Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold220
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: 1016241
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 65273 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:864252 original size:28 final size:28
Alignment explanation
Indices: 864220--864280 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
864210 GCCTTATACC
864220 ATAAATCATGAAATTGAATTATTCATTT
1 ATAAATCATGAAATTGAATTATTCATTT
864248 ATAAATCATGAAATTGAATTATTCATTT
1 ATAAATCATGAAATTGAATTATTCATTT
*
864276 TTAAA
1 ATAAA
864281 GATACTGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (28 bp):
ATAAATCATGAAATTGAATTATTCATTT
Found at i:868716 original size:36 final size:36
Alignment explanation
Indices: 868643--868716 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 36
868633 AATAGCATAA
* * * *
868643 GAAGAAGAAATTCATACAAGTAATATATTATTAAAT
1 GAAGAAGAAATTCATACAAGGAAGACATTACTAAAT
* * *
868679 GAAGGAGAAATTCATACAAGGAAGGCATTACTGAAT
1 GAAGAAGAAATTCATACAAGGAAGACATTACTAAAT
868715 GA
1 GA
868717 GCAAAGTGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (36 bp):
GAAGAAGAAATTCATACAAGGAAGACATTACTAAAT
Found at i:881828 original size:31 final size:31
Alignment explanation
Indices: 881791--881852 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
881781 ATTGTCTCAA
881791 AAAAAAAAAAAAACTCATCTTAAGAACTAAC
1 AAAAAAAAAAAAACTCATCTTAAGAACTAAC
881822 AAAAAAAAAAAAACTCATCTTAAGAACTAAC
1 AAAAAAAAAAAAACTCATCTTAAGAACTAAC
881853 CTAAAGAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.65, C:0.16, G:0.03, T:0.16
Consensus pattern (31 bp):
AAAAAAAAAAAAACTCATCTTAAGAACTAAC
Found at i:894786 original size:2 final size:2
Alignment explanation
Indices: 894775--894812 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
894765 AATATGTTTC
894775 AT AT AT -T 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 AT AT A
894813 ATTTTTAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:895691 original size:109 final size:106
Alignment explanation
Indices: 895497--895694 Score: 288
Period size: 109 Copynumber: 1.8 Consensus size: 106
895487 AAAATTCAAG
*
895497 AGGATATTTAGCAATTTGGTTAAAAGAGAAATCGAAACCCAGCACCTTAGAGAACGTTCCTCGAA
1 AGGATATTTAGCAATTTGGTTAAAAGAAAAATCGAAACCCAGCACCTTAGAGAACGTTCCTCGAA
895562 TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGGA
66 TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGGA
* * * * * * *
895603 AGGATATTTAGCTATTTGGTTTAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTC
1 AGGATATTTAGCAATTTGG-TTAA-AAGAAAAATCGAAACCCAGCACCTTAGAGAACG-TTCCTC
*
895668 GAATTTTCAAACGCAAAACATTGCCTT
63 GAATTTCCAAACGCAAAACATTGCCTT
895695 TATTATTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
106 18 0.22
107 4 0.05
108 27 0.34
109 31 0.39
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (106 bp):
AGGATATTTAGCAATTTGGTTAAAAGAAAAATCGAAACCCAGCACCTTAGAGAACGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGGA
Found at i:895970 original size:4 final size:4
Alignment explanation
Indices: 895961--895994 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
895951 AATATAATGG
*
895961 ATAA ATAA ATAA GTAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
895995 GTATCAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:898337 original size:6 final size:6
Alignment explanation
Indices: 898313--898352 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
898303 GCATTTGATT
*
898313 TTATAA TTAT-A TAATTAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTA-TAA TTATAA TTATAA TTATAA TTAT
898353 TCGATTACGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 3 0.10
6 24 0.80
7 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:902401 original size:9 final size:9
Alignment explanation
Indices: 902387--902417 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
902377 GTTAAACGAA
902387 TCGAGTTAT
1 TCGAGTTAT
*
902396 TCGAGTTAA
1 TCGAGTTAT
902405 TCGAGTTAT
1 TCGAGTTAT
902414 TCGA
1 TCGA
902418 ATCAATTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:902589 original size:21 final size:21
Alignment explanation
Indices: 902548--902590 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
902538 ACCCCAAACT
* *
902548 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
902569 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
902590 C
1 C
902591 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:903300 original size:5 final size:5
Alignment explanation
Indices: 903290--903315 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
903280 CTCAAAAATT
903290 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
903316 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:910965 original size:24 final size:24
Alignment explanation
Indices: 910950--911001 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
910940 AATCAAATTC
*
910950 AAATATATTATGCTAATATATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
910974 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
910998 AAAT
1 AAAT
911002 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:925092 original size:22 final size:22
Alignment explanation
Indices: 925067--925108 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
925057 AAAGATGATG
925067 GGGAAAGGTTATGAAGCTTATA
1 GGGAAAGGTTATGAAGCTTATA
925089 GGGAAAGGTTATGAAGCTTA
1 GGGAAAGGTTATGAAGCTTA
925109 CTTAGCCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (22 bp):
GGGAAAGGTTATGAAGCTTATA
Found at i:934515 original size:2 final size:2
Alignment explanation
Indices: 934508--934540 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
934498 ATGCAATCAG
934508 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
934541 GGCAATTCAC
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:940600 original size:20 final size:20
Alignment explanation
Indices: 940575--940614 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
940565 GACTAAATTG
* * *
940575 GAAAATGATAGAATTTTTCA
1 GAAAATAATAAAACTTTTCA
940595 GAAAATAATAAAACTTTTCA
1 GAAAATAATAAAACTTTTCA
940615 AAACTGTAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (20 bp):
GAAAATAATAAAACTTTTCA
Found at i:942089 original size:25 final size:25
Alignment explanation
Indices: 942055--942140 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
942045 ACATATATGT
942055 TCACACGAGCTATGAATCAGAATGC
1 TCACACGAGCTATGAATCAGAATGC
** ** **
942080 TCACACGAGCTGTAAAAATGGGCCTGC
1 TCACACGAGC--TATGAATCAGAATGC
*
942107 TCACACGAGCTTTGAATCAGAATGC
1 TCACACGAGCTATGAATCAGAATGC
942132 TCACACGAG
1 TCACACGAG
942141 TTGTGGGTCG
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
25 27 0.59
27 19 0.41
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.20
Consensus pattern (25 bp):
TCACACGAGCTATGAATCAGAATGC
Found at i:951100 original size:35 final size:35
Alignment explanation
Indices: 951033--951109 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
951023 ATGATGACTG
* * *
951033 ATGTGAAAGTGAATATAAGGGTGTGTTGTTCATGCC
1 ATGTG-AAGTAAATATAAGGGTATGTTATTCATGCC
**
951069 ATGTGAAGTAAATATGTGGGTATGTTATTCATGCC
1 ATGTGAAGTAAATATAAGGGTATGTTATTCATGCC
951104 ATGTGA
1 ATGTGA
951110 CAGTGATTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 31 0.86
36 5 0.14
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.35
Consensus pattern (35 bp):
ATGTGAAGTAAATATAAGGGTATGTTATTCATGCC
Found at i:951872 original size:3 final size:3
Alignment explanation
Indices: 951864--951927 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
951854 GTTAATAAAT
951864 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
951912 ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA A
951928 AAGATTCATG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:953857 original size:20 final size:19
Alignment explanation
Indices: 953804--953858 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
953794 AGGTTCTAAA
*
953804 ATTTATTTATAATTAATTAT
1 ATTTAATTATAATT-ATTAT
* * *
953824 ATGTAAATAAAATTATTAGT
1 ATTTAATTATAATTATTA-T
953844 ATTTAATTATAATTA
1 ATTTAATTATAATTA
953859 AATTAAGTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
ATTTAATTATAATTATTAT
Found at i:953877 original size:30 final size:30
Alignment explanation
Indices: 953816--953877 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
953806 TTATTTATAA
*
953816 TTAATTATATGTAAATAAAATTATTAGTAT
1 TTAATTATATGTAAATAAAATTATTACTAT
* * *
953846 TTAATTATAAT-TAAATTAAGTTGTTACTAT
1 TTAATTAT-ATGTAAATAAAATTATTACTAT
953876 TT
1 TT
953878 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (30 bp):
TTAATTATATGTAAATAAAATTATTACTAT
Found at i:963375 original size:45 final size:44
Alignment explanation
Indices: 963307--963483 Score: 196
Period size: 45 Copynumber: 4.0 Consensus size: 44
963297 CGTATACTGA
963307 GTATCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACCG
1 GTATCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACCG
* * *
963351 GTTACCATTGATTATAAAGGTGGTTGCTATGTGCTGACTCCACCG
1 G-TATCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACCG
* * ** * *
963396 GAAGTCATTAAAAATAAAGGTGGTTGCTATGTGTTTATTCCATCG
1 GTA-TCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACCG
* * * *
963441 AATATAATTGATTATAAGGGTGG-TGCTATATGTTGA-TCCACCG
1 -GTATCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACCG
963484 TGTAACGGTT
Statistics
Matches: 108, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
43 6 0.06
44 13 0.12
45 88 0.81
46 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (44 bp):
GTATCATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACCG
Found at i:963463 original size:90 final size:88
Alignment explanation
Indices: 963319--963483 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 88
963309 ATCATTGATT
** * *
963319 ATAAAGGTGGTTGCTATGTGTTGATTCCACCGGTTACCATTGATTATAAAGGTGGTTGCTATGTG
1 ATAAAGGTGGTTGCTATGTGTTGATTCCACCGAATACAATTGATTATAAAGGTGG-TGCTATATG
963384 CTGACTCCACCGGAAGTCATTAAAA
65 CTGA-TCCACCGGAAGTCATTAAAA
* * * * *
963409 ATAAAGGTGGTTGCTATGTGTTTATTCCATCGAATATAATTGATTATAAGGGTGGTGCTATATGT
1 ATAAAGGTGGTTGCTATGTGTTGATTCCACCGAATACAATTGATTATAAAGGTGGTGCTATATGC
963474 TGATCCACCG
66 TGATCCACCG
963484 TGTAACGGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
88 7 0.11
89 11 0.17
90 48 0.73
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (88 bp):
ATAAAGGTGGTTGCTATGTGTTGATTCCACCGAATACAATTGATTATAAAGGTGGTGCTATATGC
TGATCCACCGGAAGTCATTAAAA
Found at i:971141 original size:120 final size:120
Alignment explanation
Indices: 971002--971438 Score: 735
Period size: 120 Copynumber: 3.7 Consensus size: 120
970992 ATTATTAATC
* *
971002 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
971067 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
* *
971122 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAA
1 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
971187 TTTTATTAAATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
971242 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
971307 --TTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
971360 TATA-TTT-TAGTATTATATATTATGATTTTATTAGTAAATTCATATAAGAATA-TT--TATTAA
1 TATATTTTATAGTATTATATATTATGA--TT-TTAGTAAATTCATATAAGAATATTTAATATTAA
*
971420 CAATTTTATTAAATTATAT
63 GAATTTTATTAAATTATAT
971439 TTTATAACAG
Statistics
Matches: 302, Mismatches: 10, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
116 26 0.09
117 3 0.01
118 74 0.25
119 22 0.07
120 177 0.59
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (120 bp):
TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
Found at i:971245 original size:26 final size:28
Alignment explanation
Indices: 971185--971366 Score: 113
Period size: 28 Copynumber: 6.4 Consensus size: 28
971175 TCATACTAAG
* * *
971185 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
971213 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
* *
971239 AATTATATTTTATAGTATTATATATTATGATTT
1 AATTATA-TTTA-A-TA--ATATATTATTATTA
* * * * * *
971272 TAGTAAATTCATATAAGAATATTTAATATTA
1 AATTATATTTA-ATAA-TATA-TTATTATTA
* * * *
971303 AGAAT-TATTAAATTATATATTTTTATTA
1 A-ATTATATTTAATAATATATTATTATTA
971331 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
971357 AATTATATTT
1 AATTATATTT
971367 TAGTATTATA
Statistics
Matches: 118, Mismatches: 25, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
26 23 0.19
27 17 0.14
28 33 0.28
29 6 0.05
30 6 0.05
31 15 0.13
32 12 0.10
33 6 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:971664 original size:12 final size:12
Alignment explanation
Indices: 971647--971671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
971637 ATTCTATTCT
971647 ATTCAACCAAAC
1 ATTCAACCAAAC
971659 ATTCAACCAAAC
1 ATTCAACCAAAC
971671 A
1 A
971672 ATTGAATTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (12 bp):
ATTCAACCAAAC
Found at i:971707 original size:16 final size:16
Alignment explanation
Indices: 971683--971751 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
971673 TTGAATTGCT
971683 ATTACGCCTCTAATCC
1 ATTACGCCTCTAATCC
*
971699 ATTATGCCTCTAATCC
1 ATTACGCCTCTAATCC
* *
971715 ATTACGTCTCTATTCC
1 ATTACGCCTCTAATCC
*
971731 ATTACGCCTCTATTCC
1 ATTACGCCTCTAATCC
971747 ATTAC
1 ATTAC
971752 AGCGAACCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTAATCC
Found at i:977719 original size:50 final size:50
Alignment explanation
Indices: 977639--977778 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 50
977629 TATTGAGGTT
* * * * *
977639 ATGAAAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGTACCGAG
1 ATGAGAGGTCCCACATAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* *
977689 ATGAGAGGTCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCACATAAGACCATGTCTGGGACATGGCATGGGCACCGAG
** * * * *
977739 ATGAGAACTCTCATATAAGACCATATCTGGGATATGGCAT
1 ATGAGAGGTCCCACATAAGACCATGTCTGGGACATGGCAT
977779 TTGTAGTAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCACATAAGACCATGTCTGGGACATGGCATGGGCACCGAG
Found at i:983478 original size:20 final size:20
Alignment explanation
Indices: 983453--983491 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
983443 TGAGTTATTT
983453 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
983473 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
983492 GAAAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:987791 original size:27 final size:27
Alignment explanation
Indices: 987747--987798 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
987737 TTGTTTTTGG
**
987747 TTTTTTTATTTTTTA-TTTTAAAGTAA
1 TTTTTTTATTTTCAATTTTTAAAGTAA
987773 TTTTTTTATCTTTCAATTTTTAAAGT
1 TTTTTTTAT-TTTCAATTTTTAAAGT
987799 GCTTCTAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 4 0.18
28 9 0.41
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (27 bp):
TTTTTTTATTTTCAATTTTTAAAGTAA
Found at i:988147 original size:30 final size:30
Alignment explanation
Indices: 988079--988168 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
988069 GATTAAATCA
*
988079 AAATTAAAGTTTCAAGTATATATTTGA-ACC
1 AAATTAAAGTTTCAAGTATATAATT-ACACC
* *
988109 ACAATTAAAGTTTCACGTGTATAATTACACC
1 A-AATTAAAGTTTCAAGTATATAATTACACC
* *
988140 AAATTAAAATTTCATGTATATAATTACAC
1 AAATTAAAGTTTCAAGTATATAATTACAC
988169 ATTAAACCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 27 0.52
31 25 0.48
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATATAATTACACC
Found at i:988877 original size:13 final size:13
Alignment explanation
Indices: 988859--988886 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
988849 TATTGCATTA
988859 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
988872 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
988885 TT
1 TT
988887 GCCTGTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.21, T:0.64
Consensus pattern (13 bp):
TTTGTTTCGGTTC
Found at i:991246 original size:29 final size:28
Alignment explanation
Indices: 991181--991252 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
991171 TTAATTCCGA
991181 AGACG-AAAAATTTATGCAAATTGCTAT
1 AGACGAAAAAATTTATGCAAATTGCTAT
*
991208 AGACGAAAAAATTTATGTAAATTGCTAT
1 AGACGAAAAAATTTATGCAAATTGCTAT
991236 AGACGAAAAAAATTTAT
1 AGACG-AAAAAATTTAT
991253 AATTTATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
27 5 0.12
28 26 0.62
29 11 0.26
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (28 bp):
AGACGAAAAAATTTATGCAAATTGCTAT
Found at i:994977 original size:16 final size:16
Alignment explanation
Indices: 994956--994997 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
994946 TTATTAAATT
*
994956 ATATATTTTAATTATA
1 ATATATTTTAATAATA
994972 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
994987 AT-TATGTTTAA
1 ATATAT-TTTAA
994998 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:994982 original size:15 final size:15
Alignment explanation
Indices: 994947--994988 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
994937 TTAAGAATTT
*
994947 TATTAAATTAT-ATA
1 TATTTAATTATAATA
994961 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
994975 TATTTAATAATAAT
1 TATTTAATTATAAT
994989 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:999748 original size:25 final size:25
Alignment explanation
Indices: 999711--999760 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
999701 TTTCTACTAA
*
999711 AACTTTCCTTAAAATCTGTTGATTT
1 AACTTTCCATAAAATCTGTTGATTT
999736 AACTTTCCATAAAATCTGTTGATTT
1 AACTTTCCATAAAATCTGTTGATTT
999761 CAGTTCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (25 bp):
AACTTTCCATAAAATCTGTTGATTT
Found at i:1000092 original size:43 final size:43
Alignment explanation
Indices: 1000031--1000203 Score: 346
Period size: 43 Copynumber: 4.0 Consensus size: 43
1000021 TATTTTGGTC
1000031 ACTCAATTATTAATATTGTTCGATTTAATTATATAACTTTTTA
1 ACTCAATTATTAATATTGTTCGATTTAATTATATAACTTTTTA
1000074 ACTCAATTATTAATATTGTTCGATTTAATTATATAACTTTTTA
1 ACTCAATTATTAATATTGTTCGATTTAATTATATAACTTTTTA
1000117 ACTCAATTATTAATATTGTTCGATTTAATTATATAACTTTTTA
1 ACTCAATTATTAATATTGTTCGATTTAATTATATAACTTTTTA
1000160 ACTCAATTATTAATATTGTTCGATTTAATTATATAACTTTTTA
1 ACTCAATTATTAATATTGTTCGATTTAATTATATAACTTTTTA
1000203 A
1 A
1000204 AATTAAATAT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 130 1.00
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (43 bp):
ACTCAATTATTAATATTGTTCGATTTAATTATATAACTTTTTA
Found at i:1002411 original size:11 final size:11
Alignment explanation
Indices: 1002395--1002419 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1002385 GTGTATAAAT
1002395 TGTGAAATTGA
1 TGTGAAATTGA
1002406 TGTGAAATTGA
1 TGTGAAATTGA
1002417 TGT
1 TGT
1002420 AATAATAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (11 bp):
TGTGAAATTGA
Found at i:1012672 original size:20 final size:20
Alignment explanation
Indices: 1012624--1012671 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1012614 CTTTTTTTTT
1012624 CTTTTTTTTGCGCTGTTTGC
1 CTTTTTTTTGCGCTGTTTGC
1012644 CTTTTTTTTGCG-TAGTTTG-
1 CTTTTTTTTGCGCT-GTTTGC
1012663 CTTTTTTTT
1 CTTTTTTTT
1012672 TTACGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.02, C:0.15, G:0.17, T:0.67
Consensus pattern (20 bp):
CTTTTTTTTGCGCTGTTTGC
Found at i:1013269 original size:34 final size:34
Alignment explanation
Indices: 1013226--1013294 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1013216 TATAGGTAAA
1013226 ATACAAGAGTAATTGAACCCGAATAAAACTCTTT
1 ATACAAGAGTAATTGAACCCGAATAAAACTCTTT
*
1013260 ATACAAGAGTAATTGAACCCTAATAAAACTCTTT
1 ATACAAGAGTAATTGAACCCGAATAAAACTCTTT
1013294 A
1 A
1013295 AAATTATCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (34 bp):
ATACAAGAGTAATTGAACCCGAATAAAACTCTTT
Found at i:1014884 original size:43 final size:43
Alignment explanation
Indices: 1014831--1015073 Score: 212
Period size: 43 Copynumber: 5.7 Consensus size: 43
1014821 TCGCTAACTC
* ** * * *
1014831 TAGCAGCGCTTTTCTAAAAAACGCCGCTAAAGACCATAATCTT
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGATCTT
* *
1014874 TAGCGGCGCTTTTCCTACAAACGCCGCTAAAG-ACACTGACCTT
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACA-TGATCTT
* * * *
1014917 TAGCGGCAC-TTTCCCACGAACGCC-CTAAAGAGTCGT-A-CTTT
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA-ACATGATC-TT
*
1014958 TAGCGGCGCTTTGCCCACAAACGCCGCTAAAGAACATGA-CATT
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGATC-TT
* **
1015001 TAGCAGCGCTTCACCCACAAACGCCGCTAAA-AACATGATCTT
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGATCTT
* ** * *
1015043 TAGCGGCACTTTTTTCATAAACGCCACTAAA
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAA
1015074 AGTACGACTC
Statistics
Matches: 163, Mismatches: 29, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
40 1 0.01
41 17 0.10
42 63 0.39
43 82 0.50
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGATCTT
Found at i:1015003 original size:84 final size:86
Alignment explanation
Indices: 1014849--1015031 Score: 230
Period size: 84 Copynumber: 2.2 Consensus size: 86
1014839 CTTTTCTAAA
* * * * *
1014849 AAACGCCGCTAAAGA-CCATAATCTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACACTGA
1 AAACGCCGCTAAAGAGTCGTACT-TTTAGCGGCGCTTTGCCCACAAACGCCGCTAAAGACACTGA
* * *
1014913 CCTTTAGCGGCACTT-TCCCAC
65 CATTTAGCAGCACTTCACCCAC
*
1014934 GAACGCC-CTAAAGAGTCGTACTTTTAGCGGCGCTTTGCCCACAAACGCCGCTAAAGA-ACATGA
1 AAACGCCGCTAAAGAGTCGTACTTTTAGCGGCGCTTTGCCCACAAACGCCGCTAAAGACAC-TGA
*
1014997 CATTTAGCAGCGCTTCACCCAC
65 CATTTAGCAGCACTTCACCCAC
1015019 AAACGCCGCTAAA
1 AAACGCCGCTAAA
1015032 AACATGATCT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
83 2 0.02
84 55 0.66
85 21 0.25
86 5 0.06
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (86 bp):
AAACGCCGCTAAAGAGTCGTACTTTTAGCGGCGCTTTGCCCACAAACGCCGCTAAAGACACTGAC
ATTTAGCAGCACTTCACCCAC
Done.