Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold142
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: 1427168
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 17476 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:692643 original size:19 final size:20
Alignment explanation
Indices: 692607--692646 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
692597 TTATTTTAAA
692607 TTTATATAAATTAATTAAAAT
1 TTTATATAAA-TAATTAAAAT
*
692628 TTTATATAAA-ATTTAAAAT
1 TTTATATAAATAATTAAAAT
692647 CATACGTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTATATAAATAATTAAAAT
Found at i:692712 original size:23 final size:23
Alignment explanation
Indices: 692675--692719 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
692665 ATATAAATTT
* *
692675 AAATTATTATTAAATAATTATAA
1 AAATTATAATAAAATAATTATAA
*
692698 AAATTATAATAAAATATTTATA
1 AAATTATAATAAAATAATTATA
692720 GTTTAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTATAATAAAATAATTATAA
Found at i:692817 original size:21 final size:21
Alignment explanation
Indices: 692791--692874 Score: 77
Period size: 20 Copynumber: 4.1 Consensus size: 21
692781 TCTAATCAAT
*
692791 TTTTAATTTATATTATATAA-A
1 TTTTAATATAT-TTATATAATA
692812 TTTTAATATATTTATATAATA
1 TTTTAATATATTTATATAATA
* *
692833 -TTT-ATATTATTTTTATCATA
1 TTTTAATA-TATTTATATAATA
* *
692853 TTTTAAT-TTTTTATATTATA
1 TTTTAATATATTTATATAATA
692873 TT
1 TT
692875 CTTATCAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
19 3 0.06
20 34 0.64
21 14 0.26
22 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAATATATTTATATAATA
Found at i:692847 original size:31 final size:29
Alignment explanation
Indices: 692811--692881 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 29
692801 TATTATATAA
*
692811 ATTTTAAT-ATATTTATATAATATTTATATT
1 ATTTTTATCATATTT-TA-AATATTTATATT
* *
692841 ATTTTTATCATATTTTAATTTTTTATATT
1 ATTTTTATCATATTTTAAATATTTATATT
692870 ATATTCTTATCA
1 AT-TT-TTATCA
692882 AATCTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.34
30 11 0.31
31 12 0.34
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTTTATCATATTTTAAATATTTATATT
Found at i:693124 original size:17 final size:16
Alignment explanation
Indices: 693094--693127 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
693084 TGTTTCACAT
*
693094 AAAATATTACATAATA
1 AAAATATTAAATAATA
693110 AAAATAATTAAATAATA
1 AAAAT-ATTAAATAATA
693127 A
1 A
693128 TATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATTAAATAATA
Found at i:693136 original size:27 final size:28
Alignment explanation
Indices: 693092--693175 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 28
693082 CATGTTTCAC
* *
693092 ATAAAATATTACATAATAAAAATAATTAA
1 ATAAAATAATATA-AATAAAAATAATTAA
* *
693121 AT--AATAATATAAAATATAAATAAATAA
1 ATAAAATAATAT-AAATAAAAATAATTAA
*
693148 ATAAAATAATATAAATAAATAT-ATTAA
1 ATAAAATAATATAAATAAAAATAATTAA
693175 A
1 A
693176 CTTTATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
27 26 0.58
28 9 0.20
29 10 0.22
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (28 bp):
ATAAAATAATATAAATAAAAATAATTAA
Found at i:693145 original size:4 final size:4
Alignment explanation
Indices: 693111--693168 Score: 57
Period size: 4 Copynumber: 14.2 Consensus size: 4
693101 TACATAATAA
* *
693111 AAAT AATT AAAT -AAT AATAT AAA- ATAT AAAT AAAT AAAT AAAAT AATAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT
693160 AAAT AAAT A
1 AAAT AAAT A
693169 TATTAAACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
3 5 0.11
4 28 0.62
5 12 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:693182 original size:22 final size:22
Alignment explanation
Indices: 693110--693168 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
693100 TTACATAATA
693110 AAAATAAT-TAAAT-AAT-AAT
1 AAAATAATATAAATAAATAAAT
*
693129 ATAA-AATATAAATAAATAAAT
1 AAAATAATATAAATAAATAAAT
693150 AAAATAATATAAATAAATA
1 AAAATAATATAAATAAATA
693169 TATTAAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 3 0.09
19 8 0.24
20 3 0.09
21 6 0.18
22 14 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAATATAAATAAATAAAT
Found at i:693694 original size:20 final size:21
Alignment explanation
Indices: 693666--693708 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
693656 ATATATTAAT
693666 ATAAAATAAAATTTT-AATTA
1 ATAAAATAAAATTTTAAATTA
* *
693686 ATAATATAAACTTTTAAATTA
1 ATAAAATAAAATTTTAAATTA
693707 AT
1 AT
693709 TTAATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAATAAAATTTTAAATTA
Found at i:697458 original size:2 final size:2
Alignment explanation
Indices: 697415--697449 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
697405 AACCCACATA
697415 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 A
697450 CACATATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:698573 original size:26 final size:26
Alignment explanation
Indices: 698534--698590 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
698524 TTATTTTAAA
*
698534 AATTTTATTTTTATTATAATTAT-AAT
1 AATTATATTTTTATTA-AATTATGAAT
*
698560 TATTATATTTTTATTAAATTATGAAT
1 AATTATATTTTTATTAAATTATGAAT
698586 AATTA
1 AATTA
698591 AAAAATCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
AATTATATTTTTATTAAATTATGAAT
Found at i:699406 original size:12 final size:12
Alignment explanation
Indices: 699389--699413 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
699379 TAATGTTTAA
699389 AAAAATTAAATT
1 AAAAATTAAATT
699401 AAAAATTAAATT
1 AAAAATTAAATT
699413 A
1 A
699414 GTAAAATTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:699624 original size:31 final size:31
Alignment explanation
Indices: 699582--699648 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
699572 AATATTTTTT
699582 TAAA-TTTTTATTTAATTTTTAT-AAATT-TAA
1 TAAATTTTTTA-TTAA-TTTTATGAAATTATAA
*
699612 TAAATTTTTTATTAATTTTATGATATTATAA
1 TAAATTTTTTATTAATTTTATGAAATTATAA
699643 TAAATT
1 TAAATT
699649 ATAGATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 6 0.18
30 12 0.36
31 15 0.45
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (31 bp):
TAAATTTTTTATTAATTTTATGAAATTATAA
Found at i:700805 original size:24 final size:25
Alignment explanation
Indices: 700745--700805 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
700735 TTAAAATAAA
*
700745 ATAAAATATTTTTAATTAATATTTT
1 ATAAAATATTTATAATTAATATTTT
*
700770 ATATAAT-TTTATAATTAA-ATTTT
1 ATAAAATATTTATAATTAATATTTT
700793 A-AAAATATATTAT
1 ATAAAATAT-TTAT
700806 TTTAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 4 0.13
23 7 0.23
24 14 0.45
25 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAAAATATTTATAATTAATATTTT
Found at i:705527 original size:24 final size:23
Alignment explanation
Indices: 705499--705543 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
705489 AACAATTTCA
*
705499 AATATTTTTAATAAATTTTTTATT
1 AATA-TTTTAATAAACTTTTTATT
*
705523 AATATTTTATTAAACTTTTTA
1 AATATTTTAATAAACTTTTTA
705544 AATACTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
AATATTTTAATAAACTTTTTATT
Found at i:706490 original size:68 final size:68
Alignment explanation
Indices: 706381--706515 Score: 261
Period size: 68 Copynumber: 2.0 Consensus size: 68
706371 AAAATCTTTC
706381 ATTAAATTTTAACAATACAAGTCAAATGGTACTATTATTTCGGATCCTTTTCAAATCCGACCCAA
1 ATTAAATTTTAACAATACAAGTCAAATGGTACTATTATTTCGGATCCTTTTCAAATCCGACCCAA
706446 TTG
66 TTG
*
706449 ATTAAATTTTAGCAATACAAGTCAAATGGTACTATTATTTCGGATCCTTTTCAAATCCGACCCAA
1 ATTAAATTTTAACAATACAAGTCAAATGGTACTATTATTTCGGATCCTTTTCAAATCCGACCCAA
706514 TT
66 TT
706516 CAGTTTAGCC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (68 bp):
ATTAAATTTTAACAATACAAGTCAAATGGTACTATTATTTCGGATCCTTTTCAAATCCGACCCAA
TTG
Found at i:708658 original size:28 final size:28
Alignment explanation
Indices: 708613--708697 Score: 125
Period size: 28 Copynumber: 3.0 Consensus size: 28
708603 ACATGCAGCC
* * *
708613 TTTGTTACTCGAAGTCAGATGTGAGCGT
1 TTTGTTACTAGAATTCAGATATGAGCGT
*
708641 TTTGTTACTAGAATTCAGATATGAGTGT
1 TTTGTTACTAGAATTCAGATATGAGCGT
*
708669 TTTGTTACTAGAATTTAGATATGAGCGT
1 TTTGTTACTAGAATTCAGATATGAGCGT
708697 T
1 T
708698 AAATATAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (28 bp):
TTTGTTACTAGAATTCAGATATGAGCGT
Found at i:711774 original size:30 final size:29
Alignment explanation
Indices: 711728--711794 Score: 98
Period size: 30 Copynumber: 2.3 Consensus size: 29
711718 ATAAAATTTT
*
711728 AATTTATATTAAATAAATCTTTAATCTTC
1 AATTTATATTAAATAAATCTTTAATATTC
* *
711757 AATTTATATTAAAATAAATTTTTAATATTT
1 AATTTATATT-AAATAAATCTTTAATATTC
711787 AATTTATA
1 AATTTATA
711795 CACAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
AATTTATATTAAATAAATCTTTAATATTC
Found at i:711802 original size:30 final size:28
Alignment explanation
Indices: 711725--711813 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 28
711715 TTAATAAAAT
* * *
711725 TTTAATTTATATTAAATAAATCTTTAATC
1 TTTAATTTATA-AAAATAAATTTTTAATA
*
711754 TTCAATTTATATTAAAATAAATTTTTAATA
1 TTTAATTTATA--AAAATAAATTTTTAATA
*
711784 TTTAATTTATACACAAATAAATTATTAATA
1 TTTAATTTATA-A-AAATAAATTTTTAATA
711814 AAAATTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.22
30 40 0.78
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAATTTATAAAAATAAATTTTTAATA
Found at i:712116 original size:15 final size:16
Alignment explanation
Indices: 712056--712117 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
712046 GCTCTATTTT
712056 AAAATAATTAAATTTAA
1 AAAAT-ATTAAATTTAA
* * *
712073 TGTAATTATTGAATATTAA
1 --AAAATATTAAAT-TTAA
712092 AAAATATTAAATTTAA
1 AAAATATTAAATTTAA
712108 AAAAT-TTAAA
1 AAAATATTAAA
712118 AATTTTTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
15 5 0.14
16 9 0.25
17 9 0.25
18 6 0.17
19 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAATATTAAATTTAA
Found at i:712369 original size:13 final size:13
Alignment explanation
Indices: 712346--712378 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
712336 TTTAATTAAA
712346 TTTTA-TTTTTAT
1 TTTTATTTTTTAT
712358 TTTTATTTTTTAT
1 TTTTATTTTTTAT
*
712371 ATTTATTT
1 TTTTATTT
712379 CTTGACGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:712974 original size:32 final size:33
Alignment explanation
Indices: 712897--713006 Score: 105
Period size: 32 Copynumber: 3.2 Consensus size: 33
712887 ATATTATAAT
*
712897 TATATTTAAAATATTACATATTTATATAAATTTTAA
1 TATA-TTAATATATTA-ATA-TTATATAAATTTTAA
* * **
712933 TACAATAATA-ATTTTTATTATATAAATTTTAA
1 TATATTAATATATTAATATTATATAAATTTTAA
**
712965 TATATTAATATATTAATATTATATTATTTTTTAA
1 TATATTAATATATTAATATTATA-TAAATTTTAA
712999 TTATATTA
1 -TATATTA
713007 TTTATGTTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
32 23 0.38
33 12 0.20
34 11 0.18
35 11 0.18
36 3 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (33 bp):
TATATTAATATATTAATATTATATAAATTTTAA
Found at i:712990 original size:5 final size:5
Alignment explanation
Indices: 712965--713040 Score: 54
Period size: 5 Copynumber: 15.6 Consensus size: 5
712955 TAAATTTTAA
* * *
712965 TATAT TA-A- TATAT TAATAT TATAT TATTT TTTAAT TATAT TAT-T TATGT
1 TATAT TATAT TATAT T-ATAT TATAT TATAT TAT-AT TATAT TATAT TATAT
*
713014 TATACT TATAT CATA- TA-AT TATAT TAT
1 TATA-T TATAT TATAT TATAT TATAT TAT
713041 TTTTAAGATT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
3 3 0.05
4 9 0.16
5 31 0.55
6 13 0.23
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:713157 original size:15 final size:14
Alignment explanation
Indices: 713140--713202 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
713130 TTTTAATTTT
713140 TTTAAATATTAATA
1 TTTAAATATTAATA
*
713154 TTTTTAATACTT-ATA
1 -TTTAAATA-TTAATA
713169 TTT-AATA-TAA-A
1 TTTAAATATTAATA
* *
713180 TTTAAACATAAATA
1 TTTAAATATTAATA
713194 TTTAAATAT
1 TTTAAATAT
713203 AATTTTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
11 5 0.13
12 4 0.10
13 6 0.15
14 12 0.31
15 10 0.26
16 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTAAATATTAATA
Found at i:714613 original size:30 final size:30
Alignment explanation
Indices: 714578--714643 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
714568 AAAATTAAAT
*
714578 ATATTTAT-CTTAAACTTATATTTATATTCA
1 ATATTTATAC-TAAACTCATATTTATATTCA
*
714608 ATATTTATACTAAACTCATATTTATATTCG
1 ATATTTATACTAAACTCATATTTATATTCA
714638 ATATTT
1 ATATTT
714644 GTATCTCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (30 bp):
ATATTTATACTAAACTCATATTTATATTCA
Found at i:714661 original size:13 final size:14
Alignment explanation
Indices: 714638--714675 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
714628 TTTATATTCG
*
714638 ATATTTGTATCTCT
1 ATATTAGTATCTCT
714652 ATATTA-TATCTCT
1 ATATTAGTATCTCT
714665 ATATTAGTATC
1 ATATTAGTATC
714676 GAAATCCGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (14 bp):
ATATTAGTATCTCT
Found at i:715814 original size:24 final size:24
Alignment explanation
Indices: 715787--715834 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
715777 TACCAAATCC
* *
715787 ACCACCTCCATATCTACCACCATA
1 ACCACCTCCAAATCCACCACCATA
*
715811 ACCATCTCCAAATCCACCACCATA
1 ACCACCTCCAAATCCACCACCATA
715835 TGTGGTCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (24 bp):
ACCACCTCCAAATCCACCACCATA
Found at i:717668 original size:2 final size:2
Alignment explanation
Indices: 717628--717652 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
717618 GTAAATCTAA
717628 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
717653 CACACACACA
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:718428 original size:30 final size:30
Alignment explanation
Indices: 718394--718453 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
718384 TATTTTATAA
718394 AAATTAATTTGATTAACAAAAAATAAACTT
1 AAATTAATTTGATTAACAAAAAATAAACTT
718424 AAATTAATTTGATTAACAAAAAATAAACTT
1 AAATTAATTTGATTAACAAAAAATAAACTT
718454 CGGGACAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (30 bp):
AAATTAATTTGATTAACAAAAAATAAACTT
Found at i:726179 original size:25 final size:25
Alignment explanation
Indices: 726145--726194 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
726135 ACATTCTGAA
*
726145 ACACACAAAAGACTCAGAGAGTCAT
1 ACACACAAAAGACTAAGAGAGTCAT
726170 ACACACAAAAGACTAAGAGAGTCAT
1 ACACACAAAAGACTAAGAGAGTCAT
726195 CCATGATCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (25 bp):
ACACACAAAAGACTAAGAGAGTCAT
Found at i:739080 original size:17 final size:17
Alignment explanation
Indices: 739058--739092 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
739048 CAATTCAATC
739058 ACTAGAAAGAGTAAATG
1 ACTAGAAAGAGTAAATG
739075 ACTAGAAAGAGTAAATG
1 ACTAGAAAGAGTAAATG
739092 A
1 A
739093 GGGGATTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.23, T:0.17
Consensus pattern (17 bp):
ACTAGAAAGAGTAAATG
Found at i:741183 original size:13 final size:13
Alignment explanation
Indices: 741167--741191 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
741157 TTAACTGGCT
741167 GAATTAATATTAC
1 GAATTAATATTAC
741180 GAATTAATATTA
1 GAATTAATATTA
741192 ATTTAGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
GAATTAATATTAC
Found at i:748204 original size:95 final size:93
Alignment explanation
Indices: 748038--748223 Score: 327
Period size: 95 Copynumber: 2.0 Consensus size: 93
748028 AAGAAAAAAA
748038 ACAATGGCCGAAACTAGAGGAAAGCGAGACAGACGAAAGACCGAAGCTCAGAAATAAGGCCAATA
1 ACAATGGCCGAAACTAGAGGAAAGCGAGACAGACGAAAGACCGAAGCTCAGAAATAAGGCCAATA
748103 GCTCGCGTTAGGATCTTCTTCATCTCTC
66 GCTCGCGTTAGGATCTTCTTCATCTCTC
*
748131 ACAATGGCCGAAACTATAGAGGAAAGCGAGACCGACGAAAGACCGAAGCTCAGAAATAAGGCCAA
1 ACAATGGCCGAAAC--TAGAGGAAAGCGAGACAGACGAAAGACCGAAGCTCAGAAATAAGGCCAA
* *
748196 TCGTTCGCGTTAGGATCTTCTTCATCTC
64 TAGCTCGCGTTAGGATCTTCTTCATCTC
748224 CCACGGCTTT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 14 0.16
95 74 0.84
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (93 bp):
ACAATGGCCGAAACTAGAGGAAAGCGAGACAGACGAAAGACCGAAGCTCAGAAATAAGGCCAATA
GCTCGCGTTAGGATCTTCTTCATCTCTC
Found at i:748897 original size:2 final size:2
Alignment explanation
Indices: 748890--748918 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
748880 TAGTTTTTAT
748890 TC 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 TC T
748919 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:748923 original size:2 final size:2
Alignment explanation
Indices: 748918--748952 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
748908 TCTCTCTCTC
748918 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
748953 GTCCAAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:749568 original size:14 final size:14
Alignment explanation
Indices: 749549--749577 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
749539 TGTGGACTTA
749549 ACCTTTAAAGCTTG
1 ACCTTTAAAGCTTG
749563 ACCTTTAAAGCTTG
1 ACCTTTAAAGCTTG
749577 A
1 A
749578 TATTAGAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (14 bp):
ACCTTTAAAGCTTG
Found at i:751532 original size:23 final size:25
Alignment explanation
Indices: 751492--751538 Score: 71
Period size: 23 Copynumber: 1.9 Consensus size: 25
751482 TTTTTATATT
751492 AATTTTATAATTAAATTTAAATAAAA
1 AATTTTATAATT-AATTTAAATAAAA
751518 AATTTTAT-ATT-ATTTAAATAA
1 AATTTTATAATTAATTTAAATAA
751539 TAATTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
25 3 0.14
26 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTTTATAATTAATTTAAATAAAA
Found at i:751611 original size:36 final size:37
Alignment explanation
Indices: 751571--751642 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 37
751561 ACCAAAATTA
*
751571 TTAAATTTTTTATTTAAAT-TGAATC-AATTTAATTTT
1 TTAAA-TTTTTATTTAAATCTGAATCGAACTTAATTTT
*
751607 TTAAATTTTTATTTATATCTGAATCGAACTTAATTT
1 TTAAATTTTTATTTAAATCTGAATCGAACTTAATTT
751643 AAATTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 12 0.38
36 11 0.34
37 9 0.28
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (37 bp):
TTAAATTTTTATTTAAATCTGAATCGAACTTAATTTT
Found at i:752033 original size:18 final size:18
Alignment explanation
Indices: 752010--752055 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
752000 TTACTATTTA
752010 ATTAATAAATATAAAAAT
1 ATTAATAAATATAAAAAT
*
752028 ATTAAT--ATAAAAAAAT
1 ATTAATAAATATAAAAAT
*
752044 ATT-TTAAATATA
1 ATTAATAAATATA
752056 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 4 0.17
18 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTAATAAATATAAAAAT
Found at i:753999 original size:17 final size:17
Alignment explanation
Indices: 753944--753999 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
753934 TATTTAAGGT
753944 ATTTT-ATATTTATATAA
1 ATTTTAATA-TTATATAA
753961 ATTTTAATA-TAT-T-A
1 ATTTTAATATTATATAA
*
753975 ATAATTAATATTATATAA
1 AT-TTTAATATTATATAA
753993 ATTTTAA
1 ATTTTAA
754000 AATACATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 3 0.09
15 7 0.22
16 6 0.19
17 10 0.31
18 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTAATATTATATAA
Found at i:757707 original size:22 final size:22
Alignment explanation
Indices: 757656--757711 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
757646 AAACCTTAAA
*
757656 CAAATAAA-TTATTTTATTATC
1 CAAATAAATTTAATTTATTATC
757677 CAAATTAAATTTAATTTATT-TC
1 CAAA-TAAATTTAATTTATTATC
*
757699 GTAAATAAATTTA
1 -CAAATAAATTTA
757712 CCATCATCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.13
22 14 0.47
23 12 0.40
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (22 bp):
CAAATAAATTTAATTTATTATC
Found at i:758960 original size:16 final size:17
Alignment explanation
Indices: 758921--758961 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
758911 ATTTAAAAAA
758921 TTAAAATTTAATTTAAGT
1 TTAAAA-TTAATTTAAGT
758939 TT-AAATTAATTTAA-T
1 TTAAAATTAATTTAAGT
758954 TTAAAATT
1 TTAAAATT
758962 TAAAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.14
16 14 0.64
17 3 0.14
18 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTAAAATTAATTTAAGT
Found at i:759082 original size:11 final size:11
Alignment explanation
Indices: 759066--759097 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
759056 TTAAATAAAA
759066 AATTTAAATTT
1 AATTTAAATTT
759077 AATTTAAATTT
1 AATTTAAATTT
759088 -A-TTAAATTT
1 AATTTAAATTT
759097 A
1 A
759098 TCGAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.40
10 1 0.05
11 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:759086 original size:34 final size:33
Alignment explanation
Indices: 759008--759094 Score: 79
Period size: 34 Copynumber: 2.5 Consensus size: 33
758998 ATATTTATAT
* * *
759008 ATTTATAATTAAATTTTAATAAAAATATTATTTTT
1 ATTTA-AATT-AATTTAAATAAAAATATTAATTTA
759043 ATTTCAAATTAATTTAAATAAAAA-ATTTAAATTTA
1 ATTT-AAATTAATTTAAATAAAAATA-TT-AATTTA
*
759078 ATTTAAATTTA-TTAAAT
1 ATTTAAATTAATTTAAAT
759095 TTATCGAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
33 7 0.16
34 21 0.47
35 16 0.36
36 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (33 bp):
ATTTAAATTAATTTAAATAAAAATATTAATTTA
Found at i:759355 original size:2 final size:2
Alignment explanation
Indices: 759348--759378 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
759338 TTTTGTTAGG
759348 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
759379 GCATGAAACA
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:766889 original size:11 final size:11
Alignment explanation
Indices: 766875--766925 Score: 56
Period size: 10 Copynumber: 5.0 Consensus size: 11
766865 ATTTTACACG
766875 TTTTTA-ATAA
1 TTTTTATATAA
766885 TTTTTATATAA
1 TTTTTATATAA
* *
766896 TTTATAT-TTA
1 TTTTTATATAA
766906 TTTTTA-AT-A
1 TTTTTATATAA
766915 TTTTTATATAA
1 TTTTTATATAA
766926 CTTATATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 7 0.21
10 16 0.47
11 11 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTTATATAA
Found at i:766920 original size:30 final size:31
Alignment explanation
Indices: 766875--766934 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
766865 ATTTTACACG
*
766875 TTTTTAATAATTTTTATATAATTTATATTTA
1 TTTTTAATAATTTTTATATAACTTATATTTA
766906 TTTTTAAT-ATTTTTATATAACTTATATTT
1 TTTTTAATAATTTTTATATAACTTATATTT
766935 TAATATTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTTTAATAATTTTTATATAACTTATATTTA
Found at i:767060 original size:25 final size:25
Alignment explanation
Indices: 766992--767060 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
766982 ATTTACATCA
766992 AATT-TTAAATATATTAAAATATTT
1 AATTATTAAATATATTAAAATATTT
* *
767016 AATTATT-TATTTAATATAAAAT-TTT
1 AATTATTAAATAT-AT-TAAAATATTT
767041 AATTATTAAATATACTTAAA
1 AATTATTAAATATA-TTAAA
767061 TAATCAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
24 7 0.19
25 19 0.53
26 10 0.28
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTATTAAATATATTAAAATATTT
Found at i:770266 original size:52 final size:52
Alignment explanation
Indices: 770188--770292 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
770178 CGGTGGAAAA
770188 CATGAGTTAAATTGATAGGCAACTTTAAAAAAAGAAAGAAGCACCAAGAGCT
1 CATGAGTTAAATTGATAGGCAACTTTAAAAAAAGAAAGAAGCACCAAGAGCT
*
770240 CATGAGTTAAATTGATAGGCAACTTTAAAAAAAGAAAGCAGCACCAAGAGCT
1 CATGAGTTAAATTGATAGGCAACTTTAAAAAAAGAAAGAAGCACCAAGAGCT
770292 C
1 C
770293 TTCATTCTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (52 bp):
CATGAGTTAAATTGATAGGCAACTTTAAAAAAAGAAAGAAGCACCAAGAGCT
Found at i:770438 original size:2 final size:2
Alignment explanation
Indices: 770431--770456 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
770421 GGATAAATGT
770431 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
770457 ATGTAACCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:773732 original size:13 final size:13
Alignment explanation
Indices: 773716--773748 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
773706 TAATATATTG
*
773716 AAATTATTTTAAA
1 AAATTAATTTAAA
773729 AAATTAATTTAAA
1 AAATTAATTTAAA
773742 AAATTAA
1 AAATTAA
773749 ATATATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATTAATTTAAA
Found at i:773955 original size:14 final size:15
Alignment explanation
Indices: 773936--773973 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
773926 AGTTTGATAT
773936 TATTAAATTTT-TTA
1 TATTAAATTTTATTA
773950 TATTAATATTTTAATTA
1 TATTAA-ATTTT-ATTA
773967 TATTAAA
1 TATTAAA
773974 ATTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 1 0.05
17 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTAAATTTTATTA
Found at i:773982 original size:17 final size:17
Alignment explanation
Indices: 773947--773989 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
773937 ATTAAATTTT
* **
773947 TTATATTAATATTTTAA
1 TTATATTAAAATTAAAA
773964 TTATATTAAAATTAAAA
1 TTATATTAAAATTAAAA
773981 TTA-ATTAAA
1 TTATATTAAA
773990 TAATATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATATTAAAATTAAAA
Found at i:774521 original size:18 final size:18
Alignment explanation
Indices: 774481--774514 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
774471 AATATTATTA
*
774481 ATAAA-TTTTTAAAAATT
1 ATAAATTTTTTAAAAAAT
774498 ATAAATTTTTTAAAAAA
1 ATAAATTTTTTAAAAAA
774515 ATTAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATTTTTTAAAAAAT
Found at i:776131 original size:3 final size:3
Alignment explanation
Indices: 776123--776151 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
776113 TAGAAATTTA
776123 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
776152 AGTTAACAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:776451 original size:23 final size:23
Alignment explanation
Indices: 776423--776468 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
776413 TAAATTATTA
**
776423 ATTATTATATTTAATATAATAAT
1 ATTATTATAAATAATATAATAAT
*
776446 ATTATTATAAATAATATATTAAT
1 ATTATTATAAATAATATAATAAT
776469 TAATTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATTATAAATAATATAATAAT
Found at i:778467 original size:103 final size:103
Alignment explanation
Indices: 778288--778494 Score: 378
Period size: 103 Copynumber: 2.0 Consensus size: 103
778278 TATTTATTTC
*
778288 AGAACTAAGGCCATTCTTTTTGCAGTTTAACAAAGTCAATGAACCTCCAGCTTAGAGAAGAAAAT
1 AGAACAAAGGCCATTCTTTTTGCAGTTTAACAAAGTCAATGAACCTCCAGCTTAGAGAAGAAAAT
778353 AAAAGATATACTACTTGACTAAATTTTTTTACTCATAT
66 AAAAGATATACTACTTGACTAAATTTTTTTACTCATAT
*
778391 AGAACAAAGGCCGTTCTTTTTGCAGTTTAACAAAGTCAATGAACCTCCAGCTTAGAGAAGAAAAT
1 AGAACAAAGGCCATTCTTTTTGCAGTTTAACAAAGTCAATGAACCTCCAGCTTAGAGAAGAAAAT
* *
778456 AAAAGATATACTACTTGACTGAATTTTTTTACTTATAT
66 AAAAGATATACTACTTGACTAAATTTTTTTACTCATAT
778494 A
1 A
778495 ACCTAATATT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (103 bp):
AGAACAAAGGCCATTCTTTTTGCAGTTTAACAAAGTCAATGAACCTCCAGCTTAGAGAAGAAAAT
AAAAGATATACTACTTGACTAAATTTTTTTACTCATAT
Found at i:780300 original size:2 final size:2
Alignment explanation
Indices: 780293--780323 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
780283 TTAGATCAAT
780293 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
780324 TACATATGCT
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:782666 original size:18 final size:18
Alignment explanation
Indices: 782645--782679 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
782635 ATGTTTAGTC
* *
782645 TTATTTATTTTTTTAAAT
1 TTATCTATTTTTATAAAT
782663 TTATCTATTTTTATAAA
1 TTATCTATTTTTATAAA
782680 CAAATGTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATCTATTTTTATAAAT
Found at i:783783 original size:12 final size:12
Alignment explanation
Indices: 783766--783800 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
783756 GATACCTATC
783766 AATAAAATATAA
1 AATAAAATATAA
783778 AATAAAATAT-A
1 AATAAAATATAA
*
783789 ATTAAAATATAA
1 AATAAAATATAA
783801 TTTATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAAAATATAA
Found at i:783796 original size:11 final size:11
Alignment explanation
Indices: 783768--783802 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
783758 TACCTATCAA
*
783768 TAAAATATAAAA
1 TAAAATAT-AAT
783780 TAAAATATAAT
1 TAAAATATAAT
783791 TAAAATATAAT
1 TAAAATATAAT
783802 T
1 T
783803 TATAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAATATAAT
Found at i:785030 original size:2 final size:2
Alignment explanation
Indices: 785025--785050 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
785015 CCAGAGAGAA
785025 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
785051 GGATGGTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:785241 original size:19 final size:19
Alignment explanation
Indices: 785217--785258 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
785207 TAATCAAAGT
*
785217 TTTTTATTTTTAA-TATATA
1 TTTTTATTTGTAATTA-ATA
785236 TTTTTATTTGTAATTAATA
1 TTTTTATTTGTAATTAATA
785255 TTTT
1 TTTT
785259 AAAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTATTTGTAATTAATA
Found at i:785592 original size:11 final size:12
Alignment explanation
Indices: 785576--785604 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
785566 ATATAAAAAT
785576 ATAATTTTTT-A
1 ATAATTTTTTAA
785587 ATAATTTTTTAA
1 ATAATTTTTTAA
785599 ATAATT
1 ATAATT
785605 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATAATTTTTTAA
Found at i:787985 original size:29 final size:29
Alignment explanation
Indices: 787952--788010 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
787942 TTTTTTATTT
*
787952 TTAATATTTATTATAATTAATTATAATAA
1 TTAATATTTATTATAATGAATTATAATAA
*
787981 TTAATATTTATTATAATGGATTATAATAA
1 TTAATATTTATTATAATGAATTATAATAA
788010 T
1 T
788011 ATATGTTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
TTAATATTTATTATAATGAATTATAATAA
Found at i:788114 original size:15 final size:16
Alignment explanation
Indices: 788094--788199 Score: 57
Period size: 18 Copynumber: 6.7 Consensus size: 16
788084 ATAGTTAAAA
788094 TAAAAATA-ATATGAT
1 TAAAAATATATATGAT
788109 TAAAAATATATATGA-
1 TAAAAATATATATGAT
*
788124 T----AT-T-TATAAT
1 TAAAAATATATATGAT
*
788134 TAAAATAAATATAATGTAAT
1 TAAAA-ATATAT-ATG--AT
788154 TAAAAATATATATGATAT
1 TAAAAATATATATG--AT
* *
788172 TATAAATATGATACGAT
1 TAAAAATAT-ATATGAT
788189 TAAAAATATAT
1 TAAAAATATAT
788200 TTATAATCAT
Statistics
Matches: 69, Mismatches: 9, Indels: 25
0.67 0.09 0.24
Matches are distributed among these distances:
9 4 0.06
10 2 0.03
11 2 0.03
15 10 0.14
16 9 0.13
17 11 0.16
18 15 0.22
19 9 0.13
20 7 0.10
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.38
Consensus pattern (16 bp):
TAAAAATATATATGAT
Found at i:788127 original size:45 final size:45
Alignment explanation
Indices: 788071--788176 Score: 160
Period size: 45 Copynumber: 2.4 Consensus size: 45
788061 AAATATGATA
* * *
788071 ATATATTATATTTATAGTTAAAATAAAAATAATATGATTAAAAAT
1 ATATATGATATTTATAATTAAAATAAAAATAATATAATTAAAAAT
* *
788116 ATATATGATATTTATAATTAAAATAAATATAATGTAATTAAAAAT
1 ATATATGATATTTATAATTAAAATAAAAATAATATAATTAAAAAT
788161 ATATATGATA-TTATAA
1 ATATATGATATTTATAA
788177 ATATGATACG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 6 0.11
45 50 0.89
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (45 bp):
ATATATGATATTTATAATTAAAATAAAAATAATATAATTAAAAAT
Found at i:788179 original size:35 final size:33
Alignment explanation
Indices: 788138--788243 Score: 99
Period size: 35 Copynumber: 3.1 Consensus size: 33
788128 TATAATTAAA
788138 ATAAATATAATGTAATTAAAAATATATATGATATT
1 ATAAATATAAT-T-ATTAAAAATATATATGATATT
** * *
788173 ATAAATATGATACGATTAAAAATATAT-TTATAATC
1 ATAAATAT-A-ATTATTAAAAATATATATGAT-ATT
* *
788208 ATAATTA-AATTATTAAAAATATATATGTTATT
1 ATAAATATAATTATTAAAAATATATATGATATT
788240 ATAA
1 ATAA
788244 TTTAATTCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
32 20 0.35
33 3 0.05
34 3 0.05
35 29 0.51
36 1 0.02
37 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (33 bp):
ATAAATATAATTATTAAAAATATATATGATATT
Found at i:788240 original size:18 final size:18
Alignment explanation
Indices: 788140--788240 Score: 56
Period size: 18 Copynumber: 5.9 Consensus size: 18
788130 TAATTAAAAT
*
788140 AAATATA-ATGTAATTAA
1 AAATATATATGTTATTAA
* *
788157 AAATATATATGATATTAT
1 AAATATATATGTTATTAA
*
788175 AAATATGATACG--ATT-A
1 AAATAT-ATATGTTATTAA
788191 AAA-ATATAT-TTA-TAA
1 AAATATATATGTTATTAA
** **
788206 TCATA-ATTAAATTATTAA
1 AAATATA-TATGTTATTAA
788224 AAATATATATGTTATTA
1 AAATATATATGTTATTA
788241 TAATTTAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 19
0.66 0.14 0.20
Matches are distributed among these distances:
14 4 0.07
15 6 0.10
16 6 0.10
17 13 0.21
18 27 0.44
19 5 0.08
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (18 bp):
AAATATATATGTTATTAA
Found at i:788244 original size:32 final size:32
Alignment explanation
Indices: 788152--788250 Score: 90
Period size: 32 Copynumber: 3.0 Consensus size: 32
788142 ATATAATGTA
* * **
788152 ATTAAAAATATATATGATATTATAAATATGATACG
1 ATTAAAAATATATATGTTATTAT-AAT-T-AAATT
* * * *
788187 ATTAAAAATATATTTATAATCATAATTAAATT
1 ATTAAAAATATATATGTTATTATAATTAAATT
*
788219 ATTAAAAATATATATGTTATTATAATTTAATT
1 ATTAAAAATATATATGTTATTATAATTAAATT
788251 CATCATAAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
32 29 0.57
33 1 0.02
34 3 0.06
35 18 0.35
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (32 bp):
ATTAAAAATATATATGTTATTATAATTAAATT
Found at i:788397 original size:15 final size:15
Alignment explanation
Indices: 788340--788386 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
788330 ATCTTTAAAT
788340 TTATAAT-AATATATA
1 TTATAATAAATATA-A
* *
788355 TTATATTATCATATAA
1 TTATAATA-AATATAA
788371 TTATAATAAATATAA
1 TTATAATAAATATAA
788386 T
1 T
788387 ATTTAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.50
16 8 0.31
17 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATAATAAATATAA
Found at i:801372 original size:44 final size:44
Alignment explanation
Indices: 801289--801372 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
801279 TATATATATA
* * * *
801289 TATATATATATGTATGTTATCACTTTTTATTTGTTTTTTTCGTT
1 TATATATATATATATATTATCACTTTTTATCTGTATTTTTCGTT
*
801333 TATATATATATATATATTATTACTATTTT-TCTGTATTTTT
1 TATATATATATATATATTATCACT-TTTTATCTGTATTTTT
801373 GTCATTATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 30 0.88
45 4 0.12
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (44 bp):
TATATATATATATATATTATCACTTTTTATCTGTATTTTTCGTT
Found at i:809852 original size:28 final size:28
Alignment explanation
Indices: 809772--809853 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
809762 TAAATATACT
* *
809772 TTTAATAAAGTAAATTAAAAACGTAACC
1 TTTAATAATGTAAATTAAAAACTTAACC
* *
809800 TTTAATGATGTAAA-TAACAACCTTAACC
1 TTTAATAATGTAAATTAA-AAACTTAACC
* *
809828 TTTAATAATGTAAATTCAAATCTTAA
1 TTTAATAATGTAAATTAAAAACTTAA
809854 TCTAAATTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
27 3 0.07
28 40 0.89
29 2 0.04
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (28 bp):
TTTAATAATGTAAATTAAAAACTTAACC
Found at i:811908 original size:25 final size:23
Alignment explanation
Indices: 811874--811929 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
811864 TTATATTTTT
*
811874 ATATGAATATTTAAAAATATATAAA
1 ATATAAATATTTAAAAATAT-T-AA
*
811899 ATATAAATATTTTAAAATATTAA
1 ATATAAATATTTAAAAATATTAA
811922 AT-TAAATA
1 ATATAAATA
811930 AATGTATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 6 0.21
23 4 0.14
24 1 0.03
25 18 0.62
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATAAATATTTAAAAATATTAA
Found at i:812851 original size:20 final size:19
Alignment explanation
Indices: 812828--812896 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 19
812818 TAAAATTTTT
812828 TATA-AAATATATTATATA
1 TATATAAATATATTATATA
* *
812846 TGTATAAATATATGTATAAA
1 TATATAAATATAT-TATATA
812866 TATATTAAAT-TA-TATATA
1 TATA-TAAATATATTATATA
* *
812884 TAAATTAATATAT
1 TATATAAATATAT
812897 ATCGATATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 4 0.10
18 13 0.32
19 8 0.20
20 10 0.25
21 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TATATAAATATATTATATA
Found at i:812856 original size:12 final size:12
Alignment explanation
Indices: 812841--812888 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
812831 AAAATATATT
812841 ATATATGTATAA
1 ATATATGTATAA
812853 ATATATGTATAA
1 ATATATGTATAA
812865 ATATAT-TA-AA
1 ATATATGTATAA
* *
812875 TTATATATATAA
1 ATATATGTATAA
812887 AT
1 AT
812889 TAATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 7 0.22
11 4 0.12
12 21 0.66
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
ATATATGTATAA
Found at i:812882 original size:14 final size:15
Alignment explanation
Indices: 812865--812898 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
812855 ATATGTATAA
812865 ATATATTAAATT-AT
1 ATATATTAAATTAAT
812879 ATATA-TAAATTAAT
1 ATATATTAAATTAAT
812893 ATATAT
1 ATATAT
812899 CGATATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATTAAATTAAT
Found at i:812894 original size:12 final size:12
Alignment explanation
Indices: 812864--812897 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
812854 TATATGTATA
812864 AATATATTAAATT
1 AATATA-TAAATT
812877 ATATATATAAATT
1 A-ATATATAAATT
812890 AATATATA
1 AATATATA
812898 TCGATATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 8 0.40
14 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATATATAAATT
Found at i:816254 original size:22 final size:21
Alignment explanation
Indices: 816229--816274 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
816219 TATATTTTTT
816229 TATTCTAAAATAA-ATATAAAAA
1 TATT-TAAAA-AATATATAAAAA
*
816251 TA-TTAAAAAATATATAAAAT
1 TATTTAAAAAATATATAAAAA
816271 TATT
1 TATT
816275 ATTAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 2 0.10
20 15 0.71
21 2 0.10
22 2 0.10
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TATTTAAAAAATATATAAAAA
Found at i:831552 original size:20 final size:21
Alignment explanation
Indices: 831527--831618 Score: 73
Period size: 22 Copynumber: 4.3 Consensus size: 21
831517 AATTAATAGA
831527 ATATATTTAAATTATATAT-T
1 ATATATTTAAATTATATATAT
* *
831547 ATATATTTTAAAATT-TAGATGT
1 ATATA-TTT-AAATTATATATAT
*
831569 ATTTA-TTAAATTTATGATATAT
1 ATATATTTAAA-TTAT-ATATAT
* *
831591 ATATATATATATATATATATAT
1 ATATATTTAAAT-TATATATAT
831613 ATATAT
1 ATATAT
831619 ATATATATGG
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
19 3 0.05
20 9 0.16
21 8 0.14
22 31 0.54
23 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
ATATATTTAAATTATATATAT
Found at i:831592 original size:2 final size:2
Alignment explanation
Indices: 831585--831626 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
831575 TAAATTTATG
831585 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
831627 GGAAAGAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:831865 original size:2 final size:2
Alignment explanation
Indices: 831860--831903 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
831850 TCCCCCCCCC
831860 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
831902 CT
1 CT
831904 ATATATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:834742 original size:16 final size:16
Alignment explanation
Indices: 834722--834753 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
834712 AAACTGCCAA
834722 AAAAAAAAACACAAAAC
1 AAAAAAAAA-ACAAAAC
834739 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
834754 TACCACAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAAAC
Found at i:836333 original size:2 final size:2
Alignment explanation
Indices: 836320--836356 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
836310 TTTGAATGTG
*
836320 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
836357 ATTTTTAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:837684 original size:48 final size:47
Alignment explanation
Indices: 837615--837847 Score: 236
Period size: 48 Copynumber: 4.9 Consensus size: 47
837605 GGGTCTGTTA
* *
837615 AACGAGAGAAGGCTTGATTCATTTGCTAACATGTTTATGATTTCAGTT
1 AACGAGAGAAGGCATGATTCATTTGCTAAC-TGTTTATGATTTCGGTT
* *** *
837663 AACGAGAGAAGGCATGTTTCATTCATTAATCT-TTT-TGATTTTGGTT
1 AACGAGAGAAGGCATGATTCATTTGCTAA-CTGTTTATGATTTCGGTT
** * *
837709 ATTGAGAGAAGACATGATTCATTTGCTAATCTGTTTATGATTTCTGTT
1 AACGAGAGAAGGCATGATTCATTTGCTAA-CTGTTTATGATTTCGGTT
* ** * *
837757 AATGAGAGATTGCATGATTCATTCGTTAATCTGTTTATGATTTCGGTT
1 AACGAGAGAAGGCATGATTCATTTGCTAA-CTGTTTATGATTTCGGTT
* * *
837805 AACAAGAGAAAGCATGATTCATTTGCTTATCTGTTTATGATTT
1 AACGAGAGAAGGCATGATTCATTTGC-TAACTGTTTATGATTT
837848 TTCTTTCCTT
Statistics
Matches: 151, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
46 34 0.23
47 6 0.04
48 108 0.72
49 3 0.02
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (47 bp):
AACGAGAGAAGGCATGATTCATTTGCTAACTGTTTATGATTTCGGTT
Found at i:837779 original size:94 final size:96
Alignment explanation
Indices: 837615--837847 Score: 303
Period size: 94 Copynumber: 2.4 Consensus size: 96
837605 GGGTCTGTTA
* *
837615 AACGAGAGAAGGCTTGATTCATTTGCTAA-CATGTTTATGATTTCAGTTAACGAGAGAAGGCATG
1 AACGAGAGAAGACATGATTCATTTGCTAATC-TGTTTATGATTTCAGTTAACGAGAGAAGGCATG
* *
837679 TTTCATTCATTAATCT-TTT-TGATTTTGGTT
65 ATTCATTCATTAATCTGTTTATGATTTCGGTT
** * * **
837709 ATTGAGAGAAGACATGATTCATTTGCTAATCTGTTTATGATTTCTGTTAATGAGAGATTGCATGA
1 AACGAGAGAAGACATGATTCATTTGCTAATCTGTTTATGATTTCAGTTAACGAGAGAAGGCATGA
*
837774 TTCATTCGTTAATCTGTTTATGATTTCGGTT
66 TTCATTCATTAATCTGTTTATGATTTCGGTT
* *
837805 AACAAGAGAA-AGCATGATTCATTTGCTTATCTGTTTATGATTT
1 AACGAGAGAAGA-CATGATTCATTTGCTAATCTGTTTATGATTT
837848 TTCTTTCCTT
Statistics
Matches: 120, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
94 68 0.57
95 5 0.04
96 47 0.39
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (96 bp):
AACGAGAGAAGACATGATTCATTTGCTAATCTGTTTATGATTTCAGTTAACGAGAGAAGGCATGA
TTCATTCATTAATCTGTTTATGATTTCGGTT
Found at i:839105 original size:2 final size:2
Alignment explanation
Indices: 839098--839133 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
839088 GAATTTCTTC
839098 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
839134 TCTTGCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:839308 original size:17 final size:18
Alignment explanation
Indices: 839286--839329 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
839276 TTAATTAGAT
*
839286 TTATTTGAT-ATAAATTA
1 TTATTTAATAATAAATTA
*
839303 TTATTTAATAATAAATTT
1 TTATTTAATAATAAATTA
839321 TGTATTTAA
1 T-TATTTAA
839330 ATTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATTTAATAATAAATTA
Found at i:839382 original size:26 final size:23
Alignment explanation
Indices: 839331--839373 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
839321 TGTATTTAAA
839331 TTTAATAATAAAAATATATAATT
1 TTTAATAATAAAAATATATAATT
839354 TTTAATAAT-AAAATATATAA
1 TTTAATAATAAAAATATATAA
839374 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTAATAATAAAAATATATAATT
Found at i:840377 original size:2 final size:2
Alignment explanation
Indices: 840370--840419 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
840360 AAGCCCACAA
840370 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
840412 AT AT AT AT
1 AT AT AT AT
840420 TTGTGCCAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:841459 original size:2 final size:2
Alignment explanation
Indices: 841452--841476 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
841442 ATACATAGAG
841452 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
841477 GTACATGTTC
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:842029 original size:32 final size:32
Alignment explanation
Indices: 841984--842052 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
841974 TATACATGTA
* ** *
841984 GTATGCATAATAATGCATGTGTATATGTATAT
1 GTATACATAATAATGCATGTAAATATGTATAC
*
842016 GTATACATGATAATGCATGTAAATATGTATAC
1 GTATACATAATAATGCATGTAAATATGTATAC
842048 GTATA
1 GTATA
842053 TGTATATGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (32 bp):
GTATACATAATAATGCATGTAAATATGTATAC
Found at i:842057 original size:6 final size:6
Alignment explanation
Indices: 842038--842084 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
842028 ATGCATGTAA
* * * *
842038 ATATGT ATACGT ATATGT ATATGT CTATGC ATATGG ATATGT ATATG
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATG
842085 ATTAATGTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (6 bp):
ATATGT
Found at i:843207 original size:2 final size:2
Alignment explanation
Indices: 843194--843232 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
843184 TAAGGGTTTC
*
843194 AT AT AC 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
843233 ACGAAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:843734 original size:16 final size:17
Alignment explanation
Indices: 843709--843750 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
843699 TATTTAAAAA
*
843709 ATAATATTTAATA-ATT
1 ATAATTTTTAATATATT
*
843725 TTAATTTTTAATATATT
1 ATAATTTTTAATATATT
843742 ATAATTTTT
1 ATAATTTTT
843751 TTTATTCTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTTAATATATT
Found at i:845598 original size:23 final size:21
Alignment explanation
Indices: 845564--845611 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
845554 TTAAAAAATT
* *
845564 TATATTCAAATAAATTTTTAA
1 TATATTCAAATAAACTCTTAA
845585 TATATGTCTAAATAAACTCTTAA
1 TATAT-TC-AAATAAACTCTTAA
845608 TATA
1 TATA
845612 AATTAATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 2 0.09
23 16 0.70
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (21 bp):
TATATTCAAATAAACTCTTAA
Found at i:851690 original size:29 final size:28
Alignment explanation
Indices: 851636--851697 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
851626 TTTTTTATTT
851636 AATA-TAAATTTAAAATATAAAAATTAA
1 AATATTAAATTTAAAATATAAAAATTAA
851663 AATATTAAATTTAATAATA-AATAAATTAA
1 AATATTAAATTTAA-AATATAA-AAATTAA
851692 AATATT
1 AATATT
851698 TTTTTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 4 0.12
28 11 0.34
29 17 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATATTAAATTTAAAATATAAAAATTAA
Found at i:852138 original size:27 final size:27
Alignment explanation
Indices: 852101--852152 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
852091 AATATATATA
852101 ATAAGACTAGACTGATTAATTGAGTAG
1 ATAAGACTAGACTGATTAATTGAGTAG
* *
852128 ATAAGATTAGATTGATTAATTGAGT
1 ATAAGACTAGACTGATTAATTGAGT
852153 CATTTCGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (27 bp):
ATAAGACTAGACTGATTAATTGAGTAG
Found at i:852222 original size:16 final size:16
Alignment explanation
Indices: 852195--852238 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
852185 TTTTTGAGTT
*
852195 ATTTTCGAATTCAGATC
1 ATTTT-GAATTCAAATC
*
852212 GTTTTGAATTCAAATC
1 ATTTTGAATTCAAATC
852228 ATTTTGAATTC
1 ATTTTGAATTC
852239 GAATAATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (16 bp):
ATTTTGAATTCAAATC
Found at i:852247 original size:16 final size:16
Alignment explanation
Indices: 852213--852247 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
852203 ATTCAGATCG
*
852213 TTTTGAATTCAAATCA
1 TTTTGAATTCAAATAA
*
852229 TTTTGAATTCGAATAA
1 TTTTGAATTCAAATAA
852245 TTT
1 TTT
852248 CAGATTCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (16 bp):
TTTTGAATTCAAATAA
Found at i:852342 original size:14 final size:14
Alignment explanation
Indices: 852325--852352 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
852315 TTTTAATCAA
852325 TTAAGTTTAACATT
1 TTAAGTTTAACATT
852339 TTAAGTTTAACATT
1 TTAAGTTTAACATT
852353 CAAATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
TTAAGTTTAACATT
Found at i:852594 original size:22 final size:22
Alignment explanation
Indices: 852527--852599 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
852517 AAAAAATAAT
*
852527 ATTT-AAATTTAAATTTAAATC
1 ATTTCAAATTTGAATTTAAATC
**
852548 ATTTTGAATTAATG-ATTTAAATC
1 ATTTCAAATT--TGAATTTAAATC
*
852571 ATTTCAAATTTGAATTCAAATC
1 ATTTCAAATTTGAATTTAAATC
852593 ATTTCAA
1 ATTTCAA
852600 GTTCAAATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 6 0.14
22 19 0.44
23 17 0.40
24 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (22 bp):
ATTTCAAATTTGAATTTAAATC
Found at i:852628 original size:16 final size:17
Alignment explanation
Indices: 852609--852676 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 17
852599 AGTTCAAATC
852609 ATTTCGAATTCTG-ATA
1 ATTTCGAATTCTGAATA
* * * *
852625 ATTTTGAGTTC-GGATC
1 ATTTCGAATTCTGAATA
* *
852641 ATTTTGAATT-TGAATT
1 ATTTCGAATTCTGAATA
852657 ATTTCGAATTC-GAATA
1 ATTTCGAATTCTGAATA
852673 ATTT
1 ATTT
852677 TTAGATTCGG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
15 1 0.02
16 40 0.98
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (17 bp):
ATTTCGAATTCTGAATA
Found at i:859519 original size:19 final size:21
Alignment explanation
Indices: 859495--859541 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
859485 TTTGGTGATT
859495 TTTTTAAT-AAATAATT-ATA
1 TTTTTAATAAAATAATTAATA
* *
859514 TTTTTATTAAAATTATTAATA
1 TTTTTAATAAAATAATTAATA
859535 TTTTTAA
1 TTTTTAA
859542 ATAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 7 0.30
21 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTAATAAAATAATTAATA
Found at i:859582 original size:19 final size:19
Alignment explanation
Indices: 859552--859598 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
859542 ATAATTAAAA
* *
859552 TATTTATATATTTTTAATTT
1 TATTTAT-TATTATAAATTT
859572 TATTTATTATTATAAATTT
1 TATTTATTATTATAAATTT
859591 TATTTATT
1 TATTTATT
859599 TAAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTATTATTATAAATTT
Found at i:860354 original size:18 final size:17
Alignment explanation
Indices: 860306--860355 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
860296 AAAGAAATAT
* *
860306 TAAAAAATAAATTAAAAA
1 TAAAAAAT-ATTTTAAAA
860324 TAAAAAATATTTTAAAA
1 TAAAAAATATTTTAAAA
*
860341 TAAAATATACTTTTA
1 TAAAAAATA-TTTTA
860356 TTATGTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAAATATTTTAAAA
Found at i:860687 original size:33 final size:32
Alignment explanation
Indices: 860595--860687 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 32
860585 ATTATATTAA
*
860595 AAATATTAAATATTTA-TAT-AATTTTTAACGT
1 AAATATT-AATATTTATTATAAATTTTTAACAT
** * *
860626 ATTTATATAATATATATAATATAATTTTTAACAT
1 AAATAT-TAATATTTATTATA-AATTTTTAACAT
860660 AAATATTAATATTTATTATAAACTTTTT
1 AAATATTAATATTTATTATAAA-TTTTT
860688 TTAAAATTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
31 11 0.23
32 5 0.10
33 17 0.35
34 15 0.31
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (32 bp):
AAATATTAATATTTATTATAAATTTTTAACAT
Found at i:860926 original size:72 final size:70
Alignment explanation
Indices: 860826--860958 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 70
860816 TATTCATTAA
* *
860826 AATTTATATATTATATTAATTTTATTAATTACTTTTTAAATTCTATTTTAATTATTTTTAATAAA
1 AATTTATATAATATATTAATTTTATTAATTAC-TTTTAAATTATATTTTAATT-TTTTTAATAAA
860891 ATCATTG
64 ATCATTG
860898 AATTTAATATAATATATT-ATTTTATTAATTACTTTTAAATTATATTTTAATTTTTTTAATA
1 AATTT-ATATAATATATTAATTTTATTAATTACTTTTAAATTATATTTTAATTTTTTTAATA
860959 TAATTTGAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
70 9 0.16
71 19 0.33
72 19 0.33
73 11 0.19
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (70 bp):
AATTTATATAATATATTAATTTTATTAATTACTTTTAAATTATATTTTAATTTTTTTAATAAAAT
CATTG
Found at i:861163 original size:26 final size:27
Alignment explanation
Indices: 861104--861166 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
861094 CAAGTTTAAA
*
861104 ATATTAATATTATAAATTTTAAAATAT
1 ATATTTATATTATAAATTTTAAAATAT
* *
861131 ATATTTATATT-T-AATTTTAATTATTT
1 ATATTTATATTATAAATTTTAA-AATAT
861157 ATATTTATAT
1 ATATTTATAT
861167 AATTATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.25
26 14 0.44
27 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATTTATATTATAAATTTTAAAATAT
Found at i:861175 original size:20 final size:18
Alignment explanation
Indices: 861126--861184 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 18
861116 TAAATTTTAA
861126 AATA-TATATTTATATTT
1 AATATTATATTTATATTT
*
861143 AATTTTAATTATTTATATTT
1 AATATT-A-TATTTATATTT
861163 -ATA-TA-A-TTATATTT
1 AATATTATATTTATATTT
861177 AATATTAT
1 AATATTAT
861185 CAAATTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 8 0.24
15 4 0.12
16 2 0.06
17 4 0.12
18 2 0.06
19 3 0.09
20 11 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATATTATATTTATATTT
Found at i:861941 original size:29 final size:28
Alignment explanation
Indices: 861899--861954 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
861889 ATTTGATATA
* *
861899 AATTTATTTTTATACTTAAAAATTAAAT
1 AATTTATTATTATAATTAAAAATTAAAT
*
861927 AATTTAATTATTATAATTTAAAATTAAA
1 AATTT-ATTATTATAATTAAAAATTAAA
861955 GTAGAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTTATTATTATAATTAAAAATTAAAT
Found at i:862934 original size:16 final size:15
Alignment explanation
Indices: 862913--862956 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
862903 AATTTATTAA
862913 AATAAAATAAAGTTTT
1 AATAAAATAAA-TTTT
862929 AATAAAATAATTATTTT
1 AATAAAATAA--ATTTT
*
862946 ATTAAAATAAA
1 AATAAAATAAA
862957 ATAAAGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.04
16 10 0.40
17 13 0.52
18 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
AATAAAATAAATTTT
Found at i:863538 original size:25 final size:23
Alignment explanation
Indices: 863510--863572 Score: 56
Period size: 25 Copynumber: 2.7 Consensus size: 23
863500 GTTTTAAGTG
863510 TAATTTACTTTTTAAAATTTATA
1 TAATTTACTTTTTAAAATTTATA
* **
863533 CTTAATATTA-ATGGTAAAATTTATA
1 --TAAT-TTACTTTTTAAAATTTATA
*
863558 AAATTTACTTTTTAA
1 TAATTTACTTTTTAA
863573 TTACTTTGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
22 3 0.10
23 7 0.24
25 16 0.55
26 3 0.10
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (23 bp):
TAATTTACTTTTTAAAATTTATA
Found at i:863689 original size:22 final size:22
Alignment explanation
Indices: 863661--863703 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
863651 ATTATTAAAA
863661 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
863683 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
863704 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:866433 original size:60 final size:60
Alignment explanation
Indices: 866335--866448 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
866325 ACATGTCATG
* *
866335 GAATGAGCACTTCTCATTCGAATACGAGGGAATTGACTACGTAGGTCAAATTCCGTCTTA
1 GAATAAGCACTTCTCATTCGAATACGAGGGAATTGACTACGTAGATCAAATTCCGTCTTA
* * * *
866395 GAATAAGCACTTGTCATTTGAATACGATGGAATTGACTACTTAGATCAAATTCC
1 GAATAAGCACTTCTCATTCGAATACGAGGGAATTGACTACGTAGATCAAATTCC
866449 TTTTAGATCG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (60 bp):
GAATAAGCACTTCTCATTCGAATACGAGGGAATTGACTACGTAGATCAAATTCCGTCTTA
Found at i:870674 original size:4 final size:4
Alignment explanation
Indices: 870632--870657 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
870622 ATATTTTATT
870632 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
870658 TTTTTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:870857 original size:13 final size:13
Alignment explanation
Indices: 870839--870871 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
870829 ATCCGAATGC
870839 TTATTTAAAAATT
1 TTATTTAAAAATT
870852 TTATTT-AAAATT
1 TTATTTAAAAATT
*
870864 TGATTTAA
1 TTATTTAA
870872 TCTAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
TTATTTAAAAATT
Found at i:870928 original size:18 final size:18
Alignment explanation
Indices: 870905--870945 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
870895 AAAATAATAA
*
870905 ATATTAAT-TTATTTTAAT
1 ATATTAATATT-TTTAAAT
870923 ATATTAATATTTTTAAAT
1 ATATTAATATTTTTAAAT
870941 ATATT
1 ATATT
870946 TTATTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATTAATATTTTTAAAT
Found at i:870945 original size:28 final size:30
Alignment explanation
Indices: 870914--870970 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
870904 AATATTAATT
870914 TATTTTAATATATT-AATA-T-TTTTAAATA
1 TATTTTAATA-ATTAAATATTATTTTAAATA
*
870942 TATTTTATTAATTAAATATTATTTTAAAT
1 TATTTTAATAATTAAATATTATTTTAAAT
870971 TTAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 3 0.12
28 13 0.52
29 1 0.04
30 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TATTTTAATAATTAAATATTATTTTAAATA
Found at i:870974 original size:18 final size:18
Alignment explanation
Indices: 870934--870976 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
870924 TATTAATATT
870934 TTTAAATATATTTTATTAA
1 TTTAAATATATTTTA-TAA
870953 -TTAAATATTATTTTA-AA
1 TTTAAATA-TATTTTATAA
870970 TTTAAAT
1 TTTAAAT
870977 TTTTTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATATATTTTATAA
Done.