Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016633.1 Corchorus olitorius cultivar O-4 contig16666, 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: 168475
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12235 original size:12 final size:12
Alignment explanation
Indices: 12218--12244 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12208 TTTAACATTT
12218 TTGGTAATTACA
1 TTGGTAATTACA
12230 TTGGTAATTACA
1 TTGGTAATTACA
12242 TTG
1 TTG
12245 CGCAACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (12 bp):
TTGGTAATTACA
Found at i:12560 original size:14 final size:14
Alignment explanation
Indices: 12541--12574 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
12531 TTTTATAATT
12541 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
12555 ATTTTATTTTTACT
1 ATTTTATTTTTACC
12569 ATTTTA
1 ATTTTA
12575 ATTTAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:14812 original size:175 final size:165
Alignment explanation
Indices: 14576--14911 Score: 458
Period size: 166 Copynumber: 2.0 Consensus size: 165
14566 TCTTATAAAG
14576 GAAATTTGAATGTTCATCAACGAAAATAATTTGACAAACTTATAATTCGGTCTAAATTGAAAATT
1 GAAATTTGAATGTTCATCAACGAAAATAATTTGACAAACTTATAATTCGGTCTAAATTGAAAATT
*
14641 T-TAATTAATTTTTAAATAAAAAATTATACTAAATTTTAATAATGGGAATTTAGAAATATAATTG
66 TATAATTAA-TTTT---T---AAA-TA-A-TAAATTTTAATAATGGCAATTTAGAAATATAATTG
*
14705 AAAAAAGGGTACAATCGGAAAACATAAAGTTTCCCATTATTAGTA
121 AAAAAAGGATACAATCGGAAAACATAAAGTTTCCCATTATTAGTA
* * * * *
14750 GAAATTTGGATGTTCATCAATGAAAATCAATTTTACAAACTTTTAATTCGGTCTAAATTGAAATT
1 GAAATTTGAATGTTCATCAACGAAAAT-AATTTGACAAACTTATAATTCGGTCTAAATTGAAAAT
* * * *
14815 TTATAATTAATTTTTAAATAATAAATTTTAATAATGTCAATTTAGAAATATATTTGAAAAGATGA
65 TTATAATTAATTTTTAAATAATAAATTTTAATAATGGCAATTTAGAAATATAATTGAAAAAAGGA
*
14880 TACAATCGGAAAACATAAAGTTTCCCCTTATT
130 TACAATCGGAAAACATAAAGTTTCCCATTATT
14912 TGTACTTATA
Statistics
Matches: 148, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
166 69 0.47
167 1 0.01
168 2 0.01
169 3 0.02
172 1 0.01
174 25 0.17
175 40 0.27
176 7 0.05
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (165 bp):
GAAATTTGAATGTTCATCAACGAAAATAATTTGACAAACTTATAATTCGGTCTAAATTGAAAATT
TATAATTAATTTTTAAATAATAAATTTTAATAATGGCAATTTAGAAATATAATTGAAAAAAGGAT
ACAATCGGAAAACATAAAGTTTCCCATTATTAGTA
Found at i:15156 original size:21 final size:22
Alignment explanation
Indices: 15116--15156 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
15106 GACAAACTCG
*
15116 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
15138 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
15157 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:16446 original size:161 final size:160
Alignment explanation
Indices: 16185--16500 Score: 444
Period size: 161 Copynumber: 2.0 Consensus size: 160
16175 GTCATTTAAG
* * *
16185 AAATATATTTTAGAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
1 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
* *
16250 AAGTAGGTATAAGGATATTAGATTTCATTAAATAAAAATAGAGTTTTTAG-TTTTTTT-GGCCAA
66 AAGTAGGTATAAGGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTTTTTTTAGG--AA
16313 AAAATAGAGTTTTTAGTTGAGTAAAATTATAA
129 AAAATAGAGTTTTTAGTTGAGTAAAATTATAA
* *
16345 AAATATATTTAAAAAATTCTAATATATATAATTTTTTTTTAATTAAA-TAGTACAA-TGGTAAAA
1 AAATATATTTAAAAAATTCTAATATATATAA--GTTTTTTAATTAAATTAGTA-AATTGATAAAA
* *
16408 ATTAAA-TAGTTATAAGGATATTATATTTAATAAAATAAAAATAGAGTTTTTAGTTTTTTTTAAG
63 A-TAAAGTAGGTATAAGGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTTTTTTT-AG
*
16472 GGAAAAATAGAGTTTTTAGTTGAGTAAAA
126 GAAAAAATAGAGTTTTTAGTTGAGTAAAA
16501 CAATAAAAGT
Statistics
Matches: 139, Mismatches: 10, Indels: 12
0.86 0.06 0.07
Matches are distributed among these distances:
160 28 0.20
161 56 0.40
162 53 0.38
164 2 0.01
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (160 bp):
AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
AAGTAGGTATAAGGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTTTTTTTAGGAAAA
AATAGAGTTTTTAGTTGAGTAAAATTATAA
Found at i:20327 original size:31 final size:31
Alignment explanation
Indices: 20292--20383 Score: 85
Period size: 31 Copynumber: 3.3 Consensus size: 31
20282 CGAGCATCCA
20292 TGATTGCACTTCATGGCAGGCAAAGCAGAGC
1 TGATTGCACTTCATGGCAGGCAAAGCAGAGC
* *
20323 TGATTGCA--T-A---CTGTCAAA--AGA-C
1 TGATTGCACTTCATGGCAGGCAAAGCAGAGC
* *
20345 TTACTGCACTTCATGGCAGGCAAAGCAGAGC
1 TGATTGCACTTCATGGCAGGCAAAGCAGAGC
20376 TGATTGCA
1 TGATTGCA
20384 TACTGTCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 18
0.63 0.11 0.26
Matches are distributed among these distances:
22 7 0.16
23 3 0.07
24 1 0.02
25 7 0.16
28 7 0.16
29 1 0.02
30 3 0.07
31 15 0.34
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (31 bp):
TGATTGCACTTCATGGCAGGCAAAGCAGAGC
Found at i:20376 original size:53 final size:53
Alignment explanation
Indices: 20296--20401 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
20286 CATCCATGAT
20296 TGCACTTCATGGCAGGCAAAGCAGAGCTGATTGCATACTGTCAAAAGACTTAC
1 TGCACTTCATGGCAGGCAAAGCAGAGCTGATTGCATACTGTCAAAAGACTTAC
20349 TGCACTTCATGGCAGGCAAAGCAGAGCTGATTGCATACTGTCAAAAGACTTAC
1 TGCACTTCATGGCAGGCAAAGCAGAGCTGATTGCATACTGTCAAAAGACTTAC
20402 GGTCAATAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (53 bp):
TGCACTTCATGGCAGGCAAAGCAGAGCTGATTGCATACTGTCAAAAGACTTAC
Found at i:20395 original size:26 final size:26
Alignment explanation
Indices: 20313--20395 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
20303 CATGGCAGGC
20313 AAAGCAGAGCTGATTGCATACTGTCA
1 AAAGCAGAGCTGATTGCATACTGTCA
** * * *
20339 AAAGACTTA-CTGCACTT-CATGGCAGGC-
1 AAAG-CAGAGCTG-A-TTGCAT-ACTGTCA
20366 AAAGCAGAGCTGATTGCATACTGTCA
1 AAAGCAGAGCTGATTGCATACTGTCA
20392 AAAG
1 AAAG
20396 ACTTACGGTC
Statistics
Matches: 40, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
25 5 0.12
26 17 0.43
27 13 0.32
28 5 0.12
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
AAAGCAGAGCTGATTGCATACTGTCA
Found at i:27495 original size:86 final size:86
Alignment explanation
Indices: 27350--27527 Score: 302
Period size: 86 Copynumber: 2.1 Consensus size: 86
27340 GACTGATCTT
* * *
27350 GTTTGATTCTTTGAATTAGATTTGACTGGCTTTATAGAGCTTTTTACGGCGGATGTTTCATTGTC
1 GTTTGATTATTTGAATTAGATTTGACTGGCTATATAGAGCTTTTTACAGCGGATGTTTCATTGTC
27415 TACCAGCAACAATTACTCATA
66 TACCAGCAACAATTACTCATA
*
27436 GTTTGATTATTTTAATTAGATTTGACTGGCTATATAGAGCTTTTTACAGCGGATGTTTCATTGTC
1 GTTTGATTATTTGAATTAGATTTGACTGGCTATATAGAGCTTTTTACAGCGGATGTTTCATTGTC
*
27501 TGCCAGCAACAATTACTCATA
66 TACCAGCAACAATTACTCATA
*
27522 GCTTGA
1 GTTTGA
27528 CGATTTGAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (86 bp):
GTTTGATTATTTGAATTAGATTTGACTGGCTATATAGAGCTTTTTACAGCGGATGTTTCATTGTC
TACCAGCAACAATTACTCATA
Found at i:27546 original size:86 final size:86
Alignment explanation
Indices: 27359--27546 Score: 277
Period size: 86 Copynumber: 2.2 Consensus size: 86
27349 TGTTTGATTC
* * *
27359 TTTGAATTAGATTTGACTGGCTTTATAGAGCTTTTTACGGCGGATGTTTCATTGTCTACCAGCAA
1 TTTGAATCAGATTTGACTGGCTATATAGAGCTTTTTACAGCGGATGTTTCATTGTCTACCAGCAA
* **
27424 CAATTACTCATAGTTTGATTA
66 CAATTACTCATAGCTTGACGA
* * *
27445 TTTTAATTAGATTTGACTGGCTATATAGAGCTTTTTACAGCGGATGTTTCATTGTCTGCCAGCAA
1 TTTGAATCAGATTTGACTGGCTATATAGAGCTTTTTACAGCGGATGTTTCATTGTCTACCAGCAA
27510 CAATTACTCATAGCTTGACGA
66 CAATTACTCATAGCTTGACGA
* *
27531 TTTGAGTCAGTTTTGA
1 TTTGAATCAGATTTGA
27547 TGAATAACAT
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 91 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (86 bp):
TTTGAATCAGATTTGACTGGCTATATAGAGCTTTTTACAGCGGATGTTTCATTGTCTACCAGCAA
CAATTACTCATAGCTTGACGA
Found at i:32010 original size:87 final size:87
Alignment explanation
Indices: 31863--32029 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 87
31853 AGAGATGCAA
* * *
31863 TCATGGGTAAATACTAGAAATCCCGAGTCTTCTACTCATGGTCTGTTGCAGTACGTACCGAA-AA
1 TCATGGGTAAATACAAGAAATCCCGAGTCTACTACTCATGGTCTGTTGCAGAACGTACCGAAGAA
31927 ATACCAA-TCCCATTGAGACGGAC
66 A-ACCAACT-CCATTGAGACGGAC
* * *
31950 TCATGGGTAAGTGCAAGAAATCCTGAGTCTACTACTCATGGTCTGTTGCAGAAC-TCACCGAAGA
1 TCATGGGTAAATACAAGAAATCCCGAGTCTACTACTCATGGTCTGTTGCAGAACGT-ACCGAAGA
32014 AAACCAACTCCATTGA
65 AAACCAACTCCATTGA
32030 AAATTTCCTG
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
86 1 0.01
87 66 0.93
88 4 0.06
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (87 bp):
TCATGGGTAAATACAAGAAATCCCGAGTCTACTACTCATGGTCTGTTGCAGAACGTACCGAAGAA
AACCAACTCCATTGAGACGGAC
Found at i:32054 original size:99 final size:98
Alignment explanation
Indices: 31948--32242 Score: 303
Period size: 99 Copynumber: 3.0 Consensus size: 98
31938 ATTGAGACGG
*
31948 ACTCATGGGTAAGTGCAAGAAATCCTGAGTCTACTACTCATGGTCTGTTGCAGAACTCACCGAAG
1 ACTCATGGGTAAGTACAAGAAATCCTGAGTCTACTACTCATGGTCTGTTGCAGAACTCACCGAAG
32013 AAAACCAACTCCATTGAAAATTTCCTGGAGACAA
66 AAAACCAA-TCCATTGAAAATTTCCTGGAGACAA
** * * *
32047 ACTCATGGGTAAGTACTGGAATTCCTGAGTCTACCACTCATGGTCTGTTGCAGAAATCACCAGAA
1 ACTCATGGGTAAGTACAAGAAATCCTGAGTCTACTACTCATGGTCTGTTGCAGAACTCACC-GAA
* * **
32112 G-AAA-CAATTCACATTGAGAA-TTCCGTGCAGACTG
65 GAAAACCAA-TC-CATTGAAAATTTCC-TGGAGACAA
* * ** * * *
32146 ACTCATGGATAAGTACAAGAGA-CCACAAGTCTGCTACCCGTGGTCTGTTGCAGAACTCACC-AA
1 ACTCATGGGTAAGTACAAGAAATCC-TGAGTCTACTACTCATGGTCTGTTGCAGAACTCACCGAA
* * *
32209 GGAAAACCAATCCCATTCAAAGTTCCCTGGAGAC
65 -GAAAACCAAT-CCATTGAAAATTTCCTGGAGAC
32243 TGACCAAAGT
Statistics
Matches: 159, Mismatches: 28, Indels: 18
0.78 0.14 0.09
Matches are distributed among these distances:
97 2 0.01
98 12 0.08
99 134 0.84
100 11 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (98 bp):
ACTCATGGGTAAGTACAAGAAATCCTGAGTCTACTACTCATGGTCTGTTGCAGAACTCACCGAAG
AAAACCAATCCATTGAAAATTTCCTGGAGACAA
Found at i:33798 original size:4 final size:4
Alignment explanation
Indices: 33791--33818 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
33781 AGGGAAGGAA
33791 AGGG AGGG AGGG AGGG AGGG AGGG AGGG
1 AGGG AGGG AGGG AGGG AGGG AGGG AGGG
33819 GAAAGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:34016 original size:2 final size:2
Alignment explanation
Indices: 34011--34047 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
34001 AGAGGGAATC
*
34011 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34048 CACTTAGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41441 original size:22 final size:22
Alignment explanation
Indices: 41394--41441 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
41384 TATCGTTATT
* *
41394 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGGAAGGTCATA
*
41416 AAAATTTTATAAGG-AGGTCATA
1 AAAATTTCAT-AGGAAGGTCATA
41438 AAAA
1 AAAA
41442 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATA
Found at i:42652 original size:31 final size:31
Alignment explanation
Indices: 42612--42684 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
42602 TGGGTATTTA
*
42612 TAAGGTACGGGTAGTTTGAAAATTATAGGGT
1 TAAGCTACGGGTAGTTTGAAAATTATAGGGT
* *
42643 TAAGCTACGGGTAGTTTGGAAATTATGGGGT
1 TAAGCTACGGGTAGTTTGAAAATTATAGGGT
42674 TAAGCTACGGG
1 TAAGCTACGGG
42685 CACCTCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.29, C:0.07, G:0.34, T:0.30
Consensus pattern (31 bp):
TAAGCTACGGGTAGTTTGAAAATTATAGGGT
Found at i:60588 original size:35 final size:35
Alignment explanation
Indices: 60541--60612 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
60531 GATTCTCTTT
* *
60541 GATATTGGAGTTAGT-AGGATATTAAGGTGTTCAGA
1 GATATTGAAGTTAGTGAGG-TATTAAGGTATTCAGA
* *
60576 GATATTGAAGTTAGTGAGGTCTTAAGGTATTTAGA
1 GATATTGAAGTTAGTGAGGTATTAAGGTATTCAGA
60611 GA
1 GA
60613 GATATTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 29 0.91
36 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.35
Consensus pattern (35 bp):
GATATTGAAGTTAGTGAGGTATTAAGGTATTCAGA
Found at i:61575 original size:22 final size:22
Alignment explanation
Indices: 61522--61665 Score: 89
Period size: 22 Copynumber: 6.5 Consensus size: 22
61512 CATAAGATTA
** *
61522 CAAAATTTCATAGGAAGCTTTAT
1 CAAAATTTCATAGTTAG-GTTAT
*
61545 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGTTAGGTTAT
* * **
61567 CAAAGTTTCATA-TGACATTTAT
1 CAAAATTTCATAGTTA-GGTTAT
* * *
61589 CACAATTTCATAGATA-ATTAT
1 CAAAATTTCATAGTTAGGTTAT
61610 CAAAATTTCATAGGTT-GGTTAT
1 CAAAATTTCATA-GTTAGGTTAT
* * *
61632 CAAAATTTAATTGGATA-GTTAT
1 CAAAATTTCA-TAGTTAGGTTAT
*
61654 CAGAATTTCATA
1 CAAAATTTCATA
61666 AAATTATCCA
Statistics
Matches: 92, Mismatches: 23, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
21 18 0.20
22 58 0.63
23 16 0.17
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (22 bp):
CAAAATTTCATAGTTAGGTTAT
Found at i:61611 original size:21 final size:20
Alignment explanation
Indices: 61547--61622 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 20
61537 AGCTTTATTA
* *
61547 AAATTTCATAGTTAGGTTATC
1 AAATTTCATAGATA-ATTATC
* *
61568 AAAGTTTCATATGACATTTATC
1 AAA-TTTCATA-GATAATTATC
61590 ACAATTTCATAGATAATTATC
1 A-AATTTCATAGATAATTATC
61611 AAAATTTCATAG
1 -AAATTTCATAG
61623 GTTGGTTATC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
21 21 0.46
22 21 0.46
23 4 0.09
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (20 bp):
AAATTTCATAGATAATTATC
Found at i:61620 original size:65 final size:63
Alignment explanation
Indices: 61541--61673 Score: 162
Period size: 65 Copynumber: 2.1 Consensus size: 63
61531 ATAGGAAGCT
* * * *
61541 TTATTAAAATTTCATA-GTTAGGTTATCAAAGTTTCATAT-GACATTTATCACAATTTCATAGAT
1 TTATCAAAATTTCATAGGTT-GGTTATCAAAATTTAAT-TGGACAGTTATCACAATTTCATA-A-
61604 AA
62 AA
* *
61606 TTATCAAAATTTCATAGGTTGGTTATCAAAATTTAATTGGATAGTTATCAGAATTTCATAAAA
1 TTATCAAAATTTCATAGGTTGGTTATCAAAATTTAATTGGACAGTTATCACAATTTCATAAAA
61669 TTATC
1 TTATC
61674 CATTCGAAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
63 7 0.12
64 2 0.03
65 48 0.80
66 3 0.05
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (63 bp):
TTATCAAAATTTCATAGGTTGGTTATCAAAATTTAATTGGACAGTTATCACAATTTCATAAAA
Found at i:103714 original size:3 final size:3
Alignment explanation
Indices: 103622--103697 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
103612 ACAAAGTTTT
103622 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
103670 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
103698 ATATACTATA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:104720 original size:45 final size:41
Alignment explanation
Indices: 104656--104750 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 41
104646 AACAACAATT
*
104656 AATATTAGGTTTATATTGATGAATTATCTAGAAATGGTGGAGTAG
1 AATATTAGGTTTATATTGATGAATTA-C-A-AAA-GATGGAGTAG
* *
104701 AATATTAGTTTTATTTTGATGAATTACAAAAGATGGAGTAG
1 AATATTAGGTTTATATTGATGAATTACAAAAGATGGAGTAG
104742 AAT-TTAGGT
1 AATATTAGGT
104751 AGTGCACTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 5 0.11
41 12 0.26
42 3 0.07
43 1 0.02
44 1 0.02
45 24 0.52
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (41 bp):
AATATTAGGTTTATATTGATGAATTACAAAAGATGGAGTAG
Found at i:105237 original size:51 final size:53
Alignment explanation
Indices: 105181--105285 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
105171 TTGGCACAAT
105181 ATATATAGTATCAAA-TT-TATGCAAAAGTACATAAAAATAATACATAAATAA
1 ATATATAGTATCAAATTTATATGCAAAAGTACATAAAAATAATACATAAATAA
105232 ATATATAGTATCAAATTTATATGCAAAAGTACATAAAAATAATACATAAATAA
1 ATATATAGTATCAAATTTATATGCAAAAGTACATAAAAATAATACATAAATAA
105285 A
1 A
105286 AACATTATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 15 0.29
52 2 0.04
53 35 0.67
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.30
Consensus pattern (53 bp):
ATATATAGTATCAAATTTATATGCAAAAGTACATAAAAATAATACATAAATAA
Found at i:106288 original size:90 final size:89
Alignment explanation
Indices: 106175--106345 Score: 254
Period size: 90 Copynumber: 1.9 Consensus size: 89
106165 TACCCAAAAG
* *
106175 TTCCCCCCAACCCGAAATCGGGGGATTCATGATTGCCGCGCGTGAATTGTACAACGGCAATCGA-
1 TTCCCCCCAACCCGAAATCGGGGGATTCATGATTGCCGCACATGAATTGTACAACGGCAATCGAG
*
106239 AGTGCGTTTAGTCATCTGTCGGGTA
66 A-CGCGTTTAGTCATCTGTCGGGTA
* * * *
106264 TTCCCCCCACCCCCGAAATTGGGGGATTCATGATTGTCGCACATGAATTGTACAACGGTAATCGA
1 TTCCCCCCA-ACCCGAAATCGGGGGATTCATGATTGCCGCACATGAATTGTACAACGGCAATCGA
106329 GACGCGTTTAGTCATCT
65 GACGCGTTTAGTCATCT
106346 ATCAGATATT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
89 9 0.12
90 63 0.86
91 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (89 bp):
TTCCCCCCAACCCGAAATCGGGGGATTCATGATTGCCGCACATGAATTGTACAACGGCAATCGAG
ACGCGTTTAGTCATCTGTCGGGTA
Found at i:106524 original size:34 final size:34
Alignment explanation
Indices: 106481--106555 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
106471 CTGTTGGTAT
*
106481 AGGCATTCTTAGTAAGAATGATGTGTCGTTGACG
1 AGGCATTCTTAGCAAGAATGATGTGTCGTTGACG
106515 AGGCATTCTTAGCAAGAATGATGTGTCGTTGACG
1 AGGCATTCTTAGCAAGAATGATGTGTCGTTGACG
106549 AGGCATT
1 AGGCATT
106556 ACGGTTTTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (34 bp):
AGGCATTCTTAGCAAGAATGATGTGTCGTTGACG
Found at i:122169 original size:14 final size:13
Alignment explanation
Indices: 122133--122171 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
122123 ATTTTATATT
*
122133 TATAATTATATTTA
1 TATAATTA-ATTAA
122147 TATAATTAATTAA
1 TATAATTAATTAA
122160 TATAATTTAATT
1 TATAA-TTAATT
122172 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATAATTAATTAA
Found at i:123992 original size:86 final size:89
Alignment explanation
Indices: 123817--124014 Score: 298
Period size: 87 Copynumber: 2.2 Consensus size: 89
123807 TCAGATTTTC
* *
123817 TTAAGTGTTCATATCTAGTACTAGTTTTTTTTTGGATATTCTTCAATGTTTGATACTTATTTTTT
1 TTAAGTGTTAATATCTAGTAGTAG-TTTTTTTTGGATATTCTTCAATGTTTGATACTTATTTTTT
* *
123882 TTGGCATCAATGTTTGATGCTTA-T
65 TTGGCACCAATGTTTGATACTTATT
123906 TTAAG-GTTTAATATCTAGTAGTAG-TTTTTTTGGATATTCTTCAATGTTTGATA-TT-TTTGTT
1 TTAAGTG-TTAATATCTAGTAGTAGTTTTTTTTGGATATTCTTCAATGTTTGATACTTATTT-TT
123967 TTTGGCACCAATGTTTGATACTTATT
64 TTTGGCACCAATGTTTGATACTTATT
123993 TTAAGTGTTAATATCTAGTAGT
1 TTAAGTGTTAATATCTAGTAGT
124015 TTTTTGGATA
Statistics
Matches: 101, Mismatches: 4, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
85 3 0.03
86 26 0.26
87 50 0.50
88 2 0.02
89 20 0.20
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.53
Consensus pattern (89 bp):
TTAAGTGTTAATATCTAGTAGTAGTTTTTTTTGGATATTCTTCAATGTTTGATACTTATTTTTTT
TGGCACCAATGTTTGATACTTATT
Found at i:130221 original size:2 final size:2
Alignment explanation
Indices: 130214--130242 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
130204 ACAGTGAATC
130214 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 A
130243 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:130247 original size:2 final size:2
Alignment explanation
Indices: 130242--130274 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
130232 ATATATATAT
130242 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
130275 AGAAAACCAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:134279 original size:13 final size:13
Alignment explanation
Indices: 134261--134286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
134251 GTTCATAGAT
134261 GAAAACAAAAAAG
1 GAAAACAAAAAAG
134274 GAAAACAAAAAAG
1 GAAAACAAAAAAG
134287 CTTTAGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAAACAAAAAAG
Found at i:146570 original size:3 final size:3
Alignment explanation
Indices: 146562--146588 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
146552 TTCATCACAA
146562 CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG
146589 GTGCAGAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:147360 original size:27 final size:27
Alignment explanation
Indices: 147300--147372 Score: 112
Period size: 28 Copynumber: 2.7 Consensus size: 27
147290 AGGTAAGTAC
147300 TAATAATTTAGTAACTTTTTTTTGGCAA
1 TAATAATTTAGTAACTTTTTTTTGG-AA
*
147328 TTATAATTTAGTAACTTTTTTTT-GAGA
1 TAATAATTTAGTAACTTTTTTTTGGA-A
147355 TAATAATTTAGTAACTTT
1 TAATAATTTAGTAACTTT
147373 ATTTGATCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
26 1 0.02
27 19 0.45
28 22 0.52
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (27 bp):
TAATAATTTAGTAACTTTTTTTTGGAA
Found at i:148061 original size:31 final size:31
Alignment explanation
Indices: 148023--148224 Score: 217
Period size: 31 Copynumber: 6.5 Consensus size: 31
148013 ACGGTGTCCG
*
148023 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
** * * *
148054 ATATGGCACGTCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * *
148085 ATGTGGCACGCCACGTGTA-AAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* ** * *
148115 ACATATCATGCCATGTGTACCCAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* **
148146 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* **
148177 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
148208 ACGTGGCATGCCACGTG
1 ACGTGGCATGCCACGTG
148225 CACAAAAGGA
Statistics
Matches: 147, Mismatches: 23, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
30 22 0.15
31 125 0.85
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.20
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:150220 original size:44 final size:44
Alignment explanation
Indices: 150162--150248 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
150152 TTTGAATATG
*
150162 AGTTGTTAACAATCGGCCCAATCAACTTAATTACACTTCTGAAT
1 AGTTGTTAACAATCGGCCCAATCAACTTAATTACACTTATGAAT
*
150206 AGTTGTTAACAATCGGCCCAATCAAGTTAATTACACTTATGAA
1 AGTTGTTAACAATCGGCCCAATCAACTTAATTACACTTATGAA
150249 CCCATTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (44 bp):
AGTTGTTAACAATCGGCCCAATCAACTTAATTACACTTATGAAT
Found at i:161656 original size:2 final size:2
Alignment explanation
Indices: 161649--161689 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
161639 GATATTAATG
*
161649 AT AT AT AT GA- AT AT AT AC 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 AT AT AT AT A
161690 GATGTTGGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:165355 original size:24 final size:24
Alignment explanation
Indices: 165328--165376 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
165318 AATTCCTTGG
165328 ACAACTTTACTCTAGAAATAGAAT
1 ACAACTTTACTCTAGAAATAGAAT
165352 ACAACTTTACTCTAGAAATAGAAT
1 ACAACTTTACTCTAGAAATAGAAT
165376 A
1 A
165377 GTAGCAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (24 bp):
ACAACTTTACTCTAGAAATAGAAT
Found at i:168129 original size:10 final size:10
Alignment explanation
Indices: 168114--168148 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
168104 CGTTTATTAA
168114 TATATATAAT
1 TATATATAAT
168124 TATATATAAT
1 TATATATAAT
168134 AATATATATAAT
1 --TATATATAAT
168146 TAT
1 TAT
168149 TAAACGGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TATATATAAT
Done.