Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 15
Found at i:1213231 original size:20 final size:20
Alignment explanation
Indices: 1213207--1213258 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1213197 TGGAAATTGC
1213207 ATTGCGAATTTGACTTCCGT
1 ATTGCGAATTTGACTTCCGT
* *
1213227 GTTGCGAATTTGACTTCTGT
1 ATTGCGAATTTGACTTCCGT
1213247 ATTGCGAATTTG
1 ATTGCGAATTTG
1213259 GAAAATCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTGCGAATTTGACTTCCGT
Found at i:1213276 original size:21 final size:21
Alignment explanation
Indices: 1213250--1213295 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1213240 CTTCTGTATT
*
1213250 GCGAATTTGGAAAATCACAAC
1 GCGAATTCGGAAAATCACAAC
* *
1213271 GCGAATTCGGAAAATCGCAAT
1 GCGAATTCGGAAAATCACAAC
1213292 GCGA
1 GCGA
1213296 TTTACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCACAAC
Found at i:1222284 original size:16 final size:16
Alignment explanation
Indices: 1222265--1222309 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1222255 AATTCTTAAA
1222265 TTAAAATCTCTAATAT
1 TTAAAATCTCTAATAT
1222281 TTAAAATCT-TAA-AT
1 TTAAAATCTCTAATAT
**
1222295 TTTTAATCTCTAATA
1 TTAAAATCTCTAATA
1222310 ATCGTCTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 9 0.36
15 6 0.24
16 10 0.40
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATCTCTAATAT
Found at i:1222305 original size:30 final size:29
Alignment explanation
Indices: 1222252--1222309 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
1222242 TTCAAAATTC
*
1222252 TTAAATTCTTAAATTAAAATCTCTAATAT
1 TTAAAATCTTAAATTAAAATCTCTAATAT
**
1222281 TTAAAATCTTAAATTTTTAATCTCTAATA
1 TTAAAATCTTAAA-TTAAAATCTCTAATA
1222310 ATCGTCTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAAAATCTTAAATTAAAATCTCTAATAT
Found at i:1233572 original size:19 final size:20
Alignment explanation
Indices: 1233545--1233583 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1233535 TTAATAAATA
1233545 ATTTCTTAA-ATTATATTTTT
1 ATTTCTTAATATT-TATTTTT
1233565 ATTT-TTAATATTTATTTTT
1 ATTTCTTAATATTTATTTTT
1233584 TGTTACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTCTTAATATTTATTTTT
Found at i:1238588 original size:16 final size:15
Alignment explanation
Indices: 1238557--1238586 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1238547 CCTGTACATT
1238557 GCTGACTAGAAAAAA
1 GCTGACTAGAAAAAA
1238572 GCTGACTAGAAAAAA
1 GCTGACTAGAAAAAA
1238587 AGGATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (15 bp):
GCTGACTAGAAAAAA
Found at i:1241129 original size:21 final size:21
Alignment explanation
Indices: 1241103--1241233 Score: 117
Period size: 21 Copynumber: 6.3 Consensus size: 21
1241093 CATATTCACA
*
1241103 TTGCGATAATCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
**
1241124 TTGCGATAGTCCAAGTTTACG
1 TTGCGATAGTCCAAGTTCGCG
** * *
1241145 TTGCGATTTTCTAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
*
1241164 TTGCAATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
1241185 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
1241206 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
1241227 TTGCGAT
1 TTGCGAT
1241234 TTATTCCAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
19 22 0.26
21 55 0.64
23 9 0.10
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:1241151 original size:42 final size:40
Alignment explanation
Indices: 1241103--1241247 Score: 164
Period size: 42 Copynumber: 3.5 Consensus size: 40
1241093 CATATTCACA
* * **
1241103 TTGCGATAATCCAAGTTCGCGTTGCGATAGTCCAAGTTTACG
1 TTGCGATATTCCAAATT--CGTTGCGATAGTCCAAGTTCGCG
* * *
1241145 TTGCGATTTTCTAAATTCGTTGCAATAGTCCAAGTTCGCG
1 TTGCGATATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
*
1241185 TTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGA--TATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
1241227 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TATTCCAAATTCG
1241248 CAACGACTGG
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 26 0.29
42 64 0.71
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (40 bp):
TTGCGATATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
Found at i:1241205 original size:23 final size:23
Alignment explanation
Indices: 1241173--1241248 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 23
1241163 GTTGCAATAG
*
1241173 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGCGTTGCGATTTAT
*
1241196 TCCAAATT--CGTTGCGA--TAG
1 TCCAAATTCGCGTTGCGATTTAT
* *
1241215 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGCGTTGCGATTTAT
1241238 TCCAAATTCGC
1 TCCAAATTCGC
1241249 AACGACTGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 8 0.19
21 16 0.38
23 18 0.43
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (23 bp):
TCCAAATTCGCGTTGCGATTTAT
Found at i:1242128 original size:21 final size:21
Alignment explanation
Indices: 1242102--1242292 Score: 150
Period size: 21 Copynumber: 9.3 Consensus size: 21
1242092 ATTTTGGACT
* *
1242102 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1242123 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1242144 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
1242165 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
1242186 ATTGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
* *
1242207 ATCACAACGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAA
*
1242226 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1242247 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
1242268 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAACTTGGAATAA
1242287 ATCGCA
1 ATCGCA
1242293 TTGCGATAGT
Statistics
Matches: 139, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
19 51 0.37
21 58 0.42
23 30 0.22
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:1242169 original size:42 final size:42
Alignment explanation
Indices: 1242123--1242223 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 42
1242113 TTTGGAATAA
1242123 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
*
1242165 ATCGCAACGAACTTGGAATAAATTGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
*
1242207 ATCACAACGAACTTGGA
1 ATCGCAACGAACTTGGA
1242224 CTATCGCAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:1242292 original size:61 final size:61
Alignment explanation
Indices: 1242095--1242284 Score: 258
Period size: 61 Copynumber: 3.1 Consensus size: 61
1242085 CTTTACGATT
* *
1242095 TTGGACTATCGCAATGAATTTGGAATAAATCGCAA--CGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAAC
* * * * *
1242158 TTCGACTATCGCAACGAACTTGGAATAAATTGCAACGCGAACTTCGACTATCACAACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAC
*
1242219 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAC
1242280 TTGGA
1 TTGGA
1242285 AAATCGCATT
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
61 65 0.58
63 37 0.33
65 10 0.09
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (61 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAC
Found at i:1250478 original size:2 final size:2
Alignment explanation
Indices: 1250471--1250502 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1250461 GCTCATCCAC
1250471 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
1250503 GTAATGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1252551 original size:18 final size:18
Alignment explanation
Indices: 1252508--1252544 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1252498 ATATGAGCAA
*
1252508 TCATCATCTTCTTCTATT
1 TCATCATCATCTTCTATT
1252526 TCATCATCATCTTCTATT
1 TCATCATCATCTTCTATT
1252544 T
1 T
1252545 TTTCATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.27, G:0.00, T:0.54
Consensus pattern (18 bp):
TCATCATCATCTTCTATT
Found at i:1259909 original size:2 final size:2
Alignment explanation
Indices: 1259902--1259932 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1259892 GAAGATGACC
1259902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1259933 CTATGGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1266393 original size:22 final size:21
Alignment explanation
Indices: 1266368--1266431 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
1266358 CACGCTGAAT
*
1266368 GCTGAACGGTTCAACATTCAAC
1 GCTGAATGGTTC-ACATTCAAC
* *
1266390 GCTGAATGATTCAGCTTTCAAC
1 GCTGAATGGTTCA-CATTCAAC
1266412 GCTGAATGGTTC-CATTCAAC
1 GCTGAATGGTTCACATTCAAC
1266432 ATTAAACAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 7 0.19
21 1 0.03
22 28 0.78
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (21 bp):
GCTGAATGGTTCACATTCAAC
Found at i:1267564 original size:26 final size:26
Alignment explanation
Indices: 1267535--1267585 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1267525 CACATGGATA
*
1267535 TTTGAACAATTA-AATGAGATATTTGT
1 TTTGAACAA-TAGAAAGAGATATTTGT
*
1267561 TTTGAAGAATAGAAAGAGATATTTG
1 TTTGAACAATAGAAAGAGATATTTG
1267586 AATAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (26 bp):
TTTGAACAATAGAAAGAGATATTTGT
Found at i:1269017 original size:15 final size:15
Alignment explanation
Indices: 1268997--1269026 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1268987 ATCGCTCGAC
1268997 ATCGAAACTCAATCT
1 ATCGAAACTCAATCT
1269012 ATCGAAACTCAATCT
1 ATCGAAACTCAATCT
1269027 CCCGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
ATCGAAACTCAATCT
Found at i:1272396 original size:2 final size:2
Alignment explanation
Indices: 1272389--1272429 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1272379 GTAATTAGTA
1272389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1272430 CACACACTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1272957 original size:60 final size:60
Alignment explanation
Indices: 1272812--1272989 Score: 179
Period size: 60 Copynumber: 3.0 Consensus size: 60
1272802 CATAGCATGG
* * *
1272812 CTCTCA-TTATAAATTAGTCCTTAAACTTTTAAATATTACAATTTCATCCATAAACTATGA
1 CTCTCACTT-TAAATTAGTCCTCAAACTTTTTAACATTACAATTTCATCCATAAACTATGA
* * *
1272872 CTCTCACTTTAGATTAGTCCTCAAACTTTTTAACATTTCAATTTCAT-TATCAAACTATGA
1 CTCTCACTTTAAATTAGTCCTCAAACTTTTTAACATTACAATTTCATCCAT-AAACTATGA
* * *
1272932 C-CTTCA-TTCTAAATTGGTTCC-CAAACTTTTTGAACATTCCAATTTCATCC-CAAACTAT
1 CTC-TCACTT-TAAATTAG-TCCTCAAACTTTTT-AACATTACAATTTCATCCATAAACTAT
1272990 ACGTATATAC
Statistics
Matches: 100, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
59 5 0.05
60 75 0.75
61 20 0.20
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (60 bp):
CTCTCACTTTAAATTAGTCCTCAAACTTTTTAACATTACAATTTCATCCATAAACTATGA
Found at i:1273240 original size:59 final size:60
Alignment explanation
Indices: 1273104--1273251 Score: 153
Period size: 59 Copynumber: 2.5 Consensus size: 60
1273094 TATTTGGATG
* * * *
1273104 AATTTGAGGA-TGAAATTGGAATATTTAAAAGTTTGGGGACCAATTTAGAAAGAGAGTCAA
1 AATTT-AGGAGTGAAATTAGAATATATAAAAGTTTGAGGACCAATTTAGAAAGAGAATCAA
* * ** *
1273164 AACTTAGG-GATGAAATTAGAATGTATAAAAGTTTGAGGATTAA-TTA-AAACGAGAATCAC
1 AATTTAGGAG-TGAAATTAGAATATATAAAAGTTTGAGGACCAATTTAGAAA-GAGAATCAA
1273223 AATTTAGGAGTGAAATTAGAATAT-TAAAA
1 AATTTAGGAGTGAAATTAGAATATATAAAA
1273252 AATTTAAGGA
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
58 8 0.11
59 33 0.45
60 32 0.44
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (60 bp):
AATTTAGGAGTGAAATTAGAATATATAAAAGTTTGAGGACCAATTTAGAAAGAGAATCAA
Found at i:1273341 original size:20 final size:20
Alignment explanation
Indices: 1273314--1273467 Score: 101
Period size: 20 Copynumber: 7.5 Consensus size: 20
1273304 TGTAGACTAC
1273314 CGCAACGCGAAATGGAAAAT
1 CGCAACGCGAAATGGAAAAT
*
1273334 CTCAACGCGAAATGGAAAAT
1 CGCAACGCGAAATGGAAAAT
** ** *
1273354 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGAAATGGAA-AAT
* * ** ** *
1273375 CGTAATGCGATTTTCAACTAT
1 CGCAACGCGAAATGGAA-AAT
** ** *
1273396 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGAAATGGAA-AAT
*
1273417 CGCAACGCGAACTGGAAAAT
1 CGCAACGCGAAATGGAAAAT
*
1273437 CGCAACGCGAAATGAAAAAT
1 CGCAACGCGAAATGGAAAAT
1273457 CGCAACGCGAA
1 CGCAACGCGAA
1273468 TTTGCGATAG
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
20 62 0.54
21 53 0.46
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
CGCAACGCGAAATGGAAAAT
Found at i:1273384 original size:21 final size:21
Alignment explanation
Indices: 1273352--1273426 Score: 132
Period size: 21 Copynumber: 3.6 Consensus size: 21
1273342 GAAATGGAAA
1273352 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
1273373 ATCGTAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1273394 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1273415 ATCGCAACGCGA
1 ATCGCAACGCGA
1273427 ACTGGAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1280613 original size:18 final size:17
Alignment explanation
Indices: 1280589--1280628 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1280579 TTTATCAATA
1280589 TTTTTTTAAATATTAAT
1 TTTTTTTAAATATTAAT
* *
1280606 TATTTTTTTATTATTAAT
1 T-TTTTTTAAATATTAAT
1280624 TTTTT
1 TTTTT
1280629 ATCTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTTTAAATATTAAT
Found at i:1281602 original size:2 final size:2
Alignment explanation
Indices: 1281595--1281621 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1281585 AATATTTCAA
1281595 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1281622 GAATATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1285501 original size:21 final size:19
Alignment explanation
Indices: 1285477--1285515 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1285467 AATAACAGTC
1285477 AGCATATGAGAGATCTTTGGG
1 AGCATATGAG-G-TCTTTGGG
*
1285498 AGCATTTGAGGTCTTTGG
1 AGCATATGAGGTCTTTGG
1285516 AGAGTGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.33
Consensus pattern (19 bp):
AGCATATGAGGTCTTTGGG
Found at i:1287070 original size:33 final size:33
Alignment explanation
Indices: 1287033--1287111 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1287023 AAGTGTCTAA
*
1287033 TTTATGTTCGTTTTTTTAGTTTAGTGTTTAATG
1 TTTATGTTCGTTTTTTCAGTTTAGTGTTTAATG
*
1287066 TTTATGTTTGTTTTTTCAGTTTAGTGTTTAATG
1 TTTATGTTCGTTTTTTCAGTTTAGTGTTTAATG
1287099 TTTAT-TTCGTTTT
1 TTTATGTTCGTTTT
1287112 AATTTGAGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 7 0.16
33 36 0.84
ACGTcount: A:0.14, C:0.04, G:0.16, T:0.66
Consensus pattern (33 bp):
TTTATGTTCGTTTTTTCAGTTTAGTGTTTAATG
Found at i:1287305 original size:17 final size:17
Alignment explanation
Indices: 1287264--1287305 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1287254 TTTAAAAAAA
*
1287264 GAAAACACATAAATTTT
1 GAAAACCCATAAATTTT
1287281 GAATAACCCA-AAATTTTT
1 GAA-AACCCATAAA-TTTT
1287299 GAAAACC
1 GAAAACC
1287306 TTCATTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (17 bp):
GAAAACCCATAAATTTT
Found at i:1288509 original size:23 final size:21
Alignment explanation
Indices: 1288481--1288536 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
1288471 ATGTCTTTTC
1288481 TTTTTTAAAAATATATATAATT
1 TTTTTTAAAAATATATATAA-T
** * *
1288503 TTATTTTTTAATTTTATATAAT
1 TT-TTTTAAAAATATATATAAT
1288525 TTTTTTAAAAAT
1 TTTTTTAAAAAT
1288537 TATCATATTG
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
21 7 0.27
22 5 0.19
23 14 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTAAAAATATATATAAT
Found at i:1290184 original size:64 final size:64
Alignment explanation
Indices: 1290028--1290184 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 64
1290018 TTGAAGGTGT
* * ** *
1290028 ATCGATGCACATGTAGTGCATCGATGCACTCTTTTAAAATATAAACATTGAATGCAATTAGTGC
1 ATCGATGCACAAGTAGTGCATCGATGCATTCCATTAAAATATAAACATCGAATGCAATTAGTGC
* * *
1290092 ATCGATGCATAAGGCA-TGCATCGATGCATTCCATTAATAATA-AAACATCGAATGCATTTTA-T
1 ATCGATGCACAA-GTAGTGCATCGATGCATTCCATTAA-AATATAAACATCGAATGCA-ATTAGT
1290154 GC
63 GC
1290156 ATCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAAGTAGTGCATCGATGCAT
1290185 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 2 0.03
64 68 0.86
65 9 0.11
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATGCATTCCATTAAAATATAAACATCGAATGCAATTAGTGC
Found at i:1290570 original size:29 final size:29
Alignment explanation
Indices: 1290549--1290629 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
1290539 CATGTGATAT
1290549 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1290579 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1290608 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1290630 ACATATGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1297003 original size:45 final size:45
Alignment explanation
Indices: 1296946--1297033 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
1296936 GATGCACAGG
** *
1296946 TAGTGCATCGATGCACTCTTTTAA-AATATAAACATTGAATGCAAT
1 TAGTGCATCGATGCACTCCATTAATAATA-AAACATCGAATGCAAT
*
1296991 TAGTGCATCGATGCATTCCATTAATAATAAAACATCGAATGCA
1 TAGTGCATCGATGCACTCCATTAATAATAAAACATCGAATGCA
1297034 TTTTATGCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 34 0.89
46 4 0.11
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (45 bp):
TAGTGCATCGATGCACTCCATTAATAATAAAACATCGAATGCAAT
Found at i:1300526 original size:144 final size:144
Alignment explanation
Indices: 1300261--1300537 Score: 367
Period size: 144 Copynumber: 1.9 Consensus size: 144
1300251 GGGAAGTCAC
* * * * * * **
1300261 CACCAACAAGAGGATTATCATGGCTACCTCTAGGTGCTACCTTATTCCCAACCAGCTGCTCTACT
1 CACCAACAAGAGGATCATCATGGCTACCACTAGGTACAACCATATTCCCAACCAACACCTCTACT
* * * * *
1300326 GCATCATCAGAAGTAGTTTGTTTAACCATTCCATCAGCCTGATCCAACTTATCATGATCTATACC
66 GCATCATCAGAAGCAGTCTGTTTAACCACTACATCAGCCTGATCCAACTTAGCATGATCTATACC
1300391 AGCCAAAGGAGTAT
131 AGCCAAAGGAGTAT
* *
1300405 CACCAACATGAGGATCATCATGGCTACCACTAGGTACAACCATATTCCCAACTAACACCTCTACT
1 CACCAACAAGAGGATCATCATGGCTACCACTAGGTACAACCATATTCCCAACCAACACCTCTACT
* * * *
1300470 GC-TGCATCAGTAGCAGTCTGTTTAACCACTACATCATCCTGATCTAACTTGGCATGATCTATAC
66 GCAT-CATCAGAAGCAGTCTGTTTAACCACTACATCAGCCTGATCCAACTTAGCATGATCTATAC
1300534 CAGC
130 CAGC
1300538 TAAGGGAGCA
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
143 1 0.01
144 112 0.99
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (144 bp):
CACCAACAAGAGGATCATCATGGCTACCACTAGGTACAACCATATTCCCAACCAACACCTCTACT
GCATCATCAGAAGCAGTCTGTTTAACCACTACATCAGCCTGATCCAACTTAGCATGATCTATACC
AGCCAAAGGAGTAT
Found at i:1302441 original size:20 final size:20
Alignment explanation
Indices: 1302416--1302477 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
1302406 GGGATGGGCT
1302416 GTTGCTTTGCTTAAGGGTAA
1 GTTGCTTTGCTTAAGGGTAA
1302436 GTTGCTTTGCTTAAGGGTAA
1 GTTGCTTTGCTTAAGGGTAA
*
1302456 GTTGCTTTGCTTACGGGTAA
1 GTTGCTTTGCTTAAGGGTAA
1302476 GT
1 GT
1302478 CTCATCGTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.18, C:0.11, G:0.31, T:0.40
Consensus pattern (20 bp):
GTTGCTTTGCTTAAGGGTAA
Found at i:1303242 original size:7 final size:7
Alignment explanation
Indices: 1303230--1303259 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1303220 CTTTAAAGTT
1303230 CAAAAGC
1 CAAAAGC
1303237 CAAAAGC
1 CAAAAGC
1303244 CAAAAGC
1 CAAAAGC
1303251 CAAAAGC
1 CAAAAGC
1303258 CA
1 CA
1303260 CTGCTCGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.30, G:0.13, T:0.00
Consensus pattern (7 bp):
CAAAAGC
Found at i:1303438 original size:17 final size:17
Alignment explanation
Indices: 1303418--1303460 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1303408 TCTCTATCCA
1303418 CATTCTTCTTCTT-TTT
1 CATTCTTCTTCTTCTTT
* *
1303434 CCATTGTTCATCTTCTTT
1 -CATTCTTCTTCTTCTTT
1303452 CATTCTTCT
1 CATTCTTCT
1303461 CATGTTTAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.09, C:0.28, G:0.02, T:0.60
Consensus pattern (17 bp):
CATTCTTCTTCTTCTTT
Found at i:1316504 original size:2 final size:2
Alignment explanation
Indices: 1316497--1316548 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1316487 CATTCTAACA
1316497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1316539 AT AT AT AT AT
1 AT AT AT AT AT
1316549 TCAATGTCTG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1317147 original size:2 final size:2
Alignment explanation
Indices: 1317140--1317165 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1317130 AAAATGGTAA
1317140 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1317166 CCCATGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1317715 original size:19 final size:20
Alignment explanation
Indices: 1317691--1317741 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1317681 AATGACCAAT
1317691 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1317710 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1317730 AAAATCGCAACG
1 AAAATCGCAACG
1317742 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1317735 original size:20 final size:20
Alignment explanation
Indices: 1317691--1317988 Score: 147
Period size: 20 Copynumber: 14.6 Consensus size: 20
1317681 AATGACCAAT
*
1317691 AAAATCGCAACGCGA-T-ATC
1 AAAATCGCAACGCGATTGA-G
*
1317710 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
** ***
1317730 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTGAG
**
1317750 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TGAG
**
1317770 AAAATCGCAACGCGAGCTT-CC
1 AAAATCGCAACGCGA--TTGAG
**
1317791 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* *
1317814 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
** *
1317834 TGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* *
1317854 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* * *
1317877 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* * * *
1317897 AGATTCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* * *
1317917 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* * *
1317937 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* *
1317957 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
1317977 AAAATCGCAACG
1 AAAATCGCAACG
1317989 TTAAAAAGAA
Statistics
Matches: 230, Mismatches: 35, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
19 15 0.07
20 164 0.71
21 19 0.08
22 4 0.02
23 27 0.12
24 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTGAG
Found at i:1317870 original size:40 final size:40
Alignment explanation
Indices: 1317816--1317986 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 40
1317806 TTTAGAAGAA
* ** *
1317816 AATCGCAATGCGATTGATTGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
* * *
1317856 AGTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-CT-G-AGAGAATCGCAATGCGACTGAGAG
*
1317899 ATTCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
* * * *
1317939 AATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAA
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1317979 AATCGCAA
1 AATCGCAA
1317987 CGTTAAAAAG
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 78 0.68
41 3 0.03
42 2 0.02
43 32 0.28
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (40 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
Found at i:1317883 original size:63 final size:63
Alignment explanation
Indices: 1317795--1317988 Score: 259
Period size: 63 Copynumber: 3.1 Consensus size: 63
1317785 GCTTCCAAGT
* * ** *
1317795 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
* *
1317858 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
* * * * *
1317921 TCGCAATGCGA-CT-G-AGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAAA
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
1317981 TCGCAACG
1 TCGCAACG
1317989 TTAAAAAGAA
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
60 48 0.41
61 1 0.01
62 1 0.01
63 66 0.57
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:1317998 original size:20 final size:20
Alignment explanation
Indices: 1317975--1318018 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1317965 AACGCGATTT
*
1317975 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
1317995 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
1318015 AGAA
1 AGAA
1318019 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:1318003 original size:60 final size:60
Alignment explanation
Indices: 1317712--1318006 Score: 205
Period size: 60 Copynumber: 4.8 Consensus size: 60
1317702 GCGATATCAA
* * ** *
1317712 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAACG-GTCAAAAGAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAATGCGAC-TGAGAG
* ** ** * * * **
1317772 AATCGCAACGCGAGCTTCCAAGTTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTG
1 AATCGCAACGCGA-TTTAGAAAATCGCAA--CG-TTAAAAAGAAAATCGCAATGCGACTGAGAG
* * * * * * *
1317836 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAACGCGATTTAGAAAATCGCAA--CG-TTAAAAAGAAAATCGCAATGCGACTGAGAG
* * * * * * ** *** *
1317899 ATTCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAATGCGACTGAGAG
1317959 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAA
1318007 CGGTCAAAAG
Statistics
Matches: 181, Mismatches: 49, Indels: 10
0.75 0.20 0.04
Matches are distributed among these distances:
60 73 0.40
61 11 0.06
63 66 0.36
64 30 0.17
65 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (60 bp):
AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAATGCGACTGAGAG
Found at i:1318146 original size:5 final size:6
Alignment explanation
Indices: 1318096--1318143 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
1318086 GACACGTATT
1318096 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1318141 ACC
1 ACC
1318144 CGAGACGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1318963 original size:20 final size:20
Alignment explanation
Indices: 1318938--1318981 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1318928 TTTTTAACTA
*
1318938 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
1318958 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
1318978 TTCT
1 TTCT
1318982 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:1318991 original size:20 final size:20
Alignment explanation
Indices: 1318968--1319285 Score: 165
Period size: 20 Copynumber: 15.6 Consensus size: 20
1318958 TTCTTTTTAA
1318968 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1318988 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1319008 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1319028 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
1319048 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
1319071 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1319091 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1319111 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
1319131 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
1319151 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
1319174 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
1319195 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
* *** **
1319213 ACCGTTGCGATTTTTTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
1319235 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1319255 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
1319274 CGTTGCGATTTT
1 CGTTGCGATTTT
1319286 ATTGGTCATT
Statistics
Matches: 243, Mismatches: 44, Indels: 23
0.78 0.14 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.07
20 177 0.73
21 14 0.06
22 6 0.02
23 27 0.11
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:1319014 original size:40 final size:40
Alignment explanation
Indices: 1318970--1319160 Score: 238
Period size: 40 Copynumber: 4.7 Consensus size: 40
1318960 CTTTTTAACG
* *
1318970 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
1319010 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* *
1319050 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TTC-TCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
1319093 TTGCGATTCTATAAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
** *
1319133 TTGCGATTCAATCAATCGCATTGCGATT
1 TTGCGATTCTCTAAATCGCATTGCGATT
1319161 TTCTTCTAAA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
40 93 0.71
41 3 0.02
42 3 0.02
43 32 0.24
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:1319086 original size:83 final size:83
Alignment explanation
Indices: 1318978--1319140 Score: 263
Period size: 83 Copynumber: 2.0 Consensus size: 83
1318968 CGTTGCGATT
* * * * * *
1318978 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATA
*
1319043 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
1319061 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATA
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATA
1319126 AATCGCATTGCGATT
66 AATCGCATTGCGATT
1319141 CAATCAATCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATA
AATCGCATTGCGATTTTC
Found at i:1319152 original size:103 final size:103
Alignment explanation
Indices: 1318968--1319181 Score: 320
Period size: 103 Copynumber: 2.1 Consensus size: 103
1318958 TTCTTTTTAA
* * * * * * * *
1318968 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAATCGCATTG
** *
1319033 CGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCG
66 CGATTCAATCAATCGCATTGCGATTTTCTTCTAAATCG
*
1319071 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAATCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAATCGCATTG
1319136 CGATTCAATCAATCGCATTGCGATTTTCTTCTAAATCG
66 CGATTCAATCAATCGCATTGCGATTTTCTTCTAAATCG
1319174 CGTTGCGA
1 CGTTGCGA
1319182 ACTTGGAAGC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (103 bp):
CGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAATCGCATTG
CGATTCAATCAATCGCATTGCGATTTTCTTCTAAATCG
Found at i:1319181 original size:83 final size:81
Alignment explanation
Indices: 1318970--1319160 Score: 237
Period size: 83 Copynumber: 2.4 Consensus size: 81
1318960 CTTTTTAACG
* * *
1318970 TTGCGATTT--TCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTG
1 TTGCGATTTCATC-AAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTG
* * *
1319033 CGATTCTCTCAGTCGCA
65 CGATTCTATAAATCGCA
* *
1319050 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATT
1 TTGCGA-TTTCATC-AAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATT
1319115 GCGATTCTATAAATCGCA
64 GCGATTCTATAAATCGCA
*
1319133 TTGCGA-TTCAATC-AATCGCATTGCGATT
1 TTGCGATTTC-ATCAAATCGCGTTGCGATT
1319161 TTCTTCTAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
80 19 0.20
81 6 0.06
82 2 0.02
83 70 0.72
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.36
Consensus pattern (81 bp):
TTGCGATTTCATCAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGC
GATTCTATAAATCGCA
Found at i:1319275 original size:19 final size:20
Alignment explanation
Indices: 1319235--1319285 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1319225 TTTTTTTTAA
*
1319235 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
1319255 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
1319274 CGTTGCGATTTT
1 CGTTGCGATTTT
1319286 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:1322083 original size:21 final size:21
Alignment explanation
Indices: 1322053--1322259 Score: 160
Period size: 21 Copynumber: 10.0 Consensus size: 21
1322043 GATTTACATA
*
1322053 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1322074 TTCGCGTTGCGGTAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
1322095 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
1322116 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1322135 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1322158 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
1322177 TTCGCTTTGTGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
1322200 TT--CGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1322219 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
1322242 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
1322260 AATCGCAACG
Statistics
Matches: 144, Mismatches: 30, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
19 39 0.27
21 80 0.56
23 25 0.17
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1322114 original size:42 final size:40
Alignment explanation
Indices: 1322078--1322256 Score: 259
Period size: 42 Copynumber: 4.3 Consensus size: 40
1322068 TCCAAGTTCG
*
1322078 CGTTGCGGTAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1322118 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
* * *
1322160 CGTTGCGATAGTCGAAGTTCGCTTTGTGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
*
1322202 CGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1322244 CGTTGCGATAGTC
1 CGTTGCGATAGTC
1322257 CAAAATCGCA
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 28 0.22
41 2 0.02
42 99 0.77
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:1322220 original size:84 final size:82
Alignment explanation
Indices: 1322078--1322256 Score: 295
Period size: 84 Copynumber: 2.2 Consensus size: 82
1322068 TCCAAGTTCG
* *
1322078 CGTTGCGGTAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCAAAGTTCGCGTT
1322143 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
* * *
1322160 CGTTGCGATAGTCGAAGTTCGCTTTGTGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCAAAGTTCGCG
1322225 TTGCGATTTATTCCAAATT
64 TTGCGATTTATTCCAAATT
1322244 CGTTGCGATAGTC
1 CGTTGCGATAGTC
1322257 CAAAATCGCA
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
82 26 0.29
83 2 0.02
84 62 0.69
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCAAAGTTCGCGTT
GCGATTTATTCCAAATT
Found at i:1322360 original size:6 final size:6
Alignment explanation
Indices: 1322349--1322379 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1322339 GACACGTATT
*
1322349 ACCACG ACCACG ACCACG ACCCCG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
1322380 GACGAGACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1323061 original size:40 final size:40
Alignment explanation
Indices: 1322983--1323197 Score: 367
Period size: 40 Copynumber: 5.3 Consensus size: 40
1322973 TGCGATTTTG
1322983 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
* *
1323025 GATTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
*
1323065 GACTATCACAACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1323105 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1323147 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1323187 GACTATCGCAA
1 GACTATCGCAA
1323198 TGCGAATATG
Statistics
Matches: 165, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
40 104 0.63
41 3 0.02
42 58 0.35
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (40 bp):
GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
Found at i:1323136 original size:82 final size:80
Alignment explanation
Indices: 1322983--1323197 Score: 367
Period size: 82 Copynumber: 2.6 Consensus size: 80
1322973 TGCGATTTTG
*
1322983 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGATTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
*
1323048 ATCGCAACGCGAACTTT
64 ATCGCAACGCGAACTTC
*
1323065 GACTATCACAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG-A-AA
1323130 ATCGCAACGCGAACTTC
64 ATCGCAACGCGAACTTC
1323147 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
1323198 TGCGAATATG
Statistics
Matches: 127, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
80 38 0.30
81 2 0.02
82 87 0.69
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (80 bp):
GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAAT
CGCAACGCGAACTTC
Found at i:1323241 original size:21 final size:21
Alignment explanation
Indices: 1323212--1323262 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1323202 AATATGTAAA
*
1323212 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1323233 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
1323254 TCGCGTTGC
1 TCGCGTTGC
1323263 AAATTTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:1328447 original size:20 final size:20
Alignment explanation
Indices: 1328418--1328492 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
1328408 AATGTATTTT
*
1328418 GTGCACCGATGCACAAG-TAA
1 GTGCATCGATGCAC-AGTTAA
*
1328438 GTGCATCGATGCACTGTTAA
1 GTGCATCGATGCACAGTTAA
* *
1328458 GGATGCATCGATGCACGGTTTA
1 -G-TGCATCGATGCACAGTTAA
1328480 GTGCATCGATGCA
1 GTGCATCGATGCA
1328493 TACCTTCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.02
20 28 0.58
21 2 0.04
22 17 0.35
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (20 bp):
GTGCATCGATGCACAGTTAA
Found at i:1328467 original size:22 final size:20
Alignment explanation
Indices: 1328435--1328492 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 20
1328425 GATGCACAAG
*
1328435 TAAGTGCATCGATGCACTGT
1 TAAGTGCATCGATGCACGGT
1328455 TAAGGATGCATCGATGCACGGT
1 TAA-G-TGCATCGATGCACGGT
*
1328477 TTAGTGCATCGATGCA
1 TAAGTGCATCGATGCA
1328493 TACCTTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.44
21 2 0.06
22 17 0.50
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TAAGTGCATCGATGCACGGT
Found at i:1329366 original size:23 final size:23
Alignment explanation
Indices: 1329333--1329400 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1329323 ATTATTATAT
1329333 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1329356 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
1329379 GGCACTTCGTTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1329401 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1330582 original size:2 final size:2
Alignment explanation
Indices: 1330575--1330642 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1330565 ACATGACATG
1330575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1330617 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1330643 GTTATATGGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1333755 original size:20 final size:20
Alignment explanation
Indices: 1333726--1333802 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
1333716 AATGTATTTT
*
1333726 GTGCACCGATGCATAAGTAA
1 GTGCATCGATGCATAAGTAA
**
1333746 GTGCATCGATGCA-CCGTTAA
1 GTGCATCGATGCATAAG-TAA
* *
1333766 GGATGCATCGATACAT-GGTATA
1 -G-TGCATCGATGCATAAGTA-A
1333788 GTGCATCGATGCATA
1 GTGCATCGATGCATA
1333803 CCTTCATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
19 1 0.02
20 27 0.60
21 4 0.09
22 13 0.29
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (20 bp):
GTGCATCGATGCATAAGTAA
Found at i:1334660 original size:23 final size:23
Alignment explanation
Indices: 1334626--1334671 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1334616 CATTATTATA
* *
1334626 TGGCACTCCGGTGTAATTCTACG
1 TGGCACTCCGGTGCAATTATACG
*
1334649 TGGCACTTCGGTGCAATTATACG
1 TGGCACTCCGGTGCAATTATACG
1334672 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTATACG
Found at i:1337730 original size:26 final size:26
Alignment explanation
Indices: 1337694--1337748 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
1337684 AACACGTTCT
1337694 TGTTCTCCTATTGTACAACTTAAGGA
1 TGTTCTCCTATTGTACAACTTAAGGA
*
1337720 TGTTCTCCTATTGTACAACTTAAGTA
1 TGTTCTCCTATTGTACAACTTAAGGA
1337746 TGT
1 TGT
1337749 AAGCTGAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (26 bp):
TGTTCTCCTATTGTACAACTTAAGGA
Found at i:1361220 original size:17 final size:19
Alignment explanation
Indices: 1361187--1361221 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1361177 TCAACATCTC
1361187 GATTGCCCTCTTCAAACTA
1 GATTGCCCTCTTCAAACTA
1361206 GATT-CCCTC-TCAAACT
1 GATTGCCCTCTTCAAACT
1361222 GAACAAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (19 bp):
GATTGCCCTCTTCAAACTA
Found at i:1367873 original size:16 final size:18
Alignment explanation
Indices: 1367852--1367895 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
1367842 AATTAATATC
*
1367852 AATAAAAAA-A-CCTGAG
1 AATAAAAAAGAGCATGAG
1367868 AATAAACAAAGAGCATGAG
1 AATAAA-AAAGAGCATGAG
1367887 AATAAAAAA
1 AATAAAAAA
1367896 CTTTTTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 3 0.12
18 4 0.17
19 11 0.46
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (18 bp):
AATAAAAAAGAGCATGAG
Found at i:1374076 original size:25 final size:25
Alignment explanation
Indices: 1374048--1374098 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1374038 ATAAGACCCC
1374048 ATATTGCCCCAGATAAATGTACAAA
1 ATATTGCCCCAGATAAATGTACAAA
1374073 ATATTGCCCCAGATAAATGTACAAA
1 ATATTGCCCCAGATAAATGTACAAA
1374098 A
1 A
1374099 ATATGCTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.24
Consensus pattern (25 bp):
ATATTGCCCCAGATAAATGTACAAA
Found at i:1376708 original size:14 final size:14
Alignment explanation
Indices: 1376689--1376716 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1376679 TAATAGACTT
1376689 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1376703 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1376717 TGTTATCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:1384457 original size:51 final size:51
Alignment explanation
Indices: 1384398--1384498 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
1384388 TCAAGGAGAG
* *
1384398 AGTTACAAGGAGTTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTATT
1384449 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTAT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTAT
1384499 CCTTTCCTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTATT
Found at i:1386737 original size:14 final size:14
Alignment explanation
Indices: 1386718--1386761 Score: 70
Period size: 14 Copynumber: 3.0 Consensus size: 14
1386708 TAATAGACTT
1386718 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1386732 GTCTGTTTTCTACACA
1 GTCTGTTTTCT--ACA
1386748 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1386762 ATAACAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:1386750 original size:16 final size:16
Alignment explanation
Indices: 1386718--1386761 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
1386708 TAATAGACTT
1386718 GTCTGTTTTCT--ACA
1 GTCTGTTTTCTACACA
1386732 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
1386748 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1386762 ATAACAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.39
16 17 0.61
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:1389588 original size:16 final size:17
Alignment explanation
Indices: 1389560--1389594 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1389550 TTTTAACAAA
1389560 AATTTATTATAAAATAT
1 AATTTATTATAAAATAT
1389577 AATTTA-TATAAAATAT
1 AATTTATTATAAAATAT
1389593 AA
1 AA
1389595 AATTAACGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTATTATAAAATAT
Found at i:1394498 original size:54 final size:54
Alignment explanation
Indices: 1394290--1394491 Score: 296
Period size: 54 Copynumber: 3.7 Consensus size: 54
1394280 TGCATTTTTA
* * * *
1394290 CGTATCGACACTAAGTGTCCAACCCACGGAATTCATATTAAATTTATGAACAAC
1 CGTATCGGCACTAAGTGTGCAACCCACGGAATTCATAATAAATTTATGAACGAC
* * *
1394344 CGGATCGGCACTAAGTGCGCAACCCACGGAATTCATAATAAGTTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACGGAATTCATAATAAATTTATGAACGAC
*
1394398 CGTATCGGCACTAAGTGTGAAACCCACGGAATTCATAATAAATTTATGAACGAC
1 CGTATCGGCACTAAGTGTGCAACCCACGGAATTCATAATAAATTTATGAACGAC
* * **
1394452 CGTATCAGCACTAAGGGTGCAACCCACGTTATTCATAATA
1 CGTATCGGCACTAAGTGTGCAACCCACGGAATTCATAATA
1394492 GGTTTATTGT
Statistics
Matches: 132, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 132 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (54 bp):
CGTATCGGCACTAAGTGTGCAACCCACGGAATTCATAATAAATTTATGAACGAC
Found at i:1394900 original size:65 final size:62
Alignment explanation
Indices: 1394796--1394955 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 62
1394786 AATTAAATTG
* * *
1394796 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCA-CTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCAC-TACCATGCACCGATACACCTGACGA-TTT-TG-
1394860 A
62 A
* * * *
1394861 AACATCGAATGCATTTGATGCATCGATACACTAGTCATGCATCGATACACCTGACTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTA-CCATGCACCGATACACCTGACGATTTTGA
* * *
1394924 AACATCGAATGTACTTGATACATCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACT
1394956 CTTAGTGTAC
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 29 0.35
64 4 0.05
65 44 0.54
66 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (62 bp):
AACATCGAATGCATTTGATGCATCGATGCACTACCATGCACCGATACACCTGACGATTTTGA
Found at i:1396923 original size:22 final size:21
Alignment explanation
Indices: 1396898--1396938 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1396888 TATGAGAAAT
*
1396898 TGTTTTTAAAATATAAAAATGA
1 TGTTTTGAAAA-ATAAAAATGA
*
1396920 TGTTTTGAAAAATGAAAAT
1 TGTTTTGAAAAATAAAAAT
1396939 TAACTCGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTTTTGAAAAATAAAAATGA
Found at i:1400569 original size:42 final size:44
Alignment explanation
Indices: 1400522--1400616 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
1400512 TTGTGCTTCA
* *
1400522 TGCATCGATACACC-T-AACAGTGCATCGATGCA-TCCTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATGCACGCCTTGAATG
*
1400564 TGCATCGATACACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
1400608 TGCATCGAT
1 TGCATCGAT
1400617 GCACAAGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 20 0.43
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:1400587 original size:21 final size:21
Alignment explanation
Indices: 1400522--1400616 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 21
1400512 TTGTGCTTCA
*
1400522 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
*
1400542 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
1400564 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
1400585 TGCACCGATGCACGCCTTGAATG
1 TGCATCGAT--ACACCTTGAATG
1400608 TGCATCGAT
1 TGCATCGAT
1400617 GCACAAGGCC
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 17 0.28
22 13 0.22
23 19 0.32
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:1400610 original size:23 final size:23
Alignment explanation
Indices: 1400541--1400621 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
1400531 ACACCTAACA
*
1400541 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
1400563 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
1400584 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
1400607 GTGCATCGATGCACA
1 GTGCATCGATGCACA
1400622 AGGCCATGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
22 10 0.21
23 21 0.45
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:1400637 original size:43 final size:42
Alignment explanation
Indices: 1400540--1400639 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 42
1400530 TACACCTAAC
* * *
1400540 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
* * *
1400582 AGGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-GCCTTGAATGTGCATCGATACACAAGG-A
1400627 A-TGCATCGATGCA
1 AGTGCATCGATGCA
1400640 TCCATCAGGT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.48
44 23 0.48
45 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
Found at i:1403326 original size:64 final size:63
Alignment explanation
Indices: 1403250--1403439 Score: 199
Period size: 64 Copynumber: 3.0 Consensus size: 63
1403240 ATGCCCCAAT
* *
1403250 CCATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCATTTCATGCATCGATGCACATA
1 CCATGCATCGATGCACC-TGAATTATATTGAAACATCGAATGCATTTGATGCATCGATGCACA-A
* * *
1403314 CCATGCACCGATGCA-CTGAGGATTTTA-TGAAAACATCGAATGCATTTGATGTATCGATGCACC
1 CCATGCATCGATGCACCTGA--ATTATATTG-AAACATCGAATGCATTTGATGCATCGATGCA-C
*
1403377 AG
62 AA
** * *
1403379 CCATGCATCGATGCACTCTG-GCTATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
1 CCATGCATCGATGCAC-CTGAATTATATTGAAACATCGAATGCATTTGATGCATCGATGCAC
1403440 TCTTAGTGCA
Statistics
Matches: 105, Mismatches: 13, Indels: 17
0.78 0.10 0.13
Matches are distributed among these distances:
62 3 0.03
63 4 0.04
64 49 0.47
65 44 0.42
66 2 0.02
67 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
CCATGCATCGATGCACCTGAATTATATTGAAACATCGAATGCATTTGATGCATCGATGCACAA
Found at i:1403354 original size:65 final size:63
Alignment explanation
Indices: 1403280--1403439 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 63
1403270 AATTAAATTG
* *
1403280 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
1403344 A
63 A
* * * * *
1403345 AACATCGAATGCATTTGATGTATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
*
1403409 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1403440 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.35
65 49 0.58
66 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:1404779 original size:398 final size:398
Alignment explanation
Indices: 1404043--1404842 Score: 1564
Period size: 398 Copynumber: 2.0 Consensus size: 398
1404033 TGTGCAAATC
1404043 TTTTCAATTTTCTGCAAAAGCTTCCACCGAAAGTTTTAATTGCCAATTCACCTTCCTCTTGGTCG
1 TTTTCAATTTTCTGCAAAAGCTTCCACCGAAAGTTTTAATTGCCAATTCACCTTCCTCTTGGTCG
1404108 ATTTCATCGATCGATTAACTCAACATTTATGAATGATTGCATCGGCACTACGTGTGCACCCCATG
66 ATTTCATCGATCGATTAACTCAACATTTATGAATGATTGCATCGGCACTACGTGTGCACCCCATG
1404173 GAACTTATAATGAGTTGCAGTAAATAAATTCGTATTTTGATAACTATGATATACTTATGTATTGA
131 GAACTTATAATGAGTTGCAGTAAATAAATTCGTATTTTGATAACTATGATATACTTATGTATTGA
1404238 TTTCACCTCATTATTAGTATTGTCTCACTAAATAAATACTTAGCGTGTGTTGATTTTACGCGTAG
196 TTTCACCTCATTATTAGTATTGTCTCACTAAATAAATACTTAGCGTGTGTTGATTTTACGCGTAG
1404303 ATTTTAGCGAGCGGAGTAAGGAGTGCATCTGACATAGCCAATCAAGGGTCGCCTCATCAGTAACT
261 ATTTTAGCGAGCGGAGTAAGGAGTGCATCTGACATAGCCAATCAAGGGTCGCCTCATCAGTAACT
*
1404368 GTACGACAATTATGTCTACTTTTGATATTTTTAGTTGGCATGTAATAAACTTATAATAATGCTCT
326 GTACGACAATTATGTCTACTTTTGATATTGTTAGTTGGCATGTAATAAACTTATAATAATGCTCT
1404433 AAAATGTA
391 AAAATGTA
* *
1404441 TTTTCAATTTTTTGCAAAAGCTTCCACCGAAAGTTTTAATTGCCAATTTACCTTCCTCTTGGTCG
1 TTTTCAATTTTCTGCAAAAGCTTCCACCGAAAGTTTTAATTGCCAATTCACCTTCCTCTTGGTCG
1404506 ATTTCATCGATCGATTAACTCAACATTTATGAATGATTGCATCGGCACTACGTGTGCACCCCATG
66 ATTTCATCGATCGATTAACTCAACATTTATGAATGATTGCATCGGCACTACGTGTGCACCCCATG
1404571 GAACTTATAATGAGTTGCAGTAAATAAATTCGTATTTTGATAACTATGATATACTTATGTATTGA
131 GAACTTATAATGAGTTGCAGTAAATAAATTCGTATTTTGATAACTATGATATACTTATGTATTGA
1404636 TTTCACCTCATTATTAGTATTGTCTCACTAAATAAATACTTAGCGTGTGTTGATTTTACGCGTAG
196 TTTCACCTCATTATTAGTATTGTCTCACTAAATAAATACTTAGCGTGTGTTGATTTTACGCGTAG
1404701 ATTTTAGCGAGCGGAGTAAGGAGTGCATCTGACATAGCCAATCAAGGGTCGCCTCATCAGTAACT
261 ATTTTAGCGAGCGGAGTAAGGAGTGCATCTGACATAGCCAATCAAGGGTCGCCTCATCAGTAACT
*
1404766 GTACGACAATTATGTCTACTTTTGATGTTGTTAGTTGGCATGTAATAAACTTATAATAATGCTCT
326 GTACGACAATTATGTCTACTTTTGATATTGTTAGTTGGCATGTAATAAACTTATAATAATGCTCT
1404831 AAAATGTA
391 AAAATGTA
1404839 TTTT
1 TTTT
1404843 TCTTATGATG
Statistics
Matches: 398, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
398 398 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (398 bp):
TTTTCAATTTTCTGCAAAAGCTTCCACCGAAAGTTTTAATTGCCAATTCACCTTCCTCTTGGTCG
ATTTCATCGATCGATTAACTCAACATTTATGAATGATTGCATCGGCACTACGTGTGCACCCCATG
GAACTTATAATGAGTTGCAGTAAATAAATTCGTATTTTGATAACTATGATATACTTATGTATTGA
TTTCACCTCATTATTAGTATTGTCTCACTAAATAAATACTTAGCGTGTGTTGATTTTACGCGTAG
ATTTTAGCGAGCGGAGTAAGGAGTGCATCTGACATAGCCAATCAAGGGTCGCCTCATCAGTAACT
GTACGACAATTATGTCTACTTTTGATATTGTTAGTTGGCATGTAATAAACTTATAATAATGCTCT
AAAATGTA
Found at i:1404934 original size:24 final size:24
Alignment explanation
Indices: 1404906--1404995 Score: 171
Period size: 24 Copynumber: 3.8 Consensus size: 24
1404896 CTATAATTTA
1404906 ATAAATGTTTTATTATTATTACAT
1 ATAAATGTTTTATTATTATTACAT
1404930 ATAAATGTTTTATTATTATTACAT
1 ATAAATGTTTTATTATTATTACAT
1404954 ATAAATGTTTTATTATTATTACAT
1 ATAAATGTTTTATTATTATTACAT
*
1404978 ATAAATGTTTTATGATTA
1 ATAAATGTTTTATTATTA
1404996 GAAACAAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (24 bp):
ATAAATGTTTTATTATTATTACAT
Found at i:1412666 original size:2 final size:2
Alignment explanation
Indices: 1412655--1412690 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1412645 AAATAATAAA
1412655 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1412691 ATCGGGTCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1417866 original size:21 final size:21
Alignment explanation
Indices: 1417840--1417893 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1417830 TTTGATAAAA
*
1417840 TTTTATTTAAAAT-TTTATTTT
1 TTTTATTTAAAATATTGA-TTT
**
1417861 TTTTATCAAAAATATTGATTT
1 TTTTATTTAAAATATTGATTT
*
1417882 TATTATTTAAAA
1 TTTTATTTAAAA
1417894 AGTCAATAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTTAAAATATTGATTT
Found at i:1417952 original size:45 final size:44
Alignment explanation
Indices: 1417903--1418006 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 44
1417893 AAGTCAATAG
* * *
1417903 AAAAATAATATTTTAAATGATATTTAATATTAATAT-TTTTAGTAA
1 AAAAATAATATTTTAAATAATATCTAATATTAATATGTTTGA-T-A
* *
1417948 AAAAATAATATTTTAAGTAATGTCTAATATTAATATGTTTGATA
1 AAAAATAATATTTTAAATAATATCTAATATTAATATGTTTGATA
1417992 AAAAATAATATTTTA
1 AAAAATAATATTTTA
1418007 CCGAAAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 16 0.30
45 33 0.62
46 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (44 bp):
AAAAATAATATTTTAAATAATATCTAATATTAATATGTTTGATA
Found at i:1418196 original size:2 final size:2
Alignment explanation
Indices: 1418189--1418214 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1418179 GGTTATACTA
1418189 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1418215 GTGTGTGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1430757 original size:6 final size:6
Alignment explanation
Indices: 1430748--1430813 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
1430738 CTAATAATAA
* * * * *
1430748 ATAAAT ATAAAT ATATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1 ATAAAT ATAAAT ATA-A-AT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
* *
1430798 ATAATT ATAATT ATAA
1 ATAAAT ATAAAT ATAA
1430814 TTATCATCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
6 49 0.89
7 1 0.02
8 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
ATAAAT
Found at i:1430765 original size:2 final size:2
Alignment explanation
Indices: 1430752--1430800 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1430742 TAATAAATAA
*
1430752 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1430794 AT AT AT A
1 AT AT AT A
1430801 ATTATAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1430806 original size:12 final size:11
Alignment explanation
Indices: 1430758--1430806 Score: 64
Period size: 12 Copynumber: 4.3 Consensus size: 11
1430748 ATAAATATAA
1430758 ATATATATA-T
1 ATATATATATT
1430768 ATATATATATAT
1 ATATATATAT-T
1430780 ATATATATATAT
1 ATATATATAT-T
1430792 ATATATATAATT
1 ATATATAT-ATT
1430804 ATA
1 ATA
1430807 ATTATAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.25
12 25 0.69
13 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATATATATT
Found at i:1430938 original size:16 final size:17
Alignment explanation
Indices: 1430913--1430946 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1430903 CTGAAGTCTC
1430913 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
1430929 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
1430946 A
1 A
1430947 TAATGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:1441546 original size:2 final size:2
Alignment explanation
Indices: 1441539--1441579 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1441529 ATAATTTTCA
1441539 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1441580 AAGAAATAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1442408 original size:68 final size:68
Alignment explanation
Indices: 1442282--1442408 Score: 155
Period size: 68 Copynumber: 1.9 Consensus size: 68
1442272 AAATTACTGG
* * * ****
1442282 AAACATTATTATTTCTACCGATTTTGTTCTTATTGGGCATTTTACCGGGTTTGGTAAAACGCTAC
1 AAACATTATTATTTCTACCGATTTTATTATTATTAGGCATTTTACCGAAAATGGTAAAACGCTAC
1442347 CTA
66 CTA
* * * *
1442350 AAACATTATTTTTTCTATCGGTTTTATTATTATTAGGCATTTTACCGAAAATGTTAAAA
1 AAACATTATTATTTCTACCGATTTTATTATTATTAGGCATTTTACCGAAAATGGTAAAA
1442409 ACATTAATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 48 1.00
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (68 bp):
AAACATTATTATTTCTACCGATTTTATTATTATTAGGCATTTTACCGAAAATGGTAAAACGCTAC
CTA
Found at i:1442874 original size:19 final size:20
Alignment explanation
Indices: 1442850--1442887 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1442840 ACAAGAATGT
1442850 GTTTTA-TTAATGAAAAATA
1 GTTTTATTTAATGAAAAATA
*
1442869 GTTTTATTTAATTAAAAAT
1 GTTTTATTTAATGAAAAAT
1442888 TTTAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
GTTTTATTTAATGAAAAATA
Found at i:1454672 original size:3 final size:3
Alignment explanation
Indices: 1454664--1454696 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1454654 TATATATATA
1454664 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1454697 GTAGGCCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1454696 original size:23 final size:24
Alignment explanation
Indices: 1454638--1454696 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
1454628 ATCTACAAAA
1454638 ATATTTTATTA-TACTATATATAT
1 ATATTTTATTATTACTATATATAT
* *
1454661 ATATATTATTATTATTAT-TAT-T
1 ATATTTTATTATTACTATATATAT
1454683 ATTATTTTATTATT
1 A-TATTTTATTATT
1454697 GTAGGCCCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 2 0.06
23 24 0.77
24 5 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
ATATTTTATTATTACTATATATAT
Found at i:1455253 original size:20 final size:21
Alignment explanation
Indices: 1455215--1455253 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1455205 AGTTTGTTTT
*
1455215 TATTTCAATTTGGTCTGTTCA
1 TATTTCAATTTGCTCTGTTCA
1455236 TATTTCAATTT-CTCTGTT
1 TATTTCAATTTGCTCTGTT
1455254 TTGTTCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.56
Consensus pattern (21 bp):
TATTTCAATTTGCTCTGTTCA
Found at i:1455423 original size:15 final size:15
Alignment explanation
Indices: 1455388--1455465 Score: 70
Period size: 15 Copynumber: 4.9 Consensus size: 15
1455378 TTTTTCTAGG
*
1455388 TTATTTATTATTTTGTT
1 TTATTTATT-TTAT-TT
1455405 TTATTTATTTTATTT
1 TTATTTATTTTATTT
1455420 TTA-TTATTTTTATTT
1 TTATTTA-TTTTATTT
*
1455435 TTA-TTATTTTTTTCT
1 TTATTTATTTTATT-T
1455450 TTAATTTATTGTTATT
1 TT-ATTTATT-TTATT
1455466 ATCATTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
14 9 0.17
15 22 0.42
16 4 0.08
17 14 0.26
18 4 0.08
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (15 bp):
TTATTTATTTTATTT
Found at i:1458334 original size:19 final size:19
Alignment explanation
Indices: 1458312--1458369 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
1458302 ATCCAATCAG
1458312 AACAAAAAAAAAGAGAAAA
1 AACAAAAAAAAAGAGAAAA
* * *
1458331 AACAAAGGAAAAAG-CAAAG
1 AACAAA-AAAAAAGAGAAAA
1458350 AACAAATAAAAAAAGAGAAA
1 AAC-AA-AAAAAAAGAGAAA
1458370 CAAGAACAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 12 0.40
20 14 0.47
21 4 0.13
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.02
Consensus pattern (19 bp):
AACAAAAAAAAAGAGAAAA
Found at i:1459459 original size:32 final size:32
Alignment explanation
Indices: 1459423--1459509 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 32
1459413 GAATAATGGG
* *
1459423 GGCATCTTTGAAGATTCAACATCAAATGTTGA
1 GGCATCTTTGGAGATTCAACATCAAATATTGA
* * *
1459455 GGCAT-TTTCGGAGATCCAACATCGAATATTGG
1 GGCATCTTT-GGAGATTCAACATCAAATATTGA
1459487 GGCATCTTTGGAGATTCAACATC
1 GGCATCTTTGGAGATTCAACATC
1459510 CATATGTGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 3 0.06
32 41 0.87
33 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (32 bp):
GGCATCTTTGGAGATTCAACATCAAATATTGA
Found at i:1459876 original size:64 final size:64
Alignment explanation
Indices: 1459758--1459886 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 64
1459748 TGGGCGACTA
* **
1459758 TCAACAAACAACTTTCCAGTTTCATTCACAGTCAATTTCAACTTTACAGTGAAGGATATTCGAC
1 TCAACAAACAACTTTCCAGTTTCATTCACAGTCAATTTCAACTTCACAACGAAGGATATTCGAC
* * * * *
1459822 TCAACAAACAAGTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCATAACGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCACAGTCAATTTCAACTTCACAACGAAGGATATTCGAC
1459886 T
1 T
1459887 TGAAAGAACA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (64 bp):
TCAACAAACAACTTTCCAGTTTCATTCACAGTCAATTTCAACTTCACAACGAAGGATATTCGAC
Found at i:1460378 original size:36 final size:35
Alignment explanation
Indices: 1460314--1460540 Score: 141
Period size: 36 Copynumber: 6.5 Consensus size: 35
1460304 AATTTACTCA
*
1460314 AAACAAAGTTTTGTCTCTTTAGATAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCTTTAGACAGTTTCCCTTG
*
1460349 AAACAAA-TTTTGTCTCTCTTGAGGCAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCT-TT-AGACAGTTTCCCTTG
* * * *
1460385 AAACAAA-----ATCT-TTGA-ATATGTTTTCCTTG
1 AAACAAAGTTTTGTCTCTTTAGACA-GTTTCCCTTG
* * * **
1460414 AAACAAA-TTTCATCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAAGTTT--TGTCTCTTTAGACAGTTTCCCTTG
* * * * *
1460450 GAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTT
1 AAACAAAGTTTTGTCTCT-TT-AGACAGTTTCCCTTG
* *
1460487 AAATAAA-TTTTGTCTCTCTTGAGATAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCT-TT-AGACAGTTTCCCTTG
1460523 AAACAAAGTTTTGTCTCT
1 AAACAAAGTTTTGTCTCT
1460541 CTTGAAACAC
Statistics
Matches: 150, Mismatches: 27, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
28 1 0.01
29 17 0.11
30 1 0.01
31 1 0.01
32 3 0.02
34 10 0.07
35 16 0.11
36 70 0.47
37 31 0.21
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (35 bp):
AAACAAAGTTTTGTCTCTTTAGACAGTTTCCCTTG
Found at i:1460481 original size:37 final size:36
Alignment explanation
Indices: 1460426--1460545 Score: 143
Period size: 37 Copynumber: 3.3 Consensus size: 36
1460416 ACAAATTTCA
* *
1460426 TCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTG
1 TCTCTCTTGAGATAGTTTCTTTT-GAACTAAGTTTTG
* *
1460463 TCTCTCTTGAGATAGTTTCTCTTT-AAATAAATTTTG
1 TCTCTCTTGAGATAGTTTCT-TTTGAACTAAGTTTTG
** *
1460499 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAGTTTTG
1 TCTCTCTTGAGATAGTTTCTTTTG-AACTAAGTTTTG
1460536 TCTCTCTTGA
1 TCTCTCTTGA
1460546 AACACCAACC
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
35 2 0.03
36 29 0.41
37 37 0.52
38 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (36 bp):
TCTCTCTTGAGATAGTTTCTTTTGAACTAAGTTTTG
Found at i:1460602 original size:33 final size:32
Alignment explanation
Indices: 1460552--1460657 Score: 149
Period size: 33 Copynumber: 3.2 Consensus size: 32
1460542 TTGAAACACC
1460552 AACCTTTGAATATGTTTCTCTTGAAACACAAAA
1 AACCTTTGAA-ATGTTTCTCTTGAAACACAAAA
*
1460585 AACCTTAGAAATCGTTTCTCTTGAAACACAAAAA
1 AACCTTTGAAAT-GTTTCTCTTGAAACAC-AAAA
*
1460619 AAACTTTGAAAATGTTTCTCTTGAAACACAAAA
1 AACCTTTG-AAATGTTTCTCTTGAAACACAAAA
*
1460652 GACCTT
1 AACCTT
1460658 CGAGTTCGAC
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
32 2 0.03
33 33 0.51
34 26 0.40
35 4 0.06
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (32 bp):
AACCTTTGAAATGTTTCTCTTGAAACACAAAA
Found at i:1460636 original size:34 final size:34
Alignment explanation
Indices: 1460555--1460651 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 34
1460545 AAACACCAAC
* *
1460555 CTTTGAATATGTTTCTCTTGAAACAC-AAAAAAC
1 CTTTGAAAATGTTTCTCTTGAAACACAAAAAAAA
*
1460588 CTTAG-AAATCGTTTCTCTTGAAACACAAAAAAAA
1 CTTTGAAAAT-GTTTCTCTTGAAACACAAAAAAAA
1460622 CTTTGAAAATGTTTCTCTTGAAACACAAAA
1 CTTTGAAAATGTTTCTCTTGAAACACAAAA
1460652 GACCTTCGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
32 3 0.05
33 20 0.35
34 30 0.53
35 4 0.07
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (34 bp):
CTTTGAAAATGTTTCTCTTGAAACACAAAAAAAA
Found at i:1460852 original size:84 final size:83
Alignment explanation
Indices: 1460649--1460997 Score: 418
Period size: 83 Copynumber: 4.2 Consensus size: 83
1460639 TTGAAACACA
* *
1460649 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGGCTA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAA
*
1460714 GAAGGGTTATCTGTCAAC
66 GAAGGGCTATCTGTCAAC
* * * * * *
1460732 GAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATTATTTGCAACATAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAA
* *
1460797 GAAGGGCTATTTGCCAAC
66 GAAGGGCTATCTGTCAAC
* * * * *
1460815 AAAAAACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCGCATCATTTACAGCATAACTCAAGGCT
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCA
* * *
1460880 AGAAGGGTTATCTATCAGC
65 AGAAGGGCTATCTGTCAAC
* * * *
1460899 AAATACCTTTGAGTTCGACT-CTACTCAGCTCAAAGGCACAATCATTTGCAGCATATCTCAAGGC
1 AAAGACCTTCGAGTTCGACTAC-GCTCAGCTCAAAGGCAC-ATCATTTGCAGCATAACTCAAGGC
1460963 AAGAAGGGCTATCT-TC--C
64 AAGAAGGGCTATCTGTCAAC
* *
1460980 AAAGACCCTCAAGTTCGA
1 AAAGACCTTCGAGTTCGA
1460998 TTCCATTCAG
Statistics
Matches: 225, Mismatches: 38, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
81 15 0.07
82 1 0.00
83 107 0.48
84 102 0.45
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAA
GAAGGGCTATCTGTCAAC
Found at i:1460929 original size:167 final size:167
Alignment explanation
Indices: 1460646--1460974 Score: 500
Period size: 167 Copynumber: 2.0 Consensus size: 167
1460636 CTCTTGAAAC
* * *
1460646 ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTCAAGG
1 ACAAAAAACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTACAGCATAACTCAAGG
* * * *
1460711 CTAGAAGGGTTATCTGTCAACGAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCAC-ATTA
66 CTAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTAC-CTCAGCTCAAAGGCACAATCA
1460775 TTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCA
130 TTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCA
*
1460813 ACAAAAAACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCGCATCATTTACAGCATAACTCAAGG
1 ACAAAAAACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTACAGCATAACTCAAGG
* * *
1460878 CTAGAAGGGTTATCTATCAGCAAATACCTTTGAGTTCGACTCTA-CTCAGCTCAAAGGCACAATC
66 CTAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGA-T-TACCTCAGCTCAAAGGCACAATC
* *
1460942 ATTTGCAGCATATCTCAAGGCAAGAAGGGCTAT
129 ATTTGCAACATAGCTCAAGGCAAGAAGGGCTAT
1460975 CTTCCAAAGA
Statistics
Matches: 146, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
167 110 0.75
168 34 0.23
169 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (167 bp):
ACAAAAAACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTACAGCATAACTCAAGG
CTAGAAGGGTTATCTATCAACAAAGACCTTCGAGTTCGATTACCTCAGCTCAAAGGCACAATCAT
TTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCA
Found at i:1461371 original size:3 final size:3
Alignment explanation
Indices: 1461363--1461401 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1461353 ATATATATAT
*
1461363 TTA TTA TTA TTA TTA TTA ATA TT- TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1461402 TTTGTAGGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1461375 original size:9 final size:8
Alignment explanation
Indices: 1461363--1461403 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
1461353 ATATATATAT
1461363 TTATTATTA
1 TTATT-TTA
1461372 TTATTATTA
1 TTATT-TTA
*
1461381 ATATTTTA
1 TTATTTTA
1461389 TTATTTTA
1 TTATTTTA
1461397 TTATTTT
1 TTATTTT
1461404 TGTAGGCCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 17 0.57
9 13 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTATTTTA
Found at i:1461397 original size:22 final size:24
Alignment explanation
Indices: 1461357--1461401 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1461347 TATACTATAT
1461357 ATATATTTATTATTATTATTATTA
1 ATATATTTATTATTATTATTATTA
1461381 ATAT-TTTATTATT-TTATTATT
1 ATATATTTATTATTATTATTATT
1461402 TTTGTAGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 9 0.43
24 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATATATTTATTATTATTATTATTA
Found at i:1462067 original size:14 final size:14
Alignment explanation
Indices: 1462033--1462132 Score: 57
Period size: 14 Copynumber: 7.2 Consensus size: 14
1462023 TTTTTGCACC
*
1462033 TTTATTTTATTTTA
1 TTTATTTTATTATA
1462047 CTTT-TTTTA-TATA
1 -TTTATTTTATTATA
1462060 TTTATTTTATTATA
1 TTTATTTTATTATA
* *
1462074 TTT-TTAGTATTATT
1 TTTATT-TTATTATA
* *
1462088 TTTCTGGGTTATT-TA
1 TTTAT--TTTATTATA
* *
1462103 -TTATTTTGTTTTA
1 TTTATTTTATTATA
*
1462116 TTTATTTTATTTTA
1 TTTATTTTATTATA
1462130 TTT
1 TTT
1462133 TTACTTTTAC
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
12 7 0.10
13 12 0.18
14 39 0.58
15 5 0.07
16 4 0.06
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (14 bp):
TTTATTTTATTATA
Found at i:1462072 original size:16 final size:16
Alignment explanation
Indices: 1462033--1462077 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1462023 TTTTTGCACC
*
1462033 TTTATTTTATTTTACT
1 TTTATTATATTTTACT
*
1462049 TTTTTTATATATTTA-T
1 TTTATTATAT-TTTACT
1462065 TTTATTATATTTT
1 TTTATTATATTTT
1462078 TAGTATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 3 0.12
16 18 0.72
17 4 0.16
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTATATTTTACT
Found at i:1462140 original size:6 final size:6
Alignment explanation
Indices: 1462116--1462159 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
1462106 TTTTGTTTTA
*
1462116 TTTA-T TTTA-T TTTATT TTTACT TTTACT TTTACT TTTACT TTTA
1 TTTACT TTTACT TTTACT TTTACT TTTACT TTTACT TTTACT TTTA
1462160 TTATTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 9 0.24
6 28 0.76
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTACT
Found at i:1462294 original size:13 final size:13
Alignment explanation
Indices: 1462276--1462306 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1462266 CGAATAGGAT
1462276 ATTTTAAATTTTA
1 ATTTTAAATTTTA
*
1462289 ATTTTAATTTTTA
1 ATTTTAAATTTTA
1462302 ATTTT
1 ATTTT
1462307 CGCAATTAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTAAATTTTA
Found at i:1478807 original size:43 final size:43
Alignment explanation
Indices: 1478711--1479058 Score: 398
Period size: 43 Copynumber: 8.1 Consensus size: 43
1478701 TGTAAAATAA
* * * * *
1478711 AAACGCCGTAAAAAGTCAAGATTTATAGCGGCGTTTTT--AAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTGGATAC
* **
1478753 AAACGCCGCAAAAGGTTAGATCTATAGCAACATTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
** *
1478796 AAATACCGCAAAAGGTCAAGATCTATAACGGCATTTTTGGATAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTGGATAC
* * *
1478840 AAACGCCGCAAAAGGTCAGATCTATAACGACGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
* * * * **
1478882 AAACGCCGTAAAAAGTCAGATTTATAGAGGTGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
* *
1478925 AAACGCCGCAAAAGGTCATATCTATAGCAGCATTTTTGGA-AC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
* *
1478967 AAACGCCACAAAAGGTTAGATCTATAGCGGCATTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
* * *
1479010 AAACGCTGTAAAATGTCAGATCTATAGCGGCATTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCA-TTTTTGGATAC
1479054 AAACG
1 AAACG
1479059 TCGCTAATTA
Statistics
Matches: 258, Mismatches: 42, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
41 16 0.06
42 87 0.34
43 101 0.39
44 54 0.21
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGATAC
Found at i:1478942 original size:85 final size:87
Alignment explanation
Indices: 1478711--1479058 Score: 388
Period size: 85 Copynumber: 4.1 Consensus size: 87
1478701 TGTAAAATAA
* * * * * *
1478711 AAACGCCGTAAAAAGTCAAGATTTATAGCGGCGTTTTT--AAACAAACGCCGCAAAAGGTTAGAT
1 AAACGCCGCAAAAAGTCAAGATCTATAGAGGCATTTTTGGATACAAACGCCGCAAAAGGTCAGAT
*
1478774 CTATAGCAACATTTTTGGATAC
66 CTATAGCGACATTTTTGGATAC
** *
1478796 AAATACCGCAAAAGGTCAAGATCTATA-ACGGCATTTTTGGATACAAACGCCGCAAAAGGTCAGA
1 AAACGCCGCAAAAAGTCAAGATCTATAGA-GGCATTTTTGGATACAAACGCCGCAAAAGGTCAGA
* *
1478860 TCTATAACGACGTTTTTGGA-AC
65 TCTATAGCGACATTTTTGGATAC
* * ** *
1478882 AAACGCCGTAAAAAGTC-AGATTTATAGAGGTGTTTTTGGATACAAACGCCGCAAAAGGTCATAT
1 AAACGCCGCAAAAAGTCAAGATCTATAGAGGCATTTTTGGATACAAACGCCGCAAAAGGTCAGAT
1478946 CTATAGC-AGCATTTTTGGA-AC
66 CTATAGCGA-CATTTTTGGATAC
* * * * * * *
1478967 AAACGCCACAAAAGGT-TAGATCTATAGCGGCATTTTTGGATACAAACGCTGTAAAATGTCAGAT
1 AAACGCCGCAAAAAGTCAAGATCTATAGAGGCATTTTTGGATACAAACGCCGCAAAAGGTCAGAT
*
1479031 CTATAGCGGCATTTTTTGGATAC
66 CTATAGCGACA-TTTTTGGATAC
1479054 AAACG
1 AAACG
1479059 TCGCTAATTA
Statistics
Matches: 220, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
84 1 0.00
85 149 0.68
86 24 0.11
87 46 0.21
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (87 bp):
AAACGCCGCAAAAAGTCAAGATCTATAGAGGCATTTTTGGATACAAACGCCGCAAAAGGTCAGAT
CTATAGCGACATTTTTGGATAC
Found at i:1485758 original size:42 final size:44
Alignment explanation
Indices: 1485711--1485805 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
1485701 TTGTGCTTCA
* * *
1485711 TGCATCGATACACC-T-AACAGTGCATCGATGCA-TCTTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATGCACGCCTTGAATG
*
1485753 TGCATCGATACACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
1485797 TGCATCGAT
1 TGCATCGAT
1485806 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 19 0.41
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:1485799 original size:23 final size:23
Alignment explanation
Indices: 1485730--1485810 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
1485720 ACACCTAACA
* *
1485730 GTGCATCGATGCA-TCTTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
1485752 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
1485773 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
1485796 GTGCATCGATGCACA
1 GTGCATCGATGCACA
1485811 AGGCCATGCA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 10 0.22
23 21 0.46
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Done.