Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2163
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: 59531
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Found at i:8816 original size:20 final size:20
Alignment explanation
Indices: 8791--8919 Score: 73
Period size: 20 Copynumber: 5.9 Consensus size: 20
8781 GTAAAAAGAC
8791 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
8811 AGAATGCATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
8831 TA-CATGTATCGATACATCTGGGTAAAA
1 -AGAATGTATCGATACAT-T--G----A
*
8858 AGACATAATGTATCGATACATTCA
1 AG----AATGTATCGATACATTGA
*
8882 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
8902 AAAATGTATCGATACATT
1 AGAATGTATCGATACATT
8920 TGGGAAAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 30
0.68 0.08 0.24
Matches are distributed among these distances:
19 1 0.01
20 62 0.74
21 2 0.02
24 1 0.01
25 1 0.01
26 1 0.01
27 1 0.01
30 1 0.01
31 14 0.17
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:8838 original size:71 final size:71
Alignment explanation
Indices: 8743--9000 Score: 351
Period size: 71 Copynumber: 3.6 Consensus size: 71
8733 TTTTAACTAG
* *
8743 ATGTATCGATACATTATTCAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTATACAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
* *
8808 TGA-AGA
66 TCATA-C
* *
8814 ATGCATCGATACATTCATAC-ATGTATCGATACATCTGGGTAAAAAGACATAATGTATCGATACA
1 ATGTATCGATACATT-ATACAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACA
8878 TTCATAC
65 TTCATAC
* * * *
8885 ATGTATCGATACATTGA-AAAATGTATCGATACATTTGGGAAAAAAGACAGAATGTATCGATGCA
1 ATGTATCGATACATT-ATACAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACA
8949 TTCATAC
65 TTCATAC
* * *
8956 ATGTATCGATACATTTTTCAATGTATCAATACATCTGGGTAAAAA
1 ATGTATCGATACATTATACAATGTATCGATACATCTGGGTAAAAA
9001 TGTGGTTTTC
Statistics
Matches: 164, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
70 1 0.01
71 159 0.97
72 4 0.02
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (71 bp):
ATGTATCGATACATTATACAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
TCATAC
Found at i:21604 original size:20 final size:21
Alignment explanation
Indices: 21579--21635 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
21569 GTAAAAAGAC
*
21579 AGAATGTATCGATACATTGA-
1 AGAATGTATCGATACATTCAT
*
21599 AGAATGCATCGATACATTCAT
1 AGAATGTATCGATACATTCAT
*
21620 A-CATGTATCGATACAT
1 AGAATGTATCGATACAT
21636 CTGGGTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (21 bp):
AGAATGTATCGATACATTCAT
Found at i:21626 original size:71 final size:71
Alignment explanation
Indices: 21535--21687 Score: 245
Period size: 71 Copynumber: 2.2 Consensus size: 71
21525 AACTAGATGT
*
21535 ATCGATACATTATTCAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGATACATTGAA
1 ATCGATACATTATACAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGATACATTGAA
*
21600 GAATGC
66 AAATGC
* *
21606 ATCGATACATTCATAC-ATGTATCGATACATCTGGGTAAAAAGACATAATGTATCGATACATTGA
1 ATCGATACATT-ATACAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGATACATTGA
*
21670 AAAATGT
65 AAAATGC
21677 ATCGATACATT
1 ATCGATACATT
21688 TGGGAAAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
71 73 0.96
72 3 0.04
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (71 bp):
ATCGATACATTATACAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGATACATTGAA
AAATGC
Found at i:21729 original size:52 final size:51
Alignment explanation
Indices: 21599--21740 Score: 203
Period size: 52 Copynumber: 2.8 Consensus size: 51
21589 GATACATTGA
* * *
21599 AGAATGCATCGATACATTCATACATGTATCGATACATCTGGGTAAAAAGAC
1 AGAATGTATCGATACATTCATACATGTATCGATACATTTGGGAAAAAAGAC
* * * *
21650 ATAATGTATCGATACATTGAAAAATGTATCGATACATTTGGGAAAAAAAGAC
1 AGAATGTATCGATACATTCATACATGTATCGATACATTTGGG-AAAAAAGAC
*
21702 AGAATGTATCGATGCATTCATACATGTATCGATACATTT
1 AGAATGTATCGATACATTCATACATGTATCGATACATTT
21741 TTCAATGTAT
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
51 36 0.46
52 42 0.54
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (51 bp):
AGAATGTATCGATACATTCATACATGTATCGATACATTTGGGAAAAAAGAC
Found at i:21749 original size:123 final size:122
Alignment explanation
Indices: 21531--21769 Score: 313
Period size: 123 Copynumber: 2.0 Consensus size: 122
21521 TTTTAACTAG
** *
21531 ATGTATCGATACATTATTCAATGTATCGATACATCTAGGTAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTATAAAATGTATCGATACATCTAGGAAAAAAGACAGAATGTATCGATACAT
* *
21596 TGAAGAATGCATCGATACATTCATACATGTATCGATACATCTGGGTAAAAAGACATA
66 TCAAGAATGCATCGATACATTCATACATGTATCAATACATCTGGGTAAAAAGACATA
* * *
21653 ATGTATCGATACATTGA-AAAATGTATCGATACATTTGGGAAAAAAAGACAGAATGTATCGATGC
1 ATGTATCGATACATT-ATAAAATGTATCGATACATCTAGG-AAAAAAGACAGAATGTATCGATAC
* * * *
21717 ATTCATA-CATGTATCGATACATT-TTTCAATGTATCAATACATCTGGGTAAAAA
64 ATTCA-AGAATGCATCGATACATTCATAC-ATGTATCAATACATCTGGGTAAAAA
21770 TGTGGCTTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
122 35 0.35
123 65 0.64
124 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (122 bp):
ATGTATCGATACATTATAAAATGTATCGATACATCTAGGAAAAAAGACAGAATGTATCGATACAT
TCAAGAATGCATCGATACATTCATACATGTATCAATACATCTGGGTAAAAAGACATA
Found at i:25056 original size:31 final size:31
Alignment explanation
Indices: 24952--25049 Score: 133
Period size: 31 Copynumber: 3.2 Consensus size: 31
24942 CATTAGATAG
* * * *
24952 TGTATTGAAACATCTGGGTACAAACCCAGAA
1 TGTATCGATACATCTGGGTAAAAACCTAGAA
*
24983 TGTATCGATACATCTGGGTGAAAACCTAGAA
1 TGTATCGATACATCTGGGTAAAAACCTAGAA
* *
25014 TGTATCGATACATCTGGGTAAAAACTTAAAA
1 TGTATCGATACATCTGGGTAAAAACCTAGAA
25045 TGTAT
1 TGTAT
25050 TTATACAATG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (31 bp):
TGTATCGATACATCTGGGTAAAAACCTAGAA
Found at i:25790 original size:61 final size:61
Alignment explanation
Indices: 25691--25858 Score: 264
Period size: 61 Copynumber: 2.8 Consensus size: 61
25681 ATGAAGACGG
* * ** *
25691 GAAGAGTGATAAAGATGCCAATATGCCAATTCAGGGCCAACGATATTGGGCTTAAAGATGA
1 GAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGA
*
25752 GAAGAATGATAAAGGTGCTAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGA
1 GAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGA
* *
25813 AAAGAATGATAAAGGTGCCAATATGTTGATTCAAGGCCAACGATAT
1 GAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATAT
25859 CAAACTTAAA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 98 1.00
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (61 bp):
GAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGA
Found at i:26184 original size:95 final size:95
Alignment explanation
Indices: 26030--26558 Score: 669
Period size: 95 Copynumber: 5.6 Consensus size: 95
26020 GCCACCACAA
* * ** * *
26030 TGTGTGGGCTTTTGAA-AGGGTTGCCATCGACTTCTGTGGGCTCTAAGAAG-GGTTACCACCAAT
1 TGTGTGGGCTTTTGAAGA-GGTTGCCACCGACTTGTGTGGGCT-TTTGAAGAGGTTGCCACCAAC
* *
26093 TTGTGTGGGCTTTAAAGGGGTTACCAC-CAGCT
64 TTGTGTGGGCTTTAAAGGGGTTGCCACTGA-CT
* * *
26125 TGTGTGGGCTTTTGAAGAGGTTGCCACGGACTTGTGTCGGCTTTTGAAGAGGTTGCCACCGACTT
1 TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTT
* ** * *
26190 GTGTGGGTTTTGAAAAAGGTTTCCACTGATT
66 GTGTGGGCTTT-AAAGGGGTTGCCACTGACT
* * *
26221 TGTGTGGGC-TTTGAAGGGGTTGCCACTGACTTGTGTGGGC-TTTGAA-AGGGTTGCCACCGACT
1 TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTTGAAGA-GGTTGCCACCAACT
*
26283 TGTGTGGGCTTTTAAAGGGGTTGCCACCGACT
65 TGTGTGGGC-TTTAAAGGGGTTGCCACTGACT
* * * *
26315 TGTGTGGGCTTTTGAAGAGGTTGCTACCAACTTGTGTGGGCTTTTAAAGAGGTTGCCACCAATTT
1 TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTT
26380 GTGTGGGCTTTGAAA-GGGTTGCCACTGACT
66 GTGTGGGCTTT-AAAGGGGTTGCCACTGACT
* * *
26410 TGTGTGGGCTTTTCAAGAGGTTGCCACCGACTTGTGTGGGCTTTTTAAGAGGTTACCACCAACTT
1 TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTT
*
26475 GTGTGGGCTTTGAAGGGGTTGCCACTGACT
66 GTGTGGGCTTTAAAGGGGTTGCCACTGACT
*
26505 TGTGTGGGCTTTTGAAGAGGTTGCCACCAACTTGTGTGGGC-TTTGAAGAAGGTT
1 TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTTGAAG-AGGTT
26559 TCTCCACTTG
Statistics
Matches: 380, Mismatches: 42, Indels: 24
0.85 0.09 0.05
Matches are distributed among these distances:
93 1 0.00
94 64 0.17
95 262 0.69
96 51 0.13
97 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.33
Consensus pattern (95 bp):
TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTT
GTGTGGGCTTTAAAGGGGTTGCCACTGACT
Found at i:26238 original size:127 final size:126
Alignment explanation
Indices: 26030--26558 Score: 642
Period size: 127 Copynumber: 4.2 Consensus size: 126
26020 GCCACCACAA
* * * * *
26030 TGTGTGGGCTTTTGAA-AGGGTTGCCATCGACTTCTGTGGGC-TCTAAGAAGGGTTACCACCAAT
1 TGTGTGGGCTTTTGAAGA-GGTTGCCACCGACTTGTGTGGGCTTTTAA-AAAGGTTACCACCAAC
* *
26093 TTGTGTGGGCTTTAAAGGGGTTACCACCAG-CTTGTGTGGGCTTTTG-AAGAGGTTGCCACGGAC
64 TTGTGTGGGCTTTAAAGGGGTTGCCA-CAGACTTGTGTGGGC-TTTGAAAG-GGTTGCCACCGAC
26156 T
126 T
* * ** *
26157 TGTGTCGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGG-TTTTGAAAAAGGTTTCCACTGATT
1 TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTT-AAAAAGGTTACCACCAACT
* *
26221 TGTGTGGGCTTTGAAGGGGTTGCCACTGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACT
65 TGTGTGGGCTTTAAAGGGGTTGCCACAGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACT
* * * * * *
26283 TGTGTGGGCTTTTAAAGGGGTTGCCACCGACTTGTGTGGGCTTTTGAAGAGGTTGCTACCAACTT
1 TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTTAAAAAGGTTACCACCAACTT
* * *
26348 GTGTGGGCTTTTAAAGAGGTTGCCACCA-ATTTGTGTGGGCTTTGAAAGGGTTGCCACTGACT
66 GTGTGGGC-TTTAAAGGGGTTGCCA-CAGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACT
* * *
26410 TGTGTGGGCTTTTCAAGAGGTTGCCACCGACTTGTGTGGGCTTTTTAAGAGGTTACCACCAACTT
1 TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTTAAAAAGGTTACCACCAACTT
* * *
26475 GTGTGGGCTTTGAAGGGGTTGCCACTGACTTGTGTGGGCTTTTG-AAGAGGTTGCCACCAACT
66 GTGTGGGCTTTAAAGGGGTTGCCACAGACTTGTGTGGGC-TTTGAAAG-GGTTGCCACCGACT
26537 TGTGTGGGC-TTTGAAGAAGGTT
1 TGTGTGGGCTTTTGAAG-AGGTT
26559 TCTCCACTTG
Statistics
Matches: 351, Mismatches: 39, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
125 1 0.00
126 111 0.32
127 235 0.67
128 4 0.01
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.33
Consensus pattern (126 bp):
TGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTGGGCTTTTAAAAAGGTTACCACCAACTT
GTGTGGGCTTTAAAGGGGTTGCCACAGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACT
Found at i:26305 original size:158 final size:158
Alignment explanation
Indices: 26030--26552 Score: 682
Period size: 158 Copynumber: 3.3 Consensus size: 158
26020 GCCACCACAA
* * * * * * ** *
26030 TGTGTGGGCTTTTGAAAG-GGTTGCCATCGACTTCTGTGGGCTCT-AAGAAGGGTTACCACCAAT
1 TGTGTGGGCTTTTGAAAGAGGTTGCCACCAATTTGTGTGGGCTTTGAAG--GGGTTGCCACTGAC
* * *
26093 TTGTGTGGGCTTTAAAGGGGTTACCACC-AGCTTGTGTGGGCTTTTGAAGAGGTTGCCACGGACT
64 TTGTGTGGGCTTTAAA-GGGTTGCCACCGA-CTTGTGTGGGCTTTTAAAGAGGTTGCCACCGACT
*
26157 TGTGTCGGCTTTTGAAGAGGTTGCCACCGACT
127 TGTGTGGGCTTTTGAAGAGGTTGCCACCGACT
* * **
26189 TGTGTGGG-TTTTGAAAAAGGTTTCCACTGATTTGTGTGGGCTTTGAAGGGGTTGCCACTGACTT
1 TGTGTGGGCTTTTGAAAGAGGTTGCCACCAATTTGTGTGGGCTTTGAAGGGGTTGCCACTGACTT
*
26253 GTGTGGGCTTTGAAAGGGTTGCCACCGACTTGTGTGGGCTTTTAAAGGGGTTGCCACCGACTTGT
66 GTGTGGGCTTT-AAAGGGTTGCCACCGACTTGTGTGGGCTTTTAAAGAGGTTGCCACCGACTTGT
* *
26318 GTGGGCTTTTGAAGAGGTTGCTACCAACT
130 GTGGGCTTTTGAAGAGGTTGCCACCGACT
*
26347 TGTGTGGGCTTTT-AAAGAGGTTGCCACCAATTTGTGTGGGCTTTGAAAGGGTTGCCACTGACTT
1 TGTGTGGGCTTTTGAAAGAGGTTGCCACCAATTTGTGTGGGCTTTGAAGGGGTTGCCACTGACTT
* * * *
26411 GTGTGGGCTTTTCAAGAGGTTGCCACCGACTTGTGTGGGCTTTTTAAGAGGTTACCACCAACTTG
66 GTGTGGGC-TTTAAAG-GGTTGCCACCGACTTGTGTGGGCTTTTAAAGAGGTTGCCACCGACTTG
* *
26476 TGTGGGC-TTTGAAGGGGTTGCCACTGACT
129 TGTGGGCTTTTGAAGAGGTTGCCACCGACT
*
26505 TGTGTGGGCTTTTG-AAGAGGTTGCCACCAACTTGTGTGGGCTTTGAAG
1 TGTGTGGGCTTTTGAAAGAGGTTGCCACCAATTTGTGTGGGCTTTGAAG
26553 AAGGTTTCTC
Statistics
Matches: 322, Mismatches: 34, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
158 229 0.71
159 90 0.28
160 3 0.01
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.33
Consensus pattern (158 bp):
TGTGTGGGCTTTTGAAAGAGGTTGCCACCAATTTGTGTGGGCTTTGAAGGGGTTGCCACTGACTT
GTGTGGGCTTTAAAGGGTTGCCACCGACTTGTGTGGGCTTTTAAAGAGGTTGCCACCGACTTGTG
TGGGCTTTTGAAGAGGTTGCCACCGACT
Found at i:26558 original size:32 final size:31
Alignment explanation
Indices: 26030--26558 Score: 573
Period size: 32 Copynumber: 16.7 Consensus size: 31
26020 GCCACCACAA
*
26030 TGTGTGGGCTTTTGAA-AGGGTTGCCATCGACT
1 TGTGTGGGC-TTTGAAGA-GGTTGCCACCGACT
* * * * *
26062 TCTGTGGGCTCT-AAGAAGGGTTACCACCAATT
1 TGTGTGGGCTTTGAAG-A-GGTTGCCACCGACT
* * *
26094 TGTGTGGGCTTTAAAGGGGTTACCACC-AGCT
1 TGTGTGGGCTTTGAAGAGGTTGCCACCGA-CT
*
26125 TGTGTGGGCTTTTGAAGAGGTTGCCACGGACT
1 TGTGTGGGC-TTTGAAGAGGTTGCCACCGACT
*
26157 TGTGTCGGCTTTTGAAGAGGTTGCCACCGACT
1 TGTGTGGGC-TTTGAAGAGGTTGCCACCGACT
* * * * *
26189 TGTGTGGGTTTTGAAAAAGGTTTCCACTGATT
1 TGTGTGGGCTTTG-AAGAGGTTGCCACCGACT
* *
26221 TGTGTGGGCTTTGAAGGGGTTGCCACTGACT
1 TGTGTGGGCTTTGAAGAGGTTGCCACCGACT
26252 TGTGTGGGCTTTGAA-AGGGTTGCCACCGACT
1 TGTGTGGGCTTTGAAGA-GGTTGCCACCGACT
* *
26283 TGTGTGGGCTTTTAAAGGGGTTGCCACCGACT
1 TGTGTGGGC-TTTGAAGAGGTTGCCACCGACT
* *
26315 TGTGTGGGCTTTTGAAGAGGTTGCTACCAACT
1 TGTGTGGGC-TTTGAAGAGGTTGCCACCGACT
* * *
26347 TGTGTGGGCTTTTAAAGAGGTTGCCACCAATT
1 TGTGTGGGC-TTTGAAGAGGTTGCCACCGACT
*
26379 TGTGTGGGCTTTGAA-AGGGTTGCCACTGACT
1 TGTGTGGGCTTTGAAGA-GGTTGCCACCGACT
*
26410 TGTGTGGGCTTTTCAAGAGGTTGCCACCGACT
1 TGTGTGGGC-TTTGAAGAGGTTGCCACCGACT
* * *
26442 TGTGTGGGCTTTTTAAGAGGTTACCACCAACT
1 TGTGTGGGC-TTTGAAGAGGTTGCCACCGACT
* *
26474 TGTGTGGGCTTTGAAGGGGTTGCCACTGACT
1 TGTGTGGGCTTTGAAGAGGTTGCCACCGACT
*
26505 TGTGTGGGCTTTTGAAGAGGTTGCCACCAACT
1 TGTGTGGGC-TTTGAAGAGGTTGCCACCGACT
26537 TGTGTGGGCTTTGAAGAAGGTT
1 TGTGTGGGCTTTGAAG-AGGTT
26559 TCTCCACTTG
Statistics
Matches: 427, Mismatches: 55, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
30 4 0.01
31 135 0.32
32 283 0.66
33 5 0.01
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.33
Consensus pattern (31 bp):
TGTGTGGGCTTTGAAGAGGTTGCCACCGACT
Found at i:28131 original size:12 final size:12
Alignment explanation
Indices: 28116--28227 Score: 86
Period size: 12 Copynumber: 9.2 Consensus size: 12
28106 CTTTTTCCTC
*
28116 TTTTTT-TTGTT
1 TTTTTTGTTTTT
28127 TTTTTTGTTTTT
1 TTTTTTGTTTTT
* *
28139 TGTTGTTG-TTTA
1 T-TTTTTGTTTTT
*
28151 TTTTTGGTTTTT
1 TTTTTTGTTTTT
28163 TGTTTGTT-TTTTGT
1 T-TTT-TTGTTTT-T
**
28177 TTTTTTGTTGCT
1 TTTTTTGTTTTT
*
28189 TATTTTGTTTTT
1 TTTTTTGTTTTT
* *
28201 TATTTTGTTGTT
1 TTTTTTGTTTTT
28213 TTTTTTGTTTTT
1 TTTTTTGTTTTT
28225 TTT
1 TTT
28228 GCGAAAGATG
Statistics
Matches: 79, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
11 10 0.13
12 49 0.62
13 17 0.22
14 3 0.04
ACGTcount: A:0.03, C:0.01, G:0.14, T:0.82
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:28170 original size:44 final size:43
Alignment explanation
Indices: 28116--28229 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
28106 CTTTTTCCTC
*
28116 TTTTT-TTTGTTTTTTTTGTTTTTTGTTG-TTGTTTAT-TTTTGGT
1 TTTTTGTTTGTTTTTTTTGTTTTTTGTTGCTTATTT-TGTTTT--T
*
28159 TTTTTGTTTGTTTTTTGT-TTTTTTGTTGCTTATTTTGTTTTT
1 TTTTTGTTTGTTTTTTTTGTTTTTTGTTGCTTATTTTGTTTTT
28201 TATTTTG-TTGTTTTTTTTGTTTTTT-TTGC
1 T-TTTTGTTTGTTTTTTTTGTTTTTTGTTGC
28230 GAAAGATGCC
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
42 16 0.25
43 27 0.43
44 20 0.32
ACGTcount: A:0.03, C:0.02, G:0.15, T:0.81
Consensus pattern (43 bp):
TTTTTGTTTGTTTTTTTTGTTTTTTGTTGCTTATTTTGTTTTT
Found at i:28181 original size:43 final size:42
Alignment explanation
Indices: 28116--28226 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 42
28106 CTTTTTCCTC
*
28116 TTTTTTTTG-TT-TTTTTTG-TTTTTTGTTG-TTGTTTAT-TT
1 TTTTTTTTGTTTGTTTTTTGTTTTTTTGTTGCTTATTT-TGTT
28154 TTGGTTTTTTGTTTGTTTTTTGTTTTTTTGTTGCTTATTTTGTT
1 TT--TTTTTTGTTTGTTTTTTGTTTTTTTGTTGCTTATTTTGTT
*
28198 TTTTATTTTGTTGTTTTTTTTGTTTTTTT
1 TTTT-TTTTGTT-TGTTTTTTGTTTTTTT
28227 TGCGAAAGAT
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
38 2 0.03
40 7 0.11
41 2 0.03
42 9 0.15
43 18 0.29
44 24 0.39
ACGTcount: A:0.03, C:0.01, G:0.14, T:0.82
Consensus pattern (42 bp):
TTTTTTTTGTTTGTTTTTTGTTTTTTTGTTGCTTATTTTGTT
Found at i:28207 original size:51 final size:51
Alignment explanation
Indices: 28118--28225 Score: 134
Period size: 51 Copynumber: 2.1 Consensus size: 51
28108 TTTTCCTCTT
28118 TTTTTTGTTTTTTTTGTTTTTTGTTGTTGTTTATTTTTGGTT-TTTTGTTTG
1 TTTTTTGTTTTTTTTGTTTTTTGTTGTTGTTTATTTTT-GTTGTTTTGTTTG
* *
28169 TTTTTTG-TTTTTTTGTTGCTTATT-TTGTTTTTTA-TTTTGTTGTTTTTTTTG
1 TTTTTTGTTTTTTTTGTT--TT-TTGTTGTTGTTTATTTTTGTTGTTTTGTTTG
28220 TTTTTT
1 TTTTTT
28226 TTGCGAAAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
50 13 0.25
51 25 0.49
52 11 0.22
53 2 0.04
ACGTcount: A:0.03, C:0.01, G:0.15, T:0.81
Consensus pattern (51 bp):
TTTTTTGTTTTTTTTGTTTTTTGTTGTTGTTTATTTTTGTTGTTTTGTTTG
Found at i:28218 original size:24 final size:24
Alignment explanation
Indices: 28126--28225 Score: 94
Period size: 27 Copynumber: 4.0 Consensus size: 24
28116 TTTTTTTTGT
* *
28126 TTTTTTTGTTTTTTGTTGTTGTTTA
1 TTTTGTTGTTTTTT-TTGTTTTTTA
* *
28151 TTTTTGGTT-TTTTGTTTGTTTTTTG
1 -TTTT-GTTGTTTTTTTTGTTTTTTA
*
28176 TTTTTTTGTTGCTTATTTTGTTTTTTA
1 TTTTGTTGTT--TT-TTTTGTTTTTTA
28203 TTTTGTTGTTTTTTTTGTTTTTT
1 TTTTGTTGTTTTTTTTGTTTTTT
28226 TTGCGAAAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
23 2 0.03
24 17 0.28
25 10 0.16
26 11 0.18
27 21 0.34
ACGTcount: A:0.03, C:0.01, G:0.15, T:0.81
Consensus pattern (24 bp):
TTTTGTTGTTTTTTTTGTTTTTTA
Found at i:28225 original size:7 final size:7
Alignment explanation
Indices: 28118--28216 Score: 62
Period size: 7 Copynumber: 13.9 Consensus size: 7
28108 TTTTCCTCTT
28118 TTTTTTG
1 TTTTTTG
28125 TTTTTT-
1 TTTTTTG
*
28131 TTGTTT-
1 TTTTTTG
*
28137 TTTGTTG
1 TTTTTTG
* *
28144 TTGTTTA
1 TTTTTTG
*
28151 TTTTTGG
1 TTTTTTG
28158 TTTTTTG
1 TTTTTTG
28165 TTTGTTT-
1 TTT-TTTG
28172 TTTGTTT-
1 TTT-TTTG
28179 TTTTGTTG
1 TTTT-TTG
28187 CTTATTTTG
1 -TT-TTTTG
*
28196 TTTTTTA
1 TTTTTTG
28203 TTTTGTTG
1 TTTT-TTG
28211 TTTTTT
1 TTTTTT
28217 TTGTTTTTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
6 10 0.14
7 45 0.62
8 11 0.15
9 5 0.07
10 2 0.03
ACGTcount: A:0.03, C:0.01, G:0.15, T:0.81
Consensus pattern (7 bp):
TTTTTTG
Found at i:33350 original size:34 final size:33
Alignment explanation
Indices: 33235--33941 Score: 653
Period size: 34 Copynumber: 21.0 Consensus size: 33
33225 TCAAATACCT
* * *
33235 TTTTAAAGTCCACAACTCAGTGGCA-TTTTGTC
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
* * * *
33267 --TCAAAGTCCACGACTCAGTGGCA-TTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
*
33297 -TTTAAAGCCCACAATTCCGTGGCACTTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
* *
33329 ATCTTT-AAGTCCACAACTCCGTGGCAC-----CC
1 -T-TTTAAAGCCCACAACTCCGTGGCACTTTTTTC
*
33358 TTTTAAAGCCCACAATTCCGTGGCACTTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
* *
33391 ATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTC
1 -T-TTTAAAGCCCACAACTCCGTGGCACTTTTTTC
* *
33425 TGTTTAAAGCCTACAACTCCGTGGCAC-----CC
1 T-TTTAAAGCCCACAACTCCGTGGCACTTTTTTC
*
33454 TTTTAAAGCCCACAATTCCGTGGCACTTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
* *
33487 ATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTC
1 -T-TTTAAAGCCCACAACTCCGTGGCACTTTTTTC
33521 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 T-TTTAAAGCCCACAACTCCGTGGCACT-TTTTT--C
33558 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACTTTTTTC
33592 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCACT-TTTTT--C
* **
33628 TTTT-AAGTCCACAACTCCGTGGCATCTTTCTCCC
1 TTTTAAAGCCCACAACTCCGTGGCA-CTTT-TTTC
* * * * *
33662 TTCCTAAAGCCCACACAAGTCGGTGGCAACCTTCTTC
1 TT-TTAAAG-CC-CACAACTCCGTGGC-ACTTTTTTC
* *
33699 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACTTTTTTC
**
33733 TTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCA--CTTTTTT-C
* *
33769 TTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC
1 -TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
**
33803 TTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCA--CTTTTTT-C
33839 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACTTTTTTC
33873 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCACT-TTTTT--C
*
33909 TTTT-AAGTCCACAACTCCGTGGCATCTTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCA-CTTTTTTC
33942 CTTCCCAAAG
Statistics
Matches: 567, Mismatches: 59, Indels: 97
0.78 0.08 0.13
Matches are distributed among these distances:
27 3 0.01
28 43 0.08
29 3 0.01
30 27 0.05
31 18 0.03
32 7 0.01
33 99 0.17
34 147 0.26
35 94 0.17
36 35 0.06
37 75 0.13
38 15 0.03
39 1 0.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.35
Consensus pattern (33 bp):
TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
Found at i:33372 original size:62 final size:62
Alignment explanation
Indices: 33297--33423 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
33287 GCATTTTTTC
33297 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
*
33359 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTT
1 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
33421 TTT
1 TTT
33424 CTGTTTAAAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.35
Consensus pattern (62 bp):
TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
Found at i:33423 original size:96 final size:94
Alignment explanation
Indices: 33235--33939 Score: 578
Period size: 96 Copynumber: 7.0 Consensus size: 94
33225 TCAAATACCT
* * * * * *
33235 TTTTAAAGTCCACAACTCAGTGGCAT--TTTGTCTCAAAGTCCACGACTCAGTGGCA-TTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCATCCCTT-T-T-AAAGCCCACAACTCCGTGGCACTTTTTTC
* * *
33297 TTTAAAGCCCACAATTCCGTGGCACTTTTTTC
63 TTTTAAGCCCACAACTCCGTGGCACCTTTTTC
* *
33329 ATCTTT-AAGTCCACAACTCCGTGGCA-CCCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCA
1 -T-TTTAAAGCCCACAACTCCGTGGCATCCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTC-
*
33392 TCTTTAAGTCCACAACTCCGTGGCACCTTTTTC
63 T-TTTAAGCCCACAACTCCGTGGCACCTTTTTC
* *
33425 TGTTTAAAGCCTACAACTCCGTGGCA-CCCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCAT
1 T-TTTAAAGCCCACAACTCCGTGGCATCCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTC-T
*
33489 CTTTAAGTCCACAACTCCGTGGCACCTTTTTC
64 -TTTAAGCCCACAACTCCGTGGCACCTTTTTC
33521 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACT
1 T-TTTAAAGCCCACAACTCCGTGGCA-------TCCCTTTT-AAAGCCCACAACTCCGTGGCACT
33586 TTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
57 TTTTTCTTTT-AAGCCCACAACTCCGTGGCAC-CTTTTT--C
* * * *
33628 TTTT-AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAAC
1 TTTTAAAGCCCACAACTCCGTGGCA------TCCCTT-TTAAAG-CC-CACAACTCCGTGGC-AC
* * *
33692 CTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
56 TTTTTTCTTTT--AAGCCCACAACTCCGTGGCACCTTTTTC
** *
33733 TTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCT
1 TTTTAAAGCCCACAACTCCGTGGCA-TC------CC-TTTTAAAGCCCACAACTCCGTGGCACTT
* **
33798 TCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCC
58 TTTTCTTTT-AAGCCCACAACTCCGTGGCAC-C-TTTTT-C
**
33839 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTTT-AAAGCCCACAACTCCGTGGCA----TCCCTTTTAAAGCCCACAACTCCGTGGCACT-TTT
* *
33904 TTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
60 TT--CTTTTAAGCCCACAACTCCGTGGCACCTTTTT
33940 TCCTTCCCAA
Statistics
Matches: 523, Mismatches: 44, Indels: 78
0.81 0.07 0.12
Matches are distributed among these distances:
93 17 0.03
94 8 0.02
95 26 0.05
96 145 0.28
101 3 0.01
103 54 0.10
104 63 0.12
105 94 0.18
106 44 0.08
107 44 0.08
108 24 0.05
110 1 0.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (94 bp):
TTTTAAAGCCCACAACTCCGTGGCATCCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTT
TAAGCCCACAACTCCGTGGCACCTTTTTC
Found at i:33604 original size:70 final size:69
Alignment explanation
Indices: 33355--33941 Score: 677
Period size: 70 Copynumber: 8.5 Consensus size: 69
33345 CTCCGTGGCA
* *
33355 CCCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCAC-
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCACT
33418 CTTTTT
64 CTTTTT
* * *
33424 --CTGTTTAAAGCCTACAACTCCGTGGCAC-----CCTTTTAAAGCCCACAATTCCGTGGCACT-
1 CCCT-TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
33481 TTTTT
65 TTTTT
* * *
33486 -CATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACT
1 CCCT-TTTAAAGCCCACAACTCCGTGGCACTTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACT
33549 CTTTTT
64 CTTTTT
33555 CCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
33620 TTTTT
65 TTTTT
* ** * * *
33625 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGC
1 CCCTTTTAAAGCCCACAACTCCGTGGCA-CTTT-TTTCTT-TTAAAG-CC-CACAACTCCGTGGC
*
33689 AAC-CTTCTT
61 -ACTCTTTTT
* * **
33698 --CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTC
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
33761 TTTTTT
65 -TTTTT
* * * **
33767 CCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
33832 TTTT
66 TTTT
*
33836 TCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
33901 TTTTT
65 TTTTT
*
33906 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTTTTTC
1 CCCTTTTAAAGCCCACAACTCCGTGGCA-CTTTTTTC
33942 CTTCCCAAAG
Statistics
Matches: 450, Mismatches: 40, Indels: 56
0.82 0.07 0.10
Matches are distributed among these distances:
61 3 0.01
62 44 0.10
63 5 0.01
67 6 0.01
68 98 0.22
69 36 0.08
70 171 0.38
71 44 0.10
72 5 0.01
73 36 0.08
74 2 0.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (69 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
TTTT
Found at i:34020 original size:33 final size:33
Alignment explanation
Indices: 33942--34038 Score: 162
Period size: 32 Copynumber: 3.0 Consensus size: 33
33932 ATCTTTTTTC
*
33942 CTTCCCAAAGCCCACACAAGTCGGTGGCAA-CT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCT
33974 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC-T
34008 CTT-CTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC
34039 CCTCTAAGCC
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
32 29 0.47
33 29 0.47
34 4 0.06
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.18
Consensus pattern (33 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCT
Found at i:34126 original size:52 final size:51
Alignment explanation
Indices: 34043--34859 Score: 803
Period size: 52 Copynumber: 16.8 Consensus size: 51
34033 GCAACCCCTC
*
34043 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTT-CATCTT
* * ** *
34095 TAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCCCCTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTT-CATCTT
* *
34147 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTT-CATCTT
* * * *
34199 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC--CTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
* *
34248 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC--CTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
* * **
34297 TAAGTCTAATATCGCTGGCCTTGAATCAGCATATT-G-ACACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
* *
34346 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
* * *
34395 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG--CA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
*
34438 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
* * *
34481 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG--CA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
*
34524 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
* *
34567 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC-----C-TC--
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
*
34610 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTT-CATCTT
* * *
34662 TAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTT-CATCTT
34714 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTT-CATCTT
* * ** * *
34766 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--C-ATTT-TCATCTT
* * * * *
34821 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
34860 TCTTTATCAC
Statistics
Matches: 678, Mismatches: 68, Indels: 35
0.87 0.09 0.04
Matches are distributed among these distances:
43 191 0.28
44 1 0.00
45 3 0.00
47 2 0.00
48 1 0.00
49 175 0.26
50 5 0.01
52 260 0.38
54 1 0.00
55 38 0.06
56 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (51 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCATCTT
Found at i:34455 original size:43 final size:43
Alignment explanation
Indices: 34392--34753 Score: 445
Period size: 43 Copynumber: 8.0 Consensus size: 43
34382 GCATCTTCAT
* * *
34392 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
*
34435 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* * *
34478 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
*
34521 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* *
34564 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* *
34607 CTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CA-----C
*
34657 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG---------CAC
34711 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
34754 ATTTTCCATC
Statistics
Matches: 278, Mismatches: 25, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
43 196 0.71
45 2 0.01
50 1 0.00
52 76 0.27
54 1 0.00
59 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:34519 original size:86 final size:86
Alignment explanation
Indices: 34392--34753 Score: 499
Period size: 86 Copynumber: 4.0 Consensus size: 86
34382 GCATCTTCAT
* *
34392 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGC
34457 CTTGAATCAGCATATTGGCAC
66 CTTGAATCAGCATATTGGCAC
* *
34478 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGC
34543 CTTGAATCAGCATATTGGCAC
66 CTTGAATCAGCATATTGGCAC
* *
34564 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGCCCAATATAGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGC
34629 CTTGAATCAGCATATTGGCACATTTTCC
66 CTTGAATCAGCATATTGG--CA-----C
*
34657 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCACCTTTAAGTCCA
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG---------CACCTTTAAGTCCA
34722 ATATAGCTGGCCTTGAATCAGCATATTGGCAC
55 ATATAGCTGGCCTTGAATCAGCATATTGGCAC
34754 ATTTTCCATC
Statistics
Matches: 251, Mismatches: 7, Indels: 25
0.89 0.02 0.09
Matches are distributed among these distances:
86 165 0.66
88 2 0.01
93 1 0.00
95 39 0.16
97 1 0.00
102 2 0.01
104 41 0.16
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (86 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGC
CTTGAATCAGCATATTGGCAC
Found at i:35001 original size:171 final size:171
Alignment explanation
Indices: 34712--35276 Score: 1040
Period size: 171 Copynumber: 3.3 Consensus size: 171
34702 CTTTTCCACC
* *
34712 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAATG
*
34777 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCA
63 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCA
34842 TGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
128 TGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
34886 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
34951 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
35016 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
35057 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
35122 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
* *
35187 ATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCATC
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
* *
35228 TTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
35277 ATCTCTAAAA
Statistics
Matches: 384, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
171 341 0.89
172 5 0.01
174 38 0.10
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (171 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
Found at i:35049 original size:61 final size:65
Alignment explanation
Indices: 34978--35101 Score: 164
Period size: 67 Copynumber: 1.9 Consensus size: 65
34968 CGTTGACATC
* *
34978 CTTTT-TC-TCATC-TTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA
1 CTTTTCTCATCATCTTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCATCTTTATCA
* * *
35040 CTTTTCTCATCATCATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
1 CTTTTCTCATCATC--TTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCATCTT
35102 CATCTTTAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
62 5 0.10
63 2 0.04
64 5 0.10
67 40 0.77
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (65 bp):
CTTTTCTCATCATCTTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCATCTTTATCA
Found at i:35919 original size:13 final size:13
Alignment explanation
Indices: 35901--35925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35891 TTCAACGATT
35901 TGTATCGATACAA
1 TGTATCGATACAA
35914 TGTATCGATACA
1 TGTATCGATACA
35926 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:36011 original size:13 final size:13
Alignment explanation
Indices: 35993--36017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35983 ATTACTCACA
35993 TGTATCGATACAT
1 TGTATCGATACAT
36006 TGTATCGATACA
1 TGTATCGATACA
36018 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:36082 original size:52 final size:52
Alignment explanation
Indices: 36026--36146 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
36016 CACTGATCTT
*
36026 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
36078 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
36130 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
36147 TAACTCTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:46872 original size:15 final size:15
Alignment explanation
Indices: 46834--46872 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
46824 TCAAGAATAC
46834 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAAAG
* * *
46849 AATACAAAAAGAGAG
1 AAAAAAAAAAGAAAG
46864 AAAAAAAAA
1 AAAAAAAAA
46873 CCAGTATTTG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Found at i:47638 original size:12 final size:11
Alignment explanation
Indices: 47616--47691 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
47606 AGAGAAAGAA
*
47616 GAGAGAGGAGG
1 GAGATAGGAGG
47627 GATGATAGGAGG
1 GA-GATAGGAGG
*
47639 AGAGACAGGA--
1 -GAGATAGGAGG
*
47649 GAGATAGTA--
1 GAGATAGGAGG
47658 GAGATAGGAGG
1 GAGATAGGAGG
47669 GATGATAGGAGG
1 GA-GATAGGAGG
*
47681 AGAGACAGGAG
1 -GAGATAGGAG
47692 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:47648 original size:24 final size:24
Alignment explanation
Indices: 47615--47700 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
47605 AAGAGAAAGA
*
47615 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
47639 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
47657 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
47681 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
47701 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:47667 original size:42 final size:42
Alignment explanation
Indices: 47606--47724 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
47596 TAGCCCTCAA
* *
47606 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
47648 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
47690 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
47725 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:57091 original size:21 final size:18
Alignment explanation
Indices: 57067--57125 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
57057 TTTCAACAAT
57067 TTGTATCGATACAACCAGTAA
1 TTGTATCGATACAA--AGT-A
* *
57088 TTGTATTGATACATAAGTG
1 TTGTATCGATACA-AAGTA
*
57107 TTGTATCGATACAATGTA
1 TTGTATCGATACAAAGTA
57125 T
1 T
57126 CGCTACAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.12
19 12 0.38
20 3 0.09
21 12 0.38
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTGTATCGATACAAAGTA
Done.