Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3010
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: 141545
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3945 original size:40 final size:39
Alignment explanation
Indices: 3861--4044 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
3851 TTGAATGATG
* * * *
3861 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
3901 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
3941 TCCGGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
3979 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
4020 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
4045 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:3996 original size:78 final size:80
Alignment explanation
Indices: 3861--4044 Score: 207
Period size: 78 Copynumber: 2.3 Consensus size: 80
3851 TTGAATGATG
* *
3861 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
3925 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
3940 TTCCGGGCTAAG-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
4002 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
4019 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
4045 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
77 1 0.01
78 56 0.63
79 8 0.09
80 24 0.27
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATA
Found at i:11907 original size:79 final size:81
Alignment explanation
Indices: 11771--11955 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
11761 TTGAATGATG
* *
11771 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
11835 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
11850 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
11912 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
11930 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11956 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:11969 original size:40 final size:40
Alignment explanation
Indices: 11772--11955 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
11762 TGAATGATGT
* * * *
11772 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
11812 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
11852 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
11890 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
11931 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
11956 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:11977 original size:79 final size:79
Alignment explanation
Indices: 11824--11988 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
11814 GGACTAAGAT
* * **
11824 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
11889 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
11903 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
11966 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
11982 CCGAAGG
1 CCGAAGG
11989 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:17461 original size:15 final size:16
Alignment explanation
Indices: 17440--17481 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
17430 TAGCTTCTTC
17440 TTTTTTTTTCACGAAA
1 TTTTTTTTTCACGAAA
17456 TTTTTTTTTCACG-AA
1 TTTTTTTTTCACGAAA
17471 TTTTTTTTTCA
1 TTTTTTTTTCA
17482 ACTTGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTTTTTCACGAAA
Found at i:17538 original size:12 final size:11
Alignment explanation
Indices: 17519--17572 Score: 83
Period size: 11 Copynumber: 4.9 Consensus size: 11
17509 ATGGAAACCA
*
17519 AATTTTTTTTT
1 AATTTTTTTTG
17530 AA-TTTTTTTG
1 AATTTTTTTTG
17540 AATTTTTTTTG
1 AATTTTTTTTG
17551 AATTTTTTTTTG
1 AA-TTTTTTTTG
17563 AATTTTTTTT
1 AATTTTTTTT
17573 TGAAGAAACT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
10 9 0.22
11 20 0.50
12 11 0.28
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.76
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:17558 original size:23 final size:21
Alignment explanation
Indices: 17519--17572 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 21
17509 ATGGAAACCA
*
17519 AATTTTTTTTTAATTTTTTTG
1 AATTTTTTTTGAATTTTTTTG
17540 AATTTTTTTTGAATTTTTTTTTG
1 AATTTTTTTTGAA--TTTTTTTG
17563 AATTTTTTTT
1 AATTTTTTTT
17573 TGAAGAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 12 0.40
23 18 0.60
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.76
Consensus pattern (21 bp):
AATTTTTTTTGAATTTTTTTG
Found at i:17573 original size:12 final size:12
Alignment explanation
Indices: 17519--17576 Score: 88
Period size: 12 Copynumber: 5.2 Consensus size: 12
17509 ATGGAAACCA
17519 AATTTTTTTTT-
1 AATTTTTTTTTG
17530 AA--TTTTTTTG
1 AATTTTTTTTTG
17540 AA-TTTTTTTTG
1 AATTTTTTTTTG
17551 AATTTTTTTTTG
1 AATTTTTTTTTG
17563 AATTTTTTTTTG
1 AATTTTTTTTTG
17575 AA
1 AA
17577 GAAACTACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
9 7 0.16
10 2 0.05
11 12 0.27
12 23 0.52
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:24933 original size:17 final size:18
Alignment explanation
Indices: 24896--24933 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
24886 GATTGAGAGT
* *
24896 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
24914 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
24931 GAA
1 GAA
24934 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:24946 original size:13 final size:12
Alignment explanation
Indices: 24915--24969 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
24905 TGTGAAACAG
*
24915 AAAAGAAATTGA
1 AAAAGAAGTTGA
24927 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
24939 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
24951 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
24963 AAAAGAA
1 AAAAGAA
24970 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:29459 original size:29 final size:29
Alignment explanation
Indices: 29425--29498 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
29415 TCATCAACCA
*
29425 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
29454 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
29483 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
29499 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:34113 original size:207 final size:210
Alignment explanation
Indices: 33747--34170 Score: 669
Period size: 207 Copynumber: 2.0 Consensus size: 210
33737 TTGTTAATGC
* **
33747 TCGTAACTGATATCCAATGCGCCTTAGTTGCAAGATTCAGTTTCTTGGGTCAAGATTTCCAAGAT
1 TCGTAACTGAGATCCAATGCGCCTTAGTTGCAAGATTCAGTTTCTTGGACCAAGATTTCCAAGAT
*
33812 TTGAAATCTTAATTTTCTCGATTCTTGAAATTGCTCAAAATAGCAAAATTGGACCAAGATTCAGT
66 TTGAAATC------TTCTCGATTCTTGAAATCGCTCAAAATAGCAAAATTGGACCAAGATTCAGT
33877 TTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTT-TGTTTTCCTTCGTATACGCATCT
125 TTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT-TTTTCCTTCGTATACGCATCT
*
33941 AAGGCCTTTGTGACTCGTATCA
189 AAGGCCCTTGTGACTCGTATCA
* *
33963 TCGTAACTGAGATCCAATGCGCCTTAGTTGCAAGATTCGGTTTCTTGGACCAAGATTTCCTAGAT
1 TCGTAACTGAGATCCAATGCGCCTTAGTTGCAAGATTCAGTTTCTTGGACCAAGATTTCCAAGAT
*
34028 TTGAAATC-T-T-GATTCTTGAAATCGCTTAAAATAGCAAAATTGGACCAAGATTC-GATTTCTT
66 TTGAAATCTTCTCGATTCTTGAAATCGCTCAAAATAGCAAAATTGGACCAAGATTCAG-TTTCTT
34089 GATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCTTTTTCCTTCGTATACGCATCTAAGGCC
130 GATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCTTTTTCCTTCGTATACGCATCTAAGGCC
34154 CTTGTGACTCGTATCA
195 CTTGTGACTCGTATCA
34170 T
1 T
34171 TCCCCCTTCC
Statistics
Matches: 198, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
206 1 0.01
207 126 0.64
208 2 0.01
209 1 0.01
216 68 0.34
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (210 bp):
TCGTAACTGAGATCCAATGCGCCTTAGTTGCAAGATTCAGTTTCTTGGACCAAGATTTCCAAGAT
TTGAAATCTTCTCGATTCTTGAAATCGCTCAAAATAGCAAAATTGGACCAAGATTCAGTTTCTTG
ATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCTTTTTCCTTCGTATACGCATCTAAGGCCC
TTGTGACTCGTATCA
Found at i:40871 original size:20 final size:20
Alignment explanation
Indices: 40846--40900 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
40836 TGTGGTTCAA
*
40846 CTCATTCAAGCTCAAGTTAG
1 CTCATTCAAGCTCAAGTCAG
*
40866 CTCATTCATGCTCAAGTCAG
1 CTCATTCAAGCTCAAGTCAG
40886 CTCATTCAAGCTCAA
1 CTCATTCAAGCTCAA
40901 TTTAACTCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (20 bp):
CTCATTCAAGCTCAAGTCAG
Found at i:42696 original size:20 final size:20
Alignment explanation
Indices: 42648--42697 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
42638 TCGGTATTGT
**
42648 AAAAAAAAGGAAAAAAATTC
1 AAAAAAAAATAAAAAAATTC
*
42668 GAAAAAAAATAAAAAAATTC
1 AAAAAAAAATAAAAAAATTC
42688 AAAAAAAAAT
1 AAAAAAAAAT
42698 TTGTATTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (20 bp):
AAAAAAAAATAAAAAAATTC
Found at i:48402 original size:24 final size:24
Alignment explanation
Indices: 48349--48402 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
48339 AAACAAATTC
*
48349 TTTTTTTCATTTTCATCACTCGTT
1 TTTTTTTCATTTTAATCACTCGTT
* *
48373 TCTTTTTC-TTTTGAATCACTC-TC
1 TTTTTTTCATTTT-AATCACTCGTT
48396 TTTTTTT
1 TTTTTTT
48403 ATCACTCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.11, C:0.20, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTTTTCATTTTAATCACTCGTT
Found at i:50680 original size:13 final size:13
Alignment explanation
Indices: 50661--50731 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 13
50651 GTATGCAATT
50661 TTTTTTTTTGCAAA
1 TTTTTTTTT-CAAA
50675 -TTTTTTTTC---
1 TTTTTTTTTCAAA
*
50684 TTTTTTTTTCAGA
1 TTTTTTTTTCAAA
50697 TTTTTTTTTCGAAA
1 TTTTTTTTTC-AAA
* *
50711 CTTTTTTTT-AAC
1 TTTTTTTTTCAAA
50723 TTTTTTTTT
1 TTTTTTTTT
50732 TGAAGCTACG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
10 9 0.19
12 11 0.23
13 18 0.38
14 10 0.21
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:50706 original size:23 final size:23
Alignment explanation
Indices: 50661--50704 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
50651 GTATGCAATT
50661 TTTTTTTTTGCAAATTTTTTTTC
1 TTTTTTTTTGCAAATTTTTTTTC
*
50684 TTTTTTTTT-CAGATTTTTTTT
1 TTTTTTTTTGCAAATTTTTTTT
50705 TCGAAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (23 bp):
TTTTTTTTTGCAAATTTTTTTTC
Found at i:52414 original size:16 final size:15
Alignment explanation
Indices: 52395--52424 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
52385 AGTATCAATT
52395 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
52411 TTTGATTGGGATGA
1 TTTGATTGGGATGA
52425 TGGATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:53338 original size:20 final size:20
Alignment explanation
Indices: 53313--53367 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
53303 TGTGGTTCAA
*
53313 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
53333 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
53353 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
53368 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:66483 original size:23 final size:22
Alignment explanation
Indices: 66431--66483 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
66421 TCCACGTCTT
*
66431 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
66453 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
66476 TTTCTTTT
1 TTTCTTTT
66484 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:71296 original size:13 final size:12
Alignment explanation
Indices: 71278--71321 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
71268 TAAAAAAAAT
*
71278 AAAAAAACTTGA
1 AAAAAAAATTGA
*
71290 AAAAAAATTTGA
1 AAAAAAAATTGA
*
71302 AAAAAAAATTCA
1 AAAAAAAATTGA
71314 AAAAAAAA
1 AAAAAAAA
71322 GTTTTTATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:71437 original size:31 final size:31
Alignment explanation
Indices: 71367--71434 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
71357 GTATTGAAGG
* *
71367 AAAAAAAGAAGAAAAAAAAATTTGGAATTAA
1 AAAAAAAGAAGAAAAAAAAATTCGAAATTAA
71398 AAAAAAAGAAG-AAAAAAAA-TCGAAATTGAA
1 AAAAAAAGAAGAAAAAAAAATTCGAAATT-AA
71428 AAAAAAA
1 AAAAAAA
71435 AGAGTGATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 6 0.18
30 17 0.50
31 11 0.32
ACGTcount: A:0.75, C:0.01, G:0.12, T:0.12
Consensus pattern (31 bp):
AAAAAAAGAAGAAAAAAAAATTCGAAATTAA
Found at i:87287 original size:13 final size:12
Alignment explanation
Indices: 87237--87284 Score: 87
Period size: 12 Copynumber: 4.0 Consensus size: 12
87227 TAGTAGTTTC
*
87237 TTCAAAAAAAAT
1 TTCAAAAAAAAA
87249 TTCAAAAAAAAA
1 TTCAAAAAAAAA
87261 TTCAAAAAAAAA
1 TTCAAAAAAAAA
87273 TTCAAAAAAAAA
1 TTCAAAAAAAAA
87285 ATTTGGTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:87345 original size:15 final size:15
Alignment explanation
Indices: 87325--87381 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
87315 GATATCAAGT
87325 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
*
87340 TGAAAAAAAAATTAG
1 TGAAAAAAAAATTCG
87355 TGAAAAACAAAATTTCG
1 TGAAAAA-AAAA-TTCG
87372 TGAAAAAAAA
1 TGAAAAAAAA
87382 GAAGAAGCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 21 0.55
16 7 0.18
17 10 0.26
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.19
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:92861 original size:16 final size:16
Alignment explanation
Indices: 92840--92887 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
92830 TTTTCTCTTG
92840 AGTTTTCTTTAGAAGT
1 AGTTTTCTTTAGAAGT
92856 AG---T-TTTA-AA-T
1 AGTTTTCTTTAGAAGT
92866 AGTTTTCTTTAGAAGT
1 AGTTTTCTTTAGAAGT
92882 AGTTTT
1 AGTTTT
92888 AACAATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
10 3 0.12
11 2 0.08
12 4 0.15
13 2 0.08
14 4 0.15
15 2 0.08
16 9 0.35
ACGTcount: A:0.27, C:0.04, G:0.17, T:0.52
Consensus pattern (16 bp):
AGTTTTCTTTAGAAGT
Found at i:92869 original size:26 final size:26
Alignment explanation
Indices: 92840--92889 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
92830 TTTTCTCTTG
92840 AGTTTTCTTTAGAAGTAGTTTTAAAT
1 AGTTTTCTTTAGAAGTAGTTTTAAAT
92866 AGTTTTCTTTAGAAGTAGTTTTAA
1 AGTTTTCTTTAGAAGTAGTTTTAA
92890 CAATCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50
Consensus pattern (26 bp):
AGTTTTCTTTAGAAGTAGTTTTAAAT
Found at i:94484 original size:27 final size:27
Alignment explanation
Indices: 94446--94497 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
94436 TGTTTGTAGG
* *
94446 TACATGCATGGACAGCATTGAAGATAA
1 TACATGCATGGACAACAATGAAGATAA
94473 TACATGCATGGACAACAATGAAGAT
1 TACATGCATGGACAACAATGAAGAT
94498 GCTCAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (27 bp):
TACATGCATGGACAACAATGAAGATAA
Found at i:95191 original size:23 final size:22
Alignment explanation
Indices: 95154--95208 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
95144 GCCGAATTCA
*
95154 TGAACCATCTTTAATGTTTTAGTG
1 TGAACCATCTTTAAT-TGTT-GTG
*
95178 TGAACCCT-TTTAATTGTTGTG
1 TGAACCATCTTTAATTGTTGTG
95199 TGAACACATC
1 TGAAC-CATC
95209 AATAGCCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 6 0.23
24 7 0.27
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (22 bp):
TGAACCATCTTTAATTGTTGTG
Found at i:104043 original size:10 final size:10
Alignment explanation
Indices: 104008--104063 Score: 53
Period size: 9 Copynumber: 5.7 Consensus size: 10
103998 GTAATTGAAC
*
104008 AAAAAAAT-A
1 AAAAAAATCG
*
104017 AAAAAAAACG
1 AAAAAAATCG
**
104027 AGGAAAATCG
1 AAAAAAATCG
104037 AAAAAAAATC-
1 -AAAAAAATCG
104047 AAAAAAATCG
1 AAAAAAATCG
104057 AAAAAAA
1 AAAAAAA
104064 AGATTCAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 16 0.43
10 14 0.38
11 7 0.19
ACGTcount: A:0.77, C:0.07, G:0.09, T:0.07
Consensus pattern (10 bp):
AAAAAAATCG
Found at i:104044 original size:11 final size:11
Alignment explanation
Indices: 104030--104064 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
104020 AAAAACGAGG
104030 AAAATCGAAAA
1 AAAATCGAAAA
104041 AAAATC--AAA
1 AAAATCGAAAA
104050 AAAATCGAAAA
1 AAAATCGAAAA
104061 AAAA
1 AAAA
104065 GATTCAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.41
11 13 0.59
ACGTcount: A:0.77, C:0.09, G:0.06, T:0.09
Consensus pattern (11 bp):
AAAATCGAAAA
Found at i:105063 original size:14 final size:13
Alignment explanation
Indices: 105042--105079 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
105032 AAAAGTGAGA
105042 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
105054 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
105069 GAAAAAGAAAA
1 GAAAAAGAAAA
105080 AGATGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:105096 original size:6 final size:6
Alignment explanation
Indices: 104975--105082 Score: 74
Period size: 6 Copynumber: 17.5 Consensus size: 6
104965 AGTGCGAGCG
* * * *
104975 AGAAAA TGAAAA AGAAAA CGAAAA AGAAAA AGAAATT A-CAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGAAAA AGAAAA
* * ** * * *
105023 AGAAAT CGAAAA AGTGAG AGAAAA AGAAAA TGAAGAAA AGAAAA TTGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AG-A-AAA AGAAAA -AGAAAA
105074 AGAAAA AGA
1 AGAAAA AGA
105083 TGTTGAAAAA
Statistics
Matches: 75, Mismatches: 22, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
5 1 0.01
6 62 0.83
7 8 0.11
8 4 0.05
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AGAAAA
Found at i:107143 original size:27 final size:27
Alignment explanation
Indices: 107105--107156 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
107095 TGTTTGTAGG
* *
107105 TACATGCATGGACAGCATTGAAGATAA
1 TACATGCATGGACAACAATGAAGATAA
107132 TACATGCATGGACAACAATGAAGAT
1 TACATGCATGGACAACAATGAAGAT
107157 GCTTCAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (27 bp):
TACATGCATGGACAACAATGAAGATAA
Found at i:107850 original size:23 final size:22
Alignment explanation
Indices: 107813--107867 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
107803 GTCGAATTCA
*
107813 TGAACCATCTTTAATGTTTTAGTG
1 TGAACCATCTTTAAT-TGTT-GTG
*
107837 TGAACCCT-TTTAATTGTTGTG
1 TGAACCATCTTTAATTGTTGTG
107858 TGAACACATC
1 TGAAC-CATC
107868 AGTAGCTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 6 0.23
24 7 0.27
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (22 bp):
TGAACCATCTTTAATTGTTGTG
Found at i:108713 original size:26 final size:26
Alignment explanation
Indices: 108667--108716 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
108657 ATCAATTACG
*
108667 AAAGAAAACGAATTAGATTTAAATCA
1 AAAGAAAACGAATCAGATTTAAATCA
108693 AAAGAAAAC-AATCAGATTTTAAAT
1 AAAGAAAACGAATCAGA-TTTAAAT
108717 AGAAAATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (26 bp):
AAAGAAAACGAATCAGATTTAAATCA
Found at i:120346 original size:23 final size:22
Alignment explanation
Indices: 120294--120346 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
120284 TCCACGTCTT
*
120294 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
120316 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
120339 TTTCTTTT
1 TTTCTTTT
120347 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:123721 original size:151 final size:153
Alignment explanation
Indices: 123445--123750 Score: 573
Period size: 151 Copynumber: 2.0 Consensus size: 153
123435 ACCATCAATG
123445 ATCATACTACATACCTTGCCTTGAATGTGGCATCGAGTGTGAAAAATATTCTCCCTTTGTTGATC
1 ATCATACTACATACCTTGCCTTGAATGTGGCATCGAGTGTGAAAAATATTCTCCCTTTGTTGATC
*
123510 AGTTTCAACACTTTGAATATTGAGGCTACGCTTCACCACAAGAATTTCTCCTTCAACGGGTAACT
66 AGTTTCAACACTTTGAATACTGAGGCTACGCTTCACCACAAGAATTTCTCCTTCAACGGGTAACT
123575 CTAAATCTTCATCATCGGATGGC
131 CTAAATCTTCATCATCGGATGGC
123598 ATCATACTACATACCTTGCCTTGAATGTGGCATCGAGT-TG-AAAATATTCTCCC-TTGTTGATC
1 ATCATACTACATACCTTGCCTTGAATGTGGCATCGAGTGTGAAAAATATTCTCCCTTTGTTGATC
123660 AGTTTCAACACTTTGAATTACTGAGGCTACGCTTCACCACAAGAATTTCTCCTTCAACGGGTAAC
66 AGTTTCAACACTTTGAA-TACTGAGGCTACGCTTCACCACAAGAATTTCTCCTTCAACGGGTAAC
123725 TCTAAATCTTCATCATCGGATGGC
130 TCTAAATCTTCATCATCGGATGGC
123749 AT
1 AT
123751 TTCAGGTTCA
Statistics
Matches: 151, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
150 26 0.17
151 85 0.56
152 2 0.01
153 38 0.25
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (153 bp):
ATCATACTACATACCTTGCCTTGAATGTGGCATCGAGTGTGAAAAATATTCTCCCTTTGTTGATC
AGTTTCAACACTTTGAATACTGAGGCTACGCTTCACCACAAGAATTTCTCCTTCAACGGGTAACT
CTAAATCTTCATCATCGGATGGC
Found at i:125256 original size:15 final size:16
Alignment explanation
Indices: 125234--125277 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
125224 TTTTCACGAA
125234 AAATTTTTTTTTTCAC
1 AAATTTTTTTTTTCAC
*
125250 GAATTTTTTTTTTCAC
1 AAATTTTTTTTTTCAC
125266 AAAATTTTTTTT
1 -AAATTTTTTTT
125278 CAACTTGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (16 bp):
AAATTTTTTTTTTCAC
Found at i:125278 original size:15 final size:16
Alignment explanation
Indices: 125221--125279 Score: 66
Period size: 15 Copynumber: 3.6 Consensus size: 16
125211 CTTCTTCTTC
125221 TTTTTTTCACGAAAAATTT
1 TTTTTTTCACG-AAAA--T
**
125240 TTTTTTTCACGAATTT
1 TTTTTTTCACGAAAAT
125256 TTTTTTTCAC-AAAAT
1 TTTTTTTCACGAAAAT
125271 TTTTTTTCA
1 TTTTTTTCA
125280 ACTTGATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 12 0.33
16 11 0.31
18 2 0.06
19 11 0.31
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTTTTCACGAAAAT
Found at i:128290 original size:20 final size:20
Alignment explanation
Indices: 128265--128309 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
128255 TAAATACACA
128265 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
128285 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
128305 TAATT
1 TAATT
128310 CGGTTGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:136429 original size:23 final size:22
Alignment explanation
Indices: 136377--136429 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
136367 TCCACGTCTT
*
136377 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
136399 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
136422 TTTCTTTT
1 TTTCTTTT
136430 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Done.