Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006477.1 Corchorus capsularis cultivar CVL-1 contig06498, 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: 26402
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:1566 original size:78 final size:78
Alignment explanation
Indices: 1415--1570 Score: 215
Period size: 78 Copynumber: 2.0 Consensus size: 78
1405 CAGGAGGCAA
* * *
1415 GTCGACAATAGAAAGCCAAGGGTGGAGATGGCTCATGGTGACCCTATTGAAAAACCTGTATCTGT
1 GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT
*
1480 TTGCAGAAATCCT
66 TCGCAGAAATCCT
* * * *
1493 GTCGACAATAGAAAGCCAGGGGTGGAAATAGCTCGTGGTGGCCCTATTGAAAGACCTG-AACATG
1 GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAAC-TG
*
1557 TTCGTAGAAATCCT
65 TTCGCAGAAATCCT
1571 ATCTATGATA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 2 0.03
78 66 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (78 bp):
GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT
TCGCAGAAATCCT
Found at i:3123 original size:31 final size:32
Alignment explanation
Indices: 3083--3144 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
3073 CAATTTAGAA
*
3083 ATATGTTTAAAAAAAAGAATACAATTGGAAAT
1 ATATGTTTAAAAAAAAGAATACAATCGGAAAT
* **
3115 ATAT-TTTAAAAATAAGGGTACAATCGGAAA
1 ATATGTTTAAAAAAAAGAATACAATCGGAAA
3145 ACATAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.27
Consensus pattern (32 bp):
ATATGTTTAAAAAAAAGAATACAATCGGAAAT
Found at i:3233 original size:37 final size:38
Alignment explanation
Indices: 3192--3270 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
3182 TATAGATTAT
*
3192 TCATAAAGTTATGTCTATTTGAAAAGACATG-TGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
*
3229 TCATAGAGTTATGTCTATATGAAAAGACATGTATGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATG-ATGTTGA
3268 TCA
1 TCA
3271 AGTATATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 29 0.76
39 9 0.24
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (38 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
Found at i:4334 original size:15 final size:15
Alignment explanation
Indices: 4314--4343 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4304 TCCCGTTGAC
*
4314 TACTGCGATGTCCAG
1 TACTGCGATCTCCAG
4329 TACTGCGATCTCCAG
1 TACTGCGATCTCCAG
4344 CTGCCGCCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (15 bp):
TACTGCGATCTCCAG
Found at i:5846 original size:39 final size:39
Alignment explanation
Indices: 5789--5863 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
5779 GACACTTCTA
*
5789 ATAATTAAGGAAATAAATTAAATCAAGGTTTAGCCCTTG
1 ATAATTAAGGAAAGAAATTAAATCAAGGTTTAGCCCTTG
* *
5828 ATAATTAA-GATAAGAAATTGAATCCAGGTTTAGCCC
1 ATAATTAAGGA-AAGAAATTAAATCAAGGTTTAGCCC
5864 CTAGTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.06
39 30 0.94
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (39 bp):
ATAATTAAGGAAAGAAATTAAATCAAGGTTTAGCCCTTG
Found at i:14112 original size:2 final size:2
Alignment explanation
Indices: 14107--14139 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14097 AGTGTGTGTG
14107 TA TA TA 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 TA TA TA T
14140 TTCAGAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15168 original size:20 final size:21
Alignment explanation
Indices: 15143--15190 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
15133 TAAAATTATC
* *
15143 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
15163 AATTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGCAAAGTA
15184 AATTAAA
1 AATTAAA
15191 TCTAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:16555 original size:19 final size:18
Alignment explanation
Indices: 16518--16556 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
16508 TTCTTGAAAT
**
16518 AATTCTTCAATGGTCTTC
1 AATTCTTCAATAATCTTC
16536 AATTCTTCAAATAATCTTC
1 AATTCTTC-AATAATCTTC
16555 AA
1 AA
16557 ATATGAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (18 bp):
AATTCTTCAATAATCTTC
Found at i:20161 original size:26 final size:26
Alignment explanation
Indices: 20132--20311 Score: 146
Period size: 26 Copynumber: 6.6 Consensus size: 26
20122 TTGATGACTA
*
20132 ATTACCATTTTTTACTCTTTGTACTG
1 ATTACCATTTTTTACTCTTTTTACTG
* *
20158 ATTACCATATTTGACTCGTTTTTACTG
1 ATTACCATTTTTTACTC-TTTTTACTG
* *
20185 ATTACCCCTTTTCTTACTGTTTTTACTG
1 ATTA-CCATTTT-TTACTCTTTTTACTG
* * *
20213 AATACCACTTTTTACTCTTTTTACTTA
1 ATTACCATTTTTTACTCTTTTTAC-TG
*
20240 ATTACCATTTTTTTACTCTCCTTTTTTACTT
1 ATTACCA-TTTTTTA--CT-C-TTTTTACTG
* *
20271 AATACC-TTTTTTACCCCTTTTTACTG
1 ATTACCATTTTTTA-CTCTTTTTACTG
* *
20297 AATACCACTTTTTAC
1 ATTACCATTTTTTAC
20312 ACACCATTTC
Statistics
Matches: 124, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
26 42 0.34
27 31 0.25
28 24 0.19
29 11 0.09
30 2 0.02
31 7 0.06
32 7 0.06
ACGTcount: A:0.21, C:0.23, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTACCATTTTTTACTCTTTTTACTG
Found at i:20169 original size:28 final size:28
Alignment explanation
Indices: 20138--20258 Score: 101
Period size: 28 Copynumber: 4.4 Consensus size: 28
20128 ACTAATTACC
*
20138 ATTTTTTACTCTTTGTACTGATTACCAT
1 ATTTTTTACTCTTTTTACTGATTACCAT
* *
20166 A--TTTGACTCGTTTTTACTGATTACCCCT
1 ATTTTTTACTC-TTTTTACTGATTA-CCAT
* * *
20194 -TTTCTTACTGTTTTTACTGAATACC--
1 ATTTTTTACTCTTTTTACTGATTACCAT
* *
20219 ACTTTTTACTCTTTTTACTTAATTACCAT
1 ATTTTTTACTCTTTTTAC-TGATTACCAT
20248 -TTTTTTACTCT
1 ATTTTTTACTCT
20259 CCTTTTTTAC
Statistics
Matches: 72, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
26 21 0.29
27 20 0.28
28 26 0.36
29 5 0.07
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.54
Consensus pattern (28 bp):
ATTTTTTACTCTTTTTACTGATTACCAT
Found at i:20244 original size:55 final size:54
Alignment explanation
Indices: 20128--20258 Score: 144
Period size: 55 Copynumber: 2.4 Consensus size: 54
20118 TTTCTTGATG
*
20128 ACTAATTA-CCATTTTTTACTCTTTGTACTGATTACCATATTTGACTCGTTTTT
1 ACTAATTACCCATTTTTTACTCTTTGTACTGAATACCATATTTGACTCGTTTTT
* * * * *
20181 ACTGATTACCCCTTTTCTTACTGTTTTTACTGAATACCACT-TTTTACTC-TTTTT
1 ACTAATTACCCATTTT-TTACTCTTTGTACTGAATACCA-TATTTGACTCGTTTTT
20235 ACTTAATTA-CCATTTTTTTACTCT
1 AC-TAATTACCCA-TTTTTTACTCT
20259 CCTTTTTTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
53 7 0.11
54 21 0.33
55 35 0.55
56 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.52
Consensus pattern (54 bp):
ACTAATTACCCATTTTTTACTCTTTGTACTGAATACCATATTTGACTCGTTTTT
Found at i:20278 original size:16 final size:16
Alignment explanation
Indices: 20230--20284 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
20220 CTTTTTACTC
20230 TTTTTACTTAATTACCATT
1 TTTTTACTTAA-TACC--T
*
20249 TTTTTAC-T-CT-CCT
1 TTTTTACTTAATACCT
20262 TTTTTACTTAATACCT
1 TTTTTACTTAATACCT
20278 TTTTTAC
1 TTTTTAC
20285 CCCTTTTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 8 0.26
14 1 0.03
15 3 0.10
16 11 0.35
18 1 0.03
19 7 0.23
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTACTTAATACCT
Found at i:20377 original size:27 final size:26
Alignment explanation
Indices: 20313--20377 Score: 60
Period size: 28 Copynumber: 2.4 Consensus size: 26
20303 ACTTTTTACA
20313 CACCATTTCTTACTCTTTATTACTAAT
1 CACCATTT-TTACTCTTTATTACTAAT
* * *
20340 TACTC-TCTTTTACTCTTTTTTTACTGAT
1 CAC-CAT-TTTTACTC-TTTATTACTAAT
20368 CACCATTTTT
1 CACCATTTTT
20378 TTACTCCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.20, C:0.25, G:0.02, T:0.54
Consensus pattern (26 bp):
CACCATTTTTACTCTTTATTACTAAT
Found at i:20399 original size:38 final size:37
Alignment explanation
Indices: 20339--20430 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 37
20329 TTATTACTAA
*
20339 TTACTCTCTT-TTACTCTTTTTTTACTGATCAC-CATTTTT
1 TTACTCT-TTCTTACTC--TTTTTACTGATCACTC-TTTTC
*
20378 TTACTCCTTTCTTACTCTTTTTACTGATTACTCTTTTC
1 TTACT-CTTTCTTACTCTTTTTACTGATCACTCTTTTC
*
20416 TTACTCTTTTTTACT
1 TTACTCTTTCTTACT
20431 GATTACCACT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
37 9 0.19
38 22 0.47
39 8 0.17
40 8 0.17
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (37 bp):
TTACTCTTTCTTACTCTTTTTACTGATCACTCTTTTC
Found at i:20415 original size:27 final size:28
Alignment explanation
Indices: 20378--20450 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
20368 CACCATTTTT
20378 TTACTCCTTTCTTACTC-TTTTTACTGA
1 TTACTCCTTTCTTACTCTTTTTTACTGA
*
20405 TTACTCTTTTCTTACTCTTTTTTACTGA
1 TTACTCCTTTCTTACTCTTTTTTACTGA
20433 TTAC-CACTTT-TTACTCTT
1 TTACTC-CTTTCTTACTCTT
20451 CTTCTTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.15, C:0.25, G:0.03, T:0.58
Consensus pattern (28 bp):
TTACTCCTTTCTTACTCTTTTTTACTGA
Found at i:20433 original size:66 final size:64
Alignment explanation
Indices: 20262--20488 Score: 201
Period size: 66 Copynumber: 3.5 Consensus size: 64
20252 TTACTCTCCT
* * * * ** *
20262 TTTTTACTTAATAC-CTTTTTTACCCCTTTTTACTGAATACCACTTTTTACACACCATTTCTTAC
1 TTTTTACTGATTACTCTTTTTTACTCTTTTTTACTG-ATACCA-TTTTTTTACTCC-TTTCTTAC
20326 TC
63 TC
* *
20328 TTTATTACTAATTACTCTCTTTTACTCTTTTTTTACTGATCACCATTTTTTTACTCCTTTCTTAC
1 TTT-TTACTGATTACTCTTTTTTACTC-TTTTTTACTGAT-ACCATTTTTTTACTCCTTTCTTAC
20393 TC
63 TC
* * **
20395 TTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCA-CTTTTTACTCTTCTTCTTTT
1 TTTTTACTGATTACTCTTTT-TTACTCTTTTTTACTGA-TACCATTTTTTTACTCCT-TTCTTAC
20459 TC
63 TC
* *
20461 TCTTTTACTGACTAC-C-ATTTTACTCTTT
1 T-TTTTACTGATTACTCTTTTTTACTCTTT
20489 GAATTTAATT
Statistics
Matches: 137, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
64 9 0.07
65 12 0.09
66 42 0.31
67 41 0.30
68 20 0.15
69 13 0.09
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.55
Consensus pattern (64 bp):
TTTTTACTGATTACTCTTTTTTACTCTTTTTTACTGATACCATTTTTTTACTCCTTTCTTACTC
Found at i:20467 original size:39 final size:36
Alignment explanation
Indices: 20405--20488 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 36
20395 TTTTTACTGA
* *
20405 TTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTT
1 TTACTCTTTTCTTACTCTCTTTTACTGACTACCA--TT
**
20443 TTACTCTTCTTCTTTTTCTCTTTTACTGACTACCATT
1 TTACTCTT-TTCTTACTCTCTTTTACTGACTACCATT
20480 TTACTCTTT
1 TTACTCTTT
20489 GAATTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.02
37 10 0.24
38 8 0.20
39 22 0.54
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.58
Consensus pattern (36 bp):
TTACTCTTTTCTTACTCTCTTTTACTGACTACCATT
Found at i:20534 original size:21 final size:22
Alignment explanation
Indices: 20510--20753 Score: 96
Period size: 22 Copynumber: 10.9 Consensus size: 22
20500 CTGACTATCG
*
20510 TTTTACTCTTTATTGATTA-TT
1 TTTTACTCTTTATTGATTACTA
*
20531 TTTTACTTTTTTATTGATTACTA
1 TTTTAC-TCTTTATTGATTACTA
* *
20554 TTTTACTC-TTACTGATTACCA
1 TTTTACTCTTTATTGATTACTA
*
20575 --TTACTTTTTGAACTTGATTACTGA
1 TTTTACTCTTT--A-TTGATTACT-A
* *
20599 TTACCCTT-TTACTTTTATTGATTACCA
1 TT----TTACT-C-TTTATTGATTACTA
* * *
20626 TTTTACTCTTTACTAATTACCA
1 TTTTACTCTTTATTGATTACTA
* **
20648 TTTTACCCTTTACAGA-TAC-A
1 TTTTACTCTTTATTGATTACTA
* *
20668 TTTTTACTTTTTACTGATTACCT-
1 -TTTTACTCTTTATTGATTA-CTA
* *
20691 TTTTACTTTTTTACTGATTACTA
1 TTTTAC-TCTTTATTGATTACTA
*
20714 --TTACTCTTTACTGATTA-TCA
1 TTTTACTCTTTATTGATTACT-A
* *
20734 CTTTACTCTTTACTGATTAC
1 TTTTACTCTTTATTGATTAC
20754 CATTGTACCC
Statistics
Matches: 176, Mismatches: 21, Indels: 50
0.71 0.09 0.20
Matches are distributed among these distances:
19 6 0.03
20 16 0.09
21 37 0.21
22 66 0.38
23 31 0.18
24 2 0.01
27 3 0.02
28 8 0.05
29 2 0.01
30 2 0.01
31 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTTACTCTTTATTGATTACTA
Found at i:20645 original size:43 final size:43
Alignment explanation
Indices: 20592--20908 Score: 214
Period size: 43 Copynumber: 7.5 Consensus size: 43
20582 TTGAACTTGA
*
20592 TTACTGATTACCCTTTTACTTTTATTGATTACCATTTTACTCT
1 TTACTGATTACCCTTTTACTTTTACTGATTACCATTTTACTCT
* * * * *
20635 TTACTAATTACCATTTTACCCTTTACAGA-TA-CATTTTTACTTT
1 TTACTGATTACCCTTTTA-CTTTTACTGATTACCA-TTTTACTCT
* *
20678 TTACTGATTACCTTTTTACTTTTTTACTGATTA-C-TATTACTCT
1 TTACTGATTACCCTTTTAC--TTTTACTGATTACCATTTTACTCT
* * * *
20721 TTACTGATTATCAC-TTTACTCTTTACTGATTACCATTGTACCCA
1 TTACTGATTA-CCCTTTTACT-TTTACTGATTACCATTTTACTCT
* * *
20765 TTACTGACTATCTTTTTAC-TTTACTGATTACCA--TTACT-T
1 TTACTGATTACCCTTTTACTTTTACTGATTACCATTTTACTCT
* * * *
20804 CTTACT-AGTTA--CTATTACTTTTTACTAATTACCATATTGCTCT
1 -TTACTGA-TTACCCTTTTAC-TTTTACTGATTACCATTTTACTCT
* * *
20847 TTACTAATTACCATTTTACCTTTTACTGATTATCATTATT--T-T
1 TTACTGATTACCCTTTTA-CTTTTACTGATTACCATT-TTACTCT
**
20889 TTACTGATTACTATTTTACT
1 TTACTGATTACCCTTTTACT
20909 ATTTGAATTT
Statistics
Matches: 215, Mismatches: 37, Indels: 46
0.72 0.12 0.15
Matches are distributed among these distances:
38 5 0.02
39 1 0.00
40 23 0.11
41 3 0.01
42 57 0.27
43 68 0.32
44 52 0.24
45 6 0.03
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (43 bp):
TTACTGATTACCCTTTTACTTTTACTGATTACCATTTTACTCT
Found at i:20847 original size:104 final size:105
Alignment explanation
Indices: 20592--20903 Score: 327
Period size: 104 Copynumber: 2.9 Consensus size: 105
20582 TTGAACTTGA
* * *
20592 TTACTGATTACCCTTTTACT-TTTATTGATTACCATTTTACTCTTTACTAATTACCATTTTACCC
1 TTACTGATTA--CTATTACTCTTTACTAATTACCA-TTTACTCTTTACTAATTACCATTTTACCC
* * *
20656 TTTACAGATA-CATTTTTACTTTTTACTGATTACCTTTTTACTTTT
63 TTTACTGATATCATTTTTAC--TTTACTGATTACC-TATTACTTTC
* * * * *
20701 TTACTGATTACTATTACTCTTTACTGATTATCACTTTACTCTTTACTGATTACCATTGTACCCAT
1 TTACTGATTACTATTACTCTTTACTAATTACCA-TTTACTCTTTACTAATTACCATTTTACCCTT
20766 TACTGACTATC-TTTTTACTTTACTGATTACC-ATTAC-TTC
65 TACTGA-TATCATTTTTACTTTACTGATTACCTATTACTTTC
* * *
20805 TTACT-AGTTACTATTACTTTTTACTAATTACCATATTGCTCTTTACTAATTACCATTTTACCTT
1 TTACTGA-TTACTATTACTCTTTACTAATTACCAT-TTACTCTTTACTAATTACCATTTTACCCT
20869 TTACTGATTATCATTATTT--TTTACTGATTA-CTATT
64 TTACTGA-TATCATT-TTTACTTTACTGATTACCTATT
20904 TTACTATTTG
Statistics
Matches: 176, Mismatches: 19, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
103 3 0.02
104 79 0.45
105 6 0.03
106 3 0.02
107 20 0.11
108 45 0.26
109 19 0.11
110 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (105 bp):
TTACTGATTACTATTACTCTTTACTAATTACCATTTACTCTTTACTAATTACCATTTTACCCTTT
ACTGATATCATTTTTACTTTACTGATTACCTATTACTTTC
Found at i:20871 original size:22 final size:21
Alignment explanation
Indices: 20592--20908 Score: 217
Period size: 22 Copynumber: 15.0 Consensus size: 21
20582 TTGAACTTGA
*
20592 TTACTGATTACCCTTTTACTT
1 TTACTGATTACCATTTTACTT
*
20613 TTATTGATTACCATTTTACTCT
1 TTACTGATTACCATTTTACT-T
* *
20635 TTACTAATTACCATTTTACCCT
1 TTACTGATTACCATTTTA-CTT
*
20657 TTACAGA-TA-CATTTTTACTTT
1 TTACTGATTACCA-TTTTAC-TT
*
20678 TTACTGATTACCTTTTTACTTTT
1 TTACTGATTACCATTTTAC--TT
*
20701 TTACTGATTA-C-TATTACTCT
1 TTACTGATTACCATTTTACT-T
* *
20721 TTACTGATTATCACTTTACTCT
1 TTACTGATTACCATTTTACT-T
* **
20743 TTACTGATTACCATTGTACCCA
1 TTACTGATTACCATTTTA-CTT
* * *
20765 TTACTGACTATCTTTTTAC-T
1 TTACTGATTACCATTTTACTT
20785 TTACTGATTACCA--TTACTT
1 TTACTGATTACCATTTTACTT
*
20804 CTTACT-AGTTA-C-TATTACTTT
1 -TTACTGA-TTACCATTTTAC-TT
* * *
20825 TTACTAATTACCATATTGCTCT
1 TTACTGATTACCATTTTACT-T
*
20847 TTACTAATTACCATTTTACCTT
1 TTACTGATTACCATTTTA-CTT
*
20869 TTACTGATTATCATTATT--TT
1 TTACTGATTACCATT-TTACTT
*
20889 TTACTGATTACTATTTTACT
1 TTACTGATTACCATTTTACT
20909 ATTTGAATTT
Statistics
Matches: 238, Mismatches: 33, Indels: 50
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.02
19 6 0.03
20 59 0.25
21 45 0.19
22 104 0.44
23 20 0.08
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (21 bp):
TTACTGATTACCATTTTACTT
Found at i:20983 original size:30 final size:33
Alignment explanation
Indices: 20947--21013 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
20937 TTTACTCTTT
20947 ACTGATTG-CTTTTT-CTTATT-GAACTTAATC
1 ACTGATTGCCTTTTTACTTATTGGAACTTAATC
*
20977 ACTGATTGCCCTTTTTACTTTTTGGAACTTAATC
1 ACTGATTG-CCTTTTTACTTATTGGAACTTAATC
21011 ACT
1 ACT
21014 CTGATCACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 8 0.25
32 6 0.19
33 5 0.16
34 13 0.41
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (33 bp):
ACTGATTGCCTTTTTACTTATTGGAACTTAATC
Found at i:21028 original size:36 final size:34
Alignment explanation
Indices: 20955--21034 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 34
20945 TTACTGATTG
* **
20955 CTTTTT-CTTATT-GAACTTAATCACTGATTGCC
1 CTTTTTACTTTTTGGAACTTAATCACTGATCACC
20987 CTTTTTACTTTTTGGAACTTAATCACTCTGATCACC
1 CTTTTTACTTTTTGGAACTTAATCA--CTGATCACC
*
21023 TTTTTTACTTTT
1 CTTTTTACTTTT
21035 CTGACTGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 6 0.15
33 5 0.12
34 11 0.28
36 18 0.45
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.51
Consensus pattern (34 bp):
CTTTTTACTTTTTGGAACTTAATCACTGATCACC
Found at i:24564 original size:14 final size:14
Alignment explanation
Indices: 24536--24574 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
24526 CCCTTTAACT
*
24536 ATGATACTAATCTAA
1 ATGA-ACTAAACTAA
*
24551 ATGGACTAAACTAA
1 ATGAACTAAACTAA
24565 ATGAACTAAA
1 ATGAACTAAA
24575 GTTAATATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (14 bp):
ATGAACTAAACTAA
Found at i:24943 original size:28 final size:28
Alignment explanation
Indices: 24897--24970 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
24887 AAGTGAACTT
* *
24897 AAAATGACCAAAGTACCCCCT-AA-ATG
1 AAAATGACCAAAATGCCCCCTGAACATG
24923 CAAAAATGACCAAAATG-CCCCTGAACATG
1 --AAAATGACCAAAATGCCCCCTGAACATG
24952 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
24971 TATGTGACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 20 0.49
28 18 0.44
29 3 0.07
ACGTcount: A:0.46, C:0.28, G:0.12, T:0.14
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCCTGAACATG
Done.