Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010709.1 Corchorus capsularis cultivar CVL-1 contig10730, 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: 43757
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:198 original size:21 final size:21
Alignment explanation
Indices: 172--215 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
162 AAAAACTGGA
*
172 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCACCCCATTT
*
193 TTGCTATTCACCACCCCATTT
1 TTGCTAATCACCACCCCATTT
214 TT
1 TT
216 CACGTTTTTT
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:0.20, C:0.34, G:0.07, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCACCCCATTT
Found at i:517 original size:8 final size:8
Alignment explanation
Indices: 504--550 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
494 GGGGAGGCTC
504 AGTGTAAA
1 AGTGTAAA
512 AGTGTAAA
1 AGTGTAAA
*
520 AGTG-CAA
1 AGTGTAAA
*
527 AGAGT-AA
1 AGTGTAAA
*
534 AGGGTAAA
1 AGTGTAAA
542 AGTGTAAA
1 AGTGTAAA
550 A
1 A
551 AATGAGACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 11 0.33
8 22 0.67
ACGTcount: A:0.51, C:0.02, G:0.28, T:0.19
Consensus pattern (8 bp):
AGTGTAAA
Found at i:8388 original size:21 final size:22
Alignment explanation
Indices: 8363--8408 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
8353 TACTTAGGGG
**
8363 TTTGCTATTTACCGCCCCC-CT
1 TTTGCTAAATACCGCCCCCTCT
8384 TTTGCTAAATACCGCCCCCTCT
1 TTTGCTAAATACCGCCCCCTCT
8406 TTT
1 TTT
8409 TATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.13, C:0.39, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTGCTAAATACCGCCCCCTCT
Found at i:8746 original size:15 final size:14
Alignment explanation
Indices: 8695--8787 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
8685 TTATGATTAG
*
8695 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
8709 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
8722 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
8735 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
8748 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
8761 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
8774 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
8787 T
1 T
8788 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:8754 original size:52 final size:51
Alignment explanation
Indices: 8675--8793 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
8665 TTTTTGAATA
* * *
8675 TTAATTAGTTT-T-A-TGATTAGTTTTAATTAGTTAATTA-AAATTACTTAGT
1 TTAATTAGTTTATGATTAATTAGTTCTAATTAGTTAATTATAAATTA-GTA-T
* * *
8724 TT-ATTAGTTTATGTTTAATTAGTATCTAATTAGTTTATTATTAATTAGTAT
1 TTAATTAGTTTATGATTAATTAGT-TCTAATTAGTTAATTATAAATTAGTAT
8775 TTAATTAGTTTATGATTAA
1 TTAATTAGTTTATGATTAA
8794 AATGAAGGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
48 8 0.14
49 3 0.05
51 10 0.18
52 31 0.54
53 5 0.09
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.55
Consensus pattern (51 bp):
TTAATTAGTTTATGATTAATTAGTTCTAATTAGTTAATTATAAATTAGTAT
Found at i:8755 original size:26 final size:26
Alignment explanation
Indices: 8726--8793 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
8716 TACTTAGTTT
8726 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
8752 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
8778 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
8794 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:8841 original size:24 final size:25
Alignment explanation
Indices: 8802--8861 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
8792 AAAATGAAGG
*
8802 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
8825 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
8850 GAAATGAAGTTT
1 AAAATGAAGTTT
8862 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:11243 original size:31 final size:32
Alignment explanation
Indices: 11167--11248 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 32
11157 GCTAAATACC
* *
11167 CAAAAAAATGCCTTATG-TTTTGCTTTTGAGA
1 CAAAATAATCCCTTATGTTTTTGCTTTTGAGA
* * **
11198 TAAAATAATTCCTTATGTTTTTTTTTTTG-GA
1 CAAAATAATCCCTTATGTTTTTGCTTTTGAGA
* *
11229 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
11249 CAAAAATGAG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 32 0.78
32 9 0.22
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.46
Consensus pattern (32 bp):
CAAAATAATCCCTTATGTTTTTGCTTTTGAGA
Found at i:11441 original size:32 final size:32
Alignment explanation
Indices: 11392--11503 Score: 192
Period size: 32 Copynumber: 3.6 Consensus size: 32
11382 AAGGGACTAA
11392 TTTGTCCC-AAAGAAAAACATGAGGGATTTTT
1 TTTGTCCCAAAAGAAAAACATGAGGGATTTTT
11423 TTTGTCCCAAAAGAAAAACATGAGGGATTTTT
1 TTTGTCCCAAAAGAAAAACATGAGGGATTTTT
* *
11455 TTTGTCCCAAAAGAAAAACATAAGGGA-TTAT
1 TTTGTCCCAAAAGAAAAACATGAGGGATTTTT
11486 TTTGTCCCAAAAGAAAAA
1 TTTGTCCCAAAAGAAAAA
11504 ATATAATTTA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
31 29 0.37
32 49 0.63
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (32 bp):
TTTGTCCCAAAAGAAAAACATGAGGGATTTTT
Found at i:13140 original size:23 final size:22
Alignment explanation
Indices: 13106--13148 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
13096 CGAAATCTTT
*
13106 TTATAAATTTTTTTTTAACCTTC
1 TTATAAA-TTTTTGTTAACCTTC
13129 TTATGAAA-TTTTGTTAACCT
1 TTAT-AAATTTTTGTTAACCT
13149 CTCAAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 11 0.61
23 4 0.22
24 3 0.17
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (22 bp):
TTATAAATTTTTGTTAACCTTC
Found at i:13323 original size:22 final size:22
Alignment explanation
Indices: 13174--13389 Score: 90
Period size: 22 Copynumber: 9.7 Consensus size: 22
13164 AAGACCTCTA
13174 TATGAAATTTTGATAACTTC-C-C
1 TATGAAATTTTGATAA--TCACAC
* *
13196 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAATC-ACAC
* **
13219 TATGAGACGTTGATAACCTC-CA-
1 TATGAAATTTTGATAA--TCACAC
* * **
13241 TATGATATATTGATAATCACGT
1 TATGAAATTTTGATAATCACAC
* * *
13263 TATGAAAATTTAAAAACCTC-CA-
1 TATGAAATTTTGATAA--TCACAC
13285 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAATCACAC
*
13307 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAATCACAC
* * * * *
13329 TATGAAATTGTAATAACCTCGC
1 TATGAAATTTTGATAATCACAC
*
13351 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AATC-ACAC
*
13374 TATAAAATTTTGATAA
1 TATGAAATTTTGATAA
13390 ACCTCTTGTA
Statistics
Matches: 147, Mismatches: 30, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
20 5 0.03
21 7 0.05
22 92 0.63
23 38 0.26
24 4 0.03
25 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAC
Found at i:14550 original size:75 final size:75
Alignment explanation
Indices: 14464--14732 Score: 441
Period size: 75 Copynumber: 3.6 Consensus size: 75
14454 AAAATAATAA
*
14464 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAATAAATAAAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
14529 ATAATAAAGT
66 ATAATAAAGT
*
14539 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGACATTTAGGAGATATTTTAAGAAATAAAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
*
14604 ACAATAAAGT
66 ATAATAAAGT
* *
14614 TGAGAATATTTTCTAATTCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAAT-AAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAAT-
*
14678 AATAATAAAGAA
65 AATAATAAAG-T
*
14690 TGAGAATATTTCTCTAAATCTTGCCAGATTGTGGGAGATTTAG
1 TGAGAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAG
14733 AAAATATTAA
Statistics
Matches: 180, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
74 4 0.02
75 137 0.76
76 11 0.06
77 28 0.16
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (75 bp):
TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAATA
ATAATAAAGT
Found at i:15352 original size:22 final size:22
Alignment explanation
Indices: 15321--15504 Score: 110
Period size: 22 Copynumber: 8.5 Consensus size: 22
15311 TGATAACTAC
15321 AAATTTTGATAAACTCCCTATG
1 AAATTTTGATAAACTCCCTATG
** * **
15343 ATGTTTTGATAACCTCAGTATG
1 AAATTTTGATAAACTCCCTATG
* *
15365 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAAACTCCCTATG
** *
15387 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGATAAAC-TCCCTATG
*
15409 AAATTTTGAT-GAC-CCTCTTATG
1 AAATTTTGATAAACTCC-C-TATG
* * **
15431 ATATTTTGA-AAATTAAACTATG
1 AAATTTTGATAAACT-CCCTATG
* * *
15453 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAAACTCCCTATG
**
15475 AAATTTTGATATCCTCCC--TG
1 AAATTTTGATAAACTCCCTATG
15495 AAATTTTGAT
1 AAATTTTGAT
15505 TACTCCATAA
Statistics
Matches: 122, Mismatches: 32, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
20 12 0.10
21 3 0.02
22 102 0.84
23 5 0.04
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAAACTCCCTATG
Found at i:15409 original size:44 final size:44
Alignment explanation
Indices: 15321--15485 Score: 133
Period size: 44 Copynumber: 3.8 Consensus size: 44
15311 TGATAACTAC
** * *
15321 AAATTTTGATAAACTCCCTATGATGTTTTGATAACCTCAGTATG
1 AAATTTTGATAAACTCCCTATGAAATTTTGATAACATCACTATG
* * *
15365 AAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-ACTATG
1 AAATTTTGATAAACTCCCTATGAAATTTTGAT-AACATCACTATG
* * *
15409 AAATTTTGAT-GAC-CCTCTTATGATATTTTGA-AA-ATTAAACTATG
1 AAATTTTGATAAACTCC-C-TATGAAATTTTGATAACA-T-CACTATG
* * *
15453 AAATTTTGATAACCTTCATATGAAATTTTGATA
1 AAATTTTGATAAACTCCCTATGAAATTTTGATA
15486 TCCTCCCTGA
Statistics
Matches: 95, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 2 0.02
44 82 0.86
45 5 0.05
46 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (44 bp):
AAATTTTGATAAACTCCCTATGAAATTTTGATAACATCACTATG
Found at i:15705 original size:44 final size:43
Alignment explanation
Indices: 15582--15803 Score: 166
Period size: 44 Copynumber: 5.0 Consensus size: 43
15572 CCCAGAAATA
* *
15582 CCATTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAAC
1 CCATTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAAC
* * * * ** * *
15625 CTCTTTATGAAATTTTGATAACCTCTTTACAAAATTTTGTTGAC
1 C-CATTATGAAATTTTGATAATCACATTATGAAATTTTGATAAC
*
15669 CCATCTATGAAATTTTGATAATCACATTATGTAATTTTGATAAC
1 CCAT-TATGAAATTTTGATAATCACATTATGAAATTTTGATAAC
* *
15713 CTCGCTTA-GAAATTTTGATAA-CAACACTATGAAATTTTGATAATC
1 C-C-ATTATGAAATTTTGATAATC-ACATTATGAAATTTTGATAA-C
* * *
15758 CGATCTCTATGAAATTTCGATAATCAC-TCTATGAGA-TTTGATAAC
1 CCA--T-TATGAAATTTTGATAATCACAT-TATGAAATTTTGATAAC
15803 C
1 C
15804 TTCTATCAAA
Statistics
Matches: 139, Mismatches: 27, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
43 9 0.06
44 90 0.65
45 8 0.06
46 11 0.08
47 20 0.14
48 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (43 bp):
CCATTATGAAATTTTGATAATCACATTATGAAATTTTGATAAC
Found at i:15969 original size:22 final size:22
Alignment explanation
Indices: 15610--15982 Score: 174
Period size: 22 Copynumber: 16.6 Consensus size: 22
15600 AATCACATTT
* **
15610 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCACTA
**
15632 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCACTA
** * *
15654 CAAAATTTTGTTGACC-CATCTA
1 TGAAATTTTGATAACCTCA-CTA
* * *
15676 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCACTA
* *
15698 TGTAATTTTGATAACCTCGCT-
1 TGAAATTTTGATAACCTCACTA
**
15719 TAGAAATTTTGATAACAACACTA
1 T-GAAATTTTGATAACCTCACTA
*
15742 TGAAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCACTA
* * * *
15767 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCACTA
* *
15789 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCACTA
* *
15809 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCAC-TA
* *
15829 TGAAATTGAGACTTTTATAATCTTCA-TA
1 TGAAA-T-----TTTGATAA-CCTCACTA
*
15857 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCACTA
* * * *
15879 TAAAATTTTAATAACCTCCCCA
1 TGAAATTTTGATAACCTCACTA
*
15901 TGAAATATATT-AGTAACCTGA-TAA
1 TGAAAT-T-TTGA-TAACCTCACT-A
* *
15925 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCACTA
*
15947 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCACTA
*
15969 TGACATTTTGATAA
1 TGAAATTTTGATAA
15983 TCTCTTTGAT
Statistics
Matches: 264, Mismatches: 58, Indels: 58
0.69 0.15 0.15
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 21 0.08
22 168 0.64
23 10 0.04
24 16 0.06
25 17 0.06
26 4 0.02
27 2 0.01
28 7 0.03
29 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCACTA
Found at i:16105 original size:22 final size:21
Alignment explanation
Indices: 16078--16134 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 21
16068 GATCCAATGA
16078 AATTTTGGTAACCACACTATG
1 AATTTTGGTAACCACACTATG
16099 AACTTTTGGTAACCACACTATGG
1 AA-TTTTGGTAACCACACTAT-G
*
16122 AATTTTGATAACC
1 AATTTTGGTAACC
16135 TCCTCATAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 2 0.06
22 28 0.85
23 3 0.09
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (21 bp):
AATTTTGGTAACCACACTATG
Found at i:16365 original size:19 final size:20
Alignment explanation
Indices: 16334--16371 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
16324 TATTAACATT
16334 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
16353 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
16372 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:18231 original size:203 final size:203
Alignment explanation
Indices: 17854--18267 Score: 665
Period size: 203 Copynumber: 2.0 Consensus size: 203
17844 TGACTTTCTT
* * *
17854 ATAATTTAA-GGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTGT
1 ATAATTTAATGGGTCATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAGCGGATTGT
17918 GGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATAAAGTCCCTAAGA
66 GGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATAAAGTCCCTAAGA
* * *
17983 GACACATGTCACCCTTCAGGACCCGCTTGTGTAGTTTTCTAAACTCCACCGCCGGTGTATTGTAT
131 GACACATGTCACCCTTCAGGACCCGCTTCTGTAGTTTTCTAAACTCCACCGACGATGTATTGTAT
18048 AATTTGCC
196 AATTTGCC
* *
18056 ATAATTTAATGGGTCATTATTTGATACACTGACGGTGTAAATTTTGGACTCCACAAGCGGATTGT
1 ATAATTTAATGGGTCATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAGCGGATTGT
** *
18121 GGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAGA-ATTTCAATCTAGTCTCTAAG
66 GGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAA-ATATTTCAATAAAGTCCCTAAG
* *
18185 GGACACATGTCACCCTTCAGGACCCGCTTCTGTAGTTTGT-TAAACTCCACTGACGATGTATTGT
130 AGACACATGTCACCCTTCAGGACCCGCTTCTGTAGTTT-TCTAAACTCCACCGACGATGTATTGT
18249 ATAATTTGCC
194 ATAATTTGCC
18259 -TAATTTAAT
1 ATAATTTAAT
18268 ATATGTATTA
Statistics
Matches: 196, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
202 18 0.09
203 176 0.90
204 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (203 bp):
ATAATTTAATGGGTCATTATATGATACACCGACGGTGTAAATTTTGGACTCCACAAGCGGATTGT
GGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATAAAGTCCCTAAGA
GACACATGTCACCCTTCAGGACCCGCTTCTGTAGTTTTCTAAACTCCACCGACGATGTATTGTAT
AATTTGCC
Found at i:18842 original size:31 final size:30
Alignment explanation
Indices: 18786--18851 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
18776 TGACAATTTA
* *
18786 GAAATATGTTTTTTTAAAAAAGGTACAATTG
1 GAAATATG-TTTTTAAAAAAAGGTACAATCG
18817 GAAATATG-TTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTTAAAAA-AA-GGTACAATCG
18848 GAAA
1 GAAA
18852 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.26
30 2 0.06
31 21 0.68
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (30 bp):
GAAATATGTTTTTAAAAAAAGGTACAATCG
Found at i:19138 original size:32 final size:30
Alignment explanation
Indices: 19061--19155 Score: 129
Period size: 30 Copynumber: 3.1 Consensus size: 30
19051 ACTAAATACT
*
19061 AAAAAAATCCCTTATGTTTTTCTTTTGAGAC
1 AAAAAAATCCCTTATGTTTTT-TTTTGGGAC
*
19092 -AAAAAATCCATTATGTTTTTATTTTGGGAC
1 AAAAAAATCCCTTATGTTTTT-TTTTGGGAC
*
19122 AATAAAAATCCCTTATGTTTTTTTTTTGGAC
1 AA-AAAAATCCCTTATGTTTTTTTTTGGGAC
19153 AAA
1 AAA
19156 TTACTCCCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
30 28 0.49
31 11 0.19
32 18 0.32
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (30 bp):
AAAAAAATCCCTTATGTTTTTTTTTGGGAC
Found at i:19223 original size:28 final size:28
Alignment explanation
Indices: 19183--19245 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
19173 TGGAAAAGCC
19183 ACGTGGATGCCACGTAGACTTCTTGCTG
1 ACGTGGATGCCACGTAGACTTCTTGCTG
19211 ACGTGGATGCCACGTAGACTTCTTGCTG
1 ACGTGGATGCCACGTAGACTTCTTGCTG
19239 ACGTGGA
1 ACGTGGA
19246 AAAGCCACGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (28 bp):
ACGTGGATGCCACGTAGACTTCTTGCTG
Found at i:20043 original size:30 final size:30
Alignment explanation
Indices: 20009--20065 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
19999 ATTAAATCAT
*
20009 GATTGTTAGTCTTGACCATTTTTCAAAAAA
1 GATTGTTAGCCTTGACCATTTTTCAAAAAA
20039 GATTGTTAGCCTTGACCATTTTTCAAA
1 GATTGTTAGCCTTGACCATTTTTCAAA
20066 TTATGGGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (30 bp):
GATTGTTAGCCTTGACCATTTTTCAAAAAA
Found at i:20347 original size:33 final size:33
Alignment explanation
Indices: 20302--20375 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
20292 AATGGTTTAC
* *
20302 GGACTATGACTTAAGGGCACAATGATAAATTAA
1 GGACTATAACTTAAGGACACAATGATAAATTAA
**
20335 GGACTATAACTTAAGGACACAATGATGGATTAA
1 GGACTATAACTTAAGGACACAATGATAAATTAA
20368 GGACTATA
1 GGACTATA
20376 TGGCTTAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (33 bp):
GGACTATAACTTAAGGACACAATGATAAATTAA
Found at i:20505 original size:33 final size:33
Alignment explanation
Indices: 20460--20548 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
20450 GGATTGTGAC
*
20460 TTAAGGGCACAATGATGAATTAAGAACTATGAT
1 TTAAGGGCACAATGATGAATTAAAAACTATGAT
* * ** * *
20493 TTAATGGTACAATGACAAATCAAAAATTATGAT
1 TTAAGGGCACAATGATGAATTAAAAACTATGAT
*
20526 TTAAGGGCACAATAATGAATTAA
1 TTAAGGGCACAATGATGAATTAA
20549 TCAATTGAGG
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (33 bp):
TTAAGGGCACAATGATGAATTAAAAACTATGAT
Found at i:21689 original size:12 final size:12
Alignment explanation
Indices: 21674--21699 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21664 CTGCCCACGA
21674 GGCACCGCCACC
1 GGCACCGCCACC
21686 GGCACCGCCACC
1 GGCACCGCCACC
21698 GG
1 GG
21700 ACGACTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.54, G:0.31, T:0.00
Consensus pattern (12 bp):
GGCACCGCCACC
Found at i:33055 original size:29 final size:29
Alignment explanation
Indices: 32995--33057 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
32985 GCAAAAAGTC
* ** * * *
32995 CCAAAATTGAAGTTCAGGGGGTAGAATGT
1 CCAAAATTGAAATTCAAAGGGCAAAATAT
33024 CCAAAATTGAAATTCAAAGGGCAAAATAT
1 CCAAAATTGAAATTCAAAGGGCAAAATAT
33053 CCAAA
1 CCAAA
33058 CGCTACAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (29 bp):
CCAAAATTGAAATTCAAAGGGCAAAATAT
Found at i:35484 original size:155 final size:155
Alignment explanation
Indices: 35198--35505 Score: 399
Period size: 155 Copynumber: 2.0 Consensus size: 155
35188 ATGTTGACCA
* * * *
35198 TCTTGGCTAAATTTCATCTCAAACGGACTTAAGATGAAAAACTTATGCTATTTTTTCATTTAAGG
1 TCTTGGCCAAATTTCATCTCAAACAGACTTAAGATGAAAAACTTATCCTAGTTTTTCATTTAAGG
* ** ** *
35263 ACAATTTGGGGTGAGAAACCACTTCACCATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTCCA
66 ACAATTTGAGGTGAGAAACCACTTCACCACCATAGGGACCTCGATTTTACTTAGAATTTTTTCCA
*
35328 TAAG-TTTGCGGAGATAATCTAAGTC
131 T-AGCTTTACGGAGATAATCTAAGTC
35353 TCTTGGCCAAATTTCATCTCAAACAGACTT-AGAATGAAAAACTTATCCTAGTTTTTCATTTAAG
1 TCTTGGCCAAATTTCATCTCAAACAGACTTAAG-ATGAAAAACTTATCCTAGTTTTTCATTTAAG
** ** *
35417 GACAATTTGAGGTGAGAAGTCGGTTCACTACCA-AGGAGACCTCGATTTTACTTAG-ATTTTTTC
65 GACAATTTGAGGTGAGAAACCACTTCACCACCATAGG-GACCTCGATTTTACTTAGAATTTTTT-
*
35480 CCATAGCTTTATGGAGATAATCTAAG
128 CCATAGCTTTACGGAGATAATCTAAG
35506 CCTACTGGTG
Statistics
Matches: 132, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
154 14 0.11
155 118 0.89
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (155 bp):
TCTTGGCCAAATTTCATCTCAAACAGACTTAAGATGAAAAACTTATCCTAGTTTTTCATTTAAGG
ACAATTTGAGGTGAGAAACCACTTCACCACCATAGGGACCTCGATTTTACTTAGAATTTTTTCCA
TAGCTTTACGGAGATAATCTAAGTC
Found at i:41001 original size:2 final size:2
Alignment explanation
Indices: 40994--41022 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40984 AAATACTCAA
40994 AT AT 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 AT AT A
41023 GTTTAGATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43024 original size:21 final size:21
Alignment explanation
Indices: 42999--43038 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42989 TAATCCACCC
*
42999 TAAACTAATTGATAATACTAA
1 TAAACTAATTGACAATACTAA
43020 TAAACTAATTGACAATACT
1 TAAACTAATTGACAATACT
43039 TAATCATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (21 bp):
TAAACTAATTGACAATACTAA
Found at i:43129 original size:21 final size:20
Alignment explanation
Indices: 43064--43132 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 20
43054 TTCACACTTT
43064 TCAA-AATTAAATAATTA-A
1 TCAATAATTAAATAATTATA
* * * *
43082 TCAATAAATGATTAAATATAA
1 TCAATAATTAAATAATTAT-A
*
43103 TTAATAATTAAATAATTATTA
1 TCAATAATTAAATAATTA-TA
43124 TCAATAATT
1 TCAATAATT
43133 GTTATAAGCA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
18 4 0.11
19 9 0.24
21 23 0.62
22 1 0.03
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (20 bp):
TCAATAATTAAATAATTATA
Found at i:43176 original size:12 final size:12
Alignment explanation
Indices: 43159--43213 Score: 92
Period size: 12 Copynumber: 4.5 Consensus size: 12
43149 TTAATACAGG
43159 TATCGACGGATA
1 TATCGACGGATA
43171 TATCGAACGGATA
1 TATCG-ACGGATA
43184 TATCGACGGATA
1 TATCGACGGATA
*
43196 TATCGATGGATA
1 TATCGACGGATA
43208 TATCGA
1 TATCGA
43214 GGTATCAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
12 29 0.71
13 12 0.29
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:43193 original size:25 final size:24
Alignment explanation
Indices: 43159--43213 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
43149 TTAATACAGG
43159 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCG-ACGGATA
*
43184 TATCGACGGATATATCGATGGATA
1 TATCGACGGATATATCGACGGATA
43208 TATCGA
1 TATCGA
43214 GGTATCAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (24 bp):
TATCGACGGATATATCGACGGATA
Done.