Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3485.1
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: 126441
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1987 characters in sequence are not A, C, G, or T
Found at i:3979 original size:20 final size:20
Alignment explanation
Indices: 3941--3979 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3931 TAGGAAAACA
* * *
3941 TTTCTATTTTTATTCCAAAT
1 TTTCAATTTTAATTACAAAT
3961 TTTCAATTTTAATTACAAA
1 TTTCAATTTTAATTACAAA
3980 ATAATGAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTCAATTTTAATTACAAAT
Found at i:5775 original size:20 final size:21
Alignment explanation
Indices: 5745--5793 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
5735 TGGGGTATTA
5745 AATTAAATTTAATAGTAAAAT
1 AATTAAATTTAATAGTAAAAT
* *
5766 AATT-AATTTAATATTAAATT
1 AATTAAATTTAATAGTAAAAT
*
5786 AATAAAAT
1 AATTAAAT
5794 AATTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTAAATTTAATAGTAAAAT
Found at i:6791 original size:22 final size:22
Alignment explanation
Indices: 6763--6806 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
6753 TCCTGTCAAG
6763 CTTGTTAGATTGTTTCCTTGTA
1 CTTGTTAGATTGTTTCCTTGTA
6785 CTTGTTAGATTGTTTCCTTGTA
1 CTTGTTAGATTGTTTCCTTGTA
6807 GGAAAGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (22 bp):
CTTGTTAGATTGTTTCCTTGTA
Found at i:8449 original size:38 final size:38
Alignment explanation
Indices: 8407--8486 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
8397 AGCTACTAAC
*
8407 TTAAGTCATTTTTAAAGGTTCTAATTTATGAGAAGAGT
1 TTAAGTCATTTTTAAAGGTTCTAATTCATGAGAAGAGT
*
8445 TTAAGTCATTTTTAAAGGTTCTACTTCATGAGAAGAGT
1 TTAAGTCATTTTTAAAGGTTCTAATTCATGAGAAGAGT
8483 TTAA
1 TTAA
8487 ATGACGACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (38 bp):
TTAAGTCATTTTTAAAGGTTCTAATTCATGAGAAGAGT
Found at i:9463 original size:29 final size:31
Alignment explanation
Indices: 9419--9497 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 31
9409 ATTAAATTAA
9419 ATTAATA-TAATATTT-ATATATAAGATAA-AT
1 ATTAATATTAA-ATTTAATAT-TAAGATAACAT
9449 ATTAA-ATTAAATTTAATATTAAGATAATCAT
1 ATTAATATTAAATTTAATATTAAGATAA-CAT
*
9480 TTTAATATTAAA-TTAATA
1 ATTAATATTAAATTTAATA
9498 AATTACTATC
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
29 13 0.30
30 12 0.28
31 12 0.28
32 6 0.14
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTAATATTAAATTTAATATTAAGATAACAT
Found at i:9495 original size:11 final size:12
Alignment explanation
Indices: 9408--9497 Score: 50
Period size: 11 Copynumber: 7.7 Consensus size: 12
9398 AAATTAAATC
9408 TATTAA-ATTAA
1 TATTAATATTAA
9419 -ATTAATA-TAA
1 TATTAATATTAA
*
9429 TATTTATATATAA
1 TATTAATAT-TAA
* *
9442 GATAAATATTAA
1 TATTAATATTAA
9454 -ATTAA-ATTTAA
1 TATTAATA-TTAA
*
9465 TATTAAGA-TAA
1 TATTAATATTAA
9476 TCATTTTAATATTAA
1 T-A--TTAATATTAA
9491 -ATTAATA
1 TATTAATA
9498 AATTACTATC
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
10 9 0.15
11 25 0.40
12 9 0.15
13 11 0.18
14 5 0.08
15 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (12 bp):
TATTAATATTAA
Found at i:9496 original size:20 final size:18
Alignment explanation
Indices: 9446--9497 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
9436 ATATAAGATA
9446 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
9463 AATATTAAGA-TAATCATTTT
1 AATATTAA-ATTAAT-A-TTT
9483 AATATTAAATTAATA
1 AATATTAAATTAATA
9498 AATTACTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:10023 original size:13 final size:13
Alignment explanation
Indices: 10007--10042 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
9997 TTTTTCAGGA
10007 AAATTATTTAATC
1 AAATTATTTAATC
10020 AAATTATTTAATC
1 AAATTATTTAATC
*
10033 AAATTCTTTA
1 AAATTATTTA
10043 GTTGAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTATTTAATC
Found at i:16403 original size:28 final size:28
Alignment explanation
Indices: 16363--16424 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
16353 TAAGTTCACC
16363 GCAAATTCTGGATTTGTACTCTTAACTT
1 GCAAATTCTGGATTTGTACTCTTAACTT
16391 GCAAATTCTGGATTTGTACTCTTAACTT
1 GCAAATTCTGGATTTGTACTCTTAACTT
*
16419 ACAAAT
1 GCAAAT
16425 AGTATGTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (28 bp):
GCAAATTCTGGATTTGTACTCTTAACTT
Found at i:19648 original size:12 final size:12
Alignment explanation
Indices: 19626--19674 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
19616 TTAATATAAA
19626 AAAATTA-TATT
1 AAAATTATTATT
19637 AAAATTATTATT
1 AAAATTATTATT
19649 -AAATT-TTAATT
1 AAAATTATT-ATT
* *
19660 ATAATTTTTATT
1 AAAATTATTATT
19672 AAA
1 AAA
19675 TTACATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 2 0.06
11 15 0.47
12 13 0.41
13 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AAAATTATTATT
Found at i:19881 original size:46 final size:43
Alignment explanation
Indices: 19797--19888 Score: 123
Period size: 46 Copynumber: 2.1 Consensus size: 43
19787 AACAACATCT
*
19797 ATTTCATTCACCAAACACAAGAATACTATTACAGTTCTATTCC
1 ATTTCATTCACCAAACACAAGAATACTAATACAGTTCTATTCC
*
19840 ATTTCATTCAGCCAAACA-ATTGAATTACTAAATACAGTTCTATTCC
1 ATTTCATTCA-CCAAACACA-AGAA-TACT-AATACAGTTCTATTCC
19886 ATT
1 ATT
19889 ACAATTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 11 0.26
44 10 0.23
45 4 0.09
46 18 0.42
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (43 bp):
ATTTCATTCACCAAACACAAGAATACTAATACAGTTCTATTCC
Found at i:23071 original size:18 final size:15
Alignment explanation
Indices: 23024--23079 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
23014 TAACTTTGGA
*
23024 GGTGGCGGCTACGGT
1 GGTGGTGGCTACGGT
23039 GGTGGTGGCTACGGT
1 GGTGGTGGCTACGGT
*
23054 GGTGGTGGCTACGGC
1 GGTGGTGGCTACGGT
*
23069 GGTGGAGGCTA
1 GGTGGTGGCTA
23080 TGGAAGTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.09, C:0.16, G:0.54, T:0.21
Consensus pattern (15 bp):
GGTGGTGGCTACGGT
Found at i:23089 original size:30 final size:30
Alignment explanation
Indices: 23020--23092 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
23010 CTCGTAACTT
* * *
23020 TGGAGGTGGCGGCTACGGTGGTGGTGGCTA
1 TGGAGGTGGTGGCTACGGCGGTGGAGGCTA
* *
23050 CGGTGGTGGTGGCTACGGCGGTGGAGGCTA
1 TGGAGGTGGTGGCTACGGCGGTGGAGGCTA
*
23080 TGGAAGTGGTGGC
1 TGGAGGTGGTGGC
23093 GGTGGATATG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.11, C:0.14, G:0.53, T:0.22
Consensus pattern (30 bp):
TGGAGGTGGTGGCTACGGCGGTGGAGGCTA
Found at i:27537 original size:26 final size:25
Alignment explanation
Indices: 27487--27537 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 25
27477 ACTGAGTTTC
* ***
27487 GTGTATGGGTCTAATATTTTGTGTT
1 GTGTAGGGGTCTAATATTCCATGTT
27512 NGTGTAGGGGTCTAATATTCCATGTT
1 -GTGTAGGGGTCTAATATTCCATGTT
27538 ACCACCAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.18, C:0.08, G:0.27, T:0.45
Consensus pattern (25 bp):
GTGTAGGGGTCTAATATTCCATGTT
Found at i:28810 original size:29 final size:31
Alignment explanation
Indices: 28778--28842 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
28768 AAAATTATAA
* *
28778 AAAATTA-ATATATATAATTAAA-AAATATT
1 AAAATTACATAAAAATAATTAAATAAATATT
* *
28807 AAAA-AACATAAAAATAATTAAATATATATT
1 AAAATTACATAAAAATAATTAAATAAATATT
28837 AAAATT
1 AAAATT
28843 TATTAAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
28 1 0.04
29 17 0.61
30 10 0.36
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATTACATAAAAATAATTAAATAAATATT
Found at i:28851 original size:11 final size:11
Alignment explanation
Indices: 28789--28856 Score: 56
Period size: 10 Copynumber: 6.5 Consensus size: 11
28779 AAATTAATAT
28789 ATATAATTAAAA
1 ATAT-ATTAAAA
28801 A-ATATTAAAA
1 ATATATTAAAA
*
28811 A-ACA-TAAAA
1 ATATATTAAAA
*
28820 ATA-ATTAAAT
1 ATATATTAAAA
28830 ATATATT-AAA
1 ATATATTAAAA
*
28840 ATTTATTAAAA
1 ATATATTAAAA
*
28851 AGATAT
1 ATATAT
28857 ATAATAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 7 0.15
10 26 0.57
11 12 0.26
12 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (11 bp):
ATATATTAAAA
Found at i:30840 original size:34 final size:34
Alignment explanation
Indices: 30801--30869 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
30791 GTGATCTTTG
30801 TTTTATTTTTGCAAAAGAGATGAAATGAATGCCA
1 TTTTATTTTTGCAAAAGAGATGAAATGAATGCCA
30835 TTTTATTTTTGCAAAAGAGATGAAATGAATGCCA
1 TTTTATTTTTGCAAAAGAGATGAAATGAATGCCA
30869 T
1 T
30870 CTTTTTTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (34 bp):
TTTTATTTTTGCAAAAGAGATGAAATGAATGCCA
Found at i:33550 original size:22 final size:22
Alignment explanation
Indices: 33522--33566 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
33512 AACCAATGTG
33522 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
33544 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
33566 T
1 T
33567 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:37325 original size:22 final size:22
Alignment explanation
Indices: 37295--37339 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
37285 AGGGGGAGTG
*
37295 TAGGTATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
37317 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
37339 T
1 T
37340 TTTTATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:37716 original size:97 final size:98
Alignment explanation
Indices: 37550--37746 Score: 369
Period size: 97 Copynumber: 2.0 Consensus size: 98
37540 CCAAGTCCAA
37550 GTAAACATACAAGTATAAGAAACCGTTTCTAAGGCAGTTTAACTCATTATAAAGATGGAGGAAAA
1 GTAAACATACAAGTATAAGAAACCGTTTCTAAGGCAGTTTAACTCATTATAAAGATGGAGGAAAA
*
37615 GGTAATCAATTCAATATC-TATTCTCTTTCTAT
66 GGTAATCAATTCAACATCTTATTCTCTTTCTAT
*
37647 GTAAATATACAAGTATAAGAAACCGTTTCTAAGGCAGTTTAACTCATTATAAAGATGGAGGAAAA
1 GTAAACATACAAGTATAAGAAACCGTTTCTAAGGCAGTTTAACTCATTATAAAGATGGAGGAAAA
37712 GGTAATCAATTCAACATCTTATTCTCTTTCTAT
66 GGTAATCAATTCAACATCTTATTCTCTTTCTAT
37745 GT
1 GT
37747 TGAACTCTGA
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
97 81 0.84
98 16 0.16
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (98 bp):
GTAAACATACAAGTATAAGAAACCGTTTCTAAGGCAGTTTAACTCATTATAAAGATGGAGGAAAA
GGTAATCAATTCAACATCTTATTCTCTTTCTAT
Found at i:39463 original size:44 final size:45
Alignment explanation
Indices: 39386--39476 Score: 150
Period size: 44 Copynumber: 2.0 Consensus size: 45
39376 AATAACTGTC
*
39386 AACCCCCTCACCCCCCCCCCCCAAAAAAAATATATATTCAACTGG
1 AACCCCCTCACCCCCCCCCCCAAAAAAAAATATATATTCAACTGG
39431 AACCCCC-C-CCCCCCCCCCCAAAAAAAATATATATATTCAACTGG
1 AACCCCCTCACCCCCCCCCCCAAAAAAAA-ATATATATTCAACTGG
39475 AA
1 AA
39477 GCAAATAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 18 0.41
44 19 0.43
45 7 0.16
ACGTcount: A:0.37, C:0.43, G:0.04, T:0.15
Consensus pattern (45 bp):
AACCCCCTCACCCCCCCCCCCAAAAAAAAATATATATTCAACTGG
Found at i:40340 original size:30 final size:32
Alignment explanation
Indices: 40304--40363 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
40294 TACTTATCTC
*
40304 ATATTTTTACT-TT-TTTTTATGTTATATCAT
1 ATATTTTGACTATTATTTTTATGTTATATCAT
* *
40334 ATATTTTGATTATTATTTTTATTTTATATC
1 ATATTTTGACTATTATTTTTATGTTATATC
40364 CCACCTTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.36
31 2 0.08
32 14 0.56
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (32 bp):
ATATTTTGACTATTATTTTTATGTTATATCAT
Found at i:45314 original size:97 final size:97
Alignment explanation
Indices: 45201--45394 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
45191 TGCCTTATCA
45201 TCTCTGTTGCTATTTTTCTTGATCTTTCAAGGTTTGAGTTCAGCTTGTAGTTCAAAATATCATAG
1 TCTCTGTTGCTATTTTTCTTGATCTTTCAAGGTTTGAGTTCAGCTTGTAGTTCAAAATATCATAG
45266 AGAGTCCAATGTCCATAGTGAGTTTTTTCATC
66 AGAGTCCAATGTCCATAGTGAGTTTTTTCATC
45298 TCTCTGTTGCTATTTTTCTTGATCTTTCAAGGTTTGAGTTCAGCTTGTAGTTCAAAATATCATAG
1 TCTCTGTTGCTATTTTTCTTGATCTTTCAAGGTTTGAGTTCAGCTTGTAGTTCAAAATATCATAG
45363 AGAGTCCAATGTCCATAGTGAGTTTTTTCATC
66 AGAGTCCAATGTCCATAGTGAGTTTTTTCATC
45395 ATAGTGGGGG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (97 bp):
TCTCTGTTGCTATTTTTCTTGATCTTTCAAGGTTTGAGTTCAGCTTGTAGTTCAAAATATCATAG
AGAGTCCAATGTCCATAGTGAGTTTTTTCATC
Found at i:56641 original size:16 final size:16
Alignment explanation
Indices: 56620--56651 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56610 CGCACTTTAC
*
56620 CGTATCAATGTGTACT
1 CGTATCAAGGTGTACT
56636 CGTATCAAGGTGTACT
1 CGTATCAAGGTGTACT
56652 TGATTGAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (16 bp):
CGTATCAAGGTGTACT
Found at i:60113 original size:15 final size:15
Alignment explanation
Indices: 60093--60126 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
60083 AAAGAAAGTC
60093 CAAACTTAATGTCCA
1 CAAACTTAATGTCCA
*
60108 CAAACTTAATGTCCC
1 CAAACTTAATGTCCA
60123 CAAA
1 CAAA
60127 ACCAGTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (15 bp):
CAAACTTAATGTCCA
Found at i:63348 original size:36 final size:36
Alignment explanation
Indices: 63301--63370 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
63291 TTTTGCAACA
*
63301 CTTAGAAAATTTTCACACTTTGGAGAGTCACACGCC
1 CTTAGAAAATTTTCACACTTTAGAGAGTCACACGCC
63337 CTTAGAAAATTTTCACACTTTAGAGAGTCACACG
1 CTTAGAAAATTTTCACACTTTAGAGAGTCACACG
63371 GCCGTGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (36 bp):
CTTAGAAAATTTTCACACTTTAGAGAGTCACACGCC
Found at i:63592 original size:10 final size:10
Alignment explanation
Indices: 63577--63604 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
63567 ACTTATCTTG
63577 ATTTCATACT
1 ATTTCATACT
63587 ATTTCATACT
1 ATTTCATACT
63597 ATTTCATA
1 ATTTCATA
63605 TTTAAGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTTCATACT
Found at i:64098 original size:42 final size:42
Alignment explanation
Indices: 64035--64148 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
64025 CTTCGTTTTC
** * *
64035 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTTACATA-A
1 TCGATGCCATAGCCCAGCTATGGTCTTACACAT-ATT-CATATA
64078 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
64119 TCGATGCCATAGCCCAGCTATGGTCTTACA
1 TCGATGCCATAGCCCAGCTATGGTCTTACA
64149 TGAATCACAT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
40 4 0.06
41 4 0.06
42 56 0.86
43 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
Found at i:64188 original size:46 final size:45
Alignment explanation
Indices: 64120--64239 Score: 141
Period size: 47 Copynumber: 2.6 Consensus size: 45
64110 ATTCATATAT
* * * *
64120 CGATGCCATAGCCCAGCTATGGTCTTACATGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTACA-GAAGCACATATCACAC
* * * *
64166 TGATGCCATATCCTAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTC-T-TACAGAAGCACATATCACAC
64213 CGATGCCATATCCCAGATATGGTCTTA
1 CGATGCCATATCCCAGATATGGTCTTA
64240 TACGAAAATC
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
45 2 0.03
46 21 0.34
47 35 0.56
48 4 0.06
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (45 bp):
CGATGCCATATCCCAGATATGGTCTTACAGAAGCACATATCACAC
Found at i:64296 original size:31 final size:31
Alignment explanation
Indices: 64261--64378 Score: 191
Period size: 31 Copynumber: 3.8 Consensus size: 31
64251 CTTGTCACTT
*
64261 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
64292 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
64323 GTAGCCGGAGCTACCACTTTTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
64354 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
64379 TGTCATTTGT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 81 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:83103 original size:21 final size:21
Alignment explanation
Indices: 83079--83120 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
83069 ATTCTGTCCG
83079 AGCCTCGTGACAGGAATGCCA
1 AGCCTCGTGACAGGAATGCCA
83100 AGCCTCGTGACAGGAATGCCA
1 AGCCTCGTGACAGGAATGCCA
83121 GTCCAGCGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (21 bp):
AGCCTCGTGACAGGAATGCCA
Found at i:89624 original size:31 final size:31
Alignment explanation
Indices: 89548--89609 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
89538 TAGAAATTTG
89548 ATTTCTATGTAAAGTAAAATATTGAGATAAA
1 ATTTCTATGTAAAGTAAAATATTGAGATAAA
89579 ATTTCTATGTAAAGTAAAATATTGAGATAAA
1 ATTTCTATGTAAAGTAAAATATTGAGATAAA
89610 TTATGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.35
Consensus pattern (31 bp):
ATTTCTATGTAAAGTAAAATATTGAGATAAA
Found at i:91135 original size:42 final size:42
Alignment explanation
Indices: 91087--91233 Score: 188
Period size: 42 Copynumber: 3.3 Consensus size: 42
91077 CATAGTTTAA
91087 CTATGGTCTTACACATCTTCACATAAT-GATGCCATAGCCCAG
1 CTATGGTCTTACACATCTTCACAT-ATCGATGCCATAGCCCAG
* * *
91129 CTATGGTCTTATACATATTCATATATCGATGCCATAGCCCAG
1 CTATGGTCTTACACATCTTCACATATCGATGCCATAGCCCAG
91171 CTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAGCCCAG
1 CTATGGTCTTACAC---AT--C-T-TCACATATCGATGCCATAGCCCAG
91220 CTATGGTCTTACAC
1 CTATGGTCTTACAC
91234 GAATCACATA
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
41 2 0.02
42 49 0.54
45 2 0.02
48 1 0.01
49 37 0.41
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
CTATGGTCTTACACATCTTCACATATCGATGCCATAGCCCAG
Found at i:91214 original size:49 final size:48
Alignment explanation
Indices: 91141--91276 Score: 195
Period size: 49 Copynumber: 2.8 Consensus size: 48
91131 ATGGTCTTAT
*
91141 ACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATC
1 ACATA-TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACG-AATC
91191 ACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATC
1 ACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATC
* * * *
91239 ACATATCTCA-CT-GATGCCATATCCCAGATATGGTCTTA
1 ACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTA
91277 TACAGTAGCA
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
46 24 0.30
47 1 0.01
48 13 0.16
49 38 0.47
50 5 0.06
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (48 bp):
ACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATC
Found at i:91272 original size:46 final size:47
Alignment explanation
Indices: 91155--91322 Score: 178
Period size: 47 Copynumber: 3.6 Consensus size: 47
91145 ATTCATATAT
* * * *
91155 CGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCACATAT
1 CGATGCCATATCCCAGATATGGTCTTACACAG-AAGCACATATCAC--AC
* * * *
91204 CGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
* * * *
91250 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
*
91297 CGATGCCATATCTCAGATATGGTCTT
1 CGATGCCATATCCCAGATATGGTCTT
91323 GTACGGAAAT
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
46 27 0.25
47 36 0.34
48 12 0.11
49 31 0.29
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
Found at i:91335 original size:95 final size:94
Alignment explanation
Indices: 91114--91322 Score: 225
Period size: 95 Copynumber: 2.3 Consensus size: 94
91104 TTCACATAAT
* * * * *
91114 GATGCCATAGCCCAGCTATGGTCTTATAC-ATAT-TCATATAT--C-GATGCCATAGCCCAGCTA
1 GATGCCATAGCCCAGATATGGTCTTACACGA-ATCACATATCTCACTGATGCCATAGCCCAGATA
* *
91174 TGGTCTTACACGTAATCACATATCACATATC
65 TGGTCTTACACGTAAGCACATATCACA-ACC
* *
91205 GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATAT
1 GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATAGCCCAGATAT
* *
91270 GGTCTTATACAGT-AGCATATATCAC-ACC
66 GGTCTTACAC-GTAAGCACATATCACAACC
* *
91298 GATGCCATATCTCAGATATGGTCTT
1 GATGCCATAGCCCAGATATGGTCTT
91323 GTACGGAAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
91 30 0.30
92 7 0.07
93 24 0.24
94 1 0.01
95 36 0.36
96 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (94 bp):
GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATAGCCCAGATAT
GGTCTTACACGTAAGCACATATCACAACC
Found at i:91380 original size:31 final size:31
Alignment explanation
Indices: 91345--91462 Score: 184
Period size: 31 Copynumber: 3.8 Consensus size: 31
91335 CTTGCCACTT
*
91345 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
91376 GTAGCCGGTA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
*
91407 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
91438 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
91463 TGTCATTTGT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
30 2 0.03
31 76 0.95
32 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:91544 original size:50 final size:51
Alignment explanation
Indices: 91438--91566 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
91428 CACTGATCAG
* * * *
91438 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATTAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
91489 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
*
91539 GTAGCCGGAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
91567 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 43 0.61
51 27 0.39
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:94666 original size:22 final size:19
Alignment explanation
Indices: 94634--94681 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
94624 TTGTTGAGAT
94634 ATTGATGAATTAAGCTTGAA
1 ATTGATGAATTAAG-TTGAA
*
94654 ATTGATAGAAATTAAGTTTAA
1 ATTGAT-G-AATTAAGTTGAA
94675 ATT-ATGA
1 ATTGATGA
94682 TAAGGACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 1 0.04
20 8 0.32
21 8 0.32
22 7 0.28
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.38
Consensus pattern (19 bp):
ATTGATGAATTAAGTTGAA
Found at i:96791 original size:16 final size:16
Alignment explanation
Indices: 96770--96802 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
96760 TTTTTTCCTT
96770 TTTCTTTATATTT-TTA
1 TTTCTTT-TATTTATTA
96786 TTTCTTTTATTTATTA
1 TTTCTTTTATTTATTA
96802 T
1 T
96803 AACTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTTTTATTTATTA
Found at i:96819 original size:24 final size:23
Alignment explanation
Indices: 96792--96842 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
96782 TTTATTTCTT
96792 TTATTTATTATAACTATTAT-ATTA
1 TTATTTATTATAA--ATTATAATTA
*
96816 TTA--TATTTTAAATTATAATTA
1 TTATTTATTATAAATTATAATTA
96837 TTATTT
1 TTATTT
96843 CTTAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
22 7 0.30
23 1 0.04
24 3 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATTTATTATAAATTATAATTA
Found at i:96839 original size:21 final size:21
Alignment explanation
Indices: 96807--96854 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
96797 TATTATAACT
96807 ATTAT-ATTATTATATT-TTAA
1 ATTATAATTATTAT-TTCTTAA
96827 ATTATAATTATTATTTCTTAA
1 ATTATAATTATTATTTCTTAA
*
96848 ATAATAA
1 ATTATAA
96855 GTAAATACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATAATTATTATTTCTTAA
Found at i:98917 original size:9 final size:9
Alignment explanation
Indices: 98905--98938 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
98895 GAGAAAATTG
98905 AGAGAGTTA
1 AGAGAGTTA
*
98914 AGAGAGTTC
1 AGAGAGTTA
*
98923 AGAGAATTA
1 AGAGAGTTA
98932 AGAGAGT
1 AGAGAGT
98939 AGGATTTGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.32, T:0.21
Consensus pattern (9 bp):
AGAGAGTTA
Found at i:99268 original size:27 final size:23
Alignment explanation
Indices: 99217--99269 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 23
99207 TAGTAATTTG
*
99217 AATTTATTTTTAATATTTTAAAA
1 AATTTATTTTGAATATTTTAAAA
99240 AATTTATTTTAGAATAATTATTAAGAA
1 AATTTATTTT-GAAT-ATT-TTAA-AA
99267 AAT
1 AAT
99270 AATTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 10 0.40
24 3 0.12
25 3 0.12
26 4 0.16
27 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AATTTATTTTGAATATTTTAAAA
Found at i:99508 original size:24 final size:22
Alignment explanation
Indices: 99462--99509 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
99452 TTAAAGATAA
* *
99462 TAAATATAATTTATCCTATTTT
1 TAAATATAATTTATCCAAATTT
99484 TAAATATATATTTATCACAAATTT
1 TAAATATA-ATTTATC-CAAATTT
99508 TA
1 TA
99510 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 7 0.32
24 7 0.32
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAATATAATTTATCCAAATTT
Found at i:105306 original size:22 final size:23
Alignment explanation
Indices: 105247--105310 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
105237 GTTCTATTAT
* * *
105247 TAGCACGTTAAGTGCTCTCTGTT
1 TAGCACATTTAGTGCTCTCTGTA
* *
105270 TAGCACATCT-CTGCTCTCTGTA
1 TAGCACATTTAGTGCTCTCTGTA
105292 TAGCAC-TTTAGTGCTCTCT
1 TAGCACATTTAGTGCTCTCT
105311 ATTCGTTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 2 0.06
22 24 0.73
23 7 0.21
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (23 bp):
TAGCACATTTAGTGCTCTCTGTA
Found at i:113112 original size:2 final size:2
Alignment explanation
Indices: 113105--113143 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
113095 ATGGACAGGT
* * *
113105 TC TC TC TC TC TG TC TC TT TC TC TC TC TT TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
113144 TGGCATTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.41, G:0.03, T:0.56
Consensus pattern (2 bp):
TC
Found at i:119297 original size:18 final size:18
Alignment explanation
Indices: 119274--119348 Score: 105
Period size: 18 Copynumber: 4.2 Consensus size: 18
119264 CCCAACTACT
*
119274 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
119292 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* * *
119310 ATATATGTAAATAGTACC
1 GTATACGTGAATAGTACC
119328 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
119346 GTA
1 GTA
119349 AACGGTCGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Done.