Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 157 of 163
Found at i:44177158 original size:26 final size:25
Alignment explanation
Indices: 44177106--44177197 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 25
44177096 ATTTTTTAAA
*
44177106 TTTTAAAAATTCAAAAA-AGTTATAAT
1 TTTTAAAAATT-AAAAATA-TTAAAAT
44177132 TTTTAAAAATTAAAAATCATTAAAAT
1 TTTTAAAAATTAAAAAT-ATTAAAAT
* ** * *
44177158 TATTAAAAATTTATAATTTTTTTAAAT
1 TTTTAAAAA-TTA-AAAATATTAAAAT
44177185 TTTTAAAAATTAA
1 TTTTAAAAATTAA
44177198 TTAAATGCTG
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
25 6 0.11
26 28 0.51
27 18 0.33
28 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (25 bp):
TTTTAAAAATTAAAAATATTAAAAT
Found at i:44184737 original size:24 final size:24
Alignment explanation
Indices: 44184710--44184761 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
44184700 TTTTTAGAAG
* *
44184710 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
* *
44184734 ATTTGGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
44184758 ATTT
1 ATTT
44184762 GACTTACGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:44184762 original size:24 final size:24
Alignment explanation
Indices: 44184717--44184762 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
44184707 AAGATTTAGT
*
44184717 ATTTATTAGTATAATATATTTGGC
1 ATTTATTAGCATAATATATTTGGC
*
44184741 ATTTATTAGCATAATTTATTTG
1 ATTTATTAGCATAATATATTTG
44184763 ACTTACGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTGGC
Found at i:44189691 original size:18 final size:18
Alignment explanation
Indices: 44189668--44189715 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
44189658 CCATTGACCA
**
44189668 CTCCTCTCCCCGAGATTG
1 CTCCTCTCCCCGAGATCC
* *
44189686 CTCCTCTGCCCAAGATCC
1 CTCCTCTCCCCGAGATCC
*
44189704 CTCCTTTCCCCG
1 CTCCTCTCCCCG
44189716 GAGTCCCTTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.50, G:0.12, T:0.27
Consensus pattern (18 bp):
CTCCTCTCCCCGAGATCC
Found at i:44191041 original size:60 final size:61
Alignment explanation
Indices: 44190966--44191167 Score: 155
Period size: 61 Copynumber: 3.3 Consensus size: 61
44190956 TATCTCATAT
* *
44190966 CTTTTAAATCTTTTTAATTTCTTTTTTTATACCCTTAATAACATATATTTTACCAATTTAC
1 CTTTAAAATCTTTTTAATTTCATTTTTTATACCCTTAATAACATATATTTTACCAATTTAC
* * * ** * * * ** * * *
44191027 CTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTGATTTCCCT-T-CTTTGCTC-ATATTA
1 CTTTAAAATCTTTTTAATTTCATTTTTTATA--C-CCTTAATAACATATATTTTAC-CAAT-TTA
44191089 -
61 C
* *
44191089 -TTT-AAATCTTTTTAATTTCCTTTTTTATACCCTTAATAATATATATTTTACCAATTTAC
1 CTTTAAAATCTTTTTAATTTCATTTTTTATACCCTTAATAACATATATTTTACCAATTTAC
*
44191148 CTTTAAAATCTTTTAAATTT
1 CTTTAAAATCTTTTTAATTT
44191168 AAATTTGCAT
Statistics
Matches: 99, Mismatches: 31, Indels: 22
0.65 0.20 0.14
Matches are distributed among these distances:
57 5 0.05
58 6 0.06
59 6 0.06
60 23 0.23
61 41 0.41
62 6 0.06
63 6 0.06
64 6 0.06
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (61 bp):
CTTTAAAATCTTTTTAATTTCATTTTTTATACCCTTAATAACATATATTTTACCAATTTAC
Found at i:44191064 original size:121 final size:121
Alignment explanation
Indices: 44190939--44191181 Score: 427
Period size: 121 Copynumber: 2.0 Consensus size: 121
44190929 AAAAAAAACA
* *
44190939 CACGTGATTTTCCTTCTTAT-CTCATATCT-TTTAAATCTTTTTAATTTCTTTTTTTATACCCTT
1 CACGTGATTTCCCTTCTT-TGCTCATAT-TATTTAAATCTTTTTAATTTCCTTTTTTATACCCTT
44191002 AATAACATATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGT
64 AATAACATATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGT
44191060 CACGTGATTTCCCTTCTTTGCTCATATTATTTAAATCTTTTTAATTTCCTTTTTTATACCCTTAA
1 CACGTGATTTCCCTTCTTTGCTCATATTATTTAAATCTTTTTAATTTCCTTTTTTATACCCTTAA
*
44191125 TAATATATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGT
66 TAACATATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGT
44191181 C
1 C
44191182 TACCTTTCTT
Statistics
Matches: 117, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
120 2 0.02
121 115 0.98
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.51
Consensus pattern (121 bp):
CACGTGATTTCCCTTCTTTGCTCATATTATTTAAATCTTTTTAATTTCCTTTTTTATACCCTTAA
TAACATATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGT
Found at i:44193940 original size:2 final size:2
Alignment explanation
Indices: 44193933--44193964 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
44193923 AGTTTCATAA
44193933 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44193965 ATCGAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44199336 original size:27 final size:27
Alignment explanation
Indices: 44199284--44199334 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
44199274 CGATTGGTTG
*
44199284 AATTACTTAAATAATTCAACTTAAATA
1 AATTACTTAAATAATTCAAATTAAATA
* *
44199311 AATTATTTAAA-AATTTAAATTAAA
1 AATTACTTAAATAATTCAAATTAAA
44199335 ATCAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTACTTAAATAATTCAAATTAAATA
Found at i:44213994 original size:161 final size:161
Alignment explanation
Indices: 44213724--44214218 Score: 794
Period size: 161 Copynumber: 3.1 Consensus size: 161
44213714 AAAAGTGAAA
* * * *
44213724 CAAGCTTAAACTTTTGAGACTTTCAACTCGAGCTAGGCTTGATAACACCCCTAATTAGTTTTAAA
1 CAAGTTTAAACTTTTGAGACTTTCAACTCGAGCTCGGCTTGATAACACCCCTAATTAGCTTGAAA
* *
44213789 TATGTGTTGATAAGAAAGTTTTAATCAAGTGAGATAGATTATTATTTCGAGTTGAATTCGAACTT
66 TATGTGTTGATAAGAAAGGTTTAATCAAGTGAGATAGATTATTATTTCGAGTCGAATTCGAACTT
*
44213854 TAAAAGTGAAACTATACCGAGCTTTGTGTCT
131 TAAAAGTGAAACTAGACCGAGCTTTGTGTCT
* **
44213885 CAAGTTTAAACTCTTGAGACTTTCAACTTAAGCTCGGCTTGATAACACCCCTAATTAGCTTGAAA
1 CAAGTTTAAACTTTTGAGACTTTCAACTCGAGCTCGGCTTGATAACACCCCTAATTAGCTTGAAA
* * * * *
44213950 TATGTGTTGATAAGACAGGGTTAATCAAGTGAGATCGATTATTATCTCAAGTCGAATTCGAACTT
66 TATGTGTTGATAAGAAAGGTTTAATCAAGTGAGATAGATTATTATTTCGAGTCGAATTCGAACTT
* * *
44214015 TAAAAGAGAAACTAGACTGAGCTTTATGTCT
131 TAAAAGTGAAACTAGACCGAGCTTTGTGTCT
*
44214046 CAAGTTTAAACTTTTGAGACTTTCAACTCGAGCTC-GCTTGAGAACACCCCTAATTAGCTTGAAA
1 CAAGTTTAAACTTTTGAGACTTTCAACTCGAGCTCGGCTTGATAACACCCCTAATTAGCTTGAAA
*
44214110 TATGTGTTGATAAGAAAGGTTTAATCAAGTGAGATAGATTATTATTTCGACTCGAATTCGAACTT
66 TATGTGTTGATAAGAAAGGTTTAATCAAGTGAGATAGATTATTATTTCGAGTCGAATTCGAACTT
44214175 TAAAAGTGAAACTAGACCGAGCTTTGTGTCT
131 TAAAAGTGAAACTAGACCGAGCTTTGTGTCT
*
44214206 CAAGTTTCAACTT
1 CAAGTTTAAACTT
44214219 AATCTCAGCT
Statistics
Matches: 302, Mismatches: 32, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
160 127 0.42
161 175 0.58
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (161 bp):
CAAGTTTAAACTTTTGAGACTTTCAACTCGAGCTCGGCTTGATAACACCCCTAATTAGCTTGAAA
TATGTGTTGATAAGAAAGGTTTAATCAAGTGAGATAGATTATTATTTCGAGTCGAATTCGAACTT
TAAAAGTGAAACTAGACCGAGCTTTGTGTCT
Found at i:44216531 original size:12 final size:12
Alignment explanation
Indices: 44216516--44216541 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44216506 ATACACTAAA
44216516 AAATATTAAAAC
1 AAATATTAAAAC
44216528 AAATATTAAAAC
1 AAATATTAAAAC
44216540 AA
1 AA
44216542 CAAATAAATT
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:44216574 original size:18 final size:17
Alignment explanation
Indices: 44216529--44216575 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
44216519 TATTAAAACA
*
44216529 AATATTAAAACAACAAAT
1 AATATTAAAA-ATCAAAT
*
44216547 AA-ATTGAAAATCTAAAT
1 AATATTAAAAATC-AAAT
44216564 AATATTAAAAAT
1 AATATTAAAAAT
44216576 GACAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.08
17 12 0.50
18 10 0.42
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (17 bp):
AATATTAAAAATCAAAT
Found at i:44233669 original size:3 final size:3
Alignment explanation
Indices: 44233661--44233686 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44233651 GGATAATAGC
44233661 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
44233687 CGAGTACCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:44237335 original size:28 final size:28
Alignment explanation
Indices: 44237274--44237335 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
44237264 AAAGAATAGG
* *
44237274 TTTTGTTTTTAATGGAAAGAATAAGTTA
1 TTTTTTTTTTAATGGAAAGAATAAGATA
* *
44237302 TGTTTTTTTTAATGGAAATAATCAA-ATA
1 TTTTTTTTTTAATGGAAAGAAT-AAGATA
44237330 TTTTTT
1 TTTTTT
44237336 ATTTGTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.52
Consensus pattern (28 bp):
TTTTTTTTTTAATGGAAAGAATAAGATA
Found at i:44237665 original size:30 final size:30
Alignment explanation
Indices: 44237612--44237739 Score: 152
Period size: 30 Copynumber: 4.3 Consensus size: 30
44237602 TAAAATTATT
* * *
44237612 TTTGACCCCCAAAGTTTT-TAAAAAATCAAA
1 TTTGACCCCTAAA-TTTTCCAAAAATTCAAA
* *
44237642 TTTCACCCTTAAATTTTCCAAAAATTCAAA
1 TTTGACCCCTAAATTTTCCAAAAATTCAAA
*
44237672 TTTGACCCCTAAATTTTCCAAAAATTCAAG
1 TTTGACCCCTAAATTTTCCAAAAATTCAAA
* *
44237702 TTTAACCCCTAAAGTTTT-CAAAAATTAAAA
1 TTTGACCCCTAAA-TTTTCCAAAAATTCAAA
44237732 TTTGACCC
1 TTTGACCC
44237740 TATTTTAATG
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
29 4 0.05
30 76 0.90
31 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.34
Consensus pattern (30 bp):
TTTGACCCCTAAATTTTCCAAAAATTCAAA
Found at i:44241060 original size:30 final size:29
Alignment explanation
Indices: 44241026--44241107 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
44241016 GATACATAAT
*
44241026 TTTGATTTGGTGCAATTATACGCATGAAA
1 TTTGATTTGGTTCAATTATACGCATGAAA
* * *
44241055 CTTTGATTGTGGTTCAAATGTATGCATGAAA
1 -TTTGATT-TGGTTCAATTATACGCATGAAA
* *
44241086 TTTTATTTTGGTTCAATCATAC
1 TTTGA-TTTGGTTCAATTATAC
44241108 ACGTTCAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
30 21 0.51
31 20 0.49
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (29 bp):
TTTGATTTGGTTCAATTATACGCATGAAA
Found at i:44241312 original size:31 final size:29
Alignment explanation
Indices: 44241242--44241312 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
44241232 AAATCAAATT
*
44241242 TTCATGTATGAAATTACACAAAATCAACA
1 TTCATGTATAAAATTACACAAAATCAACA
* *
44241271 TTCATATATAAAATTACACATTAAACTTAA-A
1 TTCATGTATAAAATTACACA--AAA-TCAACA
44241302 TTCATGTATAA
1 TTCATGTATAA
44241313 TTTTGCGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.51
31 14 0.40
32 3 0.09
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (29 bp):
TTCATGTATAAAATTACACAAAATCAACA
Found at i:44242597 original size:18 final size:17
Alignment explanation
Indices: 44242566--44242604 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
44242556 TTTATTAATT
44242566 TTATAATATATTATATAA
1 TTATAATATATTATAT-A
* *
44242584 TTATATTATTTTATATA
1 TTATAATATATTATATA
44242601 TTAT
1 TTAT
44242605 GTGAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATAATATATTATATA
Found at i:44254417 original size:16 final size:18
Alignment explanation
Indices: 44254386--44254424 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
44254376 AAATACTATC
44254386 AAATTAAAATTATATTTT
1 AAATTAAAATTATATTTT
44254404 AAATT-AAA-TATATTTT
1 AAATTAAAATTATATTTT
44254420 AAATT
1 AAATT
44254425 GAAGATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.62
17 3 0.14
18 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAAAATTATATTTT
Found at i:44255520 original size:37 final size:36
Alignment explanation
Indices: 44255418--44255520 Score: 82
Period size: 37 Copynumber: 2.8 Consensus size: 36
44255408 AGTACGAATG
44255418 CAAAATCGAAGAGAGCATTATTTAGGAATAATGGCAA
1 CAAAATCGAAGAGAGCATTA-TTAGGAATAATGGCAA
* * ***** * *
44255455 AAAAATAG-ACCTCCCATCCCATTCGGAATAATGGCAA
1 CAAAATCGAAGAGAGCAT--TATTAGGAATAATGGCAA
44255492 CAAAATCGAAGAGAGCATTATGTAGGAAT
1 CAAAATCGAAGAGAGCATTAT-TAGGAAT
44255521 TGCTTTACAG
Statistics
Matches: 44, Mismatches: 18, Indels: 8
0.63 0.26 0.11
Matches are distributed among these distances:
36 6 0.14
37 33 0.75
38 5 0.11
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (36 bp):
CAAAATCGAAGAGAGCATTATTAGGAATAATGGCAA
Found at i:44257427 original size:6 final size:6
Alignment explanation
Indices: 44257416--44257444 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
44257406 GAGTGGGGAG
44257416 AGAGGT AGAGGT AGAGGT AGAGGT AGAGG
1 AGAGGT AGAGGT AGAGGT AGAGGT AGAGG
44257445 GACTGTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.52, T:0.14
Consensus pattern (6 bp):
AGAGGT
Found at i:44259284 original size:4 final size:4
Alignment explanation
Indices: 44259277--44259315 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
44259267 ACAAGAAAAA
*
44259277 AAAG AAAG AAAG AAAG AAAG AAAG AGAGG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AA
44259316 GAAGGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:44259295 original size:21 final size:22
Alignment explanation
Indices: 44259269--44259315 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
44259259 GCAAATAAAC
44259269 AAGAAAAAAAAGA-AAGAAAGA
1 AAGAAAAAAAAGAGAAGAAAGA
* *
44259290 AAG-AAAGAAAGAGAGGAAAGA
1 AAGAAAAAAAAGAGAAGAAAGA
44259311 AAGAA
1 AAGAA
44259316 GAAGGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 8 0.36
21 13 0.59
22 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAAAGAGAAGAAAGA
Found at i:44259413 original size:19 final size:19
Alignment explanation
Indices: 44259368--44259413 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
44259358 GTATGGTATC
*
44259368 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
**
44259387 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCGTATTTAA
44259407 TTTTTAA
1 TTTTTAA
44259414 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Found at i:44262237 original size:14 final size:14
Alignment explanation
Indices: 44262218--44262269 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
44262208 TGATTTAGTA
*
44262218 TTTAGGGTTTTAAG
1 TTTAAGGTTTTAAG
*
44262232 TTTAGGGTTTTAAG
1 TTTAAGGTTTTAAG
*
44262246 TTTAAGATTTTAAG
1 TTTAAGGTTTTAAG
44262260 TTTAAGGTTT
1 TTTAAGGTTT
44262270 AGGGTTTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (14 bp):
TTTAAGGTTTTAAG
Found at i:44262276 original size:28 final size:27
Alignment explanation
Indices: 44262225--44262284 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
44262215 GTATTTAGGG
*
44262225 TTTTAAGTTTAGGGTTTTAAGTTTAAGA
1 TTTTAAGTTTAAGGTTTTAAGTTT-AGA
*
44262253 TTTTAAGTTTAAGG-TTTAGGGTTTAGA
1 TTTTAAGTTTAAGGTTTTA-AGTTTAGA
44262280 TTTTA
1 TTTTA
44262285 GGGTTTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.52
Consensus pattern (27 bp):
TTTTAAGTTTAAGGTTTTAAGTTTAGA
Found at i:44262657 original size:45 final size:45
Alignment explanation
Indices: 44262527--44262661 Score: 207
Period size: 45 Copynumber: 3.0 Consensus size: 45
44262517 CGGAGGAGTA
* * * **
44262527 GAGTATTGCGGTGGCTCGTCAAGCTCAGCCTGATATCCTTCCCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
*
44262572 GAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
*
44262617 GAGTAGTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
44262662 TATGAGTTAG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.31
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
Found at i:44264452 original size:47 final size:47
Alignment explanation
Indices: 44264401--44264490 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
44264391 AATACATAAG
*
44264401 TTTACCAATATAATACAAAA-ATAATAATTAAATACCAAAATGGATTA
1 TTTACCAAAATAATACAAAATAT-ATAATTAAATACCAAAATGGATTA
* ** * *
44264448 TTTACTAAAATGGTACAAAATATATATTTATATACCAAAATGG
1 TTTACCAAAATAATACAAAATATATAATTAAATACCAAAATGG
44264491 TATCCACACA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
47 34 0.94
48 2 0.06
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (47 bp):
TTTACCAAAATAATACAAAATATATAATTAAATACCAAAATGGATTA
Found at i:44264590 original size:16 final size:16
Alignment explanation
Indices: 44264569--44264618 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
44264559 TGATGGAGAT
*
44264569 ATTATTTTGGTAATTA
1 ATTATTTTGATAATTA
*
44264585 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
44264600 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
44264615 ATTA
1 ATTA
44264619 GCTAGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:44265011 original size:12 final size:13
Alignment explanation
Indices: 44264982--44265014 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
44264972 TTTCTTTCTC
44264982 ATTTTATTAAACA
1 ATTTTATTAAACA
44264995 ATTTTATTAAA-A
1 ATTTTATTAAACA
44265007 ATTTTATT
1 ATTTTATT
44265015 TTATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTTATTAAACA
Found at i:44269588 original size:21 final size:21
Alignment explanation
Indices: 44269559--44269598 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44269549 TTTTTATCCT
* *
44269559 AAACCTTAAACTCTAAACCCC
1 AAACATTAAACCCTAAACCCC
44269580 AAACATTAAACCCTAAACC
1 AAACATTAAACCCTAAACC
44269599 TCAAGCCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.17
Consensus pattern (21 bp):
AAACATTAAACCCTAAACCCC
Found at i:44269746 original size:22 final size:23
Alignment explanation
Indices: 44269714--44269759 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
44269704 AGGTTCAATG
44269714 TTAAGGGTTTAA-AGTTTAGGGTT
1 TTAAGGGTTTAATA-TTTAGGGTT
44269737 TTAA-GGTTTAATATTTAGGGTT
1 TTAAGGGTTTAATATTTAGGGTT
44269759 T
1 T
44269760 GAGTTTGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (23 bp):
TTAAGGGTTTAATATTTAGGGTT
Found at i:44273644 original size:16 final size:17
Alignment explanation
Indices: 44273620--44273652 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
44273610 TCTAATTATA
*
44273620 TATTTAAATTA-TAAAT
1 TATTAAAATTATTAAAT
44273636 TATTAAAATTATTAAAT
1 TATTAAAATTATTAAAT
44273653 ACCACGTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAAATTATTAAAT
Found at i:44274100 original size:29 final size:30
Alignment explanation
Indices: 44274063--44274136 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
44274053 AGTGGATTTA
44274063 GTCCATGTA-TTTT-AATTTGATCAATTTTT
1 GTCCATGTACTTTTGAA-TTGATCAATTTTT
* *
44274092 GTCCTTGTACTTTTGGAATTGGTCAATTTTT
1 GTCCATGTACTTTT-GAATTGATCAATTTTT
44274123 GTCCCA-GTACTTTT
1 GT-CCATGTACTTTT
44274137 CAAGTTTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 8 0.21
30 4 0.11
31 22 0.58
32 4 0.11
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (30 bp):
GTCCATGTACTTTTGAATTGATCAATTTTT
Found at i:44281321 original size:28 final size:27
Alignment explanation
Indices: 44281298--44281348 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
44281288 ACTTTTGGAT
44281298 ACCCG-GGGGCAAAATGGTAATTTTGG
1 ACCCGCGGGGCAAAATGGTAATTTTGG
*
44281324 ACTCGCGGGGCAAAATGGTAATTTT
1 ACCCGCGGGGCAAAATGGTAATTTT
44281349 CGATGAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (27 bp):
ACCCGCGGGGCAAAATGGTAATTTTGG
Found at i:44281392 original size:30 final size:29
Alignment explanation
Indices: 44281358--44281515 Score: 116
Period size: 30 Copynumber: 5.3 Consensus size: 29
44281348 TCGATGAAAT
44281358 AGGGGTCAAAAATAGAATTTTGGAAAGTTC
1 AGGGGT-AAAAATAGAATTTTGGAAAGTTC
* *
44281388 AGGGGT-AAAATGGTGATTTTTGGTGAAA--TC
1 AGGGGTAAAAAT--AGAATTTT-G-GAAAGTTC
44281418 -GGGGTTAAAAATAGAATTTTGGAAAGTTC
1 AGGGG-TAAAAATAGAATTTTGGAAAGTTC
*
44281447 AGGGGT-AAAATGGTAATTTTTGGTGAAA-TT-
1 AGGGGTAAAAATAG-AA-TTTT-G-GAAAGTTC
* *
44281477 -GGGGTTAAAAATGGAATTTTGGAAAGTTT
1 AGGGG-TAAAAATAGAATTTTGGAAAGTTC
44281506 AGGGGTAAAA
1 AGGGGTAAAA
44281516 TGATAATTTT
Statistics
Matches: 105, Mismatches: 5, Indels: 37
0.71 0.03 0.25
Matches are distributed among these distances:
27 8 0.08
28 15 0.14
29 28 0.27
30 30 0.29
31 16 0.15
32 8 0.08
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.31
Consensus pattern (29 bp):
AGGGGTAAAAATAGAATTTTGGAAAGTTC
Found at i:44281407 original size:29 final size:28
Alignment explanation
Indices: 44281366--44281517 Score: 118
Period size: 29 Copynumber: 5.2 Consensus size: 28
44281356 ATAGGGGTCA
*
44281366 AAAATAGAATTTTGGAAAGTTCAGGGGT
1 AAAATGGAATTTTGGAAAGTTCAGGGGT
*
44281394 AAAATGGTGATTTTTGGTGAAA--TC-GGGGTT
1 AAAAT-G-GAATTTT-G-GAAAGTTCAGGGG-T
*
44281424 AAAAATAGAATTTTGGAAAGTTCAGGGGT
1 -AAAATGGAATTTTGGAAAGTTCAGGGGT
44281453 AAAATGGTAATTTTTGGTGAAA-TT--GGGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTCAGGGG-T
*
44281483 AAAAATGGAATTTTGGAAAGTTTAGGGGT
1 -AAAATGGAATTTTGGAAAGTTCAGGGGT
44281512 AAAATG
1 AAAATG
44281518 ATAATTTTCG
Statistics
Matches: 101, Mismatches: 5, Indels: 36
0.71 0.04 0.25
Matches are distributed among these distances:
27 8 0.08
28 21 0.21
29 24 0.24
30 24 0.24
31 16 0.16
32 8 0.08
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTCAGGGGT
Found at i:44281415 original size:59 final size:59
Alignment explanation
Indices: 44281330--44281525 Score: 302
Period size: 59 Copynumber: 3.3 Consensus size: 59
44281320 TTGGACTCGC
* * * *
44281330 GGGGCAAAATGGTAATTTTCGATGAAATAGGGGTCAAAAATAGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATAGGGGTTAAAAATAGAATTTTGGAAAGTTCA
* *
44281389 GGGGTAAAATGGTGATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATAGGGGTTAAAAATAGAATTTTGGAAAGTTCA
* * *
44281448 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATAGGGGTTAAAAATAGAATTTTGGAAAGTTCA
*
44281507 GGGGTAAAATGATAATTTT
1 GGGGTAAAATGGTAATTTT
44281526 CGGACCATCC
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 126 1.00
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATAGGGGTTAAAAATAGAATTTTGGAAAGTTCA
Found at i:44283361 original size:6 final size:6
Alignment explanation
Indices: 44283352--44283423 Score: 69
Period size: 6 Copynumber: 12.0 Consensus size: 6
44283342 ATTTTTAATG
* **
44283352 TTTAAA TTTAGTA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
44283402 TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
44283424 ATCAATTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.07
5 3 0.06
6 36 0.67
7 5 0.09
8 6 0.11
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:44283388 original size:30 final size:29
Alignment explanation
Indices: 44283354--44283422 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
44283344 TTTTAATGTT
* * *
44283354 TAAATTTAGTATTTAAATTTAAATTTAAGG
1 TAAATTTAATAATTAAATTTAAATTTAA-A
44283384 TAAATTTAAATAATTAAATTTAAATTTAAA
1 TAAATTT-AATAATTAAATTTAAATTTAAA
44283414 TAAATTTAA
1 TAAATTTAA
44283423 AATCAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 2 0.06
30 14 0.40
31 19 0.54
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (29 bp):
TAAATTTAATAATTAAATTTAAATTTAAA
Found at i:44283404 original size:31 final size:30
Alignment explanation
Indices: 44283366--44283423 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
44283356 AATTTAGTAT
*
44283366 TTAAATTTAAATTTAAGGTAAATTTAAATAA
1 TTAAATTTAAATTTAA-ATAAATTTAAATAA
44283397 TTAAATTTAAATTTAAATAAATTTAAA
1 TTAAATTTAAATTTAAATAAATTTAAA
44283424 ATCAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
TTAAATTTAAATTTAAATAAATTTAAATAA
Found at i:44283409 original size:11 final size:10
Alignment explanation
Indices: 44283373--44283433 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 10
44283363 TATTTAAATT
*
44283373 TAAATTTAAGG
1 TAAATTTAA-A
44283384 TAAATTTAAA
1 TAAATTTAAA
44283394 T-AA-TTAAA
1 TAAATTTAAA
44283402 TTTAAATTTAAA
1 --TAAATTTAAA
44283414 TAAATTTAAAA
1 TAAATTT-AAA
*
44283425 TCAATTTAA
1 TAAATTTAA
44283434 CTCTAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 11 0.26
11 20 0.47
12 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:44284166 original size:29 final size:30
Alignment explanation
Indices: 44284106--44284166 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
44284096 ACACTTTAAT
** *
44284106 TTTTTATAAAAATGATAAAAATTTAAATTA
1 TTTTTATAAAAATGATAAAAATAAAAACTA
*
44284136 TTTTTA-AAAAATTATAAAAATAAAAACTA
1 TTTTTATAAAAATGATAAAAATAAAAACTA
44284165 TT
1 TT
44284167 AAAATAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
TTTTTATAAAAATGATAAAAATAAAAACTA
Found at i:44295291 original size:21 final size:19
Alignment explanation
Indices: 44295221--44295292 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 19
44295211 CAAAATTTAT
44295221 ATTTT-TAAAAAATTTATAAA
1 ATTTTCTAAAAAA-TTA-AAA
*
44295241 ATTTTCGAAAAAATCTAAAA
1 ATTTTCTAAAAAAT-TAAAA
* *
44295261 ATTATATAAAGAAAGTTAAAA
1 ATTTTCTAAA-AAA-TTAAAA
44295282 ATTTTCTAAAA
1 ATTTTCTAAAA
44295293 TAATAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 17 0.40
21 24 0.57
22 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (19 bp):
ATTTTCTAAAAAATTAAAA
Found at i:44300513 original size:17 final size:16
Alignment explanation
Indices: 44300473--44300517 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
44300463 AGAACTATAC
**
44300473 TAATTATAATTTTATT
1 TAATTATAATTAAATT
*
44300489 TAAATATAATTAAATAT
1 TAATTATAATTAAAT-T
44300506 TAATTATAATTA
1 TAATTATAATTA
44300518 TTATATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTATAATTAAATT
Found at i:44300709 original size:20 final size:20
Alignment explanation
Indices: 44300686--44300742 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 20
44300676 TTGTGTTTTG
44300686 TTTATGATTTTTTTTAGATA
1 TTTATGATTTTTTTTAGATA
44300706 TTTA-G-TTTTGTTTACTA-ATA
1 TTTATGATTTT-TTT--TAGATA
*
44300726 TTT-TTATTTTTTTTAGA
1 TTTATGATTTTTTTTAGA
44300743 GACAAATAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 13
0.68 0.02 0.30
Matches are distributed among these distances:
18 6 0.20
19 5 0.17
20 13 0.43
21 6 0.20
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTATGATTTTTTTTAGATA
Found at i:44300993 original size:22 final size:23
Alignment explanation
Indices: 44300949--44300993 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
44300939 TTAATCTTTT
* * *
44300949 AAAAATTGCACTTTTACTATCGA
1 AAAAATTACAATTTAACTATCGA
44300972 AAAAATTACAATTTAACT-TCGA
1 AAAAATTACAATTTAACTATCGA
44300994 CATCCCTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (23 bp):
AAAAATTACAATTTAACTATCGA
Found at i:44301762 original size:20 final size:19
Alignment explanation
Indices: 44301734--44301782 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
44301724 CCACATCAGC
*
44301734 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATT-TTA
*
44301754 AAATTATTTTTATAATTTTA
1 AAATTA-TTTTAAAATTTTA
44301774 AAATTATTT
1 AAATTATTT
44301783 GCTGACGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 3 0.12
20 14 0.54
21 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AAATTATTTTAAAATTTTA
Found at i:44310893 original size:20 final size:19
Alignment explanation
Indices: 44310861--44310900 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
44310851 TGATTTTATA
44310861 TAATAATAGTATTTTAATTT
1 TAATAATAGTATTTT-ATTT
44310881 TAATACATA-TATTTTATTT
1 TAATA-ATAGTATTTTATTT
44310900 T
1 T
44310901 CAAAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 11 0.58
21 3 0.16
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
TAATAATAGTATTTTATTT
Found at i:44311062 original size:45 final size:45
Alignment explanation
Indices: 44310998--44311084 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
44310988 CTAGTAAATG
*
44310998 TTTAAATAAATTACATGGTATTTATTACAAATTATTTATATTAAT
1 TTTAAATAAATTACATGGTATTTATTACAAATTATATATATTAAT
* * **
44311043 TTTAACTAAATTCCATGGTATTTATTATTAATTATATATATT
1 TTTAAATAAATTACATGGTATTTATTACAAATTATATATATT
44311085 GGGCAAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.51
Consensus pattern (45 bp):
TTTAAATAAATTACATGGTATTTATTACAAATTATATATATTAAT
Found at i:44314611 original size:16 final size:18
Alignment explanation
Indices: 44314579--44314616 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
44314569 CAAATGTGAG
44314579 TTGTTCTCAACATAAAAA
1 TTGTTCTCAACATAAAAA
*
44314597 TTGTTC-CAA-ATAAAAG
1 TTGTTCTCAACATAAAAA
44314613 TTGT
1 TTGT
44314617 GTTGTGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 3 0.16
18 6 0.32
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (18 bp):
TTGTTCTCAACATAAAAA
Found at i:44315827 original size:2 final size:2
Alignment explanation
Indices: 44315822--44315850 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44315812 ATACCAACAT
44315822 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 T
44315851 TATTTAGAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44322501 original size:23 final size:21
Alignment explanation
Indices: 44322467--44322516 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
44322457 TTCGGAATTA
* *
44322467 AATTTTATATTTTTATTTTAT
1 AATTTTATATTTATATTTCAT
*
44322488 TATTTTAATAATTTATATTTCAT
1 AATTTT-AT-ATTTATATTTCAT
44322511 AATTTT
1 AATTTT
44322517 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 2 0.09
23 16 0.70
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
AATTTTATATTTATATTTCAT
Found at i:44325341 original size:23 final size:24
Alignment explanation
Indices: 44325301--44325346 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
44325291 CGTGTCAATG
44325301 ACATTAAAAAATATATAA-AAATA
1 ACATTAAAAAATATATAAGAAATA
*
44325324 ACATTAAATAAT-TGATAAGAAAT
1 ACATTAAAAAATAT-ATAAGAAAT
44325347 GCAAGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.75
24 4 0.20
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (24 bp):
ACATTAAAAAATATATAAGAAATA
Found at i:44327187 original size:30 final size:30
Alignment explanation
Indices: 44327152--44327220 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
44327142 AATAATTTAT
* *
44327152 ATTTTATAATTTTTAAAAAATTAAATTA-A
1 ATTTTATAATTTTAAAAAAATTAAAGTATA
*
44327181 ATTTTTATTATTTTAAAAAAATTAAAGTATA
1 A-TTTTATAATTTTAAAAAAATTAAAGTATA
44327212 ATTTTATAA
1 ATTTTATAA
44327221 ATTATAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.03
30 31 0.91
31 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (30 bp):
ATTTTATAATTTTAAAAAAATTAAAGTATA
Found at i:44331555 original size:8 final size:8
Alignment explanation
Indices: 44331542--44331580 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
44331532 TTACAAATTT
44331542 AAAAAATA
1 AAAAAATA
44331550 AAAAAATA
1 AAAAAATA
44331558 AAAAAATA
1 AAAAAATA
*
44331566 AAAAATTA
1 AAAAAATA
*
44331574 AATAAAT
1 AAAAAAT
44331581 GACTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAAAATA
Found at i:44336129 original size:7 final size:7
Alignment explanation
Indices: 44336117--44336142 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
44336107 AATATTAAAA
44336117 ATATATT
1 ATATATT
44336124 ATATATT
1 ATATATT
44336131 ATATATT
1 ATATATT
44336138 ATATA
1 ATATA
44336143 AATATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
ATATATT
Found at i:44353564 original size:12 final size:11
Alignment explanation
Indices: 44353547--44353580 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
44353537 TAATTAAAAA
44353547 TATATTTATATT
1 TATATTTA-ATT
44353559 TATATTTAATT
1 TATATTTAATT
44353570 TAATATTTAAT
1 T-ATATTTAAT
44353581 AATCGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTTAATT
Found at i:44356875 original size:3 final size:3
Alignment explanation
Indices: 44356867--44356893 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44356857 GATGTGCCCT
44356867 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
44356894 CAATTTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:44358168 original size:47 final size:49
Alignment explanation
Indices: 44358082--44358178 Score: 144
Period size: 52 Copynumber: 2.0 Consensus size: 49
44358072 AAATTAAATT
44358082 TAAGAATGTAATGAATGATTTCAATAAAAAAAGGAAAATATTCATATTAGAA
1 TAAGAATGTAATGAATGATTTCAAT--AAAAA-GAAAATATTCATATTAGAA
*
44358134 TAAGAATGTTATGAATGATTTCAAT-AAAA-AAAATATTCATATTAG
1 TAAGAATGTAATGAATGATTTCAATAAAAAGAAAATATTCATATTAG
44358179 GATATTTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
47 16 0.36
49 4 0.09
52 24 0.55
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (49 bp):
TAAGAATGTAATGAATGATTTCAATAAAAAGAAAATATTCATATTAGAA
Found at i:44359282 original size:6 final size:6
Alignment explanation
Indices: 44359239--44359272 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
44359229 TCCAATGATC
44359239 ACCATG ACCATG ACCATG ACCATG ACCATG ACCA
1 ACCATG ACCATG ACCATG ACCATG ACCATG ACCA
44359273 CCACGACCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (6 bp):
ACCATG
Found at i:44362389 original size:14 final size:14
Alignment explanation
Indices: 44362370--44362404 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
44362360 GAAAAGTAAG
*
44362370 TCATTTTCTAGAAA
1 TCATTTTCCAGAAA
44362384 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
*
44362398 TTATTTT
1 TCATTTT
44362405 TCGGTAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:44371447 original size:17 final size:17
Alignment explanation
Indices: 44371425--44371457 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
44371415 TTGATTGGAT
44371425 TGAATCATTAA-TCAATC
1 TGAATC-TTAACTCAATC
44371442 TGAATCTTAACTCAAT
1 TGAATCTTAACTCAAT
44371458 TTAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (17 bp):
TGAATCTTAACTCAATC
Found at i:44383030 original size:29 final size:27
Alignment explanation
Indices: 44382998--44383054 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
44382988 CGAGTAATTT
44382998 TTTAAATA-AAATTAGATGAAAAATAATAA
1 TTTAAATATAAATTA-A-GAAAAA-AATAA
44383027 TTTAAATATTAAATTAAGAAAAAAATAA
1 TTTAAATA-TAAATTAAGAAAAAAATAA
44383055 ATACCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 5 0.19
29 14 0.54
30 1 0.04
31 6 0.23
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
TTTAAATATAAATTAAGAAAAAAATAA
Found at i:44383360 original size:2 final size:2
Alignment explanation
Indices: 44383353--44383377 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44383343 GTTAAAAATA
44383353 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
44383378 ATCAAAACCT
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:44385702 original size:35 final size:36
Alignment explanation
Indices: 44385659--44385731 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
44385649 AAATAAAATA
* * *
44385659 AAAGATAAAATACTATAA-ATTAAAAATATTATCCT
1 AAAGATAAAATAATAGAACATTAAAAACATTATCCT
*
44385694 AAAGATAAAATAATAGAACATTAAAAACATTATTCT
1 AAAGATAAAATAATAGAACATTAAAAACATTATCCT
44385730 AA
1 AA
44385732 TAAATCCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 16 0.48
36 17 0.52
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (36 bp):
AAAGATAAAATAATAGAACATTAAAAACATTATCCT
Found at i:44387254 original size:17 final size:17
Alignment explanation
Indices: 44387232--44387267 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
44387222 ATAATAAAAA
44387232 TATTTTAT-ATTAATATT
1 TATTTTATAATTAA-ATT
44387249 TATTTTATAATTAAATT
1 TATTTTATAATTAAATT
44387266 TA
1 TA
44387268 ATAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTTATAATTAAATT
Found at i:44389996 original size:49 final size:49
Alignment explanation
Indices: 44389943--44390045 Score: 152
Period size: 49 Copynumber: 2.1 Consensus size: 49
44389933 ATTGAAAGTC
* * *
44389943 TTGATGAATTCTTTACTCGACTTAATTCTTGTTTGAATTATCTTCATTA
1 TTGATGAATTCCTTACTAGACTTAATTCTTGCTTGAATTATCTTCATTA
* *
44389992 TTGATGAATTCCTTATTAGACTTAATTCTTGCTTGAATTATCTTCGTTA
1 TTGATGAATTCCTTACTAGACTTAATTCTTGCTTGAATTATCTTCATTA
*
44390041 ATGAT
1 TTGAT
44390046 ATGCTAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.50
Consensus pattern (49 bp):
TTGATGAATTCCTTACTAGACTTAATTCTTGCTTGAATTATCTTCATTA
Found at i:44397339 original size:36 final size:36
Alignment explanation
Indices: 44397292--44397363 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
44397282 ATTAGTGTTT
44397292 GGTGAAACTGGCATGAGGCTTTAGTTCCAAATACAA
1 GGTGAAACTGGCATGAGGCTTTAGTTCCAAATACAA
*
44397328 GGTGAAGCTGGCATGAGGCTTTAGTTCCAAATACAA
1 GGTGAAACTGGCATGAGGCTTTAGTTCCAAATACAA
44397364 ACACATACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (36 bp):
GGTGAAACTGGCATGAGGCTTTAGTTCCAAATACAA
Found at i:44426449 original size:30 final size:28
Alignment explanation
Indices: 44426323--44426625 Score: 211
Period size: 29 Copynumber: 10.3 Consensus size: 28
44426313 GGGAAATTTG
* *
44426323 GGGTCAAAATGCAATTTTGGAAAAGTTT-
1 GGGTCAAAATGTAATTTT-AAAAAGTTTA
* * **
44426351 GGAGTCAAGATGCAATTTTGGGAAAGTTTA
1 GG-GTCAAAATGTAATTTT-AAAAAGTTTA
* *
44426381 AGGTCAAAATGTAATTTTAAAGAAATTTA
1 GGGTCAAAATGTAATTTTAAA-AAGTTTA
*
44426410 GGATCAAAATGTAATTTTAAATAAGTTTGA
1 GGGTCAAAATGTAATTTTAAA-AAGTTT-A
*
44426440 GGGTCAAAATGCAATTTTTAAGTAAA--TTA
1 GGGTCAAAATGTAA-TTTTAA--AAAGTTTA
* *
44426469 GGGATTAAAATGTAATTTTGATAAA-TTTA
1 GGG-TCAAAATGTAATTTT-AAAAAGTTTA
* * *
44426498 GGGGTAAAAATGTAATTTTGGAGAAGTTTTA
1 -GGGTCAAAATGTAATTTT-AAAAAG-TTTA
* *
44426529 GAGTCAAAATATAATTTTAGAAAAGTTTA
1 GGGTCAAAATGTAATTTTA-AAAAGTTTA
* * *
44426558 GGGTTAAAATATAATTTTAAAAAAGTTATG
1 GGGTCAAAATGTAATTTT-AAAAAGTT-TA
44426588 GGGTCAAAATGTAATTTTAGAAATA-TTTA
1 GGGTCAAAATGTAATTTTA-AAA-AGTTTA
*
44426617 GGGTTAAAA
1 GGGTCAAAA
44426626 CATGATTTTT
Statistics
Matches: 224, Mismatches: 33, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
28 6 0.03
29 133 0.59
30 71 0.32
31 11 0.05
32 2 0.01
33 1 0.00
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (28 bp):
GGGTCAAAATGTAATTTTAAAAAGTTTA
Found at i:44426456 original size:59 final size:57
Alignment explanation
Indices: 44426373--44426625 Score: 219
Period size: 59 Copynumber: 4.3 Consensus size: 57
44426363 CAATTTTGGG
*
44426373 AAAGTTTAAGGTCAAAATGTAATTTTAAAGAAATTTAGGATCAAAATGTAATTTTAA
1 AAAGTTTAGGGTCAAAATGTAATTTTAAAGAAATTTAGGATCAAAATGTAATTTTAA
* * * *
44426430 ATAAGTTTGAGGGTCAAAATGCAATTTTTAAGTAAA-TTAGGGATTAAAATGTAATTTTGAT
1 A-AAGTTT-AGGGTCAAAATGTAATTTTAAAG-AAATTTA-GGATCAAAATGTAATTTT-AA
* ** * *
44426491 AAA-TTTAGGGGTAAAAATGTAATTTTGGAGAAGTTTTA-GAGTCAAAATATAATTTTAGA
1 AAAGTTTA-GGGTCAAAATGTAATTTTAAAGAA-ATTTAGGA-TCAAAATGTAATTTTA-A
* * * *
44426550 AAAGTTTAGGGTTAAAATATAATTTTAAA-AAAGTTATGGGGTCAAAATGTAATTTTAGA
1 AAAGTTTAGGGTCAAAATGTAATTTTAAAGAAA-TT-TAGGATCAAAATGTAATTTTA-A
*
44426609 AATA-TTTAGGGTTAAAA
1 AA-AGTTTAGGGTCAAAA
44426626 CATGATTTTT
Statistics
Matches: 160, Mismatches: 21, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
57 1 0.01
58 16 0.10
59 110 0.69
60 31 0.19
61 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.36
Consensus pattern (57 bp):
AAAGTTTAGGGTCAAAATGTAATTTTAAAGAAATTTAGGATCAAAATGTAATTTTAA
Found at i:44433328 original size:21 final size:22
Alignment explanation
Indices: 44433304--44433352 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
44433294 AACAACGTTA
44433304 TCAAATTA-TATACAAAATTAT
1 TCAAATTAGTATACAAAATTAT
* *
44433325 TCAAA-TAGTGTACAATATTAT
1 TCAAATTAGTATACAAAATTAT
44433346 TCAAATT
1 TCAAATT
44433353 TATTAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (22 bp):
TCAAATTAGTATACAAAATTAT
Found at i:44433780 original size:31 final size:32
Alignment explanation
Indices: 44433745--44433807 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
44433735 TTAAAAGTTA
44433745 TCAAAACCTAGT-AAATATCATCAAAAT-TATC
1 TCAAAACCTAGTAAAATAT-ATCAAAATGTATC
** *
44433776 TCAAAAGGTATTAAAATATATCAAAATGTATC
1 TCAAAACCTAGTAAAATATATCAAAATGTATC
44433808 ACAATTACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (32 bp):
TCAAAACCTAGTAAAATATATCAAAATGTATC
Found at i:44434246 original size:2 final size:2
Alignment explanation
Indices: 44434239--44434264 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44434229 GATAAAGCTT
44434239 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
44434265 GTGCCTCCAG
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):
TA
Found at i:44453598 original size:31 final size:32
Alignment explanation
Indices: 44453563--44453625 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
44453553 TTAAAAGTTA
44453563 TCAAAACCTAGT-AAATATCATCAAAAT-TATC
1 TCAAAACCTAGTAAAATAT-ATCAAAATGTATC
** *
44453594 TCAAAAGGTATTAAAATATATCAAAATGTATC
1 TCAAAACCTAGTAAAATATATCAAAATGTATC
44453626 ACAATTACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (32 bp):
TCAAAACCTAGTAAAATATATCAAAATGTATC
Found at i:44459006 original size:2 final size:2
Alignment explanation
Indices: 44459001--44459027 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44458991 TTTTTAATAC
44459001 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
44459028 GAAATCGGAA
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:44463025 original size:30 final size:29
Alignment explanation
Indices: 44462963--44463026 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
44462953 AATATTTTAT
**
44462963 ATTTTTATTATTTTTAAAAATTAAATTAA
1 ATTTTTATTATTTTTAAAAACAAAATTAA
*
44462992 ATTTTTATTATTTTTTAGAAACAAAA-TATA
1 ATTTTTATTA-TTTTTAAAAACAAAATTA-A
44463022 ATTTT
1 ATTTT
44463027 ATCATAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
ATTTTTATTATTTTTAAAAACAAAATTAA
Found at i:44468070 original size:22 final size:23
Alignment explanation
Indices: 44468026--44468072 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
44468016 TACGCAAACT
44468026 AATATAAATAAATACTTTTTTATAAC
1 AATATAAATAAATAC---TTTATAAC
44468052 AATATAAATAAATAC-TTATAA
1 AATATAAATAAATACTTTATAA
44468073 GCCCTTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.29
26 15 0.71
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATAAATAAATACTTTATAAC
Found at i:44485288 original size:38 final size:38
Alignment explanation
Indices: 44485237--44485311 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
44485227 CACATCTGGG
44485237 TTGCCTCAAATACCTATATGCTCACAA-TGTTTCTTGAA
1 TTGCCTCAAATACCTATATGCTCACAAGT-TTTCTTGAA
*
44485275 TTGCCTTAAATACCTATATGCTCACAAGTTTTCTTGA
1 TTGCCTCAAATACCTATATGCTCACAAGTTTTCTTGA
44485312 CATACTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.39
Consensus pattern (38 bp):
TTGCCTCAAATACCTATATGCTCACAAGTTTTCTTGAA
Found at i:44504804 original size:15 final size:17
Alignment explanation
Indices: 44504786--44504817 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
44504776 AAATTAAAAG
44504786 TTAAAA-AAGA-AATTT
1 TTAAAATAAGAGAATTT
44504801 TTAAAATAAGAGAATTT
1 TTAAAATAAGAGAATTT
44504818 AATAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (17 bp):
TTAAAATAAGAGAATTT
Found at i:44516577 original size:15 final size:15
Alignment explanation
Indices: 44516549--44516582 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
44516539 TTTGCGTATG
44516549 TATTTATTTATTTAT
1 TATTTATTTATTTAT
* *
44516564 TATTTGTTTGTTTAT
1 TATTTATTTATTTAT
44516579 TATT
1 TATT
44516583 CATTAACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TATTTATTTATTTAT
Found at i:44516756 original size:30 final size:30
Alignment explanation
Indices: 44516720--44516790 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
44516710 AATACAACTT
*
44516720 GAACATGAACAAGTTTAAAAATAAATAAAC
1 GAACATGAACAAGTTTAAAAATAAACAAAC
44516750 GAACATGAACAAGTTTAAAAATAAACAAAC
1 GAACATGAACAAGTTTAAAAATAAACAAAC
44516780 GAACATGAACA
1 GAACATGAACA
44516791 GAGGTTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.59, C:0.13, G:0.11, T:0.17
Consensus pattern (30 bp):
GAACATGAACAAGTTTAAAAATAAACAAAC
Found at i:44517382 original size:31 final size:31
Alignment explanation
Indices: 44517344--44517416 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
44517334 AAAAATAAAA
*
44517344 ATTTTCATTTTAAGCA-TCGCGGTAAAAAATT
1 ATTTTCATTTTAAGCACT-GCCGTAAAAAATT
* *
44517375 ATTTTCATTTTAGGCACTGCCGTTAAAAATT
1 ATTTTCATTTTAAGCACTGCCGTAAAAAATT
44517406 ATTCTT-ATTTT
1 ATT-TTCATTTT
44517417 GGTTACCCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 34 0.92
32 3 0.08
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (31 bp):
ATTTTCATTTTAAGCACTGCCGTAAAAAATT
Found at i:44518276 original size:20 final size:20
Alignment explanation
Indices: 44518229--44518283 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
44518219 CACTAGTTTA
* * *
44518229 TTAAAAAAATTAGAATTAAT
1 TTAAAAAAATAAAAAATAAT
*
44518249 TCTGAAAAAATAAAAAATAAT
1 T-TAAAAAAATAAAAAATAAT
*
44518270 TTAAAAAGATAAAA
1 TTAAAAAAATAAAA
44518284 GAATTGATCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
TTAAAAAAATAAAAAATAAT
Found at i:44527741 original size:22 final size:22
Alignment explanation
Indices: 44527716--44527779 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
44527706 GAAATGAAAG
* *
44527716 CAAAACAATAAAAAAGCAATGA
1 CAAAACAGTAAAAAAACAATGA
44527738 CAAAACAGTAAAAAAACAATGA
1 CAAAACAGTAAAAAAACAATGA
44527760 CAAAACAGTAAAAAAACAAT
1 CAAAACAGTAAAAAAACAAT
44527780 AATTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.69, C:0.14, G:0.08, T:0.09
Consensus pattern (22 bp):
CAAAACAGTAAAAAAACAATGA
Found at i:44527753 original size:11 final size:11
Alignment explanation
Indices: 44527739--44527777 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
44527729 AAGCAATGAC
44527739 AAAACAGTAAA
1 AAAACAGTAAA
* * *
44527750 AAAACAATGAC
1 AAAACAGTAAA
44527761 AAAACAGTAAA
1 AAAACAGTAAA
44527772 AAAACA
1 AAAACA
44527778 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.72, C:0.13, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAACAGTAAA
Found at i:44534653 original size:18 final size:18
Alignment explanation
Indices: 44534610--44534654 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
44534600 CAAGGTCACG
* *
44534610 ATCAATAGCGTCACTAGC
1 ATCAATATCATCACTAGC
44534628 ATCAATATCATCACTAGC
1 ATCAATATCATCACTAGC
44534646 ATCAATATC
1 ATCAATATC
44534655 GATATCATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.27
Consensus pattern (18 bp):
ATCAATATCATCACTAGC
Found at i:44537054 original size:21 final size:21
Alignment explanation
Indices: 44537024--44537112 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 21
44537014 CTCACAAAGA
* *
44537024 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
44537044 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
44537065 AAAAAGAAAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
44537086 AAAAAGAAATGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
44537110 AAA
1 AAA
44537113 TCTTTTTTGT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 6 0.11
21 35 0.62
23 1 0.02
24 14 0.25
ACGTcount: A:0.55, C:0.09, G:0.22, T:0.13
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:44537105 original size:24 final size:21
Alignment explanation
Indices: 44537041--44537094 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
44537031 AAGTGAGTTA
* *
44537041 GACAAAAAGAGAAGCAACTTG
1 GACAAAAAGAAAAGTAACTTG
44537062 GACAAAAAGAAAAGTAACTTG
1 GACAAAAAGAAAAGTAACTTG
44537083 GACAAAAAGAAA
1 GACAAAAAGAAA
44537095 TGAAGTGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.59, C:0.11, G:0.20, T:0.09
Consensus pattern (21 bp):
GACAAAAAGAAAAGTAACTTG
Found at i:44546070 original size:30 final size:31
Alignment explanation
Indices: 44546005--44546077 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
44545995 GACAACAAAA
* * *
44546005 TGACTATTTTGTCACTTTTCGATAATTTTAG
1 TGACTGTTTTGTCACTTTTCGATAAGTTGAG
44546036 TGACTGTTTTGTCACATTTTC-A-AAGTTGAG
1 TGACTGTTTTGTCAC-TTTTCGATAAGTTGAG
44546066 TGACTGTTTTGT
1 TGACTGTTTTGT
44546078 TAAATGTGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.47
31 15 0.39
32 5 0.13
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (31 bp):
TGACTGTTTTGTCACTTTTCGATAAGTTGAG
Found at i:44554175 original size:23 final size:23
Alignment explanation
Indices: 44554142--44554189 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
44554132 TTTTTAGGTG
*
44554142 AATTTTCAAAATTTTAATGATTA
1 AATTTTCAAAAGTTTAATGATTA
* **
44554165 AATTTTTAAAAGTTTGGTGATTA
1 AATTTTCAAAAGTTTAATGATTA
44554188 AA
1 AA
44554190 ACATAATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (23 bp):
AATTTTCAAAAGTTTAATGATTA
Found at i:44554941 original size:15 final size:15
Alignment explanation
Indices: 44554921--44554970 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
44554911 TTAAATTACA
*
44554921 TTTTAATCACTAAAT
1 TTTTAATCATTAAAT
** *
44554936 TTTTAAAAATTACA-
1 TTTTAATCATTAAAT
44554950 TTTTAATCATTAAAT
1 TTTTAATCATTAAAT
44554965 TTTTAA
1 TTTTAA
44554971 AAATTTACTT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTAATCATTAAAT
Found at i:44554948 original size:29 final size:29
Alignment explanation
Indices: 44554913--44554975 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
44554903 TATATTATTT
44554913 AAATTACATTTTAATCACTAAATTTTTAA
1 AAATTACATTTTAATCACTAAATTTTTAA
*
44554942 AAATTACATTTTAATCATTAAATTTTTAA
1 AAATTACATTTTAATCACTAAATTTTTAA
44554971 AAATT
1 AAATT
44554976 TACTTAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (29 bp):
AAATTACATTTTAATCACTAAATTTTTAA
Found at i:44554953 original size:14 final size:15
Alignment explanation
Indices: 44554931--44554975 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
44554921 TTTTAATCAC
44554931 TAAATTTTTAAAAAT
1 TAAATTTTTAAAAAT
* **
44554946 TACA-TTTTAATCAT
1 TAAATTTTTAAAAAT
44554960 TAAATTTTTAAAAAT
1 TAAATTTTTAAAAAT
44554975 T
1 T
44554976 TACTTAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAATTTTTAAAAAT
Found at i:44562377 original size:6 final size:6
Alignment explanation
Indices: 44562368--44562402 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
44562358 TTAAAAAATG
*
44562368 TTTTTG TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
44562403 TAATAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:44564563 original size:21 final size:21
Alignment explanation
Indices: 44564534--44564573 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44564524 ACAAAATCCG
44564534 TTATAAAAAAATAATTTAAAT
1 TTATAAAAAAATAATTTAAAT
* * *
44564555 TTATCAAAAATTCATTTAA
1 TTATAAAAAAATAATTTAA
44564574 TTGATTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TTATAAAAAAATAATTTAAAT
Found at i:44564875 original size:16 final size:15
Alignment explanation
Indices: 44564836--44564871 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
44564826 ATTTGATGTT
44564836 TAAAAATTATAAAAA
1 TAAAAATTATAAAAA
* *
44564851 TATAAATTATTAAAA
1 TAAAAATTATAAAAA
44564866 TAAAAA
1 TAAAAA
44564872 ATTACATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATTATAAAAA
Found at i:44569406 original size:29 final size:29
Alignment explanation
Indices: 44569352--44569407 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
44569342 TTGATTTATT
* *
44569352 AAAAATATTGGGATTTAATGAGAATTTCA
1 AAAAATATAGGGATTTAATGAAAATTTCA
*
44569381 AAAAATATAGTGG-TTTAATTAAAATTT
1 AAAAATATAG-GGATTTAATGAAAATTT
44569408 TTGAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (29 bp):
AAAAATATAGGGATTTAATGAAAATTTCA
Found at i:44572617 original size:58 final size:58
Alignment explanation
Indices: 44572553--44572676 Score: 239
Period size: 58 Copynumber: 2.1 Consensus size: 58
44572543 TTGGAGGCGG
*
44572553 TTGCATTATTATATAAAATTAAAATGAAAACTCAGCTCTTGATAGTGAGAGAATCAAT
1 TTGCATTATTATATAAAATTAAAACGAAAACTCAGCTCTTGATAGTGAGAGAATCAAT
44572611 TTGCATTATTATATAAAATTAAAACGAAAACTCAGCTCTTGATAGTGAGAGAATCAAT
1 TTGCATTATTATATAAAATTAAAACGAAAACTCAGCTCTTGATAGTGAGAGAATCAAT
44572669 TTGCATTA
1 TTGCATTA
44572677 ATTTGAGAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (58 bp):
TTGCATTATTATATAAAATTAAAACGAAAACTCAGCTCTTGATAGTGAGAGAATCAAT
Found at i:44574253 original size:28 final size:28
Alignment explanation
Indices: 44574201--44574255 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
44574191 GTAGTATAAA
* *
44574201 TTTTGTGTTATAAATTACATCATATATT
1 TTTTGTGTTATAAATGACATAATATATT
*
44574229 TTTTGTGTTATAAATGATATAATATAT
1 TTTTGTGTTATAAATGACATAATATAT
44574256 AAAAATAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (28 bp):
TTTTGTGTTATAAATGACATAATATATT
Found at i:44575033 original size:12 final size:12
Alignment explanation
Indices: 44575016--44575040 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44575006 TTTGCTTAAG
44575016 TTCGTCCATATT
1 TTCGTCCATATT
44575028 TTCGTCCATATT
1 TTCGTCCATATT
44575040 T
1 T
44575041 ATCAATAACT
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:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TTCGTCCATATT
Found at i:44575861 original size:13 final size:13
Alignment explanation
Indices: 44575843--44575871 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
44575833 ATTTGCATTT
44575843 AATTTTTTATATA
1 AATTTTTTATATA
44575856 AATTTTTTATATA
1 AATTTTTTATATA
44575869 AAT
1 AAT
44575872 GATTTCACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTTTTTATATA
Found at i:44578975 original size:17 final size:17
Alignment explanation
Indices: 44578953--44579010 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 17
44578943 TTGGTATTTA
44578953 AATTTGATATTTTTTTT
1 AATTTGATATTTTTTTT
*
44578970 AATTTG-TA----TTTG
1 AATTTGATATTTTTTTT
*
44578982 AACTTGATATTTTTTTT
1 AATTTGATATTTTTTTT
*
44578999 AATTTGGTATTT
1 AATTTGATATTT
44579011 AAATTTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
12 8 0.26
13 2 0.06
16 2 0.06
17 19 0.61
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (17 bp):
AATTTGATATTTTTTTT
Found at i:44578996 original size:30 final size:30
Alignment explanation
Indices: 44578941--44579013 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
44578931 TTAGTATAAT
*
44578941 ATTTGGTATTTAAATTTGATATTTTTTTTA
1 ATTTGGTATTTAAACTTGATATTTTTTTTA
*
44578971 ATTT-GTATTTGAACTTGATATTTTTTTTA
1 ATTTGGTATTTAAACTTGATATTTTTTTTA
44579000 ATTTGGTATTTAAA
1 ATTTGGTATTTAAA
44579014 TTTTTTGGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 27 0.69
30 12 0.31
ACGTcount: A:0.27, C:0.01, G:0.11, T:0.60
Consensus pattern (30 bp):
ATTTGGTATTTAAACTTGATATTTTTTTTA
Found at i:44579350 original size:61 final size:60
Alignment explanation
Indices: 44579215--44579397 Score: 182
Period size: 60 Copynumber: 3.1 Consensus size: 60
44579205 AATATTTAAT
* * * * *
44579215 AAATTTAAGTACCAAATTGAATCTAAAATAAATTAGGTATTAAATTAGGAAAAAAATATC
1 AAATTTAAGTATCAAATTGAATCCAAAAGAAATTAGGTACTAAATTAGAAAAAAAATATC
** * * * *
44579275 ATGTTCAAGTATCAAATTGGATCCAAAAGAATTTAGGTACTAACTTAGAAAAAAAAATATC
1 AAATTTAAGTATCAAATTGAATCCAAAAGAAATTAGGTACTAAATTAG-AAAAAAAATATC
* *
44579336 AAATTTAAGTATCAAATTGAAT--AAAA-AAATTTAGATACCAAATT----AAAAAATATC
1 AAATTTAAGTATCAAATTGAATCCAAAAGAAA-TTAGGTACTAAATTAGAAAAAAAATATC
44579390 AAATTTAA
1 AAATTTAA
44579398 AAACCGAATA
Statistics
Matches: 102, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
54 18 0.18
58 2 0.02
59 15 0.15
60 38 0.37
61 29 0.28
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (60 bp):
AAATTTAAGTATCAAATTGAATCCAAAAGAAATTAGGTACTAAATTAGAAAAAAAATATC
Found at i:44583948 original size:18 final size:20
Alignment explanation
Indices: 44583911--44583949 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
44583901 GTTTAATATA
44583911 ACATTTTATACTTGAATTTG
1 ACATTTTATACTTGAATTTG
*
44583931 ACATTTT-TCCTT-AATTTG
1 ACATTTTATACTTGAATTTG
44583949 A
1 A
44583950 TTCGTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
ACATTTTATACTTGAATTTG
Found at i:44585190 original size:17 final size:17
Alignment explanation
Indices: 44585168--44585266 Score: 62
Period size: 17 Copynumber: 5.7 Consensus size: 17
44585158 TCTTTGACTT
44585168 TTAACCTTTCATCTTCC
1 TTAACCTTTCATCTTCC
*
44585185 TTAACCTCCCCTTGA-CTT--
1 TTAACCT----TTCATCTTCC
44585203 TTAACCTTTCATCTTCC
1 TTAACCTTTCATCTTCC
** *
44585220 TTAACCTCCCAT-TGACC
1 TTAACCTTTCATCT-TCC
*
44585237 TTTAACCTTCCATCTTCC
1 -TTAACCTTTCATCTTCC
*
44585255 TCAACCTTTCAT
1 TTAACCTTTCAT
44585267 ATTCTTGTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
14 3 0.05
15 3 0.05
16 1 0.02
17 29 0.46
18 20 0.32
19 1 0.02
20 3 0.05
21 3 0.05
ACGTcount: A:0.19, C:0.37, G:0.02, T:0.41
Consensus pattern (17 bp):
TTAACCTTTCATCTTCC
Found at i:44585207 original size:35 final size:35
Alignment explanation
Indices: 44585161--44585261 Score: 166
Period size: 35 Copynumber: 2.9 Consensus size: 35
44585151 TTCATCTTCT
*
44585161 TTGACTTTTAACCTTTCATCTTCCTTAACCTCCCC
1 TTGACTTTTAACCTTTCATCTTCCTTAACCTCCCA
44585196 TTGACTTTTAACCTTTCATCTTCCTTAACCTCCCA
1 TTGACTTTTAACCTTTCATCTTCCTTAACCTCCCA
* * *
44585231 TTGACCTTTAACCTTCCATCTTCCTCAACCT
1 TTGACTTTTAACCTTTCATCTTCCTTAACCT
44585262 TTCATATTCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.19, C:0.37, G:0.03, T:0.42
Consensus pattern (35 bp):
TTGACTTTTAACCTTTCATCTTCCTTAACCTCCCA
Found at i:44585243 original size:18 final size:18
Alignment explanation
Indices: 44585185--44585249 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
44585175 TTCATCTTCC
* *
44585185 TTAACCTCCCCTTGACTT
1 TTAACCTCCCATTGACCT
** *
44585203 TTAACCTTTCATCT-TCC-
1 TTAACCTCCCAT-TGACCT
44585220 TTAACCTCCCATTGACCT
1 TTAACCTCCCATTGACCT
*
44585238 TTAACCTTCCAT
1 TTAACCTCCCAT
44585250 CTTCCTCAAC
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
16 1 0.03
17 12 0.34
18 21 0.60
19 1 0.03
ACGTcount: A:0.20, C:0.37, G:0.03, T:0.40
Consensus pattern (18 bp):
TTAACCTCCCATTGACCT
Found at i:44590402 original size:2 final size:2
Alignment explanation
Indices: 44590395--44590450 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
44590385 AAATTCACAC
44590395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44590437 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
44590451 GTTGTGATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44590643 original size:24 final size:24
Alignment explanation
Indices: 44590609--44590654 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
44590599 ATGGATGTTC
*
44590609 AACCTTTCATCTTCCTTAACTTTT
1 AACCTTCCATCTTCCTTAACTTTT
44590633 AACCTTCCATCTTCCTTAACTT
1 AACCTTCCATCTTCCTTAACTT
44590655 CCCATTGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46
Consensus pattern (24 bp):
AACCTTCCATCTTCCTTAACTTTT
Found at i:44591203 original size:28 final size:30
Alignment explanation
Indices: 44591163--44591221 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
44591153 ATTTTCACTT
44591163 AATATTTA-ATTTTCAGTACTT-ATTTTTC
1 AATATTTATATTTTCAGTACTTAATTTTTC
* *
44591191 AATATTTATTTTTTTCAGTTCTTAATTTTTC
1 AATATTTA-TATTTTCAGTACTTAATTTTTC
44591222 GGAGTGTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
30 11 0.42
31 7 0.27
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.61
Consensus pattern (30 bp):
AATATTTATATTTTCAGTACTTAATTTTTC
Found at i:44596708 original size:28 final size:28
Alignment explanation
Indices: 44596676--44596731 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
44596666 TTCCCCCAAC
* *
44596676 TCAAAACGATAAGATTCAAACCAACAAA
1 TCAAAACAAGAAGATTCAAACCAACAAA
44596704 TCAAAACAAGAAGATTCAAACCAACAAA
1 TCAAAACAAGAAGATTCAAACCAACAAA
44596732 GAGAGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.59, C:0.21, G:0.07, T:0.12
Consensus pattern (28 bp):
TCAAAACAAGAAGATTCAAACCAACAAA
Found at i:44598900 original size:16 final size:18
Alignment explanation
Indices: 44598879--44598911 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
44598869 TATTATTTTC
44598879 AATTAA-TAAAA-TAAAT
1 AATTAATTAAAACTAAAT
44598895 AATTAATTAAAACTAAA
1 AATTAATTAAAACTAAA
44598912 AGTAATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTAATTAAAACTAAAT
Found at i:44613000 original size:24 final size:25
Alignment explanation
Indices: 44612973--44613028 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
44612963 CGACACCAAA
44612973 GAGATTTATAATTAAATATAT-ATT
1 GAGATTTATAATTAAATATATAATT
** *
44612997 GAGATAAATAATTAAATCTATAATT
1 GAGATTTATAATTAAATATATAATT
*
44613022 AAGATTT
1 GAGATTT
44613029 CATTTCATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (25 bp):
GAGATTTATAATTAAATATATAATT
Found at i:44616418 original size:3 final size:3
Alignment explanation
Indices: 44616410--44616442 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
44616400 CAGCCGCCAC
*
44616410 CTT CTT CTT ATT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
44616443 GGTGGTGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:44618232 original size:14 final size:14
Alignment explanation
Indices: 44618213--44618270 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
44618203 TTTTTAACCA
44618213 GGACCTTGAACCCT
1 GGACCTTGAACCCT
* *
44618227 GGACCTTAAATCCT
1 GGACCTTGAACCCT
**
44618241 AAACCTTGAACCTCT
1 GGACCTTGAACC-CT
* *
44618256 AGACTTTGAACCCT
1 GGACCTTGAACCCT
44618270 G
1 G
44618271 ATCCTTGATC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.26
Consensus pattern (14 bp):
GGACCTTGAACCCT
Found at i:44618914 original size:15 final size:16
Alignment explanation
Indices: 44618891--44618923 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
44618881 TTCTATTTGA
*
44618891 TTATTAAATT-TATTT
1 TTATAAAATTATATTT
44618906 TTATAAAATTATATTT
1 TTATAAAATTATATTT
44618922 TT
1 TT
44618924 GTATTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATAAAATTATATTT
Found at i:44620902 original size:2 final size:2
Alignment explanation
Indices: 44620895--44620935 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
44620885 ACTCAAAGTG
* *
44620895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A AA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44620936 AAATCAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:44620930 original size:62 final size:61
Alignment explanation
Indices: 44620853--44620987 Score: 225
Period size: 62 Copynumber: 2.2 Consensus size: 61
44620843 CATTTTTGTT
* * *
44620853 TATATATATAATTTATATATAAAATCAATGAAACTCAAAGTGTATATATATATATATATATA
1 TATATATAAAATTTATATATAAAATCAATGAAACTCAAAGTATATATATATATATA-AAATA
*
44620915 TATATATAAAATTTATATATAAAATCAATGAAACTCAAAGTATATATATATATATAAAATT
1 TATATATAAAATTTATATATAAAATCAATGAAACTCAAAGTATATATATATATATAAAATA
44620976 TATATATAAAAT
1 TATATATAAAAT
44620988 CAATGAAACT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
61 15 0.22
62 54 0.78
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (61 bp):
TATATATAAAATTTATATATAAAATCAATGAAACTCAAAGTATATATATATATATAAAATA
Found at i:44620966 original size:48 final size:48
Alignment explanation
Indices: 44620907--44621002 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
44620897 TATATATATA
44620907 TATATATATATATATAAAATTTATATATAAAATCAATGAAACTCAAAG
1 TATATATATATATATAAAATTTATATATAAAATCAATGAAACTCAAAG
44620955 TATATATATATATATAAAATTTATATATAAAATCAATGAAACTCAAAG
1 TATATATATATATATAAAATTTATATATAAAATCAATGAAACTCAAAG
44621003 CAGTATGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (48 bp):
TATATATATATATATAAAATTTATATATAAAATCAATGAAACTCAAAG
Done.