Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold486
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: 208893
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
File 2 of 2
Found at i:151601 original size:20 final size:21
Alignment explanation
Indices: 151556--151622 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 21
151546 TTATAAATTT
151556 ATTTTTTATATCATA---AT-
1 ATTTTTTATATCATATTTATA
* *
151573 ATATTTTATATCGTATTT-TA
1 ATTTTTTATATCATATTTATA
*
151593 ATTTTTTATATTATATTTATA
1 ATTTTTTATATCATATTTATA
151614 ATTTATTTA
1 ATTT-TTTA
151623 AAATTATTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 13 0.33
19 1 0.03
20 15 0.38
21 6 0.15
22 4 0.10
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (21 bp):
ATTTTTTATATCATATTTATA
Found at i:153862 original size:2 final size:2
Alignment explanation
Indices: 153855--153897 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
153845 ATTCTCCTCC
153855 AT 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 AT
153897 A
1 A
153898 CTATTATGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:153972 original size:15 final size:16
Alignment explanation
Indices: 153948--153981 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
153938 CGTATAATCA
*
153948 TATTATATTT-AAAAT
1 TATTAAATTTAAAAAT
153963 TATTAAATTTAAAAAT
1 TATTAAATTTAAAAAT
153979 TAT
1 TAT
153982 AATATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTAAATTTAAAAAT
Found at i:156969 original size:50 final size:50
Alignment explanation
Indices: 156908--157107 Score: 231
Period size: 50 Copynumber: 4.0 Consensus size: 50
156898 AGATGCTTAG
* * *
156908 AGTCAATAATTACGGTCACCTTTGTCGATTGTCAAAGGTTGATGAAGAAT
1 AGTCAACAATTACGGTCACCTTTCTCGATTGTCAAAGGTTGGTGAAGAAT
* ** * * *
156958 GGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGGTGAAAAAT
1 AGTCAACAATTACGGTCACCTTTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * * *
157008 AGTAAACAATTATGGTAACTTTTCTCGATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTTTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
157058 AGTCAACAATTAC-GACTGCCTTTCTAGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTC-ACCTTTCTCGATTGTCAAAGGTTGGTGAAGAAT
157108 TACGACCATC
Statistics
Matches: 121, Mismatches: 28, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
49 1 0.01
50 120 0.99
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTTTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:158554 original size:15 final size:16
Alignment explanation
Indices: 158529--158561 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
158519 ATAGTTTAAT
158529 ATTTTATAAAAAAATA
1 ATTTTATAAAAAAATA
*
158545 ATTTTA-AAAAATATA
1 ATTTTATAAAAAAATA
158560 AT
1 AT
158562 AATATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTTATAAAAAAATA
Found at i:159145 original size:15 final size:15
Alignment explanation
Indices: 159125--159211 Score: 70
Period size: 15 Copynumber: 5.9 Consensus size: 15
159115 TCAATTTATG
*
159125 TATATAAATATAAAA
1 TATATAAATATATAA
*
159140 TATATATATAT-TAA
1 TATATAAATATATAA
*
159154 TATATAAAT-TATTA
1 TATATAAATATATAA
* **
159168 GATATAAATATACGA
1 TATATAAATATATAA
* *
159183 TATATAAATTTATTA
1 TATATAAATATATAA
*
159198 TATAATTAATATAT
1 TAT-ATAAATATAT
159212 GAGATAAATA
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
13 1 0.02
14 20 0.36
15 27 0.48
16 8 0.14
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (15 bp):
TATATAAATATATAA
Found at i:159158 original size:12 final size:12
Alignment explanation
Indices: 159132--159211 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 12
159122 ATGTATATAA
*
159132 ATATAAAAT-AT
1 ATATAAATTAAT
*
159143 ATATATATTAAT
1 ATATAAATTAAT
*
159155 ATATAAATTATTAG
1 ATATAAATTA--AT
159169 ATATAAATATACGAT
1 ATATAAAT-TA--AT
*
159184 ATATAAATTTAT
1 ATATAAATTAAT
159196 -TATATAATTAAT
1 ATATA-AATTAAT
159208 ATAT
1 ATAT
159212 GAGATAAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 11 0.20
12 19 0.35
13 3 0.06
14 10 0.19
15 11 0.20
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (12 bp):
ATATAAATTAAT
Found at i:159172 original size:22 final size:23
Alignment explanation
Indices: 159132--159179 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
159122 ATGTATATAA
* *
159132 ATATAAAATATATATATATTAAT
1 ATATAAAATATATAGATATAAAT
*
159155 ATATAAATTAT-TAGATATAAAT
1 ATATAAAATATATAGATATAAAT
159177 ATA
1 ATA
159180 CGATATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATATAAAATATATAGATATAAAT
Found at i:159210 original size:37 final size:36
Alignment explanation
Indices: 159117--159210 Score: 86
Period size: 37 Copynumber: 2.6 Consensus size: 36
159107 TGAATAAGTC
* * *
159117 AATTTATGTATATAAAT-ATA-AAATATATATATATT
1 AATTTAT-TATATAATTAATATAAATATAGATATATA
* * *
159152 AATATA-TAAATTATTAGATATAAATATACGATATATA
1 AATTTATTATATAATTA-ATATAAATATA-GATATATA
159189 AATTTATTATATAATTAATATA
1 AATTTATTATATAATTAATATA
159211 TGAGATAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
33 6 0.13
35 8 0.18
36 7 0.16
37 16 0.36
38 8 0.18
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (36 bp):
AATTTATTATATAATTAATATAAATATAGATATATA
Found at i:160606 original size:18 final size:19
Alignment explanation
Indices: 160577--160613 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
160567 TTGTATAAGT
160577 TTATTATATTTAATATTAA
1 TTATTATATTTAATATTAA
*
160596 TTATT-TATTTAATTTTAA
1 TTATTATATTTAATATTAA
160614 AAAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTATATTTAATATTAA
Found at i:160642 original size:16 final size:16
Alignment explanation
Indices: 160614--160653 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
160604 TTAATTTTAA
160614 AAAATATATTATATATT
1 AAAATA-ATTATATATT
*
160631 AAAATAATTATATTTT
1 AAAATAATTATATATT
*
160647 AATATAA
1 AAAATAA
160654 ATATTAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATAATTATATATT
Found at i:162256 original size:2 final size:2
Alignment explanation
Indices: 162219--162247 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
162209 TTAAAAAAAT
162219 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 T
162248 GCATATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:163007 original size:5 final size:4
Alignment explanation
Indices: 162984--163022 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
162974 CTTTATTATA
* *
162984 ATTT ATTT ATTG ATAT ATTAT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT ATTT AT
163023 AATTAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (4 bp):
ATTT
Found at i:163007 original size:17 final size:14
Alignment explanation
Indices: 162975--163022 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 14
162965 ATTTTACATC
162975 TTTATTATAATTTA
1 TTTATTATAATTTA
162989 TTTATTGATATATTATA
1 TTTATT-ATA-ATT-TA
163006 TTTATT-T-ATTTA
1 TTTATTATAATTTA
163018 TTTAT
1 TTTAT
163023 AATTAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 6 0.19
15 4 0.13
16 3 0.10
17 8 0.26
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTATTATAATTTA
Found at i:170423 original size:5 final size:5
Alignment explanation
Indices: 170413--170447 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
170403 TATATTTTAG
170413 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
170448 ATATATAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:170488 original size:22 final size:22
Alignment explanation
Indices: 170437--170496 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
170427 ATAAAATAAA
*
170437 ATAAAATAAAAATATATAGTAT
1 ATAAATTAAAAATATATAGTAT
* * *
170459 A-AAGATTAAAAATATTTATTTT
1 ATAA-ATTAAAAATATATAGTAT
170481 ATAAATTAAAAA-ATAT
1 ATAAATTAAAAATATAT
170497 CCATAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.16
22 24 0.77
23 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (22 bp):
ATAAATTAAAAATATATAGTAT
Found at i:170705 original size:33 final size:33
Alignment explanation
Indices: 170667--170736 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
170657 TATTTTAAAA
**
170667 ATAATATTTATTTCTAATACTATTAAA-TTAATG
1 ATAATATTTACCTCTAATACTATTAAATTTAA-G
*
170700 ATAATATTTACCTCTAATATTATTAAATTTAAG
1 ATAATATTTACCTCTAATACTATTAAATTTAAG
170733 ATAA
1 ATAA
170737 AAATAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (33 bp):
ATAATATTTACCTCTAATACTATTAAATTTAAG
Found at i:170863 original size:2 final size:2
Alignment explanation
Indices: 170856--170884 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
170846 TGATAAGTTT
170856 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 T
170885 CAAAATTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:171622 original size:75 final size:74
Alignment explanation
Indices: 171493--171643 Score: 212
Period size: 75 Copynumber: 2.0 Consensus size: 74
171483 AGATGAATGA
* ** * *
171493 TAATCTAGATAATCTGAATGATATTTATAATCAACAAATGTTTCAGCATATTTCACAGTGCTACT
1 TAATCTAGATAATCTGAACGATAACTACAATCAACAAATATTTCAGCATATTTCACAGTGCTACT
171558 ATCAACAAC
66 ATCAACAAC
* * *
171567 TAATCTGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTCACATTGCTAC
1 TAATCT-AGATAATCTGAACGATAACTACAATCAACAAATATTTCAGCATATTTCACAGTGCTAC
*
171632 TATTAACAAC
65 TATCAACAAC
171642 TA
1 TA
171644 TAATCAACAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 6 0.09
75 61 0.91
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (74 bp):
TAATCTAGATAATCTGAACGATAACTACAATCAACAAATATTTCAGCATATTTCACAGTGCTACT
ATCAACAAC
Found at i:177132 original size:27 final size:26
Alignment explanation
Indices: 177102--177156 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
177092 CTCATTAATT
*
177102 ATATTACTTAATTTAATTAAACAA-AAA
1 ATATTAC-TAATTT-ATTAAAAAATAAA
*
177129 ATATTGCTAATTTATTAAAAAATAAA
1 ATATTACTAATTTATTAAAAAATAAA
177155 AT
1 AT
177157 CATATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.32
26 11 0.44
27 6 0.24
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (26 bp):
ATATTACTAATTTATTAAAAAATAAA
Found at i:177960 original size:10 final size:10
Alignment explanation
Indices: 177947--177990 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
177937 TTTAATTTTT
177947 ATATATTTAA
1 ATATATTTAA
177957 ATATATTTATA
1 ATATATTTA-A
*
177968 TTTATATTTAA
1 -ATATATTTAA
177979 ATATATGTTAA
1 ATATAT-TTAA
177990 A
1 A
177991 CATAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 14 0.48
11 7 0.24
12 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (10 bp):
ATATATTTAA
Found at i:183489 original size:10 final size:10
Alignment explanation
Indices: 183476--183519 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
183466 TTTAATTTTT
183476 ATATATTTAA
1 ATATATTTAA
183486 ATATATTTATA
1 ATATATTTA-A
*
183497 TTTATATTTAA
1 -ATATATTTAA
183508 ATATATGTTAA
1 ATATAT-TTAA
183519 A
1 A
183520 CATAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 14 0.48
11 7 0.24
12 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (10 bp):
ATATATTTAA
Found at i:191873 original size:13 final size:13
Alignment explanation
Indices: 191857--191909 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 13
191847 ATTATGTAAT
191857 TATATAATATAAA
1 TATATAATATAAA
* *
191870 TATAAAAAAT-AA
1 TATATAATATAAA
191882 -ATATAAT-TAAA
1 TATATAATATAAA
191893 -ATATAATATTAAA
1 TATATAATA-TAAA
191906 TATA
1 TATA
191910 ATAACGTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
10 1 0.03
11 14 0.44
12 2 0.06
13 12 0.38
14 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATATAATATAAA
Found at i:192100 original size:10 final size:11
Alignment explanation
Indices: 192071--192103 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
192061 ATATATTATC
*
192071 ATAATTAAAAA
1 ATAATTAAAAT
192082 ATAATTAAAAT
1 ATAATTAAAAT
192093 ATAA-TAAAAT
1 ATAATTAAAAT
192103 A
1 A
192104 AGATAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATTAAAAT
Found at i:192183 original size:23 final size:25
Alignment explanation
Indices: 192138--192183 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
192128 TATAAATGTT
192138 TAAATATATAAAAATTTATAAAAAA
1 TAAATATATAAAAATTTATAAAAAA
*
192163 TAAAT-TATAAACA-TTATAAAA
1 TAAATATATAAAAATTTATAAAA
192184 TTTATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 7 0.35
25 5 0.25
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAATATATAAAAATTTATAAAAAA
Found at i:192448 original size:11 final size:11
Alignment explanation
Indices: 192424--192473 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
192414 AAATATAATT
* *
192424 ATATAAATATA
1 ATATATATAAA
192435 ATATATATAAA
1 ATATATATAAA
192446 ATA-AT-TAAA
1 ATATATATAAA
192455 ATAT-TATATAA
1 ATATATATA-AA
192466 ATATATAT
1 ATATATAT
192474 TTTTTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 8 0.24
10 4 0.12
11 18 0.55
12 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATATATAAA
Found at i:192495 original size:31 final size:30
Alignment explanation
Indices: 192454--192539 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
192444 AAATAATTAA
192454 AATATTATATAAATATATATTTTTTAAAATT
1 AATA-TATATAAATATATATTTTTTAAAATT
* * *
192485 TATATAATATAAAT-TATTAATTATTAAAATT
1 AATAT-ATATAAATATA-TATTTTTTAAAATT
*
192516 AATATATATATATATA-ATTATTTT
1 AATATATATAAATATATATT-TTTT
192540 CGATATGATT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
29 2 0.05
30 13 0.30
31 29 0.66
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AATATATATAAATATATATTTTTTAAAATT
Found at i:195542 original size:1 final size:1
Alignment explanation
Indices: 195496--195531 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
195486 CTTTGTTTTG
195496 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
195532 GATGGGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:195543 original size:59 final size:59
Alignment explanation
Indices: 195456--195578 Score: 237
Period size: 59 Copynumber: 2.1 Consensus size: 59
195446 AACATATCCC
*
195456 AAAAAAAAAAAAAAAGAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAA
195515 AAAAAAAAAAAAAAAAAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAA
195574 AAAAA
1 AAAAA
195579 GAGGCAGTGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.15
Consensus pattern (59 bp):
AAAAAAAAAAAAAAAAAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAA
Found at i:200813 original size:21 final size:21
Alignment explanation
Indices: 200789--200828 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
200779 TGCATGCTTA
*
200789 TAGTAGATATTGGATTTGATT
1 TAGTAGATATTGAATTTGATT
* *
200810 TAGTTGATGTTGAATTTGA
1 TAGTAGATATTGAATTTGA
200829 ATTGATTTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (21 bp):
TAGTAGATATTGAATTTGATT
Found at i:202808 original size:24 final size:24
Alignment explanation
Indices: 202774--202819 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
202764 GATTATATTA
*
202774 TCTTGCTGATTAAAACAGAGATGT
1 TCTTGCCGATTAAAACAGAGATGT
*
202798 TCTTGCCGATTAAACCAGAGAT
1 TCTTGCCGATTAAAACAGAGAT
202820 AATCTGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (24 bp):
TCTTGCCGATTAAAACAGAGATGT
Found at i:203934 original size:17 final size:18
Alignment explanation
Indices: 203914--203948 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
203904 AAAAAGTCAC
203914 ATTAAT-CAAAATTTAAT
1 ATTAATGCAAAATTTAAT
*
203931 ATTAATGCAAATTTTAAT
1 ATTAATGCAAAATTTAAT
203949 TATTTGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAATGCAAAATTTAAT
Found at i:204472 original size:14 final size:15
Alignment explanation
Indices: 204445--204478 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
204435 TAAATTTTAA
*
204445 TTTATATTAGTATTT
1 TTTATATTAATATTT
204460 TTTA-ATTAATATTT
1 TTTATATTAATATTT
204474 TTTAT
1 TTTAT
204479 TTTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTATATTAATATTT
Found at i:204527 original size:30 final size:31
Alignment explanation
Indices: 204470--204527 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
204460 TTTAATTAAT
* *
204470 ATTTTTTATTTTTATATAAATAGATATAACG
1 ATTTTTTATTTTAATATAAATAAATATAACG
**
204501 ATTTTTTA-TTTAATATATTTAAATATA
1 ATTTTTTATTTTAATATAAATAAATATA
204528 TCGCGCTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 15 0.65
31 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTTTTTATTTTAATATAAATAAATATAACG
Found at i:205256 original size:19 final size:17
Alignment explanation
Indices: 205232--205270 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
205222 TCACTAGCTC
205232 ATATATTTATATTATACTT
1 ATATATTTATA-TATA-TT
*
205251 ATATATTTTTATATATT
1 ATATATTTATATATATT
205268 ATA
1 ATA
205271 ATTAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATTTATATATATT
Done.