Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011420.1 Corchorus capsularis cultivar CVL-1 contig11441, 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: 61619
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:193 original size:93 final size:93
Alignment explanation
Indices: 89--356 Score: 378
Period size: 93 Copynumber: 2.8 Consensus size: 93
79 GGGAAGTTGG
* * *
89 GCTAGTTGTTGTTGTCGCATATTGACATTGTTCAGAGGAGGCTGAGATGGTTGCTGTCCTAGTTG
1 GCTAGTTGTTGTTGTCGGATATTGACATTGTTAAGAGGAGGCTGAGATGGTTGTTGTCCTAGTTG
154 TTGTTGTTGTCGGAGTTGAGAC-TGCTGT
66 TTGTTGTTGTCGGAGTTGAGACTTG-TGT
* * *
182 GCTAGTTGTTGTTGTCGGTTATTGACATTGTTAAGAGGAGGCTGAGACGGTTGTTGTGCTAGTTG
1 GCTAGTTGTTGTTGTCGGATATTGACATTGTTAAGAGGAGGCTGAGATGGTTGTTGTCCTAGTTG
* *
247 TTGTTGTCGTCAGAGTTGAGACTTGTGT
66 TTGTTGTTGTCGGAGTTGAGACTTGTGT
* *
275 GCTAGTTGTTCTTGTGGGATATTGACATTGTTAAGAGGAGGCTGAGATGGCTT-TTGTTCTGCTA
1 GCTAGTTGTTGTTGTCGGATATTGACATTGTTAAGAGGAGGCTGAGATGG-TTGTTG-TC--CTA
*
339 GTTGTTGTCGTTGTCGGA
62 GTTGTTGTTGTTGTCGGA
357 CTATTTGTAT
Statistics
Matches: 154, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
93 131 0.85
94 5 0.03
96 18 0.12
ACGTcount: A:0.16, C:0.11, G:0.34, T:0.40
Consensus pattern (93 bp):
GCTAGTTGTTGTTGTCGGATATTGACATTGTTAAGAGGAGGCTGAGATGGTTGTTGTCCTAGTTG
TTGTTGTTGTCGGAGTTGAGACTTGTGT
Found at i:3643 original size:22 final size:21
Alignment explanation
Indices: 3613--3655 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3603 ACATATATAA
3613 GTTACGTAACGTTACGTAACAC
1 GTTACGTAACGTT-CGTAACAC
* *
3635 GTTATGTAACGTTCGTGACAC
1 GTTACGTAACGTTCGTAACAC
3656 CGCGACCGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (21 bp):
GTTACGTAACGTTCGTAACAC
Found at i:4918 original size:21 final size:21
Alignment explanation
Indices: 4892--4933 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4882 TTGGAGTTGA
4892 GACAGCTCTTGTGCTAATTGT
1 GACAGCTCTTGTGCTAATTGT
4913 GACAGCTCTTGTGCTAATTGT
1 GACAGCTCTTGTGCTAATTGT
4934 TGTTGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (21 bp):
GACAGCTCTTGTGCTAATTGT
Found at i:5012 original size:15 final size:15
Alignment explanation
Indices: 4988--5021 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4978 TTGTTCATGG
4988 AGTATGTGAATTTGC
1 AGTATGTGAATTTGC
* *
5003 AGTATTTGAATTTGG
1 AGTATGTGAATTTGC
5018 AGTA
1 AGTA
5022 GAGACTGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (15 bp):
AGTATGTGAATTTGC
Found at i:5981 original size:2 final size:2
Alignment explanation
Indices: 5972--6000 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5962 GTTTTTTGTT
5972 TA TA -A TA TA TA 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
6001 CTACTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6175 original size:32 final size:32
Alignment explanation
Indices: 6134--6198 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
6124 ACTGTCGATT
6134 TTGGTTTGGAGGAACCTAATCGTAACTAGACC
1 TTGGTTTGGAGGAACCTAATCGTAACTAGACC
6166 TTGGTTTGGAGGAACCTAATCGTAACTAGACC
1 TTGGTTTGGAGGAACCTAATCGTAACTAGACC
6198 T
1 T
6199 GTTCAAGGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (32 bp):
TTGGTTTGGAGGAACCTAATCGTAACTAGACC
Found at i:8251 original size:22 final size:24
Alignment explanation
Indices: 8226--8283 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
8216 TGATCCCATC
*
8226 ATGAAATTTTGATAA-CATTC-CT
1 ATGAAATTTTGATAATCATACACT
* *
8248 ATGAAATTTTAATAATGATACACT
1 ATGAAATTTTGATAATCATACACT
8272 ATGAAATTTTGA
1 ATGAAATTTTGA
8284 GAACCTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 14 0.47
23 3 0.10
24 13 0.43
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (24 bp):
ATGAAATTTTGATAATCATACACT
Found at i:8507 original size:22 final size:22
Alignment explanation
Indices: 8482--8550 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
8472 GAATTGTTAG
*
8482 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
8504 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
*
8526 TAATCACGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
8548 TAA
1 TAA
8551 ATCTTCCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:9295 original size:31 final size:32
Alignment explanation
Indices: 9239--9305 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
9229 TGGCAATTTA
* *
9239 GAAATATGTTTTAAAAAAAACGGGTATAATTG
1 GAAATATATTTTAAAAAAAACGGGTACAATTG
*
9271 GAAATATATTTTAAAAATAA-GGGTACAATTG
1 GAAATATATTTTAAAAAAAACGGGTACAATTG
9302 GAAA
1 GAAA
9306 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.30
Consensus pattern (32 bp):
GAAATATATTTTAAAAAAAACGGGTACAATTG
Found at i:17387 original size:27 final size:27
Alignment explanation
Indices: 17356--17411 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
17346 TAACTATTCA
*
17356 TTTTGGGACAAATT-AGCCCTTTAATTT
1 TTTTGGGACAAATTGA-CCCTTTAACTT
*
17383 TTTTGGTACAAATTGACCCTTTAACTT
1 TTTTGGGACAAATTGACCCTTTAACTT
17410 TT
1 TT
17412 AAAACGAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.46
Consensus pattern (27 bp):
TTTTGGGACAAATTGACCCTTTAACTT
Found at i:25108 original size:59 final size:59
Alignment explanation
Indices: 25035--25164 Score: 251
Period size: 59 Copynumber: 2.2 Consensus size: 59
25025 CCACAAACAC
*
25035 AGGATTCAATTAGTAGAGTTTAAATTTTATTAGGATCATCCTAAAAAAAGGGTGTTTTT
1 AGGATTCCATTAGTAGAGTTTAAATTTTATTAGGATCATCCTAAAAAAAGGGTGTTTTT
25094 AGGATTCCATTAGTAGAGTTTAAATTTTATTAGGATCATCCTAAAAAAAGGGTGTTTTT
1 AGGATTCCATTAGTAGAGTTTAAATTTTATTAGGATCATCCTAAAAAAAGGGTGTTTTT
25153 AGGATTCCATTA
1 AGGATTCCATTA
25165 AGATGGTGCC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 70 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (59 bp):
AGGATTCCATTAGTAGAGTTTAAATTTTATTAGGATCATCCTAAAAAAAGGGTGTTTTT
Found at i:26710 original size:321 final size:322
Alignment explanation
Indices: 25390--29116 Score: 2212
Period size: 321 Copynumber: 11.4 Consensus size: 322
25380 ATCTATTCAA
* ** * * *
25390 AATTAATTTCTAATTAAATCGAAACAAGATTTAGAAACTTGTAGAAACAAATCCTTAAATACAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AAACAAATTCTTAAATCCAAT
* * * * * **
25455 TTGGCTCATATTTGATTAGATGAATATAGATATCTTATATGGAGTATTGACGCCAAAAATCATGC
65 GTGGCTGAGATTTGATTAGATGAATATAGATATCTCA-A-GGAGTCTTGGTGCCAAAAATCATGC
* * * ** * ** *
25520 AAAACTGATATGACCCAGGGCCTGGGGATGCGTTTTTAGGC-AAAAAAC--CAT-A-TGGTACAT
128 AAAACTG--A-G--TCGGGGCC--CGGAAACGTTTTTA-GCAAAAAAACGTGATGATTATTACAC
* * * * * *
25580 GATTTTGGGTAAAATTTTGCAAAAATTGACCCA-AAATATTTTT-ATCAATTTTTAGCCACAATT
185 GATTTCGGCTAAAATTTTGCAAAAATTGA-CCAGAAA-ATTTTTCCTCAATTTTT-GGCAAAATA
* * * * * * *
25643 CTTATAAAAAATATATAATTCAATGCCAAAGATATTGAAGGGCTTCTCACGCTTCTAATATCA-T
247 CTCAT-----ATATATAATT-AACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATAT-AGT
* * *
25707 TTTTCCTAT-TTTTTTTCA
305 TTTTCTTATATTTTTCT-G
* * * * * * * *
25725 AATTAATTTCTAATTATATCAAAACATGACTCAAAAGCTCGTAAAAACAAATCCTTAAATCTAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAATTCTTAAATCCAAT
* * * * * * **
25790 ATGGCTAAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAA
65 GTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCAA
** ** * * ** *
25855 AACTGACCCGGGGCTCCATAATGCGTTTTTAGC-CAAAAAC-TG-TGA-TGGTACACGATTTCAG
130 AACTGAGTCGGGGC-CCGGAA-ACGTTTTTAGCAAAAAAACGTGATGATTATTACACGATTTCGG
* * * * *
25916 CTAAAATTTTGCAAAAATTGACCTGAAATATTTTCCCTCAATTTTAAGACACAATACTCATAAAA
193 CTAAAATTTTGCAAAAATTGACCAGAAA-ATTTTTCCTCAATTTT-TGGCAAAATACTC-----A
* * * * * *
25981 TATATATAAGTCATCGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTT-TCATA
251 TATATATAA-TTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATAGTTTTTCTTATA
26045 TTTTTCTG
315 TTTTTCTG
* *
26053 AATTAATTTCTAATTAAAACGAAACAAGATTCAGATGCTCGTAAAA-AAATT-TTAAATTCAATG
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATTCTTAAATCCAATG
* * * * * *
26116 TGGCTGATACTTGATTAGATGAATATAGATATTTTAAGAAGT-TTCGGCGCCAAAAATCATGCAA
66 TGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTT-GGTGCCAAAAATCATGCAA
* * * * *
26180 AACTAAGTCGGGGCCCTGAAACGTGTTTTTAGCAGAAAAACCGTGATGGTTAGTACACGATTTCG
130 AACTGAGTCGGGGCCCGGAAAC--GTTTTTAGCA-AAAAAACGTGATGATTATTACACGATTTCG
* * *
26245 GCTAAAATTTTGCAAAAAATGACCCAAAAAATTTTTCCGTCAATTTTTGGCTAAAATAGTCATA-
192 GCTAAAATTTTGCAAAAATTGA-CCAGAAAATTTTTCC-TCAATTTTTGGC-AAAATACTCATAT
* * * ** * *
26309 AAAT-A-T-ATGCCAAAAAGATTGGACAACTTTTGACGCTTTTAATATCGTTTTTC--ATATTTT
254 ATATAATTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATAGTTTTTCTTATATTTT
26369 TCTG
319 TCTG
* *
26373 AATTAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAACAAATTCTTAAATCCAATG
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATTCTTAAATCCAATG
** * * * * *
26438 TAACTGAGATTTG-TTAGATGAATATGGATATCTCAAAGAGTCTTGGTGCCAATAGTCATGAAAA
66 TGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCAAA
* *
26502 ACTTAGTCGGGGCCTCGGAACACG-TTTTAGTCAAAAATA-GTGATGATTATTACACGATTTCGG
131 ACTGAGTCGGGGCC-CGGAA-ACGTTTTTAG-CAAAAAAACGTGATGATTATTACACGATTTCGG
* ** * * * *
26565 CTAGAATTTTGCAAAAATTGAGTAGAAAGTTATTTCCTCAATTTTTAGTCATAATACTGATA-A-
193 CTAAAATTTTGCAAAAATTGACCAGAAAATT-TTTCCTCAATTTTT-GGCAAAATACTCATATAT
* * * * *
26628 A-AATT-ACGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATATAATTTTTCTTATTATTTAT
256 ATAATTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATAGTTTTTCTTA-TATTTTT
26691 CTG
320 CTG
* * * ***
26694 AATTAATTTCTAATTAAATTGAAACATGATTCAGATGCTTGTTTCACAAA-TCTTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATTC-TTAAATCCAAT
* * * * * * **
26758 GTAGTTGAGATTTGATTAGATAAATATAGATATATCACGGGGTCTCAGTGCCAAAAATCATGCAA
65 GTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCAA
* * * * *
26823 CACTGAATCGGGGCCCCGGAATACGTTTTTAGC-CAAAACCGTGATTTCGACTAATGTACACGAT
130 AACTGAGTCGGGG-CCCGGAA-ACGTTTTTAGCAAAAAAACGTGA--T-GA-TTAT-TACACGAT
* * * **
26887 TTTGACTAATATTTTGCAAAAATTGACCAGAAATATTTTTCCTCAATTTTTGTTTAAAATAATCA
188 TTCGGCTAAAATTTTGCAAAAATTGACCAGAAA-ATTTTTCCTCAATTTTTG-GCAAAAT-A-C-
* * * * *
26952 TAAAATATATATAATTCAACTCC-AAAAGATTGGAGGACTTTTTACGTTTTTAATAGTATCGTTT
248 T--CATATATATAATT-AACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATA-TA--GTTT
*
27016 TTC--ATATTTTTCTA
307 TTCTTATATTTTTCTG
* * *
27030 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAGAAACAAATCCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AAACAAATTCTTAAATCCAAT
* * * * * *** *
27095 GTGGCTGAGAGTTGATTAGATGAATATAGATATTTTAAGGATTTTTGACACAAAAAATCATGCAA
65 GTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCAA
* * * *
27160 AACTTAGCCGGGGTCCC-GAAACGCGTTTTTAGCAAAAAAAACCGTGATGGTTAGTACACGATTT
130 AACTGAGTCGGGG-CCCGGAAA--CGTTTTTAGC-AAAAAAA-CGTGATGATTATTACACGATTT
* * * ** * *
27224 CGGATAAAATTTTACAAAAAATGAGAAGAAAAATTTTCCTCAATTTTTGGCTAAATACTCATGAA
190 CGGCTAAAATTTTGCAAAAATTGACCAGAAAATTTTTCCTCAATTTTTGGCAAAATACTC-----
* * *
27289 ATATATATAATTTAATGCCAAAAAGATTGAAGGACTTTTCACACTTTTCATATAGTTTTTCATAT
250 ATATATATAA-TTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATAGTTTTTC---T
* *
27354 TTTTTTTTTCTG
311 TATATTTTTCTG
* * * * * *
27366 AATTAAGTTCTAATTAAATCTAAATAAGATTCAGATGCTCGTAAAAAAAATCCTTAAAAATGCAA
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATTCTT--AAATCCAA
* * * * * *
27431 TGCGACTGGGATTTGATTAGATGAATATGGATATCTCAAGGACTCTTAGCT-CCAAAAATCATGC
64 TGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTT-GGTGCCAAAAATCATGC
** * *
27495 AAAACTGA-------CCCGG-GGCGTTTTTAGCCAAAAAAACGTTATGATTATTACATGATTTCG
128 AAAACTGAGTCGGGGCCCGGAAACGTTTTTAG-CAAAAAAACGTGATGATTATTACACGATTTCG
* * * *
27552 GCTAAAATTTTGCAAAAATTGATCGGAAAGATATTTCCTCAAATTTTGGCTAAAATACTCATAAA
192 GCTAAAATTTTGCAAAAATTGACCAGAAA-ATTTTTCCTCAATTTTTGGC-AAAATACTCAT---
* * * * *
27617 AATATATAATTGAACGCCAAAAATATTGAAGGATTTTTTACG-TTTCTAATATATTTTTTCCTA-
252 -ATATATAATT-AACGCCAAAAAGATTGAAGGACTTTTCACGCTTT-TAATATAGTTTTTCTTAT
* *
27680 CTTTTTCCG
314 ATTTTTCTG
* * *
27689 AATTAATTTCTAATT-AATCGAAACAAGATTTAGATACTTGTAAAAACAAATAT-TTAAATCCAA
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAAT-TCTTAAATCCAA
* * * * * ** *
27752 TGTGGTTGAGATTTTATTAAATGAATATAGATATTTCAAGGAGTTTTGACGCAAAAAAT-ATGCA
64 TGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCA
* * * * * **** *
27816 AAACTG-GCCCGAGGCCCCAGAACGCGTTTTCAGCAAAAAAAAAAAACCGTGA-TATTACACAAT
129 AAACTGAG-TCG-GGGCCCGGAA-ACGTTTTTAGCAAAAAAACGTGA---TGATTATTACACGAT
* * * * * *
27879 TTCGGCTAATATTTTGCAAAAACTGACCCGAAATGTTTTTCCTCAATTTTTAGTCACAATACTCA
188 TTCGGCTAAAATTTTGCAAAAATTGACCAGAAA-ATTTTTCCTCAATTTTT-GGCAAAATACT--
* **
27944 CAAAATATATATAATTGAACGTCAAAAAGATTGAAGGACTTTTCACGCACTTAATATAG----T-
249 C---ATATATATAATT-AACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATAGTTTTTC
* * *
28004 GT-T-TTTTCCCG
310 TTATATTTTTCTG
* * * * * *
28015 AAATAATTTCTAATCAAAACGAAACATGATTCAAATGCTTGT--AA-AAA--C---AAT---A-G
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATTCTTAAATCCAATG
* * * * ** *
28068 T---TG-GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGTAAAAAATCATTCAAA
66 TGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCAAA
* * * * * * * *
28129 ACCGA-ACCGGGCCTCGCAACGCGTTTTTAGCCAAAAACCGTGATGATTATTATACGATTTCGGC
131 ACTGAGTCGGGGCC-CGGAA-ACGTTTTTAGCAAAAAAACGTGATGATTATTACACGATTTCGGC
** * * *
28193 TAAAATTTTGCAAAAATCT-ACTC-GAAAGAGATTTCCTCAATTTTTAGCCATAATACTTGTAAA
194 TAAAATTTTGCAAAAAT-TGAC-CAGAAA-ATTTTTCCTCAATTTTT-GGCAAAATAC---T--C
* * * * ***
28256 AAATATATAATTCAACGCAAAAAATATTGAAGGAGATTTT-ACGCTTTTAATACCCTTTTT-TTC
250 ATATATATAATT-AACGCCAAAAAGATTGAAGGA-CTTTTCACGCTTTTAATATAGTTTTTCTT-
*
28319 ACTTTTTTTTCTG
312 A--TATTTTTCTG
* *
28332 AATTAATTTCTAATTAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATAT-TTAAAT-GAA
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAAT-TCTTAAATCCAA
* * * * ** *
28395 TGTGGCTAAGATTTTATT--A-G---AT-GAT-T-TCAAGGAGTGTCGCCGCAAAAAATCATGCA
64 TGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCA
* * * * * *
28451 AAACTGAGCCGGGATCCC-GAAATGTGTTTTTAGC-CAAAAACTGTGATGGTTAGTACACGATTT
129 AAACTGAGTCGGG-GCCCGGAAA--CGTTTTTAGCAAAAAAAC-GTGATGATTATTACACGATTT
* * * * * * *
28514 TGACTAAAATTTTGCAAAAAATGACTC-GAAATTTTTTTTTTCTCATTTTTTTTGGATAAAAT-C
190 CGGCTAAAATTTTGCAAAAATTGAC-CAGAAA---ATTTTTCCTCA--ATTTTTGG-CAAAATAC
* * * * *
28577 ATAAAATATATACAATTTAAAGCTAAAAAGATT-AGAGGACTTTTCACGCTTTTAATATCGTTTT
248 -T--CATATATATAA-TTAACGCCAAAAAGATTGA-AGGACTTTTCACGCTTTTAATATAGTTTT
28641 TC--ATATTTTT-TG
308 TCTTATATTTTTCTG
* * *
28653 GATTAATTTCTAAATAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAATTCTTAAATCCAAT
* * * * * **
28718 GTGGCAGAGAGTTGATTGGATGAATAT-GTATATGTCAAGGAGACTTGACGCCAAAAATCATGCA
65 GTGGCTGAGATTTGATTAGATGAATATAG-ATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCA
* ** ** * *
28782 AAACGGAG-CTAGGCCCTCATAACGCTTTTTTAGC-CAAAAACTGTGATGCTTATTACACGATTT
129 AAACTGAGTCGGGGCCCGGA-AACG--TTTTTAGCAAAAAAAC-GTGATGATTATTACACGATTT
* * * * *
28845 CGGTTAAAATTTTGTAAAAATTGATCC-GAAAGATATTTCCTCAAATTTTGGCTAAAATACTAAT
190 CGGCTAAAATTTTGCAAAAATTGA-CCAGAAA-ATTTTTCCTCAATTTTTGGC-AAAATACTCAT
** * * * *
28909 AAAAAATATATAATTCAACAACAAAAAGATTGAAGTG-CTTTTGAC-ATTTCTAATATCGTTTTC
252 -----ATATATAATT-AACGCCAAAAAGATTGAAG-GACTTTTCACGCTTT-TAATATAGTTTTT
* **
28972 CCTAT-TTTTTCCA
309 CTTATATTTTTCTG
* * *
28985 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAATAAATCCTTAAAATCCAA
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAATTCTT-AAATCCAA
* * * ***
29050 TGTGGCTGAGATTTTATTAGATGAATATAGATATTTCAAGTAGTCTTGCAACCAAAAATCATGCA
64 TGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCA
29115 AA
129 AA
29117 TTTGAAGTCG
Statistics
Matches: 2680, Mismatches: 504, Indels: 418
0.74 0.14 0.12
Matches are distributed among these distances:
307 3 0.00
308 98 0.04
309 10 0.00
310 64 0.02
311 13 0.00
312 2 0.00
314 2 0.00
315 1 0.00
316 1 0.00
317 43 0.02
318 66 0.02
319 48 0.02
320 82 0.03
321 289 0.11
322 131 0.05
323 47 0.02
324 52 0.02
325 155 0.06
326 133 0.05
327 198 0.07
328 121 0.05
329 115 0.04
330 101 0.04
331 189 0.07
332 107 0.04
333 121 0.05
334 51 0.02
335 133 0.05
336 127 0.05
337 159 0.06
338 3 0.00
339 10 0.00
340 5 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (322 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATTCTTAAATCCAATG
TGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGCAAA
ACTGAGTCGGGGCCCGGAAACGTTTTTAGCAAAAAAACGTGATGATTATTACACGATTTCGGCTA
AAATTTTGCAAAAATTGACCAGAAAATTTTTCCTCAATTTTTGGCAAAATACTCATATATATAAT
TAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATAGTTTTTCTTATATTTTTCTG
Found at i:40525 original size:166 final size:165
Alignment explanation
Indices: 40169--40580 Score: 528
Period size: 166 Copynumber: 2.5 Consensus size: 165
40159 TACCCCGGAT
* * * *
40169 TACTTGACCGATTACTTAAATGCCCTAACTTTTGATTCTTGATGTGATTAAATAAATAGACTTTT
1 TACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAA-AAATA-ACTTTT
* * * *
40234 TGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGACTTGC
64 TGGTCATTTCTCAATGGACTTTAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGACTTGA
** * * * *
40299 TTTTGAAGTTAGAGAACTTATTTTTTTCGTCTTTTCC
129 TGATGAAGCTAGAGAACTAATCTTTTTCGTCTTTACC
*
40336 TAGTTGACAGATTACTT-AATGTCCTAACTTTTGATTCTTGAGGGGATTAAAAAAGTAATCTTTT
1 TACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAAAAA-TAA-CTTTT
*
40400 TGGTCATTTCTCAATGGA-TTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCATCAAGGA-TT
64 TGGTCATTTCTCAATGGACTTT-AATAGAGTAGTGGAATTAATAAAAGATCCCCACCAA-GACTT
40463 GATGATG-AGCTAGAGAACTAATCTTTTTCGTCTTTACC
127 GATGATGAAGCTAGAGAACTAATCTTTTTCGTCTTTACC
* * * *
40501 TACTTGGCAGATTA-TTAAAATGTCCTAACTTTTGATTTTTAAGGGGATTAAATAACTAAACTTT
1 TACTTGACAGATTACTT-AAATGTCCTAACTTTTGATTCTTGAGGGGATTAAA-AAAT-AACTTT
40565 TTGGTCATTTCTCAAT
63 TTGGTCATTTCTCAAT
40581 TGACAAATGA
Statistics
Matches: 216, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
164 2 0.01
165 46 0.21
166 147 0.68
167 21 0.10
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (165 bp):
TACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAAAAATAACTTTTTG
GTCATTTCTCAATGGACTTTAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGACTTGATG
ATGAAGCTAGAGAACTAATCTTTTTCGTCTTTACC
Found at i:46381 original size:173 final size:173
Alignment explanation
Indices: 46085--46403 Score: 545
Period size: 173 Copynumber: 1.8 Consensus size: 173
46075 ATATACAGCT
46085 TGCCAATTTTAATAGAACAATTATTTAAGCTTTTAGTGACTTCATTACACGTGAGAATCGTGATT
1 TGCCAATTTTAATAGAACAATTATTTAAGCTTTTAGTGACTTCATTACACGTGAGAATCGTGATT
*
46150 ATAAGAAAATTGATTAATTAATACCCATTAGTTTAATTAAATTATTTGCCTTGGGTTGGCAATTG
66 ATAAGAAAATTGATTAA-TAATACCCATTAGCTTAATTAAATTATTTGCCTTGGGTTGGCAATTG
*
46215 ATAAGATTATTGAATAATACAGCTCATTTCACATACATACGGTC
130 ATAAGATTATGGAATAATACAGCTCATTTCACATACATACGGTC
46259 TGCCAA-TTTAATAGAACAATTATTTAAGCTTTTAGTGACTTCATTACACGTGAGAATCGTGATT
1 TGCCAATTTTAATAGAACAATTATTTAAGCTTTTAGTGACTTCATTACACGTGAGAATCGTGATT
*
46323 ATAAGAAAATTGATT-A-AATACCCATTAGCTTAATTAAATTCATTTTGCGTTGGGGTTGGCAAT
66 ATAAGAAAATTGATTAATAATACCCATTAGCTTAATTAAATT-A-TTTGCCTT-GGGTTGGCAAT
*
46386 TGATATGATTATGGAATA
128 TGATAAGATTATGGAATA
46404 CCGCTGAATT
Statistics
Matches: 138, Mismatches: 4, Indels: 7
0.93 0.03 0.05
Matches are distributed among these distances:
170 23 0.17
171 1 0.01
172 8 0.06
173 100 0.72
174 6 0.04
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (173 bp):
TGCCAATTTTAATAGAACAATTATTTAAGCTTTTAGTGACTTCATTACACGTGAGAATCGTGATT
ATAAGAAAATTGATTAATAATACCCATTAGCTTAATTAAATTATTTGCCTTGGGTTGGCAATTGA
TAAGATTATGGAATAATACAGCTCATTTCACATACATACGGTC
Found at i:50600 original size:12 final size:12
Alignment explanation
Indices: 50583--50609 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
50573 GTTTTTTTGG
50583 TAAAAGTGGTAA
1 TAAAAGTGGTAA
50595 TAAAAGTGGTAA
1 TAAAAGTGGTAA
50607 TAA
1 TAA
50610 GGGAATGGAT
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:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (12 bp):
TAAAAGTGGTAA
Found at i:59312 original size:1 final size:1
Alignment explanation
Indices: 59306--59337 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
59296 AACAAAAGTG
59306 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
59338 GACTTACAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.