Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_pilon, whole genome shotgun sequence
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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 51
Found at i:6393971 original size:413 final size:414
Alignment explanation
Indices: 6393203--6394030 Score: 1604
Period size: 413 Copynumber: 2.0 Consensus size: 414
6393193 GAAGTATCAA
*
6393203 GATGAAAGAGGAGGGTTGACGCCACAAGTATAAAATACTTGATAAGTCGATAAAAAGTCACCAGG
1 GATGAAAGAGGAGGGTTGACACCACAAGTATAAAATACTTGATAAGTCGATAAAAAGTCACCAGG
*
6393268 ACTTAAGGAAGAGAATAATCTCACTTTGATTAATAAAAATGGTCTTCTTACAAATGATGAATGCT
66 ACTTAAGGAAGAGAATAATCTCACTTTGATTAATAAAAATGGTCTTCATACAAATGATGAATGCT
6393333 TTCCTATTTATAGGAAATGGAGGGGCATAGCCGAATAGAGACATAATGGTTCGGCCAGCCCATGT
131 TTCCTATTTATAGGAAATGGAGGGGCATAGCCGAATAGAGACATAATGGTTCGGCCAGCCCATGT
6393398 ATCTCCCTATAAAGACATAATTTAAATGCTAAAAGAGATGATGGTTTGGCCCTTGATGGAGGGAA
196 ATCTCCCTATAAAGACATAATTTAAATGCTAAAAGAGATGATGGTTTGGCCCTTGATGGAGGGAA
*
6393463 ATGATCCTTGGCCGAATAACACTTGTATCCCTTCAAATTGGCACCAAATGGGAGAAGTAATGGTG
261 ATGATCCTTGGCCGAATAACACTTGTATCCCTTCAAATTGGAACCAAATGGGAGAAGTAATGGTG
*
6393528 AATGGCCGAATGGATAGATGGCCATTCATCTTGGTGCCTAAATGAACCATATGCAAGGCACATGG
326 AATGGCCAAATGGATAGATGGCCATTCATCTTGGTGCCTAAATGAACCATATGCAAGGCACATGG
*
6393593 GGGTTGATCACATGCAAAACACAT
391 GGGCTGATCACATGCAAAACACAT
6393617 GATGAAAGAGGAGGGTTGACACCACAAGTATAAAATACTTGATAAGTCGATAAAAAGTCACCAGG
1 GATGAAAGAGGAGGGTTGACACCACAAGTATAAAATACTTGATAAGTCGATAAAAAGTCACCAGG
6393682 ACTTAAGGAAGAGAATAATCTCACTTTGATTAATAAAAATGGTCTTCATACAAATGATGAATGCT
66 ACTTAAGGAAGAGAATAATCTCACTTTGATTAATAAAAATGGTCTTCATACAAATGATGAATGCT
6393747 TTCC-ATTTATAGGAAATGGAGGGGCATAGCCGAATAGAGACATAATGGTTCGGCCAGCCCATGT
131 TTCCTATTTATAGGAAATGGAGGGGCATAGCCGAATAGAGACATAATGGTTCGGCCAGCCCATGT
6393811 ATCTCCCTATAAAGACATAATTTAAATGCTAAAAGAGATGATGGTTTGGCCCTTGATGGAGGGAA
196 ATCTCCCTATAAAGACATAATTTAAATGCTAAAAGAGATGATGGTTTGGCCCTTGATGGAGGGAA
6393876 ATGATCCTTGGCCGAATAACACTTGTATCCCTTCAAATTGGAACCAAATGGGAGAAGTAATGGTG
261 ATGATCCTTGGCCGAATAACACTTGTATCCCTTCAAATTGGAACCAAATGGGAGAAGTAATGGTG
6393941 AATGGCCAAATGGATAGATGGCCATTCATCTTGGTGCCTAAATGAACCATATGCAAGGCACATGG
326 AATGGCCAAATGGATAGATGGCCATTCATCTTGGTGCCTAAATGAACCATATGCAAGGCACATGG
6394006 GGGCTGATCACATGCAAAACACAT
391 GGGCTGATCACATGCAAAACACAT
6394030 G
1 G
6394031 GCTTGGCCGA
Statistics
Matches: 409, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
413 277 0.68
414 132 0.32
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (414 bp):
GATGAAAGAGGAGGGTTGACACCACAAGTATAAAATACTTGATAAGTCGATAAAAAGTCACCAGG
ACTTAAGGAAGAGAATAATCTCACTTTGATTAATAAAAATGGTCTTCATACAAATGATGAATGCT
TTCCTATTTATAGGAAATGGAGGGGCATAGCCGAATAGAGACATAATGGTTCGGCCAGCCCATGT
ATCTCCCTATAAAGACATAATTTAAATGCTAAAAGAGATGATGGTTTGGCCCTTGATGGAGGGAA
ATGATCCTTGGCCGAATAACACTTGTATCCCTTCAAATTGGAACCAAATGGGAGAAGTAATGGTG
AATGGCCAAATGGATAGATGGCCATTCATCTTGGTGCCTAAATGAACCATATGCAAGGCACATGG
GGGCTGATCACATGCAAAACACAT
Found at i:6401419 original size:35 final size:37
Alignment explanation
Indices: 6401350--6401425 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
6401340 ATACTATTTC
* *
6401350 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCCCCATAATCCATCATCCATTATCACACCTATAT
* *
6401387 CATCGCCATAGTCCATCAT-CA-TATCACACCTATAT
1 CATCCCCATAATCCATCATCCATTATCACACCTATAT
6401422 CATC
1 CATC
6401426 ACCAAATTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 17 0.49
36 2 0.06
37 16 0.46
ACGTcount: A:0.29, C:0.37, G:0.04, T:0.30
Consensus pattern (37 bp):
CATCCCCATAATCCATCATCCATTATCACACCTATAT
Found at i:6401906 original size:14 final size:15
Alignment explanation
Indices: 6401872--6401918 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
6401862 AATTTGGAGT
6401872 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
6401887 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
6401901 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
6401918 G
1 G
6401919 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:6413297 original size:36 final size:36
Alignment explanation
Indices: 6413274--6413416 Score: 250
Period size: 36 Copynumber: 4.0 Consensus size: 36
6413264 ATAGGCGTGA
6413274 TATGGTGATGATATAGGCGTGATAATGGTGATGGAT
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAT
* *
6413310 TATGGTGATGATATAGGCGTGATAGTGGTGATGGAA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAT
* *
6413346 TATGGTGATGAAATAGGCGTTATAATGGTGATGGAT
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAT
6413382 TATGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGA
6413417 CAGATTATAT
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 99 1.00
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAT
Found at i:6413316 original size:13 final size:13
Alignment explanation
Indices: 6413298--6413391 Score: 51
Period size: 13 Copynumber: 7.7 Consensus size: 13
6413288 AGGCGTGATA
6413298 ATGGTGATGGATT
1 ATGGTGATGGATT
6413311 ATGGTGAT-GA-T
1 ATGGTGATGGATT
*
6413322 ATAGGCG-T-GA-T
1 AT-GGTGATGGATT
*
6413333 AGTGGTGATGGAAT
1 A-TGGTGATGGATT
* *
6413347 ATGGTGATGAAAT
1 ATGGTGATGGATT
* * *
6413360 A-GGCG-T-TATA
1 ATGGTGATGGATT
6413370 ATGGTGATGGATT
1 ATGGTGATGGATT
6413383 ATGGTGATG
1 ATGGTGATG
6413392 ATATAGGCGT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
10 2 0.03
11 15 0.24
12 11 0.17
13 33 0.52
14 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.37, T:0.33
Consensus pattern (13 bp):
ATGGTGATGGATT
Found at i:6413318 original size:22 final size:22
Alignment explanation
Indices: 6413254--6413306 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
6413244 ATTTATAAGT
*
6413254 TGGTGATAATATAGGCGTGATA
1 TGGTGATGATATAGGCGTGATA
6413276 TGGTGATGATATAGGCGTGATAA
1 TGGTGATGATATAGGCGTGAT-A
6413299 TGGTGATG
1 TGGTGATG
6413307 GATTATGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (22 bp):
TGGTGATGATATAGGCGTGATA
Found at i:6413779 original size:19 final size:19
Alignment explanation
Indices: 6413755--6413804 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
6413745 GAAATCCCTT
**
6413755 TGAAAATACATGATTTTTA
1 TGAAAATACATGATTTAAA
6413774 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
6413793 TGAAGATACATG
1 TGAAAATACATG
6413805 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:6417006 original size:32 final size:33
Alignment explanation
Indices: 6416956--6417022 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
6416946 TCCACCAAAA
* *
6416956 CTCTGATTACCGCTTGATGTAAT-GCTAACCTGG
1 CTCTGATTACCACTTGATGT-ATGGCTAACCAGG
6416989 CTCTGA-TACCACTTGATGTATGGCTAACCAGG
1 CTCTGATTACCACTTGATGTATGGCTAACCAGG
6417021 CT
1 CT
6417023 TCTTCAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 2 0.06
32 23 0.74
33 6 0.19
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.31
Consensus pattern (33 bp):
CTCTGATTACCACTTGATGTATGGCTAACCAGG
Found at i:6417367 original size:22 final size:23
Alignment explanation
Indices: 6417339--6417391 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
6417329 ATTTATAAGT
6417339 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
6417361 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
6417384 TGGTGATA
1 TGGTGATA
6417392 GACTATGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:6417382 original size:36 final size:36
Alignment explanation
Indices: 6417359--6417502 Score: 252
Period size: 36 Copynumber: 4.0 Consensus size: 36
6417349 ATAGGCGTGA
*
6417359 TATGGTGATGATATAGGCGTGATAATGGTGATAGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
* *
6417395 TATGGTGATGATATAGGCGTGATAGTGGTGATGGAA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
6417431 TATGGTGATGATATAGGCGTGATAATGGTGATGGAT
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
6417467 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
6417503 AGATTGTATC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 102 1.00
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:6417438 original size:13 final size:12
Alignment explanation
Indices: 6417357--6417501 Score: 62
Period size: 11 Copynumber: 12.2 Consensus size: 12
6417347 ATATAGGCGT
6417357 GATATGGTGAT-
1 GATATGGTGATG
*
6417368 GATATAGGCG-T-
1 GATAT-GGTGATG
*
6417379 GATAATGGTGATA
1 GAT-ATGGTGATG
6417392 GACTATGGTGAT-
1 GA-TATGGTGATG
*
6417404 GATATAGGCG-T-
1 GATAT-GGTGATG
6417415 GATAGTGGTGATG
1 GATA-TGGTGATG
6417428 GAATATGGTGAT-
1 G-ATATGGTGATG
*
6417440 GATATAGGCG-T-
1 GATAT-GGTGATG
6417451 GATAATGGTGATG
1 GAT-ATGGTGATG
6417464 GATTATGGTGAT-
1 GA-TATGGTGATG
*
6417476 GATATAGGCG-T-
1 GATAT-GGTGATG
6417487 GATAATGGTGATG
1 GAT-ATGGTGATG
6417500 GA
1 GA
6417502 CAGATTGTAT
Statistics
Matches: 107, Mismatches: 8, Indels: 36
0.71 0.05 0.24
Matches are distributed among these distances:
11 44 0.41
12 28 0.26
13 30 0.28
14 5 0.05
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:6417495 original size:23 final size:23
Alignment explanation
Indices: 6417396--6417499 Score: 72
Period size: 23 Copynumber: 4.4 Consensus size: 23
6417386 GTGATAGACT
6417396 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
* *
6417419 GTGGTGATGGA-ATATG-GTGATGA
1 ATGGTGAT-GATATAGGCGTGAT-A
* * *
6417442 TATAGGCG-TGATA-ATGGTGATGGATT
1 -AT-GGTGATGATATA-GGCG-T-GATA
6417468 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
6417491 ATGGTGATG
1 ATGGTGATG
6417500 GACAGATTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 22
0.66 0.10 0.24
Matches are distributed among these distances:
22 5 0.08
23 27 0.44
24 10 0.16
25 14 0.23
26 2 0.03
27 3 0.05
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.32
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:6417885 original size:19 final size:20
Alignment explanation
Indices: 6417838--6417888 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
6417828 GAAATCCCTT
**
6417838 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
6417858 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
6417877 TGAAGATACATG
1 TGAAAATACATG
6417889 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:6418116 original size:19 final size:20
Alignment explanation
Indices: 6418069--6418119 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
6418059 GAAATCCCTT
**
6418069 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
6418089 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
6418108 TGAAGATACATG
1 TGAAAATACATG
6418120 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:6421309 original size:32 final size:33
Alignment explanation
Indices: 6421257--6421324 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
6421247 ATCCACTAAA
* *
6421257 GCTCTGATTACCGCTTGATGTAAGGCTAACCTG
1 GCTCTGATTACCACTTGATGTAAGGCTAACCAG
6421290 GCTCTGA-TACCACTTGATGTAAGGCTAACCAG
1 GCTCTGATTACCACTTGATGTAAGGCTAACCAG
6421322 GCT
1 GCT
6421325 TCTTCAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (33 bp):
GCTCTGATTACCACTTGATGTAAGGCTAACCAG
Found at i:6421668 original size:22 final size:23
Alignment explanation
Indices: 6421640--6421692 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
6421630 ATTTATAAGT
6421640 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
6421662 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
6421685 TGGTGATA
1 TGGTGATA
6421693 GACTATGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:6421683 original size:36 final size:36
Alignment explanation
Indices: 6421660--6421803 Score: 234
Period size: 36 Copynumber: 4.0 Consensus size: 36
6421650 ATAGGCGTGA
*
6421660 TATGGTGATGATATAGGCGTGATAATGGTGATAGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
** * *
6421696 TATGGTGATGATATAGGAATGATAGTGGTGATGGAA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
6421732 TATGGTGATGATATAGGCGTGATAATGGTGATGGAT
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
6421768 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
6421804 AGATTGTATC
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 98 1.00
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:6421739 original size:13 final size:12
Alignment explanation
Indices: 6421658--6421802 Score: 62
Period size: 11 Copynumber: 12.2 Consensus size: 12
6421648 ATATAGGCGT
6421658 GATATGGTGAT-
1 GATATGGTGATG
*
6421669 GATATAGGCG-T-
1 GATAT-GGTGATG
*
6421680 GATAATGGTGATA
1 GAT-ATGGTGATG
6421693 GACTATGGTGAT-
1 GA-TATGGTGATG
*
6421705 GATATAGG-AAT-
1 GATAT-GGTGATG
6421716 GATAGTGGTGATG
1 GATA-TGGTGATG
6421729 GAATATGGTGAT-
1 G-ATATGGTGATG
*
6421741 GATATAGGCG-T-
1 GATAT-GGTGATG
6421752 GATAATGGTGATG
1 GAT-ATGGTGATG
6421765 GATTATGGTGAT-
1 GA-TATGGTGATG
*
6421777 GATATAGGCG-T-
1 GATAT-GGTGATG
6421788 GATAATGGTGATG
1 GAT-ATGGTGATG
6421801 GA
1 GA
6421803 CAGATTGTAT
Statistics
Matches: 107, Mismatches: 8, Indels: 36
0.71 0.05 0.24
Matches are distributed among these distances:
11 44 0.41
12 28 0.26
13 30 0.28
14 5 0.05
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:6426961 original size:11 final size:12
Alignment explanation
Indices: 6426931--6426976 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
6426921 TTGGTGCTGG
6426931 AAACAAGATAAA
1 AAACAAGATAAA
* *
6426943 AAATAAGAT-TA
1 AAACAAGATAAA
6426954 AAACAAGATAAA
1 AAACAAGATAAA
*
6426966 GAA-AAGATAAA
1 AAACAAGATAAA
6426977 GGAATTACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:6426961 original size:23 final size:22
Alignment explanation
Indices: 6426931--6426973 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
6426921 TTGGTGCTGG
6426931 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
6426954 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
6426974 AAAGGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:6431153 original size:12 final size:12
Alignment explanation
Indices: 6431136--6431181 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
6431126 TTGGTGCTGG
6431136 AAATAAGATAAA
1 AAATAAGATAAA
*
6431148 AAATAAGAT-TA
1 AAATAAGATAAA
*
6431159 AAACAAGATAAA
1 AAATAAGATAAA
*
6431171 GAA-AAGATAAA
1 AAATAAGATAAA
6431182 GGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 17 0.59
12 12 0.41
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (12 bp):
AAATAAGATAAA
Found at i:6434684 original size:30 final size:31
Alignment explanation
Indices: 6434648--6434707 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
6434638 CTTAGCTTTA
**
6434648 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
6434678 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
6434708 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:6435576 original size:19 final size:20
Alignment explanation
Indices: 6435552--6435594 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6435542 AGCATTTATC
*
6435552 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
6435571 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
6435591 TTCA
1 TTCA
6435595 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:6437636 original size:24 final size:24
Alignment explanation
Indices: 6437609--6437683 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
6437599 TCCACAAGAC
* *
6437609 ATGTCCTTTGACGTTCCAACAGTT
1 ATGTCCTTTGAAGTTCCAAAAGTT
* * *
6437633 ATGTCATTTGAAGTTCAAAAAGAT
1 ATGTCCTTTGAAGTTCCAAAAGTT
*
6437657 ATGTCAC-TTGAAGTGCCAAAAGTT
1 ATGTC-CTTTGAAGTTCCAAAAGTT
6437681 ATG
1 ATG
6437684 ATCATTGAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (24 bp):
ATGTCCTTTGAAGTTCCAAAAGTT
Found at i:6437691 original size:24 final size:24
Alignment explanation
Indices: 6437624--6437693 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
6437614 CTTTGACGTT
* * *
6437624 CCAACAGTTATGTCATTTGAAGTT
1 CCAAAAGTTATGTCACTTGAAGTG
* *
6437648 CAAAAAGATATGTCACTTGAAGTG
1 CCAAAAGTTATGTCACTTGAAGTG
6437672 CCAAAAGTTATGATCA-TTGAAG
1 CCAAAAGTTATG-TCACTTGAAG
6437694 CTCCAAGTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 35 0.92
25 3 0.08
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (24 bp):
CCAAAAGTTATGTCACTTGAAGTG
Found at i:6438815 original size:30 final size:31
Alignment explanation
Indices: 6438779--6438838 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
6438769 CTTAGCTTTA
**
6438779 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
6438809 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
6438839 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:6439760 original size:19 final size:20
Alignment explanation
Indices: 6439736--6439778 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6439726 AGCATTTATC
*
6439736 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
6439755 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
6439775 TTCA
1 TTCA
6439779 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:6444799 original size:36 final size:36
Alignment explanation
Indices: 6444752--6444855 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6444742 AGATACATCT
6444752 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6444788 GTCCATCACCATTATCACGCCTATATCA-CACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6444823 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6444856 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
34 14 0.22
35 22 0.34
36 28 0.44
ACGTcount: A:0.31, C:0.38, G:0.05, T:0.27
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6444838 original size:23 final size:22
Alignment explanation
Indices: 6444810--6444855 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
6444800 TATCACGCCT
6444810 ATATCAC-ACCATATTCCATCACC
1 ATATCACGACCATATT--ATCACC
*
6444833 ATATCACGCCCATATTATCACC
1 ATATCACGACCATATTATCACC
6444855 A
1 A
6444856 ACTTATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 7 0.33
24 7 0.33
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (22 bp):
ATATCACGACCATATTATCACC
Found at i:6450739 original size:13 final size:12
Alignment explanation
Indices: 6450720--6450805 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
6450710 ATATGGGCGT
6450720 GATATGGTGATG
1 GATATGGTGATG
6450732 GAATATGGTGAT-
1 G-ATATGGTGATG
*
6450744 GATATAGGCG-T-
1 GATAT-GGTGATG
6450755 GATAATGGTGATG
1 GAT-ATGGTGATG
6450768 GACTATGGTGAT-
1 GA-TATGGTGATG
*
6450780 GATATAGG-CAT-
1 GATAT-GGTGATG
6450791 GATAATGGTGATG
1 GAT-ATGGTGATG
6450804 GA
1 GA
6450806 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:6450775 original size:36 final size:36
Alignment explanation
Indices: 6450702--6450806 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6450692 ATTTATAAGT
* * *
6450702 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
6450737 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
6450773 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
6450807 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:6451187 original size:19 final size:20
Alignment explanation
Indices: 6451149--6451199 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
6451139 GAAACCCCTT
*
6451149 TGAAAATGCATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
6451169 TGAATATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
6451188 TGAAAATACATG
1 TGAAAATACATG
6451200 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:6455532 original size:9 final size:8
Alignment explanation
Indices: 6455492--6455530 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
6455482 TTTTGGCTTT
6455492 TTTTTTTG
1 TTTTTTTG
6455500 TTTTTTTG
1 TTTTTTTG
*
6455508 CCTTTTTTG
1 -TTTTTTTG
6455517 -TTTTTTG
1 TTTTTTTG
6455524 TTTTTTT
1 TTTTTTT
6455531 TGAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (8 bp):
TTTTTTTG
Found at i:6456479 original size:13 final size:11
Alignment explanation
Indices: 6456438--6456522 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
6456428 ACAATCTGTC
6456438 CATCACCATTAT
1 CATCACCA-TAT
*
6456450 CA-CGCCTATAT
1 CATCACC-ATAT
6456461 CATCACCATAGT
1 CATCACCATA-T
6456473 CCATCACCATTAT
1 -CATCACCA-TAT
*
6456486 CA-CGCCTATAT
1 CATCACC-ATAT
6456497 CATCACCATATT
1 CATCACCATA-T
6456509 CCATCACCATAT
1 -CATCACCATAT
6456521 CA
1 CA
6456523 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6456482 original size:36 final size:36
Alignment explanation
Indices: 6456435--6456539 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
6456425 GATACAATCT
6456435 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6456471 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6456507 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6456540 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6457471 original size:19 final size:21
Alignment explanation
Indices: 6457447--6457498 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
6457437 CGGCCAAGAG
*
6457447 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
6457466 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
6457487 CATGTATTTTCA
1 CATGTATTTTCA
6457499 AAGGGGTATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:6457936 original size:19 final size:20
Alignment explanation
Indices: 6457912--6457960 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
6457902 TATCCTTTAT
6457912 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
6457931 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
6457951 -TATTATTATT
1 TTATT-TTATT
6457961 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:6462701 original size:19 final size:21
Alignment explanation
Indices: 6462677--6462728 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
6462667 CGGCCAAGAG
*
6462677 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
6462696 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
6462717 CATGTATTTTCA
1 CATGTATTTTCA
6462729 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:6463166 original size:19 final size:20
Alignment explanation
Indices: 6463142--6463190 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
6463132 TATCCTTTAT
6463142 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
6463161 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
6463181 -TATTATTATT
1 TTATT-TTATT
6463191 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:6484293 original size:15 final size:15
Alignment explanation
Indices: 6484269--6484304 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6484259 TTTGATAACT
*
6484269 ATTCTATCCATTTCA
1 ATTCTTTCCATTTCA
6484284 ATTCTTTCCATTTCA
1 ATTCTTTCCATTTCA
*
6484299 TTTCTT
1 ATTCTT
6484305 AATTATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTCTTTCCATTTCA
Found at i:6495500 original size:11 final size:13
Alignment explanation
Indices: 6495468--6495497 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
6495458 TGGCCAAAGA
6495468 TGAAAAGGTATGT
1 TGAAAAGGTATGT
6495481 TGAAAAGGTATG-
1 TGAAAAGGTATGT
6495493 TGAAA
1 TGAAA
6495498 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:6499988 original size:19 final size:21
Alignment explanation
Indices: 6499964--6500015 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
6499954 CGGCCAAGAA
*
6499964 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
6499983 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
6500004 CATGTATTTTCA
1 CATGTATTTTCA
6500016 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:6500757 original size:25 final size:27
Alignment explanation
Indices: 6500729--6500788 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
6500719 GCAAAAAGAA
6500729 AGAAAAGACA-AAAAGAAAAA-AAA-TC
1 AGAAAAGA-AGAAAAGAAAAAGAAATTC
*
6500754 AGAATAGAAGAAAAGAAAAAGAAATTC
1 AGAAAAGAAGAAAAGAAAAAGAAATTC
6500781 A-AAAAGAA
1 AGAAAAGAA
6500789 AGCAAGCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 1 0.03
25 17 0.57
26 9 0.30
27 3 0.10
ACGTcount: A:0.73, C:0.05, G:0.15, T:0.07
Consensus pattern (27 bp):
AGAAAAGAAGAAAAGAAAAAGAAATTC
Found at i:6503925 original size:19 final size:21
Alignment explanation
Indices: 6503901--6503952 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
6503891 CGGCCAAGAG
*
6503901 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
6503920 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
6503941 CATGTATTTTCA
1 CATGTATTTTCA
6503953 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:6517478 original size:17 final size:17
Alignment explanation
Indices: 6517450--6517500 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
6517440 AATTGGAGTG
6517450 CAAAAAGAAAGAAAAAGAT
1 CAAAAAG-AAGAAAAA-AT
6517469 -AAAAAGAAGAGAAAAAT
1 CAAAAAGAAGA-AAAAAT
6517486 CAGAAAAGAAGAAAA
1 CA-AAAAGAAGAAAA
6517501 GAAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.21
18 14 0.48
19 9 0.31
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAGAAAAAAT
Found at i:6517768 original size:20 final size:20
Alignment explanation
Indices: 6517711--6517757 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
6517701 TATATTTTAA
*
6517711 TACCTTTAAATCCTTTCTTC
1 TACCTTTAAATCTTTTCTTC
6517731 TACCTTTAAATCTTTTCTTC
1 TACCTTTAAATCTTTTCTTC
6517751 TACCTTT
1 TACCTTT
6517758 CCATTTCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (20 bp):
TACCTTTAAATCTTTTCTTC
Found at i:6532485 original size:30 final size:30
Alignment explanation
Indices: 6532449--6532515 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
6532439 AACTAATGTG
6532449 AGATGTGAAATGCATTTTAATGCTAAGTAA
1 AGATGTGAAATGCATTTTAATGCTAAGTAA
6532479 AGATGTGAAATGCATTTTAATGCTAAGTAA
1 AGATGTGAAATGCATTTTAATGCTAAGTAA
6532509 AGTATGT
1 AG-ATGT
6532516 TAGTCTCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (30 bp):
AGATGTGAAATGCATTTTAATGCTAAGTAA
Found at i:6533185 original size:17 final size:17
Alignment explanation
Indices: 6533163--6533218 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
6533153 GATTAAGATG
6533163 AAAATATATAATAAAAT
1 AAAATATATAATAAAAT
* *
6533180 AAAATAAATAATAAAAA
1 AAAATATATAATAAAAT
*
6533197 AGGAAACATAATAATAAAAT
1 A--AAATAT-ATAATAAAAT
6533217 AA
1 AA
6533219 TAAATAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 16 0.52
18 1 0.03
19 4 0.13
20 10 0.32
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (17 bp):
AAAATATATAATAAAAT
Found at i:6535515 original size:5 final size:5
Alignment explanation
Indices: 6535505--6535529 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6535495 AAGCATCTGG
6535505 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
6535530 GGAATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:6539701 original size:21 final size:21
Alignment explanation
Indices: 6539656--6539703 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
6539646 GACTTTGGAA
*
6539656 CTTTTCCTGGGATGCAACTAG
1 CTTTTCCTGGGATGCAACAAG
* *
6539677 CTTTTCCTGGGATGTAACAAT
1 CTTTTCCTGGGATGCAACAAG
6539698 CTTTTC
1 CTTTTC
6539704 TTGTGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
CTTTTCCTGGGATGCAACAAG
Found at i:6540134 original size:20 final size:20
Alignment explanation
Indices: 6540109--6540149 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6540099 AAAACTGTTA
*
6540109 AGAGTTGGCTTCCATGGTTG
1 AGAGTTGGCTGCCATGGTTG
6540129 AGAGTTGGCTGCCATGGTTG
1 AGAGTTGGCTGCCATGGTTG
6540149 A
1 A
6540150 AATCAATTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.15, G:0.37, T:0.32
Consensus pattern (20 bp):
AGAGTTGGCTGCCATGGTTG
Found at i:6541234 original size:19 final size:20
Alignment explanation
Indices: 6541210--6541252 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
6541200 CGGCCAAGAG
6541210 CATGTATCTTCATT-AAAAT
1 CATGTATCTTCATTAAAAAT
*
6541229 CATGTATTTTCATTAAAAAT
1 CATGTATCTTCATTAAAAAT
6541249 CATG
1 CATG
6541253 CATTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (20 bp):
CATGTATCTTCATTAAAAAT
Found at i:6541249 original size:20 final size:19
Alignment explanation
Indices: 6541210--6541260 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
6541200 CGGCCAAGAG
*
6541210 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
6541229 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
*
6541249 CATGCATTTTCA
1 CATGTATTTTCA
6541261 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:6545340 original size:25 final size:25
Alignment explanation
Indices: 6545289--6545340 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
6545279 AATATGAAGA
*
6545289 ATAAATAAACAAACAAAATAATATT
1 ATAAATAAACAAACAAAAGAATATT
* *
6545314 ATAAATAAAATAAAGAAAAGAAT-TT
1 ATAAAT-AAACAAACAAAAGAATATT
6545339 AT
1 AT
6545341 TCTTCGACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (25 bp):
ATAAATAAACAAACAAAAGAATATT
Found at i:6545855 original size:19 final size:19
Alignment explanation
Indices: 6545811--6545855 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
6545801 ATTTATTTTT
*
6545811 AATAATTTTTTATCTACAA
1 AATAAATTTTTATCTACAA
* *
6545830 AATTAAATTTTTATTTTCAA
1 AA-TAAATTTTTATCTACAA
6545850 AATAAA
1 AATAAA
6545856 AATATTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAAATTTTTATCTACAA
Found at i:6549725 original size:20 final size:20
Alignment explanation
Indices: 6549702--6549768 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
6549692 ATATTGACCA
6549702 TTGACCATTGACTGTTGATT
1 TTGACCATTGACTGTTGATT
* *
6549722 TTGACCATTAACCGTTGAATT
1 TTGACCATTGACTGTTG-ATT
* *
6549743 TT-TCCATTGATTGTTGATT
1 TTGACCATTGACTGTTGATT
6549762 TTGACCA
1 TTGACCA
6549769 ACATCGTCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.13
20 28 0.74
21 5 0.13
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (20 bp):
TTGACCATTGACTGTTGATT
Found at i:6550553 original size:58 final size:58
Alignment explanation
Indices: 6550433--6550565 Score: 148
Period size: 58 Copynumber: 2.3 Consensus size: 58
6550423 TATTTAATGC
* *
6550433 TTGGGTTCCTCTTCAGAGGATAACTTCCTCATCATGTTTCCTAATTTTTGTATTCTGT
1 TTGGGTTCCTCTTCAGAGGATAACTTCCCCATCATGTTTCCTAATTTATGTATTCTGT
* * * *
6550491 TTGGGTTCCTCTTCAGAGGATAA-TGTCCCCATCTTGATTT-CTGATTTATG-ATTTTTT
1 TTGGGTTCCTCTTCAGAGGATAACT-TCCCCATCATG-TTTCCTAATTTATGTATTCTGT
6550548 GTTGGGTT-CTCTTACAGA
1 -TTGGGTTCCTCTT-CAGA
6550566 AGGTAACATC
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
57 11 0.17
58 51 0.78
59 3 0.05
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.46
Consensus pattern (58 bp):
TTGGGTTCCTCTTCAGAGGATAACTTCCCCATCATGTTTCCTAATTTATGTATTCTGT
Found at i:6554068 original size:22 final size:23
Alignment explanation
Indices: 6554026--6554068 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6554016 TAAGTGCTGG
*
6554026 AAACAAGGTAAGAAAAAAGATTA
1 AAACAAGATAAGAAAAAAGATTA
*
6554049 AAACAAGATAA-ACAAAAGAT
1 AAACAAGATAAGAAAAAAGAT
6554069 AAAGAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.67, C:0.07, G:0.14, T:0.12
Consensus pattern (23 bp):
AAACAAGATAAGAAAAAAGATTA
Found at i:6559549 original size:17 final size:17
Alignment explanation
Indices: 6559523--6559556 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6559513 ATAACACTCG
6559523 AAAAAAAAAATTAAAAGT
1 AAAAAAAAAA-TAAAAGT
*
6559541 AAAATAAAAATAAAAG
1 AAAAAAAAAATAAAAG
6559557 AAAGAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAAAAAAATAAAAGT
Found at i:6560411 original size:1 final size:1
Alignment explanation
Indices: 6560407--6560463 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
6560397 TTTTGGCTTC
* ** ** * *
6560407 TTTTTGTTTTTTTTTTCCTTTTTTTTTTGCTTTTTTTTTGTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6560464 GAAAAAAATA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:6560420 original size:10 final size:10
Alignment explanation
Indices: 6560407--6560463 Score: 69
Period size: 10 Copynumber: 5.3 Consensus size: 10
6560397 TTTTGGCTTC
6560407 TTTTTGTTTTT
1 TTTTTG-TTTT
*
6560418 TTTTTCCTTTTT
1 TTTTT--GTTTT
6560430 TTTTTGCTTTT
1 TTTTTG-TTTT
6560441 TTTTTGTTTT
1 TTTTTGTTTT
6560451 TTTTTGTTTT
1 TTTTTGTTTT
6560461 TTT
1 TTT
6560464 GAAAAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 17 0.41
11 15 0.37
12 9 0.22
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:6560421 original size:11 final size:11
Alignment explanation
Indices: 6560407--6560463 Score: 80
Period size: 11 Copynumber: 5.2 Consensus size: 11
6560397 TTTTGGCTTC
6560407 TTTTTGTTTTT
1 TTTTTGTTTTT
*
6560418 TTTTTCCTTTTT
1 TTTTT-GTTTTT
*
6560430 TTTTTGCTTTT
1 TTTTTGTTTTT
6560441 TTTTTG-TTTT
1 TTTTTGTTTTT
6560451 TTTTTGTTTTT
1 TTTTTGTTTTT
6560462 TT
1 TT
6560464 GAAAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
10 10 0.24
11 21 0.51
12 10 0.24
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:6560431 original size:13 final size:12
Alignment explanation
Indices: 6560413--6560445 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
6560403 CTTCTTTTTG
6560413 TTTTTTTTTTCC
1 TTTTTTTTTTCC
*
6560425 TTTTTTTTTTGC
1 TTTTTTTTTTCC
6560437 TTTTTTTTT
1 TTTTTTTTT
6560446 GTTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTTCC
Found at i:6562066 original size:16 final size:16
Alignment explanation
Indices: 6562041--6562077 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
6562031 CTCTTTTCTT
*
6562041 CTCACGTTTAGGTTCA
1 CTCACATTTAGGTTCA
6562057 CTCACATTTAGGTTCA
1 CTCACATTTAGGTTCA
6562073 CTCAC
1 CTCAC
6562078 CTCCCATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.35
Consensus pattern (16 bp):
CTCACATTTAGGTTCA
Found at i:6570160 original size:22 final size:23
Alignment explanation
Indices: 6570118--6570160 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6570108 TATGTGCTAG
*
6570118 AAACAAGGTAAGAAAAAAGATTA
1 AAACAAGATAAGAAAAAAGATTA
*
6570141 AAACAAGATAA-ACAAAAGAT
1 AAACAAGATAAGAAAAAAGAT
6570161 AAAGAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.67, C:0.07, G:0.14, T:0.12
Consensus pattern (23 bp):
AAACAAGATAAGAAAAAAGATTA
Found at i:6573580 original size:58 final size:58
Alignment explanation
Indices: 6573504--6573613 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
6573494 GATGGGGACA
*
6573504 TTATCCTTCGAAGAGGAACCCAAACA-GAATACAAAAATTAGGAAACATGATGAGGAAG
1 TTATCCTTCGAAGAGGAACCCAAACATGAA-ACAAAAATCAGGAAACATGATGAGGAAG
* * * *
6573562 TTATCC-TCTGAATAGGAACCCAAACATTAAATAAAAATCAGGGAACATGATG
1 TTATCCTTC-GAAGAGGAACCCAAACATGAAACAAAAATCAGGAAACATGATG
6573614 GGGTTGTACA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
57 2 0.04
58 41 0.91
59 2 0.04
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (58 bp):
TTATCCTTCGAAGAGGAACCCAAACATGAAACAAAAATCAGGAAACATGATGAGGAAG
Found at i:6575403 original size:20 final size:20
Alignment explanation
Indices: 6575358--6575419 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
6575348 TCAAATTCGA
*
6575358 CAAAATCAACAATCAATGG-
1 CAAAGTCAACAATCAATGGT
* *
6575377 AAAAGTCAACGATCAATGGT
1 CAAAGTCAACAATCAATGGT
6575397 CAAAGTCAACAATCAATGGT
1 CAAAGTCAACAATCAATGGT
6575417 CAA
1 CAA
6575420 TGTTAATGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (20 bp):
CAAAGTCAACAATCAATGGT
Found at i:6580321 original size:29 final size:29
Alignment explanation
Indices: 6580279--6580365 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
6580269 GTCCCGGGGG
*
6580279 TAGGTCGCCATGCACGCCCGGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
**
6580308 TAGGTCGCCATGCACGCCCAGCGACCTGG
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
* *
6580337 TAGGTCGCCATGCATGCCCTGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
6580366 CAGCACCTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.17, C:0.39, G:0.28, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCTAC
Found at i:6580381 original size:10 final size:10
Alignment explanation
Indices: 6580374--6580466 Score: 77
Period size: 10 Copynumber: 9.3 Consensus size: 10
6580364 ACCAGCACCT
6580374 CCATGCACGC
1 CCATGCACGC
6580384 CCATGCACGC
1 CCATGCACGC
*
6580394 CCA-ACGAC-C
1 CCATGC-ACGC
6580403 TCCATGCACGC
1 -CCATGCACGC
*
6580414 CCATGTACGC
1 CCATGCACGC
* *
6580424 CCAGGCATGC
1 CCATGCACGC
*
6580434 CCA-ACGAC-C
1 CCATGC-ACGC
6580443 TCCATGCACGC
1 -CCATGCACGC
6580454 CCATGCACGC
1 CCATGCACGC
6580464 CCA
1 CCA
6580467 ACGACCTCCA
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
9 4 0.06
10 58 0.88
11 4 0.06
ACGTcount: A:0.23, C:0.48, G:0.18, T:0.11
Consensus pattern (10 bp):
CCATGCACGC
Found at i:6580388 original size:40 final size:40
Alignment explanation
Indices: 6580344--6580466 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 40
6580334 TGGTAGGTCG
**
6580344 CCATGCATGCCCTGCGACCTACCA-GCAC-CTCCATGCACGC
1 CCATGCATGCCCAACGACCT-CCATGCACGC-CCATGCACGC
* *
6580384 CCATGCACGCCCAACGACCTCCATGCACGCCCATGTACGC
1 CCATGCATGCCCAACGACCTCCATGCACGCCCATGCACGC
*
6580424 CCAGGCATGCCCAACGACCTCCATGCACGCCCATGCACGC
1 CCATGCATGCCCAACGACCTCCATGCACGCCCATGCACGC
6580464 CCA
1 CCA
6580467 ACGACCTCCA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.04
40 70 0.95
41 1 0.01
ACGTcount: A:0.22, C:0.48, G:0.18, T:0.12
Consensus pattern (40 bp):
CCATGCATGCCCAACGACCTCCATGCACGCCCATGCACGC
Found at i:6580404 original size:30 final size:30
Alignment explanation
Indices: 6580370--6580486 Score: 144
Period size: 30 Copynumber: 3.6 Consensus size: 30
6580360 ACCTACCAGC
6580370 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
6580400 ACCTCCATGCACGCCCATGTACGCCCAGGCATGCCCAACG
1 ACCTCCATGCACGCCCA--T--G--CA--C--GCCCAACG
6580440 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
6580470 ACCTCCATGCACGCCCA
1 ACCTCCATGCACGCCCA
6580487 GCTCGCCAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 20
0.79 0.00 0.21
Matches are distributed among these distances:
30 42 0.55
32 2 0.03
34 3 0.04
36 3 0.04
38 2 0.03
40 25 0.32
ACGTcount: A:0.23, C:0.49, G:0.17, T:0.11
Consensus pattern (30 bp):
ACCTCCATGCACGCCCATGCACGCCCAACG
Found at i:6580407 original size:20 final size:20
Alignment explanation
Indices: 6580384--6580456 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
6580374 CCATGCACGC
6580384 CCATGCACGCCCAACGACCT
1 CCATGCACGCCCAACGACCT
*
6580404 CCATGCACGCCC-ATGTACGC-
1 CCATGCACGCCCAACG-AC-CT
* *
6580424 CCAGGCATGCCCAACGACCT
1 CCATGCACGCCCAACGACCT
6580444 CCATGCACGCCCA
1 CCATGCACGCCCA
6580457 TGCACGCCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.23, C:0.48, G:0.18, T:0.11
Consensus pattern (20 bp):
CCATGCACGCCCAACGACCT
Found at i:6581405 original size:100 final size:102
Alignment explanation
Indices: 6581232--6581432 Score: 379
Period size: 100 Copynumber: 2.0 Consensus size: 102
6581222 ATTGTTGTTT
6581232 AAGAAATAATTTTTTTACACGTACAGAGCATTATTCCACAACATTTTTCTACGTACATATTGATT
1 AAGAAATAATTTTTTTACACGTACAGAGCATTATTCCACAACATTTTTCTACGTACATATTGATT
6581297 CGAAGAAAG-AACAATAAGGAAA-AAAGGAAAGGATA
66 CGAAGAAAGAAACAATAAGGAAAGAAAGGAAAGGATA
6581332 AAGAAATAATTTTTTTACACGTACAGAGCATTATTCCACAACATTTTTCTACGTACATATTGATT
1 AAGAAATAATTTTTTTACACGTACAGAGCATTATTCCACAACATTTTTCTACGTACATATTGATT
6581397 CGAAGAAAGAAACAATAAGGAAAGGAAAGGAAAGGA
66 CGAAGAAAGAAACAATAAGGAAA-GAAAGGAAAGGA
6581433 AATGAGCAAC
Statistics
Matches: 98, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
100 74 0.76
101 13 0.13
103 11 0.11
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (102 bp):
AAGAAATAATTTTTTTACACGTACAGAGCATTATTCCACAACATTTTTCTACGTACATATTGATT
CGAAGAAAGAAACAATAAGGAAAGAAAGGAAAGGATA
Found at i:6584128 original size:11 final size:11
Alignment explanation
Indices: 6584093--6584788 Score: 147
Period size: 11 Copynumber: 58.5 Consensus size: 11
6584083 ATTTCTATGT
* *
6584093 ATTTATTAATC
1 ATTTAATAATG
*
6584104 ATTATAAAAATG
1 ATT-TAATAATG
6584116 ATTTAATAATG
1 ATTTAATAATG
*
6584127 ATTTAAATAAATA
1 ATTT-AAT-AATG
*
6584140 ATGATT--TGATG
1 AT--TTAATAATG
*
6584151 ATTTAGTAATG
1 ATTTAATAATG
* *
6584162 ATTTGATAATA
1 ATTTAATAATG
6584173 ATCATTATATAATG
1 AT--TTA-ATAATG
*
6584187 ATTTTATAATAATT
1 A--TT-TAATAATG
* * *
6584201 ATTTAGTTATT
1 ATTTAATAATG
* *
6584212 ATTTAGTAATT
1 ATTTAATAATG
6584223 ATTATAATAATG
1 ATT-TAATAATG
6584235 ATTTAATACTAATG
1 ATTT-A-A-TAATG
6584249 ATTT-AT-A--
1 ATTTAATAATG
*
6584256 A-TTAGTAATG
1 ATTTAATAATG
6584266 ATTTAATACTAATG
1 ATTT-A-A-TAATG
6584280 ATTTAAT-A--
1 ATTTAATAATG
* *
6584288 ATTTAGTGATG
1 ATTTAATAATG
6584299 ATTTAATACTAATG
1 ATTT-A-A-TAATG
6584313 ATTTAATAATG
1 ATTTAATAATG
6584324 ATTTAATACTAATG
1 ATTT-A-A-TAATG
6584338 ATTTAATAATG
1 ATTTAATAATG
6584349 ATTT-A-AAT-
1 ATTTAATAATG
6584357 ATTTAATGATTTGATG
1 ATTTAAT-A----ATG
*
6584373 ATTTAGTAATG
1 ATTTAATAATG
*
6584384 ATTTGATAATAATC
1 A-TT--TAATAATG
*
6584398 ATTATAGTAATG
1 ATT-TAATAATG
*
6584410 ATTTGATAATAATC
1 A-TT--TAATAATG
*
6584424 ATTATAAAAATG
1 ATT-TAATAATG
*
6584436 ATTTAGTAATAATC
1 A-TT--TAATAATG
*
6584450 ATTATAAAAATG
1 ATT-TAATAATG
6584462 ATTTAATAATG
1 ATTTAATAATG
6584473 ATTT-A-AAT-
1 ATTTAATAATG
6584481 ATTTAATGATTTGATG
1 ATTTAAT-A----ATG
*
6584497 ATTTAGTAATG
1 ATTTAATAATG
*
6584508 ATTGATAATAATT
1 ATT--TAATAATG
6584521 ATTATAATAATG
1 ATT-TAATAATG
*
6584533 ATTTTATAATAATT
1 A--TT-TAATAATG
* * *
6584547 ATTTAGTTATT
1 ATTTAATAATG
* *
6584558 ATTTAGTAATT
1 ATTTAATAATG
6584569 ATTTATAATAATG
1 A-TT-TAATAATG
6584582 ATTTAATACTAATG
1 ATTT-A-A-TAATG
6584596 ATTTAATAATG
1 ATTTAATAATG
* *
6584607 ATTTAATATTT
1 ATTTAATAATG
* * * *
6584618 AATGATTTGATG
1 ATTTA-ATAATG
*
6584630 -TTTAGTAATG
1 ATTTAATAATG
*
6584640 ATTTGATAATAATT
1 A-TT--TAATAATG
6584654 ATTATAATAATG
1 ATT-TAATAATG
*
6584666 ATTTTATAATAATT
1 A--TT-TAATAATG
* * *
6584680 ATTTAGTTATT
1 ATTTAATAATG
* *
6584691 ATTTAGTAATT
1 ATTTAATAATG
6584702 ATTTATAATAATG
1 A-TT-TAATAATG
6584715 ATTTATACTAATG
1 ATTTA-A-TAATG
*
6584728 ATTTCAT-A--
1 ATTTAATAATG
*
6584736 A-TTAGTAATG
1 ATTTAATAATG
6584746 ATTTAATACTAATG
1 ATTT-A-A-TAATG
*
6584760 ATTTAATAATA
1 ATTTAATAATG
6584771 ATGTTAATAATG
1 AT-TTAATAATG
6584783 ATTTAA
1 ATTTAA
6584789 ATATTTAATG
Statistics
Matches: 523, Mismatches: 77, Indels: 170
0.68 0.10 0.22
Matches are distributed among these distances:
6 2 0.00
7 5 0.01
8 17 0.03
9 12 0.02
10 11 0.02
11 170 0.33
12 107 0.20
13 59 0.11
14 117 0.22
15 10 0.02
16 13 0.02
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (11 bp):
ATTTAATAATG
Found at i:6584174 original size:14 final size:13
Alignment explanation
Indices: 6584157--6584791 Score: 205
Period size: 14 Copynumber: 47.2 Consensus size: 13
6584147 GATGATTTAG
6584157 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
6584171 TAATCA-TTAT-A
1 TAATGATTTATAA
6584182 TAATGATTTTATAA
1 TAATGA-TTTATAA
*
6584196 TAATTATTTAGT--
1 TAATGATTTA-TAA
*
6584208 T-ATTATTTAGTAA
1 TAATGATTTA-TAA
6584221 T--T-A-TTATAA
1 TAATGATTTATAA
*
6584230 TAATGATTTAATAC
1 TAATGATTT-ATAA
6584244 TAATGATTTATAATTA
1 TAATGATTTAT-A--A
*
6584260 GTAATGATTTAATAC
1 -TAATGATTT-ATAA
6584275 TAATGATTTAATAA
1 TAATGATTT-ATAA
*
6584289 TTTAGTGATGATTTAATAC
1 --TA---ATGATTT-ATAA
6584308 TAATGA-TT-TAA
1 TAATGATTTATAA
*
6584319 TAATGATTTAATAC
1 TAATGATTT-ATAA
6584333 TAATGA-TT-TAA
1 TAATGATTTATAA
*
6584344 TAATGATTTAAATATT
1 TAATGATTT--ATA-A
6584360 TAATGATTTGATGATTTA
1 TAATGATTT-AT-A---A
6584378 GTAATGATTTGATAA
1 -TAATGATTT-ATAA
* *
6584393 TAATCA-TTATAG
1 TAATGATTTATAA
6584405 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
6584419 TAATCA-TTATAA
1 TAATGATTTATAA
*
6584431 AAATGATTTAGTAA
1 TAATGATTTA-TAA
*
6584445 TAATCA-TTATAA
1 TAATGATTTATAA
*
6584457 AAATGA-TT-TAA
1 TAATGATTTATAA
*
6584468 TAATGATTTAAATATT
1 TAATGATTT--ATA-A
6584484 TAATGATTTGATGATTTA
1 TAATGATTT-AT-A---A
*
6584502 GTAATGATTGATAA
1 -TAATGATTTATAA
*
6584516 TAATTA-TTATAA
1 TAATGATTTATAA
6584528 TAATGATTTTATAA
1 TAATGA-TTTATAA
*
6584542 TAATTATTTAGT--
1 TAATGATTTA-TAA
*
6584554 T-ATTATTTAGTAA
1 TAATGATTTA-TAA
6584567 T--T-ATTTATAA
1 TAATGATTTATAA
*
6584577 TAATGATTTAATAC
1 TAATGATTT-ATAA
6584591 TAATGA-TT-TAA
1 TAATGATTTATAA
*
6584602 TAATGATTTAATATT
1 TAATGATTT-ATA-A
*
6584617 TAATGATTTGATGTTTAG
1 TAATGATTT-A----TAA
6584635 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
6584649 TAATTA-TTATAA
1 TAATGATTTATAA
6584661 TAATGATTTTATAA
1 TAATGA-TTTATAA
*
6584675 TAATTATTTAGT--
1 TAATGATTTA-TAA
*
6584687 T-ATTATTTAGTAA
1 TAATGATTTA-TAA
6584700 T--T-ATTTATAA
1 TAATGATTTATAA
*
6584710 TAATGATTTATAC
1 TAATGATTTATAA
6584723 TAATGATTTCATAATTA
1 TAATGATTT-AT-A--A
*
6584740 GTAATGATTTAATAC
1 -TAATGATTT-ATAA
6584755 TAATGATTTAATAA
1 TAATGATTT-ATAA
6584769 TAATG---T-TAA
1 TAATGATTTATAA
6584778 TAATGATTTA-AA
1 TAATGATTTATAA
6584790 TA
1 TA
6584792 TTTAATGATT
Statistics
Matches: 493, Mismatches: 48, Indels: 162
0.70 0.07 0.23
Matches are distributed among these distances:
9 12 0.02
10 11 0.02
11 81 0.16
12 68 0.14
13 70 0.14
14 133 0.27
15 20 0.04
16 22 0.04
17 14 0.03
18 29 0.06
19 33 0.07
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:6584215 original size:25 final size:25
Alignment explanation
Indices: 6584151--6584207 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
6584141 TGATTTGATG
6584151 ATTTAGTAATGATTTGATAATAATC
1 ATTTAGTAATGATTTGATAATAATC
* *
6584176 ATTATA-TAATGATTTTATAATAATT
1 ATT-TAGTAATGATTTGATAATAATC
6584201 ATTTAGT
1 ATTTAGT
6584208 TATTATTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 2 0.07
25 24 0.86
26 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (25 bp):
ATTTAGTAATGATTTGATAATAATC
Found at i:6584264 original size:17 final size:17
Alignment explanation
Indices: 6584244--6584303 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 17
6584234 GATTTAATAC
6584244 TAATGATTTATAATTAG
1 TAATGATTTATAATTAG
*
6584261 TAATGA-TT-TAA-TAC
1 TAATGATTTATAATTAG
6584275 TAATGATTTAATAATTTAG
1 TAATGATTT-ATAA-TTAG
*
6584294 TGATGATTTA
1 TAATGATTTA
6584304 ATACTAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 8 0.23
15 5 0.14
16 2 0.06
17 9 0.26
18 1 0.03
19 10 0.29
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (17 bp):
TAATGATTTATAATTAG
Found at i:6584300 original size:33 final size:33
Alignment explanation
Indices: 6584230--6584322 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 33
6584220 ATTATTATAA
6584230 TAATGATTTAATACTAATGATTT-ATAA-TTAG
1 TAATGATTTAATACTAATGATTTAATAATTTAG
6584261 TAATGATTTAATACTAATGATTTAATAATTTAG
1 TAATGATTTAATACTAATGATTTAATAATTTAG
*
6584294 TGATGATTTAATACTAATGATTTAATAAT
1 TAATGATTTAATACTAATGATTTAATAAT
6584323 GATTTAATAC
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 23 0.39
32 4 0.07
33 32 0.54
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (33 bp):
TAATGATTTAATACTAATGATTTAATAATTTAG
Found at i:6584325 original size:58 final size:63
Alignment explanation
Indices: 6584232--6584347 Score: 188
Period size: 58 Copynumber: 1.9 Consensus size: 63
6584222 TATTATAATA
6584232 ATGATTTAATACTAATGATTTATAATTAGTAATGATTTAATACTAATGATTTAATAATTTAGTG
1 ATGATTTAATACTAATGATTTATAA-TAGTAATGATTTAATACTAATGATTTAATAATTTAGTG
6584296 ATGATTTAATACTAATGA-TT-T-A-A-TAATGATTTAATACTAATGATTTAATAAT
1 ATGATTTAATACTAATGATTTATAATAGTAATGATTTAATACTAATGATTTAATAAT
6584348 GATTTAAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
58 29 0.56
59 1 0.02
61 1 0.02
62 1 0.02
63 2 0.04
64 18 0.35
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (63 bp):
ATGATTTAATACTAATGATTTATAATAGTAATGATTTAATACTAATGATTTAATAATTTAGTG
Found at i:6584405 original size:26 final size:25
Alignment explanation
Indices: 6584379--6584726 Score: 175
Period size: 26 Copynumber: 13.7 Consensus size: 25
6584369 GATGATTTAG
*
6584379 TAATGATTTGATAATAATCATTATAG
1 TAATGATTT-ATAATAATCATTATAA
6584405 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
*
6584431 AAATGATTTAGTAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
6584457 AAATGA-TT-TAATAATGATT-T-A
1 TAATGATTTATAATAATCATTATAA
* * * *
6584478 -AAT-ATTTAATGATTTGATGATT-TAG
1 TAATGATTT-AT-A-ATAATCATTATAA
* *
6584503 TAATGATTGATAATAATTATTATAA
1 TAATGATTTATAATAATCATTATAA
* *
6584528 TAATGATTTTATAATAATTATT-TAG
1 TAATGA-TTTATAATAATCATTATAA
* * *
6584553 TTATTATTTAGTAATTAT--TTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
6584577 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTT-ATAATAATCATTATAA
* * *
6584602 TAATGATTTAATATTTAATGATTTGATGTTTAG
1 TAATGATTT-ATA-ATAATCA-TT-A----TAA
*
6584635 TAATGATTTGATAATAATTATTATAA
1 TAATGATTT-ATAATAATCATTATAA
* *
6584661 TAATGATTTTATAATAATTATT-TAG
1 TAATGA-TTTATAATAATCATTATAA
* * *
6584686 TTATTATTTAGTAATTAT--TTATAA
1 TAATGATTTA-TAATAATCATTATAA
*
6584710 TAATGATTTATACTAAT
1 TAATGATTTATAATAAT
6584727 GATTTCATAA
Statistics
Matches: 259, Mismatches: 36, Indels: 57
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.00
20 5 0.02
21 1 0.00
22 2 0.01
23 20 0.08
24 46 0.18
25 53 0.20
26 101 0.39
27 8 0.03
30 1 0.00
31 2 0.01
32 5 0.02
33 14 0.05
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (25 bp):
TAATGATTTATAATAATCATTATAA
Found at i:6584626 original size:133 final size:133
Alignment explanation
Indices: 6584436--6584737 Score: 520
Period size: 133 Copynumber: 2.3 Consensus size: 133
6584426 TATAAAAATG
* **
6584436 ATTTAGTAATAATCA-TTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATT
1 ATTTA-TAATAATGATTTATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATG-TT
6584500 TAGTAATGA-TTGATAATAATTATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAG
64 TAGTAATGATTTGATAATAATTATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAG
6584564 TAATT
129 TAATT
6584569 ATTTATAATAATGATTTAATACTAATGATTTAATAATGATTT-AATATTTAATGATTTGATGTTT
1 ATTTATAATAATGATTT-ATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGTTT
6584633 AGTAATGATTTGATAATAATTATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGT
65 AGTAATGATTTGATAATAATTATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGT
6584698 AATT
130 AATT
*
6584702 ATTTATAATAATGATTTATACTAATGATTTCATAAT
1 ATTTATAATAATGATTTATACTAATGATTTAATAAT
6584738 TAGTAATGAT
Statistics
Matches: 162, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
132 37 0.23
133 103 0.64
134 22 0.14
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (133 bp):
ATTTATAATAATGATTTATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGTTTA
GTAATGATTTGATAATAATTATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTA
ATT
Found at i:6584760 original size:32 final size:31
Alignment explanation
Indices: 6584710--6584769 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
6584700 TTATTTATAA
*
6584710 TAATGATTTATACTAATGATTTCATAATTAG
1 TAATGATTTATACTAATGATTTAATAATTAG
6584741 TAATGATTTAATACTAATGATTTAATAAT
1 TAATGATTT-ATACTAATGATTTAATAAT
6584770 AATGTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
TAATGATTTATACTAATGATTTAATAATTAG
Found at i:6584802 original size:133 final size:133
Alignment explanation
Indices: 6584458--6584781 Score: 424
Period size: 133 Copynumber: 2.4 Consensus size: 133
6584448 TCATTATAAA
* * * * * *
6584458 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGA-TTGATAATAATTA
1 AATGATTTAATAATGATGT-AATATTTAATGATCTAATG-TTTAATAATAATTTAATAATAATTA
*
6584522 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
64 ATATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
6584587 ATACT
129 ATACT
* * * * * * *
6584592 AATGATTTAATAATGATTTAATATTTAATGATTTGATGTTTAGTAATGATTTGATAATAATTATT
1 AATGATTTAATAATGATGTAATATTTAATGATCTAATGTTTAATAATAATTTAATAATAATTAAT
6584657 ATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTT-AT
66 ATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTAAT
6584721 ACT
131 ACT
* *
6584724 AATGATTTCATAATTA-GTAATGATTTAAT-A-CTAATGATTTAATAATAATGTTAATAAT
1 AATGATTTAATAATGATGTAAT-ATTTAATGATCTAATG-TTTAATAATAAT-TTAATAAT
6584782 GATTTAAATA
Statistics
Matches: 178, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
130 4 0.02
131 15 0.08
132 44 0.25
133 96 0.54
134 19 0.11
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (133 bp):
AATGATTTAATAATGATGTAATATTTAATGATCTAATGTTTAATAATAATTTAATAATAATTAAT
ATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTAAT
ACT
Found at i:6587093 original size:29 final size:29
Alignment explanation
Indices: 6587039--6587112 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
6587029 AAACCCTTAA
* *
6587039 ACAACTAATAAAATATTTTTTATATAACTA-
1 ACAACTAATAAACT-TTTTTCATATAA-TAT
6587069 A-AACTAATAAACTTTTTTCATTATAATAT
1 ACAACTAATAAACTTTTTTCA-TATAATAT
*
6587098 ACTACTAATAAACTT
1 ACAACTAATAAACTT
6587113 ACTAACTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.21
29 17 0.45
30 13 0.34
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (29 bp):
ACAACTAATAAACTTTTTTCATATAATAT
Found at i:6587250 original size:45 final size:46
Alignment explanation
Indices: 6587150--6587250 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 46
6587140 TCAACAAACA
*
6587150 ATAAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
1 ATAAAC-TAACTATTTAACTAACAAAAACTAATTAAATAATTTTTCT
*
6587197 ATATAACTAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTAACT
1 ATA-AACTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTT--CT
6587243 ATAAACTA
1 ATAAACTA
6587251 TCAAACATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
44 11 0.23
45 16 0.33
46 9 0.19
47 9 0.19
48 3 0.06
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (46 bp):
ATAAACTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTCT
Found at i:6587374 original size:17 final size:18
Alignment explanation
Indices: 6587342--6587381 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
6587332 ACTAATTAAC
* *
6587342 ATTTATAATAATAAACTA
1 ATTTAAAATAATAAACAA
6587360 ATTTAAAAT-ATAAACAA
1 ATTTAAAATAATAAACAA
6587377 ATTTA
1 ATTTA
6587382 CCTTATCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTAAAATAATAAACAA
Found at i:6587746 original size:29 final size:29
Alignment explanation
Indices: 6587701--6587791 Score: 146
Period size: 29 Copynumber: 3.1 Consensus size: 29
6587691 CGCCGGGGCA
6587701 ACCTACAAGGTCGCCGGGACTACATGGCG
1 ACCTACAAGGTCGCCGGGACTACATGGCG
*
6587730 ACCTACAAGGTCACCGGGACTACATGGCG
1 ACCTACAAGGTCGCCGGGACTACATGGCG
** *
6587759 ACCTACAAGGTCGCCCAGACTGCATGGCG
1 ACCTACAAGGTCGCCGGGACTACATGGCG
6587788 ACCT
1 ACCT
6587792 CTCCATTGGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.25, C:0.33, G:0.27, T:0.14
Consensus pattern (29 bp):
ACCTACAAGGTCGCCGGGACTACATGGCG
Found at i:6587824 original size:32 final size:32
Alignment explanation
Indices: 6587778--6587859 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
6587768 GTCGCCCAGA
6587778 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
*
6587810 CTGCATGGCTACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
6587842 CTGCATGGCGACCTCTCC
1 CTGCATGGCGACCTCTCC
6587860 TCGTATAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.10, C:0.37, G:0.26, T:0.28
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:6587988 original size:29 final size:29
Alignment explanation
Indices: 6587946--6588003 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
6587936 ATGGTATGTT
6587946 GCCTGGATTGCATGGCGTCCTACAAGATC
1 GCCTGGATTGCATGGCGTCCTACAAGATC
*
6587975 GCCTGGATTGCATGGCGTCCTACGAGATC
1 GCCTGGATTGCATGGCGTCCTACAAGATC
6588004 ACTGTAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (29 bp):
GCCTGGATTGCATGGCGTCCTACAAGATC
Found at i:6590585 original size:16 final size:17
Alignment explanation
Indices: 6590564--6590598 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6590554 ACCTATAGTT
6590564 CACATC-TTATAATATG
1 CACATCATTATAATATG
*
6590580 CACATCATTATTATATG
1 CACATCATTATAATATG
6590597 CA
1 CA
6590599 TATATGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (17 bp):
CACATCATTATAATATG
Found at i:6591423 original size:19 final size:21
Alignment explanation
Indices: 6591399--6591442 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
6591389 AGAGCATGTA
6591399 TTCA-TTAAAA-TCATGTATT
1 TTCATTTAAAAGTCATGTATT
6591418 TTCATTTAAAAGTCATGTATT
1 TTCATTTAAAAGTCATGTATT
6591439 TTCA
1 TTCA
6591443 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 6 0.26
21 13 0.57
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (21 bp):
TTCATTTAAAAGTCATGTATT
Found at i:6592175 original size:8 final size:8
Alignment explanation
Indices: 6592164--6592199 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
6592154 AAGAAAAATC
6592164 AGAAAAGA
1 AGAAAAGA
6592172 AGAAAAGA
1 AGAAAAGA
6592180 AGAAGAAGA
1 AGAA-AAGA
*
6592189 AGAAAAAA
1 AGAAAAGA
6592197 AGA
1 AGA
6592200 GAAGTTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:6592199 original size:17 final size:17
Alignment explanation
Indices: 6592152--6592203 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
6592142 GTGCAAAAAG
*
6592152 AGAAGAAAAATCAGAA-A
1 AGAAGAAAAA-AAGAAGA
*
6592169 AGAAGAAAAGAAGAAGA
1 AGAAGAAAAAAAGAAGA
6592186 AGAAGAAAAAAAG-AGA
1 AGAAGAAAAAAAGAAGA
6592202 AG
1 AG
6592204 TTCAAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 9 0.29
17 22 0.71
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (17 bp):
AGAAGAAAAAAAGAAGA
Found at i:6592627 original size:32 final size:32
Alignment explanation
Indices: 6592586--6592649 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
6592576 CAAGATATTC
6592586 CCGAGAGTAAACACGAGTGTTGAGTGGAGTGA
1 CCGAGAGTAAACACGAGTGTTGAGTGGAGTGA
6592618 CCGAGAGTAAACACGAGTGTTGAGTGGAGTGA
1 CCGAGAGTAAACACGAGTGTTGAGTGGAGTGA
6592650 TCTTATCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.38, T:0.19
Consensus pattern (32 bp):
CCGAGAGTAAACACGAGTGTTGAGTGGAGTGA
Found at i:6595699 original size:22 final size:22
Alignment explanation
Indices: 6595674--6595715 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
6595664 TTCATTATTC
*
6595674 ATAATGCTACATGTATTTTAAT
1 ATAATACTACATGTATTTTAAT
6595696 ATAATACTACATGTATTTTA
1 ATAATACTACATGTATTTTA
6595716 GCTTTTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (22 bp):
ATAATACTACATGTATTTTAAT
Found at i:6595815 original size:25 final size:25
Alignment explanation
Indices: 6595764--6595815 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
6595754 AGTATGAAGA
*
6595764 ATAAATAAACAAACAAAATAATATT
1 ATAAATAAACAAACAAAAGAATATT
* *
6595789 ATAAATATAATAAAGAAAAGAAT-TT
1 ATAAATA-AACAAACAAAAGAATATT
6595814 AT
1 AT
6595816 TCTTGGACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (25 bp):
ATAAATAAACAAACAAAAGAATATT
Found at i:6598087 original size:20 final size:20
Alignment explanation
Indices: 6598051--6598088 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6598041 ATCCTATTCC
**
6598051 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
6598071 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
6598089 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:6612926 original size:26 final size:26
Alignment explanation
Indices: 6612855--6612928 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
6612845 TTATGACTAG
* *
6612855 TGAACAGTAACGGTGTACAATGTCCT
1 TGAACAGTAACAGTGTACAGTGTCCT
6612881 TGAACAGTAACAGTGTACAGTG-CCT
1 TGAACAGTAACAGTGTACAGTGTCCT
*
6612906 GTTAACAGTAACAGTGTACAGTG
1 -TGAACAGTAACAGTGTACAGTG
6612929 GGGGAATCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 3 0.07
26 41 0.93
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (26 bp):
TGAACAGTAACAGTGTACAGTGTCCT
Found at i:6612953 original size:21 final size:22
Alignment explanation
Indices: 6612929--6612979 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
6612919 GTGTACAGTG
*
6612929 GGGGAATCAATTTC-TGTAGCA
1 GGGGAATCAAGTTCATGTAGCA
6612950 GGGGAATC-AGTTCATGTAGCA
1 GGGGAATCAAGTTCATGTAGCA
6612971 GGGGAATCA
1 GGGGAATCA
6612980 TACCCCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (22 bp):
GGGGAATCAAGTTCATGTAGCA
Found at i:6613717 original size:40 final size:40
Alignment explanation
Indices: 6613659--6613817 Score: 264
Period size: 40 Copynumber: 4.0 Consensus size: 40
6613649 ACCGTAGTGC
* *
6613659 TACATATAAGGTCATGCCCACCATATACACCAAAGTATAT
1 TACACATAAGGTCATGCCCACCATATACACCAAAGTGTAT
*
6613699 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCAAAGTGTAT
*
6613739 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCAAAGTGTAT
* *
6613779 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
1 TACACATAAGGTCATGCCCACCATATACACCAAAGTGTA
6613818 CTATAAACCT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCATGCCCACCATATACACCAAAGTGTAT
Found at i:6618503 original size:17 final size:16
Alignment explanation
Indices: 6618469--6618513 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
6618459 CCATTCCCTT
6618469 TCTTT-GAGAGAAATTC
1 TCTTTCGAGA-AAATTC
6618485 TCTTTCGAGAAAATCTC
1 TCTTTCGAGAAAAT-TC
*
6618502 TCGTTCGAGAAA
1 TCTTTCGAGAAA
6618514 CAAACACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (16 bp):
TCTTTCGAGAAAATTC
Found at i:6628008 original size:33 final size:33
Alignment explanation
Indices: 6627961--6628050 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
6627951 CAAGAACGAT
*
6627961 GTGTAAGCCTTCCCTCTATAAATCTGGGACCAC
1 GTGTAAACCTTCCCTCTATAAATCTGGGACCAC
* * *
6627994 GTGTAAACCATCCCTGTATAAATCTTGGACCAC
1 GTGTAAACCTTCCCTCTATAAATCTGGGACCAC
*
6628027 GTG-AATACCTTACCTCTATAAATC
1 GTGTAA-ACCTTCCCTCTATAAATC
6628051 GTTGACCTAG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 2 0.04
33 47 0.96
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (33 bp):
GTGTAAACCTTCCCTCTATAAATCTGGGACCAC
Found at i:6634784 original size:21 final size:21
Alignment explanation
Indices: 6634752--6634839 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
6634742 TTTTAGAGAC
*
6634752 ACTTAGCAAGGTACTTCACCT
1 ACTTACCAAGGTACTTCACCT
*
6634773 A-TTGACCAAGGTACTTCATCT
1 ACTT-ACCAAGGTACTTCACCT
* * **
6634794 ACTTACCAAGATATTTCTTCT
1 ACTTACCAAGGTACTTCACCT
* * *
6634815 ACTTACCAAGTTAATTCATCT
1 ACTTACCAAGGTACTTCACCT
6634836 ACTT
1 ACTT
6634840 CCACTTCTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (21 bp):
ACTTACCAAGGTACTTCACCT
Found at i:6636516 original size:59 final size:59
Alignment explanation
Indices: 6636424--6636538 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 59
6636414 AATAGATGGA
* *
6636424 TAAGTGTCCTATGTAACCCTCATAGTTGAAATGAAAAGAAAAACTCAATAATATGGTTG
1 TAAGTATCCTATGTAACCCTCATAGTCGAAATGAAAAGAAAAACTCAATAATATGGTTG
* * * *
6636483 TAAGTATCCTATCG-AACCCTCCTAGTCGTAATGAAATGGAAAACTCAATAATATGG
1 TAAGTATCCTAT-GTAACCCTCATAGTCGAAATGAAAAGAAAAACTCAATAATATGG
6636539 CTCTAACCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 48 0.98
60 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (59 bp):
TAAGTATCCTATGTAACCCTCATAGTCGAAATGAAAAGAAAAACTCAATAATATGGTTG
Found at i:6638673 original size:9 final size:9
Alignment explanation
Indices: 6638661--6638690 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
6638651 TCTTTCTCAG
6638661 TTTTTTTCTT
1 TTTTTTTC-T
6638671 TTTTTTTCT
1 TTTTTTTCT
6638680 TTTTTTTCT
1 TTTTTTTCT
6638689 TT
1 TT
6638691 CCTTTCCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:6638676 original size:10 final size:10
Alignment explanation
Indices: 6638661--6638690 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6638651 TCTTTCTCAG
6638661 TTTTTTTCTT
1 TTTTTTTCTT
6638671 TTTTTTTC-T
1 TTTTTTTCTT
6638680 TTTTTTTCTT
1 TTTTTTTCTT
6638690 T
1 T
6638691 CCTTTCCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:6640664 original size:60 final size:60
Alignment explanation
Indices: 6640571--6640802 Score: 365
Period size: 60 Copynumber: 3.9 Consensus size: 60
6640561 TTCATCTGAA
* * *
6640571 TTGCATTAGTGGCACCTTTCAGCAAAAATGCACAGTTAGACATTTAACTTATCATATAAC
1 TTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTATCATATAAC
* * *
6640631 TTGCATTAGTGGCGCCTTTCTGCCAAAATGCACAATTAGGCATTTAACTTATCATCTAAC
1 TTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTATCATATAAC
*
6640691 TTGCATTAGTGGCACCTTTCTGCCAAAATGCAGAGTTAGGCATTTAACTTATCATATAAC
1 TTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTATCATATAAC
** **
6640751 TTTTATTAGTGGCACCTTTCTGCCAAAACACACAGTTAGGCATTTAACTTAT
1 TTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTAT
6640803 ATGCACAGTT
Statistics
Matches: 157, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 157 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (60 bp):
TTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTATCATATAAC
Found at i:6640775 original size:120 final size:120
Alignment explanation
Indices: 6640562--6641305 Score: 508
Period size: 120 Copynumber: 6.0 Consensus size: 120
6640552 ACACTATTTT
* * * *
6640562 TCATCTGAA-TTGCATTAGTGGCACCTTTCAGCAAAAATGCACAGTTAGACATTTAACTTATCAT
1 TCATCT-AACTTGCATTAGTGGCACCTTTCTGCCAAAATGCATAGTTAGGCATTTAACTTATCAT
* *
6640626 ATAACTTGCATTAGTGGCGCCTTTCTGCCAAAATGCACAATTAGGCATTTAACTTA
65 ATAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTA
*
6640682 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCAGAGTTAGGCATTTAACTTATCATA
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCATAGTTAGGCATTTAACTTATCATA
** **
6640747 TAACTTTTATTAGTGGCACCTTTCTGCCAAAACACACAGTTAGGCATTTAACTTA
66 TAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTA
* * * ** ** **
6640802 T-ATGC-ACAGTTAGGCATT--T---AACTTATCAT-CTAACTTGCATTAG-T-GGCACCTGTC-
1 TCAT-CTA-ACTT--GCATTAGTGGCACCTT-TC-TGCCAAAATGCA-TAGTTAGGCATTTAACT
* * * * ** * ** * * *
6640856 TACCAAAATACACAGTTAGGAATTTAACTTATCATCTAACTTG-CATTAATGACACATTTCTA-C
59 TATC-ATATA-AC--TT--GCA-TT-A-GTGGCACCTTTC-TGCCA-AAATG-CACA-GT-TAGG
** *
6640919 CAAAATGCACAGTTA
110 C---ATTTA-ACTTA
* * * *
6640934 TGCATTTAACTTATCATTTAACTTGCATTAGTGGCACGTTTCTACCAAAATGCACAGCTAGGCAT
1 ------T--C--ATC---TAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCATAGTTAGGCAT
* * * *
6640999 TTAACTTATCATCTAGCTTGCATTAGTGGAACCTTTCTGCCAAAATGCATAGTTAGGCATTTAAC
53 TTAACTTATCATATAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAAC
*
6641064 TTT
118 TTA
* * * ** *
6641067 TCATCTAACTTGCATTAGTGGTACATTTCTTCCAAAATAAATAGTTAGGCATTTAACTTATCATC
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCATAGTTAGGCATTTAACTTATCATA
6641132 TAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTA
66 TAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTA
* * * *
6641187 TCATCTAACTTGCATTAGTGGCTCATTTCTGCCAAAATGCATAGTTAGGAATTTAACTTATCATC
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCATAGTTAGGCATTTAACTTATCATA
* * * * *
6641252 TAACTTGTATTAGCGACACTTTTCTTCCAAAATGCACAGTTAGGCATTTAACTT
66 TAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTT
6641306 TTCTTCATTC
Statistics
Matches: 481, Mismatches: 91, Indels: 104
0.71 0.13 0.15
Matches are distributed among these distances:
116 3 0.01
117 14 0.03
118 12 0.02
119 8 0.02
120 327 0.68
122 6 0.01
123 5 0.01
124 1 0.00
125 9 0.02
126 4 0.01
127 5 0.01
128 2 0.00
129 2 0.00
131 3 0.01
132 4 0.01
133 3 0.01
134 3 0.01
136 2 0.00
137 2 0.00
138 4 0.01
139 6 0.01
140 7 0.01
141 1 0.00
142 3 0.01
143 9 0.02
145 6 0.01
146 4 0.01
147 11 0.02
148 12 0.02
149 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (120 bp):
TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCATAGTTAGGCATTTAACTTATCATA
TAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATTTAACTTA
Found at i:6640862 original size:85 final size:85
Alignment explanation
Indices: 6640718--6640887 Score: 268
Period size: 85 Copynumber: 2.0 Consensus size: 85
6640708 TTCTGCCAAA
* ** * *
6640718 ATGCAGAGTTAGGCATTTAACTTATCATATAACTTTTATTAGTGGCACCTTTCTGCCAAAACACA
1 ATGCACAGTTAGGCATTTAACTTATCATATAACTTGCATTAGTGGCACCTGTCTACCAAAACACA
*
6640783 CAGTTAGGCATTTAACTTAT
66 CAGTTAGGAATTTAACTTAT
* *
6640803 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTGTCTACCAAAATACA
1 ATGCACAGTTAGGCATTTAACTTATCATATAACTTGCATTAGTGGCACCTGTCTACCAAAACACA
6640868 CAGTTAGGAATTTAACTTAT
66 CAGTTAGGAATTTAACTTAT
6640888 CATCTAACTT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 77 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (85 bp):
ATGCACAGTTAGGCATTTAACTTATCATATAACTTGCATTAGTGGCACCTGTCTACCAAAACACA
CAGTTAGGAATTTAACTTAT
Found at i:6640899 original size:60 final size:60
Alignment explanation
Indices: 6640803--6641305 Score: 718
Period size: 60 Copynumber: 8.4 Consensus size: 60
6640793 TTTAACTTAT
* *
6640803 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTGTCTACCAAA
1 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACATTTCTACCAAA
* * * *
6640863 ATACACAGTTAGGAATTTAACTTATCATCTAACTTGCATTAATGACACATTTCTACCAAA
1 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACATTTCTACCAAA
* * *
6640923 ATGCACAGTTATGCATTTAACTTATCATTTAACTTGCATTAGTGGCACGTTTCTACCAAA
1 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACATTTCTACCAAA
* * * * *
6640983 ATGCACAGCTAGGCATTTAACTTATCATCTAGCTTGCATTAGTGGAACCTTTCTGCCAAA
1 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACATTTCTACCAAA
* * * *
6641043 ATGCATAGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGTACATTTCTTCCAAA
1 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACATTTCTACCAAA
** * * *
6641103 ATAAATAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAA
1 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACATTTCTACCAAA
* *
6641163 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCTCATTTCTGCCAAA
1 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACATTTCTACCAAA
* * * * * * *
6641223 ATGCATAGTTAGGAATTTAACTTATCATCTAACTTGTATTAGCGACACTTTTCTTCCAAA
1 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACATTTCTACCAAA
6641283 ATGCACAGTTAGGCATTTAACTT
1 ATGCACAGTTAGGCATTTAACTT
6641306 TTCTTCATTC
Statistics
Matches: 395, Mismatches: 48, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 395 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (60 bp):
ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACATTTCTACCAAA
Found at i:6640922 original size:145 final size:145
Alignment explanation
Indices: 6640658--6640947 Score: 436
Period size: 145 Copynumber: 2.0 Consensus size: 145
6640648 TTCTGCCAAA
* * *
6640658 ATGCACAATTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCA
1 ATGCACAATTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTGTCTACCAAAATACA
* * ** * * * *
6640723 GAGTTAGGCATTTAACTTATCATATAACTTTTATTAGTGGCACCTTTCTGCCAAAACACACAGTT
66 CAGTTAGGAATTTAACTTATCATATAACTTGCATTAATGACACATTTCTACCAAAACACACAGTT
6640788 AGGCATTTAACTTAT
131 AGGCATTTAACTTAT
*
6640803 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTGTCTACCAAAATACA
1 ATGCACAATTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTGTCTACCAAAATACA
* **
6640868 CAGTTAGGAATTTAACTTATCATCTAACTTGCATTAATGACACATTTCTACCAAAATGCACAGTT
66 CAGTTAGGAATTTAACTTATCATATAACTTGCATTAATGACACATTTCTACCAAAACACACAGTT
*
6640933 ATGCATTTAACTTAT
131 AGGCATTTAACTTAT
6640948 CATTTAACTT
Statistics
Matches: 129, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
145 129 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (145 bp):
ATGCACAATTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTGTCTACCAAAATACA
CAGTTAGGAATTTAACTTATCATATAACTTGCATTAATGACACATTTCTACCAAAACACACAGTT
AGGCATTTAACTTAT
Found at i:6640950 original size:205 final size:205
Alignment explanation
Indices: 6640598--6641007 Score: 622
Period size: 205 Copynumber: 2.0 Consensus size: 205
6640588 TTCAGCAAAA
* * * *
6640598 ATGCACAGTTAGACATTTAACTTATCATATAACTTGCATTAGTGGCGCCTTTCTGCCAAAATGCA
1 ATGCACAGTTAGACATTTAACTTATCATATAACTTGCATTAGTGGCACCTGTCTACCAAAATACA
* * * * * *
6640663 CAATTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCAGAGTT
66 CAATTAGGAATTTAACTTATCATCTAACTTGCATTAATGACACATTTCTACCAAAATGCACAGTT
** * *
6640728 AGGCATTTAACTTATCATATAACTTTTATTAGTGGCACCTTTCTGCCAAAACACACAGTTAGGCA
131 AGGCATTTAACTTATCATATAACTTGCATTAGTGGCACCTTTCTACCAAAACACACAGCTAGGCA
6640793 TTTAACTTAT
196 TTTAACTTAT
* *
6640803 ATGCACAGTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTGTCTACCAAAATACA
1 ATGCACAGTTAGACATTTAACTTATCATATAACTTGCATTAGTGGCACCTGTCTACCAAAATACA
*
6640868 CAGTTAGGAATTTAACTTATCATCTAACTTGCATTAATGACACATTTCTACCAAAATGCACAGTT
66 CAATTAGGAATTTAACTTATCATCTAACTTGCATTAATGACACATTTCTACCAAAATGCACAGTT
* * * **
6640933 ATGCATTTAACTTATCATTTAACTTGCATTAGTGGCACGTTTCTACCAAAATGCACAGCTAGGCA
131 AGGCATTTAACTTATCATATAACTTGCATTAGTGGCACCTTTCTACCAAAACACACAGCTAGGCA
6640998 TTTAACTTAT
196 TTTAACTTAT
6641008 CATCTAGCTT
Statistics
Matches: 183, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
205 183 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (205 bp):
ATGCACAGTTAGACATTTAACTTATCATATAACTTGCATTAGTGGCACCTGTCTACCAAAATACA
CAATTAGGAATTTAACTTATCATCTAACTTGCATTAATGACACATTTCTACCAAAATGCACAGTT
AGGCATTTAACTTATCATATAACTTGCATTAGTGGCACCTTTCTACCAAAACACACAGCTAGGCA
TTTAACTTAT
Found at i:6647037 original size:14 final size:14
Alignment explanation
Indices: 6647004--6647040 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6646994 AACAACAATC
*
6647004 AAGCAACAAATTAT
1 AAGCCACAAATTAT
6647018 AAGCCACAAATTAT
1 AAGCCACAAATTAT
*
6647032 AGGCCACAA
1 AAGCCACAA
6647041 TAAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.22, G:0.11, T:0.16
Consensus pattern (14 bp):
AAGCCACAAATTAT
Found at i:6651037 original size:173 final size:177
Alignment explanation
Indices: 6650716--6651049 Score: 508
Period size: 173 Copynumber: 1.9 Consensus size: 177
6650706 TCCTATAAAT
*
6650716 AATAATAACTAAAGATAATATTTTAACCCAACCTTAATTCCTAATAAATAATAAATCTAATCCTA
1 AATAATAACTAAAGATAATATTTTAACCAAACCTTAATTCCTAATAAATAATAAATCTAATCCTA
*
6650781 AAAGATATGCATCATCCTATATTAAGTTATATTACAAATAATCAATATAAATTGAAATTCGTAAT
66 AAAGATATGCATCATCCTATATTAAGTGATATTACAAATAATCAATATAAATTGAAATTCGTAAT
6650846 ATTACAAAATAATGTATTAATCCCGTATAGGCTCTACCGTTCAGTAA
131 ATTACAAAATAATGTATTAATCCCGTATAGGCTCTACCGTTCAGTAA
**
6650893 AATAATAACTAAAGATAATATTTTAA-CAAAGGTT-ATTCC-AA-AAATAAT-AATC-AATCCTA
1 AATAATAACTAAAGATAATATTTTAACCAAACCTTAATTCCTAATAAATAATAAATCTAATCCTA
6650952 AAAG-TAATGC-TCATCCT-TATTAAGTGGATATTAC-AATAATCAATATAAATATTGAAAATTC
66 AAAGAT-ATGCATCATCCTATATTAAGT-GATATTACAAATAATCAATAT-AA-ATTG-AAATTC
6651013 GTAATATTTACAAAATAATGTATTAATCCCGTATAGG
126 GTAATA-TTACAAAATAATGTATTAATCCCGTATAGG
6651050 ATTTCCTGCA
Statistics
Matches: 147, Mismatches: 4, Indels: 16
0.88 0.02 0.10
Matches are distributed among these distances:
169 20 0.14
170 17 0.12
171 19 0.13
172 16 0.11
173 37 0.25
174 2 0.01
175 5 0.03
176 5 0.03
177 26 0.18
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (177 bp):
AATAATAACTAAAGATAATATTTTAACCAAACCTTAATTCCTAATAAATAATAAATCTAATCCTA
AAAGATATGCATCATCCTATATTAAGTGATATTACAAATAATCAATATAAATTGAAATTCGTAAT
ATTACAAAATAATGTATTAATCCCGTATAGGCTCTACCGTTCAGTAA
Found at i:6654601 original size:15 final size:14
Alignment explanation
Indices: 6654580--6654613 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
6654570 CTTTTTTTGG
6654580 TTTTTTTTGCCTTT
1 TTTTTTTTGCCTTT
*
6654594 TCTTTTTTGCCTTT
1 TTTTTTTTGCCTTT
6654608 TTTTTT
1 TTTTTT
6654614 GTTTTTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTTTTTGCCTTT
Found at i:6661469 original size:21 final size:19
Alignment explanation
Indices: 6661441--6661486 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
6661431 TCATCGAATC
6661441 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
6661461 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
6661480 ACTTAGT
1 A-TTAGT
6661487 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:6663798 original size:60 final size:60
Alignment explanation
Indices: 6663730--6664382 Score: 825
Period size: 60 Copynumber: 10.9 Consensus size: 60
6663720 TGTTTTCACA
* * * * *
6663730 TAACTTGCATTAGTGGCACCTTTATGCCACAATGCACAATTTGACATTTAACGTT-TCATC
1 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGACATTTAAC-TTATCATC
* * * **
6663790 TAACTTGCACTAGCGGCATCTTTCTACCAAAATGCACAGTTATG-CATAAAACTTATCATC
1 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTA-GACATTTAACTTATCATC
* * *
6663850 TAACTTGCATTAGTGACACCTTTCTACCAAAATTCACAGTTACACATTTAACTTATCATC
1 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGACATTTAACTTATCATC
* * * *
6663910 TAACTTGCATTAGTGGCACATTTCTACCAAAATACACAATCA-AGCATTTAACTTATCATC
1 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGA-CATTTAACTTATCATC
* * * *
6663970 TAACTTGCATTAGTTGTACCTTTCTATCAAAATGCACAGTTAGGCATTTAACTTATCATC
1 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGACATTTAACTTATCATC
* *
6664030 TAACTTGCATTAGTGGCACCTTTCTGCTAAAATGCACAGTTAGACATTTAACTTATCATC
1 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGACATTTAACTTATCATC
* *
6664090 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGGCATTTAACTTATCATT
1 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGACATTTAACTTATCATC
* * ** * * *
6664150 TAACATT-CATTAGTGGTACCTTTCTTCCAAAATAAATAGTTAGGCATTTAACTTATAATC
1 TAAC-TTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGACATTTAACTTATCATC
*
6664210 TAACTTGCATTAGTGGCACCTTTCT-CCAAAATGCACAGTTAGGCATTTAACTTATCATC
1 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGACATTTAACTTATCATC
* *
6664269 TAACTTGCATTAGTGGCACATTTC-AGCCAAAATGCACAGTTAGGA-ATTTAACTTGTCATC
1 TAACTTGCATTAGTGGCACCTTTCTA-CCAAAATGCACAGTTA-GACATTTAACTTATCATC
* * * * * * *
6664329 TAACTTGTATTAGCGACACCTTTATGCCAAAATGCATAGTTAGGCATTTAACTT
1 TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGACATTTAACTT
6664383 TTCTTCATTC
Statistics
Matches: 517, Mismatches: 64, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
59 59 0.11
60 454 0.88
61 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (60 bp):
TAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGACATTTAACTTATCATC
Found at i:6673787 original size:57 final size:57
Alignment explanation
Indices: 6673704--6673812 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
6673694 ATACGAGATA
** * *
6673704 TACTAAAGGATACCTAGTGTATATGGTGG-CTACGACCTTATGTGCCATACGGGACTG
1 TACTAAAGGATACCTAGTACAGATGGTGGAC-ACGACCTTAAGTGCCATACGGGACTG
* *
6673761 TACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTAAGTGTCATACGG
1 TACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTAAGTGCCATACGG
6673813 ATTATGGTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 44 0.98
58 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (57 bp):
TACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTAAGTGCCATACGGGACTG
Found at i:6673821 original size:33 final size:33
Alignment explanation
Indices: 6673783--6673849 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
6673773 CCTAGTACAG
6673783 ATGGTGGACACGACCTTAAGTGTCATACGGATT
1 ATGGTGGACACGACCTTAAGTGTCATACGGATT
*
6673816 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTAAGTGTCATACGGATT
6673849 A
1 A
6673850 GCACTACGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (33 bp):
ATGGTGGACACGACCTTAAGTGTCATACGGATT
Found at i:6674998 original size:59 final size:59
Alignment explanation
Indices: 6674917--6675033 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 59
6674907 TATGGATAAG
* * * * *
6674917 TGTCATATTGAACCCTCTTAGTCGCAATGAAAAGGCAAACTCTATAATATGGATCTAAC
1 TGTCATATTGAACACTCCTAGTCGCAATGAAAAGGAAAACTCGAAAATATGGATCTAAC
* * *
6674976 TGTCATATTGAATACTCCTAGTCGCAATTAAAAGGAAAACTCGAAAATATGGCTCTAA
1 TGTCATATTGAACACTCCTAGTCGCAATGAAAAGGAAAACTCGAAAATATGGATCTAA
6675034 ACAAACCTCC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (59 bp):
TGTCATATTGAACACTCCTAGTCGCAATGAAAAGGAAAACTCGAAAATATGGATCTAAC
Done.