Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold381
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: 370863
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.31
Warning! 21801 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:296177 original size:27 final size:27
Alignment explanation
Indices: 296147--296221 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
296137 TACTAACTCG
296147 CCAGACCTACTGGCGTATACCATCTCA
1 CCAGACCTACTGGCGTATACCATCTCA
* ** **
296174 CCAGACTTGTTGGCGTA-ACCATCTTG
1 CCAGACCTACTGGCGTATACCATCTCA
* *
296200 CCATACCTACTGGTGTTATACC
1 CCAGACCTACTGGCG-TATACC
296222 GCCACCACAA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
26 17 0.47
27 16 0.44
28 3 0.08
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (27 bp):
CCAGACCTACTGGCGTATACCATCTCA
Found at i:297728 original size:20 final size:18
Alignment explanation
Indices: 297681--297787 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
297671 CTAGATAAAC
297681 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
297698 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
297718 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
297737 ATTAAGA-TAAGTA-TTAA-
1 ATTAA-ATTAA-TATTTAAT
*
297754 ATTAAATTAAATATTAAACT
1 ATTAAATT-AATATTTAA-T
*
297774 ATTAAAATAATATT
1 ATTAAATTAATATT
297788 AATTTTAGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 16 0.23
18 8 0.11
19 20 0.29
20 25 0.36
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:300771 original size:7 final size:6
Alignment explanation
Indices: 300744--300768 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
300734 CACTCTAATC
300744 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
300769 TCTCTCTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:308341 original size:124 final size:124
Alignment explanation
Indices: 308174--308432 Score: 500
Period size: 124 Copynumber: 2.1 Consensus size: 124
308164 TTTTAATATT
308174 TATTAATTTTTAAAATTTATATTATATATTTTTAGTGCTTTCAAATATTATTAGATACTCTTTTT
1 TATTAA-TTTTAAAATTTATATTATATATTTTTAGTGCTTTCAAATATTATTAGATACTCTTTTT
308239 TTTATATATATACGTATTATGTAATTAAAATGGGTTGAACTAGCTTTTTGTTTTTATCCA
65 TTTATATATATACGTATTATGTAATTAAAATGGGTTGAACTAGCTTTTTGTTTTTATCCA
308299 TATTAATTTTAAAATTTATATTATATATTTTTAGTGCTTTCAAATATTATTAGATACTCTTTTTT
1 TATTAATTTTAAAATTTATATTATATATTTTTAGTGCTTTCAAATATTATTAGATACTCTTTTTT
308364 TTATATATATACGTATTATGTAATTAAAATGGGTTGAACTAGCTTTTTGTTTTTATCCA
66 TTATATATATACGTATTATGTAATTAAAATGGGTTGAACTAGCTTTTTGTTTTTATCCA
*
308423 AATTAATTTT
1 TATTAATTTT
308433 GGGTAAAACT
Statistics
Matches: 133, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
124 127 0.95
125 6 0.05
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (124 bp):
TATTAATTTTAAAATTTATATTATATATTTTTAGTGCTTTCAAATATTATTAGATACTCTTTTTT
TTATATATATACGTATTATGTAATTAAAATGGGTTGAACTAGCTTTTTGTTTTTATCCA
Found at i:309595 original size:31 final size:31
Alignment explanation
Indices: 309560--309619 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
309550 TTAATATATT
*
309560 ATTTGATACT-TAAATTTAGTTTTAATGTTTA
1 ATTTGATA-TGTAAATTTAGTTTCAATGTTTA
* *
309591 ATTTGGTATGTAATTTTAGTTTCAATGTT
1 ATTTGATATGTAAATTTAGTTTCAATGTT
309620 CACTTTGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.55
Consensus pattern (31 bp):
ATTTGATATGTAAATTTAGTTTCAATGTTTA
Found at i:309627 original size:31 final size:32
Alignment explanation
Indices: 309574--309639 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
309564 GATACTTAAA
* * *
309574 TTTAGTTTTAATGTTTAATTTGGTATGTAA-T
1 TTTAGTTTCAATGTTCAATTTGGTATATAAGT
*
309605 TTTAGTTTCAATGTTCACTTTGGTATATAAGT
1 TTTAGTTTCAATGTTCAATTTGGTATATAAGT
309637 TTT
1 TTT
309640 TTTAATTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (32 bp):
TTTAGTTTCAATGTTCAATTTGGTATATAAGT
Found at i:316409 original size:5 final size:5
Alignment explanation
Indices: 316399--316438 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
316389 TATAAAAGGA
316399 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAA
316439 CCCATTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:316419 original size:15 final size:16
Alignment explanation
Indices: 316392--316438 Score: 78
Period size: 15 Copynumber: 2.9 Consensus size: 16
316382 GAATCTTTAT
316392 AAAAGGAAAAAGAAAAG
1 AAAA-GAAAAAGAAAAG
316409 AAAAG-AAAAGAAAAG
1 AAAAGAAAAAGAAAAG
316424 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
316439 CCCATTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.52
16 10 0.34
17 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAG
Found at i:319685 original size:82 final size:83
Alignment explanation
Indices: 319581--319747 Score: 327
Period size: 82 Copynumber: 2.0 Consensus size: 83
319571 TATTATTTTA
319581 TATTTTATAATAAAATTTGAATTTAAAACATTATGAATAACACTATCATTTCAGTCGTAAATGTA
1 TATTTTATAATAAAATTTGAATTTAAAACATTATGAATAACACTATCATTTCAGTCGTAAATGTA
319646 TTATAATCTAATATATAT
66 TTATAATCTAATATATAT
319664 TATTTTATAA-AAAATTTGAATTTAAAACATTATGAATAACACTATCATTTCAGTCGTAAATGTA
1 TATTTTATAATAAAATTTGAATTTAAAACATTATGAATAACACTATCATTTCAGTCGTAAATGTA
319728 TTATAATCTAATATATAT
66 TTATAATCTAATATATAT
319746 TA
1 TA
319748 CTACATTAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 74 0.88
83 10 0.12
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (83 bp):
TATTTTATAATAAAATTTGAATTTAAAACATTATGAATAACACTATCATTTCAGTCGTAAATGTA
TTATAATCTAATATATAT
Found at i:340787 original size:27 final size:28
Alignment explanation
Indices: 340753--340812 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
340743 TTTCTTGAGA
* *
340753 GTTTGTAA-TTTTGGGACTCTTTGGACT
1 GTTTGTAATTTTTAGGACTCTCTGGACT
340780 GTTTGTAATTTTTAGGACTCTCTGGACT
1 GTTTGTAATTTTTAGGACTCTCTGGACT
340808 GTTTG
1 GTTTG
340813 CTTTTGGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.48
Consensus pattern (28 bp):
GTTTGTAATTTTTAGGACTCTCTGGACT
Found at i:347998 original size:125 final size:126
Alignment explanation
Indices: 347774--348307 Score: 718
Period size: 125 Copynumber: 4.3 Consensus size: 126
347764 ATTTTTGCAG
* *
347774 TCGCGCCCACGTGTACGCGCTTTTGCTACAGTAGGTCCTGGAA-AAATAATTTCGACTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * * * *
347838 TCTGAGCAAATAATATAAAAAACACTTCAAGCAGGATGCTACATGCGAAGAATTTATGAAA
66 TCTGAGCAAATAGTATAAAAAACACTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * **
347899 TCGCGCCCTAC-TGGATGCGCTTTTGCTACAGTTGGTCCAAGAAGAAATAATTTCGAGTTGACGT
1 TCGCGCCC-ACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGT
* * * *
347963 TTCTGAGCAAATAGTAT-AAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
65 TTCTGAGCAAATAGTATAAAAAACACTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * * * *
348024 TCGTGCTCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATTATTTCGAGTTGATGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * * *
348088 TCTGAGCAAATAGTATAAAAAACACTTCAAGCAGAATGCTATTTGAGAAGAATTTTTGAAA
66 TCTGAGCAAATAGTATAAAAAACACTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * * * * *
348149 TTGCGCCCTCGTGGACGCGCTTTTCCTACAGTTGGTCCTGGAAGAAATAATTTTGAGTTGATGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * * *
348214 TCTGAGCAAATAGTAT-AAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAAACACTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
348274 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
348308 CATGTTTGGG
Statistics
Matches: 352, Mismatches: 52, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
124 40 0.11
125 237 0.67
126 75 0.21
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (126 bp):
TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
TCTGAGCAAATAGTATAAAAAACACTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
Found at i:348185 original size:250 final size:250
Alignment explanation
Indices: 347744--348307 Score: 878
Period size: 250 Copynumber: 2.3 Consensus size: 250
347734 AAAATCAAAG
* * * * * * *
347744 CAGGATGATTTATCAGAAGGATTTTTGCAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGG
* *
347809 TCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAATATAAAAAACACTTCAAGCAGGA
66 TCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAATATAAAAAACACTTCAAGCAGAA
* * *
347874 TGCTACATGCGAAGAATTTATGAAATCGCGCCCTACTGGATGCGCTTTTGCTACAGTTGGTCCAA
131 TGCTACATGAGAAGAATTTATGAAATCGCGCCCTACTGGACGCGCTTTTCCTACAGTTGGTCCAA
347939 GAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAC
196 GAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAC
* *
347994 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCTCACGTGGACGCGCTTTTGCTACAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGG
* * * *
348059 TCCTGAAAAAATTATTTCGAGTTGATGTTTCTGAGCAAATAGTATAAAAAACACTTCAAGCAGAA
66 TCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAATATAAAAAACACTTCAAGCAGAA
** * * *
348124 TGCTATTTGAGAAGAATTTTTGAAATTGCGCCCT-CGTGGACGCGCTTTTCCTACAGTTGGTCCT
131 TGCTACATGAGAAGAATTTATGAAATCGCGCCCTAC-TGGACGCGCTTTTCCTACAGTTGGTCCA
* * *
348188 GGAAGAAATAATTTTGAGTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAC
195 AGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAC
348244 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
348308 CATGTTTGGG
Statistics
Matches: 285, Mismatches: 28, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
249 1 0.00
250 284 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (250 bp):
CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGG
TCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAATATAAAAAACACTTCAAGCAGAA
TGCTACATGAGAAGAATTTATGAAATCGCGCCCTACTGGACGCGCTTTTCCTACAGTTGGTCCAA
GAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAC
Found at i:351515 original size:29 final size:28
Alignment explanation
Indices: 351481--351540 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
351471 TATATTTAAC
*
351481 TTAAGGGTTAGGGTTTTGAAGTTAAGGTT
1 TTAAGGGTTAGGGTTTT-AAGTTAAGGGT
* * *
351510 TTAAGGTTTAGTGTTTTAAGTTTAGGGT
1 TTAAGGGTTAGGGTTTTAAGTTAAGGGT
351538 TTA
1 TTA
351541 GAATTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (28 bp):
TTAAGGGTTAGGGTTTTAAGTTAAGGGT
Found at i:351534 original size:14 final size:14
Alignment explanation
Indices: 351488--351539 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
351478 AACTTAAGGG
351488 TTAGGGTTTTGAAG-
1 TTAGGGTTTT-AAGT
*
351502 TTAAGGTTTTAAGGT
1 TTAGGGTTTTAA-GT
*
351517 TTAGTGTTTTAAGT
1 TTAGGGTTTTAAGT
351531 TTAGGGTTT
1 TTAGGGTTT
351540 AGAATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 2 0.06
14 20 0.62
15 10 0.31
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
TTAGGGTTTTAAGT
Found at i:351562 original size:22 final size:22
Alignment explanation
Indices: 351509--351722 Score: 206
Period size: 22 Copynumber: 9.8 Consensus size: 22
351499 AAGTTAAGGT
* *
351509 TTTAAGGTTTAGTG-TTTTAAG
1 TTTAGGGTTTAGAGTTTTTAAG
*
351530 TTTAGGGTTTAGAATTTTTAAG
1 TTTAGGGTTTAGAGTTTTTAAG
351552 TTTAGGGTTTATG-GTTTTTAAG
1 TTTAGGGTTTA-GAGTTTTTAAG
* * *
351574 TTAAGGGTTTAGGGTTTTTAGG
1 TTTAGGGTTTAGAGTTTTTAAG
*
351596 TTTAGGATTT-GTAGTTTTTAAG
1 TTTAGGGTTTAG-AGTTTTTAAG
* *
351618 TTTAGGGTTTAGTGTTTTTAGG
1 TTTAGGGTTTAGAGTTTTTAAG
*
351640 TTTAGAGTTT-GTAGTTTTTAA-
1 TTTAGGGTTTAG-AGTTTTTAAG
* * *
351661 TTTAAGGTTTTAGGGTTTTTAGG
1 TTT-AGGGTTTAGAGTTTTTAAG
*
351684 GTTAGGGTTTATGA-TTTTTAAG
1 TTTAGGGTTTA-GAGTTTTTAAG
*
351706 TTTAGGGTTTAGGGTTT
1 TTTAGGGTTTAGAGTTT
351723 GGGTTTTTTA
Statistics
Matches: 156, Mismatches: 26, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
21 18 0.12
22 132 0.85
23 6 0.04
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (22 bp):
TTTAGGGTTTAGAGTTTTTAAG
Found at i:351582 original size:44 final size:44
Alignment explanation
Indices: 351518--351722 Score: 261
Period size: 44 Copynumber: 4.6 Consensus size: 44
351508 TTTTAAGGTT
** *
351518 TAGTGTTTTAAGTTTAGGGTTTAGAATTTTTAAGTTTAGGGTTTA
1 TAGT-TTTTAAGTTTAGGGTTTAGGGTTTTTAGGTTTAGGGTTTA
* * * *
351563 TGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAGGTTTAGGATTTG
1 TAGTTTTTAAGTTTAGGGTTTAGGGTTTTTAGGTTTAGGGTTTA
* * *
351607 TAGTTTTTAAGTTTAGGGTTTAGTGTTTTTAGGTTTAGAGTTTG
1 TAGTTTTTAAGTTTAGGGTTTAGGGTTTTTAGGTTTAGGGTTTA
* *
351651 TAGTTTTTAA-TTTAAGGTTTTAGGGTTTTTAGGGTTAGGGTTTA
1 TAGTTTTTAAGTTT-AGGGTTTAGGGTTTTTAGGTTTAGGGTTTA
351695 T-GATTTTTAAGTTTAGGGTTTAGGGTTT
1 TAG-TTTTTAAGTTTAGGGTTTAGGGTTT
351723 GGGTTTTTTA
Statistics
Matches: 139, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
43 4 0.03
44 129 0.93
45 6 0.04
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (44 bp):
TAGTTTTTAAGTTTAGGGTTTAGGGTTTTTAGGTTTAGGGTTTA
Found at i:351597 original size:15 final size:15
Alignment explanation
Indices: 351579--351693 Score: 53
Period size: 15 Copynumber: 7.8 Consensus size: 15
351569 TTAAGTTAAG
351579 GGTTTAGGGTTTTTA
1 GGTTTAGGGTTTTTA
* *
351594 GGTTTAGGATTTGTA
1 GGTTTAGGGTTTTTA
* *
351609 GTTTTTA-AG--TTTA
1 G-GTTTAGGGTTTTTA
*
351622 GGGTTTAGTGTTTTTA
1 -GGTTTAGGGTTTTTA
* *
351638 GGTTTAGAGTTTGTA
1 GGTTTAGGGTTTTTA
* * *
351653 GTTTTTA---ATTTAA
1 G-GTTTAGGGTTTTTA
351666 GGTTTTAGGGTTTTTA
1 GG-TTTAGGGTTTTTA
*
351682 GGGTTAGGGTTT
1 GGTTTAGGGTTT
351694 ATGATTTTTA
Statistics
Matches: 72, Mismatches: 18, Indels: 20
0.65 0.16 0.18
Matches are distributed among these distances:
13 15 0.21
14 2 0.03
15 37 0.51
16 18 0.25
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (15 bp):
GGTTTAGGGTTTTTA
Found at i:351722 original size:29 final size:29
Alignment explanation
Indices: 351678--351751 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
351668 TTTTAGGGTT
*
351678 TTTAGGG-TTAGGGTTTATGATTTTTAAG
1 TTTAGGGTTTAGGGTTTAGGATTTTTAAG
* * *
351706 TTTAGGGTTTAGGGTTTGGGTTTTTTAGG
1 TTTAGGGTTTAGGGTTTAGGATTTTTAAG
**
351735 TTTATTGTTTAGGGTTT
1 TTTAGGGTTTAGGGTTT
351752 TACGTTAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 7 0.18
29 32 0.82
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (29 bp):
TTTAGGGTTTAGGGTTTAGGATTTTTAAG
Found at i:354282 original size:11 final size:12
Alignment explanation
Indices: 354266--354309 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
354256 ATTAAATATG
354266 AATTTGAGA-GA
1 AATTTGAGAGGA
354277 AATTTG-GAAGGA
1 AATTTGAG-AGGA
354289 AA-TTGAGAGGA
1 AATTTGAGAGGA
354300 AATTTGAGAG
1 AATTTGAGAG
354310 CGGATTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 16 0.55
12 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:355364 original size:102 final size:101
Alignment explanation
Indices: 355143--355369 Score: 265
Period size: 102 Copynumber: 2.2 Consensus size: 101
355133 ATACAGTCAT
* * * *
355143 ATGATGTCATAGAGTCTTTCATTTATGGTCTTACTCACTATACCTGGCTGCCATAGCATCTTTCA
1 ATGATGTCA-AGAGTCTTTTATCTATGGCCTTACTCACTATACCTGGCTGCCATAACATCTTTCA
* *
355208 TCTATGGTCTTATACCGTATATCTTATACATTGTACT
65 TCTATGGTCTTATACCGTATATCTTATACATTATACC
* * * * * * ** *
355245 AAGCTGCCATGACGTCTTTTATCTATGGCCTTATTCACTATACTTGGCTGTTATAACATCTTTTA
1 ATGATGTCAAGA-GTCTTTTATCTATGGCCTTACTCACTATACCTGGCTGCCATAACATCTTTCA
* *
355310 TCTATGGTCTTATACTGTATATCTTATACCTTATACC
65 TCTATGGTCTTATACCGTATATCTTATACATTATACC
*
355347 ATGATGTCAGGATGTCTTTTATC
1 ATGATGTCAAGA-GTCTTTTATC
355370 CACAGTCTTA
Statistics
Matches: 102, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
101 2 0.02
102 100 0.98
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (101 bp):
ATGATGTCAAGAGTCTTTTATCTATGGCCTTACTCACTATACCTGGCTGCCATAACATCTTTCAT
CTATGGTCTTATACCGTATATCTTATACATTATACC
Found at i:368336 original size:24 final size:24
Alignment explanation
Indices: 368283--368389 Score: 81
Period size: 25 Copynumber: 4.4 Consensus size: 24
368273 TTCTCTCCGA
*
368283 AGCTTCCCGATATTGGCTCGCTTG
1 AGCTTCCCGATATTGGCTCGCATG
* * *
368307 AACTTCCCGAT-TATGGCTTGGATG
1 AGCTTCCCGATAT-TGGCTCGCATG
* * *
368331 AGCTTCCCGTTACATGGCTCACATG
1 AGCTTCCCGATA-TTGGCTCGCATG
* * * *
368356 AGCTTCTCGTTATATGGCTCGAAAG
1 AGCTTCCCGATAT-TGGCTCGCATG
368381 AGCTTCCCG
1 AGCTTCCCG
368390 TTCACATGTT
Statistics
Matches: 63, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
23 1 0.02
24 27 0.43
25 35 0.56
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (24 bp):
AGCTTCCCGATATTGGCTCGCATG
Found at i:368356 original size:25 final size:25
Alignment explanation
Indices: 368319--368397 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
368309 CTTCCCGATT
* *
368319 ATGGCTTGGATGAGCTTCCCGTTAC
1 ATGGCTCGAATGAGCTTCCCGTTAC
* *
368344 ATGGCTC-ACATGAGCTTCTCGTTAT
1 ATGGCTCGA-ATGAGCTTCCCGTTAC
*
368369 ATGGCTCGAAAGAGCTTCCCGTTCAC
1 ATGGCTCGAATGAGCTTCCCGTT-AC
368395 ATG
1 ATG
368398 TTTGCATGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
25 39 0.89
26 5 0.11
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.30
Consensus pattern (25 bp):
ATGGCTCGAATGAGCTTCCCGTTAC
Found at i:368971 original size:22 final size:21
Alignment explanation
Indices: 368941--368985 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
368931 ACACCAAAAC
*
368941 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCG-TTTTTT
368963 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
368984 AG
1 AG
368986 CGCCGCAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGTTTTTT
Found at i:369192 original size:43 final size:43
Alignment explanation
Indices: 369140--369351 Score: 169
Period size: 43 Copynumber: 4.9 Consensus size: 43
369130 GCGCCGCTAA
* ** ***
369140 AGACCCTGATCTTTAGCGGCATTTTTTTCTCAAACGCCACAAT
1 AGACCCTGATCTATAGCGGCGCTTTCACCTCAAACGCCACAAT
* * *
369183 AGACCCTGATCTATAGCGGCGCTTTGACCACAAATGCCACGAA-
1 AGACCCTGATCTATAGCGGCGCTTTCACCTCAAACGCCAC-AAT
* * * * * *
369226 AGAACCTAATTTTTAGCGGCGCTTTCCCCTCAAACGCCGCAAT
1 AGACCCTGATCTATAGCGGCGCTTTCACCTCAAACGCCACAAT
*
369269 AGACCCTGATCTATAGCGGCGC-TTCAACCACAAACGCCACTAA-
1 AGACCCTGATCTATAGCGGCGCTTTC-ACCTCAAACGCCAC-AAT
* * * * * **
369312 AGAACCTAATCTTTAGCGACGCTTTGACCAAAAACGCCAC
1 AGACCCTGATCTATAGCGGCGCTTTCACCTCAAACGCCAC
369352 TAAATTTGGC
Statistics
Matches: 134, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
42 5 0.04
43 123 0.92
44 6 0.04
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.23
Consensus pattern (43 bp):
AGACCCTGATCTATAGCGGCGCTTTCACCTCAAACGCCACAAT
Found at i:369261 original size:86 final size:86
Alignment explanation
Indices: 369168--369336 Score: 275
Period size: 86 Copynumber: 2.0 Consensus size: 86
369158 GCATTTTTTT
** *
369168 CTCAAACGCCACAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAATGCCACGAAAGAACCT
1 CTCAAACGCCACAATAGACCCTGATCTATAGCGGCGCTTCAACCACAAACGCCACGAAAGAACCT
* *
369233 AATTTTTAGCGGCGCTTTCCC
66 AATCTTTAGCGACGCTTTCCC
* *
369254 CTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCAACCACAAACGCCACTAAAGAACCT
1 CTCAAACGCCACAATAGACCCTGATCTATAGCGGCGCTTCAACCACAAACGCCACGAAAGAACCT
369319 AATCTTTAGCGACGCTTT
66 AATCTTTAGCGACGCTTT
369337 GACCAAAAAC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (86 bp):
CTCAAACGCCACAATAGACCCTGATCTATAGCGGCGCTTCAACCACAAACGCCACGAAAGAACCT
AATCTTTAGCGACGCTTTCCC
Found at i:369355 original size:43 final size:42
Alignment explanation
Indices: 369170--369351 Score: 184
Period size: 43 Copynumber: 4.2 Consensus size: 42
369160 ATTTTTTTCT
* *
369170 CAAACGCCACAATAGACCCTGATCTATAGCGGCGCTTTGACCA
1 CAAACGCCACAA-AGAACCTAATCTATAGCGGCGCTTTGACCA
* * * ** *
369213 CAAATGCCACGAAAGAACCTAATTTTTAGCGGCGCTTTCCCCT
1 CAAACGCCAC-AAAGAACCTAATCTATAGCGGCGCTTTGACCA
* * * **
369256 CAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTCAACCA
1 CAAACGCCACAA-AGAACCTAATCTATAGCGGCGCTTTGACCA
* *
369299 CAAACGCCACTAAAGAACCTAATCTTTAGCGACGCTTTGACCA
1 CAAACGCCAC-AAAGAACCTAATCTATAGCGGCGCTTTGACCA
*
369342 AAAACGCCAC
1 CAAACGCCAC
369352 TAAATTTGGC
Statistics
Matches: 110, Mismatches: 26, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
42 2 0.02
43 104 0.95
44 4 0.04
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.19
Consensus pattern (42 bp):
CAAACGCCACAAAGAACCTAATCTATAGCGGCGCTTTGACCA
Done.