Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015163.1 Corchorus olitorius cultivar O-4 contig15196, 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: 186809
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:3364 original size:20 final size:21
Alignment explanation
Indices: 3339--3378 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3329 TAAAAACTAC
3339 AAGAACTCCG-AATGGAGTAT
1 AAGAACTCCGCAATGGAGTAT
*
3359 AAGAACTCCGCGATGGAGTA
1 AAGAACTCCGCAATGGAGTA
3379 AAAACCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
AAGAACTCCGCAATGGAGTAT
Found at i:4958 original size:6 final size:6
Alignment explanation
Indices: 4947--4978 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
4937 ATTGCCAGGT
4947 CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA CC
1 CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA CC
4979 AGCGCCACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.69, G:0.16, T:0.00
Consensus pattern (6 bp):
CCGCCA
Found at i:4986 original size:9 final size:9
Alignment explanation
Indices: 4972--5008 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
4962 CCACCGCCAC
4972 CGCCACCAG
1 CGCCACCAG
4981 CGCCACCAG
1 CGCCACCAG
*
4990 CACCACCAG
1 CGCCACCAG
4999 CGCCACCAG
1 CGCCACCAG
5008 C
1 C
5009 ACCGCCGACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.24, C:0.57, G:0.19, T:0.00
Consensus pattern (9 bp):
CGCCACCAG
Found at i:4995 original size:18 final size:18
Alignment explanation
Indices: 4974--5011 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4964 ACCGCCACCG
4974 CCACCAGCGCCACCAGCA
1 CCACCAGCGCCACCAGCA
4992 CCACCAGCGCCACCAGCA
1 CCACCAGCGCCACCAGCA
5010 CC
1 CC
5012 GCCGACGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.58, G:0.16, T:0.00
Consensus pattern (18 bp):
CCACCAGCGCCACCAGCA
Found at i:6751 original size:2 final size:2
Alignment explanation
Indices: 6746--6773 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6736 ATTATGTTTA
6746 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
6774 TCATAGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8523 original size:15 final size:16
Alignment explanation
Indices: 8503--8532 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8493 ATGTTGGACT
8503 CTTTTTC-ATTTCTTC
1 CTTTTTCTATTTCTTC
8518 CTTTTTCTATTTCTT
1 CTTTTTCTATTTCTT
8533 GGAGATCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (16 bp):
CTTTTTCTATTTCTTC
Found at i:11224 original size:31 final size:31
Alignment explanation
Indices: 11188--11247 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
11178 AAAATGGGTA
11188 GTATTTATATATCTTCATCCTTTGTTCCTGG
1 GTATTTATATATCTTCATCCTTTGTTCCTGG
11219 GTATTTATATATCTTCATCCTTTGTTCCT
1 GTATTTATATATCTTCATCCTTTGTTCCT
11248 CGTAGGCAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.17, C:0.20, G:0.10, T:0.53
Consensus pattern (31 bp):
GTATTTATATATCTTCATCCTTTGTTCCTGG
Found at i:19342 original size:13 final size:13
Alignment explanation
Indices: 19324--19348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19314 GAAAGGCTAA
19324 TAATAATTATAAG
1 TAATAATTATAAG
19337 TAATAATTATAA
1 TAATAATTATAA
19349 CTTAACTCAA
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:0.04, T:0.40
Consensus pattern (13 bp):
TAATAATTATAAG
Found at i:20592 original size:74 final size:74
Alignment explanation
Indices: 20471--20623 Score: 288
Period size: 74 Copynumber: 2.1 Consensus size: 74
20461 AGGAAGACCC
*
20471 GCTAAATCGAAATGCTAATCTATAAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAA
1 GCTAAATCGAAACGCTAATCTATAAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAA
20536 CTATAAACT
66 CTATAAACT
20545 GCTAAATCGAAACGCTAATCTATAAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAA
1 GCTAAATCGAAACGCTAATCTATAAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAA
20610 CTATAAACT
66 CTATAAACT
*
20619 ACTAA
1 GCTAA
20624 TCTATGAGCC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (74 bp):
GCTAAATCGAAACGCTAATCTATAAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAA
CTATAAACT
Found at i:20635 original size:61 final size:61
Alignment explanation
Indices: 20559--20680 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
20549 AATCGAAACG
*
20559 CTAATCTATAAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAACTATAAACTA
1 CTAATCTATAAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAACTAGAAACTA
*
20620 CTAATCTATGAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAACTAGAAACTA
1 CTAATCTATAAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAACTAGAAACTA
20681 TATCATAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.40, C:0.30, G:0.05, T:0.25
Consensus pattern (61 bp):
CTAATCTATAAGCCAACAAACCTCTTCTCCAAATAAATCTCTATGCCCAAACTAGAAACTA
Found at i:21586 original size:17 final size:17
Alignment explanation
Indices: 21544--21610 Score: 89
Period size: 17 Copynumber: 3.8 Consensus size: 17
21534 AGTGATAAGG
*
21544 TTCGTTCTTGTTGTTCTTC
1 TTCGTTC-T-TTGTTGTTC
21563 GTTCGTTCTTTGTTGTTC
1 -TTCGTTCTTTGTTGTTC
21581 TTCGTTCTTTGTTGTTC
1 TTCGTTCTTTGTTGTTC
*
21598 TTCGTTATTTGTT
1 TTCGTTCTTTGTT
21611 CCACAAAGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
17 29 0.64
18 8 0.18
19 1 0.02
20 7 0.16
ACGTcount: A:0.01, C:0.16, G:0.18, T:0.64
Consensus pattern (17 bp):
TTCGTTCTTTGTTGTTC
Found at i:26024 original size:53 final size:53
Alignment explanation
Indices: 25943--26047 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
25933 TAACATGCCC
* *
25943 CACTTTAACACGTCCCCTCACGTATAGCCCGGGACAACACCGAAACAGAACGA
1 CACTTTAACACGCCCCCTCACATATAGCCCGGGACAACACCGAAACAGAACGA
* *
25996 CACTTTAACACGCCCCCTCACATGTAGCCCGGGACAACACTGAAACAGAACG
1 CACTTTAACACGCCCCCTCACATATAGCCCGGGACAACACCGAAACAGAACG
26048 GGGCTACACG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.33, C:0.36, G:0.17, T:0.13
Consensus pattern (53 bp):
CACTTTAACACGCCCCCTCACATATAGCCCGGGACAACACCGAAACAGAACGA
Found at i:40223 original size:6 final size:6
Alignment explanation
Indices: 40212--40336 Score: 70
Period size: 6 Copynumber: 20.8 Consensus size: 6
40202 AGGGACAAAA
* * * * **
40212 TCAGGG TCAGGG TCAGGG CCAAGG CCAAGG TTGGGG TCAGGG TCAGGG
1 TCAGGG TCAGGG TCAGGG TCAGGG TCAGGG TCAGGG TCAGGG TCAGGG
* * *** * * * * * *
40260 TCAAGG ACAAAA CCAGGG TCAGGG TCAGGG TCAGGG CCAAGG CCAAGA
1 TCAGGG TCAGGG TCAGGG TCAGGG TCAGGG TCAGGG TCAGGG TCAGGG
* * *
40308 TCAGAG CCAGGG TCAAGG TCAGGG TCAGG
1 TCAGGG TCAGGG TCAGGG TCAGGG TCAGG
40337 ACACTAATTC
Statistics
Matches: 90, Mismatches: 29, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 90 1.00
ACGTcount: A:0.26, C:0.21, G:0.42, T:0.12
Consensus pattern (6 bp):
TCAGGG
Found at i:40223 original size:30 final size:30
Alignment explanation
Indices: 40183--40289 Score: 124
Period size: 30 Copynumber: 3.6 Consensus size: 30
40173 GGGCCAGCCC
* * *
40183 CAGGGCCAGGGTCAAGGCCAGGGACAAAAT
1 CAGGGTCAGGGTCAGGGCCAAGGACAAAAT
* **
40213 CAGGGTCAGGGTCAGGGCCAAGGCCAAGGT
1 CAGGGTCAGGGTCAGGGCCAAGGACAAAAT
** * *
40243 TGGGGTCAGGGTCAGGGTCAAGGACAAAAC
1 CAGGGTCAGGGTCAGGGCCAAGGACAAAAT
40273 CAGGGTCAGGGTCAGGG
1 CAGGGTCAGGGTCAGGG
40290 TCAGGGCCAA
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.27, C:0.21, G:0.42, T:0.10
Consensus pattern (30 bp):
CAGGGTCAGGGTCAGGGCCAAGGACAAAAT
Found at i:40252 original size:36 final size:32
Alignment explanation
Indices: 40212--40306 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 32
40202 AGGGACAAAA
40212 TCAGGGTCAGGGTCAGGGCCAAGGCCAAGGTTGGGG
1 TCAGGGTCAGGGTCAGGGCCAAGGCCAA----GGGG
* * **
40248 TCAGGGTCAGGGTCAAGGACAAAACC-A-GGG
1 TCAGGGTCAGGGTCAGGGCCAAGGCCAAGGGG
40278 TCAGGGTCAGGGTCAGGGCCAAGGCCAAG
1 TCAGGGTCAGGGTCAGGGCCAAGGCCAAG
40307 ATCAGAGCCA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
30 25 0.51
31 1 0.02
35 1 0.02
36 22 0.45
ACGTcount: A:0.25, C:0.21, G:0.42, T:0.12
Consensus pattern (32 bp):
TCAGGGTCAGGGTCAGGGCCAAGGCCAAGGGG
Found at i:40319 original size:36 final size:35
Alignment explanation
Indices: 40213--40331 Score: 113
Period size: 36 Copynumber: 3.5 Consensus size: 35
40203 GGGACAAAAT
* *
40213 CAGGGTCAGGGTCAGGGCCAAGGCCAAGGT---TG
1 CAGGGTCAGGGTCAGGGCCAAGGCCAAGATCAGAG
* * * * *
40245 --GGGTCAGGGTCAGGGTCAAGGACAAAACCAGGG
1 CAGGGTCAGGGTCAGGGCCAAGGCCAAGATCAGAG
40278 TCAGGGTCAGGGTCAGGGCCAAGGCCAAGATCAGAG
1 -CAGGGTCAGGGTCAGGGCCAAGGCCAAGATCAGAG
*
40314 CCAGGGTCAAGGTCAGGG
1 -CAGGGTCAGGGTCAGGG
40332 TCAGGACACT
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
30 23 0.34
33 1 0.01
36 44 0.65
ACGTcount: A:0.26, C:0.21, G:0.42, T:0.11
Consensus pattern (35 bp):
CAGGGTCAGGGTCAGGGCCAAGGCCAAGATCAGAG
Found at i:45664 original size:1 final size:1
Alignment explanation
Indices: 45658--45683 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
45648 AACATTATAG
45658 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
45684 CTCTGTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:56073 original size:17 final size:16
Alignment explanation
Indices: 56019--56069 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
56009 ATCACCCCCC
*
56019 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
56036 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
* *
56053 AGATCATCGGTGATCA
1 AGATCACCAGTGATCA
56069 A
1 A
56070 AGATTACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.10
17 26 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:57899 original size:16 final size:16
Alignment explanation
Indices: 57875--57905 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
57865 ATACAGCAAA
*
57875 AGAATAGAAATATCCC
1 AGAAGAGAAATATCCC
57891 AGAAGAGAAATATCC
1 AGAAGAGAAATATCC
57906 AAAATGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (16 bp):
AGAAGAGAAATATCCC
Found at i:61586 original size:25 final size:25
Alignment explanation
Indices: 61552--61601 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
61542 TTTAGCATTA
61552 ACTTTCCAGATCCTAGGTTCGAGGG
1 ACTTTCCAGATCCTAGGTTCGAGGG
61577 ACTTTCCAGATCCTAGGTTCGAGGG
1 ACTTTCCAGATCCTAGGTTCGAGGG
61602 CTTGTACAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (25 bp):
ACTTTCCAGATCCTAGGTTCGAGGG
Found at i:66284 original size:74 final size:73
Alignment explanation
Indices: 66195--66332 Score: 195
Period size: 74 Copynumber: 1.9 Consensus size: 73
66185 ACAGCAGGGG
* *
66195 CAAGGATTCTTTTATATACATGCACTTCAAATGAAAAAAAAAGGAAAATTTATAATTTGGCCCCC
1 CAAGAATTCTTTTATATACATGCACTTCAAATG-AAAAAAAAGGAAAATTTATAATATGGCCCCC
66260 CCAAATTGC
65 CCAAATTGC
* * * ** *
66269 CAAGAATTCTTTTATATATATGCATTTCAACTGAAAAAACTGGAAAATTTATAATATGGTCCCC
1 CAAGAATTCTTTTATATACATGCACTTCAAATGAAAAAAAAGGAAAATTTATAATATGGCCCCC
66333 TAAAATTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
73 27 0.48
74 29 0.52
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (73 bp):
CAAGAATTCTTTTATATACATGCACTTCAAATGAAAAAAAAGGAAAATTTATAATATGGCCCCCC
CAAATTGC
Found at i:67833 original size:2 final size:2
Alignment explanation
Indices: 67828--67869 Score: 52
Period size: 2 Copynumber: 21.0 Consensus size: 2
67818 TAGTAGTAAG
67828 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AGT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT
67870 GTTATATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 2 0.06
2 30 0.83
3 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68113 original size:11 final size:11
Alignment explanation
Indices: 68097--68138 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
68087 AAATAATTTA
68097 TTATATATATT
1 TTATATATATT
*
68108 TTATATATATC
1 TTATATATATT
* *
68119 ATAAATATATT
1 TTATATATATT
68130 TTATATATA
1 TTATATATA
68139 ATTGTATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATATATATT
Found at i:68385 original size:29 final size:30
Alignment explanation
Indices: 68352--68419 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
68342 CACCAACGGT
*
68352 CAAATAAGTCA-TTGAACT-TCAATTTTGGC
1 CAAATAAG-CACTTGAACTACCAATTTTGGC
68381 CAAATAAGCACTTGAACTACCAATTTTGGC
1 CAAATAAGCACTTGAACTACCAATTTTGGC
*
68411 CAGATAAGC
1 CAAATAAGC
68420 CTTTCTGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 2 0.06
29 15 0.43
30 18 0.51
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (30 bp):
CAAATAAGCACTTGAACTACCAATTTTGGC
Found at i:68523 original size:21 final size:20
Alignment explanation
Indices: 68488--68527 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
68478 AGTTTAGGGT
68488 AAATTTTTTGGAAAAGAAAAG
1 AAATTTTTTGGAAAA-AAAAG
**
68509 AAATTTTTTTTAAAAAAAA
1 AAATTTTTTGGAAAAAAAA
68528 CCATAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (20 bp):
AAATTTTTTGGAAAAAAAAG
Found at i:70301 original size:14 final size:13
Alignment explanation
Indices: 70282--70320 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
70272 AAATTGTAAA
70282 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
70295 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
70309 ATTTAAAAAATT
1 ATTTAAAAAATT
70321 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:70529 original size:125 final size:127
Alignment explanation
Indices: 70306--70563 Score: 414
Period size: 125 Copynumber: 2.0 Consensus size: 127
70296 ATTTAAGAAA
70306 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGT---AATAAA
*
70371 ATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAA
63 AT--GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
70436 AG
126 AG
*
70438 TATATTTAAAAAATTCTAATATATATACGTTTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT
1 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTTAATTAAAATAGTAAAATGGTAATAAAAT
*
70501 -TATAATGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
65 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
70563 T
1 T
70564 TTAAACAATG
Statistics
Matches: 122, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
125 61 0.50
128 5 0.04
129 1 0.01
132 28 0.23
133 27 0.22
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAATAAAATG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:81745 original size:15 final size:15
Alignment explanation
Indices: 81727--81759 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
81717 ATAATTCTTC
81727 AGACACAGCTTGACA
1 AGACACAGCTTGACA
*
81742 AGACAGAGCTTGACA
1 AGACACAGCTTGACA
81757 AGA
1 AGA
81760 AGGAATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.12
Consensus pattern (15 bp):
AGACACAGCTTGACA
Found at i:84773 original size:33 final size:35
Alignment explanation
Indices: 84714--84779 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
84704 GTAAGGCAAT
*
84714 GCCAAATTAAAGAAACAGACAGAAAATGATGGTTG
1 GCCAAATTAAAGAAAAAGACAGAAAATGATGGTTG
*
84749 GCCAAA-TAAA-AAAAAGATAGAAAATGATGGT
1 GCCAAATTAAAGAAAAAGACAGAAAATGATGGT
84780 ACAGTGAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 19 0.66
34 4 0.14
35 6 0.21
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (35 bp):
GCCAAATTAAAGAAAAAGACAGAAAATGATGGTTG
Found at i:89485 original size:29 final size:29
Alignment explanation
Indices: 89448--89575 Score: 247
Period size: 29 Copynumber: 4.4 Consensus size: 29
89438 ATTGGGACAA
*
89448 TTCAAATAAGTTGCCATGAAATGTAATTC
1 TTCAAATAAGTTGCCATGAAATGCAATTC
89477 TTCAAATAAGTTGCCATGAAATGCAATTC
1 TTCAAATAAGTTGCCATGAAATGCAATTC
89506 TTCAAATAAGTTGCCATGAAATGCAATTC
1 TTCAAATAAGTTGCCATGAAATGCAATTC
89535 TTCAAATAAGTTGCCATGAAATGCAATTC
1 TTCAAATAAGTTGCCATGAAATGCAATTC
89564 TTCAAATAAGTT
1 TTCAAATAAGTT
89576 TAGCTAATAC
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 98 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (29 bp):
TTCAAATAAGTTGCCATGAAATGCAATTC
Found at i:95631 original size:3 final size:3
Alignment explanation
Indices: 95623--95658 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
95613 CATCTATTAA
*
95623 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
95659 CTTTCTCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:101691 original size:4 final size:4
Alignment explanation
Indices: 101682--101706 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
101672 GTATAAGTAA
101682 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
101707 GACATCTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:104238 original size:2 final size:2
Alignment explanation
Indices: 104231--104275 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
104221 TGAGTGAGTA
104231 AG AG AG AG AG A- AG AG AG AG AG A- AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
104271 AG AG A
1 AG AG A
104276 TCATAAATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:104246 original size:11 final size:11
Alignment explanation
Indices: 104230--104275 Score: 83
Period size: 11 Copynumber: 4.1 Consensus size: 11
104220 GTGAGTGAGT
104230 AAGAGAGAGAG
1 AAGAGAGAGAG
104241 AAGAGAGAGAG
1 AAGAGAGAGAG
104252 AAGAGAGAGAG
1 AAGAGAGAGAG
104263 AGAGAGAGAGAG
1 A-AGAGAGAGAG
104275 A
1 A
104276 TCATAAATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 23 0.68
12 11 0.32
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (11 bp):
AAGAGAGAGAG
Found at i:112224 original size:21 final size:21
Alignment explanation
Indices: 112199--112240 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
112189 TTTTTTTTTT
112199 AAATAATTTTTTTAAAAAAAA
1 AAATAATTTTTTTAAAAAAAA
*
112220 AAATAATTTTTTTATAAAAAA
1 AAATAATTTTTTTAAAAAAAA
112241 TATGATGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATAATTTTTTTAAAAAAAA
Found at i:157406 original size:35 final size:36
Alignment explanation
Indices: 157360--157436 Score: 138
Period size: 35 Copynumber: 2.1 Consensus size: 36
157350 TAGGATTCAC
157360 TTATACTCGGTGTAAGTTATA-TTTTTTTTTCTCTT
1 TTATACTCGGTGTAAGTTATACTTTTTTTTTCTCTT
157395 TTATACTCGGTGTAAGTTATACTTTTTTTTTTCTCTT
1 TTATACTCGGTGTAAGTTATAC-TTTTTTTTTCTCTT
157432 TTATA
1 TTATA
157437 TCTTTTTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 21 0.52
37 19 0.47
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.60
Consensus pattern (36 bp):
TTATACTCGGTGTAAGTTATACTTTTTTTTTCTCTT
Found at i:163904 original size:22 final size:22
Alignment explanation
Indices: 163876--163918 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
163866 ATCATGGTAT
163876 ATAAAGCATATAAACTCCAAAA
1 ATAAAGCATATAAACTCCAAAA
163898 ATAAAGCATATAAACTCCAAA
1 ATAAAGCATATAAACTCCAAA
163919 CACTCTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (22 bp):
ATAAAGCATATAAACTCCAAAA
Found at i:166459 original size:30 final size:29
Alignment explanation
Indices: 166403--166470 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
166393 CATTTGGATG
*
166403 TTTTGCCCCTTGAACTTCAGTTTTGGACA
1 TTTTGCCCCTTGAACTTCAATTTTGGACA
**
166432 TTTTGCCGCC-TGAACTCTCAATTTTGGATG
1 TTTTGCC-CCTTGAACT-TCAATTTTGGACA
166462 TTTTGCCCC
1 TTTTGCCCC
166471 CTCTCAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (29 bp):
TTTTGCCCCTTGAACTTCAATTTTGGACA
Found at i:166641 original size:29 final size:30
Alignment explanation
Indices: 166579--166656 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
166569 ATCGTTTGAG
* *
166579 AGGGGGCAAAATGCCCAAAATTGAGAGTTT
1 AGGGGGCAAAATGTCCAAAATTGAGAGTTC
166609 AGGGGGCAAAATGTCCAAAATTGA-AGTTC
1 AGGGGGCAAAATGTCCAAAATTGAGAGTTC
*
166638 AGGGGGCAAAACGTCCAAA
1 AGGGGGCAAAATGTCCAAA
166657 CGCTACAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 22 0.49
30 23 0.51
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.17
Consensus pattern (30 bp):
AGGGGGCAAAATGTCCAAAATTGAGAGTTC
Found at i:170672 original size:1 final size:1
Alignment explanation
Indices: 170666--170692 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
170656 CTTCTTCTTC
170666 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
170693 AAATTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:173929 original size:6 final size:6
Alignment explanation
Indices: 173918--173945 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
173908 TCTTCAACAT
173918 ATATAC ATATAC ATATAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATAT
173946 GAAATGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:180024 original size:76 final size:76
Alignment explanation
Indices: 179901--180227 Score: 521
Period size: 76 Copynumber: 4.3 Consensus size: 76
179891 CGGTCTCACT
* ** * * * *
179901 GGAGACGTTCGTTTCT-TTTGTTTTTATACGGGGACACCTGGGCTGGTGTTCGACCGTTTGTGAC
1 GGAGACGATCGTTT-TGTTTGTTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGTTCGCGAC
*
179965 GAAAGTCTCTAA
65 GAAAGTCTCAAA
*
179977 GGAGACGATCGTTTTGTTTGTTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGTTCGCAACG
1 GGAGACGATCGTTTTGTTTGTTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGTTCGCGACG
*
180042 AAAGCCTCAAA
66 AAAGTCTCAAA
* *
180053 GGAGACGATCGTTTTGTTTATTTTTATACGGGGACACCAAGTTTGGTGTTCGGCCGTTCGCGACG
1 GGAGACGATCGTTTTGTTTGTTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGTTCGCGACG
180118 AAAGTCTCAAA
66 AAAGTCTCAAA
180129 GGAGACGATCGTTTTGTTTGTTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGTTCGCGACG
1 GGAGACGATCGTTTTGTTTGTTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGTTCGCGACG
180194 AAAGTCTCAAA
66 AAAGTCTCAAA
*
180205 GGAGACGATCGTTTTCTTTGTTT
1 GGAGACGATCGTTTTGTTTGTTT
180228 CTTCAAAATA
Statistics
Matches: 233, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
75 1 0.00
76 232 1.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (76 bp):
GGAGACGATCGTTTTGTTTGTTTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGTTCGCGACG
AAAGTCTCAAA
Done.