Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009557.1 Corchorus capsularis cultivar CVL-1 contig09578, 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: 89109
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:28 original size:16 final size:16
Alignment explanation
Indices: 4--89 Score: 70
Period size: 16 Copynumber: 5.4 Consensus size: 16
1 CAG
*
4 ACCCAAATTAACCCGA
1 ACCCGAATTAACCCGA
*
20 ACCCGAATTAACCTG-
1 ACCCGAATTAACCCGA
* *
35 ACCCAAATCCAACCCGA
1 ACCCGAAT-TAACCCGA
* *
52 ACCCGACTCAAGCCCGA
1 ACCCGAATTAA-CCCGA
69 ACCCG-A-TAACCCGA
1 ACCCGAATTAACCCGA
*
83 GCCCGAA
1 ACCCGAA
90 CCCAACTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
14 9 0.16
15 10 0.18
16 21 0.38
17 16 0.29
ACGTcount: A:0.36, C:0.42, G:0.13, T:0.09
Consensus pattern (16 bp):
ACCCGAATTAACCCGA
Found at i:258 original size:19 final size:17
Alignment explanation
Indices: 212--244 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
202 TCCACAAACC
212 AAAACAAAAAAAAATAA
1 AAAACAAAAAAAAATAA
229 AAAACAAAAAAAAATA
1 AAAACAAAAAAAAATA
245 TCATAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAACAAAAAAAAATAA
Found at i:331 original size:58 final size:62
Alignment explanation
Indices: 236--351 Score: 188
Period size: 58 Copynumber: 1.9 Consensus size: 62
226 TAAAAAACAA
236 AAAAAAATATCATAAAGAAAAAAGTAAAGAAGAAGGAAGAATA-AGAAAGTTCCCAATGGATT
1 AAAAAAATATCATAAAGAAAAAAGTAAAGAAGAAGGAAGAA-AGAGAAAGTTCCCAATGGATT
298 AAAAAAA-ATCAT-AA-AAAAAA-TAAAGAAGAAGGAAGAAAGAGAAAGTTCCCAATG
1 AAAAAAATATCATAAAGAAAAAAGTAAAGAAGAAGGAAGAAAGAGAAAGTTCCCAATG
352 TGAATTATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
57 1 0.02
58 32 0.60
59 6 0.11
60 2 0.04
61 5 0.09
62 7 0.13
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.14
Consensus pattern (62 bp):
AAAAAAATATCATAAAGAAAAAAGTAAAGAAGAAGGAAGAAAGAGAAAGTTCCCAATGGATT
Found at i:2459 original size:110 final size:109
Alignment explanation
Indices: 2267--2469 Score: 338
Period size: 110 Copynumber: 1.9 Consensus size: 109
2257 TCTACTATCT
* *
2267 GTGTATGGTATGATTTTCTATTTTCCTTTTTCCAGATAAAATCTCCAAATTTATATATTTGTTGG
1 GTGTATGGTATAATTTTCTATTTTCCTTTTTCCAGATAAAATCTCCAAATTTATATATTTATTGG
*
2332 GTTTAAATGCTTTGGTTACAATTAGTATAGTACCTGTAGGGTTA
66 GTTTAAATGCTTTGGTTACAAGTAGTATAGTACCTGTAGGGTTA
2376 GTGTATGGTATAATTTT-TCATTTT-CTTTTTGCCCAGATAAAATCTCCAAATTTATATATTTAT
1 GTGTATGGTATAATTTTCT-ATTTTCCTTTTT--CCAGATAAAATCTCCAAATTTATATATTTAT
2439 TGGGTTTAAATGCTTTGGTTACAAGTAGTAT
63 TGGGTTTAAATGCTTTGGTTACAAGTAGTAT
2470 CATGTAGGGC
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
108 7 0.08
109 21 0.24
110 60 0.68
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (109 bp):
GTGTATGGTATAATTTTCTATTTTCCTTTTTCCAGATAAAATCTCCAAATTTATATATTTATTGG
GTTTAAATGCTTTGGTTACAAGTAGTATAGTACCTGTAGGGTTA
Found at i:3193 original size:236 final size:230
Alignment explanation
Indices: 2763--3208 Score: 594
Period size: 236 Copynumber: 1.9 Consensus size: 230
2753 GTTGTAGATG
2763 ATTTTACTTTATAATCTATGAGTTTAGTCAAAAAATTTCTCAAATAATGAATCACCTATTTGTTA
1 ATTTTACTTTATAATCTATGAGTTTAGTCAAAAAATTTCTCAAATAA-GAATCACCTATTTGTTA
* * * * *
2828 TCATTGAAATCTTTCTATTACAAAGAACACACATAAATAAAAGCAGAAAGGTGCTCCACATTCTT
65 TCATTGAAAACTTTCTATAACAAAAAACACAAATAAATAAAAGCAGAAAGGTGCTACACATTCTT
* * *
2893 CTTGTGACTTATTGAAAATATTTGAAACTCCAATAATCAATTGAATGTGAATGTCACAAAACAAA
130 CTTGAGACTTATGGAAAATATTTGAAACTCCAATAATCAACTGAATGTGAATGTCACAAAACAAA
2958 GATCTACATCTAGAACTTAGAACTTGGGTGTATATA
195 GATCTACATCTAGAACTTAGAACTTGGGTGTATATA
* * ** *
2994 ATTTTATTTTATAATCTATGAGTTTAGTCAAAAAGTTTCTCAAAT-A-AATTGCCTTTTTGTTAT
1 ATTTTACTTTATAATCTATGAGTTTAGTCAAAAAATTTCTCAAATAAGAATCACCTATTTGTTAT
* *
3057 CTTTGAAAACTTTCTATAACAAAAAAACACCCATAAATAAATAAAAGCGGAAAGGTGCTACACAT
66 CATTGAAAACTTTCTATAAC-AAAAAACA--C--AAATAAATAAAAGCAGAAAGGTGCTACACAT
* * *
3122 GATGCTTCTTGAGACTTATGGAGAATATTTGAAACTCTAATTAATCAACTGAAT-T-CATGTGCA
126 --T-CTTCTTGAGACTTATGGAAAATATTTGAAACTCCAA-TAATCAACTGAATGTGAATGT-CA
*
3185 CAAAACAAAGATCTACATTTAGAA
186 CAAAACAAAGATCTACATCTAGAA
3209 GCAGGGGGAA
Statistics
Matches: 186, Mismatches: 19, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
228 31 0.17
229 7 0.04
230 1 0.01
231 44 0.24
233 28 0.15
235 5 0.03
236 58 0.31
237 12 0.06
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (230 bp):
ATTTTACTTTATAATCTATGAGTTTAGTCAAAAAATTTCTCAAATAAGAATCACCTATTTGTTAT
CATTGAAAACTTTCTATAACAAAAAACACAAATAAATAAAAGCAGAAAGGTGCTACACATTCTTC
TTGAGACTTATGGAAAATATTTGAAACTCCAATAATCAACTGAATGTGAATGTCACAAAACAAAG
ATCTACATCTAGAACTTAGAACTTGGGTGTATATA
Found at i:4575 original size:32 final size:33
Alignment explanation
Indices: 4517--4587 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
4507 GGGAAACTTT
* *
4517 ATATTTTCCGATTGTACCCTTA-TTTTTAAACC
1 ATATTTTCCAATTGTACCCTTATTTTTTAAAAC
4549 ATATTTT-CAATTGTACCCTTATTTTTTTAAAAC
1 ATATTTTCCAATTGTACCCTTA-TTTTTTAAAAC
4582 ATATTT
1 ATATTT
4588 CTAAATTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 13 0.37
32 7 0.20
33 15 0.43
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.51
Consensus pattern (33 bp):
ATATTTTCCAATTGTACCCTTATTTTTTAAAAC
Found at i:4781 original size:36 final size:37
Alignment explanation
Indices: 4704--4794 Score: 123
Period size: 36 Copynumber: 2.5 Consensus size: 37
4694 AATTTGGCCT
4704 TTTGTTTCCAACGTCCTACTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTACTTAATTTTGCCTTTTGTC
** *
4741 TTTGTTTCCAATCGTTGTATTTAATTTTG-C-TTTGTC
1 TTTGTTTCCAA-CGTCCTACTTAATTTTGCCTTTTGTC
*
4777 TTTGTCTCCAACGTCCTA
1 TTTGTTTCCAACGTCCTA
4795 TTTGAGCTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 5 0.11
36 16 0.34
37 12 0.26
38 14 0.30
ACGTcount: A:0.14, C:0.22, G:0.12, T:0.52
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTACTTAATTTTGCCTTTTGTC
Found at i:6262 original size:44 final size:43
Alignment explanation
Indices: 6183--6269 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
6173 GTCTCTATGT
** *
6183 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCATAAGATGGTTACCAAAATTTCAT-AGGA
*
6227 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATAGGA
1 GGTTATCAAAATTTCATAAG-ATGGTTACCAAAATTTCATAGGA
6270 TCAGGTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAAGATGGTTACCAAAATTTCATAGGA
Found at i:6315 original size:23 final size:23
Alignment explanation
Indices: 6182--6315 Score: 96
Period size: 22 Copynumber: 5.9 Consensus size: 23
6172 TGTCTCTATG
* * *
6182 TGGTTATCAAAATTTCATAAG-A
1 TGGTTATTAAAATTTCATAGGTC
*
6204 TGGTTATTATAATTTCATGAGG--
1 TGGTTATTAAAATTTCAT-AGGTC
* * *
6226 AGGTTATCAAAATTTCATA-GTG
1 TGGTTATTAAAATTTCATAGGTC
**
6248 TGGTTACCAAAATTTCATAGGATC
1 TGGTTATTAAAATTTCATAGG-TC
* * * *
6272 AGGTTATTAAAATCTCTTAGGTT
1 TGGTTATTAAAATTTCATAGGTC
*
6295 TGGTTATTGAAATTTCATAGG
1 TGGTTATTAAAATTTCATAGG
6316 GTGGTTAATT
Statistics
Matches: 88, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 48 0.55
23 21 0.24
24 17 0.19
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (23 bp):
TGGTTATTAAAATTTCATAGGTC
Found at i:6403 original size:22 final size:21
Alignment explanation
Indices: 6358--6497 Score: 113
Period size: 22 Copynumber: 6.4 Consensus size: 21
6348 ATCAAAGAGA
**
6358 TTATGAAAATTTCATAACGAGG
1 TTAT-AAAATTTCATAGTGAGG
*
6380 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAGTGAGG
*
6402 TTAACAAAATTTCATTAG-GAGG
1 TT-ATAAAATTTCA-TAGTGAGG
* * *
6424 TTACTAATATTTCATGGGGAGG
1 TTA-TAAAATTTCATAGTGAGG
* *
6446 TTATCAAAATTTTATAGTGTGG
1 TTAT-AAAATTTCATAGTGAGG
6468 TTATCAAAATTTCATA-TGAAGG
1 TTAT-AAAATTTCATAGTG-AGG
6490 TTATAAAA
1 TTATAAAA
6498 GTCTCAATTT
Statistics
Matches: 96, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
21 12 0.12
22 78 0.81
23 6 0.06
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:6572 original size:22 final size:22
Alignment explanation
Indices: 6537--6721 Score: 112
Period size: 22 Copynumber: 8.4 Consensus size: 22
6527 TGATAGAAGG
*
6537 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGAGTGA
*
6558 TTATCGAAATTTCATAGAGATCGGA
1 TTATCAAAATTTCATAGAG-T--GA
***
6583 TTATCAAAATTT-ATAGAAAAA
1 TTATCAAAATTTCATAGAGTGA
*
6604 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAG-TGA
*
6626 TTATCAAAATTT--TAAAGTGA
1 TTATCAAAATTTCATAGAGTGA
*
6646 GGTTATCAAAATTACATA-ATGTGA
1 --TTATCAAAATTTCATAGA-GTGA
* * * *
6670 TTATCAGAATTTCCTAGAGGGG
1 TTATCAAAATTTCATAGAGTGA
* * * * *
6692 TCAACAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGAGTGA
6714 TTATCAAA
1 TTATCAAA
6722 TTTTTAAAAT
Statistics
Matches: 126, Mismatches: 25, Indels: 25
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.02
20 3 0.02
21 18 0.14
22 76 0.60
23 3 0.02
24 11 0.09
25 13 0.10
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:6970 original size:22 final size:22
Alignment explanation
Indices: 6844--7312 Score: 190
Period size: 22 Copynumber: 21.5 Consensus size: 22
6834 TCAAAATTCC
*
6844 AGGGAGGATATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
***
6866 ATAAAGGTTATCAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** *
6888 AGTTTA-GTTTTCAAAATTTCAT
1 AG-GGAGGTTATCAAAATTTCAT
* *
6910 A-AGAGACTTATCAAAATTTCAT
1 AGGGAG-GTTATCAAAATTTCAT
* * * *
6932 A-GTATGTAAATCGAAATTTCAT
1 AGGGAGGT-TATCAAAATTTCAT
* *
6954 AGGGAGATTAACAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** **
6976 AATGAGGTTATCAAAAAATCAT
1 AGGGAGGTTATCAAAATTTCAT
6998 AGGGAGGTTATCAAAA-TT--T
1 AGGGAGGTTATCAAAATTTCAT
* *
7017 --GTA-GTTATCAAGATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* * * *
7036 AAGAAAGTTATCAAAATTTTAT
1 AGGGAGGTTATCAAAATTTCAT
*
7058 AGGGAGGTTTATCAAAATTTTAT
1 AGGGAGG-TTATCAAAATTTCAT
* *
7081 AGGAAGATTTATCAAAATTTCAT
1 AGGGAG-GTTATCAAAATTTCAT
* * ** *
7104 AGCGAGGTTATTACCATTTGAT
1 AGGGAGGTTATCAAAATTTCAT
* * * *
7126 AGTGTGATTATCAAAATTTCAA
1 AGGGAGGTTATCAAAATTTCAT
* * *
7148 AGTGTGATTA-CTAACAA-TTCAT
1 AGGGAGGTTATC-AA-AATTTCAT
* * * *
7170 ATGGAGGTTTTTAAATTTTCAT
1 AGGGAGGTTATCAAAATTTCAT
** * * *
7192 AACGTGATTATCAATATATT-AT
1 AGGGAGGTTATCAAAAT-TTCAT
* * * *
7214 ATGGAGATTATCAACATCTCAT
1 AGGGAGGTTATCAAAATTTCAT
** *
7236 AGTGTTGGTTATCAAAATTTTAT
1 AG-GGAGGTTATCAAAATTTCAT
** * *
7259 ATTGAGGTCT-TCAAAATTCCTT
1 AGGGAGGT-TATCAAAATTTCAT
*
7281 AGGGAGGTTAACAAAATTTCAT
1 AGGGAGGTTATCAAAATTTCAT
* *
7303 AAGAAGGTTA
1 AGGGAGGTTA
7313 AAAAAATTAT
Statistics
Matches: 324, Mismatches: 101, Indels: 44
0.69 0.22 0.09
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 1 0.00
21 8 0.02
22 238 0.73
23 62 0.19
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
AGGGAGGTTATCAAAATTTCAT
Found at i:7071 original size:23 final size:23
Alignment explanation
Indices: 7043--7112 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
7033 CATAAGAAAG
7043 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
7066 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
7089 TTATCAAAATTTCATAGCGAGGT
1 TTATCAAAATTTTATAGGGAGGT
7112 T
1 T
7113 ATTACCATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:7095 original size:46 final size:45
Alignment explanation
Indices: 7021--7112 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 45
7011 AAATTTGTAG
* * *
7021 TTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAGGT
* * *
7066 TTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGGT
1 TTATCAAAATTTCATAAGAA-AGTTATCAAAATTTCATAGCGAGGT
7112 T
1 T
7113 ATTACCATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 17 0.43
46 23 0.57
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAGGT
Found at i:7324 original size:20 final size:22
Alignment explanation
Indices: 7285--7331 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
7275 TTCCTTAGGG
* *
7285 AGGTTAACAAAATTTCATAAGA
1 AGGTTAACAAAAATTCATAAAA
7307 AGGTTAA-AAAAATT-ATAAAA
1 AGGTTAACAAAAATTCATAAAA
7327 AGGTT
1 AGGTT
7332 CTCGAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 6 0.26
22 7 0.30
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (22 bp):
AGGTTAACAAAAATTCATAAAA
Found at i:9021 original size:3 final size:3
Alignment explanation
Indices: 9013--9065 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
9003 TTTAAGAGTT
9013 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
9059 ATA ATA A
1 ATA ATA A
9066 GCATATTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:9942 original size:25 final size:24
Alignment explanation
Indices: 9914--9964 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
9904 TTTTGAACTC
9914 ATTATTCA-TTATTTAA-AATATAT
1 ATTATT-ATTTATTTAATAATATAT
9937 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
9960 ATTAT
1 ATTAT
9965 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.04
22 13 0.52
23 7 0.28
24 4 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:12392 original size:22 final size:22
Alignment explanation
Indices: 12375--12419 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
12365 ATTATGAAGT
12375 CTAAACCCAGAAACTATGAACC
1 CTAAACCCAGAAACTATGAACC
* *
12397 CTATACCCAGAAACTATAAACC
1 CTAAACCCAGAAACTATGAACC
12419 C
1 C
12420 AAAAAGGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.16
Consensus pattern (22 bp):
CTAAACCCAGAAACTATGAACC
Found at i:17874 original size:233 final size:232
Alignment explanation
Indices: 17467--17928 Score: 791
Period size: 234 Copynumber: 2.0 Consensus size: 232
17457 CTAAAATAAT
17467 CTTTTTAATTTTAAATTTTAGTGATATTTTAAGGGTTAATATGTAATCTAATATCCTTTTTAATT
1 CTTTTTAATTTTAAATTTTAGTGATATTTTAAGGGTTAATATGTAATCTAATATCCTTTTTAATT
* **
17532 TTAGAATTGGTGTAATCCAACCAGATTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAAAT
66 TTAAAATTAATGTAATCCAACCAGATTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAAAT
* * *
17597 TTTTTTTATGTTAAACATCTTATTAATTATTATTATAATTATTATATATCACTACTTTTTTTCAT
131 ATTTTTTATGTTAAACATCTTATTAATTATTATTATAATTATTATATATCACCACTTTTTTCCAT
17662 ACAAAAAAAGTATAAAATAATAACAAATTTTTTACATC
196 AC-AAAAAAGTATAAAATAATAACAAATTTTTTACATC
* * *
17700 CTTTTTAATTTTAAATTTTAGTTATATTTTTAAGGGTTAATATGTATTCTAATATTCTTTTTAAT
1 CTTTTTAATTTTAAATTTTAGTGATA-TTTTAAGGGTTAATATGTAATCTAATATCCTTTTTAAT
*
17765 TTTAAAATTAATGTAATCCAACCAGATTTTATTTCCATATTAAAAAAGTCTAAAATGATAACAAA
65 TTTAAAATTAATGTAATCCAACCAGATTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAAA
17830 -ATTTTTTATGTTAAACATCTTATTAATTATTATTATAATTATTATATATCACCACTTTTTTCCA
130 TATTTTTTATGTTAAACATCTTATTAATTATTATTATAATTATTATATATCACCACTTTTTTCCA
* *
17894 TACAAAAAAGTCTAAGATAATAACAAATTTTTTAC
195 TACAAAAAAGTATAAAATAATAACAAATTTTTTAC
17929 GTTAAACATC
Statistics
Matches: 216, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
232 30 0.14
233 89 0.41
234 97 0.45
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.46
Consensus pattern (232 bp):
CTTTTTAATTTTAAATTTTAGTGATATTTTAAGGGTTAATATGTAATCTAATATCCTTTTTAATT
TTAAAATTAATGTAATCCAACCAGATTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAAAT
ATTTTTTATGTTAAACATCTTATTAATTATTATTATAATTATTATATATCACCACTTTTTTCCAT
ACAAAAAAGTATAAAATAATAACAAATTTTTTACATC
Found at i:19954 original size:23 final size:22
Alignment explanation
Indices: 19901--19942 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19891 AAGATAATAA
*
19901 TATAGTTTTTAGAATAATCACT
1 TATACTTTTTAGAATAATCACT
19923 TATACTTTTTAGAATAATCA
1 TATACTTTTTAGAATAATCA
19943 TTGTAGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (22 bp):
TATACTTTTTAGAATAATCACT
Found at i:21308 original size:29 final size:29
Alignment explanation
Indices: 21275--21337 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
21265 TTAAACTAAA
* * *
21275 GAATTATGTAGCACGTTTATTGGTTGACG
1 GAATTATGTAGCACGTATATGGGTAGACG
*
21304 GAATTATGTAGCACGTATATGGGTAGATG
1 GAATTATGTAGCACGTATATGGGTAGACG
21333 GAATT
1 GAATT
21338 TTAATGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.35
Consensus pattern (29 bp):
GAATTATGTAGCACGTATATGGGTAGACG
Found at i:21681 original size:2 final size:2
Alignment explanation
Indices: 21674--21706 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21664 GTGTCATTAC
21674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21707 GACACCATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32722 original size:78 final size:78
Alignment explanation
Indices: 32509--32872 Score: 534
Period size: 78 Copynumber: 4.7 Consensus size: 78
32499 AATCATTACT
* * * * * * *
32509 AGTCAACACTTTTCAATTATAATTTGTAACACAATACGACAATGAAACCGTTTACAGTTAATGGT
1 AGTCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTACAGTTATTCGT
*
32574 TAAAATCATT-TCA
66 TAAAATCGTTAT-A
* * * ** * *
32587 AGTCAATACTTTTCAATCAT-TTTTGTAACATAATACGACAATGAAAGCACTTACAGTTAGTGGT
1 AGTCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTACAGTTATTCGT
32651 TAAAATCGTTATA
66 TAAAATCGTTATA
32664 AGTCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTACAGTTATTCGT
1 AGTCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTACAGTTATTCGT
32729 TAAAATCGTTATA
66 TAAAATCGTTATA
32742 AGTCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTACAGTTATTCGT
1 AGTCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTACAGTTATTCGT
32807 TAAAATCGTTATA
66 TAAAATCGTTATA
* * *
32820 AATCAATAATTTCCAATCATGATTTTGTAACATAATGCGACAATGAAACCGTT
1 AGTCAATAATTTTCAATCATGA-TTTGTAACATAATACGACAATGAAACCGTT
32873 AACCGTAACC
Statistics
Matches: 264, Mismatches: 19, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
77 67 0.25
78 168 0.64
79 29 0.11
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.35
Consensus pattern (78 bp):
AGTCAATAATTTTCAATCATGATTTGTAACATAATACGACAATGAAACCGTTTACAGTTATTCGT
TAAAATCGTTATA
Found at i:49561 original size:6 final size:6
Alignment explanation
Indices: 49545--49589 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
49535 TGTTGTGCCC
* * *
49545 GTGGCG GTGCAG GTGCAG GTGGAG GTGGAG GTGGAG GTGGAG GTG
1 GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG GTG
49590 CAGCTACTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.13, C:0.07, G:0.62, T:0.18
Consensus pattern (6 bp):
GTGGAG
Found at i:53675 original size:6 final size:6
Alignment explanation
Indices: 53664--53720 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
53654 ACTACCAATC
53664 AAAA-A AAAA-A AAAACA AAAACA AAAACA AAAACA AAAAC- AAAAC-
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
53708 AAAAC- AAAACA AA
1 AAAACA AAAACA AA
53721 TTACTTACCA
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.48
6 26 0.52
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:53717 original size:5 final size:5
Alignment explanation
Indices: 53663--53720 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
53653 TACTACCAAT
* *
53663 CAAAA AAAAA AAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA C-AAAA C-AAAA C-AAAA C-AAAA CAAAA CAAAA
53712 CAAAA CAAA
1 CAAAA CAAA
53721 TTACTTACCA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
5 27 0.54
6 23 0.46
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:67154 original size:31 final size:31
Alignment explanation
Indices: 67119--67311 Score: 161
Period size: 31 Copynumber: 6.4 Consensus size: 31
67109 CTCGGCTAAT
*
67119 TGCTCAAATAAGGGCCTAACGTT-TGCTAAAA
1 TGCTCAAATAAGGGCCTAACGTTAT-CGAAAA
* * **
67150 TGCTCAAATAAGGGCCCCATC-TT-T-GAATT
1 TGCTCAAATAAGGG-CCTAACGTTATCGAAAA
67179 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* * * **
67210 TGCTCAAATAAGGGTCCGATC-TT-T-TAATTT
1 TGCTCAAATAAGGG-CCTAACGTTATCGAA-AA
*
67240 TGC-CAAATAAGGGCCCAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
*
67270 TGCTCAAATAAGGGCCTAATGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
*
67301 TGTTCAAATAA
1 TGCTCAAATAA
67312 AGACCTGGTT
Statistics
Matches: 128, Mismatches: 22, Indels: 24
0.74 0.13 0.14
Matches are distributed among these distances:
28 8 0.06
29 29 0.23
30 13 0.10
31 70 0.55
32 8 0.06
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:67216 original size:60 final size:60
Alignment explanation
Indices: 67123--67285 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
67113 GCTAATTGCT
*
67123 CAAATAAGGGCCTAACGTT-TGCTAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
* * * *
67183 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTTGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
*
67243 CAAATAAGGGCCCAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
67286 TAATGTTATC
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
Found at i:67380 original size:31 final size:30
Alignment explanation
Indices: 67345--67512 Score: 105
Period size: 31 Copynumber: 5.6 Consensus size: 30
67335 TGCATGAGAC
67345 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-GCAAACGTT
** *
67376 AGGCCCTTATTTG-GCCAAATT-CAAA-GATG
1 AGGCCCTTATTTGAG-CATTTTGCAAACG-TT
* * * *
67405 GGGCCCTTATCTGAGAATTTTAGCAAACATT
1 AGGCCCTTATTTGAGCATTTT-GCAAACGTT
* ** * *
67436 AGGCCCTTATTTCG-CCAAATT--AAAAGATC
1 AGGCCCTTATTT-GAGCATTTTGCAAACG-TT
*
67465 AGACCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-GCAAACGTT
*
67496 AAGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
67513 ATTAGCCAAT
Statistics
Matches: 98, Mismatches: 27, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
28 5 0.05
29 35 0.36
30 2 0.02
31 51 0.52
32 5 0.05
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGCAAACGTT
Found at i:67425 original size:60 final size:60
Alignment explanation
Indices: 67344--67508 Score: 240
Period size: 60 Copynumber: 2.8 Consensus size: 60
67334 ATGCATGAGA
*
67344 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
** * * * * *
67404 GGGGCCCTTATCTGAGAATTTTAGCAAACATTAGGCCCTTATTTCGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* *
67464 CAGACCCTTATTTGAGCATTTTGGCAAACGTTAAGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
67509 AGCAATTAGC
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 88 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:69598 original size:221 final size:221
Alignment explanation
Indices: 69216--69659 Score: 741
Period size: 221 Copynumber: 2.0 Consensus size: 221
69206 GTTTTGAATT
*
69216 TTGTGAATGAAATTGTTGAGAGTGTTTTCTCCCTGTGTCTAATCCAATTTAAACAAAATTAATTA
1 TTGTGAATGAAACTGTTGAGAGTGTTTTCTCCCTGTGTCTAATCCAATTTAAACAAAATTAATTA
* * * *
69281 TAAACCGTTAAACGGATATCACATGAGGAATTGTTAGAAGGGACTGCGTGAATCTTGGGAGGCAG
66 TAAACCGTTAAACGGATATCACATGAGGAATTATTAGAAGGGACTACGTGAATCTCGGAAGGCAG
*
69346 AATATAATAATATATATTTCATTGAAAATAATACTTTCTCATCATCAAACTTTGTTAAGATATAT
131 AATATAATAATATATAATTCATTGAAAATAATACTTTCTCATCATCAAACTTTGTTAAGATATAT
69411 ATCAACTTTC-AAAACCCAATTTCAA
196 ATCAACTTTCAAAAACCCAATTTCAA
* * *
69436 TTGTGAATGAAACTGTTGAGAGTGTTTTTACTCCCT-TGTCTGATTCAATTTAAACAATATTAAT
1 TTGTGAATGAAACTGTTGAGAGTG-TTTT-CTCCCTGTGTCTAATCCAATTTAAACAAAATTAAT
*
69500 TATAAACCGTTAAACGGATATCACATGAGGAATTATTAGAAGGGACTACGTGAATC-CGGAAGGT
64 TATAAACCGTTAAACGGATATCACATGAGGAATTATTAGAAGGGACTACGTGAATCTCGGAAGGC
*
69564 GGAATTATAATAATATATAATTCATTGAAAATAATACTTTCTCATCATCAAACTTTGTTAAGATA
129 AGAA-TATAATAATATATAATTCATTGAAAATAATACTTTCTCATCATCAAACTTTGTTAAGATA
69629 TATATCAACTTTCAAAAACCCAATTTCAA
193 TATATCAACTTTCAAAAACCCAATTTCAA
69658 TT
1 TT
69660 ATTATTTTTT
Statistics
Matches: 209, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
220 31 0.15
221 155 0.74
222 23 0.11
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (221 bp):
TTGTGAATGAAACTGTTGAGAGTGTTTTCTCCCTGTGTCTAATCCAATTTAAACAAAATTAATTA
TAAACCGTTAAACGGATATCACATGAGGAATTATTAGAAGGGACTACGTGAATCTCGGAAGGCAG
AATATAATAATATATAATTCATTGAAAATAATACTTTCTCATCATCAAACTTTGTTAAGATATAT
ATCAACTTTCAAAAACCCAATTTCAA
Found at i:74835 original size:2 final size:2
Alignment explanation
Indices: 74828--74854 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
74818 ATGATTTATG
74828 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
74855 TATTATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:75765 original size:12 final size:12
Alignment explanation
Indices: 75733--75775 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
75723 TTAATACAGG
*
75733 TATCGACAGATA
1 TATCGACGGATA
75745 TATCGGACGGATA
1 TATC-GACGGATA
75758 TATCGACGGATA
1 TATCGACGGATA
75770 TATCGA
1 TATCGA
75776 GGTATCGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:78663 original size:21 final size:21
Alignment explanation
Indices: 78638--78679 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
78628 ATGTTTGGCA
*
78638 TTGTTGCCAATTTTGTTTTTT
1 TTGTTGCCAATTTTATTTTTT
*
78659 TTGTTGCCATTTTTATTTTTT
1 TTGTTGCCAATTTTATTTTTT
78680 GGAAACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.12, T:0.69
Consensus pattern (21 bp):
TTGTTGCCAATTTTATTTTTT
Found at i:79529 original size:24 final size:24
Alignment explanation
Indices: 79502--79547 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
79492 TGTTTCATGT
* *
79502 TCTTCTTCTATCTCCTTTCTTGCG
1 TCTTCTTCCATCTCATTTCTTGCG
79526 TCTTCTTCCATCTCATTTCTTG
1 TCTTCTTCCATCTCATTTCTTG
79548 TTTTCCCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.07, C:0.33, G:0.07, T:0.54
Consensus pattern (24 bp):
TCTTCTTCCATCTCATTTCTTGCG
Found at i:80969 original size:39 final size:41
Alignment explanation
Indices: 80924--81029 Score: 146
Period size: 42 Copynumber: 2.6 Consensus size: 41
80914 AAATTTCCCT
* *
80924 TGTGTTATATGTGTTTAGGGACTTTAGTA-TAG-A-TGCCTC
1 TGTGTTATATGTGTTT-GGGACTTTAGAAGGAGAATTGCCTC
80963 TGTGTTATATGTGTTTGAGGACTTTAGAAGGAGAATTGCCTC
1 TGTGTTATATGTGTTTG-GGACTTTAGAAGGAGAATTGCCTC
81005 TGTGTTATATGTGTTTGGGGACTTT
1 TGTGTTATATGTGTTT-GGGACTTT
81030 GGGGAGAGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
38 1 0.02
39 26 0.43
40 2 0.03
41 1 0.02
42 29 0.48
43 1 0.02
ACGTcount: A:0.20, C:0.08, G:0.28, T:0.43
Consensus pattern (41 bp):
TGTGTTATATGTGTTTGGGACTTTAGAAGGAGAATTGCCTC
Found at i:84093 original size:2 final size:2
Alignment explanation
Indices: 84086--84121 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
84076 TTTGTTTGTA
*
84086 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
84122 AATAAGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.