Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007311.1 Corchorus capsularis cultivar CVL-1 contig07332, 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: 37587
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:7458 original size:22 final size:22
Alignment explanation
Indices: 7426--7468 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
7416 AAAATCCTAA
7426 AACAGAGTTCCT-TTAACCCATC
1 AACAGAGTTCCTATT-ACCCATC
*
7448 AACAGATTTCCTATTACCCAT
1 AACAGAGTTCCTATTACCCAT
7469 AAAACCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (22 bp):
AACAGAGTTCCTATTACCCATC
Found at i:10219 original size:17 final size:17
Alignment explanation
Indices: 10199--10258 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
10189 ACCTGATGGG
10199 AACTTTCCCAATTTGAA
1 AACTTTCCCAATTTGAA
** **
10216 AACTTTGACAACTTGATGGG
1 AACTTTCCCAA-TT--TGAA
10236 AACTTTCCCAATTTGAA
1 AACTTTCCCAATTTGAA
10253 AACTTT
1 AACTTT
10259 GACAACTTGA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 17 0.53
18 2 0.06
19 2 0.06
20 11 0.34
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (17 bp):
AACTTTCCCAATTTGAA
Found at i:10233 original size:37 final size:37
Alignment explanation
Indices: 10114--10283 Score: 184
Period size: 37 Copynumber: 4.5 Consensus size: 37
10104 AAGTTGTTAT
* *
10114 TTGACGGGAACTTTCCCATTTTGAAAACTAAAATCTGA-AAC
1 TTGATGGGAACTTTCCCAATTTGAAAACT----T-TGACAAC
* * *** *
10155 -TGATGGGAACTTTCCCTAAATCGAAAAAACT-AAAAC
1 TTGATGGGAACTTTCCC-AATTTGAAAACTTTGACAAC
*
10191 CTGATGGGAACTTTCCCAATTTGAAAACTTTGACAAC
1 TTGATGGGAACTTTCCCAATTTGAAAACTTTGACAAC
10228 TTGATGGGAACTTTCCCAATTTGAAAACTTTGACAAC
1 TTGATGGGAACTTTCCCAATTTGAAAACTTTGACAAC
10265 TTGATGGGAACTTTCCCAA
1 TTGATGGGAACTTTCCCAA
10284 AATGAAAATG
Statistics
Matches: 111, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
35 1 0.01
36 13 0.12
37 75 0.68
40 15 0.14
41 7 0.06
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (37 bp):
TTGATGGGAACTTTCCCAATTTGAAAACTTTGACAAC
Found at i:10241 original size:20 final size:20
Alignment explanation
Indices: 10216--10278 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
10206 CCAATTTGAA
10216 AACTTTGACAACTTGATGGG
1 AACTTTGACAACTTGATGGG
** **
10236 AACTTTCCCAA-TT--TGAA
1 AACTTTGACAACTTGATGGG
10253 AACTTTGACAACTTGATGGG
1 AACTTTGACAACTTGATGGG
10273 AACTTT
1 AACTTT
10279 CCCAAAATGA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 11 0.34
18 2 0.06
19 2 0.06
20 17 0.53
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (20 bp):
AACTTTGACAACTTGATGGG
Found at i:10268 original size:17 final size:17
Alignment explanation
Indices: 10211--10268 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
10201 CTTTCCCAAT
10211 TTGAAAACTTTGACAAC
1 TTGAAAACTTTGACAAC
* ** *
10228 TTGATGGGAACTTTCCCAAT
1 TTGA---AAACTTTGACAAC
10248 TTGAAAACTTTGACAAC
1 TTGAAAACTTTGACAAC
10265 TTGA
1 TTGA
10269 TGGGAACTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 17 0.57
20 13 0.43
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (17 bp):
TTGAAAACTTTGACAAC
Found at i:10637 original size:56 final size:56
Alignment explanation
Indices: 10575--10735 Score: 207
Period size: 56 Copynumber: 2.9 Consensus size: 56
10565 TGAGCCATTT
* * * * * *
10575 ATTTACTTAATTACACCGAATTTAGCTAATTA-CTGATTTACTTAGTTTAATTATCA
1 ATTTACTTAATTGCACCGAATTAAGCTAATTACCAGA-TTACTTAATTTAAATACCA
* *
10631 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAGATTACTTAATTTAAATACCA
1 ATTTACTTAATTGCACCGAATTAAGCTAATTACCAGATTACTTAATTTAAATACCA
* * *
10687 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTTA
1 ATTTACTTAATTGCACCGAATTAAGCTAATTACCAGATTACTTAATTTA
10736 CTTCTTAAAT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
56 92 0.97
57 3 0.03
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (56 bp):
ATTTACTTAATTGCACCGAATTAAGCTAATTACCAGATTACTTAATTTAAATACCA
Found at i:14537 original size:46 final size:46
Alignment explanation
Indices: 14448--14552 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 46
14438 AACAAATCTG
* *
14448 ATTCACCGAATCAAACTTTGAAGAAATACCGCAATGCAGTAACTTT
1 ATTCACCGAATCAAACTTTGAAGAAATACCGCAACGCACTAACTTT
* ** ** *
14494 ATTCACTGAATCAAACTTTGAAGAAATAGTGCGCCGCACTAACTTG
1 ATTCACCGAATCAAACTTTGAAGAAATACCGCAACGCACTAACTTT
14540 A-TCTACCGAATCA
1 ATTC-ACCGAATCA
14553 CTCTGAACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 2 0.04
46 47 0.96
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (46 bp):
ATTCACCGAATCAAACTTTGAAGAAATACCGCAACGCACTAACTTT
Found at i:14837 original size:90 final size:89
Alignment explanation
Indices: 14511--15189 Score: 701
Period size: 90 Copynumber: 7.4 Consensus size: 89
14501 GAATCAAACT
* * * *
14511 TTGAAGAAATAGTGCGCCGCA-CTAACTTGA-TCTACCGAATCA-CTCTGAACTGTCTGAAAACG
1 TTGAAGAAATA-AGCACCGCATC-AACTTGATTC-ACCGAATCATC-CTGAACTGTTTGAAAATG
*
14573 TGCTGCACCGAGCTCACCGACTTCCAATC
62 TGCTGCACCGAGCTCACCGA-ATCCAATC
* * * * *
14602 TTTGAAGAAAT--GCACTGCATCAACTTGATTCACTGAATCATCCCGAACTGTTTGAGAATTTGC
1 -TTGAAGAAATAAGCACCGCATCAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGC
* *
14665 TGCACCGAGCTCACTGAATTCTAATC
65 TGCACCGAGCTCACCGAA-TCCAATC
* * * * *
14691 TTTGAAG--ATATGCACCGCATTAACTTGATTCACCGAACCATCCCGAACTGTTTGAAAATTTGC
1 -TTGAAGAAATAAGCACCGCATCAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGC
* *
14754 TACACCGAGCTCACTGAATCCAATC
65 TGCACCGAGCTCACCGAATCCAATC
* * * * *
14779 TCGAAGAAATAAGACACCGCCTCAACTTGATTCACCGAATCATCCTAAACTGTCTGAAAATCTGC
1 TTGAAGAAATAAG-CACCGCATCAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGC
14844 TGCACCGAGCTCACCGAATCCAATC
65 TGCACCGAGCTCACCGAATCCAATC
* * * *
14869 TTGAAGAAATAAGGCACTGCCTCAACTTGATTTACCGAATCATCCTGAACTGTTTGAAAATGTGT
1 TTGAAGAAATAA-GCACCGCATCAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGC
14934 TGCACCGAGCTCACCGAATCCAATC
65 TGCACCGAGCTCACCGAATCCAATC
* * *
14959 TTGAAGAAATAATGCACCGCATCAACTTGATTCACCAAATCATCCTGAACTGTTTGAAAATATGT
1 TTGAAGAAATAA-GCACCGCATCAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGC
* *
15024 TGCACCGAGCTCACTGAATCC-ACC
65 TGCACCGAGCTCACCGAATCCAATC
** * * * *
15048 TTTGAAGAAATAATGCACTACATTAACTTGATTCACTGAATCGTCTTGAACTGTTTGAAAATGTT
1 -TTGAAGAAATAA-GCACCGCATCAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAA---T
15113 CGAAAACGTGCTGCACCGAGCTCACCGAATCC-ATC
61 -------GTGCTGCACCGAGCTCACCGAATCCAATC
* *
15148 TTTGAAGAAATAATGCACTGCATTAACTTGATTCACCGAATC
1 -TTGAAGAAATAA-GCACCGCATCAACTTGATTCACCGAATC
15190 CAACCTTGAA
Statistics
Matches: 509, Mismatches: 57, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
87 7 0.01
88 6 0.01
89 136 0.27
90 284 0.56
91 1 0.00
92 10 0.02
93 1 0.00
100 64 0.13
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (89 bp):
TTGAAGAAATAAGCACCGCATCAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCT
GCACCGAGCTCACCGAATCCAATC
Found at i:14955 original size:180 final size:180
Alignment explanation
Indices: 14496--15189 Score: 780
Period size: 180 Copynumber: 3.8 Consensus size: 180
14486 GTAACTTTAT
* * * * *
14496 TCACTGAAT-CAAACTTTGAAGAAATAGTGCGCCGCACTAACTTGA-TCTACCGAATCA-CTCTG
1 TCACTGAATCCAATCTTTGAAGAAATAATGCACTGCATTAACTTGATTC-ACCGAATCATC-CTG
* * * *
14558 AACTGTCTGAAAACGTGCTGCACCGAGCTCACCGACTTCCAATCTTTGAAGAAAT--GCACTGCA
64 AACTGTTTGAAAATGTGCTGCACCGAGCTCACCGA-ATCCAATC-TTGAAGAAATAAGCACCGCA
* * * *
14621 TCAACTTGATTCACTGAATCATCCCGAACTGTTTGAGAATTTGCTGCACCGAGC
127 TCAACTTGATTCACCGAATCATCCTGAACTGTTTGAAAATATGCTGCACCGAGC
* * * *
14675 TCACTGAATTCTAATCTTTGAAG--AT-ATGCACCGCATTAACTTGATTCACCGAACCATCCCGA
1 TCACTGAA-TCCAATCTTTGAAGAAATAATGCACTGCATTAACTTGATTCACCGAATCATCCTGA
* * * * *
14737 ACTGTTTGAAAATTTGCTACACCGAGCTCACTGAATCCAATCTCGAAGAAATAAGACACCGCCTC
65 ACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAAG-CACCGCATC
* * *
14802 AACTTGATTCACCGAATCATCCTAAACTGTCTGAAAATCTGCTGCACCGAGC
129 AACTTGATTCACCGAATCATCCTGAACTGTTTGAAAATATGCTGCACCGAGC
* * * * *
14854 TCACCGAATCCAATC-TTGAAGAAATAAGGCACTGCCTCAACTTGATTTACCGAATCATCCTGAA
1 TCACTGAATCCAATCTTTGAAGAAATAATGCACTGCATTAACTTGATTCACCGAATCATCCTGAA
*
14918 CTGTTTGAAAATGTGTTGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAATGCACCGCATCA
66 CTGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAA-GCACCGCATCA
* *
14983 ACTTGATTCACCAAATCATCCTGAACTGTTTGAAAATATGTTGCACCGAGC
130 ACTTGATTCACCGAATCATCCTGAACTGTTTGAAAATATGCTGCACCGAGC
* * * * *
15034 TCACTGAATCC-ACCTTTGAAGAAATAATGCACTACATTAACTTGATTCACTGAATCGTCTTGAA
1 TCACTGAATCCAATCTTTGAAGAAATAATGCACTGCATTAACTTGATTCACCGAATCATCCTGAA
15098 CTGTTTGAAAATGTTCGAAAACGTGCTGCACCGAGCTCACCGAATCC-ATCTTTGAAGAAATAAT
66 CTGTTTGAAAA---T-------GTGCTGCACCGAGCTCACCGAATCCAATC-TTGAAGAAATAA-
* *
15162 GCACTGCATTAACTTGATTCACCGAATC
119 GCACCGCATCAACTTGATTCACCGAATC
15190 CAACCTTGAA
Statistics
Matches: 436, Mismatches: 56, Indels: 35
0.83 0.11 0.07
Matches are distributed among these distances:
176 9 0.02
177 13 0.03
178 63 0.14
179 77 0.18
180 197 0.45
181 11 0.03
183 1 0.00
189 3 0.01
190 62 0.14
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (180 bp):
TCACTGAATCCAATCTTTGAAGAAATAATGCACTGCATTAACTTGATTCACCGAATCATCCTGAA
CTGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCCAATCTTGAAGAAATAAGCACCGCATCAA
CTTGATTCACCGAATCATCCTGAACTGTTTGAAAATATGCTGCACCGAGC
Found at i:15313 original size:55 final size:54
Alignment explanation
Indices: 15230--15668 Score: 691
Period size: 55 Copynumber: 8.1 Consensus size: 54
15220 GAATCCAACT
*
15230 TTGACGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
1 TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
* * *
15284 TTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACCGAATCAC
1 -TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
* * * *
15339 TTTGAAGATAAACTTAAACCACCGGAGACTTTCTTGATTGACCGCACTAGATCAC
1 -TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
*
15394 TTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCAC
1 TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
15448 TTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
1 TTGAAGATAAACTTAA-ACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
*
15503 TTGAAGATAAACTTAAACCACTATAAACTTTCTTGATTGACCGCACTGGATCAC
1 TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
15557 TTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
1 TTGAAGATAAACTTAA-ACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
* ** * *
15612 TTGAAGATAAACTTAATACCACTGAAAACTTTC-TGACAGACTGCATTGGATCAC
1 TTGAAGATAAACTTAA-ACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
15666 TTG
1 TTG
15669 CAACTCGGCT
Statistics
Matches: 362, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
54 140 0.39
55 222 0.61
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (54 bp):
TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC
Found at i:15448 original size:109 final size:110
Alignment explanation
Indices: 15227--15667 Score: 703
Period size: 109 Copynumber: 4.0 Consensus size: 110
15217 TCTGAATCCA
*
15227 ACTTTGACGATAAACTTAA-ACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTTGAAG
1 ACTTTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAAG
* *
15291 ATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACCGAATC
65 ATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATC
* * * *
15337 ACTTTGAAGATAAACTTAA-ACCACCGGAGACTTTCTTGATTGACCGCACTAGATCACTTGAAGA
1 ACTTTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGA
15401 TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATC
66 TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATC
15446 AC-TTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGA
1 ACTTTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGA
**
15510 TAAACTTAAACCACTATAAACTTTCTTGATTGACCGCACTGGATC
66 TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATC
15555 AC-TTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGA
1 ACTTTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGA
* ** * *
15619 TAAACTTAATACCACTGAAAACTTTC-TGACAGACTGCATTGGATC
66 TAAACTTAA-ACCACTGGAAACTTTCTTGATTGACCGCACTGGATC
15664 ACTT
1 ACTT
15668 GCAACTCGGC
Statistics
Matches: 309, Mismatches: 19, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
108 16 0.05
109 226 0.73
110 67 0.22
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (110 bp):
ACTTTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGA
TAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATC
Found at i:15580 original size:164 final size:163
Alignment explanation
Indices: 15230--15668 Score: 702
Period size: 164 Copynumber: 2.7 Consensus size: 163
15220 GAATCCAACT
*
15230 TTGACGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTTGAAGATAA
1 TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAAGATAA
* * *
15295 ACTTAA-ACCACTGGAAACTTTCTTGATTGACCGCACCGAATCACTTTGAAGATAAACTTAAACC
65 ACTTAATACCACTGAAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAAGATAAACTTAAACC
* *
15359 ACCGGAGACTTTCTTGATTGACCGCACTAGATCAC
129 ACCAGAAACTTTCTTGATTGACCGCACTAGATCAC
*
15394 TTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAA
1 TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAA
*
15459 CTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCAC
66 CTTAATACCACTGAAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCAC
* * *
15524 TATAAACTTTCTTGATTGACCGCACTGGATCAC
131 CAGAAACTTTCTTGATTGACCGCACTAGATCAC
15557 TTGAAGATAAACTTAATACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAA
1 TTGAAGATAAACTTAA-ACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAA
** * *
15622 ACTTAATACCACTGAAAACTTTC-TGACAGACTGCATTGGATCACTTG
65 ACTTAATACCACTGAAAACTTTCTTGATTGACCGCACTGGATCACTTG
15669 CAACTCGGCT
Statistics
Matches: 257, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
163 101 0.39
164 156 0.61
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (163 bp):
TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAA
CTTAATACCACTGAAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCAC
CAGAAACTTTCTTGATTGACCGCACTAGATCAC
Found at i:16768 original size:14 final size:14
Alignment explanation
Indices: 16749--16801 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
16739 CTTCTTCTTC
16749 TTCTTTTTTCTTTT
1 TTCTTTTTTCTTTT
16763 TTCTTTTTTTCTTCTT
1 TTC-TTTTTTCTT-TT
16779 CTTCTTTTTT-TTTT
1 -TTCTTTTTTCTTTT
*
16793 ATCTTTTTT
1 TTCTTTTTT
16802 GTTGCACTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
13 8 0.23
14 5 0.14
15 11 0.31
16 8 0.23
17 3 0.09
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTTCTTTT
Found at i:16774 original size:28 final size:30
Alignment explanation
Indices: 16743--16801 Score: 95
Period size: 28 Copynumber: 2.0 Consensus size: 30
16733 CTAGAGCTTC
16743 TTCTTCTTCTT-TTTTCTTTTT-TCTTTTT
1 TTCTTCTTCTTCTTTTCTTTTTATCTTTTT
*
16771 TTCTTCTTCTTCTTTTTTTTTTATCTTTTT
1 TTCTTCTTCTTCTTTTCTTTTTATCTTTTT
16801 T
1 T
16802 GTTGCACTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 11 0.39
29 9 0.32
30 8 0.29
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (30 bp):
TTCTTCTTCTTCTTTTCTTTTTATCTTTTT
Found at i:16778 original size:31 final size:30
Alignment explanation
Indices: 16740--16801 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 30
16730 ACCCTAGAGC
*
16740 TTCTTCTTCTTCTTTTTTCTTTTTTCTTTTT
1 TTCTTCTTCTTCTTTTTT-TTTTATCTTTTT
16771 TTCTTCTTCTTCTTTTTTTTTTATCTTTTT
1 TTCTTCTTCTTCTTTTTTTTTTATCTTTTT
16801 T
1 T
16802 GTTGCACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (30 bp):
TTCTTCTTCTTCTTTTTTTTTTATCTTTTT
Found at i:18080 original size:15 final size:14
Alignment explanation
Indices: 18045--18084 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
18035 TGAAAACTCA
*
18045 TTTTTGAAAACATT
1 TTTTTGAAAAAATT
*
18059 TTCTTGAAAATAATT
1 TTTTTGAAAA-AATT
18074 TTTTTGAAAAA
1 TTTTTGAAAAA
18085 TGTCTCTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (14 bp):
TTTTTGAAAAAATT
Found at i:21371 original size:56 final size:56
Alignment explanation
Indices: 21310--21470 Score: 216
Period size: 56 Copynumber: 2.9 Consensus size: 56
21300 TGAGCCATTT
* * * *
21310 ATTTACTTAATTGCACCGAATTTAGCTAATTA-CTGATTTACTTAGTTTAATTATCA
1 ATTTACTTAATTGCACCGAATTAAGCTAATTACCAGA-TTACTTAATTTAATTACCA
* *
21366 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAGATTACTTAATTTAATTACCA
1 ATTTACTTAATTGCACCGAATTAAGCTAATTACCAGATTACTTAATTTAATTACCA
* * * *
21422 ATTTACTAAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTTA
1 ATTTACTTAATTGCACCGAATTAAGCTAATTACCAGATTACTTAATTTA
21471 CTTCTTAAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
56 93 0.97
57 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (56 bp):
ATTTACTTAATTGCACCGAATTAAGCTAATTACCAGATTACTTAATTTAATTACCA
Found at i:21427 original size:21 final size:21
Alignment explanation
Indices: 21394--21433 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21384 AATTAAGTTG
*
21394 ATTACCAGATTACTTAATTTA
1 ATTACCAGATTACTAAATTTA
21415 ATTACCA-ATTTACTAAATT
1 ATTACCAGA-TTACTAAATT
21434 GCACCGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTACCAGATTACTAAATTTA
Found at i:27537 original size:1 final size:1
Alignment explanation
Indices: 27531--27556 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
27521 AGTTAGTTAG
27531 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
27557 GTAATAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27748 original size:31 final size:31
Alignment explanation
Indices: 27710--27905 Score: 126
Period size: 31 Copynumber: 6.5 Consensus size: 31
27700 CTTGGCTAAT
*
27710 TGCTCAAATAAGGGCCTAACGTTTGTC-AAAA
1 TGCTCAAATAAGGGCCTAACG-TTATCGAAAA
* * * **
27741 TGCTCAAATAAGGGTCCGATC-TT-T-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTATCGAAAA
*
27770 TGGCT-AAATAAGGGTCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* * * **
27801 TGATCAAAT-ACGG-CTCAATC-TT-T-TAATT
1 TGCTCAAATAAGGGCCT-AA-CGTTATCGAAAA
*
27829 TGGC-CAAATAAGGGCTTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* *
27860 TGCTTAAATAAGGGCCTAACGTTATCGAAGA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
27891 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
27906 ATGGTGTCAA
Statistics
Matches: 124, Mismatches: 25, Indels: 32
0.69 0.14 0.18
Matches are distributed among these distances:
28 12 0.10
29 26 0.21
30 19 0.15
31 63 0.51
32 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:27808 original size:60 final size:58
Alignment explanation
Indices: 27714--27873 Score: 205
Period size: 59 Copynumber: 2.7 Consensus size: 58
27704 GCTAATTGCT
* *
27714 CAAATAAGGGCCTAACGTTTGTC-AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGG-CTAACG-TTATCGAAAATGCTCAAATAAGGGT-CAATCTTTTAATTTGGC
* * * *
27774 TAAATAAGGGTCTAACGTTATCGAAAATGATCAAATACGGCTCAATCTTTTAATTTGGC
1 CAAATAAGGG-CTAACGTTATCGAAAATGCTCAAATAAGGGTCAATCTTTTAATTTGGC
*
27833 CAAATAAGGGCTTAACGTTATCGAAAATGCTTAAATAAGGG
1 CAAATAAGGGC-TAACGTTATCGAAAATGCTCAAATAAGGG
27874 CCTAACGTTA
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
58 1 0.01
59 54 0.63
60 31 0.36
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (58 bp):
CAAATAAGGGCTAACGTTATCGAAAATGCTCAAATAAGGGTCAATCTTTTAATTTGGC
Found at i:27969 original size:31 final size:30
Alignment explanation
Indices: 27934--28042 Score: 123
Period size: 31 Copynumber: 3.6 Consensus size: 30
27924 ATGCGTGAGA
27934 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTT-GCAAACGT
** **
27965 TAGGCCCTTATTTG-GCTAAATT-CAAAAAT
1 TAGGCCCTTATTTGAGC-ATTTTGCAAACGT
* *
27994 GAGACCCTTATTTGAGCATTTTGACAAACGT
1 TAGGCCCTTATTTGAGCATTTTG-CAAACGT
28025 TAGGCCCTTATTTGAGCA
1 TAGGCCCTTATTTGAGCA
28043 ATTAGCCAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
29 20 0.32
30 4 0.06
31 38 0.61
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (30 bp):
TAGGCCCTTATTTGAGCATTTTGCAAACGT
Found at i:30120 original size:2 final size:2
Alignment explanation
Indices: 30113--30142 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
30103 AATAAGATTA
30113 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30143 AAAGGGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34060 original size:2 final size:2
Alignment explanation
Indices: 34053--34088 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34043 ATTAGGATTT
34053 TA TA TA TA 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 TA TA TA TA
34089 CATTTCCTTG
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):
TA
Found at i:34946 original size:2 final size:2
Alignment explanation
Indices: 34941--34970 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34931 CACTTGCTAG
34941 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
34971 TAATTGCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37212 original size:17 final size:18
Alignment explanation
Indices: 37190--37227 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
37180 TTTAGTGGGG
* *
37190 TTTTTCTCTTTGT-TTTT
1 TTTTTCTATTTATATTTT
37207 TTTTTCTATTTATATTTT
1 TTTTTCTATTTATATTTT
37225 TTT
1 TTT
37228 GGGATTATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTCTATTTATATTTT
Done.