Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 11 of 17
Found at i:1563857 original size:2 final size:2
Alignment explanation
Indices: 1563850--1563874 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1563840 TGCACTGTAT
1563850 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1563875 GTATTTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1564242 original size:5 final size:5
Alignment explanation
Indices: 1564232--1564256 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1564222 AATTTATAAA
1564232 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
1564257 AATATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:1564290 original size:14 final size:14
Alignment explanation
Indices: 1564273--1564317 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1564263 ATTATTTAAA
1564273 TAAAAATTATTTTT
1 TAAAAATTATTTTT
* *
1564287 TAAAAATTATAATTA
1 TAAAAATTAT-TTTT
1564302 TAAAAA-TATTTTT
1 TAAAAATTATTTTT
1564315 TAA
1 TAA
1564318 TATTTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 5 0.19
14 13 0.50
15 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAAAATTATTTTT
Found at i:1564604 original size:2 final size:2
Alignment explanation
Indices: 1564597--1564638 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1564587 TGTTATTTCA
1564597 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1564639 GAAAATGCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1565762 original size:16 final size:15
Alignment explanation
Indices: 1565738--1565786 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1565728 TAGTTATAAA
*
1565738 TTAACAAAAAAAATGT
1 TTAAAAAAAAAAAT-T
1565754 TTAAAAAAATAAAAATT
1 TT-AAAAAA-AAAAATT
*
1565771 TTAAAAAAAAGAATT
1 TTAAAAAAAAAAATT
1565786 T
1 T
1565787 GAGTGGCCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 7 0.24
16 8 0.28
17 8 0.28
18 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (15 bp):
TTAAAAAAAAAAATT
Found at i:1565780 original size:18 final size:18
Alignment explanation
Indices: 1565746--1565779 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1565736 AATTAACAAA
1565746 AAAAATGTTTAAAAAAAT
1 AAAAATGTTTAAAAAAAT
1565764 AAAAAT-TTTAAAAAAA
1 AAAAATGTTTAAAAAAA
1565780 AGAATTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATGTTTAAAAAAAT
Found at i:1568312 original size:97 final size:96
Alignment explanation
Indices: 1568028--1568370 Score: 327
Period size: 97 Copynumber: 3.5 Consensus size: 96
1568018 AATTTTATTT
* * * * * * *
1568028 ATCGGGGATACTTCAACCCTATTCATTCGAGGGGATATTTCAACCTCGCTTTTAAACAC-ATCAA
1 ATCGGGGACACTTCAACCC-ATTCCTCCGAGGAGATACTCCAACCCCGCTTTTAAAC-CTATCAA
* * *
1568092 AGTTTAAATCTTATTCTCACTTAAATCGTCACC
64 AGTTTAATTCTTATTCTCACTTAAATTGTCATC
** * ** * *
1568125 ATCGGAAACACTTCAATCACATT-CTCCCGAGGAGATACTCCAACCCTACTTTTAAACGTATTAA
1 ATCGGGGACACTTCAA-CCCATTCCT-CCGAGGAGATACTCCAACCCCGCTTTTAAACCTATCAA
1568189 AGTTTAAATT-TTATTCTCACTTAAATTGTCATC
64 AGTTT-AATTCTTATTCTCACTTAAATTGTCATC
*
1568222 ATCGGGGACAC-TCTAACCCTATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACCTATCAA
1 ATCGGGGACACTTC-AACCC-ATTCCTCCGAGGAGATACTCCAACCCCGCTTTTAAACCTATCAA
* ** * *
1568286 AGTTTAATTCTTCTTCTTGCTTAAATTTTAATC
64 AGTTTAATTCTTATTCTCACTTAAATTGTCATC
* * * * *
1568319 ATCGGGGATACTCTGATCCCATTCCTTCGAGGAGATACT-CAACCCCGTTTTT
1 ATCGGGGACACT-TCAACCCATTCCTCCGAGGAGATACTCCAACCCCGCTTTT
1568371 CAATCAAAAG
Statistics
Matches: 200, Mismatches: 36, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
96 21 0.10
97 167 0.83
98 11 0.05
99 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (96 bp):
ATCGGGGACACTTCAACCCATTCCTCCGAGGAGATACTCCAACCCCGCTTTTAAACCTATCAAAG
TTTAATTCTTATTCTCACTTAAATTGTCATC
Found at i:1570248 original size:24 final size:26
Alignment explanation
Indices: 1570197--1570254 Score: 84
Period size: 24 Copynumber: 2.3 Consensus size: 26
1570187 TGGGTGGCTA
*
1570197 GTCAACAAAAACCACCCTTTGTGTTT
1 GTCAACAAAAACCACCCTATGTGTTT
*
1570223 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAACCACCCTATGTGTTT
1570247 GTCAACAA
1 GTCAACAA
1570255 TGGTGGTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 15 0.50
25 2 0.07
26 13 0.43
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAACCACCCTATGTGTTT
Found at i:1570283 original size:27 final size:27
Alignment explanation
Indices: 1570244--1570309 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
1570234 CCACCATGTG
*
1570244 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
1570271 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
1570298 TTTGTCAAAAAT
1 TTTGTCAAAAAT
1570310 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:1570339 original size:24 final size:24
Alignment explanation
Indices: 1570271--1570340 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
1570261 TTACTTTGTA
* *
1570271 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
1570298 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
1570322 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
1570341 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:1570412 original size:20 final size:20
Alignment explanation
Indices: 1570387--1570424 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1570377 AAAAGGAAGC
*
1570387 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
1570407 TCCCTCATCCCTCTCAAG
1 TCCCTCATCCCTCTCAAG
1570425 CATTCTCTCT
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:0.16, C:0.50, G:0.05, T:0.29
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:1572940 original size:21 final size:22
Alignment explanation
Indices: 1572897--1572942 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1572887 TGTTCAGACA
* *
1572897 AGTAGTACTCCACAGCAGATGG
1 AGTAGTACTCCAAAACAGATGG
*
1572919 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGATGG
1572940 AGT
1 AGT
1572943 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGATGG
Found at i:1574857 original size:24 final size:26
Alignment explanation
Indices: 1574806--1574863 Score: 84
Period size: 24 Copynumber: 2.3 Consensus size: 26
1574796 TGGGTGGCTA
*
1574806 GTCAACAAAAACCACCCTTTGTGTTT
1 GTCAACAAAAACCACCCTATGTGTTT
*
1574832 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAACCACCCTATGTGTTT
1574856 GTCAACAA
1 GTCAACAA
1574864 TGGTGGTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 15 0.50
25 2 0.07
26 13 0.43
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAACCACCCTATGTGTTT
Found at i:1574892 original size:27 final size:27
Alignment explanation
Indices: 1574853--1574918 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
1574843 CCACCATGTG
*
1574853 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
1574880 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
1574907 TTTGTCAAAAAT
1 TTTGTCAAAAAT
1574919 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:1574948 original size:24 final size:24
Alignment explanation
Indices: 1574880--1574949 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
1574870 TTACTTTGTA
* *
1574880 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
1574907 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
1574931 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
1574950 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:1575021 original size:20 final size:20
Alignment explanation
Indices: 1574996--1575033 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1574986 AAAAGGAAGC
*
1574996 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
1575016 TCCCTCATCCCTCTCAAG
1 TCCCTCATCCCTCTCAAG
1575034 CATTCTCTCT
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:0.16, C:0.50, G:0.05, T:0.29
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:1575443 original size:5 final size:5
Alignment explanation
Indices: 1575433--1575496 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
1575423 AATTAATCAT
* * *
1575433 TTATA TTATA -TAAA TTTTG TTATA TTTATA TTATA TTAT- TT-T- TTATA
1 TTATA TTATA TTATA TTATA TTATA -TTATA TTATA TTATA TTATA TTATA
1575480 TTATA -TA-A TTATA TTAT
1 TTATA TTATA TTATA TTAT
1575497 GTCTAAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
3 4 0.09
4 10 0.21
5 28 0.60
6 5 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1575494 original size:25 final size:24
Alignment explanation
Indices: 1575431--1575496 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 24
1575421 ATAATTAATC
*
1575431 ATTTATATTATATAAATTTTGTTAT
1 ATTTATATTATAT-TATTTTGTTAT
1575456 ATTTATATTATATTATTTT-TTAT
1 ATTTATATTATATTATTTTGTTAT
1575479 ATTATATAATTATATTAT
1 ATT-TAT-ATTATATTAT
1575497 GTCTAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
23 7 0.18
24 8 0.21
25 23 0.61
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTTATATTATATTATTTTGTTAT
Found at i:1584349 original size:2 final size:2
Alignment explanation
Indices: 1584344--1584378 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1584334 ATTATATAAA
1584344 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1584379 AGACTGGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1585972 original size:2 final size:2
Alignment explanation
Indices: 1585965--1586010 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1585955 TTTTTAGCCT
1585965 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1586007 TA TA
1 TA TA
1586011 ATTTAGATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1588198 original size:22 final size:21
Alignment explanation
Indices: 1588157--1588204 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
1588147 CGAAAAGAAA
1588157 AGAGAAAAAAGGAAGAAATAG
1 AGAGAAAAAAGGAAGAAATAG
* *
1588178 AGAGAAAACTAGGGAGAAATAG
1 AGAGAAAA-AAGGAAGAAATAG
1588200 AGAGA
1 AGAGA
1588205 GAGCACTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.60, C:0.02, G:0.31, T:0.06
Consensus pattern (21 bp):
AGAGAAAAAAGGAAGAAATAG
Found at i:1588570 original size:24 final size:24
Alignment explanation
Indices: 1588526--1588575 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1588516 CTGATTTAGA
* *
1588526 TGATGTTGATTTTGCTCTTGTGGT
1 TGATGCTGATGTTGCTCTTGTGGT
*
1588550 TGATGCTGATGTT-CTCGTTGTTGT
1 TGATGCTGATGTTGCTC-TTGTGGT
1588574 TG
1 TG
1588576 CTGCAGCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.08, C:0.10, G:0.30, T:0.52
Consensus pattern (24 bp):
TGATGCTGATGTTGCTCTTGTGGT
Found at i:1588604 original size:9 final size:9
Alignment explanation
Indices: 1588592--1588622 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1588582 CTGATTTTGA
1588592 TGATGATAT
1 TGATGATAT
1588601 TGATGATAT
1 TGATGATAT
*
1588610 TGATGATGT
1 TGATGATAT
1588619 TGAT
1 TGAT
1588623 TATTATGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (9 bp):
TGATGATAT
Found at i:1589103 original size:2 final size:2
Alignment explanation
Indices: 1589098--1589131 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1589088 AAGATCTGAA
*
1589098 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1589132 ATTTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1591051 original size:4 final size:4
Alignment explanation
Indices: 1591044--1591076 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1591034 AGCTACTATA
1591044 TAAT TAAT TAAT TAAT TAAT TAAAT TAA- TAAT T
1 TAAT TAAT TAAT TAAT TAAT T-AAT TAAT TAAT T
1591077 TTTTTATCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.11
4 20 0.74
5 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:1592061 original size:25 final size:24
Alignment explanation
Indices: 1592005--1592062 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 24
1591995 TTTATATGAC
1592005 ATAAAAATTATATAATGTATATAA
1 ATAAAAATTATATAATGTATATAA
1592029 ATACAAAATTA-AT-ATGTATTATATA
1 ATA-AAAATTATATAATGTA-TATA-A
1592054 ATTAAAAAT
1 A-TAAAAAT
1592063 AATCACTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 5 0.17
24 9 0.30
25 14 0.47
26 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
ATAAAAATTATATAATGTATATAA
Found at i:1592367 original size:20 final size:22
Alignment explanation
Indices: 1592322--1592372 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 22
1592312 TTAATGTTAA
1592322 ATTTATTTAATTATATATATTT
1 ATTTATTTAATTATATATATTT
1592344 -TTTA-TTAA-T-TA-AT-TTT
1 ATTTATTTAATTATATATATTT
1592360 -TTTATTTAATTAT
1 ATTTATTTAATTAT
1592373 TTGACTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
16 7 0.27
17 6 0.23
18 3 0.12
19 2 0.08
20 4 0.15
21 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTATTTAATTATATATATTT
Found at i:1598138 original size:2 final size:2
Alignment explanation
Indices: 1598131--1598178 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1598121 ACTAGTTGTT
1598131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1598173 TA TA TA
1 TA TA TA
1598179 GTTTATGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1600137 original size:2 final size:2
Alignment explanation
Indices: 1600132--1600167 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1600122 CTAAACCCGA
1600132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1600168 AAATCAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1601465 original size:18 final size:20
Alignment explanation
Indices: 1601442--1601485 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 20
1601432 CAATAATTTA
*
1601442 TATTTTTTAT-TTTTAT-AT
1 TATTTTTTATGTGTTATAAT
1601460 TA-TTTTTATGTGTTATAAT
1 TATTTTTTATGTGTTATAAT
1601479 TATTTTT
1 TATTTTT
1601486 AAAATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 4 0.18
20 4 0.18
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (20 bp):
TATTTTTTATGTGTTATAAT
Found at i:1601480 original size:19 final size:17
Alignment explanation
Indices: 1601445--1601486 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
1601435 TAATTTATAT
*
1601445 TTTTTATTTTTATATTA
1 TTTTTATTGTTATATTA
1601462 TTTTTATGTGTTATAATTA
1 TTTTTAT-TGTTAT-ATTA
1601481 TTTTTA
1 TTTTTA
1601487 AAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 5 0.23
19 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTTTATTGTTATATTA
Found at i:1602429 original size:14 final size:14
Alignment explanation
Indices: 1602412--1602455 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1602402 AAGTTTAATA
1602412 AATATAATTTATTT
1 AATATAATTTATTT
*
1602426 AATATAATATATTT
1 AATATAATTTATTT
*
1602440 CATATACATTTTATTT
1 AATATA-A-TTTATTT
1602456 CTTTATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 18 0.72
15 1 0.04
16 6 0.24
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATAATTTATTT
Found at i:1602540 original size:2 final size:2
Alignment explanation
Indices: 1602533--1602565 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1602523 AAATGCAATG
1602533 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1602566 TATTAGATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1603334 original size:3 final size:3
Alignment explanation
Indices: 1603328--1603376 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1603318 TTTTAAAATA
1603328 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1603376 T
1 T
1603377 TAGCTCAGCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1605622 original size:6 final size:6
Alignment explanation
Indices: 1605592--1605664 Score: 55
Period size: 6 Copynumber: 12.3 Consensus size: 6
1605582 ATACGGTATA
* * * *
1605592 TATATT TAT-TA TATGTT TCATATT TATATT TAAAATT T-T-TG TATATT
1 TATATT TATATT TATATT T-ATATT TATATT T-ATATT TATATT TATATT
1605639 TATAATT TATA-T TATATT TATATT TA
1 TAT-ATT TATATT TATATT TATATT TA
1605665 CTTAATTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
4 2 0.04
5 10 0.19
6 25 0.47
7 16 0.30
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:1605774 original size:18 final size:18
Alignment explanation
Indices: 1605751--1605819 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
1605741 TAAAATAAAA
1605751 TAAAATAAAATAATTTAC
1 TAAAATAAAATAATTTAC
* *
1605769 TAAAATAAAATAA--AAT
1 TAAAATAAAATAATTTAC
1605785 TAAAAT-AAATAAATATTATC
1 TAAAATAAAAT-AAT-TTA-C
1605805 TAAAATCAAAATAAT
1 TAAAAT-AAAATAAT
1605820 CATTCAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
15 4 0.10
16 9 0.22
18 13 0.32
19 1 0.03
20 6 0.15
21 3 0.08
22 4 0.10
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAATAAAATAATTTAC
Found at i:1605783 original size:33 final size:36
Alignment explanation
Indices: 1605741--1605818 Score: 110
Period size: 34 Copynumber: 2.2 Consensus size: 36
1605731 TTTAATTCAT
1605741 TAAAATAAAA-TAAAATAAA-ATAAT-TTA-CTAAAA
1 TAAAATAAAATTAAAATAAATA-AATATTATCTAAAA
1605774 TAAAATAAAATTAAAATAAATAAATATTATCTAAAA
1 TAAAATAAAATTAAAATAAATAAATATTATCTAAAA
1605810 TCAAAATAA
1 T-AAAATAA
1605819 TCATTCAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
33 10 0.25
34 12 0.30
35 4 0.10
36 7 0.17
37 7 0.17
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (36 bp):
TAAAATAAAATTAAAATAAATAAATATTATCTAAAA
Found at i:1605790 original size:6 final size:5
Alignment explanation
Indices: 1605741--1605797 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
1605731 TTTAATTCAT
*
1605741 TAAAA TAAAA TAAAA TAAAA TAATTTAC TAAAA TAAAA TAAAA TTAAAA
1 TAAAA TAAAA TAAAA TAAAA TAA---AA TAAAA TAAAA TAAAA -TAAAA
1605790 T-AAA TAAA
1 TAAAA TAAA
1605798 TATTATCTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 32 0.71
6 5 0.11
8 4 0.09
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (5 bp):
TAAAA
Found at i:1606340 original size:6 final size:6
Alignment explanation
Indices: 1606329--1606360 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1606319 AAAGGCGCAG
1606329 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
1606361 GGGTCCCCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:1607686 original size:76 final size:77
Alignment explanation
Indices: 1607559--1607718 Score: 259
Period size: 76 Copynumber: 2.1 Consensus size: 77
1607549 TCAGTTTTAA
* *
1607559 AACAGAAATCATATAGATAGCATAAATGAACACAAATCCACAAAATCTACTACCTTCAGGAGAAG
1 AACAGAAATCATATAGATAGAACAAATGAACACAAATCCACAAAATCTACTACCTTCAGGAGAAG
1607624 GTTACACATCAT
66 GTTACACATCAT
* * *
1607636 AACAGAAATCATATAGATA-AACAAATGAACACAAATCCACCAAATCTACTACTTTCAGGTGAAG
1 AACAGAAATCATATAGATAGAACAAATGAACACAAATCCACAAAATCTACTACCTTCAGGAGAAG
1607700 GTTACACATCAT
66 GTTACACATCAT
*
1607712 ACCAGAA
1 AACAGAA
1607719 CCCAACACCT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
76 58 0.75
77 19 0.25
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (77 bp):
AACAGAAATCATATAGATAGAACAAATGAACACAAATCCACAAAATCTACTACCTTCAGGAGAAG
GTTACACATCAT
Found at i:1614040 original size:21 final size:20
Alignment explanation
Indices: 1614016--1614066 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1614006 GTATAACTTT
*
1614016 TTTATTATTTGATTTCATAAA
1 TTTATAATTT-ATTTCATAAA
* *
1614037 TTTATAATTTTTTTTATAAA
1 TTTATAATTTATTTCATAAA
1614057 TTTACTAATT
1 TTTA-TAATT
1614067 GAATTAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTATAATTTATTTCATAAA
Found at i:1615517 original size:71 final size:73
Alignment explanation
Indices: 1615440--1615759 Score: 237
Period size: 71 Copynumber: 4.6 Consensus size: 73
1615430 ATTAAAAATT
*
1615440 TTTTTAAGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTTAATTTTTTGGTATGATTATACG
1 TTTTTAAGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTTAATTTTTGGGTATGATTATACG
1615505 AG-TTAAA
66 AGTTTAAA
* ** * * * *** *
1615512 -ATTTAAAATATAATATATCTTTATTTATAAAAGTTTAAA-TGCGTTTCTTGGGCAT-ACTTATA
1 TTTTTAAGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTTAATTT-TTGGGTATGA-TTATA
*
1615574 TGAGTTTAAA
64 CGAGTTTAAA
* * *
1615584 TTTTTATGGTA-TA---AT-TTT-TTTGTAGAAGTTTAAA--TAAGTTTTT-TGTATGATTATAC
1 TTTTTAAGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTTAA-TTTTTGGGTATGATTATAC
*
1615640 GAGTTTATAT
65 GAGTTTA-AA
** * * * ** *
1615650 TTTTTATCGT-TAATTTATTTTTATTTATAAAAAATTAAATTT-GTTTTTGGGT-TGA-TATA--
1 TTTTTAAGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTTAATTTTTGGGTATGATTATACG
1615709 AGTTTAAA
66 AGTTTAAA
* *
1615717 TTTTTAGGGTATTATTTATCTTTATTTGTAGAAGTTTAAATTT
1 TTTTTAAGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTT
1615760 TTATTTAAAG
Statistics
Matches: 188, Mismatches: 43, Indels: 38
0.70 0.16 0.14
Matches are distributed among these distances:
65 15 0.08
66 14 0.07
67 26 0.14
68 35 0.19
69 4 0.02
70 12 0.06
71 67 0.36
72 8 0.04
73 7 0.04
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (73 bp):
TTTTTAAGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTTAATTTTTGGGTATGATTATACG
AGTTTAAA
Found at i:1615688 original size:138 final size:135
Alignment explanation
Indices: 1615440--1615757 Score: 322
Period size: 138 Copynumber: 2.3 Consensus size: 135
1615430 ATTAAAAATT
* *
1615440 TTTTTAAGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTTAATTTTTTGGTATGATTATACG
1 TTTTTAGGGTATTA--TATCTTTATTTGTAGAAGTTTAAA--TAATTTTTTGGTATGATTATACG
**
1615505 AGTTAAAATTTAAAATATAATATATCTTTATTTATAAAAGTTTAAATGCGTTTCTTGGGCATACT
62 AGTTAAAATTTAAAATATAATATATCTTTATTTATAAAAAATTAAATGCGTTT-TTGGG--T--T
* *
1615570 TATATGAGTTTAAA
122 GATATAAGTTTAAA
*
1615584 TTTTTATGGTA-TA-AT-TTT-TTTGTAGAAGTTTAAATAAGTTTTTT-GTATGATTATACGAGT
1 TTTTTAGGGTATTATATCTTTATTTGTAGAAGTTTAAATAA-TTTTTTGGTATGATTATACGAGT
* * *** * * * **
1615644 TTATATTTTTTATCGTTAATTTATTTTTATTTATAAAAAATTAAATTTGTTTTTGGGTTGATATA
65 TAAAATTTAAAAT--ATAATATATCTTTATTTATAAAAAATTAAATGCGTTTTTGGGTTGATATA
1615709 AGTTTAAA
128 AGTTTAAA
1615717 TTTTTAGGGTATTATTTATCTTTATTTGTAGAAGTTTAAAT
1 TTTTTAGGGTATTA--TATCTTTATTTGTAGAAGTTTAAAT
1615758 TTTTATTTAA
Statistics
Matches: 148, Mismatches: 17, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
133 23 0.16
134 2 0.01
135 1 0.01
136 27 0.18
137 13 0.09
138 48 0.32
139 20 0.14
140 2 0.01
143 2 0.01
144 10 0.07
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (135 bp):
TTTTTAGGGTATTATATCTTTATTTGTAGAAGTTTAAATAATTTTTTGGTATGATTATACGAGTT
AAAATTTAAAATATAATATATCTTTATTTATAAAAAATTAAATGCGTTTTTGGGTTGATATAAGT
TTAAA
Found at i:1619987 original size:42 final size:42
Alignment explanation
Indices: 1619907--1619987 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
1619897 TTTTAAAAAG
*
1619907 TAAATTTATTTTTTATAAAAATTAATTAATATTAAATTACAA
1 TAAATTTATTTTTTATAAAAATCAATTAATATTAAATTACAA
*
1619949 TAAATTTGATTTTTTATAAATAA-CAATTAA-ATTTAATTA
1 TAAATTT-ATTTTTTATAAA-AATCAATTAATATTAAATTA
1619988 TAATTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 15 0.43
43 18 0.51
44 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (42 bp):
TAAATTTATTTTTTATAAAAATCAATTAATATTAAATTACAA
Found at i:1621365 original size:30 final size:30
Alignment explanation
Indices: 1621331--1621389 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1621321 TTTATATATC
* * *
1621331 AATAAGATTAAAGTATAACGACAAAAATTA
1 AATAAAATTAAAATATAACGAAAAAAATTA
*
1621361 AATAAAATTAAAATATAATGAAAAAAATT
1 AATAAAATTAAAATATAACGAAAAAAATT
1621390 TTAATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.25
Consensus pattern (30 bp):
AATAAAATTAAAATATAACGAAAAAAATTA
Found at i:1621591 original size:18 final size:18
Alignment explanation
Indices: 1621563--1621606 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1621553 TATTTTTATT
* *
1621563 TAATTTTTAATTATAAACA
1 TAATTTATAA-TATAAAAA
1621582 T-ATTTATAATATAAAAA
1 TAATTTATAATATAAAAA
1621599 TAATTTAT
1 TAATTTAT
1621607 TAACATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 13 0.59
19 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTTATAATATAAAAA
Found at i:1622671 original size:22 final size:21
Alignment explanation
Indices: 1622618--1622682 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 21
1622608 ATTATTATTT
*
1622618 TTAATAAAATAAAAATATTTAA
1 TTAATAAATTAAAAA-ATTTAA
1622640 TTAAGT---TTAAAAAATTTATA
1 TTAA-TAAATTAAAAAATTTA-A
1622660 TTAATAAATTAAAAAA-TTAA
1 TTAATAAATTAAAAAATTTAA
1622680 TTA
1 TTA
1622683 TTATGTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
19 6 0.16
20 15 0.41
21 3 0.08
22 12 0.32
23 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAATAAATTAAAAAATTTAA
Found at i:1622976 original size:16 final size:17
Alignment explanation
Indices: 1622955--1622990 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1622945 TTTTAGATAG
*
1622955 TTTAAAGT-TATTTTAT
1 TTTAAAGTATAATTTAT
1622971 TTTAAAGTATAATTTAT
1 TTTAAAGTATAATTTAT
1622988 TTT
1 TTT
1622991 TATTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTAAAGTATAATTTAT
Found at i:1622994 original size:23 final size:21
Alignment explanation
Indices: 1622962--1623035 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 21
1622952 TAGTTTAAAG
*
1622962 TTATTTTATTTTAAAGTATAAT
1 TTATTTTATTTTAAAAT-TAAT
1622984 TTATTTTTATTTATAAAATTAAT
1 TTA-TTTTATTT-TAAAATTAAT
* *
1623007 TTAATTTATTTT--TATTAAAT
1 TTATTTTATTTTAAAATT-AAT
1623027 TTATTTTAT
1 TTATTTTAT
1623036 GATTATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.07
20 11 0.24
21 1 0.02
22 10 0.22
23 15 0.33
24 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (21 bp):
TTATTTTATTTTAAAATTAAT
Found at i:1623013 original size:24 final size:23
Alignment explanation
Indices: 1622965--1623032 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
1622955 TTTAAAGTTA
*
1622965 TTTTATTT-TAAAGTATAATTTAT
1 TTTTATTTATAAAAT-TAATTTAT
1622988 TTTTATTTATAAAATTAATTTAAT
1 TTTTATTTATAAAATTAATTT-AT
* *
1623012 TTATT-TTTATTAAATTTATTT
1 TT-TTATTTATAAAATTAATTT
1623033 TATGATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 14 0.36
24 23 0.59
25 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (23 bp):
TTTTATTTATAAAATTAATTTAT
Found at i:1623041 original size:20 final size:20
Alignment explanation
Indices: 1623004--1623051 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1622994 TTATAAAATT
**
1623004 AATTTAATTTATTTTTATTA
1 AATTTAATTTATGATTATTA
*
1623024 AATTTATTTTATGATTATATA
1 AATTTAATTTATGATTAT-TA
*
1623045 TATTTAA
1 AATTTAA
1623052 AATATTAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATTTAATTTATGATTATTA
Found at i:1623063 original size:22 final size:22
Alignment explanation
Indices: 1623037--1623081 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1623027 TTATTTTATG
1623037 ATTA-TATATATTTAAAATATTA
1 ATTATTATATATTTAAAA-ATTA
*
1623059 ATTATTATATTTTTAAAAATTA
1 ATTATTATATATTTAAAAATTA
1623081 A
1 A
1623082 AAAACAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTATTATATATTTAAAAATTA
Found at i:1623225 original size:22 final size:22
Alignment explanation
Indices: 1623186--1623227 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1623176 CAAATAGCTT
**
1623186 TTTTCAAAAAATTGAAAAAAGC
1 TTTTCAAAAAATAAAAAAAAGC
*
1623208 TTTTCAAAATATAAAAAAAA
1 TTTTCAAAAAATAAAAAAAA
1623228 TTTTATCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (22 bp):
TTTTCAAAAAATAAAAAAAAGC
Found at i:1623465 original size:70 final size:72
Alignment explanation
Indices: 1623388--1623556 Score: 177
Period size: 70 Copynumber: 2.3 Consensus size: 72
1623378 TAGAGTTATT
*
1623388 ATTTATTTCTATTTGTAAAAGTTTAAATTTATT-TTTATTTGAT-T-ATAT-AGGTTTAAATTTT
1 ATTTATTT-TATTTGTAAAA-TTTAAATTTATTATTTATTAGATATGATATGA-GTTTAAATTTT
1623449 T-AGGGTATA
63 TAAGGGTATA
* * *
1623458 ATTTATTTTGATTTGTATAAATTTAATTTTGTTATTTGTTAGATATGATATGAGTTTAAATTTTT
1 ATTTATTTT-ATTTGTA-AAATTTAAATTTATTATTTATTAGATATGATATGAGTTTAAATTTTT
* *
1623523 AATGGTGTA
64 AAGGGTATA
*
1623532 ATTTAATTTTATTTATAAAAATTTA
1 ATTT-ATTTTATTTGT-AAAATTTA
1623557 TGATCTATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
69 1 0.01
70 25 0.30
71 11 0.13
72 1 0.01
73 16 0.19
74 23 0.28
75 6 0.07
ACGTcount: A:0.33, C:0.01, G:0.11, T:0.56
Consensus pattern (72 bp):
ATTTATTTTATTTGTAAAATTTAAATTTATTATTTATTAGATATGATATGAGTTTAAATTTTTAA
GGGTATA
Found at i:1623659 original size:15 final size:15
Alignment explanation
Indices: 1623639--1623672 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1623629 AATTTTGAAG
* *
1623639 AAAGAATGAAGGAAA
1 AAAGAAAGAAGAAAA
1623654 AAAGAAAGAAGAAAA
1 AAAGAAAGAAGAAAA
1623669 AAAG
1 AAAG
1623673 GGGAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (15 bp):
AAAGAAAGAAGAAAA
Found at i:1627557 original size:20 final size:21
Alignment explanation
Indices: 1627525--1627579 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1627515 AAAAACATAA
*
1627525 TAAT-TAATATTTTAA-TTTAT
1 TAATATAAT-TTTTAACTTAAT
1627545 TAATATAATTTTTAACTTAAT
1 TAATATAATTTTTAACTTAAT
*
1627566 TAAATATTATTTTT
1 T-AATATAATTTTT
1627580 TTATTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 10 0.33
21 9 0.30
22 11 0.37
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATATAATTTTTAACTTAAT
Found at i:1627623 original size:68 final size:69
Alignment explanation
Indices: 1627508--1627636 Score: 158
Period size: 68 Copynumber: 1.9 Consensus size: 69
1627498 AAATTTTTCA
* *
1627508 TTTTTATAAAAACATAATAATTAATATTTTAATTTATTAATATAATTTTTAACTTAATTAAATAT
1 TTTTTATAAAAACATAATAATTAATATTTTAATTGATTAATATAATTTTAAACTTAATTAAATAT
1627573 TATT
66 TATT
* * *
1627577 TTTTTATTAAAA-TTAATAATTAATACATTATT-ATTGATTAA-A-AATTTTAAATTTAATTAA
1 TTTTTATAAAAACATAATAATTAAT--ATT-TTAATTGATTAATATAATTTTAAACTTAATTAA
1627637 TTTATAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
68 27 0.52
69 12 0.23
70 11 0.21
71 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (69 bp):
TTTTTATAAAAACATAATAATTAATATTTTAATTGATTAATATAATTTTAAACTTAATTAAATAT
TATT
Found at i:1628246 original size:24 final size:21
Alignment explanation
Indices: 1628208--1628258 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
1628198 AATGTATTTA
**
1628208 TATTTATTAATATAATGATAT
1 TATTTATTAATATAACAATAT
1628229 TATTTATTAATTTAATAACAATAT
1 TATTTATTAA--T-ATAACAATAT
1628253 TATTTA
1 TATTTA
1628259 ATATAACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
23 1 0.04
24 14 0.56
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTTATTAATATAACAATAT
Found at i:1628253 original size:21 final size:21
Alignment explanation
Indices: 1628207--1628264 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1628197 AAATGTATTT
* *
1628207 ATATTTATTAATATAATGATA
1 ATATTTATTAATATAATAACA
* *
1628228 TTATTTATTAATTTAATAACA
1 ATATTTATTAATATAATAACA
1628249 ATA-TTATTTAATATAA
1 ATATTTA-TTAATATAA
1628265 CAATTTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTTATTAATATAATAACA
Found at i:1628343 original size:26 final size:24
Alignment explanation
Indices: 1628313--1628382 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
1628303 ATTATTTTTA
* *
1628313 ATATTTTATTAAAAATTTTTATATT
1 ATATTTTA-TAAAAATTTATAAATT
*
1628338 ATTATTTTAATAATAAATATATAAATT
1 A-TATTTT-ATAA-AAATTTATAAATT
*
1628365 ATATTTTATAAAGATTTA
1 ATATTTTATAAAAATTTA
1628383 ATAATTAGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 5 0.14
25 5 0.14
26 15 0.41
27 12 0.32
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
ATATTTTATAAAAATTTATAAATT
Found at i:1629655 original size:19 final size:18
Alignment explanation
Indices: 1629620--1629666 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1629610 TCAATTACAT
*
1629620 AAAAT-TTTAAATCATAA
1 AAAATATTTAAATAATAA
1629637 AAAATATTTAAATAAATAA
1 AAAATATTTAAAT-AATAA
* *
1629656 TAATTATTTAA
1 AAAATATTTAA
1629667 TACATTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.20
18 7 0.28
19 13 0.52
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATTTAAATAATAA
Found at i:1630136 original size:100 final size:101
Alignment explanation
Indices: 1630018--1630204 Score: 286
Period size: 100 Copynumber: 1.9 Consensus size: 101
1630008 ATAAAAAAAA
* * * *
1630018 TCACAAATCTAAGAATATTTAATTTCATAATAGTTAATATTTTTTATAATTTTTTAATA-TTTTT
1 TCACAAATCTAAGAATATTTAATTTCATAATAGTTAATATTTTTAATAATTCTATAATACTATTT
* ** *
1630082 AAACAAATTTAATTACTCTTGACAAAAATAAGTTTG
66 AAAAAAAACTAATTACTATTGACAAAAATAAGTTTG
*
1630118 TCACAAATCTAAGAATATTTAATTTCATAATATTTAATATTTTTAATAATTCTATAATACTATTT
1 TCACAAATCTAAGAATATTTAATTTCATAATAGTTAATATTTTTAATAATTCTATAATACTATTT
1630183 AAAAAAAACTAATTACTATTGA
66 AAAAAAAACTAATTACTATTGA
1630205 TTAAAAAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
100 55 0.71
101 22 0.29
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (101 bp):
TCACAAATCTAAGAATATTTAATTTCATAATAGTTAATATTTTTAATAATTCTATAATACTATTT
AAAAAAAACTAATTACTATTGACAAAAATAAGTTTG
Found at i:1630387 original size:22 final size:19
Alignment explanation
Indices: 1630356--1630397 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
1630346 ATTTTTTATT
1630356 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
1630377 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
1630397 T
1 T
1630398 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:1638035 original size:2 final size:2
Alignment explanation
Indices: 1638028--1638082 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1638018 GTGAGTGTCT
*
1638028 TC TC TC TC GC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1638070 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
1638083 TTGCCTCATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1639289 original size:4 final size:4
Alignment explanation
Indices: 1639282--1639308 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1639272 TTTTTTTCTT
1639282 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1639309 TATCCTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1643263 original size:21 final size:21
Alignment explanation
Indices: 1643211--1643265 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
1643201 GCAAGGTGGT
1643211 TTTATATCGATACATTAACTTG
1 TTTAT-TCGATACATTAACTTG
* *
1643233 TGTA-TCGATACATTTA-TTG
1 TTTATTCGATACATTAACTTG
1643252 TTTATGTCGATACA
1 TTTAT-TCGATACA
1643266 AATTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 6 0.21
20 11 0.39
21 8 0.29
22 3 0.11
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (21 bp):
TTTATTCGATACATTAACTTG
Found at i:1648560 original size:2 final size:2
Alignment explanation
Indices: 1648548--1648588 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1648538 GTGAAGTTAC
1648548 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1648589 CATGAAGTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1652768 original size:2 final size:2
Alignment explanation
Indices: 1652761--1652788 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1652751 AGGCGAAATT
1652761 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1652789 CGTATGTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1653125 original size:4 final size:4
Alignment explanation
Indices: 1653116--1653180 Score: 75
Period size: 4 Copynumber: 17.0 Consensus size: 4
1653106 GAAAATGAAG
* *
1653116 GAAA GAAA GAAA -AAA AAAA CGAAA GAAA GAAA G-AA GAAA AAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1653163 -AAA -AAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA
1653181 TTTTATATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
3 12 0.22
4 39 0.72
5 3 0.06
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1653143 original size:24 final size:23
Alignment explanation
Indices: 1653107--1653172 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
1653097 TACACAGGTG
* *
1653107 AAAATGAAGGAAAGAAAGAAAAA
1 AAAAAGAAAGAAAGAAAGAAAAA
*
1653130 AAAAACGAAAGAAAGAAAGAAGAA
1 AAAAA-GAAAGAAAGAAAGAAAAA
1653154 AAAAAGAAA-AAA-AAAGAAA
1 AAAAAGAAAGAAAGAAAGAAA
1653173 GAAAGAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.16
22 3 0.08
23 8 0.21
24 21 0.55
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (23 bp):
AAAAAGAAAGAAAGAAAGAAAAA
Found at i:1653173 original size:33 final size:35
Alignment explanation
Indices: 1653116--1653180 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
1653106 GAAAATGAAG
*
1653116 GAAAGAAAGAAAAAAAAAACGAAAGAAAGAAAGAA
1 GAAAAAAAGAAAAAAAAAACGAAAGAAAGAAAGAA
1653151 GAAAAAAAG-AAAAAAAAA-GAAAGAAAGAAA
1 GAAAAAAAGAAAAAAAAAACGAAAGAAAGAAA
1653181 TTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 12 0.41
34 9 0.31
35 8 0.28
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (35 bp):
GAAAAAAAGAAAAAAAAAACGAAAGAAAGAAAGAA
Found at i:1653237 original size:24 final size:23
Alignment explanation
Indices: 1653181--1653238 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
1653171 AAGAAAGAAA
**
1653181 TTTTATATATTTGTATTTATAAT
1 TTTTATATATTTAAATTTATAAT
*
1653204 TTTT-TGTATTTAAAATATTAT-AT
1 TTTTATATATTT-AAAT-TTATAAT
1653227 TTTTATATATTT
1 TTTTATATATTT
1653239 TTTACATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 6 0.21
23 12 0.43
24 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (23 bp):
TTTTATATATTTAAATTTATAAT
Found at i:1653406 original size:11 final size:11
Alignment explanation
Indices: 1653392--1653453 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
1653382 CATGTCATAT
1653392 TTATTTTTATA
1 TTATTTTTATA
1653403 TTATATTTTA-A
1 TTAT-TTTTATA
*
1653414 TTATTTTTTAATT
1 TTA-TTTTT-ATA
*
1653427 TTATATTTATA
1 TTATTTTTATA
1653438 TTATTTTTATA
1 TTATTTTTATA
1653449 -TATTT
1 TTATTT
1653454 AAAGTATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 5 0.12
11 24 0.56
12 11 0.26
13 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:1653430 original size:24 final size:23
Alignment explanation
Indices: 1653395--1653452 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 23
1653385 GTCATATTTA
1653395 TTTTTATATTATATTT-TAATTAT
1 TTTTTATATTATATTTAT-ATTAT
*
1653418 TTTTTAATTTTATATTTATATTAT
1 TTTTT-ATATTATATTTATATTAT
1653442 TTTTATATATT
1 TTTT-TATATT
1653453 TAAAGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 5 0.17
24 23 0.77
25 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTTATATTATATTTATATTAT
Found at i:1653450 original size:19 final size:19
Alignment explanation
Indices: 1653367--1653454 Score: 73
Period size: 17 Copynumber: 4.9 Consensus size: 19
1653357 AAATATTTTT
* *
1653367 TTATATTTATATATTCATG
1 TTATATTTATATATTTATA
*
1653386 TCATATTTAT-T-TTTATA
1 TTATATTTATATATTTATA
1653403 TTATATTT-TAATTATTT-T-
1 TTATATTTAT-A-TATTTATA
1653421 TTA-ATTT-TATATTTATA
1 TTATATTTATATATTTATA
*
1653438 TTATTTTTATATATTTA
1 TTATATTTATATATTTA
1653455 AAGTATTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
15 5 0.09
16 3 0.05
17 19 0.34
18 7 0.12
19 19 0.34
20 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (19 bp):
TTATATTTATATATTTATA
Found at i:1654660 original size:51 final size:50
Alignment explanation
Indices: 1654568--1654674 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 50
1654558 TTTTAAAATT
1654568 ATATTATTATTATATTATTTTTAATTAAGTTAATATCATTTAATTCAATA
1 ATATTATTATTATATTATTTTTAATTAAGTTAATATCATTTAATTCAATA
* *
1654618 ATATTA-TATTATTATTATTTTTTAATTGAA-TTAATATTATTTAATTCAGTA
1 ATATTATTATTA-TATTA-TTTTTAATT-AAGTTAATATCATTTAATTCAATA
*
1654669 ACATTA
1 ATATTA
1654675 AACTCATTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
49 5 0.10
50 11 0.22
51 33 0.65
52 2 0.04
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (50 bp):
ATATTATTATTATATTATTTTTAATTAAGTTAATATCATTTAATTCAATA
Found at i:1656053 original size:16 final size:16
Alignment explanation
Indices: 1656013--1656053 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1656003 TGTTAATTTA
1656013 TTTA-AAATAATATAT
1 TTTATAAATAATATAT
1656028 TTTATCAAAT-ATATAAT
1 TTTAT-AAATAATAT-AT
1656045 TTTATAAAT
1 TTTATAAAT
1656054 TTGAGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 11 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTATAAATAATATAT
Found at i:1659020 original size:2 final size:2
Alignment explanation
Indices: 1659013--1659054 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1659003 AAGACAATAA
1659013 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1659055 TAGTGCACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1662681 original size:15 final size:16
Alignment explanation
Indices: 1662661--1662691 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1662651 AGTCGGATTC
1662661 AAAATGA-TTGAATTT
1 AAAATGATTTGAATTT
1662676 AAAATGATTTGAATTT
1 AAAATGATTTGAATTT
1662692 GAGATAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (16 bp):
AAAATGATTTGAATTT
Found at i:1664358 original size:2 final size:2
Alignment explanation
Indices: 1664351--1664380 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1664341 CGCAGTTCAG
1664351 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1664381 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1671959 original size:15 final size:15
Alignment explanation
Indices: 1671936--1671977 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1671926 AAGAGGAGGG
*
1671936 GGAACAGGATGAAGA
1 GGAACAGGAAGAAGA
*
1671951 GGAAGAGGAAGAAGA
1 GGAACAGGAAGAAGA
1671966 GGTAAC-GGAAGA
1 GG-AACAGGAAGA
1671978 GGTATGTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.48, C:0.05, G:0.43, T:0.05
Consensus pattern (15 bp):
GGAACAGGAAGAAGA
Found at i:1678867 original size:18 final size:19
Alignment explanation
Indices: 1678846--1678899 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
1678836 TTATTAAAAT
1678846 TAATTAATATATTAT-TTA
1 TAATTAATATATTATATTA
1678864 TAA-TAATATTATTATATTA
1 TAATTAATA-TATTATATTA
1678883 -AATATAATA-ATTATATT
1 TAAT-TAATATATTATATT
1678900 TAAGATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.16
18 19 0.59
19 3 0.09
20 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATTAATATATTATATTA
Found at i:1678879 original size:23 final size:23
Alignment explanation
Indices: 1678848--1678932 Score: 65
Period size: 23 Copynumber: 3.9 Consensus size: 23
1678838 ATTAAAATTA
**
1678848 ATTAATATATTATTTATAATAAT
1 ATTAATATATTAAATATAATAAT
*
1678871 ATTATTATATTAAATATAAT-A-
1 ATTAATATATTAAATATAATAAT
*
1678892 ATT-ATAT-TTAAGAT-T-ATATT
1 ATTAATATATTAA-ATATAATAAT
* *
1678912 TTTAATATATTAAATAAAATA
1 ATTAATATATTAAATATAATA
1678933 TTTATGATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
18 2 0.04
19 5 0.10
20 7 0.15
21 9 0.19
22 5 0.10
23 20 0.42
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (23 bp):
ATTAATATATTAAATATAATAAT
Found at i:1679483 original size:20 final size:19
Alignment explanation
Indices: 1679436--1679488 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
1679426 TGACTAAGTT
**
1679436 TTTTTTAAAAAAATTTTTA
1 TTTTTTAATTAAATTTTTA
1679455 TTATATTTAATTAAATTTTTAA
1 TT-T-TTTAATTAAATTTTT-A
1679477 TTTTTTAATTAA
1 TTTTTTAATTAA
1679489 CTGTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 10 0.34
21 14 0.48
22 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTTAATTAAATTTTTA
Found at i:1681192 original size:26 final size:24
Alignment explanation
Indices: 1681163--1681223 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
1681153 AAAATTATTT
*
1681163 ATAATTAATATATATTTAAATATAAA
1 ATAATTAA-A-ATAATTAAATATAAA
*
1681189 ATAATTAAAATAATTAAATAT-AT
1 ATAATTAAAATAATTAAATATAAA
*
1681212 ATAAATAAAATA
1 ATAATTAAAATA
1681224 TTCACCCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.38
24 11 0.34
25 1 0.03
26 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAATTAAAATAATTAAATATAAA
Found at i:1681459 original size:5 final size:5
Alignment explanation
Indices: 1681449--1681473 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1681439 TCATGGTCAA
1681449 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
1681474 GGGTGGCCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1681959 original size:21 final size:21
Alignment explanation
Indices: 1681917--1681961 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1681907 TTAAGTTTGA
*
1681917 ATAAAATTAATTTTGTTGTTT
1 ATAAAATTAATTTTATTGTTT
*
1681938 ATAAATATTATTTTTATT-TTT
1 ATAAA-ATTAATTTTATTGTTT
1681959 ATA
1 ATA
1681962 TATTATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
ATAAAATTAATTTTATTGTTT
Found at i:1682119 original size:19 final size:19
Alignment explanation
Indices: 1682097--1682134 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1682087 TTATGTAAAA
1682097 AATTAAAATATTA-ATTTTT
1 AATTAAAAT-TTATATTTTT
*
1682116 AATTAATATTTATATTTTT
1 AATTAAAATTTATATTTTT
1682135 TATAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTAAAATTTATATTTTT
Found at i:1683030 original size:25 final size:23
Alignment explanation
Indices: 1682973--1683031 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 23
1682963 TTTAAAAATA
1682973 TTATATATAATATATTTAAATTTT
1 TTATAT-TAATATATTTAAATTTT
*
1682997 TAACTTATTAATATATATTAAAATTTT
1 TTA--TATTAATATAT-TT-AAATTTT
1683024 TTATATTA
1 TTATATTA
1683032 TTTAACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
24 2 0.07
25 13 0.45
26 5 0.17
27 9 0.31
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATATTAATATATTTAAATTTT
Found at i:1683540 original size:13 final size:14
Alignment explanation
Indices: 1683521--1683593 Score: 82
Period size: 13 Copynumber: 5.5 Consensus size: 14
1683511 TAAATAATTC
1683521 TAAATATAATATAA
1 TAAATATAATATAA
*
1683535 -AAATATAATAAAA
1 TAAATATAATATAA
*
1683548 TAAATAT-ATTTAA
1 TAAATATAATATAA
*
1683561 TCAAT-TAATATAA
1 TAAATATAATATAA
*
1683574 TAAATATTATAT-A
1 TAAATATAATATAA
1683587 TAAATAT
1 TAAATAT
1683594 TTATAATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
12 1 0.02
13 37 0.76
14 11 0.22
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATATAATATAA
Found at i:1683621 original size:17 final size:17
Alignment explanation
Indices: 1683550--1683632 Score: 53
Period size: 17 Copynumber: 4.6 Consensus size: 17
1683540 TAATAAAATA
*
1683550 AATATATTTAATCAATT
1 AATATATTTAATCATTT
* *
1683567 AATATAATAAAT-ATTAT
1 AATATATTTAATCATT-T
*
1683584 ATATAAATATTT-ATAATTTT
1 A-AT--ATATTTAATCA-TTT
1683604 AATATATTTAATCATTT
1 AATATATTTAATCATTT
1683621 ATATCATATTTA
1 A-AT-ATATTTA
1683633 TGTGAATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
16 2 0.04
17 22 0.43
18 7 0.14
19 11 0.22
20 7 0.14
21 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATATTTAATCATTT
Found at i:1683714 original size:19 final size:18
Alignment explanation
Indices: 1683687--1683725 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1683677 TATAAATGTT
*
1683687 AGTAAATTTAGTTATAGAG
1 AGTAAATTTACTTAT-GAG
*
1683706 AGTAGATTTACTTATGAG
1 AGTAAATTTACTTATGAG
1683724 AG
1 AG
1683726 ATAGCTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (18 bp):
AGTAAATTTACTTATGAG
Found at i:1683855 original size:21 final size:20
Alignment explanation
Indices: 1683787--1683874 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
1683777 ATTTTATTTG
*
1683787 ATTAAAATTATTATT-TAAAT
1 ATTAAAA-TATAATTATAAAT
1683807 ATTAAAA-AT-ATT-T-AAT
1 ATTAAAATATAATTATAAAT
1683823 -TTAAAAT-TAATTATAAAT
1 ATTAAAATATAATTATAAAT
*
1683841 ATTAATAATATAATTTTAAAT
1 ATTAA-AATATAATTATAAAT
*
1683862 AATAAAATA-AATT
1 ATTAAAATATAATT
1683875 TTTAAATTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 15
0.78 0.03 0.20
Matches are distributed among these distances:
15 7 0.12
16 6 0.10
17 5 0.08
18 5 0.08
19 8 0.14
20 14 0.24
21 14 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTAAAATATAATTATAAAT
Found at i:1683866 original size:18 final size:20
Alignment explanation
Indices: 1683836--1683881 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1683826 AAATTAATTA
*
1683836 TAAATATTAATAATATAA-TTT
1 TAAATAATAA-AATA-AATTTT
1683857 TAAATAATAAAATAAATTTT
1 TAAATAATAAAATAAATTTT
1683877 TAAAT
1 TAAAT
1683882 TAATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 12 0.52
21 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATAAAATAAATTTT
Found at i:1683877 original size:20 final size:21
Alignment explanation
Indices: 1683830--1683881 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1683820 AATTTAAAAT
* *
1683830 TAATTATAAATATTAATAATA
1 TAATTTTAAATAATAATAATA
1683851 TAATTTTAAATAATAA-AATA
1 TAATTTTAAATAATAATAATA
1683871 -AATTTTTAAAT
1 TAA-TTTTAAAT
1683882 TAATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 12 0.43
21 14 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTTTAAATAATAATAATA
Found at i:1684901 original size:31 final size:30
Alignment explanation
Indices: 1684823--1684904 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
1684813 TATTTTTTAC
*
1684823 TATTTATTTTTAATTAATTATATAATAAAA
1 TATTTATTTTTAATTAATTACATAATAAAA
** *
1684853 TACATATTAATTAATTAATTACATAATAATAA
1 TATTTATT-TTTAATTAATTACATAATAA-AA
1684885 -ATTTATTTTTATATTAATTA
1 TATTTATTTTTA-ATTAATTA
1684905 AAAAATATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
30 9 0.21
31 31 0.74
32 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTTATTTTTAATTAATTACATAATAAAA
Found at i:1685149 original size:35 final size:36
Alignment explanation
Indices: 1685073--1685185 Score: 94
Period size: 35 Copynumber: 3.2 Consensus size: 36
1685063 TACGTTAGTT
* *
1685073 TATTA-AAATAAAATAAAATTATAATAAAATAATTA
1 TATTATAAATAAAATAAAATTAGAATAAAATAAATA
* *
1685108 TTTTATAAA-AAAATAATATTAGAATAAAATAAA-A
1 TATTATAAATAAAATAAAATTAGAATAAAATAAATA
** *
1685142 TAATTAT-AATAATAATTTAATT-TAATAAAATAAA-A
1 T-ATTATAAATAA-AATAAAATTAGAATAAAATAAATA
*
1685177 TATCATAAA
1 TATTATAAA
1685186 AGTTAAATCT
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
34 8 0.13
35 46 0.73
36 9 0.14
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (36 bp):
TATTATAAATAAAATAAAATTAGAATAAAATAAATA
Found at i:1691023 original size:20 final size:20
Alignment explanation
Indices: 1690953--1691025 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
1690943 TAGCTCGTAT
*
1690953 TATTATATTTAAATTATTTTA
1 TATTATA-TTAATTTATTTTA
* * **
1690974 TGTTTATATAAATTT-TGATA
1 T-ATTATATTAATTTATTTTA
1690994 TATTA-A-TAATTTATTTTA
1 TATTATATTAATTTATTTTA
1691012 TATTATATTAATTT
1 TATTATATTAATTT
1691026 TAAAATATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
17 5 0.13
18 9 0.23
19 4 0.10
20 10 0.26
21 6 0.15
22 5 0.13
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TATTATATTAATTTATTTTA
Found at i:1691243 original size:17 final size:18
Alignment explanation
Indices: 1691205--1691243 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1691195 AAACTAAAAA
*
1691205 GTAATTTCATATGTATAT
1 GTAATTTCATATGTAGAT
*
1691223 GTAATTTTATATG-AGAT
1 GTAATTTCATATGTAGAT
1691240 GTAA
1 GTAA
1691244 AAAAAGTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (18 bp):
GTAATTTCATATGTAGAT
Found at i:1691819 original size:22 final size:21
Alignment explanation
Indices: 1691771--1691817 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1691761 GATTGATTAC
* *
1691771 TTTTTAAGAATGTTTCACCTT
1 TTTTTAAGAATGGTTAACCTT
*
1691792 TTTTTAAGAATGGTTAATCTT
1 TTTTTAAGAATGGTTAACCTT
1691813 TTTTT
1 TTTTT
1691818 TAGGAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTTTAAGAATGGTTAACCTT
Found at i:1692079 original size:2 final size:2
Alignment explanation
Indices: 1692074--1692106 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1692064 AGTGTGTGCT
1692074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1692107 CCTAATTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1692859 original size:2 final size:2
Alignment explanation
Indices: 1692852--1692881 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1692842 AATTTTAGTG
*
1692852 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1692882 AATTCATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1693060 original size:6 final size:6
Alignment explanation
Indices: 1693044--1693140 Score: 51
Period size: 6 Copynumber: 16.2 Consensus size: 6
1693034 AAATTTAATA
* *
1693044 ATTTAT A-TTAT ATTTAT ATATAT -TATTAT A-TTAT AATTAT AGTTTA-
1 ATTTAT ATTTAT ATTTAT ATTTAT AT-TTAT ATTTAT ATTTAT A-TTTAT
** * * *
1693090 AAATAT -TTTAT ATTTAT ATTAAT TTTTAT AAATTAAT AATTTAT ATTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT --ATTTAT -ATTTAT ATTTAT
1693140 A
1 A
1693141 ATAAATTTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
5 16 0.23
6 40 0.58
7 9 0.13
8 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (6 bp):
ATTTAT
Found at i:1693165 original size:31 final size:32
Alignment explanation
Indices: 1693091--1693165 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
1693081 TATAGTTTAA
* * *
1693091 AATATTTTATATTTATATTAATTTTTATAAATT
1 AATAATTTATATTTATAATAAATTTTATAAA-T
1693124 AATAATTTATATTTATAATAAATTTTA-AAA-
1 AATAATTTATATTTATAATAAATTTTATAAAT
1693154 AATAAATTTATA
1 AAT-AATTTATA
1693166 CCCTATTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 8 0.21
32 3 0.08
33 24 0.63
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AATAATTTATATTTATAATAAATTTTATAAAT
Found at i:1693805 original size:19 final size:18
Alignment explanation
Indices: 1693771--1693820 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
1693761 TTATTTAAAA
*
1693771 TATATTAAATGT-TATTT
1 TATATTAAATTTATATTT
1693788 TATATTAATATTTATATTT
1 TATATTAA-ATTTATATTT
1693807 TATAATTAAATTTA
1 TAT-ATTAAATTTA
1693821 ATTAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 8 0.28
18 3 0.10
19 13 0.45
20 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TATATTAAATTTATATTT
Found at i:1693878 original size:25 final size:25
Alignment explanation
Indices: 1693818--1693869 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1693808 ATAATTAAAT
* * *
1693818 TTAATTAA-AAATAAATTTTATTTA
1 TTAAATAATAAATAAATTTAAATTA
1693842 TTAAATAATAAATAAATTTAAATTA
1 TTAAATAATAAATAAATTTAAATTA
1693867 TTA
1 TTA
1693870 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAATAATAAATAAATTTAAATTA
Found at i:1694108 original size:19 final size:20
Alignment explanation
Indices: 1694080--1694118 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1694070 ATTATTATTG
1694080 AAAATATA-TTATAATATTAA
1 AAAATATATTTAT-ATATTAA
1694100 AAAAT-TATTTATATATTAA
1 AAAATATATTTATATATTAA
1694119 TATTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATATATTTATATATTAA
Found at i:1696083 original size:2 final size:2
Alignment explanation
Indices: 1696078--1696105 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1696068 ATCTCCACAC
1696078 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
1696106 TAGAATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1697639 original size:4 final size:4
Alignment explanation
Indices: 1697624--1697664 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
1697614 TGAAAGCCTG
*
1697624 CTTT CCTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1697665 ATCAGTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:1701243 original size:2 final size:2
Alignment explanation
Indices: 1701236--1701262 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1701226 TATATTCGGC
1701236 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
1701263 AAAGGATATG
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:1702040 original size:23 final size:22
Alignment explanation
Indices: 1701993--1702044 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1701983 GGAGAAAAAA
*
1701993 TTTAAAATAATAGAATTTGAGT
1 TTTAAAATAATAGAATTTGAAT
*
1702015 TTTAAATATAATA-AATTTTATAT
1 TTTAAA-ATAATAGAATTTGA-AT
1702038 TTTAAAA
1 TTTAAAA
1702045 AAATTATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (22 bp):
TTTAAAATAATAGAATTTGAAT
Found at i:1702396 original size:29 final size:29
Alignment explanation
Indices: 1702338--1702396 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
1702328 ATCAAATTAG
* *
1702338 TTAAATTAAAAATTAATAGTTTATTCAAT
1 TTAAATTAAAAATTAATAGTTAATTAAAT
1702367 TTAAA-TAATAAATTAGATA-TTAATTAAAT
1 TTAAATTAA-AAATTA-ATAGTTAATTAAAT
1702396 T
1 T
1702397 GGGATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 3 0.12
29 20 0.77
30 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (29 bp):
TTAAATTAAAAATTAATAGTTAATTAAAT
Found at i:1703497 original size:14 final size:14
Alignment explanation
Indices: 1703478--1703505 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1703468 TAATTATTTA
1703478 TTTAATTTTTTTCT
1 TTTAATTTTTTTCT
1703492 TTTAATTTTTTTCT
1 TTTAATTTTTTTCT
1703506 AAATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTAATTTTTTTCT
Found at i:1704117 original size:22 final size:21
Alignment explanation
Indices: 1704079--1704130 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
1704069 CATGCATTTA
1704079 AATTAGAATATAATTTAATAA-T
1 AATTA-AATATAATTTAA-AATT
1704101 AATTAAATATAATTTTAAAATT
1 AATTAAATATAA-TTTAAAATT
1704123 AATTAAAT
1 AATTAAAT
1704131 TCTTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AATTAAATATAATTTAAAATT
Found at i:1704364 original size:86 final size:87
Alignment explanation
Indices: 1704218--1704390 Score: 242
Period size: 86 Copynumber: 2.0 Consensus size: 87
1704208 TTTATCTTTT
* * * **
1704218 TATTTAAAATTAACTTAAGAATAATATCTTAGAGAGGTAAATATATTTTTTGTCAAACTTTA-AG
1 TATTTAAAATTAACTAAAGAATAATAACTTAGAGAGATAAATATATTTTTAATCAAACTTTACAG
*
1704282 AAAGTAAGTAAGTATTTTTTAAA
66 AAA-TAAGTAAATATTTTTTAAA
* *
1704305 TATTTAAAATTAACTAAAGAATATTAAGTTAG-GAGATAAATATATTTTTAATCAAACTTTACAG
1 TATTTAAAATTAACTAAAGAATAATAACTTAGAGAGATAAATATATTTTTAATCAAACTTTACAG
*
1704369 AGATAAGTAAATATTTTTTAAA
66 AAATAAGTAAATATTTTTTAAA
1704391 CTTTGAGGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
86 44 0.58
87 32 0.42
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (87 bp):
TATTTAAAATTAACTAAAGAATAATAACTTAGAGAGATAAATATATTTTTAATCAAACTTTACAG
AAATAAGTAAATATTTTTTAAA
Found at i:1704394 original size:30 final size:26
Alignment explanation
Indices: 1704358--1704413 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 26
1704348 ATTTTTAATC
1704358 AAACTTTACAGAGATAAGTAAATATTTTTT
1 AAACTTT-CAG-GA-AA-TAAATATTTTTT
*
1704388 AAACTTTGAGGAAATAAATATTTTTT
1 AAACTTTCAGGAAATAAATATTTTTT
1704414 TTATAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 12 0.48
27 2 0.08
28 2 0.08
29 2 0.08
30 7 0.28
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (26 bp):
AAACTTTCAGGAAATAAATATTTTTT
Found at i:1704843 original size:23 final size:23
Alignment explanation
Indices: 1704799--1704864 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
1704789 ATAAATTATT
* *
1704799 TTTATTT-TTAATAAAATGATATGA
1 TTTATTTACTAATAATAT-ATA-GA
*
1704823 TTTGATTTATTAATAATATATAGA
1 TTT-ATTTACTAATAATATATAGA
*
1704847 TTTATTTACTATTAATAT
1 TTTATTTACTAATAATAT
1704865 GTTAAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.35
24 8 0.22
25 7 0.19
26 9 0.24
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (23 bp):
TTTATTTACTAATAATATATAGA
Found at i:1705150 original size:6 final size:7
Alignment explanation
Indices: 1705083--1705156 Score: 52
Period size: 7 Copynumber: 11.0 Consensus size: 7
1705073 TATCAAAATC
1705083 TATATAA
1 TATATAA
1705090 TATA-AA
1 TATATAA
1705096 T-TAATAA
1 TAT-ATAA
1705103 TATATAA
1 TATATAA
*
1705110 TA-AT-T
1 TATATAA
1705115 TATATAAA
1 TATAT-AA
*
1705123 TATGTAA
1 TATATAA
*
1705130 TATTTTAA
1 TA-TATAA
1705138 -ATATAA
1 TATATAA
1705144 T-TATAA
1 TATATAA
1705150 TATATAA
1 TATATAA
1705157 AAATATACAA
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
5 3 0.06
6 18 0.34
7 23 0.43
8 9 0.17
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (7 bp):
TATATAA
Found at i:1705152 original size:20 final size:21
Alignment explanation
Indices: 1705099--1705152 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1705089 ATATAAATTA
* *
1705099 ATAATATATAATAATTTATAT
1 ATAATATATAATATTTTAAAT
*
1705120 A-AATATGTAATATTTTAAAT
1 ATAATATATAATATTTTAAAT
1705140 ATAAT-TATAATAT
1 ATAATATATAATAT
1705153 ATAAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAATATATAATATTTTAAAT
Found at i:1707375 original size:49 final size:49
Alignment explanation
Indices: 1707307--1707406 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 49
1707297 TTTTATTTTT
* *
1707307 AAATAAGTCTACATACATCATCTTTAAAAAATAATAATTAATAAATTTA
1 AAATAAATCTACATACATCATCTTTAAAAAATAATAAATAATAAATTTA
* *
1707356 AAATAAATCTACATACATCATCTTTAAAAGATAATAAATAATAATTTTA
1 AAATAAATCTACATACATCATCTTTAAAAAATAATAAATAATAAATTTA
1707405 AA
1 AA
1707407 TTTTGATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (49 bp):
AAATAAATCTACATACATCATCTTTAAAAAATAATAAATAATAAATTTA
Done.