Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014506.1 Corchorus olitorius cultivar O-4 contig14539, 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: 67350
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Found at i:2784 original size:59 final size:58
Alignment explanation
Indices: 2710--2864 Score: 210
Period size: 59 Copynumber: 2.7 Consensus size: 58
2700 ATCAATAGAA
*
2710 TGCGCGCGTCTTCTCTATATAACTATAATTTGTAAAAATTTGTGTAACGGTTTTCTTAT
1 TGCGCGCGTCTTCTCTTTATAACTATAATTTGTAAAAATTT-TGTAACGGTTTTCTTAT
* * *
2769 TGTGCGCGTCTTCTCTTTATAACAATATTTTGTAAAAA--TTGTAACGGTTTTCTTAT
1 TGCGCGCGTCTTCTCTTTATAACTATAATTTGTAAAAATTTTGTAACGGTTTTCTTAT
*
2825 TGCACGCGACTCTTCTCTTTATAACTAT-ATTT-TAAAAATT
1 TGCGCGCG--TCTTCTCTTTATAACTATAATTTGTAAAAATT
2865 CAACTCCTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
56 29 0.35
57 4 0.05
58 17 0.20
59 34 0.40
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (58 bp):
TGCGCGCGTCTTCTCTTTATAACTATAATTTGTAAAAATTTTGTAACGGTTTTCTTAT
Found at i:2861 original size:56 final size:55
Alignment explanation
Indices: 2714--2864 Score: 196
Period size: 56 Copynumber: 2.6 Consensus size: 55
2704 ATAGAATGCG
* **
2714 CGCGTCTTCTCTATATAACTATAATTTGTAAAAATTTGTGTAACGGTTTTCTTATTGTG
1 CGCGTCTTCTCTTTATAACTAT-ATTTGTAAAAA--T-TGTAACGGTTTTCTTATTGCA
*
2773 CGCGTCTTCTCTTTATAACAATATTTTGTAAAAATTGTAACGGTTTTCTTATTGCA
1 CGCGTCTTCTCTTTATAACTATA-TTTGTAAAAATTGTAACGGTTTTCTTATTGCA
2829 CGCGACTCTTCTCTTTATAACTATATTT-TAAAAATT
1 CGCG--TCTTCTCTTTATAACTATATTTGTAAAAATT
2865 CAACTCCTTA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
56 31 0.37
57 4 0.05
58 19 0.23
59 30 0.36
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (55 bp):
CGCGTCTTCTCTTTATAACTATATTTGTAAAAATTGTAACGGTTTTCTTATTGCA
Found at i:5227 original size:45 final size:45
Alignment explanation
Indices: 5163--5252 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
5153 TTTTTCAAAT
* *
5163 GAGTTGGATTTTTAAATGTATAATCATACTATAAGAACTAAACCG
1 GAGTTGAACTTTTAAATGTATAATCATACTATAAGAACTAAACCG
**
5208 GAGTTGAACTTTTAAATGTATAATCATACTATAAGAGTTAAACCG
1 GAGTTGAACTTTTAAATGTATAATCATACTATAAGAACTAAACCG
5253 AATTAGATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (45 bp):
GAGTTGAACTTTTAAATGTATAATCATACTATAAGAACTAAACCG
Found at i:5486 original size:22 final size:22
Alignment explanation
Indices: 5460--5528 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
5450 ACTATAGCAT
5460 CAAAAAATTATAGGGAGATTAA
1 CAAAAAATTATAGGGAGATTAA
** * * *
5482 CAAAATCTCATAAGGA-AGTTAT
1 CAAAAAATTATAGGGAGA-TTAA
*
5504 C-AAAAATTATAGGAAGATT-A
1 CAAAAAATTATAGGGAGATTAA
5524 CAAAA
1 CAAAA
5529 TTTCATAGGA
Statistics
Matches: 33, Mismatches: 11, Indels: 7
0.65 0.22 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.45
22 17 0.52
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.23
Consensus pattern (22 bp):
CAAAAAATTATAGGGAGATTAA
Found at i:5493 original size:43 final size:42
Alignment explanation
Indices: 5431--5540 Score: 107
Period size: 43 Copynumber: 2.6 Consensus size: 42
5421 TCACCTAATA
* * *
5431 GAGATTATCGAAATTTCATACTATAG-CATCAAAAAATTATAGG
1 GAGATTAACAAAATTTCATACGA-AGTCATC-AAAAATTATAGG
* * *
5474 GAGATTAACAAAATCTCATAAGGAAGTTATCAAAAATTATAGG
1 GAGATTAACAAAATTTCAT-ACGAAGTCATCAAAAATTATAGG
* *
5517 AAGATT-ACAAAATTTCATAGGAAG
1 GAGATTAACAAAATTTCATACGAAG
5541 GTTTATTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
41 6 0.11
42 11 0.19
43 35 0.61
44 5 0.09
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.27
Consensus pattern (42 bp):
GAGATTAACAAAATTTCATACGAAGTCATCAAAAATTATAGG
Found at i:5573 original size:22 final size:22
Alignment explanation
Indices: 5482--5666 Score: 141
Period size: 22 Copynumber: 8.5 Consensus size: 22
5472 GGGAGATTAA
* *
5482 CAAAATCTCATAAGG-AAGTTAT
1 CAAAATTTCAT-AGGTAGGTTAT
* * *
5504 CAAAAATT-ATAGGAAGATTA-
1 CAAAATTTCATAGGTAGGTTAT
*
5524 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGTAGG-TTAT
* *
5547 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGTAGGTTAT
*
5569 CAAAATTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGTAGGTTAT
* * *
5591 CACAATTTAATAGGTA-ATTAT
1 CAAAATTTCATAGGTAGGTTAT
* * *
5612 CAGAATTACATAGCGT-GATTAT
1 CAAAATTTCATAG-GTAGGTTAT
*
5634 CAAAATTTAATAGGTA-GTTAT
1 CAAAATTTCATAGGTAGGTTAT
5655 CAAAATTTCATA
1 CAAAATTTCATA
5667 AAAATATTCA
Statistics
Matches: 131, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
20 10 0.08
21 47 0.36
22 58 0.44
23 16 0.12
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGTAGGTTAT
Found at i:7225 original size:12 final size:12
Alignment explanation
Indices: 7216--7241 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7206 TCGCCCTCGC
7216 CCTCTACCTCTG
1 CCTCTACCTCTG
7228 CCTCTACCTCTG
1 CCTCTACCTCTG
7240 CC
1 CC
7242 ACCGCCCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.54, G:0.08, T:0.31
Consensus pattern (12 bp):
CCTCTACCTCTG
Found at i:7351 original size:12 final size:12
Alignment explanation
Indices: 7342--7369 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
7332 TCGGCCTCGT
7342 CCTCTTCCTCTG
1 CCTCTTCCTCTG
7354 CCTCTTCCTCTG
1 CCTCTTCCTCTG
7366 CCTC
1 CCTC
7370 CGCCCTGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.54, G:0.07, T:0.39
Consensus pattern (12 bp):
CCTCTTCCTCTG
Found at i:7351 original size:18 final size:18
Alignment explanation
Indices: 7330--7369 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7320 ACGACCTCGA
*
7330 CCTCGGCCTCGTCCTCTT
1 CCTCGGCCTCGTCCTCTG
* *
7348 CCTCTGCCTCTTCCTCTG
1 CCTCGGCCTCGTCCTCTG
7366 CCTC
1 CCTC
7370 CGCCCTGTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.53, G:0.12, T:0.35
Consensus pattern (18 bp):
CCTCGGCCTCGTCCTCTG
Found at i:8934 original size:56 final size:55
Alignment explanation
Indices: 8873--9079 Score: 281
Period size: 56 Copynumber: 3.7 Consensus size: 55
8863 ATAACTGCAA
*
8873 TGCGCGCGTCTTCTCTTTATAACTATAATTTGAAAAAATATGTAACGCTTTTTAAT
1 TGCGCGCGTCTTCTCTTTATAACTATAATTTGAAAAAATATGTAACGGTTTTT-AT
*
8929 TGCGCGCGTCTTCTCTTTATAACTATAATTTGAAAAAATGTGTAACGGTTTTTTAT
1 TGCGCGCGTCTTCTCTTTATAACTATAATTTGAAAAAATATGTAACGG-TTTTTAT
* * * *
8985 TGCGCGCGTCTTTTCTTTATAACTATAATCTGAAAAAATCTATAACGGTTTTTAT
1 TGCGCGCGTCTTCTCTTTATAACTATAATTTGAAAAAATATGTAACGGTTTTTAT
* *
9040 TGCGCGCGCGAACCTTCTCTTTATAACTAT-ATTTCAAAAA
1 T--GCGCGCG--TCTTCTCTTTATAACTATAATTTGAAAAA
9080 TTCAACTCTT
Statistics
Matches: 136, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
55 8 0.06
56 92 0.68
57 12 0.09
58 8 0.06
59 16 0.12
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (55 bp):
TGCGCGCGTCTTCTCTTTATAACTATAATTTGAAAAAATATGTAACGGTTTTTAT
Found at i:9320 original size:6 final size:6
Alignment explanation
Indices: 9311--9386 Score: 152
Period size: 6 Copynumber: 12.7 Consensus size: 6
9301 TAAAACCTAC
9311 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
9359 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
9387 TTATAATTTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:10287 original size:59 final size:59
Alignment explanation
Indices: 10112--10287 Score: 273
Period size: 59 Copynumber: 3.0 Consensus size: 59
10102 TAGTGACTAT
* * *
10112 TTTATTAGGTAATGACATGGGGAAAACATGCACCATGGTTAGAGTTTATTAGGCAATAA
1 TTTATTAGGTAATGCCATGTGGAAAACATGCACCATGGTTAGAGTTTATTAGGCAATGA
* *
10171 TTTATTAGGTAATGCC-TCGTGGAAAGCATGCACCATGGTTAGAGTTTATTTGGCAATGA
1 TTTATTAGGTAATGCCAT-GTGGAAAACATGCACCATGGTTAGAGTTTATTAGGCAATGA
* *
10230 TTTATTAGGTAATGCCATGTGGAAAACATGCACCATGGTTAGAATTAATTAGGCAATG
1 TTTATTAGGTAATGCCATGTGGAAAACATGCACCATGGTTAGAGTTTATTAGGCAATG
10288 CCACGTGGAA
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
58 1 0.01
59 104 0.98
60 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (59 bp):
TTTATTAGGTAATGCCATGTGGAAAACATGCACCATGGTTAGAGTTTATTAGGCAATGA
Found at i:10650 original size:2 final size:2
Alignment explanation
Indices: 10637--10678 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
10627 AAAGGATTCC
10637 TA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10679 GGAGAGAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10789 original size:106 final size:106
Alignment explanation
Indices: 10661--10853 Score: 368
Period size: 106 Copynumber: 1.8 Consensus size: 106
10651 ATATATATAT
* *
10661 ATATATATATATATATATGGAGAGAGAGAGGAGTACTTAATAAGGAATTGTTTAATTTGTTATAA
1 ATATATATATATATATAGGGAGAGAGAGAGGAGAACTTAATAAGGAATTGTTTAATTTGTTATAA
10726 GAATATCATAAAATTTCAAGTTTTGTAAAGGATTTCTATTC
66 GAATATCATAAAATTTCAAGTTTTGTAAAGGATTTCTATTC
10767 ATATATATATATATATAGGGAGAGAGAGAGGAGAACTTAATAAGGAATTGTTTAATTTGTTATAA
1 ATATATATATATATATAGGGAGAGAGAGAGGAGAACTTAATAAGGAATTGTTTAATTTGTTATAA
10832 GAATATCATAAAATTTCAAGTT
66 GAATATCATAAAATTTCAAGTT
10854 CAATAACTTG
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 85 1.00
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (106 bp):
ATATATATATATATATAGGGAGAGAGAGAGGAGAACTTAATAAGGAATTGTTTAATTTGTTATAA
GAATATCATAAAATTTCAAGTTTTGTAAAGGATTTCTATTC
Found at i:13924 original size:58 final size:57
Alignment explanation
Indices: 13793--13939 Score: 174
Period size: 59 Copynumber: 2.6 Consensus size: 57
13783 ATTGCTTGTG
* * * **
13793 TCTTCTCTATATAACTATATTATGTAAAAATTTGTATAACAGTTTTCTTTTTGCGCGCG
1 TCTTCTCTTTATAACTATATTTTGTAAAAA-TTG-ATAACAGTTTTCTTATTGCGCGAA
*
13852 TCTTCTCTTTATAACTATATTTTGTAAAAATTG-TAATAGTTTTCTTATTGCGCATGAA
1 TCTTCTCTTTATAACTATATTTTGTAAAAATTGATAACAGTTTTCTTATTGCGC--GAA
*
13910 TTTTCTCTTTATAACTATA-TTT-TAAAAATT
1 TCTTCTCTTTATAACTATATTTTGTAAAAATT
13940 CAACTCCTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
56 26 0.33
57 3 0.04
58 22 0.28
59 28 0.35
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (57 bp):
TCTTCTCTTTATAACTATATTTTGTAAAAATTGATAACAGTTTTCTTATTGCGCGAA
Found at i:13936 original size:56 final size:56
Alignment explanation
Indices: 13793--13939 Score: 172
Period size: 56 Copynumber: 2.6 Consensus size: 56
13783 ATTGCTTGTG
* * **
13793 TCTTCTCTATATAACTATATTATGTAAAAATTTGTATAACAGTTTTCTTTTTGCGCGCG
1 TCTTCTCTTTATAACTATATT-TGTAAAAA-TTG-ATAACAGTTTTCTTATTGCGCGAA
*
13852 TCTTCTCTTTATAACTATATTTTGTAAAAATTG-TAATAGTTTTCTTATTGCGCATGAA
1 TCTTCTCTTTATAACTATA-TTTGTAAAAATTGATAACAGTTTTCTTATTGCGC--GAA
*
13910 TTTTCTCTTTATAACTATATTT-TAAAAATT
1 TCTTCTCTTTATAACTATATTTGTAAAAATT
13940 CAACTCCTTA
Statistics
Matches: 79, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
56 26 0.33
57 3 0.04
58 22 0.28
59 26 0.33
60 2 0.03
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (56 bp):
TCTTCTCTTTATAACTATATTTGTAAAAATTGATAACAGTTTTCTTATTGCGCGAA
Found at i:15824 original size:59 final size:58
Alignment explanation
Indices: 15761--15910 Score: 191
Period size: 59 Copynumber: 2.6 Consensus size: 58
15751 TACATTGTGT
*
15761 GCATCTTCTCTATATAACTATAATTTGTAAAAATTTATATAACGGCTTTCTTATTGCGC
1 GCATCTTCTCTTTATAACTATAATTTGTAAAAATTT-TATAACGGCTTTCTTATTGCGC
* * * *
15820 GCATCTTCTCTTTCTAACTATATTTTGTAAAAA--TTGTAACGGTTTTCTTATTGCGC
1 GCATCTTCTCTTTATAACTATAATTTGTAAAAATTTTATAACGGCTTTCTTATTGCGC
*
15876 GCAAATCTTCTCTTTATCACTAT-ATTT-TAAAAATT
1 GC--ATCTTCTCTTTATAACTATAATTTGTAAAAATT
15911 CAACTCTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
56 28 0.35
57 4 0.05
58 17 0.22
59 30 0.38
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (58 bp):
GCATCTTCTCTTTATAACTATAATTTGTAAAAATTTTATAACGGCTTTCTTATTGCGC
Found at i:15907 original size:56 final size:55
Alignment explanation
Indices: 15761--15910 Score: 185
Period size: 56 Copynumber: 2.6 Consensus size: 55
15751 TACATTGTGT
*
15761 GCATCTTCTCTATATAACTATAATTTGTAAAAATTTATATAACGGCTTTCTTATTGCGC
1 GCATCTTCTCTTTATAACTAT-ATTTGTAAAAA--T-TATAACGGCTTTCTTATTGCGC
* * *
15820 GCATCTTCTCTTTCTAACTATATTTTGTAAAAATTGTAACGGTTTTCTTATTGCGC
1 GCATCTTCTCTTTATAACTATA-TTTGTAAAAATTATAACGGCTTTCTTATTGCGC
*
15876 GCAAATCTTCTCTTTATCACTATATTT-TAAAAATT
1 GC--ATCTTCTCTTTATAACTATATTTGTAAAAATT
15911 CAACTCTTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
56 30 0.37
57 4 0.05
58 19 0.23
59 29 0.35
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (55 bp):
GCATCTTCTCTTTATAACTATATTTGTAAAAATTATAACGGCTTTCTTATTGCGC
Found at i:16904 original size:320 final size:320
Alignment explanation
Indices: 16366--17008 Score: 1205
Period size: 320 Copynumber: 2.0 Consensus size: 320
16356 AGATTATTGC
*
16366 AATGAGATTTCTATAGACTACATATAGTACCATTTTTTTTCTTTTGGCCATCAAAAATTTTAAGA
1 AATGAGATTTCTATAGACTACATATAGTACCATTTTTTTTCGTTTGGCCATCAAAAATTTTAAGA
16431 TTCCAACTTCAAGTCTAATTCGGGTTTAATTTGTTTATTAACTTCTTTATCTATTCGCTTTCATT
66 TTCCAACTTCAAGTCTAATTCGGGTTTAATTTGTTTATTAACTTCTTTATCTATTCGCTTTCATT
*
16496 CCCTAGTATTATAATTTACCTCTTAATACCCAACTATACTTATATTATTTTAGTATTTAATCTAT
131 CCCTAGAATTATAATTTACCTCTTAATACCCAACTATACTTATATTATTTTAGTATTTAATCTAT
16561 CACCATTATTCCCTTACCTATATATAGGGTAACATAACCCGGATTCTTATCCATTTTTATGCATC
196 CACCATTATTCCCTTACCTATATATAGGGTAACATAACCCGGATTCTTATCCATTTTTATGCATC
*
16626 TTCATTGTAATGTTAGATTATTTCCGATTTTATAGTAAACAATTGCATTGGCAAATGTCA
261 TTCATTGTAATGTTAGATTATTTCCGATTTTATAGTAAACAATTGCATTGGAAAATGTCA
* *
16686 AATGAGATTTCTATAGACTATATATAGTACCATTTTTTTTCGTTTGGCCATCAAAAATTTTGAGA
1 AATGAGATTTCTATAGACTACATATAGTACCATTTTTTTTCGTTTGGCCATCAAAAATTTTAAGA
16751 TTCCAACTTCAAGTCTAATTCGGGTTTAATTTGTTTATTAACTTCTTTATCTATTCGCTTTCATT
66 TTCCAACTTCAAGTCTAATTCGGGTTTAATTTGTTTATTAACTTCTTTATCTATTCGCTTTCATT
*
16816 CCCTAGAATTATAATTTACCTCTTAATATCCAACTATACTTATATTATTTTAGTATTTAATCTAT
131 CCCTAGAATTATAATTTACCTCTTAATACCCAACTATACTTATATTATTTTAGTATTTAATCTAT
* * *
16881 CACCATTATTCCCTTACCTATATATAGGGTAATATCACCCGGATTCTTATCCGTTTTTATGCATC
196 CACCATTATTCCCTTACCTATATATAGGGTAACATAACCCGGATTCTTATCCATTTTTATGCATC
16946 TTCATTGTAATGTTAGATTATTTCCGATTTTATAGTAAACAATTGCATTGGAAAATGTCA
261 TTCATTGTAATGTTAGATTATTTCCGATTTTATAGTAAACAATTGCATTGGAAAATGTCA
17006 AAT
1 AAT
17009 TATTTTCCAT
Statistics
Matches: 314, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
320 314 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (320 bp):
AATGAGATTTCTATAGACTACATATAGTACCATTTTTTTTCGTTTGGCCATCAAAAATTTTAAGA
TTCCAACTTCAAGTCTAATTCGGGTTTAATTTGTTTATTAACTTCTTTATCTATTCGCTTTCATT
CCCTAGAATTATAATTTACCTCTTAATACCCAACTATACTTATATTATTTTAGTATTTAATCTAT
CACCATTATTCCCTTACCTATATATAGGGTAACATAACCCGGATTCTTATCCATTTTTATGCATC
TTCATTGTAATGTTAGATTATTTCCGATTTTATAGTAAACAATTGCATTGGAAAATGTCA
Found at i:18206 original size:56 final size:56
Alignment explanation
Indices: 18057--18200 Score: 155
Period size: 59 Copynumber: 2.5 Consensus size: 56
18047 TAAACTACGT
* * * * *
18057 GCATCTTCTCTATATAACTATAATTTGTAAAAATTTATATAACAGTTTTCTTATTGCGC
1 GCATCTTCTCTTTCTAACTATATTTTGTAAAAA--T-TGTAACAGTTTTCTTATTGCGA
* *
18116 GCGTCTTCTCTTTCTAACTATATTTTGTAAAAATTGTAACGGTTTTCTTATTGCGA
1 GCATCTTCTCTTTCTAACTATATTTTGTAAAAATTGTAACAGTTTTCTTATTGCGA
18172 GCAAATCTTCTCTTT-TATCACTATATTTT
1 GC--ATCTTCTCTTTCTA--ACTATATTTT
18201 AAAATTCAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
56 21 0.29
57 3 0.04
58 10 0.14
59 39 0.53
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.47
Consensus pattern (56 bp):
GCATCTTCTCTTTCTAACTATATTTTGTAAAAATTGTAACAGTTTTCTTATTGCGA
Found at i:20900 original size:58 final size:60
Alignment explanation
Indices: 20763--20919 Score: 225
Period size: 58 Copynumber: 2.7 Consensus size: 60
20753 TTATCACTAC
* * *
20763 ATTGCGCGCG--TCTTCTCTATATAACCATAATTTGTAAAAATTTGTATAACAGTTTTCTT
1 ATTGCGCGCGAATCTTCTCTTTATAACTATATTTTGTAAAAATTTG-ATAACAGTTTTCTT
*
20822 ATTGCGCGCGAATCTTCTCTTTATAACTATATTTTGTAAAAA-TTG-TAACGGTTTTCTT
1 ATTGCGCGCGAATCTTCTCTTTATAACTATATTTTGTAAAAATTTGATAACAGTTTTCTT
*
20880 ATTGCGCGCGAATCTCCTCTTTATAACTATATTTTG-AAAA
1 ATTGCGCGCGAATCTTCTCTTTATAACTATATTTTGTAAAA
20920 TTCAACTCCT
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
57 4 0.04
58 47 0.52
59 10 0.11
60 3 0.03
61 27 0.30
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (60 bp):
ATTGCGCGCGAATCTTCTCTTTATAACTATATTTTGTAAAAATTTGATAACAGTTTTCTT
Found at i:29474 original size:29 final size:29
Alignment explanation
Indices: 29438--29495 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
29428 TATAGCTATT
29438 CCCAAACTTACTGTGATCAATCAATTCTA
1 CCCAAACTTACTGTGATCAATCAATTCTA
*
29467 CCCAAACTTACTGTGATCAATTAATTCTA
1 CCCAAACTTACTGTGATCAATCAATTCTA
29496 AAAACAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.33
Consensus pattern (29 bp):
CCCAAACTTACTGTGATCAATCAATTCTA
Found at i:35187 original size:2 final size:2
Alignment explanation
Indices: 35180--35246 Score: 86
Period size: 2 Copynumber: 34.0 Consensus size: 2
35170 GAGGGAAAAC
*
35180 TA TA TA TA TA -A TA TA TA -A TA TA TA -A TA TA GA TA TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
35220 TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA
35247 ATAAAAACAA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
1 3 0.05
2 51 0.88
3 4 0.07
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:35213 original size:25 final size:25
Alignment explanation
Indices: 35181--35249 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
35171 AGGGAAAACT
35181 ATATATATAATA-TATAATATATAAT
1 ATATATATAATAGTATAATATAT-AT
*
35206 ATAGATAT-ATAGTATATATATATAT
1 ATATATATAATAGTATA-ATATATAT
35231 ATATATAT-ATAGTATAATA
1 ATATATATAATAGTATAATA
35250 AAAACAACAC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.15
25 28 0.70
26 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
ATATATATAATAGTATAATATATAT
Found at i:49240 original size:2 final size:2
Alignment explanation
Indices: 49235--49272 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
49225 TCTCTCTCTC
49235 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
49273 CGTGCGCGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:50882 original size:58 final size:58
Alignment explanation
Indices: 50819--50934 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
50809 TGCACAAGTT
**
50819 ATTCTTAATATGCAAAAACAAATGAAAATCTTTGATTGTTTGCTTTGTTGATTCCATA
1 ATTCTTAATATGCAAAAACAAATGAAAATCTTTGATTGTTCACTTTGTTGATTCCATA
* * *
50877 ATTCTTAATTTGCAAAATCAATTGAAAATCTTTGATTGTTCACTTTGTTGATTCCATA
1 ATTCTTAATATGCAAAAACAAATGAAAATCTTTGATTGTTCACTTTGTTGATTCCATA
50935 TATCCACTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (58 bp):
ATTCTTAATATGCAAAAACAAATGAAAATCTTTGATTGTTCACTTTGTTGATTCCATA
Found at i:65469 original size:13 final size:13
Alignment explanation
Indices: 65453--65477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65443 AATATAAAAA
65453 TAAAATAAATTTT
1 TAAAATAAATTTT
65466 TAAAATAAATTT
1 TAAAATAAATTT
65478 AAAGAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAATAAATTTT
Found at i:66485 original size:20 final size:20
Alignment explanation
Indices: 66424--66486 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
66414 AAAGAACATA
66424 AATTTGGATATTATATAATC
1 AATTTGGATATTATATAATC
*
66444 AATATT---TATT-TGA-ACATA
1 AAT-TTGGATATTAT-ATA-ATC
66462 AATTTGGATATTATATAATC
1 AATTTGGATATTATATAATC
66482 AATTT
1 AATTT
66487 ATAACTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
17 4 0.12
18 10 0.30
20 15 0.45
21 4 0.12
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (20 bp):
AATTTGGATATTATATAATC
Found at i:66569 original size:25 final size:24
Alignment explanation
Indices: 66541--66597 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
66531 GCCGATTGTA
*
66541 AAATAAATTGAATAATAAAGATATT
1 AAATAAATTGAAAAATAAA-ATATT
* *
66566 AAATAAATTTAAAAATTAAATATT
1 AAATAAATTGAAAAATAAAATATT
66590 AAA-AAATT
1 AAATAAATT
66598 CAAGGCTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 16 0.55
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTGAAAAATAAAATATT
Done.