Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold419
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1725835
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 213561 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1032222 original size:1 final size:1
Alignment explanation
Indices: 1032216--1032283 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
1032206 CCGTGAGCGA
*** * * * ** *
1032216 CCCCCCCCCCCCCCCCCCCCCCCCCCCAAGCACGCCCCCCCACCAACCCCCCCCCCCCCCCCCTC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1032281 CCC
1 CCC
1032284 ACAGCAAGCA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.09, C:0.87, G:0.03, T:0.01
Consensus pattern (1 bp):
C
Found at i:1039649 original size:42 final size:42
Alignment explanation
Indices: 1039590--1039674 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1039580 AGCGCTTTTC
1039590 AATACTATCAGTACTTTGATTGTTTCTTTACTAGGTACGGTT
1 AATACTATCAGTACTTTGATTGTTTCTTTACTAGGTACGGTT
1039632 AATACTATCAGTACTTTGATTGTTTCTTTACTAGGTACGGTT
1 AATACTATCAGTACTTTGATTGTTTCTTTACTAGGTACGGTT
1039674 A
1 A
1039675 TCATCTCTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (42 bp):
AATACTATCAGTACTTTGATTGTTTCTTTACTAGGTACGGTT
Found at i:1071258 original size:38 final size:38
Alignment explanation
Indices: 1071207--1071282 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1071197 TCTTTATTTA
1071207 TGGTTACATTGAAATTAATGTCAAAACGGGCTTGGCCC
1 TGGTTACATTGAAATTAATGTCAAAACGGGCTTGGCCC
1071245 TGGTTACATTGAAATTAATGTCAAAACGGGCTTGGCCC
1 TGGTTACATTGAAATTAATGTCAAAACGGGCTTGGCCC
1071283 CTGTAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (38 bp):
TGGTTACATTGAAATTAATGTCAAAACGGGCTTGGCCC
Found at i:1075151 original size:2 final size:2
Alignment explanation
Indices: 1075144--1075201 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1075134 TAATAGAAGG
1075144 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1075186 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
1075202 ATCCCAGTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1080343 original size:1 final size:1
Alignment explanation
Indices: 1080325--1080383 Score: 91
Period size: 1 Copynumber: 59.0 Consensus size: 1
1080315 TATGCATATG
* * *
1080325 AAAAAATAATAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1080384 GAGATAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.95, C:0.00, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:1088631 original size:165 final size:165
Alignment explanation
Indices: 1088339--1089588 Score: 1821
Period size: 165 Copynumber: 7.5 Consensus size: 165
1088329 GAACTGNGGC
*
1088339 CACAATGGGGTGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTC
1 CACAATGGGG-GGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTC
* * * *
1088404 AGAAACTAATCAGCCAGGATAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGCAGATTCATA
65 AGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAA
1088469 GTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG
130 GTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG
* * *
1088505 CACAATGGAGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAATTCTTCTTCTCA
1 CACAATGGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
* *
1088570 GAAACTAATCAGCCAGGAAAGCTGAAACTTGTATGGAAGCATCCTCAGGCAGTGTAGATTCAAAG
66 GAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
*
1088635 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGAGGC
131 TTGTGAAAATCATGATCCCTGGGGGTAGGGTG-GGG
* * * * *
1088671 CACATTGGGGGGGGGGTGTTAAAGTTTTACCTA-GAA-ATATTGAGTAAATCTTTGAAAATCTTC
1 CACAAT-----GGGGG-GTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTC
*
1088734 TTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAATGTAGAT
60 TTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGAT
* * *
1088799 TCAAAGTTGTGAAATTCATGATCCTTGGGGGTAAGGTGGGG
125 TCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG
*
1088840 CCACAATGGGGTGGTTAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCT
1 -CACAATGGGG-GGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCT
* * * *
1088905 CAGAAACTAATCAGACAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGCAGATTCAT
64 CAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAA
*
1088970 AGTTGTGAAAATCATGATCCCTAGGGGTAGGGTGGGG
129 AGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG
* * *
1089007 CACAATGGAGGGTCAAAGTTGTACATAGGAATATATAGAGTAAATCTTTAAAATTCTTCTTCTCA
1 CACAATGGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
* * *
1089072 GAAACTAATCAGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGCAGATTCATAG
66 GAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
*
1089137 TTGTGAAAATCATGATCCCTAGGGGTAGGGTGGGG
131 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG
* *
1089172 CACAATGGAGGGTCAAAGTTGTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
1 CACAATGGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
* *
1089237 GAAACTAATCAGCCAGGAAAGCTGAAACTCGTGTGGAAGCATCCTCAGGCAGTGTAGATTCAAAG
66 GAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
* *
1089302 TAGTGAAAATCATGATCCCTGGGGGTAGGGTGAGG
131 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG
* *
1089337 CACAATGGGGGGTCGAAGTTGTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
1 CACAATGGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
* *
1089402 GAAACTAAACAGCCAGGAAAGCTGAAACTTGTG-GTGAAGTATCCTCAGGTAGTGTAGATTCAAA
66 GAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTG-GAAGCATCCTCAGGTAGTGTAGATTCAAA
* *
1089466 GTTGTGAAAA-CATGATCCCTTGGGGTAGGGTGAGGC
130 GTTGTGAAAATCATGATCCCTGGGGGTAGGGTG-GGG
* * * *
1089502 CACATTGGGGGGGGGGGGGGGTTAAAGTTTTACAAAGGAATATATAGAGTAAATCTTTTAAAA--
1 CACAAT---------GGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATC
1089565 -TCTTCTCAGAAACTAATCAGCCAG
57 TTCTTCTCAGAAACTAATCAGCCAG
1089589 ATGATTCTTT
Statistics
Matches: 994, Mismatches: 68, Indels: 39
0.90 0.06 0.04
Matches are distributed among these distances:
164 22 0.02
165 607 0.61
166 29 0.03
167 122 0.12
169 2 0.00
170 126 0.13
171 30 0.03
172 13 0.01
174 43 0.04
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (165 bp):
CACAATGGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
GAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG
Found at i:1092215 original size:2 final size:2
Alignment explanation
Indices: 1092208--1092239 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1092198 TCGTACATTA
1092208 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1092240 ATTGATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1099805 original size:2 final size:2
Alignment explanation
Indices: 1099798--1099828 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1099788 AGTTTACTCG
1099798 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1099829 TACTAAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1116680 original size:2 final size:2
Alignment explanation
Indices: 1116675--1116724 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1116665 GTGTGTGTGT
*
1116675 GA GA GA GA GA GA GA GA GA GA GA GA GA G- GG GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1116716 GA GA GA GA G
1 GA GA GA GA G
1116725 TAATGCTCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1117847 original size:118 final size:117
Alignment explanation
Indices: 1117575--1117931 Score: 467
Period size: 115 Copynumber: 3.0 Consensus size: 117
1117565 GTCTAGTTAA
* *
1117575 GGTCTTCCGTTTTCCAACGGAAGACCTTATTGTT-TTCGTTCGGTTTCTTTTTCCCTATTATTAG
1 GGTCTTCCG-TTTCCAACGGAAGACCCTCTTGTTATTC-TTCGGTTTC---TT---T-TTATTAG
* * *
1117639 GGTCTTCCGTTTCCGGAACGGAAGACCCTTTTGTTTTTCTTCGGTTTC-TTT-TTATTATTAG
57 GGTCTTCCGTTTTC--AACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTTTATTATTATTAG
*
1117700 GGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTTTTATTAGGGTCTTCCG
1 GGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTTTTATTAGGGTCTTCCG
*
1117765 TTTTCAACGGAAGACCCTCTTGTTATTCTAT-TGTTTCTTTCTATTATTATTAG
66 TTTTCAACGGAAGACCCTCTTGTTATTCT-TCGGTTTCTTT-TATTATTATTAG
1117818 GGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTC--TTT-TTAGGGTCTTCCG
1 GGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTTTTATTAGGGTCTTCCG
*
1117880 TTTTCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTTTTATCATTATTA
66 TTTTCAACGGAAGACCCTCTTGTTATTCTTCGGTTTC-TTTTATTATTATTA
1117932 TACTTTTTCT
Statistics
Matches: 215, Mismatches: 10, Indels: 24
0.86 0.04 0.10
Matches are distributed among these distances:
114 1 0.00
115 84 0.39
116 9 0.04
117 21 0.10
118 56 0.26
121 2 0.01
124 30 0.14
125 12 0.06
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (117 bp):
GGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTTTTATTAGGGTCTTCCG
TTTTCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTTTATTATTATTAG
Found at i:1117873 original size:53 final size:53
Alignment explanation
Indices: 1117814--1117922 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
1117804 TCTATTATTA
1117814 TTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTT
1 TTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTT
*
1117867 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTT
1 TTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTT
1117920 TTA
1 TTA
1117923 TCATTATTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (53 bp):
TTAGGGTCTTCCGTTTCCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTT
Found at i:1118938 original size:436 final size:433
Alignment explanation
Indices: 1118094--1119379 Score: 1850
Period size: 436 Copynumber: 3.0 Consensus size: 433
1118084 ATATTTACAA
*
1118094 GACCTTTCATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACCAAAGGGCTCTAA
1 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACCAAAGGGCTCTAA
* * *
1118159 AGTCTTTTATCTGTAGTCCTTTACTGAGGGATATTTTGTGAACAGTTATAGAAGCAAATATGTTT
66 AGTCTTTCATCTGTAGCCCTTTACTGAGGGATATTTTGTGAACGGTTATAGAAGCAAATATGTTT
* *
1118224 ATCTTACAGTTATTTATCCAAGCAATGTAATGATTTTATCGCGTGTTACGTAATTAGGGGTTTTT
131 ATCTTACAGTTATTTATCCAAGCAATGTAATGGTTTTATCGTGT-TTACGTAATTAGGGG-TTTT
* *
1118289 TGGGGCCAAAAGTCCAGCATTTTGATCACCCATATCTCAAAAAGGAAAAATATTTTGAAATAAAG
194 AGGGGCCAAAAGTCCAGAATTTTGATCACCCATATCTCAAAAAGGAAAAATATTTTGAAATAAAG
*
1118354 TATAGAAGTAAAAATGCTCAAAATGATGTACTAAATAATATGCAATTTTCAAAATTTCGTTAAAT
259 TATAGAAGTAAAGATGCTCAAAATGATGTACTAAATAATATGCAATTTTCAAAATTTCGTTAAAT
* * * *
1118419 GGCCCCTATAAGGAGTTATGGGATCGGCCCCTAAAACGTTCGTTCCTATATTTCTCAAGAACGGT
324 GG-CCCTATAAGGAGTTAAGGGATCGGCCCCTAAAACGTTCTTTCCTAAATATCTCAAGAACGGT
*
1118484 AACAAATTTCTAAACACTTGTTGAACAAAATGTGTTGAGATTTAAAT
388 AACAAA-TTCTAAACACTTGTTGAACAAAATGTGTTGAAATTTAAAT
* *
1118531 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAAGGGAACAAAGGGCTCTAA
1 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACCAAAGGGCTCTAA
1118596 AGTCTTTCATCTGTAGCCCTTTACTGAGGGATATTTTGTGAACGGTTATAGAAGCAAATATGTTT
66 AGTCTTTCATCTGTAGCCCTTTACTGAGGGATATTTTGTGAACGGTTATAGAAGCAAATATGTTT
* *
1118661 ATCTTACAGTTATTTTTCAAAGCAATGTAATGGTTTTATCGTGTATTACGTAATTAGGGGTTTTA
131 ATCTTACAGTTATTTATCCAAGCAATGTAATGGTTTTATCGTGT-TTACGTAATTAGGGGTTTTA
1118726 GGGGCCAAAAGTCCAGAATTTTGATCACCCATATCTCAAAAAGGAAAAATATTTTGAAATAAAGT
195 GGGGCCAAAAGTCCAGAATTTTGATCACCCATATCTCAAAAAGGAAAAATATTTTGAAATAAAGT
1118791 ATAGAAGTAAAGATAG-TCAAAATGATGTACTAAATAATATGCAATTTTCAAAATTTCGTTAAAT
260 ATAGAAGTAAAGAT-GCTCAAAATGATGTACTAAATAATATGCAATTTTCAAAATTTCGTTAAAT
1118855 GGACCCTATAAGGAGTTAAGGGATCGGCCCCTAAAACGTTCTTTCCTAAATATCTCAAGAACGGT
324 GG-CCCTATAAGGAGTTAAGGGATCGGCCCCTAAAACGTTCTTTCCTAAATATCTCAAGAACGGT
* *
1118920 AACAAATCTCTTAACACTTGTTAAACAAAATGTGTTGAAATTTAAAT
388 AACAAAT-TCTAAACACTTGTTGAACAAAATGTGTTGAAATTTAAAT
*
1118967 GACCTTTTATTTGATATCAAGAAGAAGGGGCTGGCCCCTCAAATTAGGGGACCAAAGGGCTCTAA
1 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACCAAAGGGCTCTAA
* * * *
1119032 AGTCTTTCATCTTTAGCTCTTTACTGAGGGATATTTTGTGAAAGGCTATAGAAGCAAATATGTTT
66 AGTCTTTCATCTGTAGCCCTTTACTGAGGGATATTTTGTGAACGGTTATAGAAGCAAATATGTTT
* ** * * * * * **
1119097 TTCTTACAACTATGTATCCAAGCAGTGTAAT-G--TCAT-GTG-TTATGTAATGAGAGATTTTTA
131 ATCTTACAGTTATTTATCCAAGCAATGTAATGGTTTTATCGTGTTTACGTAATTAG-GGGTTTTA
* * * * * * * * **
1119157 GGGGTCAAGAGTCCAAAACTATGACCACCTATATCTCAAAAAGAAAAAATATTTTGAAATGCAGT
195 GGGGCCAAAAGTCCAGAATTTTGATCACCCATATCTCAAAAAGGAAAAATATTTTGAAATAAAGT
* * * * * * * * **
1119222 ATAGAAGAAAAGATGCTAAAAATGATGTACTTAACAACATGCAATCTTCAAAATTTGGTTCAGCG
260 ATAGAAGTAAAGATGCTCAAAATGATGTACTAAATAATATGCAATTTTCAAAATTTCGTTAAATG
* * * *
1119287 GCTCCAATAAGGAGATAAGGGACCGGCCCCTAAAAC-TT-TTTCTTCTAAGATATCTCAAGAACA
325 GC-CCTATAAGGAGTTAAGGGATCGGCCCCTAAAACGTTCTTTC--CTAA-ATATCTCAAGAACG
* *
1119350 GTGACGAATTCTAAACACTTGTTGAACAAA
386 GTAACAAATTCTAAACACTTGTTGAACAAA
1119380 GCTCTTACAC
Statistics
Matches: 772, Mismatches: 69, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
429 4 0.01
430 14 0.02
431 168 0.22
432 23 0.03
433 3 0.00
435 2 0.00
436 378 0.49
437 180 0.23
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (433 bp):
GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACCAAAGGGCTCTAA
AGTCTTTCATCTGTAGCCCTTTACTGAGGGATATTTTGTGAACGGTTATAGAAGCAAATATGTTT
ATCTTACAGTTATTTATCCAAGCAATGTAATGGTTTTATCGTGTTTACGTAATTAGGGGTTTTAG
GGGCCAAAAGTCCAGAATTTTGATCACCCATATCTCAAAAAGGAAAAATATTTTGAAATAAAGTA
TAGAAGTAAAGATGCTCAAAATGATGTACTAAATAATATGCAATTTTCAAAATTTCGTTAAATGG
CCCTATAAGGAGTTAAGGGATCGGCCCCTAAAACGTTCTTTCCTAAATATCTCAAGAACGGTAAC
AAATTCTAAACACTTGTTGAACAAAATGTGTTGAAATTTAAAT
Found at i:1139937 original size:2 final size:2
Alignment explanation
Indices: 1139932--1139977 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1139922 TTTAATTATA
1139932 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1139974 TG TG
1 TG TG
1139978 GGAGGAATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1143127 original size:22 final size:22
Alignment explanation
Indices: 1143099--1143144 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1143089 TCTAAGTTTT
*
1143099 TGTTGAATACATAGGACGAATA
1 TGTTGAATACAGAGGACGAATA
1143121 TGTTGAATACAGAGGACGAATA
1 TGTTGAATACAGAGGACGAATA
1143143 TG
1 TG
1143145 CAGGTAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.26, T:0.26
Consensus pattern (22 bp):
TGTTGAATACAGAGGACGAATA
Found at i:1145503 original size:20 final size:20
Alignment explanation
Indices: 1145478--1145530 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1145468 TTGTCCGGCG
1145478 TCCGTCCGTCTGTCTGTCTC
1 TCCGTCCGTCTGTCTGTCTC
1145498 TCCGTCCGTCTGTCTGTCTC
1 TCCGTCCGTCTGTCTGTCTC
1145518 TCCGTCCGTCTGT
1 TCCGTCCGTCTGT
1145531 AAACTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.00, C:0.40, G:0.21, T:0.40
Consensus pattern (20 bp):
TCCGTCCGTCTGTCTGTCTC
Found at i:1145530 original size:16 final size:16
Alignment explanation
Indices: 1145482--1145512 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1145472 CCGGCGTCCG
*
1145482 TCCGTCTGTCTGTCTC
1 TCCGTCCGTCTGTCTC
1145498 TCCGTCCGTCTGTCT
1 TCCGTCCGTCTGTCT
1145513 GTCTCTCCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.39, G:0.19, T:0.42
Consensus pattern (16 bp):
TCCGTCCGTCTGTCTC
Found at i:1146116 original size:133 final size:131
Alignment explanation
Indices: 1145867--1146118 Score: 319
Period size: 133 Copynumber: 1.9 Consensus size: 131
1145857 TAAAAAAACA
* *
1145867 AGTTGGCCAGAAAAGCTGAAACTTGTGTGAAAGCATCCTTAGGTAACGAGATTCAAGTTTGTTCA
1 AGTTGGCCAGAAAAGCTGAAACTTGTGTGAAAGCATCCTTAAGCAACGAGATTCAAGTTTGTTCA
* * * **
1145932 ATCCATAATCCCCAGGTATACGGTGGGGCCACAATGGGGGATCGAGTTTTTACATAGAAGAAAAG
66 AACCATAATCCCCAGGGATACGGTGGGGCCACAATGGGGGATCAAAATTTTACATAGAAGAAAAG
1145997 C
131 C
* * ** * *
1145998 AGTTGGCCAGAAAAAGCTGTAACTTGTGTGAAAGCTTCCTTAAGCAGTGTTGATTCTAGTTTGTT
1 AGTTGGCCAG-AAAAGCTGAAACTTGTGTGAAAGCATCCTTAAGCAACG-AGATTCAAGTTTGTT
* *
1146063 CAAACCATGATCCCCGGGGATACGGTGGGGCCA-ATATGAGGGG-TCAAAATTTTACA
64 CAAACCATAATCCCCAGGGATACGGTGGGGCCACA-ATG-GGGGATCAAAATTTTACA
1146119 CAAAAATATA
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
131 10 0.10
132 33 0.32
133 55 0.54
134 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (131 bp):
AGTTGGCCAGAAAAGCTGAAACTTGTGTGAAAGCATCCTTAAGCAACGAGATTCAAGTTTGTTCA
AACCATAATCCCCAGGGATACGGTGGGGCCACAATGGGGGATCAAAATTTTACATAGAAGAAAAG
C
Found at i:1149798 original size:31 final size:30
Alignment explanation
Indices: 1149760--1149852 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 30
1149750 TACCATTTAT
*
1149760 TGTAGATATAGAAATTTAGCCCCCAATCACC
1 TGTAGATATAGAAATTTAG-GCCCAATCACC
*
1149791 TGTAGATATAGAAATTTAAGGCTCAATCACC
1 TGTAGATATAGAAATTT-AGGCCCAATCACC
* *
1149822 TGCAGATATAAAAATTTAGGGCCCAATCACC
1 TGTAGATATAGAAATTTA-GGCCCAATCACC
1149853 GTAATACATG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.02
31 52 0.95
32 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (30 bp):
TGTAGATATAGAAATTTAGGCCCAATCACC
Found at i:1152047 original size:16 final size:16
Alignment explanation
Indices: 1152028--1152058 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1152018 ATCTCAAAGG
1152028 TACGTTTTCTCCAGGT
1 TACGTTTTCTCCAGGT
1152044 TACGTTTTCTCCAGG
1 TACGTTTTCTCCAGG
1152059 GTACATGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.42
Consensus pattern (16 bp):
TACGTTTTCTCCAGGT
Found at i:1153512 original size:2 final size:2
Alignment explanation
Indices: 1153505--1153546 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1153495 NNNNNNNNNN
1153505 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1153547 TTCAGGGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1165428 original size:10 final size:10
Alignment explanation
Indices: 1165415--1165439 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1165405 AAAGTTTGTA
1165415 AATCATTTAT
1 AATCATTTAT
1165425 AATCATTTAT
1 AATCATTTAT
1165435 AATCA
1 AATCA
1165440 AGCAATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (10 bp):
AATCATTTAT
Found at i:1166351 original size:19 final size:19
Alignment explanation
Indices: 1166327--1166372 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1166317 ATAGCCCATT
* *
1166327 TGGGATATAATATCCTATA
1 TGGGATATAATATCCGAAA
1166346 TGGGATATAATATCCGAAA
1 TGGGATATAATATCCGAAA
1166365 TGGGATAT
1 TGGGATAT
1166373 GAATTTGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.33
Consensus pattern (19 bp):
TGGGATATAATATCCGAAA
Found at i:1172414 original size:21 final size:21
Alignment explanation
Indices: 1172390--1172461 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
1172380 CACGTCTTTT
1172390 AACCCCAAGGAACCCCAAGGA
1 AACCCCAAGGAACCCCAAGGA
1172411 AACCCCAAGGAACCCCAAGGA
1 AACCCCAAGGAACCCCAAGGA
1172432 AACCCCAAGGAAACCCCAAGGA
1 AACCCCAAGG-AACCCCAAGGA
*
1172454 TACCCCAA
1 AACCCCAA
1172462 TGACAGAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 31 0.63
22 18 0.37
ACGTcount: A:0.43, C:0.39, G:0.17, T:0.01
Consensus pattern (21 bp):
AACCCCAAGGAACCCCAAGGA
Found at i:1172416 original size:11 final size:11
Alignment explanation
Indices: 1172390--1172461 Score: 121
Period size: 11 Copynumber: 6.7 Consensus size: 11
1172380 CACGTCTTTT
1172390 AACCCCAAGG-
1 AACCCCAAGGA
1172400 AACCCCAAGGA
1 AACCCCAAGGA
1172411 AACCCCAAGG-
1 AACCCCAAGGA
1172421 AACCCCAAGGA
1 AACCCCAAGGA
1172432 AACCCCAAGGA
1 AACCCCAAGGA
1172443 AACCCCAAGGA
1 AACCCCAAGGA
*
1172454 TACCCCAA
1 AACCCCAA
1172462 TGACAGAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
10 20 0.34
11 39 0.66
ACGTcount: A:0.43, C:0.39, G:0.17, T:0.01
Consensus pattern (11 bp):
AACCCCAAGGA
Found at i:1172874 original size:173 final size:173
Alignment explanation
Indices: 1172615--1173320 Score: 1168
Period size: 173 Copynumber: 4.1 Consensus size: 173
1172605 GAACCCCAAG
* * * * * *
1172615 GAACCTCAAGGATACCCGAATACG--GTAACACAAATTTTAAACTCTTGGT-ACCCATGGGGACT
1 GAACCCCAAGGATACCCTAATACGTTGTAATACAAATGTAAAACTCTTGATAACCC-TGGGGACT
*
1172677 CATTGGTATTCCAGACACACCTCTAAGAA-CCACAGGGAACCCCAGGGATATCCCAAGGAACTCC
65 CATTGGTATTCCAGATACACCTCTAAGAATCC-CAGGGAACCCCAGGGATATCCCAAGGAACTCC
* * *
1172741 AAGAATACCCTAATTATACAGAATCATAACTCTTAATACTCCATA
129 AAGAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATA
*
1172786 GAACCCCAAGGATACCCTAATACATTGTAATACAAATGTAAAACTCTTGATAACCCTGGGGACTC
1 GAACCCCAAGGATACCCTAATACGTTGTAATACAAATGTAAAACTCTTGATAACCCTGGGGACTC
*
1172851 ATTGGTATTCCAGATACACCTCTAAGAATCCCAGGGAACCCCATGGATATCCCAAGGAACTCCAA
66 ATTGGTATTCCAGATACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAA
1172916 GAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATA
131 GAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATA
* *
1172959 AAACCCCAAGGATACCGTAATACGTTGTAATACAAATGTAAAACTCTTGATAACCCTGGGGACTC
1 GAACCCCAAGGATACCCTAATACGTTGTAATACAAATGTAAAACTCTTGATAACCCTGGGGACTC
*
1173024 ATTGGTATTCCAGATACACCTCTAAGAATCCCAGGGAACCCCATGGATATCCCAAGGAACTCCAA
66 ATTGGTATTCCAGATACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAA
1173089 GAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATA
131 GAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATA
* *
1173132 GAACCCCAAGGATACCGTAATACGTTGTAATACAAATTTAAAACTCTTGATAACCCTGGGGACTC
1 GAACCCCAAGGATACCCTAATACGTTGTAATACAAATGTAAAACTCTTGATAACCCTGGGGACTC
*
1173197 ATTGGTATTCCAGATACACCTCGAAGAATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAA
66 ATTGGTATTCCAGATACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAA
* * * *
1173262 GAATGCCCTAATAATACAGAATCATAACTCTTGATACACCACA
131 GAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATA
1173305 GAACCCCAAGGATACC
1 GAACCCCAAGGATACC
1173321 TCAAGGAACT
Statistics
Matches: 508, Mismatches: 23, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
171 21 0.04
173 481 0.95
174 6 0.01
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (173 bp):
GAACCCCAAGGATACCCTAATACGTTGTAATACAAATGTAAAACTCTTGATAACCCTGGGGACTC
ATTGGTATTCCAGATACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAA
GAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATA
Found at i:1177808 original size:21 final size:20
Alignment explanation
Indices: 1177759--1177817 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
1177749 ATTTCTATTA
1177759 TTGGGGT-TACTTGGGGTTC
1 TTGGGGTATACTTGGGGTTC
*
1177778 TAAT-GAGTATACTTGGGGTTCC
1 T--TGGGGTATACTTGGGGTT-C
*
1177800 TTGGGGTATCCTTGGGGT
1 TTGGGGTATACTTGGGGT
1177818 ACTACGAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 25 0.78
22 2 0.06
ACGTcount: A:0.12, C:0.12, G:0.37, T:0.39
Consensus pattern (20 bp):
TTGGGGTATACTTGGGGTTC
Found at i:1177813 original size:11 final size:11
Alignment explanation
Indices: 1177784--1177818 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1177774 GTTCTAATGA
*
1177784 GTATACTTGGG
1 GTATCCTTGGG
1177795 GT-TCCTTGGG
1 GTATCCTTGGG
1177805 GTATCCTTGGG
1 GTATCCTTGGG
1177816 GTA
1 GTA
1177819 CTACGAGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.11, C:0.14, G:0.37, T:0.37
Consensus pattern (11 bp):
GTATCCTTGGG
Found at i:1178083 original size:10 final size:10
Alignment explanation
Indices: 1178068--1178137 Score: 113
Period size: 10 Copynumber: 6.8 Consensus size: 10
1178058 ATTTTTGTCA
1178068 TTGGGGTTCC
1 TTGGGGTTCC
1178078 TTGGGGTATCC
1 TTGGGGT-TCC
*
1178089 TTGAGGTTCC
1 TTGGGGTTCC
1178099 TTGGGGTTTCC
1 TTGGGG-TTCC
1178110 TTGGGGTTCC
1 TTGGGGTTCC
1178120 TTGGGGTTCC
1 TTGGGGTTCC
1178130 TTGGGGTT
1 TTGGGGTT
1178138 AAAAGACGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
10 37 0.66
11 19 0.34
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (10 bp):
TTGGGGTTCC
Found at i:1178098 original size:21 final size:20
Alignment explanation
Indices: 1178068--1178137 Score: 113
Period size: 21 Copynumber: 3.4 Consensus size: 20
1178058 ATTTTTGTCA
1178068 TTGGGGTTCCTTGGGGTATCC
1 TTGGGGTTCCTTGGGGT-TCC
*
1178089 TTGAGGTTCCTTGGGGTTTCC
1 TTGGGGTTCCTTGGGG-TTCC
1178110 TTGGGGTTCCTTGGGGTTCC
1 TTGGGGTTCCTTGGGGTTCC
1178130 TTGGGGTT
1 TTGGGGTT
1178138 AAAAGACGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 12 0.26
21 33 0.72
22 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (20 bp):
TTGGGGTTCCTTGGGGTTCC
Found at i:1178106 original size:31 final size:30
Alignment explanation
Indices: 1178068--1178137 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 30
1178058 ATTTTTGTCA
1178068 TTGGGGTTCCTTGGGGTATCCTTGAGGTTCC
1 TTGGGGTTCCTTGGGGT-TCCTTGAGGTTCC
*
1178099 TTGGGGTTTCCTTGGGGTTCCTTGGGGTTCC
1 TTGGGG-TTCCTTGGGGTTCCTTGAGGTTCC
1178130 TTGGGGTT
1 TTGGGGTT
1178138 AAAAGACGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 2 0.05
31 24 0.65
32 11 0.30
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (30 bp):
TTGGGGTTCCTTGGGGTTCCTTGAGGTTCC
Found at i:1184994 original size:14 final size:15
Alignment explanation
Indices: 1184965--1184997 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
1184955 AGTTGTACAC
1184965 TTTAAAACAACACTAT
1 TTTAAAAC-ACACTAT
1184981 TTTAAAAC-CACTAT
1 TTTAAAACACACTAT
1184995 TTT
1 TTT
1184998 TTATGTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTAAAACACACTAT
Found at i:1193190 original size:22 final size:23
Alignment explanation
Indices: 1193154--1193197 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1193144 AGAAACTTCT
1193154 TTTTGTATTTTTTTTT-GTTTTG
1 TTTTGTATTTTTTTTTGGTTTTG
1193176 TTTTGT-TTTGTTTTTTGGTTTT
1 TTTTGTATTT-TTTTTTGGTTTT
1193198 TTGGGGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.15
22 12 0.60
23 5 0.25
ACGTcount: A:0.02, C:0.00, G:0.16, T:0.82
Consensus pattern (23 bp):
TTTTGTATTTTTTTTTGGTTTTG
Found at i:1199398 original size:13 final size:13
Alignment explanation
Indices: 1199380--1199404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1199370 AATTACACTC
1199380 AATTACCATTACA
1 AATTACCATTACA
1199393 AATTACCATTAC
1 AATTACCATTAC
1199405 CCCATCCCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTACCATTACA
Found at i:1206308 original size:4 final size:4
Alignment explanation
Indices: 1206301--1206481 Score: 272
Period size: 4 Copynumber: 45.2 Consensus size: 4
1206291 GTAGGATTGC
1206301 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
* * * * * *
1206349 TCTA TCTA TCTA TCCA TCCA TCCA TCCA TCCA TCCA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
* *
1206397 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCCA TCCA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
* *
1206445 TCTA TCCA TCTG TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
1206482 ATAATTAGAC
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 169 1.00
ACGTcount: A:0.24, C:0.30, G:0.01, T:0.45
Consensus pattern (4 bp):
TCTA
Found at i:1207868 original size:16 final size:18
Alignment explanation
Indices: 1207847--1207883 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1207837 ATGAATTTAT
1207847 TGTAG-ATGATTTTA-AA
1 TGTAGAATGATTTTAGAA
*
1207863 TGTAGAATGTTTTTAGAA
1 TGTAGAATGATTTTAGAA
1207881 TGT
1 TGT
1207884 CAGGATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 8 0.44
18 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (18 bp):
TGTAGAATGATTTTAGAA
Found at i:1209490 original size:15 final size:15
Alignment explanation
Indices: 1209470--1209506 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1209460 CATACCATGG
1209470 GTACAATACACAATT
1 GTACAATACACAATT
*
1209485 GTACAATATACAATT
1 GTACAATACACAATT
1209500 G-ACAATA
1 GTACAATA
1209507 TATTTTTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (15 bp):
GTACAATACACAATT
Found at i:1211343 original size:2 final size:2
Alignment explanation
Indices: 1211336--1211380 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1211326 TTTGGTAATA
1211336 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1211378 TC T
1 TC T
1211381 GTTGCCCGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1215856 original size:18 final size:18
Alignment explanation
Indices: 1215833--1215895 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
1215823 ATGGCGTAAC
1215833 CAATGGTCATAATGGACA
1 CAATGGTCATAATGGACA
** *
1215851 CAATGGGGAAAATGG-CGTAA
1 CAATGGTCATAATGGAC---A
1215871 CCAATGGTCATAATGGACA
1 -CAATGGTCATAATGGACA
1215890 CAATGG
1 CAATGG
1215896 GATTATTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
17 1 0.03
18 18 0.53
19 1 0.03
20 1 0.03
21 12 0.35
22 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (18 bp):
CAATGGTCATAATGGACA
Found at i:1215863 original size:39 final size:39
Alignment explanation
Indices: 1215819--1215896 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1215809 CCATACACAC
1215819 GAAAATGGCGTAACCAATGGTCATAATGGACACAATGGG
1 GAAAATGGCGTAACCAATGGTCATAATGGACACAATGGG
1215858 GAAAATGGCGTAACCAATGGTCATAATGGACACAATGGG
1 GAAAATGGCGTAACCAATGGTCATAATGGACACAATGGG
1215897 ATTATTAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (39 bp):
GAAAATGGCGTAACCAATGGTCATAATGGACACAATGGG
Found at i:1217434 original size:2 final size:2
Alignment explanation
Indices: 1217427--1217480 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1217417 TTGTCTGTAT
1217427 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1217469 TC TC TC TC TC TC
1 TC TC TC TC TC TC
1217481 AGAAATATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1226421 original size:2 final size:2
Alignment explanation
Indices: 1226416--1226451 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1226406 TCTCCCCCCC
1226416 CT CT CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1226452 AGCCTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1226435 original size:17 final size:17
Alignment explanation
Indices: 1226415--1226449 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1226405 CTCTCCCCCC
1226415 CCTCTCTCTCTCTCTCT
1 CCTCTCTCTCTCTCTCT
1226432 CCTCTCTCTCTCTCTCT
1 CCTCTCTCTCTCTCTCT
1226449 C
1 C
1226450 TCAGCCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (17 bp):
CCTCTCTCTCTCTCTCT
Found at i:1231216 original size:21 final size:21
Alignment explanation
Indices: 1231190--1231326 Score: 94
Period size: 21 Copynumber: 6.5 Consensus size: 21
1231180 TAAACGATAC
1231190 TAGGATAGGATTCACGCACGA
1 TAGGATAGGATTCACGCACGA
* * * *
1231211 TAGGATAGCATTAATGCATGA
1 TAGGATAGGATTCACGCACGA
* * * ** *
1231232 AAGAACAATATACACGCACGA
1 TAGGATAGGATTCACGCACGA
* *
1231253 TAGGATATGATTAACGCACGA
1 TAGGATAGGATTCACGCACGA
* * * *
1231274 TAGAACAGTATACACGCACGA
1 TAGGATAGGATTCACGCACGA
* **
1231295 TAGGATAGGATTGATACACGA
1 TAGGATAGGATTCACGCACGA
*
1231316 TAGGAAAGGAT
1 TAGGATAGGAT
1231327 AAACGATGTT
Statistics
Matches: 82, Mismatches: 34, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 82 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (21 bp):
TAGGATAGGATTCACGCACGA
Found at i:1231315 original size:42 final size:42
Alignment explanation
Indices: 1231202--1231318 Score: 162
Period size: 42 Copynumber: 2.8 Consensus size: 42
1231192 GGATAGGATT
* * *
1231202 CACGCACGATAGGATAGCATTAATGCATGAAAGAACAATATA
1 CACGCACGATAGGATAGGATTAATGCACGATAGAACAATATA
* * *
1231244 CACGCACGATAGGATATGATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAATGCACGATAGAACAATATA
* *
1231286 CACGCACGATAGGATAGGATTGATACACGATAG
1 CACGCACGATAGGATAGGATTAATGCACGATAG
1231319 GAAAGGATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (42 bp):
CACGCACGATAGGATAGGATTAATGCACGATAGAACAATATA
Found at i:1232370 original size:23 final size:21
Alignment explanation
Indices: 1232344--1232392 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1232334 CGATAAACCT
*
1232344 GATAGGATAACCGATTAACGCAC
1 GATAGGAT-ACC-ACTAACGCAC
*
1232367 GATAGGATAGCACTAACGCAC
1 GATAGGATACCACTAACGCAC
1232388 GATAG
1 GATAG
1232393 AACAGTATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.58
22 2 0.08
23 8 0.33
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.16
Consensus pattern (21 bp):
GATAGGATACCACTAACGCAC
Found at i:1232385 original size:21 final size:20
Alignment explanation
Indices: 1232359--1232430 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
1232349 GATAACCGAT
1232359 TAACGCACGATAGGATAGCA
1 TAACGCACGATAGGATAGCA
* * *
1232379 CTAACGCACGATAGAACAGTA
1 -TAACGCACGATAGGATAGCA
*
1232400 TACACGCACGATAGGATAGGA
1 TA-ACGCACGATAGGATAGCA
1232421 TAAACGCACG
1 T-AACGCACG
1232431 TTAGAACAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.05
21 40 0.93
22 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.14
Consensus pattern (20 bp):
TAACGCACGATAGGATAGCA
Found at i:1232408 original size:42 final size:42
Alignment explanation
Indices: 1232361--1232460 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
1232351 TAACCGATTA
1232361 ACGCACGATAGGATAGCACT-AACGCACGATAGAACAGTATAC
1 ACGCACGATAGGATAGCA-TAAACGCACGATAGAACAGTATAC
* *
1232403 ACGCACGATAGGATAGGATAAACGCACGTTAGAACAGTATAC
1 ACGCACGATAGGATAGCATAAACGCACGATAGAACAGTATAC
* *
1232445 ACGCATGATACGATAG
1 ACGCACGATAGGATAG
1232461 GATTGATGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (42 bp):
ACGCACGATAGGATAGCATAAACGCACGATAGAACAGTATAC
Found at i:1232448 original size:21 final size:21
Alignment explanation
Indices: 1232382--1232454 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
1232372 GATAGCACTA
1232382 ACGCACGATAGAACAGTATAC
1 ACGCACGATAGAACAGTATAC
* * * *
1232403 ACGCACGATAGGATAGGATAA
1 ACGCACGATAGAACAGTATAC
*
1232424 ACGCACGTTAGAACAGTATAC
1 ACGCACGATAGAACAGTATAC
*
1232445 ACGCATGATA
1 ACGCACGATA
1232455 CGATAGGATT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (21 bp):
ACGCACGATAGAACAGTATAC
Found at i:1239248 original size:31 final size:31
Alignment explanation
Indices: 1239206--1239276 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
1239196 CCTAGCCATC
1239206 TTTCCCCCCGGAAAAATGGCTATATAGCAGT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGT
*
1239237 TTTTCCCCCGGAAAAATGGCTATATAGCAGT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGT
1239268 TTTCCCCCC
1 TTTCCCCCC
1239277 ACGGAAAGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (31 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGT
Found at i:1239293 original size:33 final size:31
Alignment explanation
Indices: 1239206--1239296 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
1239196 CCTAGCCATC
*
1239206 TTTCCCCCCGGAAAAATGGCTATATAGCAGT
1 TTTCCCCCCGGAAAAATGACTATATAGCAGT
* *
1239237 TTTTCCCCCGGAAAAATGGCTATATAGCAGT
1 TTTCCCCCCGGAAAAATGACTATATAGCAGT
**
1239268 TTTCCCCCCACGGAAAGCTGACTATATAG
1 TTT-CCCCC-CGGAAAAATGACTATATAG
1239297 TGGGCTTTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 33 0.62
32 4 0.08
33 16 0.30
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (31 bp):
TTTCCCCCCGGAAAAATGACTATATAGCAGT
Found at i:1240755 original size:21 final size:20
Alignment explanation
Indices: 1240726--1240770 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1240716 AAAGAAATAT
*
1240726 ATGAGTGGTTGTGTATTTTTAA
1 ATGAGTGGTT-T-TACTTTTAA
1240748 ATGA-TGGTTTTACTTTTAA
1 ATGAGTGGTTTTACTTTTAA
1240767 ATGA
1 ATGA
1240771 CTGTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 12 0.55
20 1 0.05
21 5 0.23
22 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (20 bp):
ATGAGTGGTTTTACTTTTAA
Found at i:1241695 original size:32 final size:33
Alignment explanation
Indices: 1241621--1241705 Score: 118
Period size: 36 Copynumber: 2.5 Consensus size: 33
1241611 ACCCTACTAT
1241621 GGGGGAAAAGCTACTATATAGTAGCTTTTCCCCCCG
1 GGGGGAAAAGCTACTATATAGTAGCTTTT---CCCG
* *
1241657 GGGGGAAAGGCTACTATATAGTAGGTTTT-CCG
1 GGGGGAAAAGCTACTATATAGTAGCTTTTCCCG
1241689 GGGGGAAAAGCTACTAT
1 GGGGGAAAAGCTACTAT
1241706 GGGGGAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 19 0.41
36 27 0.59
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.25
Consensus pattern (33 bp):
GGGGGAAAAGCTACTATATAGTAGCTTTTCCCG
Found at i:1241722 original size:17 final size:17
Alignment explanation
Indices: 1241689--1241722 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1241679 AGGTTTTCCG
*
1241689 GGGGGAAAAGCTACTAT
1 GGGGGAAAAACTACTAT
*
1241706 GGGGGAAAAACTGCTAT
1 GGGGGAAAAACTACTAT
1241723 ACAACACCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (17 bp):
GGGGGAAAAACTACTAT
Found at i:1244510 original size:16 final size:16
Alignment explanation
Indices: 1244489--1244519 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1244479 TAGAATGCTG
1244489 GAGAAAACGTACCCAT
1 GAGAAAACGTACCCAT
1244505 GAGAAAACGTACCCA
1 GAGAAAACGTACCCA
1244520 ATTCCTAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.26, G:0.19, T:0.10
Consensus pattern (16 bp):
GAGAAAACGTACCCAT
Found at i:1244546 original size:16 final size:16
Alignment explanation
Indices: 1244527--1244602 Score: 111
Period size: 16 Copynumber: 4.9 Consensus size: 16
1244517 CCAATTCCTA
1244527 GGGTACGTTTTCTCTT
1 GGGTACGTTTTCTCTT
* *
1244543 GGGTAC-TTATC-CTA
1 GGGTACGTTTTCTCTT
1244557 GGGTACGTTTTCTCTT
1 GGGTACGTTTTCTCTT
1244573 GGGTACGTTTTCTCTT
1 GGGTACGTTTTCTCTT
*
1244589 GGGTATGTTTTCTC
1 GGGTACGTTTTCTC
1244603 CTGATACCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
14 8 0.15
15 8 0.15
16 37 0.70
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.47
Consensus pattern (16 bp):
GGGTACGTTTTCTCTT
Found at i:1244558 original size:30 final size:31
Alignment explanation
Indices: 1244522--1244602 Score: 119
Period size: 30 Copynumber: 2.6 Consensus size: 31
1244512 CGTACCCAAT
1244522 TCCTAGGGTACGTTTTCTCTTGGGTAC-TTA
1 TCCTAGGGTACGTTTTCTCTTGGGTACGTTA
*
1244552 TCCTAGGGTACGTTTTCTCTTGGGTACGTTT
1 TCCTAGGGTACGTTTTCTCTTGGGTACGTTA
* *
1244583 TCTCTTGGGTATGTTTTCTC
1 TC-CTAGGGTACGTTTTCTC
1244603 CTGATACCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 27 0.59
31 4 0.09
32 15 0.33
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (31 bp):
TCCTAGGGTACGTTTTCTCTTGGGTACGTTA
Found at i:1246003 original size:2 final size:2
Alignment explanation
Indices: 1245996--1246042 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1245986 TAAAGTACTT
1245996 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1246038 TC TC T
1 TC TC T
1246043 GTAAATCAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1249570 original size:156 final size:153
Alignment explanation
Indices: 1249310--1249794 Score: 462
Period size: 166 Copynumber: 3.1 Consensus size: 153
1249300 AATTTTGTTA
* * * *
1249310 AAGATTTTCACTATATATTCCTGTATAAAAATTTATCCCCCAATTGTGGCCCACCCTACCCCTGG
1 AAGATTTTCTCTATATATTCCTATGTAAAAA-TTATCCCCCCATTGTGGCCCACCCTACCCCT-G
* *
1249375 GGACCATGA-TTGTAACAAACTTTAATCTACACTATCTGAGGATGCTTCAACTCAAATTTGAGCT
64 GGACCATGATTTG-AACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTCAAATTTGAGCT
1249439 TTCCTGGCCTAGTA-TTTTATGAGAAT
128 TTCCTGGCCTAGTAGTTTT-TGAGAAT
* *
1249465 AAGATTTTCTCTATATATTCCTATGTAAAAATCTATCCCCCCATTGTGGTCCCACCATACCACTA
1 AAGATTTTCTCTATATATTCCTATGTAAAAAT-TATCCCCCCATTGTGG-CCCACCCTACCCCT-
* * * ** *
1249530 GGGACCATGATTTGAATAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAGTTTGAGCT
63 GGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTCAAATTTGAGCT
*
1249595 TTTCTGGCCT-GATAGTTTTTGAGAAGAAGATTTTT
128 TTCCTGGCCTAG-TAGTTTTT--G-AG-A-A----T
* * *
1249630 AAAGATTTCCTCTATATATTCCTATGTAAAACTTGATCCCCCTC-TTGTGGCCCCACCATACCCC
1 -AAGATTTTCTCTATATATTCCTATGTAAAAATT-ATCCCCC-CATTGTGG-CCCACCCTA-CCC
* * * * * **
1249694 CAGGGACTATGATATGAACAAACTTGAAACTACACTA-CTTGAGGATGCTTCCATTTTAATTTGA
61 CTGGGACCATGATTTGAACAAACTTGAATCTACACTATC-TGAGGATGCTTCCACTCAAATTTGA
*
1249758 GCATTT-CTGGCCT-GATAGTTTTTGAGAAG
125 GC-TTTCCTGGCCTAG-TAGTTTTTGAGAAT
1249787 AAGATTTT
1 AAGATTTT
1249795 TAAAGATTTC
Statistics
Matches: 282, Mismatches: 28, Indels: 39
0.81 0.08 0.11
Matches are distributed among these distances:
154 1 0.00
155 44 0.16
156 84 0.30
157 7 0.02
158 1 0.00
159 2 0.01
160 1 0.00
161 2 0.01
162 1 0.00
163 2 0.01
164 1 0.00
165 3 0.01
166 126 0.45
167 7 0.02
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Consensus pattern (153 bp):
AAGATTTTCTCTATATATTCCTATGTAAAAATTATCCCCCCATTGTGGCCCACCCTACCCCTGGG
ACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTCAAATTTGAGCTTTC
CTGGCCTAGTAGTTTTTGAGAAT
Found at i:1249634 original size:321 final size:316
Alignment explanation
Indices: 1248913--1249813 Score: 919
Period size: 321 Copynumber: 2.8 Consensus size: 316
1248903 TGTGATTTTG
* * * * *
1248913 CAAACTTGAATTTTCACTACCCGAGGATGCCTCTACA---CAAGTTTAAGCTTTTCAT-GCCAAA
1 CAAACTTGAATATACACTACCTGAGGATG-CT-TACATGCCAA-TTTGAGC-TTTCTTGGCCAAA
* *
1248974 TAGTCTTTAAAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTGAAAATTCATCCCCCA
62 TAGTTTTTAAAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCCA
* * *
1249039 TTGTGGCCTCACCCTACCCCT-----ATTATT-TAAACAAACTTTAATCTATACGATCTG-GGAA
127 TTGTGGCC-CACCCTACCCCTGGGACATGATTGT-AACAAACTTTAATCTACACTATCTGAGG-A
* * *
1249097 TGCTTCCACTCAAATTTGGGCTTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTT
189 TGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAGTAGTTTTTGAGAAGAAGATTTTTAAAGATAT
* * * * * *
1249162 TCTCTATATATAAATTTATCCCCCATTGTGGCCCGGCCCTACCCCCTGGTACCATGATTTGAA
254 TCTCTATATAAAAATCTATCCCCCATTGTGGCCCGACCATACCCACTGGGACCATGATTTGAA
* * *
1249225 CAAACTTGAATATACATTATCTGAGGATGGTTACATGCCAATTTGAGCTTTCTTGGCCAAATAGT
1 CAAACTTGAATATACACTACCTGAGGATGCTTACATGCCAATTTGAGCTTTCTTGGCCAAATAGT
* * * *
1249290 TTTTAAAAGAA-ATTTTGTTAAAGATTTTCACTATATATTCCTGTATAAAAATTTATCCCCCAAT
66 TTTTAAAAGAAGA-TTT-TTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCC-AT
1249354 TGTGGCCCACCCTACCCCTGGGGACCATGATTGTAACAAACTTTAATCTACACTATCTGAGGATG
128 TGTGGCCCACCCTACCCCT-GGGA-CATGATTGTAACAAACTTTAATCTACACTATCTGAGGATG
* * ** *
1249419 CTTCAACTCAAATTTGAGCTTTCCTGGCCTAGTA-TTTTATGAGAATAAGATTTTCTCTATATAT
191 CTTCCACTCAAATTTGAGCTTTCCTGGCCTAGTAGTTTT-TGAGAAGAAGATTTT-TAAAGATAT
*
1249483 TC-CTATGTAAAAATCTATCCCCCCATTGTGGTCCC-ACCATA-CCACTAGGGACCATGATTTGA
254 TCTCTATATAAAAATCTAT-CCCCCATTGTGG-CCCGACCATACCCACT-GGGACCATGATTTGA
1249545 A
316 A
* * * *** * **
1249546 TAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAGTTTGAGCTTT-TCTGGCCTGATAG
1 CAAACTTGAATATACACTACCTGAGGATGCTTACATGCCAATTTGAGCTTTCT-TGGCCAAATAG
* * * * *
1249610 TTTTTGAGAAGAAGATTTTTAAAGATTTCCTCTATATATTCCTATGTAAAACTTGATCCCCCTCT
65 TTTTT-AAAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCC-AT
* * * *
1249675 TGTGGCCCCACCATACCCCCAGGGACTATGATATG-AACAAACTTGAAACTACACTA-CTTGAGG
128 TGTGG-CCCACCCTA-CCCCTGGGAC-ATGAT-TGTAACAAACTTTAATCTACACTATC-TGAGG
* **
1249738 ATGCTTCCATTTTAATTTGAGCATTT-CTGGCCT-GATAGTTTTTGAGAAGAAGATTTTTAAAGA
188 ATGCTTCCACTCAAATTTGAGC-TTTCCTGGCCTAG-TAGTTTTTGAGAAGAAGATTTTTAAAGA
1249801 T-TTCCTCTATATA
251 TATT-CTCTATATA
1249814 TTCCTATGTA
Statistics
Matches: 489, Mismatches: 66, Indels: 58
0.80 0.11 0.09
Matches are distributed among these distances:
310 4 0.01
311 7 0.01
312 53 0.11
313 54 0.11
314 9 0.02
319 4 0.01
320 96 0.20
321 148 0.30
322 100 0.20
323 14 0.03
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (316 bp):
CAAACTTGAATATACACTACCTGAGGATGCTTACATGCCAATTTGAGCTTTCTTGGCCAAATAGT
TTTTAAAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCCATTGT
GGCCCACCCTACCCCTGGGACATGATTGTAACAAACTTTAATCTACACTATCTGAGGATGCTTCC
ACTCAAATTTGAGCTTTCCTGGCCTAGTAGTTTTTGAGAAGAAGATTTTTAAAGATATTCTCTAT
ATAAAAATCTATCCCCCATTGTGGCCCGACCATACCCACTGGGACCATGATTTGAA
Found at i:1249739 original size:166 final size:165
Alignment explanation
Indices: 1249465--1249846 Score: 604
Period size: 166 Copynumber: 2.3 Consensus size: 165
1249455 TTATGAGAAT
* * *
1249465 AAGATTTTCTCTATATATTCCTATGTAAAAATCTATCCCCC-CATTGTGGTCCCACCATACCACT
1 AAGATTTCCTCTATATATTCCTATGTAAAAAT-TATCCCCCTC-TTGTGGCCCCACCATACCACC
* * * *
1249529 AGGGACCATGATTTGAATAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAGTTTGAGC
64 AGGGACCATGATATGAACAAACTTGAAACTACACTACCTGAGGATGCTTCCATTTTAATTTGAGC
*
1249594 TTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTA
129 ATTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTA
* *
1249631 AAGATTTCCTCTATATATTCCTATGTAAAACTTGATCCCCCTCTTGTGGCCCCACCATACCCCCA
1 AAGATTTCCTCTATATATTCCTATGTAAAAATT-ATCCCCCTCTTGTGGCCCCACCATACCACCA
* *
1249696 GGGACTATGATATGAACAAACTTGAAACTACACTACTTGAGGATGCTTCCATTTTAATTTGAGCA
65 GGGACCATGATATGAACAAACTTGAAACTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCA
1249761 TTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTA
130 TTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTA
*
1249797 AAGATTTCCTCTATATATTCCTATGTAAAAATTCATCCCCCTATTGTGGC
1 AAGATTTCCTCTATATATTCCTATGTAAAAATT-ATCCCCCTCTTGTGGC
1249847 TCCTGTAAGC
Statistics
Matches: 199, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
165 1 0.01
166 197 0.99
167 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (165 bp):
AAGATTTCCTCTATATATTCCTATGTAAAAATTATCCCCCTCTTGTGGCCCCACCATACCACCAG
GGACCATGATATGAACAAACTTGAAACTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCAT
TTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTA
Found at i:1250889 original size:18 final size:20
Alignment explanation
Indices: 1250848--1250891 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1250838 CCATGAAAAC
*
1250848 AATAATGAATAAAGTATGAC
1 AATAATGAATAAAGTATGAA
*
1250868 AATAATG-ATCAAG-ATGAA
1 AATAATGAATAAAGTATGAA
1250886 AATAAT
1 AATAAT
1250892 CGTAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 5 0.23
20 7 0.32
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.25
Consensus pattern (20 bp):
AATAATGAATAAAGTATGAA
Found at i:1258789 original size:165 final size:166
Alignment explanation
Indices: 1258417--1258858 Score: 669
Period size: 165 Copynumber: 2.7 Consensus size: 166
1258407 TGTTTACACT
* * *
1258417 CCACCCTACCCCCGGGGACCATGATTTGAAAAAACTTAAATCTACACTACCTGAGAATGCTTCCA
1 CCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCA
* * *
1258482 TTTTAATTTGAGCTTTTGTGGCCTAATAGTTTTT--G-AGAAGATTTTTAAAGATTTCCTCTATA
66 TATTAATTTGAGCTTTTATGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTCCTCTATA
1258544 TAATCCTATGTAAAACTTGATCCCCCTATTGTGGCC
131 TAATCCTATGTAAAACTTGATCCCCCTATTGTGGCC
* * *
1258580 CCACCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTACACTACTTGAGGATGCTTCCA
1 CCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCA
1258645 TATTAATTTGAGCTTTTATGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTCCTCTATA
66 TATTAATTTGAGCTTTTATGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTCCTCTATA
* *
1258710 TATTTCTATGTAAAACTTGAT-CCCCTATTGTGGCC
131 TAATCCTATGTAAAACTTGATCCCCCTATTGTGGCC
* * *
1258745 CCACCCTACCCCCGGGGACCATAATTTGAACTAACTTGAATCTACACTACCTGAGGATGCCTCCA
1 CCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCA
* * * * *
1258810 CA-CAAGTTTAAGCTTTTTTGGCCGAATAGTTTTTGAGAAGAAGATTTTT
66 TATTAA-TTTGAGCTTTTATGGCCAAATAGTTTTTGAGAAGAAGATTTTT
1258859 GAAAAATAAT
Statistics
Matches: 253, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
163 90 0.36
164 2 0.01
165 115 0.45
166 46 0.18
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (166 bp):
CCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCA
TATTAATTTGAGCTTTTATGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTCCTCTATA
TAATCCTATGTAAAACTTGATCCCCCTATTGTGGCC
Found at i:1263043 original size:22 final size:22
Alignment explanation
Indices: 1263016--1263070 Score: 92
Period size: 24 Copynumber: 2.4 Consensus size: 22
1263006 GTCGAAGTGA
1263016 TTTTTAAGTCCCAACCACCTAT
1 TTTTTAAGTCCCAACCACCTAT
1263038 TTTTTAAGTGTCCCAACCACCTAT
1 TTTTTAA--GTCCCAACCACCTAT
1263062 TTTTTAAGT
1 TTTTTAAGT
1263071 ATTTCACCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 9 0.29
24 22 0.71
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (22 bp):
TTTTTAAGTCCCAACCACCTAT
Found at i:1263055 original size:24 final size:24
Alignment explanation
Indices: 1263023--1263070 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1263013 TGATTTTTAA
1263023 GTCCCAACCACCTATTTTTTAAGT
1 GTCCCAACCACCTATTTTTTAAGT
1263047 GTCCCAACCACCTATTTTTTAAGT
1 GTCCCAACCACCTATTTTTTAAGT
1263071 ATTTCACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (24 bp):
GTCCCAACCACCTATTTTTTAAGT
Found at i:1273085 original size:36 final size:38
Alignment explanation
Indices: 1273045--1273121 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 38
1273035 TTATTGCTTA
1273045 TATTTACAAT-TTTC-TTTAGACAAA-A-TATATTGATTG
1 TATTTAC-ATCTTTCTTTTA-ACAAATATTATATTGATTG
1273081 TATTTACATCTTTCTTTTAACAAATTATTATATTGATTG
1 TATTTACATCTTTCTTTTAACAAA-TATTATATTGATTG
1273120 TA
1 TA
1273122 AAAATGATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
35 2 0.06
36 16 0.44
37 4 0.11
38 1 0.03
39 13 0.36
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (38 bp):
TATTTACATCTTTCTTTTAACAAATATTATATTGATTG
Found at i:1277106 original size:9 final size:9
Alignment explanation
Indices: 1277072--1277141 Score: 68
Period size: 9 Copynumber: 7.7 Consensus size: 9
1277062 ACAATTTTTC
1277072 CGTTGTCTGT
1 CGTTGTC-GT
*
1277082 CGTTGTTGT
1 CGTTGTCGT
**
1277091 CAATGTCGT
1 CGTTGTCGT
1277100 CGTTGTCGT
1 CGTTGTCGT
* *
1277109 CGTCGTCGG
1 CGTTGTCGT
1277118 CGTTGTCGT
1 CGTTGTCGT
* *
1277127 CGGTGGCGT
1 CGTTGTCGT
1277136 CGTTGT
1 CGTTGT
1277142 AAACTTTTCA
Statistics
Matches: 46, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
9 40 0.87
10 6 0.13
ACGTcount: A:0.03, C:0.21, G:0.36, T:0.40
Consensus pattern (9 bp):
CGTTGTCGT
Found at i:1277789 original size:165 final size:164
Alignment explanation
Indices: 1277316--1278203 Score: 1117
Period size: 162 Copynumber: 5.4 Consensus size: 164
1277306 TTTTTTGAAA
* * *
1277316 AATATATAGAGAAAATCTTTTAAAATCTTCCTCTC-AAAACTATTAGGCAAGAAAAGCTCAAATC
1 AATATATAGAGAAAATCTTTTAAAATCTTCTTCTCAAAAACT-TTAGGCCAGAAAAGCTCAAATT
* * * *
1277380 AAAATGGAAGCATCCTCCGGTAGTGTAGATTTAAGTTTTTTTTCAAATCATGGT-CTCCGGGGGT
65 AAAATGGAAGCATCCTCAGGTAGTGTAGATTCAAG--ATTGTTCAAATCATGGTCCT-C-GGGGT
** *
1277444 AGGAAGGGGCCACAATAGGGGGATCAAGTTTTCCATAGG
126 AGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGG
* * *
1277483 AATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAATTATTTGGCCAGAAAAGCTCAAATT
1 AATATATAGAGAAAATCTTTTAAAATCTTCTTCTCAAAAACT-TTAGGCCAGAAAAGCTCAAATT
*
1277548 AAAATGGAAGCAT-C-CA-GTAGTGTAGATTCAAGATTGTTCAAATCATGGTCCTTTGGGGTAGG
65 AAAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGATTGTTCAAATCATGGTCC-TCGGGGTAGG
1277610 GTGGGGCCACAATAGGGGGATCAAGTTTTACATAGG
129 GTGGGGCCACAATAGGGGGATCAAGTTTTACATAGG
* * *
1277646 AATATATAGAGAAAAATCTTTTAAAATCTTCATCTCAAAAACTGTAGG-CAAAAAAGCTCAAATT
1 AATATATAGAG-AAAATCTTTTAAAATCTTCTTCTCAAAAACTTTAGGCCAGAAAAGCTCAAATT
* * * * *
1277710 AAAATGGAAGCATCCTTAGGTAGTGTCA-ATTCAAG-TCTGATCAATTCTTGGTCCCCGGGGGTA
65 AAAATGGAAGCATCCTCAGGTAGTGT-AGATTCAAGAT-TGTTCAAATCATGGTCCTC-GGGGTA
*
1277773 GGGTGGGGCCACAATAGGGGGATCATGTTTTACATAGG
127 GGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGG
* * * *
1277811 AATATATAGAAAAAATCTTTAAAAATCTTCTTCTCAAAAACAATTT-GGCCAGGAAAGCTCACAT
1 AATATATAGAGAAAATCTTTTAAAATCTTCTTCTCAAAAAC--TTTAGGCCAGAAAAGCTCAAAT
* * * * *
1277875 TTAAGTGGAAGCATTCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGATCCTCTGGGTAG
64 TAAAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGATTGTTCAAATCATGG-TCCTCGGGGTAG
*
1277940 GGTGGGGCCACACTAGGGGGATCAAGTTTTACATAGG
128 GGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGG
* * * *
1277977 AATATATAGAGAAAA-C-TTTAAAA--TACTTCTCAAAACCTATAAGGCCAGAAAAGCTCATATT
1 AATATATAGAGAAAATCTTTTAAAATCTTCTTCTCAAAAACT-TTAGGCCAGAAAAGCTCAAATT
*
1278038 AAAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGATTGTTCAAATCATGGATCCTCTGGGTAGG
65 AAAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGATTGTTCAAATCATGG-TCCTCGGGGTAGG
*
1278103 GTGGGGCCACACTAGGGGGATCAAGTTTTACATAGG
129 GTGGGGCCACAATAGGGGGATCAAGTTTTACATAGG
* * * *
1278139 AATATATAGAGAAAA-C-TTTAAAA--TACTTCTCAAAACCTATAAGGCCAGAAAAGCTCATATT
1 AATATATAGAGAAAATCTTTTAAAATCTTCTTCTCAAAAACT-TTAGGCCAGAAAAGCTCAAATT
1278200 AAAA
65 AAAA
1278204 NNNNNNNNNN
Statistics
Matches: 647, Mismatches: 56, Indels: 41
0.87 0.08 0.06
Matches are distributed among these distances:
160 1 0.00
161 1 0.00
162 219 0.34
163 71 0.11
164 65 0.10
165 101 0.16
166 112 0.17
167 39 0.06
168 38 0.06
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (164 bp):
AATATATAGAGAAAATCTTTTAAAATCTTCTTCTCAAAAACTTTAGGCCAGAAAAGCTCAAATTA
AAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGATTGTTCAAATCATGGTCCTCGGGGTAGGGT
GGGGCCACAATAGGGGGATCAAGTTTTACATAGG
Found at i:1278033 original size:328 final size:326
Alignment explanation
Indices: 1277316--1278203 Score: 1206
Period size: 328 Copynumber: 2.7 Consensus size: 326
1277306 TTTTTTGAAA
* *
1277316 AATATATAGAGAAAATCTTTTAAAATCTTCCTCTCAAAACTATTAGGCAAGAAAAGCTCAAATCA
1 AATATATAGAGAAAATCTTTTAAAATCTT-CTCTCAAAACTA-TAGGCCAGAAAAGCTCAAATTA
* * * *
1277381 AAATGGAAGCATCCTCCGGTAGTGTAGATTTAAGTTTTTTTTCAAATCATGGTCTCCGGGGGTAG
64 AAATGGAAGCATCCTCAGGTAGTGTAGATTCAAG--TTTGTTCAAATCATGGTCCCCGGGGGTAG
** *
1277446 GAAGGGGCCACAATAGGGGGATCAAGTTTTCCATAGGAATATATAGAGAAAATCTTTAAAAATCT
127 GGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCT
**
1277511 TCTTCTCAAAAATTATTTGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCAGTAGTGTAGATT
192 TCTTCTCAAAAACAATTTGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCAGTAGTGTAGATT
*
1277576 CAAGATTGTTCAAATCATGGTCCTTTGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTAC
257 CAAGATTGTTCAAATCATGGTCCTCTGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTAC
1277641 ATAGG
322 ATAGG
* *
1277646 AATATATAGAGAAAAATCTTTTAAAATCTTCATCTCAAAAACTGTAGG-CAAAAAAGCTCAAATT
1 AATATATAGAG-AAAATCTTTTAAAATCTTC-TCTC-AAAACTATAGGCCAGAAAAGCTCAAATT
* * * * *
1277710 AAAATGGAAGCATCCTTAGGTAGTGTCA-ATTCAAGTCTGATCAATTCTTGGTCCCCGGGGGTAG
63 AAAATGGAAGCATCCTCAGGTAGTGT-AGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAG
* *
1277774 GGTGGGGCCACAATAGGGGGATCATGTTTTACATAGGAATATATAGAAAAAATCTTTAAAAATCT
127 GGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCT
* * * *
1277839 TCTTCTCAAAAACAATTTGGCCAGGAAAGCTCACATTTAAGTGGAAGCATTCTCAGGTAGTGTAG
192 TCTTCTCAAAAACAATTTGGCCAGAAAAGCTCAAATTAAAATGGAAGCA-TC-CA-GTAGTGTAG
* *
1277904 ATTCAAGTTTGTTCAAATCATGGATCCTCT-GGGTAGGGTGGGGCCACACTAGGGGGATCAAGTT
254 ATTCAAGATTGTTCAAATCATGG-TCCTCTGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTT
1277968 TTACATAGG
318 TTACATAGG
*
1277977 AATATATAGAGAAAA-C-TTTAAAATAC-T-TCTCAAAACCTATAAGGCCAGAAAAGCTCATATT
1 AATATATAGAGAAAATCTTTTAAAAT-CTTCTCTCAAAA-CTAT-AGGCCAGAAAAGCTCAAATT
* * *
1278038 AAAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGATTGTTCAAATCATGGATCCTC-TGGGTAG
63 AAAATGGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGG-TCCCCGGGGGTAG
*
1278102 GGTGGGGCCACACTAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAA-CTTT-AAAA--T
127 GGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCT
* * * ** *
1278163 ACTTCTCAAAACCTATAAGGCCAGAAAAGCTCATATTAAAA
192 TCTTCTCAAAAACAATTTGGCCAGAAAAGCTCAAATTAAAA
1278204 NNNNNNNNNN
Statistics
Matches: 494, Mismatches: 50, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
324 33 0.07
325 4 0.01
326 11 0.02
327 8 0.02
328 247 0.50
329 8 0.02
330 61 0.12
331 111 0.22
332 11 0.02
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (326 bp):
AATATATAGAGAAAATCTTTTAAAATCTTCTCTCAAAACTATAGGCCAGAAAAGCTCAAATTAAA
ATGGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTG
GGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
CTCAAAAACAATTTGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCAGTAGTGTAGATTCAAG
ATTGTTCAAATCATGGTCCTCTGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAG
G
Found at i:1278986 original size:224 final size:223
Alignment explanation
Indices: 1278596--1279037 Score: 866
Period size: 224 Copynumber: 2.0 Consensus size: 223
1278586 NNNNNNGGGA
*
1278596 GGGGGGGGGGTATATAGGAAGAGAGAAAAATCTTCTTACAGGTACAACAACAAAAGGGGCTTGGT
1 GGGGGGGGGGGATATAGGAAGAGAGAAAAATCTTCTTACAGGTACAACAACAAAAGGGGCTTGGT
1278661 ATTTACCATAAAAAAAGAGGTGGATAAAAATTGGCAGATTTTCAATTTTTTTAGCAAGATCTACT
66 ATTTACCATAAAAAAAGAGGTGGATAAAAATTGGCAGATTTTCAATTTTTTTAGCAAGATCTACT
1278726 GTACTTAGTTGTCAAAATATTTTGATTCTGTAATGCTAATTTGATCAGAATTAAGGCAATTGTTG
131 GTACTTAGTTGTCAAAATATTTTGATTCTGTAATGCTAATTTGATCAGAATTAAGGCAATTGTTG
1278791 CTCAGGTGAGCGATGTGGCCCCNTGGGGG
196 CTCAGGTGAGCGATGTGGCCCC-TGGGGG
1278820 GGGGGGGGGGGATATAGGAAGAGAGAAAAATCTTCTTACAGGTACAACAACAAAAGGGGCTTGGT
1 GGGGGGGGGGGATATAGGAAGAGAGAAAAATCTTCTTACAGGTACAACAACAAAAGGGGCTTGGT
1278885 ATTTACCATAAAAAAAGAGGTGGATAAAAATTGGCAGATTTTCAATTTTTTTAGCAAGATCTACT
66 ATTTACCATAAAAAAAGAGGTGGATAAAAATTGGCAGATTTTCAATTTTTTTAGCAAGATCTACT
1278950 GTACTTAGTTGTCAAAATATTTTGATTCTGTAATGCTAATTTGATCAGAATTAAGGCAATTGTTG
131 GTACTTAGTTGTCAAAATATTTTGATTCTGTAATGCTAATTTGATCAGAATTAAGGCAATTGTTG
1279015 CTCAGGTGAGCGATGTGGCCCCT
196 CTCAGGTGAGCGATGTGGCCCCT
1279038 TGGCCTCTTG
Statistics
Matches: 217, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
223 1 0.00
224 216 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (223 bp):
GGGGGGGGGGGATATAGGAAGAGAGAAAAATCTTCTTACAGGTACAACAACAAAAGGGGCTTGGT
ATTTACCATAAAAAAAGAGGTGGATAAAAATTGGCAGATTTTCAATTTTTTTAGCAAGATCTACT
GTACTTAGTTGTCAAAATATTTTGATTCTGTAATGCTAATTTGATCAGAATTAAGGCAATTGTTG
CTCAGGTGAGCGATGTGGCCCCTGGGGG
Found at i:1285277 original size:4 final size:4
Alignment explanation
Indices: 1285268--1285309 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
1285258 GTTACACTGT
*
1285268 TCCG TCCG TCCG TCCG TCTG TCCG TCCG TCCG TCCG TCCG TC
1 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC
1285310 TGTCACGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.48, G:0.24, T:0.29
Consensus pattern (4 bp):
TCCG
Found at i:1286056 original size:163 final size:162
Alignment explanation
Indices: 1285844--1286234 Score: 570
Period size: 163 Copynumber: 2.4 Consensus size: 162
1285834 AGTAGCTACG
* * * * *
1285844 TCATCTCTTGGGATATAATTGGGGCTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
* *
1285909 TCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAACAAACATTGATCC
66 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACT-AAAAAA-AAACATAGATCC
*
1285974 AAGAGCTCCTCTTATGATTTAATGGATAGACA-A
129 AAGAACTCCTCTTATGATTTAATGGATAGACACA
* * *
1286007 TCATATCTTGGGATATGATAGGGACTGTTCTATATATGTGCAGTAAGGTTTTCAAAATTTAAATT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
** *
1286072 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTTCAAAAAAACATAGATCCTA
66 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAACATAGATCCAA
*
1286137 GAACTCCTTTTATGATTTAATGGATAGACACA
131 GAACTCCTCTTATGATTTAATGGATAGACACA
* * * *
1286169 TCATATCTTGGGATATGATAGGAACTGTTCCATAGATGTGCATTACGGTTTTGAAAAA-TTAAAT
1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTT-AAAAATTTAAAT
1286233 TT
65 TT
1286235 AACCCTGAGG
Statistics
Matches: 205, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
161 40 0.20
162 60 0.29
163 105 0.51
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (162 bp):
TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAACATAGATCCAA
GAACTCCTCTTATGATTTAATGGATAGACACA
Found at i:1286594 original size:189 final size:188
Alignment explanation
Indices: 1286274--1286651 Score: 738
Period size: 189 Copynumber: 2.0 Consensus size: 188
1286264 TACCTTTTGA
1286274 TGCCCTTTAAGGATCAAGAATTTATATGGTTGAGGGGTGGGGATCTCAACTGTTTTCGAGATATT
1 TGCCCTTTAAGGATCAAGAATTTATATGGTTGAGGGGTGGGGATCTCAACTGTTTTCGAGATATT
1286339 TGTGCTCTTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACTGTTTGA
66 TGTGCTCTTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACTGTTTGA
1286404 TGCCCCTTGACACAAGGAACAAGAATATATATGGTTTAAGGGTGGGGATCTCAACTGT
131 TGCCCCTTGACACAAGGAACAAGAATATATATGGTTTAAGGGTGGGGATCTCAACTGT
*
1286462 NTGCCCTTTAAGGATCAATAATTTATATGGTTGAGGGGTGGGGATCTCAACTGTTTTCGAGATAT
1 -TGCCCTTTAAGGATCAAGAATTTATATGGTTGAGGGGTGGGGATCTCAACTGTTTTCGAGATAT
1286527 TTGTGCTCTTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACTGTTTG
65 TTGTGCTCTTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACTGTTTG
1286592 ATGCCCCTTGACACAAGGAACAAGAATATATATGGTTTAAGGGTGGGGATCTCAACTGT
130 ATGCCCCTTGACACAAGGAACAAGAATATATATGGTTTAAGGGTGGGGATCTCAACTGT
1286651 T
1 T
1286652 TTGAAGATAT
Statistics
Matches: 188, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
188 1 0.01
189 187 0.99
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (188 bp):
TGCCCTTTAAGGATCAAGAATTTATATGGTTGAGGGGTGGGGATCTCAACTGTTTTCGAGATATT
TGTGCTCTTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACTGTTTGA
TGCCCCTTGACACAAGGAACAAGAATATATATGGTTTAAGGGTGGGGATCTCAACTGT
Found at i:1286753 original size:134 final size:135
Alignment explanation
Indices: 1286485--1286769 Score: 373
Period size: 134 Copynumber: 2.1 Consensus size: 135
1286475 ATCAATAATT
* * *
1286485 TATATGGTTGAGGGGTGGGGATCTCAACTGTTTTCGAGATATTTGTGCTCTTCCTGTTCAAGGGG
1 TATATGGTTTAGGGGTGGGGATCTCAACTGTTTTCGAGATATTAGTGCACTTCCTGTTCAAGGGG
* * * * *
1286550 GGTCATGACCACCCCCGGGGCCCATGACCTACATACTGTTTGATGCCCCTTGACACAAGGAACAA
66 GGTCAGGACCACCCACAGGGCCCATGACCTACATACTATTTGATGCCCCTTGACACAAGAAACAA
1286615 GAATA
131 GAATA
* * * **
1286620 TATATGGTTTAAGGGTGGGGATCTCAACTGTTTT-GAAGATATTAAG-GGACTTGCTGTTTGA-G
1 TATATGGTTTAGGGGTGGGGATCTCAACTGTTTTCG-AGATATT-AGTGCACTTCCTGTTCAAGG
1286682 GGGGTCAGGACCACCCACAGGGCCCATGACCTACATAAC-ATTTGATGCCCCTTGACATC-AGAA
64 GGGGTCAGGACCACCCACAGGGCCCATGACCTACAT-ACTATTTGATGCCCCTTGACA-CAAGAA
*
1286745 ACATGAATA
127 ACAAGAATA
1286754 TATATGGTTTAGGGGT
1 TATATGGTTTAGGGGT
1286770 CATGATTATA
Statistics
Matches: 131, Mismatches: 15, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
134 78 0.60
135 52 0.40
136 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (135 bp):
TATATGGTTTAGGGGTGGGGATCTCAACTGTTTTCGAGATATTAGTGCACTTCCTGTTCAAGGGG
GGTCAGGACCACCCACAGGGCCCATGACCTACATACTATTTGATGCCCCTTGACACAAGAAACAA
GAATA
Found at i:1306128 original size:2 final size:2
Alignment explanation
Indices: 1306121--1306148 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1306111 CCGTCACAGT
1306121 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1306149 ATAAAATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1342233 original size:273 final size:273
Alignment explanation
Indices: 1341746--1342293 Score: 1087
Period size: 273 Copynumber: 2.0 Consensus size: 273
1341736 TGTTACATTG
1341746 TAGTTTTCAAGAATATTTTTTAAACATGTTTCTTATATATTTCTATGTTAAGCGCCGCCTGAACC
1 TAGTTTTCAAGAATATTTTTTAAACATGTTTCTTATATATTTCTATGTTAAGCGCCGCCTGAACC
1341811 CCAATTTAAGGTCTGGGGTCAGGATATTTAACAATAAAGGGATTAGGATTCTGCAATAGCCAAAG
66 CCAATTTAAGGTCTGGGGTCAGGATATTTAACAATAAAGGGATTAGGATTCTGCAATAGCCAAAG
1341876 ATATATGCATAGTTATATCCAAAAAAGTCGCGTTGTAGCTTTTAAGAAGATTTTTAATCATTTTC
131 ATATATGCATAGTTATATCCAAAAAAGTCGCGTTGTAGCTTTTAAGAAGATTTTTAATCATTTTC
1341941 CTTTTTATTTTAACTTCGAACCCCGTCCAATTTTTTGTCCGAAGACCACAATTTTTAAAATTTTG
196 CTTTTTATTTTAACTTCGAACCCCGTCCAATTTTTTGTCCGAAGACCACAATTTTTAAAATTTTG
1342006 AAACTTAACTATT
261 AAACTTAACTATT
1342019 TAGTTTTCAAGAATATTTTTTAAACATGTTTCTTATATATTTCTATGTTAAGCGCCGCCTGAACC
1 TAGTTTTCAAGAATATTTTTTAAACATGTTTCTTATATATTTCTATGTTAAGCGCCGCCTGAACC
1342084 CCAATTTAAGGTCTGGGGTCAGGATATTTAACAATAAAGGGATTAGGATTCTGCAATAGCCAAAG
66 CCAATTTAAGGTCTGGGGTCAGGATATTTAACAATAAAGGGATTAGGATTCTGCAATAGCCAAAG
1342149 ATATATGCATAGTTATATCCAAAAAAGTCGCGTTGTAGCTTTTAAGAAGATTTTTAATCATTTTC
131 ATATATGCATAGTTATATCCAAAAAAGTCGCGTTGTAGCTTTTAAGAAGATTTTTAATCATTTTC
*
1342214 CTTTTTATTTTAACTTCGAACCCTGTCCAATTTTTTGTCCGAAGACCACAATTTTTAAAATTTTG
196 CTTTTTATTTTAACTTCGAACCCCGTCCAATTTTTTGTCCGAAGACCACAATTTTTAAAATTTTG
1342279 AAACTTAACTATT
261 AAACTTAACTATT
1342292 TA
1 TA
1342294 TACAAGCTTA
Statistics
Matches: 274, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
273 274 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (273 bp):
TAGTTTTCAAGAATATTTTTTAAACATGTTTCTTATATATTTCTATGTTAAGCGCCGCCTGAACC
CCAATTTAAGGTCTGGGGTCAGGATATTTAACAATAAAGGGATTAGGATTCTGCAATAGCCAAAG
ATATATGCATAGTTATATCCAAAAAAGTCGCGTTGTAGCTTTTAAGAAGATTTTTAATCATTTTC
CTTTTTATTTTAACTTCGAACCCCGTCCAATTTTTTGTCCGAAGACCACAATTTTTAAAATTTTG
AAACTTAACTATT
Found at i:1343450 original size:146 final size:146
Alignment explanation
Indices: 1342875--1343417 Score: 955
Period size: 146 Copynumber: 3.7 Consensus size: 146
1342865 GTCTGTGCAA
* *
1342875 TCGTCTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTCACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1342940 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCGAAGTCAAGGTCACGGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCGAAGTCAAGGTCACGGGC
1343005 AGAAAAAGTGCAAAAT
131 AGAAAAAGTGCAAAAT
1343021 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
1343086 TTATGACCTAAGAGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCGAAGTCAAGGTCACGGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCGAAGTCAAGGTCACGGGC
1343151 AGAAAAAGTGCAAAAT
131 AGAAAAAGTGCAAAAT
*
1343167 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACGAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * * *
1343232 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGCCATTTGGGC-ATGGTCAAGGTCACTGG
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCGA-AGTCAAGGTCACGGG
*
1343296 CAGAAAAAATGCAAAAT
130 CAGAAAAAGTGCAAAAT
1343313 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
1343378 TTATGA-TTAAAGGGTGTGTCATGACCTTGACCCAAGGTCA
66 TTATGACCT-AAGGGTGTGTCATGACCTTGACCCAAGGTCA
1343418 ATTGAGAAAG
Statistics
Matches: 380, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
145 2 0.01
146 378 0.99
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (146 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCGAAGTCAAGGTCACGGGC
AGAAAAAGTGCAAAAT
Found at i:1350629 original size:107 final size:107
Alignment explanation
Indices: 1350488--1350681 Score: 275
Period size: 107 Copynumber: 1.8 Consensus size: 107
1350478 CTTATATATT
** * * *
1350488 TTTAATAATGGCAATGTCCTATAATTCAATGACCATTCAAGGACAGAAAGATTCCAA-TACTT-A
1 TTTAATAATGAAAATATCCTATAAGTCAATGACCATTCAAGGACAGAAAGACT-CAACTACTTAA
1350551 TTTTTTGAAATTTTAGAAAAATAGAATCATAATGTTGACATAAA
65 TTTTTTGAAA-TTTAGAAAAATAGAATCATAATGTTGACATAAA
* *
1350595 TTTAATAATGAAAATATCCTATCAGTCAATGACCATTCAAGGACAGAAAGACTCAACTGCTTAAA
1 TTTAATAATGAAAATATCCTATAAGTCAATGACCATTCAAGGACAGAAAGACTCAACTACTT-AA
*
1350660 TTTTTTGAAATTTGGAAAAATA
65 TTTTTTGAAATTTAGAAAAATA
1350682 ACATTAAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
106 3 0.04
107 51 0.67
108 11 0.14
109 11 0.14
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (107 bp):
TTTAATAATGAAAATATCCTATAAGTCAATGACCATTCAAGGACAGAAAGACTCAACTACTTAAT
TTTTTGAAATTTAGAAAAATAGAATCATAATGTTGACATAAA
Found at i:1354778 original size:180 final size:179
Alignment explanation
Indices: 1354424--1354878 Score: 756
Period size: 180 Copynumber: 2.6 Consensus size: 179
1354414 GATACCATTT
*
1354424 GGAAGGCTAGGGGGGAACTCCTACAGAAATAACAGTTACAAAATGATTACATGTAGAATATCATA
1 GGAATGCTAGGGGGGAACTCCTACAGAAATAACAGTTACAAAATGATTACATGTAGAATATCATA
* *
1354489 CGATTAATATTATACACAGAT----AAAAAAAAGAAGCACCTTCTACACTAACCTTTACATCCTG
66 CGATTAATATTATACACAGATAAAAAAAAAAAAAAAACACCTTCTACACTAACCTTTACATCCTG
1354550 GGTGGGGGATTCTATTGTGGTGGTGGTCATCTTTGAAGAGAACCTAGTG
131 GGTGGGGGATTCTATTGTGGTGGTGGTCATCTTTGAAGAGAACCTAGTG
* * *
1354599 GGAATGCTAGGGGAGAACTCCTACAGAAATAACAGTTACAAAATGATTACACGCAGAATATCATA
1 GGAATGCTAGGGGGGAACTCCTACAGAAATAACAGTTACAAAATGATTACATGTAGAATATCATA
1354664 CGATTAATATTATACACAGATAAAAAAAAAAAAAAAAACACCTTCTACACTAACCTTTACATCCT
66 CGATTAATATTATACACAGAT-AAAAAAAAAAAAAAAACACCTTCTACACTAACCTTTACATCCT
1354729 GGGTGGGGGATTCTATTGTGGTGGTGGTCATCTTTGAAGAGAACCTAGTG
130 GGGTGGGGGATTCTATTGTGGTGGTGGTCATCTTTGAAGAGAACCTAGTG
* *
1354779 GGAATGCTAGGGGGGAACTCCTAAAGAAATAACAGTTACAAAATGATTACATGTAGAATGTCATA
1 GGAATGCTAGGGGGGAACTCCTACAGAAATAACAGTTACAAAATGATTACATGTAGAATATCATA
* * * *
1354844 CGATTAATAGATATACACAGACATAAAAGAAAAAA
66 CGATTAATA-TTATACACAGATAAAAAAAAAAAAA
1354879 TTACATACAC
Statistics
Matches: 259, Mismatches: 15, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
175 82 0.32
180 167 0.64
181 10 0.04
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (179 bp):
GGAATGCTAGGGGGGAACTCCTACAGAAATAACAGTTACAAAATGATTACATGTAGAATATCATA
CGATTAATATTATACACAGATAAAAAAAAAAAAAAAACACCTTCTACACTAACCTTTACATCCTG
GGTGGGGGATTCTATTGTGGTGGTGGTCATCTTTGAAGAGAACCTAGTG
Found at i:1355486 original size:28 final size:28
Alignment explanation
Indices: 1355451--1355504 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1355441 AGTAATTTTA
1355451 AAAAAGTGCAGTACTGTAGTACATATTT
1 AAAAAGTGCAGTACTGTAGTACATATTT
1355479 AAAAAGTGCAGTACTGTAGTACATAT
1 AAAAAGTGCAGTACTGTAGTACATAT
1355505 AACAATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (28 bp):
AAAAAGTGCAGTACTGTAGTACATATTT
Found at i:1367986 original size:55 final size:55
Alignment explanation
Indices: 1367870--1368014 Score: 238
Period size: 55 Copynumber: 2.7 Consensus size: 55
1367860 GAGTCTTCCA
* * *
1367870 TAAGCCTTTAGTATAAATATATAGAAAAAGCC-TTTGAGTGGGTGGAGACTATTG
1 TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTTGAGTGGGTGGAGACTATTG
*
1367924 TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTTGAGTGGGTGGAGTCTATTG
1 TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTTGAGTGGGTGGAGACTATTG
*
1367979 TAAGCCTTTGGTATCGATATATAGAGAAAGCCTTTT
1 TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTT
1368015 ATCTCATTAG
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
54 29 0.34
55 56 0.66
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (55 bp):
TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTTGAGTGGGTGGAGACTATTG
Found at i:1368037 original size:55 final size:55
Alignment explanation
Indices: 1367870--1368037 Score: 137
Period size: 55 Copynumber: 3.1 Consensus size: 55
1367860 GAGTCTTCCA
* * * * ** * *
1367870 TAAGCCTTTAGTATAAATATATAGAAAAAGCC-TTTGAGTGGGTGGAGA-CTATTG
1 TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTTGACTCAGTAGA-ATCAATTG
* ** * * *
1367924 TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTTGAGTGGGTGGAGTCTATTG
1 TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTTGACTCAGTAGAATCAATTG
* *
1367979 TAAGCCTTTGGTATCGATATATAGAGAAAGCCTTTT-ATCTCATTAGAAT-AATTGG
1 TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTTGA-CTCAGTAGAATCAATT-G
1368034 TAAG
1 TAAG
1368038 AATATAGAGT
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
54 33 0.34
55 65 0.66
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (55 bp):
TAAGCCTTTGGTATAGATATATAGAGAAAGCCTTTTGACTCAGTAGAATCAATTG
Found at i:1370633 original size:21 final size:21
Alignment explanation
Indices: 1370609--1370659 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
1370599 GTGTTAAATA
1370609 GTTCGTGTAACGTG-GGTGATC
1 GTTCGTGTAACGTGCGG-GATC
1370630 GTTCGTGTAACGTGCGGGATC
1 GTTCGTGTAACGTGCGGGATC
*
1370651 GTGCGTGTA
1 GTTCGTGTA
1370660 TCAGGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.14, C:0.16, G:0.39, T:0.31
Consensus pattern (21 bp):
GTTCGTGTAACGTGCGGGATC
Found at i:1371680 original size:11 final size:11
Alignment explanation
Indices: 1371660--1371715 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
1371650 TAAGTTAGTG
*
1371660 ATCGTCCGTGT
1 ATCGTGCGTGT
1371671 ATCGTGCGTG-
1 ATCGTGCGTGT
*
1371681 ATCGTTCGTGT
1 ATCGTGCGTGT
1371692 ATCGTGCGTG-
1 ATCGTGCGTGT
*
1371702 ATCGTTCGTGT
1 ATCGTGCGTGT
1371713 ATC
1 ATC
1371716 AGAATCGTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 18 0.46
11 21 0.54
ACGTcount: A:0.11, C:0.21, G:0.30, T:0.38
Consensus pattern (11 bp):
ATCGTGCGTGT
Found at i:1371683 original size:21 final size:21
Alignment explanation
Indices: 1371657--1371715 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1371647 CAGTAAGTTA
*
1371657 GTGATCGTCCGTGTATCGTGC
1 GTGATCGTTCGTGTATCGTGC
1371678 GTGATCGTTCGTGTATCGTGC
1 GTGATCGTTCGTGTATCGTGC
1371699 GTGATCGTTCGTGTATC
1 GTGATCGTTCGTGTATC
1371716 AGAATCGTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.10, C:0.20, G:0.32, T:0.37
Consensus pattern (21 bp):
GTGATCGTTCGTGTATCGTGC
Found at i:1371690 original size:10 final size:10
Alignment explanation
Indices: 1371657--1371711 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
1371647 CAGTAAGTTA
*
1371657 GTGATCGTCC
1 GTGATCGTGC
1371667 GTGTATCGTGC
1 GTG-ATCGTGC
*
1371678 GTGATCGTTC
1 GTGATCGTGC
1371688 GTGTATCGTGC
1 GTG-ATCGTGC
*
1371699 GTGATCGTTC
1 GTGATCGTGC
1371709 GTG
1 GTG
1371712 TATCAGAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 21 0.54
11 18 0.46
ACGTcount: A:0.09, C:0.20, G:0.35, T:0.36
Consensus pattern (10 bp):
GTGATCGTGC
Found at i:1373264 original size:48 final size:48
Alignment explanation
Indices: 1373184--1373809 Score: 932
Period size: 48 Copynumber: 13.0 Consensus size: 48
1373174 CTCATCCCCT
* * *
1373184 CCTCTACTGGTGCTGTCTGGACAGCGACGGACTCTGGTTGAGGGGTAC
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
* * *
1373232 CCTCTACTGGTGCTATCTGGACGGTGATGGACTCTGGTTGGGGGGTAT
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
* * *
1373280 CCTCTACTGGTGCTGTCTGGACAGTGATGGACTCTGGTTGGGGGGGAC
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
*
1373328 CCTCTACTGGTGCTGTCTGGACGGCGACGGACTCTGGTTGGGGGGTAC
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
* *
1373376 CCTCTACTGGTGCTGTCTGGACGGCGACGGACTCTAGTTGGGGGGTAC
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
* *
1373424 CCTCTACTGGTGCTGTCTGGACGGCGACGGACTCTAGTTGGGGGGTAC
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
* *
1373472 CCTCTACTGGTGCTGTCTGGATGGCGACGGACTCTGGTTGGGGGGTAC
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
* *
1373520 CCTCTACTGGTGCTGTCTGGACGGCGACGGACTCTAGTTGGGGGGTAC
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
*
1373568 CCTCTACTGGTGCTGTCTGGATGGTGACGGACTCTGGTTGGGGGGTAC
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
* * * *
1373616 CCTCTACTGGTGCTGTCTGGACGGTGATGAACTCTGGTTGGAGGGTAT
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
* * *
1373664 CCTCTAAC-GTTGCTGTCTGGACGGTGAGGGACTCTGGTTGGGGGGTAT
1 CCTCT-ACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
* *
1373712 CCTCTACTGGTGCTGTCTGGATC-GTGAAGGACTCTGGTTTGGGGGTAC
1 CCTCTACTGGTGCTGTCTGGA-CGGTGACGGACTCTGGTTGGGGGGTAC
* * * *
1373760 CCTCTACTGGTGCTGTCTGGACGATGACAGACTCTGTTTGGTGGGTAC
1 CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
1373808 CC
1 CC
1373810 CCACCGGCGA
Statistics
Matches: 533, Mismatches: 41, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
47 3 0.01
48 527 0.99
49 3 0.01
ACGTcount: A:0.12, C:0.23, G:0.37, T:0.28
Consensus pattern (48 bp):
CCTCTACTGGTGCTGTCTGGACGGTGACGGACTCTGGTTGGGGGGTAC
Found at i:1373843 original size:48 final size:48
Alignment explanation
Indices: 1373789--1373909 Score: 140
Period size: 48 Copynumber: 2.5 Consensus size: 48
1373779 GACGATGACA
* * *
1373789 GACTCTGTTTGGTGGGTACCC-CCAC-CGGCGACAACCTGCGTCGTGATGG
1 GACTCTGGTTGGAGGGTACCCTCC-CTC-GCGACAACCTGCGTCGT-AAGG
* **
1373838 G-CTCTGGCTGGAGGGTACCCTCCCTCTTGACAACCTGCGTCGTAAGG
1 GACTCTGGTTGGAGGGTACCCTCCCTCGCGACAACCTGCGTCGTAAGG
1373885 GACTCTGGTTGGAGGGTACCCTCCC
1 GACTCTGGTTGGAGGGTACCCTCCC
1373910 CGGTGACAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
47 4 0.06
48 54 0.87
49 4 0.06
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.23
Consensus pattern (48 bp):
GACTCTGGTTGGAGGGTACCCTCCCTCGCGACAACCTGCGTCGTAAGG
Found at i:1373917 original size:48 final size:48
Alignment explanation
Indices: 1373802--1373960 Score: 171
Period size: 48 Copynumber: 3.3 Consensus size: 48
1373792 TCTGTTTGGT
*
1373802 GGGTACCC-CCACCGGCGACAACCTGCGTCGTGATGGG-CTCTGGCTGGA
1 GGGTACCCTCC-CCGGTGACAACCTGCGTCGT-ATGGGACTCTGGCTGGA
* * *
1373850 GGGTACCCTCCCTC-TTGACAACCTGCGTCGTAAGGGACTCTGGTTGGA
1 GGGTACCCTCCC-CGGTGACAACCTGCGTCGTATGGGACTCTGGCTGGA
** * * * *
1373898 GGGTACCCTCCCCGGTGACAGTCTGCGTCATGTTGGACTCTGGCTGGG
1 GGGTACCCTCCCCGGTGACAACCTGCGTCGTATGGGACTCTGGCTGGA
*
1373946 GGGTACCATCCCCGG
1 GGGTACCCTCCCCGG
1373961 AGGTGGCCTT
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
47 5 0.05
48 85 0.91
49 3 0.03
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.21
Consensus pattern (48 bp):
GGGTACCCTCCCCGGTGACAACCTGCGTCGTATGGGACTCTGGCTGGA
Found at i:1374047 original size:13 final size:13
Alignment explanation
Indices: 1374025--1374059 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1374015 ATTTTTCTGC
*
1374025 ATAA-TAATAATA
1 ATAATTAATAAAA
1374037 ATAATTAATAAAA
1 ATAATTAATAAAA
1374050 ATAATTAATA
1 ATAATTAATA
1374060 TATTCTGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATTAATAAAA
Found at i:1376198 original size:126 final size:126
Alignment explanation
Indices: 1375968--1376210 Score: 360
Period size: 126 Copynumber: 1.9 Consensus size: 126
1375958 TTTCAATACA
*
1375968 CTGTACCAGCTGCAAAGAACTCGTTCTCTGCATCCAATCAGAAAAAGTAAAATAGTTTTTGGAGG
1 CTGTACCAGCTGCAAAGAACTCGTTCTCTGCATCCAATCAGAAAAAGTAAAATAGTTTTTGAAGG
* * * * *
1376033 GAAATTTAACATTTACAATGTATAACAAGACAACGCTAATATCCAATCAGAAAATCTTACG
66 GAAATTCAACATTCACAATATATAACAAAACAACACTAATATCCAATCAGAAAATCTTACG
* * * * * **
1376094 CTGTACCAGCTGCAAAGAATTTGTTTTCTGCATCCAATGAGTAGGAGTAAAATAGTTTTTGAAGG
1 CTGTACCAGCTGCAAAGAACTCGTTCTCTGCATCCAATCAGAAAAAGTAAAATAGTTTTTGAAGG
*
1376159 GAAGTTCAACATTCACAATATATAACAAAACAACACTAATATCCAATCAGAA
66 GAAATTCAACATTCACAATATATAACAAAACAACACTAATATCCAATCAGAA
1376211 TAAACTTAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
126 103 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (126 bp):
CTGTACCAGCTGCAAAGAACTCGTTCTCTGCATCCAATCAGAAAAAGTAAAATAGTTTTTGAAGG
GAAATTCAACATTCACAATATATAACAAAACAACACTAATATCCAATCAGAAAATCTTACG
Found at i:1376476 original size:30 final size:30
Alignment explanation
Indices: 1376440--1376497 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1376430 CTTATTTTAG
1376440 AAATAGCAGTCTTT-CAGTTCATCACACAGA
1 AAATAGCAGTCTTTCCA-TTCATCACACAGA
* *
1376470 AAATAGCAGTTTTTCCATTCATCTCACA
1 AAATAGCAGTCTTTCCATTCATCACACA
1376498 TTCAGGTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (30 bp):
AAATAGCAGTCTTTCCATTCATCACACAGA
Found at i:1380895 original size:2 final size:2
Alignment explanation
Indices: 1380888--1380917 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1380878 TTAAAAGCAT
1380888 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1380918 GGGGGGGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1397299 original size:180 final size:180
Alignment explanation
Indices: 1396998--1397783 Score: 1120
Period size: 180 Copynumber: 4.4 Consensus size: 180
1396988 AGTAAAATGG
* * * * * *
1396998 TATGCAATATTTTGCTAAAAAAGACTTAGTTCAAAAGCTGGTATTTTTTTCAGAAATAATCAGAA
1 TATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCAGTA
* * * *
1397063 ATAAAAATCCTAGAAATATGCACACCTCT-AATACATGTACAATTAATCTGCAAAAGAACAACTT
66 ATAAAAATCCTAGCAATATGCACACCTCTGATTACATGTATAATTGATCTGCAAAAGAACAACTT
1397127 TCTATCTTGAAAACTGTAGGAGGACTTATCCGTACAATGA-GGTAACCCTA
131 TCTATCTTGAAAACTGTAGGAGGACTTATCCGTACAATGAGGGT-ACCCTA
* * * *
1397177 TATGCAATATTTTGCTAAAAATTGACTAACTTCAAAAGCTGGTATTTTTGTCACAAATTATCAGT
1 TATGCAATATTTTGCCAAAAA-TGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCAGT
*
1397242 AATAAAAATCCTAGCACTATGCACACCTCTGATTA-ATGTATAATTGATCTGCAAAAGAACAAC-
65 AATAAAAATCCTAGCAATATGCACACCTCTGATTACATGTATAATTGATCTGCAAAAGAACAACT
* * * *
1397305 TTCTTATCTTGAAAACTGTAGGAGAAGTTATCCGAACAATGAGGGTACACTA
130 TTC-TATCTTGAAAACTGTAGGAGGACTTATCCGTACAATGAGGGTACCCTA
*
1397357 TATGCAATATTTTGCCAAAAATTGACTAAATTCAAAAGCTGGTATTTTTTTCATAAATTATCAGT
1 TATGCAATATTTTGCCAAAAA-TGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCAGT
** * * *
1397422 AACCAAAATCCTAGCACTATGCACACCTCTGATATA-A-GTATAACTGATCTGCAAAAGAA-AAA
65 AATAAAAATCCTAGCAATATGCACACCTCTGAT-TACATGTATAATTGATCTGCAAAAGAACAAC
* *
1397484 TTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTA
129 TTT-CTATCTTGAAAACTGTAGGAGGACTTATCCGTACAATGAGGGTACCCTA
* **
1397537 TATGCAATATTTTGCCAAAACATAACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCAAA
1 TATGCAATATTTTGCCAAAA-ATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCAGT
* * * *
1397602 AATCAAAATCCTAGCAATATGCATACCTCTGA-TATATGTTTAATTGATCTGCAAAAGAACAACT
65 AATAAAAATCCTAGCAATATGCACACCTCTGATTACATGTATAATTGATCTGCAAAAGAACAACT
1397666 TTCTATCTTGAAAACTGTAGGAGGACTTATCCGTACAATGAGGGTACCCTA
130 TTCTATCTTGAAAACTGTAGGAGGACTTATCCGTACAATGAGGGTACCCTA
* * *
1397717 TATGCAATATTGTGCCAAAAATGACAAAGTTCAAAAGCTGGTGTTTTTTTCATAAATTATCAGTA
1 TATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCAGTA
1397782 AT
66 AT
1397784 CAATTTTCAC
Statistics
Matches: 550, Mismatches: 46, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
178 2 0.00
179 69 0.13
180 463 0.84
181 16 0.03
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (180 bp):
TATGCAATATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCAGTA
ATAAAAATCCTAGCAATATGCACACCTCTGATTACATGTATAATTGATCTGCAAAAGAACAACTT
TCTATCTTGAAAACTGTAGGAGGACTTATCCGTACAATGAGGGTACCCTA
Found at i:1408315 original size:17 final size:17
Alignment explanation
Indices: 1408293--1408325 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1408283 TTACAGTGTG
*
1408293 TTATTTGACGCAATGTT
1 TTATTTGACACAATGTT
1408310 TTATTTGACACAATGT
1 TTATTTGACACAATGT
1408326 GTAACGTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (17 bp):
TTATTTGACACAATGTT
Found at i:1409891 original size:50 final size:51
Alignment explanation
Indices: 1409787--1409891 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
1409777 TATATCACGA
* * *
1409787 ATAATTAACATTTTAAGCAAAATGGTGATTTTTTATATTAAACGTTTCATT
1 ATAATAAACATTTTAAGCAAAATGGTGATTTTTTATATCAAAAGTTTCATT
* *
1409838 ATAATAAACATTTTATGCAAAATGGTGA-TTTTTATATCAAAAGTTTCGTT
1 ATAATAAACATTTTAAGCAAAATGGTGATTTTTTATATCAAAAGTTTCATT
1409888 ATAA
1 ATAA
1409892 GATTTTTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 23 0.47
51 26 0.53
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (51 bp):
ATAATAAACATTTTAAGCAAAATGGTGATTTTTTATATCAAAAGTTTCATT
Found at i:1411328 original size:134 final size:134
Alignment explanation
Indices: 1411090--1411426 Score: 502
Period size: 134 Copynumber: 2.5 Consensus size: 134
1411080 TACGGGTCTA
* * * *
1411090 CAAATATTCATACAATAAAAACAGAATTTCCCTCAACAAAA-C-ATGTTTTTTTATCCTTTCATC
1 CAAATATTCATACAATACAAACAGAATTTCCTTCAACAAAACCAATGCTTTTTTATCATTTCATC
** *
1411153 TTGT-AAGAAACTTTGTGATTCATCTGAATCCAGACTGGTAAACAGTGTTTGCATAGTCATACTC
66 TT-TCAAGAAACCATGTGATTCATCTGAATCCAGACTGGTAAACAATGTTTGCATAGTCATACTC
1411217 TTCTG
130 TTCTG
1411222 CAAATATTCATACAATACAAACAGAATTTCCTTCAACAAAACCAATGCTTTTTTATCATTTCATC
1 CAAATATTCATACAATACAAACAGAATTTCCTTCAACAAAACCAATGCTTTTTTATCATTTCATC
*
1411287 TTTCAA-AATACCATGTGATTTATCTGAATCCAGACTGGTAAACAATGTTTGCATAGTCATACTC
66 TTTCAAGAA-ACCATGTGATTCATCTGAATCCAGACTGGTAAACAATGTTTGCATAGTCATACTC
1411351 TTCTG
130 TTCTG
* * * * * *
1411356 CAAATATTCATACAATACAAACTGAATTTCCTTCATCAAAACAAATGCTGTTTGATCATTCCATC
1 CAAATATTCATACAATACAAACAGAATTTCCTTCAACAAAACCAATGCTTTTTTATCATTTCATC
1411421 TTTCAA
66 TTTCAA
1411427 CAAGAGGCCC
Statistics
Matches: 187, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
132 39 0.21
133 4 0.02
134 144 0.77
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (134 bp):
CAAATATTCATACAATACAAACAGAATTTCCTTCAACAAAACCAATGCTTTTTTATCATTTCATC
TTTCAAGAAACCATGTGATTCATCTGAATCCAGACTGGTAAACAATGTTTGCATAGTCATACTCT
TCTG
Found at i:1413009 original size:166 final size:166
Alignment explanation
Indices: 1412735--1413154 Score: 709
Period size: 166 Copynumber: 2.5 Consensus size: 166
1412725 NNNNNNNNNN
*
1412735 TTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGGCTGATTAGTTTCTG
1 TTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTG
1412800 AGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGC
66 AGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGC
*
1412865 CCCACCTTACCCCCAGGGATCATGAATTTCACAACT
131 CCCACCCTACCCCCAGGGATCATGAATTTCACAACT
*
1412901 TTGAATCTACACTACCTGAGGATGCTTCCACACAAATTTCAGCTTTCCTGGCTGATTAGTTTCTG
1 TTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTG
*
1412966 AGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCATTGTGGC
66 AGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGC
* *
1413031 CCCACCCTACCCCCGGGGGTCATGAATTTCACAACT
131 CCCACCCTACCCCCAGGGATCATGAATTTCACAACT
* * *
1413067 TTGAATCTACACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTGGCT--TTCTGGTTCT
1 TTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATT-AGTTTC-
*
1413130 TGAGAAGAAGATTTTTGAAAAATTT
64 TGAGAAGAAGATTTTT-AAAGATTT
1413155 CTCGAAATTT
Statistics
Matches: 240, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
164 2 0.01
165 4 0.02
166 227 0.95
167 7 0.03
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (166 bp):
TTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTG
AGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGC
CCCACCCTACCCCCAGGGATCATGAATTTCACAACT
Found at i:1413315 original size:8 final size:8
Alignment explanation
Indices: 1413304--1413349 Score: 83
Period size: 8 Copynumber: 5.8 Consensus size: 8
1413294 TGAAAAGTTT
1413304 ACGGACAG
1 ACGGACAG
1413312 ACGGACAG
1 ACGGACAG
1413320 ACGGACAG
1 ACGGACAG
*
1413328 ACAGACAG
1 ACGGACAG
1413336 ACGGACAG
1 ACGGACAG
1413344 ACGGAC
1 ACGGAC
1413350 GACAGACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.39, C:0.26, G:0.35, T:0.00
Consensus pattern (8 bp):
ACGGACAG
Found at i:1413332 original size:4 final size:4
Alignment explanation
Indices: 1413307--1413357 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
1413297 AAAGTTTACG
* * * *
1413307 GACA GACG GACA GACG GACA GACA GACA GACG GACA GACG GAC- GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
1413354 GACA
1 GACA
1413358 AAATGTGATC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.41, C:0.25, G:0.33, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:1433673 original size:20 final size:20
Alignment explanation
Indices: 1433648--1433689 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1433638 ACCCTTGTGT
* *
1433648 GTCTGTTTGTCTGTCCGTCC
1 GTCTGTCTGTCTGTCCGCCC
1433668 GTCTGTCTGTCTGTCCGCCC
1 GTCTGTCTGTCTGTCCGCCC
1433688 GT
1 GT
1433690 AACAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.00, C:0.33, G:0.26, T:0.40
Consensus pattern (20 bp):
GTCTGTCTGTCTGTCCGCCC
Found at i:1433981 original size:157 final size:157
Alignment explanation
Indices: 1433713--1434022 Score: 496
Period size: 157 Copynumber: 2.0 Consensus size: 157
1433703 GTCGCATTTA
* *
1433713 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTATACACAGTATTTGTTAAGGCATGCCATAT
* * * *
1433778 CGTAGGATGTATTTTTGTACAAATCGGACGTCAACTTCCTGTTAAATTAGGACTTTGCTTATTTT
66 CGTAGGATATATTTTTGTACAAATCAGACATCAACTTCCTGTTAAATGAGGACTTTGCTTATTTT
1433843 TTAGCAAACAAATTTTTGTCAAAGAAT
131 TTAGCAAACAAATTTTTGTCAAAGAAT
* *
1433870 TCTCAGCAACTGTTTATCGCAGATGCTTGGAATTTATACACAGTATTTG-TATAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTATACACAGTATTTGTTA-AGGCATGCCATA
* * * *
1433934 TCGTGGGATATATTTTTGTACCAATCAGACATTAACTTCCTGTTAAATGAGGACTTTGTTTATTT
65 TCGTAGGATATATTTTTGTACAAATCAGACATCAACTTCCTGTTAAATGAGGACTTTGCTTATTT
1433999 TTTAGCAAACAAATTTTTGTCAAA
130 TTTAGCAAACAAATTTTTGTCAAA
1434023 NAGACGTCAA
Statistics
Matches: 140, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
156 2 0.01
157 138 0.99
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (157 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTATACACAGTATTTGTTAAGGCATGCCATAT
CGTAGGATATATTTTTGTACAAATCAGACATCAACTTCCTGTTAAATGAGGACTTTGCTTATTTT
TTAGCAAACAAATTTTTGTCAAAGAAT
Found at i:1434334 original size:164 final size:164
Alignment explanation
Indices: 1434024--1434334 Score: 405
Period size: 164 Copynumber: 1.9 Consensus size: 164
1434014 TTTGTCAAAN
1434024 AGACGTCAACTTCCTGTTAAATGACGACTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCCG
1 AGACGTCAACTTCCTGTTAAATGACGACTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCCG
* * * * * * *
1434089 TCAAAGAATTCTCAGCAACTGTTTATCGCAGCTGGTTGAAATTTTTACACAGTATTTGTATAGGC
66 TCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTATATAAGC
*
1434154 ATGCTATATCGTGGGATGTATTTTTGTATCACTC
131 ATGCCATATCGTGGGATGTATTTTTGTATCACTC
* * * *
1434188 AGACGTCAA-TTCCTGTTAAATTA-GTACTTTGTTTA-TTTTAGCCAAAATTTTCAAATTAATTT
1 AGACGTCAACTTCCTGTTAAATGACG-AC--TGTTTATTTTTAGCAAAAATTTTCAAA-CAAATT
* * *
1434250 TCC-TCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTATTT
62 TCCGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTATAT
* *
1434314 AAGTATGCCATATTGTGGGAT
127 AAGCATGCCATATCGTGGGAT
1434335 ATACTTCTGT
Statistics
Matches: 126, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
162 1 0.01
163 15 0.12
164 97 0.77
165 13 0.10
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (164 bp):
AGACGTCAACTTCCTGTTAAATGACGACTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCCG
TCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTATATAAGC
ATGCCATATCGTGGGATGTATTTTTGTATCACTC
Found at i:1436731 original size:12 final size:12
Alignment explanation
Indices: 1436716--1436749 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1436706 CTGAAGTGGA
1436716 ACAGACGGACAG
1 ACAGACGGACAG
1436728 ACAGACGGACAG
1 ACAGACGGACAG
*
1436740 ACGGACGGAC
1 ACAGACGGAC
1436750 GGACGCAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.26, G:0.35, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:1436754 original size:12 final size:12
Alignment explanation
Indices: 1436719--1436754 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1436709 AAGTGGAACA
*
1436719 GACGGACAGACA
1 GACGGACAGACG
1436731 GACGGACAGACG
1 GACGGACAGACG
*
1436743 GACGGACGGACG
1 GACGGACAGACG
1436755 CAGAGGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.25, G:0.42, T:0.00
Consensus pattern (12 bp):
GACGGACAGACG
Found at i:1447181 original size:32 final size:32
Alignment explanation
Indices: 1447106--1447210 Score: 129
Period size: 32 Copynumber: 3.2 Consensus size: 32
1447096 GCTATAAAAC
* * * **
1447106 GGGGGAAAACCCACTATATAGTCAGCTTTCCG
1 GGGGGAAAAACTACTATATAGCCATTTTTCCG
*
1447138 TGGGGGAAAAACTGCTATATAGCCATTTTTCCG
1 -GGGGGAAAAACTACTATATAGCCATTTTTCCG
* *
1447171 GGGGGCAAAACTACTATATAGCCATTTTTCAG
1 GGGGGAAAAACTACTATATAGCCATTTTTCCG
1447203 GGGGGAAA
1 GGGGGAAA
1447211 GATGGCTAGG
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
32 36 0.58
33 26 0.42
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.25
Consensus pattern (32 bp):
GGGGGAAAAACTACTATATAGCCATTTTTCCG
Found at i:1447305 original size:30 final size:30
Alignment explanation
Indices: 1447269--1447344 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
1447259 CAGTCTATCG
1447269 CAGTCTATTGACCGGCGGTCCAATAGATCA
1 CAGTCTATTGACCGGCGGTCCAATAGATCA
* * *
1447299 CAGTCTATTGATCGGCGGTCTAATAGATCG
1 CAGTCTATTGACCGGCGGTCCAATAGATCA
1447329 CAGTCTATTGACCGGC
1 CAGTCTATTGACCGGC
1447345 ACAAACAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (30 bp):
CAGTCTATTGACCGGCGGTCCAATAGATCA
Found at i:1451503 original size:21 final size:21
Alignment explanation
Indices: 1451479--1451526 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1451469 AGCTACGCTC
1451479 GCTAATATCATTATATGCAAT
1 GCTAATATCATTATATGCAAT
1451500 GCTAATATCATTATATGCAAT
1 GCTAATATCATTATATGCAAT
*
1451521 GGTAAT
1 GCTAAT
1451527 TTTTCTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (21 bp):
GCTAATATCATTATATGCAAT
Found at i:1455351 original size:20 final size:20
Alignment explanation
Indices: 1455326--1455377 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1455316 ATATATATAA
1455326 AGAGAGAGAGAGAGAGGGG-T
1 AGAGAGAGAGAGAG-GGGGAT
1455346 AGAGAGAGAGAGAGGGGGAT
1 AGAGAGAGAGAGAGGGGGAT
*
1455366 AGAGATAGAGAG
1 AGAGAGAGAGAG
1455378 TAAATCTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.42, C:0.00, G:0.52, T:0.06
Consensus pattern (20 bp):
AGAGAGAGAGAGAGGGGGAT
Found at i:1455369 original size:16 final size:17
Alignment explanation
Indices: 1455327--1455377 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
1455317 TATATATAAA
1455327 GAGAGAGAGAGAGAGGG
1 GAGAGAGAGAGAGAGGG
1455344 GTAGAGAGAGAGAGAGGGG
1 G-AGAGAGAGAGAGA-GGG
* *
1455363 GATAGAGATAGAGAG
1 GAGAGAGAGAGAGAG
1455378 TAAATCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 24 0.80
19 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.53, T:0.06
Consensus pattern (17 bp):
GAGAGAGAGAGAGAGGG
Found at i:1465442 original size:18 final size:18
Alignment explanation
Indices: 1465358--1465446 Score: 63
Period size: 20 Copynumber: 4.7 Consensus size: 18
1465348 AATTAATACA
1465358 AATG-AATTATACAATGC
1 AATGAAATTATACAATGC
* *
1465375 AGATGAAATTTTTACAAGGC
1 A-ATGAAA-TTATACAATGC
* * *
1465395 AATGGAAAGTTATATAGTAC
1 AAT-GAAA-TTATACAATGC
*
1465415 AAATGAAAATTATACTATGC
1 -AATG-AAATTATACAATGC
1465435 AATGAAATTATA
1 AATGAAATTATA
1465447 AATTTATACA
Statistics
Matches: 54, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
17 1 0.02
18 11 0.20
19 8 0.15
20 28 0.52
21 6 0.11
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (18 bp):
AATGAAATTATACAATGC
Found at i:1465478 original size:2 final size:2
Alignment explanation
Indices: 1465471--1465507 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1465461 AAATTAAAAT
1465471 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1465508 TATATANNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1495278 original size:21 final size:21
Alignment explanation
Indices: 1495256--1495297 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1495246 TAGTCAACTC
1495256 TTTGAAATTGTGATGACATTCT
1 TTTG-AATTGTGATGACATTCT
**
1495278 TTTGAATTGTTTTGACATTC
1 TTTGAATTGTGATGACATTC
1495298 AAAGCATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.50
Consensus pattern (21 bp):
TTTGAATTGTGATGACATTCT
Found at i:1497456 original size:2 final size:2
Alignment explanation
Indices: 1497449--1497486 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1497439 TTAGAAAATG
1497449 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1497487 TACGTTGGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1499436 original size:26 final size:25
Alignment explanation
Indices: 1499414--1499467 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1499404 CTGTAAATCT
*
1499414 ACAATCATTATAGTATCAATAAAGTC
1 ACAAT-ATTATACTATCAATAAAGTC
* *
1499440 ACAATATTGTACTATGAATAAAGTC
1 ACAATATTATACTATCAATAAAGTC
1499465 ACA
1 ACA
1499468 TTGTGTGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (25 bp):
ACAATATTATACTATCAATAAAGTC
Found at i:1500672 original size:14 final size:13
Alignment explanation
Indices: 1500653--1500682 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1500643 AAGTACGCGG
1500653 TTTTGTTTTTGTTT
1 TTTTGTTTTT-TTT
1500667 TTTTGTTTTTTTT
1 TTTTGTTTTTTTT
1500680 TTT
1 TTT
1500683 ACTTTCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (13 bp):
TTTTGTTTTTTTT
Found at i:1503539 original size:1 final size:1
Alignment explanation
Indices: 1503533--1503565 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
1503523 TCCATTTCTC
1503533 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1503566 GCAGGATGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1515682 original size:62 final size:62
Alignment explanation
Indices: 1515585--1515772 Score: 331
Period size: 62 Copynumber: 3.0 Consensus size: 62
1515575 TAGGTCCAGT
*
1515585 AATGGAATGATGCTAGAATATGTGTTCTACAAACAAGATAATTAAACCATTACTAAATATTC
1 AATGGAATGATGCTAGAATATGTGTTCTACAAACAAGATAATTAAACCATTACTGAATATTC
* *
1515647 AATGGAAGGATGCTAGAATATGTGTTCTACAAACAAGATAATTAAACCATTATTGAATATTC
1 AATGGAATGATGCTAGAATATGTGTTCTACAAACAAGATAATTAAACCATTACTGAATATTC
* *
1515709 AATGGAATGATGCTAGAATATGTTTTCTACAAACAAGATAATTAAATCATTACTGAATATTC
1 AATGGAATGATGCTAGAATATGTGTTCTACAAACAAGATAATTAAACCATTACTGAATATTC
1515771 AA
1 AA
1515773 AAAAAAGTTT
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 119 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (62 bp):
AATGGAATGATGCTAGAATATGTGTTCTACAAACAAGATAATTAAACCATTACTGAATATTC
Found at i:1533911 original size:21 final size:21
Alignment explanation
Indices: 1533864--1533932 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
1533854 ACACCCCCGA
*
1533864 GTCCACCGGGAAAACCTCCTG
1 GTCCACCGGGAAAACCTCCGG
*
1533885 GACCACCGGGAAAACCTCCGG
1 GTCCACCGGGAAAACCTCCGG
*
1533906 GTCCACTGGCG-AAACCTCCGG
1 GTCCACCGG-GAAAACCTCCGG
1533927 GTCCAC
1 GTCCAC
1533933 TGNTCCAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.23, C:0.39, G:0.26, T:0.12
Consensus pattern (21 bp):
GTCCACCGGGAAAACCTCCGG
Found at i:1534034 original size:21 final size:21
Alignment explanation
Indices: 1534005--1534304 Score: 384
Period size: 21 Copynumber: 14.3 Consensus size: 21
1533995 GACCCCCGGA
* *
1534005 TCCACCGGGAAAACCTCCTGG
1 TCCACCGGCAAAACCTCCAGG
* * *
1534026 ACTACCGGGAAAACCTCCAGG
1 TCCACCGGCAAAACCTCCAGG
* * *
1534047 TCCACCAGCAAAACCCCCGGG
1 TCCACCGGCAAAACCTCCAGG
*
1534068 TCCACCGGCAAAGCCTCCAGG
1 TCCACCGGCAAAACCTCCAGG
*
1534089 TCCACCGGTAAAACCTCCAGG
1 TCCACCGGCAAAACCTCCAGG
**
1534110 TCCACCGGCAAAACCTCTGGG
1 TCCACCGGCAAAACCTCCAGG
* *
1534131 TCCACCGGCAAAGCCCCCAGG
1 TCCACCGGCAAAACCTCCAGG
1534152 TCCACCGGCAAAACCTCCAGG
1 TCCACCGGCAAAACCTCCAGG
1534173 TCCACCGGCAAAACCTCCAGG
1 TCCACCGGCAAAACCTCCAGG
* *
1534194 ACCACCGGCAAAGCCTCCAGG
1 TCCACCGGCAAAACCTCCAGG
*
1534215 TCCACCGGTAAAACCTCCAGG
1 TCCACCGGCAAAACCTCCAGG
*
1534236 CCCACCGGCAAAACCTCCAGG
1 TCCACCGGCAAAACCTCCAGG
* * *
1534257 ACCACCGGCAAATCCTCCTGG
1 TCCACCGGCAAAACCTCCAGG
* * *
1534278 ACCACCGGCGAAACCTCCGGG
1 TCCACCGGCAAAACCTCCAGG
1534299 TCCACC
1 TCCACC
1534305 AGGGCCTCCG
Statistics
Matches: 241, Mismatches: 38, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 241 1.00
ACGTcount: A:0.27, C:0.42, G:0.21, T:0.10
Consensus pattern (21 bp):
TCCACCGGCAAAACCTCCAGG
Found at i:1534049 original size:140 final size:139
Alignment explanation
Indices: 1533796--1534072 Score: 466
Period size: 140 Copynumber: 2.0 Consensus size: 139
1533786 CTTTAGGTTT
1533796 TCCAATCCCGTGACTTTGAAGACCCCCTAGGCCTCCTAATCCAGCGGGTCCACCACTCACACCCC
1 TCCAATCCCGTGACTTTGAAGACCCCCTAGGCCTCCTAATCCAGCGGGTCCACCACTCACACCCC
* ** * *
1533861 CGAGTCCACCGGGAAAACCTCCTGGACCACCGGGAAAACCTCCGGGTCCACTGGCGAAACCTCCG
66 CGAGTCCACCGGGAAAACCTCCTGGACCACCGGGAAAACCTCCAGGTCCACCAGCAAAACCCCCG
1533926 GGTCCACTG
131 GGTCCACTG
*
1533935 NTCCAATCCCGTGACTTTGAAGACCCCCTAGGCCTCCTAATCCAGCGGGTCCACCACTCAGACCC
1 -TCCAATCCCGTGACTTTGAAGACCCCCTAGGCCTCCTAATCCAGCGGGTCCACCACTCACACCC
*
1534000 CCG-GATCCACCGGGAAAACCTCCTGGACTACCGGGAAAACCTCCAGGTCCACCAGCAAAACCCC
65 CCGAG-TCCACCGGGAAAACCTCCTGGACCACCGGGAAAACCTCCAGGTCCACCAGCAAAACCCC
1534064 CGGGTCCAC
129 CGGGTCCAC
1534073 CGGCAAAGCC
Statistics
Matches: 129, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
139 1 0.01
140 128 0.99
ACGTcount: A:0.23, C:0.41, G:0.21, T:0.14
Consensus pattern (139 bp):
TCCAATCCCGTGACTTTGAAGACCCCCTAGGCCTCCTAATCCAGCGGGTCCACCACTCACACCCC
CGAGTCCACCGGGAAAACCTCCTGGACCACCGGGAAAACCTCCAGGTCCACCAGCAAAACCCCCG
GGTCCACTG
Done.