Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 15 of 15
Found at i:2404145 original size:3 final size:3
Alignment explanation
Indices: 2404137--2404162 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2404127 CTTGAAAATA
2404137 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2404163 AGATAGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2406620 original size:47 final size:48
Alignment explanation
Indices: 2406569--2406681 Score: 133
Period size: 46 Copynumber: 2.4 Consensus size: 48
2406559 CTTTTAAATT
*
2406569 TTTATTTTAAAAAATTATCCACTTAATTAAAATAAAAAAAA-TTT-ACA
1 TTTATTTTAAAAAACTATCCACTT-ATTAAAATAAAAAAAACTTTCACA
* ****
2406616 TTTATCTT-AAAAACTATCCACTTATTTTTTTAAAAAAAACTTTCACA
1 TTTATTTTAAAAAACTATCCACTTATTAAAATAAAAAAAACTTTCACA
2406663 TTTATTTTTAAAAAACTAT
1 TTTA-TTTTAAAAAACTAT
2406682 TATATGTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
45 12 0.22
46 17 0.31
47 14 0.25
48 3 0.05
49 9 0.16
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (48 bp):
TTTATTTTAAAAAACTATCCACTTATTAAAATAAAAAAAACTTTCACA
Found at i:2406670 original size:26 final size:25
Alignment explanation
Indices: 2406624--2406677 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
2406614 CATTTATCTT
2406624 AAAAACTATCCACTTATTTTTTTAAA
1 AAAAACTATCCACTTA-TTTTTTAAA
* *
2406650 AAAAACTTTCACATTTA-TTTTTAAA
1 AAAAACTATC-CACTTATTTTTTAAA
2406675 AAA
1 AAA
2406678 CTATTATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.44
26 9 0.36
27 5 0.20
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAAACTATCCACTTATTTTTTAAA
Found at i:2407609 original size:3 final size:3
Alignment explanation
Indices: 2407603--2407661 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
2407593 AAAAAAAAAC
* *
2407603 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2407651 TTA TTA TTA TT
1 TTA TTA TTA TT
2407662 TTCGTGGTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2412279 original size:2 final size:2
Alignment explanation
Indices: 2412272--2412308 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2412262 TTATTCCCTT
*
2412272 AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2412309 TTATATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:2414212 original size:2 final size:2
Alignment explanation
Indices: 2414205--2414236 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2414195 TTCACATTGA
2414205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2414237 GGATGGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2416275 original size:18 final size:18
Alignment explanation
Indices: 2416249--2416284 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2416239 TTTATCATAT
*
2416249 AAATTATATAATATATAA
1 AAATAATATAATATATAA
*
2416267 AAATAATATATTATATAA
1 AAATAATATAATATATAA
2416285 TTAAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATAATATAATATATAA
Found at i:2422165 original size:12 final size:12
Alignment explanation
Indices: 2422134--2422166 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2422124 ACTTATAATT
2422134 GAAAAAAA-AAA
1 GAAAAAAAGAAA
*
2422145 AAAAAAAAGAAA
1 GAAAAAAAGAAA
2422157 GAAAAAAAGA
1 GAAAAAAAGA
2422167 TAGGCTGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
GAAAAAAAGAAA
Found at i:2422282 original size:15 final size:15
Alignment explanation
Indices: 2422262--2422290 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2422252 TGGGTGTTGT
2422262 ATAGGGTGAGTATGC
1 ATAGGGTGAGTATGC
2422277 ATAGGGTGAGTATG
1 ATAGGGTGAGTATG
2422291 GGAGATTGTT
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:0.28, C:0.03, G:0.41, T:0.28
Consensus pattern (15 bp):
ATAGGGTGAGTATGC
Found at i:2424351 original size:20 final size:20
Alignment explanation
Indices: 2424326--2424367 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2424316 TATCATTCGT
2424326 ATATTTTATCATATAT-TAAA
1 ATATTTTAT-ATATATATAAA
*
2424346 ATATTTTATATTTATATAAA
1 ATATTTTATATATATATAAA
2424366 AT
1 AT
2424368 TTAATGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTTTATATATATATAAA
Found at i:2424422 original size:5 final size:5
Alignment explanation
Indices: 2424414--2424461 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
2424404 AATATTTTAT
*
2424414 TATTA TATTA TATTA TATTT TAATTA TATTA TATT- TA-TA TAATTA TAT
1 TATTA TATTA TATTA TATTA T-ATTA TATTA TATTA TATTA T-ATTA TAT
2424462 GTAGGAAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 1 0.03
4 3 0.08
5 26 0.70
6 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:2424439 original size:16 final size:16
Alignment explanation
Indices: 2424388--2424449 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
2424378 AATAATTCGT
*
2424388 ATTATA-TAAATTTTA
1 ATTATATTATATTTTA
* *
2424403 A-AATATTTTATTATTA
1 ATTATATTATATT-TTA
2424419 TATTATATTATATTTTA
1 -ATTATATTATATTTTA
2424436 ATTATATTATATTT
1 ATTATATTATATTT
2424450 ATATAATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 3 0.08
15 5 0.13
16 17 0.45
17 4 0.11
18 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATATTATATTTTA
Found at i:2426675 original size:14 final size:14
Alignment explanation
Indices: 2426658--2426688 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2426648 CATAATTATG
2426658 ACACAATAAAATAC
1 ACACAATAAAATAC
2426672 ACACAATAAAATAC
1 ACACAATAAAATAC
2426686 ACA
1 ACA
2426689 AACATTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.23, G:0.00, T:0.13
Consensus pattern (14 bp):
ACACAATAAAATAC
Found at i:2428628 original size:12 final size:12
Alignment explanation
Indices: 2428611--2428637 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2428601 TCATTGATTC
2428611 TTTCTTTTCTTT
1 TTTCTTTTCTTT
2428623 TTTCTTTTCTTT
1 TTTCTTTTCTTT
2428635 TTT
1 TTT
2428638 TTCTCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTCTTT
Found at i:2430027 original size:16 final size:16
Alignment explanation
Indices: 2429946--2430027 Score: 50
Period size: 16 Copynumber: 5.2 Consensus size: 16
2429936 ATATGACCCA
2429946 ATAATATAAATATTAATT
1 ATAATAT-AATATTAA-T
2429964 ATAAT-TAATCATT-AT
1 ATAATATAAT-ATTAAT
*
2429979 -TAAT-TAATA-CAAT
1 ATAATATAATATTAAT
* * *
2429992 -TAATTAAAAAATTAAA
1 ATAA-TATAATATTAAT
2430008 ATAATATAATATTAAT
1 ATAATATAATATTAAT
2430024 ATAA
1 ATAA
2430028 ATTTTATTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
13 6 0.12
14 9 0.18
15 4 0.08
16 19 0.38
17 7 0.14
18 5 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATATAATATTAAT
Found at i:2430260 original size:21 final size:21
Alignment explanation
Indices: 2430234--2430298 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
2430224 GTTTATACAA
2430234 AAAATTTATTTATATTA-ATAT
1 AAAATTTATTTA-ATTATATAT
2430255 AAAA-TTATATTAATTATATAT
1 AAAATTTAT-TTAATTATATAT
*
2430276 AAAATTTAATTTAACTATTATAT
1 AAAATTT-ATTTAATTA-TATAT
2430299 TTAATTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
20 8 0.21
21 15 0.39
22 8 0.21
23 7 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTTATTTAATTATATAT
Found at i:2430539 original size:18 final size:16
Alignment explanation
Indices: 2430506--2430551 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
2430496 ATTAATTTAT
*
2430506 TAAAATATTAATAATA
1 TAAAAAATTAATAATA
2430522 TAAAAAATTATATAAATA
1 TAAAAAATTA-AT-AATA
*
2430540 TATAAAATTAAT
1 TAAAAAATTAAT
2430552 TTAATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 4 0.15
18 13 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAAATTAATAATA
Found at i:2430868 original size:11 final size:12
Alignment explanation
Indices: 2430851--2430879 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2430841 AGCATTATCT
2430851 AATAATTGACTC
1 AATAATTGACTC
2430863 -ATAATTGACTC
1 AATAATTGACTC
2430874 AATAAT
1 AATAAT
2430880 AAATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (12 bp):
AATAATTGACTC
Found at i:2432097 original size:25 final size:25
Alignment explanation
Indices: 2432069--2432118 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2432059 AATTTTATCA
*
2432069 AAATTTAAATT-AAATTTTAAATTTT
1 AAATTTAAATTCAAA-CTTAAATTTT
*
2432094 AAATTTAGATTCAAACTTAAATTTT
1 AAATTTAAATTCAAACTTAAATTTT
2432119 TTTTTGGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (25 bp):
AAATTTAAATTCAAACTTAAATTTT
Found at i:2438087 original size:23 final size:23
Alignment explanation
Indices: 2438052--2438106 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
2438042 CGAGCCATAA
* * *
2438052 AACTCTGATTCTGTCATTGCCCT
1 AACTTTGAGTCTGTAATTGCCCT
2438075 AACTTTGAGTCTGTAATTGCCCT
1 AACTTTGAGTCTGTAATTGCCCT
2438098 AACTTTGAG
1 AACTTTGAG
2438107 AAAACCTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (23 bp):
AACTTTGAGTCTGTAATTGCCCT
Found at i:2438450 original size:2 final size:2
Alignment explanation
Indices: 2438443--2438482 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2438433 AATCTTCTCA
2438443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2438483 GTAACAACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2438787 original size:16 final size:16
Alignment explanation
Indices: 2438756--2438796 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2438746 TTTATGTATG
2438756 TTATAAATTTATAATT
1 TTATAAATTTATAATT
2438772 TTATCAAATTTA-AATT
1 TTAT-AAATTTATAATT
*
2438788 AT-TAAATTT
1 TTATAAATTT
2438797 TTATTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.26
15 1 0.04
16 9 0.39
17 7 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATAAATTTATAATT
Found at i:2438813 original size:22 final size:22
Alignment explanation
Indices: 2438788--2438844 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
2438778 AATTTAAATT
*
2438788 ATTAAAT-TTTTATTATTAATAA
1 ATTAAATAATTTA-TATTAATAA
**
2438810 ATTAAATAATTTATATTAATTTT
1 ATTAAATAATTTATATTAA-TAA
2438833 ATTAAATAATTT
1 ATTAAATAATTT
2438845 TAATAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTAAATAATTTATATTAATAA
Found at i:2439502 original size:31 final size:30
Alignment explanation
Indices: 2439467--2439532 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
2439457 TAATCCCATC
2439467 ATAAATAATAAAAATAACTATAATAA-ATAAT
1 ATAAATAAT-AAAATAACT-TAATAATATAAT
**
2439498 ATAAAATAATTGAATAACTTAATAATATAAT
1 AT-AAATAATAAAATAACTTAATAATATAAT
2439529 ATAA
1 ATAA
2439533 TATTGTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 8 0.26
31 16 0.52
32 7 0.23
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (30 bp):
ATAAATAATAAAATAACTTAATAATATAAT
Found at i:2439532 original size:18 final size:18
Alignment explanation
Indices: 2439470--2439532 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
2439460 TCCCATCATA
*
2439470 AATAATA-AAAATAACTAT
1 AATAATATAATATAACT-T
2439488 AATAA-ATAATATAA---
1 AATAATATAATATAACTT
*
2439502 AATAAT-TGA-ATAACTT
1 AATAATATAATATAACTT
2439518 AATAATATAATATAA
1 AATAATATAATATAA
2439533 TATTGTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
13 4 0.11
14 7 0.20
16 6 0.17
17 3 0.09
18 15 0.43
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (18 bp):
AATAATATAATATAACTT
Found at i:2447983 original size:15 final size:15
Alignment explanation
Indices: 2447965--2448040 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
2447955 GACAAATGAT
2447965 AAGGAAACGAATGGC
1 AAGGAAACGAATGGC
* * * *
2447980 AAGGACATGGATGAC
1 AAGGAAACGAATGGC
*
2447995 AAGGAAACAAATGGC
1 AAGGAAACGAATGGC
* *
2448010 AAGGACAC-AGATGAC
1 AAGGAAACGA-ATGGC
2448025 AAGGAAACGAATGGC
1 AAGGAAACGAATGGC
2448040 A
1 A
2448041 TCAAAGTTCA
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
14 1 0.02
15 44 0.96
16 1 0.02
ACGTcount: A:0.47, C:0.14, G:0.30, T:0.08
Consensus pattern (15 bp):
AAGGAAACGAATGGC
Found at i:2447999 original size:30 final size:30
Alignment explanation
Indices: 2447960--2448040 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
2447950 AGAAAGACAA
* **
2447960 ATGATAAGGAAACGAATGGCAAGGACATGG
1 ATGACAAGGAAACGAATGGCAAGGACACAG
*
2447990 ATGACAAGGAAACAAATGGCAAGGACACAG
1 ATGACAAGGAAACGAATGGCAAGGACACAG
2448020 ATGACAAGGAAACGAATGGCA
1 ATGACAAGGAAACGAATGGCA
2448041 TCAAAGTTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.47, C:0.14, G:0.30, T:0.10
Consensus pattern (30 bp):
ATGACAAGGAAACGAATGGCAAGGACACAG
Found at i:2450939 original size:17 final size:17
Alignment explanation
Indices: 2450917--2450951 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2450907 GCCATTTGTA
2450917 TTAATTTTCAAAATTTT
1 TTAATTTTCAAAATTTT
**
2450934 TTAATTTTTTAAATTTT
1 TTAATTTTCAAAATTTT
2450951 T
1 T
2450952 ATGGTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTTCAAAATTTT
Found at i:2451928 original size:18 final size:17
Alignment explanation
Indices: 2451868--2451925 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
2451858 AATCGATTAG
2451868 TTTTTAATTATATAATGT
1 TTTTTAATTATATAAT-T
* * *
2451886 ATATTAATTTTAT-ATT
1 TTTTTAATTATATAATT
*
2451902 TATTTATATTATATAATT
1 TTTTTA-ATTATATAATT
2451920 TTTTTA
1 TTTTTA
2451926 TATAAAGAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
16 4 0.13
17 8 0.27
18 18 0.60
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTAATTATATAATT
Found at i:2452135 original size:24 final size:22
Alignment explanation
Indices: 2452099--2452143 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
2452089 ATATAAGTAA
2452099 ATTTTAATAAAATTTAAAATTTAT
1 ATTTTAATAAAA-TT-AAATTTAT
2452123 ATTTTAA-ATAAATTAAATTTA
1 ATTTTAATA-AAATTAAATTTA
2452144 AATAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTTAATAAAATTAAATTTAT
Found at i:2452145 original size:15 final size:16
Alignment explanation
Indices: 2452125--2452156 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2452115 AAATTTATAT
2452125 TTTAAATAAAT-TAAA
1 TTTAAATAAATATAAA
2452140 TTTAAATAAATATAAA
1 TTTAAATAAATATAAA
2452156 T
1 T
2452157 AATATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAATAAATATAAA
Found at i:2452865 original size:10 final size:10
Alignment explanation
Indices: 2452834--2452867 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2452824 TAAAAAATTA
*
2452834 AAAAATAATT
1 AAAAATAAAT
2452844 AAAAATAAAAT
1 AAAAAT-AAAT
2452855 AAAAATAAAT
1 AAAAATAAAT
2452865 AAA
1 AAA
2452868 TTTAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:2453522 original size:19 final size:20
Alignment explanation
Indices: 2453468--2453534 Score: 91
Period size: 20 Copynumber: 3.3 Consensus size: 20
2453458 ATATAAAGTT
2453468 ATTTAAACTTAAATGATTTA
1 ATTTAAACTTAAATGATTTA
* *
2453488 ATTTAATATTTTAAATAATTT-
1 ATTTAA-A-CTTAAATGATTTA
2453509 ATTTAAACTTAAATGATTTA
1 ATTTAAACTTAAATGATTTA
2453529 ATTTAA
1 ATTTAA
2453535 TATTCTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 10 0.25
20 13 0.32
21 7 0.17
22 10 0.25
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTTAAACTTAAATGATTTA
Found at i:2455722 original size:23 final size:24
Alignment explanation
Indices: 2455696--2455765 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
2455686 ATAATCAAAT
2455696 TTTATTTTTAAAATTTAAATTT-A
1 TTTATTTTTAAAATTTAAATTTAA
*
2455719 TTTATTTTATAAAAATT-AATTTAA
1 TTTATTTT-TAAAATTTAAATTTAA
*
2455743 TTT-TTATATTAAATTTTAAATTT
1 TTTATT-T-TTAAAATTTAAATTT
2455766 GATTATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 15 0.38
24 18 0.46
25 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTTTTAAAATTTAAATTTAA
Found at i:2455731 original size:24 final size:25
Alignment explanation
Indices: 2455696--2455765 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 25
2455686 ATAATCAAAT
2455696 TTTATTTT-TAAAATTTAAATTT-A
1 TTTATTTTATAAAATTTAAATTTAA
*
2455719 TTTATTTTATAAAAATT-AATTTAA
1 TTTATTTTATAAAATTTAAATTTAA
* *
2455743 TTT-TTATATTAAATTTTAAATTT
1 TTTATTTTA-TAAAATTTAAATTT
2455766 GATTATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 17 0.44
24 17 0.44
25 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTATTTTATAAAATTTAAATTTAA
Found at i:2456301 original size:34 final size:31
Alignment explanation
Indices: 2456234--2456301 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 31
2456224 AAACTGCCTG
*
2456234 AAAAAAAAAAAAACAATAAAAACCTTTAAAA
1 AAAAAAAAAAAAACAATAAAAAACTTTAAAA
* *
2456265 AAAAAACAAAGAAAATAATAAATAAATTTTAAAA
1 AAAAAA-AAA-AAAACAATAAA-AAACTTTAAAA
2456299 AAA
1 AAA
2456302 TGAATAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.19
32 3 0.10
33 10 0.32
34 12 0.39
ACGTcount: A:0.76, C:0.06, G:0.01, T:0.16
Consensus pattern (31 bp):
AAAAAAAAAAAAACAATAAAAAACTTTAAAA
Found at i:2456820 original size:2 final size:2
Alignment explanation
Indices: 2456813--2456846 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2456803 CTTAATTGTG
2456813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2456847 ATTACAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2457159 original size:33 final size:34
Alignment explanation
Indices: 2457093--2457180 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 34
2457083 TTTATAATTT
*
2457093 TAATAATT-TTTTATTATTAATA-TTAATATTAA
1 TAATATTTATTTTATTATTAATATTTAATATTAA
* *
2457125 T-ATTTTATATTTTATTATTAATATTTATTA-TAA
1 TAATATT-TATTTTATTATTAATATTTAATATTAA
*
2457158 TAATATTTA-TTTATTATTTATAT
1 TAATATTTATTTTATTATTAATAT
2457181 ATTCATAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
31 3 0.06
32 15 0.32
33 20 0.43
34 9 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (34 bp):
TAATATTTATTTTATTATTAATATTTAATATTAA
Found at i:2457159 original size:45 final size:44
Alignment explanation
Indices: 2457064--2457159 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 44
2457054 CGATAGTAAA
* *
2457064 ATAATATTAAAATTATTATTTTATAATTTTAATAATTTTTTATT
1 ATAATATTAAAATTAATATTTTATAATTTTAATAATTATTTATT
*
2457108 ATTAATATTAATATTAATATTTTAT-ATTTTATTATTAA-TATTTATT
1 A-TAATATTAAAATTAATATTTTATAATTTTA--A-TAATTATTTATT
2457154 ATAATA
1 ATAATA
2457160 ATATTTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
44 7 0.16
45 26 0.58
46 9 0.20
47 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (44 bp):
ATAATATTAAAATTAATATTTTATAATTTTAATAATTATTTATT
Found at i:2457161 original size:15 final size:13
Alignment explanation
Indices: 2457102--2457173 Score: 66
Period size: 12 Copynumber: 5.8 Consensus size: 13
2457092 TTAATAATTT
2457102 TTTATTATTAATA
1 TTTATTATTAATA
*
2457115 -TTAATATTAATA
1 TTTATTATTAATA
2457127 -TT-TTA-T-AT-
1 TTTATTATTAATA
2457135 TTTATTATTAATA
1 TTTATTATTAATA
2457148 TTTATTATAATAATA
1 TTTATTAT--TAATA
2457163 TTTATTTATTA
1 TTTA-TTATTA
2457174 TTTATATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
9 4 0.08
10 4 0.08
11 3 0.06
12 15 0.31
13 8 0.16
14 2 0.04
15 9 0.18
16 4 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:2457164 original size:21 final size:21
Alignment explanation
Indices: 2457106--2457183 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
2457096 TAATTTTTTA
2457106 TTATTAATATTAATATTAATAT
1 TTATT-ATATTAATATTAATAT
* *
2457128 TT-TATATTTTATTATTAATAT
1 TTAT-TATATTAATATTAATAT
*
2457149 TTATTATAATAATATT--TAT
1 TTATTATATTAATATTAATAT
2457168 TTATTAT-TTATATATT
1 TTATTATATTA-ATATT
2457184 CATAATAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
18 2 0.04
19 15 0.32
21 26 0.55
22 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTATATTAATATTAATAT
Found at i:2457195 original size:32 final size:31
Alignment explanation
Indices: 2457076--2457191 Score: 84
Period size: 33 Copynumber: 3.8 Consensus size: 31
2457066 AATATTAAAA
* *
2457076 TTATTATTTTATA-ATTTTAAT-A-ATTT-T
1 TTATTATTATATATATTATAATAATATTTAT
* *
2457103 TTATTATTA-ATATTAATATTAAT-ATTTTATATT
1 TTATTATTATATA-TATTA-TAATAATATT-TA-T
*
2457136 TTATTATTAATATTTATTATAATAATATTTAT
1 TTATTATT-ATATATATTATAATAATATTTAT
2457168 TTATTATT-TATATATTCATAATAA
1 TTATTATTATATATATT-ATAATAA
2457192 ATATAAAATG
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
26 3 0.04
27 8 0.11
28 2 0.03
29 5 0.07
30 9 0.13
31 8 0.11
32 9 0.13
33 15 0.21
34 9 0.13
35 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (31 bp):
TTATTATTATATATATTATAATAATATTTAT
Done.