Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014296.1 Kokia drynarioides strain JFW-HI SEQ_129331, 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: 110665
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:276 original size:21 final size:21
Alignment explanation
Indices: 250--289 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
240 TTTTTAATAA
250 AAAATT-ATAAAAAAAGAAATG
1 AAAATTGA-AAAAAAAGAAATG
*
271 AAAATTGAAAAAATAGAAA
1 AAAATTGAAAAAAAAGAAA
290 AGGAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATTGAAAAAAAAGAAATG
Found at i:10958 original size:31 final size:30
Alignment explanation
Indices: 10908--10965 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
10898 ATCTAAATTG
10908 TTAGATTTTTATAACTTTATGTAATTTTTAGT
1 TTAGATTTTTATAACTTTA--TAATTTTTAGT
* *
10940 TTAGTTTTTTA-AATTTTATAATTTTT
1 TTAGATTTTTATAACTTTATAATTTTT
10966 TTAAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.33
31 6 0.25
32 10 0.42
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.64
Consensus pattern (30 bp):
TTAGATTTTTATAACTTTATAATTTTTAGT
Found at i:11036 original size:30 final size:28
Alignment explanation
Indices: 10996--11051 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
10986 TATTATTTTA
* *
10996 GAATTTTTTATGATTTCAGAAAAAAAATCT
1 GAATTCTTTAT-ATTT-AAAAAAAAAATCT
11026 GAATTCTTTATATTTAAAAAAAAAAT
1 GAATTCTTTATATTTAAAAAAAAAAT
11052 TATTTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
29 4 0.17
30 10 0.42
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39
Consensus pattern (28 bp):
GAATTCTTTATATTTAAAAAAAAAATCT
Found at i:18235 original size:17 final size:17
Alignment explanation
Indices: 18193--18244 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
18183 TAATTTTTAA
*
18193 TATTTTTTCTACAATTTT
1 TATTTTTT-TACAATATT
* *
18211 TATATTTTTATAATATT
1 TATTTTTTTACAATATT
18228 TATTTTTTTACAA-ATT
1 TATTTTTTTACAATATT
18244 T
1 T
18245 TTAAAAATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 4 0.14
17 18 0.62
18 7 0.24
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTTTTACAATATT
Found at i:18240 original size:34 final size:34
Alignment explanation
Indices: 18193--18341 Score: 94
Period size: 36 Copynumber: 4.2 Consensus size: 34
18183 TAATTTTTAA
18193 TATTTTTTCTACAATTTTTATATTTTTATAATATT
1 TATTTTTT-TACAATTTTTATATTTTTATAATATT
* * *
18228 TATTTTTTTACAAATTTTTAAAAATTCTA-ACATATT
1 TATTTTTTTAC-AATTTTT-ATATTTTTATA-ATATT
* *
18264 TTTATTTTTTA-ATACTTATTTATATATTTAT-ATATT
1 TAT-TTTTTTACA-A-TT-TTTATATTTTTATAATATT
* *
18300 TTTTTAGTTTTGAGAATTTTTATA-TTTTATAAT-TT
1 TATTT--TTTT-ACAATTTTTATATTTTTATAATATT
18335 T-TTTTTT
1 TATTTTTT
18342 GTTTTTTCGA
Statistics
Matches: 92, Mismatches: 9, Indels: 29
0.71 0.07 0.22
Matches are distributed among these distances:
32 3 0.03
34 6 0.07
35 27 0.29
36 30 0.33
37 20 0.22
38 5 0.05
39 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (34 bp):
TATTTTTTTACAATTTTTATATTTTTATAATATT
Found at i:28740 original size:97 final size:97
Alignment explanation
Indices: 28556--28742 Score: 218
Period size: 96 Copynumber: 1.9 Consensus size: 97
28546 ATTTTTGAAA
* *
28556 AGGATGATTGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTCA
1 AGGATGATTGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* * * * *
28621 GAATCCGAGATGAGAGACATTGCCTTGACTTT
66 AAATCAGAAATAAAAGACATTGCCTTGACTTT
* **
28653 AGGAT-ATTCGATTAT-TCCGATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTT
1 AGGATGATT-GATTATCT-CGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTT
* *
28715 CAAAATTAGAAATAAAAGAATATTGCCT
64 CAAAATCAGAAATAAAAG-ACATTGCCT
28743 CGATTTTAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
96 42 0.56
97 33 0.44
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (97 bp):
AGGATGATTGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAATCAGAAATAAAAGACATTGCCTTGACTTT
Found at i:29127 original size:58 final size:58
Alignment explanation
Indices: 29010--29350 Score: 316
Period size: 58 Copynumber: 5.9 Consensus size: 58
29000 TCGAGGGTAG
* * * * * * * *
29010 AATGGTAATTTTGGGAAAGTTTAGGGTTAGAAATAGAA-TTTTAGACA-TTCGGGGGTAA
1 AATGGTAATTTT-GGAAAGTTTCGGGGTAAAAATGGAATTTTTGGA-AGTTTGAGAGTAA
* * * *
29068 AACGGTAATTTTTGAAAGCTTCGGGGTAAAAATGGAATTTTTGGAAGTTTGAGAATAAA
1 AATGGTAATTTTGGAAAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTTGAGAGT-AA
* * * *
29127 AATGG-AATTTTGGAAAGTTTCGGGGTCAAAATGGAATTTTAGAAAGTTTGGGAGTAA
1 AATGGTAATTTTGGAAAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTTGAGAGTAA
* * * * *
29184 AATGG-AATTTTGGAAAGTTTCTAGGTTAAAAATGTAATTTTTGGAACTTTG-GGGTAA
1 AATGGTAATTTTGGAAAGTTTC-GGGGTAAAAATGGAATTTTTGGAAGTTTGAGAGTAA
* * * * * *
29241 AATGGTAAATCTCGAAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGTAA
1 AATGGTAATTTTGGAAAGTTTCGGGGT-AAAAATGGAATTTTTGGAAGTTTGAGAGTAA
* *
29300 AATGGTAACTTTTGG-AAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTTT
1 AATGGTAA-TTTTGGAAAG-TTTCGGGGTAAAAATGGAATTTTTGGAAGTTT
29351 AGGGGTCAAA
Statistics
Matches: 233, Mismatches: 41, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
57 57 0.24
58 121 0.52
59 46 0.20
60 9 0.04
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (58 bp):
AATGGTAATTTTGGAAAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTTGAGAGTAA
Found at i:29226 original size:116 final size:115
Alignment explanation
Indices: 29010--29350 Score: 363
Period size: 116 Copynumber: 2.9 Consensus size: 115
29000 TCGAGGGTAG
* * * * *
29010 AATGGTAATTTTGGGAAAGTTT-AGGGTTAGAAATAGAATTTTAGACA-TTCGGGGGTAAAACGG
1 AATGGTAATTTT-GGAAAGTTTCAGGGTCA-AAATGGAATTTTAGAAAGTT-TGGGGTAAAATGG
* * * *
29073 TAATTTTTGAAAGCTTC-GGGGTAAAAATGGAATTTTTGGAAGTTTGAGAATAAA
63 TAATTTTGGAAAGTTTCTAGGTTAAAAATGGAATTTTTGGAAGTTTG-GAAT-AA
*
29127 AATGG-AATTTTGGAAAGTTTCGGGGTCAAAATGGAATTTTAGAAAGTTTGGGAGTAAAATGG-A
1 AATGGTAATTTTGGAAAGTTTCAGGGTCAAAATGGAATTTTAGAAAGTTTGGG-GTAAAATGGTA
* * **
29190 ATTTTGGAAAGTTTCTAGGTTAAAAATGTAATTTTTGGAACTTTGGGGTAA
65 ATTTTGGAAAGTTTCTAGGTTAAAAATGGAATTTTTGGAAGTTTGGAATAA
* * * * * *
29241 AATGGTAAATCTCGAAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGT
1 AATGGTAATTTTGGAAAGTTTCAGGGTC-AAAATGGAATTTTAGAAAGTTT-GGGGTAAAATGGT
29306 AACTTTTGG-AAGTTT-TAGGGTTAAAAATGGAATTTTTGGAAGTTT
64 AA-TTTTGGAAAGTTTCTA-GGTTAAAAATGGAATTTTTGGAAGTTT
29351 AGGGGTCAAA
Statistics
Matches: 191, Mismatches: 23, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
114 7 0.04
115 61 0.32
116 77 0.40
117 40 0.21
118 6 0.03
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (115 bp):
AATGGTAATTTTGGAAAGTTTCAGGGTCAAAATGGAATTTTAGAAAGTTTGGGGTAAAATGGTAA
TTTTGGAAAGTTTCTAGGTTAAAAATGGAATTTTTGGAAGTTTGGAATAA
Found at i:29351 original size:29 final size:29
Alignment explanation
Indices: 29061--29361 Score: 228
Period size: 29 Copynumber: 10.3 Consensus size: 29
29051 TAGACATTCG
* * * *
29061 GGGGT-AAAACGGTAATTTTTGAAAGCTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTA
29090 GGGGTAAAAATGGAATTTTTGGAAGTTT-
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
** *
29118 GAGAATAAAAATGGAA-TTTTGGAAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGG-AAGTTTA
* * *
29148 GGGGTCAAAATGGAATTTTAGAAAGTTT-
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
29176 GGGAGT-AAAATGGAA-TTTTGGAAAGTTTCTA
1 GGG-GTAAAAATGGAATTTTTGG-AAG-TT-TA
* * *
29207 -GGTTAAAAATGTAATTTTTGGAACTTT-
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* * * *
29234 GGGGT-AAAATGGTAAATCTCGAAAGTTTCA
1 GGGGTAAAAATGG-AATTTTTGGAAGTTT-A
29264 -GGGTCAAAAATGGAATTTTTGGAAGTTTA
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
* *
29293 AGGGT-AAAATGGTAACTTTTGGAAGTTTTA
1 GGGGTAAAAATGG-AATTTTTGGAAG-TTTA
*
29323 GGGTTAAAAATGGAATTTTTGGAAGTTTA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
*
29352 GGGGTCAAAA
1 GGGGTAAAAA
29362 CATAATTTCT
Statistics
Matches: 218, Mismatches: 32, Indels: 44
0.74 0.11 0.15
Matches are distributed among these distances:
27 10 0.05
28 43 0.20
29 88 0.40
30 57 0.26
31 20 0.09
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTA
Found at i:30439 original size:19 final size:19
Alignment explanation
Indices: 30403--30441 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
30393 TTTTCAGTTT
* * *
30403 TTTATTATTATTATTAATA
1 TTTATTATAATAAATAATA
30422 TTTATTATAATAAATAATA
1 TTTATTATAATAAATAATA
30441 T
1 T
30442 ATTTATTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTATTATAATAAATAATA
Found at i:31140 original size:17 final size:17
Alignment explanation
Indices: 31110--31196 Score: 93
Period size: 17 Copynumber: 5.1 Consensus size: 17
31100 TTTTAATATT
* * *
31110 AATAATTTTTAATTCAA
1 AATAAATTTAAATTTAA
*
31127 AATAAATTCAAATTTAA
1 AATAAATTTAAATTTAA
*
31144 AATAAATTTAAATTCAA
1 AATAAATTTAAATTTAA
* **
31161 CACGAATTTAAATTTAA
1 AATAAATTTAAATTTAA
*
31178 AATAAATTAAAATTTAA
1 AATAAATTTAAATTTAA
31195 AA
1 AA
31197 ATTAAAAGTT
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:32616 original size:11 final size:11
Alignment explanation
Indices: 32600--32660 Score: 61
Period size: 11 Copynumber: 5.2 Consensus size: 11
32590 TTTAGGGTTT
32600 AAGAAGAGAAA
1 AAGAAGAGAAA
32611 AAGAAGA-AAA
1 AAGAAGAGAAA
*
32621 GAAGAAGAGGAA
1 -AAGAAGAGAAA
32633 AAGAAGGAGAAGAA
1 AAGAA-GAG-A-AA
32647 AGAGAAGAGAAA
1 A-AGAAGAGAAA
32659 AA
1 AA
32661 ATGGAGATGC
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 3 0.07
11 20 0.48
12 8 0.19
13 1 0.02
14 6 0.14
15 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (11 bp):
AAGAAGAGAAA
Found at i:32623 original size:14 final size:14
Alignment explanation
Indices: 32600--32654 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
32590 TTTAGGGTTT
* *
32600 AAGAAGAGAAAAAG
1 AAGAAAAGAAGAAG
32614 AAGAAAAGAAGAAG
1 AAGAAAAGAAGAAG
* *
32628 AGGAAAAGAAGGAG
1 AAGAAAAGAAGAAG
32642 AAGAAAGAGAAGA
1 AAGAAA-AGAAGA
32655 GAAAAAATGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
14 29 0.85
15 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAGAAG
Found at i:32656 original size:14 final size:13
Alignment explanation
Indices: 32612--32661 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
32602 GAAGAGAAAA
32612 AGAAGAAAAGAAG
1 AGAAGAAAAGAAG
*
32625 AAGAGGAAAAGAAGG
1 -AGAAGAAAAGAA-G
32640 AGAAGAAAGAGAAG
1 AGAAGAAA-AGAAG
32654 AGAA-AAAA
1 AGAAGAAAA
32662 TGGAGATGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 1 0.03
13 3 0.09
14 23 0.72
15 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAGAAG
Found at i:35918 original size:23 final size:23
Alignment explanation
Indices: 35883--35938 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
35873 TAGTGCGTTT
35883 CTATATTTAGCACTCTAGTGCTC
1 CTATATTTAGCACTCTAGTGCTC
* * * *
35906 CTATGTTTTGCACTTTGGTGCTC
1 CTATATTTAGCACTCTAGTGCTC
35929 CTGA-ATTTAG
1 CT-ATATTTAG
35939 TACTTTTGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (23 bp):
CTATATTTAGCACTCTAGTGCTC
Found at i:36171 original size:23 final size:22
Alignment explanation
Indices: 36121--36171 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
36111 TAAAGTATGA
* * *
36121 ATAAGTGTAATCATAAGTGATG
1 ATAAGTGAAATCATAAGTAATC
*
36143 ACAAGTGAACATCATAAGTAATC
1 ATAAGTGAA-ATCATAAGTAATC
36166 ATAAGT
1 ATAAGT
36172 ACATGAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (22 bp):
ATAAGTGAAATCATAAGTAATC
Found at i:43650 original size:24 final size:25
Alignment explanation
Indices: 43598--43654 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
43588 ATCATTTTCA
43598 CTCAGCCTTCACTTCCTTCTCTTTT
1 CTCAGCCTTCACTTCCTTCTCTTTT
43623 -TCAGCCTTCACTTCCTT-T-TTTGT
1 CTCAGCCTTCACTTCCTTCTCTTT-T
43646 CTCAGCCTT
1 CTCAGCCTT
43655 ATCATCCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 3 0.10
23 2 0.07
24 25 0.83
ACGTcount: A:0.09, C:0.37, G:0.07, T:0.47
Consensus pattern (25 bp):
CTCAGCCTTCACTTCCTTCTCTTTT
Found at i:51677 original size:11 final size:11
Alignment explanation
Indices: 51661--51692 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
51651 ATTTGATTAA
51661 ATTGATTTGTT
1 ATTGATTTGTT
51672 ATTGATTTGTT
1 ATTGATTTGTT
51683 ATTGATTTGT
1 ATTGATTTGT
51693 ATTATTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (11 bp):
ATTGATTTGTT
Found at i:51861 original size:6 final size:6
Alignment explanation
Indices: 51844--51911 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
51834 TTTGTGATCA
* * * * *
51844 AAATTT AAAGTG AAAGTG AAATTG AAATTG AAATTG GAATTG AAAGTG
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG
*
51892 -ATTTG -AATTG TAAATTG AAA
1 AAATTG AAATTG -AAATTG AAA
51912 ATCCCTATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
5 7 0.14
6 39 0.76
7 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (6 bp):
AAATTG
Found at i:52693 original size:42 final size:42
Alignment explanation
Indices: 52643--52724 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
52633 TATCTCATGG
* *
52643 GATTCTTGATGGACCTAAATCA-AACAAAATTGAATATCACGT
1 GATTCTTGATGAACCTAAATCAGAAC-AAATTAAATATCACGT
* *
52685 GATTCTTGATGAACCTGATTCAGAACAAATTAAATATCAC
1 GATTCTTGATGAACCTAAATCAGAACAAATTAAATATCAC
52725 AGGATCACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.91
43 3 0.09
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (42 bp):
GATTCTTGATGAACCTAAATCAGAACAAATTAAATATCACGT
Found at i:72222 original size:140 final size:140
Alignment explanation
Indices: 72053--72334 Score: 546
Period size: 140 Copynumber: 2.0 Consensus size: 140
72043 AATTATAATG
72053 TGAATATGTATAAATATTAAACACGAATATTTAAAAGAAAATGCTACATATAACATAGAACGTGC
1 TGAATATGTATAAATATTAAACACGAATATTTAAAAGAAAATGCTACATATAACATAGAACGTGC
*
72118 ACGCATGCACACACAAATATAAAAGGTGTGTTTGGTTGAGTGAAAAAATGAAAGGATGAAAAGAA
66 ACGCATGCACACACAAATATAAAAGGTGTGTTTGGTTGAGTGAAAAAATGAAAAGATGAAAAGAA
72183 AGGAAATGAA
131 AGGAAATGAA
72193 TGAATATGTATAAATATTAAACACGAATATTTAAAAGAAAATGCTACATATAACATAGAACGTGC
1 TGAATATGTATAAATATTAAACACGAATATTTAAAAGAAAATGCTACATATAACATAGAACGTGC
*
72258 ACGCATGCACACACAAATATAAAGGGTGTGTTTGGTTGAGTGAAAAAATGAAAAGATGAAAAGAA
66 ACGCATGCACACACAAATATAAAAGGTGTGTTTGGTTGAGTGAAAAAATGAAAAGATGAAAAGAA
72323 AGGAAATGAA
131 AGGAAATGAA
72333 TG
1 TG
72335 TTGAATGTGC
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (140 bp):
TGAATATGTATAAATATTAAACACGAATATTTAAAAGAAAATGCTACATATAACATAGAACGTGC
ACGCATGCACACACAAATATAAAAGGTGTGTTTGGTTGAGTGAAAAAATGAAAAGATGAAAAGAA
AGGAAATGAA
Found at i:84544 original size:37 final size:37
Alignment explanation
Indices: 84494--84565 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
84484 GATACATAGT
84494 TTATTTATTAATTATGTTGTATCTATATTTTTTTAGA
1 TTATTTATTAATTATGTTGTATCTATATTTTTTTAGA
84531 TTATTTATTAATTATGTTGTATCTATATTTTTTTA
1 TTATTTATTAATTATGTTGTATCTATATTTTTTTA
84566 TAATACATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.03, G:0.07, T:0.64
Consensus pattern (37 bp):
TTATTTATTAATTATGTTGTATCTATATTTTTTTAGA
Found at i:88931 original size:15 final size:17
Alignment explanation
Indices: 88906--88944 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
88896 CAATCCATGT
*
88906 TAAATAAAAATT-TAAA
1 TAAATATAAATTATAAA
88922 -AAATATAAATTATAAA
1 TAAATATAAATTATAAA
88938 TAAATAT
1 TAAATAT
88945 TAACAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 10 0.50
16 4 0.20
17 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATATAAATTATAAA
Found at i:90881 original size:18 final size:17
Alignment explanation
Indices: 90846--90885 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
90836 TAGTAAAAAC
90846 ATAATTTTATCATTATA
1 ATAATTTTATCATTATA
90863 ATAATTTATAT-ATT-T-
1 ATAATTT-TATCATTATA
90878 ATAATTTT
1 ATAATTTT
90886 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 7 0.32
16 1 0.05
17 10 0.45
18 3 0.14
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAATTTTATCATTATA
Found at i:103646 original size:4 final size:4
Alignment explanation
Indices: 103637--103665 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
103627 TGAAGAATGC
103637 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
103666 GTGAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:104262 original size:3 final size:3
Alignment explanation
Indices: 104254--104278 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
104244 GGGAAAAAAT
104254 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
104279 AAAACAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:108046 original size:18 final size:20
Alignment explanation
Indices: 108014--108053 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
108004 AAATGCTAAT
108014 AAAATCATTCAAAATAA-AA
1 AAAATCATTCAAAATAATAA
*
108033 AAAATCA-TCCAAATAATAA
1 AAAATCATTCAAAATAATAA
108052 AA
1 AA
108054 CAAAACCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAATCATTCAAAATAATAA
Found at i:108276 original size:53 final size:55
Alignment explanation
Indices: 108193--108301 Score: 168
Period size: 53 Copynumber: 2.0 Consensus size: 55
108183 ATTATAATTT
* *
108193 ATTTTTTAAAAATATATTTTCTAGTTTTTCATATTATATGTCAAAAATATGATTG
1 ATTTTATAAAAATATATTTTCTAATTTTTCATATTATATGTCAAAAATATGATTG
* *
108248 ATTTTATAAAAATCT-TTTT-TAATTTTTCATATTATATGTTAAAAATATGATTG
1 ATTTTATAAAAATATATTTTCTAATTTTTCATATTATATGTCAAAAATATGATTG
108301 A
1 A
108302 ATTGTAGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 33 0.66
54 4 0.08
55 13 0.26
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (55 bp):
ATTTTATAAAAATATATTTTCTAATTTTTCATATTATATGTCAAAAATATGATTG
Done.