Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold566
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: 21524
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:2591 original size:26 final size:27
Alignment explanation
Indices: 2469--3552 Score: 1063
Period size: 27 Copynumber: 39.7 Consensus size: 27
2459 GACCTTTTCA
* * **
2469 AAGTCCACGACTCAGTGGCATTTCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
* *
2497 AAAGTCCACAAACTCTGTGGCATCCTTTT
1 -AAGTCCAC-AACTCCGTGGCACCCTTTT
*
2526 AAGTCCACAACTCTGTGGCACCCTTTTT
1 AAGTCCACAACTCCGTGGCACCC-TTTT
*
2554 AAAGTCCACAACTCCGTGGTACCC-TTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* *
2581 AAGTCCACAACTCTGTGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
2608 AAATCCACAACTCCGTGGTACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
2635 -AGTCCACAACTCTGTTGGCACCCTTTTT
1 AAGTCCACAACTCCG-TGGCACCC-TTTT
*
2663 AAGT-CACAACTCTGTGGCACCCTTTTTT
1 AAGTCCACAACTCCGTGGCACCC--TTTT
2691 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * **
2718 AAGTCCATAACTCTGTGGCATCTTTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
* *
2746 AAGTCCACAACTCTGTGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
2773 AAGTCCAC-ACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
2799 TAGTCCACAACTCTG-GGCACCC--TT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* ** *
2823 AAGTCC-CCACTATTGTGGTACCCTTTT
1 AAGTCCACAACT-CCGTGGCACCCTTTT
*
2850 -AGTCCACAACTCTGTGG-ACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
2875 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
2902 AAGTCCA-AACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
2928 AAGTCCA-AACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
2954 AAGTCCACAACTCCGTGGCACCC-TTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
2980 AAGTCCACCACTTCGTGG--CCC--TT
1 AAGTCCACAACTCCGTGGCACCCTTTT
** *
3003 AAGTTCCACAACTCTATGTC-CTTTTCC-TTT
1 AAG-TCCACAACTCCGTGGCAC----CCTTTT
3033 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
3060 ACGTCCACAACTCCGTGGCACCCTTTTT
1 AAGTCCACAACTCCGTGGCACCC-TTTT
* * *
3088 ACATTCCACAACTCTGTGGCATTCCTTTT
1 A-AGTCCACAACTCCGTGGCA-CCCTTTT
* *
3117 AA-TACCACAACTCCGTGCCCCCCTTTT
1 AAGT-CCACAACTCCGTGGCACCCTTTT
3144 AAGTCCACAACTCCGTGG-ACCCTTTTT
1 AAGTCCACAACTCCGTGGCACCC-TTTT
*
3171 AAGTCCACAAC-CCGTGGCACTC-TTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
3196 ACGTCCATC-ACTCCATGGCATCC-TTT
1 AAGTCCA-CAACTCCGTGGCACCCTTTT
*
3222 AAGGTCCCACACTCTCCGTGGCACCCTTTT
1 AA-GT-CCACA-ACTCCGTGGCACCCTTTT
* * *
3252 AAGACCACAACTCCGTCGCCCCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
3279 AAGTCCACAACTCCGTGGCACCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
* * * **
3307 AAGTTCCATAACTCTGT-GCTCTTTTTT
1 AAG-TCCACAACTCCGTGGCACCCTTTT
* *
3334 AAGTCCACAACTTCTGTTGCACCCTTTTT
1 AAGTCCACAAC-TCCGTGGCACCC-TTTT
3363 AAAGGTCCACAACTCCGTGGCCACCCTTTTT
1 -AA-GTCCACAACTCCGTGG-CACCC-TTTT
* *
3394 TAGTCCACAACTCTGTGGCCACCCTTTT
1 AAGTCCACAACTCCGTGG-CACCCTTTT
3422 AAG-CCACAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
*
3449 CACGTCCACAAACTCCGTGGCATCCCTTTT
1 -AAGTCCAC-AACTCCGTGGCA-CCCTTTT
3479 AAGTCCACAACTCCGTGGCA-CCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
3505 AAGTCCACAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
* * * *
3533 AAATTCACAAATCGGTGGCA
1 AAGTCCACAACTCCGTGGCA
3553 ACCCATTCCA
Statistics
Matches: 903, Mismatches: 96, Indels: 113
0.81 0.09 0.10
Matches are distributed among these distances:
23 8 0.01
24 22 0.02
25 26 0.03
26 218 0.24
27 265 0.29
28 144 0.16
29 150 0.17
30 51 0.06
31 19 0.02
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.30
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:2598 original size:55 final size:53
Alignment explanation
Indices: 2469--3552 Score: 954
Period size: 55 Copynumber: 19.9 Consensus size: 53
2459 GACCTTTTCA
* * ** * *
2469 AAGTCCACGACTCAGTGGCATTTCTTTTAAAGTCCACAAACTCTGTGGCATCCTTTT
1 AAGTCCACAACTCTGTGGCA-CCCTTTT-AAGTCCAC-AACTCCGTGGCA-CCCTTT
*
2526 AAGTCCACAACTCTGTGGCACCCTTTTTAAAGTCCACAACTCCGTGGTACCCTTT
1 AAGTCCACAACTCTGTGGCACCC-TTTT-AAGTCCACAACTCCGTGGCACCCTTT
* * *
2581 AAGTCCACAACTCTGTGGCACCCTTTAAAATCCACAACTCCGTGGTACCCTTT
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
* *
2634 TAGTCCACAACTCTGTTGGCACCCTTTTTAAGT-CACAACTCTGTGGCACCCTTTTTT
1 AAGTCCACAACTCTG-TGGCACCC-TTTTAAGTCCACAACTCCGTGGCACCC---TTT
* * * **
2691 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCTGTGGCATCTTTTTT
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-C-CCTTT
*
2746 AAGTCCACAACTCTGTGGCACCCTTTAAAGTCCAC-ACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC-TTT
* * ** *
2799 TAGTCCACAACTCTG-GGCACCC--TTAAGTCC-CCACTATTGTGGTACCCTTT
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACT-CCGTGGCACCCTTT
* *
2849 TAGTCCACAACTCTGTGG-ACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC-TTT
*
2902 AAGTCCA-AACTCCGTGGCACCCTTTTAAGTCCA-AACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC-TTT
* * * *
2954 AAGTCCACAACTCCGTGGCACCC-TTAAAGTCCACCACTTCGTGG--CCC-TT
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
* *
3003 AAGTTCCACAACTCTATGTC-CTTTTCC-TTTAAGTCCACAACTCCGTGGCACCCTTTT
1 AAG-TCCACAACTCTGTGGCAC----CCTTTTAAGTCCACAACTCCGTGGCACCC-TTT
* * * * *
3060 ACGTCCACAACTCCGTGGCACCCTTTTTACATTCCACAACTCTGTGGCATTCCTTTT
1 AAGTCCACAACTCTGTGGCACCC-TTTTA-AGTCCACAACTCCGTGGCA--CCCTTT
* * *
3117 AA-TACCACAACTCCGTGCCCCCCTTTTAAGTCCACAACTCCGTGG-ACCCTTTTT
1 AAGT-CCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC--TTT
* * * * *
3171 AAGTCCACAAC-CCGTGGCACTC-TTTACGTCCATC-ACTCCATGGCATCCTTT
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCA-CAACTCCGTGGCACCCTTT
* * *
3222 AAGGTCC-CACACTCTCCGTGGCACCCTTTTAAGACCACAACTCCGTCGCCCCCTTTT
1 AA-GTCCACA-ACTCT--GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC-TTT
* * * * **
3279 AAGTCCACAACTCCGTGGCACCCCTTTTAAGTTCCATAACTCTGT-GCTCTTTTTT
1 AAGTCCACAACTCTGTGGCA-CCCTTTTAAG-TCCACAACTCCGTGGCAC-CCTTT
*
3334 AAGTCCACAACTTCTGTTGCACCCTTTTTAAAGGTCCACAACTCCGTGGCCACCCTTTTT
1 AAGTCCACAAC-TCTGTGGCACCC-TTTT-AA-GTCCACAACTCCGTGG-CACCC--TTT
*
3394 TAGTCCACAACTCTGTGGCCACCCTTTTAAG-CCACAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCTGTGG-CACCCTTTTAAGTCCACAACTCCGTGGCA-CCC-TTT
* * *
3449 CACGTCCACAAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
1 -AAGTCCAC-AACTCTGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
* * * * *
3505 AAGTCCACAACTCCGTGGCATCCCTTTTAAATTCACAAATCGGTGGCA
1 AAGTCCACAACTCTGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA
3553 ACCCATTCCA
Statistics
Matches: 863, Mismatches: 97, Indels: 137
0.79 0.09 0.12
Matches are distributed among these distances:
49 7 0.01
50 45 0.05
51 20 0.02
52 92 0.11
53 143 0.17
54 92 0.11
55 152 0.18
56 144 0.17
57 116 0.13
58 22 0.03
59 12 0.01
60 18 0.02
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.30
Consensus pattern (53 bp):
AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
Found at i:3584 original size:32 final size:32
Alignment explanation
Indices: 3538--3981 Score: 710
Period size: 32 Copynumber: 13.8 Consensus size: 32
3528 CTTTTAAATT
* *
3538 CACAAATCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3570 CACAAGTCGATGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3602 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3634 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3666 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3698 TACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3730 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3762 CACAAGTCGGTGGCAACCCATTTCAAAGCCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAG-CCCA
3795 CACAAGTCGGTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
3827 CACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
3859 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
3891 CAGAAGTTGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3923 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
3955 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
3982 TCACCATTTT
Statistics
Matches: 386, Mismatches: 23, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
32 355 0.92
33 31 0.08
ACGTcount: A:0.32, C:0.33, G:0.19, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:5242 original size:17 final size:17
Alignment explanation
Indices: 5222--5257 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5212 AAGGAAGATG
* *
5222 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
5239 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
5256 AA
1 AA
5258 ATATGAAATG
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:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:8219 original size:20 final size:20
Alignment explanation
Indices: 8172--8246 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
8162 AAAAAGACAT
*
8172 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
8191 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
8212 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
8232 AATGTATCGATACAT
1 AATGTATCGATACAT
8247 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:8240 original size:40 final size:39
Alignment explanation
Indices: 8169--8246 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
8159 GGTAAAAAGA
* *
8169 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
8208 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
8247 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:8919 original size:15 final size:15
Alignment explanation
Indices: 8899--8941 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
8889 AATTAAAGGA
8899 AAATATTAAATTATT
1 AAATATTAAATTATT
*
8914 AAATATTAAATTTTT
1 AAATATTAAATTATT
* *
8929 AAAAAATAAATTA
1 AAATATTAAATTA
8942 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTAAATTATT
Found at i:11317 original size:13 final size:12
Alignment explanation
Indices: 11297--11342 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
11287 AAATATGATA
11297 AATATATTTTACT
1 AATATATTTTA-T
*
11310 ATTATATTTTAT
1 AATATATTTTAT
*
11322 AAAATATTTTAAT
1 AATATATTTT-AT
11335 AATATATT
1 AATATATT
11343 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (12 bp):
AATATATTTTAT
Found at i:11360 original size:29 final size:31
Alignment explanation
Indices: 11309--11372 Score: 105
Period size: 29 Copynumber: 2.1 Consensus size: 31
11299 TATATTTTAC
11309 TATTATATTTTATAAAATATTTT-AATAATA
1 TATTATATTTTATAAAATATTTTAAATAATA
11339 TATTATATTTT-TAAAATATTTTGAAATAATA
1 TATTATATTTTATAAAATATTTT-AAATAATA
11370 TAT
1 TAT
11373 ATTTAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 11 0.34
30 11 0.34
31 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (31 bp):
TATTATATTTTATAAAATATTTTAAATAATA
Found at i:11367 original size:31 final size:30
Alignment explanation
Indices: 11309--11395 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 30
11299 TATATTTTAC
11309 TATTATATTTTATAAAATATTTTAATAATA
1 TATTATATTTTATAAAATATTTTAATAATA
*
11339 TATTATATTTT-TAAAATATTTTGA-AATA
1 TATTATATTTTATAAAATATTTTAATAATA
* *
11367 -A-TATATATTTA-AAAATATTATATTAATA
1 TATTATAT-TTTATAAAATATTTTAATAATA
11395 T
1 T
11396 TCTATACTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
26 5 0.10
27 13 0.27
28 8 0.16
29 12 0.24
30 11 0.22
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
TATTATATTTTATAAAATATTTTAATAATA
Found at i:11394 original size:28 final size:27
Alignment explanation
Indices: 11312--11394 Score: 64
Period size: 28 Copynumber: 3.0 Consensus size: 27
11302 ATTTTACTAT
*
11312 TATAT-TTTATAAAATATTTTAATAAT-A
1 TATATATTTA-AAAATA-TTTATTAATAA
* *
11339 TATTATATTTTTAAAATATTT-TGAAATAA
1 TA-TATA-TTTAAAAATATTTAT-TAATAA
11368 TATATATTTAAAAATATTATATTAATA
1 TATATATTTAAAAATATT-TATTAATA
11395 TTCTATACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
27 13 0.30
28 18 0.41
29 10 0.23
30 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TATATATTTAAAAATATTTATTAATAA
Found at i:11535 original size:11 final size:11
Alignment explanation
Indices: 11485--11567 Score: 59
Period size: 11 Copynumber: 7.8 Consensus size: 11
11475 ATATATATAT
11485 ATATTTATATATA
1 ATATTT-TA-ATA
* *
11498 ATATTTTGACA
1 ATATTTTAATA
*
11509 ATATATT--TA
1 ATATTTTAATA
11518 A-ATTTTAATA
1 ATATTTTAATA
11528 ATATTTTAA-A
1 ATATTTTAATA
*
11538 ATATGTTAATA
1 ATATTTTAATA
*
11549 ATA-TTTAAAA
1 ATATTTTAATA
*
11559 ATCTTTTAA
1 ATATTTTAA
11568 CAGTATTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
8 4 0.07
9 2 0.04
10 19 0.34
11 24 0.43
12 1 0.02
13 6 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (11 bp):
ATATTTTAATA
Found at i:11567 original size:21 final size:21
Alignment explanation
Indices: 11519--11567 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
11509 ATATATTTAA
*
11519 ATTTTAATAATATTTTAAAAT
1 ATTTTAATAATATTTAAAAAT
*
11540 ATGTTAATAATATTTAAAAAT
1 ATTTTAATAATATTTAAAAAT
*
11561 CTTTTAA
1 ATTTTAA
11568 CAGTATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTTAATAATATTTAAAAAT
Found at i:11782 original size:17 final size:17
Alignment explanation
Indices: 11760--11793 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11750 AATGTGTAAA
11760 TCAAAAAGATAATGCTT
1 TCAAAAAGATAATGCTT
11777 TCAAAAAGATAATGCTT
1 TCAAAAAGATAATGCTT
11794 AAGCATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
TCAAAAAGATAATGCTT
Found at i:12034 original size:7 final size:7
Alignment explanation
Indices: 12017--12048 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
12007 TCAAATTTAG
12017 TTTTTTC
1 TTTTTTC
12024 -TTTTTC
1 TTTTTTC
12030 TTTTTTC
1 TTTTTTC
12037 TTTTTT-
1 TTTTTTC
12043 TTTTTT
1 TTTTTT
12049 AGAATCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTC
Found at i:12048 original size:13 final size:13
Alignment explanation
Indices: 12017--12047 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12007 TCAAATTTAG
12017 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
12030 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
12042 TTTTTT
1 TTTTTT
12048 TAGAATCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:13152 original size:28 final size:28
Alignment explanation
Indices: 13120--13175 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
13110 GAACTCGGAA
13120 TAAAGGAGGTATGAAATGGTTACACCCC
1 TAAAGGAGGTATGAAATGGTTACACCCC
13148 TAAAGGAGGTATGAAATGGTTACACCCC
1 TAAAGGAGGTATGAAATGGTTACACCCC
13176 AACCGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (28 bp):
TAAAGGAGGTATGAAATGGTTACACCCC
Found at i:14228 original size:14 final size:14
Alignment explanation
Indices: 14196--14229 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
14186 CCAAATAATG
14196 TTATT-TTAAAATA
1 TTATTATTAAAATA
14209 -TATTATTAAAATA
1 TTATTATTAAAATA
14222 TTATTATT
1 TTATTATT
14230 TTTGCCACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 8 0.42
14 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATTATTAAAATA
Found at i:17306 original size:27 final size:27
Alignment explanation
Indices: 17267--17346 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
17257 TATTTATATT
*
17267 TATTTAT-TAAATATAATATAATAAATAA
1 TATTTATAT-AATATAATATAAGAAA-AA
17295 -ATTTATATAATAGTAAT-TAAGAAAAA
1 TATTTATATAATA-TAATATAAGAAAAA
*
17321 TATTTA-ATAAT-T-ATATAA-AATAA
1 TATTTATATAATATAATATAAGAAAAA
17344 TAT
1 TAT
17347 ATTTTTAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
23 9 0.20
24 4 0.09
26 7 0.15
27 21 0.46
28 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
TATTTATATAATATAATATAAGAAAAA
Found at i:18792 original size:22 final size:22
Alignment explanation
Indices: 18740--18811 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
18730 CTCAAAAATT
18740 TTAT-TTTAT-TA-TTTTA-AA
1 TTATATTTATATATTTTTATAA
18758 -TATATTTAAATATATTTTTAT-A
1 TTATATTT--ATATATTTTTATAA
18780 TTAATATTTATATATTTTTATAA
1 TT-ATATTTATATATTTTTATAA
18803 TTATATTTA
1 TTATATTTA
18812 AGGTGAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
17 3 0.07
18 3 0.07
20 2 0.04
21 2 0.04
22 25 0.56
23 4 0.09
24 6 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATTTATATATTTTTATAA
Done.