Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008197.1 Kokia drynarioides strain JFW-HI SEQ_122859, 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: 77504
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:7723 original size:15 final size:15
Alignment explanation
Indices: 7703--7736 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
7693 TAAGAACAAA
*
7703 AATCGTGAAATCTCT
1 AATCGTGAAATCCCT
7718 AATCGTGAAATCCCT
1 AATCGTGAAATCCCT
7733 AATC
1 AATC
7737 ATTCAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (15 bp):
AATCGTGAAATCCCT
Found at i:9548 original size:66 final size:66
Alignment explanation
Indices: 9422--9608 Score: 188
Period size: 66 Copynumber: 2.8 Consensus size: 66
9412 ACAGTAGACC
* * * * * * *
9422 CTCC-ACATCACCCTTCACATCAGCTTCTATCCC-TCCTACATCACCTTCCTCAACAGCTTCTA-
1 CTCCTACATCACCCTCCCCATCAACTTCTACCCCTTCAT-CATCACCTTCCCCAACAACTTCTAG
*
9484 CC
65 CA
* *
9486 CTTTCC-AGATCA-CCTCCACCATCAGA-TTCTACCCCTTCATCATCACCTTCCCCATCAACTTC
1 C--TCCTACATCACCCTCC-CCATCA-ACTTCTACCCCTTCATCATCACCTTCCCCAACAACTTC
9548 TAGCA
62 TAGCA
*
9553 CTCCTACATCACCCTCCCCATCAACTTCTACCCCTTCATCATCACCCTCCCCAACA
1 CTCCTACATCACCCTCCCCATCAACTTCTACCCCTTCATCATCACCTTCCCCAACA
9609 GTCAACATAA
Statistics
Matches: 101, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
64 1 0.01
65 8 0.08
66 82 0.81
67 10 0.10
ACGTcount: A:0.23, C:0.48, G:0.03, T:0.27
Consensus pattern (66 bp):
CTCCTACATCACCCTCCCCATCAACTTCTACCCCTTCATCATCACCTTCCCCAACAACTTCTAGC
A
Found at i:9599 original size:33 final size:33
Alignment explanation
Indices: 9427--9605 Score: 143
Period size: 33 Copynumber: 5.4 Consensus size: 33
9417 AGACCCTCCA
* * * * *
9427 CATCACCCTTCACATCAGCTTCTATCCC-TCCT
1 CATCACCCTCCCCATCAACTTCTACCCCTTCAT
* * * * *
9459 ACATCACCTTCCTCAACAGCTTCTACCCTTTCCA-
1 -CATCACCCTCCCCATCAACTTCTACCCCTT-CAT
*
9493 GATCA-CCTCCACCATCAGA-TTCTACCCCTTCAT
1 CATCACCCTCC-CCATCA-ACTTCTACCCCTTCAT
* * * *
9526 CATCACCTTCCCCATCAACTTCTAGCAC-TCCT
1 CATCACCCTCCCCATCAACTTCTACCCCTTCAT
9558 ACATCACCCTCCCCATCAACTTCTACCCCTTCAT
1 -CATCACCCTCCCCATCAACTTCTACCCCTTCAT
9592 CATCACCCTCCCCA
1 CATCACCCTCCCCA
9606 ACAGTCAACA
Statistics
Matches: 115, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
32 10 0.09
33 96 0.83
34 8 0.07
35 1 0.01
ACGTcount: A:0.22, C:0.47, G:0.03, T:0.27
Consensus pattern (33 bp):
CATCACCCTCCCCATCAACTTCTACCCCTTCAT
Found at i:10465 original size:16 final size:16
Alignment explanation
Indices: 10418--10467 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
10408 CGATCTTGGG
10418 TTAGGGA-TTCAAATAT
1 TTAGGGATTTC-AATAT
* **
10434 TTGGGGATTTTGATAT
1 TTAGGGATTTCAATAT
10450 TTAGGGATTTCAATAT
1 TTAGGGATTTCAATAT
10466 TT
1 TT
10468 TAAGGATTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
16 25 0.93
17 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (16 bp):
TTAGGGATTTCAATAT
Found at i:32577 original size:30 final size:30
Alignment explanation
Indices: 32541--32615 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
32531 AGATTAATGT
32541 TAAGGGTATGTAATTTTTCTTTGAAGTTGG
1 TAAGGGTATGTAATTTTTCTTTGAAGTTGG
32571 TAAGGGTATGTAATTTTTCTTTGAAGTTGG
1 TAAGGGTATGTAATTTTTCTTTGAAGTTGG
32601 TAAGGGTATGTAATT
1 TAAGGGTATGTAATT
32616 GATAAAAGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.25, C:0.03, G:0.27, T:0.45
Consensus pattern (30 bp):
TAAGGGTATGTAATTTTTCTTTGAAGTTGG
Found at i:39623 original size:16 final size:16
Alignment explanation
Indices: 39604--39645 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
39594 AATTTAGTCC
*
39604 TTATGAAATTACGT-AT
1 TTATGTAATTAC-TCAT
39620 TTATGTAATTACTCAT
1 TTATGTAATTACTCAT
39636 TTATGTAATT
1 TTATGTAATT
39646 TTGTATCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (16 bp):
TTATGTAATTACTCAT
Found at i:40068 original size:16 final size:15
Alignment explanation
Indices: 40028--40084 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
40018 TTTCTTATTT
40028 TAATAATTTTTTTAA
1 TAATAATTTTTTTAA
*
40043 TATTATATTTTTTTAA
1 TAATA-ATTTTTTTAA
***
40059 TAATAGATTTTAACAA
1 TAATA-ATTTTTTTAA
40075 TAATAATTTT
1 TAATAATTTT
40085 AAATTTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 9 0.26
16 26 0.74
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TAATAATTTTTTTAA
Found at i:40083 original size:15 final size:16
Alignment explanation
Indices: 40057--40086 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40047 ATATTTTTTT
40057 AATAATAGATTTTAAC
1 AATAATAGATTTTAAC
40073 AATAATA-ATTTTAA
1 AATAATAGATTTTAA
40087 ATTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
AATAATAGATTTTAAC
Found at i:41634 original size:37 final size:37
Alignment explanation
Indices: 41593--41673 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
41583 CGAAGTATAT
41593 AAATTGCATCCAGCGCTCATCGGTATAACCGAAATAA
1 AAATTGCATCCAGCGCTCATCGGTATAACCGAAATAA
*
41630 AAATTGCATCCAGTGCTCATCGGTATAACCGAAATAA
1 AAATTGCATCCAGCGCTCATCGGTATAACCGAAATAA
*
41667 AATTTGC
1 AAATTGC
41674 GATTTGCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (37 bp):
AAATTGCATCCAGCGCTCATCGGTATAACCGAAATAA
Found at i:50315 original size:97 final size:97
Alignment explanation
Indices: 50125--50318 Score: 225
Period size: 97 Copynumber: 2.0 Consensus size: 97
50115 CACTTTTAAA
* * * *
50125 AAGGATGTTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTC
1 AAGGATATTCGATTATCTCAATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTC
* *
50190 AGAATCAGAGATAAGAAACATTGCCTCGATTT
66 AGAATCAGAAATAAAAAACATTGCCTCGATTT
* **
50222 AAGGATATTCGATTAT-TCCAATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTT
1 AAGGATATTCGATTATCT-CAATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTT
* *
50285 C-GAAATTC-GAAATAAAATAATATTGTCTCGATTT
65 CAG-AA-TCAGAAATAAAA-AACATTGCCTCGATTT
50319 TAAAGTTTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 1 0.01
96 37 0.45
97 44 0.54
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCAATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTC
AGAATCAGAAATAAAAAACATTGCCTCGATTT
Found at i:50600 original size:29 final size:29
Alignment explanation
Indices: 50559--50720 Score: 89
Period size: 29 Copynumber: 5.5 Consensus size: 29
50549 CTGGGATGGT
*
50559 AAAATGGTAATTTTGGGAAGTTCGAGGATA
1 AAAAT-GTAATTTTGGGAAGTTCGAGGGTA
*** ** *
50589 AAAATGTAATTTTAAAAAAAATCGA-GGTC
1 AAAATGTAATTTT-GGGAAGTTCGAGGGTA
* * * *
50618 AAAATGGAAATTTGGGAAGTTTGGGGGT-
1 AAAATGTAATTTTGGGAAGTTCGAGGGTA
* *
50646 AAAATGGTAATTTT-TGAAGATTCAAGGGTA
1 AAAAT-GTAATTTTGGGAAG-TTCGAGGGTA
* **
50676 AAAATGTAATTTTTGGAAAAATC-AGGGTTA
1 AAAATGTAA-TTTTGGGAAGTTCGAGGG-TA
*
50706 AAAATGGAATTTTGG
1 AAAATGTAATTTTGG
50721 AAAAGTTTGG
Statistics
Matches: 97, Mismatches: 27, Indels: 17
0.69 0.19 0.12
Matches are distributed among these distances:
28 13 0.13
29 50 0.52
30 32 0.33
31 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (29 bp):
AAAATGTAATTTTGGGAAGTTCGAGGGTA
Found at i:50664 original size:28 final size:30
Alignment explanation
Indices: 50642--50718 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
50632 GGAAGTTTGG
50642 GGGT-AAAATGGTAATTTTTGAAGATTCAA
1 GGGTAAAAATGGTAATTTTTGAAGATTCAA
* *
50671 GGGTAAAAAT-GTAATTTTTGGAAAAATC-A
1 GGGTAAAAATGGTAATTTTT-GAAGATTCAA
50700 GGGTTAAAAATGG-AATTTT
1 GGG-TAAAAATGGTAATTTT
50719 GGAAAAGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 17 0.40
30 24 0.57
31 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (30 bp):
GGGTAAAAATGGTAATTTTTGAAGATTCAA
Found at i:50697 original size:87 final size:88
Alignment explanation
Indices: 50556--50750 Score: 227
Period size: 87 Copynumber: 2.2 Consensus size: 88
50546 TACCTGGGAT
* * *
50556 GGTAAAATGGTAATTTTGGGAAGTTCGAGGATAAAAATGTAATTTTAAAAAAAATC-GAGG-TCA
1 GGTAAAATGGTAATTTT-TGAAGTTCAAGGATAAAAATGTAATTTTAAAAAAAATCAG-GGTTAA
* *
50619 AAATGGAAATTTGG-GAAGTTTGGG
64 AAATGGAAATTTGGAAAAGTTTGGA
* ***
50643 GGTAAAATGGTAATTTTTGAAGATTCAAGGGTAAAAATGTAATTTTTGGAAAAATCAGGGTTAAA
1 GGTAAAATGGTAATTTTTGAAG-TTCAAGGATAAAAATGTAATTTTAAAAAAAATCAGGGTTAAA
*
50708 AATGGAATTTTGGAAAAGTTTGGA
65 AATGGAAATTTGGAAAAGTTTGGA
*
50732 GGTCAAAAT-ATAATTTTTG
1 GGT-AAAATGGTAATTTTTG
50751 GATAGTTTAG
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
86 4 0.04
87 47 0.51
88 16 0.17
89 20 0.22
90 5 0.05
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (88 bp):
GGTAAAATGGTAATTTTTGAAGTTCAAGGATAAAAATGTAATTTTAAAAAAAATCAGGGTTAAAA
ATGGAAATTTGGAAAAGTTTGGA
Found at i:50708 original size:30 final size:30
Alignment explanation
Indices: 50642--50724 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 30
50632 GGAAGTTTGG
* *
50642 GGGT-AAAATGGTAATTTTT-GAAGATTCAA
1 GGGTAAAAAT-GTAATTTTTGGAAAAATCAA
50671 GGGTAAAAATGTAATTTTTGGAAAAATC-A
1 GGGTAAAAATGTAATTTTTGGAAAAATCAA
*
50700 GGGTTAAAAATGGAA-TTTTGGAAAA
1 GGG-TAAAAATGTAATTTTTGGAAAA
50725 GTTTGGAGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 27 0.56
30 21 0.44
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTGGAAAAATCAA
Found at i:50740 original size:30 final size:29
Alignment explanation
Indices: 50559--50758 Score: 66
Period size: 29 Copynumber: 6.8 Consensus size: 29
50549 CTGGGATGGT
* *
50559 AAAATGGTAATTTTGGGAAG-TTCGAGGATA
1 AAAATGG-AATTTTGGAAAGTTTGGAGG-TA
* ** *** * *
50589 AAAATGTAATTTTAAAAAAAATCGAGGTC
1 AAAATGGAATTTTGGAAAGTTTGGAGGTA
* * *
50618 AAAATGGAAATTTGGGAAGTTTGGGGGT-
1 AAAATGGAATTTTGGAAAGTTTGGAGGTA
* * **
50646 AAAATGGTAATTTTTG-AAGATTCAAGGGTA
1 AAAATGG-AATTTTGGAAAGTTTGGA-GGTA
* * ** *
50676 AAAATGTAATTTTTGGAAAAATCAGG-GTTA
1 AAAATGGAA-TTTTGG-AAAGTTTGGAGGTA
*
50706 AAAATGGAATTTTGGAAAAGTTTGGAGGTC
1 AAAATGGAATTTTGG-AAAGTTTGGAGGTA
** *
50736 AAAATATAATTTTTGGATAGTTT
1 AAAATGGAA-TTTTGGAAAGTTT
50759 AGGGACCTTC
Statistics
Matches: 120, Mismatches: 41, Indels: 18
0.67 0.23 0.10
Matches are distributed among these distances:
28 12 0.10
29 51 0.43
30 49 0.41
31 6 0.05
32 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTGGAAAGTTTGGAGGTA
Found at i:54454 original size:10 final size:10
Alignment explanation
Indices: 54441--54506 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
54431 TTTTCAATAA
54441 TTTATAAAAT
1 TTTATAAAAT
54451 TTTATAAAAT
1 TTTATAAAAT
* **
54461 AGTTATGTAAT
1 -TTTATAAAAT
54472 TTTATCAAAAT
1 TTTAT-AAAAT
* *
54483 TTCA-ATAAT
1 TTTATAAAAT
54492 TTT-TAAAAT
1 TTTATAAAAT
54501 TTTATA
1 TTTATA
54507 TTTCTTTTCA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
9 13 0.31
10 16 0.38
11 13 0.31
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:54466 original size:21 final size:22
Alignment explanation
Indices: 54442--54482 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
54432 TTTCAATAAT
54442 TTATAAAATTTTAT-AAAATAG
1 TTATAAAATTTTATCAAAATAG
**
54463 TTATGTAATTTTATCAAAAT
1 TTATAAAATTTTATCAAAAT
54483 TTCAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (22 bp):
TTATAAAATTTTATCAAAATAG
Found at i:56356 original size:18 final size:18
Alignment explanation
Indices: 56324--56358 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56314 CATGGATGGC
**
56324 AGGAAAAATTCATTATAA
1 AGGAAAAATAAATTATAA
56342 AGGAAAAATAAATTATA
1 AGGAAAAATAAATTATA
56359 TATGTAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.11, T:0.26
Consensus pattern (18 bp):
AGGAAAAATAAATTATAA
Found at i:57151 original size:43 final size:41
Alignment explanation
Indices: 57037--57153 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 41
57027 TTTTATTTAT
* * *
57037 TGTGGATCACATTATTACCAAGTTTATTATTTAAAAGTGAA
1 TGTGGATCGCATTATTACCAATTTTATGATTTAAAAGTGAA
* * * *
57078 TATGG-TGCGACATTAGTATCAATTTTATGATTTAAAGGTGAAAA
1 TGTGGAT-CG-CATTATTACCAATTTTATGATTTAAAAGTG--AA
*
57122 TGTGGATCGCATGATTACCAATTTTATGATTT
1 TGTGGATCGCATTATTACCAATTTTATGATTT
57154 TAAACTTAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
40 1 0.02
41 5 0.08
42 25 0.42
43 20 0.33
44 8 0.13
45 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (41 bp):
TGTGGATCGCATTATTACCAATTTTATGATTTAAAAGTGAA
Found at i:57668 original size:43 final size:44
Alignment explanation
Indices: 57584--57678 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 44
57574 AGAAGCTTGT
* *
57584 ATTTAAAACTGAATACTGTGGATCACATAATTACCAGTTTTATG
1 ATTTAAAACTGAATACTGTGGATCAAATAATTACCAATTTTATG
** * *
57628 ATTTAAAGGTGAATA-TGTGGATCAAATGATTTCCAATTTTATG
1 ATTTAAAACTGAATACTGTGGATCAAATAATTACCAATTTTATG
57671 ATTTAAAA
1 ATTTAAAA
57679 TTTGTAAGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 31 0.70
44 13 0.30
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (44 bp):
ATTTAAAACTGAATACTGTGGATCAAATAATTACCAATTTTATG
Found at i:57829 original size:26 final size:25
Alignment explanation
Indices: 57793--57850 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 25
57783 AATTGGTAAA
57793 TTTAATGTATTTCATAAAAACTATT
1 TTTAATGTATTTCATAAAAACTATT
*
57818 TTTAATTGTATTTCATAAAAATTATT
1 TTTAA-TGTATTTCATAAAAACTATT
*
57844 TTCAATG
1 TTTAATG
57851 AAATAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (25 bp):
TTTAATGTATTTCATAAAAACTATT
Found at i:60152 original size:6 final size:6
Alignment explanation
Indices: 60113--60221 Score: 56
Period size: 6 Copynumber: 19.0 Consensus size: 6
60103 TAAAATTCTT
*
60113 TTTAAA TTT--A TTATAAGA TTT-AA TTT-AT TTTAAA TTTAAAA TTT---
1 TTTAAA TTTAAA TT-TAA-A TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* ** *
60157 TTTAAAA TTTAAA TTTAAA -TTAAG TTTAAA TTTACT TTTAAA ATTAAA
1 TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
60205 ATT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
60222 AAGTCCCATT
Statistics
Matches: 79, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
3 3 0.04
4 3 0.04
5 16 0.20
6 44 0.56
7 10 0.13
8 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:60156 original size:23 final size:24
Alignment explanation
Indices: 60113--60222 Score: 74
Period size: 23 Copynumber: 4.8 Consensus size: 24
60103 TAAAATTCTT
*
60113 TTTAAATTT--ATTATAAGATTTAA
1 TTTAAATTTAAATT-TAAAATTTAA
*
60136 TTT-ATTTTAAATTTAAAATTT--
1 TTTAAATTTAAATTTAAAATTTAA
60157 TTTAAAATTTAAATTT-AAA-TTAA
1 TTT-AAATTTAAATTTAAAATTTAA
** *
60180 GTTTAAATTTACTTTTAAAATTAAA
1 -TTTAAATTTAAATTTAAAATTTAA
* *
60205 ATT-ATTTTAAATTTAAAA
1 TTTAAATTTAAATTTAAAA
60223 AGTCCCATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
21 5 0.07
22 7 0.10
23 42 0.62
24 11 0.16
25 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAATTTAAATTTAAAATTTAA
Found at i:60222 original size:17 final size:17
Alignment explanation
Indices: 60113--60221 Score: 114
Period size: 17 Copynumber: 6.4 Consensus size: 17
60103 TAAAATTCTT
*
60113 TTTAAATTTATTATAAGA
1 TTTAAATTTATTTTAA-A
60131 TTT-AATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
60147 TTTAAAATTT-TTTAAAA
1 TTT-AAATTTATTTTAAA
** *
60164 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
60181 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
60199 ATTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
60216 TTTAAA
1 TTTAAA
60222 AAGTCCCATT
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
16 10 0.13
17 45 0.60
18 20 0.27
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:60933 original size:3 final size:3
Alignment explanation
Indices: 60927--60955 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
60917 AAAAATGTGC
60927 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
60956 TTTTTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:62063 original size:59 final size:58
Alignment explanation
Indices: 62000--62255 Score: 314
Period size: 59 Copynumber: 4.3 Consensus size: 58
61990 TACCCTCGAG
* * **
62000 CTTCCAAAAAATCCATTTTTATCCCCGAACTTCCAAAAATTCCATTTTTTACCTTGAAA
1 CTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAA
* * * *
62059 CTTCCAAAAATTCCATTTTTACCCCCGAACTTCTAAAAATTCCATTTTTAACCTCAAAA
1 CTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAA
* ** *
62118 CTTCAAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATAACATTTTCGACCCCGAAA
1 CTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATTCCATTTTTGACCCCGAAA
* * * *
62177 CTTCCAAAAATTCCATTTTTACACCCGAACCTCCAAAATTTCCATTTTTGACCCTGGAA
1 CTTCCAAAAATTCCATTTTTAC-CCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAA
*
62236 CTTTCAAAAATTACCATTTT
1 CTTCCAAAAATT-CCATTTT
62256 GCCTCAGAAT
Statistics
Matches: 171, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
58 3 0.02
59 159 0.93
60 9 0.05
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
CTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAA
Found at i:62256 original size:30 final size:29
Alignment explanation
Indices: 61985--62255 Score: 298
Period size: 29 Copynumber: 9.2 Consensus size: 29
61975 CAAACATTAT
* *
61985 ATTTTTACCCTCGAGCTTCCAAAAAATCC
1 ATTTTTACCCTCGAACTTCCAAAAATTCC
62014 ATTTTTATCCC-CGAACTTCCAAAAATTCC
1 ATTTTTA-CCCTCGAACTTCCAAAAATTCC
*
62043 ATTTTTTA-CCTTGAAACTTCCAAAAATTCC
1 A-TTTTTACCCTCG-AACTTCCAAAAATTCC
* *
62073 ATTTTTACCCCCGAACTTCTAAAAATTCC
1 ATTTTTACCCTCGAACTTCCAAAAATTCC
* * *
62102 ATTTTTAACCTCAAAACTTCAAAAAATTCC
1 ATTTTTACCCTC-GAACTTCCAAAAATTCC
**
62132 ATTTTTACCCTCGAACTTCCAAAAATAAC
1 ATTTTTACCCTCGAACTTCCAAAAATTCC
*
62161 ATTTTCGACCC-CGAAACTTCCAAAAATTCC
1 ATTTT-TACCCTCG-AACTTCCAAAAATTCC
* *
62191 ATTTTTACACC-CGAACCTCCAAAATTTCC
1 ATTTTTAC-CCTCGAACTTCCAAAAATTCC
* *
62220 ATTTTTGACCCTGGAACTTTCAAAAATTACC
1 ATTTTT-ACCCTCGAACTTCCAAAAATT-CC
62251 ATTTT
1 ATTTT
62256 GCCTCAGAAT
Statistics
Matches: 205, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
28 2 0.01
29 100 0.49
30 96 0.47
31 7 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTCCAAAAATTCC
Found at i:62303 original size:118 final size:117
Alignment explanation
Indices: 62004--62296 Score: 339
Period size: 118 Copynumber: 2.5 Consensus size: 117
61994 CTCGAGCTTC
**
62004 CAAAAAA-TCCATTTTTATCCC-CGAACTTCCAAAAATTCCATTTTTTACCTTGAAACTTCCAAA
1 CAAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAA-TCCATTTTCGACCTTGAAACTTCCAAA
* * *
62067 AATTCCATTTTTACCCCCGAACTTCTAAAAATTCCATTTTTAACCTCAAAACTT
64 AATTCCATTTTTACACCCGAACCTCCAAAAATTCCATTTTTAACCTCAAAACTT
* **
62121 CAAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATAACATTTTCGACCCCGAAACTTCCAAAA
1 CAAAAAATTCCATTTTTACCCTCGAACTTCCAAAAAT-CCATTTTCGACCTTGAAACTTCCAAAA
* * **
62186 ATTCCATTTTTACACCCGAACCTCCAAAATTTCCATTTTTGACC-CTGGAACTTT
65 ATTCCATTTTTACACCCGAACCTCCAAAAATTCCATTTTTAACCTC-AAAAC-TT
*
62240 C-AAAAATTACCA-TTTT-GCCTCAGAA-TGTCCAAAAACTCCATTTTCGACCTTGAAACT
1 CAAAAAATT-CCATTTTTACCCTC-GAACT-TCCAAAAA-TCCATTTTCGACCTTGAAACT
62297 CTCAAAATTA
Statistics
Matches: 151, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
117 17 0.11
118 127 0.84
119 7 0.05
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.32
Consensus pattern (117 bp):
CAAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCATTTTCGACCTTGAAACTTCCAAAAA
TTCCATTTTTACACCCGAACCTCCAAAAATTCCATTTTTAACCTCAAAACTT
Found at i:62389 original size:28 final size:28
Alignment explanation
Indices: 62355--62416 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
62345 CTAAATTTTC
* *
62355 CCAAAATTACCATTTTGCCCTCGTGCAT
1 CCAAAATTACCATTTTGCCCCCGGGCAT
*
62383 CCAAAATTACCATTTTGCCCCCGGGTAT
1 CCAAAATTACCATTTTGCCCCCGGGCAT
62411 CCAAAA
1 CCAAAA
62417 AGTCTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGGGCAT
Found at i:63167 original size:14 final size:15
Alignment explanation
Indices: 63139--63168 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
63129 GACCTACATG
63139 TTTTAAAAACGGTTT
1 TTTTAAAAACGGTTT
63154 TTTTAAAAAC-GTTT
1 TTTTAAAAACGGTTT
63168 T
1 T
63169 ATGGTGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (15 bp):
TTTTAAAAACGGTTT
Found at i:66923 original size:22 final size:22
Alignment explanation
Indices: 66881--66939 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
66871 CGATCTAAGG
*
66881 AAAATAAAAG-AAACAGAATTA
1 AAAATAAAAGAAAATAGAATTA
66902 AAAATAAAAGAAAATAGAATTA
1 AAAATAAAAGAAAATAGAATTA
*
66924 AAAGA-AATAGAAAATA
1 AAA-ATAAAAGAAAATA
66940 AGAAAGTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 10 0.29
22 23 0.68
23 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATAAAAGAAAATAGAATTA
Found at i:66931 original size:15 final size:16
Alignment explanation
Indices: 66906--66935 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
66896 GAATTAAAAA
66906 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
66922 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
66936 AATAAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:67770 original size:19 final size:19
Alignment explanation
Indices: 67746--67788 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
67736 AAACATAAAT
67746 TAAATACACAT-TTAAATAA
1 TAAATA-ACATATTAAATAA
* *
67765 TAAATAATATATTAAATAT
1 TAAATAACATATTAAATAA
67784 TAAAT
1 TAAAT
67789 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAACATATTAAATAA
Found at i:67935 original size:21 final size:21
Alignment explanation
Indices: 67911--67955 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
67901 CGATCTAAGG
67911 AAAAA-TAAAAGAAATAGAATT
1 AAAAATTAAAA-AAATAGAATT
67932 AAAAATTAAAAAAATAGAATT
1 AAAAATTAAAAAAATAGAATT
67953 AAA
1 AAA
67956 TGAAATAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAATTAAAAAAATAGAATT
Found at i:68792 original size:19 final size:19
Alignment explanation
Indices: 68768--68810 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
68758 AAACATAAAC
68768 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
68787 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
68806 TAAAT
1 TAAAT
68811 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Done.