Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011778.1 Corchorus capsularis cultivar CVL-1 contig11799, 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: 126568
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3985 original size:31 final size:32
Alignment explanation
Indices: 3913--3985 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
3903 CTTTGGGTTT
* * *
3913 GGGTTCGGG-TAAAATTGGGTCGGGTTGATTC
1 GGGTTCGGGTTAAAATTGGGTCAGATTAATTC
*
3944 GGGTTCGGGTTAAATTTGGGTCAGATTAATTC
1 GGGTTCGGGTTAAAATTGGGTCAGATTAATTC
3976 GGGTT-GGGTT
1 GGGTTCGGGTT
3986 TTAGCCAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.16, C:0.08, G:0.40, T:0.36
Consensus pattern (32 bp):
GGGTTCGGGTTAAAATTGGGTCAGATTAATTC
Found at i:4147 original size:20 final size:20
Alignment explanation
Indices: 4114--4152 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4104 CATAGATGAA
*
4114 ATTTTCATAAATTATTATTT
1 ATTTTCATAAATTAGTATTT
4134 ATTTTCA-AATATTAGTATT
1 ATTTTCATAA-ATTAGTATT
4153 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTCATAAATTAGTATTT
Found at i:4188 original size:22 final size:22
Alignment explanation
Indices: 4160--4201 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4150 ATTGAATTCA
4160 GGTTTTTTCAGGTTCGGGTTCG
1 GGTTTTTTCAGGTTCGGGTTCG
* *
4182 GGTTTTTTCGGGTTTGGGTT
1 GGTTTTTTCAGGTTCGGGTT
4202 TTATCGAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.10, G:0.38, T:0.50
Consensus pattern (22 bp):
GGTTTTTTCAGGTTCGGGTTCG
Found at i:4191 original size:16 final size:16
Alignment explanation
Indices: 4172--4250 Score: 79
Period size: 16 Copynumber: 4.9 Consensus size: 16
4162 TTTTTTCAGG
4172 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
*
4188 TTCGGGTTTGGGTTTT
1 TTCGGGTTCGGGTTTT
* * * *
4204 ATCGAGTTTC-AGATTT
1 TTCG-GGTTCGGGTTTT
4220 TTCGGGTTCGGGATTTT
1 TTCGGGTTCGGG-TTTT
*
4237 TTTGGGTTCGGGTT
1 TTCGGGTTCGGGTT
4251 CGGGCGGGTC
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
15 4 0.08
16 28 0.57
17 17 0.35
ACGTcount: A:0.06, C:0.10, G:0.34, T:0.49
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:5923 original size:2 final size:2
Alignment explanation
Indices: 5916--5942 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5906 TATGTATAGT
5916 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5943 GCACACAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9023 original size:20 final size:21
Alignment explanation
Indices: 9000--9059 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
8990 ATTATTATTG
*
9000 TTTTATTATTATTAATCAATT
1 TTTTATTATTATTAATCAATA
* *
9021 TTTTA-TATTATTAATTACTA
1 TTTTATTATTATTAATCAATA
* *
9041 TATTATTATTATTGATCAA
1 TTTTATTATTATTAATCAA
9060 CAATATCCCC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATTATTAATCAATA
Found at i:13278 original size:2 final size:2
Alignment explanation
Indices: 13271--13297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13261 TTGATTATTC
13271 AT AT AT 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 A
13298 GAAAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35480 original size:2 final size:2
Alignment explanation
Indices: 35475--35499 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35465 AGTAAAAAAA
35475 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35500 ACCTACATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39017 original size:44 final size:44
Alignment explanation
Indices: 38954--39041 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
38944 GGTTTAAAAT
38954 AATCCTTTATCTTTTAGTTTGTTAATTAAAGCGTATGCATCAAC
1 AATCCTTTATCTTTTAGTTTGTTAATTAAAGCGTATGCATCAAC
38998 AATCCTTTATCTTTTAGTTTGTTAATTAAAGCGTATGCATCAAC
1 AATCCTTTATCTTTTAGTTTGTTAATTAAAGCGTATGCATCAAC
39042 CATTTGTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (44 bp):
AATCCTTTATCTTTTAGTTTGTTAATTAAAGCGTATGCATCAAC
Found at i:39234 original size:30 final size:30
Alignment explanation
Indices: 39199--39260 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
39189 AGAAAGATGC
39199 TAACTATAGTTTAGAATTAGAAGATGTATG
1 TAACTATAGTTTAGAATTAGAAGATGTATG
39229 TAACTATAGTTTAGAATTAGAAGATGTATG
1 TAACTATAGTTTAGAATTAGAAGATGTATG
39259 TA
1 TA
39261 GATTAATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (30 bp):
TAACTATAGTTTAGAATTAGAAGATGTATG
Found at i:45930 original size:18 final size:17
Alignment explanation
Indices: 45898--45931 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
45888 TCTTGGTTTC
45898 GCTTCGCTTCAGCTTCA
1 GCTTCGCTTCAGCTTCA
*
45915 GCTTCTGCTTCTGCTTC
1 GCTTC-GCTTCAGCTTC
45932 TTCTGCTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.06, C:0.35, G:0.18, T:0.41
Consensus pattern (17 bp):
GCTTCGCTTCAGCTTCA
Found at i:65600 original size:28 final size:27
Alignment explanation
Indices: 65569--65627 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
65559 GTCTGGTGCC
* *
65569 AAAACTGCCATGATCAGTGTCCAAAGG
1 AAAAATGCCATGATCACTGTCCAAAGG
*
65596 AAAAATGCCATGATCACTGTGCAAAGG
1 AAAAATGCCATGATCACTGTCCAAAGG
65623 AAAAA
1 AAAAA
65628 GAAAAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (27 bp):
AAAAATGCCATGATCACTGTCCAAAGG
Found at i:66137 original size:18 final size:19
Alignment explanation
Indices: 66114--66150 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
66104 ACCCTAAACC
66114 CCACAAAAT-AAACCCCAT
1 CCACAAAATAAAACCCCAT
66132 CCACAAAATAAAACCCCAT
1 CCACAAAATAAAACCCCAT
66151 TAAAATAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.51, C:0.38, G:0.00, T:0.11
Consensus pattern (19 bp):
CCACAAAATAAAACCCCAT
Found at i:66816 original size:35 final size:36
Alignment explanation
Indices: 66761--66828 Score: 129
Period size: 35 Copynumber: 1.9 Consensus size: 36
66751 TTAATTAGAA
66761 TTTAACTTTCTGGCCAAAAAGAAATTAGGATTTAAG
1 TTTAACTTTCTGGCCAAAAAGAAATTAGGATTTAAG
66797 TTTAACTTTC-GGCCAAAAAGAAATTAGGATTT
1 TTTAACTTTCTGGCCAAAAAGAAATTAGGATTT
66829 TTTTGAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 22 0.69
36 10 0.31
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (36 bp):
TTTAACTTTCTGGCCAAAAAGAAATTAGGATTTAAG
Found at i:67241 original size:22 final size:22
Alignment explanation
Indices: 67200--67241 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
67190 GACAAACCCG
**
67200 TAACCCGAATAATATGAGAAGT
1 TAACCCGAATAATACAAGAAGT
*
67222 TAACCCGAATAATCCAAGAA
1 TAACCCGAATAATACAAGAA
67242 CATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (22 bp):
TAACCCGAATAATACAAGAAGT
Found at i:69113 original size:2 final size:2
Alignment explanation
Indices: 69063--69098 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
69053 TGTGAAGATC
69063 AT AT AT AT AT 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 AT AT AT AT AT
69099 TTTGCAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71324 original size:38 final size:38
Alignment explanation
Indices: 71273--71349 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
71263 GTTCAATGCC
71273 GGGTTTTGTTCTTTCAGATGGGAGGTGAAGGAAAGTCA
1 GGGTTTTGTTCTTTCAGATGGGAGGTGAAGGAAAGTCA
71311 GGGTTTTGTTCTTTCAGATGGGAGGTGAAGGAAAGTCA
1 GGGTTTTGTTCTTTCAGATGGGAGGTGAAGGAAAGTCA
71349 G
1 G
71350 TGCTCTTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.08, G:0.38, T:0.31
Consensus pattern (38 bp):
GGGTTTTGTTCTTTCAGATGGGAGGTGAAGGAAAGTCA
Found at i:78417 original size:19 final size:19
Alignment explanation
Indices: 78393--78434 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
78383 ATTAATGCAC
78393 TAATTGCCAATTGTATACA
1 TAATTGCCAATTGTATACA
78412 TAATTGCCAATTGTATACA
1 TAATTGCCAATTGTATACA
78431 TAAT
1 TAAT
78435 GCAGTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (19 bp):
TAATTGCCAATTGTATACA
Found at i:81082 original size:14 final size:14
Alignment explanation
Indices: 81065--81094 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
81055 TAAAATTTGA
*
81065 TTTCTTAAATGAAT
1 TTTCTTAAAAGAAT
81079 TTTCTTAAAAGAAT
1 TTTCTTAAAAGAAT
81093 TT
1 TT
81095 ATAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTCTTAAAAGAAT
Found at i:81928 original size:29 final size:30
Alignment explanation
Indices: 81896--81959 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
81886 TTGCCCCCAA
*
81896 AACTTCAATTTT-GGACATTTTACCCCCTG
1 AACTTCAATTTTGGGACATTTTACCCCCTC
* *
81925 AACTTCAATTTTGGGACGTTTTGCCCCCTC
1 AACTTCAATTTTGGGACATTTTACCCCCTC
81955 AACTT
1 AACTT
81960 AACGGCTCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (30 bp):
AACTTCAATTTTGGGACATTTTACCCCCTC
Found at i:81959 original size:30 final size:29
Alignment explanation
Indices: 81880--81959 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
81870 GTAGCGTTTA
*
81880 GACGTTTTGCCCCCAAAACTTCAATTTTG
1 GACGTTTTGCCCCCTAAACTTCAATTTTG
* * *
81909 GACATTTTACCCCCTGAACTTCAATTTTGG
1 GACGTTTTGCCCCCTAAACTTCAATTTT-G
*
81939 GACGTTTTGCCCCCTCAACTT
1 GACGTTTTGCCCCCTAAACTT
81960 AACGGCTCCG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 24 0.56
30 19 0.44
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (29 bp):
GACGTTTTGCCCCCTAAACTTCAATTTTG
Found at i:82995 original size:20 final size:19
Alignment explanation
Indices: 82943--83014 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 19
82933 CAGATTATTA
* *
82943 ATTACTTATTATTATTATTT
1 ATTAATTATTATT-TTTTTT
82963 ATTAAAGTATATTATTGTTTTTT
1 ATT-AA-T-TATTATT-TTTTTT
*
82986 ATTAATTATTAATTTCTTTT
1 ATTAATTATT-ATTTTTTTT
*
83006 ATTTATTAT
1 ATTAATTAT
83015 GACATTGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 20 0.47
21 5 0.12
22 3 0.07
23 15 0.35
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
ATTAATTATTATTTTTTTT
Found at i:84239 original size:31 final size:30
Alignment explanation
Indices: 84204--84314 Score: 114
Period size: 31 Copynumber: 3.9 Consensus size: 30
84194 GGCATGCCAC
84204 GTGTCACTTTTTGGTACACGTGGCGTGACA
1 GTGTCACTTTTTGGTACACGTGGCGTGACA
*
84234 TGTGTCACTTTTTGGTACATGTGGC---AC-
1 -GTGTCACTTTTTGGTACACGTGGCGTGACA
*
84261 --G--ACTTTTTGGTACATGTGGCGTGCCACA
1 GTGTCACTTTTTGGTACACGTGGCGTG--ACA
84289 -TGTCACTTTTTGGTACACGTGGCGTG
1 GTGTCACTTTTTGGTACACGTGGCGTG
84315 CCACGTCGGA
Statistics
Matches: 69, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
22 19 0.28
24 1 0.01
27 2 0.03
28 2 0.03
29 1 0.01
31 44 0.64
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (30 bp):
GTGTCACTTTTTGGTACACGTGGCGTGACA
Found at i:84266 original size:53 final size:53
Alignment explanation
Indices: 84209--84311 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
84199 GCCACGTGTC
** *
84209 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
84262 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
84312 GTGCCACGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:85911 original size:8 final size:8
Alignment explanation
Indices: 85898--85924 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
85888 AATATCGATC
85898 TTCCCTGT
1 TTCCCTGT
85906 TTCCCTGT
1 TTCCCTGT
85914 TTCCCTGT
1 TTCCCTGT
85922 TTC
1 TTC
85925 TGTCATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.37, G:0.11, T:0.52
Consensus pattern (8 bp):
TTCCCTGT
Found at i:92841 original size:71 final size:71
Alignment explanation
Indices: 92760--92901 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
92750 GATTGATAAC
92760 TCCACTTCTTCTTGCCTAGCACGTGTTTCTTTTTTAATATATTTGGTTATTTGGTAACAAGAGAA
1 TCCACTTCTTCTTGCCTAGCACGTGTTTCTTTTTTAATATATTTGGTTATTTGGTAACAAGAGAA
92825 GATATA
66 GATATA
92831 TCCACTTCTTCTTGCCTAGCACGTGTTTCTTTTTTAATATATTTGGTTATTTGGTAACAAGAGAA
1 TCCACTTCTTCTTGCCTAGCACGTGTTTCTTTTTTAATATATTTGGTTATTTGGTAACAAGAGAA
92896 GATATA
66 GATATA
92902 GACTCTTTGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.44
Consensus pattern (71 bp):
TCCACTTCTTCTTGCCTAGCACGTGTTTCTTTTTTAATATATTTGGTTATTTGGTAACAAGAGAA
GATATA
Found at i:99660 original size:2 final size:2
Alignment explanation
Indices: 99653--99680 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
99643 TTAACTAGGC
99653 TA 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 TA
99681 GACACTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:124486 original size:29 final size:30
Alignment explanation
Indices: 124447--124506 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
124437 CTTTAAGGTC
124447 ATTGTTA-TTATCTTTGATGTTTATCAAGT
1 ATTGTTATTTATCTTTGATGTTTATCAAGT
*
124476 ATTGTTGTTATTATCTTTGATGTTTATCAAG
1 ATTGTT-AT-TTATCTTTGATGTTTATCAAG
124507 GTAATGAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.22
32 21 0.78
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.55
Consensus pattern (30 bp):
ATTGTTATTTATCTTTGATGTTTATCAAGT
Found at i:124502 original size:16 final size:16
Alignment explanation
Indices: 124451--124502 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
124441 AAGGTCATTG
124451 TTATTATCTTTGATGT
1 TTATTATCTTTGATGT
* ** *
124467 TTATCAAGTATTGTTG-
1 TTATTATCT-TTGATGT
124483 TTATTATCTTTGATGT
1 TTATTATCTTTGATGT
124499 TTAT
1 TTAT
124503 CAAGGTAATG
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (16 bp):
TTATTATCTTTGATGT
Found at i:126431 original size:21 final size:21
Alignment explanation
Indices: 126388--126431 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
126378 TTTTTTTGGG
* *
126388 TTGCTAAATACCGCCCTAGTT
1 TTGCTAAATACCGCCCCACTT
126409 TTGCTAAATACCGCCCCACTT
1 TTGCTAAATACCGCCCCACTT
126430 TT
1 TT
126432 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCACTT
Found at i:126454 original size:14 final size:15
Alignment explanation
Indices: 126430--126473 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
126420 CGCCCCACTT
*
126430 TTTACACTTTTGCCC
1 TTTACACTTTTACCC
126445 TTTA-ACTTTTACCC
1 TTTACACTTTTACCC
126459 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
126474 ATTGAGCCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 9 0.36
15 4 0.16
16 4 0.16
17 8 0.32
ACGTcount: A:0.18, C:0.27, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:126519 original size:33 final size:33
Alignment explanation
Indices: 126477--126564 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
126467 CTTTTACATT
*
126477 GAGCCTCCCCACTAGGACGGCTCAGCCA-CGGCA
1 GAGCCTCCCCACTAGGGCGGCTCA-CCATCGGCA
*
126510 GAGCCTCCCCACTAGGGCGGCTTCACCATGGGCA
1 GAGCCTCCCCACTAGGGCGGC-TCACCATCGGCA
*
126544 G-GCCGCCCCACTAGGGCGGCT
1 GAGCCTCCCCACTAGGGCGGCT
126565 TCGC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
32 1 0.02
33 41 0.82
34 8 0.16
ACGTcount: A:0.17, C:0.41, G:0.31, T:0.11
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGGCGGCTCACCATCGGCA
Done.