Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017831.1 Corchorus olitorius cultivar O-4 contig17864, 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: 118098
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:506 original size:36 final size:36
Alignment explanation
Indices: 459--528 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
449 TTCAATAACC
* **
459 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTAATTATCATATTTCTTA
*
495 TTACATTTTTTGTAATTTTAATTATCATATTTCT
1 TTACATCTTTTGTAATTTTAATTATCATATTTCT
529 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTAATTATCATATTTCTTA
Found at i:1424 original size:205 final size:200
Alignment explanation
Indices: 1047--1456 Score: 678
Period size: 205 Copynumber: 2.0 Consensus size: 200
1037 GCTTAATAAC
* *
1047 TTTATCGATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGAAGTGAATAA
*
1112 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTGA
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTGA
1177 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCC
1242 GA-TTA
195 GATTTA
* * *
1247 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATCAAAGTTGAAGTGAATAA
1 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGAAGTGAATAA
**
1312 GATACAATGCATTACTATTATATATACAGAACTATACCAAAAAAAAAATTAGTTGAACATTAGTG
66 GATACAACACATTACTATTATATATA-A-AACTATACC---AAAAAAATTAGTTGAACATTAGTG
1377 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
126 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
*
1442 ATCTGATTTA
191 ATCCGATTTA
1452 TTTAT
1 TTTAT
1457 TATTAAGGAA
Statistics
Matches: 195, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
200 83 0.43
201 1 0.01
202 9 0.05
204 8 0.04
205 94 0.48
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (200 bp):
TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGAAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCG
ATTTA
Found at i:1563 original size:26 final size:25
Alignment explanation
Indices: 1525--1574 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
1515 ATACGTTTAC
*
1525 ACAAATACCTAAGAATTTGAATTAAA
1 ACAAATACATAAGAATTT-AATTAAA
1551 ACAAATACATAAGAATTTAATTAA
1 ACAAATACATAAGAATTTAATTAA
1575 TGTAAGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.28
Consensus pattern (25 bp):
ACAAATACATAAGAATTTAATTAAA
Found at i:1619 original size:39 final size:40
Alignment explanation
Indices: 1565--1645 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
1555 ATACATAAGA
*
1565 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
1604 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
1644 AT
1 AT
1646 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:1916 original size:132 final size:132
Alignment explanation
Indices: 1717--2244 Score: 1038
Period size: 132 Copynumber: 4.0 Consensus size: 132
1707 AATATATTTA
1717 ATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATAAATACATGTTTAC
1 ATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATAAATACATGTTTAC
1782 CCTTTAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTT
66 CCTTTAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTT
1847 TT
131 TT
1849 ATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATAAATACATGTTTAC
1 ATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATAAATACATGTTTAC
1914 CCTTTAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTT
66 CCTTTAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTT
1979 TT
131 TT
1981 ATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATAAATACATGTTTAC
1 ATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATAAATACATGTTTAC
2046 CCTTTAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTT
66 CCTTTAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTT
2111 TT
131 TT
*
2113 ATTTAATTGATAAATGAAATTACATATTGAATCTTAAAAGTTTAATTTGATAAATACATGTTTAC
1 ATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATAAATACATGTTTAC
*
2178 CCTTTAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGATCAATGGTT
66 CCTTTAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTT
2243 TT
131 TT
2245 GAAGTTTAGA
Statistics
Matches: 394, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 394 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.41
Consensus pattern (132 bp):
ATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATAAATACATGTTTAC
CCTTTAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTT
TT
Found at i:9129 original size:42 final size:42
Alignment explanation
Indices: 9070--9149 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
9060 TACAGATCAA
9070 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTTTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTTTAT
*
9112 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTT
9150 CAAGACTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTTTAT
Found at i:9137 original size:21 final size:21
Alignment explanation
Indices: 9071--9137 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
9061 ACAGATCAAG
9071 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
*** * *
9092 ATTT-A-CAAAGAATTTTTTA
1 ATTTGAGTTGAGTATTTCTTA
9111 TGATTTGAGTTGAGTATTTCTTA
1 --ATTTGAGTTGAGTATTTCTTA
9134 ATTT
1 ATTT
9138 ACAGAGAATT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 9 0.28
20 1 0.03
21 12 0.38
22 1 0.03
23 9 0.28
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (21 bp):
ATTTGAGTTGAGTATTTCTTA
Found at i:29505 original size:3 final size:3
Alignment explanation
Indices: 29499--29528 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
29489 GTTGTTGAAT
29499 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29529 CTTGAAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:36049 original size:59 final size:59
Alignment explanation
Indices: 35957--36125 Score: 338
Period size: 59 Copynumber: 2.9 Consensus size: 59
35947 GTAAACTCTT
35957 TCTAATTTTTTTTGATATCCCATCCGGTATCCAGGGCTTAGCCCTGACTAACCCGCGTC
1 TCTAATTTTTTTTGATATCCCATCCGGTATCCAGGGCTTAGCCCTGACTAACCCGCGTC
36016 TCTAATTTTTTTTGATATCCCATCCGGTATCCAGGGCTTAGCCCTGACTAACCCGCGTC
1 TCTAATTTTTTTTGATATCCCATCCGGTATCCAGGGCTTAGCCCTGACTAACCCGCGTC
36075 TCTAATTTTTTTTGATATCCCATCCGGTATCCAGGGCTTAGCCCTGACTAA
1 TCTAATTTTTTTTGATATCCCATCCGGTATCCAGGGCTTAGCCCTGACTAA
36126 TCCGGATCCG
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 110 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.35
Consensus pattern (59 bp):
TCTAATTTTTTTTGATATCCCATCCGGTATCCAGGGCTTAGCCCTGACTAACCCGCGTC
Found at i:40569 original size:61 final size:61
Alignment explanation
Indices: 40464--40588 Score: 189
Period size: 61 Copynumber: 2.0 Consensus size: 61
40454 ATTCTAGGGA
* *
40464 GAGTAATTCAAAGGAAAGTGATATTAAGGAAAGTAACAATTAAAATTCATGGAAAGTAGTTT
1 GAGTAATTCAAAGGAAAGTGATACT-AGGAAAGTAACAATTAAAATCCATGGAAAGTAGTTT
* *
40526 GAGTTATTCAAAGGAAAGTGATGCT-GTGAAAGTAACAATTAAAATCCATGGAAAGTAGTTT
1 GAGTAATTCAAAGGAAAGTGATACTAG-GAAAGTAACAATTAAAATCCATGGAAAGTAGTTT
40587 GA
1 GA
40589 AGGGTTTGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
60 1 0.02
61 35 0.60
62 22 0.38
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.27
Consensus pattern (61 bp):
GAGTAATTCAAAGGAAAGTGATACTAGGAAAGTAACAATTAAAATCCATGGAAAGTAGTTT
Found at i:49474 original size:17 final size:18
Alignment explanation
Indices: 49441--49474 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49431 ATGGAGCGAT
49441 TTCTTTTAATCTAACTTA
1 TTCTTTTAATCTAACTTA
*
49459 TTCTTTTTAT-TAACTT
1 TTCTTTTAATCTAACTT
49475 TTGATTCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCTTTTAATCTAACTTA
Found at i:52786 original size:52 final size:52
Alignment explanation
Indices: 52666--52884 Score: 339
Period size: 52 Copynumber: 4.1 Consensus size: 52
52656 AAGCTCATTT
** *
52666 AACAACAACAATTAACATATGCAAAACAAAATTATATATAGGATCAGCACTAAACAA
1 AACAACAACAACCAACATATGCAAAACAAAATTATATATAGCATCAGCACT-----A
*
52723 CAACAACAACAACCAACATATGCTAAACAAAATTATATATAGCATCAGCACTA
1 -AACAACAACAACCAACATATGCAAAACAAAATTATATATAGCATCAGCACTA
*
52776 AACAACAACAACCAACATATGCTAAACAAAATTATATATAGCATCAGCACTA
1 AACAACAACAACCAACATATGCAAAACAAAATTATATATAGCATCAGCACTA
52828 AACAACAACAACCAACATATGCAAAACAAAATTATATATAGCATCAGCACTA
1 AACAACAACAACCAACATATGCAAAACAAAATTATATATAGCATCAGCACTA
52880 AACAA
1 AACAA
52885 TTCAATTGCA
Statistics
Matches: 156, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
52 108 0.69
53 1 0.01
58 47 0.30
ACGTcount: A:0.54, C:0.22, G:0.06, T:0.18
Consensus pattern (52 bp):
AACAACAACAACCAACATATGCAAAACAAAATTATATATAGCATCAGCACTA
Found at i:61103 original size:7 final size:7
Alignment explanation
Indices: 61091--61122 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
61081 ATGAACAGAT
61091 TTGAGTC
1 TTGAGTC
61098 TTGAGTC
1 TTGAGTC
61105 TTGAGTC
1 TTGAGTC
61112 TTGAGTC
1 TTGAGTC
61119 TTGA
1 TTGA
61123 CTTGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (7 bp):
TTGAGTC
Found at i:63648 original size:36 final size:35
Alignment explanation
Indices: 63593--63678 Score: 131
Period size: 36 Copynumber: 2.5 Consensus size: 35
63583 TAAAAACAAA
*
63593 AAAAACCCCAAAAAA--TTAACTGATCACAAAATTC
1 AAAAA-CCCAAAAAATTTTAACTGATCACAAAAATC
63627 AAAAACCCAAAAAATTGTTAACTGATCACAAAAATC
1 AAAAACCCAAAAAATT-TTAACTGATCACAAAAATC
63663 AAAAACCCAAAAAATT
1 AAAAACCCAAAAAATT
63679 ACCTTGGTGG
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
33 9 0.19
34 5 0.10
36 34 0.71
ACGTcount: A:0.58, C:0.21, G:0.03, T:0.17
Consensus pattern (35 bp):
AAAAACCCAAAAAATTTTAACTGATCACAAAAATC
Found at i:64132 original size:15 final size:16
Alignment explanation
Indices: 64104--64133 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
64094 GTCTTGGTGG
64104 GTTTCCTCATTCTCTA
1 GTTTCCTCATTCTCTA
64120 GTTTCCT-ATTCTCT
1 GTTTCCTCATTCTCT
64134 GTCACTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.30, G:0.07, T:0.53
Consensus pattern (16 bp):
GTTTCCTCATTCTCTA
Found at i:77380 original size:9 final size:9
Alignment explanation
Indices: 77366--77396 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
77356 TTTTTTTCTA
77366 TCTTCAAAT
1 TCTTCAAAT
77375 TCTTCAAAT
1 TCTTCAAAT
*
77384 TCTTCCAAT
1 TCTTCAAAT
77393 TCTT
1 TCTT
77397 TCCCCACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (9 bp):
TCTTCAAAT
Found at i:90398 original size:10 final size:10
Alignment explanation
Indices: 90383--90407 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
90373 ATATAGTTTC
90383 AGAACTTGAT
1 AGAACTTGAT
90393 AGAACTTGAT
1 AGAACTTGAT
90403 AGAAC
1 AGAAC
90408 CCTGAGATGA
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:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (10 bp):
AGAACTTGAT
Found at i:93706 original size:16 final size:16
Alignment explanation
Indices: 93685--93721 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
93675 GTTTTGGCGG
93685 AAAAAGAAAATAAAAT
1 AAAAAGAAAATAAAAT
*
93701 AAAAAGAAAATAAAGT
1 AAAAAGAAAATAAAAT
93717 AAAAA
1 AAAAA
93722 CCCATTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (16 bp):
AAAAAGAAAATAAAAT
Found at i:95016 original size:3 final size:3
Alignment explanation
Indices: 95008--95076 Score: 104
Period size: 3 Copynumber: 23.3 Consensus size: 3
94998 GCTTTGCTAG
95008 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
95055 AGA GGA AGG AGA AAA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA A
95077 ACCTTAATGT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:103580 original size:103 final size:103
Alignment explanation
Indices: 103401--103606 Score: 358
Period size: 103 Copynumber: 2.0 Consensus size: 103
103391 AATCAAATTG
* * * *
103401 CACCGCAAATTTTACTTCAAAGGGCAGAGGAGTAAATCGATTGAATATATATTTTCTTCTTCATT
1 CACCGCAAATTTAACTTCAAAGGGCAAAGGAGTAAATCCATTGAATATATATTTTCCTCTTCATT
103466 GACCATTTTAGCCTCCTCTGTCTCTCCCATATCTGAGC
66 GACCATTTTAGCCTCCTCTGTCTCTCCCATATCTGAGC
*
103504 CACCGCAAATTTAACTTCAAAGGGCAAAGGAGTAAATCCATTGAATATCTATTTTCCTCTTCATT
1 CACCGCAAATTTAACTTCAAAGGGCAAAGGAGTAAATCCATTGAATATATATTTTCCTCTTCATT
*
103569 GACCATTTTAGCCTCCTCTGTCTCTCCCATCTCTGAGC
66 GACCATTTTAGCCTCCTCTGTCTCTCCCATATCTGAGC
103607 TCCCTTTCAC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (103 bp):
CACCGCAAATTTAACTTCAAAGGGCAAAGGAGTAAATCCATTGAATATATATTTTCCTCTTCATT
GACCATTTTAGCCTCCTCTGTCTCTCCCATATCTGAGC
Found at i:115094 original size:24 final size:24
Alignment explanation
Indices: 115063--115112 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
115053 CAGGGTGAAA
* * *
115063 AAACCGGCCGTTCCGAAGGAGAAG
1 AAACCGGCAGCTCCAAAGGAGAAG
115087 AAACCGGCAGCTCCAAAGGAGAAG
1 AAACCGGCAGCTCCAAAGGAGAAG
115111 AA
1 AA
115113 GCCCAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.24, G:0.30, T:0.06
Consensus pattern (24 bp):
AAACCGGCAGCTCCAAAGGAGAAG
Found at i:116312 original size:71 final size:72
Alignment explanation
Indices: 116153--116441 Score: 519
Period size: 72 Copynumber: 4.0 Consensus size: 72
116143 TCCTTTTCTT
116153 TTTCTTTAATGATTTGGG-CTTTGGCCCCTTTTCTTAATTATAGGGACTGGATTCCTTTATATAT
1 TTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTTAATTATAGGGACTGGATTCCTTTATATAT
116217 TTTGGAC
66 TTTGGAC
*
116224 TTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTTTTAATTATAGGGACTGGATTCCTTTATATAT
1 TTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTTAATTATAGGGACTGGATTCCTTTATATAT
116289 TTTGGAC
66 TTTGGAC
* * *
116296 TTTCTTTAAAGA-TTGGGCCTTTGGCCCCTTTTCTGAATTATATGGACTGGATTCCTTTATATAT
1 TTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTTAATTATAGGGACTGGATTCCTTTATATAT
116360 TTTGGAC
66 TTTGGAC
*
116367 TTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTAAATTATAGGGACTGGATTCCTTTATATAT
1 TTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTTAATTATAGGGACTGGATTCCTTTATATAT
116432 TTTGGAC
66 TTTGGAC
116439 TTT
1 TTT
116442 GGTTGCTAAA
Statistics
Matches: 208, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
71 85 0.41
72 123 0.59
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (72 bp):
TTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTTAATTATAGGGACTGGATTCCTTTATATAT
TTTGGAC
Found at i:116393 original size:143 final size:143
Alignment explanation
Indices: 116153--116441 Score: 517
Period size: 143 Copynumber: 2.0 Consensus size: 143
116143 TCCTTTTCTT
* *
116153 TTTCTTTAATGATTTGGGCTTTGGCCCCTTTTCTTAATTATAGGGACTGGATTCCTTTATATATT
1 TTTCTTTAAAGATTTGGGCTTTGGCCCCTTTTCTGAATTATAGGGACTGGATTCCTTTATATATT
* *
116218 TTGGACTTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTTTTAATTATAGGGACTGGATTCCTTT
66 TTGGACTTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTAAATTATAGGGACTGGATTCCTTT
116283 ATATATTTTGGAC
131 ATATATTTTGGAC
*
116296 TTTCTTTAAAGA-TTGGGCCTTTGGCCCCTTTTCTGAATTATATGGACTGGATTCCTTTATATAT
1 TTTCTTTAAAGATTTGGG-CTTTGGCCCCTTTTCTGAATTATAGGGACTGGATTCCTTTATATAT
116360 TTTGGACTTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTAAATTATAGGGACTGGATTCCTT
65 TTTGGACTTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTAAATTATAGGGACTGGATTCCTT
116425 TATATATTTTGGAC
130 TATATATTTTGGAC
116439 TTT
1 TTT
116442 GGTTGCTAAA
Statistics
Matches: 140, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
142 5 0.04
143 135 0.96
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (143 bp):
TTTCTTTAAAGATTTGGGCTTTGGCCCCTTTTCTGAATTATAGGGACTGGATTCCTTTATATATT
TTGGACTTTCTTTAATGATTTGGGCCTTTGGCCCCTTTTCTAAATTATAGGGACTGGATTCCTTT
ATATATTTTGGAC
Done.