Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018924.1 Corchorus olitorius cultivar O-4 contig18957, 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: 72237
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:551 original size:203 final size:202
Alignment explanation
Indices: 161--582 Score: 757
Period size: 203 Copynumber: 2.1 Consensus size: 202
151 TTATATTTTC
161 GTAGTGTACATTGTT-T--TCATTATTAATTTCTTTATTTTTTAATTAAAATCTTAAAAATTTGT
1 GTAGTGTACATTGTTATCATCATTATTAATTTCTTTATTTTTTAATTAAAATCTTAAAAATTTGT
223 AAGAGAAATTATTGTTCTTTCTTAAAATATACCAAAGGCTTTTTTCTAATCAATATATCAATATA
66 AAGAGAAATTATTGTTCTTTCTTAAAATATACCAAAGGCTTTTTTCTAATCAATATATCAATATA
288 ATGAATATTAGAATTAATTAGAGACACGTGCCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTC
131 ATGAATATTAGAATTAATTAGAGACACGTGCCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTC
353 CATATTT
196 CATATTT
360 GTAGTGTACATTGTTATCATCATATATATATGATTTC-TTA-TTTTT-ATTAAAATCTTAAAAAT
1 GTAGTGTACATTGTTATCATCAT-TAT-TA--ATTTCTTTATTTTTTAATTAAAATCTTAAAAAT
422 TTGTAAGAGAAATTATTGTTCTTTCTTAAAATATACCAAAGGCTTTTTTCTAATCAATATATCAA
62 TTGTAAGAGAAATTATTGTTCTTTCTTAAAATATACCAAAGGCTTTTTTCTAATCAATATATCAA
*
487 TATAATGAATATTAGAATTAATTAGAGACACGTGTCGAGATTTGGAGGCCTCAACATTTAAAGAG
127 TATAATGAATATTAGAATTAATTAGAGACACGTGCCGAGATTTGGAGGCCTCAACATTTAAAGAG
552 TTTCCATATTT
192 TTTCCATATTT
563 GTAGTGTACATTGTTATCAT
1 GTAGTGTACATTGTTATCAT
583 TATAGGGTTT
Statistics
Matches: 215, Mismatches: 1, Indels: 10
0.95 0.00 0.04
Matches are distributed among these distances:
199 15 0.07
200 1 0.00
202 4 0.02
203 180 0.84
204 7 0.03
205 3 0.01
206 5 0.02
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (202 bp):
GTAGTGTACATTGTTATCATCATTATTAATTTCTTTATTTTTTAATTAAAATCTTAAAAATTTGT
AAGAGAAATTATTGTTCTTTCTTAAAATATACCAAAGGCTTTTTTCTAATCAATATATCAATATA
ATGAATATTAGAATTAATTAGAGACACGTGCCGAGATTTGGAGGCCTCAACATTTAAAGAGTTTC
CATATTT
Found at i:642 original size:24 final size:24
Alignment explanation
Indices: 598--643 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
588 GGTTTATATT
* *
598 CCATGCACTGTCAGTGTATAGAGG
1 CCATACACTGTCAGTGCATAGAGG
622 CCATACACTGTCAG-GCCATAGA
1 CCATACACTGTCAGTG-CATAGA
644 ATTATGCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (24 bp):
CCATACACTGTCAGTGCATAGAGG
Found at i:2836 original size:49 final size:49
Alignment explanation
Indices: 2772--2876 Score: 192
Period size: 49 Copynumber: 2.1 Consensus size: 49
2762 CCCATGTTGT
*
2772 AGATGAAAACATATGAATCAAAATTAAAGTGCAAACTGTTAACCCAAGA
1 AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA
2821 AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA
1 AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA
*
2870 AGCTGAA
1 AGATGAA
2877 GCTAACAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.19
Consensus pattern (49 bp):
AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA
Found at i:14523 original size:41 final size:39
Alignment explanation
Indices: 14446--14524 Score: 113
Period size: 41 Copynumber: 2.0 Consensus size: 39
14436 CATAGGAGAA
*
14446 ACAAATCAAAGTTAGAGTAATAACCAGTGAGAGCAATAC
1 ACAAATCAAAGTTAGAGAAATAACCAGTGAGAGCAATAC
* *
14485 ACAAATCAAAGTTTGAGCAAATTAATCAGTGAGAGCAATA
1 ACAAATCAAAGTTAGAG-AAA-TAACCAGTGAGAGCAATA
14525 ACCAACCTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 16 0.46
40 2 0.06
41 17 0.49
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (39 bp):
ACAAATCAAAGTTAGAGAAATAACCAGTGAGAGCAATAC
Found at i:17984 original size:19 final size:20
Alignment explanation
Indices: 17936--17984 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 20
17926 AATTTGATAT
17936 TTGTA-TTA-TTAATATGTA
1 TTGTATTTATTTAATATGTA
* * *
17954 TTATGTTAATTTAATA-GTA
1 TTGTATTTATTTAATATGTA
17973 TTGTATTTATTT
1 TTGTATTTATTT
17985 TCTTCAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
18 3 0.13
19 14 0.61
20 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (20 bp):
TTGTATTTATTTAATATGTA
Found at i:22322 original size:2 final size:2
Alignment explanation
Indices: 22315--22347 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22305 CCACTGCACA
22315 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22348 AGGCTATCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23253 original size:14 final size:13
Alignment explanation
Indices: 23234--23272 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
23224 AAATTGTAAA
23234 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
23247 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
23261 ATTTAAAAAATT
1 ATTTAAAAAATT
23273 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:23480 original size:127 final size:127
Alignment explanation
Indices: 23258--23516 Score: 337
Period size: 127 Copynumber: 2.0 Consensus size: 127
23248 ATTTAAGAAA
*
23258 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAATAAAATTGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAAT---A
* * * *
23323 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 CA-GTATAAGGATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAA
23388 G
127 G
* * *
23389 TATATTTAAAAAATTCTAATATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT
1 TATATTTAAAAAATTC---TA-ATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAAT
*
23454 -CA-TA-AA-GATATTAGATTTAAATAAATAAAATTAGAGTTTTTAGTTGAATAAAACTATAAAA
62 ACAGTATAAGGATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAA
23515 G
127 G
23516 T
1 T
23517 TTAAACAATG
Statistics
Matches: 115, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
127 53 0.46
128 2 0.02
129 2 0.02
131 17 0.15
134 2 0.02
135 39 0.34
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAG
Found at i:25831 original size:22 final size:22
Alignment explanation
Indices: 25803--25893 Score: 103
Period size: 22 Copynumber: 4.0 Consensus size: 22
25793 TCTTGTCTCT
25803 GTGTGGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
25825 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
**
25847 G-GATCAGGTTATTGAAATTTCATA
1 GTG-T--GGTTATCAAAATTTCATA
* *
25871 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
25893 G
1 G
25894 AAAGGTTATC
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
21 1 0.02
22 38 0.67
24 17 0.30
25 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.40
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:25936 original size:22 final size:21
Alignment explanation
Indices: 25911--26058 Score: 104
Period size: 22 Copynumber: 6.8 Consensus size: 21
25901 ATCCAAGAGA
*
25911 TTATCAAAATATCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
25933 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
25955 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
25977 TTA-CTAATATTTCATAGGGAGG
1 TTATC-AAAATTTCATA-GGAGG
* *
25999 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
* * *
26021 TTATTAAAATTT-TTAAGTGTGG
1 TTATCAAAATTTCAT-AG-GAGG
*
26043 TTATCAAAATCTCATA
1 TTATCAAAATTTCATA
26059 TGAAAGTTTT
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
21 6 0.06
22 91 0.88
23 6 0.06
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:25963 original size:44 final size:43
Alignment explanation
Indices: 25911--26058 Score: 147
Period size: 44 Copynumber: 3.4 Consensus size: 43
25901 ATCCAAGAGA
*
25911 TTATCAAAATATCATAGCGAGGTTA-TAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTACTAA-AATTTCATAGTGTGG
* * * *
25955 TTAACAAAATTTCATAAGGAGGTTACTAATATTTCATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTACTAAAATTTCATAGTGTGG
* * * *
25999 TTATCAAAATTTTATAGTGTGGTTATTAAAATTT-TTAAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTACTAAAATTTCAT-AGTGTGG
*
26043 TTATCAAAATCTCATA
1 TTATCAAAATTTCATA
26059 TGAAAGTTTT
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
43 3 0.04
44 77 0.91
45 5 0.06
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGAGGTTACTAAAATTTCATAGTGTGG
Found at i:26058 original size:66 final size:66
Alignment explanation
Indices: 25911--26058 Score: 167
Period size: 66 Copynumber: 2.2 Consensus size: 66
25901 ATCCAAGAGA
25911 TTATCAAAATATCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
1 TTATCAAAATATCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
25976 G
66 G
* * * * ** *
25977 TTA-CTAATATTTCATAGGGAGGTTATCAA-AATTTTATAGTGTGGTTATTAAAATTT-TTAAGT
1 TTATC-AAAATATCATAGCGAGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATAAG-
*
26039 GTGG
63 GAGG
*
26043 TTATCAAAATCTCATA
1 TTATCAAAATATCATA
26059 TGAAAGTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
65 5 0.07
66 60 0.88
67 3 0.04
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (66 bp):
TTATCAAAATATCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
G
Found at i:26162 original size:21 final size:21
Alignment explanation
Indices: 26104--26375 Score: 110
Period size: 22 Copynumber: 12.5 Consensus size: 21
26094 TAAAAGTCTT
* * *
26104 AATTTCATA-AGGAGTACCAA
1 AATTTCATAGAAGATTATCAA
* *
26124 AATTTGATAGAAGGTTATC-A
1 AATTTCATAGAAGATTATCAA
* *
26144 AATCTCATAGAATGATTATCGA
1 AATTTCATAGAA-GATTATCAA
26166 AATTTCATAGAGATTGGATTATCAA
1 AATTTCATAGA-A---GATTATCAA
26191 AATTT-ATAGGAAGATTATCAA
1 AATTTCATA-GAAGATTATCAA
* *
26212 AATTTCATAG-TGTTGGTATCAA
1 AATTTCATAGAAGAT--TATCAA
* *
26234 AATTTCAAAGCAAGGTTATCAA
1 AATTTCATAG-AAGATTATCAA
* ** *
26256 AATTACATAATGAA-AAGATCGA
1 AATTTCAT-A-GAAGATTATCAA
* * * *
26278 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGA-AGATTATCAA
* *
26300 AATTTTATAGAGAGGTTATCAA
1 AATTTCATAGA-AGATTATCAA
*
26322 AATTTGATA-AAGAGGTTATCAA
1 AATTTCATAGAAGA--TTATCAA
* *
26344 ATTTTCA-A-AATGTGATTACCAA
1 AATTTCATAGAA---GATTATCAA
26366 AATTTCATAG
1 AATTTCATAG
26376 TGGTATTTAT
Statistics
Matches: 190, Mismatches: 39, Indels: 42
0.70 0.14 0.15
Matches are distributed among these distances:
20 25 0.13
21 31 0.16
22 105 0.55
23 5 0.03
24 9 0.05
25 15 0.08
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.32
Consensus pattern (21 bp):
AATTTCATAGAAGATTATCAA
Found at i:26253 original size:22 final size:22
Alignment explanation
Indices: 26121--26350 Score: 111
Period size: 22 Copynumber: 10.5 Consensus size: 22
26111 TAAGGAGTAC
*
26121 CAAAATTTGATA-GAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
26142 C-AAATCTCATA-GAATGATTAT
1 CAAAATTTCATAGGAA-GGTTAT
* *
26163 CGAAATTTCATAGAGATTGGATTAT
1 CAAAATTTCATAG-GA-AGG-TTAT
*
26188 CAAAATTT-ATAGGAAGATTAT
1 CAAAATTTCATAGGAAGGTTAT
**
26209 CAAAATTTCATAGTGTTGG-TAT
1 CAAAATTTCATAG-GAAGGTTAT
* *
26231 CAAAATTTCAAAGCAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
26253 CAAAATTACATAATGAAAAG--AT
1 CAAAATTTCAT-A-GGAAGGTTAT
* * * *
26275 CGAAATTTCATA-GAGGGGTCAA
1 CAAAATTTCATAGGA-AGGTTAT
*
26297 CAAAATTTTATA-GAGAGGTTAT
1 CAAAATTTCATAGGA-AGGTTAT
* *
26319 CAAAATTTGATA-AAGAGGTTAT
1 CAAAATTTCATAGGA-AGGTTAT
*
26341 CAAATTTTCA
1 CAAAATTTCA
26351 AAATGTGATT
Statistics
Matches: 160, Mismatches: 35, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
19 1 0.01
20 12 0.08
21 22 0.14
22 98 0.61
23 5 0.03
24 11 0.07
25 11 0.07
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:26259 original size:44 final size:45
Alignment explanation
Indices: 26157--26264 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 45
26147 CTCATAGAAT
* * *
26157 GATTATCGAAATTTCATAGAGATTGGATTATCAAAATTTATAGGAA
1 GATTATCAAAATTTCATAGAGATTGGA-TATCAAAATTTAAAGCAA
*
26203 GATTATCAAAATTTCATAGTG-TTGG-TATCAAAATTTCAAAGCAA
1 GATTATCAAAATTTCATAGAGATTGGATATCAAAATTT-AAAGCAA
* *
26247 GGTTATCAAAATTACATA
1 GATTATCAAAATTTCATA
26265 ATGAAAAGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 11 0.20
44 21 0.38
45 4 0.07
46 19 0.35
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (45 bp):
GATTATCAAAATTTCATAGAGATTGGATATCAAAATTTAAAGCAA
Found at i:26503 original size:22 final size:22
Alignment explanation
Indices: 26456--26903 Score: 193
Period size: 22 Copynumber: 20.6 Consensus size: 22
26446 CTATTGAGTA
* *
26456 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATATGGAGGTT
*
26476 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGGAGGTT
**
26498 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGGAGGTT
*
26520 TTCAAAATTTCA-A--GAGGGTT
1 ATCAAAATTTCATATGGA-GGTT
* * *
26540 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGGAGGT-T
* ***
26562 ATCAAAATTTCATAGGGAAACT
1 ATCAAAATTTCATATGGAGGTT
*
26584 AACAAAATTTCATAAT-GAGGTT
1 ATCAAAATTTCAT-ATGGAGGTT
** *
26606 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
*
26628 ATCAAAA--T--T-TGCA-GTT
1 ATCAAAATTTCATATGGAGGTT
* *
26644 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
* * *
26666 ATCAAAATTTTACAGGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
*
26688 CATCAAAATTTTATA-GCGAGGTT
1 -ATCAAAATTTCATATG-GAGGTT
*
26711 ATCACAATTTTCATAGTGTGA--TT
1 ATCA-AAATTTCATA-TG-GAGGTT
* * * *
26734 ATCAAAAATTTTAGAGTGTA-ATT
1 ATC-AAAATTTCATA-TGGAGGTT
26757 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGGAGGTT
* * * * ** *
26779 TTTAAATTTTCAAAACGTGGTT
1 ATCAAAATTTCATATGGAGGTT
** *
26801 ATCACTATATCATATGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
* * **
26823 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGGAGGTT
*
26846 ATCAAAATTTCAT-TCGGAAGTT
1 ATCAAAATTTCATAT-GGAGGTT
26868 ATCAAAATTTCATA-GTGAGGTT
1 ATCAAAATTTCATATG-GAGGTT
*
26890 AACAAAATTTCATA
1 ATCAAAATTTCATA
26904 AGTTAAAAAA
Statistics
Matches: 320, Mismatches: 76, Indels: 62
0.70 0.17 0.14
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 3 0.01
20 27 0.08
21 13 0.04
22 193 0.60
23 69 0.22
24 1 0.00
25 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGGAGGTT
Found at i:26525 original size:64 final size:64
Alignment explanation
Indices: 26457--26576 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
26447 TATTGAGTAA
* *
26457 TCAAAATTTC-AGGGAGGATATCAAAATTTCATATGAAGGT-TATCAAAATTTCATAGTTTAGTT
1 TCAAAATTTCAAGAG-GGATATCAAAATTTCATA-GAAGGTAGATCAAAATTTCATAGTTTAGTT
26520 T
64 T
* * *
26521 TCAAAATTTCAAGAGGGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAG
1 TCAAAATTTCAAGAGGGATATCAAAATTTCATAGAAGGTAGATCAAAATTTCATAG
26577 GGAAACTAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
63 4 0.08
64 42 0.86
65 3 0.06
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (64 bp):
TCAAAATTTCAAGAGGGATATCAAAATTTCATAGAAGGTAGATCAAAATTTCATAGTTTAGTTT
Found at i:26567 original size:42 final size:43
Alignment explanation
Indices: 26475--26575 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 43
26465 TCAGGGAGGA
26475 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG
* *
26518 TTTTCAAAATTTCA-A-GAGGGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGT-T-TAG
26562 -ATCAAAATTTCATA
1 TATCAAAATTTCATA
26576 GGGAAACTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
42 33 0.65
43 3 0.06
44 15 0.29
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.39
Consensus pattern (43 bp):
TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG
Found at i:26766 original size:23 final size:24
Alignment explanation
Indices: 26709--26766 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
26699 TATAGCGAGG
* *
26709 TTATC-ACAATTTTCATAGTGTGA
1 TTATCAACAATTTTCAGAGTGTAA
*
26732 TTATCAAAAATTTT-AGAGTGTAA
1 TTATCAACAATTTTCAGAGTGTAA
26755 TTA-CTAACAATT
1 TTATC-AACAATT
26767 CATATGGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 21 0.72
24 7 0.24
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (24 bp):
TTATCAACAATTTTCAGAGTGTAA
Found at i:28834 original size:60 final size:60
Alignment explanation
Indices: 28741--28860 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
28731 ACCTAATTCC
28741 AAATTTTATAATCTTATCAAACACTCCTAAGTTAGAGAGCCATTCATTTCACAAATAGGA
1 AAATTTTATAATCTTATCAAACACTCCTAAGTTAGAGAGCCATTCATTTCACAAATAGGA
*
28801 AAATTTTATAATCTTATCAAACACTCCTGAGTTAGAGAGCCATTCATTTCACAAATAGGA
1 AAATTTTATAATCTTATCAAACACTCCTAAGTTAGAGAGCCATTCATTTCACAAATAGGA
28861 GGTAAGGCAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (60 bp):
AAATTTTATAATCTTATCAAACACTCCTAAGTTAGAGAGCCATTCATTTCACAAATAGGA
Found at i:32223 original size:21 final size:22
Alignment explanation
Indices: 32189--32229 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
32179 GACAAACTCG
*
32189 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
32211 TAACCCG-ATAACCCAAGAA
1 TAACCCGAATAACCCAAGAA
32230 TATTATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:33245 original size:122 final size:127
Alignment explanation
Indices: 33043--33293 Score: 386
Period size: 122 Copynumber: 2.0 Consensus size: 127
33033 TAAGAAATAA
*
33043 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAATAAAATAG
1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-
*
33108 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTA
62 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTA
33173 T
127 T
* *
33174 ATTTAAAATATTCTAATATATATAAGTTTTTTTATT-AAATAGTAAAATGGTAAAAAT-TA-TA-
1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
*
33235 AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
66 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
33294 TTAAACAATG
Statistics
Matches: 115, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
122 55 0.48
123 2 0.02
124 2 0.02
126 2 0.02
130 20 0.17
131 34 0.30
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.39
Consensus pattern (127 bp):
ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTAT
Found at i:33400 original size:10 final size:10
Alignment explanation
Indices: 33381--33416 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
33371 ACTTTTTAAT
33381 ATAG-TATAG
1 ATAGATATAG
33390 ATAGATATAG
1 ATAGATATAG
*
33400 ATAAATATAG
1 ATAGATATAG
33410 ATAGATA
1 ATAGATA
33417 AGGAGGAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (10 bp):
ATAGATATAG
Found at i:37330 original size:61 final size:61
Alignment explanation
Indices: 37235--37358 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
37225 ATTGATAGGT
37235 GATTTGTAAGTAACATTTTAAGTCCTCTCTAAGACTTGTGACATGCCCTAACCCTGGACTG
1 GATTTGTAAGTAACATTTTAAGTCCTCTCTAAGACTTGTGACATGCCCTAACCCTGGACTG
*
37296 GATTTGTAAGTAACATTTTAAGTCCTCTTTAAGACTTGTGACATGCCCTAACCCTGGACTG
1 GATTTGTAAGTAACATTTTAAGTCCTCTCTAAGACTTGTGACATGCCCTAACCCTGGACTG
37357 GA
1 GA
37359 CTGGGGCAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (61 bp):
GATTTGTAAGTAACATTTTAAGTCCTCTCTAAGACTTGTGACATGCCCTAACCCTGGACTG
Found at i:39322 original size:2 final size:2
Alignment explanation
Indices: 39315--39349 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39305 AGAATTACAG
39315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39350 GCAGCTATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39687 original size:46 final size:46
Alignment explanation
Indices: 39620--39713 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
39610 AAAGCTCTGT
39620 ACAACGTCCGATGGCAGCAGCTCTACAAAGGCACATACAAAATCTC
1 ACAACGTCCGATGGCAGCAGCTCTACAAAGGCACATACAAAATCTC
39666 ACAACGTCCGATGGCAGCAGCTCTACAAAGGCACATACAAAATCTC
1 ACAACGTCCGATGGCAGCAGCTCTACAAAGGCACATACAAAATCTC
39712 AC
1 AC
39714 TCCGTGTATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.15
Consensus pattern (46 bp):
ACAACGTCCGATGGCAGCAGCTCTACAAAGGCACATACAAAATCTC
Found at i:40523 original size:6 final size:6
Alignment explanation
Indices: 40512--40542 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
40502 TGAAGGCTGG
*
40512 GGGGCT GGGGCT GGGGCT GGGGCT GTGGCT G
1 GGGGCT GGGGCT GGGGCT GGGGCT GGGGCT G
40543 TGGCAGTGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.16, G:0.65, T:0.19
Consensus pattern (6 bp):
GGGGCT
Found at i:47583 original size:2 final size:2
Alignment explanation
Indices: 47571--47607 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
47561 AAACCTCTTG
*
47571 AT AT AT A- AT AT AT AT AC 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
47608 TATGGGCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:51844 original size:2 final size:2
Alignment explanation
Indices: 51834--51865 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
51824 CGATATATTG
*
51834 AT AT GT 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
51866 TTTACTAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59685 original size:15 final size:16
Alignment explanation
Indices: 59661--59693 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
59651 AAAAACCACT
*
59661 AAAAATGAAAAAA-AA
1 AAAAAAGAAAAAAGAA
59676 AAAAAAGAAAAAAGAA
1 AAAAAAGAAAAAAGAA
59692 AA
1 AA
59694 GAAGGGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAAAAGAA
Found at i:70172 original size:24 final size:25
Alignment explanation
Indices: 70122--70178 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
70112 GTGGATTGTA
*
70122 AAATAAATTGAATAATTAAAACATT
1 AAATAAATTGAAGAATTAAAACATT
*
70147 AAATAAATTTAAGAATT-AAACATT
1 AAATAAATTGAAGAATTAAAACATT
70171 AAA-AAATT
1 AAATAAATT
70179 CAAGGCTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 10 0.33
25 15 0.50
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (25 bp):
AAATAAATTGAAGAATTAAAACATT
Found at i:70949 original size:14 final size:15
Alignment explanation
Indices: 70930--70963 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
70920 ATTAAATTAG
70930 TAAAAT-GGTAAAAA
1 TAAAATAGGTAAAAA
*
70944 TAAAATAGGTATAAA
1 TAAAATAGGTAAAAA
70959 TAAAA
1 TAAAA
70964 AATAGAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (15 bp):
TAAAATAGGTAAAAA
Done.