Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014612.1 Kokia drynarioides strain JFW-HI SEQ_129651, 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: 117698
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 33 characters in sequence are not A, C, G, or T
Found at i:640 original size:2 final size:2
Alignment explanation
Indices: 635--670 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
625 TTCTAGTAAC
635 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
671 TTTTTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7116 original size:22 final size:21
Alignment explanation
Indices: 7066--7116 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
7056 AAAAAATGTT
*
7066 TAAAATTATTAAATATTAAAA
1 TAAAATAATTAAATATTAAAA
*
7087 TAATATAATATAAATATTTAAAA
1 TAAAATAAT-TAAATA-TTAAAA
7110 -AAAATAA
1 TAAAATAA
7117 AATGGGCAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 7 0.28
22 12 0.48
23 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATAATTAAATATTAAAA
Found at i:9528 original size:39 final size:35
Alignment explanation
Indices: 9450--9528 Score: 95
Period size: 35 Copynumber: 2.1 Consensus size: 35
9440 ATTTTGGAGG
***
9450 ATTAAAAAGGGAAATATACTTTTATTAAGTGGGGG
1 ATTAAAAAGGGAAATATACTTTTATTAAGTGGACA
9485 ATTAAAAAGGGAAATATACTTTATTTTATTAAGTGGACA
1 ATTAAAAAGGGAAATATAC----TTTTATTAAGTGGACA
9524 ATTAA
1 ATTAA
9529 TCCTATGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 19 0.51
39 18 0.49
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (35 bp):
ATTAAAAAGGGAAATATACTTTTATTAAGTGGACA
Found at i:10277 original size:21 final size:20
Alignment explanation
Indices: 10241--10288 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 20
10231 AATTTGATTT
10241 TTTAATATGTTATATTGA-A
1 TTTAATATGTTATATTGAGA
*
10260 TTTAATATTTGTATTATTGAGGA
1 TTTAATATGT-TA-TATTGA-GA
10283 TTTAAT
1 TTTAAT
10289 GTTGTCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 9 0.38
20 2 0.08
21 6 0.25
23 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (20 bp):
TTTAATATGTTATATTGAGA
Found at i:13309 original size:18 final size:17
Alignment explanation
Indices: 13259--13310 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
13249 TATTCTTATG
13259 ATTTATTTTTAAAAAAATC
1 ATTT-TTTTT-AAAAAATC
*
13278 ATTTATTTTAAAAAATC
1 ATTTTTTTTAAAAAATC
13295 -TTATTTTTTACAAAAA
1 ATT-TTTTTTA-AAAAA
13311 AAAAATCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 2 0.07
17 14 0.48
18 9 0.31
19 4 0.14
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTTTTTAAAAAATC
Found at i:13347 original size:6 final size:6
Alignment explanation
Indices: 13336--13360 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13326 TTCGAGTTTA
13336 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
13361 TTTTTAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:13932 original size:18 final size:18
Alignment explanation
Indices: 13882--13932 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
13872 ATCTTAAAAG
* *
13882 TAATTTTTACTCTTTTTT
1 TAATTTTTATTTTTTTTT
*
13900 TAATTTTTCTGTTTTTTTT
1 TAATTTTTAT-TTTTTTTT
13919 TAATTTTTATTTTT
1 TAATTTTTATTTTT
13933 ATTAAATCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (18 bp):
TAATTTTTATTTTTTTTT
Found at i:17544 original size:10 final size:10
Alignment explanation
Indices: 17525--17557 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
17515 ATGTTGATTC
*
17525 AAATGAATAA
1 AAATGGATAA
17535 AAATGGATAA
1 AAATGGATAA
17545 AAAT-GATAA
1 AAATGGATAA
17554 AAAT
1 AAAT
17558 TGAGAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (10 bp):
AAATGGATAA
Found at i:19787 original size:6 final size:6
Alignment explanation
Indices: 19762--19800 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
19752 ACAATTCATA
* * *
19762 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
19801 ATTTTGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:24255 original size:26 final size:26
Alignment explanation
Indices: 24226--24275 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
24216 TCAAGAGTTT
* *
24226 TTTCACATTTTCCTCACTTTCCTTTC
1 TTTCACATCTTCCTCACTATCCTTTC
* *
24252 TTTCTCATCTTCCTTACTATCCTT
1 TTTCACATCTTCCTCACTATCCTT
24276 CCCTTTTCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.12, C:0.34, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTCACATCTTCCTCACTATCCTTTC
Found at i:26615 original size:19 final size:18
Alignment explanation
Indices: 26571--26636 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 18
26561 ATGTACGATC
26571 TTAAAATTAAAAT--AAAA
1 TTAAAA-TAAAATAAAAAA
26588 -TAAACATAAACATAAAAAA
1 TTAAA-ATAAA-ATAAAAAA
26607 TTAAAAT-AAATAAAAAA
1 TTAAAATAAAATAAAAAA
*
26624 TCAAAAATAAAAT
1 T-TAAAATAAAAT
26637 TTTGGTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
16 8 0.20
17 12 0.29
18 7 0.17
19 10 0.24
20 4 0.10
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
TTAAAATAAAATAAAAAA
Found at i:26629 original size:25 final size:24
Alignment explanation
Indices: 26579--26636 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
26569 TCTTAAAATT
*
26579 AAAATAAAATAAACATAAACATAA
1 AAAATAAAATAAACATAAAAATAA
* *
26603 AAAATTAAAATAAATA-AAAAATCA
1 AAAA-TAAAATAAACATAAAAATAA
26627 AAAATAAAAT
1 AAAATAAAAT
26637 TTTGGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.20
24 14 0.47
25 10 0.33
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (24 bp):
AAAATAAAATAAACATAAAAATAA
Found at i:26630 original size:18 final size:17
Alignment explanation
Indices: 26584--26634 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
26574 AAATTAAAAT
*
26584 AAAATAAACATAAACATAA
1 AAAATAAAAAT-AA-ATAA
*
26603 AAAATTAAAATAAATAA
1 AAAATAAAAATAAATAA
26620 AAAATCAAAAATAAA
1 AAAAT-AAAAATAAA
26635 ATTTTGGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.32
18 10 0.36
19 9 0.32
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAATAAAAATAAATAA
Found at i:36142 original size:9 final size:9
Alignment explanation
Indices: 36125--36155 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
36115 TATTCGCGAA
*
36125 CTTACTAAG
1 CTTAATAAG
36134 CTTAATAAG
1 CTTAATAAG
36143 CTTAATAAG
1 CTTAATAAG
36152 CTTA
1 CTTA
36156 CTCGTGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (9 bp):
CTTAATAAG
Found at i:36889 original size:24 final size:24
Alignment explanation
Indices: 36862--36911 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
36852 AATGAATAGA
36862 AACACAGAAATCCTAACCGACGAC
1 AACACAGAAATCCTAACCGACGAC
* *
36886 AACACAGATATCCTACCCGACGAC
1 AACACAGAAATCCTAACCGACGAC
36910 AA
1 AA
36912 TGTTCGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.34, G:0.12, T:0.10
Consensus pattern (24 bp):
AACACAGAAATCCTAACCGACGAC
Found at i:37908 original size:19 final size:18
Alignment explanation
Indices: 37865--37908 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
37855 ATAAAAAATG
37865 TATAAAATTATTAAATAT
1 TATAAAATTATTAAATAT
*
37883 TAAAAAATTATATAAATAT
1 TATAAAATTAT-TAAATAT
*
37902 TTTAAAA
1 TATAAAA
37909 AAGTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAAATTATTAAATAT
Found at i:43523 original size:17 final size:16
Alignment explanation
Indices: 43497--43537 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
43487 CTTTAAAAAT
*
43497 ATAAA-AAAAAATTAC
1 ATAAATAAAAAAATAC
*
43512 ATAAATAAAAAAATAT
1 ATAAATAAAAAAATAC
43528 ATAAATAAAA
1 ATAAATAAAA
43538 TTATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAATAAAAAAATAC
Found at i:43535 original size:20 final size:19
Alignment explanation
Indices: 43497--43536 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43487 CTTTAAAAAT
*
43497 ATAAAAAAAAATTACATAA
1 ATAAAAAAAAATTAAATAA
*
43516 ATAAAAAAATATATAAATAA
1 ATAAAAAAAAAT-TAAATAA
43536 A
1 A
43537 ATTATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (19 bp):
ATAAAAAAAAATTAAATAA
Found at i:50700 original size:27 final size:28
Alignment explanation
Indices: 50649--50706 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
50639 TATTTTACCC
50649 ATTTTCTTATATTTTTTCCCATCAAACAA
1 ATTTTCTTATA-TTTTTCCCATCAAACAA
* *
50678 ATTTTCTTATA-TTTTCTCATCAACCAA
1 ATTTTCTTATATTTTTCCCATCAAACAA
50705 AT
1 AT
50707 ACAAAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 16 0.59
29 11 0.41
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTTCTTATATTTTTCCCATCAAACAA
Found at i:51482 original size:3 final size:3
Alignment explanation
Indices: 51476--51508 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
51466 TTTCAAAATT
51476 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
51509 ATAGAGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54888 original size:15 final size:15
Alignment explanation
Indices: 54870--54900 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54860 ATGATCCAAA
54870 TTGACATTATAATCC
1 TTGACATTATAATCC
*
54885 TTGACGTTATAATCC
1 TTGACATTATAATCC
54900 T
1 T
54901 CAATATAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (15 bp):
TTGACATTATAATCC
Found at i:56568 original size:13 final size:13
Alignment explanation
Indices: 56550--56574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56540 GCTTTAGTTA
56550 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
56563 AAAAAAGAAAAA
1 AAAAAAGAAAAA
56575 CAAGAGCAAA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:57012 original size:18 final size:18
Alignment explanation
Indices: 56963--57054 Score: 64
Period size: 18 Copynumber: 4.9 Consensus size: 18
56953 AATAAAGAAG
56963 TAATACAAATTTAAAAATA
1 TAATA-AAATTTAAAAATA
** *
56982 T-ATAACTTATTAAAATTA
1 TAATAAAAT-TTAAAAATA
*
57000 TAATAAAATTTAAAGAAAA
1 TAATAAAATTTAAA-AATA
57019 T-ATAAAACTTTATAAAAATA
1 TAATAAAA--TT-TAAAAATA
*
57039 TAA-AAAATTTTAAAAT
1 TAATAAAATTTAAAAAT
57055 TTTAAAAAGT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
17 8 0.14
18 25 0.44
19 9 0.16
20 10 0.18
21 5 0.09
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (18 bp):
TAATAAAATTTAAAAATA
Found at i:57033 original size:28 final size:28
Alignment explanation
Indices: 57002--57081 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 28
56992 TAAAATTATA
57002 ATAAAATTTAAAGAAAATATAAAACTTT
1 ATAAAATTTAAAGAAAATATAAAACTTT
* * * *
57030 ATAAAAATATAAA-AAATTTTAAAATTTT
1 AT-AAAATTTAAAGAAAATATAAAACTTT
* *
57058 A-AAAAGTTATAGGAAAATATAAAA
1 ATAAAATTTA-AAGAAAATATAAAA
57082 ATCTTAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
26 6 0.15
27 1 0.03
28 24 0.60
29 9 0.22
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (28 bp):
ATAAAATTTAAAGAAAATATAAAACTTT
Found at i:58955 original size:21 final size:21
Alignment explanation
Indices: 58931--58985 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
58921 ATAATAGCGT
*
58931 AATTCAAATATAAAGTTTAGA
1 AATTCAAATATAAAATTTAGA
* *
58952 AATTCAAACATAAAATTTATA
1 AATTCAAATATAAAATTTAGA
*
58973 AATCCAAAT-TAAA
1 AATTCAAATATAAA
58986 TAATCCAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (21 bp):
AATTCAAATATAAAATTTAGA
Found at i:62162 original size:6 final size:6
Alignment explanation
Indices: 62151--62192 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
62141 ATATAAAAAT
*
62151 ATATTA ATATTA ATATTA ATATTA GTATTA ATATTA TATATT
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA -ATATT
62193 TTGTAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
ATATTA
Found at i:65774 original size:7 final size:7
Alignment explanation
Indices: 65762--65791 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
65752 TTTTGAAAAA
65762 GTCAACG
1 GTCAACG
65769 GTCAACG
1 GTCAACG
*
65776 ATCAACG
1 GTCAACG
65783 GTCAACG
1 GTCAACG
65790 GT
1 GT
65792 TTGACTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:71789 original size:19 final size:17
Alignment explanation
Indices: 71734--71786 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
71724 GAATAGTTAC
71734 TAACAAAAT-AAATTAA
1 TAACAAAATAAAATTAA
*
71750 TAATCCAAAATAAAAATAA
1 TAA--CAAAATAAAATTAA
71769 TAACAATAATAAAATTAA
1 TAACAA-AATAAAATTAA
71787 ATATTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 3 0.10
17 3 0.10
18 16 0.52
19 9 0.29
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.25
Consensus pattern (17 bp):
TAACAAAATAAAATTAA
Found at i:73062 original size:22 final size:21
Alignment explanation
Indices: 72995--73064 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
72985 AAGGGGTAAA
72995 GGTTTGGGTTTTAAAAGGGTTATTG
1 GGTTT-GG-TTTAAAAGGG-T-TTG
** * *
73020 GGTTTAATTTTAAAGGATTTG
1 GGTTTGGTTTAAAAGGGTTTG
73041 GGTTTGGTTATAAAAGGGTTTG
1 GGTTTGGTT-TAAAAGGGTTTG
73063 GG
1 GG
73065 CTTAGGCACA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
21 10 0.28
22 13 0.36
23 8 0.22
25 5 0.14
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (21 bp):
GGTTTGGTTTAAAAGGGTTTG
Found at i:80206 original size:41 final size:40
Alignment explanation
Indices: 80150--80325 Score: 176
Period size: 41 Copynumber: 4.6 Consensus size: 40
80140 AAACGCCACA
* *
80150 AAAGGT-AGAGCAATAGCGACGCTTATAACAAAGCGTCGCT
1 AAAGGTCATAGCAATAGCGACGCTTATGAC-AAGCGTCGCT
*
80190 AAAGGTCATAGCAATAGCGGCGC-T-T-AC---C--CGCT
1 AAAGGTCATAGCAATAGCGACGCTTATGACAAGCGTCGCT
* *
80222 AAAGGTCATAGCAATAGCAACGCTTATGAGAAAGCGTCGCT
1 AAAGGTCATAGCAATAGCGACGCTTATGA-CAAGCGTCGCT
*
80263 AAAGGTCATAG--ATAGCGACGCTTATGGTCAAGCGTCGCT
1 AAAGGTCATAGCAATAGCGACGCTTAT-GACAAGCGTCGCT
* *
80302 AAAGGTCAGAGCAATAGCGTCGCT
1 AAAGGTCATAGCAATAGCGACGCT
80326 AAAGGTCAGA
Statistics
Matches: 113, Mismatches: 10, Indels: 25
0.76 0.07 0.17
Matches are distributed among these distances:
32 25 0.22
33 1 0.01
34 2 0.02
35 1 0.01
38 2 0.02
39 35 0.31
40 8 0.07
41 39 0.35
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (40 bp):
AAAGGTCATAGCAATAGCGACGCTTATGACAAGCGTCGCT
Found at i:80245 original size:73 final size:70
Alignment explanation
Indices: 80150--80286 Score: 202
Period size: 73 Copynumber: 1.9 Consensus size: 70
80140 AAACGCCACA
* *
80150 AAAGGTAGAGCAATAGCGACGCTTATAACAAAGCGTCGCTAAAGGTCATAGCAATAGCGGCGCTT
1 AAAGGTAGAGCAATAGCAACGCTTATAACAAAGCGTCGCTAAAGGTCATAG--ATAGCGACGCTT
80215 ACCCGCT
64 ACCCGCT
* * *
80222 AAAGGTCATAGCAATAGCAACGCTTATGAGAAAGCGTCGCTAAAGGTCATAGATAGCGACGCTTA
1 AAAGGT-AGAGCAATAGCAACGCTTATAACAAAGCGTCGCTAAAGGTCATAGATAGCGACGCTTA
80287 TGGTCAAGCG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
71 12 0.20
72 6 0.10
73 41 0.69
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (70 bp):
AAAGGTAGAGCAATAGCAACGCTTATAACAAAGCGTCGCTAAAGGTCATAGATAGCGACGCTTAC
CCGCT
Found at i:80246 original size:32 final size:32
Alignment explanation
Indices: 80186--80247 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
80176 AACAAAGCGT
**
80186 CGCTAAAGGTCATAGCAATAGCGGCGCTTACC
1 CGCTAAAGGTCATAGCAATAGCAACGCTTACC
80218 CGCTAAAGGTCATAGCAATAGCAACGCTTA
1 CGCTAAAGGTCATAGCAATAGCAACGCTTA
80248 TGAGAAAGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (32 bp):
CGCTAAAGGTCATAGCAATAGCAACGCTTACC
Found at i:80325 original size:24 final size:24
Alignment explanation
Indices: 80293--80349 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
80283 CTTATGGTCA
80293 AGCGTCGCTAAAGGTCAGAGCAAT
1 AGCGTCGCTAAAGGTCAGAGCAAT
80317 AGCGTCGCTAAAGGTCAGAGCAAT
1 AGCGTCGCTAAAGGTCAGAGCAAT
*
80341 AGCGGCGCT
1 AGCGTCGCT
80350 TATGGGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.32, T:0.16
Consensus pattern (24 bp):
AGCGTCGCTAAAGGTCAGAGCAAT
Found at i:80333 original size:41 final size:41
Alignment explanation
Indices: 80218--80325 Score: 150
Period size: 39 Copynumber: 2.7 Consensus size: 41
80208 GGCGCTTACC
* *
80218 CGCTAAAGGTCATAGCAATAGCAACGCTTATGAG-AAAGCGT
1 CGCTAAAGGTCATAGCAATAGCGACGCTTATG-GTCAAGCGT
80259 CGCTAAAGGTCATAG--ATAGCGACGCTTATGGTCAAGCGT
1 CGCTAAAGGTCATAGCAATAGCGACGCTTATGGTCAAGCGT
* *
80298 CGCTAAAGGTCAGAGCAATAGCGTCGCT
1 CGCTAAAGGTCATAGCAATAGCGACGCT
80326 AAAGGTCAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
38 1 0.02
39 34 0.57
41 25 0.42
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.20
Consensus pattern (41 bp):
CGCTAAAGGTCATAGCAATAGCGACGCTTATGGTCAAGCGT
Found at i:80361 original size:65 final size:65
Alignment explanation
Indices: 80254--80406 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 65
80244 CTTATGAGAA
* ** * *
80254 AGCGTCGCTAAAGGTCATAG--ATAGCGACGCTTATGGTCAAGCGTCGCTAAAGGTCAGAGCAAT
1 AGCGTCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGAAAT
*
80317 AGCGTCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGAAAT
1 AGCGTCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGAAAT
* **
80382 AGCGGCGCT-TTGGTCAGAGCAATAG
1 AGCGTCGCTAAAGGTCAGAGCAATAG
80407 TTGCTTGTGA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
63 19 0.24
64 14 0.18
65 46 0.58
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.18
Consensus pattern (65 bp):
AGCGTCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGAAAT
Found at i:80695 original size:43 final size:43
Alignment explanation
Indices: 80638--80821 Score: 269
Period size: 43 Copynumber: 4.3 Consensus size: 43
80628 TTTGTTAATA
* * ** *
80638 TTAGTGGCATTTGTGGGAAAAATGCCACTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
80681 TTAGCGGCGTTTGTGGTATAAGTGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
80724 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
80767 TTAGCAGCGTTTATGGGATAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
80810 TTAGCGGCGTTT
1 TTAGCGGCGTTT
80822 TTTTAATAAA
Statistics
Matches: 128, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 128 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:83136 original size:18 final size:18
Alignment explanation
Indices: 83113--83155 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
83103 AAATAAGTTT
83113 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
83131 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
83149 TTAATTA
1 TTAATTA
83156 CACTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:84639 original size:22 final size:23
Alignment explanation
Indices: 84609--84658 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
84599 AAATATTTAA
84609 ATTTGGTATATAAT-ATTT-TCAT
1 ATTTGGTATA-AATAATTTATCAT
*
84631 ATTTTGTATAAATAATTTAATCAT
1 ATTTGGTATAAATAATTT-ATCAT
84655 ATTT
1 ATTT
84659 AATATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.12
22 13 0.54
24 8 0.33
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (23 bp):
ATTTGGTATAAATAATTTATCAT
Found at i:88934 original size:41 final size:43
Alignment explanation
Indices: 88845--88935 Score: 100
Period size: 41 Copynumber: 2.2 Consensus size: 43
88835 AAGGTGTGTG
*
88845 TGTGTGTATACTGTTTTGAGGCACACGAGCGTGTGTAAGGGTGA
1 TGTGTGTATA-TGTTTTAAGGCACACGAGCGTGTGTAAGGGTGA
* * *
88889 -GTGTGTAT-TGTTTTAAGGCATACG-GACGTGTGTCATGGT-A
1 TGTGTGTATATGTTTTAAGGCACACGAG-CGTGTGTAAGGGTGA
88929 TGTGTGT
1 TGTGTGT
88936 GTATACTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
40 2 0.05
41 31 0.76
43 8 0.20
ACGTcount: A:0.19, C:0.10, G:0.35, T:0.36
Consensus pattern (43 bp):
TGTGTGTATATGTTTTAAGGCACACGAGCGTGTGTAAGGGTGA
Found at i:91148 original size:5 final size:5
Alignment explanation
Indices: 91133--91176 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
91123 GAGGGCCGGG
91133 GACCA -ACCA GACCA GACCA GACCA GACCA GACCA GA-CA GACCA G
1 GACCA GACCA GACCA GACCA GACCA GACCA GACCA GACCA GACCA G
91177 CTGCTGCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.22
5 29 0.78
ACGTcount: A:0.41, C:0.39, G:0.20, T:0.00
Consensus pattern (5 bp):
GACCA
Found at i:99342 original size:9 final size:9
Alignment explanation
Indices: 99311--99435 Score: 60
Period size: 9 Copynumber: 13.6 Consensus size: 9
99301 TTTCTTAAAA
*
99311 TTTTATAAAA
1 TTTTAT-AAT
*
99321 TTTTACAAT
1 TTTTATAAT
*
99330 TTTT-TATAG
1 TTTTATA-AT
*
99339 TTTTATATT
1 TTTTATAAT
*
99348 TTTTCTAAT
1 TTTTATAAT
99357 TTTTAATAATT
1 TTTT-ATAA-T
*
99368 TTTTATTAAAA
1 TTTTA-T-AAT
*
99379 TTTAATAAT
1 TTTTATAAT
* **
99388 ATTTATAGC
1 TTTTATAAT
*
99397 TTTTATTGA-
1 TTTTA-TAAT
99406 TTTTA-AAT
1 TTTTATAAT
99414 TTTTA-AAT
1 TTTTATAAT
99422 TTTTATAAT
1 TTTTATAAT
99431 TTTTA
1 TTTTA
99436 ATAAAAGTAG
Statistics
Matches: 86, Mismatches: 20, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
7 1 0.01
8 14 0.16
9 46 0.53
10 13 0.15
11 10 0.12
12 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:99342 original size:10 final size:10
Alignment explanation
Indices: 99311--99373 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 10
99301 TTTCTTAAAA
**
99311 TTTTATAAAA
1 TTTTATAATT
*
99321 TTTTACAATT
1 TTTTATAATT
*
99331 TTTTAT-A-G
1 TTTTATAATT
99339 TTTTAT-ATT
1 TTTTATAATT
*
99348 TTTTCTAATT
1 TTTTATAATT
*
99358 TTTAATAATT
1 TTTTATAATT
99368 TTTTAT
1 TTTTAT
99374 TAAAATTTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
8 7 0.17
9 6 0.15
10 28 0.68
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:99419 original size:8 final size:8
Alignment explanation
Indices: 99406--99436 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
99396 CTTTTATTGA
99406 TTTTAAAT
1 TTTTAAAT
99414 TTTTAAAT
1 TTTTAAAT
99422 TTTTATAAT
1 TTTTA-AAT
99431 TTTTAA
1 TTTTAA
99437 TAAAAGTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTAAAT
Found at i:104437 original size:14 final size:14
Alignment explanation
Indices: 104397--104457 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
104387 TTTTAAAATC
*
104397 TATATTTACATATGA
1 TATATATACATAT-A
104412 -ATATAGTA-ATATA
1 TATATA-TACATATA
104425 TAT-TCATACATATA
1 TATAT-ATACATATA
*
104439 TATATATACACATA
1 TATATATACATATA
104453 TATAT
1 TATAT
104458 TTAAAATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
13 4 0.10
14 32 0.82
15 3 0.08
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (14 bp):
TATATATACATATA
Found at i:111076 original size:18 final size:18
Alignment explanation
Indices: 111053--111188 Score: 73
Period size: 18 Copynumber: 7.3 Consensus size: 18
111043 ATTTTAAAAT
111053 TTTTTTACAATTTTTATA
1 TTTTTTACAATTTTTATA
* *
111071 TTTTTTCCAATTTTTAAA
1 TTTTTTACAATTTTTATA
* *
111089 ATTTTTGCAA-TTTTATA
1 TTTTTTACAATTTTTATA
*
111106 TTATCATTACTAATTTTTATAA
1 TT-T-TTTAC-AATTTTTAT-A
* *
111128 ATTTATA-AATTTTTAT-
1 TTTTTTACAATTTTTATA
* *
111144 TTTTTAAATAATTTTCTATA
1 TTTTT-TACAATTTT-TATA
* *
111164 ATTTTTA-ATGATTTTAATA
1 TTTTTTACA--ATTTTTATA
111183 TTTTTT
1 TTTTTT
111189 TCATTTTAAT
Statistics
Matches: 89, Mismatches: 18, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
16 3 0.03
17 8 0.09
18 41 0.46
19 15 0.17
20 13 0.15
21 7 0.08
22 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTTTTACAATTTTTATA
Found at i:111100 original size:9 final size:9
Alignment explanation
Indices: 111054--111102 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
111044 TTTTAAAATT
111054 TTTTTACAA
1 TTTTTACAA
* *
111063 TTTTTATAT
1 TTTTTACAA
*
111072 TTTTTCCAA
1 TTTTTACAA
*
111081 TTTTTAAAA
1 TTTTTACAA
*
111090 TTTTTGCAA
1 TTTTTACAA
111099 TTTT
1 TTTT
111103 ATATTATCAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTACAA
Found at i:113031 original size:13 final size:13
Alignment explanation
Indices: 112983--113034 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
112973 AGTTTCTCAT
112983 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
112996 GGCTGTGGAAAA-
1 TGCTTTTGAAAAG
**
113008 TGCTTAAGAAAAG
1 TGCTTTTGAAAAG
113021 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
113034 T
1 T
113035 TTAGTTTAAG
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:117654 original size:20 final size:20
Alignment explanation
Indices: 117605--117654 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
117595 AAACGGGAAA
* *
117605 GAAAGAAAGGAAGGAAGAAG
1 GAAAGAAAAGAAAGAAGAAG
* *
117625 GAGAGGAAAGAAAGAAGAAG
1 GAAAGAAAAGAAAGAAGAAG
117645 GAAAGAAAAG
1 GAAAGAAAAG
117655 TAATGTGTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (20 bp):
GAAAGAAAAGAAAGAAGAAG
Done.