Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008338.1 Hibiscus syriacus cultivar Beakdansim tig00111059_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: 2210178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1405714 original size:20 final size:20
Alignment explanation
Indices: 1405689--1405803 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
1405679 AATTTGGAAA
*
1405689 ATCGCAACGTGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1405709 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1405730 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1405750 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1405770 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1405790 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1405804 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 63 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1405786 original size:40 final size:40
Alignment explanation
Indices: 1405687--1405823 Score: 168
Period size: 41 Copynumber: 3.4 Consensus size: 40
1405677 CGAATTTGGA
* * *
1405687 AAATCGCAACGTGATACTGACTATCGCAATGCGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
1405727 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTTAC
1 -AAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
1405769 -TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
1405808 ATAATCGCAATGCGAT
1 A-AATCGCAACGCGAT
1405824 TTTCAAAGCG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.39
41 44 0.54
42 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (40 bp):
AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1406320 original size:20 final size:20
Alignment explanation
Indices: 1406271--1406329 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1406261 TTTATTCTCT
* **
1406271 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1406291 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
1406311 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
1406330 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1406520 original size:25 final size:24
Alignment explanation
Indices: 1406466--1406520 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1406456 TGTTTATTAT
* *
1406466 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1406490 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1406516 TGTTT
1 TGTTT
1406521 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1407668 original size:18 final size:18
Alignment explanation
Indices: 1407647--1407694 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1407637 TCTACTTCGG
1407647 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1407665 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1407683 GAGCCATCACCT
1 GAGCCATCACCT
1407695 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1408289 original size:19 final size:20
Alignment explanation
Indices: 1408246--1408290 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1408236 CGCAACACGA
1408246 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
* *
1408266 AAATGGCTATCGTAATGC-G
1 AAATGACTATCGCAATGCGG
1408285 AAATGA
1 AAATGA
1408291 AAATCACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:1408328 original size:19 final size:19
Alignment explanation
Indices: 1408254--1408370 Score: 74
Period size: 19 Copynumber: 6.6 Consensus size: 19
1408244 GAAAATGACT
***
1408254 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
*
1408274 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1408293 ATCACAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1408307 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1408326 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
1408340 ATTGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1408359 ATCGCAATGCGA
1 ATCGCAATGCGA
1408371 TTTGTGTTTC
Statistics
Matches: 73, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
14 18 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 34 0.47
20 9 0.12
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1408362 original size:33 final size:33
Alignment explanation
Indices: 1408282--1408365 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
1408272 CTATCGTAAT
* *
1408282 GCGAAATGAAAATCACAACGACAAAATCGCAAT
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
*
1408315 GCGAAATGAAAATCGCAACGACAAAATTGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
1408348 GCGAAATGAAAATCGCAA
1 GCGAAATGAAAATCGCAA
1408366 TGCGATTTGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.12
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGACAAAATCGCAAC
Found at i:1408442 original size:20 final size:20
Alignment explanation
Indices: 1408408--1408482 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
1408398 TTGCGATTTT
*
1408408 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
1408427 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
* *
1408447 CATTTCAGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
*
1408467 CATTTTCGCGTTGCGA
1 CATTTCCGCGTTGCGA
1408483 AAGTAAGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 5 0.10
20 45 0.90
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:1408493 original size:20 final size:20
Alignment explanation
Indices: 1408449--1408508 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
1408439 GCGATAGCCA
* * *
1408449 TTTCAGCGTTGCGATAGTCAT
1 TTTC-GCGTTGCGAAAGTAAG
1408470 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
1408490 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
1408509 ACTATTCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:1408500 original size:40 final size:40
Alignment explanation
Indices: 1408409--1408502 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
1408399 TGCGATTTTC
* * *
1408409 ATTTC-GCATTGCGATAGCCATTTCCGCGTTGCGATAGCC
1 ATTTCAGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGCA
* * *
1408448 ATTTCAGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCAGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGCA
*
1408488 AGTTTC-GTGTTGCGA
1 A-TTTCAGCGTTGCGA
1408503 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 5 0.11
40 37 0.80
41 4 0.09
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (40 bp):
ATTTCAGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGCA
Found at i:1408700 original size:21 final size:20
Alignment explanation
Indices: 1408674--1408743 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1408664 CTGTCATCCC
1408674 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
1408695 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
1408716 TCAAGAGTCCCCCCCCACCGT
1 TCAAGAGT-CCCCTCCATCGT
1408737 TCAAGAG
1 TCAAGAG
1408744 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:1408776 original size:42 final size:42
Alignment explanation
Indices: 1408667--1408755 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
1408657 GACTCACCTG
* * *
1408667 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* *
1408709 TCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
1408751 TCATC
1 TCATC
1408756 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1410195 original size:14 final size:14
Alignment explanation
Indices: 1410161--1410199 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1410151 TTGATTGTTT
1410161 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1410175 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1410189 TGTTGATTTGT
1 AATTGATTTGT
1410200 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1410363 original size:19 final size:19
Alignment explanation
Indices: 1410339--1410391 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
1410329 TCAACGAGAG
*
1410339 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
*
1410358 AATCGCAATGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
1410377 AATCGCAACGAGAAA
1 AATCGCAACGCGAAA
1410392 ATCGCAATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.51, C:0.19, G:0.19, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:1410469 original size:21 final size:20
Alignment explanation
Indices: 1410422--1410498 Score: 118
Period size: 20 Copynumber: 3.8 Consensus size: 20
1410412 TTGCATTGCG
*
1410422 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1410442 ATTTTCGCTTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1410462 ATTTTTCGCGTTGCGATAGTC
1 A-TTTTCGCGTTGCGATAGCC
1410483 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
1410499 TTCCCCGTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 34 0.65
21 18 0.35
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1410757 original size:127 final size:127
Alignment explanation
Indices: 1410555--1410809 Score: 510
Period size: 127 Copynumber: 2.0 Consensus size: 127
1410545 TGAACATATC
1410555 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTGCACACATA
1 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTGCACACATA
1410620 AAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGA
66 AAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGA
1410682 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTGCACACATA
1 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTGCACACATA
1410747 AAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGA
66 AAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGA
1410809 A
1 A
1410810 GCCGGTTGTG
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 128 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (127 bp):
ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTGCACACATA
AAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAACAGTCCCAAAAGGTGA
Found at i:1410864 original size:20 final size:20
Alignment explanation
Indices: 1410848--1410924 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
1410838 ATTGCGATTT
*
1410848 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCACGTTGCGAAAG
1410868 TCAGAATCACGTTGCGAAAG
1 TCAGAATCACGTTGCGAAAG
* * *
1410888 TCAAAATCGCGTTGTGAAAG
1 TCAGAATCACGTTGCGAAAG
* *
1410908 TCAGTATCGCGTTGCGA
1 TCAGAATCACGTTGCGA
1410925 TTTTGTATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (20 bp):
TCAGAATCACGTTGCGAAAG
Found at i:1410966 original size:20 final size:20
Alignment explanation
Indices: 1410857--1410965 Score: 103
Period size: 20 Copynumber: 5.4 Consensus size: 20
1410847 TTCAGAATCT
* *
1410857 CGTTGCGAAAGTCAGAATCA
1 CGTTGCGAAAGTCAGTATCG
**
1410877 CGTTGCGAAAGTCAAAATCG
1 CGTTGCGAAAGTCAGTATCG
*
1410897 CGTTGTGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
** *
1410917 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--AAGTCAGTATCG
*
1410938 CGTTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
1410958 CATTGCGA
1 CGTTGCGA
1410966 TTTTCCAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.04
20 55 0.74
21 14 0.19
22 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:1410985 original size:41 final size:41
Alignment explanation
Indices: 1410906--1410987 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
1410896 GCGTTGTGAA
* ** *
1410906 AGTCAGTATCGCGTTGCGATTTTGTATTATCGCGTTGCGAT
1 AGTCAGTATCGCATTGCGATTTTAAATTATCGCATTGCGAT
1410947 AGTCAGTATCGCATTGCGATTTTCCAAATT-T-GCATTGCGAT
1 AGTCAGTATCGCATTGCGATTTT--AAATTATCGCATTGCGAT
1410988 TTACTTATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 31 0.89
42 1 0.03
43 3 0.09
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
AGTCAGTATCGCATTGCGATTTTAAATTATCGCATTGCGAT
Found at i:1411003 original size:20 final size:21
Alignment explanation
Indices: 1410955--1411003 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1410945 ATAGTCAGTA
*
1410955 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
1410976 TTGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1410996 TCGCATTG
1 TCGCATTG
1411004 TGAATTGGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.43
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1411048 original size:21 final size:22
Alignment explanation
Indices: 1410996--1411048 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1410986 ATTTACTTAT
*
1410996 TCGCATTGTG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
** *
1411017 TCGCAACGCGAAATT-GTAAAA
1 TCGCATTGCGAAATTGGGAAAA
1411038 TCGCATTGCGA
1 TCGCATTGCGA
1411049 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1417291 original size:31 final size:31
Alignment explanation
Indices: 1417256--1417315 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1417246 TTTCTTGTTG
*
1417256 TTGATTATTAGCTGA-AATTTAAGGATAAGTT
1 TTGATTATTAGCTGATAA-TTAAGCATAAGTT
*
1417287 TTGATTATTAGGTGATAATTAAGCATAAG
1 TTGATTATTAGCTGATAATTAAGCATAAG
1417316 AAGAGCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (31 bp):
TTGATTATTAGCTGATAATTAAGCATAAGTT
Found at i:1418990 original size:2 final size:2
Alignment explanation
Indices: 1418983--1419038 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1418973 ACATGATAGG
1418983 AT AT AT AT AT AT AT AT 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
1419025 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1419039 GTTATATTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1421413 original size:31 final size:31
Alignment explanation
Indices: 1421354--1421413 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1421344 TTTCTTGTTG
* *
1421354 TTGATTATTAGCTGAAATTTAAGGATAAGTT
1 TTGATTATTAGCTGAAATTAAAGCATAAGTT
*
1421385 TTGATTATTAGGTGATAA-TAAAGCATAAG
1 TTGATTATTAGCTGA-AATTAAAGCATAAG
1421414 AAGAGCTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.38
Consensus pattern (31 bp):
TTGATTATTAGCTGAAATTAAAGCATAAGTT
Found at i:1421894 original size:64 final size:64
Alignment explanation
Indices: 1421778--1421914 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 64
1421768 GGCAAGGTGT
* *
1421778 ATCGATGCA-CTCTTTAAAGAAGAAACATCGAATGCAAATGGTGCATCAATGCATAAGG-AGTGC
1 ATCGATGCATCCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCAATGCAT-AGGTAGTGC
* * * * * * *
1421841 ATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTAGTGC
1 ATCGATGCATCCCTTTAAAGAAG-AAACATCGAAGGCAAATGGTGCATCAATGCATAGGTAGTGC
1421905 ATCGATGCAT
1 ATCGATGCAT
1421915 TGTAGAATGC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
63 13 0.21
64 49 0.79
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (64 bp):
ATCGATGCATCCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCAATGCATAGGTAGTGC
Found at i:1422561 original size:21 final size:21
Alignment explanation
Indices: 1422536--1422605 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1422526 TGTGAACATG
1422536 TGAATTATATGAAAAGTGATA
1 TGAATTATATGAAAAGTGATA
* * *
1422557 TGAATTACATGAAAAGAAGCTA
1 TGAATTATATGAAAAG-TGATA
* *
1422579 TGAGCTTATATGAACATGTGATA
1 TGA-ATTATATGAA-AAGTGATA
1422602 TGAA
1 TGAA
1422606 AGTGTATACG
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
21 15 0.41
22 6 0.16
23 14 0.38
24 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (21 bp):
TGAATTATATGAAAAGTGATA
Found at i:1423120 original size:2 final size:2
Alignment explanation
Indices: 1423113--1423150 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1423103 ACATGATAGG
1423113 AT AT AT AT AT AT 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
1423151 GTGTATGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1428073 original size:136 final size:137
Alignment explanation
Indices: 1427812--1428194 Score: 475
Period size: 136 Copynumber: 2.8 Consensus size: 137
1427802 ATTTTAGGAA
* * *
1427812 ACATCATCCTTATATAACCAGACATCCTCATCACGAAAGAACCGTGTTATCTCAAATATCTTTAA
1 ACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
* **** * **
1427877 AGATGGCCAGGCATCCTCATCACGAAGGAATAATGTCATCCATTGATCAGAACTCCTCATCACGA
66 AGATGACCAAATGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGA
1427942 AGGAG-C
131 AGGAGTC
** *
1427948 AACATCAT-CTTAGATTGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
1 -ACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
* * *
1428012 AAGATGACCATATGTCCTCATCATGAAGGAACAATGTCATCCACCGATCAGAACTTCTCATCACG
65 AAGATGACCAAATGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACG
1428077 AAGGAGTC
130 AAGGAGTC
* * * * * **
1428085 GCTTCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAACTGTGTTATCACTATTTAT-TTCT
1 ACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTC-AAATATCTT-T
* * *
1428149 AAAAATGACCAAATGTCCTCATCACGAAGGAACAGTGTCATACACC
64 AAAGATGACCAAATGTCCTCATCACGAAGGAACAATGTCATCCACC
1428195 AGTTTGATTT
Statistics
Matches: 211, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
136 116 0.55
137 49 0.23
138 46 0.22
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (137 bp):
ACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
AGATGACCAAATGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGA
AGGAGTC
Found at i:1429841 original size:2 final size:2
Alignment explanation
Indices: 1429834--1429868 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1429824 ACCAATAATT
1429834 TA TA TA TA TA 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 TA TA TA TA TA T
1429869 TTAATCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1429993 original size:11 final size:12
Alignment explanation
Indices: 1429955--1429996 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 12
1429945 ATATTTTAAA
1429955 TTTATTACTTTAAT
1 TTTATT-CTTT-AT
1429969 TATTATTCTTTAT
1 T-TTATTCTTTAT
1429982 TTTATT-TTTAT
1 TTTATTCTTTAT
1429993 TTTA
1 TTTA
1429997 ATTACATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.33
12 5 0.19
13 3 0.11
14 5 0.19
15 5 0.19
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATTCTTTAT
Found at i:1431882 original size:2 final size:2
Alignment explanation
Indices: 1431875--1431925 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1431865 TTAATCTTAG
1431875 AT AT AT AT AT AT AT AT 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
1431917 AT AT AT AT A
1 AT AT AT AT A
1431926 ACCTAGCCAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1438095 original size:19 final size:20
Alignment explanation
Indices: 1438052--1438099 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1438042 TCTAAATCCT
*
1438052 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1438072 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1438091 TTTTCAAAA
1 TTTTCAAAA
1438100 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1439015 original size:34 final size:32
Alignment explanation
Indices: 1438953--1439022 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1438943 CCTTACAAAC
* *
1438953 TCCCTAGTTTTTCCGGGCTAAACTAAAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAAAACCTT
*
1438985 TCCCTAGCTTTTACACGGGATAAGCTAAAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAAAACCTT
1439019 TCCC
1 TCCC
1439023 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAAAACCTT
Found at i:1439477 original size:143 final size:143
Alignment explanation
Indices: 1439219--1439503 Score: 570
Period size: 143 Copynumber: 2.0 Consensus size: 143
1439209 GCTTGGAATG
1439219 TGTTTGAAGTCGTATATAGCTATTGGGGATGTTTTGGAGCCGTTTCAGGATGAGAATCAATTAAT
1 TGTTTGAAGTCGTATATAGCTATTGGGGATGTTTTGGAGCCGTTTCAGGATGAGAATCAATTAAT
1439284 AAAACTTCTTGAAGCATGGGGGGAATCAGTACCCCCTCATAGGGAATCGATTCCCTTAGTGTAAA
66 AAAACTTCTTGAAGCATGGGGGGAATCAGTACCCCCTCATAGGGAATCGATTCCCTTAGTGTAAA
1439349 ATTCAAATATTTA
131 ATTCAAATATTTA
1439362 TGTTTGAAGTCGTATATAGCTATTGGGGATGTTTTGGAGCCGTTTCAGGATGAGAATCAATTAAT
1 TGTTTGAAGTCGTATATAGCTATTGGGGATGTTTTGGAGCCGTTTCAGGATGAGAATCAATTAAT
1439427 AAAACTTCTTGAAGCATGGGGGGAATCAGTACCCCCTCATAGGGAATCGATTCCCTTAGTGTAAA
66 AAAACTTCTTGAAGCATGGGGGGAATCAGTACCCCCTCATAGGGAATCGATTCCCTTAGTGTAAA
1439492 ATTCAAATATTT
131 ATTCAAATATTT
1439504 TGACCGTTGA
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 142 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (143 bp):
TGTTTGAAGTCGTATATAGCTATTGGGGATGTTTTGGAGCCGTTTCAGGATGAGAATCAATTAAT
AAAACTTCTTGAAGCATGGGGGGAATCAGTACCCCCTCATAGGGAATCGATTCCCTTAGTGTAAA
ATTCAAATATTTA
Found at i:1439617 original size:124 final size:124
Alignment explanation
Indices: 1439397--1439645 Score: 498
Period size: 124 Copynumber: 2.0 Consensus size: 124
1439387 GGGATGTTTT
1439397 GGAGCCGTTTCAGGATGAGAATCAATTAATAAAACTTCTTGAAGCATGGGGGGAATCAGTACCCC
1 GGAGCCGTTTCAGGATGAGAATCAATTAATAAAACTTCTTGAAGCATGGGGGGAATCAGTACCCC
1439462 CTCATAGGGAATCGATTCCCTTAGTGTAAAATTCAAATATTTTGACCGTTGAACAGGGG
66 CTCATAGGGAATCGATTCCCTTAGTGTAAAATTCAAATATTTTGACCGTTGAACAGGGG
1439521 GGAGCCGTTTCAGGATGAGAATCAATTAATAAAACTTCTTGAAGCATGGGGGGAATCAGTACCCC
1 GGAGCCGTTTCAGGATGAGAATCAATTAATAAAACTTCTTGAAGCATGGGGGGAATCAGTACCCC
1439586 CTCATAGGGAATCGATTCCCTTAGTGTAAAATTCAAATATTTTGACCGTTGAACAGGGG
66 CTCATAGGGAATCGATTCCCTTAGTGTAAAATTCAAATATTTTGACCGTTGAACAGGGG
1439645 G
1 G
1439646 AATCAGTACC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (124 bp):
GGAGCCGTTTCAGGATGAGAATCAATTAATAAAACTTCTTGAAGCATGGGGGGAATCAGTACCCC
CTCATAGGGAATCGATTCCCTTAGTGTAAAATTCAAATATTTTGACCGTTGAACAGGGG
Found at i:1441004 original size:13 final size:13
Alignment explanation
Indices: 1440986--1441010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1440976 ATCAACATTG
1440986 GTCAACAGTCAAA
1 GTCAACAGTCAAA
1440999 GTCAACAGTCAA
1 GTCAACAGTCAA
1441011 TGGTGACAGT
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:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (13 bp):
GTCAACAGTCAAA
Found at i:1447035 original size:6 final size:6
Alignment explanation
Indices: 1447024--1447077 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
1447014 TTCTTCTTTT
* * *
1447024 CTTTCA CTTTCA CTTTCA CTTTTA CTTTCA CTTTCA TTTTTA CTTTCA
1 CTTTCA CTTTCA CTTTCA CTTTCA CTTTCA CTTTCA CTTTCA CTTTCA
1447072 CTTTCA
1 CTTTCA
1447078 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (6 bp):
CTTTCA
Found at i:1447045 original size:18 final size:18
Alignment explanation
Indices: 1447024--1447083 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
1447014 TTCTTCTTTT
*
1447024 CTTTCACTTTCACTTTCA
1 CTTTTACTTTCACTTTCA
1447042 CTTTTACTTTCACTTTCA
1 CTTTTACTTTCACTTTCA
*
1447060 TTTTTACTTTCACTTTCA
1 CTTTTACTTTCACTTTCA
*
1447078 TTTTTA
1 CTTTTA
1447084 TTTTTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (18 bp):
CTTTTACTTTCACTTTCA
Found at i:1447068 original size:24 final size:24
Alignment explanation
Indices: 1447019--1447094 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
1447009 AAGTTTTCTT
* *
1447019 CTTTT-CTTTCACTTTCACTTTCA
1 CTTTTACTTTCACTTTCATTTTTA
1447042 CTTTTACTTTCACTTTCATTTTTA
1 CTTTTACTTTCACTTTCATTTTTA
* * *
1447066 CTTTCACTTTCATTTTTATTTTTA
1 CTTTTACTTTCACTTTCATTTTTA
*
1447090 ATTTT
1 CTTTT
1447095 TAATTTAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 5 0.11
24 40 0.89
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (24 bp):
CTTTTACTTTCACTTTCATTTTTA
Found at i:1459249 original size:47 final size:47
Alignment explanation
Indices: 1459130--1459254 Score: 144
Period size: 47 Copynumber: 2.7 Consensus size: 47
1459120 AATATTAGTT
* * *
1459130 AACTAGAG-TCAGTTTTGAGCACCTATAGTAATTCTTGAATGTGTAAA
1 AACTAGAGCT-AGTTTTGGGCACCTCTAGTAATTCTTGAATGTATAAA
* ** * * *
1459177 AACTAGAGCTAGTATCAGACTCCTCTAGTAATTCTTGAATGTATAAC
1 AACTAGAGCTAGTTTTGGGCACCTCTAGTAATTCTTGAATGTATAAA
*
1459224 AACTAGAGCTAGTTTTGGGCACCTCTGGTAA
1 AACTAGAGCTAGTTTTGGGCACCTCTAGTAA
1459255 GAAACTCTTC
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
47 61 0.98
48 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (47 bp):
AACTAGAGCTAGTTTTGGGCACCTCTAGTAATTCTTGAATGTATAAA
Found at i:1461301 original size:16 final size:16
Alignment explanation
Indices: 1461280--1461342 Score: 110
Period size: 16 Copynumber: 4.0 Consensus size: 16
1461270 TAGTCTTACC
1461280 CTTCTTTCTTGGCCCT
1 CTTCTTTCTTGGCCCT
1461296 CTTCTTTCTTGGCCCT
1 CTTCTTTCTTGGCCCT
*
1461312 CTTCTTTCTTGCCCCT
1 CTTCTTTCTTGGCCCT
1461328 CTTCTTTCTT-GCCCT
1 CTTCTTTCTTGGCCCT
1461343 TTTTGGATCT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
15 4 0.09
16 41 0.91
ACGTcount: A:0.00, C:0.40, G:0.10, T:0.51
Consensus pattern (16 bp):
CTTCTTTCTTGGCCCT
Found at i:1461688 original size:26 final size:23
Alignment explanation
Indices: 1461640--1461685 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1461630 CACACTTGCC
1461640 ATAATGTCTTCTTCGGCATTGAT
1 ATAATGTCTTCTTCGGCATTGAT
1461663 ATAATGTCTTCTTCGGCATTGAT
1 ATAATGTCTTCTTCGGCATTGAT
1461686 GATCACAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (23 bp):
ATAATGTCTTCTTCGGCATTGAT
Found at i:1462373 original size:22 final size:22
Alignment explanation
Indices: 1462348--1462394 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1462338 CATCGGTTCA
1462348 TCCCCTTTAAAAGGTTCTTTCG
1 TCCCCTTTAAAAGGTTCTTTCG
1462370 TCCCCTTTAAAAGGTTCTTTCG
1 TCCCCTTTAAAAGGTTCTTTCG
1462392 TCC
1 TCC
1462395 TTGGAGGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.40
Consensus pattern (22 bp):
TCCCCTTTAAAAGGTTCTTTCG
Found at i:1467973 original size:20 final size:21
Alignment explanation
Indices: 1467921--1467974 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1467911 CGTTACACCA
1467921 AAGGGATCGATCCTTTTCCTC
1 AAGGGATCGATCCTTTTCCTC
* *
1467942 GA-GGAGTCGATCCTTTT-GTC
1 AAGGGA-TCGATCCTTTTCCTC
1467962 AAGGGATCGATCC
1 AAGGGATCGATCC
1467975 AAAACTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTCCTC
Found at i:1469872 original size:12 final size:12
Alignment explanation
Indices: 1469855--1469887 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1469845 GGCCATTTCT
1469855 TCTTCTTCATCC
1 TCTTCTTCATCC
1469867 TCTTCTTCATCC
1 TCTTCTTCATCC
1469879 TCTTCTTCA
1 TCTTCTTCA
1469888 CTTGAGGTGC
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:0.09, C:0.39, G:0.00, T:0.52
Consensus pattern (12 bp):
TCTTCTTCATCC
Found at i:1472508 original size:2 final size:2
Alignment explanation
Indices: 1472503--1472546 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1472493 TTTCAAAATC
*
1472503 AT AT AT GT AT AT AT AT 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
1472545 AT
1 AT
1472547 TGTATGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1472604 original size:21 final size:21
Alignment explanation
Indices: 1472460--1472604 Score: 88
Period size: 21 Copynumber: 7.0 Consensus size: 21
1472450 TATTATATAT
*
1472460 ATATATATATATTTTCAAAACC
1 ATAT-TATATATTTTCAAAATC
1472482 ATATTATATATTTTCAAAATC
1 ATATTATATATTTTCAAAATC
* * *
1472503 ATA-TATGTA-TAT-ATATAT-
1 ATATTATATATTTTCA-AAATC
* *
1472521 ATATATATATATATAT-ATATAT-
1 ATAT-TATATAT-TTTCA-AAATC
* *
1472543 ATATTGTATGTTTTCAAAA-C
1 ATATTATATATTTTCAAAATC
* *
1472563 TATATTATATGTTTTTAAAATC
1 -ATATTATATATTTTCAAAATC
*
1472585 ATATTATATAATTTCAAAAT
1 ATATTATATATTTTCAAAAT
1472605 AATACATTAT
Statistics
Matches: 100, Mismatches: 14, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
18 4 0.04
19 5 0.05
20 14 0.14
21 59 0.59
22 18 0.18
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (21 bp):
ATATTATATATTTTCAAAATC
Found at i:1473598 original size:17 final size:18
Alignment explanation
Indices: 1473575--1473618 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1473565 GGCTTTTTAA
1473575 AAGTTGCAAC-CCATTTT
1 AAGTTGCAACTCCATTTT
*
1473592 TAGTTGC-ACTCCATTTT
1 AAGTTGCAACTCCATTTT
*
1473609 AAGTCGCAAC
1 AAGTTGCAAC
1473619 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (18 bp):
AAGTTGCAACTCCATTTT
Found at i:1473633 original size:36 final size:36
Alignment explanation
Indices: 1473593--1473669 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
1473583 ACCCATTTTT
* * *
1473593 AGTTGCACTCCATTTTAAGTCGCAACATTTTTTTAA
1 AGTTGCACCCCATATTAAGTCGCAACATATTTTTAA
* *
1473629 AGTTGCGCCCCATATTAAGTCGCAACCTATTTTTAA
1 AGTTGCACCCCATATTAAGTCGCAACATATTTTTAA
1473665 AGTTG
1 AGTTG
1473670 TAACCCATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (36 bp):
AGTTGCACCCCATATTAAGTCGCAACATATTTTTAA
Found at i:1475695 original size:30 final size:31
Alignment explanation
Indices: 1475640--1475717 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 31
1475630 GTTAATAGTC
* * *
1475640 TTAATATATTTAATATGTATATTTAAT-TTTT
1 TTAATA-ATTTAATTTTTATATTTAATAATTT
*
1475671 TTAATAATTTAATTTTTATTTTTAATAATTT
1 TTAATAATTTAATTTTTATATTTAATAATTT
1475702 TT-AT-ATTTAATTTTTA
1 TTAATAATTTAATTTTTA
1475718 AATATTTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 12 0.29
30 19 0.45
31 11 0.26
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (31 bp):
TTAATAATTTAATTTTTATATTTAATAATTT
Found at i:1475699 original size:16 final size:16
Alignment explanation
Indices: 1475680--1475747 Score: 61
Period size: 16 Copynumber: 4.4 Consensus size: 16
1475670 TTTAATAATT
*
1475680 TAATTTTTATTTTTAA
1 TAATTTTTATATTTAA
1475696 TAATTTTTATATTTAA
1 TAATTTTTATATTTAA
* *
1475712 T--TTTTAAATATTTGA
1 TAATTTT-TATATTTAA
* *
1475727 TTACTTTTATATTT-A
1 TAATTTTTATATTTAA
1475742 TAATTT
1 TAATTT
1475748 AAAATAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.10
15 13 0.31
16 22 0.52
17 3 0.07
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (16 bp):
TAATTTTTATATTTAA
Found at i:1475708 original size:18 final size:20
Alignment explanation
Indices: 1475668--1475709 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1475658 ATATTTAATT
*
1475668 TTTTTAATAATTTAATTTTTA
1 TTTTTAATAATTT-ATTTATA
1475689 TTTTTAATAA-TT-TTTATA
1 TTTTTAATAATTTATTTATA
1475707 TTT
1 TTT
1475710 AATTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
20 2 0.10
21 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTAATAATTTATTTATA
Found at i:1475721 original size:24 final size:22
Alignment explanation
Indices: 1475657--1475718 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
1475647 ATTTAATATG
1475657 TATATTTAATTTTTTTAATAATTT
1 TATATTTAA--TTTTTAATAATTT
* *
1475681 AAT-TTTTATTTTTAATAATTTT
1 TATATTTAATTTTTAATAA-TTT
1475703 TATATTTAATTTTTAA
1 TATATTTAATTTTTAA
1475719 ATATTTGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 10 0.31
22 5 0.16
23 15 0.47
24 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATATTTAATTTTTAATAATTT
Found at i:1488833 original size:22 final size:21
Alignment explanation
Indices: 1488794--1488834 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1488784 GTATCATGAG
* *
1488794 TGGGTTTTTTTATTTTAAAGT
1 TGGGTTTTTTAATATTAAAGT
1488815 TGGGTTTTTTAAATATTAAA
1 TGGGTTTTTT-AATATTAAA
1488835 ATATAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (21 bp):
TGGGTTTTTTAATATTAAAGT
Found at i:1496548 original size:30 final size:30
Alignment explanation
Indices: 1496514--1496573 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1496504 TAGATGATCT
1496514 ATCCTGAGCAGCTTCCTCATTCCTCTTCCA
1 ATCCTGAGCAGCTTCCTCATTCCTCTTCCA
1496544 ATCCTGAGCAGCTTCCTCATTCCTCTTCCA
1 ATCCTGAGCAGCTTCCTCATTCCTCTTCCA
1496574 GTCCCCACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.40, G:0.10, T:0.33
Consensus pattern (30 bp):
ATCCTGAGCAGCTTCCTCATTCCTCTTCCA
Found at i:1498720 original size:21 final size:21
Alignment explanation
Indices: 1498669--1498765 Score: 106
Period size: 21 Copynumber: 4.6 Consensus size: 21
1498659 TGACCCCGAT
*
1498669 CATATGGGGATCTCTCCCGAG
1 CATATGGGGATCTCTCACGAG
* ** *
1498690 TATACAGGGATCTATCACGAG
1 CATATGGGGATCTCTCACGAG
*
1498711 CATATGGGGATTTCTCACGAG
1 CATATGGGGATCTCTCACGAG
*
1498732 CATATGGGGATTTCTCAC-AGG
1 CATATGGGGATCTCTCACGA-G
*
1498753 TATATGGGGATCT
1 CATATGGGGATCT
1498766 GTCCCATGGG
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
20 1 0.02
21 62 0.98
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (21 bp):
CATATGGGGATCTCTCACGAG
Found at i:1502154 original size:99 final size:99
Alignment explanation
Indices: 1502018--1502241 Score: 254
Period size: 99 Copynumber: 2.3 Consensus size: 99
1502008 ACCTATTATT
* * * * * *
1502018 TAACCAGTTGACATAACAACAAGGCGCAACCTATAATGTTATCCAAGAAACCATGTTTG-TTTTA
1 TAACCAGTTAAAATAACAACAAGGTGCAAACTATAATGTTATCCAAGAAAACAAGTTTGTTTTTA
* * *
1502082 CTTTTTCATAATAGACA-GAGTTTCAGCCTATAACA
66 -GTTTTCATAATAGACACCA-TTCCAGCCTATAACA
* * * * * *
1502117 TAATCAGTTAATATAACAACAAGGTTCAAACTGTAATGTTATCGAGGAAAACAAGTTTGTTTTTA
1 TAACCAGTTAAAATAACAACAAGGTGCAAACTATAATGTTATCCAAGAAAACAAGTTTGTTTTTA
* *
1502182 GTTTTCATAATATACACCATTCCAGCCTATAACT
66 GTTTTCATAATAGACACCATTCCAGCCTATAACA
*
1502216 TAACCAGTTAAAATAACACCAAGGTG
1 TAACCAGTTAAAATAACAACAAGGTG
1502242 AATGAACTTT
Statistics
Matches: 103, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
99 97 0.94
100 6 0.06
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (99 bp):
TAACCAGTTAAAATAACAACAAGGTGCAAACTATAATGTTATCCAAGAAAACAAGTTTGTTTTTA
GTTTTCATAATAGACACCATTCCAGCCTATAACA
Found at i:1503086 original size:66 final size:63
Alignment explanation
Indices: 1502970--1503129 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 63
1502960 GAATAAATTG
* *
1502970 AACATCGAATGCATTATATGCATC-ATGCACATACCATGCATCGATACACTCAAG-TTTTTATAA
1 AACATCGAATGCATT-TATGCATCGATGCACATAACATGCATCGATACACTCAAGCTATTT-T--
1503033 AA
62 AA
* * *
1503035 AACATCGAATGCATTTGATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTT-ATGCATCGATGCACATA-ACATGCATCGATACACTCAAGCTATTTTAA
* *
1503099 AACATAGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
1503130 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
64 28 0.34
65 25 0.30
66 26 0.31
67 4 0.05
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACATAACATGCATCGATACACTCAAGCTATTTTAA
Found at i:1503129 original size:17 final size:19
Alignment explanation
Indices: 1503107--1503149 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1503097 GAAACATAGA
1503107 ATGCACT-TCA-TGCATCG
1 ATGCACTCTCAGTGCATCG
*
1503124 ATGCACTCTTAGTGCATCG
1 ATGCACTCTCAGTGCATCG
1503143 ATGCACT
1 ATGCACT
1503150 AAGGGTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 2 0.09
19 14 0.61
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (19 bp):
ATGCACTCTCAGTGCATCG
Found at i:1504915 original size:17 final size:17
Alignment explanation
Indices: 1504895--1504928 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1504885 GATCCAAAGC
1504895 AATTTGGATACCAAAAT
1 AATTTGGATACCAAAAT
1504912 AATTTGGATACCAAAAT
1 AATTTGGATACCAAAAT
1504929 CTACTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
AATTTGGATACCAAAAT
Found at i:1508633 original size:23 final size:23
Alignment explanation
Indices: 1508556--1508637 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
1508546 ACACTGAACA
1508556 GTGCATCGATGCA-TCCCTTTGAAT
1 GTGCATCGATGCACT-CC-TTGAAT
* * * *
1508580 GTGCATCAAT--ACACCATGAAG
1 GTGCATCGATGCACTCCTTGAAT
* *
1508601 GTACACCGATGCACTCCTTGAAT
1 GTGCATCGATGCACTCCTTGAAT
1508624 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1508638 AAGGTCATGC
Statistics
Matches: 43, Mismatches: 12, Indels: 7
0.69 0.19 0.11
Matches are distributed among these distances:
21 11 0.26
22 3 0.07
23 20 0.47
24 9 0.21
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACTCCTTGAAT
Found at i:1518759 original size:13 final size:13
Alignment explanation
Indices: 1518741--1518765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1518731 TGATGAAAAC
1518741 CTCTTATTCTATT
1 CTCTTATTCTATT
1518754 CTCTTATTCTAT
1 CTCTTATTCTAT
1518766 CATTTACATT
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:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (13 bp):
CTCTTATTCTATT
Found at i:1520179 original size:21 final size:21
Alignment explanation
Indices: 1520153--1520206 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1520143 CCAAGTCATC
1520153 AGTATCGATACTCCATAAGGA
1 AGTATCGATACTCCATAAGGA
*
1520174 AGTATCGATACTCTATAAGGA
1 AGTATCGATACTCCATAAGGA
1520195 AGTATCGATACT
1 AGTATCGATACT
1520207 ACTCTTCCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (21 bp):
AGTATCGATACTCCATAAGGA
Found at i:1530876 original size:17 final size:18
Alignment explanation
Indices: 1530845--1530879 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1530835 ATGATATTAG
*
1530845 TTAAACAATATTAATATT
1 TTAAACAATAATAATATT
1530863 TTAAA-AATAATAATATT
1 TTAAACAATAATAATATT
1530880 ATGTTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAACAATAATAATATT
Found at i:1530928 original size:30 final size:31
Alignment explanation
Indices: 1530876--1530938 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
1530866 AAAATAATAA
*
1530876 TATTATGTTTTGTTAATAAAT-AATATTATT
1 TATTATGTTTTGATAATAAATAAATATTATT
* *
1530906 TATTATG-TTTGATATTATAATAAATATTTTT
1 TATTATGTTTTGATAATA-AATAAATATTATT
1530937 TA
1 TA
1530939 AAACAATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.29
30 10 0.36
31 10 0.36
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (31 bp):
TATTATGTTTTGATAATAAATAAATATTATT
Found at i:1531515 original size:4 final size:4
Alignment explanation
Indices: 1531506--1531532 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1531496 CAATGCATGT
1531506 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1531533 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1540689 original size:49 final size:49
Alignment explanation
Indices: 1540617--1540720 Score: 208
Period size: 49 Copynumber: 2.1 Consensus size: 49
1540607 AAAAGTAATT
1540617 ATATTACATGGAAGGTAAGCTCTTGTTTTCATTTAGAAACTTGTTAAAA
1 ATATTACATGGAAGGTAAGCTCTTGTTTTCATTTAGAAACTTGTTAAAA
1540666 ATATTACATGGAAGGTAAGCTCTTGTTTTCATTTAGAAACTTGTTAAAA
1 ATATTACATGGAAGGTAAGCTCTTGTTTTCATTTAGAAACTTGTTAAAA
1540715 ATATTA
1 ATATTA
1540721 ATTACACCTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (49 bp):
ATATTACATGGAAGGTAAGCTCTTGTTTTCATTTAGAAACTTGTTAAAA
Found at i:1543999 original size:29 final size:29
Alignment explanation
Indices: 1543946--1544025 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
1543936 TATCTTTTTT
* *
1543946 TTTCTAAAAAATTAAATAAGTCCTCAAAC
1 TTTCTAAAAAATTAATTAAGCCCTCAAAC
* *
1543975 TTTCTAAAAAATTAATTAGGCCCTCGAAC
1 TTTCTAAAAAATTAATTAAGCCCTCAAAC
* *
1544004 TTAGTCAAAAAAATCAATTAAG
1 TT--TCTAAAAAATTAATTAAG
1544026 TTCATCTATC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 27 0.64
31 15 0.36
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.30
Consensus pattern (29 bp):
TTTCTAAAAAATTAATTAAGCCCTCAAAC
Found at i:1545053 original size:53 final size:53
Alignment explanation
Indices: 1544973--1545134 Score: 290
Period size: 53 Copynumber: 3.1 Consensus size: 53
1544963 TTTAAATTTA
1544973 GTACGTAAATAAAATTACTCTTTAAGCCCCTCTGTACATATAACTAGGAAGTG
1 GTACGTAAATAAAATTACTCTTTAAGCCCCTCTGTACATATAACTAGGAAGTG
* *
1545026 GTACGTAAATAAAATTACTATTTAAGCCCCTCTGTACATATAACTAAGAAGTG
1 GTACGTAAATAAAATTACTCTTTAAGCCCCTCTGTACATATAACTAGGAAGTG
1545079 GTACGTAAATAAAATTACTCTTTAAGCCCCTCTGTACATATAACTAAGG-AGTG
1 GTACGTAAATAAAATTACTCTTTAAGCCCCTCTGTACATATAACT-AGGAAGTG
1545132 GTA
1 GTA
1545135 TGTTGGGGTA
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
53 102 0.98
54 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (53 bp):
GTACGTAAATAAAATTACTCTTTAAGCCCCTCTGTACATATAACTAGGAAGTG
Found at i:1545491 original size:14 final size:14
Alignment explanation
Indices: 1545472--1545498 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1545462 GGGCACGAAT
1545472 TTTTTACTTGGCGC
1 TTTTTACTTGGCGC
1545486 TTTTTACTTGGCG
1 TTTTTACTTGGCG
1545499 GGAAAAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.22, T:0.52
Consensus pattern (14 bp):
TTTTTACTTGGCGC
Found at i:1545996 original size:26 final size:28
Alignment explanation
Indices: 1545939--1545996 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 28
1545929 TCTTTGATAT
1545939 TAATAAATATTAACAATATAATAATTTA
1 TAATAAATATTAACAATATAATAATTTA
* **
1545967 -AATAAA-ATTAA-ATTATAATTTTTTA
1 TAATAAATATTAACAATATAATAATTTA
1545992 TAATA
1 TAATA
1545997 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 11 0.42
26 9 0.35
27 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TAATAAATATTAACAATATAATAATTTA
Found at i:1546183 original size:32 final size:32
Alignment explanation
Indices: 1546147--1546219 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 32
1546137 ACTATATAAT
1546147 TATAAAAT-ATAAACAAGTAAAATTAAAAC-ATA
1 TATAAAATAATAAA-AA-TAAAATTAAAACTATA
*
1546179 TATAATCAATAATAAAAATAAAATTAGAACTATA
1 TATAA--AATAATAAAAATAAAATTAAAACTATA
*
1546213 TTTAAAA
1 TATAAAA
1546220 GCAGTAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
32 7 0.20
33 11 0.31
34 12 0.34
35 5 0.14
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (32 bp):
TATAAAATAATAAAAATAAAATTAAAACTATA
Found at i:1547540 original size:3 final size:3
Alignment explanation
Indices: 1547532--1547580 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
1547522 TTATATTTAT
1547532 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
1547576 TAA TA
1 TAA TA
1547581 TTTAAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1548080 original size:112 final size:112
Alignment explanation
Indices: 1547884--1548305 Score: 555
Period size: 112 Copynumber: 3.8 Consensus size: 112
1547874 ATAGAATTAT
** * *
1547884 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTC-TTCTTCTTCGGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
* **
1547945 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTA
66 ATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTA
* *
1547992 GCAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
* *
1548057 ATTATGAACTCAAACTGGTAAAGCTGATCCATCAAGTGATGGATTTA
66 ATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTA
1548104 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGAT---GAGTTCTT
* * * * *** * * *
1548169 CTCATTATGAACTCTACCTGGCAATGTTGAGATATCAAATGATGAATTCAA
63 CTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATT-TA
* * *
1548220 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
*
1548285 ATTATGAACTCGAACTGGAAA
66 ATTATGAACTCTAACTGGAAA
1548306 TGTTAATGAT
Statistics
Matches: 276, Mismatches: 30, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
108 29 0.11
111 4 0.01
112 117 0.42
113 29 0.11
115 45 0.16
116 52 0.19
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTA
Found at i:1548269 original size:228 final size:220
Alignment explanation
Indices: 1547884--1548302 Score: 570
Period size: 228 Copynumber: 1.9 Consensus size: 220
1547874 ATAGAATTAT
* * *
1547884 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCGGATGAGTTCTTCTCATTA
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCGGACGAGTTCTTCTCATTA
* ** * * * *
1547949 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAGCAAAAGGTTGAACAAATTCTT
66 TGAACTTACTCTGGAAAAGCTGAGACATCAAATGATGAATTAAACAAAAGGTTGAACAAATTCTT
* * * *
1548014 CTTATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTATTATGAACTCAAACTGGTAAA
131 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGTAAA
1548079 GCTGATCCATCAAGTGATGGATTTA
196 GCTGATCCATCAAGTGATGGATTTA
*
1548104 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAACTCTTCTCATTATGAA---CTTC-TTCTTCTTC-G--GACGAGTTCTT
* * * *
1548169 CTCATTATGAACTCTAC-CTGGCAATGTTGAGATATCAAATGATGAATTCAAACAAAAGGTTGAA
59 CTCATTATGAACT-TACTCTGGAAAAGCTGAGACATCAAATGATGAATT-AAACAAAAGGTTGAA
*
1548233 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGA
122 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAA
1548298 ACTGG
187 ACTGG
1548303 AAATGTTAAT
Statistics
Matches: 170, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
220 30 0.18
223 4 0.02
224 9 0.05
225 1 0.01
227 46 0.27
228 80 0.47
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (220 bp):
GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCGGACGAGTTCTTCTCATTA
TGAACTTACTCTGGAAAAGCTGAGACATCAAATGATGAATTAAACAAAAGGTTGAACAAATTCTT
CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGTAAA
GCTGATCCATCAAGTGATGGATTTA
Found at i:1549418 original size:115 final size:115
Alignment explanation
Indices: 1549217--1549555 Score: 592
Period size: 115 Copynumber: 3.0 Consensus size: 115
1549207 GATCATGCAG
* * *
1549217 TTCATCTTTC-AATTCTAATGATTGG-TTTTGTGGTTCTTACCAAACCAGATCAGATAACTAAAA
1 TTCATCTTTCAAATTC-AATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
* * *
1549280 GAATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 GAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
*
1549331 TTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACTAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1549396 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
1549446 TTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1549511 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
66 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
1549556 TAACGTGGTA
Statistics
Matches: 215, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
114 19 0.09
115 196 0.91
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (115 bp):
TTCATCTTTCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:1549873 original size:19 final size:17
Alignment explanation
Indices: 1549849--1549897 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
1549839 AAAATAAAAG
1549849 AATAAATTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
1549868 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
1549884 AATAAATTGAATTT
1 AATAAATTGAATTT
1549898 AGAGAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 3 0.11
19 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:1550271 original size:20 final size:20
Alignment explanation
Indices: 1550248--1550338 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
1550238 TGACCCCCTC
1550248 TTTTTTTTTCTTCTTTTCTT
1 TTTTTTTTTCTTCTTTTCTT
1550268 TTTTTTCTTT-TTC-TTTC--
1 TTTTTT-TTTCTTCTTTTCTT
* * *
1550285 TTTTTCTTTCTTTTTTTCTC
1 TTTTTTTTTCTTCTTTTCTT
*
1550305 TTTCTTTTTCTT-TTTTCCTT
1 TTTTTTTTTCTTCTTTT-CTT
*
1550325 TTTTATTTT-TTCTT
1 TTTTTTTTTCTTCTT
1550339 CAAGCATAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
16 3 0.05
17 7 0.12
18 4 0.07
19 10 0.18
20 30 0.53
21 3 0.05
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTCTTCTTTTCTT
Found at i:1550275 original size:14 final size:14
Alignment explanation
Indices: 1550246--1550338 Score: 88
Period size: 14 Copynumber: 6.6 Consensus size: 14
1550236 CTTGACCCCC
*
1550246 TCTTTT-TTTTTCT
1 TCTTTTCTTTTTTT
1550259 TCTTTTCTTTTTTT
1 TCTTTTCTTTTTTT
1550273 TCTTTTTCTTTCTTTT
1 TC-TTTTCTTT-TTTT
1550289 TC-TTTC-TTTTTT
1 TCTTTTCTTTTTTT
1550301 TCTCTTTCTTTTTCTT
1 TCT-TTTCTTTTT-TT
*
1550317 T-TTTCCTTTTTTAT
1 TCTTTTCTTTTTT-T
1550331 T-TTTTCTT
1 TCTTTTCTT
1550339 CAAGCATAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
12 6 0.09
13 9 0.13
14 32 0.46
15 13 0.19
16 9 0.13
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:1550328 original size:10 final size:9
Alignment explanation
Indices: 1550249--1550320 Score: 92
Period size: 10 Copynumber: 7.7 Consensus size: 9
1550239 GACCCCCTCT
1550249 TTTTTTTTC
1 TTTTTTTTC
*
1550258 -TTCTTTTC
1 TTTTTTTTC
1550266 TTTTTTTTC
1 TTTTTTTTC
1550275 TTTTTCTTTC
1 TTTTT-TTTC
1550285 TTTTTCTTTC
1 TTTTT-TTTC
1550295 TTTTTTTCTC
1 TTTTTTT-TC
1550305 TTTCTTTTTC
1 TTT-TTTTTC
1550315 TTTTTT
1 TTTTTT
1550321 CCTTTTTTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
8 7 0.12
9 17 0.30
10 29 0.51
11 4 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1550334 original size:34 final size:32
Alignment explanation
Indices: 1550246--1550337 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 32
1550236 CTTGACCCCC
*
1550246 TCTTT-TTTTTTCTTCTTTTCTTTTTTTTCTTTT
1 TCTTTCTTTTTTCTT-TTTT-TTTTTTCTCTTTT
*
1550279 TCTTTC-TTTTTC-TTTCTTTTTTTCTCTTTCT
1 TCTTTCTTTTTTCTTTTTTTTTTTTCTCTTT-T
1550310 T-TTTCTTTTTTCCTTTTTTATTTTTTCT
1 TCTTTCTTTTTT-CTTTTTT-TTTTTTCT
1550338 TCAAGCATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
30 15 0.30
31 10 0.20
32 2 0.04
33 15 0.30
34 8 0.16
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (32 bp):
TCTTTCTTTTTTCTTTTTTTTTTTTCTCTTTT
Found at i:1563686 original size:23 final size:23
Alignment explanation
Indices: 1563635--1563689 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1563625 TTGATCGACC
**
1563635 TGTTGACTTTGACCGACTTGACT
1 TGTTGACTTTGACCGACTCCACT
*
1563658 TGTTGACTTTGATCGACTCCACT
1 TGTTGACTTTGACCGACTCCACT
1563681 CT-TTGACTT
1 -TGTTGACTT
1563690 GACAACATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (23 bp):
TGTTGACTTTGACCGACTCCACT
Found at i:1565172 original size:29 final size:29
Alignment explanation
Indices: 1565135--1565252 Score: 148
Period size: 29 Copynumber: 4.1 Consensus size: 29
1565125 TAATGCATTC
* *
1565135 CTGACTCTGCATGAGAATAATTCCCTGTT
1 CTGACTCTGCATGAGATTAATTCCCTATT
* *
1565164 CTGATTCTGCATGAGATTAATTCCTTATT
1 CTGACTCTGCATGAGATTAATTCCCTATT
* * *
1565193 CTGATTCTGCATGTGATTAATTCCCCATT
1 CTGACTCTGCATGAGATTAATTCCCTATT
* *
1565222 CTGACTCTGCATGTGATTAATTCTC-ATT
1 CTGACTCTGCATGAGATTAATTCCCTATT
1565250 CTG
1 CTG
1565253 TTTCTGTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 6 0.08
29 74 0.93
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (29 bp):
CTGACTCTGCATGAGATTAATTCCCTATT
Found at i:1565214 original size:58 final size:57
Alignment explanation
Indices: 1565130--1565268 Score: 161
Period size: 58 Copynumber: 2.4 Consensus size: 57
1565120 CACATTAATG
* * ** *
1565130 CATTCCTGACTCTGCATGAGAATAATTCCCTGTTCTGATTCTGCATGAGATTAATTCCT
1 CATT-CTGATTCTGCATGAGATTAATTCCCCATTCTGACTCTGCATGAGATTAATT-CT
* * *
1565189 TATTCTGATTCTGCATGTGATTAATTCCCCATTCTGACTCTGCATGTGATTAATTCT
1 CATTCTGATTCTGCATGAGATTAATTCCCCATTCTGACTCTGCATGAGATTAATTCT
* * *
1565246 CATTCTGTTTCTGTATGCGATTA
1 CATTCTGATTCTGCATGAGATTA
1565269 TATATTTGTT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
57 21 0.31
58 44 0.65
59 3 0.04
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42
Consensus pattern (57 bp):
CATTCTGATTCTGCATGAGATTAATTCCCCATTCTGACTCTGCATGAGATTAATTCT
Found at i:1568745 original size:2 final size:2
Alignment explanation
Indices: 1568738--1568764 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1568728 ACTATGTGAG
1568738 TA 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 TA T
1568765 TACACATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1570911 original size:9 final size:8
Alignment explanation
Indices: 1570897--1571002 Score: 56
Period size: 9 Copynumber: 12.5 Consensus size: 8
1570887 GAAAAAAAAG
1570897 AAAATAAT
1 AAAATAAT
1570905 AATAATAAT
1 AA-AATAAT
1570914 AAAATAAAT
1 AAAAT-AAT
*
1570923 GAAAAAAAT
1 -AAAATAAT
1570932 AAAAT-A-
1 AAAATAAT
1570938 AAAATAAAT
1 AAAAT-AAT
*
1570947 AAAATTGATT
1 AAAA-T-AAT
1570957 AGAAATAAT
1 A-AAATAAT
* *
1570966 ATAATAAA
1 AAAATAAT
*
1570974 AAAACAAT
1 AAAATAAT
*
1570982 GAAATAAAAT
1 -AAA-ATAAT
1570992 AAAA-AAT
1 AAAATAAT
1570999 AAAA
1 AAAA
1571003 AAACAGGGTT
Statistics
Matches: 77, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
6 5 0.06
7 8 0.10
8 21 0.27
9 27 0.35
10 13 0.17
11 3 0.04
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.22
Consensus pattern (8 bp):
AAAATAAT
Found at i:1570912 original size:36 final size:35
Alignment explanation
Indices: 1570872--1570950 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
1570862 GATTATAAAC
*
1570872 AATAAAAAGA-AATATGAAAAAAAAGAAAATAATAAT-
1 AATAAAAA-ATAA-ATG-AAAAAAAGAAAATAAAAATA
*
1570908 AATAATAAAATAAATGAAAAAAATAAAATAAAAATA
1 AATAA-AAAATAAATGAAAAAAAGAAAATAAAAATA
1570944 AATAAAA
1 AATAAAA
1570951 TTGATTAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
35 19 0.50
36 14 0.37
37 5 0.13
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (35 bp):
AATAAAAAATAAATGAAAAAAAGAAAATAAAAATA
Found at i:1570932 original size:24 final size:23
Alignment explanation
Indices: 1570905--1570950 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1570895 AGAAAATAAT
1570905 AATAATAAT-AAAATAAATGAAAAA
1 AATAA-AATAAAAATAAAT-AAAAA
1570929 AATAAAATAAAAATAAATAAAA
1 AATAAAATAAAAATAAATAAAA
1570951 TTGATTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (23 bp):
AATAAAATAAAAATAAATAAAAA
Found at i:1571002 original size:5 final size:5
Alignment explanation
Indices: 1570888--1570995 Score: 57
Period size: 5 Copynumber: 21.8 Consensus size: 5
1570878 AAGAAATATG
* *
1570888 AAAA- AAAAG AAAAT AATAAT AATAAT AAAAT -AAAT GAAA- AAAAT AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT
** * * *
1570937 AAAA- ATAAAT AAAAT TGATT AGAAAT AATAT AATAA- AAAA- ACAAT
1 AAAAT A-AAAT AAAAT AAAAT A-AAAT AAAAT AA-AAT AAAAT AAAAT
*
1570982 GAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
1570996 AATAAAAAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 17
0.72 0.12 0.15
Matches are distributed among these distances:
4 17 0.21
5 48 0.59
6 16 0.20
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1571070 original size:10 final size:9
Alignment explanation
Indices: 1571055--1571088 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1571045 AAATATTAAC
1571055 AAAAAAAAT
1 AAAAAAAAT
1571064 AAAAAAAAT
1 AAAAAAAAT
1571073 -AAAAAAAT
1 AAAAAAAAT
1571081 AAACAAAA
1 AAA-AAAA
1571089 GGATCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 11 0.48
10 4 0.17
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1572409 original size:70 final size:68
Alignment explanation
Indices: 1572331--1572557 Score: 199
Period size: 69 Copynumber: 3.1 Consensus size: 68
1572321 AACTATATAT
* * *
1572331 TATA-TATATGATTTTTAAAAAAGTTTTCAAACTATATATCATATAGTTTTCAAAGTGTTTTAAA
1 TATATTATAT-ATTTTTAAAAATGTTTTAAAACTATATAT-ATATAGTTTTCAAAATGTTTTAAA
*
1572395 AATCA
64 AATTA
* * * * *
1572400 TATATTATATACATTTTCAAAATGTTTTTTTAAACTAT-TATATA-AATTTTCAAAATGATTTAA
1 TATATTATATA-TTTTTAAAAATG--TTTTAAAACTATATATATATAGTTTTCAAAATGTTTTAA
1572463 AAACTATA
63 AAA-T-TA
*
1572471 TATATTATATATGTTTTCAAAATATTTTTTTTAAAAAACTATATATTATATAAGTTTTCAAAATG
1 TATATTATATAT-TTTT-AAAA-A--TGTTTT--AAAACTATATA-TATAT-AGTTTTCAAAATG
1572536 TTTTAAAAATTA
57 TTTTAAAAATTA
1572548 TATATTATAT
1 TATATTATAT
1572558 GTAACCCCCT
Statistics
Matches: 127, Mismatches: 14, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
69 24 0.19
70 18 0.14
71 19 0.15
72 14 0.11
73 5 0.04
75 8 0.06
76 2 0.02
77 16 0.13
78 1 0.01
79 20 0.16
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (68 bp):
TATATTATATATTTTTAAAAATGTTTTAAAACTATATATATATAGTTTTCAAAATGTTTTAAAAA
TTA
Found at i:1572557 original size:41 final size:38
Alignment explanation
Indices: 1572363--1572557 Score: 153
Period size: 36 Copynumber: 5.3 Consensus size: 38
1572353 GTTTTCAAAC
* *
1572363 TATATATCATAT-AGTTTTCAAAGTGTTTT-AAAAAT-
1 TATATATTATATAAGTTTTCAAAATGTTTTAAAAAATA
* *** *
1572398 CATATATTATATACA-TTTTCAAAATGTTTTTTTAAA-C
1 TATATATTATATA-AGTTTTCAAAATGTTTTAAAAAATA
* *
1572435 TAT-TA-TATA-AA-TTTTCAAAATGATTTAAAAACTA
1 TATATATTATATAAGTTTTCAAAATGTTTTAAAAAATA
* * *
1572469 TATATATTATATATGTTTTCAAAATATTTTTTTTAAAAAA-C
1 TATATATTATATAAGTTTTC-AAA-A--TGTTTTAAAAAATA
1572510 TATATATTATATAAGTTTTCAAAATGTTTT-AAAAAT-
1 TATATATTATATAAGTTTTCAAAATGTTTTAAAAAATA
1572546 TATATATTATAT
1 TATATATTATAT
1572558 GTAACCCCCT
Statistics
Matches: 127, Mismatches: 19, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
33 17 0.13
34 4 0.03
35 16 0.13
36 37 0.29
37 12 0.09
38 5 0.04
39 4 0.03
40 4 0.03
41 19 0.15
42 9 0.07
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (38 bp):
TATATATTATATAAGTTTTCAAAATGTTTTAAAAAATA
Found at i:1573353 original size:81 final size:81
Alignment explanation
Indices: 1573190--1573577 Score: 355
Period size: 90 Copynumber: 4.5 Consensus size: 81
1573180 TTTCCCTCAA
* * *
1573190 CACACAACAAAAGGGGAGCCAACCTAAGGATATACCTTGGGCCTATGGCCTACCAAAGATATCCT
1 CACACAACAAAA-GGGAACCAACCTAAGGATATACCTTGGGTCTA----C--CCAAGGATATCCT
1573255 TAGATCCGTAGGGTTACCTTAAG
59 TAGATCCGTAGGGTTACCTTAAG
** *
1573278 CACACAACAAAAGAAAACCAACCTAAGGATATACCTTGGGTCTACCCAAGGACATCCTTAGATCC
1 CACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGTCTACCCAAGGATATCCTTAGATCC
1573343 GTAGGGTTACCTTAAG
66 GTAGGGTTACCTTAAG
* * * *
1573359 CACACAACAAAAGGGAACTAATCTAAGGATATGCCTTGGGGTTTATGGGCCTACCCAAGGGTATC
1 CACACAACAAAAGGGAACCAACCTAAGGATATACCTT-GGG----T----CTACCCAAGGATATC
*
1573424 CTTAGATCCATAGGGTTACCTTAAG
57 CTTAGATCCGTAGGGTTACCTTAAG
* *
1573449 CACACAACAAAAGGGAACCAACCTAAGGATATGCCTTAGGGCTTGTGGGCCTACCCAAGGGTATC
1 CACACAACAAAAGGGAACCAACCTAAGGATATACCTT--GG---GT----CTACCCAAGGATATC
* * * *
1573514 CTTAGATCCATAGAGTTACCCTATG
57 CTTAGATCCGTAGGGTTACCTTAAG
* * * *
1573539 CACA-TAGAAAAGGGAACCAACCTAAGGACATGCCTTGGG
1 CACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGG
1573578 GCTAATATGC
Statistics
Matches: 265, Mismatches: 22, Indels: 30
0.84 0.07 0.09
Matches are distributed among these distances:
81 66 0.25
82 3 0.01
83 1 0.00
84 1 0.00
86 1 0.00
87 30 0.11
88 12 0.05
89 29 0.11
90 118 0.45
91 3 0.01
94 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.21
Consensus pattern (81 bp):
CACACAACAAAAGGGAACCAACCTAAGGATATACCTTGGGTCTACCCAAGGATATCCTTAGATCC
GTAGGGTTACCTTAAG
Found at i:1573440 original size:171 final size:173
Alignment explanation
Indices: 1573190--1573606 Score: 506
Period size: 171 Copynumber: 2.4 Consensus size: 173
1573180 TTTCCCTCAA
* * * *
1573190 CACACAACAAAAGGGGAGCCAACCTAAGGATATACCTT-GGGCCTATGGCCTA-CCAAAGATATC
1 CACACAACAAAA-GGGAACCAACCTAAGGATATGCCTTGGGGCTTATGGCCTACCCAAGGATATC
*
1573253 CTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAAGAAAACCAACCTAAGGATATACCTT-GG
65 CTTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGAAAACCAACCTAAGGATATACCTTAGG
* * *
1573317 -GT-CTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAG
130 TGTGCTACCCAAGGACATCCTTAGATCCATAGAGTTACCCTAAG
* * * *
1573359 CACACAACAAAAGGGAACTAATCTAAGGATATGCCTTGGGGTTTATGGGCCTACCCAAGGGTATC
1 CACACAACAAAAGGGAACCAACCTAAGGATATGCCTTGGGGCTTAT-GGCCTACCCAAGGATATC
** *
1573424 CTTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGGGAACCAACCTAAGGATATGCCTTAGG
65 CTTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGAAAACCAACCTAAGGATATACCTTA-G
** *
1573489 GCTTGTGGGCCTACCCAAGGGTATCCTTAGATCCATAGAGTTACCCTATG
129 G--TGT--G-CTACCCAAGGACATCCTTAGATCCATAGAGTTACCCTAAG
* * *
1573539 CACA-TAGAAAAGGGAACCAACCTAAGGACATGCCTTGGGGCTAATAT-GCCTACCCAAGGATAT
1 CACACAACAAAAGGGAACCAACCTAAGGATATGCCTTGGGGCT--TATGGCCTACCCAAGGATAT
1573602 CCTTA
64 CCTTA
1573607 ATTCCGTAAG
Statistics
Matches: 209, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
168 21 0.10
169 18 0.09
170 6 0.03
171 67 0.32
173 2 0.01
176 2 0.01
179 52 0.25
180 38 0.18
181 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (173 bp):
CACACAACAAAAGGGAACCAACCTAAGGATATGCCTTGGGGCTTATGGCCTACCCAAGGATATCC
TTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGAAAACCAACCTAAGGATATACCTTAGGT
GTGCTACCCAAGGACATCCTTAGATCCATAGAGTTACCCTAAG
Found at i:1573596 original size:89 final size:90
Alignment explanation
Indices: 1573314--1573606 Score: 408
Period size: 90 Copynumber: 3.3 Consensus size: 90
1573304 GGATATACCT
* * * *
1573314 TGGGTCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAAGGGAACTA
1 TGGGCCTACCCAAGGATATCCTTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGGGAACCA
* *
1573379 ATCTAAGGATATGCCTTGGGGTTTA
66 ACCTAAGGATATGCCTTGGGGCTTA
*
1573404 TGGGCCTACCCAAGGGTATCCTTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGGGAACCA
1 TGGGCCTACCCAAGGATATCCTTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGGGAACCA
* *
1573469 ACCTAAGGATATGCCTTAGGGCTTG
66 ACCTAAGGATATGCCTTGGGGCTTA
* * * * * *
1573494 TGGGCCTACCCAAGGGTATCCTTAGATCCATAGAGTTACCCTATGCACA-TAGAAAAGGGAACCA
1 TGGGCCTACCCAAGGATATCCTTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGGGAACCA
* *
1573558 ACCTAAGGACATGCCTTGGGGCTAA
66 ACCTAAGGATATGCCTTGGGGCTTA
**
1573583 TATGCCTACCCAAGGATATCCTTA
1 TGGGCCTACCCAAGGATATCCTTA
1573607 ATTCCGTAAG
Statistics
Matches: 182, Mismatches: 21, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
89 55 0.30
90 127 0.70
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (90 bp):
TGGGCCTACCCAAGGATATCCTTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGGGAACCA
ACCTAAGGATATGCCTTGGGGCTTA
Found at i:1578552 original size:89 final size:90
Alignment explanation
Indices: 1578400--1578669 Score: 296
Period size: 89 Copynumber: 3.0 Consensus size: 90
1578390 AAGGACATCA
*
1578400 TTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGAGAACCAACCTAAGGATATGCCTTGGGG
1 TTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGAGAACCAACCAAAGGATATGCCTTGGGG
*
1578465 -TTATGGGCCTATCCAAGGGTATCC
66 CTTATGGGCCTACCCAAGGGTATCC
* ***
1578489 TTAGATCCATAGGGTTACCTTAAGCACACAGCAAAA-AGAAACCAACCAAAGGATATTTGTTGGG
1 TTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGAG-AACCAACCAAAGGATATGCCTTGGG
1578553 GCTTATGGGCCTACCCAAGGGTATCC
65 GCTTATGGGCCTACCCAAGGGTATCC
* ** * * * ** * * * *
1578579 CTAGATCTGTAGGGTTACCCTATG-ACA-TAGTAAAGGGAACCAACCTAAGGACATACCTTGGGG
1 TTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGAGAACCAACCAAAGGATATGCCTTGGGG
** ** *
1578642 CCGATATGCCTACCCAAGGATATCC
66 CTTATGGGCCTACCCAAGGGTATCC
1578667 TTA
1 TTA
1578670 AGTCTGTAAG
Statistics
Matches: 151, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
88 48 0.32
89 61 0.40
90 42 0.28
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (90 bp):
TTAGATCCATAGGGTTACCTTAAGCACACAACAAAAGAGAACCAACCAAAGGATATGCCTTGGGG
CTTATGGGCCTACCCAAGGGTATCC
Found at i:1581354 original size:19 final size:18
Alignment explanation
Indices: 1581330--1581384 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
1581320 GATCAAAGCT
*
1581330 CTGGTCAATGCCGTCAACG
1 CTGGTCAACG-CGTCAACG
*
1581349 CTGGTCAACGGGTCAACG
1 CTGGTCAACGCGTCAACG
* *
1581367 CTAGTCAACGGGTCAACG
1 CTGGTCAACGCGTCAACG
1581385 GTTTCACACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 24 0.73
19 9 0.27
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (18 bp):
CTGGTCAACGCGTCAACG
Found at i:1581365 original size:18 final size:18
Alignment explanation
Indices: 1581342--1581384 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1581332 GGTCAATGCC
*
1581342 GTCAACGCTGGTCAACGG
1 GTCAACGCTAGTCAACGG
1581360 GTCAACGCTAGTCAACGG
1 GTCAACGCTAGTCAACGG
1581378 GTCAACG
1 GTCAACG
1581385 GTTTCACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.16
Consensus pattern (18 bp):
GTCAACGCTAGTCAACGG
Found at i:1582253 original size:2 final size:2
Alignment explanation
Indices: 1582246--1582275 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1582236 TTTTAAAAAC
1582246 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1582276 TCAAAATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1582315 original size:36 final size:37
Alignment explanation
Indices: 1582257--1582390 Score: 139
Period size: 38 Copynumber: 3.5 Consensus size: 37
1582247 ATATATATAT
* *
1582257 TATATATATATATATATATTCAAAATGTTTTTAAAAAC
1 TATATA-ATATATATATATTCAAAATATTTTCAAAAAC
*
1582295 TATATAATATATATGT-TTCAAAATATTTTCAAAAAC
1 TATATAATATATATATATTCAAAATATTTTCAAAAAC
*
1582331 TATATATTATATATATATATATTTCAAAATCATTTGC--AAAC
1 --TATA-TA-ATATATATATA-TTCAAAAT-ATTTTCAAAAAC
1582372 TATATAATATAATATATAT
1 TATATAATAT-ATATATAT
1582391 ATAATAAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
36 18 0.22
37 14 0.17
38 19 0.23
39 6 0.07
40 9 0.11
41 4 0.05
42 8 0.10
43 5 0.06
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (37 bp):
TATATAATATATATATATTCAAAATATTTTCAAAAAC
Found at i:1582687 original size:2 final size:2
Alignment explanation
Indices: 1582682--1582721 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1582672 ACATCAGCTT
1582682 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
1582722 ATTAATCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1596297 original size:36 final size:38
Alignment explanation
Indices: 1596237--1596310 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 38
1596227 ATATTTCAAC
1596237 AAACATCTACCAAACTTTGAAAAACCA-TTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAAACCATTTTTTCAAAG
*
1596274 AAACATTTACCAAACTTTG-AAAACCATTTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAAACCATTTTTTCAAAG
1596311 TTGGTTGCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 7 0.20
37 28 0.80
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (38 bp):
AAACATCTACCAAACTTTGAAAAACCATTTTTTCAAAG
Found at i:1599458 original size:15 final size:15
Alignment explanation
Indices: 1599438--1599469 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1599428 AAAATCTTTC
*
1599438 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
1599453 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
1599468 TT
1 TT
1599470 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:1600668 original size:37 final size:36
Alignment explanation
Indices: 1600626--1600734 Score: 157
Period size: 35 Copynumber: 3.0 Consensus size: 36
1600616 ATATTTCAAC
*
1600626 AAACATCTACCAAACTTTGAAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCATTTTTCAAAG
* *
1600663 AAACATTTACCAAATTTTGAAAACTA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
*
1600698 AAACATTTACCAAACTTTGCAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
1600735 TTGGTTGCCA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
35 32 0.50
36 6 0.09
37 26 0.41
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:1602234 original size:40 final size:42
Alignment explanation
Indices: 1602161--1602244 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
1602151 AGGAAATATA
* *
1602161 TATATATATATATACATCAACGTATTAATAAAATA-AATAAGC
1 TATATATATATATACAACAACATATTAATAAAATAGAA-AAGC
*
1602203 TATATATATATATACAACAA-ATATTTA-AAAATAGAAAAGC
1 TATATATATATATACAACAACATATTAATAAAATAGAAAAGC
1602243 TA
1 TA
1602245 CCATCTCACT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 12 0.32
41 7 0.18
42 19 0.50
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (42 bp):
TATATATATATATACAACAACATATTAATAAAATAGAAAAGC
Found at i:1602447 original size:24 final size:23
Alignment explanation
Indices: 1602409--1602457 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1602399 AAGAATTTTT
* **
1602409 TAAAATAATATAATAATGAATAA
1 TAAAATAAAATAATAAAAAATAA
1602432 TAAAATGAAAATAATAAAAAATAA
1 TAAAAT-AAAATAATAAAAAATAA
1602456 TA
1 TA
1602458 TATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
TAAAATAAAATAATAAAAAATAA
Found at i:1602530 original size:2 final size:2
Alignment explanation
Indices: 1602525--1602568 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1602515 ATAATTAAGA
*
1602525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT A- AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1602564 AT AT A
1 AT AT A
1602569 AATAAACTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1602711 original size:44 final size:47
Alignment explanation
Indices: 1602623--1602711 Score: 107
Period size: 48 Copynumber: 1.9 Consensus size: 47
1602613 GATAATTACA
*
1602623 ATATATATAGTAATAATAAACTTATAAGTAAATATTAAAGAAATATAT
1 ATATATATAGTAATAATAAACATATAAGTAAATA-TAAAGAAATATAT
1602671 ATATATATA-TATATAATAAA-ATATAA-TATAATA-AAA-AAATA
1 ATATATATAGTA-ATAATAAACATATAAGTA-AATATAAAGAAATA
1602712 AAATGAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
44 5 0.13
45 3 0.08
46 2 0.05
47 11 0.29
48 17 0.45
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (47 bp):
ATATATATAGTAATAATAAACATATAAGTAAATATAAAGAAATATAT
Found at i:1602785 original size:17 final size:18
Alignment explanation
Indices: 1602752--1602787 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1602742 ATATATACAT
*
1602752 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1602770 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1602787 A
1 A
1602788 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1604495 original size:106 final size:105
Alignment explanation
Indices: 1604306--1604824 Score: 664
Period size: 106 Copynumber: 5.0 Consensus size: 105
1604296 GTATTGTTCT
* * * * * * *
1604306 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTAATAAATTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTAGAAATTGTTTGTTGACAA
* * *
1604371 CCAGCCGTCCCTTAGTTGTGAATTTGAACTTGTGTTGTATC
65 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* *
1604412 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-AGAAATTGTTTGTTGACAA
* * *
1604477 CCAGCCGTCCCTTCGTTGTTAAGTTAAACTTGTGCTGTCTC
65 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* ** *
1604518 GGGTCCAATGCCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTA-GAAATTGTTTGTTGACAA
*
1604583 CCAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* ** *
1604624 GAATCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAG-AAATTGTTTGTTGACAA
* * *
1604689 CCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
65 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
1604730 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG----G--A--AG---TTGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGAAATTGTTTGTTGACAAC
* *
1604784 CATCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
1604824 G
1 G
1604825 GGTGGCGCGA
Statistics
Matches: 371, Mismatches: 39, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
94 52 0.14
98 1 0.00
100 1 0.00
102 1 0.00
105 6 0.02
106 310 0.84
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:1605494 original size:37 final size:37
Alignment explanation
Indices: 1605412--1605496 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
1605402 GTTTCATGGG
* * * * **
1605412 AAACGGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
1605449 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
*
1605485 GAAATTGTCTCA
1 -AAACTGTCTCA
1605497 CGGGGAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:1605697 original size:36 final size:37
Alignment explanation
Indices: 1605643--1605718 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 37
1605633 GAAACAATTT
* *
1605643 CAAAGATTTTTTTTAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
*
1605680 CAAAG-TTTGTTTCAAGGGAAACTGTCTCATGAGAGA
1 CAAAGATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1605716 CAA
1 CAA
1605719 TGGTGAGCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 31 0.86
37 5 0.14
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (37 bp):
CAAAGATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
Found at i:1606232 original size:18 final size:18
Alignment explanation
Indices: 1606205--1606240 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1606195 TGTTGAATCC
* *
1606205 CCAAAGATGCCCTAATAT
1 CCAAAAATGCCCCAATAT
1606223 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1606241 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1607314 original size:30 final size:30
Alignment explanation
Indices: 1607280--1607345 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1607270 TTGCATGTGC
1607280 TTTTTGTCCCTTTTTCTT-TTGATTTTTTCT
1 TTTTTGTCCCTTTTTCTTCTTG-TTTTTTCT
* * * *
1607310 TTTTTTTTCTTTTTTGTTCTTGTTTTTTCT
1 TTTTTGTCCCTTTTTCTTCTTGTTTTTTCT
1607340 TTTTTG
1 TTTTTG
1607346 CTTCTTTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.79
Consensus pattern (30 bp):
TTTTTGTCCCTTTTTCTTCTTGTTTTTTCT
Found at i:1607317 original size:10 final size:10
Alignment explanation
Indices: 1607302--1607359 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
1607292 TTTCTTTTGA
1607302 TTTTTTCTTT
1 TTTTTTCTTT
1607312 TTTTTTCTTT
1 TTTTTTCTTT
* *
1607322 TTTGTTCTTG
1 TTTTTTCTTT
1607332 TTTTTTCTTT
1 TTTTTTCTTT
*
1607342 TTTGCTTCTTT
1 TTT-TTTCTTT
1607353 TCTTTTT
1 T-TTTTT
1607360 TGTTTTTGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
10 29 0.73
11 9 0.22
12 2 0.05
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1607329 original size:20 final size:20
Alignment explanation
Indices: 1607302--1607359 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
1607292 TTTCTTTTGA
1607302 TTTT-TTCTTTTTTTTTCTT
1 TTTTGTTCTTTTTTTTTCTT
*
1607321 TTTTGTTCTTGTTTTTTCTT
1 TTTTGTTCTTTTTTTTTCTT
1607341 TTTTGCTTCTTTTCTTTTT
1 TTTTG-TTCTTTT-TTTTT
1607360 TGTTTTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 4 0.12
20 19 0.56
21 6 0.18
22 5 0.15
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (20 bp):
TTTTGTTCTTTTTTTTTCTT
Found at i:1607363 original size:30 final size:29
Alignment explanation
Indices: 1607290--1607366 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
1607280 TTTTTGTCCC
* *
1607290 TTTTTCTTTTGATTTTTTCTTTTTTTTTCT
1 TTTTTGTTTTG-TTTTTTCTTTTTTCTTCT
1607320 TTTTTGTTCTTGTTTTTTCTTTTTTGCTTCT
1 TTTTTGTT-TTGTTTTTTCTTTTTT-CTTCT
1607351 TTTCTT-TTTTGTTTTT
1 TTT-TTGTTTTGTTTTT
1607367 GATTGAATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 28 0.67
31 12 0.29
32 2 0.05
ACGTcount: A:0.01, C:0.10, G:0.06, T:0.82
Consensus pattern (29 bp):
TTTTTGTTTTGTTTTTTCTTTTTTCTTCT
Found at i:1612191 original size:2 final size:2
Alignment explanation
Indices: 1612143--1612175 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1612133 ATAAAAAATA
1612143 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
1612176 AAGTTATAAG
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:1612454 original size:17 final size:18
Alignment explanation
Indices: 1612423--1612458 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1612413 ATACATACGT
*
1612423 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1612441 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1612458 A
1 A
1612459 AACATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Done.