Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 9 of 131
Found at i:2813228 original size:16 final size:16
Alignment explanation
Indices: 2813204--2813237 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2813194 TTGTTGGTTC
*
2813204 AATTAAAAATTATTAA
1 AATTAAAAAATATTAA
*
2813220 AATTTAAAAATATTAA
1 AATTAAAAAATATTAA
2813236 AA
1 AA
2813238 AATCCTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTAAAAAATATTAA
Found at i:2814568 original size:22 final size:23
Alignment explanation
Indices: 2814540--2814582 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2814530 CATCTAATTC
2814540 AACCATGTAGAAACT-ACAAAAG
1 AACCATGTAGAAACTGACAAAAG
*
2814562 AACCATGTAGGAACTGACAAA
1 AACCATGTAGAAACTGACAAA
2814583 CAATCACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (23 bp):
AACCATGTAGAAACTGACAAAAG
Found at i:2819238 original size:154 final size:155
Alignment explanation
Indices: 2818953--2819497 Score: 607
Period size: 154 Copynumber: 3.5 Consensus size: 155
2818943 ATCAGAGTAA
* * * * *
2818953 CTTGATCATGAATTATATCTAATATTGATGCAAATAGATAACAATGAAGAAGGTAAAATCCTATT
1 CTTGATCATGAATTAAATCTAATAGTCATGCAAATAGATAACAATGAAGAAGGAAAAAGCCTATT
* * *
2819018 TTAAGCCCTCAAACAAGTTTATCTTCTATCTTATGCGGACCCACGATTCAGGTACGTGTTTCTAC
66 TCAAGCCCTCAAACAAGTTTATCTTCTATCTTATGTGGACCCATGATTCAGGTACGTGTTTCTAC
*
2819083 TCAATAAAATGATCCAT-TGGATAG
131 TCAATAAAAAGATCCATCTGGATAG
* * * *
2819107 CTTGATGATGAATTAAATCTAATAGTCAAGCGAACAGATAACAATGAAGAAGGAAAAAGCCTATT
1 CTTGATCATGAATTAAATCTAATAGTCATGCAAATAGATAACAATGAAGAAGGAAAAAGCCTATT
* * * * * ** *
2819172 TCAAGTCCTCAAACAAGTTTATCTTCTATCTTAAGTGGACTCTTGATT-AGGATACATAATTGTA
66 TCAAGCCCTCAAACAAGTTTATCTTCTATCTTATGTGGACCCATGATTCAGG-TACGTGTTTCTA
*
2819236 CTCAATAAAACAAAAT-CATCT-GACTAG
130 CTCAAT-AAA-AAGATCCATCTGGA-TAG
* * * * * * * * * * *
2819263 CTTGATCATTAATGAAATCAAATATTCACGCAAATAGGTGACGATGAAGAAGGTAAAATCCCATT
1 CTTGATCATGAATTAAATCTAATAGTCATGCAAATAGATAACAATGAAGAAGGAAAAAGCCTATT
* **
2819328 TCAAGCCCTCAAACAAGTTTATC-T-TATCTTATGTGGACCCATGATTCAAGCCCGTGTTTCTAC
66 TCAAGCCCTCAAACAAGTTTATCTTCTATCTTATGTGGACCCATGATTCAGGTACGTGTTTCTAC
*
2819391 TCAATAAAACAGAACCATCTGGATAG
131 TCAATAAAA-AGATCCATCTGGATAG
* *** * *
2819417 CTTGATAATGAATTAAATCTAATAGTCATGTGGAGAGATGACAATGAAGAAGGAAAAAGCCTATT
1 CTTGATCATGAATTAAATCTAATAGTCATGCAAATAGATAACAATGAAGAAGGAAAAAGCCTATT
*
2819482 TCAAGTCCTCAAACAA
66 TCAAGCCCTCAAACAA
2819498 CTACCTTAAG
Statistics
Matches: 317, Mismatches: 65, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
152 1 0.00
153 8 0.03
154 215 0.68
155 13 0.04
156 80 0.25
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (155 bp):
CTTGATCATGAATTAAATCTAATAGTCATGCAAATAGATAACAATGAAGAAGGAAAAAGCCTATT
TCAAGCCCTCAAACAAGTTTATCTTCTATCTTATGTGGACCCATGATTCAGGTACGTGTTTCTAC
TCAATAAAAAGATCCATCTGGATAG
Found at i:2819492 original size:310 final size:299
Alignment explanation
Indices: 2818930--2819653 Score: 912
Period size: 310 Copynumber: 2.4 Consensus size: 299
2818920 ATAGTACTTG
* * * * * * * *
2818930 ATAAAACAGAATGATCAGAGTAACTTGATCATGAATTATATCTAATATTGATGCAAATAGATAAC
1 ATAAAACAGAATCATCAGAATAGCTTGATCATGAATAAAATCAAATATTCATGCAAATAGATGAC
* * *
2818995 AATGAAGAAGGTAAAATCCTATTTTAAGCCCTCAAACAAGTTTATCTTCTATCTTATGCGGACCC
66 GATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATC-T-TATCTTATGCGGACCC
* * * * *
2819060 ACGATTCAGGTACGTGTTTCTACTCAATAAAATGATCCATTGGATAGCTTGATGATGAATTAAAT
129 ACGATTCAAGCACGTGTTTCTACTCAATAAAAAGAACCATTGGATAGCTTGATAATGAATTAAAT
2819125 CTAATAGTCAAGCGAACAGATAACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAACAAGT
194 CTAATAGTCAAGCGAACAGATAACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAAC-A--
*
2819190 TTATCTTCTATCTTAAGTGGACTCT-TGATTAGGATACATAATTGTACTCA
256 --A----CTACCTTAAGTGGA-TCTGTGATTAGGATACATAATTGTACTCA
* * * * * * *
2819240 ATAAAACAAAATCATCTGACTAGCTTGATCATTAATGAAATCAAATATTCACGCAAATAGGTGAC
1 ATAAAACAGAATCATCAGAATAGCTTGATCATGAATAAAATCAAATATTCATGCAAATAGATGAC
* *
2819305 GATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTTATCTTATGTGGACCCAT
66 GATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTTATCTTATGCGGACCCAC
*
2819370 GATTCAAGCCCGTGTTTCTACTCAATAAAACAGAACCATCTGGATAGCTTGATAATGAATTAAAT
131 GATTCAAGCACGTGTTTCTACTCAATAAAA-AGAACCAT-TGGATAGCTTGATAATGAATTAAAT
* * * * *
2819435 CTAATAGTCATGTGGAGAGATGACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAACAACT
194 CTAATAGTCAAGCGAACAGATAACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAACAACT
* * ** *
2819500 ACCTTAAGTGGATTTGTGATTAGGGTACATGCTTGTACTCG
259 ACCTTAAGTGGATCTGTGATTAGGATACATAATTGTACTCA
* *
2819541 ATAAAACAGAACCATCCA-AATAGCTAGATCATGAATAAAATCAAATATTCATGCAAATAGATGA
1 ATAAAACAGAATCAT-CAGAATAGCTTGATCATGAATAAAATCAAATATTCATGCAAATAGATGA
* * * *
2819605 TGATGAAGAAGGTAAATTCCCATTTCATGTCCTCAAACAAGTTTATCTT
65 CGATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTT
2819654 CTTCTATCTT
Statistics
Matches: 362, Mismatches: 48, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
300 2 0.01
301 132 0.36
302 1 0.00
305 1 0.00
308 43 0.12
309 8 0.02
310 175 0.48
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (299 bp):
ATAAAACAGAATCATCAGAATAGCTTGATCATGAATAAAATCAAATATTCATGCAAATAGATGAC
GATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTTATCTTATGCGGACCCAC
GATTCAAGCACGTGTTTCTACTCAATAAAAAGAACCATTGGATAGCTTGATAATGAATTAAATCT
AATAGTCAAGCGAACAGATAACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAACAACTAC
CTTAAGTGGATCTGTGATTAGGATACATAATTGTACTCA
Found at i:2825334 original size:58 final size:57
Alignment explanation
Indices: 2825267--2825405 Score: 143
Period size: 57 Copynumber: 2.4 Consensus size: 57
2825257 TTCCAGGGCT
* * * * *
2825267 TGAATTTTTTTTGTCCAAGTTAGTATCTAAACTTGACGATTATTTCCACATTGGGGTC
1 TGAACTTTTTTTGTCCAAGTTAGTACCTAAACTTCACGACT-GTTCCACATTGGGGTC
* ** * * *
2825325 TGAACTTTTTTTATCCAAGTTAGCCCCTGAACTTCATGACTGTTCCATATTGGGGTC
1 TGAACTTTTTTTGTCCAAGTTAGTACCTAAACTTCACGACTGTTCCACATTGGGGTC
* * *
2825382 TAAACTTTTTTGGTCCAAATTAGT
1 TGAACTTTTTTTGTCCAAGTTAGT
2825406 CTCTGATATT
Statistics
Matches: 65, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
57 33 0.51
58 32 0.49
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.42
Consensus pattern (57 bp):
TGAACTTTTTTTGTCCAAGTTAGTACCTAAACTTCACGACTGTTCCACATTGGGGTC
Found at i:2828636 original size:29 final size:30
Alignment explanation
Indices: 2828603--2828669 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
2828593 CTTAACAAGC
*
2828603 CAATGACTTAAAT-AAACTTTCGAATAGTT
1 CAATGACTTAAATAAAACTTTCGAATAATT
2828632 CAATGACTTAAATGAAAACTTTCGAATAATT
1 CAATGACTTAAAT-AAAACTTTCGAATAATT
*
2828663 CAGTGAC
1 CAATGAC
2828670 CATTTTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
31 21 0.62
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (30 bp):
CAATGACTTAAATAAAACTTTCGAATAATT
Found at i:2829519 original size:283 final size:283
Alignment explanation
Indices: 2829012--2830996 Score: 3970
Period size: 283 Copynumber: 7.0 Consensus size: 283
2829002 ACATGGTCGA
2829012 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
1 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
2829077 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
66 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
2829142 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
131 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
2829207 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
196 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
2829272 AGATTAATATTTAATGATAGTAT
261 AGATTAATATTTAATGATAGTAT
2829295 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
1 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
2829360 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
66 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
2829425 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
131 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
2829490 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
196 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
2829555 AGATTAATATTTAATGATAGTAT
261 AGATTAATATTTAATGATAGTAT
2829578 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
1 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
2829643 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
66 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
2829708 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
131 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
2829773 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
196 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
2829838 AGATTAATATTTAATGATAGTAT
261 AGATTAATATTTAATGATAGTAT
2829861 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
1 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
2829926 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
66 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
2829991 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
131 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
2830056 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
196 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
2830121 AGATTAATATTTAATGATAGTAT
261 AGATTAATATTTAATGATAGTAT
2830144 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
1 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
2830209 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
66 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
2830274 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
131 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
2830339 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
196 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
2830404 AGATTAATATTTAATGATAGTAT
261 AGATTAATATTTAATGATAGTAT
2830427 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
1 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
2830492 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
66 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
2830557 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
131 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
2830622 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
196 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
2830687 AGATTAATATTTAATGATAGTAT
261 AGATTAATATTTAATGATAGTAT
2830710 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
1 TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
2830775 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
66 TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
2830840 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
131 GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
2830905 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
196 TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
2830970 AGATTAATATTTAATGATAGTAT
261 AGATTAATATTTAATGATAGTAT
2830993 TTAA
1 TTAA
2830997 ATGCATTGTA
Statistics
Matches: 1702, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
283 1702 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (283 bp):
TTAAGGGTTATAGATGAAAGTCGAGCACATTGGTCATGGCACCGCAACAATGACTCCCAAGCACT
TGTTGCCGACCAGGTTTGGCTACAAATTAAGTTTAACTACGATCAAACCGTGTTGGCTGTCTACA
GTCCATAAAGACGGCTCATACATTAAAAATGATGAACTACAAAGTAATTATGTATATACATCGGA
TATTGAGTGTTCCGAAGGGGATGCTAATACCTTTGTTTGTACTATAAATTATATATTACACTATC
AGATTAATATTTAATGATAGTAT
Found at i:2832346 original size:3 final size:3
Alignment explanation
Indices: 2832338--2832372 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2832328 CACCGAGTCG
* *
2832338 GTT GTT GTT GTT GTT GTT GTT GCT GTT GCT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GT
2832373 GGTTTCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.06, G:0.34, T:0.60
Consensus pattern (3 bp):
GTT
Found at i:2834033 original size:17 final size:17
Alignment explanation
Indices: 2834011--2834044 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2834001 TTTGTTTATT
2834011 ACATATTATATAAATTA
1 ACATATTATATAAATTA
* *
2834028 ACATATTTTATTAATTA
1 ACATATTATATAAATTA
2834045 GACAGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
ACATATTATATAAATTA
Found at i:2835792 original size:5 final size:5
Alignment explanation
Indices: 2835756--2835789 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
2835746 AAAATTTCAC
*
2835756 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAC TCGA
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
2835790 CTCATTTCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (5 bp):
TCGAT
Found at i:2836387 original size:621 final size:621
Alignment explanation
Indices: 2835206--2836447 Score: 2484
Period size: 621 Copynumber: 2.0 Consensus size: 621
2835196 GGCCTTCCAA
2835206 GATTTCTCTACAAACGACAAAATTTAGAAGAAATCGAGAGCTTGATAGGCACACTAGCAAAGCTG
1 GATTTCTCTACAAACGACAAAATTTAGAAGAAATCGAGAGCTTGATAGGCACACTAGCAAAGCTG
2835271 GATTTTCAGATAGATAAGGGCTCGAGAGGGAAATTTGCTCGAAAGGTTATGTGTGTCAATCTTGG
66 GATTTTCAGATAGATAAGGGCTCGAGAGGGAAATTTGCTCGAAAGGTTATGTGTGTCAATCTTGG
2835336 AAAACCTCTAGTCTCTCAGATCTTGGTTAACGGAGTGGTGCAATGGGTCGAGTTTGAATCTTTTG
131 AAAACCTCTAGTCTCTCAGATCTTGGTTAACGGAGTGGTGCAATGGGTCGAGTTTGAATCTTTTG
2835401 GGCCTTGGATGCTTGTCGAGATAACACAAGGGCGCGCCAAAATCTTAACATGAAAGTGATTGAAA
196 GGCCTTGGATGCTTGTCGAGATAACACAAGGGCGCGCCAAAATCTTAACATGAAAGTGATTGAAA
2835466 ATGACACCTCGAATCCGTTTGGAATGAAATTGTTTGAGATTGCCGCGGCGGCATCTGATTTATCG
261 ATGACACCTCGAATCCGTTTGGAATGAAATTGTTTGAGATTGCCGCGGCGGCATCTGATTTATCG
2835531 GGGATAAAAAATTAAAAATTTTCTAAAATAATAATTTTTGAGAACTAAACAAGTTAATTAATGAT
326 GGGATAAAAAATTAAAAATTTTCTAAAATAATAATTTTTGAGAACTAAACAAGTTAATTAATGAT
2835596 TTAAGTTTATCATACTAAAGTATTTATTATTATTTTGCTTTGAAAAAGTTTTTAAATATACATGG
391 TTAAGTTTATCATACTAAAGTATTTATTATTATTTTGCTTTGAAAAAGTTTTTAAATATACATGG
2835661 TTTCAAATTTATGTGCTCTAACATTGAATCAGTTATATTGTAACAAAATTTTAATTTGACATGGT
456 TTTCAAATTTATGTGCTCTAACATTGAATCAGTTATATTGTAACAAAATTTTAATTTGACATGGT
2835726 AATTTTTTAATTTAATTCGAAAAATTTCACTCGATTCGATTCGATTCGATTCGATTCGACTCGAC
521 AATTTTTTAATTTAATTCGAAAAATTTCACTCGATTCGATTCGATTCGATTCGATTCGACTCGAC
2835791 TCATTTCGAAAAAAAATCAAATCGAGTTAGGATGAT
586 TCATTTCGAAAAAAAATCAAATCGAGTTAGGATGAT
2835827 GATTTCTCTACAAACGACAAAATTTAGAAGAAATCGAGAGCTTGATAGGCACACTAGCAAAGCTG
1 GATTTCTCTACAAACGACAAAATTTAGAAGAAATCGAGAGCTTGATAGGCACACTAGCAAAGCTG
2835892 GATTTTCAGATAGATAAGGGCTCGAGAGGGAAATTTGCTCGAAAGGTTATGTGTGTCAATCTTGG
66 GATTTTCAGATAGATAAGGGCTCGAGAGGGAAATTTGCTCGAAAGGTTATGTGTGTCAATCTTGG
2835957 AAAACCTCTAGTCTCTCAGATCTTGGTTAACGGAGTGGTGCAATGGGTCGAGTTTGAATCTTTTG
131 AAAACCTCTAGTCTCTCAGATCTTGGTTAACGGAGTGGTGCAATGGGTCGAGTTTGAATCTTTTG
2836022 GGCCTTGGATGCTTGTCGAGATAACACAAGGGCGCGCCAAAATCTTAACATGAAAGTGATTGAAA
196 GGCCTTGGATGCTTGTCGAGATAACACAAGGGCGCGCCAAAATCTTAACATGAAAGTGATTGAAA
2836087 ATGACACCTCGAATCCGTTTGGAATGAAATTGTTTGAGATTGCCGCGGCGGCATCTGATTTATCG
261 ATGACACCTCGAATCCGTTTGGAATGAAATTGTTTGAGATTGCCGCGGCGGCATCTGATTTATCG
2836152 GGGATAAAAAATTAAAAATTTTCTAAAATAATAATTTTTGAGAACTAAACAAGTTAATTAATGAT
326 GGGATAAAAAATTAAAAATTTTCTAAAATAATAATTTTTGAGAACTAAACAAGTTAATTAATGAT
2836217 TTAAGTTTATCATACTAAAGTATTTATTATTATTTTGCTTTGAAAAAGTTTTTAAATATACATGG
391 TTAAGTTTATCATACTAAAGTATTTATTATTATTTTGCTTTGAAAAAGTTTTTAAATATACATGG
2836282 TTTCAAATTTATGTGCTCTAACATTGAATCAGTTATATTGTAACAAAATTTTAATTTGACATGGT
456 TTTCAAATTTATGTGCTCTAACATTGAATCAGTTATATTGTAACAAAATTTTAATTTGACATGGT
2836347 AATTTTTTAATTTAATTCGAAAAATTTCACTCGATTCGATTCGATTCGATTCGATTCGACTCGAC
521 AATTTTTTAATTTAATTCGAAAAATTTCACTCGATTCGATTCGATTCGATTCGATTCGACTCGAC
2836412 TCATTTCGAAAAAAAATCAAATCGAGTTAGGATGAT
586 TCATTTCGAAAAAAAATCAAATCGAGTTAGGATGAT
2836448 AAAATAGGAC
Statistics
Matches: 621, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
621 621 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (621 bp):
GATTTCTCTACAAACGACAAAATTTAGAAGAAATCGAGAGCTTGATAGGCACACTAGCAAAGCTG
GATTTTCAGATAGATAAGGGCTCGAGAGGGAAATTTGCTCGAAAGGTTATGTGTGTCAATCTTGG
AAAACCTCTAGTCTCTCAGATCTTGGTTAACGGAGTGGTGCAATGGGTCGAGTTTGAATCTTTTG
GGCCTTGGATGCTTGTCGAGATAACACAAGGGCGCGCCAAAATCTTAACATGAAAGTGATTGAAA
ATGACACCTCGAATCCGTTTGGAATGAAATTGTTTGAGATTGCCGCGGCGGCATCTGATTTATCG
GGGATAAAAAATTAAAAATTTTCTAAAATAATAATTTTTGAGAACTAAACAAGTTAATTAATGAT
TTAAGTTTATCATACTAAAGTATTTATTATTATTTTGCTTTGAAAAAGTTTTTAAATATACATGG
TTTCAAATTTATGTGCTCTAACATTGAATCAGTTATATTGTAACAAAATTTTAATTTGACATGGT
AATTTTTTAATTTAATTCGAAAAATTTCACTCGATTCGATTCGATTCGATTCGATTCGACTCGAC
TCATTTCGAAAAAAAATCAAATCGAGTTAGGATGAT
Found at i:2836413 original size:5 final size:5
Alignment explanation
Indices: 2836377--2836410 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
2836367 AAAATTTCAC
*
2836377 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAC TCGA
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
2836411 CTCATTTCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (5 bp):
TCGAT
Found at i:2838824 original size:25 final size:25
Alignment explanation
Indices: 2838785--2838872 Score: 115
Period size: 25 Copynumber: 3.6 Consensus size: 25
2838775 ATTAGGGCCA
2838785 CCGTT-TTCAGCTCTTATGAGCTTC
1 CCGTTATTCAGCTCTTATGAGCTTC
* *
2838809 CCATTATTCAGATCTTATGAGCTTC
1 CCGTTATTCAGCTCTTATGAGCTTC
** **
2838834 ATGTTATTCAGCTCGCATGAGCTTC
1 CCGTTATTCAGCTCTTATGAGCTTC
2838859 CCGTTATTCAGCTC
1 CCGTTATTCAGCTC
2838873 GAAAGAGCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
24 4 0.08
25 49 0.92
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (25 bp):
CCGTTATTCAGCTCTTATGAGCTTC
Found at i:2838873 original size:25 final size:25
Alignment explanation
Indices: 2838785--2838904 Score: 109
Period size: 25 Copynumber: 4.9 Consensus size: 25
2838775 ATTAGGGCCA
*
2838785 CCGTT-TTCAGCTCTTATGAGCTTC
1 CCGTTATTCAGCTCGTATGAGCTTC
* * *
2838809 CCATTATTCAGATCTTATGAGCTTC
1 CCGTTATTCAGCTCGTATGAGCTTC
** *
2838834 ATGTTATTCAGCTCGCATGAGCTTC
1 CCGTTATTCAGCTCGTATGAGCTTC
* * *
2838859 CCGTTATTCAGCTCGAAAGAGCTTA
1 CCGTTATTCAGCTCGTATGAGCTTC
* * *
2838884 CTGTT-TACAGCTCATATGAGC
1 CCGTTATTCAGCTCGTATGAGC
2838905 ATACATGTAT
Statistics
Matches: 77, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
24 16 0.21
25 61 0.79
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (25 bp):
CCGTTATTCAGCTCGTATGAGCTTC
Found at i:2840164 original size:3 final size:3
Alignment explanation
Indices: 2840156--2840186 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2840146 TCGTGAGGAN
2840156 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2840187 GCATAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2841794 original size:85 final size:85
Alignment explanation
Indices: 2841696--2841852 Score: 201
Period size: 85 Copynumber: 1.8 Consensus size: 85
2841686 GTGATTTTAG
* **
2841696 TCTGCTCCACTGTAACATCAGGGAGATAAGA-CT-TGATGCTTCAACCTGCTCCACTATGACTTC
1 TCTGCTCCACTGTAACATCAGAGAGATAAGATCTGT-A-GCTTCAACCTGCTCCACTACAACTTC
2841759 AGGGAGATAAGACTGGATGCGA
64 AGGGAGATAAGACTGGATGCGA
* * * * * *
2841781 TCTGCTCTACTGTAACTTTAGAGAGATAAGATCTGTAGTTTTAATCTGCTCCACTACAACTTCAG
1 TCTGCTCCACTGTAACATCAGAGAGATAAGATCTGTAGCTTCAACCTGCTCCACTACAACTTCAG
2841846 GGAGATA
66 GGAGATA
2841853 GGATTGGCTA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
85 57 0.93
86 3 0.05
87 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (85 bp):
TCTGCTCCACTGTAACATCAGAGAGATAAGATCTGTAGCTTCAACCTGCTCCACTACAACTTCAG
GGAGATAAGACTGGATGCGA
Found at i:2841981 original size:41 final size:41
Alignment explanation
Indices: 2841922--2842071 Score: 151
Period size: 41 Copynumber: 3.5 Consensus size: 41
2841912 AACATGCCCC
*
2841922 ACTGCAACTTCAGGGAGATGAAGCTTAATATGATCTGCTCT
1 ACTGCAACTTCAGAGAGATGAAGCTTAATATGATCTGCTCT
* * *
2841963 ACTGCAACTTCAGAGAGAT-AAGATCTGTAATTTAACTTCCATCT-ATCCC
1 ACTGCAACTTCAGAGAGATGAAG--CT-TAA--T-A--T-GATCTGCT-CT
*
2842012 ACTGCAACTTCAGGGAGATGAAGCTTAATATGATCTGCTCT
1 ACTGCAACTTCAGAGAGATGAAGCTTAATATGATCTGCTCT
2842053 ACTGCAACTTCAGAGAGAT
1 ACTGCAACTTCAGAGAGAT
2842072 AAGATCTGTA
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
40 3 0.03
41 41 0.47
42 4 0.05
43 3 0.03
44 1 0.01
45 2 0.02
46 1 0.01
47 3 0.03
48 4 0.05
49 23 0.26
50 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (41 bp):
ACTGCAACTTCAGAGAGATGAAGCTTAATATGATCTGCTCT
Found at i:2842033 original size:90 final size:90
Alignment explanation
Indices: 2841919--2842117 Score: 398
Period size: 90 Copynumber: 2.2 Consensus size: 90
2841909 TTCAACATGC
2841919 CCCACTGCAACTTCAGGGAGATGAAGCTTAATATGATCTGCTCTACTGCAACTTCAGAGAGATAA
1 CCCACTGCAACTTCAGGGAGATGAAGCTTAATATGATCTGCTCTACTGCAACTTCAGAGAGATAA
2841984 GATCTGTAATTTAACTTCCATCTAT
66 GATCTGTAATTTAACTTCCATCTAT
2842009 CCCACTGCAACTTCAGGGAGATGAAGCTTAATATGATCTGCTCTACTGCAACTTCAGAGAGATAA
1 CCCACTGCAACTTCAGGGAGATGAAGCTTAATATGATCTGCTCTACTGCAACTTCAGAGAGATAA
2842074 GATCTGTAATTTAACTTCCATCTAT
66 GATCTGTAATTTAACTTCCATCTAT
2842099 CCCACTGCAACTTCAGGGA
1 CCCACTGCAACTTCAGGGA
2842118 AATCAGATTT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 109 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (90 bp):
CCCACTGCAACTTCAGGGAGATGAAGCTTAATATGATCTGCTCTACTGCAACTTCAGAGAGATAA
GATCTGTAATTTAACTTCCATCTAT
Found at i:2842273 original size:100 final size:99
Alignment explanation
Indices: 2842133--2842860 Score: 791
Period size: 100 Copynumber: 7.4 Consensus size: 99
2842123 GATTTGCTAT
* * * * * * * * ** *
2842133 CTTCAGTCTATTTAACTGTAATATCGGGGAAGTAAAATTCGCTGCTGTAGCTTCAATTTACTCTG
1 CTTCAATCT-TTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
** * * *
2842198 CTGCATTGCCTGGGAAAGTAAGATTCGCCGTTGTGG
65 CTGCAACG-CTAGGAAAGTAAGATTCGCTGTTGTAG
* * * *
2842234 CATCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCTGTCGTAGCTTCAATCTGTTTCGC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCGC
* * * *
2842299 TGCAATGCCT-GGGAAGTAAGATTTGCCT-TTGTGG
66 TGCAACG-CTAGGAAAGTAAGATTCG-CTGTTGTAG
* * * *
2842333 CTTCAATCTTTTAATTGTAATGTCGGAGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCGC
* * * *
2842398 TGCATCGCTTGGAAAGTAAGATTCGCCGTTGTGG
66 TGCAACGCTAGGAAAGTAAGATTCGCTGTTGTAG
* * *
2842432 CTTCAATC-TTT--TT--AACTGTCGGGGAAGCAAGATCCGTTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAATTGCAA-TGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
*
2842492 CTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
65 CTGCAACGCTAGGAAAGTAAGATTCGCTGTTGTAG
* * *
2842527 CTTCAATC-TTT--TT--AACTGCCGGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAATTGCAA-TGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
*
2842587 CTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
65 CTGCAACGCTAGGAAAGTAAGATTCGCTGTTGTAG
* * * *
2842622 CTTCAATCTTTTTAAATGCAATGTCAGGGAAGTAAGA-TCTGCTGTTGTAGCTTCAATCTATTCC
1 CTTCAATC-TTTTAATTGCAATGTCGGGGAAGCAAGATTC-GCTGTTGTAGCTTCAATCTGTTCC
* *
2842686 GCTGCATCGCTAGGAAAGTAAGATCCGCTGTTGTAG
64 GCTGCAACGCTAGGAAAGTAAGATTCGCTGTTGTAG
* * * *
2842722 CTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATC-TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
2842787 CTGCAACGCTAGGAAAGTAAGA-TCTGCTGTTGTAG
65 CTGCAACGCTAGGAAAGTAAGATTC-GCTGTTGTAG
* *
2842822 CTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATT
1 CTTCAATC-TTTTAATTGCAATGTCGGGGAAGCAAGATT
2842861 NNNNNNNNNN
Statistics
Matches: 554, Mismatches: 60, Indels: 27
0.86 0.09 0.04
Matches are distributed among these distances:
94 2 0.00
95 169 0.31
96 2 0.00
97 3 0.01
98 6 0.01
99 111 0.20
100 251 0.45
101 10 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (99 bp):
CTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCGC
TGCAACGCTAGGAAAGTAAGATTCGCTGTTGTAG
Found at i:2842321 original size:50 final size:49
Alignment explanation
Indices: 2842159--2842860 Score: 458
Period size: 50 Copynumber: 14.3 Consensus size: 49
2842149 TGTAATATCG
* * * * * *
2842159 GGGAAGTAAAATTCGCTGCTGTAGCTTCAAT-TTACTCTGCTGCATTGCCT
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTT-TTC-ACTGCAATGTCT
* * * * * *
2842209 GGGAAAGTAAGATTCGCCGTTGTGGCATCAATCTTTTAATTGCAATGTCG
1 GGG-AAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTCACTGCAATGTCT
** * * *
2842259 GGGAAGCGAGATTCGCTGTCGTAGCTTCAATCTGTTTCGCTGCAATGCCT
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT-TTTCACTGCAATGTCT
* * * * *
2842309 GGGAAGTAAGATTTGCCT-TTGTGGCTTCAATCTTTTAATTGTAATGTC-
1 GGGAAGTAAGATTCG-CTGTTGTAGCTTCAATCTTTTCACTGCAATGTCT
* * * * *
2842357 GGAGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCG-CTT
1 GG-GAAGTAAGATTCGCTGTTGTAGCTTCAATCT-TTTCACTGCAAT-GTC-T
* * * *
2842408 GGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTT---T--AACTGTCG
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTCACTGCAA-TGTCT
* * * * *
2842453 GGGAAGCAAGATCCGTTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT-TTTCACTGCAATGTCT
* * * *
2842502 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTT---T--AACTGCCG
1 -GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTCACTGCAA-TGTCT
* * * *
2842548 GGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT-TTTCACTGCAATGTCT
* * * * *
2842597 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAAATGCAATGTCA
1 -GGGAAGTAAGATTCGCTGTTGTAGCTTCAATC-TTTTCACTGCAATGTCT
* *
2842648 GGGAAGTAAGA-TCTGCTGTTGTAGCTTCAATCTATTCCGCTGC-ATCG-CT
1 GGGAAGTAAGATTC-GCTGTTGTAGCTTCAATCT-TTTCACTGCAAT-GTCT
* * * * *
2842697 AGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCA
1 -GGGAAGTAAGATTCGCTGTTGTAGCTTCAATC-TTTTCACTGCAATGTCT
* * *
2842748 GGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CT
1 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT-TTTCACTGCAATGTCT
* * * *
2842797 AGGAAAGTAAGA-TCTGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCA
1 -GGGAAGTAAGATTC-GCTGTTGTAGCTTCAATC-TTTTCACTGCAATGTCT
2842848 GGGAAGTAAGATT
1 GGGAAGTAAGATT
2842861 NNNNNNNNNN
Statistics
Matches: 503, Mismatches: 104, Indels: 89
0.72 0.15 0.13
Matches are distributed among these distances:
44 2 0.00
45 61 0.12
46 9 0.02
48 3 0.01
49 77 0.15
50 307 0.61
51 42 0.08
52 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (49 bp):
GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTCACTGCAATGTCT
Found at i:2843605 original size:50 final size:50
Alignment explanation
Indices: 2843479--2843605 Score: 184
Period size: 50 Copynumber: 2.5 Consensus size: 50
2843469 NNNNNCGTTG
* *
2843479 TTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTG
1 TTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAAGTAAGATCCGCTA
* ** *
2843529 TTGTAGCTTCAATCTGTTCCACTGCAATG-CTAGGAAAGTAAGATCCGCTA
1 TTGTAGCTTCAATCTTTTTAATTGCAATGTC-AGGAAAGTAAGATCCGCTA
2843579 TTGTAGCTTCAATCTTTTTAATTGCAA
1 TTGTAGCTTCAATCTTTTTAATTGCAA
2843606 ACTATGGTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
49 1 0.02
50 65 0.98
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (50 bp):
TTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGAAAGTAAGATCCGCTA
Found at i:2843870 original size:44 final size:44
Alignment explanation
Indices: 2843734--2843959 Score: 146
Period size: 44 Copynumber: 5.1 Consensus size: 44
2843724 CAGTACAGGA
* *
2843734 AGGCATGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAAACGAGAG
* * * ** *
2843778 AGGCAA-AGT-TTGTGTCTTCGACCTGCTTCGC-TGTC-AATGCAG-G
1 AGGCAAGA-TCTTTTGTCTTCAACCAGC-TC-CATCACAAACG-AGAG
2843821 AAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAAACGAGAG
1 -AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAAACGAGAG
* * * ** * *
2843866 AGGCAAGGT-TTGTGTCTTCGACTTGCTTCGCTGTCA-ATAC-AG-G
1 AGGCAAGATCTTTTGTCTTCAACCAGC-TC-C-ATCACAAACGAGAG
* * *
2843909 AAGGCAAGATCTTTTGTCTGCAACCAGCTCCATCACAACCAAGAG
1 -AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAAACGAGAG
2843954 AGGCAA
1 AGGCAA
2843960 AGTTTGTGTC
Statistics
Matches: 134, Mismatches: 30, Indels: 36
0.67 0.15 0.18
Matches are distributed among these distances:
42 3 0.02
43 36 0.27
44 55 0.41
45 37 0.28
46 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAAACGAGAG
Found at i:2844002 original size:44 final size:44
Alignment explanation
Indices: 2843778--2844003 Score: 157
Period size: 45 Copynumber: 5.1 Consensus size: 44
2843768 CAACCGAGAG
*
2843778 AGGCAAAGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
1 AGGCAAAGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
* * * * *
2843822 AGGC-AAGATCTTTTGTCTTCAACCAGC-TC-C-ATCACAAAC-GAGA
1 AGGCAAAG-T-TTGTGTCTTCGACCTGCTTCGCTGTCA-ATACAG-GA
* *
2843865 GAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCTGTCAATACAGGA
1 -AGGCAAAGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
* * * * * *
2843910 AGGC-AAGATCTTTTGTCTGCAACCAGC-TC-C-ATCACA-ACCAAGA
1 AGGCAAAG-T-TTGTGTCTTCGACCTGCTTCGCTGTCA-ATA-CAGGA
*
2843953 GAGGCAAAGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAAGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
2843998 AGGCAA
1 AGGCAA
2844004 GATCTGCTTC
Statistics
Matches: 134, Mismatches: 28, Indels: 40
0.66 0.14 0.20
Matches are distributed among these distances:
42 8 0.06
43 42 0.31
44 34 0.25
45 43 0.32
46 7 0.05
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (44 bp):
AGGCAAAGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGA
Found at i:2844109 original size:87 final size:88
Alignment explanation
Indices: 2843729--2844094 Score: 519
Period size: 88 Copynumber: 4.2 Consensus size: 88
2843719 ACTACCAGTA
* *
2843729 CAGGAAGGCATGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAAGTTTGTGTC
1 CAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTC
2843794 TTCGACCTGCTTCGCTGTCAATG
66 TTCGACCTGCTTCGCTGTCAATG
*
2843817 CAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAAACGAGAGAGGCAAGGTTTGTGTC
1 CAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTC
* *
2843882 TTCGACTTGCTTCGCTGTCAATA
66 TTCGACCTGCTTCGCTGTCAATG
* * *
2843905 CAGGAAGGCAAGATCTTTTGTCTGCAACCAGCTCCATCACAACCAAGAGAGGCAAAGTTTGTGTC
1 CAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTC
2843970 TTCGACCTGCTTCGCTGTCAATG
66 TTCGACCTGCTTCGCTGTCAATG
** * *
2843993 CAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCA-CTACAACCAATGA-AGGCAAGGCTTTGT
1 CAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAACCGA-GAGAGGCAAGG-TTTGT
* *
2844055 -T-TTCGATCC-GCTTCGCTGTTAACG
63 GTCTTCGA-CCTGCTTCGCTGTCAATG
*
2844079 GAGGAAGGCAAGATCT
1 CAGGAAGGCAAGATCT
2844095 GCTATCTTTA
Statistics
Matches: 255, Mismatches: 19, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
86 34 0.13
87 32 0.13
88 189 0.74
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (88 bp):
CAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTC
TTCGACCTGCTTCGCTGTCAATG
Found at i:2844122 original size:87 final size:87
Alignment explanation
Indices: 2843729--2844148 Score: 362
Period size: 88 Copynumber: 4.8 Consensus size: 87
2843719 ACTACCAGTA
* ** * * *
2843729 CAGGAAGGCATGATCTTTTGTCTTCAACCAGCTCCA-TCACAACCGA-GAGAGGCAAAG-TTTGT
1 CAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT-ACAACCAATGA-AGGCAAGGCTTTGT
*
2843791 GTCTTCGA-CCTGCTTCGCTGTCAATG
63 -T-TTCGATCCTGCTTCGCTGTCAACG
** * * *
2843817 CAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCACAAACGA-GAGAGGCAAGG-TTTGT
1 CAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT-ACAACCAATGA-AGGCAAGGCTTTGT
* **
2843879 GTCTTCGA-CTTGCTTCGCTGTCAATA
63 -T-TTCGATCCTGCTTCGCTGTCAACG
** ** *
2843905 CAGGAAGGCAAGATCTTTTGTCTGCAACCAGCTCCA-TCACAACCAA-GAGAGGCAAAG-TTTGT
1 CAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT-ACAACCAATGA-AGGCAAGGCTTTGT
*
2843967 GTCTTCGA-CCTGCTTCGCTGTCAATG
63 -T-TTCGATCCTGCTTCGCTGTCAACG
2843993 CAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCAATGAAGGCAAGGCTTTGTTTT
1 CAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCAATGAAGGCAAGGCTTTGTTTT
*
2844058 CGATCC-GCTTCGCTGTTAACG
66 CGATCCTGCTTCGCTGTCAACG
* * * * *
2844079 GAGGAAGGCAAGATCTGCTATCTTTAACCAGTTCCACTGCAACCGATGGAGGCAAGGCTTTGTTT
1 CAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTACAACCAATGAAGGCAAGGCTTTGTTT
2844144 TCGAT
65 TCGAT
2844149 TTTCACTGAT
Statistics
Matches: 304, Mismatches: 23, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
86 36 0.12
87 78 0.26
88 190 0.62
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (87 bp):
CAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCAATGAAGGCAAGGCTTTGTTTT
CGATCCTGCTTCGCTGTCAACG
Found at i:2845381 original size:7 final size:7
Alignment explanation
Indices: 2845369--2845420 Score: 88
Period size: 7 Copynumber: 7.6 Consensus size: 7
2845359 AGCCTCTCCA
2845369 TTTTCAT
1 TTTTCAT
2845376 TTTTCAT
1 TTTTCAT
2845383 TTTTCAT
1 TTTTCAT
2845390 TTTTCA-
1 TTTTCAT
*
2845396 TTCTCAT
1 TTTTCAT
2845403 TTTTCAT
1 TTTTCAT
2845410 TTTTCAT
1 TTTTCAT
2845417 TTTT
1 TTTT
2845421 TTGACTTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 5 0.12
7 37 0.88
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:2845397 original size:27 final size:27
Alignment explanation
Indices: 2845367--2845420 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2845357 TTAGCCTCTC
*
2845367 CATTTTCATTTTTCATTTTTCATTTTT
1 CATTCTCATTTTTCATTTTTCATTTTT
2845394 CATTCTCATTTTTCATTTTTCATTTTT
1 CATTCTCATTTTTCATTTTTCATTTTT
2845421 TTGACTTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (27 bp):
CATTCTCATTTTTCATTTTTCATTTTT
Found at i:2846402 original size:27 final size:26
Alignment explanation
Indices: 2846332--2846410 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
2846322 ATTTTTCTCA
* *
2846332 TTTTCATTTTGATCTTGATTTTGATTT
1 TTTTCATTTTCAT-TTTATTTTGATTT
* * *
2846359 TTTTCTTTCTTCTTTTTTTTTTGATTTT
1 TTTTCATT-TTCATTTTATTTTGA-TTT
2846387 TTTTCATTTTCATTTTCATTTTGA
1 TTTTCATTTTCATTTT-ATTTTGA
2846411 CTTTAATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.11, C:0.10, G:0.06, T:0.72
Consensus pattern (26 bp):
TTTTCATTTTCATTTTATTTTGATTT
Found at i:2851051 original size:3 final size:3
Alignment explanation
Indices: 2851029--2851085 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
2851019 ATATAATGAG
* *
2851029 AAT AAC AAT GAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2851075 AAT AAT AAT AA
1 AAT AAT AAT AA
2851086 CATAAAATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2856831 original size:2 final size:2
Alignment explanation
Indices: 2856824--2856848 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2856814 AAGTGATCAT
2856824 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2856849 TTGAAGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2857971 original size:24 final size:24
Alignment explanation
Indices: 2857944--2858000 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2857934 AAACCTAATT
2857944 CTAATCAAA-GCCAAATATATTATG
1 CTAAT-AAATGCCAAATATATTATG
*
2857968 CTAATAAATGCTAAATATATTATG
1 CTAATAAATGCCAAATATATTATG
*
2857992 CTCATAAAT
1 CTAATAAAT
2858001 ACTAAATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (24 bp):
CTAATAAATGCCAAATATATTATG
Found at i:2858005 original size:24 final size:24
Alignment explanation
Indices: 2857956--2858007 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
2857946 AATCAAAGCC
*
2857956 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATACT
*
2857980 AAATATATTATGCTCATAAATACT
1 AAATATATTATGCTAATAAATACT
2858004 AAAT
1 AAAT
2858008 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATACT
Found at i:2862800 original size:24 final size:24
Alignment explanation
Indices: 2862785--2862836 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2862775 AATCAAAGTC
2862785 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
2862809 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
2862833 AAAT
1 AAAT
2862837 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:2864163 original size:13 final size:13
Alignment explanation
Indices: 2864145--2864169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2864135 GTAACGCATG
2864145 ATTTGGATTCTAT
1 ATTTGGATTCTAT
2864158 ATTTGGATTCTA
1 ATTTGGATTCTA
2864170 ATGAATCATT
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:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (13 bp):
ATTTGGATTCTAT
Found at i:2866779 original size:85 final size:85
Alignment explanation
Indices: 2866690--2866854 Score: 231
Period size: 85 Copynumber: 1.9 Consensus size: 85
2866680 ACTGGGCGTG
* * * *
2866690 CTCTCATTGACATGTTATCAAAAAAGCTTTTCTAGCTGGACGCGCTTTTACACTACTGTGAAGAA
1 CTCTCATTGACATGTCATCAAAAAAGCTCTTCTAGCTGGACACGCTTTCACACTACTGTGAAGAA
2866755 AACGCGTCCAACTGGGCACA
66 AACGCGTCCAACTGGGCACA
* ** * * *
2866775 CTCTCCTTGACATGTCATCAGGAAAGCTCTTCTAGTTTGACATGCTTTCACACTACTGTGAAGAA
1 CTCTCATTGACATGTCATCAAAAAAGCTCTTCTAGCTGGACACGCTTTCACACTACTGTGAAGAA
*
2866840 AACGCGTCCAGCTGG
66 AACGCGTCCAACTGG
2866855 TTGCGCTTTC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (85 bp):
CTCTCATTGACATGTCATCAAAAAAGCTCTTCTAGCTGGACACGCTTTCACACTACTGTGAAGAA
AACGCGTCCAACTGGGCACA
Found at i:2869989 original size:28 final size:27
Alignment explanation
Indices: 2869958--2870011 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 27
2869948 ATATTTTCTG
2869958 TATT-TTTTATATATTTTTTTTATAATTC
1 TATTATTTTA-ATA-TTTTTTTATAATTC
2869986 TATTGATTTTAATATTTTTTTATAAT
1 TATT-ATTTTAATATTTTTTTATAAT
2870012 AGATAGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 16 0.67
29 3 0.12
30 5 0.21
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (27 bp):
TATTATTTTAATATTTTTTTATAATTC
Found at i:2873543 original size:103 final size:104
Alignment explanation
Indices: 2873364--2873571 Score: 400
Period size: 103 Copynumber: 2.0 Consensus size: 104
2873354 GTCACTTTTG
2873364 TTTGCCTCAGATTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTACGTTATC
1 TTTGCCTCAGATTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTACGTTATC
2873429 GTTTTGTTACGAAGTGGTCACTCTACCG-AAACTCCGTT
66 GTTTTGTTACGAAGTGGTCACTCTACCGTAAACTCCGTT
2873467 TTTGCCTCAGATTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTACGTTATC
1 TTTGCCTCAGATTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTACGTTATC
2873532 GTTTTGTTACGAAGTGGTCACTCTACCGTTAAACTCCGTT
66 GTTTTGTTACGAAGTGGTCACTCTACCG-TAAACTCCGTT
2873572 ACCTCCCTAA
Statistics
Matches: 103, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
103 93 0.90
105 10 0.10
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.42
Consensus pattern (104 bp):
TTTGCCTCAGATTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTACGTTATC
GTTTTGTTACGAAGTGGTCACTCTACCGTAAACTCCGTT
Found at i:2874744 original size:21 final size:21
Alignment explanation
Indices: 2874720--2874760 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2874710 CCTTCTCTGG
* *
2874720 TTTTATTCTTATGTAAAATTA
1 TTTTAGTCTGATGTAAAATTA
*
2874741 TTTTAGTCTGATTTAAAATT
1 TTTTAGTCTGATGTAAAATT
2874761 TACAACAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTAGTCTGATGTAAAATTA
Found at i:2883343 original size:15 final size:16
Alignment explanation
Indices: 2883323--2883359 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
2883313 AATCGGCAGC
2883323 AAAAAGAAAAA-AGAA
1 AAAAAGAAAAACAGAA
2883338 AAAAAGAAAAACAGAA
1 AAAAAGAAAAACAGAA
2883354 AGAAAA
1 A-AAAA
2883360 TTTGTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 5 0.25
17 4 0.20
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAACAGAA
Found at i:2889014 original size:21 final size:21
Alignment explanation
Indices: 2888984--2889028 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2888974 TTGCCCATAG
*
2888984 CATGTCACACCTTGAAACCAA
1 CATGTAACACCTTGAAACCAA
2889005 CATGTAACACCTTGAAACCAA
1 CATGTAACACCTTGAAACCAA
2889026 CAT
1 CAT
2889029 ATCACATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (21 bp):
CATGTAACACCTTGAAACCAA
Found at i:2891695 original size:3 final size:3
Alignment explanation
Indices: 2891673--2891746 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
2891663 TAATTTAATG
* * * *
2891673 TAT TAT CAT CTAT CAT TAT TAT TTT TAT TAT TTT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
2891719 CT-T TAC TAT TAT TAG TAT TAA TAT TAT T
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2891747 GTTGTTACTT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
2 1 0.02
3 50 0.93
4 3 0.06
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2896829 original size:23 final size:23
Alignment explanation
Indices: 2896801--2896845 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2896791 AATATTTATC
2896801 AAATCATAATCATTTAAGATGCA
1 AAATCATAATCATTTAAGATGCA
2896824 AAATCATAATCATTTAAGATGC
1 AAATCATAATCATTTAAGATGC
2896846 TTATATCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (23 bp):
AAATCATAATCATTTAAGATGCA
Found at i:2897788 original size:20 final size:20
Alignment explanation
Indices: 2897753--2897790 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2897743 TGACCACTTC
2897753 GTAATAAAACGATAACATAA
1 GTAATAAAACGATAACATAA
2897773 GTAACTAAAACG-TAACAT
1 GTAA-TAAAACGATAACAT
2897791 TTTAAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (20 bp):
GTAATAAAACGATAACATAA
Found at i:2898267 original size:76 final size:77
Alignment explanation
Indices: 2898180--2898332 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 77
2898170 ATGTAGTTTC
2898180 ATCAATTTAATAACCTATATCTTTATAATTTTTAAAGAATTAAATTAAATTTTTATTATTTT-AA
1 ATCAATTTAATAACCTATATCTTTATAATTTTTAAAGAATTAAATTAAATTTTTATTATTTTAAA
2898244 AAGACAAAAGTA
66 AAGACAAAAGTA
2898256 ATCAATTTAATAACCTATATCTTTATAATTTTTAAAGAATTAAATTAAATTTTTATTATTTTAAA
1 ATCAATTTAATAACCTATATCTTTATAATTTTTAAAGAATTAAATTAAATTTTTATTATTTTAAA
2898321 AAGACAAAAGTA
66 AAGACAAAAGTA
2898333 TAATTTTATA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 62 0.82
77 14 0.18
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (77 bp):
ATCAATTTAATAACCTATATCTTTATAATTTTTAAAGAATTAAATTAAATTTTTATTATTTTAAA
AAGACAAAAGTA
Found at i:2900242 original size:106 final size:106
Alignment explanation
Indices: 2900057--2900262 Score: 313
Period size: 106 Copynumber: 1.9 Consensus size: 106
2900047 GCATCATTCT
* *
2900057 AAAAAGTATAATTTTTAATCACCAATAAAATGGTACCACGTCATTAAAGTTTAAAGATAACAAAA
1 AAAAAGTATAATTTTTAAGCACCAATAAAATAGTACCACGTCATTAAAGTTTAAAGATAACAAAA
2900122 TATTATTACACACTCATCTATATCTAATATCTTCTATCCTA
66 TATTATTACACACTCATCTATATCTAATATCTTCTATCCTA
* * ** * *
2900163 AAAAATTATAATTTTTAGGCACCAATAAAATAGTGTCATGTCATTAAATTTTAAAGATAACAAAA
1 AAAAAGTATAATTTTTAAGCACCAATAAAATAGTACCACGTCATTAAAGTTTAAAGATAACAAAA
* * *
2900228 TATTATTATACACTCATCTGTATCTAATGTCTTCT
66 TATTATTACACACTCATCTATATCTAATATCTTCT
2900263 CCAACTTAAT
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
106 89 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (106 bp):
AAAAAGTATAATTTTTAAGCACCAATAAAATAGTACCACGTCATTAAAGTTTAAAGATAACAAAA
TATTATTACACACTCATCTATATCTAATATCTTCTATCCTA
Found at i:2900647 original size:29 final size:29
Alignment explanation
Indices: 2900593--2900652 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2900583 GAGTTCAAGT
*
2900593 GTTTGGGGTTTAGGGTTTAAGATTTAAGG
1 GTTTGGGGTTTAGGGTTCAAGATTTAAGG
* *
2900622 GTTTGGGG-TTCGGAGTTCAAGGTTTAAGG
1 GTTTGGGGTTTAGG-GTTCAAGATTTAAGG
2900651 GT
1 GT
2900653 ACAAGATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.18, C:0.03, G:0.40, T:0.38
Consensus pattern (29 bp):
GTTTGGGGTTTAGGGTTCAAGATTTAAGG
Found at i:2903890 original size:23 final size:21
Alignment explanation
Indices: 2903856--2903903 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
2903846 TGAGTGTATG
2903856 AATTAATTAATTAAAAGATTT
1 AATTAATTAATTAAAAGATTT
**
2903877 AATTAATTTGAATTAAATTATTT
1 AATTAA-TT-AATTAAAAGATTT
2903900 AATT
1 AATT
2903904 TTTTATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
23 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
AATTAATTAATTAAAAGATTT
Found at i:2906188 original size:271 final size:271
Alignment explanation
Indices: 2905690--2906232 Score: 928
Period size: 271 Copynumber: 2.0 Consensus size: 271
2905680 TGAAGAAAAG
* *
2905690 AGATCCGAAGCCGTTTTAAGAGCAAGTTGTCACGACACTTGAAGCAATCCAAGTCAGATGACCCT
1 AGATCCAAACCCGTTTTAAGAGCAAGTTGTCACGACACTTGAAGCAATCCAAGTCAGATGACCCT
*
2905755 TGGATCAAAGTTAAATCGGAAAGAAGAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTTAA
66 CGGATCAAAGTTAAATCGGAAAGAAGAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTTAA
2905820 GAGATTGTAACTCTCTTTCAAGTTATCAATAAATTTGATGTCGAATTTCCAAGTCAATATTTTAC
131 GAGATTGTAACTCTCTTTCAAGTTATCAATAAATTTGATGTCGAATTTCCAAGTCAATATTTTAC
* * * * * *
2905885 TCGAAATTTGTGTGTACAAATTTCTGGCACACCTAGTAAGACAATCTTTGTCTTTTATCTTTTCT
196 TCAAAATTTGTGTGTACAAATTTCTCGCACACCCAATAAGACAATCTTTATCTTTCATCTTTTCT
2905950 CTTGAAAGTCA
261 CTTGAAAGTCA
*
2905961 AGATCCAAACCCGTTTTAAGAGCAAGTTGTCATGACACTTGAAGCAATCCAAGTCAGATGACCCT
1 AGATCCAAACCCGTTTTAAGAGCAAGTTGTCACGACACTTGAAGCAATCCAAGTCAGATGACCCT
*
2906026 CGGATCAAAGTTAAATC-GAAGAGAATAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTTA
66 CGGATCAAAGTTAAATCGGAA-AGAAGAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTTA
* *
2906090 AGAGATTGTAACTTTCTTTCAAGTTATCAATAAATTTGACT-TTGAATTTCCAAGTCAATATTTT
130 AGAGATTGTAACTCTCTTTCAAGTTATCAATAAATTTGA-TGTCGAATTTCCAAGTCAATATTTT
*
2906154 ACTCAAAATTTGTGTGTACAAATTTCTCGCACACCCAATAGGACAATCTTTATCTTTCATCTTTT
194 ACTCAAAATTTGTGTGTACAAATTTCTCGCACACCCAATAAGACAATCTTTATCTTTCATCTTTT
2906219 CTCTTGAAAGTCA
259 CTCTTGAAAGTCA
2906232 A
1 A
2906233 AATTCAAAGT
Statistics
Matches: 256, Mismatches: 14, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
270 3 0.01
271 252 0.98
272 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (271 bp):
AGATCCAAACCCGTTTTAAGAGCAAGTTGTCACGACACTTGAAGCAATCCAAGTCAGATGACCCT
CGGATCAAAGTTAAATCGGAAAGAAGAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTTAA
GAGATTGTAACTCTCTTTCAAGTTATCAATAAATTTGATGTCGAATTTCCAAGTCAATATTTTAC
TCAAAATTTGTGTGTACAAATTTCTCGCACACCCAATAAGACAATCTTTATCTTTCATCTTTTCT
CTTGAAAGTCA
Found at i:2921854 original size:18 final size:19
Alignment explanation
Indices: 2921817--2921854 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2921807 AAGTTCGTAA
**
2921817 TTTATTATATTATGTTATT
1 TTTATTATATTATGCAATT
2921836 TTTA-TATATTATGCAATT
1 TTTATTATATTATGCAATT
2921854 T
1 T
2921855 ATAACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATTATATTATGCAATT
Found at i:2924041 original size:31 final size:31
Alignment explanation
Indices: 2923952--2924034 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 31
2923942 ATACGCCCGT
* *
2923952 ATGTATACAATTGAATCAAAATCAAAGTTTT
1 ATGTATACAATTGAATCAAAATCAAAATTTA
* *
2923983 ATATATACATTTGAATCAAAATCAAAATTTA
1 ATGTATACAATTGAATCAAAATCAAAATTTA
*
2924014 ATGTATATAATTGAATCAAAA
1 ATGTATACAATTGAATCAAAA
2924035 ATAAAATACA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.35
Consensus pattern (31 bp):
ATGTATACAATTGAATCAAAATCAAAATTTA
Found at i:2935945 original size:61 final size:61
Alignment explanation
Indices: 2935834--2935948 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
2935824 AAAATTTAAC
* * * * * *
2935834 AAATTTAACCCTCAATATTTACAAAATTTATCATTTTAGTTCTGATTCTAAAAAAATCAAT
1 AAATTTAACCCTCAATATTTACAAAATTGATCAATTTAATTATAACTCTAAAAAAATCAAT
* *
2935895 AAATTTAACTCTCAATATTTACAAAATCTGCT-AATTTAATTATAACTCTAAAAA
1 AAATTTAACCCTCAATATTTACAAAAT-TGATCAATTTAATTATAACTCTAAAAA
2935949 CTAGAAAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (61 bp):
AAATTTAACCCTCAATATTTACAAAATTGATCAATTTAATTATAACTCTAAAAAAATCAAT
Found at i:2941824 original size:112 final size:112
Alignment explanation
Indices: 2941627--2941832 Score: 396
Period size: 112 Copynumber: 1.8 Consensus size: 112
2941617 TTTTTTTTTG
2941627 GTTATGAAACTTCCTCACACATCCTTGAAATCTCGGATGAGGAACAAAAGTTTCGATTTAGTCCA
1 GTTATGAAACTTCCTCACACATCCTTGAAATCTCGGATGAGGAACAAAAGTTTCGATTTAGTCCA
2941692 CTTTAATTATAAAAATCAGCTCACCAATACGATATGGGGGCGGGGGT
66 CTTTAATTATAAAAATCAGCTCACCAATACGATATGGGGGCGGGGGT
2941739 GTTATGAAACTTCCTCACACATCCTTGAAATCTCAGG-TGAGGAACAAAAGTTTCGATTTAGTCC
1 GTTATGAAACTTCCTCACACATCCTTGAAATCTC-GGATGAGGAACAAAAGTTTCGATTTAGTCC
2941803 ACTTTAATTATAAAAATCAGCTCACCAATA
65 ACTTTAATTATAAAAATCAGCTCACCAATA
2941833 ACATATCTGA
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
112 91 0.98
113 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (112 bp):
GTTATGAAACTTCCTCACACATCCTTGAAATCTCGGATGAGGAACAAAAGTTTCGATTTAGTCCA
CTTTAATTATAAAAATCAGCTCACCAATACGATATGGGGGCGGGGGT
Found at i:2941852 original size:112 final size:112
Alignment explanation
Indices: 2941627--2941857 Score: 351
Period size: 112 Copynumber: 2.1 Consensus size: 112
2941617 TTTTTTTTTG
2941627 GTTATGAAACTTCCTCACACATCCTTGAAATCTCGGATGAGGAACAAAAGTTTCGATTTAGTCCA
1 GTTATGAAACTTCCTCACACATCCTTGAAATCTCGGATGAGGAACAAAAGTTTCGATTTAGTCCA
* *****
2941692 CTTTAATTATAAAAATCAGCTCACCAATACGATATGGGGGCGGGGGT
66 CTTTAATTATAAAAATCAGCTCACCAATACGATATCGGAAAACGGGT
2941739 GTTATGAAACTTCCTCACACATCCTTGAAATCTCAGG-TGAGGAACAAAAGTTTCGATTTAGTCC
1 GTTATGAAACTTCCTCACACATCCTTGAAATCTC-GGATGAGGAACAAAAGTTTCGATTTAGTCC
* *
2941803 ACTTTAATTATAAAAATCAGCTCACCAATAAC-ATATCTGAAAACTGGT
65 ACTTTAATTATAAAAATCAGCTCACCAAT-ACGATATCGGAAAACGGGT
2941851 G-TATGAA
1 GTTATGAA
2941858 TAGAGTAGTA
Statistics
Matches: 109, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
111 6 0.06
112 99 0.91
113 4 0.04
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (112 bp):
GTTATGAAACTTCCTCACACATCCTTGAAATCTCGGATGAGGAACAAAAGTTTCGATTTAGTCCA
CTTTAATTATAAAAATCAGCTCACCAATACGATATCGGAAAACGGGT
Found at i:2942760 original size:106 final size:106
Alignment explanation
Indices: 2942406--2942827 Score: 648
Period size: 106 Copynumber: 4.0 Consensus size: 106
2942396 TGGATTTAGA
* * * *
2942406 TTTAATAGGATATTTGGCTATTTGGTCGAACGAGAAATTGAAACCCAGCACGTTAGGGCACATTC
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
*
2942471 TCTTGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
* * *
2942512 TTTAAAAGGGATATTTTGCTATTTGGTCGAACGAGAAATAGAAACCCAGCACGTTAGGACACGTT
1 TTTAAAA-GGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTT
* *
2942577 TTCTCGAATTTTCAAAC-CAAAATATTGTCTTACTTTGAAAG
65 TTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
*
2942618 TTTAAAAGAATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* *
2942683 TCTCGAATTTCCAAACGCGAAATATTGCCTTACTTTGAAAT
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
* * * * *
2942724 TTTGAAAGGATATTCGGCTATTTGGTCGAACGAGAAATCGAAACCGAACAAGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* *
2942789 TCTCGAATTTCCAAACGCAAAATATTGTCTTACTCTGAA
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAA
2942828 TTTGAATGAA
Statistics
Matches: 288, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
105 69 0.24
106 152 0.53
107 67 0.23
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
Found at i:2943119 original size:23 final size:22
Alignment explanation
Indices: 2943093--2943136 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
2943083 ATTATTAAAG
2943093 ATGACAAAAAAATAAATAATGAA
1 ATGACAAAAAAAT-AATAATGAA
* **
2943116 ATGATAAAGTAATAATAATGA
1 ATGACAAAAAAATAATAATGA
2943137 CAAGAGTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (22 bp):
ATGACAAAAAAATAATAATGAA
Found at i:2955026 original size:52 final size:52
Alignment explanation
Indices: 2954948--2955054 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
2954938 GAGAAAAATT
* *
2954948 TAGTGCTTTCCATTGCCCTAAATTTTTCTTTCAGCCATTTACACCTTTCCTC
1 TAGTGCTTTCCATTGCCATAAATTTTTCTTTCAGCCATTTACACCTTTCCCC
* *
2955000 TAGTGCTTTCCATTGCCATAAATTTTTCTTTGAGTCATTTACACCTTTCCCC
1 TAGTGCTTTCCATTGCCATAAATTTTTCTTTCAGCCATTTACACCTTTCCCC
2955052 TAG
1 TAG
2955055 CCATTTACCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (52 bp):
TAGTGCTTTCCATTGCCATAAATTTTTCTTTCAGCCATTTACACCTTTCCCC
Found at i:2955856 original size:23 final size:20
Alignment explanation
Indices: 2955810--2955851 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
2955800 ACTCGTCAGC
2955810 TTTTCTAAAAATAAACTAAA
1 TTTTCTAAAAATAAACTAAA
2955830 TTTTCTACTAAAATAAA-TAAA
1 TTTTCTA--AAAATAAACTAAA
2955851 T
1 T
2955852 ATTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTCTAAAAATAAACTAAA
Found at i:2959921 original size:14 final size:14
Alignment explanation
Indices: 2959898--2959927 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2959888 ATACGAAAAG
*
2959898 TATATCTAAAATTT
1 TATATATAAAATTT
2959912 TATATATAAAATTT
1 TATATATAAAATTT
2959926 TA
1 TA
2959928 AAAATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATAAAATTT
Found at i:2962600 original size:2 final size:2
Alignment explanation
Indices: 2962595--2962627 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2962585 ATTTAAAGAA
2962595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2962628 AAAGGGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2966293 original size:10 final size:10
Alignment explanation
Indices: 2966249--2966297 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
2966239 TAATATTTTT
2966249 TTAAGTTATAA
1 TTAA-TTATAA
2966260 TTAATTAT-A
1 TTAATTATAA
*
2966269 TTAA-TAGT-T
1 TTAATTA-TAA
2966278 TTAATTATAA
1 TTAATTATAA
2966288 TTAATTATAA
1 TTAATTATAA
2966298 CAAGCTTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 2 0.06
9 11 0.33
10 16 0.48
11 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (10 bp):
TTAATTATAA
Found at i:2976826 original size:66 final size:66
Alignment explanation
Indices: 2976632--2976806 Score: 244
Period size: 66 Copynumber: 2.7 Consensus size: 66
2976622 ACACACAATT
* * * * *
2976632 GTGTGG-TTGGCCGTGTGACACAAGTCAGTATACCCTCCAGTTTTCACACGGCCTAGCACACGGG
1 GTGTGGCTTGGCCATGTGACACAAGTCAGTATACTCACTAGTTTTCACACGGCCTAGCACACGGA
2976696 C
66 C
* * * *
2976697 GTGTGGCTTGGCCATGTGTCACAAGTCAGTATGCTCATTATTTTTCACACGGCCTAGCACACGGA
1 GTGTGGCTTGGCCATGTGACACAAGTCAGTATACTCACTAGTTTTCACACGGCCTAGCACACGGA
2976762 C
66 C
* *
2976763 GTGTGGCTTGGCCATGTGACCCAAGTCAGTAAACTCACTAGTTT
1 GTGTGGCTTGGCCATGTGACACAAGTCAGTATACTCACTAGTTT
2976807 GGACACGGGA
Statistics
Matches: 94, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 6 0.06
66 88 0.94
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (66 bp):
GTGTGGCTTGGCCATGTGACACAAGTCAGTATACTCACTAGTTTTCACACGGCCTAGCACACGGA
C
Found at i:2983595 original size:61 final size:60
Alignment explanation
Indices: 2983500--2983619 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 60
2983490 TGCATATATA
** * *
2983500 TATATATATAATTCATAATACTATGTTCAACTCAAAGAACTTATATCATACATTCAAACTT
1 TATATATATAATTCATAATACTAAATTCAACTC-AAGAAATTAAATCATACATTCAAACTT
* * *
2983561 TATATATATAATTCATAACT-TTAAATTCAACTCAAGAAATTAAATCTTACATTCGAACT
1 TATATATATAATTCATAA-TACTAAATTCAACTCAAGAAATTAAATCATACATTCAAACT
2983620 ACATATCCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 22 0.43
61 28 0.55
62 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (60 bp):
TATATATATAATTCATAATACTAAATTCAACTCAAGAAATTAAATCATACATTCAAACTT
Found at i:2984579 original size:28 final size:28
Alignment explanation
Indices: 2984539--2984595 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
2984529 TATGTTTGTT
2984539 TTTATTATAATAA-CTTTATAATATATTA
1 TTTATTATAATAACCTTTATAAT-TATTA
*
2984567 TTTATTATTATAACCTTTATAATTATTA
1 TTTATTATAATAACCTTTATAATTATTA
2984595 T
1 T
2984596 AAAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATAATAACCTTTATAATTATTA
Found at i:2986040 original size:2 final size:2
Alignment explanation
Indices: 2986033--2986058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2986023 TTTTACCTTT
2986033 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2986059 ATTTGTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2988933 original size:33 final size:32
Alignment explanation
Indices: 2988790--2988950 Score: 115
Period size: 33 Copynumber: 4.8 Consensus size: 32
2988780 CATTGTTTAT
*
2988790 ATGTAAGATCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGATCATAGCTGGGCTATGGCAGTCTG
* * * * * *
2988822 ATGATAATACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGATCATAGCTGGGCTATGGCAGTCTG
* * * * * * * *
2988855 AACGTAAGACCATGGTTGGACCATGGCAATGTTTAT
1 -ATGTAAGATCATAGCTGGGCTATGGC-A-GTCT-G
2988891 ATGTAAGATCATAGCTGGGCTATGGCAGTCTG
1 ATGTAAGATCATAGCTGGGCTATGGCAGTCTG
* *
2988923 ATGATAAGATCATAACTGGGTTATGGCA
1 ATG-TAAGATCATAGCTGGGCTATGGCA
2988951 CTACGAATGT
Statistics
Matches: 96, Mismatches: 27, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
32 6 0.06
33 64 0.67
34 4 0.04
35 22 0.23
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (32 bp):
ATGTAAGATCATAGCTGGGCTATGGCAGTCTG
Found at i:2988947 original size:101 final size:101
Alignment explanation
Indices: 2988772--2988962 Score: 328
Period size: 101 Copynumber: 1.9 Consensus size: 101
2988762 ATGAACGTAA
* * *
2988772 GACCATGGCATTGTTTATATGTAAGATCATAGCTGGGCTATGGCATTCTGATGATAATACCATAA
1 GACCATGGCAATGTTTATATGTAAGATCATAGCTGGGCTATGGCAGTCTGATGATAAGACCATAA
*
2988837 CTGGGTTATGGCACTATGAACGTAAGACCATGGTTG
66 CTGGGTTATGGCACTACGAACGTAAGACCATGGTTG
*
2988873 GACCATGGCAATGTTTATATGTAAGATCATAGCTGGGCTATGGCAGTCTGATGATAAGATCATAA
1 GACCATGGCAATGTTTATATGTAAGATCATAGCTGGGCTATGGCAGTCTGATGATAAGACCATAA
*
2988938 CTGGGTTATGGCACTACGAATGTAA
66 CTGGGTTATGGCACTACGAACGTAA
2988963 ATGATGAATT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 84 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (101 bp):
GACCATGGCAATGTTTATATGTAAGATCATAGCTGGGCTATGGCAGTCTGATGATAAGACCATAA
CTGGGTTATGGCACTACGAACGTAAGACCATGGTTG
Found at i:2989213 original size:12 final size:12
Alignment explanation
Indices: 2989198--2989230 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2989188 CAGTAAGAGA
2989198 ATGATATGTGTC
1 ATGATATGTGTC
2989210 ATGATATGTGTC
1 ATGATATGTGTC
2989222 ATGATATGT
1 ATGATATGT
2989231 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (12 bp):
ATGATATGTGTC
Found at i:2993391 original size:202 final size:201
Alignment explanation
Indices: 2993040--2993638 Score: 783
Period size: 202 Copynumber: 3.0 Consensus size: 201
2993030 ATGTGGTTGA
*
2993040 GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATAGCTTCGGTAATATGTAAACTAGA
1 GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATGGCTTCGGTAATATGTAAAC-AGA
* * * *
2993105 CTAGTAGATCACGACATGAAAATATGTATAAGTCCATAAAGGAGATACCCATAGCGCCTTTTGTG
65 CTAGCAGATCACGACATGAAAATATGTATAAGTTCATGAGGGAGATACCCATAGCGCCTTTTGTG
* *
2993170 AAAGTTCGCTAGG-ACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGTGTAATCTACTAAG
130 AAAGTT-GC-CGGAACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGCGTAATCTACTAAG
*
2993234 CT-TTTTGG
193 CTCTTCTGG
* * * * *
2993242 GACTCATGACAATATATGACTGTATGAATATTCATGGTGATGGTTTCGGTAATATGTAAATCGGA
1 GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATGGCTTCGGTAATATGTAAA-CAGA
* * *
2993307 CTAGCAGATTATGACATGAAAATATGTATAAGTTCATGAGGGAGATACCCATAGAGCCTTTTGTG
65 CTAGCAGATCACGACATGAAAATATGTATAAGTTCATGAGGGAGATACCCATAGCGCCTTTTGTG
* * * * *
2993372 AAAGTCTGCCGGAACAGTAAACATGTGATTTTGTATGATGGCATCTGTGGCGTTATCTACTAA-A
130 AAAGT-TGCCGGAACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGCGTAATCTACTAAGC
2993436 TCTTCTGG
194 TCTTCTGG
* *
2993444 GACCCATGACAAGATATGATTGTATGAATATTCATAGTGATGGCTTCGGTAACATGTAAACCAGA
1 GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATGGCTTCGGTAATATGTAAA-CAGA
* * *
2993509 TTGGCAGATCACAACATGAAAATATGTATAAG-TCTATGAGGGAGATACCCATAGCGCCTTTTGT
65 CTAGCAGATCACGACATGAAAATATGTATAAGTTC-ATGAGGGAGATACCCATAGCGCCTTTTGT
** ** * * * * *
2993573 GAAAGTTTACTAAGACAATAAACACGTGATTTTATATGATGGTCTGTGTGGCGTAATCTGCTAAG
129 GAAAGTTGCCGGA-ACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGCGTAATCTACTAAG
2993638 C
193 C
2993639 CTTTGTGGTG
Statistics
Matches: 342, Mismatches: 48, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
201 8 0.02
202 332 0.97
203 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (201 bp):
GACCCATGACAAGATATGATTGTATGAATATTCATGGTGATGGCTTCGGTAATATGTAAACAGAC
TAGCAGATCACGACATGAAAATATGTATAAGTTCATGAGGGAGATACCCATAGCGCCTTTTGTGA
AAGTTGCCGGAACAGTAAACACGTGATTTTGTATGATGGCCTATGTGGCGTAATCTACTAAGCTC
TTCTGG
Found at i:2993655 original size:23 final size:23
Alignment explanation
Indices: 2993619--2993670 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2993609 TGATGGTCTG
2993619 TGTGGCGTAATCTGCTAAG-CCTT
1 TGTGGCGTAATCTG-TAAGACCTT
* * *
2993642 TGTGGTGTATTCTGTATGACCTT
1 TGTGGCGTAATCTGTAAGACCTT
2993665 TGTGGC
1 TGTGGC
2993671 AAGTTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.13, C:0.17, G:0.29, T:0.40
Consensus pattern (23 bp):
TGTGGCGTAATCTGTAAGACCTT
Found at i:2996543 original size:21 final size:21
Alignment explanation
Indices: 2996519--2996561 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2996509 AAATCAATAT
2996519 ATATAAAATATA-AATAATTTA
1 ATATAAAATATATAAT-ATTTA
*
2996540 ATATAAATTATATAATATTTA
1 ATATAAAATATATAATATTTA
2996561 A
1 A
2996562 AAAACATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAAAATATATAATATTTA
Found at i:2997220 original size:18 final size:18
Alignment explanation
Indices: 2997189--2997231 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2997179 TTCTTTTTAT
2997189 AAATAAATAGATCGAAAA
1 AAATAAATAGATCGAAAA
2997207 AAATGAAATA-ATCGAAAA
1 AAAT-AAATAGATCGAAAA
*
2997225 GAATAAA
1 AAATAAA
2997232 GAAAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 15 0.65
19 5 0.22
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (18 bp):
AAATAAATAGATCGAAAA
Found at i:3010103 original size:127 final size:128
Alignment explanation
Indices: 3009961--3010219 Score: 511
Period size: 127 Copynumber: 2.0 Consensus size: 128
3009951 TTTATATAAA
3009961 AAATTTAAAAAATACAATACATCAAAAACACCAAAAACATTATAATAAATGTTTCCCCACAAAGT
1 AAATTTAAAAAATACAATACATCAAAAACACCAAAAACATTATAATAAATGTTTCCCCACAAAGT
3010026 AAAAATAAATTAAAAAAAGTTTTTATACCTAAACAATACTAAGATAGGTGTAACTT-ACAAGC
66 AAAAATAAATTAAAAAAAGTTTTTATACCTAAACAATACTAAGATAGGTGTAACTTAACAAGC
3010088 AAATTTAAAAAATACAATACATCAAAAACACCAAAAACATTATAATAAATGTTTCCCCACAAAGT
1 AAATTTAAAAAATACAATACATCAAAAACACCAAAAACATTATAATAAATGTTTCCCCACAAAGT
3010153 AAAAATAAATTAAAAAAAGTTTTTATACCTAAACAATACTAAGATAGGTGTAACTTAACAAGC
66 AAAAATAAATTAAAAAAAGTTTTTATACCTAAACAATACTAAGATAGGTGTAACTTAACAAGC
3010216 AAAT
1 AAAT
3010220 GCCTCTAAAA
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 121 0.92
128 10 0.08
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (128 bp):
AAATTTAAAAAATACAATACATCAAAAACACCAAAAACATTATAATAAATGTTTCCCCACAAAGT
AAAAATAAATTAAAAAAAGTTTTTATACCTAAACAATACTAAGATAGGTGTAACTTAACAAGC
Found at i:3012517 original size:3 final size:3
Alignment explanation
Indices: 3012502--3012544 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
3012492 TGTTTATTGT
* *
3012502 TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG CTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
3012545 GTGTGTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.02, C:0.02, G:0.30, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:3026836 original size:85 final size:85
Alignment explanation
Indices: 3026693--3026855 Score: 308
Period size: 85 Copynumber: 1.9 Consensus size: 85
3026683 TAAACCATAT
*
3026693 AAGAGAAGCAACATAATACCAAAGAGAAAAGCACAATTGCCATCATAAATAACCTTTTGAATCTC
1 AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATAACCTTTTGAATCTC
3026758 AGGAGTTATATGTACAGTAC
66 AGGAGTTATATGTACAGTAC
*
3026778 AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATCACCTTTTGAATCTC
1 AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATAACCTTTTGAATCTC
3026843 AGGAGTTATATGT
66 AGGAGTTATATGT
3026856 CCAATCCTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.23
Consensus pattern (85 bp):
AAGAGAAGCAACATAATACCAAAGAGAAAAACACAATTGCCATCATAAATAACCTTTTGAATCTC
AGGAGTTATATGTACAGTAC
Found at i:3036266 original size:2 final size:2
Alignment explanation
Indices: 3036259--3036286 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3036249 CGGAGAAGAA
3036259 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3036287 GTGAAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3036770 original size:12 final size:12
Alignment explanation
Indices: 3036753--3036780 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3036743 GGAAAAATAG
3036753 CTACTTTAAGCA
1 CTACTTTAAGCA
3036765 CTACTTTAAGCA
1 CTACTTTAAGCA
3036777 CTAC
1 CTAC
3036781 GTCAATGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (12 bp):
CTACTTTAAGCA
Found at i:3040660 original size:7 final size:7
Alignment explanation
Indices: 3040648--3040693 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
3040638 AAAGAAAGGG
3040648 AGAAAAT
1 AGAAAAT
3040655 AGAAAAT
1 AGAAAAT
3040662 AGAAAA-
1 AGAAAAT
*
3040668 GGAAAA-
1 AGAAAAT
3040674 AGAAAAT
1 AGAAAAT
3040681 AGAGAAAT
1 AGA-AAAT
3040689 A-AAAA
1 AGAAAA
3040694 GGAAAATCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 13 0.37
7 17 0.49
8 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (7 bp):
AGAAAAT
Found at i:3040677 original size:26 final size:26
Alignment explanation
Indices: 3040648--3040699 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
3040638 AAAGAAAGGG
3040648 AGAAAATAGA-AAATAGAAAAGGAAAA
1 AGAAAATAGAGAAATA-AAAAGGAAAA
3040674 AGAAAATAGAGAAATAAAAAGGAAAA
1 AGAAAATAGAGAAATAAAAAGGAAAA
3040700 TCTCCCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (26 bp):
AGAAAATAGAGAAATAAAAAGGAAAA
Found at i:3047974 original size:2 final size:2
Alignment explanation
Indices: 3047967--3047991 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3047957 TACACCTCTA
3047967 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3047992 ATTTATCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3059626 original size:23 final size:21
Alignment explanation
Indices: 3059599--3059643 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
3059589 AATAAATTTT
*
3059599 AAAATTGTATAAAATTTATAAAA
1 AAAATTATAT-AAA-TTATAAAA
3059622 AAAATTATATAAATTATAAAA
1 AAAATTATATAAATTATAAAA
3059643 A
1 A
3059644 TTAGAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATTATATAAATTATAAAA
Found at i:3059635 original size:9 final size:9
Alignment explanation
Indices: 3059567--3059646 Score: 54
Period size: 9 Copynumber: 8.3 Consensus size: 9
3059557 NNNNNNNNNN
3059567 TTATAAAAA
1 TTATAAAAA
3059576 -TATAAAAAA
1 TTAT-AAAAA
*
3059585 TTCTAATAAA
1 TTATAA-AAA
* *
3059595 TTTTAAAAT
1 TTATAAAAA
*
3059604 TGTATAAAAT
1 T-TATAAAAA
3059614 TTATAAAAAAAA
1 TTAT---AAAAA
*
3059626 TTATATAAA
1 TTATAAAAA
3059635 TTATAAAAA
1 TTATAAAAA
3059644 TTA
1 TTA
3059647 GAAATTACAA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
8 3 0.05
9 28 0.49
10 18 0.32
12 8 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (9 bp):
TTATAAAAA
Found at i:3060410 original size:18 final size:18
Alignment explanation
Indices: 3060389--3060423 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3060379 TAATATTGTA
3060389 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
* *
3060407 AAATATAATTATTATTT
1 AAATAAAATAATTATTT
3060424 TTACAAGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:3068286 original size:56 final size:56
Alignment explanation
Indices: 3068222--3068333 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
3068212 CTTTTATTGC
**
3068222 CTAAAATAATAAAAATAAATTTTGAATATATTCTTATATTTTTATTATAGAATTTA
1 CTAAAATAATAAAAATAAAAATTGAATATATTCTTATATTTTTATTATAGAATTTA
3068278 CTAAAATAATAAAAATAAAAATTGAATATATTCTTATATTTTTATTATAGAATTTA
1 CTAAAATAATAAAAATAAAAATTGAATATATTCTTATATTTTTATTATAGAATTTA
3068334 TTCTTAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (56 bp):
CTAAAATAATAAAAATAAAAATTGAATATATTCTTATATTTTTATTATAGAATTTA
Found at i:3073733 original size:98 final size:97
Alignment explanation
Indices: 3073564--3073755 Score: 375
Period size: 98 Copynumber: 2.0 Consensus size: 97
3073554 TTTTCAAGTT
3073564 GAAAGACTGGAATTTGATTAATGGTCATAAATATATATATATGAACCCTAATACATCTGTCACTT
1 GAAAGACTGGAATTTGATTAATGGTCATAAATATATATATATGAACCCTAATACATCTGTCACTT
3073629 GATTCATATTTGAAATCATATTATACATAATTG
66 GATTCATATTTGAAA-CATATTATACATAATTG
3073662 GAAAGACTGGAATTTGATTAATGGTCATAAATATATATATATGAACCCTAATACATCTGTCACTT
1 GAAAGACTGGAATTTGATTAATGGTCATAAATATATATATATGAACCCTAATACATCTGTCACTT
3073727 GATTCATATTTGAAACATATTATACATAA
66 GATTCATATTTGAAACATATTATACATAA
3073756 CATATATATA
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 14 0.15
98 80 0.85
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (97 bp):
GAAAGACTGGAATTTGATTAATGGTCATAAATATATATATATGAACCCTAATACATCTGTCACTT
GATTCATATTTGAAACATATTATACATAATTG
Found at i:3074993 original size:19 final size:19
Alignment explanation
Indices: 3074962--3075003 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
3074952 TAAAAATTCT
*
3074962 AAAA-TTTATATTTATTAA
1 AAAATTTTAAATTTATTAA
* *
3074980 AAAATTTTAAATTTTTTTA
1 AAAATTTTAAATTTATTAA
3074999 AAAAT
1 AAAAT
3075004 ATATATAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATTTTAAATTTATTAA
Found at i:3078761 original size:19 final size:19
Alignment explanation
Indices: 3078730--3078771 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
3078720 TAAAAATTCT
*
3078730 AAAA-TTTATATTTATTAA
1 AAAATTTTAAATTTATTAA
* *
3078748 AAAATTTTAAATTTTTTTA
1 AAAATTTTAAATTTATTAA
3078767 AAAAT
1 AAAAT
3078772 ATATATAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATTTTAAATTTATTAA
Found at i:3098905 original size:20 final size:18
Alignment explanation
Indices: 3098868--3098934 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
3098858 CTTTATCAAA
*
3098868 TATATTTAAATTATTTAT
1 TATATTTAAATTAATTAT
3098886 TATATTTAATACTTAATTA-
1 TATATTTAA-A-TTAATTAT
* *
3098905 T-TATTAAAATTATTTATT
1 TATATTTAAATTAATTA-T
3098923 TAATATTTAAAT
1 T-ATATTTAAAT
3098935 CCGTTTCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
16 6 0.15
17 1 0.03
18 16 0.41
19 2 0.05
20 14 0.36
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTTAAATTAATTAT
Found at i:3099775 original size:96 final size:97
Alignment explanation
Indices: 3099610--3099796 Score: 295
Period size: 96 Copynumber: 1.9 Consensus size: 97
3099600 CCAGAATTAT
* * * *
3099610 GTATGAATGACATGGAAAAAAATTGTTGAAATGCCGTTCAATAATTAGAAAGGGGTCATGGATGA
1 GTATGAATGACATAGAAAAAAATTGTTGAAATGCCATTAAATAATTAGAAAGGGATCATGGATGA
* *
3099675 TGTGGTGGGAATGGTTCGTAAAATAATTTCTC
66 TGTGGTGGGAATGGTCCATAAAATAATTTCTC
* *
3099707 GTATGAATGACATAG-AAAAAATTGTTGAAATGTCATTAAATGATTAGAAAGGGATCATGGATGA
1 GTATGAATGACATAGAAAAAAATTGTTGAAATGCCATTAAATAATTAGAAAGGGATCATGGATGA
3099771 TGTGGTGGGAATGGTCCATAAAATAA
66 TGTGGTGGGAATGGTCCATAAAATAA
3099797 GTCTTCCCTA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 68 0.83
97 14 0.17
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (97 bp):
GTATGAATGACATAGAAAAAAATTGTTGAAATGCCATTAAATAATTAGAAAGGGATCATGGATGA
TGTGGTGGGAATGGTCCATAAAATAATTTCTC
Found at i:3105609 original size:19 final size:20
Alignment explanation
Indices: 3105585--3105622 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3105575 CCTTTTTACA
*
3105585 TTTCTTTTT-CTTTTCTTTT
1 TTTCTTTTTACGTTTCTTTT
3105604 TTTCTTTTTACGTTTCTTT
1 TTTCTTTTTACGTTTCTTT
3105623 GGTCTACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTCTTTTTACGTTTCTTTT
Found at i:3106135 original size:10 final size:10
Alignment explanation
Indices: 3106108--3106158 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
3106098 TTTATATTTT
3106108 TAAAAAATTA
1 TAAAAAATTA
* *
3106118 TAACAAATTC
1 TAAAAAATTA
3106128 TAAAAAATATA
1 TAAAAAAT-TA
3106139 TAAAGAAA-TA
1 TAAA-AAATTA
*
3106149 AAAAAAATTA
1 TAAAAAATTA
3106159 GAATAATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.67
11 5 0.15
12 3 0.09
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:3110151 original size:15 final size:15
Alignment explanation
Indices: 3110133--3110163 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3110123 TGAAAAATGC
3110133 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
*
3110148 AAAAAGAAAAAAGAA
1 AAAAAAAAAAAAGAA
3110163 A
1 A
3110164 TTAAGCTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:3114820 original size:15 final size:14
Alignment explanation
Indices: 3114787--3114845 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
3114777 AACTCAGCAG
* *
3114787 AATACAAATAA-AA
1 AATAAAAATAATAT
3114800 AATAAAAATAATGAT
1 AATAAAAATAAT-AT
*
3114815 AATAAAACTAATAT
1 AATAAAAATAATAT
*
3114829 AATAATAAATAAAAT
1 AATAA-AAATAATAT
3114844 AA
1 AA
3114846 ACTAAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 10 0.26
14 7 0.18
15 21 0.55
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (14 bp):
AATAAAAATAATAT
Found at i:3117684 original size:27 final size:26
Alignment explanation
Indices: 3117624--3117685 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
3117614 TATAGAATAG
* *
3117624 ATAATAATATAACCATGCATATATATT
1 ATAA-AATATAAACATGCATATACATT
*
3117651 ATTAAATATTAAACATGCATATACA-T
1 ATAAAATA-TAAACATGCATATACATT
3117677 ATGAAAATA
1 AT-AAAATA
3117686 AAAGTGCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.34
Consensus pattern (26 bp):
ATAAAATATAAACATGCATATACATT
Found at i:3117896 original size:3 final size:3
Alignment explanation
Indices: 3117888--3117936 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
3117878 AAAATGAAAC
*
3117888 TAA TAA TAA TTAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3117934 TAA
1 TAA
3117937 GTTAAACAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3129166 original size:72 final size:73
Alignment explanation
Indices: 3129024--3129167 Score: 227
Period size: 72 Copynumber: 2.0 Consensus size: 73
3129014 CTTAGACATG
** * *
3129024 TCATTAGCTCATTAAGTTTCATTGGATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTTATT
1 TCATTAGCTCATTAAAATTCATTGCATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTGATT
3129089 GCAAACCA
66 GCAAACCA
* *
3129097 TCATTAGCTCATTAAAATTCATTGCATCAACAA-TTAAGCCTCTTGAATTGTTGTCACCTTGATT
1 TCATTAGCTCATTAAAATTCATTGCATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTGATT
3129161 GCAAACC
66 GCAAACC
3129168 TTTCAAGTAG
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
72 35 0.54
73 30 0.46
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (73 bp):
TCATTAGCTCATTAAAATTCATTGCATCAACAACTTAAGCCTCTTCAATTATTGTCACCTTGATT
GCAAACCA
Found at i:3135819 original size:26 final size:26
Alignment explanation
Indices: 3135784--3135839 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
3135774 GTGGTTATTG
*
3135784 AACTCTTAAGGGAGTTGCCTACCTTGA
1 AACTCTTAAGCGAGTTGCCTACCTT-A
3135811 AACTC-TAAGCGAGTTGCCTACCTTA
1 AACTCTTAAGCGAGTTGCCTACCTTA
3135836 AACT
1 AACT
3135840 TACTGAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 5 0.18
26 18 0.64
27 5 0.18
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (26 bp):
AACTCTTAAGCGAGTTGCCTACCTTA
Found at i:3142303 original size:19 final size:20
Alignment explanation
Indices: 3142252--3142308 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
3142242 TTCCTCAACC
*
3142252 GAAAATATTTTCTGCAATAGT
1 GAAAATATTTTTTGC-ATAGT
*
3142273 CAGAAA-ATTTTTTGCA-AGT
1 GA-AAATATTTTTTGCATAGT
3142292 GAAAATATTTTTTGCAT
1 GAAAATATTTTTTGCAT
3142309 TACCAACACT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.10
19 14 0.47
20 1 0.03
21 9 0.30
22 3 0.10
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (20 bp):
GAAAATATTTTTTGCATAGT
Found at i:3154399 original size:20 final size:21
Alignment explanation
Indices: 3154360--3154401 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3154350 TAAAAAATTC
*
3154360 AAATATTAAAAATTAGAAAAA
1 AAATATTAAAAATCAGAAAAA
*
3154381 AAATA-TAAAAATCATAAAAA
1 AAATATTAAAAATCAGAAAAA
3154401 A
1 A
3154402 TAAAAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (21 bp):
AAATATTAAAAATCAGAAAAA
Found at i:3154425 original size:19 final size:19
Alignment explanation
Indices: 3154401--3154481 Score: 53
Period size: 19 Copynumber: 4.3 Consensus size: 19
3154391 ATCATAAAAA
3154401 ATAAAAATTGTAAAATTTT
1 ATAAAAATTGTAAAATTTT
* **
3154420 AT-AAAATCGTAAAAAAATT
1 ATAAAAATTGT-AAAATTTT
*
3154439 AT-AAAATATGTAGAAA-TAT
1 ATAAAAAT-TGTA-AAATTTT
*
3154458 A-AAAAATTTATAAAATTTT
1 ATAAAAA-TTGTAAAATTTT
3154477 ATAAA
1 ATAAA
3154482 GTTGTAAGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
18 10 0.21
19 28 0.60
20 9 0.19
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (19 bp):
ATAAAAATTGTAAAATTTT
Found at i:3154507 original size:57 final size:57
Alignment explanation
Indices: 3154403--3154519 Score: 139
Period size: 57 Copynumber: 2.0 Consensus size: 57
3154393 CATAAAAAAT
* *
3154403 AAAAATTGTAAAATTTTATAAAATCGTAAAAAAATTATAAAATATGT-AGAAATATA
1 AAAAATTATAAAATTTTATAAAATCGTAAAAAAACTATAAAATATGTAAGAAATATA
* * * *
3154459 AAAAATTTATAAAATTTTATAAAGTTGTAAGAAAACTATACGAA-ATGTAAAGAAATATA
1 AAAAA-TTATAAAATTTTATAAAATCGTAAAAAAACTATA-AAATATGT-AAGAAATATA
3154518 AA
1 AA
3154520 TTTCGTAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
56 5 0.10
57 33 0.65
58 2 0.04
59 11 0.22
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.31
Consensus pattern (57 bp):
AAAAATTATAAAATTTTATAAAATCGTAAAAAAACTATAAAATATGTAAGAAATATA
Found at i:3154878 original size:89 final size:88
Alignment explanation
Indices: 3154724--3154999 Score: 364
Period size: 88 Copynumber: 3.1 Consensus size: 88
3154714 TAATAAGAGC
*
3154724 AGGGGCTTAATTATTTTTTTGAAAAAAATTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAGT
1 AGGGGCTTAATTGTTTTTTTGAAAAAAATTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAGT
3154789 ATCTAATTGAGTGAAAAAAAATT
66 ATCTAATTGAGTGAAAAAAAATT
*
3154812 AGGCGCTTAATTGTTTTTTTGAAAAAAATTTAAGGGTCTTTTTTTATACATTTTTAAAGTTCAAG
1 AGGGGCTTAATTGTTTTTTTGAAAAAAATTTAAGGGTC-TTTTTTATACATTTTTAAAGTTCAAG
*
3154877 TATCCAATTGAGTG-AAAAAAATT
65 TATCTAATTGAGTGAAAAAAAATT
* * * * * * ** *
3154900 AGGGGCTTAATTTCTTTTTTTG-AAGAATTTTGAGGGCCTTTTTAATGTATTTTGAAAGTTCAAG
1 AGGGGCTTAA-TTGTTTTTTTGAAAAAAATTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAG
*
3154964 T-GCTCAATTGAGTGCAAAAAAAA--
65 TATCT-AATTGAGTG-AAAAAAAATT
3154987 AGGGGCTTAATTG
1 AGGGGCTTAATTG
3155000 CTTCTTCTTC
Statistics
Matches: 167, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
86 3 0.02
87 42 0.25
88 66 0.40
89 56 0.34
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.41
Consensus pattern (88 bp):
AGGGGCTTAATTGTTTTTTTGAAAAAAATTTAAGGGTCTTTTTTATACATTTTTAAAGTTCAAGT
ATCTAATTGAGTGAAAAAAAATT
Found at i:3170872 original size:29 final size:29
Alignment explanation
Indices: 3170830--3170891 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
3170820 AACTTGACAC
3170830 TCAACTCTCTAGGAGAGACATAAAAGCAA
1 TCAACTCTCTAGGAGAGACATAAAAGCAA
*
3170859 TCAACTCTCTAGGAGAGACATAAATGCAA
1 TCAACTCTCTAGGAGAGACATAAAAGCAA
3170888 TCAA
1 TCAA
3170892 AGTACAAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (29 bp):
TCAACTCTCTAGGAGAGACATAAAAGCAA
Found at i:3173092 original size:31 final size:33
Alignment explanation
Indices: 3173054--3173122 Score: 97
Period size: 35 Copynumber: 2.1 Consensus size: 33
3173044 ATACAATGTT
*
3173054 TAAAAA-A-ATCAAACAAATAACCTAGATAAAC
1 TAAAAATACATCAAACAAATAACCTAAATAAAC
3173085 TAAAAAAATACATCAAACAAATAACCTAAATAAAC
1 T--AAAAATACATCAAACAAATAACCTAAATAAAC
3173120 TAA
1 TAA
3173123 CATGAGAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
31 1 0.03
33 7 0.21
34 1 0.03
35 24 0.73
ACGTcount: A:0.65, C:0.16, G:0.01, T:0.17
Consensus pattern (33 bp):
TAAAAATACATCAAACAAATAACCTAAATAAAC
Found at i:3179943 original size:3 final size:3
Alignment explanation
Indices: 3179935--3179968 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
3179925 ATGTAGAAAC
* *
3179935 AAT AAT AAT AAT AAT AAT AAC ATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3179969 GCAATAAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3189660 original size:15 final size:15
Alignment explanation
Indices: 3189616--3189661 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
3189606 ACAAAAAAAT
3189616 AAAATATTTT-CT-A
1 AAAATATTTTACTGA
*
3189629 AAAATTATTTTA-GGA
1 AAAA-TATTTTACTGA
3189644 AAAATATTTTACTGA
1 AAAATATTTTACTGA
3189659 AAA
1 AAA
3189662 TTAAAGTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 4 0.15
14 13 0.48
15 10 0.37
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (15 bp):
AAAATATTTTACTGA
Found at i:3197205 original size:31 final size:30
Alignment explanation
Indices: 3197136--3197205 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
3197126 TACCCATATT
*
3197136 ATTTTTTAATTTTAAAAAAAACTATATTAT
1 ATTTTTTAATTTTAAAAAAAACTATATTAA
3197166 ATTATTTTAATATTTAATAAAAAA-T-TATTGAA
1 ATT-TTTTAAT-TTTAA-AAAAAACTATATT-AA
3197198 ATTTTTTA
1 ATTTTTTA
3197206 TAATATCTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
30 3 0.09
31 16 0.46
32 10 0.29
33 6 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
ATTTTTTAATTTTAAAAAAAACTATATTAA
Found at i:3197210 original size:33 final size:32
Alignment explanation
Indices: 3197137--3197216 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
3197127 ACCCATATTA
*
3197137 TTTTTTAAT-TTTAAAAAAAACTATATTATAT
1 TTTTTTAATATTTAAAAAAAACTATATTAAAT
*
3197168 TATTTTAATATTTAATAAAAAA-T-TATTGAAAT
1 TTTTTTAATATTTAA-AAAAAACTATATT-AAAT
3197200 TTTTTATAATATCTTAA
1 TTTTT-TAATAT-TTAA
3197217 CATTATTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 12 0.29
32 13 0.32
33 12 0.29
34 4 0.10
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (32 bp):
TTTTTTAATATTTAAAAAAAACTATATTAAAT
Found at i:3202137 original size:47 final size:47
Alignment explanation
Indices: 3202063--3202162 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 47
3202053 TATTAAGTAA
* *
3202063 TAAATATTCTATCGTTATGTGTTTGCGATGTATTAATAAAACTAACTT
1 TAAA-ATTCTATCGTTATGTGTTTGCGATGCATTAATAAAACTAACGT
* * *
3202111 TAAAATTCTATTGTTATGTGTTTGCGATGCATTAGTAAAATTAACGT
1 TAAAATTCTATCGTTATGTGTTTGCGATGCATTAATAAAACTAACGT
3202158 TAAAA
1 TAAAA
3202163 CAAGTTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 43 0.91
48 4 0.09
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (47 bp):
TAAAATTCTATCGTTATGTGTTTGCGATGCATTAATAAAACTAACGT
Found at i:3202879 original size:2 final size:2
Alignment explanation
Indices: 3202872--3202915 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
3202862 TATCATGAAA
*
3202872 AT AT AT AT TT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3202913 AT A
1 AT A
3202916 AAGGACTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3209092 original size:18 final size:18
Alignment explanation
Indices: 3209054--3209092 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3209044 ATTGCTTCTC
*
3209054 AAAAGCACTTTTGGGACA
1 AAAAGCACTTTTGAGACA
* *
3209072 AAAAGTACTTTTGAGATA
1 AAAAGCACTTTTGAGACA
3209090 AAA
1 AAA
3209093 GCATTACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (18 bp):
AAAAGCACTTTTGAGACA
Found at i:3211430 original size:15 final size:16
Alignment explanation
Indices: 3211401--3211433 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3211391 TTTTTATAAC
*
3211401 TTTTTAATATTTTTAT
1 TTTTTAATATATTTAT
3211417 TTTTTAATA-ATTTAT
1 TTTTTAATATATTTAT
3211432 TT
1 TT
3211434 GTTTTGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTAATATATTTAT
Found at i:3216686 original size:25 final size:25
Alignment explanation
Indices: 3216657--3216715 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
3216647 AGGATTAACT
3216657 GAATTAAAATTTTACTTATAAAATC
1 GAATTAAAATTTTACTTATAAAATC
3216682 GAATTAAAATTTTACTTATAAAATC
1 GAATTAAAATTTTACTTATAAAATC
3216707 GAATTAAAA
1 GAATTAAAA
3216716 GTGGGTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (25 bp):
GAATTAAAATTTTACTTATAAAATC
Found at i:3219207 original size:31 final size:30
Alignment explanation
Indices: 3219166--3219240 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
3219156 TTAATGGCTC
* **
3219166 AGTGATTAAAATGTTACAACATGTT-AATGTA
1 AGTGACTAAAATGTT--AACATGTTGAACATA
* *
3219197 AGTGACTAAAACG-TAACATTTTGAACATA
1 AGTGACTAAAATGTTAACATGTTGAACATA
3219226 AGTGACTAAAATGTT
1 AGTGACTAAAATGTT
3219241 GCCTGAGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 7 0.19
29 16 0.44
30 2 0.06
31 11 0.31
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (30 bp):
AGTGACTAAAATGTTAACATGTTGAACATA
Found at i:3221175 original size:29 final size:29
Alignment explanation
Indices: 3221142--3221202 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
3221132 CATGACACTG
*
3221142 TTTGTTATATATGCCATATCAACAAATAA
1 TTTGTTATATATGCCACATCAACAAATAA
*
3221171 TTTGTTATATATTCCACATCAACAAATAA
1 TTTGTTATATATGCCACATCAACAAATAA
3221200 TTT
1 TTT
3221203 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (29 bp):
TTTGTTATATATGCCACATCAACAAATAA
Found at i:3221587 original size:40 final size:40
Alignment explanation
Indices: 3221529--3221661 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
3221519 GCATTAACGA
* * *
3221529 CGCTTTTTAACAAACGCCGC-AATAGATCAAGAATTAGCGG
1 CGCTTTTTTAGAATCGCCGCTAA-AGATCAAGAATTAGCGG
* *
3221569 CGCTTTTTTAGAATCGCCGCTAAAGATCAAGTATTGGCGG
1 CGCTTTTTTAGAATCGCCGCTAAAGATCAAGAATTAGCGG
* * * *
3221609 CGCTTTTTGAAACAT-GCCGCTAAAGATCAAGAAATAGTGG
1 CGCTTTTTTAGA-ATCGCCGCTAAAGATCAAGAATTAGCGG
*
3221649 CGCATTTTTAGAA
1 CGCTTTTTTAGAA
3221662 ATGTCGTTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 72 0.94
41 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (40 bp):
CGCTTTTTTAGAATCGCCGCTAAAGATCAAGAATTAGCGG
Found at i:3222128 original size:14 final size:14
Alignment explanation
Indices: 3222097--3222192 Score: 63
Period size: 14 Copynumber: 6.9 Consensus size: 14
3222087 TGAGCTTTAT
3222097 TTTAGGGTTT-GTGA
1 TTTAGGGTTTAG-GA
* *
3222111 TTTAGGATTTAGGG
1 TTTAGGGTTTAGGA
* *
3222125 TTTAAGGTTTAGGGT
1 TTTAGGGTTTA-GGA
* * *
3222140 TTTATGATTTATGA
1 TTTAGGGTTTAGGA
3222154 -TTAGGGTTTA-GA
1 TTTAGGGTTTAGGA
**
3222166 GTTTAAAGTTTAGGA
1 -TTTAGGGTTTAGGA
3222181 TTTAGGGTTTAG
1 TTTAGGGTTTAG
3222193 TATTCAAGAT
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
12 2 0.03
13 8 0.13
14 38 0.61
15 14 0.23
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAGGA
Found at i:3222135 original size:21 final size:21
Alignment explanation
Indices: 3222097--3222191 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 21
3222087 TGAGCTTTAT
** *
3222097 TTTAGGGTTTGTGATTTAGGA
1 TTTAGGGTTTAAGGTTTAGGA
*
3222118 TTTAGGGTTTAAGGTTTAGGGT
1 TTTAGGGTTTAAGGTTTA-GGA
* * * * *
3222140 TTTATGATTT-ATGATTAGGG
1 TTTAGGGTTTAAGGTTTAGGA
* *
3222160 TTTAGAGTTTAAAGTTTAGGA
1 TTTAGGGTTTAAGGTTTAGGA
3222181 TTTAGGGTTTA
1 TTTAGGGTTTA
3222192 GTATTCAAGA
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 9 0.16
21 37 0.66
22 10 0.18
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.47
Consensus pattern (21 bp):
TTTAGGGTTTAAGGTTTAGGA
Found at i:3222170 original size:35 final size:35
Alignment explanation
Indices: 3222097--3222192 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
3222087 TGAGCTTTAT
*
3222097 TTTAGGGTTTGTGATTTAGGATTTAGGGTTTAAGG
1 TTTAGGGTTTATGATTTAGGATTTAGGGTTTAAGG
*
3222132 TTTAGGGTTTTATGATTTATGA-TTAGGGTTT-AGAG
1 TTTAGGG-TTTATGATTTAGGATTTAGGGTTTAAG-G
** * *
3222167 TTTAAAGTTTAGGATTTAGGGTTTAG
1 TTTAGGGTTTATGATTTAGGATTTAG
3222193 TATTCAAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
34 13 0.25
35 26 0.51
36 12 0.24
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (35 bp):
TTTAGGGTTTATGATTTAGGATTTAGGGTTTAAGG
Found at i:3227013 original size:42 final size:43
Alignment explanation
Indices: 3226967--3227065 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
3226957 GAATGGTACT
*
3226967 TTTAGTGGCATTTGCGAAAAAAGTACC-CTAAAGGTCATGTTC
1 TTTAGTGGCATTTGCGAAAAAAGCACCGCTAAAGGTCATGTTC
* * *
3227009 TTTAGTGGCGA-TTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGTGGC-ATTTGCGAAAAAAGCACCGCTAAAGGTCATGTTC
* *
3227052 TTTAGCGGCGTTTG
1 TTTAGTGGCATTTG
3227066 TGATAAGAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
42 21 0.44
43 27 0.56
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
TTTAGTGGCATTTGCGAAAAAAGCACCGCTAAAGGTCATGTTC
Found at i:3227050 original size:43 final size:43
Alignment explanation
Indices: 3226994--3227192 Score: 229
Period size: 43 Copynumber: 4.7 Consensus size: 43
3226984 AAAAAGTACC
* *
3226994 CTAAAGGTCATGTTCTTTAGTGGCGATTGTGATAAAAGCGCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
* *
3227037 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAGAGCCCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
* ** ** * * ** **
3227080 TTAAAGAACATGGCCTTTAGCGGCGCTTCTCTTTGAA-CGCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
* *
3227122 CTAAAGGTCATGATCTTTAGCGGTGTTTGTGATAAAAGCGCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
*
3227165 CTAAATGTCATGTTCTTTAGCGGCGTTT
1 CTAAAGGTCATGTTCTTTAGCGGCGTTT
3227193 ATGTGAAAGA
Statistics
Matches: 123, Mismatches: 32, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
42 29 0.24
43 94 0.76
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (43 bp):
CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
Done.