Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007844.1 Hibiscus syriacus cultivar Beakdansim tig00110198_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2094103
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:1044055 original size:45 final size:48
Alignment explanation
Indices: 1043962--1044056 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 48
1043952 TATAAATATT
* * *
1043962 TTTTAAAGTATATACATATATTAATAATATAAAAAAATATATATAAAA
1 TTTTAAAGTATATACATATATTAATAAAATAAAAAAATATAAAAAAAA
* *
1044010 TTTTAAAGTA-A-ACATA-ATTAATAAAATAAATAACTA-AAAGAAAAA
1 TTTTAAAGTATATACATATATTAATAAAATAAAAAAATATAAA-AAAAA
1044055 TT
1 TT
1044057 AAACTTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
44 2 0.05
45 23 0.56
46 5 0.12
47 1 0.02
48 10 0.24
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (48 bp):
TTTTAAAGTATATACATATATTAATAAAATAAAAAAATATAAAAAAAA
Found at i:1050501 original size:23 final size:23
Alignment explanation
Indices: 1050472--1050529 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
1050462 ACTTGTCATT
1050472 TTATTACAAAATTGTCTTTAAAA
1 TTATTACAAAATTGTCTTTAAAA
1050495 TTATTACAAAATTGTCTTTAAAA
1 TTATTACAAAATTGTCTTTAAAA
1050518 TTATTACAAAAT
1 TTATTACAAAAT
1050530 CATCACTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (23 bp):
TTATTACAAAATTGTCTTTAAAA
Found at i:1051151 original size:53 final size:53
Alignment explanation
Indices: 1051082--1051188 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
1051072 TCGTCTTGCA
1051082 CCATTTACAAAGTACATGTATAACAAAACATATTATCTAAAGATAAGATTGAT
1 CCATTTACAAAGTACATGTATAACAAAACATATTATCTAAAGATAAGATTGAT
1051135 CCATTTACAAAGTACATGTATAACAAAACATATTATCTAAAGATAAGATTGAT
1 CCATTTACAAAGTACATGTATAACAAAACATATTATCTAAAGATAAGATTGAT
1051188 C
1 C
1051189 GACGATCGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (53 bp):
CCATTTACAAAGTACATGTATAACAAAACATATTATCTAAAGATAAGATTGAT
Found at i:1064198 original size:22 final size:21
Alignment explanation
Indices: 1064134--1064198 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
1064124 TATGACCGTT
* *
1064134 TATAAATAAATAATATAAA-A
1 TATAATTAAAAAATATAAATA
*
1064154 -ATACTTAAAAAATA-AAATTTA
1 TATAATTAAAAAATATAAA--TA
1064175 TATAATTAAAAAATATAAAGTA
1 TATAATTAAAAAATATAAA-TA
1064197 TA
1 TA
1064199 CATGAATTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.09
19 11 0.31
21 1 0.03
22 17 0.49
23 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
TATAATTAAAAAATATAAATA
Found at i:1083462 original size:2 final size:2
Alignment explanation
Indices: 1083455--1083485 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1083445 TTATGGTTTT
1083455 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 T
1083486 TTTTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1085659 original size:37 final size:37
Alignment explanation
Indices: 1085609--1085682 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1085599 CTTTAAGGGT
1085609 AGTGCAAGTTGTCTGAATTCTGAAAATTTATGGGTTG
1 AGTGCAAGTTGTCTGAATTCTGAAAATTTATGGGTTG
1085646 AGTGCAAGTTGTCTGAATTCTGAAAATTTATGGGTTG
1 AGTGCAAGTTGTCTGAATTCTGAAAATTTATGGGTTG
1085683 TTGTGTAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (37 bp):
AGTGCAAGTTGTCTGAATTCTGAAAATTTATGGGTTG
Found at i:1087208 original size:39 final size:39
Alignment explanation
Indices: 1087154--1087239 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
1087144 CCTACGATGG
1087154 ATTTGATTTAGATAGTGGCATGTAATTTGATAATGTTAA
1 ATTTGATTTAGATAGTGGCATGTAATTTGATAATGTTAA
1087193 ATTTGATTTAGATAGTGGCATGTAATTTGATAATGTTAA
1 ATTTGATTTAGATAGTGGCATGTAATTTGATAATGTTAA
1087232 ATTT-ATTT
1 ATTTGATTT
1087240 TGTTAAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 4 0.09
39 43 0.91
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (39 bp):
ATTTGATTTAGATAGTGGCATGTAATTTGATAATGTTAA
Found at i:1089323 original size:32 final size:32
Alignment explanation
Indices: 1089285--1089448 Score: 134
Period size: 32 Copynumber: 5.1 Consensus size: 32
1089275 TTGATCTTAC
*
1089285 ATATATCACATCATTTAATA-TGATGATATGAC
1 ATATATCACATCATTTAA-AGTGATGATATGAT
** ** *
1089317 GCATATCACATCACCTAAAGTGATGATATAAT
1 ATATATCACATCATTTAAAGTGATGATATGAT
* * *
1089349 TTATATCACATCATTTAAAGTGATTATGTGAT
1 ATATATCACATCATTTAAAGTGATGATATGAT
* * * *
1089381 ATGTGTCACATCATTTAATA-TGATGACATAAT
1 ATATATCACATCATTTAA-AGTGATGATATGAT
* * * * *
1089413 ATATGTCACATTATTCAAGGTGATGATATGTT
1 ATATATCACATCATTTAAAGTGATGATATGAT
1089445 ATAT
1 ATAT
1089449 GACACGTCAT
Statistics
Matches: 102, Mismatches: 27, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
31 1 0.01
32 100 0.98
33 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (32 bp):
ATATATCACATCATTTAAAGTGATGATATGAT
Found at i:1090147 original size:25 final size:26
Alignment explanation
Indices: 1090103--1090154 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1090093 AATTTTTTTA
1090103 TCCTTTCATTAAACCTTTTTTATATT
1 TCCTTTCATTAAACCTTTTTTATATT
1090129 TCCTTTCATTAAACC-TTTTTATATT
1 TCCTTTCATTAAACCTTTTTTATATT
1090154 T
1 T
1090155 TTAATTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (26 bp):
TCCTTTCATTAAACCTTTTTTATATT
Found at i:1090230 original size:37 final size:37
Alignment explanation
Indices: 1090154--1090230 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
1090144 TTTTTATATT
* *
1090154 TTTAATTTTGTGAAACAAATTATATAAATATTATGAA
1 TTTAATTTTGTGAAACAAAATATATAAATATTATCAA
* * *
1090191 TTTAATTTT-TTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTGAAACAAAATATATAAATATTAT-CAA
1090228 TTT
1 TTT
1090231 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 20 0.59
37 14 0.41
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTGAAACAAAATATATAAATATTATCAA
Found at i:1091057 original size:60 final size:60
Alignment explanation
Indices: 1090981--1091097 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
1090971 ATGCAATTGT
* * *
1090981 ATTGCCTGCCTGCCTAGAAATCATTGGAAACCGGAAGAAAACCTGGTAATTGCTTTTAGA
1 ATTGCCTGACTGCCTAGAAAACATGGGAAACCGGAAGAAAACCTGGTAATTGCTTTTAGA
* * *
1091041 ATTGCTTGACTGCCTAGAAAACATGGGAAACTGGAAGAAAATCTGGTAATTGCTTTT
1 ATTGCCTGACTGCCTAGAAAACATGGGAAACCGGAAGAAAACCTGGTAATTGCTTTT
1091098 TTTTTTGGTC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (60 bp):
ATTGCCTGACTGCCTAGAAAACATGGGAAACCGGAAGAAAACCTGGTAATTGCTTTTAGA
Found at i:1098198 original size:2 final size:2
Alignment explanation
Indices: 1098191--1098215 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1098181 TGAAAAAGTA
1098191 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 A
1098216 AACTGTATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1104802 original size:59 final size:59
Alignment explanation
Indices: 1104739--1104882 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 59
1104729 TTTTGGGACC
* * * *
1104739 AATTTAGAAAGAGTGTCATAGTTTAGGAAGAAATTGGAATGTTCAAAAGTTTAAGGAT-T
1 AATTTAGAAAGAGAGTCATAGTTTAGGAAGAAAGTGAAATATTCAAAAGTTTAAGG-TCT
* * * **
1104798 AATTTAGAATGAGAGTCATAATTTGGGGGTGAAAGTGAAATATTCAAAAGTTTAAGGTCT
1 AATTTAGAAAGAGAGTCATAGTTT-AGGAAGAAAGTGAAATATTCAAAAGTTTAAGGTCT
* *
1104858 AATTTA-AAATGAGGGTTATAGTTTA
1 AATTTAGAAA-GAGAGTCATAGTTTA
1104883 AATATAATAC
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
59 24 0.35
60 44 0.65
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (59 bp):
AATTTAGAAAGAGAGTCATAGTTTAGGAAGAAAGTGAAATATTCAAAAGTTTAAGGTCT
Found at i:1107637 original size:30 final size:31
Alignment explanation
Indices: 1107603--1107675 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
1107593 ACTTTATGTC
* * *
1107603 AAATATTAATTT-AACCTTAAACTTTTA-ATG
1 AAATATCAATTTCAAACTTAAA-TTTTAGATA
*
1107633 AAATATCATTTTCAAACTTAAATTTTAGATA
1 AAATATCAATTTCAAACTTAAATTTTAGATA
*
1107664 AAATATGAATTT
1 AAATATCAATTT
1107676 GACCCTTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
30 15 0.43
31 20 0.57
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (31 bp):
AAATATCAATTTCAAACTTAAATTTTAGATA
Found at i:1110053 original size:11 final size:11
Alignment explanation
Indices: 1110037--1110061 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1110027 GGCCCTCCGA
1110037 TAATCACAAAT
1 TAATCACAAAT
1110048 TAATCACAAAT
1 TAATCACAAAT
1110059 TAA
1 TAA
1110062 AAATGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATCACAAAT
Found at i:1112753 original size:10 final size:10
Alignment explanation
Indices: 1112738--1112774 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
1112728 TTACAAATAT
1112738 AAAAAAT-CA
1 AAAAAATCCA
1112747 GAAAAAATCCA
1 -AAAAAATCCA
1112758 AAAAAATCCA
1 AAAAAATCCA
1112768 AAAAAAT
1 AAAAAAT
1112775 TAGTATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 24 0.92
11 2 0.08
ACGTcount: A:0.73, C:0.14, G:0.03, T:0.11
Consensus pattern (10 bp):
AAAAAATCCA
Found at i:1114340 original size:16 final size:16
Alignment explanation
Indices: 1114319--1114352 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1114309 CGATTAAGCA
1114319 CTGAATGATCCAAATG
1 CTGAATGATCCAAATG
*
1114335 CTGAATGATTCAAATG
1 CTGAATGATCCAAATG
1114351 CT
1 CT
1114353 ATGTATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (16 bp):
CTGAATGATCCAAATG
Found at i:1153543 original size:50 final size:52
Alignment explanation
Indices: 1153441--1153543 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 52
1153431 TTTAAAAATA
1153441 AATTATTTATTTTAAAAATAGATATACGAAGTTTATTATATTTTGGCTTAAT
1 AATTATTTATTTTAAAAATAGATATACGAAGTTTATTATATTTTGGCTTAAT
* *
1153493 AATT-TTTTTTTTAAAAATAGATATACGAA-TTTATTATATTTTGGTTTAAT
1 AATTATTTATTTTAAAAATAGATATACGAAGTTTATTATATTTTGGCTTAAT
1153543 A
1 A
1153544 TAAATATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 21 0.43
51 24 0.49
52 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (52 bp):
AATTATTTATTTTAAAAATAGATATACGAAGTTTATTATATTTTGGCTTAAT
Found at i:1156600 original size:16 final size:15
Alignment explanation
Indices: 1156579--1156608 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1156569 AATATTGAAA
1156579 CTTGAACTCGAAAAGG
1 CTTGAACTC-AAAAGG
1156595 CTTGAACTCAAAAG
1 CTTGAACTCAAAAG
1156609 AAATTTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (15 bp):
CTTGAACTCAAAAGG
Found at i:1167399 original size:23 final size:22
Alignment explanation
Indices: 1167373--1167419 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1167363 GAAAATGAGG
1167373 GAAAGAAA-AATGAAAAAAATAAA
1 GAAAGAAAGAA-GAAAAAAA-AAA
*
1167396 GAAATAAAGAAGAAAAAAAAAA
1 GAAAGAAAGAAGAAAAAAAAAA
1167418 GA
1 GA
1167420 TTTGATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 15 0.68
24 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (22 bp):
GAAAGAAAGAAGAAAAAAAAAA
Found at i:1169653 original size:116 final size:116
Alignment explanation
Indices: 1169412--1169745 Score: 478
Period size: 116 Copynumber: 2.9 Consensus size: 116
1169402 TTTTATCGTT
* * * *
1169412 AGTAACATTATCGATTTATTATATTATAATCACTCGATTGCATCCGCCAAATACGTTAAGTGTTT
1 AGTAACATTGTCGATTTATTATATTATAATCACTCGATTGCATCCACCAATTATGTTAAGTGTTT
* * *
1169477 CATTGCTGA-TT-TTTGGAATTTTTTG-CATGTATAGTATATTATTTTAGTT
66 CATTGCTAAGTTCTTTGG-ATTTTTTGTCATGTATAGGATATTATTTTAGTC
* * *
1169526 AGTAACATTGTCGATCTATTATATTATAATCACTCGATTACACCCACCAATTATGTTAAAGTGTT
1 AGTAACATTGTCGATTTATTATATTATAATCACTCGATTGCATCCACCAATTATGTT-AAGTGTT
*
1169591 TCATTGCTAAGTTCTTTGGATTTTTTGTC-TGTATAGGATGTTATTTTAGTC
65 TCATTGCTAAGTTCTTTGGATTTTTTGTCATGTATAGGATATTATTTTAGTC
* *
1169642 GGTAACGTTGTCGATTTATTATATTATAATCACTCGATTGCATCCACCAATTATGTTAAGTGTTT
1 AGTAACATTGTCGATTTATTATATTATAATCACTCGATTGCATCCACCAATTATGTTAAGTGTTT
* *
1169707 CGTTGCTAAGTTCTTTGGATTTTTTTTTCATGTATAGGA
66 CATTGCTAAGTTCTTTGGA-TTTTTTGTCATGTATAGGA
1169746 GGGATGTTTG
Statistics
Matches: 196, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
114 50 0.26
115 42 0.21
116 89 0.45
117 15 0.08
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (116 bp):
AGTAACATTGTCGATTTATTATATTATAATCACTCGATTGCATCCACCAATTATGTTAAGTGTTT
CATTGCTAAGTTCTTTGGATTTTTTGTCATGTATAGGATATTATTTTAGTC
Found at i:1172561 original size:20 final size:20
Alignment explanation
Indices: 1172467--1172835 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1172457 GATTTTCCAT
* ** *
1172467 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1172487 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1172507 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1172527 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1172547 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1172567 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1172587 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1172607 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1172627 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1172647 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1172667 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1172687 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1172707 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1172727 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1172747 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1172767 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1172787 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1172807 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1172827 AATCACAAC
1 AATCGCAAC
1172836 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1173555 original size:24 final size:24
Alignment explanation
Indices: 1173516--1173562 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1173506 AAATTTGGTC
1173516 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1173540 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1173563 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1173753 original size:12 final size:12
Alignment explanation
Indices: 1173736--1173760 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1173726 CATATATCCT
1173736 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1173748 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1173760 G
1 G
1173761 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1174898 original size:93 final size:93
Alignment explanation
Indices: 1174739--1175111 Score: 723
Period size: 93 Copynumber: 4.0 Consensus size: 93
1174729 GCAAATTGAA
1174739 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1174804 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1174832 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1174897 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1174925 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1174988 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1175016 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
1175081 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1175109 ACT
1 ACT
1175112 AAGCAATCTA
Statistics
Matches: 277, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 89 0.32
92 4 0.01
93 184 0.66
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:1175050 original size:184 final size:186
Alignment explanation
Indices: 1174739--1175111 Score: 723
Period size: 184 Copynumber: 2.0 Consensus size: 186
1174729 GCAAATTGAA
1174739 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1174804 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
1174869 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
1174925 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1174988 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
*
1175053 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
1175109 ACT
1 ACT
1175112 AAGCAATCTA
Statistics
Matches: 186, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 151 0.81
185 2 0.01
186 33 0.18
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:1176818 original size:14 final size:14
Alignment explanation
Indices: 1176799--1176888 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1176789 TTGAAATGAA
1176799 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1176813 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1176830 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1176846 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1176865 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1176879 AATCGCAACG
1 AATCGCAACG
1176889 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1176836 original size:33 final size:33
Alignment explanation
Indices: 1176791--1176905 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1176781 TCTTTTGGTT
1176791 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1176824 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1176857 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1176890 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1176906 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1176837 original size:19 final size:18
Alignment explanation
Indices: 1176798--1176910 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1176788 GTTGAAATGA
1176798 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1176813 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1176830 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1176846 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1176863 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1176879 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1176896 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1176911 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1176941 original size:14 final size:14
Alignment explanation
Indices: 1176922--1176976 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1176912 TTTGGTTTCG
1176922 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1176936 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1176955 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1176969 CGTTGCGA
1 CGTTGCGA
1176977 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1176954 original size:33 final size:33
Alignment explanation
Indices: 1176906--1176976 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1176896 AAAATCGCAA
**
1176906 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1176939 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1176972 TGCGA
1 TGCGA
1176977 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1176984 original size:33 final size:33
Alignment explanation
Indices: 1176917--1176998 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1176907 GCGATTTTGG
***
1176917 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1176950 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1176983 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1176999 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1177003 original size:20 final size:20
Alignment explanation
Indices: 1176929--1177017 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1176919 TCGCGTTGCG
1176929 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1176949 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1176962 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1176982 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1177002 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1177018 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1177138 original size:33 final size:33
Alignment explanation
Indices: 1177096--1177166 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1177086 AAATACTAAC
*
1177096 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1177129 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1177162 TGAAA
1 TGAAA
1177167 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1177565 original size:20 final size:20
Alignment explanation
Indices: 1177540--1177732 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1177530 CTTTAAATAT
1177540 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1177560 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1177582 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1177601 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1177621 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1177641 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1177661 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1177681 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1177701 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1177721 CGCGTTGCGATT
1 CGCGTTGCGATT
1177733 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1177727 original size:60 final size:60
Alignment explanation
Indices: 1177540--1177732 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1177530 CTTTAAATAT
**
1177540 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1177601 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1177661 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1177721 CGCGTTGCGATT
1 CGCGTTGCGATT
1177733 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1177813 original size:20 final size:20
Alignment explanation
Indices: 1177788--1177839 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1177778 AAGAATCGCG
*
1177788 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1177808 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1177828 TTGCGATTCTGG
1 TTGCGATTCTGG
1177840 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1178048 original size:15 final size:15
Alignment explanation
Indices: 1178012--1178051 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1178002 TATATATATA
*
1178012 TATATAAA-T-TAAG
1 TATATAAAGTATAAC
1178025 TAT-TAAAGTATAAC
1 TATATAAAGTATAAC
1178039 TATATAAAGTATA
1 TATATAAAGTATA
1178052 TAAATTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 4 0.17
13 4 0.17
14 6 0.26
15 9 0.39
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (15 bp):
TATATAAAGTATAAC
Found at i:1178775 original size:25 final size:28
Alignment explanation
Indices: 1178747--1178806 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
1178737 CAATAACTAA
*
1178747 ATTATATAA-TAAAA-T-TAATTTAAGG
1 ATTATATAATTAAAATTATAATATAAGG
1178772 ATTATATAATTAAAATTTATAATATAAGG
1 ATTATATAATTAAAA-TTATAATATAAGG
1178801 ATTATA
1 ATTATA
1178807 ATTAATATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 9 0.30
26 5 0.17
28 1 0.03
29 15 0.50
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.42
Consensus pattern (28 bp):
ATTATATAATTAAAATTATAATATAAGG
Found at i:1186174 original size:16 final size:18
Alignment explanation
Indices: 1186155--1186191 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1186145 AATAATACCC
1186155 ATTAACATTA-A-TAGAT
1 ATTAACATTAGATTAGAT
*
1186171 ATTAATATTAGATTAGAT
1 ATTAACATTAGATTAGAT
1186189 ATT
1 ATT
1186192 TATTAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (18 bp):
ATTAACATTAGATTAGAT
Found at i:1187662 original size:16 final size:18
Alignment explanation
Indices: 1187641--1187686 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
1187631 AACATTTCCA
1187641 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
1187657 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
1187677 GTAATCTTAT
1 GTAATCTTAT
1187687 ATTTCGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.31
18 5 0.19
19 2 0.08
20 11 0.42
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:1189052 original size:3 final size:3
Alignment explanation
Indices: 1189044--1189128 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
1189034 ATAAAGAGAT
1189044 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1189092 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1189129 GGGAAAATAG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1189191 original size:2 final size:2
Alignment explanation
Indices: 1189184--1189222 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1189174 CCAAATTTGA
1189184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1189223 AAAGAGGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1192857 original size:20 final size:20
Alignment explanation
Indices: 1192820--1192856 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1192810 CACTGGCCTG
*
1192820 TAACATCCAATCATTATATT
1 TAACATCCAATAATTATATT
1192840 TAACATCC-ATAA-TATAT
1 TAACATCCAATAATTATAT
1192857 ACATATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 3 0.19
20 8 0.50
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (20 bp):
TAACATCCAATAATTATATT
Found at i:1193905 original size:55 final size:54
Alignment explanation
Indices: 1193812--1194018 Score: 213
Period size: 56 Copynumber: 3.7 Consensus size: 54
1193802 CGTTTGGCCC
* * *
1193812 AAAAAA-AAAAAAATAGGGGCTCCGAAATTGAATATATCTATTAGTTGTTGTCATT
1 AAAAAACATAAAAATA-GGGCTCCGAAA-TCAATATATCTATCAGTTGTTGTCATT
* * * *
1193867 AATAAATATAAAAATAGGGTTCCGAAATCAAGTATATCTATCAGTTGTTATCATT
1 AAAAAACATAAAAATAGGGCTCCGAAATCAA-TATATCTATCAGTTGTTGTCATT
*
1193922 AAAAAACATAAAAATAGAGGCCCCGAAATCAAATATATCTATCAGTTGTTG-CAATT
1 AAAAAACATAAAAATAG-GGCTCCGAAATC-AATATATCTATCAGTTGTTGTC-ATT
* * *
1193978 AAGAAGCATAAAAATAAGGG-TCTCGGAATCGAATATATCTA
1 AAAAAACATAAAAAT-AGGGCTC-CGAAATC-AATATATCTA
1194019 GAAAATAGGG
Statistics
Matches: 129, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
54 3 0.02
55 53 0.41
56 69 0.53
57 4 0.03
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (54 bp):
AAAAAACATAAAAATAGGGCTCCGAAATCAATATATCTATCAGTTGTTGTCATT
Found at i:1194971 original size:21 final size:21
Alignment explanation
Indices: 1194945--1194986 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1194935 TTACCACAAT
1194945 AAAAACATA-TATATTTGTAAA
1 AAAAACATACT-TATTTGTAAA
*
1194966 AAAAACTTACTTATTTGTAAA
1 AAAAACATACTTATTTGTAAA
1194987 TGTATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAAACATACTTATTTGTAAA
Found at i:1195644 original size:23 final size:22
Alignment explanation
Indices: 1195605--1195654 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1195595 GTAAATTTAT
*
1195605 AAAATTTTATAAGATTA-AAAA
1 AAAATTTTATAAAATTATAAAA
*
1195626 TAAATTATTAATAAAATTATAAAA
1 AAAATT-TT-ATAAAATTATAAAA
1195650 AAAAT
1 AAAAT
1195655 CTAAAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 5 0.22
22 2 0.09
23 8 0.35
24 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATTTTATAAAATTATAAAA
Found at i:1196507 original size:3 final size:3
Alignment explanation
Indices: 1196499--1196553 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1196489 ACTAGGAAGG
1196499 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1196547 TTA TTA T
1 TTA TTA T
1196554 ATTTGTTTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1197986 original size:137 final size:135
Alignment explanation
Indices: 1197751--1198157 Score: 442
Period size: 137 Copynumber: 2.9 Consensus size: 135
1197741 CATTTCACTT
* * *
1197751 TAGTCCTTAAATTTAAGAGAATTTTTAATTTGGT-ATTCGTTTTTGCTCGAGGTTGCATTTTAAT
1 TAGTCCTT-AATTTAAGAGAAATTTTAATTTGGTCA-TCGCTTTTGCTCGAGGTTCCATTTTAAT
*
1197815 TATTTGATCCAA-AATTTGATTAAAATTGAATAGGTTAATAATTAGAGCCTCCATTTTAGGTTTA
64 TATTTGATCCAATAA-TTGATTAAAATT-AATAGGTTAAT-ATTAGAGCCTACATTTTAGGTTTA
1197879 ATTTCAAACA
126 ATTTCAAACA
* * * *
1197889 TAGTCCATTAATTTAGGAAAAATTTTAATTTGGTCATCGCTTTTGCCCAAGGTT-CATTTTAATT
1 TAGTCC-TTAATTTAAGAGAAATTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATT
* * * * * * *
1197953 ATTCGATTCAATAATCGATTAAAATTAACTAGGTTAATTATTAGAGTCTTCACTTTAGGCTTAAT
65 ATTTGATCCAATAATTGATTAAAATTAA-TAGGTTAA-TATTAGAGCCTACATTTTAGGTTTAAT
* **
1198018 TTCATATT
128 TTCAAACA
* * * *
1198026 TAGTCCTTTCATTCAAGAGAAATCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATT
1 TAGTCC-TTAATTTAAGAGAAATTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATT
* * * *
1198091 ATTTGATCCAATAATTGGTTAAAAATTGATCAGGGTTAATATTAAAGCCTATATTTTTAGGTTTA
65 ATTTGATCCAATAATTGATT-AAAATTAAT-A-GGTTAATATTAGAGCCTACA-TTTTAGGTTTA
1198156 AT
126 AT
1198158 CCCCCTAGGT
Statistics
Matches: 223, Mismatches: 36, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
136 2 0.01
137 110 0.49
138 73 0.33
139 21 0.09
140 17 0.08
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (135 bp):
TAGTCCTTAATTTAAGAGAAATTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTA
TTTGATCCAATAATTGATTAAAATTAATAGGTTAATATTAGAGCCTACATTTTAGGTTTAATTTC
AAACA
Found at i:1204730 original size:19 final size:19
Alignment explanation
Indices: 1204693--1204730 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1204683 ATTATTAAAC
*
1204693 AATATAAAAATGTAGAAAA
1 AATATAAAAATATAGAAAA
*
1204712 AATAT-AAAATATATAAAA
1 AATATAAAAATATAGAAAA
1204730 A
1 A
1204731 CAAAGACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
AATATAAAAATATAGAAAA
Found at i:1206247 original size:60 final size:60
Alignment explanation
Indices: 1206171--1206317 Score: 205
Period size: 60 Copynumber: 2.5 Consensus size: 60
1206161 AACATAATGA
1206171 ATAGTC-GGGTGATCATTTTGTAACTTTTAATAGTC-GAGGGACTCAACAAAGTAA-ATCCCT
1 ATAGTCAGGG-GATCATTTTGTAACTTTTAATAGTCAG-GGGACTCAACAAAGTAATAT-CCT
1206231 ATAGTCAGGGGATCATTTTGTAACTTTTAATAGTCAGGGGACTCAACAAAGTAATATCCT
1 ATAGTCAGGGGATCATTTTGTAACTTTTAATAGTCAGGGGACTCAACAAAGTAATATCCT
*
1206291 ATAAGT-AGGGGACCATTTGTGT-ACTTT
1 AT-AGTCAGGGGATCATTT-TGTAACTTT
1206318 ACCCTTTTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
60 69 0.85
61 12 0.15
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (60 bp):
ATAGTCAGGGGATCATTTTGTAACTTTTAATAGTCAGGGGACTCAACAAAGTAATATCCT
Found at i:1220072 original size:16 final size:16
Alignment explanation
Indices: 1220051--1220097 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
1220041 AAAAATAAAT
1220051 GAACATAAACGAACAC
1 GAACATAAACGAACAC
1220067 GAACATAAACGAACAC
1 GAACATAAACGAACAC
1220083 GAACATAAACGAACA
1 GAACATAAACGAACA
1220098 AAAATTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:1220134 original size:87 final size:87
Alignment explanation
Indices: 1220021--1220184 Score: 310
Period size: 87 Copynumber: 1.9 Consensus size: 87
1220011 AACGAAGGTA
*
1220021 TGTTCATGTTCGTTCATTTAAAAAATAAATGAACATAAACGAACACGAACATAAACGAACACGAA
1 TGTTCATGTTCGTTCATTTAAAAAATAAACGAACATAAACGAACACGAACATAAACGAACACGAA
1220086 CATAAACGAACAAAAATTTTTT
66 CATAAACGAACAAAAATTTTTT
*
1220108 TGTTCATGTTCGTTCATTTAATAAATAAACGAACATAAACGAACACGAACATAAACGAACACGAA
1 TGTTCATGTTCGTTCATTTAAAAAATAAACGAACATAAACGAACACGAACATAAACGAACACGAA
1220173 CATAAACGAACA
66 CATAAACGAACA
1220185 CGAACATAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (87 bp):
TGTTCATGTTCGTTCATTTAAAAAATAAACGAACATAAACGAACACGAACATAAACGAACACGAA
CATAAACGAACAAAAATTTTTT
Found at i:1220147 original size:10 final size:10
Alignment explanation
Indices: 1220132--1220222 Score: 65
Period size: 10 Copynumber: 9.7 Consensus size: 10
1220122 CATTTAATAA
1220132 ATAAACGAAC
1 ATAAACGAAC
1220142 ATAAACGAAC
1 ATAAACGAAC
1220152 ----ACGAAC
1 ATAAACGAAC
1220158 ATAAACGAAC
1 ATAAACGAAC
1220168 ----ACGAAC
1 ATAAACGAAC
1220174 ATAAACGAAC
1 ATAAACGAAC
** *
1220184 ACGAAC-ATAA
1 ATAAACGA-AC
1220194 ATGAACACGAAC
1 AT-AA-ACGAAC
1220206 ATAAACGAAC
1 ATAAACGAAC
1220216 ATAAACG
1 ATAAACG
1220223 TTGGAGACCC
Statistics
Matches: 63, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
6 12 0.19
9 1 0.02
10 41 0.65
11 3 0.05
12 5 0.08
13 1 0.02
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1220157 original size:16 final size:16
Alignment explanation
Indices: 1220136--1220216 Score: 153
Period size: 16 Copynumber: 5.1 Consensus size: 16
1220126 TAATAAATAA
1220136 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1220152 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1220168 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1220184 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1220200 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1220216 A
1 A
1220217 TAAACGTTGG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 63 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1220984 original size:10 final size:10
Alignment explanation
Indices: 1220969--1221016 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1220959 ATAAATGAAT
1220969 GAACATAAAC
1 GAACATAAAC
1220979 GAACATAATCAAAC
1 GAAC---AT-AAAC
1220993 GAACATAAAC
1 GAACATAAAC
*
1221003 GAACATAACC
1 GAACATAAAC
1221013 GAAC
1 GAAC
1221017 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 21 0.64
11 2 0.06
13 2 0.06
14 8 0.24
ACGTcount: A:0.56, C:0.23, G:0.10, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1221017 original size:24 final size:24
Alignment explanation
Indices: 1220969--1221017 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1220959 ATAAATGAAT
*
1220969 GAACATAAACGAACATAATCAAAC
1 GAACATAAACGAACATAACCAAAC
*
1220993 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCAAAC
1221017 G
1 G
1221018 TTCACGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.22, G:0.12, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCAAAC
Found at i:1224827 original size:24 final size:24
Alignment explanation
Indices: 1224782--1224831 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1224772 TGGTGGTTGG
*
1224782 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
1224806 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
1224830 TT
1 TT
1224832 GGTTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:1230435 original size:24 final size:24
Alignment explanation
Indices: 1230390--1230439 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1230380 TGGTGGTTGG
*
1230390 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
1230414 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
1230438 TT
1 TT
1230440 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:1241703 original size:20 final size:20
Alignment explanation
Indices: 1241678--1241716 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1241668 CTGCATTCGT
1241678 ATTTCGTAGAATAACCAGTC
1 ATTTCGTAGAATAACCAGTC
**
1241698 ATTTCGTAGTTTAACCAGT
1 ATTTCGTAGAATAACCAGT
1241717 AAATATGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (20 bp):
ATTTCGTAGAATAACCAGTC
Found at i:1242326 original size:21 final size:21
Alignment explanation
Indices: 1242287--1242326 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1242277 AGAAAAAGAA
* * *
1242287 CAAATATTTAATTATTTTTCC
1 CAAAAATTTAAGTACTTTTCC
1242308 CAAAAATTTAAGTACTTTT
1 CAAAAATTTAAGTACTTTT
1242327 GATCCCTTTA
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:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (21 bp):
CAAAAATTTAAGTACTTTTCC
Found at i:1242713 original size:20 final size:20
Alignment explanation
Indices: 1242688--1242725 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1242678 CTAAATTTCA
1242688 AAAATATAATTATTTTATAC
1 AAAATATAATTATTTTATAC
**
1242708 AAAATATTTTTATTTTAT
1 AAAATATAATTATTTTAT
1242726 CTACAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAATATAATTATTTTATAC
Found at i:1255919 original size:22 final size:21
Alignment explanation
Indices: 1255867--1255926 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
1255857 GATTTCTGGG
*
1255867 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
1255888 CAA-GGGAATCGATACCCATT
1 CAAGGGGAATCGATACCCATT
1255908 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGATACCC
1255927 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 19 0.53
21 3 0.08
22 14 0.39
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:1256004 original size:23 final size:22
Alignment explanation
Indices: 1255960--1256004 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1255950 AATCTCATAG
*
1255960 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
1255982 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
1256005 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:1257455 original size:23 final size:23
Alignment explanation
Indices: 1257422--1257489 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
1257412 ATTATTATAT
1257422 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1257445 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
1257468 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1257490 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1264234 original size:2 final size:2
Alignment explanation
Indices: 1264227--1264274 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1264217 TATGCAATAC
1264227 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
1264269 AT AT AT
1 AT AT AT
1264275 TTCTTCATAT
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):
AT
Found at i:1279882 original size:82 final size:82
Alignment explanation
Indices: 1279745--1279998 Score: 490
Period size: 82 Copynumber: 3.1 Consensus size: 82
1279735 CTCATCGTCC
1279745 TTTTGCTTATCCGGATGCCATTTCTGCAGAAACAATCCCATACTATTCAATAACAAAGAAGAAAT
1 TTTTGCTTATCCGGATGCCATTTCTGCAGAAACAATCCCATACTATTCAATAACAAAGAAGAAAT
1279810 ATATATAAAGAAATCAA
66 ATATATAAAGAAATCAA
1279827 TTTTGCTTATCCGGATGCCATTTCTGCAGAAACAATCCCATACTATTCAATAACAAAGAAGAAAT
1 TTTTGCTTATCCGGATGCCATTTCTGCAGAAACAATCCCATACTATTCAATAACAAAGAAGAAAT
*
1279892 ATATATAAGGAAATCAA
66 ATATATAAAGAAATCAA
1279909 TTTTGCTTATCCGGATGCCATTTCTGCAGAAACAATCCCATACTATTCAATAACAAAGAAGAAAT
1 TTTTGCTTATCCGGATGCCATTTCTGCAGAAACAATCCCATACTATTCAATAACAAAGAAGAAAT
1279974 ATATATAAAGAAATCAA
66 ATATATAAAGAAATCAA
*
1279991 TTTAGCTT
1 TTTTGCTT
1279999 TTGAGAAAAG
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 169 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.29
Consensus pattern (82 bp):
TTTTGCTTATCCGGATGCCATTTCTGCAGAAACAATCCCATACTATTCAATAACAAAGAAGAAAT
ATATATAAAGAAATCAA
Found at i:1280750 original size:28 final size:28
Alignment explanation
Indices: 1280714--1280773 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
1280704 GAAAACAAAG
* *
1280714 TAACTTTACTTGCAAGAAAGCCAATAAT
1 TAACTTTACTTGAAAGAAAGCCAAGAAT
1280742 TAACTTTACTTGAAAGAAAGCCAAGAAT
1 TAACTTTACTTGAAAGAAAGCCAAGAAT
1280770 TAAC
1 TAAC
1280774 ATAGAGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.27
Consensus pattern (28 bp):
TAACTTTACTTGAAAGAAAGCCAAGAAT
Found at i:1281798 original size:233 final size:233
Alignment explanation
Indices: 1281391--1281859 Score: 938
Period size: 233 Copynumber: 2.0 Consensus size: 233
1281381 AACTAATGCC
1281391 TTATTACAAATGAATGATGCAAGAAAATTTCATTGAATGGCAGTGGCACACCTGCACACGACAGT
1 TTATTACAAATGAATGATGCAAGAAAATTTCATTGAATGGCAGTGGCACACCTGCACACGACAGT
1281456 CTTCACTGGATCTTCATTAATTCGACTACCTTCACAATTGGAATAGATGCCCTCCACACTGAACA
66 CTTCACTGGATCTTCATTAATTCGACTACCTTCACAATTGGAATAGATGCCCTCCACACTGAACA
1281521 TGTGAAGACGGAGTCTCCCTGACGAATTGAAGGACGAAGAATACCATACCAGATATGACTGACAT
131 TGTGAAGACGGAGTCTCCCTGACGAATTGAAGGACGAAGAATACCATACCAGATATGACTGACAT
1281586 AACTGATAAAGAAACCGAAATAGTTTTGTCATTGCTCA
196 AACTGATAAAGAAACCGAAATAGTTTTGTCATTGCTCA
1281624 TTATTACAAATGAATGATGCAAGAAAATTTCATTGAATGGCAGTGGCACACCTGCACACGACAGT
1 TTATTACAAATGAATGATGCAAGAAAATTTCATTGAATGGCAGTGGCACACCTGCACACGACAGT
1281689 CTTCACTGGATCTTCATTAATTCGACTACCTTCACAATTGGAATAGATGCCCTCCACACTGAACA
66 CTTCACTGGATCTTCATTAATTCGACTACCTTCACAATTGGAATAGATGCCCTCCACACTGAACA
1281754 TGTGAAGACGGAGTCTCCCTGACGAATTGAAGGACGAAGAATACCATACCAGATATGACTGACAT
131 TGTGAAGACGGAGTCTCCCTGACGAATTGAAGGACGAAGAATACCATACCAGATATGACTGACAT
1281819 AACTGATAAAGAAACCGAAATAGTTTTGTCATTGCTCA
196 AACTGATAAAGAAACCGAAATAGTTTTGTCATTGCTCA
1281857 TTA
1 TTA
1281860 GTATCAATTC
Statistics
Matches: 236, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 236 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (233 bp):
TTATTACAAATGAATGATGCAAGAAAATTTCATTGAATGGCAGTGGCACACCTGCACACGACAGT
CTTCACTGGATCTTCATTAATTCGACTACCTTCACAATTGGAATAGATGCCCTCCACACTGAACA
TGTGAAGACGGAGTCTCCCTGACGAATTGAAGGACGAAGAATACCATACCAGATATGACTGACAT
AACTGATAAAGAAACCGAAATAGTTTTGTCATTGCTCA
Found at i:1283385 original size:22 final size:21
Alignment explanation
Indices: 1283340--1283397 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1283330 AAATTAAAAT
1283340 TTTAAAACTTTAAATTTCAAAC
1 TTTAAAAC-TTAAATTTCAAAC
* *
1283362 TTTAAATCTTAAATTTTAAGAC
1 TTTAAAACTTAAATTTCAA-AC
**
1283384 TTTAACCCTTAAAT
1 TTTAAAACTTAAAT
1283398 AAGATATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTAAAACTTAAATTTCAAAC
Found at i:1283420 original size:24 final size:24
Alignment explanation
Indices: 1283393--1283441 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1283383 CTTTAACCCT
1283393 TAAATAAGATATATG-ATATTAAAA
1 TAAATAAGAT-TATGTATATTAAAA
*
1283417 TAAATAAGCTTATGTATATTAAAA
1 TAAATAAGATTATGTATATTAAAA
1283441 T
1 T
1283442 GTACCCATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (24 bp):
TAAATAAGATTATGTATATTAAAA
Found at i:1284029 original size:36 final size:36
Alignment explanation
Indices: 1283989--1284061 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1283979 AATTTACTGC
1283989 TATTTTCAAGATTTTTGTAGCCAAGTTACTCTGTTT
1 TATTTTCAAGATTTTTGTAGCCAAGTTACTCTGTTT
1284025 TATTTTCAAGATTTTTGTAGCCAAGTTACTCTGTTT
1 TATTTTCAAGATTTTTGTAGCCAAGTTACTCTGTTT
1284061 T
1 T
1284062 GCTCCCCTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (36 bp):
TATTTTCAAGATTTTTGTAGCCAAGTTACTCTGTTT
Found at i:1286580 original size:114 final size:114
Alignment explanation
Indices: 1286409--1286640 Score: 308
Period size: 114 Copynumber: 2.0 Consensus size: 114
1286399 AGTCTTTATT
* * *
1286409 ATTTATATCAATTTGGTCCTAAATTAATAAAATTTACATTAATCATTTAATTAGGATCTGACATG
1 ATTTATAT-AATTTGGTCCTAAATTAATAAAATTTACATAAATCAATCAATTAGGATCTGACATG
* * *
1286474 TGTTAGCAC-TGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTA
65 TGTTAACACATGATCATGACACGTGT-ATTGGTGACACATGTCACCACCTA
* *
1286524 ATTTATAT-ATTTGGTCCTAAATTAAATAAAATTTA-ATAAATTAATCATTTCAGGATCTGACAT
1 ATTTATATAATTTGGTCCTAAATT-AATAAAATTTACATAAATCAATCAATT-AGGATCTGACAT
* * *
1286587 GTGTTAACACATGATCATGATATGTGTATTGGTGACACATGTCACCTCCTA
64 GTGTTAACACATGATCATGACACGTGTATTGGTGACACATGTCACCACCTA
1286638 ATT
1 ATT
1286641 AGAAGAAAAA
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
113 25 0.24
114 56 0.54
115 22 0.21
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (114 bp):
ATTTATATAATTTGGTCCTAAATTAATAAAATTTACATAAATCAATCAATTAGGATCTGACATGT
GTTAACACATGATCATGACACGTGTATTGGTGACACATGTCACCACCTA
Found at i:1290026 original size:29 final size:30
Alignment explanation
Indices: 1289984--1290063 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 30
1289974 ACTCAACACC
* * * *
1289984 TTATAGTCAATGGACCATTTTATTACT-TT
1 TTATAATCAATGGACCATTTAAGTACTATG
* * *
1290013 TTATAATCGATGGACTCAATAAAGTACTATG
1 TTATAATCAATGGAC-CATTTAAGTACTATG
1290044 TTATAATCAATGGACCATTT
1 TTATAATCAATGGACCATTT
1290064 GTGTACTTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 13 0.33
30 11 0.28
31 15 0.38
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (30 bp):
TTATAATCAATGGACCATTTAAGTACTATG
Found at i:1294911 original size:23 final size:23
Alignment explanation
Indices: 1294865--1294913 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1294855 CTAATTGTCA
**
1294865 TCGGTCATCTATGGCCACCGTCG
1 TCGGTCATCTATGGCCACAATCG
1294888 TCGGTCATCTATGGCCACAATCG
1 TCGGTCATCTATGGCCACAATCG
1294911 TCG
1 TCG
1294914 CTGAACACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.16, C:0.33, G:0.24, T:0.27
Consensus pattern (23 bp):
TCGGTCATCTATGGCCACAATCG
Found at i:1296241 original size:21 final size:22
Alignment explanation
Indices: 1296200--1296241 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1296190 CCATCTTTAA
* *
1296200 CAATCTGTCTCTAGTTGGCCAG
1 CAATCTGTCTCAAGATGGCCAG
1296222 CAATCTGTCT-AAGATGGCCA
1 CAATCTGTCTCAAGATGGCCA
1296242 TCCAAGCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (22 bp):
CAATCTGTCTCAAGATGGCCAG
Found at i:1311929 original size:129 final size:129
Alignment explanation
Indices: 1311699--1311967 Score: 441
Period size: 129 Copynumber: 2.1 Consensus size: 129
1311689 AATTGGAATT
* ** * *
1311699 TATATAATTTTGAAATTTAAATCTAGTAATTAATTAAGTTTTGTTACACTTATAATATTTTATGT
1 TATATAATTTTGAAATTTAAATATAACAATGAATTAAATTTTGTTACACTTATAATATTTTATGT
*
1311764 TAAAAATAAATATATTTTTCAATTTCATCCAATAATGATTATAGGCGGAGTGATAATAGATTTA
66 TAAAAATAAATATATTTTTCAATTTCATCCAATAATGATTATAGGCGGAGAGATAATAGATTTA
* *
1311828 TATATAATTTTGAAATTTAAATATAACAATGAATTAAATTTTGTTACACTTCTAGTATTTTATGT
1 TATATAATTTTGAAATTTAAATATAACAATGAATTAAATTTTGTTACACTTATAATATTTTATGT
*
1311893 TAAAAATAAATATATTTCTT-AATTTCATCCAATAATGATTATAGGTGGAGAGATAATAGATTTA
66 TAAAAATAAATATATTT-TTCAATTTCATCCAATAATGATTATAGGCGGAGAGATAATAGATTTA
1311957 TATATAATTTT
1 TATATAATTTT
1311968 ATTGAATACG
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
129 128 0.98
130 2 0.02
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (129 bp):
TATATAATTTTGAAATTTAAATATAACAATGAATTAAATTTTGTTACACTTATAATATTTTATGT
TAAAAATAAATATATTTTTCAATTTCATCCAATAATGATTATAGGCGGAGAGATAATAGATTTA
Found at i:1315242 original size:39 final size:39
Alignment explanation
Indices: 1315199--1315273 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
1315189 TTACTTGAAA
1315199 AATATATAGATTTACGTATTTTCATATATGTTGAATACG
1 AATATATAGATTTACGTATTTTCATATATGTTGAATACG
1315238 AATATATAGATTTACGTATTTTCATATATGTTGAAT
1 AATATATAGATTTACGTATTTTCATATATGTTGAAT
1315274 TAGAAGCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (39 bp):
AATATATAGATTTACGTATTTTCATATATGTTGAATACG
Found at i:1316104 original size:2 final size:2
Alignment explanation
Indices: 1316097--1316127 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1316087 TAATTTTAAT
1316097 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 T
1316128 TACGATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1318783 original size:6 final size:6
Alignment explanation
Indices: 1318772--1318806 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1318762 GCATCAATCT
*
1318772 ATGGGG ATGGGG ATGGGG ATGGGG ATGGGC ATGGG
1 ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGG
1318807 TGGGGTTTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.03, G:0.63, T:0.17
Consensus pattern (6 bp):
ATGGGG
Found at i:1318957 original size:23 final size:22
Alignment explanation
Indices: 1318917--1318974 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1318907 CGACCCAAAA
* * *
1318917 TAATAAAAAATATTATTTTTATT
1 TAAT-AAAAATAATAATTTAATT
1318940 TAATAAAAATAATAATTTAATT
1 TAATAAAAATAATAATTTAATT
*
1318962 GAA-AAAAATAATA
1 TAATAAAAATAATA
1318975 TAGAGAGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 10 0.32
22 17 0.55
23 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAATAAAAATAATAATTTAATT
Found at i:1329004 original size:130 final size:130
Alignment explanation
Indices: 1328848--1329106 Score: 428
Period size: 130 Copynumber: 2.0 Consensus size: 130
1328838 ATATTTCTAC
* *
1328848 ATTTAAATTTGAATGTTATTCGAATTAAATTATCTTGGATTTACACCGTTAAAAAATAAATATTT
1 ATTTAAATTTAAATATTATTCGAATTAAATTATCTTGGATTTACACCGTTAAAAAATAAATATTT
** * *
1328913 TAGATTTTGACTATTTTAAAATTGGATTGGTGGAGTTTAAATGTATTCAAATAATTTTGATGTTA
66 TAGATTTTGACTATTTTAAAATTAAATTGGTCGAGTTTAAATGTATTCAAATAATTCTGATGTTA
* * *
1328978 ATTTAAATTTAAATATTTTTCGAATTAAATTATCTTTGATTTAGACCGTTAAAAAATAAATATTT
1 ATTTAAATTTAAATATTATTCGAATTAAATTATCTTGGATTTACACCGTTAAAAAATAAATATTT
*
1329043 TAGATTTTGACTATTTTAAAATTAAATTGGTCGAGTTTAGATGTATTCAAATAATTCTGATGTT
66 TAGATTTTGACTATTTTAAAATTAAATTGGTCGAGTTTAAATGTATTCAAATAATTCTGATGTT
1329107 TTAACCGGTA
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 119 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (130 bp):
ATTTAAATTTAAATATTATTCGAATTAAATTATCTTGGATTTACACCGTTAAAAAATAAATATTT
TAGATTTTGACTATTTTAAAATTAAATTGGTCGAGTTTAAATGTATTCAAATAATTCTGATGTTA
Found at i:1329334 original size:3 final size:3
Alignment explanation
Indices: 1329326--1329359 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1329316 TTTTATGTTA
1329326 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1329360 CTATATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1334928 original size:201 final size:205
Alignment explanation
Indices: 1334560--1334965 Score: 775
Period size: 201 Copynumber: 2.0 Consensus size: 205
1334550 CATTTTCCTA
*
1334560 AAACATTCATCAAACTCGTAAGAACTATTGGTTAAATTATTAGTCTACCATAAAATTAATTTGAA
1 AAACATTCATCAAACACGTAAGAACTATTGGTTAAATTATTAGTCTACCATAAAATTAATTTGAA
1334625 AAAGAGATTAATTGTGTGTTATGAGCTTATTCTTATTTTAATAAATTTTAAATTTATTCTTATAA
66 AAAGAGATTAATTGTGTGTTATGAGCTTATTCTTATTTTAATAAATTTTAAATTTATTCTTATAA
1334690 GAGTAAATTTATCATAAGCTCTCCAATAAAAAGCCACCCTAAGCTCTTTGTTTGATGCTC-GCAA
131 GAGTAAATTTATCATAAGCTCTCCAATAAAAAGCCACCCTAAGCTCTTTGTTTGATGCTCTGCAA
1334754 TCATTTGGTT
196 TCATTTGGTT
1334764 AAACATTCATCAAA-AC-TAAG-ACTATTGGTTAAATTATTAGTCTACCATAAAATTAATTTGAA
1 AAACATTCATCAAACACGTAAGAACTATTGGTTAAATTATTAGTCTACCATAAAATTAATTTGAA
1334826 AAAGAGATTAATTGTGTGTTATGAGCTTATTCTTATTTTAATAAATTTTAAATTTATTCTTATAA
66 AAAGAGATTAATTGTGTGTTATGAGCTTATTCTTATTTTAATAAATTTTAAATTTATTCTTATAA
1334891 GAGTAAATTTATCATAAGCTCTCCAATAAAAAGCCACCCTAAGCTCTTTGTTTGATGCTCTGCAA
131 GAGTAAATTTATCATAAGCTCTCCAATAAAAAGCCACCCTAAGCTCTTTGTTTGATGCTCTGCAA
1334956 TCATTTGGTT
196 TCATTTGGTT
1334966 TATTTATTTC
Statistics
Matches: 200, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
201 167 0.83
202 18 0.09
203 1 0.00
204 14 0.07
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (205 bp):
AAACATTCATCAAACACGTAAGAACTATTGGTTAAATTATTAGTCTACCATAAAATTAATTTGAA
AAAGAGATTAATTGTGTGTTATGAGCTTATTCTTATTTTAATAAATTTTAAATTTATTCTTATAA
GAGTAAATTTATCATAAGCTCTCCAATAAAAAGCCACCCTAAGCTCTTTGTTTGATGCTCTGCAA
TCATTTGGTT
Found at i:1340070 original size:18 final size:17
Alignment explanation
Indices: 1340049--1340091 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1340039 ATATATACAT
1340049 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1340067 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1340084 ATAA-AATA
1 ATAATAATA
1340092 TTCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1340490 original size:37 final size:37
Alignment explanation
Indices: 1340440--1340544 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
1340430 GTGTTTGTGG
* * * *
1340440 ATCATATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
1340477 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCATATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
1340514 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1340545 GACGAAAATA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1343946 original size:2 final size:2
Alignment explanation
Indices: 1343939--1343963 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1343929 TAATGAAAAT
1343939 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
1343964 TATTTTGTTT
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:1344911 original size:21 final size:21
Alignment explanation
Indices: 1344855--1344912 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1344845 GAAGATGCGT
* *
1344855 AAGAAGAAGAAGCTGAACACG
1 AAGAAGAAGAAGATGAACAAG
* * *
1344876 AAGAACAATACGATGAA-AGAG
1 AAGAAGAAGAAGATGAACA-AG
1344897 AAGAAGAAGAAGATGA
1 AAGAAGAAGAAGATGA
1344913 GGCAATCGTA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.57, C:0.09, G:0.28, T:0.07
Consensus pattern (21 bp):
AAGAAGAAGAAGATGAACAAG
Found at i:1345781 original size:35 final size:35
Alignment explanation
Indices: 1345742--1345819 Score: 140
Period size: 35 Copynumber: 2.3 Consensus size: 35
1345732 TATATATATA
1345742 TAATATTAAATTCAGAATTGAATAAATTTTTATTC
1 TAATATTAAATTCAGAATTGAATAAATTTTTATTC
*
1345777 TAATATTAAATTTAGAATTGAATAAATTTTTATTC
1 TAATATTAAATTCAGAATTGAATAAATTTTTATTC
1345812 TAA-ATTAA
1 TAATATTAA
1345820 GTTTGGTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 5 0.12
35 37 0.88
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (35 bp):
TAATATTAAATTCAGAATTGAATAAATTTTTATTC
Found at i:1353900 original size:3 final size:3
Alignment explanation
Indices: 1353894--1353943 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1353884 ATCATCATCA
1353894 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
1353942 TA
1 TA
1353944 CAATTTCCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1354148 original size:31 final size:31
Alignment explanation
Indices: 1354110--1354179 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
1354100 AAATGGTCCC
*
1354110 TTGACTATAGAACATTACTTTGTTGAGTCTT
1 TTGACTATAAAACATTACTTTGTTGAGTCTT
*
1354141 TTGACTATAAAACATTATTTTGTTGAGTCTT
1 TTGACTATAAAACATTACTTTGTTGAGTCTT
*
1354172 TCGACTAT
1 TTGACTAT
1354180 TGAAAGTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (31 bp):
TTGACTATAAAACATTACTTTGTTGAGTCTT
Found at i:1364374 original size:3 final size:3
Alignment explanation
Indices: 1364366--1364392 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1364356 TTCTCAAACA
1364366 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1364393 TGTATCTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1364558 original size:21 final size:21
Alignment explanation
Indices: 1364532--1364571 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1364522 AGATACGGTG
1364532 TATAAGTA-TATAAAATATTAA
1 TATAAG-AGTATAAAATATTAA
*
1364553 TATAAGAGTATAAATTATT
1 TATAAGAGTATAAAATATT
1364572 TTATTGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TATAAGAGTATAAAATATTAA
Found at i:1364959 original size:17 final size:17
Alignment explanation
Indices: 1364937--1364977 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1364927 CTTTTAAATT
1364937 AAATTAAATAA-TATTTC
1 AAATTAAA-AATTATTTC
*
1364954 AAATTAAAAATTATTTT
1 AAATTAAAAATTATTTC
1364971 AAATTAA
1 AAATTAA
1364978 TCATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTAAAAATTATTTC
Found at i:1366833 original size:16 final size:16
Alignment explanation
Indices: 1366812--1366842 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1366802 TTTTATAAAT
*
1366812 TTTAATAATATAATAA
1 TTTAATAAAATAATAA
1366828 TTTAATAAAATAATA
1 TTTAATAAAATAATA
1366843 TTATATAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAATAAAATAATAA
Found at i:1375895 original size:229 final size:229
Alignment explanation
Indices: 1375314--1375997 Score: 1313
Period size: 229 Copynumber: 3.0 Consensus size: 229
1375304 ATTCTTCTAT
1375314 TGTGGTCACTTCAGCAACTGTCGCTCAACCCTCATTAATGACAGACATACCCCCGATAATTACCA
1 TGTGGTCACTTCAGCAACTGTCGCTCAACCCTCATTAATGACAGACATACCCCCGATAATTACCA
1375379 AGTAAATCCCCATATATTTAAAGAAAATTAATGTATCACCATAATATAATATCACATCAACATTA
66 AGTAAATCCCCATATATTTAAAGAAAATTAATGTATCACCATAATATAATATCACATCAACATTA
1375444 -TTTTTTTTAAAAATATCACGACAATAATTCTATTAAATTTTTAATAACAATTGATCAAAATGTA
131 TTTTTTTTTAAAAATATCACGACAATAATTCTATTAAATTTTTAATAACAATTGATCAAAATGTA
1375508 ACATTAGATATGATTTTC--AA-AATAATAATAA
196 ACATTAGATATGATTTTCAAAATAATAATAATAA
1375539 TGTGGTCACTTCAGCAACTGTCGCTCAACCCTCATTAATGACAGACATACCCCCGATAATTACCA
1 TGTGGTCACTTCAGCAACTGTCGCTCAACCCTCATTAATGACAGACATACCCCCGATAATTACCA
1375604 AGTAAATCCCCATATATTTAAAGAAAATTAATGTATCACCATAATATAATATCACATCAACATTA
66 AGTAAATCCCCATATATTTAAAGAAAATTAATGTATCACCATAATATAATATCACATCAACATTA
1375669 TTTTTTTTTAAAAATATCACGACAATAATTCTATTAAATTTTTAATAACAATTGATCAAAATGTA
131 TTTTTTTTTAAAAATATCACGACAATAATTCTATTAAATTTTTAATAACAATTGATCAAAATGTA
1375734 ACATTAGATATGATTTTCAAAATAATAATAATAA
196 ACATTAGATATGATTTTCAAAATAATAATAATAA
1375768 TGTGGTCACTTCAGCAACTGTCGCTCAACCCTCATTAATGACAGACATACCCCCGATAATTACCA
1 TGTGGTCACTTCAGCAACTGTCGCTCAACCCTCATTAATGACAGACATACCCCCGATAATTACCA
*
1375833 AGTAAGTCCCCATATATTTAAAGAAAATTAATGTATCACCATAATATAATATCACATCAACATTA
66 AGTAAATCCCCATATATTTAAAGAAAATTAATGTATCACCATAATATAATATCACATCAACATTA
**
1375898 TTTTTTTAAAAAAATATCACGACAATAATTCTATTAAATTTTTAATAACAATTGATCAAAATGTA
131 TTTTTTTTTAAAAATATCACGACAATAATTCTATTAAATTTTTAATAACAATTGATCAAAATGTA
1375963 ACATTAGATATGATTTTCAAAATAATAATAATAA
196 ACATTAGATATGATTTTCAAAATAATAATAATAA
1375997 T
1 T
1375998 AATAATAATT
Statistics
Matches: 452, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
225 130 0.29
226 82 0.18
228 2 0.00
229 238 0.53
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33
Consensus pattern (229 bp):
TGTGGTCACTTCAGCAACTGTCGCTCAACCCTCATTAATGACAGACATACCCCCGATAATTACCA
AGTAAATCCCCATATATTTAAAGAAAATTAATGTATCACCATAATATAATATCACATCAACATTA
TTTTTTTTTAAAAATATCACGACAATAATTCTATTAAATTTTTAATAACAATTGATCAAAATGTA
ACATTAGATATGATTTTCAAAATAATAATAATAA
Found at i:1381018 original size:27 final size:28
Alignment explanation
Indices: 1380956--1381022 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
1380946 CCTAAACCCG
*
1380956 AACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGAATACCACACTTAAAAA
*
1380984 AACCCGACCCGAATGCCACACTT-AAAA
1 AACCCGACCCGAATACCACACTTAAAAA
1381011 AACCCGACCCGA
1 AACCCGACCCGA
1381023 CCCGAACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 16 0.43
28 21 0.57
ACGTcount: A:0.42, C:0.37, G:0.10, T:0.10
Consensus pattern (28 bp):
AACCCGACCCGAATACCACACTTAAAAA
Found at i:1381255 original size:37 final size:38
Alignment explanation
Indices: 1381178--1381269 Score: 123
Period size: 38 Copynumber: 2.4 Consensus size: 38
1381168 TTTTCACCTT
*
1381178 AAACTCGAACCCGACCCAACCCCAATATCACACTTAAAA
1 AAACTCG-ACCCGACCCAACCCAAATATCACACTTAAAA
* * *
1381217 AAACTCGACCCGACTCGACCCAAATATCACA-TTTAAA
1 AAACTCGACCCGACCCAACCCAAATATCACACTTAAAA
*
1381254 AAACCCGACCCGACCC
1 AAACTCGACCCGACCC
1381270 GAACAAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 19 0.40
38 21 0.45
39 7 0.15
ACGTcount: A:0.40, C:0.39, G:0.08, T:0.13
Consensus pattern (38 bp):
AAACTCGACCCGACCCAACCCAAATATCACACTTAAAA
Found at i:1381279 original size:37 final size:38
Alignment explanation
Indices: 1381201--1381279 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
1381191 ACCCAACCCC
* * * *
1381201 AATATCACACTTAAAAAAACTCGACCCGACTCGACCCA
1 AATATCACACTTAAAAAAACCCGACCCGACCCGAACAA
*
1381239 AATATCACA-TTTAAAAAACCCGACCCGACCCGAACAA
1 AATATCACACTTAAAAAAACCCGACCCGACCCGAACAA
1381276 AATA
1 AATA
1381280 AAGTTTCATC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 27 0.75
38 9 0.25
ACGTcount: A:0.46, C:0.32, G:0.08, T:0.15
Consensus pattern (38 bp):
AATATCACACTTAAAAAAACCCGACCCGACCCGAACAA
Found at i:1383051 original size:23 final size:23
Alignment explanation
Indices: 1383021--1383066 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1383011 GCATCAAAGT
1383021 AAAACCAAATACTTCCAATTAAG
1 AAAACCAAATACTTCCAATTAAG
1383044 AAAACCAAATACTTCCAATTAAG
1 AAAACCAAATACTTCCAATTAAG
1383067 TAAATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAACCAAATACTTCCAATTAAG
Found at i:1386352 original size:16 final size:16
Alignment explanation
Indices: 1386327--1386357 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1386317 TATAATTTTG
*
1386327 TTAAATCTTAAAAAAC
1 TTAAAACTTAAAAAAC
1386343 TTAAAACTTAAAAAA
1 TTAAAACTTAAAAAA
1386358 ATCTAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAAACTTAAAAAAC
Found at i:1397032 original size:2 final size:2
Alignment explanation
Indices: 1397025--1397051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1397015 TGTAAGTTGT
1397025 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1397052 TCGTGTTCTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1402702 original size:24 final size:22
Alignment explanation
Indices: 1402670--1402734 Score: 98
Period size: 21 Copynumber: 3.0 Consensus size: 22
1402660 GGAAATGGGT
1402670 GGCAAAGGTGGAAGTGGCGGAGGA
1 GGCAAAGGT--AAGTGGCGGAGGA
1402694 GGCAAAGGT-AGTGGCGGAGGA
1 GGCAAAGGTAAGTGGCGGAGGA
1402715 GGCAAAGGTAA-TGGCGGAGG
1 GGCAAAGGTAAGTGGCGGAGG
1402735 CAGCGGTGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
21 30 0.75
22 1 0.03
24 9 0.22
ACGTcount: A:0.29, C:0.09, G:0.52, T:0.09
Consensus pattern (22 bp):
GGCAAAGGTAAGTGGCGGAGGA
Found at i:1405859 original size:129 final size:129
Alignment explanation
Indices: 1405629--1405886 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 129
1405619 TTCAACACCA
1405629 GTCTGATTGTAGACAATTTTACGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGC
1 GTCTGATTGTAGACAATTTTACGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGC
1405694 TGAAAACTTTTGACAACCAATCTTGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCC
66 TGAAAACTTTTGACAACCAATCTTGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCC
1405758 GTCTGATTGTAGACAATTTTACGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGC
1 GTCTGATTGTAGACAATTTTACGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGC
1405823 TGAAAACTTTTGACAACCAATCTTGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCC
66 TGAAAACTTTTGACAACCAATCTTGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCC
1405887 TGTAAATTCA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (129 bp):
GTCTGATTGTAGACAATTTTACGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGC
TGAAAACTTTTGACAACCAATCTTGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCTTTGATCC
Found at i:1408306 original size:16 final size:16
Alignment explanation
Indices: 1408282--1408315 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1408272 TATCGTCAAC
*
1408282 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1408298 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1408314 CG
1 CG
1408316 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1410650 original size:25 final size:25
Alignment explanation
Indices: 1410595--1410656 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
1410585 ATAAGTCTAG
*
1410595 ATTCAATATTTTGATACATGATCACA
1 ATTC-ATATTATGATACATGATCACA
* *
1410621 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCA-CA
1410646 ATTCATATTAT
1 ATTCATATTAT
1410657 ATGCATTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 26 0.84
26 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCACA
Found at i:1410757 original size:30 final size:31
Alignment explanation
Indices: 1410698--1410761 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1410688 GTTATATGAG
*
1410698 CTATGTGATAAAGGTATGAAAAATGATATGT
1 CTATGTGATAAAGGTATGAAAAATAATATGT
1410729 CTATGTGATAAAGGTATG-AAAATAATATGT
1 CTATGTGATAAAGGTATGAAAAATAATATGT
1410759 CTA
1 CTA
1410762 CGCGATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (31 bp):
CTATGTGATAAAGGTATGAAAAATAATATGT
Found at i:1411060 original size:24 final size:24
Alignment explanation
Indices: 1411003--1411070 Score: 86
Period size: 24 Copynumber: 2.8 Consensus size: 24
1410993 CAATATTATA
1411003 TGGCACTTCGGTGCAAAATTCTACG
1 TGGCACTTCGGTGC-AAATTCTACG
*
1411028 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-CAAATTCTACG
1411052 TGGCACTTCGGTGCAAATT
1 TGGCACTTCGGTGCAAATT
1411071 TATACGAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
23 1 0.03
24 25 0.68
25 10 0.27
26 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:1411592 original size:21 final size:21
Alignment explanation
Indices: 1411566--1411607 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1411556 TCGATGTTTT
1411566 ATGCATCGATGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
*
1411587 ATGCATCGATGTACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
1411608 CTGTTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (21 bp):
ATGCATCGATGCACTGTAGCA
Found at i:1412831 original size:18 final size:18
Alignment explanation
Indices: 1412790--1412836 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1412780 ATGTGTATTC
*
1412790 CATTCCCCTGATAATTTCA
1 CATTCCCC-GATAATTCCA
* *
1412809 TATTCCCCGGTAATTCCA
1 CATTCCCCGATAATTCCA
1412827 CATTCCCCGA
1 CATTCCCCGA
1412837 ATCAAACACG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.23, C:0.36, G:0.09, T:0.32
Consensus pattern (18 bp):
CATTCCCCGATAATTCCA
Found at i:1420310 original size:99 final size:99
Alignment explanation
Indices: 1420135--1420317 Score: 262
Period size: 99 Copynumber: 1.8 Consensus size: 99
1420125 AGGCAAGAAC
* *
1420135 AACATAATTACTTTGAATATCACTACAAAGTACAAAGTTGAAAAATCAAGAACAAGAAAAACCCA
1 AACATAATTACTTTGAATATCACTACAAAGTACAAAG-TCAAAAAACAAGAACAAGAAAAACCCA
1420200 GATTTGCAATCACTAAAATCAAATAATACAAAATA
65 GATTTGCAATCACTAAAATCAAATAATACAAAATA
* * * *
1420235 AACATAATTATTTTGAGTATCACTGCAAAGTTA-AAA-TCAAGAAAACAGGAACAAGAAAAACCC
1 AACATAATTACTTTGAATATCACTACAAAG-TACAAAGTCAA-AAAACAAGAACAAGAAAAACCC
*
1420298 AGATTTGCAATCACTCAAAT
64 AGATTTGCAATCACTAAAAT
1420318 AAAACAATGT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
98 3 0.04
99 39 0.53
100 30 0.41
101 2 0.03
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.22
Consensus pattern (99 bp):
AACATAATTACTTTGAATATCACTACAAAGTACAAAGTCAAAAAACAAGAACAAGAAAAACCCAG
ATTTGCAATCACTAAAATCAAATAATACAAAATA
Found at i:1423211 original size:21 final size:21
Alignment explanation
Indices: 1423187--1423229 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1423177 AAAATGAATT
**
1423187 ACTGGAATTTGAATTACTGAA
1 ACTGGAAAATGAATTACTGAA
1423208 ACTGGAAAATGAATTACTGAA
1 ACTGGAAAATGAATTACTGAA
1423229 A
1 A
1423230 TTTGAATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (21 bp):
ACTGGAAAATGAATTACTGAA
Found at i:1423508 original size:49 final size:50
Alignment explanation
Indices: 1423398--1423526 Score: 117
Period size: 49 Copynumber: 2.6 Consensus size: 50
1423388 AAAATTTATC
*
1423398 TATTATAAATATT-AAATATAATAAATAATATTATTTATCATAAAACTTAA
1 TATTAT-AATTTTAAAATATAATAAATAATATTATTTATCATAAAACTTAA
* * * *
1423448 TATTATTATTTTAAAATATTA-AAATAAT-TTATTTATTATTAAATA-TTAT
1 TATTATAATTTTAAAATATAATAAATAATATTATTTATCA-TAAA-ACTTAA
* **
1423497 TTTTATAATTTTATTA-ATAA-AAATAATATT
1 TATTATAATTTTAAAATATAATAAATAATATT
1423527 TTTTTTGTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
48 19 0.29
49 32 0.49
50 14 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (50 bp):
TATTATAATTTTAAAATATAATAAATAATATTATTTATCATAAAACTTAA
Found at i:1423648 original size:23 final size:23
Alignment explanation
Indices: 1423600--1423661 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1423590 GTGTTATATT
**
1423600 ATATTTTAAA-ATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
1423622 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
1423645 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
1423662 AAATAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 10 0.31
23 11 0.34
24 1 0.03
25 10 0.31
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:1423689 original size:19 final size:20
Alignment explanation
Indices: 1423637--1423689 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1423627 TTAAATATCT
1423637 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
1423656 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
1423677 TTATTAAATATAT
1 TTATTAAATATAT
1423690 AAAATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:1423702 original size:30 final size:30
Alignment explanation
Indices: 1423645--1423817 Score: 107
Period size: 29 Copynumber: 5.9 Consensus size: 30
1423635 CTTTATTAAA
1423645 ATATTATTTAAATATAT-AAA-TAATATTAT
1 ATATTA-TTAAATATATAAAATTAATATTAT
**
1423674 -TCATTATTAAATATATAAAATTTTTATTAT
1 AT-ATTATTAAATATATAAAATTAATATTAT
1423704 ATATTATTAAA-ATA-AAAATATAATATCT-T
1 ATATTATTAAATATATAAAAT-TAATAT-TAT
** *
1423733 ATATTATTATAATATA-ATTGATT-ATTTTAT
1 ATATTATTA-AATATATA-AAATTAATATTAT
* * * * *
1423763 ATAATATTAAAAATATAATATTATTA-TAA
1 ATATTATTAAATATATAAAATTAATATTAT
* *
1423792 ATATTAATAAATAAAT-AAA-TAATATT
1 ATATTATTAAATATATAAAATTAATATT
1423818 TTGATGAAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 27
0.70 0.13 0.17
Matches are distributed among these distances:
27 4 0.04
28 19 0.17
29 47 0.42
30 33 0.30
31 6 0.05
32 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
ATATTATTAAATATATAAAATTAATATTAT
Found at i:1423771 original size:15 final size:16
Alignment explanation
Indices: 1423733--1423791 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 16
1423723 ATAATATCTT
1423733 ATATTATTATAATATA
1 ATATTATTATAATATA
*
1423749 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
1423766 ATATTA--AAAATATA
1 ATATTATTATAATATA
1423780 ATATTATTATAA
1 ATATTATTATAA
1423792 ATATTAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 11 0.32
15 4 0.12
16 5 0.15
17 8 0.24
18 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:1423809 original size:29 final size:26
Alignment explanation
Indices: 1423716--1423808 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 26
1423706 ATTATTAAAA
*
1423716 TAAAAATATAATATCTTATAT--TAT
1 TAAAAATATAATATTTTATATAATAT
* *
1423740 TATAATATAATTGATTATTTTATATAATAT
1 TA-AAAAT-A-T-AATATTTTATATAATAT
1423770 TAAAAATATAATATTATTATA-AATAT
1 TAAAAATATAATATT-TTATATAATAT
1423796 TAATAAATA-AATA
1 TAA-AAATATAATA
1423809 AATAATATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
24 2 0.04
25 4 0.07
26 18 0.32
27 12 0.21
28 11 0.20
29 4 0.07
30 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (26 bp):
TAAAAATATAATATTTTATATAATAT
Found at i:1435394 original size:26 final size:26
Alignment explanation
Indices: 1435340--1435395 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1435330 ATTTGATATA
* *
1435340 TAAAAGATATATATATATATAATAGT
1 TAAAAGATATATACATATATAAAAGT
1435366 TAAAATGATA-ATACAT-TATAAAAGCT
1 TAAAA-GATATATACATATATAAAAG-T
1435392 TAAA
1 TAAA
1435396 TTTAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 7 0.27
26 15 0.58
27 4 0.15
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (26 bp):
TAAAAGATATATACATATATAAAAGT
Found at i:1438649 original size:17 final size:17
Alignment explanation
Indices: 1438627--1438664 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1438617 GGAGAACTTG
1438627 GTTGAGGATGTTAGCAA
1 GTTGAGGATGTTAGCAA
1438644 GTTGAGGATGTTAGCAA
1 GTTGAGGATGTTAGCAA
1438661 GTTG
1 GTTG
1438665 TAGTTGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (17 bp):
GTTGAGGATGTTAGCAA
Done.