Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014806.1 Kokia drynarioides strain JFW-HI SEQ_129848, 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: 395033
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:322101 original size:5 final size:5
Alignment explanation
Indices: 322091--322164 Score: 71
Period size: 5 Copynumber: 15.0 Consensus size: 5
322081 ATAGGACATT
* *
322091 ATATG ACATG ATATG ATATG AT-TCG ATATG TTATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATAT-G ATATG ATATG ATATG ATATG ATATG
* * * *
322141 ACACG TTATG AT-TG ATAAG ATATG
1 ATATG ATATG ATATG ATATG ATATG
322165 TCATGGTATG
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
4 5 0.09
5 48 0.89
6 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (5 bp):
ATATG
Found at i:322174 original size:24 final size:25
Alignment explanation
Indices: 322122--322175 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
322112 TTCGATATGT
* *
322122 TATGATATGATATGATATGACACGT
1 TATGATATGATAAGATATGACACGG
* *
322147 TATGAT-TGATAAGATATGTCATGG
1 TATGATATGATAAGATATGACACGG
322171 TATGA
1 TATGA
322176 AATATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (25 bp):
TATGATATGATAAGATATGACACGG
Found at i:326611 original size:17 final size:18
Alignment explanation
Indices: 326575--326616 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
326565 AAAACCAAAT
* *
326575 TTTAAAATTAAAAGTTCA
1 TTTACAATTAAAAGTCCA
326593 TTTACAATT-AAAGTCCA
1 TTTACAATTAAAAGTCCA
*
326610 TTAACAA
1 TTTACAA
326617 AAAACGAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (18 bp):
TTTACAATTAAAAGTCCA
Found at i:328125 original size:18 final size:18
Alignment explanation
Indices: 328102--328140 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
328092 ACCCATATCC
328102 AAAAAACCCGAACTCAAA
1 AAAAAACCCGAACTCAAA
** *
328120 AAAAAACTTGAACTTAAA
1 AAAAAACCCGAACTCAAA
328138 AAA
1 AAA
328141 TTTGAACCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.64, C:0.18, G:0.05, T:0.13
Consensus pattern (18 bp):
AAAAAACCCGAACTCAAA
Found at i:328138 original size:15 final size:15
Alignment explanation
Indices: 328120--328153 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
328110 CGAACTCAAA
*
328120 AAAAAACTTGAACTT
1 AAAAAACTTGAACCT
*
328135 AAAAAATTTGAACCT
1 AAAAAACTTGAACCT
328150 AAAA
1 AAAA
328154 TTGACTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAAACTTGAACCT
Found at i:329835 original size:14 final size:15
Alignment explanation
Indices: 329815--329850 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
329805 AAACCCAAAT
329815 CTAAAAAACTTGAAC
1 CTAAAAAACTTGAAC
* *
329830 TTAAAAAATTTGAAC
1 CTAAAAAACTTGAAC
329845 CTAAAA
1 CTAAAA
329851 TTGACTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (15 bp):
CTAAAAAACTTGAAC
Found at i:331156 original size:19 final size:17
Alignment explanation
Indices: 331134--331173 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
331124 AGAACCAAAT
331134 TTTAAAATTAAAAAGTCCA
1 TTTAAAATT--AAAGTCCA
*
331153 TTTACAATTAAAGTCCA
1 TTTAAAATTAAAGTCCA
331170 TTTA
1 TTTA
331174 CAAAAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
19 8 0.40
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (17 bp):
TTTAAAATTAAAGTCCA
Found at i:331190 original size:10 final size:10
Alignment explanation
Indices: 331175--331200 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
331165 GTCCATTTAC
331175 AAAAAATACA
1 AAAAAATACA
331185 AAAAAATACA
1 AAAAAATACA
331195 AAAAAA
1 AAAAAA
331201 CCCTTAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATACA
Found at i:332709 original size:18 final size:19
Alignment explanation
Indices: 332686--332722 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
332676 CCAAATCCGG
332686 AAAACTCGAAC-TAAAAAA
1 AAAACTCGAACTTAAAAAA
*
332704 AAAACTTGAACTTAAAAAA
1 AAAACTCGAACTTAAAAAA
332723 TCTGAACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.65, C:0.14, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAACTCGAACTTAAAAAA
Found at i:334797 original size:36 final size:36
Alignment explanation
Indices: 334654--334789 Score: 209
Period size: 36 Copynumber: 3.8 Consensus size: 36
334644 AAGTGGATAC
* *
334654 GTGGGTATGCTATTCATGCCATGTGATAGTAAATAT
1 GTGGGTATGTTATTCATGCCATGTGACAGTAAATAT
*
334690 GTGGGTATGTTATTCATGCCATGAGACAGTAAATAT
1 GTGGGTATGTTATTCATGCCATGTGACAGTAAATAT
* * *
334726 GTGAGCATGTTATTCATGCCATGTGACAGTGAATAT
1 GTGGGTATGTTATTCATGCCATGTGACAGTAAATAT
*
334762 GTGGGTATATTATTCATGCCATGTGACA
1 GTGGGTATGTTATTCATGCCATGTGACA
334790 ATGAATATAT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 90 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (36 bp):
GTGGGTATGTTATTCATGCCATGTGACAGTAAATAT
Found at i:335218 original size:23 final size:23
Alignment explanation
Indices: 335188--335574 Score: 450
Period size: 23 Copynumber: 16.8 Consensus size: 23
335178 ATTAAATGTG
335188 TTAAAAGT-TAATGTGATTTATGC
1 TTAAAAGTAT-ATGTGATTTATGC
*
335211 TAAAAAGTATATGTGATTTATGC
1 TTAAAAGTATATGTGATTTATGC
* *
335234 TTAAAAGT-TAATGTAATTTTTGC
1 TTAAAAGTAT-ATGTGATTTATGC
335257 TTAAAAGTATATGTGATTTATGC
1 TTAAAAGTATATGTGATTTATGC
* * *
335280 TTAAAGGT-TAATATGATTTTTTGC
1 TTAAAAGTAT-ATGTGA-TTTATGC
*
335304 TTAAAAGTATATGTTATTTATGC
1 TTAAAAGTATATGTGATTTATGC
*
335327 TTAAAAGT-TAATGTGATTTTTGC
1 TTAAAAGTAT-ATGTGATTTATGC
335350 TTAAAAGTATATGTGATTTATGC
1 TTAAAAGTATATGTGATTTATGC
335373 TTAAAAGTATATGTGATTTATGC
1 TTAAAAGTATATGTGATTTATGC
335396 TTAAAAGT-TAATGTGATTTATGC
1 TTAAAAGTAT-ATGTGATTTATGC
* *
335419 TTGAAAGTATATGTGATTTATGT
1 TTAAAAGTATATGTGATTTATGC
*
335442 TTAAAAGTATATGTGACTTATGC
1 TTAAAAGTATATGTGATTTATGC
* *
335465 TTAAAAATATATGTGACTTATGC
1 TTAAAAGTATATGTGATTTATGC
* * *
335488 TAAAAAAT-TAATGTGATTTTTGC
1 TTAAAAGTAT-ATGTGATTTATGC
*
335511 TTAAAAGTACATGTGATTTATTG-
1 TTAAAAGTATATGTGATTTA-TGC
335534 TTAAAAGT-TAATGTGATTTATGC
1 TTAAAAGTAT-ATGTGATTTATGC
* *
335557 TCAAATG-ATAATGTGATT
1 TTAAAAGTAT-ATGTGATT
335575 AATGTGTAAA
Statistics
Matches: 316, Mismatches: 32, Indels: 32
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.02
23 285 0.90
24 23 0.07
25 1 0.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (23 bp):
TTAAAAGTATATGTGATTTATGC
Found at i:347966 original size:19 final size:19
Alignment explanation
Indices: 347942--347980 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
347932 AATGGAAAGA
347942 TAGTATATTTGTTTTGAGT
1 TAGTATATTTGTTTTGAGT
347961 TAGTATATTTGTTTTGAGT
1 TAGTATATTTGTTTTGAGT
347980 T
1 T
347981 CTTTTGGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (19 bp):
TAGTATATTTGTTTTGAGT
Found at i:349473 original size:105 final size:105
Alignment explanation
Indices: 349287--349639 Score: 440
Period size: 105 Copynumber: 3.4 Consensus size: 105
349277 TGTATTATTT
* * * *
349287 GAGTTGCGATTTTAAATCAACTAACTTAAATAAATTTAGGTTGCGATCTTAAATCAATTAACATT
1 GAGTTGCGATCTTAAATCAACTAACTCAAATAAATTTAGGTTGAGATCTTAAATCAACTAACATT
* * * *
349352 AATAATATCAGCTATGAATGTACGTCAGCAAGCTATTTAG
66 AATAATATCAGCTATGAACGTAGGTCAGCAAGTTGTTTAG
* * *
349392 GAGTTGTGATCTTAAATCAGCTAACTCAAATAAATTTAGGTTGAGATCTTAAATCAACTAACCTT
1 GAGTTGCGATCTTAAATCAACTAACTCAAATAAATTTAGGTTGAGATCTTAAATCAACTAACATT
* ** * *
349457 AATAATGTCAATTATGAACGTAGGTCAACGAA-TTGCTTAG
66 AATAATATCAGCTATGAACGTAGGTCAGC-AAGTTGTTTAG
* * * * * *
349497 GAGTTGTGATCTTGAATCAGCTAACTCAAATAAATTCAGGTTGCA-ATCTTAAATCAGCTAACTT
1 GAGTTGCGATCTTAAATCAACTAACTCAAATAAATTTAGGTTG-AGATCTTAAATCAACTAACAT
* * *
349561 TAATAATATCAGCTGTGAACATAGGTCAGCGAGTTGTTTAG
65 TAATAATATCAGCTATGAACGTAGGTCAGCAAGTTGTTTAG
*
349602 GAGTTGCAATCTTAAATCAACTAACTCAAATAAATTTA
1 GAGTTGCGATCTTAAATCAACTAACTCAAATAAATTTA
349640 ATCACGAGAT
Statistics
Matches: 212, Mismatches: 33, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
104 1 0.00
105 208 0.98
106 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (105 bp):
GAGTTGCGATCTTAAATCAACTAACTCAAATAAATTTAGGTTGAGATCTTAAATCAACTAACATT
AATAATATCAGCTATGAACGTAGGTCAGCAAGTTGTTTAG
Found at i:354713 original size:26 final size:26
Alignment explanation
Indices: 354677--354733 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
354667 GTGAGCTTTC
*
354677 ATCAAAATGTCACGTCTCAAATCTGG
1 ATCATAATGTCACGTCTCAAATCTGG
*
354703 ATCATAATGTCACGTCTCAAATTTGG
1 ATCATAATGTCACGTCTCAAATCTGG
354729 ATCAT
1 ATCAT
354734 TCGGAACACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (26 bp):
ATCATAATGTCACGTCTCAAATCTGG
Found at i:358736 original size:52 final size:52
Alignment explanation
Indices: 358658--358942 Score: 392
Period size: 52 Copynumber: 5.5 Consensus size: 52
358648 AACTGAAATT
* * *
358658 GGTCCGATGACCATGTGTTATCGTGAGTATAAGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
358710 GGTCCGATGACTATGTGCCATCGTGAGTATATGAATCCTTTACGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
358762 GGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * * *
358814 GGTCCGATGACAATATATCATCGTGAGTATATGAATCCTTTACGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * ** *
358866 GGTCTGATGACTATGTGTCATCGTGAGTATACGAATTTTTTACGGATTA-AA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * * *
358917 GGTTCGATAACTCTATGTCATCGTGA
1 GGTCCGATGACTATGTGTCATCGTGA
358943 ATATCAAATA
Statistics
Matches: 206, Mismatches: 27, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
51 22 0.11
52 184 0.89
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:362812 original size:14 final size:14
Alignment explanation
Indices: 362795--362835 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
362785 ATTGTAATTT
*
362795 AAAAAGAAA-AAAG
1 AAAAAAAAAGAAAG
362808 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
362822 AAAGAAAAAGAAAG
1 AAAAAAAAAGAAAG
362836 GTAATGCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:362816 original size:10 final size:11
Alignment explanation
Indices: 362797--362834 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
362787 TGTAATTTAA
362797 AAAGAAAAAAG
1 AAAGAAAAAAG
362808 AAA-AAAAAAG
1 AAAGAAAAAAG
*
362818 AAAGAAAGAA-
1 AAAGAAAAAAG
362828 AAAGAAA
1 AAAGAAA
362835 GGTAATGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:363617 original size:56 final size:58
Alignment explanation
Indices: 363523--363650 Score: 188
Period size: 57 Copynumber: 2.2 Consensus size: 58
363513 TAAGATGGTC
* * *
363523 TTTTTACTTACATTTGTATTTTTTTTATTTTATGTTGTTTCAAGC-TTTTTAAATTAATG
1 TTTTTAATTA-ATTTGTA-TTTTTTTATTTCATATTGTTTCAAGCTTTTTTAAATTAATG
*
363582 TTTTTAATTAATTTGTA-TTTTTTATTTCATATTGTTTCAAGCTTTTTTTAATTAATG
1 TTTTTAATTAATTTGTATTTTTTTATTTCATATTGTTTCAAGCTTTTTTAAATTAATG
363639 TTTTTAATTAAT
1 TTTTTAATTAAT
363651 AAATATATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
56 23 0.36
57 25 0.39
58 7 0.11
59 9 0.14
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (58 bp):
TTTTTAATTAATTTGTATTTTTTTATTTCATATTGTTTCAAGCTTTTTTAAATTAATG
Found at i:363630 original size:58 final size:56
Alignment explanation
Indices: 363523--363650 Score: 177
Period size: 56 Copynumber: 2.2 Consensus size: 56
363513 TAAGATGGTC
* * *
363523 TTTTTACTTACATTTGTATTTTTTTTATTTTATGTTGTTTCAAGCTTTTTAAATTAATG
1 TTTTTAATTA-ATTTGTA-TTTTTTTATTTCATATTGTTTCAAGCTTTTT-AATTAATG
363582 TTTTTAATTAATTTGTA-TTTTTTATTTCATATTGTTTCAAGCTTTTTTTAATTAATG
1 TTTTTAATTAATTTGTATTTTTTTATTTCATATTGTTTCAAGC--TTTTTAATTAATG
363639 TTTTTAATTAAT
1 TTTTTAATTAAT
363651 AAATATATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
56 23 0.36
57 20 0.31
58 12 0.19
59 9 0.14
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (56 bp):
TTTTTAATTAATTTGTATTTTTTTATTTCATATTGTTTCAAGCTTTTTAATTAATG
Found at i:363644 original size:13 final size:13
Alignment explanation
Indices: 363626--363650 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
363616 TTTCAAGCTT
363626 TTTTTAATTAATG
1 TTTTTAATTAATG
363639 TTTTTAATTAAT
1 TTTTTAATTAAT
363651 AAATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:363666 original size:56 final size:55
Alignment explanation
Indices: 363547--363666 Score: 152
Period size: 57 Copynumber: 2.2 Consensus size: 55
363537 TGTATTTTTT
* *** *
363547 TTATTTT-ATGTTGTTTCAAGCTTTTTAAATTAATGTTTTTAATTAATTTGTATT
1 TTATTTTCATATTGTTTCAAGCTTTTTAAATTAATGTTTTTAATTAATAAATATA
* *
363601 TTTTATTTCATATTGTTTCAAGCTTTTTTTAATTAATGTTTTTAATTAATAAATATA
1 TTAT-TTTCATATTGTTTCAAGC-TTTTTAAATTAATGTTTTTAATTAATAAATATA
363658 TTATTTTCA
1 TTATTTTCA
363667 AGTTTTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
54 3 0.05
55 3 0.05
56 18 0.33
57 31 0.56
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (55 bp):
TTATTTTCATATTGTTTCAAGCTTTTTAAATTAATGTTTTTAATTAATAAATATA
Found at i:365012 original size:22 final size:20
Alignment explanation
Indices: 364978--365017 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
364968 AAATAGGTAC
*
364978 CATTTTATTATTAACTACAAT
1 CATTTTATAATTAA-TACAAT
364999 CATTATTATAATTAATACA
1 CATT-TTATAATTAATACA
365018 TGTTGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (20 bp):
CATTTTATAATTAATACAAT
Found at i:365110 original size:7 final size:7
Alignment explanation
Indices: 365098--365122 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
365088 TTTACACTAA
365098 ATATGTT
1 ATATGTT
365105 ATATGTT
1 ATATGTT
365112 ATATGTT
1 ATATGTT
365119 ATAT
1 ATAT
365123 ATGATATATT
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:0.12, T:0.56
Consensus pattern (7 bp):
ATATGTT
Found at i:365241 original size:204 final size:195
Alignment explanation
Indices: 364803--365207 Score: 668
Period size: 204 Copynumber: 2.0 Consensus size: 195
364793 ATCATGAATC
* *
364803 ATTATTATAATTAATCCATGTTGTTTTACTCATTTTTATTTTTAAGTATTATATTATATTTTACT
1 ATTATTATAATTAATACATGTTCTTTTA-TCATTTTTATTTTTAAGTATTATATTATATTTTACT
364868 TTCTAATATAATTTTAAATATTATTTACACTAAATATGTTATATGTTATATATGATATATTTTTA
65 TTCTAATATAATTTTAAATATTATTTACACTAAATATGTTATATGTTATATATGATATATTTTTA
364933 ATTTATATATATATATATATATTCACTTGCAAAGCAAATAGGTACCATTTTATTATTAACTACAA
130 ATTTATATATATATATATATATTCACTTGCAAAGCAAATAGGTACCATTTTATTATTAACTACAA
364998 T
195 T
* *
364999 CATTATTATAATTAATACATGTTGTTTTACTCATTTTTATTTTTAAGTATTGTATTATATTTTAC
1 -ATTATTATAATTAATACATGTTCTTTTA-TCATTTTTATTTTTAAGTATTATATTATATTTTAC
365064 TTTCTAATATAATTTTAAATATTATTTACACTAAATATGTTATATGTTATATGTTATATATGATA
64 TTTCTAATATAATTTTAAATATTATTTACACT--A-A----ATATGTTATATGTTATATATGATA
*
365129 TATTTTTAATTTTTATATATATATATATATTCACTTGCAAAGCAAATAGGTACCATTTTATTATT
122 TATTTTTAATTTATATATATATATATATATTCACTTGCAAAGCAAATAGGTACCATTTTATTATT
365194 AACTACAAT
187 AACTACAAT
365203 -TTATT
1 ATTATT
365208 TTTATTTTTT
Statistics
Matches: 198, Mismatches: 3, Indels: 9
0.94 0.01 0.04
Matches are distributed among these distances:
197 94 0.47
199 1 0.01
200 1 0.01
202 5 0.03
204 97 0.49
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (195 bp):
ATTATTATAATTAATACATGTTCTTTTATCATTTTTATTTTTAAGTATTATATTATATTTTACTT
TCTAATATAATTTTAAATATTATTTACACTAAATATGTTATATGTTATATATGATATATTTTTAA
TTTATATATATATATATATATTCACTTGCAAAGCAAATAGGTACCATTTTATTATTAACTACAAT
Found at i:366020 original size:30 final size:32
Alignment explanation
Indices: 365986--366046 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
365976 AGTAAAAGTG
*
365986 CATTTTTAAAGGATTAAA-T-TAAAATTTTAT
1 CATTTTTAAAGGATCAAAGTGTAAAATTTTAT
* *
366016 CATTTTTAGAGGGTCAAAGTGTAAAATTTTA
1 CATTTTTAAAGGATCAAAGTGTAAAATTTTA
366047 AAAAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 15 0.58
31 1 0.04
32 10 0.38
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (32 bp):
CATTTTTAAAGGATCAAAGTGTAAAATTTTAT
Found at i:367225 original size:39 final size:37
Alignment explanation
Indices: 367152--367228 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
367142 CACAATAAGA
* * *
367152 AAAAAAGGAATGGAGAGATTTTATTCTACCAAAAAGG
1 AAAAAAGGAATGGAAAGATTATATTCAACCAAAAAGG
* *
367189 AAAAAAGGAATGGAAAGATTGATATATGAACGAAAAAGG
1 AAAAAAGGAATGGAAAGATT-ATAT-TCAACCAAAAAGG
367228 A
1 A
367229 TCATATGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 19 0.58
38 3 0.09
39 11 0.33
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.18
Consensus pattern (37 bp):
AAAAAAGGAATGGAAAGATTATATTCAACCAAAAAGG
Found at i:367565 original size:23 final size:24
Alignment explanation
Indices: 367536--367582 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
367526 TGAATTATAA
*
367536 AATATTAGAAA-ATTATTTAAAAT
1 AATATTAAAAATATTATTTAAAAT
367559 AATATTAAAAATATTATTTAAAAT
1 AATATTAAAAATATTATTTAAAAT
367583 GATAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
AATATTAAAAATATTATTTAAAAT
Found at i:367566 original size:11 final size:12
Alignment explanation
Indices: 367549--367582 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
367539 ATTAGAAAAT
367549 TATTTAAAATAA
1 TATTTAAAATAA
* *
367561 TATTAAAAATAT
1 TATTTAAAATAA
367573 TATTTAAAAT
1 TATTTAAAAT
367583 GATAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:374607 original size:19 final size:20
Alignment explanation
Indices: 374583--374630 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
374573 TAAAGTTATG
* *
374583 TTAATTAGGTTTAATTA-AA
1 TTAATTAAGATTAATTAGAA
*
374602 TTAATTAAGATTAATTAGAT
1 TTAATTAAGATTAATTAGAA
374622 TTAATTAAG
1 TTAATTAAG
374631 GTATAAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
TTAATTAAGATTAATTAGAA
Found at i:374680 original size:26 final size:26
Alignment explanation
Indices: 374644--374695 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
374634 TAAAAGTAGA
*
374644 AAAATTGTAAAAAATATCATTTTCTT
1 AAAATTATAAAAAATATCATTTTCTT
*
374670 AAAATTATAAAAAGTATCATTTTCTT
1 AAAATTATAAAAAATATCATTTTCTT
374696 TCTATCTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (26 bp):
AAAATTATAAAAAATATCATTTTCTT
Found at i:375514 original size:22 final size:22
Alignment explanation
Indices: 375486--375556 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
375476 CGAGTCTAGA
*
375486 ACTTCGATTCTCTCTGATCAAC
1 ACTTCGATTCTCTCTGATCAGC
*
375508 ACTTCGATGT-TTTCT-ACTCAGC
1 ACTTCGAT-TCTCTCTGA-TCAGC
375530 ACTTCGATTCTCTCTGATCAGC
1 ACTTCGATTCTCTCTGATCAGC
375552 ACTTC
1 ACTTC
375557 AGTGTTCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.05
22 38 0.90
23 2 0.05
ACGTcount: A:0.20, C:0.31, G:0.11, T:0.38
Consensus pattern (22 bp):
ACTTCGATTCTCTCTGATCAGC
Found at i:375549 original size:44 final size:44
Alignment explanation
Indices: 375486--375579 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 44
375476 CGAGTCTAGA
*
375486 ACTTCGATTCTCTCTGATCAACACTTC-GATGTTTTCTACTCAGC
1 ACTTCGATTCTCTCTGATCAACACTTCAG-TGTTCTCTACTCAGC
* *
375530 ACTTCGATTCTCTCTGATCAGCACTTCAGTGTTCTCTACTTAGC
1 ACTTCGATTCTCTCTGATCAACACTTCAGTGTTCTCTACTCAGC
375574 ACTTCG
1 ACTTCG
375580 GTGCTATCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 45 0.98
45 1 0.02
ACGTcount: A:0.19, C:0.30, G:0.13, T:0.38
Consensus pattern (44 bp):
ACTTCGATTCTCTCTGATCAACACTTCAGTGTTCTCTACTCAGC
Found at i:375565 original size:22 final size:22
Alignment explanation
Indices: 375486--375579 Score: 81
Period size: 22 Copynumber: 4.3 Consensus size: 22
375476 CGAGTCTAGA
*
375486 ACTTCGAT-TCTCTCTGATCAAC
1 ACTTCGATGT-TCTCTGATCAGC
*
375508 ACTTCGATGTTTTCT-ACTCAGC
1 ACTTCGATGTTCTCTGA-TCAGC
375530 ACTTCGAT-TCTCTCTGATCAGC
1 ACTTCGATGT-TCTCTGATCAGC
*
375552 ACTTC-AGTGTTCTCT-ACTTAGC
1 ACTTCGA-TGTTCTCTGA-TCAGC
375574 ACTTCG
1 ACTTCG
375580 GTGCTATCTA
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
21 4 0.07
22 53 0.88
23 3 0.05
ACGTcount: A:0.19, C:0.30, G:0.13, T:0.38
Consensus pattern (22 bp):
ACTTCGATGTTCTCTGATCAGC
Found at i:375589 original size:22 final size:22
Alignment explanation
Indices: 375549--375598 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
375539 CTCTCTGATC
* *
375549 AGCACTTCAGTGTTCTCTACTT
1 AGCACTTCAGTGCTATCTACTT
* *
375571 AGCACTTCGGTGCTATCTATTT
1 AGCACTTCAGTGCTATCTACTT
375593 AGCACT
1 AGCACT
375599 ATGGGGCTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (22 bp):
AGCACTTCAGTGCTATCTACTT
Found at i:375611 original size:22 final size:22
Alignment explanation
Indices: 375562--375611 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
375552 ACTTCAGTGT
*
375562 TCTCTACTTAGCACTTCGGTGC
1 TCTCTACTTAGCACTTCGGGGC
* *
375584 TATCTATTTAGCACTAT-GGGGC
1 TCTCTACTTAGCACT-TCGGGGC
375606 TCTCTA
1 TCTCTA
375612 GTGTAGTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (22 bp):
TCTCTACTTAGCACTTCGGGGC
Found at i:379611 original size:23 final size:24
Alignment explanation
Indices: 379578--379633 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 24
379568 AATCTTCCAA
379578 TTAAACTCTGTTTATTTGTTTCA-
1 TTAAACTCTGTTTATTTGTTTCAG
*
379601 TTGAACTCTGTTTATTTGTTTCAG
1 TTAAACTCTGTTTATTTGTTTCAG
379625 TTAAACTCT
1 TTAAACTCT
379634 TATTAGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAG
Found at i:381415 original size:15 final size:16
Alignment explanation
Indices: 381386--381418 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
381376 GTTTGATAAA
381386 AAAGAAAAATGAGAGG
1 AAAGAAAAATGAGAGG
*
381402 AAAG-AAAATTAGAGG
1 AAAGAAAAATGAGAGG
381417 AA
1 AA
381419 TGATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (16 bp):
AAAGAAAAATGAGAGG
Found at i:384979 original size:23 final size:23
Alignment explanation
Indices: 384927--384979 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
384917 GGGGAGGTCG
* **
384927 AAATT-AAATTGTAATTTTTACG
1 AAATTAAAATTATAATTTTTAAA
* *
384949 ATAGTAAAATTATAATTTTTAAA
1 AAATTAAAATTATAATTTTTAAA
384972 AAATTAAA
1 AAATTAAA
384980 TCAAAATTGT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATTAAAATTATAATTTTTAAA
Found at i:385337 original size:6 final size:6
Alignment explanation
Indices: 385326--385356 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
385316 TAATATATAT
*
385326 TAATTA TAATTA TGATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA TAATTA T
385357 GAGTCATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:385349 original size:18 final size:18
Alignment explanation
Indices: 385326--385394 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
385316 TAATATATAT
385326 TAATTATAATTATGATTA
1 TAATTATAATTATGATTA
*
385344 TAATTATAATTATGAGTCA
1 TAATTATAATTATGA-TTA
* *
385363 TGAATTATGATTGATGA-TG
1 T-AATTATAATT-ATGATTA
*
385382 TAATTAGAATTAT
1 TAATTATAATTAT
385395 TAAAATTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 2 0.05
18 23 0.55
19 4 0.10
20 9 0.21
21 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (18 bp):
TAATTATAATTATGATTA
Done.