Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009081.1 Hibiscus syriacus cultivar Beakdansim tig00112523_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: 1718667
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1466512 original size:52 final size:52
Alignment explanation
Indices: 1466386--1466514 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1466376 TAGTTTACTT
**
1466386 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1466438 T-G-AAAATCGCAACGACATAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1466491 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1466515 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1466551 original size:14 final size:14
Alignment explanation
Indices: 1466532--1466588 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1466522 TTTCATTTCG
1466532 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1466546 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
* *
1466563 CGCATTGCAATTCTGT
1 CG--TTGCGATTCTTT
1466579 CGTTGCGATT
1 CGTTGCGATT
1466589 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 15 0.43
16 7 0.20
17 8 0.23
19 5 0.14
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1466557 original size:33 final size:33
Alignment explanation
Indices: 1466515--1466607 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1466505 CAAAATCGCA
*
1466515 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
* *
1466548 TTGCGATTTTCATTTCGCATTGCAATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1466581 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1466608 TTGGTTTCGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1466615 original size:19 final size:19
Alignment explanation
Indices: 1466510--1466624 Score: 97
Period size: 19 Copynumber: 6.6 Consensus size: 19
1466500 GAAACCAAAA
*
1466510 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1466529 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1466545 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * *
1466562 TCGCATTGC-A-ATTC-TG
1 TCGCGTTGCGATTTTCATT
1466578 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1466595 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1466614 TCGTGTTGCGA
1 TCGCGTTGCGA
1466625 AAGTAAACTA
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
14 13 0.17
15 1 0.01
16 11 0.14
17 11 0.14
18 1 0.01
19 39 0.51
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1468567 original size:14 final size:14
Alignment explanation
Indices: 1468548--1468583 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1468538 ATTGTTTAAT
1468548 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1468562 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
1468576 TGATTTGT
1 TGATTTGT
1468584 GTTGTATACC
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:1468634 original size:20 final size:20
Alignment explanation
Indices: 1468606--1468835 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
1468596 AAATTTCAGT
* * *
1468606 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1468626 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1468646 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1468666 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1468686 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1468706 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1468726 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1468746 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1468766 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1468786 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1468806 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1468826 GTTGCGATTT
1 GTTGCGATTT
1468836 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1468852 original size:21 final size:21
Alignment explanation
Indices: 1468822--1468904 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1468812 ATTTTCATAT
*
1468822 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1468843 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1468864 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1468885 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1468905 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1468895 original size:42 final size:43
Alignment explanation
Indices: 1468802--1468900 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1468792 ATTTATGTGT
* *
1468802 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1468843 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1468885 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1468901 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1469687 original size:16 final size:16
Alignment explanation
Indices: 1469666--1469696 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1469656 AAATTTAAAT
*
1469666 TTTATTTTTTTAATTA
1 TTTATTTTATTAATTA
1469682 TTTATTTTATTAATT
1 TTTATTTTATTAATT
1469697 GTGTCTTGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTTATTAATTA
Found at i:1472240 original size:22 final size:22
Alignment explanation
Indices: 1472187--1472240 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1472177 ATGAAAGAAG
*
1472187 ATAAATA-TAAAAAATAATTAT
1 ATAAATATTAAAAAATAATCAT
** * *
1472208 ATTTATTTTAAAATATAATCAT
1 ATAAATATTAAAAAATAATCAT
1472230 ATAAATATTAA
1 ATAAATATTAA
1472241 GATTTAAATC
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATATTAAAAAATAATCAT
Found at i:1483309 original size:2 final size:2
Alignment explanation
Indices: 1483302--1483334 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1483292 TTGTTAAAAT
1483302 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 T
1483335 TGGTTCTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1485618 original size:15 final size:15
Alignment explanation
Indices: 1485598--1485636 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1485588 CAATAGCTAG
1485598 GATAATTAAATAAAA
1 GATAATTAAATAAAA
1485613 GATAATTAAATAAAA
1 GATAATTAAATAAAA
1485628 -ATAATTAAA
1 GATAATTAAA
1485637 ATAAGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
GATAATTAAATAAAA
Found at i:1485638 original size:15 final size:14
Alignment explanation
Indices: 1485599--1485646 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
1485589 AATAGCTAGG
1485599 ATAATTAAATAAAA
1 ATAATTAAATAAAA
1485613 GATAATTAAATAAAA
1 -ATAATTAAATAAAA
*
1485628 ATAATTAAAATAAGA
1 ATAATT-AAATAAAA
1485643 ATAA
1 ATAA
1485647 ACTTATTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 6 0.19
15 25 0.81
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (14 bp):
ATAATTAAATAAAA
Found at i:1491633 original size:75 final size:76
Alignment explanation
Indices: 1491533--1491729 Score: 263
Period size: 75 Copynumber: 2.6 Consensus size: 76
1491523 GTTGTACAAT
* * *
1491533 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
** *
1491597 AAACTGTTTAG
66 AAACCATTCAG
* * * *
1491608 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
1491672 AAACCATTCAG
66 AAACCATTCAG
* *
1491683 GGGGAAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCCGAGCA
1491730 ATCTGTAATT
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
75 83 0.78
76 6 0.06
77 17 0.16
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
AAACCATTCAG
Found at i:1492333 original size:17 final size:17
Alignment explanation
Indices: 1492311--1492354 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1492301 TTCATAAATC
1492311 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
1492328 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
1492345 -AAATATCCAA
1 CAAA-ATCCAA
1492355 AAAGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:1492346 original size:9 final size:8
Alignment explanation
Indices: 1492306--1492357 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
1492296 CACTATTCAT
1492306 AAATCC-A
1 AAATCCAA
1492313 AAATCCAA
1 AAATCCAA
*
1492321 CAATCCACA
1 AAATCCA-A
1492330 AAAT-CAA
1 AAATCCAA
1492337 ACAATCCAA
1 A-AATCCAA
1492346 AATATCCAA
1 AA-ATCCAA
1492355 AAA
1 AAA
1492358 GTTGAAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 8 0.21
8 14 0.37
9 16 0.42
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATCCAA
Found at i:1493151 original size:18 final size:18
Alignment explanation
Indices: 1493128--1493164 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1493118 TAATCCGGAT
1493128 CAAGATGGAAATATTGAC
1 CAAGATGGAAATATTGAC
1493146 CAAGATGGAAATATTGAC
1 CAAGATGGAAATATTGAC
1493164 C
1 C
1493165 TAGGAGGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (18 bp):
CAAGATGGAAATATTGAC
Found at i:1494205 original size:21 final size:21
Alignment explanation
Indices: 1494179--1494218 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1494169 CAGAACCCCA
*
1494179 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1494200 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1494219 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1494247 original size:20 final size:21
Alignment explanation
Indices: 1494201--1494261 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1494191 TTCCCCTGTG
1494201 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1494224 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1494244 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1494262 TGTACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1498101 original size:22 final size:21
Alignment explanation
Indices: 1498059--1498098 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1498049 GAGTTTGTTT
*
1498059 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1498080 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1498099 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1500089 original size:75 final size:77
Alignment explanation
Indices: 1500005--1500201 Score: 258
Period size: 74 Copynumber: 2.6 Consensus size: 77
1499995 GTTGTACAAT
* * * *
1500005 GGGGGAATCGGTACCCCCT-TGGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAAC
** *
1500069 AAAACTGTTTA-
66 AAAACCATTCAG
* *
1500080 GGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAAC
*
1500143 CAAACCATTCAG
66 AAAACCATTCAG
* *
1500155 GGGGGAATCGGTTCCTTCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCA
1500202 ATCTGTAATT
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
74 45 0.42
75 37 0.35
76 1 0.01
77 23 0.22
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (77 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAAC
AAAACCATTCAG
Found at i:1501982 original size:14 final size:14
Alignment explanation
Indices: 1501963--1501992 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1501953 TAACAGACTT
1501963 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1501977 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1501991 GT
1 GT
1501993 TTCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:1518510 original size:17 final size:18
Alignment explanation
Indices: 1518488--1518521 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1518478 ATATGTTAAA
*
1518488 TAATTAA-TAGTTTTGAT
1 TAATTAAGTAATTTTGAT
1518505 TAATTAAGTAATTTTGA
1 TAATTAAGTAATTTTGA
1518522 ACCAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (18 bp):
TAATTAAGTAATTTTGAT
Found at i:1518972 original size:39 final size:39
Alignment explanation
Indices: 1518909--1518988 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
1518899 ATGATTATCA
* * *
1518909 GTACCTTCGGGTCTCGATGTAAGTTTCTTTCACTAGTTT
1 GTACCTTCGAGTCTCGATGCAAGTTTCTTCCACTAGTTT
*
1518948 GTACCTTCGAGTCTTGATGCAAGTTTCTTCCACTAGTTT
1 GTACCTTCGAGTCTCGATGCAAGTTTCTTCCACTAGTTT
1518987 GT
1 GT
1518989 GATTTTATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.42
Consensus pattern (39 bp):
GTACCTTCGAGTCTCGATGCAAGTTTCTTCCACTAGTTT
Found at i:1519549 original size:2 final size:2
Alignment explanation
Indices: 1519542--1519582 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1519532 TCAGAATTTA
1519542 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
1519583 ACATCTTAAA
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:1519654 original size:5 final size:5
Alignment explanation
Indices: 1519644--1519673 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1519634 GGGCGTAAAT
1519644 GAGTC GAGTC GAGTC GAGTC GAGTTC GAGT
1 GAGTC GAGTC GAGTC GAGTC GAG-TC GAGT
1519674 ATTGCTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.20, C:0.17, G:0.40, T:0.23
Consensus pattern (5 bp):
GAGTC
Found at i:1523381 original size:3 final size:3
Alignment explanation
Indices: 1523373--1523398 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1523363 CCATGTGAAT
1523373 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1523399 GCATAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1523488 original size:2 final size:2
Alignment explanation
Indices: 1523481--1523513 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1523471 ACTAAATTTC
1523481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1523514 CGAACGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1524724 original size:35 final size:35
Alignment explanation
Indices: 1524685--1524764 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
1524675 AACACAATCA
1524685 TCAATTACATTATAAA-CTCCAAAATCCAAAATACT
1 TCAATTACATTATAAACCT-CAAAATCCAAAATACT
* *
1524720 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTATAAACCTCAAAATCCAAAATACT
*
1524755 TTAATTACAT
1 TCAATTACAT
1524765 ACCCAACCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 39 0.95
36 2 0.05
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTATAAACCTCAAAATCCAAAATACT
Found at i:1524779 original size:35 final size:35
Alignment explanation
Indices: 1524704--1524780 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
1524694 TTATAAACTC
* * *
1524704 CAAAATCCAAAATACTTCAATTACATTCTAAACCT
1 CAAATTCCAAAATACTTCAATTACATCCCAAACCT
* *
1524739 CAAATTCCAAAATACTTTAATTACATACCCAACCCT
1 CAAATTCCAAAATACTTCAATTACAT-CCCAAACCT
1524775 -AAATTC
1 CAAATTC
1524781 ATAATTCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
35 30 0.83
36 6 0.17
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (35 bp):
CAAATTCCAAAATACTTCAATTACATCCCAAACCT
Found at i:1525614 original size:36 final size:35
Alignment explanation
Indices: 1525574--1525651 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
1525564 ATTGGTCATG
*
1525574 TAATTGAAATATTTTTGGAATTT-GAGGTTTAGAATA
1 TAATTGAAACA-TTTTGGAATTTAG-GGTTTAGAATA
* *
1525610 TAATTGAAGCATTTTGGAATTTAGGGTTTAGAATG
1 TAATTGAAACATTTTGGAATTTAGGGTTTAGAATA
1525645 TAATTGA
1 TAATTGA
1525652 TAATTGTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 28 0.74
36 10 0.26
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
TAATTGAAACATTTTGGAATTTAGGGTTTAGAATA
Found at i:1537852 original size:73 final size:73
Alignment explanation
Indices: 1537769--1537910 Score: 248
Period size: 73 Copynumber: 1.9 Consensus size: 73
1537759 TAAATTTACG
* *
1537769 TTCTCTATCAATTCCTAAATTATTATTATTATTTTATTTTGATTCTTCCATTAACATGTCATAGA
1 TTCTATATCAATTCCTAAATTATTATTATTATTCTATTTTGATTCTTCCATTAACATGTCATAGA
1537834 CTCGGAAA
66 CTCGGAAA
* *
1537842 TTCTATATCAATTCTTAAATTATTATTATTATTCTATTTTGATTCTTCCATTAATATGTCATAGA
1 TTCTATATCAATTCCTAAATTATTATTATTATTCTATTTTGATTCTTCCATTAACATGTCATAGA
1537907 CTCG
66 CTCG
1537911 AAAGTCACAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (73 bp):
TTCTATATCAATTCCTAAATTATTATTATTATTCTATTTTGATTCTTCCATTAACATGTCATAGA
CTCGGAAA
Found at i:1539132 original size:2 final size:2
Alignment explanation
Indices: 1539121--1539204 Score: 55
Period size: 2 Copynumber: 47.5 Consensus size: 2
1539111 GAACCCGAAA
* * *
1539121 AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1539158 -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT -T 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
1539194 AT AT AT AT AT A
1 AT AT AT AT AT A
1539205 ATCGGGGTGG
Statistics
Matches: 67, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
1 11 0.16
2 56 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1539142 original size:9 final size:8
Alignment explanation
Indices: 1539120--1539206 Score: 54
Period size: 9 Copynumber: 10.4 Consensus size: 8
1539110 TGAACCCGAA
*
1539120 AATATTAT
1 AATATAAT
1539128 ATATATAATT
1 A-ATATAA-T
*
1539138 AATATAAA
1 AATATAAT
1539146 AATATAA-
1 AATATAAT
*
1539153 AATATTAT
1 AATATAAT
1539161 ATATATAATT
1 A-ATATAA-T
1539171 AATATAA-
1 AATATAAT
*
1539178 AATATTAT
1 AATATAAT
1539186 -ATATATAT
1 AATATA-AT
1539194 ATATATATAT
1 A-ATATA-AT
1539204 AAT
1 AAT
1539207 CGGGGTGGGG
Statistics
Matches: 64, Mismatches: 6, Indels: 17
0.74 0.07 0.20
Matches are distributed among these distances:
7 16 0.25
8 11 0.17
9 24 0.38
10 13 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AATATAAT
Found at i:1539155 original size:33 final size:35
Alignment explanation
Indices: 1539118--1539206 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 35
1539108 CCTGAACCCG
1539118 AAAATATTATATATATAATTAATATAAAA-A-TAT
1 AAAATATTATATATATAATTAATATAAAATATTAT
1539151 AAAATATTATATATATAATTAATATAAAATATTAT
1 AAAATATTATATATATAATTAATATAAAATATTAT
*
1539186 ATATATATATATATATATAAT
1 A-AAATAT-TATATATATAAT
1539207 CGGGGTGGGG
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
33 29 0.57
34 1 0.02
35 4 0.08
36 5 0.10
37 12 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (35 bp):
AAAATATTATATATATAATTAATATAAAATATTAT
Found at i:1541394 original size:16 final size:16
Alignment explanation
Indices: 1541375--1541406 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1541365 TCTCTCGACT
1541375 ATTAAAAATTACAAAA
1 ATTAAAAATTACAAAA
*
1541391 ATTATAAATTACAAAA
1 ATTAAAAATTACAAAA
1541407 TGATAATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTAAAAATTACAAAA
Found at i:1541412 original size:15 final size:16
Alignment explanation
Indices: 1541380--1541412 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1541370 CGACTATTAA
*
1541380 AAATTACAAAAATTAT
1 AAATTACAAAAATGAT
1541396 AAATTAC-AAAATGAT
1 AAATTACAAAAATGAT
1541411 AA
1 AA
1541413 TTTGATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (16 bp):
AAATTACAAAAATGAT
Found at i:1547747 original size:22 final size:22
Alignment explanation
Indices: 1547721--1547776 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1547711 GAAATACGGT
* * *
1547721 ATGAACAATACCGTGAACAGTC
1 ATGAACAATACCATAAACAGTA
*
1547743 ATGAACAGTACCATAAACAGTA
1 ATGAACAATACCATAAACAGTA
1547765 ATGAACAATACC
1 ATGAACAATACC
1547777 CTGCTACAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.18
Consensus pattern (22 bp):
ATGAACAATACCATAAACAGTA
Found at i:1547856 original size:20 final size:21
Alignment explanation
Indices: 1547820--1547861 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
1547810 ATGTTAGAGG
1547820 GGTATCGATACCCCTGCTACA
1 GGTATCGATACCCCTGCTACA
1547841 GGTATCGATA-CCCTGCTACA
1 GGTATCGATACCCCTGCTACA
1547861 G
1 G
1547862 TACTGCTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (21 bp):
GGTATCGATACCCCTGCTACA
Found at i:1548140 original size:23 final size:23
Alignment explanation
Indices: 1548122--1548182 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1548112 CGCGTAAAAA
*
1548122 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
1548145 TACACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
1548168 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1548183 TATAGTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:1550119 original size:103 final size:103
Alignment explanation
Indices: 1549935--1550152 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
1549925 GTCGAGGGTC
1549935 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATAC
*
1550000 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
1550038 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAA-ACACATA
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGT-AAGACACATA
*
1550102 CTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
65 CTTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
*
1550141 TATATGGTCCTT
1 TATGTGGTCCTT
1550153 ATGGACATTA
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 109 0.98
104 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATAC
TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1550202 original size:23 final size:23
Alignment explanation
Indices: 1550169--1550234 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
1550159 ATTATTATAT
*
1550169 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* * *
1550192 GTCACTCCGGTGCAATTATACGT
1 GGCACTACGGTGCAATTATACGC
*
1550215 GGCACTTCGGTGCAATTATA
1 GGCACTACGGTGCAATTATA
1550235 TGAGCTGTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1550781 original size:103 final size:103
Alignment explanation
Indices: 1550556--1550773 Score: 402
Period size: 103 Copynumber: 2.1 Consensus size: 103
1550546 TTCGAGGGTC
1550556 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATAC
*
1550621 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
1550659 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAA-ACACATA
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGT-AAGACACATA
*
1550723 CTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
65 CTTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
1550762 TATGTGGTCCTT
1 TATGTGGTCCTT
1550774 ATGGACATTA
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
103 110 0.98
104 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATAC
TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1550825 original size:23 final size:23
Alignment explanation
Indices: 1550790--1550855 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
1550780 ATTATTATAT
* * *
1550790 GGCACTACAGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTATACGC
* *
1550813 GTCACTCCGGTGCAATTATACGT
1 GGCACTCCGGTGCAATTATACGC
*
1550836 GGCACTTCGGTGCAATTATA
1 GGCACTCCGGTGCAATTATA
1550856 TGAGCTGTGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTATACGC
Found at i:1551071 original size:621 final size:621
Alignment explanation
Indices: 1549881--1551132 Score: 2450
Period size: 621 Copynumber: 2.0 Consensus size: 621
1549871 GATAATGCCC
* *
1549881 ATATATGTGTCATGAGAGCTAGGGGTATAGTTGGCATGCCAAGAGTCGAGGGTCTATGTGGTCCT
1 ATATATATATCATGAGAGCTAGGGGTATAGTTGGCATGCCAAGAGTCGAGGGTCTATGTGGTCCT
1549946 TCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTTGATCCTTGG
66 TCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTTGATCCTTGG
1550011 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAC
131 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAC
1550076 ATGTGTGAAGTCTGGTGAAACACATACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
196 ATGTGTGAAGTCTGGTGAAACACATACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
*
1550141 TATATGGTCCTTATGGACATTATTATATGGCACTACGGTGCAATTCTACGCGTCACTCCGGTGCA
261 TATATGGTCCTTATGGACATTATTATATGGCACTACAGTGCAATTCTACGCGTCACTCCGGTGCA
1550206 ATTATACGTGGCACTTCGGTGCAATTATATGAGCTGTGGTGACAGCATTAGTGCACAACCTCTAT
326 ATTATACGTGGCACTTCGGTGCAATTATATGAGCTGTGGTGACAGCATTAGTGCACAACCTCTAT
*
1550271 GTACTCGCTTATCTTTAGTTCTCACATGTGTATCATGGGCTATTAAATAGATAATATTAATAAAG
391 GTACTCGCATATCTTTAGTTCTCACATGTGTATCATGGGCTATTAAATAGATAATATTAATAAAG
1550336 TGATATGATAATATGTTTGTTTCCTTGTGGAATTTCATGTGTGATATTGATTGTACAAATGGTAA
456 TGATATGATAATATGTTTGTTTCCTTGTGGAATTTCATGTGTGATATTGATTGTACAAATGGTAA
1550401 CTTATAAGACCATATGATGAAAGGAATCAATGATAGTGATAAAATAAGAAAGAAATGAAGATGAT
521 CTTATAAGACCATATGATGAAAGGAATCAATGATAGTGATAAAATAAGAAAGAAATGAAGATGAT
1550466 AATATAGTTGTTTGGGTGTACGTGTTTTATGATAGT
586 AATATAGTTGTTTGGGTGTACGTGTTTTATGATAGT
*
1550502 ATATATATATCATGAGAGCTAGGGGTATAGTTGGCATGCCAAGATTCGAGGGTCTATGTGGTCCT
1 ATATATATATCATGAGAGCTAGGGGTATAGTTGGCATGCCAAGAGTCGAGGGTCTATGTGGTCCT
1550567 TCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTTGATCCTTGG
66 TCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTTGATCCTTGG
1550632 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAC
131 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAC
1550697 ATGTGTGAAGTCTGGTGAAACACATACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
196 ATGTGTGAAGTCTGGTGAAACACATACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
*
1550762 TATGTGGTCCTTATGGACATTATTATATGGCACTACAGTGCAATTCTACGCGTCACTCCGGTGCA
261 TATATGGTCCTTATGGACATTATTATATGGCACTACAGTGCAATTCTACGCGTCACTCCGGTGCA
1550827 ATTATACGTGGCACTTCGGTGCAATTATATGAGCTGTGGTGACAGCATTAGTGCACAACCTCTAT
326 ATTATACGTGGCACTTCGGTGCAATTATATGAGCTGTGGTGACAGCATTAGTGCACAACCTCTAT
1550892 GTACTCGCATATCTTTAGTTCTCACATGTGTATCATGGGCTATTAAATAGATAATATTAATAAAG
391 GTACTCGCATATCTTTAGTTCTCACATGTGTATCATGGGCTATTAAATAGATAATATTAATAAAG
1550957 TGATATGATAATATGTTTGTTTCCTTGTGGAATTTCATGTGTGATATTGATTGTACAAATGGTAA
456 TGATATGATAATATGTTTGTTTCCTTGTGGAATTTCATGTGTGATATTGATTGTACAAATGGTAA
1551022 CTTATAAGACCATATGATGAAAGGAATCAATGATAGTGATAAAATAAGAAAGAAATGAAGATGAT
521 CTTATAAGACCATATGATGAAAGGAATCAATGATAGTGATAAAATAAGAAAGAAATGAAGATGAT
1551087 AATATAGTTGTTTGGGTGTACGTGTTTTATGATAGT
586 AATATAGTTGTTTGGGTGTACGTGTTTTATGATAGT
1551123 ATATATATAT
1 ATATATATAT
1551133 ATATGGTTTA
Statistics
Matches: 625, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
621 625 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (621 bp):
ATATATATATCATGAGAGCTAGGGGTATAGTTGGCATGCCAAGAGTCGAGGGTCTATGTGGTCCT
TCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTTGATCCTTGG
CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAC
ATGTGTGAAGTCTGGTGAAACACATACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
TATATGGTCCTTATGGACATTATTATATGGCACTACAGTGCAATTCTACGCGTCACTCCGGTGCA
ATTATACGTGGCACTTCGGTGCAATTATATGAGCTGTGGTGACAGCATTAGTGCACAACCTCTAT
GTACTCGCATATCTTTAGTTCTCACATGTGTATCATGGGCTATTAAATAGATAATATTAATAAAG
TGATATGATAATATGTTTGTTTCCTTGTGGAATTTCATGTGTGATATTGATTGTACAAATGGTAA
CTTATAAGACCATATGATGAAAGGAATCAATGATAGTGATAAAATAAGAAAGAAATGAAGATGAT
AATATAGTTGTTTGGGTGTACGTGTTTTATGATAGT
Found at i:1556742 original size:31 final size:32
Alignment explanation
Indices: 1556707--1556769 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
1556697 TCATTTAAAT
1556707 CCGACCTCATACGAAAAT-TATATATCATTCA
1 CCGACCTCATACGAAAATATATATATCATTCA
* * *
1556738 CCGACCTGATCCGAAAATATATATATTATTCA
1 CCGACCTCATACGAAAATATATATATCATTCA
1556770 TCCTACTCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (32 bp):
CCGACCTCATACGAAAATATATATATCATTCA
Found at i:1561127 original size:6 final size:6
Alignment explanation
Indices: 1561116--1561151 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1561106 AAGTCATGGA
*
1561116 TGAAAG TGAAAG TGAAAG TGAAAG TGAAGG TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
1561152 GTTACTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:1564904 original size:16 final size:16
Alignment explanation
Indices: 1564883--1564915 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1564873 AAAAAAAAAT
1564883 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1564899 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1564915 T
1 T
1564916 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1569730 original size:40 final size:41
Alignment explanation
Indices: 1569686--1569766 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
1569676 AAAATTATAT
*
1569686 GGATTTTATTAAAAA-GAATACACGAATATTATCTTTAATC
1 GGATTTTATTAAAAAGGAATACACGAATATCATCTTTAATC
*
1569726 GGATTTTATTAAAAAGGAATACACGAATATCGTCTTTAATC
1 GGATTTTATTAAAAAGGAATACACGAATATCATCTTTAATC
1569767 ATTTAATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 15 0.39
41 23 0.61
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (41 bp):
GGATTTTATTAAAAAGGAATACACGAATATCATCTTTAATC
Found at i:1572650 original size:31 final size:31
Alignment explanation
Indices: 1572615--1572673 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
1572605 AGTTGTATAG
1572615 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1572646 ATTATTTAAATTTCAGTATTGTAAAACT
1 ATTATTTAAATTTCAGTATTGTAAAACT
1572674 CTTTTAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGTAAAACTAAA
Found at i:1581039 original size:11 final size:11
Alignment explanation
Indices: 1581020--1581050 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1581010 ATACCTAACA
1581020 TTTACTTTTCAT
1 TTTA-TTTTCAT
1581032 TTTATTTTCAT
1 TTTATTTTCAT
1581043 TTTATTTT
1 TTTATTTT
1581051 AATACCCCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTCAT
Found at i:1583401 original size:140 final size:140
Alignment explanation
Indices: 1583150--1583428 Score: 526
Period size: 140 Copynumber: 2.0 Consensus size: 140
1583140 CTGTGTTTGG
1583150 TTTGTTTGGCAGGAATGTATAATTACTGTGTTGGTTGAAAGAATATGAGATTACTAGAATGTATA
1 TTTGTTTGGCAGGAATGTATAATTACTGTGTTGGTTGAAAGAATATGAGATTACTAGAATGTATA
1583215 TTTTACCAAATTGTTCTTGTGCTATATGTGGTTACAAGTGGAATTCTAAATATTTAAATTAAAAT
66 TTTTACCAAATTGTTCTTGTGCTATATGTGGTTACAAGTGGAATTCTAAATATTTAAATTAAAAT
1583280 A-TCATATAA
131 ATTCATATAA
1583289 TTTGTTTGGCAGGAATGTATAATTACTGTGTTTGGTTGAAAGAATATGAGATTACTAGAATGTAT
1 TTTGTTTGGCAGGAATGTATAATTACTGTG-TTGGTTGAAAGAATATGAGATTACTAGAATGTAT
1583354 ATTTTACCAAATTGTTCTTGTGCTATATGT-GTTAACAAGTGGAATTCTAAATATTTAAATTAAA
65 ATTTTACCAAATTGTTCTTGTGCTATATGTGGTT-ACAAGTGGAATTCTAAATATTTAAATTAAA
1583418 ATATTCATATA
129 ATATTCATATA
1583429 TAAAAAAGCA
Statistics
Matches: 137, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
139 33 0.24
140 97 0.71
141 7 0.05
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (140 bp):
TTTGTTTGGCAGGAATGTATAATTACTGTGTTGGTTGAAAGAATATGAGATTACTAGAATGTATA
TTTTACCAAATTGTTCTTGTGCTATATGTGGTTACAAGTGGAATTCTAAATATTTAAATTAAAAT
ATTCATATAA
Found at i:1595118 original size:31 final size:31
Alignment explanation
Indices: 1595083--1595304 Score: 417
Period size: 31 Copynumber: 7.2 Consensus size: 31
1595073 GGTCATAATA
1595083 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
1595114 TAAACTGTTCATATGTGTCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
1595145 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
1595176 TAAACTGTTCATATTTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
1595207 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
1595238 TAAACTGTTCATATATGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
1595269 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
1595300 TAAAC
1 TAAAC
1595305 CCTCGACACT
Statistics
Matches: 185, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 185 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:1595980 original size:64 final size:63
Alignment explanation
Indices: 1595814--1596037 Score: 238
Period size: 64 Copynumber: 3.5 Consensus size: 63
1595804 TAATGAAGGT
* ** *
1595814 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGAT-TTAGTATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGTT--TATTATTAATGGG
* ** *
1595878 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGTTT-ATTATTAATGGG
* * **
1595942 ATGCATCGATGCACTACTTATGCATCGATGTATGAATTGTATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATG--TTTATTATTAATGGG
** *
1596005 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
1596038 CATTCAAATA
Statistics
Matches: 136, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
63 3 0.02
64 125 0.92
65 5 0.04
66 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGTTTATTATTAATGGG
Found at i:1597420 original size:18 final size:17
Alignment explanation
Indices: 1597393--1597436 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
1597383 GTCATATATG
*
1597393 TCCCGTAGGACCACTACA
1 TCCCGAAGGA-CACTACA
1597411 TCCCGAAGG--ACTACA
1 TCCCGAAGGACACTACA
1597426 TCCCGAAGGAC
1 TCCCGAAGGAC
1597437 TATTATACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 15 0.65
18 8 0.35
ACGTcount: A:0.30, C:0.36, G:0.20, T:0.14
Consensus pattern (17 bp):
TCCCGAAGGACACTACA
Found at i:1597425 original size:15 final size:15
Alignment explanation
Indices: 1597405--1597438 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1597395 CCGTAGGACC
1597405 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
1597420 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
1597435 ACTA
1 ACTA
1597439 TTATACCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1597564 original size:29 final size:29
Alignment explanation
Indices: 1597522--1597602 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
1597512 TTTCATATGT
1597522 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1597550 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1597579 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1597603 ATATCACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1598071 original size:45 final size:45
Alignment explanation
Indices: 1598004--1598109 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
1597994 TGCACTACTT
* * *
1598004 GTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATT-AATGG
1 GTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAGA
* *
1598048 GATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGA
1 G-TGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
1598094 GTGCATCGATGCACTA
1 GTGCATCGATGCACTA
1598110 CCTGTGCATC
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
44 1 0.02
45 40 0.75
46 12 0.23
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (45 bp):
GTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:1598195 original size:14 final size:14
Alignment explanation
Indices: 1598176--1598203 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1598166 GCACTATGAA
1598176 AATATGCATCGATG
1 AATATGCATCGATG
1598190 AATATGCATCGATG
1 AATATGCATCGATG
1598204 CACTCTGCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
AATATGCATCGATG
Found at i:1602334 original size:16 final size:16
Alignment explanation
Indices: 1602313--1602345 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1602303 TAATAAATAA
1602313 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1602329 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1602345 A
1 A
1602346 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1602426 original size:10 final size:10
Alignment explanation
Indices: 1602411--1602485 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1602401 CATTTAATAA
1602411 ATAAACGAAC
1 ATAAACGAAC
1602421 ATAAACGAAC
1 ATAAACGAAC
1602431 ----ACGAAC
1 ATAAACGAAC
1602437 ATAAACGAAC
1 ATAAACGAAC
** *
1602447 ACGAAC-ATAA
1 ATAAACGA-AC
1602457 ATGAACACGAAC
1 AT-AA-ACGAAC
1602469 ATAAACGAAC
1 ATAAACGAAC
1602479 ATAAACG
1 ATAAACG
1602486 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1602436 original size:16 final size:16
Alignment explanation
Indices: 1602415--1602479 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1602405 TAATAAATAA
1602415 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1602431 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1602447 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1602463 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1602479 A
1 A
1602480 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1603247 original size:14 final size:14
Alignment explanation
Indices: 1603230--1603285 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1603220 AATGAACATA
*
1603230 AACGAACATAATCG
1 AACGAACATAACCG
1603244 AACGAACAT-A---
1 AACGAACATAACCG
*
1603254 AACGAACATAACCA
1 AACGAACATAACCG
1603268 AACGAACATAACCG
1 AACGAACATAACCG
1603282 AACG
1 AACG
1603286 TTCACGAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1603250 original size:24 final size:24
Alignment explanation
Indices: 1603210--1603284 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
1603200 GATTGTGTTA
*
1603210 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1603234 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
1603258 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
1603282 AAC
1 AAC
1603285 GTTCACGAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1605660 original size:29 final size:28
Alignment explanation
Indices: 1605569--1605649 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 28
1605559 TTTCATATGT
1605569 TCATGTACTCATGTCATTTCTCTTGTGA
1 TCATGTACTCATGTCATTTCTCTTGTGA
1605597 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTA-CTCATGTCATTTCTCTTGTGA
1605626 TCATGTACCTCATGTCATGTTCTC
1 TCATGTA-CTCATGTCAT-TTCTC
1605650 ATATCACATG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.44
Consensus pattern (28 bp):
TCATGTACTCATGTCATTTCTCTTGTGA
Found at i:1609301 original size:21 final size:21
Alignment explanation
Indices: 1609274--1609351 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
1609264 TATTCCACAA
1609274 CCATTTTAGATGCCACCGCAG
1 CCATTTTAGATGCCACCGCAG
* ** * *
1609295 GCATTTTAGATGGTATCGCAA
1 CCATTTTAGATGCCACCGCAG
* * *
1609316 CCATTTTCGATGCCACTGTAG
1 CCATTTTAGATGCCACCGCAG
*
1609337 CCATTTCAGATGCCA
1 CCATTTTAGATGCCA
1609352 ACACCGCAAC
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (21 bp):
CCATTTTAGATGCCACCGCAG
Found at i:1611637 original size:59 final size:60
Alignment explanation
Indices: 1611553--1611695 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 60
1611543 GGTCAGATTT
* * * * *
1611553 CCCCACGAAGGCTCGCTTTATGATCCGCACC-TTCCAACATGGCGTCAGCTCAGACAGAA
1 CCCCGCGAAGGCGCGCTTCATGATCCGCACCTTTCCAACATGGCGCCAACTCAGACAGAA
* * * * *
1611612 CCCCGCGAAGGCGCGCCTCATGATCCGCACCTTTCCACCTTGGTGCCAACTCGGACAGAA
1 CCCCGCGAAGGCGCGCTTCATGATCCGCACCTTTCCAACATGGCGCCAACTCAGACAGAA
** *
1611672 CCATGTGAAGGCGCGCTTCATGAT
1 CCCCGCGAAGGCGCGCTTCATGAT
1611696 TTGCGCTTTG
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 27 0.39
60 42 0.61
ACGTcount: A:0.22, C:0.36, G:0.23, T:0.19
Consensus pattern (60 bp):
CCCCGCGAAGGCGCGCTTCATGATCCGCACCTTTCCAACATGGCGCCAACTCAGACAGAA
Found at i:1612282 original size:17 final size:17
Alignment explanation
Indices: 1612260--1612344 Score: 86
Period size: 17 Copynumber: 5.0 Consensus size: 17
1612250 GTGATTATTG
1612260 ATTATTTTATATTTTTA
1 ATTATTTTATATTTTTA
*
1612277 ATTATTTTATATTATTAA
1 ATTATTTTATATT-TTTA
1612295 TATTATTTTATATTTTTA
1 -ATTATTTTATATTTTTA
* *
1612313 A-TA-TCTACTA-TATTA
1 ATTATTTTA-TATTTTTA
*
1612328 ATTATTTTATAATTTTA
1 ATTATTTTATATTTTTA
1612345 TGAGGTGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
15 8 0.14
16 8 0.14
17 21 0.38
18 6 0.11
19 13 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATTTTATATTTTTA
Found at i:1612301 original size:19 final size:18
Alignment explanation
Indices: 1612260--1612316 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
1612250 GTGATTATTG
*
1612260 ATTATTTTATATTTTTA-
1 ATTATTTTATATTTTAAT
1612277 ATTATTTTATATTATTAAT
1 ATTATTTTATATT-TTAAT
1612296 ATTATTTTATATTTTTAAT
1 ATTATTTTATA-TTTTAAT
1612315 AT
1 AT
1612317 CTACTATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
17 13 0.36
18 3 0.08
19 18 0.50
20 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTATTTTATATTTTAAT
Found at i:1617695 original size:39 final size:39
Alignment explanation
Indices: 1617587--1617697 Score: 108
Period size: 34 Copynumber: 3.0 Consensus size: 39
1617577 AATTTGGTTC
1617587 GGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCA
1 GGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCA
** * * ***
1617626 AATTAATCGAAGCAAAA---ATTTG---GTTAATTAAGTT
1 GGTTAATCGAACCAAAATTTATTTGAAAATT-ATTAACCA
1617660 GGTTAATCGAACCAAAATTTATTTGAAAATTATTAACC
1 GGTTAATCGAACCAAAATTTATTTGAAAATTATTAACC
1617698 GAACCGAATT
Statistics
Matches: 52, Mismatches: 13, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
33 2 0.04
34 19 0.37
36 5 0.10
37 5 0.10
39 19 0.37
40 2 0.04
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (39 bp):
GGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCA
Found at i:1617712 original size:29 final size:29
Alignment explanation
Indices: 1617675--1617734 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
1617665 ATCGAACCAA
* *
1617675 AATTTATTTGAAAATTATTAACCGAACCG
1 AATTAATTTAAAAATTATTAACCGAACCG
1617704 AATTAATTTAAAAATTATTAACCGAACCG
1 AATTAATTTAAAAATTATTAACCGAACCG
1617733 AA
1 AA
1617735 ATAACCGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (29 bp):
AATTAATTTAAAAATTATTAACCGAACCG
Found at i:1617929 original size:16 final size:17
Alignment explanation
Indices: 1617905--1617948 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1617895 AACATTTTAC
* *
1617905 AATTAATTTAAA-TAAT
1 AATTTATTTAAACAAAT
1617921 AATTTATTTAAACAAAT
1 AATTTATTTAAACAAAT
*
1617938 AATTTGTTTAA
1 AATTTATTTAA
1617949 TTTTTAATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
AATTTATTTAAACAAAT
Found at i:1619023 original size:36 final size:36
Alignment explanation
Indices: 1618948--1619030 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
1618938 ATTTTAGGAT
*
1618948 TTAAGATT-AAAATAATCAAGGCGTTTAAGACACGT
1 TTAAGATTAAAAATAATCAAGGCGTTTAAGACACGC
** * **
1618983 TTAAGATTAAAAATAATCAAGTTGTTTAAGGCGTGC
1 TTAAGATTAAAAATAATCAAGGCGTTTAAGACACGC
*
1619019 TTAAGATCAAAA
1 TTAAGATTAAAA
1619031 TAAAGAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 8 0.20
36 32 0.80
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (36 bp):
TTAAGATTAAAAATAATCAAGGCGTTTAAGACACGC
Found at i:1620345 original size:113 final size:112
Alignment explanation
Indices: 1620017--1621059 Score: 1609
Period size: 113 Copynumber: 9.4 Consensus size: 112
1620007 TTGTCGGTTT
* ** *
1620017 GTGTCGATACTTTATGAAAATGTATTAATCCATAACAATATAAGAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1620081 GGTCTAAAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1620128 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
1620193 AGTCTATAAATGAAAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1620240 GTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTTAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGG-TAAAAAAATGACAAAAC
*
1620305 CGGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
1620353 GTGTCGATACTTTAT--AAATGTATCGATCAATAA-TACATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1620415 GGTCTATAAATGAC-AAACA--TAAA-CACTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1620458 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
1620523 AGTCTATAAATGACAAAACAGGTAAAGCGTTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * * *
1620570 GTGGCGATACTTTATAAAAATGTATCGATCCATAATAATATAAGAGGTAAAAAAAACGATAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
*
1620635 CGGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
1620683 GTGTCGATACTTTATAAAAATGTATCGATCAATAATAACATAACAGGTAAAAAAAATGATAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
* * *
1620748 CGGTCTATAAATGACAAAACAAGTAAAGCGCTACTGGATATATCGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1620796 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
1620861 GGTCTATAAATGACAAAACAGGTAAAGCGCTA-CTGATATATTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
1620907 GTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAATAGGTAAAAAAATGACAAAACA
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1620972 GGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
1621019 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAT
1621060 TGTTGAAAAC
Statistics
Matches: 848, Mismatches: 73, Indels: 21
0.90 0.08 0.02
Matches are distributed among these distances:
105 34 0.04
106 4 0.00
107 16 0.02
108 44 0.05
109 36 0.04
110 9 0.01
111 166 0.20
112 260 0.31
113 279 0.33
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1620639 original size:330 final size:333
Alignment explanation
Indices: 1620017--1621053 Score: 1690
Period size: 330 Copynumber: 3.1 Consensus size: 333
1620007 TTGTCGGTTT
** * * * *
1620017 GTGTCGATACTTTATGAAAATGTATTAATCCATAACAATATAAGAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTAT-AAAATGTATCGATCAATAA-TACATAACAGGTAAAAAAATGACAAAACC
*
1620081 GGTCTAAAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
64 GGTCTATAAATGACAAAACA-GTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* *
1620146 AATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAATCAGTCTATAAATGAAAAAA
128 AATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACCAGTCTATAAATGACAAAA
1620211 CAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAAT
193 CAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAAT
1620276 AATATAACAGGTTAAAAAAATGACAAAACCGGTTTATAAATGACAAAACAGGTAAAGCGCTACCG
258 AATATAACAGG-TAAAAAAATGACAAAACCGGTTTATAAATGACAAAACAGGTAAAGCGCTACCG
1620341 GATATATTGAAA
322 GATATATTGAAA
1620353 GTGTCGATACTTTAT-AAATGTATCGATCAATAATACATAACAGGTAAAAAAATGACAAAACCGG
1 GTGTCGATACTTTATAAAATGTATCGATCAATAATACATAACAGGTAAAAAAATGACAAAACCGG
*
1620417 TCTATAAATGAC-AAACA-TAAA-CACTACCGGATATATTGAAAGTGTCGATACTTTATAAAAAT
66 TCTATAAATGACAAAACAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAAT
*
1620479 GTATCTATCCATAACAATATAACATGTAAAAAAATGACAAAACCAGTCTATAAATGACAAAACAG
131 GTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACCAGTCTATAAATGACAAAACAG
* *
1620544 GTAAAGCGTTACCGGATATGTTGATAGTGGCGATACTTTATAAAAATGTATCGATCCATAATAAT
196 GTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAAT
* * *
1620609 ATAAGAGGTAAAAAAAACGATAAAACCGGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGAT
261 ATAACAGGT-AAAAAAATGACAAAACCGGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGAT
1620674 ATATTGAAA
325 ATATTGAAA
*
1620683 GTGTCGATACTTTATAAAAATGTATCGATCAATAATAACATAACAGGTAAAAAAAATGATAAAAC
1 GTGTCGATACTTTAT-AAAATGTATCGATCAATAAT-ACATAACAGGT-AAAAAAATGACAAAAC
* *
1620748 CGGTCTATAAATGACAAAACAAGTAAAGCGCTACTGGATATATCGAAAGTGTCGATACTTTATAA
63 CGGTCTATAAATGACAAAAC-AGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
* *
1620813 AAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
127 AAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACCAGTCTATAAATGACAAA
* *
1620878 ACAGGTAAAGCGCTA-CTGATATATTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
192 ACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
* * * *
1620942 TAATATAATAGGTAAAAAAATGACAAAACAGGTCTATAAATGACAAAACATGTAAAGCGCTACCG
257 TAATATAACAGGTAAAAAAATGACAAAACCGGTTTATAAATGACAAAACAGGTAAAGCGCTACCG
1621007 GATATATTGAAA
322 GATATATTGAAA
*
1621019 GTGTCGATACTTTATAAAAATGTATCGATCCATAA
1 GTGTCGATACTTTAT-AAAATGTATCGATCAATAA
1621054 CAATATTGTT
Statistics
Matches: 657, Mismatches: 34, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
329 1 0.00
330 249 0.38
331 4 0.01
332 19 0.03
333 25 0.04
334 74 0.11
335 4 0.01
336 109 0.17
337 62 0.09
338 110 0.17
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (333 bp):
GTGTCGATACTTTATAAAATGTATCGATCAATAATACATAACAGGTAAAAAAATGACAAAACCGG
TCTATAAATGACAAAACAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAAT
GTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACCAGTCTATAAATGACAAAACAG
GTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAAT
ATAACAGGTAAAAAAATGACAAAACCGGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATA
TATTGAAA
Found at i:1621390 original size:19 final size:19
Alignment explanation
Indices: 1621366--1621404 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1621356 TCGAATGCAT
1621366 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1621385 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1621404 T
1 T
1621405 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1621421 original size:65 final size:63
Alignment explanation
Indices: 1621303--1621511 Score: 219
Period size: 65 Copynumber: 3.3 Consensus size: 63
1621293 TATTCAAAGG
* *
1621303 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
1621365 TTC
61 TTT
1621368 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * ** * **
1621433 GATGCATCGATGCAC-AGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTT
*
1621496 CATGCATCGATGCACT
1 CATGCACCGATGCACT
1621512 TGGTGCACCG
Statistics
Matches: 126, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
63 43 0.34
64 37 0.29
65 44 0.35
66 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:1629078 original size:21 final size:21
Alignment explanation
Indices: 1629036--1629079 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1629026 ACCCCGGGAG
* *
1629036 CTAGTTGTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1629057 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1629078 CT
1 CT
1629080 CCTCCTCCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.34, G:0.18, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1630101 original size:19 final size:19
Alignment explanation
Indices: 1630077--1630115 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1630067 TCGAATGCAT
1630077 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1630096 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1630115 T
1 T
1630116 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1630216 original size:64 final size:65
Alignment explanation
Indices: 1630063--1630223 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
1630053 GAATTAATTG
* * *** *
1630063 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
1630128 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
1630191 A
65 A
1630192 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1630224 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1630238 original size:64 final size:64
Alignment explanation
Indices: 1630063--1630243 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
1630053 GAATTAATTG
* * * *
1630063 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
1630128 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
1630192 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
1630244 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 48 0.48
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:1636261 original size:22 final size:22
Alignment explanation
Indices: 1636236--1636280 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1636226 AAACAATTTT
*
1636236 AATAAGATT-ATTTAATTAATTA
1 AATAAGATTAATTAAATT-ATTA
*
1636258 AATAATATTAATTAAATTATTA
1 AATAAGATTAATTAAATTATTA
1636280 A
1 A
1636281 TGTTTAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATAAGATTAATTAAATTATTA
Found at i:1636603 original size:2 final size:2
Alignment explanation
Indices: 1636596--1636622 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1636586 GTTTGAATTT
1636596 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
1636623 TGTAGTTTGA
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:1636812 original size:2 final size:2
Alignment explanation
Indices: 1636769--1636799 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1636759 TTCATTTTGT
1636769 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
1636800 TAGCAATATA
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:1638224 original size:16 final size:15
Alignment explanation
Indices: 1638182--1638225 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
1638172 TATAATGTGA
1638182 ATATGGTGC-TTG-C
1 ATATGGTGCATTGTC
*
1638195 ATATGGTCCATTGTC
1 ATATGGTGCATTGTC
1638210 ATATAGGTGCATTGTC
1 ATAT-GGTGCATTGTC
1638226 GCACTTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 8 0.31
14 3 0.12
15 5 0.19
16 10 0.38
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (15 bp):
ATATGGTGCATTGTC
Found at i:1639546 original size:2 final size:2
Alignment explanation
Indices: 1639539--1639578 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1639529 CTTCTGTTGC
1639539 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1639579 TACAAAGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1643210 original size:48 final size:48
Alignment explanation
Indices: 1643155--1643252 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
1643145 ATCCAATTAA
1643155 CTAAATTGAGAGACAAGAATTTCGATAATCTGTCAGTTTCAACTAATT
1 CTAAATTGAGAGACAAGAATTTCGATAATCTGTCAGTTTCAACTAATT
1643203 CTAAATTGAGAGACAAGAATTTCGATAATCTGTCAGTTTCAACTAATT
1 CTAAATTGAGAGACAAGAATTTCGATAATCTGTCAGTTTCAACTAATT
1643251 CT
1 CT
1643253 CTCCGCACAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (48 bp):
CTAAATTGAGAGACAAGAATTTCGATAATCTGTCAGTTTCAACTAATT
Found at i:1666847 original size:24 final size:24
Alignment explanation
Indices: 1666818--1666881 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
1666808 TTGTAACTTT
* *
1666818 TTTATAAACTCATTTATTGATTCG
1 TTTATAAACTCATTTATCGACTCG
* *
1666842 TTTATAAATTTATTTATCGACTCG
1 TTTATAAACTCATTTATCGACTCG
* * *
1666866 ATTATAAGCTCGTTTA
1 TTTATAAACTCATTTA
1666882 CTCGGTTCTC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (24 bp):
TTTATAAACTCATTTATCGACTCG
Found at i:1667092 original size:23 final size:23
Alignment explanation
Indices: 1667047--1667098 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1667037 TTAAAAGTGA
* *
1667047 GTTAAATAAATATGTTTGTGAAC
1 GTTAAATAAATATGTTCGCGAAC
*
1667070 GTTAAATGAATATGTTCGCGAAC
1 GTTAAATAAATATGTTCGCGAAC
*
1667093 GCTAAA
1 GTTAAA
1667099 CGAACGAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
GTTAAATAAATATGTTCGCGAAC
Found at i:1673159 original size:20 final size:20
Alignment explanation
Indices: 1673117--1673159 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1673107 CGAATAATTT
* * *
1673117 AATCGAATATATAATTTTGA
1 AATCGAATATAAAATCTTAA
1673137 AATCGAATATAAAATCTTAA
1 AATCGAATATAAAATCTTAA
1673157 AAT
1 AAT
1673160 TCATTTACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (20 bp):
AATCGAATATAAAATCTTAA
Found at i:1676031 original size:4 final size:4
Alignment explanation
Indices: 1676022--1676048 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1676012 AAAATAAAGA
1676022 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1676049 ACCATTACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1677014 original size:270 final size:270
Alignment explanation
Indices: 1676523--1677064 Score: 1039
Period size: 270 Copynumber: 2.0 Consensus size: 270
1676513 ATCATGCTCA
1676523 CCCATAGTAAAATATGAGTGCTTAAGCCAGAGAGATTCGGAATAACCTTCCATAAGGAAACTGCT
1 CCCATAGTAAAATATGAGTGCTTAAGCCAGAGAGATTCGGAATAACCTTCCATAAGGAAACTGCT
1676588 AGATAGCACTCACTAAACAGATGGTCCCTAGTCTCCGTAGTTTCATTATAGATTATGCATGAACC
66 AGATAGCACTCACTAAACAGATGGTCCCTAGTCTCCGTAGTTTCATTATAGATTATGCATGAACC
*
1676653 AATGGTAACAATTCCCATTCTTTGGAGCCTCTCCCTAGTTGGGAGTCTATCCAGAAGTGACATCT
131 AATGGTAACAATTCCCATTCTTTGGAGCCTCTCCATAGTTGGGAGTCTATCCAGAAGTGACATCT
* *
1676718 ATGTAATCATGCTATATTTTGGGACGTGTAGAGGAAACCATATCAATTTGTGCCATGAGACTTTT
196 ATGTAATCATGCTATATTTGGGGACGTGTAGAGGAAACCATATCAATTTGTACCATGAGACTTTT
1676783 CTTCTTTTAC
261 CTTCTTTTAC
1676793 CCCATAGTAAAATATGAGTGCTTAAGCCAGAGAGATTCGGAATAACCTTCCATAAGGAAACTGCT
1 CCCATAGTAAAATATGAGTGCTTAAGCCAGAGAGATTCGGAATAACCTTCCATAAGGAAACTGCT
*
1676858 AGATAGCACTCACTAAACAGATGGTCCCTAGTCTCCGTAGTTTCATTGTAGATTATGCATGAACC
66 AGATAGCACTCACTAAACAGATGGTCCCTAGTCTCCGTAGTTTCATTATAGATTATGCATGAACC
1676923 AATGGTAACAATTCCCATTCTTTGGAGCCTCTCCATAGTTGGGAGTCTATCCAGAAGTGACATCT
131 AATGGTAACAATTCCCATTCTTTGGAGCCTCTCCATAGTTGGGAGTCTATCCAGAAGTGACATCT
*
1676988 ATGTAATCATGCTATGTTTGGGGACGTGTAGAGGAAACCATATCAATTTGTACCATGAGACTTTT
196 ATGTAATCATGCTATATTTGGGGACGTGTAGAGGAAACCATATCAATTTGTACCATGAGACTTTT
1677053 CTTCTTTTAC
261 CTTCTTTTAC
1677063 CC
1 CC
1677065 GTAGTTCTTT
Statistics
Matches: 267, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
270 267 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (270 bp):
CCCATAGTAAAATATGAGTGCTTAAGCCAGAGAGATTCGGAATAACCTTCCATAAGGAAACTGCT
AGATAGCACTCACTAAACAGATGGTCCCTAGTCTCCGTAGTTTCATTATAGATTATGCATGAACC
AATGGTAACAATTCCCATTCTTTGGAGCCTCTCCATAGTTGGGAGTCTATCCAGAAGTGACATCT
ATGTAATCATGCTATATTTGGGGACGTGTAGAGGAAACCATATCAATTTGTACCATGAGACTTTT
CTTCTTTTAC
Found at i:1683470 original size:32 final size:32
Alignment explanation
Indices: 1683421--1683496 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
1683411 CTTAATTTGG
* *
1683421 TAGATATGCTCCTCAGGTTTGATTGTTTCAAC
1 TAGAAATGCTCCCCAGGTTTGATTGTTTCAAC
1683453 TAGAAATGCTCCCCAGGTTTGATTGTTTCAAC
1 TAGAAATGCTCCCCAGGTTTGATTGTTTCAAC
1683485 TAGAAATGCTCC
1 TAGAAATGCTCC
1683497 AAGCATAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (32 bp):
TAGAAATGCTCCCCAGGTTTGATTGTTTCAAC
Found at i:1687483 original size:23 final size:22
Alignment explanation
Indices: 1687448--1687490 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1687438 ATAATTATTT
1687448 AAAAAATTAAATAAAAAATACC
1 AAAAAATTAAATAAAAAATACC
*
1687470 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
1687491 ATTTTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATACC
Found at i:1690211 original size:20 final size:20
Alignment explanation
Indices: 1690186--1690239 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1690176 TATTCCCTCG
1690186 TAATCTTACATTCCCACTGA
1 TAATCTTACATTCCCACTGA
1690206 TAATCTTACATTCCCACTGA
1 TAATCTTACATTCCCACTGA
1690226 TAATCTTACATTCC
1 TAATCTTACATTCC
1690240 GTGAATCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.37
Consensus pattern (20 bp):
TAATCTTACATTCCCACTGA
Found at i:1693640 original size:21 final size:20
Alignment explanation
Indices: 1693616--1693673 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
1693606 ATGTAGTATT
1693616 ATATAAATATATAATAAAGTA
1 ATATAAATA-ATAATAAAGTA
* *
1693637 ATATATATAATAATATACGTA
1 ATATAAATAATAATA-AAGTA
*
1693658 AAAT-AATACATAATAA
1 ATATAAATA-ATAATAA
1693674 TATACATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
ATATAAATAATAATAAAGTA
Found at i:1693652 original size:12 final size:12
Alignment explanation
Indices: 1693635--1693686 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
1693625 TATAATAAAG
*
1693635 TAATATATATAA
1 TAATATACATAA
*
1693647 TAATATACGTAA
1 TAATATACATAA
1693659 -AATAATACATAA
1 TAAT-ATACATAA
1693671 TAATATACATAA
1 TAATATACATAA
1693683 -AATA
1 TAATA
1693687 AATGTGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 7 0.20
12 25 0.71
13 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.33
Consensus pattern (12 bp):
TAATATACATAA
Found at i:1696375 original size:18 final size:18
Alignment explanation
Indices: 1696354--1696421 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
1696344 GTTGCAAGAG
1696354 CAGTCTTCATTGC-TAGAT
1 CAGTCTTCATT-CTTAGAT
1696372 CAGTCTTCATTCTTAGAT
1 CAGTCTTCATTCTTAGAT
1696390 CAGTCTTCATTCTTAGAT
1 CAGTCTTCATTCTTAGAT
*
1696408 CAATCTTCATTCTT
1 CAGTCTTCATTCTT
1696422 TTCCTGGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
17 1 0.02
18 47 0.98
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (18 bp):
CAGTCTTCATTCTTAGAT
Found at i:1696622 original size:52 final size:53
Alignment explanation
Indices: 1696562--1696702 Score: 160
Period size: 54 Copynumber: 2.7 Consensus size: 53
1696552 ATTTACAGTT
*
1696562 ATCAAGAAACCCCT-AAAATTAGGCTTAACTTCTCTCAAAAATTCA-AAAAAAA
1 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCT-TCAAAAATTCATAAAAAAA
* ** ** ** *
1696614 ATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTCAAAAATTCA-TAAAAAAA
*
1696668 ATCAAGAAACCCCTAAAAATTAAGCTTAATTTCTT
1 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTT
1696703 TGAACGTTCA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
52 23 0.31
53 16 0.22
54 35 0.47
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.27
Consensus pattern (53 bp):
ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTCAAAAATTCATAAAAAAA
Found at i:1696679 original size:54 final size:54
Alignment explanation
Indices: 1696609--1697248 Score: 617
Period size: 54 Copynumber: 11.7 Consensus size: 54
1696599 AAAATTCAAA
* ** * * * * *
1696609 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
** * * * * ***
1696663 AAAACATCAAGAAACCCCTAAAAATTA-AGCTTAATTTCTTTGAACGTTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGA-CTTAGTTTCTTTAAAAACTCATTTG
* * * *
1696717 AGAAAAATCAGGAAACTT-TCGAAAATCAGACTTAATTTCTTT-AAAACACATTTG
1 A-AAACATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* * *
1696771 AAAAGCGTCAAGAAACTTCTAAAAATTAGACTTAGTTTCTTTAAAAACTCATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* * *
1696826 AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAACACATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* * *
1696879 AAAAGCGTCAAGAAACTTCTAAAAATTAGACTTAGTTTCTTTAAAAACTCATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* * * * *
1696934 AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* * * *
1696988 AAATCATCAAGAAACTTCTGAAAATAAGACATAGTTTCTTTAAAAACTCACTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* * * * *
1697042 AAAATCGTCAAGAAACTTCTAAAAATAATACTTATTTTCTTTAAAAACTCATTT-
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* * * **
1697096 AAAATGATCAAGAAACTT-TCGAAAATCGGAATTAGTTTCTAAAAAAACTCATTTG
1 AAAA-CATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* * ***
1697151 AAAATAGTCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAATAAA
1 AAAACA-TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
* *
1697206 AAATACCATGTCAAGAAACCTCTGAAAATCAGACGTAGTTTCT
1 AAA-A-CA--TCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
1697249 AAAAACACAT
Statistics
Matches: 489, Mismatches: 80, Indels: 30
0.82 0.13 0.05
Matches are distributed among these distances:
53 18 0.04
54 288 0.59
55 147 0.30
56 3 0.01
57 1 0.00
58 32 0.07
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (54 bp):
AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG
Found at i:1697209 original size:109 final size:109
Alignment explanation
Indices: 1696609--1697202 Score: 552
Period size: 109 Copynumber: 5.5 Consensus size: 109
1696599 AAAATTCAAA
* ** * * * * * *
1696609 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTGAAAA--CATCA
1 AAAATATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACT-AATTGAAAATGCATCA
** * * * ***
1696672 AGAAACCCCTAAAAATTA-AGCTTAATTTCTTTGAACGTTCATTTG
65 AGAAACTTCTAAAAATTAGA-ATTAGTTTCTTTAAAAACTCATTTG
* * * * *
1696717 AGAAAAATCAGGAAACTT-TCGAAAATCAGACTTAATTTCTTTAAAACAC-ATTTGAAAA-GCGT
1 A-AAATATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAA-ACTAATTGAAAATGCAT
*
1696779 CAAGAAACTTCTAAAAATTAGACTTAGTTTCTTTAAAAACTCATTTG
63 CAAGAAACTTCTAAAAATTAGAATTAGTTTCTTTAAAAACTCATTTG
* * *
1696826 -AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACAC-ATTTGAAAA-GCGTC
1 AAAAT-ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAA-ACTAATTGAAAATGCATC
*
1696888 AAGAAACTTCTAAAAATTAGACTTAGTTTCTTTAAAAACTCATTTG
64 AAGAAACTTCTAAAAATTAGAATTAGTTTCTTTAAAAACTCATTTG
* * * *
1696934 -AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTG-AAAT-CATC
1 AAAAT-ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAAC-TAATTGAAAATGCATC
* * *
1696996 AAGAAACTTCTGAAAATAAGACA-TAGTTTCTTTAAAAACTCACTTG
64 AAGAAACTTCTAAAAATTAGA-ATTAGTTTCTTTAAAAACTCATTTG
* * * * * * *
1697042 AAAATCGTCAAGAAACTTCTAAAAATAATACTTATTTTCTTTAAAAACTCATTTAAAATG-ATCA
1 AAAAT-ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAATTGAAAATGCATCA
* ** **
1697106 AGAAACTT-TCGAAAATCGGAATTAGTTTCTAAAAAAACTCATTTG
65 AGAAACTTCT-AAAAATTAGAATTAGTTTCTTTAAAAACTCATTTG
1697151 AAAATAGTCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAAT
1 AAAATA-TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAAT
1697203 AAAAAATACC
Statistics
Matches: 422, Mismatches: 47, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
107 5 0.01
108 205 0.49
109 210 0.50
110 2 0.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (109 bp):
AAAATATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTAATTGAAAATGCATCAA
GAAACTTCTAAAAATTAGAATTAGTTTCTTTAAAAACTCATTTG
Found at i:1699276 original size:43 final size:41
Alignment explanation
Indices: 1699226--1699335 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 41
1699216 TTTTTAATCT
* *
1699226 TTTTTTTCTTTTTCTTCTATTTTTTCTCTTTCTTTTTCTCTTTC
1 TTTTTTTCTTTTTCTTCT-GTGTTTCTCTTT-TTTTT-TCTTTC
*
1699270 -TTTTTTCTGTTTTTTTCTGTGTTTCTCTTTTTTTTTCTTTC
1 TTTTTTTCT-TTTTCTTCTGTGTTTCTCTTTTTTTTTCTTTC
* *
1699311 TTTTTTTCTTTCTTTTTTTGTGTTT
1 TTTTTTTCTTT-TTCTTCTGTGTTT
1699336 TTTTTATATA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
41 8 0.14
42 25 0.42
43 18 0.31
44 8 0.14
ACGTcount: A:0.01, C:0.15, G:0.05, T:0.79
Consensus pattern (41 bp):
TTTTTTTCTTTTTCTTCTGTGTTTCTCTTTTTTTTTCTTTC
Found at i:1699309 original size:53 final size:54
Alignment explanation
Indices: 1699210--1699339 Score: 162
Period size: 53 Copynumber: 2.4 Consensus size: 54
1699200 TCTGTCCATT
1699210 TCTTT-TTTTTTAATCT-TTTTTTTCTTTTTCTTCTATTTTTTCTCTTTCTTTTTC
1 TCTTTCTTTTTT--TCTGTTTTTTTCTTTTTCTTCTATTTTTTCTCTTTCTTTTTC
* *
1699264 TCTTTC-TTTTTTCTGTTTTTTTCTGTGTTTC-TCT-TTTTTTTTCTTTCTTTTTT
1 TCTTTCTTTTTTTCTGTTTTTTTCT-T-TTTCTTCTATTTTTTCTCTTTCTTTTTC
*
1699317 TCTTTCTTTTTTTGTGTTTTTTT
1 TCTTTCTTTTTTTCTGTTTTTTT
1699340 TATATATCTT
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
52 3 0.04
53 32 0.47
54 29 0.43
55 4 0.06
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (54 bp):
TCTTTCTTTTTTTCTGTTTTTTTCTTTTTCTTCTATTTTTTCTCTTTCTTTTTC
Found at i:1699338 original size:24 final size:24
Alignment explanation
Indices: 1699291--1699340 Score: 52
Period size: 23 Copynumber: 2.1 Consensus size: 24
1699281 TTTTTCTGTG
*
1699291 TTTCTCTTT-TTTTTTCT-TTCTTT
1 TTTCTCTTTCTTTTTT-TGTTTTTT
1699314 TTT-TCTTTCTTTTTTTGTGTTTTT
1 TTTCTCTTTCTTTTTTTGT-TTTTT
1699338 TTT
1 TTT
1699341 ATATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
22 6 0.26
23 10 0.43
24 7 0.30
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.84
Consensus pattern (24 bp):
TTTCTCTTTCTTTTTTTGTTTTTT
Found at i:1699340 original size:12 final size:12
Alignment explanation
Indices: 1699225--1699329 Score: 81
Period size: 12 Copynumber: 8.4 Consensus size: 12
1699215 TTTTTTAATC
1699225 TTTTT-TTTCTT
1 TTTTTCTTTCTT
*
1699236 TTTCTTCTAT-TT
1 TTT-TTCTTTCTT
*
1699248 TTTCTCTTTCTT
1 TTTTTCTTTCTT
*
1699260 TTTCTCTTTCTT
1 TTTTTCTTTCTT
* *
1699272 TTTTCTGTTTTTTT
1 TTTT-T-CTTTCTT
1699286 CTGTGTTTCTCTT-TT
1 -T-T-TTTCT-TTCTT
1699301 TTTTTCTTTCTT
1 TTTTTCTTTCTT
1699313 TTTTTCTTTCTT
1 TTTTTCTTTCTT
1699325 TTTTT
1 TTTTT
1699330 GTGTTTTTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
11 9 0.12
12 48 0.62
13 4 0.05
14 6 0.08
15 4 0.05
16 4 0.05
17 2 0.03
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:1699353 original size:42 final size:42
Alignment explanation
Indices: 1699264--1699357 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
1699254 TTTCTTTTTC
* *
1699264 TCTTTC-TTTTTTCTGTTTTTTTCTGTGTTTCTCTTTTTTTT
1 TCTTTCTTTTTTTCTGTTTTTTTCTGTGTTTCTCTTTTTATA
*
1699305 TCTTTCTTTTTTTCT-TTCTTTTTTTGTGTTT-T-TTTTATATA
1 TCTTTCTTTTTTTCTGTT-TTTTTCTGTGTTTCTCTTTT-TATA
1699346 TCTTTTCTTTTT
1 TC-TTTCTTTTT
1699358 CTCTCTATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
40 4 0.09
41 13 0.28
42 29 0.63
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (42 bp):
TCTTTCTTTTTTTCTGTTTTTTTCTGTGTTTCTCTTTTTATA
Found at i:1699357 original size:53 final size:53
Alignment explanation
Indices: 1699245--1699359 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 53
1699235 TTTTCTTCTA
* * * *
1699245 TTTTTTCTCTTTCTTTTTCTCTTTCTTTTTTCTGTTTTTTTCTGTGTTTCTCT
1 TTTTTTTTCTTTCTTTTTCTCTTTCTTTTTTCTGTTTTTTTCTGTATATATCT
*
1699298 TTTTTTTTCTTTCTTTTTTTCTTTCTTTTTT-TGTGTTTTTT-T-TATATATCT
1 TTTTTTTTCTTTCTTTTTCTCTTTCTTTTTTCTGT-TTTTTTCTGTATATATCT
1699349 TTTCTTTTTCT
1 TTT-TTTTTCT
1699360 CTCTATGTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
51 9 0.16
52 11 0.20
53 35 0.64
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.78
Consensus pattern (53 bp):
TTTTTTTTCTTTCTTTTTCTCTTTCTTTTTTCTGTTTTTTTCTGTATATATCT
Found at i:1700750 original size:21 final size:23
Alignment explanation
Indices: 1700709--1700759 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1700699 ATGCACATGC
1700709 AAATG-AAAAGATACAAAAATGG
1 AAATGCAAAAGATACAAAAATGG
* *
1700731 GAATGCAAAA-ATAC-AAAATGT
1 AAATGCAAAAGATACAAAAATGG
1700752 AAATGCAA
1 AAATGCAA
1700760 CAAAGGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.52
22 8 0.32
23 4 0.16
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (23 bp):
AAATGCAAAAGATACAAAAATGG
Found at i:1703478 original size:14 final size:13
Alignment explanation
Indices: 1703436--1703504 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 13
1703426 GTAGTATTAT
*
1703436 AAAT-ATATAATA
1 AAATAATATACTA
*
1703448 AAGTAATATA-TA
1 AAATAATATACTA
*
1703460 TAATAATATACGTA
1 AAATAATATAC-TA
1703474 AAATAA-ATAC-A
1 AAATAATATACTA
*
1703485 TAATAATATACATA
1 AAATAATATAC-TA
1703499 AAATAA
1 AAATAA
1703505 ATGTGTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 6 0.13
12 17 0.38
13 9 0.20
14 13 0.29
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.30
Consensus pattern (13 bp):
AAATAATATACTA
Found at i:1703514 original size:25 final size:25
Alignment explanation
Indices: 1703459--1703506 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1703449 AGTAATATAT
*
1703459 ATAATAATATACGTAAAATAAATAC
1 ATAATAATATACATAAAATAAATAC
1703484 ATAATAATATACATAAAATAAAT
1 ATAATAATATACATAAAATAAAT
1703507 GTGTAATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (25 bp):
ATAATAATATACATAAAATAAATAC
Found at i:1709530 original size:15 final size:15
Alignment explanation
Indices: 1709512--1709578 Score: 54
Period size: 15 Copynumber: 4.8 Consensus size: 15
1709502 ATATATTTAA
1709512 ATTAAATATATAAAT
1 ATTAAATATATAAAT
* *
1709527 ATTATATATATATAT
1 ATTAAATATATAAAT
1709542 ATT-AAT-T-T-AAT
1 ATTAAATATATAAAT
* *
1709553 -TTAAATTTATTAAT
1 ATTAAATATATAAAT
*
1709567 ATTATATATATA
1 ATTAAATATATA
1709579 TATAATTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
10 2 0.05
11 5 0.12
12 2 0.05
13 2 0.05
14 5 0.12
15 24 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTAAATATATAAAT
Found at i:1709550 original size:40 final size:38
Alignment explanation
Indices: 1709498--1709582 Score: 125
Period size: 40 Copynumber: 2.2 Consensus size: 38
1709488 ATCGGGTCGA
1709498 ATATATATATTTAAATTAAATATATAAATATTATATAT
1 ATATATATATTTAAATTAAATATATAAATATTATATAT
* * *
1709536 ATATATATTAATTTAATTTAAATTTATTAATATTATATAT
1 ATATATA-T-ATTTAAATTAAATATATAAATATTATATAT
1709576 ATATATA
1 ATATATA
1709583 ATTATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
38 7 0.17
39 1 0.02
40 34 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
ATATATATATTTAAATTAAATATATAAATATTATATAT
Found at i:1712325 original size:8 final size:8
Alignment explanation
Indices: 1712312--1712336 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1712302 AAATTAAACT
1712312 GAAGAGAA
1 GAAGAGAA
1712320 GAAGAGAA
1 GAAGAGAA
1712328 GAAGAGAA
1 GAAGAGAA
1712336 G
1 G
1712337 GGAAGCATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
GAAGAGAA
Found at i:1713029 original size:47 final size:47
Alignment explanation
Indices: 1712960--1713056 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
1712950 AAACATTTGT
1712960 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1713007 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1713054 AAA
1 AAA
1713057 CACCAAGTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.23
Consensus pattern (47 bp):
AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
Found at i:1713077 original size:21 final size:21
Alignment explanation
Indices: 1713046--1713090 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
1713036 AAACAACTTA
1713046 ATAAGCAAAAACACCAAGTAGC
1 ATAAGCAAAAACACCAAGTA-C
1713068 ATAA-CAAAAACACCAAGTAC
1 ATAAGCAAAAACACCAAGTAC
1713088 ATA
1 ATA
1713091 CACTACAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.17
21 15 0.65
22 4 0.17
ACGTcount: A:0.58, C:0.22, G:0.09, T:0.11
Consensus pattern (21 bp):
ATAAGCAAAAACACCAAGTAC
Found at i:1715852 original size:19 final size:19
Alignment explanation
Indices: 1715828--1715870 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1715818 TTTTAATTTT
1715828 TGGATAAAATAACAATCGC
1 TGGATAAAATAACAATCGC
1715847 TGGATAAAATAACAATCGC
1 TGGATAAAATAACAATCGC
1715866 TGGAT
1 TGGAT
1715871 TTAAATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (19 bp):
TGGATAAAATAACAATCGC
Found at i:1716779 original size:42 final size:42
Alignment explanation
Indices: 1716720--1716803 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
1716710 TTGTATTAAC
* *
1716720 AATCATGACCGTGTACATAATATGAGCAAGTGTAAGTTCTTT
1 AATCATGACCATGTACATAATACGAGCAAGTGTAAGTTCTTT
*
1716762 AATCATGACCATGTACATAATACGAGCGAGTGTAAGTTCTTT
1 AATCATGACCATGTACATAATACGAGCAAGTGTAAGTTCTTT
1716804 CATTCTTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (42 bp):
AATCATGACCATGTACATAATACGAGCAAGTGTAAGTTCTTT
Found at i:1717887 original size:70 final size:71
Alignment explanation
Indices: 1717759--1717902 Score: 263
Period size: 70 Copynumber: 2.0 Consensus size: 71
1717749 AATATTCAGT
*
1717759 TTTTGCCTTGTTCCATTTTTATACAGTTTTTGGAATGGTTGTGAACTTGAATGAAAGCACAAGGG
1 TTTTGCCTTGTTCCATTTTTATACAGTTTTTGGAATAGTTGTGAACTTGAATGAAAGCACAAGGG
1717824 AGGCCA
66 AGGCCA
*
1717830 TTTTGCCTTGTTCCATTTTTATACAG-TTTTGGAATAGTTGTGAGCTTGAATGAAAGCACAAGGG
1 TTTTGCCTTGTTCCATTTTTATACAGTTTTTGGAATAGTTGTGAACTTGAATGAAAGCACAAGGG
1717894 AGGCCA
66 AGGCCA
1717900 TTT
1 TTT
1717903 ACCCCATCAA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 45 0.63
71 26 0.37
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (71 bp):
TTTTGCCTTGTTCCATTTTTATACAGTTTTTGGAATAGTTGTGAACTTGAATGAAAGCACAAGGG
AGGCCA
Done.