Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004662.1 Kokia drynarioides strain JFW-HI SEQ_118205, 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: 65562
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:977 original size:20 final size:20
Alignment explanation
Indices: 952--991 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
942 AAGTTGGAAT
952 GGAGTTTTCCTCCAAAGATG
1 GGAGTTTTCCTCCAAAGATG
972 GGAGTTTTCCTCCAAAGATG
1 GGAGTTTTCCTCCAAAGATG
992 TTGTTGGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (20 bp):
GGAGTTTTCCTCCAAAGATG
Found at i:2410 original size:21 final size:21
Alignment explanation
Indices: 2384--2447 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
2374 TAGTAGGCTG
2384 TGTGCCGGTGTTTTCAAGCTA
1 TGTGCCGGTGTTTTCAAGCTA
* *
2405 TGTGCC--TAG---T-AGGCTG
1 TGTGCCGGT-GTTTTCAAGCTA
2421 TGTGCCGGTGTTTTCAAGCTA
1 TGTGCCGGTGTTTTCAAGCTA
2442 TGTGCC
1 TGTGCC
2448 TAGTAGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 10 0.31
17 2 0.06
18 1 0.03
19 1 0.03
20 2 0.06
21 16 0.50
ACGTcount: A:0.12, C:0.20, G:0.31, T:0.36
Consensus pattern (21 bp):
TGTGCCGGTGTTTTCAAGCTA
Found at i:2484 original size:37 final size:37
Alignment explanation
Indices: 2359--2468 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
2349 CTTACACAAA
* *
2359 TTCAGGCTATATGCCTAGTAGGCTGTGTGCCGGTGTT
1 TTCAAGCTATGTGCCTAGTAGGCTGTGTGCCGGTGTT
2396 TTCAAGCTATGTGCCTAGTAGGCTGTGTGCCGGTGTT
1 TTCAAGCTATGTGCCTAGTAGGCTGTGTGCCGGTGTT
2433 TTCAAGCTATGTGCCTAGTAGGCT-TCGTGCCGGTGT
1 TTCAAGCTATGTGCCTAGTAGGCTGT-GTGCCGGTGT
2469 ATTTGGGCTT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
36 1 0.01
37 69 0.99
ACGTcount: A:0.14, C:0.20, G:0.32, T:0.35
Consensus pattern (37 bp):
TTCAAGCTATGTGCCTAGTAGGCTGTGTGCCGGTGTT
Found at i:5802 original size:212 final size:210
Alignment explanation
Indices: 5437--5836 Score: 611
Period size: 212 Copynumber: 1.9 Consensus size: 210
5427 CATCAATTAA
*
5437 TAGACCAAATTGTAATGCCACATCCTTGAATGTAATCGTACTCTCACCGTACAAAAGATGGAATG
1 TAGACCAAATTGTAATGCCACATCCTTGAATGTAATCGTACACTCACCGTACAAAAGATGGAATG
* * * * * *
5502 TGTGTCTCGGGTTTCCATCTTTCCAACAAAGCATTGATAAGTGTCGACTCCAATTTAGTCCTTCC
66 TGTGTCTCAGATCTCCATCTTTCCAACAAAGCACTGATAAGTGTCGACTACAATTTAGTCCTGCC
* * * *
5567 AAGCATATGAGACACGTGCAAGAATCTCGCTTCTTCCAGGTGTTGTTCAATAACACGCGGTGCTC
131 AAGCATACGAGACACGTGCAAGAATCCCGCTTCGTCCAAGTGTTGTTCAATAACACGCGGTGCTC
5632 TCGCACTTAAATTGG
196 TCGCACTTAAATTGG
* * * * *
5647 TAGACCAAGTTGTAATGCCACATCCTTGAGTGTAATTGTACACTCACCGTATAGAAGATGGAATA
1 TAGACCAAATTGTAATGCCACATCCTTGAATGTAATCGTACACTCACCGTACAAAAGATGG-A-A
* * *
5712 TGTGTGTCTCAGATCTCCATCTTTCCAGCAAAGCACTGATAAGTGTGGGCTACAATTTAGTCCTG
64 TGTGTGTCTCAGATCTCCATCTTTCCAACAAAGCACTGATAAGTGTCGACTACAATTTAGTCCTG
5777 CCAAGCATACGAGACACGTGCAAGAATCCCGCTTCGTCCAAGTGTTGTTCAATAACACGC
129 CCAAGCATACGAGACACGTGCAAGAATCCCGCTTCGTCCAAGTGTTGTTCAATAACACGC
5837 CTAGCTCTCT
Statistics
Matches: 169, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
210 55 0.33
211 1 0.01
212 113 0.67
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (210 bp):
TAGACCAAATTGTAATGCCACATCCTTGAATGTAATCGTACACTCACCGTACAAAAGATGGAATG
TGTGTCTCAGATCTCCATCTTTCCAACAAAGCACTGATAAGTGTCGACTACAATTTAGTCCTGCC
AAGCATACGAGACACGTGCAAGAATCCCGCTTCGTCCAAGTGTTGTTCAATAACACGCGGTGCTC
TCGCACTTAAATTGG
Found at i:6587 original size:17 final size:17
Alignment explanation
Indices: 6565--6598 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6555 AAAATTTTTG
6565 TATATAAAATTGTATAA
1 TATATAAAATTGTATAA
*
6582 TATATATAATTGTATAA
1 TATATAAAATTGTATAA
6599 AACTGGCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TATATAAAATTGTATAA
Found at i:6814 original size:17 final size:17
Alignment explanation
Indices: 6792--6825 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6782 AAAATTTTTG
6792 TATATAAAATTGTATAA
1 TATATAAAATTGTATAA
*
6809 TATATATAATTGTATAA
1 TATATAAAATTGTATAA
6826 AACTGGCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TATATAAAATTGTATAA
Found at i:6950 original size:227 final size:227
Alignment explanation
Indices: 6555--7014 Score: 893
Period size: 227 Copynumber: 2.0 Consensus size: 227
6545 ATATATTTTT
6555 AAAATTTTTGTATATAAAATTGTATAATATATATAATTGTATAAAACTGGCCTAAATCCCCTGTA
1 AAAATTTTTGTATATAAAATTGTATAATATATATAATTGTATAAAACTGGCCTAAATCCCCTGTA
6620 ATAGTTTTTTTAACTCAAATTCGTAATTGTTTTCTAGTATTATAAAACATTTATTTTTCGTTGGG
66 ATAGTTTTTTTAACTCAAATTCGTAATTGTTTTCTAGTATTATAAAACATTTATTTTTCGTTGGG
6685 GATAAACCAGTGTAAGCAATGAACAAATAAAATAACGAAGAAATTAAAAAGATCGAACACATAAA
131 GATAAACCAGTGTAAGCAATGAACAAATAAAATAACGAAGAAATTAAAAAGATCGAACACATAAA
*
6750 TTTTATGTAAAAAAAATTTTCTGAAAAGGATA
196 TTTTACGTAAAAAAAATTTTCTGAAAAGGATA
*
6782 AAAATTTTTGTATATAAAATTGTATAATATATATAATTGTATAAAACTGGCCTAAATCTCCTGTA
1 AAAATTTTTGTATATAAAATTGTATAATATATATAATTGTATAAAACTGGCCTAAATCCCCTGTA
6847 ATAGTTTTTTTAACTCAAATTCGTAATTGTTTTCTAGTATTATAAAACATTTATTTTTCGTTGGG
66 ATAGTTTTTTTAACTCAAATTCGTAATTGTTTTCTAGTATTATAAAACATTTATTTTTCGTTGGG
*
6912 GATAAACCAGTGTAAGCAATGAACAAATAAAATAACGAAGAAATTAAAAAGTTCGAACACATAAA
131 GATAAACCAGTGTAAGCAATGAACAAATAAAATAACGAAGAAATTAAAAAGATCGAACACATAAA
6977 TTTTACGTAAAAAAAATTTTCTGAAAAGGATA
196 TTTTACGTAAAAAAAATTTTCTGAAAAGGATA
7009 AAAATT
1 AAAATT
7015 ATGGACAAAA
Statistics
Matches: 230, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
227 230 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (227 bp):
AAAATTTTTGTATATAAAATTGTATAATATATATAATTGTATAAAACTGGCCTAAATCCCCTGTA
ATAGTTTTTTTAACTCAAATTCGTAATTGTTTTCTAGTATTATAAAACATTTATTTTTCGTTGGG
GATAAACCAGTGTAAGCAATGAACAAATAAAATAACGAAGAAATTAAAAAGATCGAACACATAAA
TTTTACGTAAAAAAAATTTTCTGAAAAGGATA
Found at i:21498 original size:12 final size:12
Alignment explanation
Indices: 21481--21505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21471 ATGAACTAAC
21481 AGAAAAAAAAAA
1 AGAAAAAAAAAA
21493 AGAAAAAAAAAA
1 AGAAAAAAAAAA
21505 A
1 A
21506 AGGAAATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:21501 original size:13 final size:13
Alignment explanation
Indices: 21483--21507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21473 GAACTAACAG
21483 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
21496 AAAAAAAAAAAG
1 AAAAAAAAAAAG
21508 GAAATTCAAT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:23659 original size:58 final size:59
Alignment explanation
Indices: 23593--23706 Score: 203
Period size: 58 Copynumber: 1.9 Consensus size: 59
23583 TTAGCTTTAC
* *
23593 AGTGTTATTCTTGCAGCTATATAATTTCATTTTGCTAGTTAGATTTAAG-AATTAACAA
1 AGTGTTATTCTTGCAGCTACATAATTTCACTTTGCTAGTTAGATTTAAGAAATTAACAA
23651 AGTGTTATTCTTGCAGCTACATAATTTCACTTTGCTAGTTAGATTTAAGAAATTAA
1 AGTGTTATTCTTGCAGCTACATAATTTCACTTTGCTAGTTAGATTTAAGAAATTAA
23707 AATTTCTTAC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
58 47 0.89
59 6 0.11
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (59 bp):
AGTGTTATTCTTGCAGCTACATAATTTCACTTTGCTAGTTAGATTTAAGAAATTAACAA
Found at i:24508 original size:21 final size:21
Alignment explanation
Indices: 24482--24522 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
24472 TCAAAATGAC
24482 ATAATTTT-ACCTTTTAACTTA
1 ATAATTTTGA-CTTTTAACTTA
24503 ATAATTTTGACTTTTAACTT
1 ATAATTTTGACTTTTAACTT
24523 TAAAAAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAATTTTGACTTTTAACTTA
Found at i:24991 original size:20 final size:20
Alignment explanation
Indices: 24968--25016 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
24958 TAAAAATTTG
24968 AAAAAAAAAAAACAAAATAT
1 AAAAAAAAAAAACAAAATAT
* ** **
24988 AAAAAAGAAGGACTGAATAT
1 AAAAAAAAAAAACAAAATAT
25008 AAAAAAAAA
1 AAAAAAAAA
25017 GATAAAAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (20 bp):
AAAAAAAAAAAACAAAATAT
Found at i:25307 original size:12 final size:12
Alignment explanation
Indices: 25290--25315 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25280 TAAATTAAAC
25290 ATTTATAAATAT
1 ATTTATAAATAT
25302 ATTTATAAATAT
1 ATTTATAAATAT
25314 AT
1 AT
25316 GAATAAATTT
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):
ATTTATAAATAT
Found at i:28016 original size:11 final size:11
Alignment explanation
Indices: 28000--28027 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
27990 TTTGTAGGTC
28000 AAATAATATTA
1 AAATAATATTA
28011 AAATAATATTA
1 AAATAATATTA
28022 AAATAA
1 AAATAA
28028 CCTCCACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATATTA
Found at i:29562 original size:22 final size:23
Alignment explanation
Indices: 29537--29579 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
29527 AAAATAAAAG
29537 ATTTAATT-AGAAAT-AAAAGTTT
1 ATTTAATTGA-AAATCAAAAGTTT
*
29559 ATTTCATTGAAAATCAAAAGT
1 ATTTAATTGAAAATCAAAAGT
29580 CAAAAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (23 bp):
ATTTAATTGAAAATCAAAAGTTT
Found at i:35645 original size:25 final size:25
Alignment explanation
Indices: 35617--35692 Score: 61
Period size: 25 Copynumber: 3.1 Consensus size: 25
35607 AAGAAACTAA
35617 AAATTTTATGTTAAGTAATTGAGAT
1 AAATTTTATGTTAAGTAATTGAGAT
* * * *
35642 AAATTATGAAAGTTCA-TAACT-A-A-
1 AAATT-T-TATGTTAAGTAATTGAGAT
*
35665 AAATATTATGTTAAGTAATTGAGAT
1 AAATTTTATGTTAAGTAATTGAGAT
35690 AAA
1 AAA
35693 ATTATGAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 12
0.63 0.16 0.21
Matches are distributed among these distances:
21 5 0.14
22 5 0.14
23 5 0.14
24 2 0.06
25 9 0.25
26 5 0.14
27 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (25 bp):
AAATTTTATGTTAAGTAATTGAGAT
Found at i:35667 original size:48 final size:49
Alignment explanation
Indices: 35611--35721 Score: 190
Period size: 48 Copynumber: 2.3 Consensus size: 49
35601 TTATATAAGA
35611 AACTAAAAATTTTATGTTAAGTAATTGAGAT-AAATTATGAAAGT-TCAT
1 AACTAAAAATTTTATGTTAAGTAATTGAGATAAAATTATGAAA-TATCAT
*
35659 AACTAAAAATATTATGTTAAGTAATTGAGATAAAATTATGAAATATCAT
1 AACTAAAAATTTTATGTTAAGTAATTGAGATAAAATTATGAAATATCAT
35708 AACTAAAAATTTTA
1 AACTAAAAATTTTA
35722 AATTAAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
48 31 0.53
49 28 0.47
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (49 bp):
AACTAAAAATTTTATGTTAAGTAATTGAGATAAAATTATGAAATATCAT
Found at i:36002 original size:21 final size:20
Alignment explanation
Indices: 35963--36002 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
35953 TTATAATTAT
35963 AAAAATTCAAATAATTTTTA
1 AAAAATTCAAATAATTTTTA
35983 AAAACATT-AAATAGATTTTT
1 AAAA-ATTCAAATA-ATTTTT
36003 GAGTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (20 bp):
AAAAATTCAAATAATTTTTA
Found at i:36049 original size:19 final size:19
Alignment explanation
Indices: 36021--36073 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
36011 TCCACATTTA
*
36021 ATTTTATATAATTTTTAAT
1 ATTTTTTATAATTTTTAAT
* *
36040 ATTTTTTATAACTTCTAAT
1 ATTTTTTATAATTTTTAAT
*
36059 -TTTTATTATTATTTT
1 ATTTT-TTATAATTTT
36074 GAAGCCATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTTTATAATTTTTAAT
Found at i:36701 original size:19 final size:17
Alignment explanation
Indices: 36677--36711 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
36667 AAATAACAAA
36677 TTTAAAATATAGATATATG
1 TTTAAAA-ATA-ATATATG
36696 TTTAAAAATAATATAT
1 TTTAAAAATAATATAT
36712 AATAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
TTTAAAAATAATATATG
Found at i:37409 original size:13 final size:13
Alignment explanation
Indices: 37391--37440 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
37381 TCTAGCATTG
*
37391 TTTTTAAGAAATA
1 TTTTTAAGAAGTA
*
37404 TTTTTAAGAAGTG
1 TTTTTAAGAAGTA
*
37417 TTTTGAA-AAGTA
1 TTTTTAAGAAGTA
*
37429 TTTTTAAAAAGT
1 TTTTTAAGAAGT
37441 TTGATTTAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (13 bp):
TTTTTAAGAAGTA
Found at i:37823 original size:17 final size:18
Alignment explanation
Indices: 37803--37840 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
37793 TTAACATTAC
*
37803 TTTTA-ATTTAAAATACT
1 TTTTATATTAAAAATACT
*
37820 TTTTATATTAAAAATGCT
1 TTTTATATTAAAAATACT
37838 TTT
1 TTT
37841 AAAAATATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTTATATTAAAAATACT
Found at i:37841 original size:17 final size:16
Alignment explanation
Indices: 37800--37842 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
37790 TGTTTAACAT
*
37800 TACTTTTAATTTAAAA
1 TACTTTTAATTAAAAA
37816 TACTTTTTATATTAAAAA
1 TAC-TTTTA-ATTAAAAA
*
37834 TGCTTTTAA
1 TACTTTTAA
37843 AAATATCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.17
17 10 0.43
18 9 0.39
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (16 bp):
TACTTTTAATTAAAAA
Found at i:45408 original size:11 final size:13
Alignment explanation
Indices: 45389--45423 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
45379 TTTTGACAAG
*
45389 GCACACACACCTT
1 GCACACACACTTT
45402 GCACACACACTTT
1 GCACACACACTTT
45415 GCACACACA
1 GCACACACA
45424 GACGTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.43, G:0.09, T:0.14
Consensus pattern (13 bp):
GCACACACACTTT
Found at i:50363 original size:39 final size:40
Alignment explanation
Indices: 50277--50363 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 40
50267 CTCTGGTATT
* *
50277 GTGACATTGGAGTCAATAAGAGTAATTTGTCCTCGATGTC
1 GTGACATTGAAGTCAATAAGAGTAAATTGTCCTCGATGTC
** *
50317 GCAACATTGAAGTC-ATAAGGGTAAATTGTCCTC-AGTGTC
1 GTGACATTGAAGTCAATAAGAGTAAATTGTCCTCGA-TGTC
50356 GTGACATT
1 GTGACATT
50364 AGGAGGTCAG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.03
39 27 0.69
40 11 0.28
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
GTGACATTGAAGTCAATAAGAGTAAATTGTCCTCGATGTC
Found at i:62031 original size:16 final size:17
Alignment explanation
Indices: 62012--62045 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
62002 TATGTTGTAT
62012 TAAAAATA-TTAAAATA
1 TAAAAATATTTAAAATA
*
62028 TAAATATATTTAAAATA
1 TAAAAATATTTAAAATA
62045 T
1 T
62046 TGAGCTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATATTTAAAATA
Found at i:62367 original size:24 final size:24
Alignment explanation
Indices: 62340--62391 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
62330 TTTTTTACTG
*
62340 TTTTAATTGCTATTTTGGTGCTT-T
1 TTTTAATTACTATTTTGGTG-TTGT
**
62364 TTTTTTTTACTATTTTGGTGTTGT
1 TTTTAATTACTATTTTGGTGTTGT
62388 TTTT
1 TTTT
62392 GCTATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.10, C:0.06, G:0.15, T:0.69
Consensus pattern (24 bp):
TTTTAATTACTATTTTGGTGTTGT
Found at i:62400 original size:23 final size:24
Alignment explanation
Indices: 62349--62402 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
62339 GTTTTAATTG
* **
62349 CTATTTTGGTGCTTTTTTTTTTTA
1 CTATTTTGGTGCTTGTTTTTGCTA
62373 CTATTTTGGTG-TTGTTTTTGCTA
1 CTATTTTGGTGCTTGTTTTTGCTA
*
62396 TTATTTT
1 CTATTTT
62403 TTGTTACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.09, C:0.07, G:0.15, T:0.69
Consensus pattern (24 bp):
CTATTTTGGTGCTTGTTTTTGCTA
Found at i:62402 original size:12 final size:12
Alignment explanation
Indices: 62387--62431 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
62377 TTTGGTGTTG
62387 TTTTTGCTATTA
1 TTTTTGCTATTA
* *
62399 TTTTTTGTTACTA
1 -TTTTTGCTATTA
*
62412 TTTTTGCTATCA
1 TTTTTGCTATTA
62424 TTTTTGCT
1 TTTTTGCT
62432 GCTGTTTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (12 bp):
TTTTTGCTATTA
Found at i:62405 original size:13 final size:13
Alignment explanation
Indices: 62387--62428 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
62377 TTTGGTGTTG
62387 TTTTTGCTATTAT
1 TTTTTGCTATTAT
* *
62400 TTTTTGTTACTA-
1 TTTTTGCTATTAT
*
62412 TTTTTGCTATCAT
1 TTTTTGCTATTAT
62425 TTTT
1 TTTT
62429 GCTGCTGTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.14, C:0.10, G:0.07, T:0.69
Consensus pattern (13 bp):
TTTTTGCTATTAT
Found at i:65378 original size:4 final size:4
Alignment explanation
Indices: 65369--65434 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
65359 AAATAAACGG
* * * *
65369 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GCAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
65419 G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
65435 GTAATGTGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.79
5 8 0.15
ACGTcount: A:0.64, C:0.02, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:65391 original size:17 final size:17
Alignment explanation
Indices: 65369--65401 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
65359 AAATAAACGG
65369 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
65386 GAAAGAAAGAAAGGAA
1 GAAAGAAAGAAAGGAA
65402 GCAGGAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Done.