Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold480.1
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: 1027035
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.32
Warning! 12152 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:954295 original size:17 final size:18
Alignment explanation
Indices: 954273--954306 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
954263 CGTTTTAATT
*
954273 AATATT-TTTTATTTAAA
1 AATATTATTATATTTAAA
954290 AATATTATTATATTTAA
1 AATATTATTATATTTAA
954307 TTAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTATTATATTTAAA
Found at i:955057 original size:19 final size:19
Alignment explanation
Indices: 955043--955086 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
955033 ATTTAATATT
955043 TTTTA-TAAAATTTAAACA
1 TTTTATTAAAATTTAAACA
955061 TTTTATTAAAATTTAAACA
1 TTTTATTAAAATTTAAACA
955080 TTTTATT
1 TTTTATT
955087 TTACTAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTATTAAAATTTAAACA
Found at i:958279 original size:31 final size:31
Alignment explanation
Indices: 958199--958263 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
958189 TATTTTGATC
* *
958199 CAATTAAGCACATGAACTCGGCTTCTTAGTT
1 CAATTAAGCACATGAACTTGGCTGCTTAGTT
958230 CAATTAAGCACATGAACTTGGCTGCTTAGTT
1 CAATTAAGCACATGAACTTGGCTGCTTAGTT
958261 CAA
1 CAA
958264 ATTGGCACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (31 bp):
CAATTAAGCACATGAACTTGGCTGCTTAGTT
Found at i:960197 original size:30 final size:31
Alignment explanation
Indices: 960162--960226 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
960152 TAGTAATAAA
960162 ATAAATTA-TTAATATAATTAATTAT-TTTTT
1 ATAAATTATTTAATATAA-TAATTATATTTTT
* *
960192 ATAAATTATTTAATATTATAATTTTATTTTT
1 ATAAATTATTTAATATAATAATTATATTTTT
960223 ATAA
1 ATAA
960227 TAAATATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
ATAAATTATTTAATATAATAATTATATTTTT
Found at i:960210 original size:17 final size:17
Alignment explanation
Indices: 960162--960212 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 17
960152 TAGTAATAAA
*
960162 ATAAATTA-TTAATATA
1 ATAAATTATTTAATATT
*
960178 ATTAATTATTT--T-TT
1 ATAAATTATTTAATATT
960192 ATAAATTATTTAATATT
1 ATAAATTATTTAATATT
960209 ATAA
1 ATAA
960213 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 8 0.29
17 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATAAATTATTTAATATT
Found at i:960230 original size:34 final size:31
Alignment explanation
Indices: 960161--960231 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 31
960151 TTAGTAATAA
960161 AATAAATTATTAATATAATTAATTATTTTTT
1 AATAAATTATTAATATAATTAATTATTTTTT
*
960192 -ATAAATTATTTAATATTA-TAATTTTATTTTTAT
1 AATAAATTA-TTAATATAATTAA--TTATTTTT-T
960225 AATAAAT
1 AATAAAT
960232 ATACATTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
30 11 0.32
31 8 0.24
32 8 0.24
33 1 0.03
34 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
AATAAATTATTAATATAATTAATTATTTTTT
Found at i:960558 original size:22 final size:23
Alignment explanation
Indices: 960505--960560 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
960495 CCCATTTTTA
* * *
960505 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
960528 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
960550 ATTAAAATTAA
1 ATTAAAATTAA
960561 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:960573 original size:16 final size:16
Alignment explanation
Indices: 960536--960575 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
960526 TTAATAAAAT
* *
960536 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
960552 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
960568 TAAAATTA
1 TAAAATTA
960576 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:960654 original size:59 final size:61
Alignment explanation
Indices: 960585--960764 Score: 256
Period size: 68 Copynumber: 2.9 Consensus size: 61
960575 ATCAAATTAT
*
960585 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
*
960650 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTATATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
960713 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
960765 ACAAACTTGA
Statistics
Matches: 108, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
59 47 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 53 0.49
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:960681 original size:9 final size:9
Alignment explanation
Indices: 960648--960675 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
960638 TTTATCAAAT
960648 TATTAATTG
1 TATTAATTG
960657 TATTAATTG
1 TATTAATTG
960666 TATTAATTG
1 TATTAATTG
960675 T
1 T
960676 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:960685 original size:68 final size:68
Alignment explanation
Indices: 960564--960734 Score: 310
Period size: 68 Copynumber: 2.5 Consensus size: 68
960554 AAATTAATTG
*
960564 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
960627 TGA
66 TGA
960630 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
960695 TGA
66 TGA
*
960698 TTAGTATATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
960735 TGTAACAAAA
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
66 26 0.26
68 75 0.74
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:960855 original size:23 final size:24
Alignment explanation
Indices: 960829--960879 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
960819 GTAAATAAAC
960829 TTAAAATAAAAA-ACTAT-TATAT-T
1 TTAAAA-AAAAATA-TATATATATAT
960852 TTAAAAAAAAATATATATATATAT
1 TTAAAAAAAAATATATATATATAT
960876 TTAA
1 TTAA
960880 TATTTTTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.32
23 12 0.48
24 5 0.20
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAAAAAAAAATATATATATATAT
Found at i:961193 original size:18 final size:17
Alignment explanation
Indices: 961170--961204 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
961160 TATGATATTG
*
961170 ATTATTATAAAATATTTT
1 ATTATTA-AAAAAATTTT
961188 ATTATTAAAAAAATTTT
1 ATTATTAAAAAAATTTT
961205 TGATGGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTAAAAAAATTTT
Found at i:961376 original size:20 final size:20
Alignment explanation
Indices: 961345--961382 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
961335 ACAATAGAAT
961345 ATCAATTTTTTTAGAAAATTA
1 ATCAATTTTTTTA-AAAATTA
961366 ATCAA-TTTTTTAAAAAT
1 ATCAATTTTTTTAAAAAT
961383 AATTTTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
ATCAATTTTTTTAAAAATTA
Found at i:961380 original size:18 final size:20
Alignment explanation
Indices: 961345--961385 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
961335 ACAATAGAAT
*
961345 ATCAATTTTTTTAGAAAATTA
1 ATCAATTTTTTTA-AAAAATA
961366 ATCAA-TTTTTT-AAAAATA
1 ATCAATTTTTTTAAAAAATA
961384 AT
1 AT
961386 TTTTCGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (20 bp):
ATCAATTTTTTTAAAAAATA
Found at i:962015 original size:36 final size:36
Alignment explanation
Indices: 961965--962051 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 36
961955 TTTCTTTTTT
* * **
961965 TATTGTTGTT-TTGTTGTTATTTCGTTATTATATTGC
1 TATTGTT-TTATTGTTATTATTTCGATATTATATAAC
* *
962001 TATTGTTTTATTGTTATTGTTTGGATATTATATAAC
1 TATTGTTTTATTGTTATTATTTCGATATTATATAAC
*
962037 TCTTG-TTTATTGTTA
1 TATTGTTTTATTGTTA
962052 ATTTTGCTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 12 0.28
36 31 0.72
ACGTcount: A:0.18, C:0.05, G:0.15, T:0.62
Consensus pattern (36 bp):
TATTGTTTTATTGTTATTATTTCGATATTATATAAC
Found at i:966001 original size:49 final size:50
Alignment explanation
Indices: 965923--966020 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 50
965913 TATGTATTTG
*
965923 GAAGATCGAATAAAAAAAAGAAAAAGAGTGGATTCTTTGAGTGTAAGTTA
1 GAAGATCGAATAAAAAAAAGAAAAAGAGTGGATTCTTGGAGTGTAAGTTA
965973 GAAGATCGAAT-AAAAAAAGAAAAAGAGTGGATTCTTGGAGTGTAAGTT
1 GAAGATCGAATAAAAAAAAGAAAAAGAGTGGATTCTTGGAGTGTAAGTT
966021 TGATTCTGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 36 0.77
50 11 0.23
ACGTcount: A:0.47, C:0.04, G:0.26, T:0.23
Consensus pattern (50 bp):
GAAGATCGAATAAAAAAAAGAAAAAGAGTGGATTCTTGGAGTGTAAGTTA
Found at i:970841 original size:41 final size:41
Alignment explanation
Indices: 970779--970860 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
970769 AGTTTAGTCC
*
970779 TAATTTTAAGTAAATCGATAAATATATAAAATTGTTCAATT
1 TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
970820 TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
1 TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
970861 AGATAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (41 bp):
TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
Found at i:973170 original size:44 final size:43
Alignment explanation
Indices: 973114--973200 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 43
973104 ATTTTTTTAA
973114 TTTTAAAATACTTTTTTTTTAAATTTT-TTTTAA-TTTTAAAATAT
1 TTTTAAAATAC--TTTTTTT-AATTTTATTTTAATTTTTAAAATAT
973158 TTTTAAAATACTTTTTTTAATTTTAATTTTAATTTTTAAAATA
1 TTTTAAAATACTTTTTTTAATTTT-ATTTTAATTTTTAAAATA
973201 AATTTTTGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
41 6 0.15
42 7 0.17
43 6 0.15
44 21 0.52
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (43 bp):
TTTTAAAATACTTTTTTTAATTTTATTTTAATTTTTAAAATAT
Found at i:973200 original size:33 final size:31
Alignment explanation
Indices: 973105--973183 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 31
973095 TTATTTTTTA
*
973105 TTTTTTTAATTTTAAAATACTTTTTTTTTAAAT--
1 TTTTTTTAATTTTAAAATA----TTTTTAAAATAC
973138 TTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAATATTTTTAAAATAC
973169 TTTTTTTAATTTTAA
1 TTTTTTTAATTTTAA
973184 TTTTAATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 9 0.21
31 15 0.35
33 19 0.44
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:973207 original size:33 final size:31
Alignment explanation
Indices: 973106--973207 Score: 89
Period size: 33 Copynumber: 3.2 Consensus size: 31
973096 TATTTTTTAT
***
973106 TTTTTTAATTTTAAAATACTTTTT-TTTTAAA
1 TTTTTTAATTTTAAAATA-TTTTTAAAATAAA
**
973137 TTTTTTTTAATTTTAAAATATTTTTAAAATACT
1 --TTTTTTAATTTTAAAATATTTTTAAAATAAA
**
973170 TTTTTTAATTTTAATTTTAATTTTTAAAATAAA
1 TTTTTTAATTTTAA-AAT-ATTTTTAAAATAAA
973203 TTTTT
1 TTTTT
973208 GGTATTTATT
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
31 14 0.25
32 6 0.11
33 37 0.65
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (31 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAAA
Found at i:981990 original size:28 final size:29
Alignment explanation
Indices: 981954--982013 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
981944 ATTGAAAATA
981954 TTTAATTTT-AGAATTTAGTCCATTTACT
1 TTTAATTTTAAGAATTTAGTCCATTTACT
* * * *
981982 TTTATTTTTAAGAATTTATTCCTTTTATT
1 TTTAATTTTAAGAATTTAGTCCATTTACT
982011 TTT
1 TTT
982014 CAAATTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.62
Consensus pattern (29 bp):
TTTAATTTTAAGAATTTAGTCCATTTACT
Found at i:983396 original size:15 final size:14
Alignment explanation
Indices: 983366--983403 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
983356 ACCTAATTGA
983366 TTTCTATTTTAGTTT
1 TTTCT-TTTTAGTTT
*
983381 TTTCTTTTTAGCTT
1 TTTCTTTTTAGTTT
983395 TTT-TTTTTA
1 TTTCTTTTTA
983404 AGTTGACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 11 0.50
15 5 0.23
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTCTTTTTAGTTT
Found at i:989758 original size:163 final size:161
Alignment explanation
Indices: 989480--989966 Score: 523
Period size: 163 Copynumber: 3.0 Consensus size: 161
989470 TTGAGTCGAG
* * * *
989480 GCAAGG-GGATTTTATCTAAAACCGCCCCCAAT-ATGCCCTGAAAA-TTCAGCCAAGTAACTAAC
1 GCAAGGTGGATTTTATCTAGAACCGCCCCC-ATCATG-CCTGAAAATTTCAGCTAAGAAACCAAC
* **
989542 ATGCCTAGCCTCTGAACTCGATTGTCAGATAAAAGAAAGACCTATAAGGTGAGGTTGAAACCTGA
64 ATGCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGACCTATAAGGTGAGGTTGAAACCCAA
* * *
989607 AAAGTTAGGTTATTTTTCCTCATATATGTTCGGA
129 AAAGTTAGATTATTTCTCC-CATATAAGTTCGGA
* * * *
989641 GCAAGGTGGATTTTATCTAGAACCACTCCCATCCTGCCATGAAAATTTCAGCTATGAAACCAACA
1 GCAAGGTGGATTTTATCTAGAACCGCCCCCATCATGCC-TGAAAATTTCAGCTAAGAAACCAACA
* *
989706 TGCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGCCCTATAGGGTGAGGTTGAAACCCAAA
65 TGCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGACCTATAAGGTGAGGTTGAAACCCAAA
* * *
989771 AAGTTCGATTGTTTCTCCCATATAAGTTCGGG
130 AAGTTAGATTATTTCTCCCATATAAGTTCGGA
* * * * * *
989803 GCAAGGTGGATTTTATCTAGAACTGCCCCACAACTTGTCCCGAAAATTTCAGATAAGAAATCAAC
1 GCAAGGTGGATTTTATCTAGAACCGCCCC-CATCATG-CCTGAAAATTTCAGCTAAGAAACCAAC
* * * * * * * *
989868 ATGCCTAGCCTCCGACCTCAATTGTGAGAAAAAAAAAAAAGACTTAATAGGGGGAGGTTGAAACC
64 ATGCCTAGCCTCCGAACTCGATTGTCAG--ATAAAAGAAAGACCT-ATAAGGTGAGGTTGAAACC
* * * * *
989933 CAAAAATTTCGGTTTTTTC-CCCATGTAAGTTCGG
126 CAAAAAGTTAGATTATTTCTCCCATATAAGTTCGG
989967 TTGAAACTCG
Statistics
Matches: 277, Mismatches: 40, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
161 10 0.04
162 66 0.24
163 140 0.51
164 2 0.01
165 25 0.09
166 34 0.12
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (161 bp):
GCAAGGTGGATTTTATCTAGAACCGCCCCCATCATGCCTGAAAATTTCAGCTAAGAAACCAACAT
GCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGACCTATAAGGTGAGGTTGAAACCCAAAA
AGTTAGATTATTTCTCCCATATAAGTTCGGA
Found at i:991615 original size:20 final size:21
Alignment explanation
Indices: 991590--991628 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
991580 ATTTCTAATT
*
991590 TATATTTTTA-AATTATTTGA
1 TATATTTTAACAATTATTTGA
991610 TATATTTTAACAATTATTT
1 TATATTTTAACAATTATTT
991629 ATTTTACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (21 bp):
TATATTTTAACAATTATTTGA
Found at i:993764 original size:9 final size:9
Alignment explanation
Indices: 993750--993777 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
993740 GATTTAAAAG
993750 AAAATTAAA
1 AAAATTAAA
993759 AAAATTAAA
1 AAAATTAAA
993768 AAAATTAAA
1 AAAATTAAA
993777 A
1 A
993778 TGTCAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATTAAA
Found at i:994484 original size:13 final size:13
Alignment explanation
Indices: 994466--994490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
994456 CATGAACTCA
994466 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
994479 TTTTCTTTTTTT
1 TTTTCTTTTTTT
994491 TTTGGTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:1000532 original size:3 final size:3
Alignment explanation
Indices: 1000526--1000557 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
1000516 ATAATAATAA
1000526 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT T
1000558 TTAGAGTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1000549 original size:13 final size:13
Alignment explanation
Indices: 1000526--1000558 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1000516 ATAATAATAA
1000526 TATTA-TTATTAT
1 TATTATTTATTAT
1000538 TATTATTTATTAT
1 TATTATTTATTAT
1000551 TATTATTT
1 TATTATTT
1000559 TAGAGTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:1002877 original size:15 final size:16
Alignment explanation
Indices: 1002854--1002892 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1002844 TCCAATCTTG
* *
1002854 AACCTTAAAAAC-TCA
1 AACCCTAAAAACATAA
1002869 AACCCTAAAAACATAA
1 AACCCTAAAAACATAA
1002885 AACCCTAA
1 AACCCTAA
1002893 CTCTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.15
Consensus pattern (16 bp):
AACCCTAAAAACATAA
Found at i:1008305 original size:20 final size:20
Alignment explanation
Indices: 1008280--1008319 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1008270 TTTCTGGCTC
1008280 AGTTCTGTTCTCTTTTGCAT
1 AGTTCTGTTCTCTTTTGCAT
1008300 AGTTCTGTTCTCTTTTGCAT
1 AGTTCTGTTCTCTTTTGCAT
1008320 CAAAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.20, G:0.15, T:0.55
Consensus pattern (20 bp):
AGTTCTGTTCTCTTTTGCAT
Found at i:1008759 original size:3 final size:3
Alignment explanation
Indices: 1008747--1008776 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1008737 TTTAGGGATC
1008747 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1008777 TCTTTTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1013391 original size:78 final size:78
Alignment explanation
Indices: 1013262--1013418 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
1013252 AAGGTATCGG
1013262 TGCTCAAATTGAACATCTTGCTCGATTCCCTAATAATCATGAGTAAAACAAAAATGAGCTTCAAA
1 TGCTCAAATTGAACATCTTGCTCGATTCCCTAATAATCATGAGTAAAACAAAAATGAGCTTCAAA
1013327 ATATACAAAAACA
66 ATATACAAAAACA
*
1013340 TGCTCAAATTGAACGTCTTGCTCGATTCCCTAATAATCATGAGTAAAACAAAAATGAGCTTCAAA
1 TGCTCAAATTGAACATCTTGCTCGATTCCCTAATAATCATGAGTAAAACAAAAATGAGCTTCAAA
1013405 ATATACAAAAACA
66 ATATACAAAAACA
1013418 T
1 T
1013419 TGAATATCTA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (78 bp):
TGCTCAAATTGAACATCTTGCTCGATTCCCTAATAATCATGAGTAAAACAAAAATGAGCTTCAAA
ATATACAAAAACA
Found at i:1014377 original size:14 final size:15
Alignment explanation
Indices: 1014351--1014381 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1014341 TCCGGGTTCA
1014351 TCAACACATTTTTCT
1 TCAACACATTTTTCT
1014366 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
1014380 TC
1 TC
1014382 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:1017266 original size:2 final size:2
Alignment explanation
Indices: 1017259--1017285 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1017249 CCTCCCTCAA
1017259 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 A
1017286 AACTGAGCAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1022502 original size:38 final size:38
Alignment explanation
Indices: 1022460--1022537 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
1022450 GATGTGTATG
* *
1022460 TAGATATATATAGTCATGTGTATAAATTATAGAACATA
1 TAGATATATATAGTCATGTGCATAAATTATAAAACATA
*
1022498 TAGATATATATAGTCGTGTGCATAAATTATAAAACATA
1 TAGATATATATAGTCATGTGCATAAATTATAAAACATA
1022536 TA
1 TA
1022538 AAAATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (38 bp):
TAGATATATATAGTCATGTGCATAAATTATAAAACATA
Done.