Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018751.1 Corchorus olitorius cultivar O-4 contig18784, 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: 41964
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:181 original size:29 final size:30
Alignment explanation
Indices: 144--203 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
134 CAATTCTTCC
*
144 TCTTGAAATAAATCTTCAAA-GTCTTCAAA
1 TCTTCAAATAAATCTTCAAAGGTCTTCAAA
*
173 TCTTCAAATAAGTCTTCAAATGGTCTTCAAA
1 TCTTCAAATAAATCTTCAAA-GGTCTTCAAA
204 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (30 bp):
TCTTCAAATAAATCTTCAAAGGTCTTCAAA
Found at i:1476 original size:14 final size:14
Alignment explanation
Indices: 1457--1484 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1447 ATGCATGCAG
1457 ACTCTCTATTATAC
1 ACTCTCTATTATAC
1471 ACTCTCTATTATAC
1 ACTCTCTATTATAC
1485 TATGCATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
ACTCTCTATTATAC
Found at i:1688 original size:14 final size:15
Alignment explanation
Indices: 1669--1698 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1659 CAATCAAAGC
1669 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
1683 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
1698 A
1 A
1699 TTAGAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:2075 original size:21 final size:21
Alignment explanation
Indices: 2051--2105 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2041 GGCTTGGAAT
* *
2051 GGTGATGGCACGGGCATAGCC
1 GGTGGTGGCACGGGCATAACC
*
2072 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
2093 GGTGGTGGCACGG
1 GGTGGTGGCACGG
2106 TGAATGGTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:2476 original size:32 final size:32
Alignment explanation
Indices: 2433--2502 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
2423 GCGGAGGAGT
*
2433 CCGGGCGTGGCCAGGTAGATGGCTCGG-GTGG
1 CCGGGCGTGGCCAGGCAGATGGCTCGGCGTGG
* *
2464 CCGGGCTGTGGCCAGGCATATGTCTCGGCGTGG
1 CCGGGC-GTGGCCAGGCAGATGGCTCGGCGTGG
2497 CTCGGG
1 C-CGGG
2503 TATGGCCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 6 0.18
32 18 0.55
33 5 0.15
34 4 0.12
ACGTcount: A:0.09, C:0.26, G:0.47, T:0.19
Consensus pattern (32 bp):
CCGGGCGTGGCCAGGCAGATGGCTCGGCGTGG
Found at i:5408 original size:28 final size:27
Alignment explanation
Indices: 5392--5449 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
5382 CAAAAACTTT
5392 TTTTATGACGCAGAAACAAAAAACAAA
1 TTTTATGACGCAGAAACAAAAAACAAA
*
5419 TTTTATGACGCAGAAA-AACAAAACAGA
1 TTTTATGACGCAGAAACAA-AAAACAAA
5446 TTTT
1 TTTT
5450 TTTTTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (27 bp):
TTTTATGACGCAGAAACAAAAAACAAA
Found at i:5933 original size:16 final size:15
Alignment explanation
Indices: 5895--5936 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
5885 ACAGAGATTG
*
5895 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
5910 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
5925 ACTAGAAAACAA
1 AC-AGAAAACAA
5937 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:7363 original size:29 final size:30
Alignment explanation
Indices: 7326--7386 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
7316 CAATTCTTCC
*
7326 TCTTGAAATAAATCTTCAAA-GTCTTCAAA
1 TCTTCAAATAAATCTTCAAAGGTCTTCAAA
*
7355 TCTTCAAATAAGTCTTCAAATGGTCTTCAAA
1 TCTTCAAATAAATCTTCAAA-GGTCTTCAAA
7386 T
1 T
7387 ACGAACTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.64
31 10 0.36
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (30 bp):
TCTTCAAATAAATCTTCAAAGGTCTTCAAA
Found at i:7382 original size:11 final size:12
Alignment explanation
Indices: 7355--7387 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
7345 AGTCTTCAAA
7355 TCTTCAAATAAG
1 TCTTCAAATAAG
*
7367 TCTTCAAAT-GG
1 TCTTCAAATAAG
7378 TCTTCAAATA
1 TCTTCAAATA
7388 CGAACTTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (12 bp):
TCTTCAAATAAG
Found at i:9832 original size:38 final size:39
Alignment explanation
Indices: 9743--9845 Score: 147
Period size: 39 Copynumber: 2.7 Consensus size: 39
9733 AATCAATTAA
* *
9743 TTTCCAAAATTTTCTTTTGGGA-TATCTTAAACTTTTATT
1 TTTCCAAAATCTTCTTTTGGGATTA-CCTAAACTTTTATT
*
9782 TTTCCAAAATCTTCTTTTGGGATTACCTAGACTTTTA-T
1 TTTCCAAAATCTTCTTTTGGGATTACCTAAACTTTTATT
*
9820 TTTCCAAAATCTTCTTTTGGAATTAC
1 TTTCCAAAATCTTCTTTTGGGATTAC
9846 TTAATTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
38 26 0.44
39 31 0.53
40 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.50
Consensus pattern (39 bp):
TTTCCAAAATCTTCTTTTGGGATTACCTAAACTTTTATT
Found at i:10308 original size:15 final size:15
Alignment explanation
Indices: 10288--10317 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10278 TAATTAATGG
10288 CAAGTAAATATGATA
1 CAAGTAAATATGATA
10303 CAAGTAAATATGATA
1 CAAGTAAATATGATA
10318 TACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
CAAGTAAATATGATA
Found at i:11059 original size:11 final size:11
Alignment explanation
Indices: 11043--11071 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
11033 CATTTTTATG
11043 CTCAAAATCAA
1 CTCAAAATCAA
11054 CTCAAAATCAA
1 CTCAAAATCAA
11065 CTCAAAA
1 CTCAAAA
11072 AAGTAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (11 bp):
CTCAAAATCAA
Found at i:11596 original size:13 final size:13
Alignment explanation
Indices: 11573--11619 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
11563 TTAAAAAAAT
*
11573 AAAAAATATTTGA
1 AAAAAAAATTTGA
* *
11586 AAAACAAATTTTA
1 AAAAAAAATTTGA
*
11599 AAAAAAAAATTGA
1 AAAAAAAATTTGA
11612 AAAAAAAA
1 AAAAAAAA
11620 AATCTAAACC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:11608 original size:14 final size:14
Alignment explanation
Indices: 11568--11622 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
11558 AGGCATTAAA
11568 AAAATAAAAAATATTT
1 AAAA-AAAAAAT-TTT
* *
11584 GAAAAACAAATTTT
1 AAAAAAAAAATTTT
**
11598 AAAAAAAAAATTGA
1 AAAAAAAAAATTTT
11612 AAAAAAAAAAT
1 AAAAAAAAAAT
11623 CTAAACCCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 24 0.73
15 6 0.18
16 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (14 bp):
AAAAAAAAAATTTT
Found at i:12983 original size:30 final size:31
Alignment explanation
Indices: 12921--12990 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
12911 CACTTATTTC
*
12921 CCTGAATTGACACAGCCCGATAACGTTATAT
1 CCTGAATTGACACAGCCCGATAACGGTATAT
* *
12952 CCTGAATTGACACAAG-TCG-TAACGGTGTAT
1 CCTGAATTGACAC-AGCCCGATAACGGTATAT
12982 CCTGAATTG
1 CCTGAATTG
12991 CATTTTCGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 18 0.51
31 15 0.43
32 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (31 bp):
CCTGAATTGACACAGCCCGATAACGGTATAT
Found at i:14967 original size:18 final size:18
Alignment explanation
Indices: 14924--14981 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
14914 AGTACAGCAG
14924 ATGAACATGTGTTGACC-A
1 ATGAACATGTGTTG-CCTA
* *
14942 ATAAGAACATGTTTTGCTTA
1 AT--GAACATGTGTTGCCTA
14962 ATGAACATGTGTTGCCTA
1 ATGAACATGTGTTGCCTA
14980 AT
1 AT
14982 ATTTATGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 18 0.55
19 1 0.03
20 14 0.42
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (18 bp):
ATGAACATGTGTTGCCTA
Found at i:26327 original size:24 final size:23
Alignment explanation
Indices: 26272--26327 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
26262 GAATTAGTAT
*
26272 TATTGAAATTTCAATTATTGTTA
1 TATTGAAATTTCAATTACTGTTA
* *
26295 T-TGTTAAATCTTCTATTACTGTTA
1 TAT-TGAAAT-TTCAATTACTGTTA
26319 TATTGAAAT
1 TATTGAAAT
26328 GAAACCATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
22 1 0.04
23 6 0.23
24 18 0.69
25 1 0.04
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (23 bp):
TATTGAAATTTCAATTACTGTTA
Found at i:27553 original size:18 final size:17
Alignment explanation
Indices: 27532--27600 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 17
27522 AAAAATCCAG
*
27532 AAAAATTTGAAAAAAATT
1 AAAAAATTG-AAAAAATT
27550 AAAAAATTGAAAAAATT
1 AAAAAATTGAAAAAATT
*
27567 -AAAGATT-AAAAAGA-T
1 AAAAAATTGAAAAA-ATT
27582 --AAAATT-AAAAAATT
1 AAAAAATTGAAAAAATT
27596 AAAAA
1 AAAAA
27601 TAAGAAAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
13 1 0.02
14 11 0.25
15 6 0.14
16 10 0.23
17 8 0.18
18 8 0.18
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (17 bp):
AAAAAATTGAAAAAATT
Found at i:27579 original size:9 final size:8
Alignment explanation
Indices: 27542--27600 Score: 63
Period size: 8 Copynumber: 7.6 Consensus size: 8
27532 AAAAATTTGA
27542 AAAAAATT
1 AAAAAATT
27550 AAAAAATT
1 AAAAAATT
27558 GAAAAAATT
1 -AAAAAATT
*
27567 -AAAGATT
1 AAAAAATT
27574 AAAAAGA-T
1 AAAAA-ATT
27582 --AAAATT
1 AAAAAATT
27588 AAAAAATT
1 AAAAAATT
27596 AAAAA
1 AAAAA
27601 TAAGAAAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
5 1 0.02
6 4 0.09
7 6 0.14
8 23 0.53
9 9 0.21
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (8 bp):
AAAAAATT
Found at i:27588 original size:14 final size:14
Alignment explanation
Indices: 27542--27599 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
27532 AAAAATTTGA
27542 AAAAAATTAAAAAATT
1 AAAAAATT--AAAATT
27558 GAAAAAATTAAAGATT
1 -AAAAAATTAAA-ATT
27574 AAAAAGA-TAAAATT
1 AAAAA-ATTAAAATT
27588 AAAAAATTAAAA
1 AAAAAATTAAAA
27600 ATAAGAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.03
14 13 0.34
15 12 0.32
16 4 0.11
17 8 0.21
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (14 bp):
AAAAAATTAAAATT
Found at i:29438 original size:13 final size:13
Alignment explanation
Indices: 29409--29437 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29399 AAAAAAAGGG
29409 AAAAGAAATGAAA
1 AAAAGAAATGAAA
29422 AAAAGAAA-GAAA
1 AAAAGAAATGAAA
29434 AAAA
1 AAAA
29438 ACAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAGAAATGAAA
Found at i:30046 original size:31 final size:29
Alignment explanation
Indices: 30010--30078 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
30000 TGATTTTATA
30010 CTTAATTGCTTGAAATCGATAACGTTATATC
1 CTTAATTGCTTG-AATCG-TAACGTTATATC
* ** *
30041 TTTAATTGCTTGTTTTGTAACGTTATATC
1 CTTAATTGCTTGAATCGTAACGTTATATC
30070 CTTAATTGC
1 CTTAATTGC
30079 ATGAGGCAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 20 0.61
30 2 0.06
31 11 0.33
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.46
Consensus pattern (29 bp):
CTTAATTGCTTGAATCGTAACGTTATATC
Found at i:31086 original size:107 final size:108
Alignment explanation
Indices: 30949--31233 Score: 266
Period size: 107 Copynumber: 2.7 Consensus size: 108
30939 AGATCACCCC
* * * *
30949 CGATCAA-TCAAAATAAGCTTAAGAGAGACCACCCCCGATCGA-T-CCAAATAAGT-TGAAGAAA
1 CGATCAATTCGAAATAAACTGAAGAAAGACCACCCCCGATC-ATTGCCAAATAA-TCTGAAGAAA
* *
31010 GACTACCCCAGATCAATCCAAA-TCAAATTGAAGAACGACCATCC-T
64 GACCACCCCAGATCAATCCAAACT-AAATTGAAAAACGACCA-CCGT
**
31055 CGATC-ATTCTGAAATAAACTGAAGAAAGACCA-CCCCGATCATTGTGAAATAATCTGAAGAAAG
1 CGATCAATTC-GAAATAAACTGAAGAAAGACCACCCCCGATCATTGCCAAATAATCTGAAGAAAG
* * **
31118 ACCACCCCAGATTAGTCTGAACTAAATTGAAAAACGACCACCGT
65 ACCACCCCAGATCAATCCAAACTAAATTGAAAAACGACCACCGT
* * * * * * *
31162 CGATCAATTCGAACTAAATTGTAGAACGACCACCCTCGATCATT-CCGAAATAAACTG-AGCAAC
1 CGATCAATTCGAAATAAACTGAAGAAAGACCACCCCCGATCATTGCC-AAATAATCTGAAG-AAA
31225 GACCACCCC
64 GACCACCCC
31234 CGACCATTTT
Statistics
Matches: 147, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
105 2 0.01
106 19 0.13
107 91 0.62
108 35 0.24
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.18
Consensus pattern (108 bp):
CGATCAATTCGAAATAAACTGAAGAAAGACCACCCCCGATCATTGCCAAATAATCTGAAGAAAGA
CCACCCCAGATCAATCCAAACTAAATTGAAAAACGACCACCGT
Found at i:31311 original size:144 final size:144
Alignment explanation
Indices: 30923--31482 Score: 585
Period size: 144 Copynumber: 3.9 Consensus size: 144
30913 CCGATTAGAA
* * * * ** * * *
30923 GAAATAAACAGAAGAAAGATCACCCCCGATCA-ATCAAAATAAGCTTAAGAGAGACCACCCCCGA
1 GAAATAAACTGAAGAAAGACCACCCCCGACCATTTTGAAATAATCTGAAGAAAGACCACCCCCGA
* * * * *
30987 TCGATCC-AAATAAGTTGAAGAAAGACTACCC-CAGATCAATCCAAA-TCAAATTGAAGAACGAC
66 TCAATCCGAACTAAATTGAAGAACGACCACCCTC-GATCAATCCAAACT-AAATTGAAGAACGAC
* *
31049 CATCCTCGATCATTCT
129 CACCCTCGATCATTCC
* * *
31065 GAAATAAACTGAAGAAAGACCA-CCCCGATCATTGTGAAATAATCTGAAGAAAGACCACCCCAGA
1 GAAATAAACTGAAGAAAGACCACCCCCGACCATTTTGAAATAATCTGAAGAAAGACCACCCCCGA
* * * * * * * *
31129 TTAGTCTGAACTAAATTGAAAAACGACCACCGTCGATCAATTCGAACTAAATTGTAGAACGACCA
66 TCAATCCGAACTAAATTGAAGAACGACCACCCTCGATCAATCCAAACTAAATTGAAGAACGACCA
31194 CCCTCGATCATTCC
131 CCCTCGATCATTCC
* * *
31208 GAAATAAACTG-AGCAACGACCACCCCCGACCATTTTGAAATAATTTGAAGAAAGACTACCCCCG
1 GAAATAAACTGAAG-AAAGACCACCCCCGACCATTTTGAAATAATCTGAAGAAAGACCACCCCCG
* * * * *
31272 GTCAATCCAAACTAAATTGAAGGACAACCACCCTCGATCAATCCAAACTAAATTGAAAAACGACC
65 ATCAATCCGAACTAAATTGAAGAACGACCACCCTCGATCAATCCAAACTAAATTGAAGAACGACC
* *
31337 ACCCTTGGTCATTCC
130 ACCCTCGATCATTCC
* * * * *
31352 GAAATAAACTGAAGAAAGACCACCCCCGATCAATCTT-AAATAAACTGAAGAAAAACCACCCTCG
1 GAAATAAACTGAAGAAAGACCACCCCCGA-CCATTTTGAAATAATCTGAAGAAAGACCACCCCCG
* * * * * * * *
31416 ATCAATCCGAACTAAATTGAAGAACGCCCACCCTCAATCATTTCAAAATAAACTGATGAAAGACC
65 ATCAATCCGAACTAAATTGAAGAACGACCACCCTCGATCAATCCAAACTAAATTGAAGAACGACC
31481 AC
130 AC
31483 TCGGGTCAAT
Statistics
Matches: 343, Mismatches: 67, Indels: 14
0.81 0.16 0.03
Matches are distributed among these distances:
141 9 0.03
142 49 0.14
143 74 0.22
144 204 0.59
145 7 0.02
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.18
Consensus pattern (144 bp):
GAAATAAACTGAAGAAAGACCACCCCCGACCATTTTGAAATAATCTGAAGAAAGACCACCCCCGA
TCAATCCGAACTAAATTGAAGAACGACCACCCTCGATCAATCCAAACTAAATTGAAGAACGACCA
CCCTCGATCATTCC
Found at i:31449 original size:36 final size:36
Alignment explanation
Indices: 30923--31516 Score: 370
Period size: 36 Copynumber: 16.6 Consensus size: 36
30913 CCGATTAGAA
** * * *
30923 GAAATAAACAGAAGAAAGATCACCCCCGATCAAT-C
1 GAAATAAATTGAAGAACGACCACCCTCGATCAATCC
* * * *
30958 AAAATAAGCTT-AAGAGA-GACCACCCCCGATCGATCC
1 GAAATAA-ATTGAAGA-ACGACCACCCTCGATCAATCC
* * *
30994 -AAATAAGTTGAAGAAAGACTACCC-CAGATCAATCC
1 GAAATAAATTGAAGAACGACCACCCTC-GATCAATCC
* * *
31029 -AAATCAAATTGAAGAACGACCATCCTCGATCATTCT
1 GAAAT-AAATTGAAGAACGACCACCCTCGATCAATCC
* * * **
31065 GAAATAAACTGAAGAAAGACCACCC-CGATCATTGT
1 GAAATAAATTGAAGAACGACCACCCTCGATCAATCC
* * * *
31100 GAAAT-AATCTGAAGAAAGACCACCC-CAGATTAGTCT
1 GAAATAAAT-TGAAGAACGACCACCCTC-GATCAATCC
* * * *
31136 GAACTAAATTGAAAAACGACCACCGTCGATCAATTC
1 GAAATAAATTGAAGAACGACCACCCTCGATCAATCC
* * *
31172 GAACTAAATTGTAGAACGACCACCCTCGATCATTCC
1 GAAATAAATTGAAGAACGACCACCCTCGATCAATCC
* * * * **
31208 GAAATAAACTG-AGCAACGACCACCCCCGACCATTTT
1 GAAATAAATTGAAG-AACGACCACCCTCGATCAATCC
* * * * *
31244 GAAATAATTTGAAGAAAGACTACCCCCGGTCAATCC
1 GAAATAAATTGAAGAACGACCACCCTCGATCAATCC
* *
31280 -AAACTAAATTGAAGGACAACCACCCTCGATCAATCC
1 GAAA-TAAATTGAAGAACGACCACCCTCGATCAATCC
* * * *
31316 -AAACTAAATTGAAAAACGACCACCCTTGGTCATTCC
1 GAAA-TAAATTGAAGAACGACCACCCTCGATCAATCC
* * * *
31352 GAAATAAACTGAAGAAAGACCACCCCCGATCAATCT
1 GAAATAAATTGAAGAACGACCACCCTCGATCAATCC
* * **
31388 TAAATAAACTGAAGAAAAACCACCCTCGATCAATCC
1 GAAATAAATTGAAGAACGACCACCCTCGATCAATCC
* * * * *
31424 GAACTAAATTGAAGAACGCCCACCCTCAATCATTTC
1 GAAATAAATTGAAGAACGACCACCCTCGATCAATCC
* * * * *
31460 AAAATAAACTGATGAAAGACCA--CTCGGGTCAATCTC
1 GAAATAAATTGAAGAACGACCACCCTC-GATCAATC-C
** *
31496 GAAATTCATTGAAGAAAGACC
1 GAAATAAATTGAAGAACGACC
31517 GTCCTGGATC
Statistics
Matches: 440, Mismatches: 100, Indels: 37
0.76 0.17 0.06
Matches are distributed among these distances:
34 9 0.02
35 94 0.21
36 323 0.73
37 14 0.03
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.18
Consensus pattern (36 bp):
GAAATAAATTGAAGAACGACCACCCTCGATCAATCC
Found at i:31449 original size:108 final size:108
Alignment explanation
Indices: 30923--31482 Score: 451
Period size: 108 Copynumber: 5.2 Consensus size: 108
30913 CCGATTAGAA
* * * * * * *
30923 GAAATAAACAGAAGAAAGATCACCCCCGATCAATC-AAAATAAGCTTAAGAGAGACCACCCCCGA
1 GAAATAAACTGAAGAAAGACCACCCCCGATCAATCTGAAATAAACTGAAGAAAGACCACCCTCGA
* * * * *
30987 TCGATCC-AAATAAGTTGAAGAAAGACTACCCCAGATCAATCC
66 TCAATCCGAAATAAATTGAAGAACGACCACCCCAGATCATTCC
* * * * *
31029 -AAATCAAATTGAAGAACGACCATCCTCGATCATTCTGAAATAAACTGAAGAAAGACCACCC-CG
1 GAAAT-AAACTGAAGAAAGACCACCCCCGATCAATCTGAAATAAACTGAAGAAAGACCACCCTCG
* ** * * * *
31092 ATCATTGTGAAAT-AATCTGAAGAAAGACCACCCCAGATTAGTCT
65 ATCAATCCGAAATAAAT-TGAAGAACGACCACCCCAGATCATTCC
* * ** * * * *
31136 GAACTAAATTGAA-AAACGACCACCGTCGATCAAT-TCGAACTAAATTGTAGAACGACCACCCTC
1 GAAATAAACTGAAGAAA-GACCACCCCCGATCAATCT-GAAATAAACTGAAGAAAGACCACCCTC
* * * * **
31199 GATCATTCCGAAATAAACTG-AGCAACGACCACCCCCGACCATTTT
64 GATCAATCCGAAATAAATTGAAG-AACGACCACCCCAGATCATTCC
** * * * * *
31244 GAAATAATTTGAAGAAAGACTACCCCCGGTCAATC-CAAACTAAATTGAAGGACA-ACCACCCTC
1 GAAATAAACTGAAGAAAGACCACCCCCGATCAATCTGAAA-TAAACTGAA-GAAAGACCACCCTC
* ** *
31307 GATCAATCC-AAACTAAATTGAAAAACGACCACCCTTGGTCATTCC
64 GATCAATCCGAAA-TAAATTGAAGAACGACCACCCCAGATCATTCC
* *
31352 GAAATAAACTGAAGAAAGACCACCCCCGATCAATCTTAAATAAACTGAAGAAAAACCACCCTCGA
1 GAAATAAACTGAAGAAAGACCACCCCCGATCAATCTGAAATAAACTGAAGAAAGACCACCCTCGA
* * *
31417 TCAATCCGAACTAAATTGAAGAACGCCCACCCTCA-ATCATTTC
66 TCAATCCGAAATAAATTGAAGAACGACCACCC-CAGATCATTCC
* *
31460 AAAATAAACTGATGAAAGACCAC
1 GAAATAAACTGAAGAAAGACCAC
31483 TCGGGTCAAT
Statistics
Matches: 360, Mismatches: 74, Indels: 38
0.76 0.16 0.08
Matches are distributed among these distances:
105 4 0.01
106 34 0.09
107 101 0.28
108 208 0.58
109 13 0.04
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.18
Consensus pattern (108 bp):
GAAATAAACTGAAGAAAGACCACCCCCGATCAATCTGAAATAAACTGAAGAAAGACCACCCTCGA
TCAATCCGAAATAAATTGAAGAACGACCACCCCAGATCATTCC
Found at i:32702 original size:2 final size:2
Alignment explanation
Indices: 32691--32720 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
32681 AAATGATAAG
32691 AT AT -T 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
32721 AAAGAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33321 original size:25 final size:24
Alignment explanation
Indices: 33293--33340 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
33283 AAGTGTTATT
33293 TTTTATTCTTCTTT-CTTTTCTTTTC
1 TTTTATTCTT-TTTACTTTT-TTTTC
*
33318 TTTTCTTCTTTTTACTTTTTTTT
1 TTTTATTCTTTTTACTTTTTTTT
33341 ATCACATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTATTCTTTTTACTTTTTTTTC
Found at i:35771 original size:14 final size:14
Alignment explanation
Indices: 35754--35782 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35744 CAATCATAAA
35754 ATAGCCCAACAATT
1 ATAGCCCAACAATT
35768 ATAGCCCAACAATT
1 ATAGCCCAACAATT
35782 A
1 A
35783 AAAGAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.07, T:0.21
Consensus pattern (14 bp):
ATAGCCCAACAATT
Found at i:36502 original size:12 final size:14
Alignment explanation
Indices: 36487--36519 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
36477 TTTTTCTCTC
36487 TTTTTTTGTA-TA-
1 TTTTTTTGTAGTAG
36499 TTTTTTTGTAGTAG
1 TTTTTTTGTAGTAG
36513 TTTTTTT
1 TTTTTTT
36520 TCTACTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 2 0.11
14 7 0.37
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (14 bp):
TTTTTTTGTAGTAG
Found at i:40317 original size:11 final size:11
Alignment explanation
Indices: 40297--40331 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40287 TTGGCAGCGC
40297 AACAAAAATAA
1 AACAAAAATAA
*
40308 AACGAAAATAA
1 AACAAAAATAA
*
40319 AACAAAAACAA
1 AACAAAAATAA
40330 AA
1 AA
40332 AACAGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.80, C:0.11, G:0.03, T:0.06
Consensus pattern (11 bp):
AACAAAAATAA
Done.