Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008449.1 Hibiscus syriacus cultivar Beakdansim tig00111254_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: 1344907
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:586647 original size:19 final size:19
Alignment explanation
Indices: 586625--586690 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
586615 AAAAATGGCT
586625 ATCGCAACACGAAATGAAA
1 ATCGCAACACGAAATGAAA
*
586644 ATCGC-A-ACG--A-GAGA
1 ATCGCAACACGAAATGAAA
* *
586658 ATCACAACGCGAAATGAAA
1 ATCGCAACACGAAATGAAA
*
586677 ATCGCAACGCGAAA
1 ATCGCAACACGAAA
586691 CCAAAAGACA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
14 7 0.19
15 2 0.05
16 2 0.05
17 3 0.08
18 2 0.05
19 21 0.57
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.09
Consensus pattern (19 bp):
ATCGCAACACGAAATGAAA
Found at i:586696 original size:19 final size:19
Alignment explanation
Indices: 586657--586696 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
586647 GCAACGAGAG
**
586657 AATCACAACGCGAAATGAA
1 AATCACAACGCGAAACCAA
*
586676 AATCGCAACGCGAAACCAA
1 AATCACAACGCGAAACCAA
586695 AA
1 AA
586697 GACAAAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.25, G:0.15, T:0.07
Consensus pattern (19 bp):
AATCACAACGCGAAACCAA
Found at i:586709 original size:12 final size:12
Alignment explanation
Indices: 586692--586717 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
586682 AACGCGAAAC
586692 CAAAAGACAAAA
1 CAAAAGACAAAA
586704 CAAAAGACAAAA
1 CAAAAGACAAAA
586716 CA
1 CA
586718 GTGTTACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.19, G:0.08, T:0.00
Consensus pattern (12 bp):
CAAAAGACAAAA
Found at i:587104 original size:96 final size:93
Alignment explanation
Indices: 586789--587166 Score: 595
Period size: 94 Copynumber: 4.1 Consensus size: 93
586779 ATGGATTGTA
* *
586789 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
586854 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
586882 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
586947 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
586976 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACACA
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAAT--ACACA
*
587041 GTTTAGCAGAATTGGCAGCAACCGAATAAAT
63 GTTTAGCAGAATTGGCAGCAACCGAACAAAT
*
587072 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACATTGTTAATA-AAT----AG
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAA-AGAATACACAG
* * *
587132 TTTAGCAGTATTGGTAGCAACCGAATAAAT
64 TTTAGCAGAATTGGCAGCAACCGAACAAAT
587162 TTACT
1 TTACT
587167 AAGCAATCTA
Statistics
Matches: 273, Mismatches: 7, Indels: 13
0.93 0.02 0.04
Matches are distributed among these distances:
90 35 0.13
93 4 0.01
94 144 0.53
95 19 0.07
96 70 0.26
97 1 0.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:587114 original size:190 final size:184
Alignment explanation
Indices: 586789--587166 Score: 591
Period size: 190 Copynumber: 2.0 Consensus size: 184
586779 ATGGATTGTA
*
586789 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
586853 TTAGCAGAATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
66 TTAGCAGAATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
586918 TAACTTCACAGTGTTAA-AGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 TAACTTCACAGTGTTAATA-AAT----AGTTTAGCAGAATTGGCAGCAACCGAACAAAT
*
586976 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACACA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAAT--ACACA
* *
587041 GTTTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAA
64 GTTTAGCAGAATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAA
* * * *
587105 TACTAACTTCACATTGTTAATAAATAGTTTAGCAGTATTGGTAGCAACCGAATAAAT
128 TACTAACTTCACAGTGTTAATAAATAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
587162 TTACT
1 TTACT
587167 AAGCAATCTA
Statistics
Matches: 178, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
186 34 0.19
187 4 0.02
188 51 0.29
189 19 0.11
190 69 0.39
191 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (184 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
TAACTTCACAGTGTTAATAAATAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:588897 original size:40 final size:38
Alignment explanation
Indices: 588853--588965 Score: 128
Period size: 33 Copynumber: 3.1 Consensus size: 38
588843 TCTTTTGGTT
** *
588853 GAAATGAAAATCGCAATGAGATAATGAAAATCGCAACGC
1 GAAATGACTATCGCAACGAGA-AATGAAAATCGCAACGC
588892 GGAAATGACTATCGCAACGAG--A-G--AATCGCAACGC
1 -GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
* *
588926 GAAATGACTATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
588964 GA
1 GA
588966 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
33 19 0.30
34 11 0.17
35 1 0.02
36 2 0.03
37 1 0.02
38 12 0.19
40 17 0.27
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (38 bp):
GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
Found at i:588898 original size:20 final size:19
Alignment explanation
Indices: 588853--588965 Score: 101
Period size: 19 Copynumber: 6.1 Consensus size: 19
588843 TCTTTTGGTT
* *
588853 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
588872 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
588892 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
588910 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
588926 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
588945 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
588964 GA
1 GA
588966 TTTTGGTTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 32 0.42
20 27 0.36
21 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:589030 original size:20 final size:19
Alignment explanation
Indices: 588961--589031 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
588951 AAAATCGCAA
** *
588961 TGCGATTTTGGTTTCTCGT
1 TGCGATTTTCATTTCGCGT
588980 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
588999 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
589019 TGCGATTTTCATT
1 TGCGATTTTCATT
589032 CTCGAAACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:589599 original size:20 final size:20
Alignment explanation
Indices: 589576--589669 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
589566 CGATAGTCAG
*
589576 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACTT
* * *
589596 ATTCGCATTGTGATTTTCCTA
1 ATTCGCATTGCGA-TTTACTT
589617 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* * *
589637 AATCACGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
589657 ATTCGCATTGCGA
1 ATTCGCATTGCGA
589670 ATTATGAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 44 0.73
21 16 0.27
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:589624 original size:41 final size:40
Alignment explanation
Indices: 589576--589669 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 40
589566 CGATAGTCAG
* * * *
589576 ATTCGCATTGCGATTTACGTATTCGCATTGTGATTTTCCTA
1 ATTCGCATTGCGATTTACGTAATCACATTGCGA-TTTACTA
* * *
589617 ATTCGCATTGCGATTTACTTAATCACGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACTA
589657 ATTCGCATTGCGA
1 ATTCGCATTGCGA
589670 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 18 0.39
41 28 0.61
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.41
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACTA
Found at i:589690 original size:21 final size:21
Alignment explanation
Indices: 589666--589721 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
589656 TATTCGCATT
*
589666 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
589687 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
589707 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
589722 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:589730 original size:21 final size:21
Alignment explanation
Indices: 589659--589731 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
589649 ATTTACTTAT
* *
589659 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
589680 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
589700 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
589721 TTGCATTGCGA
1 TCGCAATGCGA
589732 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:589834 original size:21 final size:22
Alignment explanation
Indices: 589782--589834 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
589772 ATTTACTTAT
589782 TCGCATTGCG-AATTGTGAAAA
1 TCGCATTGCGAAATTGTGAAAA
* **
589803 ACGCAACGCGAAATTG-GAAAA
1 TCGCATTGCGAAATTGTGAAAA
589824 TCGCATTGCGA
1 TCGCATTGCGA
589835 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGTGAAAA
Found at i:590989 original size:11 final size:11
Alignment explanation
Indices: 590968--591005 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
590958 ATATTCTTAA
590968 TTTTA-TTTAT
1 TTTTATTTTAT
590978 TTTTATTTTATT
1 TTTTATTTTA-T
590990 TTTTATTTTAT
1 TTTTATTTTAT
*
591001 ATTTA
1 TTTTA
591006 CATATTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 9 0.36
12 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:590992 original size:12 final size:12
Alignment explanation
Indices: 590968--591000 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
590958 ATATTCTTAA
590968 TTTTA-TTTA-T
1 TTTTATTTTATT
590978 TTTTATTTTATT
1 TTTTATTTTATT
590990 TTTTATTTTAT
1 TTTTATTTTAT
591001 ATTTACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 4 0.19
12 12 0.57
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:591456 original size:54 final size:54
Alignment explanation
Indices: 591374--591518 Score: 263
Period size: 54 Copynumber: 2.7 Consensus size: 54
591364 TTTATTTAAA
*
591374 AAAAATAAATAGGTTGACCGAATACCTTATTTCTTACCTAATCTGTGTCTTACC
1 AAAAATAAATAGGTTGACCGGATACCTTATTTCTTACCTAATCTGTGTCTTACC
*
591428 AAAAATAAATAGGTTGACCGGATACCTTATTTCTTACCTAATTTGTGTCTTACC
1 AAAAATAAATAGGTTGACCGGATACCTTATTTCTTACCTAATCTGTGTCTTACC
*
591482 AACAATAAATAGGTTGACCGGATACCTTATTTCTTAC
1 AAAAATAAATAGGTTGACCGGATACCTTATTTCTTAC
591519 TTGAAAGGGC
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (54 bp):
AAAAATAAATAGGTTGACCGGATACCTTATTTCTTACCTAATCTGTGTCTTACC
Found at i:592408 original size:23 final size:21
Alignment explanation
Indices: 592382--592463 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 21
592372 CCTTTAAGTC
592382 TTTAGTTATTCATTTTTTCCCT-T
1 TTTAGTTATTCATTTTTT---TAT
*
592405 TTTAATT-TATCATTTTTTTAT
1 TTTAGTTAT-TCATTTTTTTAT
592426 TTTAGTTATTCATTTTTTTTAAT
1 TTTAGTTATTCA-TTTTTTT-AT
592449 TTTAGTGTATT-ATTT
1 TTTAGT-TATTCATTT
592464 ATTTGTTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
20 1 0.02
21 10 0.20
22 12 0.24
23 24 0.47
24 4 0.08
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTAGTTATTCATTTTTTTAT
Found at i:592428 original size:21 final size:21
Alignment explanation
Indices: 592414--592463 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
592404 TTTTAATTTA
592414 TCATTTTTTTATTTTAGTTAT
1 TCATTTTTTTATTTTAGTTAT
592435 TCATTTTTTTTAATTTTAGTGTAT
1 TCA-TTTTTTT-ATTTTAGT-TAT
592459 T-ATTT
1 TCATTT
592464 ATTTGTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 3 0.12
22 10 0.38
23 9 0.35
24 4 0.15
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (21 bp):
TCATTTTTTTATTTTAGTTAT
Found at i:592713 original size:6 final size:6
Alignment explanation
Indices: 592702--592728 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
592692 GAATTGAATT
592702 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
592729 TCGCAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:593898 original size:20 final size:20
Alignment explanation
Indices: 593867--593980 Score: 147
Period size: 20 Copynumber: 5.7 Consensus size: 20
593857 GAATATGTAA
* *
593867 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
593887 ATCACAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
593907 ATCGCAAAGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
593927 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * *
593947 GTCGCAACGCAATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
593967 ATCGCAATGCGATT
1 ATCGCAACGCGATT
593981 TTCAAAGCGC
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:594180 original size:22 final size:22
Alignment explanation
Indices: 594155--594197 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
594145 GGCGACATCC
594155 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
594177 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
594198 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:594623 original size:19 final size:19
Alignment explanation
Indices: 594577--594626 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
594567 AACGACAGAA
*
594577 TCGCAATGCGATTTTAGTT
1 TCGCATTGCGATTTTAGTT
* *
594596 TTGCGTTGCGATTTTCA-TT
1 TCGCATTGCGATTTT-AGTT
594615 TCGCATTGCGAT
1 TCGCATTGCGAT
594627 AGTCAAATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTAGTT
Found at i:594688 original size:20 final size:20
Alignment explanation
Indices: 594583--594689 Score: 76
Period size: 20 Copynumber: 5.5 Consensus size: 20
594573 AGAATCGCAA
*
594583 TGCGATTTT-AGTTTT-GCGT
1 TGCGATTTTCA-TTTTCGTGT
**
594602 TGCGATTTTCA-TTTCGCAT
1 TGCGATTTTCATTTTCGTGT
** ** *
594621 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGTGT
* **
594641 TGTGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
594661 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
*
594681 TGCTATTTT
1 TGCGATTTT
594690 AAGTTTCAGA
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
18 3 0.04
19 21 0.29
20 48 0.67
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:594696 original size:20 final size:20
Alignment explanation
Indices: 594653--594696 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
594643 TGATAGTCAT
* *
594653 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
*
594673 TTTCGTGTTGCTATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
594693 TTTC
1 TTTC
594697 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:596298 original size:20 final size:20
Alignment explanation
Indices: 596273--596322 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
596263 AGTTTACTTT
596273 CGCAACGCGAAAATGACTAC
1 CGCAACGCGAAAATGACTAC
*
596293 CGCAACGCGAAAATGACTAT
1 CGCAACGCGAAAATGACTAC
*
596313 TGCAACGCGA
1 CGCAACGCGA
596323 TTTTGACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.28, G:0.22, T:0.12
Consensus pattern (20 bp):
CGCAACGCGAAAATGACTAC
Found at i:596436 original size:20 final size:20
Alignment explanation
Indices: 596382--596437 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
596372 GCGATTCTCT
**
596382 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
596402 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
596422 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
596438 CGTTTTATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:598475 original size:14 final size:14
Alignment explanation
Indices: 598438--598496 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
598428 TTGCATGTTT
*
598438 AATTGATTTATAAA
1 AATTGATTTGTAAA
598452 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
598466 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
598481 TATTGATGTGTAAA
1 AATTGATTTGTAAA
598495 AA
1 AA
598497 ATTCTTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
14 26 0.72
15 10 0.28
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:598651 original size:20 final size:20
Alignment explanation
Indices: 598598--598651 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
598588 AGGTACATTT
* **
598598 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCAAAAGACAAAA
*
598618 TCGCAATGCAAAAGACAAAA
1 TCGCAACGCAAAAGACAAAA
*
598638 TCGCAACGCGAAAG
1 TCGCAACGCAAAAG
598652 CCAATTCGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCAAAAGACAAAA
Found at i:598719 original size:20 final size:20
Alignment explanation
Indices: 598694--598971 Score: 193
Period size: 20 Copynumber: 14.8 Consensus size: 20
598684 GCGATTTTCT
* *
598694 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
598714 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
598734 CATTGCGATACTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
598754 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
598774 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
598788 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
* *
598807 ACGTTGCAATAATCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
*
598828 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
598842 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
* *
598861 ACGTTGCAATAATCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
598882 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
598902 CG-TGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
598915 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
598935 CATTGTGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
598955 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
598972 GAATGTGTAA
Statistics
Matches: 200, Mismatches: 35, Indels: 46
0.71 0.12 0.16
Matches are distributed among these distances:
13 4 0.02
14 30 0.15
16 3 0.01
17 1 0.00
18 2 0.01
19 8 0.04
20 148 0.74
21 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:598782 original size:94 final size:94
Alignment explanation
Indices: 598662--598836 Score: 278
Period size: 94 Copynumber: 1.9 Consensus size: 94
598652 CCAATTCGCG
* * * *
598662 TTGCGATAATCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTGCGATAATC
1 TTGCGATAATCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACACGTTGCAATAATC
598727 AAATTCGCATTGCGATACTCAAATTCACA
66 AAATTCGCATTGCGATACTCAAATTCACA
* * *
598756 TTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAGACGTTGCAATAATC
1 TTGCGATAATCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACACGTTGCAATAATC
*
598821 AAATTCGCGTTGCGAT
66 AAATTCGCATTGCGAT
598837 TTTCTCGTTG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 73 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (94 bp):
TTGCGATAATCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACACGTTGCAATAATC
AAATTCGCATTGCGATACTCAAATTCACA
Found at i:598823 original size:54 final size:54
Alignment explanation
Indices: 598736--598890 Score: 256
Period size: 54 Copynumber: 2.9 Consensus size: 54
598726 CAAATTCGCA
* ** * * *
598736 TTGCGATACTCAAATTCACATTGCGATAGTCAAATTCGCGTTGCGATTTTCTCG
1 TTGCGATAGTCAAATAGACGTTGCAATAATCAAATTCGCGTTGCGATTTTCTCG
598790 TTGCGATAGTCAAATAGACGTTGCAATAATCAAATTCGCGTTGCGATTTTCTCG
1 TTGCGATAGTCAAATAGACGTTGCAATAATCAAATTCGCGTTGCGATTTTCTCG
598844 TTGCGATAGTCAAATAGACGTTGCAATAATCAAATTCGCGTTGCGAT
1 TTGCGATAGTCAAATAGACGTTGCAATAATCAAATTCGCGTTGCGAT
598891 AGTCAAATTC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
TTGCGATAGTCAAATAGACGTTGCAATAATCAAATTCGCGTTGCGATTTTCTCG
Found at i:598950 original size:73 final size:74
Alignment explanation
Indices: 598790--598971 Score: 201
Period size: 73 Copynumber: 2.5 Consensus size: 74
598780 GATTTTCTCG
* * *
598790 TTGCGATAGTCAAA-TAGACGTTGCAATAATCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGT
1 TTGCGATAGTCAAATTAG-CGTTGCGATAATCAAATTCGCGTTGCGATTTTCTAGTTGCGATAAT
*
598854 CAAATAGACG
65 CAAATAGACA
* * * *
598864 TTGCAATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG-TGCGATTTT-TGAGTTGCGATAAT
1 TTGCGATAGTCAAATTAGCGTTGCGATAATCAAATTCGCGTTGCGATTTTCT-AGTTGCGATAAT
*
598927 CAAATTCG-CA
65 CAAA-TAGACA
* * *
598937 TTGTGATAGTCAAATTTGCGTTGCGATATTCAAAT
1 TTGCGATAGTCAAATTAGCGTTGCGATAATCAAAT
598972 GAATGTGTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
72 1 0.01
73 54 0.59
74 34 0.37
75 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (74 bp):
TTGCGATAGTCAAATTAGCGTTGCGATAATCAAATTCGCGTTGCGATTTTCTAGTTGCGATAATC
AAATAGACA
Found at i:599194 original size:140 final size:140
Alignment explanation
Indices: 598942--599211 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
598932 TCGCATTGTG
* *
598942 ATAGTCAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
* *
599007 TAGCAATGTTCAAACTGAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
599072 AATACACATA
131 AATACACATA
599082 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
599147 TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
599212 TACAACGTTT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:599294 original size:18 final size:18
Alignment explanation
Indices: 599271--599305 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
599261 AAGCCGGTTG
*
599271 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
599289 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
599306 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:601361 original size:14 final size:14
Alignment explanation
Indices: 601342--601378 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
601332 TCCCGTGGCA
601342 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
601356 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
601370 TTCTTCTTC
1 TT-TTCTTC
601379 TTATTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:601378 original size:3 final size:3
Alignment explanation
Indices: 601370--601408 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
601360 CTTCGGGGAT
* * *
601370 TTC TTC TTC TTA TTT TTC TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
601409 AGGGTTATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:601387 original size:15 final size:15
Alignment explanation
Indices: 601369--601408 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
601359 TCTTCGGGGA
601369 TTTCTTCTTCTTATT
1 TTTCTTCTTCTTATT
*
601384 TTTCTTCTTCTTCTT
1 TTTCTTCTTCTTATT
601399 TTTCTTCTTC
1 TTTCTTCTTC
601409 AGGGTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCTTCTTCTTATT
Found at i:601617 original size:24 final size:24
Alignment explanation
Indices: 601583--601636 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
601573 CTGAAACATC
*
601583 ATCAAAATCCGATTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
601607 ATCAAAGTCCGGGTATTGACCAGG
1 ATCAAAATCCGAGTATTGACCAAG
601631 ATCAAA
1 ATCAAA
601637 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:602482 original size:20 final size:20
Alignment explanation
Indices: 602458--602548 Score: 121
Period size: 20 Copynumber: 4.5 Consensus size: 20
602448 AAATTCAGTG
* * *
602458 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
602478 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
602498 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
602518 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
602538 TTGCGATAGTC
1 TTGCGATAGTC
602549 GGAAAATCGC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
19 1 0.02
20 61 0.97
21 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:604840 original size:10 final size:10
Alignment explanation
Indices: 604827--604864 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
604817 TGAATATTCT
604827 TTTGTTCTTA
1 TTTGTTCTTA
604837 TTTGTTCTTA
1 TTTGTTCTTA
*
604847 -GTGTTCTTA
1 TTTGTTCTTA
604856 TTTGTTCTT
1 TTTGTTCTT
604865 GAATTGTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.08, C:0.11, G:0.13, T:0.68
Consensus pattern (10 bp):
TTTGTTCTTA
Found at i:606690 original size:21 final size:19
Alignment explanation
Indices: 606666--606713 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
606656 AAATGTATTA
606666 TTTTCTCTATTATTTTTCCTT
1 TTTTCTCTATT-TTTTT-CTT
*
606687 TTTTCCTTCTGTTTTTTTCTT
1 TTTT-C-TCTATTTTTTTCTT
606708 TTTTCT
1 TTTTCT
606714 AGATTGTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 11 0.46
22 6 0.25
23 5 0.21
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTCTCTATTTTTTTCTT
Found at i:609178 original size:37 final size:36
Alignment explanation
Indices: 609137--609329 Score: 133
Period size: 37 Copynumber: 5.6 Consensus size: 36
609127 ATTATATTAG
609137 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATATATAAGTGACCAAATAGGTAG-TTACCCTAA
** * *** *
609174 ATAATAGT-CGAGTGACCAAA-A--CA--TAAATTAG
1 ATAATA-TATAAGTGACCAAATAGGTAGTTACCCTAA
609205 ATAATATATAAGTGACCAAATAGGTAGTCTACCCTAA
1 ATAATATATAAGTGACCAAATAGGTAGT-TACCCTAA
* *** *
609242 ATAATA-ATAGAGTGACCAAA-A--CA--TAAATTAG
1 ATAATATATA-AGTGACCAAATAGGTAGTTACCCTAA
609273 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATATATAAGTGACCAAATAGGTAG-TTACCCTAA
609310 ATAATA-ATCAAGTGACCAAA
1 ATAATATAT-AAGTGACCAAA
609330 ACACAAATTA
Statistics
Matches: 115, Mismatches: 24, Indels: 34
0.66 0.14 0.20
Matches are distributed among these distances:
30 1 0.01
31 40 0.35
32 5 0.04
34 4 0.03
36 7 0.06
37 57 0.50
38 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (36 bp):
ATAATATATAAGTGACCAAATAGGTAGTTACCCTAA
Found at i:609219 original size:31 final size:31
Alignment explanation
Indices: 609184--609360 Score: 122
Period size: 31 Copynumber: 5.3 Consensus size: 31
609174 ATAATAGTCG
609184 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
** * **
609215 AGTGACCAAATAGGT-AGTCTACCCTAAATAATAATA
1 AGTGACCAAA-ACATAAAT-TA-GAT-AAT-AT-ATA
609251 GAGTGACCAAAACATAAATTAGATAATATATA
1 -AGTGACCAAAACATAAATTAGATAATATATA
** ** **
609283 AGTGACCAAATAGGTAGTTTACCCTAAATAATAATCA
1 AGTGACCAAA-ACATAAATTA-GAT-AAT-AT-AT-A
*
609320 AGTGACCAAAACACAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
609351 AGTGACCAAA
1 AGTGACCAAA
609361 TAAGTAGTTT
Statistics
Matches: 109, Mismatches: 23, Indels: 28
0.68 0.14 0.17
Matches are distributed among these distances:
31 33 0.30
32 15 0.14
33 6 0.06
34 12 0.11
35 6 0.06
36 14 0.13
37 23 0.21
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (31 bp):
AGTGACCAAAACATAAATTAGATAATATATA
Found at i:609221 original size:68 final size:68
Alignment explanation
Indices: 609041--609378 Score: 490
Period size: 68 Copynumber: 5.0 Consensus size: 68
609031 TTTTGAAAAA
* * *
609041 AAATAATAATCTAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATATGTAGTTTGC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
609106 CCT
66 CCT
* * * * * *
609109 GAATAAAAAT--A-T-A-TATGAA-TTATATTAGATAATATATAAGTGACCAAATAGGTAGTTTA
1 AAATAATAATCGAGTGACCA-AAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTA
609168 CCCT
65 CCCT
* *
609172 AAATAATAGTCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTCTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
609237 CCT
66 CCT
*
609240 AAATAATAATAGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
609305 CCT
66 CCT
* * *
609308 AAATAATAATCAAGTGACCAAAACACAAATTAGATAATATATAAGTGACCAAATAAGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
609373 CCT
66 CCT
609376 AAA
1 AAA
609379 AAAATCCCTA
Statistics
Matches: 240, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
63 48 0.20
64 3 0.01
65 2 0.01
66 2 0.01
67 3 0.01
68 182 0.76
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (68 bp):
AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
CCT
Found at i:611056 original size:29 final size:29
Alignment explanation
Indices: 611024--611093 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
611014 GTAATTGATG
*
611024 TTTAGTCCTTTAGTTTTTGTTAATACCAT
1 TTTAGCCCTTTAGTTTTTGTTAATACCAT
* * ** *
611053 TTTAACCCTTAAGTTTTTGTTTTTACTAT
1 TTTAGCCCTTTAGTTTTTGTTAATACCAT
611082 TTTAGCCCTTTA
1 TTTAGCCCTTTA
611094 AATTTCTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.56
Consensus pattern (29 bp):
TTTAGCCCTTTAGTTTTTGTTAATACCAT
Found at i:613354 original size:2 final size:2
Alignment explanation
Indices: 613347--613380 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
613337 TGTACTATTA
613347 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
613381 CTTTCCATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:615541 original size:12 final size:12
Alignment explanation
Indices: 615524--615548 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
615514 CTTTCCTTTC
615524 TTGCAATGTCAA
1 TTGCAATGTCAA
615536 TTGCAATGTCAA
1 TTGCAATGTCAA
615548 T
1 T
615549 GTGATCTCTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TTGCAATGTCAA
Found at i:616996 original size:54 final size:54
Alignment explanation
Indices: 616909--617332 Score: 618
Period size: 54 Copynumber: 7.9 Consensus size: 54
616899 ATACCGAATG
* *
616909 GGCAGTATGTGTGCAACCTAACAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
616963 GGCACTATGTGTGTAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
617017 GGCACTATGTATGCAACCTAAGAAATTCATAATAAG-TTATAAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
617070 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
617124 GGCACTGTGTGTGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
617178 GGCACTATGTATGCAACCTAAGAAATTCATAATAAG-TTATGAATTTCCATATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * * *
617231 GGCACTATGTGTTCAACCTCACGAAATTCTTAATGATTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCT-AAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * *
617286 GGCACTATGTGTGCAACTCCACGTAATTCATAATGAGTTTATGAATT
1 GGCACTATGTGTGCAAC-CTAAGAAATTCATAATAAGTTTATGAATT
617333 ATTGTATCGT
Statistics
Matches: 332, Mismatches: 34, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
53 82 0.25
54 193 0.58
55 56 0.17
56 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
Found at i:617051 original size:108 final size:108
Alignment explanation
Indices: 616909--617332 Score: 627
Period size: 107 Copynumber: 3.9 Consensus size: 108
616899 ATACCGAATG
* *
616909 GGCAGTATGTGTGCAACCTAACAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
*
616974 TGTAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATT
66 TGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATT
* * *
617017 GGCACTATGTATGCAACCTAAGAAATTCATAATAAG-TTATAAATTTTCGTATTGGCACTATGTG
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
**
617081 TGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
66 TGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATT
* * * *
617124 GGCACTGTGTGTGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTA
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
617189 TGCAACCTAAGAAATTCATAATAAG-TTATGAATTTCCATATT
66 TGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATT
* * * * *
617231 GGCACTATGTGTTCAACCTCACGAAATTCTTAATGATTTTATGAATTTCCGTATTGGCACTATGT
1 GGCACTATGTGTGCAACCT-AAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGT
* * * *
617296 GTGCAACTCCACGTAATTCATAATGAGTTTATGAATT
65 GTGCAAC-CTAAGAAATTCATAATAAGTTTATGAATT
617333 ATTGTATCGT
Statistics
Matches: 282, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
107 129 0.46
108 129 0.46
109 15 0.05
110 9 0.03
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (108 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
TGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATT
Found at i:617180 original size:161 final size:160
Alignment explanation
Indices: 616909--617332 Score: 641
Period size: 161 Copynumber: 2.6 Consensus size: 160
616899 ATACCGAATG
* *
616909 GGCAGTATGTGTGCAACCTAACAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
* *
616974 TGTAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTATGCAACCTAAG
66 TGCAACTTAAG-AATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTATGCAACCTAAG
* *
617039 AAATTCATAATAAGTTATAAATTTTCGTATT
130 AAATTCATAATAAGTTATAAATTTCCATATT
* *
617070 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTGTGTG
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
*
617135 TGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTATGCAACCTAAG
66 TGCAACTTAAGAA-TTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTATGCAACCTAAG
*
617200 AAATTCATAATAAGTTATGAATTTCCATATT
130 AAATTCATAATAAGTTATAAATTTCCATATT
* * * * *
617231 GGCACTATGTGTTCAACCTCACGAAATTCTTAATGATTTTATGAATTTCCGTATTGGCACTATGT
1 GGCACTATGTGTGCAACCT-AAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGT
* * *
617296 GTGCAACTCCACGTAATTCATAATGAGTTTATGAATT
65 GTGCAACT-TAAG-AATTCATAATAAGTTTATGAATT
617333 ATTGTATCGT
Statistics
Matches: 239, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
160 2 0.01
161 166 0.69
162 47 0.20
163 22 0.09
164 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (160 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
TGCAACTTAAGAATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTATGCAACCTAAGA
AATTCATAATAAGTTATAAATTTCCATATT
Found at i:623514 original size:54 final size:54
Alignment explanation
Indices: 623432--623748 Score: 508
Period size: 54 Copynumber: 5.9 Consensus size: 54
623422 TTACCGAATA
*
623432 GGCACTATATGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
623486 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCTTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
623540 GACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * *
623594 GGCACTATGTGTGCAACTTAAGAAGTTCATAATAATTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
623648 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * * *
623702 GGCACTATGTGTGCAACCCCACGTAATTCATAATGAGTTTGTGAATT
1 GGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATT
623749 ATTGTATCAG
Statistics
Matches: 242, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
54 217 0.90
55 25 0.10
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
Found at i:624464 original size:20 final size:20
Alignment explanation
Indices: 624439--624489 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
624429 CGCGATTTTC
624439 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
* * *
624459 CAAATTCACAATATAGAAGT
1 CAAATTCGCAACACAGAAGT
624479 CAAATTCGCAA
1 CAAATTCGCAA
624490 AGCAAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:624533 original size:19 final size:20
Alignment explanation
Indices: 624483--624525 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
624473 AGAAGTCAAA
* *
624483 TTCGCAAAGC-AAATTTATT
1 TTCGCAATGCGAATTTTATT
624502 TTCGCAATGCGAATTTTATT
1 TTCGCAATGCGAATTTTATT
624522 TTCG
1 TTCG
624526 AATTCGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (20 bp):
TTCGCAATGCGAATTTTATT
Found at i:624662 original size:22 final size:22
Alignment explanation
Indices: 624637--624687 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
624627 TCACTCTCTA
*
624637 CGACGACATCCGTCCCCATCTC
1 CGACGACATCCGTCCCCATATC
**
624659 CGACGACATGTGTCCCCATATC
1 CGACGACATCCGTCCCCATATC
624681 CGACGAC
1 CGACGAC
624688 CCCCTCTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.43, G:0.18, T:0.18
Consensus pattern (22 bp):
CGACGACATCCGTCCCCATATC
Found at i:625127 original size:19 final size:20
Alignment explanation
Indices: 625072--625116 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
625062 GCGATTTTAG
*
625072 TTTCGCGATGCGAATTTCAT
1 TTTCGCGTTGCGAATTTCAT
625092 TTTCGCGTTGCGAATTTCAT
1 TTTCGCGTTGCGAATTTCAT
625112 TTTCG
1 TTTCG
625117 TTTTCGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTCAT
Found at i:626815 original size:21 final size:21
Alignment explanation
Indices: 626791--626831 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
626781 AGGGGAGTTA
*
626791 CGTGATGAGGTCGGTGCTTTG
1 CGTGATGAGGTCGGTACTTTG
626812 CGTGATGAGGTCGGTACTTT
1 CGTGATGAGGTCGGTACTTT
626832 ACATGACGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.39, T:0.34
Consensus pattern (21 bp):
CGTGATGAGGTCGGTACTTTG
Found at i:626895 original size:21 final size:21
Alignment explanation
Indices: 626871--626951 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
626861 AGGTATGGTC
*
626871 TTTACGTGGTGAGGTAGCTAT
1 TTTACGTGATGAGGTAGCTAT
* *
626892 TTTACGCGATGA--TA-ATGAT
1 TTTACGTGATGAGGTAGCT-AT
* * *
626911 GCTTTACGTGGTGAGGTATCTAC
1 --TTTACGTGATGAGGTAGCTAT
626934 TTTACGTGATGAGGTAGC
1 TTTACGTGATGAGGTAGC
626952 CGCTCTACGT
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
18 1 0.02
19 4 0.09
21 36 0.80
23 3 0.07
24 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (21 bp):
TTTACGTGATGAGGTAGCTAT
Found at i:626903 original size:42 final size:43
Alignment explanation
Indices: 626857--626949 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
626847 TGCATGGTGT
* *
626857 GATGAGGTATGGT-CTTTACGTGGTGAGGTAGCTATTTTACGC
1 GATGAGGTATGATGCTTTACGTGGTGAGGTAGCTACTTTACGC
* *
626899 GATGA--TAATGATGCTTTACGTGGTGAGGTATCTACTTTACGT
1 GATGAGGT-ATGATGCTTTACGTGGTGAGGTAGCTACTTTACGC
626941 GATGAGGTA
1 GATGAGGTA
626950 GCCGCTCTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
40 1 0.02
41 4 0.09
42 36 0.84
43 1 0.02
44 1 0.02
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.35
Consensus pattern (43 bp):
GATGAGGTATGATGCTTTACGTGGTGAGGTAGCTACTTTACGC
Found at i:627069 original size:4 final size:4
Alignment explanation
Indices: 627060--627096 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
627050 TTTTTCGGCA
627060 TTAT TTAT TTAT TTAT TTAT TTA- TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
627097 TTAGCGGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:627268 original size:21 final size:21
Alignment explanation
Indices: 627240--627323 Score: 134
Period size: 21 Copynumber: 4.0 Consensus size: 21
627230 GATTCACCTG
627240 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
627261 -CTATCGTTCAAGAGTCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
627282 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
627303 TCATTGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
627324 CCACCATTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.19, C:0.37, G:0.18, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:627333 original size:21 final size:21
Alignment explanation
Indices: 627241--627335 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
627231 ATTCACCTGT
627241 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * *
627262 TATCGTTCAAGAGTCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
*
627283 CATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
*
627304 CATTGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
627325 CACCATTCAAG
1 CATCGTTCAAG
627336 TGCCCGATTC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:628764 original size:16 final size:14
Alignment explanation
Indices: 628735--628768 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
628725 TGTAAATAAG
628735 AATTGTTTTTGTTT
1 AATTGTTTTTGTTT
628749 AATTGATTTGTTGTTT
1 AATTG-TTT-TTGTTT
628765 AATT
1 AATT
628769 TCAATCTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 3 0.17
16 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (14 bp):
AATTGTTTTTGTTT
Found at i:629076 original size:18 final size:18
Alignment explanation
Indices: 629053--629088 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
629043 AAGCCGGTTG
629053 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
629071 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
629089 CCTTTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:631284 original size:24 final size:24
Alignment explanation
Indices: 631250--631303 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
631240 CTGAAACATC
*
631250 ATCAAAATCCGAGTATTGACGAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
631274 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
631298 ATCAAA
1 ATCAAA
631304 CTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:631449 original size:12 final size:12
Alignment explanation
Indices: 631428--631461 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
631418 GGTTGTGGGT
*
631428 TTTGAGATTGTG
1 TTTGATATTGTG
631440 TTTGATATTGTG
1 TTTGATATTGTG
*
631452 TTTGGTATTG
1 TTTGATATTG
631462 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:632231 original size:17 final size:17
Alignment explanation
Indices: 632209--632243 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
632199 AAAACATTTG
632209 TGTTGCGAAATAAAAAT
1 TGTTGCGAAATAAAAAT
*
632226 TGTTGCGAAATTAAAAT
1 TGTTGCGAAATAAAAAT
632243 T
1 T
632244 CGTGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (17 bp):
TGTTGCGAAATAAAAAT
Found at i:632251 original size:20 final size:20
Alignment explanation
Indices: 632208--632395 Score: 106
Period size: 20 Copynumber: 9.5 Consensus size: 20
632198 CAAAACATTT
*
632208 GTGTTGCGAAA-TAAAAAT-
1 GTGTTGCGAAATTAAAATTC
632226 -TGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
632245 GTGTTGCG-AATTCGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
* **
632265 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAATTC
* *
632285 GTGTTGCG-ATTTAGAAAATC
1 GTGTTGCGAAATTA-AAATTC
* ** *
632305 TTGTTGCGAAAAGGAAACTT-
1 GTGTTGCG-AAATTAAAATTC
*
632325 GTGTTGCGAAA-AAGAAATTC
1 GTGTTGCGAAATTA-AAATTC
* *
632345 GCGTTGCG-AATTCAAAAATC
1 GTGTTGCGAAATT-AAAATTC
* * *
632365 ATGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATTAAAATTC
632385 AGTGTTGCGAA
1 -GTGTTGCGAA
632396 TTTGGAAAAT
Statistics
Matches: 127, Mismatches: 27, Indels: 29
0.69 0.15 0.16
Matches are distributed among these distances:
17 10 0.08
18 7 0.06
19 19 0.15
20 67 0.53
21 22 0.17
22 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:632282 original size:40 final size:40
Alignment explanation
Indices: 632208--632395 Score: 159
Period size: 40 Copynumber: 4.8 Consensus size: 40
632198 CAAAACATTT
* **
632208 GTGTTGCGAAATA-AAAAT--TGTTGCGAAATTAAAATTC
1 GTGTTGCGAATTAGAAAATCGTGTTGCGAAAACAAAATTC
* *
632245 GTGTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATTC
1 GTGTTGCGAATTAGAAAATCGTGTTGCGAAAACAAAATTC
* * * *
632285 GTGTTGCGATTTAGAAAATCTTGTTGCGAAAAGGAAACTT-
1 GTGTTGCGAATTAGAAAATCGTGTTGCGAAAA-CAAAATTC
** * * ** *
632325 GTGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAAAAATC
1 GTGTTGCGAATTAGAAAATCGTGTTGCGAAAACAAAATTC
* * *
632365 ATGTTGCGAATTTGAAATTCAGTGTTGCGAA
1 GTGTTGCGAATTAGAAAATC-GTGTTGCGAA
632396 TTTGGAAAAT
Statistics
Matches: 118, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
37 11 0.09
38 5 0.04
39 4 0.03
40 84 0.71
41 14 0.12
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (40 bp):
GTGTTGCGAATTAGAAAATCGTGTTGCGAAAACAAAATTC
Found at i:632312 original size:60 final size:60
Alignment explanation
Indices: 632208--632395 Score: 165
Period size: 60 Copynumber: 3.2 Consensus size: 60
632198 CAAAACATTT
* *
632208 GTGTTGCGAAATAA-AAATT---GTTGCGAAATT-AAAATTCGTGTTGCGAATTCGAAAATC
1 GTGTTGCGAAA-AAGAAATTCGCGTTGCG-AATTCAAAAATCATGTTGCGAATTCGAAAATC
* * * * *** * *
632265 GAGTTGCGAAAACA-AAATTCGTGTTGCG-ATTTAGAAAATCTTGTTGCGAAAAGGAAACTT
1 GTGTTGCGAAAA-AGAAATTCGCGTTGCGAATTCA-AAAATCATGTTGCGAATTCGAAAATC
* *
632325 GTGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAAAAATCATGTTGCGAATTTGAAATTC
1 GTGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAAAAATCATGTTGCGAATTCGAAAATC
632385 AGTGTTGCGAA
1 -GTGTTGCGAA
632396 TTTGGAAAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
56 1 0.01
57 16 0.15
58 3 0.03
59 2 0.02
60 69 0.66
61 14 0.13
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (60 bp):
GTGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAAAAATCATGTTGCGAATTCGAAAATC
Found at i:632412 original size:21 final size:21
Alignment explanation
Indices: 632338--632480 Score: 91
Period size: 20 Copynumber: 7.0 Consensus size: 21
632328 TTGCGAAAAA
*
632338 GAAATTCGCGTTGCGAA-TTC
1 GAAATTCGCGTTGCGAATTTG
* * **
632358 AAAAATCATGTTGCGAATTT-
1 GAAATTCGCGTTGCGAATTTG
*
632378 GAAATTCAGTGTTGCGAATTTG
1 GAAATTC-GCGTTGCGAATTTG
* *
632400 GAAAATCGCGTTGCG-ATTGTA
1 GAAATTCGCGTTGCGAATT-TG
* *
632421 GAAACT-GAGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
* * *
632441 GAAACT-GTGTTGCGAAATTG
1 GAAATTCGCGTTGCGAATTTG
* *
632461 G-AGTTTGCGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
632481 TTGGTCATTT
Statistics
Matches: 98, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.02
20 60 0.61
21 30 0.31
22 6 0.06
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (21 bp):
GAAATTCGCGTTGCGAATTTG
Found at i:638580 original size:21 final size:21
Alignment explanation
Indices: 638556--638611 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
638546 AAAAATGGTA
638556 AGTATCGATACTCTTATGGGG
1 AGTATCGATACTCTTATGGGG
638577 AGTATCGATACTCTTATGGGG
1 AGTATCGATACTCTTATGGGG
638598 AGTATCGATACTCT
1 AGTATCGATACTCT
638612 ACCCTTGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (21 bp):
AGTATCGATACTCTTATGGGG
Found at i:640252 original size:22 final size:23
Alignment explanation
Indices: 640215--640257 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
640205 GCGGCGGCAG
640215 CCACCGCAGGAATCCT-TTTCCT
1 CCACCGCAGGAATCCTCTTTCCT
**
640237 CCACCGCAGGGGTCCTCTTTC
1 CCACCGCAGGAATCCTCTTTC
640258 TCTGTCCCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.14, C:0.42, G:0.19, T:0.26
Consensus pattern (23 bp):
CCACCGCAGGAATCCTCTTTCCT
Found at i:645041 original size:29 final size:29
Alignment explanation
Indices: 644995--645050 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
644985 AAACTATTAG
*
644995 TTTTCTCTCATTGGTACGTCGTTTATTCA
1 TTTTCTCTCATTGATACGTCGTTTATTCA
* *
645024 TTTTCTGTCGTTGATACGTCGTTTATT
1 TTTTCTCTCATTGATACGTCGTTTATT
645051 GACCGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.12, C:0.18, G:0.16, T:0.54
Consensus pattern (29 bp):
TTTTCTCTCATTGATACGTCGTTTATTCA
Found at i:650673 original size:45 final size:46
Alignment explanation
Indices: 650607--650714 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 46
650597 AGTGCACGAA
650607 GAGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGC-CT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A-CTCT
* *
650652 GAGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAACTCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTCT
*
650698 GAGTGCATAGATGCATA
1 GAGTGCATCGATGCATA
650715 GTATGTGCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 30 0.54
46 23 0.41
47 3 0.05
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTCT
Found at i:650958 original size:21 final size:21
Alignment explanation
Indices: 650910--650958 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
650900 AAATTGATCT
* *
650910 TTGAAGATTTGGAGTAATAAT
1 TTGAATATTTGGAGTAATAAA
650931 TTG-ATATTT-GAGTAATTAAA
1 TTGAATATTTGGAGTAA-TAAA
650951 TTGAATAT
1 TTGAATAT
650959 ACTTAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (21 bp):
TTGAATATTTGGAGTAATAAA
Found at i:655888 original size:18 final size:18
Alignment explanation
Indices: 655867--655905 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
655857 ACTAGGCATA
655867 AATTAGTCATATCAATAG
1 AATTAGTCATATCAATAG
655885 AATTAGTCATATCAATAG
1 AATTAGTCATATCAATAG
655903 AAT
1 AAT
655906 CTAAATGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (18 bp):
AATTAGTCATATCAATAG
Found at i:656768 original size:20 final size:20
Alignment explanation
Indices: 656726--656768 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
656716 TTATTTTCAT
* *
656726 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
656746 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
656766 TTT
1 TTT
656769 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:658692 original size:64 final size:63
Alignment explanation
Indices: 658624--658831 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 63
658614 TGCACGAAGA
* *
658624 GTGCATCGATGCATAAAATGCATTTGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-CCTGAGTGCATCGATGCATGAATG
* *
658688 GTGCATCGATGCATCAAATGCATTCGATTTTTTCATAAA-ACTCTGAGTGCATCGATGCAT-AAT
1 GTGCATCGATGCATAAAATGCATTCGA-TGTTTCA-AAATAC-CTGAGTGCATCGATGCATGAAT
*
658751 AT
63 -G
* * * * * *
658753 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGTATTGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA--AATACC-TGAGTGCATCGATGCAT-GAA
658816 TG
62 TG
658818 GTGCATCGATGCAT
1 GTGCATCGATGCAT
658832 GGATTGGTGC
Statistics
Matches: 121, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 43 0.36
65 68 0.56
66 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCTGAGTGCATCGATGCATGAATG
Found at i:658828 original size:20 final size:20
Alignment explanation
Indices: 658805--658844 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
658795 ATGGTGTATT
658805 GATGCATGGATTGGTGCATC
1 GATGCATGGATTGGTGCATC
658825 GATGCATGGATTGGTGCATC
1 GATGCATGGATTGGTGCATC
658845 ACTTTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.35, T:0.30
Consensus pattern (20 bp):
GATGCATGGATTGGTGCATC
Found at i:665057 original size:21 final size:22
Alignment explanation
Indices: 665023--665067 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
665013 CAAATTATCA
*
665023 AAATCTGGTAAATC-ATAGTAG
1 AAATCTGATAAATCTATAGTAG
* *
665044 AAATCTGATTAATCTATATTAG
1 AAATCTGATAAATCTATAGTAG
665066 AA
1 AA
665068 GAACAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (22 bp):
AAATCTGATAAATCTATAGTAG
Found at i:665620 original size:119 final size:119
Alignment explanation
Indices: 665421--665658 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
665411 ATATTTGACA
665421 GGAAGAAGAAGATAAGAATAAAATAAAAGTAGCATATAAACCACAGAACTAAAGGTGATTTTGGG
1 GGAAGAAGAAGATAAGAATAAAATAAAAGTAGCATATAAACCACAGAACTAAAGGTGATTTTGGG
665486 AAAAGGACGAAAACGAAATTAATGGTAGAAATAAGGTTTTTCAAATAAATTAGG
66 AAAAGGACGAAAACGAAATTAATGGTAGAAATAAGGTTTTTCAAATAAATTAGG
665540 GGAAGAAGAAGATAAGAATAAAATAAAAGTAGCATATAAACCACAGAACTAAAGGTGATTTTGGG
1 GGAAGAAGAAGATAAGAATAAAATAAAAGTAGCATATAAACCACAGAACTAAAGGTGATTTTGGG
665605 AAAAGGACGAAAACGAAATTAATGGTAGAAATAAGGTTTTTCAAATAAATTAGG
66 AAAAGGACGAAAACGAAATTAATGGTAGAAATAAGGTTTTTCAAATAAATTAGG
665659 AAAATAAAGT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.50, C:0.07, G:0.22, T:0.21
Consensus pattern (119 bp):
GGAAGAAGAAGATAAGAATAAAATAAAAGTAGCATATAAACCACAGAACTAAAGGTGATTTTGGG
AAAAGGACGAAAACGAAATTAATGGTAGAAATAAGGTTTTTCAAATAAATTAGG
Found at i:669941 original size:19 final size:19
Alignment explanation
Indices: 669917--669973 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
669907 GCGATTTTGA
669917 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
669936 AAAATGTGTTGCGATAATT
1 AAAATGTGTTGCGATAGTT
*
669955 AAAATGTGTTGCGAGAGTT
1 AAAATGTGTTGCGATAGTT
669974 TGAAAAACGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:670458 original size:40 final size:40
Alignment explanation
Indices: 670403--670619 Score: 246
Period size: 40 Copynumber: 5.5 Consensus size: 40
670393 ACCAGTTGTT
*
670403 GCGAACTTCGACTATCGTAACGAATTTGGAAAATCGCAAC
1 GCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAAC
670443 GCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAAC
1 GCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAAC
* * * *
670483 GTGAACTTGGACTATCACAATGAATTTGGAAAATCGCAAC
1 GCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAAC
* **
670523 GCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAA-
1 GCGAACTTCGACTATCGCAAC--GAATTTGGAAAATCGCAAC
* * * * * *
670564 -CGAATTTGGACAAACG-TA--AATTTGGAAAATAGCAAC
1 GCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAAC
*
670600 GCGAACTTGGACTATCGCAA
1 GCGAACTTCGACTATCGCAA
670620 AATCGCGTTA
Statistics
Matches: 147, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
35 13 0.09
37 13 0.09
38 1 0.01
39 1 0.01
40 104 0.71
42 15 0.10
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
GCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAAC
Found at i:670459 original size:21 final size:21
Alignment explanation
Indices: 670403--670565 Score: 131
Period size: 21 Copynumber: 8.0 Consensus size: 21
670393 ACCAGTTGTT
* *
670403 GCGAACTTCGACTATCGTAA-
1 GCGAACTTGGACTATCGCAAC
* **
670423 -CGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAAC
*
670443 GCGAACTTCGACTATCGCAA-
1 GCGAACTTGGACTATCGCAAC
* **
670463 -CGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAAC
* *
670483 GTGAACTTGGACTATCACAA-
1 GCGAACTTGGACTATCGCAAC
* * **
670503 -TGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAAC
*
670523 GCGAACTTCGACTATCGCAAC
1 GCGAACTTGGACTATCGCAAC
*
670544 GTGAACTTGGACTATCGCAAC
1 GCGAACTTGGACTATCGCAAC
670565 G
1 G
670566 AATTTGGACA
Statistics
Matches: 108, Mismatches: 29, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
19 44 0.41
21 64 0.59
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAC
Found at i:671970 original size:20 final size:19
Alignment explanation
Indices: 671940--671977 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
671930 TTCTGGGTTA
671940 TAGTATGATATTATTCTTG
1 TAGTATGATATTATTCTTG
*
671959 TAGTATTGATATTGTTCTT
1 TAGTA-TGATATTATTCTT
671978 ACAATATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (19 bp):
TAGTATGATATTATTCTTG
Found at i:672005 original size:15 final size:15
Alignment explanation
Indices: 671982--672021 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
671972 GTTCTTACAA
*
671982 TATCTATACTATGAT
1 TATCGATACTATGAT
*
671997 TATCGATACAATGAT
1 TATCGATACTATGAT
*
672012 TACCGATACT
1 TATCGATACT
672022 GTGAGTACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (15 bp):
TATCGATACTATGAT
Found at i:686905 original size:44 final size:43
Alignment explanation
Indices: 686849--686950 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 43
686839 ATGCATAGCA
* *
686849 TAGTGCATCGATGCACATTCAAGGAATGCATCGGTGCA-TCTT
1 TAGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTCTT
* *
686891 TATGGTGTATCGATGCACATTCAAGGGATGCATTGGTACACTCTT
1 TA--GTGTATCGATGCACATTCAAGGAATGCATCGGTACACTCTT
686936 TAGTGTATCGATGCA
1 TAGTGTATCGATGCA
686951 TGATATACAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
42 2 0.04
43 13 0.25
44 32 0.60
45 6 0.11
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (43 bp):
TAGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTCTT
Found at i:692807 original size:65 final size:65
Alignment explanation
Indices: 692694--692848 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 65
692684 TACACTCAGG
* *
692694 GTGCATCGGTACACT-AATTACATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGG-T
1 GTGCATCGGTACA-TAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCT
692757 CT
65 -T
* * * **
692759 GTGCATCGGTACATAAAATGCATTCGATGTTTTAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACATAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
* * *
692824 GTGCATCGATACACAAAACACATTC
1 GTGCATCGGTACATAAAATACATTC
692849 TAAATGGGTG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 1 0.01
65 75 0.97
66 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACATAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
Found at i:695515 original size:44 final size:43
Alignment explanation
Indices: 695455--695556 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 43
695445 ATGCATAGCA
* * * *
695455 TAGTGCATCAATGCACATTTAAGGAATGCATCGGTGCA-TCTT
1 TAGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTCTT
* *
695497 CATGGTGTATCGATGCACATTCAAGGGATGCATCGGTACACTCTT
1 --TAGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTCTT
695542 TAGTGTATCGATGCA
1 TAGTGTATCGATGCA
695557 TGTTGCACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 14 0.28
44 32 0.64
45 4 0.08
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (43 bp):
TAGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTCTT
Found at i:701834 original size:21 final size:21
Alignment explanation
Indices: 701808--701884 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
701798 TAAAATAGAG
*
701808 AAGGGATCGATCCTTTTCTCT
1 AAGGGATCGATCCTTTTCTCA
* **
701829 AAGGGACCGATCC-TTTCAAA
1 AAGGGATCGATCCTTTTCTCA
*
701849 AAGGGATCGAT-CTTTTCTCCC
1 AAGGGATCGATCCTTTTCT-CA
*
701870 AAGGGATTGATCCTT
1 AAGGGATCGATCCTT
701885 AGATAGACAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 18 0.41
21 22 0.50
22 3 0.07
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTCTCA
Found at i:707236 original size:20 final size:20
Alignment explanation
Indices: 707211--707347 Score: 105
Period size: 20 Copynumber: 6.8 Consensus size: 20
707201 ATTTTTCTCT
707211 AAGGGATCGATCCTTTTGAA
1 AAGGGATCGATCCTTTTGAA
* *
707231 AAGGGATCGATCATTTCTCCAA
1 AAGGGATCGATCCTTT-T-GAA
* *
707253 AA-GAATCTATCCTTTTGAA
1 AAGGGATCGATCCTTTTGAA
** *
707272 AAGGGATAAATCCTTTTAAA
1 AAGGGATCGATCCTTTTGAA
* * ***
707292 AAGAGACCGATCCTTTCTCCT
1 AAGGGATCGATCCTTT-TGAA
* *
707313 GAGGGATCGACCCTTTTGAA
1 AAGGGATCGATCCTTTTGAA
*
707333 AAGGGATCAATCCTT
1 AAGGGATCGATCCTT
707348 AGTTGGACAT
Statistics
Matches: 86, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
19 4 0.05
20 54 0.63
21 24 0.28
22 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (20 bp):
AAGGGATCGATCCTTTTGAA
Found at i:707285 original size:61 final size:61
Alignment explanation
Indices: 707211--707347 Score: 166
Period size: 61 Copynumber: 2.2 Consensus size: 61
707201 ATTTTTCTCT
* * * * * *
707211 AAGGGATCGATCCTTTTGAAAAGGGATCGATCATTTCTCCAAAAGAATCTATCCTTTTGAA
1 AAGGGATCAATCCTTTTAAAAAGAGACCGATCATTTCTCCAAAAGAATCGACCCTTTTGAA
* * ** * *
707272 AAGGGATAAATCCTTTTAAAAAGAGACCGATCCTTTCTCCTGAGGGATCGACCCTTTTGAA
1 AAGGGATCAATCCTTTTAAAAAGAGACCGATCATTTCTCCAAAAGAATCGACCCTTTTGAA
707333 AAGGGATCAATCCTT
1 AAGGGATCAATCCTT
707348 AGTTGGACAT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (61 bp):
AAGGGATCAATCCTTTTAAAAAGAGACCGATCATTTCTCCAAAAGAATCGACCCTTTTGAA
Found at i:712710 original size:60 final size:60
Alignment explanation
Indices: 712616--712743 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
712606 AAGGGTAAAA
*
712616 TACACAAATAGTCTCCCGACTATAAGATACTACTTTATCGAGTCTC-CCGACTATTAAAAGT
1 TACA-AAATAGTCCCCCGACTATAAGATACTACTTTATCGAGTC-CACCGACTATTAAAAGT
* * ** * **
712677 TACAAAATGGTCCCCCGACTATAGGATGTTACTTTATTGAGTCCATTGACTATTAAAAGT
1 TACAAAATAGTCCCCCGACTATAAGATACTACTTTATCGAGTCCACCGACTATTAAAAGT
712737 TACAAAA
1 TACAAAA
712744 CATTCACTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.02
60 53 0.91
61 4 0.07
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.30
Consensus pattern (60 bp):
TACAAAATAGTCCCCCGACTATAAGATACTACTTTATCGAGTCCACCGACTATTAAAAGT
Found at i:716296 original size:54 final size:55
Alignment explanation
Indices: 716238--716349 Score: 122
Period size: 55 Copynumber: 2.1 Consensus size: 55
716228 TTCGGGGTTT
* * * *
716238 AAAAGAAGAAAAAGAA-AA-AATGAACGAGAAAAAAG-AGAAGGAATTCGAGTCTAA
1 AAAAG-AGAAAAAAAACAACAATAAAC-AGAAAAAAGAAGAACGAATTCGAGGCTAA
* * *
716292 AAAAGGGAAAAAAAACAACAATAAACAGAAAAGAGAAGAACGAATTCGGGGCTAA
1 AAAAGAGAAAAAAAACAACAATAAACAGAAAAAAGAAGAACGAATTCGAGGCTAA
716347 AAA
1 AAA
716350 GGGAAAGACA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
53 8 0.17
54 15 0.31
55 25 0.52
ACGTcount: A:0.62, C:0.08, G:0.21, T:0.08
Consensus pattern (55 bp):
AAAAGAGAAAAAAAACAACAATAAACAGAAAAAAGAAGAACGAATTCGAGGCTAA
Found at i:717806 original size:14 final size:15
Alignment explanation
Indices: 717777--717806 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
717767 ATTTTTTATC
717777 TTTTAAAATTATTTT
1 TTTTAAAATTATTTT
717792 TTTTAAAATTATTTT
1 TTTTAAAATTATTTT
717807 AAAATGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAAAATTATTTT
Found at i:719986 original size:18 final size:18
Alignment explanation
Indices: 719963--719999 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
719953 TGATCCACTA
*
719963 ATGGTGTTAAGGTAACAT
1 ATGGTGTTAAGGCAACAT
719981 ATGGTGTTAAGGCAACAT
1 ATGGTGTTAAGGCAACAT
719999 A
1 A
720000 GGGTATGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (18 bp):
ATGGTGTTAAGGCAACAT
Found at i:725046 original size:188 final size:188
Alignment explanation
Indices: 724697--725318 Score: 912
Period size: 188 Copynumber: 3.3 Consensus size: 188
724687 ATTCAACTTC
* * * * *
724697 ACTACTTTTTTGTGAAAATTAGATTCGAAGTTGATTTGATTCCACTACTCTTTCGTGGAGACTTC
1 ACTACTCTTCTGTGAAGATCAGATTCGAAGTTGATTTGATTCCACTACTCTTTCATGGAGACTTC
* * * *
724762 ATACTTTGCTGAAAAATCCGTTCCACTACTTTTACGTGGAGAGCGAACTTTGATCTTGTTCCTGC
66 ATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGCTCCTGC
* * * * * *
724827 TTCACTACTCTT-TAATGAATGCTTGATTTGAATAACTTGAACAAAAAGAATCTGTTTA
131 TTCACTACTCTTCT-GTGAAGGCTTAATTTGAATGACTTGAACAGAAGGAATCTGTTTA
* * * *
724885 ACTACTCTTCCT-TGAAGATCAGATTCAAAGTTGATTTGATTCCACTACTTTTTCGTGGAGATTT
1 ACTACTCTT-CTGTGAAGATCAGATTCGAAGTTGATTTGATTCCACTACTCTTTCATGGAGACTT
** *
724949 CATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGAAAATTTTGATCTTGCTCATG
65 CATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGCTCCTG
* *
725014 CTTCACTACTCTTCTGTGAAGGCTTAATTTGAATGACTTGAACAGAAGGAATATGTTTT
130 CTTCACTACTCTTCTGTGAAGGCTTAATTTGAATGACTTGAACAGAAGGAATCTGTTTA
*
725073 ACTACTCTTATGTGAAGATTC-GATTCGAAGTTGATTTGATTCCACTACTCTTTCATGGA-ACTT
1 ACTACTCTTCTGTGAAGA-TCAGATTCGAAGTTGATTTGATTCCACTACTCTTTCATGGAGACTT
*
725136 CATACTTTGCTGAAAAATCCGTTCCACTACTCTTCTGTGGAGAGCGAATTTTGATCTTGCTCCTG
65 CATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGCTCCTG
*
725201 CTTCACTACTCTTCTGTGAAGGCTTAATTTGAATGACTTGAACAGAAGGAATCTGTTTC
130 CTTCACTACTCTTCTGTGAAGGCTTAATTTGAATGACTTGAACAGAAGGAATCTGTTTA
* * *
725260 ACTAATCTTCTGTGAAGATCATATTCGAAGTTGATTT-AATCCACTACTCTTTCATGGAG
1 ACTACTCTTCTGTGAAGATCAGATTCGAAGTTGATTTGATTCCACTACTCTTTCATGGAG
725319 CCCTAAGGAC
Statistics
Matches: 391, Mismatches: 37, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
186 22 0.06
187 153 0.39
188 212 0.54
189 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (188 bp):
ACTACTCTTCTGTGAAGATCAGATTCGAAGTTGATTTGATTCCACTACTCTTTCATGGAGACTTC
ATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGCTCCTGC
TTCACTACTCTTCTGTGAAGGCTTAATTTGAATGACTTGAACAGAAGGAATCTGTTTA
Found at i:725387 original size:20 final size:20
Alignment explanation
Indices: 725359--725401 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
725349 CTGACAGGTG
725359 ACCCAAAGGATTTACAAATT
1 ACCCAAAGGATTTACAAATT
* *
725379 ACCCGAAGGTTTTACAAATT
1 ACCCAAAGGATTTACAAATT
725399 ACC
1 ACC
725402 TGGAGACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (20 bp):
ACCCAAAGGATTTACAAATT
Found at i:725412 original size:20 final size:20
Alignment explanation
Indices: 725369--725412 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
725359 ACCCAAAGGA
**
725369 TTTACAAATTACCCGAAGGT
1 TTTACAAATTACCCGAAGAC
* *
725389 TTTACAAATTACCTGGAGAC
1 TTTACAAATTACCCGAAGAC
725409 TTTA
1 TTTA
725413 ACTTTCTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
TTTACAAATTACCCGAAGAC
Found at i:729288 original size:6 final size:6
Alignment explanation
Indices: 729254--729382 Score: 80
Period size: 6 Copynumber: 23.2 Consensus size: 6
729244 ACTTCACCTG
* * * *
729254 AAGAAA AA-AAA GAGAAA ATGAAA GA-AAA AAGAAA AGGAAA AAG--A
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** * *
729298 AA-AAA AAGAAA AAGAAA AA-ATG AAGATA AAGAAA ATG-AA AA-AAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* * * *
729342 ATGAAA AAAAAA AAG-AA AAGAAA GA-AAA AAGAAA AGGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A
729383 TAAACAAAAA
Statistics
Matches: 92, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
4 3 0.03
5 29 0.32
6 60 0.65
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (6 bp):
AAGAAA
Found at i:729301 original size:38 final size:36
Alignment explanation
Indices: 729258--729376 Score: 107
Period size: 38 Copynumber: 3.1 Consensus size: 36
729248 CACCTGAAGA
729258 AAAAAAAGAGAAAATGAAAGAAAAAAGAAAAGGAAAAAG
1 AAAAAAA-AGAAAA-GAAA-AAAAAAGAAAAGGAAAAAG
* *
729297 AAAAAAAAGAAAAAGAAAAAATGAAGATAAA-GAAAATG
1 AAAAAAAAG-AAAAGAAAAAA-AAAGA-AAAGGAAAAAG
* *
729335 AAAAAAAATGAAAA-AAAAAAAGAAAAGAAAGAAAAAAG
1 AAAAAAAA-GAAAAGAAAAAAA-AAGA-AAAGGAAAAAG
729373 AAAA
1 AAAA
729377 GGAAAATAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
37 15 0.22
38 37 0.55
39 15 0.22
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (36 bp):
AAAAAAAAGAAAAGAAAAAAAAAGAAAAGGAAAAAG
Found at i:729348 original size:9 final size:10
Alignment explanation
Indices: 729268--729352 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 10
729258 AAAAAAAGAG
729268 AAAATGAAAGA
1 AAAATGAAA-A
*
729279 AAAAAGAAAA
1 AAAATGAAAA
*
729289 GGAAAAAGAAAA
1 --AAAATGAAAA
729301 AAAA-GAAAA
1 AAAATGAAAA
*
729310 AGAAA--AAATG
1 A-AAATGAAA-A
* *
729320 AAGAT-AAAG
1 AAAATGAAAA
729329 AAAATGAAAA
1 AAAATGAAAA
729339 AAAATGAAAA
1 AAAATGAAAA
729349 AAAA
1 AAAA
729353 AAAGAAAAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
9 16 0.25
10 29 0.46
11 8 0.13
12 10 0.16
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (10 bp):
AAAATGAAAA
Found at i:729382 original size:50 final size:51
Alignment explanation
Indices: 729297--729392 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 51
729287 AAGGAAAAAG
*
729297 AAAAAAAAGAAAAAGAAAAAATGAAGATAAAGAAAATGAAA-AAAAATGAAA
1 AAAAAAAAGAAAAAGAAAAAATAAAGATAAAGAAAAT-AAACAAAAATGAAA
729348 AAAAAAAAG-AAAAGAAAGAAA-AAAGA-AAAGGAAAATAAACAAAAA
1 AAAAAAAAGAAAAAGAAA-AAATAAAGATAAA-GAAAATAAACAAAAA
729393 GGGGGTTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
49 6 0.15
50 23 0.56
51 12 0.29
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (51 bp):
AAAAAAAAGAAAAAGAAAAAATAAAGATAAAGAAAATAAACAAAAATGAAA
Found at i:729391 original size:22 final size:21
Alignment explanation
Indices: 729257--729392 Score: 116
Period size: 21 Copynumber: 6.1 Consensus size: 21
729247 TCACCTGAAG
729257 AAAA-AAAAGAGAAAATGAAAGAA
1 AAAAGAAAAG-GAAAA--AAAGAA
729280 AAAAGAAAAGGAAAAAGAA-AA
1 AAAAGAAAAGGAAAAA-AAGAA
* *
729301 AAAAGAAAAAGAAAAAATGAA
1 AAAAGAAAAGGAAAAAAAGAA
*
729322 GATAAAGAAAATGAAAAAAAATGAA
1 -A-AAAGAAAA-GGAAAAAAA-GAA
*
729347 AAAA-AAAAAGAAAAGAAAGAA
1 AAAAGAAAAGGAAAA-AAAGAA
*
729368 AAAAGAAAAGGAAAATAAACAA
1 AAAAGAAAAGGAAAA-AAAGAA
729390 AAA
1 AAA
729393 GGGGGTTTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 19
0.76 0.08 0.15
Matches are distributed among these distances:
20 1 0.01
21 31 0.33
22 27 0.29
23 20 0.21
24 12 0.13
25 3 0.03
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.04
Consensus pattern (21 bp):
AAAAGAAAAGGAAAAAAAGAA
Found at i:729393 original size:21 final size:22
Alignment explanation
Indices: 729260--729392 Score: 119
Period size: 22 Copynumber: 5.9 Consensus size: 22
729250 CCTGAAGAAA
729260 AAAAAGAGAAAATGAAAGAAAAAAG
1 AAAAAGA-AAAA--AAAGAAAAAAG
* *
729285 AAAAGGAAAAAGAA-AAAAAAG
1 AAAAAGAAAAAAAAGAAAAAAG
*
729306 AAAAAGAAAAAATGAAG-ATAAAG
1 AAAAAGAAAAAA--AAGAAAAAAG
*
729329 AAAATGAAAAAAAATGAAAAAA-
1 AAAAAGAAAAAAAA-GAAAAAAG
*
729351 AAAAAGAAAAGAAAGAAAAAAG
1 AAAAAGAAAAAAAAGAAAAAAG
* * *
729373 AAAAGGAAAATAAACAAAAA
1 AAAAAGAAAAAAAAGAAAAA
729393 GGGGGTTTAT
Statistics
Matches: 90, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
21 26 0.29
22 32 0.36
23 22 0.24
24 4 0.04
25 6 0.07
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.05
Consensus pattern (22 bp):
AAAAAGAAAAAAAAGAAAAAAG
Found at i:730837 original size:134 final size:134
Alignment explanation
Indices: 730609--730902 Score: 389
Period size: 134 Copynumber: 2.2 Consensus size: 134
730599 ATCAAATTTT
* * * *
730609 ATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAAAATCCCCATATCTGATTTTCCCTCAAGAA
1 ATTCAATATTCCCTGAAGAACAGTGGAATGAATAAAAATCCCCAGATCTGATTTTCCCTCAAGAA
* * * * * *
730674 GAAGCGAAACATATCCATTTCTTTGAAGATTTGATATTCCTTTAGTAACAGTGAAACAAGTTTGA
66 GAAGCGAAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGAAACAAGTATGA
*
730739 CTTG
131 CTCG
* *
730743 ATTCAATTTTCCCT-AAGTAACAGTGGAAT-AACTAAAAATCCCCGGATCTGATTTTCCCTCAAG
1 ATTCAATATTCCCTGAAG-AACAGTGGAATGAA-TAAAAATCCCCAGATCTGATTTTCCCTCAAG
*
730806 AAGAAGC-AGAACAAATCTC-TCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
64 AAGAAGCGA-AACAAATC-CATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGAAACAAGT
*
730869 ATGCCTCG
127 ATGACTCG
730877 ATTCAATATTCCCTGAAGAACAGTGG
1 ATTCAATATTCCCTGAAGAACAGTGG
730903 TATGGATCAA
Statistics
Matches: 140, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
133 6 0.04
134 130 0.93
135 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (134 bp):
ATTCAATATTCCCTGAAGAACAGTGGAATGAATAAAAATCCCCAGATCTGATTTTCCCTCAAGAA
GAAGCGAAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGAAACAAGTATGA
CTCG
Found at i:731286 original size:20 final size:20
Alignment explanation
Indices: 731261--731299 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
731251 ATCGCCACCG
731261 CTAGTACAAGACTCCCGACA
1 CTAGTACAAGACTCCCGACA
731281 CTAGTACAAGACTCCCGAC
1 CTAGTACAAGACTCCCGAC
731300 GTCGCCACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.36, G:0.15, T:0.15
Consensus pattern (20 bp):
CTAGTACAAGACTCCCGACA
Found at i:741540 original size:24 final size:24
Alignment explanation
Indices: 741513--741572 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
741503 CTTAATTTTG
*
741513 TTCTGATTTCTGTTCTGGATTCTA
1 TTCTGATTTCTGTTCTGAATTCTA
*
741537 TTCTGA-TACTTGTTCTGAATTCTA
1 TTCTGATTTC-TGTTCTGAATTCTA
*
741561 TTTTGATTTCTG
1 TTCTGATTTCTG
741573 ATATCTCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 26 0.87
25 2 0.07
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (24 bp):
TTCTGATTTCTGTTCTGAATTCTA
Found at i:741740 original size:2 final size:2
Alignment explanation
Indices: 741733--741759 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
741723 GGGATGGGGG
741733 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 T
741760 GTTTTAAAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:743689 original size:12 final size:12
Alignment explanation
Indices: 743672--743713 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
743662 CCGACCCGAC
743672 CCGACCTGTTGA
1 CCGACCTGTTGA
* *
743684 CCGACCCGTTGTC
1 CCGACCTGTTG-A
743697 CCGACCTGTTGA
1 CCGACCTGTTGA
743709 CCGAC
1 CCGAC
743714 GTTAACCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.14, C:0.40, G:0.24, T:0.21
Consensus pattern (12 bp):
CCGACCTGTTGA
Found at i:746219 original size:24 final size:24
Alignment explanation
Indices: 746192--746255 Score: 128
Period size: 24 Copynumber: 2.7 Consensus size: 24
746182 ATTTTCGACT
746192 TGAATTCTGTTCTGATATATGACC
1 TGAATTCTGTTCTGATATATGACC
746216 TGAATTCTGTTCTGATATATGACC
1 TGAATTCTGTTCTGATATATGACC
746240 TGAATTCTGTTCTGAT
1 TGAATTCTGTTCTGAT
746256 TTCTGTTCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATATGACC
Found at i:746230 original size:12 final size:12
Alignment explanation
Indices: 746192--746297 Score: 74
Period size: 12 Copynumber: 8.9 Consensus size: 12
746182 ATTTTCGACT
746192 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
746204 TG-ATATATGACC
1 TGAAT-TCTGTTC
746216 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
746228 TG-ATATATGACC
1 TGAAT-TCTGTTC
746240 TGAATTCTGTTC
1 TGAATTCTGTTC
*
746252 TGATTTCTGTTC
1 TGAATTCTGTTC
* *
746264 TGGATTCTATTC
1 TGAATTCTGTTC
* *
746276 TGTA-CCTGTTC
1 TGAATTCTGTTC
746287 TGAATTCTGTT
1 TGAATTCTGTT
746298 TTAATTTCTG
Statistics
Matches: 68, Mismatches: 21, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
11 12 0.18
12 52 0.76
13 4 0.06
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:746270 original size:24 final size:24
Alignment explanation
Indices: 746192--746297 Score: 115
Period size: 24 Copynumber: 4.5 Consensus size: 24
746182 ATTTTCGACT
*
746192 TGAATTCTGTTCTGATATATGACC
1 TGAATTCTGTTCTGATATCTGACC
*
746216 TGAATTCTGTTCTGATATATGACC
1 TGAATTCTGTTCTGATATCTGACC
* **
746240 TGAATTCTGTTCTGATTTCTGTTC
1 TGAATTCTGTTCTGATATCTGACC
* * * **
746264 TGGATTCTATTCTG-TACCTGTTC
1 TGAATTCTGTTCTGATATCTGACC
746287 TGAATTCTGTT
1 TGAATTCTGTT
746298 TTAATTTCTG
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 16 0.22
24 56 0.78
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGACC
Found at i:750544 original size:9 final size:10
Alignment explanation
Indices: 750525--750575 Score: 63
Period size: 9 Copynumber: 5.2 Consensus size: 10
750515 GGGATTTAAA
750525 ATATATATATT
1 ATATAT-TATT
750536 ATAT-TTATT
1 ATATATTATT
750545 AT-TATTATT
1 ATATATTATT
750554 ATTATATTATT
1 A-TATATTATT
750565 AT-TATTATT
1 ATATATTATT
750574 AT
1 AT
750576 TACTAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.03
9 21 0.57
10 3 0.08
11 12 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATATTATT
Found at i:750548 original size:3 final size:3
Alignment explanation
Indices: 750540--750577 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
750530 TATATTATAT
750540 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
750578 CTAATAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:751149 original size:18 final size:19
Alignment explanation
Indices: 751108--751151 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
751098 CATCTTAAGG
*
751108 TTTTTAATTTATTTTTCTA
1 TTTTTATTTTATTTTTCTA
*
751127 -CTTTATTTTA-TTTTCTA
1 TTTTTATTTTATTTTTCTA
751144 TTTTTATT
1 TTTTTATT
751152 AATTTGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTATTTTATTTTTCTA
Found at i:753828 original size:24 final size:24
Alignment explanation
Indices: 753801--753895 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
753791 ATTTTCGACT
* *
753801 TGAATTCTGTTCTGATATATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
753825 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* * * *
753849 TGGATTCTATTCTGATACCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
753873 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
753896 ATCTCCGTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:753839 original size:12 final size:12
Alignment explanation
Indices: 753801--753893 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
753791 ATTTTCGACT
753801 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
753813 TG-ATATATGACC
1 TGAAT-TCTGTTC
753825 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
753837 TGATTTCTGATC
1 TGAATTCTGTTC
* *
753849 TGGATTCTATTC
1 TGAATTCTGTTC
*
753861 TG-ATACCTGTTC
1 TGAAT-TCTGTTC
*
753873 TGAATTCTGTTT
1 TGAATTCTGTTC
*
753885 TGATTTCTG
1 TGAATTCTG
753894 ATATCTCCGT
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 4 0.07
12 52 0.87
13 4 0.07
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:753839 original size:48 final size:49
Alignment explanation
Indices: 753787--753895 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 49
753777 AAATATTTTA
* *
753787 TCTGATTTTC-GA-CTTGAATTCTGTTCTGATATATGACCTGAATTCTGT
1 TCTGATTTTCTGATC-TGAATTCTATTCTGATACATGACCTGAATTCTGT
* * **
753835 TCTGA-TTTCTGATCTGGATTCTATTCTGATACCTGTTCTGAATTCTGT
1 TCTGATTTTCTGATCTGAATTCTATTCTGATACATGACCTGAATTCTGT
*
753883 TTTGA-TTTCTGAT
1 TCTGATTTTCTGAT
753896 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 4 0.08
48 47 0.90
49 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.49
Consensus pattern (49 bp):
TCTGATTTTCTGATCTGAATTCTATTCTGATACATGACCTGAATTCTGT
Found at i:754813 original size:17 final size:18
Alignment explanation
Indices: 754791--754829 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
754781 TCATCTTGAG
*
754791 AGTATCGATAC-CCCCTT
1 AGTATCGATACTCCCCTA
754808 AGTATCGATACTCCCCTA
1 AGTATCGATACTCCCCTA
754826 AGTA
1 AGTA
754830 CCAATACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (18 bp):
AGTATCGATACTCCCCTA
Done.