Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1173
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: 68176
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:371 original size:52 final size:52
Alignment explanation
Indices: 311--439 Score: 188
Period size: 52 Copynumber: 2.5 Consensus size: 52
301 CTTAATTGTT
*
311 CACAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTC
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTC
** * *
362 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTC
*
415 CACAATCGAGGATACTCCAACCCCG
1 CACAATCGGGGATACTCCAACCCCG
440 TTATTTCCGA
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
51 1 0.01
52 51 0.76
53 15 0.22
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (52 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTC
Found at i:510 original size:51 final size:51
Alignment explanation
Indices: 450--670 Score: 214
Period size: 51 Copynumber: 4.3 Consensus size: 51
440 TTATTTCCGA
* * *** *
450 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATA-TTGGTTTCTCATAATC
1 GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACTAATTTTC-CACAATC
* *
501 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACTAATTTTCCACAATC
* * * * **
552 GGGGATACTCCAACCCTAGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACTAATTTTCC-ACAATC
* * *
604 GGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAAATTTT-CACAATC
1 GGGGATACTCCAACCCCAG-CTTTATTTCC-AAAACA-CTAATTTTCCACAATC
*
656 GAGGATACTCCAACC
1 GGGGATACTCCAACC
671 TCATTATTTC
Statistics
Matches: 143, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
51 79 0.55
52 50 0.35
53 7 0.05
54 7 0.05
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACTAATTTTCCACAATC
Found at i:627 original size:52 final size:51
Alignment explanation
Indices: 496--670 Score: 205
Period size: 52 Copynumber: 3.4 Consensus size: 51
486 TGGTTTCTCA
* *
496 TAATCGGGGATACTCCAACCCCAGTTTTA-TTTCTAAAACACTAATTTTCC
1 TAATCGGGGATACTCCAACCCCAGTTTTATTTTCAAAAACACCAATTTTCC
* *
546 ACAATCGGGGATACTCCAACCCTAGTTTTATTTTC-AAAACACCAATTTTCC
1 -TAATCGGGGATACTCCAACCCCAGTTTTATTTTCAAAAACACCAATTTTCC
* *
597 TTTAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAAATTTTCAC
1 --TAATCGGGGATACTCCAACCCCAG-TTTTATTTTCAAAAACACC-AATTTTC-C
*
652 -AATCGAGGATACTCCAACC
1 TAATCGGGGATACTCCAACC
671 TCATTATTTC
Statistics
Matches: 108, Mismatches: 10, Indels: 11
0.84 0.08 0.09
Matches are distributed among these distances:
51 43 0.40
52 49 0.45
53 8 0.07
54 7 0.06
55 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.31
Consensus pattern (51 bp):
TAATCGGGGATACTCCAACCCCAGTTTTATTTTCAAAAACACCAATTTTCC
Found at i:795 original size:107 final size:108
Alignment explanation
Indices: 604--804 Score: 255
Period size: 107 Copynumber: 1.9 Consensus size: 108
594 TCCTTTAATC
*
604 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTTCACAACCGAGGATACTCCAA
* * *
669 CCTCATTATTTCATCGGGGATACTCCAACTCTGTTACCTCCGA
66 CCCCACTATTTCATAGGGGATACTCCAACTCTGTTACCTCCGA
* * * * * * *
712 GGGGATACTCCAATTTCGATTTTATTTCC-TAATCATCGATTTTTCACAACC-AGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTTCACAACCGA-GGATACTCCA
*
775 ACCCCGCTATTTTCA-AGGGGATACTCCAAC
65 ACCCCACTA-TTTCATAGGGGATACTCCAAC
805 CTCGTTATTA
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
106 1 0.01
107 46 0.58
108 32 0.41
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (108 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTTCACAACCGAGGATACTCCAA
CCCCACTATTTCATAGGGGATACTCCAACTCTGTTACCTCCGA
Found at i:3249 original size:16 final size:15
Alignment explanation
Indices: 3214--3256 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3204 ATTTAAATTT
3214 AAAATTTCTAAAATA
1 AAAATTTCTAAAATA
*
3229 AAAATTTCTATAATA
1 AAAATTTCTAAAATA
*
3244 AAAAATT-TAAAAT
1 AAAATTTCTAAAAT
3257 TAATTAGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATTTCTAAAATA
Found at i:4119 original size:41 final size:40
Alignment explanation
Indices: 4074--4152 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
4064 ATAGTTGATT
* *
4074 GGGATGAAATTGACAAGCCAACTAAGAGTGAATGGTTGACC
1 GGGATGAAACTGACAAGCCAACTAAGAGT-AAAGGTTGACC
* *
4115 GGGATGAAACTGATAAGTCAACTAAGAGTAAAGGTTGA
1 GGGATGAAACTGACAAGCCAACTAAGAGTAAAGGTTGA
4153 TTAAGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 8 0.24
41 26 0.76
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.20
Consensus pattern (40 bp):
GGGATGAAACTGACAAGCCAACTAAGAGTAAAGGTTGACC
Found at i:4310 original size:81 final size:81
Alignment explanation
Indices: 4116--4340 Score: 211
Period size: 81 Copynumber: 2.8 Consensus size: 81
4106 TGGTTGACCG
** * ** *
4116 GGATGAAACTGATAAGTCAACTAAGAGTAAAGGTTGATTAAGAAAAAATTGACAAGTCAATAAAG
1 GGATGAAACCAATAAGTCAACTAAGAGTGAAGGTTGACCAAGAAAAAATTGACAAGTCAACAAAG
4181 AATGAAGTATTAACAA
66 AATGAAGTATTAACAA
** * * * * * * * *
4197 GGACAAAATCTATAAGTCAATTGAGAGAGAAGGTTAACCAAGATAAAATTGACAAGTCAGCAAAG
1 GGATGAAACCAATAAGTCAACTAAGAGTGAAGGTTGACCAAGAAAAAATTGACAAGTCAACAAAG
* *
4262 AATGAAGTGTTGACTAA
66 AATGAAGTATTAAC-AA
* * * * *
4279 -GATGAAACCAATAAATCAACTAAAAGTGAAGGTTGACCACG-ACAAATCTGACAATTCAACAA
1 GGATGAAACCAATAAGTCAACTAAGAGTGAAGGTTGACCAAGAAAAAAT-TGACAAGTCAACAA
4341 TGAGTAATGG
Statistics
Matches: 110, Mismatches: 32, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
80 4 0.04
81 104 0.95
82 2 0.02
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.20
Consensus pattern (81 bp):
GGATGAAACCAATAAGTCAACTAAGAGTGAAGGTTGACCAAGAAAAAATTGACAAGTCAACAAAG
AATGAAGTATTAACAA
Found at i:4403 original size:41 final size:41
Alignment explanation
Indices: 4336--4422 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
4326 CTGACAATTC
* * * **
4336 AACAATGAGTAATGGGTTGACTGAGATGGAATTGATGAGTA
1 AACAATAAGTAATGGGGTGACTGAGATGAAACCGATGAGTA
* *
4377 AACAATAAGTTATGGGGTGA-TCGAGATGAAACCGATGAGTC
1 AACAATAAGTAATGGGGTGACT-GAGATGAAACCGATGAGTA
4418 AACAA
1 AACAA
4423 AGATTGTAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.39, C:0.09, G:0.29, T:0.23
Consensus pattern (41 bp):
AACAATAAGTAATGGGGTGACTGAGATGAAACCGATGAGTA
Found at i:10084 original size:28 final size:28
Alignment explanation
Indices: 10044--10448 Score: 533
Period size: 28 Copynumber: 14.7 Consensus size: 28
10034 CATAATGGAT
* *
10044 CTGACTTATGGGCTTTGAAAGGATGCTA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
*
10072 CTGACTTGTGGGCTTTGAAGGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
10100 CTGACTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* * *
10128 CTAACTTGTGGGCTTTGAAAAGGGTGTCA
1 CTGACTTGTGGGCTTTG-AAAGGATGCCA
*
10157 CTGACTTATGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
** * *
10185 CAAACTTATGGGCTTTGAAAAGGGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGATGCCA
* *
10214 CTAACTTGTGGGCTTTGAAAAGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
*
10242 CTGACTTGTGGGCTTTGAAAAGGGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGATGCCA
10271 CTGACTTGTGGGCTTTG--A--ATG---
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
10292 --GACTTGTGGGCTTTGAAA-GATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* *
10317 CTGACTTGTGGACTTTGAAAAGGGTGCCA
1 CTGACTTGTGGGCTTTG-AAAGGATGCCA
10346 CTGACTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
10374 CTGACTTGTGGGCTTTGAAAGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
* *
10402 CTGACTTGTGGGCTTTAAAAGGATGCGA
1 CTGACTTGTGGGCTTTGAAAGGATGCCA
*
10430 CTGACTTATGGGCTTTGAA
1 CTGACTTGTGGGCTTTGAA
10449 GAAATGAACG
Statistics
Matches: 334, Mismatches: 30, Indels: 26
0.86 0.08 0.07
Matches are distributed among these distances:
19 15 0.04
21 1 0.00
22 3 0.01
24 2 0.01
26 1 0.00
27 14 0.04
28 201 0.60
29 97 0.29
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (28 bp):
CTGACTTGTGGGCTTTGAAAGGATGCCA
Found at i:10181 original size:57 final size:57
Alignment explanation
Indices: 10044--10448 Score: 534
Period size: 57 Copynumber: 7.3 Consensus size: 57
10034 CATAATGGAT
* *
10044 CTGACTTATGGGCTTTGAAAGGATGCTACTGACTTGTGGGCTTTG--AAGGGATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGG-TGCCA
* *
10100 CTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGGTGTCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCA
* ** *
10157 CTGACTTATGGGCTTTGAAAGGATGCCACAAACTTATGGGCTTTGAAAAGGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCA
* *
10214 CTAACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCA
*
10271 CTGACTTGTGGGCTTTG--A--ATG-----GACTTGTGGGCTTTG-AAA-GATGCCA
1 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCA
* * *
10317 CTGACTTGTGGACTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCA
1 CTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCA
* *
10374 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-AAAAGGATGCGA
1 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCA
*
10430 CTGACTTATGGGCTTTGAA
1 CTGACTTGTGGGCTTTGAA
10449 GAAATGAACG
Statistics
Matches: 313, Mismatches: 22, Indels: 28
0.86 0.06 0.08
Matches are distributed among these distances:
46 22 0.07
47 3 0.01
48 15 0.05
49 1 0.00
51 2 0.01
53 3 0.01
55 1 0.00
56 114 0.36
57 147 0.47
58 5 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (57 bp):
CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCA
Found at i:10341 original size:75 final size:76
Alignment explanation
Indices: 10217--10448 Score: 324
Period size: 75 Copynumber: 2.9 Consensus size: 76
10207 GGTGCCACTA
10217 ACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGG
1 ACTTGTGGGCTTTG-AAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGG
10282 GCTTTGAATG-G
65 GCTTTGAATGCG
*
10293 ACTTGTGGGCTTTGAAAGATGCCACTGACTTGTGGACTTTGAAAAGGGTGCCACTGACTTGTGGG
1 ACTTGTGGGCTTTGAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGG
10358 CTTTGAAAGGATGCCACTG
66 CTTTG--A--ATG---C-G
* * *
10377 ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-AAAAGGATGCGACTGACTTATGG
1 ACTTGTGGGCTTTGAAA-GATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGG
10441 GCTTTGAA
65 GCTTTGAA
10449 GAAATGAACG
Statistics
Matches: 141, Mismatches: 5, Indels: 16
0.87 0.03 0.10
Matches are distributed among these distances:
75 55 0.39
76 14 0.10
77 1 0.01
79 3 0.02
80 1 0.01
82 1 0.01
84 44 0.31
85 22 0.16
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.30
Consensus pattern (76 bp):
ACTTGTGGGCTTTGAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGG
CTTTGAATGCG
Found at i:11735 original size:21 final size:22
Alignment explanation
Indices: 11711--11752 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11701 TTGTTCGTTT
11711 TCTTGG-CTTTTTCTTTTTTTA
1 TCTTGGTCTTTTTCTTTTTTTA
*
11732 TCTTGGTTTTTTTCTTTTTTT
1 TCTTGGTCTTTTTCTTTTTTT
11753 GTACGAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.02, C:0.12, G:0.10, T:0.76
Consensus pattern (22 bp):
TCTTGGTCTTTTTCTTTTTTTA
Found at i:26123 original size:20 final size:19
Alignment explanation
Indices: 26086--26132 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
26076 AGCTTTTCAT
26086 CATGCATTTTTACTATGTTC
1 CATGCATTTTTACTATG-TC
26106 CATGCATTTTTAAC-ATGTC
1 CATGCATTTTT-ACTATGTC
26125 CA-GCATTT
1 CATGCATTT
26133 CATTAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.23
19 4 0.15
20 14 0.54
21 2 0.08
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (19 bp):
CATGCATTTTTACTATGTC
Found at i:30648 original size:20 final size:20
Alignment explanation
Indices: 30620--30714 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
30610 TTTTCACAAT
30620 TTGTATCGATACATTGTT-CA
1 TTGTATCGATACATT-TTACA
* *
30640 TTATATCGATACATTTTGCA
1 TTGTATCGATACATTTTACA
*
30660 TTGTATCGATACATTGCT-CA
1 TTGTATCGATACATT-TTACA
30680 TTGTATCGATACATTTTACA
1 TTGTATCGATACATTTTACA
*
30700 ATGTATCGATACATT
1 TTGTATCGATACATT
30715 CAGGCATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
19 3 0.04
20 63 0.94
21 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTTTACA
Found at i:30667 original size:40 final size:40
Alignment explanation
Indices: 30620--30714 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
30610 TTTTCACAAT
* *
30620 TTGTATCGATACATTGTTCATTATATCGATACATTTTGCA
1 TTGTATCGATACATTGCTCATTATATCGATACATTTTACA
*
30660 TTGTATCGATACATTGCTCATTGTATCGATACATTTTACA
1 TTGTATCGATACATTGCTCATTATATCGATACATTTTACA
*
30700 ATGTATCGATACATT
1 TTGTATCGATACATT
30715 CAGGCATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (40 bp):
TTGTATCGATACATTGCTCATTATATCGATACATTTTACA
Found at i:33184 original size:51 final size:51
Alignment explanation
Indices: 33041--33184 Score: 177
Period size: 50 Copynumber: 2.8 Consensus size: 51
33031 ATCCCAGCTC
* **
33041 TATTTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACTCTGATTT
1 TATTTTCAAAACATCAATTTTTCACAATCGGGGATACTCCAACTCTGATTT
* * *
33092 T-TTTT-AAAAGCATCGATTTATCGCAATCGGGGATACTCCAACT-TCGATTT
1 TATTTTCAAAA-CATCAATTTTTCACAATCGGGGATACTCCAACTCT-GATTT
* *
33142 TATTTTCAAAACACCAATTTTTCACAATTGGGGATACTCCAAC
1 TATTTTCAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
33185 CCCGGTATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
49 5 0.06
50 38 0.48
51 32 0.41
52 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (51 bp):
TATTTTCAAAACATCAATTTTTCACAATCGGGGATACTCCAACTCTGATTT
Found at i:33290 original size:28 final size:28
Alignment explanation
Indices: 33247--33354 Score: 103
Period size: 28 Copynumber: 3.8 Consensus size: 28
33237 ATTTTTCATA
*
33247 ATCGGGGGTACTCCAACCCTATTATGTC
1 ATCGGGGGTACTCCAACCCCATTATGTC
* *
33275 ATTGGGGGTACTCCAACCCCGTTATGTC
1 ATCGGGGGTACTCCAACCCCATTATGTC
* * * * *
33303 ATCGGGGATACTCTAATCCCGTTATTTC
1 ATCGGGGGTACTCCAACCCCATTATGTC
33331 --CGAGGGGATACTCCAACTCCCATT
1 ATCG-GGGG-TACTCCAAC-CCCATT
33355 TTATTTCTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
26 2 0.03
27 3 0.05
28 55 0.85
29 5 0.08
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (28 bp):
ATCGGGGGTACTCCAACCCCATTATGTC
Found at i:33393 original size:51 final size:51
Alignment explanation
Indices: 33334--33449 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
33324 TTATTTCCGA
* *
33334 GGGGATACTCCAACTCCCATTTTATTTCTAAAATACCAAATTTTC-ACAATC
1 GGGGATACTCCAACTCCAATTTTATTTCTAAAACA-CAAATTTTCTACAATC
* * * *
33385 GGGGATACTCCAACTCTAATTTTATTTTTAAAACACTAATTTTCTATAATC
1 GGGGATACTCCAACTCCAATTTTATTTCTAAAACACAAATTTTCTACAATC
*
33436 AGGGATACTCCAAC
1 GGGGATACTCCAAC
33450 CCTGTTATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 8 0.14
51 49 0.86
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACTCCAATTTTATTTCTAAAACACAAATTTTCTACAATC
Found at i:33468 original size:79 final size:78
Alignment explanation
Indices: 33385--33565 Score: 227
Period size: 78 Copynumber: 2.3 Consensus size: 78
33375 TTTCACAATC
* * * * * *
33385 GGGGATACTCCAACTCTAATTTTATTTTTAAAACACTAATTTTCTATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCAATTTTAGTTTCAAAACACCAATTTTATATAATCA-GGATACTCCAAC
*
33450 CCTGTTATTTCCGA
65 CCTATTATTTCCGA
* * *
33464 GGGGATACTCCAACCCCGATTTTAGTTTCAAAATACCGATTTTATATAATCAGGATACTCCAACC
1 GGGGATACTCCAACCCCAATTTTAGTTTCAAAACACCAATTTTATATAATCAGGATACTCCAACC
* *
33529 CTATTTTTTCTGA
66 CTATTATTTCCGA
* *
33542 GGGGATACTTCAACCCCGATTTTA
1 GGGGATACTCCAACCCCAATTTTA
33566 CTACCAAAAC
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 46 0.52
79 43 0.48
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (78 bp):
GGGGATACTCCAACCCCAATTTTAGTTTCAAAACACCAATTTTATATAATCAGGATACTCCAACC
CTATTATTTCCGA
Found at i:33574 original size:78 final size:78
Alignment explanation
Indices: 33414--33602 Score: 234
Period size: 78 Copynumber: 2.4 Consensus size: 78
33404 TTTTATTTTT
** *
33414 AAAACACTAATTTTCTATAATCAGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACC
1 AAAACACCGATTTTCTATAATCA-GGATACTCCAACCCTATTATTTCCGAGGGGATACTCCAACC
* **
33479 CCGATTTTAGTTTC
65 CCGATTTTACTACC
* * * * *
33493 AAAATACCGATTTTATATAATCAGGATACTCCAACCCTATTTTTTCTGAGGGGATACTTCAACCC
1 AAAACACCGATTTTCTATAATCAGGATACTCCAACCCTATTATTTCCGAGGGGATACTCCAACCC
33558 CGATTTTACTACC
66 CGATTTTACTACC
* * *
33571 AAAACATCGATTTTCCATAATCGGGGATACTC
1 AAAACACCGATTTTCTATAATC-AGGATACTC
33603 TAGCCCCGTT
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 66 0.71
79 27 0.29
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (78 bp):
AAAACACCGATTTTCTATAATCAGGATACTCCAACCCTATTATTTCCGAGGGGATACTCCAACCC
CGATTTTACTACC
Found at i:44926 original size:20 final size:20
Alignment explanation
Indices: 44901--44953 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
44891 GTTACAAGCT
44901 ATGTATCGATACATT-T-CTTC
1 ATGTATCGATACATTGTAC--C
44921 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
44941 ATGTATCGATACA
1 ATGTATCGATACA
44954 AATAGTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:45028 original size:19 final size:19
Alignment explanation
Indices: 44983--45056 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
44973 CTGCCAGTTT
**
44983 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
45004 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
45023 CATGTATCGATACAAAGCAG
1 CATGTATCGATACAATG-AA
*
45043 CATGTATCAATACA
1 CATGTATCGATACA
45057 TCTGGGTGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
19 18 0.38
20 14 0.30
21 15 0.32
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:54640 original size:20 final size:21
Alignment explanation
Indices: 54611--54651 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
54601 TGTTTTTGAA
54611 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
54630 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
54652 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:54801 original size:13 final size:13
Alignment explanation
Indices: 54783--54821 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
54773 ATAATCCCAC
*
54783 TGTATCGATACAG
1 TGTATCGATACAA
54796 TGTATCGATACAA
1 TGTATCGATACAA
54809 TGTATCGATACAA
1 TGTATCGATACAA
54822 ATAATGCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:61025 original size:13 final size:13
Alignment explanation
Indices: 61007--61031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60997 CATTTTATGG
61007 TGTATCGATACAA
1 TGTATCGATACAA
61020 TGTATCGATACA
1 TGTATCGATACA
61032 TACTATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:61803 original size:13 final size:13
Alignment explanation
Indices: 61785--61810 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61775 CAATTTTTTG
61785 TGTATCGATACAT
1 TGTATCGATACAT
61798 TGTATCGATACAT
1 TGTATCGATACAT
61811 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:61875 original size:21 final size:21
Alignment explanation
Indices: 61849--61924 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
61839 CTGCCAAGAA
61849 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTT
*****
61870 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTT
61890 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTT
61911 ATGTATCGATACAT
1 ATGTATCGATACAT
61925 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTT
Found at i:61895 original size:20 final size:20
Alignment explanation
Indices: 61870--61942 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
61860 CATCTTTTTT
61870 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*****
61890 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TGCAAC
61911 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
61931 ATGTATCGATAC
1 ATGTATCGATAC
61943 TTTGAATTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:61906 original size:41 final size:41
Alignment explanation
Indices: 61849--61942 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
61839 CTGCCAAGAA
61849 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
61890 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
61931 ATGTATCGATAC
1 ATGTATCGATAC
61943 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
Found at i:62544 original size:16 final size:16
Alignment explanation
Indices: 62523--62554 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
62513 CCTTAATAAG
62523 GTAATTCACGCATTCT
1 GTAATTCACGCATTCT
62539 GTAATTCACGCATTCT
1 GTAATTCACGCATTCT
62555 CTCCTTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (16 bp):
GTAATTCACGCATTCT
Found at i:64422 original size:13 final size:13
Alignment explanation
Indices: 64404--64440 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
64394 TAATCACCCA
64404 GTATCGATACAGT
1 GTATCGATACAGT
*
64417 GTATCGATACATT
1 GTATCGATACAGT
64430 GTATCGATACA
1 GTATCGATACA
64441 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (13 bp):
GTATCGATACAGT
Found at i:64454 original size:20 final size:20
Alignment explanation
Indices: 64429--64506 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
64419 ATCGATACAT
64429 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
64449 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
*
64474 TGTATCGATACACAA-AAACA
1 TGTATCGATACA-AAGAAAAA
64494 TGTATCGATACAA
1 TGTATCGATACAA
64507 TTTGGTCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
19 1 0.02
20 30 0.62
25 16 0.33
26 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:66539 original size:15 final size:15
Alignment explanation
Indices: 66519--66549 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
66509 ATTTCGTTTG
*
66519 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
66534 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
66549 G
1 G
66550 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Done.