Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2234
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: 77305
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:11579 original size:17 final size:17
Alignment explanation
Indices: 11557--11589 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11547 TTATTTTTAT
11557 TTTCCATTATTATATTA
1 TTTCCATTATTATATTA
11574 TTTCCATTATTATATT
1 TTTCCATTATTATATT
11590 GGAACTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTCCATTATTATATTA
Found at i:11669 original size:2 final size:2
Alignment explanation
Indices: 11657--11713 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
11647 GTTATGATTC
*
11657 TA TA CA TA TA TA 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 TA TA TA TA TA TA
11699 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
11714 GTTCTCATTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13118 original size:81 final size:81
Alignment explanation
Indices: 13027--13184 Score: 298
Period size: 81 Copynumber: 2.0 Consensus size: 81
13017 ATATATAGAT
* *
13027 ATAAATCATAAATTATGGTTTAGAGTATCTAATATGAAAGAAATGGAGGGTTCATTTGTTGATCA
1 ATAAATCATAAATTATGGTTTAGAGTATCTAATATGAAAGAAATGGAGGGTTCATATGTTGACCA
13092 TTAATCAATGATATAA
66 TTAATCAATGATATAA
13108 ATAAATCATAAATTATGGTTTAGAGTATCTAATATGAAAGAAATGGAGGGTTCATATGTTGACCA
1 ATAAATCATAAATTATGGTTTAGAGTATCTAATATGAAAGAAATGGAGGGTTCATATGTTGACCA
13173 TTAATCAATGAT
66 TTAATCAATGAT
13185 CAAATTAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.35
Consensus pattern (81 bp):
ATAAATCATAAATTATGGTTTAGAGTATCTAATATGAAAGAAATGGAGGGTTCATATGTTGACCA
TTAATCAATGATATAA
Found at i:13370 original size:2 final size:2
Alignment explanation
Indices: 13363--13402 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
13353 CAAGTAGACA
13363 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
13403 TTTAAAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13745 original size:6 final size:6
Alignment explanation
Indices: 13701--13759 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
13691 GTTTGATTTG
* * * *
13701 GGGAAT GGGAG- GGAGAGT GGG-GT GGGGGT GGGGGT GGGAGT GGGAAT
1 GGGAGT GGGAGT GG-GAGT GGGAGT GGGAGT GGGAGT GGGAGT GGGAGT
13748 GGGAGT GGGAGT
1 GGGAGT GGGAGT
13760 CGGTGCATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 7 0.15
6 37 0.80
7 2 0.04
ACGTcount: A:0.17, C:0.00, G:0.68, T:0.15
Consensus pattern (6 bp):
GGGAGT
Found at i:14444 original size:20 final size:21
Alignment explanation
Indices: 14414--14452 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14404 TTGTAAAATA
*
14414 AATATAAATAATTTTATTTTT
1 AATATAAATAATATTATTTTT
14435 AATA-AAATAATATTATTT
1 AATATAAATAATATTATTT
14453 AATTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATAAATAATATTATTTTT
Found at i:14452 original size:25 final size:26
Alignment explanation
Indices: 14410--14465 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
14400 ATATTTGTAA
*
14410 AATAAATATAAATAATTTTATTT-TT
1 AATAAATATAAATAATTTAATTTATT
*
14435 AATAAA-ATAATATTATTTAATTTATT
1 AATAAATATAA-ATAATTTAATTTATT
14461 AATAA
1 AATAA
14466 TATCTAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 16 0.59
26 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAAATATAAATAATTTAATTTATT
Found at i:17496 original size:48 final size:48
Alignment explanation
Indices: 17401--17496 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
17391 AATTTAAATA
* *
17401 AAAAATTAAACTCGTTTAAAAAATGAATTGAACTTTGGTTCTCACTTT
1 AAAAATTAAACTCGTTTAAAAAATGAATTGAACCTTGATTCTCACTTT
* * *
17449 AAAAATTAGACTCGTTTAAAAAAT-AGATTGATCCTTGATTCTTACTTT
1 AAAAATTAAACTCGTTTAAAAAATGA-ATTGAACCTTGATTCTCACTTT
17497 CAAAGCTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
47 1 0.02
48 41 0.98
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (48 bp):
AAAAATTAAACTCGTTTAAAAAATGAATTGAACCTTGATTCTCACTTT
Found at i:17577 original size:26 final size:26
Alignment explanation
Indices: 17521--17605 Score: 72
Period size: 26 Copynumber: 3.4 Consensus size: 26
17511 AGTCTAATCT
17521 ATTTTATAATTATATAATATATATTA
1 ATTTTATAATTATATAATATATATTA
* *
17547 ATTTTATATTTTTAT-ATAT-TATGTA
1 ATTTTATAATTATATAATATATAT-TA
* *
17572 ATTTT-T-ATCATATAA-ATATAGGTA
1 ATTTTATAATTATATAATATATA-TTA
*
17596 ATATTATAAT
1 ATTTTATAAT
17606 ATAAACATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
23 6 0.13
24 13 0.28
25 12 0.26
26 15 0.33
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (26 bp):
ATTTTATAATTATATAATATATATTA
Found at i:21986 original size:2 final size:2
Alignment explanation
Indices: 21942--21970 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21932 CCATACTTGT
21942 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
21971 TAGTATGGAG
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:22249 original size:2 final size:2
Alignment explanation
Indices: 22242--22278 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22232 GTTATCACAT
22242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22279 GAGTATAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24072 original size:2 final size:2
Alignment explanation
Indices: 24065--24091 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24055 TTTTCCACTT
24065 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 T
24092 TGCATTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26235 original size:298 final size:298
Alignment explanation
Indices: 25699--26298 Score: 1137
Period size: 298 Copynumber: 2.0 Consensus size: 298
25689 TCTTTTGTCA
*
25699 TGGGATAAAATATGCCATCTTCAAAAATCTATCCACAACTATCATTATGGAATCTTTCTGTCTTT
1 TGGGATAAAATATGCCATCTTCAAAAATCTATCCACAACTACCATTATGGAATCTTTCTGTCTTT
* *
25764 AAGTTCGAGGTAGTCTAAGAACAAAATACATACTTACATCTTCCCAAGGTGTAGTTAGAATAGGA
66 AAGTTCGAGGTAGTCTAAGAACAAAATACATACTTACATATTCCCAAGGTATAGTTAGAATAGGA
*
25829 AAAGGCATGTATAATCCTGTATTTTGGCTTTTGGATTTAGCCAAGTGACAGGTTTTGAATCTTTA
131 AAAGGCATGTATAATCCTGTATTTTGGCTTTTGGATTTAGCCAAGTGACACGTTTTGAATCTTTA
*
25894 GATATGCCTATTGACATTTATTTTAAGCTTTGACCAATAGAAATTTTCTTTAACTAAGGCCACAG
196 GATATGCCTATTGACATTTATTTTAAGCTTTAACCAATAGAAATTTTCTTTAACTAAGGCCACAG
*
25959 CTTCATCTCGTCCAAAGTGTCCTGCTAATCCTCCGTTG
261 CTTCATCTCGTCCAAAGTGTCCTACTAATCCTCCGTTG
25997 TGGGATAAAATATGCCATCTTCAAAAATCTATCCACAACTACCATTATGGAATCTTTCTGTCTTT
1 TGGGATAAAATATGCCATCTTCAAAAATCTATCCACAACTACCATTATGGAATCTTTCTGTCTTT
26062 AAGTTCGAGGTAGTCTAAGAACAAAATACATACTTACATATTCCCAAGGTATAGTTAGAATAGGA
66 AAGTTCGAGGTAGTCTAAGAACAAAATACATACTTACATATTCCCAAGGTATAGTTAGAATAGGA
*
26127 AAAGGCATGTATAATCCTGTATTTTGGCTTTTGGATTTAGCCAAGTGACACGTTTTGAATCTTTG
131 AAAGGCATGTATAATCCTGTATTTTGGCTTTTGGATTTAGCCAAGTGACACGTTTTGAATCTTTA
26192 GATATGCCTATTGACATTTATTTTAAGCTTTAACCAATAGAAATTTTCTTTAACTAAGGCCACAG
196 GATATGCCTATTGACATTTATTTTAAGCTTTAACCAATAGAAATTTTCTTTAACTAAGGCCACAG
26257 CTTCATCTCGTCCAAAGTGTCCTACTAATCCTCCGTTG
261 CTTCATCTCGTCCAAAGTGTCCTACTAATCCTCCGTTG
26295 TGGG
1 TGGG
26299 CCTCTCAAAT
Statistics
Matches: 295, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
298 295 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (298 bp):
TGGGATAAAATATGCCATCTTCAAAAATCTATCCACAACTACCATTATGGAATCTTTCTGTCTTT
AAGTTCGAGGTAGTCTAAGAACAAAATACATACTTACATATTCCCAAGGTATAGTTAGAATAGGA
AAAGGCATGTATAATCCTGTATTTTGGCTTTTGGATTTAGCCAAGTGACACGTTTTGAATCTTTA
GATATGCCTATTGACATTTATTTTAAGCTTTAACCAATAGAAATTTTCTTTAACTAAGGCCACAG
CTTCATCTCGTCCAAAGTGTCCTACTAATCCTCCGTTG
Found at i:29754 original size:18 final size:19
Alignment explanation
Indices: 29727--29763 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29717 GTAATCACAT
29727 AAATCGGTGATT-CTAAAA
1 AAATCGGTGATTCCTAAAA
*
29745 AAATCTGTGATTCCTAAAA
1 AAATCGGTGATTCCTAAAA
29764 TTTGTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (19 bp):
AAATCGGTGATTCCTAAAA
Found at i:34389 original size:40 final size:39
Alignment explanation
Indices: 34319--34397 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
34309 CTCATTTTAT
34319 TATTTATAATTAATATTATAAAAATTTATTTTTATATTAA
1 TATTTATAATTAATATTATAAAAA-TTATTTTTATATTAA
*
34359 TATTTATAATTAA-ATTTAAATAAAAA-TATTTTTTTATTA
1 TATTTATAATTAATA-TT--ATAAAAATTATTTTTATATTA
34398 TTTAAATAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
39 1 0.03
40 27 0.77
42 7 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (39 bp):
TATTTATAATTAATATTATAAAAATTATTTTTATATTAA
Found at i:34536 original size:2 final size:2
Alignment explanation
Indices: 34531--34556 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34521 GTGAACACAC
34531 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
34557 TAAGTTTGTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38982 original size:2 final size:2
Alignment explanation
Indices: 38975--39017 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
38965 GAGTACACCG
*
38975 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39017 A
1 A
39018 ATTATCTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39654 original size:19 final size:19
Alignment explanation
Indices: 39626--39667 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
39616 CCTAATATAA
39626 AAATTATTTTAAAAAATTT
1 AAATTATTTTAAAAAATTT
*
39645 AAATTTTTTTAAAAAATTT
1 AAATTATTTTAAAAAATTT
39664 AAAT
1 AAAT
39668 CTTTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATTATTTTAAAAAATTT
Found at i:40459 original size:2 final size:2
Alignment explanation
Indices: 40452--40487 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40442 AATGTAAATA
40452 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
40488 GGTCTAGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44059 original size:28 final size:29
Alignment explanation
Indices: 44017--44086 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
44007 CAGCCTTTAA
* *
44017 TTATACCCAACTAAGCTCTTAACCTAT-A-
1 TTATACCTAAATAAGCTC-TAACCTATAAT
* *
44045 TTGTACCTAAATAAGCTCTAACCTTTAAT
1 TTATACCTAAATAAGCTCTAACCTATAAT
44074 TTATACCTAAATA
1 TTATACCTAAATA
44087 CACCCTTTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 7 0.20
28 16 0.46
29 12 0.34
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (29 bp):
TTATACCTAAATAAGCTCTAACCTATAAT
Found at i:44084 original size:29 final size:28
Alignment explanation
Indices: 43996--44086 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 28
43986 TATTACACTC
* * *
43996 AAATAAGCCCTCAGCCTTTAATTATACCC
1 AAATAAGCTCT-AACCTTTAATTATACCT
* * *
44025 AACTAAGCTCTTAACCTAT-ATTGTACCT
1 AAATAAGCTC-TAACCTTTAATTATACCT
44053 AAATAAGCTCTAACCTTTAATTTATACCT
1 AAATAAGCTCTAACCTTTAA-TTATACCT
44082 AAATA
1 AAATA
44087 CACCCTTTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 7 0.14
28 17 0.34
29 25 0.50
30 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATAAGCTCTAACCTTTAATTATACCT
Found at i:45307 original size:34 final size:35
Alignment explanation
Indices: 45207--45310 Score: 103
Period size: 35 Copynumber: 3.0 Consensus size: 35
45197 TATATAATTA
* *
45207 AAATAGTTTA-ATTTAA-ATTATTATTTAATAATAAT
1 AAATAATTTATATTTAATATTA--ATTTAAAAATAAT
45242 AAATAATTTATATTTAA-ATTTAA-TTATAAAATATAT
1 AAATAATTTATATTTAATA-TTAATTTA-AAAATA-AT
45278 AAAT-ATTTATA-TTAATATTAATTTAAAAATAAT
1 AAATAATTTATATTTAATATTAATTTAAAAATAAT
45311 TTTTTATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
33 2 0.03
34 17 0.28
35 26 0.43
36 13 0.21
37 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (35 bp):
AAATAATTTATATTTAATATTAATTTAAAAATAAT
Found at i:46899 original size:19 final size:21
Alignment explanation
Indices: 46877--46918 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
46867 CCTCATGGGA
46877 TTCATTTT-T-TATTTTTATT
1 TTCATTTTATATATTTTTATT
*
46896 TTCATTTTATATGTTTTTATT
1 TTCATTTTATATATTTTTATT
46917 TT
1 TT
46919 AGGAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 11 0.55
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (21 bp):
TTCATTTTATATATTTTTATT
Found at i:48244 original size:21 final size:21
Alignment explanation
Indices: 48202--48244 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
48192 AGAATAAATT
*
48202 AAATATAATTATAATATAAAA
1 AAATATAATTATAAAATAAAA
*
48223 AAATATGAATT-TAAAATTAAA
1 AAATAT-AATTATAAAATAAAA
48244 A
1 A
48245 TTAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATATAATTATAAAATAAAA
Found at i:51903 original size:17 final size:17
Alignment explanation
Indices: 51883--51916 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
51873 AAATAAAAAC
51883 TAAACTTAATTAAATTT
1 TAAACTTAATTAAATTT
* *
51900 TAAATTTAATTTAATTT
1 TAAACTTAATTAAATTT
51917 AATTTTTTTA
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):
TAAACTTAATTAAATTT
Found at i:52099 original size:16 final size:16
Alignment explanation
Indices: 52078--52109 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52068 TTGCGTGCTA
52078 ACTCACTTCCTTTTCT
1 ACTCACTTCCTTTTCT
52094 ACTCACTTCCTTTTCT
1 ACTCACTTCCTTTTCT
52110 TAAGTATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.00, T:0.50
Consensus pattern (16 bp):
ACTCACTTCCTTTTCT
Found at i:58264 original size:40 final size:40
Alignment explanation
Indices: 58220--58299 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
58210 TGTACTTGTA
58220 ATTGTATCCAAAATCTTCTTATTTTATTTTAATCTTTCAC
1 ATTGTATCCAAAATCTTCTTATTTTATTTTAATCTTTCAC
*
58260 ATTGTATCCAAAGTCTTCTTATTTTATTTTAATCTTTCAC
1 ATTGTATCCAAAATCTTCTTATTTTATTTTAATCTTTCAC
58300 CTTTTTCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.53
Consensus pattern (40 bp):
ATTGTATCCAAAATCTTCTTATTTTATTTTAATCTTTCAC
Found at i:62241 original size:2 final size:2
Alignment explanation
Indices: 62234--62259 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62224 GTGTATGTGA
62234 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
62260 TCACTAACCT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64134 original size:2 final size:2
Alignment explanation
Indices: 64127--64156 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
64117 TTAGTATGTA
64127 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
64157 CTTATGTATA
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):
AT
Found at i:70274 original size:103 final size:103
Alignment explanation
Indices: 70095--70302 Score: 398
Period size: 103 Copynumber: 2.0 Consensus size: 103
70085 TTATAATAAA
*
70095 CTTTTTCCTATTATACCCTTTTCAATAGAGTTTTTCATGAATAATACAATTGGCTTTGAAATTGA
1 CTTTTTCCTATTATACCCTTTTCAATAGAGTTTTTCATGAATAATACAATTGGCTTTGAAATTAA
70160 TTATAAAATTAAGTACTGATAATATTACTATTACTAAT
66 TTATAAAATTAAGTACTGATAATATTACTATTACTAAT
*
70198 CTTTTTTCTATTATACCCTTTTCAATAGAGTTTTTCATGAATAATACAATTGGCTTTGAAATTAA
1 CTTTTTCCTATTATACCCTTTTCAATAGAGTTTTTCATGAATAATACAATTGGCTTTGAAATTAA
70263 TTATAAAATTAAGTACTGATAATATTACTATTACTAAT
66 TTATAAAATTAAGTACTGATAATATTACTATTACTAAT
70301 CT
1 CT
70303 ATCGTTACTT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (103 bp):
CTTTTTCCTATTATACCCTTTTCAATAGAGTTTTTCATGAATAATACAATTGGCTTTGAAATTAA
TTATAAAATTAAGTACTGATAATATTACTATTACTAAT
Found at i:74655 original size:546 final size:547
Alignment explanation
Indices: 73092--74739 Score: 3111
Period size: 547 Copynumber: 3.0 Consensus size: 547
73082 TCCAGTGCTC
*
73092 CCCAGCAATATATTGATAGGCCTTCTAGGACTACGATGCTTCTGGCTTGTGGCATACTGACTTTA
1 CCCAACAATATATTGATAGGCCTTCTAGGACTACGATGCTTCTGGCTTGTGGCATACTGACTTTA
*
73157 ATATCAACAACCTCCGTCAAGCCTCTGCTATTTCAAACTATAATATGCCACATGGGATTCATTGC
66 ATATCAACACCCTCCGTCAAGCCTCTGCTATTTCAAACTATAATATGCCACATGGGATTCATTGC
*
73222 CTTCCTCAGAAATGCACTTGGTCATTACTTGCTATTACAGTACTATTATCCTTTCAGGTTTATTT
131 CTTCCTCAGAAATGCACTCGGTCATTACTTGCTATTACAGTACTATTATCCTTTCAGGTTTATTT
*
73287 CACTCTCTCTGGGTTGAAGTGATCTATGAGCCACAGCGTATTTCTGACAAAACTTACACAGCATA
196 CACTCTCTCTGGGTTAAAGTGATCTATGAGCCACAGCGTATTTCTGACAAAACTTACACAGCATA
*
73352 GGAGCTCATTCTCTTGATCAATAACTCATAAAGAAAGAAACAATATTGCAAGTATGGCTTGCTTA
261 GGAGCTCATTCTCTTGATCAATAACTCATAAAGAAAGAAACAATATTGCAAGTATGGCTTGCTTG
*
73417 TCTCCCATTCAAAAAAAAAATCCAATATTAGCTTAGCTGCTAAACATAGCAAAGCTAAAACCCCA
326 TCTCCCATTCAAAATAAAAATCCAATATTAGCTTAGCTGCTAAACATAGCAAAGCTAAAACCCCA
*
73482 AAAGGTGATCTTTTCATTTCAGCTCTAGAAGCACCGCATGCACTGAGTTCATTGAGTACCTTAAT
391 AAAGGTGATCTTTTCATTTCAGCTCTAGAAGCACCGCATGCATTGAGTTCATTGAGTACCTTAAT
73547 CACAATGAAACCTTGCAGCATCAAGTTCCAACCACACAATCAGTTTTAGTCACCATACTCCCTTA
456 CACAATGAAACCTTGCAGCATCAAGTTCCAACCACACAATCAGTTTTAGTCACCATACTCCCTTA
73612 GAGAACTTCTCAGTGAACTCCAGATGA
521 GAGAACTTCTCAGTGAACTCCAGATGA
73639 CCCAACAATATATTGATAGGCCTTCTAGGACTACGATGCTTCTGGCTTGTGGCATACTGACTTTA
1 CCCAACAATATATTGATAGGCCTTCTAGGACTACGATGCTTCTGGCTTGTGGCATACTGACTTTA
73704 ATATCAACACCCTCCGTCAAGCCTCTGCTATTTCAAACTATAATATGCCACATGGGATTCATTGC
66 ATATCAACACCCTCCGTCAAGCCTCTGCTATTTCAAACTATAATATGCCACATGGGATTCATTGC
*
73769 CTTCCTCAGAAATGCACTCGGTCATTACTTGCTATTACAGTACAATTATCCTTTCAGGTTTATTT
131 CTTCCTCAGAAATGCACTCGGTCATTACTTGCTATTACAGTACTATTATCCTTTCAGGTTTATTT
* * *
73834 CACTCTCTCTGGGTTAAAGTGATCTATGAGCCACAGCCTATTTCTGACACAACTTACACTGCATA
196 CACTCTCTCTGGGTTAAAGTGATCTATGAGCCACAGCGTATTTCTGACAAAACTTACACAGCATA
73899 GGAGCTCATTCTCTTGATCAATAACTCATAAAGAAAGAAACAATATTGCAAGTATGGCTTGCTTG
261 GGAGCTCATTCTCTTGATCAATAACTCATAAAGAAAGAAACAATATTGCAAGTATGGCTTGCTTG
73964 TCTCCCATTCAAAATAAAAATCCAATATTAGCTTAGCTGCTAAACATAGCAAAGCTAAAACCCCA
326 TCTCCCATTCAAAATAAAAATCCAATATTAGCTTAGCTGCTAAACATAGCAAAGCTAAAACCCCA
*
74029 AAAGGTGATCTTTTCATTTCAGCTCTAGAAGCACTGCATGCATTGAGTTCATTGAGTACCTTAAT
391 AAAGGTGATCTTTTCATTTCAGCTCTAGAAGCACCGCATGCATTGAGTTCATTGAGTACCTTAAT
74094 CACAATGAAACCTTGCAGCATCAAGTTCCAACCACACAATCAGTTTTAGTCACCATACTCCCTTA
456 CACAATGAAACCTTGCAGCATCAAGTTCCAACCACACAATCAGTTTTAGTCACCATACTCCCTTA
74159 GAGAACTTCTCAGTGAACTCCAGATGA
521 GAGAACTTCTCAGTGAACTCCAGATGA
*
74186 CCCAACAATATATTGATAGGCCTTCTAGGACTACGATGCTT-TGGGCTTGTGGAATACTGACTTT
1 CCCAACAATATATTGATAGGCCTTCTAGGACTACGATGCTTCT-GGCTTGTGGCATACTGACTTT
* **
74250 AATATCAACACCCTCCGCCAAGCCTCTGCTATTTCAAACTATAATATGCCACATTAGATTCATTG
65 AATATCAACACCCTCCGTCAAGCCTCTGCTATTTCAAACTATAATATGCCACATGGGATTCATTG
*
74315 CCTTCCTCAGAAATGCACTCGGTCATTACTTGCTATTACTGTACTATTATCC-TTCAGGTTTATT
130 CCTTCCTCAGAAATGCACTCGGTCATTACTTGCTATTACAGTACTATTATCCTTTCAGGTTTATT
*
74379 TCACTCTCTCTGGGTTAAAGTGATCTATGAGCCACAGCGTATTTCTGACAGAACTTACACAGCAT
195 TCACTCTCTCTGGGTTAAAGTGATCTATGAGCCACAGCGTATTTCTGACAAAACTTACACAGCAT
74444 AGGAGCTCATTCTCTTGATCAATAACTCATAAAGAAAGAAACAATATTGCAAGTATGGCTTGCTT
260 AGGAGCTCATTCTCTTGATCAATAACTCATAAAGAAAGAAACAATATTGCAAGTATGGCTTGCTT
74509 GTCTCCCATTCAAAATAAAAATCCAATATTAGCTTAGCTGCTAAACATAGCAAAGCTAAAACCCC
325 GTCTCCCATTCAAAATAAAAATCCAATATTAGCTTAGCTGCTAAACATAGCAAAGCTAAAACCCC
74574 AAAAGGTGATCTTTTCATTTCAGCTCTAGAAGCACCGCATGCATTGAGTTCATTGAGTACCTTAA
390 AAAAGGTGATCTTTTCATTTCAGCTCTAGAAGCACCGCATGCATTGAGTTCATTGAGTACCTTAA
74639 TCACAATGAAACCTTGCAGCATCAAGTTCCAACCACACAATCAGTTTTAGTCACCATACTCCCTT
455 TCACAATGAAACCTTGCAGCATCAAGTTCCAACCACACAATCAGTTTTAGTCACCATACTCCCTT
74704 AGAGAACTTCTCAGTGAACTCCAGATGA
520 AGAGAACTTCTCAGTGAACTCCAGATGA
74732 CCCAACAA
1 CCCAACAA
74740 ACATATTCGG
Statistics
Matches: 1078, Mismatches: 22, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
546 370 0.34
547 708 0.66
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (547 bp):
CCCAACAATATATTGATAGGCCTTCTAGGACTACGATGCTTCTGGCTTGTGGCATACTGACTTTA
ATATCAACACCCTCCGTCAAGCCTCTGCTATTTCAAACTATAATATGCCACATGGGATTCATTGC
CTTCCTCAGAAATGCACTCGGTCATTACTTGCTATTACAGTACTATTATCCTTTCAGGTTTATTT
CACTCTCTCTGGGTTAAAGTGATCTATGAGCCACAGCGTATTTCTGACAAAACTTACACAGCATA
GGAGCTCATTCTCTTGATCAATAACTCATAAAGAAAGAAACAATATTGCAAGTATGGCTTGCTTG
TCTCCCATTCAAAATAAAAATCCAATATTAGCTTAGCTGCTAAACATAGCAAAGCTAAAACCCCA
AAAGGTGATCTTTTCATTTCAGCTCTAGAAGCACCGCATGCATTGAGTTCATTGAGTACCTTAAT
CACAATGAAACCTTGCAGCATCAAGTTCCAACCACACAATCAGTTTTAGTCACCATACTCCCTTA
GAGAACTTCTCAGTGAACTCCAGATGA
Found at i:76202 original size:18 final size:19
Alignment explanation
Indices: 76176--76217 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
76166 ATTGTTTTTC
76176 TTTTT-GTTTTTT-TATTT
1 TTTTTCGTTTTTTCTATTT
*
76193 TTTTTCGTTTTTTCTTTTT
1 TTTTTCGTTTTTTCTATTT
76212 TTTTTC
1 TTTTTC
76218 AGGGAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (19 bp):
TTTTTCGTTTTTTCTATTT
Found at i:76518 original size:20 final size:21
Alignment explanation
Indices: 76476--76519 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
76466 ATTGATGTAT
* * *
76476 TTTTGAATAATAATTAATTTA
1 TTTTAAATAATAAATAATATA
76497 TTTTAAATAA-AAATAATATA
1 TTTTAAATAATAAATAATATA
76517 TTT
1 TTT
76520 ATTTTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTTAAATAATAAATAATATA
Done.