Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016875.1 Corchorus olitorius cultivar O-4 contig16908, 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: 39295
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2714 original size:16 final size:17
Alignment explanation
Indices: 2688--2719 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2678 AGTGCAAATT
2688 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
2705 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
2720 ACGCAATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:3011 original size:19 final size:19
Alignment explanation
Indices: 2976--3012 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2966 AAACAATTAA
*
2976 CAAGAAAACAGTGAATAAT
1 CAAGAAAACAATGAATAAT
*
2995 CAAGAAAACAATTAATAA
1 CAAGAAAACAATGAATAA
3013 AAACCTCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (19 bp):
CAAGAAAACAATGAATAAT
Found at i:7344 original size:15 final size:16
Alignment explanation
Indices: 7320--7359 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7310 AGAGGTTGAA
*
7320 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
7335 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
7351 AGAAAACAA
1 AGAAAACAA
7360 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:8837 original size:29 final size:30
Alignment explanation
Indices: 8805--8864 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
8795 AATTCTTTCC
* * *
8805 TCTTGAAATAATTCTTTAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
8834 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
8865 CACGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
31 9 0.35
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:10755 original size:21 final size:21
Alignment explanation
Indices: 10731--10785 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
10721 GGCATGGAAT
*
10731 GGTGATGATACGGGCTTAACC
1 GGTGATGACACGGGCTTAACC
* *
10752 GGTGGTGGCACGGGCTTAACC
1 GGTGATGACACGGGCTTAACC
* *
10773 AGTGATGGCACGG
1 GGTGATGACACGG
10786 TGTATGGCCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (21 bp):
GGTGATGACACGGGCTTAACC
Found at i:13993 original size:18 final size:17
Alignment explanation
Indices: 13949--13996 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
13939 ACGCAGAAAC
13949 AAAATTTTTTATGACGCA
1 AAAATTTTTT-TGACGCA
**
13967 GAATTTTTTTTTGACGCA
1 -AAAATTTTTTTGACGCA
13985 AAAACTTTTTTT
1 AAAA-TTTTTTT
13997 TTTTATCGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.08
18 14 0.58
19 8 0.33
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (17 bp):
AAAATTTTTTTGACGCA
Found at i:14391 original size:15 final size:16
Alignment explanation
Indices: 14367--14406 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
14357 AGAGGTTGAA
*
14367 AGAAAGCAATTA-AAT
1 AGAAAACAATTATAAT
*
14382 AGAAAACAATTATACT
1 AGAAAACAATTATAAT
14398 AGAAAACAA
1 AGAAAACAA
14407 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTATAAT
Found at i:19291 original size:26 final size:26
Alignment explanation
Indices: 19258--19309 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
19248 TGGGACTAAA
19258 AAAGAAATTCGA-ATTAGAAGGAAAGT
1 AAAGAAATT-GATATTAGAAGGAAAGT
*
19284 AAAGAAATTTATATTAGAAGGAAAGT
1 AAAGAAATTGATATTAGAAGGAAAGT
19310 GTACGAGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.54, C:0.02, G:0.21, T:0.23
Consensus pattern (26 bp):
AAAGAAATTGATATTAGAAGGAAAGT
Found at i:20973 original size:20 final size:20
Alignment explanation
Indices: 20948--20986 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20938 AAGAGTTAGA
*
20948 AATAACTAATTTTTAATAAT
1 AATAACTAATTATTAATAAT
20968 AATAACTAATTATTAATAA
1 AATAACTAATTATTAATAA
20987 ATTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAACTAATTATTAATAAT
Found at i:21570 original size:41 final size:41
Alignment explanation
Indices: 21506--22378 Score: 1065
Period size: 41 Copynumber: 21.1 Consensus size: 41
21496 GGAATAAGAC
*
21506 AAAGTAAACAACACCTTCTGGTGGGGAAGGGCAAAAC-GGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGGA
* * *
21547 AAATTAAACAACACCTTCCGGTGGGGAAGGGTAAAGC-AGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAA-CTGGGA
* * * *
21588 AAAGAAAACAACACCTTCCGGTAGGGAAAGACAAACT-GGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* * *
21628 AAAGGTAGACAACACCTTCTGGTGAGGAAGGGCAAACTGGGA
1 AAA-GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
*
21670 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTTGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* * *
21711 AATGTAAACAACACCTTCCAGTGAGGAAGGGCAAACTGGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* *
21752 AAAGCAAACAACACCTTTCGGTGGGGAAGGGCAAACTGGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* *
21793 AATGTAAACAACACCTTCCGGTGCGGAAGGGCAAACTGGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* *
21834 AAAGTAAACAACACCTTCTGGTGGGGAAGGGAAAACTGGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* ** *
21875 AAAGTAAACAACACCTTCTGGTGCAGAAGGGCAAACTAGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* * * * *
21916 AATGTAAACAACACTTTCTGGTGGGGAAGGGCAAAGTGCGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
*
21957 AAAGTAAACAACACCTT-CTGTGGGGAAGGGCAAACTGGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* * * * *
21997 AATGTAAACAACACCTTCTGGTGCGGAAGGGTAAACTGGTA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* * *
22038 AAAGCAAACAACACTTTCCGGT-GGGAAGGGCAAACTAGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* *
22078 AATGTAAACAACACCTTCCGGTGTGGAAGGGCAAACTGGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
*
22119 AAAGTAAACAACACCTTTCGGTGGGGAAGGGCAAACTGGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* *
22160 AAAGTAAACAACACCTTCCGGTGCGGAAGGGCAAACTGAGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* *
22201 AATGTAAACAACACTTTCCGGTGGGGAAGGGCAAACTGGGA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
* **
22242 AAAGTAAA-AACACCTTCCGGTGAGGAAGGGCAATTTGGGAA
1 AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-A
** **
22283 AAGCAGACTTAAACAACACCTTCCAATGGGGAAGGGCAATTTGGGAA
1 AA--AG---TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-A
* **
22330 AAGCAGACTTAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGA
1 AA--AG---TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
22376 AAA
1 AAA
22379 AGCAGACTCA
Statistics
Matches: 726, Mismatches: 93, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
40 105 0.14
41 531 0.73
42 6 0.01
43 2 0.00
44 1 0.00
46 7 0.01
47 74 0.10
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (41 bp):
AAAGTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA
Found at i:22492 original size:48 final size:47
Alignment explanation
Indices: 22205--22475 Score: 360
Period size: 48 Copynumber: 5.9 Consensus size: 47
22195 CTGAGAAATG
* * **
22205 TAAACAACACTTTCCGGTGGGGAAGGGCAAACTGGG-AAA--AG---
1 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAGCAGACT
* *
22246 TAAA-AACACCTTCCGGTGAGGAAGGGCAATTTGGGAAAAGCAGACT
1 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAGCAGACT
*
22292 TAAACAACACCTTCCAATGGGGAAGGGCAATTTGGGAAAAGCAGACT
1 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAGCAGACT
22339 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAAGCAGACT
1 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGG-AAAAGCAGACT
* * *
22387 CAAACAACACCTTCCGACT-TGGAAGGGCAATTTGGGAAACAACAGACT
1 TAAACAACACCTTCCGA-TGGGGAAGGGCAATTTGGGAAA-AGCAGACT
*
22435 TAAACAACACCTTTCGATGGGGAAGGGCAATTTGGGAAAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAG
22476 TGGAAACAAG
Statistics
Matches: 204, Mismatches: 15, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
40 27 0.13
41 7 0.03
43 2 0.01
46 4 0.02
47 79 0.39
48 84 0.41
49 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (47 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAGCAGACT
Found at i:22492 original size:96 final size:94
Alignment explanation
Indices: 22246--22475 Score: 356
Period size: 95 Copynumber: 2.4 Consensus size: 94
22236 CTGGGAAAAG
* * *
22246 TAAA-AACACCTTCCGGTGAGGAAGGGCAATTTGGGAAAAGCAGACTTAAACAACACCTTCCAAT
1 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAGCAGACTCAAACAACACCTTCCAAT
*
22310 GGGGAAGGGCAATTTGGGAAAAGCAGACT
66 GGGGAAGGGCAATTTGGGAAAAACAGACT
22339 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAAGCAGACTCAAACAACACCTTCCGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGG-AAAAGCAGACTCAAACAACACCTTCC-A
* *
22404 CT-TGGAAGGGCAATTTGGGAAACAACAGACT
64 ATGGGGAAGGGCAATTTGGGAAA-AACAGACT
*
22435 TAAACAACACCTTTCGATGGGGAAGGGCAATTTGGGAAAAG
1 TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAG
22476 TGGAAACAAG
Statistics
Matches: 126, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
93 4 0.03
94 29 0.23
95 49 0.39
96 44 0.35
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.17
Consensus pattern (94 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAGCAGACTCAAACAACACCTTCCAAT
GGGGAAGGGCAATTTGGGAAAAACAGACT
Found at i:23118 original size:50 final size:49
Alignment explanation
Indices: 23027--23210 Score: 183
Period size: 50 Copynumber: 3.7 Consensus size: 49
23017 CCCTTTACTT
* * * *
23027 AAAGATTCTCATTCTTAATT-CAATTTTATCAAAAGTTAATCTTTTAGTTC
1 AAAGA-TCTCATTTTTATTTACAA-TTAATCAAAAATTAATCTTTTAGTTC
* * * *
23077 AAGGCTCTCAATTTTATTTACAAGTTAATCAAAAATCAATCTTTTAGTTC
1 AAAGATCTCATTTTTATTTACAA-TTAATCAAAAATTAATCTTTTAGTTC
* * * * *
23127 AAAGATCTCATTTTTATTGT-TAATTAACCAAAAGTTTAATCTTTTAATCC
1 AAAGATCTCATTTTTATT-TACAATTAATCAAAA-ATTAATCTTTTAGTTC
23177 AAAGATCTCATTTTTATTTACAAATTAATCAAAA
1 AAAGATCTCATTTTTATTTAC-AATTAATCAAAA
23211 GCTTCGATCT
Statistics
Matches: 109, Mismatches: 20, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
49 21 0.19
50 76 0.70
51 12 0.11
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (49 bp):
AAAGATCTCATTTTTATTTACAATTAATCAAAAATTAATCTTTTAGTTC
Found at i:23453 original size:50 final size:50
Alignment explanation
Indices: 23365--23639 Score: 453
Period size: 50 Copynumber: 5.5 Consensus size: 50
23355 TATCCAAAAA
* * *
23365 TTTTAGCTTAAAGATTACATTTTT-TCATAAATCAATCAAAAATCTTATC
1 TTTTAGCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATC
* * * *
23414 TTTTAACTTAAAGATGACATTTTTATCATCAATCAATCAAAAATCTTATC
1 TTTTAGCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATC
23464 TTTTAGCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATC
1 TTTTAGCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATC
*
23514 TTTTATCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATC
1 TTTTAGCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATC
*
23564 TTTTATCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATC
1 TTTTAGCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATC
*
23614 TTTTAGCTTAAAGATTGCATTTTTAT
1 TTTTAGCTTAAAGATTACATTTTTAT
23640 AACTTTACCA
Statistics
Matches: 215, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
49 22 0.10
50 193 0.90
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (50 bp):
TTTTAGCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATC
Found at i:23520 original size:30 final size:30
Alignment explanation
Indices: 23484--23618 Score: 80
Period size: 30 Copynumber: 5.2 Consensus size: 30
23474 AAGATTACAT
23484 TTTTATCATCAATCAACCAAAAATCTCATC
1 TTTTATCATCAATCAACCAAAAATCTCATC
*
23514 TTTTATC-T---T-----AAAGAT-TACAT-
1 TTTTATCATCAATCAACCAAAAATCT-CATC
23534 TTTTATCATCAATCAACCAAAAATCTCATC
1 TTTTATCATCAATCAACCAAAAATCTCATC
*
23564 TTTTATC-T---T-----AAAGAT-TACAT-
1 TTTTATCATCAATCAACCAAAAATCT-CATC
23584 TTTTATCATCAATCAACCAAAAATCTCATC
1 TTTTATCATCAATCAACCAAAAATCTCATC
23614 TTTTA
1 TTTTA
23619 GCTTAAAGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 48
0.60 0.03 0.37
Matches are distributed among these distances:
20 16 0.21
21 18 0.23
24 2 0.03
26 2 0.03
29 18 0.23
30 21 0.27
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.40
Consensus pattern (30 bp):
TTTTATCATCAATCAACCAAAAATCTCATC
Found at i:23705 original size:100 final size:99
Alignment explanation
Indices: 23365--23686 Score: 380
Period size: 100 Copynumber: 3.2 Consensus size: 99
23355 TATCCAAAAA
* * * * * *
23365 TTTTAGCTTAAAGATTACATTTTT-TCATAAATCAATCAAAAATCTTATCTTTTAACTTAAAGAT
1 TTTTATCTCAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAGCTTAAAGAT
* * * *
23429 GACATTTTTATCATCAATCAATCAAAAATCTTATC
66 TACATTTTTATCA-CAATCAACCAAAAATCTAACC
* * *
23464 TTTTAGCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTATCTTAAAGAT
1 TTTTATCTCAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAGCTTAAAGAT
* *
23529 TACATTTTTATCATCAATCAACCAAAAATCTCATC
66 TACATTTTTATCA-CAATCAACCAAAAATCTAACC
*
23564 TTTTATCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAGCTTAAAGAT
1 TTTTATCTCAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAGCTTAAAGAT
* * ** **
23629 TGCATTTTTAT-A-ACTTTACCAAAGTTCTAACC
66 TACATTTTTATCACAATCAACCAAAAATCTAACC
*
23661 TTTTTTCAATCAAAGATTACATTTTT
1 TTTTATC--TCAAAGATTACATTTTT
23687 TTTATTAATT
Statistics
Matches: 201, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
97 19 0.09
99 41 0.20
100 141 0.70
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (99 bp):
TTTTATCTCAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAGCTTAAAGAT
TACATTTTTATCACAATCAACCAAAAATCTAACC
Found at i:23705 original size:150 final size:149
Alignment explanation
Indices: 23365--23686 Score: 425
Period size: 150 Copynumber: 2.2 Consensus size: 149
23355 TATCCAAAAA
* * * * *
23365 TTTTAGCTTAAAGATTACATTTTT-TCATAAATCAATCAAAAATCTTATCTTTTAACTTAAAGAT
1 TTTTATCTCAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAACTTAAAGAT
* *
23429 GACATTTTTATCATCAATCAATCAAAAATCTTATCTTTTAGCTTAAAGATTACATTTTTATCATC
66 GACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAGCTTAAAGATTACATTTTTATCA-C
* *
23494 AATCAACCAAAAATCTCATC
130 AATCAACCAAAAATCTAACC
* *
23514 TTTTATCTTAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTATCTTAAAGAT
1 TTTTATCTCAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAACTTAAAGAT
* *
23579 TACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAGCTTAAAGATTGCATTTTTAT-A-A
66 GACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAGCTTAAAGATTACATTTTTATCACA
* ** **
23642 CTTTACCAAAGTTCTAACC
131 ATCAACCAAAAATCTAACC
*
23661 TTTTTTCAATCAAAGATTACATTTTT
1 TTTTATC--TCAAAGATTACATTTTT
23687 TTTATTAATT
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
147 19 0.12
149 40 0.26
150 93 0.61
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (149 bp):
TTTTATCTCAAAGATTACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAACTTAAAGAT
GACATTTTTATCATCAATCAACCAAAAATCTCATCTTTTAGCTTAAAGATTACATTTTTATCACA
ATCAACCAAAAATCTAACC
Found at i:26594 original size:5 final size:5
Alignment explanation
Indices: 26584--26611 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
26574 CACTTTTCTC
26584 TTAGT TTAGT TTAGT TTAGT TTAGT TTA
1 TTAGT TTAGT TTAGT TTAGT TTAGT TTA
26612 TTATTCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (5 bp):
TTAGT
Found at i:33208 original size:26 final size:26
Alignment explanation
Indices: 33179--33228 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
33169 ATCCGGCGCT
*
33179 CCATAGCCCG-ACACCTTCTCTTTCCG
1 CCATAACCCGAAC-CCTTCTCTTTCCG
33205 CCATAACCCGAACCCTTCTCTTTC
1 CCATAACCCGAACCCTTCTCTTTC
33229 ATTCTCATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.18, C:0.46, G:0.08, T:0.28
Consensus pattern (26 bp):
CCATAACCCGAACCCTTCTCTTTCCG
Found at i:35967 original size:23 final size:23
Alignment explanation
Indices: 35937--35982 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35927 AAACAAATGA
35937 ATCTTCACTCAAAATTCTGCTTT
1 ATCTTCACTCAAAATTCTGCTTT
35960 ATCTTCACTCAAAATTCTGCTTT
1 ATCTTCACTCAAAATTCTGCTTT
35983 GAAATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.43
Consensus pattern (23 bp):
ATCTTCACTCAAAATTCTGCTTT
Done.