Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1462
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: 29179
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:77 original size:17 final size:18
Alignment explanation
Indices: 37--78 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
27 TTAAAAAATA
37 TATTTATATTATTCAAAC
1 TATTTATATTATTCAAAC
* * *
55 TTTTTA-ATTTTTTAAAC
1 TATTTATATTATTCAAAC
72 TATTTAT
1 TATTTAT
79 GTTCGATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTATATTATTCAAAC
Found at i:1683 original size:22 final size:23
Alignment explanation
Indices: 1658--1725 Score: 88
Period size: 22 Copynumber: 3.0 Consensus size: 23
1648 ACGTTTATGA
1658 TTATAATT-AATATACAAATAAT
1 TTATAATTAAATATACAAATAAT
*
1680 TTAT-ATTAAATATATAAATAA-
1 TTATAATTAAATATACAAATAAT
*
1701 TTATAATTAAATATTACATATAAT
1 TTATAATTAAATA-TACAAATAAT
1725 T
1 T
1726 AATGATATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
21 7 0.18
22 24 0.62
23 7 0.18
24 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
TTATAATTAAATATACAAATAAT
Found at i:1744 original size:43 final size:45
Alignment explanation
Indices: 1657--1757 Score: 111
Period size: 43 Copynumber: 2.3 Consensus size: 45
1647 TACGTTTATG
*
1657 ATTATAATT-AATA-TACAAATAATTTATATTAAATATATAAATA
1 ATTATAATTAAATATTACAAATAATTTATATGAAATATATAAATA
* * * *
1700 ATTATAATTAAATATTACATATAA-TTA-ATGATATGTATATATA
1 ATTATAATTAAATATTACAAATAATTTATATGAAATATATAAATA
* *
1743 ATTTTAACTAAATAT
1 ATTATAATTAAATAT
1758 ATATATAGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 34 0.69
44 7 0.14
45 8 0.16
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (45 bp):
ATTATAATTAAATATTACAAATAATTTATATGAAATATATAAATA
Found at i:2258 original size:18 final size:18
Alignment explanation
Indices: 2223--2260 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2213 TAGTATTCTC
2223 TTTTAAACCCAATAATTA
1 TTTTAAACCCAATAATTA
*
2241 TTTTCAAACCTAAT-ATTA
1 TTTT-AAACCCAATAATTA
2259 TT
1 TT
2261 AAATCTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAAACCCAATAATTA
Found at i:2361 original size:51 final size:52
Alignment explanation
Indices: 2304--2447 Score: 184
Period size: 52 Copynumber: 2.8 Consensus size: 52
2294 CATACTTATT
* *
2304 TTAAAAAATAATTTAAGATTAAATATAAAATATTTTTTAATTTTTA-T-TCTA
1 TTAAAAAGTAATTCAAGATTAAATATAAAATATTTTTT-ATTTTTATTATCTA
* * * *
2355 TTAAAAAGTAATTCAAGATTGAATATAAAATAGTTTTTATTTTTATTATTTT
1 TTAAAAAGTAATTCAAGATTAAATATAAAATATTTTTTATTTTTATTATCTA
* * *
2407 TTAAATAGTAATTCAAGATTTAATATAAAATATATTTTATT
1 TTAAAAAGTAATTCAAGATTAAATATAAAATATTTTTTATT
2448 ATTTTTAAGT
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
50 7 0.09
51 35 0.43
52 39 0.48
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (52 bp):
TTAAAAAGTAATTCAAGATTAAATATAAAATATTTTTTATTTTTATTATCTA
Found at i:2418 original size:52 final size:51
Alignment explanation
Indices: 2302--2752 Score: 280
Period size: 51 Copynumber: 8.9 Consensus size: 51
2292 CCCATACTTA
* * *
2302 TTTTAAAAAATAATTTAAGATTAAATATAAAATATTTTTTAATTTTTA-T-TC
1 TTTTAAATAGTAATTTAAGATT-AATATAAAATATTTTTT-ATTTTTATTATT
* * * *
2353 TATTAAAAAGTAATTCAAGATTGAATATAAAATAGTTTTTATTTTTATTATT
1 TTTTAAATAGTAATTTAAGATT-AATATAAAATATTTTTTATTTTTATTATT
*
2405 TTTTAAATAGTAATTCAAGATTTAATATAAAATA-----TA-TTTTATTA-T
1 TTTTAAATAGTAATTTAAGA-TTAATATAAAATATTTTTTATTTTTATTATT
* * * * ** * *
2450 TTTTAAGTACTAATTCAAGATTAACATAAAAGATATTTTAAATTTGTATTAAT
1 TTTTAAATAGTAATTTAAGATTAATAT-AAA-ATATTTTTTATTTTTATTATT
* * * *
2503 TGTTAAATATTAATTTGAGACTAAGTAT----T-TTTTTTATTTTTATTATTT
1 TTTTAAATAGTAATTTAAGATTAA-TATAAAATATTTTTTATTTTTATTA-TT
** * *
2551 TTTTAAATAAAAATTTGAGATT-TTATATAAATATTTTTTTATTTTTATT-TT
1 TTTTAAATAGTAATTTAAGATTAATATA-AAATA-TTTTTTATTTTTATTATT
* * *
2602 TTTTAAATAGTAATTTTAA-ATTTATTTAAAATA-TTTTTAATTTT-TTATT
1 TTTTAAATAGTAA-TTTAAGATTAATATAAAATATTTTTTATTTTTATTATT
* * * * *
2651 ATTTAAA-AGTCAAATTTAAAATTATTATAAAATATTTTTTAATTTTATTATC
1 TTTTAAATAGT--AATTTAAGATTAATATAAAATATTTTTTATTTTTATTATT
* * *
2703 TTTCAAAAAGTAATTT-AGATTTAATA-AAACATAGGTTTTTATTTTATATT
1 TTTTAAATAGTAATTTAAGA-TTAATATAAA-ATA-TTTTTTATTTT-TATT
2753 TTATAATAAT
Statistics
Matches: 320, Mismatches: 46, Indels: 66
0.74 0.11 0.15
Matches are distributed among these distances:
44 6 0.02
45 22 0.07
46 14 0.04
47 15 0.05
48 25 0.08
49 23 0.07
50 25 0.08
51 83 0.26
52 62 0.19
53 43 0.13
54 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (51 bp):
TTTTAAATAGTAATTTAAGATTAATATAAAATATTTTTTATTTTTATTATT
Found at i:2465 original size:45 final size:46
Alignment explanation
Indices: 2302--2489 Score: 146
Period size: 52 Copynumber: 3.9 Consensus size: 46
2292 CCCATACTTA
* * * * *
2302 TTTTAAAAAATAATTTAAGATTAAATATAAAATATTTTTTAATTTTTATT
1 TTTTAAATACTAATTCAAGATTTAATATAAAATATATTTT-A---TTATT
* * * *
2352 CTATTAAAAAGTAATTCAAGATTGAATATAAAATAGTTTTTATTTTTATTATT
1 -TTTTAAATACTAATTCAAGATTTAATATAAAATA-----TA-TTTTATTATT
*
2405 TTTTAAATAGTAATTCAAGATTTAATATAAAATATATTTTATTA-T
1 TTTTAAATACTAATTCAAGATTTAATATAAAATATATTTTATTATT
* * *
2450 TTTTAAGTACTAATTCAAGA-TTAACATAAAAGATATTTTA
1 TTTTAAATACTAATTCAAGATTTAATATAAAATATATTTTA
2490 AATTTGTATT
Statistics
Matches: 119, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
44 18 0.15
45 19 0.16
46 8 0.07
47 2 0.02
51 30 0.25
52 31 0.26
53 5 0.04
56 2 0.02
57 4 0.03
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (46 bp):
TTTTAAATACTAATTCAAGATTTAATATAAAATATATTTTATTATT
Found at i:2617 original size:51 final size:50
Alignment explanation
Indices: 2531--2754 Score: 154
Period size: 50 Copynumber: 4.4 Consensus size: 50
2521 GACTAAGTAT
**
2531 TTTTTTTATTTTTATTATTTTTTTAAATAAAAATTTGAGATTTTATATAAATA
1 TTTTTTTATTTTTA-T-TTTTTTTAAATAGTAATTT-AGATTTTATATAAATA
* *
2584 TTTTTTTATTTTTATTTTTTTTAAATAGTAATTTTA-AATTTATTTAAA-A
1 TTTTTTTATTTTTATTTTTTTTAAATAGTAA-TTTAGATTTTATATAAATA
* * * *
2633 TATTTTTAATTTTT-TATTATTTAAA-AGTCAAATTTAAAATTATTATA-AAATA
1 T-TTTTTTATTTTTATTTTTTTTAAATAGT--AATTT-AGATT-TTATATAAATA
* * * * * *
2685 -TTTTTTAATTTTATTATCTTTCAAAAAGTAATTTAGATTTAATAAAACATA
1 TTTTTTTATTTTTATT-TTTTTTAAATAGTAATTTAGATTTTATATAA-ATA
**
2736 GGTTTTTATTTTATATTTT
1 TTTTTTTATTTT-TATTTT
2755 ATAATAATAT
Statistics
Matches: 136, Mismatches: 20, Indels: 31
0.73 0.11 0.17
Matches are distributed among these distances:
48 3 0.02
49 18 0.13
50 40 0.29
51 29 0.21
52 25 0.18
53 21 0.15
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (50 bp):
TTTTTTTATTTTTATTTTTTTTAAATAGTAATTTAGATTTTATATAAATA
Found at i:2626 original size:50 final size:49
Alignment explanation
Indices: 2531--2731 Score: 158
Period size: 50 Copynumber: 4.0 Consensus size: 49
2521 GACTAAGTAT
** * *
2531 TTTTTTTATTTTTATTATTTTTTTAAATAAAAATTTGAGATTTTATATAAATA
1 TTTTTTTATTTTTA-T-TTTTTTTAAATAGTAATTTTA-AATTTATATAAA-A
*
2584 TTTTTTTATTTTTATTTTTTTTAAATAGTAATTTTAAATTTATTTAAAA
1 TTTTTTTATTTTTATTTTTTTTAAATAGTAATTTTAAATTTATATAAAA
* * * * *
2633 TATTTTTAATTTTT-TATTATTTAAA-AGTCAAATTTAAAATTATTATAAAA
1 T-TTTTTTATTTTTATTTTTTTTAAATAGT-AATTTTAAATTTA-TATAAAA
* * * * *
2683 TATTTTTTAATTTTATTATCTTTCAAAAAGTAA-TTTAGATTTA-ATAAAA
1 T-TTTTTTATTTTTATT-TTTTTTAAATAGTAATTTTAAATTTATATAAAA
2732 CATAGGTTTT
Statistics
Matches: 123, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
48 3 0.02
49 28 0.23
50 39 0.32
51 27 0.22
52 9 0.07
53 17 0.14
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (49 bp):
TTTTTTTATTTTTATTTTTTTTAAATAGTAATTTTAAATTTATATAAAA
Found at i:2638 original size:43 final size:48
Alignment explanation
Indices: 2590--2701 Score: 126
Period size: 49 Copynumber: 2.4 Consensus size: 48
2580 AATATTTTTT
* * *
2590 TATTTTT-ATTTTTT-TTA-AATAGT-AATTTTAAATTTATT-TAAAA
1 TATTTTTAATTTTTTATTATAAAAGTCAAATTTAAAATTATTATAAAA
2633 TATTTTTAATTTTTTATTATTTAAAAGTCAAATTTAAAATTATTATAAAA
1 TATTTTTAATTTTTTATTA--TAAAAGTCAAATTTAAAATTATTATAAAA
2683 TATTTTTTAATTTTATTAT
1 TA-TTTTTAATTTT-TTAT
2702 CTTTCAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
43 7 0.12
44 7 0.12
45 3 0.05
48 5 0.09
49 13 0.23
50 7 0.12
51 11 0.19
52 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (48 bp):
TATTTTTAATTTTTTATTATAAAAGTCAAATTTAAAATTATTATAAAA
Found at i:3147 original size:21 final size:21
Alignment explanation
Indices: 3109--3160 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
3099 AATAAAATAA
*
3109 AAAATTATTTGAATTTTTAATT
1 AAAATAATTTGAATTTTT-ATT
*
3131 AAAA-AATTT-AATATTTTTTT
1 AAAATAATTTGAAT-TTTTATT
3151 AAAATAATTT
1 AAAATAATTT
3161 TATTATACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.35
21 13 0.50
22 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AAAATAATTTGAATTTTTATT
Found at i:3685 original size:25 final size:23
Alignment explanation
Indices: 3639--3688 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 23
3629 TAATTTACTT
3639 AATTTAATTATATTTAAAAATTA
1 AATTTAATTATATTTAAAAATTA
*
3662 AATTTAATCTAATTTTTAAAAATTA
1 AATTTAAT-T-ATATTTAAAAATTA
3687 AA
1 AA
3689 ATAACTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 8 0.33
24 1 0.04
25 15 0.62
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTAATTATATTTAAAAATTA
Found at i:4378 original size:116 final size:118
Alignment explanation
Indices: 4215--4445 Score: 349
Period size: 116 Copynumber: 2.0 Consensus size: 118
4205 ATTCCCTAGA
* * * *
4215 TGAATTGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTATAATT
1 TGAAATGGAAGGAACCCTTTAAAGATATATGTATTATGATTCATTTTCATGCCTAATTTAGAATT
4280 TTTATCCTGCTTTTCAGTTTTCAATT-TGGG-GTTTTAACTGAAATGATGAAT
66 TTTATCCTGCTTTTCAGTTTTCAATTATGGGTGTTTTAACTGAAATGATGAAT
* * *
4331 TGAAATGGAAGGAACCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTAGAATT
1 TGAAATGGAAGGAACCCTTTAAAGATATATGTATTATGATTCATTTTCATGCCTAATTTAGAATT
* * * *
4396 TTTATCTTGCTTTTCGGTTTTCAATTATGGGTTTTTTAGCTGAAATGATG
66 TTTATCCTGCTTTTCAGTTTTCAATTATGGGTGTTTTAACTGAAATGATG
4446 TTTAGGGTTA
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
116 82 0.80
117 4 0.04
118 16 0.16
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (118 bp):
TGAAATGGAAGGAACCCTTTAAAGATATATGTATTATGATTCATTTTCATGCCTAATTTAGAATT
TTTATCCTGCTTTTCAGTTTTCAATTATGGGTGTTTTAACTGAAATGATGAAT
Found at i:4658 original size:134 final size:135
Alignment explanation
Indices: 4326--4713 Score: 575
Period size: 136 Copynumber: 2.9 Consensus size: 135
4316 ACTGAAATGA
* *
4326 TGAATTGAAATGGAAGGAACCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* * * *
4391 GAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGGTTA
66 TAATTTTTATCTTGCTTTTCAGTTTTCAATTATGGG-GTTTTAGCTGAAATGATGTTCAGGGTTA
4456 GGTCTT
130 GGTCTT
* * * *
4462 TGAATTGAAATGGAAGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* **
4527 TAATTTTTATCTTTCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATG-TCAGGGTTTA
66 TAATTTTTATCTTGCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGAAATGATGTTCAGGG-TTA
4591 GGTCTT
130 GGTCTT
* * *
4597 TGAATTG-AATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* *
4661 TAATTTTTATCCTGCTTTTCAGTTTTCAATT-TGGGGTTTTAACTGAAATGATG
66 TAATTTTTATCTTGCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGAAATGATG
4714 AATTGAAATG
Statistics
Matches: 227, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
133 19 0.08
134 85 0.37
135 31 0.14
136 92 0.41
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (135 bp):
TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
TAATTTTTATCTTGCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGAAATGATGTTCAGGGTTAG
GTCTT
Found at i:4782 original size:116 final size:116
Alignment explanation
Indices: 4597--4830 Score: 362
Period size: 116 Copynumber: 2.0 Consensus size: 116
4587 TTTAGGTCTT
* * *
4597 TGAATTGAATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTAT
1 TGAATTGAATGGAAGGAACCCTTTAAAGATATATGTATTATGATTCATTTTCATGCCTAATTTAG
4662 AATTTTTATCCTGCTTTTCAGTTTTCAATT-TGGGGTTTTAACTGAAATGA
66 AATTTTTATCCTGCTTTTCAGTTTTCAATTATGGGGTTTTAACTGAAATGA
* * *
4712 TGAATTGAAATGGAAGGAACCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTA
1 TGAATTG-AATGGAAGGAACCCTTTAAAGATATATGTATTATGATTCATTTTCATGCCTAATTTA
* * * *
4777 GAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGTTTTTAGCTGAAATGA
65 GAATTTTTATCCTGCTTTTCAGTTTTCAATTATGGGGTTTTAACTGAAATGA
4829 TG
1 TG
4831 TTTAGGGTTA
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
115 7 0.07
116 80 0.75
117 20 0.19
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (116 bp):
TGAATTGAATGGAAGGAACCCTTTAAAGATATATGTATTATGATTCATTTTCATGCCTAATTTAG
AATTTTTATCCTGCTTTTCAGTTTTCAATTATGGGGTTTTAACTGAAATGA
Found at i:5024 original size:385 final size:386
Alignment explanation
Indices: 4215--5625 Score: 2402
Period size: 386 Copynumber: 3.6 Consensus size: 386
4205 ATTCCCTAGA
4215 TGAATTGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTATAATT
1 TGAA-TGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTATAATT
4280 TTTATCCTGCTTTTCAGTTTTCAATTTGGGGTTTTAACTGAAATGATGAATTGAAATGGAAGGAA
65 TTTATCCTGCTTTTCAGTTTTCAATTTGGGGTTTTAACTGAAATGATGAATTGAAATGGAAGGAA
4345 CCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTAGAATTTTTATCTTGCTTTT
130 CCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTAGAATTTTTATCTTGCTTTT
4410 CGGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGGTTAGGTCTTTGAATTGAAATGG
195 CGGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGGTTAGGTCTTTGAATTGAAATGG
4475 AAGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTATAATTTTTATCTT
260 AAGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTATAATTTTTATCTT
4540 TCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATGTCAGGGTTTAGGTCTTTGAAT
325 TCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATGTCAGGGTTTAGGTCTTTGAAT
4602 TGAATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTATAATTT
1 TGAATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTATAATTT
4667 TTATCCTGCTTTTCAGTTTTCAATTTGGGGTTTTAACTGAAATGATGAATTGAAATGGAAGGAAC
66 TTATCCTGCTTTTCAGTTTTCAATTTGGGGTTTTAACTGAAATGATGAATTGAAATGGAAGGAAC
4732 CGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTAGAATTTTTATCTTGCTTTTC
131 CGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTAGAATTTTTATCTTGCTTTTC
4797 GGTTTTCAATTATGGG-TTTTTAGCTGAAATGATGTTTAGGGTTAGGTCTTTGAATTGAAATGGA
196 GGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGGTTAGGTCTTTGAATTGAAATGGA
4861 AGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTATAATTTTTATCTTT
261 AGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTATAATTTTTATCTTT
4926 CTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATGTCAGGGTTTAGGTCTTTGAAT
326 CTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATGTCAGGGTTTAGGTCTTTGAAT
4987 TGAATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTATAATTT
1 TGAATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTATAATTT
5052 TTATCCTGCTTTTCAGTTTTCAATTTGGGGTTTTAACTGAAATGATGAATTGAAATGGAAGGAAC
66 TTATCCTGCTTTTCAGTTTTCAATTTGGGGTTTTAACTGAAATGATGAATTGAAATGGAAGGAAC
5117 CGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTAGAATTTTTATCTTGCTTTTC
131 CGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTAGAATTTTTATCTTGCTTTTC
5182 GGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGGTTAGGTCTTTGAATTGAAATGGA
196 GGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGGTTAGGTCTTTGAATTGAAATGGA
5247 AGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTATAATTTTTATCTTT
261 AGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTATAATTTTTATCTTT
5312 CTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATGTCAGGGTTTAGGTCTTTGAAT
326 CTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATGTCAGGGTTTAGGTCTTTGAAT
* ** * * *
5373 TGAATGGAAGGAACCCTTTAAAGCTATGTGTATCATGATTCATTTTCATG-CTCACTTTGTAATA
1 TGAATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCT-AATTTATAATT
* * * * *
5437 TTTATCTTGCTTTTCTGTTTTCAACTATGGGTTTTTAGCTGAAATGATGTCAGGGTTTAGGTCTT
65 TTTATCCTGCTTTTCAGTTTTCAA-TTTGGGGTTTTAACTGAAATGATG--A------A-----T
* * * * * * * *
5502 TGAATTGAAACGCAAGGGACCCTTTAAAGCTATATTTATTATGATTCATTTTCGTGCTTAACTTA
116 TGAAATG----G-AAGGAACCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTA
* *
5567 TAATTTTTATCTTGCTTTTCGGTTTCCAATTATGGG---TTTAGCTGAAATGATG-TTAGGGT
176 GAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGGT
5626 CTATGTTGCT
Statistics
Matches: 982, Mismatches: 21, Indels: 28
0.95 0.02 0.03
Matches are distributed among these distances:
385 387 0.39
386 458 0.47
387 25 0.03
389 1 0.00
395 1 0.00
400 7 0.01
401 7 0.01
402 16 0.02
404 1 0.00
405 79 0.08
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (386 bp):
TGAATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTATAATTT
TTATCCTGCTTTTCAGTTTTCAATTTGGGGTTTTAACTGAAATGATGAATTGAAATGGAAGGAAC
CGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTAGAATTTTTATCTTGCTTTTC
GGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGGTTAGGTCTTTGAATTGAAATGGA
AGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTATAATTTTTATCTTT
CTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATGTCAGGGTTTAGGTCTTTGAAT
Found at i:5064 original size:134 final size:135
Alignment explanation
Indices: 4712--5098 Score: 582
Period size: 135 Copynumber: 2.9 Consensus size: 135
4702 ACTGAAATGA
* *
4712 TGAATTGAAATGGAAGGAACCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* * * *
4777 GAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGTTTTTAGCTGAAATGATGTTTAGGGTTAG
66 TAATTTTTATCTTGCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGAAATGATGTTCAGGGTTAG
4842 GTCTT
131 GTCTT
* * * *
4847 TGAATTGAAATGGAAGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* **
4912 TAATTTTTATCTTTCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATG-TCAGGGTTTA
66 TAATTTTTATCTTGCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGAAATGATGTTCAGGG-TTA
4976 GGTCTT
130 GGTCTT
* * *
4982 TGAATTG-AATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* *
5046 TAATTTTTATCCTGCTTTTCAGTTTTCAATT-TGGGGTTTTAACTGAAATGATG
66 TAATTTTTATCTTGCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGAAATGATG
5099 AATTGAAATG
Statistics
Matches: 227, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
133 19 0.08
134 85 0.37
135 123 0.54
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (135 bp):
TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
TAATTTTTATCTTGCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGAAATGATGTTCAGGGTTAG
GTCTT
Found at i:5167 original size:116 final size:117
Alignment explanation
Indices: 4982--5216 Score: 357
Period size: 116 Copynumber: 2.0 Consensus size: 117
4972 TTTAGGTCTT
* * *
4982 TGAATTGAATGGAAGGAACCCTTTAAAGCTATATGTATTTTGATTCATTTTCATGCCTAATTTAT
1 TGAATTGAATGGAAGGAACCCTTTAAAGATATATGTATTATGATTCATTTTCATGCCTAATTTAG
5047 AATTTTTATCCTGCTTTTCAGTTTTCAATT-TGGG-GTTTTAACTGAAATGA
66 AATTTTTATCCTGCTTTTCAGTTTTCAATTATGGGTGTTTTAACTGAAATGA
* * *
5097 TGAATTGAAATGGAAGGAACCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTA
1 TGAATTG-AATGGAAGGAACCCTTTAAAGATATATGTATTATGATTCATTTTCATGCCTAATTTA
* * * *
5162 GAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGTTTTTTAGCTGAAATGA
65 GAATTTTTATCCTGCTTTTCAGTTTTCAATTATGGGTGTTTTAACTGAAATGA
5215 TG
1 TG
5217 TTTAGGGTTA
Statistics
Matches: 107, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
115 7 0.07
116 80 0.75
117 4 0.04
118 16 0.15
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (117 bp):
TGAATTGAATGGAAGGAACCCTTTAAAGATATATGTATTATGATTCATTTTCATGCCTAATTTAG
AATTTTTATCCTGCTTTTCAGTTTTCAATTATGGGTGTTTTAACTGAAATGA
Found at i:5441 original size:134 final size:135
Alignment explanation
Indices: 5097--5625 Score: 733
Period size: 134 Copynumber: 3.9 Consensus size: 135
5087 ACTGAAATGA
* *
5097 TGAATTGAAATGGAAGGAACCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* * *
5162 GAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGG-TT
66 TAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGG-GTTTTAGCTGAAATGATG-TCAGGGTTT
5226 AGGTCTT
129 AGGTCTT
* * * *
5233 TGAATTGAAATGGAAGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTTAATTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* * **
5298 TAATTTTTATCTTTCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATGTCAGGGTTTAG
66 TAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGGTTTTAGCTGAAATGATGTCAGGGTTTAG
5363 GTCTT
131 GTCTT
* * * * *
5368 TGAATTG-AATGGAAGGAACCCTTTAAAGCTATGTGTATCATGATTCATTTTCATGCTCACTTTG
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* * * *
5432 TAATATTTATCTTGCTTTTCTGTTTTCAACTATGGGTTTTTAGCTGAAATGATGTCAGGGTTTAG
66 TAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGGTTTTAGCTGAAATGATGTCAGGGTTTAG
5497 GTCTT
131 GTCTT
* * * * * * *
5502 TGAATTGAAACGCAAGGGACCCTTTAAAGCTATATTTATTATGATTCATTTTCGTGCTTAACTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
* *
5567 TAATTTTTATCTTGCTTTTCGGTTTCCAATTAT-GGG-TTTAGCTGAAATGATGTTAGGGT
66 TAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGGTTTTAGCTGAAATGATGTCAGGGT
5626 CTATGTTGCT
Statistics
Matches: 345, Mismatches: 46, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
133 22 0.06
134 125 0.36
135 106 0.31
136 92 0.27
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (135 bp):
TGAATTGAAATGGAAGGAACCCTTTAAAGCTATCTGTATTATGATTCATTTTCATGCTTAATTTA
TAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGGTTTTAGCTGAAATGATGTCAGGGTTTAG
GTCTT
Found at i:5599 original size:269 final size:269
Alignment explanation
Indices: 5097--5625 Score: 751
Period size: 269 Copynumber: 2.0 Consensus size: 269
5087 ACTGAAATGA
* * *
5097 TGAATTGAAATGGAAGGAACCGTTTAAAGATATCTGTATTATGATTCATTTTCATGCTTAATTTA
1 TGAATTGAAATGGAAGGAACCCTTTAAAGATATCTGTATCATGATTCATTTTCATGCTCAATTTA
* * *
5162 GAATTTTTATCTTGCTTTTCGGTTTTCAATTATGGGTTTTTTAGCTGAAATGATGTTTAGGGTTA
66 GAATATTTATCTTGCTTTTCGGTTTTCAACTATGGGTTTTTTAGCTGAAATGATGTTCAGGGTTA
* * * * *
5227 GGTCTTTGAATTGAAATGGAAGGAACCCTTTAAAGCTGTCTGAATTGTGATTCATTTTCATACTT
131 GGTCTTTGAATTGAAACGCAAGGAACCCTTTAAAGCTATATGAATTATGATTCATTTTCATACTT
* * * **
5292 AATTTATAATTTTTATCTTTCTTTTCAGTTTTCAATTATGGGGTTTTAGCTGCTATGATGTCAGG
196 AACTTATAATTTTTATCTTGCTTTTCAGTTTCCAATTAT-GGG-TTTAGCTGAAATGATGTCAGG
5357 GTTTAGGTCTT
259 GTTTAGGTCTT
* * *
5368 TGAATTG-AATGGAAGGAACCCTTTAAAGCTATGTGTATCATGATTCATTTTCATGCTCACTTT-
1 TGAATTGAAATGGAAGGAACCCTTTAAAGATATCTGTATCATGATTCATTTTCATGCTCAATTTA
*
5431 GTAATATTTATCTTGCTTTTCTGTTTTCAACTATGGG-TTTTTAGCTGAAATGATG-TCAGGGTT
66 G-AATATTTATCTTGCTTTTCGGTTTTCAACTATGGGTTTTTTAGCTGAAATGATGTTCAGGG-T
* ** * *
5494 TAGGTCTTTGAATTGAAACGCAAGGGACCCTTTAAAGCTATATTTATTATGATTCATTTTCGTGC
129 TAGGTCTTTGAATTGAAACGCAAGGAACCCTTTAAAGCTATATGAATTATGATTCATTTTCATAC
* *
5559 TTAACTTATAATTTTTATCTTGCTTTTCGGTTTCCAATTATGGGTTTAGCTGAAATGATGTTAGG
194 TTAACTTATAATTTTTATCTTGCTTTTCAGTTTCCAATTATGGGTTTAGCTGAAATGATGTCAGG
5624 GT
259 GT
5626 CTATGTTGCT
Statistics
Matches: 229, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
267 20 0.09
268 8 0.03
269 112 0.49
270 82 0.36
271 7 0.03
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (269 bp):
TGAATTGAAATGGAAGGAACCCTTTAAAGATATCTGTATCATGATTCATTTTCATGCTCAATTTA
GAATATTTATCTTGCTTTTCGGTTTTCAACTATGGGTTTTTTAGCTGAAATGATGTTCAGGGTTA
GGTCTTTGAATTGAAACGCAAGGAACCCTTTAAAGCTATATGAATTATGATTCATTTTCATACTT
AACTTATAATTTTTATCTTGCTTTTCAGTTTCCAATTATGGGTTTAGCTGAAATGATGTCAGGGT
TTAGGTCTT
Found at i:8416 original size:2 final size:2
Alignment explanation
Indices: 8409--8438 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8399 CTCTTAACTC
*
8409 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8439 GATTTCAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11858 original size:2 final size:2
Alignment explanation
Indices: 11851--11875 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11841 TCATGCAAAG
11851 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
11876 AAATAACTCT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:14785 original size:2 final size:2
Alignment explanation
Indices: 14767--14802 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
14757 ATCCTATCCC
* *
14767 AT AT TT AT AT CT 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
14803 GTCTTAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:24817 original size:2 final size:2
Alignment explanation
Indices: 24810--24868 Score: 81
Period size: 2 Copynumber: 31.5 Consensus size: 2
24800 GCTCTATGTC
*
24810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24851 AT A- AT AT A- AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
24869 AACCAAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
1 4 0.08
2 47 0.92
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:28482 original size:19 final size:20
Alignment explanation
Indices: 28449--28488 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
28439 TTTAAAAAAT
*
28449 AAATAATAAATAATTTTAAA
1 AAATAATAAAAAATTTTAAA
28469 AAAT-ATAAAAAATTTTAAA
1 AAATAATAAAAAATTTTAAA
28488 A
1 A
28489 TATCAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATAAAAAATTTTAAA
Done.