Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008709.1 Hibiscus syriacus cultivar Beakdansim tig00111758_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: 3030657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 15
Found at i:1534445 original size:20 final size:20
Alignment explanation
Indices: 1534416--1534453 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1534406 TTTCAAAGTA
1534416 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
1534436 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
1534454 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:1534522 original size:45 final size:45
Alignment explanation
Indices: 1534473--1534582 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
1534463 GAACATCGAA
1534473 TGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAG
1 TGCATTTTATGCATCGATGCACA-AGCCATGCATCGATGCACTCAG
* *
1534518 TGCATTTGATGCATCGATGTACAAGCCATGCATCGATGCACTCAG
1 TGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAG
*
1534563 -GC-TATTT-TGAATCGATGCAC
1 TGCAT-TTTATGCATCGATGCAC
1534583 TCTTAGTGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
43 12 0.21
44 5 0.09
45 41 0.71
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (45 bp):
TGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAG
Found at i:1540324 original size:23 final size:22
Alignment explanation
Indices: 1540253--1540334 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
1540243 ACACTTAATA
1540253 GTGCATCGATGCATCCCTTAGAAT
1 GTGCATCGATGCA-CCCTT-GAAT
* * *
1540277 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
1540298 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
1540321 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1540335 AAGGAGATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 14 0.29
22 3 0.06
23 19 0.40
24 12 0.25
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:1543119 original size:45 final size:46
Alignment explanation
Indices: 1543035--1543128 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 46
1543025 CATTTTATGT
* *
1543035 ATCGATGCACATACCATGCATCGATGCACTCAGTGTA-TTTGATAC
1 ATCGATGCACATACCAAGCATCGATGCACTCAGTGTATTTTGAAAC
*
1543080 ATCGATGTACA-AGCCAAGCATCGATGCACTCAG-GATATTTTGAAAC
1 ATCGATGCACATA-CCAAGCATCGATGCACTCAGTG-TATTTTGAAAC
1543126 ATC
1 ATC
1543129 AAATGCATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
44 2 0.05
45 31 0.72
46 10 0.23
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (46 bp):
ATCGATGCACATACCAAGCATCGATGCACTCAGTGTATTTTGAAAC
Found at i:1544934 original size:13 final size:13
Alignment explanation
Indices: 1544912--1544945 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1544902 AAGGGGAGTA
*
1544912 ATTTTCAAAATTG
1 ATTTTCAAAAATG
1544925 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1544937 ATTTTCAAA
1 ATTTTCAAA
1544946 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1545354 original size:64 final size:65
Alignment explanation
Indices: 1545285--1545440 Score: 226
Period size: 65 Copynumber: 2.4 Consensus size: 65
1545275 ACACCCTAAT
* *
1545285 TCGAATGCATTTTGTGTACCGATGCACA-ACCATGCATTGATGCACTCCTGA-TTTTATTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGACTCTT-TTGAAAC
1545348 A
65 A
* *
1545349 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCTTGACTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGACTCTTTTGAAACA
* * *
1545414 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
1545441 CCCAAGTGTA
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 27 0.33
65 52 0.63
66 3 0.04
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGACTCTTTTGAAACA
Found at i:1548547 original size:2 final size:2
Alignment explanation
Indices: 1548540--1548618 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
1548530 ATGTATCGTT
* * *
1548540 AC AC AC AC AC AC AC AC GC GC GC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1548582 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1548619 TATATATATA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.47, C:0.49, G:0.04, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1548623 original size:2 final size:2
Alignment explanation
Indices: 1548618--1548655 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1548608 ACACACACAC
1548618 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
1548656 TCCATACTTA
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:1549265 original size:20 final size:20
Alignment explanation
Indices: 1549240--1549281 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1549230 CATTATTCCG
* *
1549240 TAACCATATACCATAGAAAA
1 TAACCATAAACAATAGAAAA
*
1549260 TAACCATAAACAATAGACAA
1 TAACCATAAACAATAGAAAA
1549280 TA
1 TA
1549282 GCCCAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19
Consensus pattern (20 bp):
TAACCATAAACAATAGAAAA
Found at i:1549378 original size:33 final size:33
Alignment explanation
Indices: 1549341--1549404 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1549331 ACCGTAGTGC
1549341 TAATCCGTATGACACATAAGGTCATGTCCACCA
1 TAATCCGTATGACACATAAGGTCATGTCCACCA
*
1549374 TAATCCGTATGACACATAAGGTCGTGTCCAC
1 TAATCCGTATGACACATAAGGTCATGTCCAC
1549405 TTTCTGTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCATGTCCACCA
Found at i:1554471 original size:73 final size:74
Alignment explanation
Indices: 1554391--1554527 Score: 195
Period size: 74 Copynumber: 1.9 Consensus size: 74
1554381 CGTTAATTGT
* ** *
1554391 AGTTAGATACATGTACCCTATTTCGTTA-GAAGCGGTGCATTCGTGTCTTCTTTCAGTTAAATTT
1 AGTTAGATACATGTACCATATTTCGTTATGAAGCAATGCATTCGTGTCTTCTTTCAATTAAATTT
1554455 ATATTTTTC
66 ATATTTTTC
* * * *
1554464 AGTTAGATATATGTATCATATTTTGTTATGAAGCAATGTATTCGTGTCTTCTTTCAATTAAATT
1 AGTTAGATACATGTACCATATTTCGTTATGAAGCAATGCATTCGTGTCTTCTTTCAATTAAATT
1554528 AAAATTGTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
73 24 0.44
74 31 0.56
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (74 bp):
AGTTAGATACATGTACCATATTTCGTTATGAAGCAATGCATTCGTGTCTTCTTTCAATTAAATTT
ATATTTTTC
Found at i:1560971 original size:20 final size:20
Alignment explanation
Indices: 1560946--1560984 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1560936 TGTACGGATG
1560946 CAGTTTGAATGATCTAATAA
1 CAGTTTGAATGATCTAATAA
*
1560966 CAGTTTGAATGATGTAATA
1 CAGTTTGAATGATCTAATA
1560985 GCAATTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (20 bp):
CAGTTTGAATGATCTAATAA
Found at i:1560992 original size:20 final size:20
Alignment explanation
Indices: 1560949--1560992 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1560939 ACGGATGCAG
*
1560949 TTTGAATGATCTAATAACAG
1 TTTGAATGATCTAATAACAA
* *
1560969 TTTGAATGATGTAATAGCAA
1 TTTGAATGATCTAATAACAA
1560989 TTTG
1 TTTG
1560993 TGTATAAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (20 bp):
TTTGAATGATCTAATAACAA
Found at i:1570283 original size:17 final size:18
Alignment explanation
Indices: 1570260--1570300 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
1570250 CTATATATAT
1570260 TTATATTTT-TCAAAACTA
1 TTATATTTTAT-AAAACTA
1570278 -TATATTTTATAAAACTA
1 TTATATTTTATAAAACTA
1570295 TTATAT
1 TTATAT
1570301 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATATTTTATAAAACTA
Found at i:1570345 original size:45 final size:43
Alignment explanation
Indices: 1570251--1570355 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 43
1570241 AAAGGTATAC
* * *
1570251 TATATATATTTATAT-TTTTCAAAACTATATATTTTATAAAAC
1 TATATATATATATATATATTCAAAACTATATATTTTATAAAAA
* *
1570293 TAT-TATATATATATATATTCCAAACTAT-TATTTACTTTCAAAAA
1 TATATATATATATATATATTCAAAACTATATATTT--TAT-AAAAA
1570337 TATATATATATATATATAT
1 TATATATATATATATATAT
1570356 ATATTTTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
41 15 0.28
42 14 0.26
43 2 0.04
44 7 0.13
45 15 0.28
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (43 bp):
TATATATATATATATATATTCAAAACTATATATTTTATAAAAA
Found at i:1570616 original size:20 final size:20
Alignment explanation
Indices: 1570591--1570683 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1570581 TTTTCCCAAT
1570591 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1570611 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1570631 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1570652 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1570673 TCGCAATGCGA
1 TCGCAATGCGA
1570684 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1570633 original size:41 final size:41
Alignment explanation
Indices: 1570588--1570683 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1570578 CGATTTTCCC
1570588 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1570629 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1570670 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1570684 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1570637 original size:21 final size:20
Alignment explanation
Indices: 1570591--1570683 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1570581 TTTTCCCAAT
*
1570591 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1570611 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1570631 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1570652 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1570673 TCGCAATGCGA
1 TCGCAATGCGA
1570684 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1570696 original size:41 final size:41
Alignment explanation
Indices: 1570610--1570744 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1570600 GAATAAGTAA
* * *
1570610 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1570651 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1570692 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1570733 TTCGCAACGCGA
1 ATCGCAACGCGA
1570745 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1570697 original size:20 final size:20
Alignment explanation
Indices: 1570672--1570766 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1570662 AATTGGGAAA
*
1570672 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1570692 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1570713 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1570733 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1570753 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1570767 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1571267 original size:20 final size:20
Alignment explanation
Indices: 1571242--1571279 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1571232 CGATTCTCTC
1571242 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1571262 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1571280 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1572620 original size:18 final size:18
Alignment explanation
Indices: 1572599--1572643 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1572589 TCCACTTCGG
*
1572599 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1572617 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1572635 GAGCCATCA
1 GAGCCATCA
1572644 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1573170 original size:19 final size:20
Alignment explanation
Indices: 1573116--1573182 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1573106 TAGTTTACTT
* *
1573116 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1573136 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1573156 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1573175 TCGCAACG
1 TCGCAACG
1573183 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1573217 original size:19 final size:18
Alignment explanation
Indices: 1573195--1573243 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1573185 AAAATCGCAA
1573195 TGCGATTTGTGTTTCGCGT
1 TGCGATTT-TGTTTCGCGT
**
1573214 TGCGATTTCATTTCGCGT
1 TGCGATTTTGTTTCGCGT
1573232 TGCGATTTTGTT
1 TGCGATTTTGTT
1573244 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.08, C:0.16, G:0.27, T:0.49
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1573269 original size:19 final size:19
Alignment explanation
Indices: 1573206--1573328 Score: 105
Period size: 20 Copynumber: 6.7 Consensus size: 19
1573196 GCGATTTGTG
1573206 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
1573224 TTTCGCGTTGCGATTTT--
1 TTTCGCGTTGCGATTTTCA
*
1573241 GTT---GTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
1573257 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
1573276 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
1573296 TTTCGCGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
1573315 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
1573329 AAGTAAACTA
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
14 11 0.13
16 2 0.02
17 2 0.02
18 13 0.15
19 28 0.33
20 29 0.34
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1573326 original size:39 final size:37
Alignment explanation
Indices: 1573195--1573328 Score: 111
Period size: 39 Copynumber: 3.6 Consensus size: 37
1573185 AAAATCGCAA
1573195 TGCGATTTGT-GTTTCGCGTTGCGATTTCATTTCGCGT
1 TGCGATTT-TAGTTTCGCGTTGCGATTTCATTTCGCGT
*
1573232 TGCGATTTT-G-TT---GTTGCGATTTTCATTTCGCAT
1 TGCGATTTTAGTTTCGCGTTGCGA-TTTCATTTCGCGT
*** *
1573265 TGCGATAGCCA-TTTCCGCGTTGCGATAGTCATTTCGCGT
1 TGCGAT-TTTAGTTT-CGCGTTGCGAT-TTCATTTCGCGT
*
1573304 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-AGTTTCGCGTTGCGA
1573329 AAGTAAACTA
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
32 7 0.09
33 18 0.24
35 4 0.05
36 2 0.03
37 8 0.11
38 1 0.01
39 33 0.43
40 3 0.04
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (37 bp):
TGCGATTTTAGTTTCGCGTTGCGATTTCATTTCGCGT
Found at i:1575195 original size:14 final size:14
Alignment explanation
Indices: 1575176--1575211 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1575166 ATTGTTTAAT
1575176 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1575190 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1575204 TGATTTGT
1 TGATTTGT
1575212 TTAATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1575350 original size:19 final size:19
Alignment explanation
Indices: 1575328--1575427 Score: 123
Period size: 14 Copynumber: 5.8 Consensus size: 19
1575318 ATCGCAACGA
1575328 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1575347 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1575365 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1575379 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1575398 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1575412 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1575428 TTTTCATTTC
Statistics
Matches: 72, Mismatches: 0, Indels: 20
0.78 0.00 0.22
Matches are distributed among these distances:
14 22 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 19 0.26
19 21 0.29
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1575375 original size:51 final size:52
Alignment explanation
Indices: 1575299--1575415 Score: 182
Period size: 51 Copynumber: 2.3 Consensus size: 52
1575289 AAAACAGACT
***
1575299 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGAAATG-AA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
*
1575350 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
*
1575402 ATCGCAACGAGAAA
1 ATCGCAACGCGAAA
1575416 ATCGCAATGC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 45 0.76
52 14 0.24
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (52 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:1575440 original size:33 final size:33
Alignment explanation
Indices: 1575348--1575427 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
1575338 ATGCGAAATG
1575348 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
1575381 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
1575414 AAATCGCAATGCGA
1 AAATCGCAATGCGA
1575428 TTTTCATTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (33 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGA
Found at i:1575503 original size:20 final size:20
Alignment explanation
Indices: 1575446--1575503 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1575436 TCGCATTGCG
* *
1575446 ATTTTCTCGTTGCGATAACC
1 ATTTTCACGTTGCGATAGCC
*
1575466 ATTTTCGCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
1575486 ATTTTCACGTTGCGATAG
1 ATTTTCACGTTGCGATAG
1575504 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCACGTTGCGATAGCC
Found at i:1575881 original size:14 final size:14
Alignment explanation
Indices: 1575862--1575897 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1575852 ATTGTTTAAT
1575862 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1575876 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1575890 TGATTTGT
1 TGATTTGT
1575898 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1577192 original size:24 final size:24
Alignment explanation
Indices: 1577136--1577194 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
1577126 AGTCAGTATT
* *
1577136 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
1577160 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
1577184 CGAATTTTGAT
1 CGAAATTTGAT
1577195 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:1577386 original size:12 final size:12
Alignment explanation
Indices: 1577369--1577393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1577359 ATATAATCCT
1577369 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1577381 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1577393 G
1 G
1577394 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1579711 original size:19 final size:19
Alignment explanation
Indices: 1579689--1579786 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1579679 GGAAATTACT
1579689 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1579708 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1579722 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1579741 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
1579755 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1579774 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1579787 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.50
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1579731 original size:33 final size:33
Alignment explanation
Indices: 1579689--1579782 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1579679 GGAAATTACT
1579689 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1579722 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1579755 ATCGTAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1579783 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1579964 original size:14 final size:14
Alignment explanation
Indices: 1579945--1579981 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1579935 CATCAATTAA
1579945 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1579959 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1579973 ACAAATCAA
1 ACAAATCAA
1579982 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1581403 original size:21 final size:21
Alignment explanation
Indices: 1581337--1581403 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1581327 GTGAATCGGG
*
1581337 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1581357 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1581379 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1581400 CTCT
1 CTCT
1581404 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1581422 original size:42 final size:41
Alignment explanation
Indices: 1581337--1581459 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1581327 GTGAATCGGG
* * * * *
1581337 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1581379 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1581421 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1581460 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1583524 original size:33 final size:33
Alignment explanation
Indices: 1583467--1583565 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1583457 ACGAGATAAT
*
1583467 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1583501 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1583534 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1583566 GCGAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1583559 original size:19 final size:19
Alignment explanation
Indices: 1583442--1583607 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
1583432 TCTTTTGGTT
* *
1583442 GAAATGAAAATCACAACGA
1 GAAATGAAAATCGCAACGC
*
1583461 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1583481 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1583499 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1583515 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1583533 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1583548 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1583568 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1583587 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1583606 GA
1 GA
1583608 TTTTGGTTTC
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.36
20 44 0.37
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1583636 original size:19 final size:19
Alignment explanation
Indices: 1583603--1583647 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1583593 AAAATCGCAA
**
1583603 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
1583622 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
1583641 TGCGATT
1 TGCGATT
1583648 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1584286 original size:20 final size:20
Alignment explanation
Indices: 1584201--1584294 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1584191 CGCTAAGTAA
*
1584201 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
1584221 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1584241 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1584262 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1584282 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1584295 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1584313 original size:41 final size:41
Alignment explanation
Indices: 1584283--1584378 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
1584273 ATAGTCAGTA
* * *
1584283 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
1584324 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
1584365 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1584379 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:1584327 original size:20 final size:20
Alignment explanation
Indices: 1584283--1584375 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1584273 ATAGTCAGTA
* **
1584283 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1584304 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
1584324 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
1584345 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1584365 TCGCATTGCGA
1 TCGCATTGCGA
1584376 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:1593042 original size:37 final size:37
Alignment explanation
Indices: 1592985--1593089 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1592975 CTTTTTCGTC
*
1592985 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
1593022 TTGCTAGGATTCAAACTCCTAAAAATAGGATATAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1593059 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1593090 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1593646 original size:2 final size:2
Alignment explanation
Indices: 1593626--1593668 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1593616 TTTTTAATAC
* *
1593626 TA TA TT TA T- TA TT 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 TA
1593667 TA
1 TA
1593669 CTTTTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1593943 original size:2 final size:2
Alignment explanation
Indices: 1593936--1593976 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1593926 TTTACTCATT
1593936 TA TA TA 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 TA TA TA T
1593977 TAATATTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1594046 original size:26 final size:29
Alignment explanation
Indices: 1593982--1594047 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 29
1593972 TATATTAATA
*
1593982 TTTCATTTATTTATTTTTCCTTTAATTTT
1 TTTCATTTATTTATTATTCCTTTAATTTT
* * *
1594011 TTTTACTTATTT-TTATT-C-TTCATTTT
1 TTTCATTTATTTATTATTCCTTTAATTTT
1594037 TTTCATTTATT
1 TTTCATTTATT
1594048 CATTTTTTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 16 0.52
27 1 0.03
28 4 0.13
29 10 0.32
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTCATTTATTTATTATTCCTTTAATTTT
Found at i:1594047 original size:20 final size:19
Alignment explanation
Indices: 1594022--1594064 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 19
1594012 TTTACTTATT
1594022 TTTATTCTTCATTTTTTTCA
1 TTTATTCTTCA-TTTTTTCA
1594042 TTTA---TTCATTTTTTCA
1 TTTATTCTTCATTTTTTCA
1594058 TTTATTC
1 TTTATTC
1594065 ATTTTTCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 7
0.74 0.00 0.26
Matches are distributed among these distances:
16 12 0.60
17 4 0.20
20 4 0.20
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTCTTCATTTTTTCA
Found at i:1594051 original size:8 final size:8
Alignment explanation
Indices: 1594038--1594068 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1594028 CTTCATTTTT
1594038 TTCATTTA
1 TTCATTTA
*
1594046 TTCATTTT
1 TTCATTTA
1594054 TTCATTTA
1 TTCATTTA
1594062 TTCATTT
1 TTCATTT
1594069 TTCCCTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (8 bp):
TTCATTTA
Found at i:1594051 original size:17 final size:17
Alignment explanation
Indices: 1594029--1594070 Score: 77
Period size: 16 Copynumber: 2.5 Consensus size: 17
1594019 ATTTTTATTC
1594029 TTCATTTTTTTCATTTA
1 TTCATTTTTTTCATTTA
1594046 TTCA-TTTTTTCATTTA
1 TTCATTTTTTTCATTTA
1594062 TTCATTTTT
1 TTCATTTTT
1594071 CCCTCTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCATTTTTTTCATTTA
Found at i:1598522 original size:31 final size:32
Alignment explanation
Indices: 1598487--1598571 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 32
1598477 AGATCCAATC
1598487 AAGAACAAAAAAGAAAAGAAGAAAA-A-AAACA
1 AAGAA-AAAAAAGAAAAGAAGAAAAGAGAAACA
1598518 AAGAAAAAAAA-ACAAAGAA-AAAAGAGAAACA
1 AAGAAAAAAAAGA-AAAGAAGAAAAGAGAAACA
*
1598549 AA-AGAAAAAAAGAAAAAAAGAAA
1 AAGA-AAAAAAAGAAAAGAAGAAA
1598572 GAACAAAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
29 5 0.11
30 14 0.30
31 24 0.51
32 4 0.09
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (32 bp):
AAGAAAAAAAAGAAAAGAAGAAAAGAGAAACA
Found at i:1598524 original size:9 final size:8
Alignment explanation
Indices: 1598493--1598571 Score: 86
Period size: 9 Copynumber: 9.2 Consensus size: 8
1598483 AATCAAGAAC
1598493 AAAAAAGA
1 AAAAAAGA
*
1598501 AAAGAAGAA
1 AAAAAAG-A
*
1598510 AAAAAACA
1 AAAAAAGA
*
1598518 AAGAAAAAA
1 AA-AAAAGA
1598527 AAACAAAGA
1 AAA-AAAGA
1598536 AAAAAGAGA
1 AAAAA-AGA
1598545 AACAAAAGA
1 AA-AAAAGA
1598554 AAAAAAGA
1 AAAAAAGA
1598562 AAAAAAGA
1 AAAAAAGA
1598570 AA
1 AA
1598572 GAACAAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
8 28 0.46
9 30 0.49
10 3 0.05
ACGTcount: A:0.84, C:0.04, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1598524 original size:26 final size:26
Alignment explanation
Indices: 1598495--1598593 Score: 92
Period size: 27 Copynumber: 3.7 Consensus size: 26
1598485 TCAAGAACAA
* *
1598495 AAAAGAAAAGAAGAAAAAAAACAAAG
1 AAAAGAAAAAAAGAAAAAAAACAAAC
* * *
1598521 AAAAAAAAACAAAGAAAAAAGAGAAAC
1 AAAAGAAAA-AAAGAAAAAAAACAAAC
*
1598548 AAAAGAAAAAAAGAAAAAAAGAAAGAAC
1 AAAAGAAAAAAAGAAAAAAA-ACA-AAC
*
1598576 AAAA-ATCAAAAAGAAAAA
1 AAAAGA-AAAAAAGAAAAA
1598594 GGGACAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
26 18 0.30
27 24 0.40
28 18 0.30
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.01
Consensus pattern (26 bp):
AAAAGAAAAAAAGAAAAAAAACAAAC
Found at i:1598525 original size:14 final size:14
Alignment explanation
Indices: 1598508--1598567 Score: 70
Period size: 13 Copynumber: 4.4 Consensus size: 14
1598498 AGAAAAGAAG
1598508 AAAAAAAACAAAGA
1 AAAAAAAACAAAGA
1598522 AAAAAAAACAAAG-
1 AAAAAAAACAAAGA
* * *
1598535 AAAAAAGAGAAACA
1 AAAAAAAACAAAGA
*
1598549 AAAGAAAA-AAAGA
1 AAAAAAAACAAAGA
1598562 AAAAAA
1 AAAAAA
1598568 GAAAGAACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 19 0.50
14 19 0.50
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAGA
Found at i:1598535 original size:27 final size:27
Alignment explanation
Indices: 1598505--1598594 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
1598495 AAAAGAAAAG
*
1598505 AAGAAAAAAAACAAAGAAAAAAAAACA
1 AAGAAAAAAAAGAAAGAAAAAAAAACA
* * *
1598532 AAGAAAAAAGAGAAACAAAAGAAAA-A
1 AAGAAAAAAAAGAAAGAAAAAAAAACA
* *
1598558 AAG-AAAAAAAGAAAGAACAAAAATCA
1 AAGAAAAAAAAGAAAGAAAAAAAAACA
*
1598584 AA-AAGAAAAAG
1 AAGAAAAAAAAG
1598595 GGACAAAAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
25 16 0.31
26 14 0.27
27 21 0.41
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (27 bp):
AAGAAAAAAAAGAAAGAAAAAAAAACA
Found at i:1598573 original size:31 final size:30
Alignment explanation
Indices: 1598493--1598574 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 30
1598483 AATCAAGAAC
*
1598493 AAAAAAGAAAAGAAGAAA-AAAAACAAAGA
1 AAAAAAGAAAAAAAGAAAGAAAAACAAAGA
* *
1598522 AAAAAA-AACAAAGAAAAAAGAGAAACAAAAGA
1 AAAAAAGAA-AAA-AAGAAAGAAAAAC-AAAGA
1598554 AAAAAAGAAAAAAAGAAAGAA
1 AAAAAAGAAAAAAAGAAAGAA
1598575 CAAAAATCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.05
29 8 0.19
30 5 0.12
31 12 0.28
32 14 0.33
33 2 0.05
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (30 bp):
AAAAAAGAAAAAAAGAAAGAAAAACAAAGA
Found at i:1598577 original size:45 final size:45
Alignment explanation
Indices: 1598491--1598593 Score: 108
Period size: 45 Copynumber: 2.3 Consensus size: 45
1598481 CCAATCAAGA
*
1598491 ACAAAAAAGAAAAGAAGAAAAAAAACAAAGAAAAAAAAACAAAGA
1 ACAAAAAAGAAAAAAAGAAAAAAAACAAAGAAAAAAAAACAAAGA
* *
1598536 A-AAAAGAGAAACAAAAGAAAAAAAGA-AAA-AAAGAAAGAACAAA-A
1 ACAAAAAAGAAA-AAAAGAAAAAAA-ACAAAGAAA-AAAAAACAAAGA
1598580 ATC-AAAAAGAAAAA
1 A-CAAAAAAGAAAAA
1598594 GGGACAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
44 16 0.33
45 32 0.65
46 1 0.02
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.01
Consensus pattern (45 bp):
ACAAAAAAGAAAAAAAGAAAAAAAACAAAGAAAAAAAAACAAAGA
Found at i:1599272 original size:22 final size:22
Alignment explanation
Indices: 1599199--1599272 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
1599189 GCTACCCCAT
* *
1599199 CAAACCGTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
1599221 CAAACC-TTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1599242 CAAACCTTTGAGCATCAAATAC
1 CAAACCTTTGAGCATCAAATGC
1599264 CAAACCTTT
1 CAAACCTTT
1599273 ACCAAACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.41
22 29 0.59
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:1600303 original size:106 final size:106
Alignment explanation
Indices: 1600100--1601580 Score: 2181
Period size: 106 Copynumber: 14.0 Consensus size: 106
1600090 ATATCGTGCC
* * * * * * * * *
1600100 ACTCAAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTATCAA-CAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
**
1600164 AATTTTGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1600205 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
1600270 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1600311 ACTTCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1600376 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1600417 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
1600482 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1600523 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1600588 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1600629 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1600694 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1600735 ACTCCATACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
1600800 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1600841 ACTCCATACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
1600906 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1600947 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAAAAACTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
1601012 AATTTCAGAGCCAATTTCAACTTCACGGAGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1601053 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * * *
1601118 AATTTTAGAGCTAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1601159 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
1601224 AATTTCAGAGCCAATTTCAACTTCACAACGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1601265 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * * * *
1601330 AATTTTAGAGCCAATTTTAACTTCTCAGCGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
1601371 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAA-CAA-AA-TT-T
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCC
*
1601431 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
1601471 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-TGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAACTTCC
** * *
1601535 CGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1601577 ACTC
1 ACTC
1601581 AGAACAATGC
Statistics
Matches: 1252, Mismatches: 113, Indels: 21
0.90 0.08 0.02
Matches are distributed among these distances:
99 1 0.00
100 73 0.06
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 50 0.04
106 1114 0.89
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1602364 original size:37 final size:37
Alignment explanation
Indices: 1602311--1602407 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
1602301 CCTTTTCGTC
1602311 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* * *
1602348 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
* *
1602385 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
1602408 GATAGGATCC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:1602979 original size:23 final size:23
Alignment explanation
Indices: 1602885--1602980 Score: 69
Period size: 23 Copynumber: 4.3 Consensus size: 23
1602875 TTTTTTACAC
*
1602885 TATATA-TTATTA-TTATATATG
1 TATATATTTATTATTTATATATA
* *
1602906 CATATATTTTTTATTTAT-T-TA
1 TATATATTTATTATTTATATATA
* * *
1602927 TAT-TCATTTGGTTATTTTTTTA-A
1 TATAT-ATTT-ATTATTTATATATA
1602950 TACTATATTTATTATTTATATATA
1 TA-TATATTTATTATTTATATATA
1602974 TATATAT
1 TATATAT
1602981 ATATACTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
20 1 0.02
21 12 0.21
22 13 0.23
23 22 0.39
24 8 0.14
25 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (23 bp):
TATATATTTATTATTTATATATA
Found at i:1603200 original size:33 final size:31
Alignment explanation
Indices: 1603119--1603207 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 31
1603109 TATAAACCAA
*
1603119 TTATCATTATATGTATACTTTTATATTTGGTTT
1 TTAT-ATTATAT-TATATTTTTATATTTGGTTT
* *
1603152 ATATATT-TATT-TATTTTTATTTTTGGTTTTT
1 TTATATTATATTATATTTTTATATTTGG--TTT
*
1603183 TTATATTATATTATATTTTCATATT
1 TTATATTATATTATATTTTTATATT
1603208 ACTATTATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 13 0.28
30 1 0.02
31 12 0.26
32 7 0.15
33 13 0.28
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.66
Consensus pattern (31 bp):
TTATATTATATTATATTTTTATATTTGGTTT
Found at i:1603206 original size:18 final size:19
Alignment explanation
Indices: 1603180--1603215 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1603170 ATTTTTGGTT
*
1603180 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
1603198 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
1603216 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:1603259 original size:2 final size:2
Alignment explanation
Indices: 1603252--1603282 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1603242 TTTACTCATT
1603252 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 T
1603283 TAATATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1603299 original size:4 final size:4
Alignment explanation
Indices: 1603286--1603335 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
1603276 TATATATTAA
*
1603286 TATT TCATT TATT TATT TATT TATT T-TT CCT-TT TATT TTTT TATT TATT
1 TATT T-ATT TATT TATT TATT TATT TATT --TATT TATT TATT TATT TATT
1603335 T
1 T
1603336 TTATTCTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 3 0.08
4 30 0.75
5 7 0.17
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1603336 original size:12 final size:12
Alignment explanation
Indices: 1603292--1603360 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
1603282 TTAATATTTC
*
1603292 ATTTATTTATTT
1 ATTTATTTTTTT
*
1603304 ATTTATTTTTCCT
1 ATTTATTTTT-TT
1603317 -TTTATTTTTTT
1 ATTTATTTTTTT
1603328 ATTTATTTTTATT
1 ATTTATTTTT-TT
* * *
1603341 CTTCATTTTTTC
1 ATTTATTTTTTT
1603353 ATTT-TTTT
1 ATTTATTTT
1603361 CATTTTTTCC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
11 5 0.11
12 30 0.65
13 11 0.24
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:1603349 original size:24 final size:26
Alignment explanation
Indices: 1603288--1603360 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 26
1603278 TATATTAATA
*
1603288 TTTCATTTATTTATTTATTTATTTTTCC
1 TTTCATTT-TTTATTTATTT-TTATTCC
*
1603316 TTTTATTTTTTTATTTATTTTTATT-C
1 TTTCA-TTTTTTATTTATTTTTATTCC
1603342 -TTCATTTTTTCATTT-TTTT
1 TTTCATTTTTT-ATTTATTTT
1603361 CATTTTTTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 10 0.25
25 7 0.17
26 1 0.03
27 4 0.10
28 15 0.38
29 3 0.08
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTCATTTTTTATTTATTTTTATTCC
Found at i:1604080 original size:24 final size:23
Alignment explanation
Indices: 1604046--1604099 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1604036 AAAAGTAATT
*
1604046 AAATTATTATTCA-TATATTTTATA
1 AAATTAATATT-AGTATATTTTA-A
*
1604070 AAATTAATATTAGTTTATTTTAA
1 AAATTAATATTAGTATATTTTAA
1604093 AAATTAA
1 AAATTAA
1604100 ATGTATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATTAATATTAGTATATTTTAA
Found at i:1604154 original size:14 final size:15
Alignment explanation
Indices: 1604128--1604160 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1604118 TAAATAATAA
1604128 TTAAATATATTTAAC
1 TTAAATATATTTAAC
*
1604143 TTAAAT-TATTTAAT
1 TTAAATATATTTAAC
1604157 TTAA
1 TTAA
1604161 TAACGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAATATATTTAAC
Found at i:1604212 original size:24 final size:24
Alignment explanation
Indices: 1604185--1604236 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1604175 TTAGTATAAC
*
1604185 TATAAAATTATTATTTA-TATATTT
1 TATAAAATTAATA-TTAGTATATTT
*
1604209 TATAAAATTAATATTAGTTTATTT
1 TATAAAATTAATATTAGTATATTT
1604233 TATA
1 TATA
1604237 CGTTTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATAAAATTAATATTAGTATATTT
Found at i:1610779 original size:3 final size:3
Alignment explanation
Indices: 1610766--1610826 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
1610756 AATTAATTAA
*
1610766 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- AAT AAT AGA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
1610812 AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT
1610827 TATCTAACCT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 5 0.10
3 44 0.88
4 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1612257 original size:18 final size:17
Alignment explanation
Indices: 1612234--1612267 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1612224 TAACATTATA
1612234 TATCATATAATATATATG
1 TATCATATAAT-TATATG
1612252 TATCATATAATTATAT
1 TATCATATAATTATAT
1612268 AATTATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
TATCATATAATTATATG
Found at i:1612785 original size:84 final size:84
Alignment explanation
Indices: 1612665--1614014 Score: 1326
Period size: 84 Copynumber: 16.3 Consensus size: 84
1612655 GCTCGACAAT
* * * * * * *
1612665 TTTA-TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGTCTTGGAGCTGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1612729 GTAGTCAAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* *
1612748 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1612813 GTAGTCAAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * * ** * *
1612832 TTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAG
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAG
* *
1612897 TGTAATCGAACTCG-AGG-G
65 CGTAATCGAACTCGAAGGTC
* * * *
1612915 TGT--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCTTGGAGCTGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1612978 GTAGTCGAACTCAAAGGTC
66 GTAATCGAACTCGAAGGTC
*
1612997 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1613062 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * ** * * * * * * * *
1613081 TTTTGGTCACATATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAG
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAG
* * *
1613146 TGTAATTGAACTCGAGGGTC
65 CGTAATCGAACTCGAAGGTC
* *
1613166 TTTA----GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1613227 ATAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * *
1613246 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGTCTTGGAGCTGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1613311 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * *** * * * * * * *
1613330 TTTTGGTCAAAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAG
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAG
* *
1613395 TGTAATTGAACTCG-AGGTC
65 CGTAATCGAACTCGAAGGTC
* * * * * *
1613414 TTTA----GCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTACCTTAGAGATGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* * *
1613475 ATAGTCGAACTCGAAGGTT
66 GTAATCGAACTCGAAGGTC
* * *
1613494 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATAATGTGCCTTGGAGCTGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1613559 GTAATCGAACTCGAATGTAT
66 GTAATCGAACTCGAAGGT-C
* * * * * * * * *
1613579 TTTAG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAACTGAG
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAG
* * *
1613643 TGTAATCGAATTCGAGGGTC
65 CGTAATCGAACTCGAAGGTC
* * * * *
1613663 --T--TTGGCAGATAGCCCTTCTCGACTTAAGCTGTGCTGTAAATGATGTACCTTGGAGCTGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
**
1613724 GTAATCGAACTCGAATATC
66 GTAATCGAACTCGAAGGTC
* * * * *
1613743 TTTGGTTGGCAGATAACCATTCTCGACTTAAGTTATACTGTAAATGATATGCCTTGGAGCTGAGC
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1613808 GTAGTCGAACTCGAAAGTC
66 GTAATCGAACTCGAAGGTC
* * * * * * * *
1613827 TTTTAG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTTA
1 -TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGA
* *
1613891 GTGTAATCGAACTCGAGGGTC
64 GCGTAATCGAACTCGAAGGTC
* * * * *
1613912 --T--CTGGCAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTGTCTTGGAGCTGAGT
1 TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
1613973 GTAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * *
1613992 TTTGGTTGGTAGATAGCCCTTCT
1 TTTAGTTGGCAGATAACCCTTCT
1614015 AACATTGAGT
Statistics
Matches: 1028, Mismatches: 208, Indels: 61
0.79 0.16 0.05
Matches are distributed among these distances:
79 19 0.02
80 141 0.14
81 148 0.14
82 6 0.01
83 6 0.01
84 573 0.56
85 135 0.13
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
TTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAATCGAACTCGAAGGTC
Found at i:1613127 original size:249 final size:249
Alignment explanation
Indices: 1612673--1614014 Score: 2110
Period size: 249 Copynumber: 5.4 Consensus size: 249
1612663 ATTTTATTGA
* * * * * * *
1612673 CAGATAACCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTCAAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
1612738 CTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATATGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* *
1612803 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
131 GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
* *
1612868 GCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTGTTTGG
196 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
*
1612922 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
1612987 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* *
1613052 GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTCACATATAACCCTTCTAGCCTTGAGTTAT
131 GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
* * *
1613117 ACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGAGGGTCTTTAG
196 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
*
1613171 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
1613236 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGTCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* * *
1613301 GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTCAAAGATAACTCTTCTAGCCTTGAGTTAT
131 GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
* *
1613366 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGA-GGTCTTTAG
196 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * * *
1613419 CAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTACCTTAGAGATGAGCATAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
1613484 CTCGAAGGTTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATAATGTGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* * *
1613549 GGAGCTGAGCGTAATCGAACTCGAATGTATTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTAT
131 GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
* * *
1613614 GTTGTAAATGATGTGCCCTCGAAACTGAGTGTAATCGAATTCGAGGGTCTTTGG
196 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * *
1613668 CAGATAGCCCTTCTCGACTTAAGCTGTGCTGTAAATGATGTACCTTGGAGCTGAGCGTAATCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
** * * * *
1613733 CTCGAATATCTTTGGTTGGCAGATAACCATTCTCGACTTAAGTTATACTGTAAATGATATGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* * *
1613798 GGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTAT
131 GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
* *
1613863 GCTGTAAATGATGTGCCCTCGAAGCTTAGTGTAATCGAACTCGAGGGTCTCTGG
196 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * *
1613917 CAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTGTCTTGGAGCTGAGTGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
1613982 CTCGAAGGTCTTTGGTTGGTAGATAGCCCTTCT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1614015 AACATTGAGT
Statistics
Matches: 1010, Mismatches: 82, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
248 231 0.23
249 779 0.77
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (249 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
Found at i:1616685 original size:345 final size:345
Alignment explanation
Indices: 1616054--1616743 Score: 1353
Period size: 345 Copynumber: 2.0 Consensus size: 345
1616044 TTCATGGATT
1616054 TCTCTAGATATGGTGACACCACATGTGCGCCAAACAATTGTTGGTAAAGCTCCTTATATGTCATA
1 TCTCTAGATATGGTGACACCACATGTGCGCCAAACAATTGTTGGTAAAGCTCCTTATATGTCATA
1616119 GGATCGAAATGTTTTTATTTTCTATGAGACATGTGAATGTAATGAAAAAAAGAGAAAAATAATGC
66 GGATCGAAATGTTTTTATTTTCTATGAGACATGTGAATGTAATGAAAAAAAGAGAAAAATAATGC
*
1616184 GAAATATGCAGGAATGCATGATGCATGCAACGTTCGAGGCATTGATCCGAAAAATGTGTCTGCTA
131 GAAATATACAGGAATGCATGATGCATGCAACGTTCGAGGCATTGATCCGAAAAATGTGTCTGCTA
1616249 TTAGAAATAATCCTTATTGGAGACAAAAGTGTTTTATCTTTTAAGAGACAAAAATATCCTGACAA
196 TTAGAAATAATCCTTATTGGAGACAAAAGTGTTTTATCTTTTAAGAGACAAAAATATCCTGACAA
*
1616314 CTTCTGATATGTTGACTAGTCTTCTAACTTCTTTTGTTACTGGTTGAACATCCTGTCGAACCGCT
261 CTTCTGATATGTTGACTAGTCTTCTAACTTCTTTTGTTACCGGTTGAACATCCTGTCGAACCGCT
1616379 CTGGCTTCTCTGGATGAACC
326 CTGGCTTCTCTGGATGAACC
1616399 TCTCTAGATATGGTGACACCACATGTGCGCCAAACAATTGTTGGTAAAGCTCCTTATATGTCATA
1 TCTCTAGATATGGTGACACCACATGTGCGCCAAACAATTGTTGGTAAAGCTCCTTATATGTCATA
1616464 GGATCGAAATGTTTTTATTTTCTATGAGACATGTGAATGTAATGAAAAAAAGAGAAAAATAATGC
66 GGATCGAAATGTTTTTATTTTCTATGAGACATGTGAATGTAATGAAAAAAAGAGAAAAATAATGC
1616529 GAAATATACAGGAATGCATGATGCATGCAACGTTCGAGGCATTGATCCGAAAAATGTGTCTGCTA
131 GAAATATACAGGAATGCATGATGCATGCAACGTTCGAGGCATTGATCCGAAAAATGTGTCTGCTA
*
1616594 TTAGAAATAATCCTTATTGGAGACAAAAGTGTTTTATCTTTTAAGAGAGAAAAATATCCTGACAA
196 TTAGAAATAATCCTTATTGGAGACAAAAGTGTTTTATCTTTTAAGAGACAAAAATATCCTGACAA
1616659 CTTCTGATATGTTGACTAGTCTTCTAACTTCTTTTGTTACCGGTTGAACATCCTGTCGAACCGCT
261 CTTCTGATATGTTGACTAGTCTTCTAACTTCTTTTGTTACCGGTTGAACATCCTGTCGAACCGCT
1616724 CTGGCTTCTCTGGATGAACC
326 CTGGCTTCTCTGGATGAACC
1616744 GTGAAAATGC
Statistics
Matches: 342, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
345 342 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (345 bp):
TCTCTAGATATGGTGACACCACATGTGCGCCAAACAATTGTTGGTAAAGCTCCTTATATGTCATA
GGATCGAAATGTTTTTATTTTCTATGAGACATGTGAATGTAATGAAAAAAAGAGAAAAATAATGC
GAAATATACAGGAATGCATGATGCATGCAACGTTCGAGGCATTGATCCGAAAAATGTGTCTGCTA
TTAGAAATAATCCTTATTGGAGACAAAAGTGTTTTATCTTTTAAGAGACAAAAATATCCTGACAA
CTTCTGATATGTTGACTAGTCTTCTAACTTCTTTTGTTACCGGTTGAACATCCTGTCGAACCGCT
CTGGCTTCTCTGGATGAACC
Found at i:1617332 original size:14 final size:14
Alignment explanation
Indices: 1617306--1617339 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1617296 TTAGTAAGGT
1617306 AAATCAAAATAAAA
1 AAATCAAAATAAAA
1617320 AAAT-AAAAGTAAAA
1 AAATCAAAA-TAAAA
1617334 AAATCA
1 AAATCA
1617340 TACCACACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 13 0.72
15 1 0.06
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (14 bp):
AAATCAAAATAAAA
Found at i:1618372 original size:3 final size:3
Alignment explanation
Indices: 1618359--1618410 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
1618349 AATTAATTAA
*
1618359 AAT AGT AAT AAT AAT AAT AAT AA- AAT AA- AAT AAT AGA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
*
1618402 AAT ACT AAT
1 AAT AAT AAT
1618411 TGTCTAACCT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 5 0.12
3 35 0.85
4 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1619841 original size:18 final size:17
Alignment explanation
Indices: 1619818--1619851 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1619808 TAACATTATA
1619818 TATCATATAATATATATG
1 TATCATATAAT-TATATG
1619836 TATCATATAATTATAT
1 TATCATATAATTATAT
1619852 AATTATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
TATCATATAATTATATG
Found at i:1624539 original size:20 final size:18
Alignment explanation
Indices: 1624496--1624556 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
1624486 AGATCGTCAA
*
1624496 TATTTTTTATTGTATTTT
1 TATTTTTTATTGTATCTT
*
1624514 TCTTTTTTATATCGTATCTT
1 TATTTTTTAT-T-GTATCTT
*
1624534 TATTTTCTT-TTGT-TTTT
1 TATTTT-TTATTGTATCTT
1624551 TATTTT
1 TATTTT
1624557 CAATAAGTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 9 0.25
18 11 0.31
19 2 0.06
20 12 0.33
21 2 0.06
ACGTcount: A:0.13, C:0.07, G:0.05, T:0.75
Consensus pattern (18 bp):
TATTTTTTATTGTATCTT
Found at i:1629037 original size:20 final size:21
Alignment explanation
Indices: 1629008--1629051 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1628998 CTCAAAATCA
*
1629008 TTTTTCAAAATTTC-ATTTTGC
1 TTTTTCAAAA-TCCAATTTTGC
1629029 TTTTT-AAAATCCAATTTTGC
1 TTTTTCAAAATCCAATTTTGC
1629049 TTT
1 TTT
1629052 CAGAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 14 0.67
21 5 0.24
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTTCAAAATCCAATTTTGC
Found at i:1636729 original size:15 final size:15
Alignment explanation
Indices: 1636705--1636737 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1636695 TGGTAGATCC
*
1636705 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
1636720 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
1636735 AAA
1 AAA
1636738 AAAGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.15, G:0.24, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:1640049 original size:12 final size:12
Alignment explanation
Indices: 1640032--1640058 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1640022 TAAATTTCTT
1640032 CAAATTGGACGG
1 CAAATTGGACGG
1640044 CAAATTGGACGG
1 CAAATTGGACGG
1640056 CAA
1 CAA
1640059 TTTTGAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.15
Consensus pattern (12 bp):
CAAATTGGACGG
Found at i:1649594 original size:27 final size:27
Alignment explanation
Indices: 1649546--1649600 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1649536 AATCAAGTAC
* *
1649546 CCGAATTTGAATACCCCAACTAGGGGA
1 CCGAATTTGAACACACCAACTAGGGGA
* * *
1649573 CCGAATTTGAACGCACCTACTAGTGGA
1 CCGAATTTGAACACACCAACTAGGGGA
1649600 C
1 C
1649601 GAGCCTTTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (27 bp):
CCGAATTTGAACACACCAACTAGGGGA
Found at i:1649902 original size:13 final size:13
Alignment explanation
Indices: 1649884--1649926 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 13
1649874 ATATAAATTA
1649884 AAATTAAATATTT
1 AAATTAAATATTT
1649897 AAATTATGAATATATAT
1 AAATTA--AATAT-T-T
1649914 AAATTAAATATTT
1 AAATTAAATATTT
1649927 TTATATTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 7 0.27
14 1 0.04
15 10 0.38
16 1 0.04
17 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
AAATTAAATATTT
Found at i:1650207 original size:2 final size:2
Alignment explanation
Indices: 1650200--1650226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1650190 CAACTTAAAT
1650200 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
1650227 CTCGAATTGA
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:1651076 original size:2 final size:2
Alignment explanation
Indices: 1651071--1651111 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1651061 CCTAGCCAAG
1651071 AT AT AT AT 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 AT AT AT AT A
1651112 ATAACAACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1659148 original size:56 final size:54
Alignment explanation
Indices: 1659033--1659157 Score: 124
Period size: 54 Copynumber: 2.3 Consensus size: 54
1659023 ATAGCATTTA
* * * * *** *
1659033 AATTATATATGAATTATATCAATTTAAACTATAATCAATTTTTTTAATAAATAT
1 AATTATATATAAATTAGATCAATTTAAACTATAATAAATATAAATAAAAAATAT
* *
1659087 TATTATATATAAATTAGATCAATTTAAATTATAATAAAAATATAAATAAAAAATAT
1 AATTATATATAAATTAGATCAATTTAAACTATAAT--AAATATAAATAAAAAATAT
*
1659143 AATTATCATAAAAAT
1 AATTAT-ATATAAAT
1659158 GTATTTTAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
54 31 0.55
56 18 0.32
57 7 0.12
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (54 bp):
AATTATATATAAATTAGATCAATTTAAACTATAATAAATATAAATAAAAAATAT
Found at i:1664752 original size:63 final size:63
Alignment explanation
Indices: 1664649--1664777 Score: 213
Period size: 63 Copynumber: 2.0 Consensus size: 63
1664639 ACACGAGAAG
* *
1664649 CATTGCCATTTCGGGATCGTGCAACAGCTCGAACATGAACAGCAGCTGCATGAGCTGCACTTA
1 CATTGACATTTCGGGATCGTGCAACAGCTCGAACACGAACAGCAGCTGCATGAGCTGCACTTA
* * *
1664712 CATTGACATTTCGGGATTGTGCAACAGCTTGAACACGAACAGCAGTTGCATGAGCTGCACTTA
1 CATTGACATTTCGGGATCGTGCAACAGCTCGAACACGAACAGCAGCTGCATGAGCTGCACTTA
1664775 CAT
1 CAT
1664778 CGTGATTTCG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (63 bp):
CATTGACATTTCGGGATCGTGCAACAGCTCGAACACGAACAGCAGCTGCATGAGCTGCACTTA
Found at i:1664846 original size:45 final size:45
Alignment explanation
Indices: 1664745--1664834 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
1664735 ACAGCTTGAA
*
1664745 CACGAACAGCAGTTGCATGAGCTGCACTTACATCGTGATTTCGGG
1 CACGAACAGCAGTCGCATGAGCTGCACTTACATCGTGATTTCGGG
*
1664790 CACGAACAGCAGTCGCTTGAGCTGCACTTACATCGTGATTTCGGG
1 CACGAACAGCAGTCGCATGAGCTGCACTTACATCGTGATTTCGGG
1664835 ATTGGCCAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.23, C:0.26, G:0.27, T:0.24
Consensus pattern (45 bp):
CACGAACAGCAGTCGCATGAGCTGCACTTACATCGTGATTTCGGG
Found at i:1664877 original size:108 final size:108
Alignment explanation
Indices: 1664685--1664884 Score: 287
Period size: 108 Copynumber: 1.9 Consensus size: 108
1664675 GCTCGAACAT
*
1664685 GAACAGCAGCTGCATGAGCTGCACTTACATTGACATTTCGGGATTGTGCAACAGCTTGAACACGA
1 GAACAGCAGCTGCATGAGCTGCACTTACATCGACATTTCGGGATTGTGCAACAGCTTGAACACGA
* *
1664750 ACAGCAGTTGCATGAGCTGCACTTACATCGTGATTTCGGGCAC
66 ACAGCAGTCGCAAGAGCTGCACTTACATCGTGATTTCGGGCAC
* ** * *
1664793 GAACAGCAG-TCGCTTGAGCTGCACTTACATCGTGATTTCGGGATTG-GCCAGCAGCTTGAACAT
1 GAACAGCAGCT-GCATGAGCTGCACTTACATCGACATTTCGGGATTGTG-CAACAGCTTGAACAC
*
1664856 GAACAGCAGTCGCAAGTGCTGCACTTACA
64 GAACAGCAGTCGCAAGAGCTGCACTTACA
1664885 CGAACTGCAG
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 2 0.02
108 79 0.98
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (108 bp):
GAACAGCAGCTGCATGAGCTGCACTTACATCGACATTTCGGGATTGTGCAACAGCTTGAACACGA
ACAGCAGTCGCAAGAGCTGCACTTACATCGTGATTTCGGGCAC
Found at i:1667359 original size:17 final size:18
Alignment explanation
Indices: 1667326--1667359 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1667316 CCGTTTTTAG
1667326 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
1667344 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
1667360 GACCGGCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:1668060 original size:22 final size:21
Alignment explanation
Indices: 1668035--1668075 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1668025 TATAAAAAAT
1668035 TATTTTTATTAAATATTTTTGA
1 TATTTTTATTAAAT-TTTTTGA
*
1668057 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
1668076 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:1679123 original size:36 final size:36
Alignment explanation
Indices: 1679072--1679146 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
1679062 CATCGTCGGG
* *
1679072 AAGCTCGTAGAATTTTGGATGCTAATTTAAATTACA
1 AAGCTCGTAGAATTTTGAAAGCTAATTTAAATTACA
*
1679108 AAGCTCGTAGGATTTTGAAAGCTAATTTAAATTACA
1 AAGCTCGTAGAATTTTGAAAGCTAATTTAAATTACA
1679144 AAG
1 AAG
1679147 TGTGTTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (36 bp):
AAGCTCGTAGAATTTTGAAAGCTAATTTAAATTACA
Found at i:1683888 original size:34 final size:30
Alignment explanation
Indices: 1683850--1683918 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
1683840 TTGATATAAC
1683850 AATTTAAGGCAAAATAGCTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GCTTTTGGACTT-AATTG
*
1683884 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGCTTTTGGACTTAATTG
1683913 AATTTA
1 AATTTA
1683919 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGCTTTTGGACTTAATTG
Found at i:1683929 original size:29 final size:30
Alignment explanation
Indices: 1683859--1683918 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1683849 CAATTTAAGG
*
1683859 CAAAATAGCTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1683890 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1683919 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1684024 original size:21 final size:19
Alignment explanation
Indices: 1683998--1684095 Score: 106
Period size: 21 Copynumber: 4.8 Consensus size: 19
1683988 AGGGTGTCAA
1683998 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA--CCTGC
1684019 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA--CCTGC
*
1684040 AGTGCATCAATGCACCTGCAC
1 AGTGCATCCATGCACCTG--C
* *
1684061 TAGTGCATCGATGCACATGC
1 -AGTGCATCCATGCACCTGC
1684081 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1684096 TCAAACACCG
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
19 18 0.26
20 1 0.01
21 34 0.49
22 16 0.23
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.21
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGC
Found at i:1684068 original size:22 final size:22
Alignment explanation
Indices: 1684040--1684081 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1684030 GCATCCCTGC
*
1684040 AGTGCATCAATGCACCTGCACT
1 AGTGCATCAATGCACATGCACT
*
1684062 AGTGCATCGATGCACATGCA
1 AGTGCATCAATGCACATGCA
1684082 GTGCATCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (22 bp):
AGTGCATCAATGCACATGCACT
Found at i:1684161 original size:21 final size:21
Alignment explanation
Indices: 1684135--1684177 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1684125 TGCATCCTTT
*
1684135 TGTGCATCGATGCATC-AAGGC
1 TGTGCATCCATGCA-CGAAGGC
1684156 TGTGCATCCATGCACGAAGGC
1 TGTGCATCCATGCACGAAGGC
1684177 T
1 T
1684178 ATAACAGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (21 bp):
TGTGCATCCATGCACGAAGGC
Found at i:1684310 original size:20 final size:22
Alignment explanation
Indices: 1684272--1684311 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1684262 TTTGAGTAGA
1684272 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1684294 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1684312 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1686330 original size:25 final size:24
Alignment explanation
Indices: 1686277--1686330 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
1686267 ATATGCACTT
1686277 AATTTTAACAAATGGTATTGATATC
1 AATTTTAACAAATGGTATTGATA-C
*
1686302 AATTTTCAACAATTGGTATTGCATA-
1 AATTTT-AACAAATGGTATTG-ATAC
1686327 AATT
1 AATT
1686331 ATTTTAGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 10 0.38
26 13 0.50
27 3 0.12
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (24 bp):
AATTTTAACAAATGGTATTGATAC
Found at i:1686981 original size:20 final size:22
Alignment explanation
Indices: 1686911--1686988 Score: 85
Period size: 21 Copynumber: 3.7 Consensus size: 22
1686901 AGGGTGTCAA
*
1686911 AGTGCATCCATGCATCCCT--AC
1 AGTGCATCCATGCA-CCATGCAC
1686932 AGTGCATCCATGCA-CATGCAC
1 AGTGCATCCATGCACCATGCAC
*
1686953 TAGTGCATCGATGCACCATGCA-
1 -AGTGCATCCATGCACCATGCAC
1686975 A-TGCATCCATGCAC
1 AGTGCATCCATGCAC
1686989 TCAAACACCA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
19 2 0.04
20 12 0.24
21 17 0.34
22 13 0.26
23 6 0.12
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (22 bp):
AGTGCATCCATGCACCATGCAC
Found at i:1687457 original size:34 final size:32
Alignment explanation
Indices: 1687418--1687487 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1687408 TTTTGTAAAG
* *
1687418 GGGAAAGGTTCTAGCTTATCTCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTATCCCG-G-AAAAACTA
*
1687452 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTATCCCGGAAAAACTA
1687484 GGGA
1 GGGA
1687488 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTATCCCGGAAAAACTA
Found at i:1689368 original size:35 final size:35
Alignment explanation
Indices: 1689323--1689398 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
1689313 GTCATGTTCA
1689323 AAATTACAAAACACTTCAATTACATTCTAAACCCT
1 AAATTACAAAACACTTCAATTACATTCTAAACCCT
* * * **
1689358 AAATTCCAAAATACTTTAATTGTATTCTAAACCCT
1 AAATTACAAAACACTTCAATTACATTCTAAACCCT
1689393 AAATTA
1 AAATTA
1689399 AAGTATTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (35 bp):
AAATTACAAAACACTTCAATTACATTCTAAACCCT
Found at i:1689433 original size:35 final size:36
Alignment explanation
Indices: 1689393--1689468 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1689383 TCTAAACCCT
1689393 AAATTAAAGTA-TTTTAAAATTTAGAGTTTAAAATA
1 AAATTAAAGTATTTTTAAAATTTAGAGTTTAAAATA
* * * * *
1689428 TAATTAAATTATTTTTGAAATTTAGGGTTTAGAATA
1 AAATTAAAGTATTTTTAAAATTTAGAGTTTAAAATA
1689464 AAATT
1 AAATT
1689469 GAGGACTGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 9 0.26
36 25 0.74
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (36 bp):
AAATTAAAGTATTTTTAAAATTTAGAGTTTAAAATA
Found at i:1690048 original size:60 final size:60
Alignment explanation
Indices: 1689954--1690128 Score: 194
Period size: 60 Copynumber: 2.9 Consensus size: 60
1689944 ATAGTTGGGT
* * * * * *
1689954 GACCATTTTATAACTTTTAATAGT-TAGAGAACTCAATAAAGCAATATCCTATAGTCGA-A
1 GACCATTTTGTAACTTTTGATAGTCGA-AGGACTCAACAAAGCAATATCCTATAATCGAGA
* * * *
1690013 GGTCCATTTTGTAACTTTTGATAGTCGAAGGACTCAACAAAGCAACATTCTATAATCGTGA
1 -GACCATTTTGTAACTTTTGATAGTCGAAGGACTCAACAAAGCAATATCCTATAATCGAGA
* *
1690074 GACTATTTTGTAACTTTTGATAGTCGAATGACTCAACAAAGC-ATCATCCTATAAT
1 GACCATTTTGTAACTTTTGATAGTCGAAGGACTCAACAAAGCAAT-ATCCTATAAT
1690129 TAGGTGACCA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 94 0.97
61 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTGATAGTCGAAGGACTCAACAAAGCAATATCCTATAATCGAGA
Found at i:1695707 original size:23 final size:23
Alignment explanation
Indices: 1695677--1695721 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1695667 ATTATTTTTT
1695677 TTTAAAATTTCGAAGTTAAAAAA
1 TTTAAAATTTCGAAGTTAAAAAA
* *
1695700 TTTAAAATTTTGAGGTTAAAAA
1 TTTAAAATTTCGAAGTTAAAAA
1695722 TTATACGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (23 bp):
TTTAAAATTTCGAAGTTAAAAAA
Found at i:1704627 original size:29 final size:29
Alignment explanation
Indices: 1704589--1704671 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1704579 CTCACCTAAC
*
1704589 TAAATTGATGTAAGCAATAACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
1704619 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
1704648 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1704672 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:1707448 original size:15 final size:15
Alignment explanation
Indices: 1707428--1707466 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1707418 CTACATGGAG
1707428 CGATGAAGAAAGTTT
1 CGATGAAGAAAGTTT
*
1707443 CGATGAAGAAGGTTT
1 CGATGAAGAAAGTTT
1707458 CGATGAAGA
1 CGATGAAGA
1707467 GGAACAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (15 bp):
CGATGAAGAAAGTTT
Found at i:1711473 original size:20 final size:20
Alignment explanation
Indices: 1711448--1711487 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1711438 TTTTGGTGCA
1711448 GAGGGAA-TCGATCCCCCCTT
1 GAGGGAACT-GATCCCCCCTT
*
1711468 GAGGGAACTGATTCCCCCTT
1 GAGGGAACTGATCCCCCCTT
1711488 TTAAGGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
GAGGGAACTGATCCCCCCTT
Found at i:1717679 original size:15 final size:15
Alignment explanation
Indices: 1717659--1717688 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1717649 CTTTCTCACA
1717659 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
1717674 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
1717689 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:1717743 original size:24 final size:24
Alignment explanation
Indices: 1717687--1717737 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
1717677 GTTGTTGTAA
*
1717687 TTCCAGCCTCGTCCAAGACCTCGAC
1 TTCCA-CCTCGTCCAAGACCTCAAC
*
1717712 TTCCACCTCGTCCATGACCTCTAAC
1 TTCCACCTCGTCCAAGACCTC-AAC
1717737 T
1 T
1717738 CTACCTTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.20, C:0.43, G:0.12, T:0.25
Consensus pattern (24 bp):
TTCCACCTCGTCCAAGACCTCAAC
Found at i:1719005 original size:29 final size:29
Alignment explanation
Indices: 1718962--1719044 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1718952 CTCACCTAAC
1718962 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
1718992 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
*
1719021 TAAATGATATAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1719045 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:1719300 original size:16 final size:16
Alignment explanation
Indices: 1719279--1719318 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1719269 ATATTTTATT
1719279 CCCCATATTAGAGGAA
1 CCCCATATTAGAGGAA
1719295 CCCCATATTAGAGGAA
1 CCCCATATTAGAGGAA
*
1719311 CCGCATAT
1 CCCCATAT
1719319 AAAATGACGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (16 bp):
CCCCATATTAGAGGAA
Found at i:1722641 original size:27 final size:27
Alignment explanation
Indices: 1722609--1722660 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1722599 TTGATTATGT
1722609 TTATGGGGCGAGATAAGTTTTCTTTGG
1 TTATGGGGCGAGATAAGTTTTCTTTGG
* *
1722636 TTATGGGGTGAGATACGTTTTCTTT
1 TTATGGGGCGAGATAAGTTTTCTTT
1722661 TGTTGAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.08, G:0.31, T:0.44
Consensus pattern (27 bp):
TTATGGGGCGAGATAAGTTTTCTTTGG
Found at i:1722975 original size:21 final size:20
Alignment explanation
Indices: 1722941--1722979 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1722931 TAATATGAAG
1722941 GTTGAAATAGAAAACTAAAAA
1 GTTGAAATAGAAAA-TAAAAA
1722962 GTTGAAA-AGTAAAATAAA
1 GTTGAAATAG-AAAATAAA
1722980 TAAGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.21
Consensus pattern (20 bp):
GTTGAAATAGAAAATAAAAA
Found at i:1729106 original size:11 final size:11
Alignment explanation
Indices: 1729090--1729114 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1729080 TTCTTTTCAT
1729090 TTTATTTACTG
1 TTTATTTACTG
1729101 TTTATTTACTG
1 TTTATTTACTG
1729112 TTT
1 TTT
1729115 TTACCATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTATTTACTG
Found at i:1738764 original size:23 final size:23
Alignment explanation
Indices: 1738734--1738782 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1738724 TGGTGGTTGG
*
1738734 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
1738757 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
1738780 TTT
1 TTT
1738783 GGTTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:1743233 original size:20 final size:21
Alignment explanation
Indices: 1743208--1743251 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1743198 GAAAATGTTA
*
1743208 AAAAATATTAATG-TTTAAGT
1 AAAAATAATAATGTTTTAAGT
1743228 AAAAATAATAATGTTTTAAGT
1 AAAAATAATAATGTTTTAAGT
1743249 AAA
1 AAA
1743252 TTTTTATCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
AAAAATAATAATGTTTTAAGT
Done.