Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold100
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: 1174989
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 153044 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1081336 original size:21 final size:21
Alignment explanation
Indices: 1081310--1081540 Score: 265
Period size: 21 Copynumber: 10.9 Consensus size: 21
1081300 ATATAGACCA
*
1081310 TTTCTCGTAATTACGAGATCT
1 TTTCTCGTAATAACGAGATCT
*
1081331 TTTCTCGTAATAACGATATCT
1 TTTCTCGTAATAACGAGATCT
1081352 TTTC-CTGTAATAACGAGATCT
1 TTTCTC-GTAATAACGAGATCT
*
1081373 TTTCTCGTAATTAA-GAGATAAT
1 TTTCTCGTAA-TAACGAGAT-CT
** *
1081395 TAACTCGTAATAACGATATCT
1 TTTCTCGTAATAACGAGATCT
1081416 TTTC-CTGTAATAACGAGATCT
1 TTTCTC-GTAATAACGAGATCT
*
1081437 TTTCTCGTAATTAA-GAGATAAT
1 TTTCTCGTAA-TAACGAGAT-CT
** *
1081459 TAACTCGTAATAACGATATCT
1 TTTCTCGTAATAACGAGATCT
1081480 TTTC-CTGTAATAACGAGATCT
1 TTTCTC-GTAATAACGAGATCT
1081501 TTTCTCGTAATAACGAGATCT
1 TTTCTCGTAATAACGAGATCT
*
1081522 TTTCTCATAATAACGAGAT
1 TTTCTCGTAATAACGAGAT
1081541 AATTTACCCG
Statistics
Matches: 178, Mismatches: 20, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.02
21 140 0.79
22 35 0.20
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.39
Consensus pattern (21 bp):
TTTCTCGTAATAACGAGATCT
Found at i:1081404 original size:22 final size:23
Alignment explanation
Indices: 1081376--1081474 Score: 77
Period size: 22 Copynumber: 4.6 Consensus size: 23
1081366 GAGATCTTTT
1081376 CTCGTAATTAA-GAGATAATTAA
1 CTCGTAATTAACGAGATAATTAA
* ** **
1081398 CTCGTAA-TAACGATATCTTTTC
1 CTCGTAATTAACGAGATAATTAA
* **
1081420 CT-GTAA-TAACGAGAT-CTTTT
1 CTCGTAATTAACGAGATAATTAA
1081440 CTCGTAATTAA-GAGATAATTAA
1 CTCGTAATTAACGAGATAATTAA
1081462 CTCGTAA-TAACGA
1 CTCGTAATTAACGA
1081475 TATCTTTTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
20 5 0.08
21 27 0.44
22 29 0.48
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (23 bp):
CTCGTAATTAACGAGATAATTAA
Found at i:1081490 original size:85 final size:85
Alignment explanation
Indices: 1081316--1081562 Score: 261
Period size: 85 Copynumber: 2.9 Consensus size: 85
1081306 ACCATTTCTC
* * * * ** *
1081316 GTAATTACGAGATCTTTTCTCGTAATAACGATATCTTTTC-CTGTAATAACGAGAT-CTTTTCTC
1 GTAATAACGAGATCTTTTCTCGTAATAACGAGATCTTTTCTC-ATAATAACGAGATAATTAACCC
* ** **
1081379 GTAATTAA-GAGATAATTAACT
65 GTAA-TAACGATATCTTTTCCT
* *
1081400 CGTAATAACGATATCTTTTC-CTGTAATAACGAGATCTTTTCTCGTAATTAA-GAGATAATTAAC
1 -GTAATAACGAGATCTTTTCTC-GTAATAACGAGATCTTTTCTCATAA-TAACGAGATAATTAAC
*
1081463 TCGTAATAACGATATCTTTTCCT
63 CCGTAATAACGATATCTTTTCCT
*
1081486 GTAATAACGAGATCTTTTCTCGTAATAACGAGATCTTTTCTCATAATAACGAGATAATTTACCCG
1 GTAATAACGAGATCTTTTCTCGTAATAACGAGATCTTTTCTCATAATAACGAGATAATTAACCCG
*
1081551 TAATTACGATAT
66 TAATAACGATAT
1081563 AATGAAAACT
Statistics
Matches: 139, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
84 4 0.03
85 113 0.81
86 22 0.16
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (85 bp):
GTAATAACGAGATCTTTTCTCGTAATAACGAGATCTTTTCTCATAATAACGAGATAATTAACCCG
TAATAACGATATCTTTTCCT
Found at i:1081554 original size:64 final size:64
Alignment explanation
Indices: 1081310--1081519 Score: 361
Period size: 64 Copynumber: 3.3 Consensus size: 64
1081300 ATATAGACCA
* * **
1081310 TTTCTCGTAATTACGAGAT-CTTTTCTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT
1 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT
1081373 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT
1 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT
1081437 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT
1 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT
1081501 TTTCTCGTAA-TAACGAGAT
1 TTTCTCGTAATTAA-GAGAT
1081520 CTTTTCTCAT
Statistics
Matches: 141, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
63 21 0.15
64 120 0.85
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.39
Consensus pattern (64 bp):
TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT
Found at i:1083340 original size:19 final size:20
Alignment explanation
Indices: 1083294--1083341 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
1083284 ATGATATTAG
1083294 GTTTTGCATCGGTGGTCGTTT
1 GTTTTGCATCGGTGGTCG-TT
1083315 GTTTTGCATCGGT-GTC-TT
1 GTTTTGCATCGGTGGTCGTT
1083333 GATTTTGCA
1 G-TTTTGCA
1083342 AAAGAGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.12
19 7 0.27
20 3 0.12
21 13 0.50
ACGTcount: A:0.08, C:0.15, G:0.29, T:0.48
Consensus pattern (20 bp):
GTTTTGCATCGGTGGTCGTT
Found at i:1083820 original size:2 final size:2
Alignment explanation
Indices: 1083813--1083886 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
1083803 GTATGAATAT
1083813 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
1083855 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
1083887 ATATACCCTG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1086315 original size:33 final size:33
Alignment explanation
Indices: 1086273--1086336 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1086263 CGTTACTGAT
*
1086273 TCCTTAAGTAAATGAAAACACAAAATCAAATCA
1 TCCTTAAGTAAATGAAAACACAAAATAAAATCA
* * *
1086306 TCCTTAAGTAAATTAATACACCAAATAAAAT
1 TCCTTAAGTAAATGAAAACACAAAATAAAAT
1086337 AAAATTATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (33 bp):
TCCTTAAGTAAATGAAAACACAAAATAAAATCA
Found at i:1098079 original size:127 final size:127
Alignment explanation
Indices: 1097853--1098110 Score: 498
Period size: 127 Copynumber: 2.0 Consensus size: 127
1097843 TTTAAAAATG
* *
1097853 TTATCATATACGTACAACATTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG
1 TTATCACATACGTACAACACTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG
1097918 TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT
66 TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT
1097980 TTATCACATACGTACAACACTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG
1 TTATCACATACGTACAACACTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG
1098045 TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT
66 TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT
1098107 TTAT
1 TTAT
1098111 TTTGGAATTT
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 129 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (127 bp):
TTATCACATACGTACAACACTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG
TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT
Found at i:1105274 original size:2 final size:2
Alignment explanation
Indices: 1105267--1105315 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1105257 CAGAAAAGCT
1105267 TC TC TC TC TC TC TC TC T- 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
1105308 TC TC TC TC
1 TC TC TC TC
1105316 AAAATTTTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1115154 original size:140 final size:145
Alignment explanation
Indices: 1114892--1115179 Score: 433
Period size: 140 Copynumber: 2.0 Consensus size: 145
1114882 CAGTATAAAA
*
1114892 TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAGAAAAAAAAATATATTCTGGATAATATATCAT
1 TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAGAAAAAAAAATATATTCCGG--AATATATCAT
* * *
1114957 AATATCATAAGTTAGTTTTTTACCTCGATAATTTTAATATAAACAACATATATGTTGTTATCGAC
64 AATATCATAAGTTAGTTTTTGACCTCGATAATTTCAATATAAACAACATATATGTTGTAATCGAC
* *
1115022 AATGGATGGTTTGAAGC
129 AATGGATAGATTGAAGC
*
1115039 TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAG-AAAAAAAATCTATTCCGG-ATA-AT-AT-A
1 TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAGAAAAAAAAATATATTCCGGAATATATCATAA
* * *
1115099 TATCATAAGTTAGTTTTTGACCTCGATAGTTTCACTATCAACAACATATATGTTGTAATCGACAA
66 TATCATAAGTTAGTTTTTGACCTCGATAATTTCAATATAAACAACATATATGTTGTAATCGACAA
1115164 TGGATAGATTGAAGC
131 TGGATAGATTGAAGC
1115179 T
1 T
1115180 CCTATTTGTC
Statistics
Matches: 131, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
140 74 0.56
141 2 0.02
142 2 0.02
143 3 0.02
146 16 0.12
147 34 0.26
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (145 bp):
TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAGAAAAAAAAATATATTCCGGAATATATCATAA
TATCATAAGTTAGTTTTTGACCTCGATAATTTCAATATAAACAACATATATGTTGTAATCGACAA
TGGATAGATTGAAGC
Found at i:1115266 original size:19 final size:18
Alignment explanation
Indices: 1115214--1115257 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1115204 GTACTGAATC
1115214 AAAAGTGTATAAAAATAA
1 AAAAGTGTATAAAAATAA
1115232 AAAAGTGTATAAAAATAA
1 AAAAGTGTATAAAAATAA
1115250 AGAAAGTG
1 A-AAAGTG
1115258 ATGGAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (18 bp):
AAAAGTGTATAAAAATAA
Found at i:1117867 original size:2 final size:2
Alignment explanation
Indices: 1117860--1117923 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1117850 ACCGTCATTT
1117860 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
1117902 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
1117924 CCTTCTGTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1118469 original size:2 final size:2
Alignment explanation
Indices: 1118462--1118515 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1118452 TTTGAAAATT
1118462 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
1118504 TC TC TC TC TC TC
1 TC TC TC TC TC TC
1118516 CTTATTTGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1121469 original size:8 final size:8
Alignment explanation
Indices: 1121456--1121489 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1121446 GTAACTGAGT
1121456 ATTTATTA
1 ATTTATTA
*
1121464 ATTTATTT
1 ATTTATTA
1121472 ATTTATT-
1 ATTTATTA
1121479 ATTTATTA
1 ATTTATTA
1121487 ATT
1 ATT
1121490 AATCAGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
ATTTATTA
Found at i:1125123 original size:19 final size:20
Alignment explanation
Indices: 1125091--1125130 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1125081 AAAGCAATAG
**
1125091 AACTTTTTTTAAAAC-TTTT
1 AACTTTTTCAAAAACATTTT
1125110 AACTTTTTCAAAAACATTTT
1 AACTTTTTCAAAAACATTTT
1125130 A
1 A
1125131 CTCAATGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (20 bp):
AACTTTTTCAAAAACATTTT
Found at i:1135760 original size:4 final size:4
Alignment explanation
Indices: 1135753--1135826 Score: 51
Period size: 4 Copynumber: 17.8 Consensus size: 4
1135743 TTAGTAAATT
* * *
1135753 AGTA AGTA AGTA AGTGCA ACTGCA AGTA AGTA CGTA AGTA AGTA ACTA
1 AGTA AGTA AGTA AGT--A A--GTA AGTA AGTA AGTA AGTA AGTA AGTA
* * *
1135801 AGTA AGAA AGGA AGAA AGT- AGTA AGT
1 AGTA AGTA AGTA AGTA AGTA AGTA AGT
1135827 GTGAAGCATA
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
3 3 0.05
4 47 0.85
6 4 0.07
8 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.26, T:0.20
Consensus pattern (4 bp):
AGTA
Found at i:1140288 original size:178 final size:178
Alignment explanation
Indices: 1139988--1140337 Score: 666
Period size: 178 Copynumber: 2.0 Consensus size: 178
1139978 GAAAGATGAA
1139988 GTCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCCT
1 GTCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCCT
1140053 AATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCAA
66 AATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCAA
1140118 CTACAGTTCTTATCGACCACATCATACATAG-AGGCGGGGGGGGGGGG
131 CTACAGTTCTTATCGACCACATCATACATAGAAGGCGGGGGGGGGGGG
1140165 GNTCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCC
1 G-TCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCC
1140230 TAATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCA
65 TAATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCA
* *
1140295 ACTACAGTTCTTATCGACCACATCATACATAGANGGTGGGGGG
130 ACTACAGTTCTTATCGACCACATCATACATAGAAGGCGGGGGG
1140338 CTTTCAATGC
Statistics
Matches: 169, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
177 1 0.01
178 160 0.95
179 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (178 bp):
GTCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCCT
AATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCAA
CTACAGTTCTTATCGACCACATCATACATAGAAGGCGGGGGGGGGGGG
Found at i:1147355 original size:12 final size:11
Alignment explanation
Indices: 1147336--1147367 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
1147326 CTTTAGAAGC
1147336 AAAAAAAACAA
1 AAAAAAAACAA
1147347 AACAAAAAACAA
1 AA-AAAAAACAA
1147359 AAAAAAAAC
1 AAAAAAAAC
1147368 CCGAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:1148548 original size:12 final size:12
Alignment explanation
Indices: 1148520--1148564 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1148510 ATCACATTTT
1148520 GTCTGTC-GTCC
1 GTCTGTCTGTCC
*
1148531 GTCTGTCTGTCT
1 GTCTGTCTGTCC
*
1148543 GTCTGTCCGTCC
1 GTCTGTCTGTCC
1148555 GTCTGTCTGT
1 GTCTGTCTGT
1148565 AAACTTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.00, C:0.31, G:0.27, T:0.42
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:1148562 original size:4 final size:4
Alignment explanation
Indices: 1148519--1148564 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1148509 GATCACATTT
* * *
1148519 TGTC TGTC -GTC CGTC TGTC TGTC TGTC TGTC CGTC CGTC TGTC TGT
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
1148565 AAACTTTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.00, C:0.30, G:0.26, T:0.43
Consensus pattern (4 bp):
TGTC
Found at i:1148794 original size:61 final size:61
Alignment explanation
Indices: 1148729--1148847 Score: 220
Period size: 61 Copynumber: 2.0 Consensus size: 61
1148719 GAAATTTTCA
* *
1148729 AAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATC
1 AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATC
1148790 AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATC
1 AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATC
1148848 CTCAGGTAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATC
Found at i:1149461 original size:333 final size:331
Alignment explanation
Indices: 1148790--1149968 Score: 1719
Period size: 333 Copynumber: 3.5 Consensus size: 331
1148780 AAGCATCATC
* *
1148790 AAAATCTTCTTCTCATG-AAC-AATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
1 AAAATCTTCTTCTCA-GAAACTAAT-CAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* * * *
1148853 GTAGTGTAGATTCTAATTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
64 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAAAGGGGGG
* * * * *
1148918 TCGAAGTTTTACATAGGAATATACAGATTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGG
129 TCGAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGA
* * * * *
1148983 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTTCTAATTTGTGAAAATA
194 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTA-AATTCAAAGTTGTGAAAATC
* *
1149048 ATGATCCCCGGTGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTTACATAGGAATATAAAGAG
258 ATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGG-TCGAAGTTTTACATAGGAATATATAGAG
1149113 TAAATCTTTA
322 TAAATCTTTA
* * *
1149123 AAAATCTTCTTCTCATG-AAC-CATAAGACCAGGACAGCTGAAACTTGTGTGGAAGCATCCTCAG
1 AAAATCTTCTTCTCA-GAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* * * * * **
1149186 GAAGTGTAGATTCATAGTTGTGAAAATCATG-GCCTTCGGGGGTAGGGTGGGGCCACGATTGGGG
64 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCC-CCGGGGGTAGGGTGGGGCCACAAAGGGGG
*
1149250 GTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTTATGAACCATAAG
128 GTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAG
* *
1149315 ACCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATTAAAAGTTGTGAAAATC
193 ACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATC
*
1149380 ATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGTAGTCGAAGTTTTACATAGGAATATATAGAG
258 ATGATCCCCGGGGGTAGGGTGGGGCCACAATGGG-GGTCGAAGTTTTACATAGGAATATATAGAG
*
1149445 TAAATCTTAAA
322 TAAATCTT-TA
*
1149456 AAAATCTTTTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
1 AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
* * **
1149521 AGTGTAGATGCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGATGGTC
66 AGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAAAGGGGGGTC
* * * * *
1149586 GAACTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTTTTCTCA-GAAAC-TAATCAG
131 GAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAA-GA-
*
1149649 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
194 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCA
*
1149714 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT
259 TGATCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGGTCGAAGTTTTACATAGGAATATATAGAGT
1149779 AAATCTTTA
323 AAATCTTTA
* *
1149788 AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTTAAACTTGTGTGGAAGCGTCCTCAGGT
1 AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
* *
1149853 AGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAAAGGGGGGTC
66 AGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAAAGGGGGGTC
*
1149918 -AAAGTTTAACAAAGGAATATATATG-GTAAATCTTTAAAAATCTTCTTCTCA
131 GAAA-TTTAACATAGGAATATATA-GAGTAAATCTTTAAAAATCTTCTTCTCA
1149969 GAAACTAATC
Statistics
Matches: 768, Mismatches: 66, Indels: 25
0.89 0.08 0.03
Matches are distributed among these distances:
331 5 0.01
332 257 0.33
333 497 0.65
334 9 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (331 bp):
AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
AGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAAAGGGGGGTC
GAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGACC
AGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATG
ATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAA
TCTTTA
Found at i:1149662 original size:499 final size:499
Alignment explanation
Indices: 1148790--1149984 Score: 1814
Period size: 499 Copynumber: 2.4 Consensus size: 499
1148780 AAGCATCATC
*
1148790 AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
1 AAAATCTTCTTCTCATGAACCATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
* * * *
1148855 AGTGTAGATTCTAATTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTC
66 AGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTC
* * * *
1148920 GAAGTTTTACATAGGAATATACAGATTAAATCTTTAAAAATCTTCTTCTCATGAACCATAA--GG
131 GAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA-GAAAC-TAATCAG
* * *
1148983 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTTCTAATTTGTGAAAATA
194 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTGCAAAGTTGTGAAAATA
* *
1149048 ATGATCCCCGGTGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTTACATAGGAATATAAAGAG
259 ATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAACTTTTACATAGGAATATAAAGAG
* *
1149113 TAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGACCAGGACAGCTGAAACTTGTGTGGAAGC
324 TAAATCTTTAAAAATCTTCTTCTCATGAACAATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGC
* * ** *
1149178 ATCCTCAGGAAGTGTAGATTCATAGTTGTGAAAATCATGGCCTTCGGGGGTAGGGTGGGGCCACG
389 ATCCTCAGGAAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACA
*
1149243 ATTGGGGGTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA
454 ATGGGGGGTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA
* * *
1149289 AAAATCTTCTTCTTATGAACCATAAGACCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAGGT
1 AAAATCTTCTTCTCATGAACCATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
* **
1149354 AGTGTAAATTAAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGTAGTC
66 AGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTC
* *
1149419 GAAGTTTTACATAGGAATATATAGAGTAAATCTTAAAAAAATCTTTTTCTCAGAAACTAATCAGC
131 GAAGTTTTACATAGGAATATATAGAGTAAATCTT-TAAAAATCTTCTTCTCAGAAACTAATCAGC
* *
1149484 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGA-TGCAAAGTTGTGAAAATCA
195 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTGCAAAGTTGTGAAAATAA
* *
1149548 TGATCCCCGGGGGTAGGGTGGGGCCACAATGGATGG-TCGAACTTTTACATAGGAATATATAGAG
260 TGATCCCCGGGGGTAGGGTGGGGCCACAATGG-GGGATCGAACTTTTACATAGGAATATAAAGAG
* *
1149612 TAAATCTTTAAAAATCTTTTTCTCA-GAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAA
324 TAAATCTTTAAAAATCTTCTTCTCATG-AAC-AATAAGACCAGGAAAGCTGAAACTTGTGTGGAA
*
1149675 GCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCA
387 GCATCCTCAGGAAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCA
* *
1149740 CAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA
452 CAATGGGGGGTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA
* * * *
1149788 AAAATCTTCTTCTCA-GAAAC-TAATCAGCCAGGAAAGCTTAAACTTGTGTGGAAGCGTCCTCAG
1 AAAATCTTCTTCTCATGAACCATAA--AACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* *
1149851 GTAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAAAGGGGGG
64 GTAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
* * *
1149916 TCAAAGTTTAACAAAGGAATATATATG-GTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCA
129 TCGAAGTTTTACATAGGAATATATA-GAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCA
1149980 GCCAG
193 GCCAG
1149985 ATGATTCTTT
Statistics
Matches: 631, Mismatches: 56, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
497 3 0.00
498 39 0.06
499 521 0.83
500 68 0.11
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (499 bp):
AAAATCTTCTTCTCATGAACCATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT
AGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTC
GAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCC
AGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTGCAAAGTTGTGAAAATAAT
GATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAACTTTTACATAGGAATATAAAGAGTA
AATCTTTAAAAATCTTCTTCTCATGAACAATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCAT
CCTCAGGAAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAT
GGGGGGTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA
Found at i:1149969 original size:166 final size:167
Alignment explanation
Indices: 1148790--1149984 Score: 1761
Period size: 166 Copynumber: 7.2 Consensus size: 167
1148780 AAGCATCATC
* *
1148790 AAAATCTTCTTCTCATG-AAC-AATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
1 AAAATCTTCTTCTCATGAAACTAAT-CAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* * *
1148853 GTAGTGTAGATTCTAATTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
65 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
* *
1148918 TCGAAGTTTTACATAGGAATATACAGATTAAATCTTTA
130 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA
* *
1148956 AAAATCTTCTTCTCATGAACCATAA--GGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
1 AAAATCTTCTTCTCATGAAAC-TAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* * * * *
1149019 GAAGTGTAGACTTCTAATTTGTGAAAATAATGATCCCCGGTGGTAGGGTGGGGCCACAATGGGGG
65 GTAGTGTAGA-TTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
* *
1149084 ATCGAAGTTTTACATAGGAATATAAAGAGTAAATCTTTA
129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA
* * *
1149123 AAAATCTTCTTCTCATG-AAC-CATAAGACCAGGACAGCTGAAACTTGTGTGGAAGCATCCTCAG
1 AAAATCTTCTTCTCATGAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* * * * * *
1149186 GAAGTGTAGATTCATAGTTGTGAAAATCATG-GCCTTCGGGGGTAGGGTGGGGCCACGATTGGGG
65 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCC-CCGGGGGTAGGGTGGGGCCACAATGGGGG
* *
1149250 GTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA
129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA
* * * *
1149289 AAAATCTTCTTCTTATG-AAC-CATAAGACCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAG
1 AAAATCTTCTTCTCATGAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* * **
1149352 GTAGTGTAAATTAAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGTAG
65 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG
*
1149417 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTAAA
130 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTT-TA
*
1149456 AAAATCTTTTTCTCA-GAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAATCTTCTTCTCATGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* **
1149520 TAGTGTAGATGCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGATGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
*
1149585 CGAACTTTTACATAGGAATATATAGAGTAAATCTTTA
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA
*
1149622 AAAATCTTTTTCTCA-GAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAATCTTCTTCTCATGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
1149686 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
1149751 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA
* *
1149788 AAAATCTTCTTCTCA-GAAACTAATCAGCCAGGAAAGCTTAAACTTGTGTGGAAGCGTCCTCAGG
1 AAAATCTTCTTCTCATGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
1149852 TAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAAAGGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
* * *
1149917 CAAAGTTTAACAAAGGAATATATATG-GTAAATCTTTA
131 CGAAGTTTTACATAGGAATATATA-GAGTAAATCTTTA
1149954 AAAATCTTCTTCTCA-GAAACTAATCAGCCAG
1 AAAATCTTCTTCTCATGAAACTAATCAGCCAG
1149985 ATGATTCTTT
Statistics
Matches: 946, Mismatches: 70, Indels: 26
0.91 0.07 0.02
Matches are distributed among these distances:
164 1 0.00
165 2 0.00
166 636 0.67
167 301 0.32
168 4 0.00
169 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (167 bp):
AAAATCTTCTTCTCATGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA
Found at i:1151248 original size:2 final size:2
Alignment explanation
Indices: 1151241--1151276 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1151231 TTGTTAGCAC
1151241 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
1151277 GGGGGAGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1157320 original size:3 final size:3
Alignment explanation
Indices: 1157305--1157334 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1157295 GACTTTCTCA
*
1157305 TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1157335 ATCCAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1158182 original size:437 final size:438
Alignment explanation
Indices: 1157355--1158610 Score: 2108
Period size: 437 Copynumber: 2.9 Consensus size: 438
1157345 GTCCAGGCCG
* *
1157355 TAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGG
1 TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
* * * *
1157420 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTGTTTAGTTCTTCAAGGTCAGGCTTTTGATAAA
66 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA
*
1157485 AAATATTGTCGGGACCATAACACAATACTCCTTTAACATACAGACTTTTAACTTGTATCATAGAT
131 AAATATTGTCGGGACCATAACACAAGA--CCTTTAACATACAGACTTTTAACTTGTATCATAGAT
*
1157550 AGATGGTATATAACCTAGTTCAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCA
194 AGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAA-TTTTATTTCA
*
1157615 AGGTCATATTTGAAAAAACTTCATTGTTCAACTT-CTGAATATACTTTGACAGAAGGACTTCAAA
258 AGGTCATATTAGAAAAAACTTCATTGTTCAA-TTCCTGAATATACTTTGACAGAAGGACTTCAAA
* *
1157679 CTTGAAACAAAGAACAACAATAATACACTTAGGTGTACTATT-AATTAATATTTGACATTGACCT
322 CTTTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAA-TAATATTTGACATTGACCT
1157743 TGTTTTACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA
386 TGTTTTACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA
* * *
1157796 TAACTTTATTACCCTTTGACATTAAGACTTCAAACGTAGAACATAGGTAGATGGTATTGAGAAGG
1 TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
**
1157861 AGTGCACGAGACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA
66 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA
* * *
1157926 AAATAATGTCCGGACCATAACACAAGA-CTTTAACATACAGACTTTTAACTTGTATCATAGATAA
131 AAATATTGTCGGGACCATAACACAAGACCTTTAACATACAGACTTTTAACTTGTATCATAGATAG
1157990 ATGGTATATAACCTAGTTGAACCTTACCAAAA-TTTTGACCTTGACCTAGAATTTTCATTTCAAG
196 ATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTT-ATTTCAAG
1158054 GTCATATTAGAAAAAACTTCATTGTTCAATTCCTGAATATACTTTGACAGAAGGACTTCAAACTT
260 GTCATATTAGAAAAAACTTCATTGTTCAATTCCTGAATATACTTTGACAGAAGGACTTCAAACTT
*
1158119 TAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATACTATTTGACATTGACCTTGTT
325 TAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACATTGACCTTGTT
*
1158184 TTACTCAAGGTCAAATTAAGATAAAAGTAATAAAATTTTGTCTGGGTCA
390 TTACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA
* *
1158233 TAACTTTAATACCCTTTGACATTAAGACTTCAATCTTGGAACATAGGTATATGGTATTGAGAAGG
1 TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
* *
1158298 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTATTTCAAGGTCAAGCTTTTCATAAA
66 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA
1158363 AAATATTGTCGGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCAT-GAA
131 AAATATTGTCGGGACCATAACACAAGA--CCTTTAACATACAGACTTTTAACTTGTATCATAG-A
* *
1158427 TAGATGGTATATTACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAAAAATTTTATTTC
193 TAGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCT-AGAATTTTATTTC
* * * *
1158492 AAAGTCAAATTAGAAAAAACTTCATTGTTCAACTCCTGAATATGCTTTGACAGAAGGACTTCAAA
257 AAGGTCATATTAGAAAAAACTTCATTGTTCAATTCCTGAATATACTTTGACAGAAGGACTTCAAA
1158557 CTTTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTG
322 CTTTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTG
1158611 TTAAATTTGC
Statistics
Matches: 766, Mismatches: 40, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
436 6 0.01
437 341 0.45
438 69 0.09
439 1 0.00
440 65 0.08
441 277 0.36
442 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (438 bp):
TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA
AAATATTGTCGGGACCATAACACAAGACCTTTAACATACAGACTTTTAACTTGTATCATAGATAG
ATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTATTTCAAGG
TCATATTAGAAAAAACTTCATTGTTCAATTCCTGAATATACTTTGACAGAAGGACTTCAAACTTT
AAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACATTGACCTTGTTT
TACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA
Found at i:1159657 original size:2 final size:2
Alignment explanation
Indices: 1159650--1159693 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1159640 AGCTGCACCA
* *
1159650 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1159692 TC
1 TC
1159694 ATGTTTGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:1167268 original size:2 final size:2
Alignment explanation
Indices: 1167263--1167295 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1167253 GACCCCCCCC
*
1167263 CT CT CT CT CT CT CT -T TT 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
1167296 TTTCTCTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
CT
Found at i:1167285 original size:17 final size:18
Alignment explanation
Indices: 1167263--1167302 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
1167253 GACCCCCCCC
1167263 CTCTCTCTCTCTCT-TTT
1 CTCTCTCTCTCTCTCTTT
1167280 CTCTCTCTCTCTCTCTTT
1 CTCTCTCTCTCTCTCTTT
1167298 -TCTCT
1 CTCTCT
1167303 ATGTATGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.57
Consensus pattern (18 bp):
CTCTCTCTCTCTCTCTTT
Found at i:1167287 original size:19 final size:19
Alignment explanation
Indices: 1167263--1167302 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1167253 GACCCCCCCC
1167263 CTCTCTCTCTCTCTTTTCT
1 CTCTCTCTCTCTCTTTTCT
1167282 CTCTCTCTCTCTCTTTTCT
1 CTCTCTCTCTCTCTTTTCT
1167301 CT
1 CT
1167303 ATGTATGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.57
Consensus pattern (19 bp):
CTCTCTCTCTCTCTTTTCT
Found at i:1173968 original size:16 final size:14
Alignment explanation
Indices: 1173936--1173962 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1173926 AGAGTTTATA
1173936 ATATATAACATGTT
1 ATATATAACATGTT
1173950 ATATATAACATGT
1 ATATATAACATGT
1173963 ATTATAGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATATAACATGTT
Done.