Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008578.1 Corchorus capsularis cultivar CVL-1 contig08599, 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: 78187
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:279 original size:3 final size:3
Alignment explanation
Indices: 271--302 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
261 ATTTCTTACT
271 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
303 TTTTTTGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:9515 original size:103 final size:103
Alignment explanation
Indices: 9336--9542 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
9326 ACTAAACTCA
9336 AGCTTCAATTCAATTTTGGCAAACCATACTTCTTTTCTAAACGTTTTAAAGCCAACTTTTCTTTT
1 AGCTTCAATTCAATTTTGGCAAACCATACTTCTTTTCTAAACGTTTTAAAGCCAACTTTTCTTTT
9401 ACTCTCTTTTTTTTTTCCAATTATTAATCTAATTTCGT
66 ACTCTCTTTTTTTTTTCCAATTATTAATCTAATTTCGT
9439 AGCTTCAATTCAATTTTGGCAAACCATACTTCTTTTCTAAACGTTTTAAAGCCAACTTTTCTTTT
1 AGCTTCAATTCAATTTTGGCAAACCATACTTCTTTTCTAAACGTTTTAAAGCCAACTTTTCTTTT
9504 ACTCTCTTTTTTTTTTCCAATTATTAATCTAATTTCGT
66 ACTCTCTTTTTTTTTTCCAATTATTAATCTAATTTCGT
9542 A
1 A
9543 AATTACGTTT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (103 bp):
AGCTTCAATTCAATTTTGGCAAACCATACTTCTTTTCTAAACGTTTTAAAGCCAACTTTTCTTTT
ACTCTCTTTTTTTTTTCCAATTATTAATCTAATTTCGT
Found at i:10898 original size:5 final size:6
Alignment explanation
Indices: 10871--10897 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10861 TATACTCTTC
10871 TTTTCT TTTTCT TTTTCT TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTT
10898 CCTTAGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:11860 original size:15 final size:15
Alignment explanation
Indices: 11840--11868 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11830 ATCATTCTTG
11840 AGAAGAAGAAGAATA
1 AGAAGAAGAAGAATA
11855 AGAAGAAGAAGAAT
1 AGAAGAAGAAGAAT
11869 GGGTCCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.07
Consensus pattern (15 bp):
AGAAGAAGAAGAATA
Found at i:12535 original size:1 final size:1
Alignment explanation
Indices: 12529--12553 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12519 ATTACCAGGG
12529 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12554 GACATGGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16378 original size:20 final size:20
Alignment explanation
Indices: 16353--16395 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
16343 TTGCCTACGA
*
16353 AAAAGATTACGACAAAAAAG
1 AAAAGACTACGACAAAAAAG
*
16373 AAAAGACTACGACAAAAGAG
1 AAAAGACTACGACAAAAAAG
16393 AAA
1 AAA
16396 TTTAGCGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.65, C:0.12, G:0.16, T:0.07
Consensus pattern (20 bp):
AAAAGACTACGACAAAAAAG
Found at i:20527 original size:11 final size:11
Alignment explanation
Indices: 20513--20542 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20503 TATACTATAT
20513 CAATTTTGTAA
1 CAATTTTGTAA
20524 CAATTTTGTAA
1 CAATTTTGTAA
*
20535 AAATTTTG
1 CAATTTTG
20543 AATCGATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (11 bp):
CAATTTTGTAA
Found at i:23071 original size:331 final size:331
Alignment explanation
Indices: 21954--23111 Score: 1196
Period size: 331 Copynumber: 3.5 Consensus size: 331
21944 ATATAATTTT
* * * * * *
21954 TTTAATTAGAAATTAATTCAGAAAAAGGTTGGAAAAGTC-ATATTAGAAGCGTGAGA-AACCCTT
1 TTTAATTAGAAATTAATTCGGAAAAA-ATAGGAAAA-ACGATATTAGAAGCGTGA-ATAGCTCTT
* ** * * *
22017 CATTCTTTTTGGCATTGAGTTATATAATTTT-TATTAGTATTGTGGTCC-AAAATTGAGGAGAAA
63 CAATCTTTTTGGTGTTGAATTATAT-ATTTTCTATGAGTATCGTGG-CCAAAAATTGAGGAGAAA
* * * * * *
22080 TTTCTCATGTCAATTTTTGTAAGATTTTAGCTGAAATCGTGTATTAACCATCACAT-TTTTTTGA
126 TTTCTCAGGTCAATTTTTATAAAATTTTAGCCGAAATCGTGTA-TAATCAT--CATGGTTTTTGA
* * *
22144 CTAAAAAGGCGTTCCGGAGTCCCGACTCAGTTTTGCACGATTTTTGGCGCTAAGTCTCATTGAAA
188 CTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCAAGTCTCATTG--A
* *
22209 ATCTATATCTATATCTATCTAACCAAATCTTACCCATATTGGATTTAAGGATTTGTTTTTACGAG
251 A---ATATCTATATCTATCTAACCAAATCTTAACCACATTGGATTTAAGGATTTGTTTTTACGAG
* *
22274 CATATGAATCATGTTTCGA
313 CATCTAAATCATGTTTCGA
* * *
22293 TTCAATTAGGAATTAATTCGGAAAAAAATAGGTAAAACGATATTAGAAGCGTGAATAGCCTCTT-
1 TTTAATTAGAAATTAATTCGG-AAAAAATAGGAAAAACGATATTAGAAGCGTGAATAG-CTCTTC
*
22357 AATCTTTTTGGTGTTGAATTATATATTTTCTATGAGTATCGTGGCCAAAAATTGA-GAAAAATTC
64 AATCTTTTTGGTGTTGAATTATATATTTTCTATGAGTATCGTGGCCAAAAATTGAGGAGAAATT-
* *
22421 TTTC-GAGTCAATTTTTACAAAATTTTAGCCGAAATCGTG-----T-ATCATGGTTTTTGACTAA
128 TCTCAG-GTCAATTTTTATAAAATTTTAGCCGAAATCGTGTATAATCATCATGGTTTTTGACTAA
* * * * * * *
22479 AAACGCATTTCGG-GACCCTGTCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTG---TAT
192 AAACGCGTTCCGGAG-CCCCGACTCAGTTTTGCACGATTTTTGGCGCCAAGTCTCATTGAAATAT
* ** * * * **
22540 CTATATTTATCTAATGAAATCTTAGCTACATTGGATTTAAGGATTT-TTTTTACAAGCATCTCGA
256 CTATATCTATCTAACCAAATCTTAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAA
**
22604 TCCGGTTTCGA
321 TCATGTTTCGA
* * *
22615 TTTAATTAGAAATTAATTCGG-AAAAATAGGAAAAAAAACAATATTAGAAGCGTGAAAAGCCCTT
1 TTTAATTAGAAATTAATTCGGAAAAAATAGG---AAAAACGATATTAGAAGCGTGAATAGCTCTT
* * * * **
22679 CAATCTTTTTGGCGTTGAATTATATATTTTTTTATGAATATGGTGGCCGGAAATTGAGGAGAAAT
63 CAATCTTTTTGGTGTTGAATTATATA-TTTTCTATGAGTATCGTGGCCAAAAATTGAGGAGAAAT
*
22744 TTCTCAGGTCAATTTTT-TCAAAATTTTAGCTGAAATCGTGTACTAATCATCATGGTTTTTGACT
127 TTCTCAGGTCAATTTTTAT-AAAATTTTAGCCGAAATCGTGTA-TAATCATCATGGTTTTTGACT
* * **
22808 AAAAACGCGTTCTGGAGCCCCGGCTCAGTTTTGCACGATTTGGGGCGCCAAGTCTCATTGAAATA
190 AAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCAAGTCTCATTGAAATA
* * * *
22873 TCTATATCCATCTAGCCAAAT-TTCAACCACACTGGATTTGAGGATTTGTTTTTACGAGCATCTA
255 TCTATATCTATCTAACCAAATCTT-AACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTA
*
22937 AATCATGTTTCAA
319 AATCATGTTTCGA
* * * *
22950 TTTAATTAGAAATTAATTAGGAAAAAATAGGAAAACCGATATTAGAAACGTGAATAGCTTTTCAA
1 TTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAATAGCTCTTCAA
* * * *
23015 T-TTTTTAGTGTTGAATTATATATTTTCTATGAGTATCGTGG-TAAAAGATCGAGGAGAATTGTT
66 TCTTTTTGGTGTTGAATTATATATTTTCTATGAGTATCGTGGCCAAAA-ATTGAGGAGAAAT-TT
* * *
23078 TTGA-TTCAATTTTTATAAAATTTTAGCCGAAATC
129 CTCAGGTCAATTTTTATAAAATTTTAGCCGAAATC
23112 TAACCATCAC
Statistics
Matches: 676, Mismatches: 108, Indels: 78
0.78 0.13 0.09
Matches are distributed among these distances:
320 9 0.01
322 46 0.07
323 90 0.13
324 58 0.09
325 8 0.01
330 7 0.01
331 174 0.26
332 27 0.04
333 31 0.05
334 37 0.05
335 43 0.06
336 9 0.01
338 16 0.02
339 112 0.17
340 9 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (331 bp):
TTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAATAGCTCTTCAA
TCTTTTTGGTGTTGAATTATATATTTTCTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTTCT
CAGGTCAATTTTTATAAAATTTTAGCCGAAATCGTGTATAATCATCATGGTTTTTGACTAAAAAC
GCGTTCCGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCAAGTCTCATTGAAATATCTATA
TCTATCTAACCAAATCTTAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCATG
TTTCGA
Found at i:23190 original size:2 final size:2
Alignment explanation
Indices: 23183--23217 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23173 GACTCAAAAG
23183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23218 AATTGCAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23393 original size:3 final size:3
Alignment explanation
Indices: 23387--23419 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
23377 TATTATTATT
23387 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23420 GCATATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:33397 original size:18 final size:18
Alignment explanation
Indices: 33374--33408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33364 TAACTGGTTC
* *
33374 AAACATTAACAATCTCAG
1 AAACATCAACAACCTCAG
33392 AAACATCAACAACCTCA
1 AAACATCAACAACCTCA
33409 TTAACCCCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.29, G:0.03, T:0.17
Consensus pattern (18 bp):
AAACATCAACAACCTCAG
Found at i:36686 original size:14 final size:14
Alignment explanation
Indices: 36662--36699 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
36652 TGCCTAAAAG
36662 CAAAAAGAAAAAGAA
1 CAAAAA-AAAAAGAA
*
36677 TAAAAAAAAAAGAA
1 CAAAAAAAAAAGAA
36691 CAAAAAAAA
1 CAAAAAAAA
36700 CAAAAAGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.84, C:0.05, G:0.08, T:0.03
Consensus pattern (14 bp):
CAAAAAAAAAAGAA
Found at i:42137 original size:21 final size:21
Alignment explanation
Indices: 42111--42154 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42101 AATAAGAAGG
*
42111 TTGCTAAAT-ACCGTCCTATTT
1 TTGCT-AATCACCGTCCCATTT
*
42132 TTGCTATTCACCGTCCCATTT
1 TTGCTAATCACCGTCCCATTT
42153 TT
1 TT
42155 TACATTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (21 bp):
TTGCTAATCACCGTCCCATTT
Found at i:42245 original size:33 final size:33
Alignment explanation
Indices: 42202--42300 Score: 150
Period size: 33 Copynumber: 3.1 Consensus size: 33
42192 TTTGCCTTTA
*
42202 GCCAC-GCGGAGCCTACCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
42234 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
* *
42267 GCCACGGC-TAGCCGCCCCACTAGGACGGC-CT
1 GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
42298 GCC
1 GCC
42301 CTGGCTAAGC
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
31 5 0.08
32 24 0.38
33 34 0.54
ACGTcount: A:0.16, C:0.43, G:0.29, T:0.11
Consensus pattern (33 bp):
GCCACGGCGGAGCCTCCCCACTAGGACGGCTCT
Found at i:42290 original size:32 final size:32
Alignment explanation
Indices: 42217--42317 Score: 143
Period size: 32 Copynumber: 3.1 Consensus size: 32
42207 GCGGAGCCTA
* *
42217 CCCACTAGGACGGCTCTGCCACGGCGGAGCCTC
1 CCCACTAGGACGGCTCTGCCACGGC-TAGCCGC
42250 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
42282 CCCACTAGGACGGC-CTGCC-CTGGCTAAGCCGC
1 CCCACTAGGACGGCTCTGCCAC-GGCT-AGCCGC
42314 CCCA
1 CCCA
42318 GTGGGGCGGC
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
30 1 0.02
31 9 0.14
32 29 0.45
33 25 0.39
ACGTcount: A:0.16, C:0.45, G:0.28, T:0.12
Consensus pattern (32 bp):
CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
Found at i:51664 original size:14 final size:13
Alignment explanation
Indices: 51647--51706 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 13
51637 ATGCATAAAC
*
51647 ACACATACGTATGT
1 ACACATACATAT-T
51661 ACACATACATATT
1 ACACATACATATT
*
51674 ATACATAC--A-T
1 ACACATACATATT
*
51684 ACACATACATACAT
1 ACACATACATA-TT
51698 ACACATACA
1 ACACATACA
51707 GACATACGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 8 0.21
11 1 0.03
12 1 0.03
13 8 0.21
14 21 0.54
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (13 bp):
ACACATACATATT
Found at i:51681 original size:4 final size:4
Alignment explanation
Indices: 51663--51743 Score: 57
Period size: 4 Copynumber: 21.5 Consensus size: 4
51653 ACGTATGTAC
* *
51663 ACAT ACAT ATTAT ACAT ACAT AC-- ACAT ACAT ACAT AC-- ACAT ACAG
1 ACAT ACAT A-CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
51708 ACAT ACGT GCAT ACAT ATAT AC-- ACAT ACAT GCAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
51744 GTATGGGCTG
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
2 6 0.10
4 49 0.84
5 3 0.05
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:51697 original size:18 final size:18
Alignment explanation
Indices: 51628--51713 Score: 73
Period size: 18 Copynumber: 4.7 Consensus size: 18
51618 TTGCTAGGAC
* *
51628 CATACATACATGCATAAA
1 CATACATACATACATACA
* * **
51646 CACACATACGTATGTACA
1 CATACATACATACATACA
*
51664 CATACATATTATACATACA
1 CATACATA-CATACATACA
* *
51683 TACACATACATACATACA
1 CATACATACATACATACA
*
51701 CATACAGACATAC
1 CATACATACATAC
51714 GTGCATACAT
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
18 38 0.76
19 12 0.24
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.23
Consensus pattern (18 bp):
CATACATACATACATACA
Found at i:51711 original size:14 final size:14
Alignment explanation
Indices: 51674--51743 Score: 86
Period size: 14 Copynumber: 4.9 Consensus size: 14
51664 CATACATATT
51674 ATACATACATACAC
1 ATACATACATACAC
51688 ATACATACATACAC
1 ATACATACATACAC
* *
51702 ATACAGACATACGTGC
1 ATACATACATAC--AC
*
51718 ATACATATATACAC
1 ATACATACATACAC
*
51732 ATACATGCATAC
1 ATACATACATAC
51744 GTATGGGCTG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
14 36 0.77
16 11 0.23
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.23
Consensus pattern (14 bp):
ATACATACATACAC
Found at i:51711 original size:22 final size:22
Alignment explanation
Indices: 51684--51743 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
51674 ATACATACAT
*
51684 ACACATACATACATACACATAC
1 ACACATACATGCATACACATAC
* * * *
51706 AGACATACGTGCATACATATAT
1 ACACATACATGCATACACATAC
51728 ACACATACATGCATAC
1 ACACATACATGCATAC
51744 GTATGGGCTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.45, C:0.27, G:0.07, T:0.22
Consensus pattern (22 bp):
ACACATACATGCATACACATAC
Found at i:51723 original size:30 final size:30
Alignment explanation
Indices: 51687--51745 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
51677 CATACATACA
51687 CATACATACATACACATACA-GACATACGTG
1 CATACATACATACACATACATG-CATACGTG
*
51717 CATACATATATACACATACATGCATACGT
1 CATACATACATACACATACATGCATACGT
51746 ATGGGCTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.24
Consensus pattern (30 bp):
CATACATACATACACATACATGCATACGTG
Found at i:59794 original size:16 final size:16
Alignment explanation
Indices: 59769--59809 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
59759 CTTTGTCCTT
59769 TGGAACTGCATTTATA
1 TGGAACTGCATTTATA
*
59785 TGGAATTGCATTTATA
1 TGGAACTGCATTTATA
59801 TGGAACTGC
1 TGGAACTGC
59810 TACATCACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (16 bp):
TGGAACTGCATTTATA
Found at i:68480 original size:8 final size:8
Alignment explanation
Indices: 68467--68496 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
68457 AGGTATAATT
68467 AAAAATAA
1 AAAAATAA
68475 AAAAATAAA
1 AAAAAT-AA
68484 AAAAATAA
1 AAAAATAA
68492 AAAAA
1 AAAAA
68497 AAACTGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:68498 original size:10 final size:9
Alignment explanation
Indices: 68467--68497 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
68457 AGGTATAATT
68467 AAAAAT-AA
1 AAAAATAAA
68475 AAAAATAAA
1 AAAAATAAA
68484 AAAAATAAA
1 AAAAATAAA
68493 AAAAA
1 AAAAA
68498 AACTGGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:69759 original size:16 final size:16
Alignment explanation
Indices: 69738--69769 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
69728 ATATTTAAAT
*
69738 GACCAAAATCTGAAAA
1 GACCAAAACCTGAAAA
69754 GACCAAAACCTGAAAA
1 GACCAAAACCTGAAAA
69770 TTAGAGGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
GACCAAAACCTGAAAA
Found at i:70385 original size:110 final size:109
Alignment explanation
Indices: 70217--70475 Score: 430
Period size: 110 Copynumber: 2.4 Consensus size: 109
70207 TAAATTAAAA
** *
70217 TGGTAAAAATAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTA
1 TGGTAAAAATAAAGTAATTATA-AAAATATTAG-ATTTAATCAAATGAAAATAGAGTTTTTAGTA
70281 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTT
64 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAA-TTTTT
**
70328 TGGTAAAAATAAAGTAATTATAAAGCTATTAGATTTAATCAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAAATATTAGATTTAATCAAATGAAAATAGAGTTTTTAGTAGA
*
70393 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
70437 TGGTAAAAATAAAGTAATTATAAAAATATTAGATTTAAT
1 TGGTAAAAATAAAGTAATTATAAAAATATTAGATTTAAT
70476 TTAATTGAAT
Statistics
Matches: 139, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
109 42 0.30
110 76 0.55
111 21 0.15
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAAATATTAGATTTAATCAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:70507 original size:109 final size:112
Alignment explanation
Indices: 70217--70514 Score: 373
Period size: 110 Copynumber: 2.7 Consensus size: 112
70207 TAAATTAAAA
**
70217 TGGTAAAAATAAAAAAATTATATAAAATATT-G----AATTTAATTAAATGAAAATAGAGTTTTT
1 TGGTAAAAATAAAGTAATTATA-AAAATATTAGATTTAATTTAATT-AATGAAAATAGAG-TTTT
70277 AGTAGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTT
63 AGTAG-ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTT
** *
70328 TGGTAAAAATAAAGTAATTATAAAGCTATTAGATTTAA--TCA--AATGAAAATAGAGTTTTTAG
1 TGGTAAAAATAAAGTAATTATAAAAATATTAGATTTAATTTAATTAATGAAAATAGAG-TTTTAG
*
70389 TAGAATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAA-TTTTT
65 TAG-ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTT
*
70437 TGGTAAAAATAAAGTAATTATAAAAATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAAATATTAGATTTAATTTAATT-AATGAAAATAGAGTTT-TA
*
70502 GTAAAATAAAATT
64 GT-AGATAAAATT
70515 ATAATAGTTG
Statistics
Matches: 164, Mismatches: 11, Indels: 21
0.84 0.06 0.11
Matches are distributed among these distances:
109 41 0.25
110 68 0.41
111 23 0.14
113 5 0.03
114 24 0.15
115 3 0.02
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (112 bp):
TGGTAAAAATAAAGTAATTATAAAAATATTAGATTTAATTTAATTAATGAAAATAGAGTTTTAGT
AGATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTTT
Found at i:75584 original size:44 final size:45
Alignment explanation
Indices: 75507--75594 Score: 108
Period size: 44 Copynumber: 1.9 Consensus size: 45
75497 ATTGAATAAA
*
75507 TTGAAAAAAAAATAAAGAACCAAAGCAATAAAAGATAAATGACAATAG
1 TTGAAAAAAAAATAAAG-A-CAAAGCAAGAAAAGAT-AATGACAATAG
* *
75555 TTGAAAAAAAAA-AAAG-CAAAGCGAGAAAAGGTAATGACAA
1 TTGAAAAAAAAATAAAGACAAAGCAAGAAAAGATAATGACAA
75595 CACACCTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 8 0.22
44 13 0.35
47 4 0.11
48 12 0.32
ACGTcount: A:0.64, C:0.08, G:0.16, T:0.12
Consensus pattern (45 bp):
TTGAAAAAAAAATAAAGACAAAGCAAGAAAAGATAATGACAATAG
Found at i:76937 original size:109 final size:109
Alignment explanation
Indices: 76741--77015 Score: 455
Period size: 109 Copynumber: 2.5 Consensus size: 109
76731 ACTATTATAG
* *
76741 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
76806 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
76855 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
76920 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
76964 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
77016 TATATATTTT
Statistics
Matches: 157, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 7 0.04
109 124 0.79
110 3 0.02
111 2 0.01
114 21 0.13
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Done.