Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011946.1 Corchorus capsularis cultivar CVL-1 contig11967, 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: 65618
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:12203 original size:10 final size:11
Alignment explanation
Indices: 12185--12216 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
12175 GATTAATTAA
12185 TATTTTTTTAT
1 TATTTTTTTAT
12196 TATTTTTTTAT
1 TATTTTTTTAT
12207 TATTTTTTTA
1 TATTTTTTTA
12217 AGCAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TATTTTTTTAT
Found at i:13328 original size:5 final size:5
Alignment explanation
Indices: 13312--13341 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
13302 ATCGAAAAAT
13312 ATAAA A-AAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
13342 ATTTCGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:15749 original size:33 final size:33
Alignment explanation
Indices: 15711--15794 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
15701 AGCACAAGTG
*
15711 ACCGGCCACGCGACTTGGAGATGCC-CTCGCAAC
1 ACCGGCCACGCGACATGGAGATGCCTCTC-CAAC
* * *
15744 ACCGGCCATGCGACATGGAGATGCCTGTCCATC
1 ACCGGCCACGCGACATGGAGATGCCTCTCCAAC
15777 ACCGGCCACGCGACATGG
1 ACCGGCCACGCGACATGG
15795 CCAAGCCTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.21, C:0.37, G:0.29, T:0.13
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGCCTCTCCAAC
Found at i:15803 original size:33 final size:32
Alignment explanation
Indices: 15711--15818 Score: 99
Period size: 33 Copynumber: 3.3 Consensus size: 32
15701 AGCACAAGTG
* * * * *
15711 ACCGGCCACGCGACTTGGAGATGCCCTCGCAAC
1 ACCGGCCACGCGACATGGACAAG-CCTGGCCAC
* * * *
15744 ACCGGCCATGCGACATGGAGATGCCTGTCCATC
1 ACCGGCCACGCGACATGGACAAGCCTGGCCA-C
*
15777 ACCGGCCACGCGACATGGCCAAGCCTGGCCAC
1 ACCGGCCACGCGACATGGACAAGCCTGGCCAC
15809 ACCCGGCCAC
1 A-CCGGCCAC
15819 ATGACTCGGC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 7 0.11
33 56 0.89
ACGTcount: A:0.21, C:0.41, G:0.27, T:0.11
Consensus pattern (32 bp):
ACCGGCCACGCGACATGGACAAGCCTGGCCAC
Found at i:15830 original size:33 final size:33
Alignment explanation
Indices: 15793--15855 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
15783 CACGCGACAT
*
15793 GGCCAAGC-CTGGCCACACCCGGCCACATGACTC
1 GGCCAAGCTC-GGCCACAACCGGCCACATGACTC
* *
15826 GGCCATGCTCGGCCACAACCGGCCATATGA
1 GGCCAAGCTCGGCCACAACCGGCCACATGA
15856 TCCTTTAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.96
34 1 0.04
ACGTcount: A:0.22, C:0.41, G:0.25, T:0.11
Consensus pattern (33 bp):
GGCCAAGCTCGGCCACAACCGGCCACATGACTC
Found at i:16342 original size:19 final size:18
Alignment explanation
Indices: 16320--16358 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16310 ACACAAGTCA
16320 AGTTAATCAATAAAAGTTG
1 AGTTAATCAAT-AAAGTTG
* *
16339 AGTTGATTAATAAAGTTG
1 AGTTAATCAATAAAGTTG
16357 AG
1 AG
16359 GATTATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (18 bp):
AGTTAATCAATAAAGTTG
Found at i:16785 original size:8 final size:8
Alignment explanation
Indices: 16772--16805 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
16762 CACCTTCTTG
16772 AAAAATTC
1 AAAAATTC
16780 AAAAATTC
1 AAAAATTC
*
16788 AGAAACTTC
1 A-AAAATTC
16797 AAAAATTC
1 AAAAATTC
16805 A
1 A
16806 TAACTGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:16897 original size:10 final size:10
Alignment explanation
Indices: 16884--16914 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
16874 ATCGAAAACT
16884 ATAAAAAAAA
1 ATAAAAAAAA
16894 AT-AAAAAAA
1 ATAAAAAAAA
16903 ATAAAAAAAA
1 ATAAAAAAAA
16913 AT
1 AT
16915 TTCGACCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
ATAAAAAAAA
Found at i:16899 original size:9 final size:9
Alignment explanation
Indices: 16887--16912 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
16877 GAAAACTATA
16887 AAAAAAAAT
1 AAAAAAAAT
16896 AAAAAAAAT
1 AAAAAAAAT
16905 AAAAAAAA
1 AAAAAAAA
16913 ATTTCGACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:22307 original size:33 final size:33
Alignment explanation
Indices: 22269--22375 Score: 119
Period size: 33 Copynumber: 3.2 Consensus size: 33
22259 AGCACAAGTG
* *
22269 ACCGGCCACGTGACTTGGAGATGCCC-GCGCAAC
1 ACCGGCCACGCGACATGGAGATGCCCGGC-CAAC
* *
22302 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACATGGAGATGCCCGGCCAAC
** *
22335 ACCGGCCACGCGACATGGCCAAGCCCGGCC-AC
1 ACCGGCCACGCGACATGGAGATGCCCGGCCAAC
22367 AACCGGCCA
1 -ACCGGCCA
22376 TATGATCCTT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.02
33 60 0.95
34 2 0.03
ACGTcount: A:0.22, C:0.40, G:0.29, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGCCCGGCCAAC
Found at i:31072 original size:57 final size:57
Alignment explanation
Indices: 31009--31130 Score: 208
Period size: 57 Copynumber: 2.1 Consensus size: 57
30999 CCCCCTGGGC
31009 GCCCATGTAGATGGCTTGTGCGCCCAAGGCATTGCTCTCAGCCCCCATGTCGTCACT
1 GCCCATGTAGATGGCTTGTGCGCCCAAGGCATTGCTCTCAGCCCCCATGTCGTCACT
* * * *
31066 GCCCATGTAGATGGCTTGTGCGCCCAGGGCGTTGCTCTCATCCCCCATGTCGTCAGT
1 GCCCATGTAGATGGCTTGTGCGCCCAAGGCATTGCTCTCAGCCCCCATGTCGTCACT
31123 GCCCATGT
1 GCCCATGT
31131 GCTTGCTGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.25
Consensus pattern (57 bp):
GCCCATGTAGATGGCTTGTGCGCCCAAGGCATTGCTCTCAGCCCCCATGTCGTCACT
Found at i:33071 original size:13 final size:14
Alignment explanation
Indices: 33048--33097 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
33038 CCTTCATTCA
33048 TTTTCATTTTCATT
1 TTTTCATTTTCATT
*
33062 TTTTCA-TTTCTTT
1 TTTTCATTTTCATT
*
33075 TTTTCTTTTTTC-TT
1 TTTTC-ATTTTCATT
33089 TTTTC-TTTT
1 TTTTCATTTT
33098 TTTTGAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 4 0.12
13 11 0.34
14 13 0.41
15 4 0.12
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCATTTTCATT
Found at i:33100 original size:8 final size:7
Alignment explanation
Indices: 33054--33099 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
33044 TTCATTTTCA
33054 TTTTCATT
1 TTTTC-TT
*
33062 TTTTCAT
1 TTTTCTT
*
33069 TTCT-TT
1 TTTTCTT
33075 TTTTCTT
1 TTTTCTT
33082 TTTTCTT
1 TTTTCTT
33089 TTTTCTT
1 TTTTCTT
33096 TTTT
1 TTTT
33100 TTGAAAGGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
6 4 0.12
7 24 0.73
8 5 0.15
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:33529 original size:70 final size:69
Alignment explanation
Indices: 33300--33672 Score: 450
Period size: 70 Copynumber: 5.4 Consensus size: 69
33290 GTCTTGGAAG
* ** * *
33300 ACTGACTTCATATGGAAATGAACTTGGCTTATGGAAAAGCCCC----TGCTTGGATGGAACCAAG
1 ACTGAC-TCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCTTGGATGGAACCAAA
33361 GCTAA
65 GCTAA
* * * *** *
33366 ACTAACTCATATGGAAACGAGTTTGGCTAGTTGAAAAG-CCCTTGCTGCTTGGATGGAACCAAGG
1 ACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCTTGGATGGAACCAAAG
33430 CTAA
66 CTAA
* * *
33434 ATTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCTTGGATGGAACCAAAG
1 ACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCTTGGATGGAACCAAAG
*
33499 CTTGA
66 C-TAA
*
33504 ACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGTTTGGATGGAACCAAAG
1 ACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCTTGGATGGAACCAAAG
*
33569 CTTGA
66 C-TAA
* * * * *
33574 ACTGGCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATACTTGGATGGAACCAAAA
1 ACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCTTGGATGGAACCAAAG
33639 CTAA
66 CTAA
* * *
33643 ACTGACTCGTGTGGAAACGAGTTTGACTTG
1 ACTGACTCATATGGAAACGAGTTTGGCTTG
33673 AAAACTTAAA
Statistics
Matches: 269, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
64 3 0.01
65 26 0.10
66 5 0.02
68 55 0.20
69 52 0.19
70 128 0.48
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (69 bp):
ACTGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCTTGGATGGAACCAAAG
CTAA
Found at i:33697 original size:39 final size:38
Alignment explanation
Indices: 33635--33711 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
33625 GGATGGAACC
* * *
33635 AAAACTAAACTGACTCGTGTGGAAACGAGTTTGACTTG
1 AAAACTAAACTGACCCGTATGGAAACAAGTTTGACTTG
*
33673 AAAACTTAAACTGACCCGTATGGAAACAAGTTTGGCTTG
1 AAAAC-TAAACTGACCCGTATGGAAACAAGTTTGACTTG
33712 TGGAAAAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 5 0.15
39 29 0.85
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (38 bp):
AAAACTAAACTGACCCGTATGGAAACAAGTTTGACTTG
Found at i:34345 original size:15 final size:14
Alignment explanation
Indices: 34325--34381 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
34315 TTCTTCATTC
*
34325 TCTTTTTTTTCTTT
1 TCTTTTTTTTTTTT
34339 TCTTTTTTTCTTTTT
1 TCTTTTTTT-TTTTT
34354 TCTTTTCTTTTTTTT
1 TCTTTT-TTTTTTTT
*
34369 TACTTTCTTTTTT
1 T-CTTTTTTTTTT
34382 ACATGCACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
14 9 0.24
15 22 0.58
16 7 0.18
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (14 bp):
TCTTTTTTTTTTTT
Found at i:34354 original size:20 final size:20
Alignment explanation
Indices: 34329--34367 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
34319 TCATTCTCTT
34329 TTTTTTCTTTTCTTTTTTTC
1 TTTTTTCTTTTCTTTTTTTC
34349 TTTTTTCTTTTCTTTTTTT
1 TTTTTTCTTTTCTTTTTTT
34368 TTACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (20 bp):
TTTTTTCTTTTCTTTTTTTC
Found at i:34365 original size:31 final size:32
Alignment explanation
Indices: 34311--34379 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
34301 CCCTAGAGCC
34311 TCTTTTCTTCATTCTCTTTTTTTTCTTTT-CTT
1 TCTTTTCTTCATTCTCTTTTTTTT-TTTTACTT
**
34343 T-TTTTCTTTTTTCT-TTTCTTTTTTTTTACTT
1 TCTTTTCTTCATTCTCTTT-TTTTTTTTTACTT
34374 TCTTTT
1 TCTTTT
34380 TTACATGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 7 0.22
31 20 0.62
32 5 0.16
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (32 bp):
TCTTTTCTTCATTCTCTTTTTTTTTTTTACTT
Found at i:34375 original size:20 final size:20
Alignment explanation
Indices: 34332--34379 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
34322 TTCTCTTTTT
*
34332 TTTCTTTTCTTTTTTTCTTT
1 TTTCTTTTCTTTTTTTCTTC
34352 TTTCTTTTCTTTTTTT-TTAC
1 TTTCTTTTCTTTTTTTCTT-C
34372 TTTCTTTT
1 TTTCTTTT
34380 TTACATGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTCTTTTCTTTTTTTCTTC
Found at i:34382 original size:12 final size:11
Alignment explanation
Indices: 34327--34383 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
34317 CTTCATTCTC
34327 TTTTTTTT-CTT
1 TTTTTTTTAC-T
*
34338 TTCTTTTTTTCT
1 TT-TTTTTTACT
*
34350 TTTTTCTTTTCT
1 TTTTT-TTTACT
34362 TTTTTTTTACT
1 TTTTTTTTACT
34373 TTCTTTTTTAC
1 TT-TTTTTTAC
34384 ATGCACTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
11 12 0.29
12 28 0.68
13 1 0.02
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTACT
Found at i:34716 original size:24 final size:26
Alignment explanation
Indices: 34689--34742 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
34679 TTCACCCTTC
* *
34689 CTTTCACTTTC-ATTTTCATT-TTTT
1 CTTTCACTTTCAAATTTCATTCATTT
34713 CTTTCACTTTCAAATTTCATTCATTT
1 CTTTCACTTTCAAATTTCATTCATTT
34739 CTTT
1 CTTT
34743 TGGATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 11 0.42
25 8 0.31
26 7 0.27
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (26 bp):
CTTTCACTTTCAAATTTCATTCATTT
Found at i:35158 original size:45 final size:44
Alignment explanation
Indices: 35100--35184 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 44
35090 TGGAAAACCA
35100 TTTTATCAAAAACCTTTTGAAAACCATGACTCTTTTTGAAAAAGGC
1 TTTTATCAAAAACCTTTTGAAAACCATGA--CTTTTTGAAAAAGGC
35146 TTTTATC-AAAACCTTTTGAAAACCATGACTTTTTGAAAA
1 TTTTATCAAAAACCTTTTGAAAACCATGACTTTTTGAAAA
35185 CCATCGTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
43 11 0.28
45 21 0.54
46 7 0.18
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (44 bp):
TTTTATCAAAAACCTTTTGAAAACCATGACTTTTTGAAAAAGGC
Found at i:35215 original size:16 final size:18
Alignment explanation
Indices: 35194--35234 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
35184 ACCATCGTTC
35194 CTTTTTTCCT-TTC-TTT
1 CTTTTTTCCTCTTCTTTT
*
35210 CTTTTTT-TTCTTCTTTT
1 CTTTTTTCCTCTTCTTTT
35227 CTTTTTTC
1 CTTTTTTC
35235 TCTGGGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 10 0.48
17 10 0.48
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
CTTTTTTCCTCTTCTTTT
Found at i:35217 original size:17 final size:17
Alignment explanation
Indices: 35195--35233 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
35185 CCATCGTTCC
35195 TTTTTTCCTT-TCTTTCT
1 TTTTTTCCTTCT-TTTCT
*
35212 TTTTTTTCTTCTTTTCT
1 TTTTTTCCTTCTTTTCT
35229 TTTTT
1 TTTTT
35234 CTCTGGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCCTTCTTTTCT
Found at i:41714 original size:10 final size:10
Alignment explanation
Indices: 41699--41724 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41689 CTAATGAGAC
41699 TTTTTTTTCT
1 TTTTTTTTCT
41709 TTTTTTTTCT
1 TTTTTTTTCT
41719 TTTTTT
1 TTTTTT
41725 ATGTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:47360 original size:122 final size:124
Alignment explanation
Indices: 47076--47377 Score: 364
Period size: 122 Copynumber: 2.4 Consensus size: 124
47066 CCTAGCATGA
* * *
47076 CCCCGACTGGCAGGAGATCGGCACGAACCATCCCTAACCAAGTATGGGAAGAATAACGCCCTCAA
1 CCCCGACTGGCAGGAGATCGGCACGAACCATCCTTGACCAAGTATGGGAAGAAGAACGCCCT-AA
*
47141 AAGGGTTCAACGCCAACCGACGAGCACCAAGCATAAGCTGGCCTCGATCAAAGATATGGC
65 AAGGGCTCAACGCCAACCGACGAGCACCAAGCATAAGCTGGCCTCGATCAAAGATATGGC
* * * * *
47201 CCCCAACTGGCAGGAGATTGGCACAAACCATCATTGACCAAGTATGGGAAGACAGCAC-CCCT-A
1 CCCCGACTGGCAGGAGATCGGCACGAACCATCCTTGACCAAGTATGGGAAGA-AGAACGCCCTAA
** * * *
47264 AAGGGCTCAACGCCAGTCGACGAGCGCC-GGTTC-TAAG-TCGGCCTCGGTCAAAG-TATGGC
65 AAGGGCTCAACGCCAACCGACGAGCACCAAG--CATAAGCT-GGCCTCGATCAAAGATATGGC
* * *
47323 CCCCGATTGGCAGGAGATCGGCACGAACCATCCTTGACCAAATAAGGGAAGAAGA
1 CCCCGACTGGCAGGAGATCGGCACGAACCATCCTTGACCAAGTATGGGAAGAAGA
47378 GCATCCTCAA
Statistics
Matches: 151, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
121 2 0.01
122 53 0.35
123 42 0.28
124 1 0.01
125 50 0.33
126 3 0.02
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Consensus pattern (124 bp):
CCCCGACTGGCAGGAGATCGGCACGAACCATCCTTGACCAAGTATGGGAAGAAGAACGCCCTAAA
AGGGCTCAACGCCAACCGACGAGCACCAAGCATAAGCTGGCCTCGATCAAAGATATGGC
Found at i:54687 original size:32 final size:33
Alignment explanation
Indices: 54651--54713 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
54641 TTAAATCGCA
** *
54651 AATTTTTTTTTTTTAG-AAAAATCGGAAAAAGG
1 AATTTTTTTTTTAAAGAAAAAAACGGAAAAAGG
54683 AATTTTTTTTTTAAAGAAAAAAACGGAAAAA
1 AATTTTTTTTTTAAAGAAAAAAACGGAAAAA
54714 AACAAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.37
Consensus pattern (33 bp):
AATTTTTTTTTTAAAGAAAAAAACGGAAAAAGG
Found at i:61521 original size:59 final size:59
Alignment explanation
Indices: 61455--61576 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
61445 GGAATAAAAG
61455 ATCAATCCATCAACAATCAAATTGTAATCCTAGGTTTTCATGCAACTCATGCAAAAACT
1 ATCAATCCATCAACAATCAAATTGTAATCCTAGGTTTTCATGCAACTCATGCAAAAACT
61514 ATCAATCCATCAACAATCAAATTGTAATCCTAGGTTTTCATGCAACTCATGCAAAAACT
1 ATCAATCCATCAACAATCAAATTGTAATCCTAGGTTTTCATGCAACTCATGCAAAAACT
61573 ATCA
1 ATCA
61577 TATGACTCAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (59 bp):
ATCAATCCATCAACAATCAAATTGTAATCCTAGGTTTTCATGCAACTCATGCAAAAACT
Done.