Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_183
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: 140823
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1437 original size:42 final size:42
Alignment explanation
Indices: 1356--1441 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 42
1346 TTGGTTTTCA
1356 GCAATAAGTGTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
1 GCAATAAGTGTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
1398 GCAATAAGTGTTCACGGTTGCGAGATTGGCACTAA-TGTGCGG
1 GCAATAAGTG-TCACGGTTGCGAGATTGGCACTAAGTGTGCGG
1440 GC
1 GC
1442 TTGAAATGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 19 0.44
43 24 0.56
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.24
Consensus pattern (42 bp):
GCAATAAGTGTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
Found at i:1482 original size:29 final size:29
Alignment explanation
Indices: 1424--1495 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
1414 GTTGCGAGAT
* *
1424 TGGCACTAA-TGTGCGGGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATACA
*
1452 TGGCACTAAGTGTGCGAG-TTTAAAGTACA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TACA
1481 TGGCAC-AAGTGTGCG
1 TGGCACTAAGTGTGCG
1496 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 23 0.59
29 16 0.41
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATACA
Found at i:1610 original size:40 final size:40
Alignment explanation
Indices: 1518--1825 Score: 431
Period size: 40 Copynumber: 8.0 Consensus size: 40
1508 AAGCACTATG
* *
1518 TGTGCGAACTGATATATCC-GGATAAGACCCGAAGGCA-T
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
1556 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
*
1596 TGTGCGAATTGATATATCCGGGCTAAGACCTGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
*
1636 TGTGCGAATTGATATATCCGGGATAAGACCCGAA-GCA-T
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
1674 TGTGCGAATTGATATAT-C-GGC-AAGA-CCGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
*
1710 TGTGCGAA-TGATATATCCGGGCTAAGA-CCGAAGGCAAT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
*
1748 TGTGC-AAGTTGATACATCCGGGCTAAGACCCGAAGGCATT
1 TGTGCGAA-TTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * * *
1788 CGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCA
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCA
1826 ATTGAGCTTG
Statistics
Matches: 244, Mismatches: 15, Indels: 20
0.87 0.05 0.07
Matches are distributed among these distances:
34 5 0.02
35 15 0.06
36 12 0.05
37 6 0.02
38 55 0.23
39 38 0.16
40 112 0.46
41 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (40 bp):
TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
Found at i:1847 original size:80 final size:77
Alignment explanation
Indices: 1540--1873 Score: 281
Period size: 80 Copynumber: 4.3 Consensus size: 77
1530 TATATCCGGA
* * *
1540 TAAGACCCGAAGGCATT-GTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA
1 TAAGA-CCGAAGGCATTCGTGCGAA-TGATATACCCGGGCTAAGA-CCGAAGGCAATTGAGC-AA
* *
1604 -TTGATATATCCGGGC
62 GTGGATACATCCGGGC
* * * *
1619 TAAGACCTGAAGGCATTTGTGCGAATTGATATATCCGGGATAAGACCCGAA-GC-ATTGTGCGAA
1 TAAGACC-GAAGGCATTCGTGCGAA-TGATATACCCGGGCTAAGA-CCGAAGGCAATTGAGC-AA
* *
1682 -TTGATATAT-C-GGC
62 GTGGATACATCCGGGC
* * * *
1695 -AAGACCGAAGGCATTTGTGCGAATGATATATCCGGGCTAAGACCGAAGGCAATTGTGCAAGTTG
1 TAAGACCGAAGGCATTCGTGCGAATGATATACCCGGGCTAAGACCGAAGGCAATTGAGCAAGTGG
1759 ATACATCCGGGC
66 ATACATCCGGGC
* * * **
1771 TAAGACCCGAAGGCATTCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGAGCTTG
1 TAAGA-CCGAAGGCATTCGTGCGA-ATGATATACCCGGGCTAAGA-CCGAAGGCAATTGAGCAAG
* *
1836 TGGTTATATCCGGGC
63 TGGATACATCCGGGC
1851 TAA-ATTCCGAAGAGCATTCGTGC
1 TAAGA--CCGAAG-GCATTCGTGC
1874 TAGTGAGGTA
Statistics
Matches: 226, Mismatches: 16, Indels: 24
0.85 0.06 0.09
Matches are distributed among these distances:
72 5 0.02
73 22 0.10
74 32 0.14
75 7 0.03
76 6 0.03
77 5 0.02
78 37 0.16
79 33 0.15
80 69 0.31
81 10 0.04
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (77 bp):
TAAGACCGAAGGCATTCGTGCGAATGATATACCCGGGCTAAGACCGAAGGCAATTGAGCAAGTGG
ATACATCCGGGC
Found at i:1955 original size:40 final size:40
Alignment explanation
Indices: 1721--1958 Score: 157
Period size: 40 Copynumber: 6.0 Consensus size: 40
1711 GTGCGAATGA
* * * *
1721 TATATCCGGGCTAAG-ACCGAAG-GCAATT-GTGCAAGTTGA
1 TATATCCGGGCTAAGTTCCGAAGAGC-ATTCGTGC-TGGTGT
* ** *
1760 TACATCCGGGCTAAGACCCGAAG-GCATTCGTGC-GAGTTGC
1 TATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTG-G-TGT
* * ** * *
1800 TATACCCGGGTTAAGACCCGAAG-GCAATT-GAGCTTGTGGT
1 TATATCCGGGCTAAGTTCCGAAGAGC-ATTCGTGCTGGT-GT
* * *
1840 TATATCCGGGCTAAATTCCGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGT
** *
1880 GGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGT
* * * *
1920 TATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTG
1 TATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTG
1959 ACATGTATTC
Statistics
Matches: 159, Mismatches: 31, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
38 1 0.01
39 18 0.11
40 129 0.81
41 11 0.07
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.24
Consensus pattern (40 bp):
TATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGT
Found at i:4413 original size:13 final size:13
Alignment explanation
Indices: 4395--4419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4385 TAATGGTATA
4395 TTGAATCCATGAC
1 TTGAATCCATGAC
4408 TTGAATCCATGA
1 TTGAATCCATGA
4420 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:6196 original size:47 final size:47
Alignment explanation
Indices: 6072--6485 Score: 498
Period size: 47 Copynumber: 9.1 Consensus size: 47
6062 GAAATGATAG
6072 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
6119 T-A-G-CTAATGG-CGA--TG-TGAATGTG-AAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
6158 TAAGGCCTAATGGCCGATGTGATGACTGTGAAAGTGTATATATGTGAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-A
* * *
6206 TAGGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
6253 TAAGGCCTAATGGCCGATGTGATGACTGTGAAAGTGTATATATGTGAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-A
* * * **
6301 TAGGGCTTAATGGCCGATGTGATGAATGCGAAAGTGTATATGCGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* **
6348 TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGCGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
6395 TAAGGCTTAATGGCC-A-ATG-TG-A--TG-AAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
6435 CAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
6482 TAAG
1 TAAG
6486 TCTCGAAGGG
Statistics
Matches: 320, Mismatches: 30, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
39 17 0.05
40 33 0.10
41 6 0.02
42 9 0.03
43 9 0.03
44 10 0.03
45 5 0.02
46 11 0.03
47 136 0.43
48 84 0.26
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:6241 original size:95 final size:94
Alignment explanation
Indices: 6072--6420 Score: 534
Period size: 95 Copynumber: 3.8 Consensus size: 94
6062 GAAATGATAG
6072 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATA--GC-TAATGG-CGA-
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCTTAATGGCCGAT
*
6132 -TG-TGAATGTG-AAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATGTGTGA
*
6158 TAAGGCCTAATGGCCGATGTGATGACTGTGAAAGTGTATATATGTGAATAGGGCTTAATGGCCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-ATAGGGCTTAATGGCCGA
6223 TGTGATGAATGTGAAAGTGTATATGTGTGA
65 TGTGATGAATGTGAAAGTGTATATGTGTGA
*
6253 TAAGGCCTAATGGCCGATGTGATGACTGTGAAAGTGTATATATGTGAATAGGGCTTAATGGCCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-ATAGGGCTTAATGGCCGA
* *
6318 TGTGATGAATGCGAAAGTGTATATGCGTGA
65 TGTGATGAATGTGAAAGTGTATATGTGTGA
* ** * *
6348 TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGCGTGATAAGGCTTAATGGCCAAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCTTAATGGCCGAT
6413 GTGATGAA
66 GTGATGAA
6421 GTGTATATAT
Statistics
Matches: 244, Mismatches: 10, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
86 45 0.18
87 3 0.01
89 2 0.01
90 6 0.02
91 3 0.01
93 2 0.01
94 33 0.14
95 150 0.61
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (94 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCTTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATGTGTGA
Found at i:6398 original size:142 final size:140
Alignment explanation
Indices: 6072--6470 Score: 516
Period size: 134 Copynumber: 2.9 Consensus size: 140
6062 GAAATGATAG
* *
6072 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT-A-G-CTAATGG-CGAT
1 TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCGAT
* *
6133 GTGA--ATGTGAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGACTGTGAAAGTGTA
66 GTGATGATGTGAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGCGAAAGTGTA
*
6196 TATATGTGAA
131 TATACGTGAA
*
6206 TAGGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCGAT
1 TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCGAT
* *
6271 GTGATGACTGTGAAAGTGTATATATGTGAATAGGGCTTAATGGCCGATGTGATGAATGCGAAAGT
66 GTGATGA-TGTG-AAGTGTATATATGTG-ATAAGGCCTAATGGCCGATGTGATGAATGCGAAAGT
*
6336 GTATATGCGTG-A
128 GTATATACGTGAA
* *
6348 TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGCGTGATAAGGCTTAATGGCC-A-
1 TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCGAT
* * * * * * * *
6411 ATG-TGA--TGAAGTGTATATATGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTG
66 GTGATGATGTGAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGCGAAAGTG
6471 CATAAATGTG
Statistics
Matches: 236, Mismatches: 20, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
134 75 0.32
135 16 0.07
136 3 0.01
137 7 0.03
138 8 0.03
139 3 0.01
140 3 0.01
141 5 0.02
142 75 0.32
143 41 0.17
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (140 bp):
TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCGAT
GTGATGATGTGAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGCGAAAGTGTA
TATACGTGAA
Found at i:6660 original size:37 final size:37
Alignment explanation
Indices: 6606--6681 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
6596 GAGTTCTAAG
* *
6606 GACCCGATGACTACGTGTGGGGATTTTGTCCGGGTAA
1 GACCCGATAACTACGTGTGGGGATTATGTCCGGGTAA
*
6643 GACCCGATAACTTCGTGTGGGGATTATGTCCGGGTAA
1 GACCCGATAACTACGTGTGGGGATTATGTCCGGGTAA
6680 GA
1 GA
6682 TTTCGTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.26
Consensus pattern (37 bp):
GACCCGATAACTACGTGTGGGGATTATGTCCGGGTAA
Found at i:9179 original size:31 final size:31
Alignment explanation
Indices: 9133--9207 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
9123 ACGGTTACTA
*
9133 GGCCGAAGCCTTTTCATAAATCATATCACTG
1 GGCCAAAGCCTTTTCATAAATCATATCACTG
* * *
9164 GGCCAAAGCTTTTTCATAAATTATTTCACTG
1 GGCCAAAGCCTTTTCATAAATCATATCACTG
**
9195 GGCTGAAGCCTTT
1 GGCCAAAGCCTTT
9208 ACTGTAAACG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (31 bp):
GGCCAAAGCCTTTTCATAAATCATATCACTG
Found at i:9278 original size:42 final size:42
Alignment explanation
Indices: 9231--9322 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
9221 TAGCCTATAG
* * **
9231 GCCCATTTCAATATCACATGTAAT-GTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACT-AATAAATGTATGCAA
9273 GCCCATTTCAATATCACATGAAATACTAATAAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACTAATAAATGTATGCAA
9315 GCCCATTT
1 GCCCATTT
9323 GGGGAGACTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACTAATAAATGTATGCAA
Found at i:9519 original size:26 final size:26
Alignment explanation
Indices: 9467--9616 Score: 248
Period size: 26 Copynumber: 5.8 Consensus size: 26
9457 CCTCTTTAAT
9467 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
9492 AACTGGGGCATAAACCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
*
9518 AACTGGGGCATAAGCCCTTTTCGTTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
*
9544 AACTGGGGCATAAGCCGTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
9570 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
9596 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
9617 GCACTTCCTC
Statistics
Matches: 115, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 10 0.09
26 105 0.91
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:10519 original size:27 final size:27
Alignment explanation
Indices: 10419--10502 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
10409 GGGCATATTC
* *
10419 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
10446 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
10473 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
10500 GTC
1 GTC
10503 TTTTTACCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
27 53 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:10571 original size:27 final size:27
Alignment explanation
Indices: 10554--10606 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
10544 GGGTGTTTTG
10554 GTAAATCTACAAACCAAGGGTATTTCA
1 GTAAATCTACAAACCAAGGGTATTTCA
* * *
10581 GTAATTTTACAAACCAATGGTATTTC
1 GTAAATCTACAAACCAAGGGTATTTC
10607 CATAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (27 bp):
GTAAATCTACAAACCAAGGGTATTTCA
Found at i:10634 original size:29 final size:27
Alignment explanation
Indices: 10561--10885 Score: 145
Period size: 27 Copynumber: 12.0 Consensus size: 27
10551 TTGGTAAATC
10561 TACAAACCAAGGGTATTTCAGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
*
10588 TACAAACCAATGGTATTTCCA-TAATTTT
1 TACAAACCAAGGGTATTT-CAGTAA-TTT
* * ** *
10616 TAGAAAGTCAAGGGTATTTTTGTAACTT
1 TACAAA-CCAAGGGTATTTCAGTAATTT
** * ** **
10644 TGTAAATCTGGGGTATTTTGGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
*** **
10671 TACAAATTGAGGGTATTTTGGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
* * **
10698 CACAAACC-AGTGATATTTTGGTAATTT
1 TACAAACCAAG-GGTATTTCAGTAATTT
** * **
10725 TACAAAGTAGGGGTATTTTGGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
*** *
10752 TACAAATTGAGGGTATTTCGGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
* * *
10779 TACAAACCAGGGGTATTTTAGCAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
* * * **
10806 TATAGACTAA-GGTATTTTGGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
** * * **
10832 TACTGATCGAGGGTATTTTGGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
** * *
10859 TGTAAA-CAAGGGCATTTTAGTAATTT
1 TACAAACCAAGGGTATTTCAGTAATTT
10885 T
1 T
10886 GTAAATCGAG
Statistics
Matches: 235, Mismatches: 56, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
26 39 0.17
27 166 0.71
28 17 0.07
29 13 0.06
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.41
Consensus pattern (27 bp):
TACAAACCAAGGGTATTTCAGTAATTT
Found at i:10715 original size:54 final size:53
Alignment explanation
Indices: 10655--10897 Score: 217
Period size: 54 Copynumber: 4.5 Consensus size: 53
10645 GTAAATCTGG
* * *
10655 GGTATTTTGGTAATTTTACAAATTGA-GGGTATTTTGGTAATTTCACAAACCA
1 GGTATTTTGGTAATTTTACAAATCGAGGGGTATTTTGGTAATTTTACAAACAA
* *
10707 GTGATATTTTGGTAATTTTACAAA--GTAGGGGTATTTTGGTAATTTTACAAATTGAG
1 G-G-TATTTTGGTAATTTTACAAATCG-AGGGGTATTTTGGTAATTTTACAAA--CAA
* * * * * *
10763 GGTATTTCGGTAATTTTACAAA-CCAGGGGTATTTTAGCAATTTTATAGACTAA
1 GGTATTTTGGTAATTTTACAAATCGAGGGGTATTTTGGTAATTTTACAAAC-AA
** **
10816 GGTATTTTGGTAATTTTACTGATCGA-GGGTATTTTGGTAATTTTGTAAACAA
1 GGTATTTTGGTAATTTTACAAATCGAGGGGTATTTTGGTAATTTTACAAACAA
* * **
10868 GGGCATTTTAGTAATTTTGTAAATCGAGGG
1 -GGTATTTTGGTAATTTTACAAATCGAGGG
10898 TAAAACAGTA
Statistics
Matches: 154, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
52 4 0.03
53 62 0.40
54 86 0.56
55 1 0.01
56 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (53 bp):
GGTATTTTGGTAATTTTACAAATCGAGGGGTATTTTGGTAATTTTACAAACAA
Found at i:10753 original size:81 final size:81
Alignment explanation
Indices: 10653--10858 Score: 288
Period size: 81 Copynumber: 2.6 Consensus size: 81
10643 TTGTAAATCT
* *
10653 GGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAACCAGTGATATTTTG
1 GGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAACCAGGGATATTTTA
* *
10718 GTAATTTTACAAAGTA
66 GCAATTTTACAAACTA
* * *
10734 GGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGGGGTATTTTA
1 GGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAACCAGGGATATTTTA
* *
10799 GCAATTTTATAGACTA
66 GCAATTTTACAAACTA
* ** *
10815 -AGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTT
1 GGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTT
10859 TGTAAACAAG
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 39 0.35
81 72 0.65
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (81 bp):
GGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAAACCAGGGATATTTTA
GCAATTTTACAAACTA
Found at i:10881 original size:26 final size:26
Alignment explanation
Indices: 10841--10890 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
10831 TTACTGATCG
* *
10841 AGGGTATTTTGGTAATTTTGTAAACA
1 AGGGCATTTTAGTAATTTTGTAAACA
10867 AGGGCATTTTAGTAATTTTGTAAA
1 AGGGCATTTTAGTAATTTTGTAAA
10891 TCGAGGGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.04, G:0.22, T:0.42
Consensus pattern (26 bp):
AGGGCATTTTAGTAATTTTGTAAACA
Found at i:10907 original size:27 final size:27
Alignment explanation
Indices: 10877--10981 Score: 142
Period size: 27 Copynumber: 3.9 Consensus size: 27
10867 AGGGCATTTT
*
10877 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
10904 AGTAATTCTGTAAATCAAGGGTAAAA-
1 AGTAATTCTGTAAATCGAGGGTAAAAC
10930 ATGGTAATTCTGTAAATCGAGGGTAAAAC
1 A--GTAATTCTGTAAATCGAGGGTAAAAC
*
10959 -GATAATTCTATAAATCGAGGGTA
1 AG-TAATTCTGTAAATCGAGGGTA
10982 CTTTGGTAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
26 2 0.03
27 44 0.63
28 24 0.34
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:10952 original size:55 final size:55
Alignment explanation
Indices: 10878--10981 Score: 165
Period size: 55 Copynumber: 1.9 Consensus size: 55
10868 GGGCATTTTA
* *
10878 GTAATTTTGTAAATCGAGGGTAAAAC-AGTAATTCTGTAAATCAAGGGTAAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACGA-TAATTCTATAAATCAAGGGTAAAAATG
*
10933 GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTATAAATCAAGGGTA
10982 CTTTGGTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
55 44 0.98
56 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (55 bp):
GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTATAAATCAAGGGTAAAAATG
Found at i:12676 original size:27 final size:27
Alignment explanation
Indices: 12548--12675 Score: 168
Period size: 27 Copynumber: 4.7 Consensus size: 27
12538 CCAAATTGTT
12548 TAAAATTACCGAAATACCCCC-AGTTTG
1 TAAAATTACCGAAATACCCCCGA-TTTG
12575 TAAAATTACCGAAATACCCCCGATTTG
1 TAAAATTACCGAAATACCCCCGATTTG
**
12602 TAAAATTATTGAAATACCCCCGATTTG
1 TAAAATTACCGAAATACCCCCGATTTG
** **
12629 TAAAATTACTAAAATACCCCTTATTTG
1 TAAAATTACCGAAATACCCCCGATTTG
* *
12656 TAAAATTATCAAAATACCCC
1 TAAAATTACCGAAATACCCC
12676 TGTAGGGTAA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 91 0.99
28 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.30
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCCCGATTTG
Found at i:12685 original size:27 final size:27
Alignment explanation
Indices: 12574--12688 Score: 72
Period size: 27 Copynumber: 4.3 Consensus size: 27
12564 CCCCCAGTTT
** ** **
12574 GTAAAATTACCGAAATACCCCCGATTT
1 GTAAAATTACTAAAATACCCCTTATGG
* * ** **
12601 GTAAAATTATTGAAATACCCCCGATTT
1 GTAAAATTACTAAAATACCCCTTATGG
**
12628 GTAAAATTACTAAAATACCCCTTATTT
1 GTAAAATTACTAAAATACCCCTTATGG
12655 GTAAAATTA-TCAAAATACCCCTGTA-GG
1 GTAAAATTACT-AAAATACCCCT-TATGG
12682 GTAAAAT
1 GTAAAAT
12689 GATTGTTTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.01
27 75 0.96
28 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (27 bp):
GTAAAATTACTAAAATACCCCTTATGG
Found at i:15575 original size:90 final size:90
Alignment explanation
Indices: 15422--15590 Score: 223
Period size: 90 Copynumber: 1.9 Consensus size: 90
15412 TACCAATGCC
* * * *
15422 ATATCCCAGATATGGCCTTACATGGGATCACAACTCGATGCTAATGCCATGTCCCAGACATGGTC
1 ATATCCCAGATATGGCCTTACATGAGAACACAACTCGATGCCAATGCCATATCCCAGACATGGTC
*
15487 TTACATGGGATCTCCTATTAAATTT
66 TTACACGGGATCTCCTATTAAATTT
* * ** *
15512 ATATCCCAGATATGGTCTTACATGATAACACATACT-GATGCCAATGCCATATCCTGGATATGGT
1 ATATCCCAGATATGGCCTTACATGAGAACACA-ACTCGATGCCAATGCCATATCCCAGACATGGT
*
15576 CTTATACGGGATCTC
65 CTTACACGGGATCTC
15591 ATCACCCCAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
90 64 0.96
91 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (90 bp):
ATATCCCAGATATGGCCTTACATGAGAACACAACTCGATGCCAATGCCATATCCCAGACATGGTC
TTACACGGGATCTCCTATTAAATTT
Found at i:22600 original size:46 final size:45
Alignment explanation
Indices: 22531--22701 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 45
22521 TTAACCCGCC
* *
22531 CCTAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCAT
* *
22576 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTC--A-GAC--GTTCGCAT
* * *
22626 -CTCA-CGAACTCGGACTCAACTCAACGAGTTC-GAACATTCGCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCAG-ACGTTCGCAT
22669 CCGTAAGTGAACTCGGACTCAACTCAACGAGTT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTT
22702 TGGATGCTCA
Statistics
Matches: 105, Mismatches: 10, Indels: 21
0.77 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 55 0.52
47 26 0.25
48 3 0.03
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
CCTAAGTGAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCAT
Found at i:22650 original size:93 final size:93
Alignment explanation
Indices: 22538--22708 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
22528 GCCCCTAAGT
* *
22538 GAACTCGGACTCAACTCAACGAGCTC-AGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGA-ACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
22602 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* *
22631 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCGTAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
22696 CGAGTTTGGATGC
66 CGAGTTCGGATGC
22709 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 71 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:22724 original size:46 final size:46
Alignment explanation
Indices: 22531--22724 Score: 159
Period size: 46 Copynumber: 4.2 Consensus size: 46
22521 TTAACCCGCC
* * * *
22531 CCTAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTC-GCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTC-GGATGCTCAACAT
22576 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTACAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACAT
* * * *** *
22626 -CTCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTC-GCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACAT
*
22669 CCGTAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCTCAACCAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAA-CAT
22717 CCT-AGTGA
1 CCTAAGTGA
22725 CATGTCACTT
Statistics
Matches: 117, Mismatches: 19, Indels: 25
0.73 0.12 0.16
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 7 0.06
46 65 0.56
47 29 0.25
48 8 0.07
49 1 0.01
50 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACAT
Found at i:34754 original size:30 final size:30
Alignment explanation
Indices: 34696--34754 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
34686 ATTTTTGGGT
* * **
34696 CTAGGGGTAAAATGGTTATTTTGTCAAAGC
1 CTAGGGATAAAATGGTCATTTTACCAAAGC
*
34726 CTAGGGATAGAATGGTCATTTTACCAAAG
1 CTAGGGATAAAATGGTCATTTTACCAAAG
34755 TTATAATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (30 bp):
CTAGGGATAAAATGGTCATTTTACCAAAGC
Found at i:35242 original size:46 final size:45
Alignment explanation
Indices: 35095--35262 Score: 155
Period size: 46 Copynumber: 3.6 Consensus size: 45
35085 ATTGTGAGCT
*
35095 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGA-G-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTC--TA-GACGTAGCC
* * *
35141 AATGTAAGACCATGTCTGGGACATGGCATCAGCAT-TGAGACAGGT-GCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCT-AGAC--GTAGCC
* *
35189 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCTAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCTAGACGT-AGCC
* *
35235 AGTGTAAGACATGTCTGGTACCTGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
35263 GACTACGAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
44 2 0.02
45 3 0.03
46 48 0.48
47 28 0.28
48 19 0.19
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCTAGACGTAGCC
Found at i:36447 original size:13 final size:13
Alignment explanation
Indices: 36429--36456 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36419 GTGTGAGCCA
36429 CATGAGCCATCAG
1 CATGAGCCATCAG
36442 CATGAGCCATCAG
1 CATGAGCCATCAG
36455 CA
1 CA
36457 CGAACATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.14
Consensus pattern (13 bp):
CATGAGCCATCAG
Found at i:45417 original size:16 final size:17
Alignment explanation
Indices: 45384--45417 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45374 TCGGGCAATA
*
45384 ACCATGCATTTCCAAAC
1 ACCATGCATATCCAAAC
45401 ACCATGCATAT-CAAAC
1 ACCATGCATATCCAAAC
45417 A
1 A
45418 TAGTATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (17 bp):
ACCATGCATATCCAAAC
Found at i:45959 original size:75 final size:75
Alignment explanation
Indices: 45864--46035 Score: 283
Period size: 75 Copynumber: 2.3 Consensus size: 75
45854 AAAGAAAAAT
* * *
45864 TAGGATTATACCCTAATTAATAGAGAAGGCAAAT-GAAAGGTTAGAAAAATGAATTATATTCTTT
1 TAGGATTATTCCCTTATTAATAGAGAAGGCAAATAGAAA-GTTAGAAAAAAGAATTATATTCTTT
*
45928 CCAAAATAATA
65 CCAAAAGAATA
*
45939 TAGGATTATTCTCTTATTAATAGAGAAGGCAAATAGAAAGTTAGAAAAAAGAATTATATTCTTTC
1 TAGGATTATTCCCTTATTAATAGAGAAGGCAAATAGAAAGTTAGAAAAAAGAATTATATTCTTTC
46004 CAAAAGAATA
66 CAAAAGAATA
46014 TAGGATTATTCCCTTATTAATA
1 TAGGATTATTCCCTTATTAATA
46036 TAAAGTTAAA
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
75 86 0.96
76 4 0.04
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (75 bp):
TAGGATTATTCCCTTATTAATAGAGAAGGCAAATAGAAAGTTAGAAAAAAGAATTATATTCTTTC
CAAAAGAATA
Found at i:46258 original size:137 final size:138
Alignment explanation
Indices: 46052--46334 Score: 433
Period size: 137 Copynumber: 2.1 Consensus size: 138
46042 TAAAAAAAGA
* **
46052 AATTATATTCTTTCCAAAATAATATTAATTTCCATATCTTTTATATTTTGATTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAA
* ** *
46117 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAAAATTTTGTATGAATCAAATT
66 TATAATTATTTATATTAATAAATTCAGTAAAATATATACAATTAAAATTTTATATGAATCAAATT
*
46182 CATATAAT
131 CACATAAT
* *
46190 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTC-TTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAA
* * *
46254 TATAATTATTTATATTAATAAATTCAGTCAAATCTATACAATTAATATTTTATATGAATCAAATT
66 TATAATTATTTATATTAATAAATTCAGTAAAATATATACAATTAAAATTTTATATGAATCAAATT
*
46319 CACATATT
131 CACATAAT
46327 AATTATAT
1 AATTATAT
46335 CTATGTTCTC
Statistics
Matches: 131, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
137 96 0.73
138 35 0.27
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAA
TATAATTATTTATATTAATAAATTCAGTAAAATATATACAATTAAAATTTTATATGAATCAAATT
CACATAAT
Found at i:49301 original size:54 final size:54
Alignment explanation
Indices: 49231--49363 Score: 212
Period size: 54 Copynumber: 2.5 Consensus size: 54
49221 GTCATTCAGA
* * *
49231 GGGATTTAGCCTAGACTAGTAATCCCGACATTGCTATATGAGTTACTACTATGG
1 GGGATTTAGCCTAGACTGGTAATCCCGACATTGCTATATAAGTTACTACTACGG
*
49285 GGGATTTAGCCTAGACTGGTAATCCCGACATTGCTCTATAAGTTACTACTACGG
1 GGGATTTAGCCTAGACTGGTAATCCCGACATTGCTATATAAGTTACTACTACGG
**
49339 GAAATTTAGCCTAGACTGGTAATCC
1 GGGATTTAGCCTAGACTGGTAATCC
49364 TGCCGTAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 73 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (54 bp):
GGGATTTAGCCTAGACTGGTAATCCCGACATTGCTATATAAGTTACTACTACGG
Found at i:50224 original size:14 final size:14
Alignment explanation
Indices: 50205--50232 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50195 AATTAGGCCA
50205 TGTTAAATACCATT
1 TGTTAAATACCATT
50219 TGTTAAATACCATT
1 TGTTAAATACCATT
50233 GAAGTCTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TGTTAAATACCATT
Found at i:54966 original size:46 final size:48
Alignment explanation
Indices: 54844--54968 Score: 170
Period size: 46 Copynumber: 2.7 Consensus size: 48
54834 CATGAGAGCC
*
54844 AATGTAAGACCATGTCTGGGACATGGCATCGG-TATTAAGACGAGTGCT
1 AATGTAAGACCATGTCTGGGACATGGCATCGGCTATCAAGAC-AGTGCT
* *
54892 AATGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CAAGA-TGTGTT
1 AATGTAAGACCATGTCTGGGACATGGCATCGGCTATCAAGACAGTGCT
*
54936 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AATGTAAGACCATGTCTGGGACATGGCATCGGC
54969 ACCTTACCCC
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
44 12 0.17
45 14 0.20
46 19 0.27
47 16 0.23
48 9 0.13
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
AATGTAAGACCATGTCTGGGACATGGCATCGGCTATCAAGACAGTGCT
Found at i:57013 original size:22 final size:22
Alignment explanation
Indices: 56985--57029 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
56975 AAGCTCCTAA
*
56985 AGTGCAAAACCTAGTTTAATCT
1 AGTGCAAAAACTAGTTTAATCT
57007 AGTGCAAAAACTAGTTTAATCT
1 AGTGCAAAAACTAGTTTAATCT
57029 A
1 A
57030 CTACACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (22 bp):
AGTGCAAAAACTAGTTTAATCT
Found at i:64365 original size:13 final size:13
Alignment explanation
Indices: 64349--64373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64339 TGGACTGTCC
64349 CGTAGGACCGTCA
1 CGTAGGACCGTCA
64362 CGTAGGACCGTC
1 CGTAGGACCGTC
64374 GTTAGGGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (13 bp):
CGTAGGACCGTCA
Found at i:64969 original size:59 final size:59
Alignment explanation
Indices: 64887--65007 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
64877 ATTTAGGAAT
*
64887 ATGAATATACGTTTATCGAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGC
1 ATGAATATACGTTTATAGAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGC
64946 ATGAATATACGTTTATAGAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGC
1 ATGAATATACGTTTATAGAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGC
65005 ATG
1 ATG
65008 TTAAAAGGAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.32
Consensus pattern (59 bp):
ATGAATATACGTTTATAGAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGC
Found at i:65036 original size:41 final size:41
Alignment explanation
Indices: 64991--65106 Score: 103
Period size: 34 Copynumber: 3.1 Consensus size: 41
64981 TAAGAAAGCA
64991 TTGAAATTTATTGCATGTTAAAAGGATAAATATAAATATTC
1 TTGAAATTTATTGCATGTTAAAAGGATAAATATAAATATTC
* * **
65032 TTG-AA--CA-TGCATGATT--AA-GAT-AAGA-AAGCA---
1 TTGAAATTTATTGCATG-TTAAAAGGATAAATATAAATATTC
65062 TTGAAATTTATTGCATGTTAAAAGGATAAATATAAATATTC
1 TTGAAATTTATTGCATGTTAAAAGGATAAATATAAATATTC
65103 TTGA
1 TTGA
65107 GGATTAGGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 26
0.61 0.09 0.30
Matches are distributed among these distances:
30 3 0.06
31 2 0.04
33 6 0.11
34 9 0.17
35 5 0.09
36 5 0.09
37 9 0.17
38 6 0.11
40 2 0.04
41 7 0.13
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (41 bp):
TTGAAATTTATTGCATGTTAAAAGGATAAATATAAATATTC
Found at i:65070 original size:71 final size:71
Alignment explanation
Indices: 64963--65106 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
64953 TACGTTTATA
64963 GAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGCATGTTAAAAGGATAAATATAAAT
1 GAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGCATGTTAAAAGGATAAATATAAAT
65028 ATTCTT
66 ATTCTT
65034 GAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGCATGTTAAAAGGATAAATATAAAT
1 GAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGCATGTTAAAAGGATAAATATAAAT
65099 ATTCTT
66 ATTCTT
65105 GA
1 GA
65107 GGATTAGGTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (71 bp):
GAACATGCATGATTAAGATAAGAAAGCATTGAAATTTATTGCATGTTAAAAGGATAAATATAAAT
ATTCTT
Found at i:82136 original size:43 final size:44
Alignment explanation
Indices: 82089--82171 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 44
82079 TATATGATTG
*
82089 ATATTGAAATGGAAAAGATGAAAAATG-AATATGAGATGAGAAA
1 ATATTGAAATGGAAAAGATGAAAAATGAAATATGAAATGAGAAA
* * *
82132 ATATTTAAATGGCAAAGATGAGAAATGAAATATGAAATGA
1 ATATTGAAATGGAAAAGATGAAAAATGAAATATGAAATGA
82172 TGAATTGAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 24 0.69
44 11 0.31
ACGTcount: A:0.54, C:0.01, G:0.22, T:0.23
Consensus pattern (44 bp):
ATATTGAAATGGAAAAGATGAAAAATGAAATATGAAATGAGAAA
Found at i:94207 original size:18 final size:18
Alignment explanation
Indices: 94181--94218 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
94171 ACTCAGGTTG
*
94181 CAAAGTTGCGAGCCCATC
1 CAAACTTGCGAGCCCATC
*
94199 CAAACTTGCGAGCTCATC
1 CAAACTTGCGAGCCCATC
94217 CA
1 CA
94219 GAGTTGTGAG
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:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (18 bp):
CAAACTTGCGAGCCCATC
Found at i:97518 original size:42 final size:42
Alignment explanation
Indices: 97413--97574 Score: 182
Period size: 43 Copynumber: 3.8 Consensus size: 42
97403 TGATATGTTT
* * *
97413 TTTCGTGTAAGACCATGTATGGGACGTTGGCATCG-ACTTATGA
1 TTTCATGTAAGACCATGTCTGGGACATTGGCATCGTA-TT-TGA
* *
97456 TTTACACGTAAGACCATGTCTGGGACATTAGCATCGTATTTGA
1 TTT-CATGTAAGACCATGTCTGGGACATTGGCATCGTATTTGA
* *
97499 TTTCATGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGA
1 TTTCATGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGA
* * * *
97542 TTACATGTAAGACCACGTCTAGGACGTTGGCAT
1 TTTCATGTAAGACCATGTCTGGGACATTGGCAT
97575 TGTACAAGTT
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
42 28 0.28
43 43 0.43
44 29 0.29
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
TTTCATGTAAGACCATGTCTGGGACATTGGCATCGTATTTGA
Found at i:111384 original size:74 final size:73
Alignment explanation
Indices: 111254--111401 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 73
111244 TCTTACGTGA
*
111254 TTCCAATCGATCGAGCATCCAATGATCTATAAAGAGAGAAAAATAACTGTGTAAGAACTAATGCT
1 TTCCAATCGATCGAGCATCAAATGATCTATAAAGAGAGAAAAATAACTGTGTAAGAACTAATGCT
111319 TAGTAAGC
66 TAGTAAGC
*
111327 TTCCGATCGATCGAGCATCAAATGATCTATAAAAGAGAGAAAAATAACTGTGTAAGAACTAATGC
1 TTCCAATCGATCGAGCATCAAATGATCTAT-AAAGAGAGAAAAATAACTGTGTAAGAACTAATGC
111392 TTAGTAAGC
65 TTAGTAAGC
111401 T
1 T
111402 CGTATGAAGG
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 28 0.39
74 44 0.61
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (73 bp):
TTCCAATCGATCGAGCATCAAATGATCTATAAAGAGAGAAAAATAACTGTGTAAGAACTAATGCT
TAGTAAGC
Found at i:112149 original size:20 final size:20
Alignment explanation
Indices: 112099--112162 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
112089 TCGAAATGCT
*
112099 AATAGAGGCACCGTAGTGCA
1 AATAGAGGCACCGAAGTGCA
*
112119 AATAAAGAGGCATCGAAGTGCA
1 AAT--AGAGGCACCGAAGTGCA
*
112141 AATAGAGGCACCAAAGTGCA
1 AATAGAGGCACCGAAGTGCA
112161 AA
1 AA
112163 CCTGTACAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 20 0.53
22 18 0.47
ACGTcount: A:0.44, C:0.17, G:0.27, T:0.12
Consensus pattern (20 bp):
AATAGAGGCACCGAAGTGCA
Found at i:117287 original size:32 final size:31
Alignment explanation
Indices: 117220--117287 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 31
117210 TTAATCATTG
* * *
117220 AACTTGACAATTATTCCTATATTGGGGCTTG
1 AACTTGACAATTATTCCTATATTAGGGCCTA
* * *
117251 AACTTGGCAATTTGTTCCTATGTTAGGGCCTA
1 AACTTGACAA-TTATTCCTATATTAGGGCCTA
117283 AACTT
1 AACTT
117288 TAAGGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (31 bp):
AACTTGACAATTATTCCTATATTAGGGCCTA
Found at i:117440 original size:16 final size:17
Alignment explanation
Indices: 117419--117451 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
117409 TTACCAAATT
117419 TAAACCCGAAAA-AAAA
1 TAAACCCGAAAATAAAA
117435 TAAACCCGAAAATAAAA
1 TAAACCCGAAAATAAAA
117452 ATGTGTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (17 bp):
TAAACCCGAAAATAAAA
Found at i:119196 original size:17 final size:17
Alignment explanation
Indices: 119150--119198 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
119140 AAAATATGAT
*
119150 TTTAAAGTAACTAATTA
1 TTTAAAGTAATTAATTA
**
119167 GATAATAGT-ATTAATTA
1 TTTAA-AGTAATTAATTA
119184 TTTAAAGTAATTAAT
1 TTTAAAGTAATTAAT
119199 GATATTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 3 0.12
17 19 0.76
18 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (17 bp):
TTTAAAGTAATTAATTA
Found at i:119585 original size:27 final size:27
Alignment explanation
Indices: 119555--119607 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
119545 ATTTTAAAGG
119555 TTCAATTTCCATTATAGGAAGAGACTA
1 TTCAATTTCCATTATAGGAAGAGACTA
119582 TTCAATTTCCATTATAGGAAGAGACT
1 TTCAATTTCCATTATAGGAAGAGACT
119608 GACCCCCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (27 bp):
TTCAATTTCCATTATAGGAAGAGACTA
Found at i:129472 original size:26 final size:26
Alignment explanation
Indices: 129436--129489 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
129426 CATTTGGAAA
129436 TCATACCAACAAATTCCAATATTCTT
1 TCATACCAACAAATTCCAATATTCTT
129462 TCATACCAACAAATTCCAATATTCTT
1 TCATACCAACAAATTCCAATATTCTT
129488 TC
1 TC
129490 TTTCTTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (26 bp):
TCATACCAACAAATTCCAATATTCTT
Found at i:135453 original size:49 final size:49
Alignment explanation
Indices: 135397--135579 Score: 188
Period size: 50 Copynumber: 3.7 Consensus size: 49
135387 CTGGTACGCA
* *
135397 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATTC-GTTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTA-TCGGATACATG
* ** * *
135446 TAGTAGCCTGCACTTAGTACTACACATGTAACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC-AATTATCGGATACATG
* ** * * * *
135496 TAGTAGCCAGCACTTAGTACTACACACATGATCGAAGTTATCGGGTACGTA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCGGATACATG
*
135547 TAGTAGCTTGCACTTAGTACTACACATGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
135580 TCACAATAGA
Statistics
Matches: 107, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 33 0.31
50 39 0.36
51 35 0.33
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCGGATACATG
Found at i:135856 original size:27 final size:27
Alignment explanation
Indices: 135826--135879 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
135816 TCATACAACC
*
135826 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAATAATAATTTAACATTCAATT
* **
135853 CATGTGATAATAATTTGCCATTCAATT
1 CATGTAATAATAATTTAACATTCAATT
135880 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (27 bp):
CATGTAATAATAATTTAACATTCAATT
Found at i:140049 original size:27 final size:27
Alignment explanation
Indices: 140019--140196 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
140009 ATATCGAGTC
* *
140019 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
140046 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
140073 CGCACACTTAGTGCCACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
140101 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
140128 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
140155 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
140182 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
140197 GTACAATTTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:140158 original size:82 final size:81
Alignment explanation
Indices: 140040--140195 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
140030 TGCTATATAA
*
140040 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCCACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
140105 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
140122 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
140186 CACTTAGTGC
65 CACTTAGTGC
140196 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.