Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017567.1 Corchorus olitorius cultivar O-4 contig17600, 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: 165815
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:313 original size:84 final size:85
Alignment explanation
Indices: 174--356 Score: 296
Period size: 84 Copynumber: 2.1 Consensus size: 85
164 TACATAGTAA
* * *
174 GGTGGAGGAGACGGCGGTGGTGGTGATCTGTATTTGTAACGTGGTGGAGGTGGTGGGGGTGGTGA
1 GGTGGAGGAGACGGCGGTGGTGGTGATCTATATTTGTAAC--GGTGGAGGTGGTGGGGGAGGGGA
239 CTTGTATTTGTAGATAAAAGGT
64 CTTGTATTTGTAGATAAAAGGT
*
261 GGTGGAGGAGACGGTGGTGGTGGTGATCTATATTTGTAAC-GTGGAGGTGGTGGGGGAGGGGACT
1 GGTGGAGGAGACGGCGGTGGTGGTGATCTATATTTGTAACGGTGGAGGTGGTGGGGGAGGGGACT
325 TGTATTTGTAGATAAAAGGT
66 TGTATTTGTAGATAAAAGGT
*
345 GGAGGAGGAGAC
1 GGTGGAGGAGAC
357 TTGTATGAAT
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
84 53 0.58
87 38 0.42
ACGTcount: A:0.21, C:0.05, G:0.46, T:0.27
Consensus pattern (85 bp):
GGTGGAGGAGACGGCGGTGGTGGTGATCTATATTTGTAACGGTGGAGGTGGTGGGGGAGGGGACT
TGTATTTGTAGATAAAAGGT
Found at i:15361 original size:26 final size:26
Alignment explanation
Indices: 15313--15362 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
15303 AAAAAAGTTT
* * *
15313 GATATAAAGATAAAATGAGTTAAAAG
1 GATATAAACATAAAAGGAATTAAAAG
*
15339 GATATAAACATAGAAGGAATTAAA
1 GATATAAACATAAAAGGAATTAAA
15363 GAAAAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.18, T:0.22
Consensus pattern (26 bp):
GATATAAACATAAAAGGAATTAAAAG
Found at i:15489 original size:16 final size:16
Alignment explanation
Indices: 15468--15501 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
15458 TTTTTTTTCG
15468 TGTCAAAACTAGTTTT
1 TGTCAAAACTAGTTTT
15484 TGTCAAAACTAGTTTT
1 TGTCAAAACTAGTTTT
15500 TG
1 TG
15502 ACACAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (16 bp):
TGTCAAAACTAGTTTT
Found at i:16443 original size:21 final size:19
Alignment explanation
Indices: 16418--16472 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
16408 TGTTGCTCTA
*
16418 ATAATTTCATCTGTACAAT
1 ATAATCTCATCTGTACAAT
* *
16437 ACCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAAT
16458 ATAATCTCATCTGTA
1 ATAATCTCATCTGTA
16473 TAGTTGCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 14 0.47
21 16 0.53
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (19 bp):
ATAATCTCATCTGTACAAT
Found at i:16464 original size:19 final size:20
Alignment explanation
Indices: 16426--16472 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
16416 TAATAATTTC
16426 ATCTGTACAATACCTAATCTA
1 ATCTGTACAATA-CTAATCTA
* *
16447 ATCTGTACAGTA-TAATCTC
1 ATCTGTACAATACTAATCTA
16466 ATCTGTA
1 ATCTGTA
16473 TAGTTGCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.54
21 11 0.46
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (20 bp):
ATCTGTACAATACTAATCTA
Found at i:17082 original size:13 final size:13
Alignment explanation
Indices: 17064--17088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17054 CAAAAACAAC
17064 TGAAAAACACTTT
1 TGAAAAACACTTT
17077 TGAAAAACACTT
1 TGAAAAACACTT
17089 CTGGATTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (13 bp):
TGAAAAACACTTT
Found at i:18416 original size:21 final size:19
Alignment explanation
Indices: 18371--18428 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
18361 CTGTTTAGCA
18371 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
18390 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
18411 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
18429 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:19245 original size:6 final size:6
Alignment explanation
Indices: 19231--19275 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
19221 AAAACACCAC
*
19231 TTCTG- TTCTGT TTCTGT TTCTGT TTCTGT TTCTGT TTCTAT TTCT
1 TTCTGT TTCTGT TTCTGT TTCTGT TTCTGT TTCTGT TTCTGT TTCT
19276 TCCCTCTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.02, C:0.18, G:0.13, T:0.67
Consensus pattern (6 bp):
TTCTGT
Found at i:21143 original size:4 final size:4
Alignment explanation
Indices: 21136--21167 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
21126 GAACAATGAA
21136 AAAG AAAG AAAG AAAG AAAG -AA- AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
21168 GGGGGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.15
4 22 0.85
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:28143 original size:6 final size:6
Alignment explanation
Indices: 28132--28160 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28122 TCCTCAAACA
28132 CCGTCG CCGTCG CCGTCG CCGTCG CCGTC
1 CCGTCG CCGTCG CCGTCG CCGTCG CCGTC
28161 CTTCCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.31, T:0.17
Consensus pattern (6 bp):
CCGTCG
Found at i:28446 original size:133 final size:132
Alignment explanation
Indices: 28208--28592 Score: 635
Period size: 133 Copynumber: 2.9 Consensus size: 132
28198 AACCAAGCCA
* * * *
28208 GAATGAATGGATGGTACATTGACCCCTACGAGGTAATATAAATGTCACACTTTGCTTATGTTACA
1 GAATGGATGCATGGTACATTGACCCTTACGAGGTAACATAAATGTCACACTTTGCTTATGTTACA
* *
28273 TGAAACCTTCATGTCTTTGTCTGACATTATATCCCGAGTCCAAAAATACTCGAGGTTAATGACTA
66 AGAAATCTT-ATGTCTTTGTCTGACATTATATCCCGAGTCCAAAAATACTCGAGGTTAATGACTA
28338 ATT
130 ATT
28341 GAATGGATGCATGGTACATTGACCCTTACGAGGTAACATAAATGTCACACTTTGCTTATGTTACA
1 GAATGGATGCATGGTACATTGACCCTTACGAGGTAACATAAATGTCACACTTTGCTTATGTTACA
* * *
28406 AGAAATCTGTATGTCTTTGTCTGACATTATATTCCGAGTCCAAAAATACTCAATGTTAATGACTA
66 AGAAATCT-TATGTCTTTGTCTGACATTATATCCCGAGTCCAAAAATACTCGAGGTTAATGACTA
28471 ATT
130 ATT
*
28474 GAATGGATGCATGGTACATTGACCCTTACAAGGTAACATAAATGTCACACTTTGCTTATGTTACA
1 GAATGGATGCATGGTACATTGACCCTTACGAGGTAACATAAATGTCACACTTTGCTTATGTTACA
*
28539 AGAAATCTCTATGTCTTTGTCTGACATTATATCCCCGAGTCCAAAAATATTCGA
66 AGAAATCT-TATGTCTTTGTCTGACATTATAT-CCCGAGTCCAAAAATACTCGA
28593 TGTCATGTCA
Statistics
Matches: 236, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
133 217 0.92
134 19 0.08
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (132 bp):
GAATGGATGCATGGTACATTGACCCTTACGAGGTAACATAAATGTCACACTTTGCTTATGTTACA
AGAAATCTTATGTCTTTGTCTGACATTATATCCCGAGTCCAAAAATACTCGAGGTTAATGACTAA
TT
Found at i:39408 original size:11 final size:11
Alignment explanation
Indices: 39392--39416 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39382 ATCTCTTCAT
39392 TTTCATTATAA
1 TTTCATTATAA
39403 TTTCATTATAA
1 TTTCATTATAA
39414 TTT
1 TTT
39417 ACGAAGATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTCATTATAA
Found at i:41391 original size:22 final size:22
Alignment explanation
Indices: 41366--41411 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
41356 TCACCCTTAT
*
41366 ATCGCGACATGACAGAGGCAAC
1 ATCGCGACATGACAAAGGCAAC
41388 ATCGCGACATGACAAAGGCAAC
1 ATCGCGACATGACAAAGGCAAC
41410 AT
1 AT
41412 AGAAGAGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.26, G:0.24, T:0.11
Consensus pattern (22 bp):
ATCGCGACATGACAAAGGCAAC
Found at i:63673 original size:4 final size:4
Alignment explanation
Indices: 63664--63690 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
63654 ACTTTATCTT
63664 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
63691 CGTTTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:69512 original size:19 final size:19
Alignment explanation
Indices: 69488--69545 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
69478 CTGTTTAGCA
69488 ACTGTACAAATGAGATTAC
1 ACTGTACAAATGAGATTAC
* * *
69507 ACTGTATAAATTAGATTAGAT
1 ACTGTACAAATGAGATT--AC
*
69528 ACTGTACAGATGAGATTA
1 ACTGTACAAATGAGATTA
69546 TTAGAGCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (19 bp):
ACTGTACAAATGAGATTAC
Found at i:69543 original size:21 final size:20
Alignment explanation
Indices: 69488--69545 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
69478 CTGTTTAGCA
69488 ACTGTACAAATGAGATT-AC
1 ACTGTACAAATGAGATTAAC
* * *
69507 ACTGTATAAATTAGATTAGAT
1 ACTGTACAAATGAGATTA-AC
*
69528 ACTGTACAGATGAGATTA
1 ACTGTACAAATGAGATTA
69546 TTAGAGCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (20 bp):
ACTGTACAAATGAGATTAAC
Found at i:69746 original size:19 final size:20
Alignment explanation
Indices: 69691--69748 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
69681 GCTGCTCTAT
69691 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTA-C
* * *
69712 TATTCTAATTTGTACAGT-C
1 TAATCTCATCTGTACAGTAC
69731 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
69749 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:75537 original size:15 final size:15
Alignment explanation
Indices: 75499--75540 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
75489 CAAGTCATGA
75499 AGTACCAAATTTCGG
1 AGTACCAAATTTCGG
75514 A-T--C-AATTTCGG
1 AGTACCAAATTTCGG
75525 AGTACCAAATTTCGG
1 AGTACCAAATTTCGG
75540 A
1 A
75541 TCATGTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
11 9 0.39
12 2 0.09
14 2 0.09
15 10 0.43
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (15 bp):
AGTACCAAATTTCGG
Found at i:78429 original size:29 final size:29
Alignment explanation
Indices: 78379--78434 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
78369 GGCAAGACGT
* * * *
78379 CCCAGAATTGAAGTTTAGAGGGGAAAATG
1 CCCAAAATTGAAGTTCACAGGGCAAAATG
78408 CCCAAAATTGAAGTTCACAGGGCAAAA
1 CCCAAAATTGAAGTTCACAGGGCAAAA
78435 CATCCAAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (29 bp):
CCCAAAATTGAAGTTCACAGGGCAAAATG
Found at i:84911 original size:3 final size:3
Alignment explanation
Indices: 84903--84933 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
84893 GCCAAAAAGC
84903 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT G
84934 ATGGACATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:88403 original size:18 final size:18
Alignment explanation
Indices: 88382--88440 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
88372 TCATTTTGAA
88382 TGAAAATGATAGTACTAC
1 TGAAAATGATAGTACTAC
* ** *
88400 TG-AAATGGTCA-TTTTGAA
1 TGAAAATGAT-AGTACT-AC
88418 TGAAAATGATAGTACTAC
1 TGAAAATGATAGTACTAC
88436 TGAAA
1 TGAAA
88441 TGGTCATTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
17 8 0.28
18 13 0.45
19 8 0.28
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (18 bp):
TGAAAATGATAGTACTAC
Found at i:88405 original size:36 final size:36
Alignment explanation
Indices: 88333--88452 Score: 210
Period size: 36 Copynumber: 3.4 Consensus size: 36
88323 AGAACTGGTC
*
88333 AAATGGTTATTTTGAATGAAAATG--A-TACTACTG
1 AAATGGTCATTTTGAATGAAAATGATAGTACTACTG
88366 AAATGGTCATTTTGAATGAAAATGATAGTACTACTG
1 AAATGGTCATTTTGAATGAAAATGATAGTACTACTG
88402 AAATGGTCATTTTGAATGAAAATGATAGTACTACTG
1 AAATGGTCATTTTGAATGAAAATGATAGTACTACTG
88438 AAATGGTCATTTTGA
1 AAATGGTCATTTTGA
88453 TATTGTAAAG
Statistics
Matches: 83, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
33 23 0.28
35 1 0.01
36 59 0.71
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.35
Consensus pattern (36 bp):
AAATGGTCATTTTGAATGAAAATGATAGTACTACTG
Found at i:94232 original size:2 final size:2
Alignment explanation
Indices: 94225--94262 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
94215 AATATAATGA
94225 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
94263 CAACATCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:106119 original size:12 final size:13
Alignment explanation
Indices: 106099--106128 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
106089 TTTTTTTTTT
106099 TTTTCTTTTTGGC
1 TTTTCTTTTTGGC
106112 TTTT-TTTTTGGC
1 TTTTCTTTTTGGC
106124 TTTTC
1 TTTTC
106129 ATTATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.73
Consensus pattern (13 bp):
TTTTCTTTTTGGC
Found at i:107822 original size:13 final size:13
Alignment explanation
Indices: 107806--107830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
107796 TTTAAACTCT
107806 TTTTTTTTTACCA
1 TTTTTTTTTACCA
107819 TTTTTTTTTACC
1 TTTTTTTTTACC
107831 GATAACAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTACCA
Found at i:108253 original size:2 final size:2
Alignment explanation
Indices: 108246--108275 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
108236 AACTTCCCTC
108246 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
108276 TCATAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114056 original size:39 final size:41
Alignment explanation
Indices: 114008--114114 Score: 128
Period size: 39 Copynumber: 2.7 Consensus size: 41
113998 ATACGACCGT
* * **
114008 TATGGCTACTCTTCACATGTAATTTACACTTTTGTTATT-G
1 TATGTCTACTATTCACATGTAATTTACACTTCAGTTATTGG
* * *
114048 -ATTTCTACTATTCACGTGTAATATACACTTCAGTTATTGG
1 TATGTCTACTATTCACATGTAATTTACACTTCAGTTATTGG
*
114088 TATGTCTGCTATTCACATGTAATTTAC
1 TATGTCTACTATTCACATGTAATTTAC
114115 TTACACTCTT
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
39 31 0.57
40 1 0.02
41 22 0.41
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (41 bp):
TATGTCTACTATTCACATGTAATTTACACTTCAGTTATTGG
Found at i:118595 original size:97 final size:97
Alignment explanation
Indices: 118484--118678 Score: 327
Period size: 97 Copynumber: 2.0 Consensus size: 97
118474 ATTGAAATAT
118484 TTAAAACTTAATTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAATCCAAA
1 TTAAAACTTAATTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAATCCAAA
*
118549 ATTTACACCGCCGGTGTATCAAATAATTACCC
66 ATTTACACAGCCGGTGTATCAAATAATTACCC
* * * * * *
118581 TTAAAACTTAATTAATTCAGAAAATGGACATGTGTCAATTCCATAACCCGCTTGTGGAGTCTAAA
1 TTAAAACTTAATTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAATCCAAA
118646 ATTTACACAGCCGGTGTATCAAATAATTACCC
66 ATTTACACAGCCGGTGTATCAAATAATTACCC
118678 T
1 T
118679 ATTATTATAA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (97 bp):
TTAAAACTTAATTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAATCCAAA
ATTTACACAGCCGGTGTATCAAATAATTACCC
Found at i:130030 original size:122 final size:122
Alignment explanation
Indices: 129813--130059 Score: 494
Period size: 122 Copynumber: 2.0 Consensus size: 122
129803 AGTTAAACAC
129813 TTTGAATTTCTTAATATTGCATTTCACTCACTTACCAAGTACACTAGAAGAGAGCATAGCTTTGC
1 TTTGAATTTCTTAATATTGCATTTCACTCACTTACCAAGTACACTAGAAGAGAGCATAGCTTTGC
129878 ACTTGATTGTTATTGCTGTTGTGGTTACCTATCTCTAGTCATCATCATAATGCCAAA
66 ACTTGATTGTTATTGCTGTTGTGGTTACCTATCTCTAGTCATCATCATAATGCCAAA
129935 TTTGAATTTCTTAATATTGCATTTCACTCACTTACCAAGTACACTAGAAGAGAGCATAGCTTTGC
1 TTTGAATTTCTTAATATTGCATTTCACTCACTTACCAAGTACACTAGAAGAGAGCATAGCTTTGC
130000 ACTTGATTGTTATTGCTGTTGTGGTTACCTATCTCTAGTCATCATCATAATGCCAAA
66 ACTTGATTGTTATTGCTGTTGTGGTTACCTATCTCTAGTCATCATCATAATGCCAAA
130057 TTT
1 TTT
130060 TAGCTAACCA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 125 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (122 bp):
TTTGAATTTCTTAATATTGCATTTCACTCACTTACCAAGTACACTAGAAGAGAGCATAGCTTTGC
ACTTGATTGTTATTGCTGTTGTGGTTACCTATCTCTAGTCATCATCATAATGCCAAA
Found at i:148733 original size:20 final size:19
Alignment explanation
Indices: 148703--148744 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
148693 GATCTCTTTG
148703 TACCAAAAAGAAATATATTAT
1 TACCAAAAAGAAA-ATATT-T
148724 TACC-AAAAGAAAATATTT
1 TACCAAAAAGAAAATATTT
148742 TAC
1 TAC
148745 TTGTTTTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
20 8 0.38
21 4 0.19
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.29
Consensus pattern (19 bp):
TACCAAAAAGAAAATATTT
Found at i:148932 original size:21 final size:20
Alignment explanation
Indices: 148906--148956 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
148896 CGCTACTCTA
148906 ATAATCTCATTTGTACA-GT
1 ATAATCTCATTTGTACACGT
*
148925 ACCTAATCTAATTTGTACACGT
1 A--TAATCTCATTTGTACACGT
148947 ATAATCTCAT
1 ATAATCTCAT
148957 CTATATAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 8 0.30
21 15 0.56
22 3 0.11
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (20 bp):
ATAATCTCATTTGTACACGT
Found at i:150515 original size:23 final size:24
Alignment explanation
Indices: 150484--150538 Score: 87
Period size: 23 Copynumber: 2.3 Consensus size: 24
150474 ACATAGATTC
150484 TATATATTCTATATA-ATA-ATAT
1 TATATATTCTATATATATATATAT
150506 TACTATATTCTATATATATATATAT
1 TA-TATATTCTATATATATATATAT
150531 TATATATT
1 TATATATT
150539 ATTATAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.07
23 13 0.43
24 9 0.30
25 6 0.20
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATATTCTATATATATATATAT
Found at i:150516 original size:32 final size:32
Alignment explanation
Indices: 150480--150544 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
150470 TGCTACATAG
*
150480 ATTCTATATATTCTATATAATA-ATATTACTAT
1 ATTCTATATA-TATATATAATATATATTACTAT
* *
150512 ATTCTATATATATATATATTATATATTATTAT
1 ATTCTATATATATATATAATATATATTACTAT
150544 A
1 A
150545 AAGTGTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTCTATATATATATATAATATATATTACTAT
Found at i:153148 original size:12 final size:12
Alignment explanation
Indices: 153133--153174 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
153123 CTCTGTTCTT
153133 CTTC-TTCTTCTC
1 CTTCTTTCTT-TC
153145 CTTCTTTCTTTC
1 CTTCTTTCTTTC
* *
153157 TTTCTTTCTTTT
1 CTTCTTTCTTTC
153169 CTTCTT
1 CTTCTT
153175 CTTATCGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
CTTCTTTCTTTC
Done.