Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012375.1 Corchorus capsularis cultivar CVL-1 contig12396, 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: 51186
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1151 original size:331 final size:331
Alignment explanation
Indices: 2--2496 Score: 2873
Period size: 331 Copynumber: 7.6 Consensus size: 331
1 A
* * * * * *
2 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGTTTCAAATACTCGTAAAAACAAATCATT
1 TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * *
67 AAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGATATTTTGAGGAGTCTTGGTGCCAAAA
66 AAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGCAGTCTTGGCGCCAAAA
* * * * * *
132 ATCAAGAAAATCTGAGTC-GAGG-CCCTGAACCGCGTTTTAAGCCAAAAACCCTGATAGTTAGTA
131 ATCATGCAAATCTGAGTCAG-GGCCCCGGAA-CGCGTTTTTAGCCAAAAACCGTGATTGTTAGTA
* * * *
195 CACGATTTCGGCGAAAATTTTGCAACAATTGATCCAAAATA-TTTTCCGTTAATTTTTGGCCACC
194 CAC-ATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCC-TTAATTTTTGGCCACA
* * *
259 GTACTCATATAAAATATATAATTAACC-CCCAAAGGATTGAAGGGATTTTCAAGCTTTTACTATC
257 GTACTCATATAAAATATATAATTAACCGCCAAAAGGATTGAAGGGATTTTCAAGCTTCTAATATC
323 GTTTTTCCTATT
322 GTTTTTCC-A-T
* ** * **
335 TTTTTTCCGAATAAATTTCTAATTAAATTAAAACAAGATTTAGATGCTCAAAAAAAAAACAAATC
1 TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCAGATGCTC---GTAAAAACAAATC
* * ** * *
400 CGTAAATTCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTCGAGCAATCTTGGTGCCA
63 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGCAGTCTTGGCGCCA
* * * *
465 AAAATCATACAAATCT--G--A--GCCCCGTAACACGTTTTTAGCC-AAAA-----ATCG-T-G-
128 AAAATCATGCAAATCTGAGTCAGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGT
* * * **
515 ----ATTTCGGCTAAAATTTTGCAAAAATGGACCCGAAATATTTTCCCTTAATTTTTGGCCACCT
193 ACACATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTTAATTTTTGGCCACAG
* * *
576 TACTCATATAAAATATATAATTAACCTCCATAAGGATTGAAGGGATTTTCAAGGTTCTAATATCG
258 TACTCATATAAAATATATAATTAACCGCCAAAAGGATTGAAGGGATTTTCAAGCTTCTAATATCG
641 TTTTTCC-T
323 TTTTTCCAT
* * * * *
649 ATTTTTTGCGAATAAATTTTTGATTAAATCGAAACAAGATTTAAATGCTCGTAAAAAGAAATCCT
1 -TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
* *** *
714 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGTTTTCTTGGAGCCAAA
65 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGCAGTCTTGGCGCCAAA
* * ** *
779 AATTCTTGCAAATCTGTGTTGGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATTGTTACTG
130 AA-TCATGCAAATCTGAGTCAGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATTGTTA--G
* * * *
844 TACA-ATTTCTGCTAAAAATTTGCAAAAATTGACCCAAAATATTTTTCCTTAATTTTT-TCCATA
192 TACACATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTTAATTTTTGGCCACA
*
907 ATACTCATA-AAAATATATAATTAACCGCCAAAAGGATTGAA-GGACTTTTCAAGCTTCTAATAT
257 GTACTCATATAAAATATATAATTAACCGCCAAAAGGATTGAAGGGA-TTTTCAAGCTTCTAATAT
970 CGTTTTTCC-T
321 CGTTTTTCCAT
980 TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCATG-TGCTCGTAAAAACAAATCCT
1 TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCA-GATGCTCGTAAAAACAAATCCT
* * * * * *
1044 TAAATGCAATATGACTGAGATTTGGTTAGATAAATATAGATATTTCGAGCAGTCTTGTCGCAAAA
65 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGCAGTCTTGGCGC-CAA
* *
1109 AAATTCATGCAAATCTGAGTCAGGACCCCGGAACGCGTTTTTAGCCAAAAACGGTGATTGTTAGT
129 AAA-TCATGCAAATCTGAGTCAGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGT
* *
1174 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTATTTGGCCTT
193 ACAC-ATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTTAATT-TTTGGCC-A
* * *
1239 C-GTACTCATATATAATATATAATTAACCTCCAAAAAGATTGAAGGGATTTTCAAGCTTCTAATA
255 CAGTACTCATATAAAATATATAATTAACCGCCAAAAGGATTGAAGGGATTTTCAAGCTTCTAATA
1303 TCGTTTTTCCTAAT
320 TCGTTTTTCC--AT
* * **
1317 TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAATATTCAGATCCTTTTAAAAACAAATCCTT
1 TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * * * * * *
1382 AAATCCAACGTGGTTGATATTTTGTTAGATAAATATAGTTATTTCGAGCAGTCTAGCCGCCAAAA
66 AAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGCAGTCTTGGCGCCAAAA
* * * * *
1447 ATCATGCAAATCTGAGACGGGGCCCCGGAACGCATTTTTAGCCAAAAACAGTGATGGTTAGTACA
131 ATCATGCAAATCTGAGTCAGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGTACA
* *
1512 CGATTTCGGCTAAAATTTTGCAAAAATTG-CCCAAAATATTTTCCCTTAATTTTTGGCCACCGTA
196 C-ATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTTAATTTTTGGCCACAGTA
* * * * * *
1576 CTCATATATAATATATGATTAACCTCCAGAAGGATTGAATGGATTTTCAAACTTCTAATATCGTT
260 CTCATATAAAATATATAATTAACCGCCAAAAGGATTGAAGGGATTTTCAAGCTTCTAATATCGTT
1641 TTTCCTAT
325 TTTCC-AT
* *
1649 TTTTTTCCGAATAAATTT-TAGATTAAATCGAAA-AATGATTCAGATGCTCGTAAAGACGAATCC
1 TTTTTTCCGAATAAATTTCT-GATTAAATCGAAACAA-GATTCAGATGCTCGTAAAAACAAATCC
* * * *
1712 TTAAATCCAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT-GTGCCAA
64 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGCAGTCTTGGCGCCAA
* * * * *
1776 AAATCATGCAAATTTGAGTCGGGGCCCCGGAACGCGTTTTTTGCCAAAAACCATGATGGTTAGTA
129 AAATCATGCAAATCTGAGTCAGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGTA
* ***
1841 CACGATTTCGGCTAAAATTTTACAAAAATTGA-CCACAAATATTTTTCCTTAA-TTTT-AAAACA
194 CAC-ATTTCGGCTAAAATTTTGCAAAAATTGACCCA-AAATATTTTTCCTTAATTTTTGGCCACA
* * * *
1903 ATACTCATA-ATAGATATATATTTAACCGCCAAAATGATTGAA-GGACTTTTCAAGCTTCTAATA
257 GTACTCATATA-AAATATATAATTAACCGCCAAAAGGATTGAAGGGA-TTTTCAAGCTTCTAATA
*
1966 TCATTTTTCACAT
320 TCGTTTTTC-CAT
*
1979 TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCAGATGCTTGT-AAAA-AAATCCTT
1 TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * *
2042 AAATCCAATGTGGCTGATATTTTGTTAGATGAATATAGATATTTCGGGCAGTCTTGGCGCCAAAA
66 AAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGCAGTCTTGGCGCCAAAA
* *
2107 ATCATGCAAATCTGAG-CAAGGGCCCTGGAACGCGTTTTTAG-CAAAAACCGTGA-TG--CGTAC
131 ATCATGCAAATCTGAGTC-AGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGTAC
* ** *
2167 ACGATTTTGGCTAAAATTTTGCAAAAATTGACATGAAAA-ATTTTTCCTT-ATTTTT-TCTCACA
195 AC-ATTTCGGCTAAAATTTTGCAAAAATTGAC-CCAAAATATTTTTCCTTAATTTTTGGC-CACA
* * * *
2229 GTACTCATAAAAATATATATAATTAACCGCCAAAAGGATTGAAGGAATTTTCAAGCTTTTTTATA
257 GTACTCATATAAA-ATATATAATTAACCGCCAAAAGGATTGAAGGGATTTTCAAGC-TTCTAATA
*
2294 TTGTTTTTCC-T
320 TCGTTTTTCCAT
* * * *
2305 ATTTTTTCTGAATAAATTTCTTATTAAATCGAGACAAAATTCAGATGCTCGTAAAAACAAATCCT
1 -TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
* * * * *
2370 TAAATCCAATGTGGTTGAGATTTGGTTCGATGAATATAGATATTTTGAGCAGCCTTGACGCCAAA
65 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGCAGTCTTGGCGCCAAA
* * * * *
2435 AATCATGCAAATCT-AGTC-GAGGCCTCGAAACGTGTTTTTAGCCAAAAATCCATGATGGTTAG
130 AATCATGCAAATCTGAGTCAG-GGCCCCGGAACGCGTTTTTAGCCAAAAA-CCGTGATTGTTAG
2497 ACATCGAACT
Statistics
Matches: 1860, Mismatches: 229, Indels: 146
0.83 0.10 0.07
Matches are distributed among these distances:
312 70 0.04
313 10 0.01
314 1 0.00
315 44 0.02
316 74 0.04
317 45 0.02
319 19 0.01
320 4 0.00
322 1 0.00
323 1 0.00
324 4 0.00
325 50 0.03
326 17 0.01
327 87 0.05
328 107 0.06
329 145 0.08
330 234 0.13
331 276 0.15
332 132 0.07
333 176 0.09
334 77 0.04
335 90 0.05
336 86 0.05
337 110 0.06
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (331 bp):
TTTTTTCCGAATAAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
AAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGCAGTCTTGGCGCCAAAA
ATCATGCAAATCTGAGTCAGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGTACA
CATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTTAATTTTTGGCCACAGTAC
TCATATAAAATATATAATTAACCGCCAAAAGGATTGAAGGGATTTTCAAGCTTCTAATATCGTTT
TTCCAT
Found at i:4023 original size:33 final size:32
Alignment explanation
Indices: 3981--4077 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 32
3971 CTTTTACACT
3981 GAGTCTCCCCACTAGGACGGCTCAGCCACGGCG
1 GAGTCTCCCCACTAGGACGGCTCA-CCACGGCG
4014 GAGTCTCCCCACTGAGGA-GGCTCAACCACGGCG
1 GAGTCTCCCCACT-AGGACGGCTC-ACCACGGCG
* * *
4047 GAGCCTCCCCACTGGGGCGGCTTCACCACGG
1 GAGTCTCCCCACTAGGACGGC-TCACCACGG
4078 GCAGGCCGCC
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
32 2 0.04
33 48 0.84
34 7 0.12
ACGTcount: A:0.18, C:0.39, G:0.31, T:0.12
Consensus pattern (32 bp):
GAGTCTCCCCACTAGGACGGCTCACCACGGCG
Found at i:4049 original size:17 final size:17
Alignment explanation
Indices: 3999--4049 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
3989 CCACTAGGAC
*
3999 GGCTCAGCCACGGCGGA
1 GGCTCAACCACGGCGGA
* * * *
4016 GTCTC-CCCACTGAGGA
1 GGCTCAACCACGGCGGA
4032 GGCTCAACCACGGCGGA
1 GGCTCAACCACGGCGGA
4049 G
1 G
4050 CCTCCCCACT
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.20, C:0.35, G:0.35, T:0.10
Consensus pattern (17 bp):
GGCTCAACCACGGCGGA
Found at i:4406 original size:21 final size:21
Alignment explanation
Indices: 4380--4423 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4370 GAAAACTGGA
*
4380 TTGCTAAAT-ACCGCCTCATTT
1 TTGCT-AATCACCGCCCCATTT
*
4401 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
4422 TT
1 TT
4424 TACGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:4524 original size:19 final size:20
Alignment explanation
Indices: 4492--4529 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4482 CTCGGCTATT
*
4492 TTATTTATAAAAAATAATTA
1 TTATTTATAAAAAAAAATTA
4512 TTATTTA-AAAAAAAAATT
1 TTATTTATAAAAAAAAATT
4530 GGTCTAGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTATTTATAAAAAAAAATTA
Found at i:4576 original size:32 final size:33
Alignment explanation
Indices: 4535--4609 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 33
4525 AAATTGGTCT
4535 AGCCGCCCCACCAGGGCGGCCTG-CCGTGGCAA
1 AGCCGCCCCACCAGGGCGGCCTGCCCGTGGCAA
*** **
4567 AGCCGCCCCAGTGGGGCGGCCTGCCCGTGGTGA
1 AGCCGCCCCACCAGGGCGGCCTGCCCGTGGCAA
4600 AGCCGCCCCA
1 AGCCGCCCCA
4610 GTGGGGAGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 20 0.54
33 17 0.46
ACGTcount: A:0.13, C:0.43, G:0.36, T:0.08
Consensus pattern (33 bp):
AGCCGCCCCACCAGGGCGGCCTGCCCGTGGCAA
Found at i:4603 original size:33 final size:32
Alignment explanation
Indices: 4548--4615 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
4538 CGCCCCACCA
4548 GGGCGGCCTGCCGTGGCAAAGCCGCCCCAGTG
1 GGGCGGCCTGCCGTGGCAAAGCCGCCCCAGTG
**
4580 GGGCGGCCTGCCCGTGGTGAAGCCGCCCCAGTG
1 GGGCGGCCTG-CCGTGGCAAAGCCGCCCCAGTG
4613 GGG
1 GGG
4616 AGACTCCGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.10, C:0.35, G:0.44, T:0.10
Consensus pattern (32 bp):
GGGCGGCCTGCCGTGGCAAAGCCGCCCCAGTG
Found at i:4636 original size:32 final size:33
Alignment explanation
Indices: 4566--4636 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
4556 TGCCGTGGCA
* *
4566 AAGCCGCCCCAGTGGGGCGGCCTGCCCGTGGTG
1 AAGCCGCCCCAGTGGGGCAGACTGCCCGTGGTG
4599 AAGCCGCCCCAGTGGGG-AGACT-CCGCGTGGCTG
1 AAGCCGCCCCAGTGGGGCAGACTGCC-CGTGG-TG
4632 -AGCCG
1 AAGCCG
4637 TCCTAGTGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.06
32 13 0.38
33 19 0.56
ACGTcount: A:0.13, C:0.35, G:0.41, T:0.11
Consensus pattern (33 bp):
AAGCCGCCCCAGTGGGGCAGACTGCCCGTGGTG
Found at i:13842 original size:8 final size:8
Alignment explanation
Indices: 13829--13857 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
13819 CAACCATCAT
13829 TCATATAA
1 TCATATAA
13837 TCATATAA
1 TCATATAA
13845 TCATATAA
1 TCATATAA
13853 TCATA
1 TCATA
13858 GTTCACACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (8 bp):
TCATATAA
Found at i:15494 original size:2 final size:2
Alignment explanation
Indices: 15487--15519 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
15477 TTTATTTAAC
*
15487 AT AT AT AT GT 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 A
15520 CACACTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15564 original size:27 final size:26
Alignment explanation
Indices: 15523--15574 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
15513 ATATATACAC
15523 ACTTATGTGTGATTAGTGATTTAGTT
1 ACTTATGTGTGATTAGTGATTTAGTT
*
15549 ACTTATAGTTTGATTAGTGATTTAGT
1 ACTTAT-GTGTGATTAGTGATTTAGT
15575 GATTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.50
Consensus pattern (26 bp):
ACTTATGTGTGATTAGTGATTTAGTT
Found at i:16459 original size:3 final size:3
Alignment explanation
Indices: 16446--16501 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
16436 AGAAATCTAA
* * * * *
16446 ATC ACC ATC ATC ATA ATC ATT ATG ATT ATC ATC ATC ATC ATC ATC ATCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT-C
16495 ATC ATC A
1 ATC ATC A
16502 AATCATACTC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:22884 original size:2 final size:2
Alignment explanation
Indices: 22877--22901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22867 TGATAAGTGA
22877 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 A
22902 CTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26291 original size:2 final size:2
Alignment explanation
Indices: 26284--26312 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26274 ATTTTTATTG
26284 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
26313 TTGAATTTTT
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:38405 original size:51 final size:50
Alignment explanation
Indices: 38329--38432 Score: 199
Period size: 51 Copynumber: 2.1 Consensus size: 50
38319 AAATGAATAC
38329 AAATATAATAAACAAAACATTAGAAAATTAACTATTGACACTTGTCAAAGA
1 AAATATAATAAACAAAACATTAGAAAATTAACTATTGACACTTGTCAAA-A
38380 AAATATAATAAACAAAACATTAGAAAATTAACTATTGACACTTGTCAAAA
1 AAATATAATAAACAAAACATTAGAAAATTAACTATTGACACTTGTCAAAA
38430 AAA
1 AAA
38433 GCAAATGCCA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 4 0.08
51 49 0.92
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.25
Consensus pattern (50 bp):
AAATATAATAAACAAAACATTAGAAAATTAACTATTGACACTTGTCAAAA
Found at i:45419 original size:23 final size:22
Alignment explanation
Indices: 45389--45431 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
45379 AAACCTTCAT
45389 CTTTTTTTTTCTCTTTGTTTTGC
1 CTTTTTTTTTCT-TTTGTTTTGC
*
45412 CTTTTTTTTTCTTTTTTTTT
1 CTTTTTTTTTCTTTTGTTTT
45432 AAATGTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (22 bp):
CTTTTTTTTTCTTTTGTTTTGC
Found at i:48936 original size:99 final size:99
Alignment explanation
Indices: 48817--49015 Score: 371
Period size: 99 Copynumber: 2.0 Consensus size: 99
48807 AATTACCATA
* *
48817 AATAAACCATCTACCTACCAAATACACAAATAAATAAATTACAAATTAAATTCACATTCCGTGAG
1 AATAAACCATCTACCTACCAAATACACAAATAAACAAATTACAAATTAAACTCACATTCCGTGAG
*
48882 ACTTGAACCCATGACCTTACGGTTCAGACACGAT
66 ACTTGAACCCAGGACCTTACGGTTCAGACACGAT
48916 AATAAACCATCTACCTACCAAATACACAAATAAACAAATTACAAATTAAACTCACATTCCGTGAG
1 AATAAACCATCTACCTACCAAATACACAAATAAACAAATTACAAATTAAACTCACATTCCGTGAG
48981 ACTTGAACCCAGGACCTTACGGTTCAGACACGAT
66 ACTTGAACCCAGGACCTTACGGTTCAGACACGAT
49015 A
1 A
49016 CACCTACCAG
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.23
Consensus pattern (99 bp):
AATAAACCATCTACCTACCAAATACACAAATAAACAAATTACAAATTAAACTCACATTCCGTGAG
ACTTGAACCCAGGACCTTACGGTTCAGACACGAT
Done.