Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013429.1 Corchorus olitorius cultivar O-4 contig13462, 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: 69517
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1314 original size:10 final size:10
Alignment explanation
Indices: 1299--1338 Score: 53
Period size: 10 Copynumber: 3.7 Consensus size: 10
1289 TTATTGTGCA
1299 TTGTGTGGAT
1 TTGTGTGGAT
1309 TTGTGTGGGTAAT
1 TTGTGT-GG--AT
1322 TTGTGTGGAT
1 TTGTGTGGAT
1332 TTGTGTG
1 TTGTGTG
1339 AATAATTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 15 0.56
11 2 0.07
12 2 0.07
13 8 0.30
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (10 bp):
TTGTGTGGAT
Found at i:1344 original size:23 final size:23
Alignment explanation
Indices: 1299--1346 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1289 TTATTGTGCA
**
1299 TTGTGTGGATTTGTGTGGGTAAT
1 TTGTGTGGATTTGTGTGAATAAT
1322 TTGTGTGGATTTGTGTGAATAAT
1 TTGTGTGGATTTGTGTGAATAAT
1345 TT
1 TT
1347 CGGCTAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (23 bp):
TTGTGTGGATTTGTGTGAATAAT
Found at i:4091 original size:2 final size:2
Alignment explanation
Indices: 4080--4116 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4070 TATTTCAACA
4080 AT AT -T 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
4117 CTAGAACATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4275 original size:24 final size:24
Alignment explanation
Indices: 4243--4295 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
4233 CCAAGGAAAC
4243 TTAAACATCCATGCAAATAAAAAG
1 TTAAACATCCATGCAAATAAAAAG
* *
4267 TTAAACATCCATGCAAATCAAATG
1 TTAAACATCCATGCAAATAAAAAG
4291 TTAAA
1 TTAAA
4296 TATTGTTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.25
Consensus pattern (24 bp):
TTAAACATCCATGCAAATAAAAAG
Found at i:10114 original size:23 final size:23
Alignment explanation
Indices: 10087--10132 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
10077 TCTCTACATT
*
10087 CTCTTGTCCTTTT-CATAGTTCAA
1 CTCTTGT-CTTTTCCATACTTCAA
10110 CTCTTGTCTTTTCCATACTTCAA
1 CTCTTGTCTTTTCCATACTTCAA
10133 TTCTCTACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.17, C:0.28, G:0.07, T:0.48
Consensus pattern (23 bp):
CTCTTGTCTTTTCCATACTTCAA
Found at i:13362 original size:2 final size:2
Alignment explanation
Indices: 13355--13430 Score: 125
Period size: 2 Copynumber: 38.0 Consensus size: 2
13345 TCTTTTATGG
* *
13355 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
13397 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13431 CAATTTATGT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13382 original size:18 final size:18
Alignment explanation
Indices: 13359--13429 Score: 142
Period size: 18 Copynumber: 3.9 Consensus size: 18
13349 TTATGGTATA
13359 TATATATATATATATATG
1 TATATATATATATATATG
13377 TATATATATATATATATG
1 TATATATATATATATATG
13395 TATATATATATATATATG
1 TATATATATATATATATG
13413 TATATATATATATATAT
1 TATATATATATATATAT
13430 ACAATTTATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TATATATATATATATATG
Found at i:15856 original size:33 final size:33
Alignment explanation
Indices: 15812--15879 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
15802 TATTTAACAT
* *
15812 ATGCATGATCTCCTTCTTCTACCTTTCTTTATC
1 ATGCATAATCTCCTCCTTCTACCTTTCTTTATC
15845 ATGCATAATCTCCTCCTTCTACCTTTCTTTATC
1 ATGCATAATCTCCTCCTTCTACCTTTCTTTATC
15878 AT
1 AT
15880 TAAAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.31, G:0.04, T:0.47
Consensus pattern (33 bp):
ATGCATAATCTCCTCCTTCTACCTTTCTTTATC
Found at i:15954 original size:33 final size:33
Alignment explanation
Indices: 15912--16010 Score: 189
Period size: 33 Copynumber: 3.0 Consensus size: 33
15902 ATACTACCTT
15912 GCATATTAGTGGCACCTGAAGTTGTCACATCAA
1 GCATATTAGTGGCACCTGAAGTTGTCACATCAA
15945 GCATATTAGTGGCACCTGAAGTTGTCACATCAA
1 GCATATTAGTGGCACCTGAAGTTGTCACATCAA
*
15978 GCATATTTGTGGCACCTGAAGTTGTCACATCAA
1 GCATATTAGTGGCACCTGAAGTTGTCACATCAA
16011 AAATATAGTA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (33 bp):
GCATATTAGTGGCACCTGAAGTTGTCACATCAA
Found at i:16061 original size:29 final size:29
Alignment explanation
Indices: 16015--16075 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
16005 CATCAAAAAT
* * *
16015 ATAGTATTACTTTAACACGAGAAGTTGTC
1 ATAGTATCACTTTAACACCAGAACTTGTC
* * *
16044 ATAGTATCATTTTGACACCTGAACTTGTC
1 ATAGTATCACTTTAACACCAGAACTTGTC
16073 ATA
1 ATA
16076 TTAAGGATGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (29 bp):
ATAGTATCACTTTAACACCAGAACTTGTC
Found at i:16791 original size:17 final size:17
Alignment explanation
Indices: 16766--16799 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16756 GATTGTAGTA
16766 ATGAATATCATGGAGAT
1 ATGAATATCATGGAGAT
*
16783 ATGACTATCATGGAGAT
1 ATGAATATCATGGAGAT
16800 TATTCTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (17 bp):
ATGAATATCATGGAGAT
Found at i:17509 original size:35 final size:35
Alignment explanation
Indices: 17462--17531 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
17452 TCGGGTAGTG
17462 CAAATTTGATTGAAGACTCCCGAAAAGCCAGTATT
1 CAAATTTGATTGAAGACTCCCGAAAAGCCAGTATT
* * * * *
17497 CAAATTTTATTGAAGGCTCCGGAAGAGCTAGTATT
1 CAAATTTGATTGAAGACTCCCGAAAAGCCAGTATT
17532 GTTTTATCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (35 bp):
CAAATTTGATTGAAGACTCCCGAAAAGCCAGTATT
Found at i:21760 original size:191 final size:191
Alignment explanation
Indices: 21429--21812 Score: 741
Period size: 191 Copynumber: 2.0 Consensus size: 191
21419 GAAGCAAACG
*
21429 ATAACTGCCACATCATCTAATCATGAGGAAATTTTAGTAATACATGAGGAAAGCCGAGAATGTGT
1 ATAACTGCCACATCATCTAATCATGAGGAAATTTTAGCAATACATGAGGAAAGCCGAGAATGTGT
21494 TTGGTTGAGGTCTGTGGTAAAACACATTCGTGAGACATGTGGCTTGTCTTCTGGAAAAATGACTG
66 TTGGTTGAGGTCTGTGGTAAAACACATTCGTGAGACATGTGGCTTGTCTTCTGGAAAAATGACTG
21559 TGACGATCATATATGAAGATAATACTGCTTGTATAGCTCAATTGAAAGATGGGTACATTAA
131 TGACGATCATATATGAAGATAATACTGCTTGTATAGCTCAATTGAAAGATGGGTACATTAA
*
21620 ATAACTGTCACATCATCTAATCATGAGGAAATTTTAGCAATACATGAGGAAAGCCGAGAATGTGT
1 ATAACTGCCACATCATCTAATCATGAGGAAATTTTAGCAATACATGAGGAAAGCCGAGAATGTGT
21685 TTGGTTGAGGTCTGTGGTAAAACACATTCGTGAGACATGTGGCTTGTCTTCTGGAAAAATGACTG
66 TTGGTTGAGGTCTGTGGTAAAACACATTCGTGAGACATGTGGCTTGTCTTCTGGAAAAATGACTG
*
21750 TGATGATCATATATGAAGATAATACTGCTTGTATAGCTCAATTGAAAGATGGGTACATTAA
131 TGACGATCATATATGAAGATAATACTGCTTGTATAGCTCAATTGAAAGATGGGTACATTAA
21811 AT
1 AT
21813 GAGATGGGGC
Statistics
Matches: 190, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
191 190 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (191 bp):
ATAACTGCCACATCATCTAATCATGAGGAAATTTTAGCAATACATGAGGAAAGCCGAGAATGTGT
TTGGTTGAGGTCTGTGGTAAAACACATTCGTGAGACATGTGGCTTGTCTTCTGGAAAAATGACTG
TGACGATCATATATGAAGATAATACTGCTTGTATAGCTCAATTGAAAGATGGGTACATTAA
Found at i:29566 original size:30 final size:30
Alignment explanation
Indices: 29530--29591 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
29520 TTCATAGTGA
29530 TGCAATTTGATAAAGAGATTAGAGTTAACC
1 TGCAATTTGATAAAGAGATTAGAGTTAACC
29560 TGCAATTTGATAAAGAGATTAGAGTTAACC
1 TGCAATTTGATAAAGAGATTAGAGTTAACC
29590 TG
1 TG
29592 AAGAGCAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.31
Consensus pattern (30 bp):
TGCAATTTGATAAAGAGATTAGAGTTAACC
Found at i:30785 original size:2 final size:2
Alignment explanation
Indices: 30780--30812 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30770 TTTTTAAGCC
30780 TA TA 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 TA TA T
30813 TGCACTAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31510 original size:43 final size:41
Alignment explanation
Indices: 31369--31692 Score: 323
Period size: 43 Copynumber: 7.7 Consensus size: 41
31359 CCAATAACCA
* * *
31369 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTTCT
1 AAAGTCCCCAAACACATTTATAACACAGGGGC-A-TCT-ATTCC
* * *
31413 AAAGTCCTCAAACACATTTATGACACAGAGGCATCTATAT-C
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTAT-TCC
*
31454 AAAGTCCCCAAACACAATTATAACACAGGGGCAGCTCTATTCC
1 AAAGTCCCCAAACACATTTATAACACAGGGGCA--TCTATTCC
** *
31497 AAAGTCCTTAAACACATTTATAACACAGAGGCATCTATAT-C
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTAT-TCC
* *
31538 AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCT-CTCTA
1 AAAGTCCCCAAACACATTTATAACACAGGGGC-AT-CTATTC-C
* * * * *
31581 AAAGTCCTCAAACACATTTATAACACAGAGGCATCCATACT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTATTCC
* *
31622 AAAGTCCCCAAACACATTTATAACAGAGGGACACCTCTA-TCTC
1 AAAGTCCCCAAACACATTTATAACACAGGGGCA--TCTATTC-C
*
31665 AAAGTCCTCAAACACATTTATAACACAG
1 AAAGTCCCCAAACACATTTATAACACAG
31693 AGGGATTTTT
Statistics
Matches: 233, Mismatches: 34, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
41 96 0.41
42 12 0.05
43 97 0.42
44 28 0.12
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (41 bp):
AAAGTCCCCAAACACATTTATAACACAGGGGCATCTATTCC
Found at i:31531 original size:84 final size:83
Alignment explanation
Indices: 31369--31695 Score: 462
Period size: 84 Copynumber: 3.9 Consensus size: 83
31359 CCAATAACCA
31369 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTTCT-AAAGTCCTCAAACACATTTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGC-A--CTCTTTCTCAAAGTCCTCAAACACATTTA
*
31433 TGACACAGAGGCATCTATATC
63 TAACACAGAGGCATCTATATC
*
31454 AAAGTCCCCAAACACAATTATAACACAGGGGCAGCTCTATTC-CAAAGTCCTTAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCA-CTCT-TTCTCAAAGTCCTCAAACACATTTAT
31518 AACACAGAGGCATCTATATC
64 AACACAGAGGCATCTATATC
* * * *
31538 AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTCTAAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCACT-CTTTCTCAAAGTCCTCAAACACATTTATA
*
31603 ACACAGAGGCATCCATA-C
65 ACACAGAGGCATCTATATC
* * * *
31621 TAAAGTCCCCAAACACATTTATAACAGAGGGACACCTCTATCTCAAAGTCCTCAAACACATTTAT
1 -AAAGTCCCCAAACACAATTATAACACAGGGGCA-CTCTTTCTCAAAGTCCTCAAACACATTTAT
31686 AACACAGAGG
64 AACACAGAGG
31696 GATTTTTCTT
Statistics
Matches: 222, Mismatches: 14, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
83 8 0.04
84 181 0.82
85 33 0.15
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (83 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCACTCTTTCTCAAAGTCCTCAAACACATTTATAA
CACAGAGGCATCTATATC
Found at i:31670 original size:168 final size:169
Alignment explanation
Indices: 31369--31695 Score: 518
Period size: 168 Copynumber: 1.9 Consensus size: 169
31359 CCAATAACCA
*
31369 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTCTAAAGTCCTCAAACACATTTAT
* * * *
31434 GACACAGAGGCATCTATATCAAAGTCCCCAAACACAATTATAACACAGGGGCAGCTCTATTCCAA
66 AACACAGAGGCATCCATATCAAAGTCCCCAAACACAATTATAACACAGGGACACCTCTATTCCAA
*
31499 AGTCCTTAAACACATTTATAACACAGAGGCATCTATATC
131 AGTCCTCAAACACATTTATAACACAGAGGCATCTATATC
*
31538 AAAGTCCCCAAACACATTTATAACACAGGGGCAA-TC-CTCTCTAAAAGTCCTCAAACACATTTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTCT-AAAGTCCTCAAACACATTTA
* *
31601 TAACACAGAGGCATCCATA-CTAAAGTCCCCAAACACATTTATAACAGAGGGACACCTCTA-TCT
65 TAACACAGAGGCATCCATATC-AAAGTCCCCAAACACAATTATAACACAGGGACACCTCTATTC-
31664 CAAAGTCCTCAAACACATTTATAACACAGAGG
128 CAAAGTCCTCAAACACATTTATAACACAGAGG
31696 GATTTTTCTT
Statistics
Matches: 146, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
167 8 0.05
168 105 0.72
169 33 0.23
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (169 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTCTAAAGTCCTCAAACACATTTAT
AACACAGAGGCATCCATATCAAAGTCCCCAAACACAATTATAACACAGGGACACCTCTATTCCAA
AGTCCTCAAACACATTTATAACACAGAGGCATCTATATC
Found at i:33934 original size:33 final size:35
Alignment explanation
Indices: 33897--33967 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 35
33887 TCTAAGTTTC
33897 TTAATTAAAATAGTAAAATGGTAAAAA-AAAAT-T
1 TTAATTAAAATAGTAAAATGGTAAAAATAAAATAT
*
33930 TTAATTAAAATAGTAAATTGGTAAAAATAAAATAT
1 TTAATTAAAATAGTAAAATGGTAAAAATAAAATAT
33965 TTA
1 TTA
33968 CAAAGAGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 26 0.74
34 5 0.14
35 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (35 bp):
TTAATTAAAATAGTAAAATGGTAAAAATAAAATAT
Found at i:34249 original size:85 final size:85
Alignment explanation
Indices: 34125--34286 Score: 254
Period size: 85 Copynumber: 1.9 Consensus size: 85
34115 TAAAAAATTA
* *
34125 TAATATATATAAGTTTTGTAATTATAATAGTAAAAATGGTAAAAATAAAATAGTCATAAAGAGAT
1 TAATATATATAAGTTTTGTAATTAAAATAATAAAAATGGTAAAAATAAAATAGTCATAAAGAGAT
*
34190 TAGATTTAATTAGAAACTTC
66 TAGATCTAATTAGAAACTTC
* * *
34210 TAATATATTTAAGGTTTTTTAATTAAAATAAT-AAAATGGTAAAAATAAAATAGTTATAAAGAGA
1 TAATATATATAA-GTTTTGTAATTAAAATAATAAAAATGGTAAAAATAAAATAGTCATAAAGAGA
34274 TTAGATCTAATTA
65 TTAGATCTAATTA
34287 AATAAAAATA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
85 54 0.77
86 16 0.23
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (85 bp):
TAATATATATAAGTTTTGTAATTAAAATAATAAAAATGGTAAAAATAAAATAGTCATAAAGAGAT
TAGATCTAATTAGAAACTTC
Found at i:35908 original size:2 final size:2
Alignment explanation
Indices: 35901--35926 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35891 ATGAAATTGA
35901 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
35927 GAATATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44740 original size:3 final size:3
Alignment explanation
Indices: 44732--44763 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
44722 ATCAAGCCCT
44732 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
44764 TTTTAGTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:45627 original size:13 final size:13
Alignment explanation
Indices: 45606--45642 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
45596 GATAATTCTT
45606 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
45619 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
45632 ATTGACCCTCC
1 TTTGACCCTCC
45643 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.41, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:66293 original size:72 final size:74
Alignment explanation
Indices: 66184--66371 Score: 246
Period size: 72 Copynumber: 2.6 Consensus size: 74
66174 AGTTGTGAGA
* *
66184 ACAGAAAGT-TGTATTGAAGGTGAATCTGATGCTTGTGAAGCTGAA-ACAAGCAAAGAAGAAAAA
1 ACAGAAAGTGCGTATTGAAGGTGAATCTGATGCATGTGAAGCTGAACACAAGCAAAGAAGAAAAA
* *
66247 GTTTTGATG
66 GCTTTAATG
* *
66256 ACAGAACA-TG-GTATTGAAGGTGACTCTGATGCATGTGAAGCT-AACACAAGCAAAGAAGAAAC
1 ACAGAA-AGTGCGTATTGAAGGTGAATCTGATGCATGTGAAGCTGAACACAAGCAAAGAAGAAAA
66318 AGCTTTAATG
65 AGCTTTAATG
*
66328 ACAGAAAGTTGCGTA--GAAGGCGAATCTGATGCATGTGAAGCTGA
1 ACAGAAAG-TGCGTATTGAAGGTGAATCTGATGCATGTGAAGCTGA
66372 CACCAATAAA
Statistics
Matches: 102, Mismatches: 7, Indels: 13
0.84 0.06 0.11
Matches are distributed among these distances:
71 3 0.03
72 92 0.90
73 4 0.04
74 3 0.03
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (74 bp):
ACAGAAAGTGCGTATTGAAGGTGAATCTGATGCATGTGAAGCTGAACACAAGCAAAGAAGAAAAA
GCTTTAATG
Found at i:69474 original size:21 final size:23
Alignment explanation
Indices: 69450--69498 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
69440 GTTAAGTCAA
69450 TAAAAAA-TATTTTTTAATTA-T
1 TAAAAAAGTATTTTTTAATTACT
69471 TAAAAAAGTATTTTTTAATTACT
1 TAAAAAAGTATTTTTTAATTACT
69494 TAAAA
1 TAAAA
69499 TAAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 7 0.27
22 13 0.50
23 6 0.23
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAAAAAGTATTTTTTAATTACT
Done.