Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019781.1 Corchorus olitorius cultivar O-4 contig19814, 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: 70373
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2294 original size:13 final size:13
Alignment explanation
Indices: 2257--2297 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
2247 TTATGCACCC
2257 AAAACATTTAT-T
1 AAAACATTTATAT
*
2269 AAAAC-TTTTTAT
1 AAAACATTTATAT
*
2281 AAAGCATTTATAT
1 AAAACATTTATAT
2294 AAAA
1 AAAA
2298 GCAGTAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 4 0.17
12 10 0.43
13 9 0.39
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (13 bp):
AAAACATTTATAT
Found at i:3700 original size:20 final size:19
Alignment explanation
Indices: 3663--3710 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
3653 TTTATTCCCA
* *
3663 ATTTTCTCTTTATTTTCCTT
1 ATTTTCTTTTTATCTTCC-T
*
3683 ATTTTCTTTTTCTCTTCCT
1 ATTTTCTTTTTATCTTCCT
3702 -TTTTCTTTT
1 ATTTTCTTTT
3711 CTTTCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
19 1 0.04
20 15 0.60
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTCTTTTTATCTTCCT
Found at i:3704 original size:26 final size:27
Alignment explanation
Indices: 3664--3720 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
3654 TTATTCCCAA
*
3664 TTTTCTCTTTATTTTCCTTAT-TTTCT
1 TTTTCTCTTCATTTTCCTTATCTTTCT
* * *
3690 TTTTCTCTTCCTTTTTCTTTTCTTTCT
1 TTTTCTCTTCATTTTCCTTATCTTTCT
3717 TTTT
1 TTTT
3721 TTCCCTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTCTCTTCATTTTCCTTATCTTTCT
Found at i:3717 original size:9 final size:8
Alignment explanation
Indices: 3664--3757 Score: 62
Period size: 8 Copynumber: 10.8 Consensus size: 8
3654 TTATTCCCAA
*
3664 TTTTCTCT
1 TTTTTTCT
3672 TTATTTTCCT
1 TT-TTTT-CT
*
3682 TATTTTCT
1 TTTTTTCT
*
3690 TTTTCTCT
1 TTTTTTCT
3698 TCCTTTTTCT
1 T--TTTTTCT
3708 TTTCTTTCT
1 TTT-TTTCT
3717 TTTTTTCCCT
1 TTTTTT--CT
*
3727 TTTTCTTTT
1 TTTT-TTCT
*
3736 TTTTTTCC
1 TTTTTTCT
*
3744 CTTTTTCT
1 TTTTTTCT
3752 TTTTTT
1 TTTTTT
3758 TTCCCTGTTG
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
8 29 0.43
9 20 0.30
10 16 0.24
11 2 0.03
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCT
Found at i:3723 original size:44 final size:45
Alignment explanation
Indices: 3669--3754 Score: 122
Period size: 44 Copynumber: 1.9 Consensus size: 45
3659 CCCAATTTTC
*
3669 TCTTTATTTTCCTTATTTTCTTTTTCTCTT-CCTTTTTCTTTTCTT
1 TCTTTATTTTCCCT-TTTTCTTTTTCTCTTCCCTTTTTCTTTTCTT
* *
3714 TCTTT-TTTTCCCTTTTTCTTTTTTTTTTCCCTTTTTCTTTT
1 TCTTTATTTTCCCTTTTTCTTTTTCTCTTCCCTTTTTCTTTT
3755 TTTTTCCCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 13 0.35
44 19 0.51
45 5 0.14
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (45 bp):
TCTTTATTTTCCCTTTTTCTTTTTCTCTTCCCTTTTTCTTTTCTT
Found at i:3728 original size:19 final size:18
Alignment explanation
Indices: 3706--3763 Score: 82
Period size: 18 Copynumber: 3.1 Consensus size: 18
3696 CTTCCTTTTT
3706 CTTTTCTTTCTTTTTTTCC
1 CTTTTCTTT-TTTTTTTCC
3725 CTTTTTCTTTTTTTTTTCC
1 C-TTTTCTTTTTTTTTTCC
3744 CTTTT-TCTTTTTTTTTCC
1 CTTTTCT-TTTTTTTTTCC
3762 CT
1 CT
3764 GTTGGGCCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.03
18 17 0.46
19 11 0.30
20 8 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (18 bp):
CTTTTCTTTTTTTTTTCC
Found at i:3737 original size:27 final size:27
Alignment explanation
Indices: 3685--3735 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
3675 TTTTCCTTAT
*
3685 TTTCTTTTTCTCTTCCTTTTTCTTTTC
1 TTTCTTTTTCTCTCCCTTTTTCTTTTC
3712 TTTCTTTTT-T-TCCCTTTTTCTTTT
1 TTTCTTTTTCTCTCCCTTTTTCTTTT
3736 TTTTTTCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.57
26 1 0.04
27 9 0.39
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTCTTTTTCTCTCCCTTTTTCTTTTC
Found at i:3759 original size:18 final size:19
Alignment explanation
Indices: 3707--3763 Score: 98
Period size: 19 Copynumber: 3.0 Consensus size: 19
3697 TTCCTTTTTC
3707 TTTTCTTTCTTTTTTTCCCT
1 TTTTCTTT-TTTTTTTCCCT
3727 TTTTCTTTTTTTTTTCCCT
1 TTTTCTTTTTTTTTTCCCT
3746 TTTTC-TTTTTTTTTCCCT
1 TTTTCTTTTTTTTTTCCCT
3764 GTTGGGCCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.35
19 16 0.43
20 8 0.22
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTTTTTTTCCCT
Found at i:17353 original size:5 final size:5
Alignment explanation
Indices: 17338--17387 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
17328 TAATATTAAA
*
17338 AATAT -ATAT AATAT AATAT AATAT -ATAT AATAAT AA-AT ACTAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT
17386 AA
1 AA
17388 ATGAATTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 11 0.28
5 24 0.62
6 4 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:17362 original size:19 final size:19
Alignment explanation
Indices: 17328--17387 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
17318 CAAAAATTAT
*
17328 TAATATTAAA-AATATATA
1 TAATAATAAATAATATATA
17346 TAAT-ATAATATAATATATA
1 TAATAATAA-ATAATATATA
*
17365 TAATAATAAATACTATAATA
1 TAATAATAAATAATAT-ATA
17385 TAA
1 TAA
17388 ATGAATTGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 3 0.08
18 5 0.14
19 18 0.50
20 10 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATAATAAATAATATATA
Found at i:17363 original size:12 final size:11
Alignment explanation
Indices: 17339--17386 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
17329 AATATTAAAA
17339 ATATATATAAT
1 ATATATATAAT
17350 ATA-ATATAAT
1 ATATATATAAT
17360 ATATATAATAAT
1 ATATAT-ATAAT
*
17372 AAATACTATAAT
1 ATATA-TATAAT
17384 ATA
1 ATA
17387 AATGAATTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 10 0.31
11 5 0.16
12 16 0.50
13 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATATATAAT
Found at i:17363 original size:17 final size:16
Alignment explanation
Indices: 17341--17387 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
17331 TATTAAAAAT
17341 ATATATAATATAATATA
1 ATATATAATATAATA-A
17358 ATATAT-ATAATAATAA
1 ATATATAAT-ATAATAA
17374 ATACTATAATATAA
1 ATA-TATAATATAA
17388 ATGAATTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.22
17 19 0.70
18 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATATAATATAATAA
Found at i:17388 original size:14 final size:13
Alignment explanation
Indices: 17338--17389 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 13
17328 TAATATTAAA
*
17338 AATATATATAATAT
1 AATATAAAT-ATAT
17352 AATATAATATATAT
1 AATATAA-ATATAT
17366 AATAATAAATACTAT
1 AAT-ATAAATA-TAT
17381 AATATAAAT
1 AATATAAAT
17390 GAATTGGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAAATATAT
Found at i:19599 original size:2 final size:2
Alignment explanation
Indices: 19592--19621 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19582 ATCCAAATTA
19592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19622 TTTGTTATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20830 original size:30 final size:30
Alignment explanation
Indices: 20794--21207 Score: 675
Period size: 30 Copynumber: 13.7 Consensus size: 30
20784 ACTCTCTAAA
20794 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
20824 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
20854 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
20884 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
20914 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
20944 TGACACCAGAAGCTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
20974 TGACACCAGAAGCTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
21004 TGACACCAGAAGCTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
21034 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
21064 TGACACCAGAAGTTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
21094 TGACACCAGAAGCTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
21124 TGACACCATAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * * *
21154 TGACACCATAAGTTGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
21186 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
21208 TTTACCTTTC
Statistics
Matches: 368, Mismatches: 14, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
30 341 0.93
31 3 0.01
32 24 0.07
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:21233 original size:36 final size:32
Alignment explanation
Indices: 20755--21241 Score: 149
Period size: 30 Copynumber: 15.6 Consensus size: 32
20745 TAATATATGT
*
20755 TGACACCAGAAGTTGTCACAATTTATTTTACTCTCTAAA
1 TGACACCAGAAGTTGT--C-A-TAATTTTA-T-TC-AAA
* * * *
20794 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* * * *
20824 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* * * *
20854 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* * * *
20884 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
** * * *
20914 TGACACCAGAAGTTGTCAT-GGTCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* ** * * *
20944 TGACACCAGAAGCTGTCAT-GGTCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* ** * * *
20974 TGACACCAGAAGCTGTCAT-GGTCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* ** * * *
21004 TGACACCAGAAGCTGTCAT-GGTCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* * * *
21034 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* * * *
21064 TGACACCAGAAGTTGTCATGA-TGT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* * * * *
21094 TGACACCAGAAGCTGTCATGA-TGT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* * * * *
21124 TGACACCATAAGTTGTCATGA-TCT-TGCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
* *
21154 TGACACCATAAGTTGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATAATTTTATTCAAA
*
21186 TGACACCAGAAGTTGTCATGATTTTACCTTTCATAA
1 TGACACCAGAAGTTGTCATAATTTTA---TTCA-AA
*
21222 TGACACAAGAAGTTGTCATA
1 TGACACCAGAAGTTGTCATA
21242 TGCACTATTA
Statistics
Matches: 419, Mismatches: 21, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
30 341 0.81
31 3 0.01
32 30 0.07
34 2 0.00
35 6 0.01
36 20 0.05
37 1 0.00
39 16 0.04
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (32 bp):
TGACACCAGAAGTTGTCATAATTTTATTCAAA
Found at i:23315 original size:32 final size:33
Alignment explanation
Indices: 23253--23315 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
23243 ATACTGAATA
**
23253 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
* *
23286 ATATTG-CCCTGTAGTGGCATAAACCCATGA
1 ATATTGCCCCTGAAGAGGCATAAACCCATGA
23316 AAAGATCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
Found at i:25633 original size:24 final size:23
Alignment explanation
Indices: 25606--25657 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
25596 AGGTTGCGCA
*
25606 AACTTCAGGGTTCAACCTGGCCCC
1 AACTTCAGGGGT-AACCTGGCCCC
* **
25630 AACTTGAGGGGTAAGTTGGCCCC
1 AACTTCAGGGGTAACCTGGCCCC
25653 AACTT
1 AACTT
25658 GGAGTTCGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (23 bp):
AACTTCAGGGGTAACCTGGCCCC
Found at i:28637 original size:58 final size:58
Alignment explanation
Indices: 28542--28654 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 58
28532 ATTAATCAAA
*
28542 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCGAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCT
* *
28600 TATCGAGTGACATGTTTTTTTATTAGATGTC-T-AAAAAAGACGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATG-CATAAAAAAAGACGTTTTAGGACCGAG
28655 ACATGATGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 35 0.70
59 14 0.28
60 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGGCT
Found at i:29954 original size:36 final size:36
Alignment explanation
Indices: 29907--29976 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
29897 TTCAATAACC
* *
29907 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
29943 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
29977 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:30833 original size:204 final size:201
Alignment explanation
Indices: 30486--30895 Score: 748
Period size: 204 Copynumber: 2.0 Consensus size: 201
30476 GCTTAATAAC
*
30486 TTTATCAATGGTGAATGTTATTAATTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
* *
30551 ATATAACACATTATTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGA
66 ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGA
30616 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
30681 GATTTA
196 GATTTA
* *
30687 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATCAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
30752 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
65 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
30817 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
128 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
30882 TCCGATTTA
193 TCCGATTTA
30891 TTTAT
1 TTTAT
30896 TATTAAGGAA
Statistics
Matches: 201, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
201 24 0.12
202 61 0.30
203 1 0.00
204 115 0.57
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
GATTTA
Found at i:38602 original size:22 final size:21
Alignment explanation
Indices: 38577--38661 Score: 80
Period size: 22 Copynumber: 3.9 Consensus size: 21
38567 CAAGGTTTCT
* *
38577 TATGGAGTTTATCACAATTTTA
1 TATGGAG-TTATCAAAATTTAA
* * *
38599 TATGTAATTATCAAAATTTCA
1 TATGGAGTTATCAAAATTTAA
*
38620 TATGGTGGTTATCAAAATTTAA
1 TATGG-AGTTATCAAAATTTAA
*
38642 TAAGGTAGTTATCAAAATTT
1 TATGG-AGTTATCAAAATTT
38662 CATAAAAATG
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.31
22 36 0.69
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (21 bp):
TATGGAGTTATCAAAATTTAA
Found at i:38666 original size:22 final size:22
Alignment explanation
Indices: 38606--38666 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
38596 TTATATGTAA
* *
38606 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTCATAAGGTAG
*
38628 TTATCAAAATTTAATAAGGTAG
1 TTATCAAAATTTCATAAGGTAG
38650 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
38667 AAATGTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGTAG
Found at i:41213 original size:15 final size:16
Alignment explanation
Indices: 41186--41215 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41176 TATCGAGATT
41186 ATCATATTATAATTTA
1 ATCATATTATAATTTA
41202 ATCATA-TATAATTT
1 ATCATATTATAATTT
41216 CCTAGAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
ATCATATTATAATTTA
Found at i:41623 original size:60 final size:60
Alignment explanation
Indices: 41559--41685 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
41549 ATAATTTGGC
* * * * *
41559 CAAATAAAGGTCTGATCTTTTAA-TTAGGTCAAATAAGGGCCTAATGGTATCGAAAATGCT
1 CAAATAAAGGCCCGATCTTTTAATTTA-GCCAAATAAAGGCCTAACGGTATCGAAAATGCT
* * *
41619 CAAATAAGGGCCCGGTCTTTTAATTTAGCCAAATAAAGGCCTAACGTTATCGAAAATGCT
1 CAAATAAAGGCCCGATCTTTTAATTTAGCCAAATAAAGGCCTAACGGTATCGAAAATGCT
41679 CAAATAA
1 CAAATAA
41686 GGATCTGGCG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 55 0.95
61 3 0.05
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (60 bp):
CAAATAAAGGCCCGATCTTTTAATTTAGCCAAATAAAGGCCTAACGGTATCGAAAATGCT
Found at i:41686 original size:60 final size:60
Alignment explanation
Indices: 41574--41687 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
41564 AAAGGTCTGA
* * *
41574 TCTTTTAATTAGGTCAAATAAGGGCCTAATGGTATCGAAAATGCTCAAATAAGGGCCCGG
1 TCTTTTAATTAGGCCAAATAAAGGCCTAACGGTATCGAAAATGCTCAAATAAGGGCCCGG
*
41634 TCTTTTAATTTA-GCCAAATAAAGGCCTAACGTTATCGAAAATGCTCAAATAAGG
1 TCTTTTAA-TTAGGCCAAATAAAGGCCTAACGGTATCGAAAATGCTCAAATAAGG
41688 ATCTGGCGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 46 0.94
61 3 0.06
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (60 bp):
TCTTTTAATTAGGCCAAATAAAGGCCTAACGGTATCGAAAATGCTCAAATAAGGGCCCGG
Found at i:42200 original size:21 final size:19
Alignment explanation
Indices: 42155--42212 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
42145 TTGTTTAGCA
42155 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
42174 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
42195 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
42213 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:44303 original size:27 final size:29
Alignment explanation
Indices: 44250--44311 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
44240 TAATTAAGGT
* *
44250 GAGACTCAAAGAAAGATCTAGGTTTAGGA
1 GAGACTCAAAGAAAGATCCAAGTTTAGGA
* *
44279 GAGATTCAAAG-AAGATCCAAG-TTAGGT
1 GAGACTCAAAGAAAGATCCAAGTTTAGGA
44306 GAGACT
1 GAGACT
44312 TGGGAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 10 0.36
28 8 0.29
29 10 0.36
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.21
Consensus pattern (29 bp):
GAGACTCAAAGAAAGATCCAAGTTTAGGA
Found at i:47658 original size:21 final size:23
Alignment explanation
Indices: 47634--47679 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 23
47624 CTCACATCTC
*
47634 TTTTCTTG-TGAAGA-TTTT-AT
1 TTTTCTTGTTGAAAATTTTTAAT
47654 TTTT-TTGTTGAAAATTTTTAAT
1 TTTTCTTGTTGAAAATTTTTAAT
47676 TTTT
1 TTTT
47680 TCTTTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 4 0.18
22 6 0.27
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.65
Consensus pattern (23 bp):
TTTTCTTGTTGAAAATTTTTAAT
Found at i:48383 original size:14 final size:14
Alignment explanation
Indices: 48364--48406 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
48354 GAAAAAAATT
48364 AAAAAAGAAAGAAA
1 AAAAAAGAAAGAAA
**
48378 AAAAAATTAAGAAA
1 AAAAAAGAAAGAAA
*
48392 GAAAAAGAAAAGAAA
1 AAAAAAG-AAAGAAA
48407 CACTATTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (14 bp):
AAAAAAGAAAGAAA
Found at i:48402 original size:22 final size:23
Alignment explanation
Indices: 48352--48402 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
48342 CAAATCCAAT
48352 AAGAAAAAAATTAAAAAAGAAAG
1 AAGAAAAAAATTAAAAAAGAAAG
*
48375 AA-AAAAAAATTAAGAAAGAAA-
1 AAGAAAAAAATTAAAAAAGAAAG
48396 AAGAAAA
1 AAGAAAA
48403 GAAACACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (23 bp):
AAGAAAAAAATTAAAAAAGAAAG
Found at i:54328 original size:10 final size:10
Alignment explanation
Indices: 54323--54357 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
54313 ATGTCGATTT
54323 CGGTCGGTTA
1 CGGTCGGTTA
54333 CGGTCGGTTA
1 CGGTCGGTTA
54343 CGGTCGGTTA
1 CGGTCGGTTA
54353 CGGTC
1 CGGTC
54358 AGTTTCTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.09, C:0.23, G:0.40, T:0.29
Consensus pattern (10 bp):
CGGTCGGTTA
Found at i:55947 original size:7 final size:7
Alignment explanation
Indices: 55909--55939 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
55899 AGTTTTTTTT
55909 AAAA-AA
1 AAAAGAA
55915 AAAAGAA
1 AAAAGAA
55922 AAAAGAA
1 AAAAGAA
55929 AAAAGAA
1 AAAAGAA
55936 AAAA
1 AAAA
55940 AATGAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:56664 original size:26 final size:26
Alignment explanation
Indices: 56635--56690 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
56625 ATTAAAATCA
*
56635 TATGTGTGTATATATATATATATATG
1 TATGTATGTATATATATATATATATG
* * *
56661 TATGTATGTATGTATGTATGTATATG
1 TATGTATGTATATATATATATATATG
56687 TATG
1 TATG
56691 CAAGAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (26 bp):
TATGTATGTATATATATATATATATG
Found at i:56690 original size:4 final size:4
Alignment explanation
Indices: 56657--56683 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
56647 TATATATATA
56657 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
56684 ATGTATGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:57069 original size:98 final size:98
Alignment explanation
Indices: 56912--57098 Score: 365
Period size: 98 Copynumber: 1.9 Consensus size: 98
56902 CGTATTAATT
56912 AATATAAATTAATTTGATTGCAAAAGAATGCAGGTTTAACTTACAACTAGACAAAACAAAATTAA
1 AATATAAATTAATTTGATTGCAAAAGAATGCAGGTTTAACTTACAACTAGACAAAACAAAATTAA
56977 TATAAATATACTCGTATATAATTCGTATTTAAA
66 TATAAATATACTCGTATATAATTCGTATTTAAA
*
57010 AATATAAATTAATTTGATTGCAAAAGAATGCAGGTTTAACTTACTACTAGACAAAACAAAATTAA
1 AATATAAATTAATTTGATTGCAAAAGAATGCAGGTTTAACTTACAACTAGACAAAACAAAATTAA
57075 TATAAATATACTCGTATATAATTC
66 TATAAATATACTCGTATATAATTC
57099 TATACAAAAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.33
Consensus pattern (98 bp):
AATATAAATTAATTTGATTGCAAAAGAATGCAGGTTTAACTTACAACTAGACAAAACAAAATTAA
TATAAATATACTCGTATATAATTCGTATTTAAA
Done.