Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008474.1 Kokia drynarioides strain JFW-HI SEQ_123149, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 227884
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:2371 original size:13 final size:14
Alignment explanation
Indices: 2334--2370 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2324 AAAAAATATT
* *
2334 AATTTTTTTTCGTA
1 AATTATTTTTCGAA
2348 AATTATTTTTCGAA
1 AATTATTTTTCGAA
2362 AATTATTTT
1 AATTATTTT
2371 CAGTGAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (14 bp):
AATTATTTTTCGAA
Found at i:2527 original size:22 final size:22
Alignment explanation
Indices: 2467--2527 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
2457 AAAAACTCAA
2467 ATATGTGTCAATTGTCA-TAAG
1 ATATGTGTCAATTGTCATTAAG
* ** * *
2488 ATCT-TAACAGATTTTCATTGAG
1 ATATGTGTCA-ATTGTCATTAAG
2510 ATATGTGTCAATTGTCAT
1 ATATGTGTCAATTGTCAT
2528 GAAACATTAC
Statistics
Matches: 28, Mismatches: 9, Indels: 5
0.67 0.21 0.12
Matches are distributed among these distances:
20 3 0.11
21 9 0.32
22 13 0.46
23 3 0.11
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (22 bp):
ATATGTGTCAATTGTCATTAAG
Found at i:9966 original size:23 final size:22
Alignment explanation
Indices: 9940--9987 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
9930 TACCATCTAA
9940 TTTTGGATCAAGAGCTTAGTTGG
1 TTTTGGATCAAGAG-TTAGTTGG
* **
9963 TTTTGTATGTAGAGTTAGTTGG
1 TTTTGGATCAAGAGTTAGTTGG
9985 TTT
1 TTT
9988 ATTGCTTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.19, C:0.04, G:0.29, T:0.48
Consensus pattern (22 bp):
TTTTGGATCAAGAGTTAGTTGG
Found at i:26783 original size:21 final size:22
Alignment explanation
Indices: 26759--26801 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
26749 AAATTCGCTG
*
26759 GGTTCGATT-TTTTTTAATTTT
1 GGTTCAATTCTTTTTTAATTTT
*
26780 GGTTCAATTCTTTTTTATTTTT
1 GGTTCAATTCTTTTTTAATTTT
26802 CAATCCTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.67
Consensus pattern (22 bp):
GGTTCAATTCTTTTTTAATTTT
Found at i:28675 original size:17 final size:17
Alignment explanation
Indices: 28642--28675 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28632 ATACAATTTT
* *
28642 ATTTTTAATATTTTAAA
1 ATTTTTAAAATTCTAAA
28659 ATTTTTAAAATTCTAAA
1 ATTTTTAAAATTCTAAA
28676 TAACCTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTAAAATTCTAAA
Found at i:32798 original size:23 final size:23
Alignment explanation
Indices: 32772--32830 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
32762 TTATTATTAA
*
32772 ATGATCTTTATTCTTTTTTAGGT
1 ATGATCTTTATCCTTTTTTAGGT
*
32795 ATGATTTTTATCCTTTTTTAGGT
1 ATGATCTTTATCCTTTTTTAGGT
32818 ATGATCTTTATCC
1 ATGATCTTTATCC
32831 CTTTAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.58
Consensus pattern (23 bp):
ATGATCTTTATCCTTTTTTAGGT
Found at i:36756 original size:2 final size:2
Alignment explanation
Indices: 36749--36774 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36739 AATGAGATCA
36749 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
36775 CCCTTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44499 original size:30 final size:30
Alignment explanation
Indices: 44463--44557 Score: 154
Period size: 30 Copynumber: 3.2 Consensus size: 30
44453 CAACTTAACA
*
44463 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
*
44493 AACAAATACCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
* *
44523 AACAAACGCCTCAAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
44553 AACAA
1 AACAA
44558 TAAAATAAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.21
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:44605 original size:14 final size:14
Alignment explanation
Indices: 44582--44616 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
44572 TACAATATCC
*
44582 AAATAATAACAACA
1 AAATAGTAACAACA
44596 AAATAGTAACAACA
1 AAATAGTAACAACA
*
44610 TAATAGT
1 AAATAGT
44617 GAAATTGTAG
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:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:55102 original size:12 final size:12
Alignment explanation
Indices: 55085--55114 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55075 GTTATGCATC
*
55085 AATTAATTAACA
1 AATTAATTAAAA
55097 AATTAATTAAAA
1 AATTAATTAAAA
55109 AATTAA
1 AATTAA
55115 GCTCTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
AATTAATTAAAA
Found at i:55405 original size:20 final size:20
Alignment explanation
Indices: 55355--55403 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
55345 CCGAACTTCG
*
55355 AACTCAAAACTCTAATTATA
1 AACTCAAAACCCTAATTATA
55375 AACTCAAAACCCTAATTATA
1 AACTCAAAACCCTAATTATA
55395 AACTTCAAA
1 AAC-TCAAA
55404 CCTTAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (20 bp):
AACTCAAAACCCTAATTATA
Found at i:57084 original size:17 final size:18
Alignment explanation
Indices: 57049--57086 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
57039 ATTTTTATTA
* *
57049 TTTTTTAAATATGATTTT
1 TTTTTTAAATATAAATTT
57067 TTTTTTAAAT-TAAATTT
1 TTTTTTAAATATAAATTT
57084 TTT
1 TTT
57087 AAATAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTTAAATATAAATTT
Found at i:57643 original size:14 final size:14
Alignment explanation
Indices: 57624--57659 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
57614 AATGATAGTT
57624 GTTAAATTCATTAA
1 GTTAAATTCATTAA
57638 GTTAAATTCATTAA
1 GTTAAATTCATTAA
57652 GTTAAATT
1 GTTAAATT
57660 ATGTTATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (14 bp):
GTTAAATTCATTAA
Found at i:58238 original size:28 final size:28
Alignment explanation
Indices: 58206--58262 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
58196 AATATAGTAT
58206 TAAAAATAATTTCCTAAGCTGTAAATCC
1 TAAAAATAATTTCCTAAGCTGTAAATCC
58234 TAAAAATAATTTCCTAAGCTGTAAATCC
1 TAAAAATAATTTCCTAAGCTGTAAATCC
58262 T
1 T
58263 TACTTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (28 bp):
TAAAAATAATTTCCTAAGCTGTAAATCC
Found at i:60195 original size:2 final size:2
Alignment explanation
Indices: 60188--60234 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
60178 ACATAATTTG
* *
60188 AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60230 AT AT A
1 AT AT A
60235 AACACACGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:60559 original size:17 final size:15
Alignment explanation
Indices: 60530--60569 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
60520 AAATATTAAA
60530 TAAATAAAAAATTATT
1 TAAATAAAAAATT-TT
60546 TAAATAATAAAATTTT
1 TAAATAA-AAAATTTT
60562 TAAA-AAAA
1 TAAATAAAA
60570 TATTGATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.09
15 2 0.09
16 13 0.57
17 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATAAAAAATTTT
Found at i:61016 original size:17 final size:17
Alignment explanation
Indices: 60994--61027 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
60984 AAAAAAATTC
*
60994 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
61011 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
61028 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:62062 original size:22 final size:22
Alignment explanation
Indices: 62036--62080 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
62026 TAAAAAGTTC
62036 ATTTAATTTACAATATTAAACT
1 ATTTAATTTACAATATTAAACT
62058 ATTTAATTTACAATATTAAACT
1 ATTTAATTTACAATATTAAACT
62080 A
1 A
62081 AGTTATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTAATTTACAATATTAAACT
Found at i:64145 original size:28 final size:28
Alignment explanation
Indices: 64111--64168 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
64101 ATTATTAAAT
64111 AAATTCAAATT-TAAACAGAATTAATTCC
1 AAATTC-AATTATAAACAGAATTAATTCC
**
64139 AAATTCAATTATAAACTTAATTAATTCC
1 AAATTCAATTATAAACAGAATTAATTCC
64167 AA
1 AA
64169 CAGAAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (28 bp):
AAATTCAATTATAAACAGAATTAATTCC
Found at i:66957 original size:25 final size:26
Alignment explanation
Indices: 66908--66959 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
66898 AACCTTCTGT
* *
66908 TTCCTTTTCTTCTTCAAAACTTTTGC
1 TTCCTTTCCTTCTTCAAAACATTTGC
66934 TTCCTTTCCTTCTTCAAAA-ATTTGC
1 TTCCTTTCCTTCTTCAAAACATTTGC
66959 T
1 T
66960 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.17, C:0.27, G:0.04, T:0.52
Consensus pattern (26 bp):
TTCCTTTCCTTCTTCAAAACATTTGC
Found at i:67103 original size:27 final size:26
Alignment explanation
Indices: 67043--67108 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
67033 ATAGTTTTGA
67043 CAAAGGCACCACTAGTGCCACCTACC
1 CAAAGGCACCACTAGTGCCACCTACC
* * * *
67069 CAGTAGGCACCATTGGTGCCGCCTACC
1 CA-AAGGCACCACTAGTGCCACCTACC
67096 CTAAAGGCACCAC
1 C-AAAGGCACCAC
67109 CTGTTAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 2 0.06
27 29 0.91
28 1 0.03
ACGTcount: A:0.27, C:0.39, G:0.20, T:0.14
Consensus pattern (26 bp):
CAAAGGCACCACTAGTGCCACCTACC
Found at i:69535 original size:29 final size:30
Alignment explanation
Indices: 69503--69680 Score: 111
Period size: 29 Copynumber: 6.1 Consensus size: 30
69493 AAATAGTAAG
69503 TTTGAACACTTCG-GGGCAAAATGGTAATT
1 TTTGAACACTTCGAGGGCAAAATGGTAATT
* *
69532 TTTGGATACTT-GAGGGCAAAATGGTAATT
1 TTTGAACACTTCGAGGGCAAAATGGTAATT
* * * * *
69561 TTGGAAAAGTTCG-GAGTCAAAAAT-GAAATT
1 TTTGAACACTTCGAG-GGC-AAAATGGTAATT
* *
69591 TTTGGACA-TTCGAGGGTAAAATGGTAA-T
1 TTTGAACACTTCGAGGGCAAAATGGTAATT
* * * **
69619 TTAGAAAAAGTTCGAGGTTAAAAATGG-AATT
1 TTTG-AACACTTCGAGG-GCAAAATGGTAATT
* * *
69650 TTTGGA-AGTTCGAGGGTAAAATGGTAATT
1 TTTGAACACTTCGAGGGCAAAATGGTAATT
69679 TT
1 TT
69681 GAAAAAGTTT
Statistics
Matches: 115, Mismatches: 23, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
28 17 0.15
29 58 0.50
30 24 0.21
31 16 0.14
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (30 bp):
TTTGAACACTTCGAGGGCAAAATGGTAATT
Found at i:69843 original size:59 final size:59
Alignment explanation
Indices: 69520--70049 Score: 380
Period size: 59 Copynumber: 9.1 Consensus size: 59
69510 ACTTCGGGGC
* * * * *
69520 AAAATGGTAATTTTTGGATACTT-GAGGGCAAAATGGTAATTTTGGAAAAGTTCG-GAGTCA
1 AAAATGG-AA-TTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGAAAAAGTTCGAG-GTTA
* * *
69580 AAAATGAAATTTTTGGACA-TTCGAGGGTAAAATGGTAATTTAGAAAAAGTTCGAGGTTA
1 AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGAAAAAGTTCGAGGTTA
**
69639 AAAATGGAATTTTTGG-AAGTTCGAGGGTAAAATGGTAATTTTGAAAAAGTTTAAGGTTA
1 AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGAAAAAGTTCGAGGTTA
** * * * * * * *
69698 AAGTTGGAATTTTAG-AAGTTCGAGGGTTAAATAGTAATTTTGGAAAAGTTTGGGGTCAA
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGAAAAAGTTCGAGGT-TA
* * *
69757 AAAATGGAATTTTTGGACA-TTCGAGGGTGAAATGGTAATTTTGAAAAAAGTTCGAGGTAA
1 AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTG-AAAAAGTTCGAGGTTA
* * *** * *
69817 AAAATGGAATTTTGAAAAGTT-TAGGGTTAAAAATGG-AATTTTTTGACA-TTCGAGGGT-
1 AAAATGGAATTTTGGAAAGTTCGAGGG-T-AAAATGGTAATTTTGAAAAAGTTCGAGGTTA
* * * *
69874 GAAATGGTAATTTTGAAAAGTTCGA-GTTAAAAAATGG-AATTTTG-AAAAGTT-TAGGGTTA
1 AAAATGG-AATTTTGGAAAGTTCGAGGGT--AAAATGGTAATTTTGAAAAAGTTCGA-GGTTA
* * * * * * *
69933 AAAATAGAATTTTGGAAAGTT-TAGTGTTAAAAT-GTAATTTTTAAAAAGTTTG-GGGTC
1 AAAATGGAATTTTGGAAAGTTCGAG-GGTAAAATGGTAATTTTGAAAAAGTTCGAGGTTA
* * * *
69990 AAAATGGAATTTTGGAAAGTT-TAGGGTCAAAATGG-AATTTTGGAAAA-TTTGAGGGTA
1 AAAATGGAATTTTGGAAAGTTCGAGGGT-AAAATGGTAATTTTGAAAAAGTTCGAGGTTA
70047 AAA
1 AAA
70050 TTATAATTTT
Statistics
Matches: 386, Mismatches: 60, Indels: 51
0.78 0.12 0.10
Matches are distributed among these distances:
56 7 0.02
57 70 0.18
58 106 0.27
59 131 0.34
60 54 0.14
61 18 0.05
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.33
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGAAAAAGTTCGAGGTTA
Found at i:69972 original size:57 final size:57
Alignment explanation
Indices: 69904--70125 Score: 227
Period size: 57 Copynumber: 3.9 Consensus size: 57
69894 TTCGAGTTAA
*
69904 AAAATGGAATTTTGAAAAGTTT-AGGGTTAAAAATAGAATTTTGGAAAGTTTAGTGTT
1 AAAATGGAATTTTGAAAAGTTTAAGGG-TAAAAATAGAATTTTGGAAAGTTTAGTGTC
* * * * * *
69961 AAAATGTAATTTTTAAAAAGTTT-GGGGTCAAAATGGAATTTTGGAAAGTTTAGGGTC
1 AAAATGGAA-TTTTGAAAAGTTTAAGGGTAAAAATAGAATTTTGGAAAGTTTAGTGTC
* * * * *
70018 AAAATGGAATTTTGGAAAA-TTTGAGGGTAAAATTATAATTTTTAGAAAGTTCA-TGTC
1 AAAATGGAATTTT-GAAAAGTTTAAGGGTAAAAATAGAA-TTTTGGAAAGTTTAGTGTC
* * * *
70075 AATAATGGAATTTTGGAATGTTTAAGGGTAAAAATATAATTTTGGACAGTT
1 AA-AATGGAATTTTGAAAAGTTTAAGGGTAAAAATAGAATTTTGGAAAGTT
70126 CAGGGACCTT
Statistics
Matches: 136, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
56 7 0.05
57 74 0.54
58 55 0.40
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (57 bp):
AAAATGGAATTTTGAAAAGTTTAAGGGTAAAAATAGAATTTTGGAAAGTTTAGTGTC
Found at i:70059 original size:29 final size:27
Alignment explanation
Indices: 69520--70050 Score: 169
Period size: 28 Copynumber: 18.2 Consensus size: 27
69510 ACTTCGGGGC
* * * *
69520 AAAATGGTAATTTTTGGATACTTGAGGGC
1 AAAATGG-AA-TTTTGGAAAATTTAGGGT
* *
69549 AAAATGGTAATTTTGGAAAAGTTCGGAGT
1 AAAATGG-AATTTTGGAAAATTTAGG-GT
* * *
69578 CAAAAATGAAATTTTTGG-ACATTCGAGGGT
1 --AAAATGGAA-TTTTGGAAAATT-TAGGGT
* * * *
69608 AAAATGGTAATTTAGAAAAAGTTCGAGGTT
1 AAAATGG-AATTTTGGAAAA-TT-TAGGGT
* *
69638 AAAAATGGAATTTTTGG-AAGTTCGAGGGT
1 -AAAATGGAA-TTTTGGAAAATT-TAGGGT
* *
69667 AAAATGGTAATTTTGAAAAAGTTTAAGGTT
1 AAAATGG-AATTTTGGAAAA-TTT-AGGGT
* * * *
69697 AAAGTTGGAATTTTAG-AAGTTCGAGGGT
1 AAA-ATGGAATTTTGGAAAATT-TAGGGT
* * *
69725 TAAATAGTAATTTTGGAAAAGTTTGGGGT
1 AAAAT-GGAATTTTGGAAAA-TTTAGGGT
* *
69754 CAAAAAATGGAATTTTTGG-ACATTCGAGGGT
1 ---AAAATGGAA-TTTTGGAAAATT-TAGGGT
* * * *
69785 GAAATGGTAATTTTGAAAAAAGTTCGAGGT
1 AAAATGG-AATTTTG-GAAAATTTAG-GGT
69815 AAAAAATGGAATTTT-GAAAAGTTTAGGGTT
1 --AAAATGGAATTTTGGAAAA-TTTAGGG-T
* * *
69845 AAAAATGGAATTTTTTG-ACATTCGAGGGT
1 -AAAATGGAA-TTTTGGAAAATT-TAGGGT
* * * *
69874 GAAATGGTAATTTT-GAAAAGTTCGAGTT
1 AAAATGG-AATTTTGGAAAATTTAG-GGT
69902 AAAAAATGGAATTTT-GAAAAGTTTAGGGTT
1 --AAAATGGAATTTTGGAAAA-TTTAGGG-T
* * *
69932 AAAAATAGAATTTTGGAAAGTTTAGTGTT
1 -AAAATGGAATTTTGGAAAATTTAG-GGT
* ** *
69961 AAAATGTAATTTTTAAAAAGTTTGGGGT
1 AAAATGGAATTTTGGAAAA-TTTAGGGT
*
69989 CAAAATGGAATTTTGGAAAGTTTAGGGT
1 -AAAATGGAATTTTGGAAAATTTAGGGT
70017 CAAAATGGAATTTTGGAAAATTTGAGGGT
1 -AAAATGGAATTTTGGAAAATTT-AGGGT
70046 AAAAT
1 AAAAT
70051 TATAATTTTT
Statistics
Matches: 375, Mismatches: 80, Indels: 95
0.68 0.15 0.17
Matches are distributed among these distances:
27 3 0.01
28 125 0.33
29 114 0.30
30 73 0.19
31 44 0.12
32 16 0.04
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.33
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAAATTTAGGGT
Found at i:70115 original size:29 final size:28
Alignment explanation
Indices: 69549--70130 Score: 238
Period size: 29 Copynumber: 19.9 Consensus size: 28
69539 ACTTGAGGGC
*
69549 AAAATGGTAATTTTGGAAAAG-TTCGGAGTCA
1 AAAATGG-AATTTTGG-AAAGTTTAGG-GT-A
* * *
69580 AAAATGAAATTTTTGGACA-TTCGAGGGT-
1 AAAATGGAA-TTTTGGAAAGTT-TAGGGTA
* * * *
69608 AAAATGGTAATTTAGAAAAAGTTCGAGGTTA
1 AAAATGG-AATTTTG-GAAAGTT-TAGGGTA
*
69639 AAAATGGAATTTTTGG-AAGTTCGAGGGT-
1 AAAATGGAA-TTTTGGAAAGTT-TAGGGTA
* *
69667 AAAATGGTAATTTTGAAAAAGTTTAAGGTTA
1 AAAATGG-AATTTTG-GAAAGTTT-AGGGTA
** * *
69698 AAGTTGGAATTTTAG-AAGTTCGAGGGT-
1 AAAATGGAATTTTGGAAAGTT-TAGGGTA
* * *
69725 TAAATAGTAATTTTGGAAAAGTTTGGGGTCAA
1 AAAAT-GGAATTTTGG-AAAGTTTAGGGT--A
* *
69757 AAAATGGAATTTTTGGACA-TTCGAGGGT-
1 AAAATGGAA-TTTTGGAAAGTT-TAGGGTA
* * *
69785 GAAATGGTAATTTTGAAAAAAG-TTCGAGGTAA
1 AAAATGG-AATTTTG--GAAAGTTTAG-GGT-A
*
69817 AAAATGGAATTTTGAAAAGTTTAGGGTTA
1 AAAATGGAATTTTGGAAAGTTTAGGG-TA
* * *
69846 AAAATGGAATTTTTTGACA-TTCGAGGGT-
1 AAAATGGAA-TTTTGGAAAGTT-TAGGGTA
* * * *
69874 GAAATGGTAATTTTGAAAAG-TTCGAGTTAA
1 AAAATGG-AATTTTGGAAAGTTTAG-GGT-A
*
69904 AAAATGGAATTTTGAAAAGTTTAGGGTTA
1 AAAATGGAATTTTGGAAAGTTTAGGG-TA
* * *
69933 AAAATAGAATTTTGGAAAGTTTAGTGTT
1 AAAATGGAATTTTGGAAAGTTTAGGGTA
* ** * *
69961 AAAATGTAATTTTTAAAAAGTTTGGGGTC
1 AAAATGGAA-TTTTGGAAAGTTTAGGGTA
*
69990 AAAATGGAATTTTGGAAAGTTTAGGGTC
1 AAAATGGAATTTTGGAAAGTTTAGGGTA
*
70018 AAAATGGAATTTTGGAAAATTTGAGGGTA
1 AAAATGGAATTTTGGAAAGTTT-AGGGTA
* ** * * *
70047 AAATTATAATTTTTAGAAAGTTCA-TGTCA
1 AAAATGGAA-TTTTGGAAAGTTTAGGGT-A
* *
70076 ATAATGGAATTTTGGAATGTTTAAGGGTA
1 AAAATGGAATTTTGGAAAGTTT-AGGGTA
** * *
70105 AAAATATAATTTTGGACAGTTCAGGG
1 AAAATGGAATTTTGGAAAGTTTAGGG
70131 ACCTTTTGGG
Statistics
Matches: 413, Mismatches: 92, Indels: 95
0.69 0.15 0.16
Matches are distributed among these distances:
27 3 0.01
28 126 0.31
29 141 0.34
30 81 0.20
31 46 0.11
32 16 0.04
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTAGGGTA
Found at i:71226 original size:3 final size:3
Alignment explanation
Indices: 71218--71243 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
71208 CATTTTCTTT
71218 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
71244 CATTCAATGC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:71959 original size:17 final size:17
Alignment explanation
Indices: 71937--71978 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
71927 TAAATTTAAT
*
71937 TTTAAATTTATAATAAA
1 TTTAAATTTACAATAAA
*
71954 TTTAAATTTCCAATAAA
1 TTTAAATTTACAATAAA
71971 TTTAAATT
1 TTTAAATT
71979 CTGTTGGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAATTTACAATAAA
Found at i:72560 original size:16 final size:16
Alignment explanation
Indices: 72541--72574 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
72531 ATATAAAATG
*
72541 AACTTGAAATAATTCA
1 AACTTAAAATAATTCA
72557 AACTTAAAATAATTCA
1 AACTTAAAATAATTCA
72573 AA
1 AA
72575 TTTAGACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (16 bp):
AACTTAAAATAATTCA
Found at i:73476 original size:31 final size:31
Alignment explanation
Indices: 73423--73485 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
73413 CAACCCATTG
* *
73423 ATTTAAATAAAAAATTTTAAATAGTTAAATA
1 ATTTAAATAAAAAATATCAAATAGTTAAATA
* * *
73454 ATTTAAATAAAAACTATCAAATATTTTAATA
1 ATTTAAATAAAAAATATCAAATAGTTAAATA
73485 A
1 A
73486 CCATTACGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (31 bp):
ATTTAAATAAAAAATATCAAATAGTTAAATA
Found at i:78409 original size:20 final size:21
Alignment explanation
Indices: 78380--78418 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
78370 GACTTGCTGA
*
78380 TTTTATTATG-ATTTTAATCT
1 TTTTAGTATGAATTTTAATCT
78400 TTTTAGTATGAATTTTAAT
1 TTTTAGTATGAATTTTAAT
78419 TATTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (21 bp):
TTTTAGTATGAATTTTAATCT
Found at i:78424 original size:21 final size:21
Alignment explanation
Indices: 78379--78424 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
78369 AGACTTGCTG
*
78379 ATTTTATTATGATTTTAATCT
1 ATTTTAGTATGATTTTAATCT
78400 -TTTTAGTATGAATTTTAAT-T
1 ATTTTAGTATG-ATTTTAATCT
78420 ATTTT
1 ATTTT
78425 TATTTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (21 bp):
ATTTTAGTATGATTTTAATCT
Found at i:78929 original size:16 final size:17
Alignment explanation
Indices: 78901--78939 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
78891 CGGTAATTAT
78901 ATTAAATTTCAAATAAA
1 ATTAAATTTCAAATAAA
*
78918 ATTAAA-TTCAAATCAA
1 ATTAAATTTCAAATAAA
78934 ATTAAA
1 ATTAAA
78940 ATTTTTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTAAATTTCAAATAAA
Found at i:89985 original size:35 final size:35
Alignment explanation
Indices: 89946--90012 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
89936 CAAATTGCTT
*
89946 CAAATTAAAGTAGAA-CACTAAATATCAAATTTTAA
1 CAAATTAAAGTAGAAGCACTAAA-ATAAAATTTTAA
*
89981 CAAATTAAAGTAGAAGGACTAAAATAAAATTT
1 CAAATTAAAGTAGAAGCACTAAAATAAAATTT
90013 AAACCATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 23 0.79
36 6 0.21
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (35 bp):
CAAATTAAAGTAGAAGCACTAAAATAAAATTTTAA
Found at i:90189 original size:59 final size:59
Alignment explanation
Indices: 90097--90268 Score: 200
Period size: 59 Copynumber: 2.9 Consensus size: 59
90087 TTAATGTAAC
** ** * *
90097 ATTTGATACCTGAACTTGGTACTTTTTCCTAATTTGATACTTAAACTTTTTTTGACCAA
1 ATTTGATAATTGAACTTGACACTTTTTCCTAATTTGATACCTAAACTTTTTTTAACCAA
* * * *
90156 ATTTGGTAATTGAATTTGACACTTTTTCCTAATTCGATACCTAAACTTTTTTTAACCCA
1 ATTTGATAATTGAACTTGACACTTTTTCCTAATTTGATACCTAAACTTTTTTTAACCAA
* * * * * *
90215 ATTTGATACTTGAACTTGACATTTTTTTCTATTTTGGTACCTAAGCTTTTTTTA
1 ATTTGATAATTGAACTTGACACTTTTTCCTAATTTGATACCTAAACTTTTTTTA
90269 GATTCAATTT
Statistics
Matches: 94, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 94 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (59 bp):
ATTTGATAATTGAACTTGACACTTTTTCCTAATTTGATACCTAAACTTTTTTTAACCAA
Found at i:90605 original size:90 final size:90
Alignment explanation
Indices: 90440--90605 Score: 208
Period size: 90 Copynumber: 1.8 Consensus size: 90
90430 AAAGATTAAG
* * **
90440 TACCAAATTAGGAAAAAGAGTCAAGTTCATGTACCAAATTGGACCCCAAAAAGTTGAAGTACCAA
1 TACCAAATTAAGAAAAAGAGTCAAGTTCATGTACCAAATTGCACCAAAAAAAGTTGAAGTACCAA
* **
90505 CTTCTAAAAAAGTGTCAAGGGTAGA
66 ATTAGAAAAAAGTGTCAAGGGTAGA
* * * *
90530 TACCAAATTAAGAAAAAGTGTCAAGTTTGA-GTACCAAATTGCACCAAAAAAAGTTTAGGTACCA
1 TACCAAATTAAGAAAAAGAGTCAAG-TTCATGTACCAAATTGCACCAAAAAAAGTTGAAGTACCA
*
90594 AATTAGGAAAAA
65 AATTAGAAAAAA
90606 TTATCAAGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
90 60 0.95
91 3 0.05
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (90 bp):
TACCAAATTAAGAAAAAGAGTCAAGTTCATGTACCAAATTGCACCAAAAAAAGTTGAAGTACCAA
ATTAGAAAAAAGTGTCAAGGGTAGA
Found at i:91603 original size:22 final size:22
Alignment explanation
Indices: 91571--91617 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
91561 AAATAGGAGG
* *
91571 GAAAAAACTCAAGTATTAAATT
1 GAAAAAACTCAAGTATCAAAAT
*
91593 GAAAAAGCTCAAGTATCAAAAT
1 GAAAAAACTCAAGTATCAAAAT
91615 GAA
1 GAA
91618 TTTTGAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (22 bp):
GAAAAAACTCAAGTATCAAAAT
Found at i:94888 original size:29 final size:30
Alignment explanation
Indices: 94833--94895 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
94823 AATTTGTGAG
94833 AATTAGATCAAATCGAAATTTAATCTATAA
1 AATTAGATCAAATCGAAATTTAATCTATAA
*
94863 AATTAGA-CAAAATC-AAAGTTT-ATCTATAC
1 AATTAGATC-AAATCGAAA-TTTAATCTATAA
94892 AATT
1 AATT
94896 TCGCATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.33
Consensus pattern (30 bp):
AATTAGATCAAATCGAAATTTAATCTATAA
Found at i:97972 original size:20 final size:21
Alignment explanation
Indices: 97929--97971 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
97919 TTGGGAGGTT
97929 GGAAAATTAAAAACAGAAAGG
1 GGAAAATTAAAAACAGAAAGG
*
97950 GGAAAA-TAAAAAGGAGAAAGG
1 GGAAAATTAAAAA-CAGAAAGG
97971 G
1 G
97972 ATATGGTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.60, C:0.02, G:0.30, T:0.07
Consensus pattern (21 bp):
GGAAAATTAAAAACAGAAAGG
Found at i:98131 original size:18 final size:16
Alignment explanation
Indices: 98086--98132 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
98076 CATTGTTATT
*
98086 GCTCTCTTTGTTCTTC
1 GCTCTCTTTATTCTTC
*
98102 GTTCTCTTTATTCTTC
1 GCTCTCTTTATTCTTC
98118 GCTCTACATTTATTC
1 GCTCT-C-TTTATTC
98133 AAATAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 18 0.69
17 1 0.04
18 7 0.27
ACGTcount: A:0.09, C:0.28, G:0.09, T:0.55
Consensus pattern (16 bp):
GCTCTCTTTATTCTTC
Found at i:103529 original size:30 final size:30
Alignment explanation
Indices: 103495--103611 Score: 111
Period size: 30 Copynumber: 4.0 Consensus size: 30
103485 GGTAAACTAA
103495 TAAAATAAAGGACTAAATT-TAAAATTTGAG
1 TAAAATAAAGGACT-AATTATAAAATTTGAG
*
103525 TAAAATACAGGGACTAATTATAAAA-TT---
1 TAAAATA-AAGGACTAATTATAAAATTTGAG
* * *
103552 TAAAATAAGGGACTAAATT-TATAAGTTGAG
1 TAAAATAAAGGACT-AATTATAAAATTTGAG
*
103582 TAAAATACAGCGACTAATTATAAAATTTGA
1 TAAAATAAAG-GACTAATTATAAAATTTGA
103612 CCAGTAATTT
Statistics
Matches: 72, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
26 11 0.15
27 13 0.18
30 25 0.35
31 23 0.32
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.30
Consensus pattern (30 bp):
TAAAATAAAGGACTAATTATAAAATTTGAG
Found at i:103541 original size:31 final size:30
Alignment explanation
Indices: 103495--103611 Score: 120
Period size: 31 Copynumber: 4.0 Consensus size: 30
103485 GGTAAACTAA
*
103495 TAAAATAAAGGACTAAATT-TAAAATTTGAG
1 TAAAATAAGGGACT-AATTATAAAATTTGAG
103525 TAAAATACAGGGACTAATTATAAAA-TT---
1 TAAAATA-AGGGACTAATTATAAAATTTGAG
* *
103552 TAAAATAAGGGACTAAATT-TATAAGTTGAG
1 TAAAATAAGGGACT-AATTATAAAATTTGAG
*
103582 TAAAATACAGCGACTAATTATAAAATTTGA
1 TAAAATA-AGGGACTAATTATAAAATTTGA
103612 CCAGTAATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
26 11 0.15
27 13 0.18
30 24 0.33
31 25 0.34
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.30
Consensus pattern (30 bp):
TAAAATAAGGGACTAATTATAAAATTTGAG
Found at i:103565 original size:26 final size:27
Alignment explanation
Indices: 103525--103609 Score: 93
Period size: 27 Copynumber: 3.0 Consensus size: 27
103515 AAAATTTGAG
103525 TAAAATACAGGGACTAATTATAAAATT
1 TAAAATACAGGGACTAATTATAAAATT
*
103552 TAAAATA-AGGGACTAAATT-TATAAGTT
1 TAAAATACAGGGACT-AATTATA-AAATT
*
103579 GAGTAAAATACAGCGACTAATTATAAAATT
1 ---TAAAATACAGGGACTAATTATAAAATT
103609 T
1 T
103610 GACCAGTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
26 9 0.19
27 16 0.33
30 15 0.31
31 8 0.17
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (27 bp):
TAAAATACAGGGACTAATTATAAAATT
Found at i:103565 original size:57 final size:57
Alignment explanation
Indices: 103495--103609 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
103485 GGTAAACTAA
* *
103495 TAAAATAAAGGACTAAATTTAAAATTTGAGTAAAATACAGGGACTAATTATAAAATT
1 TAAAATAAAGGACTAAATTTAAAAGTTGAGTAAAATACAGCGACTAATTATAAAATT
* *
103552 TAAAATAAGGGACTAAATTTATAAGTTGAGTAAAATACAGCGACTAATTATAAAATT
1 TAAAATAAAGGACTAAATTTAAAAGTTGAGTAAAATACAGCGACTAATTATAAAATT
103609 T
1 T
103610 GACCAGTAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.30
Consensus pattern (57 bp):
TAAAATAAAGGACTAAATTTAAAAGTTGAGTAAAATACAGCGACTAATTATAAAATT
Found at i:104319 original size:19 final size:19
Alignment explanation
Indices: 104295--104333 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
104285 CATGTAATGG
*
104295 CGAATTTTGATGGAAAATA
1 CGAATTTTGACGGAAAATA
104314 CGAATTTTGACGGAAAATA
1 CGAATTTTGACGGAAAATA
104333 C
1 C
104334 TTAAAACGAA
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:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (19 bp):
CGAATTTTGACGGAAAATA
Found at i:105914 original size:176 final size:175
Alignment explanation
Indices: 105550--105932 Score: 497
Period size: 176 Copynumber: 2.2 Consensus size: 175
105540 CCTGCAGAAA
* ** * *
105550 ACTGTTTCGAGGTTTATTA-GGATTGCATACTGGCAGTTTTTAAACTTTTTCAGTACGACTTTCT
1 ACTGTTTCGAGGTTTATTAGGGATTGCATACTAGCAGTAGTTAAACTTTTCCAGTACAACTTTCT
* * *
105614 GTCATCCAAGGTGGTTTCTTTTACAATATTCACGGTGAAGTTAGATAGCCTCATTGTTTCTTCGA
66 GTCATCCAAGGTGGTTACTTTTACAATATTCACGGTGAAGTTAGATAGCCTCATCGTATCTTCGA
* * * **
105679 GTCAAAGAACTGTAAACCCTGCATTGTGTCAATACCATACAAAAG
131 GTCAAAGAACTATAAACCATACATTACGTCAATACCATACAAAAG
*
105724 ACTGTCTT-GAGGTTTATTAGGGATTTGGATACTAGCAGTCGAGTTAAACTTTTCC-GATACAAC
1 ACTGT-TTCGAGGTTTATTAGGGA-TTGCATACTAGCAGT--AGTTAAACTTTTCCAG-TACAAC
* * * * * *
105787 -TTCTGTCGTCCGAGGTGGTTACTTTTACAATATTCTCGGTGAAGTTAGAT-GGCTTATCGTATG
61 TTTCTGTCATCCAAGGTGGTTACTTTTACAATATTCACGGTGAAGTTAGATAGCCTCATCGTATC
*
105850 TTCGAGTCAAAGAACTATAAACTATACATTACGTCAATACCATACAAAAG
126 TTCGAGTCAAAGAACTATAAACCATACATTACGTCAATACCATACAAAAG
105900 ACTGTTTCGAGGTTTATTAGGGATTGCATACTA
1 ACTGTTTCGAGGTTTATTAGGGATTGCATACTA
105933 AAACATCAAG
Statistics
Matches: 180, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
174 16 0.09
175 16 0.09
176 85 0.47
177 47 0.26
178 16 0.09
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (175 bp):
ACTGTTTCGAGGTTTATTAGGGATTGCATACTAGCAGTAGTTAAACTTTTCCAGTACAACTTTCT
GTCATCCAAGGTGGTTACTTTTACAATATTCACGGTGAAGTTAGATAGCCTCATCGTATCTTCGA
GTCAAAGAACTATAAACCATACATTACGTCAATACCATACAAAAG
Found at i:106738 original size:84 final size:84
Alignment explanation
Indices: 106642--106810 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
106632 AGAAGAACTG
106642 ATTTGCTCTTTGATCTAATGTATAAGGACTAATTTACCTGTTTTTTGAGTAAAGGGGATAAAATT
1 ATTTGCTCTTTGATCTAATGTATAAGGACTAATTTACCTGTTTTTTGAGTAAAGGGGATAAAATT
106707 CAAATTGATTTCTAATGCT
66 CAAATTGATTTCTAATGCT
*
106726 ATTTGCTCTTTGATCTAATGTATAAGGACTAATTTACCTGTTTTTTGCGTAAAGGGGATAAAATT
1 ATTTGCTCTTTGATCTAATGTATAAGGACTAATTTACCTGTTTTTTGAGTAAAGGGGATAAAATT
*
106791 GAAATTGATTTCTAATGCT
66 CAAATTGATTTCTAATGCT
106810 A
1 A
106811 GGGCCTCTAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (84 bp):
ATTTGCTCTTTGATCTAATGTATAAGGACTAATTTACCTGTTTTTTGAGTAAAGGGGATAAAATT
CAAATTGATTTCTAATGCT
Found at i:109630 original size:24 final size:24
Alignment explanation
Indices: 109598--109645 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
109588 TATAGTAATC
109598 ACTTTTGTTTCGAATTTCTCTTTT
1 ACTTTTGTTTCGAATTTCTCTTTT
*
109622 ACTTTTGTTTCGAGTTTCTCTTTT
1 ACTTTTGTTTCGAATTTCTCTTTT
109646 TCCTTTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.17, G:0.10, T:0.62
Consensus pattern (24 bp):
ACTTTTGTTTCGAATTTCTCTTTT
Found at i:110315 original size:15 final size:15
Alignment explanation
Indices: 110291--110341 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
110281 TTAGCTGGAG
110291 AAAAATTTTCCCATA
1 AAAAATTTTCCCATA
* *
110306 AAAAAATTT-CCATG
1 AAAAATTTTCCCATA
*
110320 CAAAATTTTCCCATA
1 AAAAATTTTCCCATA
110335 AAAAATT
1 AAAAATT
110342 CAGAAACATG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAAATTTTCCCATA
Found at i:112859 original size:40 final size:42
Alignment explanation
Indices: 112814--112895 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
112804 AATCTAAGCC
* *
112814 GATAAACTCAGCTATT-CC-ATATAATCAGAAAAACGAGAAA
1 GATAAACTCAGCGATTCCCAATATAATCAAAAAAACGAGAAA
* *
112854 GATAAACTCAGCGATTCCCAATATGATTAAAAAAACGAGAAA
1 GATAAACTCAGCGATTCCCAATATAATCAAAAAAACGAGAAA
112896 CAGGTTATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 15 0.42
41 2 0.06
42 19 0.53
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (42 bp):
GATAAACTCAGCGATTCCCAATATAATCAAAAAAACGAGAAA
Found at i:114246 original size:20 final size:20
Alignment explanation
Indices: 114211--114275 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
114201 AAACGCATAA
**
114211 AAAAATAACATTCAAACAAC
1 AAAAATAACAACCAAACAAC
*
114231 AAAAATAACAACCAAAACAGC
1 AAAAATAACAACC-AAACAAC
*
114252 AGTGAAAATAACAACAAAACAAC
1 A---AAAATAACAACCAAACAAC
114275 A
1 A
114276 TTAAAAACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.31
21 7 0.19
23 7 0.19
24 11 0.31
ACGTcount: A:0.66, C:0.20, G:0.05, T:0.09
Consensus pattern (20 bp):
AAAAATAACAACCAAACAAC
Found at i:114282 original size:23 final size:24
Alignment explanation
Indices: 114231--114282 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
114221 TTCAAACAAC
*
114231 AAAAATAACAACCAAAACAGCAGT
1 AAAAATAACAACCAAAACAACAGT
* *
114255 GAAAATAACAA-CAAAACAACATT
1 AAAAATAACAACCAAAACAACAGT
114278 AAAAA
1 AAAAA
114283 CAATAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.10
Consensus pattern (24 bp):
AAAAATAACAACCAAAACAACAGT
Found at i:114296 original size:21 final size:21
Alignment explanation
Indices: 114267--114306 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
114257 AAATAACAAC
**
114267 AAAACAACATTAAAAACAATA
1 AAAACAACAACAAAAACAATA
*
114288 AAAATAACAACAAAAACAA
1 AAAACAACAACAAAAACAA
114307 CAAGAAAAAT
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:0.75, C:0.15, G:0.00, T:0.10
Consensus pattern (21 bp):
AAAACAACAACAAAAACAATA
Found at i:114304 original size:56 final size:56
Alignment explanation
Indices: 114211--114343 Score: 148
Period size: 56 Copynumber: 2.4 Consensus size: 56
114201 AAACGCATAA
* * * *
114211 AAAAATAACATT-CAAACAACAAAAATAACAACCAAAACAGC-AGTGAAAATAACAAC
1 AAAAA-AACATTAAAAACAACAAAAATAACAACAAAAACAACAAG-AAAAATAACAAC
* * *
114267 AAAACAACATTAAAAACAATAAAAATAACAACAAAAACAACAAGAAAAATAACAGC
1 AAAAAAACATTAAAAACAACAAAAATAACAACAAAAACAACAAGAAAAATAACAAC
114323 AAAAAAACA--AGAAAACAACAA
1 AAAAAAACATTA-AAAACAACAA
114344 CCAAAACAGT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
54 1 0.02
55 15 0.23
56 47 0.72
57 2 0.03
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.08
Consensus pattern (56 bp):
AAAAAAACATTAAAAACAACAAAAATAACAACAAAAACAACAAGAAAAATAACAAC
Found at i:114308 original size:24 final size:23
Alignment explanation
Indices: 114281--114351 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
114271 CAACATTAAA
114281 AACAATAAAAATAACAACAAAAAC
1 AACAA-AAAAATAACAACAAAAAC
*
114305 AACAAGAAAAATAACAGCAAAAA-
1 AACAA-AAAAATAACAACAAAAAC
* * *
114328 AACAAGAAAACAACAACCAAAAC
1 AACAAAAAAATAACAACAAAAAC
114351 A
1 A
114352 GTAAAAAAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 13 0.32
23 6 0.15
24 21 0.52
ACGTcount: A:0.73, C:0.18, G:0.04, T:0.04
Consensus pattern (23 bp):
AACAAAAAAATAACAACAAAAAC
Found at i:114351 original size:12 final size:12
Alignment explanation
Indices: 114225--114351 Score: 68
Period size: 12 Copynumber: 11.1 Consensus size: 12
114215 ATAACATTCA
*
114225 AACAACAAAAAT
1 AACAACAAAAAC
*
114237 AACAACCAAAAC
1 AACAACAAAAAC
* *** *
114249 AGCAGTGAAAAT
1 AACAACAAAAAC
114261 AACAAC-AAAAC
1 AACAACAAAAAC
**
114272 AAC-A-TTAAA-
1 AACAACAAAAAC
* *
114281 AACAATAAAAAT
1 AACAACAAAAAC
114293 AACAACAAAAAC
1 AACAACAAAAAC
* *
114305 AACAAGAAAAAT
1 AACAACAAAAAC
*
114317 AACAGCAAAAA-
1 AACAACAAAAAC
*
114328 AACAA-GAAAAC
1 AACAACAAAAAC
*
114339 AACAACCAAAAC
1 AACAACAAAAAC
114351 A
1 A
114352 GTAAAAAAGC
Statistics
Matches: 86, Mismatches: 23, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
9 3 0.03
10 9 0.10
11 19 0.22
12 55 0.64
ACGTcount: A:0.70, C:0.19, G:0.05, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:117454 original size:2 final size:2
Alignment explanation
Indices: 117449--117480 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
117439 ACACACATAA
117449 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
117481 GGTACCGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:144972 original size:123 final size:123
Alignment explanation
Indices: 144753--144990 Score: 352
Period size: 123 Copynumber: 1.9 Consensus size: 123
144743 TGATTGCACG
* * *
144753 TAAGTGTTTATTTCTTTTGATTTAAGGGTTGAAGAAAGATTATGGGTATAAAGAAAATATATGTG
1 TAAGTGTGTATTTCTTTTGATTTAAGGATTGAAGAAAGATTATGAGTATAAAGAAAATATATGTG
* *
144818 GATTGAAATTTAATTTTGTTGACGTCGTTGTTATTGCAGTAATGAAAAAGGCATCAGT
66 GATTGAAATTTAACTTTGTTGACGCCGTTGTTATTGCAGTAATGAAAAAGGCATCAGT
* * * * *
144876 TAAGTGTGTATTT-TTTCTTATTTAAGGATTGATGAAGGGTTATGAGTATAAAGAAAGTATATGT
1 TAAGTGTGTATTTCTTT-TGATTTAAGGATTGAAGAAAGATTATGAGTATAAAGAAAATATATGT
**
144940 GGATTGAGCTTTAACTTTGTTGACGCCGTTGTTATTGCAGTAATGAAAAAG
65 GGATTGAAATTTAACTTTGTTGACGCCGTTGTTATTGCAGTAATGAAAAAG
144991 ACGTGAATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
122 3 0.03
123 99 0.97
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (123 bp):
TAAGTGTGTATTTCTTTTGATTTAAGGATTGAAGAAAGATTATGAGTATAAAGAAAATATATGTG
GATTGAAATTTAACTTTGTTGACGCCGTTGTTATTGCAGTAATGAAAAAGGCATCAGT
Found at i:145022 original size:123 final size:123
Alignment explanation
Indices: 144763--145041 Score: 330
Period size: 123 Copynumber: 2.3 Consensus size: 123
144753 TAAGTGTTTA
* * * * * *
144763 TTTCTTTTGATTTAAGGGTTGAAGAAAGATTATGGGTATAAAGAAAATATATGTGGATTGAAATT
1 TTTC-TTTAATTTAAGGATTGATGAAGGGTTATGAGTATAAAGAAAATATATGTGGATTGAAATT
* * * * * *
144828 TAATTTTGTTGACGTCGTTGTTATTGCAGTAATGAAAAAGGCATCAGTTAAGTGTGTAT
65 TAACTTTGTTGACGCCGTTGTTATTGCAGTAATGAAAAAGACATCAATTAAATGCGTAT
* * **
144887 TTT-TTCTTATTTAAGGATTGATGAAGGGTTATGAGTATAAAGAAAGTATATGTGGATTGAGCTT
1 TTTCTT-TAATTTAAGGATTGATGAAGGGTTATGAGTATAAAGAAAATATATGTGGATTGAAATT
* *
144951 TAACTTTGTTGACGCCGTTGTTATTGCAGTAATGAAAAAGACGTGAATTAAATGCGT-T
65 TAACTTTGTTGACGCCGTTGTTATTGCAGTAATGAAAAAGACATCAATTAAATGCGTAT
*
145009 TTTCCTTTAATTTAAGAATTGATG-AGGGATTAT
1 TTT-CTTTAATTTAAGGATTGATGAAGGG-TTAT
145042 CAATAAAAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
122 10 0.08
123 117 0.89
124 5 0.04
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (123 bp):
TTTCTTTAATTTAAGGATTGATGAAGGGTTATGAGTATAAAGAAAATATATGTGGATTGAAATTT
AACTTTGTTGACGCCGTTGTTATTGCAGTAATGAAAAAGACATCAATTAAATGCGTAT
Found at i:145752 original size:17 final size:17
Alignment explanation
Indices: 145727--145777 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
145717 CAATGAATCT
*
145727 GATTGATTTTAGATTCG
1 GATTAATTTTAGATTCG
*
145744 GATTAATTTAAG-TTCG
1 GATTAATTTTAGATTCG
* *
145760 AATTCAATTTTATATTCG
1 GATT-AATTTTAGATTCG
145778 AACCATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 7 0.26
17 16 0.59
18 4 0.15
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (17 bp):
GATTAATTTTAGATTCG
Found at i:146620 original size:24 final size:23
Alignment explanation
Indices: 146593--146637 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
146583 ATATTGTTCT
146593 TGAACATGTTTAATTATATGTTTA
1 TGAACATGTTTAATTA-ATGTTTA
*
146617 TGAACATGTTTATTTAATGTT
1 TGAACATGTTTAATTAATGTT
146638 CACGAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
TGAACATGTTTAATTAATGTTTA
Found at i:152473 original size:26 final size:25
Alignment explanation
Indices: 152409--152482 Score: 85
Period size: 25 Copynumber: 2.9 Consensus size: 25
152399 ATCAGTAACA
*
152409 TAATAATAATTATTAAATGTTGGAT
1 TAATAAAAATTATTAAATGTTGGAT
** * **
152434 TTTTAAAAAATATTAAATGTTTTAT
1 TAATAAAAATTATTAAATGTTGGAT
152459 TAAATAAAAATTATTAAATGTTGG
1 T-AATAAAAATTATTAAATGTTGG
152483 CATGTATACG
Statistics
Matches: 37, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
25 20 0.54
26 17 0.46
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (25 bp):
TAATAAAAATTATTAAATGTTGGAT
Found at i:159986 original size:72 final size:72
Alignment explanation
Indices: 159896--160038 Score: 277
Period size: 72 Copynumber: 2.0 Consensus size: 72
159886 GAAAATTTGG
*
159896 CATTCAATATATCTACGGTGTGATCTGTATCAATCTACATTGGAATCGAGTTAGTCTGTACAATA
1 CATTCAATATATCTACGGTGTGATCTGTATCAATCTACATTAGAATCGAGTTAGTCTGTACAATA
159961 GTTTTAC
66 GTTTTAC
159968 CATTCAATATATCTACGGTGTGATCTGTATCAATCTACATTAGAATCGAGTTAGTCTGTACAATA
1 CATTCAATATATCTACGGTGTGATCTGTATCAATCTACATTAGAATCGAGTTAGTCTGTACAATA
160033 GTTTTA
66 GTTTTA
160039 GTCAAGGTAG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (72 bp):
CATTCAATATATCTACGGTGTGATCTGTATCAATCTACATTAGAATCGAGTTAGTCTGTACAATA
GTTTTAC
Found at i:166231 original size:2 final size:2
Alignment explanation
Indices: 166224--166248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
166214 AATTATGATA
166224 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
166249 CACATAAGAT
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:169565 original size:56 final size:56
Alignment explanation
Indices: 169500--169614 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
169490 AGTCGATGCA
*
169500 TAAGTCTCTTAAAAGGAAATATATAGCTCAAATGTAATTTGTATTTTTGAAAATCC
1 TAAGTCTCTTAAAAGGAAATATATAGCTCAAATGTAATTTGTATGTTTGAAAATCC
*
169556 TAAGTCTCTTAAAAGGAAATATATAGCTCAAATGTAATTTGTATGTTTGAAAATTC
1 TAAGTCTCTTAAAAGGAAATATATAGCTCAAATGTAATTTGTATGTTTGAAAATCC
169612 TAA
1 TAA
169615 AATTTACCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (56 bp):
TAAGTCTCTTAAAAGGAAATATATAGCTCAAATGTAATTTGTATGTTTGAAAATCC
Found at i:174087 original size:2 final size:2
Alignment explanation
Indices: 174080--174113 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
174070 GAGCCTGCAC
174080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
174114 TCAAGTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:174496 original size:99 final size:98
Alignment explanation
Indices: 174325--174522 Score: 369
Period size: 99 Copynumber: 2.0 Consensus size: 98
174315 ACTTGGTCAG
174325 ATTAGTCTCTATTATTAAATAATCAATTTAGTCCTATAAGGTCAAATTGAAACAAAGTTAACATT
1 ATTAGTCTCTATTATTAAATAATCAATTTAGTCCTATAAGGTCAAATTGAAACAAAGTTAACATT
* *
174390 TACAAAAAAAAAAGAATCTATTTATTCTTTTTAT
66 TAC-AAAAAAAAAGAATCGATTTAATCTTTTTAT
174424 ATTAGTCTCTATTATTAAATAATCAATTTAGTCCTATAAGGTCAAATTGAAACAAAGTTAACATT
1 ATTAGTCTCTATTATTAAATAATCAATTTAGTCCTATAAGGTCAAATTGAAACAAAGTTAACATT
174489 TACAAAAAAAAAGAATCGATTTAATCTTTTTAT
66 TACAAAAAAAAAGAATCGATTTAATCTTTTTAT
174522 A
1 A
174523 CAGTAAATGT
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
98 29 0.30
99 68 0.70
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (98 bp):
ATTAGTCTCTATTATTAAATAATCAATTTAGTCCTATAAGGTCAAATTGAAACAAAGTTAACATT
TACAAAAAAAAAGAATCGATTTAATCTTTTTAT
Found at i:182234 original size:36 final size:37
Alignment explanation
Indices: 182171--182244 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
182161 GTAATGAACA
* *
182171 TAAAATAATATTTTTATTTAAATTATTA-AATATAAT
1 TAAAATAATATTTTTATTCAAATTATTATAATAAAAT
182207 TAAAAT-ATATTTATTCATTCAAA-TATTATAATAAAAT
1 TAAAATAATATTT-TT-ATTCAAATTATTATAATAAAAT
182244 T
1 T
182245 TTTTTCAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 6 0.18
36 13 0.39
37 14 0.42
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (37 bp):
TAAAATAATATTTTTATTCAAATTATTATAATAAAAT
Found at i:184758 original size:21 final size:21
Alignment explanation
Indices: 184734--184774 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
184724 TTTTAAACTC
184734 ATTTTT-TTAATATAATAATTG
1 ATTTTTATTAATAT-ATAATTG
*
184755 ATTTTTATTATTATATAATT
1 ATTTTTATTAATATATAATT
184775 AAATAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTATTAATATATAATTG
Found at i:185330 original size:31 final size:31
Alignment explanation
Indices: 185295--185355 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
185285 AAAAAAACTT
* *
185295 AATAGCCTAGTGCCTTGAATAAAATTTTTTG
1 AATAGCCTAGTGACTTGAATAAAACTTTTTG
** *
185326 AATAGTTTAGTGACTTGAATGAAACTTTTT
1 AATAGCCTAGTGACTTGAATAAAACTTTTT
185356 AAACAATTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (31 bp):
AATAGCCTAGTGACTTGAATAAAACTTTTTG
Found at i:190769 original size:2 final size:2
Alignment explanation
Indices: 190762--190791 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
190752 TTAAAACCTT
190762 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
190792 GGAAAGACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:197280 original size:32 final size:32
Alignment explanation
Indices: 197239--197306 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
197229 ATTTTCAATT
*
197239 TTTAAATTATTTTGGGTTTGTGTTATTTTAAA
1 TTTAAATTATTTTGGGTTTGGGTTATTTTAAA
*
197271 TTTAAATTATTTTGGGTTTGGGTTATTTTAAT
1 TTTAAATTATTTTGGGTTTGGGTTATTTTAAA
197303 TTTA
1 TTTA
197307 GGGTTATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (32 bp):
TTTAAATTATTTTGGGTTTGGGTTATTTTAAA
Found at i:202956 original size:88 final size:84
Alignment explanation
Indices: 202774--202956 Score: 231
Period size: 84 Copynumber: 2.1 Consensus size: 84
202764 TTGCCACCAT
* * * *
202774 AAATGAAAAATTTTCAATTCAGTCCTCTTATAAATAGATAAACTATATATTAATATATAGTGAAA
1 AAATGAAAAATTTTCAATTCAGTCCTCTTATAAATAAATAAACTATAAACTAATATATAGTAAAA
**
202839 TTGCACTTCAACCCCCCCC
66 TTGCACTTCAACCCCCCAA
* * *
202858 AAACGAAAAAATTTCAATTCAGTCCTCTTATAAATAAATAAACAAATTATAAACTACTATATAGT
1 AAATGAAAAATTTTCAATTCAGTCCTCTTATAAATAAATAAAC----TATAAACTAATATATAGT
*
202923 AAAATTGCACTTTAACCCCCCTAA
62 AAAATTGCACTTCAACCCCCC-AA
202947 AAATGAAAAA
1 AAATGAAAAA
202957 GATTATGTTC
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
84 40 0.48
88 34 0.41
89 9 0.11
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (84 bp):
AAATGAAAAATTTTCAATTCAGTCCTCTTATAAATAAATAAACTATAAACTAATATATAGTAAAA
TTGCACTTCAACCCCCCAA
Found at i:203524 original size:2 final size:2
Alignment explanation
Indices: 203519--203546 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
203509 AGAAAAAAGT
203519 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
203547 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:204664 original size:18 final size:18
Alignment explanation
Indices: 204641--204685 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
204631 AGTAATTTAA
204641 TTGGATCTTTCTACCAAC
1 TTGGATCTTTCTACCAAC
204659 TTGGATCTTTCTACCAAC
1 TTGGATCTTTCTACCAAC
204677 TTGGATCTT
1 TTGGATCTT
204686 AGCTTGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.42
Consensus pattern (18 bp):
TTGGATCTTTCTACCAAC
Found at i:206253 original size:21 final size:22
Alignment explanation
Indices: 206221--206262 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
206211 AATTTTATCA
* *
206221 TTTTACTTTTTTTTTTCAATTG
1 TTTTACTTTTTTATTTAAATTG
206243 TTTTA-TTTTTTATTTAAATT
1 TTTTACTTTTTTATTTAAATT
206263 TAGCTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTACTTTTTTATTTAAATTG
Found at i:207710 original size:17 final size:18
Alignment explanation
Indices: 207688--207723 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
207678 ATTTTCAACT
207688 CATTCATTCAT-GATTTA
1 CATTCATTCATAGATTTA
*
207705 CATTCATTTATAGATTTA
1 CATTCATTCATAGATTTA
207723 C
1 C
207724 GAGTTCAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (18 bp):
CATTCATTCATAGATTTA
Found at i:208811 original size:22 final size:23
Alignment explanation
Indices: 208786--208844 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
208776 ATCGGAGTAG
*
208786 GGGAGAGGGATGGT-GGGGAAGA
1 GGGAGAGGGATGATGGGGGAAGA
*
208808 GGGAGAGGGATGATGGGGGAAGT
1 GGGAGAGGGATGATGGGGGAAGA
*
208831 GGAGAGAAGGATGA
1 GG-GAGAGGGATGA
208845 AAAATGGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 13 0.41
23 9 0.28
24 10 0.31
ACGTcount: A:0.31, C:0.00, G:0.59, T:0.10
Consensus pattern (23 bp):
GGGAGAGGGATGATGGGGGAAGA
Found at i:218688 original size:6 final size:6
Alignment explanation
Indices: 218677--218702 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
218667 TTATATATAC
218677 TGGCAA TGGCAA TGGCAA TGGCAA TG
1 TGGCAA TGGCAA TGGCAA TGGCAA TG
218703 TTATAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.19
Consensus pattern (6 bp):
TGGCAA
Done.