Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009004.1 Corchorus capsularis cultivar CVL-1 contig09025, 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: 47022
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:1456 original size:31 final size:30
Alignment explanation
Indices: 1418--1515 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 30
1408 TGATTTGGCC
1418 AAATAAGGGCCTAACGTTATCGAAAATGCTT
1 AAATAAGGGCCTAAC-TTATCGAAAATGCTT
* * * **
1449 AAATAAGGTCCCAATCTT-T-TAATTTGGC-T
1 AAATAAGGGCCTAA-CTTATCGAAAAT-GCTT
* *
1478 AAATAAGGGTCTAACATTATCGAAAATGCTC
1 AAATAAGGGCCTAAC-TTATCGAAAATGCTT
1509 AAATAAG
1 AAATAAG
1516 AGTCTGGCAT
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
28 1 0.02
29 17 0.35
30 6 0.12
31 24 0.49
32 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (30 bp):
AAATAAGGGCCTAACTTATCGAAAATGCTT
Found at i:1456 original size:65 final size:61
Alignment explanation
Indices: 1352--1515 Score: 197
Period size: 60 Copynumber: 2.6 Consensus size: 61
1342 GCTAATTGTT
* * * *
1352 CAAATAAGAGCCTAACGTT-TGCAAAAATGCTCAAATAAGGGTCCGATCCGATCTTTTGATTTGG
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGT-C---CCAATCTTTTAATTTGG
1416 C
61 C
*
1417 CAAATAAGGGCCTAACGTTATCGAAAATGCTTAAATAA-GGTCCCAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCCAATCTTTTAATTTGGC
* * *
1477 TAAATAAGGGTCTAACATTATCGAAAATGCTCAAATAAG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAG
1516 AGTCTGGCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
60 50 0.57
63 1 0.01
64 3 0.03
65 33 0.38
66 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (61 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCCAATCTTTTAATTTGGC
Found at i:1719 original size:60 final size:59
Alignment explanation
Indices: 1562--1720 Score: 219
Period size: 60 Copynumber: 2.7 Consensus size: 59
1552 GATACCAGGC
* * * * *
1562 CCTTATTTGAGCATTTTAGAAAACGTTAGGCCCTTATGTGGCCAAGTTAAAAGATCGAG
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCGAG
* *
1621 CCATTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTAGCCAAATTAAAAGATCAGAT
1 CC-TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATC-GAG
* *
1682 TCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTT
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
1721 GAACAATAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
59 2 0.02
60 83 0.94
61 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (59 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCGAG
Found at i:3737 original size:21 final size:22
Alignment explanation
Indices: 3702--3748 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3692 ATTTAATTAC
3702 TTTACATACTGTTAATAATTTA
1 TTTACATACTGTTAATAATTTA
*
3724 TTTA-ATATTGTTAATAATTTA
1 TTTACATACTGTTAATAATTTA
3745 TTTA
1 TTTA
3749 TGCAAGTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTACATACTGTTAATAATTTA
Found at i:3914 original size:31 final size:31
Alignment explanation
Indices: 3872--3931 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3862 AAATTGATCA
* *
3872 AATTTTGAAACGTTTAGTACCTATTTGAGTC
1 AATTTTAAAACGTTTAGTACCAATTTGAGTC
3903 AATTTTAAAACGTTTAGTACCAATTTGAG
1 AATTTTAAAACGTTTAGTACCAATTTGAG
3932 CCGGTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (31 bp):
AATTTTAAAACGTTTAGTACCAATTTGAGTC
Found at i:3959 original size:9 final size:9
Alignment explanation
Indices: 3947--3976 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
3937 TTAAAATGTT
3947 AAAAAATAA
1 AAAAAATAA
3956 AAAAAATAA
1 AAAAAATAA
3965 AAAAAATAA
1 AAAAAATAA
3974 AAA
1 AAA
3977 TACATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:3993 original size:10 final size:10
Alignment explanation
Indices: 3939--4000 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
3929 GAGCCGGTTT
*
3939 AAAATGTTAA
1 AAAATATTAA
3949 AAAATA--AA
1 AAAATATTAA
3957 AAAA-A-TAA
1 AAAATATTAA
* *
3965 AAAAAATAAA
1 AAAATATTAA
3975 AATACATATTAA
1 AA-A-ATATTAA
3987 AAAATATTAA
1 AAAATATTAA
3997 AAAA
1 AAAA
4001 ACCACGTAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 1 0.02
8 12 0.28
9 1 0.02
10 20 0.47
11 2 0.05
12 7 0.16
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (10 bp):
AAAATATTAA
Found at i:24022 original size:19 final size:19
Alignment explanation
Indices: 23984--24025 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
23974 AACTCGTACT
*
23984 TATATATATAGTATAGATA
1 TATATATATAGTATACATA
24003 TATATATATA-TATACCATA
1 TATATATATAGTATA-CATA
24022 TATA
1 TATA
24026 AAAGTACGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
TATATATATAGTATACATA
Found at i:36882 original size:3 final size:3
Alignment explanation
Indices: 36876--36914 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
36866 AATTTTTGAA
36876 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
36915 TCCATATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42424 original size:28 final size:28
Alignment explanation
Indices: 42393--42465 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
42383 TAATAAACAT
* *
42393 AACAAAACCAACAAAATTACTGCAAAAA
1 AACAAAGCCAACAAAATTACTACAAAAA
*
42421 AACAAAGCCAACAAAATTACTACCAAAA
1 AACAAAGCCAACAAAATTACTACAAAAA
42449 AACAAAGCCAACAAAAT
1 AACAAAGCCAACAAAAT
42466 CCACACGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.63, C:0.23, G:0.04, T:0.10
Consensus pattern (28 bp):
AACAAAGCCAACAAAATTACTACAAAAA
Found at i:43158 original size:6 final size:6
Alignment explanation
Indices: 43141--43178 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
43131 GTACTTTTAT
43141 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
43179 ATGACTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:43390 original size:22 final size:22
Alignment explanation
Indices: 43365--43613 Score: 63
Period size: 22 Copynumber: 11.5 Consensus size: 22
43355 ATTACACTAT
*
43365 TTTTGATGACA-TCCTTATGAAA
1 TTTTGATAACATTCC-TATGAAA
*
43387 TTTTGATAATATTCCTATGAAA
1 TTTTGATAACATTCCTATGAAA
**
43409 TTAAGAT-A-ATTACACTAT----
1 TTTTGATAACATT-C-CTATGAAA
* * *
43427 TTTTTATGACGT-CCTTATGAAA
1 TTTTGATAACATTCCT-ATGAAA
*
43449 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACATTCCTATGAAA
** *
43471 TTTCAATAACGA-TACTATGAAA
1 TTTTGATAAC-ATTCCTATGAAA
* * * ** *
43493 TTTCGAGAACCTTTTTATAAAA
1 TTTTGATAACATTCCTATGAAA
** * * *
43515 TTTTTTTTAGCCTTCTTATGAAA
1 -TTTTGATAACATTCCTATGAAA
* * * * *
43538 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACATTCCTATGAAA
*
43560 TTTTGA-AGAC-CTCACTATGAAA
1 TTTTGATA-ACATTC-CTATGAAA
* *
43582 TTTTGTTAAC-TTCCAAATGAAA
1 TTTTGATAACATTCC-TATGAAA
43604 TTTTGATAAC
1 TTTTGATAAC
43614 CAACACTATA
Statistics
Matches: 166, Mismatches: 43, Indels: 36
0.68 0.18 0.15
Matches are distributed among these distances:
17 2 0.01
18 7 0.04
19 1 0.01
20 4 0.02
21 5 0.03
22 125 0.75
23 22 0.13
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TTTTGATAACATTCCTATGAAA
Found at i:43424 original size:62 final size:62
Alignment explanation
Indices: 43322--43472 Score: 214
Period size: 62 Copynumber: 2.5 Consensus size: 62
43312 ATATTCATAC
* * * * *
43322 GAAATTATGATAACCTTCCTGT-TAATTATGATAATTACACTATTTTTGATGACATCCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTAAGATAATTACACTATTTTTGATGACATCCTTAT
* * *
43383 GAAATTTTGATAATATTCCTATGAAATTAAGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTAAGATAATTACACTATTTTTGATGACATCCTTAT
*
43445 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACATTCCTATGAAATT
43473 TCAATAACGA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
61 18 0.23
62 61 0.77
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (62 bp):
GAAATTTTGATAACATTCCTATGAAATTAAGATAATTACACTATTTTTGATGACATCCTTAT
Found at i:43724 original size:22 final size:22
Alignment explanation
Indices: 43686--43745 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
43676 AAAACCTCCA
*
43686 TATG-AATTGTCAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* *
43708 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
43730 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
43746 CCTTGCTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:43754 original size:22 final size:22
Alignment explanation
Indices: 43710--43982 Score: 143
Period size: 22 Copynumber: 12.6 Consensus size: 22
43700 AATCACACTC
* *
43710 TGAAATTTTGATAATC-ACACTA
1 TGAAATTTTGATAAACTTC-CTA
* * *
43732 TGAAATTGTGATAACCTTGCTA
1 TGAAATTTTGATAAACTTCCTA
43754 TGAAATTTTGATAAAACTTCCTA
1 TGAAATTTTGAT-AAACTTCCTA
* *
43777 TAAAATTTTGATAAATCTCCCTA
1 TGAAATTTTGATAAA-CTTCCTA
* *
43800 TAAAATTTTGAT-AACCTCCTTA
1 TGAAATTTTGATAAACTTCC-TA
* *
43822 TGAAATCTTAAT-AA----CTA
1 TGAAATTTTGATAAACTTCCTA
* * *
43839 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAAACTTCCTA
** * *
43860 TGATTTTTTGAT-AATTTCATTA
1 TGAAATTTTGATAAACTTC-CTA
** * *
43882 TGAAATTTTGATCTACATACTA
1 TGAAATTTTGATAAACTTCCTA
* * * *
43904 TGAAATTTTGATAACCCTCTTC
1 TGAAATTTTGATAAACTTCCTA
***
43926 TGAAATTTTGA-AAACTAAATTA
1 TGAAATTTTGATAAACT-TCCTA
* *
43948 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAAACTTCCTA
43970 TGAAATTTTGATA
1 TGAAATTTTGATA
43983 TCCTCCCTGA
Statistics
Matches: 189, Mismatches: 48, Indels: 28
0.71 0.18 0.11
Matches are distributed among these distances:
16 8 0.04
17 3 0.02
18 1 0.01
21 12 0.06
22 122 0.65
23 43 0.23
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAAACTTCCTA
Found at i:43948 original size:66 final size:64
Alignment explanation
Indices: 43878--44000 Score: 167
Period size: 66 Copynumber: 1.9 Consensus size: 64
43868 TGATAATTTC
* *
43878 ATTATGAAATTTTGATCTACATAC-TATGAAATTTTGATAACCCTCTTCTGAAATTTTGAAAACT
1 ATTATGAAATTTTGAT-AACATACATATGAAATTTTGAT-ACCCTC-CCTGAAATTTTGAAAACT
43942 AA
63 AA
* * *
43944 ATTATGAAATTTTGATAACCTTCATATGAAATTTTGATATCCTCCCTGAAATTTTGA
1 ATTATGAAATTTTGATAACATACATATGAAATTTTGATACCCTCCCTGAAATTTTGA
44001 TTACTCCATA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
64 12 0.24
65 9 0.18
66 30 0.59
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (64 bp):
ATTATGAAATTTTGATAACATACATATGAAATTTTGATACCCTCCCTGAAATTTTGAAAACTAA
Found at i:44026 original size:64 final size:66
Alignment explanation
Indices: 43902--44030 Score: 154
Period size: 64 Copynumber: 2.0 Consensus size: 66
43892 ATCTACATAC
* * * * *
43902 TATGAAATTTTGATAACCCTCTTCTGAAATTTTGAAAACTAAATTATGAAATTTTGATAACCTTC
1 TATGAAATTTTGATAACCCTCTCCTGAAATTTTGAAAACTAAATAATAAAAGTTTAATAACCTTC
43967 A
66 A
* ** **
43968 TATGAAATTTTGAT-ATCCTC-CCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTC
1 TATGAAATTTTGATAACCCTCTCCTGAAATTTTGAAAACTAAATAATAAAAGTTTAATAACCTTC
44031 CTAATTTGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 34 0.64
65 5 0.09
66 14 0.26
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (66 bp):
TATGAAATTTTGATAACCCTCTCCTGAAATTTTGAAAACTAAATAATAAAAGTTTAATAACCTTC
A
Found at i:44132 original size:22 final size:22
Alignment explanation
Indices: 44107--44186 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
44097 AATCACATTT
* *
44107 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
44129 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
44151 TCAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
44173 TGAAATTTTGATAA
1 TGAAATTTTGATAA
44187 TCACATTATG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:44196 original size:22 final size:22
Alignment explanation
Indices: 44083--44196 Score: 88
Period size: 22 Copynumber: 5.2 Consensus size: 22
44073 AAAATACCAC
* *
44083 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCACAT
* * * *
44105 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCACAT
*
44127 TATGAAATTTTGATAACCTC-T
1 TATGAAATTTTGATAACCACAT
* * * *
44148 CTATCAAATTTTGTTGACC-CCT
1 -TATGAAATTTTGATAACCACAT
*
44170 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAACCACAT
44193 TATG
1 TATG
44197 TGATTTTGGT
Statistics
Matches: 73, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
21 2 0.03
22 69 0.95
23 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAT
Found at i:44204 original size:44 final size:44
Alignment explanation
Indices: 44082--44196 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
44072 AAAAATACCA
* * * *
44082 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * *
44126 TTATGAAATTTTGATAACCTC-TCTATCAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCT
44170 CTATGAAATTTTGATAATCACATTATG
1 CTATGAAATTTTGATAATCACATTATG
44197 TGATTTTGGT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
43 1 0.02
44 53 0.96
45 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:44374 original size:37 final size:37
Alignment explanation
Indices: 44281--44376 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 37
44271 ATCTAACCCC
* * *
44281 AAATAGGACGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGAAAACAAAGACAAAAAGCAAAATT
** *
44318 AAATACAACGATT-AGAAACAAAGACAAAAGGCAAAATT
1 AAATAGGACG-TTGA-AAACAAAGACAAAAAGCAAAATT
44356 AAATAGGACGTTGAAAACAAA
1 AAATAGGACGTTGAAAACAAA
44377 AAGTCAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
37 17 0.35
38 31 0.65
ACGTcount: A:0.56, C:0.11, G:0.19, T:0.14
Consensus pattern (37 bp):
AAATAGGACGTTGAAAACAAAGACAAAAAGCAAAATT
Found at i:45451 original size:20 final size:19
Alignment explanation
Indices: 45422--45472 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
45412 TTAACAAAAT
45422 ATGAATAAAGGTTTTGTAAA
1 ATGAA-AAAGGTTTTGTAAA
45442 ATGAAGAAAGGTTTTGTAAA
1 ATGAA-AAAGGTTTTGTAAA
*
45462 AAGAAAAAGGT
1 ATGAAAAAGGT
45473 AATGAACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (19 bp):
ATGAAAAAGGTTTTGTAAA
Found at i:46389 original size:43 final size:43
Alignment explanation
Indices: 46267--46396 Score: 188
Period size: 44 Copynumber: 3.0 Consensus size: 43
46257 CATGAAGAAG
*
46267 TTTAATGGGTAACCAACTTAATAGGGAGTGGATTTTTTTTTAT
1 TTTAATGGGTAACCAACTTAATAGGGAGTGGTTTTTTTTTTAT
46310 TTTAATGGGTAACCAACTTAATAGGGAGTGGCTTTTTTTTTTAT
1 TTTAATGGGTAACCAACTTAATAGGGAGTGG-TTTTTTTTTTAT
* * * **
46354 TTTAATGGGTAACTAATTTAATAAGGAGCAGTTTTTTTATTTA
1 TTTAATGGGTAACCAACTTAATAGGGAGTGGTTTTTTT-TTTA
46397 AATGTAATGA
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
43 38 0.48
44 41 0.52
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.45
Consensus pattern (43 bp):
TTTAATGGGTAACCAACTTAATAGGGAGTGGTTTTTTTTTTAT
Found at i:46910 original size:15 final size:15
Alignment explanation
Indices: 46890--46920 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46880 ATGTGTTAAA
46890 AAAGAAAATTATTAT
1 AAAGAAAATTATTAT
46905 AAAGAAAATTATTAT
1 AAAGAAAATTATTAT
46920 A
1 A
46921 CTAATTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
AAAGAAAATTATTAT
Done.