Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011674.1 Kokia drynarioides strain JFW-HI SEQ_126666, 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: 92100
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:973 original size:35 final size:34
Alignment explanation
Indices: 934--1011 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
924 GGGAAGGCTT
* *
934 TTTGTTTTCTTTTTTGCATCTGGTTTCTTTACTGG
1 TTTGTTTTCTTCTTAG-ATCTGGTTTCTTTACTGG
* * *
969 TTTGTTTTTCTTCTTAGTTTTGTTTTCTTTACTGG
1 TTTG-TTTTCTTCTTAGATCTGGTTTCTTTACTGG
*
1004 TTTATTTT
1 TTTGTTTT
1012 GTATGGTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
34 4 0.11
35 22 0.61
36 10 0.28
ACGTcount: A:0.06, C:0.12, G:0.14, T:0.68
Consensus pattern (34 bp):
TTTGTTTTCTTCTTAGATCTGGTTTCTTTACTGG
Found at i:978 original size:18 final size:17
Alignment explanation
Indices: 957--1011 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
947 TTGCATCTGG
957 TTTCTTTACTGGTTTGTT
1 TTTCTTTACTGGTTT-TT
*
975 TTTC-TT-CTTAGTTTTGT
1 TTTCTTTAC-TGGTTTT-T
992 TTTCTTTACTGGTTTATT
1 TTTCTTTACTGGTTT-TT
1010 TT
1 TT
1012 GTATGGTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
16 2 0.07
17 12 0.40
18 14 0.47
19 2 0.07
ACGTcount: A:0.07, C:0.11, G:0.13, T:0.69
Consensus pattern (17 bp):
TTTCTTTACTGGTTTTT
Found at i:1146 original size:27 final size:26
Alignment explanation
Indices: 1116--1168 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1106 AAAATTTTTG
1116 GTTACCCAACTATAAAAAGTTACAAAA
1 GTTACCCAACTAT-AAAAGTTACAAAA
* * *
1143 GTTATCTAACTATGAAAGTTACAAAA
1 GTTACCCAACTATAAAAGTTACAAAA
1169 TGATCACTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.26
Consensus pattern (26 bp):
GTTACCCAACTATAAAAGTTACAAAA
Found at i:4447 original size:15 final size:16
Alignment explanation
Indices: 4427--4456 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4417 AATTAATTAA
4427 TTTTAG-TTGATTGGG
1 TTTTAGTTTGATTGGG
4442 TTTTAGTTTGATTGG
1 TTTTAGTTTGATTGG
4457 TATGGATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (16 bp):
TTTTAGTTTGATTGGG
Found at i:6168 original size:20 final size:20
Alignment explanation
Indices: 6145--6188 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
6135 TTTTATAATG
**
6145 TTTTAAATAATTTTCTATTA
1 TTTTAAATAATTTGATATTA
**
6165 TTTTTTATAATTTGATATTA
1 TTTTAAATAATTTGATATTA
6185 TTTT
1 TTTT
6189 TACATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTAAATAATTTGATATTA
Found at i:6233 original size:10 final size:10
Alignment explanation
Indices: 6219--6289 Score: 66
Period size: 10 Copynumber: 7.6 Consensus size: 10
6209 TAAAAATTAT
6219 ATTTTTAAT-
1 ATTTTTAATA
6228 ATTTTT-AT-
1 ATTTTTAATA
*
6236 ATTTTT-CTA
1 ATTTTTAATA
6245 TATTTTT-ATA
1 -ATTTTTAATA
6255 ATATTTTAA-A
1 AT-TTTTAATA
6265 ATTTTT-ATA
1 ATTTTTAATA
6274 ATTTTTAATA
1 ATTTTTAATA
6284 ATTTTT
1 ATTTTT
6290 CTACCATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
8 10 0.19
9 19 0.35
10 24 0.44
11 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:6237 original size:8 final size:8
Alignment explanation
Indices: 6215--6280 Score: 60
Period size: 9 Copynumber: 7.4 Consensus size: 8
6205 TTTTTAAAAA
6215 TTATATTT
1 TTATATTT
6223 TTAATATTT
1 TT-ATATTT
6232 TTATATTTT
1 TTATA-TTT
6241 TCTATATTT
1 T-TATATTT
6250 TTATAATATT
1 TTAT-AT-TT
*
6260 TTAAAATTT
1 TT-ATATTT
6269 TTATAATTT
1 TTAT-ATTT
6278 TTA
1 TTA
6281 ATAATTTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
8 9 0.18
9 29 0.59
10 10 0.20
11 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (8 bp):
TTATATTT
Found at i:6268 original size:19 final size:19
Alignment explanation
Indices: 6215--6289 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
6205 TTTTTAAAAA
6215 TTAT-ATTTTTAAT-ATTT
1 TTATAATTTTTAATAATTT
*
6232 TTAT-ATTTTT-CTATATTT
1 TTATAATTTTTAATA-ATTT
6250 TTATAATATTTTAA-AATTT
1 TTATAAT-TTTTAATAATTT
6269 TTATAATTTTTAATAATTT
1 TTATAATTTTTAATAATTT
6288 TT
1 TT
6290 CTACCATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.02
17 10 0.20
18 14 0.28
19 20 0.40
20 5 0.10
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATAATTTTTAATAATTT
Found at i:6268 original size:29 final size:29
Alignment explanation
Indices: 6216--6289 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
6206 TTTTAAAAAT
* * *
6216 TATA-TTTT-TAATATTTTTATATTTTTC
1 TATATTTTTATAATATTTTAAAATTTTTA
6243 TATATTTTTATAATATTTTAAAATTTTTA
1 TATATTTTTATAATATTTTAAAATTTTTA
6272 TA-ATTTTTAATAAT-TTTT
1 TATATTTTT-ATAATATTTT
6290 CTACCATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.10
28 14 0.34
29 23 0.56
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (29 bp):
TATATTTTTATAATATTTTAAAATTTTTA
Found at i:7902 original size:29 final size:29
Alignment explanation
Indices: 7832--7904 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
7822 GTACTCTTTA
* *
7832 TAAA-TTAGTAATTTAGTCTCTTTATTTT
1 TAAATTTAGAAATTTAGTCTCTCTATTTT
** *
7860 TATTTTTAGGAATTTAGTCTCTCTATTTTT
1 TAAATTTAGAAATTTAGTCTCTCTA-TTTT
7890 TAAATTTA-AAATTTA
1 TAAATTTAGAAATTTA
7905 AGTCCAATTG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 2 0.06
29 24 0.67
30 10 0.28
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (29 bp):
TAAATTTAGAAATTTAGTCTCTCTATTTT
Found at i:8467 original size:2 final size:2
Alignment explanation
Indices: 8462--8489 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8452 ATACACACAC
8462 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
8490 GTAGATGGAA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13591 original size:22 final size:22
Alignment explanation
Indices: 13555--13615 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
13545 CGATCTAAGG
13555 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
13576 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
13598 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
13616 GGAAGTCGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 11 0.30
22 25 0.68
23 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:13606 original size:15 final size:16
Alignment explanation
Indices: 13581--13610 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13571 GAATTAAAAA
13581 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
13597 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
13611 AATAGGGAAG
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:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:14436 original size:19 final size:19
Alignment explanation
Indices: 14412--14454 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
14402 AAACATAAAT
14412 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
14431 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
14450 TAAAT
1 TAAAT
14455 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:22008 original size:28 final size:28
Alignment explanation
Indices: 21968--22023 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
21958 TGAGAAGTTA
*
21968 TTCCAATTATTAATGAACACATGAACTG
1 TTCCAATTATTAATAAACACATGAACTG
21996 TTCCAATTATTAATAAACACATGAACTG
1 TTCCAATTATTAATAAACACATGAACTG
22024 CTGATTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (28 bp):
TTCCAATTATTAATAAACACATGAACTG
Found at i:28172 original size:2 final size:2
Alignment explanation
Indices: 28165--28191 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28155 AACCTACACA
28165 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 A
28192 AGCGAGTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29057 original size:46 final size:46
Alignment explanation
Indices: 29003--29100 Score: 180
Period size: 46 Copynumber: 2.2 Consensus size: 46
28993 ATCACACTTC
*
29003 GTTC-TTCGCCTTGTGTACTGTAGAACGTAAGATCATGATTCTTTT
1 GTTCTTTCGCCTTGTGTACTGTAGAACGTAAGATCATGATTCGTTT
29048 GTTCTTTCGCCTTGTGTACTGTAGAACGTAAGATCATGATTCGTTT
1 GTTCTTTCGCCTTGTGTACTGTAGAACGTAAGATCATGATTCGTTT
29094 GTTCTTT
1 GTTCTTT
29101 TTCAACCGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 4 0.08
46 47 0.92
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.44
Consensus pattern (46 bp):
GTTCTTTCGCCTTGTGTACTGTAGAACGTAAGATCATGATTCGTTT
Found at i:35438 original size:18 final size:16
Alignment explanation
Indices: 35406--35449 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
35396 ATGGAATAAG
35406 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
35422 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
35436 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
35450 ACCTTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:39717 original size:41 final size:41
Alignment explanation
Indices: 39660--39738 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
39650 TTGTTTGGGC
39660 ATCATGCTTGTGCTTTTTCATGTGAAATAAAACAAAATAGA
1 ATCATGCTTGTGCTTTTTCATGTGAAATAAAACAAAATAGA
39701 ATCATGCTTGTGCTTTTTCATGTGAAATAAAACAAAAT
1 ATCATGCTTGTGCTTTTTCATGTGAAATAAAACAAAAT
39739 CTGAAATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (41 bp):
ATCATGCTTGTGCTTTTTCATGTGAAATAAAACAAAATAGA
Found at i:46791 original size:3 final size:3
Alignment explanation
Indices: 46783--46835 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
46773 ATTTAAAACG
46783 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
46831 ATT AT
1 ATT AT
46836 AATAAGAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:47357 original size:3 final size:3
Alignment explanation
Indices: 47308--47337 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
47298 TTAATGTAAA
47308 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47338 GAGATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:51009 original size:2 final size:2
Alignment explanation
Indices: 51002--51036 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50992 AAATTCTTTA
51002 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 A
51037 ATAAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53025 original size:100 final size:100
Alignment explanation
Indices: 52913--53112 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
52903 ACCATTTTTT
52913 ACAAAAAAAAGTTGATTAAGTTTACTATTACCTATTCATGAAAAATATGTTTGGAAAAAATAGAT
1 ACAAAAAAAAGTTGATTAAGTTTACTATTACCTATTCATGAAAAATATGTTTGGAAAAAATAGAT
52978 GAATTAAAAATATGAATTAAATTTGAGTTTAAATA
66 GAATTAAAAATATGAATTAAATTTGAGTTTAAATA
53013 ACAAAAAAAAGTTGATTAAGTTTACTATTACCTATTCATGAAAAATATGTTTGGAAAAAATAGAT
1 ACAAAAAAAAGTTGATTAAGTTTACTATTACCTATTCATGAAAAATATGTTTGGAAAAAATAGAT
53078 GAATTAAAAATATGAATTAAATTTGAGTTTAAATA
66 GAATTAAAAATATGAATTAAATTTGAGTTTAAATA
53113 TTTTAGATCT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (100 bp):
ACAAAAAAAAGTTGATTAAGTTTACTATTACCTATTCATGAAAAATATGTTTGGAAAAAATAGAT
GAATTAAAAATATGAATTAAATTTGAGTTTAAATA
Found at i:56171 original size:31 final size:30
Alignment explanation
Indices: 56127--56186 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
56117 TTTCTTTAAA
**
56127 TTAATATTATAAGTGGTTTTTAAATTATAC
1 TTAATATTATAAGTGGTAATTAAATTATAC
*
56157 TTAATTATTCTAAGTGGTAATTAAATTATA
1 TTAA-TATTATAAGTGGTAATTAAATTATA
56187 TTTCGTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.48
Consensus pattern (30 bp):
TTAATATTATAAGTGGTAATTAAATTATAC
Found at i:56553 original size:20 final size:20
Alignment explanation
Indices: 56516--56553 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56506 TTAAAAAAGT
*
56516 TTGCTGGAATATGAATTTTG
1 TTGCTGGAAAATGAATTTTG
*
56536 TTGCTGGAAAATGGATTT
1 TTGCTGGAAAATGAATTT
56554 GGATAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCTGGAAAATGAATTTTG
Found at i:56779 original size:28 final size:29
Alignment explanation
Indices: 56746--56809 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
56736 TTTTAAAAAC
56746 TATTTAAATA-ATTTAA-ATAATAAAATA
1 TATTTAAATACATTTAAGATAATAAAATA
* *
56773 TGATTTAAGTAGCATTTAAGATAATATAATA
1 T-ATTTAAATA-CATTTAAGATAATAAAATA
56804 TATTTA
1 TATTTA
56810 TAGGAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 1 0.03
28 8 0.26
30 11 0.35
31 11 0.35
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (29 bp):
TATTTAAATACATTTAAGATAATAAAATA
Found at i:57219 original size:9 final size:9
Alignment explanation
Indices: 57205--57235 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
57195 TTATTAATTT
57205 AAAATTTTA
1 AAAATTTTA
57214 AAAATTTTA
1 AAAATTTTA
*
57223 AAAAATTTA
1 AAAATTTTA
57232 AAAA
1 AAAA
57236 AAATTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATTTTA
Found at i:58653 original size:20 final size:19
Alignment explanation
Indices: 58615--58653 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
58605 TTGTAATGGA
* *
58615 TATATTTTAATATTTAAAT
1 TATAGTTTAATATTCAAAT
58634 TATAGTTTATATATTCAAAT
1 TATAGTTTA-ATATTCAAAT
58654 CAAATTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
TATAGTTTAATATTCAAAT
Found at i:59229 original size:21 final size:20
Alignment explanation
Indices: 59205--59244 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
59195 TTCATGGAAT
*
59205 CAAGTATATAATTATTATGTC
1 CAAGTATATAACTA-TATGTC
*
59226 CAAGTTTATAACTATATGT
1 CAAGTATATAACTATATGT
59245 TTTATAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (20 bp):
CAAGTATATAACTATATGTC
Found at i:61627 original size:19 final size:20
Alignment explanation
Indices: 61605--61642 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61595 ACTTTATTTT
*
61605 ATAAT-TTAAATTTCAAAAA
1 ATAATATTAAATTACAAAAA
*
61624 ATAATATTTAATTACAAAA
1 ATAATATTAAATTACAAAA
61643 TGATTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAATATTAAATTACAAAAA
Found at i:65161 original size:15 final size:15
Alignment explanation
Indices: 65143--65177 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
65133 AAAATTAAAG
*
65143 AAATAAATATTGTAA
1 AAATAAATATTATAA
*
65158 AAATAGATATTATAA
1 AAATAAATATTATAA
65173 AAATA
1 AAATA
65178 TTGGTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
AAATAAATATTATAA
Found at i:72834 original size:16 final size:16
Alignment explanation
Indices: 72813--72858 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
72803 AATCATTATG
72813 AATATAATTTAATAAA
1 AATATAATTTAATAAA
*
72829 AATATAA-TT-AT-TA
1 AATATAATTTAATAAA
*
72842 AATATGATTTAATAAA
1 AATATAATTTAATAAA
72858 A
1 A
72859 TTTTTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
13 7 0.29
14 4 0.17
15 4 0.17
16 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AATATAATTTAATAAA
Found at i:72889 original size:10 final size:10
Alignment explanation
Indices: 72876--72912 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
72866 TATAATTATT
72876 TTATATTAAA
1 TTATATTAAA
72886 TTATATTAAA
1 TTATATTAAA
* *
72896 ATATTTTAAA
1 TTATATTAAA
72906 TTATATT
1 TTATATT
72913 TTGAAATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTATATTAAA
Found at i:73929 original size:61 final size:60
Alignment explanation
Indices: 73789--73948 Score: 169
Period size: 61 Copynumber: 2.6 Consensus size: 60
73779 AATTATAACA
*
73789 AAATTGATAAATTTGATAAATGTTGAGGGCTAAATTTATTGAATTTTTAAGAACTAGAACT
1 AAATTGATAAATTTG-TAAATATTGAGGGCTAAATTTATTGAATTTTTAAGAACTAGAACT
* * * * * * * *
73850 AAAATGACAAATTTTGTAAACATTGAGGGTTAAATTTATTGAGTTTTTTAGATCTAGGA-T
1 AAATTGATAAA-TTTGTAAATATTGAGGGCTAAATTTATTGAATTTTTAAGAACTAGAACT
* *
73910 CAAATTGATAGAATATGTAAATATTGAAGGACTAAATTT
1 -AAATTGATA-AATTTGTAAATATTG-AGGGCTAAATTT
73949 TTTATCAAGC
Statistics
Matches: 80, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
60 1 0.01
61 63 0.79
62 16 0.20
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.38
Consensus pattern (60 bp):
AAATTGATAAATTTGTAAATATTGAGGGCTAAATTTATTGAATTTTTAAGAACTAGAACT
Found at i:74067 original size:20 final size:21
Alignment explanation
Indices: 74030--74068 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
74020 TTTAATTTCG
* *
74030 AAAAATTAAATGATTAAATCA
1 AAAAATTAAATAACTAAATCA
74051 AAAAATT-AATAACTAAAT
1 AAAAATTAAATAACTAAAT
74069 AACTAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAAATTAAATAACTAAATCA
Found at i:81899 original size:15 final size:15
Alignment explanation
Indices: 81879--81929 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
81869 ATACAATATT
81879 TATATTTTTTAATTA
1 TATATTTTTTAATTA
*
81894 TATA-TTTTTAATTT
1 TATATTTTTTAATTA
* *
81908 TGAGAATTTTTAATTTA
1 T-ATATTTTTTAA-TTA
81925 TATAT
1 TATAT
81930 ATCTTTTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 10 0.36
15 6 0.21
16 9 0.32
17 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
TATATTTTTTAATTA
Found at i:83963 original size:21 final size:22
Alignment explanation
Indices: 83924--83964 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
83914 ATTTAGATAA
*
83924 TTTTTTAAGAGTATTAAATATT
1 TTTTTTAAGAGTATAAAATATT
*
83946 TTTTTTAA-ATTATAAAATA
1 TTTTTTAAGAGTATAAAATA
83965 AAAAAAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTTTTAAGAGTATAAAATATT
Found at i:91589 original size:22 final size:22
Alignment explanation
Indices: 91563--91620 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
91553 GCCAAGTCAA
91563 ACCGTTGACCAGCCATTGACCG
1 ACCGTTGACCAGCCATTGACCG
* * **
91585 ACCGTTGATCGGCTGTTGACCG
1 ACCGTTGACCAGCCATTGACCG
*
91607 ACCGTTGACTAGCC
1 ACCGTTGACCAGCC
91621 GTTAACCAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.22
Consensus pattern (22 bp):
ACCGTTGACCAGCCATTGACCG
Found at i:91592 original size:11 final size:11
Alignment explanation
Indices: 91563--91615 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
91553 GCCAAGTCAA
91563 ACCGTTGACC-
1 ACCGTTGACCG
*
91573 AGCCATTGACCG
1 A-CCGTTGACCG
*
91585 ACCGTTGATCG
1 ACCGTTGACCG
* *
91596 GCTGTTGACCG
1 ACCGTTGACCG
91607 ACCGTTGAC
1 ACCGTTGAC
91616 TAGCCGTTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 1 0.03
11 31 0.94
12 1 0.03
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (11 bp):
ACCGTTGACCG
Found at i:91661 original size:7 final size:7
Alignment explanation
Indices: 91641--91706 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
91631 CATTGATCAG
91641 TCGTTGA
1 TCGTTGA
91648 -CTGTTGA
1 TC-GTTGA
*
91655 TCATTGA
1 TCGTTGA
91662 TCGTTGA
1 TCGTTGA
91669 TCGTTGA
1 TCGTTGA
*
91676 -CTTTGA
1 TCGTTGA
*
91682 CCGTTGA
1 TCGTTGA
*
91689 CCGTTGA
1 TCGTTGA
*
91696 -CCTTGA
1 TCGTTGA
91702 TCGTT
1 TCGTT
91707 AACTTTTTCG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
6 11 0.22
7 37 0.76
8 1 0.02
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (7 bp):
TCGTTGA
Found at i:91686 original size:20 final size:20
Alignment explanation
Indices: 91641--91706 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
91631 CATTGATCAG
* *
91641 TCGTTGACTGTTGATCATTGA
1 TCGTTGACCGTTGA-CCTTGA
* *
91662 TCGTTGATCGTTGACTTTGA
1 TCGTTGACCGTTGACCTTGA
*
91682 CCGTTGACCGTTGACCTTGA
1 TCGTTGACCGTTGACCTTGA
91702 TCGTT
1 TCGTT
91707 AACTTTTTCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 26 0.68
21 12 0.32
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
TCGTTGACCGTTGACCTTGA
Done.