Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 6 of 113
Found at i:1520630 original size:18 final size:17
Alignment explanation
Indices: 1520602--1520655 Score: 74
Period size: 18 Copynumber: 3.2 Consensus size: 17
1520592 TTAATTTACT
1520602 TAAATATTTATTAATAA
1 TAAATATTTATTAATAA
1520619 TAAATAATTTATTAATAA
1 TAAAT-ATTTATTAATAA
* *
1520637 AAAATA-TTATTTATAA
1 TAAATATTTATTAATAA
1520653 TAA
1 TAA
1520656 GATTCGAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 11 0.33
17 6 0.18
18 16 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATATTTATTAATAA
Found at i:1522093 original size:13 final size:13
Alignment explanation
Indices: 1522075--1522100 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1522065 ATTTGAGCCC
1522075 ATTTTAACCCTAT
1 ATTTTAACCCTAT
1522088 ATTTTAACCCTAT
1 ATTTTAACCCTAT
1522101 CTATTGCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTAACCCTAT
Found at i:1524426 original size:91 final size:91
Alignment explanation
Indices: 1524262--1524439 Score: 295
Period size: 91 Copynumber: 2.0 Consensus size: 91
1524252 GATGCCTTAA
* *
1524262 GCCACGATTTACTTGATATGGATGGAAGCAAATATATGCCTGAGGTAAGTCTTCTTGTTAATTTC
1 GCCACGATGTACTTGATATGGATGGAAACAAATATATGCCTGAGGTAAGTCTTCTTGTTAATTTC
*
1524327 CTGCGAAGATTTGAAGAATCTTATGT
66 CTGCGAAGATTTGAAAAATCTTATGT
*
1524353 GCCATGATGTACTTGATATGGATGGAAACAAATATATG-CTAGAGGTAAGTCTTCTTGTTAATTT
1 GCCACGATGTACTTGATATGGATGGAAACAAATATATGCCT-GAGGTAAGTCTTCTTGTTAATTT
*
1524417 GCTGCGAAGATTTGAAAAATCTT
65 CCTGCGAAGATTTGAAAAATCTT
1524440 CTTTCCTTTA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 2 0.02
91 79 0.98
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (91 bp):
GCCACGATGTACTTGATATGGATGGAAACAAATATATGCCTGAGGTAAGTCTTCTTGTTAATTTC
CTGCGAAGATTTGAAAAATCTTATGT
Found at i:1532822 original size:211 final size:203
Alignment explanation
Indices: 1532457--1532850 Score: 637
Period size: 211 Copynumber: 1.9 Consensus size: 203
1532447 CTGTGGATAT
1532457 GATATCCGCAAGATCTAATTCTAATGAGGCCGAAAAATTGGCCCGCAACATGGAAAACTTTTGGC
1 GATATCCGCAAGATCTAATTCTAATGAGGCCGAAAAATTGGCCCGCAACATGGAAAACTTTTGGC
1532522 AGAGCTGCTGGTACTACGTCCCTGCCCATTGGCTGATGTTGATGAGGCGTTCAAAATTAAAAAAC
66 AGAGCTGCTGGTACTACGTCCCTGCCCATTGGCTGATGTTGATGAGGCGTTCAAAATTAAAAAAC
*
1532587 GACGCCCACCGTGGGGTTCGAACCCACGACCACAAGGGTAAGAGCCTTGCGCTATACTAGACTGT
131 GACGCCCACCGTGGGGCTCGAACCCACGACCACAAGGGTAAGAGCCTTGCGCTATACTAGACTGT
1532652 GGGCTGTG
196 GGGCTGTG
* *
1532660 GATATCCGCAAGATCTAATTCTAATGAGGCCGAACAATTGGCCCGCAACATGGAAAACTTTTGGT
1 GATATCCGCAAGATCTAATTCTAATGAGGCCGAAAAATTGGCCCGCAACATGGAAAACTTTTGGC
* * *
1532725 AGTGCTGCTGGTAGCCTGGTACTACGTCCCTGCCCATTGGTTGATGTTGATGAGTCGTT-AAGAA
66 A--G-AGC---T-G-CTGGTACTACGTCCCTGCCCATTGGCTGATGTTGATGAGGCGTTCAA-AA
*
1532789 TTAAAAAACGACGCCCACCGTGGGGCTCGAACCCACGACCACAAGGTTAAGAGCCTTGCGCT
122 TTAAAAAACGACGCCCACCGTGGGGCTCGAACCCACGACCACAAGGGTAAGAGCCTTGCGCT
1532851 CTACCGACTG
Statistics
Matches: 175, Mismatches: 7, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
203 64 0.37
205 1 0.01
206 2 0.01
209 1 0.01
210 3 0.02
211 104 0.59
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (203 bp):
GATATCCGCAAGATCTAATTCTAATGAGGCCGAAAAATTGGCCCGCAACATGGAAAACTTTTGGC
AGAGCTGCTGGTACTACGTCCCTGCCCATTGGCTGATGTTGATGAGGCGTTCAAAATTAAAAAAC
GACGCCCACCGTGGGGCTCGAACCCACGACCACAAGGGTAAGAGCCTTGCGCTATACTAGACTGT
GGGCTGTG
Found at i:1535286 original size:114 final size:113
Alignment explanation
Indices: 1535082--1535309 Score: 348
Period size: 114 Copynumber: 2.0 Consensus size: 113
1535072 ACTATATTTG
* * *
1535082 AGTTTAGTTTAATTTTATGTTAGATTTGTCAAATTATATTTATTATTGTGATTGTAACTTATAAT
1 AGTTTAATTTAATTTTATGTTAGATTTGTCAAATTATATTTAATACTGTGATTGTAACTTATAAT
* *
1535147 AGGATAGATTGGAGGGTCTTTCAAGAGGTTGGGAGTTAGACCATTCAT
66 AGGATAGATTGGAGGGTCTTTCAAGAGGTTGGAAGTTAGAACATTCAT
* *
1535195 AGTTTAATTTAATTTTATGTTATATTTGTCAAATTGTATTTTAATACTGTGATTGTAACTTATAA
1 AGTTTAATTTAATTTTATGTTAGATTTGTCAAATTATA-TTTAATACTGTGATTGTAACTTATAA
* * * *
1535260 TAGGATGGATTGGGGGGTTTTTCAAGAGGTTGGAAGTTAGAACGTTCAT
65 TAGGATAGATTGGAGGGTCTTTCAAGAGGTTGGAAGTTAGAACATTCAT
1535309 A
1 A
1535310 TAAGTTTGTG
Statistics
Matches: 103, Mismatches: 11, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
113 35 0.34
114 68 0.66
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.43
Consensus pattern (113 bp):
AGTTTAATTTAATTTTATGTTAGATTTGTCAAATTATATTTAATACTGTGATTGTAACTTATAAT
AGGATAGATTGGAGGGTCTTTCAAGAGGTTGGAAGTTAGAACATTCAT
Found at i:1538089 original size:18 final size:19
Alignment explanation
Indices: 1538048--1538089 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1538038 AAAAAAAACC
* *
1538048 ATAAATACAAATTAATTTT
1 ATAAATACAAAATAATATT
1538067 A-AAATA-AAAATAATATT
1 ATAAATACAAAATAATATT
1538084 ATAAAT
1 ATAAAT
1538090 GATTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 9 0.45
19 1 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAATACAAAATAATATT
Found at i:1538251 original size:31 final size:32
Alignment explanation
Indices: 1538226--1538308 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 32
1538216 ATTAATCACA
*
1538226 TTAAAA-ATAAATATCATATTAATTAATAAAT
1 TTAAAATATAAATATCACATTAATTAATAAAT
* **
1538257 TTAAAATTTAAATATCACATTAA--AA-ATTT
1 TTAAAATATAAATATCACATTAATTAATAAAT
*
1538286 TTAAAATTTAAATATCACATTAA
1 TTAAAATATAAATATCACATTAA
1538309 ATATTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 25 0.53
30 2 0.04
31 6 0.13
32 14 0.30
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (32 bp):
TTAAAATATAAATATCACATTAATTAATAAAT
Found at i:1538298 original size:29 final size:29
Alignment explanation
Indices: 1538256--1538315 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1538246 AATTAATAAA
1538256 TTTAAAATTTAAATATCACATTAAAAATT
1 TTTAAAATTTAAATATCACATTAAAAATT
*
1538285 TTTAAAATTTAAATATCACATTAAATATT
1 TTTAAAATTTAAATATCACATTAAAAATT
1538314 TT
1 TT
1538316 ATTGTAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTAAAATTTAAATATCACATTAAAAATT
Found at i:1564256 original size:11 final size:12
Alignment explanation
Indices: 1564228--1564260 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1564218 TAAAAATTTT
*
1564228 AAATTTAATTCG
1 AAATTTAATTCA
1564240 AAATTTAATT-A
1 AAATTTAATTCA
1564251 AAATTTAATT
1 AAATTTAATT
1564261 TTTAAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (12 bp):
AAATTTAATTCA
Found at i:1564433 original size:19 final size:20
Alignment explanation
Indices: 1564411--1564475 Score: 80
Period size: 19 Copynumber: 3.2 Consensus size: 20
1564401 TATATAAAAA
1564411 TAAAATAAT-AAATTTTAAT
1 TAAAATAATAAAATTTTAAT
*
1564430 TAAAATAATAAAAATATATATAT
1 TAAAATAAT-AAAAT-TTTA-AT
1564453 TAAAAT-ATAAAATTTTAAT
1 TAAAATAATAAAATTTTAAT
1564472 TAAA
1 TAAA
1564476 TTCGTAAGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 15 0.38
20 3 0.08
21 9 0.22
22 5 0.12
23 8 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAATAATAAAATTTTAAT
Found at i:1566776 original size:14 final size:16
Alignment explanation
Indices: 1566757--1566790 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
1566747 CAACCAAGAC
1566757 AAAAAATAA-AAT-TA
1 AAAAAATAATAATATA
1566771 AAAAAATAATAATATA
1 AAAAAATAATAATATA
1566787 AAAA
1 AAAA
1566791 CTCCAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 3 0.17
16 6 0.33
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAATAATAATATA
Found at i:1571118 original size:179 final size:178
Alignment explanation
Indices: 1570767--1571128 Score: 449
Period size: 179 Copynumber: 2.0 Consensus size: 178
1570757 ATGGTCCAAT
* ** * *
1570767 TAAATTGAGCCTTTTTGGATATGGGAATTTGATTATATGCCAAAGTCGTCCACTGTTGCTTATGT
1 TAAATTGAGCCTTTTTGGATATGGGAATTTGATTATATGCCAAAGTCGTCAACCCTTGCTCATGG
* *
1570832 CCCAAATATTTGTGTACAGAAACAATTTAAACTTGTCAGAAATATTAATCTTTTAAGCTGTATGG
66 CCCAAATATTTGTGCACAGAAACAATTTAAACTTGTCAGAAATATAAATCTTTTAAGCTGTATGG
* * * * * * * * * *
1570897 TATTCGAAGTGGGCAAATTCTCCATTATAGATACGGTGCTTTCTTTTG
131 GATTCAAAATAGGAAAATTATCCAATACAGATACGATGCTTTCTTATG
* *
1570945 TAAATTGTGCCTTTTTGGATATGGGCATTTGATTATATGCCAAAGGTC-TCAACCCTTGCTCATG
1 TAAATTGAGCCTTTTTGGATATGGGAATTTGATTATATGCCAAA-GTCGTCAACCCTTGCTCATG
** * * *
1571009 GCTTAAATGGTTTTTGCACAGAAACAATTTAACCTTGTCAGAAATATAAATCTTTTAAGCTGTAT
65 GCCCAAAT-ATTTGTGCACAGAAACAATTTAAACTTGTCAGAAATATAAATCTTTTAAGCTGTAT
* *
1571074 GGGAGTT-AAAATAGGAAAATTATCCAATGCAGATATGATGCTTTCTTATG
129 GGGA-TTCAAAATAGGAAAATTATCCAATACAGATACGATGCTTTCTTATG
1571124 TAAAT
1 TAAAT
1571129 ATTTTAAGCC
Statistics
Matches: 155, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
178 59 0.38
179 94 0.61
180 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (178 bp):
TAAATTGAGCCTTTTTGGATATGGGAATTTGATTATATGCCAAAGTCGTCAACCCTTGCTCATGG
CCCAAATATTTGTGCACAGAAACAATTTAAACTTGTCAGAAATATAAATCTTTTAAGCTGTATGG
GATTCAAAATAGGAAAATTATCCAATACAGATACGATGCTTTCTTATG
Found at i:1573123 original size:2 final size:2
Alignment explanation
Indices: 1573118--1573155 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1573108 AAAAAAAAAA
1573118 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
1573156 TAGACTATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1575350 original size:2 final size:2
Alignment explanation
Indices: 1575343--1575379 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1575333 TACTTCCACA
1575343 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 A
1575380 CTATTAATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1575971 original size:14 final size:14
Alignment explanation
Indices: 1575952--1575981 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1575942 GGTATCAGAG
1575952 CGAGGTTCCAGGTT
1 CGAGGTTCCAGGTT
*
1575966 CGAGGTTCTAGGTT
1 CGAGGTTCCAGGTT
1575980 CG
1 CG
1575982 TGGGTCCAAG
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:0.13, C:0.20, G:0.37, T:0.30
Consensus pattern (14 bp):
CGAGGTTCCAGGTT
Found at i:1584411 original size:29 final size:29
Alignment explanation
Indices: 1584369--1584430 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
1584359 GATCCTTACG
1584369 CTTACAGATTTTCTTTTTTAATATATTTT
1 CTTACAGATTTTCTTTTTTAATATATTTT
*
1584398 CTTACAGTTTTTCTTTTTTAATATATTTT
1 CTTACAGATTTTCTTTTTTAATATATTTT
1584427 CTTA
1 CTTA
1584431 AACTGCGACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.63
Consensus pattern (29 bp):
CTTACAGATTTTCTTTTTTAATATATTTT
Found at i:1584442 original size:29 final size:29
Alignment explanation
Indices: 1584381--1584443 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
1584371 TACAGATTTT
* * ****
1584381 CTTTTTTAATATATTTTCTTACAGTTTTT
1 CTTTTTTAATATATTTTCTTAAACTGCGA
1584410 CTTTTTTAATATATTTTCTTAAACTGCGA
1 CTTTTTTAATATATTTTCTTAAACTGCGA
1584439 CTTTT
1 CTTTT
1584444 CTTGTATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.05, T:0.60
Consensus pattern (29 bp):
CTTTTTTAATATATTTTCTTAAACTGCGA
Found at i:1585524 original size:2 final size:2
Alignment explanation
Indices: 1585517--1585555 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1585507 TTTTCAACGT
*
1585517 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1585556 TGGCGTCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1587949 original size:2 final size:2
Alignment explanation
Indices: 1587944--1587970 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1587934 ACACACACAC
1587944 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
1587971 AACGTTTCAT
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:1589639 original size:15 final size:16
Alignment explanation
Indices: 1589608--1589642 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1589598 ATTTTTATAA
*
1589608 AAATAAATTTAATATT
1 AAATAAATTTAAAATT
1589624 AAATAAA-TTAAAATT
1 AAATAAATTTAAAATT
1589639 AAAT
1 AAAT
1589643 TTTTTATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAAATTTAAAATT
Found at i:1592593 original size:2 final size:2
Alignment explanation
Indices: 1592586--1592619 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1592576 TAAAATTAAC
*
1592586 AT AT AT AT AC 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
1592620 TGCTTTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1598543 original size:85 final size:85
Alignment explanation
Indices: 1598454--1598622 Score: 286
Period size: 85 Copynumber: 2.0 Consensus size: 85
1598444 GAAGACTGCT
1598454 TTTGAAATTGCAAATTTGTAAAATAAACAAGTGTTAATTGACCCTATCTTTTTTCT-ATTTCCCT
1 TTTGAAATTGCAAATTTGTAAAATAAACAAGTGTTAATTGACCCTATCTTTTTTCTCATTT-CCT
*
1598518 TATTTTTACATTTATATTTGC
65 TATTTTAACATTTATATTTGC
* *
1598539 TTTGAAATTGCAAATTTGTAAAATGAACAAGTGTTAATTGACCCTATCTTTTTTTTCATTTCCTT
1 TTTGAAATTGCAAATTTGTAAAATAAACAAGTGTTAATTGACCCTATCTTTTTTCTCATTTCCTT
*
1598604 GTTTTAACATTTATATTTG
66 ATTTTAACATTTATATTTG
1598623 AACAAATATC
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 75 0.95
86 4 0.05
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (85 bp):
TTTGAAATTGCAAATTTGTAAAATAAACAAGTGTTAATTGACCCTATCTTTTTTCTCATTTCCTT
ATTTTAACATTTATATTTGC
Found at i:1605611 original size:4 final size:4
Alignment explanation
Indices: 1605582--1605634 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
1605572 CATTTTTATT
*
1605582 TTTA TTT- TTTA TTCTA TTTA --TA TTTA TTTA TTAA TTTA TTT- TTTGA
1 TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A
1605628 TTTA TTT
1 TTTA TTT
1605635 GTTCTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
2 2 0.05
3 6 0.15
4 26 0.63
5 7 0.17
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1605621 original size:22 final size:22
Alignment explanation
Indices: 1605576--1605622 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1605566 TGAGCTCATT
* *
1605576 TTTATTTTTATTTTTTATTCTA
1 TTTATATTTATTTTTAATTCTA
1605598 TTTATATTTATTTATTAATT-TA
1 TTTATATTTATTT-TTAATTCTA
1605620 TTT
1 TTT
1605623 TTTGATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATATTTATTTTTAATTCTA
Found at i:1606555 original size:58 final size:58
Alignment explanation
Indices: 1606442--1606746 Score: 428
Period size: 57 Copynumber: 5.3 Consensus size: 58
1606432 TTTTTCAATG
* *
1606442 ATTTTCC-T-AAAATAAAAATTTTCAAAAAA-ATTTTTTAAGGAAAAGTTAAAAGTATCA
1 ATTTTCCTTGAAAATAAAAATTTT-AAAAAATATTTTTGAAGG-AAAGTTGAAAGTATCA
*
1606499 ATTTTCCTTGAAAATAAAAATTTTAAAAAATATTTTTGGAGGAAAGTTGAAAGTATCA
1 ATTTTCCTTGAAAATAAAAATTTTAAAAAATATTTTTGAAGGAAAGTTGAAAGTATCA
* *
1606557 ATTTTTCTTGAAAATAAAAA-TTTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCA
1 ATTTTCCTTGAAAATAAAAATTTTAAAAAATATTTTTGAAGGAAAGTTGAAAGTATCA
1606614 ATTTTCCTTGAAAAT-AAAATTTTAAAAAATATTTTTGAAGGAAAAGTTGAAAGTATCA
1 ATTTTCCTTGAAAATAAAAATTTTAAAAAATATTTTTGAAGG-AAAGTTGAAAGTATCA
** *
1606672 ATTTT--TTGAAAATAAAAATTTCT-AAAAATATTTTTGAAAAAAAGTTGAAAGTATTA
1 ATTTTCCTTGAAAATAAAAATTT-TAAAAAATATTTTTGAAGGAAAGTTGAAAGTATCA
* *
1606728 ATTTTCTTTAAAAATAAAA
1 ATTTTCCTTGAAAATAAAA
1606747 TTTCTTGAAA
Statistics
Matches: 227, Mismatches: 12, Indels: 17
0.89 0.05 0.07
Matches are distributed among these distances:
56 32 0.14
57 98 0.43
58 74 0.33
59 23 0.10
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (58 bp):
ATTTTCCTTGAAAATAAAAATTTTAAAAAATATTTTTGAAGGAAAGTTGAAAGTATCA
Found at i:1606617 original size:27 final size:27
Alignment explanation
Indices: 1606587--1606677 Score: 69
Period size: 32 Copynumber: 3.2 Consensus size: 27
1606577 TTTAAAAAAT
1606587 ATTTTTGAAGAAAAGTTGAAAGTATCA
1 ATTTTTGAAGAAAAGTTGAAAGTATCA
* * * **
1606614 ATTTTCCTTGAAAATAAAATTTTAAAAAAT--
1 A-TTT--TTG--AAGAAAAGTTGAAAGTATCA
1606644 ATTTTTGAAGGAAAAGTTGAAAGTATCA
1 ATTTTTGAA-GAAAAGTTGAAAGTATCA
1606672 ATTTTT
1 ATTTTT
1606678 TGAAAATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 15
0.65 0.14 0.21
Matches are distributed among these distances:
25 2 0.04
26 11 0.24
27 4 0.09
28 9 0.20
29 3 0.07
30 4 0.09
32 13 0.28
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (27 bp):
ATTTTTGAAGAAAAGTTGAAAGTATCA
Found at i:1606752 original size:17 final size:18
Alignment explanation
Indices: 1606730--1606768 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1606720 AAGTATTAAT
1606730 TTTCTTTAAAAAT-AAAA
1 TTTCTTTAAAAATAAAAA
*
1606747 TTTC-TTGAAAATAAAAA
1 TTTCTTTAAAAATAAAAA
1606764 TTTCT
1 TTTCT
1606769 AAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTCTTTAAAAATAAAAA
Found at i:1606757 original size:74 final size:74
Alignment explanation
Indices: 1606671--1606820 Score: 255
Period size: 74 Copynumber: 2.0 Consensus size: 74
1606661 TGAAAGTATC
* *
1606671 AATTTTTTGAAAATAAAAATTTCTAAAAATATTTTTGAAAAAAAGTTGAAAGTATTAATTTTCTT
1 AATTTCTTGAAAATAAAAATTTCTAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCTT
1606736 TAAAAATAA
66 TAAAAATAA
* *
1606745 AATTTCTTGAAAATAAAAATTTCTAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTT
1 AATTTCTTGAAAATAAAAATTTCTAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCTT
*
1606810 TTAAAATAA
66 TAAAAATAA
1606819 AA
1 AA
1606821 ATTTTAAAGA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.40
Consensus pattern (74 bp):
AATTTCTTGAAAATAAAAATTTCTAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCTT
TAAAAATAA
Found at i:1606773 original size:16 final size:17
Alignment explanation
Indices: 1606730--1606775 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1606720 AAGTATTAAT
1606730 TTTCTTTAAAAAT-AAAA
1 TTTC-TTAAAAATAAAAA
*
1606747 TTTCTTGAAAATAAAAA
1 TTTCTTAAAAATAAAAA
1606764 TTTC-TAAAAATA
1 TTTCTTAAAAATA
1606776 TTTTTGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (17 bp):
TTTCTTAAAAATAAAAA
Found at i:1606962 original size:21 final size:21
Alignment explanation
Indices: 1606923--1606962 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1606913 TGAATCATTA
**
1606923 TTCTTTTTTTTTTTATTTTAT
1 TTCTTTTTTCCTTTATTTTAT
*
1606944 TTCTTTTTTCCTTTCTTTT
1 TTCTTTTTTCCTTTATTTT
1606963 CTTAAAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (21 bp):
TTCTTTTTTCCTTTATTTTAT
Found at i:1610066 original size:15 final size:14
Alignment explanation
Indices: 1610038--1610076 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1610028 GCAAATGTTC
*
1610038 TTTTCATGCATGTA
1 TTTTCATTCATGTA
1610052 TTTTCATTCATTGTA
1 TTTTCATTCA-TGTA
*
1610067 TTCTCATTCA
1 TTTTCATTCA
1610077 ATACATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.18, G:0.08, T:0.54
Consensus pattern (14 bp):
TTTTCATTCATGTA
Found at i:1618450 original size:44 final size:44
Alignment explanation
Indices: 1618342--1618695 Score: 380
Period size: 45 Copynumber: 8.1 Consensus size: 44
1618332 TCAAAAGCAA
* * * * *
1618342 TTTATTTTTTCAAAGTTGTGGTGCCTCTGTTTAGATGAGC-AT-
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTG
* *
1618384 TTTA-TTTTTGAAA---GTTGAGCCTCTGATTAGATGGGCTTTG
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTG
* * *
1618424 TTTATTTTTTCAAAGTCGTTGAGCCTCTAATTAGAAGAGCTTTT
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTG
* * *
1618468 TCTTTTTTTTTTAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTG
1 T-TTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTG
*
1618513 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTT
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTG
* * *
1618557 TTTATATTTTCAAAGTCGTTGAGCCTCTAATTAGAGGAGCTTTG
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTG
* * * * *
1618601 TTTATGATTCTCAAGGTCGTTGTGCCTCT-ACTTAGAGGAGCTTTG
1 TTTAT-TTTTTCAAAGTCGTTGAGCCTCTGA-TTAGATGAGCTTTG
* * * * *
1618646 TTTATGATTCTCAAGGTCGTTGTGCCTCTGCTTAGATGAGCTTTG
1 TTTAT-TTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTG
1618691 TTTAT
1 TTTAT
1618696 GATTCTTAAG
Statistics
Matches: 273, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
38 19 0.07
39 1 0.00
40 4 0.01
41 16 0.06
42 4 0.01
44 109 0.40
45 120 0.44
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.45
Consensus pattern (44 bp):
TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTTG
Found at i:1618495 original size:89 final size:88
Alignment explanation
Indices: 1618397--1618695 Score: 384
Period size: 89 Copynumber: 3.4 Consensus size: 88
1618387 ATTTTTGAAA
1618397 GTTGAGCCTCTGATTAGATGG-GCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTAATTAGAAG
1 GTTGAGCCTCTGATTAGA-GGAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTAATTAGAAG
* *
1618461 AGCTTTTTCTTTTTTTTTTAAAGTC
65 AGCTTTTT-TTTTATTTTCAAAGTC
* *
1618486 GTTGAGCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGA
1 GTTGAGCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTAATTAGAAGA
*
1618551 GCTTTTTTTATATTTTCAAAGTC
66 GCTTTTTTTTTATTTTCAAAGTC
* * * * * * *
1618574 GTTGAGCCTCTAATTAGAGGAGCTTTGTTTATGATTCTCAAGGTCGTTGTGCCTCTACTTAGAGG
1 GTTGAGCCTCTGATTAGAGGAGCTTTGTTTAT-TTTTTCAAAGTCGTTGAGCCTCTAATTAGAAG
* * * *
1618639 AGCTTTGTTTATGATTCTCAAGGTC
65 AGCTTT-TTTTTTATTTTCAAAGTC
* * *
1618664 GTTGTGCCTCTGCTTAGATGAGCTTTGTTTAT
1 GTTGAGCCTCTGATTAGAGGAGCTTTGTTTAT
1618696 GATTCTTAAG
Statistics
Matches: 185, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
88 46 0.25
89 98 0.53
90 41 0.22
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.44
Consensus pattern (88 bp):
GTTGAGCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTAATTAGAAGA
GCTTTTTTTTTATTTTCAAAGTC
Found at i:1618785 original size:11 final size:11
Alignment explanation
Indices: 1618769--1618830 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
1618759 GGGTAAGCCC
1618769 ATTTTTTTTTT
1 ATTTTTTTTTT
1618780 ATTTTTTTTTT
1 ATTTTTTTTTT
* *
1618791 ATTTTATATTT
1 ATTTTTTTTTT
* *
1618802 -TTTGTATTTT
1 ATTTTTTTTTT
*
1618812 ATTTTTATTATT
1 ATTTTT-TTTTT
1618824 ATTTTTT
1 ATTTTTT
1618831 ATATACATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 6 0.15
11 25 0.62
12 9 0.22
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (11 bp):
ATTTTTTTTTT
Found at i:1618795 original size:16 final size:16
Alignment explanation
Indices: 1618770--1618828 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
1618760 GGTAAGCCCA
1618770 TTTTTT-TTTTATTTT
1 TTTTTTATTTTATTTT
*
1618785 TTTTTTATTTTATATT
1 TTTTTTATTTTATTTT
*
1618801 TTTTGTATTTTATTTT
1 TTTTTTATTTTATTTT
*
1618817 TATTATTATTTT
1 T-TTTTTATTTT
1618829 TTATATACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 6 0.16
16 23 0.62
17 8 0.22
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTTTATTTTATTTT
Found at i:1618809 original size:27 final size:26
Alignment explanation
Indices: 1618772--1618830 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
1618762 TAAGCCCATT
* * *
1618772 TTTTTTTTATTTTTTTTTTATTTTATA
1 TTTTTTGTATTTTATTTTTATTAT-TA
1618799 TTTTTTGTATTTTATTTTTATTATTA
1 TTTTTTGTATTTTATTTTTATTATTA
1618825 TTTTTT
1 TTTTTT
1618831 ATATACATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (26 bp):
TTTTTTGTATTTTATTTTTATTATTA
Found at i:1618879 original size:15 final size:15
Alignment explanation
Indices: 1618852--1618891 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1618842 TTTTTCTTTC
1618852 ATTT-TTATCTTATGT
1 ATTTATTAT-TTATGT
*
1618867 ATTTATTATTTATTT
1 ATTTATTATTTATGT
1618882 ATTTATTATT
1 ATTTATTATT
1618892 ACTATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (15 bp):
ATTTATTATTTATGT
Found at i:1619063 original size:44 final size:41
Alignment explanation
Indices: 1618971--1619068 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
1618961 ATATATATAT
*
1618971 TTATCTAATTATATATTATAATTTATCTATTATTTATTTTTAG
1 TTATCT-ATTA-ATATTATAATTTATCTATTATTTATTTTTAA
* * * *
1619014 TTATCTGTTAATATTATTATTTATCTGGTTATTTTTCTTTTAAA
1 TTATCTATTAATATTATAATTTATCT-ATTATTTAT-TTTT-AA
1619058 TTATCTATTAA
1 TTATCTATTAA
1619069 CATTTTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
41 15 0.33
42 10 0.22
43 10 0.22
44 11 0.24
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (41 bp):
TTATCTATTAATATTATAATTTATCTATTATTTATTTTTAA
Found at i:1619471 original size:19 final size:19
Alignment explanation
Indices: 1619447--1619488 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1619437 GCTATTCCGG
1619447 CCAAGTTTGAAGTTTTCGA
1 CCAAGTTTGAAGTTTTCGA
*
1619466 CCAAGTTTGAAGTTTTCGG
1 CCAAGTTTGAAGTTTTCGA
1619485 CCAA
1 CCAA
1619489 CTTTCCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (19 bp):
CCAAGTTTGAAGTTTTCGA
Found at i:1619641 original size:16 final size:17
Alignment explanation
Indices: 1619616--1619661 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
1619606 TTCGAATTCT
*
1619616 AGAAAGAAGGAAGAGA-
1 AGAAAAAAGGAAGAGAG
1619632 AGAAAAAAGGAAAGAGAG
1 AGAAAAAAGG-AAGAGAG
1619650 AGAAGAAAAGGA
1 AGAA-AAAAGGA
1619662 GGGTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 9 0.35
17 6 0.23
18 5 0.19
19 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
AGAAAAAAGGAAGAGAG
Found at i:1620218 original size:58 final size:56
Alignment explanation
Indices: 1620051--1620257 Score: 229
Period size: 58 Copynumber: 3.6 Consensus size: 56
1620041 CAAAAAAATT
* *
1620051 ATTTTTGAA-GAAAAGTTGAAAGTATCAATTTTCTTTAAAATTAAAAGTTTTCAAAAAGT
1 ATTTTT-AAGGAAAAATTGAAAGTATCAATTTTC-TTAAAATT-AAAG-TTTCAAAAAGA
* * * *
1620110 ATTTTTGAGGAAAATTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAATGA
1 ATTTTTAAGGAAAAATTGAAAGTATCAA-TTTTCTTAAAATTAAAGTTTCAAAAA-GA
* * *
1620168 ATTTTTAAGGAAAAATTAAAAATATCAATTTTCTTCGAAATTAAAGTTTC-AAAAGA
1 ATTTTTAAGGAAAAATTGAAAGTATCAATTTTCTT-AAAATTAAAGTTTCAAAAAGA
*
1620224 ATATTTTTAGGAAAAAGTTGAAAGTATCAATTTT
1 AT-TTTTAAGGAAAAA-TTGAAAGTATCAATTTT
1620258 TCCTGCACAA
Statistics
Matches: 127, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
56 4 0.03
57 32 0.25
58 55 0.43
59 31 0.24
60 5 0.04
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (56 bp):
ATTTTTAAGGAAAAATTGAAAGTATCAATTTTCTTAAAATTAAAGTTTCAAAAAGA
Found at i:1624199 original size:8 final size:8
Alignment explanation
Indices: 1624185--1624246 Score: 72
Period size: 8 Copynumber: 7.9 Consensus size: 8
1624175 AGATGATGAA
1624185 AAAAAAAT
1 AAAAAAAT
*
1624193 GAAAAAAT
1 AAAAAAAT
**
1624201 -GGAAAAT
1 AAAAAAAT
1624208 AAAAAAAT
1 AAAAAAAT
1624216 AAAAAAAT
1 AAAAAAAT
1624224 AAAAAAAT
1 AAAAAAAT
* *
1624232 GAGAAAAT
1 AAAAAAAT
1624240 AAAAAAA
1 AAAAAAA
1624247 AAGATTCAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 5 0.11
8 39 0.89
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1624220 original size:32 final size:32
Alignment explanation
Indices: 1624185--1624246 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
1624175 AGATGATGAA
*
1624185 AAAAAAATGAAAAAATG-GAAAATAAAAAAAT
1 AAAAAAATAAAAAAATGAGAAAATAAAAAAAT
1624216 AAAAAAATAAAAAAATGAGAAAATAAAAAAA
1 AAAAAAATAAAAAAATGAGAAAATAAAAAAA
1624247 AAGATTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (32 bp):
AAAAAAATAAAAAAATGAGAAAATAAAAAAAT
Found at i:1625531 original size:22 final size:22
Alignment explanation
Indices: 1625501--1625554 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1625491 TATTTTGATG
*
1625501 GAATTTTTGAGAACTC-AAATGA
1 GAATCTTTGAG-ACTCAAAATGA
**
1625523 GAATCTTTGAGTTTCAAAATGA
1 GAATCTTTGAGACTCAAAATGA
1625545 GAATCTTTGA
1 GAATCTTTGA
1625555 AGAGTGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (22 bp):
GAATCTTTGAGACTCAAAATGA
Found at i:1625564 original size:22 final size:22
Alignment explanation
Indices: 1625517--1625559 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1625507 TTGAGAACTC
**
1625517 AAATGAGAATCTTTGAGTTTCA
1 AAATGAGAATCTTTGAGAGTCA
1625539 AAATGAGAATCTTTGAAGAGT
1 AAATGAGAATCTTTG-AGAGT
1625560 GAAATCCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (22 bp):
AAATGAGAATCTTTGAGAGTCA
Found at i:1626130 original size:41 final size:42
Alignment explanation
Indices: 1626085--1626380 Score: 375
Period size: 41 Copynumber: 7.1 Consensus size: 42
1626075 TTATTTTTCT
* *
1626085 AAAGTCGTGGTGCCTCTATTTAGA-AAGCAATTTACTTTCCA
1 AAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
* *
1626126 AAAGTTGAGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC-
1 AAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
* *
1626167 AAAGTTATAGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
1 AAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
* * * * * *
1626209 AAAGTTGAGGTGCCTCTGTTTAAAAGAGCAATTTATTTTTC-
1 AAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
*
1626250 AAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
1 AAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
* ** * * *
1626292 AAAGTTGAGGTGCCTCTGCTTAAAAGAGCAATTTACTTTTC-
1 AAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
* *
1626333 AAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCA
1 AAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
1626375 AAAGTT
1 AAAGTT
1626381 AAGCCTTTGA
Statistics
Matches: 215, Mismatches: 36, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
41 127 0.59
42 88 0.41
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (42 bp):
AAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCA
Found at i:1626212 original size:83 final size:83
Alignment explanation
Indices: 1626073--1626502 Score: 503
Period size: 83 Copynumber: 5.2 Consensus size: 83
1626063 TCAATGAGTC
* ** *
1626073 ATTTATTTTTCTAAAGTCGTGGTGCCTCTATTTAGA-AAGCAATTTACTTTCCAAAAGTTGAGGT
1 ATTTACTTTTC-AAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGTTGAGGT
* *
1626137 GCCTCTGTTTAGAGGAGCA
65 GCCTCTGTTTAAAAGAGCA
* *
1626156 ATTTACTTTCCAAAGTTATAGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGTTGAGGTG
1 ATTTACTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGTTGAGGTG
1626221 CCTCTGTTTAAAAGAGCA
66 CCTCTGTTTAAAAGAGCA
*
1626239 ATTTATTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGTTGAGGTG
1 ATTTACTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGTTGAGGTG
*
1626304 CCTCTGCTTAAAAGAGCA
66 CCTCTGTTTAAAAGAGCA
* *
1626322 ATTTACTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTT-A--AG
1 ATTTACTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGTTGAGGTG
* * ** *
1626384 CCTTTGATTAGGAGAGCC
66 CCTCTGTTTAAAAGAGCA
* * * * * * * **
1626402 ATTTACTTTTCAAAAGTCATTGAGCCTCTGA-TTAGAGGAGCCATTTATTTTTTC-AAAGTCGTT
1 ATTTACTTTTC-AAAGTTATGGTGCCTCT-ATTTAGAGGAGCAATTTA-CTTTCCAAAAGTTGAG
* * * * *
1626465 GAGCCTCTGATTAGATGAGCC
63 GTGCCTCTGTTTAAAAGAGCA
1626486 ATTTACTTTTCAAAGTT
1 ATTTACTTTTCAAAGTT
1626503 GTTGAGCCTC
Statistics
Matches: 309, Mismatches: 31, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
80 25 0.08
81 34 0.11
82 28 0.09
83 194 0.63
84 28 0.09
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (83 bp):
ATTTACTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGTTGAGGTG
CCTCTGTTTAAAAGAGCA
Found at i:1626508 original size:41 final size:41
Alignment explanation
Indices: 1626110--1626655 Score: 420
Period size: 42 Copynumber: 13.0 Consensus size: 41
1626100 CTATTTAGAA
* ** * *
1626110 AGCAATTTACTTTCCAAAAGTTGAGGTGCCTCTGTTTAGAGG
1 AGCAATTTACTTTTC-AAAGTTGTTGAGCCTCTGATTAGAGG
* * * *
1626152 AGCAATTTACTTTCCAAAGTTATAGTGCCTCT-ATTTAGAGG
1 AGCAATTTACTTTTCAAAGTTGTTGAGCCTCTGA-TTAGAGG
* ** * * * *
1626193 AGCAATTTACTTTCCAAAAGTTGAGGTGCCTCTGTTTAAAAG
1 AGCAATTTACTTTTC-AAAGTTGTTGAGCCTCTGATTAGAGG
* * * *
1626235 AGCAATTTATTTTTCAAAGTTATGGTGCCTCT-ATTTAGAGG
1 AGCAATTTACTTTTCAAAGTTGTTGAGCCTCTGA-TTAGAGG
* ** * * * *
1626276 AGCAATTTACTTTCCAAAAGTTGAGGTGCCTCTGCTTAAAAG
1 AGCAATTTACTTTTC-AAAGTTGTTGAGCCTCTGATTAGAGG
* * *
1626318 AGCAATTTACTTTTCAAAGTTATGGTGCCTCT-ATTTAGAGG
1 AGCAATTTACTTTTCAAAGTTGTTGAGCCTCTGA-TTAGAGG
* * *
1626359 AGCAATTTACTTTTCAAA--AGTTAAGCCTTTGATTAG-GAG
1 AGCAATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAGAG-G
* **
1626398 AGCCATTTACTTTTCAAAAGTCATTGAGCCTCTGATTAGAGG
1 AGCAATTTACTTTTC-AAAGTTGTTGAGCCTCTGATTAGAGG
* * * *
1626440 AGCCATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATG
1 AGCAATTTA-CTTTTCAAAGTTGTTGAGCCTCTGATTAGAGG
* *
1626482 AGCCATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAAAGG
1 AGCAATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAGAGG
* * *
1626523 AGCCATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGG
1 AGCAATTTA-CTTTTCAAAGTTGTTGAGCCTCTGATTAGAGG
** *
1626565 AGCTTTGTTTATTCATTTTCAAAGTCGTTGAGCCTCTGATTAGAGG
1 AGC--AATTTA--C-TTTTCAAAGTTGTTGAGCCTCTGATTAGAGG
* ** *
1626611 AACTTTGTTTATCTTTCCAAAGTTGTTGAGCCTCTGATTAGAGG
1 AGC--AATTTA-CTTTTCAAAGTTGTTGAGCCTCTGATTAGAGG
1626655 A
1 A
1626656 ACCTTGTTTA
Statistics
Matches: 428, Mismatches: 57, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
38 1 0.00
39 25 0.06
40 4 0.01
41 144 0.34
42 170 0.40
43 6 0.01
44 34 0.08
45 3 0.01
46 41 0.10
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (41 bp):
AGCAATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAGAGG
Found at i:1626530 original size:83 final size:82
Alignment explanation
Indices: 1626137--1626701 Score: 381
Period size: 83 Copynumber: 6.7 Consensus size: 82
1626127 AAGTTGAGGT
* * * * * * *
1626137 GCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTATAGTGCCTCT-ATTTAGAGGAGCAATTT
1 GCCTCTGATTAGA-GAGCCATTTACTTTTCAAAGTCATTGAGCCTCTGA-TTAGAGGAGCCATTT
* * ** *
1626201 A-CTTTCCAAAAGTTGAGGT
64 ATCTTTTC-AAAGTCGTTGA
* * * * * * * *
1626220 GCCTCTGTTTAAAAGAGCAATTTATTTTTCAAAGTTATGGTGCCTCT-ATTTAGAGGAGCAATTT
1 GCCTCTGATT-AGAGAGCCATTTACTTTTCAAAGTCATTGAGCCTCTGA-TTAGAGGAGCCATTT
* * ** *
1626284 A-CTTTCCAAAAGTTGAGGT
64 ATCTTTTC-AAAGTCGTTGA
* * * * * * *
1626303 GCCTCTGCTTAAAAGAGCAATTTACTTTTCAAAGTTATGGTGCCTCT-ATTTAGAGGAGCAATTT
1 GCCTCTGATT-AGAGAGCCATTTACTTTTCAAAGTCATTGAGCCTCTGA-TTAGAGGAGCCATTT
* *
1626367 A-CTTTTCAAA--AGTTAA
64 ATCTTTTCAAAGTCGTTGA
*
1626383 GCCTTTGATTAGGAGAGCCATTTACTTTTCAAAAGTCATTGAGCCTCTGATTAGAGGAGCCATTT
1 GCCTCTGATTA-GAGAGCCATTTACTTTTC-AAAGTCATTGAGCCTCTGATTAGAGGAGCCATTT
*
1626448 ATTTTTTCAAAGTCGTTGA
64 ATCTTTTCAAAGTCGTTGA
** *
1626467 GCCTCTGATTAGATGAGCCATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAAAGGAGCCATTTA
1 GCCTCTGATTAGA-GAGCCATTTACTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCATTTA
*
1626532 TTTTTTCAAAGTCGTTGA
65 TCTTTTCAAAGTCGTTGA
** * *
1626550 GCCTCTGATTAGAGGAGCTTTGTTTATTCATTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAACT
1 GCCTCTGATTAGA-GAGC--CATTTA--C-TTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGC-
** * *
1626615 TTGTTTATCTTTCCAAAGTTGTTGA
59 -CATTTATCTTTTCAAAGTCGTTGA
* * * * *
1626640 GCCTCTGATTAGAGGAACCTTGTTTATGTTTTTCAAAGTCATTAAGCCTCTGCTTAGAGGAG
1 GCCTCTGATTAGA-GAGCC--ATTTA--CTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAG
1626702 TTTTGATCAA
Statistics
Matches: 419, Mismatches: 46, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
79 1 0.00
80 25 0.06
81 29 0.07
82 12 0.03
83 213 0.51
84 32 0.08
85 4 0.01
87 1 0.00
88 31 0.07
89 29 0.07
90 42 0.10
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (82 bp):
GCCTCTGATTAGAGAGCCATTTACTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCATTTAT
CTTTTCAAAGTCGTTGA
Found at i:1626553 original size:125 final size:127
Alignment explanation
Indices: 1626344--1626701 Score: 397
Period size: 125 Copynumber: 2.8 Consensus size: 127
1626334 AAGTTATGGT
* * * *
1626344 GCCTCT-ATTTAGAGGAGCAATTTACTTTTCAAA--AGTTAAGCCTTTGATT-AGGAGAGCCATT
1 GCCTCTGA-TTAGAGGAGCAATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAAAG-GAGCCATT
*
1626405 TA-CTTTTCAAAAGTCATTGAGCCTCTGATTAGAGGAGC-CATTTATT-TTTTCAAAGTCGTTGA
64 TATTTTTTC-AAAGTCATTGAGCCTCTGATTAGAGGAGCTCATTTATTATTTTCAAAGTCGTTGA
* *
1626467 GCCTCTGATTAGATGAGCCATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAAAGGAGCCATTTA
1 GCCTCTGATTAGAGGAGCAATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAAAGGAGCCATTTA
* **
1626532 TTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTGTTTATTCATTTTCAAAGTCGTTGA
66 TTTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGC-TCATTTATT-ATTTTCAAAGTCGTTGA
* ** * * *
1626596 GCCTCTGATTAGAGGAACTTTGTTTATCTTTCCAAAGTTGTTGAGCCTCTGATTAGAGGAACCTT
1 GCCTCTGATTAGAGGAGC--AATTTA-CTTTTCAAAGTTGTTGAGCCTCTGATTAAAGGAGCC--
* * *
1626661 GTTTATGTTTTTCAAAGTCATTAAGCCTCTGCTTAGAGGAG
61 ATTTAT-TTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAG
1626702 TTTTGATCAA
Statistics
Matches: 199, Mismatches: 21, Indels: 18
0.84 0.09 0.08
Matches are distributed among these distances:
123 29 0.15
124 1 0.01
125 51 0.26
126 7 0.04
127 6 0.03
129 32 0.16
131 4 0.02
132 33 0.17
134 5 0.03
135 31 0.16
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (127 bp):
GCCTCTGATTAGAGGAGCAATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAAAGGAGCCATTTA
TTTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTCATTTATTATTTTCAAAGTCGTTGA
Found at i:1626907 original size:14 final size:13
Alignment explanation
Indices: 1626886--1626932 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 13
1626876 ATTTTTTTAA
1626886 TTATTTTTATTTT
1 TTATTTTTATTTT
* *
1626899 TTAATTTTTGTATT
1 TT-ATTTTTATTTT
*
1626913 TTATTTTTA-TTA
1 TTATTTTTATTTT
1626925 TTATTTTT
1 TTATTTTT
1626933 TTATATACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 9 0.32
13 8 0.29
14 11 0.39
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
TTATTTTTATTTT
Found at i:1626912 original size:16 final size:17
Alignment explanation
Indices: 1626878--1626914 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1626868 GTAAGCCCAT
*
1626878 TTTTTTAATTATTTTTA
1 TTTTTTAATTATTTGTA
1626895 TTTTTTAATT-TTTGTA
1 TTTTTTAATTATTTGTA
1626911 TTTT
1 TTTT
1626915 ATTTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTTAATTATTTGTA
Found at i:1627007 original size:62 final size:62
Alignment explanation
Indices: 1626890--1627008 Score: 140
Period size: 62 Copynumber: 1.9 Consensus size: 62
1626880 TTTTAATTAT
* *
1626890 TTTTATTTTTTAATTTTTGTATTTTATTTTTATTATTATTTTTTTATATACATATATTTTTC
1 TTTTATTTTTTAATTTATGTATTTTATTTTTATTATTATTTATTTATATACATATATTTTTC
1626952 TTTTA-TTTTT-ATCTTATGTA-TTTATTATTTATTTATTATTACTATTTAT-TA-ATATAT
1 TTTTATTTTTTAAT-TTATGTATTTTATT-TTTA-TTATTATT--TATTTATATACATATAT
1627009 ATATCCTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
60 8 0.16
61 15 0.30
62 19 0.38
63 2 0.04
64 6 0.12
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (62 bp):
TTTTATTTTTTAATTTATGTATTTTATTTTTATTATTATTTATTTATATACATATATTTTTC
Found at i:1627070 original size:12 final size:12
Alignment explanation
Indices: 1627053--1627105 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
1627043 TTTTCTGTTA
*
1627053 ATATTTATATAT
1 ATATTTATCTAT
1627065 ATATTTATCTGAT
1 ATATTTATCT-AT
*
1627078 -TATATAT-TAT
1 ATATTTATCTAT
1627088 A-ATTTATCTAT
1 ATATTTATCTAT
1627099 -TATTTAT
1 ATATTTAT
1627106 TTTTAGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
10 7 0.21
11 10 0.29
12 15 0.44
13 2 0.06
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (12 bp):
ATATTTATCTAT
Found at i:1627100 original size:21 final size:22
Alignment explanation
Indices: 1627057--1627143 Score: 103
Period size: 21 Copynumber: 4.2 Consensus size: 22
1627047 CTGTTAATAT
1627057 TTATATA-TA-TATTTATCTGA
1 TTATATATTATTATTTATCTGA
*
1627077 TTATATATTATAATTTATCT-A
1 TTATATATTATTATTTATCTGA
* * *
1627098 TTATTTATTTTTAGTTATCTG-
1 TTATATATTATTATTTATCTGA
1627119 TTA-ATATTATTATTTATCTGA
1 TTATATATTATTATTTATCTGA
1627140 TTAT
1 TTAT
1627144 TTTCCTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
20 21 0.39
21 25 0.46
22 8 0.15
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (22 bp):
TTATATATTATTATTTATCTGA
Found at i:1627720 original size:16 final size:17
Alignment explanation
Indices: 1627699--1627734 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1627689 GATTCTAGAG
*
1627699 AGAAGGGAA-AGAAGAA
1 AGAAGGGAAGAGAAAAA
1627715 AGAAGGGAAGAGAAAAA
1 AGAAGGGAAGAGAAAAA
1627732 AGA
1 AGA
1627735 GAAGAAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AGAAGGGAAGAGAAAAA
Found at i:1627729 original size:21 final size:22
Alignment explanation
Indices: 1627700--1627743 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1627690 ATTCTAGAGA
* *
1627700 GAAGGGAAAGAAGA-AAGAAGG
1 GAAGAGAAAAAAGAGAAGAAGG
1627721 GAAGAGAAAAAAGAGAAGAAGG
1 GAAGAGAAAAAAGAGAAGAAGG
1627743 G
1 G
1627744 TTCTACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (22 bp):
GAAGAGAAAAAAGAGAAGAAGG
Found at i:1628075 original size:6 final size:6
Alignment explanation
Indices: 1628064--1628111 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
1628054 AATTGTTTAA
* * *
1628064 TATTTT TATTTT TATTTT TATTTA TCTTTT TA--TT TATTTT CATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
1628110 TA
1 TA
1628112 CTTAGTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 4 0.12
6 30 0.88
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:1628099 original size:16 final size:16
Alignment explanation
Indices: 1628080--1628136 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
1628070 TATTTTTATT
1628080 TTTATTTATCTTTTTA
1 TTTATTTATCTTTTTA
1628096 TTTATTT-TCATTTTTA
1 TTTATTTATC-TTTTTA
*
1628112 CTTAGTTTAT-TTTATTA
1 TTTA-TTTATCTTT-TTA
1628129 TTTTATTT
1 -TTTATTT
1628137 CTTTTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 2 0.06
16 19 0.56
17 9 0.26
18 4 0.12
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTATTTATCTTTTTA
Found at i:1628100 original size:28 final size:30
Alignment explanation
Indices: 1628068--1628136 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
1628058 GTTTAATATT
*
1628068 TTTATTTTTATTTTTATTTA-TCT-TTTTA
1 TTTATTTTTATTTTTACTTAGTCTATTTTA
* *
1628096 TTTATTTTCATTTTTACTTAGTTTATTTTA
1 TTTATTTTTATTTTTACTTAGTCTATTTTA
1628126 -TTA-TTTTATTT
1 TTTATTTTTATTT
1628137 CTTTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 25 0.71
29 5 0.14
30 5 0.14
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (30 bp):
TTTATTTTTATTTTTACTTAGTCTATTTTA
Found at i:1628859 original size:10 final size:9
Alignment explanation
Indices: 1628833--1628896 Score: 58
Period size: 10 Copynumber: 6.7 Consensus size: 9
1628823 GGGCTCATTC
1628833 TTATTTTTA
1 TTATTTTTA
*
1628842 TTTTTTTTTA
1 -TTATTTTTA
1628852 TTAATTTTATA
1 TT-ATTTT-TA
1628863 TTATTTTATA
1 TTATTTT-TA
*
1628873 TTATTATTA
1 TTATTTTTA
1628882 TTATTTATT-
1 TTATTT-TTA
1628891 TTATTT
1 TTATTT
1628897 ATCTCTTCTG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
9 15 0.32
10 28 0.60
11 4 0.09
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTTTA
Found at i:1628861 original size:19 final size:18
Alignment explanation
Indices: 1628837--1628895 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 18
1628827 TCATTCTTAT
1628837 TTTTATTTTTTTTTATTAA
1 TTTTATTTTTTTTTATT-A
*
1628856 TTTTATATTATTTTATATTA
1 TTTTAT-TT-TTTTTTATTA
1628876 TTATTATTATTTATTTTATT
1 TT-TTATT-TTT-TTTTATT
1628896 TATCTCTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
21 19 0.58
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTTTTATTA
Found at i:1628866 original size:24 final size:23
Alignment explanation
Indices: 1628833--1628898 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
1628823 GGGCTCATTC
* *
1628833 TTATT-TTTATTTTTTTTTATTAA
1 TTATTATTTATTTTATATTATT-A
1628856 TT-TTATATTATTTTATATTATTA
1 TTATTAT-TTATTTTATATTATTA
1628879 TTATTATTTATTTTAT-TTAT
1 TTATTATTTATTTTATATTAT
1628899 CTCTTCTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
22 6 0.16
23 15 0.39
24 17 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TTATTATTTATTTTATATTATTA
Found at i:1628898 original size:19 final size:18
Alignment explanation
Indices: 1628849--1628895 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1628839 TTATTTTTTT
*
1628849 TTATTAATTTTA-TATTA
1 TTATTTATTTTATTATTA
*
1628866 -T-TTTATATTATTATTA
1 TTATTTATTTTATTATTA
1628882 TTATTTATTTTATT
1 TTATTTATTTTATT
1628896 TATCTCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 1 0.04
18 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTATTTTATTATTA
Found at i:1629668 original size:11 final size:11
Alignment explanation
Indices: 1629652--1629696 Score: 56
Period size: 10 Copynumber: 3.9 Consensus size: 11
1629642 TTCCCTATTT
1629652 TTTTATTTTTA
1 TTTTATTTTTA
1629663 TTTTA-TTTTA
1 TTTTATTTTTA
1629673 TTTTATTCTTTTA
1 TTTTA-T-TTTTA
1629686 TTATTATTTTT
1 TT-TTATTTTT
1629697 TCAATGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.33
11 5 0.17
12 4 0.13
13 8 0.27
14 3 0.10
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:1629684 original size:24 final size:24
Alignment explanation
Indices: 1629647--1629695 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1629637 TGATATTCCC
*
1629647 TATTTTTTTATTTTTATT-TTATTT
1 TATTTTATTA-TTTTATTATTATTT
*
1629671 TATTTTATTCTTTTATTATTATTT
1 TATTTTATTATTTTATTATTATTT
1629695 T
1 T
1629696 TTCAATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (24 bp):
TATTTTATTATTTTATTATTATTT
Found at i:1629840 original size:56 final size:57
Alignment explanation
Indices: 1629711--1629959 Score: 326
Period size: 58 Copynumber: 4.3 Consensus size: 57
1629701 TGATTTTCCT
** *
1629711 AAAATAAAAATTTTCAAAAAAATATTTTTG-GGGAAGGTTGAAAGTATCAA-TTTTCTTTA
1 AAAAT-AAAATTTT--AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC-TTA
*
1629770 AAAATAAAATTTTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAATTTTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA
* * *
1629827 AAAATAAAA-TTT-AAAAATATTTTTGAAGGAAAAGTTGAAAGTATTAATTTTTCTTG
1 AAAATAAAATTTTAAAAAATATTTTTG-AGAAAAAGTTGAAAGTATCAATTTTTCTTA
* *
1629883 AAAATAAAAATTTTTAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTA
1 AAAAT-AAAATTTTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA
1629941 AAAATAAAATTTCTAAAAA
1 AAAATAAAATTT-TAAAAA
1629960 TAAAATTTCT
Statistics
Matches: 172, Mismatches: 11, Indels: 15
0.87 0.06 0.08
Matches are distributed among these distances:
55 13 0.08
56 50 0.29
57 39 0.23
58 52 0.30
59 18 0.10
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.38
Consensus pattern (57 bp):
AAAATAAAATTTTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA
Found at i:1629908 original size:114 final size:113
Alignment explanation
Indices: 1629728--1629961 Score: 348
Period size: 114 Copynumber: 2.1 Consensus size: 113
1629718 AAATTTTCAA
* * *
1629728 AAAAATATTTTTGGGGAAGGTTGAAAGTATCAATTTTCTTTAAAAATAAAATTTTAAAAAATATT
1 AAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCTTGAAAAATAAAATTTTAAAAAATATT
* *
1629793 TTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAA-TT-T
66 TTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCT
* *
1629839 AAAAATATTTTTGAAGGAAAAGTTGAAAGTATTAATTTTTCTTG-AAAATAAAAATTTTTAAAAA
1 AAAAATATTTTTG--GGAAAAGTTGAAAGTATCAA-TTTTCTTGAAAAAT-AAAATTTTAAAAAA
1629903 TATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCT
62 TATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCT
1629955 AAAAATA
1 AAAAATA
1629962 AAATTTCTAA
Statistics
Matches: 110, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
111 13 0.12
113 22 0.20
114 65 0.59
115 2 0.02
116 8 0.07
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.38
Consensus pattern (113 bp):
AAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCTTGAAAAATAAAATTTTAAAAAATATT
TTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCT
Found at i:1629959 original size:16 final size:15
Alignment explanation
Indices: 1629934--1629972 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
1629924 AGTATCAATT
1629934 TTTCTTAAAAATAAAA
1 TTTC-TAAAAATAAAA
1629950 TTTCTAAAAATAAAA
1 TTTCTAAAAATAAAA
1629965 TTTCTAAA
1 TTTCTAAA
1629973 GATATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTCTAAAAATAAAA
Found at i:1629960 original size:57 final size:56
Alignment explanation
Indices: 1629728--1629961 Score: 321
Period size: 56 Copynumber: 4.1 Consensus size: 56
1629718 AAATTTTCAA
** *
1629728 AAAAATATTTTTG-GGGAAGGTTGAAAGTATCAA-TTTTCTTTAAAAATAAAATTTT
1 AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAAATTTT
*
1629783 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAA-TTT
1 -AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTT
* * *
1629839 AAAAATATTTTTGAAGGAAAAGTTGAAAGTATTAATTTTTCTTGAAAATAAAAATTTTT
1 AAAAATATTTTTG-AGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAA-TTTT
*
1629898 AAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCT
1 AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTT-T
1629955 AAAAATA
1 AAAAATA
1629962 AAATTTCTAA
Statistics
Matches: 161, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
55 13 0.08
56 52 0.32
57 44 0.27
58 36 0.22
59 16 0.10
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.38
Consensus pattern (56 bp):
AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTT
Found at i:1629967 original size:72 final size:72
Alignment explanation
Indices: 1629883--1630019 Score: 190
Period size: 72 Copynumber: 1.9 Consensus size: 72
1629873 ATTTTTCTTG
* *
1629883 AAAATAAAAATTTTTAAAAATATTTTTGAGAAAAAATTGAAAGTA-TCAA-TTTTTCTTAAAAAT
1 AAAATAAAAATTTCTAAAAATATTTTTAAG-AAAAATTG-AAGTACTCAATTTTTTCTT-AAAAT
1629946 AAAATTTCTA
63 AAAATTTCTA
* *
1629956 AAAAT-AAAATTTCTAAAGATATTTTTAAGAAAAGTTGAAGTACTCAATTTTTTCTTAAAATAAA
1 AAAATAAAAATTTCTAAAAATATTTTTAAGAAAAATTGAAGTACTCAATTTTTTCTTAAAATAAA
1630020 TCTCCAAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 5 0.09
71 19 0.33
72 29 0.50
73 5 0.09
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (72 bp):
AAAATAAAAATTTCTAAAAATATTTTTAAGAAAAATTGAAGTACTCAATTTTTTCTTAAAATAAA
ATTTCTA
Found at i:1630165 original size:17 final size:18
Alignment explanation
Indices: 1630126--1630168 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1630116 TCATTATTCC
* *
1630126 CTTTTTTTTTTTATTTTT
1 CTTTTCTTTTTTACTTTT
*
1630144 ATTTTCTTTTTT-CTTTT
1 CTTTTCTTTTTTACTTTT
1630161 CTTTTCTT
1 CTTTTCTT
1630169 GGAATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (18 bp):
CTTTTCTTTTTTACTTTT
Found at i:1632666 original size:23 final size:21
Alignment explanation
Indices: 1632639--1632681 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1632629 TACTTCTTTG
*
1632639 AAAAATTTTAAATTTCATCCAT
1 AAAAAATTTAAATTTCA-CCAT
1632661 AAAAAATTTAAATTTCACCAT
1 AAAAAATTTAAATTTCACCAT
1632682 CGAAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAAATTTAAATTTCACCAT
Found at i:1632691 original size:22 final size:22
Alignment explanation
Indices: 1632640--1632691 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1632630 ACTTCTTTGA
1632640 AAAAT-TTTAAATTTCATCCAT
1 AAAATATTTAAATTTCATCCAT
*
1632661 AAAAAATTTAAATTTCA-CCAT
1 AAAATATTTAAATTTCATCCAT
*
1632682 CGAAATATTT
1 -AAAATATTT
1632692 TACTCATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATATTTAAATTTCATCCAT
Found at i:1654302 original size:22 final size:22
Alignment explanation
Indices: 1654277--1654329 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1654267 ATCTGAAAAT
1654277 AAGAAAGAGAAAGAAAGA-AAGA
1 AAGAAAGAGAAAGAAAGAGAA-A
* *
1654299 AAGAAAGAGATAGAGAGAGAAA
1 AAGAAAGAGAAAGAAAGAGAAA
1654321 AAGAAAGAG
1 AAGAAAGAG
1654330 GCTTTTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (22 bp):
AAGAAAGAGAAAGAAAGAGAAA
Found at i:1663090 original size:254 final size:253
Alignment explanation
Indices: 1662642--1663144 Score: 918
Period size: 254 Copynumber: 2.0 Consensus size: 253
1662632 GCTGCCTATC
1662642 TTCATTGGTGACTCTCTTCCTATATATTTTGCAATGTTTCGCGCTAACTGAATTTGATTCAATTC
1 TTCATTGGTGACTCTCTTCCTATATATTTTGCAATGTTTCGCGCTAACTGAATTTGATTCAATTC
* *
1662707 GAAAACTCGTATCCTCTACTAATCGGCCAATGCAGTGCTCATCTGCAGTCAAAAGCATATTCATA
66 GAAAACTCGCATCCTCTACTAATCGGCCAATGCAGTGCTCATCTGCAGTCAAAAGCACATTCATA
1662772 CCCTGGAAAAATGATCTTCTCATCAGCCTTTCACTTACATTGTATATTACAATTTTCAGTCTAAT
131 CCCTGGAAAAATGATCTTCTCATCAGCCTTTCACTTACATTGTATATTACAATTTTCAGTCTAAT
1662837 CTTTTCTTTCCTTCTTTT-TTTTCCCTAAATCCTTAAGCAATTTTAGCAAATCTTTTCT
196 CTTTTCTTTCCTTCTTTTCTTTT-CCTAAATCCTTAAGCAATTTTAGCAAATCTTTTCT
* *
1662895 TTCATTGGTGACTCTCTTCCTATATATTTTTGCAGTGTTTCGCGCTAACTGAATTTGATTCAGTT
1 TTCATTGGTGACTCTCTTCCTATATA-TTTTGCAATGTTTCGCGCTAACTGAATTTGATTCAATT
1662960 CGAAAACTCGCATCCTCTACTAATCGGCCAATGCAGTGCTCATCTGCAGTCAAAAGCACATTCAT
65 CGAAAACTCGCATCCTCTACTAATCGGCCAATGCAGTGCTCATCTGCAGTCAAAAGCACATTCAT
*
1663025 ACCCTGGAAAAATGATCTTCTCATCAGCCTTTCACTTACGTTGTATATTACAATTTTCAGTCTAA
130 ACCCTGGAAAAATGATCTTCTCATCAGCCTTTCACTTACATTGTATATTACAATTTTCAGTCTAA
* *
1663090 TCTTTTCTTTCTTTCTTTTCTTTTCCTAATTCCTTAAGCAATTTTAGCAAATCTT
195 TCTTTTCTTTCCTTCTTTTCTTTTCCTAAATCCTTAAGCAATTTTAGCAAATCTT
1663145 CATCTCGGTT
Statistics
Matches: 241, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
253 26 0.11
254 211 0.88
255 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.40
Consensus pattern (253 bp):
TTCATTGGTGACTCTCTTCCTATATATTTTGCAATGTTTCGCGCTAACTGAATTTGATTCAATTC
GAAAACTCGCATCCTCTACTAATCGGCCAATGCAGTGCTCATCTGCAGTCAAAAGCACATTCATA
CCCTGGAAAAATGATCTTCTCATCAGCCTTTCACTTACATTGTATATTACAATTTTCAGTCTAAT
CTTTTCTTTCCTTCTTTTCTTTTCCTAAATCCTTAAGCAATTTTAGCAAATCTTTTCT
Found at i:1663274 original size:21 final size:21
Alignment explanation
Indices: 1663231--1663274 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1663221 AAGGTTGGAA
1663231 ATTTACTGACAAAAAAAGGAAT
1 ATTTACTGACAAAAAAA-GAAT
*
1663253 ATTTACTGCCAAAATAAA-AAT
1 ATTTACTGACAAAA-AAAGAAT
1663274 A
1 A
1663275 GAAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 13 0.65
23 3 0.15
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (21 bp):
ATTTACTGACAAAAAAAGAAT
Found at i:1667724 original size:3 final size:3
Alignment explanation
Indices: 1667716--1667745 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1667706 AAGATTACAA
1667716 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1667746 GAATTTAAGA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1673301 original size:18 final size:19
Alignment explanation
Indices: 1673270--1673324 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 19
1673260 GATGCATTTG
* *
1673270 AGGATGATATATTTGTGGT
1 AGGAGGATACATTTGTGGT
*
1673289 AGGA-GATACATTTGAGGT
1 AGGAGGATACATTTGTGGT
*
1673307 -GGAGGATACATTTATGGT
1 AGGAGGATACATTTGTGGT
1673325 GGATAATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 3 0.10
18 24 0.77
19 4 0.13
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.35
Consensus pattern (19 bp):
AGGAGGATACATTTGTGGT
Found at i:1676937 original size:20 final size:21
Alignment explanation
Indices: 1676887--1676966 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
1676877 AAACAACAAA
*
1676887 AAAATTATTAAATTTTAAATAT
1 AAAA-TATAAAATTTTAAATAT
1676909 AAAATATAAAATTTTAAAT-T
1 AAAATATAAAATTTTAAATAT
*** *
1676929 AATAA-ATAAAAAAATAAAAAT
1 AA-AATATAAAATTTTAAATAT
**
1676950 AAAATATTTAATTTTAA
1 AAAATATAAAATTTTAA
1676967 TTATTTTTCA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 15 0.33
21 26 0.58
22 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATATAAAATTTTAAATAT
Found at i:1676948 original size:29 final size:28
Alignment explanation
Indices: 1676886--1676949 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1676876 AAAACAACAA
* *
1676886 AAAAATTATTAAATTTTAAATATAAAAT
1 AAAAATTATTAAATTATAAATAAAAAAT
1676914 ATAAAATT-TTAAATTAATAAATAAAAAAAT
1 A-AAAATTATTAAATT-ATAAAT-AAAAAAT
1676944 AAAAAT
1 AAAAAT
1676950 AAAATATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 8 0.26
29 16 0.52
30 7 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
AAAAATTATTAAATTATAAATAAAAAAT
Found at i:1677158 original size:22 final size:21
Alignment explanation
Indices: 1677129--1677169 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1677119 CAAAATTTTA
* *
1677129 AATTTAAATTTTAATAAAATT
1 AATTTAAAATTAAATAAAATT
1677150 AATTATAAAATTAAATAAAA
1 AATT-TAAAATTAAATAAAA
1677170 AACACACACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTTAAAATTAAATAAAATT
Found at i:1677248 original size:50 final size:49
Alignment explanation
Indices: 1677185--1677327 Score: 166
Period size: 50 Copynumber: 2.9 Consensus size: 49
1677175 ACACCCCATT
* *
1677185 CTACCTTCCAATGCACCCAACCTCACCCAATCTCACTCCACCCCTCCACC
1 CTACCCTCAAATGCACCC-ACCTCACCCAATCTCACTCCACCCCTCCACC
* *
1677235 CTACCCTCAAATGCACCCTACCTCACCCAATCTCACCCCACCTCTCCACC
1 CTACCCTCAAATGCACCC-ACCTCACCCAATCTCACTCCACCCCTCCACC
* *
1677285 TTACCCTCCAAA-G--CCCACCCCACCCAATCTCACGTCCTACCCC
1 CTACCCT-CAAATGCACCCACCTCACCCAATCTCAC-TCC-ACCCC
1677328 ACCCCTCACC
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
47 16 0.20
48 5 0.06
49 4 0.05
50 52 0.64
51 4 0.05
ACGTcount: A:0.24, C:0.56, G:0.03, T:0.17
Consensus pattern (49 bp):
CTACCCTCAAATGCACCCACCTCACCCAATCTCACTCCACCCCTCCACC
Found at i:1677780 original size:18 final size:18
Alignment explanation
Indices: 1677753--1677789 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1677743 ATAGTGATTT
*
1677753 TTTTTCTTTTGGCTTTTG
1 TTTTTATTTTGGCTTTTG
*
1677771 TTTTTATTTTTGCTTTTG
1 TTTTTATTTTGGCTTTTG
1677789 T
1 T
1677790 AATTTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.08, G:0.14, T:0.76
Consensus pattern (18 bp):
TTTTTATTTTGGCTTTTG
Found at i:1685744 original size:17 final size:17
Alignment explanation
Indices: 1685722--1685756 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1685712 AAATTGTTGG
1685722 TTTTTTTTTTC-TTTCT
1 TTTTTTTTTTCATTTCT
1685738 TTTTTTTTTTCATTTCT
1 TTTTTTTTTTCATTTCT
1685755 TT
1 TT
1685757 AAAGATAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTCATTTCT
Found at i:1688311 original size:36 final size:33
Alignment explanation
Indices: 1688270--1688339 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 33
1688260 TAATTAATAA
*
1688270 GGTAAAATTAATATGATAATATAGTTAGTTTCAAAT
1 GGTAAAATT-A-A-GATAATATAGTTAATTTCAAAT
* *
1688306 GGTAAAGTTAAGATAATGTAGTTAATTTCAAAT
1 GGTAAAATTAAGATAATATAGTTAATTTCAAAT
1688339 G
1 G
1688340 AGAATCCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 21 0.68
34 1 0.03
35 1 0.03
36 8 0.26
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (33 bp):
GGTAAAATTAAGATAATATAGTTAATTTCAAAT
Found at i:1698069 original size:10 final size:10
Alignment explanation
Indices: 1698054--1698092 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1698044 GTATCCATTG
1698054 TATCTATATC
1 TATCTATATC
* *
1698064 TATCTATTTA
1 TATCTATATC
*
1698074 TATATATATC
1 TATCTATATC
1698084 TATCTATAT
1 TATCTATAT
1698093 ATATATATGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (10 bp):
TATCTATATC
Found at i:1698083 original size:16 final size:16
Alignment explanation
Indices: 1698058--1698112 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
1698048 CCATTGTATC
* *
1698058 TATATCTATCTATTTA
1 TATATATATCTATCTA
1698074 TATATATATCTATCTA
1 TATATATATCTATCTA
*
1698090 TATATATA--TATGTA
1 TATATATATCTATCTA
1698104 TATATATAT
1 TATATATAT
1698113 TTTGTGGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.37
16 22 0.63
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (16 bp):
TATATATATCTATCTA
Found at i:1698083 original size:20 final size:20
Alignment explanation
Indices: 1698058--1698100 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1698048 CCATTGTATC
*
1698058 TATATCTATCTATTTATATA
1 TATATCTATCTATATATATA
1698078 TATATCTATCTATATATATA
1 TATATCTATCTATATATATA
1698098 TAT
1 TAT
1698101 GTATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATCTATCTATATATATA
Found at i:1698095 original size:4 final size:4
Alignment explanation
Indices: 1698058--1698112 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
1698048 CCATTGTATC
* * * * * *
1698058 TATA TCTA TCTA TTTA TATA TATA TCTA TCTA TATA TATA TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1698106 TATA TAT
1 TATA TAT
1698113 TTTGTGGGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (4 bp):
TATA
Found at i:1698111 original size:14 final size:14
Alignment explanation
Indices: 1698054--1698112 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
1698044 GTATCCATTG
* *
1698054 TATCTATATCTATC
1 TATCTATATATATA
*
1698068 TATTTATATATATA
1 TATCTATATATATA
1698082 TCTATCTATATATATA
1 --TATCTATATATATA
*
1698098 TATGTATATATATA
1 TATCTATATATATA
1698112 T
1 T
1698113 TTTGTGGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
14 25 0.66
16 13 0.34
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (14 bp):
TATCTATATATATA
Found at i:1704093 original size:34 final size:34
Alignment explanation
Indices: 1704050--1704118 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1704040 AGTAGTACTA
*
1704050 CTTTTGATATGAAGTATGCAACCTAGTGAAATGG
1 CTTTTGATATGAAGCATGCAACCTAGTGAAATGG
*
1704084 CTTTTGATATGAGGCATGCAACCTAGTGAAATGG
1 CTTTTGATATGAAGCATGCAACCTAGTGAAATGG
1704118 C
1 C
1704119 AGATACAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (34 bp):
CTTTTGATATGAAGCATGCAACCTAGTGAAATGG
Found at i:1704260 original size:86 final size:87
Alignment explanation
Indices: 1704114--1704287 Score: 314
Period size: 86 Copynumber: 2.0 Consensus size: 87
1704104 ACCTAGTGAA
*
1704114 ATGGCAGATACAGAATGCAACAATAAATTTCATGGAACCAGACCAACATTAAAGGACATAAATTA
1 ATGGCAGATACAGAATGCAACAATAAATTTCATGGAACCAGACCAACATTAAAGGACATAAACTA
1704179 AAGCTTTTAGGCGCACAGCAAG
66 AAGCTTTTAGGCGCACAGCAAG
*
1704201 ATGGCAGATACAGAATGCAACAA-CAATTTCATGGAACCAGACCAACATTAAAGGACATAAACTA
1 ATGGCAGATACAGAATGCAACAATAAATTTCATGGAACCAGACCAACATTAAAGGACATAAACTA
*
1704265 CAGCTTTTAGGCGCACAGCAAG
66 AAGCTTTTAGGCGCACAGCAAG
1704287 A
1 A
1704288 ACATGTTGGC
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
86 61 0.73
87 23 0.27
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (87 bp):
ATGGCAGATACAGAATGCAACAATAAATTTCATGGAACCAGACCAACATTAAAGGACATAAACTA
AAGCTTTTAGGCGCACAGCAAG
Found at i:1707422 original size:16 final size:19
Alignment explanation
Indices: 1707384--1707425 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1707374 TTACAAATTT
*
1707384 AATTATTTCATTTATATAT
1 AATTATTTCATTTATATAA
1707403 AATT-TTTCATTT-T-TAA
1 AATTATTTCATTTATATAA
1707419 AATTATT
1 AATTATT
1707426 ATTCTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.29
17 3 0.14
18 8 0.38
19 4 0.19
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTATTTCATTTATATAA
Found at i:1712118 original size:16 final size:15
Alignment explanation
Indices: 1712097--1712126 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1712087 AATATGATGA
1712097 TAATTATTTTATTTTT
1 TAATTATTTT-TTTTT
1712113 TAATTATTTTTTTT
1 TAATTATTTTTTTT
1712127 AAATATCGAT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TAATTATTTTTTTTT
Found at i:1722544 original size:21 final size:21
Alignment explanation
Indices: 1722519--1722570 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
1722509 ACCGGAATAC
1722519 AAGAAAATTTAATT-AAT-AT
1 AAGAAAATTTAATTAAATAAT
* *
1722538 ATGAGAATTTAATTAAATAAT
1 AAGAAAATTTAATTAAATAAT
1722559 AAGAAAATTTAA
1 AAGAAAATTTAA
1722571 AACAATATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (21 bp):
AAGAAAATTTAATTAAATAAT
Found at i:1730073 original size:29 final size:29
Alignment explanation
Indices: 1730025--1730082 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1730015 AGATTGGATA
*
1730025 CTTAAACAAGGGTTAAGTCAATTAGCCCT
1 CTTAAACAAGGGCTAAGTCAATTAGCCCT
*
1730054 CTTAAACAAGGGCTATGTCAATTAGCCCT
1 CTTAAACAAGGGCTAAGTCAATTAGCCCT
1730083 GCAGGGGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (29 bp):
CTTAAACAAGGGCTAAGTCAATTAGCCCT
Found at i:1732994 original size:84 final size:84
Alignment explanation
Indices: 1732853--1733014 Score: 225
Period size: 84 Copynumber: 1.9 Consensus size: 84
1732843 CAAGCATTTT
** * *
1732853 AGTGCATAGATATGTACACTTATGTGTCATATGTGGTTATAGGATAGAATTTCCTCTGTTTAACT
1 AGTGCATAGATACATACACTTATGTATCATATGTGGTTATAGGATAGAATTTACTCTGTTTAACT
1732918 TACCTCCACAACATATCGA
66 TACCTCCACAACATATCGA
* ** * * * *
1732937 AGTGCATAGATACATACGCTTATGTATTGTATGTGGTTATCGGTTAGGATTTACTCTGTTTGACT
1 AGTGCATAGATACATACACTTATGTATCATATGTGGTTATAGGATAGAATTTACTCTGTTTAACT
1733002 TACCTCCACAACA
66 TACCTCCACAACA
1733015 AAGCTGACCG
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 67 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (84 bp):
AGTGCATAGATACATACACTTATGTATCATATGTGGTTATAGGATAGAATTTACTCTGTTTAACT
TACCTCCACAACATATCGA
Found at i:1746391 original size:16 final size:16
Alignment explanation
Indices: 1746372--1746413 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1746362 TCTTAATACT
1746372 TATTTTAATTAAAAAA
1 TATTTTAATTAAAAAA
*
1746388 TATTAT-ATATAAAAAA
1 TATTTTAAT-TAAAAAA
*
1746404 TTTTTTAATT
1 TATTTTAATT
1746414 TTTAATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 2 0.10
16 17 0.81
17 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTTAATTAAAAAA
Found at i:1752196 original size:33 final size:33
Alignment explanation
Indices: 1752159--1752247 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
1752149 GGGTAGTGGT
*
1752159 ATTGGTGCTGGAGTTGGGCTTGTTGGAACTGGA
1 ATTGGTGCTGGAGTTGGGCTTGTTGGAACCGGA
* *
1752192 ATTGGTGCTGGAGTTGGACTTGTTGGAACCGGT
1 ATTGGTGCTGGAGTTGGGCTTGTTGGAACCGGA
* *
1752225 GTTGGTGCTGGAGTTGGGATTGT
1 ATTGGTGCTGGAGTTGGGCTTGT
1752248 CGGGAGTGGC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.13, C:0.09, G:0.43, T:0.35
Consensus pattern (33 bp):
ATTGGTGCTGGAGTTGGGCTTGTTGGAACCGGA
Found at i:1756589 original size:72 final size:72
Alignment explanation
Indices: 1756421--1756671 Score: 227
Period size: 72 Copynumber: 3.5 Consensus size: 72
1756411 GAATGTTGAT
** * * ** * * *
1756421 ATTATATTTTTGAAATTATGTAATTTTAATAAATACCGCATTTTT-AG-TATAAAAATGTAGTGA
1 ATTATATTTTCAAAATTATATAATTTTAATAAAAACCAAATTTTTAAGATA-AAAAATGCAATGG
*
1756484 ATATTGAA
65 ATATTAAA
* * * * * **
1756492 ACTATACTTTGAAAATTCTAAAATTTTAATAAAAACCTTATTTTTAAGATAAAAAATGCAATGGA
1 ATTATATTTTCAAAATTATATAATTTTAATAAAAACCAAATTTTTAAGATAAAAAATGCAATGGA
1756557 TATTAAA
66 TATTAAA
* * ** * ** *
1756564 ATTATATTTTCAAAATTCTATAATTTTAATAAAGATGAAATTTTTAAAATAAAAAAACACAATAG
1 ATTATATTTTCAAAATTATATAATTTTAATAAAAACCAAATTTTTAAGAT-AAAAAATGCAATGG
*
1756629 ATGTTAAA
65 ATATTAAA
*
1756637 ATTATATTTTCAAAATTATATAATTTTAACAAAAA
1 ATTATATTTTCAAAATTATATAATTTTAATAAAAA
1756672 TCATGTTTTT
Statistics
Matches: 146, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
71 35 0.24
72 59 0.40
73 52 0.36
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (72 bp):
ATTATATTTTCAAAATTATATAATTTTAATAAAAACCAAATTTTTAAGATAAAAAATGCAATGGA
TATTAAA
Found at i:1756659 original size:73 final size:73
Alignment explanation
Indices: 1756484--1756694 Score: 217
Period size: 73 Copynumber: 2.9 Consensus size: 73
1756474 AATGTAGTGA
* * * * * * * * ** *
1756484 ATATTGAAACTATACTTTGAAAATTCTAAAATTTTAATAAAAACCTTATTTTTAAGAT-AAAAAA
1 ATATTAAAATTATATTTTCAAAATTATATAATTTTAACAAAAATCAAATTTTTAAAATAAAAAAA
** *
1756548 TGCAATGG
66 CACAATAG
* * * *
1756556 ATATTAAAATTATATTTTCAAAATTCTATAATTTTAATAAAGATGAAATTTTTAAAATAAAAAAA
1 ATATTAAAATTATATTTTCAAAATTATATAATTTTAACAAAAATCAAATTTTTAAAATAAAAAAA
1756621 CACAATAG
66 CACAATAG
* **
1756629 ATGTTAAAATTATATTTTCAAAATTATATAATTTTAACAAAAATCATGTTTTTAAAATTAAAAAA
1 ATATTAAAATTATATTTTCAAAATTATATAATTTTAACAAAAATCAAATTTTTAAAA-TAAAAAA
1756694 A
65 A
1756695 GGCATCGAAT
Statistics
Matches: 116, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
72 47 0.41
73 61 0.53
74 8 0.07
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (73 bp):
ATATTAAAATTATATTTTCAAAATTATATAATTTTAACAAAAATCAAATTTTTAAAATAAAAAAA
CACAATAG
Found at i:1757460 original size:38 final size:40
Alignment explanation
Indices: 1757372--1757460 Score: 91
Period size: 38 Copynumber: 2.3 Consensus size: 40
1757362 ATTGTTTAAT
1757372 TATTATTTTAGAAAATTTTTACATTTAATTTACTATTTCTA
1 TATTATTTTA-AAAATTTTTACATTTAATTTACTATTTCTA
*
1757413 TCA--AATTTAAAAA-TTTTACA-TTAATTT-C-ATTTTCTAA
1 T-ATTATTTTAAAAATTTTTACATTTAATTTACTA-TTTCT-A
1757450 TATTATTTTAA
1 TATTATTTTAA
1757461 TCAATGTCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
35 1 0.02
36 7 0.17
37 9 0.22
38 13 0.32
39 4 0.10
40 5 0.12
41 1 0.02
42 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (40 bp):
TATTATTTTAAAAATTTTTACATTTAATTTACTATTTCTA
Found at i:1760701 original size:21 final size:22
Alignment explanation
Indices: 1760669--1760711 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1760659 GTCATTAAAT
1760669 ATTAAATCTATTT-ATATCCTC
1 ATTAAATCTATTTGATATCCTC
*
1760690 ATTAAA-CATATTTGATCTCCTC
1 ATTAAATC-TATTTGATATCCTC
1760712 CGCGATACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 11 0.58
22 7 0.37
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTAAATCTATTTGATATCCTC
Found at i:1763899 original size:20 final size:20
Alignment explanation
Indices: 1763870--1763966 Score: 70
Period size: 22 Copynumber: 4.6 Consensus size: 20
1763860 TTTATATTTT
*
1763870 AAATACTTATATTTTAATAA
1 AAATAATTATATTTTAATAA
*
1763890 AAATAATTATAATTTAATAA
1 AAATAATTATATTTTAATAA
* * * *
1763910 ATAATCATAACTATTTGAATAT
1 A-AATAATTA-TATTTTAATAA
1763932 AAATAAATTATTATTTATAA-AA
1 AAAT-AATTA-TATTT-TAATAA
*
1763954 ATCATAATTATAT
1 A-AATAATTATAT
1763967 AAAAATTATA
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
20 19 0.32
21 12 0.20
22 24 0.41
23 4 0.07
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (20 bp):
AAATAATTATATTTTAATAA
Found at i:1763913 original size:18 final size:18
Alignment explanation
Indices: 1763869--1763979 Score: 59
Period size: 18 Copynumber: 5.8 Consensus size: 18
1763859 ATTTATATTT
* *
1763869 TAAATACTTATATTTTAA
1 TAAATAATTATAATTTAA
1763887 TAAAAATAATTATAATTTAA
1 T--AAATAATTATAATTTAA
*
1763907 TAAATAATCATAACTATTTGAATA
1 TAAATAATTAT-A--ATTT--A-A
*
1763931 TAAATAAATTATTATTT-A
1 TAAAT-AATTATAATTTAA
*
1763949 TAAA-AATCATAA-TTATA
1 TAAATAATTATAATTTA-A
1763966 TAAA-AATTATAATT
1 TAAATAATTATAATT
1763980 ATTTGAATAG
Statistics
Matches: 73, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
15 2 0.03
16 6 0.08
17 12 0.16
18 16 0.22
19 1 0.01
20 16 0.22
21 4 0.05
22 4 0.05
23 1 0.01
24 6 0.08
25 5 0.07
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (18 bp):
TAAATAATTATAATTTAA
Found at i:1763925 original size:42 final size:41
Alignment explanation
Indices: 1763879--1763960 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
1763869 TAAATACTTA
*
1763879 TATTTTAATAAAAAT-AATTATAATTTAATAAATAATCATAAC
1 TATTTGAATAAAAATAAATTATAATTT-ATAAA-AATCATAAC
* *
1763921 TATTTGAATATAAATAAATTATTATTTATAAAAATCATAA
1 TATTTGAATAAAAATAAATTATAATTTATAAAAATCATAA
1763961 TTATATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 8 0.22
42 18 0.50
43 10 0.28
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (41 bp):
TATTTGAATAAAAATAAATTATAATTTATAAAAATCATAAC
Found at i:1763969 original size:17 final size:17
Alignment explanation
Indices: 1763947--1763981 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1763937 AATTATTATT
1763947 TATAAAAATCATAATTA
1 TATAAAAATCATAATTA
*
1763964 TATAAAAATTATAATTA
1 TATAAAAATCATAATTA
1763981 T
1 T
1763982 TTGAATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TATAAAAATCATAATTA
Found at i:1774358 original size:1 final size:1
Alignment explanation
Indices: 1774352--1774377 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1774342 GCACCAGTTG
1774352 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1774378 CTGTATCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1778427 original size:28 final size:26
Alignment explanation
Indices: 1778372--1778424 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1778362 TATATCATTT
*
1778372 ATTTTTTATATTAATATTTATATAAA
1 ATTTTTTACATTAATATTTATATAAA
*
1778398 ATTTTTTACATTAGTATTTATATAAA
1 ATTTTTTACATTAATATTTATATAAA
1778424 A
1 A
1778425 AATATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTTTTACATTAATATTTATATAAA
Found at i:1779695 original size:6 final size:6
Alignment explanation
Indices: 1779686--1779729 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
1779676 AGCGCAACCA
*
1779686 CAACCG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CA
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CA
1779730 GCCACTGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.48, C:0.36, G:0.16, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:1785005 original size:7 final size:7
Alignment explanation
Indices: 1784989--1785038 Score: 72
Period size: 7 Copynumber: 7.7 Consensus size: 7
1784979 TGCAATTGGT
1784989 ATTA-TA
1 ATTATTA
1784995 ATTATTA
1 ATTATTA
1785002 ATTATTA
1 ATTATTA
1785009 ATTATTA
1 ATTATTA
1785016 ATTATT-
1 ATTATTA
1785022 ATTATT-
1 ATTATTA
1785028 ATTATT-
1 ATTATTA
1785034 ATTAT
1 ATTAT
1785039 GACAAGTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.49
7 22 0.51
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTATTA
Found at i:1785008 original size:3 final size:3
Alignment explanation
Indices: 1784988--1785038 Score: 66
Period size: 3 Copynumber: 16.0 Consensus size: 3
1784978 GTGCAATTGG
*
1784988 TAT TAT AAT TAT TAAT TAT TAAT TAT TAAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT T-AT TAT T-AT TAT TAT TAT TAT TAT TAT
1785036 TAT
1 TAT
1785039 GACAAGTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 34 0.79
4 9 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1791905 original size:6 final size:6
Alignment explanation
Indices: 1791896--1791922 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1791886 TTCGTAGAGG
1791896 ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATA
1791923 TATAATCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:1794226 original size:22 final size:22
Alignment explanation
Indices: 1794201--1794249 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1794191 TATATAACGA
1794201 GATTTTTCAA-TTTATTAATTTT
1 GATTTTT-AATTTTATTAATTTT
*
1794223 GATTTTTAATTTTTTTAATTTT
1 GATTTTTAATTTTATTAATTTT
*
1794245 AATTT
1 GATTT
1794250 AATTTGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
GATTTTTAATTTTATTAATTTT
Found at i:1795866 original size:2 final size:2
Alignment explanation
Indices: 1795859--1795891 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1795849 TGAATTTGTC
1795859 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 A
1795892 CATAGTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1799107 original size:42 final size:42
Alignment explanation
Indices: 1799023--1799108 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
1799013 AGGTTAACAT
** *
1799023 GGCATACAATTTGTTAACTGTTCAAATGGGTTTAGGGTTTAA
1 GGCATACAATTTGTTAACTGTTCAAATGGGTCGAGGGCTTAA
1799065 GGCATACAATTTGTTAACTGTTCAAATGGG-CGAGGAGCTTAA
1 GGCATACAATTTGTTAACTGTTCAAATGGGTCGAGG-GCTTAA
1799107 GG
1 GG
1799109 GAATGAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 3 0.08
42 37 0.93
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33
Consensus pattern (42 bp):
GGCATACAATTTGTTAACTGTTCAAATGGGTCGAGGGCTTAA
Found at i:1803432 original size:1 final size:1
Alignment explanation
Indices: 1803426--1803461 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
1803416 CAAGGAAAGC
**
1803426 TTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1803462 GCATTTATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:1804267 original size:140 final size:140
Alignment explanation
Indices: 1804008--1804280 Score: 440
Period size: 140 Copynumber: 1.9 Consensus size: 140
1803998 TGAAACCTTC
* * * * *
1804008 TCACATACTAGCCACGTCTACGTAATCTCCAATCTGCATGCGTCAAGGAAAAAGTTAAGGACAAA
1 TCACATAATAGCCACGTCTAAGTAATCTCCAATCTGCATACGTCAAGGAAAAAGTTAAAGAAAAA
* *
1804073 GCTTGAACATAGGTAAGACAATGATTGATGCCACTACAAAGTGAGATTCTGCCTACCTC-AAGCT
66 GCTTGAACATAGGTAAGACAATGACTGATGCCACTACAAAGTGAGATTCCGCCTACCTCAAAGCT
1804137 AAGCCTTCTT
131 AAGCCTTCTT
*
1804147 TCACATAATAGCCACGTCTAAGTAATCTCCAATCTGCATATGTCAAGGAAAAAGTTAAAAGAAAA
1 TCACATAATAGCCACGTCTAAGTAATCTCCAATCTGCATACGTCAAGGAAAAAGTT-AAAGAAAA
* *
1804212 AGCTTGAGCATAGGTAAGACAATGACTGATGCCGCTACAAAGTGAGATTCCGCCTACCTCAAAGC
65 AGCTTGAACATAGGTAAGACAATGACTGATGCCACTACAAAGTGAGATTCCGCCTACCTCAAAGC
1804277 TAAG
130 TAAG
1804281 TTCACCTAAG
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
139 52 0.43
140 62 0.51
141 8 0.07
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (140 bp):
TCACATAATAGCCACGTCTAAGTAATCTCCAATCTGCATACGTCAAGGAAAAAGTTAAAGAAAAA
GCTTGAACATAGGTAAGACAATGACTGATGCCACTACAAAGTGAGATTCCGCCTACCTCAAAGCT
AAGCCTTCTT
Found at i:1808971 original size:20 final size:21
Alignment explanation
Indices: 1808946--1808990 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1808936 GATTAAAACG
1808946 ATATATTATTT-ATAAA-TTAA
1 ATATATTATTTCA-AAATTTAA
*
1808966 ATATATTTTTTCAAAATTTAA
1 ATATATTATTTCAAAATTTAA
1808987 ATAT
1 ATAT
1808991 TAAAAGTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATATTATTTCAAAATTTAA
Done.