Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018677.1 Corchorus olitorius cultivar O-4 contig18710, 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: 34312
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:92 original size:33 final size:33
Alignment explanation
Indices: 22--103 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
12 GCGACCTAGC
* * **
22 CGCGACTCAGTCGCGATCCGCAGGCGATCAATC
1 CGCGGCTCCGTCGCGATCCGCAGGCGATCAAGA
* *
55 CGCGGCTCCGTCGCGATCCGCATGCGATCGAGA
1 CGCGGCTCCGTCGCGATCCGCAGGCGATCAAGA
88 CGCGGCTCCGTCGCGA
1 CGCGGCTCCGTCGCGA
104 GCGACCATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.16, C:0.38, G:0.32, T:0.15
Consensus pattern (33 bp):
CGCGGCTCCGTCGCGATCCGCAGGCGATCAAGA
Found at i:5381 original size:81 final size:81
Alignment explanation
Indices: 5288--5449 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
5278 GGTATACCAA
5288 CAAAAAAGAAAAGAAGGCAAATTTGCATAAATCAACAGAGGAGGATCCAAGATGTTTTAACTTTT
1 CAAAAAAGAAAAGAAGGCAAATTTGCATAAATCAACAGAGGAGGATCCAAGATGTTTTAACTTTT
*
5353 AAGTGTGTGTGTGTGT
66 AAGTGTGTGTCTGTGT
*
5369 CAAAAAGGAAAAGAAGGCAAATTTGCATAAATCAACAGAGGAGGATCCAAGATGTTTTAACTTTT
1 CAAAAAAGAAAAGAAGGCAAATTTGCATAAATCAACAGAGGAGGATCCAAGATGTTTTAACTTTT
5434 AAGTGTGTGTCTGTGT
66 AAGTGTGTGTCTGTGT
5450 GTGTGTGTGT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.27
Consensus pattern (81 bp):
CAAAAAAGAAAAGAAGGCAAATTTGCATAAATCAACAGAGGAGGATCCAAGATGTTTTAACTTTT
AAGTGTGTGTCTGTGT
Found at i:5443 original size:2 final size:2
Alignment explanation
Indices: 5436--5468 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5426 TAACTTTTAA
*
5436 GT GT GT GT CT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
5469 AAAAAGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
GT
Found at i:6965 original size:28 final size:28
Alignment explanation
Indices: 6934--7018 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 28
6924 CAGCAAGGTG
* *
6934 AAAACAGCAAGCTCAAAACAGCAACTCT
1 AAAACAGCAAGCTCAAAACAGCAAATCA
6962 AAAACAGCAAGCTCAAAACAGCAAATCA
1 AAAACAGCAAGCTCAAAACAGCAAATCA
* *
6990 AAAACAGTAA-ATCAAAAACAGCAAATCA
1 AAAACAGCAAGCTC-AAAACAGCAAATCA
7018 A
1 A
7019 TTAAGACTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 2 0.04
28 50 0.96
ACGTcount: A:0.58, C:0.24, G:0.09, T:0.09
Consensus pattern (28 bp):
AAAACAGCAAGCTCAAAACAGCAAATCA
Found at i:6968 original size:42 final size:42
Alignment explanation
Indices: 6907--7013 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
6897 GAAAACAAGT
* * * * *
6907 AAACAACAAATCAATAACAGCAAGGTGAAAACAGCAAGCTC-A
1 AAACAGCAAATCAAAAACAGCAAGCTCAAAACAGCAA-ATCAA
* *
6949 AAACAGCAACTCTAAAACAGCAAGCTCAAAACAGCAAATCAA
1 AAACAGCAAATCAAAAACAGCAAGCTCAAAACAGCAAATCAA
*
6991 AAACAGTAAATCAAAAACAGCAA
1 AAACAGCAAATCAAAAACAGCAA
7014 ATCAATTAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.04
42 52 0.96
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.09
Consensus pattern (42 bp):
AAACAGCAAATCAAAAACAGCAAGCTCAAAACAGCAAATCAA
Found at i:6993 original size:14 final size:14
Alignment explanation
Indices: 6907--7018 Score: 95
Period size: 14 Copynumber: 8.0 Consensus size: 14
6897 GAAAACAAGT
*
6907 AAACAACAAATCAA
1 AAACAGCAAATCAA
* * *
6921 TAACAGCAAGGT-GA
1 AAACAGCAA-ATCAA
*
6935 AAACAGCAAGCTC-A
1 AAACAGCAA-ATCAA
* *
6949 AAACAGCAACTCTA
1 AAACAGCAAATCAA
*
6963 AAACAGCAAGCTC-A
1 AAACAGCAA-ATCAA
6977 AAACAGCAAATCAA
1 AAACAGCAAATCAA
*
6991 AAACAGTAAATCAA
1 AAACAGCAAATCAA
7005 AAACAGCAAATCAA
1 AAACAGCAAATCAA
7019 TTAAGACTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
13 5 0.06
14 75 0.89
15 4 0.05
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.10
Consensus pattern (14 bp):
AAACAGCAAATCAA
Found at i:10499 original size:17 final size:17
Alignment explanation
Indices: 10465--10504 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
10455 CGTCTTTTTA
**
10465 TTTTCTGATTTTTCTCT
1 TTTTCTGATTTTGATCT
*
10482 TTTTTTGATTTTGATCT
1 TTTTCTGATTTTGATCT
10499 TTTTCT
1 TTTTCT
10505 ATCTCTAGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.72
Consensus pattern (17 bp):
TTTTCTGATTTTGATCT
Found at i:11749 original size:65 final size:65
Alignment explanation
Indices: 11643--11772 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
11633 TCGTACTGCT
*
11643 CGAATCTCCTCCTTTGTCGTTAAAGCTTCTATCTTTCTTCTTCGCTTCACTCTTTTCTTCTTCAG
1 CGAATCTCCTCCTTTGTCGTTAAAGCTTCTATCTTTATTCTTCGCTTCACTCTTTTCTTCTTCAG
*
11708 CGAATCTCCTCCTTTGTCGTTAAAGCTTCTTTCTTTATTCTTCGCTTCACTCTTTTCTTCTTCAG
1 CGAATCTCCTCCTTTGTCGTTAAAGCTTCTATCTTTATTCTTCGCTTCACTCTTTTCTTCTTCAG
11773 TGAGCCTTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.12, C:0.30, G:0.09, T:0.48
Consensus pattern (65 bp):
CGAATCTCCTCCTTTGTCGTTAAAGCTTCTATCTTTATTCTTCGCTTCACTCTTTTCTTCTTCAG
Found at i:14307 original size:27 final size:29
Alignment explanation
Indices: 14254--14307 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
14244 TTTCAGATGC
*
14254 AATCTAGATAATTAAGAGATGAATTAGCT
1 AATCTAGATAATTAAAAGATGAATTAGCT
14283 AATCTA-A-AATTAAAAG-TGAACTTAG
1 AATCTAGATAATTAAAAGATGAA-TTAG
14308 AATGACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.17
27 12 0.52
28 1 0.04
29 6 0.26
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (29 bp):
AATCTAGATAATTAAAAGATGAATTAGCT
Found at i:18173 original size:267 final size:265
Alignment explanation
Indices: 17684--18219 Score: 833
Period size: 267 Copynumber: 2.0 Consensus size: 265
17674 TATTAACGAA
* * * *
17684 TTGGGTTTAAGAATATCAGATTTAGATTTCAAGACATCTGGCTTGACAATTTGGGCTTCATGGAG
1 TTGGGTCTAAGAATATCAGATTTAGACTTCAAGACATCTGGCTTGACAATTTGGACTTCATGGAC
* * *
17749 TCAAACGGGTCTAATGGACAAACTGGCCGAAATAAGACAAAATCAATAGTTTCTCCAAATCTATA
66 TCAAACGGGCCTAATGGACAAACTGGCCAAAATAAGACAAAATCAATAATTTCTCCAAATCTATA
*
17814 CTATATATAAAAGTACGAATAATAAGAAATTTTATATTTTCCGATTCTACTAAATTTTTCCAAAA
131 CTATATATAAAAGTACGAATAATAAGAAACTTTATATTTTCCGATTCTACTAAATTTTTCCAAAA
*
17879 ATATTTCTAATTTTTCATTACTTTTTTTTTAAAAAAAAATTGTCATTACTTAAAATTAGACTTTT
196 ATATTTCTAATTTTTCATTACTTTTTTTTT--AAAAAAATTGTCATCACTTAAAATTAGACTTTT
17944 ATGCAAT
259 ATGCAAT
* *
17951 TTGGGTCTAAGAATATCAGATTTAGACTTCAAGACATCTGGTTTGGCAATTTGGACTTCATGGAC
1 TTGGGTCTAAGAATATCAGATTTAGACTTCAAGACATCTGGCTTGACAATTTGGACTTCATGGAC
** *
18016 TCAAACGGGCCTAATGGACCTACTGGCCAAAATGAGACAAAATCAATAATTTCTCCAAATCTATA
66 TCAAACGGGCCTAATGGACAAACTGGCCAAAATAAGACAAAATCAATAATTTCTCCAAATCTATA
* * * * * * * *
18081 CTATATATAAAAGTACGAATAAT-GGAAAACTTTATGTTTTCTGATTGTA-TCATTTTTTTCGAA
131 CTATATATAAAAGTACGAATAATAAG-AAACTTTATATTTTCCGATTCTACTAAATTTTTCCAAA
18144 AATATTTCTAATTTTTCATTACTTTTTTTTTAAAAAAATTGTCATCACTTAAAATTAGACTTTTA
195 AATATTTCTAATTTTTCATTACTTTTTTTTTAAAAAAATTGTCATCACTTAAAATTAGACTTTTA
18209 TGCAAT
260 TGCAAT
18215 TTGGG
1 TTGGG
18220 CTTCATGGAT
Statistics
Matches: 246, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
264 44 0.18
266 42 0.17
267 160 0.65
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (265 bp):
TTGGGTCTAAGAATATCAGATTTAGACTTCAAGACATCTGGCTTGACAATTTGGACTTCATGGAC
TCAAACGGGCCTAATGGACAAACTGGCCAAAATAAGACAAAATCAATAATTTCTCCAAATCTATA
CTATATATAAAAGTACGAATAATAAGAAACTTTATATTTTCCGATTCTACTAAATTTTTCCAAAA
ATATTTCTAATTTTTCATTACTTTTTTTTTAAAAAAATTGTCATCACTTAAAATTAGACTTTTAT
GCAAT
Found at i:18396 original size:215 final size:214
Alignment explanation
Indices: 17996--18425 Score: 657
Period size: 215 Copynumber: 2.0 Consensus size: 214
17986 ATCTGGTTTG
17996 GCAATTTGGACTTCATGGACTCAAACGGGCCTAATGGACCTACTGGCCAAAATGAGACAAAATCA
1 GCAATTTGGACTTCATGGACTCAAACGGGCCTAATGGACCTACTGGCCAAAATGAGACAAAATCA
* * *
18061 ATAATTTCTCCAAATCTATACTATATATAAAAGTACGAATAATGGAAAACTTTATGTTTTCTGAT
66 ATAATTTATCCAAATCTATACTATATATAAAAGTACGAATAATGGAAAACTTTATGTTTTCCGAC
* * * ****
18126 TGTATCATTTTTTTCGAAAATATTTCTAATTTTTCATTACTTTTTTTTTAAAAAAATTGTCATCA
131 TGTACCATTTTTTTCGAAAATATTTATAATTTGTCATTACTTTTTAAAAAAAAAAATTGTCATCA
18191 CTTAAAATTAGACTTTTAT
196 CTTAAAATTAGACTTTTAT
* * *
18210 GCAATTTGGGCTTCATGGATTCAAACGGGCCTAATGGACCTACTAGGCCGAAATGAGACAAAATC
1 GCAATTTGGACTTCATGGACTCAAACGGGCCTAATGGACCTACT-GGCCAAAATGAGACAAAATC
* * *
18275 AATAGTTTATCCAAATCTATACTATATATAAAATTACGAATAATGGAAAATTTTATGTTTTCCGA
65 AATAATTTATCCAAATCTATACTATATATAAAAGTACGAATAATGGAAAACTTTATGTTTTCCGA
*
18340 CTGTACCATTTTTTTC-AAATATATTTATAGTTTGTCATTA-TTTTTAAAAAAAAAAAATTGTCA
130 CTGTACCATTTTTTTCGAAA-ATATTTATAATTTGTCATTACTTTTT-AAAAAAAAAAATTGTCA
*
18403 TTACTTAAAATTAGACTTTTAT
193 TCACTTAAAATTAGACTTTTAT
18425 G
1 G
18426 TTTTATATAT
Statistics
Matches: 195, Mismatches: 18, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
214 50 0.26
215 145 0.74
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (214 bp):
GCAATTTGGACTTCATGGACTCAAACGGGCCTAATGGACCTACTGGCCAAAATGAGACAAAATCA
ATAATTTATCCAAATCTATACTATATATAAAAGTACGAATAATGGAAAACTTTATGTTTTCCGAC
TGTACCATTTTTTTCGAAAATATTTATAATTTGTCATTACTTTTTAAAAAAAAAAATTGTCATCA
CTTAAAATTAGACTTTTAT
Found at i:20399 original size:21 final size:22
Alignment explanation
Indices: 20360--20435 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 22
20350 GGAGATTAAC
* * *
20360 AAAATCTCACAAGGAGGTTATT
1 AAAATATCATAAGAAGGTTATT
* * *
20382 AAAA-ATTATAGGAAGGTTA-C
1 AAAATATCATAAGAAGGTTATT
20402 AAAATATCATAAGAAGGTTTATT
1 AAAATATCATAAGAAGG-TTATT
*
20425 AAAATTTCATA
1 AAAATATCATA
20436 GTTAGGTTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
20 4 0.10
21 20 0.49
22 7 0.17
23 10 0.24
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.30
Consensus pattern (22 bp):
AAAATATCATAAGAAGGTTATT
Found at i:20450 original size:22 final size:22
Alignment explanation
Indices: 20395--20545 Score: 82
Period size: 22 Copynumber: 6.9 Consensus size: 22
20385 AATTATAGGA
* *
20395 AGGTTA-CAAAATATCATAAG-A
1 AGGTTATCAAAATTTCAT-AGTT
*
20416 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATCAAAATTTCATAGTT
*
20439 AGGTTATCAAAAGTTTCATA-TGG
1 AGGTTATCAAAA-TTTCATAGT-T
* * *
20462 AGTTTATCATAATTTCATAGGT
1 AGGTTATCAAAATTTCATAGTT
* * *
20484 A-ATTATCAAAATTTAATAGGGT
1 AGGTTATCAAAATTTCATA-GTT
*
20506 -GGTTATCAAAATTTTATAGGATT
1 AGGTTATCAAAATTTCATA-G-TT
*
20529 A--TTATTAAAATTTCATA
1 AGGTTATCAAAATTTCATA
20546 AAAATATTCA
Statistics
Matches: 103, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
21 17 0.17
22 56 0.54
23 30 0.29
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTT
Found at i:20491 original size:21 final size:21
Alignment explanation
Indices: 20420--20545 Score: 92
Period size: 22 Copynumber: 5.8 Consensus size: 21
20410 ATAAGAAGGT
* * *
20420 TTATTAAAATTTCATAGTTAGG
1 TTATCAAAATTTCATAGGTA-A
*
20442 TTATCAAAAGTTTCATATGG-AGT
1 TTATCAAAA-TTTCATA-GGTA-A
*
20465 TTATCATAATTTCATAGGTAA
1 TTATCAAAATTTCATAGGTAA
* **
20486 TTATCAAAATTTAATAGGGTGG
1 TTATCAAAATTTCATA-GGTAA
* *
20508 TTATCAAAATTTTATAGGATTA
1 TTATCAAAATTTCATAGG-TAA
*
20530 TTATTAAAATTTCATA
1 TTATCAAAATTTCATA
20546 AAAATATTCA
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
21 18 0.21
22 49 0.58
23 17 0.20
24 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTAA
Found at i:20533 original size:44 final size:43
Alignment explanation
Indices: 20420--20541 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 43
20410 ATAAGAAGGT
* * * * * *
20420 TTATTAAAATTTCATAGTTAGGTTATCAAAAGTTTCATATGGAGT
1 TTATCAAAATTTCATAGGTA-ATTATCAAAA-TTTAATAGGGAGG
* *
20465 TTATCATAATTTCATAGGTAATTATCAAAATTTAATAGGGTGG
1 TTATCAAAATTTCATAGGTAATTATCAAAATTTAATAGGGAGG
* * *
20508 TTATCAAAATTTTATAGGATTATTATTAAAATTT
1 TTATCAAAATTTCATAGG-TAATTATCAAAATTT
20542 CATAAAAATA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 25 0.39
44 22 0.34
45 17 0.27
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGTAATTATCAAAATTTAATAGGGAGG
Found at i:21574 original size:19 final size:21
Alignment explanation
Indices: 21526--21583 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
21516 ATATCCTTTG
*
21526 ATGAGTAGTTTTTTTTAATCAT
1 ATGAGTAGTTTTATTTAA-CAT
*
21548 ATGGGTAGTTTTATTTAA-A-
1 ATGAGTAGTTTTATTTAACAT
21567 ATGAGTAGTTTTTATTT
1 ATGAGTAG-TTTTATTT
21584 TGTTTTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 7 0.22
20 9 0.28
22 16 0.50
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (21 bp):
ATGAGTAGTTTTATTTAACAT
Found at i:23270 original size:58 final size:58
Alignment explanation
Indices: 23174--23283 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
23164 ATTAATCAAA
*
23174 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
* * *
23232 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACC
23284 GAGGCATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 32 0.68
59 15 0.32
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
Found at i:25143 original size:201 final size:199
Alignment explanation
Indices: 24798--25203 Score: 751
Period size: 201 Copynumber: 2.0 Consensus size: 199
24788 GCTTAATAAC
24798 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
24863 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGA
65 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGA
24928 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
130 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCC
24993 GATTTA
194 GATTTA
24999 TTTATCAATGGTGAATGTTATTAA-TTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
*
25063 ATACAACACATTACTATTATATATATAGAACTATACCAAAAAAATTAGTTGAACATTAGTGGTTG
66 ATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTG
25128 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
129 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
25193 GATTTA
194 GATTTA
25199 TTTAT
1 TTTAT
25204 TATTAAGGAA
Statistics
Matches: 201, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
199 64 0.32
200 19 0.09
201 118 0.59
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (199 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGAT
TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGA
TTTA
Found at i:30528 original size:204 final size:202
Alignment explanation
Indices: 30178--30576 Score: 717
Period size: 204 Copynumber: 2.0 Consensus size: 202
30168 TATATATATA
* *
30178 GCTGCACGTATGTTAATAATTGATAAATCATATATTCTACACATGCATACTTTTTATTTTCATAA
1 GCTGCACGTATGTTAATAATTGATAAATCATATATTCCACACATACATACTTTTTATTTTCATAA
*
30243 ATTTTGATTAATTAATCATCAAAATCTGGTCATTTAGTTTAAAGAGATTTGAAATAATTAATCTC
66 ATTTTGATTAATTAATCATCAAAATCTGGTCATTTAATTTAAAGAGATTTGAAATAATTAATCTC
*
30308 ATTGAACGAACAAAAAAAAACCTTAAATTATTATATAATTATGGTTATCTTTAATAATGAAGGTA
131 ATTGAACGAAC-AAAAAAAA-CTTAAATTATTATATAATTATGGTTATCTTCAATAATGAAGGTA
30373 AGCACGTGC
194 AGCACGTGC
*
30382 GCTGCACGTATGTTAATAATTGATAAATCATATATTCCACACATACGTACTTTTTATTTTCATAA
1 GCTGCACGTATGTTAATAATTGATAAATCATATATTCCACACATACATACTTTTTATTTTCATAA
*
30447 ATTTTGATTAATTAATCATCAAAATCTGGTCATTTAATTTACAGAGATTTGAAATAATTAATCTC
66 ATTTTGATTAATTAATCATCAAAATCTGGTCATTTAATTTAAAGAGATTTGAAATAATTAATCTC
*
30512 ATTGAATGAACAAAAAAAACTTAAATTATTATATAATTATGGTTATCTTCAATAATGAAGGTAAG
131 ATTGAACGAACAAAAAAAACTTAAATTATTATATAATTATGGTTATCTTCAATAATGAAGGTAAG
30577 GTTATCAATT
Statistics
Matches: 188, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
202 45 0.24
203 8 0.04
204 135 0.72
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (202 bp):
GCTGCACGTATGTTAATAATTGATAAATCATATATTCCACACATACATACTTTTTATTTTCATAA
ATTTTGATTAATTAATCATCAAAATCTGGTCATTTAATTTAAAGAGATTTGAAATAATTAATCTC
ATTGAACGAACAAAAAAAACTTAAATTATTATATAATTATGGTTATCTTCAATAATGAAGGTAAG
CACGTGC
Found at i:31936 original size:56 final size:58
Alignment explanation
Indices: 31844--31956 Score: 135
Period size: 56 Copynumber: 2.0 Consensus size: 58
31834 ATTAATCAAA
*
31844 TATCAAGTGACATGTTCTATATTAGATGCATAAAAAAA-A-GTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTATATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
* * * *
31900 TATCGAGTGACATGTTTTTTTATTAGATGTC-T-AAAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACATG-TTCTATATTAGATG-CATAAAAAAAGACGTTTTAGGACCAAGGC
31957 ATGATGCTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
56 19 0.40
57 14 0.29
58 15 0.31
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTATATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:33260 original size:36 final size:36
Alignment explanation
Indices: 33213--33282 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
33203 TTCAATAACC
* *
33213 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
33249 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
33283 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
Done.