Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009458.1 Kokia drynarioides strain JFW-HI SEQ_124165, 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: 60885
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:613 original size:6 final size:6
Alignment explanation
Indices: 588--637 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
578 CTTTATTTAT
* * *
588 TTTAAA TTTGAAA -GTAAA TTTAAA TTCAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
635 TTT
1 TTT
638 TTAAACAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
5 7 0.20
6 25 0.71
7 3 0.09
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:628 original size:23 final size:24
Alignment explanation
Indices: 591--636 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
581 TATTTATTTT
*
591 AAATTTGAAAGTAAATTTAAATTC
1 AAATTTGAAAATAAATTTAAATTC
615 AAATTT-AAAATAAATTTAAATT
1 AAATTTGAAAATAAATTTAAATT
637 TTTAAACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (24 bp):
AAATTTGAAAATAAATTTAAATTC
Found at i:8509 original size:1 final size:1
Alignment explanation
Indices: 8503--8527 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
8493 AGTGGTACAG
8503 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
8528 GGAGAGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12293 original size:29 final size:27
Alignment explanation
Indices: 12256--12321 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 27
12246 TATATTTACG
* *
12256 ATTTGATTAATGATATTAATATTTTGATA
1 ATTTAATTAATGATATTAAAATTTT-A-A
* *
12285 ATTTAATTAATTATTTTAAAATTTTAA
1 ATTTAATTAATGATATTAAAATTTTAA
*
12312 ATTAAATTAA
1 ATTTAATTAA
12322 AATATGGAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 10 0.31
28 1 0.03
29 21 0.66
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
ATTTAATTAATGATATTAAAATTTTAA
Found at i:12307 original size:20 final size:20
Alignment explanation
Indices: 12270--12308 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12260 GATTAATGAT
*
12270 ATTAATATTTTGATAATTTA
1 ATTAATATTTTGAAAATTTA
12290 ATTAATTATTTT-AAAATTT
1 ATTAA-TATTTTGAAAATTT
12309 TAAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTAATATTTTGAAAATTTA
Found at i:32590 original size:2 final size:2
Alignment explanation
Indices: 32583--32611 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32573 AGAATACTAT
32583 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 T
32612 CTTATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37149 original size:24 final size:23
Alignment explanation
Indices: 37121--37165 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
37111 TTGATAATAT
*
37121 TTATTTTTAATATATTATTTAAAA
1 TTATTTATAATATATT-TTTAAAA
37145 TTATTTATAATATATTTTTAA
1 TTATTTATAATATATTTTTAA
37166 CTTTTAAATA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATTTATAATATATTTTTAAAA
Found at i:37155 original size:37 final size:37
Alignment explanation
Indices: 37081--37165 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 37
37071 TTAGGGAAAG
* * *
37081 ATATTT-TATTTAATAATTTTGTTATAATTTTTGATA
1 ATATTTATTTTTAATAATTATGTTAAAATTTTTGATA
37117 ATATTTATTTTTAATATATTAT-TTAAAATTATTT-ATA
1 ATATTTATTTTTAATA-ATTATGTTAAAATT-TTTGATA
37154 ATA--TATTTTTAA
1 ATATTTATTTTTAA
37166 CTTTTAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
35 9 0.21
36 6 0.14
37 21 0.49
38 7 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (37 bp):
ATATTTATTTTTAATAATTATGTTAAAATTTTTGATA
Found at i:39694 original size:36 final size:36
Alignment explanation
Indices: 39644--39712 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
39634 AAACAACTTA
* *
39644 CTTACACCGGTGTAAGTATGATTGCTTTAATCATAG
1 CTTACACCGATGTAAGTATAATTGCTTTAATCATAG
39680 CTTACACCGATGTAAGTATAATTGCTTTAATCA
1 CTTACACCGATGTAAGTATAATTGCTTTAATCA
39713 AGTTTGGGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (36 bp):
CTTACACCGATGTAAGTATAATTGCTTTAATCATAG
Found at i:41305 original size:12 final size:12
Alignment explanation
Indices: 41288--41313 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41278 TTTAAGTATG
41288 ATTAATTTTAAA
1 ATTAATTTTAAA
41300 ATTAATTTTAAA
1 ATTAATTTTAAA
41312 AT
1 AT
41314 ATTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTAATTTTAAA
Found at i:41512 original size:20 final size:21
Alignment explanation
Indices: 41471--41513 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
41461 TAATTTACTT
41471 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
41492 TAATTTTATTTTGTT-GTTAG
1 TAATTTAATTTTGTTAGTTAG
41512 TA
1 TA
41514 GTAGTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:41809 original size:30 final size:30
Alignment explanation
Indices: 41773--41879 Score: 114
Period size: 30 Copynumber: 3.6 Consensus size: 30
41763 TAAACTTGGC
*
41773 TAATTAATTTTCAAAATATAATATACAAAA
1 TAATTAATTATCAAAATATAATATACAAAA
***
41803 TAATTAATTATC-AAA-ATAATAT-CCCCA
1 TAATTAATTATCAAAATATAATATACAAAA
*
41830 TCATATT-ATTGACCAAAATATAATATACAAAA
1 T-A-ATTAATT-ATCAAAATATAATATACAAAA
41862 TAATTAATTATCAAAATA
1 TAATTAATTATCAAAATA
41880 ATATCCCCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
27 3 0.05
28 11 0.18
29 8 0.13
30 25 0.41
31 11 0.18
32 3 0.05
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (30 bp):
TAATTAATTATCAAAATATAATATACAAAA
Found at i:41817 original size:16 final size:16
Alignment explanation
Indices: 41773--41822 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
41763 TAAACTTGGC
*
41773 TAATTAATTTTCAAAA
1 TAATTAATTATCAAAA
41789 T-A-TAA-TATACAAAA
1 TAATTAATTAT-CAAAA
41803 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
41819 TAAT
1 TAAT
41823 ATCCCCATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 2 0.07
14 9 0.31
15 2 0.07
16 13 0.45
17 3 0.10
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:41847 original size:59 final size:59
Alignment explanation
Indices: 41784--41898 Score: 221
Period size: 59 Copynumber: 1.9 Consensus size: 59
41774 AATTAATTTT
41784 CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC
1 CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC
*
41843 CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATTTTATT
1 CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATATTATT
41899 TTGTTGTTAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (59 bp):
CAAAATATAATATACAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTGAC
Found at i:41945 original size:397 final size:398
Alignment explanation
Indices: 41494--42246 Score: 1391
Period size: 397 Copynumber: 1.9 Consensus size: 398
41484 TTAGTTAGTA
*
41494 ATTTTATTTTGTTGTTAGTAGTAGTAAATAAAAAATATTGTTCATATTTATTGATTTAAAATTTA
1 ATTTTATTTTGTTGTTAGTAGTAGTAAATAAAAAATATTATTCATATTTATTGATTTAAAATTTA
41559 ATAATGTTTAAATTTTGTTAGTTAGTAACTTTATTATACAAGTCATAAGATTGTTTAATAAAATG
66 ATAATGTTTAAATTTTGTTAGTTAGTAACTTTATTATACAAGTCATAAGATTGTTTAATAAAATG
41624 TGAAAGAAAACTATTACAAGTATTTATTAAAATAAACAATAATCCATTTTTAAGTTATAATTAAA
131 TGAAAGAAAACTATTACAAGTATTTATTAAAATAAACAATAATCCATTTTTAAGTTATAATTAAA
*
41689 ATTAGTTACAAGTATGAAATTAAAAAATTTATTATTTTAT-AAAAATAAGAGAGTTTTAATAATT
196 ATTAGTTACAAGTATGAAATTAAAAAAATTATTATTTTATAAAAAATAAGAGAGTTTTAATAATT
* * ** *
41753 CACAAAAAATTAAACTTGGCTAATTAATTTTCAAAATATAATATACAAAATAATTAATTATCAAA
261 CACAAAAAATTAAACCTAGCTAATTAATTACCAAAATATAATATAAAAAATAATTAATTATCAAA
41818 ATAATATCCCCATCATATTATTGACCAAAATATAATATACAAAATAATTAATTATCAAAATAATA
326 ATAATATCCCCATCATATTATTGACCAAAATATAATATACAAAATAATTAATTATCAAAATAATA
41883 TCCCCATC
391 TCCCCATC
*
41891 ATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTATTCATATTTATTGATTTAAAATTTA
1 ATTTTATTTTGTTGTTAGTAGTAGTAAATAAAAAATATTATTCATATTTATTGATTTAAAATTTA
41956 ATAATGTTTAAATTTTGTTAGTTAGTAACTTTATTATACAAGTCATAAGATTGTTTAATAAAATG
66 ATAATGTTTAAATTTTGTTAGTTAGTAACTTTATTATACAAGTCATAAGATTGTTTAATAAAATG
42021 TGAAAGAAAACTATTACAAGTATTTATTAAAATAAACAATAATCCATTTTTAAGTTATAATTAAA
131 TGAAAGAAAACTATTACAAGTATTTATTAAAATAAACAATAATCCATTTTTAAGTTATAATTAAA
42086 ATTAGTTACAAGTATGAAATTAAAAAAATTATTATTTTATAAAAAATAAGAGAGTTTTAATAATT
196 ATTAGTTACAAGTATGAAATTAAAAAAATTATTATTTTATAAAAAATAAGAGAGTTTTAATAATT
*
42151 CACAAAAAGTTAAACCTAGCTAATTAATTACCAAAATATAATATAAAAAATAATTAATTATCAAA
261 CACAAAAAATTAAACCTAGCTAATTAATTACCAAAATATAATATAAAAAATAATTAATTATCAAA
* * *
42216 ATAATATCCTCATCATATTATTTACTAAAAT
326 ATAATATCCCCATCATATTATTGACCAAAAT
42247 GGTACAAAAT
Statistics
Matches: 343, Mismatches: 12, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
397 232 0.68
398 111 0.32
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (398 bp):
ATTTTATTTTGTTGTTAGTAGTAGTAAATAAAAAATATTATTCATATTTATTGATTTAAAATTTA
ATAATGTTTAAATTTTGTTAGTTAGTAACTTTATTATACAAGTCATAAGATTGTTTAATAAAATG
TGAAAGAAAACTATTACAAGTATTTATTAAAATAAACAATAATCCATTTTTAAGTTATAATTAAA
ATTAGTTACAAGTATGAAATTAAAAAAATTATTATTTTATAAAAAATAAGAGAGTTTTAATAATT
CACAAAAAATTAAACCTAGCTAATTAATTACCAAAATATAATATAAAAAATAATTAATTATCAAA
ATAATATCCCCATCATATTATTGACCAAAATATAATATACAAAATAATTAATTATCAAAATAATA
TCCCCATC
Found at i:42216 original size:16 final size:16
Alignment explanation
Indices: 42171--42220 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
42161 TAAACCTAGC
*
42171 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
42187 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
42201 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
42217 TAAT
1 TAAT
42221 ATCCTCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:43593 original size:43 final size:43
Alignment explanation
Indices: 43511--43595 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
43501 ATTAACATGT
* * * *
43511 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATGACTTGACTCGTATTAATATGATTACATGTTAC
* *
43554 TAAATTATATGACTTTACTCTTATTAATAT-ATTAACATGTTA
1 TAAATTATATGACTTGACTCGTATTAATATGATT-ACATGTTA
43596 TTAGTTGTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 2 0.06
43 33 0.94
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAATTATATGACTTGACTCGTATTAATATGATTACATGTTAC
Found at i:44234 original size:45 final size:45
Alignment explanation
Indices: 44154--44290 Score: 168
Period size: 45 Copynumber: 3.0 Consensus size: 45
44144 GCATAGCTCA
* * *
44154 TCAAGCCAATGATATCAGCCTCAGTTTGACAAGCCACCGCAATAC
1 TCAAACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* *
44199 TCAAACCAAGGATATCAGCCTCAATTTGATGAGCCACCGCAATAC
1 TCAAACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * * * *
44244 TCAAGA-GAAGGATATCAGACTGAGTTTGACGAGCCATCGCGATAC
1 TCAA-ACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
44289 TC
1 TC
44291 TATTCCTCCC
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
45 78 0.99
46 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (45 bp):
TCAAACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:45256 original size:21 final size:21
Alignment explanation
Indices: 45232--45274 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
45222 AATACGTAAC
45232 GTACGTTGGAGAGTGTAAACG
1 GTACGTTGGAGAGTGTAAACG
45253 GTACGTTGGAGAGTGTAAACG
1 GTACGTTGGAGAGTGTAAACG
45274 G
1 G
45275 GGTCAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.40, T:0.23
Consensus pattern (21 bp):
GTACGTTGGAGAGTGTAAACG
Found at i:47761 original size:4 final size:4
Alignment explanation
Indices: 47741--47806 Score: 71
Period size: 4 Copynumber: 16.2 Consensus size: 4
47731 AACACATTAC
* * * *
47741 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
47789 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
47807 CTGTTTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.81
5 7 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:47775 original size:17 final size:15
Alignment explanation
Indices: 47741--47802 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 15
47731 AACACATTAC
47741 CTTTCTTTCCTTCTT
1 CTTTCTTTCCTTCTT
47756 CTTTCTTTCC-TC-T
1 CTTTCTTTCCTTCTT
*
47769 CCTTC-TTCC-T-TT
1 CTTTCTTTCCTTCTT
47781 CTTTCTTT-CTT-TT
1 CTTTCTTTCCTTCTT
47794 CTTTCTTTC
1 CTTTCTTTC
47803 TTTCCTGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
12 11 0.27
13 18 0.44
14 2 0.05
15 10 0.24
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTTCTTTCCTTCTT
Found at i:47799 original size:25 final size:24
Alignment explanation
Indices: 47740--47806 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
47730 AAACACATTA
47740 CCTTTCTTTCCTTC-TTCTTTCTTT
1 CCTTTCTTT-CTTCTTTCTTTCTTT
* *
47764 CCTCTCCTTCTTCCTTTCTTTCTTT
1 CCTTTCTTTCTT-CTTTCTTTCTTT
*
47789 CTTTTCTTTCTTTCTTTC
1 CCTTTCTTTC-TTCTTTC
47807 CTGTTTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.09
24 8 0.23
25 22 0.63
26 2 0.06
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (24 bp):
CCTTTCTTTCTTCTTTCTTTCTTT
Found at i:53520 original size:15 final size:14
Alignment explanation
Indices: 53483--53521 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
53473 CATATAATTT
53483 TTTAAATTAATATA
1 TTTAAATTAATATA
**
53497 TTTTTATTATATATA
1 TTTAAATTA-ATATA
53512 TTTAAATTAA
1 TTTAAATTAA
53522 ATTAAAAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAAATTAATATA
Found at i:59335 original size:29 final size:28
Alignment explanation
Indices: 59293--59363 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
59283 ATCGGAGTTA
* *
59293 AAAATGAGACTTTTTGGATACC-TGGGGGC
1 AAAATGGGAATTTTTGG--ACCATGGGGGC
*
59322 AAAATGGTAA-TTTTGGACCTATGGGGGC
1 AAAATGGGAATTTTTGGACC-ATGGGGGC
59350 AAAATGGGAATTTT
1 AAAATGGGAATTTT
59364 GGAAAAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 3 0.09
28 22 0.63
29 10 0.29
ACGTcount: A:0.31, C:0.10, G:0.30, T:0.30
Consensus pattern (28 bp):
AAAATGGGAATTTTTGGACCATGGGGGC
Found at i:59376 original size:28 final size:28
Alignment explanation
Indices: 59315--59393 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
59305 TTTGGATACC
* **
59315 TGGGGGCAAAATGGTAATTTTGGACCTA
1 TGGGGGCAAAATGGGAATTTTGGACAAA
59343 TGGGGGCAAAATGGGAATTTTGGA-AAA
1 TGGGGGCAAAATGGGAATTTTGGACAAA
* *
59370 GTTGGGGGTTAAAATCGGAATTTT
1 --TGGGGG-CAAAATGGGAATTTT
59394 TAGACACCCG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
27 1 0.02
28 23 0.53
29 6 0.14
30 13 0.30
ACGTcount: A:0.30, C:0.06, G:0.34, T:0.29
Consensus pattern (28 bp):
TGGGGGCAAAATGGGAATTTTGGACAAA
Found at i:59468 original size:59 final size:57
Alignment explanation
Indices: 59405--59619 Score: 175
Period size: 59 Copynumber: 3.7 Consensus size: 57
59395 AGACACCCGA
* **
59405 GGGTAAAAGGGTAATTTTTAGAAGTTTTTGGGTCAAAATCGAGATTTTTGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTAGAA-AATTTGGGTCAAAAT-GAGATTTTTGGAAGTTTGG
* ** * *
59464 GGGTAAAATAGCCATTTTTGGAAAAATTGAGGTCAAAAAT-AGAATTTTTGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTAGAAAATTTG-GGTC-AAAATGAG-ATTTTTGGAAGTTTGG
* * * * * **
59523 TGGTAAAATGGTAATTTCTAAAAAAATTGGGGTCAAAATG-GAATTTTGGAAAGTTTAA
1 GGGTAAAATGGTAATTT-TTAGAAAATTTGGGTCAAAATGAGATTTTTGG-AAGTTTGG
* *
59581 GGGTAAAAAT-GTAATTTTTAGAAAGTTCGGGGTCAAAAT
1 GGGT-AAAATGGTAATTTTTAGAAAATT-TGGGTCAAAAT
59620 ATAATTTTGG
Statistics
Matches: 124, Mismatches: 24, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
57 14 0.11
58 38 0.31
59 60 0.48
60 12 0.10
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTAGAAAATTTGGGTCAAAATGAGATTTTTGGAAGTTTGG
Found at i:59472 original size:29 final size:29
Alignment explanation
Indices: 59417--59665 Score: 97
Period size: 29 Copynumber: 8.5 Consensus size: 29
59407 GTAAAAGGGT
* ** *
59417 AATTTTTAGAAGTTTTTGGGTCAAAATCG
1 AATTTTTGGAAGTTTGGGGGTCAAAATAG
59446 AGATTTTTGGAAGTTTGGGGGT-AAAATAG
1 A-ATTTTTGGAAGTTTGGGGGTCAAAATAG
* ** *
59475 CCATTTTTGGAAAAATT-GAGGTCAAAAATAG
1 -AATTTTTGG-AAGTTTGGGGGTC-AAAATAG
* *
59506 AATTTTTGGAAGTTTGGTGGT-AAAATGG
1 AATTTTTGGAAGTTTGGGGGTCAAAATAG
*** ** *
59534 TAATTTCTAAAAAAATT-GGGGTCAAAATGG
1 -AATTT-TTGGAAGTTTGGGGGTCAAAATAG
** *
59564 AA-TTTTGGAAAGTTTAAGGGTAAAAAT-G
1 AATTTTTGG-AAGTTTGGGGGTCAAAATAG
* * *
59592 TAATTTTTAGAAAG-TTCGGGGTCAAAATAT
1 -AATTTTT-GGAAGTTTGGGGGTCAAAATAG
*
59622 AA-TTTTGGATAAGTTT-GGGATCAGAAAT-G
1 AATTTTTGG--AAGTTTGGGGGTCA-AAATAG
59651 -ATTTTTGGAAAGTTT
1 AATTTTTGG-AAGTTT
59666 AGGGACCTCC
Statistics
Matches: 165, Mismatches: 35, Indels: 41
0.68 0.15 0.17
Matches are distributed among these distances:
27 2 0.01
28 24 0.15
29 73 0.44
30 58 0.35
31 8 0.05
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAAGTTTGGGGGTCAAAATAG
Found at i:59577 original size:58 final size:54
Alignment explanation
Indices: 59434--59640 Score: 162
Period size: 58 Copynumber: 3.5 Consensus size: 54
59424 AGAAGTTTTT
* * * **
59434 GGGTCAAAATCGAGATTTTTGGAAGTTTGGGGGTAAAATAGCCATTTTTGGAAAAATTG
1 GGGTCAAAAT--AGAATTTTGGAAGTTT-GGGGTAAAAT-G-TAATTTTAAAAAAATTG
*
59493 AGGTCAAAAATAGAATTTTTGGAAGTTTGGTGGTAAAATGGTAATTTCTAAAAAAATTG
1 GGGTC-AAAATAGAA-TTTTGGAAGTTTGG-GGTAAAAT-GTAATTT-TAAAAAAATTG
* * * * *
59552 GGGTCAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTAGAAAGTTCG
1 GGGTCAAAATAGAATTTTGG-AAGTTT-GGGGT-AAAATGTAATTTTAAAAAAATT-G
*
59610 GGGTCAAAATATAATTTTGGATAAGTTTGGG
1 GGGTCAAAATAGAATTTTGG--AAGTTTGGG
59641 ATCAGAAATG
Statistics
Matches: 122, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
57 13 0.11
58 54 0.44
59 50 0.41
60 5 0.04
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (54 bp):
GGGTCAAAATAGAATTTTGGAAGTTTGGGGTAAAATGTAATTTTAAAAAAATTG
Done.