Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016019.1 Corchorus capsularis cultivar CVL-1 contig16040, 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: 55618
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9324 original size:22 final size:22
Alignment explanation
Indices: 9299--9367 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
9289 GAATTGTTAG
9299 TAATCACACTCTGAAATTTTGA
1 TAATCACACTCTGAAATTTTGA
*
9321 TAATCACAC-CATGAAATTGTGA
1 TAATCACACTC-TGAAATTTTGA
* * * *
9343 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTCTGAAATTTTGA
9365 TAA
1 TAA
9368 ATCTTCTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATCACACTCTGAAATTTTGA
Found at i:9384 original size:23 final size:23
Alignment explanation
Indices: 9356--9435 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
9346 CCTCGCTATG
9356 AAATTTTGATAAATCTTCTTATA
1 AAATTTTGATAAATCTTCTTATA
* * *
9379 AAATTTTGATAAACCTCCATATA
1 AAATTTTGATAAATCTTCTTATA
* *
9402 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCTTATA
*
9424 AAATCTTGATAA
1 AAATTTTGATAA
9436 CTACAAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
22 16 0.33
23 32 0.67
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCTTATA
Found at i:9420 original size:45 final size:46
Alignment explanation
Indices: 9334--9435 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 46
9324 TCACACCATG
* *
9334 AAATTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTCTTATA
1 AAATTTTGATAAACCTCGCTATAAAATTTTGATAAATCTTCTTATA
* *
9379 AAATTTTGATAAACCTC-CATATAAAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAACCTCGC-TATAAAATTTTGATAAATCTTCTTATA
*
9424 AAATCTTGATAA
1 AAATTTTGATAA
9436 CTACAAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
45 28 0.56
46 22 0.44
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (46 bp):
AAATTTTGATAAACCTCGCTATAAAATTTTGATAAATCTTCTTATA
Found at i:9527 original size:22 final size:22
Alignment explanation
Indices: 9502--9604 Score: 138
Period size: 22 Copynumber: 4.7 Consensus size: 22
9492 GTTAATTTCC
9502 CTATGAAATTTTGATCTACATA
1 CTATGAAATTTTGATCTACATA
*
9524 CTATGAAATTTTG--CTAACACTT
1 CTATGAAATTTTGATCT-ACA-TA
*
9546 TTATGAAATTTTGATCTACATA
1 CTATGAAATTTTGATCTACATA
* *
9568 TTATGAAATTTTGATCTAAATA
1 CTATGAAATTTTGATCTACATA
9590 CTATGAAATTTTGAT
1 CTATGAAATTTTGAT
9605 AACACTTTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.03
21 3 0.04
22 62 0.86
23 3 0.04
24 2 0.03
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.44
Consensus pattern (22 bp):
CTATGAAATTTTGATCTACATA
Found at i:9573 original size:66 final size:66
Alignment explanation
Indices: 9503--9626 Score: 221
Period size: 66 Copynumber: 1.9 Consensus size: 66
9493 TTAATTTCCC
* * *
9503 TATGAAATTTTGATCTACATACTATGAAATTTTGCTAACACTTTTATGAAATTTTGATCTACATA
1 TATGAAATTTTGATCTAAATACTATGAAATTTTGATAACACTTTAATGAAATTTTGATCTACATA
9568 T
66 T
9569 TATGAAATTTTGATCTAAATACTATGAAATTTTGATAACACTTTAATGAAATTTTGAT
1 TATGAAATTTTGATCTAAATACTATGAAATTTTGATAACACTTTAATGAAATTTTGAT
9627 AACATTCACA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (66 bp):
TATGAAATTTTGATCTAAATACTATGAAATTTTGATAACACTTTAATGAAATTTTGATCTACATA
T
Found at i:9577 original size:44 final size:43
Alignment explanation
Indices: 9503--9648 Score: 156
Period size: 44 Copynumber: 3.3 Consensus size: 43
9493 TTAATTTCCC
* *
9503 TATGAAATTTTGATCTACATACTATGAAATTTTGCTAACACTTT
1 TATGAAATTTTGATCTACATATTATGAAATTTTGCTAACA-TTA
9547 TATGAAATTTTGATCTACATATTATGAAATTTTGATCTAA-A-TA
1 TATGAAATTTTGATCTACATATTATGAAATTTTG--CTAACATTA
* *
9590 CTATGAAATTTTGAT-AACACT-TTAATGAAATTTTGATAACATTCA
1 -TATGAAATTTTGATCTACA-TATT-ATGAAATTTTGCTAACATT-A
*
9635 CATGAAATTTTGAT
1 TATGAAATTTTGAT
9649 ATCCTCCCAG
Statistics
Matches: 89, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
42 3 0.03
43 7 0.08
44 73 0.82
45 2 0.02
46 4 0.04
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (43 bp):
TATGAAATTTTGATCTACATATTATGAAATTTTGCTAACATTA
Found at i:9617 original size:22 final size:20
Alignment explanation
Indices: 9503--9649 Score: 116
Period size: 22 Copynumber: 6.8 Consensus size: 20
9493 TTAATTTCCC
* *
9503 TATGAAATTTTGATCTACATAC
1 TATGAAATTTTGAT-AACAT-T
*
9525 TATGAAATTTTGCTAACACTTT
1 TATGAAATTTTGATAACA--TT
*
9547 TATGAAATTTTGATCTACATAT
1 TATGAAATTTTGAT-AACAT-T
*
9569 TATGAAATTTTGATCTAA-ATAC
1 TATGAAATTTTGA--TAACAT-T
9591 TATGAAATTTTGATAACACTT
1 TATGAAATTTTGATAACA-TT
9612 TAATGAAATTTTGATAACATT
1 T-ATGAAATTTTGATAACATT
*
9633 CACATGAAATTTTGATA
1 --TATGAAATTTTGATA
9650 TCCTCCCAGA
Statistics
Matches: 105, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
20 3 0.03
21 8 0.08
22 88 0.84
23 5 0.05
24 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (20 bp):
TATGAAATTTTGATAACATT
Found at i:9640 original size:66 final size:66
Alignment explanation
Indices: 9504--9648 Score: 213
Period size: 66 Copynumber: 2.2 Consensus size: 66
9494 TAATTTCCCT
* * * *
9504 ATGAAATTTTGATCTACATACTATGAAATTTTGCTAACACTTTTATGAAATTTTGATCTACATAT
1 ATGAAATTTTGATCTAAATACTATGAAATTTTGATAACACTTTAATGAAATTTTGATCAACATAT
*
9569 T
66 C
9570 ATGAAATTTTGATCTAAATACTATGAAATTTTGATAACACTTTAATGAAATTTTGAT-AACAT-T
1 ATGAAATTTTGATCTAAATACTATGAAATTTTGATAACACTTTAATGAAATTTTGATCAACATAT
9633 CAC
66 --C
9636 ATGAAATTTTGAT
1 ATGAAATTTTGAT
9649 ATCCTCCCAG
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
64 1 0.01
65 4 0.06
66 67 0.93
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (66 bp):
ATGAAATTTTGATCTAAATACTATGAAATTTTGATAACACTTTAATGAAATTTTGATCAACATAT
C
Found at i:11074 original size:22 final size:22
Alignment explanation
Indices: 11043--11094 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
11033 TCACATTTTC
11043 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* *
11064 GAAATTTTGATAACTTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
11086 AAAATTTTG
1 AAAATTTTG
11095 TCGACCTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:25878 original size:22 final size:22
Alignment explanation
Indices: 25852--25895 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25842 ATTTTACCAT
25852 AAACATATCCTTATGTATTGGA
1 AAACATATCCTTATGTATTGGA
25874 AAACATATCCTTATGTATTGGA
1 AAACATATCCTTATGTATTGGA
25896 TATAGCATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (22 bp):
AAACATATCCTTATGTATTGGA
Found at i:26068 original size:22 final size:22
Alignment explanation
Indices: 26043--26653 Score: 165
Period size: 22 Copynumber: 28.0 Consensus size: 22
26033 ATAATCCCAT
26043 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
26065 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
26087 TATGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** ***** *
26109 TAAAAAAAAAAAATTTAACCTTCT
1 TATGAAATTTTGA-T-AACCTTCC
* * *
26133 TATAAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
26155 TAAGGAATTTTGA-AGATC-TCAG
1 TATGAAATTTTGATA-ACCTTC-C
26177 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
26199 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
26222 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * * *
26243 ATAGGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
26266 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
26287 ATATG-AATTGTT-AGTAATCATAC
1 -TATGAAATT-TTGA-TAACCTTCC
* *
26310 TCTGAAATTTTGATAATCACAT--
1 TATGAAATTTTGATAA-C-CTTCC
26332 TATGAAATTTTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
26354 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
26377 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
26400 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
26422 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* * *
26439 TA-CAAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
26460 TATGATTTTTTGATAACC-TCA
1 TATGAAATTTTGATAACCTTCC
* * *
26481 TCATGAAATTTTGTTAATCTCCC
1 T-ATGAAATTTTGATAACCTTCC
*** * *
26504 TATGAAATTTTGATCTGCATAC
1 TATGAAATTTTGATAACCTTCC
* * *
26526 TATGAAATTTTGAAAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
26548 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
26570 TATAAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
26591 ATAATAAAAGTTTAATAATCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
26615 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
26632 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
26654 CAGAAATACC
Statistics
Matches: 418, Mismatches: 129, Indels: 84
0.66 0.20 0.13
Matches are distributed among these distances:
16 11 0.03
17 11 0.03
18 2 0.00
19 2 0.00
20 2 0.00
21 20 0.05
22 267 0.64
23 82 0.20
24 21 0.05
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:26384 original size:23 final size:23
Alignment explanation
Indices: 26336--26437 Score: 102
Period size: 23 Copynumber: 4.5 Consensus size: 23
26326 TCACATTATG
* *
26336 AAATTTTGAT-AA-CCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATA
26358 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
26381 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
* * *
26404 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
26426 AAATCTTGATAA
1 AAATTTTGATAA
26438 CTACAAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
22 26 0.38
23 39 0.57
24 3 0.04
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:26435 original size:45 final size:44
Alignment explanation
Indices: 26314--26437 Score: 142
Period size: 45 Copynumber: 2.8 Consensus size: 44
26304 TCATACTCTG
** * *
26314 AAATTTTGATAATCACATTATGAAATTTTGAT-AACCTCGCTATG
1 AAATTTTGATAATTTC-TTATGAAATTTTGATAAACCTCCCTATA
* *
26358 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AAT-TTCTTATGAAATTTTGATAAACCTCCCTATA
*
26404 AAATTTTGATAACTTTCTTATGAAATCTTGATAA
1 AAATTTTGATAA-TTTCTTATGAAATTTTGATAA
26438 CTACAAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
44 10 0.15
45 35 0.52
46 22 0.33
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (44 bp):
AAATTTTGATAATTTCTTATGAAATTTTGATAAACCTCCCTATA
Found at i:26779 original size:22 final size:21
Alignment explanation
Indices: 26666--26835 Score: 94
Period size: 22 Copynumber: 7.8 Consensus size: 21
26656 GAAATACCAC
26666 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAA-CACAT
* * * *
26688 TCTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAA-CACAT
* * *
26710 TCTGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAA-CACAT
* * * *
26732 TATAAAATTTTGTTGATC-CCT
1 TATGAAATTTTGAT-AACACAT
*
26753 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAA-CACAT
* *
26776 TATGTAATTTTGATAACATCGCT
1 TATGAAATTTTGATAACA-C-AT
*
26799 T-TGGAATTTTGATAACAACAT
1 TATGAAATTTTGATAAC-ACAT
26820 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
26836 TCTTCCTATA
Statistics
Matches: 117, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
21 11 0.09
22 100 0.85
23 6 0.05
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTGATAACACAT
Found at i:26828 original size:88 final size:88
Alignment explanation
Indices: 26665--26831 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
26655 AGAAATACCA
* * * * **
26665 CTATGAAATTTTTGTAATCACATTCTGAAAATTTGATAACCTCTTTCTGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACATCCTTCTGAAATTTTGATAACAAC
*
26730 TTTATAAAATTTTGTTGATCCCT
66 ATTATAAAATTTTGTTGATCCCT
* * *
26753 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACATCGCTT-TGGAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACATC-CTTCTGAAATTTTGATAACA
*
26816 ACATTATGAAATTTTG
64 ACATTATAAAATTTTG
26832 ATAATCTTCC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 4 0.06
88 60 0.91
89 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACATCCTTCTGAAATTTTGATAACAAC
ATTATAAAATTTTGTTGATCCCT
Found at i:26971 original size:22 final size:21
Alignment explanation
Indices: 26942--27299 Score: 146
Period size: 22 Copynumber: 16.5 Consensus size: 21
26932 AAATTGAGAC
*
26942 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCCTATGAAA
* *
26963 TTTTGATAACCACGCTATAAAA
1 TTTTGATAACCTC-CTATGAAA
*
26985 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CCTATGAAA
*
27007 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCCT-ATGAAA
* * *
27029 TTCTGTTAACCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
27051 TTCTT-ATAACCTCGTTATGACA
1 TT-TTGATAACCTC-CTATGAAA
* *
27073 TTTTGATAATCT-CTTTGATAA
1 TTTTGATAACCTCCTATGA-AA
** *
27094 CCTTTCT-ATAAAAT--TGTGAAA
1 --TTT-TGATAACCTCCTATGAAA
* *
27115 --AT--TAACCACTCTATGAAA
1 TTTTGATAACCTC-CTATGAAA
** *
27133 TTTCAATAACCAAT-CTAAGAAA
1 TTTTGATAACC--TCCTATGAAA
*
27155 TTTTAATAACCTGATCCTATGAAA
1 TTTTGATAACC---TCCTATGAAA
* *
27179 TTTTGGTAACCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
*
27201 TTTTGATAACTTCCATATGAAA
1 TTTTGATAACCTCC-TATGAAA
* * * *
27223 TTTTGGTAACCACACTACGGAA
1 TTTTGATAACCTC-CTATGAAA
27245 TTTTGATAACCTCCTCATGAAA
1 TTTTGATAACCTCCT-ATGAAA
* * *
27267 TTATAATAACCATCTTATGAAA
1 TTTTGATAACC-TCCTATGAAA
27289 TTTTGATAACC
1 TTTTGATAACC
27300 ACATAGAGAC
Statistics
Matches: 251, Mismatches: 57, Indels: 57
0.69 0.16 0.16
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
18 6 0.02
20 4 0.02
21 17 0.07
22 185 0.74
23 18 0.07
24 17 0.07
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:27234 original size:44 final size:43
Alignment explanation
Indices: 27125--27299 Score: 165
Period size: 44 Copynumber: 4.0 Consensus size: 43
27115 ATTAACCACT
*** * *
27125 CTATGAAATTTCAATAACCA-ATCTAAGAAATTTTAATAACCTGATC
1 CTATGAAATTTTGGTAACCACA-CTATGAAATTTTGATAACC---TC
*
27171 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTC
1 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTC
* *
27214 CATATGAAATTTTGGTAACCACACTACGGAATTTTGATAACCTC
1 C-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTC
* ** *
27258 CTCATGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 CT-ATGAAATTTTGGTAACCA-CACTATGAAATTTTGATAACC
27300 ACATAGAGAC
Statistics
Matches: 110, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
43 4 0.04
44 71 0.65
45 1 0.01
46 33 0.30
47 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (43 bp):
CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTC
Found at i:27276 original size:66 final size:66
Alignment explanation
Indices: 27117--27302 Score: 166
Period size: 66 Copynumber: 2.8 Consensus size: 66
27107 TTGTGAAAAT
* * * * *
27117 TAACCACTCTATGAAATT-TCAATAACCAATC-TAAGAAATTTTAATAACCTGATC-CTATGAAA
1 TAACCACACTATGAAATTAT-AATAACC-ATCATATGAAATTTTGATAACC--A-CACTACGGAA
*
27179 TTTTGG
61 TTTTGA
* * * *
27185 TAACCACACTATGAAATTTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTACGGAATTTT
1 TAACCACACTATGAAATTATAATAACCAT-CATATGAAATTTTGATAACCACACTACGGAATTTT
27249 GA
65 GA
* *
27251 TAACCTC-CTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCACA
1 TAACCACACT-ATGAAATTATAATAACCATCATATGAAATTTTGATAACCACA
27303 TAGAGACAAG
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
65 3 0.03
66 53 0.55
67 4 0.04
68 36 0.37
69 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (66 bp):
TAACCACACTATGAAATTATAATAACCATCATATGAAATTTTGATAACCACACTACGGAATTTTG
A
Found at i:27485 original size:19 final size:20
Alignment explanation
Indices: 27454--27491 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27444 GTTTAATCTT
27454 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
27473 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
27492 ACTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:27749 original size:31 final size:31
Alignment explanation
Indices: 27689--27751 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
27679 TAATGGTAAT
* *
27689 TTAGAAATATGTTTTTAAAAAATGAGTACAA
1 TTAGAAATATGATTTTAAAAAAAGAGTACAA
*
27720 TTAGAAATAT-ATTTTAAAAATAAGGGTACAA
1 TTAGAAATATGATTTTAAAAA-AAGAGTACAA
27751 T
1 T
27752 CGGAAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.35
Consensus pattern (31 bp):
TTAGAAATATGATTTTAAAAAAAGAGTACAA
Found at i:28733 original size:31 final size:31
Alignment explanation
Indices: 28697--28837 Score: 183
Period size: 31 Copynumber: 4.5 Consensus size: 31
28687 TCCTTTTGTG
* * **
28697 CATGTGGCATGCCACGTGCCATTTTTTGAAA
1 CATGTGGCATGCCACGTGTCACTTTTTGGTA
28728 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CATGTGGCATGCCACGTGTCACTTTTTGGTA
* * * *
28759 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CATGTGGCATGCCACGTGTCACTTTTTGGTA
*
28790 CATGTGGCATGCCACATGTCACTTTTTGGTA
1 CATGTGGCATGCCACGTGTCACTTTTTGGTA
* *
28821 CACGTGGCGTGCCACGT
1 CATGTGGCATGCCACGT
28838 CGGACACCGT
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 94 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (31 bp):
CATGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:34240 original size:69 final size:69
Alignment explanation
Indices: 34129--34266 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
34119 GGTACTTCCA
34129 AAGTTGCAAATGTCACCTTTGAGTAGAAAGAGTTTAATGCCTCTTAAGCAGATTCTGAAGCTCTC
1 AAGTTGCAAATGTCACCTTTGAGTAGAAAGAGTTTAATGCCTCTTAAGCAGATTCTGAAGCTCTC
34194 AAGT
66 AAGT
34198 AAGTTGCAAATGTCACCTTTGAGTAGAAAGAGTTTAATGCCTCTTAAGCAGATTCTGAAGCTCTC
1 AAGTTGCAAATGTCACCTTTGAGTAGAAAGAGTTTAATGCCTCTTAAGCAGATTCTGAAGCTCTC
34263 AAGT
66 AAGT
34267 TTGAGTACGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (69 bp):
AAGTTGCAAATGTCACCTTTGAGTAGAAAGAGTTTAATGCCTCTTAAGCAGATTCTGAAGCTCTC
AAGT
Found at i:43695 original size:160 final size:159
Alignment explanation
Indices: 43415--43732 Score: 555
Period size: 160 Copynumber: 2.0 Consensus size: 159
43405 TCAAACAACC
43415 CATCCTTTTATGATGTGAAATGTTTCCTCACATATAAATCCTCAACAATCTCCCCCGATTTACAT
1 CATCCTTTTATGATGTGAAATGTTTCCTCACATATAAATCCTCAACAATCTCCCCCGATTTACAT
*
43480 GTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCCGTCAAGTCTTAAGCCAATTACCGGTCATCC
66 GTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCAGTCAAGTCTTAAGCCAATTACCGGTCATCC
43545 AAGACATAACCCGTGGAGTGCGAGGGCCG
131 AAGACATAACCCGTGGAGTGCGAGGGCCG
* * **
43574 CATCCTTTTATGTTGTGAGATGTTTCCTCACATATAAATCCTCAACAATCTCCCTTGATTTTACA
1 CATCCTTTTATGATGTGAAATGTTTCCTCACATATAAATCCTCAACAATCTCCCCCGA-TTTACA
*
43639 TGTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCAGTCAAGTCTTAAGTCAATTACCGGTCATC
65 TGTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCAGTCAAGTCTTAAGCCAATTACCGGTCATC
* *
43704 CAATACTTAACCCGTGGAGTGCGAGGGCC
130 CAAGACATAACCCGTGGAGTGCGAGGGCC
43733 CAACACTCCG
Statistics
Matches: 150, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
159 54 0.36
160 96 0.64
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (159 bp):
CATCCTTTTATGATGTGAAATGTTTCCTCACATATAAATCCTCAACAATCTCCCCCGATTTACAT
GTGAGTCCTCATCTCTCCCCCGTGCGGCCCAACCAGTCAAGTCTTAAGCCAATTACCGGTCATCC
AAGACATAACCCGTGGAGTGCGAGGGCCG
Found at i:55364 original size:2 final size:2
Alignment explanation
Indices: 55357--55383 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55347 TGTATACTAT
55357 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 T
55384 TATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.