Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_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: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 40
Found at i:1313063 original size:25 final size:25
Alignment explanation
Indices: 1313015--1313063 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1313005 AGCCATAAGA
* * *
1313015 AACATGCCATAAGAGCAGAGAAAAG
1 AACATGCCACAAGAACAGAAAAAAG
*
1313040 AACATGCCACAAGAACATAAAAAA
1 AACATGCCACAAGAACAGAAAAAA
1313064 CGTGTCATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.57, C:0.18, G:0.16, T:0.08
Consensus pattern (25 bp):
AACATGCCACAAGAACAGAAAAAAG
Found at i:1313640 original size:55 final size:56
Alignment explanation
Indices: 1313558--1313699 Score: 189
Period size: 55 Copynumber: 2.6 Consensus size: 56
1313548 GGGCATTTTC
* * * *
1313558 TAGATATATTCAATTTCGGGCT-CCTATTTTTATGCTTCTTAATGGCAACAATTGA
1 TAGATATACTCAATTTCGGGATCCCTATTTTTATGCTTCTTAATGACAACAACTGA
* * * *
1313613 TATATATACTCGATTTTGGG-TCTCTATTTTTATGCTTCTTAATGACAACAACTGA
1 TAGATATACTCAATTTCGGGATCCCTATTTTTATGCTTCTTAATGACAACAACTGA
*
1313668 TAGATATATTCAATTTCGGGATCCCTATTTTT
1 TAGATATACTCAATTTCGGGATCCCTATTTTT
1313700 TTGGGCCCTG
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
54 1 0.01
55 62 0.85
56 10 0.14
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (56 bp):
TAGATATACTCAATTTCGGGATCCCTATTTTTATGCTTCTTAATGACAACAACTGA
Found at i:1314132 original size:13 final size:14
Alignment explanation
Indices: 1314116--1314145 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1314106 AAAAGAAAAT
1314116 AATAAAAT-CTAAA
1 AATAAAATACTAAA
1314129 AATAAAATACTAAA
1 AATAAAATACTAAA
1314143 AAT
1 AAT
1314146 TGTTAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAAATACTAAA
Found at i:1317645 original size:18 final size:17
Alignment explanation
Indices: 1317624--1317659 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1317614 TAAAAAGTTA
1317624 TAATTTTTTTGTATAGTC
1 TAATTTTTTT-TATAGTC
1317642 TAATTTTTTTTATAGTC
1 TAATTTTTTTTATAGTC
1317659 T
1 T
1317660 GAGGTGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (17 bp):
TAATTTTTTTTATAGTC
Found at i:1318412 original size:41 final size:41
Alignment explanation
Indices: 1318356--1318644 Score: 488
Period size: 41 Copynumber: 7.0 Consensus size: 41
1318346 AGATTCGCAA
* * *
1318356 TGCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAATTCGT
1 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
*
1318397 TGCGACAGGCAAAGTTCGCATTGCGATTCATTCCAATTCGT
1 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
1318438 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
1 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
1318479 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
1 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
* * *
1318520 TGCGACAGACGAAGTTCGCATTGCGATTCATTCTAATTCAT
1 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
1318561 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
1 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
* *
1318602 TGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGT
1 TGCGACAGGCGAAGTTCGCATTGCGATTCATTCC-AATTCGT
1318644 T
1 T
1318645 ACGATAGTCC
Statistics
Matches: 234, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
41 226 0.97
42 8 0.03
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (41 bp):
TGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
Found at i:1319587 original size:33 final size:33
Alignment explanation
Indices: 1319545--1319610 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1319535 ATATTTGGAC
*
1319545 TATCGCAACGAATTTGTAATGAATCGCAACGCG
1 TATCGCAACGAATTTGGAATGAATCGCAACGCG
1319578 TATCGCAACGAATTTGGAATGAATCGCAACGCG
1 TATCGCAACGAATTTGGAATGAATCGCAACGCG
1319611 AACTTCGCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (33 bp):
TATCGCAACGAATTTGGAATGAATCGCAACGCG
Found at i:1319647 original size:20 final size:21
Alignment explanation
Indices: 1319579--1319669 Score: 91
Period size: 20 Copynumber: 4.4 Consensus size: 21
1319569 CGCAACGCGT
*
1319579 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* **
1319600 ATCGCAACGCGAACTTCGCCTG-
1 ATCGCAA--CGAACTTGGAATGA
1319622 -TCGCAACGAA-TTGGAATGA
1 ATCGCAACGAACTTGGAATGA
*
1319641 ATCGCAATGAA-TTGGAATGA
1 ATCGCAACGAACTTGGAATGA
1319661 ATCGCAACG
1 ATCGCAACG
1319670 CGAACTTCGA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.09
19 4 0.07
20 26 0.46
21 13 0.23
23 9 0.16
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATGA
Found at i:1320665 original size:21 final size:21
Alignment explanation
Indices: 1320640--1320694 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1320630 AGGGTTAATA
*
1320640 CCTTTAGATGAAATGACTTAAT
1 CCTTTAGATGAAAGGACTT-AT
* *
1320662 -CTTTAAATTAAAGGACTTAT
1 CCTTTAGATGAAAGGACTTAT
*
1320682 CCTTTTGATGAAA
1 CCTTTAGATGAAA
1320695 AGTGCTTAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (21 bp):
CCTTTAGATGAAAGGACTTAT
Found at i:1326610 original size:23 final size:23
Alignment explanation
Indices: 1326556--1326610 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1326546 CAACTCATAT
*
1326556 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTACCACGTAG
* *
1326579 AATTGCACCGAAGTACCGCGTAG
1 AAATGCACCGAAGTACCACGTAG
*
1326602 AAATACACC
1 AAATGCACC
1326611 ATAGTGCCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.15
Consensus pattern (23 bp):
AAATGCACCGAAGTACCACGTAG
Found at i:1330300 original size:3 final size:3
Alignment explanation
Indices: 1330288--1330326 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1330278 TTAATCCGAG
1330288 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1330327 ATATTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1330534 original size:3 final size:3
Alignment explanation
Indices: 1330526--1330564 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
1330516 ATCCGAGATG
1330526 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
1330565 CGAACGAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1330675 original size:225 final size:224
Alignment explanation
Indices: 1330302--1330730 Score: 605
Period size: 225 Copynumber: 1.9 Consensus size: 224
1330292 AATAATAATA
* * * *
1330302 ATAATAATAATAATAATAATAATAAATATTATTATATAATCGAACGAAGCAAAATAAATAAAAAT
1 ATAATAATAATAATAATAATAATAAATAATAATAAATAATCGAACGAAACAAAATAAATAAAAAT
* * * **
1330367 CAAAGTAGAGGTAAGAAATTGGTTTACTCATATTTAGACATTGAATCGAATGAGTAGAGTAACAT
66 CAAAATAGAAGTAAGAAATTGGTTTACTCATATGTAGACACGGAATCGAATGAGTAGAGTAACAT
* *
1330432 AAATCAAAGAAGAATTTTGTTGAGGCCTGTGTGAACAATTTCCTTAAGACATATTCGTCCTCTCC
131 AAATCAAAGAAGAATTTTGTTGAGGCATGTATGAACAATTTCCTTAAGACATATTCGTCCTCTCC
*
1330497 TCGGTGCTTAAAATGGTTAATCCGAGATG
196 TAGGTGCTTAAAATGGTTAATCCGAGATG
*
1330526 ATAATAATAATAATAATAATAAT-AATAATAATAAATAATCGAACGAAACAAAATAATTATATAG
1 ATAATAATAATAATAATAATAATAAATAATAATAAATAATCGAACGAAACAAAATAA--ATA-AA
* * *
1330590 AATTAAAATAGAAG-AATGAAACTT-G-TTACTCATGTGTAGACACGGAATCGAATGAGTGGAGT
63 AATCAAAATAGAAGTAA-GAAA-TTGGTTTACTCATATGTAGACACGGAATCGAATGAGTAGAGT
* * * *
1330652 AACATAAATCGAAGAATAATTTTGTTGAGGCATGTATGAACATTTTCCTTAAGACATATTTGTCC
126 AACATAAATCAAAGAAGAATTTTGTTGAGGCATGTATGAACAATTTCCTTAAGACATATTCGTCC
1330717 TCTCCTAGGTGCTT
191 TCTCCTAGGTGCTT
1330731 TGAGTAACGT
Statistics
Matches: 180, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
223 29 0.16
224 23 0.13
225 109 0.61
226 17 0.09
227 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (224 bp):
ATAATAATAATAATAATAATAATAAATAATAATAAATAATCGAACGAAACAAAATAAATAAAAAT
CAAAATAGAAGTAAGAAATTGGTTTACTCATATGTAGACACGGAATCGAATGAGTAGAGTAACAT
AAATCAAAGAAGAATTTTGTTGAGGCATGTATGAACAATTTCCTTAAGACATATTCGTCCTCTCC
TAGGTGCTTAAAATGGTTAATCCGAGATG
Found at i:1334347 original size:31 final size:31
Alignment explanation
Indices: 1334309--1334447 Score: 210
Period size: 31 Copynumber: 4.5 Consensus size: 31
1334299 TAGTTACGTC
* *
1334309 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAATAGACTAAATGTTA
1334340 GGGGACCATATTGCAAATAGACTAAATGTT-
1 GGGGACCATATTGCAAATAGACTAAATGTTA
*
1334370 GAGGGATCATATTGC-AATAGACTAAATGTTA
1 G-GGGACCATATTGCAAATAGACTAAATGTTA
*
1334401 GGGGACCATATTGAAAATAGACTAAATGTTA
1 GGGGACCATATTGCAAATAGACTAAATGTTA
*
1334432 GGGGACTATATTGCAA
1 GGGGACCATATTGCAA
1334448 GTTTTAAAAG
Statistics
Matches: 99, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
30 27 0.27
31 72 0.73
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.26
Consensus pattern (31 bp):
GGGGACCATATTGCAAATAGACTAAATGTTA
Found at i:1334411 original size:61 final size:60
Alignment explanation
Indices: 1334309--1334447 Score: 199
Period size: 61 Copynumber: 2.2 Consensus size: 60
1334299 TAGTTACGTC
* *
1334309 GGGGACCATATTGCAAACAGACTAAATGTTGGGGGACCATATTGCAAATAGACTAAATGTT-
1 GGGGA-CATATTGC-AACAGACTAAATGTTAGGGGACCATATTGAAAATAGACTAAATGTTA
*
1334370 GAGGGATCATATTGCAATAGACTAAATGTTAGGGGACCATATTGAAAATAGACTAAATGTTA
1 G-GGGA-CATATTGCAACAGACTAAATGTTAGGGGACCATATTGAAAATAGACTAAATGTTA
1334432 GGGGACTATATTGCAA
1 GGGGAC-ATATTGCAA
1334448 GTTTTAAAAG
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
60 1 0.01
61 57 0.80
62 13 0.18
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.26
Consensus pattern (60 bp):
GGGGACATATTGCAACAGACTAAATGTTAGGGGACCATATTGAAAATAGACTAAATGTTA
Found at i:1334465 original size:29 final size:29
Alignment explanation
Indices: 1334423--1334485 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1334413 GAAAATAGAC
* * *
1334423 TAAATGTTAGGGGAC-TATATTGCAAGTTT
1 TAAAAGTTAGGGGACTTA-AATGAAAGTTT
*
1334452 TAAAAGTTGGGGGACTTAAATGAAAGTTT
1 TAAAAGTTAGGGGACTTAAATGAAAGTTT
1334481 TAAAA
1 TAAAA
1334486 AATTTCAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (29 bp):
TAAAAGTTAGGGGACTTAAATGAAAGTTT
Found at i:1334535 original size:10 final size:10
Alignment explanation
Indices: 1334520--1334585 Score: 57
Period size: 10 Copynumber: 6.5 Consensus size: 10
1334510 TACCCTATTA
1334520 TTTATTGTTT
1 TTTATTGTTT
*
1334530 TTTATTATTAAT
1 TTTATTGTT--T
1334542 TTTATATG-TT
1 TTTAT-TGTTT
1334552 TTTATTG--T
1 TTTATTGTTT
*
1334560 TTTATTATTT
1 TTTATTGTTT
1334570 TTTATTGTTT
1 TTTATTGTTT
1334580 CTTTAT
1 -TTTAT
1334586 AAGTCTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.15
9 2 0.04
10 24 0.52
11 5 0.11
12 7 0.15
13 1 0.02
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (10 bp):
TTTATTGTTT
Found at i:1334585 original size:18 final size:18
Alignment explanation
Indices: 1334541--1334579 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1334531 TTATTATTAA
1334541 TTTTA-TATGTTTTTATTG
1 TTTTATTAT-TTTTTATTG
1334559 TTTTATTATTTTTTATTG
1 TTTTATTATTTTTTATTG
1334577 TTT
1 TTT
1334580 CTTTATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (18 bp):
TTTTATTATTTTTTATTG
Found at i:1334724 original size:23 final size:24
Alignment explanation
Indices: 1334690--1334744 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
1334680 CATAATGAAA
*
1334690 AATTAAATATTG-ATTTTAAAGTAT
1 AATTAAATATTGAATATTAAA-TAT
*
1334714 AATTAAA-ATTGAATATTGAATAT
1 AATTAAATATTGAATATTAAATAT
1334737 AATTAAAT
1 AATTAAAT
1334745 TATTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (24 bp):
AATTAAATATTGAATATTAAATAT
Found at i:1335469 original size:31 final size:31
Alignment explanation
Indices: 1335424--1335531 Score: 171
Period size: 31 Copynumber: 3.5 Consensus size: 31
1335414 CTTTTAAAAC
**
1335424 TTGCAATACAGTCCCCCAACATTTAGTCTAT
1 TTGCAATATGGTCCCCCAACATTTAGTCTAT
* *
1335455 TTTCAATATGGTCCCTCAACATTTAGTCTAT
1 TTGCAATATGGTCCCCCAACATTTAGTCTAT
*
1335486 TTGCAATATGGTCCCCCAACATTTAGTCCAT
1 TTGCAATATGGTCCCCCAACATTTAGTCTAT
1335517 TTGCAATATGGTCCC
1 TTGCAATATGGTCCC
1335532 TGATGTAACT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCTAT
Found at i:1337695 original size:18 final size:18
Alignment explanation
Indices: 1337672--1337721 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1337662 GAGTGGTCAA
* *
1337672 TGGGAGTGGGAGTGGGAG
1 TGGGAGTGAGAGTGCGAG
1337690 TGGGAGTGAGAGTGCGAG
1 TGGGAGTGAGAGTGCGAG
1337708 TGGGAGTGAGAGTG
1 TGGGAGTGAGAGTG
1337722 AGAATGGACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.02, G:0.60, T:0.18
Consensus pattern (18 bp):
TGGGAGTGAGAGTGCGAG
Found at i:1337724 original size:6 final size:6
Alignment explanation
Indices: 1337672--1337721 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
1337662 GAGTGGTCAA
* * *
1337672 TGGGAG TGGGAG TGGGAG TGGGAG TGAGAG TGCGAG TGGGAG TGAGAG
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG
1337720 TG
1 TG
1337722 AGAATGGACG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.20, C:0.02, G:0.60, T:0.18
Consensus pattern (6 bp):
TGGGAG
Found at i:1337888 original size:29 final size:29
Alignment explanation
Indices: 1337843--1337900 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1337833 GTATTAGCCG
* *
1337843 TAGGTCGCCATGCCTTCCGGGCGATCTAC
1 TAGGTCGCCATGCCTTCCCGGCGAGCTAC
*
1337872 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGAGCTAC
1337901 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGAGCTAC
Found at i:1337977 original size:10 final size:10
Alignment explanation
Indices: 1337964--1338024 Score: 59
Period size: 10 Copynumber: 5.7 Consensus size: 10
1337954 CGACCGAGGC
1337964 CATCCGAGAG
1 CATCCGAGAG
*
1337974 CATCCGAGAC
1 CATCCGAGAG
1337984 CATCCGACCGAGG
1 CATCCGA--GA-G
1337997 CCATCCGAGAG
1 -CATCCGAGAG
* *
1338008 CATTCGAGAC
1 CATCCGAGAG
1338018 CATCCGA
1 CATCCGA
1338025 CCGAGGCCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 30 0.71
11 1 0.02
12 4 0.10
14 7 0.17
ACGTcount: A:0.28, C:0.36, G:0.25, T:0.11
Consensus pattern (10 bp):
CATCCGAGAG
Found at i:1337986 original size:20 final size:20
Alignment explanation
Indices: 1337957--1338024 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
1337947 GGCCATCCGA
*
1337957 CCGAGGCCATCCGAGAGCAT
1 CCGAGACCATCCGAGAGCAT
1337977 CCGAGACCATCC----G-A-
1 CCGAGACCATCCGAGAGCAT
*
1337991 CCGAGGCCATCCGAGAGCAT
1 CCGAGACCATCCGAGAGCAT
*
1338011 TCGAGACCATCCGA
1 CCGAGACCATCCGA
1338025 CCGAGGCCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
14 11 0.29
15 1 0.03
16 1 0.03
18 1 0.03
19 1 0.03
20 23 0.61
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.10
Consensus pattern (20 bp):
CCGAGACCATCCGAGAGCAT
Found at i:1337992 original size:34 final size:34
Alignment explanation
Indices: 1337949--1338038 Score: 171
Period size: 34 Copynumber: 2.6 Consensus size: 34
1337939 GCATATGAGG
1337949 CCATCCGACCGAGGCCATCCGAGAGCATCCGAGA
1 CCATCCGACCGAGGCCATCCGAGAGCATCCGAGA
*
1337983 CCATCCGACCGAGGCCATCCGAGAGCATTCGAGA
1 CCATCCGACCGAGGCCATCCGAGAGCATCCGAGA
1338017 CCATCCGACCGAGGCCATCCGA
1 CCATCCGACCGAGGCCATCCGA
1338039 CTGAGCTATG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.26, C:0.39, G:0.26, T:0.10
Consensus pattern (34 bp):
CCATCCGACCGAGGCCATCCGAGAGCATCCGAGA
Found at i:1338146 original size:29 final size:29
Alignment explanation
Indices: 1338113--1338168 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1338103 GAGCGAGGGT
*
1338113 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
1338142 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
1338169 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:1338441 original size:44 final size:43
Alignment explanation
Indices: 1338377--1338459 Score: 121
Period size: 44 Copynumber: 1.9 Consensus size: 43
1338367 TCTTCTCTCT
* *
1338377 AATTCTCTCAAGTTCAAATCTCTCCATTCTCAACATTTCTATG
1 AATTCTCTCAAGTCCAAATCTCTCCATTATCAACATTTCTATG
* *
1338420 AATTCTCTCCAAGTCCTAATCTCTCTATTATCAACATTTC
1 AATTCTCT-CAAGTCCAAATCTCTCCATTATCAACATTTC
1338460 ATATTTACAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 8 0.23
44 27 0.77
ACGTcount: A:0.28, C:0.29, G:0.04, T:0.40
Consensus pattern (43 bp):
AATTCTCTCAAGTCCAAATCTCTCCATTATCAACATTTCTATG
Found at i:1338548 original size:24 final size:24
Alignment explanation
Indices: 1338516--1338562 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1338506 TTTCTTTTCT
**
1338516 CAGTTGCTTTTTGGGTGAGAATTC
1 CAGTTGCTTTTCAGGTGAGAATTC
1338540 CAGTTGCTTTTCAGGTGAGAATT
1 CAGTTGCTTTTCAGGTGAGAATT
1338563 TTAACTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (24 bp):
CAGTTGCTTTTCAGGTGAGAATTC
Found at i:1350319 original size:28 final size:28
Alignment explanation
Indices: 1350288--1350346 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
1350278 TTTTCGCCCT
1350288 CCTTAAAATTTTATAAGTTCAAGTTCAC
1 CCTTAAAATTTTATAAGTTCAAGTTCAC
* * *
1350316 CCTTGAAATTTTATAAGTTTAAGTTCGC
1 CCTTAAAATTTTATAAGTTCAAGTTCAC
1350344 CCT
1 CCT
1350347 CCCTTACTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.41
Consensus pattern (28 bp):
CCTTAAAATTTTATAAGTTCAAGTTCAC
Found at i:1358417 original size:16 final size:16
Alignment explanation
Indices: 1358398--1358428 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1358388 CATCTTCAAC
1358398 CAAATTGCTTCTTTAT
1 CAAATTGCTTCTTTAT
1358414 CAAATTGCTTCTTTA
1 CAAATTGCTTCTTTA
1358429 CTGGCTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (16 bp):
CAAATTGCTTCTTTAT
Found at i:1365356 original size:10 final size:10
Alignment explanation
Indices: 1365341--1365415 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
1365331 CATTTAATAA
1365341 ATAAACGAAC
1 ATAAACGAAC
1365351 ATAAACGAAC
1 ATAAACGAAC
1365361 ----ACGAAC
1 ATAAACGAAC
*
1365367 ATAAACAAAC
1 ATAAACGAAC
** *
1365377 ACGAAC-ATAA
1 ATAAACGA-AC
1365387 ATGAACACGAAC
1 AT-AA-ACGAAC
1365399 ATAAACGAAC
1 ATAAACGAAC
1365409 ATAAACG
1 ATAAACG
1365416 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1365366 original size:16 final size:16
Alignment explanation
Indices: 1365345--1365409 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1365335 TAATAAATAA
1365345 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1365361 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
1365377 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1365393 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1365409 A
1 A
1365410 TAAACGTTGG
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:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1366516 original size:14 final size:14
Alignment explanation
Indices: 1366499--1366554 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
1366489 AATGAGCATA
1366499 AACGAACATAACCG
1 AACGAACATAACCG
*
1366513 AACGGACAT-A---
1 AACGAACATAACCG
1366523 AACGAACATAACCG
1 AACGAACATAACCG
1366537 AACGAACATAACCG
1 AACGAACATAACCG
1366551 AACG
1 AACG
1366555 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1366522 original size:24 final size:24
Alignment explanation
Indices: 1366495--1366553 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
1366485 AATGAATGAG
*
1366495 CATAAACGAACATAACCGAACGGA
1 CATAAACGAACATAACCGAACGAA
1366519 CATAAACGAACATAACCGAACGAA
1 CATAAACGAACATAACCGAACGAA
*
1366543 CATAACCGAAC
1 CATAAACGAAC
1366554 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.27, G:0.14, T:0.08
Consensus pattern (24 bp):
CATAAACGAACATAACCGAACGAA
Found at i:1373659 original size:21 final size:21
Alignment explanation
Indices: 1373633--1373830 Score: 156
Period size: 21 Copynumber: 9.5 Consensus size: 21
1373623 GTTTCCAGAT
**
1373633 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1373654 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
1373675 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * * * *
1373695 TCGAAATGCGATAGTCGAAGT-
1 TCGCAATGCGA-ACTTGGACTA
*
1373716 TCGTAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
1373737 TTGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * *
1373757 TCGTAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
1373778 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
1373799 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
1373820 TCGCATTGCGA
1 TCGCAATGCGA
1373831 TTTACATATT
Statistics
Matches: 140, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
20 31 0.22
21 108 0.77
22 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1373704 original size:62 final size:62
Alignment explanation
Indices: 1373637--1373810 Score: 251
Period size: 62 Copynumber: 2.8 Consensus size: 62
1373627 CCAGATTCGC
*
1373637 AATGCGATTTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGA
1 AATGCGATATTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGA
* * * * * *
1373699 AATGCGATAGTCGAAGT-TCGTAATGCGAACTTGGACTATTGCAATGCGAATATGTAAATCGT
1 AATGCGATA-TTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGA
* *
1373761 AATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA
1 AATGCGATATTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA
1373811 CTTCGACTAT
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
61 2 0.02
62 90 0.94
63 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (62 bp):
AATGCGATATTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGA
Found at i:1373761 original size:41 final size:42
Alignment explanation
Indices: 1373716--1373830 Score: 128
Period size: 41 Copynumber: 2.8 Consensus size: 42
1373706 TAGTCGAAGT
* * *
1373716 TCGTAATGCGAACTTGGACTATTGCAATGCGAA-TATGTA-AA
1 TCGTAATGCGAACTTCGACTATCGCAATGCGAACT-TGGACAA
* *
1373757 TCGTAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTA
1 TCGTAATGCGA-ACTTCGACTATCGCAATGCGAACTTGGACAA
* *
1373799 TCGCAATGCGAACTTCGACTATCGCATTGCGA
1 TCGTAATGCGAACTTCGACTATCGCAATGCGA
1373831 TTTACATATT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 32 0.52
42 30 0.48
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (42 bp):
TCGTAATGCGAACTTCGACTATCGCAATGCGAACTTGGACAA
Found at i:1373885 original size:21 final size:21
Alignment explanation
Indices: 1373763--1373918 Score: 117
Period size: 21 Copynumber: 7.5 Consensus size: 21
1373753 TAAATCGTAA
*
1373763 TGCGATAGTCGACTATCGCAA
1 TGCGATAGTCGACTATCGCAT
* * *
1373784 TGCGA-ACTTGGACTATCGCAA
1 TGCGATA-GTCGACTATCGCAT
*
1373805 TGCGA-ACTTCGACTATCGCAT
1 TGCGATA-GTCGACTATCGCAT
*
1373826 TGCGAT--T-TACATATTCGCAT
1 TGCGATAGTCGAC-TA-TCGCAT
* * *
1373846 TGCGATAGTTGAAGT-TCGCGT
1 TGCGATAGTCG-ACTATCGCAT
1373867 TGCGATAGTCGACTATCGCAT
1 TGCGATAGTCGACTATCGCAT
* **
1373888 TGCGATAGTCCAAAATCGCAT
1 TGCGATAGTCGACTATCGCAT
1373909 TGCGATAGTC
1 TGCGATAGTC
1373919 CAAAAATCGC
Statistics
Matches: 112, Mismatches: 14, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 15 0.13
21 89 0.79
22 1 0.01
23 1 0.01
24 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCGACTATCGCAT
Found at i:1373927 original size:22 final size:21
Alignment explanation
Indices: 1373840--1373929 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
1373830 ATTTACATAT
** **
1373840 TCGCATTGCGATAGTTGAAGT
1 TCGCATTGCGATAGTCCAAAA
* * **
1373861 TCGCGTTGCGATAGTCGACTA
1 TCGCATTGCGATAGTCCAAAA
1373882 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
1373903 TCGCATTGCGATAGTCCAAAAA
1 TCGCATTGCGATAGTCC-AAAA
1373925 TCGCA
1 TCGCA
1373930 ACGACTGGTG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
21 50 0.85
22 9 0.15
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAA
Found at i:1374662 original size:21 final size:21
Alignment explanation
Indices: 1374636--1374722 Score: 120
Period size: 21 Copynumber: 4.1 Consensus size: 21
1374626 CACCAGTCGT
*
1374636 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTCGACTATCGCAA
**
1374657 TGCGATAGTCGACTATCGCAA
1 TGCGATTTTCGACTATCGCAA
*
1374678 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTCGACTATCGCAA
**
1374699 TGCGAACTTCGACTATCGCAA
1 TGCGATTTTCGACTATCGCAA
1374720 TGC
1 TGC
1374723 AAATATGTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCGATTTTCGACTATCGCAA
Found at i:1374683 original size:42 final size:42
Alignment explanation
Indices: 1374636--1374751 Score: 155
Period size: 42 Copynumber: 2.8 Consensus size: 42
1374626 CACCAGTCGT
1374636 TGCGATTTTGGACTATCGCAATGCGATAGTCGACTATCGCAA
1 TGCGATTTTGGACTATCGCAATGCGATAGTCGACTATCGCAA
*
1374678 TGCGATTTTGGACTATCGCAATGCGA-ACTTCGACTATCGCAA
1 TGCGATTTTGGACTATCGCAATGCGATA-GTCGACTATCGCAA
* * * * *
1374720 TGCAAATATGTA-AATCGCAATGCGATAGTCGA
1 TGCGATTTTGGACTATCGCAATGCGATAGTCGA
1374752 AGTTCGCATT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
41 17 0.26
42 48 0.74
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (42 bp):
TGCGATTTTGGACTATCGCAATGCGATAGTCGACTATCGCAA
Found at i:1374764 original size:21 final size:21
Alignment explanation
Indices: 1374734--1374911 Score: 193
Period size: 21 Copynumber: 8.5 Consensus size: 21
1374724 AATATGTAAA
* *
1374734 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
1374755 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
1374776 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* * *
1374796 ATCGCATTGCTAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
1374817 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
1374838 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
1374859 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* **
1374879 ATCGCATTGCGATAGTCTAAAA
1 -TCGCATTGCGATAGTCCAAGT
1374901 TCGCATTGCGA
1 TCGCATTGCGA
1374912 ATCTGGAAAT
Statistics
Matches: 134, Mismatches: 16, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
20 19 0.14
21 113 0.84
22 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:1374794 original size:83 final size:83
Alignment explanation
Indices: 1374707--1374884 Score: 272
Period size: 83 Copynumber: 2.1 Consensus size: 83
1374697 AATGCGAACT
*
1374707 TCGACTATCGCAATGCAAATATGTA-A-A-TCGCAATGCGATAGTCGAAGTTCGCATTGCGATAG
1 TCGACTATCGCAATGC---TATGTACATATTCGCAATGCGATAGTCCAAGTTCGCATTGCGATAG
1374769 TCCAAGTTCGCATTGCGATAG
63 TCCAAGTTCGCATTGCGATAG
* * *
1374790 TCGACTATCGCATTGCTATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCC
1 TCGACTATCGCAATGCTATGTACATATTCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCC
1374855 AAGTTCGCATTGCGATAG
66 AAGTTCGCATTGCGATAG
1374873 TCGACTATCGCA
1 TCGACTATCGCA
1374885 TTGCGATAGT
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
80 5 0.06
81 1 0.01
82 1 0.01
83 81 0.92
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (83 bp):
TCGACTATCGCAATGCTATGTACATATTCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCC
AAGTTCGCATTGCGATAG
Found at i:1374885 original size:83 final size:83
Alignment explanation
Indices: 1374734--1374888 Score: 292
Period size: 83 Copynumber: 1.9 Consensus size: 83
1374724 AATATGTAAA
*
1374734 TCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATC
1 TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATC
1374799 GCATTGCTATTTACATAT
66 GCATTGCTATTTACATAT
*
1374817 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATC
1 TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATC
1374882 GCATTGC
66 GCATTGC
1374889 GATAGTCTAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (83 bp):
TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATC
GCATTGCTATTTACATAT
Found at i:1374933 original size:83 final size:83
Alignment explanation
Indices: 1374732--1374911 Score: 265
Period size: 83 Copynumber: 2.2 Consensus size: 83
1374722 CAAATATGTA
* * *
1374732 AATCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTA
1 AATCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTA
*
1374797 TCGCATTGCTATTTACAT
66 TCGCATTGCTATCTACAT
* *
1374815 ATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTA
1 AATCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTA
1374880 TCGCATTGCGATAGTCTA-A-
66 TCGCATTGC--TA-TCTACAT
1374899 AATCGCATTGCGA
1 AATCGCATTGCGA
1374912 ATCTGGAAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
83 71 0.80
84 12 0.13
85 3 0.03
86 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (83 bp):
AATCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTA
TCGCATTGCTATCTACAT
Found at i:1375737 original size:47 final size:45
Alignment explanation
Indices: 1375662--1375771 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 45
1375652 TATAAAATCC
*
1375662 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* * *
1375707 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* *
1375754 CTTGCCA-TTATTCCATAA
1 CTTACCATTTATCCCATAA
1375772 CCATATCCCA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
44 9 0.16
45 10 0.17
46 2 0.03
47 37 0.64
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:1377228 original size:67 final size:67
Alignment explanation
Indices: 1377120--1377254 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
1377110 ACAACTTGAA
1377120 ATTGATCACCGTTTGTTTTAAACGAAACTAAATCGATATATGAACATAATATATAAAAATAATCT
1 ATTGATCACCGTTTGTTTTAAACGAAACTAAATCGATATATGAACATAATATATAAAAATAATCT
1377185 CC
66 CC
* *
1377187 ATTGATCCCCGTTTGTTTTAAACGAAACTACATCGATATATGAACATAATATATAAAAATAATCT
1 ATTGATCACCGTTTGTTTTAAACGAAACTAAATCGATATATGAACATAATATATAAAAATAATCT
1377252 CC
66 CC
1377254 A
1 A
1377255 AATTATTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (67 bp):
ATTGATCACCGTTTGTTTTAAACGAAACTAAATCGATATATGAACATAATATATAAAAATAATCT
CC
Found at i:1383102 original size:23 final size:23
Alignment explanation
Indices: 1383068--1383120 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1383058 CACTATGTAT
*
1383068 CGATACCCTCTTTGAATGGGTAC
1 CGATACCATCTTTGAATGGGTAC
1383091 CGATACCATCTTTGAATGGGTAC
1 CGATACCATCTTTGAATGGGTAC
*
1383114 TGATACC
1 CGATACC
1383121 CCCATAAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (23 bp):
CGATACCATCTTTGAATGGGTAC
Found at i:1383624 original size:13 final size:13
Alignment explanation
Indices: 1383606--1383643 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1383596 AAACTACATA
1383606 TTTTCAAACATTG
1 TTTTCAAACATTG
*
1383619 TTTTCAAACATAG
1 TTTTCAAACATTG
1383632 TTTTCAAA-ATTG
1 TTTTCAAACATTG
1383644 CCCATTAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:1389044 original size:25 final size:25
Alignment explanation
Indices: 1389006--1389054 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1388996 TTAGAATGTT
*
1389006 TGAAAATAAAACTT-AAAATAAAAA
1 TGAAAATAAAACTTGAAAAGAAAAA
1389030 TGAAAATGAAAACTTGAAAAGAAAA
1 TGAAAAT-AAAACTTGAAAAGAAAA
1389055 GAAAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 7 0.32
26 8 0.36
ACGTcount: A:0.67, C:0.04, G:0.10, T:0.18
Consensus pattern (25 bp):
TGAAAATAAAACTTGAAAAGAAAAA
Found at i:1389855 original size:3 final size:3
Alignment explanation
Indices: 1389845--1389901 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
1389835 GTATTTTTTT
*
1389845 TAA T-A TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1389890 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1389902 ATAAAAAATG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1394117 original size:2 final size:2
Alignment explanation
Indices: 1394110--1394141 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1394100 TGAAAGATAA
1394110 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
1394142 GAAAATTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1396937 original size:30 final size:30
Alignment explanation
Indices: 1396870--1397054 Score: 163
Period size: 30 Copynumber: 6.2 Consensus size: 30
1396860 GCGGAGGATT
* *
1396870 CGGAGGCAGAGGAAGCATAGGAAGAGGCGG
1 CGGAGGCGGAGGAAGCGTAGGAAGAGGCGG
* *
1396900 TGGAGGCGGATGAAGCGTAGGAAGAGGCGG
1 CGGAGGCGGAGGAAGCGTAGGAAGAGGCGG
* * * * * **
1396930 CGGAGGCGGATGAAACGTAGTAATACGCAC
1 CGGAGGCGGAGGAAGCGTAGGAAGAGGCGG
* * ** * * **
1396960 CGAAGGCGGAGGAAACGTATTAATACGCAC
1 CGGAGGCGGAGGAAGCGTAGGAAGAGGCGG
* * **
1396990 CGGAGGCGGATGAAGCGTAGTAACTGGCGG
1 CGGAGGCGGAGGAAGCGTAGGAAGAGGCGG
1397020 CGGAGGCGGAGGAAGCGTAGGAAGAGGCGG
1 CGGAGGCGGAGGAAGCGTAGGAAGAGGCGG
1397050 CGGAG
1 CGGAG
1397055 TAGAGGTTTG
Statistics
Matches: 128, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 128 1.00
ACGTcount: A:0.30, C:0.16, G:0.45, T:0.09
Consensus pattern (30 bp):
CGGAGGCGGAGGAAGCGTAGGAAGAGGCGG
Found at i:1397054 original size:60 final size:60
Alignment explanation
Indices: 1396894--1397054 Score: 180
Period size: 60 Copynumber: 2.7 Consensus size: 60
1396884 GCATAGGAAG
* *
1396894 AGGCGGTGGAGGCGGATGAAGCGTAGGAAGAGGCGGCGGAGGCGGATGAAACGTAGTAAT
1 AGGCGGCGGAGGCGGAGGAAGCGTAGGAAGAGGCGGCGGAGGCGGATGAAACGTAGTAAT
* ** * * ** * * ** *
1396954 ACGCACCGAAGGCGGAGGAAACGTATTAATACGCACCGGAGGCGGATGAAGCGTAGTAACT
1 AGGCGGCGGAGGCGGAGGAAGCGTAGGAAGAGGCGGCGGAGGCGGATGAAACGTAGTAA-T
1397015 -GGCGGCGGAGGCGGAGGAAGCGTAGGAAGAGGCGGCGGAG
1 AGGCGGCGGAGGCGGAGGAAGCGTAGGAAGAGGCGGCGGAG
1397055 TAGAGGTTTG
Statistics
Matches: 75, Mismatches: 25, Indels: 2
0.74 0.25 0.02
Matches are distributed among these distances:
60 74 0.99
61 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.45, T:0.10
Consensus pattern (60 bp):
AGGCGGCGGAGGCGGAGGAAGCGTAGGAAGAGGCGGCGGAGGCGGATGAAACGTAGTAAT
Found at i:1400086 original size:9 final size:9
Alignment explanation
Indices: 1400072--1400158 Score: 66
Period size: 10 Copynumber: 9.0 Consensus size: 9
1400062 GGCTGCTGGA
1400072 AACCGGTTT
1 AACCGGTTT
1400081 AACCGGTTTT
1 AACCGG-TTT
*
1400091 CAAACGGTTCT
1 -AACCGGTT-T
*
1400102 GACCGGTTT
1 AACCGGTTT
*
1400111 GACCGGTTT
1 AACCGGTTT
*
1400120 CAACCGGTTCG
1 -AACCGGTT-T
1400131 AACCGGTTT
1 AACCGGTTT
* *
1400140 GACCGGTCTG
1 AACCGGT-TT
1400150 AACCGGTTT
1 AACCGGTTT
1400159 GATCGGTCTG
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
9 23 0.37
10 33 0.53
11 6 0.10
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1400135 original size:29 final size:30
Alignment explanation
Indices: 1400072--1400157 Score: 113
Period size: 29 Copynumber: 2.9 Consensus size: 30
1400062 GGCTGCTGGA
* *
1400072 AACCGGTTTAACCGGTTTTCAAACGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
1400103 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* *
1400131 AACCGGTTTGACCGGTCTGAACCGGTT
1 AACCGGTTTGACCGGTTTCAACCGGTT
1400158 TGATCGGTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.02
29 36 0.72
30 13 0.26
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:1400165 original size:9 final size:9
Alignment explanation
Indices: 1400095--1400171 Score: 73
Period size: 10 Copynumber: 8.1 Consensus size: 9
1400085 GGTTTTCAAA
1400095 CGGTTCTGAC
1 CGGTT-TGAC
1400105 CGGTTTGAC
1 CGGTTTGAC
*
1400114 CGGTTTCAAC
1 CGGTTT-GAC
*
1400124 CGGTTCGAAC
1 CGGTTTG-AC
1400134 CGGTTTGAC
1 CGGTTTGAC
*
1400143 CGGTCTGAAC
1 CGGTTTG-AC
*
1400153 CGGTTTGAT
1 CGGTTTGAC
*
1400162 CGGTCTGAC
1 CGGTTTGAC
1400171 C
1 C
1400172 CGACCGACCG
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
9 27 0.49
10 28 0.51
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:1400166 original size:19 final size:19
Alignment explanation
Indices: 1400072--1400169 Score: 83
Period size: 19 Copynumber: 5.1 Consensus size: 19
1400062 GGCTGCTGGA
* * *
1400072 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
* *
1400092 AAACGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
1400112 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
1400131 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
1400150 AACCGGTTTGATCGGTCTG
1 AACCGGTTTGACCGGTCTG
1400169 A
1 A
1400170 CCCGACCGAC
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.03
19 39 0.59
20 19 0.29
21 6 0.09
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:1407383 original size:22 final size:22
Alignment explanation
Indices: 1407355--1407402 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1407345 GCTGCTGGAA
*
1407355 ACCGTTGACCCGACCCGACCCG
1 ACCGTTGACCCGACCCGACACG
1407377 ACCGTTGACCCGACCCGACACG
1 ACCGTTGACCCGACCCGACACG
1407399 ACCG
1 ACCG
1407403 GACCGTTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.48, G:0.23, T:0.08
Consensus pattern (22 bp):
ACCGTTGACCCGACCCGACACG
Found at i:1407400 original size:27 final size:27
Alignment explanation
Indices: 1407361--1407413 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1407351 GGAAACCGTT
*
1407361 GACCCGACCCGACCCGACCGTTGACCC
1 GACCCGACACGACCCGACCGTTGACCC
*
1407388 GACCCGACACGACCGGACCGTTGACC
1 GACCCGACACGACCCGACCGTTGACC
1407414 GTTGACCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.47, G:0.25, T:0.08
Consensus pattern (27 bp):
GACCCGACACGACCCGACCGTTGACCC
Found at i:1407415 original size:7 final size:7
Alignment explanation
Indices: 1407403--1407433 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1407393 GACACGACCG
1407403 GACCGTT
1 GACCGTT
1407410 GACCGTT
1 GACCGTT
1407417 GACCGTT
1 GACCGTT
1407424 GACCGTT
1 GACCGTT
1407431 GAC
1 GAC
1407434 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1411050 original size:15 final size:15
Alignment explanation
Indices: 1411030--1411071 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1411020 TTTCATCCCA
1411030 TAAAATTATAAATAG
1 TAAAATTATAAATAG
* *
1411045 TAAAA-TATTGAATAT
1 TAAAATTA-TAAATAG
1411060 TAAAATTATAAA
1 TAAAATTATAAA
1411072 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (15 bp):
TAAAATTATAAATAG
Found at i:1413837 original size:28 final size:28
Alignment explanation
Indices: 1413806--1413871 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
1413796 TATATAAATT
1413806 TATCAATTTTGCTTATATCGTATATTCG
1 TATCAATTTTGCTTATATCGTATATTCG
1413834 TATCAATTTTGCTTATATCGTATATTCG
1 TATCAATTTTGCTTATATCGTATATTCG
*
1413862 CATCAATTTT
1 TATCAATTTT
1413872 TCCCTCGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (28 bp):
TATCAATTTTGCTTATATCGTATATTCG
Found at i:1417165 original size:18 final size:16
Alignment explanation
Indices: 1417128--1417169 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
1417118 ACTTTCTTAA
1417128 CATTATCA-TATATAT
1 CATTATCATTATATAT
*
1417143 TATTATCATTATATCTAT
1 CATTATCATTATA--TAT
1417161 CATTATCAT
1 CATTATCAT
1417170 CAAATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
18 11 0.50
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (16 bp):
CATTATCATTATATAT
Found at i:1417252 original size:26 final size:26
Alignment explanation
Indices: 1417223--1417307 Score: 63
Period size: 26 Copynumber: 3.4 Consensus size: 26
1417213 TCATATCACA
*
1417223 CATATATCATTTCACCAATAAACACC
1 CATAAATCATTTCACCAATAAACACC
**
1417249 CATAAATCATAATT--CCTGT-AACA--
1 CATAAATCAT--TTCACCAATAAACACC
* * *
1417272 CATATATCATTTCACCAAGAAATACC
1 CATAAATCATTTCACCAATAAACACC
1417298 CATAAATCAT
1 CATAAATCAT
1417308 AATTCTTGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
21 2 0.05
23 11 0.26
24 3 0.07
25 4 0.09
26 21 0.49
28 2 0.05
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (26 bp):
CATAAATCATTTCACCAATAAACACC
Found at i:1417277 original size:49 final size:49
Alignment explanation
Indices: 1417220--1417323 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
1417210 ATATCATATC
*
1417220 ACACATATATCATTTCACCAATAAACACCCATAAATCATAATTCCTGTA
1 ACACATATATCATTTCACCAAGAAACACCCATAAATCATAATTCCTGTA
* *
1417269 ACACATATATCATTTCACCAAGAAATACCCATAAATCATAATTCTTGTA
1 ACACATATATCATTTCACCAAGAAACACCCATAAATCATAATTCCTGTA
1417318 ACACAT
1 ACACAT
1417324 TTCCTATCAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.29
Consensus pattern (49 bp):
ACACATATATCATTTCACCAAGAAACACCCATAAATCATAATTCCTGTA
Found at i:1417484 original size:23 final size:23
Alignment explanation
Indices: 1417457--1417501 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1417447 CACCACAGCT
1417457 CGTATAAATGCACCGAAGTGCCG
1 CGTATAAATGCACCGAAGTGCCG
*
1417480 CGTATAAATGCACCGTAGTGCC
1 CGTATAAATGCACCGAAGTGCC
1417502 ATATAATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTATAAATGCACCGAAGTGCCG
Found at i:1422294 original size:21 final size:21
Alignment explanation
Indices: 1422257--1422300 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1422247 ACTTTCTTAA
*
1422257 CATTATCATATATATTATTAT
1 CATTATCATATATATTATCAT
*
1422278 CATTATC-TCTATCATTATCAT
1 CATTATCATATAT-ATTATCAT
1422299 CA
1 CA
1422301 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
CATTATCATATATATTATCAT
Found at i:1422386 original size:26 final size:26
Alignment explanation
Indices: 1422352--1422447 Score: 66
Period size: 26 Copynumber: 3.4 Consensus size: 26
1422342 TCATATCACA
*
1422352 CATATATCATTTCACCAATAAACACC
1 CATAAATCATTTCACCAATAAACACC
* * *
1422378 CATAAATCATAATTCCTGTAACATATATATCACA
1 CATAAATCAT--TT-C---ACCA-ATA-AACACC
* *
1422412 CATATATCATTTCACCAAGAAACACC
1 CATAAATCATTTCACCAATAAACACC
1422438 CATAAATCAT
1 CATAAATCAT
1422448 AATTCTTGTA
Statistics
Matches: 52, Mismatches: 10, Indels: 16
0.67 0.13 0.21
Matches are distributed among these distances:
26 22 0.42
27 2 0.04
28 5 0.10
29 1 0.02
31 1 0.02
32 5 0.10
33 3 0.06
34 13 0.25
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (26 bp):
CATAAATCATTTCACCAATAAACACC
Found at i:1422414 original size:60 final size:61
Alignment explanation
Indices: 1422339--1422460 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 61
1422329 TTCTTTCAGT
*
1422339 ATATCATATCACACATATATCATTTCACCAATAAACACCCATAAATCATAATTCCTGTAAC
1 ATATCATATCACACATATATCATTTCACCAAGAAACACCCATAAATCATAATTCCTGTAAC
*
1422400 ATAT-ATATCACACATATATCATTTCACCAAGAAACACCCATAAATCATAATTCTTGTAAC
1 ATATCATATCACACATATATCATTTCACCAAGAAACACCCATAAATCATAATTCCTGTAAC
1422460 A
1 A
1422461 CATTTCCTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 55 0.93
61 4 0.07
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (61 bp):
ATATCATATCACACATATATCATTTCACCAAGAAACACCCATAAATCATAATTCCTGTAAC
Found at i:1422622 original size:23 final size:23
Alignment explanation
Indices: 1422595--1422687 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
1422585 GTCACCACAA
*
1422595 CTCGTATAAATGCACCGAAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
*
1422618 CTCGTAGAAATGCACCGTAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
* * *
1422641 CACGTAGGATTGCACCGAAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
* * *
1422664 CGCGTAGAAATGCACTGTAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
1422687 C
1 C
1422688 ATATAATGTC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (23 bp):
CTCGTAGAAATGCACCGAAGTGC
Found at i:1424207 original size:19 final size:19
Alignment explanation
Indices: 1424180--1424217 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1424170 GTATCGATGC
1424180 ATTCCCTATCGGTGCATCG
1 ATTCCCTATCGGTGCATCG
* *
1424199 ATTCGCTATCTGTGCATCG
1 ATTCCCTATCGGTGCATCG
1424218 GTGCATAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (19 bp):
ATTCCCTATCGGTGCATCG
Found at i:1424324 original size:21 final size:21
Alignment explanation
Indices: 1424292--1424334 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1424282 TGTTTATTTA
1424292 ATTGAGAGTGCATCAATGCAC
1 ATTGAGAGTGCATCAATGCAC
*
1424313 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCAATGCAC
1424334 A
1 A
1424335 CAACCCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCAATGCAC
Found at i:1430099 original size:100 final size:103
Alignment explanation
Indices: 1429921--1430122 Score: 322
Period size: 100 Copynumber: 2.0 Consensus size: 103
1429911 CTAGAGTACT
* *
1429921 TGAACATATAATTCCTTGTATTTATGACAAATTTATCAAAAAAAAATTAGAGTCTAATATTATTT
1 TGAACAAATAATTCCTTGTATTTATGACAAATTTATC-AAAAAAAATTAGAGTCTAAGATTATTT
1429986 GATGATTCAAATTTATTCAAATAAATTA-TTAACATATG
65 GATGATTCAAATTTATTCAAATAAATTATTTAACATATG
* *
1430024 TGAACAAATACTTCCTTGTATTTATGCCAAATTTATC-AAAAAAA-TAGCA-TCTAAGATTATTT
1 TGAACAAATAATTCCTTGTATTTATGACAAATTTATCAAAAAAAATTAG-AGTCTAAGATTATTT
1430086 GATGATTCAAATTTATTCAAATAAATTATTTAACATA
65 GATGATTCAAATTTATTCAAATAAATTATTTAACATA
1430123 AGTATTAATT
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
100 43 0.46
101 16 0.17
103 34 0.37
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (103 bp):
TGAACAAATAATTCCTTGTATTTATGACAAATTTATCAAAAAAAATTAGAGTCTAAGATTATTTG
ATGATTCAAATTTATTCAAATAAATTATTTAACATATG
Found at i:1434976 original size:15 final size:15
Alignment explanation
Indices: 1434956--1434985 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1434946 ACTTTAGGCG
1434956 TGTAGTCAATTGCGT
1 TGTAGTCAATTGCGT
*
1434971 TGTAGTTAATTGCGT
1 TGTAGTCAATTGCGT
1434986 CCATCAGTAA
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:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
TGTAGTCAATTGCGT
Found at i:1437309 original size:20 final size:20
Alignment explanation
Indices: 1437286--1437372 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
1437276 AAGTCCAATT
1437286 TCGCAACGCGAATA-GTTAAA
1 TCGCAACGCGAATATG-TAAA
**
1437306 TCGCAACGATAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
1437326 TCGCAAGGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* * * *
1437346 TTGCAACACTAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
1437366 TCGCAAC
1 TCGCAAC
1437373 ACATAAGTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 54 0.98
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:1437330 original size:40 final size:40
Alignment explanation
Indices: 1437286--1437372 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
1437276 AAGTCCAATT
1437286 TCGCAACGCGAATA-GTTAAATCGCAACGA-TAATATGTAAA
1 TCGCAACGCGAATATG-TAAATCGCAAC-ACTAATATGTAAA
* * *
1437326 TCGCAAGGCGAATATGTAAATTGCAACACTAATTTGTAAA
1 TCGCAACGCGAATATGTAAATCGCAACACTAATATGTAAA
1437366 TCGCAAC
1 TCGCAAC
1437373 ACATAAGTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.02
40 39 0.95
41 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (40 bp):
TCGCAACGCGAATATGTAAATCGCAACACTAATATGTAAA
Found at i:1437389 original size:20 final size:20
Alignment explanation
Indices: 1437366--1437411 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1437356 AATTTGTAAA
*
1437366 TCGCAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
1437386 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
1437406 TCGCAA
1 TCGCAA
1437412 AGCGCGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.17
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:1437591 original size:22 final size:22
Alignment explanation
Indices: 1437566--1437608 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1437556 CTACGGTGAC
* *
1437566 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCACATATCCGGCGAA
1437588 ATCCGTCCACATATCCGGCGA
1 ATCCGTCCACATATCCGGCGA
1437609 CTCCCCTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCCGTCCACATATCCGGCGAA
Found at i:1437982 original size:20 final size:20
Alignment explanation
Indices: 1437935--1437996 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
1437925 AAACTTAAAT
*
1437935 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1437955 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1437975 TCGCAACGTTGCGAAAATGAAA
1 TCGCAAC---GCGAAAATGAAA
1437997 TTTGCGTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 26 0.68
23 12 0.32
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1438039 original size:20 final size:20
Alignment explanation
Indices: 1438000--1438039 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1437990 AATGAAATTT
* *
1438000 GCGTTGCGATTTTCATTTTC
1 GCGTTGCGATTTTAAGTTTC
1438020 GCGTTGCGATTTTAAGTTTC
1 GCGTTGCGATTTTAAGTTTC
1438040 AGAAACTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.47
Consensus pattern (20 bp):
GCGTTGCGATTTTAAGTTTC
Found at i:1439842 original size:21 final size:21
Alignment explanation
Indices: 1439818--1439869 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1439808 GATAATGGTG
* *
1439818 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGATGAGGTAGCTA
1439839 CTTTACGTGATGAGGTAGCTA
1 CTTTACGTGATGAGGTAGCTA
1439860 CTTTACGTGA
1 CTTTACGTGA
1439870 GATTGTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.37
Consensus pattern (21 bp):
CTTTACGTGATGAGGTAGCTA
Found at i:1440200 original size:21 final size:21
Alignment explanation
Indices: 1440149--1440267 Score: 112
Period size: 21 Copynumber: 5.7 Consensus size: 21
1440139 AATTCACCTG
* * *
1440149 TCATCGTTCAAGAAGCCTCTC
1 TCATCGTTCAAGAGGCCCCTA
* * *
1440170 TTATAGTTCAAAAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
* *
1440191 TCATCCTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* *
1440212 CCATCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTA
* *
1440233 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* *
1440254 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
1440268 CCCGATTCAC
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:1440201 original size:42 final size:42
Alignment explanation
Indices: 1440149--1440256 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 42
1440139 AATTCACCTG
* **
1440149 TCATCGTTCAAGAAGCCTCTCTTATAGTTCAAAAGGCCCCTA
1 TCATCGTTCAAGAAGCCCCTCCCATAGTTCAAAAGGCCCCTA
* * * * *
1440191 TCATCCTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAAGCCCCTCCCATAGTTCAAAAGGCCCCTA
* *
1440233 TCATCGTTCAAGAGGTCCCTCCCA
1 TCATCGTTCAAGAAGCCCCTCCCA
1440257 CCGTTCAAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (42 bp):
TCATCGTTCAAGAAGCCCCTCCCATAGTTCAAAAGGCCCCTA
Found at i:1440262 original size:42 final size:42
Alignment explanation
Indices: 1440175--1440267 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
1440165 CTCTCTTATA
* *
1440175 GTTCAAAAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCATC
1 GTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACC
* * *
1440217 GTTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCCCTCCCACC
1 GTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACC
1440259 GTTCAAGAG
1 GTTCAAGAG
1440268 CCCGATTCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
GTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACC
Found at i:1441789 original size:20 final size:20
Alignment explanation
Indices: 1441761--1441801 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1441751 TACACTTTCA
*
1441761 CAACGCGAAAGTCAAAATCG
1 CAACACGAAAGTCAAAATCG
*
1441781 CAACACGAAAGTCAAATTCG
1 CAACACGAAAGTCAAAATCG
1441801 C
1 C
1441802 GTTGCGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.27, G:0.17, T:0.12
Consensus pattern (20 bp):
CAACACGAAAGTCAAAATCG
Found at i:1441819 original size:14 final size:14
Alignment explanation
Indices: 1441797--1441826 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1441787 GAAAGTCAAA
1441797 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
*
1441811 TTCGTGTTGCGATT
1 TTCGCGTTGCGATT
1441825 TT
1 TT
1441827 GAATTTCGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.17, G:0.27, T:0.50
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:1441839 original size:20 final size:20
Alignment explanation
Indices: 1441810--1441862 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1441800 GCGTTGCGAT
*
1441810 TTTCGTGTTGCGATTTTGAA
1 TTTCGCGTTGCGATTTTGAA
*
1441830 TTTCGCGTTGCGATTTTGAT
1 TTTCGCGTTGCGATTTTGAA
*
1441850 TTTTGCGTTGCGA
1 TTTCGCGTTGCGA
1441863 ATTCAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.11, C:0.13, G:0.26, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTGAA
Found at i:1442339 original size:18 final size:18
Alignment explanation
Indices: 1442316--1442351 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1442306 AAGTCGGTTG
1442316 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
*
1442334 TGATTGTGATTTTGATTT
1 TGATTGGGATTTTGATTT
1442352 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.25, T:0.58
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:1444646 original size:24 final size:24
Alignment explanation
Indices: 1444619--1444710 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
1444609 TTGAAACATC
*
1444619 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
* *
1444643 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
*
1444667 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
* * *
1444691 ATCAAATTTCGAATATTGAC
1 ATCAAAGTCCGAGTATTGAC
1444711 TAGTACTCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAGTATTGACCAAG
Found at i:1445657 original size:20 final size:20
Alignment explanation
Indices: 1445629--1445696 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
1445619 AAATAAAAGC
*
1445629 TGTTACGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
1445649 TGTTGCG-AATTCGAAAATT-G
1 TGTTGCGAAATT--AAAATTCG
*
1445669 AT-TTGCGAAATCAAAATTCG
1 -TGTTGCGAAATTAAAATTCG
1445689 TGTTGCGA
1 TGTTGCGA
1445697 TTTAGAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
19 11 0.28
20 19 0.47
21 10 0.25
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:1445767 original size:20 final size:18
Alignment explanation
Indices: 1445741--1445901 Score: 72
Period size: 20 Copynumber: 8.1 Consensus size: 18
1445731 TTATGAAAAA
1445741 TAAATTCGCGTTGCGAATT
1 TAAATTCGCGTTGCG-ATT
*
1445760 TGAAATTC-CGTATTTCGAATT
1 T-AAATTCGCG--TTGCG-ATT
* * *
1445781 TGACTTCTGTGTTGCGATT
1 TAAATTC-GCGTTGCGATT
*
1445800 TACAAATTCACGTTGCGATT
1 T--AAATTCGCGTTGCGATT
1445820 TAACTATTCGCGTTGCGATT
1 TAA--ATTCGCGTTGCGATT
**
1445840 TACATATTATCGTTGCGATT
1 TA-A-ATTCGCGTTGCGATT
*
1445860 TAACTATTCACGTTGCGAATT
1 TAA--ATTCGCGTTGCG-ATT
* *
1445881 TGGAAAATCGCGTTGCAATT
1 T--AAATTCGCGTTGCGATT
1445901 T
1 T
1445902 TGGAACCTAT
Statistics
Matches: 111, Mismatches: 17, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
18 2 0.02
19 8 0.07
20 71 0.64
21 27 0.24
22 1 0.01
23 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (18 bp):
TAAATTCGCGTTGCGATT
Found at i:1445838 original size:40 final size:40
Alignment explanation
Indices: 1445791--1445877 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
1445781 TGACTTCTGT
*
1445791 GTTGCGATTTACAAATTCA-CGTTGCGATTTAACTATTCGC
1 GTTGCGATTTACAAATT-ATCGTTGCGATTTAACTATTCAC
*
1445831 GTTGCGATTTACATATTATCGTTGCGATTTAACTATTCAC
1 GTTGCGATTTACAAATTATCGTTGCGATTTAACTATTCAC
1445871 GTTGCGA
1 GTTGCGA
1445878 ATTTGGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (40 bp):
GTTGCGATTTACAAATTATCGTTGCGATTTAACTATTCAC
Found at i:1447008 original size:21 final size:20
Alignment explanation
Indices: 1446963--1447007 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1446953 TAAATTTGTT
1446963 TAAAATATAACAGCAGCACC
1 TAAAATATAACAGCAGCACC
*
1446983 TAAAATATAAGCAGCGGCA-C
1 TAAAATATAA-CAGCAGCACC
1447003 TAAAA
1 TAAAA
1447008 ACAATAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.51, C:0.20, G:0.13, T:0.16
Consensus pattern (20 bp):
TAAAATATAACAGCAGCACC
Found at i:1447448 original size:36 final size:36
Alignment explanation
Indices: 1447407--1447519 Score: 103
Period size: 36 Copynumber: 3.3 Consensus size: 36
1447397 GAATTTCGAG
1447407 TTCGAGTCGAACTTGAAAATTTTAAACTCACGAGTT
1 TTCGAGTCGAACTTGAAAATTTTAAACTCACGAGTT
* ** * * **
1447443 TTCGAGTCGAGC-T--CCATTTCAAAGTTTTCGAG--
1 TTCGAGTCGAACTTGAAAATTTTAAA-CTCACGAGTT
*
1447475 -TCGAGTCGAACTTGAAAATTTTAAGCTCACGAGTT
1 TTCGAGTCGAACTTGAAAATTTTAAACTCACGAGTT
1447510 TTCGAGTCGA
1 TTCGAGTCGA
1447520 GCTCCATTTC
Statistics
Matches: 55, Mismatches: 15, Indels: 14
0.65 0.18 0.17
Matches are distributed among these distances:
31 10 0.18
32 1 0.02
33 12 0.22
34 11 0.20
35 1 0.02
36 20 0.36
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (36 bp):
TTCGAGTCGAACTTGAAAATTTTAAACTCACGAGTT
Found at i:1447479 original size:31 final size:31
Alignment explanation
Indices: 1447444--1447553 Score: 96
Period size: 31 Copynumber: 3.4 Consensus size: 31
1447434 TCACGAGTTT
1447444 TCGAGTCGAGCTCCATTTCAAAGTTTTCGAG
1 TCGAGTCGAGCTCCATTTCAAAGTTTTCGAG
* ** * * **
1447475 TCGAGTCGAACTTGAAAATTT-TAAGCTCACGAG
1 TCGAGTCGAGC-T--CCATTTCAAAGTTTTCGAG
1447508 TTTTCGAGTCGAGCTCCATTTCAAAGTTTTCGAG
1 ---TCGAGTCGAGCTCCATTTCAAAGTTTTCGAG
1447542 TCGAGTCGAGCT
1 TCGAGTCGAGCT
1447554 TAGCAATACT
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
31 22 0.38
32 1 0.02
33 12 0.21
34 12 0.21
35 1 0.02
36 10 0.17
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (31 bp):
TCGAGTCGAGCTCCATTTCAAAGTTTTCGAG
Found at i:1447479 original size:67 final size:67
Alignment explanation
Indices: 1447400--1447550 Score: 284
Period size: 67 Copynumber: 2.2 Consensus size: 67
1447390 CAATTCAGAA
1447400 TTTCGAGTTCGAGTCGAACTTGAAAATTTTAAACTCACGAGTTTTCGAGTCGAGCTCCATTTCAA
1 TTTCGAG-TCGAGTCGAACTTGAAAATTTTAAACTCACGAGTTTTCGAGTCGAGCTCCATTTCAA
1447465 AGT
65 AGT
*
1447468 TTTCGAGTCGAGTCGAACTTGAAAATTTTAAGCTCACGAGTTTTCGAGTCGAGCTCCATTTCAAA
1 TTTCGAGTCGAGTCGAACTTGAAAATTTTAAACTCACGAGTTTTCGAGTCGAGCTCCATTTCAAA
1447533 GT
66 GT
1447535 TTTCGAGTCGAGTCGA
1 TTTCGAGTCGAGTCGA
1447551 GCTTAGCAAT
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
67 75 0.91
68 7 0.09
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (67 bp):
TTTCGAGTCGAGTCGAACTTGAAAATTTTAAACTCACGAGTTTTCGAGTCGAGCTCCATTTCAAA
GT
Found at i:1447496 original size:26 final size:26
Alignment explanation
Indices: 1447441--1447496 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
1447431 AACTCACGAG
* * *
1447441 TTTTCGAGTCGAGCTCCATTTCAAAG
1 TTTTCGAGTCGAGCTCAACTTCAAAA
*
1447467 TTTTCGAGTCGAG-TCGAACTTGAAAA
1 TTTTCGAGTCGAGCTC-AACTTCAAAA
1447493 TTTT
1 TTTT
1447497 AAGCTCACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.38
Consensus pattern (26 bp):
TTTTCGAGTCGAGCTCAACTTCAAAA
Found at i:1453861 original size:11 final size:11
Alignment explanation
Indices: 1453822--1453909 Score: 99
Period size: 11 Copynumber: 7.9 Consensus size: 11
1453812 AGCTCGAAAC
1453822 TCAAGCTCGAT
1 TCAAGCTCGAT
** *
1453833 TGGAGGTCGATT
1 TCAAGCTCGA-T
*
1453845 TTAAGCTCGAT
1 TCAAGCTCGAT
1453856 TCAAGCTC-AT
1 TCAAGCTCGAT
1453866 TCTAAGCTCGAT
1 TC-AAGCTCGAT
1453878 TCAAGCTC-AT
1 TCAAGCTCGAT
1453888 TCTAAGCTCGAT
1 TC-AAGCTCGAT
1453900 TCAAGCTCGA
1 TCAAGCTCGA
1453910 CGGGTTTTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.12
11 41 0.63
12 16 0.25
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (11 bp):
TCAAGCTCGAT
Found at i:1453874 original size:22 final size:22
Alignment explanation
Indices: 1453846--1453907 Score: 124
Period size: 22 Copynumber: 2.8 Consensus size: 22
1453836 AGGTCGATTT
1453846 TAAGCTCGATTCAAGCTCATTC
1 TAAGCTCGATTCAAGCTCATTC
1453868 TAAGCTCGATTCAAGCTCATTC
1 TAAGCTCGATTCAAGCTCATTC
1453890 TAAGCTCGATTCAAGCTC
1 TAAGCTCGATTCAAGCTC
1453908 GACGGGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (22 bp):
TAAGCTCGATTCAAGCTCATTC
Found at i:1456700 original size:21 final size:21
Alignment explanation
Indices: 1456654--1456715 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
1456644 TCTCGTCCCT
*
1456654 AAGCCGTTGAGCTTTTGTTCTT
1 AAGCCGTTGAGC-TTTGTTCTC
*
1456676 AAGCCGTTGTGCTTTGTTGC-C
1 AAGCCGTTGAGCTTTGTT-CTC
*
1456697 AAGCC-TATGGGCTTTGTTC
1 AAGCCGT-TGAGCTTTGTTC
1456716 GTCGTGGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 21 0.60
22 12 0.34
ACGTcount: A:0.13, C:0.21, G:0.26, T:0.40
Consensus pattern (21 bp):
AAGCCGTTGAGCTTTGTTCTC
Found at i:1457622 original size:22 final size:22
Alignment explanation
Indices: 1457597--1458125 Score: 726
Period size: 22 Copynumber: 24.0 Consensus size: 22
1457587 ATAATAAATT
**
1457597 TTTTAAAATAAATCAATTTATA
1 TTTTAAAATAAATCAATCCATA
1457619 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1457641 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1457663 TTTTAAAATAAAAT-TTTACATA
1 TTTTAAAAT-AAATCAATCCATA
1457685 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1457707 TTTTAAAATAAAAT-TTTACATA
1 TTTTAAAAT-AAATCAATCCATA
1457729 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1457751 TTTTAAAATAAAAT-TTTACATA
1 TTTTAAAAT-AAATCAATCCATA
1457773 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1457795 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1457817 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
1457839 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1457861 TTTTAAAATAAAAT-TGTCCATA
1 TTTTAAAAT-AAATCAATCCATA
1457883 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1457905 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1457927 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
*
1457949 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*** *
1457971 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
1457993 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *
1458015 TTTTAAAATAAACCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1458037 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
1458059 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
1458081 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1458103 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1458125 T
1 T
1458126 AAATTTTAAA
Statistics
Matches: 448, Mismatches: 49, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
21 20 0.04
22 408 0.91
23 20 0.04
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1459999 original size:18 final size:19
Alignment explanation
Indices: 1459976--1460014 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1459966 CACCTAAAAA
1459976 TTTAAAA-TTATTATATAT
1 TTTAAAACTTATTATATAT
* *
1459994 TTTAAAACTTTTTATGTAT
1 TTTAAAACTTATTATATAT
1460013 TT
1 TT
1460015 CATATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTAAAACTTATTATATAT
Found at i:1463897 original size:2 final size:2
Alignment explanation
Indices: 1463885--1463923 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
1463875 AGAATATGCG
1463885 AT AT GAT 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
1463924 GATAATGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1464096 original size:21 final size:21
Alignment explanation
Indices: 1464072--1464130 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
1464062 TTCTATGTGG
* *
1464072 TCCTTCGGGATATATATGTAA
1 TCCTTCGGAACATATATGTAA
* *
1464093 TCCTTTGGAACATATATGTAG
1 TCCTTCGGAACATATATGTAA
*
1464114 TTCTTCGAGACACATAT
1 TCCTTCG-GA-ACATAT
1464131 TTGGTCTTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 22 0.73
22 2 0.07
23 6 0.20
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:1471221 original size:83 final size:83
Alignment explanation
Indices: 1471044--1471337 Score: 286
Period size: 83 Copynumber: 3.6 Consensus size: 83
1471034 TCTTACGCGT
* * * * * * *
1471044 CGTTT-TAAAAAAACACCGTTAAAATACAAATATTTTGTGGCATTTGTTA-AAAAAAGCAACTGT
1 CGTTTGTATAAAAACACCGCTAAAGTACAAATATTTTGCGGCATTTGTTATAAAAACGCCACTAT
*
1471107 AGATTACACCTATTGCGG
66 AGATTACACCTATTGCAG
* * * * * **
1471125 AGTTTGTACAAAAACGCCGCTAAAGTATAAATATTTTGCGGCATTTTTTATCCAAACGCCACTAT
1 CGTTTGTATAAAAACACCGCTAAAGTACAAATATTTTGCGGCATTTGTTATAAAAACGCCACTAT
*
1471190 AGATTACACCTATTGCTG
66 AGATTACACCTATTGCAG
* * *** * * * * * *
1471208 CGTTTTTATAAAAATACCGCTTTTGTATAAATATTTTGTGGCGTTTGGTATTAAAACGCCACTAC
1 CGTTTGTATAAAAACACCGCTAAAGTACAAATATTTTGCGGCATTTGTTATAAAAACGCCACTAT
1471273 AGATTACACCTATTGCAG
66 AGATTACACCTATTGCAG
* * * *
1471291 CATTTGCATAAAAACGCCGCTAAAGTACAAATATTTTTGCGACATTT
1 CGTTTGTATAAAAACACCGCTAAAGTACAAATA-TTTTGCGGCATTT
1471338 CTTGAAAAAG
Statistics
Matches: 168, Mismatches: 42, Indels: 3
0.79 0.20 0.01
Matches are distributed among these distances:
81 4 0.02
82 37 0.22
83 117 0.70
84 10 0.06
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (83 bp):
CGTTTGTATAAAAACACCGCTAAAGTACAAATATTTTGCGGCATTTGTTATAAAAACGCCACTAT
AGATTACACCTATTGCAG
Found at i:1471681 original size:73 final size:73
Alignment explanation
Indices: 1471562--1471711 Score: 273
Period size: 73 Copynumber: 2.1 Consensus size: 73
1471552 AAAAGTTATG
* * *
1471562 CATAAAATTAATACTTAACAACAGAATACATTAAAATTTAGAAACATTAAAGTTATGCATAAACA
1 CATAAAATTAATACTTAACAACAAAATACATTAAAATTTAGAAACATTAAAATTATGCATAAAAA
1471627 GTCTTCAC
66 GTCTTCAC
1471635 CATAAAATTAATACTTAACAACAAAATACATTAAAATTTAGAAACATTAAAATTATGCATAAAAA
1 CATAAAATTAATACTTAACAACAAAATACATTAAAATTTAGAAACATTAAAATTATGCATAAAAA
1471700 GTCTTCAC
66 GTCTTCAC
1471708 CATA
1 CATA
1471712 TTGTTCACTT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (73 bp):
CATAAAATTAATACTTAACAACAAAATACATTAAAATTTAGAAACATTAAAATTATGCATAAAAA
GTCTTCAC
Found at i:1476638 original size:19 final size:20
Alignment explanation
Indices: 1476599--1476638 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1476589 TAAGTGTTAA
*
1476599 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
1476619 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
1476638 T
1 T
1476639 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:1476901 original size:36 final size:36
Alignment explanation
Indices: 1476832--1476901 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1476822 ATTGCCCAGA
* ***
1476832 GGGAACAGATTCCCCCCTAGGGGGTATTGATTCCCC
1 GGGAACAGATTCCCCCCCAGGGGGTACCAATTCCCC
1476868 GGGAACAGATTCCCCCCCAGGGGGTACCAATTCC
1 GGGAACAGATTCCCCCCCAGGGGGTACCAATTCC
1476902 ACCCCAGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.21, C:0.33, G:0.27, T:0.19
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCCAGGGGGTACCAATTCCCC
Found at i:1481809 original size:19 final size:19
Alignment explanation
Indices: 1481785--1481826 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1481775 TAAGTTACAA
*
1481785 TTGATGTAATTGTAAGACT
1 TTGATGAAATTGTAAGACT
* *
1481804 TTGATGAAATTGTGAGATT
1 TTGATGAAATTGTAAGACT
1481823 TTGA
1 TTGA
1481827 ATTGACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.43
Consensus pattern (19 bp):
TTGATGAAATTGTAAGACT
Found at i:1482047 original size:24 final size:23
Alignment explanation
Indices: 1482007--1482052 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1481997 TTAATTTAGA
*
1482007 TATTTATAAATTTAATTTATTTT
1 TATTTATAAATTTAATTAATTTT
1482030 TATTTA-ATAATTTAAATTAATTT
1 TATTTATA-AATTT-AATTAATTT
1482053 AGCTCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 11 0.55
24 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTATAAATTTAATTAATTTT
Found at i:1482617 original size:12 final size:12
Alignment explanation
Indices: 1482601--1482752 Score: 66
Period size: 12 Copynumber: 13.6 Consensus size: 12
1482591 ATATATACAC
1482601 ATATATACTTAT
1 ATATATACTTAT
*
1482613 GTATATACTTAT
1 ATATATACTTAT
1482625 AT-TATACTT-T
1 ATATATACTTAT
1482635 ATA-ATTA-TATAT
1 ATATA-TACT-TAT
*
1482647 AGATATA-TATAGT
1 ATATATACT-TA-T
1482660 ATATATACTTAT
1 ATATATACTTAT
**
1482672 ATATA-AAGTAT
1 ATATATACTTAT
1482683 -TA-ATA--TAT
1 ATATATACTTAT
* * *
1482691 ATACACACATAT
1 ATATATACTTAT
*
1482703 GTATATACTTAT
1 ATATATACTTAT
*
1482715 A-AT-TAATTA-
1 ATATATACTTAT
1482724 ATATATA--TAT
1 ATATATACTTAT
1482734 ATATATA-TATAT
1 ATATATACT-TAT
1482746 ATATATA
1 ATATATA
1482753 TTAATTATAA
Statistics
Matches: 110, Mismatches: 13, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
8 3 0.03
9 6 0.05
10 24 0.22
11 18 0.16
12 48 0.44
13 10 0.09
14 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (12 bp):
ATATATACTTAT
Found at i:1482647 original size:2 final size:2
Alignment explanation
Indices: 1482640--1482753 Score: 75
Period size: 2 Copynumber: 59.5 Consensus size: 2
1482630 ACTTTATAAT
* *
1482640 TA TA TA TA GA TA TA TA TA GTA TA TA TA CT- TA TA TA TA AA GTA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA
* * * *
1482682 T- TA -A TA TA TA TA CA CA CA TA TG TA TA TA CT- TA TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
1482720 -A T- TA -A 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 T
1482754 TAATTATAAG
Statistics
Matches: 91, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
1 9 0.10
2 77 0.85
3 5 0.05
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1482664 original size:19 final size:19
Alignment explanation
Indices: 1482640--1482676 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1482630 ACTTTATAAT
*
1482640 TATATATAGATATATATAG
1 TATATATACATATATATAG
*
1482659 TATATATACTTATATATA
1 TATATATACATATATATA
1482677 AAGTATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (19 bp):
TATATATACATATATATAG
Found at i:1483019 original size:2 final size:2
Alignment explanation
Indices: 1483012--1483067 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1483002 ATCATACATA
1483012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1483054 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1483068 TGTTTCAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1483282 original size:128 final size:132
Alignment explanation
Indices: 1483138--1483401 Score: 287
Period size: 137 Copynumber: 2.0 Consensus size: 132
1483128 CTGATATTTA
1483138 TAATTATTTCAATTTGAT-TC-C-CC-TGT-TT-TTTAATATATTTAAAT-TTTAATTTGTAATT
1 TAATTATTTCAATTTGATCTCTCACCATGTGTTATTTAATATATTTAAATATTT-ATTTGTAATT
* * *
1483196 TTATATTT-TTCAATTTAGTCCTTAAAATTATATTTGTAT-ATGAAATTG-ACACATGCTTATTT
65 TCATATTTGTTCAATTTAGTCATTAAAATTAT-TTT-TATCA--AAATTGAACA-ATACTTATTT
1483258 ATATTTTT
125 ATATTTTT
* * * *
1483266 TAATTGTTTCGATTTGATCTCTCATCCATGTGTGTTATTTAATTTATTTAAATATTTGTTTGTAA
1 TAATTATTTCAATTTGATCTCTCA-CCA--TGTGTTATTTAATATATTTAAATATTTATTTGTAA
* * *
1483331 TTTCATGTTTGTTCAGTTTAGTCATTAAAATTATTTTTATCAAAATTGAACAATATTTATTTATA
63 TTTCATATTTGTTCAATTTAGTCATTAAAATTATTTTTATCAAAATTGAACAATACTTATTTATA
1483396 TTTTT
128 TTTTT
1483401 T
1 T
1483402 GTAATTTACT
Statistics
Matches: 113, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
128 16 0.14
129 2 0.02
130 1 0.01
132 2 0.02
135 26 0.23
136 8 0.07
137 34 0.30
138 24 0.21
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (132 bp):
TAATTATTTCAATTTGATCTCTCACCATGTGTTATTTAATATATTTAAATATTTATTTGTAATTT
CATATTTGTTCAATTTAGTCATTAAAATTATTTTTATCAAAATTGAACAATACTTATTTATATTT
TT
Found at i:1487295 original size:24 final size:24
Alignment explanation
Indices: 1487243--1487295 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1487233 GCCCAGTGAT
* *
1487243 AGATGTAGAATAAGGAGCAGAATC
1 AGATGTAGAAGAAGAAGCAGAATC
* **
1487267 GGATGTAGAAGAAGAAGCAGGTTC
1 AGATGTAGAAGAAGAAGCAGAATC
1487291 AGATG
1 AGATG
1487296 GGACAATATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.34, T:0.17
Consensus pattern (24 bp):
AGATGTAGAAGAAGAAGCAGAATC
Found at i:1490279 original size:39 final size:40
Alignment explanation
Indices: 1490220--1490298 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 40
1490210 GTCAAAAGTG
1490220 TTGGTGTAGTGTGAGTGGTATATCCTAGGTTCTTTATAGTA
1 TTGGTGTAG-GTGAGTGGTATATCCTAGGTTCTTTATAGTA
1490261 TTGGTGTA-GTGAGTGGTATATCCTAGGTTCTTTATAGT
1 TTGGTGTAGGTGAGTGGTATATCCTAGGTTCTTTATAGT
1490299 GGGTGTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 30 0.79
41 8 0.21
ACGTcount: A:0.19, C:0.08, G:0.29, T:0.44
Consensus pattern (40 bp):
TTGGTGTAGGTGAGTGGTATATCCTAGGTTCTTTATAGTA
Found at i:1490757 original size:42 final size:43
Alignment explanation
Indices: 1490671--1490784 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 43
1490661 CTTGTGGAAG
* * *
1490671 ACATATA-TTATTTTTCAT-GTAAATTCACTCTCTTAAAAACCT
1 ACATATAGTCATTTTTCATAG-AAATGCACTATCTTAAAAACCT
*
1490713 ACATATAGTCATTTTTCATAGAAATGCCCTATCTTAAAAA-CT
1 ACATATAGTCATTTTTCATAGAAATGCACTATCTTAAAAACCT
* *
1490755 ACATATAGTCAATTTTCATATAAATGCACT
1 ACATATAGTCATTTTTCATAGAAATGCACT
1490785 TTGTTGAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
42 36 0.57
43 26 0.41
44 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (43 bp):
ACATATAGTCATTTTTCATAGAAATGCACTATCTTAAAAACCT
Found at i:1497894 original size:27 final size:27
Alignment explanation
Indices: 1497854--1497911 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
1497844 CCCGATGGGA
*
1497854 ACGAGGGGTGCTGCAGCAAAGGTGGAG
1 ACGAGGGGTACTGCAGCAAAGGTGGAG
1497881 ACGAGGGGTACTGCAGCAAAGGTGGAG
1 ACGAGGGGTACTGCAGCAAAGGTGGAG
1497908 ACGA
1 ACGA
1497912 AGCAATCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.45, T:0.10
Consensus pattern (27 bp):
ACGAGGGGTACTGCAGCAAAGGTGGAG
Done.