Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013656.1 Kokia drynarioides strain JFW-HI SEQ_128684, 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: 288284
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 136 characters in sequence are not A, C, G, or T
Found at i:915 original size:6 final size:6
Alignment explanation
Indices: 904--948 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
894 AATTTTGAAA
* *
904 TTAAAT TTAAAT TTAAA- TTAAAT TTAAA- ATAAAT CTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
949 ATAAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 9 0.26
6 25 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:923 original size:17 final size:16
Alignment explanation
Indices: 901--958 Score: 89
Period size: 17 Copynumber: 3.5 Consensus size: 16
891 GTTAATTTTG
*
901 AAATTAAATTTAAATTT
1 AAATTAAATTTAAA-AT
918 AAATTAAATTTAAAAT
1 AAATTAAATTTAAAAT
934 AAATCTAAATTTAAAAT
1 AAAT-TAAATTTAAAAT
951 AAATTAAA
1 AAATTAAA
959 AAGGAGACCC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
16 9 0.23
17 30 0.77
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAAATTTAAAAT
Found at i:924 original size:11 final size:11
Alignment explanation
Indices: 904--958 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
894 AATTTTGAAA
904 TTAAATTTAAAT
1 TTAAA-TTAAAT
916 TTAAATTAAAT
1 TTAAATTAAAT
*
927 TTAAAATAAAT
1 TTAAATTAAAT
*
938 CTAAATTTAAA-
1 TTAAA-TTAAAT
*
949 ATAAATTAAA
1 TTAAATTAAA
959 AAGGAGACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 5 0.13
11 24 0.63
12 9 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:3840 original size:25 final size:25
Alignment explanation
Indices: 3804--3878 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
3794 GATGATGAAT
*
3804 ATATTCTATTTGGCTCGTAAGAGCG
1 ATATTCTGTTTGGCTCGTAAGAGCG
3829 ATATTCTGTTTGGCTCGTAAGAGTCG
1 ATATTCTGTTTGGCTCGTAAGAG-CG
* *
3855 A-ACTCTGTTTGGGCTCATAAGAGC
1 ATATTCTGTTT-GGCTCGTAAGAGC
3879 TAAACTCTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
25 31 0.69
26 14 0.31
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (25 bp):
ATATTCTGTTTGGCTCGTAAGAGCG
Found at i:3876 original size:26 final size:25
Alignment explanation
Indices: 3815--3898 Score: 98
Period size: 26 Copynumber: 3.3 Consensus size: 25
3805 TATTCTATTT
*
3815 GGCTCGTAAGAGCGATATTCTGTTT-
1 GGCTCGTAAGAGCGA-ACTCTGTTTG
3840 GGCTCGTAAGAGTCGAACTCTGTTTG
1 GGCTCGTAAGAG-CGAACTCTGTTTG
* * *
3866 GGCTCATAAGAGCTAAACTCTGTCTG
1 GGCTCGTAAGAGC-GAACTCTGTTTG
3892 GGCTCGT
1 GGCTCGT
3899 TTAAGTTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
25 21 0.41
26 30 0.59
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (25 bp):
GGCTCGTAAGAGCGAACTCTGTTTG
Found at i:5772 original size:51 final size:51
Alignment explanation
Indices: 5647--5835 Score: 229
Period size: 51 Copynumber: 3.6 Consensus size: 51
5637 TTTCATTTAA
* ** *
5647 TACTCACGATGACA-TATAGTCATCGAACCTCTTGTTCCA-CATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATCAT-GG-ATTCATT
* * *
5700 TACTCACGATGACTCTAAGTCATAGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATCATGGATTCATT
* * *
5751 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATCATGGATTCATT
5802 TACTCACGATGACACTTAGTCATCGGACCCTTTA
1 TACTCACGATGACACTTAGTCATCGGA-CCTTTA
5836 GTTTATAGCT
Statistics
Matches: 120, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
51 78 0.65
52 14 0.12
53 27 0.22
54 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATCATGGATTCATT
Found at i:6862 original size:28 final size:28
Alignment explanation
Indices: 6822--6879 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
6812 TTGCACTTTT
6822 CTCAATTTAATCCTTTTTACTTAATTAA
1 CTCAATTTAATCCTTTTTACTTAATTAA
6850 CTCAATTTAATCCTTTTTACTTAATTAA
1 CTCAATTTAATCCTTTTTACTTAATTAA
6878 CT
1 CT
6880 AAGTAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (28 bp):
CTCAATTTAATCCTTTTTACTTAATTAA
Found at i:9135 original size:31 final size:31
Alignment explanation
Indices: 9100--9166 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
9090 AAGTAAGTGA
9100 TTTTAATCAAAATTAAGGAATTAAAATTCAT
1 TTTTAATCAAAATTAAGGAATTAAAATTCAT
9131 TTTTAATCAAAATTAAGGAATTAAAATTCAT
1 TTTTAATCAAAATTAAGGAATTAAAATTCAT
9162 TTTTA
1 TTTTA
9167 TTCTTCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (31 bp):
TTTTAATCAAAATTAAGGAATTAAAATTCAT
Found at i:9938 original size:25 final size:26
Alignment explanation
Indices: 9903--9953 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
9893 AGGCGATGAA
* *
9903 GATATTTTGTCT-GGCTCGTAAGAGC
1 GATATTCTGTCTGGGATCGTAAGAGC
9928 GATATTCTGTCTGGGATCGTAAGAGC
1 GATATTCTGTCTGGGATCGTAAGAGC
9954 AAAACTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (26 bp):
GATATTCTGTCTGGGATCGTAAGAGC
Found at i:11299 original size:21 final size:21
Alignment explanation
Indices: 11262--11309 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
11252 ACTTCTACTA
*
11262 ATACAAGTGACAATTCTATCG
1 ATACAAGTGACAATTCTACCG
**
11283 ATACAAGTGACTCTTCTACCG
1 ATACAAGTGACAATTCTACCG
*
11304 AAACAA
1 ATACAA
11310 CTCTTACTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (21 bp):
ATACAAGTGACAATTCTACCG
Found at i:12077 original size:24 final size:24
Alignment explanation
Indices: 12027--12077 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
12017 CAAGACCAAA
*
12027 TTAGCTCTCACGAACCCAGAACGG
1 TTAGCTCTCACGAACCCAGAACAG
* * * *
12051 TTAGCTCTTATGAGCCCAGAATAG
1 TTAGCTCTCACGAACCCAGAACAG
12075 TTA
1 TTA
12078 ACTAGTAATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (24 bp):
TTAGCTCTCACGAACCCAGAACAG
Found at i:17371 original size:24 final size:24
Alignment explanation
Indices: 17343--17403 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
17333 AGAAATAATC
* *
17343 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGCTTAGTTG
*
17367 TTTCAATTAAACTCTGCTTAGTTG
1 TTTCAGTTAAACTCTGCTTAGTTG
* *
17391 TTTGAGTCAAACT
1 TTTCAGTTAAACT
17404 TCTATTAGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.48
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGCTTAGTTG
Found at i:20406 original size:14 final size:12
Alignment explanation
Indices: 20385--20427 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 12
20375 GTTCCTAAAC
20385 TTTTTAATTTAT
1 TTTTTAATTTAT
*
20397 TTGGTTTAATATAT
1 TT--TTTAATTTAT
20411 TTTTTAAATTTAT
1 TTTTT-AATTTAT
20424 TTTT
1 TTTT
20428 ATATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 11 0.42
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTTAATTTAT
Found at i:34466 original size:120 final size:120
Alignment explanation
Indices: 34253--34495 Score: 477
Period size: 120 Copynumber: 2.0 Consensus size: 120
34243 ATCTTCATCA
34253 TTGATCTCTTTCTGTGACATGCTATATGTCTCTGACTCAGCACCTTGAGATCCATATCTCACAGG
1 TTGATCTCTTTCTGTGACATGCTATATGTCTCTGACTCAGCACCTTGAGATCCATATCTCACAGG
*
34318 CTTTGGTCCCACACCACTAACATTCACTTCCCTATTCGAACTCCCTCCCAAAGAT
66 CTTTGGTCCCACACCACTAACATTCACTTCACTATTCGAACTCCCTCCCAAAGAT
34373 TTGATCTCTTTCTGTGACATGCTATATGTCTCTGACTCAGCACCTTGAGATCCATATCTCACAGG
1 TTGATCTCTTTCTGTGACATGCTATATGTCTCTGACTCAGCACCTTGAGATCCATATCTCACAGG
34438 CTTTGGTCCCACACCACTAACATTCACTTCACTATTCGAACTCCCTCCCAAAGAT
66 CTTTGGTCCCACACCACTAACATTCACTTCACTATTCGAACTCCCTCCCAAAGAT
34493 TTG
1 TTG
34496 GAACGAGCAG
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 122 1.00
ACGTcount: A:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (120 bp):
TTGATCTCTTTCTGTGACATGCTATATGTCTCTGACTCAGCACCTTGAGATCCATATCTCACAGG
CTTTGGTCCCACACCACTAACATTCACTTCACTATTCGAACTCCCTCCCAAAGAT
Found at i:39233 original size:19 final size:18
Alignment explanation
Indices: 39209--39261 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
39199 AAATAAAACC
39209 ATATTTATATATATAAATA
1 ATATTTATATATATAAA-A
* *
39228 ATATTTATTTA-ATTAAA
1 ATATTTATATATATAAAA
39245 ATATTTA-AT-TATAAAA
1 ATATTTATATATATAAAA
39261 A
1 A
39262 CGTAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
18 4 0.14
19 10 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTATATATATAAAA
Found at i:40529 original size:2 final size:2
Alignment explanation
Indices: 40522--40555 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40512 AAAAAGATAA
40522 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
40556 GTTGTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42176 original size:18 final size:17
Alignment explanation
Indices: 42136--42179 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
42126 TTTATAGTTG
42136 TAATTAATTTAAAATTTT
1 TAATTAA-TTAAAATTTT
* *
42154 CAATTAATTAAATTTATT
1 TAATTAATTAAAATT-TT
42172 TAATTAAT
1 TAATTAAT
42180 GTTGAACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTAATTAAAATTTT
Found at i:47185 original size:25 final size:25
Alignment explanation
Indices: 47151--47210 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
47141 TTGTCAAAAG
47151 ATCAAATTGATAACTGTTATCTTGT
1 ATCAAATTGATAACTGTTATCTTGT
*
47176 ATCAAATTGATAACTGTTATGTTGT
1 ATCAAATTGATAACTGTTATCTTGT
**
47201 AGAAAATTGA
1 ATCAAATTGA
47211 CTTAACAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (25 bp):
ATCAAATTGATAACTGTTATCTTGT
Found at i:55376 original size:19 final size:19
Alignment explanation
Indices: 55352--55389 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
55342 GTACACAAAG
*
55352 AGTAAGCTCGACTTCTAAC
1 AGTAAGCTCAACTTCTAAC
55371 AGTAAGCTCAACTTCTAAC
1 AGTAAGCTCAACTTCTAAC
55390 TTACTGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (19 bp):
AGTAAGCTCAACTTCTAAC
Found at i:83941 original size:123 final size:123
Alignment explanation
Indices: 83713--83959 Score: 341
Period size: 123 Copynumber: 2.0 Consensus size: 123
83703 CCACCCCGTC
* ** ** *
83713 CACCACCTCTGCCTCTTCCACTAGCTGATCCTGTTGATGTGCCCCTACCACCACGACCCCTTCCA
1 CACCACCTCTGCCTCTTCCACCAGCTGAGACTGTTGATGCACCCCTACCACCACGAACCCTTCCA
* * * *
83778 CCAGACTTCACAGGAGACTCCAAATCTTTAATATCCTCTTCATCACTTTCGTCAATAT
66 CCAGACTTCACAGGAGACTCCAAATCTTTAACATCATCTTCATCACTTCCATCAATAT
* * * * *
83836 CACCACCTCTGCCTCTTCCGCCAGCTGGGACTTTTGATGCACCCCTGCCACCACGAACCTTTCCA
1 CACCACCTCTGCCTCTTCCACCAGCTGAGACTGTTGATGCACCCCTACCACCACGAACCCTTCCA
* *
83901 CCTGACTTTACAGGAGACTCCAAATCTTTAACATCATCTTCATCACTTCCATCAATAT
66 CCAGACTTCACAGGAGACTCCAAATCTTTAACATCATCTTCATCACTTCCATCAATAT
83959 C
1 C
83960 TACAGCTTTT
Statistics
Matches: 107, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
123 107 1.00
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (123 bp):
CACCACCTCTGCCTCTTCCACCAGCTGAGACTGTTGATGCACCCCTACCACCACGAACCCTTCCA
CCAGACTTCACAGGAGACTCCAAATCTTTAACATCATCTTCATCACTTCCATCAATAT
Found at i:86673 original size:42 final size:42
Alignment explanation
Indices: 86610--86775 Score: 192
Period size: 42 Copynumber: 4.0 Consensus size: 42
86600 TTCCCCAGTG
* *
86610 ACAAGCACAAGCAATGGTATCTTCGGTGGTACATCTGCAAGT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAGT
*
86652 ACAAGCACAGGCAATGATATCTTTGGTGGTACATCTGC-AGCT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAG-T
* ** * * * **
86694 ACAAGCACGGGCTCTGGTTTATTTGGTGGTACATCAGCATCT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAGT
*
86736 ACAAGCACAGGCAAT-GTCGTCTTTGGTGGTACATCTGCAA
1 ACAAGCACAGGCAATGGT-ATCTTTGGTGGTACATCTGCAA
86776 CAAGCAAAGG
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
41 4 0.04
42 98 0.96
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (42 bp):
ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAGT
Found at i:89979 original size:42 final size:42
Alignment explanation
Indices: 89896--90092 Score: 229
Period size: 42 Copynumber: 4.8 Consensus size: 42
89886 TGGCAAAGAC
* * * *
89896 GTACCACCAAAAATACTACTACCTGTGC-T-T-GTTGCAGAT
1 GTACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGAT
* *
89935 GTACCAGCAAAGATGCCATTGCCTGTGCTTGTAGTTGCAGAT
1 GTACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGAT
* * * *
89977 GTACCACCAAATAAACCAGTGCCCGTGCTTGTAGTTGCAGAT
1 GTACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGAT
* * * *
90019 GTACCACCAAAGTTACCATTGCCTTTTCTTGTACTTGCAGAT
1 GTACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGAT
* *
90061 GTACCACCGAAGATACCATTGCTTGTGCTTGT
1 GTACCACCAAAGATACCATTGCCTGTGCTTGT
90093 CACTAGGGAA
Statistics
Matches: 130, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
39 22 0.17
40 1 0.01
41 1 0.01
42 106 0.82
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (42 bp):
GTACCACCAAAGATACCATTGCCTGTGCTTGTAGTTGCAGAT
Found at i:99419 original size:2 final size:2
Alignment explanation
Indices: 99412--99462 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
99402 GCTTTGAAAC
99412 AT AT AT 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 AT AT AT
99454 AT AT AT AT A
1 AT AT AT AT A
99463 ATCTAATTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:100252 original size:29 final size:31
Alignment explanation
Indices: 100219--100276 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
100209 ACAACGGGAA
*
100219 AAAGCGCTTTCACG-T-GGGCGCTTTTTTGT
1 AAAGCGCTTTCACGTTAGCGCGCTTTTTTGT
100248 AAAGCGCTTTCACGTTAGCGCGCTTTTTT
1 AAAGCGCTTTCACGTTAGCGCGCTTTTTT
100277 CTAACACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 1 0.04
31 11 0.42
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (31 bp):
AAAGCGCTTTCACGTTAGCGCGCTTTTTTGT
Found at i:101698 original size:59 final size:59
Alignment explanation
Indices: 101573--101699 Score: 132
Period size: 59 Copynumber: 2.2 Consensus size: 59
101563 TAGCACCTCA
* * * * *
101573 ATTTTTTTAATTAAATAAAAGAGGTTTCGATAATTAGTGTATCAGCATTTTAAAAAATT
1 ATTTTTTTAATTAAATAAAAGAGGTGTCGATAATTAATGTATCAACACTTCAAAAAATT
* * * * *
101632 -TAATTTTTAATTAGAT-AAAGGGGATGTCGATCATTAATGTGTCAACACTTCAAAAAATT
1 AT-TTTTTTAATTAAATAAAAGAGG-TGTCGATAATTAATGTATCAACACTTCAAAAAATT
101691 ATTTTTTTA
1 ATTTTTTTA
101700 TTTCATAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
58 7 0.13
59 46 0.85
60 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.42
Consensus pattern (59 bp):
ATTTTTTTAATTAAATAAAAGAGGTGTCGATAATTAATGTATCAACACTTCAAAAAATT
Found at i:104557 original size:42 final size:42
Alignment explanation
Indices: 104498--104673 Score: 225
Period size: 42 Copynumber: 4.3 Consensus size: 42
104488 TTCCCCAGTG
* *
104498 ACAAGCACAAGCAATGGTATCTTCGGTGGTACATCTGCAAG-T
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGC-AGCT
*
104540 ACAAGCACAGGAAATGGTATCTTTGGTGGTACATCTGCAGCT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAGCT
* * * * * *
104582 ACAAGCACGGGCACTGGTTTATTTGGTGGTGCATCAGCAGCT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAGCT
*
104624 ACAAGCACAGGCAATGGCATCTTTGGTGGTACATCTGCA---
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAGCT
104663 ACAAGCACAGG
1 ACAAGCACAGG
104674 TAGTAGTAGT
Statistics
Matches: 116, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
39 11 0.09
41 2 0.02
42 103 0.89
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (42 bp):
ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAGCT
Found at i:117599 original size:13 final size:13
Alignment explanation
Indices: 117568--117602 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
117558 GAAATTTCTT
*
117568 AAAGAAAGTAAAA
1 AAAGAGAGTAAAA
117581 AAAGAGAGTAAAA
1 AAAGAGAGTAAAA
117594 AAAGAGAGT
1 AAAGAGAGT
117603 TAGTAGACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.09
Consensus pattern (13 bp):
AAAGAGAGTAAAA
Found at i:118770 original size:25 final size:23
Alignment explanation
Indices: 118700--118827 Score: 93
Period size: 23 Copynumber: 5.4 Consensus size: 23
118690 ACACTAGCGC
118700 GCCCTCTGT-TTAGCACGTT-TCGT
1 GCCCTCTGTATTAGCAC-TTGT-GT
* *
118723 GCCCTTTGT-TTAGCACCGTGTGT
1 GCCCTCTGTATTAGCA-CTTGTGT
*
118746 GCCCTTTGTTATTAGCACTTCGTGT
1 GCCCTCTG-TATTAGCACTT-GTGT
118771 GCCCTCTG-ATTAGCACTTTGTGT
1 GCCCTCTGTATTAGCAC-TTGTGT
* ** *
118794 TCCCTCTGTTACCCAGCACTTATGT
1 GCCCTCTG-TA-TTAGCACTTGTGT
118819 GCCCTCTGT
1 GCCCTCTGT
118828 TAAGTACTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
23 44 0.51
24 8 0.09
25 30 0.34
26 5 0.06
ACGTcount: A:0.11, C:0.30, G:0.20, T:0.39
Consensus pattern (23 bp):
GCCCTCTGTATTAGCACTTGTGT
Found at i:123992 original size:25 final size:25
Alignment explanation
Indices: 123964--124013 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
123954 TCCTCCAGAG
123964 TTAGACAAGATTCATAATGTTTTAC
1 TTAGACAAGATTCATAATGTTTTAC
123989 TTAGACAAGATTCATAATGTTTTAC
1 TTAGACAAGATTCATAATGTTTTAC
124014 ATGTGTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (25 bp):
TTAGACAAGATTCATAATGTTTTAC
Found at i:126061 original size:25 final size:23
Alignment explanation
Indices: 126006--126089 Score: 84
Period size: 23 Copynumber: 3.6 Consensus size: 23
125996 AGCATGTTTC
*
126006 GTGCCCTCTG-TTCAGAACTGT-GT
1 GTGCCCTCTGATT-AGCACT-TCGT
*
126029 GTGCCCTCTGTTATTAGTACTTCGT
1 GTGCCCTCTG--ATTAGCACTTCGT
*
126054 GTGCCCTCTGATTAGCACTTTGT
1 GTGCCCTCTGATTAGCACTTCGT
126077 GTGCCCTCT-ATTA
1 GTGCCCTCTGATTA
126090 CCCAACACTT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.07
23 30 0.56
24 1 0.02
25 17 0.31
26 2 0.04
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.39
Consensus pattern (23 bp):
GTGCCCTCTGATTAGCACTTCGT
Found at i:132550 original size:19 final size:19
Alignment explanation
Indices: 132520--132564 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
132510 AGTTTTCATG
*
132520 ATTTTATATTTTATCATTGT
1 ATTTT-TATTTTATCATTGC
*
132540 ATTTTTATTTTGTCATTGC
1 ATTTTTATTTTATCATTGC
132559 ATTTTT
1 ATTTTT
132565 GTTAATTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (19 bp):
ATTTTTATTTTATCATTGC
Found at i:133165 original size:16 final size:16
Alignment explanation
Indices: 133132--133176 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
133122 CAGTCACTTG
* *
133132 AAAAAGAAAAAATGAGA
1 AAAAAGAAGAAA-CAGA
*
133149 AAAAGGAAGAAACAGA
1 AAAAAGAAGAAACAGA
133165 AAAAAGAAGAAA
1 AAAAAGAAGAAA
133177 AAAAATTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (16 bp):
AAAAAGAAGAAACAGA
Found at i:137223 original size:21 final size:21
Alignment explanation
Indices: 137185--137237 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
137175 GTGCGTATTG
137185 AGGAAGAGAAAGAAGAAGAGA
1 AGGAAGAGAAAGAAGAAGAGA
* * *
137206 AGGAGGAGAAATAGGAAGA-A
1 AGGAAGAGAAAGAAGAAGAGA
*
137226 A-GAAAAGAAAGA
1 AGGAAGAGAAAGA
137238 GAGCAGGAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 8 0.31
20 2 0.08
21 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
AGGAAGAGAAAGAAGAAGAGA
Found at i:146684 original size:18 final size:16
Alignment explanation
Indices: 146661--146696 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
146651 TTTAGTAAAT
146661 ATTAAATTGAGGAATGAA
1 ATTAAATTGA--AATGAA
146679 ATTAAATTGAAATGAA
1 ATTAAATTGAAATGAA
146695 AT
1 AT
146697 GGTATTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
ATTAAATTGAAATGAA
Found at i:147323 original size:52 final size:52
Alignment explanation
Indices: 147238--147529 Score: 435
Period size: 52 Copynumber: 5.6 Consensus size: 52
147228 GTAAATGCAA
* * *
147238 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCATTTACAGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * ** * *
147290 GAGTTTTGATGATTATGTGTCATTGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* *
147342 AAGATCCGTTGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
*
147394 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
*
147446 GAA-GTCCGATGACTATGTGTCATCGTGAGCATATGAATCCCTTT-CGGATTAT
1 -AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTAT
147498 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
147530 CAAATGAGAA
Statistics
Matches: 217, Mismatches: 20, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
51 2 0.01
52 208 0.96
53 7 0.03
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:165472 original size:12 final size:12
Alignment explanation
Indices: 165455--165489 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
165445 AAACTTTTGC
*
165455 TTTTATTTTCTA
1 TTTTATTTTATA
*
165467 TTTTATTTTATC
1 TTTTATTTTATA
165479 TTTTATTTTAT
1 TTTTATTTTAT
165490 GCTCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:165477 original size:17 final size:17
Alignment explanation
Indices: 165455--165489 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
165445 AAACTTTTGC
165455 TTTTAT-TTTCTATTTTA
1 TTTTATCTTT-TATTTTA
165472 TTTTATCTTTTATTTTA
1 TTTTATCTTTTATTTTA
165489 T
1 T
165490 GCTCTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATCTTTTATTTTA
Found at i:167856 original size:13 final size:14
Alignment explanation
Indices: 167837--167869 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
167827 ATAGCAATAT
*
167837 TTCTTTTTCTTTTC
1 TTCTTTTTCTCTTC
167851 -TCTTTTTCTCTTC
1 TTCTTTTTCTCTTC
167864 TTCTTT
1 TTCTTT
167870 CTCAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTTTTTCTCTTC
Found at i:170847 original size:14 final size:14
Alignment explanation
Indices: 170816--170853 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
170806 GCATAAAATT
*
170816 TAAAACGAAACAAG
1 TAAAAGGAAACAAG
170830 TAAAAGTGAAACAA-
1 TAAAAG-GAAACAAG
170844 TAAAAGGAAA
1 TAAAAGGAAA
170854 TATAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 11 0.50
15 7 0.32
ACGTcount: A:0.66, C:0.08, G:0.16, T:0.11
Consensus pattern (14 bp):
TAAAAGGAAACAAG
Found at i:171674 original size:29 final size:29
Alignment explanation
Indices: 171616--171674 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
171606 AGGATGTAAG
* * **
171616 TATGGAAAAACTTCAACACCGTTCGGGCA
1 TATGAAAAAACTTCAACACCGTACCAGCA
*
171645 TATGAAAAAACTTCAACACTGTACCAGCA
1 TATGAAAAAACTTCAACACCGTACCAGCA
171674 T
1 T
171675 CATCTTTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (29 bp):
TATGAAAAAACTTCAACACCGTACCAGCA
Found at i:179591 original size:271 final size:271
Alignment explanation
Indices: 179108--179648 Score: 1037
Period size: 271 Copynumber: 2.0 Consensus size: 271
179098 ACTGAAAAAC
179108 TAGAACTGATGGGTTTGTCATGACATAGACAAAACCATGTTGCGACATGGGGGTAGATTACTAAA
1 TAGAACTGATGGGTTTGTCATGACATAGACAAAACCATGTTGCGACATGGGGGTAGATTACTAAA
*
179173 AGTTCAAGACTGATGGGTTTGTCGTGACACAAGGAGAGCTACGTCACGATAAGCAGGGCACTGGC
66 AGTTCAAGACTGATGGGTTTGTCGTGACACAAGGAGAGCTACATCACGATAAGCAGGGCACTGGC
*
179238 AGGTTGGTTGTGACTTACTAGGGTTACGTCGCAACATCGTCTGTAATTTTTTGTAGGGTTGACCC
131 AGGTTGGTTGCGACTTACTAGGGTTACGTCGCAACATCGTCTGTAATTTTTTGTAGGGTTGACCC
179303 GACTCAATTACTCAACTCGACTTCTTAAAACCCTATTTACCCGATTTTTATCACTTAAAACCTAA
196 GACTCAATTACTCAACTCGACTTCTTAAAACCCTATTTACCCGATTTTTATCACTTAAAACCTAA
179368 TTTTCACACCT
261 TTTTCACACCT
179379 TAGAACTGATGGGTTTGTCATGACATAGACAAAACCATGTTGCGACATGGGGGTAGATTACTAAA
1 TAGAACTGATGGGTTTGTCATGACATAGACAAAACCATGTTGCGACATGGGGGTAGATTACTAAA
*
179444 AGTTCAAGACTGATGGGTTTGTCGTGACACAAGGAGAGCTACATCGCGATAAGCAGGGCACTGGC
66 AGTTCAAGACTGATGGGTTTGTCGTGACACAAGGAGAGCTACATCACGATAAGCAGGGCACTGGC
*
179509 AGGTTGGTTGCGACTTACTAGGGTTACGTCGCTACATCGTCTGTAATTTTTTGTAGGGTTGACCC
131 AGGTTGGTTGCGACTTACTAGGGTTACGTCGCAACATCGTCTGTAATTTTTTGTAGGGTTGACCC
*
179574 GACTCAATTACTCAACTCGACTTCTTAAAACCCTATTTACTCGATTTTTATCACTTAAAACCTAA
196 GACTCAATTACTCAACTCGACTTCTTAAAACCCTATTTACCCGATTTTTATCACTTAAAACCTAA
179639 TTTTCACACC
261 TTTTCACACC
179649 CCTTATATAT
Statistics
Matches: 265, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
271 265 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (271 bp):
TAGAACTGATGGGTTTGTCATGACATAGACAAAACCATGTTGCGACATGGGGGTAGATTACTAAA
AGTTCAAGACTGATGGGTTTGTCGTGACACAAGGAGAGCTACATCACGATAAGCAGGGCACTGGC
AGGTTGGTTGCGACTTACTAGGGTTACGTCGCAACATCGTCTGTAATTTTTTGTAGGGTTGACCC
GACTCAATTACTCAACTCGACTTCTTAAAACCCTATTTACCCGATTTTTATCACTTAAAACCTAA
TTTTCACACCT
Found at i:183788 original size:12 final size:12
Alignment explanation
Indices: 183771--183805 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
183761 AAACTTTTGC
*
183771 TTTTATTTTCTA
1 TTTTATTTTATA
*
183783 TTTTATTTTATC
1 TTTTATTTTATA
183795 TTTTATTTTAT
1 TTTTATTTTAT
183806 GCTCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:183793 original size:17 final size:17
Alignment explanation
Indices: 183771--183805 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
183761 AAACTTTTGC
183771 TTTTAT-TTTCTATTTTA
1 TTTTATCTTT-TATTTTA
183788 TTTTATCTTTTATTTTA
1 TTTTATCTTTTATTTTA
183805 T
1 T
183806 GCTCTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATCTTTTATTTTA
Found at i:191741 original size:9 final size:9
Alignment explanation
Indices: 191727--191753 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
191717 TAGGGACCAG
191727 ACTTGAAGA
1 ACTTGAAGA
191736 ACTTGAAGA
1 ACTTGAAGA
191745 ACTTGAAGA
1 ACTTGAAGA
191754 CTGACTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (9 bp):
ACTTGAAGA
Found at i:196594 original size:13 final size:14
Alignment explanation
Indices: 196570--196598 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
196560 AACCACATAT
196570 TACAATTCTTAAAA
1 TACAATTCTTAAAA
196584 TACAA-TCTTAAAA
1 TACAATTCTTAAAA
196597 TA
1 TA
196599 AAAACAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
TACAATTCTTAAAA
Found at i:210698 original size:17 final size:17
Alignment explanation
Indices: 210678--210716 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
210668 ATTGTCTTCA
210678 CATTTTAATTGTCCATG
1 CATTTTAATTGTCCATG
* **
210695 CATTTTATTTGTTGATG
1 CATTTTAATTGTCCATG
210712 CATTT
1 CATTT
210717 GCATTGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.54
Consensus pattern (17 bp):
CATTTTAATTGTCCATG
Found at i:216233 original size:15 final size:16
Alignment explanation
Indices: 216213--216244 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
216203 TTATCATAAA
216213 TTTTTTTCTT-CTTTT
1 TTTTTTTCTTCCTTTT
216228 TTTTTTTCTTCCTTTT
1 TTTTTTTCTTCCTTTT
216244 T
1 T
216245 CTCATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTCTTCCTTTT
Found at i:217356 original size:21 final size:21
Alignment explanation
Indices: 217332--217376 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
217322 TTTCATTTCA
*
217332 TTCTCTTCTTCTT-TTTCTTCC
1 TTCTCTTCCTCTTCTTTC-TCC
217353 TTCTCTTCCTCTTCTTTCTCC
1 TTCTCTTCCTCTTCTTTCTCC
217374 TTC
1 TTC
217377 ATCTGGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTCTTCCTCTTCTTTCTCC
Found at i:227112 original size:21 final size:22
Alignment explanation
Indices: 227088--227137 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
227078 GGTTGGTCAT
*
227088 GACATAGACATGC-TGTGTTGC
1 GACATAGACATGCTTCTGTTGC
* *
227109 GACATACACATTCTTCTGTTGC
1 GACATAGACATGCTTCTGTTGC
*
227131 AACATAG
1 GACATAG
227138 GGGGTTGGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (22 bp):
GACATAGACATGCTTCTGTTGC
Found at i:238561 original size:13 final size:13
Alignment explanation
Indices: 238551--238586 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
238541 TGATTTAATC
238551 AATTAATTTAACT
1 AATTAATTTAACT
*
238564 AATTAAATTAACT
1 AATTAATTTAACT
238577 ACATTAATTT
1 A-ATTAATTT
238587 CTCAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTAATTTAACT
Found at i:243889 original size:10 final size:10
Alignment explanation
Indices: 243874--243898 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
243864 TCAAGCGAAC
243874 GCTTTCATCG
1 GCTTTCATCG
243884 GCTTTCATCG
1 GCTTTCATCG
243894 GCTTT
1 GCTTT
243899 AATCCACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.28, G:0.20, T:0.44
Consensus pattern (10 bp):
GCTTTCATCG
Found at i:249065 original size:14 final size:14
Alignment explanation
Indices: 249046--249072 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
249036 AGTAAATTTC
249046 TTTTTTTTTTTGAT
1 TTTTTTTTTTTGAT
249060 TTTTTTTTTTTGA
1 TTTTTTTTTTTGA
249073 ACAATCTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTTGAT
Found at i:267862 original size:18 final size:18
Alignment explanation
Indices: 267839--267885 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
267829 CGGAAGGATT
267839 AGCATACTGGCTCATTTG
1 AGCATACTGGCTCATTTG
* *
267857 AGCATACTGACTCGTTTG
1 AGCATACTGGCTCATTTG
267875 AGCATTACTGG
1 AGCA-TACTGG
267886 ATCGTAAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (18 bp):
AGCATACTGGCTCATTTG
Found at i:268597 original size:21 final size:23
Alignment explanation
Indices: 268573--268628 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 23
268563 CTTGTTTCGA
268573 TAGAAGACT-T-ACTTGTATTGG
1 TAGAAGACTGTCACTTGTATTGG
268594 TAG-A-ACTGTCACTTGTATTGG
1 TAGAAGACTGTCACTTGTATTGG
*
268615 TAGAAGTCTG-CACT
1 TAGAAGACTGTCACT
268629 ATTCTTAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.10
20 2 0.07
21 17 0.57
22 5 0.17
23 3 0.10
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (23 bp):
TAGAAGACTGTCACTTGTATTGG
Found at i:276890 original size:17 final size:17
Alignment explanation
Indices: 276864--276905 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
276854 TTAGCATTCT
276864 TGCA-TTTTATTGTGC-C
1 TGCATTTTTATTGT-CAC
276880 TGCATTTTTATTGTCAC
1 TGCATTTTTATTGTCAC
276897 TGCATTTTT
1 TGCATTTTT
276906 TTTGGTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (17 bp):
TGCATTTTTATTGTCAC
Found at i:279325 original size:18 final size:18
Alignment explanation
Indices: 279298--279335 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
279288 AAACCAAGAT
279298 TGATTCGTTGGATCTTGC
1 TGATTCGTTGGATCTTGC
*
279316 TGATTTGTTGGATCTTGC
1 TGATTCGTTGGATCTTGC
279334 TG
1 TG
279336 TTACAAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.13, G:0.29, T:0.47
Consensus pattern (18 bp):
TGATTCGTTGGATCTTGC
Found at i:281654 original size:19 final size:19
Alignment explanation
Indices: 281632--281676 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
281622 TTATATTAGG
281632 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
281651 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
281670 ATTTAAT
1 ATTTAAT
281677 TTATGTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Done.