Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold156
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: 2697547
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 14 of 14
Found at i:2621799 original size:39 final size:37
Alignment explanation
Indices: 2621744--2621824 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 37
2621734 TGGGCGTGAC
*
2621744 AATAAAAAATATTTTTTAAATAATAATATTTA-ATAAA
1 AATAAAAAATATTTTTTAAATAA-AATATTAACATAAA
*
2621781 AATATAAAATGATATTTTTT-AATTAAATATTAACATAAA
1 AATA-AAAA--ATATTTTTTAAATAAAATATTAACATAAA
2621820 AATAA
1 AATAA
2621825 TTTTTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
37 4 0.11
38 12 0.32
39 13 0.34
40 9 0.24
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (37 bp):
AATAAAAAATATTTTTTAAATAAAATATTAACATAAA
Found at i:2622803 original size:2 final size:2
Alignment explanation
Indices: 2622796--2622833 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2622786 TCAAACTTTC
*
2622796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2622834 TATTCAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2625599 original size:2 final size:2
Alignment explanation
Indices: 2625594--2625623 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2625584 TGATTTTTTC
2625594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2625624 ATTTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2627104 original size:27 final size:28
Alignment explanation
Indices: 2627052--2627104 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
2627042 TTTTTTAAAA
**
2627052 AATTTATTTTTATATTAATATTAATATT
1 AATTTATTTTTATATTAATAAAAATATT
2627080 AATTTA-TTTTA-ATTAAATAAAAATA
1 AATTTATTTTTATATT-AATAAAAATA
2627105 AAAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 3 0.14
27 13 0.59
28 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AATTTATTTTTATATTAATAAAAATATT
Found at i:2628168 original size:17 final size:16
Alignment explanation
Indices: 2628138--2628180 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
2628128 TTATTTACTT
2628138 TTAAAATATATTTAATTA
1 TTAAAA-AT-TTTAATTA
*
2628156 TTATAAAATTTTAATTT
1 TTA-AAAATTTTAATTA
2628173 TTAAAAAT
1 TTAAAAAT
2628181 AATATCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.22
17 10 0.43
18 5 0.22
19 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAAAATTTTAATTA
Found at i:2636047 original size:2 final size:2
Alignment explanation
Indices: 2636040--2636065 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2636030 CAACAACAAT
2636040 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
2636066 TCAAAGTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2647397 original size:30 final size:29
Alignment explanation
Indices: 2647275--2647389 Score: 135
Period size: 30 Copynumber: 3.9 Consensus size: 29
2647265 TTTTAATTAT
*
2647275 TTTTTAATTTTT-ATAT-TATTAAATAAA
1 TTTTTAATTTTTAATTTGTATTAAATAAA
* * *
2647302 TTTTTTATTTTTAATTTATATTTAAGTAAA
1 TTTTTAATTTTTAATTTGTA-TTAAATAAA
* *
2647332 TTTTAAATATTTAATTTGTATCTAAATAAA
1 TTTTTAATTTTTAATTTGTAT-TAAATAAA
2647362 TTTTTAATTTTTAATTTGTATGTAAATA
1 TTTTTAATTTTTAATTTGTAT-TAAATA
2647390 TGTTTTTATT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
27 11 0.15
28 3 0.04
29 3 0.04
30 56 0.77
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTTAATTTTTAATTTGTATTAAATAAA
Found at i:2655385 original size:15 final size:15
Alignment explanation
Indices: 2655367--2655409 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2655357 TTATTTAATT
2655367 ATTATTTAAAATATA
1 ATTATTTAAAATATA
*
2655382 ATTAATTAAAAT-TA
1 ATTATTTAAAATATA
*
2655396 ATTTATTTTAAATA
1 A-TTATTTAAAATA
2655410 AAAAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATTTAAAATATA
Found at i:2657956 original size:15 final size:16
Alignment explanation
Indices: 2657936--2657973 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2657926 TGATAATTAG
2657936 TTAAATTCAAAAATA-
1 TTAAATTCAAAAATAT
**
2657951 TTAAATTTTAAAATAT
1 TTAAATTCAAAAATAT
2657967 TTAAATT
1 TTAAATT
2657974 AGTTGATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAATTCAAAAATAT
Found at i:2659393 original size:15 final size:17
Alignment explanation
Indices: 2659373--2659406 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
2659363 TGATTTAAAA
2659373 ATTTTAA-AAGTA-TCG
1 ATTTTAATAAGTATTCG
2659388 ATTTTAATAAGTATTCG
1 ATTTTAATAAGTATTCG
2659405 AT
1 AT
2659407 CACACTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTTTAATAAGTATTCG
Found at i:2661002 original size:20 final size:19
Alignment explanation
Indices: 2660958--2661002 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2660948 AATAGATTCG
2660958 TTTTAAAATAATAATTTTA
1 TTTTAAAATAATAATTTTA
**
2660977 AATTAAAATAATATATTTTA
1 TTTTAAAATAATA-ATTTTA
2660997 TTTTAA
1 TTTTAA
2661003 TTTAATTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTAAAATAATAATTTTA
Found at i:2661261 original size:16 final size:15
Alignment explanation
Indices: 2661238--2661302 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
2661228 AATAAAAATA
2661238 AATTAATTAAAATTT
1 AATTAATTAAAATTT
**
2661253 AATTTAATTAATTTATT
1 AA-TTAATTAAAAT-TT
* *
2661270 AAATAATTAATATTT
1 AATTAATTAAAATTT
*
2661285 AATAAATATAAAATTT
1 AATTAAT-TAAAATTT
2661301 AA
1 AA
2661303 ATCTTTTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
15 9 0.22
16 27 0.68
17 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAATTAAAATTT
Found at i:2668677 original size:3 final size:3
Alignment explanation
Indices: 2668657--2668707 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
2668647 GCAAAAGCTT
* *
2668657 TTC TTT TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2668705 TTC
1 TTC
2668708 CCTTGCCCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:2673571 original size:23 final size:22
Alignment explanation
Indices: 2673545--2673587 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2673535 AAATTTTAAT
2673545 ATTTTAATAAATATATTATATAA
1 ATTTTAATAAATATA-TATATAA
*
2673568 ATTTTAATAAATTTATATAT
1 ATTTTAATAAATATATATAT
2673588 TTATATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTAATAAATATATATATAA
Found at i:2673598 original size:33 final size:31
Alignment explanation
Indices: 2673529--2673598 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 31
2673519 GTGTTATGTA
*
2673529 ATTAT-TAAATTTTAATATTTTAATAAATAT
1 ATTATATAAATTTTAATAATTTAATAAATAT
**
2673559 ATTATATAAATTTTAATAAATTTATATATTTAT
1 ATTATATAAATTTTAAT-AATTTA-ATAAATAT
2673592 ATTATAT
1 ATTATAT
2673599 TTATATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 5 0.15
31 11 0.32
32 5 0.15
33 13 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTATATAAATTTTAATAATTTAATAAATAT
Found at i:2673599 original size:11 final size:11
Alignment explanation
Indices: 2673583--2673612 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2673573 AATAAATTTA
2673583 TATATTTATAT
1 TATATTTATAT
2673594 TATATTTATAT
1 TATATTTATAT
2673605 TATTATTT
1 TA-TATTT
2673613 TTAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2673604 original size:19 final size:18
Alignment explanation
Indices: 2673554--2673604 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2673544 TATTTTAATA
*
2673554 AATATATTATATAAATTTT
1 AATATATT-TATATATTTT
*
2673573 AATAAATTTATATATTTAT
1 AATATATTTATATATTT-T
*
2673592 ATTATATTTATAT
1 AATATATTTATAT
2673605 TATTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATATTTATATATTTT
Found at i:2673637 original size:17 final size:17
Alignment explanation
Indices: 2673580--2673646 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 17
2673570 TTTAATAAAT
* *
2673580 TTATATATTTATATTATAT
1 TTATAT-TTTAT-TTTTAA
2673599 TTATATTATTATTTTTAAAA
1 TTATATT-TTATTTTT--AA
2673619 TTATATTTTATTTTTAA
1 TTATATTTTATTTTTAA
*
2673636 TTATTTTTTAT
1 TTATATTTTAT
2673647 AATAAATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.29
18 4 0.10
19 18 0.43
20 8 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTTTATTTTTAA
Found at i:2674371 original size:21 final size:19
Alignment explanation
Indices: 2674322--2674364 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2674312 ATTTATCGTA
*
2674322 TTTTAT-TTATATTATTTT
1 TTTTATATTGTATTATTTT
*
2674340 TTTTATATTGTATTATATT
1 TTTTATATTGTATTATTTT
2674359 TTTTAT
1 TTTTAT
2674365 GTTTTGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTATATTGTATTATTTT
Found at i:2675296 original size:19 final size:19
Alignment explanation
Indices: 2675274--2675353 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 19
2675264 TTCGATAGAA
2675274 AAAAAATTAAATATAATAT
1 AAAAAATTAAATATAATAT
* *
2675293 AAAATA-TAAA-ATGATAT
1 AAAAAATTAAATATAATAT
2675310 AAAAAATATAAATATAAAATAT
1 AAAAAAT-TAAATAT--AATAT
* *
2675332 ATTAAAATT-TATATAATAT
1 A-AAAAATTAAATATAATAT
2675351 AAA
1 AAA
2675354 TTATTAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
17 11 0.23
18 5 0.10
19 15 0.31
20 2 0.04
21 4 0.08
22 6 0.12
23 5 0.10
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAAAATTAAATATAATAT
Found at i:2675309 original size:17 final size:16
Alignment explanation
Indices: 2675276--2675381 Score: 74
Period size: 17 Copynumber: 6.3 Consensus size: 16
2675266 CGATAGAAAA
2675276 AAAAT-TAAATATAATAT
1 AAAATATAAA-AT-ATAT
2675293 AAAATATAAAATGATAT
1 AAAATATAAAAT-ATAT
*
2675310 AAAAAATATAAATATA-
1 AAAATATA-AAATATAT
*
2675326 AAATATATTAAAATTTAT
1 AAA-ATA-TAAAATATAT
* *
2675344 ATAATATAAATTAT-T
1 AAAATATAAAATATAT
*
2675359 AATATATCAAAATTATAT
1 AAAATAT-AAAA-TATAT
2675377 AAAAT
1 AAAAT
2675382 TTTTAAATAA
Statistics
Matches: 70, Mismatches: 11, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
15 6 0.09
16 12 0.17
17 35 0.50
18 17 0.24
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (16 bp):
AAAATATAAAATATAT
Found at i:2675322 original size:25 final size:25
Alignment explanation
Indices: 2675279--2675360 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
2675269 TAGAAAAAAA
2675279 ATTAAATATAATATAAAATATAAAATGAT
1 ATTAAA-A-AATAT-AAATATAAAAT-AT
2675308 A-TAAAAAATATAAATATAAAATAT
1 ATTAAAAAATATAAATATAAAATAT
**
2675332 ATTAAAATTTATATAATAT-AAAT-T
1 ATTAAAAAATATA-AATATAAAATAT
2675356 ATTAA
1 ATTAA
2675361 TATATCAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
24 9 0.18
25 24 0.49
26 10 0.20
27 1 0.02
28 4 0.08
29 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (25 bp):
ATTAAAAAATATAAATATAAAATAT
Found at i:2675350 original size:32 final size:31
Alignment explanation
Indices: 2675314--2675378 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
2675304 TGATATAAAA
*
2675314 AATATAAA-TATAAAATATATTAAAATTTATAT
1 AATATAAATTAT-AAATATATCAAAA-TTATAT
*
2675346 AATATAAATTATTAATATATCAAAATTATAT
1 AATATAAATTATAAATATATCAAAATTATAT
2675377 AA
1 AA
2675379 AATTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 8 0.27
32 19 0.63
33 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
AATATAAATTATAAATATATCAAAATTATAT
Found at i:2675916 original size:45 final size:47
Alignment explanation
Indices: 2675866--2675956 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 47
2675856 TATTTAAAAG
2675866 TATTATTT-AT-AT-ATTT-TTATAATTAAATTTAAATAAAAATATATT
1 TATTATTTAATAATAATTTATTA-AATT-AATTTAAATAAAAATATATT
2675911 TATTATTTGAATAATAATTTAGTTAAATTAATTTAAATAAAAATAT
1 TATTATTT-AATAATAATTTA-TTAAATTAATTTAAATAAAAATAT
2675957 TATATTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
45 8 0.20
47 2 0.05
48 2 0.05
49 21 0.52
50 4 0.10
51 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (47 bp):
TATTATTTAATAATAATTTATTAAATTAATTTAAATAAAAATATATT
Found at i:2675918 original size:23 final size:26
Alignment explanation
Indices: 2675886--2676009 Score: 89
Period size: 23 Copynumber: 4.7 Consensus size: 26
2675876 ATATTTTTAT
2675886 AATTAAATTTAAATAAAAATATA-TT-
1 AATT-AATTTAAATAAAAATATAGTTA
* * * *
2675911 TATT-ATTTGAATAATAATTTAGTTA
1 AATTAATTTAAATAAAAATATAGTTA
*
2675936 AATTAATTTAAATAAAAATATTATATTTA
1 AATTAATTTAAAT-AAAA-A-TATAGTTA
2675965 AATTCAATTTAATATGAAAAA-ATA-TTA
1 AATT-AATTTAA-AT-AAAAATATAGTTA
2675992 AATTCAA-TTAAATAAAAA
1 AATT-AATTTAAATAAAAA
2676010 CTTAACTCTT
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
23 14 0.17
24 7 0.09
25 8 0.10
26 11 0.14
27 13 0.16
28 4 0.05
29 10 0.12
30 8 0.10
31 6 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
AATTAATTTAAATAAAAATATAGTTA
Found at i:2676883 original size:12 final size:11
Alignment explanation
Indices: 2676857--2676881 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2676847 TTTGATATTT
2676857 AAATTTATAAA
1 AAATTTATAAA
2676868 AAATTTATAAA
1 AAATTTATAAA
2676879 AAA
1 AAA
2676882 ATAATATAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTTATAAA
Found at i:2677232 original size:17 final size:19
Alignment explanation
Indices: 2677184--2677233 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2677174 TTTTTAATCT
2677184 TATTTTATATTAAAGATTA
1 TATTTTATATTAAAGATTA
* *
2677203 TATTATTAAATTAAATA-TA
1 TATT-TTATATTAAAGATTA
2677222 TATTTT-TATTAA
1 TATTTTATATTAA
2677234 TTATTAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.19
18 2 0.07
19 10 0.37
20 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TATTTTATATTAAAGATTA
Found at i:2678144 original size:3 final size:3
Alignment explanation
Indices: 2678136--2678169 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2678126 GAAGATGAAC
2678136 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2678170 AGTTTCTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:2678204 original size:6 final size:6
Alignment explanation
Indices: 2678193--2678226 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2678183 AGAGCTTGAT
2678193 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTC
2678227 AGCTTCTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTTCCC
Found at i:2678232 original size:18 final size:18
Alignment explanation
Indices: 2678193--2678232 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2678183 AGAGCTTGAT
*
2678193 CTTCCCCTTCCCCTTCCC
1 CTTCCCCTTCCCCTTCAC
*
2678211 CTTCCCCTTCCCCTTCAG
1 CTTCCCCTTCCCCTTCAC
2678229 CTTC
1 CTTC
2678233 TGCTGCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.60, G:0.03, T:0.35
Consensus pattern (18 bp):
CTTCCCCTTCCCCTTCAC
Found at i:2678527 original size:6 final size:6
Alignment explanation
Indices: 2678518--2678562 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
2678508 CTGCCCCTGT
* *
2678518 TTCAGC TTCAGC TTCAGC TTCAGC TTCAGA TTCAAC TTCAGC TTC
1 TTCAGC TTCAGC TTCAGC TTCAGC TTCAGC TTCAGC TTCAGC TTC
2678563 TGGGATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (6 bp):
TTCAGC
Found at i:2681554 original size:2 final size:2
Alignment explanation
Indices: 2681549--2681581 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
2681539 AACATGTTAC
2681549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
2681582 TTTTGTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2682146 original size:22 final size:22
Alignment explanation
Indices: 2682103--2682166 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
2682093 ATAATTAAAA
2682103 AATATATATAAATA--AATATATT
1 AATATATA-AAATATTAAT-TATT
* * *
2682125 AATTTTTATAATATTAATTATT
1 AATATATAAAATATTAATTATT
2682147 AATATATAAAATATTAATTA
1 AATATATAAAATATTAATTA
2682167 CTATTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 4 0.12
22 27 0.79
23 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATATAAAATATTAATTATT
Found at i:2682153 original size:15 final size:15
Alignment explanation
Indices: 2682117--2682164 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2682107 TATATAAATA
2682117 AATATATTAATT-TT
1 AATATATTAATTATT
*
2682131 TATAATATTAATTATT
1 AAT-ATATTAATTATT
* *
2682147 AATATATAAAATATT
1 AATATATTAATTATT
2682162 AAT
1 AAT
2682165 TACTATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATATTAATTATT
Found at i:2682162 original size:18 final size:17
Alignment explanation
Indices: 2682141--2682185 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2682131 TATAATATTA
2682141 ATTATTAATATATAAAAT
1 ATTATTAATAT-TAAAAT
*
2682159 ATTAATTACTATTAAAAT
1 ATT-ATTAATATTAAAAT
2682177 ATTA-TAATA
1 ATTATTAATA
2682186 AAAATACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 1 0.04
18 12 0.50
19 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATTAATATTAAAAT
Found at i:2683454 original size:1 final size:1
Alignment explanation
Indices: 2683448--2683472 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2683438 CACATGAAAT
2683448 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
2683473 AACATTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2684445 original size:2 final size:2
Alignment explanation
Indices: 2684438--2684479 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2684428 AAGCCAAGGC
2684438 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
2684480 TCCTAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2686163 original size:18 final size:20
Alignment explanation
Indices: 2686129--2686169 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
2686119 AATAAATTCT
2686129 AAAAATTCTCAAGAAAAATA
1 AAAAATTCTCAAGAAAAATA
*
2686149 AAAAATTCT-AA-AAAATTA
1 AAAAATTCTCAAGAAAAATA
2686167 AAA
1 AAA
2686170 TAAAAAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAAATTCTCAAGAAAAATA
Found at i:2686174 original size:29 final size:30
Alignment explanation
Indices: 2686107--2686175 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
2686097 TAAGATCTAA
2686107 AAAATAAAAATAAATAAATTCTAAAAATTC
1 AAAATAAAAATAAATAAATTCTAAAAATTC
** *
2686137 TCAAGAAAAATAAA-AAATTCTAAAAAATT-
1 AAAATAAAAATAAATAAATTCT-AAAAATTC
2686166 AAAATAAAAA
1 AAAATAAAAA
2686176 ATCCAGTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.70, C:0.06, G:0.01, T:0.23
Consensus pattern (30 bp):
AAAATAAAAATAAATAAATTCTAAAAATTC
Found at i:2690644 original size:30 final size:30
Alignment explanation
Indices: 2690608--2690671 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
2690598 AACACAAGAA
2690608 ATAAGAGAATAATTAGACTAGGTAATCTAT
1 ATAAGAGAATAATTAGACTAGGTAATCTAT
2690638 ATAAGAGAATAATTAGACTAGGTAATCTAT
1 ATAAGAGAATAATTAGACTAGGTAATCTAT
2690668 ATAA
1 ATAA
2690672 CTCAAGCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (30 bp):
ATAAGAGAATAATTAGACTAGGTAATCTAT
Found at i:2694053 original size:18 final size:17
Alignment explanation
Indices: 2694016--2694049 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2694006 TAATGAGTAC
*
2694016 TTATAAATACTTTTTAA
1 TTATAAAAACTTTTTAA
*
2694033 TTATAAAAATTTTTTAA
1 TTATAAAAACTTTTTAA
2694050 ATTAAACTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAAAAACTTTTTAA
Found at i:2696908 original size:21 final size:20
Alignment explanation
Indices: 2696884--2696945 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
2696874 ATTAAAATAT
*
2696884 TATTTTATATTAATATTTATA
1 TATTTTATATTAA-ATTTAAA
2696905 TA-TTTATAATTAAATTTAAA
1 TATTTTAT-ATTAAATTTAAA
*
2696925 TAATTTTTTATT--ATTTAAA
1 T-ATTTTATATTAAATTTAAA
2696944 TA
1 TA
2696946 ATATTTGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 1 0.03
19 8 0.22
20 12 0.33
21 11 0.31
22 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTATATTAAATTTAAA
Done.