Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011720.1 Corchorus capsularis cultivar CVL-1 contig11741, 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: 17590
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:988 original size:21 final size:18
Alignment explanation
Indices: 949--1000 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
939 AACGTTGAAG
*
949 TTATAACCTTAATTTTTTT
1 TTATAACCTTAA-GTTTTT
968 TTATAACCTCTATAGTTTTT
1 TTATAACCT-TA-AGTTTTT
988 TTAGTAACCTTAA
1 TTA-TAACCTTAA
1001 TAGATGTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 10 0.34
20 12 0.41
21 7 0.24
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (18 bp):
TTATAACCTTAAGTTTTT
Found at i:1003 original size:21 final size:20
Alignment explanation
Indices: 949--1003 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
939 AACGTTGAAG
*
949 TTATAACCTTAAT-TTTTTT
1 TTATAACCTTAATAGTTTTT
968 TTATAACCTCT-ATAGTTTTT
1 TTATAACCT-TAATAGTTTTT
988 TTAGTAACCTTAATAG
1 TTA-TAACCTTAATAG
1004 ATGTGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 11 0.35
20 10 0.32
21 10 0.32
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (20 bp):
TTATAACCTTAATAGTTTTT
Found at i:1706 original size:13 final size:13
Alignment explanation
Indices: 1688--1716 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1678 ACTCATAAAC
1688 TTTGGAAAACAAG
1 TTTGGAAAACAAG
1701 TTTGGAAAACAAG
1 TTTGGAAAACAAG
1714 TTT
1 TTT
1717 TCTAAAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (13 bp):
TTTGGAAAACAAG
Found at i:4499 original size:31 final size:32
Alignment explanation
Indices: 4459--4524 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
4449 AAACTTTATG
* *
4459 TTTTCCGATTGTACCCCTTTTTAAAAAATATA
1 TTTTCCGATTATACCCCTTTTTAAAAAATACA
*
4491 TTTT-CGATTATACCCTTTTTTAAAAAATACA
1 TTTTCCGATTATACCCCTTTTTAAAAAATACA
4522 TTT
1 TTT
4525 CTAAATTGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.47
Consensus pattern (32 bp):
TTTTCCGATTATACCCCTTTTTAAAAAATACA
Found at i:8561 original size:21 final size:22
Alignment explanation
Indices: 8441--8588 Score: 113
Period size: 22 Copynumber: 6.7 Consensus size: 22
8431 CATAGTGTTG
*
8441 TTATCAAAATTTCA-AAGCGAGA
1 TTATCAAAATTTCATAA-AGAGA
* * *
8463 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGA
* * * * *
8485 TTATTAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGAGA
* * *
8507 TCAACAAAATTTTATAAAGAGA
1 TTATCAAAATTTCATAAAGAGA
*
8529 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGA
* *
8551 TTATCAAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAAA-GAGA
8573 TTA-CAAAAATTTCATA
1 TTATC-AAAATTTCATA
8589 GTGGTTTTTT
Statistics
Matches: 96, Mismatches: 26, Indels: 7
0.74 0.20 0.05
Matches are distributed among these distances:
21 4 0.04
22 89 0.93
23 3 0.03
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGA
Found at i:8695 original size:20 final size:20
Alignment explanation
Indices: 8670--8721 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
8660 TTATGGAGTA
* * *
8670 ATCAAACTTTTAGGGATGAT
1 ATCAAAATTTCAGGGAGGAT
8690 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
8710 ATCAAAATTTCA
1 ATCAAAATTTCA
8722 TAGTTTAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
ATCAAAATTTCAGGGAGGAT
Found at i:8758 original size:22 final size:20
Alignment explanation
Indices: 8689--9486 Score: 153
Period size: 22 Copynumber: 37.8 Consensus size: 20
8679 TTAGGGATGA
** *
8689 TATCAAAATTTCAGGGAGGA
1 TATCAAAATTTCATAGAGGT
8709 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAG---AGGT
*
8731 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCAT-AGA-GGT
*
8753 TATCAAAATTTCATAGAATGT
1 TATCAAAATTTCATAG-AGGT
* *
8774 AGATCAAAATTTCATAGGAGCT
1 -TATCAAAATTTCATA-GAGGT
* * *
8796 TAACCAAATTTCATAATGAGTT
1 TATCAAAATTTCAT-A-GAGGT
**
8818 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATA--GAGGT
*
8840 TATCAAAATTT-GT--A-GT
1 TATCAAAATTTCATAGAGGT
* *
8856 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCAT-AG-AGGT
*
8878 TATCAAAATTT--TATAGG-
1 TATCAAAATTTCATAGAGGT
* *
8895 -AACAAAATTTTATAAAGAGGT
1 TATCAAAATTTCAT--AGAGGT
*
8916 TATCAGAATTTCATAGAGAGGT
1 TATCAAAATTTCAT--AGAGGT
* *
8938 TATCAAATTTTCAGA-ATGTGAT
1 TATCAAAATTTCATAGA-G-G-T
* *
8960 TA-CAAAAATTCCATAGTGG-
1 TATC-AAAATTTCATAGAGGT
**
8979 TA-C----TTT-AGGGAAGGT
1 TATCAAAATTTCATAG-AGGT
*
8994 TATCAAAATTTCATAGTATGAT
1 TATCAAAATTTCATAG-A-GGT
* *
9016 TA-CCAAA-TT-A-GGAAGGT
1 TATCAAAATTTCATAG-AGGT
* * * *
9033 TATTAAACTTTTATTATGGAGGA
1 TATCAAAATTTCA-TA--GAGGT
**
9056 TATCAAAATTTCAGGGAGGATAT
1 TATCAAAATTTCATAGAGG---T
9079 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAG---AGGT
* *
9101 TTTCAAATTTTCATAAGACGGT
1 TATCAAAATTTCAT-AGA-GGT
**
9123 TATCAAAATTTCATAGTATGCA
1 TATCAAAATTTCATAG-A-GGT
* * *
9145 GATTAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATA--GAGGT
*
9167 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCAT-A-GAGGT
*
9189 TATCAAAAAATT-ATAGGGAGGT
1 TATC-AAAATTTCATA--GAGGT
*
9211 TATCAAAATTT-GT--A-GT
1 TATCAAAATTTCATAGAGGT
* *
9227 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCAT-AG-AGGT
*
9249 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATA--GAGG-T
* *
9272 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATA-G-AG-GT
9295 TATCAAAATTTCATAGTAAGGT
1 TATCAAAATTTCATAG--AGGT
* *
9317 TATCAAAATTTCATAGTGTAAT
1 TATCAAAATTTCATAGAG--GT
* *
9339 TATCAAAATTTCAGAGTATGAT
1 TATCAAAATTTCATAG-A-GGT
9361 TA-CTAATAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATA--GAGGT
* * * *
9383 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCAT-A-GAGGT
* *
9405 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATA--GAGGT
* * *
9427 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA--G-AGGT
* *
9450 TATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCA-T-AGAGGT
9472 TATCAAAATTTCATA
1 TATCAAAATTTCATA
9487 CTGAGATCTT
Statistics
Matches: 568, Mismatches: 124, Indels: 172
0.66 0.14 0.20
Matches are distributed among these distances:
13 2 0.00
14 4 0.01
15 2 0.00
16 34 0.06
17 8 0.01
18 7 0.01
19 8 0.01
20 34 0.06
21 44 0.08
22 321 0.57
23 97 0.17
24 5 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (20 bp):
TATCAAAATTTCATAGAGGT
Found at i:9278 original size:23 final size:23
Alignment explanation
Indices: 9226--9332 Score: 128
Period size: 23 Copynumber: 4.7 Consensus size: 23
9216 AAATTTGTAG
* * *
9226 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGAAGGT
* *
9248 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGAAGGT
* *
9271 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGAAGGT
*
9294 TTATCAAAATTTCATAGTAAGG-
1 TTATCAAAATTTCATAGGAAGGT
9316 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
9333 TGTAATTATC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
22 34 0.46
23 40 0.54
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGAAGGT
Found at i:9546 original size:23 final size:22
Alignment explanation
Indices: 9515--9560 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
9505 CTTAGGGAGG
*
9515 TTAACAAAATTTCATAAAAAGGT
1 TTAAAAAAATTT-ATAAAAAGGT
9538 TTAAAAAAATTTATAAAAAGGT
1 TTAAAAAAATTTATAAAAAGGT
9560 T
1 T
9561 CTCGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (22 bp):
TTAAAAAAATTTATAAAAAGGT
Found at i:10605 original size:27 final size:25
Alignment explanation
Indices: 10553--10614 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
10543 TCATTATTCT
* *
10553 TAAAACATATTTTTAAATTGTTATTA
1 TAAAATATA-TTTTAAATTGTCATTA
*
10579 TCAAAATATATTTTAATTATGTCATTA
1 T-AAAATATATTTTAAAT-TGTCATTA
*
10606 TTAAATATA
1 TAAAATATA
10615 CTGCCTCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (25 bp):
TAAAATATATTTTAAATTGTCATTA
Found at i:10837 original size:17 final size:16
Alignment explanation
Indices: 10794--10846 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
10784 ACAATGTTTG
* *
10794 ATAGGAAGG-AAATAA
1 ATAGCAAGGAAAAGAA
10809 ATAAGCAAGGAAAAGAA
1 AT-AGCAAGGAAAAGAA
*
10826 ATAGCAAGGGAAAGGAA
1 ATAGCAA-GGAAAAGAA
10843 ATAG
1 ATAG
10847 GGAGGAAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 11 0.34
17 19 0.59
ACGTcount: A:0.58, C:0.04, G:0.28, T:0.09
Consensus pattern (16 bp):
ATAGCAAGGAAAAGAA
Found at i:11885 original size:2 final size:2
Alignment explanation
Indices: 11878--11934 Score: 50
Period size: 2 Copynumber: 30.0 Consensus size: 2
11868 AGGTTTAGGT
* * *
11878 TA TA TA TA TA TA TA TA TA TCA TA TA TA -A AA TA AA TA TA -A AA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
11919 TA TA T- TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA
11935 ATAAATGGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
1 4 0.09
2 40 0.87
3 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:11928 original size:7 final size:7
Alignment explanation
Indices: 11878--11934 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
11868 AGGTTTAGGT
11878 TATAT-A
1 TATATAA
11884 TATATATA
1 TATATA-A
*
11892 TATATCA
1 TATATAA
11899 TATATAA
1 TATATAA
11906 -A-ATAA
1 TATATAA
11911 -ATATAA
1 TATATAA
* *
11917 AATATAT
1 TATATAA
11924 TATATAA
1 TATATAA
11931 TATA
1 TATA
11935 ATAAATGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
5 5 0.12
6 10 0.24
7 21 0.50
8 6 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:12392 original size:15 final size:16
Alignment explanation
Indices: 12365--12394 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12355 TGGTAGGAAC
12365 TAGGAAGGAAAGAAAT
1 TAGGAAGGAAAGAAAT
12381 TAGGAA-GAAAGAAA
1 TAGGAAGGAAAGAAA
12395 CAAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.10
Consensus pattern (16 bp):
TAGGAAGGAAAGAAAT
Found at i:14180 original size:16 final size:16
Alignment explanation
Indices: 14157--14240 Score: 118
Period size: 16 Copynumber: 5.4 Consensus size: 16
14147 CGGGTTCGGG
14157 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
14173 CGGATTCGGATATTTT
1 CGGGTTCGGGTATTTT
* *
14189 CGGGTTTGAGTATTTT
1 CGGGTTCGGGTATTTT
14205 CGGGTTC-GGTA-TTT
1 CGGGTTCGGGTATTTT
14219 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
14235 CGGGTT
1 CGGGTT
14241 AGGGCTTGGA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
14 10 0.17
15 7 0.12
16 41 0.71
ACGTcount: A:0.10, C:0.12, G:0.35, T:0.44
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:14260 original size:23 final size:23
Alignment explanation
Indices: 14233--14286 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
14223 TTCGGGTATT
**
14233 TTCGGGTTAGGGCTTGGATCGGG
1 TTCGGGTTAGGGCCCGGATCGGG
* *
14256 TTCGGGTTTGGGCCCGGGTCGGG
1 TTCGGGTTAGGGCCCGGATCGGG
14279 TTCGGGTT
1 TTCGGGTT
14287 CACTTTCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.04, C:0.17, G:0.48, T:0.31
Consensus pattern (23 bp):
TTCGGGTTAGGGCCCGGATCGGG
Found at i:14822 original size:31 final size:31
Alignment explanation
Indices: 14787--14858 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
14777 TAAATTGTAG
* *
14787 CAAATTAAAACAAAT-TAAGTATTAAATTAAA
1 CAAATTAAAA-AAATGCAAGCATTAAATTAAA
* ** *
14818 CAAATCATCAAAATGCAAGCCTTAAATTAAA
1 CAAATTAAAAAAATGCAAGCATTAAATTAAA
14849 CAAATTAAAA
1 CAAATTAAAA
14859 GCTAATGGAC
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.25
Consensus pattern (31 bp):
CAAATTAAAAAAATGCAAGCATTAAATTAAA
Found at i:15187 original size:2 final size:2
Alignment explanation
Indices: 15180--15205 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15170 CATTATTAAG
15180 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
15206 TCCTTTTACG
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:15912 original size:44 final size:43
Alignment explanation
Indices: 15843--16447 Score: 289
Period size: 44 Copynumber: 14.0 Consensus size: 43
15833 TTCTGTGTAG
* * * * *
15843 TTATCAAAATTTTATAATGAGGTTATCGAAATTTCATAGTGTTA
1 TTATCAAAATTTCAT-AGGATGTTATCAAAATTTCATAGTGTGA
***
15887 TTATCAAAATTTCATAGCGATGTTATCAAAATTTCATAAG-AAAA
1 TTATCAAAATTTCATAG-GATGTTATCAAAATTTCAT-AGTGTGA
* *
15931 GTTATCAAAATTTCACAGTG-TGGTTATCAAAATTTCATAGTATGA
1 -TTATCAAAATTTCATAG-GAT-GTTATCAAAATTTCATAGTGTGA
* * *
15976 TTA-CAAAAATTTCATAAGG-TAGTTCTTAAAATTTCATAGTAT-A
1 TTATC-AAAATTTCAT-AGGAT-GTTATCAAAATTTCATAGTGTGA
* ** * *
16019 GTTACCAAAATTTTTTAGGA-GATTATTAAAATTTC--AGTGTGG
1 -TTATCAAAATTTCATAGGATG-TTATCAAAATTTCATAGTGTGA
* * *
16061 TTATCAAAATTTCATAGAGACGTTATCCAAATTTCATGGTGTGA
1 TTATCAAAATTTCATAG-GATGTTATCAAAATTTCATAGTGTGA
* * * * * * *
16105 TTATCAAAATTTCATAAGAAGGTTTTCAAACTTGCATAATGTGG
1 TTATCAAAATTTCAT-AGGATGTTATCAAAATTTCATAGTGTGA
* * * * * *
16149 TTATCAAAATTTCAGAAGA--TTACCAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGGATGTTATCAAAATTTCATAGTGTGA
* * * * *
16190 TTACCAAAATTTCATAGGTAGGTTACCAAAACTTTTATATTGTGA
1 TTATCAAAATTTCATAGG-ATGTTATCAAAA-TTTCATAGTGTGA
* ** *
16235 -TATTAAAATTTCATA-GAAATTAACAAAATTTCATAAG-GATG-
1 TTATCAAAATTTCATAGGATGTTATCAAAATTTCAT-AGTG-TGA
** **
16276 TTA-CTAAAATTTCATAGTGCGGTTATCAAAATTTCATAGATAAGCA
1 TTATC-AAAATTTCATAG-GATGTTATCAAAATTTCATAG-TGTG-A
* ** * *
16322 --ATC-AAATTTCA-AGGAGGAAATCGAAATTTCATAGAGT-A
1 TTATCAAAATTTCATAGGATGTTATCAAAATTTCATAGTGTGA
* * * *
16360 GTTGTCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGTGG
1 -TTATCAAAATTTCATA-GGATGTTATCAAAATTTCATAGTGTGA
* * * * *
16405 TTTTCGAAATTTCATAAAGA-GATTACCAAAATTTCATGGTGTG
1 TTATCAAAATTTCAT-AGGATG-TTATCAAAATTTCATAGTGTG
16448 GTTACCATGA
Statistics
Matches: 432, Mismatches: 88, Indels: 82
0.72 0.15 0.14
Matches are distributed among these distances:
38 1 0.00
41 73 0.17
42 50 0.12
43 34 0.08
44 222 0.51
45 52 0.12
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGATGTTATCAAAATTTCATAGTGTGA
Found at i:16007 original size:89 final size:88
Alignment explanation
Indices: 15841--16398 Score: 251
Period size: 85 Copynumber: 6.5 Consensus size: 88
15831 GTTTCTGTGT
* * * * *
15841 AGTTATCAAAATTTTATAATGAGGTTATCGAAATTTCATAGTGTTATTATCAAAATTTCATAGCG
1 AGTTATCAAAATTTCACAATGAGGTTATCAAAATTTCATAGTATGATTATCAAAATTTCATAGCG
15906 ATGTTATCAAAATTTCATAAGAAA
66 ATGTTATCAAAATTTCAT-AGAAA
* *
15930 AGTTATCAAAATTTCACAGTGTGGTTATCAAAATTTCATAGTATGATTA-CAAAAATTTCATAAG
1 AGTTATCAAAATTTCACAATGAGGTTATCAAAATTTCATAGTATGATTATC-AAAATTTCAT-AG
* * * *
15994 -G-TAGTTCTTAAAATTTCATAGTAT
64 CGAT-GTTATCAAAATTTCATAGAAA
* *** * * * * * *
16018 AGTTACCAAAATTT-TTTAGGAGATTATTAAAATTTC--AGTGTGGTTATCAAAATTTCATAGAG
1 AGTTATCAAAATTTCACAATGAGGTTATCAAAATTTCATAGTATGATTATCAAAATTTCATAGCG
* * ***
16080 ACGTTATCCAAATTTCAT-GGTG
66 ATGTTATCAAAATTTCATAGAAA
* * * * * * * * *
16102 TGATTATCAAAATTTCATAA-GAAGGTTTTCAAACTTGCATAATGTGGTTATCAAAATTTCAGA-
1 AG-TTATCAAAATTTCACAATG-AGGTTATCAAAATTTCATAGTATGATTATCAAAATTTCATAG
* * **
16165 AGA--TTACCAAAATTTCATAGGGA
64 CGATGTTATCAAAATTTCATAGAAA
* * * * * * * * *
16188 GGTTACCAAAATTTCA-TAGGTAGGTTACCAAAACTTTTATATTGTGA-TATTAAAATTTCATA-
1 AGTTATCAAAATTTCACAATG-AGGTTATCAAAA-TTTCATAGTATGATTATCAAAATTTCATAG
** * *
16250 -GAAATTAACAAAATTTCATA-AGGA
64 CGATGTTATCAAAATTTCATAGA-AA
* * * * *
16274 TGTTA-CTAAAATTTCATAGTGCGGTTATCAAAATTTCATAGATAAGCA--ATC-AAATTTCA-A
1 AGTTATC-AAAATTTCACAATGAGGTTATCAAAATTTCATAG-TATG-ATTATCAAAATTTCATA
* ** * **
16334 G-GAGGAAATCGAAATTTCATAGAGT
63 GCGATGTTATCAAAATTTCATAGAAA
* * **
16359 AGTTGTCAAAATTTCATAGGGAGGTTATCAAAATTTCATA
1 AGTTATCAAAATTTCACAATGAGGTTATCAAAATTTCATA
16399 ATGTGGTTTT
Statistics
Matches: 364, Mismatches: 81, Indels: 52
0.73 0.16 0.10
Matches are distributed among these distances:
84 8 0.02
85 157 0.43
86 72 0.20
87 19 0.05
88 39 0.11
89 67 0.18
90 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (88 bp):
AGTTATCAAAATTTCACAATGAGGTTATCAAAATTTCATAGTATGATTATCAAAATTTCATAGCG
ATGTTATCAAAATTTCATAGAAA
Found at i:16133 original size:22 final size:22
Alignment explanation
Indices: 15842--16441 Score: 161
Period size: 22 Copynumber: 27.7 Consensus size: 22
15832 TTTCTGTGTA
*
15842 GTTATCAAAATTTTATAATG-AG
1 GTTATCAAAATTTCATAA-GAAG
* *
15864 GTTATCGAAATTTCAT-AG-TG
1 GTTATCAAAATTTCATAAGAAG
* * *
15884 TTATTATCAAAATTTCAT-AGCGAT
1 --GTTATCAAAATTTCATAAG-AAG
*
15908 GTTATCAAAATTTCATAAGAAAA
1 GTTATCAAAATTTCATAAG-AAG
* **
15931 GTTATCAAAATTTCA-CAGTGTG
1 GTTATCAAAATTTCATAAG-AAG
*
15953 GTTATCAAAATTTCAT-AGTATG
1 GTTATCAAAATTTCATAAG-AAG
* *
15975 ATTA-CAAAAATTTCATAAGGTA-
1 GTTATC-AAAATTTCATAA-GAAG
* *
15997 GTTCTTAAAATTTCAT-AGTATA-
1 GTTATCAAAATTTCATAAG-A-AG
* * * *
16019 GTTACCAAAATTT-TTTAGGAG
1 GTTATCAAAATTTCATAAGAAG
* * *
16040 ATTATTAAAATTTCAGT--G-TG
1 GTTATCAAAATTTCA-TAAGAAG
*
16060 GTTATCAAAATTTCAT-AGAGAC
1 GTTATCAAAATTTCATAAGA-AG
* **
16082 GTTATCCAAATTTCAT--GGTG
1 GTTATCAAAATTTCATAAGAAG
16102 TGATTATCAAAATTTCATAAGAAG
1 -G-TTATCAAAATTTCATAAGAAG
* * * *
16126 GTTTTCAAACTTGCATAATG-TG
1 GTTATCAAAATTTCATAA-GAAG
16148 GTTATCAAAATTTC---AGAAG
1 GTTATCAAAATTTCATAAGAAG
* * * *
16167 ATTACCAAAATTTCATAGGGAG
1 GTTATCAAAATTTCATAAGAAG
* * *
16189 GTTACCAAAATTTCATAGGTAG
1 GTTATCAAAATTTCATAAGAAG
* * * *
16211 GTTACCAAAACTTTTATATTG--T
1 GTTATCAAAA-TTTCATA-AGAAG
* *
16233 GATATTAAAATTTCAT-AGAA-
1 GTTATCAAAATTTCATAAGAAG
* * * *
16253 ATTAACAAAATTTCATAAGGAT
1 GTTATCAAAATTTCATAAGAAG
**
16275 GTTA-CTAAAATTTCAT-AGTGCG
1 GTTATC-AAAATTTCATAAG-AAG
*
16297 GTTATCAAAATTTCAT-AGATAA
1 GTTATCAAAATTTCATAAGA-AG
** *
16319 GCAATC-AAATTTC--AAGGAG
1 GTTATCAAAATTTCATAAGAAG
** * *
16338 GAAATCGAAATTTCATAGAGTA-
1 GTTATCAAAATTTCATA-AGAAG
* * *
16360 GTTGTCAAAATTTCATAGGGAG
1 GTTATCAAAATTTCATAAGAAG
*
16382 GTTATCAAAATTTCATAATG-TG
1 GTTATCAAAATTTCATAA-GAAG
* *
16404 GTTTTCGAAATTTCATAA-AGAG
1 GTTATCAAAATTTCATAAGA-AG
* *
16426 ATTACCAAAATTTCAT
1 GTTATCAAAATTTCAT
16442 GGTGTGGTTA
Statistics
Matches: 431, Mismatches: 100, Indels: 94
0.69 0.16 0.15
Matches are distributed among these distances:
18 1 0.00
19 22 0.05
20 40 0.09
21 37 0.09
22 294 0.68
23 33 0.08
24 4 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGAAG
Found at i:16159 original size:66 final size:65
Alignment explanation
Indices: 15843--16441 Score: 372
Period size: 66 Copynumber: 9.2 Consensus size: 65
15833 TTCTGTGTAG
* * ** *
15843 TTATCAAAATTTTATAATGAGGTTATCGAAATTTCATAGTGTTATTATCAAAATTTCATAGCGAT
1 TTATCAAAATTTCATAA-GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTG-T
15908 G-
64 GA
* * *
15909 TTATCAAAATTTCATAAGAAAAGTTATCAAAATTTCACAGTGTGGTTATCAAAATTTCATAGTAT
1 TTATCAAAATTTCATAAG--AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGT
15974 GA
64 GA
* * * * * **
15976 TTA-CAAAAATTTCATAAG-GTAGTTCTTAAAATTTCATAGTATAGTTACCAAAATTTTTTAG-G
1 TTATC-AAAATTTCATAAGAG--GTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTG
*
16038 AGA
63 TGA
* * * ** * *
16041 TTATTAAAATTTCAGT--GTGGTTATCAAAATTTCATAGAGACGTTATCCAAATTTCATGGTGTG
1 TTATCAAAATTTCA-TAAGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGTG
16104 A
65 A
* * * * **
16105 TTATCAAAATTTCATAAGAAGGTTTTCAAACTTGCATAATGTGGTTATCAAAATTTC--AG-AAG
1 TTATCAAAATTTCATAAG-AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGTG
16167 A
65 A
* * * * * *
16168 TTACCAAAATTTCATAGGGAGGTTACCAAAATTTCATAG-GTAGGTTACCAAAACTTTTATATTG
1 TTATCAAAATTTCATA-AGAGGTTATCAAAATTTCATAGTGT-GGTTATCAAAA-TTTCATAGTG
16232 TGA
63 TGA
* ** *
16235 -TATTAAAATTTCAT-AGAAATTAACAAAATTTCATAAG-GAT-GTTA-CTAAAATTTCATAGTG
1 TTATCAAAATTTCATAAGAGGTTATCAAAATTTCAT-AGTG-TGGTTATC-AAAATTTCATAGTG
* *
16295 CGG
63 TGA
* * ** * ** * *
16298 TTATCAAAATTTCATAGATAAGCAATC-AAATTTCA-AG-GAGGAAATCGAAATTTCATAGAGT-
1 TTATCAAAATTTCATA-AGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGTG
16359 A
65 A
* * * * * ** *
16360 GTTGTCAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGTGGTTTTCGAAATTTCATAAAGA
1 -TTATCAAAATTTCATA-AGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGT
16425 GA
64 GA
*
16427 TTACCAAAATTTCAT
1 TTATCAAAATTTCAT
16442 GGTGTGGTTA
Statistics
Matches: 406, Mismatches: 95, Indels: 64
0.72 0.17 0.11
Matches are distributed among these distances:
62 2 0.00
63 120 0.30
64 68 0.17
65 29 0.07
66 131 0.32
67 56 0.14
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (65 bp):
TTATCAAAATTTCATAAGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGTGTGA
Found at i:16279 original size:64 final size:64
Alignment explanation
Indices: 16194--16315 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 64
16184 GGGAGGTTAC
* * * *
16194 CAAAATTTCATAGGTAGGTTACCAAAACTTTTATATTG-TGATATTAAAATTTCATAGAAATTAA
1 CAAAATTTCATAGGTAGGTTACCAAAA-TTTCATAGTGCGGATATCAAAATTTCATAGAAATTAA
* * *
16258 CAAAATTTCATAAGG-ATGTTACTAAAATTTCATAGTGCGGTTATCAAAATTTCATAGA
1 CAAAATTTCAT-AGGTAGGTTACCAAAATTTCATAGTGCGGATATCAAAATTTCATAGA
16316 TAAGCAATCA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
63 8 0.16
64 38 0.78
65 3 0.06
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (64 bp):
CAAAATTTCATAGGTAGGTTACCAAAATTTCATAGTGCGGATATCAAAATTTCATAGAAATTAA
Done.