Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 15 of 15
Found at i:2560690 original size:20 final size:21
Alignment explanation
Indices: 2560652--2560692 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2560642 TTTAAATAAG
* *
2560652 ATTTTAAATATTTTTAAAATA
1 ATTTTAAATATTATAAAAATA
2560673 ATTTT-AATATTATAAAAATA
1 ATTTTAAATATTATAAAAATA
2560693 TTAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTTAAATATTATAAAAATA
Found at i:2564067 original size:26 final size:26
Alignment explanation
Indices: 2564018--2564070 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
2564008 TTTTAATATT
*
2564018 AATATATTATATTATTTTTATTTAAA
1 AATATATTATATTATTATTATTTAAA
*
2564044 AATATATTA-ATTATTATTATTTTAA
1 AATATATTATATTATTATTATTTAAA
2564069 AA
1 AA
2564071 GTTTTGTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATATATTATATTATTATTATTTAAA
Found at i:2565259 original size:26 final size:27
Alignment explanation
Indices: 2565223--2565274 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
2565213 AAAAATTTAT
2565223 ATTACTTTTTAA-AATAAAATTAAAAA
1 ATTACTTTTTAATAATAAAATTAAAAA
* **
2565249 ATTATTTTTTAATTTTAAAATTAAAA
1 ATTACTTTTTAATAATAAAATTAAAA
2565275 TTAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTACTTTTTAATAATAAAATTAAAAA
Found at i:2576322 original size:24 final size:21
Alignment explanation
Indices: 2576280--2576332 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 21
2576270 GACCTAATTT
2576280 ATTTTTATTATATAATATATTA
1 ATTTTTATTATATAATATA-TA
*
2576302 ATTTTATATTTATATATTATATA
1 ATTTT-TA-TTATATAATATATA
2576325 ATTTTTAT
1 ATTTTTAT
2576333 GGTATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.04
22 7 0.25
23 9 0.32
24 11 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTATTATATAATATATA
Found at i:2576581 original size:41 final size:40
Alignment explanation
Indices: 2576482--2576586 Score: 108
Period size: 41 Copynumber: 2.5 Consensus size: 40
2576472 TAAAAAATAT
*
2576482 AATATAGATAATTTTAAATAAATTTGAATTATTTATTTACA
1 AATATAAATAA-TTTAAATAAATTTGAATTATTTATTTACA
* *
2576523 AATATAAATACATTTAAATAAATTTTATATT-TTATATTT-TA
1 AATATAAATA-ATTTAAATAAATTTGA-ATTATT-TATTTACA
2576564 AAT-TAAATTAATCTTAAATAAAT
1 AATATAAA-TAAT-TTAAATAAAT
2576587 ATAAATAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
40 6 0.11
41 41 0.73
42 9 0.16
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.47
Consensus pattern (40 bp):
AATATAAATAATTTAAATAAATTTGAATTATTTATTTACA
Found at i:2577275 original size:35 final size:33
Alignment explanation
Indices: 2577215--2577311 Score: 113
Period size: 34 Copynumber: 2.8 Consensus size: 33
2577205 GCCTTACAAT
*
2577215 TCTATCTTTTAACAAGTTAAGATAAAACCTATTC
1 TCTATCTTTTTACAAGTTAAGATAAAA-CTATTC
* *
2577249 TCTATCTTTTTACAGGTTAAGAATAAAACTCTTC
1 TCTATCTTTTTACAAGTTAAG-ATAAAACTATTC
* * *
2577283 TTTATCTTTTTTAAAAGCTAAGATAAAAC
1 TCTATC-TTTTTACAAGTTAAGATAAAAC
2577312 CTCTCAATCA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 36 0.67
35 18 0.33
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.40
Consensus pattern (33 bp):
TCTATCTTTTTACAAGTTAAGATAAAACTATTC
Found at i:2578719 original size:15 final size:15
Alignment explanation
Indices: 2578699--2578732 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2578689 CAAGTTAAAT
2578699 TTAATTT-TTTTATTA
1 TTAATTTATTTTA-TA
2578714 TTAATTTATTTTATA
1 TTAATTTATTTTATA
2578729 TTAA
1 TTAA
2578733 ATGTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTAATTTATTTTATA
Found at i:2578993 original size:6 final size:6
Alignment explanation
Indices: 2578982--2579011 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2578972 TCATAGTACC
2578982 TTTTCT TTTTCT TTTTCT TTTT-T TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T
2579012 ATATTTCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTCT
Found at i:2579132 original size:17 final size:18
Alignment explanation
Indices: 2579107--2579168 Score: 53
Period size: 17 Copynumber: 3.7 Consensus size: 18
2579097 TAATTTAGTA
*
2579107 ATTTATATTATTTTATAT
1 ATTTATATTATATTATAT
2579125 ATTT-TATTATATTATA-
1 ATTTATATTATATTATAT
* **
2579141 A-TAATATT-TAAAATAT
1 ATTTATATTATATTATAT
2579157 -TTTATATTATAT
1 ATTTATATTATAT
2579169 CAATTTTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
15 6 0.18
16 11 0.32
17 13 0.38
18 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATATTATATTATAT
Found at i:2579161 original size:27 final size:28
Alignment explanation
Indices: 2579131--2579205 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
2579121 ATATATTTTA
2579131 TTATATTATAAT-AATATTTAA-A-ATATT
1 TTATATTAT-ATCAAT-TTTAATACATATT
2579158 TTATATTATATCAATTTTAATACATATT
1 TTATATTATATCAATTTTAATACATATT
* * *
2579186 TTATTTTTTATAAATTTTAA
1 TTATATTATATCAATTTTAA
2579206 AAATATATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.17
27 13 0.31
28 22 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATATTATATCAATTTTAATACATATT
Found at i:2579257 original size:14 final size:14
Alignment explanation
Indices: 2579238--2579277 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2579228 ATTTTTATTT
2579238 TTTATATATATATA
1 TTTATATATATATA
2579252 TTTATATA-ATTATA
1 TTTATATATA-TATA
2579266 TTTA-ATAT-TATA
1 TTTATATATATATA
2579278 AATGTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.17
13 4 0.17
14 16 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATATATATATA
Found at i:2579294 original size:18 final size:20
Alignment explanation
Indices: 2579242--2579294 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2579232 TTATTTTTTA
*
2579242 TATATATATATTTATATAAT
1 TATATTTATATTTATATAAT
2579262 TATATTTA-ATATTATA-AA-
1 TATATTTATAT-TTATATAAT
*
2579280 TGTATTTATATTTAT
1 TATATTTATATTTAT
2579295 GAGAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 11 0.38
19 6 0.21
20 12 0.41
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TATATTTATATTTATATAAT
Found at i:2579453 original size:19 final size:19
Alignment explanation
Indices: 2579429--2579475 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2579419 ATGAATAAAA
* *
2579429 AAAAGATAGAGAAAGAGAG
1 AAAAGAAAGACAAAGAGAG
2579448 AAAAGAAAGACAAAGAGA-
1 AAAAGAAAGACAAAGAGAG
*
2579466 AACAGAAAGA
1 AAAAGAAAGA
2579476 AGGAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.68, C:0.04, G:0.26, T:0.02
Consensus pattern (19 bp):
AAAAGAAAGACAAAGAGAG
Found at i:2579582 original size:27 final size:27
Alignment explanation
Indices: 2579552--2579604 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2579542 TTTTAATTAT
2579552 TTTTAAGATATT-ATATATTTATATAAA
1 TTTTAAGATATTAAT-TATTTATATAAA
* *
2579579 TTTTAATATATTAATTTTTTATATAA
1 TTTTAAGATATTAATTATTTATATAA
2579605 TTTCGATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTAAGATATTAATTATTTATATAAA
Found at i:2580430 original size:27 final size:24
Alignment explanation
Indices: 2580383--2580433 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
2580373 TATTGTTTAA
*
2580383 ATTAAAATTAAAACAAATTTAAAT
1 ATTAAAATTAAAAAAAATTTAAAT
2580407 ATTAAATATTAAAAAAATTATTTAAAT
1 ATTAAA-ATTAAAAAAA--ATTTAAAT
2580434 TTACTCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 9 0.39
27 8 0.35
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
ATTAAAATTAAAAAAAATTTAAAT
Found at i:2580637 original size:28 final size:30
Alignment explanation
Indices: 2580599--2580668 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
2580589 AATTATTTCA
* *
2580599 ATTTATTTTAATA-ATTTTTTAAAATTTTT
1 ATTTATATTAATATATTTTTTAAAATTTGT
*
2580628 A-TTATATTAAAATATTTTTTAAAATTTGT
1 ATTTATATTAATATATTTTTTAAAATTTGT
*
2580657 ATTTAAATTAAT
1 ATTTATATTAAT
2580669 TTTAAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 9 0.26
29 17 0.50
30 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
ATTTATATTAATATATTTTTTAAAATTTGT
Found at i:2581110 original size:19 final size:18
Alignment explanation
Indices: 2581072--2581106 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2581062 TTCATATATC
2581072 TTTTTTTTTCTCTTTAAT
1 TTTTTTTTTCTCTTTAAT
2581090 TTTTTTTCTTC-CTTTAA
1 TTTTTTT-TTCTCTTTAA
2581107 ATTTCTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTTTCTCTTTAAT
Found at i:2587708 original size:36 final size:35
Alignment explanation
Indices: 2587668--2587735 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
2587658 TAAATCGTGT
* *
2587668 TTAAATATATTTTTTTTAT-TGTATTATTTTTATTTA
1 TTAAATATATTGTATTTATAT-T-TTATTTTTATTTA
2587704 TTAAATATATTGTATTTATATTTTATTTTTAT
1 TTAAATATATTGTATTTATATTTTATTTTTAT
2587736 GTCAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 10 0.34
36 18 0.62
37 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (35 bp):
TTAAATATATTGTATTTATATTTTATTTTTATTTA
Found at i:2587745 original size:36 final size:36
Alignment explanation
Indices: 2587669--2587745 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
2587659 AAATCGTGTT
* * * *
2587669 TAAATATATTTTTTTTATTGTATTATTTTTATTTAT
1 TAAATATATTGTATTTATTGTATTATTTTTATTCAA
2587705 TAAATATATTGTATTTATAT-T-TTATTTTTATGTCAA
1 TAAATATATTGTATTTAT-TGTATTATTTTTAT-TCAA
2587741 TAAAT
1 TAAAT
2587746 TTTATTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 10 0.29
36 24 0.69
37 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (36 bp):
TAAATATATTGTATTTATTGTATTATTTTTATTCAA
Found at i:2587851 original size:19 final size:18
Alignment explanation
Indices: 2587815--2587857 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2587805 TAATTTATAA
*
2587815 TATTAATTATTATATTTT
1 TATTAATTATGATATTTT
2587833 TAATTAATTAATGAT-TTTT
1 T-ATTAATT-ATGATATTTT
2587852 TATTAA
1 TATTAA
2587858 GATTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.27
19 12 0.55
20 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TATTAATTATGATATTTT
Found at i:2588762 original size:16 final size:18
Alignment explanation
Indices: 2588752--2588791 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
2588742 TTATTTCTTT
2588752 TATTATTTATTACATTTA
1 TATTATTTATTACATTTA
*
2588770 TATTATTT-GTA-ATTTA
1 TATTATTTATTACATTTA
2588786 TATTAT
1 TATTAT
2588792 AGATGATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 2 0.10
18 8 0.38
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTATTTATTACATTTA
Found at i:2592249 original size:17 final size:16
Alignment explanation
Indices: 2592223--2592308 Score: 57
Period size: 16 Copynumber: 5.1 Consensus size: 16
2592213 GAATTATCTA
*
2592223 TTTAAATTTAAGTATAT
1 TTTAAATTTAAAT-TAT
*
2592240 TTTAATTTTAAATTAT
1 TTTAAATTTAAATTAT
*
2592256 TTTAAATTAAAATAATTAT
1 TTTAAATT--TA-AATTAT
*
2592275 ATTTAATAATTAAATTA-
1 -TTTAA-ATTTAAATTAT
* *
2592292 ATTAAATTTAATTTAT
1 TTTAAATTTAAATTAT
2592308 T
1 T
2592309 ATTTATACGA
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
15 8 0.15
16 14 0.26
17 11 0.21
18 6 0.11
19 7 0.13
20 5 0.09
21 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:2592268 original size:16 final size:17
Alignment explanation
Indices: 2592223--2592269 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2592213 GAATTATCTA
*
2592223 TTTAAATTTAAGTATAT
1 TTTAAATTTAAATATAT
*
2592240 TTTAATTTTAAAT-TAT
1 TTTAAATTTAAATATAT
*
2592256 TTTAAATTAAAATA
1 TTTAAATTTAAATA
2592270 ATTATATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATATAT
Found at i:2592287 original size:22 final size:22
Alignment explanation
Indices: 2592260--2592303 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2592250 AATTATTTTA
*
2592260 AATTAAAATAATTATATTTAAT
1 AATTAAAATAATTAAATTTAAT
*
2592282 AATTAAATTAATTAAATTTAAT
1 AATTAAAATAATTAAATTTAAT
2592304 TTATTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTAAAATAATTAAATTTAAT
Found at i:2593179 original size:26 final size:27
Alignment explanation
Indices: 2593151--2593223 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
2593141 TATCCATGTT
2593151 TATTTAAGTAAATTTTTATATTTTATTA
1 TATTTAA-TAAATTTTTATATTTTATTA
*
2593179 TATTTAATAAAATTTTATATTTT-TTA
1 TATTTAATAAATTTTTATATTTTATTA
*
2593205 TATTTAAATAAATATTTAT
1 TATTT-AATAAATTTTTAT
2593224 TTTAAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 8 0.20
27 26 0.63
28 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (27 bp):
TATTTAATAAATTTTTATATTTTATTA
Found at i:2593224 original size:16 final size:16
Alignment explanation
Indices: 2593205--2593294 Score: 55
Period size: 17 Copynumber: 5.8 Consensus size: 16
2593195 ATATTTTTTA
2593205 TATTTAAATAAATATT
1 TATTTAAATAAATATT
*
2593221 TATTTTAAATAAAAATT
1 TA-TTTAAATAAATATT
* * *
2593238 CCA-TTATATTAAACATT
1 -TATTTA-AATAAATATT
* *
2593255 TATTTAGATAAA-CTT
1 TATTTAAATAAATATT
*
2593270 TA---AATTAAATATT
1 TATTTAAATAAATATT
2593283 TATTTAAATAAA
1 TATTTAAATAAA
2593295 AATTAAAATT
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
12 5 0.09
13 4 0.07
15 4 0.07
16 16 0.30
17 24 0.44
18 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (16 bp):
TATTTAAATAAATATT
Found at i:2593300 original size:28 final size:28
Alignment explanation
Indices: 2593208--2593301 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 28
2593198 TTTTTTATAT
2593208 TTAAA-TAAATATTTATTTTAAATAAAAA
1 TTAAATTAAATATTTA-TTTAAATAAAAA
* * **
2593236 TTCCATTATATTAAACATTTATTTAGATAAACT
1 TT--A--A-ATTAAATATTTATTTAAATAAAAA
2593269 TTAAATTAAATATTTATTTAAATAAAAA
1 TTAAATTAAATATTTATTTAAATAAAAA
2593297 TTAAA
1 TTAAA
2593302 ATTTATTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
28 27 0.52
29 1 0.02
30 1 0.02
31 1 0.02
32 1 0.02
33 12 0.23
34 9 0.17
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (28 bp):
TTAAATTAAATATTTATTTAAATAAAAA
Found at i:2593308 original size:22 final size:23
Alignment explanation
Indices: 2593270--2593341 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 23
2593260 AGATAAACTT
2593270 TAAATTAAATATTTATTTAAATAA
1 TAAATTAAA-ATTTATTTAAATAA
*
2593294 -AAATTAAAATTTATTTAATTAAA
1 TAAATTAAAATTTATTTAAAT-AA
2593317 TTAAATATCAAAATTTATTTAAATA
1 -TAAAT-T-AAAATTTATTTAAATA
2593342 TAATAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 11 0.27
23 10 0.24
25 4 0.10
26 2 0.05
27 14 0.34
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATTAAAATTTATTTAAATAA
Found at i:2593329 original size:27 final size:27
Alignment explanation
Indices: 2593279--2593363 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
2593269 TTAAATTAAA
* * *
2593279 TATTTATTTAAA-TAAAAATTAAAATT
1 TATTTAATTAAATTAAATATAAAAATT
*
2593305 TATTTAATTAAATTAAATATCAAAATT
1 TATTTAATTAAATTAAATATAAAAATT
* *
2593332 TATTTAAATATAATAAAATATAAAAATT
1 TATTTAATTA-AATTAAATATAAAAATT
2593360 TATT
1 TATT
2593364 ACGTAAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
26 11 0.22
27 21 0.41
28 19 0.37
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTTAATTAAATTAAATATAAAAATT
Found at i:2593359 original size:28 final size:27
Alignment explanation
Indices: 2593287--2593363 Score: 102
Period size: 28 Copynumber: 2.9 Consensus size: 27
2593277 AATATTTATT
* *
2593287 TAAATAAAA-ATTAAAATTTATTTAAT
1 TAAATAAAATATAAAAATTTATTTAAA
* *
2593313 TAAATTAAATATCAAAATTTATTTAAA
1 TAAATAAAATATAAAAATTTATTTAAA
2593340 TATAATAAAATATAAAAATTTATT
1 TA-AATAAAATATAAAAATTTATT
2593364 ACGTAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 8 0.18
27 17 0.39
28 19 0.43
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATAAAATATAAAAATTTATTTAAA
Found at i:2596118 original size:16 final size:17
Alignment explanation
Indices: 2596078--2596120 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2596068 AAAATATTTC
2596078 ATTTATATTTAAATTAAA
1 ATTTA-ATTTAAATTAAA
*
2596096 ATGTAATTT-AATTAAA
1 ATTTAATTTAAATTAAA
*
2596112 TTTTAATTT
1 ATTTAATTT
2596121 TATAATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 14 0.64
17 4 0.18
18 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAATTTAAATTAAA
Found at i:2596163 original size:38 final size:39
Alignment explanation
Indices: 2596121--2596207 Score: 96
Period size: 38 Copynumber: 2.3 Consensus size: 39
2596111 ATTTTAATTT
2596121 TATAATAATTAAATATATCA-TTAATAATAAAAATT-AAA
1 TATAATAATTAAATA-ATCATTTAATAATAAAAATTGAAA
*
2596159 TATAATTAGA-T-AATAATTATTTAATAATAAAAATTGAAA
1 TATAA-TA-ATTAAATAATCATTTAATAATAAAAATTGAAA
2596198 -ATAAT-ATTAA
1 TATAATAATTAA
2596208 TAAATTAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
35 1 0.02
36 1 0.02
37 5 0.12
38 28 0.67
39 6 0.14
40 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (39 bp):
TATAATAATTAAATAATCATTTAATAATAAAAATTGAAA
Found at i:2596174 original size:11 final size:11
Alignment explanation
Indices: 2596122--2596177 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
2596112 TTTTAATTTT
2596122 ATAATAATTAA
1 ATAATAATTAA
*
2596133 ATATATCATTAATA
1 ATA-ATAATT-A-A
*
2596147 ATAAAAATTAA
1 ATAATAATTAA
*
2596158 AT-ATAATTAG
1 ATAATAATTAA
2596168 ATAATAATTA
1 ATAATAATTA
2596178 TTTAATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 8 0.22
11 13 0.36
12 6 0.17
13 5 0.14
14 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
ATAATAATTAA
Found at i:2596182 original size:25 final size:24
Alignment explanation
Indices: 2596122--2596174 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
2596112 TTTTAATTTT
*
2596122 ATAATAATTAAATATATCATTAATA
1 ATAAAAATTAAATATA-CATTAATA
2596147 ATAAAAATTAAATATA-ATTAGATA
1 ATAAAAATTAAATATACATTA-ATA
2596171 ATAA
1 ATAA
2596175 TTATTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
24 7 0.27
25 15 0.58
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAAAAATTAAATATACATTAATA
Found at i:2597791 original size:21 final size:23
Alignment explanation
Indices: 2597766--2597824 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 23
2597756 ATAAATCGAT
*
2597766 TAAATTATAATTTAAATTT-TTA
1 TAAATTATAATTTAAATTTAATA
* *
2597788 -AAATTTTAATTTTAATTTAATA
1 TAAATTATAATTTAAATTTAATA
2597810 TAAATTA-AATTTAAA
1 TAAATTATAATTTAAA
2597825 ATAATTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 16 0.53
22 9 0.30
23 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAATTATAATTTAAATTTAATA
Found at i:2597873 original size:29 final size:30
Alignment explanation
Indices: 2597819--2597895 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
2597809 ATAAATTAAA
* * *
2597819 TTTAAAATAATTTAATAATTTATTTTTTAT
1 TTTAAAATAATTTAAAAATATATTTTATAT
2597849 TTTAAAA-AATATTAAAAATAT-TTTTATAT
1 TTTAAAATAAT-TTAAAAATATATTTTATAT
*
2597878 TTTATAATTAAATTTAAA
1 TTTA-AAAT-AATTTAAA
2597896 TAAAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 14 0.36
30 17 0.44
31 5 0.13
32 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTAAAATAATTTAAAAATATATTTTATAT
Found at i:2599014 original size:16 final size:16
Alignment explanation
Indices: 2598916--2599028 Score: 72
Period size: 17 Copynumber: 7.1 Consensus size: 16
2598906 GAAATAATTG
* *
2598916 ATTTAAATTAATAATAT
1 ATTTAATTTATTAA-AT
2598933 ATTTAATTTATTATAAT
1 ATTTAATTTATTA-AAT
* * *
2598950 AGTTATTTTATTATA-
1 ATTTAATTTATTAAAT
* * *
2598965 AGTTAA-TTA-GATAT
1 ATTTAATTTATTAAAT
* *
2598979 ATTATAA-TGATAAAATT
1 ATT-TAATTTATTAAA-T
2598996 ATTTAATTTATTAAAT
1 ATTTAATTTATTAAAT
2599012 ATTTAATTTATTAAAT
1 ATTTAATTTATTAAAT
2599028 A
1 A
2599029 ATTGATTTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
13 3 0.04
14 5 0.06
15 10 0.13
16 24 0.31
17 34 0.44
18 1 0.01
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (16 bp):
ATTTAATTTATTAAAT
Found at i:2599036 original size:16 final size:16
Alignment explanation
Indices: 2598998--2599036 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2598988 ATAAAATTAT
*
2598998 TTAATTTATTAAATAT
1 TTAATTTATTAAATAA
2599014 TTAATTTATTAAATAA
1 TTAATTTATTAAATAA
*
2599030 TTGATTT
1 TTAATTT
2599037 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTAATTTATTAAATAA
Found at i:2599084 original size:59 final size:61
Alignment explanation
Indices: 2599018--2599160 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 61
2599008 AAATATTTAA
2599018 TTTATTAAATAATTGATTTTTTTATTTTAT-A-AAATT-TTAAAATAATTATTTAATATATT
1 TTTATTAAATAATT-ATTTTTTTATTTTATAATAAATTATTAAAATAATTATTTAATATATT
* ** * *
2599077 TTTATTAAATAATTA--TTTTAATTTTATAATTAAATTATTATTATAATTATTTATTTTATT
1 TTTATTAAATAATTATTTTTTTATTTTATAA-TAAATTATTAAAATAATTATTTAATATATT
* * *
2599137 TTAATAAAATAATTATTTTATTAT
1 TTTATTAAATAATTATTTTTTTAT
2599161 ACTTTTATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
56 11 0.16
57 1 0.01
58 1 0.01
59 19 0.28
60 32 0.46
62 5 0.07
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (61 bp):
TTTATTAAATAATTATTTTTTTATTTTATAATAAATTATTAAAATAATTATTTAATATATT
Found at i:2599102 original size:22 final size:22
Alignment explanation
Indices: 2599050--2599124 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 22
2599040 TATTTTATAA
2599050 AATTTTA-AAATAATTATTTAAT
1 AATTTTATAAATAATTATTT-AT
2599072 ATATTTTTATTAAATAATTATTT-T
1 A-A-TTTTA-TAAATAATTATTTAT
*
2599096 AATTTTATAATTAAATTATTATTAT
1 AATTTTATAAAT-AATTA-T-TTAT
2599121 AATT
1 AATT
2599125 ATTTATTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
21 4 0.09
22 11 0.25
23 3 0.07
24 9 0.20
25 5 0.11
26 12 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTTATAAATAATTATTTAT
Found at i:2599105 original size:17 final size:17
Alignment explanation
Indices: 2599062--2599128 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
2599052 TTTTAAAATA
2599062 ATTATT-TAATATATTTTT
1 ATTATTATAAT-TA-TTTT
*
2599080 ATTA-AATAATTATTTT
1 ATTATTATAATTATTTT
**
2599096 AATT-TTATAATTAAATT
1 -ATTATTATAATTATTTT
2599113 ATTATTATAATTATTT
1 ATTATTATAATTATTT
2599129 ATTTTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
16 7 0.18
17 24 0.62
18 8 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATTATAATTATTTT
Found at i:2599151 original size:38 final size:37
Alignment explanation
Indices: 2599109--2599182 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 37
2599099 TTTATAATTA
2599109 AATTATTATTATAATTA-TTTATTTTATTTTAATAAAAT
1 AATTATT-TTATAA-TACTTTATTTTATTTTAATAAAAT
*
2599147 AATTATTTTATTATACTTTTATTTTATTTTAATAAA
1 AATTATTTTATAATAC-TTTATTTTATTTTAATAAA
2599183 TCAACCATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 2 0.06
37 5 0.15
38 26 0.79
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (37 bp):
AATTATTTTATAATACTTTATTTTATTTTAATAAAAT
Found at i:2600175 original size:28 final size:28
Alignment explanation
Indices: 2600144--2600198 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
2600134 TTATATAATT
* *
2600144 ATTTATTTGATTTAGTAATTAAATTATC
1 ATTTATGTGAATTAGTAATTAAATTATC
*
2600172 ATTTATGTGAATTAGTAATTGAATTAT
1 ATTTATGTGAATTAGTAATTAAATTAT
2600199 TTATTTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (28 bp):
ATTTATGTGAATTAGTAATTAAATTATC
Found at i:2600207 original size:25 final size:25
Alignment explanation
Indices: 2600140--2600207 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 25
2600130 CAGATTATAT
*
2600140 AATTATTTATTTGATTTAGTAATTA
1 AATTATTTATTTGAATTAGTAATTA
* *
2600165 AATTATCATTTATGTGAATTAGTAATTG
1 AA-T-T-ATTTATTTGAATTAGTAATTA
2600193 AATTATTTATTTGAA
1 AATTATTTATTTGAA
2600208 AGAGGTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 12 0.33
26 2 0.06
27 2 0.06
28 20 0.56
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.51
Consensus pattern (25 bp):
AATTATTTATTTGAATTAGTAATTA
Found at i:2602120 original size:13 final size:13
Alignment explanation
Indices: 2602102--2602127 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2602092 AGCTTTTATA
2602102 TCTGCTTAAACTT
1 TCTGCTTAAACTT
2602115 TCTGCTTAAACTT
1 TCTGCTTAAACTT
2602128 GATGAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
TCTGCTTAAACTT
Found at i:2602856 original size:30 final size:29
Alignment explanation
Indices: 2602822--2602893 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
2602812 ATTTTAAAAA
2602822 TAAATTTTAAA-ATTTATTTAAATTTATTTT
1 TAAATTTTAAATATTTATTTAAA--TATTTT
* *
2602852 TAAA-TTTAATATTTTTATTTAAATCTTTT
1 TAAATTTTAA-ATATTTATTTAAATATTTT
*
2602881 TAAATATTAAATA
1 TAAATTTTAAATA
2602894 AATTTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
29 16 0.46
30 9 0.26
31 10 0.29
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
TAAATTTTAAATATTTATTTAAATATTTT
Found at i:2603765 original size:28 final size:28
Alignment explanation
Indices: 2603719--2603834 Score: 95
Period size: 28 Copynumber: 4.4 Consensus size: 28
2603709 TTTTACTTTT
2603719 AATTATATTT-TATATATAATATAAATAA
1 AATTATATTTATATA-ATAATATAAATAA
*
2603747 AATTATATTTATATAATAAT-T--TTAA
1 AATTATATTTATATAATAATATAAATAA
* * * *
2603772 AA-TATA-TAATATAAT-ATATTATTTA
1 AATTATATTTATATAATAATATAAATAA
*
2603797 TATTATATGTTATATAATAATATAAAT-A
1 AATTATAT-TTATATAATAATATAAATAA
*
2603825 ATTTATATTT
1 AATTATATTT
2603835 CTAAATCTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
22 2 0.03
23 9 0.13
24 4 0.06
25 9 0.13
26 4 0.06
27 3 0.04
28 30 0.42
29 10 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
AATTATATTTATATAATAATATAAATAA
Found at i:2603799 original size:23 final size:23
Alignment explanation
Indices: 2603727--2603799 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
2603717 TTAATTATAT
*
2603727 TTTATATATAATATAA-ATA-AA
1 TTTATATATAATATAATATATTA
* *
2603748 ATTATAT-TTATATAATA-ATT-
1 TTTATATATAATATAATATATTA
*
2603768 TTAAAATATATAATATAATATATTA
1 TT--TATATATAATATAATATATTA
2603793 TTTATAT
1 TTTATAT
2603800 TATATGTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
20 9 0.24
21 7 0.18
22 4 0.11
23 13 0.34
24 3 0.08
25 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATATATAATATAATATATTA
Found at i:2603826 original size:45 final size:42
Alignment explanation
Indices: 2603716--2603826 Score: 103
Period size: 39 Copynumber: 2.8 Consensus size: 42
2603706 CTATTTTACT
*
2603716 TTTA-ATTATATTTTATAT-ATAATATAAAT-A-AAATTATA
1 TTTATATTATATATTATATAATAATATAAATAATAAATTATA
* * * *
2603754 TTTATATAATA-ATTTTAAAAT-ATATAATATAATATA-T-TA
1 TTTATATTATATATTATATAATAATATAA-ATAATAAATTATA
*
2603793 TTTATATTATATGTTATATAATAATATAAATAAT
1 TTTATATTATATATTATATAATAATATAAATAAT
2603827 TTATATTTCT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
38 14 0.25
39 21 0.37
40 14 0.25
41 8 0.14
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (42 bp):
TTTATATTATATATTATATAATAATATAAATAATAAATTATA
Done.