Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007138.1 Corchorus capsularis cultivar CVL-1 contig07159, 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: 44940
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3782 original size:31 final size:31
Alignment explanation
Indices: 3746--3813 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
3736 AAAAAGGGGC
3746 AATCAGCAATTAAAGTTCAATAAGAAA-AAGT
1 AATCAGCAATT-AAGTTCAATAAGAAAGAAGT
** *
3777 AATCAGTGATTAAGTTCAATAAGAAAGATGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
3808 AATCAG
1 AATCAG
3814 TAAAAGGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (31 bp):
AATCAGCAATTAAGTTCAATAAGAAAGAAGT
Found at i:3972 original size:105 final size:108
Alignment explanation
Indices: 3849--4051 Score: 304
Period size: 105 Copynumber: 1.9 Consensus size: 108
3839 AGTAAAGTGA
* *
3849 TAATCAGTAAAGAGTAATAAAAATTAGTAAATCAGTAATTAAGT-AAA-A-ATTGACCAGAGTCA
1 TAATCAGTAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAACCAGAGTCA
*
3911 AGGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
66 AAGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
* **
3954 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATTAGAGTC
1 TAATCAGTAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAACCAGAGTC
* *
4019 AAAGTAATAGTAATCAGTAAATCGATAATTAAG
65 AAAGTAATAGAAATCAGTAAATCAATAATTAAG
4052 AGTTAAAATG
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 42 0.49
107 3 0.03
108 1 0.01
109 40 0.47
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (108 bp):
TAATCAGTAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAACCAGAGTCA
AAGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
Found at i:3984 original size:54 final size:53
Alignment explanation
Indices: 3849--4051 Score: 209
Period size: 54 Copynumber: 3.8 Consensus size: 53
3839 AGTAAAGTGA
* * *
3849 TAATCAGTAAAGAGTAATAAAAATTAGTAAATCAGTAATTAAGT--AA-AAAT
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
* * *
3899 TGACCAGAGTCAAG-GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
1 TAATC--AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAAT
* *
3954 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAAT
* * * *
4008 TAATTAGAGTCAA-AGTAATAGTAATCAGTAAATCGATAATTAAG
1 TAA-T-CAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAG
4052 AGTTAAAATG
Statistics
Matches: 127, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
50 3 0.02
51 28 0.22
52 6 0.05
53 6 0.05
54 43 0.34
55 36 0.28
56 5 0.04
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (53 bp):
TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
Found at i:4077 original size:109 final size:103
Alignment explanation
Indices: 3856--4051 Score: 257
Period size: 109 Copynumber: 1.8 Consensus size: 103
3846 TGATAATCAG
* * *
3856 TAAAGAGTAATAAAAATTAGTAAATCAGTAATTAAGTAAAAATTGACCAGAGTCAAGGTAATAGA
1 TAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGTAAAAATTAACCAGAGTCAAAGTAATAGA
*
3921 AATCAGTAAATCAATAATTAAGTGAAAAGAAATTAATCA
66 AATCAGTAAATCAATAATTAAGTGAAAAGAAAGTAAT-A
* **
3960 GTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATTAGAGTCAAAGTA
1 -TAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGT--AAA-A-ATTAACCAGAGTCAAAGTA
* *
4025 ATAGTAATCAGTAAATCGATAATTAAG
61 ATAGAAATCAGTAAATCAATAATTAAG
4052 AGTTAAAATG
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
105 35 0.44
107 3 0.04
108 1 0.01
109 40 0.51
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.26
Consensus pattern (103 bp):
TAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGTAAAAATTAACCAGAGTCAAAGTAATAGA
AATCAGTAAATCAATAATTAAGTGAAAAGAAAGTAATA
Found at i:4329 original size:43 final size:42
Alignment explanation
Indices: 4274--4593 Score: 238
Period size: 43 Copynumber: 7.7 Consensus size: 42
4264 AAAGGGTAAA
*
4274 AAGAGTAAAATAGTAATCAGTAAAAATTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
*
4317 AAGAGTAAAATAGTAGTCAGTAAAAAGTAAATA-GTAAT---C
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAAC
* * * * ***
4356 ---AGTAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCGGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
* * * *
4395 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAAAGGTAATCAAC
** *
4438 AAGAAGTAAAA-AGGTAATCAGTAAAAAACAAAAGGCAATCAGTA-
1 AAG-AGTAAAATA-GTAATCAGTAAAAAGTAAAAGGTAATCA--AC
* * * *
4482 AAAAGTAAAAGAGTAATCAGTAAAAA--AAAAGG--AGCAGAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCA-AC
* *
4521 AATAGT-AAAGAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
*
4563 AAGAGTAAAATAGTAATCAGTACAAAGTAAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA
4594 GAATAATCAG
Statistics
Matches: 224, Mismatches: 32, Indels: 43
0.75 0.11 0.14
Matches are distributed among these distances:
35 1 0.00
36 28 0.12
38 20 0.09
39 9 0.04
40 2 0.01
41 11 0.05
42 32 0.14
43 97 0.43
44 24 0.11
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
Found at i:4375 original size:22 final size:23
Alignment explanation
Indices: 4269--4368 Score: 95
Period size: 21 Copynumber: 4.5 Consensus size: 23
4259 ACCTGAAAGG
4269 GTAAAAAGAGTAAAATAGTAATCA
1 GTAAAAA-AGTAAAATAGTAATCA
* *
4293 GT-AAAAATTAAGAA-GGTAATCA
1 GTAAAAAAGTAA-AATAGTAATCA
* * *
4315 --ACAAGAGTAAAATAGTAGTCA
1 GTAAAAAAGTAAAATAGTAATCA
4336 GT-AAAAAGT-AAATAGTAATCA
1 GTAAAAAAGTAAAATAGTAATCA
4357 GTAAAAAAGTAA
1 GTAAAAAAGTAA
4369 TAAGTAAGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
20 2 0.03
21 25 0.42
22 23 0.39
23 7 0.12
24 2 0.03
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.21
Consensus pattern (23 bp):
GTAAAAAAGTAAAATAGTAATCA
Found at i:4381 original size:22 final size:22
Alignment explanation
Indices: 4338--4606 Score: 133
Period size: 21 Copynumber: 12.7 Consensus size: 22
4328 AGTAGTCAGT
**
4338 AAAAAGTAAAT-AGTAATCAGTA
1 AAAAAGT-AATCAGTAAGAAGTA
*
4360 AAAAAGTAATAAGTAAGAAGT-
1 AAAAAGTAATCAGTAAGAAGTA
* * *
4381 AAAAGGAAATCGGTAAG-AGTA
1 AAAAAGTAATCAGTAAGAAGTA
* *
4402 AAAAGGTGATCAGTAA-AGAGT-
1 AAAAAGTAATCAGTAAGA-AGTA
*
4423 AAAAAGCTAATCAGCAAGAAGTA
1 AAAAAG-TAATCAGTAAGAAGTA
*
4446 AAAAGGTAATCAGTAA-AA--A
1 AAAAAGTAATCAGTAAGAAGTA
* *
4465 ACAAAAGGCAATCAGTAAAAAGTA
1 A-AAAA-GTAATCAGTAAGAAGTA
*
4489 AAAGAGTAATCAGT-A-AA--A
1 AAAAAGTAATCAGTAAGAAGTA
* * *
4507 AAAAAG-GAGCAG-AAAATAGT-
1 AAAAAGTAATCAGTAAGA-AGTA
* *
4527 AAAGAGTAATCAGTAAAAAGTA
1 AAAAAGTAATCAGTAAGAAGTA
* * **
4549 AGAAGGTAATCAACAAG-AGTA
1 AAAAAGTAATCAGTAAGAAGTA
*
4570 AAATAGTAATCAGTACA-AAGTA
1 AAAAAGTAATCAGTA-AGAAGTA
*
4592 AAGAA-TAATCAGTAA
1 AAAAAGTAATCAGTAA
4607 AATAGTGATG
Statistics
Matches: 188, Mismatches: 37, Indels: 46
0.69 0.14 0.17
Matches are distributed among these distances:
17 5 0.03
18 7 0.04
19 3 0.02
20 14 0.07
21 77 0.41
22 71 0.38
23 9 0.05
24 2 0.01
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (22 bp):
AAAAAGTAATCAGTAAGAAGTA
Found at i:4384 original size:21 final size:21
Alignment explanation
Indices: 4335--4606 Score: 161
Period size: 22 Copynumber: 12.9 Consensus size: 21
4325 AATAGTAGTC
**
4335 AGTAAAAAGTAAAT-AGTAATC
1 AGTAAAAAGT-AATCAGTAAGA
*
4356 AGTAAAAAAGTAATAAGTAAGA
1 AGT-AAAAAGTAATCAGTAAGA
* * *
4378 AGTAAAAGGAAATCGGTAAG-
1 AGTAAAAAGTAATCAGTAAGA
*
4398 AGTAAAAAGGTGATCAGTAA-A
1 AGTAAAAA-GTAATCAGTAAGA
*
4419 GAGTAAAAAGCTAATCAGCAAGA
1 -AGTAAAAAG-TAATCAGTAAGA
*
4442 AGTAAAAAGGTAATCAGTAAAA
1 AGTAAAAA-GTAATCAGTAAGA
** * * *
4464 AACAAAAGGCAATCAGTAAAA
1 AGTAAAAAGTAATCAGTAAGA
4485 AGTAAAAGAGTAATCAGTAA-A
1 AGTAAAA-AGTAATCAGTAAGA
* * *
4506 A--AAAAAG-GAGCAG-AAAA
1 AGTAAAAAGTAATCAGTAAGA
* *
4523 TAGTAAAGAGTAATCAGTAAAA
1 -AGTAAAAAGTAATCAGTAAGA
* **
4545 AGTAAGAAGGTAATCAACAAG-
1 AGTAA-AAAGTAATCAGTAAGA
4566 AGTAAAATAGTAATCAGTACA-A
1 AGTAAAA-AGTAATCAGTA-AGA
4588 AGTAAAGAA-TAATCAGTAA
1 AGTAAA-AAGTAATCAGTAA
4607 AATAGTGATG
Statistics
Matches: 196, Mismatches: 35, Indels: 41
0.72 0.13 0.15
Matches are distributed among these distances:
16 2 0.01
17 5 0.03
18 3 0.02
19 4 0.02
20 15 0.08
21 78 0.40
22 86 0.44
23 3 0.02
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (21 bp):
AGTAAAAAGTAATCAGTAAGA
Found at i:4534 original size:38 final size:41
Alignment explanation
Indices: 4441--4545 Score: 130
Period size: 38 Copynumber: 2.6 Consensus size: 41
4431 AATCAGCAAG
*
4441 AAGTAAAA-AGGTAATCAGTAAAAAACAAAAGGCAATCAGTAAA
1 AAGTAAAAGA-GTAATCAGT-AAAAACAAAAGG-AAGCAGTAAA
4484 AAGTAAAAGAGTAATCAGTAAAAA-AAAAGG-AGCAG-AAA
1 AAGTAAAAGAGTAATCAGTAAAAACAAAAGGAAGCAGTAAA
4522 ATAGT-AAAGAGTAATCAGTAAAAA
1 A-AGTAAAAGAGTAATCAGTAAAAA
4546 GTAAGAAGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
38 23 0.39
39 7 0.12
41 6 0.10
42 5 0.08
43 17 0.29
44 1 0.02
ACGTcount: A:0.61, C:0.07, G:0.18, T:0.14
Consensus pattern (41 bp):
AAGTAAAAGAGTAATCAGTAAAAACAAAAGGAAGCAGTAAA
Found at i:9331 original size:20 final size:19
Alignment explanation
Indices: 9282--9322 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
9272 GTCGTTAGTT
9282 ACGTGCCGTCACGTGACTA
1 ACGTGCCGTCACGTGACTA
9301 ACGTGCCGTCACGTGACTA
1 ACGTGCCGTCACGTGACTA
9320 ACG
1 ACG
9323 GTTCCGTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (19 bp):
ACGTGCCGTCACGTGACTA
Found at i:9517 original size:24 final size:23
Alignment explanation
Indices: 9472--9516 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
9462 CCCTACCCTT
*
9472 TTTTTTATTTCTTTTACTTTTTA
1 TTTTTTATTTCTCTTACTTTTTA
9495 TTTTTTATTTTCTCTT-CTTTTT
1 TTTTTTA-TTTCTCTTACTTTTT
9517 TCTTCTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTATTTCTCTTACTTTTTA
Found at i:10885 original size:24 final size:24
Alignment explanation
Indices: 10858--10905 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
10848 CTATTTAGTC
10858 CTTCTCAAACACTAGCTAAGTGTA
1 CTTCTCAAACACTAGCTAAGTGTA
10882 CTTCTCAAACACTAGCTAAGTGTA
1 CTTCTCAAACACTAGCTAAGTGTA
10906 TCAAGATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (24 bp):
CTTCTCAAACACTAGCTAAGTGTA
Found at i:11522 original size:32 final size:32
Alignment explanation
Indices: 11462--11522 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
11452 CCCCTATAAC
****
11462 AAAACATATGACAATGGACATTGCCAAAAAAA
1 AAAACATATGACAATGGACAACAACAAAAAAA
11494 AAAACATATGACAATGGACAACAACAAAA
1 AAAACATATGACAATGGACAACAACAAAA
11523 GGGTAGATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.13
Consensus pattern (32 bp):
AAAACATATGACAATGGACAACAACAAAAAAA
Found at i:14633 original size:24 final size:23
Alignment explanation
Indices: 14606--14730 Score: 64
Period size: 24 Copynumber: 5.2 Consensus size: 23
14596 CTTTTGTACT
14606 AATGTTGTCATGATTTTTCTGATC
1 AATGTTGTCATG-TTTTTCTGATC
**
14630 AATGTCCTACAT-TTCTTT-TG-TAC
1 AATGTTGT-CATGTT-TTTCTGAT-C
14653 TAATGTTGTCATGTTTTTTCTGATC
1 -AATGTTGTCATG-TTTTTCTGATC
**
14678 AATGTCCTACAT-TTCTTT-TG-TAC
1 AATGTTGT-CATGTT-TTTCTGAT-C
*
14701 TACTGTTGTCATGATTTTTCTGATC
1 -AATGTTGTCATG-TTTTTCTGATC
14726 AATGT
1 AATGT
14731 CCTACATTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 32
0.64 0.09 0.27
Matches are distributed among these distances:
22 2 0.03
23 16 0.21
24 39 0.52
25 16 0.21
26 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (23 bp):
AATGTTGTCATGTTTTTCTGATC
Found at i:14649 original size:48 final size:48
Alignment explanation
Indices: 14593--14764 Score: 317
Period size: 48 Copynumber: 3.6 Consensus size: 48
14583 TGAAAGCACG
14593 TTTCTTTTGTACTAATGTTGTCATGATTTTTCTGATCAATGTCCTACA
1 TTTCTTTTGTACTAATGTTGTCATGATTTTTCTGATCAATGTCCTACA
*
14641 TTTCTTTTGTACTAATGTTGTCATGTTTTTTCTGATCAATGTCCTACA
1 TTTCTTTTGTACTAATGTTGTCATGATTTTTCTGATCAATGTCCTACA
*
14689 TTTCTTTTGTACTACTGTTGTCATGATTTTTCTGATCAATGTCCTACA
1 TTTCTTTTGTACTAATGTTGTCATGATTTTTCTGATCAATGTCCTACA
*
14737 TTTCTTTTGTACTACTGTTGTCATGATT
1 TTTCTTTTGTACTAATGTTGTCATGATT
14765 CAGTATCAAG
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 121 1.00
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.52
Consensus pattern (48 bp):
TTTCTTTTGTACTAATGTTGTCATGATTTTTCTGATCAATGTCCTACA
Found at i:22713 original size:104 final size:104
Alignment explanation
Indices: 22533--22742 Score: 375
Period size: 104 Copynumber: 2.0 Consensus size: 104
22523 TCAGACCCTA
* *
22533 TTTTTAATTTCTTTTTCCTTTTCTCAAGGAAAATGTAACTTTTTGTAAATGAATTTATTTCTAAT
1 TTTTTAATTTCTTTTTCCTTTTCTCAAGGAAAATGTAACTTCTTGTAAATGAATTTATTTCTAAA
22598 GGAGAATCAAGTACCGAAGAATATCGAGGAAAAAGTATG
66 GGAGAATCAAGTACCGAAGAATATCGAGGAAAAAGTATG
*
22637 TTTTTAATTTCTTTTTCCTTTTCTTAAGGAAAATGTAACTTCTTGTAAATGAATTTATTTCTAAA
1 TTTTTAATTTCTTTTTCCTTTTCTCAAGGAAAATGTAACTTCTTGTAAATGAATTTATTTCTAAA
* *
22702 GGAGAATCAAGTGCTGAAGAATATCGAGGAAAAAGTATG
66 GGAGAATCAAGTACCGAAGAATATCGAGGAAAAAGTATG
22741 TT
1 TT
22743 GCTGTTTTTG
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (104 bp):
TTTTTAATTTCTTTTTCCTTTTCTCAAGGAAAATGTAACTTCTTGTAAATGAATTTATTTCTAAA
GGAGAATCAAGTACCGAAGAATATCGAGGAAAAAGTATG
Found at i:25040 original size:19 final size:19
Alignment explanation
Indices: 25016--25052 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
25006 AGAGCCATCG
25016 CCTATGACCAACGTATCTT
1 CCTATGACCAACGTATCTT
25035 CCTATGACCAACGTATCT
1 CCTATGACCAACGTATCT
25053 GTTCCAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.30
Consensus pattern (19 bp):
CCTATGACCAACGTATCTT
Found at i:29156 original size:84 final size:83
Alignment explanation
Indices: 28992--29145 Score: 245
Period size: 84 Copynumber: 1.8 Consensus size: 83
28982 GTTCCACGTA
* * *
28992 CCATTTTTCATGCATTAATTCGTTAGGCATAGCTTGACGTCGTTTAGCATCTTTCGTCGCCGGTG
1 CCATTTTTCATGCATTAATTCGTTACGCATAGCTTGACGACGTTTAGCATCTTTCGTCGCAGGTG
29057 ATACAAATATGGGTTGTG
66 ATACAAATATGGGTTGTG
* * *
29075 CCATTTTTCATGCATTAAATTTGTTACGTATAGCTTGACGACGTTTAGCATCTTTCGTCGCATGT
1 CCATTTTTCATGCATT-AATTCGTTACGCATAGCTTGACGACGTTTAGCATCTTTCGTCGCAGGT
29140 GATACA
65 GATACA
29146 CATTGGGGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
83 16 0.25
84 48 0.75
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (83 bp):
CCATTTTTCATGCATTAATTCGTTACGCATAGCTTGACGACGTTTAGCATCTTTCGTCGCAGGTG
ATACAAATATGGGTTGTG
Found at i:32505 original size:54 final size:54
Alignment explanation
Indices: 32423--32530 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
32413 AATTGATATA
32423 GATAAATCTTCTATCATTTTTAGCTCTAATACACAAGAGAAACTTAGATTATTT
1 GATAAATCTTCTATCATTTTTAGCTCTAATACACAAGAGAAACTTAGATTATTT
* * *
32477 GATAAATCTTCTATCCTTTTTAGCTCTAATACACCAGAGAATCTTAGATTATTT
1 GATAAATCTTCTATCATTTTTAGCTCTAATACACAAGAGAAACTTAGATTATTT
32531 ATCATGGGGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (54 bp):
GATAAATCTTCTATCATTTTTAGCTCTAATACACAAGAGAAACTTAGATTATTT
Found at i:32878 original size:19 final size:20
Alignment explanation
Indices: 32841--32878 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
32831 GCGTTTGGCA
*
32841 TTGTTGCCATTTTTGTTTTC
1 TTGTTGCCATTTTTCTTTTC
32861 TTGTTGCCA-TTTTCTTTT
1 TTGTTGCCATTTTTCTTTT
32879 TTCGGCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.05, C:0.16, G:0.13, T:0.66
Consensus pattern (20 bp):
TTGTTGCCATTTTTCTTTTC
Found at i:33444 original size:7 final size:7
Alignment explanation
Indices: 33432--33475 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
33422 ATATGTCTTC
33432 TTCTTTT
1 TTCTTTT
33439 TTC-TTT
1 TTCTTTT
33445 TTCTTTT
1 TTCTTTT
33452 TTCTTTT
1 TTCTTTT
33459 TTCTTTT
1 TTCTTTT
*
33466 ATCTTTT
1 TTCTTTT
33473 TTC
1 TTC
33476 ATTCTACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (7 bp):
TTCTTTT
Found at i:33448 original size:13 final size:13
Alignment explanation
Indices: 33427--33473 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
33417 TTGTAATATG
*
33427 TCTTCTTCTTTTT
1 TCTTTTTCTTTTT
33440 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
*
33453 TCTTTTTTCTTTTA
1 TC-TTTTTCTTTTT
33467 TCTTTTT
1 TCTTTTT
33474 TCATTCTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
TCTTTTTCTTTTT
Found at i:34614 original size:54 final size:54
Alignment explanation
Indices: 34532--34639 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
34522 AATTGATATA
34532 GATAAATCTTCTATCATTTTTAGCTCTAATACACAAGAGAAACTTAGATTATTT
1 GATAAATCTTCTATCATTTTTAGCTCTAATACACAAGAGAAACTTAGATTATTT
* * *
34586 GATAAATCTTCTATCCTTTTTAGCTCTAATACACCAGAGAATCTTAGATTATTT
1 GATAAATCTTCTATCATTTTTAGCTCTAATACACAAGAGAAACTTAGATTATTT
34640 ATCATGGGGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (54 bp):
GATAAATCTTCTATCATTTTTAGCTCTAATACACAAGAGAAACTTAGATTATTT
Found at i:38033 original size:11 final size:11
Alignment explanation
Indices: 38019--38061 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
38009 TTGAAAACGT
*
38019 AACAAAAATAA
1 AACAAAAACAA
38030 AACAAAAACAA
1 AACAAAAACAA
*
38041 AACGAAAACGAA
1 AACAAAAAC-AA
*
38053 AAAAAAAAC
1 AACAAAAAC
38062 CGAGAACAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.79, C:0.14, G:0.05, T:0.02
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:38039 original size:17 final size:18
Alignment explanation
Indices: 38019--38060 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
38009 TTGAAAACGT
*
38019 AACAAAAATAAAAC-AAA
1 AACAAAAAGAAAACGAAA
*
38036 AACAAAACGAAAACGAAA
1 AACAAAAAGAAAACGAAA
38054 AA-AAAAA
1 AACAAAAA
38061 CCGAGAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.81, C:0.12, G:0.05, T:0.02
Consensus pattern (18 bp):
AACAAAAAGAAAACGAAA
Found at i:38964 original size:93 final size:93
Alignment explanation
Indices: 38857--39026 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 93
38847 CATTGTTTGA
* * * *
38857 ACTTTTATAATTTTAGTCGACTAAAAACTTTATTTTTATTTAATTAAATCTAATATCCTTATAAT
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
38922 TATTTTATTTTTACCATTTTACTATTTT
66 TATTTTATTTTTACCATTTTACTATTTT
* *
38950 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
39015 TATTTTATTTTT
66 TATTTTATTTTT
39027 TTTCCAAATT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (93 bp):
ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTTATTTTTACCATTTTACTATTTT
Found at i:39519 original size:31 final size:31
Alignment explanation
Indices: 39481--39544 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
39471 GAGTAACATT
39481 GAATTATTTCCTTTGACTTATAAGGTTAGAG
1 GAATTATTTCCTTTGACTTATAAGGTTAGAG
39512 GAATTATTTCCTTTGACTTATAAGGTTAGAG
1 GAATTATTTCCTTTGACTTATAAGGTTAGAG
39543 GA
1 GA
39545 GTCAATCGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (31 bp):
GAATTATTTCCTTTGACTTATAAGGTTAGAG
Found at i:44918 original size:1 final size:1
Alignment explanation
Indices: 44914--44940 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
44904 ACAATTTTTG
44914 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.