Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008460.1 Hibiscus syriacus cultivar Beakdansim tig00111273_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: 2854393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 15
Found at i:1523925 original size:19 final size:19
Alignment explanation
Indices: 1523903--1523984 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
1523893 GAAACACAAA
1523903 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1523922 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1523938 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
1523954 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1523973 TCGCATTGCGAT
1 TCGCATTGCGAT
1523985 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.17
16 8 0.15
18 9 0.17
19 28 0.52
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1524003 original size:20 final size:19
Alignment explanation
Indices: 1523939--1524023 Score: 91
Period size: 20 Copynumber: 4.4 Consensus size: 19
1523929 GCGATTTTGT
*
1523939 CGTTGCGAT-TTCATTTCG
1 CGTTGCGATAGTCATTTCG
**
1523957 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
1523976 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1523996 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
1524016 TGTTGCGA
1 CGTTGCGA
1524024 AAGTAAACTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
18 9 0.16
19 22 0.39
20 23 0.40
21 3 0.05
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1526136 original size:22 final size:22
Alignment explanation
Indices: 1526111--1526154 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1526101 GATTTAGATA
1526111 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1526133 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1526155 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1526367 original size:20 final size:20
Alignment explanation
Indices: 1526342--1526435 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1526332 GATTATGTAT
1526342 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1526362 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1526382 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1526403 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1526423 TATCGCATTGCGA
1 TATCGCGTTGCGA
1526436 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1526407 original size:41 final size:42
Alignment explanation
Indices: 1526362--1526538 Score: 123
Period size: 41 Copynumber: 4.3 Consensus size: 42
1526352 CGAAAGTCAG
* * * *
1526362 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
1526403 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
1526445 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
** ** * *
1526486 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
1526527 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
1526539 TTTACTTATT
Statistics
Matches: 117, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
40 3 0.03
41 111 0.95
42 3 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:1526436 original size:20 final size:20
Alignment explanation
Indices: 1526322--1526436 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1526312 CGCTTTGAAA
*
1526322 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1526343 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1526363 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1526383 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1526404 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1526424 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1526437 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1526454 original size:21 final size:20
Alignment explanation
Indices: 1526425--1526558 Score: 142
Period size: 21 Copynumber: 6.5 Consensus size: 20
1526415 ATAGTCAGTA
*
1526425 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
1526446 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
1526466 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
1526487 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
1526507 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
1526528 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
1526548 TCGCATTGCGA
1 TCGCATTGCGA
1526559 ATTGGGAAAA
Statistics
Matches: 91, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
20 44 0.48
21 47 0.52
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:1526475 original size:82 final size:81
Alignment explanation
Indices: 1526405--1526558 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 81
1526395 TTTTTTATTA
* *
1526405 TCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTATTC
1 TCGCATTGCGAT--TCACGTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTC
1526468 GCATTGCGAATTTCCCAAT
64 GCATTGCG-ATTTCCCAAT
* * *
1526487 TCGCGTTGCGATTTACTTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGC
1 TCGCATTGCGATTCACGTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGC
1526552 ATTGCGA
66 ATTGCGA
1526559 ATTGGGAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
80 2 0.03
81 3 0.05
82 60 0.92
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (81 bp):
TCGCATTGCGATTCACGTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGC
ATTGCGATTTCCCAAT
Found at i:1526539 original size:41 final size:41
Alignment explanation
Indices: 1526425--1526561 Score: 256
Period size: 41 Copynumber: 3.3 Consensus size: 41
1526415 ATAGTCAGTA
* *
1526425 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1526466 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1526507 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1526548 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1526562 GGGAAAATCG
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1527629 original size:20 final size:20
Alignment explanation
Indices: 1527579--1527628 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1527569 TAAATTCAAA
1527579 TATTTAAAT-TATTTTATAT
1 TATTTAAATATATTTTATAT
*
1527598 T-TATAAAATATATTTT-TAT
1 TAT-TTAAATATATTTTATAT
1527617 TATTT-AATATAT
1 TATTTAAATATAT
1527629 AAACACAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 8 0.31
19 11 0.42
20 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTAAATATATTTTATAT
Found at i:1530163 original size:29 final size:31
Alignment explanation
Indices: 1530129--1530203 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1530119 AATTTATTAC
*
1530129 ATATATTTTATTATTAAT-TTAA-TTT-AAAA
1 ATATATTTTATTATT-ATCTAAATTTTAAAAA
* *
1530158 ATATATATTATTCTTATCTAAATTTTAAAAA
1 ATATATTTTATTATTATCTAAATTTTAAAAA
1530189 ATATATTTTATTATT
1 ATATATTTTATTATT
1530204 TTAACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 2 0.05
29 16 0.42
30 3 0.08
31 17 0.45
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (31 bp):
ATATATTTTATTATTATCTAAATTTTAAAAA
Found at i:1530165 original size:31 final size:27
Alignment explanation
Indices: 1530129--1530203 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 27
1530119 AATTTATTAC
1530129 ATATATTTTATTATTAATTTAATTTAAAAA
1 ATATATTTTATTATTAA---AATTTAAAAA
* *
1530159 TATATATTATTCTTATCTAAATTTTAAAAA
1 -ATATATT-TTATTAT-TAAAATTTAAAAA
1530189 ATATATTTTATTATT
1 ATATATTTTATTATT
1530204 TTAACTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.03
28 6 0.15
29 7 0.18
30 9 0.23
31 7 0.18
32 6 0.15
33 3 0.08
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATATTTTATTATTAAAATTTAAAAA
Found at i:1530212 original size:29 final size:29
Alignment explanation
Indices: 1530129--1530212 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
1530119 AATTTATTAC
* *
1530129 ATATATTTTATTATTAATTTAA-TTTAAAA
1 ATATATATT-TTATTATTTTAATTTTAAAA
* * *
1530158 ATATATATTATTCTTATCTAAATTTTAAAA
1 ATATATATT-TTATTATTTTAATTTTAAAA
1530188 A-ATATATTTTATTATTTTAACTTTT
1 ATATATATTTTATTATTTTAA-TTTT
1530213 TGAATATTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 9 0.20
29 28 0.62
30 8 0.18
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATATATTTTATTATTTTAATTTTAAAA
Found at i:1530330 original size:20 final size:20
Alignment explanation
Indices: 1530298--1530351 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1530288 TTTCAAAATA
* *
1530298 TTTTAACATAAAAT-ATATAT
1 TTTTAA-ATAAAATAAAACAT
1530318 TTTTAAATAAAAATAAAACAT
1 TTTTAAAT-AAAATAAAACAT
*
1530339 TTTTAAATTAAAT
1 TTTTAAATAAAAT
1530352 TAATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.52
21 12 0.41
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTTAAATAAAATAAAACAT
Found at i:1531562 original size:38 final size:38
Alignment explanation
Indices: 1531520--1531607 Score: 126
Period size: 38 Copynumber: 2.3 Consensus size: 38
1531510 TTTTTCTAAA
1531520 ATTTTCGATTGAACCGAAAATATTAACTTAATCATAAG
1 ATTTTCGATTGAACCGAAAATATTAACTTAATCATAAG
*
1531558 ATTTTC-AGTAT-AACCGAAAATATTAACTTATTCATAAG
1 ATTTTCGA-T-TGAACCGAAAATATTAACTTAATCATAAG
*
1531596 ATTTTCGGTTGA
1 ATTTTCGATTGA
1531608 CAGCTGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
37 2 0.05
38 41 0.93
39 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (38 bp):
ATTTTCGATTGAACCGAAAATATTAACTTAATCATAAG
Found at i:1531917 original size:20 final size:20
Alignment explanation
Indices: 1531870--1531909 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1531860 TATAAGGGAA
1531870 AGTTTAAGAAACAATCGTTT
1 AGTTTAAGAAACAATCGTTT
1531890 AGTTTAAGAAACAATCGTTT
1 AGTTTAAGAAACAATCGTTT
1531910 TATTTAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
AGTTTAAGAAACAATCGTTT
Found at i:1532646 original size:39 final size:39
Alignment explanation
Indices: 1532532--1532649 Score: 136
Period size: 39 Copynumber: 3.1 Consensus size: 39
1532522 CTTACTATAA
*
1532532 AATAAAAATATAAAATTATCCACGTGTAGAATTTTACAT
1 AATAAAAATATAAAATTATCCACGTATAGAATTTTACAT
* * * ** *
1532571 GATAAAACT-TAAACTTAAACAC--ACA-ATATTTTACAT
1 AATAAAAATATAAAATTATCCACGTATAGA-ATTTTACAT
1532607 AATAAAAATATAAAATTATCCACGTATAGAATTTTACAT
1 AATAAAAATATAAAATTATCCACGTATAGAATTTTACAT
1532646 AATA
1 AATA
1532650 TTGAAATTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
35 1 0.02
36 17 0.28
37 10 0.16
38 10 0.16
39 22 0.36
40 1 0.02
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (39 bp):
AATAAAAATATAAAATTATCCACGTATAGAATTTTACAT
Found at i:1534139 original size:35 final size:38
Alignment explanation
Indices: 1534073--1534142 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 38
1534063 TACTAATATG
*
1534073 TAATAAATAGATTATAAATGACTAATCTATTAATTTTT
1 TAATAAATAGATTAAAAATGACTAATCTATTAATTTTT
1534111 TAATAAATA-A-TAAAAAT-ACTAAAT-TATTAATT
1 TAATAAATAGATTAAAAATGACT-AATCTATTAATT
1534143 AATAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
35 11 0.37
36 9 0.30
37 1 0.03
38 9 0.30
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (38 bp):
TAATAAATAGATTAAAAATGACTAATCTATTAATTTTT
Found at i:1538925 original size:24 final size:24
Alignment explanation
Indices: 1538898--1538959 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1538888 CGTTCGTGAA
*
1538898 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
1538922 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
* *
1538946 CGTTAATTTATGTT
1 CGTTCAGTTATGTT
1538960 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:1540484 original size:10 final size:10
Alignment explanation
Indices: 1540469--1540553 Score: 72
Period size: 10 Copynumber: 8.7 Consensus size: 10
1540459 GGGTCTCCAA
1540469 CGTTTATGTT
1 CGTTTATGTT
1540479 CGTTTATGTT
1 CGTTTATGTT
1540489 CGTTTATGTT
1 CGTTTATGTT
1540499 CG----TGTT
1 CGTTTATGTT
*
1540505 CATTTATGTT
1 CGTTTATGTT
*
1540515 CGTGTT-CGTTT
1 CGT-TTATG-TT
* *
1540526 ATGTTTGTGTT
1 -CGTTTATGTT
1540537 CGTTTATGTT
1 CGTTTATGTT
1540547 CGTTTAT
1 CGTTTAT
1540554 TTATTAAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
6 5 0.08
10 44 0.73
11 8 0.13
12 3 0.05
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1540510 original size:16 final size:16
Alignment explanation
Indices: 1540485--1540549 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1540475 TGTTCGTTTA
1540485 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1540501 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1540517 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
1540533 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1540549 T
1 T
1540550 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1540511 original size:26 final size:26
Alignment explanation
Indices: 1540475--1540549 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
1540465 CCAACGTTTA
1540475 TGTTCGTTTATGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCGTTTATGTTCG
*
1540501 TGTTCATTTATGTTCG----TGTTCG
1 TGTTCGTTTATGTTCGTTTATGTTCG
* *
1540523 T-TTATGTTTGTGTTCGTTTATGTTCG
1 TGTT-CGTTTATGTTCGTTTATGTTCG
1540549 T
1 T
1540550 TTATTTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
21 2 0.05
22 16 0.40
26 22 0.55
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.59
Consensus pattern (26 bp):
TGTTCGTTTATGTTCGTTTATGTTCG
Found at i:1540640 original size:16 final size:16
Alignment explanation
Indices: 1540619--1540650 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1540609 AAAAAAATTT
1540619 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1540635 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1540651 CTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1546447 original size:24 final size:25
Alignment explanation
Indices: 1546418--1546465 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1546408 CACCAATGTA
* *
1546418 TTAGCA-AGAGGCTTCATAATTATG
1 TTAGCAGAAAGGCTTCAGAATTATG
1546442 TTAGCAGAAAGGCTTCAGAATTAT
1 TTAGCAGAAAGGCTTCAGAATTAT
1546466 AGCTTAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (25 bp):
TTAGCAGAAAGGCTTCAGAATTATG
Found at i:1556665 original size:21 final size:20
Alignment explanation
Indices: 1556625--1556668 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1556615 ATATTTTTTT
*
1556625 TAAAATAATCATATATAAAA
1 TAAAATAATCATATAAAAAA
1556645 TAAATATAAT-ATAATAAAAAA
1 TAAA-ATAATCAT-ATAAAAAA
1556666 TAA
1 TAA
1556669 TTTTACCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAATAATCATATAAAAAA
Found at i:1561445 original size:17 final size:18
Alignment explanation
Indices: 1561408--1561445 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1561398 CTAAAAATTA
*
1561408 AATAAATAAAATATTCAC
1 AATAAATAAAATATACAC
*
1561426 AATAATTAAAATA-ACAC
1 AATAAATAAAATATACAC
1561443 AAT
1 AAT
1561446 TTCAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAATAAAATATACAC
Found at i:1567462 original size:53 final size:53
Alignment explanation
Indices: 1567402--1567509 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
1567392 CCAACAAAAA
1567402 GAAAACGAAGCCTAGTTGATAATGCAATTACAATAACGATGAAGACAGCACTG
1 GAAAACGAAGCCTAGTTGATAATGCAATTACAATAACGATGAAGACAGCACTG
1567455 GAAAACGAAGCCTAGTTGATAATGCAATTACAATAACGATGAAGACAGCACTG
1 GAAAACGAAGCCTAGTTGATAATGCAATTACAATAACGATGAAGACAGCACTG
1567508 GA
1 GA
1567510 TCACATAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.19
Consensus pattern (53 bp):
GAAAACGAAGCCTAGTTGATAATGCAATTACAATAACGATGAAGACAGCACTG
Found at i:1568225 original size:114 final size:114
Alignment explanation
Indices: 1568071--1568411 Score: 380
Period size: 114 Copynumber: 2.9 Consensus size: 114
1568061 ACAACTCAAA
** * * * *
1568071 CAACCGATAAACATCGAAT-TCTTCAGATGTTTCATTACTACATAACTACCAAGTATCAAGCAGG
1 CAACCGATAAA-ATCGAATCT-TTCA-ATGTTTCACAACTACATATCTAACAACTATCAAGCAAG
*
1568135 CTAGAGTATCTGAAGAGTTCGAAGTTAACATAAATGCAAAATAACAACTCTG
63 CTAGAGTATCTGAAGAATTCGAAGTTAACATAAATGCAAAATAACAACTCTG
*
1568187 CAACCGATCAAATCGAATCTTTCAATGTTTCACAACTACATATCTAACAACTATCAAGCAAGCTA
1 CAACCGATAAAATCGAATCTTTCAATGTTTCACAACTACATATCTAACAACTATCAAGCAAGCTA
* * * * *
1568252 GAGTATCTGAA-AATTTTGAAGCTACCATAGATGCAAAATAACGACTCTG
66 GAGTATCTGAAGAA-TTCGAAGTTAACATAAATGCAAAATAACAACTCTG
** * * * * **
1568301 CAACAAAAAAAAATCAAATCTTTCAATGTTTCACAACCACGTGTATCTGGCAACTATCAAGCAAG
1 CAAC-CGATAAAATCGAATCTTTCAATGTTTCACAACTAC--ATATCTAACAACTATCAAGCAAG
* * * *
1568366 CTAGAGTATCCGAAGAATTCGAAGTTATCATGAATGCAAAGTAACA
63 CTAGAGTATCTGAAGAATTCGAAGTTAACATAAATGCAAAATAACA
1568412 TATACAATCA
Statistics
Matches: 189, Mismatches: 30, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
113 1 0.01
114 80 0.42
115 40 0.21
116 11 0.06
117 55 0.29
118 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (114 bp):
CAACCGATAAAATCGAATCTTTCAATGTTTCACAACTACATATCTAACAACTATCAAGCAAGCTA
GAGTATCTGAAGAATTCGAAGTTAACATAAATGCAAAATAACAACTCTG
Found at i:1569957 original size:107 final size:108
Alignment explanation
Indices: 1569846--1570065 Score: 406
Period size: 107 Copynumber: 2.0 Consensus size: 108
1569836 TAACTATTTC
* **
1569846 AATTTAATTATTTTATTTATAATACAAAAATTATGTAATTTATTATTTTATCTTATTAGTTCAAT
1 AATTTAATTATTTTATTTATAATACAAAAATTAAGTAATTTATTATTTTATCTTATTAGAACAAT
1569911 TAGTAATATGAGATAAATTA-TAAATAAAATATATGATGATAA
66 TAGTAATATGAGATAAATTATTAAATAAAATATATGATGATAA
1569953 AATTTAATTATTTTATTTATAATACAAAAATTAAGTAATTTATTATTTTATCTTATTAGAACAAT
1 AATTTAATTATTTTATTTATAATACAAAAATTAAGTAATTTATTATTTTATCTTATTAGAACAAT
1570018 TAGTAATATGAGATAAATTATTAAATAAAATATATGATGATAA
66 TAGTAATATGAGATAAATTATTAAATAAAATATATGATGATAA
1570061 AATTT
1 AATTT
1570066 TGGCTAAATT
Statistics
Matches: 109, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 82 0.75
108 27 0.25
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (108 bp):
AATTTAATTATTTTATTTATAATACAAAAATTAAGTAATTTATTATTTTATCTTATTAGAACAAT
TAGTAATATGAGATAAATTATTAAATAAAATATATGATGATAA
Found at i:1574147 original size:29 final size:30
Alignment explanation
Indices: 1574114--1574172 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1574104 CCCGAAGGAC
1574114 CTATCCA-AGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
*
1574143 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
1574173 TGTCCATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAAATCCTCGGTAA
Found at i:1574191 original size:29 final size:30
Alignment explanation
Indices: 1574117--1574211 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 30
1574107 GAAGGACCTA
* * *
1574117 TCCA-AGGTCATAAAAATCCTCGGTAACTA
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* *
1574146 TCCAGAGGTCATAAAGATCCTCGGTAA-TG
1 TCCATAGGTCACAAAGATCCTCGGTAACTG
* * * *
1574175 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGATCCTCGGT-AACTG
1574206 TCCATA
1 TCCATA
1574212 TGTTCCTTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.44
30 23 0.42
31 8 0.15
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (30 bp):
TCCATAGGTCACAAAGATCCTCGGTAACTG
Found at i:1574289 original size:32 final size:32
Alignment explanation
Indices: 1574173--1574295 Score: 103
Period size: 32 Copynumber: 3.9 Consensus size: 32
1574163 TCCTCGGTAA
* * * *
1574173 TGTCCATAGGTCCCGAAGAACCTAGGT-AAAC
1 TGTCCATATGTTCCGTAGAACATAGGTAAAAC
* ** * *
1574204 TGTCCATATGTTCCTTAG-A-ATATTTTATAC
1 TGTCCATATGTTCCGTAGAACATAGGTAAAAC
*
1574234 TGTCCATATG-TCTCG-AAAGACATAGGTAAAAC
1 TGTCCATATGTTC-CGTAGA-ACATAGGTAAAAC
1574266 TGTCCATATGTTCCGTAGAACATAGGTAAA
1 TGTCCATATGTTCCGTAGAACATAGGTAAA
1574296 CCCTCAATCT
Statistics
Matches: 70, Mismatches: 15, Indels: 13
0.71 0.15 0.13
Matches are distributed among these distances:
29 6 0.09
30 15 0.21
31 15 0.21
32 30 0.43
33 4 0.06
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
TGTCCATATGTTCCGTAGAACATAGGTAAAAC
Found at i:1575826 original size:21 final size:21
Alignment explanation
Indices: 1575802--1575846 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1575792 TTTTGTTCGG
* *
1575802 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1575823 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1575844 TTG
1 TTG
1575847 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1579176 original size:30 final size:30
Alignment explanation
Indices: 1579142--1579214 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1579132 CCCGAAGGAC
1579142 CTATCCAGAGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
*
1579172 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGTAA
* *
1579202 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1579215 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAAATCCTCGGTAA
Found at i:1579238 original size:31 final size:31
Alignment explanation
Indices: 1579200--1579327 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
1579190 GATCCTCGGT
* *
1579200 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* ** *
1579231 AACTGTCCATATGTTCCTTAGAACATAGTTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
1579262 TATTGTCCATATGTCTCGAA-AGACATAGGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* *
1579294 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
1579325 AAC
1 AAC
1579328 CCTCGACTCT
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
30 1 0.01
31 50 0.66
32 24 0.32
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:1579308 original size:63 final size:62
Alignment explanation
Indices: 1579203--1579321 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 62
1579193 CCTCGGTAAC
* *
1579203 TGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGTTATAT
1 TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGTTATAT
* *
1579265 TGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATAG
1 TGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAG
1579322 GTAAACCCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 1 0.02
62 22 0.43
63 28 0.55
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (62 bp):
TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGTTATAT
Found at i:1580777 original size:21 final size:21
Alignment explanation
Indices: 1580753--1580797 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1580743 TTTTGTTCGG
* *
1580753 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1580774 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1580795 TTG
1 TTG
1580798 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1588264 original size:43 final size:43
Alignment explanation
Indices: 1588215--1588299 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
1588205 AAACAAAATG
* *
1588215 TCATAAGCATGCATAAACAAAGACCTGAATCAAACATGTAACT
1 TCATAAGCATGCATAAACAAAAACCCGAATCAAACATGTAACT
1588258 TCATAAGCATGCATAAACAAAAACCCGAATCAAACATGTAAC
1 TCATAAGCATGCATAAACAAAAACCCGAATCAAACATGTAAC
1588300 AATATTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.48, C:0.22, G:0.11, T:0.19
Consensus pattern (43 bp):
TCATAAGCATGCATAAACAAAAACCCGAATCAAACATGTAACT
Found at i:1595543 original size:19 final size:17
Alignment explanation
Indices: 1595488--1595552 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 17
1595478 GCTTACACAT
*
1595488 TAAAAATATT--AAATA
1 TAAAAATATTAAAAAAA
1595503 TAAAAATATTAAAAAAA
1 TAAAAATATTAAAAAAA
*
1595520 T-AAAATATTATTAGAAAA
1 TAAAAATATTA--AAAAAA
*
1595538 TAAAAATAGTAAAAA
1 TAAAAATATTAAAAA
1595553 CATCATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
15 10 0.24
16 9 0.22
17 8 0.20
18 6 0.15
19 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
TAAAAATATTAAAAAAA
Found at i:1609828 original size:174 final size:173
Alignment explanation
Indices: 1609539--1609883 Score: 681
Period size: 174 Copynumber: 2.0 Consensus size: 173
1609529 ATATCTGATG
1609539 CATATTCAGACATGGTTATAGGAGTACGTCGAGTAATCCTACTCATACATCTGTCCACCCCCCTC
1 CATATTCAGACATGGTTATAGGAGTACGTCGAGTAATCCTACTCATACATCTGTCCACCCCCCTC
1609604 TTCCATGTAGCGTTGAATACTGGAGTCCTGAGTTCCTTTCTGGGATGTTGATAAATCTAGTGAAA
66 TTCCATGTAGCGTTGAATACTGGAGTCCTGAGTTCCTTTCTGGGATGTTGATAAATCTAGTGAAA
1609669 TGCTTTTCATTCATGCTTCCTTCAAGTTGTCGTACTCAGAATT
131 TGCTTTTCATTCATGCTTCCTTCAAGTTGTCGTACTCAGAATT
1609712 CATATTCAGACATGGTTTATAGGAGTACGTCGAGTAATCCTACTCATACATCTGTCCACCCCCCT
1 CATATTCAGACATGG-TTATAGGAGTACGTCGAGTAATCCTACTCATACATCTGTCCACCCCCCT
1609777 CTTCCATGTAGCGTTGAATACTGGAGTCCTGAGTTCCTTTCTGGGATGTTGATAAATCTAGTGAA
65 CTTCCATGTAGCGTTGAATACTGGAGTCCTGAGTTCCTTTCTGGGATGTTGATAAATCTAGTGAA
1609842 ATGCTTTTCATTCATGCTTCCTTCAAGTTGTCGTACTCAGAA
130 ATGCTTTTCATTCATGCTTCCTTCAAGTTGTCGTACTCAGAA
1609884 ATTCCGATAC
Statistics
Matches: 171, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 15 0.09
174 156 0.91
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (173 bp):
CATATTCAGACATGGTTATAGGAGTACGTCGAGTAATCCTACTCATACATCTGTCCACCCCCCTC
TTCCATGTAGCGTTGAATACTGGAGTCCTGAGTTCCTTTCTGGGATGTTGATAAATCTAGTGAAA
TGCTTTTCATTCATGCTTCCTTCAAGTTGTCGTACTCAGAATT
Found at i:1610935 original size:23 final size:23
Alignment explanation
Indices: 1610909--1610956 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1610899 ATAAAGTACA
* *
1610909 ATAACATACTAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1610932 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1610955 AT
1 AT
1610957 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1611411 original size:23 final size:23
Alignment explanation
Indices: 1611376--1611448 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1611366 ATACTTTACA
* *
1611376 ATATAAGCACTACTTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1611399 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1611422 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
1611445 ATAT
1 ATAT
1611449 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1611830 original size:22 final size:22
Alignment explanation
Indices: 1611796--1611864 Score: 88
Period size: 20 Copynumber: 3.2 Consensus size: 22
1611786 ATACTTTACA
*
1611796 ATATAAGCACTACCTATACATT
1 ATATAAGCGCTACCTATACATT
*
1611818 ATATAAACGCTACC--TACATT
1 ATATAAGCGCTACCTATACATT
*
1611838 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTA-TACATT
1611861 ATAT
1 ATAT
1611865 TTTTACCTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 19 0.47
22 12 0.30
23 9 0.22
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (22 bp):
ATATAAGCGCTACCTATACATT
Found at i:1612230 original size:21 final size:21
Alignment explanation
Indices: 1612205--1612279 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 21
1612195 GATAGATACT
1612205 TTACA-ATATAACCACTACCTA
1 TTACATATATAA-CACTACCTA
1612226 TTACATTATATAACGA-TACCTA
1 TTACA-TATATAAC-ACTACCTA
*
1612248 TTACATTATATAA-GCTACCTA
1 TTACA-TATATAACACTACCTA
1612269 TTACATCATAT
1 TTACAT-ATAT
1612280 TTTTACTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
20 1 0.02
21 20 0.42
22 20 0.42
23 7 0.15
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (21 bp):
TTACATATATAACACTACCTA
Found at i:1612248 original size:22 final size:22
Alignment explanation
Indices: 1612210--1612279 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
1612200 ATACTTTACA
*
1612210 ATATAACCACTACCTATTACATT
1 ATATAACGA-TACCTATTACATT
1612233 ATATAACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* *
1612255 ATATAA-GCTACCTATTACATC
1 ATATAACGATACCTATTACATT
1612276 ATAT
1 ATAT
1612280 TTTTACTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 17 0.39
22 19 0.43
23 8 0.18
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:1612417 original size:415 final size:427
Alignment explanation
Indices: 1611023--1612476 Score: 2493
Period size: 414 Copynumber: 3.5 Consensus size: 427
1611013 TATTACATTA
1611023 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1611088 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
1611153 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
1611218 AATAATAATATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAT
196 AATAAT-A-ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAT
1611283 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACA
259 ATCTTAAAACTCACTC-AAAGATAACCTT-AATTAATGTTTTCCACAGTG-AAAAAGTATGGACA
* *
1611348 CTTTTATAAAAATGATAGATACTTTACAATATAAGCACTACTTATTACATTATATAAACGCTACC
321 CTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACC
1611413 TATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
386 TATTACATTATATAA-CGCTACCTATTACATCATATTTTTACC
* *
1611456 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGATTGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1611521 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATA-T-ATTTAATAA-TTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
1611583 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
1611648 -ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTAT-ATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
* *
1611711 CTT-AAACTCACTCAAAGATAACCTAAATTAATGTTTT-C-CAGTGAAAAAGTATAGACACTTTT
261 CTTAAAACTCACTCAAAGATAACCTTAATTAATGTTTTCCACAGTGAAAAAGTATGGACACTTTT
1611773 ATAAAAAGGATAGATACTTTACAATATAAGCACTACCTA-TACATTATATAAACGCTACC---TA
326 ATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTA
1611834 CATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 CATTATATAA-CGCTACCTATTACATCATATTTTTACC
1611872 TATTATATTGAAAGTGTCCATACTTTTTATAAAAA-GATCGATACTTCTTTTAAAGTTA-GTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
1611935 TTATGTTTCAA-TTTTTTTAATAG-GTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
1611998 ATTTGCACAAAAAA-TATTTGATTGTTTTGATATTTTATAAAATATTA-TTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
1612061 AATAATAATATATATCGT-ACGT-AAAAA-AAATCATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
1612123 CTTAAAACTCACTCAAGGATAACCTTAATTAATGTTTTCCACAGTGAAAAAGTATGGACACTTTT
261 CTTAAAACTCACTCAAAGATAACCTTAATTAATGTTTTCCACAGTGAAAAAGTATGGACACTTTT
* *
1612188 AT-AAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATAT-AACGATACCTATTA
326 ATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTA
*
1612251 CATTATATAA-GCTACCTATTACATCATATTTTTACT
391 CATTATATAACGCTACCTATTACATCATATTTTTACC
1612287 TA-TATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
1612351 TTATGTTTCAA-TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA-TAATTTAATAA-TTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
1612413 ATTTGCACAAAAAATTATTTGATTGTTTTGATA-TTTAT-AAATAATATTTAGAA-TTTAAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
1612475 AA
196 AA
1612477 AACAAATCAA
Statistics
Matches: 985, Mismatches: 19, Indels: 53
0.93 0.02 0.05
Matches are distributed among these distances:
411 18 0.02
412 47 0.05
413 65 0.07
414 168 0.17
415 152 0.15
416 131 0.13
417 35 0.04
419 20 0.02
420 55 0.06
421 5 0.01
422 1 0.00
423 12 0.01
424 11 0.01
425 10 0.01
426 19 0.02
427 41 0.04
428 1 0.00
429 5 0.01
430 67 0.07
431 9 0.01
432 1 0.00
433 112 0.11
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.41
Consensus pattern (427 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
CTTAAAACTCACTCAAAGATAACCTTAATTAATGTTTTCCACAGTGAAAAAGTATGGACACTTTT
ATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTA
CATTATATAACGCTACCTATTACATCATATTTTTACC
Found at i:1612739 original size:38 final size:38
Alignment explanation
Indices: 1612685--1612765 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
1612675 TCAAGTTGTA
* *
1612685 GATTTTGATTTCCTTTTGCTTGGCATCATA-GAGATTTG
1 GATTTGGATTTCCTTTTGCTT-GCACCATATGAGATTTG
* *
1612723 GATTTGGATTTTCTTTTGCTTGCACCATATGAGCTTTG
1 GATTTGGATTTCCTTTTGCTTGCACCATATGAGATTTG
1612761 GATTT
1 GATTT
1612766 TGATGAGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 7 0.18
38 31 0.82
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (38 bp):
GATTTGGATTTCCTTTTGCTTGCACCATATGAGATTTG
Found at i:1613057 original size:18 final size:17
Alignment explanation
Indices: 1613034--1613069 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1613024 CGAAATATAT
1613034 ATTGAAATTCAAACTCAA
1 ATTGAAATT-AAACTCAA
*
1613052 ATTGAAATTAAATTCAA
1 ATTGAAATTAAACTCAA
1613069 A
1 A
1613070 CTCCAATAAG
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:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
ATTGAAATTAAACTCAA
Found at i:1613366 original size:25 final size:25
Alignment explanation
Indices: 1613332--1613381 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1613322 ATTATTTTTC
*
1613332 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1613357 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1613382 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1613684 original size:23 final size:23
Alignment explanation
Indices: 1613658--1613720 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1613648 ATATAAGCAC
1613658 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1613681 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1613704 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1613721 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1614174 original size:23 final size:23
Alignment explanation
Indices: 1614148--1614210 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1614138 ATATAAGCAC
1614148 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1614171 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
* *
1614194 TACTTATTACATCATAT
1 TACCTATTACATTATAT
1614211 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1614402 original size:490 final size:490
Alignment explanation
Indices: 1613482--1614557 Score: 2116
Period size: 490 Copynumber: 2.2 Consensus size: 490
1613472 ATATTTATAA
**
1613482 TTTTTAATTTAATAATAATATATATTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1613547 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
1613612 TATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
131 TATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
1613677 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
1613742 TGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTTTCAATT
261 TGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTTTCAATT
1613807 TTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
326 TTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
1613872 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAACATTAACCAA
391 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAACATTAACCAA
1613937 AGATAATAATAAATATGTAATATATATGTTTATTG
456 AGATAATAATAAATATGTAATATATATGTTTATTG
1613972 TTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1614037 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
1614102 TATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
131 TATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
*
1614167 ACGATACCTATTACATTATATAAGCGCTACTTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
*
1614232 TGTCCATACTTTTTATAAAAATGATCGATATTTTTTTTAAAAGTTATGTAATTTATGTTTCAATT
261 TGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTTTCAATT
1614297 TTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
326 TTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
1614362 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAACATTAACCAA
391 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAACATTAACCAA
1614427 AGATAATAATAAATATGTAATATATATGTTTATTG
456 AGATAATAATAAATATGTAATATATATGTTTATTG
1614462 TTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1614527 AAATTAATATCTTAAAACTCACTCAAAAGAT
66 AAATTAATATCTTAAAACTCACTCAAAAGAT
1614558 GTATATACCT
Statistics
Matches: 582, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
490 582 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (490 bp):
TTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
TATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
TGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTTTCAATT
TTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAACATTAACCAA
AGATAATAATAAATATGTAATATATATGTTTATTG
Found at i:1614613 original size:25 final size:25
Alignment explanation
Indices: 1614556--1614621 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
1614546 CACTCAAAAG
*
1614556 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
1614581 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
1614606 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
1614622 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:1617577 original size:183 final size:183
Alignment explanation
Indices: 1617085--1617577 Score: 844
Period size: 183 Copynumber: 2.7 Consensus size: 183
1617075 TTAAAATTAC
* * *
1617085 CGACACTTTTTTAAATGGTATCGATACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAA
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* * *
1617150 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCAGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
1617215 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
1617268 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTATCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
1617333 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACTGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
1617398 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
1617451 CGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* * * *
1617515 TATTAAAAAGTGTCAATACATGTTGTAGACCTATTCACGCATAAAACCGGTATATTTATACCG
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
1617578 ATAGCATTGC
Statistics
Matches: 293, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 290 0.99
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:1619096 original size:9 final size:9
Alignment explanation
Indices: 1619081--1619149 Score: 84
Period size: 9 Copynumber: 7.7 Consensus size: 9
1619071 ACTTGTTTGG
1619081 ATCATCATC
1 ATCATCATC
*
1619090 TTCATCATC
1 ATCATCATC
1619099 ATCATCATC
1 ATCATCATC
*
1619108 ATCGTCATC
1 ATCATCATC
*
1619117 ATCTTCATC
1 ATCATCATC
*
1619126 GTCATCATC
1 ATCATCATC
*
1619135 ATCGTCATC
1 ATCATCATC
*
1619144 TTCATC
1 ATCATC
1619150 GTCAGCTTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.38
Consensus pattern (9 bp):
ATCATCATC
Found at i:1619101 original size:15 final size:15
Alignment explanation
Indices: 1619081--1619149 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
1619071 ACTTGTTTGG
*
1619081 ATCATCATCTTCATC
1 ATCATCATCATCATC
1619096 ATCATCATCATCATC
1 ATCATCATCATCATC
* *
1619111 GTCATCATCTTCATC
1 ATCATCATCATCATC
* *
1619126 GTCATCATCATCGTC
1 ATCATCATCATCATC
*
1619141 ATCTTCATC
1 ATCATCATC
1619150 GTCAGCTTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.38
Consensus pattern (15 bp):
ATCATCATCATCATC
Found at i:1619104 original size:18 final size:18
Alignment explanation
Indices: 1619081--1619164 Score: 96
Period size: 18 Copynumber: 4.7 Consensus size: 18
1619071 ACTTGTTTGG
1619081 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
1619099 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* *
1619117 ATCTTCATCGTCATCATC
1 ATCATCATCTTCATCATC
* *
1619135 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
1619153 AGCTTCATCTTC
1 ATCATCATCTTC
1619165 TGCGACCGCT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:1619158 original size:12 final size:12
Alignment explanation
Indices: 1619085--1619161 Score: 82
Period size: 12 Copynumber: 6.4 Consensus size: 12
1619075 GTTTGGATCA
* *
1619085 TCATCTTCATCA
1 TCATCGTCATCT
* *
1619097 TCATCATCATCA
1 TCATCGTCATCT
* *
1619109 TCGTCATCATCT
1 TCATCGTCATCT
*
1619121 TCATCGTCATCA
1 TCATCGTCATCT
1619133 TCATCGTCATCT
1 TCATCGTCATCT
*
1619145 TCATCGTCAGCT
1 TCATCGTCATCT
1619157 TCATC
1 TCATC
1619162 TTCTGCGACC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 57 1.00
ACGTcount: A:0.22, C:0.34, G:0.06, T:0.38
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:1619164 original size:6 final size:6
Alignment explanation
Indices: 1619081--1619149 Score: 84
Period size: 6 Copynumber: 11.5 Consensus size: 6
1619071 ACTTGTTTGG
* * * *
1619081 ATCATC ATCTTC ATCATC ATCATC ATCATC GTCATC ATCTTC ATCGTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* *
1619129 ATCATC ATCGTC ATCTTC ATC
1 ATCATC ATCATC ATCATC ATC
1619150 GTCAGCTTCA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.38
Consensus pattern (6 bp):
ATCATC
Found at i:1620968 original size:199 final size:198
Alignment explanation
Indices: 1620628--1621790 Score: 2077
Period size: 199 Copynumber: 5.9 Consensus size: 198
1620618 TTTAAATTAG
*
1620628 TATCGACACAAACTAAAATGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1620693 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
* *
1620758 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCCTATTTTCCATTCATTCTGGACCA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CCCTGTTTTCCATTCATTCTGGACCA
1620823 AAAA
195 AAAA
* *
1620827 TATCGACACCAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
1620892 TTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
1620957 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
*
1621022 AAC
196 AAA
*
1621025 TATCGACACGAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
1621090 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGACGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
1621155 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC-A
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
1621219 AAA
196 AAA
* *
1621222 TATCG--AC--AC-AAAACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAT
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1621282 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
* * *
1621347 GAGACTTTTTATATGTGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
1621412 AAA
196 AAA
1621415 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
1621480 TTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTAGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
* *
1621545 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTTATTCTGGAACA
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
1621610 AAAA
195 AAAA
1621614 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
1621679 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGGA
1621744 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
129 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
1621791 GGCCATATTA
Statistics
Matches: 930, Mismatches: 26, Indels: 15
0.96 0.03 0.02
Matches are distributed among these distances:
192 173 0.19
193 11 0.01
195 4 0.00
197 10 0.01
198 221 0.24
199 449 0.48
200 62 0.07
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
AAA
Found at i:1621955 original size:19 final size:19
Alignment explanation
Indices: 1621909--1621957 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1621899 TTATATTCAC
*
1621909 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
* *
1621928 GTACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1621947 ATACAAAATTA
1 ATACAAAATTA
1621958 ACCCTACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1623871 original size:21 final size:21
Alignment explanation
Indices: 1623846--1623889 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1623836 CCCCTTATGC
1623846 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
1623867 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
1623888 CT
1 CT
1623890 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:1626100 original size:17 final size:18
Alignment explanation
Indices: 1626078--1626120 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1626068 ATATATCCGG
1626078 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1626095 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1626115 TATCAT
1 TATCAT
1626121 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1626129 original size:20 final size:19
Alignment explanation
Indices: 1626083--1626129 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1626073 TCCGGTATCA
1626083 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1626102 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1626123 TTTTACC
1 TTTTACC
1626130 TTTTATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1626288 original size:20 final size:20
Alignment explanation
Indices: 1626261--1626307 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1626251 TCCGGTAACG
1626261 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1626280 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1626301 TTTTACC
1 TTTTACC
1626308 TGGTATACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1626707 original size:8 final size:8
Alignment explanation
Indices: 1626694--1626723 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1626684 TTACACAAAA
1626694 ATTATTTG
1 ATTATTTG
1626702 ATTATTTG
1 ATTATTTG
1626710 ATTATTTG
1 ATTATTTG
1626718 A-TATTT
1 ATTATTT
1626724 TAAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (8 bp):
ATTATTTG
Found at i:1635528 original size:102 final size:102
Alignment explanation
Indices: 1635411--1635614 Score: 408
Period size: 102 Copynumber: 2.0 Consensus size: 102
1635401 AATACCTGGA
1635411 TGAATATATAAGATACATGCTATAATTTTACTTCTTTATCATCATGCGCCACTAAGGGAAAAACA
1 TGAATATATAAGATACATGCTATAATTTTACTTCTTTATCATCATGCGCCACTAAGGGAAAAACA
1635476 TAGATGGTACTATGTAAATAGTCAATTGAGACCACAT
66 TAGATGGTACTATGTAAATAGTCAATTGAGACCACAT
1635513 TGAATATATAAGATACATGCTATAATTTTACTTCTTTATCATCATGCGCCACTAAGGGAAAAACA
1 TGAATATATAAGATACATGCTATAATTTTACTTCTTTATCATCATGCGCCACTAAGGGAAAAACA
1635578 TAGATGGTACTATGTAAATAGTCAATTGAGACCACAT
66 TAGATGGTACTATGTAAATAGTCAATTGAGACCACAT
1635615 GATTAAATCA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (102 bp):
TGAATATATAAGATACATGCTATAATTTTACTTCTTTATCATCATGCGCCACTAAGGGAAAAACA
TAGATGGTACTATGTAAATAGTCAATTGAGACCACAT
Found at i:1639205 original size:23 final size:23
Alignment explanation
Indices: 1639179--1639223 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1639169 TCAATGATAT
*
1639179 ATCAAAC-CTTATTATAATAATTA
1 ATCAAACTC-TATCATAATAATTA
*
1639202 ATCAGACTCTATCATAATAATT
1 ATCAAACTCTATCATAATAATT
1639224 CAAAACGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (23 bp):
ATCAAACTCTATCATAATAATTA
Found at i:1640523 original size:16 final size:17
Alignment explanation
Indices: 1640502--1640534 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1640492 CCAATAACAC
*
1640502 ACATATA-TCATGTTAA
1 ACATATACTCATATTAA
1640518 ACATATACTCATATTAA
1 ACATATACTCATATTAA
1640535 TGAATTCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36
Consensus pattern (17 bp):
ACATATACTCATATTAA
Found at i:1641146 original size:24 final size:24
Alignment explanation
Indices: 1641112--1641183 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
1641102 AAATGGAGAT
* *
1641112 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
1641136 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
1641160 ATCAAAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
1641184 GTAATGTATC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1641183 original size:12 final size:12
Alignment explanation
Indices: 1641114--1641183 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
1641104 ATGGAGATAT
* *
1641114 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
1641126 CATAATTCAGAT
1 CAGAATTCAGAA
1641138 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1641150 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
1641162 CAAAAATCAGAA
1 CAGAATTCAGAA
1641174 CAGAATTCAG
1 CAGAATTCAG
1641184 GTAATGTATC
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1644431 original size:23 final size:24
Alignment explanation
Indices: 1644403--1644456 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
1644393 AAATTCAACA
1644403 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
1644426 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
1644450 AAGAAAA
1 AAGAAAA
1644457 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:1644461 original size:24 final size:23
Alignment explanation
Indices: 1644403--1644462 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
1644393 AAATTCAACA
1644403 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
1644426 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
1644450 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
1644463 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:1649702 original size:13 final size:13
Alignment explanation
Indices: 1649684--1649708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1649674 GTCAACAGTC
1649684 AACGGGTCGGGTA
1 AACGGGTCGGGTA
1649697 AACGGGTCGGGT
1 AACGGGTCGGGT
1649709 CGGAGTATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:1650978 original size:153 final size:150
Alignment explanation
Indices: 1650750--1651133 Score: 417
Period size: 153 Copynumber: 2.5 Consensus size: 150
1650740 GGGATGTTAC
* * * * * * * * *
1650750 ATCACCTCATTTATGAAATTGTTTACCACATTTAATAATTGAACAGACCCTATCATAATAATCTC
1 ATCACCTAATTTCTGAACTTGTTGAGCACATTTAATAATTGATCAAATCCTATCATAATAATTTC
* * * *
1650815 ATCATAACTTTTTAGTAACATAACACCTCAAAATGACTTTTCAGTGATATTTGAATAAAAAACGT
66 ACCATGACTTTTTAGTAACATAACACCTCAAAATGACTTTTCAAT-ATATATGAATAAAAAACGT
*
1650880 CATTTTTCTTTTCAGTGATAT
130 CAATTTTCTTTTCAGTGATAT
* * * * ***
1650901 ATCACCTAATTTTTTTAACTTTTTAGTGTTTATTTAATAATTGATCAAATCCTATCATAATAATT
1 ATCACCTAA-TTTCTGAACTTGTT-GAGCACATTTAATAATTGATCAAATCCTATCATAATAATT
* *** ** * **
1650966 TCACCATGACTTTTCAGTGGTATTTCACCTCAAAATTACTTTTCAATATATATGAATTCAAAACG
64 TCACCATGACTTTTTAGTAACATAACACCTCAAAATGACTTTTCAATATATATGAATAAAAAACG
1651031 TCAATTTTCTTTTCAGTGATAT
129 TCAATTTTCTTTTCAGTGATAT
* * * *
1651053 ATTACCTCATTTCTGAACTTGTTGAGCACATTTAATAATTGATCATATCTTATCATAATAATTTC
1 ATCACCTAATTTCTGAACTTGTTGAGCACATTTAATAATTGATCAAATCCTATCATAATAATTTC
* *
1651118 ACAATGACATTTTAGT
66 ACCATGACTTTTTAGT
1651134 GATATATAAA
Statistics
Matches: 188, Mismatches: 43, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
150 49 0.26
151 19 0.10
152 53 0.28
153 67 0.36
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (150 bp):
ATCACCTAATTTCTGAACTTGTTGAGCACATTTAATAATTGATCAAATCCTATCATAATAATTTC
ACCATGACTTTTTAGTAACATAACACCTCAAAATGACTTTTCAATATATATGAATAAAAAACGTC
AATTTTCTTTTCAGTGATAT
Found at i:1651755 original size:5 final size:5
Alignment explanation
Indices: 1651745--1651774 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1651735 TTCTAACATG
1651745 ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
1651775 TGAGTTACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1660298 original size:14 final size:15
Alignment explanation
Indices: 1660281--1660314 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1660271 TCATAGTATT
1660281 ATATTTTAAAG-AAA
1 ATATTTTAAAGTAAA
*
1660295 ATATTTTAAGGTAAA
1 ATATTTTAAAGTAAA
1660310 ATATT
1 ATATT
1660315 GATGAGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (15 bp):
ATATTTTAAAGTAAA
Found at i:1664281 original size:28 final size:29
Alignment explanation
Indices: 1664250--1664308 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
1664240 TTAAAAAAAT
1664250 AAATCACCATTTTT-AATATATGACTTTC
1 AAATCACCATTTTTGAATATATGACTTTC
*
1664278 AAATCATCATTTTTGAATATATGACTTTC
1 AAATCACCATTTTTGAATATATGACTTTC
1664307 AA
1 AA
1664309 GGTTGTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.42
Consensus pattern (29 bp):
AAATCACCATTTTTGAATATATGACTTTC
Found at i:1664627 original size:25 final size:25
Alignment explanation
Indices: 1664598--1664659 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
1664588 CTTAATTTAG
*
1664598 TAAAATATTAATAAATATGAGTATT
1 TAAAATATTAATAAATATGAATATT
* * *
1664623 TAAAATTATT-TTAAATTTTAATATT
1 TAAAA-TATTAATAAATATGAATATT
*
1664648 TAATATATTAAT
1 TAAAATATTAAT
1664660 TATTTATAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
24 4 0.14
25 21 0.72
26 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
TAAAATATTAATAAATATGAATATT
Found at i:1664873 original size:17 final size:17
Alignment explanation
Indices: 1664840--1664875 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1664830 ATAAATATTA
1664840 TACTTATGAAAATTGTT
1 TACTTATGAAAATTGTT
1664857 TACTTATGAAAATTGTT
1 TACTTATGAAAATTGTT
1664874 TA
1 TA
1664876 AAAATTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (17 bp):
TACTTATGAAAATTGTT
Found at i:1669753 original size:16 final size:17
Alignment explanation
Indices: 1669722--1669754 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1669712 TTAAGAACTC
*
1669722 AGCAAACAGTAAATCGA
1 AGCAAAAAGTAAATCGA
1669739 AGCAAAAAG-AAATCGA
1 AGCAAAAAGTAAATCGA
1669755 GATTTTCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.15, G:0.18, T:0.09
Consensus pattern (17 bp):
AGCAAAAAGTAAATCGA
Found at i:1671217 original size:21 final size:21
Alignment explanation
Indices: 1671191--1671232 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1671181 TTTTATCAAC
*
1671191 CATCCTGGACCGTCATGTCAG
1 CATCCTGGACCGTCATATCAG
1671212 CATCCTGGACCGTCATATCAG
1 CATCCTGGACCGTCATATCAG
1671233 TACAGTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.24
Consensus pattern (21 bp):
CATCCTGGACCGTCATATCAG
Found at i:1672007 original size:4 final size:4
Alignment explanation
Indices: 1671998--1672022 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1671988 ATTATAATAC
1671998 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
1672023 ATGTTCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1673083 original size:18 final size:17
Alignment explanation
Indices: 1673029--1673077 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1673019 TTGGACCCTT
* *
1673029 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1673047 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1673065 AGTGCATTCGATG
1 AGTGCA-TCGATG
1673078 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1673182 original size:65 final size:65
Alignment explanation
Indices: 1673049--1673208 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
1673039 TGCACTAAGA
* *
1673049 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCACAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
* * * *
1673113 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCAGTGCATCGGTGCATGGTA-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCAT-G-AC
1673177 T-
64 TG
* *
1673178 GTGCATCGATGCATGAAATGAATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
1673209 CAATTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.33
65 54 0.64
66 2 0.02
67 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
Found at i:1673589 original size:22 final size:22
Alignment explanation
Indices: 1673561--1673605 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1673551 TGAAATCAAT
1673561 TTTGAAAATTACTCCAAATTAC
1 TTTGAAAATTACTCCAAATTAC
1673583 TTTGAAAATTACTCCAAATTAC
1 TTTGAAAATTACTCCAAATTAC
1673605 T
1 T
1673606 CCCCCTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (22 bp):
TTTGAAAATTACTCCAAATTAC
Found at i:1681803 original size:65 final size:64
Alignment explanation
Indices: 1681670--1681825 Score: 181
Period size: 65 Copynumber: 2.4 Consensus size: 64
1681660 TGCACTAAGA
* * * *
1681670 GTGCATCGATGCATCAAGTGCATTCAATGTTTCAAAATAGCCAGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
* * * *
1681734 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCAGTGCATCGGTGCATGGTA-
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAAACAGCCACAGTGCATCGATGCAT-G-AC
1681798 T-
63 TG
* *
1681799 GTGCATCGATGCATGAAATGTATTCGA
1 GTGCATCGATGCATCAAATGCATTCGA
1681826 ATTTCAATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 27 0.34
65 49 0.62
66 2 0.03
67 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
Found at i:1681819 original size:19 final size:19
Alignment explanation
Indices: 1681780--1681819 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1681770 AACATCCTCA
* **
1681780 GTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATGAAAT
1681799 GTGCATCGATGCATGAAAT
1 GTGCATCGATGCATGAAAT
1681818 GT
1 GT
1681820 ATTCGAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATGAAAT
Found at i:1684671 original size:30 final size:30
Alignment explanation
Indices: 1684637--1684708 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
1684627 TGTATTGTCC
*
1684637 GGATTAGCACTATGGTGTAAGCTTAGTGCA
1 GGATTAGCACTATGGCGTAAGCTTAGTGCA
*
1684667 GGATTAACACTATGGCGTAAGCTTAGTGCA
1 GGATTAGCACTATGGCGTAAGCTTAGTGCA
*
1684697 GGTTTAGCACTA
1 GGATTAGCACTA
1684709 CGATACAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
GGATTAGCACTATGGCGTAAGCTTAGTGCA
Found at i:1685712 original size:58 final size:60
Alignment explanation
Indices: 1685578--1685714 Score: 147
Period size: 58 Copynumber: 2.3 Consensus size: 60
1685568 AGAATTGCAT
* ** *
1685578 CCATAAGGACTTACCCTAGGCTTGAAGGGCGTAGGTGTCAACCTAAGGGAGAACCTTGGGT
1 CCATAAGGACTTACCCTAGGCTCGAA-GGCGTAGGTGTCAACCTAAGGGAGAACCTCAGGC
* * **
1685639 CCATAAGGTCTTACCCTA-GC-CGAA-GCGTAGGTGCTC-ACCTGAGGGAGTGCCATCAGGC
1 CCATAAGGACTTACCCTAGGCTCGAAGGCGTAGGTG-TCAACCTAAGGGAGAACC-TCAGGC
1685697 CCATAAGGACTTACCCTA
1 CCATAAGGACTTACCCTA
1685715 TGCACACAGC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
57 21 0.32
58 22 0.34
59 3 0.05
60 2 0.03
61 17 0.26
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (60 bp):
CCATAAGGACTTACCCTAGGCTCGAAGGCGTAGGTGTCAACCTAAGGGAGAACCTCAGGC
Found at i:1685883 original size:35 final size:35
Alignment explanation
Indices: 1685820--1685887 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1685810 CATAGGTCCT
* * *
1685820 TAAGGAATTACCAGCTCGATCGATCTGAACCTATA
1 TAAGGAATTACCAACTCGACCGAGCTGAACCTATA
* *
1685855 TAAGGAATTACCAATTTGACCGAGCTGAACCTA
1 TAAGGAATTACCAACTCGACCGAGCTGAACCTA
1685888 CATAGACTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (35 bp):
TAAGGAATTACCAACTCGACCGAGCTGAACCTATA
Found at i:1686722 original size:19 final size:19
Alignment explanation
Indices: 1686700--1686745 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
1686690 GCAGGTCAGT
1686700 GGTCAGGTCAAAGTCAATA
1 GGTCAGGTCAAAGTCAATA
*
1686719 GGTC-GGTTCAAAGTCAATG
1 GGTCAGG-TCAAAGTCAATA
1686738 GGTCAGGT
1 GGTCAGGT
1686746 TAAATAGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (19 bp):
GGTCAGGTCAAAGTCAATA
Found at i:1687653 original size:11 final size:11
Alignment explanation
Indices: 1687637--1687664 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1687627 ACAATTAATT
1687637 AATTTTAAATA
1 AATTTTAAATA
1687648 AATTTTAAATA
1 AATTTTAAATA
1687659 AATTTT
1 AATTTT
1687665 GGGATGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTTTAAATA
Found at i:1689634 original size:20 final size:20
Alignment explanation
Indices: 1689609--1689673 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
1689599 AAAATAATAA
1689609 TAAATTTAATATTTTAAAAT
1 TAAATTTAATATTTTAAAAT
*
1689629 TAAATTTGATATGTATT-AAA-
1 TAAATTTAATAT-T-TTAAAAT
1689649 TAAA--TAATATTTTTAAAAT
1 TAAATTTAATA-TTTTAAAAT
*
1689668 AAAATT
1 TAAATT
1689674 AAAAATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
17 2 0.06
18 8 0.23
19 4 0.11
20 15 0.43
21 4 0.11
22 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TAAATTTAATATTTTAAAAT
Found at i:1689837 original size:24 final size:23
Alignment explanation
Indices: 1689776--1689837 Score: 54
Period size: 24 Copynumber: 2.5 Consensus size: 23
1689766 TTTCTTTATA
*
1689776 TATAATCATTAAATTTAATTTAATT
1 TATAAT-A-TAAAGTTAATTTAATT
*
1689801 TATCAATAAAAAGTTAATTTAATAAT
1 TAT-AATATAAAGTTAATTTAAT--T
1689827 TAT-ATATAAAG
1 TATAATATAAAG
1689838 GAATTATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 20 0.65
25 4 0.13
26 7 0.23
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (23 bp):
TATAATATAAAGTTAATTTAATT
Found at i:1693507 original size:35 final size:35
Alignment explanation
Indices: 1693459--1693528 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1693449 TTTTACTTGT
* *
1693459 TCAAGATCCTGTCTAAATCTGGTCAAGCCTAGAGA
1 TCAAGATCATGTCTAAATCTGGTCAAACCTAGAGA
1693494 TCAAGATCATGTCTAAATCTGGTCAAACCTAGAGA
1 TCAAGATCATGTCTAAATCTGGTCAAACCTAGAGA
1693529 CCCAACTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (35 bp):
TCAAGATCATGTCTAAATCTGGTCAAACCTAGAGA
Found at i:1695669 original size:22 final size:20
Alignment explanation
Indices: 1695654--1695692 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1695644 ATTTTTGTGT
1695654 TTTTTAAATATAATTTTTTA
1 TTTTTAAATATAATTTTTTA
*
1695674 TTTTTAAATA-ATTTTTTTA
1 TTTTTAAATATAATTTTTTA
1695693 AATTACTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAAATATAATTTTTTA
Found at i:1699118 original size:22 final size:22
Alignment explanation
Indices: 1699093--1699142 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1699083 TTATCTCGTG
1699093 AATATATGTTGTTTAGATAATC
1 AATATATGTTGTTTAGATAATC
1699115 AATATATGTTGTTTAGATAATC
1 AATATATGTTGTTTAGATAATC
1699137 AATATA
1 AATATA
1699143 GCGTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (22 bp):
AATATATGTTGTTTAGATAATC
Found at i:1706697 original size:36 final size:36
Alignment explanation
Indices: 1706657--1706795 Score: 224
Period size: 36 Copynumber: 3.9 Consensus size: 36
1706647 ACAGTGCTAG
*
1706657 ACATTGATACACGAATGTACCAAAGCTGATATAATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
1706693 ACATTGATACACGAATGTACCAAAGCTGATATGTTA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
**
1706729 ACATTGATACACGAAAATACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
1706765 ATATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1706796 ATACTCAAAT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:1710140 original size:19 final size:19
Alignment explanation
Indices: 1710116--1710161 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1710106 TATAAGTTTT
**
1710116 TATGAATAGTACTATATGG
1 TATGAATAGTACTATACAG
1710135 TATGAATAGTACTATACAG
1 TATGAATAGTACTATACAG
1710154 TATGAATA
1 TATGAATA
1710162 TTATCGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (19 bp):
TATGAATAGTACTATACAG
Found at i:1710783 original size:20 final size:20
Alignment explanation
Indices: 1710749--1710819 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
1710739 TCTTAGGGTA
1710749 GTATCGGTA-CCCCCATAGG
1 GTATCGGTACCCCCCATAGG
1710768 GTATCGGTACCCCCCATAGG
1 GTATCGGTACCCCCCATAGG
*
1710788 GTATCGGTACCCCTCATAGG
1 GTATCGGTACCCCCCATAGG
*
1710808 GTATCGATACCC
1 GTATCGGTACCC
1710820 TATATAATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 9 0.18
20 40 0.82
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.23
Consensus pattern (20 bp):
GTATCGGTACCCCCCATAGG
Found at i:1710945 original size:170 final size:173
Alignment explanation
Indices: 1710655--1710989 Score: 649
Period size: 170 Copynumber: 2.0 Consensus size: 173
1710645 TATAATCATA
1710655 CATATAATATCCAAATTATTATTCCAAATATCATGACTCGATCCTTAATATCTTAGAACAAAGAA
1 CATATAATATCCAAATTATTATTCCAAATATCATGACTCGATCCTTAATATCTTAGAACAAAGAA
1710720 AAGCTCAATTTCTATTTTCTCTTAGGGTAGTATCGGTACCCCCATAGGGTATCGGTACCCCCCAT
66 AAGCTCAATTTCTATTTTCTCTTAGGGTAGTATCGGTACCCCCATAGGGTATCGGTACCCCCCAT
1710785 AGGGTATCGGTACCCCTCATAGGGTATCGATACCCTATATAAT
131 AGGGTATCGGTACCCCTCATAGGGTATCGATACCCTATATAAT
1710828 CATAT-ATATCCAAATTATTATTCCAAATATCATGACTCGATCCTT-A-ATCTTAGAACAAAGAA
1 CATATAATATCCAAATTATTATTCCAAATATCATGACTCGATCCTTAATATCTTAGAACAAAGAA
1710890 AAGCTCAATTTCTATTTTCTCTTAGGGTAGTATCGGTACCCCCATAGGGTATCGGTACCCCCCAT
66 AAGCTCAATTTCTATTTTCTCTTAGGGTAGTATCGGTACCCCCATAGGGTATCGGTACCCCCCAT
1710955 AGGGTATCGGTACCCCTCATAGGGTATCGATACCC
131 AGGGTATCGGTACCCCTCATAGGGTATCGATACCC
1710990 CCTACATAAT
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
170 116 0.72
171 1 0.01
172 40 0.25
173 5 0.03
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (173 bp):
CATATAATATCCAAATTATTATTCCAAATATCATGACTCGATCCTTAATATCTTAGAACAAAGAA
AAGCTCAATTTCTATTTTCTCTTAGGGTAGTATCGGTACCCCCATAGGGTATCGGTACCCCCCAT
AGGGTATCGGTACCCCTCATAGGGTATCGATACCCTATATAAT
Found at i:1710953 original size:20 final size:20
Alignment explanation
Indices: 1710919--1710991 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
1710909 TCTTAGGGTA
1710919 GTATCGGTA-CCCCCATAGG
1 GTATCGGTACCCCCCATAGG
1710938 GTATCGGTACCCCCCATAGG
1 GTATCGGTACCCCCCATAGG
*
1710958 GTATCGGTACCCCTCATAGG
1 GTATCGGTACCCCCCATAGG
*
1710978 GTATCGATACCCCC
1 GTATCGGTACCCCC
1710992 TACATAATCT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
19 9 0.18
20 41 0.82
ACGTcount: A:0.21, C:0.34, G:0.23, T:0.22
Consensus pattern (20 bp):
GTATCGGTACCCCCCATAGG
Found at i:1713001 original size:12 final size:12
Alignment explanation
Indices: 1712984--1713024 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1712974 ACTATACAAT
1712984 ATGAACAATACC
1 ATGAACAATACC
*
1712996 ATGAACAGTA--
1 ATGAACAATACC
1713006 ATGAACAATACC
1 ATGAACAATACC
*
1713018 GTGAACA
1 ATGAACA
1713025 GTGATGAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.49, C:0.20, G:0.15, T:0.17
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:1713040 original size:22 final size:22
Alignment explanation
Indices: 1712984--1713040 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1712974 ACTATACAAT
*
1712984 ATGAACAATACCATGAACAGTA
1 ATGAACAATACCGTGAACAGTA
*
1713006 ATGAACAATACCGTGAACAGTG
1 ATGAACAATACCGTGAACAGTA
*
1713028 ATGAACAGTACCG
1 ATGAACAATACCG
1713041 AATGCTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (22 bp):
ATGAACAATACCGTGAACAGTA
Found at i:1713095 original size:21 final size:22
Alignment explanation
Indices: 1713062--1713102 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1713052 TTTTCCAGAT
* *
1713062 TGCTGCAGAGGTATCGATACCA
1 TGCTACAGAGGTACCGATACCA
1713084 TGCTACAG-GGTACCGATAC
1 TGCTACAGAGGTACCGATAC
1713103 TCTACTACAG
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:0.24, G:0.27, T:0.22
Consensus pattern (22 bp):
TGCTACAGAGGTACCGATACCA
Found at i:1713664 original size:20 final size:19
Alignment explanation
Indices: 1713622--1713674 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
1713612 TTTTAGGGTA
1713622 GTATCGATACCCCCATAGG
1 GTATCGATACCCCCATAGG
* *
1713641 GTATCGGTACCCCTCATAGT
1 GTATCGATACCCC-CATAGG
1713661 GTATCGATACCCCC
1 GTATCGATACCCCC
1713675 TGCATAATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.25
Consensus pattern (19 bp):
GTATCGATACCCCCATAGG
Found at i:1722147 original size:12 final size:12
Alignment explanation
Indices: 1722130--1722158 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1722120 AGATGAGCCT
1722130 GAGCAGCCCGAG
1 GAGCAGCCCGAG
1722142 GAGCAGCCCGAG
1 GAGCAGCCCGAG
1722154 GAGCA
1 GAGCA
1722159 AGCACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAG
Found at i:1729352 original size:29 final size:29
Alignment explanation
Indices: 1729270--1729353 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 29
1729260 TAAAATATAT
* * *
1729270 AACTTTTAAAAGTTACAAATTTTAGTCCCTA
1 AACTTTCAAAACTTAC--ATTTTAGCCCCTA
* ** * *
1729301 CACTTTTCAAAGTTTATACTTTAGCCCCTA
1 AAC-TTTCAAAACTTACATTTTAGCCCCTA
1729331 AACTTTCAAAACTTACATTTTAG
1 AACTTTCAAAACTTACATTTTAG
1729354 TCACTAGTCC
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
29 16 0.40
30 13 0.32
31 2 0.05
32 9 0.22
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (29 bp):
AACTTTCAAAACTTACATTTTAGCCCCTA
Found at i:1747493 original size:19 final size:19
Alignment explanation
Indices: 1747466--1747504 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1747456 CATGTTCTGA
* *
1747466 TAAATTTAAAAAATTTATT
1 TAAAATTAAAAAATATATT
1747485 TAAAATTAAAAAATATATT
1 TAAAATTAAAAAATATATT
1747504 T
1 T
1747505 TTATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATTAAAAAATATATT
Found at i:1749205 original size:22 final size:22
Alignment explanation
Indices: 1749177--1749232 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1749167 GGATAATTAT
1749177 GTCCCGAAGGACCACTAGATAC
1 GTCCCGAAGGACCACTAGATAC
* *
1749199 GTCCCGAACGACCACTGGATAC
1 GTCCCGAAGGACCACTAGATAC
*
1749221 GTCCCAAAGGAC
1 GTCCCGAAGGAC
1749233 TAATATACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.34, G:0.23, T:0.12
Consensus pattern (22 bp):
GTCCCGAAGGACCACTAGATAC
Found at i:1749635 original size:150 final size:150
Alignment explanation
Indices: 1749364--1749667 Score: 572
Period size: 150 Copynumber: 2.0 Consensus size: 150
1749354 TATGTGTAAC
* * * *
1749364 TATATATTTCATATCATATCACATGTATCACAAGTGCATATGTTCATGTAGATCATTTCATATGT
1 TATATATTTCATATCATATCACATGTATCACAAGCGCATATATTCACGTAGATCATTTCATATGG
1749429 CTTATATCATTCCTCATTTGTTCATGTAAACTCGCATGTCATATCTTGTTCACATATGTTCATAT
66 CTTATATCATTCCTCATTTGTTCATGTAAACTCGCATGTCATATCTTGTTCACATATGTTCATAT
1749494 ATACATCACATAACACATAG
131 ATACATCACATAACACATAG
1749514 TATATATTTCATATCATATCACATGTATCACAAGCGCATATATTCACGTAGATCATTTCATATGG
1 TATATATTTCATATCATATCACATGTATCACAAGCGCATATATTCACGTAGATCATTTCATATGG
1749579 CTTATATCATTCCTCATTTGTTCATGTAAACTCGCATGTCATATCTTGTTCACATATGTTCATAT
66 CTTATATCATTCCTCATTTGTTCATGTAAACTCGCATGTCATATCTTGTTCACATATGTTCATAT
1749644 ATACATCACATAACACATAG
131 ATACATCACATAACACATAG
1749664 TATA
1 TATA
1749668 GCATATAAAC
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (150 bp):
TATATATTTCATATCATATCACATGTATCACAAGCGCATATATTCACGTAGATCATTTCATATGG
CTTATATCATTCCTCATTTGTTCATGTAAACTCGCATGTCATATCTTGTTCACATATGTTCATAT
ATACATCACATAACACATAG
Found at i:1750017 original size:2 final size:2
Alignment explanation
Indices: 1750012--1750037 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1750002 ATATTATTCT
1750012 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
1750038 ACTCATGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1752539 original size:10 final size:10
Alignment explanation
Indices: 1752524--1752563 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1752514 TTTATCACAC
1752524 CAAATTCTCT
1 CAAATTCTCT
1752534 CAAATTCTCT
1 CAAATTCTCT
1752544 -AAATTTCTCT
1 CAAA-TTCTCT
*
1752554 CAAATACTCT
1 CAAATTCTCT
1752564 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1752641 original size:17 final size:18
Alignment explanation
Indices: 1752606--1752646 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1752596 CTATTCTATA
*
1752606 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
1752624 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
1752641 TTTACT
1 TTTACT
1752647 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:1752902 original size:111 final size:111
Alignment explanation
Indices: 1752708--1753040 Score: 567
Period size: 111 Copynumber: 3.0 Consensus size: 111
1752698 TGGAAATCAT
*
1752708 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
1752773 TATTTAGTTAATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1752819 ATATCTCGACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1752884 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAATAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1752930 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * * * *
1752995 TAATTAGTTGATTTATTTAATACACGACTATTATAATAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1753041 TTTTTGCAAT
Statistics
Matches: 209, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 209 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1754575 original size:18 final size:18
Alignment explanation
Indices: 1754552--1754586 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1754542 GCAGCCACCG
*
1754552 CAGCCATTTATGATGCCA
1 CAGCCATATATGATGCCA
1754570 CAGCCATATATGATGCC
1 CAGCCATATATGATGCC
1754587 GCCATTGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (18 bp):
CAGCCATATATGATGCCA
Found at i:1754611 original size:27 final size:27
Alignment explanation
Indices: 1754581--1754637 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1754571 AGCCATATAT
1754581 GATGCCGCCATTGCCTTTTCATTACCA
1 GATGCCGCCATTGCCTTTTCATTACCA
1754608 GATGCCGCCATTGCCTTTTCATTACCA
1 GATGCCGCCATTGCCTTTTCATTACCA
1754635 GAT
1 GAT
1754638 ATCGTCGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.33
Consensus pattern (27 bp):
GATGCCGCCATTGCCTTTTCATTACCA
Found at i:1758324 original size:51 final size:51
Alignment explanation
Indices: 1758222--1758355 Score: 130
Period size: 51 Copynumber: 2.6 Consensus size: 51
1758212 CCCCTACGTG
* * * *
1758222 GCGTATAGCGCGG-AGC-AGGGGGGCGCTATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGTA-CAAGGGGCGCGCTATACTCCACGTGTAACCAAATCA
* * *
1758272 GCGTATAGTGCGGTACAAGGGGTGCGCTATACTCCACGTGGT-GCCAAATCA
1 GCGTATAGCGCGGTACAAGGGGCGCGCTATACTCCACGT-GTAACCAAATCA
* * * *
1758323 GCATATAGCGCGGTTCAGGGGGCGCGCTTTACT
1 GCGTATAGCGCGGTACAAGGGGCGCGCTATACT
1758356 ACTACGGGTG
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
50 13 0.19
51 54 0.78
52 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (51 bp):
GCGTATAGCGCGGTACAAGGGGCGCGCTATACTCCACGTGTAACCAAATCA
Found at i:1759951 original size:12 final size:13
Alignment explanation
Indices: 1759933--1759962 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1759923 TAAAATGCCC
*
1759933 TTAAAAAATTTCT
1 TTAAAAATTTTCT
1759946 TTAAAAATTTTCT
1 TTAAAAATTTTCT
1759959 TTAA
1 TTAA
1759963 TTTGTCATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAAAAATTTTCT
Done.