Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3125.1
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: 159524
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.31
Warning! 9554 characters in sequence are not A, C, G, or T
Found at i:2284 original size:16 final size:15
Alignment explanation
Indices: 2263--2299 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
2253 TAGCTTCTTC
2263 TTTTTTTCACGAAATT
1 TTTTTTTCACG-AATT
2279 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
2294 TTTTTT
1 TTTTTT
2300 CAACTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.19, C:0.11, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:2355 original size:12 final size:12
Alignment explanation
Indices: 2338--2396 Score: 93
Period size: 12 Copynumber: 5.0 Consensus size: 12
2328 AAAGGAAACC
2338 TTTTTTTTTGAA
1 TTTTTTTTTGAA
2350 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
2362 TTTTTTTTCGAA
1 TTTTTTTTTGAA
*
2374 -TTTTTTTTCAA
1 TTTTTTTTTGAA
2385 TTTTTTTTTGAA
1 TTTTTTTTTGAA
2397 GAAACTACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.21
12 33 0.79
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:2369 original size:23 final size:23
Alignment explanation
Indices: 2338--2392 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
2328 AAAGGAAACC
* *
2338 TTTTTTTTTGAATTTTTTTTTGAA
1 TTTTTTTTCGAA-TTTTTTTTCAA
2362 TTTTTTTTCGAATTTTTTTTCAA
1 TTTTTTTTCGAATTTTTTTTCAA
2385 TTTTTTTT
1 TTTTTTTT
2393 TGAAGAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.15, C:0.04, G:0.05, T:0.76
Consensus pattern (23 bp):
TTTTTTTTCGAATTTTTTTTCAA
Found at i:9338 original size:15 final size:15
Alignment explanation
Indices: 9320--9351 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9310 CATTTCACTA
9320 TTATGTATTTTATAT
1 TTATGTATTTTATAT
*
9335 TTATGTCTTTTATAT
1 TTATGTATTTTATAT
9350 TT
1 TT
9352 TTCTTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTATTTTATAT
Found at i:17274 original size:36 final size:36
Alignment explanation
Indices: 17234--17335 Score: 111
Period size: 36 Copynumber: 2.8 Consensus size: 36
17224 TAATACATAA
*
17234 GTATGTATATATATAAATAAGTTAAAAAATATGTAC
1 GTATGTATATATATATATAAGTTAAAAAATATGTAC
* *
17270 GTATGT-TAGA-AT-TATAAAGTATATAAAAATATGTAT
1 GTATGTATATATATATAT-AAGT-TA-AAAAATATGTAC
* *
17306 GTATGTATGTATATATATAAGCTAAAAAAT
1 GTATGTATATATATATATAAGTTAAAAAAT
17336 GTTTATGAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
33 2 0.04
34 6 0.11
35 5 0.09
36 29 0.54
37 4 0.07
38 5 0.09
39 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (36 bp):
GTATGTATATATATATATAAGTTAAAAAATATGTAC
Found at i:17389 original size:18 final size:18
Alignment explanation
Indices: 17366--17400 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
17356 ATATATACAC
17366 ATATATAATAAGATATAT
1 ATATATAATAAGATATAT
17384 ATATATAATAAGATATA
1 ATATATAATAAGATATA
17401 AAGATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
ATATATAATAAGATATAT
Found at i:17421 original size:20 final size:22
Alignment explanation
Indices: 17366--17415 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 22
17356 ATATATACAC
17366 ATATATAATAAGATAT----AT
1 ATATATAATAAGATATAAAGAT
17384 ATATATAATAAGATATAAAGAT
1 ATATATAATAAGATATAAAGAT
17406 ATATA-AATAA
1 ATATATAATAA
17416 TTATAATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 16 0.57
21 5 0.18
22 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (22 bp):
ATATATAATAAGATATAAAGAT
Found at i:19790 original size:19 final size:19
Alignment explanation
Indices: 19766--19805 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
19756 GAGTGATAGA
19766 TAGCGTACACTAAAGAGTC
1 TAGCGTACACTAAAGAGTC
*
19785 TAGCGTACACTATAGAGTC
1 TAGCGTACACTAAAGAGTC
19804 TA
1 TA
19806 AGCGGCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (19 bp):
TAGCGTACACTAAAGAGTC
Found at i:37458 original size:36 final size:36
Alignment explanation
Indices: 37418--37519 Score: 111
Period size: 36 Copynumber: 2.8 Consensus size: 36
37408 TAATACATAA
*
37418 GTATGTATATATATAAATAAGTTAAAAAATATGTAC
1 GTATGTATATATATATATAAGTTAAAAAATATGTAC
* *
37454 GTATGT-TAGA-AT-TATAAAGTATATAAAAATATGTAT
1 GTATGTATATATATATAT-AAGT-TA-AAAAATATGTAC
* *
37490 GTATGTATGTATATATATAAGCTAAAAAAT
1 GTATGTATATATATATATAAGTTAAAAAAT
37520 GTTTATGAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
33 2 0.04
34 6 0.11
35 5 0.09
36 29 0.54
37 4 0.07
38 5 0.09
39 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (36 bp):
GTATGTATATATATATATAAGTTAAAAAATATGTAC
Found at i:37573 original size:18 final size:18
Alignment explanation
Indices: 37550--37584 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
37540 ATATATACAC
37550 ATATATAATAAGATATAT
1 ATATATAATAAGATATAT
37568 ATATATAATAAGATATA
1 ATATATAATAAGATATA
37585 AAGATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
ATATATAATAAGATATAT
Found at i:37605 original size:20 final size:22
Alignment explanation
Indices: 37550--37599 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 22
37540 ATATATACAC
37550 ATATATAATAAGATAT----AT
1 ATATATAATAAGATATAAAGAT
37568 ATATATAATAAGATATAAAGAT
1 ATATATAATAAGATATAAAGAT
37590 ATATA-AATAA
1 ATATATAATAA
37600 TTATAATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 16 0.57
21 5 0.18
22 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (22 bp):
ATATATAATAAGATATAAAGAT
Found at i:39974 original size:19 final size:19
Alignment explanation
Indices: 39950--39989 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
39940 GAGTGATAGA
39950 TAGCGTACACTAAAGAGTC
1 TAGCGTACACTAAAGAGTC
*
39969 TAGCGTACACTATAGAGTC
1 TAGCGTACACTAAAGAGTC
39988 TA
1 TA
39990 AGCGGCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (19 bp):
TAGCGTACACTAAAGAGTC
Found at i:45635 original size:47 final size:47
Alignment explanation
Indices: 45563--45917 Score: 557
Period size: 47 Copynumber: 7.4 Consensus size: 47
45553 CCCTTCGGGA
* * * *
45563 CTTATCACATTTATACACTTTCACATCCATCACATCGGGCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45610 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45657 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45706 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45755 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45804 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
45851 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45898 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
45918 GTACATCAAT
Statistics
Matches: 293, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 149 0.51
49 144 0.49
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:45690 original size:49 final size:49
Alignment explanation
Indices: 45563--45915 Score: 569
Period size: 49 Copynumber: 7.4 Consensus size: 49
45553 CCCTTCGGGA
* * *
45563 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGGCATTTGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45610 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45657 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45706 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45755 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45804 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
45851 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45898 CCTATCACATATATATAC
1 CTTATCACATATATATAC
45916 TTGTACATCA
Statistics
Matches: 289, Mismatches: 11, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
46 1 0.00
47 136 0.47
49 152 0.53
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:48383 original size:27 final size:26
Alignment explanation
Indices: 48348--48444 Score: 119
Period size: 25 Copynumber: 3.8 Consensus size: 26
48338 TGTTCTGACC
* *
48348 CACAACTCGTGTGAGCA-AGCCCAATTT
1 CACAGCTCGTGTGAGCATA--CCGATTT
* *
48375 CATAGCTCGTGAGAGCATACCGATTT
1 CACAGCTCGTGTGAGCATACCGATTT
48401 -ACAGCTCGTGTGAGCATACCGA-TT
1 CACAGCTCGTGTGAGCATACCGATTT
48425 CACAGCTCGTGTGAGCATAC
1 CACAGCTCGTGTGAGCATAC
48445 ATGTACATGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.03
25 39 0.63
26 6 0.10
27 14 0.23
28 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCATACCGATTT
Found at i:49553 original size:20 final size:20
Alignment explanation
Indices: 49520--49558 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49510 GCCACATGGT
*
49520 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATAGTATC
49540 TTGG-TTGTGATTATAGTAT
1 TTGGCTTGTG-TTATAGTAT
49559 TTTGAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.15, C:0.05, G:0.28, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATAGTATC
Found at i:50292 original size:12 final size:12
Alignment explanation
Indices: 50275--50304 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
50265 TCAGTGAGTT
50275 ACACGAGCACGG
1 ACACGAGCACGG
*
50287 ACACGAGCTCGG
1 ACACGAGCACGG
50299 ACACGA
1 ACACGA
50305 CCCTATGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.33, G:0.30, T:0.03
Consensus pattern (12 bp):
ACACGAGCACGG
Found at i:50834 original size:75 final size:75
Alignment explanation
Indices: 50708--50848 Score: 219
Period size: 75 Copynumber: 1.9 Consensus size: 75
50698 AAAAACCAGA
**
50708 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAATTAATTACATTCATTCCAAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATTACATTCATTCCAAA
50773 AGGATATAGG
66 AGGATATAGG
* ** * *
50783 ATTATTCCCTTATTAATAGATAAGGTAAATGGAAAGTTAGAAAAAGGAATTATATTCTTTCCAAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATTACATTCATTCCAAA
50848 A
66 A
50849 TAATATTAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (75 bp):
ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATTACATTCATTCCAAA
AGGATATAGG
Found at i:50956 original size:17 final size:17
Alignment explanation
Indices: 50923--50957 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
50913 GGGTTTAAGG
50923 TTTTAATTAATATAATT
1 TTTTAATTAATATAATT
50940 TTTTATATTAATA-AATT
1 TTTTA-ATTAATATAATT
50957 T
1 T
50958 GGTAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAATTAATATAATT
Found at i:51113 original size:44 final size:44
Alignment explanation
Indices: 51049--51134 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
51039 AGTTTGTACA
51049 TATAATGTGTTTAATGTTTAACCATCAAATTAAAT-TAATTCACT
1 TATAATGTGTTTAATGTTTAACCATCAAATT-AATGTAATTCACT
* **
51093 TATAATGTGTTTAATTTTTAAGTATCAAATTAATGTAATTCA
1 TATAATGTGTTTAATGTTTAACCATCAAATTAATGTAATTCA
51135 ATAATTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 3 0.08
44 35 0.92
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (44 bp):
TATAATGTGTTTAATGTTTAACCATCAAATTAATGTAATTCACT
Found at i:71513 original size:21 final size:22
Alignment explanation
Indices: 71479--71520 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
71469 TCAATTTCTC
*
71479 AATCCAATATATATATTTCAAT
1 AATCCAATATATATAATTCAAT
*
71501 AATCTAATA-ATATAATTCAA
1 AATCCAATATATATAATTCAA
71521 GTTACACGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
AATCCAATATATATAATTCAAT
Found at i:75273 original size:28 final size:27
Alignment explanation
Indices: 75255--75356 Score: 107
Period size: 28 Copynumber: 3.7 Consensus size: 27
75245 TCAAAGTTTG
75255 CCACAAAGGCTATTTTTTTAAGAGTTCA
1 CCACAAAGGCTATTTTTTTAA-AGTTCA
* * *
75283 CCATACAA-GTTATTCTTTTTAGAGTTCA
1 CCACA-AAGGCTATT-TTTTTAAAGTTCA
* * *
75311 CCACAAAGGCTATTCTTTTCATAGTTCG
1 CCACAAAGGCTATT-TTTTTAAAGTTCA
75339 CCACAAAGGCTATTTTTT
1 CCACAAAGGCTATTTTTT
75357 AATGTCGTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
27 6 0.10
28 49 0.78
29 8 0.13
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (27 bp):
CCACAAAGGCTATTTTTTTAAAGTTCA
Found at i:81434 original size:16 final size:15
Alignment explanation
Indices: 81413--81452 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
81403 TTTTGTATTT
81413 TTTTAATATTAAATAA
1 TTTTAATATTAAA-AA
*
81429 TTTTAAGATTAAAAA
1 TTTTAATATTAAAAA
*
81444 TATTAATAT
1 TTTTAATAT
81453 AATCGATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTTAATATTAAAAA
Found at i:87635 original size:19 final size:18
Alignment explanation
Indices: 87581--87629 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
87571 TAGTAATTTT
*
87581 TATAATTTGTCTATATTT-C
1 TATAATTT-TATA-ATTTAC
87600 TATAATTTTATAATTTAC
1 TATAATTTTATAATTTAC
87618 TATAAGTTTTAT
1 TATAA-TTTTAT
87630 TTTTTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
19 14 0.52
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (18 bp):
TATAATTTTATAATTTAC
Found at i:89352 original size:39 final size:39
Alignment explanation
Indices: 89309--89385 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
89299 ACGAAAATGC
*
89309 GTTTTCAGCAAATTGACAGGAAAATCCTTCTAACTAGAA
1 GTTTTCAGCAAATTGACAAGAAAATCCTTCTAACTAGAA
* * ** *
89348 GTTTTTAGCAGATTGGTAAGAAAATGCTTCTAACTAGA
1 GTTTTCAGCAAATTGACAAGAAAATCCTTCTAACTAGA
89386 CGCGTTTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (39 bp):
GTTTTCAGCAAATTGACAAGAAAATCCTTCTAACTAGAA
Found at i:89574 original size:93 final size:93
Alignment explanation
Indices: 89415--89600 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
89405 CATTGAAAAC
*
89415 GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAGGGTTTAGATTT
1 GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTT
89480 TTGTTAAAGTAGGGTTATGGTTAGGTTT
66 TTGTTAAAGTAGGGTTATGGTTAGGTTT
89508 GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTT
1 GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTT
89573 TTGTTAAAGTAGGGTTATGGTTAGGTTT
66 TTGTTAAAGTAGGGTTATGGTTAGGTTT
89601 TGTATGTTTT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (93 bp):
GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTT
TTGTTAAAGTAGGGTTATGGTTAGGTTT
Found at i:94494 original size:18 final size:18
Alignment explanation
Indices: 94471--94514 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
94461 CATTATTTGT
**
94471 ATAAAATAATTCTAAAAA
1 ATAAAATAATTAAAAAAA
*
94489 ATAAAAAAATTAAAAAAA
1 ATAAAATAATTAAAAAAA
94507 ATTAAAAT
1 A-TAAAAT
94515 TAAAATTAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAAAATAATTAAAAAAA
Found at i:94503 original size:6 final size:6
Alignment explanation
Indices: 94494--94539 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
94484 AAAAAATAAA
*
94494 AAAATT AAAA-- AAAATT AAAATT AAAATT AGAAATAT GAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT A-AAAT-T AAAATT AAAA
94540 AAATTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.12
6 21 0.62
7 8 0.24
8 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (6 bp):
AAAATT
Found at i:94504 original size:16 final size:16
Alignment explanation
Indices: 94483--94547 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
94473 AAAATAATTC
94483 TAAAAAATAA-AAAAAT
1 TAAAAAA-AATAAAAAT
*
94499 TAAAAAAAATTAAAAT
1 TAAAAAAAATAAAAAT
*
94515 TAAAATTAGAAATATGAAAT
1 TAAAA--A-AAATA-AAAAT
*
94535 TAAAAAAATTAAA
1 TAAAAAAAATAAA
94548 TTTATCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
15 2 0.05
16 18 0.46
17 4 0.10
18 2 0.05
19 4 0.10
20 9 0.23
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
TAAAAAAAATAAAAAT
Found at i:96688 original size:43 final size:42
Alignment explanation
Indices: 96625--96782 Score: 226
Period size: 43 Copynumber: 3.7 Consensus size: 42
96615 ATGTTCCAAT
*
96625 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATT-GC
*
96668 ACCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGAC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTG-C
*
96711 ATCGATTTGAGATTTCGTGTAAGACCATAGTTGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATT-GC
** *
96754 ATCGATACGAGATTTCCATGTAAGACCAT
1 ATCGATTTGAGATTT-CGTGTAAGACCAT
96783 GTCTGGGGCA
Statistics
Matches: 105, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.01
43 91 0.87
44 13 0.12
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (42 bp):
ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGC
Found at i:101246 original size:27 final size:27
Alignment explanation
Indices: 101188--101254 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
101178 AGAGAGTCCA
* *
101188 TTGGGACATTAAATACAGGGTAATCTG
1 TTGGGACAATAAACACAGGGTAATCTG
* * *
101215 CTGGGACAGTAAACACAGGGTAGT-TCG
1 TTGGGACAATAAACACAGGGTAATCT-G
101242 TTGGGACAATAAA
1 TTGGGACAATAAA
101255 AATGGGTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.24
Consensus pattern (27 bp):
TTGGGACAATAAACACAGGGTAATCTG
Found at i:103613 original size:12 final size:12
Alignment explanation
Indices: 103591--103625 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
103581 AGTAACCTCA
103591 CAGGCCCGTGTGC
1 CAGG-CCGTGTGC
103604 CAGGCCGTGTGC
1 CAGGCCGTGTGC
*
103616 TAGGCCGTGT
1 CAGGCCGTGT
103626 AATAGCCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.09, C:0.31, G:0.40, T:0.20
Consensus pattern (12 bp):
CAGGCCGTGTGC
Found at i:105374 original size:25 final size:24
Alignment explanation
Indices: 105346--105427 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 24
105336 GTATGTTTTC
105346 ACGAGCTGTAAATCAGTAAGCTCAT
1 ACGAGCTG-AAATCAGTAAGCTCAT
*
105371 ACGAGCTGAGAATCGGTAAGCTC-T
1 ACGAGCTGA-AATCAGTAAGCTCAT
* *
105395 CACGAGCTACAAATCAATAAGCTCAT
1 -ACGAGCT-GAAATCAGTAAGCTCAT
105421 ACGAGCT
1 ACGAGCT
105428 ATGGTGTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 2 0.04
25 45 0.92
26 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (24 bp):
ACGAGCTGAAATCAGTAAGCTCAT
Found at i:105398 original size:50 final size:50
Alignment explanation
Indices: 105315--105430 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
105305 ATACATGTAT
* * * * ** *
105315 GCTCATACGAGCTATGAATTGGTATGTTTTCACGAGCTGTAAATCAGTAA
1 GCTCATACGAGCTATGAATCGGTAAGCTCTCACGAGCTACAAATCAATAA
105365 GCTCATACGAGCTGA-GAATCGGTAAGCTCTCACGAGCTACAAATCAATAA
1 GCTCATACGAGCT-ATGAATCGGTAAGCTCTCACGAGCTACAAATCAATAA
105415 GCTCATACGAGCTATG
1 GCTCATACGAGCTATG
105431 GTGTATCCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.02
50 55 0.96
51 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (50 bp):
GCTCATACGAGCTATGAATCGGTAAGCTCTCACGAGCTACAAATCAATAA
Found at i:109641 original size:101 final size:102
Alignment explanation
Indices: 109515--109699 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
109505 AAAGTGATGG
* *
109515 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGATAATGGTCACATGTGCAGT
109578 ACAATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
65 ACAATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
* * *
109616 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATGGTAATGGTCACATGTGCAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGGTCACATGTGCAGTA
* *
109681 CTATGTGCAGGCTAGTATG
66 CAATGTGCAGGCTACTATG
109700 TGAACCAGAC
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.53
102 31 0.41
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGGTCACATGTGCAGTA
CAATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
Found at i:109642 original size:51 final size:49
Alignment explanation
Indices: 109511--109701 Score: 213
Period size: 51 Copynumber: 3.8 Consensus size: 49
109501 CATGAAAGTG
* *
109511 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATGT
* * *
109560 ATAGGTCGCATGTGTAGTACAATGTGCAGGCTACTATGCGTACCGAATAGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAAT-GT
* * * * *
109611 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAAT-GT
* *
109662 AATGGTCACATGTGCAGTACTATGTGCAGGCTAGTATGTG
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
109702 AACCAGACAT
Statistics
Matches: 118, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 6 0.05
50 37 0.31
51 74 0.63
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (49 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATGT
Found at i:143665 original size:27 final size:26
Alignment explanation
Indices: 143635--143692 Score: 98
Period size: 27 Copynumber: 2.2 Consensus size: 26
143625 ATCATGACAT
*
143635 GCAATGTTAGTGTCGCAACATGGTGA
1 GCAATGTTAGTGTCGCAACACGGTGA
143661 GGCAATGTTAGTGTCGCAACACGGTGA
1 -GCAATGTTAGTGTCGCAACACGGTGA
143688 GCAAT
1 GCAAT
143693 TTTTGACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (26 bp):
GCAATGTTAGTGTCGCAACACGGTGA
Found at i:158581 original size:27 final size:26
Alignment explanation
Indices: 158551--158608 Score: 98
Period size: 27 Copynumber: 2.2 Consensus size: 26
158541 ATCATGACAT
*
158551 GCAATGTTAGTGTCGCAACATGGTGA
1 GCAATGTTAGTGTCGCAACACGGTGA
158577 GGCAATGTTAGTGTCGCAACACGGTGA
1 -GCAATGTTAGTGTCGCAACACGGTGA
158604 GCAAT
1 GCAAT
158609 TTTTGACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (26 bp):
GCAATGTTAGTGTCGCAACACGGTGA
Done.