Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012051.1 Kokia drynarioides strain JFW-HI SEQ_127049, 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: 31368
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2836 original size:30 final size:29
Alignment explanation
Indices: 2802--3034 Score: 210
Period size: 30 Copynumber: 7.9 Consensus size: 29
2792 ATTCAAGGTC
*
2802 AAAATGTAATTTTGGAAAAGTTTAGGTGTA
1 AAAATGTAATTTTGGAAAAGTTTAGG-GTT
2832 AAAATGTAATTTTAGG-AAAGTTT-GGGTT
1 AAAATGTAATTTT-GGAAAAGTTTAGGGTT
* ** *
2860 AAAATGTGATTTTGGTGAAGTTCAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTT
* * *
2889 AAAATGCT-ATTTTGTAGAAGTTTAAGGGTC
1 AAAATG-TAATTTTGGAAAAGTTT-AGGGTT
*
2919 AAAATGCAATTTTGGAAAAGTTTAGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTAG-GGTT
*
2949 AAAATGTAA-TTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT
2978 AAAATGTAATTTT--AAAGTAGTTTGAGGGTT
1 AAAATGTAATTTTGGAAA--AGTTT-AGGGTT
* * *
3008 AAAATATGATTTTTTG-AAAGTTTAGGG
1 AAAATGT-AATTTTGGAAAAGTTTAGGG
3035 ACCTTTTGGG
Statistics
Matches: 171, Mismatches: 18, Indels: 29
0.78 0.08 0.13
Matches are distributed among these distances:
27 2 0.01
28 22 0.13
29 56 0.33
30 82 0.48
31 7 0.04
32 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTT
Found at i:2940 original size:59 final size:58
Alignment explanation
Indices: 2798--3012 Score: 233
Period size: 59 Copynumber: 3.7 Consensus size: 58
2788 GAGAATTCAA
*
2798 GGTCAAAATGTAATTTTGGAAAAGTTTAGGTGTAAAAATGTAATTT-TAGGAAAGTTT--G
1 GGTCAAAATGTAATTTTGGAAAAGTTTAGG-GTTAAAATGTAATTTGTA-G-AAGTTTAAG
* * ** * *
2856 GGTTAAAATGTGATTTTGGTGAAGTTCAGGGTTAAAATGCTATTTTGTAGAAGTTTAAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATG-TAATTTGTAGAAGTTTAAG
* * *
2915 GGTCAAAATGCAATTTTGGAAAAGTTTAGAGGTTAAAATGTAATTTGGAAAAGTTTAAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTGTAGAAGTTTAAG
2974 GGTCAAAATGTAATTTT--AAAGTAGTTTGAGGGTTAAAAT
1 GGTCAAAATGTAATTTTGGAAA--AGTTT-AGGGTTAAAAT
3013 ATGATTTTTT
Statistics
Matches: 132, Mismatches: 17, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
57 17 0.13
58 31 0.23
59 72 0.55
60 12 0.09
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
GGTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTGTAGAAGTTTAAG
Found at i:3576 original size:17 final size:17
Alignment explanation
Indices: 3542--3575 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3532 CAAAAACTCC
3542 TCTCTTCTCTCTCTTTT
1 TCTCTTCTCTCTCTTTT
3559 TCTCTTCTCTCT-TTTT
1 TCTCTTCTCTCTCTTTT
3575 T
1 T
3576 TGAGTGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TCTCTTCTCTCTCTTTT
Found at i:3641 original size:20 final size:21
Alignment explanation
Indices: 3592--3642 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
3582 AGTTTCTCCG
3592 GCGTCGACTACTCCCGCCGAC
1 GCGTCGACTACTCCCGCCGAC
*
3613 GGGCGTCGACTACTCCCGCCGTC
1 --GCGTCGACTACTCCCGCCGAC
3636 -CGTCGAC
1 GCGTCGAC
3643 CACCATTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.26
23 20 0.74
ACGTcount: A:0.12, C:0.45, G:0.27, T:0.16
Consensus pattern (21 bp):
GCGTCGACTACTCCCGCCGAC
Found at i:3788 original size:95 final size:95
Alignment explanation
Indices: 3617--3789 Score: 310
Period size: 95 Copynumber: 1.8 Consensus size: 95
3607 GCCGACGGGC
3617 GTCGACTACTCCCGCCGTCCGTCGACCACCATTGGTTGCCACCATCGTCCCCGTCGCCACCATCC
1 GTCGACTACTCCCGCCGTCCGTCGACCACCATTGGTTGCCACCATCGTCCCCGTCGCCACCATCC
***
3682 GGGGNCTTTTTTTGAGTGAGTTTCTCCGGT
66 GGGGTAATTTTTTGAGTGAGTTTCTCCGGT
*
3712 GTCGACTACTCCCGCCGTCCGTCGACCACCGTTGGTTGCCACCATCGTCCCCGTCGCCACCATCC
1 GTCGACTACTCCCGCCGTCCGTCGACCACCATTGGTTGCCACCATCGTCCCCGTCGCCACCATCC
3777 GGGGTAATTTTTT
66 GGGGTAATTTTTT
3790 TCTTTTAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.12, C:0.38, G:0.23, T:0.27
Consensus pattern (95 bp):
GTCGACTACTCCCGCCGTCCGTCGACCACCATTGGTTGCCACCATCGTCCCCGTCGCCACCATCC
GGGGTAATTTTTTGAGTGAGTTTCTCCGGT
Found at i:4008 original size:6 final size:6
Alignment explanation
Indices: 3997--4028 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3987 ATTATTTTCG
*
3997 AAATAA AAATAA AAATAA AAATAA AAGTAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AA
4029 CTAATATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:5042 original size:48 final size:48
Alignment explanation
Indices: 4970--5092 Score: 174
Period size: 48 Copynumber: 2.6 Consensus size: 48
4960 GAATTAGTCT
* * *
4970 ACTTCTCAGTATCTCATTAGGAAGATGACCGCTTTATTGTTTTAATCC
1 ACTTCTCAGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTAACCC
* * * * *
5018 ACTTCTCTGTATCTCATCAAGAAGACGATCGCTTTATTGCTTTGACCC
1 ACTTCTCAGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTAACCC
5066 ACTTCTCAGTATCTCATCAGGAAGATG
1 ACTTCTCAGTATCTCATCAGGAAGATG
5093 GGTTTGAAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (48 bp):
ACTTCTCAGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTAACCC
Found at i:5405 original size:39 final size:39
Alignment explanation
Indices: 5231--5423 Score: 165
Period size: 39 Copynumber: 4.9 Consensus size: 39
5221 TAGATGGCCA
* *
5231 CAATCCGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTG
1 CAATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGATG
* * * *
5270 CAATCTGCCCCAGGCTCGGTGGTAAGAGATTGACT-GATGG
1 CAATCTGCCCCAAGCTC-GAGGTAAGAGATCGAATGGAT-G
** * *
5310 TGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGATG
1 CAATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGATG
* * * ** *
5349 CAATCTGCCTCAGGCTCGAGGTAAGAGATTGGCT-TATG
1 CAATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGATG
* * * *
5387 CTGATCTACCCCAAGCTCGGGGTAAAAGATCGAATGG
1 C-AATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGG
5424 CTGTAATTTA
Statistics
Matches: 116, Mismatches: 33, Indels: 9
0.73 0.21 0.06
Matches are distributed among these distances:
38 4 0.03
39 80 0.69
40 32 0.28
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (39 bp):
CAATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGATG
Found at i:5411 original size:78 final size:77
Alignment explanation
Indices: 5238--5501 Score: 321
Period size: 78 Copynumber: 3.4 Consensus size: 77
5228 CCACAATCCG
* * * * * *
5238 CCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCGGTGGTAAGAGATTGA
1 CCCCAAGCTCGGGGTAAAAGATCGAATGGATGCAATCTGCCTCAGGCTC-GAGGTAAGAGATTGG
*
5303 CTGATGGTGATCTG
65 CTGAT-GTGATCTA
5317 CCCCAAGCTCGGGGTAAAAGATCGAATGGATGCAATCTGCCTCAGGCTCGAGGTAAGAGATTGGC
1 CCCCAAGCTCGGGGTAAAAGATCGAATGGATGCAATCTGCCTCAGGCTCGAGGTAAGAGATTGGC
*
5382 TTATGCTGATCTA
66 TGATG-TGATCTA
* * * * * *
5395 CCCCAAGCTCGGGGTAAAAGATCGAATGGCTGTAATTTACCTTAGGCTCAAGGTAAGAGATTGGC
1 CCCCAAGCTCGGGGTAAAAGATCGAATGGATGCAATCTGCCTCAGGCTCGAGGTAAGAGATTGGC
5460 TGATAGTGATCTA
66 TGAT-GTGATCTA
* * * * *
5473 CCACAGGCTCGGGATAAGAGATCGGATGG
1 CCCCAAGCTCGGGGTAAAAGATCGAATGG
5502 CCACAATCTG
Statistics
Matches: 163, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
77 1 0.01
78 116 0.71
79 46 0.28
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (77 bp):
CCCCAAGCTCGGGGTAAAAGATCGAATGGATGCAATCTGCCTCAGGCTCGAGGTAAGAGATTGGC
TGATGTGATCTA
Found at i:5528 original size:156 final size:157
Alignment explanation
Indices: 5238--5536 Score: 350
Period size: 156 Copynumber: 1.9 Consensus size: 157
5228 CCACAATCCG
* * * **
5238 CCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCTGCCCCAGGCTCGGTGGTAAGAGATTGA
1 CCCCAAGCTCGAGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGAAGGTAAGAGATTGA
* * * * ** *
5303 CTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGATGCAATCTGCCTCAGGCTCGA
66 CTGATAGTGATCTACCACAAGCTCGGGATAAAAGATCGAATGGACACAATCTGCCTCAGGATCGA
5368 GGTAAGAGATTGGCTTATGCTGATCTA
131 GGTAAGAGATTGGCTTATGCTGATCTA
* * * ** *
5395 CCCCAAGCTCGGGGTAAAAGATCGAATGGCTGTAATTTACCTTAGGCTC-AAGGTAAGAGATTGG
1 CCCCAAGCTCGAGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGAAGGTAAGAGATTGA
* * * * * *
5459 CTGATAGTGATCTACCACAGGCTCGGGATAAGAGATCGGATGGCCACAATCTGACC-CGGGATTG
66 CTGATAGTGATCTACCACAAGCTCGGGATAAAAGATCGAATGGACACAATCTG-CCTCAGGATCG
*
5523 GGGTAAGAGATTGG
130 AGGTAAGAGATTGG
5537 AATCTTCAAT
Statistics
Matches: 116, Mismatches: 25, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
156 73 0.63
157 43 0.37
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (157 bp):
CCCCAAGCTCGAGGTAAAAGATCGAATGGCTGCAATCTACCCCAGGCTCGAAGGTAAGAGATTGA
CTGATAGTGATCTACCACAAGCTCGGGATAAAAGATCGAATGGACACAATCTGCCTCAGGATCGA
GGTAAGAGATTGGCTTATGCTGATCTA
Found at i:5999 original size:50 final size:50
Alignment explanation
Indices: 5811--6056 Score: 187
Period size: 50 Copynumber: 4.9 Consensus size: 50
5801 CCATCTTGTT
* * * ** *
5811 TTCTAAGGTACTAAGTTCGCCGGTGCGGCCTCAACCTTTTTCGTCACATC
1 TTCTAAGGTACCAAGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATC
* * * * * *
5861 TTTTACGGTGCCGAA-TTCACCGTCGTGGCCTCAATCC-TTCCCTTCATC-TC
1 TTCTAAGGTACC-AAGTTCACCGTTGCGGCCTCAA-CCTTTCCCATCA-CATC
* ** * * * *
5911 TTC-ATGGTACCGGGTTCACCGTAGCAGCCTTAATCTTTCCCATCACATC
1 TTCTAAGGTACCAAGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATC
** **
5960 TTCTAAGGTACCAAGTTCGTCGTTGCGGCCTCAACCTTTCCTTTCACATC
1 TTCTAAGGTACCAAGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATC
* *
6010 TTCTAAGGTACCAAATTCACCGTCGCGGCCTCAATCC-TTCCCTATCA
1 TTCTAAGGTACCAAGTTCACCGTTGCGGCCTCAA-CCTTTCCC-ATCA
6057 AACTTGTAGA
Statistics
Matches: 148, Mismatches: 39, Indels: 17
0.73 0.19 0.08
Matches are distributed among these distances:
48 2 0.01
49 34 0.23
50 102 0.69
51 10 0.07
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.32
Consensus pattern (50 bp):
TTCTAAGGTACCAAGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATC
Found at i:7001 original size:13 final size:13
Alignment explanation
Indices: 6985--7014 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6975 CTTTTTTTTA
6985 TTTTCATTTTCCT
1 TTTTCATTTTCCT
*
6998 TTTTCTTTTTCCT
1 TTTTCATTTTCCT
7011 TTTT
1 TTTT
7015 TCTTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCATTTTCCT
Found at i:12638 original size:25 final size:25
Alignment explanation
Indices: 12610--12673 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
12600 CAATTTATTG
*
12610 ATAAAATTAAATAAAATAACTAAGC
1 ATAAAATTAAATAAAAAAACTAAGC
* *
12635 ATAAAAGTAAATGAAAAAAATTAAGC
1 ATAAAATTAAAT-AAAAAAACTAAGC
* *
12661 ATAAGATAAAATA
1 ATAAAATTAAATA
12674 CGAGATTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.22
Consensus pattern (25 bp):
ATAAAATTAAATAAAAAAACTAAGC
Found at i:12748 original size:30 final size:30
Alignment explanation
Indices: 12709--13085 Score: 447
Period size: 30 Copynumber: 12.6 Consensus size: 30
12699 AAATAAAAAA
* *
12709 GGGTTAAAATATAATTTTGGAAAAGTTTGG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
*
12739 GGGTAAAAATGTAATTTTAGG-AAAG-TTAG
1 GGGTTAAAATGTAATTTT-GGAAAAGTTTAG
* * **
12768 GGGTTAAAATGTGATTATGGTTAAGTTTA-
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
* * * * *
12797 GGGTTAAAATATTATTTTAGAGAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
* *
12827 GGGTCAAAATGAAATTTTGGAAAAGTTTAG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
* * ** *
12857 GGGTCAAAATGTAACTTTGGAAAAGCATAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
*
12887 GGCTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
* ** *
12917 GGGTAAAAAAATAATTTTGGAAAGGTTTAG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
12947 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
*
12977 GGGTTAAAATGTAATTTTGGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
13007 GGGTTAAAA-GTTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATG-TAATTTTGGAAAAGTTTAG
* *
13037 GGGTTAAAATGTAATTTTAGAAAAATTTAG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
* *
13067 GGGTCAAAATGTATTTTTG
1 GGGTTAAAATGTAATTTTG
13086 ATGTAGTTTG
Statistics
Matches: 294, Mismatches: 47, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
28 2 0.01
29 45 0.15
30 244 0.83
31 3 0.01
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTAG
Found at i:19293 original size:41 final size:39
Alignment explanation
Indices: 19256--19359 Score: 129
Period size: 41 Copynumber: 2.6 Consensus size: 39
19246 TTTCGGTGGA
*
19256 AGTCTT-CTAGGTATCGGTAGAACTGATGTTGTTTCGGT
1 AGTCTTGCAAGGTATCGGTAGAACTGATGTTGTTTCGGT
*
19294 AGTTTTGGCCAAGGTATCGGTAGAACTGATGTTGTTTCGGT
1 AGTCTT-G-CAAGGTATCGGTAGAACTGATGTTGTTTCGGT
* *
19335 AGTTTTGGCGAAGGTATCAGTAGAA
1 AGTCTT-GC-AAGGTATCGGTAGAA
19360 GTCCTAAGCC
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
38 5 0.08
40 1 0.02
41 53 0.90
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.36
Consensus pattern (39 bp):
AGTCTTGCAAGGTATCGGTAGAACTGATGTTGTTTCGGT
Found at i:21476 original size:2 final size:2
Alignment explanation
Indices: 21463--21708 Score: 101
Period size: 2 Copynumber: 124.0 Consensus size: 2
21453 ATCTAAAATT
* * *
21463 TA TA TG TA TA TA TA TA TA TA TA GA TA TA TA TA -A CA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * * * * * * *
21505 TG TA AA AA AA TA TA TA TG TT TA TA -A AA TA GA TA TG TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
21546 TA TA TG GA TA TA TA TA -A TA GTA TA TA TG TA AA AA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
21588 TA TA TA TA TA TA TA TA TA -A AA TA GA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
21629 -A AA TA GTA TA TA TG TA TA AA AA TA TA TG GA TA TA -A AA T- TGA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* * * *
21670 TA TG TA TA TA TA TA TA TA TA AA AA TA GTA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
21709 AAATATACAA
Statistics
Matches: 184, Mismatches: 48, Indels: 24
0.72 0.19 0.09
Matches are distributed among these distances:
1 7 0.04
2 169 0.92
3 8 0.04
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (2 bp):
TA
Found at i:21572 original size:69 final size:67
Alignment explanation
Indices: 21445--21715 Score: 241
Period size: 67 Copynumber: 4.0 Consensus size: 67
21435 TTTTAATAAA
* ** * *
21445 ATATATGTATCTAAAATTTATATGTATATATATATATATAGATATATATAACAGTATATATGTAA
1 ATATATGTATATAAAATAGATATG--TATA-A-ATATATGGATATATATAATAGTATATATGTAA
21510 AAAAAT
62 AAAAAT
*
21516 ATATATGTTTATAAAATAGATATGTATAAATATATGGATATATATAATAGTATATATGTAAAAAA
1 ATATATGTATATAAAATAGATATGTATAAATATATGGATATATATAATAGTATATATGTAAAAAA
21581 AT
66 AT
* * * ** * ** * *
21583 ATATATATATAT-ATATATATATAAAATAGATATGTATATATATATAAAATAGTATATATGT-AT
1 ATATATGTATATAAAATAGATAT-GTATA-A-ATATATGGATATATATAATAGTATATATGTAAA
21646 AAAA-
63 AAAAT
* * * * *
21650 ATATATGGATATAAAATTGATATGTATATATATAT--ATATA-AAAATAGTATATATGT-ATAAA
1 ATATATGTATATAAAATAGATATGTATAAATATATGGATATATATAATAGTATATATGTAAAAAA
21711 AT
66 AT
21713 ATA
1 ATA
21716 CAATTTGTAA
Statistics
Matches: 169, Mismatches: 26, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
62 22 0.13
63 8 0.05
65 5 0.03
66 8 0.05
67 62 0.37
68 14 0.08
69 30 0.18
71 20 0.12
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (67 bp):
ATATATGTATATAAAATAGATATGTATAAATATATGGATATATATAATAGTATATATGTAAAAAA
AT
Found at i:21580 original size:67 final size:66
Alignment explanation
Indices: 21445--21715 Score: 246
Period size: 69 Copynumber: 4.0 Consensus size: 66
21435 TTTTAATAAA
* ** * *
21445 ATATATGTATCTAAAATTTATATGTATATATATATATATAGATATATATAACAGTATATATGTAA
1 ATATATGTATATAAAATAGATATG--TATA-A-ATATATAGATATATAAAATAGTATATATGT-A
21510 AAAAAT
61 AAAAAT
* * *
21516 ATATATGTTTATAAAATAGATATGTATAAATATATGGATATATATAATAGTATATATGTAAAAAA
1 ATATATGTATATAAAATAGATATGTATAAATATATAGATATATAAAATAGTATATATGTAAAAAA
21581 -
66 T
* * * ** * * *
21581 ATATATATATATATATATATATATAAAATAGATATGTATATATATATAAAATAGTATATATGTAT
1 ATATATGTATATA-AAATAGATAT-GTATA-A-ATATATAGATATATAAAATAGTATATATGTAA
21646 AAAA-
62 AAAAT
* * * *
21650 ATATATGGATATAAAATTGATATGTAT--ATATATATATATA-AAAATAGTATATATGTATAAAA
1 ATATATGTATATAAAATAGATATGTATAAATATATAGATATATAAAATAGTATATATGTAAAAAA
21712 T
66 T
21713 ATA
1 ATA
21716 CAATTTGTAA
Statistics
Matches: 170, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
62 22 0.13
63 15 0.09
65 11 0.06
66 14 0.08
67 33 0.19
68 9 0.05
69 46 0.27
71 20 0.12
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (66 bp):
ATATATGTATATAAAATAGATATGTATAAATATATAGATATATAAAATAGTATATATGTAAAAAA
T
Found at i:21620 original size:23 final size:24
Alignment explanation
Indices: 21469--21708 Score: 100
Period size: 23 Copynumber: 10.4 Consensus size: 24
21459 AATTTATATG
*
21469 TATATATATATATAT-AGATA-TA
1 TATATATATATATATAAAATAGTA
* * * *
21491 TATAACAGTATATATGTAAAAAAATA
1 TAT-ATA-TATATATATAAAATAGTA
* *
21517 TATATGT-T-TATAAAATAGATATGTA
1 TATATATATATATATAA-A-ATA-GTA
* *
21542 TAAATATATGGATATATATAATAGTA
1 TATATATAT--ATATATAAAATAGTA
* * * * *
21568 TATATGTAAAAAAAT-ATATA-TA
1 TATATATATATATATAAAATAGTA
21590 TATATATATATATATAAAATAG-A
1 TATATATATATATATAAAATAGTA
*
21613 TATGTATATATATATAAAATAG--
1 TATATATATATATATAAAATAGTA
*
21635 --TATATATGTATA-AAAATA-TA
1 TATATATATATATATAAAATAGTA
** * * *
21655 TGGATATA-AAAT-TGATAT-GTA
1 TATATATATATATATAAAATAGTA
21676 TATATATATATATA-AAAATAGTA
1 TATATATATATATATAAAATAGTA
*
21699 TATATGTATA
1 TATATATATA
21709 AAATATACAA
Statistics
Matches: 156, Mismatches: 40, Indels: 43
0.65 0.17 0.18
Matches are distributed among these distances:
19 6 0.04
20 10 0.06
21 13 0.08
22 32 0.21
23 45 0.29
24 15 0.10
25 11 0.07
26 15 0.10
27 3 0.02
28 1 0.01
29 5 0.03
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
TATATATATATATATAAAATAGTA
Found at i:30105 original size:3 final size:3
Alignment explanation
Indices: 30097--30151 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
30087 ATTAAGGCAT
* *
30097 AAG AAG AAG AAAG AA- AAG AAG AAG AAA AAG AAG -AG AAGG AAG AAA
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG
30142 AAG AAG AAG A
1 AAG AAG AAG A
30152 TGTTGCCCCG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:30562 original size:18 final size:18
Alignment explanation
Indices: 30536--30574 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
30526 CATGCATTTC
30536 TTTTAATTGTCATTGCAT
1 TTTTAATTGTCATTGCAT
* *
30554 TTTTTATTGTCTTTGCAT
1 TTTTAATTGTCATTGCAT
30572 TTT
1 TTT
30575 ATTTGTTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.64
Consensus pattern (18 bp):
TTTTAATTGTCATTGCAT
Found at i:30580 original size:17 final size:17
Alignment explanation
Indices: 30536--30580 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
30526 CATGCATTTC
*
30536 TTTTAATTGTCATTGCA
1 TTTTATTTGTCATTGCA
* *
30553 TTTTTTATTGTCTTTGCA
1 TTTTAT-TTGTCATTGCA
30571 TTTTATTTGT
1 TTTTATTTGT
30581 TCTAGCATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (17 bp):
TTTTATTTGTCATTGCA
Done.