Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001727.1 Kokia drynarioides strain JFW-HI SEQ_113428, 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: 131725
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1020 original size:23 final size:23
Alignment explanation
Indices: 990--1055 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
980 CATTAAGGAA
*
990 CACTGTGTGTGCTTATTGTTCAG
1 CACTGTGTGTGCTTACTGTTCAG
*
1013 CACTGTGTGTGCTTACTGATCAG
1 CACTGTGTGTGCTTACTGTTCAG
1036 CACTGTGTGTGCTTACTGTT
1 CACTGTGTGTGCTTACTGTT
1056 GCCCAGCACT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.14, C:0.20, G:0.26, T:0.41
Consensus pattern (23 bp):
CACTGTGTGTGCTTACTGTTCAG
Found at i:3800 original size:29 final size:29
Alignment explanation
Indices: 3744--3802 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3734 TTGTGGAAAA
** *
3744 GGTGAAAAACTTGTTCATTGAGAGTTTGT
1 GGTGAAAAACTTGTTCATAAAGAATTTGT
* *
3773 GGTGAAGAACTTGTTCGTAAAGAATTTGT
1 GGTGAAAAACTTGTTCATAAAGAATTTGT
3802 G
1 G
3803 TCAAGGTGGA
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:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (29 bp):
GGTGAAAAACTTGTTCATAAAGAATTTGT
Found at i:11836 original size:22 final size:22
Alignment explanation
Indices: 11789--11831 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
11779 CCGTCGATAT
*
11789 TATTTTTTAATTTTTTTTAAAA
1 TATTTTTTAATTTTATTTAAAA
*
11811 TATTTATTTTATTTTATTTAA
1 TATTT-TTTAATTTTATTTAA
11832 GTATTCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTTTTAATTTTATTTAAAA
Found at i:34486 original size:16 final size:18
Alignment explanation
Indices: 34462--34504 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
34452 CTACATTTAT
34462 TTTTATTTTCA-TTTTCA
1 TTTTATTTTCATTTTTCA
34479 TTTT-TTTTCATTTTTCA
1 TTTTATTTTCATTTTTCA
34496 TTTTATTTT
1 TTTTATTTT
34505 ATTATGCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.25
17 14 0.58
18 4 0.17
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATTTTCATTTTTCA
Found at i:37457 original size:19 final size:18
Alignment explanation
Indices: 37426--37465 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
37416 GTTTTCTATG
* *
37426 TTAGAAAACAAAATATAT
1 TTAGAAAAAAAAAGATAT
37444 TTAGAAAAAAAAAAGATAT
1 TTAG-AAAAAAAAAGATAT
37463 TTA
1 TTA
37466 TCTAGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (18 bp):
TTAGAAAAAAAAAGATAT
Found at i:39686 original size:20 final size:22
Alignment explanation
Indices: 39639--39686 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
39629 CCCAATTAAC
*
39639 TCAAATTATTTAATTAAAAATT
1 TCAAATTATTTAATCAAAAATT
* *
39661 TAAAATT-TTT-ATCAAAATTT
1 TCAAATTATTTAATCAAAAATT
39681 TCAAAT
1 TCAAAT
39687 CGAATCGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.59
21 3 0.14
22 6 0.27
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (22 bp):
TCAAATTATTTAATCAAAAATT
Found at i:41472 original size:53 final size:53
Alignment explanation
Indices: 41414--41518 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
41404 AAATTTAGTC
* *
41414 TATTTACTTTTTTTTTTAAAAATTTAG-TCTCTATACTATTCAGTTTCCAAAAA
1 TATTTACTTTTATTTTTAAAAATTTAGTTC-CTATACTATTCAATTTCCAAAAA
* *
41467 TATTTACTTTTATTTTTAGAAATTTAGTTCCTATACTATTCAATTTTCAAAA
1 TATTTACTTTTATTTTTAAAAATTTAGTTCCTATACTATTCAATTTCCAAAA
41519 TTCAGGTCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
53 45 0.96
54 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.51
Consensus pattern (53 bp):
TATTTACTTTTATTTTTAAAAATTTAGTTCCTATACTATTCAATTTCCAAAAA
Found at i:42588 original size:19 final size:20
Alignment explanation
Indices: 42564--42604 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
42554 AGGGGGAAAG
42564 TGGGAGAAAAT-AAAAGTTT
1 TGGGAGAAAATAAAAAGTTT
42583 TGGGAGAAAATAAAAAGTTT
1 TGGGAGAAAATAAAAAGTTT
42603 TG
1 TG
42605 AGGGTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (20 bp):
TGGGAGAAAATAAAAAGTTT
Found at i:42875 original size:21 final size:21
Alignment explanation
Indices: 42851--42890 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42841 ATCTTTGCTA
**
42851 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAAACAAAACTATT
42872 AAGTTAAAAAACAAAACTA
1 AAGTTAAAAAACAAAACTA
42891 CGTCGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAAACAAAACTATT
Found at i:43322 original size:27 final size:27
Alignment explanation
Indices: 43272--43323 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
43262 GGGATGAGAG
*
43272 GGAGTAAAAGTTTTGGAGGGAAAGTGA
1 GGAGTAAAAGTTTTGGAGGAAAAGTGA
43299 GGAGTAAAAGTTTTTGGA-GAAAAGT
1 GGAGTAAAAG-TTTTGGAGGAAAAGT
43324 AAAAGACTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.37, T:0.25
Consensus pattern (27 bp):
GGAGTAAAAGTTTTGGAGGAAAAGTGA
Found at i:43392 original size:9 final size:9
Alignment explanation
Indices: 43380--43417 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
43370 GATATTTGAT
43380 TTATTCGAA
1 TTATTCGAA
*
43389 TTATTCAAA
1 TTATTCGAA
*
43398 TTATTCGAG
1 TTATTCGAA
43407 TTATTCGAA
1 TTATTCGAA
43416 TT
1 TT
43418 CGAAAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:52283 original size:5 final size:5
Alignment explanation
Indices: 52273--52302 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
52263 ATACTAAATC
52273 GATTT GATTT GATTT GATTT GATTT GATTT
1 GATTT GATTT GATTT GATTT GATTT GATTT
52303 CATTCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
GATTT
Found at i:52460 original size:16 final size:15
Alignment explanation
Indices: 52443--52471 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52433 TTTTTCTTTC
52443 TCTCT-CAAAATTTT
1 TCTCTACAAAATTTT
52457 TCTCTACAAAATTTT
1 TCTCTACAAAATTTT
52472 CATACGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (15 bp):
TCTCTACAAAATTTT
Found at i:54149 original size:29 final size:29
Alignment explanation
Indices: 54107--54216 Score: 123
Period size: 29 Copynumber: 3.8 Consensus size: 29
54097 GGCGTCCTTT
* * *
54107 ATAGAATCAACCACAAAAGCTCACATTTA
1 ATAGAATTAGCCACAAAGGCTCACATTTA
*
54136 ATAGATTTAGCCACAAAGGCTCACATTTA
1 ATAGAATTAGCCACAAAGGCTCACATTTA
* * *
54165 ATA-AAATCGACCACAAAGGCTCACATTGA
1 ATAGAATTAG-CCACAAAGGCTCACATTTA
* *
54194 AGAGAATCAGCCACAAAGGCTCA
1 ATAGAATTAGCCACAAAGGCTCA
54217 AATTAACATA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 3 0.04
29 61 0.91
30 3 0.04
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.19
Consensus pattern (29 bp):
ATAGAATTAGCCACAAAGGCTCACATTTA
Found at i:64816 original size:12 final size:12
Alignment explanation
Indices: 64801--64839 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
64791 AGAGAAGGAT
64801 GAAGAAAAAGAA
1 GAAGAAAAAGAA
*
64813 GAAGGAAAAGAA
1 GAAGAAAAAGAA
*
64825 GAAGAGAAAGAA
1 GAAGAAAAAGAA
64837 GAA
1 GAA
64840 ACAAAACCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAGAA
Found at i:67761 original size:3 final size:3
Alignment explanation
Indices: 67753--67780 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
67743 AAGGACCCAA
67753 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
67781 GGTTTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:68634 original size:145 final size:144
Alignment explanation
Indices: 68195--68633 Score: 586
Period size: 144 Copynumber: 3.0 Consensus size: 144
68185 CTTGGGAAAT
* * * *
68195 TTTTTTATTTTTTAACAATTTCGAAATAAAAGTTTTAATTTTTCAA-AAAAATAATGATTTTCTT
1 TTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTT-AAGAAAAATAGTGATTTTC-T
* * *
68259 TAA-AAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTAGTTATTTTAATGAAAAAGTT
64 TAACAAAAAAAAGTTTAGATTTTTAAAAATAAAAATAT-TTTTTAGTCATTTTAATGAAAAAATT
*
68323 TAAATATTTAAACAAAG
128 TAAATTTTTAAACAAAG
* * *
68340 -TTTTGATTTCTTAACTATTTCAAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTCTT-
1 TTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTTTCTTA
*
68403 -CAAAAATAGAAGGTTTAGATTTTTAAAATTAAAAATCTATTTTTTAGTCATTTTAATGAAAAAA
66 ACAAAAA-A-AA-GTTTAGATTTTTAAAAATAAAAA--TATTTTTTAGTCATTTTAATGAAAAAA
*
68467 TTTAAAATTTTAAACAAA-
126 TTTAAATTTTTAAACAAAG
68485 TTTTTGATTTTTTAACTATTTCGAAATAAAA-TTTTGATTTTTAAGAAAAATAGTGATTTTCTTA
1 TTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTTTCTTA
* * * **
68549 ACAAAAAAAAGTTTAAATTTTCAAAAATAAAAATATGTTTTTAGTCATTTTAAAGAAAAAATACA
66 ACAAAAAAAAGTTTAGATTTTTAAAAATAAAAATAT-TTTTTAGTCATTTTAATGAAAAAATTTA
68614 AATTTTTAAACAAAG
130 AATTTTTAAACAAAG
68629 TTTTT
1 TTTTT
68634 TTTGTTTTCG
Statistics
Matches: 259, Mismatches: 23, Indels: 25
0.84 0.07 0.08
Matches are distributed among these distances:
142 7 0.03
143 43 0.17
144 78 0.30
145 55 0.21
146 67 0.26
147 9 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (144 bp):
TTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTTTCTTA
ACAAAAAAAAGTTTAGATTTTTAAAAATAAAAATATTTTTTAGTCATTTTAATGAAAAAATTTAA
ATTTTTAAACAAAG
Found at i:69176 original size:16 final size:15
Alignment explanation
Indices: 69145--69187 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
69135 TTATTTATTC
*
69145 TTATTTTATATTTAT
1 TTATTTTATATCTAT
69160 TTATTTTCATATCTAT
1 TTATTTT-ATATCTAT
69176 TTATATTTATAT
1 TTAT-TTTATAT
69188 TTTTTACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 15 0.60
17 3 0.12
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTTATATCTAT
Found at i:69420 original size:48 final size:47
Alignment explanation
Indices: 69364--69463 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 47
69354 TAGCTTTTCA
*
69364 TTAAATTTAGTCAACTTAATTAATTCTCCTATTTTATTTCTATTCGTT
1 TTAAATTTAGTCAACTTAATTAATTCTCCTATTTTATTACTATTC-TT
*
69412 TTAAATTTAGTCAATTTAATTAATTCTCCTATTTTATTACTATTCTT
1 TTAAATTTAGTCAACTTAATTAATTCTCCTATTTTATTACTATTCTT
69459 TTAAA
1 TTAAA
69464 ACAGAAAACT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 7 0.14
48 43 0.86
ACGTcount: A:0.30, C:0.13, G:0.03, T:0.54
Consensus pattern (47 bp):
TTAAATTTAGTCAACTTAATTAATTCTCCTATTTTATTACTATTCTT
Found at i:98198 original size:17 final size:16
Alignment explanation
Indices: 98162--98215 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
98152 ATGTTACAGA
98162 AGAAGA-GAAAAGAA-
1 AGAAGAGGAAAAGAAG
98176 ATGAAGATGGAAAAGAAG
1 A-GAAGA-GGAAAAGAAG
*
98194 AGAAG-GAAAAAGAAG
1 AGAAGAGGAAAAGAAG
98209 AAGAAGA
1 -AGAAGA
98216 AGCTGTCTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 1 0.03
15 14 0.42
16 5 0.15
17 12 0.36
18 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (16 bp):
AGAAGAGGAAAAGAAG
Found at i:104027 original size:24 final size:24
Alignment explanation
Indices: 104000--104047 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
103990 TTTCTACAAC
104000 TACACCTTAACTAAACAAAATTTA
1 TACACCTTAACTAAACAAAATTTA
*
104024 TACACCTTACCTAAACAAAATTTA
1 TACACCTTAACTAAACAAAATTTA
104048 ACTTACATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (24 bp):
TACACCTTAACTAAACAAAATTTA
Found at i:104223 original size:22 final size:22
Alignment explanation
Indices: 104210--104260 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
104200 GAGCGCTTAA
*
104210 GTGCTATACGGAGAGCATGAAT
1 GTGCTAAACGGAGAGCATGAAT
104232 GTGCTAAACGGAGAGCACT-AAT
1 GTGCTAAACGGAGAGCA-TGAAT
104254 GTGCTAA
1 GTGCTAA
104261 TAAATGGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (22 bp):
GTGCTAAACGGAGAGCATGAAT
Found at i:106571 original size:278 final size:277
Alignment explanation
Indices: 106072--106628 Score: 965
Period size: 278 Copynumber: 2.0 Consensus size: 277
106062 TAACACACCC
* * * *
106072 AGGACACACCCCTGTGTGCGGGTCGTGTGTGCCTAAAATGCCTAGAACTCAACTCAACATCACAT
1 AGGACACACCCCTGTGTGCAGGCCATGTATGCCTAAAATGCCTAGAACTCAACTCAACATCACAT
*
106137 ATTTTACTAGGTATCTAAACCAATTCATACCTCAATGTTACCATGAATTAAAACACACCTAAAAA
66 ATTTGACTAGGTATCTAAACCAATTCATACCTCAATGTTACCATGAATTAAAACACACCTAAAAA
*
106202 CATCAAAAACATAATTCAATTATCCATTCAAGGCTACATACGATCACCTACGTATTGTCACATTT
131 CATCAAAAACATAATTCAATTATCCATTCAAGGCTACATACGATCACCTACGTATAGTCACATTT
106267 CAAATAGCATATGAACATATCAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTACAAT
196 CAAATAGCATATGAACATATCAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTACAAT
106332 TTCAAAAGATCATTTCA
261 TTCAAAAGATCATTTCA
* *
106349 AGGACACACGCCC-GTGTGCAGGCCATGTATGCCTAAAATGCCTAGAACTCAACTTAACCTTCAC
1 AGGACACAC-CCCTGTGTGCAGGCCATGTATGCCTAAAATGCCTAGAACTCAACTCAA-CATCAC
*
106413 ATATTTGACTAGGTATCTAAACCAATTCATACCTTAATGTTACCATGAATTAAAACACACCTAAA
64 ATATTTGACTAGGTATCTAAACCAATTCATACCTCAATGTTACCATGAATTAAAACACACCTAAA
* * *
106478 AAGATCAAAAACATAATTCGATTATCCATTCAAGGTTACATACGATCACCTACGTATAGTCACAT
129 AACATCAAAAACATAATTCAATTATCCATTCAAGGCTACATACGATCACCTACGTATAGTCACAT
106543 TTCAAATAGCATATGAACAT-TCCAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTAC
194 TTCAAATAGCATATGAACATAT-CAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTAC
106607 AATTTCAAAAGATCATTTCA
258 AATTTCAAAAGATCATTTCA
106627 AG
1 AG
106629 ACATCAACAC
Statistics
Matches: 265, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
277 49 0.18
278 216 0.82
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (277 bp):
AGGACACACCCCTGTGTGCAGGCCATGTATGCCTAAAATGCCTAGAACTCAACTCAACATCACAT
ATTTGACTAGGTATCTAAACCAATTCATACCTCAATGTTACCATGAATTAAAACACACCTAAAAA
CATCAAAAACATAATTCAATTATCCATTCAAGGCTACATACGATCACCTACGTATAGTCACATTT
CAAATAGCATATGAACATATCAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTACAAT
TTCAAAAGATCATTTCA
Found at i:108480 original size:24 final size:25
Alignment explanation
Indices: 108432--108477 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
108422 AGTTGTAAAG
108432 AGAAAATTCTCTAAGAGATTATTTC
1 AGAAAATTCTCTAAGAGATTATTTC
108457 AGAAAATT-TCT-AGAGA-TATTT
1 AGAAAATTCTCTAAGAGATTATTT
108478 TTCTTATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 5 0.24
24 3 0.14
25 8 0.38
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (25 bp):
AGAAAATTCTCTAAGAGATTATTTC
Found at i:113894 original size:102 final size:102
Alignment explanation
Indices: 113645--114412 Score: 840
Period size: 102 Copynumber: 7.5 Consensus size: 102
113635 AAAGTTGCAA
* * * * * *
113645 TGGATCGGATTAAAACTAACAATAG-TGAATCCCAATCTCCCTGAAGTTTCAGTGGAATGGAGTG
1 TGGATCAGATTAAAACTAATAGTAGCAG-ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTG
* * *
113709 AAGTTATAACACCAAATCTTATATTCC-TGAA-TTGC-AA
65 AAGTTACAACACCAAATCCTATA-TCCTTGAAGTT-CTAG
* * * *
113746 TGTATCAGATTAAAACTAATTGTAGTAGATCTCAATCT-CCTCGAAGTTGCAATGGAATGGAGTG
1 TGGATCAGATTAAAACTAATAGTAGCAGATCTCAATCTCCCT-GAAGTTGCAGTGGAATGGAGTG
*
113810 AAGTTACAACACCAAATGCTATATCCTTGAAGTTCTAG
65 AAGTTACAACACCAAATCCTATATCCTTGAAGTTCTAG
* * * * *
113848 TGAATCAGATTAAAACTAATAGTAGCGGATCTGAATCTCCCTGAAGTTGTAGTGGAATGAAGTGA
1 TGGATCAGATTAAAACTAATAGTAGCAGATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGA
* * * *
113913 AGTTACAATACCAAATTCTATATCCTTGAATTTTTAG
66 AGTTACAACACCAAATCCTATATCCTTGAAGTTCTAG
* * * * * *
113950 TGGATCGGACTAAACCTAACAGTAGCATATCTCAATCT-CCTAGAAGTTGCAATGGAATGGAGTG
1 TGGATCAGATTAAAACTAATAGTAGCAGATCTCAATCTCCCT-GAAGTTGCAGTGGAATGGAGTG
*
114014 AAGTTACAACACCAAATCCAATATCCTTGAAGTTAC-AG
65 AAGTTACAACACCAAATCCTATATCCTTGAAGTT-CTAG
* * * * *
114052 TGGATC-GAATTAAAACTAATAGTAGTAGATCTTAATCTCCTTGAAGTTGCAATCGAATGGAGTG
1 TGGATCAG-ATTAAAACTAATAGTAGCAGATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTG
* *
114116 AAGTTACAACACCAAATTCTATATCCTTGAAGTTGTAG
65 AAGTTACAACACCAAATCCTATATCCTTGAAGTTCTAG
* * * *
114154 TGGAT-TGAATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTTGTAGTGGAATGGAGTG
1 TGGATCAG-ATTAAAACTAATAGTAGCAGATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTG
* * *
114218 AAGCTACATCACCAAATCCTATATCCTTGAAGTTGTAG
65 AAGTTACAACACCAAATCCTATATCCTTGAAGTTCTAG
* *
114256 TGGATCAGATTAAAACTAATAGTAAC-GAATCTCAATCTCCCTGAAGTTGTAGTGGAATGGAGTG
1 TGGATCAGATTAAAACTAATAGTAGCAG-ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTG
* *
114320 AAGTTACAACACCAAATCCTATATCCCTT-ATGTTGTAG
65 AAGTTACAACACCAAATCCTATAT-CCTTGAAGTTCTAG
** * * * * * * * *
114358 TATAT-TGATTAAAACTAAAAATAACGGATCTCAATCTCCTTAAAGTTGTAGTGGA
1 TGGATCAGATTAAAACTAATAGTAGCAGATCTCAATCTCCCTGAAGTTGCAGTGGA
114413 TCGGATTAAA
Statistics
Matches: 574, Mismatches: 77, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
100 6 0.01
101 122 0.21
102 436 0.76
103 10 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (102 bp):
TGGATCAGATTAAAACTAATAGTAGCAGATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGA
AGTTACAACACCAAATCCTATATCCTTGAAGTTCTAG
Found at i:114203 original size:306 final size:303
Alignment explanation
Indices: 113636--114345 Score: 978
Period size: 306 Copynumber: 2.3 Consensus size: 303
113626 CTATTCCCTA
* * * * * *
113636 AAGTTGCAATGGATCGGATTAAAACTAACAATAGTGAATCCCAATCTCCCTGAAGTTTCAGTGGA
1 AAGTTGTAGTGGATCGGATTAAAACTAACAGTAG-CAATCTCAATCTCCCTGAAGTTGCAGTGGA
* * * *
113701 ATGGAGTGAAGTTATAACACCAAATCTTATATTCCTGAATTGCAATGTATCAGATTAAAACTAAT
65 ATGGAGTGAAGTTACAACACCAAATCCTATA-TCCTGAATTACAATGGATCAGATTAAAACTAAT
* *
113766 TGTAGTAGATCTCAATCTCCTCGAAGTTGCAATGGAATGGAGTGAAGTTACAACACCAAATGCTA
129 AGTAGTAGATCTCAATCTCCTCGAAGTTGCAATCGAATGGAGTGAAGTTACAACACCAAATGCTA
* * * *
113831 TATCCTTGAAGTTCTAGTGAATCAGATTAAAACTAATAGTAGCGGATCTGAATCTCCCTGAAGTT
194 TATCCTTGAAGTTCTAGTGAATCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTT
* *
113896 GTAGTGGAATGAAGTGAAGTTACAAT-ACCAAATTCTATATCCTTG
259 GTAGTGGAATGAAGTGAAGCTAC-ATCACCAAATCCTATATCCTTG
* * * * *
113941 AATTTTTAGTGGATCGGACTAAACCTAACAGTAGCATATCTCAATCT-CCTAGAAGTTGCAATGG
1 AAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCA-ATCTCAATCTCCCT-GAAGTTGCAGTGG
* *
114005 AATGGAGTGAAGTTACAACACCAAATCCAATATCCTTGAAGTTACAGTGGATC-GAATTAAAACT
64 AATGGAGTGAAGTTACAACACCAAATCCTATATCC-TGAA-TTACAATGGATCAG-ATTAAAACT
* * *
114069 AATAGTAGTAGATCTTAATCTCCTTGAAGTTGCAATCGAATGGAGTGAAGTTACAACACCAAATT
126 AATAGTAGTAGATCTCAATCTCCTCGAAGTTGCAATCGAATGGAGTGAAGTTACAACACCAAATG
* * *
114134 CTATATCCTTGAAGTTGTAGTGGAT-TGAATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAA
191 CTATATCCTTGAAGTTCTAGTGAATCAG-ATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAA
*
114198 AGTTGTAGTGGAATGGAGTGAAGCTACATCACCAAATCCTATATCCTTG
255 AGTTGTAGTGGAATGAAGTGAAGCTACATCACCAAATCCTATATCCTTG
* * * *
114247 AAGTTGTAGTGGATCAGATTAAAACTAATAGTAACGAATCTCAATCTCCCTGAAGTTGTAGTGGA
1 AAGTTGTAGTGGATCGGATTAAAACTAACAGTAGC-AATCTCAATCTCCCTGAAGTTGCAGTGGA
114312 ATGGAGTGAAGTTACAACACCAAATCCTATATCC
65 ATGGAGTGAAGTTACAACACCAAATCCTATATCC
114346 CTTATGTTGT
Statistics
Matches: 354, Mismatches: 42, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
304 7 0.02
305 84 0.24
306 259 0.73
307 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (303 bp):
AAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAATCTCAATCTCCCTGAAGTTGCAGTGGAA
TGGAGTGAAGTTACAACACCAAATCCTATATCCTGAATTACAATGGATCAGATTAAAACTAATAG
TAGTAGATCTCAATCTCCTCGAAGTTGCAATCGAATGGAGTGAAGTTACAACACCAAATGCTATA
TCCTTGAAGTTCTAGTGAATCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTTGT
AGTGGAATGAAGTGAAGCTACATCACCAAATCCTATATCCTTG
Found at i:114446 original size:52 final size:51
Alignment explanation
Indices: 114139--114456 Score: 191
Period size: 52 Copynumber: 6.2 Consensus size: 51
114129 AAATTCTATA
* * * *
114139 TCCTTGAAGTTGTAGTGGATTGAATTAAAACTAACAGTAGCAGATCTCAATC
1 TCCTTAAAGTTGTAGTGGA-TGGATTAAAACTAACAGTAACAAATCTCAATC
* * * * * * *
114191 TCCCTAAAGTTGTAGTGGAATGGAGTGAAGCT-ACA-TCACCAAATC-CTATA
1 TCCTTAAAGTTGTAGTGG-ATGGATTAAAACTAACAGT-AACAAATCTCAATC
* * * *
114241 TCCTTGAAGTTGTAGTGGATCAGATTAAAACTAATAGTAACGAATCTCAATC
1 TCCTTAAAGTTGTAGTGGAT-GGATTAAAACTAACAGTAACAAATCTCAATC
* * * * * * ** *
114293 TCCCTGAAGTTGTAGTGGAATGGAGT-GAAGTTACAACACCAAATC-CTATATC
1 TCCTTAAAGTTGTAGTGG-ATGGATTAAAACTAACAGTAACAAATCTC-A-ATC
* ** * * * **
114345 -CCTT-ATGTTGTAGTATATTGATTAAAACTAAAAATAACGGATCTCAATC
1 TCCTTAAAGTTGTAGTGGATGGATTAAAACTAACAGTAACAAATCTCAATC
* * *
114394 TCCTTAAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCATATCTTAATC
1 TCCTTAAAGTTGTAGTGGAT-GGATTAAAACTAACAGTAACAAATCTCAATC
*
114446 TCCCTAAAGTT
1 TCCTTAAAGTT
114457 ACAATGAAAT
Statistics
Matches: 195, Mismatches: 57, Indels: 28
0.70 0.20 0.10
Matches are distributed among these distances:
49 10 0.05
50 53 0.27
51 44 0.23
52 85 0.44
53 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (51 bp):
TCCTTAAAGTTGTAGTGGATGGATTAAAACTAACAGTAACAAATCTCAATC
Found at i:118509 original size:18 final size:18
Alignment explanation
Indices: 118488--118522 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
118478 AATTAAAAAC
*
118488 AAATAAAGCAAGAAAAGT
1 AAATAAAGAAAGAAAAGT
118506 AAATAAAGAAAGAAAAG
1 AAATAAAGAAAGAAAAG
118523 GAGCTTGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.17, T:0.09
Consensus pattern (18 bp):
AAATAAAGAAAGAAAAGT
Found at i:123198 original size:31 final size:31
Alignment explanation
Indices: 123160--123219 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
123150 AAAGACAATA
123160 AAGTAAAATCCTATAGAATTATAAAAAAACT
1 AAGTAAAATCCTATAGAATTATAAAAAAACT
123191 AAGTAAAATCCTATAGAATTATAAAAAAA
1 AAGTAAAATCCTATAGAATTATAAAAAAA
123220 AATGCTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.07, T:0.25
Consensus pattern (31 bp):
AAGTAAAATCCTATAGAATTATAAAAAAACT
Done.