Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011930.1 Corchorus capsularis cultivar CVL-1 contig11951, 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: 84150
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:14095 original size:50 final size:50
Alignment explanation
Indices: 14041--14151 Score: 159
Period size: 50 Copynumber: 2.2 Consensus size: 50
14031 CGCATCAGAA
* * *
14041 ACAGTTCGAAGGATAGGCGGAAGACGATCCTTTTAATATTAAATTGGAAG
1 ACAGTTCGAAGGATAAGCGGAAGACAATCCTTTTAAGATTAAATTGGAAG
* * *
14091 ACAGTTCAAAGGATAAGTGGAAGACAATCCTTTTAAGATTGAATTGGAAG
1 ACAGTTCGAAGGATAAGCGGAAGACAATCCTTTTAAGATTAAATTGGAAG
*
14141 ACAATTCGAAG
1 ACAGTTCGAAG
14152 AAGTTGATTC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (50 bp):
ACAGTTCGAAGGATAAGCGGAAGACAATCCTTTTAAGATTAAATTGGAAG
Found at i:16114 original size:16 final size:16
Alignment explanation
Indices: 16093--16125 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16083 AATCCTACAT
16093 GAACAAGCAGACAAAA
1 GAACAAGCAGACAAAA
16109 GAACAAGCAGACAAAA
1 GAACAAGCAGACAAAA
16125 G
1 G
16126 GAGAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.18, G:0.21, T:0.00
Consensus pattern (16 bp):
GAACAAGCAGACAAAA
Found at i:18303 original size:34 final size:34
Alignment explanation
Indices: 18264--18395 Score: 131
Period size: 34 Copynumber: 3.8 Consensus size: 34
18254 AGTCAAGGTA
*
18264 ATAGTAATCAGTAAATCAATAATCAAGTAAAAAG
1 ATAGTAATCAGTAAATCAATAATTAAGTAAAAAG
** * *
18298 ATAGTAATCAGTAAATTGATAATTAAG-AGTCAAGG
1 ATAGTAATCAGTAAATCAATAATTAAGTA--AAAAG
* * *
18333 TAATGGTAACCAGTAAATCAGTAATTAAGTAAAAAG
1 --ATAGTAATCAGTAAATCAATAATTAAGTAAAAAG
**
18369 ATAGTAATCAGTAAATTGATAATTAAG
1 ATAGTAATCAGTAAATCAATAATTAAG
18396 AGTCAAGGTA
Statistics
Matches: 76, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
33 1 0.01
34 46 0.61
35 3 0.04
36 3 0.04
37 22 0.29
38 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (34 bp):
ATAGTAATCAGTAAATCAATAATTAAGTAAAAAG
Found at i:18318 original size:18 final size:17
Alignment explanation
Indices: 18264--18318 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
18254 AGTCAAGGTA
*
18264 ATAGTAATCAGTAAATC
1 ATAGTAATCAGTAAATG
*
18281 A-A-TAATCAAGTAAAAAG
1 ATAGTAATC-AGT-AAATG
18298 ATAGTAATCAGTAAATTG
1 ATAGTAATCAGTAAA-TG
18316 ATA
1 ATA
18319 ATTAAGAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
15 5 0.17
16 4 0.13
17 8 0.27
18 8 0.27
19 5 0.17
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (17 bp):
ATAGTAATCAGTAAATG
Found at i:18334 original size:71 final size:71
Alignment explanation
Indices: 18252--18486 Score: 294
Period size: 71 Copynumber: 3.3 Consensus size: 71
18242 GAAATTAATC
18252 AGAGTCAAGGTAATAGTAATCAGTAAATCAATAATCAAGTAAAAAGATAGTAATCAGTAAATTGA
1 AGAGTCAAGGTAATAGTAATCAGTAAATCAATAATCAAGTAAAAAGATAGTAATCAGTAAATTGA
18317 TAATTA
66 TAATTA
* * * *
18323 AGAGTCAAGGTAATGGTAACCAGTAAATCAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGA
1 AGAGTCAAGGTAATAGTAATCAGTAAATCAATAATCAAGTAAAAAGATAGTAATCAGTAAATTGA
18388 TAATTA
66 TAATTA
* * * * * *
18394 AGAGTCAAGGTAAGAGATTAATCAGTAATTAAAGAGTCTAGGT-AAAA-ATAGTAATCAGTAAAT
1 AGAGTCAAGGTAATAG--TAATCAGTAAATCAATAATC-AAGTAAAAAGATAGTAATCAGTAAAT
*
18457 CGATAATTA
63 TGATAATTA
* * *
18466 AAAGTTAAGGTGATCAGTAAT
1 AGAGTCAAGGTAAT-AGTAAT
18487 TAAGAGTCGA
Statistics
Matches: 141, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
71 85 0.60
72 34 0.24
73 19 0.13
74 3 0.02
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (71 bp):
AGAGTCAAGGTAATAGTAATCAGTAAATCAATAATCAAGTAAAAAGATAGTAATCAGTAAATTGA
TAATTA
Found at i:18454 original size:33 final size:31
Alignment explanation
Indices: 18388--18454 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
18378 AGTAAATTGA
*
18388 TAATTAAGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
*
18419 TAATTAAAGAGTCTAGGTAA-AAATAGTAATCAG
1 TAATT-AAGAGTCAAGGTAAGAAAT--TAATCAG
18452 TAA
1 TAA
18455 ATCGATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 8 0.26
32 13 0.42
33 10 0.32
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:18855 original size:26 final size:26
Alignment explanation
Indices: 18820--18977 Score: 86
Period size: 26 Copynumber: 6.1 Consensus size: 26
18810 AATTAGTTTT
18820 AAAGAGTAAGAAATGGTGA-TCAGTAAA
1 AAAG-GTAAGAAATGGT-ATTCAGTAAA
*
18847 AAAGGTAAGAAGTGGTATTCAGTAAA
1 AAAGGTAAGAAATGGTATTCAGTAAA
*
18873 AAGGGATAA-AAATGGTA---A--AAA
1 AAAGG-TAAGAAATGGTATTCAGTAAA
* *
18894 AGA-GTAA-AAATGGTATTAAGTAAAA
1 AAAGGTAAGAAATGGTATTCAGT-AAA
* *
18919 AAGGAGAGTAAAAAAATGGTAATTAAGT-AA
1 AA--AG-GT-AAGAAATGGT-ATTCAGTAAA
18949 AAAGAGTAA-AAAGTGGTATTCAGTAAA
1 AAAG-GTAAGAAA-TGGTATTCAGTAAA
18976 AA
1 AA
18978 CAGAAAGAAA
Statistics
Matches: 107, Mismatches: 7, Indels: 34
0.72 0.05 0.23
Matches are distributed among these distances:
19 11 0.10
20 1 0.01
21 4 0.04
22 1 0.01
23 1 0.01
25 5 0.05
26 39 0.36
27 18 0.17
28 5 0.05
29 2 0.02
30 6 0.06
31 7 0.07
32 7 0.07
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.20
Consensus pattern (26 bp):
AAAGGTAAGAAATGGTATTCAGTAAA
Found at i:18917 original size:16 final size:16
Alignment explanation
Indices: 18896--18951 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 16
18886 GGTAAAAAAG
18896 AGTAAAAATGGTATTA
1 AGTAAAAATGGTATTA
* * *
18912 AGTAAAAAAGGAGAGTA
1 AGTAAAAATGG-TATTA
18929 A--AAAAATGGTAATTA
1 AGTAAAAATGGT-ATTA
18944 AGTAAAAA
1 AGTAAAAA
18952 GAGTAAAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
15 11 0.37
16 10 0.33
17 9 0.30
ACGTcount: A:0.59, C:0.00, G:0.20, T:0.21
Consensus pattern (16 bp):
AGTAAAAATGGTATTA
Found at i:18920 original size:28 final size:28
Alignment explanation
Indices: 18889--19023 Score: 100
Period size: 28 Copynumber: 4.7 Consensus size: 28
18879 TAAAAATGGT
18889 AAAAAAGAGTAAAAATGGTATTAAGTAA
1 AAAAAAGAGTAAAAATGGTATTAAGTAA
*
18917 AAAAGGAGAGTAAAAAAATGGTAATTAAGT--
1 AAAA-AAGAGT--AAAAATGGT-ATTAAGTAA
*
18947 -AAAAAGAGTAAAAAGTGGTATTCAGTAA
1 AAAAAAGAGTAAAAA-TGGTATTAAGTAA
** * *
18975 AAACAGAA-AG-AAAAGGGGTAATCAGTAA
1 AAA-A-AAGAGTAAAAATGGTATTAAGTAA
*
19003 AAAAAAGGGTAAAATATGGTA
1 AAAAAAGAGTAAAA-ATGGTA
19024 ATCAGTACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 25
0.71 0.08 0.21
Matches are distributed among these distances:
26 13 0.15
27 6 0.07
28 27 0.32
29 18 0.21
30 3 0.04
31 11 0.13
32 7 0.08
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.19
Consensus pattern (28 bp):
AAAAAAGAGTAAAAATGGTATTAAGTAA
Found at i:19659 original size:31 final size:31
Alignment explanation
Indices: 19621--19699 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 31
19611 CCGAATTATG
*
19621 ATATATATAATATATTTTTATATT-TTATGTT
1 ATATATATAATATATTTTGATATTCTTAT-TT
*
19652 ATATATATAATTATATATCTGATATTCTTATTT
1 ATATATATAA-TATAT-TTTGATATTCTTATTT
19685 ATATAT-TAATA-ATTT
1 ATATATATAATATATTT
19700 CAAAATACCA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 1 0.02
30 2 0.05
31 12 0.29
32 8 0.19
33 15 0.36
34 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (31 bp):
ATATATATAATATATTTTGATATTCTTATTT
Found at i:23007 original size:30 final size:30
Alignment explanation
Indices: 22971--23035 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
22961 GGGGATGATC
22971 AAGGATTGCAAGGAAGCATGGACAAGCTTA
1 AAGGATTGCAAGGAAGCATGGACAAGCTTA
* *
23001 AAGGATTGCAAGGAAGTATGGACAAGTTTA
1 AAGGATTGCAAGGAAGCATGGACAAGCTTA
23031 AAGGA
1 AAGGA
23036 GAGGATGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.31, T:0.18
Consensus pattern (30 bp):
AAGGATTGCAAGGAAGCATGGACAAGCTTA
Found at i:28298 original size:30 final size:30
Alignment explanation
Indices: 28264--28323 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
28254 AAAGGAGAGG
*
28264 ATGGAATCGCAAAGTCTCATGAAGATGCCA
1 ATGGAATCGCAAAGCCTCATGAAGATGCCA
*
28294 ATGGAATCGCAAAGCCTCATGGAGATGCCA
1 ATGGAATCGCAAAGCCTCATGAAGATGCCA
28324 TTATAAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (30 bp):
ATGGAATCGCAAAGCCTCATGAAGATGCCA
Found at i:29528 original size:43 final size:45
Alignment explanation
Indices: 29451--29535 Score: 129
Period size: 43 Copynumber: 1.9 Consensus size: 45
29441 AACATTACAT
* * *
29451 TCATTTCTTATCTTTTACTATTTTATTCTATAAACTATAATTCTG
1 TCATTTATTATCTTTTACTAGTTTAATCTATAAACTATAATTCTG
29496 TCATTTATT-TCTTTTACT-GTTTAATCTATAAACTATAATT
1 TCATTTATTATCTTTTACTAGTTTAATCTATAAACTATAATT
29536 ATGTTGCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 20 0.54
44 9 0.24
45 8 0.22
ACGTcount: A:0.28, C:0.14, G:0.02, T:0.55
Consensus pattern (45 bp):
TCATTTATTATCTTTTACTAGTTTAATCTATAAACTATAATTCTG
Found at i:30092 original size:11 final size:11
Alignment explanation
Indices: 30052--30099 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
30042 TGACTATATG
30052 ATATAGTCTAT
1 ATATAGTCTAT
* * *
30063 ATATAATATCT
1 ATATAGTCTAT
*
30074 CT-TAGTCTAT
1 ATATAGTCTAT
30084 ATATAGTCTAT
1 ATATAGTCTAT
30095 ATATA
1 ATATA
30100 AAATATGCTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 6 0.21
11 22 0.79
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (11 bp):
ATATAGTCTAT
Found at i:34312 original size:2 final size:2
Alignment explanation
Indices: 34299--34344 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
34289 TCGTTTGGCC
* *
34299 AT AT AA AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34341 -T AT A
1 AT AT A
34345 GTAATAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:35347 original size:31 final size:30
Alignment explanation
Indices: 35292--35364 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
35282 GCATGCCACA
*
35292 TGTCACTTTTGGTACATGTAGCGTGACACG
1 TGTCACTTTTTGTACATGTAGCGTGACACG
* * *
35322 TGTCACCTTTTTGTATATGTGGCGTGCCACG
1 TGTCA-CTTTTTGTACATGTAGCGTGACACG
35353 TGTCA-TTTTTGT
1 TGTCACTTTTTGT
35365 TCACGTGGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 7 0.18
30 5 0.13
31 26 0.68
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (30 bp):
TGTCACTTTTTGTACATGTAGCGTGACACG
Found at i:38244 original size:14 final size:14
Alignment explanation
Indices: 38225--38254 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38215 TGAAAATAGG
*
38225 ATTATTATTCTATT
1 ATTATTATTATATT
38239 ATTATTATTATATT
1 ATTATTATTATATT
38253 AT
1 AT
38255 CACAAGTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:45669 original size:31 final size:31
Alignment explanation
Indices: 45631--45692 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
45621 CGACTAAACG
45631 TGCTAATTTAAATCTTAATCTTGATAATTTT
1 TGCTAATTTAAATCTTAATCTTGATAATTTT
45662 TGCTAATTTAAATCTTAATCTTGATAATTTT
1 TGCTAATTTAAATCTTAATCTTGATAATTTT
45693 ATTATTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (31 bp):
TGCTAATTTAAATCTTAATCTTGATAATTTT
Found at i:47415 original size:17 final size:16
Alignment explanation
Indices: 47362--47411 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
47352 TCACCCCCCT
47362 GATCACCAGTGATCTAA
1 GATCACCAGTGATC-AA
47379 GATCACCAGTGATGCAA
1 GATCACCAGTGAT-CAA
**
47396 GATCACTGGTGATCAA
1 GATCACCAGTGATCAA
47412 AGATTACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 26 0.87
18 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
GATCACCAGTGATCAA
Found at i:51646 original size:21 final size:20
Alignment explanation
Indices: 51622--51660 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
51612 TTATTAATAC
*
51622 TTAGTTACAAATCAATAATGT
1 TTAGTCACAAAT-AATAATGT
*
51643 TTAGTCCCAAATAATAAT
1 TTAGTCACAAATAATAAT
51661 ATTTGACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (20 bp):
TTAGTCACAAATAATAATGT
Found at i:55210 original size:39 final size:38
Alignment explanation
Indices: 55165--55268 Score: 129
Period size: 39 Copynumber: 2.7 Consensus size: 38
55155 AAATTTCCCT
* *
55165 TGTGTTATATGTGTTTAGGGACTTT-AGTATAGATGCCTC
1 TGTGTTATATGTGTTT-GGGACTTTGAG-AGAGATGCCCC
*
55204 TGTGTTATATGTGTTTGAGGACTTTGAGAGAGTTGCCCC
1 TGTGTTATATGTGTTTG-GGACTTTGAGAGAGATGCCCC
*
55243 TGTGTTATGTGTGTTTGGGGACTTTG
1 TGTGTTATATGTGTTT-GGGACTTTG
55269 GGGAGAGAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
38 1 0.02
39 54 0.93
40 3 0.05
ACGTcount: A:0.16, C:0.10, G:0.31, T:0.43
Consensus pattern (38 bp):
TGTGTTATATGTGTTTGGGACTTTGAGAGAGATGCCCC
Found at i:57407 original size:20 final size:20
Alignment explanation
Indices: 57382--57419 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
57372 GCCATGCTTC
57382 TGTCTCTGCCGCAACTATAT
1 TGTCTCTGCCGCAACTATAT
57402 TGTCTCTGCCGCAACTAT
1 TGTCTCTGCCGCAACTAT
57420 GACACTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (20 bp):
TGTCTCTGCCGCAACTATAT
Found at i:59016 original size:35 final size:35
Alignment explanation
Indices: 58977--59105 Score: 114
Period size: 35 Copynumber: 3.7 Consensus size: 35
58967 TGTTGAAGCC
* *
58977 CCCAAGTATTGAATGAAGAATGATTTGTTGGAGTA
1 CCCAAGTATTGAATGAAGAAGGAGTTGTTGGAGTA
* * * *
59012 CCCAACTGTTGAATGATGAAGGAGTTGTTGGAGTC
1 CCCAAGTATTGAATGAAGAAGGAGTTGTTGGAGTA
* * * * * * * *
59047 CCCAAGTGTTAAACGATGAAGGGGTTGCTGGTGTC
1 CCCAAGTATTGAATGAAGAAGGAGTTGTTGGAGTA
* *
59082 CCCAAGTGTTGAATGAGGAAGGAG
1 CCCAAGTATTGAATGAAGAAGGAG
59106 CTTTAATCTT
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (35 bp):
CCCAAGTATTGAATGAAGAAGGAGTTGTTGGAGTA
Found at i:63032 original size:39 final size:39
Alignment explanation
Indices: 62891--63033 Score: 207
Period size: 39 Copynumber: 3.7 Consensus size: 39
62881 AAATTTCCCT
* * * *
62891 TGTGTTATATGTGTTTAGGGACTTT-AGTATAGATGCCTC
1 TGTGTTATATGTGTTTGGGGACTTTGAG-AGAGTTGCCCC
* * *
62930 TGAGTTATATGTGTTTGAGGACATTGAGAGAGTTGCCCC
1 TGTGTTATATGTGTTTGGGGACTTTGAGAGAGTTGCCCC
62969 TGTGTTATATGTGTTTGGGGACTTTGAGAGAGTTGCCCC
1 TGTGTTATATGTGTTTGGGGACTTTGAGAGAGTTGCCCC
63008 TGTGTTATATGTGTTTGGGGACTTTG
1 TGTGTTATATGTGTTTGGGGACTTTG
63034 GGGAGAGAGA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
39 91 0.98
40 2 0.02
ACGTcount: A:0.18, C:0.10, G:0.31, T:0.41
Consensus pattern (39 bp):
TGTGTTATATGTGTTTGGGGACTTTGAGAGAGTTGCCCC
Found at i:67086 original size:21 final size:21
Alignment explanation
Indices: 67061--67101 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
67051 ACAATTTATG
* *
67061 AGTGTTCAACAGCAGCAAATA
1 AGTGTTCAACAACAACAAATA
67082 AGTGTTCAACAACAACAAAT
1 AGTGTTCAACAACAACAAAT
67102 CTGTGCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (21 bp):
AGTGTTCAACAACAACAAATA
Found at i:70058 original size:20 final size:21
Alignment explanation
Indices: 70033--70080 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
70023 TAAAATTATC
* *
70033 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
70053 AATTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGCAAAGTA
70074 AATTAAA
1 AATTAAA
70081 TCTAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:82065 original size:21 final size:19
Alignment explanation
Indices: 82033--82071 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
82023 CAATCAAGCA
82033 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
82052 AATCATAGCATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
82072 ATGAGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
AATCAAGATTCAAAGCATC
Found at i:83877 original size:13 final size:13
Alignment explanation
Indices: 83831--83878 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
83821 TATCATTTTT
83831 TCTCTTTTCTTAC
1 TCTCTTTTCTTAC
* *
83844 TCT-TTTTACTAAT
1 TCTCTTTT-CTTAC
83857 TACTCTTTTCTTAC
1 T-CTCTTTTCTTAC
83871 TCTCTTTT
1 TCTCTTTT
83879 ATTTATTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 4 0.14
13 14 0.50
14 6 0.21
15 4 0.14
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCTTTTCTTAC
Found at i:83893 original size:29 final size:28
Alignment explanation
Indices: 83834--83906 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
83824 CATTTTTTCT
*
83834 CTTTTCTTACTCT-TTTTACTAATTACT
1 CTTTTCTTACTCTCTTTTACTAATTACA
* *
83861 CTTTTCTTACTCTCTTTTATTTATTACCA
1 CTTTTCTTACTCTCTTTTACTAATTA-CA
83890 C-TTT-TTACTCTTCTTTT
1 CTTTTCTTACTC-TCTTTT
83907 TTCTTATACT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 19 0.47
28 19 0.47
29 2 0.05
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (28 bp):
CTTTTCTTACTCTCTTTTACTAATTACA
Found at i:84042 original size:35 final size:36
Alignment explanation
Indices: 84003--84150 Score: 174
Period size: 35 Copynumber: 3.9 Consensus size: 36
83993 CACTTTGCTC
*
84003 TTACTGATTACTGTTTTACTC-TTACTGATTACCTT
1 TTACTGATTACTATTTTACTCTTTACTGATTACCTT
*
84038 TTACTGATTACTATTTTACTCTTTGCTGA-TACCTT
1 TTACTGATTACTATTTTACTCTTTACTGATTACCTT
*
84073 CTACTGATTACTATTTTACTCTTTACTGATTACCTTCTTACTTT
1 TTACTGATTACTATTTTACTCTTTACTGATTA----C---C-TT
*
84117 TTACTGATTACTATTTTACTCCTTACTGATTACC
1 TTACTGATTACTATTTTACTCTTTACTGATTACC
Statistics
Matches: 97, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
35 53 0.55
36 8 0.08
37 1 0.01
40 2 0.02
43 1 0.01
44 32 0.33
ACGTcount: A:0.21, C:0.22, G:0.07, T:0.51
Consensus pattern (36 bp):
TTACTGATTACTATTTTACTCTTTACTGATTACCTT
Found at i:84102 original size:22 final size:22
Alignment explanation
Indices: 84074--84149 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
84064 TGATACCTTC
84074 TACTGATTACTATTTTACTCTT
1 TACTGATTACTATTTTACTCTT
* *
84096 TACTGATTACCT-TCTTACTTTT
1 TACTGATTA-CTATTTTACTCTT
*
84118 TACTGATTACTATTTTACTCCT
1 TACTGATTACTATTTTACTCTT
84140 TACTGATTAC
1 TACTGATTAC
84150 C
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 2 0.04
22 43 0.91
23 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.51
Consensus pattern (22 bp):
TACTGATTACTATTTTACTCTT
Found at i:84142 original size:15 final size:15
Alignment explanation
Indices: 84080--84143 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
84070 CTTCTACTGA
*
84080 TTACTATTTTACTCT
1 TTACTATTTTACTCC
*
84095 TTACTGA--TTACCTTC
1 TTACT-ATTTTA-CTCC
**
84110 TTACT-TTTTACTGA
1 TTACTATTTTACTCC
84124 TTACTATTTTACTCC
1 TTACTATTTTACTCC
84139 TTACT
1 TTACT
84144 GATTACC
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
14 10 0.26
15 27 0.71
16 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.55
Consensus pattern (15 bp):
TTACTATTTTACTCC
Done.