Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022682.1 Corchorus olitorius cultivar O-4 contig22715, 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: 49288
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:48 original size:30 final size:31
Alignment explanation
Indices: 12--72 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
2 TTCTCTCCTG
12 TTACAAATTATATGC-AATGTCATGGAACTA
1 TTACAAATTATATGCAAATGTCATGGAACTA
42 TTACAAATTATATGCAAATGTCATGGAACTA
1 TTACAAATTATATGCAAATGTCATGGAACTA
73 GAACCTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (31 bp):
TTACAAATTATATGCAAATGTCATGGAACTA
Found at i:586 original size:14 final size:17
Alignment explanation
Indices: 542--597 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
532 GAAGTAGTCC
*
542 AATTAATATAATGACCA
1 AATTAATATGATGACCA
559 AATTAATATGATGACCA
1 AATTAATATGATGACCA
576 AATTAATATGATGACCA
1 AATTAATATGATGACCA
593 AATTA
1 AATTA
598 GATTTTACGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (17 bp):
AATTAATATGATGACCA
Found at i:664 original size:15 final size:14
Alignment explanation
Indices: 641--678 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
631 GACTCAAGGG
*
641 CTAAATGAAAACTTA
1 CTAATTGAAAA-TTA
656 CTAATTG-AAATTA
1 CTAATTGAAAATTA
669 CTAATTGAAA
1 CTAATTGAAA
679 CTGCAATCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 10 0.48
14 5 0.24
15 6 0.29
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (14 bp):
CTAATTGAAAATTA
Found at i:671 original size:13 final size:13
Alignment explanation
Indices: 653--678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
643 AAATGAAAAC
653 TTACTAATTGAAA
1 TTACTAATTGAAA
666 TTACTAATTGAAA
1 TTACTAATTGAAA
679 CTGCAATCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TTACTAATTGAAA
Found at i:694 original size:18 final size:18
Alignment explanation
Indices: 671--707 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
661 TGAAATTACT
671 AATTGAAACTGCAATCCA
1 AATTGAAACTGCAATCCA
689 AATTGAAACTGCAATCCA
1 AATTGAAACTGCAATCCA
707 A
1 A
708 TGTAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (18 bp):
AATTGAAACTGCAATCCA
Found at i:901 original size:18 final size:18
Alignment explanation
Indices: 878--935 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
868 CCTAAGCGAA
*
878 AAAATAGAAACAAAATTG
1 AAAATAGAAAAAAAATTG
**
896 AAAATAGGAAAAAAAAAAG
1 AAAATA-GAAAAAAAATTG
915 AAAA-AGAAAAAAAATTTG
1 AAAATAGAAAAAAAA-TTG
933 AAA
1 AAA
936 TAAATTAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 9 0.27
18 11 0.33
19 13 0.39
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (18 bp):
AAAATAGAAAAAAAATTG
Found at i:3694 original size:34 final size:34
Alignment explanation
Indices: 3651--3718 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
3641 CTCCAATAGT
3651 CTGAAATCTTGGTTAAATGATTAAAACCATCTTG
1 CTGAAATCTTGGTTAAATGATTAAAACCATCTTG
3685 CTGAAATCTTGGTTAAATGATTAAAACCATCTTG
1 CTGAAATCTTGGTTAAATGATTAAAACCATCTTG
3719 GTGACTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (34 bp):
CTGAAATCTTGGTTAAATGATTAAAACCATCTTG
Found at i:4504 original size:130 final size:129
Alignment explanation
Indices: 4353--4762 Score: 581
Period size: 130 Copynumber: 3.2 Consensus size: 129
4343 TTAAAAGTAT
* * *
4353 GTTGCCTTAGTGATTTTGATGGTATTTTAC-CAACAGATTTTTTAATTGTTGCAAATGCTTACAG
1 GTTGCCTAAGTGATTTTGATGGTATTTTACACAACA-CTTTTTTAATTGTT-CAAATGCTTACAA
* * ** * * *
4417 TTTTCATAACAACAAAAACAAAGTCATTGCGAAATCATAATTTATTCATAACAATTTTATAAAAT
64 TTTTCGTAACAACAAAAACAAAGTCATTGCGATATCATAAACTATTCGTAACAACTTTATAAAAA
*
4482 T
129 C
* *
4483 GTTACCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTATT-TTCGAATGCTTACAA
1 GTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTA--ATTGTTCAAATGCTTACAA
4547 TTTTCGTAACAACAAAAACAAAGTCATTGCGATATCATAAACTATTCGTAACAACTTTATAAAAA
64 TTTTCGTAACAACAAAAACAAAGTCATTGCGATATCATAAACTATTCGTAACAACTTTATAAAAA
4612 C
129 C
* * * *
4613 GTTGCCTAAGTGATTTTGATGGCATTTTACACAACACTTTTTTAGTCGTTTCCAATGCTTACAAT
1 GTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTG-TTCAAATGCTTACAAT
** *
4678 TTTCGTAACAACAAAAACAAAGTTGTTTCGATATCATAAACTATTCGTAACAACTTTATAAAAAC
65 TTTCGTAACAACAAAAACAAAGTCATTGCGATATCATAAACTATTCGTAACAACTTTATAAAAAC
4743 GTTGCCTAAGTGATTTTGAT
1 GTTGCCTAAGTGATTTTGAT
4763 CACAGCACCT
Statistics
Matches: 254, Mismatches: 21, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
128 1 0.00
130 243 0.96
131 7 0.03
132 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (129 bp):
GTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTGTTCAAATGCTTACAATT
TTCGTAACAACAAAAACAAAGTCATTGCGATATCATAAACTATTCGTAACAACTTTATAAAAAC
Found at i:4804 original size:121 final size:121
Alignment explanation
Indices: 4642--4859 Score: 285
Period size: 121 Copynumber: 1.8 Consensus size: 121
4632 TGGCATTTTA
* * * * * *
4642 CACAACACTTTTTTAGTCGTTTCCAATGCTTACAATTTTCGTAACAACAAAAAC-AAAGTTGTTT
1 CACAACACCTTTTTAGTCGTTGCCAATACTTACAATATTCGTAACAACAAAAACTAAAG-TGCTA
*
4706 CGATATCATAAACTATTCGTAACAACTTTATAAAAACGTTGCCTAAGTGATTTTGAT
65 CGAAATCATAAACTATTCGTAACAACTTTATAAAAACGTTGCCTAAGTGATTTTGAT
* * * * *** *
4763 CACAGCACCTTTTTAGTTGTTGCCAATATTTACAGTATTCGTAACAACAACTTCTTAAGTGCTAC
1 CACAACACCTTTTTAGTCGTTGCCAATACTTACAATATTCGTAACAACAAAAACTAAAGTGCTAC
4828 GAAATCATAAACTATTCGTAACAACTTTATAA
66 GAAATCATAAACTATTCGTAACAACTTTATAA
4860 GTCGTTGCAC
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
121 78 0.96
122 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (121 bp):
CACAACACCTTTTTAGTCGTTGCCAATACTTACAATATTCGTAACAACAAAAACTAAAGTGCTAC
GAAATCATAAACTATTCGTAACAACTTTATAAAAACGTTGCCTAAGTGATTTTGAT
Found at i:10139 original size:2 final size:2
Alignment explanation
Indices: 10132--10157 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10122 AACTTAATTT
10132 TA 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
10158 ACTGAAACTG
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):
TA
Found at i:10505 original size:20 final size:20
Alignment explanation
Indices: 10477--10516 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10467 TGCCGCTTAT
10477 TTATCTATGAGATTATATTC
1 TTATCTATGAGATTATATTC
* *
10497 TTATTTATGAGATTTTATTC
1 TTATCTATGAGATTATATTC
10517 ACAAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (20 bp):
TTATCTATGAGATTATATTC
Found at i:11047 original size:7 final size:7
Alignment explanation
Indices: 11035--11059 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11025 GTACTAGAGA
11035 CAATGGG
1 CAATGGG
11042 CAATGGG
1 CAATGGG
11049 CAATGGG
1 CAATGGG
11056 CAAT
1 CAAT
11060 TTAGTAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (7 bp):
CAATGGG
Found at i:12461 original size:19 final size:18
Alignment explanation
Indices: 12437--12472 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12427 TGAAGGCTCA
12437 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
12456 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
12473 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:15057 original size:25 final size:25
Alignment explanation
Indices: 15025--15074 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
15015 GGGAGGAGAG
15025 GAAAGAAG-ACAAA-AGGGTTGTCAC
1 GAAAGAAGTA-AAACAGGGTTGTCAC
15049 GAAACGAAGTAAAACAGGGTTGTCAC
1 GAAA-GAAGTAAAACAGGGTTGTCAC
15075 CAAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 7 0.30
26 12 0.52
ACGTcount: A:0.44, C:0.14, G:0.28, T:0.14
Consensus pattern (25 bp):
GAAAGAAGTAAAACAGGGTTGTCAC
Found at i:17314 original size:29 final size:28
Alignment explanation
Indices: 17273--17329 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
17263 GTTTTTCTGA
17273 TTTTGGTTAAGTGCGGGTTGTGCACTTG
1 TTTTGGTTAAGTGCGGGTTGTGCACTTG
* *
17301 TTTTTGTTCAAGTGTGGGTTGTGCACTTG
1 TTTTGGTT-AAGTGCGGGTTGTGCACTTG
17330 GGATTGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.46
Consensus pattern (28 bp):
TTTTGGTTAAGTGCGGGTTGTGCACTTG
Found at i:17336 original size:29 final size:29
Alignment explanation
Indices: 17281--17337 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
17271 GATTTTGGTT
***
17281 AAGTGCGGGTTGTGCACTTGTTTTTGTTC
1 AAGTGCGGGTTGTGCACTTGGGATTGTTC
*
17310 AAGTGTGGGTTGTGCACTTGGGATTGTT
1 AAGTGCGGGTTGTGCACTTGGGATTGTT
17338 TTGAGTGTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.12, C:0.11, G:0.35, T:0.42
Consensus pattern (29 bp):
AAGTGCGGGTTGTGCACTTGGGATTGTTC
Found at i:20859 original size:18 final size:19
Alignment explanation
Indices: 20836--20875 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
20826 TTCTTGAGAA
20836 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
20854 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
20873 AAT
1 AAT
20876 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:23796 original size:21 final size:21
Alignment explanation
Indices: 23754--23799 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
23744 GCCCATTCAT
**
23754 CGTGCCACCACCGGTTAAGCC
1 CGTGCCACCACCGGCCAAGCC
*
23775 CGTGCCACCACCGGCCATGCC
1 CGTGCCACCACCGGCCAAGCC
23796 CGTG
1 CGTG
23800 GCATCGCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.46, G:0.26, T:0.13
Consensus pattern (21 bp):
CGTGCCACCACCGGCCAAGCC
Found at i:24714 original size:19 final size:18
Alignment explanation
Indices: 24683--24718 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24673 AAGGGTAGTT
*
24683 AAAAAAAATTGCTTTCAA
1 AAAAAAAAGTGCTTTCAA
24701 AAAAAAGAAGTGCTTTCA
1 AAAAAA-AAGTGCTTTCA
24719 TGCAAGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (18 bp):
AAAAAAAAGTGCTTTCAA
Found at i:26271 original size:11 final size:11
Alignment explanation
Indices: 26255--26280 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26245 AGATAATTTC
26255 TTTTCTTCTAG
1 TTTTCTTCTAG
26266 TTTTCTTCTAG
1 TTTTCTTCTAG
26277 TTTT
1 TTTT
26281 TTAGGCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:30713 original size:15 final size:16
Alignment explanation
Indices: 30680--30719 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
30670 TTACTTTGCT
30680 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
30696 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
30711 TTGCTTTCT
1 TTGTTTTCT
30720 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:32892 original size:8 final size:8
Alignment explanation
Indices: 32863--33051 Score: 51
Period size: 8 Copynumber: 23.8 Consensus size: 8
32853 AAAAAGAAAA
32863 AGATAAAT
1 AGATAAAT
* * *
32871 AGGTATAG
1 AGATAAAT
32879 AGATAAAT
1 AGATAAAT
32887 AGATAAAT
1 AGATAAAT
*
32895 AGGTAGCTAAAA
1 A-G-A--TAAAT
32907 AGGAT-AAT
1 A-GATAAAT
32915 A-AT-AAT
1 AGATAAAT
*
32921 AAATAAAT
1 AGATAAAT
32929 AGAT-AAT
1 AGATAAAT
*
32936 AGCTAAATT
1 AGATAAA-T
32945 A-ATAAAT
1 AGATAAAT
32952 A-A-AAA-
1 AGATAAAT
*
32957 A-AT-ATT
1 AGATAAAT
*
32963 AAATAAAT
1 AGATAAAT
32971 AGAT-AAT
1 AGATAAAT
* *
32978 AAATAAAA
1 AGATAAAT
32986 AGATAAAT
1 AGATAAAT
*
32994 AGTAAATAAGT
1 AG---ATAAAT
33005 AGATAATAGT
1 AGATAA-A-T
* * *
33015 TGAAAAAA
1 AGATAAAT
*
33023 AAATAAAT
1 AGATAAAT
33031 AGATAAAT
1 AGATAAAT
33039 AG-TAAAT
1 AGATAAAT
*
33046 AAATAA
1 AGATAA
33052 TAAAAAAATC
Statistics
Matches: 133, Mismatches: 29, Indels: 38
0.67 0.14 0.19
Matches are distributed among these distances:
5 3 0.02
6 10 0.08
7 25 0.19
8 69 0.52
9 5 0.04
10 6 0.05
11 8 0.06
12 7 0.05
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (8 bp):
AGATAAAT
Found at i:32927 original size:4 final size:4
Alignment explanation
Indices: 32918--33060 Score: 63
Period size: 4 Copynumber: 37.8 Consensus size: 4
32908 GGATAATAAT
* ** * * *
32918 AATA AATA AATA GAT- AATA GCTA AATT AATA AATA AAAA AAT- ATTA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * *
32964 AATA AATA GAT- AATA AATA AA-A AGATA AAT- AGTA AATA AGTA GAT-
1 AATA AATA AATA AATA AATA AATA A-ATA AATA AATA AATA AATA AATA
** * *
33009 AATA GTTGA AA-A AA-A AATA AATA GATA AAT- AGTA AATA AAT- AATA
1 AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
33054 AAAA AAT
1 AATA AAT
33061 CTTTTTGGTC
Statistics
Matches: 98, Mismatches: 30, Indels: 22
0.65 0.20 0.15
Matches are distributed among these distances:
3 23 0.23
4 72 0.73
5 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:32936 original size:15 final size:15
Alignment explanation
Indices: 32912--32991 Score: 78
Period size: 15 Copynumber: 5.6 Consensus size: 15
32902 TAAAAAGGAT
32912 AATA-ATAATAAATA
1 AATAGATAATAAATA
**
32926 AATAGATAATAGCTA
1 AATAGATAATAAATA
32941 AAT---TAATAAATA
1 AATAGATAATAAATA
* * *
32953 AAAAAATATTAAATA
1 AATAGATAATAAATA
32968 AATAGATAATAAATA
1 AATAGATAATAAATA
*
32983 AAAAGATAA
1 AATAGATAA
32992 ATAGTAAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
12 9 0.17
14 4 0.08
15 39 0.75
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (15 bp):
AATAGATAATAAATA
Found at i:32978 original size:7 final size:7
Alignment explanation
Indices: 32912--33047 Score: 55
Period size: 7 Copynumber: 18.7 Consensus size: 7
32902 TAAAAAGGAT
32912 AATAAT-
1 AATAATA
32918 AATAAATA
1 AAT-AATA
32926 AATAGAT-
1 AATA-ATA
*
32933 AATAGCTA
1 AATA-ATA
32941 AATTAATA
1 AA-TAATA
*
32949 AATAAAAA
1 AAT-AATA
*
32957 AATATTA
1 AATAATA
32964 AATAAATA
1 AAT-AATA
*
32972 GATAATA
1 AATAATA
32979 AATAA-A
1 AATAATA
*
32985 AA-GATA
1 AATAATA
*
32991 AATAGTA
1 AATAATA
32998 AATAAGTA
1 AATAA-TA
*
33006 GATAATA
1 AATAATA
** *
33013 GTTGAAAA
1 AAT-AATA
*
33021 AAAAATA
1 AATAATA
33028 AATAGATA
1 AATA-ATA
*
33036 AATAGTA
1 AATAATA
33043 AATAA
1 AATAA
33048 ATAATAAAAA
Statistics
Matches: 96, Mismatches: 22, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
5 1 0.01
6 9 0.09
7 46 0.48
8 38 0.40
9 2 0.02
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:32983 original size:34 final size:33
Alignment explanation
Indices: 32945--33060 Score: 108
Period size: 34 Copynumber: 3.4 Consensus size: 33
32935 TAGCTAAATT
*
32945 AATAAATAAAAAAATATTAAATAAATAGATAATA
1 AATAAA-AAAAAAATAATAAATAAATAGATAATA
* * *
32979 AATAAAAAGATAAATAGTAAATAAGTAGATAATA
1 AATAAAAA-AAAAATAATAAATAAATAGATAATA
** * *
33013 GTTGAAAAAAAAATAAATAGATAAATAG-TAAATA
1 AATAAAAAAAAAAT-AATAAATAAATAGAT-AATA
*
33047 AATAATAAAAAAAT
1 AATAAAAAAAAAAT
33061 CTTTTTGGTC
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
33 8 0.12
34 57 0.88
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (33 bp):
AATAAAAAAAAAATAATAAATAAATAGATAATA
Found at i:32992 original size:27 final size:26
Alignment explanation
Indices: 32912--32994 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 26
32902 TAAAAAGGAT
*
32912 AATAATAATAAATAAATAGATAATAGCTA
1 AATAATAATAAATAAAAAGATAA-A--TA
*
32941 AATTAATAAATAAA-AAAATA-TTAAATA
1 AA-TAAT-AATAAATAAAA-AGATAAATA
32968 AATAGATAATAAATAAAAAGATAAATA
1 AATA-ATAATAAATAAAAAGATAAATA
32995 GTAAATAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
26 9 0.20
27 16 0.36
29 3 0.07
30 10 0.22
31 7 0.16
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (26 bp):
AATAATAATAAATAAAAAGATAAATA
Found at i:32992 original size:42 final size:42
Alignment explanation
Indices: 32915--32994 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
32905 AAAGGATAAT
** *
32915 AATAATAAATAAATAGATAATAGCTAAATTAATAAATAAAAA
1 AATAATAAATAAATAGATAATAAATAAATAAATAAATAAAAA
*
32957 AATATTAAATAAATAGATAATAAATAAA-AAGATAAATA
1 AATAATAAATAAATAGATAATAAATAAATAA-ATAAATA
32995 GTAAATAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 32 0.97
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (42 bp):
AATAATAAATAAATAGATAATAAATAAATAAATAAATAAAAA
Found at i:33814 original size:31 final size:31
Alignment explanation
Indices: 33776--33837 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
33766 GAGTTTTGTA
* *
33776 AAACTTTTGAATCGTCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
33807 AAACTTTTGAATCGCCTATCATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
33838 TTTCGAATAT
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:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATT
Found at i:33975 original size:93 final size:93
Alignment explanation
Indices: 33873--34057 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 93
33863 TTTTTTAAAT
* *
33873 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* *
33938 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
*
33966 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAGCTA
1 TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
34031 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
34058 ATTAAAAAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:40337 original size:2 final size:2
Alignment explanation
Indices: 40330--40382 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
40320 TTATAAACTT
* *
40330 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40372 TA -A TA GTA TA T
1 TA TA TA -TA TA T
40383 TAAAATAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:40951 original size:20 final size:21
Alignment explanation
Indices: 40926--40965 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
40916 AAATACTTAC
40926 GAATTAGTAATC-AGGAAAAA
1 GAATTAGTAATCAAGGAAAAA
40946 GAATTAGTAATCAAGGAAAA
1 GAATTAGTAATCAAGGAAAA
40966 TCTATCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (21 bp):
GAATTAGTAATCAAGGAAAAA
Found at i:42908 original size:20 final size:20
Alignment explanation
Indices: 42883--42986 Score: 68
Period size: 20 Copynumber: 5.1 Consensus size: 20
42873 TCAAATAGTA
*
42883 ACTAAAATCCTAAATCGGGG
1 ACTAAAATCCTAAATCAGGG
* * **
42903 ACTAAATTGCATCAAAT-AGTA
1 ACTAAAAT-CCT-AAATCAGGG
42924 ACTAAAATCCTAAATCAGGG
1 ACTAAAATCCTAAATCAGGG
* * **
42944 ACTAAATTGCATTAAAT-AGTA
1 ACTAAAAT-C-CTAAATCAGGG
*
42965 AATAAAATCCTAAATCAGGG
1 ACTAAAATCCTAAATCAGGG
42985 AC
1 AC
42987 CAAATTGCAT
Statistics
Matches: 59, Mismatches: 19, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
19 9 0.15
20 22 0.37
21 19 0.32
22 9 0.15
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.24
Consensus pattern (20 bp):
ACTAAAATCCTAAATCAGGG
Found at i:42910 original size:41 final size:41
Alignment explanation
Indices: 42857--43149 Score: 218
Period size: 41 Copynumber: 7.2 Consensus size: 41
42847 TTTCTAAAAC
**
42857 CAGGGACCAAATTAAATCAAATAGTAACTAAAATCCTAAAT
1 CAGGGACCAAATTGCATCAAATAGTAACTAAAATCCTAAAT
* *
42898 CGGGGACTAAATTGCATCAAATAGTAACTAAAATCCTAAAT
1 CAGGGACCAAATTGCATCAAATAGTAACTAAAATCCTAAAT
* * *
42939 CAGGGACTAAATTGCATTAAATAGTAAATAAAATCCTAAAT
1 CAGGGACCAAATTGCATCAAATAGTAACTAAAATCCTAAAT
** * * ** *
42980 CAGGGACCAAATTGCATTTAATCAGGAAAT-TGAT-TTGAAAT
1 CAGGGACCAAATTGCATCAAAT-AGTAACTAAAATCCT-AAAT
* *** * *
43021 TAGGGACCAAGCCGCAT-AAATTA-AAAATAAAATCCTAAAT
1 CAGGGACCAAATTGCATCAAA-TAGTAACTAAAATCCTAAAT
* * * * * * *
43061 CAGTGG-CGAAATTGAATTAATTAATAAATGAAATCCTAAAT
1 CAG-GGACCAAATTGCATCAAATAGTAACTAAAATCCTAAAT
* * * * * *
43102 CAGGGACAAAATTGAATCAATTAATAAATGAAATCCTAAAT
1 CAGGGACCAAATTGCATCAAATAGTAACTAAAATCCTAAAT
43143 CAGGGAC
1 CAGGGAC
43150 TAAGGTGAAA
Statistics
Matches: 210, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
39 4 0.02
40 22 0.10
41 178 0.85
42 6 0.03
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (41 bp):
CAGGGACCAAATTGCATCAAATAGTAACTAAAATCCTAAAT
Found at i:45592 original size:27 final size:29
Alignment explanation
Indices: 45549--45624 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
45539 GAGTGGACTT
**
45549 AAAATGACCAACGTGCCCCT-GA-ATATG
1 AAAATGACCAAAATGCCCCTGGATATATG
* * * *
45576 CAAATGACTAAAATGCCCCTGGATTTTTG
1 AAAATGACCAAAATGCCCCTGGATATATG
45605 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
45625 AGGTGATCCA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 16 0.41
28 2 0.05
29 21 0.54
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGGATATATG
Found at i:46879 original size:23 final size:23
Alignment explanation
Indices: 46830--46879 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
46820 GAACTTACTT
* ** *
46830 AAATATCTATGATGTGTAAGGTT
1 AAATATCTATGATGTCTAAAATC
46853 AAATATCTATGATGTCTAAAATC
1 AAATATCTATGATGTCTAAAATC
46876 AAAT
1 AAAT
46880 TAAAGGAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (23 bp):
AAATATCTATGATGTCTAAAATC
Found at i:47140 original size:2 final size:2
Alignment explanation
Indices: 47133--47158 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47123 ATTAATTAAT
47133 TA 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
47159 CTAGTTAAAG
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):
TA
Done.