Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2474
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: 37469
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:192 original size:16 final size:17
Alignment explanation
Indices: 160--191 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
150 GAAAGCAAAG
160 TCCAATTCAAGATAAAA
1 TCCAATTCAAGATAAAA
177 TCCAA-TCAA-ATAAAA
1 TCCAATTCAAGATAAAA
192 AAAAAGAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.56, C:0.19, G:0.03, T:0.22
Consensus pattern (17 bp):
TCCAATTCAAGATAAAA
Found at i:717 original size:11 final size:12
Alignment explanation
Indices: 703--731 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
693 GTAATTTAAA
703 AAATTTTAA-TT
1 AAATTTTAATTT
714 AAATTTTAATTT
1 AAATTTTAATTT
726 AAATTT
1 AAATTT
732 ATTCAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AAATTTTAATTT
Found at i:837 original size:19 final size:18
Alignment explanation
Indices: 813--855 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
803 AATTATATTA
* *
813 AATAAAAATATTATTAATT
1 AATAAAAATATT-TAAACT
832 AAT-AAAATATTTAAACT
1 AATAAAAATATTTAAACT
849 AATAAAA
1 AATAAAA
856 TTCAACTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 7 0.33
18 11 0.52
19 3 0.14
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAAAATATTTAAACT
Found at i:853 original size:17 final size:18
Alignment explanation
Indices: 817--856 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
807 ATATTAAATA
* *
817 AAAATATTATTAATTAAT
1 AAAATATTATAAACTAAT
835 AAAATATT-TAAACTAAT
1 AAAATATTATAAACTAAT
852 AAAAT
1 AAAAT
857 TCAACTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATTATAAACTAAT
Found at i:3614 original size:19 final size:19
Alignment explanation
Indices: 3590--3628 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3580 ATATTAAAAA
3590 ATATTTTAT-AATAATATTT
1 ATATTTTATAAATAA-ATTT
3609 ATATTTTATAAATAAATTT
1 ATATTTTATAAATAAATTT
3628 A
1 A
3629 AATAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTTTATAAATAAATTT
Found at i:4220 original size:16 final size:16
Alignment explanation
Indices: 4201--4232 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4191 TAGATATAGT
4201 TTAATGTTTTTTTAAA
1 TTAATGTTTTTTTAAA
*
4217 TTAATTTTTTTTTAAA
1 TTAATGTTTTTTTAAA
4233 AAAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TTAATGTTTTTTTAAA
Found at i:4379 original size:18 final size:21
Alignment explanation
Indices: 4341--4381 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
4331 TTATTTAAAT
4341 TTAATTATAAAATATATAATA
1 TTAATTATAAAATATATAATA
4362 TTAA-TATAAAA-A-ATAATA
1 TTAATTATAAAATATATAATA
4380 TT
1 TT
4382 TTAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 7 0.35
21 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAATTATAAAATATATAATA
Found at i:4385 original size:20 final size:21
Alignment explanation
Indices: 4339--4389 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
4329 TTTTATTTAA
4339 ATTTAATTATAAAATATATAAT
1 ATTTAA-TATAAAATATATAAT
4361 A-TTAATATAAAA-A-ATAAT
1 ATTTAATATAAAATATATAAT
4379 ATTTTAATATA
1 A-TTTAATATA
4390 TTTTGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 6 0.22
19 1 0.04
20 15 0.56
21 4 0.15
22 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTAATATAAAATATATAAT
Found at i:4392 original size:10 final size:12
Alignment explanation
Indices: 4373--4405 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
4363 TAATATAAAA
4373 AATAATATTTT-
1 AATAATATTTTG
4384 AAT-ATATTTTG
1 AATAATATTTTG
4395 AATAATATTTT
1 AATAATATTTT
4406 TTTAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.35
11 6 0.30
12 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (12 bp):
AATAATATTTTG
Found at i:4448 original size:16 final size:16
Alignment explanation
Indices: 4429--4473 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
4419 TAAATTATTA
4429 AATTTTTAATATTTAT
1 AATTTTTAATATTTAT
* *
4445 AATTTTTACTTAATTAT
1 AATTTTTA-ATATTTAT
*
4462 AATTTTTTATAT
1 AATTTTTAATAT
4474 AAAAATTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTTAATATTTAT
Found at i:4461 original size:17 final size:16
Alignment explanation
Indices: 4401--4468 Score: 70
Period size: 17 Copynumber: 4.4 Consensus size: 16
4391 TTTGAATAAT
4401 ATTTTT-TTAATTATA
1 ATTTTTATTAATTATA
**
4416 ATTTAAATT-ATTA-A
1 ATTTTTATTAATTATA
* *
4430 ATTTTTAATATTTATA
1 ATTTTTATTAATTATA
4446 ATTTTTACTTAATTATA
1 ATTTTTA-TTAATTATA
4463 ATTTTT
1 ATTTTT
4469 TATATAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
14 7 0.17
15 11 0.27
16 10 0.24
17 13 0.32
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTATTAATTATA
Found at i:4838 original size:4 final size:4
Alignment explanation
Indices: 4829--4856 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4819 ATCCCGTTGC
4829 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
4857 TGTGGTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:5277 original size:34 final size:33
Alignment explanation
Indices: 5232--5449 Score: 260
Period size: 34 Copynumber: 6.5 Consensus size: 33
5222 TAAAAACCAT
*
5232 CATTTAATCAACAATGGCAACCTACCAAATCTAC
1 CATTTAATCAACAATGGTAACCTACCAAATC-AC
*
5266 CATTTAGTCAACAATGGTAAGCC-ACCAAATCACC
1 CATTTAATCAACAATGGTAA-CCTACCAAATCA-C
* * **
5300 CATTTAATCAATAATGGTAAGCTACCAAATTTC
1 CATTTAATCAACAATGGTAACCTACCAAATCAC
* *
5333 TCATTTAATCAACAATGGTAAGCTACCAAATCTCC
1 -CATTTAATCAACAATGGTAACCTACCAAATC-AC
* *
5368 CATTTAGTCAACAATGGCAAACC-ACCAAATCACC
1 CATTTAATCAACAATGG-TAACCTACCAAATCA-C
*
5402 CATTTAATCAACAATGGTAAACTACCAAATCAC
1 CATTTAATCAACAATGGTAACCTACCAAATCAC
5435 CATTTAATCAACAAT
1 CATTTAATCAACAAT
5450 TCTCCCACTT
Statistics
Matches: 159, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
33 22 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CATTTAATCAACAATGGTAACCTACCAAATCAC
Found at i:5345 original size:68 final size:67
Alignment explanation
Indices: 5232--5449 Score: 294
Period size: 68 Copynumber: 3.2 Consensus size: 67
5222 TAAAAACCAT
* * *
5232 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAATC
5297 ACC
65 ACC
* * * *
5300 CATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAATC
1 CATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAATC
*
5365 TCC
65 ACC
* * * *
5368 CATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAATC
1 CATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAATC
5433 A-C
65 ACC
5435 CATTTAATCAACAAT
1 CATTTAATCAACAAT
5450 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATCA
CC
Found at i:5407 original size:102 final size:102
Alignment explanation
Indices: 5231--5449 Score: 350
Period size: 102 Copynumber: 2.2 Consensus size: 102
5221 GTAAAAACCA
* *
5231 TCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 TCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAAT
* * **
5296 CACCCATTTAATCAATAATGGTAAGCTACCAAATTTC
66 CACCCATTTAATCAACAATGGTAAACTACCAAATCAC
* * *
5333 TCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAAT
1 TCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAAT
5398 CACCCATTTAATCAACAATGGTAAACTACCAAATCAC
66 CACCCATTTAATCAACAATGGTAAACTACCAAATCAC
5435 -CATTTAATCAACAAT
1 TCATTTAATCAACAAT
5450 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
101 15 0.14
102 93 0.86
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (102 bp):
TCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAAT
CACCCATTTAATCAACAATGGTAAACTACCAAATCAC
Found at i:8367 original size:171 final size:171
Alignment explanation
Indices: 8082--8423 Score: 675
Period size: 171 Copynumber: 2.0 Consensus size: 171
8072 GCTCACAGAA
8082 AGGTAGGCTTACTGTTTTGAGTCCAAGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTT
1 AGGTAGGCTTACTGTTTTGAGTCCAAGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTT
8147 CTGACATATGGCCCAATCTACGATGCCACATCATTGTTGATTCTTCATCCGAACTGATTGTCGCA
66 CTGACATATGGCCCAATCTACGATGCCACATCATTGTTGATTCTTCATCCGAACTGATTGTCGCA
8212 ACAGATGCGTCTGCCTCCTGCAATGTCTCTCCTTTAAGCAT
131 ACAGATGCGTCTGCCTCCTGCAATGTCTCTCCTTTAAGCAT
*
8253 AGGTAGGCTTACTGTTTTGAGTCCAGGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTT
1 AGGTAGGCTTACTGTTTTGAGTCCAAGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTT
8318 CTGACATATGGCCCAATCTACGATGCCACATCATTGTTGATTCTTCATCCGAACTGATTGTCGCA
66 CTGACATATGGCCCAATCTACGATGCCACATCATTGTTGATTCTTCATCCGAACTGATTGTCGCA
8383 ACAGATGCGTCTGCCTCCTGCAATGTCTCTCCTTTAAGCAT
131 ACAGATGCGTCTGCCTCCTGCAATGTCTCTCCTTTAAGCAT
8424 GTATAGATTT
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 170 1.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (171 bp):
AGGTAGGCTTACTGTTTTGAGTCCAAGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTT
CTGACATATGGCCCAATCTACGATGCCACATCATTGTTGATTCTTCATCCGAACTGATTGTCGCA
ACAGATGCGTCTGCCTCCTGCAATGTCTCTCCTTTAAGCAT
Found at i:10061 original size:34 final size:33
Alignment explanation
Indices: 10016--10231 Score: 170
Period size: 34 Copynumber: 6.4 Consensus size: 33
10006 AAAAACTTAC
*
10016 CATTTAATCAACAATGGCAACCTACCAAATCTAT
1 CATTTAATCAACAATGGTAACCTACCAAATC-AT
*
10050 CATTTAGTCAACAATGGTAAGCC-ACCAAATCACT
1 CATTTAATCAACAATGGTAA-CCTACCAAATCA-T
* * * *
10084 TATTTAATCAATAATGGTAAGCTATCAAATTTC-T
1 CATTTAATCAACAATGGTAACCTACCAAA--TCAT
*** *
10118 CATTTAATCAACAATGGTAGGTTACC-AATCTCT
1 CATTTAATCAACAATGGTAACCTACCAAATC-AT
* ** *
10151 CATTTAGTCAACAATGACAAACC-ATCAAATCACCT
1 CATTTAATCAACAATG-GTAACCTACCAAATCA--T
* * *
10186 CATTTAATCAACAACGGTAAACTACCAAATCAC
1 CATTTAATCAACAATGGTAACCTACCAAATCAT
10219 CATTTAATCAACA
1 CATTTAATCAACA
10232 GTTTTCAGAG
Statistics
Matches: 143, Mismatches: 27, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
31 2 0.01
33 35 0.24
34 79 0.55
35 25 0.17
36 2 0.01
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (33 bp):
CATTTAATCAACAATGGTAACCTACCAAATCAT
Found at i:10129 original size:68 final size:68
Alignment explanation
Indices: 10016--10231 Score: 229
Period size: 68 Copynumber: 3.2 Consensus size: 68
10006 AAAAACTTAC
* * * * * *
10016 CATTTAATCAACAATGGCAACCTACCAAATCTATCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGGCAAACTATCAAATATCTCATTTAATCAACAATGGTAAGCTACCAAATC
10081 ACT
66 ACT
* * * * * * *
10084 TATTTAATCAATAATGGTAAGCTATCAAATTTCTCATTTAATCAACAATGGTAGGTTACC-AATC
1 CATTTAATCAACAATGGCAAACTATCAAATATCTCATTTAATCAACAATGGTAAGCTACCAAATC
*
10148 TCT
66 ACT
* * * * * *
10151 CATTTAGTCAACAATGACAAACCATCAAATCACCTCATTTAATCAACAACGGTAAACTACCAAAT
1 CATTTAATCAACAATGGCAAACTATCAAAT-ATCTCATTTAATCAACAATGGTAAGCTACCAAAT
10216 CAC-
65 CACT
10219 CATTTAATCAACA
1 CATTTAATCAACA
10232 GTTTTCAGAG
Statistics
Matches: 119, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
67 29 0.24
68 85 0.71
69 5 0.04
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (68 bp):
CATTTAATCAACAATGGCAAACTATCAAATATCTCATTTAATCAACAATGGTAAGCTACCAAATC
ACT
Found at i:10193 original size:102 final size:101
Alignment explanation
Indices: 10014--10231 Score: 267
Period size: 102 Copynumber: 2.1 Consensus size: 101
10004 GTAAAAACTT
** *
10014 ACCATTTAATCAACAATGGCAACCTACCAAATCTATCATTTAGTCAACAATGGTAAGCCACCAAA
1 ACCATTTAATCAACAATGGCAACCTACCAAATCTATCATTTAGTCAACAATGACAAACCACCAAA
* * * * * *
10079 TCACTTATTTAATCAATAATGGTAAGCTATCAAATT
66 TCACTCATTTAATCAACAACGGTAAACTACCAAATC
* * *** * *
10115 TCTCATTTAATCAACAATGGTAGGTTACC-AATCTCTCATTTAGTCAACAATGACAAACCATCAA
1 AC-CATTTAATCAACAATGGCAACCTACCAAATCTATCATTTAGTCAACAATGACAAACCACCAA
10179 ATCACCTCATTTAATCAACAACGGTAAACTACCAAATC
65 ATCA-CTCATTTAATCAACAACGGTAAACTACCAAATC
10217 ACCATTTAATCAACA
1 ACCATTTAATCAACA
10232 GTTTTCAGAG
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
101 48 0.49
102 50 0.51
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (101 bp):
ACCATTTAATCAACAATGGCAACCTACCAAATCTATCATTTAGTCAACAATGACAAACCACCAAA
TCACTCATTTAATCAACAACGGTAAACTACCAAATC
Found at i:11756 original size:404 final size:404
Alignment explanation
Indices: 11007--11786 Score: 1544
Period size: 404 Copynumber: 1.9 Consensus size: 404
10997 CAGTTTCATG
11007 TACAAAGGGCATATGGAAGCAAAATAATCTCTTTCAGCTTCCAGGAAAGAAGAATCTGTCGAGGC
1 TACAAAGGGCATATGGAAGCAAAATAATCTCTTTCAGCTTCCAGGAAAGAAGAATCTGTCGAGGC
11072 CCCATTGAAGCTTGACGAAGACCCTTGGACTTGGGCTATGGAGTTATTAGAATGTGCGTCTTCTA
66 CCCATTGAAGCTTGACGAAGACCCTTGGACTTGGGCTATGGAGTTATTAGAATGTGCGTCTTCTA
11137 CTAGTGAAGAAGGATAAGAAGAAGCAAAAGAGTGAGATCTCCATGTCAATGGAGATAGCAATGGC
131 CTAGTGAAGAAGGATAAGAAGAAGCAAAAGAGTGAGATCTCCATGTCAATGGAGATAGCAATGGC
11202 GACAAACTAGAGGGCTGATTAGGAACCAATGTAGACACAAGAACTAAAAACACAACCAATGGTAT
196 GACAAACTAGAGGGCTGATTAGGAACCAATGTAGACACAAGAACTAAAAACACAACCAATGGTAT
11267 AACAAGGAATAAAACCAGATTCAATGAAGAATTAGACCAGAAAGATGAAGGTTTCGGAGGCTTTT
261 AACAAGGAATAAAACCAGATTCAATGAAGAATTAGACCAGAAAGATGAAGGTTTCGGAGGCTTTT
11332 CATAGTTATTATGAGGTGCCATAACTTCCAACAGTCTTCAATAAAATTCTGCCATAACTTCCCTC
326 CATAGTTATTATGAGGTGCCATAACTTCCAACAGTCTTCAATAAAATTCTGCCATAACTTCCCTC
11397 TCAATAAATGCATC
391 TCAATAAATGCATC
11411 TACAAAGGGCATATTGGAAGCAAAATAATCTCTTTCAGCTTCCAGGAAAGAAGAATCTGTCGAGG
1 TACAAAGGGCATA-TGGAAGCAAAATAATCTCTTTCAGCTTCCAGGAAAGAAGAATCTGTCGAGG
11476 CCCCATTGAAGCTTGACGAAGACCCTT-GACTTGGGCTATGGAGTTATTAGAATGTGCGTCTTCT
65 CCCCATTGAAGCTTGACGAAGACCCTTGGACTTGGGCTATGGAGTTATTAGAATGTGCGTCTTCT
11540 ACTAGTGAAGAAGGATAAGAAGAAGCAAAAGAGTGAGATCTCCATGTCAATGGAGATAGCAATGG
130 ACTAGTGAAGAAGGATAAGAAGAAGCAAAAGAGTGAGATCTCCATGTCAATGGAGATAGCAATGG
11605 CGACAAACTAGAGGGCTGATTAGGAACCAATGTAGACACAAGAACTAAAAACACAACCAATGGTA
195 CGACAAACTAGAGGGCTGATTAGGAACCAATGTAGACACAAGAACTAAAAACACAACCAATGGTA
11670 TAACAAGGAATAAAACCAGATTCAATGAAGAATTAGACCAGAAAGATGAAGGTTTCGGAGGCTTT
260 TAACAAGGAATAAAACCAGATTCAATGAAGAATTAGACCAGAAAGATGAAGGTTTCGGAGGCTTT
11735 TCATAGTTATTATGAGGTGCCATAACTTCCAACAGTCTTCAATAAAATTCTG
325 TCATAGTTATTATGAGGTGCCATAACTTCCAACAGTCTTCAATAAAATTCTG
11787 GCGTTCAAAT
Statistics
Matches: 375, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
404 297 0.79
405 78 0.21
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (404 bp):
TACAAAGGGCATATGGAAGCAAAATAATCTCTTTCAGCTTCCAGGAAAGAAGAATCTGTCGAGGC
CCCATTGAAGCTTGACGAAGACCCTTGGACTTGGGCTATGGAGTTATTAGAATGTGCGTCTTCTA
CTAGTGAAGAAGGATAAGAAGAAGCAAAAGAGTGAGATCTCCATGTCAATGGAGATAGCAATGGC
GACAAACTAGAGGGCTGATTAGGAACCAATGTAGACACAAGAACTAAAAACACAACCAATGGTAT
AACAAGGAATAAAACCAGATTCAATGAAGAATTAGACCAGAAAGATGAAGGTTTCGGAGGCTTTT
CATAGTTATTATGAGGTGCCATAACTTCCAACAGTCTTCAATAAAATTCTGCCATAACTTCCCTC
TCAATAAATGCATC
Found at i:14332 original size:8 final size:8
Alignment explanation
Indices: 14314--14363 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
14304 TTTTAGATAT
14314 AATAT-AA
1 AATATAAA
14321 AATATAAA
1 AATATAAA
*
14329 AATAAAAA
1 AATATAAA
14337 AAT-TAAA
1 AATATAAA
*
14344 ATATGATTAA
1 A-AT-ATAAA
14354 AATATAAA
1 AATATAAA
14362 AA
1 AA
14364 AGATATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
7 9 0.26
8 20 0.57
9 2 0.06
10 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (8 bp):
AATATAAA
Found at i:14734 original size:38 final size:37
Alignment explanation
Indices: 14691--14811 Score: 154
Period size: 38 Copynumber: 3.2 Consensus size: 37
14681 GTTTCCAATT
*
14691 AAATTACATACCAATTAAAATCCATTTGCATGGAACAA
1 AAATTATATACCAATTAAAA-CCATTTGCATGGAACAA
* * *
14729 AAATTATAGACCAATTAAAACCAATTTGCA-AGAAAAA
1 AAATTATATACCAATTAAAACC-ATTTGCATGGAACAA
* *
14766 AAATTATGTACCAATTAAAACTCATTTGCATGAAACAA
1 AAATTATATACCAATTAAAAC-CATTTGCATGGAACAA
14804 AAATTATA
1 AAATTATA
14812 GGGGTAATCA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
37 33 0.47
38 37 0.53
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.26
Consensus pattern (37 bp):
AAATTATATACCAATTAAAACCATTTGCATGGAACAA
Found at i:14779 original size:37 final size:37
Alignment explanation
Indices: 14691--14812 Score: 142
Period size: 37 Copynumber: 3.2 Consensus size: 37
14681 GTTTCCAATT
* * *
14691 AAATTACA-TACCAATTAAAATCCATTTGCATGGAACAA
1 AAATTATAGTACCAATTAAAA-CCATTTGCA-AGAAAAA
14729 AAATTATAG-ACCAATTAAAACCAATTTGCAAGAAAAA
1 AAATTATAGTACCAATTAAAACC-ATTTGCAAGAAAAA
*
14766 AAATTAT-GTACCAATTAAAACTCATTTGCATGAAACAA
1 AAATTATAGTACCAATTAAAAC-CATTTGCAAGAAA-AA
14804 AAATTATAG
1 AAATTATAG
14813 GGGTAATCAG
Statistics
Matches: 74, Mismatches: 4, Indels: 11
0.83 0.04 0.12
Matches are distributed among these distances:
36 1 0.01
37 37 0.50
38 35 0.47
39 1 0.01
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (37 bp):
AAATTATAGTACCAATTAAAACCATTTGCAAGAAAAA
Found at i:15230 original size:2 final size:2
Alignment explanation
Indices: 15223--15247 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15213 TCAACGGATC
15223 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15248 AACCAACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15469 original size:2 final size:2
Alignment explanation
Indices: 15462--15500 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
15452 CTTTTTCTCT
15462 TA 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 TA T
15501 TAAAAAAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17020 original size:22 final size:22
Alignment explanation
Indices: 16995--17036 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
16985 TAAAAAAAAT
16995 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATT-ATATTTATA
17017 TATTTTTATAATTATATTTA
1 TATTTTTATAATTATATTTA
17037 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATAATTATATTTATA
Found at i:17068 original size:17 final size:18
Alignment explanation
Indices: 17030--17083 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
17020 TTTTATAATT
17030 ATATTTAAATA-AA-AATA
1 ATATTTAAATATAATAA-A
* *
17047 TTATTTTAAT-TAATAAA
1 ATATTTAAATATAATAAA
*
17064 ATATTTAAATATATTAAA
1 ATATTTAAATATAATAAA
17082 AT
1 AT
17084 TCAACTCAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTTAAATATAATAAA
Found at i:18815 original size:14 final size:14
Alignment explanation
Indices: 18796--18822 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18786 ATTTATAAAA
18796 TTCTTTTTTTCTTT
1 TTCTTTTTTTCTTT
18810 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
18823 GCACTATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTCTTTTTTTCTTT
Found at i:20580 original size:23 final size:24
Alignment explanation
Indices: 20554--20607 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
20544 ATAATTTTAT
* * *
20554 TTAATTTTAATTTTAAA-AATATA
1 TTAATATTAATATAAAATAATATA
*
20577 TTAATATTAATATAAAATAATATT
1 TTAATATTAATATAAAATAATATA
20601 TTAATAT
1 TTAATAT
20608 ATTTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTAATATTAATATAAAATAATATA
Found at i:20616 original size:22 final size:24
Alignment explanation
Indices: 20553--20626 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 24
20543 AATAATTTTA
*
20553 TTTAATTTTAATTTTAAA-AATAT
1 TTTAATATTAATTTTAAATAATAT
* * *
20576 ATTAATATTAATATAAAATAATAT
1 TTTAATATTAATTTTAAATAATAT
*
20600 TTTAATA-T-ATTTTAAATAATAA
1 TTTAATATTAATTTTAAATAATAT
20622 TTTAA
1 TTTAA
20627 GTAGATGAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 16 0.38
23 15 0.36
24 11 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAATATTAATTTTAAATAATAT
Found at i:21998 original size:17 final size:19
Alignment explanation
Indices: 21963--21999 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21953 ATATTGTAAT
21963 TATTTTACATTAATATTTA
1 TATTTTACATTAATATTTA
*
21982 TATTTTTCA-TAAT-TTTA
1 TATTTTACATTAATATTTA
21999 T
1 T
22000 TAAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTACATTAATATTTA
Found at i:22018 original size:19 final size:20
Alignment explanation
Indices: 21994--22032 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
21984 TTTTTCATAA
21994 TTTTATTAAATAAAA-ATAT
1 TTTTATTAAATAAAATATAT
*
22013 TTTTATTAATTAAAATATAT
1 TTTTATTAAATAAAATATAT
22033 AATCCATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTATTAAATAAAATATAT
Found at i:22732 original size:16 final size:16
Alignment explanation
Indices: 22713--22751 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
22703 ATTATAGTAT
*
22713 TTAATTTTTATTTAAA
1 TTAATTTTTATTAAAA
*
22729 TTAATATTTATTAAAA
1 TTAATTTTTATTAAAA
*
22745 TTTATTT
1 TTAATTT
22752 AATTTTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAATTTTTATTAAAA
Found at i:23341 original size:23 final size:23
Alignment explanation
Indices: 23314--23357 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
23304 TAACTATAAA
23314 TATT-AATATTTAAATTTTAAATT
1 TATTAAATA-TTAAATTTTAAATT
*
23337 TATTAAATATTATATTTTAAA
1 TATTAAATATTAAATTTTAAA
23358 AATTATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAAATATTAAATTTTAAATT
Found at i:23363 original size:24 final size:24
Alignment explanation
Indices: 23314--23365 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
23304 TAACTATAAA
*
23314 TATT-AATATTTAAATTTTAAATT
1 TATTAAATATTTAAATTTTAAAAT
*
23337 TATTAAATA-TTATATTTTAAAAAT
1 TATTAAATATTTAAATTTT-AAAAT
23361 TATTA
1 TATTA
23366 TATGAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTAAATATTTAAATTTTAAAAT
Found at i:25038 original size:20 final size:20
Alignment explanation
Indices: 24982--25056 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 20
24972 TTGAATTTAG
*
24982 TTATATATTTAATATTATTTTAT
1 TTATATATTT-ATA-AATTTT-T
* *
25005 TTA-ATTTTTTTAAATTTTT
1 TTATATATTTATAAATTTTT
* *
25024 TTATATATTTATAAAATCTTA
1 TTATATATTTAT-AAATTTTT
25045 TT-TATATTTATA
1 TTATATATTTATA
25057 TTTTAAATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 5 0.12
20 20 0.47
21 10 0.23
22 5 0.12
23 3 0.07
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATATATTTATAAATTTTT
Found at i:26564 original size:31 final size:30
Alignment explanation
Indices: 26529--26612 Score: 84
Period size: 32 Copynumber: 2.8 Consensus size: 30
26519 TTAAGATATA
*
26529 ATATGAATATATGAATATTTTAAAATTTAT
1 ATATGAATATATAAATATTTTAAAATTTAT
* *
26559 GATATGAATTATTTTAAT-TTATTAAAATTTAT
1 -ATATGAA-TATATAAATATT-TTAAAATTTAT
*
26591 ATA-AAATATA-AAATATTTTAAA
1 ATATGAATATATAAATATTTTAAA
26613 TATAATTATG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
28 8 0.18
29 5 0.11
30 2 0.04
31 12 0.27
32 18 0.40
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (30 bp):
ATATGAATATATAAATATTTTAAAATTTAT
Found at i:28968 original size:27 final size:27
Alignment explanation
Indices: 28932--29010 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
28922 AAACAACAAG
28932 CCATCATTTTTTACAAACAAAAAGGAA
1 CCATCATTTTTTACAAACAAAAAGGAA
* * * **
28959 CCATCGTTTTTGACAGACGCAAAGGAA
1 CCATCATTTTTTACAAACAAAAAGGAA
*
28986 CCACCATTTTTTACAAACACAAAAG
1 CCATCATTTTTTACAAACA-AAAAG
29011 ATGATTTTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (27 bp):
CCATCATTTTTTACAAACAAAAAGGAA
Found at i:35276 original size:12 final size:12
Alignment explanation
Indices: 35261--35285 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35251 TAATATTTAA
35261 TAATTTTTAATT
1 TAATTTTTAATT
35273 TAATTTTTAATT
1 TAATTTTTAATT
35285 T
1 T
35286 TTTAATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATTTTTAATT
Found at i:35281 original size:22 final size:20
Alignment explanation
Indices: 35224--35291 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
35214 AATTCATAAA
35224 TTAATTTACATATTT-ATTTCT
1 TTAATTTA-ATATTTAATTT-T
** *
35245 AAAATATAATATTTAATAATTT
1 TTAATTTAATATTTAAT--TTT
*
35267 TTAATTTAATTTTTAATTTT
1 TTAATTTAATATTTAATTTT
35287 TTAAT
1 TTAAT
35292 ATTTTATAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
20 14 0.38
21 7 0.19
22 14 0.38
23 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATTTAATATTTAATTTT
Found at i:35595 original size:16 final size:17
Alignment explanation
Indices: 35574--35625 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
35564 TCGATTATTA
35574 TAATTATTT-TATATAT
1 TAATTATTTATATATAT
35590 TAATTATTTATATATA-
1 TAATTATTTATATATAT
*
35606 T-ATATATATATATATAT
1 TAAT-TATTTATATATAT
35623 TAA
1 TAA
35626 ACCATGCACC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 2 0.06
16 21 0.68
17 7 0.23
18 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTATTTATATATAT
Found at i:35603 original size:2 final size:2
Alignment explanation
Indices: 35598--35622 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35588 ATTAATTATT
35598 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 T
35623 TAAACCATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.