Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1472
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: 78153
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:599 original size:18 final size:17
Alignment explanation
Indices: 565--606 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
555 GAGTACATTA
**
565 TTAAAAAAAAAGGAGTT
1 TTAAAAAAAAAACAGTT
582 TTAAAAGAAAAAACAGTT
1 TTAAAA-AAAAAACAGTT
600 TTAAAAA
1 TTAAAAA
607 CAGGAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.24
Consensus pattern (17 bp):
TTAAAAAAAAAACAGTT
Found at i:2093 original size:141 final size:139
Alignment explanation
Indices: 1834--2106 Score: 397
Period size: 141 Copynumber: 1.9 Consensus size: 139
1824 TTACTTCTTC
* *
1834 TTAAATAATCTTATTATTAATAATAAGGTTATTTGGTGTTTATATATTAACAATATTTTTTTTGA
1 TTAAATAATCTTATTATTAACAATAAGGTTATTTGGTGTTTATACATTAACAATATTTTTTTTGA
*
1899 AATATTAAACACAATGATTTAACATTACTAATAATCTAATATATTATACCAAATACTAGAATTTA
66 AATATTAAACACAATGATTTAACATCACTAATAATCTAATATATTATACCAAATACTAGAATTTA
1964 AGCTTCTCA
131 AGCTTCTCA
* * *
1973 TTAAATGATCTTATTATTAACAATGAA-GTTATTTTGGTG-TTATACATTAAATAATCTTTTTTT
1 TTAAATAATCTTATTATTAACAAT-AAGGTTA-TTTGGTGTTTATACATT-AACAATATTTTTTT
* * * * *
2036 TGGAAATATTTAACATAATGATTTAATATCACTAATAATCTATTATATTATATCAAATACTAGAA
63 T-GAAATATTAAACACAATGATTTAACATCACTAATAATCTAATATATTATACCAAATACTAGAA
2101 TTTAAG
127 TTTAAG
2107 ATCACTAGTG
Statistics
Matches: 119, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
139 34 0.29
140 22 0.18
141 63 0.53
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (139 bp):
TTAAATAATCTTATTATTAACAATAAGGTTATTTGGTGTTTATACATTAACAATATTTTTTTTGA
AATATTAAACACAATGATTTAACATCACTAATAATCTAATATATTATACCAAATACTAGAATTTA
AGCTTCTCA
Found at i:3663 original size:21 final size:20
Alignment explanation
Indices: 3615--3660 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
3605 TTTTAAAATT
3615 TTAAAATATATGAAATAAAA
1 TTAAAATATATGAAATAAAA
3635 TTAAAATATTAT-AAA-AATAA
1 TTAAAATA-TATGAAATAA-AA
3655 TTAAAA
1 TTAAAA
3661 ATAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
TTAAAATATATGAAATAAAA
Found at i:8238 original size:52 final size:52
Alignment explanation
Indices: 8181--8298 Score: 175
Period size: 52 Copynumber: 2.3 Consensus size: 52
8171 AATTAACTAG
* * *
8181 ATGTATCGATACATT-AATAAATGTATCGATACATCTGGGTAAAAAAAATAGA
1 ATGTATCGATACATTGAA-AAATATATCGATACATCTAGGTAAAAAAAACAGA
* *
8233 ATGTATCGATACATTGAAAAATATATCGATATATCTAGGTAGAAAAAACAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAAAAACAGA
8285 ATGTATCGATACAT
1 ATGTATCGATACAT
8299 GTACTGTTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 58 0.97
53 2 0.03
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAAAAACAGA
Found at i:28636 original size:19 final size:18
Alignment explanation
Indices: 28607--28649 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28597 AATTACATCT
28607 TTTAT-AAATATATAAATA
1 TTTATAAAATATA-AAATA
28625 TTTATAAAATATAAAATA
1 TTTATAAAATATAAAATA
*
28643 GTTATAA
1 TTTATAA
28650 TTGTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
TTTATAAAATATAAAATA
Found at i:28863 original size:16 final size:16
Alignment explanation
Indices: 28838--28871 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
28828 TATTACTTTA
28838 ATTTTTAAAAAT-ATT
1 ATTTTTAAAAATAATT
28853 ATTTTTGAAAAATAATT
1 ATTTTT-AAAAATAATT
28870 AT
1 AT
28872 CTAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTTTAAAAATAATT
Found at i:30989 original size:8 final size:8
Alignment explanation
Indices: 30976--31014 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
30966 TCAATTATCA
30976 ATTTTTAT
1 ATTTTTAT
30984 ATTTTTTAT
1 A-TTTTTAT
*
30993 ATTTTTTT
1 ATTTTTAT
31001 ATTTTTAT
1 ATTTTTAT
31009 -TTTTTA
1 ATTTTTA
31015 CTCAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 6 0.21
8 14 0.50
9 8 0.29
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
ATTTTTAT
Found at i:30991 original size:9 final size:9
Alignment explanation
Indices: 30977--31006 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30967 CAATTATCAA
30977 TTTTTATAT
1 TTTTTATAT
30986 TTTTTATAT
1 TTTTTATAT
30995 TTTTT-TAT
1 TTTTTATAT
31003 TTTT
1 TTTT
31007 ATTTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTATAT
Found at i:31038 original size:18 final size:18
Alignment explanation
Indices: 31006--31053 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
30996 TTTTTATTTT
31006 TATTTTTT-ACT-CAAAA
1 TATTTTTTAACTACAAAA
31022 TATTTTTTAACTACAAAA
1 TATTTTTTAACTACAAAA
*
31040 T-TATCTTTAACTAC
1 TAT-TTTTTAACTAC
31054 TATTAAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 8 0.29
17 4 0.14
18 16 0.57
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTTTTTAACTACAAAA
Found at i:31851 original size:30 final size:30
Alignment explanation
Indices: 31817--31891 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
31807 AGCTTTGAAA
*
31817 GTAAGTATATTTTTTGCTCAACT-TTAAGA-G
1 GTAAGTATATTTTTT--TCAAATATTAAGAGG
*
31847 GTAAGTAGT-TTTTTTTTAAATATTAAGAGG
1 GTAAGTA-TATTTTTTTCAAATATTAAGAGG
*
31877 GTAAATATATTTTTT
1 GTAAGTATATTTTTT
31892 ATAAAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 4 0.11
29 7 0.18
30 26 0.68
31 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (30 bp):
GTAAGTATATTTTTTTCAAATATTAAGAGG
Found at i:31872 original size:29 final size:30
Alignment explanation
Indices: 31840--31902 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
31830 TTGCTCAACT
* * *
31840 TTAAGA-GGTAAGTAGT-TTTTTTTTAAATA
1 TTAAGAGGGTAAATA-TATTTTTTATAAAAA
31869 TTAAGAGGGTAAATATATTTTTTATAAAAA
1 TTAAGAGGGTAAATATATTTTTTATAAAAA
31899 TTAA
1 TTAA
31903 AAAAAGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.44
Consensus pattern (30 bp):
TTAAGAGGGTAAATATATTTTTTATAAAAA
Found at i:32902 original size:16 final size:17
Alignment explanation
Indices: 32841--32902 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 17
32831 TTAAAATTGT
*
32841 AAATATTT-AATATCTA
1 AAATATTTAAATATCAA
*
32857 AAATTTTTAAATATCAAA
1 AAATATTTAAATATC-AA
**
32875 AAATAAAATAAATAT-AA
1 AAAT-ATTTAAATATCAA
32892 AAATATTTAAA
1 AAATATTTAAA
32903 AAATATAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
16 12 0.33
17 12 0.33
18 5 0.14
19 7 0.19
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATTTAAATATCAA
Found at i:33048 original size:16 final size:17
Alignment explanation
Indices: 33029--33064 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
33019 GAAAAATCAA
33029 ATAAATA-AAAAATTTT
1 ATAAATATAAAAATTTT
33045 ATAAATATAAAAATTTT
1 ATAAATATAAAAATTTT
33062 ATA
1 ATA
33065 CCTAACCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAATATAAAAATTTT
Found at i:37266 original size:10 final size:10
Alignment explanation
Indices: 37251--37301 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
37241 GAACATGTTT
37251 TATAAAATAA
1 TATAAAATAA
37261 TATAAAATTAA
1 TATAAAA-TAA
* *
37272 AATAAGATAA
1 TATAAAATAA
* *
37282 GATAAGATAA
1 TATAAAATAA
37292 -ATAAAATAA
1 TATAAAATAA
37301 T
1 T
37302 GAGAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 8 0.23
10 19 0.54
11 8 0.23
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (10 bp):
TATAAAATAA
Found at i:37281 original size:26 final size:24
Alignment explanation
Indices: 37252--37300 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
37242 AACATGTTTT
*
37252 ATAAAATAATATAAAATTAAAATAAG
1 ATAAAATAAGAT-AAA-TAAAATAAG
*
37278 ATAAGATAAGATAAATAAAATAA
1 ATAAAATAAGATAAATAAAATAA
37301 TGAGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (24 bp):
ATAAAATAAGATAAATAAAATAAG
Found at i:38433 original size:23 final size:23
Alignment explanation
Indices: 38398--38448 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
38388 TTATTTGTAT
**
38398 ATTAA-TTTTTTAAATTATTAAA
1 ATTAATTTTTTTAAAAAATTAAA
38420 ATTAATTTTTTTAAAAAATTAAA
1 ATTAATTTTTTTAAAAAATTAAA
38443 A-TAATT
1 ATTAATT
38449 AACAGCAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTAATTTTTTTAAAAAATTAAA
Found at i:38858 original size:22 final size:21
Alignment explanation
Indices: 38802--38859 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
38792 AATTTTTAAA
*
38802 TAAA-ATAATTTTATCATTTTT
1 TAAATATAATTTT-TTATTTTT
* * *
38823 TAATTTTAAATTTTTATTATTT
1 TAAATATAATTTTTTATT-TTT
38845 TAAATATAATTTTTT
1 TAAATATAATTTTTT
38860 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TAAATATAATTTTTTATTTTT
Found at i:39954 original size:17 final size:17
Alignment explanation
Indices: 39910--39954 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
39900 TTATCTAATA
39910 ATAAAAATATATTT-TT
1 ATAAAAATATATTTATT
*
39926 A-AAATA-AT-TTTATT
1 ATAAAAATATATTTATT
39940 ATAAAAATATATTTA
1 ATAAAAATATATTTA
39955 AATTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
13 3 0.13
14 5 0.22
15 8 0.35
16 3 0.13
17 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAAAATATATTTATT
Found at i:40360 original size:31 final size:33
Alignment explanation
Indices: 40310--40370 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
40300 AAAAATTTAT
40310 ATTTTAATTTTTTAATATTT-T-TAATTATGAA
1 ATTTTAATTTTTTAATATTTGTGTAATTATGAA
*
40341 ATTTTAATTTCTTT-TTATTTGTGTAATTAT
1 ATTTTAATTT-TTTAATATTTGTGTAATTAT
40371 ACAAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 15 0.58
32 4 0.15
33 7 0.27
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (33 bp):
ATTTTAATTTTTTAATATTTGTGTAATTATGAA
Found at i:40966 original size:32 final size:32
Alignment explanation
Indices: 40930--40998 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
40920 TTATTATATA
40930 TTTATATAAATTTTAAAATATTAATAATTTAT
1 TTTATATAAATTTTAAAATATTAATAATTTAT
* * * *
40962 TTTATGTAAATTTTAATATTTTAATATTTTAT
1 TTTATATAAATTTTAAAATATTAATAATTTAT
*
40994 ATTAT
1 TTTAT
40999 TTTTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (32 bp):
TTTATATAAATTTTAAAATATTAATAATTTAT
Found at i:41005 original size:12 final size:12
Alignment explanation
Indices: 40988--41033 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
40978 TATTTTAATA
40988 TTTTATATTATT
1 TTTTATATTATT
41000 TTTTAT-TATATT
1 TTTTATAT-TATT
41012 TTTTA-ATTATT
1 TTTTATATTATT
*
41023 TTTCATATTAT
1 TTTTATATTAT
41034 GTTTGTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTATATTATT
Found at i:41016 original size:40 final size:40
Alignment explanation
Indices: 40905--41024 Score: 99
Period size: 40 Copynumber: 3.0 Consensus size: 40
40895 TATTCAGATT
40905 ATATTTT-TATTA-TTTTTATTATATATTTATATAA-ATTTTA
1 ATATTTTATATTATTTTTTATTATAT-TTT-T-TAATATTTTA
* * * *
40945 AAATATTAATAATT-TATTTTATGTA-A-ATTTTAATATTTTA
1 ATAT-TTTAT-ATTATTTTTTAT-TATATTTTTTAATATTTTA
40985 ATATTTTATATTATTTTTTATTATATTTTTTAATTATTTT
1 ATATTTTATATTATTTTTTATTATATTTTTTAA-TATTTT
41025 TCATATTATG
Statistics
Matches: 62, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
38 5 0.08
39 15 0.24
40 19 0.31
41 10 0.16
42 1 0.02
43 10 0.16
44 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (40 bp):
ATATTTTATATTATTTTTTATTATATTTTTTAATATTTTA
Found at i:45271 original size:20 final size:21
Alignment explanation
Indices: 45226--45275 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
45216 TACAATTTGC
*
45226 ATCGATACAAATAGTAAATGT
1 ATCGATACAAATAGTAAATAT
*
45247 ATCGATACAAA-AGTGAATAT
1 ATCGATACAAATAGTAAATAT
45267 ATCGATACA
1 ATCGATACA
45276 TGCCTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (21 bp):
ATCGATACAAATAGTAAATAT
Found at i:50022 original size:28 final size:28
Alignment explanation
Indices: 49949--50340 Score: 421
Period size: 28 Copynumber: 13.8 Consensus size: 28
49939 AAAAAAGGTA
* *
49949 CCACTAACTTGTGTGGTCTTTGAAAGGTTATG
1 CCACTGACTTGTG-GG-CTTTGAAAGG--GTG
49981 CCACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * *
50009 TCACTAACTTGTGGGTTTTG-AAGGGTA
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
50036 CCACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * *
50064 CCACTAACTTGTGGGCTTTGAGAGGTTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
50092 CTACTGACTTGTGAGCTTT-AGAAGGGTG
1 CCACTGACTTGTGGGCTTTGA-AAGGGTG
*
50120 CCACTGATTTGTGTGGGCTTTGAAAGGGTG
1 CCACTGA-CT-TGTGGGCTTTGAAAGGGTG
*
50150 CCACTGACTTGTGGGCTTTGAAAGTGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
50178 CCATTGACTTGTGGGCTTTG-AAGAGGTG
1 CCACTGACTTGTGGGCTTTGAAAG-GGTG
* *
50206 CCACTGATTTGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * *
50234 CCACTGACTTATGGTCTTTTGAAAAGATA
1 CCACTGACTTGTGGGC-TTTGAAAGGGTG
* * *
50263 CCACTAACTTATGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * **
50291 CCACTAACTTGTGGGCTTTGAAAAGAAG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
50319 CCACTGACCTGTGGGCTTTGAA
1 CCACTGACTTGTGGGCTTTGAA
50341 GAGATGAACG
Statistics
Matches: 310, Mismatches: 42, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
27 27 0.09
28 206 0.66
29 29 0.09
30 33 0.11
31 3 0.01
32 12 0.04
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.32
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTGAAAGGGTG
Found at i:50166 original size:114 final size:112
Alignment explanation
Indices: 49949--50340 Score: 457
Period size: 113 Copynumber: 3.4 Consensus size: 112
49939 AAAAAAGGTA
* *
49949 CCACTAACTTGTGTGGTCTTTGAAAGGTTATGCCACTGACTTGTGGGCTTTGAAAGGGTGTCACT
1 CCACTAACTTGTG-GG-CTTTGAGAGG-T-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* *
50014 AACTTGTGGGTTTTG-AAGGGTACCACTGACTTGTGGGCTTTGAAAGGGTG
62 GACTTGTGGGCTTTGAAAGGGTACCACTGACTTGTGGGCTTTGAAAGGGTG
* *
50064 CCACTAACTTGTGGGCTTTGAGAGGTTGCTACTGACTTGTGAGCTTT-AGAAGGGTGCCACTGAT
1 CCACTAACTTGTGGGCTTTGAGAGGTTGCCACTGACTTGTGGGCTTTGA-AAGGGTGCCACTGA-
* * *
50128 TTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGTGTG
64 CT-TGTGGGCTTTGAAAGGGTACCACTGACTTGTGGGCTTTGAAAGGGTG
* * * *
50178 CCATTGACTTGTGGGCTTTGAAGAGG-TGCCACTGATTTGTGGGCTTTGAAAGGATGCCACTGAC
1 CCACTAACTTGTGGGCTTTG-AGAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGAC
* * * * * * *
50242 TTATGGTCTTTTGAAAAGATACCACTAACTTATGGGCTTTGAAAGGATG
65 TTGTGGGC-TTTGAAAGGGTACCACTGACTTGTGGGCTTTGAAAGGGTG
* * ** *
50291 CCACTAACTTGTGGGCTTTGAAAAGAAGCCACTGACCTGTGGGCTTTGAA
1 CCACTAACTTGTGGGCTTTGAGAGGTTGCCACTGACTTGTGGGCTTTGAA
50341 GAGATGAACG
Statistics
Matches: 237, Mismatches: 32, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
110 1 0.00
111 31 0.13
112 10 0.04
113 92 0.39
114 84 0.35
115 19 0.08
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.32
Consensus pattern (112 bp):
CCACTAACTTGTGGGCTTTGAGAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
TGTGGGCTTTGAAAGGGTACCACTGACTTGTGGGCTTTGAAAGGGTG
Found at i:50287 original size:141 final size:139
Alignment explanation
Indices: 49981--50343 Score: 433
Period size: 141 Copynumber: 2.6 Consensus size: 139
49971 AAAGGTTATG
* * * * *
49981 CCACTGACTTGTGGGCTTTGAAAGGGTGTCACTAACTTGTGGGTTTTGAAGGGTACCACTGACTT
1 CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGTGCCACTGACTT
* * * *
50046 GTGGGCTTTGAA-AGGGTGCCACTAACTTGTGGGCTTTGAGAGGTTGCTACTGACTTGTGAGCTT
66 GTGGGCTTTGAAGA-GGTGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGAGCTT
* * *
50110 TAGAAGGGTG
130 TAGAAAGATA
** * *
50120 CCACTGATTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGTGTGCCATTGA
1 CCACT-AACT-TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAG-GTGCCACTGA
* *
50185 CTTGTGGGCTTTGAAGAGGTGCCACTGATTTGTGGGCTTTGAAAGGATGCCACTGACTTATG-GT
63 CTTGTGGGCTTTGAAGAGGTGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGAG-
*
50249 CTTTTGAAAAGATA
127 CTTTAG-AAAGATA
* * ** *
50263 CCACTAACTTATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAAGCCACTGACC
1 CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTG-AAAGGTGCCACTGACT
50328 TGTGGGCTTTGAAGAG
65 TGTGGGCTTTGAAGAG
50344 ATGAACGTTC
Statistics
Matches: 189, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
139 5 0.03
140 1 0.01
141 100 0.53
142 73 0.39
143 10 0.05
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (139 bp):
CCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGTGCCACTGACTT
GTGGGCTTTGAAGAGGTGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGAGCTTT
AGAAAGATA
Found at i:51576 original size:1 final size:1
Alignment explanation
Indices: 51572--51665 Score: 53
Period size: 1 Copynumber: 94.0 Consensus size: 1
51562 CTAGACCCCC
* * * * * ** * * *
51572 TTTTTTGTTTGTTTGTTTTTTTTGTTTTTTTGTTTTTGGTTTTTTTTTCTATTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * *
51637 TCTTGGTTTTTTTTGTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
51666 GGTACGAAGG
Statistics
Matches: 67, Mismatches: 26, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (1 bp):
T
Found at i:51588 original size:8 final size:8
Alignment explanation
Indices: 51572--51665 Score: 71
Period size: 8 Copynumber: 10.6 Consensus size: 8
51562 CTAGACCCCC
51572 TTTTTTGT
1 TTTTTTGT
*
51580 TTGTTTGTT
1 TTTTTTG-T
51589 TTTTTTGT
1 TTTTTTGT
51597 TTTTTTGT
1 TTTTTTGT
*
51605 TTTTGGTTTT
1 TTTT--TTGT
*
51615 TTTTTCTAT
1 TTTTT-TGT
51624 TTTTTTGTTT
1 TTTTTTG--T
51634 TTTTCTTGGTT
1 TTTT-TT-G-T
51645 TTTTTTGT
1 TTTTTTGT
*
51653 TTTTTTAT
1 TTTTTTGT
51661 TTTTT
1 TTTTT
51666 GGTACGAAGG
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
8 34 0.47
9 15 0.21
10 14 0.19
11 8 0.11
12 1 0.01
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (8 bp):
TTTTTTGT
Found at i:51605 original size:21 final size:21
Alignment explanation
Indices: 51572--51664 Score: 68
Period size: 21 Copynumber: 4.3 Consensus size: 21
51562 CTAGACCCCC
*
51572 TTTTTTGTTTGTTTGTTTTTT
1 TTTTTTATTTGTTTGTTTTTT
51593 TTGTTTT-TTTGTTT-TTGGTTTT
1 TT-TTTTATTTGTTTGTT--TTTT
*
51615 TTTTTCTATTTTTTTGTTTTTT
1 TTTTT-TATTTGTTTGTTTTTT
*
51637 TCTTGGTT-TTT-TTTGTTTTTT
1 T-TT-TTTATTTGTTTGTTTTTT
51658 TATTTTT
1 T-TTTTT
51665 TGGTACGAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
20 4 0.07
21 25 0.42
22 19 0.32
23 9 0.15
24 3 0.05
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (21 bp):
TTTTTTATTTGTTTGTTTTTT
Found at i:54393 original size:13 final size:13
Alignment explanation
Indices: 54375--54399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54365 AAACAGGAAT
54375 TGTATCGATACAA
1 TGTATCGATACAA
54388 TGTATCGATACA
1 TGTATCGATACA
54400 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:54489 original size:13 final size:13
Alignment explanation
Indices: 54471--54495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54461 ATTACTCAAA
54471 TGTATCGATACAT
1 TGTATCGATACAT
54484 TGTATCGATACA
1 TGTATCGATACA
54496 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:70847 original size:116 final size:116
Alignment explanation
Indices: 70643--70873 Score: 390
Period size: 116 Copynumber: 2.0 Consensus size: 116
70633 ACAGTATAAT
* * *
70643 GATCTAACCGAGTTAAACTCATCCCTGGTGAAATGATGCGATACCTCTCGAAATGTGACTGATTA
1 GATCTAACCGAGTTAAACTCAACCCAGGTGAAATGATGCGACACCTCTCGAAATGTGACTGATTA
* *
70708 CTTAAGTAATGAAACTTGTTTATTATCACTTATTCATTGGCGTTTATTAAC
66 CTTAAGTAATGAAACTCGTTTATTATCACTTATTCATTGGCGTATATTAAC
* *
70759 GATCTAACCGAGTTAAACTCAACCCAGGTGAAATGATGCGACACCTCTCGAAATGTGATTTATTA
1 GATCTAACCGAGTTAAACTCAACCCAGGTGAAATGATGCGACACCTCTCGAAATGTGACTGATTA
*
70824 CTTAAGTAATGAAACTCGTTTATTGTCACTTATTCATTGGCGTATATTAA
66 CTTAAGTAATGAAACTCGTTTATTATCACTTATTCATTGGCGTATATTAA
70874 GATATCAATC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 107 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (116 bp):
GATCTAACCGAGTTAAACTCAACCCAGGTGAAATGATGCGACACCTCTCGAAATGTGACTGATTA
CTTAAGTAATGAAACTCGTTTATTATCACTTATTCATTGGCGTATATTAAC
Found at i:78072 original size:24 final size:21
Alignment explanation
Indices: 78030--78083 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 21
78020 ATTTTCAATT
78030 TTTTTAATTTCAAAAATTTTGAA
1 TTTTTAATTTCAAAAA-TTTG-A
***
78053 TATTTTAATTTCACTTATTTGA
1 T-TTTTAATTTCAAAAATTTGA
78075 TTTTTAATT
1 TTTTTAATT
78084 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.30
22 2 0.07
23 5 0.19
24 12 0.44
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTTTAATTTCAAAAATTTGA
Done.