Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold204
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: 1152859
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31
Warning! 64757 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:762974 original size:17 final size:18
Alignment explanation
Indices: 762952--762987 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
762942 CGGTGGTTTG
*
762952 ACTTAAACTC-TTCTGTA
1 ACTTAAACCCATTCTGTA
762969 ACTTAAACCCATTCTGTA
1 ACTTAAACCCATTCTGTA
762987 A
1 A
762988 TTTGTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (18 bp):
ACTTAAACCCATTCTGTA
Found at i:766248 original size:18 final size:18
Alignment explanation
Indices: 766225--766262 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
766215 TGTTATCAGT
766225 AAGTACTTGATACGAATA
1 AAGTACTTGATACGAATA
*
766243 AAGTACTTGATACTAATA
1 AAGTACTTGATACGAATA
766261 AA
1 AA
766263 TTGATATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (18 bp):
AAGTACTTGATACGAATA
Found at i:771275 original size:19 final size:19
Alignment explanation
Indices: 771253--771306 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
771243 AATGTTCGTA
*
771253 AAAGTACTCAAATAACCTT
1 AAAGTACTCAAATAACATT
*
771272 AAAGAACTCAAATAACATT
1 AAAGTACTCAAATAACATT
* *
771291 AAATTACTGAAATAAC
1 AAAGTACTCAAATAAC
771307 TATATATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.24
Consensus pattern (19 bp):
AAAGTACTCAAATAACATT
Found at i:775341 original size:2 final size:2
Alignment explanation
Indices: 775334--775385 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
775324 GTTTGGGAGG
775334 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
775376 GA GA GA GA GA
1 GA GA GA GA GA
775386 ATGCACTCTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:797148 original size:20 final size:20
Alignment explanation
Indices: 797123--797160 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
797113 AACAAAAATC
797123 TTATATCACACCCCTAGGGT
1 TTATATCACACCCCTAGGGT
797143 TTATATCACACCCCTAGG
1 TTATATCACACCCCTAGG
797161 CGAATTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (20 bp):
TTATATCACACCCCTAGGGT
Found at i:798910 original size:38 final size:38
Alignment explanation
Indices: 798859--798935 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
798849 GACAGTACTT
798859 AAAATCCCTTTTACATGCGTATGCACCTAAATAATGCA
1 AAAATCCCTTTTACATGCGTATGCACCTAAATAATGCA
*
798897 AAAATCCCTTTTACATGCGTATGCACCTAATTAATGCA
1 AAAATCCCTTTTACATGCGTATGCACCTAAATAATGCA
798935 A
1 A
798936 TTATGAGCCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.30
Consensus pattern (38 bp):
AAAATCCCTTTTACATGCGTATGCACCTAAATAATGCA
Found at i:799576 original size:180 final size:175
Alignment explanation
Indices: 799226--799762 Score: 723
Period size: 180 Copynumber: 3.0 Consensus size: 175
799216 GGCTGCCAAA
*
799226 AGGGTACACTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
*
799291 GATCAATTGTACATATATCAGAGGTGTGCATATTTCTAGGATTTTGATTTCTGATACTTTTTGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATA-TTCTA-GATTTTGATTT-TAATA--TTTTGAA
*
799356 AAAAATACCACCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
126 AAAAATACCACCTTTTGAACTTAGTCATTTTTTTGCAAAATATTGCATAT
* * *
799406 AGGGTACCCTCATTGTACGGATAACTCCTCCGACAGTTTTCAAGATAGGAATTTGTTCTTTTGTA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
* * *
799471 GATCAATTGTACATATATCAAAAGTGTGCATATTGCTAGATTTTGATTTTTAATAATTTATGACA
66 GATCAATTGTACATATATCAGAGGTGTGCATATT-CTAGATTTTGA-TTTTAAT-ATTT-TGAAA
* *
799536 AAAATACCAGCC-TTTGAACTTAGTCATTTTTTTTGCAAAATATTACATAA
127 AAAATACCA-CCTTTTGAACTTAGTCA-TTTTTTTGCAAAATATTGCATAT
* *
799586 AGGGTACCCTCA-T-TACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
* * *
799649 GATCAATTGTATATGTATATTAGAGGTGTGCATATT-TCGATTTCTGA---TAAT-TTTTGAAAA
66 GATCAATTGTACA--TATATCAGAGGTGTGCATATTCTAGATTT-TGATTTTAATATTTTGAAAA
* *
799709 AAATACCACCTTTTGAACTTAGTCA-CTTTTTGCAAAAAATTGCATAT
128 AAATACCACCTTTTGAACTTAGTCATTTTTTTGCAAAATATTGCATAT
799756 AGGGTAC
1 AGGGTAC
799763 TCCATTTCAC
Statistics
Matches: 322, Mismatches: 25, Indels: 30
0.85 0.07 0.08
Matches are distributed among these distances:
170 25 0.08
171 2 0.01
172 27 0.08
173 3 0.01
175 4 0.01
178 67 0.21
179 44 0.14
180 150 0.47
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (175 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTCTAGATTTTGATTTTAATATTTTGAAAAAAA
TACCACCTTTTGAACTTAGTCATTTTTTTGCAAAATATTGCATAT
Found at i:800823 original size:15 final size:15
Alignment explanation
Indices: 800803--800833 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
800793 ACAGAATATG
800803 GGACATATGAAGGAA
1 GGACATATGAAGGAA
*
800818 GGACATATGAATGAA
1 GGACATATGAAGGAA
800833 G
1 G
800834 ACTTGCTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.32, T:0.16
Consensus pattern (15 bp):
GGACATATGAAGGAA
Found at i:805486 original size:322 final size:322
Alignment explanation
Indices: 804892--805673 Score: 1115
Period size: 322 Copynumber: 2.4 Consensus size: 322
804882 GTGAATATGC
* * * * * *
804892 AAAATAAGCAAAGTCGTCATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
* * * *
804957 ATATGGCATGCCAAAACAAATAGTGTGTTTAAATTTCAAGCATCTGCGATATATAGTTGCTGAGA
66 ATATGGCATGCCAAAACAAATAGTGTG-TAAAAATTCAAGCATCTGCGATAAACAGTTGCTGAGA
805022 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATTTAACAGGAAGT
130 AA----T-A--GAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATTTAACAGGAAGT
* *
805087 TGACGCCCGATTGGTTAAAAAATATATCCCACGATATGGCATGCTTAAACAAATATTGTGTTAAA
188 TGACACCCGATTGGTTAAAAAATATATCCCACGATATGGCATGCCTAAACAAATATTGTGTTAAA
805152 ATGTCAAGCATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAAATTTT
253 ATGTCAAGCATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTG-AAAATTTT
805217 GATTAA
317 GATTAA
*
805223 AAAATAAGCAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
* * *
805288 ATATGGCATGCCAAAACAAATAGTGTGAAAAAATTCAAGCATCTGCGATAAACATTTGCTGA-CA
66 ATATGGCATGCCAAAACAAATAGTGTGTAAAAATTCAAGCATCTGCGATAAACAGTTGCTGAGAA
* *
805352 A-A-AAA-TTGTTTGAAAATTTTTGCTAAAAATGAACAAAGTCGTCATTTAACAGGAAGTTGACA
131 ATAGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAA---GTCATTTAACAGGAAGTTGACA
** * ** *
805414 TGCGATTGG-TACAAAAATATATCCCACGATATGGCATGCCTATACAAATATTGTGTTTTAATTT
193 CCCGATTGGTTA-AAAAATATATCCCACGATATGGCATGCCTAAACAAATATTGTGTTAAAATGT
* *
805478 TAAGCATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTA
257 CAAGCATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGATTA
805543 A
322 A
* *
805544 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATAAATCCCACG
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
** * *
805609 ATATGGCATGCCTTAACAAACACTGTGTAAAAATGTCAAGCATCTGCGATAAACAGTTGCTGAGA
66 ATATGGCATGCCAAAACAAATAGTGTGTAAAAAT-TCAAGCATCTGCGATAAACAGTTGCTGAGA
805674 TAAATGCGAC
Statistics
Matches: 409, Mismatches: 36, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
319 30 0.07
320 3 0.01
321 106 0.26
322 153 0.37
323 1 0.00
329 2 0.00
330 29 0.07
331 85 0.21
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (322 bp):
AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
ATATGGCATGCCAAAACAAATAGTGTGTAAAAATTCAAGCATCTGCGATAAACAGTTGCTGAGAA
ATAGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATTTAACAGGAAGTTGACACCC
GATTGGTTAAAAAATATATCCCACGATATGGCATGCCTAAACAAATATTGTGTTAAAATGTCAAG
CATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGATTAA
Found at i:805521 original size:154 final size:159
Alignment explanation
Indices: 805220--805669 Score: 502
Period size: 167 Copynumber: 2.8 Consensus size: 159
805210 AAATTTTGAT
*
805220 TAAAAAATAAGCAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCC
1 TAAAAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCC
* * * * * * *
805285 ACAATATGGCATGCCAAAACAAATAGTGTG-AAAAAATTCAAGCATCTGCGATAAACATTTGCTG
66 ACGATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTA
**
805349 ACAAAAAATTGTTTGAAAA-T-TTTT-GC
131 ACAAAAAATTGTACGAAAATTATTTTGGC
* * *
805375 T-AAAAATGAA-CAAAGTCGTCATTTAACAGGAAGTTGACATGCGATTGGTACAAAAATATATCC
1 TAAAAAAT-AAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCC
* *** * *
805438 CACGATATGGCATGCCTATACAAATATTGTGTTTTAATTTTAAGCATCTGCGATAAATAGTTGCT
65 CACGATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCT
* *** *
805503 AAGAAATCTTTG-ACGAAAATTTGTTTGAAAATTTTGGT
130 AACAAAAAATTGTACGAAAA-----TT----ATTTTGGC
*
805541 TAAAAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATAAATCCC
1 TAAAAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCC
* *
805606 ACGATATGGCATGCCT-TAACAAACACTGTGTAAAAATGTCAAGCATCTGCGATAAACAGTTGCT
66 ACGATATGGCATGCCTAT-ACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCT
805670 GAGATAAATG
Statistics
Matches: 243, Mismatches: 35, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
154 87 0.36
155 36 0.15
160 1 0.00
165 4 0.02
166 5 0.02
167 110 0.45
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (159 bp):
TAAAAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCC
ACGATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTA
ACAAAAAATTGTACGAAAATTATTTTGGC
Found at i:807361 original size:167 final size:168
Alignment explanation
Indices: 806989--807607 Score: 897
Period size: 167 Copynumber: 3.6 Consensus size: 168
806979 TCACACTTTT
* * * * *
806989 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCATTACATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
*
807054 CCACTCTTAC-CTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
66 CCA--CTAACACTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTT---GTTATGGG
*
807118 ACTTTGACCACAATAATGACCCTGTTTTATCCAAAAATTGACC
126 ACTTTGACCACAATAATGACTCTGTTTTATCCAAAAATTGACC
807161 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
*
807226 CCACTAACACTTCGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTG-T-TTATGGGACTA
66 CCACTAACACTT-GGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGTTATGGGACTT
* *
807289 TGACCACAATAATGACTCTGTTTTATCCTAAAATTGACA
130 TGACCACAATAATGACTCTGTTTTATCCAAAAATTGACC
*
807328 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCAAT-AAATTTATACCAAATGTTTAT
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTAC-ATGAAATTTATACCAAATGTTTAT
* *
807392 ACCACTAATACTTTGGTCAAGTTTGAAAATCAGCATTGGTCGATA-TTTTTGTTGGAGTTATGGG
65 ACCACTAACAC-TTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTT---GTTATGGG
* * * *
807456 ACTTTGTCCACAATAATGACTCCGTTTTATCCCAAAATTCACC
126 ACTTTGACCACAATAATGACTCTGTTTTATCCAAAAATTGACC
807499 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
* *** *
807564 CCACTAATACCTTGGTCAAGTTCCTGAATCAGCCTTGGTCGATA
66 CCACTAACA-CTTGGTCAAGTTCGAAAATCAGCATTGGTCGATA
807608 TTAGTATACT
Statistics
Matches: 411, Mismatches: 25, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
166 6 0.01
167 147 0.36
168 4 0.01
170 6 0.01
171 146 0.36
172 102 0.25
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (168 bp):
TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
CCACTAACACTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGTTATGGGACTTT
GACCACAATAATGACTCTGTTTTATCCAAAAATTGACC
Found at i:807606 original size:338 final size:339
Alignment explanation
Indices: 806989--807607 Score: 1055
Period size: 338 Copynumber: 1.8 Consensus size: 339
806979 TCACACTTTT
* *
806989 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCATTACATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCAATAAATTTATACCAAATGTTTATA
**
807054 CCACTCTTACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
*
807119 CTTTGACCACAATAATGACCCTGTTTTATCCAAAAATTGACCTTGTAAGCGCTCTCATGCCTACA
131 CTTTGACCACAATAATGACCCTGTTTTATCCAAAAATTCACCTTGTAAGCGCTCTCATGCCTACA
807184 AATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAACACTTCGGTCAAGTTC
196 AATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAACACTTCGGTCAAGTTC
*
807249 GAAAATCAGCATTGGTCGATACTTTTTGTTTATGGGACTATGACCACAATAATGACTCTGTTTTA
261 CAAAATCAGCATTGGTCGATACTTTTTGTTTATGGGACTATGACCACAATAATGACTCTGTTTTA
807314 TCCTAAAATTGACA
326 TCCTAAAATTGACA
* *
807328 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCAATAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCAATAAATTTATACCAAATGTTTATA
* *
807393 CCACTAATACTTTGGTCAAGTTTGAAAATCAGCATTGGTCGATA-TTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
* *
807457 CTTTGTCCACAATAATGACTCC-GTTTTATCCCAAAATTCACCTTGTAAGCGCTCTCATGCCTAC
131 CTTTGACCACAATAATGAC-CCTGTTTTATCCAAAAATTCACCTTGTAAGCGCTCTCATGCCTAC
*
807521 AAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAATACCTT-GGTCAAGT
195 AAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAACA-CTTCGGTCAAGT
** *
807585 TCCTGAATCAGCCTTGGTCGATA
259 TCCAAAATCAGCATTGGTCGATA
807608 TTAGTATACT
Statistics
Matches: 262, Mismatches: 16, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
338 156 0.60
339 106 0.40
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (339 bp):
TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCAATAAATTTATACCAAATGTTTATA
CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
CTTTGACCACAATAATGACCCTGTTTTATCCAAAAATTCACCTTGTAAGCGCTCTCATGCCTACA
AATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAACACTTCGGTCAAGTTC
CAAAATCAGCATTGGTCGATACTTTTTGTTTATGGGACTATGACCACAATAATGACTCTGTTTTA
TCCTAAAATTGACA
Found at i:807609 original size:171 final size:172
Alignment explanation
Indices: 806989--807607 Score: 950
Period size: 171 Copynumber: 3.6 Consensus size: 172
806979 TCACACTTTT
* * * * *
806989 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCATTACATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
**
807054 CCACTCTTACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
807119 CTTTGACCACAATAATGAC-CCTGTTTTATCCAAAAATTGACC
131 CTTTGACCACAATAATGACTCC-GTTTTATCCAAAAATTGACC
807161 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
*
807226 CCACTAACA-CTTCGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTG-T----TTATGGG
66 CCACTAATACCTT-GGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
* * * *
807285 ACTATGACCACAATAATGACTCTGTTTTATCCTAAAATTGACA
130 ACTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
*
807328 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCAAT-AAATTTATACCAAATGTTTAT
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTAC-ATGAAATTTATACCAAATGTTTAT
* *
807392 ACCACTAATACTTTGGTCAAGTTTGAAAATCAGCATTGGTCGATA-TTTTTGTTGGAGTTATGGG
65 ACCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
* * *
807456 ACTTTGTCCACAATAATGACTCCGTTTTATCCCAAAATTCACC
130 ACTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
807499 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
*** *
807564 CCACTAATACCTTGGTCAAGTTCCTGAATCAGCCTTGGTCGATA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATA
807608 TTAGTATACT
Statistics
Matches: 408, Mismatches: 29, Indels: 21
0.89 0.06 0.05
Matches are distributed among these distances:
166 6 0.01
167 144 0.35
168 5 0.01
170 2 0.00
171 147 0.36
172 104 0.25
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (172 bp):
TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA
CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
Found at i:807898 original size:2 final size:2
Alignment explanation
Indices: 807891--807924 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
807881 CTATATTTAC
807891 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
807925 CTGGTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:819998 original size:2 final size:2
Alignment explanation
Indices: 819949--819987 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
819939 GCTTTTCATA
819949 CT CT CT CT CT CT CT CT CT CT 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 CT C
819988 CATGATCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:820117 original size:2 final size:2
Alignment explanation
Indices: 820110--820137 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
820100 CACTGTAATT
820110 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
820138 TCTCTCTCTC
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:820181 original size:2 final size:2
Alignment explanation
Indices: 820137--820164 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
820127 CACACACACA
820137 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
820165 GAGTCTATCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:824388 original size:166 final size:165
Alignment explanation
Indices: 824013--824557 Score: 821
Period size: 166 Copynumber: 3.3 Consensus size: 165
824003 TAAAGAATCA
* *
824013 TCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCTATATATTCCTATGTAAAAC
1 TCTGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAATATATTCCTATGTAAAAC
*
824078 TTCGACCCTCCATTGTGGCTCCACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATTTAC
66 TTCGACCCTCCATTGTGGCTCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATATAC
*
824142 ACTACCTGAGGAT-TCTTCCAAACAAGTTTCAGCTT
131 ACTACCTGAGGATGT-TTCCACACAAGTTTCAGCTT
*
824177 TCCTGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAAAATATTCCTATGTAAAA
1 T-CTGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAATATATTCCTATGTAAAA
* *
824242 CTTCGACCCTCCATTGTGGCTCCACCCTACCCCCGGGGGTAATGAATTTCACAACTTTGAATATA
65 CTTCGACCCTCCATTGTGGCTCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATATA
*
824307 CACTACCTGAGGATGTTTCCACACAAGTTTCAACTT
130 CACTACCTGAGGATGTTTCCACACAAGTTTCAGCTT
* *
824343 TCGTGGCTGATGAGTTTCTGAGAAGAAGATTTCTAAAGGTTTCCTCAATATATTCCTATGTAAAA
1 TC-TGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAATATATTCCTATGTAAAA
* * * *
824408 CTTCGACCCCCCATTGTGGCCCCACCCTACCCACGGGGGGTCATGATTTTTCTCAACTTTGAATA
65 CTTCGACCCTCCATTGTGGCTCCACCCTACCC-CCGGGGGTCATGA-TTTTCACAACTTTGAATA
* *
824473 TACACTACCTGATGATGCTTCCACACAAGTTTCAGCTTT
128 TACACTACCTGAGGATGTTTCCACACAAGTTTCAGC-TT
* *
824512 TCTGGCTTTATG-GTTTTTGAGAAGAAGATTTTTGAAA-ATTT-CTCAA
1 TCTGGC-TGATGAGTTTCTGAGAAGAAGATTTTT-AAAGATTTCCTCAA
824558 ATTTTTTCAT
Statistics
Matches: 348, Mismatches: 24, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
164 1 0.00
165 95 0.27
166 149 0.43
167 17 0.05
168 75 0.22
169 11 0.03
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (165 bp):
TCTGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAATATATTCCTATGTAAAAC
TTCGACCCTCCATTGTGGCTCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATATAC
ACTACCTGAGGATGTTTCCACACAAGTTTCAGCTT
Found at i:824667 original size:95 final size:95
Alignment explanation
Indices: 824504--824693 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
824494 CACACAAGTT
824504 TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT
1 TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT
824569 AATTTCTAATTATCTCCCCTTGAAAAAAGG
66 AATTTCTAATTATCTCCCCTTGAAAAAAGG
824599 TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT
1 TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT
824664 AATTTCTAATTATCTCCCCTTGAAAAAAGG
66 AATTTCTAATTATCTCCCCTTGAAAAAAGG
824694 CGTGACCCTT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (95 bp):
TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT
AATTTCTAATTATCTCCCCTTGAAAAAAGG
Found at i:824749 original size:11 final size:11
Alignment explanation
Indices: 824733--824771 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
824723 CATTCAGTCA
824733 ACTGAAAGGTG
1 ACTGAAAGGTG
*
824744 ACTGAAAGGTA
1 ACTGAAAGGTG
*
824755 ACTGAAAAGTG
1 ACTGAAAGGTG
824766 ACTGAA
1 ACTGAA
824772 TGGCATAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.28, T:0.18
Consensus pattern (11 bp):
ACTGAAAGGTG
Found at i:827227 original size:12 final size:12
Alignment explanation
Indices: 827210--827249 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
827200 TTTCCTCTGC
827210 GTCCGTCTGTCT
1 GTCCGTCTGTCT
* *
827222 GTCCGTCCGTCA
1 GTCCGTCTGTCT
827234 GTCCGTCTGTCT
1 GTCCGTCTGTCT
827246 GTCC
1 GTCC
827250 CACTTCAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.38, G:0.25, T:0.35
Consensus pattern (12 bp):
GTCCGTCTGTCT
Found at i:834621 original size:8 final size:8
Alignment explanation
Indices: 834608--834677 Score: 86
Period size: 8 Copynumber: 8.8 Consensus size: 8
834598 CCGGGCGTCC
*
834608 GTCCGTGT
1 GTCCGTGG
834616 GTCCGTGG
1 GTCCGTGG
*
834624 GTCCGTGT
1 GTCCGTGG
834632 GTCCGTGG
1 GTCCGTGG
* *
834640 GTCTGTGT
1 GTCCGTGG
*
834648 GTCCGTGC
1 GTCCGTGG
834656 GTCCGTGG
1 GTCCGTGG
*
834664 GTCCGTGC
1 GTCCGTGG
834672 GTCCGT
1 GTCCGT
834678 CCGTCACACT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 53 1.00
ACGTcount: A:0.00, C:0.27, G:0.41, T:0.31
Consensus pattern (8 bp):
GTCCGTGG
Found at i:834629 original size:16 final size:16
Alignment explanation
Indices: 834607--834677 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
834597 GCCGGGCGTC
834607 CGTCCGTGTGTCCGTG
1 CGTCCGTGTGTCCGTG
*
834623 GGTCCGTGTGTCCGTG
1 CGTCCGTGTGTCCGTG
* *
834639 GGTCTGTGTGTCCGTG
1 CGTCCGTGTGTCCGTG
*
834655 CGTCCGTGGGTCCGTG
1 CGTCCGTGTGTCCGTG
834671 CGTCCGT
1 CGTCCGT
834678 CCGTCACACT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.00, C:0.28, G:0.41, T:0.31
Consensus pattern (16 bp):
CGTCCGTGTGTCCGTG
Found at i:834651 original size:24 final size:24
Alignment explanation
Indices: 834607--834682 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 24
834597 GCCGGGCGTC
* *
834607 CGTCCGTGTGTCCGTGGGTCCGTG
1 CGTCCGTGGGTCCGTGCGTCCGTG
* * *
834631 TGTCCGTGGGTCTGTGTGTCCGTG
1 CGTCCGTGGGTCCGTGCGTCCGTG
*
834655 CGTCCGTGGGTCCGTGCGTCCGTC
1 CGTCCGTGGGTCCGTGCGTCCGTG
834679 CGTC
1 CGTC
834683 ACACTTTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.00, C:0.30, G:0.39, T:0.30
Consensus pattern (24 bp):
CGTCCGTGGGTCCGTGCGTCCGTG
Found at i:834977 original size:172 final size:172
Alignment explanation
Indices: 834691--835143 Score: 834
Period size: 172 Copynumber: 2.6 Consensus size: 172
834681 TCACACTTTT
* *
834691 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTTATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* * *
834756 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTCATCGAA
834821 CTATGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
131 CTATGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
834863 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
*
834928 CCACGAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTCATCGAA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTCATCGAA
*
834993 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
131 CTATGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
835035 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
*
835100 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCCTTGGTCGATA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATA
835144 GACTCGATAC
Statistics
Matches: 272, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
172 272 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (172 bp):
TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTCATCGAA
CTATGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
Found at i:837737 original size:21 final size:21
Alignment explanation
Indices: 837713--837779 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
837703 ATCTGCCACC
837713 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
*
837734 ACTTGTCAGAT-CTTGATGTCG
1 ACTTGTCAGATAATT-ATGTCG
* *
837755 ACTTGTCAGATAATCATGTTG
1 ACTTGTCAGATAATTATGTCG
837776 ACTT
1 ACTT
837780 ATAATATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.93
22 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:837854 original size:21 final size:20
Alignment explanation
Indices: 837838--837905 Score: 82
Period size: 21 Copynumber: 3.3 Consensus size: 20
837828 CTGTCAGATA
837838 ATTATGTTAACTTGTCAAAT
1 ATTATGTTAACTTGTCAAAT
* **
837858 CTTCATGTCGACTTGTCAAAT
1 ATT-ATGTTAACTTGTCAAAT
*
837879 AATTATGTTAACTTGTCAGAT
1 -ATTATGTTAACTTGTCAAAT
837900 ATTATG
1 ATTATG
837906 ATGACAGGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 8 0.21
21 29 0.74
22 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
ATTATGTTAACTTGTCAAAT
Found at i:838010 original size:21 final size:21
Alignment explanation
Indices: 837984--838077 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
837974 ATGGTTATTT
* *
837984 TCTGACAAGTAAACATAAAGA
1 TCTGACAAGTTAACATAAATA
* *
838005 TCTGACAAGTTGACATTAATA
1 TCTGACAAGTTAACATAAATA
**
838026 TCTGACAAGTCGACAT-AATCA
1 TCTGACAAGTTAACATAAAT-A
* *
838047 TCTGACAATTTAACATAATTA
1 TCTGACAAGTTAACATAAATA
838068 TCTGACAAGT
1 TCTGACAAGT
838078 GGTGGCAGAT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
20 3 0.05
21 56 0.92
22 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (21 bp):
TCTGACAAGTTAACATAAATA
Found at i:838043 original size:42 final size:42
Alignment explanation
Indices: 837984--838077 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
837974 ATGGTTATTT
* *
837984 TCTGACAAGTAAACATAAAGATCTGACAAGTTGACATTAA-TA
1 TCTGACAAGTAAACATAAACATCTGACAAGTTAACA-TAATTA
** * *
838026 TCTGACAAGTCGACATAATCATCTGACAATTTAACATAATTA
1 TCTGACAAGTAAACATAAACATCTGACAAGTTAACATAATTA
838068 TCTGACAAGT
1 TCTGACAAGT
838078 GGTGGCAGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 3 0.07
42 42 0.93
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (42 bp):
TCTGACAAGTAAACATAAACATCTGACAAGTTAACATAATTA
Found at i:839435 original size:160 final size:161
Alignment explanation
Indices: 839150--839511 Score: 539
Period size: 160 Copynumber: 2.3 Consensus size: 161
839140 ACTTCAAATT
* * * * * *
839150 AATTTTTATAAGTCCAAGGGCCATTACTCTGTCGAAAATTGCTCGATCGTACCCAATATCCAACT
1 AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGATCGATCATACCCAAAATCCAACT
* *
839215 TGACCTAGATATTATCGTGATAAACCTGTATACTAAATTTCATTTCAAAATGTTCATCCTCTGCG
66 TGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAAAATGTTCATCCTCTGCG
*
839280 AAGAAAATGAGCGGAAACTGCAAAAAACTAG
131 AAGAAAATGAGCGGAAACTGCAAAAAACTAA
*
839311 AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGATCTATCATACCCAAAAT-CAGAC
1 AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGATCGATCATACCCAAAATCCA-AC
* * *
839375 TTG-CCTAGATATTATCATGATTAACCTGTATACCAAATTTTATTTCAATATGTTCATCCTCTGC
65 TTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAAAATGTTCATCCTCTGC
* * *
839439 GAAGAAAATGAGCGGAAACTTCAATAAATTAA
130 GAAGAAAATGAGCGGAAACTGCAAAAAACTAA
* *
839471 AATTTTTCTACATCTAAGGGCCATAACTCTGTCGAAAATTG
1 AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTG
839512 TTCATCCTCT
Statistics
Matches: 182, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
160 125 0.69
161 57 0.31
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (161 bp):
AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGATCGATCATACCCAAAATCCAACT
TGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAAAATGTTCATCCTCTGCG
AAGAAAATGAGCGGAAACTGCAAAAAACTAA
Found at i:855060 original size:172 final size:172
Alignment explanation
Indices: 854774--855395 Score: 1064
Period size: 172 Copynumber: 3.6 Consensus size: 172
854764 GTATCGAGTC
* ** * ** *
854774 TATCGACCAAGGCTGATTTAGGAACTTGACCAAGGTATTAAAGGTATAAACATTTAGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT
*
854839 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTAAAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTAAAAGGTCAATTTTTGGATAAAACG
854904 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
*
854946 TATCGACAAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT
*
855011 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTATAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTAAAAGGTCAATTTTTGGATAAAACG
* *
855076 GAGTTATTATTGTGGTCAAAGTCCCGTAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
* *
855118 TATCGGCCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTTGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT
* * * *
855183 TAATGAACATCCGTCTAAATTTGTAGGCATGATAACGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTAAAAGGTCAATTTTTGGATAAAACG
855248 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
* *
855290 TATCGACCAATGCTGATTTTAGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT
855355 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTA
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTA
855396 CAAAAAAGTG
Statistics
Matches: 422, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
172 422 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (172 bp):
TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT
TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTAAAAGGTCAATTTTTGGATAAAACG
GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
Found at i:855773 original size:12 final size:12
Alignment explanation
Indices: 855746--855778 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
855736 ATCACATTTT
*
855746 GTCTGT-CGTTC
1 GTCTGTCCGTCC
855757 GTCTGTCCGTCC
1 GTCTGTCCGTCC
855769 GTCTGTCCGT
1 GTCTGTCCGT
855779 AAACTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.00, C:0.33, G:0.27, T:0.39
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:856227 original size:166 final size:167
Alignment explanation
Indices: 855971--856334 Score: 523
Period size: 166 Copynumber: 2.1 Consensus size: 167
855961 AGAACCAGAA
* * * * * *
855971 AGCCAGAAAATCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATT
1 AGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAAATTCAAAGTTATGAAAAT
* *
856036 CATGACCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGGGTCGAAGTTTAACATAGGAATATATAG
66 CATGAACCCCGGGGGTAGGGTGGGGCCACAATGGGGGGGGCGAAGTTTAACATAGGAATATATAG
*
856100 AGTAAATCTTTAGAAATCTTCTTCTCAGAAACTAATC
131 AGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
*
856137 AGCCAGGAAAGCTGAAACTTTTGTGAAAGCATCCTCAGGTAGTGTAAATTCAAAGTTATGAAAAT
1 AGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAAATTCAAAGTTATGAAAAT
* *
856202 CATGAACCCGGGGGGTAGGGTGGGGCCACAATGGGGGGAGGGGGGGGGGCGAAGTTTTACATAGG
66 CATGAACCCCGGGGGTAGGGTGGGGCCACAAT---------GGGGGGGGCGAAGTTTAACATAGG
856267 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
122 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
*
856313 AGCCAGGAAAGTTGAAACTTGT
1 AGCCAGGAAAGCTGAAACTTGT
856335 TATTTGTTTA
Statistics
Matches: 174, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
166 88 0.51
176 86 0.49
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (167 bp):
AGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAAATTCAAAGTTATGAAAAT
CATGAACCCCGGGGGTAGGGTGGGGCCACAATGGGGGGGGCGAAGTTTAACATAGGAATATATAG
AGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
Found at i:859453 original size:11 final size:11
Alignment explanation
Indices: 859437--859461 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
859427 TATCCACGTT
859437 GGCATCTAGAA
1 GGCATCTAGAA
859448 GGCATCTAGAA
1 GGCATCTAGAA
859459 GGC
1 GGC
859462 CAAGCGCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (11 bp):
GGCATCTAGAA
Found at i:861267 original size:2 final size:2
Alignment explanation
Indices: 861260--861289 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
861250 TTAAAAGCAT
861260 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
861290 TTTTCAGTCT
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):
GA
Found at i:863004 original size:30 final size:30
Alignment explanation
Indices: 862968--863028 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
862958 AGGGAAACGT
862968 TGATTTATATGAAATGCTATTCCAATAGGA
1 TGATTTATATGAAATGCTATTCCAATAGGA
* *
862998 TGATTTATATGAATTGTTATTCCAATAGGA
1 TGATTTATATGAAATGCTATTCCAATAGGA
863028 T
1 T
863029 TATTCTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.41
Consensus pattern (30 bp):
TGATTTATATGAAATGCTATTCCAATAGGA
Found at i:867858 original size:30 final size:30
Alignment explanation
Indices: 867822--867879 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
867812 AAAGGCGAGG
*
867822 CTCCGCCTCGCTTTCTATGGACTTTACCGA
1 CTCCGCCTCGCCTTCTATGGACTTTACCGA
867852 CTCCGCCTCGCCTTCTATGGACTTTACC
1 CTCCGCCTCGCCTTCTATGGACTTTACC
867880 AACCCCACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.12, C:0.40, G:0.16, T:0.33
Consensus pattern (30 bp):
CTCCGCCTCGCCTTCTATGGACTTTACCGA
Found at i:871915 original size:1 final size:1
Alignment explanation
Indices: 871909--871934 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
871899 GCCCTCTCCC
871909 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
871935 TCGGGAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:872592 original size:18 final size:18
Alignment explanation
Indices: 872569--872604 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
872559 GGGACATTGT
872569 AAATTATACACCGGTAAG
1 AAATTATACACCGGTAAG
872587 AAATTATACACCGGTAAG
1 AAATTATACACCGGTAAG
872605 TTTTTGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (18 bp):
AAATTATACACCGGTAAG
Found at i:882727 original size:2 final size:2
Alignment explanation
Indices: 882720--882753 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
882710 TTTATAGGTG
882720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
882754 CACCTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:900482 original size:165 final size:166
Alignment explanation
Indices: 900239--900595 Score: 457
Period size: 165 Copynumber: 2.1 Consensus size: 166
900229 TCCATGAAGC
* *
900239 CCTCTACCAAAACTGTGAAATTCATGGCCCCTGGGTCAGACGTTCAGGCTCTAGGGTGGGGCCAC
1 CCTCTACCAAAACTGTAAAATTCAAGGCCCCTGGGTCAGACGTTCAGGCTCTAGGGTGGGGCCAC
*
900304 TTTGGCCATATAGTGAAAATGTATTAAATCTTAGAAAA-TCTTTTCTTCTTCCATATACATTTCA
66 TTTGGCCATATAGTGAAAATGTATTAAATCTTAGAAAATTCTTTTCTTCTCCCATATACATTTCA
900368 ATAAAACTGAGTGTATGGTTATGATATCCACTGACT
131 ATAAAACTGAGTGTATGGTTATGATATCCACTGACT
* * ** *
900404 CCTCTACCAAAATTGTAAAATTCAAAGG-GCCTGGGTCAGGGGTTCAGGCTTTAGGGTGGGGCCA
1 CCTCTACCAAAACTGTAAAATTC-AAGGCCCCTGGGTCAGACGTTCAGGCTCTAGGGTGGGGCCA
** *
900468 CTTTGGTGATATAGTGAAAATGTATTAAATCTTAGAAAATCTTCTTTTCTTCTCCCATATATATT
65 CTTTGGCCATATAGTGAAAATGTATTAAATCTTAGAAAA--TTCTTTTCTTCTCCCATATACATT
* * * ** * * * **
900533 TGAATAAATCTTAGTACATGGTTATTATGTCAAAGGACT
128 TCAATAAAACTGAGTGTATGGTTATGATATCCACTGACT
* * *
900572 CCTTTACCTAAGCTGTAAAATTCA
1 CCTCTACCAAAACTGTAAAATTCA
900596 TTACCTCTGG
Statistics
Matches: 163, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
165 90 0.55
166 3 0.02
167 1 0.01
168 69 0.42
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (166 bp):
CCTCTACCAAAACTGTAAAATTCAAGGCCCCTGGGTCAGACGTTCAGGCTCTAGGGTGGGGCCAC
TTTGGCCATATAGTGAAAATGTATTAAATCTTAGAAAATTCTTTTCTTCTCCCATATACATTTCA
ATAAAACTGAGTGTATGGTTATGATATCCACTGACT
Found at i:906616 original size:17 final size:17
Alignment explanation
Indices: 906594--906626 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
906584 CTGGTACTGT
906594 ACCAGTTATCGGCTAAG
1 ACCAGTTATCGGCTAAG
906611 ACCAGTTATCGGCTAA
1 ACCAGTTATCGGCTAA
906627 ACTGAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (17 bp):
ACCAGTTATCGGCTAAG
Found at i:907747 original size:4 final size:4
Alignment explanation
Indices: 907716--907803 Score: 117
Period size: 4 Copynumber: 22.5 Consensus size: 4
907706 GCATTATAGG
* * * *
907716 ATCT ATCC ATCC ATCG ATCT ATCG ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
*
907764 ATCT ATCT ATCT ATCT ATCT ATC- -TCT ATCT TTCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
907804 AGATTCAACT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.03
4 73 0.97
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.47
Consensus pattern (4 bp):
ATCT
Found at i:907940 original size:17 final size:17
Alignment explanation
Indices: 907918--907953 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
907908 ATATCGCCAG
907918 TGTTTGGGGTTTTTGTT
1 TGTTTGGGGTTTTTGTT
* *
907935 TGTTTGGGTTTTTTTTT
1 TGTTTGGGGTTTTTGTT
907952 TG
1 TG
907954 GGGGGGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (17 bp):
TGTTTGGGGTTTTTGTT
Found at i:912489 original size:13 final size:13
Alignment explanation
Indices: 912471--912501 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
912461 TTATTAGTAA
912471 AAAAAACAAAAAC
1 AAAAAACAAAAAC
*
912484 AAAAAACAAAAAG
1 AAAAAACAAAAAC
912497 AAAAA
1 AAAAA
912502 CAATTCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:913590 original size:21 final size:21
Alignment explanation
Indices: 913541--913624 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
913531 ATTTTTCAAT
913541 TAATTATGTCGACATGCAAGA
1 TAATTATGTCGACATGCAAGA
* * *
913562 TAAATATGTTGATATGCAAGA
1 TAATTATGTCGACATGCAAGA
* * * *
913583 TAGTTATGTCAACATGTAACA
1 TAATTATGTCGACATGCAAGA
* * *
913604 TAACTATGTTGACATGTAAGA
1 TAATTATGTCGACATGCAAGA
913625 AAACTACAAT
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (21 bp):
TAATTATGTCGACATGCAAGA
Found at i:913612 original size:42 final size:42
Alignment explanation
Indices: 913544--913624 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
913534 TTTCAATTAA
* * *
913544 TTATGTCGACATGCAAGATAAATATGTTGATATGCAAGATAG
1 TTATGTCAACATGCAACATAAATATGTTGACATGCAAGATAG
* * *
913586 TTATGTCAACATGTAACATAACTATGTTGACATGTAAGA
1 TTATGTCAACATGCAACATAAATATGTTGACATGCAAGA
913625 AAACTACAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (42 bp):
TTATGTCAACATGCAACATAAATATGTTGACATGCAAGATAG
Found at i:914110 original size:20 final size:20
Alignment explanation
Indices: 914085--914124 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
914075 TGCCAGTTAT
914085 AAACACAATAATGTAAAGCA
1 AAACACAATAATGTAAAGCA
914105 AAACACAATAATGTAAAGCA
1 AAACACAATAATGTAAAGCA
914125 GTAAACGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15
Consensus pattern (20 bp):
AAACACAATAATGTAAAGCA
Found at i:915275 original size:63 final size:63
Alignment explanation
Indices: 915161--915317 Score: 199
Period size: 63 Copynumber: 2.5 Consensus size: 63
915151 CTACCTACTG
* * * * *** *
915161 ATGTCAACATGCAACTCATTTATGTTAACATGCAACTTCTTTATGTCGACATGCAACTTATTT
1 ATGTCGACATGCAACTAAGTTATGTTAACATGCAAATAAATTATGTCGACATGCAACATATTT
*
915224 ATGTCGACATGCAACTAAGTTATGTTAACATGCAAGATAAATT-TGTTGACATGCAACATATTT
1 ATGTCGACATGCAACTAAGTTATGTTAACATGCAA-ATAAATTATGTCGACATGCAACATATTT
* *
915287 ATGTCGACATGCAACTTAGTTATGTTGACAT
1 ATGTCGACATGCAACTAAGTTATGTTAACAT
915318 ACAACTTATA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 79 0.96
64 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (63 bp):
ATGTCGACATGCAACTAAGTTATGTTAACATGCAAATAAATTATGTCGACATGCAACATATTT
Found at i:915324 original size:21 final size:21
Alignment explanation
Indices: 915167--915326 Score: 169
Period size: 21 Copynumber: 7.6 Consensus size: 21
915157 ACTGATGTCA
* *
915167 ACATGCAACTCATTTATGTTA
1 ACATGCAACTTATTTATGTTG
* *
915188 ACATGCAACTTCTTTATGTCG
1 ACATGCAACTTATTTATGTTG
*
915209 ACATGCAACTTATTTATGTCG
1 ACATGCAACTTATTTATGTTG
* * *
915230 ACATGCAACTAAGTTATGTTA
1 ACATGCAACTTATTTATGTTG
* * *
915251 ACATGCAAGATAAATT-TGTTG
1 ACATGCAA-CTTATTTATGTTG
* *
915272 ACATGCAACATATTTATGTCG
1 ACATGCAACTTATTTATGTTG
*
915293 ACATGCAACTTAGTTATGTTG
1 ACATGCAACTTATTTATGTTG
*
915314 ACATACAACTTAT
1 ACATGCAACTTAT
915327 AAGTTGCATG
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
20 3 0.03
21 107 0.93
22 5 0.04
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (21 bp):
ACATGCAACTTATTTATGTTG
Found at i:915356 original size:21 final size:21
Alignment explanation
Indices: 915332--915407 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
915322 CTTATAAGTT
915332 GCATGTCAACATATTTATCTC
1 GCATGTCAACATATTTATCTC
* ** ** *
915353 GCATGTAAACATAACTAAGTT
1 GCATGTCAACATATTTATCTC
*
915374 GCATGTCAACATATTCATCTC
1 GCATGTCAACATATTTATCTC
*
915395 GTATGTCAACATA
1 GCATGTCAACATA
915408 AAAAAGTTGC
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (21 bp):
GCATGTCAACATATTTATCTC
Found at i:915385 original size:42 final size:42
Alignment explanation
Indices: 915325--915463 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 42
915315 CATACAACTT
*
915325 ATAAGTTGCATGTCAACATATTTATCTCGCATGTAAACATAA
1 ATAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATAA
* * *
915367 CTAAGTTGCATGTCAACATATTCATCTCGTATGTCAACATAA
1 ATAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATAA
* ** * ** * *
915409 AAAAGTTGCATGTTGACATAATCAAGTTGCATGTCAACATAA
1 ATAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATAA
*
915451 ATAAGTTCCATGT
1 ATAAGTTGCATGT
915464 TGACATAAAT
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (42 bp):
ATAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATAA
Found at i:915421 original size:21 final size:21
Alignment explanation
Indices: 915397--915537 Score: 104
Period size: 21 Copynumber: 6.7 Consensus size: 21
915387 TTCATCTCGT
915397 ATGTCAACATAAAAAAGTTGC
1 ATGTCAACATAAAAAAGTTGC
** **
915418 ATGTTGACATAATCAAGTTGC
1 ATGTCAACATAAAAAAGTTGC
* *
915439 ATGTCAACATAAATAAGTTCC
1 ATGTCAACATAAAAAAGTTGC
** *
915460 ATGTTGACATAAATATA-TTGC
1 ATGTCAACATAAA-AAAGTTGC
* ** **
915481 ATGTCAGCATATTAATCTTGC
1 ATGTCAACATAAAAAAGTTGC
* *
915502 ATGTTAACATAAATAAGTTGC
1 ATGTCAACATAAAAAAGTTGC
* *
915523 AAGTCGACATAAAAA
1 ATGTCAACATAAAAA
915538 GGCACCATCC
Statistics
Matches: 86, Mismatches: 32, Indels: 4
0.70 0.26 0.03
Matches are distributed among these distances:
20 1 0.01
21 84 0.98
22 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (21 bp):
ATGTCAACATAAAAAAGTTGC
Found at i:915464 original size:42 final size:42
Alignment explanation
Indices: 915397--915535 Score: 158
Period size: 42 Copynumber: 3.3 Consensus size: 42
915387 TTCATCTCGT
*
915397 ATGTCAACATAAAAAAGTTGCATGTTGACAT-AATCAAGTTGC
1 ATGTCAACATAAATAAGTTGCATGTTGACATAAAT-AAGTTGC
*
915439 ATGTCAACATAAATAAGTTCCATGTTGACATAAATATA-TTGC
1 ATGTCAACATAAATAAGTTGCATGTTGACATAAATA-AGTTGC
* * * *
915481 ATGTCAGCAT-ATTAATCTTGCATGTTAACATAAATAAGTTGC
1 ATGTCAACATAAATAA-GTTGCATGTTGACATAAATAAGTTGC
* *
915523 AAGTCGACATAAA
1 ATGTCAACATAAA
915536 AAGGCACCAT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
41 5 0.06
42 71 0.88
43 5 0.06
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (42 bp):
ATGTCAACATAAATAAGTTGCATGTTGACATAAATAAGTTGC
Found at i:915470 original size:63 final size:62
Alignment explanation
Indices: 915403--915537 Score: 148
Period size: 63 Copynumber: 2.1 Consensus size: 62
915393 TCGTATGTCA
* * * *
915403 ACATAAAAAAGTTGCATGT-TGACATAATCAA-GTTGCATGTCAACATAAATAAGTTCCATGTTG
1 ACATAAAAAA-TTGCATGTCAG-CAT-ATCAATCTTGCATGTCAACATAAATAAGTTCCAAGTCG
* * * *
915466 ACATAAATATATTGCATGTCAGCATATTAATCTTGCATGTTAACATAAATAAGTTGCAAGTCG
1 ACATAAA-AAATTGCATGTCAGCATATCAATCTTGCATGTCAACATAAATAAGTTCCAAGTCG
915529 ACATAAAAA
1 ACATAAAAA
915538 GGCACCATCC
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
62 5 0.08
63 52 0.87
64 3 0.05
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (62 bp):
ACATAAAAAATTGCATGTCAGCATATCAATCTTGCATGTCAACATAAATAAGTTCCAAGTCG
Found at i:915650 original size:21 final size:21
Alignment explanation
Indices: 915619--915703 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 21
915609 ATCTGATTGC
* *
915619 AATTTTCTTGCATGTCAACGT
1 AATTATCTTGCATGTCAACAT
* *
915640 AATTATGTTGCATGTTAACAT
1 AATTATCTTGCATGTCAACAT
915661 AATTATCTTGCATGTCAACAT
1 AATTATCTTGCATGTCAACAT
* * *
915682 ATTTATCTTGCATATCGACAT
1 AATTATCTTGCATGTCAACAT
915703 A
1 A
915704 TTTGATTGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (21 bp):
AATTATCTTGCATGTCAACAT
Found at i:918434 original size:33 final size:33
Alignment explanation
Indices: 918394--918470 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
918384 AGCCATCTTT
918394 CCCCCCGGAAAAATGGCTATATAGCAGTTCATC
1 CCCCCCGGAAAAATGGCTATATAGCAGTTCATC
**
918427 CCCCCCGGAAAAATGGCTATATAGCAGTTTTTC
1 CCCCCCGGAAAAATGGCTATATAGCAGTTCATC
*
918460 CCCCACGGAAA
1 CCCCCCGGAAA
918471 GCTGACTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (33 bp):
CCCCCCGGAAAAATGGCTATATAGCAGTTCATC
Found at i:926754 original size:28 final size:28
Alignment explanation
Indices: 926714--926769 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
926704 CTCTAGCAAA
926714 TTGTAATGTTAACAAAATGCGGTTATAT
1 TTGTAATGTTAACAAAATGCGGTTATAT
926742 TTGTAATGTTAACAAAATGCGGTTATAT
1 TTGTAATGTTAACAAAATGCGGTTATAT
926770 AAACCAACGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (28 bp):
TTGTAATGTTAACAAAATGCGGTTATAT
Found at i:929647 original size:2 final size:2
Alignment explanation
Indices: 929640--929688 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
929630 TCTAATGACC
929640 AG AG AG AG AG AG 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 AG AG AG AG AG AG
929682 AG AG AG A
1 AG AG AG A
929689 CTGGGTTCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:932836 original size:2 final size:2
Alignment explanation
Indices: 932829--932868 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
932819 TCTTATTAAT
932829 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
932869 TGGATGGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:933139 original size:326 final size:325
Alignment explanation
Indices: 932547--933193 Score: 1285
Period size: 326 Copynumber: 2.0 Consensus size: 325
932537 GAAGGTTACA
932547 ATGGATAATAGACTCTGCAAGTTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATATG
1 ATGGATAATAGACTCTGCAAGTTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATATG
932612 ATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAAA
66 ATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAAA
932677 GCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATAA
131 GCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATAA
932742 TGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGTC
196 TGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGTC
932807 GTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGG
261 GTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGG
932872 ATGGATAATAGACTCTGCAAGTTTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATAT
1 ATGGATAATAGACTCTGCAAG-TTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATAT
932937 GATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAA
65 GATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAA
933002 AGCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATA
130 AGCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATA
933067 ATGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGT
195 ATGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGT
933132 CGTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
260 CGTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
933194 TGAGAGTGAG
Statistics
Matches: 321, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
325 21 0.07
326 300 0.93
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (325 bp):
ATGGATAATAGACTCTGCAAGTTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATATG
ATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAAA
GCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATAA
TGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGTC
GTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGG
Found at i:933233 original size:2 final size:2
Alignment explanation
Indices: 933155--933214 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
933145 TCTTATTAAT
*
933155 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GT GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
933197 GA GT GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
933215 ATTTAGTTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:936429 original size:2 final size:2
Alignment explanation
Indices: 936422--936469 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
936412 TAATGCATGA
936422 AG AG AG AG AG AG 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 AG AG AG AG AG AG
936464 AG AG AG
1 AG AG AG
936470 GTGTAAATCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:948644 original size:17 final size:17
Alignment explanation
Indices: 948624--948666 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
948614 GTGCAAACAT
* *
948624 GGATATAGTGAATTCTC
1 GGATATAGCGAATTCCC
948641 GGATATAGCGAATTCCC
1 GGATATAGCGAATTCCC
*
948658 AGATATAGC
1 GGATATAGC
948667 AAAGTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (17 bp):
GGATATAGCGAATTCCC
Found at i:948744 original size:15 final size:16
Alignment explanation
Indices: 948724--948763 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
948714 ATTTTACGGT
*
948724 TATAACGAATT-CGGA
1 TATAACGAATTAAGGA
948739 TATAACGAATTAAGGA
1 TATAACGAATTAAGGA
*
948755 TATAGCGAA
1 TATAACGAA
948764 CTGATTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (16 bp):
TATAACGAATTAAGGA
Found at i:949056 original size:16 final size:16
Alignment explanation
Indices: 949035--949066 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
949025 CGAATTCAGT
949035 TTACGGATATAACAAA
1 TTACGGATATAACAAA
949051 TTACGGATATAACAAA
1 TTACGGATATAACAAA
949067 GTAATTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (16 bp):
TTACGGATATAACAAA
Found at i:950472 original size:180 final size:179
Alignment explanation
Indices: 950170--950708 Score: 963
Period size: 180 Copynumber: 3.0 Consensus size: 179
950160 CCTACATGTT
* * *
950170 TATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCT-AGTATTTTTTTCATGAATTATCGG
1 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGA-TA-TTTTTTCATAAATTATCCG
*
950234 AAATCGAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACT
64 AAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACT
*
950299 TCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACCATGAGGGTACCCTA
129 TCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTA
*
950350 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGTTGATATTTTTTCAATAAATTATCCGA
1 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGATATTTTTTC-ATAAATTATCCGA
*
950415 AATCAAAATCCTAGCAATATGCACACATCTGATATATGTACAATTGATCTGCAAAAGAACAACTT
65 AATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTT
950480 CCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTA
130 CCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTA
*
950530 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCCGA
1 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGATATTTTTTC-ATAAATTATCCGA
950595 AATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTT
65 AATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTT
950660 CCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCT
130 CCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCT
950709 TTTGGCAGCC
Statistics
Matches: 346, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
179 7 0.02
180 338 0.98
181 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (179 bp):
TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGATATTTTTTCATAAATTATCCGAA
ATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTTC
CTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTA
Found at i:953694 original size:22 final size:19
Alignment explanation
Indices: 953653--953697 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
953643 ACGGTCAAAA
953653 TTATATATAATCAAAATTT
1 TTATATATAATCAAAATTT
* *
953672 TTATCATATAATTAACAACTT
1 TTAT-ATATAATCAA-AATTT
953693 TTATA
1 TTATA
953698 ACATTGGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 10 0.45
21 8 0.36
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATATATAATCAAAATTT
Found at i:957482 original size:24 final size:26
Alignment explanation
Indices: 957448--957499 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
957438 AAAATGTTTT
*
957448 AATTTCAAATTAATCC-AAGAGCAAA
1 AATTTCAAATTAATCCAAAAAGCAAA
957473 AATTT-AAATTAATCCAAAAAGCAAA
1 AATTTCAAATTAATCCAAAAAGCAAA
957498 AA
1 AA
957500 ACTACATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (26 bp):
AATTTCAAATTAATCCAAAAAGCAAA
Found at i:958797 original size:4 final size:4
Alignment explanation
Indices: 958752--958790 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
958742 GTTTCACCCT
* *
958752 GTCC GTCT GTCT GTCC GTCC GTCC GTCC GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
958791 TGTCTGTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.44, G:0.26, T:0.31
Consensus pattern (4 bp):
GTCC
Found at i:966944 original size:17 final size:19
Alignment explanation
Indices: 966922--966957 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
966912 TCTGTAAGTA
966922 AAAAT-ATTCCTT-TTTTT
1 AAAATAATTCCTTATTTTT
966939 AAAATAATTCCTTATTTTT
1 AAAATAATTCCTTATTTTT
966958 TTTTCTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 7 0.41
19 5 0.29
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAATAATTCCTTATTTTT
Found at i:967318 original size:4 final size:4
Alignment explanation
Indices: 967309--967352 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
967299 TACCCTTGTG
* * *
967309 TGTC TGTC TGTC CGTC CGTC TGTC TGTC TGTC CGTC TGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
967353 CGTCCGTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.32, G:0.25, T:0.43
Consensus pattern (4 bp):
TGTC
Found at i:967331 original size:12 final size:12
Alignment explanation
Indices: 967310--967359 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
967300 ACCCTTGTGT
*
967310 GTCTGTCTGTCC
1 GTCTGTCCGTCC
* * *
967322 GTCCGTCTGTCT
1 GTCTGTCCGTCC
*
967334 GTCTGTCCGTCT
1 GTCTGTCCGTCC
967346 GTCTGTCCGTCC
1 GTCTGTCCGTCC
967358 GT
1 GT
967360 AACAAAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:967331 original size:16 final size:16
Alignment explanation
Indices: 967310--967359 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
967300 ACCCTTGTGT
967310 GTCTGTCTGTCCGTCC
1 GTCTGTCTGTCCGTCC
*
967326 GTCTGTCTGTCTGTCC
1 GTCTGTCTGTCCGTCC
967342 GTCTGTCTGTCCGTCC
1 GTCTGTCTGTCCGTCC
967358 GT
1 GT
967360 AACAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40
Consensus pattern (16 bp):
GTCTGTCTGTCCGTCC
Found at i:967658 original size:167 final size:167
Alignment explanation
Indices: 967383--968508 Score: 1682
Period size: 165 Copynumber: 6.8 Consensus size: 167
967373 GTCGCATTTA
*
967383 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTAT-AGGCATGCCATA
* *
967447 TCATGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAACGACGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTT
* **
967512 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAA
130 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
967550 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACAGTATTGGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
*
967615 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGA-GTACTTTG-TT-TAT
66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACG-ACTTTGCTTATTT
**
967677 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAA
130 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
967715 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACAGTATTGGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
* *
967780 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
*
967845 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
131 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
967882 TCTCAGCAGCTATTTATCGCAGATGCTTGAAA-TTTATACACAATATTTGTATAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTA-ACACAGTATTTGTATAGGCATGCCATA
* *
967946 TCGTGGGATATATTTTTGTACCAATCGG-CGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TT
65 TCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTT
*
968009 TTTAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATT
130 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
*
968047 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
* * * * * *
968112 TGTGGGATATATTTTTGTATCAATCGGACGTCAAACTTCCTGTGAAATGATGACTTTGTTTA-TT
66 CGTGGGATATATTTTTGTACCAATCGGACG-CCAACTTCCTGTTAAATGACGACTTTGCTTATTT
968176 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * *
968214 TCTCAGCAGCTATTTATCGCAGATGCTTAAAATTTTTACACAGTGTTTGT-TAAGGCATGCCGTA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTAT-AGGCATGCCATA
* *
968278 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GTACTTTG-TT-TA
65 TCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACG-ACTTTGCTTATT
*
968340 TTTTAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
129 TTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
968379 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
* * * * * * * *
968444 TGTGGAATATATTTCTGTACCAATCGAATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
968509 GCATATTCAC
Statistics
Matches: 882, Mismatches: 61, Indels: 32
0.90 0.06 0.03
Matches are distributed among these distances:
165 420 0.48
166 75 0.09
167 386 0.44
168 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (167 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:968014 original size:332 final size:331
Alignment explanation
Indices: 967381--968508 Score: 1771
Period size: 332 Copynumber: 3.4 Consensus size: 331
967371 CTGTCGCATT
* *
967381 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGT-TAAGGCATGCCA
1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTAT-AGGCATGCCA
* *
967445 TATCATGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAACGACGACTTTGCTTAT
65 TATCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTAT
** * *
967510 TTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAATCTCAGCAACTGTTTATCGCAGATG
130 TTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATG
*
967575 CTTGAAATTTTAACACAGTATTGGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATC
195 CTTGAAATTTT-ACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATC
*
967640 GGACGCCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTTC
259 GGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTTC
967705 GTCAAAGA
324 GTCAAAGA
* * * *
967713 AATCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACAGTATTGGTATAGGCATGCCAT
1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT
* *
967778 ATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATT
66 ATCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATT
967843 TTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGC
131 TTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGC
*
967908 TTGAAATTTATACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCG
196 TTGAAATTT-TACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCG
*
967973 G-CGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTC
260 GACGTCAACTTCCTGTTAAATGA-GTACTTTGTTTA-TTTTAGCCAAAATTTTCAAACAAATTTT
968036 CGTCAAAGA
323 CGTCAAAGA
*
968045 TTTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT
1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT
* * * * * *
968110 ATTGTGGGATATATTTTTGTATCAATCGGACGTCAAACTTCCTGTGAAATGATGACTTTGTTTA-
66 ATCGTGGGATATATTTTTGTACCAATCGGACG-CCAACTTCCTGTTAAATGACGACTTTGCTTAT
*
968174 TTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATG
130 TTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATG
* * *
968239 CTTAAAATTTTTACACAGTGTTTGT-TAAGGCATGCCGTATCGTGGGATATATTTTTGTACCAAT
195 CTTGAAA-TTTTACACAGTATTTGTAT-AGGCATGCCATATCGTGGGATATATTTTTGTACCAAT
968303 CGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTT
258 CGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTT
*
968368 CCTCAAAGA
323 CGTCAAAGA
* * * *
968377 TTTCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCTAT
1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT
* * * * * * * *
968442 ATTGTGGAATATATTTCTGTACCAATCGAATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATT
66 ATCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATT
968507 TT
131 TT
968509 GCATATTCAC
Statistics
Matches: 735, Mismatches: 51, Indels: 20
0.91 0.06 0.02
Matches are distributed among these distances:
331 55 0.07
332 618 0.84
333 62 0.08
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (331 bp):
TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT
ATCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATT
TTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGC
TTGAAATTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGG
ACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTTCGT
CAAAGA
Found at i:979700 original size:17 final size:18
Alignment explanation
Indices: 979680--979713 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
979670 AACCCTCAGT
979680 TTAGCCGA-TAACTGGTC
1 TTAGCCGATTAACTGGTC
979697 TTAGCCGATTAACTGGT
1 TTAGCCGATTAACTGGT
979714 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (18 bp):
TTAGCCGATTAACTGGTC
Found at i:982155 original size:17 final size:17
Alignment explanation
Indices: 982117--982155 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
982107 TTAAAAATTC
*
982117 CTTTAAATTTAACCTTT
1 CTTTAAATTTAACCATT
* *
982134 TTTTAAATTTAAGCATT
1 CTTTAAATTTAACCATT
982151 CTTTA
1 CTTTA
982156 TATATTTGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.54
Consensus pattern (17 bp):
CTTTAAATTTAACCATT
Found at i:987793 original size:13 final size:13
Alignment explanation
Indices: 987775--987804 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
987765 GTAGAGTGTA
987775 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
987788 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
987801 TTTT
1 TTTT
987805 GCAACAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:990790 original size:23 final size:23
Alignment explanation
Indices: 990760--990816 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
990750 ATTGCAGTTT
990760 GATTGACACAACGCACACAGACG
1 GATTGACACAACGCACACAGACG
*
990783 GATTGACACAACGCGCACAGACG
1 GATTGACACAACGCACACAGACG
990806 GATATGA-ACAA
1 GAT-TGACACAA
990817 AAGTTCACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 29 0.91
24 3 0.09
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (23 bp):
GATTGACACAACGCACACAGACG
Found at i:995042 original size:21 final size:21
Alignment explanation
Indices: 995018--995095 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 21
995008 GCATATCATT
* *
995018 GCATTAAAATCTCATAGAATA
1 GCATTAAAATATCATACAATA
** * *
995039 GCATTGGAATCTCATACCATA
1 GCATTAAAATATCATACAATA
* *
995060 GCATTGAAATATCATACCATA
1 GCATTAAAATATCATACAATA
*
995081 GCA-TACAATATCATA
1 GCATTAAAATATCATA
995096 GATTCTCATT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 10 0.20
21 39 0.80
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (21 bp):
GCATTAAAATATCATACAATA
Found at i:995362 original size:21 final size:21
Alignment explanation
Indices: 995326--995403 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
995316 CATTTCACTT
*
995326 TCTCATAGCAAAGCA-TACAAA
1 TCTCATAGCATAGCATTA-AAA
*
995347 TCTCATAGCATTGCATTAAAA
1 TCTCATAGCATAGCATTAAAA
* * *
995368 TCTCGTAGCATATCATTTAAA
1 TCTCATAGCATAGCATTAAAA
* *
995389 TCGCATACCATAGCA
1 TCTCATAGCATAGCA
995404 AAGCATAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
21 44 0.96
22 2 0.04
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28
Consensus pattern (21 bp):
TCTCATAGCATAGCATTAAAA
Found at i:997800 original size:7 final size:7
Alignment explanation
Indices: 997788--997817 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
997778 CTTGATTTAA
997788 AAAACAC
1 AAAACAC
997795 AAAACAC
1 AAAACAC
*
997802 AAAACAT
1 AAAACAC
997809 AAAACAC
1 AAAACAC
997816 AA
1 AA
997818 GTGGGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.73, C:0.23, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAACAC
Found at i:1007037 original size:53 final size:53
Alignment explanation
Indices: 1006970--1007074 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
1006960 ATTTCTAAAG
* * *
1006970 AAAAAAAAGAAAAATACAAAAATACATTTTCGGGTTAAAATTTTAATTAATTA
1 AAAAAAAAGAAAAATACAAAAATACATATACGGGTTAAAATTTTAACTAATTA
*
1007023 AAAAAAAATG-AAAATACAAAAATACATATACGGGTTAAAGTTTTAACTAATT
1 AAAAAAAA-GAAAAATACAAAAATACATATACGGGTTAAAATTTTAACTAATT
1007075 GGCCCTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
53 46 0.98
54 1 0.02
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29
Consensus pattern (53 bp):
AAAAAAAAGAAAAATACAAAAATACATATACGGGTTAAAATTTTAACTAATTA
Found at i:1009230 original size:48 final size:47
Alignment explanation
Indices: 1009178--1009273 Score: 122
Period size: 48 Copynumber: 2.0 Consensus size: 47
1009168 GTAAGTATTC
*
1009178 ATGTTGT-AGAATATGATTTTTACAGATATCAAAAACATCCATCACAGA
1 ATGTTGTCA-AATAGGATTTTTACAGATATC-AAAACATCCATCACAGA
* * * *
1009226 ATGTTGTCAAATAGGATTTTTGCAGATATCGAAACATTCATCCCAGA
1 ATGTTGTCAAATAGGATTTTTACAGATATCAAAACATCCATCACAGA
1009273 A
1 A
1009274 AATTTTACAG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
47 15 0.36
48 26 0.62
49 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (47 bp):
ATGTTGTCAAATAGGATTTTTACAGATATCAAAACATCCATCACAGA
Found at i:1009800 original size:1 final size:1
Alignment explanation
Indices: 1009794--1009819 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1009784 AGAATATACG
1009794 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1009820 GGTATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1014951 original size:2 final size:2
Alignment explanation
Indices: 1014944--1015024 Score: 155
Period size: 2 Copynumber: 41.0 Consensus size: 2
1014934 TGTGGACCAT
1014944 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- 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
1014985 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
1015025 CTTTAATTCA
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 77 0.99
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1017369 original size:414 final size:411
Alignment explanation
Indices: 1016546--1017374 Score: 1523
Period size: 413 Copynumber: 2.0 Consensus size: 411
1016536 TACTCTGAAA
**
1016546 GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAGCCCCCCCACCCCCATTAAATACTGAT
1 GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAGCCCCCCCACCCCCACCAAATACTGAT
*
1016611 AATGTTATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATGTA
66 AATGTAATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATGTA
1016676 ATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTAAT
131 ATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTAAT
1016741 TGTAATTTAATCGATTACTTTTGAAAGGAATCAACTACATCGCTTGTCACAATCAACGTTATTTC
196 TGTAATTTAATCGATTACTTTTGAAAGGAATCAACTACATCGCTTGTCACAATCAACGTTATTTC
* *
1016806 TTATTTTCTAACGATACAATGGGTTAATTGAAGTTGAAAACACGTGTGAATGAAATCTAGGCATT
261 TTATCTTCTAACGATACAATGGGTTAATTGAAGCTGAAAACACGTGTGAATGAAATCTAGGCATT
*
1016871 AAAATATGCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAACTATAAGATAACATTTA
326 AAAATATCCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAACTATAAGATAACATTTA
1016936 CGTACATTTATTTTTTCTTCT
391 CGTACATTTATTTTTTCTTCT
*
1016957 GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAGCCCCCCCCCCCCTCCACCAAATACTG
1 GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAG-CCCCCCCACCC-CCACCAAATACTG
1017022 ATAATGTAATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATG
64 ATAATGTAATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATG
1017087 TAATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTA
129 TAATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTA
*
1017152 ATTGTAATTTAATCGATTACTTTTGACAGGAATCAACTACATCGCTTGTCACAATCAACGGTTAT
194 ATTGTAATTTAATCGATTACTTTTGAAAGGAATCAACTACATCGCTTGTCACAATCAAC-GTTAT
* *
1017217 TTCTTATCTTCTAATGATACAATGGGTTAATTGAAGCTGAACACACGTGTGAATGAAATCTAGGC
258 TTCTTATCTTCTAACGATACAATGGGTTAATTGAAGCTGAAAACACGTGTGAATGAAATCTAGGC
* *
1017282 ATTGAAATATCCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAATTATAAGATAACAT
323 ATTAAAATATCCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAACTATAAGATAACAT
1017347 TTACGTACATTTATTTTTTCTTCT
388 TTACGTACATTTATTTTTTCTTCT
1017371 GTCA
1 GTCA
1017375 TTGATTTTTT
Statistics
Matches: 403, Mismatches: 12, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
411 39 0.10
412 10 0.02
413 198 0.49
414 156 0.39
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (411 bp):
GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAGCCCCCCCACCCCCACCAAATACTGAT
AATGTAATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATGTA
ATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTAAT
TGTAATTTAATCGATTACTTTTGAAAGGAATCAACTACATCGCTTGTCACAATCAACGTTATTTC
TTATCTTCTAACGATACAATGGGTTAATTGAAGCTGAAAACACGTGTGAATGAAATCTAGGCATT
AAAATATCCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAACTATAAGATAACATTTA
CGTACATTTATTTTTTCTTCT
Found at i:1020005 original size:21 final size:21
Alignment explanation
Indices: 1019976--1020050 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
1019966 TATGCTATGC
* *
1019976 TATGGTATGCGATTTAAATGA
1 TATGCTATGAGATTTAAATGA
*
1019997 TATGCTATGAGATTTTAATGCA
1 TATGCTATGAGATTTAAATG-A
* ** *
1020019 -ATACTATGAGATTTGTATGC
1 TATGCTATGAGATTTAAATGA
*
1020039 TTTGCTATGAGA
1 TATGCTATGAGA
1020051 AATCGAAATG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (21 bp):
TATGCTATGAGATTTAAATGA
Found at i:1026208 original size:2 final size:2
Alignment explanation
Indices: 1026201--1026251 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1026191 GACCGAGCCC
1026201 CT CT 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 CT CT
1026243 CT CT CT CT C
1 CT CT CT CT C
1026252 AACAGAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1027130 original size:2 final size:2
Alignment explanation
Indices: 1027123--1027185 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1027113 CGCCTAAACG
1027123 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
1027165 TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
1027186 TGTAAGGTGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1028611 original size:4 final size:4
Alignment explanation
Indices: 1028602--1028643 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
1028592 AAAGTTTACA
* * *
1028602 GACG GACG GACG GACA GACA GACG GACA GACG GAC- GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC
1028644 AAAATGTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.33, C:0.26, G:0.40, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:1030582 original size:2 final size:2
Alignment explanation
Indices: 1030577--1030642 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1030567 TTATATACGA
1030577 CT CT 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 CT CT
1030619 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
1030643 TATTTTTTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1031157 original size:1 final size:1
Alignment explanation
Indices: 1031151--1031180 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1031141 TTAGACCGTC
1031151 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1031181 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1031246 original size:1 final size:1
Alignment explanation
Indices: 1031242--1031273 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
1031232 TTTTAGCCGC
1031242 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1031274 GGATTACAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1048649 original size:112 final size:112
Alignment explanation
Indices: 1048452--1048782 Score: 565
Period size: 111 Copynumber: 3.0 Consensus size: 112
1048442 TCCCCCGATT
* *
1048452 CACATACTCACACTCACAAACCAATTGACAGTGAGACTGCCTCCCTTCATACCCACCCACACACT
1 CACATACTCACACTCACAAACCAATTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT
* * *
1048517 TACCAATGAATGGTGCATCCTTGTCGTTGGGACCTGCCGCCCCTAGA
66 TACCAATGGATGGTGCATCCTTGTCGTTAGGACCCGCCGCCCCTAGA
*
1048564 CACATACTCACACTCACAAACCAATTGACAGTGAGATTACCTCCCTTCACACCCACCCACACACT
1 CACATACTCACACTCACAAACCAATTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT
* *
1048629 TACCAATGGATAGTGCATCCTTGTCGTTAGGACCCGCTG-CCCTAGA
66 TACCAATGGATGGTGCATCCTTGTCGTTAGGACCCGCCGCCCCTAGA
*
1048675 CACATACTCACACTCACAAACCAACTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT
1 CACATACTCACACTCACAAACCAATTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT
*
1048740 TACCAATGGAGGGTGCATCCTTGTCGTTAGGACCCGCCGCCCC
66 TACCAATGGATGGTGCATCCTTGTCGTTAGGACCCGCCGCCCC
1048783 CTTCACACCC
Statistics
Matches: 205, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
111 106 0.52
112 99 0.48
ACGTcount: A:0.27, C:0.37, G:0.15, T:0.21
Consensus pattern (112 bp):
CACATACTCACACTCACAAACCAATTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT
TACCAATGGATGGTGCATCCTTGTCGTTAGGACCCGCCGCCCCTAGA
Found at i:1057148 original size:101 final size:101
Alignment explanation
Indices: 1056965--1057168 Score: 336
Period size: 101 Copynumber: 2.0 Consensus size: 101
1056955 TCTGTAAAAC
* * * *
1056965 AATCACAGAAAGAGAGTCACTGGTAAAGTACATTATAACTTGAAAAAAAAGATTTAAGGCAACAA
1 AATCAAAGAAAGAGAGTCACTGGTAAAATACATGATAACTTGAAAAAAAAGATTTAAGACAACAA
*
1057030 ATAAAAAACAATGTATTGCTGCATACTGAGAAATGA
66 ATAAAAAAAAATGTATTGCTGCATACTGAGAAATGA
* *
1057066 AATCAAAGAAAGAGTGTCACTGGTAAAATACATGATAACTTGACAAAAAAGATTTAAGACAACAA
1 AATCAAAGAAAGAGAGTCACTGGTAAAATACATGATAACTTGAAAAAAAAGATTTAAGACAACAA
*
1057131 ATAAAAAAAAATTTATTGCTGCATACTGAGAAATGA
66 ATAAAAAAAAATGTATTGCTGCATACTGAGAAATGA
1057167 AA
1 AA
1057169 AATTGTGTAT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (101 bp):
AATCAAAGAAAGAGAGTCACTGGTAAAATACATGATAACTTGAAAAAAAAGATTTAAGACAACAA
ATAAAAAAAAATGTATTGCTGCATACTGAGAAATGA
Found at i:1087310 original size:177 final size:177
Alignment explanation
Indices: 1087065--1087634 Score: 781
Period size: 177 Copynumber: 3.2 Consensus size: 177
1087055 ACTTGAAAGA
** * * * * *
1087065 CTTGGATGCTGAATCTGAGTCC-TAAATTCCAGATGCTGGAGGAGGTTAAGGTTGTTGGACCAGG
1 CTTGGATGCTGAATCTGAG-CCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG
* * * * *
1087129 TTAAAGTTTTTGTTGCAGGTGCCCTTTGAT-AGTAATATCTAAGTTACTGCTGGTCCGT-ACTTC
65 TTAAAGTTTTTGTTGCAGGTGCCCTCTGATGA-TTATATCTTAGTTACTACTTGTCC-TAACTTC
* * * *
1087192 ACCAAACTTGCATTGATGGTGTGTCTTATGATACTGATGCACCAGGCAGG
128 ACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGG
* * *
1087242 CTTGGATGCTGAATCTGAGCTATAGGTTACAGATGCTGAAGGAGGTTAAGGTTTTTAGAGCTGGT
1 CTTGGATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGT
1087307 TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTTGTCCTAACTTCACC
66 TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTTGTCCTAACTTCACC
*
1087372 AGACTTCCATGGATGGTGTGTCTTATGCTACTGATGCACCAGACAGG
131 AGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGG
*
1087419 CTT-GATTGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG
1 CTTGGA-TGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG
*** * *
1087483 TTAAAGTTTTTGAAACAGGTGCCCTCTGATGATTATATCTTAGTTATTACTTGTCCTAACTACAC
65 TTAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTTGTCCTAACTTCAC
* * *
1087548 CGGACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACA-G
130 CAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGG
* * *
1087595 CTTGAATGCTGAGTCTGAGCCATAGGTTTCAGACGCTGGA
1 CTTGGATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGA
1087635 TATGGTTAAG
Statistics
Matches: 352, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
176 39 0.11
177 312 0.89
178 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (177 bp):
CTTGGATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGT
TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTTGTCCTAACTTCACC
AGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGG
Found at i:1088558 original size:36 final size:32
Alignment explanation
Indices: 1088516--1088580 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 32
1088506 TATTGCAAAA
1088516 TATAATATTGTATCCTATGATCGATATTGTATATTC
1 TATAATATTGTAT--TAT-AT-GATATTGTATATTC
1088552 TATAATATTGTATTATATGATATTGTATA
1 TATAATATTGTATTATATGATATTGTATA
1088581 ATATGATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 11 0.38
33 2 0.07
34 3 0.10
36 13 0.45
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (32 bp):
TATAATATTGTATTATATGATATTGTATATTC
Found at i:1088574 original size:15 final size:15
Alignment explanation
Indices: 1088515--1088590 Score: 62
Period size: 15 Copynumber: 4.7 Consensus size: 15
1088505 ATATTGCAAA
*
1088515 ATATAATATTGTATCCT
1 ATATGATATTGTAT--T
1088532 ATGATCGATATTGTATATT
1 AT-AT-GATATTG--TATT
* *
1088551 CTATAATATTGTATT
1 ATATGATATTGTATT
*
1088566 ATATGATATTGTATA
1 ATATGATATTGTATT
1088581 ATATGATATT
1 ATATGATATT
1088591 AGTTTCTGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
15 26 0.53
17 8 0.16
18 4 0.08
19 8 0.16
21 3 0.06
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.49
Consensus pattern (15 bp):
ATATGATATTGTATT
Found at i:1088687 original size:15 final size:15
Alignment explanation
Indices: 1088556--1088703 Score: 73
Period size: 15 Copynumber: 9.1 Consensus size: 15
1088546 ATATTCTATA
*
1088556 ATATTGTATTATATG
1 ATATTGTATAATATG
1088571 ATATTGTATAATATG
1 ATATTGTATAATATG
*
1088586 ATATTAGTTTCTGTAATATAG
1 ATATT-G----TATAATAT-G
* * *
1088607 A-ATTATATCACATG
1 ATATTGTATAATATG
* *
1088621 AAAATGTATAATATG
1 ATATTGTATAATATG
* *
1088636 ATACTGTAATATTATATA
1 ATATTGT-ATA--ATATG
* * *
1088654 ACATTGTATCATACG
1 ATATTGTATAATATG
1088669 ATATTGTATAATATG
1 ATATTGTATAATATG
1088684 ATATTGGTTTATAATATG
1 ATATT-G--TATAATATG
1088702 AT
1 AT
1088704 GTATTATCGC
Statistics
Matches: 99, Mismatches: 21, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
14 2 0.02
15 58 0.59
16 5 0.05
17 2 0.02
18 20 0.20
20 10 0.10
21 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (15 bp):
ATATTGTATAATATG
Found at i:1088751 original size:98 final size:97
Alignment explanation
Indices: 1088552--1088769 Score: 248
Period size: 98 Copynumber: 2.2 Consensus size: 97
1088542 TTGTATATTC
* * *
1088552 TATAATATTGTATTATATGATATTGTATAATATGATATTAGTTTCTGTAATATAGAATTATATCA
1 TATAATATTGTATCATATGATATTGTATAATATGATATTAGGTTCTATAATATAGAATTATATCA
1088617 CATGAAAATGTATAATATGATACTGTAATATTA
66 CATGAAAATGTATAATATGATACTGTAATA-TA
* * *
1088650 TATAACATTGTATCATACGATATTGTATAATATGATATT-GGTT-TATAATATGATGTATTATCG
1 TATAATATTGTATCATATGATATTGTATAATATGATATTAGGTTCTATAATAT-A-GAATTAT--
* **
1088713 CATCACATGAAATTGTATTGTATGAT-CTTGTAA-A-A
62 -ATCACATGAAAATGTATAATATGATAC-TGTAATATA
*
1088748 TATATTATTGTATCATATGATA
1 TATAATATTGTATCATATGATA
1088770 CAATATGTAT
Statistics
Matches: 102, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
96 7 0.07
97 4 0.04
98 62 0.61
100 2 0.02
101 27 0.26
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (97 bp):
TATAATATTGTATCATATGATATTGTATAATATGATATTAGGTTCTATAATATAGAATTATATCA
CATGAAAATGTATAATATGATACTGTAATATA
Found at i:1090867 original size:21 final size:21
Alignment explanation
Indices: 1090843--1090896 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1090833 ATTTTAATAA
1090843 TATGCTATGAGATTTGTATGC
1 TATGCTATGAGATTTGTATGC
1090864 TATGCTATGAGATTTGTATGC
1 TATGCTATGAGATTTGTATGC
1090885 TATGCTATGAGA
1 TATGCTATGAGA
1090897 AATTGAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (21 bp):
TATGCTATGAGATTTGTATGC
Found at i:1090878 original size:42 final size:42
Alignment explanation
Indices: 1090817--1090896 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1090807 AAATTTATGC
* *
1090817 TATGCTATGGTATGCGATTT-TAATAATATGCTATGAGATTTG
1 TATGCTATGCTATGAGATTTGT-ATAATATGCTATGAGATTTG
**
1090859 TATGCTATGCTATGAGATTTGTATGCTATGCTATGAGA
1 TATGCTATGCTATGAGATTTGTATAATATGCTATGAGA
1090897 AATTGAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.41
Consensus pattern (42 bp):
TATGCTATGCTATGAGATTTGTATAATATGCTATGAGATTTG
Found at i:1091167 original size:21 final size:21
Alignment explanation
Indices: 1091141--1091216 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
1091131 ATGAGAGTGT
* *
1091141 ATGCTATGGTATGAGATTCCA
1 ATGCTATGCTATGAGATTTCA
1091162 ATGCTATGCTATGAGATTTCA
1 ATGCTATGCTATGAGATTTCA
*
1091183 ACGCTATGCTATGAGATTTCA
1 ATGCTATGCTATGAGATTTCA
1091204 ATGCTATGCTATG
1 ATGCTATGCTATG
1091217 CTATGGTGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (21 bp):
ATGCTATGCTATGAGATTTCA
Found at i:1091563 original size:10 final size:10
Alignment explanation
Indices: 1091534--1091576 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
1091524 TTGCGTAAAT
1091534 TATATTA-TG
1 TATATTATTG
* *
1091543 TAAAGTATTG
1 TATATTATTG
*
1091553 TTTATTATTG
1 TATATTATTG
1091563 TATATTATTG
1 TATATTATTG
1091573 TATA
1 TATA
1091577 ATATGATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 5 0.19
10 22 0.81
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (10 bp):
TATATTATTG
Found at i:1095800 original size:2 final size:2
Alignment explanation
Indices: 1095793--1095838 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1095783 CAGGTACCGG
1095793 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
1095835 TC TC
1 TC TC
1095839 GGGGTAGGGG
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1100281 original size:27 final size:27
Alignment explanation
Indices: 1100248--1100409 Score: 236
Period size: 27 Copynumber: 6.0 Consensus size: 27
1100238 TCATCCCCAG
*
1100248 GATCGTCTGCTTCCACTTCTAGATCCC
1 GATCGTCTGCCTCCACTTCTAGATCCC
*
1100275 GATCGTCTGCTTCCACTTCTAGATCCC
1 GATCGTCTGCCTCCACTTCTAGATCCC
*
1100302 GATCGGCTGCCTCCACTTCTAGATCCC
1 GATCGTCTGCCTCCACTTCTAGATCCC
*
1100329 GATCGTCTGCTTCCACTTCTAGATCCC
1 GATCGTCTGCCTCCACTTCTAGATCCC
* *
1100356 CATCGGCTGCCTCCACTTCTAGATCCC
1 GATCGTCTGCCTCCACTTCTAGATCCC
**
1100383 CTTCGGT-TGCCTCCACTTCTAGATCCC
1 GATC-GTCTGCCTCCACTTCTAGATCCC
1100410 CCTCGTATCC
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
27 124 0.99
28 1 0.01
ACGTcount: A:0.14, C:0.40, G:0.15, T:0.31
Consensus pattern (27 bp):
GATCGTCTGCCTCCACTTCTAGATCCC
Found at i:1100394 original size:81 final size:81
Alignment explanation
Indices: 1100248--1100409 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 81
1100238 TCATCCCCAG
* * * *
1100248 GATCGTCTGCTTCCACTTCTAGATCCCGATCGTCTGCTTCCACTTCTAGATCCCGATCGGCTGCC
1 GATCGTCTGCTTCCACTTCTAGATCCCCATCGGCTGCCTCCACTTCTAGATCCCCATCGGCTGCC
1100313 TCCACTTCTAGATCCC
66 TCCACTTCTAGATCCC
* *
1100329 GATCGTCTGCTTCCACTTCTAGATCCCCATCGGCTGCCTCCACTTCTAGATCCCCTTCGGTTGCC
1 GATCGTCTGCTTCCACTTCTAGATCCCCATCGGCTGCCTCCACTTCTAGATCCCCATCGGCTGCC
1100394 TCCACTTCTAGATCCC
66 TCCACTTCTAGATCCC
1100410 CCTCGTATCC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.14, C:0.40, G:0.15, T:0.31
Consensus pattern (81 bp):
GATCGTCTGCTTCCACTTCTAGATCCCCATCGGCTGCCTCCACTTCTAGATCCCCATCGGCTGCC
TCCACTTCTAGATCCC
Found at i:1100482 original size:18 final size:18
Alignment explanation
Indices: 1100441--1100593 Score: 114
Period size: 18 Copynumber: 8.6 Consensus size: 18
1100431 GGTCTACGTC
* * *
1100441 TGGGTTTCCTAGGGGGGT
1 TGGGTTTTCTTGGGGGAT
* *
1100459 TTGGTTTTCTTGGTGGAT
1 TGGGTTTTCTTGGGGGAT
* *
1100477 TGGG-TTTCCTGGGGGGT
1 TGGGTTTTCTTGGGGGAT
* *
1100494 TGGGTTTCCTAGGGGGAT
1 TGGGTTTTCTTGGGGGAT
** *
1100512 TGGGTTCCCTGGGGGGAT
1 TGGGTTTTCTTGGGGGAT
*
1100530 TGGG-TTTCCTGAGGGGAT
1 TGGGTTTTCTTG-GGGGAT
* *
1100548 TGGGTTTCCTAGGGGGAT
1 TGGGTTTTCTTGGGGGAT
*
1100566 TGGG-TTTCTTGGGAGCAT
1 TGGGTTTTCTTGGG-GGAT
*
1100584 CGGGTTTTCT
1 TGGGTTTTCT
1100594 GTCGGGTTTA
Statistics
Matches: 104, Mismatches: 26, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
17 24 0.23
18 71 0.68
19 9 0.09
ACGTcount: A:0.07, C:0.12, G:0.44, T:0.37
Consensus pattern (18 bp):
TGGGTTTTCTTGGGGGAT
Found at i:1100484 original size:17 final size:17
Alignment explanation
Indices: 1100453--1100578 Score: 126
Period size: 18 Copynumber: 7.2 Consensus size: 17
1100443 GGTTTCCTAG
* *
1100453 GGGGGTTTGGTTTTCTT
1 GGGGGATTGGGTTTCTT
* *
1100470 GGTGGATTGGGTTTCCT
1 GGGGGATTGGGTTTCTT
* *
1100487 GGGGGGTTGGGTTTCCTA
1 GGGGGATTGGGTTT-CTT
* *
1100505 GGGGGATTGGGTTCCCTG
1 GGGGGATTGGGTT-TCTT
*
1100523 GGGGGATTGGGTTTCCT
1 GGGGGATTGGGTTTCTT
*
1100540 GAGGGGATTGGGTTTCCTA
1 G-GGGGATTGGGTTT-CTT
1100559 GGGGGATTGGGTTTCTT
1 GGGGGATTGGGTTTCTT
1100576 GGG
1 GGG
1100579 AGCATCGGGT
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
17 32 0.36
18 54 0.61
19 2 0.02
ACGTcount: A:0.06, C:0.10, G:0.47, T:0.37
Consensus pattern (17 bp):
GGGGGATTGGGTTTCTT
Found at i:1100492 original size:36 final size:35
Alignment explanation
Indices: 1100441--1100578 Score: 179
Period size: 36 Copynumber: 3.9 Consensus size: 35
1100431 GGTCTACGTC
* * *
1100441 TGGGTTTCCTAGGGGGGTTTGGTTTTCTTGGTGGAT
1 TGGGTTTCCT-GGGGGGATTGGGTTTCTTGGGGGAT
*
1100477 TGGGTTTCCTGGGGGG-TTGGGTTTCCTAGGGGGAT
1 TGGGTTTCCTGGGGGGATTGGGTTT-CTTGGGGGAT
* *
1100512 TGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT
1 TGGGTTTCCTGGGGGGATTGGGTTTCTTG-GGGGAT
*
1100548 TGGGTTTCCTAGGGGGATTGGGTTTCTTGGG
1 TGGGTTTCCTGGGGGGATTGGGTTTCTTGGG
1100579 AGCATCGGGT
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
34 7 0.08
35 33 0.37
36 50 0.56
ACGTcount: A:0.07, C:0.11, G:0.46, T:0.37
Consensus pattern (35 bp):
TGGGTTTCCTGGGGGGATTGGGTTTCTTGGGGGAT
Found at i:1100530 original size:53 final size:54
Alignment explanation
Indices: 1100441--1100571 Score: 192
Period size: 53 Copynumber: 2.4 Consensus size: 54
1100431 GGTCTACGTC
* * ** * * *
1100441 TGGGTTTCCTAGGGGGGTTTGGTTTTCTTGGTGGATTGGGTTTCCTG-GGGGGT
1 TGGGTTTCCTAGGGGGATTGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT
1100494 TGGGTTTCCTAGGGGGATTGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT
1 TGGGTTTCCTAGGGGGATTGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT
1100548 TGGGTTTCCTAGGGGGATTGGGTT
1 TGGGTTTCCTAGGGGGATTGGGTT
1100572 TCTTGGGAGC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 41 0.59
54 29 0.41
ACGTcount: A:0.07, C:0.11, G:0.46, T:0.37
Consensus pattern (54 bp):
TGGGTTTCCTAGGGGGATTGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT
Found at i:1100719 original size:90 final size:90
Alignment explanation
Indices: 1100562--1101193 Score: 1066
Period size: 90 Copynumber: 7.0 Consensus size: 90
1100552 TTTCCTAGGG
* * ** *
1100562 GGATTGGGTTTCTTGGGAGCATCGGGTTTTCTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
*
1100627 AAGCTTCGGATAATCGTCGGGGTTA
66 AAGCTTCGGATAATCGTCGGGTTTA
* * *
1100652 GTATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGGTTAGGACTTGCATAATCGTCGGGGGT
1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
1100717 AAGCTTCGGATAATCGTCGGGTTTA
66 AAGCTTCGGATAATCGTCGGGTTTA
* * *
1100742 GGATTGGCTTTCTTGGAAGCATCACGTTTACTGTCGGGGTTAGGACTTGCATAATCGTCGGGGGT
1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
1100807 AAGCTTCGGATAATCGTCGGGTTTA
66 AAGCTTCGGATAATCGTCGGGTTTA
*
1100832 GGATTGGCTTTCTTGGAAGCATCACGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
1100897 AAGCTTCGGATAATCGTCGGGTTTA
66 AAGCTTCGGATAATCGTCGGGTTTA
* *
1100922 GGATTGGCATTCTTGGAAGCATCAAGTTTACTGTCGGCTTTAGGACTTGCATAATCGTCGGGTGT
1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
1100987 AAGCTTCGGATAATCGTCGGGTTTA
66 AAGCTTCGGATAATCGTCGGGTTTA
* *
1101012 GTATTGGCTTTCTTGGAAGCATCACGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
1101077 AAGCTTCGGATAATCGTCGGGTTTA
66 AAGCTTCGGATAATCGTCGGGTTTA
* *
1101102 GTATTGGCTTTCTTGGAAGCATCAAGTTAACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
* * *
1101167 ATGCTTCGGATAATCGTAGAGTTTA
66 AAGCTTCGGATAATCGTCGGGTTTA
1101192 GG
1 GG
1101194 TTTAGGGTTA
Statistics
Matches: 516, Mismatches: 26, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 516 1.00
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (90 bp):
GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT
AAGCTTCGGATAATCGTCGGGTTTA
Found at i:1104454 original size:13 final size:13
Alignment explanation
Indices: 1104432--1104474 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1104422 TACTTGCTAG
*
1104432 AAAAAGAAAAAAC
1 AAAAACAAAAAAC
1104445 AAAAACAAAAAAC
1 AAAAACAAAAAAC
* * *
1104458 AAATACCAAAAAT
1 AAAAACAAAAAAC
1104471 AAAA
1 AAAA
1104475 TAAAAAGGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.81, C:0.12, G:0.02, T:0.05
Consensus pattern (13 bp):
AAAAACAAAAAAC
Found at i:1111923 original size:2 final size:2
Alignment explanation
Indices: 1111916--1111959 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1111906 TAAAGACTGA
1111916 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
1111958 TC
1 TC
1111960 GTTTTAATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1118514 original size:31 final size:31
Alignment explanation
Indices: 1118472--1118531 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1118462 TAGTAACTTT
*
1118472 TATCAAGTCTGTAAAAACATTGACCCAGTTC
1 TATCAACTCTGTAAAAACATTGACCCAGTTC
*
1118503 TATCAACTCTGTATAAACATTGACCCAGT
1 TATCAACTCTGTAAAAACATTGACCCAGT
1118532 CACCAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (31 bp):
TATCAACTCTGTAAAAACATTGACCCAGTTC
Done.