Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010175.1 Corchorus capsularis cultivar CVL-1 contig10196, 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: 70548
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:228 original size:25 final size:25
Alignment explanation
Indices: 179--262 Score: 127
Period size: 25 Copynumber: 3.4 Consensus size: 25
169 AAATGATGGA
*
179 AAATG-AGTTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
*
202 AAATGAAGTTTGGAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
227 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
*
252 GAATGAAGTTT
1 AAATGAAGTTT
263 AGGGTTTGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 42 0.76
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.35
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:7343 original size:6 final size:6
Alignment explanation
Indices: 7332--7368 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
7322 CTCTGAGTTC
7332 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT T
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT T
7369 ATCATTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTCTT
Found at i:13480 original size:19 final size:19
Alignment explanation
Indices: 13456--13494 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
13446 AGGATGATGC
13456 AGAAGATGATTCAATACCA
1 AGAAGATGATTCAATACCA
13475 AGAAGATGATTCAATACCA
1 AGAAGATGATTCAATACCA
13494 A
1 A
13495 TCACCTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (19 bp):
AGAAGATGATTCAATACCA
Found at i:16329 original size:23 final size:23
Alignment explanation
Indices: 16295--16338 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
16285 CATAACTAAT
16295 AATAATGATATCACCTACTCAGA
1 AATAATGATATCACCTACTCAGA
* **
16318 AATAATGGTATCTTCTACTCA
1 AATAATGATATCACCTACTCA
16339 ATTGTTAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (23 bp):
AATAATGATATCACCTACTCAGA
Found at i:16929 original size:2 final size:2
Alignment explanation
Indices: 16922--16953 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16912 AAATTATACA
16922 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
16954 CACATTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19421 original size:9 final size:8
Alignment explanation
Indices: 19395--19430 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
19385 GGTCCCTTTG
19395 TTTTTATT
1 TTTTTATT
**
19403 TTTTCCTT
1 TTTTTATT
19411 TTTTTATT
1 TTTTTATT
19419 TTTTTATT
1 TTTTTATT
19427 TTTT
1 TTTT
19431 GGGGTTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTATT
Found at i:20243 original size:45 final size:46
Alignment explanation
Indices: 20174--20264 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
20164 TAATAGAGTA
*
20174 GTGGAATTACTAAAAGATCCCTACCCC-GAATTACTGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCAGAATTAATGATGAGCTGG
* *
20219 GTGGAATTACTAAAAGATCTCTACCCCAGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCAGAATTAATGATGAGCTGG
20265 AGAAGTAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 26 0.62
46 16 0.38
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (46 bp):
GTGGAATTACTAAAAGATCCCTACCCCAGAATTAATGATGAGCTGG
Found at i:20961 original size:165 final size:165
Alignment explanation
Indices: 20678--21155 Score: 561
Period size: 165 Copynumber: 2.9 Consensus size: 165
20668 AACATATGGA
* * ** * * * * *
20678 AATTACTAAAAGATCCCCACCCCAGATTAATGAGGAGCGAGAGAACTAATTTTTTTTTGTCTTTT
1 AATTAATAAAAGATCTCCACCAAAGATTGATGATGAGCTAGAGAACTAA-TCTTTTTCGTC-TTT
* * * * *
20743 TCC-ACTTGACCGATTACTTAAATGCCCTAACTTTTGATTCTTGAGGTGATTAAATAACTAGACT
64 ACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-ACT
* *
20807 TTTTGTTCATTTCTCAATTAACTTTAATAGAGTAGTGG
128 TTTTGGTCATTTCTCAATTAACTTGAATAGAGTAGTGG
* * * ** * * *
20845 AATTACTAAAAGATC-CCTACCAAAGCTTGCTTTTGGAGTTAGAGAACTTATTTTTTTCGT-TTT
1 AATTAATAAAAGATCTCC-ACCAAAGATTGATGAT-GAGCTAGAGAACTAATCTTTTTCGTCTTT
* * * * *
20908 -CCTATTTGGTAGATTACTTAAATGTCCTAACTTTTGATTTTTTAGGGGATTAAATAAGTAATCT
64 ACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CT
*
20972 TTTTGGTCATTTCTCAATGAACTTGAATAGAGTAGTGG
128 TTTTGGTCATTTCTCAATTAACTTGAATAGAGTAGTGG
* *
21010 AATTAATAAAAGATCTCCATCAAGGATTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTAC
1 AATTAATAAAAGATCTCCACCAAAGATTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTAC
*
21075 CTACTTGGCAGATTACTTAAATGT-CTAACTTTTCATTCTTGAGGGGATTAAATAACTAAACTTT
66 CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTT
21139 TTGGTCATTTCTCAATT
130 TTGGTCATTTCTCAATT
21156 GACAAATGAC
Statistics
Matches: 262, Mismatches: 41, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
164 25 0.10
165 164 0.63
166 29 0.11
167 32 0.12
168 12 0.05
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (165 bp):
AATTAATAAAAGATCTCCACCAAAGATTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTAC
CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTT
TGGTCATTTCTCAATTAACTTGAATAGAGTAGTGG
Found at i:21999 original size:23 final size:23
Alignment explanation
Indices: 21955--21999 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
21945 ATTTAATTAG
* * *
21955 TGTTCATGAACACGTTCGTTTAT
1 TGTTCATGAACAAGTCCATTTAT
*
21978 TGTTCATGAATAAGTCCATTTA
1 TGTTCATGAACAAGTCCATTTA
22000 AACGAGCCGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (23 bp):
TGTTCATGAACAAGTCCATTTAT
Found at i:22933 original size:14 final size:14
Alignment explanation
Indices: 22909--22946 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
22899 AAACGAGCCA
22909 CTCCTCTCTCCCCTT
1 CTCC-CTCTCCCCTT
22924 CTCCCTCTCCCCTT
1 CTCCCTCTCCCCTT
*
22938 CTTCCTCTC
1 CTCCCTCTC
22947 TAGTACTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (14 bp):
CTCCCTCTCCCCTT
Found at i:28253 original size:21 final size:22
Alignment explanation
Indices: 28218--28263 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
28208 ACTAATATAA
*
28218 TAATTACATAAAATATATTATTT
1 TAATTACA-AAAATATATTAATT
28241 TAATTAC-AAAATATATTAATT
1 TAATTACAAAAATATATTAATT
28262 TA
1 TA
28264 CATATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.68
23 7 0.32
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATTACAAAAATATATTAATT
Found at i:28908 original size:2 final size:2
Alignment explanation
Indices: 28901--28944 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
28891 AAGATTTGTA
28901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
28944 A
1 A
28945 AAATTACGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29011 original size:31 final size:31
Alignment explanation
Indices: 28963--29021 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28953 AGTTTTGAGA
* *
28963 AACTTTTGAAATGCCTATTATATCCTTATTT
1 AACTTTTAAAATACCTATTATATCCTTATTT
28994 AACTTTTAAAATACCTATTATATCCTTA
1 AACTTTTAAAATACCTATTATATCCTTA
29022 CTTATCTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (31 bp):
AACTTTTAAAATACCTATTATATCCTTATTT
Found at i:29962 original size:109 final size:103
Alignment explanation
Indices: 29781--29993 Score: 282
Period size: 109 Copynumber: 2.0 Consensus size: 103
29771 ATAATGTAAA
* * *
29781 AATTAAATAACAATATCCTTATCATTTTTTTTGTTTTTTTTCGAATATCTCAGCCTTATAATTTA
1 AATTAAATAACAATATCCTTATCATTTTTTTTGTTTTTTTTCGAATATCCCAACCTTAAAATTTA
** *
29846 TAATGTAAAGTAGGGTTATTTTGTTCAAGAATTAATAT
66 TAATGTAAAACAGGATTATTTTGTTCAAGAATTAATAT
* *
29884 AATTAATTAACAATATCCTTAAATCAATTTTTTTGTTTTCTTTTTTCCGAATATCCCAACCTTAA
1 AATTAAATAACAATATCCTT--ATC-ATTTTTTT-TGTT-TTTTTT-CGAATATCCCAACCTTAA
* *
29949 AATTTATAATGTAAAACCGGATTATTTTGTTGAAGAATTAATAT
60 AATTTATAATGTAAAACAGGATTATTTTGTTCAAGAATTAATAT
29993 A
1 A
29994 TCCAATTAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
103 19 0.20
105 3 0.03
106 8 0.09
107 3 0.03
108 6 0.06
109 55 0.59
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (103 bp):
AATTAAATAACAATATCCTTATCATTTTTTTTGTTTTTTTTCGAATATCCCAACCTTAAAATTTA
TAATGTAAAACAGGATTATTTTGTTCAAGAATTAATAT
Found at i:30203 original size:31 final size:31
Alignment explanation
Indices: 30168--30233 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
30158 AACTTTATGT
* * *
30168 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCATT-TTCTTCAAAACATA
30199 TTTCCAATTGTACCATTTTCTTCAAAACATA
1 TTTCCAATTGTACCATTTTCTTCAAAACATA
30230 TTTC
1 TTTC
30234 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (31 bp):
TTTCCAATTGTACCATTTTCTTCAAAACATA
Found at i:30734 original size:22 final size:22
Alignment explanation
Indices: 30706--30845 Score: 122
Period size: 22 Copynumber: 6.3 Consensus size: 22
30696 TGTCTCTATG
*
30706 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
30728 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
30751 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
30772 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
30794 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
30818 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
30840 TGGTTA
1 TGGTTA
30846 ATCATCACAA
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
21 3 0.03
22 72 0.76
23 3 0.03
24 17 0.18
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:30935 original size:22 final size:22
Alignment explanation
Indices: 30910--31006 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
30900 ACGTTATAAG
30910 AATTTCATAGTGGGGTTAACAA
1 AATTTCATAGTGGGGTTAACAA
*
30932 AATTTCATTAG-GAGGTT-ACTAA
1 AATTTCA-TAGTGGGGTTAAC-AA
* * *
30954 TATTTCAT-GGGGAGGTTATCAA
1 AATTTCATAGTGG-GGTTAACAA
* * * * *
30976 AATTTTACAGTGTGGTTATCAC
1 AATTTCATAGTGGGGTTAACAA
30998 AATTTCATA
1 AATTTCATA
31007 TGAAGGTTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
20 1 0.02
21 4 0.07
22 46 0.81
23 6 0.11
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (22 bp):
AATTTCATAGTGGGGTTAACAA
Found at i:31095 original size:22 final size:22
Alignment explanation
Indices: 31043--31297 Score: 121
Period size: 22 Copynumber: 11.6 Consensus size: 22
31033 TAAGGAATAC
*
31043 CAAAATTTGATAGAAG-G-TTAT
1 CAAAATTTCATAG-AGTGATTAT
*
31064 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGTGATTAT
**
31085 TGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAG-T--GATTAT
**
31110 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
31131 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAG-TGATTAT
* * * * *
31153 CAAAATCTCAAAGCGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
* *
31175 CAAAATTACATA-ATGTAATTAT
1 CAAAATTTCATAGA-GTGATTAT
* * * * *
31197 CAGAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGAGTGATTAT
* * * *
31219 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
* * * *
31241 CAAAATTTAATAAAGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
* *
31263 CAAATTTTCA-AAATGTGATTA-
1 CAAAATTTCATAGA-GTGATTAT
31284 CAAAAATTTCATAG
1 C-AAAATTTCATAG
31298 TGGTATTTCT
Statistics
Matches: 178, Mismatches: 42, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.01
20 10 0.06
21 24 0.13
22 121 0.68
23 4 0.02
24 5 0.03
25 12 0.07
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGAGTGATTAT
Found at i:31491 original size:22 final size:22
Alignment explanation
Indices: 31380--31935 Score: 232
Period size: 22 Copynumber: 25.5 Consensus size: 22
31370 ATGGAGTAAC
* *
31380 CAAAATTTC--AGGAAGGATAT
1 CAAAATTTCATAGGGAGGTTAT
* * *
31400 CAAAATTTCATATGAAGATTAT
1 CAAAATTTCATAGGGAGGTTAT
* ** *
31422 GAAAATTTCATAGTTTA-GTTCT
1 CAAAATTTCATAG-GGAGGTTAT
* * *
31444 CAAAATTTTACA-AGACGGTTAT
1 CAAAATTTCATAGGGA-GGTTAT
* *
31466 CAAAATTTCATAGGGAGATTAA
1 CAAAATTTCATAGGGAGGTTAT
**
31488 CAAAATTTCATAATGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
**
31510 CAAAAAATCATAGGGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
*
31532 CAAAA-TT--T--GTA-GTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * * *
31548 CAAGATTTCATAAGAAAGTTAT
1 CAAAATTTCATAGGGAGGTTAT
*
31570 CAAAATTTTATAGGGAGGTTTAT
1 CAAAATTTCATAGGGAGG-TTAT
*
31593 CAAAATTGT-ATA-GGACGATTTAT
1 CAAAATT-TCATAGGGA-G-GTTAT
**
31616 CAAAATTTCATAGCAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * * *
31638 CAAAATTTTATAGTGTGATTAT
1 CAAAATTTCATAGGGAGGTTAT
* * *
31660 CAAAATTTCAGAGTGTGGTTA-
1 CAAAATTTCATAGGGAGGTTAT
* *
31681 CTAACAA-TTAATATGGAGGTT-T
1 C-AA-AATTTCATAGGGAGGTTAT
* ** *
31703 TAAAATTTTCATAACGTGGTTAT
1 CAAAA-TTTCATAGGGAGGTTAT
* * *
31726 CAATATATCATATGGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * **
31748 CAACATCTCATAGTGTTGGTTAT
1 CAAAATTTCATAG-GGAGGTTAT
* *
31771 CAAAATTTCATTGGGAAGTTAT
1 CAAAATTTCATAGGGAGGTTAT
** *
31793 CAAAATTTCATATTGA-GTTCTT
1 CAAAATTTCATAGGGAGGTT-AT
* *
31815 CAAAA-TTCTTAGGGAGGTTAA
1 CAAAATTTCATAGGGAGGTTAT
* * * * *
31836 CCAAATTTCATAAGAATGTTAAA
1 CAAAATTTCATAGGGAGGTT-AT
* *** *
31859 AAAAATTT-ATAAAAAGGTTCT
1 CAAAATTTCATAGGGAGGTTAT
* * * *
31880 CGAAATTCCATA-GTATCGTTAT
1 CAAAATTTCATAGGGA-GGTTAT
* *
31902 TAAAATTTCATAGGAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
31924 CAAAATTTCATA
1 CAAAATTTCATA
31936 ATGGGATCAT
Statistics
Matches: 395, Mismatches: 109, Indels: 62
0.70 0.19 0.11
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
19 2 0.01
20 12 0.03
21 26 0.07
22 274 0.69
23 66 0.17
24 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGGTTAT
Found at i:31594 original size:23 final size:23
Alignment explanation
Indices: 31566--31667 Score: 102
Period size: 23 Copynumber: 4.5 Consensus size: 23
31556 CATAAGAAAG
31566 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
31589 TTATCAAAATTGTATA-GGACGAT
1 TTATCAAAATTTTATAGGGA-GGT
* **
31612 TTATCAAAATTTCATAGCAAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * *
31634 TTATCAAAATTTTATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
31656 TTATCAAAATTT
1 TTATCAAAATTT
31668 CAGAGTGTGG
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
21 1 0.02
22 31 0.48
23 32 0.49
24 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:31638 original size:45 final size:45
Alignment explanation
Indices: 31566--31669 Score: 131
Period size: 46 Copynumber: 2.3 Consensus size: 45
31556 CATAAGAAAG
* **
31566 TTATCAAAATTTTATAGGGAGGTTTATCAAAATTGTATAG-GACGA
1 TTATCAAAATTTCATAGCAAGGTTTATCAAAATTGTATAGTG-CGA
* *
31611 TTTATCAAAATTTCATAGCAAGG-TTATCAAAATTTTATAGTGTGA
1 -TTATCAAAATTTCATAGCAAGGTTTATCAAAATTGTATAGTGCGA
31656 TTATCAAAATTTCA
1 TTATCAAAATTTCA
31670 GAGTGTGGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 14 0.27
45 18 0.35
46 20 0.38
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAGCAAGGTTTATCAAAATTGTATAGTGCGA
Found at i:31792 original size:45 final size:45
Alignment explanation
Indices: 31719--31804 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
31709 TTTCATAACG
* * *
31719 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
31764 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
31805 TTGAGTTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:39453 original size:19 final size:19
Alignment explanation
Indices: 39424--39466 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
39414 GTTAAAGAAA
39424 TTGCA-TTTTGTTTTGTGT
1 TTGCATTTTTGTTTTGTGT
39442 TTGCATTTTTGTTTTGTGT
1 TTGCATTTTTGTTTTGTGT
39461 TTGCAT
1 TTGCAT
39467 AATTTTCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.65
Consensus pattern (19 bp):
TTGCATTTTTGTTTTGTGT
Found at i:43982 original size:11 final size:11
Alignment explanation
Indices: 43958--43992 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
43948 TTGACAGCAC
43958 AACAAAAACAA
1 AACAAAAACAA
* *
43969 AACGAAAACGA
1 AACAAAAACAA
43980 AACAAAAACAA
1 AACAAAAACAA
43991 AA
1 AA
43993 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:48300 original size:4 final size:4
Alignment explanation
Indices: 48291--48334 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
48281 AATAGTCAAG
48291 AAGA AAGA AAG- AA-A AAGA AA-A CAAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA AAGA AA
48335 CAAGCAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 5 0.14
4 30 0.83
5 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:60685 original size:3 final size:3
Alignment explanation
Indices: 60677--60727 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
60667 TTTCTACCAA
60677 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
60725 AAT
1 AAT
60728 GACGAAACAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:63871 original size:20 final size:20
Alignment explanation
Indices: 63833--63872 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
63823 AATACACATA
*
63833 AAAATAGCAAAAAGCATAGG
1 AAAATAGCAAAAAGAATAGG
* *
63853 AAAATAGCTATAAGAATAGG
1 AAAATAGCAAAAAGAATAGG
63873 GTTAATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATAGCAAAAAGAATAGG
Found at i:64445 original size:2 final size:2
Alignment explanation
Indices: 64438--64465 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
64428 TTTTAGTGTA
64438 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
64466 TTTTTTTAGC
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):
AT
Found at i:65306 original size:31 final size:31
Alignment explanation
Indices: 65271--65350 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
65261 GGTGCAAAAC
*
65271 GCAGCAAATTAAAAGATCTGGGGTGCGCGTA
1 GCAGCAGATTAAAAGATCTGGGGTGCGCGTA
65302 GCAGCAGATTAAAAGATCTGGGGTGCGCGTA
1 GCAGCAGATTAAAAGATCTGGGGTGCGCGTA
65333 GCAGCAGATTAAAAGATC
1 GCAGCAGATTAAAAGATC
65351 AGAGCGATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (31 bp):
GCAGCAGATTAAAAGATCTGGGGTGCGCGTA
Found at i:65953 original size:17 final size:17
Alignment explanation
Indices: 65927--65963 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
65917 TCCCTCTCAT
65927 GGTACCAGGTAACATGA
1 GGTACCAGGTAACATGA
* *
65944 GGTACTAGGTAGCATGA
1 GGTACCAGGTAACATGA
65961 GGT
1 GGT
65964 GCTGGATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.22
Consensus pattern (17 bp):
GGTACCAGGTAACATGA
Found at i:68130 original size:22 final size:22
Alignment explanation
Indices: 68080--68131 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
68070 AAATAAAATA
*
68080 TTCA-TATGAAATTATGATAAC
1 TTCACTATTAAATTATGATAAC
*
68101 TTCTCTATTAAATTATGATAA-
1 TTCACTATTAAATTATGATAAC
68122 TTACACTATT
1 TT-CACTATT
68132 TTTTATGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (22 bp):
TTCACTATTAAATTATGATAAC
Found at i:68171 original size:22 final size:22
Alignment explanation
Indices: 68146--68684 Score: 154
Period size: 22 Copynumber: 24.7 Consensus size: 22
68136 ATGATCCCAT
68146 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** **
68168 TATGAAATTTTAATAACGATAT
1 TATGAAATTTTGATAACCTTCC
* * * **
68190 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** * *
68212 TAT-AATTTTTTTTTAACATTCT
1 TATGAA-ATTTTGATAACCTTCC
* *
68234 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
68256 TAGGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
68278 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
68300 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
68323 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
** * * *
68344 ATAT-AATATAGTGATGACC-ACGT
1 -TATGAA-ATTTTGATAACCTTC-C
* * * *
68367 TATGAAAATTTAAAAATC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
68388 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* *
68411 T-TGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
68432 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
68454 TATGAAATTTTGATGAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
68477 TAT-AACATTTTGATAAACCTCCC
1 TATGAA-ATTTTGAT-AACCTTCC
* * *
68500 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
68522 TATAAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
68539 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
68560 TATGATTTTTTAATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
68582 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
68604 CATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
68626 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
68648 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
68670 TATGAAATTTTGATA
1 TATGAAATTTTGATA
68685 TCCTCCCTGA
Statistics
Matches: 378, Mismatches: 103, Indels: 71
0.68 0.19 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
21 32 0.08
22 270 0.71
23 59 0.16
24 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:68535 original size:45 final size:46
Alignment explanation
Indices: 68442--68537 Score: 117
Period size: 45 Copynumber: 2.1 Consensus size: 46
68432 TATGAAATTG
* * * *
68442 TGAT-AACCTCGCTATGAAATTTTGATGAATCTTCCTATAACATTT
1 TGATAAACCTCCCTATAAAATTTTGATGAATCTTCCTATAAAATCT
*
68487 TGATAAACCTCCCTATAAAATTTTGAT-AA-CTTTCTTATAAAATCT
1 TGATAAACCTCCCTATAAAATTTTGATGAATC-TTCCTATAAAATCT
68532 TGATAA
1 TGATAA
68538 CTACAAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
44 1 0.02
45 23 0.52
46 20 0.45
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (46 bp):
TGATAAACCTCCCTATAAAATTTTGATGAATCTTCCTATAAAATCT
Found at i:68813 original size:22 final size:22
Alignment explanation
Indices: 68785--69015 Score: 159
Period size: 22 Copynumber: 10.5 Consensus size: 22
68775 GAAATACCAC
*
68785 TATGAAAGTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
68807 TATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
* * *
68829 TATAAAATTTTGTTGATCC-CTT
1 TATGAAATTTTGAT-AACCTCTT
* * * *
68851 TATGAAATTCTGATAATCACAT
1 TATGAAATTTTGATAACCTCTT
* *
68873 TATGTAATTTTGATAACCTCACT
1 TATGAAATTTTGATAACCTC-TT
** **
68896 T-TGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTCTT
*
68917 TATGAAATTTTGATAATCT-TT
1 TATGAAATTTTGATAACCTCTT
*
68938 CTAT-AAATTTTGATAATCCGATCTC
1 -TATGAAATTTTGATAA-CC--TCTT
* * * *
68963 TATGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAACCTCTT
* *
68985 TATGAGA-TTTGATAACCT-TC
1 TATGAAATTTTGATAACCTCTT
*
69005 TATCAAATTTT
1 TATGAAATTTT
69016 CGTACTCCTT
Statistics
Matches: 162, Mismatches: 36, Indels: 23
0.73 0.16 0.10
Matches are distributed among these distances:
20 7 0.04
21 26 0.16
22 107 0.66
23 5 0.03
24 5 0.03
25 12 0.07
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:69068 original size:22 final size:21
Alignment explanation
Indices: 69039--69178 Score: 88
Period size: 22 Copynumber: 6.4 Consensus size: 21
69029 AAATTGAGAC
69039 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
69060 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
69082 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
69104 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* * *
69126 TTTTGTTAACCACACTGTGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
69148 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
69170 TTTTGATAA
1 TTTTGATAA
69179 TGGTCTAATG
Statistics
Matches: 91, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
21 11 0.12
22 76 0.84
23 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:69779 original size:30 final size:31
Alignment explanation
Indices: 69745--69809 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
69735 TGGCAATTTA
* * *
69745 GAAATATGTTTTAATAA-AAGGTTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
69775 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
69806 GAAA
1 GAAA
69810 ACATAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Done.