Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012782.1 Corchorus olitorius cultivar O-4 contig12815, 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: 64862
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:1593 original size:2 final size:2
Alignment explanation
Indices: 1586--1614 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1576 ATAACTTCTT
1586 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 T
1615 TAATTTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2166 original size:18 final size:18
Alignment explanation
Indices: 2143--2177 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2133 GTTTTAAAAA
*
2143 AATAAAAAAATATATAAT
1 AATAAAAAAATAAATAAT
*
2161 AATAAATAAATAAATAA
1 AATAAAAAAATAAATAA
2178 ATAAAAGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAAAAAATAAATAAT
Found at i:2170 original size:4 final size:4
Alignment explanation
Indices: 2137--2191 Score: 53
Period size: 4 Copynumber: 14.5 Consensus size: 4
2127 AAATAGGTTT
* * *
2137 TAAA AAAA TAAA AAAA TATA T-AA T-AA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
*
2183 -AGA TAAA TA
1 TAAA TAAA TA
2192 GGTTTAGGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 7 0.17
4 34 0.83
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:2188 original size:15 final size:15
Alignment explanation
Indices: 2138--2191 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
2128 AATAGGTTTT
2138 AAAA-AAATAAA-AA
1 AAAATAAATAAATAA
*
2151 AATATATAAT-AATAA
1 AAAATA-AATAAATAA
2166 ATAAATAAATAAATAA
1 A-AAATAAATAAATAA
*
2182 AAGATAAATA
1 AAAATAAATA
2192 GGTTTAGGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 3 0.09
14 3 0.09
15 17 0.52
16 10 0.30
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATAAATAAATAA
Found at i:2188 original size:26 final size:26
Alignment explanation
Indices: 2137--2188 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
2127 AAATAGGTTT
*
2137 TAAAAAAATAAAAAAATATATAATAA
1 TAAAAAAATAAAAAAATATAAAATAA
* *
2163 TAAATAAATAAATAAATA-AAAGATAA
1 TAAAAAAATAAAAAAATATAAA-ATAA
2189 ATAGGTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (26 bp):
TAAAAAAATAAAAAAATATAAAATAA
Found at i:2309 original size:27 final size:27
Alignment explanation
Indices: 2279--2372 Score: 75
Period size: 27 Copynumber: 3.8 Consensus size: 27
2269 ATAAGCAAAT
2279 AGAT-AATAGCTAAATTAATAAATAAAA
1 AGATAAATAGCTAAATTAATAAAT-AAA
2306 AGATAAATAGC---A--AATAAAT---
1 AGATAAATAGCTAAATTAATAAATAAA
*
2325 AGAT-AATAGTTAAATTAATAAATAATA
1 AGATAAATAGCTAAATTAATAAATAA-A
*
2352 AGATAAATAG-TAAATAAATAA
1 AGATAAATAGCTAAATTAATAA
2373 TAGATAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 22
0.69 0.03 0.28
Matches are distributed among these distances:
18 5 0.09
19 4 0.07
21 1 0.02
23 14 0.26
25 1 0.02
27 18 0.33
28 11 0.20
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.27
Consensus pattern (27 bp):
AGATAAATAGCTAAATTAATAAATAAA
Found at i:2319 original size:42 final size:42
Alignment explanation
Indices: 2272--2381 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 42
2262 AATAATAATA
*
2272 AGCAAATAGATAATAGCTAAATTAATAAATAAAAAGATAAAT
1 AGCAAATAGATAATAGATAAATTAATAAATAAAAAGATAAAT
* *
2314 AGCAAATAAATAGATAATAGTTAAATTAATAAATAATAAGATAAAT
1 AGC----AAATAGATAATAGATAAATTAATAAATAAAAAGATAAAT
* *
2360 AGTAAATAAATAATAGATAAAT
1 AGCAAATAGATAATAGATAAAT
2382 AACTATAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
42 20 0.34
46 39 0.66
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (42 bp):
AGCAAATAGATAATAGATAAATTAATAAATAAAAAGATAAAT
Found at i:2332 original size:46 final size:46
Alignment explanation
Indices: 2275--2371 Score: 167
Period size: 46 Copynumber: 2.1 Consensus size: 46
2265 AATAATAAGC
2275 AAATAGATAATAGCTAAATTAATAAATAAAAAGATAAATAGCAAAT
1 AAATAGATAATAGCTAAATTAATAAATAAAAAGATAAATAGCAAAT
* * *
2321 AAATAGATAATAGTTAAATTAATAAATAATAAGATAAATAGTAAAT
1 AAATAGATAATAGCTAAATTAATAAATAAAAAGATAAATAGCAAAT
2367 AAATA
1 AAATA
2372 ATAGATAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (46 bp):
AAATAGATAATAGCTAAATTAATAAATAAAAAGATAAATAGCAAAT
Found at i:2339 original size:19 final size:19
Alignment explanation
Indices: 2317--2383 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
2307 GATAAATAGC
*
2317 AAATAAATAGATAATAGTT
1 AAATAAATAAATAATAGTT
* *
2336 AAATTAATAAATAATAAGATA
1 AAATAAATAAATAAT-AG-TT
*
2357 AATAGTAAATAAATAATAGAT
1 AA-A-TAAATAAATAATAGTT
2378 AAATAA
1 AAATAA
2384 CTATAAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.42
20 3 0.08
21 5 0.13
22 3 0.08
23 11 0.29
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.28
Consensus pattern (19 bp):
AAATAAATAAATAATAGTT
Found at i:2380 original size:15 final size:15
Alignment explanation
Indices: 2317--2383 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 15
2307 GATAAATAGC
2317 AAATAAATAGATA-AT
1 AAATAAATA-ATAGAT
** *
2332 AGTTAAATTAATAAAT
1 AAATAAA-TAATAGAT
2348 -AATAAGATAAATAG-T
1 AAATAA-AT-AATAGAT
2363 AAATAAATAATAGAT
1 AAATAAATAATAGAT
2378 AAATAA
1 AAATAA
2384 CTATAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
14 5 0.12
15 22 0.54
16 14 0.34
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.28
Consensus pattern (15 bp):
AAATAAATAATAGAT
Found at i:2383 original size:11 final size:11
Alignment explanation
Indices: 2342--2383 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
2332 AGTTAAATTA
2342 ATAAATAATAAG
1 ATAAATAAT-AG
* *
2354 ATAAATAGTAA
1 ATAAATAATAG
2365 ATAAATAATAG
1 ATAAATAATAG
2376 ATAAATAA
1 ATAAATAA
2384 CTATAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (11 bp):
ATAAATAATAG
Found at i:5279 original size:155 final size:153
Alignment explanation
Indices: 4999--5279 Score: 377
Period size: 155 Copynumber: 1.8 Consensus size: 153
4989 CTCCAATTAC
* *
4999 TTAAAATTAAAATGGTAAAAATAAAATATTTATAAAAATATTAAATTTAATTAAATAAAAATACA
1 TTAAAATTAAAATGGTAAAAATAAAATAGTTATAAAAAGATTAAATTTAATTAAATAAAAATACA
* * *
5064 GTTGTAGTAGAATAAAACTGTAAAAGTTTAAAAAATATCATTTAAGAAATAAATTTAAAAAATTC
66 GTTGTAGTAGAATAAAACTATAAAAGTTTAAAAAATAGCATTTAAGAAATAAATTGAAAAAATTC
5129 TAATATATCTAAGTTTTTTAAAA
131 TAATATATCTAAGTTTTTTAAAA
* * * *
5152 TTAAAATACTAAAATGTTAAAGATAAAATAGTTATAAAGAGATTAGATTTAATTAAATAAAAATA
1 TTAAAAT--TAAAATGGTAAAAATAAAATAGTTATAAAAAGATTAAATTTAATTAAATAAAAATA
* * * * * *
5217 GAGTTTTTAGTTGAATAAAACTATAAAAG-TT-AACAATGGCATTTAAGAAATATATTCGAAAAA
64 CAG-TTGTAGTAGAATAAAACTATAAAAGTTTAAAAAATAGCATTTAAGAAATAAATT-GAAAAA
5280 TAAGGGTATA
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
153 7 0.06
154 21 0.19
155 59 0.54
156 22 0.20
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.34
Consensus pattern (153 bp):
TTAAAATTAAAATGGTAAAAATAAAATAGTTATAAAAAGATTAAATTTAATTAAATAAAAATACA
GTTGTAGTAGAATAAAACTATAAAAGTTTAAAAAATAGCATTTAAGAAATAAATTGAAAAAATTC
TAATATATCTAAGTTTTTTAAAA
Found at i:6535 original size:40 final size:40
Alignment explanation
Indices: 6456--6767 Score: 398
Period size: 40 Copynumber: 7.8 Consensus size: 40
6446 CAACCTAAAA
* *
6456 CCAATTGGCATTGAACTTGCCTTGATTCACATTCAAATTTT
1 CCAATTGACATTGAACTTGCCTT-ATTCACATCCAAATTTT
*
6497 CCAATTAACATTGAACTTGCCTTATTCACATCCAAATTTT
1 CCAATTGACATTGAACTTGCCTTATTCACATCCAAATTTT
*
6537 CCAATTGACATTGAACTAGCCTTGATTCACATCCAAATTTT
1 CCAATTGACATTGAACTTGCCTT-ATTCACATCCAAATTTT
** *
6578 CCAATCAACATTGAACTTGCCTTATTCACATCC-AGTTTT
1 CCAATTGACATTGAACTTGCCTTATTCACATCCAAATTTT
* * * *
6617 CCCAAATGATATTGAACTTGCCTTATTCACATCCAACTTTC
1 -CCAATTGACATTGAACTTGCCTTATTCACATCCAAATTTT
* *
6658 CCAAATGACATTGAACTTGCCTTATTCACATCC-AA--TC
1 CCAATTGACATTGAACTTGCCTTATTCACATCCAAATTTT
* * *
6695 CCAAATGACATTGAACTTGCCTTGATTCACATTCAAATTTC
1 CCAATTGACATTGAACTTGCCTT-ATTCACATCCAAATTTT
*
6736 CCAATTAACATTGAACTTGCCTTTATTCACAT
1 CCAATTGACATTGAACTTGCC-TTATTCACAT
6768 TGGCCCTCAA
Statistics
Matches: 243, Mismatches: 20, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
37 25 0.10
38 9 0.04
39 8 0.03
40 108 0.44
41 91 0.37
42 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.35
Consensus pattern (40 bp):
CCAATTGACATTGAACTTGCCTTATTCACATCCAAATTTT
Found at i:6591 original size:81 final size:80
Alignment explanation
Indices: 6464--6767 Score: 443
Period size: 81 Copynumber: 3.8 Consensus size: 80
6454 AACCAATTGG
* *
6464 CATTGAACTTGCCTTGATTCACATTCAAATTTTCCAATTAACATTGAACTTGCCTTATTCACATC
1 CATTGAACTTGCCTTGATTCACATCCAAATTTCCCAATTAACATTGAACTTGCCTTATTCACATC
*
6529 CAAATTTTCCAATTGA
66 C-AATTTTCCAAATGA
* * *
6545 CATTGAACTAGCCTTGATTCACATCCAAATTTTCCAATCAACATTGAACTTGCCTTATTCACATC
1 CATTGAACTTGCCTTGATTCACATCCAAATTTCCCAATTAACATTGAACTTGCCTTATTCACATC
*
6610 CAGTTTTCCCAAATGA
66 CAATTTT-CCAAATGA
* * * *
6626 TATTGAACTTGCCTT-ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTATTCACATC
1 CATTGAACTTGCCTTGATTCACATCCAAATTTCCCAATTAACATTGAACTTGCCTTATTCACATC
*
6690 CAA--TCCCAAATGA
66 CAATTTTCCAAATGA
*
6703 CATTGAACTTGCCTTGATTCACATTCAAATTTCCCAATTAACATTGAACTTGCCTTTATTCACAT
1 CATTGAACTTGCCTTGATTCACATCCAAATTTCCCAATTAACATTGAACTTGCC-TTATTCACAT
6768 TGGCCCTCAA
Statistics
Matches: 201, Mismatches: 19, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
77 22 0.11
78 35 0.17
79 10 0.05
80 51 0.25
81 83 0.41
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.36
Consensus pattern (80 bp):
CATTGAACTTGCCTTGATTCACATCCAAATTTCCCAATTAACATTGAACTTGCCTTATTCACATC
CAATTTTCCAAATGA
Found at i:6769 original size:21 final size:21
Alignment explanation
Indices: 6627--6769 Score: 68
Period size: 20 Copynumber: 7.2 Consensus size: 21
6617 CCCAAATGAT
6627 ATTGAACTTGCCTT-ATTCAC
1 ATTGAACTTGCCTTAATTCAC
** * * * *
6647 ATCCAACTTTCC-CAAATGAC
1 ATTGAACTTGCCTTAATTCAC
6667 ATTGAACTTGCCTT-ATTCAC
1 ATTGAACTTGCCTTAATTCAC
** * * *
6687 ATCCAA--T-CC-CAAATGAC
1 ATTGAACTTGCCTTAATTCAC
*
6704 ATTGAACTTGCCTTGATTCAC
1 ATTGAACTTGCCTTAATTCAC
* * * * *
6725 ATTCAAATTTCC-CAATTAAC
1 ATTGAACTTGCCTTAATTCAC
*
6745 ATTGAACTTGCCTTTATTCAC
1 ATTGAACTTGCCTTAATTCAC
6766 ATTG
1 ATTG
6770 GCCCTCAATG
Statistics
Matches: 80, Mismatches: 35, Indels: 15
0.62 0.27 0.12
Matches are distributed among these distances:
17 10 0.12
18 1 0.01
19 1 0.01
20 46 0.57
21 22 0.28
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (21 bp):
ATTGAACTTGCCTTAATTCAC
Found at i:7165 original size:41 final size:41
Alignment explanation
Indices: 7108--7188 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
7098 TACGCGGTAC
**
7108 ATTCACATTTAACTTTCCCAATCAACATTGAACTTGCCTTG
1 ATTCACATCCAACTTTCCCAATCAACATTGAACTTGCCTTG
* **
7149 ATTCACATCCAACTTTCCTAATTGACATTGAACTTGCCTT
1 ATTCACATCCAACTTTCCCAATCAACATTGAACTTGCCTT
7189 ATTAAAAGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.28, C:0.27, G:0.07, T:0.37
Consensus pattern (41 bp):
ATTCACATCCAACTTTCCCAATCAACATTGAACTTGCCTTG
Found at i:7182 original size:20 final size:20
Alignment explanation
Indices: 7112--7193 Score: 56
Period size: 20 Copynumber: 4.0 Consensus size: 20
7102 CGGTACATTC
* * *
7112 ACATTTAACTTTCCCAATCA
1 ACATTGAACTTTCCTAATTA
* * *
7132 ACATTGAACTTGCCTTGATTC
1 ACATTGAACTTTCC-TAATTA
** *
7153 ACATCCAACTTTCCTAATTG
1 ACATTGAACTTTCCTAATTA
* *
7173 ACATTGAACTTGCCTTATTA
1 ACATTGAACTTTCCTAATTA
7193 A
1 A
7194 AAGCACCTCC
Statistics
Matches: 45, Mismatches: 16, Indels: 2
0.71 0.25 0.03
Matches are distributed among these distances:
20 32 0.71
21 13 0.29
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (20 bp):
ACATTGAACTTTCCTAATTA
Found at i:7418 original size:33 final size:33
Alignment explanation
Indices: 7379--7444 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
7369 ACATGTGGAG
*
7379 GATCTGAAGCTAATCAAAAGTGTTCTTGAGGAT
1 GATCTGAAGCTAATCAAAAGTGTTCTTAAGGAT
* * * *
7412 GATCTGAAGGTAGTCAAAGGTGTTGTTAAGGAT
1 GATCTGAAGCTAATCAAAAGTGTTCTTAAGGAT
7445 ATTGTTGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (33 bp):
GATCTGAAGCTAATCAAAAGTGTTCTTAAGGAT
Found at i:16641 original size:72 final size:72
Alignment explanation
Indices: 16535--16671 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 72
16525 TGAAGATCTT
* * *
16535 GGTTTGTGGGATTCTAGTTTTGATGCAAAGTTTTCTGCTGAAGTCTTAAGATTGTCAAAAATTGA
1 GGTTTGTGGGATTCTAGTTTAGATGCAAAATTTTCTGCTGAAATCTTAAGATTGTCAAAAATTGA
16600 CTTTGAA
66 CTTTGAA
* *
16607 GGTTTGTGGGATTCTAGTTTAGATG-AGAAATTTTCTGCTGAAATTTTCAGATTGTCAAAAATTG
1 GGTTTGTGGGATTCTAGTTTAGATGCA-AAATTTTCTGCTGAAATCTTAAGATTGTCAAAAATTG
16671 A
65 A
16672 TCTTGATGGA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 1 0.02
72 58 0.98
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (72 bp):
GGTTTGTGGGATTCTAGTTTAGATGCAAAATTTTCTGCTGAAATCTTAAGATTGTCAAAAATTGA
CTTTGAA
Found at i:23608 original size:1 final size:1
Alignment explanation
Indices: 23604--23638 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
23594 TTTCCTTGCC
23604 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23639 CTCGTATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25387 original size:25 final size:23
Alignment explanation
Indices: 25337--25389 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
25327 GGCGGTCCAA
* **
25337 ACCGCCCGAACCGTCTAAAATTG
1 ACCGCCCGAACCGACTAAAACCG
25360 ACCGCCCGAAACCGACTTAAAACCG
1 ACCGCCCG-AACCGAC-TAAAACCG
25385 ACCGC
1 ACCGC
25390 TCGGTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.32
24 6 0.24
25 11 0.44
ACGTcount: A:0.32, C:0.40, G:0.17, T:0.11
Consensus pattern (23 bp):
ACCGCCCGAACCGACTAAAACCG
Found at i:25831 original size:11 final size:11
Alignment explanation
Indices: 25815--25844 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
25805 TTCAAAAAAT
25815 AAAACCGACTA
1 AAAACCGACTA
*
25826 AAAACCGATTA
1 AAAACCGACTA
25837 AAAACCGA
1 AAAACCGA
25845 AAACCGACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.23, G:0.10, T:0.10
Consensus pattern (11 bp):
AAAACCGACTA
Found at i:26421 original size:64 final size:65
Alignment explanation
Indices: 26318--26441 Score: 198
Period size: 64 Copynumber: 1.9 Consensus size: 65
26308 CCGCATGGGC
*
26318 ATATAATGATTTGGTTTACATGCTTAAAAATTCTAATCAAAATCACATAG-TTACCTTTATGTAT
1 ATATAATGATTTGGTTTACATGCTTAAAAATCCTAATCAAAATCACATAGTTTACCTTTATGTAT
* *
26382 ATATAATCG-TTTGGTTTATATGCTTAAAAATCCTTATCAAAATCACATAGTTTACCTTTA
1 ATATAAT-GATTTGGTTTACATGCTTAAAAATCCTAATCAAAATCACATAGTTTACCTTTA
26442 CGTTTAGCTA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 45 0.82
65 10 0.18
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (65 bp):
ATATAATGATTTGGTTTACATGCTTAAAAATCCTAATCAAAATCACATAGTTTACCTTTATGTAT
Found at i:27190 original size:3 final size:3
Alignment explanation
Indices: 27184--27219 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
27174 CATAGGATGA
27184 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
27220 GTTGGAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:37042 original size:180 final size:176
Alignment explanation
Indices: 36560--37047 Score: 393
Period size: 176 Copynumber: 2.8 Consensus size: 176
36550 CGGTCTATTT
* * * * * * *
36560 AATATTACATAATTCT-TGCTACAAATG-ATCGATTTAGGTGATTCAAATGTCTATTAAAATG-T
1 AATATTACATAATT-TATACTTCAAATGTAT-GATTAAGCTAATTCAACTATCTATTAAAA-GAT
* * * *** *
36622 TGTTCCATGATCTAGAACAACCATGAAGGAC-TCAAAAGCTAAATGTAATGTTTCAAGTATAAAA
63 TGTTTCATGATATAAAACTTTCATGAAGGACAT-AAAAGCTAAATTTAATGTTTCAAGTATAAAA
* * *
36686 AATGCTTCCAAAAAATTAGTTTTCGGTTAGCGAGAATGGATAGCCTACTA
127 AATGCTTCCAAAAAATCAGTTTTCGGTTAGCGAGAATAGAGAGCCTACTA
* * * * * *
36736 AATATTACATAATTTATTCTTTAAATGTATGATTAAGGTAATTCAAGTGTCTGTTAAAAGATTGT
1 AATATTACATAATTTATACTTCAAATGTATGATTAAGCTAATTCAACTATCTATTAAAAGATTGT
* * ** * * *
36801 TTCATGATATAAAACTTTTATGAAGGACATGAAAGCTAAATTCGATATTTCAGGAATAAAAAATG
66 TTCATGATATAAAACTTTCATGAAGGACATAAAAGCTAAATTTAATGTTTCAAGTATAAAAAATG
* * * *
36866 CTTCCCAAAAATCAGTAATTTCGGTTGGCGGGAAATAGACGA-TCTACTTAA
131 CTTCCAAAAAATCAGT--TTTCGGTTAGCGAG-AATAGA-GAGCCTAC-T-A
* * * *
36917 ATATATTATATAAATTT-TAC-TCAAGATGTCTGATTGAGCTGATTCAACTATCTATTAAAAG-T
1 A-ATATTACAT-AATTTATACTTCAA-ATGTATGATTAAGCTAATTCAACTATCTATTAAAAGAT
* * * ** *
36979 T-TTTCATGATTTACAACTTTCATGAATGATTTAAAAGGTAAATTTAATGTTTCAAGTAT-AAAA
63 TGTTTCATGATATAAAACTTTCATGAAGGACATAAAAGCTAAATTTAATGTTTCAAGTATAAAAA
37042 ATGCTT
128 ATGCTT
37048 TCGGAAAATT
Statistics
Matches: 248, Mismatches: 51, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
175 2 0.01
176 114 0.46
177 3 0.01
178 12 0.05
179 19 0.08
180 47 0.19
181 7 0.03
182 39 0.16
183 5 0.02
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (176 bp):
AATATTACATAATTTATACTTCAAATGTATGATTAAGCTAATTCAACTATCTATTAAAAGATTGT
TTCATGATATAAAACTTTCATGAAGGACATAAAAGCTAAATTTAATGTTTCAAGTATAAAAAATG
CTTCCAAAAAATCAGTTTTCGGTTAGCGAGAATAGAGAGCCTACTA
Found at i:53370 original size:28 final size:28
Alignment explanation
Indices: 53326--53404 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
53316 TTGTTATTAT
*
53326 AAAT-AAATTAAAAAAAGTTTATTTCCA
1 AAATAAAATTTAAAAAAGTTTATTTCCA
*
53353 AAATAAAATTTAAAAAAGTTT-TGGTGCCA
1 AAATAAAATTTAAAAAAGTTTAT--TTCCA
*
53382 AAA-AAAA-TTAAAAATGTTTATTT
1 AAATAAAATTTAAAAAAGTTTATTT
53405 TTTGGTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
26 1 0.02
27 16 0.36
28 20 0.45
29 7 0.16
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (28 bp):
AAATAAAATTTAAAAAAGTTTATTTCCA
Found at i:56219 original size:25 final size:24
Alignment explanation
Indices: 56182--56232 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
56172 TAATGCAATA
*
56182 TTTTGGCCATCTTTTGTTTTCTTTG
1 TTTTGGCCATC-TTTCTTTTCTTTG
* *
56207 TTTTGGTCTTCTTTCTTTTCTTTG
1 TTTTGGCCATCTTTCTTTTCTTTG
56231 TT
1 TT
56233 GCCTGAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.02, C:0.16, G:0.14, T:0.69
Consensus pattern (24 bp):
TTTTGGCCATCTTTCTTTTCTTTG
Found at i:61366 original size:33 final size:33
Alignment explanation
Indices: 61268--61398 Score: 145
Period size: 33 Copynumber: 3.8 Consensus size: 33
61258 AAAAACTGAA
* ****
61268 TGGGAACTTTCCCAATTTGAAAACTTAAAAGTTAA
1 TGGGAACTTTCCCAA-TTAAAAACTTAAAA-CCGG
61303 TGGGAACTTTCCCAATTTTTAAAAACTTAAAACCGG
1 TGGGAACTTTCCCAA---TTAAAAACTTAAAACCGG
* * *
61339 TGGGAACTTTCCCGATTAAAAATTTAAAACTGG
1 TGGGAACTTTCCCAATTAAAAACTTAAAACCGG
61372 TGGGAACTTTCCCAATTAAAAACTTAA
1 TGGGAACTTTCCCAATTAAAAACTTAA
61399 TGAAATTCTT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 41 0.49
35 15 0.18
36 14 0.17
37 14 0.17
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (33 bp):
TGGGAACTTTCCCAATTAAAAACTTAAAACCGG
Found at i:61438 original size:18 final size:19
Alignment explanation
Indices: 61415--61450 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
61405 TCTTTTTTGA
61415 TTTTTG-AGTTTTGAAAAT
1 TTTTTGTAGTTTTGAAAAT
*
61433 TTTTTGTATTTTTGAAAA
1 TTTTTGTAGTTTTGAAAA
61451 CCTTTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (19 bp):
TTTTTGTAGTTTTGAAAAT
Found at i:62136 original size:23 final size:23
Alignment explanation
Indices: 62073--62136 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
62063 GGAACTAAAT
62073 CCAAAGTATAAACTAGAAATCTAAG
1 CCAAAGTAT-AACTA-AAATCTAAG
* ** *
62098 CCCAAGCCTAACTAAAATTTAAG
1 CCAAAGTATAACTAAAATCTAAG
*
62121 CCAAAGTATAATTAAA
1 CCAAAGTATAACTAAA
62137 GTTCAAAGGC
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
23 20 0.65
24 5 0.16
25 6 0.19
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.22
Consensus pattern (23 bp):
CCAAAGTATAACTAAAATCTAAG
Found at i:63553 original size:39 final size:42
Alignment explanation
Indices: 63510--63593 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 42
63500 GTTTTTTTTG
* *
63510 AAAGCTA-GGTTTTT-TTG-CTTGGGAATCTTGTGTAAAAAA
1 AAAGCTAGGGTTTTTCTTGCCTTGGGAATCGTCTGTAAAAAA
*
63549 AAAGCTAGGGTTTTTCTTGCTCTTGGGAATCGTCTGTAAGAAA
1 AAAGCTAGGGTTTTTCTTGC-CTTGGGAATCGTCTGTAAAAAA
63592 AA
1 AA
63594 TGGGAAAGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 7 0.18
40 7 0.18
41 3 0.08
43 21 0.55
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.36
Consensus pattern (42 bp):
AAAGCTAGGGTTTTTCTTGCCTTGGGAATCGTCTGTAAAAAA
Found at i:63700 original size:2 final size:2
Alignment explanation
Indices: 63693--63720 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
63683 GAATAGTAGG
63693 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
63721 CTGCCTAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.