Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_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: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 17
Found at i:1667082 original size:45 final size:45
Alignment explanation
Indices: 1666986--1667074 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
1666976 CTACACAATC
* *
1666986 CAATAATCGAAAGGAACTAATCATTTGATTTTACTTTTGGCAACA
1 CAATAATCGAAAGGAACTAATAATTTGATTTTACTTTTGCCAACA
*
1667031 CAATAATC-AAATGAACTAATAATTTGATTTTACTTTTGACCAAC
1 CAATAATCGAAAGGAACTAATAATTTGATTTTACTTTTG-CCAAC
1667075 CCGATAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 28 0.70
45 12 0.30
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (45 bp):
CAATAATCGAAAGGAACTAATAATTTGATTTTACTTTTGCCAACA
Found at i:1667208 original size:19 final size:18
Alignment explanation
Indices: 1667184--1667226 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 18
1667174 AAACACAATC
1667184 AATAATTATTATAATATTT
1 AATAATTATTATAATA-TT
1667203 AATAATTATTATAATATT
1 AATAATTATTATAATATT
1667221 AATAAT
1 AATAAT
1667227 AATATAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAATTATTATAATATT
Found at i:1667362 original size:86 final size:91
Alignment explanation
Indices: 1667259--1667519 Score: 415
Period size: 86 Copynumber: 2.9 Consensus size: 91
1667249 TGTATTAATA
1667259 GCTTTAGCAGTTTGCCCTCGCCAATAAGTCATGTATGAACTATAAACCATAAATGAATAA-ATTT
1 GCTTTAGCAGTTTGCCCTCGCCAATAAGTCATGTATGAACTATAAACCATAAATGAATAAGATTT
*
1667323 GCACGACTACCCAG-TTAAT-A-GCT
66 GCACGACTACCCAGAATAATCATGCT
1667346 GCTTTA-CAGTTTGCCCTCGCCAATAAGTCATGTATGAACTATAAACCATAAATGAATAATGATT
1 GCTTTAGCAGTTTGCCCTCGCCAATAAGTCATGTATGAACTATAAACCATAAATGAATAA-GATT
*
1667410 TGCACGACTACCCAGAAATATTCATGCT
65 TGCACGACTACCCAG-AATAATCATGCT
*
1667438 GCTTTAGCAGTTTGCCCTCGCCAATAATTCATTGTATGAACTATAAACCATAAATGAATAAATGA
1 GCTTTAGCAGTTTGCCCTCGCCAATAAGTCA-TGTATGAACTATAAACCATAAATGAAT-AA-GA
1667503 TTTGCACGACTACCCAG
63 TTTGCACGACTACCCAG
1667520 GAAATATCAT
Statistics
Matches: 162, Mismatches: 3, Indels: 10
0.93 0.02 0.06
Matches are distributed among these distances:
86 53 0.33
87 6 0.04
88 18 0.11
90 3 0.02
91 1 0.01
92 9 0.06
93 23 0.14
94 27 0.17
95 22 0.14
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (91 bp):
GCTTTAGCAGTTTGCCCTCGCCAATAAGTCATGTATGAACTATAAACCATAAATGAATAAGATTT
GCACGACTACCCAGAATAATCATGCT
Found at i:1667631 original size:76 final size:76
Alignment explanation
Indices: 1667538--1667684 Score: 242
Period size: 76 Copynumber: 1.9 Consensus size: 76
1667528 ATTGTACAAC
* *
1667538 AAAATTTGAGATGAACGTGAACTAAAATAAAAAATATTTATTTAAATTTAC-ATACTTCCAACTT
1 AAAAATTGAGATAAACGTGAACTAAAAT-AAAAATATTTATTTAAATTTACAATACTTCCAACTT
1667602 ATAAAAAATAAA
65 ATAAAAAATAAA
* *
1667614 AAAAATTGAGATAAACGTGAATTAAAATAAAGATATTTATTTAAATTTACAATACTTCCAACTTA
1 AAAAATTGAGATAAACGTGAACTAAAATAAAAATATTTATTTAAATTTACAATACTTCCAACTTA
1667679 TAAAAA
66 TAAAAA
1667685 TATGTAAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
75 21 0.32
76 45 0.68
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (76 bp):
AAAAATTGAGATAAACGTGAACTAAAATAAAAATATTTATTTAAATTTACAATACTTCCAACTTA
TAAAAAATAAA
Found at i:1680669 original size:82 final size:82
Alignment explanation
Indices: 1680330--1680644 Score: 434
Period size: 82 Copynumber: 3.8 Consensus size: 82
1680320 ATTTAGATCT
* * * * * * *
1680330 TGGCAGCATGCAACAGTTCATCATTCAACTTGATTCGATCATGGTAGCATACAACAATTCACCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
*
1680395 TCGA-TCTAATTCAATCA
66 TCAATTC-AATTCAATCA
* *
1680412 TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATTATGGTAGCATGCAATAATTCACCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
1680477 TCAATTCAATTCAATCA
66 TCAATTCAATTCAATCA
*
1680494 TGGCAGCATACAATAATCCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
1680559 TCAATTCAATTCAATCA
66 TCAATTCAATTCAATCA
* * * ** * * * *
1680576 TGGCAGCATACAATACTTCACCATTCAACCTGATTCAACCACGGTAGCATACCATAATTCATCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
1680641 TCAA
66 TCAA
1680645 CTTGACTTTA
Statistics
Matches: 211, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
82 209 0.99
83 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (82 bp):
TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
TCAATTCAATTCAATCA
Found at i:1680677 original size:41 final size:41
Alignment explanation
Indices: 1680346--1680669 Score: 341
Period size: 41 Copynumber: 7.9 Consensus size: 41
1680336 CATGCAACAG
* *
1680346 TTCATCATTCAACTTGATTCGATCATGGTAGCATACAACAA
1 TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
* * * *
1680387 TTCACCATTCGA-TCTAATTCAATCATGGCAGCATACAATAA
1 TTCATCATTCAACT-TGATTCAATCATGGTAGCATACAATAA
** * *
1680428 TTCATCATTCAACTTGATTTGATTATGGTAGCATGCAATAA
1 TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
* * *
1680469 TTCACCATTCAA-TTCAATTCAATCATGGCAGCATACAATAA
1 TTCATCATTCAACTT-GATTCAATCATGGTAGCATACAATAA
* ** *
1680510 TCCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAA
1 TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
* * *
1680551 TTCATCATTCAA-TTCAATTCAATCATGGCAGCATACAATAC
1 TTCATCATTCAACTT-GATTCAATCATGGTAGCATACAATAA
* * * * *
1680592 TTCACCATTCAACCTGATTCAACCACGGTAGCATACCATAA
1 TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
* *
1680633 TTCATCATTCAACTTGACTT-TATCATGGTAACATACA
1 TTCATCATTCAACTTGA-TTCAATCATGGTAGCATACA
1680670 TTTATTCACA
Statistics
Matches: 226, Mismatches: 50, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
40 5 0.02
41 215 0.95
42 6 0.03
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (41 bp):
TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
Found at i:1682041 original size:21 final size:21
Alignment explanation
Indices: 1682017--1682056 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1682007 GCGTAGAATT
1682017 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
1682038 TGTCCTGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
1682057 AAACACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:1682087 original size:18 final size:18
Alignment explanation
Indices: 1682064--1682099 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1682054 ATAAAACACA
1682064 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
1682082 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
1682100 ATATAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:1682099 original size:46 final size:46
Alignment explanation
Indices: 1682017--1682143 Score: 191
Period size: 46 Copynumber: 2.7 Consensus size: 46
1682007 GCGTAGAATT
*
1682017 TGTCCCGAAGGACCACATAGATGTCCTGAAGGACCACATAAAACACATA
1 TGTCCCGAAGGACCAC-T--ATGTCCCGAAGGACCACATAAAACACATA
*
1682066 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACATATAACACATA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACATAAAACACATA
* *
1682112 TATCCCGAAGGACCACTATGTTCCGAAGGACC
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACC
1682144 GCGTAGACCC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
46 57 0.77
48 1 0.01
49 16 0.22
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (46 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGGACCACATAAAACACATA
Found at i:1683011 original size:24 final size:20
Alignment explanation
Indices: 1682958--1683015 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1682948 TTCCCATTGA
*
1682958 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
1682978 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
1683001 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1683016 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:1690534 original size:3 final size:3
Alignment explanation
Indices: 1690526--1690634 Score: 134
Period size: 3 Copynumber: 35.7 Consensus size: 3
1690516 GGCCTGTTTG
**
1690526 TAA TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
1690571 TAA TAA TAAA TAA -AA TAA TAA TAAA TAA TATA TAA -AA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA
1690617 TAA TAAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TA
1690635 GAAATAGAGA
Statistics
Matches: 94, Mismatches: 4, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
2 6 0.06
3 73 0.78
4 15 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1692157 original size:564 final size:560
Alignment explanation
Indices: 1691079--1692208 Score: 1555
Period size: 564 Copynumber: 2.0 Consensus size: 560
1691069 TGTAATTTGG
* * * *
1691079 AAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCGGATGAGTTCTTCTCA
1 AAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
1691144 TTATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTGTGATAGAGTCATGCAAAAG
66 TTATGAACTCTACCTGGAAA--TTGAT-ATGATCCATCGA--TATGTGA-AGAGTCAAGCAAAAA
* *
1691209 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCTATCTGG
125 GTTGAACAAACTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCTATCTGG
* * * *
1691274 CAATGCTGATCCATCGAATGATGAATTCAAGTAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
190 AAAAGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGCTCTTCTCATTATGAACT
*
1691339 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAA
255 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGTTGATCCATCAA
* * *
1691404 GTGATGGATTTGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAG
320 GTGATGAATTTGAACAAAAAGTTAAACAAGCTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAG
* *
1691469 ATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCAAATGATGAATTCAAGCAA
385 ATGAGTTCTTCTCATTATAAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAGCAA
**
1691534 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
450 AAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
1691599 TGAACTCTACCT-GAAATGTTGATCCATC-AAGTGATGGATTTGAAC
515 TGAACTCGACCTGGAAATGCTGATCCATCGAA-TGATGGATTTGAAC
1691644 AAAA-GGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
1691708 TTATGAACTCTACCTGGAAA-TG-T-TGATCCATCGA-ATGATG-A-ATTCAAGTAAAAAGTTGA
66 TTATGAACTCTACCTGGAAATTGATATGATCCATCGATATG-TGAAGAGTCAAGCAAAAAGTTGA
* * *
1691767 ACAAATTCTTCTCATTATGAACTTCTTATTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTT
130 ACAAACTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC----T--A----
* * ** *
1691832 CTCTGGAAAAGTTGATCCATC-AAGTGATGGATTTGAGCAAAATGTTGAACAAGCTCTTCTCATT
185 -TCTGGAAAAGCTGATCCATCGAA-TGATGAATTCAAGCAAAAAGTTGAACAAGCTCTTCTCATT
*
1691896 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGA
248 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAAAGTTGA
* * *
1691960 TCCATCAAGTGATGAATTTGAGCAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
312 TCCATCAAGTGATGAATTTGAACAAAAAGTTAAACAAGCTCTTCTCATTATGAACTTCCTCTTCC
* * * *
1692025 TTCTTCAGATGAGTTCTTCTCATTATAAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGGA
377 TTCTTCAGATGAGTTCTTCTCATTATAAACTCTAC-CTGGAAAAGCTGATCCATCAAATGATGAA
** *
1692089 TTTGAGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
441 TTCAAGCAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
*
1692154 TTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGGATTTGAAC
506 TTCTCATTATGAACTCGACCTGGAAATGCTGATCCATCGAATGATGGATTTGAAC
1692209 CTTTGCTAAA
Statistics
Matches: 501, Mismatches: 47, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
553 62 0.12
554 1 0.00
555 2 0.00
556 2 0.00
557 1 0.00
558 9 0.02
559 1 0.00
560 1 0.00
561 2 0.00
563 6 0.01
564 380 0.76
565 32 0.06
566 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (560 bp):
AAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTACCTGGAAATTGATATGATCCATCGATATGTGAAGAGTCAAGCAAAAAGTTGAA
CAAACTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCTATCTGGAAAAGC
TGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGTTGATCCATCAAGTGATG
AATTTGAACAAAAAGTTAAACAAGCTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGT
TCTTCTCATTATAAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAAGTT
GAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
CGACCTGGAAATGCTGATCCATCGAATGATGGATTTGAAC
Found at i:1692200 original size:113 final size:113
Alignment explanation
Indices: 1691264--1692206 Score: 1378
Period size: 113 Copynumber: 8.4 Consensus size: 113
1691254 ATGAGTTCTT
* * * * ** *
1691264 CTCTATCTGGCAATGCTGATCCATCGAA-TGATGAATTCAAGTAAAAAGTTGAACAAGTTCTTCT
1 CTCTACCTGGAAATGTTGATCCATC-AAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCT
1691328 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
65 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
1691377 CTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGTTCTTCTC
1 CTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCTC
*
1691442 ATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * **
1691490 CTCTACCTGGAAATGCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
1 CTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCTC
1691555 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
1691603 CTCTACCT-GAAATGTTGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGTTCTTCTC
1 CTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCTC
*
1691667 ATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* ** * *
1691715 CTCTACCTGGAAATGTTGATCCATCGAA-TGATGAATTCAAGTAAAAAGTTGAACAAATTCTTCT
1 CTCTACCTGGAAATGTTGATCCATC-AAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCT
* * *
1691779 CATTATGAACTTCTTATTTCTTTTTCAGATGAGTTCTTCTCATTATGAA
65 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1691828 CT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAATGTTGAACAAGCTCTTCT
1 CTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCT
1691892 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
65 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1691941 CT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTGAGCAAAAAGTTGAACAAGCTCTTCT
1 CTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCT
*
1692005 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAA
65 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * **
1692054 CT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAACTCTTCT
1 CTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCT
1692118 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
65 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
1692167 CTCGACCTGGTAATGCTGATCCATCGAA-TGATGGATTTGA
1 CTCTACCTGGAAATGTTGATCCATC-AAGTGATGGATTTGA
1692207 ACCTTTGCTA
Statistics
Matches: 758, Mismatches: 65, Indels: 14
0.91 0.08 0.02
Matches are distributed among these distances:
112 109 0.14
113 644 0.85
114 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
CTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
Found at i:1692633 original size:22 final size:22
Alignment explanation
Indices: 1692608--1692662 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1692598 GATAAAGCTT
*
1692608 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1692630 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1692652 TCATCTTTGAA
1 TCATCTTTGAA
1692663 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1694096 original size:75 final size:73
Alignment explanation
Indices: 1694002--1694175 Score: 195
Period size: 74 Copynumber: 2.3 Consensus size: 73
1693992 CATGATGTTG
* * * * *
1694002 TGGGCCTTCAGCATGCCCCAACATTGGCTAATACAAGTGTTCAAAATGCATCAACAATTCTGGTT
1 TGGGCTTTCAGCATGCCCCAACATTGACTAATA-AA-TATTCAAAATACATCAACAATTCTGATT
1694067 CTGATTGAAA
64 CTGATTGAAA
* * * ** * *
1694077 TGGGCTTTCAGCATGCCCCAACATTTTACTGATAAATATTCAGAATATTTTAACATTTCTGATTC
1 TGGGCTTTCAGCATGCCCCAACA-TTGACTAATAAATATTCAAAATACATCAACAATTCTGATTC
1694142 TGATTGAAA
65 TGATTGAAA
* *
1694151 AGGGTTTTCAGCATGCCCCAACATT
1 TGGGCTTTCAGCATGCCCCAACATT
1694176 TGCTTCTTGT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
73 2 0.02
74 51 0.61
75 24 0.29
76 7 0.08
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (73 bp):
TGGGCTTTCAGCATGCCCCAACATTGACTAATAAATATTCAAAATACATCAACAATTCTGATTCT
GATTGAAA
Found at i:1695458 original size:114 final size:114
Alignment explanation
Indices: 1695256--1695477 Score: 372
Period size: 114 Copynumber: 1.9 Consensus size: 114
1695246 ACGATCATGC
* * *
1695256 AATTCATCTTCCTAATCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAA
1 AATTCATCTTCCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
1695321 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCAACTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCAACTATGAGCA
* * *
1695370 AATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTCCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
* *
1695435 GAACACTTCCAGAAGATGTTATTGGGTCTCCTTATTTCTACTA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCAACTA
1695478 CGAGAACGTG
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (114 bp):
AATTCATCTTCCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCAACTATGAGCA
Found at i:1697616 original size:14 final size:14
Alignment explanation
Indices: 1697597--1697652 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 14
1697587 CTCCCATTTT
1697597 TCTTTTTTTTTTCC
1 TCTTTTTTTTTTCC
1697611 TC--TTTTTTTTCC
1 TCTTTTTTTTTTCC
*
1697623 TCATTTTTCCTTTTTCA
1 TC-TTTTT--TTTTTCC
1697640 TCTTTTTTCTTTT
1 TCTTTTTT-TTTT
1697653 TTTGCTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
12 12 0.34
14 3 0.09
15 7 0.20
16 5 0.14
17 8 0.23
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (14 bp):
TCTTTTTTTTTTCC
Found at i:1697654 original size:17 final size:17
Alignment explanation
Indices: 1697615--1697654 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1697605 TTTTCCTCTT
*
1697615 TTTTTTCCTCATTTTTC
1 TTTTTTCATCATTTTTC
* *
1697632 CTTTTTCATCTTTTTTC
1 TTTTTTCATCATTTTTC
1697649 TTTTTT
1 TTTTTT
1697655 TGCTTTCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTCATCATTTTTC
Found at i:1701802 original size:66 final size:66
Alignment explanation
Indices: 1701732--1701934 Score: 243
Period size: 66 Copynumber: 3.2 Consensus size: 66
1701722 TTCACCCCCG
1701732 TAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCACCATC
1 TAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCACCATC
1701797 T
66 T
* ** * *
1701798 TAAGTTCACCCCTCAACTT------CTT--TT-ACCACTCCATCTA-TTTTCCACCC-ACTTCC-
1 TAAGTTCACCCCTCAA-TTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTC-ACCA
*
1701851 -CG
64 TCT
1701853 TAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCACCATC
1 TAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCACCATC
1701918 T
66 T
1701919 TAAGTTCACCCCTCAA
1 TAAGTTCACCCCTCAA
1701935 CTTCTTTTAC
Statistics
Matches: 110, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
54 2 0.02
55 17 0.15
56 1 0.01
57 10 0.09
58 12 0.11
59 2 0.02
60 3 0.03
61 3 0.03
62 2 0.02
63 12 0.11
64 10 0.09
65 1 0.01
66 33 0.30
67 2 0.02
ACGTcount: A:0.25, C:0.40, G:0.03, T:0.32
Consensus pattern (66 bp):
TAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCACCATC
T
Found at i:1701827 original size:58 final size:58
Alignment explanation
Indices: 1701753--1701959 Score: 208
Period size: 58 Copynumber: 3.5 Consensus size: 58
1701743 CTCAATTCCA
* *
1701753 CAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCACCATCTTAAGTTCACCCCT
1 CAACTTCTTTTACCACTCCATCAATTTTTTAACCCGTCACCATCTTAAGTTCACCCCT
* ** * * *
1701811 CAACTTCTTTTACCACTCCATCTA-TTTTCCACCC-ACTTCC--CGTAAGTTCACCCCT
1 CAACTTCTTTTACCACTCCATCAATTTTTTAACCCGTC-ACCATCTTAAGTTCACCCCT
1701866 CAA-TTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCACCATCTTAAGTTCACCC
1 CAACTT------CTT--TT-ACCACTCCATCAATTTTTTAACCCGTCACCATCTTAAGTTCACCC
1701930 CT
57 CT
*
1701932 CAACTTCTTTTACCACTCCATCTATTTT
1 CAACTTCTTTTACCACTCCATCAATTTT
1701960 CCACCCACTT
Statistics
Matches: 119, Mismatches: 15, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
54 2 0.02
55 17 0.14
56 1 0.01
57 10 0.08
58 37 0.31
59 2 0.02
60 3 0.03
61 3 0.03
62 2 0.02
63 12 0.10
64 10 0.08
65 1 0.01
66 17 0.14
67 2 0.02
ACGTcount: A:0.23, C:0.39, G:0.03, T:0.35
Consensus pattern (58 bp):
CAACTTCTTTTACCACTCCATCAATTTTTTAACCCGTCACCATCTTAAGTTCACCCCT
Found at i:1701874 original size:121 final size:121
Alignment explanation
Indices: 1701728--1701972 Score: 490
Period size: 121 Copynumber: 2.0 Consensus size: 121
1701718 CCTCTTCACC
1701728 CCCGTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCAC
1 CCCGTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCAC
1701793 CATCTTAAGTTCACCCCTCAACTTCTTTTACCACTCCATCTATTTTCCACCCACTT
66 CATCTTAAGTTCACCCCTCAACTTCTTTTACCACTCCATCTATTTTCCACCCACTT
1701849 CCCGTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCAC
1 CCCGTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCAC
1701914 CATCTTAAGTTCACCCCTCAACTTCTTTTACCACTCCATCTATTTTCCACCCACTT
66 CATCTTAAGTTCACCCCTCAACTTCTTTTACCACTCCATCTATTTTCCACCCACTT
1701970 CCC
1 CCC
1701973 CTTTAAGCCT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 124 1.00
ACGTcount: A:0.23, C:0.41, G:0.03, T:0.33
Consensus pattern (121 bp):
CCCGTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCCATCAATTTTTTAACCCGTCAC
CATCTTAAGTTCACCCCTCAACTTCTTTTACCACTCCATCTATTTTCCACCCACTT
Found at i:1702422 original size:22 final size:23
Alignment explanation
Indices: 1702395--1702445 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
1702385 AACCTGCATT
1702395 TATAATTAAAT-T-TATCATTTTA
1 TATAA-TAAATATATATCATTTTA
1702417 TATAATAAATATACTATCATTTTA
1 TATAATAAATATA-TATCATTTTA
1702441 TATAA
1 TATAA
1702446 AAAAACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.19
22 6 0.23
24 15 0.58
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
TATAATAAATATATATCATTTTA
Found at i:1704751 original size:163 final size:163
Alignment explanation
Indices: 1704481--1704818 Score: 534
Period size: 163 Copynumber: 2.1 Consensus size: 163
1704471 ATAATGAAAT
* * * * *
1704481 CGGTTTTATCATATTTTTATCTGTTATATTGTTATGTATTGATATATTTTTATAAAGTATCAATA
1 CGGTTTTGTCATATTTTTACCTGCTATATTGTTATGTATCGATACATTTTTATAAAGTATCAATA
* * *
1704546 CTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTTCAAAAGTGTCGATACTTATTTGAATAAAA
66 CTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATAAAA
1704611 TCGATACTTTCAACATATCCGGCA-GCTCTTTAC
131 TCGATACTTTCAACATATCCGGCAGGCT-TTTAC
*
1704644 CGGTTTTGTCATATTTTTACCTGCTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATA
1 CGGTTTTGTCATATTTTTACCTGCTATATTGTTATGTATCGATACATTTTTATAAAGTATCAATA
**
1704709 CTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAA
66 CTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATAAAA
* *
1704774 TCGATACTTTCAACATATCCGGTAGGGTTTTAC
131 TCGATACTTTCAACATATCCGGCAGGCTTTTAC
*
1704807 CAGTTTTGTCAT
1 CGGTTTTGTCAT
1704819 TATGAAACTG
Statistics
Matches: 160, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
163 158 0.99
164 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (163 bp):
CGGTTTTGTCATATTTTTACCTGCTATATTGTTATGTATCGATACATTTTTATAAAGTATCAATA
CTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATAAAA
TCGATACTTTCAACATATCCGGCAGGCTTTTAC
Found at i:1704935 original size:161 final size:161
Alignment explanation
Indices: 1704537--1705031 Score: 496
Period size: 163 Copynumber: 3.1 Consensus size: 161
1704527 TTTTTATAAA
* * * * * * *
1704537 GTATCAATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTTCAAAAGTGTCGATACTTATT
1 GTATCGATACTTTATAGACGCTATTACTGCTTTTCTCTTAAATTCCAAAAATGTCAATACTTATT
* ** * * * * ** *
1704602 TGAATAAAATCGATACTTTCAACATATCCGGCAGCTCTTTACCGGTTTTGTCATATTTTTACCTG
66 TAAATGGAATCAATACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATA-TTGAACCGG
* * ** * * * * * *
1704667 CTATATTGTTA-TGTATC-GATACATTTTTAT
130 TTTTATCATAATTTTACCTAATATATTGTTAT
* * * *
1704697 AAAGTATCGATACTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTT
1 ---GTATCGATACTTTATAGACGCTATTACTGCTTTTCTCTTAAATTCCAAAAATGTCAATACTT
* * *
1704762 ATTTAAATGGAATCGATACTTTCAACATATCCGGTAGGGTTTTACC-AGTTTTGTCAT-TATGAA
63 ATTTAAATGGAATCAATACTTTCAACATATCCGGTAGCGCTTTACCGA-TTTTGTCATAT-TG-A
* **
1704825 ACTGGTTTTATCATAATTTTACCTGTTATATTGTTAT
125 ACCGGTTTTATCATAATTTTACCTAATATATTGTTAT
* * *
1704862 GTATCGATACTTTATAGACGTTATTAC-GCTTTTCTCTTAAATTCTAAAAATGTTAATACTTATT
1 GTATCGATACTTTATAGACGCTATTACTGCTTTTCTCTTAAATTCCAAAAATGTCAATACTTATT
* * *
1704926 TCAATGGAATCAATACTTTCAACATATCTGGTAGCGCTTTACCGATTTTTTCATATTGAACCGGT
66 TAAATGGAATCAATACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATATTGAACCGGT
*
1704991 TTTATCATATTTTTACCTAATATATTGTTAT
131 TTTATCATAATTTTACCTAATATATTGTTAT
1705022 GTATCGATAC
1 GTATCGATAC
1705032 ATATTTTAAT
Statistics
Matches: 283, Mismatches: 42, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
160 44 0.16
161 81 0.29
162 28 0.10
163 116 0.41
164 4 0.01
165 10 0.04
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (161 bp):
GTATCGATACTTTATAGACGCTATTACTGCTTTTCTCTTAAATTCCAAAAATGTCAATACTTATT
TAAATGGAATCAATACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATATTGAACCGGT
TTTATCATAATTTTACCTAATATATTGTTAT
Found at i:1706769 original size:34 final size:34
Alignment explanation
Indices: 1706715--1706786 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
1706705 AGGGGTTTAA
*
1706715 AAATAAAATAAAAGATAAAATTAATAAATAA-TT
1 AAATAAAAGAAAAGATAAAATTAATAAATAATTT
*
1706748 AAATAAAAGATAAGGATAAAATTAATAAATAATTT
1 AAATAAAAGA-AAAGATAAAATTAATAAATAATTT
1706783 AAAT
1 AAAT
1706787 TTAAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 9 0.26
34 20 0.57
35 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (34 bp):
AAATAAAAGAAAAGATAAAATTAATAAATAATTT
Found at i:1710051 original size:18 final size:19
Alignment explanation
Indices: 1710028--1710068 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1710018 CTTAATCGCG
1710028 AAAATT-AAAATTTAAATC
1 AAAATTAAAAATTTAAATC
*
1710046 AAAATTAAAAATTTAATTC
1 AAAATTAAAAATTTAAATC
1710065 AAAA
1 AAAA
1710069 ATACCTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATTAAAAATTTAAATC
Found at i:1711798 original size:3 final size:3
Alignment explanation
Indices: 1711778--1711843 Score: 53
Period size: 3 Copynumber: 21.0 Consensus size: 3
1711768 GGCCCTGTAA
* * * *
1711778 AAT AAT AAA AAT ATT AAT AAT AAAT AAT AAT ACT AAA AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
1711824 AAAT AAAT AAAT AAT -AT AAT
1 -AAT -AAT -AAT AAT AAT AAT
1711844 GCTTGTGGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 36 0.69
4 14 0.27
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1711805 original size:22 final size:23
Alignment explanation
Indices: 1711777--1711840 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
1711767 GGGCCCTGTA
1711777 AAATAATAAA-AATATTAATAAT
1 AAATAATAAATAATATTAATAAT
* *
1711799 AAATAATAATACTAAAAATAATAAT
1 AAATAATAA-A-TAATATTAATAAT
1711824 AAATAAATAAATAATAT
1 AAAT-AATAAATAATAT
1711841 AATGCTTGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 9 0.26
23 1 0.03
24 4 0.12
25 15 0.44
26 5 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATAATAAATAATATTAATAAT
Found at i:1711836 original size:15 final size:13
Alignment explanation
Indices: 1711778--1711839 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 13
1711768 GGCCCTGTAA
1711778 AATAAT-AAAAAT
1 AATAATAAAAAAT
* *
1711790 ATTAATAATAAAT
1 AATAATAAAAAAT
1711803 AATAATACTAAAAAT
1 AATAATA--AAAAAT
1711818 AATAATAAATAAAT
1 AATAATAAA-AAAT
1711832 AAATAATA
1 -AATAATA
1711840 TAATGCTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 5 0.12
13 13 0.32
14 4 0.10
15 19 0.46
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAAAAAAT
Found at i:1712213 original size:3 final size:3
Alignment explanation
Indices: 1712198--1712242 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
1712188 GGCCCTGCAA
* *
1712198 AAT AAT AAA AAT AAT AAT AAAT ACT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
1712243 ATATATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1712228 original size:25 final size:25
Alignment explanation
Indices: 1712198--1712245 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1712188 GGCCCTGCAA
1712198 AATAATAAAAATAATAATAAATACT
1 AATAATAAAAATAATAATAAATACT
*
1712223 AATAATAATAATAATAATAAATA
1 AATAATAAAAATAATAATAAATA
1712246 TATATTTAAA
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:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (25 bp):
AATAATAAAAATAATAATAAATACT
Found at i:1712229 original size:19 final size:19
Alignment explanation
Indices: 1712197--1712243 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1712187 GGGCCCTGCA
1712197 AAATAATAAAAATAATAAT
1 AAATAATAAAAATAATAAT
* *
1712216 AAATACTAATAATAATAAT
1 AAATAATAAAAATAATAAT
1712235 -AATAATAAA
1 AAATAATAAA
1712244 TATATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAATAAAAATAATAAT
Found at i:1712629 original size:123 final size:120
Alignment explanation
Indices: 1712412--1712631 Score: 293
Period size: 123 Copynumber: 1.8 Consensus size: 120
1712402 AAAAGATCTG
* **
1712412 AGTTGAGCTTTGAATTGGATATCATTCGTTGTGGTTGAAATCCAATCTAAAGATGAATGTTGTGG
1 AGTTGAGCCTTGAATTGGATATCATTCGACGTGGTTGAAATCCAATCTAAAGATGAATGTTGT-G
* *
1712477 TGAGCACGATTCCTTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGA
65 TGAGCACAATTCCTTTCGCCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGA
* *
1712533 AGTTGAGCCTTGAATTGGATATCCTTCGACGTGAAGTTGAAATCCAATCTAAATATGAATGTTGC
1 AGTTGAGCCTTGAATTGGATATCATTCGACGTG--GTTGAAATCCAATCTAAAGATGAATGTTG-
1712598 T-TCGAGTC-CAATATCC-TTCGCCGTGAAGTTGAAA
63 TGT-GAG-CACAAT-TCCTTTCGCCGTGAAGTTGAAA
1712632 TTGGCTCTGA
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
121 29 0.34
122 1 0.01
123 51 0.59
124 5 0.06
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (120 bp):
AGTTGAGCCTTGAATTGGATATCATTCGACGTGGTTGAAATCCAATCTAAAGATGAATGTTGTGT
GAGCACAATTCCTTTCGCCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGA
Found at i:1723630 original size:3 final size:3
Alignment explanation
Indices: 1723607--1723672 Score: 64
Period size: 3 Copynumber: 21.3 Consensus size: 3
1723597 GACCCTGCAA
* *
1723607 AAT AAT AA- AAT -AT TAT AAAT AAT AAT AAT AAT AAT ACT AAAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT AAT
1723652 AAT AAAT AAT AAAT AAT AAT A
1 AAT -AAT AAT -AAT AAT AAT A
1723673 TATTTTTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
2 4 0.07
3 40 0.74
4 10 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1723634 original size:10 final size:10
Alignment explanation
Indices: 1723607--1723672 Score: 64
Period size: 10 Copynumber: 6.4 Consensus size: 10
1723597 GACCCTGCAA
1723607 AATAATAAA-
1 AATAATAAAT
*
1723616 ATATTATAAAT
1 A-ATAATAAAT
1723627 AATAATAATAAT
1 AATAAT-A-AAT
*
1723639 AATACTAAAT
1 AATAATAAAT
1723649 AATAATAAAT
1 AATAATAAAT
1723659 AATAA-ATAAT
1 AATAATA-AAT
1723669 AATA
1 AATA
1723673 TATTTTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
9 2 0.04
10 35 0.73
11 3 0.06
12 8 0.17
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
AATAATAAAT
Found at i:1726056 original size:160 final size:162
Alignment explanation
Indices: 1725860--1726183 Score: 602
Period size: 162 Copynumber: 2.0 Consensus size: 162
1725850 GTAATGAATA
1725860 TGAGGATGTTCATTCCACATGAGTTAAGGGGCCCGTTTGATGTTTGGAT-G-GGTGGTCCCTCTG
1 TGAGGATGTTCATTCCACATGAGTTAAGGGGCCCGTTTGATGTTTGGATGGTGGTGGTCCCTCTG
1725923 ATCTGTTGTATGATTGTCAAGTGGCACCCCACTGATCGCGTGCTCCGATAATTTGGTTTTGTACA
66 ATCTGTTGTATGATTGTCAAGTGGCACCCCACTGATCGCGTGCTCCGATAATTTGG-TTTGTACA
1725988 ACCAATTCCGGAGCACCTAG-AATATTGACCAGT
130 ACCAATTCCGGAGCACCTAGAAATA-TGACCAGT
1726021 TGAGGATGTTCATTCCAC-TGAGTTAAGGGGCCCGTTTGATGTTTGGATGGTGGTGGTCCCTCTG
1 TGAGGATGTTCATTCCACATGAGTTAAGGGGCCCGTTTGATGTTTGGATGGTGGTGGTCCCTCTG
1726085 ATCTGTTGTATGATTGTCAAGTGGCACCCCACTGATCGCGTGCTCCGATAATTTGGTTTGTACAA
66 ATCTGTTGTATGATTGTCAAGTGGCACCCCACTGATCGCGTGCTCCGATAATTTGGTTTGTACAA
1726150 CCAATTCCGGAGCACCTAGAAATATGACCAGT
131 CCAATTCCGGAGCACCTAGAAATATGACCAGT
1726182 TG
1 TG
1726184 TATAACACAG
Statistics
Matches: 160, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
160 30 0.19
161 57 0.36
162 73 0.46
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (162 bp):
TGAGGATGTTCATTCCACATGAGTTAAGGGGCCCGTTTGATGTTTGGATGGTGGTGGTCCCTCTG
ATCTGTTGTATGATTGTCAAGTGGCACCCCACTGATCGCGTGCTCCGATAATTTGGTTTGTACAA
CCAATTCCGGAGCACCTAGAAATATGACCAGT
Found at i:1727923 original size:11 final size:12
Alignment explanation
Indices: 1727892--1727932 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
1727882 AACATTATCC
1727892 ATTT-ATTTCTT
1 ATTTCATTTCTT
1727903 ATCCTTCATTT-TT
1 AT--TTCATTTCTT
1727916 ATTTCATTTCTT
1 ATTTCATTTCTT
1727928 ATTTC
1 ATTTC
1727933 CAATATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 9 0.35
12 7 0.27
13 6 0.23
14 4 0.15
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTCATTTCTT
Found at i:1731752 original size:22 final size:22
Alignment explanation
Indices: 1731727--1731768 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1731717 TCCATCATCA
**
1731727 TCACCATTTCATTATCATTCCT
1 TCACCATTAAATTATCATTCCT
1731749 TCACCATTAAATTATCATTC
1 TCACCATTAAATTATCATTC
1731769 ATTTATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (22 bp):
TCACCATTAAATTATCATTCCT
Found at i:1731907 original size:16 final size:16
Alignment explanation
Indices: 1731873--1731919 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
1731863 ATATCATCTC
*
1731873 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
1731889 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
1731904 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
1731917 TAT
1 TAT
1731920 TTCCAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:1731921 original size:12 final size:13
Alignment explanation
Indices: 1731894--1731922 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1731884 TTTCTTATCC
1731894 TTTCATTTCTTTA
1 TTTCATTTCTTTA
1731907 TTTCATTTC-TTA
1 TTTCATTTCTTTA
1731919 TTTC
1 TTTC
1731923 CAATATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:1734874 original size:31 final size:31
Alignment explanation
Indices: 1734836--1734990 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
1734826 AGGGTCGAGG
1734836 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1734867 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1734898 GTTTACCTATGTTCTTCGGAACATACGG-CT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1734928 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1734959 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1734990 G
1 G
1734991 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 27 0.24
31 85 0.75
32 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1734950 original size:61 final size:62
Alignment explanation
Indices: 1734836--1734979 Score: 236
Period size: 61 Copynumber: 2.3 Consensus size: 62
1734826 AGGGTCGAGG
* * *
1734836 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACT
1734898 GTTTACCTATGTTCTTCGGAACATACGG-CTGTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACT
* *
1734959 GATTACCTAGGTTCTTCGGAA
1 GTTTACCTATGTTCTTCGGAA
1734980 TCTATGGACT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
61 51 0.66
62 26 0.34
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACT
Found at i:1738195 original size:31 final size:31
Alignment explanation
Indices: 1738157--1738312 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
1738147 AGGGTCGAGG
1738157 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1738188 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1738219 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1738250 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1738281 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1738312 G
1 G
1738313 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1746147 original size:51 final size:51
Alignment explanation
Indices: 1746091--1746194 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
1746081 TAAAATACAA
1746091 TTAATAAGTAAATCTTGATACACACTTTTTATTTGTTGTTAAAAACGTGAT
1 TTAATAAGTAAATCTTGATACACACTTTTTATTTGTTGTTAAAAACGTGAT
1746142 TTAATAAGTAAATCTTGATACACACTTTTTATTTGTTGTTAAAAACGTGAT
1 TTAATAAGTAAATCTTGATACACACTTTTTATTTGTTGTTAAAAACGTGAT
1746193 TT
1 TT
1746195 TAAGAAAACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (51 bp):
TTAATAAGTAAATCTTGATACACACTTTTTATTTGTTGTTAAAAACGTGAT
Found at i:1747125 original size:94 final size:87
Alignment explanation
Indices: 1747003--1747190 Score: 279
Period size: 94 Copynumber: 2.1 Consensus size: 87
1746993 CGTCGAAACC
1747003 GATCTTTACCTATTGTTTTCGAGCCACTGACCGCCGAAACTCTCTTCCGAGGCTTCACAATTTGG
1 GATC-TTACCTATTGTTTTCGAGCCACTGACCGCCGAAACTCTCTTCC---G-TTCACAATTTGG
1747068 ACAAGAGTCACCTTGATATGAAGCGAGGAAT
61 ACAAGAGTCA-C---ATATGAAGCGAGGAAT
1747099 GATCTTACCTATTG-TTTCGAGCCACTGACCGCCGAAACTCTCTTCCGTTCACAATTTGGACAAG
1 GATCTTACCTATTGTTTTCGAGCCACTGACCGCCGAAACTCTCTTCCGTTCACAATTTGGACAAG
1747163 AGTCACATATGAAGCGAGGAAT
66 AGTCACATATGAAGCGAGGAAT
*
1747185 GGTCTT
1 GATCTT
1747191 CGTGAGGCCA
Statistics
Matches: 91, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
86 21 0.23
89 1 0.01
90 22 0.24
91 1 0.01
94 32 0.35
95 10 0.11
96 4 0.04
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (87 bp):
GATCTTACCTATTGTTTTCGAGCCACTGACCGCCGAAACTCTCTTCCGTTCACAATTTGGACAAG
AGTCACATATGAAGCGAGGAAT
Found at i:1756771 original size:3 final size:3
Alignment explanation
Indices: 1756763--1756852 Score: 65
Period size: 3 Copynumber: 30.0 Consensus size: 3
1756753 CTGTAATATG
* * * * * *
1756763 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA CAG TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1756808 TAA TAA TTA TAA CAA TTA TAA TAA TTA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1756853 AACAGGCAAA
Statistics
Matches: 65, Mismatches: 20, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
2 2 0.03
3 61 0.94
4 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1756811 original size:9 final size:9
Alignment explanation
Indices: 1756799--1756846 Score: 78
Period size: 9 Copynumber: 5.3 Consensus size: 9
1756789 ATAATAACAG
1756799 TAATAATTA
1 TAATAATTA
1756808 TAATAATTA
1 TAATAATTA
*
1756817 TAACAATTA
1 TAATAATTA
1756826 TAATAATTA
1 TAATAATTA
*
1756835 TAATAATAA
1 TAATAATTA
1756844 TAA
1 TAA
1756847 AAATAAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
TAATAATTA
Found at i:1757369 original size:124 final size:124
Alignment explanation
Indices: 1757087--1757737 Score: 932
Period size: 124 Copynumber: 5.3 Consensus size: 124
1757077 CTTCTTATTT
* ** * *
1757087 AGATGAGTTCTTCTCATTATAAAC-ACTTCT-GAAAATGTTGATGCTAATCTATCTCCTTCTGAG
1 AGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAA-GTTGATGCTGATCTATCTCCTTCTGTG
* * * *
1757150 ATAGA-TCATACAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTT
65 ATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * * *
1757208 AGATGAGTTCTTCTCATTATAAACTTTCTCTAGAAAAGTTGATGTTGATCTATCTCCTTCTGTGA
1 AGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
*
1757273 TAAAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
66 TAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
1757332 AGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTATGTGA
1 AGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
* *
1757397 TAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTC
66 TAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * * * *
1757456 AGATGAGTTTTTTTTATTATGAACTTTTTCTGGAAAAGTTGATGTTAATCTATCTCCTTCTGTGA
1 AGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
*
1757521 TAGAGGCATGCAAAAGGTTGAACAAGCTCTTCTCATTATG-A-------TTCCTTCTTC
66 TAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
1757572 AGATGAGTTCTTCTTATTATGAACTTTTTATGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
1 AGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
*
1757637 TAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
66 TAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * *
1757696 AGATGAGTTCTTCTCATTATGAAC-TCTTCCGGAAATGTTGAT
1 AGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGAT
1757738 CCATCGAATG
Statistics
Matches: 478, Mismatches: 40, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
116 107 0.22
117 1 0.00
121 24 0.05
122 31 0.06
123 63 0.13
124 252 0.53
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (124 bp):
AGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
TAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
Found at i:1757641 original size:240 final size:241
Alignment explanation
Indices: 1757087--1757737 Score: 954
Period size: 240 Copynumber: 2.7 Consensus size: 241
1757077 CTTCTTATTT
* * ** * *
1757087 AGATGAGTTCTTCTCATTATAAAC-ACTTCT-GAAAATGTTGATGCTAATCTATCTCCTTCTGAG
1 AGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAA-GTTGATGCTGATCTATCTCCTTCTGTG
* * * * *
1757150 ATAGA-TCATACAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATGA
65 ATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGA
* * * * *
1757214 GTTCTTCTCATTATAAACTTTCTCTAGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAAAGT
130 GTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGTTAATCTATCTCCTTCTGTGATAAAGG
1757279 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
195 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA-----T-TTCCTTCTTC
*
1757332 AGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTATGTGA
1 AGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
1757397 TAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGA
66 TAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGA
* * * *
1757462 GTTTTTTTTATTATGAACTTTTTCTGGAAAAGTTGATGTTAATCTATCTCCTTCTGTGATAGAGG
130 GTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGTTAATCTATCTCCTTCTGTGATAAAGG
1757527 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATG-A-TTCCTTCTTC
195 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAATTTCCTTCTTC
*
1757572 AGATGAGTTCTTCTTATTATGAACTTTTTATGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
1 AGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
1757637 TAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
66 TAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGA
* * *
1757702 GTTCTTCTCATTATGAAC-TCTTCCGGAAATGTTGAT
130 GTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGAT
1757738 CCATCGAATG
Statistics
Matches: 372, Mismatches: 29, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
239 15 0.04
240 151 0.41
241 1 0.00
245 22 0.06
246 33 0.09
247 49 0.13
248 101 0.27
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (241 bp):
AGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGA
TAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAG
TTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGTTAATCTATCTCCTTCTGTGATAAAGGC
ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAATTTCCTTCTTC
Found at i:1758478 original size:18 final size:18
Alignment explanation
Indices: 1758455--1758489 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1758445 TATATGAAAC
1758455 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
1758473 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
1758490 GATAAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:1758870 original size:15 final size:14
Alignment explanation
Indices: 1758850--1758900 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
1758840 TCTTTCACTC
1758850 ATTTTTTTTCATTTT
1 ATTTTTTTTCA-TTT
* *
1758865 ATTTTTCTTTTATTA
1 ATTTTT-TTTCATTT
*
1758880 ATTTTTCTTCA-TT
1 ATTTTTTTTCATTT
1758893 ATTTTTTT
1 ATTTTTTT
1758901 AGTATTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
13 8 0.28
14 3 0.10
15 14 0.48
16 4 0.14
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTTTTTCATTT
Found at i:1758884 original size:30 final size:31
Alignment explanation
Indices: 1758832--1758900 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
1758822 ATATTGACCC
* *
1758832 TTATTTTCTCTTTCACTCATTTTTTTTCATT-
1 TTATTTT-TCTTTCACTAATTTTTCTTCATTA
* *
1758863 TTATTTTTCTTTTATTAATTTTTCTTCATTA
1 TTATTTTTCTTTCACTAATTTTTCTTCATTA
1758894 TT-TTTTT
1 TTATTTTT
1758901 AGTATTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.14, C:0.13, G:0.00, T:0.72
Consensus pattern (31 bp):
TTATTTTTCTTTCACTAATTTTTCTTCATTA
Found at i:1758894 original size:28 final size:26
Alignment explanation
Indices: 1758852--1758926 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 26
1758842 TTTCACTCAT
*
1758852 TTTTTTTCATTTTATTTTTCTT-TTATTAA
1 TTTTTTTCA--TTATTTTT-TTAGTATT-A
1758881 TTTTTCTTCATTATTTTTTTAGTATTA
1 TTTTT-TTCATTATTTTTTTAGTATTA
*
1758908 TTTTTTTCATCATTTTTTT
1 TTTTTTTCATTATTTTTTT
1758927 CTTCAAGCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 13 0.31
27 8 0.19
28 12 0.29
29 5 0.12
30 4 0.10
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (26 bp):
TTTTTTTCATTATTTTTTTAGTATTA
Found at i:1758922 original size:26 final size:28
Alignment explanation
Indices: 1758875--1758926 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
1758865 ATTTTTCTTT
*
1758875 TATTAATTTTTCTTCATTATTTTTTTAG
1 TATTAATTTTTCTTCATCATTTTTTTAG
1758903 TATT-ATTTTT-TTCATCATTTTTTT
1 TATTAATTTTTCTTCATCATTTTTTT
1758927 CTTCAAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 6 0.26
28 4 0.17
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (28 bp):
TATTAATTTTTCTTCATCATTTTTTTAG
Found at i:1758925 original size:14 final size:15
Alignment explanation
Indices: 1758881--1758931 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
1758871 CTTTTATTAA
*
1758881 TTTTTCTTCATTATT
1 TTTTTCATCATTATT
1758896 TTTTT-AGT-ATTATT
1 TTTTTCA-TCATTATT
1758910 TTTTTCATCATT-TT
1 TTTTTCATCATTATT
1758924 TTTCTTCA
1 TTT-TTCA
1758932 AGCATAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 17 0.55
15 14 0.45
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTTCATCATTATT
Found at i:1771857 original size:3 final size:3
Alignment explanation
Indices: 1771816--1771903 Score: 61
Period size: 3 Copynumber: 29.0 Consensus size: 3
1771806 ATTGGGCCTG
* * * * *
1771816 TAA TATA TAA TAA AAA TATT TAT TAA TAA AAA T-A TAA TAA TAG TAA
1 TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1771862 TAA TTA TAA CAA TTA TAA TAA TTA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1771904 AACAGGCAAA
Statistics
Matches: 64, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
2 2 0.03
3 57 0.89
4 5 0.08
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1774789 original size:28 final size:28
Alignment explanation
Indices: 1774758--1774813 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1774748 TCATACTCTA
1774758 AAAATTTCAAATTAATTATCATATATTT
1 AAAATTTCAAATTAATTATCATATATTT
1774786 AAAATTTCAAATTAATTATCATATATTT
1 AAAATTTCAAATTAATTATCATATATTT
1774814 TAGATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (28 bp):
AAAATTTCAAATTAATTATCATATATTT
Found at i:1775630 original size:64 final size:63
Alignment explanation
Indices: 1775424--1775631 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
1775414 TTTCAGAGTG
** *
1775424 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACACCGAATGCATT
1 ATGCACCGATGCACCAA-CCATGCATCGATGCACTCA-GG--TATTTTGAAACATCGAATGCATT
1775487 TC
62 TC
*
1775489 ATGCACCGATGCA-CATACTATGCATCGATGCACTCAGAGT-TTTATGAAAACATCGAATGCATT
1 ATGCACCGATGCACCA-ACCATGCATCGATGCACTCAG-GTATTT-TG-AAACATCGAATGCATT
*
1775552 TG
62 TC
* * * *
1775554 ATGCATCGATGCACCAGCCATGCATCGATGCTCTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCACCGATGCACCAACCATGCATCGATGCACTCAGG-TATTTTGAAACATCGAATGCATTTC
*
1775618 ATGCATCGATGCAC
1 ATGCACCGATGCAC
1775632 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 50 0.40
65 65 0.52
66 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (63 bp):
ATGCACCGATGCACCAACCATGCATCGATGCACTCAGGTATTTTGAAACATCGAATGCATTTC
Found at i:1781490 original size:23 final size:22
Alignment explanation
Indices: 1781419--1781500 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
1781409 ACACTTAACA
1781419 GTGCATCGATGCATCCCATTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * *
1781443 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
1781464 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
1781487 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1781501 AAGGCCATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:1784379 original size:64 final size:66
Alignment explanation
Indices: 1784221--1784380 Score: 206
Period size: 65 Copynumber: 2.5 Consensus size: 66
1784211 AAATAAATTG
* *
1784221 AACATCGAATGCATTTCATGCA-CTGATGCA-CATACTATGCATCGATGCACTCAGAGTTTTATG
1 AACATCGAATGCATTTCATGCATC-GATGCACCATACCATGCATCGATGCACTCAGAGTGTTATG
1784284 AA
65 AA
* *
1784286 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCAG-GCTAGTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAG-T-GTTAT
1784348 G-A
64 GAA
*
1784350 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
1784381 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
64 32 0.37
65 49 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTGTTATGA
A
Found at i:1784396 original size:64 final size:64
Alignment explanation
Indices: 1784221--1784400 Score: 194
Period size: 65 Copynumber: 2.8 Consensus size: 64
1784211 AAATAAATTG
*
1784221 AACATCGAATGCATTTCATGCA-CTGATGCACATACTA-TGCATCGATGCACTCAGAGTTTTATG
1 AACATCGAATGCATTTCATGCATC-GATGCAC-T-CTAGTGCATCGATGCACTCAGAGTGTTATG
1784284 AA
63 AA
*
1784286 AACATCGAATGCATTTGATGCATCGATGCAC-C-AGCCATGCATCGATGCACTCAG-GCTAGTT-
1 AACATCGAATGCATTTCATGCATCGATGCACTCTAG---TGCATCGATGCACTCAGAG-T-GTTA
1784347 TG-A
61 TGAA
* *
1784350 AACATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTC-TAGTGCATCGATGCACT
1784401 AAGGGTGCAA
Statistics
Matches: 101, Mismatches: 4, Indels: 21
0.80 0.03 0.17
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
64 45 0.45
65 49 0.49
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTAGTGCATCGATGCACTCAGAGTGTTATGAA
Found at i:1788452 original size:13 final size:13
Alignment explanation
Indices: 1788396--1788460 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
1788386 TTTTAAATTG
* *
1788396 CATTTTTATACAT
1 CATTTTTAAAAAT
*
1788409 CACTTTTAAAAATT
1 CATTTTTAAAAA-T
*
1788423 CATTTTT-ACAA-
1 CATTTTTAAAAAT
1788434 CATTTTTAAAAAT
1 CATTTTTAAAAAT
1788447 CATTTTTGAAAAAT
1 CATTTTT-AAAAAT
1788461 TATACTCGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
11 7 0.17
12 3 0.07
13 19 0.45
14 13 0.31
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (13 bp):
CATTTTTAAAAAT
Found at i:1790894 original size:21 final size:21
Alignment explanation
Indices: 1790870--1790930 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1790860 AACTTTGAAA
1790870 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1790891 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1790905 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1790926 AAATG
1 AAATG
1790931 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1790976 original size:36 final size:36
Alignment explanation
Indices: 1790862--1790981 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
1790852 TGGTAACCAA
1790862 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1790899 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
1790934 CTTTGAAAAATAGTTTTTCAAAATTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
1790971 -GTTGAAAAATG
1 CTTTGAAAAATG
1790982 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 36 0.47
36 14 0.18
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1795441 original size:21 final size:21
Alignment explanation
Indices: 1795417--1795482 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
1795407 AACTTTGAAA
1795417 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1795438 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1795452 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1795473 AAATGTTTTT
1 AAATGGTTTT
1795483 TTGAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
19 4 0.11
20 4 0.11
21 14 0.40
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.47
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1795501 original size:34 final size:35
Alignment explanation
Indices: 1795410--1795525 Score: 157
Period size: 35 Copynumber: 3.3 Consensus size: 35
1795400 GGTAACCAAC
*
1795410 TTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTG-AAAAAT-GTTTTCAAAGTTTGGTAAATGTTTT
1795447 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAAAT-GTTTTCAAAGTTTGGTAAATGTTTT
*
1795482 TTTGAAAAAT-TTTTCAAAGTTTGGTAGATG-TTT
1 TTTGAAAAATGTTTTCAAAGTTTGGTAAATGTTTT
*
1795515 GTTGAAAAATG
1 TTTGAAAAATG
1795526 ATAATGGGAT
Statistics
Matches: 74, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
33 12 0.16
34 19 0.26
35 34 0.46
36 5 0.07
37 4 0.05
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (35 bp):
TTTGAAAAATGTTTTCAAAGTTTGGTAAATGTTTT
Found at i:1795524 original size:69 final size:68
Alignment explanation
Indices: 1795375--1795525 Score: 173
Period size: 69 Copynumber: 2.2 Consensus size: 68
1795365 AAGTGGGAGA
1795375 TTGTTGAAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAA
1 TTGTTGAAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAAT-GTTTTCAAAGTTTGGTAA
1795440 ATGT
65 ATGT
* *****
1795444 TTCTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTTTTTG-AAAAAT-TTTTCAAAGTTTGG
1 TT-GTTGAAAAATGGTTTTC-AAGTTTGGT-AA-CCAACTTTGAAAAAATGTTTTCAAAGTTTGG
*
1795506 TAGATGT
62 TAAATGT
1795513 TTGTTGAAAAATG
1 TTGTTGAAAAATG
1795526 ATAATGGGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
68 3 0.04
69 42 0.61
70 12 0.17
71 8 0.12
72 4 0.06
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (68 bp):
TTGTTGAAAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATGTTTTCAAAGTTTGGTAAA
TGT
Found at i:1799772 original size:23 final size:23
Alignment explanation
Indices: 1799745--1799797 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1799735 TCGGGATAAT
*
1799745 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCCGTGCAAACC
1799768 TATGTGGCACTTCCGTGCAAACC
1 TATGTGGCACTTCCGTGCAAACC
1799791 TATGTGG
1 TATGTGG
1799798 TCTTTCGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TATGTGGCACTTCCGTGCAAACC
Found at i:1806744 original size:21 final size:21
Alignment explanation
Indices: 1806718--1806780 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1806708 AGGATTTAAT
1806718 TTTAATTGG-TAGGATTTAGGG
1 TTTAA-TGGTTAGGATTTAGGG
*
1806739 TTTAATGGTTAGGTTTTAGGG
1 TTTAATGGTTAGGATTTAGGG
*
1806760 -TT-ATGTTTAGGA-TT-GGG
1 TTTAATGGTTAGGATTTAGGG
1806777 TTTA
1 TTTA
1806781 GGGTTTAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 8 0.22
20 5 0.14
21 16 0.44
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.48
Consensus pattern (21 bp):
TTTAATGGTTAGGATTTAGGG
Found at i:1807910 original size:15 final size:15
Alignment explanation
Indices: 1807854--1807950 Score: 69
Period size: 15 Copynumber: 6.3 Consensus size: 15
1807844 CGGCTGTGCC
1807854 TTCTTCTCCTCTTCT
1 TTCTTCTCCTCTTCT
* *
1807869 TTATTCTCTTCCTCCTTCCC
1 TT-CT-TC-TCCT-CTT-CT
1807889 TTC-TCTCCTCTTCT
1 TTCTTCTCCTCTTCT
*
1807903 TTCTTCTCCTCCTCT
1 TTCTTCTCCTCTTCT
1807918 TTCTT-T-CTCCTTC-
1 TTCTTCTCCT-CTTCT
1807931 TTC-TCTCCCTCTTCT
1 TTCTTCT-CCTCTTCT
1807946 TTCTT
1 TTCTT
1807951 TGCTTCTTCC
Statistics
Matches: 64, Mismatches: 6, Indels: 23
0.69 0.06 0.25
Matches are distributed among these distances:
12 1 0.02
13 6 0.09
14 12 0.19
15 25 0.39
16 6 0.09
17 4 0.06
18 4 0.06
19 3 0.05
20 3 0.05
ACGTcount: A:0.01, C:0.42, G:0.00, T:0.57
Consensus pattern (15 bp):
TTCTTCTCCTCTTCT
Found at i:1807936 original size:19 final size:19
Alignment explanation
Indices: 1807893--1807928 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1807883 CTTCCCTTCT
*
1807893 CTCCTC-TTCTTTCTTCTC
1 CTCCTCTTTCTTTCTCCTC
1807911 CTCCTCTTTCTTTCTCCT
1 CTCCTCTTTCTTTCTCCT
1807929 TCTTCTCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (19 bp):
CTCCTCTTTCTTTCTCCTC
Found at i:1807941 original size:25 final size:24
Alignment explanation
Indices: 1807852--1807949 Score: 69
Period size: 25 Copynumber: 4.0 Consensus size: 24
1807842 GGCGGCTGTG
* *
1807852 CCTTCTTCTCCTCTTCTTTATTCTCTT
1 CCTTCTTCTCCTCCTC-TTCTT-TC-T
* * *
1807879 CCTCCTTC-CCTTCTCTCCTCTTCT
1 CCTTCTTCTCCTCCTCTTCT-TTCT
1807903 --TTCTTCTCCTCCTCTTTCTTTCT
1 CCTTCTTCTCCTCCTC-TTCTTTCT
1807926 CCTTCTTCT-CTCCCTCTTCTTTCT
1 CCTTCTTCTCCT-CCTCTTCTTTCT
1807950 TTGCTTCTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
22 5 0.09
23 10 0.18
24 14 0.25
25 15 0.26
26 6 0.11
27 7 0.12
ACGTcount: A:0.01, C:0.44, G:0.00, T:0.55
Consensus pattern (24 bp):
CCTTCTTCTCCTCCTCTTCTTTCT
Found at i:1807958 original size:15 final size:14
Alignment explanation
Indices: 1807897--1807980 Score: 53
Period size: 15 Copynumber: 5.8 Consensus size: 14
1807887 CCTTCTCTCC
*
1807897 TCTTCTTTCTTCTCC
1 TCTTCTTTCTT-TCT
*
1807912 TCCTCTTTCTTTCT
1 TCTTCTTTCTTTCT
* * *
1807926 CCTTC-TTCTCTCCC
1 TCTTCTTTCT-TTCT
1807940 TCTTCTTTCTTTGCT
1 TCTTCTTTCTTT-CT
* *
1807955 TCTTCCTTCTTTGGT
1 TCTTCTTTCTTT-CT
*
1807970 TCCTCTTTCTT
1 TCTTCTTTCTT
1807981 CTCCGGTTCT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
13 4 0.08
14 12 0.23
15 37 0.70
ACGTcount: A:0.00, C:0.37, G:0.04, T:0.60
Consensus pattern (14 bp):
TCTTCTTTCTTTCT
Found at i:1809345 original size:16 final size:15
Alignment explanation
Indices: 1809324--1809357 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1809314 TTAAAAGTAA
1809324 AATTTAGATTTTATAT
1 AATTTA-ATTTTATAT
*
1809340 AATTTATTTTTATAT
1 AATTTAATTTTATAT
1809355 AAT
1 AAT
1809358 CATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
AATTTAATTTTATAT
Found at i:1809366 original size:23 final size:23
Alignment explanation
Indices: 1809340--1809408 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
1809330 GATTTTATAT
1809340 AATTTATTTTTATATAATCATTA
1 AATTTATTTTTATATAATCATTA
* * * *
1809363 AATTAATTTTAATATAATTAATA
1 AATTTATTTTTATATAATCATTA
* * * *
1809386 ATTTTAATTTTATTTAATGATTA
1 AATTTATTTTTATATAATCATTA
1809409 TATATATATT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (23 bp):
AATTTATTTTTATATAATCATTA
Found at i:1809389 original size:61 final size:61
Alignment explanation
Indices: 1809289--1809403 Score: 135
Period size: 61 Copynumber: 1.9 Consensus size: 61
1809279 CACAATAATA
* * **
1809289 TATATACTCATTAAATTGAGTTTTTTTAAAAGTAAAA-TTTAGATTTTATATAATTTATTTT
1 TATATAATCATTAAATTGAATTTTAATAAAAGTAAAATTTTA-ATTTTATATAATTTATTTT
* * *
1809350 TATATAATCATTAAATT-AATTTTAATATAATTAATAATTTTAATTTTATTTAAT
1 TATATAATCATTAAATTGAATTTTAATAAAAGTAA-AATTTTAATTTTATATAAT
1809404 GATTATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
60 12 0.27
61 29 0.64
62 4 0.09
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (61 bp):
TATATAATCATTAAATTGAATTTTAATAAAAGTAAAATTTTAATTTTATATAATTTATTTT
Found at i:1809538 original size:20 final size:21
Alignment explanation
Indices: 1809509--1809549 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1809499 AGTTTTCATG
*
1809509 AAAATTTTAAATTTA-TATTA
1 AAAATATTAAATTTATTATTA
1809529 AAAATATTAAATTTATTATTA
1 AAAATATTAAATTTATTATTA
1809550 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATATTAAATTTATTATTA
Found at i:1810422 original size:30 final size:28
Alignment explanation
Indices: 1810349--1810425 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 28
1810339 TGGCCACCCC
*
1810349 AAAATTTTAAAAATTATAATTTAGACCTT
1 AAAATTTTAAAAAAT-TAATTTAGACCTT
*
1810378 AAAATTTTCCAAAAAATTAATTTAGTCCCTCT
1 AAAATTTT--AAAAAATTAATTTAG-ACCT-T
*
1810410 AATATTTTAAAAAATT
1 AAAATTTTAAAAAATT
1810426 CATATTAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 8 0.20
30 16 0.39
31 9 0.22
32 8 0.20
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (28 bp):
AAAATTTTAAAAAATTAATTTAGACCTT
Found at i:1811128 original size:22 final size:22
Alignment explanation
Indices: 1811076--1811208 Score: 73
Period size: 22 Copynumber: 6.1 Consensus size: 22
1811066 CAAAGAAACT
1811076 AAAA-ATAT-AATGAAAATAA-A
1 AAAATATATAAAT-AAAATAATA
*
1811096 TAAATAGTATAAATAAAATAATA
1 AAAATA-TATAAATAAAATAATA
1811119 AAAATATATATATATAAAA-ATATA
1 AAAATATATA-A-ATAAAATA-ATA
* ** *
1811143 AAAATGTATGTATAATATAAT-
1 AAAATATATAAATAAAATAATA
* *
1811164 AAAATACA-AAATAGTAATAATA
1 AAAATATATAAATA-AAATAATA
* * *
1811186 ATAATAAATAAATGAAA-AATA
1 AAAATATATAAATAAAATAATA
1811207 AA
1 AA
1811209 TATACATATA
Statistics
Matches: 85, Mismatches: 17, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
20 6 0.07
21 17 0.20
22 29 0.34
23 16 0.19
24 17 0.20
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.28
Consensus pattern (22 bp):
AAAATATATAAATAAAATAATA
Found at i:1811135 original size:24 final size:24
Alignment explanation
Indices: 1811090--1811165 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
1811080 ATATAATGAA
*
1811090 AATAAATAA-ATAGTATAAATAAAAT
1 AATAAA-AATATA-TATATATAAAAT
1811115 AATAAAAATATATATATATAAAA-
1 AATAAAAATATATATATATAAAAT
* * *
1811138 ATATAAAAATGTATGTATAATATAAT
1 A-ATAAAAATATATATAT-ATAAAAT
1811164 AA
1 AA
1811166 AATACAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
23 1 0.02
24 26 0.60
25 15 0.35
26 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (24 bp):
AATAAAAATATATATATATAAAAT
Found at i:1811947 original size:37 final size:37
Alignment explanation
Indices: 1811854--1811955 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
1811844 ATGCTTGTGG
* * ** * * *
1811854 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
1811891 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
1811928 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1811956 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:1813026 original size:106 final size:106
Alignment explanation
Indices: 1812708--1814190 Score: 2217
Period size: 106 Copynumber: 14.0 Consensus size: 106
1812698 GCATTGTTCC
* * * * * *
1812708 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
1812773 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
1812814 GAGTCCAATATCATTCGCTGTGAAGTTAAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * * * *
1812873 TCAGCCGCCCCTTCTTCGTGAAGTTGAGCTTGTGTTATCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
1812915 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1812979 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1813020 GAGTCCAATATCCTACGATGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1813085 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1813126 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1813191 CCAGCGGTCCCTTCGGCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1813232 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1813297 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1813338 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1813403 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1813444 GAGTCAAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1813509 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1813550 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAAATTGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AAATTGGGAAGTTGTTTATTGACA
1813615 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
1813657 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1813722 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-G
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1813762 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACA
1 -GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * *
1813827 ACTAGCAGTCCCTTCATCGTGAAGTTGAACTTGAGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1813869 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
1813934 CCAACGGTCCATTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1813975 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1814040 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1814081 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
1814146 CCAGCGATCCCTTCGTTGTGAAGTTGAACTAGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1814187 GAGT
1 GAGT
1814191 GGCACGATAT
Statistics
Matches: 1250, Mismatches: 116, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
100 77 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 6 0.00
106 1057 0.85
107 98 0.08
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1815038 original size:22 final size:22
Alignment explanation
Indices: 1815012--1815086 Score: 150
Period size: 22 Copynumber: 3.4 Consensus size: 22
1815002 ATGTTTGGTT
1815012 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
1815034 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
1815056 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTC
1815078 AAAGGTTTG
1 AAAGGTTTG
1815087 ATGGGGTAGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (22 bp):
AAAGGTTTGGCATTTGATGCTC
Found at i:1815759 original size:15 final size:16
Alignment explanation
Indices: 1815723--1815765 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1815713 TTCTTTTCTT
*
1815723 CTTTTTTGCTTCTTTTC
1 CTTTTTTG-TTCTTTGC
1815740 C-TTTTTGTT-TTTGC
1 CTTTTTTGTTCTTTGC
1815754 CTTTTTTGTTCT
1 CTTTTTTGTTCT
1815766 GATTGAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 5 0.22
15 10 0.43
16 7 0.30
17 1 0.04
ACGTcount: A:0.00, C:0.19, G:0.09, T:0.72
Consensus pattern (16 bp):
CTTTTTTGTTCTTTGC
Found at i:1819195 original size:19 final size:19
Alignment explanation
Indices: 1819162--1819198 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1819152 TGCAGATGAT
1819162 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
1819181 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
1819199 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:1820479 original size:22 final size:21
Alignment explanation
Indices: 1820453--1820507 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 21
1820443 AAATATAATG
1820453 AAATAAATAAATAGTATA-AAAA
1 AAATAAA-AAATA-TATATAAAA
*
1820475 AAATAAAAAATATATATATAA
1 AAATAAAAAATATATATAAAA
1820496 AAATATAAAAAT
1 AAATA-AAAAAT
1820508 GTATGTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 4 0.13
21 13 0.43
22 13 0.43
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AAATAAAAAATATATATAAAA
Found at i:1820561 original size:22 final size:25
Alignment explanation
Indices: 1820513--1820567 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 25
1820503 AAAATGTATG
**
1820513 TAATATATAAAATACTAAATAGTAA
1 TAATATATAAAATACTAAATAAAAA
1820538 TAATA-ATAAAA-A-TAAATAAAAA
1 TAATATATAAAATACTAAATAAAAA
1820560 TAA-ATATA
1 TAATATATA
1820568 CATATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 14 0.52
23 1 0.04
24 6 0.22
25 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
TAATATATAAAATACTAAATAAAAA
Found at i:1820777 original size:23 final size:23
Alignment explanation
Indices: 1820743--1820789 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
1820733 ACGCAAAGAA
1820743 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
1820766 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
1820789 A
1 A
1820790 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:1821246 original size:37 final size:37
Alignment explanation
Indices: 1821205--1821297 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
1821195 ATGCTTGTGG
* * *
1821205 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
1821242 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
1821279 ATCCTATTTTTAAGAGTTT
1 ATCCTATTTTTAGGAGTTT
1821298 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:1822384 original size:20 final size:20
Alignment explanation
Indices: 1822355--1822431 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
1822345 TTGTTAGACA
1822355 GGGGGAATCGGTACCCCTGG
1 GGGGGAATCGGTACCCCTGG
*
1822375 GGGGGGATCGGTACCCCT-G
1 GGGGGAATCGGTACCCCTGG
1822394 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTA-CCCCTGG
* *
1822415 GGGGAAATCTGTACCCC
1 GGGGGAATCGGTACCCC
1822432 CTGGACATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.25
20 26 0.51
21 12 0.24
ACGTcount: A:0.16, C:0.27, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCTGG
Found at i:1822838 original size:24 final size:24
Alignment explanation
Indices: 1822809--1822870 Score: 124
Period size: 24 Copynumber: 2.6 Consensus size: 24
1822799 CCCCTTACTC
1822809 TAACACTTCTCCCCTTTAACACCT
1 TAACACTTCTCCCCTTTAACACCT
1822833 TAACACTTCTCCCCTTTAACACCT
1 TAACACTTCTCCCCTTTAACACCT
1822857 TAACACTTCTCCCC
1 TAACACTTCTCCCC
1822871 CTTTTTGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (24 bp):
TAACACTTCTCCCCTTTAACACCT
Found at i:1823969 original size:20 final size:19
Alignment explanation
Indices: 1823933--1823979 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1823923 CTAAATCCTT
*
1823933 TTTCAAAATTTCATTTTGAC
1 TTTCAAAATCTCATTTTG-C
*
1823953 TTTCAAAATCT-ATTTTTGT
1 TTTCAAAATCTCA-TTTTGC
1823972 TTTCAAAA
1 TTTCAAAA
1823980 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:1826250 original size:20 final size:21
Alignment explanation
Indices: 1826208--1826265 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
1826198 CCAAACATTG
1826208 GTATCGATATTAG-C-CTTACA
1 GTATCGATATT-GCCTCTTACA
1826228 GTATCGATATTGCCTCTTA-A
1 GTATCGATATTGCCTCTTACA
* *
1826248 GTATCAATACT-CCTCTTA
1 GTATCGATATTGCCTCTTA
1826266 TGTTATTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 8 0.24
20 22 0.65
21 4 0.12
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (21 bp):
GTATCGATATTGCCTCTTACA
Found at i:1830364 original size:630 final size:639
Alignment explanation
Indices: 1828077--1830619 Score: 4582
Period size: 632 Copynumber: 4.0 Consensus size: 639
1828067 TTTGTACGAA
1828077 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCT-CCCTTTAATCTTTTTACAACTTT
1828142 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
65 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGA-
1828207 ATATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCTC
129 ATATTTTTTTGAATTGAATCGAGAAATGTAA-TTTTTTACATATGGACTGTTTTGTCTCTCTCTC
* *
1828272 GATAACTGGCAAATTGTTTAAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTGG
193 GATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGCACGTTTGG
1828337 GCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTG
258 GCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTG
* * *
1828402 ATTGGAGGAAGTTGTTTGTTTTTGATGAAGAACACTCTTTTGATTTCTTTCCCCTGAGATCAGTG
323 ATTGGAGGAAGTTGTTTGTTTTTGTTAAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTG
* *
1828467 ATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAGGCACT
388 ATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAAAATGGAAGCACT
1828532 CGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAA
453 CGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAA
1828597 GAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTA
518 GAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTA
* * *
1828662 CTATTA-GGTTTGGGTTTTAGAGAATGATCCCTGGT--ATTCAACATAAGCATTTAG
583 CTATTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAGCTTTTAG
*
1828716 -TTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCTTAAATCTTTTTACAACTTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCTTTAATCTTTTTACAACTTTT
1828780 TAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTG---
66 TAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAAT
1828842 ATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTACATATGGACTGTTTTGTCTCTCTCTCGAT
131 ATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTACATATGGACTGTTTTGTCTCTCTCTCGAT
*
1828907 AACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTGGGCG
196 AACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGCACGTTTGGGCG
1828972 TTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTGATT
261 TTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTGATT
*
1829037 GGAGGAAGTTGTTTGTTTTTTTTAAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTGATG
326 GGAGGAAGTTGTTTGTTTTTGTTAAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTGATG
1829102 G-GTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTC-AAATGGAAGCACTCGT
391 GTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAAAATGGAAGCACTCGT
1829165 TGGTA-GGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAAGAA
456 TGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAAGAA
*
1829229 CTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCTATTCTACTA
521 CTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTACTA
1829294 TTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAGCTTTTAG
586 TTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAGCTTTTAG
1829348 TTTTG--ATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCTTTAATCTTTTTACAACTTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCTTTAATCTTTTTACAAC-TTT
*
1829411 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGAATTGAT
65 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGA-
1829476 ATATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCTC
129 ATATTTTTTTGAATTGAATCGAGAAATGTAA-TTTTTTACATATGGACTGTTTTGTCTCTCTCTC
*
1829541 GATAACTGGAAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTG-TGCACGTTTGG
193 GATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGCACGTTTGG
1829605 GCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTG
258 GCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTG
1829670 ATTGGAGGAAGTTGTTTGTTTATT-TTAAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
323 ATTGGAGGAAGTTGTTTGTTT-TTGTTAAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
1829734 GATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAAAATGGAAGCAC
387 GATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAAAATGGAAGCAC
1829799 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
452 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
*
1829864 AGAACTCAATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGC-TTTTCCTTTGCCAATTCT
517 AGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCT
*
1829928 ACTATTAGGGATTGGGTTTTGGAGAATGATCCCTGATACATTCAACATAAGCTTTTAG
582 ACTATTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAGCTTTTAG
1829986 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCT-CCCTTTAATCTTTTTACAACTTT
*
1830051 TTAAACCAATTTCCA-T-TTTTATTCTTTTCTTTCGTATATTTGTTTGATTAAATTTGATTTG-A
65 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAA
1830113 TA-TTTTTTGAATTGAATCGAGAAATGTAA-TTTTTACATATGGA-TGTTTTGTCTCTCTCTCGA
130 TATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTACATATGGACTGTTTTGTCTCTCTCTCGA
1830175 TAACTGGCAAA-TG-TTTAGGG-TTTCGTCCATTCGTCTAGGGTTTGTGTGTTGCACGTTTGGGC
195 TAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGCACGTTTGGGC
1830237 GTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTGAT
260 GTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTGAT
* *
1830302 TGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTGAT
325 TGGAGGAAGTTGTTTGTTTTTGTTAAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTGAT
* *
1830367 GGTGTTGTGACTGTTAATCCTTCCAAAGATG-TTTGAAGAGGGGATTTCAGAATGG-A-CACTCG
390 GGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAAAATGGAAGCACTCG
*
1830429 TTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTATGCAAAAGATTGCGGGGGAAGA
455 TTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAAGA
* *
1830494 ACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTGCCTTTGCTAATTCTACT
520 ACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTACT
*
1830559 ATTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAACTTTTAG
585 ATTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAGCTTTTAG
1830614 TTTTGA
1 TTTTGA
1830620 GAAAATGGGA
Statistics
Matches: 1852, Mismatches: 32, Indels: 51
0.96 0.02 0.03
Matches are distributed among these distances:
627 112 0.06
628 79 0.04
629 179 0.10
630 221 0.12
631 101 0.05
632 339 0.18
633 47 0.03
635 27 0.01
636 173 0.09
637 218 0.12
638 183 0.10
639 101 0.05
640 52 0.03
641 20 0.01
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (639 bp):
TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCTTTAATCTTTTTACAACTTTT
TAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAAT
ATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTACATATGGACTGTTTTGTCTCTCTCTCGAT
AACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGCACGTTTGGGCG
TTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTGATT
GGAGGAAGTTGTTTGTTTTTGTTAAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTGATG
GTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAAAATGGAAGCACTCGT
TGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAAGAA
CTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTACTA
TTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAGCTTTTAG
Found at i:1834774 original size:15 final size:15
Alignment explanation
Indices: 1834754--1834783 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1834744 TCCCACTGTT
1834754 CTTTTAAGCTATTAA
1 CTTTTAAGCTATTAA
*
1834769 CTTTTAAGTTATTAA
1 CTTTTAAGCTATTAA
1834784 TAAAGATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (15 bp):
CTTTTAAGCTATTAA
Found at i:1835050 original size:29 final size:30
Alignment explanation
Indices: 1834981--1835038 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1834971 ATTAACGAAC
1834981 AGAGATAAA--ATATATTATATATAAAAAA
1 AGAGATAAATTATATATTATATATAAAAAA
* *
1835009 AGAGATTAATTATATATTCTA-ATAAAAAA
1 AGAGATAAATTATATATTATATATAAAAAA
1835038 A
1 A
1835039 AGGGTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
29 9 0.35
30 9 0.35
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (30 bp):
AGAGATAAATTATATATTATATATAAAAAA
Found at i:1841197 original size:182 final size:180
Alignment explanation
Indices: 1840893--1841267 Score: 675
Period size: 182 Copynumber: 2.1 Consensus size: 180
1840883 TCTTATGATT
1840893 AGTACATACTATTAACTGACGGGGAACCTGAATGTTATAAAAAAGTGTTGAACTATGTTTTGATA
1 AGTACATA-TATTAACTGACGGGGAACCTGAATGTTATAAAAAAGTGTTGAACTATGTTTTGATA
1840958 ACAATTTATGGAAAAAAAATGTTTTTGGACTTGAATTGAATTTGTTCAAAGTTTTCAAAAATAAT
65 ACAATTTATGGAAAAAAAATGTTTTTGGACTTGAATTGAATTTGTTCAAAGTTTTCAAAAATAAT
1841023 TCAAAGTCCATTTAACTTGGAATTGAG-ATAAAATGTTTTTCTGGACAAG-
130 TCAAAGTCCATTTAACTTGGAATTGAGCATAAAATGTTTTTCTGGACAAGA
1841072 AGTACATATATTGAACTGACGGGGAGAACCTGAATGTTAT-AAAAAGTGTTGAACTATGTTTTGA
1 AGTACATATATT-AACTGAC-GGG-GAACCTGAATGTTATAAAAAAGTGTTGAACTATGTTTTG-
1841136 TATAACAATTTATGGAAAAAAAATGTTTTTGGACTTGAATTGAATTTGTTCAAAGTTTTCAAAAA
62 -ATAACAATTTATGGAAAAAAAATGTTTTTGGACTTGAATTGAATTTGTTCAAAGTTTTCAAAAA
1841201 TAATTCAAAGTCCATTTAACTTGGAATTGAGCATAAAATGTTTTTCTGGACAAGA
126 TAATTCAAAGTCCATTTAACTTGGAATTGAGCATAAAATGTTTTTCTGGACAAGA
1841256 AGTACATATATT
1 AGTACATATATT
1841268 TTCTACAGTA
Statistics
Matches: 189, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
178 4 0.02
179 15 0.08
180 26 0.14
181 15 0.08
182 95 0.50
183 22 0.12
184 12 0.06
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (180 bp):
AGTACATATATTAACTGACGGGGAACCTGAATGTTATAAAAAAGTGTTGAACTATGTTTTGATAA
CAATTTATGGAAAAAAAATGTTTTTGGACTTGAATTGAATTTGTTCAAAGTTTTCAAAAATAATT
CAAAGTCCATTTAACTTGGAATTGAGCATAAAATGTTTTTCTGGACAAGA
Found at i:1842763 original size:20 final size:19
Alignment explanation
Indices: 1842719--1842763 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1842709 GATTTTCGTT
* * *
1842719 TGAAAACTAAAATGGATTT
1 TGAAAACCAAAATGAATTA
1842738 TGAAAACCAAAATGAAATTA
1 TGAAAACCAAAATG-AATTA
1842758 TGAAAA
1 TGAAAA
1842764 AAGATTTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (19 bp):
TGAAAACCAAAATGAATTA
Found at i:1844153 original size:20 final size:20
Alignment explanation
Indices: 1844120--1844169 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1844110 CTCATAAACA
1844120 GTACCGATACTGTTCATAAG
1 GTACCGATACTGTTCATAAG
* * *
1844140 GTATCGATATTGTTTATAAG
1 GTACCGATACTGTTCATAAG
1844160 GTACCGATAC
1 GTACCGATAC
1844170 CAAAGGTAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (20 bp):
GTACCGATACTGTTCATAAG
Found at i:1846529 original size:18 final size:18
Alignment explanation
Indices: 1846508--1846561 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1846498 GGTGCAACCA
1846508 AAAAATAGGTTGCAACTT
1 AAAAATAGGTTGCAACTT
1846526 -AAAATA---TGCAACTT
1 AAAAATAGGTTGCAACTT
*
1846540 AAAAATAGGTTGCAATTT
1 AAAAATAGGTTGCAACTT
1846558 AAAA
1 AAAA
1846562 TAAAATTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 8 0.26
15 6 0.19
17 6 0.19
18 11 0.35
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (18 bp):
AAAAATAGGTTGCAACTT
Found at i:1846531 original size:17 final size:17
Alignment explanation
Indices: 1846509--1846563 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
1846499 GTGCAACCAA
1846509 AAAATAGGTTGCAACTT
1 AAAATAGGTTGCAACTT
1846526 AAAATA---TGCAACTT
1 AAAATAGGTTGCAACTT
*
1846540 AAAAATAGGTTGCAATTT
1 -AAAATAGGTTGCAACTT
1846558 AAAATA
1 AAAATA
1846564 AAATTTTCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 8 0.24
15 6 0.18
17 12 0.36
18 7 0.21
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (17 bp):
AAAATAGGTTGCAACTT
Found at i:1852579 original size:20 final size:20
Alignment explanation
Indices: 1852554--1852592 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1852544 ATATTTATCA
1852554 ATATTTCTAATAATATAATT
1 ATATTTCTAATAATATAATT
* *
1852574 ATATTTTTAATATTATAAT
1 ATATTTCTAATAATATAAT
1852593 AAATAATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTTCTAATAATATAATT
Found at i:1852613 original size:15 final size:17
Alignment explanation
Indices: 1852581--1852628 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1852571 ATTATATTTT
*
1852581 TAATAT-TATAATA-AA
1 TAATATATATATTATAA
*
1852596 TAATCATTTATATTATAA
1 TAAT-ATATATATTATAA
1852614 TAATATATATATTAT
1 TAATATATATATTAT
1852629 TTTTATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.14
16 2 0.07
17 16 0.57
18 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATATATATATTATAA
Found at i:1852768 original size:30 final size:29
Alignment explanation
Indices: 1852734--1852806 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 29
1852724 TTTATATATT
1852734 AATATTAATA-AATAATCTAATATTTTAATA
1 AATATTAATATAATAAT-TAATATTTTAA-A
*
1852764 AATATTAAAATATAATAATTAATATTTTTAA
1 AATATT--AATATAATAATTAATATTTTAAA
1852795 AATA-TAATATAA
1 AATATTAATATAA
1852807 CACTATTACT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
28 7 0.18
30 7 0.18
31 5 0.13
32 14 0.36
33 6 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
AATATTAATATAATAATTAATATTTTAAA
Found at i:1852775 original size:20 final size:20
Alignment explanation
Indices: 1852738--1852776 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1852728 TATATTAATA
**
1852738 TTAATAAATAATCTAATATT
1 TTAATAAATAATAAAATATT
*
1852758 TTAATAAATATTAAAATAT
1 TTAATAAATAATAAAATAT
1852777 AATAATTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATAAATAATAAAATATT
Found at i:1852782 original size:20 final size:23
Alignment explanation
Indices: 1852692--1852803 Score: 68
Period size: 23 Copynumber: 4.8 Consensus size: 23
1852682 ATAGAAATAG
* *
1852692 TATTATTAAATTATTAATAATGAA
1 TATTATTAAAATA-TAATAATTAA
* **
1852716 TAATATT-ATTTAT-AT-ATTAA
1 TATTATTAAAATATAATAATTAA
* * *
1852736 TATTAATAAATAATCTAATATTTTAA
1 TATT-ATTAA-AATATAATA-ATTAA
*
1852762 TAAATATTAAAATATAATAATTAA
1 T-ATTATTAAAATATAATAATTAA
*
1852786 TATTTTTAAAATATAATA
1 TATTATTAAAATATAATA
1852804 TAACACTATT
Statistics
Matches: 66, Mismatches: 15, Indels: 15
0.69 0.16 0.16
Matches are distributed among these distances:
20 7 0.11
21 4 0.06
22 2 0.03
23 21 0.32
24 13 0.20
25 8 0.12
26 9 0.14
27 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
TATTATTAAAATATAATAATTAA
Found at i:1852910 original size:30 final size:32
Alignment explanation
Indices: 1852843--1852911 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 32
1852833 ATAATTTATG
* *
1852843 ATATTTTTATTTCAATAAAATATACCAATATTA
1 ATATTTTTATTTCAATAAAATATA-CAAAAATA
1852876 ATATTTTTA-TT-AATAAAATTATA-AAAAATA
1 ATATTTTTATTTCAATAAAA-TATACAAAAATA
1852906 ATATTT
1 ATATTT
1852912 AATAACAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 11 0.33
31 7 0.21
32 6 0.18
33 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (32 bp):
ATATTTTTATTTCAATAAAATATACAAAAATA
Found at i:1852956 original size:23 final size:26
Alignment explanation
Indices: 1852904--1852978 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 26
1852894 TTATAAAAAA
*
1852904 TAATATTTAATAACAAATAAATTATTT
1 TAATATTT-ATAACAAATAAATTATAT
1852931 TAATATTT-TAA-AAAT-AATTATAT
1 TAATATTTATAACAAATAAATTATAT
* *
1852954 TAAGT-TTTATGATAAATAATATTAT
1 TAA-TATTTATAACAAATAA-ATTAT
1852979 TTATTGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 13 0.32
24 7 0.17
25 7 0.17
26 1 0.02
27 13 0.32
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (26 bp):
TAATATTTATAACAAATAAATTATAT
Found at i:1857559 original size:24 final size:25
Alignment explanation
Indices: 1857527--1857575 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
1857517 AGGTGGTGTT
1857527 CACCTTTTTTGGAGCATTC-TGACA
1 CACCTTTTTTGGAGCATTCTTGACA
1857551 CACCTTTTTTGGAGCATTCTTGACA
1 CACCTTTTTTGGAGCATTCTTGACA
1857576 TGTTGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.39
Consensus pattern (25 bp):
CACCTTTTTTGGAGCATTCTTGACA
Found at i:1866522 original size:15 final size:15
Alignment explanation
Indices: 1866502--1866536 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1866492 TATTCACGGG
1866502 CTGCTCCGACACCTA
1 CTGCTCCGACACCTA
*
1866517 CTGCTCCGACACCTG
1 CTGCTCCGACACCTA
1866532 CTGCT
1 CTGCT
1866537 GATGATCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.46, G:0.17, T:0.23
Consensus pattern (15 bp):
CTGCTCCGACACCTA
Found at i:1867999 original size:15 final size:15
Alignment explanation
Indices: 1867979--1868021 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1867969 AACAAGAATT
1867979 GAGAAAGAATCAAGA
1 GAGAAAGAATCAAGA
1867994 GAGAAAGAATCAAGA
1 GAGAAAGAATCAAGA
*
1868009 GAGAAAGCATCAA
1 GAGAAAGAATCAA
1868022 ACCTCAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.58, C:0.09, G:0.26, T:0.07
Consensus pattern (15 bp):
GAGAAAGAATCAAGA
Found at i:1875680 original size:52 final size:52
Alignment explanation
Indices: 1875597--1875704 Score: 198
Period size: 52 Copynumber: 2.1 Consensus size: 52
1875587 GGAAAAACAA
* *
1875597 TATCGATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTTAAAGGAGAG
1 TATCAATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAG
1875649 TATCAATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAG
1 TATCAATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAG
1875701 TATC
1 TATC
1875705 GATACTCATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.38
Consensus pattern (52 bp):
TATCAATATTGTTCTTCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAG
Found at i:1875732 original size:52 final size:52
Alignment explanation
Indices: 1875612--1875717 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
1875602 ATATTGTTCT
* * ** *
1875612 TCAATTAGTGTATAATGAAAGAGTTTTTAAAGGAGAGTATCAATATTGTTCT
1 TCAAGTAGTGTATAATGAAAGAGTTTTCAAAGGAGAGTATCAATATCATTCA
* *
1875664 TCAATTAGTGTATAATGAAAGAGTTTTCAAAGGAGAGTATCGATACTCATTCA
1 TCAAGTAGTGTATAATGAAAGAGTTTTCAAAGGAGAGTATCAATA-TCATTCA
1875717 T
1 T
1875718 GGAGTATCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 43 0.90
53 5 0.10
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (52 bp):
TCAAGTAGTGTATAATGAAAGAGTTTTCAAAGGAGAGTATCAATATCATTCA
Found at i:1877227 original size:56 final size:57
Alignment explanation
Indices: 1877135--1877242 Score: 166
Period size: 56 Copynumber: 1.9 Consensus size: 57
1877125 TTATGACCCG
*
1877135 AGAGTTCTAAGTAAATAAAATAACTAATTCCTAAATAAAATAATTAAA-AATCCAGTT
1 AGAGCTCTAAGTAAATAAAATAACTAATTCCTAAATAAAATAA-TAAATAATCCAGTT
**
1877192 AGAGCTCTAAGTAAAT-AAATAGTTAATTCCTAAATAAAATAATAAATAATC
1 AGAGCTCTAAGTAAATAAAATAACTAATTCCTAAATAAAATAATAAATAATC
1877243 AAACTAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
55 4 0.09
56 28 0.60
57 15 0.32
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (57 bp):
AGAGCTCTAAGTAAATAAAATAACTAATTCCTAAATAAAATAATAAATAATCCAGTT
Found at i:1881028 original size:3 final size:3
Alignment explanation
Indices: 1881020--1881131 Score: 152
Period size: 3 Copynumber: 36.7 Consensus size: 3
1881010 TTTAAATTTT
** *
1881020 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1881068 TTA TTA TAA TTA TTA TTA TCA TTA TTTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
1881114 TTA TATA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TT
1881132 TAATAAATAA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
3 89 0.94
4 6 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1881285 original size:26 final size:27
Alignment explanation
Indices: 1881249--1881311 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
1881239 CCTAGCCACC
*
1881249 CCCAGCCGCCTCTGA-GCTTCCAGAAT
1 CCCAGCCGCCTCTGATGCTTCAAGAAT
1881275 CCCAGCCGCCTCTGATGCTTCAAGAAT
1 CCCAGCCGCCTCTGATGCTTCAAGAAT
1881302 CCCAGCCGCC
1 CCCAGCCGCC
1881312 GCCTCACTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 15 0.43
27 20 0.57
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.17
Consensus pattern (27 bp):
CCCAGCCGCCTCTGATGCTTCAAGAAT
Found at i:1883381 original size:17 final size:18
Alignment explanation
Indices: 1883336--1883382 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
1883326 CTTTTCAAAC
1883336 TTTTTA-TTT-TTTATTA
1 TTTTTATTTTATTTATTA
**
1883352 TTTTTATAATATTTA-TA
1 TTTTTATTTTATTTATTA
1883369 TTTTTATTTTATTT
1 TTTTTATTTTATTT
1883383 GCAAGTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 6 0.24
17 15 0.60
18 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTATTTTATTTATTA
Found at i:1883404 original size:13 final size:15
Alignment explanation
Indices: 1883373--1883409 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1883363 TTTATATTTT
1883373 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
1883388 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
1883401 TA-TTTATTT
1 TATTTTATTT
1883410 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:1887273 original size:30 final size:30
Alignment explanation
Indices: 1887237--1887298 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1887227 CCAAGTTTGA
1887237 CTTGCAATCTTCTTTCGATTAGCAAATTAT
1 CTTGCAATCTTCTTTCGATTAGCAAATTAT
1887267 CTTGCAATCTTCTTTCGATTAGCAAATTAT
1 CTTGCAATCTTCTTTCGATTAGCAAATTAT
1887297 CT
1 CT
1887299 ATCGATTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.44
Consensus pattern (30 bp):
CTTGCAATCTTCTTTCGATTAGCAAATTAT
Found at i:1890560 original size:23 final size:23
Alignment explanation
Indices: 1890534--1890586 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1890524 AAAAAAACCA
*
1890534 TGTTTATAAGAACCGAAAAACTT
1 TGTTTACAAGAACCGAAAAACTT
* * * *
1890557 TGTTTACCATAATCGAAAAATTT
1 TGTTTACAAGAACCGAAAAACTT
1890580 TGTTTAC
1 TGTTTAC
1890587 CAGAGCTGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (23 bp):
TGTTTACAAGAACCGAAAAACTT
Done.