Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008311.1 Hibiscus syriacus cultivar Beakdansim tig00111002_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: 1790494
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1418111 original size:21 final size:22
Alignment explanation
Indices: 1418087--1418134 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1418077 AGCTAATGTA
*
1418087 TAATACATAGGAGCTAA-AAAT
1 TAATACACAGGAGCTAACAAAT
* *
1418108 TAATGCACATGAGCTAACAAAT
1 TAATACACAGGAGCTAACAAAT
*
1418130 GAATA
1 TAATA
1418135 ATTAAGCATG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (22 bp):
TAATACACAGGAGCTAACAAAT
Found at i:1420703 original size:14 final size:14
Alignment explanation
Indices: 1420680--1420709 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1420670 GTGTTGCAAC
1420680 AAAACAAAAAAGAA
1 AAAACAAAAAAGAA
*
1420694 AAAACCAAAAAGAA
1 AAAACAAAAAAGAA
1420708 AA
1 AA
1420710 TAAATAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAAGAA
Found at i:1447734 original size:17 final size:17
Alignment explanation
Indices: 1447712--1447764 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
1447702 TTCATGTATT
1447712 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
* *
1447729 TAGTTCATTCATTAAAC
1 TAGTTCATTAATCAAAC
1447746 TAGTGT-ATTAATCAAAC
1 TAGT-TCATTAATCAAAC
1447763 TA
1 TA
1447765 ACTATTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 30 0.97
18 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:1456302 original size:13 final size:13
Alignment explanation
Indices: 1456286--1456310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1456276 TTAGAAAAAC
1456286 AAAAAGGAAAATA
1 AAAAAGGAAAATA
1456299 AAAAAGGAAAAT
1 AAAAAGGAAAAT
1456311 GACATAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (13 bp):
AAAAAGGAAAATA
Found at i:1460387 original size:13 final size:13
Alignment explanation
Indices: 1460369--1460399 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1460359 CTCAAATTTT
1460369 GTTATACATGGAA
1 GTTATACATGGAA
1460382 GTTATACATGGAA
1 GTTATACATGGAA
1460395 GTTAT
1 GTTAT
1460400 TGCATGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (13 bp):
GTTATACATGGAA
Found at i:1466699 original size:33 final size:33
Alignment explanation
Indices: 1466657--1466756 Score: 182
Period size: 33 Copynumber: 3.0 Consensus size: 33
1466647 CCTAGTACAG
1466657 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
* *
1466690 ATGGTGGACACGATCTTATGTATCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
1466723 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
1466756 A
1 A
1466757 GCACTACAGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:1475036 original size:50 final size:50
Alignment explanation
Indices: 1474977--1475118 Score: 223
Period size: 50 Copynumber: 2.8 Consensus size: 50
1474967 ACTGCTCTAA
1474977 AATGAAAGTTAAATGCATAACGGTGCATTTTCGACATAAAAGATGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTTCGACATAAAAGATGCCACT
* *
1475027 AATGAAAGTTAAATGCATAACAGTGCATTTTTGACATAAAAGATGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTTCGACATAAAAGATGCCACT
* * *
1475077 AATTAAAGTTAAATGCATAATGGTGTATTTTC-ATCATAAAAG
1 AATGAAAGTTAAATGCATAACGGTGCATTTTCGA-CATAAAAG
1475119 GGGCCACTCA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 83 0.99
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (50 bp):
AATGAAAGTTAAATGCATAACGGTGCATTTTCGACATAAAAGATGCCACT
Found at i:1481237 original size:20 final size:20
Alignment explanation
Indices: 1481212--1481262 Score: 93
Period size: 21 Copynumber: 2.5 Consensus size: 20
1481202 ATTGATGTGT
1481212 GTATCGATACTAGTAGGAAG
1 GTATCGATACTAGTAGGAAG
1481232 GTATCGAATACTAGTAGGAAG
1 GTATCG-ATACTAGTAGGAAG
1481253 GTATCGATAC
1 GTATCGATAC
1481263 CATGTATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.25
Consensus pattern (20 bp):
GTATCGATACTAGTAGGAAG
Found at i:1481792 original size:50 final size:50
Alignment explanation
Indices: 1481716--1481815 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
1481706 ACTCTTCTAA
* **
1481716 AATGAAAGTTAAATGCATAACGGTGCATTTTTGGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACAGTGCATTTTCAGCATAAAAGGTGCCACT
* *
1481766 AATGAAAGTTAAATGCATAATAGTGCATTTTCAGCATAAAAGGTGTCACT
1 AATGAAAGTTAAATGCATAACAGTGCATTTTCAGCATAAAAGGTGCCACT
1481816 CATGGTATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (50 bp):
AATGAAAGTTAAATGCATAACAGTGCATTTTCAGCATAAAAGGTGCCACT
Found at i:1488082 original size:9 final size:8
Alignment explanation
Indices: 1488053--1488144 Score: 54
Period size: 9 Copynumber: 11.6 Consensus size: 8
1488043 TTTAAGACTC
1488053 ATTATAAT
1 ATTATAAT
1488061 ATTAGT-AT
1 ATTA-TAAT
1488069 AATTATACAT
1 -ATTATA-AT
*
1488079 ATTATGAT
1 ATTATAAT
1488087 AATT-TAAT
1 -ATTATAAT
1488095 -TTAT-AT
1 ATTATAAT
*
1488101 AGTTTTAAT
1 A-TTATAAT
1488110 ATTA-AAT
1 ATTATAAT
*
1488117 ATTATAGT
1 ATTATAAT
1488125 ATTAATAAT
1 ATT-ATAAT
1488134 ATT-T-AT
1 ATTATAAT
1488140 ATTAT
1 ATTAT
1488145 GTATTTAGTA
Statistics
Matches: 66, Mismatches: 6, Indels: 25
0.68 0.06 0.26
Matches are distributed among these distances:
6 9 0.14
7 10 0.15
8 22 0.33
9 23 0.35
10 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (8 bp):
ATTATAAT
Found at i:1488155 original size:29 final size:30
Alignment explanation
Indices: 1488116--1488173 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1488106 TAATATTAAA
1488116 TATTATAGTATTAATAAT-ATTTATATTATG
1 TATTATAGTATTAATAATAATTTAT-TTATG
* *
1488146 TATT-TAGTATTTATATTAATTTATTTAT
1 TATTATAGTATTAATAATAATTTATTTAT
1488174 AAATTAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (30 bp):
TATTATAGTATTAATAATAATTTATTTATG
Found at i:1494632 original size:19 final size:20
Alignment explanation
Indices: 1494594--1494636 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1494584 GAAACCCCTT
*
1494594 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
1494614 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
1494633 TGAA
1 TGAA
1494637 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:1495379 original size:20 final size:21
Alignment explanation
Indices: 1495338--1495379 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1495328 AATGATCATC
* *
1495338 TATAAGCTAAGATAACATGTA
1 TATAAGCTAAGATAAAAGGTA
1495359 TATAAGCT-AGATAAAAGGTA
1 TATAAGCTAAGATAAAAGGTA
1495379 T
1 T
1495380 TGAATGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.29
Consensus pattern (21 bp):
TATAAGCTAAGATAAAAGGTA
Found at i:1503184 original size:20 final size:20
Alignment explanation
Indices: 1503137--1503186 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1503127 TTATGAGTAA
*
1503137 TTAAAATATGTTTAAAGTGT
1 TTAAAATGTGTTTAAAGTGT
1503157 TTAAAATGTGTTTAAAGCT-T
1 TTAAAATGTGTTTAAAG-TGT
1503177 TTAAAATGTG
1 TTAAAATGTG
1503187 AAAAAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.44
Consensus pattern (20 bp):
TTAAAATGTGTTTAAAGTGT
Found at i:1503346 original size:28 final size:28
Alignment explanation
Indices: 1503289--1503346 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1503279 AAAAAGTTTG
*
1503289 AACAGTCATATTTTTAAGTAAGAGTGTC
1 AACAGTCATATTTTTAAGTAAGACTGTC
*
1503317 AACAGTCATATTTTTAAGTAAGACTTTC
1 AACAGTCATATTTTTAAGTAAGACTGTC
1503345 AA
1 AA
1503347 AACGTTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (28 bp):
AACAGTCATATTTTTAAGTAAGACTGTC
Found at i:1503415 original size:20 final size:20
Alignment explanation
Indices: 1503387--1503424 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1503377 TATAGTAAGT
*
1503387 TTAAGAGTTTCAAAACTTTC
1 TTAAAAGTTTCAAAACTTTC
1503407 TTAAAAGTTTCAAAACTT
1 TTAAAAGTTTCAAAACTT
1503425 CATATGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (20 bp):
TTAAAAGTTTCAAAACTTTC
Found at i:1505137 original size:3 final size:3
Alignment explanation
Indices: 1505129--1505198 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
1505119 ACCTAGTTGT
1505129 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1505176 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
1505199 TCATATTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1505308 original size:39 final size:40
Alignment explanation
Indices: 1505265--1505343 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
1505255 TAAATTCTGA
*
1505265 ATTTCTTAAATT-TTTC-CATTATAACATTCTAAATT-TTTT
1 ATTTCTTAAATTATTTCACA-T-TAACAATCTAAATTATTTT
1505304 ATTTCTTAAATTATTTCACATTAACAATCTAAATTATTTT
1 ATTTCTTAAATTATTTCACATTAACAATCTAAATTATTTT
1505344 TTAAAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 25 0.69
40 9 0.25
41 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (40 bp):
ATTTCTTAAATTATTTCACATTAACAATCTAAATTATTTT
Found at i:1507027 original size:64 final size:63
Alignment explanation
Indices: 1506858--1507037 Score: 202
Period size: 64 Copynumber: 2.8 Consensus size: 63
1506848 GAATAAATTG
* * * * *
1506858 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* *
1506922 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
1506985 A
63 A
* * * *
1506986 AACATCAAATGTATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
1507038 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 90 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:1513448 original size:232 final size:234
Alignment explanation
Indices: 1513018--1513486 Score: 867
Period size: 232 Copynumber: 2.0 Consensus size: 234
1513008 ATCATCGAAA
1513018 AATCATCGGTTTATTCATGCTATTCATCTTTAAAACCTGTTTACATCATTAAATCGTGCAAAACA
1 AATCATCGGTTTATT-ATGCTATTCATCTTTAAAACCTGTTTACATCATTAAATCGTGCAAAACA
1513083 ACTCCTCATCCCTCTCAATCCGAATTTTCAAGGTAATATTTCAAAAACCTCTATTTTATTGATTT
65 ACTCCTCATCCCTCTCAATCCGAATTTTCAAGGTAATATTTCAAAAACCTCTATTTTATTGATTT
1513148 TTAATTTTAGAACTAGTTTGATTAGTTCTATGATGACATTATATTGGGCATTGATGTTTGTTGGT
130 TTAATTTTAGAACTAGTTTGATTAGTTCTATGATGACATTATATTGGGCATTGATGTTTGTTGGT
1513213 TCTAAACTAGATTTTACTACCAATTTCGTCAAAAATAAAC
195 TCTAAACTAGATTTTACTACCAATTTCGTCAAAAATAAAC
1513253 AATCATCGGTTTA-T-TGCTATTCATCTTTAAAACCTGTTTACATCATTAAATCGTGCAAAACAA
1 AATCATCGGTTTATTATGCTATTCATCTTTAAAACCTGTTTACATCATTAAATCGTGCAAAACAA
1513316 CT-C-C-TCCCTCTCAATCCGAATTTTCAAGGTAATATTTCAAAAACCTCTATTTTATTGATTTT
66 CTCCTCATCCCTCTCAATCCGAATTTTCAAGGTAATATTTCAAAAACCTCTATTTTATTGATTTT
1513378 TAATTTTAGAACTAGTTTTGATTAGTTCTATGATGAACATTATATTGGGCATTGATTGTTTGTTG
131 TAATTTTAGAACTAG-TTTGATTAGTTCTATGATG-ACATTATATTGGGCATTGA-TGTTTGTTG
1513443 GTTCTAAACTAGATTTTACTACCAATTTCGTCAAAAATAAAC
193 GTTCTAAACTAGATTTTACTACCAATTTCGTCAAAAATAAAC
1513485 AA
1 AA
1513487 ATTTTCAAGA
Statistics
Matches: 231, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
229 73 0.32
230 20 0.09
231 20 0.09
232 104 0.45
234 1 0.00
235 13 0.06
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (234 bp):
AATCATCGGTTTATTATGCTATTCATCTTTAAAACCTGTTTACATCATTAAATCGTGCAAAACAA
CTCCTCATCCCTCTCAATCCGAATTTTCAAGGTAATATTTCAAAAACCTCTATTTTATTGATTTT
TAATTTTAGAACTAGTTTGATTAGTTCTATGATGACATTATATTGGGCATTGATGTTTGTTGGTT
CTAAACTAGATTTTACTACCAATTTCGTCAAAAATAAAC
Found at i:1515808 original size:64 final size:64
Alignment explanation
Indices: 1515733--1515854 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
1515723 GCATAAATCC
* *
1515733 ATGCATTGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCATGCATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTC
1515796 T
64 T
** **
1515797 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCA
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCA
1515855 AAGCAATGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 2 0.04
63 6 0.12
64 42 0.84
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
Found at i:1515896 original size:63 final size:64
Alignment explanation
Indices: 1515761--1515919 Score: 187
Period size: 63 Copynumber: 2.5 Consensus size: 64
1515751 GAATAAATTG
*** * * * * * *
1515761 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCAATGCACTAGGCTATTATTAA
*
1515825 AACATCGAATGCATTTCATGCATCGATGCA-AAGCAATGCACCAATGCACTCAGGCTATT-TTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCAATGCACT-AGGCTATTATTAA
* *
1515888 AACATCGAATGTATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1515920 CTTGGTTCAC
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 45 0.56
64 36 0.44
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCAATGCACTAGGCTATTATTAA
Found at i:1522262 original size:14 final size:14
Alignment explanation
Indices: 1522240--1522270 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1522230 TCCTTAGTGT
*
1522240 GGAGTTAAGGTAGA
1 GGAGCTAAGGTAGA
1522254 GGAGCTAAGGTAGA
1 GGAGCTAAGGTAGA
1522268 GGA
1 GGA
1522271 TGTAGTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.45, T:0.16
Consensus pattern (14 bp):
GGAGCTAAGGTAGA
Found at i:1523056 original size:13 final size:13
Alignment explanation
Indices: 1523035--1523099 Score: 103
Period size: 13 Copynumber: 4.9 Consensus size: 13
1523025 CTTGTCTCAT
*
1523035 TCTTCTTTCTCTTA
1 TCTT-TTTCTCTTC
1523049 TCTTTTTCTCTTC
1 TCTTTTTCTCTTC
1523062 TCTTTTTCTCTTC
1 TCTTTTTCTCTTC
1523075 TCTTTTTCTCTTC
1 TCTTTTTCTCTTC
*
1523088 TCCTTTTCTCTT
1 TCTTTTTCTCTT
1523100 TATCTTTCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
13 45 0.92
14 4 0.08
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTTTTCTCTTC
Found at i:1523083 original size:21 final size:21
Alignment explanation
Indices: 1523059--1523100 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1523049 TCTTTTTCTC
* *
1523059 TTCTCTTTTTCTCTTCTCTTT
1 TTCTCTTCTCCTCTTCTCTTT
*
1523080 TTCTCTTCTCCTTTTCTCTTT
1 TTCTCTTCTCCTCTTCTCTTT
1523101 ATCTTTCCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
TTCTCTTCTCCTCTTCTCTTT
Found at i:1531830 original size:42 final size:42
Alignment explanation
Indices: 1531745--1531978 Score: 344
Period size: 42 Copynumber: 5.6 Consensus size: 42
1531735 CGAAGTTATG
1531745 ATGCTTTAAATCGATGTAGTTTAAGT-CATTGTTGCCAATGA
1 ATGCTTTAAATCGATGTAGTTTAAGTCCATTGTTGCCAATGA
*
1531786 ATGCTTTAAATCGATGTAGTTTAAGTCCATTGTTGTCAATGA
1 ATGCTTTAAATCGATGTAGTTTAAGTCCATTGTTGCCAATGA
* * * *
1531828 ATGCTATAAATTGATGTTGTTTAAGTTCATTGTTGCCAATGA
1 ATGCTTTAAATCGATGTAGTTTAAGTCCATTGTTGCCAATGA
* * **
1531870 ATGCTTTATATCGATGTTGTTTAAGTCCATTGTTGTTAATGA
1 ATGCTTTAAATCGATGTAGTTTAAGTCCATTGTTGCCAATGA
* **
1531912 ATGCTTTAAATCGATGTTGTTTAAGTCCATTGTTGCCAACAA
1 ATGCTTTAAATCGATGTAGTTTAAGTCCATTGTTGCCAATGA
*
1531954 ATGCTTTTAATCGATGTAGTTTAAG
1 ATGCTTTAAATCGATGTAGTTTAAG
1531979 CCCGCTGCTG
Statistics
Matches: 173, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
41 26 0.15
42 147 0.85
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (42 bp):
ATGCTTTAAATCGATGTAGTTTAAGTCCATTGTTGCCAATGA
Found at i:1534722 original size:6 final size:6
Alignment explanation
Indices: 1534697--1534758 Score: 63
Period size: 6 Copynumber: 10.3 Consensus size: 6
1534687 GTACATCATC
* * * * *
1534697 TTTGCA TTTATA TTCGTA TTTATA TTTGTA TTTGTA TTTGTA TTTAT-
1 TTTGTA TTTGTA TTTGTA TTTGTA TTTGTA TTTGTA TTTGTA TTTGTA
1534744 TTTCGTA TTTGTA TT
1 TTT-GTA TTTGTA TT
1534759 CATATTTGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
5 3 0.07
6 39 0.87
7 3 0.07
ACGTcount: A:0.19, C:0.05, G:0.11, T:0.65
Consensus pattern (6 bp):
TTTGTA
Found at i:1534728 original size:18 final size:18
Alignment explanation
Indices: 1534697--1534764 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
1534687 GTACATCATC
*
1534697 TTTGCATTTATATTCGTA
1 TTTGTATTTATATTCGTA
* * *
1534715 TTTATATTTGTATTTGTA
1 TTTGTATTTATATTCGTA
*
1534733 TTTGTATTTATTTTCGTA
1 TTTGTATTTATATTCGTA
*
1534751 TTTGTATTCATATT
1 TTTGTATTTATATT
1534765 TGTGTATATC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.21, C:0.06, G:0.10, T:0.63
Consensus pattern (18 bp):
TTTGTATTTATATTCGTA
Found at i:1534729 original size:24 final size:23
Alignment explanation
Indices: 1534697--1534765 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
1534687 GTACATCATC
* *
1534697 TTTGCATTTATATTCGTATTTAT
1 TTTGTATTTGTATTCGTATTTAT
*
1534720 ATTTGTATTTGTATTTGTATTTAT
1 -TTTGTATTTGTATTCGTATTTAT
*
1534744 TTTCGTATTTGTATTCATATTT
1 TTT-GTATTTGTATTCGTATTT
1534766 GTGTATATCG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 3 0.08
24 36 0.92
ACGTcount: A:0.20, C:0.06, G:0.10, T:0.64
Consensus pattern (23 bp):
TTTGTATTTGTATTCGTATTTAT
Found at i:1534767 original size:12 final size:12
Alignment explanation
Indices: 1534702--1534765 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
1534692 TCATCTTTGC
1534702 ATTTATATTCGT
1 ATTTATATTCGT
*
1534714 ATTTATATTTGT
1 ATTTATATTCGT
* *
1534726 ATTTGTATTTGT
1 ATTTATATTCGT
*
1534738 ATTTATTTTCGT
1 ATTTATATTCGT
* *
1534750 ATTTGTATTCAT
1 ATTTATATTCGT
1534762 ATTT
1 ATTT
1534766 GTGTATATCG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.22, C:0.05, G:0.09, T:0.64
Consensus pattern (12 bp):
ATTTATATTCGT
Found at i:1537026 original size:14 final size:14
Alignment explanation
Indices: 1537007--1537034 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1536997 TTGCGGATTT
1537007 TGTTGCGGTTGCGG
1 TGTTGCGGTTGCGG
1537021 TGTTGCGGTTGCGG
1 TGTTGCGGTTGCGG
1537035 ATGGTGCGGA
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:0.00, C:0.14, G:0.50, T:0.36
Consensus pattern (14 bp):
TGTTGCGGTTGCGG
Found at i:1539034 original size:16 final size:16
Alignment explanation
Indices: 1539015--1539056 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1539005 TGAGAAAAAT
1539015 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
*
1539031 TTAATTTAATTTTAAA
1 TTAATTTAAATTTAAA
*
1539047 ATAATGTTAA
1 TTAAT-TTAA
1539057 TAAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:1542646 original size:163 final size:164
Alignment explanation
Indices: 1542369--1542679 Score: 525
Period size: 163 Copynumber: 1.9 Consensus size: 164
1542359 GGCGAGAAAT
* * *
1542369 CAAAGGCTCATATAGGTGCGCGCTTTTGTAGCCTTTTGAAGAGACGCAAGGCGCACCTCTTTTAG
1 CAAAGGCTCATATAGGTGCGCGATTTGGTAGCCTTTTAAAGAGACGCAAGGCGCACCTCTTTTAG
*
1542434 CGCTTTACTGTCCCTCATTCTTTTGTTCAGTTTTGTAGTGGATAAATTGTTCCAACTTCAACGTG
66 CGCTTTACTGTCCCTCATTCTTTTGTTCAGTTTTGTAGTAGATAAATTGTTCCAACTTCAACGTG
1542499 ACAACTATTTATGGTTTTAAGTGGGGTGATAAAC
131 ACAACTATTTATGGTTTTAAGTGGGGTGATAAAC
* * *
1542533 CAAAGGCTCGTATAGGTGCGCGATTTGGTAGCCTTTTAAAGAGGCGCAAGGCGCACCTC-TTTGG
1 CAAAGGCTCATATAGGTGCGCGATTTGGTAGCCTTTTAAAGAGACGCAAGGCGCACCTCTTTTAG
* * *
1542597 CGCTTTACTGTCCCTCGTTCTTTTGTTCAGTTTTGTAGTAGATAAATTGTTCTAACTTGAACGTG
66 CGCTTTACTGTCCCTCATTCTTTTGTTCAGTTTTGTAGTAGATAAATTGTTCCAACTTCAACGTG
1542662 ACAACTATTTATGGTTTT
131 ACAACTATTTATGGTTTT
1542680 GTGGAGTCAA
Statistics
Matches: 137, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
163 83 0.61
164 54 0.39
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (164 bp):
CAAAGGCTCATATAGGTGCGCGATTTGGTAGCCTTTTAAAGAGACGCAAGGCGCACCTCTTTTAG
CGCTTTACTGTCCCTCATTCTTTTGTTCAGTTTTGTAGTAGATAAATTGTTCCAACTTCAACGTG
ACAACTATTTATGGTTTTAAGTGGGGTGATAAAC
Found at i:1545831 original size:48 final size:49
Alignment explanation
Indices: 1545760--1545857 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 49
1545750 TGCGATAACA
*
1545760 TTAGTTAGTTTACGTCTTTTATAAGGAT-AAAGGTTTTAACATTCGATT
1 TTAGTTAGTTTAAGTCTTTTATAAGGATAAAAGGTTTTAACATTCGATT
1545808 TTAGTTAGTTTAAGTCTTTTATAAGGATAAAAGGTTTTAACATTCGATT
1 TTAGTTAGTTTAAGTCTTTTATAAGGATAAAAGGTTTTAACATTCGATT
1545857 T
1 T
1545858 ACTGGTGGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 27 0.56
49 21 0.44
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (49 bp):
TTAGTTAGTTTAAGTCTTTTATAAGGATAAAAGGTTTTAACATTCGATT
Found at i:1555661 original size:19 final size:22
Alignment explanation
Indices: 1555639--1555681 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1555629 GATATATTAA
1555639 AATAA-AAA-AATAATA-TAAT
1 AATAATAAATAATAATAGTAAT
*
1555658 AATAATAAATATTAATAGTAAT
1 AATAATAAATAATAATAGTAAT
1555680 AA
1 AA
1555682 ATATAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 6 0.30
22 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAATAAATAATAATAGTAAT
Found at i:1555673 original size:16 final size:16
Alignment explanation
Indices: 1555632--1555685 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
1555622 TTGAAAAGAT
*
1555632 ATATTAA-AATAAAAAA
1 ATATTAATAAT-AATAA
1555648 ATAATATAATAATAATAA
1 AT-AT-TAATAATAATAA
*
1555666 ATATTAATAGTAATAA
1 ATATTAATAATAATAA
1555682 ATAT
1 ATAT
1555686 AAAAGGGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 17 0.52
17 4 0.12
18 9 0.27
19 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
ATATTAATAATAATAA
Found at i:1556445 original size:19 final size:19
Alignment explanation
Indices: 1556389--1556451 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1556379 CTATTTAAAC
**
1556389 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
1556409 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1556429 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1556448 TAAA
1 TAAA
1556452 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1558113 original size:16 final size:15
Alignment explanation
Indices: 1558092--1558121 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1558082 GAACCAAATA
1558092 TGTTTTTTTTCTGCAC
1 TGTTTTTTTT-TGCAC
1558108 TGTTTTTTTTTGCA
1 TGTTTTTTTTTGCA
1558122 TTGCATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.07, C:0.13, G:0.13, T:0.67
Consensus pattern (15 bp):
TGTTTTTTTTTGCAC
Found at i:1563598 original size:21 final size:22
Alignment explanation
Indices: 1563565--1563605 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1563555 GGTTAAAATA
1563565 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
1563587 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
1563606 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:1564321 original size:75 final size:76
Alignment explanation
Indices: 1564244--1564390 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 76
1564234 AAAATACCTA
*
1564244 AAAAAAT-AAAATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACA
1 AAAAAATAAAAATAATATTCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACA
1564307 AAGATAAAGAT
66 AAGATAAAGAT
* * * *
1564318 AAAATATAAAAATAATATTCTAAAACTTAATTAAAATATTAAAAACCTATTTAAACTTAAATACA
1 AAAAAATAAAAATAATATTCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACA
1564383 AAGATAAA
66 AAGATAAA
1564391 ATATAATGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 6 0.09
75 29 0.44
76 31 0.47
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (76 bp):
AAAAAATAAAAATAATATTCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACA
AAGATAAAGAT
Found at i:1564406 original size:76 final size:75
Alignment explanation
Indices: 1564250--1564417 Score: 230
Period size: 76 Copynumber: 2.2 Consensus size: 75
1564240 CCTAAAAAAA
*
1564250 TAAAATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA
1 TAAAATAATATTCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA
1564315 GATAAAATAT
66 GATAAAATAT
* * * *
1564325 AAAAATAATATTCTAAAACTTAATTAAAATATTAAAAACCTATTTAAACTTAAATACAAAGATAA
1 TAAAATAATATTCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAA
* *
1564390 A-ATATAATGTT
65 AGATAAAAT-AT
* *
1564401 TAAAATATTATCCTAAA
1 TAAAATAATATTCTAAA
1564418 TTTGAGTTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
75 35 0.43
76 46 0.57
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.32
Consensus pattern (75 bp):
TAAAATAATATTCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA
GATAAAATAT
Found at i:1572845 original size:20 final size:21
Alignment explanation
Indices: 1572817--1572867 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1572807 GCATGAATGA
*
1572817 TGGATTATGTTGATGATGGAGT
1 TGGA-TATGTTGATGATAGAGT
* *
1572839 TGG-TATGATGATGATATAGT
1 TGGATATGTTGATGATAGAGT
1572859 TGGATATGT
1 TGGATATGT
1572868 CCAATTAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 17 0.71
21 4 0.17
22 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.41
Consensus pattern (21 bp):
TGGATATGTTGATGATAGAGT
Found at i:1577778 original size:11 final size:11
Alignment explanation
Indices: 1577762--1577792 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1577752 ATGAATGATG
1577762 AATAAAATAAC
1 AATAAAATAAC
*
1577773 AATAAAATAAT
1 AATAAAATAAC
1577784 AATAAAATA
1 AATAAAATA
1577793 CTATCCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (11 bp):
AATAAAATAAC
Found at i:1578679 original size:54 final size:54
Alignment explanation
Indices: 1578617--1579217 Score: 629
Period size: 54 Copynumber: 11.1 Consensus size: 54
1578607 CGATACAGTC
* * * * **
1578617 ATTCATAAACTTATTATGAATTTTGTGGGTTGCACACACAGTGCTAATATGGTA
1 ATTCATAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGCCAATACGAAA
** * * *
1578671 ATTCATAAACTCATTATGAATTACGTGGGGTTGTACACATAGCGCCAATACAAAA
1 ATTCATAAACTCATTATGAATTTTGT-GGGTTGCACACATAGTGCCAATACGAAA
* *
1578726 ATTCATAAACTGATTATGAATTTTGTGGGTTGCAAACATAGTGCCAATACGAAA
1 ATTCATAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGCCAATACGAAA
* ** * * **
1578780 ATTCATAAACTCATTAAGAATTTCATGGGTTGCACACATAATGCCAATATGGTA
1 ATTCATAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGCCAATACGAAA
** * * *
1578834 ATTCATAAACTCATTATGAATTAGGTGGGGTTTCACACATAGTGCCATTACGATA
1 ATTCATAAACTCATTATGAATTTTGT-GGGTTGCACACATAGTGCCAATACGAAA
* ** * *
1578889 ATTCATAAACTCATTATGAATTATGCAAGGTTGCACACATAGTGCTAATA-TAGAA
1 ATTCATAAACTCATTATGAATTTTG-TGGGTTGCACACATAGTGCCAATACGA-AA
* * *
1578944 ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGTC-ATATGAAA
1 ATTCATAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGCCAATACGAAA
* * *
1578997 ATTCATAAACTCATTATGAATTACCTG-GGGTTGCACACATAATGCCAACAC-AATA
1 ATTCATAAACTCATTATGAATT--TTGTGGGTTGCACACATAGTGCCAATACGAA-A
* * ** * *
1579052 ATTCATAAACTAATTATAAATTACGTGGGGTTGCACACATATTGTCAATACGAAA
1 ATTCATAAACTCATTATGAATTTTGT-GGGTTGCACACATAGTGCCAATACGAAA
** * * *
1579107 ATTTTTAAACTCGTTACT-AATTTTGTGGGTTGCACACATAGTGCTAATA-TAGAA
1 ATTCATAAACTCATTA-TGAATTTTGTGGGTTGCACACATAGTGCCAATACGA-AA
* *
1579161 ATTCATAAACTCATTATGAATTTTGTGGGTTGCATACATAGTGCCAATACGATA
1 ATTCATAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGCCAATACGAAA
1579215 ATT
1 ATT
1579218 GCAACATATA
Statistics
Matches: 450, Mismatches: 81, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
53 30 0.07
54 219 0.49
55 198 0.44
56 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (54 bp):
ATTCATAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGCCAATACGAAA
Found at i:1578894 original size:163 final size:163
Alignment explanation
Indices: 1578617--1579217 Score: 751
Period size: 163 Copynumber: 3.7 Consensus size: 163
1578607 CGATACAGTC
* * * * *
1578617 ATTCATAAACTTATTATGAATTTTGTGGGTTGCACACACAGTGCTAATATGGTAATTCATAAACT
1 ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCCAATATGGAAATTCATAAACT
* * * *
1578682 CATTATGAATTACGTGGGGTTGTACACATAGCGCCAATACAAAAATTCATAAACTGATTATGAAT
66 CATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACAATAATTCATAAACTAATTATGAAT
* *
1578747 TTTGTGGGTTGCAAACATAGTGCCAATACGAAA
131 TATGTGGGTTGCACACATAGTGCCAATACGAAA
* * * *
1578780 ATTCATAAACTCATTAAGAATTTCATGGGTTGCACACATAATGCCAATATGGTAATTCATAAACT
1 ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCCAATATGGAAATTCATAAACT
* * * * *
1578845 CATTATGAATTAGGTGGGGTTTCACACATAGTGCCATTACGATAATTCATAAACTCATTATGAAT
66 CATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACAATAATTCATAAACTAATTATGAAT
** * *
1578910 TATGCAAGGTTGCACACATAGTGCTAATA-TAGAA
131 TATG-TGGGTTGCACACATAGTGCCAATACGA-AA
* *
1578944 ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGTC-ATATGAAAATTCATAAACT
1 ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCCAATATGGAAATTCATAAACT
* * * *
1579008 CATTATGAATTACCTGGGGTTGCACACATAATGCCAACACAATAATTCATAAACTAATTATAAAT
66 CATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACAATAATTCATAAACTAATTATGAAT
* * *
1579073 TACGTGGGGTTGCACACATATTGTCAATACGAAA
131 TATGT-GGGTTGCACACATAGTGCCAATACGAAA
** * * * *
1579107 ATTTTTAAACTCGTTACT-AATTTTGTGGGTTGCACACATAGTGCTAATATAGAAATTCATAAAC
1 ATTCATAAACTCATTA-TGAATTTCGTGGGTTGCACACATAGTGCCAATATGGAAATTCATAAAC
** * *
1579171 TCATTATGAATTTTGT-GGGTTGCATACATAGTGCCAATACGATAATT
65 TCATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACAATAATT
1579218 GCAACATATA
Statistics
Matches: 374, Mismatches: 58, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
163 280 0.75
164 94 0.25
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (163 bp):
ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCCAATATGGAAATTCATAAACT
CATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACAATAATTCATAAACTAATTATGAAT
TATGTGGGTTGCACACATAGTGCCAATACGAAA
Found at i:1579030 original size:218 final size:217
Alignment explanation
Indices: 1578617--1579217 Score: 769
Period size: 218 Copynumber: 2.8 Consensus size: 217
1578607 CGATACAGTC
* ** * * * *
1578617 ATTCATAAACTTATTATGAATTTTGT-GGGTTGCACACACAGTGCTAATATGGTAATTCATAAAC
1 ATTCATAAACTAATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGATAATTCATAAAC
* * * * * *
1578681 TCATTATGAATTACGTG-GGGTTGTACACATAGCGCCAATACAAAAATTCATAAACTGATTATGA
66 TCATTATGAATTA--TGAGGGTTGCACACATAGTGCTAATATAGAAATTCATAAACTCATTATGA
*
1578745 ATTTTGTGGGTTGCAAACATAGTGCCAATACGAAAATTCATAAACTCATTAAGAATTTCATGGGT
129 ATTTTGTGGGTTGCAAACATAGTGCCAATACGAAAATTCATAAACTCATTAAGAATTACATGGGT
* ***
1578810 TGCACACATAATGCCAATATGGTA
194 TGCACACATAATGCCAACACAATA
* * * *
1578834 ATTCATAAACTCATTATGAATTAGGTGGGGTTTCACACATAGTGCCATTACGATAATTCATAAAC
1 ATTCATAAACTAATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGATAATTCATAAAC
*
1578899 TCATTATGAATTATGCAAGGTTGCACACATAGTGCTAATATAGAAATTCATAAACTCATTATGAA
66 TCATTATGAATTATG-AGGGTTGCACACATAGTGCTAATATAGAAATTCATAAACTCATTATGAA
* * * * * *
1578964 TTTCGTGGGTTGCACACATAGTGTC-ATATGAAAATTCATAAACTCATTATGAATTACCTGGGGT
130 TTTTGTGGGTTGCAAACATAGTGCCAATACGAAAATTCATAAACTCATTAAGAATTACAT-GGGT
1579028 TGCACACATAATGCCAACACAATA
194 TGCACACATAATGCCAACACAATA
* * * * **
1579052 ATTCATAAACTAATTATAAATTACGTGGGGTTGCACACATATTGTCAATACGAAAATTTTTAAAC
1 ATTCATAAACTAATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGATAATTCATAAAC
* * *
1579117 TCGTTACT-AATTTTGTGGGTTGCACACATAGTGCTAATATAGAAATTCATAAACTCATTATGAA
66 TCATTA-TGAATTATGAGGGTTGCACACATAGTGCTAATATAGAAATTCATAAACTCATTATGAA
* *
1579181 TTTTGTGGGTTGCATACATAGTGCCAATACGATAATT
130 TTTTGTGGGTTGCAAACATAGTGCCAATACGAAAATT
1579218 GCAACATATA
Statistics
Matches: 332, Mismatches: 46, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
216 2 0.01
217 122 0.37
218 207 0.62
219 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (217 bp):
ATTCATAAACTAATTATGAATTACGTGGGGTTGCACACATAGTGCCAATACGATAATTCATAAAC
TCATTATGAATTATGAGGGTTGCACACATAGTGCTAATATAGAAATTCATAAACTCATTATGAAT
TTTGTGGGTTGCAAACATAGTGCCAATACGAAAATTCATAAACTCATTAAGAATTACATGGGTTG
CACACATAATGCCAACACAATA
Found at i:1585213 original size:55 final size:54
Alignment explanation
Indices: 1585101--1585646 Score: 624
Period size: 55 Copynumber: 10.1 Consensus size: 54
1585091 TGACATGGTC
* * * *
1585101 ATTCATAAACTCATTATGAATTCTGTGGGTTGCACACACAGTGCCAATACAGTA
1 ATTCATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGAA
**
1585155 ATTCATAAACTCATTATGAATTATGTGGGGTTGCACACATAGTGCCTTTACGGAA
1 ATTCATAAACTCATTATGAATTATGT-GGGTTGCACACATAGTGCCAATACGGAA
* * * *
1585210 ATTCATAAACTCATTATGAATTTTGTGGGATGCACACTTAGTGCCGATACGGAA
1 ATTCATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGAA
* * * *
1585264 ATGT-ATAAACTCATTATGAATT-TCATGGGTTGCACATATAGTTCCAATA-TGATA
1 AT-TCATAAACTCATTATGAATTAT-GTGGGTTGCACACATAGTGCCAATACGGA-A
* * * *
1585318 ATTCAT--ACTCATTATGAATTACGTGGGGTTGCATACATAGTGCCAATATGGTA
1 ATTCATAAACTCATTATGAATTATGT-GGGTTGCACACATAGTGCCAATACGGAA
* * * * *
1585371 ATTCATAAACTCATTATAAATTACGTAGGGTTGCACACATAGTGGCAATATGAAA
1 ATTCATAAACTCATTATGAATTATGT-GGGTTGCACACATAGTGCCAATACGGAA
* *
1585426 ATTCATAAACTCATTATGAATT-TCGTGGGTTGCACACATAGTGACAATATGGAA
1 ATTCATAAACTCATTATGAATTAT-GTGGGTTGCACACATAGTGCCAATACGGAA
* * *
1585480 ATTCATAAACTCACTATGAATTACATG-GGGTAGCACACATAGTGCCAATACGGTA
1 ATTCATAAACTCATTATGAATT--ATGTGGGTTGCACACATAGTGCCAATACGGAA
* * *
1585535 ATTCATAAACTCACTATGAATTACT-TGGGGTTGCACACATAGTGTCAATACTGAA
1 ATTCATAAACTCATTATGAATTA-TGT-GGGTTGCACACATAGTGCCAATACGGAA
* *
1585590 ATTCATAAACTCGTTATGAATT-TCGTGGGTTGCACACATAGTGCCAATACGGTA
1 ATTCATAAACTCATTATGAATTAT-GTGGGTTGCACACATAGTGCCAATACGGAA
1585644 ATT
1 ATT
1585647 GCAACATATA
Statistics
Matches: 424, Mismatches: 49, Indels: 38
0.83 0.10 0.07
Matches are distributed among these distances:
52 15 0.04
53 33 0.08
54 170 0.40
55 204 0.48
56 1 0.00
57 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (54 bp):
ATTCATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGCCAATACGGAA
Found at i:1585485 original size:109 final size:108
Alignment explanation
Indices: 1585101--1585640 Score: 640
Period size: 109 Copynumber: 5.0 Consensus size: 108
1585091 TGACATGGTC
* ** *
1585101 ATTCATAAACTCATTATGAA-TTCTGTGGGTTGCACACACAGTGCCAATACAGTAATTCATAAAC
1 ATTCATAAACTCATTATGAATTTC-GTGGGTTGCACACATAGTGCCAATATGGAAATTCATAAAC
* ** *
1585165 TCATTATGAATTATGTGGGGTTGCACACATAGTGCCTTTACGGAA
65 TCATTATGAATTACGT-GGGTTGCACACATAGTGCCAATACGAAA
* * * * *
1585210 ATTCATAAACTCATTATGAATTTTGTGGGATGCACACTTAGTGCCGATACGGAAATGT-ATAAAC
1 ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCCAATATGGAAAT-TCATAAAC
* * * * * *
1585274 TCATTATGAATTTCATGGGTTGCACATATAGTTCCAATATGATA
65 TCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGAAA
* * *
1585318 ATTCAT--ACTCATTATGAATTACGTGGGGTTGCATACATAGTGCCAATATGGTAATTCATAAAC
1 ATTCATAAACTCATTATGAATTTCGT-GGGTTGCACACATAGTGCCAATATGGAAATTCATAAAC
* * *
1585381 TCATTATAAATTACGTAGGGTTGCACACATAGTGGCAATATGAAA
65 TCATTATGAATTACGT-GGGTTGCACACATAGTGCCAATACGAAA
*
1585426 ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGACAATATGGAAATTCATAAACT
1 ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCCAATATGGAAATTCATAAACT
* * * **
1585491 CACTATGAATTACATGGGGTAGCACACATAGTGCCAATACGGTA
66 CATTATGAATTACGT-GGGTTGCACACATAGTGCCAATACGAAA
* * * *
1585535 ATTCATAAACTCACTATGAATTACTTGGGGTTGCACACATAGTGTCAATACT-GAAATTCATAAA
1 ATTCATAAACTCATTATGAATTTCGT-GGGTTGCACACATAGTGCCAATA-TGGAAATTCATAAA
* *
1585599 CTCGTTATGAATTTCGTGGGTTGCACACATAGTGCCAATACG
64 CTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACG
1585641 GTAATTGCAA
Statistics
Matches: 368, Mismatches: 54, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
106 17 0.05
107 43 0.12
108 57 0.15
109 183 0.50
110 67 0.18
111 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (108 bp):
ATTCATAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCCAATATGGAAATTCATAAACT
CATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGAAA
Found at i:1585950 original size:20 final size:20
Alignment explanation
Indices: 1585925--1585978 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
1585915 AAGCTGAATA
1585925 GTATCGATACCCCTCCTATG
1 GTATCGATACCCCTCCTATG
* *
1585945 GTATCGATACTTCTCTTCTATG
1 GTATCGATAC--CCCTCCTATG
*
1585967 GTATTGATACCC
1 GTATCGATACCC
1585979 ACATCGGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (20 bp):
GTATCGATACCCCTCCTATG
Found at i:1589006 original size:29 final size:29
Alignment explanation
Indices: 1588973--1589028 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1588963 AATCTATTTT
*
1588973 CCCCCTAAAAAT-TTATAACTTCAAGTTTG
1 CCCCCT-AAAATCCTATAACTTCAAGTTTG
*
1589002 CCCCCTAAAATCCTATAAGTTCAAGTT
1 CCCCCTAAAATCCTATAACTTCAAGTT
1589029 CTCCCTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (29 bp):
CCCCCTAAAATCCTATAACTTCAAGTTTG
Found at i:1589185 original size:14 final size:15
Alignment explanation
Indices: 1589166--1589205 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1589156 TTGACAGACT
*
1589166 AAAAATAT-ATTTTG
1 AAAAATATAATTATG
1589180 AAAAAT-TAATTATG
1 AAAAATATAATTATG
1589194 AAAAATA-AATTA
1 AAAAATATAATTA
1589206 CATTTTCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
AAAAATATAATTATG
Found at i:1589499 original size:23 final size:23
Alignment explanation
Indices: 1589468--1589512 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1589458 ACAATGTTAA
*
1589468 AAAAAATATTATTTAATTATATT
1 AAAAAATATTATTTAACTATATT
* *
1589491 AAAATATATTCTTTAACTATAT
1 AAAAAATATTATTTAACTATAT
1589513 AAATTAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAAAATATTATTTAACTATATT
Found at i:1590522 original size:69 final size:71
Alignment explanation
Indices: 1590448--1590590 Score: 182
Period size: 76 Copynumber: 2.0 Consensus size: 71
1590438 ATTTTAAACA
* * * *
1590448 TTATATTTTATC-TTTTA-ATTTTAGTTCAAATAGTTTTTAGTATTTTAATTATGTTTTAGGATA
1 TTATATTTTATCTTTTTAGATTTTAGTTCAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATA
1590511 TTATTT
66 TTATTT
*
1590517 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATC--T-TTTTA-G-ATTTTAGTTCAAATAGGTTTTAGTATTTTAATTAGGATTTA
1590582 GAATATTAT
61 GAATATTAT
1590591 ATTACTTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
69 12 0.19
73 5 0.08
76 45 0.73
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (71 bp):
TTATATTTTATCTTTTTAGATTTTAGTTCAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATA
TTATTT
Found at i:1590535 original size:32 final size:32
Alignment explanation
Indices: 1590481--1590543 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1590471 GTTCAAATAG
1590481 TTTTTAGTATTTTAATTATGTTTTAGGATATTA
1 TTTTTAGTATTTTAATTATGTTTTAGG-TATTA
*
1590514 TTTTTA-TATTTT-ATCTTTGTTTTAGGTATT
1 TTTTTAGTATTTTAAT-TATGTTTTAGGTATT
1590544 TTAGTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 6 0.21
32 16 0.57
33 6 0.21
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.65
Consensus pattern (32 bp):
TTTTTAGTATTTTAATTATGTTTTAGGTATTA
Found at i:1590576 original size:19 final size:19
Alignment explanation
Indices: 1590548--1590610 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1590538 GGTATTTTAG
*
1590548 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
1590567 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
1590586 ATTATATTACTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
1590607 TTTA
1 TTTA
1590611 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.54
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:1591282 original size:19 final size:18
Alignment explanation
Indices: 1591231--1591279 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
1591221 AATCTCTTTA
1591231 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
*
1591250 TTTCTTTTATTTAATTATT
1 ATT-TTTTATTTAATTATT
1591269 ATTTTTTATTT
1 ATTTTTTATTT
1591280 TAAAAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:1591352 original size:8 final size:7
Alignment explanation
Indices: 1591325--1591367 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
1591315 TTACTATTAA
1591325 TATTTTT
1 TATTTTT
*
1591332 TATTATAT
1 TATT-TTT
1591340 TATTTTT
1 TATTTTT
1591347 TCATTTTT
1 T-ATTTTT
*
1591355 TATTATT
1 TATTTTT
1591362 TATTTT
1 TATTTT
1591368 ATTTTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
7 17 0.57
8 13 0.43
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (7 bp):
TATTTTT
Found at i:1591358 original size:18 final size:19
Alignment explanation
Indices: 1591337--1591372 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1591327 TTTTTTATTA
1591337 TATTATTT-TTTCATTTTT
1 TATTATTTATTTCATTTTT
*
1591355 TATTATTTATTTTATTTT
1 TATTATTTATTTCATTTT
1591373 AATATATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (19 bp):
TATTATTTATTTCATTTTT
Found at i:1594317 original size:12 final size:11
Alignment explanation
Indices: 1594285--1594309 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1594275 TTTCATTCCA
1594285 TTTATTTTATT
1 TTTATTTTATT
1594296 TTTATTTTATT
1 TTTATTTTATT
1594307 TTT
1 TTT
1594310 TTCTTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:1595983 original size:19 final size:19
Alignment explanation
Indices: 1595959--1595996 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1595949 CATTTTATTT
*
1595959 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
1595978 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
1595997 AATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:1596771 original size:19 final size:18
Alignment explanation
Indices: 1596720--1596768 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1596710 AATCTATTTA
1596720 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
1596739 TTTATTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
1596758 ATTTTTTATTT
1 ATTTTTTATTT
1596769 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:1596835 original size:23 final size:21
Alignment explanation
Indices: 1596809--1596860 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
1596799 TATTTTTTAC
1596809 TTTTAATATTTATTATTATATTA
1 TTTTAATATTTA-T-TTATATTA
** *
1596832 TTTTTCTA-TTATTTATTTTA
1 TTTTAATATTTATTTATATTA
1596852 TTTTAATAT
1 TTTTAATAT
1596861 ATCATTTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
22 3 0.13
23 6 0.26
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTAATATTTATTTATATTA
Found at i:1597648 original size:32 final size:32
Alignment explanation
Indices: 1597612--1597817 Score: 113
Period size: 32 Copynumber: 6.6 Consensus size: 32
1597602 TTATAAGCAT
* *
1597612 CAAACTTAGAACATAACACTT-TCAAAA-CTCAA
1 CAAACTTAAAACATAACAATTCT-AAAATC-CAA
* *
1597644 CAAACTTAAAATATAACAATTCTAATATCCAA
1 CAAACTTAAAACATAACAATTCTAAAATCCAA
** * * *
1597676 CAAACTTAAAACATAATTATTCCAATACCCAA
1 CAAACTTAAAACATAACAATTCTAAAATCCAA
* * * * * * *
1597708 TAAACATAAAACATAATAGTTTTAATATACAA
1 CAAACTTAAAACATAACAATTCTAAAATCCAA
* *
1597740 CAAACTTAAAAACATAATAA---TAATATCCAA
1 CAAACTT-AAAACATAACAATTCTAAAATCCAA
* * * *
1597770 CAATCATAAAACATAATAATT-T--CATCCAA
1 CAAACTTAAAACATAACAATTCTAAAATCCAA
* *
1597799 CAAAGTTAAAACATTACAA
1 CAAACTTAAAACATAACAA
1597818 GTTCACTGTT
Statistics
Matches: 140, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
29 32 0.23
30 14 0.10
31 1 0.01
32 80 0.57
33 13 0.09
ACGTcount: A:0.54, C:0.19, G:0.01, T:0.26
Consensus pattern (32 bp):
CAAACTTAAAACATAACAATTCTAAAATCCAA
Found at i:1597808 original size:29 final size:29
Alignment explanation
Indices: 1597641--1597812 Score: 130
Period size: 32 Copynumber: 5.6 Consensus size: 29
1597631 TTTCAAAACT
* *
1597641 CAACAAACTTAAAATATAACAATTCTAATATC
1 CAACAAACTTAAAACATAATAA---TAATATC
* *
1597673 CAACAAACTTAAAACATAATTATTCCAATACC
1 CAACAAACTTAAAACATAA-TAAT--AATATC
* * * *
1597705 CAATAAACATAAAACATAATAGTTTTAATATA
1 CAACAAACTTAAAACATAATA---ATAATATC
1597737 CAACAAACTTAAAAACATAATAATAATATC
1 CAACAAACTT-AAAACATAATAATAATATC
* * *
1597767 CAACAATCATAAAACATAATAAT-TTCATC
1 CAACAAACTTAAAACATAATAATAAT-ATC
*
1597796 CAACAAAGTTAAAACAT
1 CAACAAACTTAAAACAT
1597813 TACAAGTTCA
Statistics
Matches: 114, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.01
29 30 0.26
30 15 0.13
31 2 0.02
32 52 0.46
33 12 0.11
34 2 0.02
ACGTcount: A:0.55, C:0.18, G:0.01, T:0.26
Consensus pattern (29 bp):
CAACAAACTTAAAACATAATAATAATATC
Found at i:1598840 original size:17 final size:17
Alignment explanation
Indices: 1598820--1598857 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1598810 TTAATAGAGT
*
1598820 TAGTTCATTGATCAAAC
1 TAGTTCATTCATCAAAC
*
1598837 TAGTTCATTCATTAAAC
1 TAGTTCATTCATCAAAC
1598854 TAGT
1 TAGT
1598858 GTATTAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (17 bp):
TAGTTCATTCATCAAAC
Found at i:1603261 original size:12 final size:12
Alignment explanation
Indices: 1603244--1603285 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1603234 CTAATGATGG
1603244 AATAATAAAATA
1 AATAATAAAATA
*
1603256 AATAATAAGATA
1 AATAATAAAATA
*
1603268 AATAATGAAATGA
1 AATAATAAAAT-A
1603281 AATAA
1 AATAA
1603286 AAGGAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:1603336 original size:22 final size:21
Alignment explanation
Indices: 1603310--1603350 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1603300 GCTACGGAAT
1603310 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
*
1603332 TTGATGGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
1603351 AATGGTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:1607514 original size:29 final size:27
Alignment explanation
Indices: 1607480--1607572 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 27
1607470 TGGCTCTGCT
1607480 TTCTTTTTGAATTTCTTATTTTTCTTTTC
1 TTCTTTTTGAATTTCTT-TTTTT-TTTTC
1607509 TTCTTTTCTGAATTCTTCTTCTTTTTGTCTTTC
1 TTCTTTT-TGAA-T-TTCTT-TTTTT-T-TTTC
*
1607542 TTTCTTTTTAAATTTCTTTTTATTTTTTC
1 -TTCTTTTTGAATTTCTTTTT-TTTTTTC
1607571 TT
1 TT
1607573 TGCACGCCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
28 2 0.04
29 11 0.20
30 8 0.15
31 8 0.15
32 12 0.22
33 7 0.13
34 7 0.13
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (27 bp):
TTCTTTTTGAATTTCTTTTTTTTTTTC
Found at i:1607542 original size:15 final size:14
Alignment explanation
Indices: 1607480--1607550 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 14
1607470 TGGCTCTGCT
*
1607480 TTCTTTTTGAATTTC
1 TTCTTTTTG-TTTTC
* *
1607495 TTATTTTTCTTTTC
1 TTCTTTTTGTTTTC
1607509 TTCTTTTCTGAATTCTTC
1 TTCTTTT-TG--TT-TTC
1607527 TTCTTTTTGTCTTTC
1 TTCTTTTTGT-TTTC
1607542 TTTCTTTTT
1 -TTCTTTTT
1607551 AAATTTCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.22
15 12 0.27
16 9 0.20
17 4 0.09
18 10 0.22
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (14 bp):
TTCTTTTTGTTTTC
Found at i:1607559 original size:34 final size:32
Alignment explanation
Indices: 1607492--1607573 Score: 87
Period size: 34 Copynumber: 2.5 Consensus size: 32
1607482 CTTTTTGAAT
*
1607492 TTCTTA-TTTTTCTTTTCTTCTTTTCTGAATTC
1 TTCTTATTTTTTC-TTTCTTCTTTTCTAAATTC
*
1607524 TTCTTCTTTTTGTCTTTCTTTCTTTT-TAAATTTC
1 TTCTTATTTTT-TCTTTC-TTCTTTTCTAAA-TTC
*
1607558 TTTTTATTTTTTCTTT
1 TTCTTATTTTTTCTTT
1607574 GCACGCCAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
32 5 0.12
33 16 0.38
34 21 0.50
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (32 bp):
TTCTTATTTTTTCTTTCTTCTTTTCTAAATTC
Found at i:1607573 original size:29 final size:30
Alignment explanation
Indices: 1607478--1607573 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 30
1607468 CTTGGCTCTG
*
1607478 CTTTCTTTTTGAATTTCTTATTTTTCTTTT
1 CTTTCTTTTTAAATTTCTTATTTTTCTTTT
* * *
1607508 C-TTCTTTTCTGAATTCTTCTTCTTTTTGTCTTT
1 CTTTCTTTT-T-AAAT-TTCTTATTTTTCT-TTT
1607541 CTTTCTTTTTAAATTTCTT-TTTATT-TTTT
1 CTTTCTTTTTAAATTTCTTATTT-TTCTTTT
1607570 CTTT
1 CTTT
1607574 GCACGCCAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
29 14 0.25
30 6 0.11
31 9 0.16
32 14 0.25
33 5 0.09
34 7 0.13
ACGTcount: A:0.09, C:0.16, G:0.03, T:0.72
Consensus pattern (30 bp):
CTTTCTTTTTAAATTTCTTATTTTTCTTTT
Found at i:1616655 original size:23 final size:24
Alignment explanation
Indices: 1616612--1616664 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1616602 TTTCTTTCTT
1616612 TTTCTTCTTTTCAAGTGCTTTCAA
1 TTTCTTCTTTTCAAGTGCTTTCAA
* * *
1616636 TTTCTTCTTTT-GAGTGCTTTGAT
1 TTTCTTCTTTTCAAGTGCTTTCAA
1616659 TTTCTT
1 TTTCTT
1616665 TGCTGGATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTCAAGTGCTTTCAA
Found at i:1620319 original size:24 final size:25
Alignment explanation
Indices: 1620283--1620330 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1620273 GTGAACTATA
1620283 ATATATAATAATAACTTA-TATCAC
1 ATATATAATAATAACTTATTATCAC
*
1620307 ATAT-TAATGAATAAGTTATTATCA
1 ATATATAAT-AATAACTTATTATCA
1620331 TAATAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 12 0.57
25 5 0.24
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
ATATATAATAATAACTTATTATCAC
Found at i:1624944 original size:11 final size:11
Alignment explanation
Indices: 1624928--1624966 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1624918 GATACATTTA
1624928 AAATTTAGCCT
1 AAATTTAGCCT
*
1624939 AAATTTATCC-
1 AAATTTAGCCT
*
1624949 AATTTTAGCCT
1 AAATTTAGCCT
1624960 AAATTTA
1 AAATTTA
1624967 TCCAATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (11 bp):
AAATTTAGCCT
Found at i:1624956 original size:21 final size:21
Alignment explanation
Indices: 1624931--1624977 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1624921 ACATTTAAAA
1624931 TTTAGCCTAAATTTATCCAAT
1 TTTAGCCTAAATTTATCCAAT
1624952 TTTAGCCTAAATTTATCCAAT
1 TTTAGCCTAAATTTATCCAAT
1624973 TTTAG
1 TTTAG
1624978 TCTACATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (21 bp):
TTTAGCCTAAATTTATCCAAT
Found at i:1628114 original size:17 final size:17
Alignment explanation
Indices: 1628094--1628133 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1628084 AATAAGCTAC
* *
1628094 TTCATTCATACATTTAG
1 TTCATTAATACAGTTAG
*
1628111 TTCATTAATAGAGTTAG
1 TTCATTAATACAGTTAG
1628128 TTCATT
1 TTCATT
1628134 GATCAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
TTCATTAATACAGTTAG
Found at i:1628145 original size:17 final size:17
Alignment explanation
Indices: 1628125--1628174 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1628115 TTAATAGAGT
*
1628125 TAGTTCATTGATCAAAC
1 TAGTTCATTAATCAAAC
* *
1628142 TAGTTCATTCATTAAAC
1 TAGTTCATTAATCAAAC
*
1628159 TAGTGCATTAATCAAA
1 TAGTTCATTAATCAAA
1628175 ATAACTCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:1631709 original size:18 final size:17
Alignment explanation
Indices: 1631668--1631701 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1631658 CATTGTTTGC
1631668 TGTTGATTATAATGTTA
1 TGTTGATTATAATGTTA
*
1631685 TGATTGATTGTAATGTT
1 TG-TTGATTATAATGTT
1631702 GTTGTTGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.13
18 13 0.87
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (17 bp):
TGTTGATTATAATGTTA
Found at i:1638341 original size:16 final size:17
Alignment explanation
Indices: 1638320--1638353 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1638310 TCAGATTTTT
*
1638320 TAAAAATATATTTTTAA
1 TAAAATTATATTTTTAA
*
1638337 TAAAATTTTATTTTTAA
1 TAAAATTATATTTTTAA
1638354 GTGAGAATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAATTATATTTTTAA
Found at i:1638659 original size:10 final size:10
Alignment explanation
Indices: 1638640--1638674 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
1638630 TATCAAGTTC
*
1638640 TCAAGGCATA
1 TCAAGACATA
1638650 TCAAGACATA
1 TCAAGACATA
1638660 TCAAGACATA
1 TCAAGACATA
1638670 TCAAG
1 TCAAG
1638675 TCGACCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (10 bp):
TCAAGACATA
Found at i:1639140 original size:21 final size:21
Alignment explanation
Indices: 1639116--1639159 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1639106 AGCGTTGCCT
1639116 TCCGATATACCCGCAATAATG
1 TCCGATATACCCGCAATAATG
* ** *
1639137 TCCGTTATGGCCGCAATAGTG
1 TCCGATATACCCGCAATAATG
1639158 TC
1 TC
1639160 TGCTATGTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (21 bp):
TCCGATATACCCGCAATAATG
Found at i:1639166 original size:21 final size:21
Alignment explanation
Indices: 1639126--1639166 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1639116 TCCGATATAC
*
1639126 CCGCAATAATGTCCGTTATGG
1 CCGCAATAATGTCCGCTATGG
* *
1639147 CCGCAATAGTGTCTGCTATG
1 CCGCAATAATGTCCGCTATG
1639167 TCTGAAATCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
CCGCAATAATGTCCGCTATGG
Found at i:1644945 original size:65 final size:64
Alignment explanation
Indices: 1644860--1645011 Score: 207
Period size: 65 Copynumber: 2.4 Consensus size: 64
1644850 CCTGGGGTGT
* * * * * *
1644860 ATCGGTACACTAATTACATTCAATGTTTTAA-AAGAGCCAAGAGTGTATCGATGCATGGTCTATG
1 ATCGGTACACAAAATGCATTCAATGTTTCAATAA-AACCAAGAGTGCATCGATGCATGGT-TATG
1644924 C
64 C
* *
1644925 ATCGGTACATAAAATGCATTCAATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGTTATGC
1 ATCGGTACACAAAATGCATTCAATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGTTATGC
1644989 ATCGGTACACAAAATGCATTCAA
1 ATCGGTACACAAAATGCATTCAA
1645012 ATTAGGGTGT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 27 0.35
65 48 0.62
66 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGGTACACAAAATGCATTCAATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGTTATGC
Found at i:1647659 original size:44 final size:44
Alignment explanation
Indices: 1647585--1647699 Score: 137
Period size: 44 Copynumber: 2.6 Consensus size: 44
1647575 GAGTGTATCG
* * *
1647585 GTACAC-TGCATAGTGTATCGATGCACATTC-AAGGAATGCATTA
1 GTACACTTTCATAGTGTATCGATGCACATTCAAAGG-ATGAATCA
* * *
1647628 GTGCACCTTT-ATAGTGTATCGATGCATATTCAAAGGATGAATCG
1 GTACA-CTTTCATAGTGTATCGATGCACATTCAAAGGATGAATCA
1647672 GTACACTTTCATAGTGTATCGATGCACA
1 GTACACTTTCATAGTGTATCGATGCACA
1647700 GTGCAGAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
43 8 0.13
44 47 0.78
45 5 0.08
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
GTACACTTTCATAGTGTATCGATGCACATTCAAAGGATGAATCA
Found at i:1654336 original size:21 final size:21
Alignment explanation
Indices: 1654307--1654359 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1654297 ATTCTGACTA
1654307 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1654328 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1654349 TCGCAATGCGA
1 TCGCATTGCGA
1654360 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1654374 original size:20 final size:20
Alignment explanation
Indices: 1654349--1654482 Score: 178
Period size: 20 Copynumber: 6.7 Consensus size: 20
1654339 TTTTCCTAAT
1654349 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1654369 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
** *
1654390 TCGCAATTAGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1654410 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1654430 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1654450 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1654470 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1654483 CTGACTACCG
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 84 0.87
21 13 0.13
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1654474 original size:60 final size:61
Alignment explanation
Indices: 1654349--1654482 Score: 207
Period size: 60 Copynumber: 2.2 Consensus size: 61
1654339 TTTTCCTAAT
** *
1654349 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAATTAGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATTACGAAAATCGCAATGAGATTACGTAAA
* * *
1654410 TCGCAATGCGAATACGTAAATCGCAATGCG-ATTACGTAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATTACGAAAATCGCAATGAGATTACGTAAA
1654470 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1654483 CTGACTACCG
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
60 38 0.57
61 29 0.43
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (61 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATTACGAAAATCGCAATGAGATTACGTAAA
Found at i:1654495 original size:40 final size:39
Alignment explanation
Indices: 1654349--1654502 Score: 132
Period size: 40 Copynumber: 3.8 Consensus size: 39
1654339 TTTTCCTAAT
* * * ** *
1654349 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATTACGT-AACCGCAATGCG-ATTACGTAAA
** * *
1654390 TCGCAATTAGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGT-AACCGCAATGCGATTACGTAAA
*
1654430 TCGCAATGCGATTACGTAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGT-AACCGCAATGCGATTACGTAAA
1654470 TCGCAATGCGAATCTGAC-T-ACCGCAATGCGATT
1 TCGCAATGCG-AT-T-ACGTAACCGCAATGCGATT
1654503 TACATAGCGT
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
40 66 0.67
41 28 0.29
42 2 0.02
43 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (39 bp):
TCGCAATGCGATTACGTAACCGCAATGCGATTACGTAAA
Found at i:1654703 original size:22 final size:22
Alignment explanation
Indices: 1654678--1654739 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
1654668 GGCGATATCC
1654678 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1654700 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
* *
1654718 GTCTCCATCTCCGACAAAATCA
1 GTCCCCATCTCCGACGAAATCA
1654740 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.31, C:0.39, G:0.13, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1655192 original size:20 final size:20
Alignment explanation
Indices: 1655076--1655184 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
1655066 CGATTCTGTC
*
1655076 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
** ** **
1655095 GTTGCGATAGTCAAATTCAC
1 GTTGCGATTTTCATTTTCGT
**
1655115 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1655135 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1655155 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
1655175 GTTACGATTT
1 GTTGCGATTT
1655185 AAAGTTTCAG
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 11 0.14
20 67 0.86
ACGTcount: A:0.16, C:0.17, G:0.21, T:0.47
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:1657082 original size:20 final size:20
Alignment explanation
Indices: 1657057--1657140 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
1657047 ATAATAGTTT
*
1657057 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
1657077 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1657093 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1657111 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1657131 ACTATCGCAA
1 ACTATCGCAA
1657141 CGAAAGAATC
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.13
16 4 0.08
17 4 0.08
18 3 0.06
20 35 0.66
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1657119 original size:54 final size:54
Alignment explanation
Indices: 1657057--1657161 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
1657047 ATAATAGTTT
*
1657057 ACTATCGCAATGCAAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAAATG
1 ACTATCGCAATGCAAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAAATG
* **
1657111 ACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCGAAA
1 ACTATCGCAATGCAAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAA
1657162 TGAAAATCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (54 bp):
ACTATCGCAATGCAAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAAATG
Found at i:1657319 original size:20 final size:20
Alignment explanation
Indices: 1657185--1657326 Score: 154
Period size: 20 Copynumber: 7.5 Consensus size: 20
1657175 GTGATTCTCT
**
1657185 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
* *
1657205 CATTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
*
1657225 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
**
1657245 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
*
1657264 CGTTGCGAT--TC----TCT
1 CGTTGCGATAGTCATTTTCG
1657278 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1657298 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1657318 CGTTACGAT
1 CGTTGCGAT
1657327 TTTAAGTTTC
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.10
16 2 0.02
17 2 0.02
19 14 0.13
20 76 0.72
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1657851 original size:18 final size:19
Alignment explanation
Indices: 1657812--1657853 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1657802 CTCACCTGTC
1657812 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1657833 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1657851 ATC
1 ATC
1657854 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1657914 original size:42 final size:42
Alignment explanation
Indices: 1657807--1657928 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
1657797 CCTGACTCAC
* * *
1657807 CTGTCATCGTTCAAGAGG--CCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCCCT-CCC-AACATTCAAGAGGCCA
* ** *
1657849 CTATCATCCCTCAAGA-GTCCCCTCCCACCATTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGT-CCCTCCCAACATTCAAGAGGCCA
* * *
1657891 CTGTCATCGTTGAAGAGGTCCCTCTCAACATTCTAGAG
1 CTGTCATCGTTCAAGAGGTCCCTCCCAACATTCAAGAG
1657929 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
41 1 0.02
42 54 0.86
43 5 0.08
44 3 0.05
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGTCCCTCCCAACATTCAAGAGGCCA
Found at i:1659289 original size:14 final size:14
Alignment explanation
Indices: 1659270--1659305 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1659260 ATTGTTTAAT
1659270 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1659284 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1659298 TGATTTGT
1 TGATTTGT
1659306 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1659456 original size:33 final size:33
Alignment explanation
Indices: 1659406--1659492 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
1659396 AAAACAGACT
* **
1659406 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
1659440 ATCGCAATGCGAAATGAAAATTGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1659473 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCG-AAATGAAA
1659493 TTTTCATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 30 0.64
34 17 0.36
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1659545 original size:19 final size:19
Alignment explanation
Indices: 1659492--1659585 Score: 117
Period size: 19 Copynumber: 5.2 Consensus size: 19
1659482 CGAAAATGAA
1659492 ATTTTCATTTTCGCATTGCG
1 ATTTTCA-TTTCGCATTGCG
*
1659512 A--TTCA-CTCG--TTGCG
1 ATTTTCATTTCGCATTGCG
*
1659526 ATTTTCATTTCGTATTGCG
1 ATTTTCATTTCGCATTGCG
*
1659545 ATTTTCATTTCACATTGCG
1 ATTTTCATTTCGCATTGCG
1659564 ATTTTCATTTCGCATTGCG
1 ATTTTCATTTCGCATTGCG
1659583 ATT
1 ATT
1659586 CTCTCGTTGT
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.11
17 3 0.05
18 4 0.06
19 43 0.67
20 1 0.02
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.48
Consensus pattern (19 bp):
ATTTTCATTTCGCATTGCG
Found at i:1659619 original size:20 final size:19
Alignment explanation
Indices: 1659596--1659682 Score: 93
Period size: 20 Copynumber: 4.4 Consensus size: 19
1659586 CTCTCGTTGT
* *
1659596 GATAGTCATTTCCGCGTTAC
1 GATAGTCATTT-CGCATTGC
*
1659616 GATAGTCAATTCGCATTGC
1 GATAGTCATTTCGCATTGC
* *
1659635 AATAGTCATTTCCGTATTGC
1 GATAGTCATTT-CGCATTGC
*
1659655 GATAGTCATATTCGCGTTGC
1 GATAGTCAT-TTCGCATTGC
1659675 GATAGTCA
1 GATAGTCA
1659683 AATGAATGTC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 15 0.27
20 39 0.70
21 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (19 bp):
GATAGTCATTTCGCATTGC
Found at i:1659658 original size:39 final size:40
Alignment explanation
Indices: 1659597--1659682 Score: 120
Period size: 39 Copynumber: 2.2 Consensus size: 40
1659587 TCTCGTTGTG
*
1659597 ATAGTCATTTCCGCGTTACGATAGTCA-ATTCGCATTGCA
1 ATAGTCATTTCCGCATTACGATAGTCATATTCGCATTGCA
* * * *
1659636 ATAGTCATTTCCGTATTGCGATAGTCATATTCGCGTTGCG
1 ATAGTCATTTCCGCATTACGATAGTCATATTCGCATTGCA
1659676 ATAGTCA
1 ATAGTCA
1659683 AATGAATGTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 24 0.59
40 17 0.41
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (40 bp):
ATAGTCATTTCCGCATTACGATAGTCATATTCGCATTGCA
Found at i:1661903 original size:3 final size:3
Alignment explanation
Indices: 1661895--1661924 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1661885 CTTTGGGGAT
1661895 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1661925 AGTGTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1663025 original size:20 final size:20
Alignment explanation
Indices: 1663002--1663062 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1662992 TTGCGATAGT
* *
1663002 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
1663022 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
1663042 C-GTATTCGCATTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
1663062 C
1 C
1663063 GTATTTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTTA
Found at i:1663063 original size:20 final size:20
Alignment explanation
Indices: 1663012--1663126 Score: 97
Period size: 20 Copynumber: 5.3 Consensus size: 20
1663002 CAGAATCTCG
1663012 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
1663032 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1663052 TTGCGATTTACGTATTTATGTAATCGCA
1 TTGCGATTTACG----TA--T--TCGCA
* ** *
1663080 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
1663101 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1663121 TTGCGA
1 TTGCGA
1663127 ATTAGGAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.01
20 46 0.60
21 10 0.13
23 1 0.01
24 2 0.03
25 1 0.01
26 1 0.01
28 11 0.14
29 4 0.05
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1663147 original size:21 final size:21
Alignment explanation
Indices: 1663123--1663168 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1663113 TATTCGCATT
1663123 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1663144 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1663165 GCGA
1 GCGA
1663169 TAGTCAGAAT
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:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1666131 original size:82 final size:80
Alignment explanation
Indices: 1665903--1666120 Score: 265
Period size: 81 Copynumber: 2.7 Consensus size: 80
1665893 AAAATGGGCT
* ** * * *
1665903 TTTAGCGACGTTTTTTGAACAAACGGTGGTAAATACTCGTACTTTAGTGGTGTTTTCATAAAACG
1 TTTAGCGGCG-TTTTTGAACAAACGCCGCTAAAAACTCGTACTTTAGTGGCGTTTTCATAAAACG
*
1665968 CCGCTAATTACTATAC
65 CCACTAATTACTATAC
* * ** * *
1665984 TTTAGCGGCGTTTTAAGCACAAACGCCGCTAAAGGCCCGTACATTAGTGGCGTTTTCATATAAAC
1 TTTAGCGGCGTTTT-TGAACAAACGCCGCTAAAAACTCGTACTTTAGTGGCGTTTTCATA-AAAC
*
1666049 GCCACTAGTTACTATAC
64 GCCACTAATTACTATAC
* *
1666066 TTTAGCGGCGTTTTTGTACAAACGCCGCTAAAAACTCATACTTTAGTGGCGTTTT
1 TTTAGCGGCGTTTTTGAACAAACGCCGCTAAAAACTCGTACTTTAGTGGCGTTTT
1666121 AAACACAAAC
Statistics
Matches: 115, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 4 0.03
81 78 0.68
82 33 0.29
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (80 bp):
TTTAGCGGCGTTTTTGAACAAACGCCGCTAAAAACTCGTACTTTAGTGGCGTTTTCATAAAACGC
CACTAATTACTATAC
Found at i:1666150 original size:42 final size:42
Alignment explanation
Indices: 1665932--1666224 Score: 215
Period size: 42 Copynumber: 7.1 Consensus size: 42
1665922 CAAACGGTGG
* * * *
1665932 TAAATACTCGTACTTTAGTGGTGTTTTCA-TA-AAACGCCGC
1 TAAATACTTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGC
* * *
1665972 TAATTAC-TATACTTTAGCGGCGTTTTAAGCACAAACGCCGC
1 TAAATACTTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGC
** ** * * * * *
1666013 TAAAGGCCCGTACATTAGTGGCGTTTTCA-TATAAACGCCAC
1 TAAATACTTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGC
** * * * *
1666054 TAGTTAC-TATACTTTAGCGGCGTTTT-TGTACAAACGCCGC
1 TAAATACTTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGC
* ** * *
1666094 TAAAAACTCATACTTTAGTGGCGTTTTAAACACAAACGTCGC
1 TAAATACTTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGC
* * **
1666136 TAAATGCTTGTACTTTAGTAGCGTTTTAAGCACAAACTTCGC
1 TAAATACTTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGC
** *
1666178 TAAATAAATGTACTTTAGTGGCGTTTGT-A-CATAAACGCCGC
1 TAAATACTTGTACTTTAGTGGCGTTT-TAAGCACAAACGCCGC
1666219 TAAATA
1 TAAATA
1666225 TTTAGTCTTT
Statistics
Matches: 194, Mismatches: 52, Indels: 13
0.75 0.20 0.05
Matches are distributed among these distances:
39 16 0.08
40 36 0.19
41 57 0.29
42 84 0.43
43 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (42 bp):
TAAATACTTGTACTTTAGTGGCGTTTTAAGCACAAACGCCGC
Found at i:1666205 original size:123 final size:120
Alignment explanation
Indices: 1665941--1666222 Score: 269
Period size: 123 Copynumber: 2.3 Consensus size: 120
1665931 GTAAATACTC
* * ** *
1665941 GTACTTTAGTGGTGTTT-TCATAAAACGCCGCTAATTACTATACTTTAGCGGCGTTTTAAGCACA
1 GTACTTTAGTGGCGTTTGT-A-CAAACGCCGCTAAAAACTATACTTTAGCGGCGTTTTAAACACA
* * * * * * *
1666005 AACGCCGCTAAAGGCCCGTACATTAGTGGCGTTTTCATATAAACGCCACTAGTTACT
64 AACGCCGCTAAAGGCCCGTACATTAGTAGCGTTTTAACACAAACGCCACTAATAAAT
* * *
1666062 ATACTTTAGCGGCGTTTTTGTACAAACGCCGCTAAAAACTCATACTTTAGTGGCGTTTTAAACAC
1 GTACTTTAGTGGCG--TTTGTACAAACGCCGCTAAAAACT-ATACTTTAGCGGCGTTTTAAACAC
* * ** * ** *
1666127 AAACGTCGCTAAATGCTTGTACTTTAGTAGCGTTTTAAGCACAAACTTCGCTAAATAAAT
63 AAACGCCGCTAAAGGCCCGTACATTAGTAGCGTTTTAA-CACAAACGCCACT-AATAAAT
1666187 GTACTTTAGTGGCGTTTGTACATAAACGCCGCTAAA
1 GTACTTTAGTGGCGTTTGTAC--AAACGCCGCTAAA
1666223 TATTTAGTCT
Statistics
Matches: 128, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
121 11 0.09
122 15 0.12
123 64 0.50
124 9 0.07
125 29 0.23
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (120 bp):
GTACTTTAGTGGCGTTTGTACAAACGCCGCTAAAAACTATACTTTAGCGGCGTTTTAAACACAAA
CGCCGCTAAAGGCCCGTACATTAGTAGCGTTTTAACACAAACGCCACTAATAAAT
Found at i:1669324 original size:43 final size:43
Alignment explanation
Indices: 1669235--1669497 Score: 359
Period size: 43 Copynumber: 6.1 Consensus size: 43
1669225 CAAATGATAT
* * * * *
1669235 TAAATGCATAGTCAATAGC-GCGTTTGTAAAGGA-AAACGTCGT
1 TAAATACACAGTCAATAGCGGCGTTTATAAA-GACAAACGCCGC
* * **
1669277 TAAATACACAGTCAATAACGGCATTTATAAAGACAAACGCTAC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
* *
1669320 TAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAACGCCGC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
1669363 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
* * * *
1669406 TAAATACACAGTCAATAGCAGCGTTTATAAAGACAAATGCAGT
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
*
1669449 TAAATACACAGTCAATAGCGGCATTTATAAAGACAAACGCCGC
1 TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
1669492 TAAATA
1 TAAATA
1669498 TATTTGTCTT
Statistics
Matches: 193, Mismatches: 26, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
42 18 0.09
43 175 0.91
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.21
Consensus pattern (43 bp):
TAAATACACAGTCAATAGCGGCGTTTATAAAGACAAACGCCGC
Found at i:1673550 original size:20 final size:19
Alignment explanation
Indices: 1673511--1673564 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1673501 TTAGCCAGTT
1673511 TTGGTATCGATAAC-AAGGG
1 TTGGTATCGAT-ACTAAGGG
1673530 TTGGTATCGATACTGAAGGG
1 TTGGTATCGATACT-AAGGG
* *
1673550 TGGGTATCAATACTA
1 TTGGTATCGATACTA
1673565 TAGGACTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 2 0.06
19 12 0.39
20 17 0.55
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGGTATCGATACTAAGGG
Found at i:1676577 original size:15 final size:14
Alignment explanation
Indices: 1676542--1676582 Score: 66
Period size: 13 Copynumber: 2.9 Consensus size: 14
1676532 TTAAATGGAA
1676542 ATAAGAAATGAAAG
1 ATAAGAAATGAAAG
1676556 A-AAGAAATGAAATG
1 ATAAGAAATGAAA-G
1676570 ATAAGAAATGAAA
1 ATAAGAAATGAAA
1676583 AGGGATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.44
14 3 0.12
15 11 0.44
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.15
Consensus pattern (14 bp):
ATAAGAAATGAAAG
Found at i:1680477 original size:17 final size:17
Alignment explanation
Indices: 1680455--1680488 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1680445 GCATCATCTA
*
1680455 TAAGAAATGGTTATGGT
1 TAAGAAATGGATATGGT
1680472 TAAGAAATGGATATGGT
1 TAAGAAATGGATATGGT
1680489 AAAAGTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.32
Consensus pattern (17 bp):
TAAGAAATGGATATGGT
Found at i:1688712 original size:20 final size:21
Alignment explanation
Indices: 1688666--1688725 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
1688656 TTCCCCTGTG
1688666 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1688689 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1688709 GGGGGGATCGATTCCCT
1 GGGGGAATCGGTTCCCT
1688726 ATGCACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1700450 original size:21 final size:20
Alignment explanation
Indices: 1700422--1700460 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1700412 CATTGCCGAA
*
1700422 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
1700442 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
1700461 GACCTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:1705202 original size:13 final size:13
Alignment explanation
Indices: 1705184--1705218 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
1705174 TTCCTTGTTT
1705184 TCTTTTTCTTCAA
1 TCTTTTTCTTCAA
1705197 TCTTTTTTCTTCAA
1 TC-TTTTTCTTCAA
1705211 T-TTTTTCT
1 TCTTTTTCT
1705219 AAATTTCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.33
13 2 0.10
14 12 0.57
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (13 bp):
TCTTTTTCTTCAA
Found at i:1712416 original size:19 final size:20
Alignment explanation
Indices: 1712392--1712440 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1712382 TATATATAAG
1712392 TATTTATATA-GTGTAT-GTA
1 TATTTATATATGT-TATAGTA
1712411 TATTTATATATGTTATAGTA
1 TATTTATATATGTTATAGTA
1712431 TATATTATAT
1 TAT-TTATAT
1712441 TTGAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 13 0.48
20 8 0.30
21 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (20 bp):
TATTTATATATGTTATAGTA
Found at i:1712438 original size:12 final size:11
Alignment explanation
Indices: 1712380--1712647 Score: 74
Period size: 11 Copynumber: 23.6 Consensus size: 11
1712370 TAAGCATTAA
*
1712380 TATATATATAAG
1 TATATATAT-AT
* *
1712392 TATTTATATAG
1 TATATATATAT
* *
1712403 TGTATGTATAT
1 TATATATATAT
*
1712414 T-TATATATGT
1 TATATATATAT
1712424 TATAGTATATAT
1 TATA-TATATAT
* *
1712436 TATATTTGA-AA
1 TATATAT-ATAT
* *
1712447 AATATATATAA
1 TATATATATAT
*
1712458 TATATTACATAGT
1 TATA-TATATA-T
1712471 GTATTATATATAT
1 -TA-TATATATAT
1712484 TATAGTATATTAT
1 TATA-TATA-TAT
* *
1712497 T-TTTAAATATT
1 TATATATATA-T
1712508 TATATATAATAGT
1 TATATAT-ATA-T
*
1712521 TGATAT-TATTT
1 T-ATATATATAT
*
1712532 TAAAATATATAT
1 T-ATATATATAT
1712544 TATAT-TATCAT
1 TATATATAT-AT
* *
1712555 T-TAAAAATAT
1 TATATATATAT
*
1712565 ATAGTATGTATATT
1 -TA-TATATATA-T
*
1712579 TAAATATATAT
1 TATATATATAT
*
1712590 TAT-TATAT-G
1 TATATATATAT
*
1712599 TATATGTATAT
1 TATATATATAT
*
1712610 GTATATGTATAT
1 -TATATATATAT
1712622 T-TAT-TATAT
1 TATATATATAT
1712631 TAT-TATATTAT
1 TATATATA-TAT
1712642 TA-ATAT
1 TATATAT
1712648 TAATATCAAT
Statistics
Matches: 191, Mismatches: 37, Indels: 57
0.67 0.13 0.20
Matches are distributed among these distances:
9 10 0.05
10 33 0.17
11 58 0.30
12 58 0.30
13 18 0.09
14 12 0.06
15 2 0.01
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (11 bp):
TATATATATAT
Found at i:1712527 original size:33 final size:31
Alignment explanation
Indices: 1712472--1712548 Score: 91
Period size: 33 Copynumber: 2.4 Consensus size: 31
1712462 TTACATAGTG
* *
1712472 TATTATATATATTATAGTATATTATTTTTAAA
1 TATT-TATATATAATAGTATATTATTTTAAAA
1712504 TATTTATATATAATAGTTGATATTATTTTAAAA
1 TATTTATATATAATAG-T-ATATTATTTTAAAA
*
1712537 TATATATTATAT
1 TATTTA-TATAT
1712549 TATCATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 11 0.28
32 5 0.13
33 18 0.46
34 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (31 bp):
TATTTATATATAATAGTATATTATTTTAAAA
Found at i:1712540 original size:25 final size:26
Alignment explanation
Indices: 1712503--1712578 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 26
1712493 TTATTTTTAA
*
1712503 ATATTT-ATATATAATAGTTGATATT
1 ATATTTAAAATATAATAGTTGATATT
1712528 AT-TTTAAAATAT-ATA-TT-ATATT
1 ATATTTAAAATATAATAGTTGATATT
1712550 ATCATTTAAAA-ATATATAGTATGTATATT
1 AT-ATTTAAAATATA-ATAGT-TG-ATATT
1712579 TAAATATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
22 7 0.17
23 4 0.10
24 13 0.32
25 10 0.24
26 1 0.02
27 1 0.02
29 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (26 bp):
ATATTTAAAATATAATAGTTGATATT
Found at i:1712579 original size:23 final size:24
Alignment explanation
Indices: 1712527--1712603 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
1712517 TAGTTGATAT
* * *
1712527 TATTTTAAAATATATATTATATTA
1 TATTTAAAAATATATAGTATAGTA
1712551 TCATTTAAAAATATATAGTAT-GTA
1 T-ATTTAAAAATATATAGTATAGTA
* *
1712575 TATTTAAATATATATTATTATATGTA
1 TATTTAAAAATATA-TAGTATA-GTA
1712601 TAT
1 TAT
1712604 GTATATGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 12 0.27
24 9 0.20
25 17 0.39
26 6 0.14
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (24 bp):
TATTTAAAAATATATAGTATAGTA
Found at i:1712589 original size:25 final size:24
Alignment explanation
Indices: 1712523--1712603 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 24
1712513 ATAATAGTTG
1712523 ATAT-TAT-TTTAAAATATATATT
1 ATATGTATATTTAAAATATATATT
1712545 ATAT-TATCATTTAAAA-ATATA-T
1 ATATGTAT-ATTTAAAATATATATT
1712567 AGTATGTATATTTAAATATATATTATT
1 A-TATGTATATTTAAA-ATATA-TATT
1712594 ATATGTATAT
1 ATATGTATAT
1712604 GTATATGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
22 9 0.18
23 15 0.29
24 11 0.22
25 3 0.06
26 11 0.22
27 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (24 bp):
ATATGTATATTTAAAATATATATT
Done.