Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007069.1 Corchorus capsularis cultivar CVL-1 contig07090, 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: 21513
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:80 original size:31 final size:31
Alignment explanation
Indices: 56--194 Score: 149
Period size: 31 Copynumber: 4.5 Consensus size: 31
46 TTTGGTTAAT
56 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
* * * * **
87 TGTTCAAATAAGGGTCTGATATTT--TAATT
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
* *
116 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGCTAAAA
* * *
147 TGCTCAAATAAGAGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
178 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
195 GTCTCATGCG
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
29 20 0.23
30 3 0.03
31 65 0.74
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGCTAAAA
Found at i:258 original size:31 final size:29
Alignment explanation
Indices: 223--451 Score: 160
Period size: 31 Copynumber: 7.6 Consensus size: 29
213 ACTGACACCG
*
223 GGCCCTTATTTGAGCATTTTCGATAATGTTA
1 GGCCCTTATTTGAGCATTTT-GA-AACGTTA
254 GGCCCTTATTTGAGCATTTTCGATAACGTTA
1 GGCCCTTATTTGAGCATTTT-GA-AACGTTA
** ** * **
285 GATCCTTATTTG-GCCAAATT-AAAAGATCG
1 GGCCCTTATTTGAG-CATTTTGAAACG-TTA
314 GGCCCTTATTTGAGCATTTTTGATAACGTTA
1 GGCCCTTATTTGAGCA-TTTTGA-AACGTTA
** * **
345 GGCCCTTATTTG-GCCAAATT-AAAAGATCG
1 GGCCCTTATTTGAG-CATTTTGAAACG-TTA
*
374 GGCCCTTAGTTGAGCATTTTGGCAAACGTTA
1 GGCCCTTATTTGAGCATTTT-G-AAACGTTA
* *
405 GGCTCTTATTTGAGCATTTTGACAAATGTTA
1 GGCCCTTATTTGAGCATTTTG--AAACGTTA
436 GGCCCTTATTTGAGCA
1 GGCCCTTATTTGAGCA
452 ATTAGCGTTT
Statistics
Matches: 155, Mismatches: 30, Indels: 26
0.73 0.14 0.12
Matches are distributed among these distances:
28 6 0.04
29 31 0.20
30 9 0.06
31 102 0.66
32 7 0.05
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (29 bp):
GGCCCTTATTTGAGCATTTTGAAACGTTA
Found at i:323 original size:60 final size:60
Alignment explanation
Indices: 254--416 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
244 GATAATGTTA
*
254 GGCCCTTATTTGAGCATTTTCGATAACGTTAGATCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
* *
314 GGCCCTTATTTGAGCATTTTTGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
* * * *
374 GGCCCTTAGTTGAGCATTTTGGCA-AACGTTAGGCTCTTATTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACGTTAGACCCTTATTTG
417 AGCATTTTGA
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 95 0.99
61 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
Found at i:325 original size:29 final size:29
Alignment explanation
Indices: 288--381 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
278 AACGTTAGAT
288 CCTTATTTGGCCAAATTAAAAGATCGGGC
1 CCTTATTTGGCCAAATTAAAAGATCGGGC
** * **
317 CCTTATTTGAG-CATTTTTGATAACG-TTAGGC
1 CCTTATTTG-GCCA-AATT-A-AAAGATCGGGC
348 CCTTATTTGGCCAAATTAAAAGATCGGGC
1 CCTTATTTGGCCAAATTAAAAGATCGGGC
377 CCTTA
1 CCTTA
382 GTTGAGCATT
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 3 0.06
29 21 0.43
30 6 0.12
31 16 0.33
32 3 0.06
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (29 bp):
CCTTATTTGGCCAAATTAAAAGATCGGGC
Found at i:742 original size:7 final size:7
Alignment explanation
Indices: 732--763 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
722 GGAAGAAGGG
*
732 AAAAAAA
1 AAAAAAC
739 AAAAAAC
1 AAAAAAC
746 AAAAAAC
1 AAAAAAC
753 AAAAAAC
1 AAAAAAC
760 AAAA
1 AAAA
764 CAGAAAAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:776 original size:6 final size:5
Alignment explanation
Indices: 732--798 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
722 GGAAGAAGGG
*
732 AAAA- AAAAA AAAAC AAAA- AACAA- AAAAC AAAAC AGAAAAGC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AA-AAC AAAAC AAAAC --AAAA-C AAAAC
* *
778 AAAAC GAAAC AAAAA AAAAC A
1 AAAAC AAAAC AAAAC AAAAC A
799 GACAGAACGT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
4 8 0.15
5 35 0.67
6 4 0.08
7 4 0.08
8 1 0.02
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:782 original size:18 final size:17
Alignment explanation
Indices: 731--800 Score: 65
Period size: 19 Copynumber: 4.1 Consensus size: 17
721 AGGAAGAAGG
*
731 GAAAA-AAAAAAAAACA
1 GAAAACAAAACAAAACA
*
747 AAAAACAAAAAACAAAACA
1 GAAAAC--AAAACAAAACA
766 GAAAAGCAAAACAAAAC-
1 GAAAA-CAAAACAAAACA
*
783 G-AAACAAAAAAAAACA
1 GAAAACAAAACAAAACA
799 GA
1 GA
801 CAGAACGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
15 10 0.23
16 8 0.18
17 1 0.02
18 10 0.23
19 14 0.32
20 1 0.02
ACGTcount: A:0.80, C:0.13, G:0.07, T:0.00
Consensus pattern (17 bp):
GAAAACAAAACAAAACA
Found at i:3622 original size:22 final size:22
Alignment explanation
Indices: 3597--4066 Score: 134
Period size: 22 Copynumber: 21.5 Consensus size: 22
3587 TCCAATTATA
*
3597 AAATTTTGAAAACCTTCCTATG
1 AAATTTTGATAACCTTCCTATG
* ** *
3619 AAATTTTAATAACGATACTAT-
1 AAATTTTGATAACCTTCCTATG
* * **
3640 AGAATTTCGAGAACCTTTTTATG
1 A-AATTTTGATAACCTTCCTATG
* ** * *
3663 AATTTTTTTTAATCTTCTTATG
1 AAATTTTGATAACCTTCCTATG
* *
3685 AAATTTTGTTAACC-TCACTAAG
1 AAATTTTGATAACCTTC-CTATG
* *
3707 GAATTTTGA-AGACC-TCAATATG
1 AAATTTTGATA-ACCTTC-CTATG
*
3729 AAATTTTGATAA-CTTCCCAATG
1 AAATTTTGATAACCTT-CCTATG
* *
3751 AAATTTTGATAACCAATACTATG
1 AAATTTTGATAACC-TTCCTATG
* *
3774 AGATGTTGATAACC-TCCATATG
1 AAATTTTGATAACCTTCC-TATG
* * * * *
3796 ATATATTGATAACC-ACGTTATA
1 AAATTTTGATAACCTTC-CTATG
* * *
3818 AAAATTTAAAAACC-TCCATATG
1 AAATTTTGATAACCTTCC-TATG
* * *
3840 -AATTGTT-AGTAATC-ACACTCTG
1 AAATT-TTGA-TAACCTTC-CTATG
* *
3862 AAATTTTGATAA-ATCACACTATG
1 AAATTTTGATAACCT-TC-CTATG
**
3885 AAATGGTGATAACC-TCGCTATG
1 AAATTTTGATAACCTTC-CTATG
* *
3907 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGAT-AACCTTCCTATG
* *
3930 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTTCCTATG
* * *
3953 AAATTTTGATAACTTTCTTAGG
1 AAATTTTGATAACCTTCCTATG
* * *
3975 AAATCTTGACAA-----CTA-C
1 AAATTTTGATAACCTTCCTATG
*
3991 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTTCCTATG
** *
4013 ATTTTTTGATAACC-TCATTATG
1 AAATTTTGATAACCTTC-CTATG
* * * *
4035 TAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTTCCTATG
4057 AAATTTTGAT
1 AAATTTTGAT
4067 TTACATACTG
Statistics
Matches: 325, Mismatches: 93, Indels: 60
0.68 0.19 0.13
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
21 15 0.05
22 213 0.66
23 82 0.25
24 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTTCCTATG
Found at i:3783 original size:45 final size:45
Alignment explanation
Indices: 3725--3810 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
3715 AAGACCTCAA
* * *
3725 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAATAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAATAC
* *
3770 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
3811 CGTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAATAC
Found at i:3876 original size:23 final size:23
Alignment explanation
Indices: 3850--3964 Score: 99
Period size: 23 Copynumber: 5.0 Consensus size: 23
3840 AATTGTTAGT
*
3850 AATCACACTCTGAAATTTTGATA
1 AATCACACTATGAAATTTTGATA
**
3873 AATCACACTATGAAATGGTGAT-
1 AATCACACTATGAAATTTTGATA
* * *
3895 AACCTCGCTATGAAATTTTGATA
1 AATCACACTATGAAATTTTGATA
* *
3918 AATCTTC-CTATAAAATTTTGATA
1 AATC-ACACTATGAAATTTTGATA
* * * *
3941 AACCTCCCTATAAAATTTTGATA
1 AATCACACTATGAAATTTTGATA
3964 A
1 A
3965 CTTTCTTAGG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.24
23 57 0.73
24 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (23 bp):
AATCACACTATGAAATTTTGATA
Found at i:3940 original size:45 final size:46
Alignment explanation
Indices: 3860--3964 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 46
3850 AATCACACTC
* *
3860 TGAAATTTTGATAAATCACACTATGAAATGGTGAT-AACCTCGCTA
1 TGAAATTTTGATAAATCACACTATAAAATGGTGATAAACCTCCCTA
* **
3905 TGAAATTTTGATAAATCTTC-CTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATAAATC-ACACTATAAAATGGTGATAAACCTCCCTA
*
3951 TAAAATTTTGATAA
1 TGAAATTTTGATAA
3965 CTTTCTTAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 29 0.56
46 23 0.44
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (46 bp):
TGAAATTTTGATAAATCACACTATAAAATGGTGATAAACCTCCCTA
Found at i:4111 original size:22 final size:22
Alignment explanation
Indices: 4086--4144 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
4076 GTGAACCTCT
4086 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAAACTAAA
* * **
4107 GTATGCAATTTTGATAACCTTCA
1 -TATGAAATTTTGATAAACTAAA
4130 TATGAAATTTTGATA
1 TATGAAATTTTGATA
4145 TCCTCCCTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAAACTAAA
Found at i:4321 original size:22 final size:22
Alignment explanation
Indices: 4269--4493 Score: 126
Period size: 22 Copynumber: 10.3 Consensus size: 22
4259 AATCACATTT
*
4269 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
4291 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
4313 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
4335 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
4357 TGTAATTTTCATAACCTCGTTT-
1 TGAAATTTTGATAACCTC-TTTA
*
4379 TGAAATTTTAATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
** *
4401 T-AAATTTTGATAATTTGATCTCTA
1 TGAAATTTTGATAA---CCTCTTTA
* *
4425 TGAAATTTTGATAA-TTACTCTA
1 TGAAATTTTGATAACCT-CTTTA
*
4447 TGAGA-TTTGATAACCT-TTTA
1 TGAAATTTTGATAACCTCTTTA
* * *
4467 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
4487 TGAAATT
1 TGAAATT
4494 GAAACTTTTA
Statistics
Matches: 156, Mismatches: 33, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
19 4 0.03
20 18 0.12
21 26 0.17
22 88 0.56
23 2 0.01
24 3 0.02
25 12 0.08
26 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.44
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:4364 original size:44 final size:44
Alignment explanation
Indices: 4244--4563 Score: 131
Period size: 44 Copynumber: 7.2 Consensus size: 44
4234 AGAAATACCA
* * *
4244 CTATGAAACTTTTG-TAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * * *
4288 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * *
4332 CTATGAAATTCTGATAATCACATTATGTAATTTTCATAACCTCGT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACC-CCT
* * * * ***
4377 -TTTGAAATTTTAATAATCTTC-CTAT-AAATTTTGATAATTTGATCT
1 CTATGAAATTTTGATAATC-ACATTATGAAATTTTGATAA---CCCCT
* * *
4422 CTATGAAATTTTGATAATTAC-TCTATGAGA-TTTGATAA-CCTT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCT
* * * * * *
4464 TTATCAAATTTTGGTACTC-C-TTATGAAATTGAAACTTTTATAA-CCTT
1 CTATGAAATTTTGATAATCACATTATGAAA-T-----TTTGATAACCCCT
* * *
4511 CATATGAAATTTTGATAACCACACTAT-AAATTTTGATAACCGCT
1 C-TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
*
4555 CCATGAAAT
1 CTATGAAAT
4564 ATTAGTAACC
Statistics
Matches: 198, Mismatches: 58, Indels: 41
0.67 0.20 0.14
Matches are distributed among these distances:
40 6 0.03
41 2 0.01
42 15 0.08
43 29 0.15
44 80 0.40
45 5 0.03
46 26 0.13
47 13 0.07
48 15 0.08
49 4 0.02
50 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:4403 original size:88 final size:86
Alignment explanation
Indices: 4244--4409 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 86
4234 AGAAATACCA
* * * *
4244 CTATGAAACTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAACTTCTGTAATCACATTATGAAAATTTCATAACCTCTTTATGAAATTTTAATAA-CTC
4309 TTTATAAAATTTTGTTGACCCCT
65 TTTAT-AAATTTTGTTGACCCCT
* *
4332 CTATGAAA-TTCTGATAATCACATTATGTAATTTTCATAACCTCGTTT-TGAAATTTTAATAA-T
1 CTATGAAACTTCTG-TAATCACATTATGAAAATTTCATAACCTC-TTTATGAAATTTTAATAACT
4394 CTTCCTATAAATTTTG
64 CTT--TATAAATTTTG
4410 ATAATTTGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
86 4 0.06
87 12 0.18
88 49 0.72
89 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (86 bp):
CTATGAAACTTCTGTAATCACATTATGAAAATTTCATAACCTCTTTATGAAATTTTAATAACTCT
TTATAAATTTTGTTGACCCCT
Found at i:4434 original size:25 final size:22
Alignment explanation
Indices: 4379--4459 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 22
4369 AACCTCGTTT
* *
4379 TGAAATTTTAATAATCTTC-CTA
1 TGAAATTTTGATAAT-TACTCTA
4401 T-AAATTTTGATAATTTGATCTCTA
1 TGAAATTTTGATAA-TT-A-CTCTA
4425 TGAAATTTTGATAATTACTCTA
1 TGAAATTTTGATAATTACTCTA
*
4447 TGAGA-TTTGATAA
1 TGAAATTTTGATAA
4460 CCTTTTATCA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
21 20 0.39
22 11 0.22
23 2 0.04
24 6 0.12
25 12 0.24
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (22 bp):
TGAAATTTTGATAATTACTCTA
Found at i:4604 original size:22 final size:22
Alignment explanation
Indices: 4513--4858 Score: 122
Period size: 22 Copynumber: 16.0 Consensus size: 22
4503 ATAACCTTCA
4513 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
4535 TAT-AAATTTTGATAACCGCTC
1 TATGAAATTTTGATAACCACAC
* * *
4556 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
* *
4577 TAATGAAATTTTGTTAATCACAC
1 T-ATGAAATTTTGATAACCACAC
* *
4600 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCACAC
* * *
4622 TATGACATTTTGATAA--TCTC
1 TATGAAATTTTGATAACCACAC
* *
4642 TTTGATAACCTTTCT-ATAA--A-AT
1 TATGA-AA--TTT-TGATAACCACAC
*
4664 TGTGATAA---T--TAACCATC-C
1 TATGA-AATTTTGATAACCA-CAC
**
4682 TATGAAATTTCAATAACCA-ACC
1 TATGAAATTTTGATAACCACA-C
* * **
4704 TAAGAAATTTTAATAACCTGATC
1 TATGAAATTTTGATAACCACA-C
* * *
4727 TTATAAAATTAT-AGTAACTACAC
1 -TATGAAATTTTGA-TAACCACAC
*
4750 TATGAAATGTT-AGTAACCACAC
1 TATGAAATTTTGA-TAACCACAC
*
4772 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCACAC
*
4794 TATGAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCACAC
* * *
4815 TCATGAAATTATAATAACCATC-T
1 T-ATGAAATTTTGATAACCA-CAC
*
4838 TGTGAAATTTTGATAACCACA
1 TATGAAATTTTGATAACCACA
4859 TAGAAACAAG
Statistics
Matches: 245, Mismatches: 50, Indels: 58
0.69 0.14 0.16
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 3 0.01
18 4 0.02
20 7 0.03
21 26 0.11
22 170 0.69
23 17 0.07
24 14 0.06
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:4811 original size:44 final size:45
Alignment explanation
Indices: 4732--4858 Score: 136
Period size: 44 Copynumber: 2.9 Consensus size: 45
4722 TGATCTTATA
* *
4732 AAATTATAGTAACTACACTATGAAATGTT-AGTAACCACACT-ATG
1 AAATTATAGTAACCACACTATGAAATTTTGA-TAACCACACTCATG
* * *
4776 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTC-CTCATG
1 AAATTATAGTAACCACACTATGAAATTTTGATAACCACACTCATG
* * *
4820 AAATTATAATAACCATC-TTGTGAAATTTTGATAACCACA
1 AAATTATAGTAACCA-CACTATGAAATTTTGATAACCACA
4859 TAGAAACAAG
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
43 2 0.03
44 64 0.94
45 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.32
Consensus pattern (45 bp):
AAATTATAGTAACCACACTATGAAATTTTGATAACCACACTCATG
Found at i:5174 original size:25 final size:24
Alignment explanation
Indices: 5132--5180 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
5122 GTCTAAATTG
* *
5132 AAAATTTTAATAATTTTTAAATAAT
1 AAAATTATAATAAATTTT-AATAAT
*
5157 AAAATTATACTAAATTTTAATAAT
1 AAAATTATAATAAATTTTAATAAT
5181 GGAAATTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAATTATAATAAATTTTAATAAT
Found at i:6496 original size:31 final size:31
Alignment explanation
Indices: 6460--6525 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
6450 TGACAATTTA
* *
6460 GAAATATGTTTTGAAAATAAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
6491 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
6522 GAAA
1 GAAA
6526 ATATAAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:6561 original size:2 final size:2
Alignment explanation
Indices: 6554--6587 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
6544 TTCGTACTTT
*
6554 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
6588 TTACTAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10539 original size:51 final size:50
Alignment explanation
Indices: 10484--10586 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 50
10474 CAATTCTCTT
*
10484 AAATTCTCTCAACCTTCAAGCTTTCAAAACTCAATCATTCAAAATCATCTC
1 AAATTCTCTCAACCTTCAAACTTTCAAAACTCAATCATTCAAAATCAT-TC
10535 AAATTCTCTCAACCTTCAAACTTTCAAAACTCAATCATTCAAAATCATTC
1 AAATTCTCTCAACCTTCAAACTTTCAAAACTCAATCATTCAAAATCATTC
10585 AA
1 AA
10587 GTAAAACAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 4 0.08
51 47 0.92
ACGTcount: A:0.40, C:0.28, G:0.01, T:0.31
Consensus pattern (50 bp):
AAATTCTCTCAACCTTCAAACTTTCAAAACTCAATCATTCAAAATCATTC
Found at i:11806 original size:70 final size:71
Alignment explanation
Indices: 11703--11844 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 71
11693 AAGCCTGTCC
11703 ATTTTATTTTTTTAATATTTTTTCTTAAATAATAATAAATATTTTAATTACATATTAAACTTTTT
1 ATTTTATTTTTTTAATATTTTTTCTTAAATAATAATAAATATTTTAATTACATATTAAACTTTTT
11768 TTAACA
66 TTAACA
11774 ATTTTATTTTTTTAATA-TTTTTCTTAAATAATAATAAATATTTTAATTACATATTAAACTTTTT
1 ATTTTATTTTTTTAATATTTTTTCTTAAATAATAATAAATATTTTAATTACATATTAAACTTTTT
11838 TTAACA
66 TTAACA
11844 A
1 A
11845 AATCATTATG
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 54 0.76
71 17 0.24
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (71 bp):
ATTTTATTTTTTTAATATTTTTTCTTAAATAATAATAAATATTTTAATTACATATTAAACTTTTT
TTAACA
Found at i:13804 original size:28 final size:28
Alignment explanation
Indices: 13750--13824 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 28
13740 AATTTGTAAC
*
13750 TTTTGGACGTTTTGCCCCTTGAACTTCAA
1 TTTTGGACGTTTT-ACCCTTGAACTTCAA
*
13779 TTTTGGACATTTTACCCTTGAACTTCAA
1 TTTTGGACGTTTTACCCTTGAACTTCAA
*
13807 TTGTGGGACGTTTTACCC
1 TT-TTGGACGTTTTACCC
13825 CCTCAACCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 16 0.39
29 25 0.61
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (28 bp):
TTTTGGACGTTTTACCCTTGAACTTCAA
Found at i:14031 original size:30 final size:29
Alignment explanation
Indices: 13995--14052 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
13985 CGTTAGGTTG
13995 AGGGGGCAAAACATCCCAAAATTGAAGTTT
1 AGGGGGCAAAACAT-CCAAAATTGAAGTTT
** *
14025 AGGGGGCAAAATGTCTAAAATTGAAGTT
1 AGGGGGCAAAACATCCAAAATTGAAGTT
14053 CAATGGGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (29 bp):
AGGGGGCAAAACATCCAAAATTGAAGTTT
Found at i:20173 original size:34 final size:34
Alignment explanation
Indices: 20135--20199 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
20125 TATATAATAT
20135 ATATAACTATAATTGATGAAAAAAAAAAAGAGTG
1 ATATAACTATAATTGATGAAAAAAAAAAAGAGTG
*
20169 ATATAACTATAATTGATGCAAAAAAAAAAGA
1 ATATAACTATAATTGATGAAAAAAAAAAAGA
20200 AAAAAGAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.23
Consensus pattern (34 bp):
ATATAACTATAATTGATGAAAAAAAAAAAGAGTG
Done.