Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012446.1 Corchorus capsularis cultivar CVL-1 contig12467, 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: 10228
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Found at i:1019 original size:333 final size:332
Alignment explanation
Indices: 365--1972 Score: 2516
Period size: 333 Copynumber: 4.8 Consensus size: 332
355 TGGAAGAGAT
* *
365 AGCCGGGCCCCCGGAACGCGTTTTTAGTAAAAAACCGTAATGGTTAGTACATGATTTCGGCTAAA
1 AGCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAA
* * * * *
430 ATTTTGCAAAATTTGACCCGAAACGTTTCTCCTCAATTTTCGGCAATAAATAATCATGAAAAAAA
66 ATTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATA
* * *
495 TACAATTCAACGCCAAAAGATTGAAGGGCTTCTCACGAATGTAATATCATTTTTCCTATTTTTTT
131 TACAACTCAACGCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTTT
*
560 CGAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAAT-ACTTAATTCC
196 CGAATTAATTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCA-TTAATTCC
*
624 AAAGTGGGTGATCTTTCACTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAAATCAT
260 AAAGTGGGTGATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCC-AAAAATCAT
689 GCAAAACTG
324 GCAAAACTG
**
698 AGCCGGGCCCCCGGAACGCGTTTGAAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAA
1 AGCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAA
* *
763 ATTTTGCAAAATTTGACCCGAAACGTTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATA
66 ATTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATA
* *
828 TACAACTCAACATCAAAAAGATTGAAGGCCTTCTCACGCATGTAATATCATTTTTCCTATTTTTT
131 TACAACTCAAC-GCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTT
* * *
893 TCGAATTAATTCCTAATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCATTGATTCC
195 TCGAATTAATTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCATTAATTCC
* * * *
958 AAGGTGGGTGATCTTTCGTTATATGAATATAGATATTGCAATGAGTCTTGTTGTCAAAAATCATT
260 AAAGTGGGTGATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATG
*
1023 CAAAACTT
325 CAAAACTG
* * * *
1031 AGCCGGGCCTCCAGAACGCGTTTTTAGTCAAAAATCGTGATGGTTAGTACATGATTTCTGCTAAA
1 AGCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAA
* *
1096 ATTTTGCAAAATTTGATCCTAAACATTTCTCCTCAATTTTCGGCCTTAAATACTCATGAAAAATA
66 ATTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATA
* * * *
1161 TATAATTTAACGCCAAAAAGATTGAAGGGTTTCTCACGCATGTAATATCATTTTTCCTATTTTTT
131 TACAACTCAACG-CAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTT
* *
1226 TCGAATTAATTTCTAATTAAATAGAAACCGGATTGAGATGCTCGTAAAAACAAATCATTAATTCC
195 TCGAATTAATTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCATTAATTCC
* * * * *
1291 AAGGTGGGTGATCTTTCGTTATATGAATATAGATATTGTAATGAGTCTTGTTGTCAAAAATCATT
260 AAAGTGGGTGATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATG
*
1356 CAAAACTT
325 CAAAACTG
* * * * *
1364 AGCCGGGCCTCCAGAACACGTTTTTAGTTAAAAACCGTGATGGTTAGTAAATGATTTCGGCTAAA
1 AGCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAA
* *
1429 ATTTTGCAAATTTTGATCCGAAACATTTCTCCTCAATTTTTGGCCATAAATACTCATGAAAAATA
66 ATTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATA
* *
1494 TACAACTCAACGCAAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTATTCTTATTTTTT
131 TACAACTCAACGC-AAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTT
* * ** *
1559 TCGAATTAGTTTCTGATTAAATCGAAACCGGGTTGAGATGCTCGTAAAAGGAAATCCTTAATTCC
195 TCGAATTAATTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCATTAATTCC
1624 AAAGTGGGTGATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATG
260 AAAGTGGGTGATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATG
1689 CAAAACTG
325 CAAAACTG
1697 AGCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAA
1 AGCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAA
* * * *
1762 ATTTTGCAAAATTTGGTCCGAAACATTTCTCCTCAATTTTTGGCCATAAGTACTTATGAAAAATA
66 ATTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATA
** * *
1827 TACAACTCAACAAAAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCAATTTTCTTATTTCTT
131 TACAACTCAAC-GCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTT-TT
* * *
1892 TTCGAATTAATTTCTGATTAAATCGAAACCGGGTTGAGATGCTCGTAAAAAGAAATCCTTAATTC
194 TTCGAATTAATTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCATTAATTC
*
1957 CATAGTGGGTGATCTT
259 CAAAGTGGGTGATCTT
1973 GTAGACACCC
Statistics
Matches: 1183, Mismatches: 86, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
332 1 0.00
333 942 0.80
334 239 0.20
335 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (332 bp):
AGCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAA
ATTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATA
TACAACTCAACGCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTTT
CGAATTAATTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCATTAATTCCA
AAGTGGGTGATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGC
AAAACTG
Found at i:5935 original size:27 final size:26
Alignment explanation
Indices: 5883--5979 Score: 108
Period size: 26 Copynumber: 3.7 Consensus size: 26
5873 CAGTAATCAA
* * *
5883 TAAAAAGAGTAAGGAACGGTATTCAG
1 TAAAAAGAGTAAGAAAAGATATTCAG
*
5909 TAAAAAGAATAAGAAAAGAGTCA-TCAG
1 TAAAAAGAGTAAGAAAAGA-T-ATTCAG
*
5936 TAAAAAGAGTAGGAAATA-ATATTCAG
1 TAAAAAGAGTAAGAAA-AGATATTCAG
5962 TAAAAAGAGTAAGAAAAG
1 TAAAAAGAGTAAGAAAAG
5980 CGCGATAGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
25 2 0.03
26 35 0.59
27 20 0.34
28 2 0.03
ACGTcount: A:0.56, C:0.05, G:0.22, T:0.18
Consensus pattern (26 bp):
TAAAAAGAGTAAGAAAAGATATTCAG
Found at i:5941 original size:53 final size:53
Alignment explanation
Indices: 5878--5979 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
5868 GTAATCAGTA
**
5878 ATCAATAAAAAGAGTAAGG-AACGGTATTCAGTAAAAAGAATAAGAAAAGAGTC
1 ATCAATAAAAAGAGT-AGGAAACAATATTCAGTAAAAAGAATAAGAAAAGAGTC
* * *
5931 ATCAGTAAAAAGAGTAGGAAATAATATTCAGTAAAAAGAGTAAGAAAAG
1 ATCAATAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAATAAGAAAAG
5980 CGCGATAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 3 0.07
53 40 0.93
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.18
Consensus pattern (53 bp):
ATCAATAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAATAAGAAAAGAGTC
Found at i:6112 original size:35 final size:35
Alignment explanation
Indices: 6053--6119 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
6043 TTGAAAAAGC
* * * *
6053 AATCAGTAAAGAGTAAAATGGTAAAAGGTAATGGT
1 AATCAGTAAACAATAAAATAGTAAAAAGTAATGGT
*
6088 AATCAGTAAACAATGAAATAGTAAAAAGTAAT
1 AATCAGTAAACAATAAAATAGTAAAAAGTAAT
6120 CAGTAAAGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.54, C:0.04, G:0.19, T:0.22
Consensus pattern (35 bp):
AATCAGTAAACAATAAAATAGTAAAAAGTAATGGT
Found at i:6189 original size:22 final size:22
Alignment explanation
Indices: 6150--6439 Score: 197
Period size: 21 Copynumber: 13.5 Consensus size: 22
6140 GAATAATAGA
*
6150 GTAATCAGT-GAAAG-AAAATG
1 GTAATCAGTAAAAAGTAAAATG
** *
6170 GTAAAGAGTAAAAAGTAAAAAG
1 GTAATCAGTAAAAAGTAAAATG
*
6192 GTAATCAGTAAAAAATAAAATG
1 GTAATCAGTAAAAAGTAAAATG
* *
6214 GTAATCAGT-AAGAGTAAAATA
1 GTAATCAGTAAAAAGTAAAATG
* * *
6235 GTAATCGGCAAAAAGTAAAA-A
1 GTAATCAGTAAAAAGTAAAATG
*
6256 GTAATCAGTAAGAAGTAAAA-G
1 GTAATCAGTAAAAAGTAAAATG
* *
6277 GTAAACAGT-AAGAGTATAAA-G
1 GTAATCAGTAAAAAGTA-AAATG
* * *
6298 GTAATCAGTGAAGAGTAAAAAG
1 GTAATCAGTAAAAAGTAAAATG
* * * * *
6320 ATAATTAGT-AAGAGTCAAATA
1 GTAATCAGTAAAAAGTAAAATG
** *
6341 GTAATCAGTAAAAAACAAAAAGG
1 GTAATCAGT-AAAAAGTAAAATG
* *
6364 GCAATCAGTAAAAAGT-AAAGG
1 GTAATCAGTAAAAAGTAAAATG
*
6385 GTAATCAGAAAAAAAGTAAAATG
1 GTAATCAG-TAAAAAGTAAAATG
* * * *
6408 GTAGTTAGTAAAGAGT--AATA
1 GTAATCAGTAAAAAGTAAAATG
6428 GTAATCAGTAAA
1 GTAATCAGTAAA
6440 GAGTTTTCAA
Statistics
Matches: 212, Mismatches: 48, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
20 25 0.12
21 89 0.42
22 74 0.35
23 24 0.11
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.20
Consensus pattern (22 bp):
GTAATCAGTAAAAAGTAAAATG
Found at i:6264 original size:106 final size:106
Alignment explanation
Indices: 6149--6397 Score: 268
Period size: 106 Copynumber: 2.3 Consensus size: 106
6139 GGAATAATAG
* *
6149 AGTAATCAGTGA-AAG-AAAATGGTAAAGAGTAAAAAGTAAAAAGGTAATCAGTAAAAAATAAAA
1 AGTAATCAGTAAGAAGTAAAA-GGTAAACAGT-AAAAGTAAAAAGGTAATCAGTAAAAAATAAAA
* *
6212 TGGTAATCAGTAAGAGTAAAATAGTAATCGGCAAAAAGTAAAA
64 AGATAATCAGTAAGAGTAAAATAGTAATCGGCAAAAAGTAAAA
* * * * *
6255 AGTAATCAGTAAGAAGTAAAAGGTAAACAGTAAGAGTATAAAGGTAATCAGTGAAGAGTAAAAAG
1 AGTAATCAGTAAGAAGTAAAAGGTAAACAGTAAAAGTAAAAAGGTAATCAGTAAAAAATAAAAAG
* * * * **
6320 ATAATTAGTAAGAGTCAAATAGTAATCAGTAAAAAACAAAA
66 ATAATCAGTAAGAGTAAAATAGTAATCGGCAAAAAGTAAAA
* * * * *
6361 AGGGCAATCAGTAAAAAGTAAAGGGTAATCAGAAAAA
1 A--GTAATCAGTAAGAAGTAAAAGGTAAACAGTAAAA
6398 AAGTAAAATG
Statistics
Matches: 118, Mismatches: 21, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
106 74 0.63
107 12 0.10
108 32 0.27
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.18
Consensus pattern (106 bp):
AGTAATCAGTAAGAAGTAAAAGGTAAACAGTAAAAGTAAAAAGGTAATCAGTAAAAAATAAAAAG
ATAATCAGTAAGAGTAAAATAGTAATCGGCAAAAAGTAAAA
Found at i:6345 original size:43 final size:41
Alignment explanation
Indices: 6248--6351 Score: 113
Period size: 43 Copynumber: 2.5 Consensus size: 41
6238 ATCGGCAAAA
* *
6248 AGTAAAAAGTAATCAGTAAGAAGTAAAAGGTAAACAGTAAG
1 AGTATAAAGTAATCAGTAAGAAGTAAAAGATAAACAGTAAG
**
6289 AGTATAAAGGTAATCAGTGAAG-AGTAAAAAGATAATTAGTAAG
1 AGTATAAA-GTAATCAGT-AAGAAGT-AAAAGATAAACAGTAAG
6332 AGTCA-AATAGTAATCAGTAA
1 AGT-ATAA-AGTAATCAGTAA
6352 AAAACAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
41 7 0.13
42 14 0.26
43 31 0.57
44 2 0.04
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (41 bp):
AGTATAAAGTAATCAGTAAGAAGTAAAAGATAAACAGTAAG
Found at i:6647 original size:35 final size:34
Alignment explanation
Indices: 6604--6684 Score: 117
Period size: 35 Copynumber: 2.4 Consensus size: 34
6594 AATAGTGAAG
* *
6604 AGTAAAGAGTAATCAGCAAAGTAAAATGGTAAAA
1 AGTAAAGAGTAATCAGCAAAGAAAAAGGGTAAAA
* *
6638 AGTAAAAGAGTAATCAGTAAAGAAAAAGGGTAAAG
1 AGT-AAAGAGTAATCAGCAAAGAAAAAGGGTAAAA
6673 AGTAAAGAGTAA
1 AGTAAAGAGTAA
6685 AGAGAAGAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 12 0.29
35 30 0.71
ACGTcount: A:0.57, C:0.04, G:0.23, T:0.16
Consensus pattern (34 bp):
AGTAAAGAGTAATCAGCAAAGAAAAAGGGTAAAA
Found at i:6664 original size:20 final size:20
Alignment explanation
Indices: 6636--6680 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6626 AAAATGGTAA
* *
6636 AAAGTAAAAGAGTAATCAGT
1 AAAGAAAAAGAGTAAACAGT
* *
6656 AAAGAAAAAGGGTAAAGAGT
1 AAAGAAAAAGAGTAAACAGT
6676 AAAGA
1 AAAGA
6681 GTAAAGAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.13
Consensus pattern (20 bp):
AAAGAAAAAGAGTAAACAGT
Found at i:6679 original size:14 final size:14
Alignment explanation
Indices: 6662--6776 Score: 60
Period size: 14 Copynumber: 8.4 Consensus size: 14
6652 CAGTAAAGAA
6662 AAAGGGTAAAGAGT
1 AAAGGGTAAAGAGT
*
6676 AAAGAGTAAAGAG-
1 AAAGGGTAAAGAGT
* *
6689 -AAGAGTAATGAGT
1 AAAGGGTAAAGAGT
** *
6702 AAA-GAAAAAAATGGT
1 AAAGGGTAAAGA--GT
6717 AAAGGGTAAAGAGT
1 AAAGGGTAAAGAGT
*
6731 --AGAGTAAAGAGT
1 AAAGGGTAAAGAGT
** **
6743 AATCGGTAAAGAAA
1 AAAGGGTAAAGAGT
*
6757 AAATGGTAAAGAGT
1 AAAGGGTAAAGAGT
*
6771 GAAGGG
1 AAAGGG
6777 AAGTCAGTAA
Statistics
Matches: 72, Mismatches: 22, Indels: 14
0.67 0.20 0.13
Matches are distributed among these distances:
12 22 0.31
13 3 0.04
14 37 0.51
15 5 0.07
16 5 0.07
ACGTcount: A:0.53, C:0.01, G:0.31, T:0.15
Consensus pattern (14 bp):
AAAGGGTAAAGAGT
Found at i:6686 original size:7 final size:7
Alignment explanation
Indices: 6632--6744 Score: 76
Period size: 7 Copynumber: 16.6 Consensus size: 7
6622 AAGTAAAATG
*
6632 GTAAAAA
1 GTAAAGA
6639 GTAAAAGA
1 GT-AAAGA
**
6647 GTAATCA
1 GTAAAGA
6654 GTAAAGA
1 GTAAAGA
* *
6661 -AAAAGG
1 GTAAAGA
6667 GTAAAGA
1 GTAAAGA
6674 GTAAAGA
1 GTAAAGA
6681 GTAAAGA
1 GTAAAGA
6688 G--AAGA
1 GTAAAGA
*
6693 GTAATGA
1 GTAAAGA
6700 GTAAAGA
1 GTAAAGA
* *
6707 -AAAAAA
1 GTAAAGA
*
6713 TGGTAAAGG
1 --GTAAAGA
6722 GTAAAGA
1 GTAAAGA
6729 GT--AGA
1 GTAAAGA
6734 GTAAAGA
1 GTAAAGA
6741 GTAA
1 GTAA
6745 TCGGTAAAGA
Statistics
Matches: 80, Mismatches: 17, Indels: 18
0.70 0.15 0.16
Matches are distributed among these distances:
5 10 0.12
6 8 0.10
7 53 0.66
8 6 0.08
9 3 0.04
ACGTcount: A:0.57, C:0.01, G:0.27, T:0.15
Consensus pattern (7 bp):
GTAAAGA
Found at i:6694 original size:19 final size:19
Alignment explanation
Indices: 6670--6744 Score: 78
Period size: 19 Copynumber: 3.8 Consensus size: 19
6660 AAAAAGGGTA
6670 AAGAGTAAAGAGTAAAGAG
1 AAGAGTAAAGAGTAAAGAG
* *
6689 AAGAGTAATGAGTAAAGAAA
1 AAGAGTAAAGAGTAAAG-AG
* *
6709 AAAATGGTAAAGGGTAAAGAG
1 AAGA--GTAAAGAGTAAAGAG
*
6730 TAGAGTAAAGAGTAA
1 AAGAGTAAAGAGTAA
6745 TCGGTAAAGA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 26 0.59
20 4 0.09
21 3 0.07
22 11 0.25
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (19 bp):
AAGAGTAAAGAGTAAAGAG
Found at i:6703 original size:26 final size:27
Alignment explanation
Indices: 6634--6706 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
6624 GTAAAATGGT
**
6634 AAAA-AGTAAAAGAGTAATCAGTAAAGA
1 AAAAGAGT-AAAGAGTAAAGAGTAAAGA
*
6661 AAAAGGGTAAAGAGTAAAGAGTAAAG-
1 AAAAGAGTAAAGAGTAAAGAGTAAAGA
* *
6687 AGAAGAGTAATGAGTAAAGA
1 AAAAGAGTAAAGAGTAAAGA
6707 AAAAAATGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
26 17 0.44
27 20 0.51
28 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.26, T:0.14
Consensus pattern (27 bp):
AAAAGAGTAAAGAGTAAAGAGTAAAGA
Found at i:6730 original size:48 final size:47
Alignment explanation
Indices: 6636--6770 Score: 177
Period size: 48 Copynumber: 2.9 Consensus size: 47
6626 AAAATGGTAA
* *
6636 AAAGTAAAAGAGTAATCAGTAAAG-AAAAAGGGTAAAGAGTAAAGAGT
1 AAAGT-AAAGAGTAATGAGTAAAGAAAAAATGGTAAAGAGTAAAGAGT
*
6683 AAAG-AGAAGAGTAATGAGTAAAGAAAAAAATGGTAAAGGGTAAAGAGT
1 AAAGTA-AAGAGTAATGAGTAAAG-AAAAAATGGTAAAGAGTAAAGAGT
*
6731 AGAGTAAAGAGTAATCG-GTAAAGAAAAAATGGTAAAGAGT
1 AAAGTAAAGAGTAAT-GAGTAAAGAAAAAATGGTAAAGAGT
6771 GAAGGGAAGT
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
45 1 0.01
46 16 0.21
47 20 0.26
48 39 0.50
49 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.27, T:0.16
Consensus pattern (47 bp):
AAAGTAAAGAGTAATGAGTAAAGAAAAAATGGTAAAGAGTAAAGAGT
Found at i:6787 original size:35 final size:36
Alignment explanation
Indices: 6731--6843 Score: 124
Period size: 35 Copynumber: 3.2 Consensus size: 36
6721 GGTAAAGAGT
* * *
6731 AGAGTAAAGAGTAA-TCGGTAAAGAAAAAATGGTAA
1 AGAGTAAAGAGGAACCCAGTAAAGAAAAAATGGTAA
* ** * *
6766 AGAGTGAAG-GGAAGTCAGTAAAG-AAGAATGGTGA
1 AGAGTAAAGAGGAACCCAGTAAAGAAAAAATGGTAA
*
6800 AGAGTAAAGAGTAACCCAGTAAAGAAAAAATGGTAA
1 AGAGTAAAGAGGAACCCAGTAAAGAAAAAATGGTAA
6836 AGAGTAAA
1 AGAGTAAA
6844 ATATTAATCA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
34 20 0.31
35 27 0.42
36 17 0.27
ACGTcount: A:0.52, C:0.04, G:0.28, T:0.15
Consensus pattern (36 bp):
AGAGTAAAGAGGAACCCAGTAAAGAAAAAATGGTAA
Found at i:6813 original size:69 final size:69
Alignment explanation
Indices: 6535--6840 Score: 248
Period size: 69 Copynumber: 4.6 Consensus size: 69
6525 TAAAGAGTAA
* * *
6535 AGTAAAGAG-AGATCGGTAAAGAAAAAATGGTAAAGAGTGAAGGGAAGCCAGTAAAGAAGAATAG
1 AGTAAAGAGTA-ATCAGTAAAGAAAAAATGGTAAAGAGTGAAGGGAAGTCAGTAAAGAAGAATGG
6599 TGAAG
65 TGAAG
* * * * * * *
6604 AGTAAAGAGTAATCAGCAAAG-TAAAATGGTAAAAAGTAAAAGAGTAA-TCAGTAAAGAAAAAGG
1 AGTAAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGT-GAAG-GGAAGTCAGTAAAGAAGAATG
*
6667 GTAAAG
64 GTGAAG
** * * * * *
6673 AGTAAAGAGTAA--AG-AGAAG-AGTAATGAGTAAAGA---AA--AAAAT-GGTAAAG-GGTAAA
1 AGTAAAGAGTAATCAGTA-AAGAAAAAATG-GTAAAGAGTGAAGGGAAGTCAGTAAAGAAG-AAT
6727 GAGT--AG
63 G-GTGAAG
*
6733 AGTAAAGAGTAATCGGTAAAGAAAAAATGGTAAAGAGTGAAGGGAAGTCAGTAAAGAAGAATGGT
1 AGTAAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTGAAGGGAAGTCAGTAAAGAAGAATGGT
6798 GAAG
66 GAAG
*
6802 AGTAAAGAGTAACCCAGTAAAGAAAAAATGGTAAAGAGT
1 AGTAAAGAGTAA-TCAGTAAAGAAAAAATGGTAAAGAGT
6841 AAAATATTAA
Statistics
Matches: 185, Mismatches: 30, Indels: 43
0.72 0.12 0.17
Matches are distributed among these distances:
60 14 0.08
61 11 0.06
62 14 0.08
63 6 0.03
64 2 0.01
65 2 0.01
66 1 0.01
67 14 0.08
68 29 0.16
69 64 0.35
70 28 0.15
ACGTcount: A:0.53, C:0.04, G:0.28, T:0.15
Consensus pattern (69 bp):
AGTAAAGAGTAATCAGTAAAGAAAAAATGGTAAAGAGTGAAGGGAAGTCAGTAAAGAAGAATGGT
GAAG
Found at i:6942 original size:21 final size:21
Alignment explanation
Indices: 6882--6948 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
6872 CGGCAAAGGA
* *
6882 TAAAATGGTAACTAGTAATCAG
1 TAAAATAGTAA-TGGTAATCAG
* * *
6904 TACAA-AGTAAAGAATAATCAG
1 TAAAATAGTAATG-GTAATCAG
6925 TAAAATAGTAATGGTAATCAG
1 TAAAATAGTAATGGTAATCAG
6946 TAA
1 TAA
6949 TTCAGTGAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.25
Consensus pattern (21 bp):
TAAAATAGTAATGGTAATCAG
Found at i:8475 original size:333 final size:332
Alignment explanation
Indices: 7421--10228 Score: 4179
Period size: 332 Copynumber: 8.5 Consensus size: 332
7411 CGTTGCGACA
*
7421 GATCTTTCATTATATGAATATAGATATTGCAATGAGTGTTGTTGCCAAAAATCATGCAAAACTGA
1 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
* * **
7486 GCCGGGCCCTCGGAACGCTTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGAAAAAA
66 GCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
*** *
7551 TTTTGCAAAATTTGATTTTAAACATTTCTCCTCAATTTTCGGCCTTAAATACTCATGAAAAATAT
131 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATAT
*** * *
7616 ACAACTCAACAAAAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCAATTTTCATATTTTTTT
196 ACAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTA--TTTTT
* * * * *
7681 TCGAATTAATTTCTAATTAAATCGAAACC-AAGTTGAGATGCTCGTAAAAAGAAATCCTTAATTC
259 TAGAATTAGTTTCTGATTAAATCGAAACCGGA-TTGAGATGCTCGTAAAAACAAATCCTTAATTC
7745 CAAAGTGGGT
323 CAAAGTGGGT
* * *
7755 GATCTTTCATTATATGAATATAGATATTGCAATAAGTCTTGTTGACAAAAATCATGCAAAAATGA
1 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
* *
7820 GCCGGGCTCCCGGAACGCGGTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
66 GCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
* * *
7885 TTTTGCAAAATTTGTTCCGATACATTTCTCGTCAATTTAT-GGCCATAAATACTCATGAAAAAAT
131 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTT-TCGGCCATAAATACTCATG-AAAAAT
*** * *
7949 ATACAACTCAACAAAAAAAAGATTGAAGGGCTTCTCACACATGTAATATCAATTTTCCTATTTTT
194 ATACAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTA--TTT
* *
8014 TTTCGAATTAGTTTCTGATTAAATCGAAACCAGATTGAGATGCAT-GTAAAAACAAATCCTTAAT
257 TTTAGAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGC-TCGTAAAAACAAATCCTTAAT
8078 TCCAAAGTGGGT
321 TCCAAAGTGGGT
* * *
8090 GATCTTTCATTATCTGAATATAGATATTGCAATGAGTCTTGTTGCAAAAAATCATGCAAAATTGA
1 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
* *
8155 GCCAGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCTGCTAAAA
66 GCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
* * * *
8220 TTTTGCAAAATTTTATCCTAAACATTTCTCCTGAATTTTCGGCCTTAAATACTCATGAAAAATAT
131 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATAT
* * * * *
8285 ATAATTTAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCAATTTTCTTATTTCTTT
196 ACAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTT-TTT
* *
8350 CGAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACATATCCTTAATTCCA
260 AGAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAATTCCA
*
8415 AAGAGGGT
325 AAGTGGGT
*
8423 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCCAAACTGA
1 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
* *
8488 GCCGGGCCCCCGGGAA-ACGTTTTTAGTCAAAAACCGTGATGGTTATTACATGATTTCGGCTAAA
66 GCCGGGCCCCC-GGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAA
* * * * *
8552 ATTTTGCAAAATTTGATCCTAAGCAATTCTCCTCAATTTTCGGTCGTAAATACTCATGAAAAATA
130 ATTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATA
* * *
8617 TATAACTTAACGCCAAAAAGATTGAAGTGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTT
195 TACAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTT
8682 AGAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAATTCCA
260 AGAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAATTCCA
8747 AAGTGGGT
325 AAGTGGGT
*
8755 GATCTTTCATTATATGAATATAGATATTGCAATGAGTGTTGTTGCCAAAAATCATGCAAAACTGA
1 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
* * **
8820 GCCCGGCCCTCGGAACGCGTTTTTAGTCAAAAACCGTGACCGTTAGTACATGATTTCGGCTAAAA
66 GCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
8885 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATAT
131 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATAT
*
8950 ACAACTCAACGCCAAAAAGATTGAAGGTCTTCTCACGCATGTAATATCATTTTTCCTATTTTTTA
196 ACAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTTA
9015 GAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAATTCCAA
261 GAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAATTCCAA
*
9080 GGTGGGT
326 AGTGGGT
* *
9087 GATCTTTCGTTATATGAATATAGATATTGCAATGAGTGTTGTTGCCAAAAATCATGCAAAACTGA
1 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
*
9152 GCCGGGCCCTCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
66 GCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
9217 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTTCGGCCATAAATACTCATGAAAAATA
131 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAA-TTTTCGGCCATAAATACTCATGAAAAATA
* * *
9282 TATAACTTAACGCCAAAAAGATTGAACGGCTTCTCACGCATGTAATATCATTTTTCCTATTTCTT
195 TACAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTT-TT
* * *
9347 TCGAATTAGTTTCTGATTAAATCGAAACCGGATTTAGATGCTCGTAAAAACAAATCATTAATTCC
259 TAGAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAATTCC
9412 AAAGTGGGT
324 AAAGTGGGT
* * * * *
9421 GATATTTCGTTATATGAATATAGATATTGCAATGAGTCTTGTTGTCAAAAATCATTCAAAACTTA
1 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
* * *
9486 GGCGGGCCTCCGGAACGCGTTTTTAGTTAAAAACC------G-T--T-C------T--GCTAAAA
66 GCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
* * *
9533 TTTTGCAAAATTTGATCCTAAACATTTCTCCTGAATTTTCGGCCGTAAATACTCATGAAAAATAT
131 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATAT
* * * *
9598 AAAACTCAACGCCAAAATGATTGAAGGACTTGTCACGCATGTAATATCATTTTTCCTATTTTTTT
196 ACAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTA-TTTTTT
* * *
9663 AAAACTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAAAAAAAATCCTTAATTC
260 AGAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGT--AAAAACAAATCCTTAATTC
9728 CAAAGTGGGT
323 CAAAGTGGGT
* * *
9738 GATCTTTCCTTATATGAAAATAGATATTGCAATAAGTCTTGTTGCCAAAAATCATGCAAAACTGA
1 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
* *
9803 GCCGGGCTCCCGGAACGCGTTTTTAGTCAAAAACCGTGATCGTTAGTACATGATTTCGGCTAAAA
66 GCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
* * *
9868 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTTGGCCGTAAATACTCATGTAAAATAT
131 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATAT
* * *
9933 ACAACTCAACGCCGAAATGATTGAAGGTCTTCTCACGCATGTAATATCATTTTTCCTATTTTTTA
196 ACAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTTA
* * * *
9998 GAATTAGTTTCTGATTAAATCGAAACCGAATTGAGATGCTCGTAAAAATAAATCCTGAATTACAA
261 GAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAATTCCAA
*
10063 GGTGGGT
326 AGTGGGT
* *
10070 GATCTTTCGTTATATGAATATAGATATTGCAATGAGTGTTGTTGCCAAAAATCATGCAAAACTGA
1 GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
* * *
10135 GTCGGGCCCTCGAAACGCGTTTTTAGTCAAAAACC------G-T-G---ATGATTTCGGCTAAAA
66 GCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
* *
10189 TTTTGCAAAATTCGACCCGAAACATTTCTCCTCAATTTTC
131 TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTC
Statistics
Matches: 2280, Mismatches: 162, Indels: 77
0.91 0.06 0.03
Matches are distributed among these distances:
315 124 0.05
316 43 0.02
317 116 0.05
318 1 0.00
321 53 0.02
323 1 0.00
324 3 0.00
325 2 0.00
326 2 0.00
327 2 0.00
328 1 0.00
331 4 0.00
332 664 0.29
333 392 0.17
334 441 0.19
335 429 0.19
336 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (332 bp):
GATCTTTCATTATATGAATATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGA
GCCGGGCCCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAA
TTTTGCAAAATTTGATCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATAT
ACAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCATGTAATATCATTTTTCCTATTTTTTA
GAATTAGTTTCTGATTAAATCGAAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAATTCCAA
AGTGGGT
Done.