Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2699
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: 92263
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3916 original size:19 final size:19
Alignment explanation
Indices: 3884--4001 Score: 66
Period size: 19 Copynumber: 6.3 Consensus size: 19
3874 TCTTTATATT
*
3884 TTTTTAGAATTTTTTTGAAA
1 TTTTTATAA-TTTTTTGAAA
3904 TTTTTATAATTTTTT-AAA
1 TTTTTATAATTTTTTGAAA
*** *
3922 -AAATATAAATTTTTG-AA
1 TTTTTATAATTTTTTGAAA
*
3939 TTTTTATAAATATTTT-AAA
1 TTTTTAT-AATTTTTTGAAA
* * *
3958 TTTTAAAAATTATTTTGAAC
1 TTTTTATAATT-TTTTGAAA
* *
3978 TTTTGAAAATTATTTTG-AA
1 TTTTTATAATT-TTTTGAAA
3997 TTTTT
1 TTTTT
4002 TTGTATTTTT
Statistics
Matches: 75, Mismatches: 17, Indels: 13
0.71 0.16 0.12
Matches are distributed among these distances:
17 12 0.16
18 9 0.12
19 28 0.37
20 26 0.35
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTTATAATTTTTTGAAA
Found at i:4001 original size:20 final size:19
Alignment explanation
Indices: 3932--4001 Score: 88
Period size: 19 Copynumber: 3.6 Consensus size: 19
3922 AAATATAAAT
3932 TTTTGAATTTTTATAAA-TA
1 TTTTGAATTTTTA-AAATTA
* *
3951 TTTTAAATTTTAAAAATTA
1 TTTTGAATTTTTAAAATTA
*
3970 TTTTGAACTTTTGAAAATTA
1 TTTTGAA-TTTTTAAAATTA
3990 TTTTGAATTTTT
1 TTTTGAATTTTT
4002 TTGTATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
18 3 0.07
19 23 0.52
20 18 0.41
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (19 bp):
TTTTGAATTTTTAAAATTA
Found at i:5993 original size:5 final size:5
Alignment explanation
Indices: 5983--6008 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5973 AGAATGAAGG
5983 CTGTT CTGTT CTGTT CTGTT CTGTT C
1 CTGTT CTGTT CTGTT CTGTT CTGTT C
6009 AATTCATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.19, T:0.58
Consensus pattern (5 bp):
CTGTT
Found at i:9042 original size:13 final size:13
Alignment explanation
Indices: 9024--9051 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9014 CTTGTACAAG
9024 TAAACTTCATAAA
1 TAAACTTCATAAA
9037 TAAACTTCATAAA
1 TAAACTTCATAAA
9050 TA
1 TA
9052 GAGAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTTCATAAA
Found at i:9510 original size:20 final size:20
Alignment explanation
Indices: 9485--9524 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9475 AATATTTTTC
*
9485 AGTAAATCATTTTACAGAAA
1 AGTAAAGCATTTTACAGAAA
*
9505 AGTAAAGCATTTTCCAGAAA
1 AGTAAAGCATTTTACAGAAA
9525 TCATTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (20 bp):
AGTAAAGCATTTTACAGAAA
Found at i:19534 original size:23 final size:23
Alignment explanation
Indices: 19490--19537 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
19480 TTATCCCATT
** *
19490 ATTGAAATTCTATTTTTTAAAAC
1 ATTGAAATTCTAAATTTCAAAAC
*
19513 ATTGAAATTTTAAATTTCAAAAC
1 ATTGAAATTCTAAATTTCAAAAC
19536 AT
1 AT
19538 CAAAATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTGAAATTCTAAATTTCAAAAC
Found at i:20492 original size:6 final size:7
Alignment explanation
Indices: 20476--20501 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20466 TTGTACATGG
20476 AAAAACA
1 AAAAACA
20483 AAAAACA
1 AAAAACA
20490 AAAAACA
1 AAAAACA
20497 AAAAA
1 AAAAA
20502 AGGAGAGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:24243 original size:25 final size:25
Alignment explanation
Indices: 24196--24245 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
24186 CTATCTCTCC
* *
24196 TAGGGTTAGAGTTTTTTAATTTTGG
1 TAGGGTTAGAGGTTTTAAATTTTGG
24221 TAGGGTTAG-GGTTTTAAAGTTTTGG
1 TAGGGTTAGAGGTTTTAAA-TTTTGG
24246 GTTATGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (25 bp):
TAGGGTTAGAGGTTTTAAATTTTGG
Found at i:35360 original size:17 final size:17
Alignment explanation
Indices: 35338--35370 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35328 ACATGTTTAT
35338 TTATTAGAA-AATTTAAA
1 TTATTA-AATAATTTAAA
35355 TTATTAAATAATTTAA
1 TTATTAAATAATTTAA
35371 TTAAAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTATTAAATAATTTAAA
Found at i:36025 original size:334 final size:329
Alignment explanation
Indices: 35394--35997 Score: 741
Period size: 328 Copynumber: 1.8 Consensus size: 329
35384 AAGTTAGAGA
* *
35394 AGACTAAATGACAAGAAAAGACCCATTTCTAAAAAAAATTACGAAAATGGGTCGTTTTGTTCAAA
1 AGACTAAATGACAAGAAAAGACCCATTTCTAAAAAAAATTACGAAAATGGGTCATTTTGCTCAAA
* * * * * * * * *
35459 AATTATTGAAAGGACCGATTTCCCTAAAAGACACTGAGTTGGCATTGTTTTTAGGGGAAACGCAG
66 AAGTATAGAAAGGACCAATTTCCCAAAAAGACACCGAGCTAGCATTGTTTTTAGGAGAAACGCAA
* * * *
35524 AAAAGCGCGTCCAGCTCAGCGTTGTTTCCCTGATGACCAGTAAAACGCGTCTATGTCAGCACGCT
131 AAAAGCACGTCCAGCTCAGCGTTGTTTCCC--ATGA-CAG--AAACGCGCCCACGTCAGCACGCT
* * * * *
35589 TTAGTATAGCGCTTCCACGTGGGCGTGCTTTTGCCCGTTGTCCAACGGTCAACTCCAACGGCTAT
191 TTAGTAAAGCGCTTCCACGTAGGCGCGCTTTTGCCCGCTGTCCAACGGTCAACTCCAACGACTAT
* *
35654 TTTAACTAGCCGTTGGACCCCAATGGTAAAAAAAAAAATTATAAACCCCCATACCTTTCTTATAC
256 TTGAACTAGCCATTGGACCCCAATGGTAAAAAAAAAAATTATAAACCCCCATACCTTTCTTATAC
35719 ACAATTATC
321 ACAATTATC
* * *
35728 AGACTAAATGACCAGAAAAGGCCCATTTCTAAACAAAATTACGAAAATGGGTCATTTTGCTCAAA
1 AGACTAAATGACAAGAAAAGACCCATTTCTAAAAAAAATTACGAAAATGGGTCATTTTGCTCAAA
* * * *
35793 AAGTACTAGAAAGGGCCAATTTCCCAAAAATACACCGAGCTAGCGTTGTTTTTAGGAGAAACGTA
66 AAGTA-TAGAAAGGACCAATTTCCCAAAAAGACACCGAGCTAGCATTGTTTTTAGGAGAAACGCA
* * * * **
35858 AAAAATCACGTCTAGGTCAGCGAATT-TTTCCC-TGA-AG-AACGCGCCCGCGTCAGTGCGCTTT
130 AAAAAGCACGTCCAGCTCAGCG--TTGTTTCCCATGACAGAAACGCGCCCACGTCAGCACGCTTT
* * * *
35919 AGTAAAGTGCTTCCACGTAGGCGCGTTTTTGCCC-CTGCTCCAACGGTCAACTCTAATGACTATT
193 AGTAAAGCGCTTCCACGTAGGCGCGCTTTTGCCCGCTG-TCCAACGGTCAACTCCAACGACTATT
35983 TGAACTAGCCATTGG
257 TGAACTAGCCATTGG
35998 TAGCCATTGG
Statistics
Matches: 227, Mismatches: 39, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
327 2 0.01
328 83 0.37
331 2 0.01
333 3 0.01
334 64 0.28
335 65 0.29
336 6 0.03
337 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (329 bp):
AGACTAAATGACAAGAAAAGACCCATTTCTAAAAAAAATTACGAAAATGGGTCATTTTGCTCAAA
AAGTATAGAAAGGACCAATTTCCCAAAAAGACACCGAGCTAGCATTGTTTTTAGGAGAAACGCAA
AAAAGCACGTCCAGCTCAGCGTTGTTTCCCATGACAGAAACGCGCCCACGTCAGCACGCTTTAGT
AAAGCGCTTCCACGTAGGCGCGCTTTTGCCCGCTGTCCAACGGTCAACTCCAACGACTATTTGAA
CTAGCCATTGGACCCCAATGGTAAAAAAAAAAATTATAAACCCCCATACCTTTCTTATACACAAT
TATC
Found at i:39213 original size:20 final size:20
Alignment explanation
Indices: 39174--39213 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39164 CCTCTACAGT
* * *
39174 CTAAAATTTTCAACTTTTTC
1 CTAAAATTTCCAAATATTTC
39194 CTAAAATTTCCAAATATTTC
1 CTAAAATTTCCAAATATTTC
39214 TGATTTAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (20 bp):
CTAAAATTTCCAAATATTTC
Found at i:45177 original size:23 final size:23
Alignment explanation
Indices: 45141--45191 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
45131 GTGGAGATGG
* *
45141 TGTAATATCTCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
45164 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
45187 AGTAA
1 TGTAA
45192 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:47311 original size:59 final size:60
Alignment explanation
Indices: 47247--47434 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 60
47237 TTATAGTATC
47247 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAA-T
* * * * * * * *
47308 ATATATTTTAATTAT-AATATATTTA-ATAAGAATTATGTTAA-T-TT-A-TATTTTA-CAGTAT
1 ATATATTATGATT-TGAGTAAATTCATATAAGAA-TA--TTAATTATTAAGAATTTTATTA-AAT
47366 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 -ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAA-T
47428 ATATATT
1 ATATATT
47435 TTAATTATAA
Statistics
Matches: 97, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
57 4 0.04
58 4 0.04
59 29 0.30
60 16 0.16
61 36 0.37
62 4 0.04
63 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (60 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:47417 original size:120 final size:120
Alignment explanation
Indices: 47236--47466 Score: 435
Period size: 120 Copynumber: 1.9 Consensus size: 120
47226 CAAATTTTCA
*
47236 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
1 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
*
47301 TTAAATTATATATTTTAATTATAATATATTTAATAAGAATTATGTTAATTTATAT
66 TTAAATTATATATTTTAATTATAATATATTTAATAAGAATCATGTTAATTTATAT
47356 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
1 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
*
47421 TTAAATTATATATTTTAATTATAATATATTTAATAATAATCATGTT
66 TTAAATTATATATTTTAATTATAATATATTTAATAAGAATCATGTT
47467 TAAATATGAT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (120 bp):
TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
TTAAATTATATATTTTAATTATAATATATTTAATAAGAATCATGTTAATTTATAT
Found at i:47454 original size:15 final size:15
Alignment explanation
Indices: 47419--47460 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
47409 TTAAGAATTT
*
47419 TATTAAATTAT-ATA
1 TATTTAATTATAATA
47433 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
47447 TATTTAATAATAAT
1 TATTTAATTATAAT
47461 CATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:47588 original size:157 final size:157
Alignment explanation
Indices: 47403--47719 Score: 571
Period size: 157 Copynumber: 2.0 Consensus size: 157
47393 ATAAGAATAT
*
47403 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATCATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATCATGTTT
* *
47468 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
47533 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
*
47560 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATCATGTTT
*
47625 AATTATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
47690 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
47717 TAA
1 TAA
47720 GGGTATTCTA
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATCATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:47600 original size:18 final size:17
Alignment explanation
Indices: 47572--47606 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
47562 ATTATTAAGA
*
47572 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
47589 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
47607 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:47606 original size:16 final size:16
Alignment explanation
Indices: 47572--47629 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
47562 ATTATTAAGA
47572 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
47589 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
47605 A-TTTAA-TAATAAT-T
1 ATTTTAATTAA-AATAT
47619 ATGTTTAATTA
1 AT-TTTAATTA
47630 TGATTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.14
15 8 0.22
16 10 0.28
17 7 0.19
18 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:47863 original size:16 final size:16
Alignment explanation
Indices: 47842--47877 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
47832 GATTTGCTAT
47842 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
47858 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
47874 TACA
1 TACA
47878 GCGAACGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:55663 original size:17 final size:17
Alignment explanation
Indices: 55617--55651 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55607 GAGAATGGAA
55617 AATAAAG-AAAAAAAGT
1 AATAAAGAAAAAAAAGT
55633 AATAAAGAAAAAAAAGT
1 AATAAAGAAAAAAAAGT
55650 AA
1 AA
55652 AACAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (17 bp):
AATAAAGAAAAAAAAGT
Found at i:63440 original size:17 final size:16
Alignment explanation
Indices: 63406--63470 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
63396 ATGATATAAC
**
63406 AAAAATAATTAATTAT
1 AAAAATAATTAAAAAT
63422 AAAAAGTAATTAAAAAT
1 AAAAA-TAATTAAAAAT
* *
63439 AATAATAA-TATAATAT
1 AAAAATAATTA-AAAAT
63455 AATAAATAATTTAAAA
1 AA-AAATAA-TTAAAA
63471 CAATTATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.05
16 14 0.37
17 18 0.47
18 2 0.05
19 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
AAAAATAATTAAAAAT
Found at i:63441 original size:23 final size:24
Alignment explanation
Indices: 63409--63470 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
63399 ATATAACAAA
*
63409 AATAATTAATTATAAAAAGTAAT-T
1 AATAAATAATTATAAAAA-TAATAT
* *
63433 AA-AAATAATAAT-AATATAATAT
1 AATAAATAATTATAAAAATAATAT
63455 AATAAATAATT-TAAAA
1 AATAAATAATTATAAAA
63471 CAATTATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
21 4 0.13
22 7 0.23
23 17 0.57
24 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
AATAAATAATTATAAAAATAATAT
Found at i:63456 original size:33 final size:33
Alignment explanation
Indices: 63403--63479 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
63393 ACAATGATAT
*
63403 AACAAAAATAATTAATTATAA-AAAGTAATTAAA
1 AACAATAATAATTAATTATAATAAA-TAATTAAA
* *
63436 AATAATAATAATATAA-TATAATAAATAATTTAA
1 AACAATAATAAT-TAATTATAATAAATAATTAAA
*
63469 AACAATTATAA
1 AACAATAATAA
63480 AAACAATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 31 0.84
34 6 0.16
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (33 bp):
AACAATAATAATTAATTATAATAAATAATTAAA
Found at i:64502 original size:20 final size:20
Alignment explanation
Indices: 64479--64516 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
64469 TACACATTTC
64479 ACAATTCATATCAAAATCTG
1 ACAATTCATATCAAAATCTG
* *
64499 ACAATTGATATTAAAATC
1 ACAATTCATATCAAAATC
64517 CCGTTATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (20 bp):
ACAATTCATATCAAAATCTG
Found at i:66978 original size:12 final size:12
Alignment explanation
Indices: 66961--67030 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
66951 TTAATTTAAT
66961 CGAACATGTTCA
1 CGAACATGTTCA
**
66973 CGAACAT-TAAA
1 CGAACATGTTCA
66984 CGAACATGTTCA
1 CGAACATGTTCA
* *
66996 TGAACAT-TTAA
1 CGAACATGTTCA
*
67007 TTGAACATGTTCA
1 -CGAACATGTTCA
*
67020 TGAACAATGTT
1 CGAAC-ATGTT
67031 AATAAACAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
11 12 0.26
12 27 0.57
13 8 0.17
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (12 bp):
CGAACATGTTCA
Found at i:67012 original size:24 final size:24
Alignment explanation
Indices: 66954--67025 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
66944 TATTCATTTA
*
66954 ATTTAATCGAACATGTTCACGAAC
1 ATTTAATCGAACATGTTCATGAAC
*
66978 A-TTAAACGAACATGTTCATGAAC
1 ATTTAATCGAACATGTTCATGAAC
*
67001 ATTTAATTGAACATGTTCATGAAC
1 ATTTAATCGAACATGTTCATGAAC
67025 A
1 A
67026 ATGTTAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 21 0.49
24 22 0.51
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (24 bp):
ATTTAATCGAACATGTTCATGAAC
Found at i:67014 original size:47 final size:46
Alignment explanation
Indices: 66937--67025 Score: 124
Period size: 47 Copynumber: 1.9 Consensus size: 46
66927 TTTAATATTC
**
66937 ACGAACATATTCATTTAATTTAATCGAACATGTTCACGAACATTAA
1 ACGAACATATTCATGAAATTTAATCGAACATGTTCACGAACATTAA
* * *
66983 ACGAACATGTTCATGAACATTTAATTGAACATGTTCATGAACA
1 ACGAACATATTCATGAA-ATTTAATCGAACATGTTCACGAACA
67026 ATGTTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 14 0.38
47 23 0.62
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (46 bp):
ACGAACATATTCATGAAATTTAATCGAACATGTTCACGAACATTAA
Found at i:74918 original size:29 final size:29
Alignment explanation
Indices: 74879--74935 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
74869 AGCAAGCAAT
74879 TTTTTTTTGGTAATTTAGTCGTAACCCAA
1 TTTTTTTTGGTAATTTAGTCGTAACCCAA
74908 TTTTTTTTGGTAATTTAGTCGTAACCCA
1 TTTTTTTTGGTAATTTAGTCGTAACCCA
74936 TCATAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTTTTTTGGTAATTTAGTCGTAACCCAA
Found at i:78178 original size:11 final size:11
Alignment explanation
Indices: 78161--78190 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
78151 GTTGCAATTG
78161 ATATTATTGCT
1 ATATTATTGCT
*
78172 CTATTATTGCT
1 ATATTATTGCT
78183 ATATTATT
1 ATATTATT
78191 TAACAAAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (11 bp):
ATATTATTGCT
Found at i:82902 original size:3 final size:3
Alignment explanation
Indices: 82894--82936 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
82884 CCACGAAGCC
82894 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
82937 AACAAACTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:83337 original size:18 final size:18
Alignment explanation
Indices: 83311--83359 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
83301 CTGCGAATTG
*
83311 CGAGCTCACCAAGAA-CTA
1 CGAGCTCACCAA-AATATA
*
83329 CGAGTTCACCAAAATATA
1 CGAGCTCACCAAAATATA
83347 CGAGCTCACCAAA
1 CGAGCTCACCAAA
83360 TGTGCGAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.41, C:0.31, G:0.14, T:0.14
Consensus pattern (18 bp):
CGAGCTCACCAAAATATA
Found at i:83367 original size:17 final size:17
Alignment explanation
Indices: 83311--83393 Score: 62
Period size: 17 Copynumber: 4.8 Consensus size: 17
83301 CTGCGAATTG
**
83311 CGAGCTCACCAAGAACTA
1 CGAGCTCACCAA-ATGTA
* *
83329 CGAGTTCACCAAAATATA
1 CGAGCTCACC-AAATGTA
*
83347 CGAGCTCACCAAATGTG
1 CGAGCTCACCAAATGTA
*
83364 CGAGCTCATCAACACTGT-
1 CGAGCTCACCAA-A-TGTA
83382 -GAGCTCACCAAA
1 CGAGCTCACCAAA
83394 GCCTGAGAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.02
17 26 0.48
18 22 0.41
19 5 0.09
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (17 bp):
CGAGCTCACCAAATGTA
Found at i:83431 original size:29 final size:30
Alignment explanation
Indices: 83382--83445 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
83372 TCAACACTGT
* * **
83382 GAGCTCACCAAAGCCTGAGAGCTCATTTGC
1 GAGCTAACCAAAGCATGAGAGCTCACCTGC
83412 GAGCTAACC-AAGCATGAGAGCTCACCTGC
1 GAGCTAACCAAAGCATGAGAGCTCACCTGC
83441 GAGCT
1 GAGCT
83446 CTTCACTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (30 bp):
GAGCTAACCAAAGCATGAGAGCTCACCTGC
Done.