Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015068.1 Corchorus capsularis cultivar CVL-1 contig15089, 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: 27385
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Found at i:68 original size:27 final size:26
Alignment explanation
Indices: 38--94 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
28 TTAATAAAAA
*
38 TTAAAAAAATCAATTTTTCTGTTTTTT
1 TTAAAAAAA-CAATTTTTCTCTTTTTT
* * *
65 TT-AAAGAACCATTTTTTTCTTTTTT
1 TTAAAAAAACAATTTTTCTCTTTTTT
90 TTAAA
1 TTAAA
95 GAAGAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 16 0.64
26 7 0.28
27 2 0.08
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.56
Consensus pattern (26 bp):
TTAAAAAAACAATTTTTCTCTTTTTT
Found at i:78 original size:25 final size:25
Alignment explanation
Indices: 50--97 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
40 AAAAAAATCA
*
50 ATTTTTCTGTTTTTTTTAAAGAACC
1 ATTTTTCTCTTTTTTTTAAAGAACC
*
75 ATTTTTTTCTTTTTTTTAAAGAA
1 ATTTTTCTCTTTTTTTTAAAGAA
98 GAAAATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.60
Consensus pattern (25 bp):
ATTTTTCTCTTTTTTTTAAAGAACC
Found at i:129 original size:23 final size:22
Alignment explanation
Indices: 84--124 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
74 CATTTTTTTC
*
84 TTTTTTTTAAAGAAGAAAATGA
1 TTTTTTTTAAAGAAAAAAATGA
106 TTTTTTTTAAA-AAAAAAAT
1 TTTTTTTTAAAGAAAAAAAT
125 TTGATACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TTTTTTTTAAAGAAAAAAATGA
Found at i:2577 original size:22 final size:22
Alignment explanation
Indices: 2531--2578 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2521 ATGATCCCAT
* * *
2531 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTAATAACCATAC
*
2553 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTAATAACCATAC
2575 TATG
1 TATG
2579 GAATCTCGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTAATAACCATAC
Found at i:2729 original size:22 final size:21
Alignment explanation
Indices: 2657--3043 Score: 97
Period size: 22 Copynumber: 17.9 Consensus size: 21
2647 CTCAATATAA
*
2657 AATTTTGATAACTTCCCA-ATG
1 AATTTTGATAACCT-CCATATG
**
2678 AAATTTTGATAACCAACACTATG
1 -AATTTTGATAACCTCCA-TATG
*
2701 AGATGTTGATAACCTCCATATG
1 A-ATTTTGATAACCTCCATATG
* * *
2723 AATTGTT-AGTAATCATAC-TCTG
1 AATT-TTGA-TAA-CCTCCATATG
2745 AAATTTTGATAA--TCACACTATG
1 -AATTTTGATAACCTC-CA-TATG
* *
2767 TAATTGTGATAACCTCGC-CATG
1 -AATTTTGATAACCTC-CATATG
* *
2789 AAATTTTGATAAATCGTCC-TATAA
1 -AATTTTGAT-AA-CCTCCATAT-G
* *
2813 AATTTTGATATACCTCCCTATAA
1 AATTTTGATA-ACCTCCATAT-G
* * *
2836 AATTTTGATAACTTTCTTATG
1 AATTTTGATAACCTCCATATG
* *
2857 AAATCTTGATAA-CT--ACA--
1 -AATTTTGATAACCTCCATATG
*
2874 AATTTTGATAACCTCCTTATG
1 AATTTTGATAACCTCCATATG
*
2895 ATTTTTTGATAACCT-CATTATG
1 A-ATTTTGATAACCTCCA-TATG
* * *
2917 AAATTTTGTTAATCTCCCTATG
1 -AATTTTGATAACCTCCATATG
* * *
2939 AAATTTTGATCTACATAC-TATG
1 -AATTTTGAT-AACCTCCATATG
*
2961 AAATTTTGATAACC-CTCTTATG
1 -AATTTTGATAACCTC-CATATG
* * *
2983 AAATTTTGATAACATTCATACG
1 -AATTTTGATAACCTCCATATG
* * *
3005 AAATTTTGATATCCTCCCTA-A
1 -AATTTTGATAACCTCCATATG
*
3026 AATTTTGATTA-CTCCATA
1 AATTTTGATAACCTCCATA
3044 ATAAAAGTTT
Statistics
Matches: 274, Mismatches: 59, Indels: 67
0.69 0.15 0.17
Matches are distributed among these distances:
16 10 0.04
17 2 0.01
19 9 0.03
20 10 0.04
21 11 0.04
22 167 0.61
23 59 0.22
24 6 0.02
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (21 bp):
AATTTTGATAACCTCCATATG
Found at i:2817 original size:23 final size:23
Alignment explanation
Indices: 2768--2846 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
2758 CACACTATGT
* *
2768 AATTGTGAT-AACCTCGCC-ATGA
1 AATTTTGATAAACCTC-CCTATAA
*
2790 AATTTTGATAAATCGT-CCTATAA
1 AATTTTGATAAA-CCTCCCTATAA
*
2813 AATTTTGATATACCTCCCTATAA
1 AATTTTGATAAACCTCCCTATAA
2836 AATTTTGATAA
1 AATTTTGATAA
2847 CTTTCTTATG
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 12 0.26
23 33 0.70
24 2 0.04
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (23 bp):
AATTTTGATAAACCTCCCTATAA
Found at i:2961 original size:44 final size:44
Alignment explanation
Indices: 2651--3034 Score: 198
Period size: 44 Copynumber: 8.8 Consensus size: 44
2641 GAAGATCTCA
* *
2651 ATATAAAATTTTGATAA-CTTCCCAATGAAATTTTGATAACCA-AC
1 ATATGAAATTTTGATAATC-TCCCTATGAAATTTTGATAA-CATAC
* * * *
2695 ACTATGAGATGTTGATAACCTCCATATG-AATTGTT-AGTAATCATAC
1 A-TATGAAATTTTGATAATCTCCCTATGAAATT-TTGA-TAA-CATAC
* * * * * *
2741 -TCTGAAATTTTGATAATCACACTATGTAATTGTGATAACCT-C
1 ATATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACATAC
** * * *
2783 GCCATGAAATTTTGATAAATCGT-CCTATAAAATTTTGATATACCTCC
1 -ATATGAAATTTTGAT-AATC-TCCCTATGAAATTTTGATA-ACATAC
* * * * *
2830 CTATAAAATTTTGATAA-CTTTCTTATGAAATCTTGATAAC-TAC
1 ATATGAAATTTTGATAATC-TCCCTATGAAATTTTGATAACATAC
* * ** *
2873 -----AAATTTTGATAACCTCCTTATGATTTTTTGATAACCT-C
1 ATATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACATAC
* *
2911 ATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATAC
1 A-TATGAAATTTTGATAATCTCCCTATGAAATTTTGAT-AACATAC
*
2957 -TATGAAATTTTGATAA-C-CCTCTTATGAAATTTTGATAACATTC
1 ATATGAAATTTTGATAATCTCC-C-TATGAAATTTTGATAACATAC
*
3000 ATACGAAATTTTGAT-ATCCTCCCTA--AAATTTTGAT
1 ATATGAAATTTTGATAAT-CTCCCTATGAAATTTTGAT
3035 TACTCCATAA
Statistics
Matches: 266, Mismatches: 44, Indels: 62
0.72 0.12 0.17
Matches are distributed among these distances:
38 30 0.11
39 2 0.01
42 13 0.05
43 12 0.05
44 116 0.44
45 69 0.26
46 23 0.09
47 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (44 bp):
ATATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACATAC
Found at i:3165 original size:22 final size:22
Alignment explanation
Indices: 3140--3264 Score: 87
Period size: 22 Copynumber: 5.7 Consensus size: 22
3130 AATCACATTT
*
3140 TGAAAATTTGATAACCTTTTTA
1 TGAAAATTTGATAACCTCTTTA
*
3162 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
3184 T-AAAATTTTGTTGA-CTCCTTTA
1 TGAAAA-TTTGATAACCT-CTTTA
* * *
3206 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * *
3228 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
*
3250 TGAAATTTTGATAAC
1 TGAAAATTTGATAAC
3265 AACGCTATGA
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
21 7 0.09
22 68 0.83
23 7 0.09
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:3278 original size:88 final size:88
Alignment explanation
Indices: 3116--3281 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 88
3106 GAAATACCAC
* * ** ** *
3116 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTTTTTATGAAATTTTGATAACCTCT
1 TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTGCTTATGAAATTTTGATAACAACG
*
3181 TTATAAAATTTTGTTGACTCCTT
66 CTATAAAATTTTGTTGACTCCTT
* *
3204 TATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 TATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCT-GCTTATGAAATTTTGATAACAA
*
3267 CGCTATGAAATTTTG
64 CGCTATAAAATTTTG
3282 ATAATCTTCC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 4 0.06
88 59 0.91
89 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (88 bp):
TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTGCTTATGAAATTTTGATAACAACG
CTATAAAATTTTGTTGACTCCTT
Found at i:3300 original size:21 final size:23
Alignment explanation
Indices: 3204--3342 Score: 92
Period size: 22 Copynumber: 6.2 Consensus size: 23
3194 TTGACTCCTT
* **
3204 TATGAAATTCTGATAATC-ACAT
1 TATGAAATTTTGATAATCAACGC
* **
3226 TATGTAATTTTGATAA-CCTCGC
1 TATGAAATTTTGATAATCAACGC
*
3248 TTTGAAATTTTGATAA-CAACGC
1 TATGAAATTTTGATAATCAACGC
**
3270 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAATCAACGC
* * *
3292 TAT-AAATTTCGATAATCGGATCTC
1 TATGAAATTTTGATAATC--AACGC
* *
3316 TATGAAATTTCGATAATC-ACTC
1 TATGAAATTTTGATAATCAACGC
3338 TATGA
1 TATGA
3343 GATTGGATAA
Statistics
Matches: 96, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
21 14 0.15
22 60 0.62
23 4 0.04
24 4 0.04
25 14 0.15
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (23 bp):
TATGAAATTTTGATAATCAACGC
Found at i:3421 original size:22 final size:22
Alignment explanation
Indices: 3396--3534 Score: 83
Period size: 22 Copynumber: 6.3 Consensus size: 22
3386 TGAGACTTTC
3396 ATAACCTTCATATGAAATTTTG
1 ATAACCTTCATATGAAATTTTG
* * *
3418 ATAACC-ACACTATAAAATTTTA
1 ATAACCTTCA-TATGAAATTTTG
* ** *
3440 ATAACCTCCCCATGAAATATT-
1 ATAACCTTCATATGAAATTTTG
*
3461 AGTAACC-TCCTAATGAAATTTTG
1 A-TAACCTTCAT-ATGAAATTTTG
* *
3484 TTAACC-ACACTATGAAATTCTT-
1 ATAACCTTCA-TATGAAATT-TTG
*
3506 ATAACCTTGC-TATGACATTTTG
1 ATAACCTT-CATATGAAATTTTG
3528 ATAACCT
1 ATAACCT
3535 CTTTGATAAC
Statistics
Matches: 90, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
21 7 0.08
22 78 0.87
23 4 0.04
24 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.35
Consensus pattern (22 bp):
ATAACCTTCATATGAAATTTTG
Found at i:3613 original size:22 final size:22
Alignment explanation
Indices: 3567--3739 Score: 104
Period size: 22 Copynumber: 7.8 Consensus size: 22
3557 TTGTGATAAT
* **
3567 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTGA
*
3589 TAACCAACCTAAGAAATTTTGA
1 TAACCAACCTATGAAATTTTGA
* *
3611 TAA-CATGATCCTATGATATTTTGG
1 TAACCA--A-CCTATGAAATTTTGA
3635 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTGA
** * *
3657 TAA-CTTCTGTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTGA
*
3679 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTGA
* * *
3701 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTGA
* *
3723 TAACCATCTTATGAAAT
1 TAACCAACCTATGAAAT
3740 CACCTACTCT
Statistics
Matches: 119, Mismatches: 23, Indels: 18
0.74 0.14 0.11
Matches are distributed among these distances:
21 6 0.05
22 92 0.77
23 5 0.04
24 15 0.13
25 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTGA
Found at i:3651 original size:46 final size:44
Alignment explanation
Indices: 3575--3718 Score: 150
Period size: 44 Copynumber: 3.2 Consensus size: 44
3565 ATTAACCACC
*** *
3575 CTATGAAATTTCAATAACCA-ACCTAAGAAATTTTGATAACATGATC-
1 CTATGAAATTTTGGTAACCACA-CTATGAAATTTTGATAAC-T--TCT
*
3621 CTATGATATTTTGGTAACCACACTATGAAATTTTGATAACTTCT
1 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTCT
* * *
3665 GTATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTCT
3708 CTCATGAAATT
1 CT-ATGAAATT
3719 ATAATAACCA
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
43 3 0.04
44 47 0.55
45 1 0.01
46 33 0.39
47 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (44 bp):
CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTCT
Found at i:3727 original size:44 final size:44
Alignment explanation
Indices: 3635--3728 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
3625 GATATTTTGG
* * * **
3635 TAACCACACTATGAAATTTTGATAACTTCTGTATGAAATTTTGG
1 TAACCACACTATGAAATTTTGATAACTCCTGCATGAAATTATAA
*
3679 TAACCACACTATGGAATTTTGATAACCTCCT-CATGAAATTATAA
1 TAACCACACTATGAAATTTTGATAA-CTCCTGCATGAAATTATAA
3723 TAACCA
1 TAACCA
3729 TCTTATGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 39 0.91
45 4 0.09
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (44 bp):
TAACCACACTATGAAATTTTGATAACTCCTGCATGAAATTATAA
Found at i:3916 original size:20 final size:19
Alignment explanation
Indices: 3879--3916 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3869 TATTGGCATT
3879 TAAAAATTGAAATTAAAAG
1 TAAAAATTGAAATTAAAAG
3898 TAAAATATT-AAATTTAAAA
1 TAAAA-ATTGAAA-TTAAAA
3917 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAAAATTGAAATTAAAAG
Found at i:4209 original size:13 final size:13
Alignment explanation
Indices: 4174--4217 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 13
4164 TAAATTGAAA
4174 TTTTATAATTAAT
1 TTTTATAATTAAT
4187 TTTTAAATAATTAAT
1 TTTT--ATAATTAAT
4202 TTTTATAATGTAAT
1 TTTTATAAT-TAAT
4216 TT
1 TT
4218 AGAAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.32
14 6 0.21
15 13 0.46
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TTTTATAATTAAT
Found at i:4899 original size:29 final size:31
Alignment explanation
Indices: 4864--4921 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
4854 TGACAATTTA
*
4864 GAAATATGTTTT-AAAA-AAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
4893 GAAATATATTTTAAAAATAAGGGTACAAT
1 GAAATATATTTTAAAAATAAGGGTACAAT
4922 CGAAAAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.42
30 4 0.15
31 11 0.42
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.31
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATTG
Found at i:10554 original size:141 final size:136
Alignment explanation
Indices: 10305--10573 Score: 423
Period size: 141 Copynumber: 1.9 Consensus size: 136
10295 AAACTATTTG
* * *
10305 AACAGTGAACGCCCTTAAAGAAGCAACAACCGTACACCAAAATTTCATATTCCAAATATATTCTG
1 AACAGTGAACACCCTTAAAGAAGCAACAACCATACACCAAAATTTCATATTCCAAACATATTCTG
*
10370 AAATTTTGTAGAAGTCAATGAATTGACTACATTTCCTGCATGTTCTTCCCCTTTTGTGCAAACAT
66 AAATTTTCTAGAAGTCAATGAATTGACTACATTTCCTGCATGTTCTTCCCCTTTTGTGCAAACAT
10435 ATTCCA
131 ATTCCA
*
10441 AACAGTGAACACCCTTGAAGAAGCAACAACCATACACCAAAATTTCACATCATATTCCAAACATA
1 AACAGTGAACACCCTTAAAGAAGCAACAACCATACACCAAAA-TT----TCATATTCCAAACATA
*
10506 TTCTGAAATTTTCT-GTTAGTCAATGAATTGACTACATTTCCTGCATGTTCTTCCCCTTTTGTGC
61 TTCTGAAATTTTCTAG-AAGTCAATGAATTGACTACATTTCCTGCATGTTCTTCCCCTTTTGTGC
10570 AAAC
125 AAAC
10574 TATAACTTCA
Statistics
Matches: 121, Mismatches: 6, Indels: 7
0.90 0.04 0.05
Matches are distributed among these distances:
136 39 0.32
137 2 0.02
140 1 0.01
141 79 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (136 bp):
AACAGTGAACACCCTTAAAGAAGCAACAACCATACACCAAAATTTCATATTCCAAACATATTCTG
AAATTTTCTAGAAGTCAATGAATTGACTACATTTCCTGCATGTTCTTCCCCTTTTGTGCAAACAT
ATTCCA
Found at i:12328 original size:28 final size:27
Alignment explanation
Indices: 12296--12349 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
12286 TAAAAGTAAG
*
12296 TAATATTAAATTAAAACCCCAAAATACA
1 TAATAATAAATT-AAACCCCAAAATACA
* *
12324 TAATAATACATTAAACCCCAAGATAC
1 TAATAATAAATTAAACCCCAAAATAC
12350 CTATCCCTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.24
Consensus pattern (27 bp):
TAATAATAAATTAAACCCCAAAATACA
Found at i:17170 original size:17 final size:18
Alignment explanation
Indices: 17148--17183 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17138 GTCACGTGTC
*
17148 TTCTAT-TTTTTTCTTTT
1 TTCTATCTTTATTCTTTT
17165 TTCTATCTTTATTCTTTT
1 TTCTATCTTTATTCTTTT
17183 T
1 T
17184 AGTAAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (18 bp):
TTCTATCTTTATTCTTTT
Found at i:17210 original size:21 final size:21
Alignment explanation
Indices: 17186--17239 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
17176 TTCTTTTTAG
17186 TAAGTTTAGCCCTAATTTCAC
1 TAAGTTTAGCCCTAATTTCAC
* *
17207 TAAGTTTAACCTTAATTTCAC
1 TAAGTTTAGCCCTAATTTCAC
17228 TAAGTTTAGCCC
1 TAAGTTTAGCCC
17240 CAAATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (21 bp):
TAAGTTTAGCCCTAATTTCAC
Found at i:21533 original size:17 final size:17
Alignment explanation
Indices: 21511--21547 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
21501 TGTATACGGA
21511 AAAAAATGTCAACCTCT
1 AAAAAATGTCAACCTCT
21528 AAAAAATGTCAACCTCT
1 AAAAAATGTCAACCTCT
21545 AAA
1 AAA
21548 GAATTTGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (17 bp):
AAAAAATGTCAACCTCT
Found at i:22219 original size:219 final size:220
Alignment explanation
Indices: 21732--22363 Score: 890
Period size: 219 Copynumber: 2.9 Consensus size: 220
21722 TTTTTAAAGT
*
21732 CAAAATTGTGAAATTCAGTATCCCCAAACTGATATATTTTATACCCAAATCATTTCTCATCATCC
1 CAAAA-TGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCC
*
21797 CCAAATAATCATATGCACCATTCCGAAATTCTTTAGAAATTGACATTTTCTCATATACACAAATT
65 CCAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGACATTTTCTCATATACACAAATT
** * *
21862 TTACTTTAAAAAGTGTTTTAATCCATATTTTAGGGATCTAATTAATTGAACAAACCACGTCTATA
130 GGACTTTAAAAAGTGCTTTAATCCATATTTTA-GCATCTAATTAATTGAACAAACCACGTCTATA
* * *
21927 TGATTTTAGTGTCGTCTCATAATTAAA
194 TGATTTTAGCGCCATCTCATAATTAAA
* * *
21954 CAAAATGTAAAATTCAGTATCCCCAAAATGATATACTTTATACCCAAATCATTTTTCATCATCCC
1 CAAAATGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCC
* * * *
22019 CAATTAATCTTATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTCTCATATACACAAATTG
66 CAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGACATTTTCTCATATACACAAATTG
* * * * *
22084 GACTTTAAAAGGTGCTTTAA-GCATATTTT-TCATTCTAATTAATTGAATAAACCACGTTTATAT
131 GACTTTAAAAAGTGCTTTAATCCATATTTTAGCA-TCTAATTAATTGAACAAACCACGTCTATAT
22147 GATTTTAGCGCCATCTCATAATTAAA
195 GATTTTAGCGCCATCTCATAATTAAA
* *
22173 CAAAATGTGAAATTCAGTATCCCCAAACTGATTTACTTTATACCCAAATCATTTCTCACCATCCC
1 CAAAATGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCC
22238 CAAATAATCATATGCA-CAGTTCCCAAATTCTTTAGAAATTG-CTATTTTCTCATATACAC----
66 CAAATAATCATATGCACCA-TTCCCAAATTCTTTAGAAATTGAC-ATTTTCTCATATACACAAAT
* * * *
22297 ---ACTTTAAAAAGTGCTTTAATCCATATTTTAGGGATCTAATTAATTGAATAAATCATGTCTAT
129 TGGACTTTAAAAAGTGCTTTAATCCATATTTTA-GCATCTAATTAATTGAACAAACCACGTCTAT
22359 ATGAT
193 ATGAT
22364 GGTGGAAAAT
Statistics
Matches: 367, Mismatches: 37, Indels: 20
0.87 0.09 0.05
Matches are distributed among these distances:
212 18 0.05
213 8 0.02
214 30 0.08
215 1 0.00
218 4 0.01
219 161 0.44
220 8 0.02
221 132 0.36
222 5 0.01
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (220 bp):
CAAAATGTGAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCC
CAAATAATCATATGCACCATTCCCAAATTCTTTAGAAATTGACATTTTCTCATATACACAAATTG
GACTTTAAAAAGTGCTTTAATCCATATTTTAGCATCTAATTAATTGAACAAACCACGTCTATATG
ATTTTAGCGCCATCTCATAATTAAA
Found at i:22422 original size:11 final size:11
Alignment explanation
Indices: 22408--22497 Score: 58
Period size: 11 Copynumber: 7.5 Consensus size: 11
22398 GGAAAAAGAA
22408 AAGAAAAAATT
1 AAGAAAAAATT
22419 AAGAAAAAA--
1 AAGAAAAAATT
***
22428 AAGGGTGAAATT
1 AA-GAAAAAATT
22440 AAGAAAAAATTT
1 AAGAAAAAA-TT
22452 AAGAAAAAATAT
1 AAGAAAAAAT-T
22464 ACAACGTATAAAAACTT
1 --AA-G-A-AAAAA-TT
22481 AAGAAAAAATT
1 AAGAAAAAATT
22492 AAGAAA
1 AAGAAA
22498 TTGGGGAAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
9 2 0.03
10 4 0.06
11 22 0.35
12 19 0.31
13 1 0.02
14 3 0.05
15 3 0.05
16 1 0.02
17 6 0.10
18 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.12, T:0.18
Consensus pattern (11 bp):
AAGAAAAAATT
Found at i:22552 original size:33 final size:33
Alignment explanation
Indices: 22525--22631 Score: 196
Period size: 33 Copynumber: 3.2 Consensus size: 33
22515 GAAAAAATTT
*
22525 AAGAAAAGAAATTGATAAAAGGAGAAAACGGAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAG
22558 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAG
*
22591 AAGAAAAGAAATTGATAAAAGCAGAAAACAGAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAG
22624 AAGAAAAG
1 AAGAAAAG
22632 GAAGAAGAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.63, C:0.05, G:0.24, T:0.08
Consensus pattern (33 bp):
AAGAAAAGAAATTGATAAAAGCAGAAAACGGAG
Found at i:24994 original size:22 final size:22
Alignment explanation
Indices: 24965--25046 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
24955 TGAATATTTT
24965 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* *
24987 TATTAAATTTTGATAAAC-ACGC
1 TATGAAATTTTGAT-AACTACCC
*
25009 TATGAAATTTTGATAATTTA-CC
1 TATGAAATTTTGATAA-CTACCC
*
25031 TATGAAATTGTGATAA
1 TATGAAATTTTGATAA
25047 ACTCAATGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.04
22 45 0.88
23 4 0.08
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:25078 original size:44 final size:43
Alignment explanation
Indices: 24965--25092 Score: 130
Period size: 44 Copynumber: 2.9 Consensus size: 43
24955 TGAATATTTT
* **
24965 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAAACACGC
1 TATGAAATTTTGATAACTA-CCTATGAAATTTTGATAAACACAA
* * *
25009 TATGAAATTTTGATAATTTACCTATGAAATTGTGATAAACTCAA
1 TATGAAATTTTGATAA-CTACCTATGAAATTTTGATAAACACAA
* * * * *
25053 TGTGAAACTTTGATAACCTAACTATGCAATTTTAATAAAC
1 TATGAAATTTTGATAA-CTACCTATGAAATTTTGATAAAC
25093 CTTCCTATAT
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
44 67 0.97
45 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (43 bp):
TATGAAATTTTGATAACTACCTATGAAATTTTGATAAACACAA
Done.