Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold285
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: 926752
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 6 of 6
Found at i:866369 original size:34 final size:34
Alignment explanation
Indices: 866330--866430 Score: 130
Period size: 34 Copynumber: 3.0 Consensus size: 34
866320 AAATATCTTA
* * * *
866330 CTCACCTAACACATTACCTAACACACATAATATT
1 CTCACCAAATACATCACCTAACACACATAACATT
* * *
866364 TTCACCAAATACATCACTTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACATAACATT
*
866398 CTCACCAAATACATCACCTAACACACCTAACAT
1 CTCACCAAATACATCACCTAACACACATAACAT
866431 GCTTTACTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.24
Consensus pattern (34 bp):
CTCACCAAATACATCACCTAACACACATAACATT
Found at i:868250 original size:2 final size:2
Alignment explanation
Indices: 868243--868274 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
868233 TGAGGTTTGA
868243 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
868275 GCTAGGAATC
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:871118 original size:19 final size:20
Alignment explanation
Indices: 871096--871136 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
871086 TATATAAATA
871096 TTTTTATATTATATT-TATT
1 TTTTTATATTATATTATATT
871115 TTTTTATATTATATTATATT
1 TTTTTATATTATATTATATT
871135 TT
1 TT
871137 AATTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTATATTATATTATATT
Found at i:871143 original size:19 final size:19
Alignment explanation
Indices: 871093--871150 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
871083 ATATATATAA
871093 ATATTTTTA-TATTATATT
1 ATATTTTTATTATTATATT
*
871111 -TATTTTTTTATATTATATT
1 ATATTTTTAT-TATTATATT
* *
871130 ATATTTTAATTATTATTTT
1 ATATTTTTATTATTATATT
871149 AT
1 AT
871151 TGTATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 7 0.21
19 19 0.58
20 7 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATATTTTTATTATTATATT
Found at i:871145 original size:24 final size:24
Alignment explanation
Indices: 871099--871150 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
871089 ATAAATATTT
* *
871099 TTATATTATATTTATTTTTTTATA
1 TTATATTATATTTATATTATTATA
*
871123 TTATATTATATTT-TAATTATTATT
1 TTATATTATATTTAT-ATTATTATA
871147 TTAT
1 TTAT
871151 TGTATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATATTATATTTATATTATTATA
Found at i:873743 original size:21 final size:22
Alignment explanation
Indices: 873682--873744 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
873672 ATAACGAGGG
*
873682 TTATCAAAATTATATCAATGATA
1 TTATCAAAATTATAACAAT-ATA
*
873705 TT-T-AAGATTACTAA-AATA-A
1 TTATCAAAATTA-TAACAATATA
873724 TTATCAAAATTATAACAATAT
1 TTATCAAAATTATAACAATAT
873745 CTAAAGTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 19 0.59
22 3 0.09
23 2 0.06
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTATAACAATATA
Found at i:878269 original size:130 final size:127
Alignment explanation
Indices: 877994--878319 Score: 341
Period size: 130 Copynumber: 2.5 Consensus size: 127
877984 ACGAGAAATT
*
877994 TAATATTTTGGAGATAATAACGGGGTTGGAGTATCCTCTCGAAAATAATGGGGTTGGAGTATCCC
1 TAATATTTTGGAAATAA-AACGGGGTTGGAGTATCC-CTCGAAAATAATGGGGTTGGAGTATCCC
* * * *
878059 CGATTGTGAAAAATCGATAATTTAGAAATAAGGCAAAAGTTGAAGTGTCCATGATTATAGAAAA
64 CAATTATGAAAAATCAATAATTTAGAAATAAGGCAAAAGTTGAAGTATCCATGATTATAGAAAA
* * * * * *
878123 TAGATGTTTCGAAAATAAAATCGAGATTGGAGTATCCACGT-GAAAATAATGGGGTTAGAGTATC
1 TA-ATATTTTGGAAATAAAA-CGGGGTTGGAGTATCC-C-TCGAAAATAATGGGGTTGGAGTATC
* * * **** *
878187 CTCAATTATGAGAAATCAATATTTTAGAAATAAGGCCGGGGTTGAAGTATCCATGATTGT-GAGA
62 CCCAATTATGAAAAATCAATAATTTAGAAATAAGGCAAAAGTTGAAGTATCCATGATTATAGA-A
*
878251 GA
126 AA
* * *
878253 TCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAATATCC
1 T-AATATTTTGGAAATAAA-ACGGGGTTGGAGTAT-CCCTCGAAAATAATGGGGTTGGAGTATCC
878318 CC
63 CC
878320 GATGAAATAA
Statistics
Matches: 158, Mismatches: 31, Indels: 15
0.77 0.15 0.07
Matches are distributed among these distances:
129 7 0.04
130 147 0.93
131 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (127 bp):
TAATATTTTGGAAATAAAACGGGGTTGGAGTATCCCTCGAAAATAATGGGGTTGGAGTATCCCCA
ATTATGAAAAATCAATAATTTAGAAATAAGGCAAAAGTTGAAGTATCCATGATTATAGAAAA
Found at i:878404 original size:51 final size:51
Alignment explanation
Indices: 878349--878448 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 51
878339 AGTATCCCCA
**
878349 ATTGTGAAAAATTAATGTTTTGGAAATAAAATCGAAGTTGGAATATCCCTG
1 ATTGTGAAAAATTAATGTTTTAAAAATAAAATCGAAGTTGGAATATCCCTG
* * ** ** *
878400 ATTGTGGAGAATTGGTGTTTTAAAAATAAAATCGGGGTTGGAGTATCCC
1 ATTGTGAAAAATTAATGTTTTAAAAATAAAATCGAAGTTGGAATATCCC
878449 CTCAGAAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (51 bp):
ATTGTGAAAAATTAATGTTTTAAAAATAAAATCGAAGTTGGAATATCCCTG
Found at i:878475 original size:79 final size:78
Alignment explanation
Indices: 878385--878664 Score: 341
Period size: 79 Copynumber: 3.6 Consensus size: 78
878375 TAAAATCGAA
* * * * * *
878385 GTTGGAATATCCCTGATTGTGGAGAATTGGTGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTAT-GAGAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
878450 TC-AGAAATAACGGG
65 TCGA-AAATAACGGG
* * *
878464 GTTGGAGTATCCCCGATTATGAAAATTTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCA
1 GTTGGAGTATCCCCGATTATGAGAA-TTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
*
878529 TCGAAAATGACGGG
65 TCGAAAATAACGGG
* * * *
878543 GTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAGCCTGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAG-AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
*
878608 TCGAAAATAACGGA
65 TCGAAAATAACGGG
* * *
878622 GTTGGAGTATCTCCGATGA--AAAATTGATGTTTTAGAAATAAAA
1 GTTGGAGTATCCCCGATTATGAGAATTGATGTTTTAGAAATAAAA
878665 TGGGGATTGG
Statistics
Matches: 173, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
76 19 0.11
77 1 0.01
78 4 0.02
79 146 0.84
80 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (78 bp):
GTTGGAGTATCCCCGATTATGAGAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCT
CGAAAATAACGGG
Found at i:881012 original size:20 final size:19
Alignment explanation
Indices: 880987--881093 Score: 109
Period size: 20 Copynumber: 5.7 Consensus size: 19
880977 AAAATGCCTG
*
880987 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
881007 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
881027 AATGTATCGATAC------
1 AATGTATCGATACAATGAA
*
881040 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
881060 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
881080 AATGTATCGATACA
1 AATGTATCGATACA
881094 TCTAGGTAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
13 13 0.17
19 1 0.01
20 60 0.80
21 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:881049 original size:33 final size:33
Alignment explanation
Indices: 881007--881076 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
880997 TACATTGTAA
881007 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
881040 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
881073 AATG
1 AATG
881077 CAAAATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:881049 original size:53 final size:53
Alignment explanation
Indices: 880987--881093 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 53
880977 AAAATGCCTG
* *
880987 AATGTATCGATACATTGTA-AAATGTATCGATACAATG-AGCAATGTATCGATAC
1 AATGTATCGATACAATG-AGAAATGTATCGATACAATGCA-AAATGTATCGATAC
*
881040 AATGTATCGATACAATGAGCAATGTATCGATACAATGCAAAATGTATCGATAC
1 AATGTATCGATACAATGAGAAATGTATCGATACAATGCAAAATGTATCGATAC
881093 A
1 A
881094 TCTAGGTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
52 1 0.02
53 47 0.96
54 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (53 bp):
AATGTATCGATACAATGAGAAATGTATCGATACAATGCAAAATGTATCGATAC
Found at i:881075 original size:13 final size:13
Alignment explanation
Indices: 881026--881056 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
881016 ATACAATGAG
881026 CAATGTATCGATA
1 CAATGTATCGATA
881039 CAATGTATCGATA
1 CAATGTATCGATA
881052 CAATG
1 CAATG
881057 AGCAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:881814 original size:15 final size:15
Alignment explanation
Indices: 881754--881830 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
881744 TATTAGTATG
*
881754 ATTTAAAAATAATTA
1 ATTTTAAAATAATTA
*
881769 ATTTT-AAAT-GTTA
1 ATTTTAAAATAATTA
* *
881782 ATTGTGTTTAAATGATTA
1 A-T-T-TTAAAATAATTA
881800 ATTTTAAAATAATTA
1 ATTTTAAAATAATTA
* *
881815 ATTTTTAAATGATTA
1 ATTTTAAAATAATTA
881830 A
1 A
881831 AGTTTTATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 4 0.08
14 5 0.10
15 29 0.58
16 3 0.06
17 5 0.10
18 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
ATTTTAAAATAATTA
Found at i:883524 original size:14 final size:14
Alignment explanation
Indices: 883482--883539 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
883472 ACTTGTAAAA
*
883482 ATAAT-TAAAATAT
1 ATAATATAAATTAT
883495 AT-ATATAAA-TATT
1 ATAATATAAATTA-T
* *
883508 ATATTATAATTTAT
1 ATAATATAAATTAT
883522 ATAATATAAATTAT
1 ATAATATAAATTAT
883536 -TAAT
1 ATAAT
883540 GTATATATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.11
13 13 0.35
14 18 0.49
15 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATATAAATTAT
Found at i:883539 original size:22 final size:22
Alignment explanation
Indices: 883496--883546 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
883486 TTAAAATATA
* *
883496 TATATAAATATTATATTATAATT
1 TATAT-AATATTAAATTATAATG
883519 TATATAATA-TAAATTATTAATG
1 TATATAATATTAAATTA-TAATG
883541 TATATA
1 TATATA
883547 TCAAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 14 0.56
23 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TATATAATATTAAATTATAATG
Found at i:884536 original size:14 final size:14
Alignment explanation
Indices: 884505--884535 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
884495 TTCAAAGTAA
884505 TTTTAATAGATGAT
1 TTTTAATAGATGAT
884519 TTTTAA-AGATGAT
1 TTTTAATAGATGAT
884532 TTTT
1 TTTT
884536 TTGTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (14 bp):
TTTTAATAGATGAT
Found at i:885040 original size:2 final size:2
Alignment explanation
Indices: 885033--885071 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
885023 TCTTACTCTT
885033 TA TA TA 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 TA TA TA T
885072 GAGATTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:887899 original size:2 final size:2
Alignment explanation
Indices: 887892--887925 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
887882 TGAGGTTTAA
887892 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
887926 GCTAGGAATC
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):
AT
Found at i:890763 original size:19 final size:20
Alignment explanation
Indices: 890741--890781 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
890731 TATATAAATA
890741 TTTTTATATTATATT-TATT
1 TTTTTATATTATATTATATT
890760 TTTTTATATTATATTATATT
1 TTTTTATATTATATTATATT
890780 TT
1 TT
890782 AATTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTATATTATATTATATT
Found at i:890788 original size:19 final size:19
Alignment explanation
Indices: 890738--890795 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
890728 ATATATATAA
890738 ATATTTTTA-TATTATATT
1 ATATTTTTATTATTATATT
*
890756 -TATTTTTTTATATTATATT
1 ATATTTTTAT-TATTATATT
* *
890775 ATATTTTAATTATTATTTT
1 ATATTTTTATTATTATATT
890794 AT
1 AT
890796 TGTATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 7 0.21
19 19 0.58
20 7 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATATTTTTATTATTATATT
Found at i:890790 original size:24 final size:24
Alignment explanation
Indices: 890744--890795 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
890734 ATAAATATTT
* *
890744 TTATATTATATTTATTTTTTTATA
1 TTATATTATATTTATATTATTATA
*
890768 TTATATTATATTT-TAATTATTATT
1 TTATATTATATTTAT-ATTATTATA
890792 TTAT
1 TTAT
890796 TGTATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATATTATATTTATATTATTATA
Found at i:893387 original size:21 final size:22
Alignment explanation
Indices: 893326--893388 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
893316 ATAACGAGGG
*
893326 TTATCAAAATTATATCAATGATA
1 TTATCAAAATTATAACAAT-ATA
*
893349 TT-T-AAGATTACTAA-AATA-A
1 TTATCAAAATTA-TAACAATATA
893368 TTATCAAAATTATAACAATAT
1 TTATCAAAATTATAACAATAT
893389 CTAAAGTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 19 0.59
22 3 0.09
23 2 0.06
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTATAACAATATA
Found at i:897972 original size:28 final size:28
Alignment explanation
Indices: 897919--897976 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
897909 GAAATAAAGC
*
897919 CGGGGTTGGAGTATTCCCTCGAAAATAA
1 CGGGGTTGGAATATTCCCTCGAAAATAA
897947 CGGGGTTGGAATA-TCCC-CGATGAAATAA
1 CGGGGTTGGAATATTCCCTCGA--AAATAA
897975 CG
1 CG
897977 AGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 3 0.11
27 4 0.15
28 20 0.74
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAATATTCCCTCGAAAATAA
Found at i:898226 original size:80 final size:75
Alignment explanation
Indices: 898080--898309 Score: 277
Period size: 80 Copynumber: 3.0 Consensus size: 75
898070 AATAAATCGG
898080 GGTTGGAGTATCCCCTC-AGAAATACGGGGTTGGAGTATCCCCGATTATGAAAATTTGATGTTTT
1 GGTTGGAGTATCCCCTCGA-AAATACGGGGTTGGAGTAT-CCCGATTATGAAAA-TTGATGTTTT
898144 AGAAATAAAACCGA
63 AGAAATAAAACC-A
* * *
898158 GGTTTGGAGTAATCCCATCGAAAATGACGGGGTTGGAGTATCCCGATTATGAGAAATTAATATTT
1 GG-TTGGAGT-ATCCCCTCGAAAAT-ACGGGGTTGGAGTATCCCGATTATGA-AAATTGATGTTT
* *
898223 TAGAAATAAAGCCT
62 TAGAAATAAAACCA
* *
898237 GGTTGGAGTATCCCCTCGAAAATAAACGGAGTTGGAGTATCTCCGATGA--AAAATTGATGTTTT
1 GGTTGGAGTATCCCCTCGAAAAT--ACGGGGTTGGAGTATC-CCGATTATGAAAATTGATGTTTT
898300 AGAAATAAAA
63 AGAAATAAAA
898310 TGGGGATTGG
Statistics
Matches: 133, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
76 20 0.15
77 14 0.11
78 24 0.18
79 15 0.11
80 41 0.31
81 19 0.14
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (75 bp):
GGTTGGAGTATCCCCTCGAAAATACGGGGTTGGAGTATCCCGATTATGAAAATTGATGTTTTAGA
AATAAAACCA
Found at i:900732 original size:20 final size:18
Alignment explanation
Indices: 900679--900753 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 18
900669 AAAATTAGCG
900679 TACATGAGCAATGTATCG-
1 TACATGA-CAATGTATCGA
900697 -A-AT-ACAATGTATCGA
1 TACATGACAATGTATCGA
900712 TACATGAGCAATGTAATCGA
1 TACATGA-CAATGT-ATCGA
900732 TTACAATGA-AATGTATCGA
1 -TAC-ATGACAATGTATCGA
900751 TAC
1 TAC
900754 TCTAGGTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 3 0.06
17 3 0.06
18 4 0.08
19 11 0.22
20 10 0.20
21 3 0.06
22 4 0.08
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (18 bp):
TACATGACAATGTATCGA
Found at i:904850 original size:10 final size:11
Alignment explanation
Indices: 904832--904861 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
904822 TCTTTCTATA
904832 TATATATAGAT
1 TATATATAGAT
904843 TA-ATATAGAT
1 TATATATAGAT
904853 TATATATAG
1 TATATATAG
904862 GTAATGAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (11 bp):
TATATATAGAT
Found at i:907790 original size:2 final size:2
Alignment explanation
Indices: 907783--907811 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
907773 TTGTAAATAG
907783 AT AT AT AT AT A- 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
907812 GGCGAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:907801 original size:15 final size:15
Alignment explanation
Indices: 907778--907808 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
907768 TGAGGTTGTA
907778 AATAGATATATATAT
1 AATAGATATATATAT
*
907793 AATATATATATATAT
1 AATAGATATATATAT
907808 A
1 A
907809 TATGGCGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
AATAGATATATATAT
Found at i:910709 original size:18 final size:19
Alignment explanation
Indices: 910688--910732 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
910678 TATATATAAA
910688 TATTTTTTTATATTAAT-T
1 TATTTTTTTATATTAATAT
910706 TATTTTTTTATATTAATAT
1 TATTTTTTTATATTAATAT
910725 TATATTTT
1 TAT-TTTT
910733 AATTAGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 17 0.68
19 4 0.16
20 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTTTTATATTAATAT
Found at i:910733 original size:18 final size:17
Alignment explanation
Indices: 910680--910756 Score: 72
Period size: 16 Copynumber: 4.6 Consensus size: 17
910670 AAAAATAGTA
*
910680 TATATAAATATTT-TTT
1 TATATTAATATTTATTT
910696 TATATTAATTTATTT-TTT
1 TATATTAA--TATTTATTT
910714 TATATTAATATTATATTT
1 TATATTAATATT-TATTT
* *
910732 TA-ATTAGTATTTATGT
1 TATATTAATATTTATTT
910748 TATA-TAATA
1 TATATTAATA
910757 GTAATTACAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
16 21 0.40
17 10 0.19
18 21 0.40
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATATTAATATTTATTT
Done.