Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008591.1 Hibiscus syriacus cultivar Beakdansim tig00111540_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: 1730314
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1540808 original size:131 final size:131
Alignment explanation
Indices: 1540570--1540824 Score: 345
Period size: 131 Copynumber: 1.9 Consensus size: 131
1540560 ATCATCAAAT
* * * * * *
1540570 TCACCATCAATTGGAGTCCACAGCCTGCAGAAAAAGGACGTGTGATTCATAATAATTTCTTTGAG
1 TCACCATCAATTGGAGTCCAAAGCCAGCAGAAAAAGGAAGTGTGACTCATAATAATTGCTTAGAG
1540635 AAAAAACATCACCATTAAGAAGTATGGTTTATGACTAGTGTTAAAACAGAGAACTTCTACATCAA
66 AAAAAACATCACCATTAAGAAGTATGGTTTATGACTAGTGTTAAAACAGAGAACTTCTACATCAA
1540700 C
131 C
*
1540701 TCACCGTCAATTGGAGTCCAAAGCCAGCAGAAAAAGGATAG-GTGACTCATAATAATTGCTTA-A
1 TCACCATCAATTGGAGTCCAAAGCCAGCAGAAAAAGGA-AGTGTGACTCATAATAATTGCTTAGA
** * * * *
1540764 GAGAAAGGCATCATCATTGAGAAGCT-TGGTTTATGACTATTGTTAAAACTGAGAACTTCTA
65 GA-AAAAACATCACCATTAAGAAG-TATGGTTTATGACTAGTGTTAAAACAGAGAACTTCTA
1540825 AGTTCTTATA
Statistics
Matches: 108, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
130 3 0.03
131 103 0.95
132 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (131 bp):
TCACCATCAATTGGAGTCCAAAGCCAGCAGAAAAAGGAAGTGTGACTCATAATAATTGCTTAGAG
AAAAAACATCACCATTAAGAAGTATGGTTTATGACTAGTGTTAAAACAGAGAACTTCTACATCAA
C
Found at i:1540918 original size:2 final size:2
Alignment explanation
Indices: 1540911--1540935 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1540901 TTTTCTACCT
1540911 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 T
1540936 TTCATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1546677 original size:166 final size:166
Alignment explanation
Indices: 1546398--1546730 Score: 513
Period size: 166 Copynumber: 2.0 Consensus size: 166
1546388 GATGGTATAC
* *
1546398 GTCCAATGTATGGAATGGAAGAAGAGATGGTCGTTCATGTCTTGAGAGACTGCGCATATGCTCAG
1 GTCCAATGTATGGAATGGAAGAAGAGACGATCGTTCATGTCTTGAGAGACTGCGCATATGCTCAG
* ** * * * *
1546463 GAAACGTTTGTTTGTGTTGGAGTACAAGGTGGGTTTTTTCTGGTCAACTTGTATCTCCATTAGAT
66 GAAACGTTTATTTGTGCCGGAGCACAAGGTGGGTTTTGTCTAGTCAACTTCTATCTCCATTAGAT
* *
1546528 TGGCTCGATTTGGCAATCTCTGCCATGAAGGTTGAT
131 TGGCTCGATTTGGCAATCTATGCCATGAAGATTGAT
* * *
1546564 GTCCAATGTGTGGAATGGAAGAAGAGACGATCGTTCATGTCTTGAGTGACTGTGCATATGCTCAG
1 GTCCAATGTATGGAATGGAAGAAGAGACGATCGTTCATGTCTTGAGAGACTGCGCATATGCTCAG
*
1546629 GAAACTTTTATTTGTGCCGGAGCACAAGGTGGGTTTTGTCTAGTCAACTTCTATCTCCATTAGAT
66 GAAACGTTTATTTGTGCCGGAGCACAAGGTGGGTTTTGTCTAGTCAACTTCTATCTCCATTAGAT
* *
1546694 TTGCTCGATTTGGTAATCTATGCCATGAAGATTGAT
131 TGGCTCGATTTGGCAATCTATGCCATGAAGATTGAT
1546730 G
1 G
1546731 ATCTAGCTTG
Statistics
Matches: 150, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
166 150 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (166 bp):
GTCCAATGTATGGAATGGAAGAAGAGACGATCGTTCATGTCTTGAGAGACTGCGCATATGCTCAG
GAAACGTTTATTTGTGCCGGAGCACAAGGTGGGTTTTGTCTAGTCAACTTCTATCTCCATTAGAT
TGGCTCGATTTGGCAATCTATGCCATGAAGATTGAT
Found at i:1552093 original size:21 final size:20
Alignment explanation
Indices: 1552069--1552116 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1552059 TATTTTTTTT
*
1552069 AAAAATAGTATTAAATTATTA-
1 AAAAATAGTA-TAAA-AATTAG
*
1552090 AAAAAAAGTATAAAAATTAG
1 AAAAATAGTATAAAAATTAG
1552110 AAAAATA
1 AAAAATA
1552117 TGAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 10 0.43
21 9 0.39
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAAATAGTATAAAAATTAG
Found at i:1561311 original size:14 final size:15
Alignment explanation
Indices: 1561292--1561329 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1561282 TCTCCATCTC
1561292 TAATTTTTTT-TACA
1 TAATTTTTTTATACA
*
1561306 TAATTTTATTTATATA
1 TAATTTT-TTTATACA
1561322 TAATTTTT
1 TAATTTTT
1561330 CAATGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTATACA
Found at i:1562104 original size:24 final size:24
Alignment explanation
Indices: 1562072--1562125 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1562062 GTATTCGAAA
*
1562072 TTTGATCTTGGTCGATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1562096 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1562120 TTTGAT
1 TTTGAT
1562126 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1564621 original size:20 final size:20
Alignment explanation
Indices: 1564568--1564622 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1564558 GTTTTCCTTG
* * *
1564568 AATTTGCAACGTGAAAGTCA
1 AATTCGCAACGCGATAGTCA
**
1564588 AATTCGCATTGCGATAGTCA
1 AATTCGCAACGCGATAGTCA
1564608 AATTCGCAACGCGAT
1 AATTCGCAACGCGAT
1564623 TGTCGCGTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
AATTCGCAACGCGATAGTCA
Found at i:1567502 original size:47 final size:44
Alignment explanation
Indices: 1567404--1567521 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 44
1567394 GCAACCATGC
* * *
1567404 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATTGGAA
* * *
1567448 AAATAAGCTTACGAGCTTATGGAATTTAAATGATAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGACAAGTATATTGGAA
*
1567495 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
1567522 ATGGTAAGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
44 24 0.38
45 1 0.02
46 1 0.02
47 38 0.59
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATTGGAA
Found at i:1568398 original size:21 final size:21
Alignment explanation
Indices: 1568374--1568491 Score: 130
Period size: 21 Copynumber: 5.6 Consensus size: 21
1568364 GTGAATCGGG
* * *
1568374 CTCTTGAACGGTGAGAGAGAC
1 CTCTTGAACGATGAGAGGGGC
*
1568395 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
1568416 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
1568437 ATCTTAAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1568458 CTCTTGAACGAT-AGGAGGTGC
1 CTCTTGAACGATGA-GAGGGGC
*
1568479 CTCTTAAACGATG
1 CTCTTGAACGATG
1568492 GCAGGTGCAT
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
20 1 0.01
21 79 0.99
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1568447 original size:42 final size:42
Alignment explanation
Indices: 1568374--1568496 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
1568364 GTGAATCGGG
* * * *
1568374 CTCTTGAACGGTGAGAGAGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTAAACGATGACAGGGGC
* *
1568416 CTCTTGAACGGTGGGAGGGGCATCTTAAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTAAACGATGACAGGGGC
* * * *
1568458 CTCTTGAACGATAGGAGGTGCCTCTTAAACGATGGCAGG
1 CTCTTGAACGGTGGGAGGGGCCTCTTAAACGATGACAGG
1568497 TGCATCGGGC
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.25, C:0.20, G:0.35, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTAAACGATGACAGGGGC
Found at i:1568502 original size:63 final size:63
Alignment explanation
Indices: 1568371--1568502 Score: 151
Period size: 63 Copynumber: 2.1 Consensus size: 63
1568361 CATGTGAATC
* * * * *
1568371 GGGC-TCTTGAACGGTGAGAGAGACCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAG
1 GGGCATCTTAAACGATGAGAGAGACCTCTTGAACGATGACAGGGGCCTCTTAAACGATGGCAG
* * * *
1568433 GGGCATCTTAAACGATGAGAGGGGCCTCTTGAACGAT-AGGAGGTGCCTCTTAAACGATGGCAG
1 GGGCATCTTAAACGATGAGAGAGACCTCTTGAACGATGA-CAGGGGCCTCTTAAACGATGGCAG
*
1568496 GTGCATC
1 GGGCATC
1568503 GGGCTTCTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
62 5 0.09
63 53 0.91
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (63 bp):
GGGCATCTTAAACGATGAGAGAGACCTCTTGAACGATGACAGGGGCCTCTTAAACGATGGCAG
Found at i:1570688 original size:20 final size:20
Alignment explanation
Indices: 1570646--1570688 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1570636 CGAAACTAAA
* * *
1570646 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGAATTTAAGT
*
1570666 TTCGTGTTGCGAATTTAAGT
1 TTCGCGTTGCGAATTTAAGT
1570686 TTC
1 TTC
1570689 AAAAACTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTAAGT
Found at i:1571046 original size:22 final size:22
Alignment explanation
Indices: 1571019--1571069 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1571009 GATGGAGATA
*
1571019 GACGGATTTCGTCGGAGATGTG
1 GACGGATTTCGTCGGAGATGGG
1571041 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
1571063 GATGGAT
1 GACGGAT
1571070 ATCACCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.43, T:0.25
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1571217 original size:20 final size:20
Alignment explanation
Indices: 1571192--1571267 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
1571182 ATAAACGCGC
1571192 TTTGACTTCTGTGTTGTGAA
1 TTTGACTTCTGTGTTGTGAA
*
1571212 TTTGACTTATGTGTTGTGAA
1 TTTGACTTCTGTGTTGTGAA
* *
1571232 TTTGACTTTTGTGTTATGAA
1 TTTGACTTCTGTGTTGTGAA
1571252 TTTGACTTCTGTGTTG
1 TTTGACTTCTGTGTTG
1571268 CGATTTTACA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.53
Consensus pattern (20 bp):
TTTGACTTCTGTGTTGTGAA
Found at i:1571372 original size:41 final size:41
Alignment explanation
Indices: 1571287--1571401 Score: 151
Period size: 41 Copynumber: 2.8 Consensus size: 41
1571277 AAATTCACGT
* * * * **
1571287 TGCGATTTACAAATTCACGTTGCG-ATTTACAAATTCGCGT
1 TGCGATTTACATATTCGCGTTGCGAATTTAGAAAATCGCAA
1571327 TGCGATTTACATATTCGCGTTGCGAATTTAGAAAATCGCAA
1 TGCGATTTACATATTCGCGTTGCGAATTTAGAAAATCGCAA
* *
1571368 TGCGATTCACATATTCGCGTTGCGAATTTGGAAA
1 TGCGATTTACATATTCGCGTTGCGAATTTAGAAA
1571402 CTGTGTTGCG
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 22 0.33
41 44 0.67
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (41 bp):
TGCGATTTACATATTCGCGTTGCGAATTTAGAAAATCGCAA
Found at i:1571372 original size:61 final size:61
Alignment explanation
Indices: 1571264--1571392 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 61
1571254 TGACTTCTGT
* ** *
1571264 GTTGCGATTTTACAAATTCACGTTGCGATTTACAAATTCACGTTGCGATTTACAAATTCGC
1 GTTGCGATTTTACAAATTCACGTTGCGATTTACAAAATCACAATGCGATTCACAAATTCGC
* * * * *
1571325 GTTGCGA-TTTACATATTCGCGTTGCGAATTTAGAAAATCGCAATGCGATTCACATATTCGC
1 GTTGCGATTTTACAAATTCACGTTGCG-ATTTACAAAATCACAATGCGATTCACAAATTCGC
1571386 GTTGCGA
1 GTTGCGA
1571393 ATTTGGAAAC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 17 0.29
61 41 0.71
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (61 bp):
GTTGCGATTTTACAAATTCACGTTGCGATTTACAAAATCACAATGCGATTCACAAATTCGC
Found at i:1571391 original size:20 final size:20
Alignment explanation
Indices: 1571264--1571392 Score: 159
Period size: 20 Copynumber: 6.3 Consensus size: 20
1571254 TGACTTCTGT
*
1571264 GTTGCGATTTTACAAATTCAC
1 GTTGCGA-TTTACAAATTCGC
*
1571285 GTTGCGATTTACAAATTCAC
1 GTTGCGATTTACAAATTCGC
1571305 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
1571325 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
* *
1571345 GTTGCGAATTTAGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** * *
1571366 AATGCGATTCACATATTCGC
1 GTTGCGATTTACAAATTCGC
1571386 GTTGCGA
1 GTTGCGA
1571393 ATTTGGAAAC
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
20 72 0.77
21 22 0.23
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:1574093 original size:23 final size:24
Alignment explanation
Indices: 1574030--1574096 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
1574020 TTAATAAAAA
*
1574030 TATTTATGTCTTTGTGAT-ATG-T
1 TATTTATGTCTTTGTGATCACGTT
*
1574052 TA-TT-TGTCTTTATGA-CACGTT
1 TATTTATGTCTTTGTGATCACGTT
1574073 TATTTATGTCTTTGT-ATCACGTT
1 TATTTATGTCTTTGTGATCACGTT
1574096 T
1 T
1574097 TTCTCTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 12 0.32
21 5 0.14
22 5 0.14
23 15 0.41
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.57
Consensus pattern (24 bp):
TATTTATGTCTTTGTGATCACGTT
Found at i:1576566 original size:38 final size:38
Alignment explanation
Indices: 1576515--1576591 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
1576505 TACTCATGCT
* *
1576515 TAAATTTATCAGATTTCCACTATATTGGTTGATTTTAC
1 TAAATTTATCAGATTTACACTATATTGGGTGATTTTAC
1576553 TAAATTTATCAGATTTACACTATATTGGGTGATTTTAC
1 TAAATTTATCAGATTTACACTATATTGGGTGATTTTAC
1576591 T
1 T
1576592 TCTTGTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (38 bp):
TAAATTTATCAGATTTACACTATATTGGGTGATTTTAC
Found at i:1586985 original size:34 final size:33
Alignment explanation
Indices: 1586931--1586998 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
1586921 CTTGTGGGTA
1586931 TACCGTACGCGTCACCTTTAGTAAGGAAAATCT
1 TACCGTACGCGTCACCTTTAGTAAGGAAAATCT
* *
1586964 TACCGTACCGTGTTACCTTTAGTAAGGAAAATCT
1 TACCGTA-CGCGTCACCTTTAGTAAGGAAAATCT
1586998 T
1 T
1586999 CTAGGTACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (33 bp):
TACCGTACGCGTCACCTTTAGTAAGGAAAATCT
Found at i:1593352 original size:2 final size:2
Alignment explanation
Indices: 1593339--1593371 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1593329 TATTCAACAA
*
1593339 AT AT AT AC 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
1593372 CGCAACAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1596746 original size:132 final size:129
Alignment explanation
Indices: 1596343--1596746 Score: 386
Period size: 132 Copynumber: 3.1 Consensus size: 129
1596333 CCAAATAAAA
* * *
1596343 CGGTTGGGCCCTTTTTTATGTATTTTTTAAAAATTAAAAACAATTTTTATA-TAAAAAAATTAAA
1 CGGTTGGGCCCTTTTTTGTGTATCTTTT--AAATTAAAAACAGTTTTTATACTAAAAAAATTAAA
* * * * *
1596407 CCCCCAAGCAATTGGGTCTATAGCTCAGCGATGGTACTGCAGATCAAGAGTTCAACTGTTCGAAC
64 CCCTCAAGCAATTGGGTCTATAGCTCAGTGGTAGTACTGCAGATCAAGAGTTCAACGGTTCGAAC
*
1596472 T
129 C
* * * * *
1596473 CGGTTGGGCCATTTTTTGTCTATCTTTTAAATGAAAAACAG-TTTT-TAC-ATAAAAATTAGACC
1 CGGTTGGGCCCTTTTTTGTGTATCTTTTAAATTAAAAACAGTTTTTATACTAAAAAAATTAAACC
* * * ** * *
1596535 CTCTAGCAATTGGGTTTATAACCCTGTTGTGGATACTTAACTGCAGATCAAGAGTTCAACGATTC
66 CTCAAGCAATTGGGTCTAT-A-GCT-CAGTGG-TA-GT-ACTGCAGATCAAGAGTTCAACGGTTC
1596600 GAACC
125 GAACC
* * * *
1596605 TGGTCGGGCCCTTTATCGTGTATCTTTTAAATTAAAAACAGTTTTTATATACTAAAAAAATTAAA
1 CGGTTGGGCCCTTTTTTGTGTATCTTTTAAATTAAAAACAG-TTTT-TATACTAAAAAAATTAAA
* * * * * *
1596670 CCCTAAATCAATTGGGTCTATAGCTCAGTGGCAGTACTGCAGTTCAAG-TTGTCACCGGTTCGAA
64 CCCTCAAGCAATTGGGTCTATAGCTCAGTGGTAGTACTGCAGATCAAGAGT-TCAACGGTTCGAA
1596734 CC
128 CC
1596736 CGGTTTGGGCC
1 CGG-TTGGGCC
1596747 GGTTTTTTTT
Statistics
Matches: 215, Mismatches: 45, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
126 30 0.14
127 5 0.02
128 13 0.06
129 2 0.01
130 26 0.12
131 28 0.13
132 69 0.32
133 1 0.00
134 7 0.03
135 3 0.01
136 4 0.02
137 27 0.13
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (129 bp):
CGGTTGGGCCCTTTTTTGTGTATCTTTTAAATTAAAAACAGTTTTTATACTAAAAAAATTAAACC
CTCAAGCAATTGGGTCTATAGCTCAGTGGTAGTACTGCAGATCAAGAGTTCAACGGTTCGAACC
Found at i:1607338 original size:16 final size:16
Alignment explanation
Indices: 1607302--1607340 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1607292 TCTGATTCAT
1607302 TTAAAAAATAAATTTA
1 TTAAAAAATAAATTTA
*
1607318 ATAAAATAATAAA-TTA
1 TTAAAA-AATAAATTTA
1607334 TTAAAAA
1 TTAAAAA
1607341 TATTACGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.65
17 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAAAATAAATTTA
Found at i:1609085 original size:5 final size:5
Alignment explanation
Indices: 1609069--1609119 Score: 70
Period size: 5 Copynumber: 10.4 Consensus size: 5
1609059 CGTAAATACA
*
1609069 TATTT T-TTT TATTT TATTT TATTT TATTT TATTT TTTTT TAGTTT T-TTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT
1609118 TA
1 TA
1609120 GAAATTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 8 0.20
5 29 0.71
6 4 0.10
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (5 bp):
TATTT
Found at i:1610730 original size:44 final size:47
Alignment explanation
Indices: 1610656--1610752 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 47
1610646 TTATTTTCGT
*
1610656 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAA-GCATGAGAACTAGATATCATGCGGTTAGGATTTA
* *
1610703 TTTTT-GAATAAA-CATGAGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAATAAAGCATGAGAACTAGATATCATGCGGTTAGGATTTA
1610748 TTTTT
1 TTTTT
1610753 ATGGATAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
44 26 0.57
45 8 0.17
46 7 0.15
47 5 0.11
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (47 bp):
TTTTTCGAATAAAGCATGAGAACTAGATATCATGCGGTTAGGATTTA
Found at i:1620459 original size:27 final size:29
Alignment explanation
Indices: 1620413--1620533 Score: 89
Period size: 27 Copynumber: 4.3 Consensus size: 29
1620403 GAAGAAATAA
*
1620413 AAGAGAAAAAAAT-GAGAAAAT-AAGAAA-
1 AAGAGAAAAAGATGGA-AAAATGAAGAAAG
**
1620440 AA-AGAAAAATGATGGAAAAAACAA-AAAG
1 AAGAGAAAAA-GATGGAAAAATGAAGAAAG
* *
1620468 AA-AGAAAAAGAAGAAAAAATGAA-AAAGGG
1 AAGAGAAAAAGATGGAAAAATGAAGAAA--G
*
1620497 AAGAGAACAA-ATGGAAAAATGAAGAAA-
1 AAGAGAAAAAGATGGAAAAATGAAGAAAG
1620524 AAGAGAAAAA
1 AAGAGAAAAA
1620534 TGAAAAAAGA
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
26 7 0.09
27 33 0.43
28 13 0.17
29 14 0.18
30 9 0.12
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.06
Consensus pattern (29 bp):
AAGAGAAAAAGATGGAAAAATGAAGAAAG
Found at i:1620530 original size:8 final size:9
Alignment explanation
Indices: 1620499--1620547 Score: 52
Period size: 8 Copynumber: 5.7 Consensus size: 9
1620489 AAAAAGGGAA
1620499 GAGAACAAAT
1 GAGAA-AAAT
1620509 G-GAAAAAT
1 GAGAAAAAT
1620517 GAAGAAAAA-
1 G-AGAAAAAT
1620526 GAGAAAAAT
1 GAGAAAAAT
1620535 GA-AAAAA-
1 GAGAAAAAT
1620542 GAGAAA
1 GAGAAA
1620548 TGAAAAGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 2 0.06
8 20 0.57
9 6 0.17
10 7 0.20
ACGTcount: A:0.69, C:0.02, G:0.22, T:0.06
Consensus pattern (9 bp):
GAGAAAAAT
Found at i:1620548 original size:14 final size:15
Alignment explanation
Indices: 1620520--1620553 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1620510 GAAAAATGAA
1620520 GAAAAAGAGAAAAAT
1 GAAAAAGAGAAAAAT
*
1620535 GAAAAA-AGAGAAAT
1 GAAAAAGAGAAAAAT
1620549 GAAAA
1 GAAAA
1620554 GGAGGGTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (15 bp):
GAAAAAGAGAAAAAT
Found at i:1622146 original size:51 final size:51
Alignment explanation
Indices: 1621633--1622326 Score: 868
Period size: 51 Copynumber: 13.4 Consensus size: 51
1621623 AGTGAAGCAA
**
1621633 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
**
1621684 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
*
1621735 ACAAGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
** *
1621786 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
* *
1621837 ACAAGTTTATTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
* *
1621888 ACAAGTTTATTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
*
1621939 ACAAGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
**
1621990 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
**
1622041 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
* * * * * * * *
1622092 ACACGTTTTTTGAAGATCGAGTCTTATACTCCCTGATGGAATAGAGAGCAG
1 ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
* * * * *
1622143 ACACGTTTACTGAAGATTATTTGAGTCTTATACT-TCCTGAACGAATAGGGAGCAG
1 ACAAGTTTATTGAAG---A-TTGAGTCCTATACTCT-CTGAAGGAATAGGGAGCGG
* * * * * *
1622198 ACACGTTTACTGAAGATTACTCGAGTCTTATACTCTCTGATGGAATAGAGAGCAG
1 ACAAGTTTATTGAAGA-T--T-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
* * * * * *
1622253 ACACGTTTACTGAAGATTACTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAG
1 ACAAGTTTATTGAAGA-T--T-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
* *
1622308 ACACGTTTACTGAAGATTG
1 ACAAGTTTATTGAAGATTG
1622327 TTCGAGTCTT
Statistics
Matches: 600, Mismatches: 34, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
51 453 0.75
52 4 0.01
54 3 0.00
55 139 0.23
56 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (51 bp):
ACAAGTTTATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
Found at i:1624024 original size:5 final size:5
Alignment explanation
Indices: 1624008--1624058 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
1623998 CGTAAATACA
* *
1624008 TATTT T-TTT TATTT TATTT TATTT TATTA TATTT TTTTT TAGTTT T-TTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT
1624057 TA
1 TA
1624059 GAAATTTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 8 0.21
5 27 0.69
6 4 0.10
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:1644783 original size:16 final size:17
Alignment explanation
Indices: 1644748--1644793 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1644738 AGTCCTTAAT
*
1644748 ATTTAAATATTATATTA
1 ATTTAAATATAATATTA
*
1644765 ATTTAATTATAAT-TTA
1 ATTTAAATATAATATTA
*
1644781 ATTCAAAT-TAATA
1 ATTTAAATATAATA
1644794 AATTTAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 11 0.46
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAAATATAATATTA
Found at i:1648917 original size:24 final size:26
Alignment explanation
Indices: 1648872--1648923 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
1648862 CGTTCGTGAA
*
1648872 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
1648898 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
1648922 CG
1 CG
1648924 AACAGAGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:1649192 original size:10 final size:10
Alignment explanation
Indices: 1649177--1649241 Score: 76
Period size: 10 Copynumber: 5.9 Consensus size: 10
1649167 TTTTTTTTTA
1649177 TTCGTTTATG
1 TTCGTTTATG
1649187 TTCGTTTATTGTG
1 TTCGTTTA---TG
1649200 TTCGTTTATG
1 TTCGTTTATG
1649210 TTCGTTTATTGTG
1 TTCGTTTA---TG
1649223 TTCGTTTATG
1 TTCGTTTATG
1649233 TTCGTTTAT
1 TTCGTTTAT
1649242 TATTTAAATG
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 29 0.59
13 20 0.41
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.62
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:1649203 original size:23 final size:23
Alignment explanation
Indices: 1649177--1649242 Score: 132
Period size: 23 Copynumber: 2.9 Consensus size: 23
1649167 TTTTTTTTTA
1649177 TTCGTTTATGTTCGTTTATTGTG
1 TTCGTTTATGTTCGTTTATTGTG
1649200 TTCGTTTATGTTCGTTTATTGTG
1 TTCGTTTATGTTCGTTTATTGTG
1649223 TTCGTTTATGTTCGTTTATT
1 TTCGTTTATGTTCGTTTATT
1649243 ATTTAAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.62
Consensus pattern (23 bp):
TTCGTTTATGTTCGTTTATTGTG
Found at i:1649244 original size:13 final size:13
Alignment explanation
Indices: 1649182--1649244 Score: 66
Period size: 13 Copynumber: 5.3 Consensus size: 13
1649172 TTTTATTCGT
1649182 TTATGTTCGTTTA
1 TTATGTTCGTTTA
*
1649195 TTGTGTTCG--T-
1 TTATGTTCGTTTA
1649205 TTATGTTCGTTTA
1 TTATGTTCGTTTA
*
1649218 TTGTGTTCG--T-
1 TTATGTTCGTTTA
1649228 TTATGTTCGTTTA
1 TTATGTTCGTTTA
1649241 TTAT
1 TTAT
1649245 TTAAATGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
10 16 0.40
11 2 0.05
12 2 0.05
13 20 0.50
ACGTcount: A:0.11, C:0.08, G:0.19, T:0.62
Consensus pattern (13 bp):
TTATGTTCGTTTA
Found at i:1649285 original size:21 final size:21
Alignment explanation
Indices: 1649259--1649306 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1649249 ATGAACGAAC
*
1649259 ATGAACAAGCTATATTCTTTA
1 ATGAACAAGCTATATTCCTTA
*
1649280 ATGAACAAGTTATATTCCTTA
1 ATGAACAAGCTATATTCCTTA
1649301 ATGAAC
1 ATGAAC
1649307 GAACATGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (21 bp):
ATGAACAAGCTATATTCCTTA
Found at i:1652811 original size:21 final size:22
Alignment explanation
Indices: 1652787--1652833 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
1652777 TCTAATATTT
*
1652787 TATAATTTATATTAAAT-TTAA
1 TATAATTTATATTAAATATAAA
* *
1652808 TAT-ATTTTTCTTAAATATAAA
1 TATAATTTATATTAAATATAAA
1652829 TATAA
1 TATAA
1652834 ATAACAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.52
21 9 0.43
22 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATAATTTATATTAAATATAAA
Found at i:1653270 original size:31 final size:29
Alignment explanation
Indices: 1653189--1653290 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 29
1653179 AAAAATGAAT
* *
1653189 ACTTTATGTACCTATTTTGACC-AAAAAT-
1 ACTTTA-GTACTTATTTAGACCAAAAAATA
* * *
1653217 AGTTTAGATACCTATTTTGACCAAAAATATA
1 ACTTTAG-TACTTATTTAGACCAAAAA-ATA
* *
1653248 ACTTTGGGTACTTATTTAGACCAAAAAATT
1 ACTTT-AGTACTTATTTAGACCAAAAAATA
1653278 ACTTTAGTACTTA
1 ACTTTAGTACTTA
1653291 AATGAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.02
28 19 0.31
29 11 0.18
30 9 0.15
31 21 0.34
32 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (29 bp):
ACTTTAGTACTTATTTAGACCAAAAAATA
Found at i:1660583 original size:396 final size:395
Alignment explanation
Indices: 1659502--1660911 Score: 948
Period size: 396 Copynumber: 3.5 Consensus size: 395
1659492 AATGTCGCAG
* * * * * *
1659502 CTCAGCTGGATT-AGATT-TGGTGCCTTGTTGAAAAGCATTATGTATATCCTCTAGTGATCTTGC
1 CTCAACTGGATTAAG-TTCTGGT-CCTTTTTGGAAAGCATTATGTATATCTTCCAGAGATCTTGC
* * * ** * * * *
1659565 ATCAACAACAGGTAAATCTGAATTGGTG-TCTGCATGACCCTGGTGATTCTCAATCATGCTAGGA
64 CTCGACAACAGGTAATTCTGAGGTGG-GATCTGCATGATCCAGGTGATTCTCAATCATACTTGGA
* * * * *
1659629 AGAATTACTTCCTC-GACATCTACTCCTCCATGGAGTTGCTTAAAAGCCAAATCAATGTCTTTCA
128 AGAATTACTTCCTCAG-CATCCACTCTTTCATGAAGTTGCTTAAAAGCCAAATCAATATC-TTCA
* * * * * ** *
1659693 ATGATCTTGCTTCAAGAACAGG-CAGCTCCACGTTGATC-TC-TGTCTTCA-TTGCTTCGATTTC
191 ACGATCTTGCTTCAAGAACAGGACTGCTCAACATTGATCGACACCTC-T-AGTT-CTTCTATTTC
* * * * * * *
1659754 ATCATAGCCAAATTTT--GGTTC-ACTGGCAGTGT-TCAGACTATTTTCTTGAATACCAGAGACG
253 TTCA-ATCC--ATTTTCAGATTCAACT-GCA-T-TATCATA--ACTTCCTTGAAAACCAGAGA-G
* ** * ** * * * * *
1659815 CCATGATTAGCTTCAATCTCTTCACCAGAAACCACATCATGTTGCTCCA-TGTCTGCTGATCCAT
309 CCATTACCAACTTCAATCTCTT--TGAGAAACCACAACATGCTGCTCCACT-TCAGATGAACCAT
* * * ** ** *
1659879 T-TCTAAAGCCAGCAGAAAG-AGGCAG
371 TCT-TCAAGTCTGTGGACTGTA-GCAA
** * * * * *
1659904 CTCCGCTGGATTAGGCTCTGGGCATTTTTGGAAAGCATTATGTATATCCTCCAGAGATCTTGCCT
1 CTCAACTGGATTAAGTTCTGGTCCTTTTTGGAAAGCATTATGTATATCTTCCAGAGATCTTGCCT
* * * * *
1659969 TGACAACAGGTAATTCTG-GAGTGGGATCTGCATGATTCAGGTGATTCTCAATCGTGCTTGTAAG
66 CGACAACAGGTAATTCTGAG-GTGGGATCTGCATGATCCAGGTGATTCTCAATCATACTTGGAAG
* * *
1660033 AATTACTTCCTCTGCATCAACGTC-ATCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAACC
130 AATTACTTCCTCAGCATCCAC-TCTTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAA-C
* * * * * *
1660097 AATCTTGCCTCACGAACA-GACTGCTCAACATTGGTCGACATCTCTATTTCTTCTATTTCTTCAT
193 GATCTTGCTTCAAGAACAGGACTGCTCAACATTGATCGACACCTCTAGTTCTTCTATTTCTTCA-
* ** * * *
1660161 ATTCATTTTTTGATTCAACTGCATTATTC-TCATTTTCTTGAAAACCAGAG-GCCATCTCACCAA
257 ATCCATTTTCAGATTCAACTGCATTA-TCATAACTTCCTTGAAAACCAGAGAGCCAT-T-ACCAA
** * *
1660224 CTTCAATCTCTTT-ATTAACCACATCATGCTGCTCTACTTCAG-TCGAACCATT-TCTCAAGTTC
319 CTTCAATCTCTTTGAGAAACCACAACATGCTGCTCCACTTCAGAT-GAACCATTCT-TCAAG-TC
1660286 AT-T-GACTGTAGCAA
381 -TGTGGACTGTAGCAA
**
1660300 CTCAACTGGATTAAGTTCTGGTCCTTTTTGGAAAGCATTATGTATATCTTCGGGAGATCTTGCCT
1 CTCAACTGGATTAAGTTCTGGTCCTTTTTGGAAAGCATTATGTATATCTTCCAGAGATCTTGCCT
* * *
1660365 CGACAA-AGGGTAATTCTGAGGTGGGATCTGAATGATCCAGGAGATTCTCAATCATACTTGGAAT
66 CGACAACA-GGTAATTCTGAGGTGGGATCTGCATGATCCAGGTGATTCTCAATCATACTTGGAAG
* *
1660429 AATTACTTCCTCAGCATCCACTCTTTCATTAAGTTGCTTAAAAGCCAAAACAATATCTTCAATCG
130 AATTACTTCCTCAGCATCCACTCTTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAA-CG
* ** * *
1660494 ATCTTGCTTCAAGAACAGGTAACT-C-CAA-GTTGATCTTCGCCT-TCCGTTCTTC-AGTTTCTT
194 ATCTTGCTTCAAGAACAGG--ACTGCTCAACATTGATCGACACCTCT-AGTTCTTCTA-TTTCTT
* * * * * *
1660554 C-A-CCATTTTCAGGTTCACAGGTAGCATTATCATAACTTCCTTGAATATCAGAGACGGCATTGC
255 CAATCCATTTTCAGATTCA-A-CT-GCATTATCATAACTTCCTTGAAAACCAGAGA-GCCATTAC
* * * *
1660617 TAACTTCAATCTCTTTGGAAGAAACTACAACATGCTGCTCCACTTCTGATGATCCATTCTTCAAG
316 CAACTTCAATCTCTTT-G-AGAAACCACAACATGCTGCTCCACTTCAGATGAACCATTCTTCAAG
* **
1660682 TCTGTGGACTGTGGCGG
379 TCTGTGGACTGTAGCAA
* * * * * * * * * *
1660699 CTGAGCTGGATTACGTTCT-GTACCTTTTTGCAAACCATTACGTATAT-TCCCCAGATACCTCGC
1 CTCAACTGGATTAAGTTCTGGT-CCTTTTTGGAAAGCATTATGTATATCT-TCCAGAGATCTTGC
* * * ** * *
1660762 CTCGACAACAGTTAAATCCGACTTGGTATCTGCATGATCCAGCTGATTCTCAATCATACTTGGAA
64 CTCGACAACAGGTAATTCTGAGGTGGGATCTGCATGATCCAGGTGATTCTCAATCATACTTGGAA
* * *
1660827 GAATTACTTCCTCAACATCCACT-TCTTCATGAAGTTGCTTAAAAGCTAAATCAATATCTTCTAC
129 GAATTACTTCCTCAGCATCCACTCT-TTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAAC
*
1660891 TGATATTGCTTCAAGAACAGG
193 -GATCTTGCTTCAAGAACAGG
1660912 CAGTTCCACA
Statistics
Matches: 812, Mismatches: 147, Indels: 101
0.77 0.14 0.10
Matches are distributed among these distances:
393 11 0.01
394 2 0.00
395 9 0.01
396 278 0.34
397 15 0.02
398 13 0.02
399 252 0.31
400 9 0.01
401 8 0.01
402 198 0.24
403 14 0.02
404 3 0.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (395 bp):
CTCAACTGGATTAAGTTCTGGTCCTTTTTGGAAAGCATTATGTATATCTTCCAGAGATCTTGCCT
CGACAACAGGTAATTCTGAGGTGGGATCTGCATGATCCAGGTGATTCTCAATCATACTTGGAAGA
ATTACTTCCTCAGCATCCACTCTTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAACGAT
CTTGCTTCAAGAACAGGACTGCTCAACATTGATCGACACCTCTAGTTCTTCTATTTCTTCAATCC
ATTTTCAGATTCAACTGCATTATCATAACTTCCTTGAAAACCAGAGAGCCATTACCAACTTCAAT
CTCTTTGAGAAACCACAACATGCTGCTCCACTTCAGATGAACCATTCTTCAAGTCTGTGGACTGT
AGCAA
Found at i:1664377 original size:161 final size:162
Alignment explanation
Indices: 1664065--1664389 Score: 602
Period size: 161 Copynumber: 2.0 Consensus size: 162
1664055 TTGTGTTTGG
1664065 GTTCTAGTTAAACTTTTGTTAGAAGCGTGAAGAAGGTGAGGTTTTGTTCCTGTAGTGATTCGGTT
1 GTTCTAGTTAAACTTTTGTTAGAAGCGTGAAGAAGGTGAGGTTTTGTTCCTGTAGTGATTCGGTT
1664130 TTAGGCATTTTCGGTGAGGGTTTGTGGTGGTTCGGGTAAGGATAGCTACTTCCGAGGGTGGCCGG
66 TTAGGCATTTTCGGTGAGGGTTTGTGGTGGTTCGGGTAAGGATAGCTACTTCCGAGGGTGGCCGG
*
1664195 TGTTGTTCTGTTGGATTGAAGTGATGGTGGCC
131 TGTTGTTCTGTTGGATTGAAGTGATGATGGCC
1664227 GTTCTAGTTAAACTTTTGTTAGAAGCGTGAAGAAGGTGAGG-TTTGTTCCTGTAGTGATTCGGTT
1 GTTCTAGTTAAACTTTTGTTAGAAGCGTGAAGAAGGTGAGGTTTTGTTCCTGTAGTGATTCGGTT
1664291 TTAGGCATTTTCGGTGA-GGTTTGTGGTGGTTCGGGTAAGGATAGCTACTTCCGAGGGTGGCCGG
66 TTAGGCATTTTCGGTGAGGGTTTGTGGTGGTTCGGGTAAGGATAGCTACTTCCGAGGGTGGCCGG
1664355 TG-TGTTCTGTTGGATTTTGAAGTGATGATGGCC
131 TGTTGTTCTGTTGGA--TTGAAGTGATGATGGCC
1664388 GT
1 GT
1664390 CGAACAGGGT
Statistics
Matches: 160, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
159 12 0.08
160 49 0.31
161 58 0.36
162 41 0.26
ACGTcount: A:0.17, C:0.11, G:0.35, T:0.37
Consensus pattern (162 bp):
GTTCTAGTTAAACTTTTGTTAGAAGCGTGAAGAAGGTGAGGTTTTGTTCCTGTAGTGATTCGGTT
TTAGGCATTTTCGGTGAGGGTTTGTGGTGGTTCGGGTAAGGATAGCTACTTCCGAGGGTGGCCGG
TGTTGTTCTGTTGGATTGAAGTGATGATGGCC
Found at i:1676253 original size:19 final size:19
Alignment explanation
Indices: 1676229--1676274 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1676219 TGGTGCTTAA
*
1676229 AAGGATTTTGCCTATTCAG
1 AAGGATTTTACCTATTCAG
1676248 AAGGATTTTACCTATTCAG
1 AAGGATTTTACCTATTCAG
1676267 AAGGATTT
1 AAGGATTT
1676275 CAGAGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (19 bp):
AAGGATTTTACCTATTCAG
Found at i:1676460 original size:9 final size:9
Alignment explanation
Indices: 1676437--1676466 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1676427 ATAAAAGAGA
1676437 AAAAATGAG
1 AAAAATGAG
1676446 AAAAATGAG
1 AAAAATGAG
1676455 AAAAATGA-
1 AAAAATGAG
1676463 AAAA
1 AAAA
1676467 TGATGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (9 bp):
AAAAATGAG
Found at i:1676517 original size:8 final size:8
Alignment explanation
Indices: 1676506--1676542 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
1676496 GAAAAGGGAA
1676506 GAAAAAAT
1 GAAAAAAT
1676514 G-AAAAAT
1 GAAAAAAT
*
1676521 GAAAAAAA
1 GAAAAAAT
1676529 G-AAAAAT
1 GAAAAAAT
1676536 GAAAAAA
1 GAAAAAA
1676543 AGAGAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
7 13 0.52
8 12 0.48
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:1676517 original size:18 final size:16
Alignment explanation
Indices: 1676418--1676542 Score: 73
Period size: 15 Copynumber: 7.6 Consensus size: 16
1676408 TATTTTGCTT
*
1676418 GAAGAAGAAAT-AAAA
1 GAAGAAAAAATGAAAA
1676433 G-AGAAAAAATGAGAAA
1 GAAGAAAAAATGA-AAA
1676449 -AATGAGAAAAATGAAAAA
1 GAA-GA-AAAAATG-AAAA
* *
1676467 TGATGGAAAAAACGAAAA
1 -GA-AGAAAAAATGAAAA
1676485 GAA-AAAAAATGGAAAA
1 GAAGAAAAAAT-GAAAA
1676501 GGGAAGAAAAAATGAAAA
1 --GAAGAAAAAATGAAAA
* *
1676519 -ATGAAAAAAAGAAAA
1 GAAGAAAAAATGAAAA
*
1676534 -ATGAAAAAA
1 GAAGAAAAAA
1676543 AGAGAAATAA
Statistics
Matches: 90, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.09
15 30 0.33
16 9 0.10
17 4 0.04
18 22 0.24
19 14 0.16
20 3 0.03
ACGTcount: A:0.71, C:0.01, G:0.20, T:0.08
Consensus pattern (16 bp):
GAAGAAAAAATGAAAA
Found at i:1676526 original size:15 final size:15
Alignment explanation
Indices: 1676506--1676554 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1676496 GAAAAGGGAA
*
1676506 GAAAAAATGAAAAAT
1 GAAAAAAAGAAAAAT
1676521 GAAAAAAAGAAAAAT
1 GAAAAAAAGAAAAAT
*
1676536 GAAAAAAAGAGAAAT
1 GAAAAAAAGAAAAAT
1676551 -AAAA
1 GAAAA
1676555 GGAGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 4 0.12
15 28 0.88
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:1678073 original size:55 final size:54
Alignment explanation
Indices: 1677883--1678240 Score: 399
Period size: 55 Copynumber: 6.7 Consensus size: 54
1677873 GTTGAAGATT
1677883 GAGTCCTATACTCTCTGAA-GAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTTTC
1677933 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTTTC
1677984 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATT-TTC
* * * *
1678039 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTT-TTATGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAGATT-TTC
* * * ** **
1678094 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTTTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTTTC
* * ** ** *
1678148 TGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTT
1 -GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGATT-TTC
* * * * *
1678205 GAGTCTTTTACTCCCTGAATGAATAGGGAGCAGACA
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1678241 CGTTTGCCAA
Statistics
Matches: 277, Mismatches: 21, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
50 19 0.07
51 80 0.29
54 6 0.02
55 128 0.46
56 42 0.15
57 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (54 bp):
GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTTTC
Found at i:1678153 original size:110 final size:108
Alignment explanation
Indices: 1677881--1678240 Score: 450
Period size: 110 Copynumber: 3.3 Consensus size: 108
1677871 TTGTTGAAGA
* *
1677881 TTGAGTCCTATACTCTCTGAAGAATAGGGAGCGGACAAGTTCGTTGAAGA---T-TGAGTCCTAT
1 TTGAGTCCTATACTCCCTGAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTTTCTGAGTTCTAT
* * *
1677942 ACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAGA---
66 ACTCTCTGAAGGAATAGAGAGCGGACACGTT-TTATGAAGATTG
*
1677982 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC-GAGTTCT
1 TTGAGTCCTATACTCCCTGAA-GAATAGGGAGCGGACAAGTTCGTTGAAGATT-TTCTGAGTTCT
1678046 ATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTG
64 ATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTG
* ** **
1678091 TTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTTTCTGAGTTCT
1 TT-GAGTCCTATACTCCCTGAA-GAATAGGGAGCGGACAAGTTCGTTGAAGATTTTCTGAGTTCT
*
1678156 ATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTG
64 ATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTA-TGAAGATTG
* * *
1678202 TTTGAGTCTTTTACTCCCTGAATGAATAGGGAGCAGACA
1 -TTGAGTCCTATACTCCCTGAA-GAATAGGGAGCGGACA
1678241 CGTTTGCCAA
Statistics
Matches: 227, Mismatches: 18, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
101 21 0.09
102 29 0.13
105 1 0.00
106 44 0.19
109 5 0.02
110 86 0.38
111 39 0.17
112 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (108 bp):
TTGAGTCCTATACTCCCTGAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTTTCTGAGTTCTAT
ACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTG
Found at i:1678262 original size:166 final size:164
Alignment explanation
Indices: 1677933--1678313 Score: 425
Period size: 166 Copynumber: 2.3 Consensus size: 164
1677923 GTTGAAGATT
* * * ** *
1677933 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TTGAGTCCTATAC
1 GAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTCATTGAAGATTTTTGAGTCCTATAC
* * *
1677995 TCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGG
66 TCTCTGAAGGAATAGAGAGCGGACAAGTTCATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGG
* **
1678060 AATAGAGAGCGGACACGTTTTATGAAGATTGTTC
131 AATAGAGAGCAGACACGTTTTACCAAGATTGTTC
* * *
1678094 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTTTCTGAGTTCTATA
1 GAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTCATTGAAGATTTT-TGAGTCCTATA
** * * *
1678159 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTTGAG-TCTTTTACTCCCTGA
65 CTCTCTGAAGGAATAGAGAGCGGACAAG-TTCATTGAAGATTGTTCGAGTTC-TATACTCCCTGA
* * *
1678223 ATGAATAGGGAGCAGACACG-TTTGCCAAGGATTGTTC
128 AGGAATAGAGAGCAGACACGTTTTACCAA-GATTGTTC
* * *
1678260 GAG-TCTTATACTCCTTGAAAGAAAAGGGAGCAGACCCG-TCATTAGAAGATTTTT
1 GAGTTC-TATACTCCCTGAAAGAATAGGGAGCGGACCCGTTCATT-GAAGATTTTT
1678314 CAAGTATCAC
Statistics
Matches: 184, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
161 42 0.23
164 1 0.01
165 49 0.27
166 92 0.50
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (164 bp):
GAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACCCGTTCATTGAAGATTTTTGAGTCCTATAC
TCTCTGAAGGAATAGAGAGCGGACAAGTTCATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGG
AATAGAGAGCAGACACGTTTTACCAAGATTGTTC
Found at i:1678273 original size:55 final size:54
Alignment explanation
Indices: 1677883--1678290 Score: 354
Period size: 55 Copynumber: 7.6 Consensus size: 54
1677873 GTTGAAGATT
* * * *
1677883 GAGTCCTATACTCTCTGAA-GAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTG-TGAAGATTGTTC
* * * *
1677933 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTG-TGAAGATTGTTC
* * * *
1677984 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTG-TGAAGATTGTTC
* * *
1678039 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACACG-TTTGTGAAGATTGTTC
* * *
1678094 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATT-TTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTT-GTGAAGATTGTTC
* * * * *
1678148 TGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTT
1 -GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACACG-TTT-GTGAAGATTGTTC
* * * **
1678205 GAG-TCTTTTACTCCCTGAATGAATAGGGAGCAGACACGTTTGCCAAGGATTGTTC
1 GAGTTC-TATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGTGAA-GATTGTTC
* * *
1678260 GAG-TCTTATACTCCTTGAAAGAAAAGGGAGC
1 GAGTTC-TATACTCCCTGAAGGAATAGGGAGC
1678291 AGACCCGTCA
Statistics
Matches: 318, Mismatches: 28, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
50 19 0.06
51 80 0.25
54 10 0.03
55 163 0.51
56 44 0.14
57 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (54 bp):
GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTGTGAAGATTGTTC
Found at i:1685102 original size:16 final size:16
Alignment explanation
Indices: 1685081--1685115 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1685071 CAAATCAATC
1685081 AGAGGGTCCAAAACAG
1 AGAGGGTCCAAAACAG
1685097 AGAGGGTCCAAAACAG
1 AGAGGGTCCAAAACAG
1685113 AGA
1 AGA
1685116 AGATCAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.31, T:0.06
Consensus pattern (16 bp):
AGAGGGTCCAAAACAG
Found at i:1707976 original size:3 final size:3
Alignment explanation
Indices: 1707968--1707994 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1707958 TATCGGTAAT
1707968 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1707995 CAAAACCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1711712 original size:16 final size:17
Alignment explanation
Indices: 1711683--1711716 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1711673 CTCGAGTTTC
1711683 TTATAAAATAAAAGATA
1 TTATAAAATAAAAGATA
*
1711700 TTAT-AAATTAAAGATA
1 TTATAAAATAAAAGATA
1711716 T
1 T
1711717 AAATTGTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
TTATAAAATAAAAGATA
Found at i:1716790 original size:18 final size:17
Alignment explanation
Indices: 1716763--1716807 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1716753 ATACGTTAAG
1716763 AATTAAAAAAGTTTAAAA
1 AATTAAAAAA-TTTAAAA
*
1716781 AATTAGAAAATTTAAAA
1 AATTAAAAAATTTAAAA
1716798 TAATATAAAA
1 -AAT-TAAAA
1716808 TAGAAATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (17 bp):
AATTAAAAAATTTAAAA
Found at i:1722970 original size:30 final size:32
Alignment explanation
Indices: 1722923--1722984 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
1722913 AGAAGTCACC
1722923 CTTACCTAAATTTTATGTAATAAA-ATATATA
1 CTTACCTAAATTTTATGTAATAAATATATATA
1722954 CTTACCTAAA-TTTATGTAATAAATATATATA
1 CTTACCTAAATTTTATGTAATAAATATATATA
1722985 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (32 bp):
CTTACCTAAATTTTATGTAATAAATATATATA
Found at i:1722983 original size:2 final size:2
Alignment explanation
Indices: 1722976--1723004 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1722966 TATGTAATAA
1722976 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 A
1723005 AAGTGATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1726023 original size:38 final size:39
Alignment explanation
Indices: 1725942--1726023 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 39
1725932 TCTGTCCCAC
* * *
1725942 TAAATTTAAATTATGATTTTTTTAAAAAGTTAAAATTTT
1 TAAATTTAAATTATGATTATTTTAAAAAGTTAAAACTTA
* *
1725981 TAAATTT-GATTATGATTATTTTAAATAA-TTAAACCTTA
1 TAAATTTAAATTATGATTATTTTAAA-AAGTTAAAACTTA
1726019 TAAAT
1 TAAAT
1726024 AGATAATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 28 0.76
39 9 0.24
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (39 bp):
TAAATTTAAATTATGATTATTTTAAAAAGTTAAAACTTA
Done.