Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3204
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: 80092
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5085 original size:40 final size:40
Alignment explanation
Indices: 5037--5201 Score: 214
Period size: 40 Copynumber: 4.2 Consensus size: 40
5027 GGACTAAGAT
5037 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
5077 CCGAAGGCATTTGTGCTAGTTA-TATATCCGGGCTAAG--
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
*
5114 CCGAAGGCATTTGTG-TAGTTACTATTATCTGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTA-TATCCGGGCTAAGTC
* * * * *
5154 TCGAAGGCATTTTGTGCAGAGTTGCTATAT-CAGGCTAAATC
1 CCGAAGGCA-TTTGTGC-TAGTTACTATATCCGGGCTAAGTC
5195 CCGAAGG
1 CCGAAGG
5202 TACTTGGGTT
Statistics
Matches: 110, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
36 6 0.05
37 17 0.15
38 12 0.11
39 15 0.14
40 30 0.27
41 20 0.18
42 3 0.03
43 7 0.06
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
Found at i:6306 original size:22 final size:23
Alignment explanation
Indices: 6278--6320 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
6268 AAAGCTCTGA
6278 CAGGGAGAT-TCTAAGTCGTATG
1 CAGGGAGATATCTAAGTCGTATG
6300 CAGGGAGATATCTAAGTCGTA
1 CAGGGAGATATCTAAGTCGTA
6321 AAATGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (23 bp):
CAGGGAGATATCTAAGTCGTATG
Found at i:12115 original size:24 final size:25
Alignment explanation
Indices: 12053--12130 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 25
12043 CATAAAATTC
12053 CATAGAAACATTTACCTAACCCATTAT
1 CATAGAAA-ATTTACCTAA-CCATTAT
* * *
12080 CATTGGACATTTACCTAA-CATTAT
1 CATAGAAAATTTACCTAACCATTAT
*
12104 CATAGCAAATTTA-CTGAACCATT-T
1 CATAGAAAATTTACCT-AACCATTAT
12128 CAT
1 CAT
12131 GGATACATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
23 2 0.05
24 22 0.51
25 4 0.09
26 10 0.23
27 5 0.12
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.33
Consensus pattern (25 bp):
CATAGAAAATTTACCTAACCATTAT
Found at i:13174 original size:29 final size:27
Alignment explanation
Indices: 13132--13219 Score: 99
Period size: 26 Copynumber: 3.2 Consensus size: 27
13122 GAGAAACGTC
*
13132 CTGGTGGCTATGCACAAATAATCTGATTT
1 CTGGTGGCTCTGCACAAAT-ATCTG-TTT
* *
13161 CTGGTGGCTCTGCACATATATCTG-TC
1 CTGGTGGCTCTGCACAAATATCTGTTT
*
13187 CTGGTGGCTCTGC-CACAATATCTGTAT
1 CTGGTGGCTCTGCACA-AATATCTGTTT
13214 CTGGTG
1 CTGGTG
13220 ACTTCGTCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
25 2 0.04
26 21 0.41
27 6 0.12
28 5 0.10
29 17 0.33
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCACAAATATCTGTTT
Found at i:13217 original size:27 final size:25
Alignment explanation
Indices: 13132--13237 Score: 97
Period size: 27 Copynumber: 3.9 Consensus size: 25
13122 GAGAAACGTC
*
13132 CTGGTGGCTATGCACAAATAATCTGATTT
1 CTGGTGGCTCTGCAC-AAT-ATCTG--TT
*
13161 CTGGTGGCTCTGCACATATATCTGTC
1 CTGGTGGCTCTGCACA-ATATCTGTT
13187 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTG-CACAATATCTGT-T
*
13214 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-G-CACAATATCTG
13238 GTAGCCTCGC
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
26 22 0.32
27 24 0.35
28 6 0.09
29 16 0.24
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.34
Consensus pattern (25 bp):
CTGGTGGCTCTGCACAATATCTGTT
Found at i:29904 original size:40 final size:40
Alignment explanation
Indices: 29849--29933 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
29839 AACAAGTCTT
29849 AATAGATATATCAATTCACTATTAGCATTATGAATACAAA
1 AATAGATATATCAATTCACTATTAGCATTATGAATACAAA
* *
29889 AATAGATATATCAATTCATTATTAGCATTATGAATACAGA
1 AATAGATATATCAATTCACTATTAGCATTATGAATACAAA
29929 AATAG
1 AATAG
29934 TGCTAACGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (40 bp):
AATAGATATATCAATTCACTATTAGCATTATGAATACAAA
Found at i:31804 original size:18 final size:18
Alignment explanation
Indices: 31781--31827 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
31771 TCGTTGCGTT
*
31781 ATTTTGAAAACAATTATC
1 ATTTTGGAAACAATTATC
31799 ATTTTGGAAACAATTATC
1 ATTTTGGAAACAATTATC
31817 ATTTTGGAAAC
1 ATTTTGGAAAC
31828 GCGCCCTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
ATTTTGGAAACAATTATC
Found at i:32320 original size:30 final size:31
Alignment explanation
Indices: 32244--32326 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
32234 TCAGTTTCGA
32244 CATAT-ACTAGGCCGAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
*
32274 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
32305 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTAGGCCGAAGCCTTT
32327 ACTGTAAGCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 18 0.35
31 33 0.65
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTTCATAAAT
Found at i:32574 original size:25 final size:25
Alignment explanation
Indices: 32546--32615 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
32536 CTCTTTTAAT
32546 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
32571 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
32596 AACTAGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
32616 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 37 0.90
26 4 0.10
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:33573 original size:27 final size:27
Alignment explanation
Indices: 33547--33675 Score: 120
Period size: 27 Copynumber: 4.7 Consensus size: 27
33537 ATCTACAAAC
*
33547 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCAGTAATTTTGTAAAT
*
33574 CAATGGTATTTCTA-TAATTTT-TGAAAGT
1 CAAGGGTATTTC-AGTAATTTTGT-AAA-T
33602 CAAGGGTATTTCTA-TAATTTTGTAAAT
1 CAAGGGTATTTC-AGTAATTTTGTAAAT
* ** **
33629 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTGTAAAT
**
33656 TGAGGGTATTTCAGTAATTT
1 CAAGGGTATTTCAGTAATTT
33676 CACAAACCAG
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.01
27 58 0.69
28 24 0.29
29 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.43
Consensus pattern (27 bp):
CAAGGGTATTTCAGTAATTTTGTAAAT
Found at i:33717 original size:54 final size:54
Alignment explanation
Indices: 33540--33720 Score: 195
Period size: 54 Copynumber: 3.3 Consensus size: 54
33530 TTGGTAAATC
*
33540 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTT
1 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAGTGGTATTT-TGATAATTT
** * * * *
33594 TTGAAAGTCAAGGGTATTTCTA-TAATTTTGTAAATCAGGGGTATTTTGGTAATTT
1 TACAAA-CCAAGGGTATTTC-AGTAATTTTGTAAACCAGTGGTATTTTGATAATTT
*** ***
33649 TACAAATTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTTTGATAATTT
1 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAGTGGTATTTTGATAATTT
*
33703 TACAAACCAGGGGTATTT
1 TACAAACCAAGGGTATTT
33721 TGGTAATTCT
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
53 1 0.01
54 57 0.56
55 43 0.42
56 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (54 bp):
TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAGTGGTATTTTGATAATTT
Found at i:33721 original size:27 final size:27
Alignment explanation
Indices: 33605--33728 Score: 110
Period size: 27 Copynumber: 4.6 Consensus size: 27
33595 TGAAAGTCAA
** *
33605 GGGTATTTCT-ATAATTTTGTAAATCAG
1 GGGTATTT-TGATAATTTTACAAACCAG
* **
33632 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTGATAATTTTACAAACCAG
* *
33658 AGGGTA-TTTCAGTAATTTCACAAACCAG
1 -GGGTATTTTGA-TAATTTTACAAACCAG
*
33686 TGGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGATAATTTTACAAACCAG
*
33713 GGGTATTTTGGTAATT
1 GGGTATTTTGATAATT
33729 CTATCCTATA
Statistics
Matches: 77, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
26 5 0.06
27 67 0.87
28 5 0.06
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGATAATTTTACAAACCAG
Found at i:33721 original size:81 final size:81
Alignment explanation
Indices: 33606--33761 Score: 208
Period size: 81 Copynumber: 1.9 Consensus size: 81
33596 GAAAGTCAAG
** * * *
33606 GGTATTTCTATAATTTTGTAAATCAGGGGTATTTTGGTAATTTTA-CAAATTGAGGGTATTTCAG
1 GGTATTTCTATAATTTTACAAACCAGGGGTATTTTGGTAATTCTATCAAATAG-GGGTATTTCAG
33670 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
** *
33687 GGTATTT-TGATAATTTTACAAACCAGGGGTATTTTGGTAATTCTATCCTATAGGGGTATTTTAG
1 GGTATTTCT-ATAATTTTACAAACCAGGGGTATTTTGGTAATTCTATCAAATAGGGGTATTTCAG
33751 TAATTTCACAA
65 TAATTTCACAA
33762 TCAAGGGTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
80 1 0.02
81 60 0.92
82 4 0.06
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (81 bp):
GGTATTTCTATAATTTTACAAACCAGGGGTATTTTGGTAATTCTATCAAATAGGGGTATTTCAGT
AATTTCACAAACCAGT
Found at i:33768 original size:27 final size:27
Alignment explanation
Indices: 33626--33768 Score: 82
Period size: 27 Copynumber: 5.3 Consensus size: 27
33616 TAATTTTGTA
* *
33626 AATC-AGGGGTATTTTGGTAATTTTAC
1 AATCAAGGGGTATTTTAGTAATTTCAC
** *
33652 AAATTGA-GGGTATTTCAGTAATTTCAC
1 -AATCAAGGGGTATTTTAGTAATTTCAC
* * * *
33679 AAACCAGTGGTATTTT-GATAATTTTAC
1 AATCAAGGGGTATTTTAG-TAATTTCAC
* * *
33706 AAACCAGGGGTATTTTGGTAA-TT--C
1 AATCAAGGGGTATTTTAGTAATTTCAC
*
33730 TATCCTATAGGGGTATTTTAGTAATTTCAC
1 AAT-C-A-AGGGGTATTTTAGTAATTTCAC
33760 AATCAAGGG
1 AATCAAGGG
33769 TAAAACGGTA
Statistics
Matches: 90, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
24 2 0.02
25 1 0.01
26 6 0.07
27 72 0.80
28 5 0.06
29 1 0.01
30 3 0.03
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (27 bp):
AATCAAGGGGTATTTTAGTAATTTCAC
Found at i:33798 original size:27 final size:27
Alignment explanation
Indices: 33760--33851 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
33750 GTAATTTCAC
*
33760 AATCAAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
33787 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
* * *
33814 AATCGAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
33841 AATCGAGGGTA
1 AATCGAGGGTA
33852 CTTTGGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:36282 original size:30 final size:31
Alignment explanation
Indices: 36201--36292 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
36191 TCAGTCTCGA
36201 CATAT-ACTAGGCCGAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
*
36231 CATATCACTAGGCCAAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
* *
36262 CATATCACT-GGTCGAAGCCTTTACTATAAAT
1 CATATCACTAGGCCGAAGCCTTTTC-ATAAAT
36293 GGTATGGCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
30 17 0.30
31 39 0.70
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTTCATAAAT
Found at i:36554 original size:25 final size:26
Alignment explanation
Indices: 36503--36572 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 26
36493 CTCTTTTAAT
36503 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTCTGATA
* *
36528 AATTGGGGCAAAGCCCTTTTC-GGTA
1 AACTGGGGCAAAGCCCTTTTCTGATA
* *
36553 AACTAGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
36573 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 35 0.90
26 4 0.10
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (26 bp):
AACTGGGGCAAAGCCCTTTTCTGATA
Found at i:37386 original size:27 final size:27
Alignment explanation
Indices: 37356--37420 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
37346 GGGCATATTC
37356 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
** * *
37383 GTCACATTACCCTACAAGGGCTTTATG
1 GTCATTTTACCATACAAGGGCTTTACG
*
37410 GTCTTTTTACC
1 GTCATTTTACC
37421 TATTAGGGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:37540 original size:28 final size:27
Alignment explanation
Indices: 37478--37570 Score: 118
Period size: 27 Copynumber: 3.4 Consensus size: 27
37468 ATCTACAAAC
*
37478 CAAGGGTATTTC-AGTAATTTTGTAAAC
1 CAAGGGTATTTCTA-TAATTTTGTAAAT
*
37505 CAATGGTATTTCTATAATTTT-TGAAAGT
1 CAAGGGTATTTCTATAATTTTGT-AAA-T
37533 CAAGGGTATTTCTATAATTTTGTAAAT
1 CAAGGGTATTTCTATAATTTTGTAAAT
*
37560 CAGGGGTATTT
1 CAAGGGTATTT
37571 TGGTAATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.02
27 32 0.55
28 24 0.41
29 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (27 bp):
CAAGGGTATTTCTATAATTTTGTAAAT
Found at i:37577 original size:27 final size:27
Alignment explanation
Indices: 37547--37659 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 27
37537 GGTATTTCTA
**
37547 TAATTTTGTAAATCAGGGGTATTTTGG
1 TAATTTTACAAATCAGGGGTATTTTGG
* *
37574 TAATTTTACAAAT-TGAGGGTATTTCGG
1 TAATTTTACAAATCAG-GGGTATTTTGG
* * *
37601 TAATTTCACAAACCAGTGGTATTTTGG
1 TAATTTTACAAATCAGGGGTATTTTGG
*
37628 TAATTTTACAAA-CTAGGTGTATTTTGG
1 TAATTTTACAAATC-AGGGGTATTTTGG
37655 TAATT
1 TAATT
37660 CTATCCTACA
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.03
27 68 0.96
28 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
TAATTTTACAAATCAGGGGTATTTTGG
Found at i:37578 original size:55 final size:53
Alignment explanation
Indices: 37459--37639 Score: 175
Period size: 54 Copynumber: 3.3 Consensus size: 53
37449 TACAAAGGTG
* * * *
37459 TTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTATTTCA-TAATTTTGTAAACCAGTGGTA
* ** * *
37513 TTTCT-ATAATTTTTGAAAGTCAAGGGTATTTCTATAATTTTGTAAATCAGGGGTA
1 TTT-TGGTAATTTTACAAA-TCAAGGGTATTTC-ATAATTTTGTAAACCAGTGGTA
** * ***
37568 TTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTATTTC-ATAATTTTGTAAACCAGTGGTA
37622 TTTTGGTAATTTTACAAA
1 TTTTGGTAATTTTACAAA
37640 CTAGGTGTAT
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
54 57 0.56
55 44 0.43
56 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (53 bp):
TTTTGGTAATTTTACAAATCAAGGGTATTTCATAATTTTGTAAACCAGTGGTA
Found at i:37699 original size:27 final size:26
Alignment explanation
Indices: 37557--37699 Score: 94
Period size: 27 Copynumber: 5.3 Consensus size: 26
37547 TAATTTTGTA
*
37557 AATCAGGGGTATTTTGGTAATTTTAC
1 AATCAGGGGTATTTTGGTAATTTCAC
* *
37583 AAAT-TGAGGGTATTTCGGTAATTTCAC
1 -AATCAG-GGGTATTTTGGTAATTTCAC
* * *
37610 AAACCAGTGGTATTTTGGTAATTTTAC
1 -AATCAGGGGTATTTTGGTAATTTCAC
* *
37637 AAACTAGGTGTATTTTGGTAA-TTCTATC
1 AATC-AGGGGTATTTTGGTAATTTC-A-C
* **
37665 -CTACAGGGGTATTTCAGTAATTTCAC
1 AAT-CAGGGGTATTTTGGTAATTTCAC
37691 AATCGAGGG
1 AATC-AGGG
37700 TAAAACGGTA
Statistics
Matches: 89, Mismatches: 18, Indels: 18
0.71 0.14 0.14
Matches are distributed among these distances:
26 8 0.09
27 75 0.84
28 6 0.07
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (26 bp):
AATCAGGGGTATTTTGGTAATTTCAC
Found at i:37725 original size:27 final size:26
Alignment explanation
Indices: 37691--37782 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 26
37681 GTAATTTCAC
37691 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAA-GGTAATTTTGTA
*
37718 AA-CTGAGGGTAAAATGGTTATTTTGTA
1 AATC-GAGGGTAAAA-GGTAATTTTGTA
* *
37745 AATCGAGGGTAAAAGGATAATTCTATA
1 AATCGAGGGTAAAAGG-TAATTTTGTA
*
37772 AATCAAGGGTA
1 AATCGAGGGTA
37783 CTTTGGTAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.05
27 52 0.93
28 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (26 bp):
AATCGAGGGTAAAAGGTAATTTTGTA
Found at i:52320 original size:40 final size:40
Alignment explanation
Indices: 52272--52435 Score: 262
Period size: 40 Copynumber: 4.2 Consensus size: 40
52262 GGACTAAGAT
52272 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
52312 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAG--
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
*
52350 CCGAAGGCATTTGTGCTAGTTACTATATCTGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
* * * *
52390 TCGAAGGCATTTGTGCAAGTTGCTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
52429 CCGAAGG
1 CCGAAGG
52436 TACTTGGGTT
Statistics
Matches: 115, Mismatches: 7, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
38 37 0.32
39 14 0.12
40 64 0.56
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
Found at i:52401 original size:78 final size:77
Alignment explanation
Indices: 52272--52425 Score: 263
Period size: 78 Copynumber: 2.0 Consensus size: 77
52262 GGACTAAGAT
*
52272 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTA
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA
52337 TATCCGGGCTAAG
66 TATCC-GGCTAAG
* * *
52350 CCGAAGGCATTTGTGCTAGTTACTATATCTGGGCTAAGTCTCGAAGGCATTTGTGCAAGTTGCTA
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA
52415 TATCCGGCTAA
66 TATCCGGCTAA
52426 ATCCCGAAGG
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 6 0.08
78 66 0.92
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA
TATCCGGCTAAG
Found at i:53536 original size:18 final size:18
Alignment explanation
Indices: 53513--53547 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
53503 GTACAGGGAG
53513 ATATCTAAGTCGTAATGC
1 ATATCTAAGTCGTAATGC
53531 ATATCTAAGTCGTAATG
1 ATATCTAAGTCGTAATG
53548 GGTCAGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
ATATCTAAGTCGTAATGC
Found at i:60485 original size:77 final size:78
Alignment explanation
Indices: 60355--60530 Score: 284
Period size: 77 Copynumber: 2.2 Consensus size: 78
60345 TCGGATGATA
60355 ACCGGACTAAGATCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
1 ACCGGACTAAG-TCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
*
60420 GTGCTAGTTACTAT
65 GTGCGAGTTACTAT
60434 ACCGGACTAAGTCCGAAGGCATTTGTGCTAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 ACCGGACTAAGTCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
60498 TGCGAGTTGCTAT
66 TGCGAGTTACTAT
*
60511 ATCCGG-CTAAATCCCGAAGG
1 A-CCGGACTAAGT-CCGAAGG
60531 TACTTGGGTT
Statistics
Matches: 92, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
77 50 0.54
78 31 0.34
79 11 0.12
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.27
Consensus pattern (78 bp):
ACCGGACTAAGTCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTAT
Found at i:60500 original size:39 final size:40
Alignment explanation
Indices: 60368--60530 Score: 262
Period size: 39 Copynumber: 4.2 Consensus size: 40
60358 GGACTAAGAT
60368 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
*
60408 CCGAAGGCATTTGTGCTAGTTACTATA-CCGGACTAAGT-
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
60446 CCGAAGGCATTTGTGCTAG-TACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
* * *
60485 CCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
60524 CCGAAGG
1 CCGAAGG
60531 TACTTGGGTT
Statistics
Matches: 115, Mismatches: 5, Indels: 7
0.91 0.04 0.06
Matches are distributed among these distances:
37 7 0.06
38 29 0.25
39 43 0.37
40 36 0.31
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
Found at i:72002 original size:22 final size:22
Alignment explanation
Indices: 71959--72012 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
71949 TAGCCCATGC
* *
71959 ATCACCCAAATTCATTGTCTAT
1 ATCACCCAAAATCATTGGCTAT
* *
71981 ATCACGCAAAATCTTTGGCTAT
1 ATCACCCAAAATCATTGGCTAT
* *
72003 TTCCCCCAAA
1 ATCACCCAAA
72013 GTTCCTTTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.31
Consensus pattern (22 bp):
ATCACCCAAAATCATTGGCTAT
Found at i:75671 original size:95 final size:90
Alignment explanation
Indices: 75488--75672 Score: 230
Period size: 95 Copynumber: 2.0 Consensus size: 90
75478 ATGTAATAAA
* * *
75488 ACTTAAAAACATCCACTTACCCAAGATTTTAAGAAATCCACACCAATACGTTAGGCACGATGCTC
1 ACTTAAAAACATCCACTTACCCAAGATTTTAAGAAATCAACACCAATACGTTAGGCACAATCCTC
*
75553 AAAATCCCAACTCGGAATATTCCTT
66 AAAACCCCAACTCGGAATATTCCTT
* *
75578 ACTTAAAAGAACATCCAC-TATCCAAGA-TTTAAGAAATCAACACCCAATACGTTAGGGCCATAA
1 ACTT-AAA-AACATCCACTTACCCAAGATTTTAAGAAATCAACA-CCAATACGTTA-GG-CACAA
*
75641 TTCCTTCAAAACCCCAACTCGGAATGTTCCTT
61 -TCC-TCAAAACCCCAACTCGGAATATTCCTT
75673 CATTATTTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
90 18 0.22
91 22 0.27
92 11 0.14
93 3 0.04
94 2 0.02
95 25 0.31
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (90 bp):
ACTTAAAAACATCCACTTACCCAAGATTTTAAGAAATCAACACCAATACGTTAGGCACAATCCTC
AAAACCCCAACTCGGAATATTCCTT
Done.