Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010582.1 Corchorus capsularis cultivar CVL-1 contig10603, 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: 42170
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:20074 original size:16 final size:16
Alignment explanation
Indices: 20053--20086 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
20043 CTTCATTTAC
20053 ATCCTCCTAACTTTTT
1 ATCCTCCTAACTTTTT
20069 ATCCTCCTAACTTTTT
1 ATCCTCCTAACTTTTT
20085 AT
1 AT
20087 GGGGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (16 bp):
ATCCTCCTAACTTTTT
Found at i:22872 original size:419 final size:410
Alignment explanation
Indices: 22279--23182 Score: 1449
Period size: 419 Copynumber: 2.2 Consensus size: 410
22269 AATGGCGACG
* * *
22279 CATAATGAACATA-TGTTTTCAATTCAAGTTTTGCATGATTTAATTTATCTTTATTATATGCCAA
1 CATAATGAACA-AGTGTTTTCATTTTAAG-TTTGTATGATTTAATTTATCTTTATTATATGCCAA
* * *
22343 AAGAGGTATTGTTTGAAAGAAGGAGAAGGTGACGCGTGATGGCTTGTTCTTAGTTTTATCTTTAA
64 AAGAGGTATTGTTTGAAAGAAGGAGAAGGCGACGCGTAATGACTTGTTCTTAGTTTTATCTTTAA
* **
22408 TATAGTATGTATCAAATTAATTGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTTGTTAAG
129 TATAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTCATTAAG
*
22473 AAACAAAAAATGACGGCGCATAATAAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTA-
194 AAACAAAAAATGACGGCGCATAATAAACAAGTGTTTTCATTTTAAGTGTGTATGATTTAATTTAC
*
22537 TTTATTATATGTCAAAAAAGGTATTGTTTGAAAGGAGGAAAAGACGGCGCGTAGAT-ACTTGTTC
259 TTTATTATATGTCAAAAAAGGTATTGTTTGAAAGGAGGAAAAGACGGCGCGTA-ATGACTTATTC
22601 TTAGTTTTATCTTTAATATAGTATGTATCAAATTAAATGAGGAATTGTATCAGAAAATACGACAA
323 TTAGTTTTATCTTT-A-ATA-TA-G-------TTAAATGAGGAATTGTATCAGAAAATACGACAA
22666 AAATTAGTTTGTTAAGAAACAAAAAATGACGGCA
377 AAATTAGTTTGTTAAGAAACAAAAAATGACGGCA
*
22700 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGA-TTAAGTTTATCTTTATTATATGTCAAA
1 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAA-TTTATCTTTATTATATGCCAAA
* *
22764 AGAGGTATTGTTTGAAAGGAGGA-AAGGCGGCGCGTAATGACTTGTTCTTAGTTTTATCTTTAAT
65 AGAGGTATTGTTTGAAAGAAGGAGAAGGCGACGCGTAATGACTTGTTCTTAGTTTTATCTTTAAT
22828 ATAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTCATTAAGA
130 ATAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTCATTAAGA
* *
22893 AACAAAAAATGACGGCGCATAATGAACACGTGTTTTCATTTTAAGTGTGTATGATTTAATTTATC
195 AACAAAAAATGACGGCGCATAATAAACAAGTGTTTTCATTTTAAGTGTGTATGATTTAATTTA-C
* * *
22958 TTTATTATATGTCTAAAGAGGTATTGTTTGAAAGGAGGAAAAGGCGGCGCGTAATGACTTATTCT
259 TTTATTATATGTCAAAAAAGGTATTGTTTGAAAGGAGGAAAAGACGGCGCGTAATGACTTATTCT
*
23023 TAGTTTTATCTTTAATATAGTTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTTGT
324 TAGTTTTATCTTTAATATAGTTAAATGAGGAATTGTATCAGAAAATACGACAAAAATTAGTTTGT
23088 TAAGAAACAAAAAATGACGGCA
389 TAAGAAACAAAAAATGACGGCA
23110 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTATCTTTATTATATGCCAAAA
1 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTATCTTTATTATATGCCAAAA
23175 GAGGTATT
66 GAGGTATT
23183 AATGTTTTTT
Statistics
Matches: 456, Mismatches: 21, Indels: 23
0.91 0.04 0.05
Matches are distributed among these distances:
410 133 0.29
411 4 0.01
417 1 0.00
418 2 0.00
419 166 0.36
420 55 0.12
421 95 0.21
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (410 bp):
CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTATCTTTATTATATGCCAAAA
GAGGTATTGTTTGAAAGAAGGAGAAGGCGACGCGTAATGACTTGTTCTTAGTTTTATCTTTAATA
TAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTCATTAAGAA
ACAAAAAATGACGGCGCATAATAAACAAGTGTTTTCATTTTAAGTGTGTATGATTTAATTTACTT
TATTATATGTCAAAAAAGGTATTGTTTGAAAGGAGGAAAAGACGGCGCGTAATGACTTATTCTTA
GTTTTATCTTTAATATAGTTAAATGAGGAATTGTATCAGAAAATACGACAAAAATTAGTTTGTTA
AGAAACAAAAAATGACGGCA
Found at i:22875 original size:210 final size:211
Alignment explanation
Indices: 22279--23182 Score: 1437
Period size: 210 Copynumber: 4.3 Consensus size: 211
22269 AATGGCGACG
* * * *
22279 CATAATGAACATA-TGTTTTCAATTCAAGTTTTGCATGATTTAATTTATCTTTATTATATGCCAA
1 CATAATGAACA-AGTGTTTTCATTTTAAG-TTTGTATGATTTAATTTATCTTTATTATATGTCAA
* * * * * *
22343 AAGAGGTATTGTTTGAAAGAAGGAGAAGGTGACGCGTGATGGCTTGTTCTTAGTTTTATCTTTAA
64 AAGAGGTATTGTTTGAAAGGAGGAAAAGGCGGCGCGTAATGACTTGTTCTTAGTTTTATCTTTAA
*
22408 TATAGTATGTATCAAATTAATTGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTTGTTAAG
129 TATAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTTGTTAAG
*
22473 AAACAAAAAATGACGGCG
194 AAACAAAAAATGACGGCA
*
22491 CATAATAAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTA--TTTATTATATGTCAAAA
1 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTATCTTTATTATATGTCAAAA
* *
22554 AAGGTATTGTTTGAAAGGAGGAAAAGACGGCGCGTAGAT-ACTTGTTCTTAGTTTTATCTTTAAT
66 GAGGTATTGTTTGAAAGGAGGAAAAGGCGGCGCGTA-ATGACTTGTTCTTAGTTTTATCTTTAAT
*
22618 ATAGTATGTATCAAATTAAATGAGGAATTGTATCAGAAAATACGACAAAAATTAGTTTGTTAAGA
130 ATAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTTGTTAAGA
22683 AACAAAAAATGACGGCA
195 AACAAAAAATGACGGCA
22700 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGA-TTAAGTTTATCTTTATTATATGTCAAA
1 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAA-TTTATCTTTATTATATGTCAAA
22764 AGAGGTATTGTTTGAAAGGAGG-AAAGGCGGCGCGTAATGACTTGTTCTTAGTTTTATCTTTAAT
65 AGAGGTATTGTTTGAAAGGAGGAAAAGGCGGCGCGTAATGACTTGTTCTTAGTTTTATCTTTAAT
**
22828 ATAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTCATTAAGA
130 ATAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTTGTTAAGA
*
22893 AACAAAAAATGACGGCG
195 AACAAAAAATGACGGCA
* * *
22910 CATAATGAACACGTGTTTTCATTTTAAGTGTGTATGATTTAATTTATCTTTATTATATGTCTAAA
1 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTATCTTTATTATATGTCAAAA
*
22975 GAGGTATTGTTTGAAAGGAGGAAAAGGCGGCGCGTAATGACTTATTCTTAGTTTTATCTTT-A-A
66 GAGGTATTGTTTGAAAGGAGGAAAAGGCGGCGCGTAATGACTTGTTCTTAGTTTTATCTTTAATA
23038 TA-TA-G-------TTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTTGTTAAGAA
131 TAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTTGTTAAGAA
23094 ACAAAAAATGACGGCA
196 ACAAAAAATGACGGCA
*
23110 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTATCTTTATTATATGCCAAAA
1 CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTATCTTTATTATATGTCAAAA
23175 GAGGTATT
66 GAGGTATT
23183 AATGTTTTTT
Statistics
Matches: 650, Mismatches: 34, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
200 133 0.20
207 1 0.00
208 6 0.01
209 193 0.30
210 197 0.30
211 97 0.15
212 23 0.04
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (211 bp):
CATAATGAACAAGTGTTTTCATTTTAAGTTTGTATGATTTAATTTATCTTTATTATATGTCAAAA
GAGGTATTGTTTGAAAGGAGGAAAAGGCGGCGCGTAATGACTTGTTCTTAGTTTTATCTTTAATA
TAGTATGTATCAAATTAAATGAGGAATTGTCTCAGAAAATACGACAAAAATTAGTTTGTTAAGAA
ACAAAAAATGACGGCA
Found at i:25602 original size:2 final size:2
Alignment explanation
Indices: 25595--25621 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25585 TTGACTTAGC
25595 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
25622 TGTGCCTATT
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
Found at i:26977 original size:22 final size:22
Alignment explanation
Indices: 26907--27319 Score: 168
Period size: 22 Copynumber: 19.0 Consensus size: 22
26897 TTATCCTTCT
*
26907 TATGAAATATTT-TTAACCTCTC-
1 TATGAAAT-TTTGATAACCTC-CA
* * *
26929 TAAGAAATTTTGA-AGATCTCAA
1 TATGAAATTTTGATA-ACCTCCA
*
26951 TATGAAATTTTGATAACTTCTCA
1 TATGAAATTTTGATAACCTC-CA
26974 -ATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCA
* * * **
26995 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCA
* * *
27017 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
27039 TATG-AATTGTT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
*
27060 CTCTGAAATTTTGATAA--TCACA
1 -TATGAAATTTTGATAACCTC-CA
*
27082 CTATGAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCTC-CA
*
27105 TATGAAATTTTGATAAATCTTCC-
1 TATGAAATTTTGAT-AA-CCTCCA
*
27128 TAT-AGAATTTTGATAAACCTCCC
1 TATGA-AATTTTGAT-AACCTCCA
* * * * *
27151 TATAAAATATTGATAACTTTCT
1 TATGAAATTTTGATAACCTCCA
* *
27173 TATGAAATCTTAATAA----C-
1 TATGAAATTTTGATAACCTCCA
* * *
27190 TA-CAAATTTTGATAAGCTCCT
1 TATGAAATTTTGATAACCTCCA
* * *
27211 TATGAAATTTTGATTTACATAC-
1 TATGAAATTTTGA-TAACCTCCA
*
27233 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CA
* **
27255 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
* * *
27276 CTATAAAATTTTTATAACCTTCA
1 -TATGAAATTTTGATAACCTCCA
*
27299 TATGAAATTTTGATATCCTCC
1 TATGAAATTTTGATAACCTCC
27320 CTGAATTTTA
Statistics
Matches: 298, Mismatches: 62, Indels: 62
0.71 0.15 0.15
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
20 3 0.01
21 21 0.07
22 209 0.70
23 45 0.15
24 7 0.02
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:26998 original size:44 final size:44
Alignment explanation
Indices: 26907--27318 Score: 203
Period size: 44 Copynumber: 9.5 Consensus size: 44
26897 TTATCCTTCT
* * * *
26907 TATGAAATATTT-TTAACCTCTCTAAGAAATTTTGA-AGATCTCAA
1 TATGAAAT-TTTGATAACCTCTCTATGAAATTTTGATA-ACCTCCA
* *
26951 TATGAAATTTTGATAACTTCTCAATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCTCTATGAAATTTTGATAACCTCCA
* * * * * *
26995 TATGATATATTGATAACCACGT-TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTC-TCTATGAAATTTTGATAACCTCCA
* * * *
27039 TATG-AATTGTT-AGTAATCACACTCTGAAATTTTGATAA--TCACA
1 TATGAAATT-TTGA-TAACCTCTCTATGAAATTTTGATAACCTC-CA
* * *
27082 CTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTCC-
1 -TATGAAATTTTGATAACCTCTCTATGAAATTTTGAT-AA-CCTCCA
* * * * * *
27128 TAT-AGAATTTTGATAAACCTCCCTATAAAATATTGATAACTTTCT
1 TATGA-AATTTTGAT-AACCTCTCTATGAAATTTTGATAACCTCCA
* * * * *
27173 TATGAAATCTTAATAA-----CTA-CAAATTTTGATAAGCTCCT
1 TATGAAATTTTGATAACCTCTCTATGAAATTTTGATAACCTCCA
* * * *
27211 TATGAAATTTTGATTTACAT-ACTATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGA-TAACCTCTCTATGAAATTTTGATAACCTC-CA
* ** * * *
27255 TATGAAATTTTGA-AAACTAAACTATAAAATTTTTATAACCTTCA
1 TATGAAATTTTGATAACCT-CTCTATGAAATTTTGATAACCTCCA
*
27299 TATGAAATTTTGATATCCTC
1 TATGAAATTTTGATAACCTC
27319 CCTGAATTTT
Statistics
Matches: 285, Mismatches: 54, Indels: 58
0.72 0.14 0.15
Matches are distributed among these distances:
38 25 0.09
39 5 0.02
42 4 0.01
43 12 0.04
44 181 0.64
45 35 0.12
46 20 0.07
47 1 0.00
48 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCTCTATGAAATTTTGATAACCTCCA
Found at i:27136 original size:23 final size:23
Alignment explanation
Indices: 27065--27166 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 23
27055 TCACACTCTG
* * * *
27065 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* * *
27087 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* *
27109 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
27132 GAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
27155 AAATATTGATAA
1 AAATTTTGATAA
27167 CTTTCTTATG
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
22 27 0.42
23 38 0.58
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:27357 original size:19 final size:19
Alignment explanation
Indices: 27304--27347 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
27294 CTTCATATGA
27304 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
*
27323 AATTTTAATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
27342 AATTTT
1 AATTTT
27348 TGATTACTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:27613 original size:22 final size:22
Alignment explanation
Indices: 27496--27658 Score: 99
Period size: 22 Copynumber: 7.5 Consensus size: 22
27486 TGTTGATCCT
* *
27496 TCTATGAAATTCTGATAATAAC
1 TCTATGAAATTTTGATAATCAC
* **
27518 AT-TATGTAATTTTGATAAAAAC
1 -TCTATGAAATTTTGATAATCAC
* *
27540 ACTATGAAATTTTGATAATC-T
1 TCTATGAAATTTTGATAATCAC
*
27561 TCATAT-AATTTTTGATAATCCGATC
1 TC-TATGAAATTTTGATAAT-C-A-C
*
27586 TCTATGAAATTTCGATAATCAC
1 TCTATGAAATTTTGATAATCAC
*
27608 TCTATGAGA-TTTGATAA-C-C
1 TCTATGAAATTTTGATAATCAC
* * *
27627 TTCTATCAAATTTTGGTACTC-C
1 -TCTATGAAATTTTGATAATCAC
27649 T-TATGAAATT
1 TCTATGAAATT
27659 GAGACTTTTA
Statistics
Matches: 110, Mismatches: 20, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
19 1 0.01
20 16 0.15
21 27 0.25
22 47 0.43
23 2 0.02
24 4 0.04
25 13 0.12
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (22 bp):
TCTATGAAATTTTGATAATCAC
Found at i:27693 original size:22 final size:22
Alignment explanation
Indices: 27542--27784 Score: 80
Period size: 22 Copynumber: 10.9 Consensus size: 22
27532 ATAAAAACAC
*
27542 TATGAAATTTTGATAATCTTCA
1 TATGAAATTTTGATAACCTTCA
*
27564 TAT-AATTTTTGATAATCCGATCTC-
1 TATGAAATTTTGATAA-CC--T-TCA
*
27588 TATGAAATTTCGATAATCAC-TC-
1 TATGAAATTTTGATAA-C-CTTCA
*
27610 TATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAACCTTCA
* * *
27630 TATCAAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATA-ACCTTCA
*
27652 TGAAATTGAGACTTTT-ATAACCTTCA
1 T---A-TGA-AATTTTGATAACCTTCA
**
27678 TATGAAATTTTGATAA-CAACA
1 TATGAAATTTTGATAACCTTCA
* * *
27699 CTATAAAATTTTGATAACCTCCC
1 -TATGAAATTTTGATAACCTTCA
* * *
27722 CATGAAATATT-AGTAACC-TCC
1 TATGAAATTTTGA-TAACCTTCA
* *
27743 TAATGAAATTTTGTTAACC-ACA
1 T-ATGAAATTTTGATAACCTTCA
27765 CTATGAAATTCTT-ATAACCT
1 -TATGAAATT-TTGATAACCT
27785 CGCTACGACA
Statistics
Matches: 165, Mismatches: 31, Indels: 49
0.67 0.13 0.20
Matches are distributed among these distances:
19 1 0.01
20 8 0.05
21 35 0.21
22 80 0.48
23 6 0.04
24 4 0.02
25 19 0.12
26 7 0.04
27 5 0.03
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:27946 original size:22 final size:21
Alignment explanation
Indices: 27921--27977 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
27911 TACACTATGG
*
27921 AATTTTGATAACCTCCTCATGA
1 AATTTTGATAACCT-CTCATAA
* * * *
27943 AATTATAATAATCATCTTATAA
1 AATTTTGATAA-CCTCTCATAA
27965 AATTTTGATAACC
1 AATTTTGATAACC
27978 ACATAGAGAC
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (21 bp):
AATTTTGATAACCTCTCATAA
Found at i:28171 original size:19 final size:20
Alignment explanation
Indices: 28140--28177 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28130 TATTAACATT
28140 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
28159 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
28178 AATAATAGTA
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:30054 original size:32 final size:30
Alignment explanation
Indices: 29987--30050 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
29977 GGCAATTTAG
* * *
29987 AAATATGTTTTAAAAAAGGGGTAGAATTGG
1 AAATATGTTTTAAAAAAGGGGTACAATCGA
30017 AAATATGTTTTAAGAATAA-GGGTACAATCGA
1 AAATATGTTTTAA-AA-AAGGGGTACAATCGA
30048 AAA
1 AAA
30051 ATATAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 13 0.45
31 14 0.48
32 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.28
Consensus pattern (30 bp):
AAATATGTTTTAAAAAAGGGGTACAATCGA
Found at i:36589 original size:154 final size:157
Alignment explanation
Indices: 36285--36589 Score: 501
Period size: 154 Copynumber: 2.0 Consensus size: 157
36275 GTCAATGGAT
*
36285 TAGTAGAATTTATAATTTTTCTAAATAAACGAAAAATTGAAAAAGGAAAAAAATAGTAGAGAAAA
1 TAGTAGAATTTATAATTTTTCTAAATAAACGAAAAAATGAAAAAGGAAAAAAATAGTAGAGAAAA
*
36350 ATAGTCAACGGATTAGTAGAATACTCTGGAAAAAAAAACAGAAAGATTAGTAGAGTATAATTTCT
66 ATAGTCAACGGATTAGTAG-ATACTCTGGAAAAAAAAACAGAAAGATTAGTAGAGTAGAATTTCT
36415 CTAAAAAATAAATACATTAAAAAATTGA
130 CTAAAAAATAAATACATTAAAAAATTGA
* *
36443 TAGTAGAGTTTATAATTTTTTTAAATAAAC-AAAAAATGAAAAAGGAAAAAAATAGTAGAGAAAA
1 TAGTAGAATTTATAATTTTTCTAAATAAACGAAAAAATGAAAAAGGAAAAAAATAGTAGAGAAAA
*
36507 ATAGTCAACGGATTAG-AG-TACTCTGGCAAAAAAAAA-AGAAAGATTAGTAGATTAGAATTTCT
66 ATAGTCAACGGATTAGTAGATACTCTGG-AAAAAAAAACAGAAAGATTAGTAGAGTAGAATTTCT
* *
36569 CTAAAAGATAAATACCTTAAA
130 CTAAAAAATAAATACATTAAA
36590 GAAGTCCTAT
Statistics
Matches: 139, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
154 51 0.37
155 9 0.06
156 2 0.01
157 49 0.35
158 28 0.20
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (157 bp):
TAGTAGAATTTATAATTTTTCTAAATAAACGAAAAAATGAAAAAGGAAAAAAATAGTAGAGAAAA
ATAGTCAACGGATTAGTAGATACTCTGGAAAAAAAAACAGAAAGATTAGTAGAGTAGAATTTCTC
TAAAAAATAAATACATTAAAAAATTGA
Found at i:36758 original size:31 final size:31
Alignment explanation
Indices: 36720--36779 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
36710 TATGTTAGAC
36720 AAATAAGGATATAATAGGC-ATTTCAAAAGTT
1 AAATAAGGATATAATAGGCGA-TTCAAAAGTT
*
36751 AAATAAGGGTATAATAGGCGATTCAAAAG
1 AAATAAGGATATAATAGGCGATTCAAAAG
36780 CTTTACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (31 bp):
AAATAAGGATATAATAGGCGATTCAAAAGTT
Found at i:36811 original size:143 final size:143
Alignment explanation
Indices: 36660--36948 Score: 524
Period size: 143 Copynumber: 2.0 Consensus size: 143
36650 ATAAATAATA
*
36660 ATAAAATCAACAGAATTAAAAATTATTTGTATAATGGCAATTGTTAGAAATATGTTAGACAAATA
1 ATAAAATCAACAGAATTAAAAATTATTTGTATAATGGCAATTGTTAGAAATATGTTAAACAAATA
36725 AGGATATAATAGGCATTTCAAAAGTTAAATAAGGGTATAATAGGCGATTCAAAAGCTTTACAAAA
66 AGGATATAATAGGCATTTCAAAAGTTAAATAAGGGTATAATAGGCGATTCAAAAGCTTTACAAAA
36790 CTCATACTTTTAT
131 CTCATACTTTTAT
*
36803 ATAAAATCAACAGAATTAAAAATTATTTGTATAATGGCAATTTTTAGAAATATGTTAAACAAATA
1 ATAAAATCAACAGAATTAAAAATTATTTGTATAATGGCAATTGTTAGAAATATGTTAAACAAATA
* *
36868 AGGATATAATAGGCGTTTCAAAAGTTAAATAAGGGTATAATAGGCGATTCAAAAGTTTTACAAAA
66 AGGATATAATAGGCATTTCAAAAGTTAAATAAGGGTATAATAGGCGATTCAAAAGCTTTACAAAA
* *
36933 CTCGTATTTTTAT
131 CTCATACTTTTAT
36946 ATA
1 ATA
36949 TAGTATAGAT
Statistics
Matches: 140, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
143 140 1.00
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (143 bp):
ATAAAATCAACAGAATTAAAAATTATTTGTATAATGGCAATTGTTAGAAATATGTTAAACAAATA
AGGATATAATAGGCATTTCAAAAGTTAAATAAGGGTATAATAGGCGATTCAAAAGCTTTACAAAA
CTCATACTTTTAT
Found at i:36899 original size:31 final size:31
Alignment explanation
Indices: 36863--36924 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
36853 TATGTTAAAC
*
36863 AAATAAGGATATAATAGGCGTTTCAAAAGTT
1 AAATAAGGATATAATAGGCGATTCAAAAGTT
*
36894 AAATAAGGGTATAATAGGCGATTCAAAAGTT
1 AAATAAGGATATAATAGGCGATTCAAAAGTT
36925 TTACAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (31 bp):
AAATAAGGATATAATAGGCGATTCAAAAGTT
Found at i:37775 original size:15 final size:16
Alignment explanation
Indices: 37749--37781 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
37739 TATATATGGG
37749 ATAAATAATAATTATT
1 ATAAATAATAATTATT
37765 ATAAA-AATAATTATT
1 ATAAATAATAATTATT
37780 AT
1 AT
37782 TTATTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAATAATAATTATT
Found at i:37993 original size:3 final size:3
Alignment explanation
Indices: 37985--38030 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
37975 TGGATGGATG
37985 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38031 ATATACTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39717 original size:14 final size:14
Alignment explanation
Indices: 39698--39729 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39688 TAATAATTGC
39698 GACTGTAACAAAAA
1 GACTGTAACAAAAA
*
39712 GACTGTAACGAAAA
1 GACTGTAACAAAAA
39726 GACT
1 GACT
39730 ATATAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.19, T:0.16
Consensus pattern (14 bp):
GACTGTAACAAAAA
Done.