Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001301.1 Kokia drynarioides strain JFW-HI SEQ_112707, 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: 109001
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:4747 original size:13 final size:13
Alignment explanation
Indices: 4709--4739 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
4699 AAACATGTTA
4709 TTTTTGTTTTTTC
1 TTTTTGTTTTTTC
4722 TTTTTGTTTTTTC
1 TTTTTGTTTTTTC
4735 TTTTT
1 TTTTT
4740 TTTATTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (13 bp):
TTTTTGTTTTTTC
Found at i:7379 original size:21 final size:21
Alignment explanation
Indices: 7327--7380 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
7317 ACCTACAAAA
*
7327 CATTATGTTTGTAACTCTCCT
1 CATTATGTTTGTAACTCTCAT
* *
7348 CA-AAAGTTTTGTAACTCTCAT
1 CATTATG-TTTGTAACTCTCAT
7369 CATTATGTTTGT
1 CATTATGTTTGT
7381 TTTAAATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (21 bp):
CATTATGTTTGTAACTCTCAT
Found at i:11852 original size:130 final size:130
Alignment explanation
Indices: 11701--11973 Score: 528
Period size: 130 Copynumber: 2.1 Consensus size: 130
11691 AATTTAATAT
11701 ATATTAAATTTAAATTTTATCATGTGTAATTTTTATTAATTTATAAAAATATAAAAGAAACAACT
1 ATATT-AATTTAAATTTTATCATGTGTAATTTTTATTAATTTATAAAAATATAAAAGAAACAACT
*
11766 ATATTATAATCCTTACTTTATAACATAAATAATTTTTTAATTAAATTAATATTTATTTATCTCGT
65 ATATTATAATCCTTACTTTATAACATAAATAACTTTTTAATTAAATTAATATTTATTTATCTCGT
11831 G
130 G
11832 ATATTAATTTAAATTTTATCATGTGTAATTTTTATTAATTTATAAAAATATAAAAGAAACAACTA
1 ATATTAATTTAAATTTTATCATGTGTAATTTTTATTAATTTATAAAAATATAAAAGAAACAACTA
11897 TATTATAATCCTTACTTTATAACATAAATAACTTTTTAATTAAATTAATATTTATTTATCTCGTG
66 TATTATAATCCTTACTTTATAACATAAATAACTTTTTAATTAAATTAATATTTATTTATCTCGTG
11962 ATATTAATTTAA
1 ATATTAATTTAA
11974 TCAATAATAT
Statistics
Matches: 141, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
130 136 0.96
131 5 0.04
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.47
Consensus pattern (130 bp):
ATATTAATTTAAATTTTATCATGTGTAATTTTTATTAATTTATAAAAATATAAAAGAAACAACTA
TATTATAATCCTTACTTTATAACATAAATAACTTTTTAATTAAATTAATATTTATTTATCTCGTG
Found at i:15190 original size:17 final size:18
Alignment explanation
Indices: 15170--15222 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
15160 GTAATTCACC
15170 AAAAATTTTAATCAA-TT
1 AAAAATTTTAATCAACTT
*
15187 AAAAATATTAATAGCAACTT
1 AAAAATTTTAAT--CAACTT
*
15207 AAAATTTTATAATCAA
1 AAAAATTT-TAATCAA
15223 GGAAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.38
19 6 0.21
20 8 0.28
21 4 0.14
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAAATTTTAATCAACTT
Found at i:23643 original size:22 final size:22
Alignment explanation
Indices: 23606--23661 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
23596 AATTTATTTT
23606 TTTATAAATTTTTATAATACATA
1 TTTATAAA-TTTTATAATACATA
*
23629 TTTATAAATTTTATAATATATA
1 TTTATAAATTTTATAATACATA
23651 TTTATAAATTT
1 TTTATAAATTT
23662 ACATGCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTATAAATTTTATAATACATA
Found at i:23656 original size:8 final size:8
Alignment explanation
Indices: 23626--23695 Score: 54
Period size: 8 Copynumber: 8.6 Consensus size: 8
23616 TTTATAATAC
23626 ATATTTAT
1 ATATTTAT
*
23634 AAATTT-T
1 ATATTTAT
*
23641 ATA-ATAT
1 ATATTTAT
23648 ATATTTAT
1 ATATTTAT
* *
23656 AAATTTAC
1 ATATTTAT
*
23664 ATGCTTTTAT
1 AT--ATTTAT
23674 ATATTTAT
1 ATATTTAT
23682 ATATTATAT
1 ATATT-TAT
23691 ATATT
1 ATATT
23696 CAAAATAATA
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
6 1 0.02
7 7 0.15
8 25 0.53
9 8 0.17
10 6 0.13
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (8 bp):
ATATTTAT
Found at i:24524 original size:2 final size:2
Alignment explanation
Indices: 24517--24547 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24507 TTTAATAATT
24517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24548 TAAATGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25452 original size:5 final size:5
Alignment explanation
Indices: 25442--25473 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
25432 TTATATTTGT
25442 TTTTC TTTTC TTTTC TTTTC TTCTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC T
25474 CTCATATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:26576 original size:21 final size:21
Alignment explanation
Indices: 26518--26599 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 21
26508 TTTTTATTAC
26518 GAGTGGTTCATCCACAACGAT
1 GAGTGGTTCATCCACAACGAT
*** * *
26539 GAGCAATTTATCTACAACGAT
1 GAGTGGTTCATCCACAACGAT
*
26560 GAGTGGTTCATCCACAATGAT
1 GAGTGGTTCATCCACAACGAT
* *
26581 GAGTGTTTTATCCACAACG
1 GAGTGGTTCATCCACAACG
26600 TAGTGTAAGG
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (21 bp):
GAGTGGTTCATCCACAACGAT
Found at i:26591 original size:42 final size:42
Alignment explanation
Indices: 26518--26599 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
26508 TTTTTATTAC
*
26518 GAGTGGTTCATCCACAACGATGAGCAATTTATCTACAACGAT
1 GAGTGGTTCATCCACAACGATGAGCAATTTATCCACAACGAT
* ***
26560 GAGTGGTTCATCCACAATGATGAGTGTTTTATCCACAACG
1 GAGTGGTTCATCCACAACGATGAGCAATTTATCCACAACG
26600 TAGTGTAAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (42 bp):
GAGTGGTTCATCCACAACGATGAGCAATTTATCCACAACGAT
Found at i:30394 original size:26 final size:24
Alignment explanation
Indices: 30355--30406 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
30345 TCCAAATTAA
*
30355 AAATTAGAAACAAATAAACAAGAAC
1 AAATTAGAAACAAAGAAACAA-AAC
*
30380 AAATATAGTAACAAAGAAACAAAAC
1 AAAT-TAGAAACAAAGAAACAAAAC
30405 AA
1 AA
30407 GATGGATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.69, C:0.12, G:0.08, T:0.12
Consensus pattern (24 bp):
AAATTAGAAACAAAGAAACAAAAC
Found at i:30588 original size:26 final size:27
Alignment explanation
Indices: 30559--30609 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
30549 AAAGATGGTT
*
30559 AAAAATCTTCTAAAT-AAAACTCAAGA
1 AAAAATCTTCAAAATAAAAACTCAAGA
* *
30585 AAAATTCTTGAAAATAAAAACTCAA
1 AAAAATCTTCAAAATAAAAACTCAA
30610 AGAGAGAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.59, C:0.14, G:0.04, T:0.24
Consensus pattern (27 bp):
AAAAATCTTCAAAATAAAAACTCAAGA
Found at i:32310 original size:3 final size:3
Alignment explanation
Indices: 32302--32332 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
32292 TTTTGGTTAT
*
32302 TTC TTC TTC TTA TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
32333 AAAATTAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:32968 original size:3 final size:3
Alignment explanation
Indices: 32962--33005 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
32952 AGAAGAAGAA
32962 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
33006 AGAAATCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:38544 original size:20 final size:20
Alignment explanation
Indices: 38515--38553 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38505 TTAGAAAAGG
*
38515 TCAACGGTCAAAGTCAACGA
1 TCAACAGTCAAAGTCAACGA
38535 TCAACAGTCAAAGTCAACG
1 TCAACAGTCAAAGTCAACG
38554 GTTGGTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (20 bp):
TCAACAGTCAAAGTCAACGA
Found at i:38570 original size:18 final size:18
Alignment explanation
Indices: 38547--38592 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
38537 AACAGTCAAA
* *
38547 GTCAACGGTTGGTCAATG
1 GTCAACGGTCGATCAATG
*
38565 GTCAACGATCGATCAATG
1 GTCAACGGTCGATCAATG
38583 GTCAACGGTC
1 GTCAACGGTC
38593 AATGGTCGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (18 bp):
GTCAACGGTCGATCAATG
Found at i:38586 original size:25 final size:25
Alignment explanation
Indices: 38556--38609 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
38546 AGTCAACGGT
*
38556 TGGTCAATGGTCAACGATCGATCAA
1 TGGTCAACGGTCAACGATCGATCAA
* * *
38581 TGGTCAACGGTCAATGGTCGGTCAA
1 TGGTCAACGGTCAACGATCGATCAA
38606 TGGT
1 TGGT
38610 TAATTAGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (25 bp):
TGGTCAACGGTCAACGATCGATCAA
Found at i:38667 original size:6 final size:6
Alignment explanation
Indices: 38625--38649 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38615 AGCTTGACTC
38625 GGTTTG GGTTTG GGTTTG GGTTTG G
1 GGTTTG GGTTTG GGTTTG GGTTTG G
38650 TTCAAATGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (6 bp):
GGTTTG
Found at i:38715 original size:23 final size:23
Alignment explanation
Indices: 38669--38731 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
38659 GTTTAGGTTA
*
38669 TTGGGTTTA-ATTTT-AAAGGAT
1 TTGGGTTTAGGTTTTAAAAGGAT
*
38690 TTGGGTTTAGGTTTTAAAAGGGT
1 TTGGGTTTAGGTTTTAAAAGGAT
38713 TTGGGTTT-GGATTTTAAAA
1 TTGGGTTTAGG-TTTTAAAA
38732 AAAGTTTGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.24
22 6 0.16
23 22 0.59
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (23 bp):
TTGGGTTTAGGTTTTAAAAGGAT
Found at i:38738 original size:24 final size:22
Alignment explanation
Indices: 38689--38747 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
38679 TTTTAAAGGA
**
38689 TTTGGGTTTAGGTTTTAAAAGGG
1 TTTGGGTTT-GGTTTTAAAAAAG
38712 TTTGGGTTTGGATTTTAAAAAAAG
1 TTTGGGTTTGG-TTTT-AAAAAAG
*
38736 TTTGAGTTTGGT
1 TTTGGGTTTGGT
38748 GATGATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 2 0.06
23 14 0.45
24 15 0.48
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.46
Consensus pattern (22 bp):
TTTGGGTTTGGTTTTAAAAAAG
Found at i:41816 original size:18 final size:18
Alignment explanation
Indices: 41793--41841 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
41783 AAAGTTAACG
41793 GTCAACGATCAACGATCA
1 GTCAACGATCAACGATCA
**
41811 GTCAAC-AGTCAACGATTG
1 GTCAACGA-TCAACGATCA
*
41829 GTCAACGGTCAAC
1 GTCAACGATCAAC
41842 TTGGCTTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (18 bp):
GTCAACGATCAACGATCA
Found at i:41941 original size:22 final size:21
Alignment explanation
Indices: 41895--41942 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
41885 TAGGTTATTG
*
41895 GGTTTAATTTTAAAGGATTTG
1 GGTTTAATTTTAAAGGATTTA
41916 GGTTTAAGTTTTAAAAGG-TTTA
1 GGTTTAA-TTTT-AAAGGATTTA
41938 GGTTT
1 GGTTT
41943 GGTGATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 12 0.50
23 5 0.21
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (21 bp):
GGTTTAATTTTAAAGGATTTA
Found at i:44000 original size:3 final size:3
Alignment explanation
Indices: 43994--44022 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
43984 TATATAATAT
43994 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
44023 TGATGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:44027 original size:3 final size:3
Alignment explanation
Indices: 44021--44082 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
44011 AGAAGAAGAA
44021 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
44069 GAG GAT GAG GAT GA
1 GAT GAT GAT GAT GA
44083 AACGACAGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:44493 original size:29 final size:29
Alignment explanation
Indices: 44446--44502 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
44436 AGATATTTAT
* *
44446 TTTATTATATTATTGTTTTGTTTTAATTA
1 TTTATTATATTATAGTTTTATTTTAATTA
44475 TTTATTATATTA-AGATTTTATTTTAATT
1 TTTATTATATTATAG-TTTTATTTTAATT
44503 TTAGGATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTATTATATTATAGTTTTATTTTAATTA
Found at i:44518 original size:16 final size:15
Alignment explanation
Indices: 44497--44526 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
44487 AGATTTTATT
44497 TTAATTTTAGGATTTA
1 TTAATTTTA-GATTTA
44513 TTAATTTTAGATTT
1 TTAATTTTAGATTT
44527 TTTTATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (15 bp):
TTAATTTTAGATTTA
Found at i:45649 original size:21 final size:21
Alignment explanation
Indices: 45624--45664 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45614 TTTTTTTAAG
45624 AAAATTCAAATCTAATTAAAT
1 AAAATTCAAATCTAATTAAAT
*
45645 AAAATTTAAATCTAATTAAA
1 AAAATTCAAATCTAATTAAA
45665 AATGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATTCAAATCTAATTAAAT
Found at i:49997 original size:60 final size:60
Alignment explanation
Indices: 49904--50023 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
49894 TTGAGGCTTT
49904 GAGTTAAGCATGATTCACTAATTGTCTCTGAATTGAAGAAGTTACACCAAGACTGACGTG
1 GAGTTAAGCATGATTCACTAATTGTCTCTGAATTGAAGAAGTTACACCAAGACTGACGTG
49964 GAGTTAAGCATGATTCACTAATTGTCTCTGAATTGAAGAAGTTACACCAAGACTGACGTG
1 GAGTTAAGCATGATTCACTAATTGTCTCTGAATTGAAGAAGTTACACCAAGACTGACGTG
50024 AAGAGGTAGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (60 bp):
GAGTTAAGCATGATTCACTAATTGTCTCTGAATTGAAGAAGTTACACCAAGACTGACGTG
Found at i:58386 original size:27 final size:21
Alignment explanation
Indices: 58310--58374 Score: 130
Period size: 21 Copynumber: 3.1 Consensus size: 21
58300 ACTAATCAAA
58310 ATTAAAATGATTTTTATATTT
1 ATTAAAATGATTTTTATATTT
58331 ATTAAAATGATTTTTATATTT
1 ATTAAAATGATTTTTATATTT
58352 ATTAAAATGATTTTTATATTT
1 ATTAAAATGATTTTTATATTT
58373 AT
1 AT
58375 GAATATTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTAAAATGATTTTTATATTT
Found at i:59212 original size:25 final size:25
Alignment explanation
Indices: 59178--59228 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
59168 AAGTTATATC
*
59178 ATTGAAAGATTCAACAAATCTCTCG
1 ATTGAAAGATTCAACAAATCCCTCG
*
59203 ATTGAAAGATTCAACATATCCCTCG
1 ATTGAAAGATTCAACAAATCCCTCG
59228 A
1 A
59229 GAAGTGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (25 bp):
ATTGAAAGATTCAACAAATCCCTCG
Found at i:61988 original size:31 final size:30
Alignment explanation
Indices: 61951--62025 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 30
61941 AAAAGATTAG
61951 GTACCAAATTAAAAAAAAAAGTCGAGTTCAA
1 GTACCAAATTAAAAAAAAAA-TCGAGTTCAA
61982 GTACCAAATTAAGAAAAAAAATCGAGTTCAA
1 GTACCAAATTAA-AAAAAAAATCGAGTTCAA
62013 GTACCAAATTAAA
1 GTACCAAATTAAA
62026 CCCCAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
30 1 0.02
31 34 0.79
32 8 0.19
ACGTcount: A:0.55, C:0.13, G:0.12, T:0.20
Consensus pattern (30 bp):
GTACCAAATTAAAAAAAAAATCGAGTTCAA
Found at i:62077 original size:31 final size:32
Alignment explanation
Indices: 62036--62099 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
62026 CCCCAAAAAA
*
62036 TTTAAATACCAACTTAA-AAAAACGTGTC-AAG
1 TTTAAATACCAAATTAAGAAAAA-GTGTCTAAG
*
62067 TTTAAGTACCAAATTAAGAAAAAGTGTCTAAG
1 TTTAAATACCAAATTAAGAAAAAGTGTCTAAG
62099 T
1 T
62100 ACCAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 20 0.69
32 9 0.31
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (32 bp):
TTTAAATACCAAATTAAGAAAAAGTGTCTAAG
Found at i:75876 original size:20 final size:20
Alignment explanation
Indices: 75851--75891 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
75841 AATTGTTTTA
*
75851 ATTAAAAAAAATTATATTAT
1 ATTAAAAAAAATTAAATTAT
**
75871 ATTAAAAGGAATTAAATTAT
1 ATTAAAAAAAATTAAATTAT
75891 A
1 A
75892 AATTTACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
ATTAAAAAAAATTAAATTAT
Found at i:75940 original size:29 final size:29
Alignment explanation
Indices: 75884--75940 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
75874 AAAAGGAATT
* *
75884 AAATTATAAATTTACTAATAGTTTAATAA
1 AAATTATAAATTTACTAATACTTAAATAA
* *
75913 AAATTTTAAATTTATTAATACTTAAATA
1 AAATTATAAATTTACTAATACTTAAATA
75941 GTAAATTGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (29 bp):
AAATTATAAATTTACTAATACTTAAATAA
Found at i:76261 original size:30 final size:32
Alignment explanation
Indices: 76225--76293 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
76215 GATTTCATTT
* *
76225 CAGTCACTTAA-CTT-TGAAAAAATGACAAAA
1 CAGTCACTTAATATTATCAAAAAATGACAAAA
*
76255 CAGTCAC-TAATATTATCAAAAAGTGACAAAA
1 CAGTCACTTAATATTATCAAAAAATGACAAAA
76286 CAGTCACT
1 CAGTCACT
76294 GATTAATAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 3 0.09
30 9 0.27
31 21 0.64
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (32 bp):
CAGTCACTTAATATTATCAAAAAATGACAAAA
Found at i:76887 original size:18 final size:19
Alignment explanation
Indices: 76864--76909 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
76854 GGTATCTCCA
*
76864 TTTTTTCTCTTCTCCT-TT
1 TTTTTTCTATTCTCCTCTT
*
76882 TTTTTTTTATTCTCCTCTT
1 TTTTTTCTATTCTCCTCTT
76901 TTTTCTTCT
1 TTTT-TTCT
76910 TTTTCTCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 14 0.61
19 6 0.26
20 3 0.13
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTCTATTCTCCTCTT
Found at i:76888 original size:21 final size:22
Alignment explanation
Indices: 76864--76920 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
76854 GGTATCTCCA
76864 TTTTTTCTCTTCTCCTTTTT-T
1 TTTTTTCTCTTCTCCTTTTTCT
* *
76885 TTTTTAT-TCTCCTCTTTTTTCT
1 TTTTT-TCTCTTCTCCTTTTTCT
76907 TCTTTTTCTCTTCT
1 T-TTTTTCTCTTCT
76921 TAAACCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 16 0.55
22 4 0.14
23 9 0.31
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTTCTCTTCTCCTTTTTCT
Found at i:90111 original size:25 final size:26
Alignment explanation
Indices: 90072--90122 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
90062 CCTTTATAGC
*
90072 TTGTCAGGTAACCAAGCTCATAAAAT
1 TTGTCAAGTAACCAAGCTCATAAAAT
90098 TTGTCAAG-AACCAAGCTCATAAAAT
1 TTGTCAAGTAACCAAGCTCATAAAAT
90123 GTATGTCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (26 bp):
TTGTCAAGTAACCAAGCTCATAAAAT
Found at i:94042 original size:77 final size:77
Alignment explanation
Indices: 93950--94101 Score: 295
Period size: 77 Copynumber: 2.0 Consensus size: 77
93940 AATGAGTTAG
93950 AAATCACTTTAAAACAATAGATTAACTTAGTATTACAAGAACTACCATTTTTAAACTAAAAATAA
1 AAATCACTTTAAAACAATAGATTAACTTAGTATTACAAGAACTACCATTTTTAAACTAAAAATAA
94015 GTTTAAAGTCAA
66 GTTTAAAGTCAA
*
94027 AAATCACTTTAAAACAATAGATTAACTTAGTATTACAAGAACTACCATTTTTAAACTAAAAATAG
1 AAATCACTTTAAAACAATAGATTAACTTAGTATTACAAGAACTACCATTTTTAAACTAAAAATAA
94092 GTTTAAAGTC
66 GTTTAAAGTC
94102 CTTAGATCTA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (77 bp):
AAATCACTTTAAAACAATAGATTAACTTAGTATTACAAGAACTACCATTTTTAAACTAAAAATAA
GTTTAAAGTCAA
Found at i:95038 original size:21 final size:21
Alignment explanation
Indices: 95014--95077 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
95004 TATAAGAACA
*
95014 CTTACTAAGTATATGCAAACC
1 CTTAGTAAGTATATGCAAACC
* *
95035 CTTAAGGAATGT-TATGCAAACA
1 CTT-AGTAA-GTATATGCAAACC
*
95057 CTTAGTAAGTATATGCGAACC
1 CTTAGTAAGTATATGCAAACC
95078 TCTTGTATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.06
21 15 0.44
22 15 0.44
23 2 0.06
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (21 bp):
CTTAGTAAGTATATGCAAACC
Found at i:95066 original size:43 final size:42
Alignment explanation
Indices: 94989--95077 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 42
94979 TTATGATGTG
94989 AACCCTTAAGGAAGATATAAGAACACTTACTAAGTATATGCA
1 AACCCTTAAGGAAGATATAAGAACACTTACTAAGTATATGCA
* * * *
95031 AACCCTTAAGGAATGTTATGCA-AACACTTAGTAAGTATATGCG
1 AACCCTTAAGGAA-GATAT-AAGAACACTTACTAAGTATATGCA
95074 AACC
1 AACC
95078 TCTTGTATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 13 0.32
43 27 0.66
44 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (42 bp):
AACCCTTAAGGAAGATATAAGAACACTTACTAAGTATATGCA
Found at i:98314 original size:16 final size:17
Alignment explanation
Indices: 98273--98308 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
98263 TTGTTTTCAA
98273 TTTATTTTGTTTTTTTT
1 TTTATTTTGTTTTTTTT
*
98290 TTTCTTTTGTTTTTTTT
1 TTTATTTTGTTTTTTTT
98307 TT
1 TT
98309 AGTTTGCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.89
Consensus pattern (17 bp):
TTTATTTTGTTTTTTTT
Found at i:101316 original size:55 final size:54
Alignment explanation
Indices: 101203--101344 Score: 144
Period size: 55 Copynumber: 2.6 Consensus size: 54
101193 GTCGTGTCTT
* * * *
101203 TGCCCGTGTGTGTATTTGAAATTGGGTCACACGGCCATGTCCCAGCCCGAGTGTC
1 TGCCCGTGTGTG-ATTTCAAATTGGGTCACACAGCCATGTCCCAACCCGAGTGCC
* * *
101258 TGCCCGTGTGTGATTTCAAAGTTGGGTCACACAGTCGTGTTCCAACCC-ATGTGCC
1 TGCCCGTGTGTGATTTCAAA-TTGGGTCACACAGCCATGTCCCAACCCGA-GTGCC
* *
101313 TGCCCATGTGT-ATGTTCAAAATAGGGTCACAC
1 TGCCCGTGTGTGAT-TTC-AAATTGGGTCACAC
101345 GACCGTCTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
54 10 0.14
55 61 0.82
56 3 0.04
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (54 bp):
TGCCCGTGTGTGATTTCAAATTGGGTCACACAGCCATGTCCCAACCCGAGTGCC
Found at i:105026 original size:46 final size:46
Alignment explanation
Indices: 104933--105041 Score: 119
Period size: 46 Copynumber: 2.3 Consensus size: 46
104923 TTGGCCAGGG
* * *
104933 CTTAATATCCATATTCTCCAATCCGCAACATATGTAAGAAATGGGAA
1 CTTAA-ATCCATATTCTCCAATCCACAACATATGCAAGAAATAGGAA
* * **
104980 CTTAAATCCATATTCTCCAGTCCACAACGTATGCAAGAGCTAGGAA
1 CTTAAATCCATATTCTCCAATCCACAACATATGCAAGAAATAGGAA
* **
105026 CCTGCATCCATATTCT
1 CTTAAATCCATATTCT
105042 TTAGTCTGTA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
46 47 0.90
47 5 0.10
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (46 bp):
CTTAAATCCATATTCTCCAATCCACAACATATGCAAGAAATAGGAA
Found at i:106072 original size:91 final size:90
Alignment explanation
Indices: 105934--106104 Score: 222
Period size: 91 Copynumber: 1.9 Consensus size: 90
105924 AACCTCCGAT
* *
105934 TGAGTTGGTGTTATAGGTTAATCAGGTACCAATTGGGTTAGAAAATTATGAAAAATGTT-TTTTT
1 TGAGTTGGTGTCATAGGTTAACCAGGTACCAATTGGGTTAGAAAATTATG-AAAAT-TTCTTTTT
105998 ATATTTAAAATGAGTCAAATCCTTGAA
64 ATATTTAAAATGAGTCAAATCCTTGAA
* * **
106025 TGAGTTGGTGTCATTGGTTAACC-GAGTACTAACTT-GGTTAGGGAATTATGAAAATTTCTTTTT
1 TGAGTTGGTGTCATAGGTTAACCAG-GTACCAA-TTGGGTTAGAAAATTATGAAAATTTCTTTTT
*
106088 GTATTTAAAATGAGTCA
64 ATATTTAAAATGAGTCA
106105 TATTATTTGA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
89 2 0.03
90 27 0.39
91 39 0.56
92 2 0.03
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (90 bp):
TGAGTTGGTGTCATAGGTTAACCAGGTACCAATTGGGTTAGAAAATTATGAAAATTTCTTTTTAT
ATTTAAAATGAGTCAAATCCTTGAA
Found at i:106897 original size:9 final size:9
Alignment explanation
Indices: 106883--106909 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
106873 CATTTAATAA
106883 ATAATTAAT
1 ATAATTAAT
106892 ATAATTAAT
1 ATAATTAAT
106901 ATAATTAAT
1 ATAATTAAT
106910 TATTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATAATTAAT
Found at i:106900 original size:13 final size:13
Alignment explanation
Indices: 106876--106932 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
106866 ATTTAGTCAT
106876 TTAATA-AA-TAA
1 TTAATATAATTAA
106887 TTAATATAATTAA
1 TTAATATAATTAA
*
106900 TATAAT-TAATTATT
1 T-TAATATAATTA-A
*
106914 TTAATA-AATTAT
1 TTAATATAATTAA
106926 TTAATAT
1 TTAATAT
106933 TTTAATTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
11 6 0.15
12 9 0.23
13 19 0.49
14 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATATAATTAA
Found at i:106982 original size:16 final size:17
Alignment explanation
Indices: 106946--106982 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
106936 AATTTTATTT
106946 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
*
106963 -AATAGTAAA-TTTAAA
1 TAATAATAAATTTTAAA
106978 TAATA
1 TAATA
106983 TTCTTCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:107035 original size:15 final size:15
Alignment explanation
Indices: 107015--107071 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
107005 ATTCAATATT
107015 AATATTTTAATAATA
1 AATATTTTAATAATA
*
107030 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
107049 AATATATTAATAATA
1 AATATTTTAATAATA
*
107064 AATGTTTT
1 AATATTTT
107072 GTAGTATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Done.