Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011371.1 Corchorus capsularis cultivar CVL-1 contig11392, 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: 64813
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:2179 original size:24 final size:24
Alignment explanation
Indices: 2152--2203 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
2142 TTGTCCATGG
2152 TTCCTTGCAATCCTTGATCATCCC
1 TTCCTTGCAATCCTTGATCATCCC
2176 TTCCTTGCAATCCTTGATCATCCC
1 TTCCTTGCAATCCTTGATCATCCC
2200 TTCC
1 TTCC
2204 ATGATCTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (24 bp):
TTCCTTGCAATCCTTGATCATCCC
Found at i:8649 original size:24 final size:24
Alignment explanation
Indices: 8622--8674 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
8612 CTTGTCCATG
*
8622 CTTCCTTGCAATCCTTGATCATTC
1 CTTCCTTGCAATCCTTGATCATCC
8646 CTTCCTTGCAATCCTTGATCATCC
1 CTTCCTTGCAATCCTTGATCATCC
8670 CTTCC
1 CTTCC
8675 ATGATCTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.40
Consensus pattern (24 bp):
CTTCCTTGCAATCCTTGATCATCC
Found at i:18346 original size:1 final size:1
Alignment explanation
Indices: 18340--18419 Score: 70
Period size: 1 Copynumber: 80.0 Consensus size: 1
18330 GCCAGGTCGC
* * ** * * * *
18340 AAAAAAAAAAAAAAAAAAACAAAAAACAAAAAAAATCAAAAACAAAAAAAAGACAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
18405 AACAAAAAATAAAAA
1 AAAAAAAAAAAAAAA
18420 TTGCGACAGG
Statistics
Matches: 60, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.88, C:0.09, G:0.01, T:0.03
Consensus pattern (1 bp):
A
Found at i:18380 original size:27 final size:27
Alignment explanation
Indices: 18339--18419 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
18329 AGCCAGGTCG
18339 CAAAAAAAAAAAAAAA-AAAACAAAAAA
1 CAAAAAAAAAAAAAAACAAAA-AAAAAA
** *
18366 CAAAAAAAATCAAAAACAAAAAAAAGA
1 CAAAAAAAAAAAAAAACAAAAAAAAAA
* *
18393 CAAAAAACAAAAAACAA-AAAATAAAAA
1 CAAAAAA-AAAAAAAAACAAAAAAAAAA
18420 TTGCGACAGG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 34 0.77
28 10 0.23
ACGTcount: A:0.86, C:0.10, G:0.01, T:0.02
Consensus pattern (27 bp):
CAAAAAAAAAAAAAAACAAAAAAAAAA
Found at i:23433 original size:41 final size:41
Alignment explanation
Indices: 23330--23435 Score: 167
Period size: 41 Copynumber: 2.6 Consensus size: 41
23320 AATTAAGTAA
* *
23330 AAACAACAGTCAAAGTCTTAAATCAGGGTAATTAAGAAAGTC
1 AAAC-ACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAGTC
* *
23372 AAACATAGTTAAAGTCTTAATTCATGGTAATTAAGAAAGTC
1 AAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAGTC
23413 AAACACAGTTAAAGTCTTAATTC
1 AAACACAGTTAAAGTCTTAATTC
23436 CCATGATCTT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 55 0.93
42 4 0.07
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.27
Consensus pattern (41 bp):
AAACACAGTTAAAGTCTTAATTCAGGGTAATTAAGAAAGTC
Found at i:27382 original size:29 final size:30
Alignment explanation
Indices: 27318--27384 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
27308 AAGTCCCATT
***
27318 TTGCCCCCTGAACTTATATCAGTTGGACGCT
1 TTGCCCCCTGAACTTATATCA-TTGGACAAA
27349 TTGCCCCCTGAACTT-TAATC-TTGGACAAA
1 TTGCCCCCTGAACTTAT-ATCATTGGACAAA
27378 TTGCCCC
1 TTGCCCC
27385 TTAAACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 13 0.41
30 1 0.03
31 18 0.56
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (30 bp):
TTGCCCCCTGAACTTATATCATTGGACAAA
Found at i:28248 original size:2 final size:2
Alignment explanation
Indices: 28241--28271 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28231 AAATTTGTGG
28241 AT 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 AT A
28272 AACTAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28551 original size:20 final size:20
Alignment explanation
Indices: 28522--28562 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28512 AAAAAAAAAG
* *
28522 ACACATATACATATATATAC
1 ACACACATACATATACATAC
28542 ACACACATACATATACATAC
1 ACACACATACATATACATAC
28562 A
1 A
28563 TACATCTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (20 bp):
ACACACATACATATACATAC
Found at i:33041 original size:30 final size:30
Alignment explanation
Indices: 33005--33064 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
32995 ATAGGAGAGG
*
33005 ATGGAATCGCAAAGTCTCATGAAGATGCCA
1 ATGGAATCGCAAAGCCTCATGAAGATGCCA
* *
33035 ATGGAATCGCAACGCCTCATGCAGATGCCA
1 ATGGAATCGCAAAGCCTCATGAAGATGCCA
33065 TTAAGATGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.18
Consensus pattern (30 bp):
ATGGAATCGCAAAGCCTCATGAAGATGCCA
Found at i:40784 original size:25 final size:25
Alignment explanation
Indices: 40750--40800 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
40740 TTTCGACTCT
40750 CACTCCAAATAATCGGATGGAGGCC
1 CACTCCAAATAATCGGATGGAGGCC
40775 CACTCCAAATAATCGGATGGAGGCC
1 CACTCCAAATAATCGGATGGAGGCC
40800 C
1 C
40801 TTTCCCATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (25 bp):
CACTCCAAATAATCGGATGGAGGCC
Found at i:47041 original size:30 final size:30
Alignment explanation
Indices: 47007--47066 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
46997 ATAGAAGAGG
*
47007 ATGGAATCGCAAAGTCTCATGAAGATGCCA
1 ATGGAATCGCAAAGCCTCATGAAGATGCCA
*
47037 ATGGAATCGCAAAGCCTCATGGAGATGCCA
1 ATGGAATCGCAAAGCCTCATGAAGATGCCA
47067 TTTGATCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (30 bp):
ATGGAATCGCAAAGCCTCATGAAGATGCCA
Found at i:48211 original size:22 final size:22
Alignment explanation
Indices: 48171--48222 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
48161 CCTGGGCCAA
**
48171 AGTTGTCCAAGTTCAGGGCAGG
1 AGTTGTCCAAGACCAGGGCAGG
*
48193 AGTTGTCCAAGACCTGGGCAGG
1 AGTTGTCCAAGACCAGGGCAGG
*
48215 ACTTGTCC
1 AGTTGTCC
48223 TATAATTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (22 bp):
AGTTGTCCAAGACCAGGGCAGG
Found at i:48274 original size:22 final size:22
Alignment explanation
Indices: 48246--48293 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
48236 CTTTTCAATA
* * *
48246 GTCCAAGTCCTGGGGAGGAGTT
1 GTCCAAGTCCTAGGCAGGACTT
48268 GTCCAAGTCCTAGGCAGGACTT
1 GTCCAAGTCCTAGGCAGGACTT
48290 GTCC
1 GTCC
48294 TGTTTTTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (22 bp):
GTCCAAGTCCTAGGCAGGACTT
Found at i:53889 original size:13 final size:13
Alignment explanation
Indices: 53871--53900 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
53861 TAAACTAAAG
53871 CAATTAAAAAAAA
1 CAATTAAAAAAAA
53884 CAATTAAAAAAAA
1 CAATTAAAAAAAA
53897 CAAT
1 CAAT
53901 AATAAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTAAAAAAAA
Found at i:54384 original size:27 final size:27
Alignment explanation
Indices: 54307--54528 Score: 141
Period size: 27 Copynumber: 8.0 Consensus size: 27
54297 TAATATATCC
*
54307 TACTCCTTTTTACTGATTACCATTTTC-
1 TACT-CTTTTTACTGATTACCCTTTTCT
* *
54334 TACCTTCTTCTTTTACTAACTACCCTTTTCT
1 TA-C-TC-T-TTTTACTGATTACCCTTTTCT
* *
54365 TACTCTTTTTATTGATTA-CCATTT-T
1 TACTCTTTTTACTGATTACCCTTTTCT
*
54390 TACT-TTCTTACTGATTACCCTTTTCT
1 TACTCTTTTTACTGATTACCCTTTTCT
* *
54416 TACTCTGTTTTTACTAATTACCCTTTACT
1 TACTC--TTTTTACTGATTACCCTTTTCT
* * *
54445 TACTTTTTTCTTTTACTGAATACCATTTT-T
1 TAC---TCT-TTTTACTGATTACCCTTTTCT
* * *
54475 TTCTCTTTTTTACTGAATACCATTTT-T
1 TACTC-TTTTTACTGATTACCCTTTTCT
* *
54502 TACTCTTTTCTATTGATTACCATTTTC
1 TACTCTTTT-TACTGATTACCCTTTTC
54529 ACTTTACTAA
Statistics
Matches: 155, Mismatches: 23, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
24 11 0.07
25 10 0.06
26 14 0.09
27 50 0.32
28 4 0.03
29 26 0.17
30 22 0.14
31 17 0.11
32 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.55
Consensus pattern (27 bp):
TACTCTTTTTACTGATTACCCTTTTCT
Found at i:54409 original size:51 final size:56
Alignment explanation
Indices: 54307--54500 Score: 168
Period size: 58 Copynumber: 3.4 Consensus size: 56
54297 TAATATATCC
54307 TACTCCTTTTTACTGATTACCATTTTCTACCTTCTTCTTTTACTAACTACCCTTTTCT
1 TACT-CTTTTTACTGATTACCATTTTCTACCTTCTTC-TTTACTAACTACCCTTTTCT
* * *
54365 TACTCTTTTTATTGATTACCATTTT-TA-C-T-TTC-TTACTGATTACCCTTTTCT
1 TACTCTTTTTACTGATTACCATTTTCTACCTTCTTCTTTACTAACTACCCTTTTCT
* * * * * *
54416 TACTCTGTTTTTACTAATTACCCTTTACTTACTTTTTTCTTTTACTGAA-TACCATTTT-T
1 TACTC--TTTTTACTGATTACCATTTTC-TACCTTCTTC-TTTACT-AACTACCCTTTTCT
* *
54475 TTCTCTTTTTTACTGAATACCATTTT
1 TACTC-TTTTTACTGATTACCATTTT
54501 TTACTCTTTT
Statistics
Matches: 110, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
51 22 0.20
53 19 0.17
54 1 0.01
55 3 0.03
56 2 0.02
57 21 0.19
58 23 0.21
59 5 0.05
60 13 0.12
61 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (56 bp):
TACTCTTTTTACTGATTACCATTTTCTACCTTCTTCTTTACTAACTACCCTTTTCT
Found at i:54478 original size:81 final size:80
Alignment explanation
Indices: 54316--54474 Score: 180
Period size: 80 Copynumber: 1.9 Consensus size: 80
54306 CTACTCCTTT
* * *
54316 TTACTGATTACCATTTTCTACCTTCTTCTTTTACTAACTACCCTTTTCTTACTCTTTTTATTGAT
1 TTACTGATTACCATTTTCTACCTTCTTCTTTTACTAACTACCCTTTACTTACTCTTTTTACTGAA
54381 TACCATTTTTACTTTC
66 TACCATTTTTA-TTTC
* * *
54397 TTACTGATTACCCTTTTCTTA-C-TCTGT-TTTTACTAATTACCCTTTACTTACTTTTTTCTTTT
1 TTACTGATTACCATTTTC-TACCTTCT-TCTTTTACTAACTACCCTTTACTTAC---TCT-TTTT
54459 ACTGAATACCATTTTT
60 ACTGAATACCATTTTT
54475 TTCTCTTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
80 25 0.38
81 19 0.29
82 2 0.03
83 2 0.03
84 18 0.27
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (80 bp):
TTACTGATTACCATTTTCTACCTTCTTCTTTTACTAACTACCCTTTACTTACTCTTTTTACTGAA
TACCATTTTTATTTC
Found at i:54497 original size:111 final size:113
Alignment explanation
Indices: 54313--54528 Score: 262
Period size: 111 Copynumber: 1.9 Consensus size: 113
54303 ATCCTACTCC
* * * *
54313 TTTTTACTGATTACCATTTTCTACCTTCTTCTTTTACTAACTACCCTTTTCTTACTCTTTTTATT
1 TTTTTACTAATTACCATTTACTACCTTCTTCTTTTACTAACTACCATTTTCTTACTCTTTTTACT
* *
54378 GATTACCA-TTTTTACT-TTCT-TACTGATTACCCTTTTCTTACTCTG
66 GAATACCATTTTTTACTCTTCTCTACTGATTACCATTTTCTTACTCTG
* * * *
54423 TTTTTACTAATTACCCTTTACTTACTTTTTTCTTTTACTGAA-TACCATTTT-TTTCTCTTTTTT
1 TTTTTACTAATTACCATTTAC-TACCTTCTTCTTTTACT-AACTACCATTTTCTTACTC-TTTTT
* *
54486 ACTGAATACCATTTTTTACTCTTTTCTATTGATTACCATTTTC
63 ACTGAATACCATTTTTTACTCTTCTCTACTGATTACCATTTTC
54529 ACTTTACTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
110 23 0.26
111 37 0.42
112 10 0.11
113 3 0.03
114 15 0.17
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.56
Consensus pattern (113 bp):
TTTTTACTAATTACCATTTACTACCTTCTTCTTTTACTAACTACCATTTTCTTACTCTTTTTACT
GAATACCATTTTTTACTCTTCTCTACTGATTACCATTTTCTTACTCTG
Found at i:54541 original size:21 final size:21
Alignment explanation
Indices: 54517--54556 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54507 TTTTCTATTG
*
54517 ATTACCATTTTCACTTTACTA
1 ATTACCATTTACACTTTACTA
* *
54538 ATTACTATTTACTCTTTAC
1 ATTACCATTTACACTTTAC
54557 CATTTCACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTACCATTTACACTTTACTA
Found at i:54555 original size:7 final size:7
Alignment explanation
Indices: 54539--54658 Score: 66
Period size: 7 Copynumber: 16.7 Consensus size: 7
54529 ACTTTACTAA
*
54539 TTACTAT
1 TTACTCT
54546 TTACTCT
1 TTACTCT
54553 TTAC-CAT
1 TTACTC-T
*
54560 TTCACTTT
1 TT-ACTCT
**
54568 TTACTGA
1 TTACTCT
54575 TTACTCT
1 TTACTCT
*
54582 TTACTTT
1 TTACTCT
54589 TTAC-CATT
1 TTACTC--T
*
54597 TTACCCT
1 TTACTCT
**
54604 TTACTGA
1 TTACTCT
54611 TTACTCT
1 TTACTCT
*
54618 TTACTTT
1 TTACTCT
54625 TTAC-CATT
1 TTACTC--T
54633 TTACTCT
1 TTACTCT
**
54640 TTACTGA
1 TTACTCT
54647 TTACTCT
1 TTACTCT
54654 TTACT
1 TTACT
54659 TTTTTACCAT
Statistics
Matches: 85, Mismatches: 19, Indels: 18
0.70 0.16 0.15
Matches are distributed among these distances:
6 1 0.01
7 67 0.79
8 15 0.18
9 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:54578 original size:36 final size:36
Alignment explanation
Indices: 54518--54678 Score: 243
Period size: 36 Copynumber: 4.5 Consensus size: 36
54508 TTTCTATTGA
* * * *
54518 TTACCATTTT-CACTTTACTAATTACTATTTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
* *
54553 TTACCATTTCACTTTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
54589 TTACCATTTTACCCTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
54625 TTACCATTTTACTCTTTACTGATTACTCTTTACTTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTAC-TTT
54662 TTACCATTTTACTCTTT
1 TTACCATTTTACTCTTT
54679 TTAACTTAAT
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 9 0.08
36 85 0.75
37 20 0.18
ACGTcount: A:0.20, C:0.23, G:0.02, T:0.55
Consensus pattern (36 bp):
TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
Found at i:54765 original size:40 final size:40
Alignment explanation
Indices: 54702--54790 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
54692 TAAATACCAT
**
54702 CTTTTGAC-CTTAATTACTGATTTAATAACT-ACTTCTTTTA
1 CTTTT-ACTCTTAATTACAAATTTAAT-ACTCACTTCTTTTA
* * *
54742 CTTTTACTCTTAATTACAAATTTACTGCTCCCTTCTTTTA
1 CTTTTACTCTTAATTACAAATTTAATACTCACTTCTTTTA
54782 CTTTTACTC
1 CTTTTACTC
54791 CATTCTACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.10
40 38 0.90
ACGTcount: A:0.24, C:0.22, G:0.03, T:0.51
Consensus pattern (40 bp):
CTTTTACTCTTAATTACAAATTTAATACTCACTTCTTTTA
Found at i:54963 original size:81 final size:80
Alignment explanation
Indices: 54868--55091 Score: 263
Period size: 80 Copynumber: 2.8 Consensus size: 80
54858 TGCCATTTTT
* * *
54868 CCGATTACTTCTTTTACTTTCTCTCTTAATTATCAATTTACTGATTAATTTTTTTTACTTTTACT
1 CCGATTACTTCTTTTACTTTCTCTCTTAATTATCAATTTACTGATT-ACTTTTCTTACTTTCACT
**
54933 CTTAATTACTGATTGA
65 CTTAATTACCAATTGA
* * *
54949 CTGATTACTTCTTTTACTTCCTCTCTTAATTATCAATTTACTGATTACTTTTCTTACTTTCACTT
1 CCGATTACTTCTTTTACTTTCTCTCTTAATTATCAATTTACTGATTACTTTTCTTACTTTCACTC
* *
55014 TTAGTTACCAATTTA
66 TTAATTACCAATTGA
** * * * *
55029 CCGATTACCCCTTTTACTTT-TACTCTTAATTACCAAGTTACTGCTTACTTCTT-GTACTTTCAC
1 CCGATTACTTCTTTTACTTTCT-CTCTTAATTATCAATTTACTGATTACTT-TTCTTACTTTCAC
55092 CCCATTCTTC
Statistics
Matches: 123, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
79 1 0.01
80 76 0.62
81 46 0.37
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (80 bp):
CCGATTACTTCTTTTACTTTCTCTCTTAATTATCAATTTACTGATTACTTTTCTTACTTTCACTC
TTAATTACCAATTGA
Found at i:55088 original size:40 final size:40
Alignment explanation
Indices: 54870--55088 Score: 228
Period size: 40 Copynumber: 5.5 Consensus size: 40
54860 CCATTTTTCC
*
54870 GATTACTTCTTTTACTTTCT-CTCTTAATTATCAATTTACT
1 GATTACTTCTTTTACTTT-TACTCTTAATTACCAATTTACT
* * ** *
54910 GATTAATTTTTTTTACTTTTACTCTTAATTACTGATTGACT
1 GATT-ACTTCTTTTACTTTTACTCTTAATTACCAATTTACT
* *
54951 GATTACTTCTTTTACTTCCT-CTCTTAATTATCAATTTACT
1 GATTACTTCTTTTACTT-TTACTCTTAATTACCAATTTACT
* * * *
54991 GATTACTT-TTCTTACTTTCACTTTTAGTTACCAATTTACC
1 GATTACTTCTT-TTACTTTTACTCTTAATTACCAATTTACT
** *
55031 GATTACCCCTTTTACTTTTACTCTTAATTACCAAGTTACT
1 GATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACT
* *
55071 GCTTACTTCTTGTACTTT
1 GATTACTTCTTTTACTTT
55089 CACCCCATTC
Statistics
Matches: 143, Mismatches: 30, Indels: 12
0.77 0.16 0.06
Matches are distributed among these distances:
39 2 0.01
40 106 0.74
41 35 0.24
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (40 bp):
GATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACT
Found at i:55119 original size:32 final size:32
Alignment explanation
Indices: 55067--55375 Score: 435
Period size: 32 Copynumber: 9.7 Consensus size: 32
55057 ATTACCAAGT
* * * *
55067 TACTGCTTACTTCTTGTACTTTCACCCCATTC
1 TACTGATTACTTCTTTTACTTTTACTCCATTC
* *
55099 TTCTGATTTCTTCTTTTACTTTTACTCCATTC
1 TACTGATTACTTCTTTTACTTTTACTCCATTC
55131 TACTGATTACTTCTTTTA-TTCTTACTCCATTC
1 TACTGATTACTTCTTTTACTT-TTACTCCATTC
* * *
55163 TGCTGATTACTTTTTTTACTTTTACTCAATTC
1 TACTGATTACTTCTTTTACTTTTACTCCATTC
* *
55195 TATTGATTACTTATTTTACTTTTACTCCATT-
1 TACTGATTACTTCTTTTACTTTTACTCCATTC
55226 TACTGATTACTTCTTTTACTTTTACTCCATTC
1 TACTGATTACTTCTTTTACTTTTACTCCATTC
* *
55258 TACTGATTATTTCTTTTACTTTTACTCCATTT
1 TACTGATTACTTCTTTTACTTTTACTCCATTC
*
55290 TACTGATTACTTCCTCTTACTTTTACTCCATT-
1 TACTGATTACTT-CTTTTACTTTTACTCCATTC
*
55322 TACTGATTACTTCCTCTTACTTTTACTCCATTC
1 TACTGATTACTT-CTTTTACTTTTACTCCATTC
55355 TACTGATTACTTCTTTTACTT
1 TACTGATTACTTCTTTTACTT
55376 CTTTAGCTTA
Statistics
Matches: 250, Mismatches: 22, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
31 31 0.12
32 187 0.75
33 32 0.13
ACGTcount: A:0.18, C:0.24, G:0.04, T:0.54
Consensus pattern (32 bp):
TACTGATTACTTCTTTTACTTTTACTCCATTC
Found at i:55239 original size:127 final size:128
Alignment explanation
Indices: 55058--55375 Score: 437
Period size: 127 Copynumber: 2.5 Consensus size: 128
55048 TTACTCTTAA
* * * * * * *
55058 TTAC-CAAGTTACTGCTTACTTCTTGTACTTTCACCCCATTCTTCTGATTTCTTCTTTTACTTTT
1 TTACTCAATTTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTTTT
* * *
55122 ACTCCATTCTACTGATTACTTCTTTTA-TTCTTACTCCATTCTGCTGATTACTT-TTTTTACTT
66 ACTCCATTCTACTGATTACTTCTTTTACTT-TTACTCCATTCTACTGATTACTTCCTCTTACTT
* *
55184 TTACTCAATTCTATTGATTACTTATTTTACTTTTACTCCATT-TACTGATTACTTCTTTTACTTT
1 TTACTCAATT-TACTGATTACTTCTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTTT
* *
55248 TACTCCATTCTACTGATTATTTCTTTTACTTTTACTCCATTTTACTGATTACTTCCTCTTACTT
65 TACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGATTACTTCCTCTTACTT
* *
55312 TTACTCCATTTACTGATTACTTCCTCTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTT
1 TTACTCAATTTACTGATTACTT-CTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTT
55376 CTTTAGCTTA
Statistics
Matches: 168, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
126 4 0.02
127 83 0.49
128 60 0.36
129 21 0.12
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.53
Consensus pattern (128 bp):
TTACTCAATTTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTTTT
ACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGATTACTTCCTCTTACTT
Found at i:55246 original size:159 final size:160
Alignment explanation
Indices: 55066--55375 Score: 448
Period size: 159 Copynumber: 1.9 Consensus size: 160
55056 AATTACCAAG
* *
55066 TTACTGCTTACTTCTTGTACTTTCACCCCATTCTTCTGATT-TCTTCTTTTACTTTTACTCCATT
1 TTACTGATTACTTCTTGTACTTTCACCCCATTCTACTGATTAT-TTCTTTTACTTTTACTCCATT
* * * *
55130 CTACTGATTACTT-CTTTTA-TTCTTACTCCATTCTGCTGATTACTT-TTTTTACTTTTACTCAA
65 CTACTGATTACTTCCTCTTACTT-TTACTCCATT-TACTGATTACTTCCTCTTACTTTTACTCAA
*
55192 TTCTATTGATTACTTATTTTACTTTTACTCCAT
128 TTCTACTGATTACTTATTTTACTTTTACTCCAT
* * * *
55225 TTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGATTATTTCTTTTACTTTTACTCCATTT
1 TTACTGATTACTTCTTGTACTTTCACCCCATTCTACTGATTATTTCTTTTACTTTTACTCCATTC
*
55290 TACTGATTACTTCCTCTTACTTTTACTCCATTTACTGATTACTTCCTCTTACTTTTACTCCATTC
66 TACTGATTACTTCCTCTTACTTTTACTCCATTTACTGATTACTTCCTCTTACTTTTACTCAATTC
*
55355 TACTGATTACTTCTTTTACTT
131 TACTGATTACTTATTTTACTT
55376 CTTTAGCTTA
Statistics
Matches: 134, Mismatches: 13, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
159 80 0.60
160 52 0.39
161 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.04, T:0.54
Consensus pattern (160 bp):
TTACTGATTACTTCTTGTACTTTCACCCCATTCTACTGATTATTTCTTTTACTTTTACTCCATTC
TACTGATTACTTCCTCTTACTTTTACTCCATTTACTGATTACTTCCTCTTACTTTTACTCAATTC
TACTGATTACTTATTTTACTTTTACTCCAT
Found at i:63402 original size:16 final size:16
Alignment explanation
Indices: 63381--63412 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
63371 AATCCTACGT
63381 GAACAAACAAACAAAA
1 GAACAAACAAACAAAA
*
63397 GAACAAGCAAACAAAA
1 GAACAAACAAACAAAA
63413 AGAGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.19, G:0.09, T:0.00
Consensus pattern (16 bp):
GAACAAACAAACAAAA
Done.