Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3673
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: 17638
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1934 original size:12 final size:12
Alignment explanation
Indices: 1913--1947 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1903 ATGGATATGC
1913 AATG-ATGAATG
1 AATGCATGAATG
1924 AATGCATGAATG
1 AATGCATGAATG
1936 AATGCATGAATG
1 AATGCATGAATG
1948 TCAAATGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.26
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:3502 original size:23 final size:23
Alignment explanation
Indices: 3471--3530 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
3461 TAATGATGTG
3471 AATAATAAAATAT-ATAAATATAA
1 AATAATAAAATATCA-AAATATAA
* *
3494 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATA-TAA
3518 AATAATAATAATA
1 AATAATAA-AATA
3531 ATATGACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 17 0.55
24 10 0.32
25 4 0.13
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
AATAATAAAATATCAAAATATAA
Found at i:3511 original size:8 final size:7
Alignment explanation
Indices: 3475--3514 Score: 53
Period size: 8 Copynumber: 5.3 Consensus size: 7
3465 GATGTGAATA
3475 ATAAAAT
1 ATAAAAT
3482 ATATAAAT
1 ATA-AAAT
3490 ATAAAAT
1 ATAAAAT
3497 ATTAAAAT
1 A-TAAAAT
3505 ATCAAAAT
1 AT-AAAAT
3513 AT
1 AT
3515 TAGAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 9 0.30
8 21 0.70
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (7 bp):
ATAAAAT
Found at i:3513 original size:16 final size:15
Alignment explanation
Indices: 3475--3521 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
3465 GATGTGAATA
3475 ATAAAATA-TATAAAT
1 ATAAAATATTA-AAAT
3490 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
3505 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
3521 A
1 A
3522 ATAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:3521 original size:8 final size:8
Alignment explanation
Indices: 3471--3521 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
3461 TAATGATGTG
*
3471 AATAATAA
1 AATATTAA
3479 AATA-TATA
1 AATATTA-A
3487 AATA-TAA
1 AATATTAA
3494 AATATTAA
1 AATATTAA
*
3502 AATATCAA
1 AATATTAA
*
3510 AATATTAG
1 AATATTAA
3518 AATA
1 AATA
3522 ATAATAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
7 7 0.18
8 31 0.82
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:3548 original size:18 final size:17
Alignment explanation
Indices: 3521--3564 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3511 ATATTAGAAT
* *
3521 AATAATAATAATATGACA
1 AATAAAAATAAAAT-ACA
*
3539 AATAAAAATAAAATAGA
1 AATAAAAATAAAATACA
3556 AATAAAAAT
1 AATAAAAAT
3565 GTACATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (17 bp):
AATAAAAATAAAATACA
Found at i:3721 original size:22 final size:24
Alignment explanation
Indices: 3669--3722 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
3659 ATAAAAAATG
3669 TACATAATATAGTGTTAAAAATACA
1 TACATAATATAG-GTTAAAAATACA
* *
3694 TACATAATATA-GTT-AAGATATA
1 TACATAATATAGGTTAAAAATACA
3716 TACATAA
1 TACATAA
3723 GATAACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 13 0.48
23 3 0.11
25 11 0.41
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (24 bp):
TACATAATATAGGTTAAAAATACA
Found at i:3751 original size:14 final size:14
Alignment explanation
Indices: 3732--3795 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 14
3722 AGATAACATG
3732 TAAAAATATATATA
1 TAAAAATATATATA
3746 TAAAAATAATATAATA
1 TAAAAAT-ATAT-ATA
* *
3762 TTAAAGATATATACA
1 -TAAAAATATATATA
3777 TAAAATAGTATAATATA
1 TAAAA-A-TAT-ATATA
3794 TA
1 TA
3796 TAAGTAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.28
15 7 0.17
16 10 0.25
17 12 0.30
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (14 bp):
TAAAAATATATATA
Found at i:3780 original size:31 final size:30
Alignment explanation
Indices: 3732--3792 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3722 AGATAACATG
*
3732 TAAAAATATATATATAAAAATAATATAATAT
1 TAAAAATATATACAT-AAAATAATATAATAT
* *
3763 TAAAGATATATACATAAAATAGTATAATAT
1 TAAAAATATATACATAAAATAATATAATAT
3793 ATATAAGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (30 bp):
TAAAAATATATACATAAAATAATATAATAT
Found at i:3864 original size:24 final size:23
Alignment explanation
Indices: 3750--3871 Score: 71
Period size: 24 Copynumber: 5.3 Consensus size: 23
3740 TATATATAAA
3750 AATAATATAATATT-AAAGATAT
1 AATAATATAATATTAAAAGATAT
* * *
3772 -ATACATAAAATAGTATAATATATAT
1 AATA-ATATAATA-T-TAAAAGATAT
*
3797 AAGTAATATAGA-ATTTAAA-ATAT
1 AA-TAATATA-ATATTAAAAGATAT
*
3820 ACCT-A-AT-ATATTAAAAGATAT
1 A-ATAATATAATATTAAAAGATAT
3841 ATATAATATAATATTAAGAA-ATAT
1 A-ATAATATAATATTAA-AAGATAT
3865 AATAATA
1 AATAATA
3872 ACAAAAAGGA
Statistics
Matches: 76, Mismatches: 10, Indels: 27
0.67 0.09 0.24
Matches are distributed among these distances:
19 1 0.01
20 6 0.08
21 11 0.14
22 9 0.12
23 15 0.20
24 16 0.21
25 9 0.12
26 6 0.08
27 3 0.04
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.35
Consensus pattern (23 bp):
AATAATATAATATTAAAAGATAT
Found at i:3871 original size:44 final size:46
Alignment explanation
Indices: 3750--3871 Score: 126
Period size: 46 Copynumber: 2.7 Consensus size: 46
3740 TATATATAAA
* * * *
3750 AATAATATAATATTAAAGATATATACATAAAATAGTATAATATATAT
1 AATAATATAATATT-AAGAAATATACATAATATAGTAAAAGATATAT
* * *
3797 AAGTAATATAGA-ATTTA-AAATATACCTAATATATTAAAAGATATAT
1 AA-TAATATA-ATATTAAGAAATATACATAATATAGTAAAAGATATAT
3843 -ATAATATAATATTAAGAAATATA-ATAATA
1 AATAATATAATATTAAGAAATATACATAATA
3872 ACAAAAAGGA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
43 1 0.02
44 16 0.26
45 8 0.13
46 23 0.37
47 3 0.05
48 10 0.16
49 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.35
Consensus pattern (46 bp):
AATAATATAATATTAAGAAATATACATAATATAGTAAAAGATATAT
Found at i:4426 original size:30 final size:30
Alignment explanation
Indices: 4348--4482 Score: 157
Period size: 30 Copynumber: 4.5 Consensus size: 30
4338 TAGGTACAAG
* *
4348 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
4378 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
4408 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
4438 TGGTGGTGGAAAAGGAGTGGCTGGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
4468 TGGTGGTGGAAAAGG
1 TGGTGGTGGAAAAGG
4483 CTAAGATTTA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 2 0.02
30 90 0.98
ACGTcount: A:0.21, C:0.04, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:5274 original size:78 final size:79
Alignment explanation
Indices: 5183--5724 Score: 348
Period size: 84 Copynumber: 6.4 Consensus size: 79
5173 GTTTTTAAAT
*
5183 CAACTCATATTGCGAGAAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAAATTCCTGTT
1 CAACTCATATTGCGAGAAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTT-AATTCCTGTT
5248 TAATTTAT-TTTT-A-
64 TAATTTATATTTTAAG
* * * *
5261 CAACTCATATTGCGAG-AGATGAGTTGAGCCTCGGCTCACATGCTGAGGAATTTTTAATTCCTAT
1 CAACTCATATTGCGAGAAGGTGAGTTGAGCCTCGG---ACACGCTGAGGTATTTTTAATTCCTGT
5325 TTAATTTATACTTTTCAAAAG
63 TTAATTTATA-TTTT---AAG
5346 TCAACTCATATTGCGA-AAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTGAATT-CTGT
1 -CAACTCATATTGCGAGAAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTT-AATTCCTGT
* *
5409 TTAGTTTATATTTTTCAAAAAAAAT
63 TTAATTTATA-TTTT-------AAG
* * * *
5434 CGACTCATATTGCGAG-AGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTCT
1 CAACTCATATTGCGAGAAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTTAATTCCTG--T
* *
5498 TTAATTTCTACTTTTCCAAAAT
63 TTAATTTATA-TTTT----AAG
* * * * *
5520 CAACTTATATTGCGAG-AGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAGTTTCTGT
1 CAACTCATATTGCGAGAAGGTGAGTTGAGCCTCGG---ACACGCTGAGGTATTTTTAATTCCTG-
* * *
5584 TTTTTTAATTTCTGTTTTTCAAAAAT
62 ---TTTAATTTAT-ATTTT----AAG
* * * *
5610 CAACTCATATTGCGAGAA-GTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTT
1 CAACTCATATTGCGAGAAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTTAATTCCTGTTT
** *
5674 TTTTTATATTTTTCAAAAAT
65 AATTTATA-TTTT----AAG
5694 CAACTCATATTGCGAG-AGGTGAGTTGAGCCT
1 CAACTCATATTGCGAGAAGGTGAGTTGAGCCT
5725 TTTAATTCCT
Statistics
Matches: 394, Mismatches: 38, Indels: 58
0.80 0.08 0.12
Matches are distributed among these distances:
76 1 0.00
77 15 0.04
78 33 0.08
79 16 0.04
80 4 0.01
83 1 0.00
84 80 0.20
85 6 0.02
86 69 0.18
87 54 0.14
88 50 0.13
89 13 0.03
90 50 0.13
91 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (79 bp):
CAACTCATATTGCGAGAAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTTAATTCCTGTTTA
ATTTATATTTTAAG
Found at i:5462 original size:173 final size:168
Alignment explanation
Indices: 5179--5724 Score: 555
Period size: 173 Copynumber: 3.2 Consensus size: 168
5169 TTCTGTTTTT
* * *
5179 AAATCAACTCATATTGCGAGAAGGTGAGTTGAGCCTCAAG--ACACGCTGAGGTATTTTTAAATT
1 AAATCAACTCATATTGCGAG-AGGTGAGTTGAGCCTC-GGCCACACGCTGAGGTATTTTCAGATT
*
5242 CCTG-TTTAA-TT-TATTTTT-----A-CAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTC
64 -CTGTTTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG---
* *
5298 ACATGCTGAGG-AATTTTTAATTCCTATTTAATTTATACTTTTCA
125 ACACGCTGAGGTAA-TTTCAATTCCTATTTAATTTATACTTTTCA
* * *
5342 AAAGTCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGG-GACACGCTGAGGTATTTT-TGAATT
1 AAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACGCTGAGGTATTTTCAG-ATT
* *
5405 CTG-TTTAGTTTATATTTTTCAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
64 CTGTTTTAATTTATATTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG
* * *
5469 ACACGCTGAGGTAATTTCAATTTCTGTCTTTAATTTCTACTTTTCCA
125 ACACGCTGAGGTAATTTCAA-TTC-CTATTTAATTTATACTTTT-CA
* * *
5516 AAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAGTTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-CACACGCTGAGGTATTTTCAGATTC
* * * *
5581 TGTTTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGA
65 TG---TTTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGA
* * ** *
5646 CACGCTGAGGTAATTTCAATTTCTGTTTTTTTTATATTTTTCAA
126 CACGCTGAGGTAATTTCAATTCCTATTTAATTTATACTTTTC-A
5690 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5725 TTTAATTCCT
Statistics
Matches: 323, Mismatches: 33, Indels: 43
0.81 0.08 0.11
Matches are distributed among these distances:
162 8 0.02
163 41 0.13
164 23 0.07
171 15 0.05
172 6 0.02
173 80 0.25
174 55 0.17
175 23 0.07
176 58 0.18
179 14 0.04
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (168 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCACACGCTGAGGTATTTTCAGATTCT
GTTTTAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGC
TGAGGTAATTTCAATTCCTATTTAATTTATACTTTTCA
Found at i:5848 original size:141 final size:139
Alignment explanation
Indices: 5586--5920 Score: 471
Period size: 141 Copynumber: 2.4 Consensus size: 139
5576 GTTTCTGTTT
*
5586 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC-TCAAGACACG
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTCAACACACG
* * * * *
5650 CTGAGGTAATTTCAATTTCTGTTTTTTTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTG
66 CTAAGGTAATTTCAATTTCTGTTTTATTCATAGTTTTCAAAAATCAACTCATATTGCGAGAGGTA
5715 AGTTGAGCC
131 AGTTGAGCC
* * *
5724 TTTTAATTCCTGTTTTTTCAAATATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGC-TCAC
1 TTTTAATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT--CAACAC
* *
5788 ATGCTAAGGT-ATTTCCAATTTCTGTTTTAATTCAT-GTTTTCAAAAATTAACTCATATTGCGAG
63 ACGCTAAGGTAATTT-CAATTTCTGTTTT-ATTCATAGTTTTCAAAAATCAACTCATATTGCGAG
5851 AGGTAAGTTGAGCC
126 AGGTAAGTTGAGCC
* * *
5865 TTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTT
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
5921 TTAATTTCTG
Statistics
Matches: 175, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
138 11 0.06
139 41 0.23
140 46 0.26
141 72 0.41
142 5 0.03
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (139 bp):
TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTCAACACACG
CTAAGGTAATTTCAATTTCTGTTTTATTCATAGTTTTCAAAAATCAACTCATATTGCGAGAGGTA
AGTTGAGCC
Found at i:5885 original size:54 final size:55
Alignment explanation
Indices: 5812--5929 Score: 188
Period size: 54 Copynumber: 2.2 Consensus size: 55
5802 CCAATTTCTG
*
5812 TTTTAA-TTC-ATGTTTTCAAAAATTAACTCATATTGCGAGAGGTAAGTTGAGCC
1 TTTTAATTTCTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCC
* *
5865 TTTTAATTTCTAT-TTTTCAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCC
1 TTTTAATTTCTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCC
5919 TTTTAATTTCT
1 TTTTAATTTCT
5930 GTTCATATTG
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
53 6 0.10
54 52 0.87
55 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (55 bp):
TTTTAATTTCTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCC
Found at i:7120 original size:17 final size:16
Alignment explanation
Indices: 7098--7147 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
7088 CCTAAAGGTG
*
7098 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTT-TT
7115 ATTTTACTCTTATTTTT
1 ATTTTA-TCTTATTTTT
*
7132 ATTTTATTTTATTTTT
1 ATTTTATCTTATTTTT
7148 TTCCCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 9 0.30
17 14 0.47
18 7 0.23
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTATCTTATTTTT
Found at i:7203 original size:12 final size:12
Alignment explanation
Indices: 7186--7234 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
7176 TATATACATC
7186 ATAATAAAAAAT
1 ATAATAAAAAAT
*
7198 ATAATAAAATAT
1 ATAATAAAAAAT
*
7210 ATATACAAAAAAT
1 ATA-ATAAAAAAT
*
7223 AT-TTAAAAAAT
1 ATAATAAAAAAT
7234 A
1 A
7235 CCTTTTCCGG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 8 0.26
12 14 0.45
13 9 0.29
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATAAAAAAT
Found at i:7347 original size:11 final size:11
Alignment explanation
Indices: 7331--7365 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
7321 CCCTTCCCCC
7331 CTCCCTTCTCT
1 CTCCCTTCTCT
7342 CTCCCTTCTCT
1 CTCCCTTCTCT
7353 CTTCCC-TCTCT
1 C-TCCCTTCTCT
7364 CT
1 CT
7366 TCTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:8196 original size:22 final size:23
Alignment explanation
Indices: 8168--8249 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 23
8158 AATTTTTTTA
8168 ATATATATTATATGAATA-ATTT
1 ATATATATTATATGAATATATTT
* *
8190 ATATATAATATTATGTATATATTT
1 ATATATATTA-TATGAATATATTT
* *
8214 -TA-ATATTATCAATTATATATCTTT
1 ATATATATTAT--ATGA-ATATATTT
8238 ATACTATATTAT
1 ATA-TATATTAT
8250 TTCTAATACT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
21 1 0.02
22 14 0.30
23 11 0.24
24 11 0.24
25 2 0.04
27 7 0.15
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATATATTATATGAATATATTT
Found at i:8470 original size:26 final size:24
Alignment explanation
Indices: 8420--8477 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
8410 TTCCATGTAC
* *
8420 ATATTTTTATACTATCTTATGTAT
1 ATATTTTTATACTATATTATATAT
*
8444 ATATTTTTAAATACTATATTGTATAT
1 ATATTTTT--ATACTATATTATATAT
8470 ATATTTTT
1 ATATTTTT
8478 TTTTTCTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 8 0.28
26 21 0.72
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (24 bp):
ATATTTTTATACTATATTATATAT
Found at i:11846 original size:15 final size:16
Alignment explanation
Indices: 11826--11859 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11816 ATTCAACAGT
*
11826 TTAATCAT-TAAAATA
1 TTAATCATATAAAAAA
11841 TTAATCATATAAAAAA
1 TTAATCATATAAAAAA
11857 TTA
1 TTA
11860 TGAAAGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAATCATATAAAAAA
Found at i:14066 original size:18 final size:18
Alignment explanation
Indices: 14043--14199 Score: 210
Period size: 18 Copynumber: 8.8 Consensus size: 18
14033 CGTTTACAGT
*
14043 ACTATTCACGTATATGGC
1 ACTATTCACGTATACGGC
* *
14061 ACTATTCACGTATA-TGT
1 ACTATTCACGTATACGGC
*
14078 ACTATTAACGTATACGGC
1 ACTATTCACGTATACGGC
*
14096 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
14114 A-TATTCACGTATATGGC
1 ACTATTCACGTATACGGC
* *
14131 ACTATTCACGTATATGGT
1 ACTATTCACGTATACGGC
*
14149 ACTATTAACGTATACGGC
1 ACTATTCACGTATACGGC
*
14167 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
14185 ACTATTCACGTATAC
1 ACTATTCACGTATAC
14200 AGTAGTTGGG
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
17 29 0.24
18 93 0.76
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:14089 original size:35 final size:36
Alignment explanation
Indices: 14041--14199 Score: 250
Period size: 35 Copynumber: 4.5 Consensus size: 36
14031 ACCGTTTACA
* *
14041 GTACTATTCACGTATATGGCACTATTCACGTATA-T
1 GTACTATTCACGTATACGGCACTATTCACGTATACG
*
14076 GTACTATTAACGTATACGGCACTATTCACGTATACG
1 GTACTATTCACGTATACGGCACTATTCACGTATACG
* *
14112 GTA-TATTCACGTATATGGCACTATTCACGTATATG
1 GTACTATTCACGTATACGGCACTATTCACGTATACG
*
14147 GTACTATTAACGTATACGGCACTATTCACGTATACG
1 GTACTATTCACGTATACGGCACTATTCACGTATACG
14183 GTACTATTCACGTATAC
1 GTACTATTCACGTATAC
14200 AGTAGTTGGG
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
35 64 0.57
36 48 0.43
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (36 bp):
GTACTATTCACGTATACGGCACTATTCACGTATACG
Found at i:14178 original size:71 final size:71
Alignment explanation
Indices: 14041--14198 Score: 300
Period size: 71 Copynumber: 2.2 Consensus size: 71
14031 ACCGTTTACA
14041 GTACTATTCACGTATATGGCACTATTCACGTATATGTACTATTAACGTATACGGCACTATTCACG
1 GTACTATTCACGTATATGGCACTATTCACGTATATGTACTATTAACGTATACGGCACTATTCACG
14106 TATACG
66 TATACG
14112 GTA-TATTCACGTATATGGCACTATTCACGTATATGGTACTATTAACGTATACGGCACTATTCAC
1 GTACTATTCACGTATATGGCACTATTCACGTATAT-GTACTATTAACGTATACGGCACTATTCAC
14176 GTATACG
65 GTATACG
14183 GTACTATTCACGTATA
1 GTACTATTCACGTATA
14199 CAGTAGTTGG
Statistics
Matches: 85, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
70 31 0.36
71 42 0.49
72 12 0.14
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (71 bp):
GTACTATTCACGTATATGGCACTATTCACGTATATGTACTATTAACGTATACGGCACTATTCACG
TATACG
Done.