Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015819.1 Corchorus olitorius cultivar O-4 contig15852, 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: 133682
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1251 original size:3 final size:3
Alignment explanation
Indices: 1243--1280 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
1233 TATTATGTCT
1243 ATA ATA ATA ATA ATA AT- ATA ATA TATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT
1281 CCTTCTACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:5650 original size:24 final size:24
Alignment explanation
Indices: 5623--5668 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
5613 ACCGCCTCCA
*
5623 ACACC-AACACTCGTCCGTACCACG
1 ACACCGAA-ACTCGTCCGAACCACG
*
5647 ACACCGAAACTGGTCCGAACCA
1 ACACCGAAACTCGTCCGAACCA
5669 AATCGCCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.33, C:0.41, G:0.15, T:0.11
Consensus pattern (24 bp):
ACACCGAAACTCGTCCGAACCACG
Found at i:28684 original size:6 final size:6
Alignment explanation
Indices: 28670--28706 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
28660 TGGGCTGAGG
28670 AAAAA- AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AA
28707 TTCGCGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:35005 original size:13 final size:13
Alignment explanation
Indices: 34989--35016 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34979 GTTGAAACTG
34989 AAAAACAGAGCAA
1 AAAAACAGAGCAA
35002 AAAAACAGAGCAA
1 AAAAACAGAGCAA
35015 AA
1 AA
35017 CCATGAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAACAGAGCAA
Found at i:38937 original size:31 final size:31
Alignment explanation
Indices: 38899--39036 Score: 170
Period size: 31 Copynumber: 4.5 Consensus size: 31
38889 GGTGTCCAAC
* **
38899 GTGGCATGCCATGTGTATAAAAAAGCGACAT
1 GTGGCATGCCACGTGTACCAAAAAGCGACAT
*
38930 GTGGCATGCCATGTGTACCAAAAAGCGACAT
1 GTGGCATGCCACGTGTACCAAAAAGCGACAT
* * *
38961 GTGACACGCCACGTGTACCAAAAAGTGA-AT
1 GTGGCATGCCACGTGTACCAAAAAGCGACAT
** * *
38991 GTGGCACACCACGTGTACCAAAAAGTGACAC
1 GTGGCATGCCACGTGTACCAAAAAGCGACAT
39022 GTGGCATGCCACGTG
1 GTGGCATGCCACGTG
39037 CACAAAATGA
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 28 0.29
31 67 0.71
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (31 bp):
GTGGCATGCCACGTGTACCAAAAAGCGACAT
Found at i:39007 original size:61 final size:62
Alignment explanation
Indices: 38918--39036 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
38908 CATGTGTATA
** * *
38918 AAAAAGCGACATGTGGCATGCCATGTGTACCAAAAAGCGACATGTGACACGCCACGTGTACC
1 AAAAAGCGACATGTGGCACACCACGTGTACCAAAAAGCGACACGTGACACGCCACGTGTACC
* * * *
38980 AAAAAGTGA-ATGTGGCACACCACGTGTACCAAAAAGTGACACGTGGCATGCCACGTG
1 AAAAAGCGACATGTGGCACACCACGTGTACCAAAAAGCGACACGTGACACGCCACGTG
39037 CACAAAATGA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
61 41 0.84
62 8 0.16
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.16
Consensus pattern (62 bp):
AAAAAGCGACATGTGGCACACCACGTGTACCAAAAAGCGACACGTGACACGCCACGTGTACC
Found at i:40239 original size:29 final size:29
Alignment explanation
Indices: 40186--40260 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
40176 ACATGCAGAG
* * *
40186 GAGGTAAAACGTCCCAGAATTGAAGTTCA-
1 GAGGTAAAATGT-CCAAAATTGAAGCTCAT
40215 GAAGGTAAAATGTCCAAAATTGAAGCTCAT
1 G-AGGTAAAATGTCCAAAATTGAAGCTCAT
*
40245 G-GGCAAAATGTCCAAA
1 GAGGTAAAATGTCCAAA
40261 CTACAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 14 0.35
29 15 0.38
30 11 0.28
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (29 bp):
GAGGTAAAATGTCCAAAATTGAAGCTCAT
Found at i:54231 original size:27 final size:27
Alignment explanation
Indices: 54176--54231 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
54166 TATATACATC
* *
54176 TATTATTTGGAATAAATATATTATTTA
1 TATTATATGGAATAAATATATAATTTA
54203 TATTATATGGAATAAA-ATATAATTATA
1 TATTATATGGAATAAATATATAATT-TA
54230 TA
1 TA
54232 CATATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (27 bp):
TATTATATGGAATAAATATATAATTTA
Found at i:54288 original size:27 final size:24
Alignment explanation
Indices: 54242--54291 Score: 64
Period size: 27 Copynumber: 2.0 Consensus size: 24
54232 CATATTTTAA
54242 TATTTATATAAATAAAAATATAAT
1 TATTTATATAAATAAAAATATAAT
*
54266 TATTATATATATAATATATAATATAA
1 TATT-TATATA-AATA-AAAATATAA
54292 ACGAACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 6 0.27
26 4 0.18
27 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTTATATAAATAAAAATATAAT
Found at i:57059 original size:18 final size:18
Alignment explanation
Indices: 57036--57073 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
57026 TCCTGTCGGG
57036 GATG-TTCTATAGCCTATA
1 GATGTTTCTAT-GCCTATA
*
57054 GATGTTTCTATGCTTATA
1 GATGTTTCTATGCCTATA
57072 GA
1 GA
57074 ATCTATGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (18 bp):
GATGTTTCTATGCCTATA
Found at i:59260 original size:26 final size:26
Alignment explanation
Indices: 59208--59263 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
59198 TAGTATAATT
* **
59208 AAAACAAGTTTTAGATATGTAGCAAA
1 AAAACAAGTTTTAGATATGAAAAAAA
*
59234 AAAACAAGTTTTAGATCTGAAAAAAA
1 AAAACAAGTTTTAGATATGAAAAAAA
59260 AAAA
1 AAAA
59264 AAACTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.23
Consensus pattern (26 bp):
AAAACAAGTTTTAGATATGAAAAAAA
Found at i:79289 original size:18 final size:18
Alignment explanation
Indices: 79262--79298 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
79252 ATTTGAAAGT
*
79262 CTAATGAAATCGTAAATC
1 CTAATAAAATCGTAAATC
*
79280 CTAATAAAATTGTAAATC
1 CTAATAAAATCGTAAATC
79298 C
1 C
79299 CAATCAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (18 bp):
CTAATAAAATCGTAAATC
Found at i:83453 original size:72 final size:72
Alignment explanation
Indices: 83372--83520 Score: 262
Period size: 72 Copynumber: 2.1 Consensus size: 72
83362 ACAATTTCAA
* *
83372 AGTATATATTATAACATACGCGTTAATATATACACGACTTTTTTAACTATCAGTCACATGGTCTG
1 AGTATATATTATAACATACGCGTTAATATATACACGACTTTTTTAACCACCAGTCACATGGTCTG
83437 ATGATGG
66 ATGATGG
* *
83444 AGTATATATTATAACATACGCGTTAATATATACACGATTTTTTTAACCACCAGTCACGTGGTCTG
1 AGTATATATTATAACATACGCGTTAATATATACACGACTTTTTTAACCACCAGTCACATGGTCTG
83509 ATGATGG
66 ATGATGG
83516 AGTAT
1 AGTAT
83521 TTCCAGTAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (72 bp):
AGTATATATTATAACATACGCGTTAATATATACACGACTTTTTTAACCACCAGTCACATGGTCTG
ATGATGG
Found at i:87660 original size:88 final size:88
Alignment explanation
Indices: 87507--87679 Score: 301
Period size: 88 Copynumber: 2.0 Consensus size: 88
87497 AGAGTTTTCC
* * *
87507 TTATTTAGGGTCGATACAACGACCTGATTTGATTTGAATTAGTAGAATCCAATATCAAAGAGTTT
1 TTATTTAGGATCGATACAACAACCTGATTTGACTTGAATTAGTAGAATCCAATATCAAAGAGTTT
87572 TGTACCAAAAAATAATTAACCCT
66 TGTACCAAAAAATAATTAACCCT
* *
87595 TTATTTAGGATCGATACAGCAACCTGATTTGACTTGAATTAGTAGAATCCAATATCAAAGGGTTT
1 TTATTTAGGATCGATACAACAACCTGATTTGACTTGAATTAGTAGAATCCAATATCAAAGAGTTT
87660 TGTACCAAAAAATAATTAAC
66 TGTACCAAAAAATAATTAAC
87680 ATATTATTGT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (88 bp):
TTATTTAGGATCGATACAACAACCTGATTTGACTTGAATTAGTAGAATCCAATATCAAAGAGTTT
TGTACCAAAAAATAATTAACCCT
Found at i:98689 original size:20 final size:20
Alignment explanation
Indices: 98664--98704 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
98654 CATGTCATGG
98664 AAGATAAATTTGGTTTTGCA
1 AAGATAAATTTGGTTTTGCA
98684 AAGATAAATTTGGTTTTGCA
1 AAGATAAATTTGGTTTTGCA
98704 A
1 A
98705 GGTTAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
AAGATAAATTTGGTTTTGCA
Found at i:102664 original size:2 final size:2
Alignment explanation
Indices: 102657--102696 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
102647 ATTTGCTTAC
102657 AT AT 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 AT AT
102697 GGATTGGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102864 original size:20 final size:20
Alignment explanation
Indices: 102839--102880 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
102829 TGGTTAGGTC
102839 AAGATGTTATTGTTCCTTCT
1 AAGATGTTATTGTTCCTTCT
102859 AAGATGTTATTGTTCCTTCT
1 AAGATGTTATTGTTCCTTCT
102879 AA
1 AA
102881 TCCCATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (20 bp):
AAGATGTTATTGTTCCTTCT
Found at i:104368 original size:21 final size:21
Alignment explanation
Indices: 104342--104384 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
104332 CATGCATATA
104342 TTTTTATTTTATAGCATTGTT
1 TTTTTATTTTATAGCATTGTT
104363 TTTTTATTTTATAGCATTGTT
1 TTTTTATTTTATAGCATTGTT
104384 T
1 T
104385 ACGCGGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.05, G:0.09, T:0.67
Consensus pattern (21 bp):
TTTTTATTTTATAGCATTGTT
Found at i:111858 original size:51 final size:51
Alignment explanation
Indices: 111798--111926 Score: 240
Period size: 51 Copynumber: 2.5 Consensus size: 51
111788 ACTTGACACT
111798 AGAACCTTCAACTTCAGTGAGACCAAGCAAAGAAACCGAATCAACTATACC
1 AGAACCTTCAACTTCAGTGAGACCAAGCAAAGAAACCGAATCAACTATACC
* *
111849 AGAACCTTCAACTTCAGTGAGACCAAGCAAAGAAACCGACTCAACTGTACC
1 AGAACCTTCAACTTCAGTGAGACCAAGCAAAGAAACCGAATCAACTATACC
111900 AGAACCTTCAACTTCAGTGAGACCAAG
1 AGAACCTTCAACTTCAGTGAGACCAAG
111927 AAGGTCGCGG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (51 bp):
AGAACCTTCAACTTCAGTGAGACCAAGCAAAGAAACCGAATCAACTATACC
Found at i:114397 original size:60 final size:59
Alignment explanation
Indices: 114292--114453 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 59
114282 TTAGGCTAAT
* * ** *
114292 TGCTCAGAT-AAGACCCAACGTTTGTGAAAA-TGCTCAAAGAAGGGCAAAG-AAAAACAAA
1 TGCTCAAATCAAGGCCCAACG-TTGCAAAAATTGCTCAAATAAGGGCAAAGCAAAAA-AAA
* * *
114350 TTCTTAAATCAAGGCCCAACGTTGCAAAAAATTGCTCAAATAAGGGCAAGGCAAAAAAAA
1 TGCTCAAATCAAGGCCCAACGTTGC-AAAAATTGCTCAAATAAGGGCAAAGCAAAAAAAA
** * *
114410 TGCTCAAATCAAGGCCTGATGTTGCCAAAATTGCTCAAATAAGG
1 TGCTCAAATCAAGGCCCAACGTTGCAAAAATTGCTCAAATAAGG
114454 CCCCGCCGTC
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
58 9 0.10
59 32 0.37
60 40 0.47
61 5 0.06
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (59 bp):
TGCTCAAATCAAGGCCCAACGTTGCAAAAATTGCTCAAATAAGGGCAAAGCAAAAAAAA
Found at i:114415 original size:28 final size:29
Alignment explanation
Indices: 114318--114423 Score: 85
Period size: 28 Copynumber: 3.6 Consensus size: 29
114308 AACGTTTGTG
* *
114318 AAAATGCTCAAA-GAAGGGCAAAG-AAAA
1 AAAATGCTCAAATCAAGGGCAAGGCAAAA
* * *
114345 ACAAATTCTTAAATCAAGGCCCAACGTTGC-AAA
1 A-AAATGCTCAAATCAAGG-GCAA-G--GCAAAA
*
114378 AAATTGCTCAAAT-AAGGGCAAGGCAAAA
1 AAAATGCTCAAATCAAGGGCAAGGCAAAA
114406 AAAATGCTCAAATCAAGG
1 AAAATGCTCAAATCAAGG
114424 CCTGATGTTG
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
27 3 0.05
28 24 0.40
29 9 0.15
30 6 0.10
31 4 0.07
32 9 0.15
33 5 0.08
ACGTcount: A:0.50, C:0.17, G:0.18, T:0.15
Consensus pattern (29 bp):
AAAATGCTCAAATCAAGGGCAAGGCAAAA
Found at i:114712 original size:2 final size:2
Alignment explanation
Indices: 114707--114735 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
114697 TTTATATACA
114707 AT 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 AT A
114736 GGAGTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:116108 original size:28 final size:29
Alignment explanation
Indices: 116072--116127 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
116062 ATGCTTGGGA
116072 CTTAATTGAGCAATTTT-GC-AACATTGGC
1 CTTAATTGAGC-ATTTTCGCAAACATTGGC
*
116100 CTTATTTGAGCATTTTCGCAAACATTGG
1 CTTAATTGAGCATTTTCGCAAACATTGG
116128 GGGCCTATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (29 bp):
CTTAATTGAGCATTTTCGCAAACATTGGC
Found at i:118154 original size:29 final size:29
Alignment explanation
Indices: 118122--118178 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
118112 AACATCCCAA
* *
118122 AATTGAAGTTTAG-GGGACAAAATGTCCAG
1 AATTGAAGTTCAGAGGG-CAAAACGTCCAG
118151 AATTGAAGTTCAGAGGGCAAAACGTCCA
1 AATTGAAGTTCAGAGGGCAAAACGTCCA
118179 AACGCTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (29 bp):
AATTGAAGTTCAGAGGGCAAAACGTCCAG
Found at i:120203 original size:24 final size:26
Alignment explanation
Indices: 120171--120223 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
120161 TCTAGAAGTT
120171 TATGTTGC-AG-CTAAAGACCATTTC
1 TATGTTGCAAGCCTAAAGACCATTTC
*
120195 TATGTTGCAGAGCCTGAAGACCATTTC
1 TATGTTGCA-AGCCTAAAGACCATTTC
120222 TA
1 TA
120224 CTATTATGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
26 2 0.08
27 15 0.60
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (26 bp):
TATGTTGCAAGCCTAAAGACCATTTC
Found at i:124641 original size:31 final size:32
Alignment explanation
Indices: 124589--124652 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
124579 GTATTCTTTC
124589 AAAAGAAATTATGTTTTTTTTCCAACAATTTA
1 AAAAGAAATTATGTTTTTTTTCCAACAATTTA
*
124621 AAAAGAAATTATG-TTTTTTTCCAGCAATTTA
1 AAAAGAAATTATGTTTTTTTTCCAACAATTTA
124652 A
1 A
124653 TTATATTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (32 bp):
AAAAGAAATTATGTTTTTTTTCCAACAATTTA
Found at i:125138 original size:31 final size:31
Alignment explanation
Indices: 125077--125134 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
125067 GAGTTTTGTA
*
125077 AAACTTTTGAATCGCCTATTATATCCTTATT
1 AAACTTTTGAATCGCCTATCATATCCTTATT
125108 AAACTTTTGAATCGCCTATCATA-CCTT
1 AAACTTTTGAATCGCCTATCATATCCTT
125135 TATTTTTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.41
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATATCCTTATT
Found at i:125258 original size:8 final size:8
Alignment explanation
Indices: 125235--125275 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
125225 TATCCTTATA
125235 ACTATTTT
1 ACTATTTT
125243 A-T-TTTT
1 ACTATTTT
125249 ACTATTTT
1 ACTATTTT
125257 ACTATTTT
1 ACTATTTT
125265 ACTATTTT
1 ACTATTTT
125273 ACT
1 ACT
125276 TTTATAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 5 0.16
7 2 0.06
8 24 0.77
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (8 bp):
ACTATTTT
Found at i:125279 original size:22 final size:22
Alignment explanation
Indices: 125235--125289 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
125225 TATCCTTATA
125235 ACTATTTTA-TTTTTACTATTTT
1 ACTATTTTACTTTTTAC-ATTTT
125257 ACTATTTTACTATTTTAC-TTTT
1 ACTATTTTACT-TTTTACATTTT
125279 A-TAGTTTTACT
1 ACTA-TTTTACT
125290 CAATTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.07
22 21 0.70
23 1 0.03
24 6 0.20
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.64
Consensus pattern (22 bp):
ACTATTTTACTTTTTACATTTT
Found at i:127018 original size:21 final size:22
Alignment explanation
Indices: 126994--127038 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
126984 TAATAACATT
* *
126994 TTTTTGTC-AAGAAAAGATTTA
1 TTTTGGTCAAAGAAAAGAATTA
127015 TTTTGGTCAAAGAAAAGAATTA
1 TTTTGGTCAAAGAAAAGAATTA
127037 TT
1 TT
127039 GCATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (22 bp):
TTTTGGTCAAAGAAAAGAATTA
Found at i:130975 original size:32 final size:33
Alignment explanation
Indices: 130912--130975 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
130902 ATTTAGGTGC
130912 TGGCAACTGTATGAACATGGAATTTTTAATTTT
1 TGGCAACTGTATGAACATGGAATTTTTAATTTT
* *
130945 TGGCAATTGTATGAACAT-GACTTTTTAATTT
1 TGGCAACTGTATGAACATGGAATTTTTAATTT
130976 AAAGAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (33 bp):
TGGCAACTGTATGAACATGGAATTTTTAATTTT
Done.