Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014982.1 Corchorus capsularis cultivar CVL-1 contig15003, 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: 164460
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1575 original size:6 final size:6
Alignment explanation
Indices: 1564--1601 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1554 TATAATCTGC
1564 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1602 GCTTTGCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:8713 original size:6 final size:6
Alignment explanation
Indices: 8702--8733 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
8692 TATAATCTGC
8702 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
8734 GCTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:29139 original size:18 final size:17
Alignment explanation
Indices: 29113--29151 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
29103 AGGGTTCTTT
*
29113 GATTCCCGGAAACTAAAA
1 GATTACCGGAAA-TAAAA
*
29131 GATTACCGGGAATAAAA
1 GATTACCGGAAATAAAA
29148 GATT
1 GATT
29152 CCTACAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (17 bp):
GATTACCGGAAATAAAA
Found at i:31648 original size:2 final size:2
Alignment explanation
Indices: 31641--31673 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31631 CTTTTTCAAG
31641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31674 GATAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37636 original size:16 final size:16
Alignment explanation
Indices: 37615--37646 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37605 TATAATGAAA
37615 TATATTATGAGCGACT
1 TATATTATGAGCGACT
37631 TATATTATGAGCGACT
1 TATATTATGAGCGACT
37647 ATAAGTCGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (16 bp):
TATATTATGAGCGACT
Found at i:50177 original size:125 final size:125
Alignment explanation
Indices: 49955--50205 Score: 493
Period size: 125 Copynumber: 2.0 Consensus size: 125
49945 GAGTATCATC
49955 TATGGTAACCCAGATACAGATATTAGGGGTGGATCCCAGGTTTTTCTTGAGTGGGGGCACATTAT
1 TATGGTAACCCAGATACAGATATTAGGGGTGGATCCCAGGTTTTTCTTGAGTGGGGGCACATTAT
50020 TAAGTATATTTATATATTAGTTTCTTTTTAAAAAAACATTTGAATTTCAACAAAGAAAAG
66 TAAGTATATTTATATATTAGTTTCTTTTTAAAAAAACATTTGAATTTCAACAAAGAAAAG
*
50080 TATGGTAACCCAGATACAGATATTAGGGGTGGATCCCAGGTTTTTCTTGGGTGGGGGCACATTAT
1 TATGGTAACCCAGATACAGATATTAGGGGTGGATCCCAGGTTTTTCTTGAGTGGGGGCACATTAT
50145 TAAGTATATTTATATATTAGTTTCTTTTTAAAAAAACATTTGAATTTCAACAAAGAAAAG
66 TAAGTATATTTATATATTAGTTTCTTTTTAAAAAAACATTTGAATTTCAACAAAGAAAAG
50205 T
1 T
50206 TCTACTGTTA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (125 bp):
TATGGTAACCCAGATACAGATATTAGGGGTGGATCCCAGGTTTTTCTTGAGTGGGGGCACATTAT
TAAGTATATTTATATATTAGTTTCTTTTTAAAAAAACATTTGAATTTCAACAAAGAAAAG
Found at i:50832 original size:30 final size:31
Alignment explanation
Indices: 50782--50841 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 31
50772 TTTACTTATA
50782 CTAAATTTTTATCTTTTTTTCCTTCATAGTG
1 CTAAATTTTTATCTTTTTTTCCTTCATAGTG
50813 CTAAATTTTTATC-TTTTTTCCTTCATAGT
1 CTAAATTTTTATCTTTTTTTCCTTCATAGT
50842 ATAATGGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.20, C:0.17, G:0.05, T:0.58
Consensus pattern (31 bp):
CTAAATTTTTATCTTTTTTTCCTTCATAGTG
Found at i:54755 original size:46 final size:46
Alignment explanation
Indices: 54695--54861 Score: 193
Period size: 46 Copynumber: 3.8 Consensus size: 46
54685 CGATCATATG
54695 TATCAATCACTGAATCAAATGTTCAAACGTGTCATTCGAGATCACA
1 TATCAATCACTGAATCAAATGTTCAAACGTGTCATTCGAGATCACA
* *
54741 TATCAATCACTGAATTAAATGTTTAAACGTGTCATTCGAGAT--CA
1 TATCAATCACTGAATCAAATGTTCAAACGTGTCATTCGAGATCACA
* * ** **
54785 TGT--ATCA--AAATCAAATGTTCAAACGTACCATTCGAGATCATG
1 TATCAATCACTGAATCAAATGTTCAAACGTGTCATTCGAGATCACA
** *
54827 TATCAATCACTGAATCAAATACTCGAACGTGTCAT
1 TATCAATCACTGAATCAAATGTTCAAACGTGTCAT
54862 AATCTAATTT
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
40 26 0.27
42 6 0.06
44 8 0.08
46 58 0.59
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (46 bp):
TATCAATCACTGAATCAAATGTTCAAACGTGTCATTCGAGATCACA
Found at i:54817 original size:40 final size:40
Alignment explanation
Indices: 54707--54832 Score: 144
Period size: 40 Copynumber: 3.0 Consensus size: 40
54697 TCAATCACTG
* *
54707 AATCAAATGTTCAAACGTGTCATTCGAGATCACATATCAATCACTG
1 AATCAAATGTTCAAACGTGTCATTCGAGAT--CATGT--ATCA--A
* *
54753 AATTAAATGTTTAAACGTGTCATTCGAGATCATGTATCAA
1 AATCAAATGTTCAAACGTGTCATTCGAGATCATGTATCAA
**
54793 AATCAAATGTTCAAACGTACCATTCGAGATCATGTATCAA
1 AATCAAATGTTCAAACGTGTCATTCGAGATCATGTATCAA
54833 TCACTGAATC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
40 36 0.50
42 4 0.06
44 4 0.06
46 28 0.39
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (40 bp):
AATCAAATGTTCAAACGTGTCATTCGAGATCATGTATCAA
Found at i:61548 original size:30 final size:29
Alignment explanation
Indices: 61479--61552 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 29
61469 GTAGCGTTTA
61479 GACGTTTTGTCCCCC-GAACTTCAATCTTG
1 GACGTTTTG-CCCCCTGAACTTCAATCTTG
* *
61508 GACATTTTGCCCCCTGAACTTCAATTTTGG
1 GACGTTTTGCCCCCTGAACTTCAATCTT-G
61538 GACGTTTTGCCCCCT
1 GACGTTTTGCCCCCT
61553 CAACCTAACG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.12
29 20 0.50
30 15 0.38
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (29 bp):
GACGTTTTGCCCCCTGAACTTCAATCTTG
Found at i:61741 original size:29 final size:30
Alignment explanation
Indices: 61689--61762 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
61679 CGTTAGGTTG
*
61689 AGGGGGCAAAACGTCCCAAAATTGAAATTT
1 AGGGGGCAAAACGTCCCAAAATTGAAATTC
* * *
61719 AGGGGGCAAAATGT-CCAAGATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAATTC
*
61748 GGGGGGCAAAACGTC
1 AGGGGGCAAAACGTC
61763 TAAACGCTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTGAAATTC
Found at i:62473 original size:79 final size:79
Alignment explanation
Indices: 62342--62496 Score: 310
Period size: 79 Copynumber: 2.0 Consensus size: 79
62332 TTAATGTTAA
62342 TCTTGTGATATGTAGGGAACTTCCTCTATATTTGTAACCATGATATTTAATATAGAGAGATTAAA
1 TCTTGTGATATGTAGGGAACTTCCTCTATATTTGTAACCATGATATTTAATATAGAGAGATTAAA
62407 TTTGTTTAAACAAG
66 TTTGTTTAAACAAG
62421 TCTTGTGATATGTAGGGAACTTCCTCTATATTTGTAACCATGATATTTAATATAGAGAGATTAAA
1 TCTTGTGATATGTAGGGAACTTCCTCTATATTTGTAACCATGATATTTAATATAGAGAGATTAAA
62486 TTTGTTTAAAC
66 TTTGTTTAAAC
62497 TAAAGTAAAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (79 bp):
TCTTGTGATATGTAGGGAACTTCCTCTATATTTGTAACCATGATATTTAATATAGAGAGATTAAA
TTTGTTTAAACAAG
Found at i:62991 original size:37 final size:37
Alignment explanation
Indices: 62941--63011 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
62931 AGGAAAATGA
*
62941 GAACTAACTTGAAATATATTCCTATTGTTTCTGACTT
1 GAACTAACTTGAAATATATTCCTATTATTTCTGACTT
*
62978 GAACTAATTTGAAATATATTCCTATTATTTCTGA
1 GAACTAACTTGAAATATATTCCTATTATTTCTGA
63012 ATGCAGGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (37 bp):
GAACTAACTTGAAATATATTCCTATTATTTCTGACTT
Found at i:65747 original size:15 final size:16
Alignment explanation
Indices: 65727--65756 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
65717 ATGTTTGGGA
65727 ATTTTAAT-TCATATT
1 ATTTTAATGTCATATT
65742 ATTTTAATGTCATAT
1 ATTTTAATGTCATAT
65757 CAAATTTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTTAATGTCATATT
Found at i:75007 original size:13 final size:13
Alignment explanation
Indices: 74989--75017 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
74979 AAGAAAAATA
74989 TATGGAATAAGTG
1 TATGGAATAAGTG
75002 TATGGAATAAGTG
1 TATGGAATAAGTG
75015 TAT
1 TAT
75018 ATTTCTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (13 bp):
TATGGAATAAGTG
Found at i:77497 original size:30 final size:30
Alignment explanation
Indices: 77463--77521 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
77453 GCATCTTTTG
77463 AGTCCCATAAGCCTTACAGTATCTTCACCC
1 AGTCCCATAAGCCTTACAGTATCTTCACCC
* *
77493 AGTCCGATAAGCCTTACATTATCTTCACC
1 AGTCCCATAAGCCTTACAGTATCTTCACC
77522 TGAAGCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.34, G:0.10, T:0.29
Consensus pattern (30 bp):
AGTCCCATAAGCCTTACAGTATCTTCACCC
Found at i:89603 original size:21 final size:21
Alignment explanation
Indices: 89546--89591 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
89536 GAGGATGGCA
* *
89546 ATGAGCTTGAAATGGAAGGAG
1 ATGACCTTGAAATTGAAGGAG
89567 ATGACCTTGAAATTGAAGGAG
1 ATGACCTTGAAATTGAAGGAG
89588 ATGA
1 ATGA
89592 TGTTGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (21 bp):
ATGACCTTGAAATTGAAGGAG
Found at i:105369 original size:24 final size:24
Alignment explanation
Indices: 105342--105459 Score: 166
Period size: 24 Copynumber: 4.9 Consensus size: 24
105332 CAGTTTTAGG
*
105342 GATAATGCCCCCATTCCCTTTAGA
1 GATAATGCCCCCATTCCCTTCAGA
105366 GATAATGCCCCCATTCCCTTCAGA
1 GATAATGCCCCCATTCCCTTCAGA
*
105390 GATAATGCCCCCATTTCCTTCAGCA
1 GATAATGCCCCCATTCCCTTCAG-A
* * *
105415 -ATAATGCCTCCATTCTCTTCAGG
1 GATAATGCCCCCATTCCCTTCAGA
*
105438 GATAATGCCACCATTCCCTTCA
1 GATAATGCCCCCATTCCCTTCA
105460 TGGCTGATGG
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
24 83 0.99
25 1 0.01
ACGTcount: A:0.25, C:0.35, G:0.12, T:0.29
Consensus pattern (24 bp):
GATAATGCCCCCATTCCCTTCAGA
Found at i:105476 original size:48 final size:48
Alignment explanation
Indices: 105339--105586 Score: 229
Period size: 48 Copynumber: 5.2 Consensus size: 48
105329 GTTCAGTTTT
* * * * * *
105339 AGGGATAATGCCCCCATTCCCTTTA-GAGATAATGCCCCCATTCCCTTC
1 AGGGATAATGCCACCATTCCCTTCATG-GCTGATGCCACCATTCTCTTC
* * * * *
105387 AGAGATAATGCCCCCATTTCCTTCA--GCAATAATGCCTCCATTCTCTTC
1 AGGGATAATGCCACCATTCCCTTCATGGC--TGATGCCACCATTCTCTTC
*
105435 AGGGATAATGCCACCATTCCCTTCATGGCTGATGGCACCATTCTCTTC
1 AGGGATAATGCCACCATTCCCTTCATGGCTGATGCCACCATTCTCTTC
* * * * *
105483 ATGGCTGATGCCACCATTCTCTTCATGGTTGATGCCACCATTCTCTTC
1 AGGGATAATGCCACCATTCCCTTCATGGCTGATGCCACCATTCTCTTC
* * *
105531 ATGGCTAATGCCACC---CCCTTCATGGCTGATGCCACCATTCCCTTC
1 AGGGATAATGCCACCATTCCCTTCATGGCTGATGCCACCATTCTCTTC
* *
105576 ATGGCTAATGC
1 AGGGATAATGC
105587 TCGCATTACC
Statistics
Matches: 174, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
45 38 0.22
46 1 0.01
48 133 0.76
50 2 0.01
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (48 bp):
AGGGATAATGCCACCATTCCCTTCATGGCTGATGCCACCATTCTCTTC
Found at i:105476 original size:72 final size:72
Alignment explanation
Indices: 105343--105586 Score: 207
Period size: 72 Copynumber: 3.4 Consensus size: 72
105333 AGTTTTAGGG
* * * * * * *
105343 ATAATGCCCCCATTCCCTTTAGAGATAATGCCCCCATTCCCTTCA-GAGATAATGCCCCCATT-T
1 ATAATGCCACCATTCTCTTCAGGGATAATGCCACCATTCCCTTCATG-GCTAATGCCACCATTCT
105406 CCTTCA-GC
65 -CTTCAGGC
* * *
105414 AATAATGCCTCCATTCTCTTCAGGGATAATGCCACCATTCCCTTCATGGCTGATGGCACCATTCT
1 -ATAATGCCACCATTCTCTTCAGGGATAATGCCACCATTCCCTTCATGGCTAATGCCACCATTCT
105479 CTTCATGGC
65 CTTCA-GGC
* * * * * *
105488 -TGATGCCACCATTCTCTTCATGGTTGATGCCACCATTCTCTTCATGGCTAATGCCACC---CCC
1 ATAATGCCACCATTCTCTTCAGGGATAATGCCACCATTCCCTTCATGGCTAATGCCACCATTCTC
105549 TTCATGGC
66 TTCA-GGC
* * * *
105557 -TGATGCCACCATTCCCTTCATGGCTAATGC
1 ATAATGCCACCATTCTCTTCAGGGATAATGC
105587 TCGCATTACC
Statistics
Matches: 147, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
69 37 0.25
72 106 0.72
73 2 0.01
74 2 0.01
ACGTcount: A:0.21, C:0.34, G:0.15, T:0.30
Consensus pattern (72 bp):
ATAATGCCACCATTCTCTTCAGGGATAATGCCACCATTCCCTTCATGGCTAATGCCACCATTCTC
TTCAGGC
Found at i:105593 original size:24 final size:24
Alignment explanation
Indices: 105418--105586 Score: 209
Period size: 24 Copynumber: 7.2 Consensus size: 24
105408 TTCAGCAATA
* * * * *
105418 ATGCCTCCATTCTCTTCAGGGATA
1 ATGCCACCATTCCCTTCATGGCTG
105442 ATGCCACCATTCCCTTCATGGCTG
1 ATGCCACCATTCCCTTCATGGCTG
* *
105466 ATGGCACCATTCTCTTCATGGCTG
1 ATGCCACCATTCCCTTCATGGCTG
* *
105490 ATGCCACCATTCTCTTCATGGTTG
1 ATGCCACCATTCCCTTCATGGCTG
* *
105514 ATGCCACCATTCTCTTCATGGCTA
1 ATGCCACCATTCCCTTCATGGCTG
105538 ATGCCACC---CCCTTCATGGCTG
1 ATGCCACCATTCCCTTCATGGCTG
*
105559 ATGCCACCATTCCCTTCATGGCTA
1 ATGCCACCATTCCCTTCATGGCTG
105583 ATGC
1 ATGC
105587 TCGCATTACC
Statistics
Matches: 128, Mismatches: 14, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
21 19 0.15
24 109 0.85
ACGTcount: A:0.18, C:0.34, G:0.17, T:0.31
Consensus pattern (24 bp):
ATGCCACCATTCCCTTCATGGCTG
Found at i:114471 original size:29 final size:28
Alignment explanation
Indices: 114414--114469 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
114404 TTAGATTTTT
* *
114414 TTTTTCTTTTAGGTATATAGTAGTCATA
1 TTTTTCTTTGAGGTATATAGTAATCATA
114442 TTTTT-TTTGAGGTATATAGTAATCATA
1 TTTTTCTTTGAGGTATATAGTAATCATA
114469 T
1 T
114470 ATATATGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (28 bp):
TTTTTCTTTGAGGTATATAGTAATCATA
Found at i:120330 original size:30 final size:30
Alignment explanation
Indices: 120274--120342 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
120264 CTAATTTTAT
*
120274 CCTGAATTGACACAAATCGATAACGTTTGAA
1 CCTGAATTGACACAAA-CGATAACGTTAGAA
*
120305 CCTGAATTGACACAAGA-GCTAACGTTAGAA
1 CCTGAATTGACACAA-ACGATAACGTTAGAA
*
120335 TCTGAATT
1 CCTGAATT
120343 ATAATTTGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 18 0.53
31 15 0.44
32 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (30 bp):
CCTGAATTGACACAAACGATAACGTTAGAA
Found at i:120419 original size:19 final size:19
Alignment explanation
Indices: 120395--120431 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
120385 CAATTATTTT
*
120395 GGCATATTCATCTCTAACC
1 GGCATATTAATCTCTAACC
120414 GGCATATTAATCTCTAAC
1 GGCATATTAATCTCTAAC
120432 ACATCGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (19 bp):
GGCATATTAATCTCTAACC
Found at i:122848 original size:22 final size:22
Alignment explanation
Indices: 122807--122848 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
122797 GACAAACCCG
**
122807 TAACCCGAATAATCTGAGAAGC
1 TAACCCGAATAATCCAAGAAGC
*
122829 TAACCCGAATTATCCAAGAA
1 TAACCCGAATAATCCAAGAA
122849 TATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (22 bp):
TAACCCGAATAATCCAAGAAGC
Found at i:123383 original size:31 final size:31
Alignment explanation
Indices: 123338--123396 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
123328 TATGTTAGAC
*
123338 AAATAAGGATATAAT-TGGCGTTTCAAAAATT
1 AAATAAGGACATAATAT-GCGTTTCAAAAATT
* *
123369 AAATAAGGGCATAATATGTGTTTCAAAA
1 AAATAAGGACATAATATGCGTTTCAAAA
123397 GTTTTACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.31
Consensus pattern (31 bp):
AAATAAGGACATAATATGCGTTTCAAAAATT
Found at i:124750 original size:7 final size:7
Alignment explanation
Indices: 124738--124762 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
124728 TCAATGGTTC
124738 GAGAGTG
1 GAGAGTG
124745 GAGAGTG
1 GAGAGTG
124752 GAGAGTG
1 GAGAGTG
124759 GAGA
1 GAGA
124763 CAGCCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.56, T:0.12
Consensus pattern (7 bp):
GAGAGTG
Found at i:125697 original size:22 final size:22
Alignment explanation
Indices: 125672--125725 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
125662 ATGACCTCCT
*
125672 TATGAAATTTTGATAATC-A-AC
1 TATGAAATTTTAATAA-CGATAC
125693 GTATGAAATTTTAATAACGATAC
1 -TATGAAATTTTAATAACGATAC
125716 TATGAAATTT
1 TATGAAATTT
125726 CGAGAATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 1 0.03
22 26 0.90
23 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTAATAACGATAC
Found at i:125830 original size:23 final size:22
Alignment explanation
Indices: 125801--126209 Score: 161
Period size: 22 Copynumber: 18.8 Consensus size: 22
125791 TGAAGACCTT
125801 ACTATGAAATTTTGATAACCAAC
1 ACTATGAAATTTTGATAACC-AC
* * *
125824 ACTATGAGATATTGAT-ACCTC
1 ACTATGAAATTTTGATAACCAC
* *
125845 -CATATGATATATTGATAACCAC
1 AC-TATGAAATTTTGATAACCAC
* * * *
125867 ATTATGAAAATTTAAAAAGCTC-C
1 ACTATGAAATTTTGATAA-C-CAC
*
125890 A-TATG-AATTGTT-AGTAATCAC
1 ACTATGAAATT-TTGA-TAACCAC
* * *
125911 ACTCTGAAATTGTGATAATCAC
1 ACTATGAAATTTTGATAACCAC
*
125933 ACTATGAAATTGTGATAACCTA-
1 ACTATGAAATTTTGATAACC-AC
* *
125955 GCTATGGAATTTTGATAAACCATC
1 ACTATGAAATTTTGAT-AACCA-C
* **
125979 -CTATAAAATTTTGATAAACGTC
1 ACTATGAAATTTTGAT-AACCAC
* * **
126001 CCTATAAAATTTTGATAACTTC
1 ACTATGAAATTTTGATAACCAC
* *
126023 -CTTATGCAATCTTG--AA--A-
1 AC-TATGAAATTTTGATAACCAC
* *
126040 ACTA-CAAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCAC
* ** *
126061 CCTATGATTTTTTGATAACCTC
1 ACTATGAAATTTTGATAACCAC
* * * *
126083 ATTATGAAATTTTGTTAATCTC
1 ACTATGAAATTTTGATAACCAC
* * *
126105 CCTATGAAATTTTGATTTA-CAT
1 ACTATGAAATTTTGA-TAACCAC
126127 ACTATGAAATTTTGATAACC-C
1 ACTATGAAATTTTGATAACCAC
* * * *
126148 TCTTATGAAATTTTGAAAACTAA
1 AC-TATGAAATTTTGATAACCAC
* *
126171 ACTATGAAAATTTGATAACCTTC
1 ACTATGAAATTTTGATAACC-AC
*
126194 A-TATAAAATTTTGATA
1 ACTATGAAATTTTGATA
126210 TCCTCCCTAA
Statistics
Matches: 292, Mismatches: 65, Indels: 59
0.70 0.16 0.14
Matches are distributed among these distances:
16 6 0.02
17 2 0.01
18 3 0.01
20 4 0.01
21 27 0.09
22 186 0.64
23 63 0.22
24 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCAC
Found at i:126074 original size:22 final size:22
Alignment explanation
Indices: 126045--126228 Score: 144
Period size: 22 Copynumber: 8.5 Consensus size: 22
126035 TGAAAACTAC
126045 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
126067 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
* *
126089 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
* * *
126111 AAATTTTGATTTACAT-ACTATG
1 AAATTTTGA-TAACCTCCCTATG
*
126133 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CCTATG
* **
126155 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CCCTATG
* * * *
126177 AAAATTTGATAACCTTCATATA
1 AAATTTTGATAACCTCCCTATG
*
126199 AAATTTTGATATCCTCCCTA--
1 AAATTTTGATAACCTCCCTATG
126219 AAATTTTGAT
1 AAATTTTGAT
126229 TATTCCATAA
Statistics
Matches: 123, Mismatches: 33, Indels: 14
0.72 0.19 0.08
Matches are distributed among these distances:
20 10 0.08
21 6 0.05
22 100 0.81
23 7 0.06
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:126133 original size:44 final size:43
Alignment explanation
Indices: 125802--126209 Score: 182
Period size: 44 Copynumber: 9.4 Consensus size: 43
125792 GAAGACCTTA
* * * *
125802 CTATGAAATTTTGATAACCAACACTATGAGATATTGATACCTCC
1 CTATGAAATTTTGATAA-CATCACTATGAAATTTTGATAACTCC
* * * * * * *
125846 ATATGATATATTGATAACCA-CATTATGAAAATTTAAAAAGCTCC
1 CTATGAAATTTTGATAA-CATCACTATGAAATTTTGATAA-CTCC
* * *
125890 ATATG-AATTGTT-AGTAATCA-CACTCTGAAATTGTGATAA-TCAC
1 CTATGAAATT-TTGA-TAA-CATCACTATGAAATTTTGATAACTC-C
* * *
125933 ACTATGAAATTGTGATAACCT-AGCTATGGAATTTTGATAAAC-CATC
1 -CTATGAAATTTTGATAACATCA-CTATGAAATTTTGAT-AACTC--C
* * * *
125979 CTATAAAATTTTGATAAACGTCCCTATAAAATTTTGATAACTTCC
1 CTATGAAATTTTGAT-AACATCACTATGAAATTTTGATAAC-TCC
* * * *
126024 TTATGCAATCTTG--AA-A--ACTA-CAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACATCACTATGAAATTTTGATAA-CTCC
** * * *
126062 CTATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCC
1 CTATGAAATTTTGATAACATCACTATGAAATTTTGATAA-CTCC
*
126106 CTATGAAATTTTGATTTACAT-ACTATGAAATTTTGATAAC-CC
1 CTATGAAATTTTGA-TAACATCACTATGAAATTTTGATAACTCC
* * * *
126148 TCTTATGAAATTTTGAAAAC-TAAACTATGAAAATTTGATAACCTTC
1 -C-TATGAAATTTTGATAACAT-CACTATGAAATTTTGATAA-CTCC
* *
126194 ATATAAAATTTTGATA
1 CTATGAAATTTTGATA
126210 TCCTCCCTAA
Statistics
Matches: 272, Mismatches: 62, Indels: 60
0.69 0.16 0.15
Matches are distributed among these distances:
38 23 0.08
39 4 0.01
40 2 0.01
42 7 0.03
43 25 0.09
44 152 0.56
45 39 0.14
46 19 0.07
47 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (43 bp):
CTATGAAATTTTGATAACATCACTATGAAATTTTGATAACTCC
Found at i:126645 original size:22 final size:22
Alignment explanation
Indices: 126360--126715 Score: 125
Period size: 22 Copynumber: 16.0 Consensus size: 22
126350 TCTTTATGAA
* *
126360 ATAACCTCTCTATAAAATTTTG
1 ATAACCTCCCTATGAAATTTTG
* *
126382 TTGACC-CCTCTATGAAATTTTG
1 ATAACCTCC-CTATGAAATTTTG
* ** *
126404 ATAATCAT-ATTATGTAATTTTG
1 ATAA-CCTCCCTATGAAATTTTG
** *
126426 ATAACCTCGTTTTGAAATTTTG
1 ATAACCTCCCTATGAAATTTTG
** * *
126448 ATAACAACACTATAAAATTTTG
1 ATAACCTCCCTATGAAATTTTG
* *
126470 ATAATCTTCCTAT-AAATTTTG
1 ATAACCTCCCTATGAAATTTTG
** **
126491 ATAATCCGATCATTATGAAATTTCA
1 ATAA-CC--TCCCTATGAAATTTTG
* * * *
126516 ATAATCACTCTATGAGA-TTTG
1 ATAACCTCCCTATGAAATTTTG
* *
126537 ATAACCT-TCTATCAAATTTTG
1 ATAACCTCCCTATGAAATTTTG
* * *
126558 GT-A-CTCCTTATGAAATTGAAACTTTT
1 ATAACCTCCCTATGAAA-T-----TTTG
* * *
126584 ATAATCTTCATATGAAATTTTG
1 ATAACCTCCCTATGAAATTTTG
* * *
126606 ATAACCACACTATTAAATTTTG
1 ATAACCTCCCTATGAAATTTTG
* *
126628 ATAACCTCCCCATGAAATATT-
1 ATAACCTCCCTATGAAATTTTG
*
126649 AGTAACCTCCTTATGAAATTTTG
1 A-TAACCTCCCTATGAAATTTTG
* * ** *
126672 TTAACCACATTATGAAATTTTT
1 ATAACCTCCCTATGAAATTTTG
* * *
126694 ATAACATCGCTATGACATTTTG
1 ATAACCTCCCTATGAAATTTTG
126716 GTAATCTCTT
Statistics
Matches: 238, Mismatches: 76, Indels: 40
0.67 0.21 0.11
Matches are distributed among these distances:
19 2 0.01
20 14 0.06
21 29 0.12
22 161 0.68
23 1 0.00
24 5 0.02
25 10 0.04
26 4 0.02
27 2 0.01
28 10 0.04
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
ATAACCTCCCTATGAAATTTTG
Found at i:126911 original size:22 final size:22
Alignment explanation
Indices: 126727--126912 Score: 128
Period size: 22 Copynumber: 8.4 Consensus size: 22
126717 TAATCTCTTC
* * * *
126727 GATAACCTTTCTATAAAATTGT
1 GATAACCATCCTATGAAATTTT
* *
126749 GATAGCCA-CACTATGAAATTTC
1 GATAACCATC-CTATGAAATTTT
* * *
126771 AATAACCTTCCTAAGAAATTTT
1 GATAACCATCCTATGAAATTTT
* *
126793 TATAACCTGATCCTCTGAAATTTT
1 GATAACC--ATCCTATGAAATTTT
*
126817 GATAA-CTTCCATATGAAATTTT
1 GATAACCATCC-TATGAAATTTT
* * *
126839 GGTGACCA-CACTATGGAATTTT
1 GATAACCATC-CTATGAAATTTT
*
126861 GATAACC-TCCTCATGAAATTAT
1 GATAACCATCCT-ATGAAATTTT
* *
126883 AATAACCATCTTATGAAATTTT
1 GATAACCATCCTATGAAATTTT
126905 GATAACCA
1 GATAACCA
126913 CATAAAGACA
Statistics
Matches: 124, Mismatches: 30, Indels: 20
0.71 0.17 0.11
Matches are distributed among these distances:
21 5 0.04
22 96 0.77
23 7 0.06
24 16 0.13
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
GATAACCATCCTATGAAATTTT
Found at i:129899 original size:231 final size:228
Alignment explanation
Indices: 129496--130076 Score: 923
Period size: 231 Copynumber: 2.5 Consensus size: 228
129486 TTAAAAACGT
* * * * *
129496 ATGAATGATTGAAGAAATCAAATGGTTGGTAAAAAGTTTAAAACTGACTGTTGAGAGCCATTCCT
1 ATGAATGATTGAAGAAATGAAATGCTTGGAAAAAAGTTAAAAACTGACTGTTGAGAGACATTCCT
* * * *
129561 AAGTTAAAAAGCTGTCATCCTATATCCTTACATGAATGTTACTTAAATCTCCCATTAACTTGTTC
66 AAGTTAAAAAGCTGCCATCCTATATCCTTACATAAATGGTACTTAAATCTCCCATTAACGTGTTC
129626 CTTTTAATTGTTAAAAAACATTCTTTTGTTACAGTTTTCTTTCGTTTTTCATTAAAGGGTAATTA
131 CTTTTAATTGTTAAAAAACATTCTTTTGTTACAGTTTTCTTTCGTTTTTCATTAAAGGGT-A--A
129691 TAAAGGAGTTTTAATTCAGAATGATGAGGCAAAAAA
193 TAAAGGAGTTTTAATTCAGAATGATGAGGCAAAAAA
129727 ATGAATGATTGAAGAAATGAAATGCTTGGAAAAAAGTTAAAAACTGACTGTTGAGAGACATTCCT
1 ATGAATGATTGAAGAAATGAAATGCTTGGAAAAAAGTTAAAAACTGACTGTTGAGAGACATTCCT
* *
129792 AAGTTAAAAAGCTGCCATCCTATATCTTTACATAAATGGTACTTAAATCTCCTATTAACGTGTTC
66 AAGTTAAAAAGCTGCCATCCTATATCCTTACATAAATGGTACTTAAATCTCCCATTAACGTGTTC
* * *
129857 CTTTTAATTGTTAAAGAACGTTGTTTTGTTACAGTTTTCTTTCGTTTTTCATTAAAGGGTAATAA
131 CTTTTAATTGTTAAAAAACATTCTTTTGTTACAGTTTTCTTTCGTTTTTCATTAAAGGGTAATAA
*
129922 AGGAGTTTTAATTCAGAATGATGAGGCCAAAAA
196 AGGAGTTTTAATTCAGAATGATGAGGCAAAAAA
* ** * *
129955 ATGAATGATTGAAGAATTGGCATGCTTGGAAAAATGTTAAAAACTGAGTGTTGAGAGACATTCCT
1 ATGAATGATTGAAGAAATGAAATGCTTGGAAAAAAGTTAAAAACTGACTGTTGAGAGACATTCCT
* *
130020 AAGTTAAAAAGCTGCC--CTTATATCCTTACATAAATGGTACATAAATCTCCCATTAAC
66 AAGTTAAAAAGCTGCCATCCTATATCCTTACATAAATGGTACTTAAATCTCCCATTAAC
130077 TTCTTCCATT
Statistics
Matches: 326, Mismatches: 24, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
226 37 0.11
228 112 0.34
230 1 0.00
231 176 0.54
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (228 bp):
ATGAATGATTGAAGAAATGAAATGCTTGGAAAAAAGTTAAAAACTGACTGTTGAGAGACATTCCT
AAGTTAAAAAGCTGCCATCCTATATCCTTACATAAATGGTACTTAAATCTCCCATTAACGTGTTC
CTTTTAATTGTTAAAAAACATTCTTTTGTTACAGTTTTCTTTCGTTTTTCATTAAAGGGTAATAA
AGGAGTTTTAATTCAGAATGATGAGGCAAAAAA
Found at i:130132 original size:28 final size:28
Alignment explanation
Indices: 130100--130156 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
130090 TGATTTCTAT
130100 TAAAGTCATTATTATAAATTTATAACGG
1 TAAAGTCATTATTATAAATTTATAACGG
130128 TAAAGTCATTATTATAAATTTATAACGG
1 TAAAGTCATTATTATAAATTTATAACGG
130156 T
1 T
130157 TAATTCTTTT
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:0.07, G:0.11, T:0.40
Consensus pattern (28 bp):
TAAAGTCATTATTATAAATTTATAACGG
Found at i:130855 original size:24 final size:24
Alignment explanation
Indices: 130827--130874 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
130817 TCAGAACTTT
*
130827 TATATCAGAA-ATTGATGAGAAAAA
1 TATATCAGAAGA-TCATGAGAAAAA
130851 TATATCAGAAGATCATGAGAAAAA
1 TATATCAGAAGATCATGAGAAAAA
130875 AGAAAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (24 bp):
TATATCAGAAGATCATGAGAAAAA
Found at i:131486 original size:35 final size:34
Alignment explanation
Indices: 131447--131517 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 34
131437 AACCAAAGAT
131447 TCTACAAAACAAAT-AAATATGCAATTTCAGAATTA
1 TCTACAAAACAAATCAAA-ATGCAA-TTCAGAATTA
*
131482 TCTACAAAACAAATCAAAATGCAATTCTGAATTA
1 TCTACAAAACAAATCAAAATGCAATTCAGAATTA
131516 TC
1 TC
131518 ATATGAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 11 0.32
35 20 0.59
36 3 0.09
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (34 bp):
TCTACAAAACAAATCAAAATGCAATTCAGAATTA
Found at i:133226 original size:32 final size:33
Alignment explanation
Indices: 133190--133265 Score: 84
Period size: 35 Copynumber: 2.3 Consensus size: 33
133180 CAAAAAAAAT
*
133190 ATAATTTAA-TTGAATAA-TTATATTTATTATAC
1 ATAATTTAAGTTGAATAACTTATATTTATGAT-C
*
133222 ATAATAATAAAGTTGAATAACTTATATTTATGATC
1 ATAAT--TTAAGTTGAATAACTTATATTTATGATC
*
133257 TTAATTTAA
1 ATAATTTAA
133266 ACTTGTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
32 5 0.14
33 3 0.08
34 3 0.08
35 13 0.36
36 12 0.33
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (33 bp):
ATAATTTAAGTTGAATAACTTATATTTATGATC
Found at i:133513 original size:31 final size:29
Alignment explanation
Indices: 133478--133536 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
133468 GCTAATTACT
*
133478 TTTTAAAAATACAATATATGTTTTATTTTTC
1 TTTTAAAAATA-AATAT-TATTTTATTTTTC
*
133509 TTTTAAAAATAATTATTATTTTATTTTT
1 TTTTAAAAATAAATATTATTTTATTTTT
133537 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 11 0.42
30 4 0.15
31 11 0.42
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTAAAAATAAATATTATTTTATTTTTC
Found at i:134678 original size:4 final size:4
Alignment explanation
Indices: 134669--134700 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
134659 CACCACTTGT
134669 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
134701 CTTACTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:140313 original size:2 final size:2
Alignment explanation
Indices: 140306--140330 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
140296 TATTTGGCCT
140306 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
140331 TCTTTTGTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:141967 original size:2 final size:2
Alignment explanation
Indices: 141960--141996 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
141950 ATGTACCTCA
141960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
141997 GAGTTATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:148389 original size:15 final size:15
Alignment explanation
Indices: 148355--148399 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
148345 TTTAATTGAT
*
148355 TAAATAATTA-AAAA
1 TAAAAAATTACAAAA
148369 TAAAAAAATTACAAAA
1 T-AAAAAATTACAAAA
148385 TAAAAAATTACAAAA
1 TAAAAAATTACAAAA
148400 GGGACCTACC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 1 0.04
15 22 0.79
16 5 0.18
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAAAAATTACAAAA
Found at i:150240 original size:15 final size:15
Alignment explanation
Indices: 150220--150281 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 15
150210 CTGTCATTGA
150220 AGAAAATGCAGGCCC
1 AGAAAATGCAGGCCC
*
150235 AGAAAATGCAGTCCC
1 AGAAAATGCAGGCCC
*
150250 AAAAAATGCAGGCCC
1 AGAAAATGCAGGCCC
* *
150265 AGAAAATCCACGCCC
1 AGAAAATGCAGGCCC
150280 AG
1 AG
150282 TAAGGAGGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.42, C:0.29, G:0.21, T:0.08
Consensus pattern (15 bp):
AGAAAATGCAGGCCC
Found at i:152872 original size:24 final size:24
Alignment explanation
Indices: 152845--152891 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
152835 CAGCATTTCT
*
152845 TTTGCTAAATTGTGTAGTTATGGA
1 TTTGCTAAATTGTGCAGTTATGGA
152869 TTTGCTAAATTGTGCAGTTATGG
1 TTTGCTAAATTGTGCAGTTATGG
152892 GGTTAAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (24 bp):
TTTGCTAAATTGTGCAGTTATGGA
Found at i:153399 original size:29 final size:30
Alignment explanation
Indices: 153349--153421 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
153339 ATCACTTTAG
***
153349 ATAGTAGAGGGACCATTTTGCAGAA-AAAA
1 ATAGTAGAGGGACCAAAATGCAGAATAAAA
** *
153378 ATAGTAGAGGGACCAAAATGCAGAATTCAT
1 ATAGTAGAGGGACCAAAATGCAGAATAAAA
153408 ATAGTAGAGGGACC
1 ATAGTAGAGGGACC
153422 TCCCTTGTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.19
Consensus pattern (30 bp):
ATAGTAGAGGGACCAAAATGCAGAATAAAA
Found at i:156085 original size:22 final size:23
Alignment explanation
Indices: 156060--156103 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
156050 CGGCCAAAAA
* *
156060 TATAATGAAAAAATAA-AATAAT
1 TATAACGAAAAAAAAAGAATAAT
156082 TATAACGAAAAAAAAAGAATAA
1 TATAACGAAAAAAAAAGAATAA
156104 AAAAGAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (23 bp):
TATAACGAAAAAAAAAGAATAAT
Found at i:157838 original size:2 final size:2
Alignment explanation
Indices: 157826--157856 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
157816 CCTATTATGG
157826 AT AT A- 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
157857 CTTTTGCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:159861 original size:27 final size:27
Alignment explanation
Indices: 159831--159985 Score: 143
Period size: 27 Copynumber: 5.5 Consensus size: 27
159821 CAGAATATCC
159831 ATGATGATGATGATCATAGCTCCGGA-A
1 ATGATGATGATGATCATAGCTCC-GACA
* *
159858 ATGATGATGATCATGGCCATAGCTCCAATC-
1 ATGATGATGATGAT---CATAGCTCCGA-CA
* * * *
159888 ATCATGATGATGATTATAGCTCCTACC
1 ATGATGATGATGATCATAGCTCCGACA
*
159915 ATGATGATGATGATCATAGCTCTGACCA
1 ATGATGATGATGATCATAGCTCCGA-CA
* *
159943 TGATGATGATGATGGTCATAGCTCCGACC
1 --ATGATGATGATGATCATAGCTCCGACA
159972 ATGATGATGATGAT
1 ATGATGATGATGAT
159986 GATGATGATA
Statistics
Matches: 104, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
26 1 0.01
27 56 0.54
28 1 0.01
29 2 0.02
30 44 0.42
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (27 bp):
ATGATGATGATGATCATAGCTCCGACA
Found at i:159867 original size:30 final size:29
Alignment explanation
Indices: 159831--160015 Score: 144
Period size: 30 Copynumber: 6.3 Consensus size: 29
159821 CAGAATATCC
159831 ATGATGATGATGATCATAGCTCCGGAAATG
1 ATGATGATGATGATCATAGCTCC-GAAATG
* ** *
159861 ATGATGATCATGGCCATAGCTCC--AATC
1 ATGATGATGATGATCATAGCTCCGAAATG
* * * **
159888 ATCATGATGATGATTATAGCTCC--TACC
1 ATGATGATGATGATCATAGCTCCGAAATG
* *
159915 ATGATGATGATGATCATAGCTCTGACCATG
1 ATGATGATGATGATCATAGCTCCGA-AATG
*
159945 ATGATGATGATGGTCATAGCTCCGACCATGATG
1 ATGATGATGATGATCATAGCTCCGA--A--ATG
* * *
159978 ATGATGATGATGATGATAGCTCTGACTATG
1 ATGATGATGATGATCATAGCTCCGA-AATG
160008 ATGATGAT
1 ATGATGAT
160016 CATAGCTCTG
Statistics
Matches: 125, Mismatches: 24, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
27 43 0.34
30 55 0.44
31 1 0.01
32 1 0.01
33 25 0.20
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (29 bp):
ATGATGATGATGATCATAGCTCCGAAATG
Found at i:159983 original size:57 final size:57
Alignment explanation
Indices: 159830--159986 Score: 178
Period size: 57 Copynumber: 2.7 Consensus size: 57
159820 TCAGAATATC
* * *
159830 CATGATGATGATGATCATAGCTCCGGA-AATGATGATGATCATGGCCATAGCTCCAATCAT
1 CATGATGATGATG-TCATAGCTCC-GACCATGATGATGATGAT-G-CATAGCTCCAACCAT
* **
159890 CATGATGATGAT-T-ATAGCTCCTACCATGATGATGATGAT-CATAGCTCTGACCAT
1 CATGATGATGATGTCATAGCTCCGACCATGATGATGATGATGCATAGCTCCAACCAT
*
159944 GATGATGATGATGGTCATAGCTCCGACCATGATGATGATGATG
1 CATGATGATGAT-GTCATAGCTCCGACCATGATGATGATGATG
159987 ATGATGATAG
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
54 23 0.27
56 2 0.02
57 46 0.55
58 1 0.01
60 12 0.14
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (57 bp):
CATGATGATGATGTCATAGCTCCGACCATGATGATGATGATGCATAGCTCCAACCAT
Found at i:160008 original size:27 final size:27
Alignment explanation
Indices: 159829--160031 Score: 137
Period size: 27 Copynumber: 7.2 Consensus size: 27
159819 ATCAGAATAT
* *
159829 CCATGATGATGATGATCATAGCTCCGGA
1 CCATGATGATGATGATGATAGCT-CTGA
* * **
159857 -AATGATGATGATCATGGCCATAGCTCCAA
1 CCATGATGATGATGAT-G--ATAGCTCTGA
* * *
159886 TCATCATGATGATGATTATAGCTCCT-A
1 CCATGATGATGATGATGATAGCT-CTGA
*
159913 CCATGATGATGATGATCATAGCTCTGA
1 CCATGATGATGATGATGATAGCTCTGA
*
159940 CCATGATGATGATGATGGTCATAGCTCCGA
1 CCATGATGATGATGAT-G--ATAGCTCTGA
159970 CCATGATGATGATGATGATGATGATAGCTCTGA
1 CC------ATGATGATGATGATGATAGCTCTGA
*
160003 -C-T-ATGATGATGATCATAGCTCTGA
1 CCATGATGATGATGATGATAGCTCTGA
160027 CCATG
1 CCATG
160032 GTGTGTATGG
Statistics
Matches: 140, Mismatches: 17, Indels: 37
0.72 0.09 0.19
Matches are distributed among these distances:
24 21 0.15
25 2 0.01
26 3 0.02
27 57 0.41
28 1 0.01
29 2 0.01
30 29 0.21
32 1 0.01
33 9 0.06
35 1 0.01
36 14 0.10
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (27 bp):
CCATGATGATGATGATGATAGCTCTGA
Done.