Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007919.1 Corchorus capsularis cultivar CVL-1 contig07940, 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: 53742
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:7058 original size:18 final size:17
Alignment explanation
Indices: 7031--7066 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
7021 TTTCTCTTCA
7031 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
7048 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
7066 T
1 T
7067 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:13209 original size:25 final size:27
Alignment explanation
Indices: 13161--13211 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
13151 TTGTCATAGC
*
13161 TTTAGTTTAATTTAGTTTTGCTTTATT
1 TTTAGATTAATTTAGTTTTGCTTTATT
*
13188 TTTAGATTAA-TT-GTTTTTCTTTAT
1 TTTAGATTAATTTAGTTTTGCTTTAT
13212 AATTGATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 2 0.09
27 9 0.41
ACGTcount: A:0.20, C:0.04, G:0.10, T:0.67
Consensus pattern (27 bp):
TTTAGATTAATTTAGTTTTGCTTTATT
Found at i:14284 original size:16 final size:17
Alignment explanation
Indices: 14239--14345 Score: 66
Period size: 16 Copynumber: 6.7 Consensus size: 17
14229 GTTTTCTCAG
14239 GTCATTTGGGTTTC-GA
1 GTCATTTGGGTTTCGGA
*
14255 GTCATCTGGG-TTCGGA
1 GTCATTTGGGTTTCGGA
*
14271 -TTATTTGGGTTTCGG-
1 GTCATTTGGGTTTCGGA
* * * *
14286 GTCATTCGGATCTCAG-
1 GTCATTTGGGTTTCGGA
**
14302 GTCATACGGGTTTCGG-
1 GTCATTTGGGTTTCGGA
* *
14318 GTCATTCGGGTCTCGG-
1 GTCATTTGGGTTTCGGA
*
14334 GTCATTCGGGTT
1 GTCATTTGGGTT
14346 CCTAGTCATT
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
15 10 0.14
16 63 0.86
ACGTcount: A:0.11, C:0.18, G:0.34, T:0.37
Consensus pattern (17 bp):
GTCATTTGGGTTTCGGA
Found at i:14315 original size:32 final size:32
Alignment explanation
Indices: 14277--14345 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
14267 CGGATTATTT
14277 GGGTTTCGGGTCATTCGGATCTCAGGTCATAC
1 GGGTTTCGGGTCATTCGGATCTCAGGTCATAC
* * *
14309 GGGTTTCGGGTCATTCGGGTCTCGGGTCATTC
1 GGGTTTCGGGTCATTCGGATCTCAGGTCATAC
14341 GGGTT
1 GGGTT
14346 CCTAGTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.10, C:0.20, G:0.36, T:0.33
Consensus pattern (32 bp):
GGGTTTCGGGTCATTCGGATCTCAGGTCATAC
Found at i:14327 original size:9 final size:9
Alignment explanation
Indices: 14281--14344 Score: 59
Period size: 9 Copynumber: 7.8 Consensus size: 9
14271 TTATTTGGGT
14281 TTCGGGTCA
1 TTCGGGTCA
*
14290 TTCGGATC-
1 TTCGGGTCA
*
14298 -TCAGGTCA
1 TTCGGGTCA
*
14306 TACGGGT--
1 TTCGGGTCA
14313 TTCGGGTCA
1 TTCGGGTCA
14322 TTCGGGTC-
1 TTCGGGTCA
14330 -TCGGGTCA
1 TTCGGGTCA
14338 TTCGGGT
1 TTCGGGT
14345 TCCTAGTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
7 18 0.42
9 25 0.58
ACGTcount: A:0.11, C:0.22, G:0.34, T:0.33
Consensus pattern (9 bp):
TTCGGGTCA
Found at i:14354 original size:32 final size:32
Alignment explanation
Indices: 14277--14376 Score: 96
Period size: 32 Copynumber: 3.1 Consensus size: 32
14267 CGGATTATTT
* * * *
14277 GGGTTTCGGGTCATTCGGATCTCAGGTCATAC
1 GGGTTCCGAGTCATTCGGGTCTCGGGTCATAC
* * *
14309 GGGTTTCGGGTCATTCGGGTCTCGGGTCATTC
1 GGGTTCCGAGTCATTCGGGTCTCGGGTCATAC
*
14341 GGGTTCCTAGTCATTCGGGT-TCCGGGTC-TACC
1 GGGTTCCGAGTCATTCGGGTCT-CGGGTCATA-C
14373 GGGT
1 GGGT
14377 CTCGGGTTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 2 0.03
32 57 0.97
ACGTcount: A:0.10, C:0.23, G:0.35, T:0.32
Consensus pattern (32 bp):
GGGTTCCGAGTCATTCGGGTCTCGGGTCATAC
Found at i:14354 original size:48 final size:46
Alignment explanation
Indices: 14233--14383 Score: 119
Period size: 48 Copynumber: 3.2 Consensus size: 46
14223 CAGACAGTTT
* * * * * *
14233 TCTCAGGTCATTTGGGTTTCGAGTCATCTGGG-TTCGGATTATTTGGG
1 TCTCGGGTCATTCGGG-TTCTAGTCATC-GGGTTTCGGGTCATTCGGG
* *
14280 TTTCGGGTCATTC-GGATCTCAGGTCATACGGGTTTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGGTTCT-A-GTCAT-CGGGTTTCGGGTCATTCGGG
* *
14328 TCTCGGGTCATTCGGGTTCCTAGTCATTCGGGTTCCGGGTC-TACCGGG
1 TCTCGGGTCATTCGGGTT-CTAGTCA-TCGGGTTTCGGGTCAT-TCGGG
14376 TCTCGGGT
1 TCTCGGGT
14384 TGGGTGGGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 15
0.76 0.11 0.14
Matches are distributed among these distances:
45 2 0.02
46 3 0.04
47 19 0.23
48 53 0.63
49 5 0.06
50 2 0.02
ACGTcount: A:0.11, C:0.21, G:0.33, T:0.35
Consensus pattern (46 bp):
TCTCGGGTCATTCGGGTTCTAGTCATCGGGTTTCGGGTCATTCGGG
Found at i:15158 original size:11 final size:11
Alignment explanation
Indices: 15144--15181 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15134 ATTCATAACA
15144 AATTTATAATT
1 AATTTATAATT
15155 AATTTATAATT
1 AATTTATAATT
15166 -ATTTGATAATT
1 AATTT-ATAATT
*
15177 TATTT
1 AATTT
15182 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:15817 original size:9 final size:8
Alignment explanation
Indices: 15804--15921 Score: 61
Period size: 7 Copynumber: 14.9 Consensus size: 8
15794 TATTCGGGTT
15804 TCGGGTCA
1 TCGGGTCA
15812 TACGGGTC-
1 T-CGGGTCA
15820 TCGGGTCA
1 TCGGGTCA
*
15828 CTCGGGTTA
1 -TCGGGTCA
15837 -CGGGTCA
1 TCGGGTCA
*
15844 TTCGGGT-T
1 -TCGGGTCA
15852 TCGGGTCA
1 TCGGGTCA
* *
15860 TCTGGTTA
1 TCGGGTCA
15868 -CGGGTCA
1 TCGGGTCA
*
15875 TTTGGGTC-
1 -TCGGGTCA
*
15883 TCGAGTCA
1 TCGGGTCA
**
15891 TCTGGGTTG
1 TC-GGGTCA
15900 T-GGGTCA
1 TCGGGTCA
15907 TCCGGGTC-
1 T-CGGGTCA
15915 TCGGGTC
1 TCGGGTC
15922 GAGCGGGTTC
Statistics
Matches: 82, Mismatches: 16, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
7 39 0.48
8 11 0.13
9 32 0.39
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.31
Consensus pattern (8 bp):
TCGGGTCA
Found at i:15823 original size:16 final size:14
Alignment explanation
Indices: 15797--15936 Score: 100
Period size: 16 Copynumber: 8.9 Consensus size: 14
15787 CTCAGGTTAT
15797 TCGGGTTTCGGGTCA
1 TCGGG-TTCGGGTCA
15812 TACGGGTCTCGGGTCA
1 T-CGGGT-TCGGGTCA
15828 CTCGGGTTACGGGTCA
1 -TCGGGTT-CGGGTCA
15844 TTCGGGTTTCGGGTCA
1 -TCGGG-TTCGGGTCA
*
15860 TCTGGTTACGGGTCA
1 TCGGGTT-CGGGTCA
* *
15875 TTTGGGTCTCGAGTCA
1 -TCGGGT-TCGGGTCA
*
15891 TCTGGGTTGTGGGTCA
1 TC-GGGTT-CGGGTCA
15907 TCCGGGTCTCGGGTCGA
1 T-CGGGT-TCGGGTC-A
*
15924 GCGGGTTCGGGTC
1 TCGGGTTCGGGTC
15937 GTTTACTTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.02
15 23 0.23
16 70 0.69
17 7 0.07
ACGTcount: A:0.09, C:0.21, G:0.39, T:0.31
Consensus pattern (14 bp):
TCGGGTTCGGGTCA
Found at i:15835 original size:32 final size:31
Alignment explanation
Indices: 15797--15936 Score: 156
Period size: 32 Copynumber: 4.5 Consensus size: 31
15787 CTCAGGTTAT
* *
15797 TCGGGTTTCGGGTCATACGGGTCTCGGGTCA
1 TCGGGTTACGGGTCATTCGGGTCTCGGGTCA
*
15828 CTCGGGTTACGGGTCATTCGGGTTTCGGGTCA
1 -TCGGGTTACGGGTCATTCGGGTCTCGGGTCA
* * *
15860 TCTGGTTACGGGTCATTTGGGTCTCGAGTCA
1 TCGGGTTACGGGTCATTCGGGTCTCGGGTCA
** *
15891 TCTGGGTTGTGGGTCATCCGGGTCTCGGGTCGA
1 TC-GGGTTACGGGTCATTCGGGTCTCGGGTC-A
*
15924 GCGGGTT-CGGGTC
1 TCGGGTTACGGGTC
15937 GTTTACTTTT
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
31 34 0.37
32 55 0.60
33 2 0.02
ACGTcount: A:0.09, C:0.21, G:0.39, T:0.31
Consensus pattern (31 bp):
TCGGGTTACGGGTCATTCGGGTCTCGGGTCA
Found at i:15882 original size:63 final size:63
Alignment explanation
Indices: 15800--15921 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
15790 AGGTTATTCG
* * * *
15800 GGTTTCGGGTCATACGGGTCTCGGGTCA-CTCGGGTTACGGGTCATTCGGGTTTCGGGTCATCT
1 GGTTACGGGTCATACGGGTCTCGAGTCATCT-GGGTTACGGGTCATCCGGGTCTCGGGTCATCT
** **
15863 GGTTACGGGTCATTTGGGTCTCGAGTCATCTGGGTTGTGGGTCATCCGGGTCTCGGGTC
1 GGTTACGGGTCATACGGGTCTCGAGTCATCTGGGTTACGGGTCATCCGGGTCTCGGGTC
15922 GAGCGGGTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
63 48 0.96
64 2 0.04
ACGTcount: A:0.09, C:0.21, G:0.38, T:0.32
Consensus pattern (63 bp):
GGTTACGGGTCATACGGGTCTCGAGTCATCTGGGTTACGGGTCATCCGGGTCTCGGGTCATCT
Found at i:15935 original size:63 final size:62
Alignment explanation
Indices: 15798--15936 Score: 154
Period size: 63 Copynumber: 2.2 Consensus size: 62
15788 TCAGGTTATT
* * * *
15798 CGGGTTTCGGGTCATACGGGTCTCGGGTCACTCGGGTTACGGGTCATTCGGGTTTCGGGTCAT
1 CGGG-TTCGGGTCATACGGGTCTCGAGTCACTCGGGTTACGGGTCATCCGGGTCTCGGGTCAG
* ** **
15861 CTGGTTACGGGTCATTTGGGTCTCGAGTCA-TCTGGGTTGTGGGTCATCCGGGTCTCGGGTCGAG
1 CGGGTT-CGGGTCATACGGGTCTCGAGTCACTC-GGGTTACGGGTCATCCGGGTCTCGGGTC-AG
15925 CGGGTTCGGGTC
1 CGGGTTCGGGTC
15937 GTTTACTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
62 4 0.06
63 53 0.84
64 6 0.10
ACGTcount: A:0.09, C:0.22, G:0.40, T:0.30
Consensus pattern (62 bp):
CGGGTTCGGGTCATACGGGTCTCGAGTCACTCGGGTTACGGGTCATCCGGGTCTCGGGTCAG
Found at i:19716 original size:2 final size:2
Alignment explanation
Indices: 19711--19741 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19701 TTTTTTTATG
*
19711 AT AT AT AT CT 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 AT A
19742 GCAAATGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20436 original size:13 final size:13
Alignment explanation
Indices: 20411--20451 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
20401 GACTTTTTCC
20411 AAAAA-AAAA-AA
1 AAAAACAAAACAA
20422 AAAAACAAAACAA
1 AAAAACAAAACAA
20435 AAAAACAAAAACAA
1 AAAAAC-AAAACAA
20449 AAA
1 AAA
20452 CTTGAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 8 0.30
14 10 0.37
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAACAA
Found at i:20438 original size:19 final size:19
Alignment explanation
Indices: 20414--20450 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20404 TTTTTCCAAA
20414 AAAAAAAAAAAAACAAAAC
1 AAAAAAAAAAAAACAAAAC
*
20433 AAAAAAACAAAAACAAAA
1 AAAAAAAAAAAAACAAAA
20451 ACTTGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAACAAAAC
Found at i:20452 original size:6 final size:6
Alignment explanation
Indices: 20410--20452 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
20400 AGACTTTTTC
* *
20410 CAAAAA -AAAAA AAAAAA CAAAACA AAAAAA CAAAAA CAAAAA C
1 CAAAAA CAAAAA CAAAAA CAAAA-A CAAAAA CAAAAA CAAAAA C
20453 TTGAATTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 5 0.16
6 22 0.69
7 5 0.16
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:29081 original size:39 final size:39
Alignment explanation
Indices: 29014--29158 Score: 172
Period size: 39 Copynumber: 3.7 Consensus size: 39
29004 TTTTGACGGA
*
29014 ATCTTTCCCTAAATTGAAAATTTTGAAAA-ATGGATGGG
1 ATCTTTCCCTAAATTGAAAACTTTGAAAACATGGATGGG
*
29052 ATCTTTCCCTAAATTTGAAAACTTTGAAAACTTGG-TGGG
1 ATCTTTCCCTAAA-TTGAAAACTTTGAAAACATGGATGGG
* * *
29091 ATCTTTCGCTAAATCT-AAAACCTTGGAAAACAT-GATAGG
1 ATCTTTCCCTAAAT-TGAAAA-CTTTGAAAACATGGATGGG
* *
29130 ATCTTTCCCTAAATTGAAAGCATTGAAAA
1 ATCTTTCCCTAAATTGAAAACTTTGAAAA
29159 TTATTCTTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
38 27 0.30
39 61 0.67
40 3 0.03
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (39 bp):
ATCTTTCCCTAAATTGAAAACTTTGAAAACATGGATGGG
Found at i:29104 original size:77 final size:77
Alignment explanation
Indices: 29014--29158 Score: 188
Period size: 77 Copynumber: 1.9 Consensus size: 77
29004 TTTTGACGGA
* * * *
29014 ATCTTTCCCTAAAT-TGAAAA-TTTTGAAAA-ATGGATGGGATCTTTCCCTAAATTTGAAAACTT
1 ATCTTTCCCTAAATCT-AAAACCTTGGAAAACAT-GATAGGATCTTTCCCTAAA-TTGAAAACAT
29076 TGAAAACTTGGTGGG
63 TGAAAACTTGGTGGG
* *
29091 ATCTTTCGCTAAATCTAAAACCTTGGAAAACATGATAGGATCTTTCCCTAAATTGAAAGCATTGA
1 ATCTTTCCCTAAATCTAAAACCTTGGAAAACATGATAGGATCTTTCCCTAAATTGAAAACATTGA
29156 AAA
66 AAA
29159 TTATTCTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
77 31 0.53
78 26 0.44
79 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (77 bp):
ATCTTTCCCTAAATCTAAAACCTTGGAAAACATGATAGGATCTTTCCCTAAATTGAAAACATTGA
AAACTTGGTGGG
Found at i:29972 original size:18 final size:18
Alignment explanation
Indices: 29924--29972 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
29914 TTCTTCTTAT
29924 TAATATATTGGAAATTAAAC
1 TAAT-TATT-GAAATTAAAC
*
29944 TAAACTA-TGAAATTAAAC
1 T-AATTATTGAAATTAAAC
29962 TAATTATTGAA
1 TAATTATTGAA
29973 TTTCATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 1 0.04
20 3 0.12
21 2 0.08
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (18 bp):
TAATTATTGAAATTAAAC
Found at i:30102 original size:25 final size:25
Alignment explanation
Indices: 30058--30124 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
30048 TAAAACCTAG
* * * *
30058 GCCCAAATGCACAAAGAAATCATAA
1 GCCCAAGTGCATAAATAAATCAAAA
*
30083 GCCTAAGTGCATAAATAAATCAAAA
1 GCCCAAGTGCATAAATAAATCAAAA
**
30108 GCCCAAGCACATAAATA
1 GCCCAAGTGCATAAATA
30125 GGTTAGAAGC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.15
Consensus pattern (25 bp):
GCCCAAGTGCATAAATAAATCAAAA
Found at i:30263 original size:20 final size:20
Alignment explanation
Indices: 30234--30274 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
30224 CTTTTTTCTT
*
30234 CTCTTTTTCTTCTTCCCTCC
1 CTCTTCTTCTTCTTCCCTCC
*
30254 CTCTTCTTCTTCTTCCTTCC
1 CTCTTCTTCTTCTTCCCTCC
30274 C
1 C
30275 CGTAACTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (20 bp):
CTCTTCTTCTTCTTCCCTCC
Found at i:30853 original size:26 final size:27
Alignment explanation
Indices: 30824--30874 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
30814 AGCTCTTGCT
*
30824 CTAAAAACCTC-TGCTTTTCTCTCTTG
1 CTAAAAACCTCAAGCTTTTCTCTCTTG
*
30850 CTAAAACCCTCAAGCTTTTCTCTCT
1 CTAAAAACCTCAAGCTTTTCTCTCT
30875 CCCAAAACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (27 bp):
CTAAAAACCTCAAGCTTTTCTCTCTTG
Found at i:32730 original size:24 final size:24
Alignment explanation
Indices: 32685--32730 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
32675 ACTAACTTGG
* *
32685 TAACAAAGTCCAAAATGGACTAAC
1 TAACAAAGTCCAAAACGAACTAAC
32709 TAACAAAAG-CCAAAACGAACTA
1 TAAC-AAAGTCCAAAACGAACTA
32731 CCTGACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.54, C:0.22, G:0.11, T:0.13
Consensus pattern (24 bp):
TAACAAAGTCCAAAACGAACTAAC
Found at i:35582 original size:3 final size:3
Alignment explanation
Indices: 35574--35637 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
35564 TGGCAGCTGT
*
35574 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
35622 AGG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG A
35638 TAGCCATGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35852 original size:25 final size:25
Alignment explanation
Indices: 35818--35910 Score: 89
Period size: 25 Copynumber: 3.8 Consensus size: 25
35808 CAAACAGAGG
*
35818 AGCTCACTGCCATGAAGCTCGTTGA
1 AGCTCACTGCCAGGAAGCTCGTTGA
* **
35843 AGCTCACTGCCAGGAAGTTCACTGA
1 AGCTCACTGCCAGGAAGCTCGTTGA
** *
35868 AGCTTGCTGCTAGGAAGCTCGTTGA
1 AGCTCACTGCCAGGAAGCTCGTTGA
** *
35893 A-CTTGCTGCTAGGAAGCT
1 AGCTCACTGCCAGGAAGCT
35911 GATAGAGATA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
24 17 0.29
25 41 0.71
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.25
Consensus pattern (25 bp):
AGCTCACTGCCAGGAAGCTCGTTGA
Found at i:35902 original size:24 final size:25
Alignment explanation
Indices: 35831--35910 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
35821 TCACTGCCAT
** *
35831 GAAGCTCGTTGAAGCTCACTGCCAG
1 GAAGCTCGTTGAAGCTTGCTGCTAG
* **
35856 GAAGTTCACTGAAGCTTGCTGCTAG
1 GAAGCTCGTTGAAGCTTGCTGCTAG
35881 GAAGCTCGTTGAA-CTTGCTGCTAG
1 GAAGCTCGTTGAAGCTTGCTGCTAG
35905 GAAGCT
1 GAAGCT
35911 GATAGAGATA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 17 0.37
25 29 0.63
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (25 bp):
GAAGCTCGTTGAAGCTTGCTGCTAG
Found at i:39598 original size:20 final size:19
Alignment explanation
Indices: 39553--39598 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
39543 TGAATCATGC
39553 TTTTTTTTAATTAAATATT
1 TTTTTTTTAATTAAATATT
* *
39572 TAATTTTTTAATTAAATATG
1 T-TTTTTTTAATTAAATATT
39592 TTTTTTT
1 TTTTTTT
39599 ATTCAATACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTTTAATTAAATATT
Found at i:40287 original size:23 final size:22
Alignment explanation
Indices: 40244--40290 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
40234 AATTATATAA
* *
40244 TTTAATAAAATACATTGAAAAT
1 TTTAATAAAATACAATAAAAAT
*
40266 TTTAATGAAAATATAATAAAAAT
1 TTTAAT-AAAATACAATAAAAAT
40289 TT
1 TT
40291 CAGCGAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
TTTAATAAAATACAATAAAAAT
Found at i:46933 original size:11 final size:11
Alignment explanation
Indices: 46907--47073 Score: 164
Period size: 11 Copynumber: 15.1 Consensus size: 11
46897 GAAATTAGGC
*
46907 AAAAGAAGACGG
1 AAAA-AAGACTG
*
46919 AAAAAAGACTA
1 AAAAAAGACTG
*
46930 AAAAAATACTG
1 AAAAAAGACTG
46941 --AAAA-A--G
1 AAAAAAGACTG
46947 AAAAAAGACTG
1 AAAAAAGACTG
* *
46958 AAAGAAGACTA
1 AAAAAAGACTG
46969 AAAAGAAGACTG
1 AAAA-AAGACTG
46981 AAAAAAGACTG
1 AAAAAAGACTG
*
46992 AAACAAGACTG
1 AAAAAAGACTG
47003 AAAGAGAAGACTG
1 AAA-A-AAGACTG
*
47016 AAATAAGACTG
1 AAAAAAGACTG
47027 AAAGAGAAGACTG
1 AAA-A-AAGACTG
47040 AAAAAAGACTG
1 AAAAAAGACTG
*
47051 AAAGAAGACTG
1 AAAAAAGACTG
*
47062 AAAGAAGACTG
1 AAAAAAGACTG
47073 A
1 A
47074 CTTATTTCAA
Statistics
Matches: 132, Mismatches: 13, Indels: 21
0.80 0.08 0.13
Matches are distributed among these distances:
6 1 0.01
8 5 0.04
9 5 0.04
11 86 0.65
12 15 0.11
13 20 0.15
ACGTcount: A:0.60, C:0.09, G:0.22, T:0.09
Consensus pattern (11 bp):
AAAAAAGACTG
Found at i:46950 original size:28 final size:27
Alignment explanation
Indices: 46918--46975 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
46908 AAAGAAGACG
*
46918 GAAAAAAGACTAAAAAAATACTGAAAAA
1 GAAAAAAGACTAAAAAAAGACT-AAAAA
* *
46946 GAAAAAAGACTGAAAGAAGACTAAAAA
1 GAAAAAAGACTAAAAAAAGACTAAAAA
46973 GAA
1 GAA
46976 GACTGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.69, C:0.07, G:0.16, T:0.09
Consensus pattern (27 bp):
GAAAAAAGACTAAAAAAAGACTAAAAA
Found at i:46952 original size:17 final size:18
Alignment explanation
Indices: 46930--46965 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
46920 AAAAAGACTA
*
46930 AAAAAATACTGAAA-AAG
1 AAAAAAGACTGAAAGAAG
46947 AAAAAAGACTGAAAGAAG
1 AAAAAAGACTGAAAGAAG
46965 A
1 A
46966 CTAAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.69, C:0.06, G:0.17, T:0.08
Consensus pattern (18 bp):
AAAAAAGACTGAAAGAAG
Found at i:46952 original size:18 final size:19
Alignment explanation
Indices: 46929--47058 Score: 57
Period size: 24 Copynumber: 6.1 Consensus size: 19
46919 AAAAAAGACT
*
46929 AAAAAAATACTGAAA-AAG
1 AAAAAAAGACTGAAAGAAG
46947 -AAAAAAGACTGAAAGAAG
1 AAAAAAAGACTGAAAGAAG
*
46965 ACTAAAAAGAAGACTGAAAAAAG
1 ---AAAAA-AAGACTGAAAGAAG
*
46988 ACTGAAACAAGACTGAAAGAGAAG
1 A---AAAAAAGACTG-AA-AGAAG
*
47012 ACTGAAATAAGACTGAAAGAGAAG
1 A---AAAAAAGACTG-AA-AGAAG
47036 ACTGAAAAAAGACTGAAAGAAG
1 A---AAAAAAGACTGAAAGAAG
47058 A
1 A
47059 CTGAAAGAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
17 13 0.14
18 3 0.03
20 1 0.01
22 17 0.18
23 20 0.21
24 41 0.43
ACGTcount: A:0.62, C:0.08, G:0.21, T:0.09
Consensus pattern (19 bp):
AAAAAAAGACTGAAAGAAG
Found at i:46966 original size:39 final size:41
Alignment explanation
Indices: 46907--47069 Score: 119
Period size: 39 Copynumber: 4.0 Consensus size: 41
46897 GAAATTAGGC
*
46907 AAAAGAAGACGGAAAAAAGACTAAAAA-AATACTGAAAAAG
1 AAAAGAAGACGGAAAAAAGACTAAAAAGAAGACTGAAAAAG
* *
46947 AAAA-AAGACTGAAAGAAGACTAAAAAGAAGACTGAAAAAAG
1 AAAAGAAGACGGAAAAAAGACTAAAAAGAAGACTG-AAAAAG
* * * *
46988 ACTGAAACAAGACTGAAAGAGAAGACT-GAAATAAGACTG--AAAG
1 A---AAAGAAGACGGAAA-A-AAGACTAAAAAGAAGACTGAAAAAG
* *
47031 ---AGAAGACTGAAAAAAGACT-GAAAGAAGACTGAAAGAAG
1 AAAAGAAGACGGAAAAAAGACTAAAAAGAAGACTGAAA-AAG
47069 A
1 A
47070 CTGACTTATT
Statistics
Matches: 103, Mismatches: 8, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
35 17 0.17
36 1 0.01
37 12 0.12
38 3 0.03
39 20 0.19
40 10 0.10
41 7 0.07
43 4 0.04
44 3 0.03
45 10 0.10
46 10 0.10
47 6 0.06
ACGTcount: A:0.61, C:0.09, G:0.21, T:0.09
Consensus pattern (41 bp):
AAAAGAAGACGGAAAAAAGACTAAAAAGAAGACTGAAAAAG
Found at i:47011 original size:35 final size:34
Alignment explanation
Indices: 46907--47073 Score: 186
Period size: 35 Copynumber: 5.0 Consensus size: 34
46897 GAAATTAGGC
* * * *
46907 AAAAGAAGACGGAAAAAAGACTAAAAAAATACTG
1 AAAAGAAGACTGAAAAAAGACTGAAAGAAGACTG
*
46941 --AA-AA-A--GAAAAAAGACTGAAAGAAGACTA
1 AAAAGAAGACTGAAAAAAGACTGAAAGAAGACTG
*
46969 AAAAGAAGACTGAAAAAAGACTGAAACAAGACTG
1 AAAAGAAGACTGAAAAAAGACTGAAAGAAGACTG
*
47003 AAAGAGAAGACTGAAATAAGACTGAAAGAGAAGACTG
1 AAA-AGAAGACTGAAAAAAGACTG-AA-AGAAGACTG
*
47040 AAAA-AAGACTGAAAGAAGACTGAAAGAAGACTG
1 AAAAGAAGACTGAAAAAAGACTGAAAGAAGACTG
47073 A
1 A
47074 CTTATTTCAA
Statistics
Matches: 115, Mismatches: 9, Indels: 19
0.80 0.06 0.13
Matches are distributed among these distances:
28 19 0.17
30 3 0.03
31 4 0.03
32 3 0.03
33 10 0.09
34 26 0.23
35 36 0.31
36 3 0.03
37 11 0.10
ACGTcount: A:0.60, C:0.09, G:0.22, T:0.09
Consensus pattern (34 bp):
AAAAGAAGACTGAAAAAAGACTGAAAGAAGACTG
Found at i:47017 original size:24 final size:23
Alignment explanation
Indices: 46946--47073 Score: 172
Period size: 24 Copynumber: 5.6 Consensus size: 23
46936 TACTGAAAAA
46946 GAAAAAAGACTG-AAAGAAGACT
1 GAAAAAAGACTGAAAAGAAGACT
*
46968 AAAAAGAAGACTGAAAA-AAGACT
1 GAAAA-AAGACTGAAAAGAAGACT
*
46991 GAAACAAGACTGAAAGAGAAGACT
1 GAAAAAAGACTGAAA-AGAAGACT
*
47015 GAAATAAGACTGAAAGAGAAGACT
1 GAAAAAAGACTGAAA-AGAAGACT
47039 GAAAAAAGACTG-AAAGAAGACT
1 GAAAAAAGACTGAAAAGAAGACT
*
47061 GAAAGAAGACTGA
1 GAAAAAAGACTGA
47074 CTTATTTCAA
Statistics
Matches: 95, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
22 33 0.35
23 19 0.20
24 43 0.45
ACGTcount: A:0.58, C:0.09, G:0.23, T:0.09
Consensus pattern (23 bp):
GAAAAAAGACTGAAAAGAAGACT
Found at i:47147 original size:36 final size:36
Alignment explanation
Indices: 47066--47311 Score: 329
Period size: 36 Copynumber: 6.9 Consensus size: 36
47056 AGACTGAAAG
* *
47066 AAGACTGACTTA-TTTCAAGGAAATTAGGTAAA-AG
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
*
47100 AAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
* * *
47136 AAGACTGGCTTAATTTTAAGGAAATTAGGTAAA-AG
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
* * *
47171 AAGACTGGCTTAGTTTCCAGGAAACTAAGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
*
47207 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
* * *
47243 ATGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGA
1 AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
*
47279 AAGACTGGCTT-GATTTCAAGGAAATTAAGTAAA
1 AAGACTGGCTTAG-TTTCAAGGAAATTAGGTAAA
47312 AGGACACATG
Statistics
Matches: 186, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
34 11 0.06
35 48 0.26
36 127 0.68
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (36 bp):
AAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAA
Found at i:47161 original size:71 final size:71
Alignment explanation
Indices: 47066--47313 Score: 365
Period size: 71 Copynumber: 3.5 Consensus size: 71
47056 AGACTGAAAG
*
47066 AAGACTGACTT-ATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGT
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGT
47130 AAAGAA
66 AAAGAA
* * *
47136 AAGACTGGCTTAATTTTAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCCAGGAAACTAAGT
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGT
47201 AAAGAA
66 AAAGAA
* * * *
47207 AAGACTGGCTTAGTTTCAAGGAAACTAGGT-AAAGAAATGACTGGCTTAATTTCAAGGAAATTAG
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAG-AA-GACTGGCTTAGTTTCAAGGAAATTAA
*
47271 GTAAAGGA
64 GTAAAGAA
* *
47279 AAGACTGGCTTGATTTCAAGGAAATTAAGTAAAAG
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAG
47314 GACACATGCT
Statistics
Matches: 158, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
70 14 0.09
71 85 0.54
72 55 0.35
73 4 0.03
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (71 bp):
AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGT
AAAGAA
Found at i:47228 original size:107 final size:106
Alignment explanation
Indices: 47062--47312 Score: 371
Period size: 107 Copynumber: 2.4 Consensus size: 106
47052 AAGAAGACTG
* * * *
47062 AAAGAAGACTGACTTA-TTTCAAGGAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGGAAATT
1 AAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAAAAAGACTGGCTTAGTTTCAAGGAAACT
*
47126 AAGTAAAGAAAAGACTGGCTTAATTTTAAGGAAATTAGGTA
66 AAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
* *
47167 AAAGAAGACTGGCTTAGTTTCCAGGAAACTAAGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAAC
1 AAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGTAAA-AAAAGACTGGCTTAGTTTCAAGGAAAC
* *
47232 TAGGTAAAGAAATGACTGGCTTAATTTCAAGGAAATTAGGTA
65 TAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
*
47274 AAGGAAAGACTGGCTT-GATTTCAAGGAAATTAAGTAAAA
1 AAAG-AAGACTGGCTTAG-TTTCAAGGAAATTAAGTAAAA
47313 GGACACATGC
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
105 15 0.12
106 17 0.13
107 69 0.53
108 29 0.22
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (106 bp):
AAAGAAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAAAAAGACTGGCTTAGTTTCAAGGAAACT
AAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTAGGTA
Found at i:47390 original size:36 final size:34
Alignment explanation
Indices: 47350--47468 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 34
47340 AATTAAGTAA
*
47350 AATAAAGAACTTAATTCAGTGTAATTGAGTGAGGTC
1 AATAAAGAACTTAATTCAG-GTAATTAAGTGA-GTC
* *
47386 AATAAA-AGGCTTAATTTAGGGTAATTAAGT-AG--
1 AATAAAGA-ACTTAATTCA-GGTAATTAAGTGAGTC
*
47418 AATAAAGAACTTAATTCAAGGTAATTAAGTGAAATC
1 AATAAAGAACTTAATTC-AGGTAATTAAGTG-AGTC
47454 AATAAAGAACTTAAT
1 AATAAAGAACTTAAT
47469 CTAAAAAAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
32 24 0.35
33 2 0.03
34 2 0.03
35 2 0.03
36 38 0.55
37 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (34 bp):
AATAAAGAACTTAATTCAGGTAATTAAGTGAGTC
Found at i:47431 original size:32 final size:32
Alignment explanation
Indices: 47340--47447 Score: 110
Period size: 32 Copynumber: 3.2 Consensus size: 32
47330 CAGGAATGGA
* *
47340 AATTAAGTAAAATAAAGAACTTAATTCAGTGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
* * *
47372 AATTGAGTGAGGTCAATAAA-AGGCTTAATTTAGGGT
1 AATTAAGT-A-G--AATAAAGA-ACTTAATTCAGGGT
*
47408 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
47440 AATTAAGT
1 AATTAAGT
47448 GAAATCAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
32 32 0.52
33 2 0.03
34 1 0.02
35 2 0.03
36 24 0.39
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.31
Consensus pattern (32 bp):
AATTAAGTAGAATAAAGAACTTAATTCAGGGT
Found at i:47467 original size:68 final size:68
Alignment explanation
Indices: 47340--47468 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 68
47330 CAGGAATGGA
* ** *
47340 AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTGAGTGAGGTCAATAAAAGGCTTAATTTAG
1 AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAAATCAATAAAAGACTTAATTTAG
47405 GGT
66 GGT
*
47408 AATTAAGTAGAATAAAGAACTTAATTCAAG-GTAATTAAGTGAAATCAAT-AAAGAACTTAAT
1 AATTAAGTAAAATAAAGAACTTAATTC-AGTGTAATTAAGTGAAATCAATAAAAG-ACTTAAT
47469 CTAAAAAAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 4 0.07
68 48 0.89
69 2 0.04
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.29
Consensus pattern (68 bp):
AATTAAGTAAAATAAAGAACTTAATTCAGTGTAATTAAGTGAAATCAATAAAAGACTTAATTTAG
GGT
Done.