Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold497
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: 133896
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.32
Warning! 4803 characters in sequence are not A, C, G, or T
Found at i:92 original size:21 final size:21
Alignment explanation
Indices: 61--118 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
51 GTACAGGCTG
*
61 CAGCAAGGGAAGCAGAAGCTA
1 CAGCGAGGGAAGCAGAAGCTA
* * * * *
82 TAGCGATGGAAGTAAAAGCTG
1 CAGCGAGGGAAGCAGAAGCTA
103 CAGCGAGGGAAGCAGA
1 CAGCGAGGGAAGCAGA
119 GCAGCGTCAA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.36, T:0.09
Consensus pattern (21 bp):
CAGCGAGGGAAGCAGAAGCTA
Found at i:480 original size:43 final size:43
Alignment explanation
Indices: 427--568 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 43
417 ATCTGCCAAA
* * * * ***
427 TTTAGTGGCGTTTTTTTAAAAAACGCCACTAAAGGTGTTGGCC
1 TTTAGCGGCGTTTTTTGAAAAAGCGCCACTAAAGATAAGGGCC
* *
470 TTTAGCGGCG-TTTTTGATAAAAGCGCCGCTAAAGATAAGGGTC
1 TTTAGCGGCGTTTTTTGA-AAAAGCGCCACTAAAGATAAGGGCC
* * * * *
513 TTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTC
1 TTTAGCGGCGTTTTTTGAAAAAGCGCCACTAAAGATAAGGGCC
*
556 TTTAGCGGTGTTT
1 TTTAGCGGCGTTT
569 GTGGGGGAAG
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
42 6 0.07
43 71 0.87
44 5 0.06
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTTGAAAAAGCGCCACTAAAGATAAGGGCC
Found at i:816 original size:43 final size:43
Alignment explanation
Indices: 469--805 Score: 388
Period size: 43 Copynumber: 7.8 Consensus size: 43
459 AGGTGTTGGC
* * ** *
469 CTTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGATAAGGGT
1 CTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGT
* * * *
512 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGT
* * ** ** *
555 CTTTAGCGGTGTTTGTGGGGGAAGCGCCGCTAAAGATTTGGTT
1 CTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGT
* * *** *
598 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTACAGATCAGGGT
1 CTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGT
* * *
641 CTTTTGCAGCATTTGTGGGAAAAGCGCCGCTACAGATCAGGGT
1 CTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGT
* * *
684 CTTTTGCAGCGTTTGTGGGAAAAGCACCGCTACAGATCAGGGT
1 CTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGT
*
727 CTTTTGCGGCATTTGTGGGAAAAGCGCCGCTACAA-ATCAGGGT
1 CTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTA-AAGATCAGGGT
*
770 CTTTTGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGA
1 CTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGA
806 CCCTAATCTT
Statistics
Matches: 254, Mismatches: 38, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
42 2 0.01
43 251 0.99
44 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (43 bp):
CTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGT
Found at i:1079 original size:22 final size:21
Alignment explanation
Indices: 1046--1090 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
1036 ATTTGCGGCG
*
1046 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
1067 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
1089 CT
1 CT
1091 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:3764 original size:18 final size:18
Alignment explanation
Indices: 3743--3780 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3733 ATTTGGGTAA
3743 AACCGAAAAAATTCGGTT
1 AACCGAAAAAATTCGGTT
**
3761 AACCGACCAAATTCGGTT
1 AACCGAAAAAATTCGGTT
3779 AA
1 AA
3781 TCGGTCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (18 bp):
AACCGAAAAAATTCGGTT
Found at i:4126 original size:9 final size:9
Alignment explanation
Indices: 4106--4172 Score: 93
Period size: 9 Copynumber: 7.4 Consensus size: 9
4096 GTAGTGATTC
4106 AATTCGGTT
1 AATTCGGTT
4115 AATTCAGG-T
1 AATTC-GGTT
*
4124 AATCCGGTT
1 AATTCGGTT
4133 AATTCGGTT
1 AATTCGGTT
4142 AATTCAGG-T
1 AATTC-GGTT
4151 AATTCGGTT
1 AATTCGGTT
4160 AATTCGGTT
1 AATTCGGTT
4169 AATT
1 AATT
4173 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
8 4 0.08
9 44 0.85
10 4 0.08
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4138 original size:27 final size:27
Alignment explanation
Indices: 4106--4172 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
4096 GTAGTGATTC
4106 AATTCGGTTAATTCAGGTAATCCGGTT
1 AATTCGGTTAATTCAGGTAATCCGGTT
*
4133 AATTCGGTTAATTCAGGTAATTCGGTT
1 AATTCGGTTAATTCAGGTAATCCGGTT
4160 AATTCGGTTAATT
1 AATTCGGTTAATT
4173 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (27 bp):
AATTCGGTTAATTCAGGTAATCCGGTT
Found at i:7553 original size:20 final size:19
Alignment explanation
Indices: 7513--7551 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
7503 TAAATATATT
7513 TTTTATTTTTTTACTTTAAA
1 TTTTATTTTTTTA-TTTAAA
7533 TTTTATTTTTATT-TTTAAA
1 TTTTATTTTT-TTATTTAAA
7552 ATAAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 10 0.56
21 2 0.11
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTTTTTATTTAAA
Found at i:11673 original size:20 final size:21
Alignment explanation
Indices: 11645--11683 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
11635 AATTTTTTTT
*
11645 CTTATAAAT-AAAAAAATTCC
1 CTTAAAAATGAAAAAAATTCC
*
11665 CTTAAAAATGTAAAAAATT
1 CTTAAAAATGAAAAAAATT
11684 AATTAATTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (21 bp):
CTTAAAAATGAAAAAAATTCC
Found at i:18498 original size:19 final size:19
Alignment explanation
Indices: 18457--18501 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
18447 TTGTTTGACA
18457 ATTT-TTTGTATTTTTGCT
1 ATTTCTTTGTATTTTTGCT
*
18475 TTTTCTTTGTATTTTATG-T
1 ATTTCTTTGTATTTT-TGCT
18494 ATTTCTTT
1 ATTTCTTT
18502 TCAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 18 0.78
20 2 0.09
ACGTcount: A:0.11, C:0.07, G:0.09, T:0.73
Consensus pattern (19 bp):
ATTTCTTTGTATTTTTGCT
Found at i:22334 original size:17 final size:17
Alignment explanation
Indices: 22312--22347 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
22302 AGAAATTTGA
* *
22312 ACATACCTATATCGAAC
1 ACATACCAATATCAAAC
22329 ACATACCAATATCAAAC
1 ACATACCAATATCAAAC
22346 AC
1 AC
22348 CTTCTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (17 bp):
ACATACCAATATCAAAC
Found at i:34490 original size:62 final size:60
Alignment explanation
Indices: 34369--34494 Score: 150
Period size: 62 Copynumber: 2.1 Consensus size: 60
34359 TATATTTGTA
* ****
34369 TAAATTATTTTTATATTGTTTCATTTAATAAAATAAAGGTTGTTTTGAATATTTTAATAG
1 TAAATTATTTTTATATTGTTTCATTTAATAAAATAAAGGTTCTTTTGAATAAGGCAATAG
34429 TAAATTATTTTTATATT-TTGTCCTATTTAATAAAATAGAA-GTTCTTTTGAATAAGGCAATAG
1 TAAATTATTTTTATATTGTT-T-C-ATTTAATAAAATA-AAGGTTCTTTTGAATAAGGCAATAG
34491 -AAAT
1 TAAAT
34495 AATGCAACAT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
59 2 0.04
60 18 0.32
61 5 0.09
62 30 0.53
63 2 0.04
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (60 bp):
TAAATTATTTTTATATTGTTTCATTTAATAAAATAAAGGTTCTTTTGAATAAGGCAATAG
Found at i:37857 original size:126 final size:126
Alignment explanation
Indices: 37527--38164 Score: 824
Period size: 126 Copynumber: 5.1 Consensus size: 126
37517 GCAAAGTAGG
** * *
37527 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTGT-AGTAATTTTACTAACAGTGCATC
1 AACTACTGTAGAAAAAGAATGTCCACGTGGGAGCTTTTT-TCAGTAATTTTGCTGACAGTGCATC
*
37591 CTGCTTGAAGCGTTTTTGACAC-A-TTTTT-ATAACCGTCTTCTCAAAATTATTTTTTCA-A
65 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA
* * ** *
37649 GCACTACTGTAGAAAAAGAATGTCTACGTGAAAGCTTTTTTTCAGTAATTTTGCTGGCAGTGCAT
1 -AACTACTGTAGAAAAAGAATGTCCACGTGGGAGC-TTTTTTCAGTAATTTTGCTGACAGTGCAT
* * *
37714 CTTGCTTAAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAATATTATTTTTTTC-GA
64 CCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTA-TTTTTTCAGA
* * * *
37777 AATTACTATAGAAAAAGAGTGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAATGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * * * * * *
37842 TGTTTGAAGCATTTTTTACACTATTTTTTCAGAACCATCTTTTAAAAATTATTTTTTCAGG
66 TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA
* * * *
37903 AACTACTATAGAAAAAAAAAG-CCTACGTGGGAGCTTTTTTCAGTAATTTTACTGACAGTGCATC
1 AACTACTGTAGAAAAAGAATGTCC-ACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * *
37967 CTACTTGAACCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTA-TTTTTCAGG
65 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA
* * *
38028 AACTACTGTAGAAAAAAAATTGTCCACGTGGGAGCTTTTTTCAGTAATTTTGTTGATAGTGCATC
1 AACTACTGTAGAAAAAGAA-TGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * *
38093 CTGCTTGAAGCGTTTTTGACATTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCAGA
65 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA
38155 AACTACTGTA
1 AACTACTGTA
38165 TAAGAAAAAT
Statistics
Matches: 445, Mismatches: 58, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
123 29 0.07
124 45 0.10
125 37 0.08
126 261 0.59
127 65 0.15
128 8 0.02
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (126 bp):
AACTACTGTAGAAAAAGAATGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA
Found at i:38345 original size:34 final size:34
Alignment explanation
Indices: 38273--38358 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
38263 TTTCAAAAAA
*
38273 CTAAACCCTAATTTAATTAATTTTCTTTAAAACT
1 CTAAACCCTAATTTAATTAATTTTCTTTAAAACC
* * *
38307 CTAAACCCTAATTTAATTTA-TTTGTTTAAACCCC
1 CTAAACCCTAATTTAATTAATTTTCTTTAAA-ACC
**
38341 CTAAAATCTAATTTAATT
1 CTAAACCCTAATTTAATT
38359 CTTTTTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 9 0.20
34 36 0.80
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.43
Consensus pattern (34 bp):
CTAAACCCTAATTTAATTAATTTTCTTTAAAACC
Found at i:38914 original size:21 final size:21
Alignment explanation
Indices: 38890--38933 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
38880 AAAGTGCCTG
*
38890 ATTACCTACAAATGCTAAAGC
1 ATTACCAACAAATGCTAAAGC
*
38911 ATTACCAACAAATGCTGAAGC
1 ATTACCAACAAATGCTAAAGC
38932 AT
1 AT
38934 CAAAAGTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (21 bp):
ATTACCAACAAATGCTAAAGC
Found at i:44692 original size:20 final size:20
Alignment explanation
Indices: 44661--44707 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
44651 GTTGTTAAAC
*
44661 ATATTATTTATAAATATTTAT
1 ATATT-TTTATAAATAATTAT
*
44682 ATATTTTTATAATTAATTAT
1 ATATTTTTATAAATAATTAT
44702 A-ATTTT
1 ATATTTT
44708 GTATTATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 14 0.58
21 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTTATAAATAATTAT
Found at i:54898 original size:21 final size:21
Alignment explanation
Indices: 54850--54904 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
54840 CGAATACGCC
*
54850 AACAGAAGCTTG-AA-AGCTG
1 AACAGAAGCTAGTAAGAGCTG
* *
54869 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTAGTAAGAGCTG
*
54890 AACATAAGCTAGTAA
1 AACAGAAGCTAGTAA
54905 AAGTTGATCC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 10 0.34
20 2 0.07
21 17 0.59
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTAGTAAGAGCTG
Found at i:57249 original size:23 final size:23
Alignment explanation
Indices: 57219--57269 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
57209 TTTAAATGTA
57219 AAAAAT-AAAATAACTAAATTTTT
1 AAAAATAAAAATAACT-AATTTTT
57242 AAAAATAAAAATAACTAATTTTT
1 AAAAATAAAAATAACTAATTTTT
57265 AAAAA
1 AAAAA
57270 ATAAGTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAATAAAAATAACTAATTTTT
Found at i:57270 original size:24 final size:25
Alignment explanation
Indices: 57217--57273 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 25
57207 CTTTTAAATG
57217 TAAAAAAT-AAAATAACTAAATTTT
1 TAAAAAATAAAAATAACTAAATTTT
57241 T-AAAAATAAAAATAACT-AATTTT
1 TAAAAAATAAAAATAACTAAATTTT
57264 TAAAAAATAA
1 TAAAAAATAA
57274 GTCAATGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (25 bp):
TAAAAAATAAAAATAACTAAATTTT
Found at i:66354 original size:150 final size:151
Alignment explanation
Indices: 66082--66382 Score: 586
Period size: 150 Copynumber: 2.0 Consensus size: 151
66072 TGTATGTGTT
66082 GGGATACATTAATATTTGTCTAAGAATCCAGTAGTTCGTTTGCTTTGAGTAAGATTAGGTTTGGA
1 GGGATACATTAATATTTGTCTAAGAATCCAGTAGTTCGTTTGCTTTGAGTAAGATTAGGTTTGGA
66147 CAAAGATTTTTTATATTAGAATCCACTTGATTCGAATTTAATTTAAATACTAAAAAATATTTTTA
66 CAAAGATTTTTTATATTAGAATCCACTTGATTCGAATTTAATTTAAATACTAAAAAATATTTTTA
66212 ACATTTAAATTTAATTATAAA
131 ACATTTAAATTTAATTATAAA
66233 GGGATACATTAAT-TTTGTCTAAGAATCCAGTAGTTCGTTTGCTTTGAGTAAGATTAGGTTTGGA
1 GGGATACATTAATATTTGTCTAAGAATCCAGTAGTTCGTTTGCTTTGAGTAAGATTAGGTTTGGA
*
66297 CAAAGATTTTTTATATTAGAATCCACTTGGTTCGAATTTAATTTAAATACTAAAAAATATTTTTA
66 CAAAGATTTTTTATATTAGAATCCACTTGATTCGAATTTAATTTAAATACTAAAAAATATTTTTA
66362 ACATTTAAATTTAATTATAAA
131 ACATTTAAATTTAATTATAAA
66383 AATATATAAA
Statistics
Matches: 149, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
150 136 0.91
151 13 0.09
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (151 bp):
GGGATACATTAATATTTGTCTAAGAATCCAGTAGTTCGTTTGCTTTGAGTAAGATTAGGTTTGGA
CAAAGATTTTTTATATTAGAATCCACTTGATTCGAATTTAATTTAAATACTAAAAAATATTTTTA
ACATTTAAATTTAATTATAAA
Found at i:68864 original size:3 final size:3
Alignment explanation
Indices: 68858--68887 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
68848 GACTTCAAAG
*
68858 ATT ATT ATT ATT ATT ATT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
68888 TGTTTCAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:69608 original size:6 final size:6
Alignment explanation
Indices: 69597--69624 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
69587 TTAGTTTGAT
69597 CCATCA CCATCA CCATCA CCATCA CCAT
1 CCATCA CCATCA CCATCA CCATCA CCAT
69625 TGCCATGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CCATCA
Found at i:85097 original size:31 final size:31
Alignment explanation
Indices: 85037--85105 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
85027 TTATAAAATG
*
85037 GTCACTGAACTATTTGAAAGTATTCATTTAA
1 GTCACTGAACTATTTGAAAATATTCATTTAA
* * *
85068 GTCATTGAACTATTTGAAAATTTTTATTTAA
1 GTCACTGAACTATTTGAAAATATTCATTTAA
*
85099 GCCACTG
1 GTCACTG
85106 GACTGTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (31 bp):
GTCACTGAACTATTTGAAAATATTCATTTAA
Found at i:95808 original size:15 final size:15
Alignment explanation
Indices: 95788--95818 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
95778 GGAGAGAATG
95788 TCACGGGCCGCAGTT
1 TCACGGGCCGCAGTT
95803 TCACGGGCCGCAGTT
1 TCACGGGCCGCAGTT
95818 T
1 T
95819 AAAGCCCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.23
Consensus pattern (15 bp):
TCACGGGCCGCAGTT
Found at i:98036 original size:24 final size:25
Alignment explanation
Indices: 97959--98038 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
97949 AAGCTGTTTC
** * *
97959 GAGCCATATAACGGGAAACTCATGT
1 GAGCCATATAACGGGAAGTTTAAGT
* * * *
97984 GAGTCATGTAATGGGAAGTTT-CGT
1 GAGCCATATAACGGGAAGTTTAAGT
98008 AGAGCCAT-TAACGGGAAGTTTAAGT
1 -GAGCCATATAACGGGAAGTTTAAGT
98033 GAGCCA
1 GAGCCA
98039 ATATTAGGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
24 20 0.47
25 23 0.53
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.24
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGTTTAAGT
Found at i:98107 original size:25 final size:24
Alignment explanation
Indices: 98056--98109 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
98046 GAAGTTCTGG
*
98056 AGAGCCATTAGCGAGAAGCTCATA
1 AGAGCCATTAGCGAGAAGCTCAGA
* * *
98080 AGAGCCATTTATCGGGAAGCTCCGA
1 AGAGCCA-TTAGCGAGAAGCTCAGA
98105 AGAGC
1 AGAGC
98110 AATAAACATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (24 bp):
AGAGCCATTAGCGAGAAGCTCAGA
Found at i:112325 original size:17 final size:16
Alignment explanation
Indices: 112305--112338 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
112295 AATAAAACAC
112305 TAAAAATATATATTTTT
1 TAAAAATATA-ATTTTT
*
112322 TAAAAATTTAATTTTT
1 TAAAAATATAATTTTT
112338 T
1 T
112339 TTAAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAAAATATAATTTTT
Found at i:113382 original size:29 final size:29
Alignment explanation
Indices: 113323--113376 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
113313 ATGTATAAAC
*
113323 TTGTATTGTGTTTATATATATATTTTATA
1 TTGTATTGTATTTATATATATATTTTATA
113352 TTGTATTGTATTT-TAT-TATATTTTA
1 TTGTATTGTATTTATATATATATTTTA
113377 AATATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.38
28 3 0.12
29 12 0.50
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (29 bp):
TTGTATTGTATTTATATATATATTTTATA
Found at i:113385 original size:27 final size:29
Alignment explanation
Indices: 113318--113379 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
113308 CGTATATGTA
*
113318 TAAACTTGTATTGTGTTTATATATATATTT
1 TAAA-TTGTATTGTATTTATATATATATTT
*
113348 TATATTGTATTGTATTT-TAT-TATATTT
1 TAAATTGTATTGTATTTATATATATATTT
113375 TAAAT
1 TAAAT
113380 ATTATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 11 0.38
28 3 0.10
29 12 0.41
30 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.60
Consensus pattern (29 bp):
TAAATTGTATTGTATTTATATATATATTT
Found at i:117869 original size:2 final size:2
Alignment explanation
Indices: 117862--117891 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
117852 NNNNNNNNNN
117862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117892 GAGCCAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:122273 original size:2 final size:2
Alignment explanation
Indices: 122266--122304 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
122256 AAAGTAAAAG
* *
122266 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
122305 AAGAGAGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:123335 original size:32 final size:32
Alignment explanation
Indices: 123255--123342 Score: 110
Period size: 31 Copynumber: 2.8 Consensus size: 32
123245 GGGGACTTAG
*
123255 TAAG-ATTTTTTT-AAAAATTTAAGACTTTAA
1 TAAGAATTTTTTTAAAAAATTTAAAACTTTAA
* *
123285 TAAGAA-TTATTTAAAAAATTTAAAAGTTTAA
1 TAAGAATTTTTTTAAAAAATTTAAAACTTTAA
*
123316 TGAGAATTTTTTTAAAAAATTTTAAAA
1 TAAGAATTTTTTTAAAAAA-TTTAAAA
123343 AAATTGGAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.18
31 22 0.45
32 11 0.22
33 7 0.14
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (32 bp):
TAAGAATTTTTTTAAAAAATTTAAAACTTTAA
Found at i:126533 original size:23 final size:24
Alignment explanation
Indices: 126504--126557 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
126494 TTTTTTTACT
*
126504 AAAAAAATTC-CTTAAAAATACAA
1 AAAAAAAATCACTTAAAAATACAA
* * *
126527 AATAAAAATCATTTAAAAATGCAA
1 AAAAAAAATCACTTAAAAATACAA
126551 AAAAAAA
1 AAAAAAA
126558 CCCTAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.69, C:0.09, G:0.02, T:0.20
Consensus pattern (24 bp):
AAAAAAAATCACTTAAAAATACAA
Found at i:126684 original size:19 final size:18
Alignment explanation
Indices: 126662--126697 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
126652 TTTTTTTTAA
126662 AAAATTTATGAAAGTTTTT
1 AAAATTTATG-AAGTTTTT
*
126681 AAAATTTTTGAAGTTTT
1 AAAATTTATGAAGTTTT
126698 ACATACTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (18 bp):
AAAATTTATGAAGTTTTT
Done.