Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011543.1 Kokia drynarioides strain JFW-HI SEQ_126529, 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: 47527
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:6638 original size:35 final size:35
Alignment explanation
Indices: 6596--6677 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
6586 TCTTTAAGTC
* *
6596 TCCCAGTAATTTAACTCATACGAGTTTTTCAAGAT
1 TCCCAGTAATTTAACTCATACGAGCTCTTCAAGAT
* *
6631 TCTCAGTAATTTAACTCATACGAGCTCTTCCAGAT
1 TCCCAGTAATTTAACTCATACGAGCTCTTCAAGAT
6666 TCCCAGTAATTT
1 TCCCAGTAATTT
6678 TTAGCTCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (35 bp):
TCCCAGTAATTTAACTCATACGAGCTCTTCAAGAT
Found at i:6734 original size:19 final size:19
Alignment explanation
Indices: 6710--6765 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
6700 GTAAATTGCT
6710 CTTACGAGCCAGTATCGCG
1 CTTACGAGCCAGTATCGCG
* * *
6729 CTTACGAGCCAATATTGCT
1 CTTACGAGCCAGTATCGCG
*
6748 CTTACAAGCCAGTATCGC
1 CTTACGAGCCAGTATCGC
6766 TTAAACGAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (19 bp):
CTTACGAGCCAGTATCGCG
Found at i:6815 original size:19 final size:19
Alignment explanation
Indices: 6791--6874 Score: 109
Period size: 19 Copynumber: 4.5 Consensus size: 19
6781 NNNNNNTACA
6791 AGCCAGTATCGCTTAAACG
1 AGCCAGTATCGCTTAAACG
6810 AGCCAGTATCGCTTAAACG
1 AGCCAGTATCGCTTAAACG
*
6829 AGCCAGTATCGCTCT-TACG
1 AGCCAGTATCGCT-TAAACG
* *
6848 AGCCAGTAT-GCTCAAGCG
1 AGCCAGTATCGCTTAAACG
*
6866 AGTCAGTAT
1 AGCCAGTAT
6875 TGCTATTCCT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
18 13 0.22
19 44 0.76
20 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (19 bp):
AGCCAGTATCGCTTAAACG
Found at i:15019 original size:17 final size:17
Alignment explanation
Indices: 14999--15035 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
14989 ACTACAATGC
14999 AAATGTACTAACAAATA
1 AAATGTACTAACAAATA
* *
15016 AAATGTAGTGACAAATA
1 AAATGTACTAACAAATA
15033 AAA
1 AAA
15036 ATGAAATGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (17 bp):
AAATGTACTAACAAATA
Found at i:15038 original size:18 final size:18
Alignment explanation
Indices: 14999--15052 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
14989 ACTACAATGC
* *
14999 AAATGTACTAACAAAT-A
1 AAATGTAATGACAAATAA
*
15016 AAATGTAGTGACAAATAA
1 AAATGTAATGACAAATAA
* *
15034 AAATGAAATGACAACTAA
1 AAATGTAATGACAAATAA
15052 A
1 A
15053 TGCTATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATGTAATGACAAATAA
Found at i:19532 original size:69 final size:68
Alignment explanation
Indices: 19406--19555 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 68
19396 TATACGGAAC
* *
19406 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGACAACAGTGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT-GACAACAGAGAGCACACACAG
19471 TGCT
65 TGCT
* * *
19475 AAACAGATAGTACACAAAGTACTAATCAGAGGGCACACAAAGTGCT-A-ATCAGAGAGCACACAC
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGACAACAGAGAGCACACAC
19538 AGTGCT
63 AGTGCT
19544 AATAACAGAGAG
1 -A-AACAGAGAG
19556 CACGAGACGT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
69 32 0.46
70 13 0.19
71 18 0.26
72 7 0.10
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (68 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGACAACAGAGAGCACACACAGT
GCT
Found at i:19573 original size:23 final size:23
Alignment explanation
Indices: 19406--19579 Score: 140
Period size: 23 Copynumber: 7.5 Consensus size: 23
19396 TATACGGAAC
* * *
19406 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
19428 -AACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
19449 GGACAACAGTGAGCACACACAGTGCT
1 --A-AACAGAGAGCACACACAGTGCT
* * * *
19475 AAACAGATAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* * *
19498 AATCAGAGGGCACACAAAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
19521 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
19544 AATAACAGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
19569 AAACAGAGAGC
1 AAACAGAGAGC
19580 GTGCTAGTGT
Statistics
Matches: 124, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
21 16 0.13
22 1 0.01
23 66 0.53
24 3 0.02
25 29 0.23
26 9 0.07
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:21290 original size:47 final size:47
Alignment explanation
Indices: 21221--21408 Score: 288
Period size: 47 Copynumber: 3.9 Consensus size: 47
21211 ACGGATGTTA
*
21221 CACTGTGTGTGCTTCTGTTACCCAACACTGTGTGTGCTTCTGTTCAG
1 CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTTCAG
21268 CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTTACCCAG
1 CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTT---CAG
*
21318 CACTGTGTGTGCTTCTATTACCCAGCACTGTGTGTGCTTCTGTTCAG
1 CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTTCAG
* * *
21365 CACTGTGTGTGCTTCTGTTTCTCCAGCACT-TATGCGCTTCTGTT
1 CACTGTGTGTGCTTCTGTTAC-CCAGCACTGTGTGTGCTTCTGTT
21409 TCCCCAGCAC
Statistics
Matches: 131, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
47 77 0.59
48 8 0.06
50 46 0.35
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.39
Consensus pattern (47 bp):
CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTTCAG
Found at i:21404 original size:97 final size:98
Alignment explanation
Indices: 21221--21419 Score: 321
Period size: 97 Copynumber: 2.0 Consensus size: 98
21211 ACGGATGTTA
*
21221 CACTGTGTGTGCTTCTGTTACCCAACACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
1 CACTGTGTGTGCTTCTATTACCCAACACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
* *
21286 TACCCAGCACTGTGTGTGCTTCTG-TTACCCAG
66 TACCCAGCACTGTATGCGCTTCTGTTTACCCAG
*
21318 CACTGTGTGTGCTTCTATTACCCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
1 CACTGTGTGTGCTTCTATTACCCAACACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
* *
21383 TTCTCCAGCACT-TATGCGCTTCTGTTTCCCCAG
66 TAC-CCAGCACTGTATGCGCTTCTGTTTACCCAG
21416 CACT
1 CACT
21420 TACTTCGGTA
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
97 75 0.80
98 19 0.20
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (98 bp):
CACTGTGTGTGCTTCTATTACCCAACACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
TACCCAGCACTGTATGCGCTTCTGTTTACCCAG
Found at i:21421 original size:25 final size:25
Alignment explanation
Indices: 21221--21419 Score: 277
Period size: 25 Copynumber: 8.2 Consensus size: 25
21211 ACGGATGTTA
*
21221 CACTGTGTGTGCTTCTGTTACCCAA
1 CACTGTGTGTGCTTCTGTTACCCAG
21246 CACTGTGTGTGCTTCTGTT---CAG
1 CACTGTGTGTGCTTCTGTTACCCAG
21268 CACTGTGTGTGCTTCTGTTACCCAG
1 CACTGTGTGTGCTTCTGTTACCCAG
21293 CACTGTGTGTGCTTCTGTTACCCAG
1 CACTGTGTGTGCTTCTGTTACCCAG
*
21318 CACTGTGTGTGCTTCTATTACCCAG
1 CACTGTGTGTGCTTCTGTTACCCAG
21343 CACTGTGTGTGCTTCTGTT---CAG
1 CACTGTGTGTGCTTCTGTTACCCAG
*
21365 CACTGTGTGTGCTTCTGTTTCTCCAG
1 CACTGTGTGTGCTTCTGTTAC-CCAG
* * *
21391 CACT-TATGCGCTTCTGTTTCCCCAG
1 CACTGTGTGTGCTTCTG-TTACCCAG
21416 CACT
1 CACT
21420 TACTTCGGTA
Statistics
Matches: 160, Mismatches: 6, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
22 43 0.27
25 107 0.67
26 10 0.06
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (25 bp):
CACTGTGTGTGCTTCTGTTACCCAG
Found at i:23137 original size:17 final size:17
Alignment explanation
Indices: 23117--23153 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
23107 ACTACAATGC
23117 AAATGTACTAACAAATA
1 AAATGTACTAACAAATA
* *
23134 AAATGTAGTGACAAATA
1 AAATGTACTAACAAATA
23151 AAA
1 AAA
23154 ATGAAATGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (17 bp):
AAATGTACTAACAAATA
Found at i:23156 original size:18 final size:18
Alignment explanation
Indices: 23117--23170 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
23107 ACTACAATGC
* *
23117 AAATGTACTAACAAAT-A
1 AAATGTAATGACAAATAA
*
23134 AAATGTAGTGACAAATAA
1 AAATGTAATGACAAATAA
* *
23152 AAATGAAATGACAACTAA
1 AAATGTAATGACAAATAA
23170 A
1 A
23171 TGCTATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATGTAATGACAAATAA
Found at i:27650 original size:69 final size:68
Alignment explanation
Indices: 27524--27673 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 68
27514 TATACGGAAC
* *
27524 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGACAACAGTGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT-GACAACAGAGAGCACACACAG
27589 TGCT
65 TGCT
* * *
27593 AAACAGATAGTACACAAAGTACTAATCAGAGGGCACACAAAGTGCT-A-ATCAGAGAGCACACAC
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGACAACAGAGAGCACACAC
27656 AGTGCT
63 AGTGCT
27662 AATAACAGAGAG
1 -A-AACAGAGAG
27674 CACGAGACGT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
69 32 0.46
70 13 0.19
71 18 0.26
72 7 0.10
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (68 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGACAACAGAGAGCACACACAGT
GCT
Found at i:27691 original size:23 final size:23
Alignment explanation
Indices: 27524--27697 Score: 140
Period size: 23 Copynumber: 7.5 Consensus size: 23
27514 TATACGGAAC
* * *
27524 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
27546 -AACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
27567 GGACAACAGTGAGCACACACAGTGCT
1 --A-AACAGAGAGCACACACAGTGCT
* * * *
27593 AAACAGATAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* * *
27616 AATCAGAGGGCACACAAAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
27639 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
27662 AATAACAGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
27687 AAACAGAGAGC
1 AAACAGAGAGC
27698 GTGCTAGTGT
Statistics
Matches: 124, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
21 16 0.13
22 1 0.01
23 66 0.53
24 3 0.02
25 29 0.23
26 9 0.07
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:29408 original size:47 final size:47
Alignment explanation
Indices: 29339--29526 Score: 288
Period size: 47 Copynumber: 3.9 Consensus size: 47
29329 ACGGATGTTA
*
29339 CACTGTGTGTGCTTCTGTTACCCAACACTGTGTGTGCTTCTGTTCAG
1 CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTTCAG
29386 CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTTACCCAG
1 CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTT---CAG
*
29436 CACTGTGTGTGCTTCTATTACCCAGCACTGTGTGTGCTTCTGTTCAG
1 CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTTCAG
* * *
29483 CACTGTGTGTGCTTCTGTTTCTCCAGCACT-TATGCGCTTCTGTT
1 CACTGTGTGTGCTTCTGTTAC-CCAGCACTGTGTGTGCTTCTGTT
29527 TCCCCAGCAC
Statistics
Matches: 131, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
47 77 0.59
48 8 0.06
50 46 0.35
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.39
Consensus pattern (47 bp):
CACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGCTTCTGTTCAG
Found at i:29522 original size:97 final size:98
Alignment explanation
Indices: 29339--29537 Score: 321
Period size: 97 Copynumber: 2.0 Consensus size: 98
29329 ACGGATGTTA
*
29339 CACTGTGTGTGCTTCTGTTACCCAACACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
1 CACTGTGTGTGCTTCTATTACCCAACACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
* *
29404 TACCCAGCACTGTGTGTGCTTCTG-TTACCCAG
66 TACCCAGCACTGTATGCGCTTCTGTTTACCCAG
*
29436 CACTGTGTGTGCTTCTATTACCCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
1 CACTGTGTGTGCTTCTATTACCCAACACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
* *
29501 TTCTCCAGCACT-TATGCGCTTCTGTTTCCCCAG
66 TAC-CCAGCACTGTATGCGCTTCTGTTTACCCAG
29534 CACT
1 CACT
29538 TACTTCGGTA
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
97 75 0.80
98 19 0.20
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (98 bp):
CACTGTGTGTGCTTCTATTACCCAACACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGT
TACCCAGCACTGTATGCGCTTCTGTTTACCCAG
Found at i:29539 original size:25 final size:25
Alignment explanation
Indices: 29339--29537 Score: 277
Period size: 25 Copynumber: 8.2 Consensus size: 25
29329 ACGGATGTTA
*
29339 CACTGTGTGTGCTTCTGTTACCCAA
1 CACTGTGTGTGCTTCTGTTACCCAG
29364 CACTGTGTGTGCTTCTGTT---CAG
1 CACTGTGTGTGCTTCTGTTACCCAG
29386 CACTGTGTGTGCTTCTGTTACCCAG
1 CACTGTGTGTGCTTCTGTTACCCAG
29411 CACTGTGTGTGCTTCTGTTACCCAG
1 CACTGTGTGTGCTTCTGTTACCCAG
*
29436 CACTGTGTGTGCTTCTATTACCCAG
1 CACTGTGTGTGCTTCTGTTACCCAG
29461 CACTGTGTGTGCTTCTGTT---CAG
1 CACTGTGTGTGCTTCTGTTACCCAG
*
29483 CACTGTGTGTGCTTCTGTTTCTCCAG
1 CACTGTGTGTGCTTCTGTTAC-CCAG
* * *
29509 CACT-TATGCGCTTCTGTTTCCCCAG
1 CACTGTGTGTGCTTCTG-TTACCCAG
29534 CACT
1 CACT
29538 TACTTCGGTA
Statistics
Matches: 160, Mismatches: 6, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
22 43 0.27
25 107 0.67
26 10 0.06
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (25 bp):
CACTGTGTGTGCTTCTGTTACCCAG
Found at i:33539 original size:24 final size:26
Alignment explanation
Indices: 33494--33543 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
33484 ATTTATTATT
33494 TTGAAAAAAAGGTAGATGAAAGATTG
1 TTGAAAAAAAGGTAGATGAAAGATTG
**
33520 TTGAAAAAGTGGTA-AT-AAAGATTG
1 TTGAAAAAAAGGTAGATGAAAGATTG
33544 AAAGAAGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 2 0.09
26 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (26 bp):
TTGAAAAAAAGGTAGATGAAAGATTG
Found at i:35628 original size:7 final size:7
Alignment explanation
Indices: 35616--35640 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35606 AGTAGAGGTG
35616 GGGCGTT
1 GGGCGTT
35623 GGGCGTT
1 GGGCGTT
35630 GGGCGTT
1 GGGCGTT
35637 GGGC
1 GGGC
35641 TCCTATAGAA
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:0.00, C:0.16, G:0.60, T:0.24
Consensus pattern (7 bp):
GGGCGTT
Found at i:37616 original size:19 final size:19
Alignment explanation
Indices: 37592--37629 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
37582 ATATTTTTTT
37592 CCAAATTA-AAGAAAAAAAA
1 CCAAATTAGAA-AAAAAAAA
37611 CCAAATTAGAAAAAAAAAA
1 CCAAATTAGAAAAAAAAAA
37630 AAATAAACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.74, C:0.11, G:0.05, T:0.11
Consensus pattern (19 bp):
CCAAATTAGAAAAAAAAAA
Found at i:37628 original size:20 final size:19
Alignment explanation
Indices: 37592--37630 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
37582 ATATTTTTTT
*
37592 CCAAATTAAAGAAAAAAAA
1 CCAAATTAAAAAAAAAAAA
37611 CCAAATTAGAAAAAAAAAAA
1 CCAAATTA-AAAAAAAAAAA
37631 AATAAACGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.74, C:0.10, G:0.05, T:0.10
Consensus pattern (19 bp):
CCAAATTAAAAAAAAAAAA
Found at i:37706 original size:23 final size:23
Alignment explanation
Indices: 37680--37725 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
37670 ATGTTTAGTT
*
37680 ATTTACTTTTTTAATTTAATTTA
1 ATTTAATTTTTTAATTTAATTTA
* *
37703 ATTTAATTTTTTTATTTTATTTA
1 ATTTAATTTTTTAATTTAATTTA
37726 CTTTTTCACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTAATTTTTTAATTTAATTTA
Found at i:39483 original size:17 final size:16
Alignment explanation
Indices: 39450--39480 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39440 CTCATCTTAT
*
39450 TTTTTATTTTAAATTA
1 TTTTAATTTTAAATTA
39466 TTTTAATTTTAAATT
1 TTTTAATTTTAAATT
39481 TATATCTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATTTTAAATTA
Found at i:40991 original size:18 final size:19
Alignment explanation
Indices: 40968--41009 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
40958 AAGTTTTAAA
*
40968 AGTAAAAACT-AAAAATAG
1 AGTAAAAACTGAAAAAGAG
40986 AGT-AAAACTGAAAAAGAG
1 AGTAAAAACTGAAAAAGAG
41004 AGTAAA
1 AGTAAA
41010 TATCAAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.64, C:0.05, G:0.17, T:0.14
Consensus pattern (19 bp):
AGTAAAAACTGAAAAAGAG
Found at i:41547 original size:23 final size:23
Alignment explanation
Indices: 41514--41559 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41504 TATATGAAAT
* *
41514 ATAAATTTTAAATATTTTTAAAA
1 ATAAATATTAAATATTTATAAAA
*
41537 ATAAATATTAATTATTTATAAAA
1 ATAAATATTAAATATTTATAAAA
41560 TTTAATTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAAATATTAAATATTTATAAAA
Found at i:41578 original size:20 final size:21
Alignment explanation
Indices: 41553--41600 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
41543 ATTAATTATT
*
41553 TATAAAATT-TAATTAGAATA
1 TATAAAATTATAATTAAAATA
*
41573 TAT-AAATTATATTTAAAATA
1 TATAAAATTATAATTAAAATA
*
41593 TTTAAAAT
1 TATAAAAT
41601 AACCATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 5 0.22
20 14 0.61
21 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TATAAAATTATAATTAAAATA
Found at i:42002 original size:3 final size:3
Alignment explanation
Indices: 41994--42045 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
41984 TAATTTCCTA
41994 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42042 TAT T
1 TAT T
42046 CGTTTCAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42966 original size:97 final size:96
Alignment explanation
Indices: 42786--42973 Score: 231
Period size: 97 Copynumber: 1.9 Consensus size: 96
42776 ACGAAGAGGA
* ** *
42786 TATTCGATTATCTTGATTTGTAGAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATC
1 TATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAAAATC
*
42851 AAAGATAAGGAAACATTGCCTCGATTAAGGG
66 AAAGATAAAGAAACATTGCCTCGATTAAGGG
* *
42882 TATTCGATTAT-TTCGATTTGAAGAAAAAATTGCACCTGGTGAGTTAAGGCACAA-ATTTTCAAA
1 TATTCGATTATCTT-GATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTCAAA
*
42945 ATTCAAA-ATAAA-AGAATATTGCCTCGATT
63 A-TCAAAGATAAAGA-AACATTGCCTCGATT
42974 TTAAAAGCTT
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
95 2 0.03
96 21 0.27
97 51 0.65
98 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (96 bp):
TATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAAAATC
AAAGATAAAGAAACATTGCCTCGATTAAGGG
Found at i:43400 original size:30 final size:30
Alignment explanation
Indices: 43269--43497 Score: 176
Period size: 29 Copynumber: 7.8 Consensus size: 30
43259 TTCGGGGAGT
* *
43269 AAAAATGGATTTTTTTGGAAATTTCG-GGATC
1 AAAAATGGA-ATTTTTGGAAGTTTCGAGG-TC
** *
43300 AAAAATGGCGTTTTTGGAAG-TTCGGGAGT-
1 AAAAATGGAATTTTTGGAAGTTTCGAG-GTC
* * *
43329 AAAAATAGAATTTTTAGAAG-TTCGGGGGT-
1 AAAAATGGAATTTTTGGAAGTTTC-GAGGTC
*
43358 -AAAATGGAATTTTTGGGAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
*
43387 GAAAAT-GAGATTTTTGGAAG-TTCGAAGGT-
1 AAAAATGGA-ATTTTTGGAAGTTTCG-AGGTC
* *
43416 AAAAATGGAATTTTTGGAAGTTTTG-GGGC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
* *
43445 AAAAATGGGATTTTTGGAAG-TTCGGGGGT-
1 AAAAATGGAATTTTTGGAAGTTTC-GAGGTC
43474 AAAAATGGAATTTTTGGATAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
43498 AGGGACCTTC
Statistics
Matches: 164, Mismatches: 19, Indels: 30
0.77 0.09 0.14
Matches are distributed among these distances:
28 24 0.15
29 87 0.53
30 42 0.26
31 11 0.07
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTC
Found at i:43400 original size:58 final size:58
Alignment explanation
Indices: 43300--43497 Score: 240
Period size: 58 Copynumber: 3.4 Consensus size: 58
43290 TTTCGGGATC
** * *
43300 AAAAATGGCGTTTTTGGAAG-TTCGGGAGTAAAAAT-AGAATTTTTAGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGG-GCAAAAATGAG-ATTTTTGGAAGTTCGGGGGT
* * * **
43358 -AAAATGGAATTTTTGGGAGTTTCGAGGTCGAAAATGAGATTTTTGGAAGTTCGAAGGT
1 AAAAATGGAATTTTTGGAAGTTTCG-GGGCAAAAATGAGATTTTTGGAAGTTCGGGGGT
* *
43416 AAAAATGGAATTTTTGGAAGTTTTGGGGCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGGCAAAAATGAGATTTTTGGAAGTTCGGGGGT
43474 AAAAATGGAATTTTTGGATAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
43498 AGGGACCTTC
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
57 16 0.13
58 72 0.61
59 31 0.26
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTTCGGGGCAAAAATGAGATTTTTGGAAGTTCGGGGGT
Found at i:43401 original size:87 final size:87
Alignment explanation
Indices: 43239--43496 Score: 249
Period size: 87 Copynumber: 2.9 Consensus size: 87
43229 CGTGGTTTAA
* * *
43239 AAAAATGGAATTATTAGACA-TTCGGGGAGTAAAAATGGATTTTTTTGGAAATTTCGGGATCAAA
1 AAAAATGGAATTTTTAGA-AGTTCGGGG-GT-AAAATGGA-ATTTTTGGAAGTTTCGGGATCAAA
* *
43303 AATGGCGTTTTTGGAAGTTCG-GGAGT
62 AATGGCATTTTTGGAAGTTCGAAG-GT
* * *
43329 AAAAATAGAATTTTTAGAAGTTCGGGGGTAAAATGGAATTTTTGGGAGTTTCGAGG-TCGAAAAT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTTCG-GGATCAAAAAT
43393 GAG-ATTTTTGGAAGTTCGAAGGT
65 G-GCATTTTTGGAAGTTCGAAGGT
* * ** * *
43416 AAAAATGGAATTTTTGGAAGTTTTGGGGCAAAAATGGGATTTTTGGAAG-TTCGGGGGT-AAAAA
1 AAAAATGGAATTTTTAGAAG-TTCGGGGGTAAAATGGAATTTTTGGAAGTTTC-GGGATCAAAAA
*
43479 TGGAATTTTTGGATAGTT
64 TGGCATTTTTGGA-AGTT
43497 TAGGGACCTT
Statistics
Matches: 143, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
86 1 0.01
87 75 0.52
88 41 0.29
89 3 0.02
90 23 0.16
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (87 bp):
AAAAATGGAATTTTTAGAAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTTCGGGATCAAAAATG
GCATTTTTGGAAGTTCGAAGGT
Found at i:45285 original size:6 final size:6
Alignment explanation
Indices: 45274--45355 Score: 59
Period size: 6 Copynumber: 14.5 Consensus size: 6
45264 AATTGGATAT
*
45274 TTTAAA TTTAAA TTT--A TATAAA TTTAAA TTTCAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * * * *
45319 TTTAAA -ATAAA CTTAAT TTTAAA -ATAAA TTCAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
45356 CAATAGGCCC
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
4 6 0.10
5 9 0.16
6 40 0.69
7 3 0.05
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:45313 original size:17 final size:17
Alignment explanation
Indices: 45276--45355 Score: 108
Period size: 17 Copynumber: 4.8 Consensus size: 17
45266 TTGGATATTT
*
45276 TAAATTTAAATTT-ATA
1 TAAATTTAAATTTAAAA
*
45292 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
45309 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
45326 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
45343 TAAATTCAAATTT
1 TAAATTTAAATTT
45356 CAATAGGCCC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 13 0.23
17 43 0.77
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:46042 original size:47 final size:47
Alignment explanation
Indices: 45966--46079 Score: 147
Period size: 47 Copynumber: 2.4 Consensus size: 47
45956 GTTCAGTTCT
* * *
45966 CAGTATCTCATTAGGAAGCTAACCGTTTATTGCTTCGACCTGCTTCC
1 CAGTGTCTCATCAGGAAGCTAACCGTTTATCGCTTCGACCTGCTTCC
* ** * *
46013 CAGTGTCTCATCAAGAAGCTAACTTTTTATCGCTTCGATCTGCTTCT
1 CAGTGTCTCATCAGGAAGCTAACCGTTTATCGCTTCGACCTGCTTCC
*
46060 CAATGTCTCATCAGGAAGCT
1 CAGTGTCTCATCAGGAAGCT
46080 GGGGTTCGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (47 bp):
CAGTGTCTCATCAGGAAGCTAACCGTTTATCGCTTCGACCTGCTTCC
Found at i:46684 original size:27 final size:27
Alignment explanation
Indices: 46654--46714 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
46644 TCAAAAATTC
*
46654 TATTAAAAAGAGGATAAAAGGAAACAA
1 TATTAAAAAGAGGATAAAAGAAAACAA
* *
46681 TATTAAAAAGAGGATCAAAGAAAATAA
1 TATTAAAAAGAGGATAAAAGAAAACAA
46708 TCATTAA
1 T-ATTAA
46715 TTGAAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.61, C:0.05, G:0.15, T:0.20
Consensus pattern (27 bp):
TATTAAAAAGAGGATAAAAGAAAACAA
Done.