Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold84
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: 4163231
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 246351 characters in sequence are not A, C, G, or T
File 1 of 11
Found at i:3495 original size:24 final size:24
Alignment explanation
Indices: 3463--3541 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 24
3453 AAATCTGTCA
* *
3463 TTCTCTTTTGTTTTCTTCTTTCTT
1 TTCTTTTTTGTTTTCTTCTTTATT
*
3487 TTCTTTTTTTTTTTCCTT-TTTATT
1 TTCTTTTTTGTTTT-CTTCTTTATT
*
3511 TTCTGTTTGTTCGTTTTTCTTGCTTTTTT
1 TTCT-TTT-TT-G-TTTTCTT-CTTTATT
3540 TT
1 TT
3542 GTTGTCCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
24 21 0.49
25 6 0.14
26 2 0.05
27 3 0.07
28 4 0.09
29 7 0.16
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.77
Consensus pattern (24 bp):
TTCTTTTTTGTTTTCTTCTTTATT
Found at i:7449 original size:18 final size:19
Alignment explanation
Indices: 7426--7464 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
7416 GGGGTGTTCC
7426 AAAGGTT-CACTTA-AAGAA
1 AAAGGTTGCA-TTACAAGAA
7444 AAAGGTTGCATTACAAGAA
1 AAAGGTTGCATTACAAGAA
7463 AA
1 AA
7465 CCAAGACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (19 bp):
AAAGGTTGCATTACAAGAA
Found at i:13590 original size:60 final size:62
Alignment explanation
Indices: 13515--13650 Score: 147
Period size: 64 Copynumber: 2.2 Consensus size: 62
13505 TTAACTTAAA
* * * *
13515 TAAATGAACTAAACTCATG-CATTAACT-ATTCCAGCAACTAG-TTAATTTAAGAAGCAAAA-T
1 TAAATAAACTAAACTCATGTCAATAAATAATTCCAGAAACTAGATTAA-TTAA-AAGCAAAACT
* *
13575 TAAATAAACTTAACTCATGCTTCAATAAATAATTCTAGAAACTAGATTAATTAAAAGCAAAACT
1 TAAATAAACTAAACTCATG--TCAATAAATAATTCCAGAAACTAGATTAATTAAAAGCAAAACT
13639 TAAATAAA-TAAA
1 TAAATAAACTAAA
13651 GGTTCAACAA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
60 17 0.27
63 17 0.27
64 25 0.40
65 4 0.06
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (62 bp):
TAAATAAACTAAACTCATGTCAATAAATAATTCCAGAAACTAGATTAATTAAAAGCAAAACT
Found at i:16705 original size:16 final size:17
Alignment explanation
Indices: 16680--16714 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16670 CACACTTATT
16680 TTCTCAATTTTTT-TTC
1 TTCTCAATTTTTTCTTC
*
16696 TTCTCCATTTTTTCTTC
1 TTCTCAATTTTTTCTTC
16713 TT
1 TT
16715 TTTGCTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTCAATTTTTTCTTC
Found at i:20161 original size:849 final size:849
Alignment explanation
Indices: 18524--20224 Score: 3384
Period size: 849 Copynumber: 2.0 Consensus size: 849
18514 AAAACTGAAG
*
18524 AAAGATAACAATTGAAACCTCACAACAAACCTTATATTCACTCTGAAAGAAAGAAATTGATAACA
1 AAAGATAACAATTGAAACCTCACAACAAACCTTATATCCACTCTGAAAGAAAGAAATTGATAACA
18589 CTCACGCTCGTGTTTGCACTCGTATGTTGGCTTTTACCTCCTCTCTATTGTGCTCACGTTCTCGT
66 CTCACGCTCGTGTTTGCACTCGTATGTTGGCTTTTACCTCCTCTCTATTGTGCTCACGTTCTCGT
18654 GCCTTTTTCCACTCTTTCTTTTCTCGTAACTTTGTAAGCAGACTTGCCAAGGCTTAATCGTAGGC
131 GCCTTTTTCCACTCTTTCTTTTCTCGTAACTTTGTAAGCAGACTTGCCAAGGCTTAATCGTAGGC
18719 TTAGGGGTCAGTCACAAATTTGGGAAACAAAGGGAATAATGAATAGGGATAGGGTAGGCTGAACA
196 TTAGGGGTCAGTCACAAATTTGGGAAACAAAGGGAATAATGAATAGGGATAGGGTAGGCTGAACA
18784 AAAAAGAAAAAAACAAATTCAGGTTGAGTGTGGCGTTGAGGTAGAAGAGATAGGGGTAGAAAATC
261 AAAAAGAAAAAAACAAATTCAGGTTGAGTGTGGCGTTGAGGTAGAAGAGATAGGGGTAGAAAATC
18849 AATCTTTGTGGATGGGGATTAGAAAAGATGATTACTATAAAAAGAAAAAATAATAATTCCAACAC
326 AATCTTTGTGGATGGGGATTAGAAAAGATGATTACTATAAAAAGAAAAAATAATAATTCCAACAC
18914 TCTTTTTTTTGAATTTTCATTTTGTTTTCTTTTAACACTTCTGATTTCAATAAGAAACTTGCAAA
391 TCTTTTTTTTGAATTTTCATTTTGTTTTCTTTTAACACTTCTGATTTCAATAAGAAACTTGCAAA
18979 TACAACTTGAAAATTTTTTTTCAAATTTTTTTCGAATGTTTTTTTTCACTTCACAAACCTATTCC
456 TACAACTTGAAAATTTTTTTTCAAATTTTTTTCGAATGTTTTTTTTCACTTCACAAACCTATTCC
19044 AGCTTGTCATCGTAAGTCCGTACTTCGCATTTAATGGCTCTGATACCAAATGATACGATCTGCCT
521 AGCTTGTCATCGTAAGTCCGTACTTCGCATTTAATGGCTCTGATACCAAATGATACGATCTGCCT
19109 CGGCGTTGAGCCGAGTCGTATTTAGAATCACCCAATCGTCTACAAAGAAGTAAGGAACAAATGAA
586 CGGCGTTGAGCCGAGTCGTATTTAGAATCACCCAATCGTCTACAAAGAAGTAAGGAACAAATGAA
19174 TACCTAACAAGTATAATTGGTGAAATAGGCTAAATATTGTTTTATAATATCAAAGGTTCAGAAAA
651 TACCTAACAAGTATAATTGGTGAAATAGGCTAAATATTGTTTTATAATATCAAAGGTTCAGAAAA
19239 ATGGCTAAATAGATGTGTTCGGTAATAGTAAAAATGATGGAAGAATAATGGCTCAAGAAACAAGT
716 ATGGCTAAATAGATGTGTTCGGTAATAGTAAAAATGATGGAAGAATAATGGCTCAAGAAACAAGT
19304 AAGAACCAACACTAATAAGTGTCGACCCAACACTTATACGTTTAAAGAGATGGACAGAAAATTCA
781 AAGAACCAACACTAATAAGTGTCGACCCAACACTTATACGTTTAAAGAGATGGACAGAAAATTCA
19369 ATCA
846 ATCA
19373 AAAGATAACAATTGAAACCTCACAACAAACCTTATATCCACTCTGAAAGAAAGAAATTGATAACA
1 AAAGATAACAATTGAAACCTCACAACAAACCTTATATCCACTCTGAAAGAAAGAAATTGATAACA
19438 CTCACGCTCGTGTTTGCACTCGTATGTTGGCTTTTACCTCCTCTCTATTGTGCTCACGTTCTCGT
66 CTCACGCTCGTGTTTGCACTCGTATGTTGGCTTTTACCTCCTCTCTATTGTGCTCACGTTCTCGT
19503 GCCTTTTTCCACTCTTTCTTTTCTCGTAACTTTGTAAGCAGACTTGCCAAGGCTTAATCGTAGGC
131 GCCTTTTTCCACTCTTTCTTTTCTCGTAACTTTGTAAGCAGACTTGCCAAGGCTTAATCGTAGGC
19568 TTAGGGGTCAGTCACAAATTTGGGAAACAAAGGGAATAATGAATAGGGATAGGGTAGGCTGAACA
196 TTAGGGGTCAGTCACAAATTTGGGAAACAAAGGGAATAATGAATAGGGATAGGGTAGGCTGAACA
19633 AAAAAGAAAAAAACAAATTCAGGTTGAGTGTGGCGTTGAGGTAGAAGAGATAGGGGTAGAAAATC
261 AAAAAGAAAAAAACAAATTCAGGTTGAGTGTGGCGTTGAGGTAGAAGAGATAGGGGTAGAAAATC
19698 AATCTTTGTGGATGGGGATTAGAAAAGATGATTACTATAAAAAGAAAAAATAATAATTCCAACAC
326 AATCTTTGTGGATGGGGATTAGAAAAGATGATTACTATAAAAAGAAAAAATAATAATTCCAACAC
19763 TCTTTTTTTTGAATTTTCATTTTGTTTTCTTTTAACACTTCTGATTTCAATAAGAAACTTGCAAA
391 TCTTTTTTTTGAATTTTCATTTTGTTTTCTTTTAACACTTCTGATTTCAATAAGAAACTTGCAAA
19828 TACAACTTGAAAATTTTTTTTCAAATTTTTTTCGAATGTTTTTTTTCACTTCACAAACCTATTCC
456 TACAACTTGAAAATTTTTTTTCAAATTTTTTTCGAATGTTTTTTTTCACTTCACAAACCTATTCC
19893 AGCTTGTCATCGTAAGTCCGTACTTCGCATTTAATGGCTCTGATACCAAATGATACGATCTGCCT
521 AGCTTGTCATCGTAAGTCCGTACTTCGCATTTAATGGCTCTGATACCAAATGATACGATCTGCCT
19958 CGGCGTTGAGCCGAGTCGTATTTAGAATCACCCAATCGTCTACAAAGAAGTAAGGAACAAATGAA
586 CGGCGTTGAGCCGAGTCGTATTTAGAATCACCCAATCGTCTACAAAGAAGTAAGGAACAAATGAA
20023 TACCTAACAAGTATAATTGGTGAAATAGGCTAAATATTGTTTTATAATATCAAAGGTTCAGAAAA
651 TACCTAACAAGTATAATTGGTGAAATAGGCTAAATATTGTTTTATAATATCAAAGGTTCAGAAAA
*
20088 ATGGCTAAATAGATGTGTTCGGTAATAGTAAAATTGATGGAAGAATAATGGCTCAAGAAACAAGT
716 ATGGCTAAATAGATGTGTTCGGTAATAGTAAAAATGATGGAAGAATAATGGCTCAAGAAACAAGT
20153 AAGAACCAACACTAATAAGTGTCGACCCAACACTTATACGTTTAAAGAGATGGACAGAAAATTCA
781 AAGAACCAACACTAATAAGTGTCGACCCAACACTTATACGTTTAAAGAGATGGACAGAAAATTCA
20218 ATCA
846 ATCA
20222 AAA
1 AAA
20225 CCTCGACCTG
Statistics
Matches: 850, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
849 850 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (849 bp):
AAAGATAACAATTGAAACCTCACAACAAACCTTATATCCACTCTGAAAGAAAGAAATTGATAACA
CTCACGCTCGTGTTTGCACTCGTATGTTGGCTTTTACCTCCTCTCTATTGTGCTCACGTTCTCGT
GCCTTTTTCCACTCTTTCTTTTCTCGTAACTTTGTAAGCAGACTTGCCAAGGCTTAATCGTAGGC
TTAGGGGTCAGTCACAAATTTGGGAAACAAAGGGAATAATGAATAGGGATAGGGTAGGCTGAACA
AAAAAGAAAAAAACAAATTCAGGTTGAGTGTGGCGTTGAGGTAGAAGAGATAGGGGTAGAAAATC
AATCTTTGTGGATGGGGATTAGAAAAGATGATTACTATAAAAAGAAAAAATAATAATTCCAACAC
TCTTTTTTTTGAATTTTCATTTTGTTTTCTTTTAACACTTCTGATTTCAATAAGAAACTTGCAAA
TACAACTTGAAAATTTTTTTTCAAATTTTTTTCGAATGTTTTTTTTCACTTCACAAACCTATTCC
AGCTTGTCATCGTAAGTCCGTACTTCGCATTTAATGGCTCTGATACCAAATGATACGATCTGCCT
CGGCGTTGAGCCGAGTCGTATTTAGAATCACCCAATCGTCTACAAAGAAGTAAGGAACAAATGAA
TACCTAACAAGTATAATTGGTGAAATAGGCTAAATATTGTTTTATAATATCAAAGGTTCAGAAAA
ATGGCTAAATAGATGTGTTCGGTAATAGTAAAAATGATGGAAGAATAATGGCTCAAGAAACAAGT
AAGAACCAACACTAATAAGTGTCGACCCAACACTTATACGTTTAAAGAGATGGACAGAAAATTCA
ATCA
Found at i:37825 original size:18 final size:18
Alignment explanation
Indices: 37802--37837 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
37792 AAACCCTAGA
37802 ATTCTTT-TGAATCTGATT
1 ATTCTTTGTG-ATCTGATT
37820 ATTCTTTGTGATCTGATT
1 ATTCTTTGTGATCTGATT
37838 TTTTTAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (18 bp):
ATTCTTTGTGATCTGATT
Found at i:44002 original size:18 final size:18
Alignment explanation
Indices: 43979--44013 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43969 AAACCCTAGA
43979 ATTCTTT-TGAATCTGATT
1 ATTCTTTGTG-ATCTGATT
43997 ATTCTTTGTGATCTGAT
1 ATTCTTTGTGATCTGAT
44014 GTTTTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.20, C:0.11, G:0.14, T:0.54
Consensus pattern (18 bp):
ATTCTTTGTGATCTGATT
Found at i:48570 original size:29 final size:29
Alignment explanation
Indices: 48501--48571 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
48491 GGTGCATTAC
* *
48501 AAAGATCGAAAGGTATACAGTGAAAAACA
1 AAAGATCCAAAGGTATACAGCGAAAAACA
*
48530 AAAGATCGAAAGGTATACAGCGAAAAGA-A
1 AAAGATCCAAAGGTATACAGCGAAAA-ACA
48559 AAAG-TACCAAAGG
1 AAAGAT-CCAAAGG
48572 GACCGGTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 1 0.03
29 36 0.95
30 1 0.03
ACGTcount: A:0.55, C:0.11, G:0.23, T:0.11
Consensus pattern (29 bp):
AAAGATCCAAAGGTATACAGCGAAAAACA
Found at i:69774 original size:24 final size:24
Alignment explanation
Indices: 69747--69823 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
69737 AAATGAATGC
69747 ATATTAGCTGCAAATAATGATGGA
1 ATATTAGCTGCAAATAATGATGGA
* * *
69771 ATA-TGGCTTGCACTAGTATAT-AT-GC
1 ATATTAGC-TGCA--AATA-ATGATGGA
69796 ATATTAGCTGCAAATAATGATGGA
1 ATATTAGCTGCAAATAATGATGGA
69820 ATAT
1 ATAT
69824 GGCTTGCACT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 2 0.05
23 8 0.20
24 12 0.30
25 8 0.20
26 8 0.20
27 2 0.05
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (24 bp):
ATATTAGCTGCAAATAATGATGGA
Found at i:69800 original size:49 final size:49
Alignment explanation
Indices: 69743--69842 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
69733 ATTCAAATGA
69743 ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
1 ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
69792 ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
1 ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
69841 AT
1 AT
69843 CTTTCTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (49 bp):
ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
Found at i:69831 original size:24 final size:24
Alignment explanation
Indices: 69755--69831 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
69745 GCATATTAGC
69755 TGCAAATAATGATGGAATATGGCT
1 TGCAAATAATGATGGAATATGGCT
* * *
69779 TGCACTAGTATAT-AT-GCATATTAGC-
1 TGCA--AATA-ATGATGGAATA-TGGCT
69804 TGCAAATAATGATGGAATATGGCT
1 TGCAAATAATGATGGAATATGGCT
69828 TGCA
1 TGCA
69832 CTAGTATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 2 0.05
23 8 0.20
24 12 0.30
25 8 0.20
26 8 0.20
27 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (24 bp):
TGCAAATAATGATGGAATATGGCT
Found at i:75349 original size:42 final size:40
Alignment explanation
Indices: 75302--75385 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 40
75292 TTTTGAGGTG
* * * *
75302 TGATTTCATGTAAGACCATGTCTGGGACATTGGCTTCGTATA
1 TGATTT-ATATAAGACCATGTCTCGGACAGTGGCATCG-ATA
* *
75344 TGATTTGTATAAGACCCTGTCTCGGACAGTGGCATCGATA
1 TGATTTATATAAGACCATGTCTCGGACAGTGGCATCGATA
75384 TG
1 TG
75386 TGTTAACATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
40 5 0.14
41 25 0.69
42 6 0.17
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (40 bp):
TGATTTATATAAGACCATGTCTCGGACAGTGGCATCGATA
Found at i:89846 original size:20 final size:20
Alignment explanation
Indices: 89821--89867 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
89811 AGCTCGTTTC
*
89821 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
89841 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
89861 CAGCTCA
1 CAGCTCA
89868 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:91497 original size:17 final size:17
Alignment explanation
Indices: 91475--91507 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
91465 TAGACTGTAG
91475 CACCTGGCAAATAGTAT
1 CACCTGGCAAATAGTAT
91492 CACCTGGCAAATAGTA
1 CACCTGGCAAATAGTA
91508 CCGCTTGACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (17 bp):
CACCTGGCAAATAGTAT
Found at i:96540 original size:27 final size:27
Alignment explanation
Indices: 96502--96553 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
96492 TCATTGAAGC
*
96502 ATCTTCATTGCTGTCCATGCATGTATT
1 ATCTTCAATGCTGTCCATGCATGTATT
*
96529 ATCTTCAATGCTGTCTATGCATGTA
1 ATCTTCAATGCTGTCCATGCATGTA
96554 CCTACAAACA
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:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (27 bp):
ATCTTCAATGCTGTCCATGCATGTATT
Found at i:96954 original size:20 final size:20
Alignment explanation
Indices: 96907--96956 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
96897 AACGAGTTCA
*
96907 TTGAGCTAGAATCGAGCTTAT
1 TTGAGCTA-AATCGAGCTAAT
*
96928 TTAAGCTAAA-CGAGCTAAAT
1 TTGAGCTAAATCGAGCT-AAT
96948 TTGAGCTAA
1 TTGAGCTAA
96957 GTCAGCTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (20 bp):
TTGAGCTAAATCGAGCTAAT
Found at i:98611 original size:16 final size:18
Alignment explanation
Indices: 98577--98615 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
98567 TTTTCTTTCG
98577 TTTCTTTTTCAACATTTT
1 TTTCTTTTTCAACATTTT
98595 TTTCTTTTTC-A-ATTTT
1 TTTCTTTTTCAACATTTT
98611 TTTCT
1 TTTCT
98616 CATTCTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.48
17 1 0.05
18 10 0.48
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTTTTCAACATTTT
Found at i:98624 original size:18 final size:16
Alignment explanation
Indices: 98590--98632 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
98580 CTTTTTCAAC
*
98590 ATTTTTTTCTTTTTCA
1 ATTTTTTTCTTTCTCA
98606 ATTTTTTTCTCATTCTCA
1 ATTTTTTTCT--TTCTCA
98624 ATTTCTTTT
1 ATTT-TTTT
98633 TCAATTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 10 0.43
18 9 0.39
19 4 0.17
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTTTCTTTCTCA
Found at i:98641 original size:27 final size:28
Alignment explanation
Indices: 98595--98661 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
98585 TCAACATTTT
98595 TTTCTTTTTCAATTTTTTTCTCATTC-TCAA
1 TTTCTTTTTCAA--TTTTTCT-ATTCTTCAA
**
98625 TTTCTTTTTCAA-TTTTCTATTCTTCGT
1 TTTCTTTTTCAATTTTTCTATTCTTCAA
98652 TTTCTTTTTC
1 TTTCTTTTTC
98662 TCTCACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 4 0.12
27 18 0.53
30 12 0.35
ACGTcount: A:0.12, C:0.19, G:0.01, T:0.67
Consensus pattern (28 bp):
TTTCTTTTTCAATTTTTCTATTCTTCAA
Found at i:98688 original size:18 final size:17
Alignment explanation
Indices: 98667--98761 Score: 59
Period size: 18 Copynumber: 5.4 Consensus size: 17
98657 TTTTCTCTCA
*
98667 CTTTTTTATTTCTTTTTT
1 CTTTTTAATTTC-TTTTT
*
98685 CTTTTACAATTTCTTTTT
1 CTTTT-TAATTTCTTTTT
** *
98703 CTTTTTCGTTTTCTATTT
1 CTTTTT-AATTTCTTTTT
* *
98721 CTTTTTCACTTTCCTTTT
1 CTTTTT-AATTTCTTTTT
*
98739 CTTTTT--CTTCTTTTT
1 CTTTTTAATTTCTTTTT
98754 CATTTTTA
1 C-TTTTTA
98762 TTACAATGTG
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
15 8 0.13
16 5 0.08
18 43 0.70
19 5 0.08
ACGTcount: A:0.08, C:0.18, G:0.01, T:0.73
Consensus pattern (17 bp):
CTTTTTAATTTCTTTTT
Found at i:98759 original size:6 final size:6
Alignment explanation
Indices: 98625--98747 Score: 77
Period size: 6 Copynumber: 20.0 Consensus size: 6
98615 TCATTCTCAA
* * * ** *
98625 TTTCTT TTTCAAT TTTCTAT TCTTCGT TTTCTT TTTCTC TCACTT TTT-TA
1 TTTCTT TTTC-TT TTTCT-T T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** * *
98675 TTTCTTT TTTCTT TTACAA TTTCTT TTTCTT TTTCGT TTTCTA TTTCTT
1 TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
** *
98724 TTTCAC TTTCCT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT
98748 CTTTTTCATT
Statistics
Matches: 85, Mismatches: 27, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
5 4 0.05
6 64 0.75
7 14 0.16
8 3 0.04
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:100552 original size:20 final size:20
Alignment explanation
Indices: 100529--100577 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
100519 GGGTTAAGAT
*
100529 TGAGCTGAATTGTGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
100549 TGAGCTTACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
*
100569 TGGGCTGAA
1 TGAGCTGAA
100578 CTAAGTTAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:103839 original size:14 final size:15
Alignment explanation
Indices: 103794--103845 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 15
103784 TCACTCTCAT
*
103794 TTTCTTTTTCGATTTCT
1 TTTCTTTTTC--TTTCA
103811 TGTTCTTTTTCTTTCA
1 T-TTCTTTTTCTTTCA
103827 TTTCTTTTT-TTTCA
1 TTTCTTTTTCTTTCA
103841 TTTCT
1 TTTCT
103846 CGATTTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 10 0.30
15 8 0.24
16 5 0.15
17 1 0.03
18 9 0.27
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (15 bp):
TTTCTTTTTCTTTCA
Found at i:106197 original size:10 final size:10
Alignment explanation
Indices: 106182--106219 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
106172 TTGGGTTAAG
106182 ATTGAGCTGA
1 ATTGAGCTGA
106192 ATTGAGCTTGA
1 ATTGAGC-TGA
106203 A-TGAGCTGA
1 ATTGAGCTGA
*
106212 CTTGAGCT
1 ATTGAGCT
106220 CGCGTGAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:106227 original size:20 final size:20
Alignment explanation
Indices: 106184--106221 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
106174 GGGTTAAGAT
*
106184 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
*
106204 TGAGCTGACTTGAGCTCG
1 TGAGCTGAATTGAGCTCG
106222 CGTGAGGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.29
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:108258 original size:33 final size:33
Alignment explanation
Indices: 108192--108265 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
108182 TAATAAAATC
*
108192 GAAAAAGAAGAAAAAGAAAAGGCAAGTGAAAAA
1 GAAAAAGAAGAAAAAGAAAAGGCAAATGAAAAA
*
108225 GAAAAAGAA-AAAAAGAGAATGG-AAATGAGAAAA
1 GAAAAAGAAGAAAAAGA-AAAGGCAAATGA-AAAA
108258 GAAAAAGA
1 GAAAAAGA
108266 GAAGTGAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 12 0.32
33 25 0.68
ACGTcount: A:0.70, C:0.01, G:0.24, T:0.04
Consensus pattern (33 bp):
GAAAAAGAAGAAAAAGAAAAGGCAAATGAAAAA
Found at i:108283 original size:28 final size:26
Alignment explanation
Indices: 108219--108291 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 26
108209 AAAGGCAAGT
108219 GAAAAAGAAAAAGAAAAAAAGAGAATGGA
1 GAAAAAG-AAAAG--AAAAAGAGAATGGA
**
108248 -AATGAGAAAAGAAAAAGAGAAGTGAGA
1 GAAAAAGAAAAGAAAAAGAGAA-TG-GA
*
108275 GAAAAAGAAAACAAAAA
1 GAAAAAGAAAAGAAAAA
108292 AAGAGAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
25 10 0.28
26 2 0.06
27 7 0.19
28 17 0.47
ACGTcount: A:0.71, C:0.01, G:0.23, T:0.04
Consensus pattern (26 bp):
GAAAAAGAAAAGAAAAAGAGAATGGA
Found at i:110193 original size:21 final size:23
Alignment explanation
Indices: 110148--110194 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
110138 TCACCTGCAA
* *
110148 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
110171 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
110192 TAA
1 TAA
110195 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:115466 original size:16 final size:16
Alignment explanation
Indices: 115445--115487 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
115435 CTTCTTTTTC
115445 TTTTTTTTTCACGAAA
1 TTTTTTTTTCACGAAA
*
115461 TTTTTTTTTCACGAAT
1 TTTTTTTTTCACGAAA
115477 TTTTTTTTTCA
1 TTTTTTTTTCA
115488 ACTTGATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.65
Consensus pattern (16 bp):
TTTTTTTTTCACGAAA
Found at i:115542 original size:12 final size:12
Alignment explanation
Indices: 115525--115571 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
115515 ATGGAAACCA
115525 TTTTTTTTGAAT
1 TTTTTTTTGAAT
115537 TTTTTTTTGAAT
1 TTTTTTTTGAAT
* *
115549 TTTTTTTTCAAA
1 TTTTTTTTGAAT
115561 TTTTTTTTGAA
1 TTTTTTTTGAA
115572 GAACTACTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.72
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:115543 original size:13 final size:13
Alignment explanation
Indices: 115525--115568 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
115515 ATGGAAACCA
115525 TTTTTTTTGAA-T
1 TTTTTTTTGAATT
115537 TTTTTTTTGAATT
1 TTTTTTTTGAATT
**
115550 TTTTTTTCAAATT
1 TTTTTTTTGAATT
115563 TTTTTT
1 TTTTTT
115569 GAAGAACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:116307 original size:21 final size:23
Alignment explanation
Indices: 116262--116308 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
116252 TCACCTGCAA
* *
116262 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
116285 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
116306 TAA
1 TAA
116309 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:118844 original size:37 final size:37
Alignment explanation
Indices: 118796--118866 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
118786 ACGACATAAG
118796 AAGCGGGGTGACACTACGATA-TAGTGTAGAATCTAAT
1 AAGCGGGGTGACACTACGATACT-GTGTAGAATCTAAT
*
118833 AAGCGGGGTGACACTACGATACTGTGTGGAATCT
1 AAGCGGGGTGACACTACGATACTGTGTAGAATCT
118867 TTCTTTCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
37 31 0.97
38 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (37 bp):
AAGCGGGGTGACACTACGATACTGTGTAGAATCTAAT
Found at i:125872 original size:23 final size:23
Alignment explanation
Indices: 125832--125895 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
125822 TAAACACAAA
* *
125832 ATTTTGTAAAGCCTTTGTAGCAT
1 ATTTTGTGAAGCCATTGTAGCAT
* *
125855 ATTTTGTGAAGTCATTGTGGCAT
1 ATTTTGTGAAGCCATTGTAGCAT
* *
125878 ATTCTGTGAAGCCTTTGT
1 ATTTTGTGAAGCCATTGT
125896 GGTGAGATCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (23 bp):
ATTTTGTGAAGCCATTGTAGCAT
Found at i:125896 original size:23 final size:23
Alignment explanation
Indices: 125840--125897 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
125830 AAATTTTGTA
* *
125840 AAGCCTTTGTAGCATATTTTGTG
1 AAGCCTTTGTGGCATATTCTGTG
* *
125863 AAGTCATTGTGGCATATTCTGTG
1 AAGCCTTTGTGGCATATTCTGTG
125886 AAGCCTTTGTGG
1 AAGCCTTTGTGG
125898 TGAGATCTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.40
Consensus pattern (23 bp):
AAGCCTTTGTGGCATATTCTGTG
Found at i:128050 original size:235 final size:234
Alignment explanation
Indices: 127640--128121 Score: 713
Period size: 235 Copynumber: 2.1 Consensus size: 234
127630 CCCTTGCCGT
* * * **
127640 CCACCCCATTGTTGCCTTGTGGGGAAGATCCTTTCCTCTTTTGGTGAGTTGATTTTCCCCCAATA
1 CCACCCCATTGTTTCCTTGTGGGGAAGATCATTTCCTCTATTGGTGAGTCAATTTTCCCCCAATA
* *
127705 CCCTCCGTTCCACTCAATGATCCACTTTTGGTGCCTATGTTCCCCCTATTGCCAAATTCTCCCCA
66 CCCCCCGTTCCACTCAATGATCCACTTTCGGTGCCTATGTTCCCCCTATTGCCAAATTCTCCCCA
127770 CTTACCATACCTTGGCCAACCATGCACCTACATACCCTCAAATCTTCATTTTTATTTTTATTCTC
131 CTTACCATACCTTGGCCAACCATGCACCTACATACCCTCAAATCTTCATTTTTATTTTTATTCTC
* *
127835 CTCATCTCATATTTTTTATCTTTTCTCTTCCTCCTACCA
196 CTCATCTCATATTTTTTATCTTTTATCCTCCTCCTACCA
*
127874 CCACCCCATTGTTTCCTTGTGGGGAAGATTATTTCCTCTATTGAG-GAGTCAATTTTCCCCCAAT
1 CCACCCCATTGTTTCCTTGTGGGGAAGATCATTTCCTCTATTG-GTGAGTCAATTTTCCCCCAAT
* * *
127938 ACCTCCCCTTTTCACTCCATGATCCACTTTCGGTGCCTATGTTCCCCCTATTGCCAAATTCTCTC
65 ACC-CCCCGTTCCACTCAATGATCCACTTTCGGTGCCTATGTTCCCCCTATTGCCAAATTCTC-C
* * * *
128003 CC-CTTATCGTACCTTGGCCGACCATGCACCTAGATACCC-CTAAATCTTCATTTTTATTTTTAT
128 CCACTTACCATACCTTGGCCAACCATGCACCTACATACCCTC-AAATCTTCATTTTTATTTTTAT
* * *
128066 TCTCCTTATCTCATCTTTTTTCTCTTTTATCCTCCTCCTACCA
192 TCTCCTCATCTCATATTTTTTATCTTTTATCCTCCTCCTACCA
128109 CCA-CCCATT-TTTC
1 CCACCCCATTGTTTC
128122 TACATTTTGC
Statistics
Matches: 224, Mismatches: 20, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
233 4 0.02
234 66 0.29
235 151 0.67
236 3 0.01
ACGTcount: A:0.18, C:0.34, G:0.10, T:0.39
Consensus pattern (234 bp):
CCACCCCATTGTTTCCTTGTGGGGAAGATCATTTCCTCTATTGGTGAGTCAATTTTCCCCCAATA
CCCCCCGTTCCACTCAATGATCCACTTTCGGTGCCTATGTTCCCCCTATTGCCAAATTCTCCCCA
CTTACCATACCTTGGCCAACCATGCACCTACATACCCTCAAATCTTCATTTTTATTTTTATTCTC
CTCATCTCATATTTTTTATCTTTTATCCTCCTCCTACCA
Found at i:129459 original size:35 final size:35
Alignment explanation
Indices: 129432--129557 Score: 173
Period size: 35 Copynumber: 3.6 Consensus size: 35
129422 ATTGATATTT
* * *
129432 TGATTCGTATGTTAAGCATGCTATTATTCTGGTTA
1 TGATTCGCATGTTAAGCATGCTATTATTATGATTA
* *
129467 TGATTCGCATGTTAAGCATTCTATTATTTTGATTA
1 TGATTCGCATGTTAAGCATGCTATTATTATGATTA
*
129502 TGATTCGCATGTTAAGCATGCTATTATTTTGATTA
1 TGATTCGCATGTTAAGCATGCTATTATTATGATTA
*
129537 TGACTT-GCATGTTAAACATGC
1 TGA-TTCGCATGTTAAGCATGC
129558 CATTGTGTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 82 0.98
36 2 0.02
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.44
Consensus pattern (35 bp):
TGATTCGCATGTTAAGCATGCTATTATTATGATTA
Found at i:141600 original size:10 final size:9
Alignment explanation
Indices: 141577--141643 Score: 71
Period size: 10 Copynumber: 6.9 Consensus size: 9
141567 TGCTAATAAC
*
141577 GAGCTCAAT
1 GAGCTGAAT
141586 GAGCTGAATT
1 GAGCTGAA-T
141596 GAGCTCGAAT
1 GAGCT-GAAT
141606 GAGCTTGAAT
1 GAGC-TGAAT
*
141616 AAGCTGAATT
1 GAGCTGAA-T
141626 GAGCTCGAAT
1 GAGCT-GAAT
141636 GAGCTGAA
1 GAGCTGAA
141644 CCGCATGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
9 14 0.28
10 29 0.58
11 7 0.14
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (9 bp):
GAGCTGAAT
Found at i:141965 original size:78 final size:75
Alignment explanation
Indices: 141882--142028 Score: 181
Period size: 78 Copynumber: 1.9 Consensus size: 75
141872 TATGTTAGAT
**
141882 TCGAATATATATGTAAATACATGA-ATAAGT-CTTGAATTTAGATAAAGGTATGAGTATGTATAT
1 TCGAATATATATACAAATACAT-ATATAAGTCCTTGAATTTAGATAAA-GTATGA--ATGT-TAT
141945 ATATGTATATAATGC
61 ATATGTATATAATGC
* * * *
141960 TCGAATATATATACATATATATATATAAGTCCTTGAATTTAGTTAAAGTATGAATGTTGTATATG
1 TCGAATATATATACAAATACATATATAAGTCCTTGAATTTAGATAAAGTATGAATGTTATATATG
142025 TATA
66 TATA
142029 AATTCTTGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
75 11 0.18
76 4 0.07
77 1 0.02
78 30 0.49
79 15 0.25
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.39
Consensus pattern (75 bp):
TCGAATATATATACAAATACATATATAAGTCCTTGAATTTAGATAAAGTATGAATGTTATATATG
TATATAATGC
Found at i:142497 original size:41 final size:41
Alignment explanation
Indices: 142449--142528 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
142439 TGATCGAATG
* *
142449 TTTCAGACTTTACATCTAGCAGGTTTGACGCCGGTGAAATA
1 TTTCAGACTTTACATCTAGCAGGCTTAACGCCGGTGAAATA
** *
142490 TTTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTGAAA
1 TTTCAGACTTTACATCTAGCAGGCTTAACGCCGGTGAAA
142529 CAATTCGGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (41 bp):
TTTCAGACTTTACATCTAGCAGGCTTAACGCCGGTGAAATA
Found at i:142548 original size:41 final size:41
Alignment explanation
Indices: 142450--142551 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 41
142440 GATCGAATGT
* * * * *
142450 TTCAGACTTTACA-TCTAGCAGGTTTGACGCCGGTGAAATAT
1 TTCAGACTATA-AGTCTAGCAGGCTTAACGCCGGTGAAACAA
* * *
142491 TTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTGAAACAA
1 TTCAGACTATAAGTCTAGCAGGCTTAACGCCGGTGAAACAA
*
142532 TTCGGACTATAAGTCTAGCA
1 TTCAGACTATAAGTCTAGCA
142552 AGCTAAAAGC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (41 bp):
TTCAGACTATAAGTCTAGCAGGCTTAACGCCGGTGAAACAA
Found at i:150809 original size:16 final size:17
Alignment explanation
Indices: 150790--150822 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
150780 TAACCGTAAG
150790 ATTAA-TTAAATTAATT
1 ATTAATTTAAATTAATT
*
150806 ATTAATTTAATTTAATT
1 ATTAATTTAAATTAATT
150823 TGACAGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTAATTTAAATTAATT
Found at i:171115 original size:20 final size:20
Alignment explanation
Indices: 171078--171116 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
171068 GTTAAATAAG
*
171078 TAATTAAATAAGTAAAAATT
1 TAATTAAATAAGGAAAAATT
* *
171098 TAATTTAATAAGGCAAAAT
1 TAATTAAATAAGGAAAAAT
171117 AGCATCATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (20 bp):
TAATTAAATAAGGAAAAATT
Found at i:172074 original size:41 final size:42
Alignment explanation
Indices: 171931--172249 Score: 264
Period size: 41 Copynumber: 7.8 Consensus size: 42
171921 TGAGTCCAGC
* * *
171931 AGGCTTCATGCCAGTGATTTATATCAGGCT-TTGTGTCTAGT
1 AGGCTTCGTGCCAGTGATTTATATCAGGCTCTAGTGCCTAGT
* * * * * *
171972 AGACTCCGTGTC-G-GCATGTTCTATCAGGCTCT-GTGCATACT
1 AGGCTTCGTGCCAGTG-AT-TTATATCAGGCTCTAGTGCCTAGT
* * *
172013 AGGTTTCGTGCCAATGATTTATATCTGGCT-TAGTGCCTAGT
1 AGGCTTCGTGCCAGTGATTTATATCAGGCTCTAGTGCCTAGT
* * *
172054 AGCCTTCGTGCCAGTGATTTATATTAGGCTCTA-TGCCTAGC
1 AGGCTTCGTGCCAGTGATTTATATCAGGCTCTAGTGCCTAGT
* *
172095 AAGCTTCGTGCC-GATGATTTATATCAGGCTCTA-TGCCTAGC
1 AGGCTTCGTGCCAG-TGATTTATATCAGGCTCTAGTGCCTAGT
* * * * *
172136 AGGCTTAGTGTCAGTGATTTATATTAGGTTC-AGTGCCTAGC
1 AGGCTTCGTGCCAGTGATTTATATCAGGCTCTAGTGCCTAGT
* * * * **
172177 AGGCTTGGTGCCGGTGATTTATACCAGGCTCTA-TACCTACC
1 AGGCTTCGTGCCAGTGATTTATATCAGGCTCTAGTGCCTAGT
*
172218 AGGCTTAGTAG-CAGTGATTTATATCAGGCTCT
1 AGGCTTCGT-GCCAGTGATTTATATCAGGCTCT
172250 GTGTCGGTGT
Statistics
Matches: 224, Mismatches: 42, Indels: 24
0.77 0.14 0.08
Matches are distributed among these distances:
39 1 0.00
40 6 0.03
41 208 0.93
42 8 0.04
43 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (42 bp):
AGGCTTCGTGCCAGTGATTTATATCAGGCTCTAGTGCCTAGT
Found at i:172174 original size:123 final size:123
Alignment explanation
Indices: 172027--172249 Score: 299
Period size: 123 Copynumber: 1.8 Consensus size: 123
172017 TTCGTGCCAA
* ** *
172027 TGATTTATATCTGGCTTAGTGCCTAGTAGCCTTCGTGCCAGTGATTTATATTAGGCTCTATGCCT
1 TGATTTATATCTGGCTTAGTGCCTAGCAGCCTTCGTGCCAGTGATTTATACCAGGCTCTATACCT
* * *
172092 AGCAAGCTTCGT-GCCGATGATTTATATCAGGCTCTATGCCTAGCAGGCTTAGTGTCAG
66 ACCAAGCTTAGTAGCAG-TGATTTATATCAGGCTCTATGCCTAGCAGGCTTAGTGTCAG
* * *
172150 TGATTTATAT-TAGG-TTCAGTGCCTAGCAGGCTTGGTGCCGGTGATTTATACCAGGCTCTATAC
1 TGATTTATATCT-GGCTT-AGTGCCTAGCAGCCTTCGTGCCAGTGATTTATACCAGGCTCTATAC
*
172213 CTACCAGGCTTAGTAGCAGTGATTTATATCAGGCTCT
64 CTACCAAGCTTAGTAGCAGTGATTTATATCAGGCTCT
172250 GTGTCGGTGT
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
122 3 0.03
123 80 0.93
124 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (123 bp):
TGATTTATATCTGGCTTAGTGCCTAGCAGCCTTCGTGCCAGTGATTTATACCAGGCTCTATACCT
ACCAAGCTTAGTAGCAGTGATTTATATCAGGCTCTATGCCTAGCAGGCTTAGTGTCAG
Found at i:179135 original size:50 final size:50
Alignment explanation
Indices: 179026--179222 Score: 200
Period size: 50 Copynumber: 3.9 Consensus size: 50
179016 ATATTTGGGT
* * * *
179026 GATGAGA--TCCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA-C--CGA
*
179077 GATTATGAGAGGTCCCATGTAAGACCATATCGGGGACATGGCATTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGA
** * * *
179130 GATGAGAGGTCCCCCGTAAGACCATGTCTGAGACATGGCATGGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGA
* ** *
179180 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTG
1 GATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTG
179223 ATAGTACAAG
Statistics
Matches: 121, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
50 77 0.64
51 1 0.01
53 3 0.02
54 6 0.05
55 1 0.01
56 33 0.27
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGA
Found at i:193652 original size:183 final size:183
Alignment explanation
Indices: 193339--193709 Score: 708
Period size: 183 Copynumber: 2.0 Consensus size: 183
193329 TAAAAAGTGC
* *
193339 AAAAA-TTGAGTTCTACATGTTAGAGGTGTCCAATTGTTATGAAATTTTAAATTGGAGGTCTTTA
1 AAAAAGTTGAGTTCTACATGTTAGAAGTGTCCAATCGTTATGAAATTTTAAATTGGAGGTCTTTA
193403 TATGGTAATTATACCATTGGTTAAGTTATGGACAAAAATGGACATGAGATAAGTGAAATAGGAAA
66 TATGGTAATTATACCATTGGTTAAGTTATGGACAAAAATGGACATGAGATAAGTGAAATAGGAAA
193468 TTTTTAAGTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGGA
131 TTTTTAAGTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGGA
193521 AAAAAGTTGAGTTCTACATGTTAGAAGTGTCCAATCGTTATGAAATTTTAAATTGGAGGTCTTTA
1 AAAAAGTTGAGTTCTACATGTTAGAAGTGTCCAATCGTTATGAAATTTTAAATTGGAGGTCTTTA
193586 TATGGTAATTATACCATTGGTTAAGTTATGGACAAAAATGGACATGAGATAAGTGAAATAGGAAA
66 TATGGTAATTATACCATTGGTTAAGTTATGGACAAAAATGGACATGAGATAAGTGAAATAGGAAA
*
193651 TTTTTAAGTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGGG
131 TTTTTAAGTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGGA
193704 AAAAAG
1 AAAAAG
193710 ATGGCAAATT
Statistics
Matches: 185, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
182 5 0.03
183 180 0.97
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (183 bp):
AAAAAGTTGAGTTCTACATGTTAGAAGTGTCCAATCGTTATGAAATTTTAAATTGGAGGTCTTTA
TATGGTAATTATACCATTGGTTAAGTTATGGACAAAAATGGACATGAGATAAGTGAAATAGGAAA
TTTTTAAGTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGGA
Found at i:194837 original size:14 final size:13
Alignment explanation
Indices: 194815--194948 Score: 57
Period size: 12 Copynumber: 10.2 Consensus size: 13
194805 AAGTGTTTTC
*
194815 TTTCTTCAAGTGTT
1 TTTCATCAAGT-TT
194829 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
194843 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
* *
194855 TTAATTACCAAGTTTTT
1 TT--TCATCAAG--TTT
* *
194872 TTTTATTAAG-TT
1 TTTCATCAAGTTT
* *
194884 TTGCATTAAGTTCT
1 TTTCATCAAGTT-T
194898 TTT--T-AAG-TT
1 TTTCATCAAGTTT
194907 TTTCATCAAG-TT
1 TTTCATCAAGTTT
*
194919 TTCCATCAAGTTT
1 TTTCATCAAGTTT
*
194932 TTAATCATTAAGTTT
1 TT--TCATCAAGTTT
194947 TT
1 TT
194949 CAATTAAGCT
Statistics
Matches: 96, Mismatches: 10, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
9 4 0.04
10 1 0.01
11 4 0.04
12 28 0.29
13 14 0.15
14 18 0.19
15 22 0.23
17 5 0.05
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:194938 original size:12 final size:12
Alignment explanation
Indices: 194826--194938 Score: 59
Period size: 12 Copynumber: 8.9 Consensus size: 12
194816 TTCTTCAAGT
194826 GTTTTTCATCAA
1 GTTTTTCATCAA
*
194838 GTTCTTTTATCAA
1 GTT-TTTCATCAA
*
194851 GTTTTTAATTACCAA
1 GTTTTTCA-T--CAA
* *
194866 GTTTTTTTTTATTAA
1 G---TTTTTCATCAA
* *
194881 GTTTTGCATTAA
1 GTTTTTCATCAA
*
194893 GTTCTTT--TTAA
1 GTT-TTTCATCAA
194904 GTTTTTCATCAA
1 GTTTTTCATCAA
*
194916 GTTTTCCATCAA
1 GTTTTTCATCAA
*
194928 GTTTTTAATCA
1 GTTTTTCATCA
194939 TTAAGTTTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
10 3 0.04
11 7 0.09
12 42 0.52
13 14 0.17
15 7 0.09
17 1 0.01
18 6 0.08
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.54
Consensus pattern (12 bp):
GTTTTTCATCAA
Found at i:197653 original size:25 final size:25
Alignment explanation
Indices: 197618--197680 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
197608 TTGAGTCTAG
*
197618 CAGGCTTTGTGCCGATGATTTATAT
1 CAGGCTCTGTGCCGATGATTTATAT
*
197643 CAGGCTCTGTGCCGGTGATTTATAT
1 CAGGCTCTGTGCCGATGATTTATAT
*
197668 CAGGCTCTATGCC
1 CAGGCTCTGTGCC
197681 TAGCAGGCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.35
Consensus pattern (25 bp):
CAGGCTCTGTGCCGATGATTTATAT
Found at i:197755 original size:41 final size:41
Alignment explanation
Indices: 197692--197811 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 41
197682 AGCAGGCTCC
* * * * *
197692 GCTCGGTGCCTAGCAGGATTCGTGCCAGTAATTTATATC-A
1 GCTCTGTGCCTAGCAGGCTTCGTGTCGGTGATTTATATCAA
* *
197732 GGTTTAGTGCCTAGCAGGCTTCGTGTCGGTGATTTATATCAA
1 GCTCT-GTGCCTAGCAGGCTTCGTGTCGGTGATTTATATCAA
*
197774 GCTCTGTGCCTAGCAGGCTTTGTGTCGGTGATTTATAT
1 GCTCTGTGCCTAGCAGGCTTCGTGTCGGTGATTTATAT
197812 TAGGCTTGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.03
41 62 0.91
42 4 0.06
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (41 bp):
GCTCTGTGCCTAGCAGGCTTCGTGTCGGTGATTTATATCAA
Found at i:198931 original size:53 final size:53
Alignment explanation
Indices: 198864--198989 Score: 216
Period size: 53 Copynumber: 2.4 Consensus size: 53
198854 TTGGAATAAG
* *
198864 TATTTAGTTGCTGGAATAAATTACTCATCTTTGTTAATTGAGTTCATCTTAGT
1 TATTTAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGT
*
198917 TATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGT
1 TATTTAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGT
198970 TAATTTAGTTGCTGGAATAA
1 T-ATTTAGTTGCTGGAATAA
198990 TTTATTGTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
53 51 0.75
54 17 0.25
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (53 bp):
TATTTAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGT
Found at i:198965 original size:19 final size:19
Alignment explanation
Indices: 198941--198979 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
198931 AATAAATTAC
198941 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
198960 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
198979 T
1 T
198980 GCTGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:199105 original size:9 final size:9
Alignment explanation
Indices: 199091--199126 Score: 72
Period size: 9 Copynumber: 4.0 Consensus size: 9
199081 TATGTGCTTA
199091 AATGTGTTT
1 AATGTGTTT
199100 AATGTGTTT
1 AATGTGTTT
199109 AATGTGTTT
1 AATGTGTTT
199118 AATGTGTTT
1 AATGTGTTT
199127 GTTAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (9 bp):
AATGTGTTT
Found at i:199393 original size:24 final size:24
Alignment explanation
Indices: 199366--199437 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
199356 GGGCTTTTAA
199366 ATCAATTAAAGGAGAGCATTATAC
1 ATCAATTAAAGGAGAGCATTATAC
199390 ATC-ATTCAAA--AGAGC-TGT-TAC
1 ATCAATT-AAAGGAGAGCAT-TATAC
* * *
199411 ATTATTTAAAGGAAAGCATTATAC
1 ATCAATTAAAGGAGAGCATTATAC
199435 ATC
1 ATC
199438 CTTTAAATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
21 9 0.24
22 8 0.22
23 8 0.22
24 12 0.32
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (24 bp):
ATCAATTAAAGGAGAGCATTATAC
Found at i:199793 original size:52 final size:52
Alignment explanation
Indices: 199731--200051 Score: 624
Period size: 52 Copynumber: 6.2 Consensus size: 52
199721 GTATTTAAGT
**
199731 AGCAGCTTAAGATATCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
1 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
199783 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
1 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
199835 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
1 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
199887 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
1 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
199939 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
1 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
199991 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
1 AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
200043 AGCAGCTTA
1 AGCAGCTTA
200052 TTTTAAACCC
Statistics
Matches: 267, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 267 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (52 bp):
AGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAATAATAGAC
Found at i:215166 original size:29 final size:29
Alignment explanation
Indices: 215124--215196 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
215114 TTAGATATTA
* *
215124 TTAAATATGTCCTAATTAGTTTAGGTGCT
1 TTAAATATGTCCTAATTAGTTCAAGTGCT
*
215153 TTAAATATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGCT
215182 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
215197 ACTAATATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGCT
Found at i:221125 original size:12 final size:12
Alignment explanation
Indices: 221110--221172 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
221100 TCAGGCTCTC
221110 TTTCAATTTCTT
1 TTTCAATTTCTT
*
221122 TTTCCACTCTTTCTT
1 TTT-CA--ATTTCTT
221137 TTTC---TTCTT
1 TTTCAATTTCTT
221146 TTTCAATTTCTT
1 TTTCAATTTCTT
*
221158 TTTCAATCTCTT
1 TTTCAATTTCTT
221170 TTT
1 TTT
221173 GCTTTTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
12 22 0.51
13 2 0.05
14 1 0.02
15 9 0.21
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:221225 original size:15 final size:15
Alignment explanation
Indices: 221202--221248 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
221192 TTTTGAAATC
221202 TCATTTTCATCTT-TT
1 TCATTTTCAT-TTCTT
*
221217 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
221232 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
221248 T
1 T
221249 GTTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:252346 original size:28 final size:28
Alignment explanation
Indices: 252298--252388 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 28
252288 GCCCAATTGT
*
252298 CACACTG-TTACTGTATGGGGCTAAGGCC
1 CACACTGATT-CTGTATTGGGCTAAGGCC
*
252326 CACACTGATTCTATATTGGGCTATA-GCC
1 CACACTGATTCTGTATTGGGCTA-AGGCC
* * *
252354 CATATTGATTCTGTATTGGGCTAAGGCT
1 CACACTGATTCTGTATTGGGCTAAGGCC
252382 CACACTG
1 CACACTG
252389 TACTATTACT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.02
28 48 0.92
29 3 0.06
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (28 bp):
CACACTGATTCTGTATTGGGCTAAGGCC
Found at i:254240 original size:18 final size:18
Alignment explanation
Indices: 254219--254278 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
254209 GACCTCACTC
254219 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** * *
254237 TCTTTTTCAATCTCTTAT
1 TCTTTTTTGATTTCTTTT
254255 TCTTTTCTTTCGATTTCTTTT
1 TC-TTT-TTT-GATTTCTTTT
254276 TCT
1 TCT
254279 CGCTCGCACT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
18 16 0.52
19 3 0.10
20 3 0.10
21 9 0.29
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.70
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:257102 original size:13 final size:13
Alignment explanation
Indices: 257086--257115 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
257076 TTTAAACAAA
*
257086 TTAATTAACTTAT
1 TTAATTAACTAAT
257099 TTAATTAACTAAT
1 TTAATTAACTAAT
257112 TTAA
1 TTAA
257116 CTATCAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:257825 original size:24 final size:24
Alignment explanation
Indices: 257798--257845 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
257788 AAAACTTCAA
257798 CTTACTCCTCAAACTTATGATACT
1 CTTACTCCTCAAACTTATGATACT
257822 CTTACTCCTCAAACTTATGATACT
1 CTTACTCCTCAAACTTATGATACT
257846 TACACTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.38
Consensus pattern (24 bp):
CTTACTCCTCAAACTTATGATACT
Found at i:261348 original size:24 final size:24
Alignment explanation
Indices: 261316--261395 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
261306 GATAACTCTT
*
261316 GAAAGTATGTTTGCTTGTAATTAA
1 GAAAATATGTTTGCTTGTAATTAA
* *
261340 GAAAATATG-TT--TT-TATTTTA
1 GAAAATATGTTTGCTTGTAATTAA
* * *
261360 GAATATGTATTTGCTTGTAATTAA
1 GAAAATATGTTTGCTTGTAATTAA
261384 GAAAATATGTTT
1 GAAAATATGTTT
261396 TTATTTTAGA
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
20 11 0.27
21 4 0.10
23 4 0.10
24 22 0.54
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (24 bp):
GAAAATATGTTTGCTTGTAATTAA
Found at i:270880 original size:14 final size:14
Alignment explanation
Indices: 270861--270892 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
270851 CTTTTCTCTC
*
270861 TTTCTTTTCTTTAA
1 TTTCTTTACTTTAA
270875 TTTCTTTACTTTAA
1 TTTCTTTACTTTAA
270889 TTTC
1 TTTC
270893 ATTCTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTCTTTACTTTAA
Found at i:271664 original size:19 final size:19
Alignment explanation
Indices: 271640--271737 Score: 115
Period size: 19 Copynumber: 4.8 Consensus size: 19
271630 AATCTTCGAG
271640 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
271659 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
271678 GATATATGCAATCTTAGATAT
1 G--ATATGTAATCTTAGATAT
271699 GATATGTAATCTTAGAAGATAT
1 GATATGTAATCTT---AGATAT
*
271721 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
271738 GATTTAATTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
19 30 0.43
20 3 0.04
21 19 0.27
22 8 0.11
23 10 0.14
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:271686 original size:21 final size:21
Alignment explanation
Indices: 271641--271703 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
271631 ATCTTCGAGG
*
271641 ATATGTAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
271660 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
271681 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
271702 AT
1 AT
271704 GTAATCTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 18 0.44
21 23 0.56
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:271747 original size:22 final size:23
Alignment explanation
Indices: 271703--271747 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
271693 AGATATGATA
*
271703 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
271726 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
271748 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:293858 original size:16 final size:17
Alignment explanation
Indices: 293827--293859 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
293817 ATACATATTG
293827 ATTAACACACTAATTAA
1 ATTAACACACTAATTAA
*
293844 ATTAAGACA-TAATTAA
1 ATTAACACACTAATTAA
293860 TATAGACTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (17 bp):
ATTAACACACTAATTAA
Found at i:295249 original size:17 final size:17
Alignment explanation
Indices: 295214--295257 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
295204 CATAACTCGA
*
295214 TTTATTTTCTCTCTATT
1 TTTATTTTTTCTCTATT
* *
295231 TTTATTTTTTCTTTCTT
1 TTTATTTTTTCTCTATT
295248 TTTCATTTTT
1 TTT-ATTTTT
295258 ATTTTCTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTTTCTCTATT
Found at i:295250 original size:18 final size:18
Alignment explanation
Indices: 295218--295270 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
295208 ACTCGATTTA
*
295218 TTTTCTCTCTATTTTTATT
1 TTTTCTTTCT-TTTTTATT
*
295237 TTTTCTTTCTTTTTCATT
1 TTTTCTTTCTTTTTTATT
295255 TTTAT-TTTCTTCTTTT
1 TTT-TCTTTCTT-TTTT
295271 TTTCTCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCTTTCTTTTTTATT
Found at i:295260 original size:24 final size:25
Alignment explanation
Indices: 295218--295281 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
295208 ACTCGATTTA
*
295218 TTTTCTCTCTATTTTTATTTT-TTCT
1 TTTTTTCTC-ATTTTTATTTTCTTCT
295243 TTCTTTT-TCATTTTTATTTTCTTCT
1 TT-TTTTCTCATTTTTATTTTCTTCT
295268 TTTTTTCTCATTTT
1 TTTTTTCTCATTTT
295282 CTCCATGGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
24 15 0.43
25 17 0.49
26 3 0.09
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTTCTCATTTTTATTTTCTTCT
Found at i:298008 original size:20 final size:20
Alignment explanation
Indices: 297983--298021 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
297973 TACTTTCTTC
297983 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
298003 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
298022 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:298370 original size:50 final size:50
Alignment explanation
Indices: 298277--298415 Score: 136
Period size: 50 Copynumber: 2.8 Consensus size: 50
298267 TACTACAAAT
* * * * * ** * *
298277 GCCATATCCCATATATGGTCTTACATGAGAGTTCTCATATCAGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCAGTGCCAAC
* * * *
298327 GTCATGTCCCCGACATTGTCTTACG-GGGCACCTCTCATCTCAGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACGTGGG-ACCTCTCATATCAGTGCCAAC
*
298377 GCCATGTCCCAGACATGGTCTTATGTGGGACCTCTCATA
1 GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATA
298416 ACCTCAATAA
Statistics
Matches: 69, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
49 2 0.03
50 64 0.93
51 3 0.04
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCAGTGCCAAC
Found at i:298889 original size:90 final size:90
Alignment explanation
Indices: 298790--298960 Score: 324
Period size: 90 Copynumber: 1.9 Consensus size: 90
298780 ACATTCATCA
*
298790 AAACAGTCCTTGACTCGAACTTTGGCAAAATTATGATTTTGCCCCTAAACTTTTACATATTTACA
1 AAACAGTCCTTGACTCAAACTTTGGCAAAATTATGATTTTGCCCCTAAACTTTTACATATTTACA
298855 CTTTTGCTCGAAAACTCAGAAATTC
66 CTTTTGCTCGAAAACTCAGAAATTC
*
298880 AAACAGTCCTTGACTCAAACTTTGGCAAAATTATGATTTTGCCCCTAAACTTTTGCATATTTACA
1 AAACAGTCCTTGACTCAAACTTTGGCAAAATTATGATTTTGCCCCTAAACTTTTACATATTTACA
298945 CTTTTGCTCGAAAACT
66 CTTTTGCTCGAAAACT
298961 TCATCCCTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (90 bp):
AAACAGTCCTTGACTCAAACTTTGGCAAAATTATGATTTTGCCCCTAAACTTTTACATATTTACA
CTTTTGCTCGAAAACTCAGAAATTC
Found at i:301618 original size:17 final size:16
Alignment explanation
Indices: 301596--301629 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
301586 AAGACATATT
301596 AATTAACACACTAATTA
1 AATTAACACA-TAATTA
*
301613 AATTAAGACATAATTA
1 AATTAACACATAATTA
301629 A
1 A
301630 TATAGACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (16 bp):
AATTAACACATAATTA
Found at i:301626 original size:16 final size:16
Alignment explanation
Indices: 301586--301629 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
301576 AAATAACATC
301586 AAGACAT-ATT-AATT
1 AAGACATAATTAAATT
*
301600 AACACACTAATTAAATT
1 AAGACA-TAATTAAATT
301617 AAGACATAATTAA
1 AAGACATAATTAA
301630 TATAGACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 5 0.20
15 1 0.04
16 10 0.40
17 9 0.36
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (16 bp):
AAGACATAATTAAATT
Found at i:307352 original size:11 final size:11
Alignment explanation
Indices: 307336--307360 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
307326 GCGATTATTG
307336 TATTTATTGTA
1 TATTTATTGTA
307347 TATTTATTGTA
1 TATTTATTGTA
307358 TAT
1 TAT
307361 AAAGGGACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TATTTATTGTA
Found at i:308666 original size:24 final size:25
Alignment explanation
Indices: 308629--308695 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
308619 TACTGTTATT
* * * *
308629 CAGCTCGGAGGAGCTTACC-ATTTA
1 CAGCTCGTAAGAGCATACCGATTCA
308653 CAGCTCGTAAGAGCATACCGATTCA
1 CAGCTCGTAAGAGCATACCGATTCA
* **
308678 AAGCTCGTGTGAGCATAC
1 CAGCTCGTAAGAGCATAC
308696 ATGTATCCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 16 0.46
25 19 0.54
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.22
Consensus pattern (25 bp):
CAGCTCGTAAGAGCATACCGATTCA
Found at i:316410 original size:6 final size:6
Alignment explanation
Indices: 316399--316508 Score: 80
Period size: 6 Copynumber: 17.3 Consensus size: 6
316389 TTTTTTCTCA
* *
316399 TTTTCT TTTTCT TTTTCT TCCTT-T TTTTCT TTTTCT TTTCTCA TTTTCT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTT-TCT TTTTCT
* * * *
316448 TTTATCT TTCTCT TGTTAT TTTTC- TTTTCT TTTCCTCAT TTTCATTT
1 TTT-TCT TTTTCT TTTTCT TTTTCT TTTTCT TTT--TC-T TTT--TCT
316495 TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TT
316509 CAATTGATCT
Statistics
Matches: 83, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
5 7 0.08
6 52 0.63
7 12 0.14
8 6 0.07
9 6 0.07
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.75
Consensus pattern (6 bp):
TTTTCT
Found at i:316439 original size:43 final size:42
Alignment explanation
Indices: 316391--316507 Score: 146
Period size: 43 Copynumber: 2.6 Consensus size: 42
316381 ATCAAACTTT
316391 TTTTCTCATTTTCTTTTTCTTTTTCTTCCTT-TTTTTCTTTTTC
1 TTTTCTCATTTTCTTTTTCTTTTTCTT-CTTATTTTTC-TTTTC
* *
316434 TTTTCTCATTTTCTTTTATCTTTCTCTTGTTATTTTTCTTTTC
1 TTTTCTCATTTTCTTTT-TCTTTTTCTTCTTATTTTTCTTTTC
316477 TTTTCCTCATTTTCATTTTTTTCTTTTTCTT
1 TTTT-CTCATTTTC---TTTTTCTTTTTCTT
316508 TCAATTGATC
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
43 28 0.43
44 24 0.37
46 9 0.14
47 4 0.06
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (42 bp):
TTTTCTCATTTTCTTTTTCTTTTTCTTCTTATTTTTCTTTTC
Found at i:316509 original size:19 final size:18
Alignment explanation
Indices: 316404--316509 Score: 74
Period size: 19 Copynumber: 5.9 Consensus size: 18
316394 TCTCATTTTC
*
316404 TTTTTCTTTTTCTTCCTT
1 TTTTTCTTTTTCTTTCTT
*
316422 TTTTTCTTTTTCTTTTCTC
1 TTTTTCTTTTTC-TTTCTT
* *
316441 ATTTTCTTTTATCTTTCTC
1 TTTTTCTTTT-TCTTTCTT
* *
316460 TTGTTATTTTTCTTTTCTT
1 TTTTTCTTTTTC-TTTCTT
** * *
316479 TTCCTCATTTTC---ATT
1 TTTTTCTTTTTCTTTCTT
316494 TTTTTCTTTTTCTTTC
1 TTTTTCTTTTTCTTTC
316510 AATTGATCTA
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
15 11 0.17
18 14 0.21
19 39 0.59
20 2 0.03
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.75
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTCTT
Found at i:321624 original size:35 final size:35
Alignment explanation
Indices: 321579--321676 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 35
321569 AAAAATCCCA
*
321579 CCACAACACCAGT-CCTCTTTCAATTAACATCCTG
1 CCACAACACCAATACCTCTTTCAATTAACATCCTG
* *
321613 CCACAAACACCAATACTTCTTTCAATTAACATCCTA
1 CCAC-AACACCAATACCTCTTTCAATTAACATCCTG
* * * * *
321649 CAAGAACATCAATACTTCTTCCAATTAA
1 CCACAACACCAATACCTCTTTCAATTAA
321677 TATCAAGAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
34 4 0.07
35 30 0.55
36 21 0.38
ACGTcount: A:0.37, C:0.33, G:0.03, T:0.28
Consensus pattern (35 bp):
CCACAACACCAATACCTCTTTCAATTAACATCCTG
Found at i:321636 original size:36 final size:35
Alignment explanation
Indices: 321594--321676 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 35
321584 ACACCAGTCC
*
321594 TCTTTCAATTAACATCCTGCCACA-AACACCAATACT
1 TCTTTCAATTAACATCCT-ACA-AGAACACCAATACT
*
321630 TCTTTCAATTAACATCCTACAAGAACATCAATACT
1 TCTTTCAATTAACATCCTACAAGAACACCAATACT
*
321665 TCTTCCAATTAA
1 TCTTTCAATTAA
321677 TATCAAGAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 1 0.02
35 24 0.56
36 18 0.42
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.31
Consensus pattern (35 bp):
TCTTTCAATTAACATCCTACAAGAACACCAATACT
Found at i:326531 original size:28 final size:28
Alignment explanation
Indices: 326491--326552 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
326481 GGTTCCCTTT
*
326491 TCCAAGATAATGACAATTGAAGGACTCA
1 TCCAAGATAATGAAAATTGAAGGACTCA
326519 TCCAAGATAATGAAAATTGAAGGACTCA
1 TCCAAGATAATGAAAATTGAAGGACTCA
326547 TCCAAG
1 TCCAAG
326553 TTTTGATAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (28 bp):
TCCAAGATAATGAAAATTGAAGGACTCA
Found at i:331892 original size:23 final size:23
Alignment explanation
Indices: 331855--331900 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
331845 AGAATTGAAC
* * *
331855 TGAAAGTAAACCTAAAGTCTAAA
1 TGAAAGGAAAACTAAAATCTAAA
331878 TGAAAGGAAAACTAAAATCTAAA
1 TGAAAGGAAAACTAAAATCTAAA
331901 ATTACAAAGA
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:0.57, C:0.11, G:0.13, T:0.20
Consensus pattern (23 bp):
TGAAAGGAAAACTAAAATCTAAA
Found at i:344919 original size:52 final size:51
Alignment explanation
Indices: 344851--344982 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 51
344841 ATAAACAAAT
* *
344851 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTAACATGA
1 GAGTTACATAAAGCATGACTTAATTTAATGATGCAAAC-TTAACTAACATGA
* * * *
344903 GAGTTATATAAAGCATGCCATAATTT-ATTATGCAAACTTAACTAACATGA
1 GAGTTACATAAAGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA
* **
344953 GAGTTACATAATGCATGACTTTCTTTAATG
1 GAGTTACATAAAGCATGACTTAATTTAATG
344983 CAAAACACAT
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
50 33 0.50
51 12 0.18
52 21 0.32
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (51 bp):
GAGTTACATAAAGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA
Found at i:355446 original size:27 final size:27
Alignment explanation
Indices: 355416--355559 Score: 159
Period size: 27 Copynumber: 5.3 Consensus size: 27
355406 ATTCGTGGGG
** *
355416 AAATGACCAAAATACCCTCGAAAGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* * *
355443 AAATGATTGAACTACCCTCGATGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* *
355470 AAATGACTGAACTACCCTCGATGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
355497 AAATGA-TCGAAATACTCCT-GAAGGGTA
1 AAATGACT-GAAATAC-CCTCGAAGGGTA
*
355524 AAATGACTGAAATACCC-CCATAGGGTA
1 AAATGACTGAAATACCCTCGA-AGGGTA
355551 AAATGACTG
1 AAATGACTG
355560 TTATACTCCT
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.04
27 94 0.92
28 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (27 bp):
AAATGACTGAAATACCCTCGAAGGGTA
Found at i:355814 original size:26 final size:26
Alignment explanation
Indices: 355737--355814 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
355727 ACATATACTG
* * * *
355737 TTACTGGCAGCTTTACTACGTTACTG
1 TTACTGGCAGCTTTGCTACGATATTA
* * *
355763 TTATTGGTAGCTTTGCTTC-ATCATTA
1 TTACTGGCAGCTTTGCTACGAT-ATTA
*
355789 TTACTGGCAGCTTTGCTGCGATATTA
1 TTACTGGCAGCTTTGCTACGATATTA
355815 GTGTGCTGGC
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
25 1 0.03
26 37 0.93
27 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTACGATATTA
Found at i:355959 original size:28 final size:28
Alignment explanation
Indices: 355919--356003 Score: 134
Period size: 28 Copynumber: 3.0 Consensus size: 28
355909 ATTGTACCAA
355919 TTACTGTATTGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
*
355947 TTACTATATTGGGCTAAGGCCTACACACTG
1 TTACTGTATTGGGCTAAGGCC--CACACTG
*
355977 TTACTGTAATGGGCTAAGGCCCACACT
1 TTACTGTATTGGGCTAAGGCCCACACT
356004 ATACTGCTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
28 26 0.50
30 26 0.50
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTG
Found at i:362494 original size:27 final size:27
Alignment explanation
Indices: 362464--362736 Score: 318
Period size: 27 Copynumber: 10.1 Consensus size: 27
362454 ATTCGTGGGC
*
362464 AAATGACCGAAATACCCTCGATGGCTA
1 AAATGACCGAAATACCCTCGATGGGTA
*
362491 AAATGACCGAAATACCCTCGATGGATA
1 AAATGACCGAAATACCCTCGATGGGTA
* * *
362518 AACTAATCGAAATACCCTCGATGGGTA
1 AAATGACCGAAATACCCTCGATGGGTA
* * *
362545 AAATGATCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGATGGGTA
* * *
362572 AACTGACCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGATGGGTA
* * *
362599 AAATAACCG-AATACCGTCAATGGGTA
1 AAATGACCGAAATACCCTCGATGGGTA
* *
362625 AAATGACCGAATTACCCTCAATGGGTA
1 AAATGACCGAAATACCCTCGATGGGTA
* *
362652 AAATGACCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGATGGGTA
* *
362679 AAATGATCGAAATACTCCT-GAAGGGTA
1 AAATGACCGAAATAC-CCTCGATGGGTA
*
362706 AAATGACCGAAATACCCT-AATAGGGTA
1 AAATGACCGAAATACCCTCGAT-GGGTA
362733 AAAT
1 AAAT
362737 TACTATTATA
Statistics
Matches: 216, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
26 27 0.12
27 186 0.86
28 3 0.01
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGATGGGTA
Found at i:362714 original size:134 final size:135
Alignment explanation
Indices: 362464--362736 Score: 390
Period size: 134 Copynumber: 2.0 Consensus size: 135
362454 ATTCGTGGGC
* * * * *
362464 AAATGACCGAAATACCCTCGATGGCTAAAATGACCGAAATACCCTCGATGGATAAACTAATCGAA
1 AAATAACCGAAATACCCTCAATGGCTAAAATGACCGAAATACCCTCAATGGATAAAATAACCGAA
* * *
362529 ATACCCTCGATGGGTAAAATGATCGAAATACCCTTGAAGGGTAAACTGACCGAAATACCCTCAA-
66 ATACCCTCAAAGGGTAAAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCT-AAT
362593 AGGGTA
130 AGGGTA
* * * * *
362599 AAATAACCG-AATACCGTCAATGGGTAAAATGACCGAATTACCCTCAATGGGTAAAATGACCGAA
1 AAATAACCGAAATACCCTCAATGGCTAAAATGACCGAAATACCCTCAATGGATAAAATAACCGAA
362663 ATACCCTCAAAGGGTAAAATGATCGAAATACTCC-TGAAGGGTAAAATGACCGAAATACCCTAAT
66 ATACCCTCAAAGGGTAAAATGATCGAAATAC-CCTTGAAGGGTAAAATGACCGAAATACCCTAAT
362727 AGGGTA
130 AGGGTA
362733 AAAT
1 AAAT
362737 TACTATTATA
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
133 2 0.02
134 111 0.90
135 10 0.08
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (135 bp):
AAATAACCGAAATACCCTCAATGGCTAAAATGACCGAAATACCCTCAATGGATAAAATAACCGAA
ATACCCTCAAAGGGTAAAATGATCGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCTAATA
GGGTA
Found at i:363162 original size:30 final size:30
Alignment explanation
Indices: 363095--363183 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
363085 ACTACATTGT
*
363095 ACTGATTACTATATTGGGCTAAGGCCCACA-
1 ACTG-TTACTGTATTGGGCTAAGGCCCACAC
363125 A-TGTTACTGTATTGGGCTAAGGCCCACAC
1 ACTGTTACTGTATTGGGCTAAGGCCCACAC
*
363154 ACTGTTACTGTAATGGGCTAAGGCCCACAC
1 ACTGTTACTGTATTGGGCTAAGGCCCACAC
363184 TATACCGCTA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 24 0.44
29 3 0.05
30 28 0.51
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (30 bp):
ACTGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:363205 original size:33 final size:29
Alignment explanation
Indices: 363109--363213 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 29
363099 ATTACTATAT
* * *
363109 TGGGCTAAGGCCCACA-A-TGTTACTGTAT
1 TGGGCTAAGGCCCACACACCGCTACTG-AA
* *
363137 TGGGCTAAGGCCCACACACTGTTACTGTAA
1 TGGGCTAAGGCCCACACACCGCTACTG-AA
363167 TGGGCTAAGGCCCACACTATACCGCTACTGAA
1 TGGGCTAAGGCCCACAC---ACCGCTACTGAA
*
363199 TAGGGCTTAGGCCCA
1 T-GGGCTAAGGCCCA
363214 GACTGTTACT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
28 16 0.24
29 1 0.01
30 27 0.40
32 3 0.04
33 20 0.30
ACGTcount: A:0.26, C:0.27, G:0.25, T:0.23
Consensus pattern (29 bp):
TGGGCTAAGGCCCACACACCGCTACTGAA
Found at i:365435 original size:33 final size:33
Alignment explanation
Indices: 365393--365459 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
365383 AAATACATGA
365393 CATAGTTTCTTTTAAACAATTACCATTCATTTC
1 CATAGTTTCTTTTAAACAATTACCATTCATTTC
365426 CATAGTTTCTTTTAAACAATTACCATTCATTTC
1 CATAGTTTCTTTTAAACAATTACCATTCATTTC
365459 C
1 C
365460 TTTTCATGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (33 bp):
CATAGTTTCTTTTAAACAATTACCATTCATTTC
Found at i:366363 original size:55 final size:55
Alignment explanation
Indices: 366275--366403 Score: 197
Period size: 55 Copynumber: 2.3 Consensus size: 55
366265 ATGGTCGACG
*
366275 CCGTGTAACTCATTAACTTGGGCCACACAGCCAACCACACG-TCCGTATAACTAGC
1 CCGTGTAACTCATTGACTTGGGCCACACAGCCAACCACACGCT-CGTATAACTAGC
* * * *
366330 CCGTGTAACTCATTGACTTGGGTCACACGGCCAACCACACGCTCGTGTGACTAGC
1 CCGTGTAACTCATTGACTTGGGCCACACAGCCAACCACACGCTCGTATAACTAGC
366385 CCGTGTAACTCATTGACTT
1 CCGTGTAACTCATTGACTT
366404 TCTTTCGTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
55 67 0.99
56 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (55 bp):
CCGTGTAACTCATTGACTTGGGCCACACAGCCAACCACACGCTCGTATAACTAGC
Found at i:372231 original size:37 final size:36
Alignment explanation
Indices: 372177--372253 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 36
372167 GAACTGACTA
372177 AACCGTAGCTCGTATACCACTAAATGTAACACCCCT
1 AACCGTAGCTCGTATACCACTAAATGTAACACCCCT
372213 AACCTGTAGCTCGTATACCACTAAATGTAACACCCCT
1 AACC-GTAGCTCGTATACCACTAAATGTAACACCCCT
372250 AACC
1 AACC
372254 CGTATCTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 4 0.10
37 36 0.90
ACGTcount: A:0.34, C:0.34, G:0.10, T:0.22
Consensus pattern (36 bp):
AACCGTAGCTCGTATACCACTAAATGTAACACCCCT
Found at i:373545 original size:20 final size:20
Alignment explanation
Indices: 373517--373554 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
373507 AATACTATGA
373517 ACCACTCCATTTACTTTCTT
1 ACCACTCCATTTACTTTCTT
*
373537 ACCATTCCATTTACTTTC
1 ACCACTCCATTTACTTTC
373555 CATTGCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (20 bp):
ACCACTCCATTTACTTTCTT
Found at i:373563 original size:16 final size:16
Alignment explanation
Indices: 373538--373568 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
373528 TACTTTCTTA
373538 CCATTCCATTTACTTT
1 CCATTCCATTTACTTT
*
373554 CCATTGCATTTACTT
1 CCATTCCATTTACTT
373569 AGCATAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.29, G:0.03, T:0.48
Consensus pattern (16 bp):
CCATTCCATTTACTTT
Found at i:380662 original size:96 final size:96
Alignment explanation
Indices: 380510--380689 Score: 342
Period size: 96 Copynumber: 1.9 Consensus size: 96
380500 AGACGAACTC
*
380510 GATTTCTTAAGGTTAGTACTCGATAATGTTTTTGACTTTGGCATCTTAACTGTTAATCAATTTTT
1 GATTTCTTAAGGTTAGTACTCGATAATGTTTTCGACTTTGGCATCTTAACTGTTAATCAATTTTT
380575 GGAAAAGTGTTCTAAAAACGTAGATGAGCTT
66 GGAAAAGTGTTCTAAAAACGTAGATGAGCTT
*
380606 GATTTCTTATGGTTAGTACTCGATAATGTTTTCGACTTTGGCATCTTAACTGTTAATCAATTTTT
1 GATTTCTTAAGGTTAGTACTCGATAATGTTTTCGACTTTGGCATCTTAACTGTTAATCAATTTTT
380671 GGAAAAGTGTTCTAAAAAC
66 GGAAAAGTGTTCTAAAAAC
380690 CCTTAATTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (96 bp):
GATTTCTTAAGGTTAGTACTCGATAATGTTTTCGACTTTGGCATCTTAACTGTTAATCAATTTTT
GGAAAAGTGTTCTAAAAACGTAGATGAGCTT
Found at i:384252 original size:15 final size:14
Alignment explanation
Indices: 384224--384253 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
384214 TCTTTCGTTC
384224 TCTTTTCCTCTTCT
1 TCTTTTCCTCTTCT
384238 TCTTTTCCTTCTTCT
1 TCTTTTCC-TCTTCT
384253 T
1 T
384254 ACCTCTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTTCCTCTTCT
Found at i:387539 original size:21 final size:21
Alignment explanation
Indices: 387496--387540 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
387486 ACAATATTCT
* **
387496 TTATCTGGTAGCTTGTCTGCA
1 TTATCTGGTAGCTTGGCCACA
*
387517 TTATCTGGTGGCTTGGCCACA
1 TTATCTGGTAGCTTGGCCACA
387538 TTA
1 TTA
387541 GTGTGTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (21 bp):
TTATCTGGTAGCTTGGCCACA
Found at i:389875 original size:25 final size:25
Alignment explanation
Indices: 389816--389877 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
389806 CAACCCGTAC
*
389816 AAGCTTACCATTATTCAGATAAGAG
1 AAGCTTACCGTTATTCAGATAAGAG
* *
389841 AAGCTTACCGTTATTCAGCTTAGAG
1 AAGCTTACCGTTATTCAGATAAGAG
*
389866 TAGCTTACCGTT
1 AAGCTTACCGTT
389878 TACAACTCGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (25 bp):
AAGCTTACCGTTATTCAGATAAGAG
Found at i:398223 original size:116 final size:115
Alignment explanation
Indices: 398093--398470 Score: 295
Period size: 116 Copynumber: 3.2 Consensus size: 115
398083 TTATGTTTTC
398093 TATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCTTTAATATTTTATTTACG
1 TATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCTTTAATATTTTATTTA-G
* *
398158 AGTTTTTATTTCAATAAATGACGTTATATAAAATAATAAATTAATATACAT
65 AGTTTTTATTTCAATAAATGAAGTAATATAAAATAATAAATTAATATACAT
* * * ** * ** ** **
398209 TATATTATTTATTAATTTTTATTTACTTTATATGATATTAGGACTTATAATAAAGCTAAAATAAA
1 TATAATATATATTAATTGTTATCAAC--T-T-T-ACA-TAGGA-TTA-AA-ATTGCTTTAATATT
* * * **
398274 TAATTTA-A-TTTAATT-TTT-AATAAAT-AAGATGATGATAACTAAT-ATATAATT-ATGT-TT
57 TTATTTAGAGTTT--TTATTTCAATAAATGAAG-TAAT-ATAA--AATAATA-AATTAATATACA
398331 T
115 T
*
398332 CTATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCCTTAATATTTTATTTAA
1 -TATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCTTTAATATTTTATTT-A
* **
398397 GAGTTCTTATTTCAATAAATGAAGTAATAGCAAATAATAAATTAATATACAT
64 GAGTTTTTATTTCAATAAATGAAGTAATATAAAATAATAAATTAATATACAT
* * *
398449 TATATTATTTATTAATTTTTAT
1 TATAATATATATTAATTGTTAT
398471 TTACTTTATA
Statistics
Matches: 194, Mismatches: 42, Indels: 52
0.67 0.15 0.18
Matches are distributed among these distances:
115 19 0.10
116 51 0.26
117 10 0.05
118 18 0.09
119 6 0.03
120 2 0.01
121 5 0.03
122 19 0.10
123 12 0.06
124 31 0.16
125 21 0.11
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (115 bp):
TATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCTTTAATATTTTATTTAGA
GTTTTTATTTCAATAAATGAAGTAATATAAAATAATAAATTAATATACAT
Found at i:398444 original size:240 final size:240
Alignment explanation
Indices: 398021--398501 Score: 899
Period size: 240 Copynumber: 2.0 Consensus size: 240
398011 TCTTTAAAAG
398021 AAGCTAAAATAAATAATTTAATTTAATTTTTAATAAATAAGATGATGATAACTAATATATAATTA
1 AAGCTAAAATAAATAATTTAATTTAATTTTTAATAAATAAGATGATGATAACTAATATATAATTA
*
398086 TGTTTTCTATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCTTTAATATTTT
66 TGTTTTCTATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCCTTAATATTTT
* * * * *
398151 ATTTACGAGTTTTTATTTCAATAAATGACGTTATATAAAATAATAAATTAATATACATTATATTA
131 ATTTAAGAGTTCTTATTTCAATAAATGAAGTAATAGAAAATAATAAATTAATATACATTATATTA
398216 TTTATTAATTTTTATTTACTTTATATGATATTAGGACTTATAATA
196 TTTATTAATTTTTATTTACTTTATATGATATTAGGACTTATAATA
398261 AAGCTAAAATAAATAATTTAATTTAATTTTTAATAAATAAGATGATGATAACTAATATATAATTA
1 AAGCTAAAATAAATAATTTAATTTAATTTTTAATAAATAAGATGATGATAACTAATATATAATTA
398326 TGTTTTCTATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCCTTAATATTTT
66 TGTTTTCTATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCCTTAATATTTT
*
398391 ATTTAAGAGTTCTTATTTCAATAAATGAAGTAATAGCAAATAATAAATTAATATACATTATATTA
131 ATTTAAGAGTTCTTATTTCAATAAATGAAGTAATAGAAAATAATAAATTAATATACATTATATTA
398456 TTTATTAATTTTTATTTACTTTATATGATATTAGGACTTATAATA
196 TTTATTAATTTTTATTTACTTTATATGATATTAGGACTTATAATA
398501 A
1 A
398502 TTTAGTATTA
Statistics
Matches: 234, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
240 234 1.00
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (240 bp):
AAGCTAAAATAAATAATTTAATTTAATTTTTAATAAATAAGATGATGATAACTAATATATAATTA
TGTTTTCTATAATATATATTAATTGTTATCAACTTTACATAGGATTAAAATTGCCTTAATATTTT
ATTTAAGAGTTCTTATTTCAATAAATGAAGTAATAGAAAATAATAAATTAATATACATTATATTA
TTTATTAATTTTTATTTACTTTATATGATATTAGGACTTATAATA
Found at i:399803 original size:28 final size:28
Alignment explanation
Indices: 399774--399987 Score: 230
Period size: 28 Copynumber: 7.5 Consensus size: 28
399764 CTACAACATG
* * *
399774 CAGTAATAGTCTGGGCCTTAGCCCTATG
1 CAGTAATAGTGTGGGCCTTAGCCCAATA
*
399802 CAGTAACAGTACAGTGTGGGCCTTAGCCCGATA
1 CAGT-A-A-T--AGTGTGGGCCTTAGCCCAATA
* * * *
399835 CAGTAACAATGTGAGCCTTAGCCCGATA
1 CAGTAATAGTGTGGGCCTTAGCCCAATA
* *
399863 CCGTAATAGTGTGGGCCTTAACCCAATA
1 CAGTAATAGTGTGGGCCTTAGCCCAATA
* * *
399891 TAGTAAAAGTGTGGGCCTTAGTCCAATA
1 CAGTAATAGTGTGGGCCTTAGCCCAATA
*
399919 CAGTAAGAGTGTGGGCCTTAGCCCAATA
1 CAGTAATAGTGTGGGCCTTAGCCCAATA
* *
399947 CAGAAATAGTGTGGGCCTTAGCCTAATA
1 CAGTAATAGTGTGGGCCTTAGCCCAATA
*
399975 CAGTAACAGTGTG
1 CAGTAATAGTGTG
399988 ATAATGCAAC
Statistics
Matches: 156, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
28 129 0.83
29 1 0.01
30 1 0.01
31 2 0.01
32 1 0.01
33 22 0.14
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (28 bp):
CAGTAATAGTGTGGGCCTTAGCCCAATA
Found at i:400121 original size:26 final size:26
Alignment explanation
Indices: 400082--400136 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
400072 AACACACCAA
400082 TATCGCAGCAAAGCTACCAGTAAAAG
1 TATCGCAGCAAAGCTACCAGTAAAAG
* * * *
400108 TATCGTAGCGAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAAAAG
400134 TAT
1 TAT
400137 ATGTGGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTACCAGTAAAAG
Found at i:400356 original size:27 final size:27
Alignment explanation
Indices: 400324--400392 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
400314 GGTTTAACAA
* *
400324 TCATTTTACCCTTTGGGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* **
400351 TTATTTTACCCTTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
400378 TCATTTTACCCTTCG
1 TCATTTTACCCTTCG
400393 GGTGCAAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.46
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCAG
Found at i:413625 original size:40 final size:40
Alignment explanation
Indices: 413579--413657 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
413569 ATTTGGATTG
413579 TCATTAGGACCAAGATCATTCTTGTTTCTAGCCATTTTTT
1 TCATTAGGACCAAGATCATTCTTGTTTCTAGCCATTTTTT
413619 TCATTAGGACCAAGATCATTCTTGTTTCTAGCCATTTTT
1 TCATTAGGACCAAGATCATTCTTGTTTCTAGCCATTTTT
413658 CTCGTTCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (40 bp):
TCATTAGGACCAAGATCATTCTTGTTTCTAGCCATTTTTT
Found at i:419520 original size:11 final size:11
Alignment explanation
Indices: 419504--419607 Score: 67
Period size: 11 Copynumber: 9.7 Consensus size: 11
419494 CCTCTTCTTC
419504 TTTTTTTTCAA
1 TTTTTTTTCAA
419515 TTTTTTTTCAA
1 TTTTTTTTCAA
419526 -TTTTTTTC--
1 TTTTTTTTCAA
* * **
419534 TTTCTCTCTCTTT
1 TTT-TTTTTC-AA
*
419547 TTTTTTGTTCGA
1 TTTTTT-TTCAA
*
419559 -TTTTTTTCAC
1 TTTTTTTTCAA
*
419569 TTTTTTTTGAA
1 TTTTTTTTCAA
419580 TTTTTTTTCAA
1 TTTTTTTTCAA
*
419591 TTTTCTTTC--
1 TTTTTTTTCAA
419600 TTTTTTTT
1 TTTTTTTT
419608 TTTAATCCAA
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
9 9 0.12
10 15 0.21
11 42 0.58
12 2 0.03
13 5 0.07
ACGTcount: A:0.10, C:0.12, G:0.03, T:0.75
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:421483 original size:43 final size:43
Alignment explanation
Indices: 421435--421547 Score: 158
Period size: 41 Copynumber: 2.7 Consensus size: 43
421425 ACGGTAAATC
* *
421435 CAACAACCCATGTTTATCTTCTCCTCTTTTTAAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
*
421478 CAACAACCTAAGATTATCTTCT-C-CTTTTTAAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
* * *
421519 CAAAAACCCAAAATTATCATCTCCTCTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTT
421548 CTTAGGAAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
41 36 0.59
42 2 0.03
43 23 0.38
ACGTcount: A:0.27, C:0.26, G:0.02, T:0.45
Consensus pattern (43 bp):
CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTT
Found at i:433004 original size:12 final size:13
Alignment explanation
Indices: 432989--433017 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
432979 TTTCTCACTC
432989 TTTTCTTTTTC-T
1 TTTTCTTTTTCAT
433001 TTTTCTTTTTCAT
1 TTTTCTTTTTCAT
433014 TTTT
1 TTTT
433018 TTCTTCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTCAT
Found at i:433024 original size:18 final size:17
Alignment explanation
Indices: 432971--433025 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 17
432961 TGTAACTCAA
*
432971 TTTCTTTTTTTCTCACTCT
1 TTTCTTTTTTTCT-TCT-T
*
432990 TTTCTTTTTCTTTTTCTT
1 TTTCTTTTT-TTCTTCTT
433008 TTTCATTTTTTTCTTCTT
1 TTTC-TTTTTTTCTTCTT
433026 GTTTTTGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 12 0.39
19 16 0.52
20 3 0.10
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTTTTTCTTCTT
Found at i:437152 original size:4 final size:4
Alignment explanation
Indices: 437143--437219 Score: 145
Period size: 4 Copynumber: 19.2 Consensus size: 4
437133 CTTTTAAAAG
437143 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
437191 GTAT GTAT GTAT GTAT GTAT GTAT ATAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
437220 ACAAGGTACT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:444517 original size:95 final size:94
Alignment explanation
Indices: 444339--444524 Score: 219
Period size: 95 Copynumber: 2.0 Consensus size: 94
444329 ATGACCTGTG
* * *
444339 AATCAGACATTAACCATTACACAGTGCTACTCACACGAGATATGAAGAATCCACAACACATGCAA
1 AATCAGACATTAACCATTACACAATGCTACTCACACGAGATATGAAGAATACACAACACATACAA
* **
444404 AATTTTAGTCATCAGTAAGGTATCCAGTA
66 AATCTTAACCATCAGTAAGGTATCCAGTA
* * * * * * * * *
444433 AATCGAGACATTAATCATTACATAATGTTTCTCACATGAGCTGTGAAGAATACACAATATATACA
1 AATC-AGACATTAACCATTACACAATGCTACTCACACGAGATATGAAGAATACACAACACATACA
*
444498 AAATCTTAACCATCGGTAAGGTATCCA
65 AAATCTTAACCATCAGTAAGGTATCCA
444525 CCACCGGTAC
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
94 4 0.05
95 71 0.95
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (94 bp):
AATCAGACATTAACCATTACACAATGCTACTCACACGAGATATGAAGAATACACAACACATACAA
AATCTTAACCATCAGTAAGGTATCCAGTA
Found at i:449368 original size:50 final size:52
Alignment explanation
Indices: 449258--449389 Score: 144
Period size: 50 Copynumber: 2.6 Consensus size: 52
449248 ATGAACAAAT
* *
449258 AAGTTACTTAATGCAAGACTTAATTTAATGATACAGACTTAAACTAACATGG
1 AAGTTACATAATGCATGACTTAATTTAATGATACAGACTTAAACTAACATGG
* * * * *
449310 GAGTTACATAATGCATGTCATT-ATTT-ATGATGCATACTT-AACTAGCATGG
1 AAGTTACATAATGCATGAC-TTAATTTAATGATACAGACTTAAACTAACATGG
* * *
449360 AAGTTACATAATGCATAACTTTATTAAATG
1 AAGTTACATAATGCATGACTTAATTTAATG
449390 TAGAACACAC
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
49 2 0.03
50 29 0.44
51 14 0.21
52 19 0.29
53 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (52 bp):
AAGTTACATAATGCATGACTTAATTTAATGATACAGACTTAAACTAACATGG
Found at i:457078 original size:296 final size:298
Alignment explanation
Indices: 456338--457078 Score: 751
Period size: 298 Copynumber: 2.5 Consensus size: 298
456328 CACATTTTGC
* * * * * * * *
456338 ATAAAACCTTAAATTTACTACTCAA-TCAAAATTTTATTTTACT-TTTTTAATACATTTTAGTTT
1 ATAAAATCTTTAATTTACCACTCAACT-AAAATGTTATTTTAATATATTTAA-ACATCTTAATTT
* * * * * * *
456401 TATTATGCACACTTT-TTACCTCCATGAATTG--TATAT--CTATATTATTATTTAAGCTCCTGA
64 TACTATG-ACACTTTATTACTTCCATCATTTGTATATATAACTATACTATTATTTAAGCTACTTA
* * * * * * * *** * * *
456461 TTGAGTTGATATTACTCACAACCAAACCACCAACTTGGTTAGGAAAATTATAGGCATACCCTTCT
128 CTGAGTTGATGTCACCCTCAATCGAGTTACCAACTCGGTTAGGAAAATTATAGGCATACCATTCC
* * * * *
456526 GTAATTAAAATAAATTATATTATTCGAGGGTACTTTAGTTTTTTTTATTTAAAAAACCAATACAA
193 ATAATTAAAATAAACTATATTATTCAAGGCTACTTTAGTTTTTTATATTTAAAAAACCAATACAA
* * * **
456591 ATAAGCATACGGTGGGATTTGGACCCAAACTAATTGTATTA
258 ATAAGCATACGGTGAGATTCGAACCCAAACTAATTACATTA
* * *
456632 GTAAAATCTTTAATTTACCACTCAACTAACATGTTATTTTAATATATTTAAACATTTTAATTTTA
1 ATAAAATCTTTAATTTACCACTCAACTAAAATGTTATTTTAATATATTTAAACATCTTAATTTTA
* * * * *
456697 TTATGACACTTTATTACTTTCATCATTTGTATATCTATCTATAGTATTATTTAAGCTACTTACTG
66 CTATGACACTTTATTACTTCCATCATTTGTATATATAACTATACTATTATTTAAGCTACTTACTG
456762 AGTTGATGTCACCCTCAATCGAGTTACCAACTCGGTTAGGAAAATTA-AGGACATACCATTCCAT
131 AGTTGATGTCACCCTCAATCGAGTTACCAACTCGGTTAGGAAAATTATAGG-CATACCATTCCAT
* * *
456826 AATTAAAATAAGCTATATTATTCAAGGCTATTTTAGTCTTTTTAT-TTTAAAAAACTAATA-AAA
195 AATTAAAATAAACTATATTATTCAAGGCTACTTTAGT-TTTTTATATTTAAAAAACCAATACAAA
** *
456889 -AATGCATATTGTGAGATTCGAACCCAAACTATTTACATTA
259 TAA-GCATACGGTGAGATTCGAACCCAAACTAATTACATTA
* * *
456929 ATAAAATTTTTAATTTACCACTCAACTAAAACT-TTATTTTGAT-T-TTTATACATCTTAATTTT
1 ATAAAATCTTTAATTTACCACTCAACTAAAA-TGTTATTTTAATATATTTAAACATCTTAATTTT
456991 ACTATGTACACTTTATTACTTCCATCATTTGTATATATACACT-TACTATTATTTAAGCT-CTTG
65 ACTATG-ACACTTTATTACTTCCATCATTTGTATATATA-ACTATACTATTATTTAAGCTACTT-
* *
457054 A-TGGAGTTGGTGTCACCTTCAATCG
127 ACT-GAGTTGATGTCACCCTCAATCG
457079 GGTCACCTTC
Statistics
Matches: 373, Mismatches: 59, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
293 7 0.02
294 64 0.17
295 32 0.09
296 73 0.20
297 74 0.20
298 117 0.31
299 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (298 bp):
ATAAAATCTTTAATTTACCACTCAACTAAAATGTTATTTTAATATATTTAAACATCTTAATTTTA
CTATGACACTTTATTACTTCCATCATTTGTATATATAACTATACTATTATTTAAGCTACTTACTG
AGTTGATGTCACCCTCAATCGAGTTACCAACTCGGTTAGGAAAATTATAGGCATACCATTCCATA
ATTAAAATAAACTATATTATTCAAGGCTACTTTAGTTTTTTATATTTAAAAAACCAATACAAATA
AGCATACGGTGAGATTCGAACCCAAACTAATTACATTA
Found at i:457085 original size:15 final size:15
Alignment explanation
Indices: 457065--457100 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
457055 TGGAGTTGGT
457065 GTCACCTTCAA-TCGG
1 GTCACCTTCAACT-GG
457080 GTCACCTTCAACTGG
1 GTCACCTTCAACTGG
457095 GTCACC
1 GTCACC
457101 AACTTGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (15 bp):
GTCACCTTCAACTGG
Found at i:459659 original size:16 final size:16
Alignment explanation
Indices: 459621--459659 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
459611 CTTTTTCTTT
*
459621 CAAAAAAGAAAAAGAA
1 CAAAAAAGAAAAACAA
459637 -AAGAAAAGAAAAACAA
1 CAA-AAAAGAAAAACAA
459653 CAAAAAA
1 CAAAAAA
459660 AAAGAGACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 2 0.10
16 16 0.80
17 2 0.10
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (16 bp):
CAAAAAAGAAAAACAA
Found at i:463290 original size:12 final size:13
Alignment explanation
Indices: 463263--463295 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
463253 TCTTTGATAT
463263 ATTATTTTATTTTA
1 ATTA-TTTATTTTA
463277 ATTATTTA-TTTA
1 ATTATTTATTTTA
463289 ATTATTT
1 ATTATTT
463296 TATCTAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 4 0.21
14 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTATTTATTTTA
Done.