Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 31
Found at i:2041316 original size:21 final size:21
Alignment explanation
Indices: 2041290--2041353 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
2041280 ATCAAATTGT
2041290 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
2041311 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
* *
2041332 CTAGGGGGTACTGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
2041353 C
1 C
2041354 TGTCTAACGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.16
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:2041732 original size:34 final size:32
Alignment explanation
Indices: 2041693--2041762 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
2041683 TTTTGTAAAG
*
2041693 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2041727 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2041759 GGGA
1 GGGA
2041763 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2044692 original size:21 final size:20
Alignment explanation
Indices: 2044653--2044774 Score: 154
Period size: 20 Copynumber: 6.0 Consensus size: 20
2044643 TCAGATTGTT
2044653 CAGGGGGTACAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
2044673 CAGGGGGTACAGATTCCCCCC
1 CAGGGGGTACAGATT-CCCCC
* *
2044694 CAGGGAGAACAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
* *
2044714 CGGGGGGTACCGATTCCCCCC
1 CAGGGGGTACAGATT-CCCCC
* *
2044735 CAAGGGGAACAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
* *
2044755 CAAGGGGTACCGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
2044775 TGTCTAATGG
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
20 54 0.61
21 34 0.39
ACGTcount: A:0.21, C:0.38, G:0.28, T:0.13
Consensus pattern (20 bp):
CAGGGGGTACAGATTCCCCC
Found at i:2044706 original size:41 final size:41
Alignment explanation
Indices: 2044656--2044774 Score: 186
Period size: 41 Copynumber: 2.9 Consensus size: 41
2044646 GATTGTTCAG
* *
2044656 GGGGTACAGATTCCCCCCAGGGGGTACAGATTCCCCCCC-A
1 GGGGAACAGATTCCCCCCAGGGGGTACCGATTCCCCCCCAA
*
2044696 GGGAGAACAGATTCCCCCCGGGGGGTACCGATTCCCCCCCAA
1 GGG-GAACAGATTCCCCCCAGGGGGTACCGATTCCCCCCCAA
*
2044738 GGGGAACAGATTCCCCCCAAGGGGTACCGATTCCCCC
1 GGGGAACAGATTCCCCCCAGGGGGTACCGATTCCCCC
2044775 TGTCTAATGG
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 3 0.04
41 65 0.90
42 4 0.06
ACGTcount: A:0.21, C:0.38, G:0.28, T:0.13
Consensus pattern (41 bp):
GGGGAACAGATTCCCCCCAGGGGGTACCGATTCCCCCCCAA
Found at i:2047021 original size:68 final size:64
Alignment explanation
Indices: 2046949--2047109 Score: 175
Period size: 68 Copynumber: 2.4 Consensus size: 64
2046939 CCGTTTTTTT
* * **
2046949 AAACTATATATTATACTTTTTCAAAATATTTTAAAAAACTATTTACTATGTTTTCTA-AACCGCT
1 AAACTATATATTATA-TTTTTCAAAATA-TTT-AAAAACTATATA-TATGCTTTC-AGAA-CAAT
2047013 TTA-A
60 TTAGA
*
2047017 AAACTATATATTATATGCTTTCAAAACTATTTAAAAACTATATATATGCTTTCAGAACAATTTAG
1 AAACTATATATTATAT-TTTTCAAAA-TATTTAAAAACTATATATATGCTTTCAGAACAATTTAG
2047082 A
64 A
2047083 AAACTATATATATATATTTTT-AAAATA
1 AAACTATATAT-TATATTTTTCAAAATA
2047110 AATTTTCAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
64 2 0.02
65 10 0.12
66 25 0.30
67 17 0.21
68 26 0.32
69 2 0.02
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (64 bp):
AAACTATATATTATATTTTTCAAAATATTTAAAAACTATATATATGCTTTCAGAACAATTTAGA
Found at i:2047050 original size:34 final size:34
Alignment explanation
Indices: 2046949--2047099 Score: 120
Period size: 34 Copynumber: 4.5 Consensus size: 34
2046939 CCGTTTTTTT
*
2046949 AAACTATATATTATACT-TTTTCAAAA-TATTTTAA
1 AAACTATATATTATA-TGCTTTCAAAACTA-TTTAA
* * **
2046983 AAA--ACTAT-TTACTATGTTTTCTAAACCGCTTTAA
1 AAACTA-TATATTA-TATGCTTTC-AAAACTATTTAA
2047017 AAACTATATATTATATGCTTTCAAAACTATTTAA
1 AAACTATATATTATATGCTTTCAAAACTATTTAA
* *
2047051 AAAC--TATA-TATATGCTTTCAGAACAATTTAGA
1 AAACTATATATTATATGCTTTCAAAACTATTTA-A
2047083 AAACTATATATATATAT
1 AAACTATATAT-TATAT
2047100 TTTTAAAATA
Statistics
Matches: 95, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
31 20 0.21
32 14 0.15
33 10 0.11
34 31 0.33
35 11 0.12
36 9 0.09
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (34 bp):
AAACTATATATTATATGCTTTCAAAACTATTTAA
Found at i:2047086 original size:32 final size:31
Alignment explanation
Indices: 2046949--2047095 Score: 114
Period size: 35 Copynumber: 4.4 Consensus size: 31
2046939 CCGTTTTTTT
* * *
2046949 AAACTATATATTATACTTTTTCAAAATATTTTAAA
1 AAACTATATA-TATGC--TTTCAAAACAATTT-AA
* * * **
2046984 AAACTATTTACTATGTTTTCTAAACCGCTTTAA
1 AAACTATATA-TATGCTTTC-AAAACAATTTAA
*
2047017 AAACTATATATTATATGCTTTCAAAACTATTTAA
1 AAAC--TATA-TATATGCTTTCAAAACAATTTAA
*
2047051 AAACTATATATATGCTTTCAGAACAATTTAGA
1 AAACTATATATATGCTTTCAAAACAATTTA-A
2047083 AAACTATATATAT
1 AAACTATATATAT
2047096 ATATTTTTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
31 20 0.22
32 18 0.20
33 10 0.11
34 19 0.21
35 23 0.25
36 2 0.02
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (31 bp):
AAACTATATATATGCTTTCAAAACAATTTAA
Found at i:2052264 original size:3 final size:3
Alignment explanation
Indices: 2052258--2052294 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2052248 AATGATGATG
*
2052258 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2052295 ATATCATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2057416 original size:25 final size:25
Alignment explanation
Indices: 2057367--2057431 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
2057357 TAAAAGACAG
* *
2057367 GTTTATAAAACTTTAAAACGGGTGA
1 GTTTATAAAATTTTAAAACGAGTGA
2057392 GTTTATAAAATTTTAAGAA-GAGTGA
1 GTTTATAAAATTTTAA-AACGAGTGA
* *
2057417 ATTTATGAAATTTTA
1 GTTTATAAAATTTTA
2057432 GACAACGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (25 bp):
GTTTATAAAATTTTAAAACGAGTGA
Found at i:2065451 original size:16 final size:16
Alignment explanation
Indices: 2065430--2065468 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2065420 TGACCTTCGG
*
2065430 CTTTGATCAAAGTTGA
1 CTTTGACCAAAGTTGA
**
2065446 CTTTGACCAGCGTTGA
1 CTTTGACCAAAGTTGA
2065462 CTTTGAC
1 CTTTGAC
2065469 TTTGACCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (16 bp):
CTTTGACCAAAGTTGA
Found at i:2070812 original size:37 final size:38
Alignment explanation
Indices: 2070770--2070910 Score: 169
Period size: 37 Copynumber: 3.8 Consensus size: 38
2070760 AATTACAGTA
*
2070770 TTATATTCCAATCAAATATAAATTCAT-AATAATATAT
1 TTATATTTCAATCAAATATAAATTCATAAATAATATAT
* ** *
2070807 TTATATTTTAATTGAATATAAATTCATCAATAATATAT
1 TTATATTTCAATCAAATATAAATTCATAAATAATATAT
* *
2070845 TTGTATTT-AATCAAATATAAATTTATAAATAATATAT
1 TTATATTTCAATCAAATATAAATTCATAAATAATATAT
*** *
2070882 ACCTATTTCAATCTAATATAAATTCATAA
1 TTATATTTCAATCAAATATAAATTCATAA
2070911 TTTTAATTGA
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
37 53 0.60
38 35 0.40
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (38 bp):
TTATATTTCAATCAAATATAAATTCATAAATAATATAT
Found at i:2071675 original size:20 final size:19
Alignment explanation
Indices: 2071643--2071698 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
2071633 GATCCACAAC
*
2071643 GATATAACAGGTAAAAATAT
1 GATAAAACAGGTAAAAA-AT
* *
2071663 GATAAAACCGGTATCAAAAT
1 GATAAAACAGGTA-AAAAAT
2071683 GATAAAACAGGTAAAA
1 GATAAAACAGGTAAAA
2071699 TGCTACCGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.20
Consensus pattern (19 bp):
GATAAAACAGGTAAAAAAT
Found at i:2071706 original size:180 final size:182
Alignment explanation
Indices: 2071261--2071729 Score: 723
Period size: 181 Copynumber: 2.6 Consensus size: 182
2071251 GATCCAAATT
* * **
2071261 AAAAATGTATCGATCCACAACGATATAACAGGT-AAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
** * * * * *
2071325 AAATTGGTAAAGCGGTACCAGATATATTCAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
2071390 GTTAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTTGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * *
2071442 AAAAATGTATCGATCCACAACAATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
2071507 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
2071571 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTT-A
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
*
2071622 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
2071687 AAACAGGTAAAATGCTACCGG--ATATTGAAAGTGTCGATACTTT
66 AAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
2071730 CGTAAGTACG
Statistics
Matches: 264, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
178 22 0.08
180 81 0.31
181 98 0.37
182 63 0.24
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:2073960 original size:21 final size:21
Alignment explanation
Indices: 2073936--2073979 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2073926 AAGACAATCA
2073936 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2073957 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2073978 AG
1 AG
2073980 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2074055 original size:33 final size:33
Alignment explanation
Indices: 2074013--2074078 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2074003 AAATAGATGG
*
2074013 AGTGGTGAAAGAAGTAAAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGTGA
**
2074046 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGTGA
2074079 TCTTAAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGTGA
Found at i:2075419 original size:185 final size:185
Alignment explanation
Indices: 2075107--2075443 Score: 629
Period size: 185 Copynumber: 1.8 Consensus size: 185
2075097 CAGCATAAAG
*
2075107 TGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAGTTATAATGTAATAG
1 TGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAG
* *
2075172 GTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATATGTCTACAACCTATA
66 GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATA
2075237 TCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAAA
131 TCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAAA
* *
2075292 TGTCGATACCTTTTCAAAAAGTGTTGATTGAAAAAACATCGGAACCTATAATTATAATGTAATAG
1 TGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAG
2075357 GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATA
66 GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATA
2075422 TCGACACTTTTTAATATTGTGT
131 TCGACACTTTTTAATATTGTGT
2075444 TCATACTTTT
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 147 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (185 bp):
TGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAG
GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATA
TCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAAAAAAA
Found at i:2078658 original size:23 final size:22
Alignment explanation
Indices: 2078632--2078710 Score: 100
Period size: 23 Copynumber: 3.9 Consensus size: 22
2078622 AAATATGATG
2078632 TAATAGGTAGCGCTTATATAATT
1 TAATAGGTAGCGCTTATATAA-T
2078655 TAATAGGTAGCGCTTATATAAT
1 TAATAGGTAGCGCTTATATAAT
2078677 T-A-A--TAG-G--TATATAAT
1 TAATAGGTAGCGCTTATATAAT
2078692 TAATAGGTAGCGCTTATAT
1 TAATAGGTAGCGCTTATAT
2078711 TGTAAAGTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
15 9 0.18
16 1 0.02
17 2 0.04
18 3 0.06
19 3 0.06
20 2 0.04
21 1 0.02
22 7 0.14
23 21 0.43
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (22 bp):
TAATAGGTAGCGCTTATATAAT
Found at i:2078689 original size:15 final size:15
Alignment explanation
Indices: 2078669--2078700 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2078659 AGGTAGCGCT
2078669 TATATAATTAATAGG
1 TATATAATTAATAGG
2078684 TATATAATTAATAGG
1 TATATAATTAATAGG
2078699 TA
1 TA
2078701 GCGCTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (15 bp):
TATATAATTAATAGG
Found at i:2079616 original size:23 final size:23
Alignment explanation
Indices: 2079560--2079616 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2079550 TTAGTTATAA
*
2079560 AATATGTCAATATAAGCACTACCT
1 AATATGT-TATATAAGCACTACCT
* ** *
2079584 ATTACATTATATAAGCGCTACCT
1 AATATGTTATATAAGCACTACCT
2079607 AATATGTTAT
1 AATATGTTAT
2079617 TGTACTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (23 bp):
AATATGTTATATAAGCACTACCT
Found at i:2079670 original size:23 final size:23
Alignment explanation
Indices: 2079644--2079687 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2079634 AAGGTTAAAT
**
2079644 ATCTATTTTATTATATAAGCGCA
1 ATCTATTACATTATATAAGCGCA
2079667 ATCTATTACATTATATAAGCG
1 ATCTATTACATTATATAAGCG
2079688 TTACCTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (23 bp):
ATCTATTACATTATATAAGCGCA
Found at i:2085342 original size:23 final size:23
Alignment explanation
Indices: 2085295--2085344 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2085285 AATAACATAT
**
2085295 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
2085318 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
2085341 TAGG
1 TAGG
2085345 CATTTAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:2085404 original size:87 final size:87
Alignment explanation
Indices: 2085258--2085420 Score: 308
Period size: 87 Copynumber: 1.9 Consensus size: 87
2085248 AATGTTATAT
2085258 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
2085323 AGCGCTTATATAATAAAATAGG
66 AACGCTTATATAATAAAATAGG
*
2085345 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
2085410 AACGCTTATAT
66 AACGCTTATAT
2085421 TGACCTATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AACGCTTATATAATAAAATAGG
Found at i:2085922 original size:199 final size:198
Alignment explanation
Indices: 2085438--2086143 Score: 702
Period size: 200 Copynumber: 3.5 Consensus size: 198
2085428 TTTTCGAAGT
* * * * * *
2085438 AAATCAGTATATTTATATCGGTAACATTGCAAATTTACCTATTACATTATTATTATCGGTTATGA
1 AAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGA
* ** *
2085503 TGTTTTTTA-GATCTATACAATTT-TAAATGTATCGACACTTTATGATTGCACCTGGTTGGGCAT
66 TGTTTTTTAGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCT-GTT-----T
** * *
2085566 TCATATTTCATTCT-GAAAAAAGTATCGACACAAACTAACAACGTGTCGATACATTAT-TTAGAC
125 TGGTA-TTCATTCTGGACAAAAGTATCGACACAAATTAACAA-GTGTCGATACATTATGTT-GAC
*
2085629 ATATTCTCTCATA
187 ATATTTTCT-ATA
* * * **
2085642 AAATCGCTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTA-CGGGTTTCA
1 AAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATC-GGTTTTG
**
2085706 ATG--TTTCGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCT-TTTTGGT
65 ATGTTTTTTAGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCA-CCTGTTTTGGT
* * * *
2085768 ATTCATTCTGGACCAAAAGTATCGACACAAATTTAGCAAGTGTCGATACTTTATGCTGACGTATT
129 ATTCATTCTGGA-CAAAAGTATCGACACAAA-TTAACAAGTGTCGATACATTATGTTGACATATT
*
2085833 TTATATA
192 TTCTATA
* * * * * **
2085840 AAATTGGTATATTTATATCGATTATATTGTAAATTTACCTAATACATTATAATTATCAATTTTGA
1 AAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGA
*
2085905 TG-TTTTTAGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG-TGCACCTCG-TTTGTG
66 TGTTTTTTAGGATCGATACTTTTTATAAATGTATCGACACTTTATG-GTTGCACCT-GTTTTG-G
* * * * *
2085967 CATTCATCCTGGACAATAAGTTTCAACACAAATTACACAAGTGTCGATACATTATGTTGACCTAT
128 TATTCATTCTGGACAA-AAGTATCGACACAAATTA-ACAAGTGTCGATACATTATGTTGACATAT
2086032 TTTCTA-A
191 TTTCTATA
* * * * *
2086039 TTAACCGATATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTTG
1 -AAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTG
* *
2086104 ATGTTTTTTTGG-TCGATAC-TTGTATAAAATGTATCGACAC
65 ATGTTTTTTAGGATCGATACTTTTTAT-AAATGTATCGACAC
2086144 ATATTTAGGT
Statistics
Matches: 418, Mismatches: 65, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
197 8 0.02
198 65 0.16
199 99 0.24
200 138 0.33
201 7 0.02
202 3 0.01
203 14 0.03
204 81 0.19
205 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (198 bp):
AAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGA
TGTTTTTTAGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCTGTTTTGGTAT
TCATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTTGACATATTTTCT
ATA
Found at i:2089084 original size:198 final size:198
Alignment explanation
Indices: 2088666--2089221 Score: 776
Period size: 198 Copynumber: 2.8 Consensus size: 198
2088656 TTTATTTACA
* *
2088666 AAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTATACCAGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
* * * *
2088731 CAAAATCACATATTACATTATAATTATGGGTTTCAATGTTTTCGGTATCGACACTTTTAATAAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT-GGGATCGACACTTTTAATAAAT
* * *
2088796 GTATCGACACTTTGTGCGTTCATCCTTTTTGGCATCCATTCTGAAAAAAAGTATCGACACAAATT
130 GTATCGACACTTTATGCGTTCACCCTTTTTGACATCCATTCTGAAAAAAAGTATCGACACAAATT
2088861 TAAC
195 TAAC
* * * * *
2088865 AAGTGTCGCTAAATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACTGGTTACATTG
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
* * *
2088930 TAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTGGGATCGACACTGTTTGA-AAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTGGGATCGACACT-TTTAATAAAT
* * *
2088994 GTATCGACACTTTATGCGTTCACCCTTTTTGACATCCATTTTGGACAAAAATTAT-GACAC-AAT
130 GTATCGACACTTTATGCGTTCACCCTTTTTGACATCCATTCT-GAAAAAAAGTATCGACACAAAT
*
2089057 ATTAAG
194 -TTAAC
* * * *
2089063 AAGTGTCGATACATATTATAGACATATTCTCTCATAAAACTGGTATATGTATACCGGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
* *
2089128 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGATCGAAACTTTTAATAAATG
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTGGGATCGACACTTTTAATAAATG
* * *
2089193 TATCGAAACTTTATGTGTGCAACCCTTTT
131 TATCGACACTTTATGCGTTC-ACCCTTTT
2089222 GGATCGACAC
Statistics
Matches: 314, Mismatches: 38, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
197 7 0.02
198 190 0.61
199 117 0.37
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (198 bp):
AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTA
CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTGGGATCGACACTTTTAATAAATG
TATCGACACTTTATGCGTTCACCCTTTTTGACATCCATTCTGAAAAAAAGTATCGACACAAATTT
AAC
Found at i:2089349 original size:249 final size:250
Alignment explanation
Indices: 2088968--2089419 Score: 653
Period size: 249 Copynumber: 1.8 Consensus size: 250
2088958 GGTTTCGATG
* *
2088968 TTTTGGGATCGACACTGTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCCAT
1 TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCCAT
* * * * *
2089033 TTTGGACAAAAATTATGACACAATATTAAGAAGTGTCGATACATATTATAGACATATTCTCTCAT
66 TCTGGACAAAAAGTATGACACAATACTAAGAAATGTCGATAAATATTATAGACATATTCTCTCAT
*
2089098 AAAACTGGTATATGTATACCGGTTATATT-ACAAAATTAC-CTATTACATTATAATTATGGGTTT
131 AAAACTGGTATATGTATACCGGTTAAATTGA-AAAATTACTC-ATTACATTATAATTATGGGTTT
2089161 CGATGTTTTTGGATCGAAACTTTTAATAAATGTATCGAAACTTTATGTGTGCAACCC
194 CGATGTTTTTGGATCGAAACTTTTAATAAATGTATCGAAACTTTATGTGTGCAACCC
* * * *
2089218 TTTT-GGATCGACACTCTATGAAAATGTATCGACTCTTTGTAG-GTTCACGCTTTTTGGCATCCA
1 TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTAT-GCGTTCACCCTTTTTGACATCCA
* * * * *
2089281 TTCTGGAGAAAAAGTATCGACACAATACTAATAAATGTCGATAAATGTTGTAGACATATT-TTTC
65 TTCTGGACAAAAAGTAT-GACACAATACTAAGAAATGTCGATAAATATTATAGACATATTCTCTC
* * *
2089345 ATAAAATTGGTATATTTATACTGGTTAAATTGAAAAATTACTCATTACATTATAATTATGGGTTT
129 ATAAAACTGGTATATGTATACCGGTTAAATTGAAAAATTACTCATTACATTATAATTATGGGTTT
2089410 CGATGTTTTT
194 CGATGTTTTT
2089420 TGGGTCTTTA
Statistics
Matches: 178, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
249 135 0.76
250 43 0.24
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (250 bp):
TTTTGGGATCGACACTCTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCCAT
TCTGGACAAAAAGTATGACACAATACTAAGAAATGTCGATAAATATTATAGACATATTCTCTCAT
AAAACTGGTATATGTATACCGGTTAAATTGAAAAATTACTCATTACATTATAATTATGGGTTTCG
ATGTTTTTGGATCGAAACTTTTAATAAATGTATCGAAACTTTATGTGTGCAACCC
Found at i:2092074 original size:20 final size:19
Alignment explanation
Indices: 2092029--2092086 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2092019 CCGGTAGCGC
*
2092029 TTTACCGATTTTATCATTT
1 TTTACCGGTTTTATCATTT
*
2092048 TGATACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCAT-TT
* *
2092069 TTTACCTGTTATATCATT
1 TTTACCGGTTTTATCATT
2092087 GTGGATCGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.06
20 27 0.84
21 3 0.09
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:2092319 original size:182 final size:182
Alignment explanation
Indices: 2091995--2092470 Score: 690
Period size: 182 Copynumber: 2.6 Consensus size: 182
2091985 TGTACTTATG
* * *
2091995 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGATTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAGTTT
2092060 TATCATATTTTTACCTGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
2092125 AGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATAC-TTATATT
131 AGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGAT-CTTTATATT
* * * *
2092177 AAAGTACCGACACTTTAAATATATCCGGTAGCTCTTTATCGGTTTTATCATTTCGATACCAGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAGTTT
* *
2092242 TGTCATATTTTTACATGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
* * *
2092307 AGTCGTTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCTTTATATT
131 AGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATCTTTATATT
** * * * *
2092359 AAAGTATCGACACGCTCAATATATCCGGTAAG-GATTTACCGGTATTGTCTTTTCG-TGACCAGT
1 AAAGTATCGACACTTTCAATATATCCGGT-AGCGCTTTACCGGTTTTATCATTTCGAT-ACCAGT
* * *
2092422 TTTATCGATATTTTTACCTGTTATATTGA-TATAGATCGATACATTTTTA
64 TTTATC-ATATTTTTACCTGTTATA-TCATTGTGGATCGATACATTTTTA
2092471 ATTTGGATCG
Statistics
Matches: 262, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
181 2 0.01
182 221 0.84
183 37 0.14
184 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCAGTTT
TATCATATTTTTACCTGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
AGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATCTTTATATT
Found at i:2096986 original size:26 final size:26
Alignment explanation
Indices: 2096933--2096986 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2096923 GCAGGATGTC
* *
2096933 ATTTATAAAATTTTAAAGGGAGATAA
1 ATTTATAAAATTTTAAAGGGACAAAA
*
2096959 ATTTATAAAATTTT-ATGGAGACAAAA
1 ATTTATAAAATTTTAAAGG-GACAAAA
2096985 AT
1 AT
2096987 AGATTTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.12
26 21 0.88
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (26 bp):
ATTTATAAAATTTTAAAGGGACAAAA
Found at i:2097018 original size:18 final size:17
Alignment explanation
Indices: 2096997--2097038 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2096987 AGATTTTCAA
2096997 TAAAAAATATTAAAAATC
1 TAAAAAATA-TAAAAATC
* *
2097015 TAAAATATATAAAAATT
1 TAAAAAATATAAAAATC
2097032 TAAAAAA
1 TAAAAAA
2097039 CTTAAAGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATATAAAAATC
Found at i:2098007 original size:27 final size:26
Alignment explanation
Indices: 2097949--2098007 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2097939 ATATTTAAAA
*
2097949 TATTTATTTAATTTTTAAAATCATAT
1 TATTTATTTAATTTTTAAAATAATAT
* * *
2097975 TATTTATTTATTTATTTGAATTAATAT
1 TATTTATTTAATT-TTTAAAATAATAT
2098002 TATTTA
1 TATTTA
2098008 ATTTGTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TATTTATTTAATTTTTAAAATAATAT
Found at i:2098119 original size:18 final size:19
Alignment explanation
Indices: 2098098--2098134 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2098088 AAGATTAGAT
*
2098098 TAAATATT-TAATTTTAAA
1 TAAATATTATAATATTAAA
2098116 TAAATATTATAATATTAAA
1 TAAATATTATAATATTAAA
2098135 AATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATATTATAATATTAAA
Found at i:2098147 original size:28 final size:26
Alignment explanation
Indices: 2098111--2098174 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 26
2098101 ATATTTAATT
2098111 TTAAATAAATATTATAATATTAAAAA
1 TTAAATAAATATTATAATATTAAAAA
* *
2098137 TAATAAATAAATATTATGATTTTAAAAA
1 T--TAAATAAATATTATAATATTAAAAA
2098165 TTAAATAAAT
1 TTAAATAAAT
2098175 TATTCTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 10 0.29
28 24 0.71
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
TTAAATAAATATTATAATATTAAAAA
Found at i:2098843 original size:27 final size:28
Alignment explanation
Indices: 2098813--2098874 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
2098803 TATAAATTAG
2098813 AAAATTTTAAAAAAATTT-GGTTAATTCA
1 AAAATTTT-AAAAAATTTCGGTTAATTCA
*
2098841 AAAATTTTAAAAAATTTCGGTTAATTCG
1 AAAATTTTAAAAAATTTCGGTTAATTCA
2098869 AAAATT
1 AAAATT
2098875 AACCGAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (28 bp):
AAAATTTTAAAAAATTTCGGTTAATTCA
Found at i:2102741 original size:19 final size:19
Alignment explanation
Indices: 2102719--2102759 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2102709 TAGTATTTTG
2102719 TCCTGTAATTACTATATCA
1 TCCTGTAATTACTATATCA
2102738 TCCTGTAATTACTATATCA
1 TCCTGTAATTACTATATCA
2102757 TCC
1 TCC
2102760 ACGTAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (19 bp):
TCCTGTAATTACTATATCA
Found at i:2103779 original size:17 final size:17
Alignment explanation
Indices: 2103757--2103796 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
2103747 CAATTCGAAG
2103757 TGACTGAGCATTTGGAT
1 TGACTGAGCATTTGGAT
2103774 TGACTGAGCATTTGGAT
1 TGACTGAGCATTTGGAT
2103791 TGACTG
1 TGACTG
2103797 CATAATCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (17 bp):
TGACTGAGCATTTGGAT
Found at i:2107619 original size:14 final size:15
Alignment explanation
Indices: 2107593--2107621 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2107583 GAAATTATAT
2107593 TTTAATATTTAATTA
1 TTTAATATTTAATTA
2107608 TTTAAT-TTTAATTA
1 TTTAATATTTAATTA
2107622 AAAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATATTTAATTA
Found at i:2113212 original size:36 final size:37
Alignment explanation
Indices: 2113137--2113217 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
2113127 ACCCATTCTA
*
2113137 TTTTC-AACAAACATCTACCAAACTTTGAAAAACATT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACATT
*
2113173 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACA-T
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACATT
2113209 TTTTCAAAG
1 TTTTCAAAG
2113218 TTGGTTGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 15 0.36
37 27 0.64
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (37 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACATT
Found at i:2117225 original size:16 final size:17
Alignment explanation
Indices: 2117194--2117227 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2117184 CGTATCGCCG
*
2117194 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
2117211 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
2117227 A
1 A
2117228 AGTGAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:2117715 original size:36 final size:37
Alignment explanation
Indices: 2117638--2117713 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
2117628 CCCATTCTTA
2117638 TTTTC-AACAAACATCTACCAAACTTTAAAAAACATT
1 TTTTCAAACAAACATCTACCAAACTTTAAAAAACATT
* * *
2117674 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACATT
1 TTTTCAAACAAACATCTACCAAACTTTAAAAAACATT
2117711 TTT
1 TTT
2117714 CATAGTTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 5 0.14
37 31 0.86
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (37 bp):
TTTTCAAACAAACATCTACCAAACTTTAAAAAACATT
Found at i:2120755 original size:16 final size:16
Alignment explanation
Indices: 2120718--2120761 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2120708 TTGTTTTATT
* *
2120718 TATTATTATTATTTTGA
1 TATTATTATTA-TATCA
2120735 T-TTATTATTATATCA
1 TATTATTATTATATCA
2120750 TATTATTATTAT
1 TATTATTATTAT
2120762 TAAATAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 19 0.79
17 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTATTATTATATCA
Found at i:2122203 original size:18 final size:16
Alignment explanation
Indices: 2122171--2122208 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
2122161 TTTAGTCACT
2122171 ATTTATTTATATTTTA
1 ATTTATTTATATTTTA
2122187 ATTTAATTTATTATTTTA
1 ATTT-ATTTA-TATTTTA
2122205 ATTT
1 ATTT
2122209 TATATGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 5 0.25
18 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTATTTATATTTTA
Found at i:2122332 original size:33 final size:33
Alignment explanation
Indices: 2122270--2122332 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2122260 ATTCATATAA
* *
2122270 ATATATATTAAATAATATGTTTTTATTTATTTT
1 ATATATATTAAATAATATCTTATTATTTATTTT
2122303 ATATATATTAAATAAATATCTTATT-TTTAT
1 ATATATATTAAAT-AATATCTTATTATTTAT
2122333 AAATTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (33 bp):
ATATATATTAAATAATATCTTATTATTTATTTT
Found at i:2122341 original size:33 final size:33
Alignment explanation
Indices: 2122265--2122346 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 33
2122255 TATTTATTCA
* *
2122265 TATAAA-TATATATTAAATAATATGTTTTTATT
1 TATAAATTATATATTAAATAATATCTTATTATT
**
2122297 TAT-TTTATATATATTAAATAAATATCTTATT-TT
1 TATAAAT-TATATATTAAAT-AATATCTTATTATT
2122330 TATAAATTATATATTAA
1 TATAAATTATATATTAA
2122347 TCTATGTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
32 3 0.08
33 27 0.68
34 10 0.25
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (33 bp):
TATAAATTATATATTAAATAATATCTTATTATT
Found at i:2122475 original size:19 final size:18
Alignment explanation
Indices: 2122439--2122477 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2122429 TCATTTTCTG
2122439 ATATTTATTAATAAATAA
1 ATATTTATTAATAAATAA
* *
2122457 ATATCTTATTTATATATAA
1 ATAT-TTATTAATAAATAA
2122476 AT
1 AT
2122478 TAATAGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTTATTAATAAATAA
Found at i:2123063 original size:21 final size:20
Alignment explanation
Indices: 2123013--2123063 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
2123003 TTTATACTTA
2123013 TTATTTTCATAATATTTATAT
1 TTATTTT-ATAATATTTATAT
* *
2123034 GTATATTATCAATATTTCAT-T
1 TTATTTTAT-AATATTT-ATAT
2123055 TTATTTTAT
1 TTATTTTAT
2123064 TCCATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATTTTATAATATTTATAT
Found at i:2126349 original size:15 final size:15
Alignment explanation
Indices: 2126326--2126362 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2126316 TTTGGGATCA
*
2126326 ATACCTTTTGCATAC
1 ATACATTTTGCATAC
2126341 ATACATTTTGCATAC
1 ATACATTTTGCATAC
*
2126356 ATTCATT
1 ATACATT
2126363 ATTCATTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (15 bp):
ATACATTTTGCATAC
Found at i:2129069 original size:24 final size:23
Alignment explanation
Indices: 2129026--2129070 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
2129016 GTTCATAATG
2129026 AGAAGAATTCATATGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
2129049 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
2129071 AGCTTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 10 0.50
25 3 0.15
ACGTcount: A:0.51, C:0.04, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:2130914 original size:33 final size:33
Alignment explanation
Indices: 2130852--2130914 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2130842 ATTCATATAA
** *
2130852 ATATATATTAAATAATATGTTTTTATTTATTTT
1 ATATATATTAAATAATATCCTATTATTTATTTT
2130885 ATATATATTAAATAAATATCCTATT-TTTAT
1 ATATATATTAAAT-AATATCCTATTATTTAT
2130915 AAATTATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 18 0.69
34 8 0.31
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (33 bp):
ATATATATTAAATAATATCCTATTATTTATTTT
Found at i:2130925 original size:37 final size:33
Alignment explanation
Indices: 2130852--2130925 Score: 76
Period size: 37 Copynumber: 2.1 Consensus size: 33
2130842 ATTCATATAA
* ** *
2130852 ATATATATTAAATAATATGTTTTTATTTATTTT
1 ATATATATTAAATAATATATTTTTATAAATTAT
2130885 ATATATATTAAATAAATATCCTATTTTTATAAATTAT
1 ATATATATTAAAT-AATA---TATTTTTATAAATTAT
2130922 ATAT
1 ATAT
2130926 TAATCTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 13 0.39
34 4 0.12
37 16 0.48
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (33 bp):
ATATATATTAAATAATATATTTTTATAAATTAT
Found at i:2137079 original size:14 final size:14
Alignment explanation
Indices: 2137056--2137088 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2137046 TGGATTCTTC
*
2137056 TGGTGTGGCGGTGG
1 TGGTGAGGCGGTGG
2137070 TGGTGAGGCGGTGG
1 TGGTGAGGCGGTGG
2137084 TGGTG
1 TGGTG
2137089 TGGCAGCGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.06, G:0.64, T:0.27
Consensus pattern (14 bp):
TGGTGAGGCGGTGG
Found at i:2137478 original size:14 final size:14
Alignment explanation
Indices: 2137456--2137505 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
2137446 TAACAAGAAT
2137456 TATATAATAATAAG
1 TATATAATAATAAG
* *
2137470 TATAAAATAACAAG
1 TATATAATAATAAG
2137484 TATATAATAATAA-
1 TATATAATAATAAG
2137497 TATATAATA
1 TATATAATA
2137506 TAAAAACGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
13 9 0.28
14 23 0.72
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (14 bp):
TATATAATAATAAG
Found at i:2137732 original size:65 final size:65
Alignment explanation
Indices: 2137628--2137887 Score: 259
Period size: 65 Copynumber: 3.9 Consensus size: 65
2137618 ATCTTGCTTC
* * * ** *
2137628 ACTACTCTTTTGTGAAGGCTTGATTGCATCACTTCACTACTCTTTTGTGAAGGATGAATTACTTT
1 ACTACTCTTCTGTAAAGGCTGGATTGCATTGCTTCACTACTCTTTTGTAAAGGATGAATTACTTT
* * *
2137693 ACTACTCTACTGTAAAGGCTGGATTGCATTGCTTTACTACTCTTTTGTAAAGGCCAGATTGCATT
1 ACTACTCTTCTGTAAAGGCTGGATTGCATTGCTTCACTACTCTTTTGTAAA-G---GA-TGAATT
2137758 ACTTT
61 ACTTT
* * * * * * ** *
2137763 ACTACTCTTTTGTAAAGGCTTGATTGCATTGCTTTACTAATCATTTGTAAAGGTTGGGTTGCTTT
1 ACTACTCTTCTGTAAAGGCTGGATTGCATTGCTTCACTACTCTTTTGTAAAGGATGAATTACTTT
* ** * * *
2137828 ACTACTCTGCTGTAAAGGCTGGATCACATTGCTCCACTACTCTTTTGTGAAGGCTGAATT
1 ACTACTCTTCTGTAAAGGCTGGATTGCATTGCTTCACTACTCTTTTGTAAAGGATGAATT
2137888 TGAATTAAGA
Statistics
Matches: 159, Mismatches: 31, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
65 98 0.62
66 2 0.01
69 3 0.02
70 56 0.35
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (65 bp):
ACTACTCTTCTGTAAAGGCTGGATTGCATTGCTTCACTACTCTTTTGTAAAGGATGAATTACTTT
Found at i:2137883 original size:35 final size:35
Alignment explanation
Indices: 2137621--2137883 Score: 231
Period size: 35 Copynumber: 7.8 Consensus size: 35
2137611 TGACTTTATC
* * *
2137621 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTGCA
1 TTGCTTTACTACTCTTTTGTAAAGGCTGGATTGCA
** * * *
2137656 TCACTTCACTACTCTTTTGTGAA----GGA-TGAA
1 TTGCTTTACTACTCTTTTGTAAAGGCTGGATTGCA
* **
2137686 TTACTTTACTACTCTACTGTAAAGGCTGGATTGCA
1 TTGCTTTACTACTCTTTTGTAAAGGCTGGATTGCA
**
2137721 TTGCTTTACTACTCTTTTGTAAAGGCCAGATTGCA
1 TTGCTTTACTACTCTTTTGTAAAGGCTGGATTGCA
* *
2137756 TTACTTTACTACTCTTTTGTAAAGGCTTGATTGCA
1 TTGCTTTACTACTCTTTTGTAAAGGCTGGATTGCA
* * *
2137791 TTGCTTTACTAATCATTTGTAAAGGTTGG---G--
1 TTGCTTTACTACTCTTTTGTAAAGGCTGGATTGCA
** **
2137821 TTGCTTTACTACTCTGCTGTAAAGGCTGGATCACA
1 TTGCTTTACTACTCTTTTGTAAAGGCTGGATTGCA
** *
2137856 TTGCTCCACTACTCTTTTGTGAAGGCTG
1 TTGCTTTACTACTCTTTTGTAAAGGCTG
2137884 AATTTGAATT
Statistics
Matches: 184, Mismatches: 34, Indels: 20
0.77 0.14 0.08
Matches are distributed among these distances:
30 45 0.24
31 2 0.01
32 1 0.01
34 3 0.02
35 133 0.72
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (35 bp):
TTGCTTTACTACTCTTTTGTAAAGGCTGGATTGCA
Found at i:2138465 original size:63 final size:61
Alignment explanation
Indices: 2138076--2138591 Score: 508
Period size: 61 Copynumber: 8.4 Consensus size: 61
2138066 AATCTGCAAT
* * * *
2138076 GTTGACTTCTTTTCACAAAGAAGTCAATGATTGA--CTA--G-GGAGTC-AGAAATAACAAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGAGGAGTCAAG-AATAACAAA
* * * * * * * *
2138132 GGTTGACATCTCTTCAAGAGGAAGTCAATGATTGACTCTACTGAGGAGTTAGGGATAATAAGG
1 -GTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGAGGAGTCAAGAATAACAA-A
* * * *
2138195 GTTGACTTCTTTTCATGAGGAAGTCAATGATTGACTCTACTGAGGAGTTAAGAATAACAAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGAGGAGTCAAGAATAACAAA
* * * * *
2138256 GTTGATTTCTCATCATGAGGAAGTCAAGGATTGACTCTATTGAGGAGTCAAGAATAATAAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGAGGAGTCAAGAATAACAAA
* * ** * *
2138317 GTTGATTTCTCTTCACAAGGAAGTCAAAAATTGACTCTACCGAGGAGTCAGGAATAACAAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGAGGAGTCAAGAATAACAAA
* * **
2138378 GCTGACTTCT-TGTCACGAGGAAGTCAAGGATTGACTCTACTGAGGAATCAAGGAATAACAGGG
1 GTTGACTTCTCT-TCACGAGGAAGTCAAGGATTGACTCTACTGAGGAGTCAA-GAATAACA-AA
* * * *
2138441 GTTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCATATAATAAAAAA
1 GTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGAGGAGTCA-AGAATAACAAA
* * * * * *
2138503 GTTCGACTTCTCTTTACGAGGAAGTCAAAGG-TTAACTCTACTGAGGAGTCAGGGAGAATAAA
1 GTT-GACTTCTCTTCACGAGGAAGTC-AAGGATTGACTCTACTGAGGAGTCAAGAATAACAAA
* *
2138565 GTTGACTTCTCGTCATGAGGAAGTCAA
1 GTTGACTTCTCTTCACGAGGAAGTCAA
2138592 TGAATAATAG
Statistics
Matches: 384, Mismatches: 61, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
57 29 0.08
59 3 0.01
60 3 0.01
61 167 0.43
62 85 0.22
63 92 0.24
64 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (61 bp):
GTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGAGGAGTCAAGAATAACAAA
Found at i:2138669 original size:62 final size:62
Alignment explanation
Indices: 2138594--2139264 Score: 729
Period size: 62 Copynumber: 10.8 Consensus size: 62
2138584 GAAGTCAATG
** * * *
2138594 AATAATAGGGATTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTTTACTGAGGAGTCAGA
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGA
* * * * * * * *
2138656 GATAATATAGATTGACTCCTCTTCATGAGTAAGTCAAAGATTAACTTTACTGAGGAGTCAGA
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGA
* * * * * * *
2138718 AATAATAAAAATTGACTTCTCTTTTCAAGGAAGTTAAAGATTGACTATACTGAGGAGTTAGGG
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCA-GA
* * * *
2138781 AATAATAAAGGTTAAATTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAAA
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGA
* * * * * *
2138843 AATAATAAAGATTGACTTTTCTTTACAAGGAAGTCAAGGATTGACTATACTGAGGAGTCCGT
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGA
* * * * * * *
2138905 GATAACAAAGATTGATTTCTCTTCACGAGAAAGTCAAAGATTGACTTTACTGAGGAGTCAGGG
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCA-GA
* * *
2138968 AATAACAAAGGTTGACTTCTCTTTACGAGGAAGTC-AAGCATTGACTCTACTGAGGAGTCGGGA
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAG-ATTGACTCTACTGAGGAGTC-AGA
* * * * * *
2139031 AATAATAAAGATTGATTTATCTTCACGAGGAAGTTAAATATTGACTCTACTGAGCAGTCAGGA
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCA-GA
* * * * *
2139094 AATAACAAAGGTTGACTTCTCTTTATGAAGAAGTAAAAGATTGACTCTACAT-AGGAGTCAG-
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTAC-TGAGGAGTCAGA
* * * *
2139155 GA-AATAAAGATTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTATTGAGGAGTCAGA
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGA
* * * *
2139216 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAAGATTGATTCTA
1 AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTA
2139265 GAAAACAAAA
Statistics
Matches: 501, Mismatches: 98, Indels: 20
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.00
60 48 0.10
61 2 0.00
62 246 0.49
63 201 0.40
64 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (62 bp):
AATAATAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAGA
Found at i:2138735 original size:163 final size:162
Alignment explanation
Indices: 2138418--2138738 Score: 421
Period size: 163 Copynumber: 2.0 Consensus size: 162
2138408 TTGACTCTAC
* * *
2138418 TGAGGAATCAAGGAATAACAGGGGTTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTG
1 TGAGGAATCAAGGAATAACAGGGATTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTACTG
* * * *
2138483 AGGAGTCATATAATAAAAAAGTTCGACTTCTCTTTACGAGGAAGTCAAAGGTTAACTCTACTGAG
66 AGGAGTCAGATAATAAAAAAGTTCGACTCCTCTTCACGAGGAAGTCAAAGATTAACTCTACTGAG
** *
2138548 GAGTCAGGGAGAATAAAGTTGACTTCTCGTCA
131 GAGTCAGAAAGAATAAAATTGACTTCTCGTCA
* * *
2138580 TGAGGAAGTCAATGAATAATAGGGATTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTTTACT
1 TGAGGAA-TCAAGGAATAACAGGGATTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTACT
* * * * * *
2138645 GAGGAGTCAGA-GATAATATAGATT-GACTCCTCTTCATGAGTAAGTCAAAGATTAACTTTACTG
65 GAGGAGTCAGATAATAAAAAAG-TTCGACTCCTCTTCACGAGGAAGTCAAAGATTAACTCTACTG
*
2138708 AGGAGTCAGAAATAATAAAAATTGACTTCTC
129 AGGAGTCAGAAAGAAT-AAAATTGACTTCTC
2138739 TTTTCAAGGA
Statistics
Matches: 136, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
162 60 0.44
163 76 0.56
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (162 bp):
TGAGGAATCAAGGAATAACAGGGATTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTACTG
AGGAGTCAGATAATAAAAAAGTTCGACTCCTCTTCACGAGGAAGTCAAAGATTAACTCTACTGAG
GAGTCAGAAAGAATAAAATTGACTTCTCGTCA
Found at i:2138927 original size:187 final size:186
Alignment explanation
Indices: 2138605--2139259 Score: 780
Period size: 187 Copynumber: 3.5 Consensus size: 186
2138595 ATAATAGGGA
* * *
2138605 TTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTTTACTGAGGAGTCAGAGATAATATAGATTG
1 TTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTACTGAGGAGTCAGAAATAATAAAGATTG
* * * * * * * *
2138670 ACTCCTCTTCATGAGTAAGTCAAAGATTAACTTTACTGAGGAGTCAGAAATAATAAAAATTGACT
66 ACTTCTCTTCACGAGGAAGTCAAAGATTGACTATACTGAGGAGTCAG-GATAACAAAGATTGACT
* *
2138735 TCTCTTTTCAAGGAAGTTAAAGATTGACTATACTGAGGAGTTAGGGAATAATAAAGG
130 TCTCTTTTCAAGGAAGTAAAAGATTGACTATACTGAGGAGTCAGGGAATAATAAAGG
* * * * *
2138792 TTAAATTCTCTTTACGAGGAAGTCAAAGATTGACTCTACTGAGGAGTCAAAAATAATAAAGATTG
1 TTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTACTGAGGAGTCAGAAATAATAAAGATTG
* * * * * *
2138857 ACTTTTCTTTACAAGGAAGTCAAGGATTGACTATACTGAGGAGTCCGTGATAACAAAGATTGATT
66 ACTTCTCTTCACGAGGAAGTCAAAGATTGACTATACTGAGGAGTCAG-GATAACAAAGATTGACT
** * * * * *
2138922 TCTCTTCACGAGAAAGTCAAAGATTGACTTTACTGAGGAGTCAGGGAATAACAAAGG
130 TCTCTTTTCAAGGAAGTAAAAGATTGACTATACTGAGGAGTCAGGGAATAATAAAGG
* ** *
2138979 TTGACTTCTCTTTACGAGGAAGTCAAGCATTGACTCTACTGAGGAGTCGGGAAATAATAAAGATT
1 TTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTACTGAGGAGTC-AGAAATAATAAAGATT
* * * * * * *
2139044 GATTTATCTTCACGAGGAAGTTAAATATTGACTCTACTGAGCAGTCAGGAAATAACAAAGGTTGA
65 GACTTCTCTTCACGAGGAAGTCAAAGATTGACTATACTGAGGAGTCAGG--ATAACAAAGATTGA
* * *
2139109 CTTCTCTTTATGAA-GAAGTAAAAGATTGACTCTACAT-AGGAGTCA-GG-A-AATAAAGA
128 CTTCTCTTT-TCAAGGAAGTAAAAGATTGACTATAC-TGAGGAGTCAGGGAATAATAAAGG
* * *
2139165 TTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTATTGAGGAGTCAGAAATAACAAAGGTTG
1 TTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTACTGAGGAGTCAGAAATAATAAAGATTG
2139230 ACTTCTCTTCACGAGGAAGTCAAAGATTGA
66 ACTTCTCTTCACGAGGAAGTCAAAGATTGA
2139260 TTCTAGAAAA
Statistics
Matches: 394, Mismatches: 69, Indels: 12
0.83 0.15 0.03
Matches are distributed among these distances:
185 40 0.10
186 50 0.13
187 202 0.51
188 54 0.14
189 46 0.12
190 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (186 bp):
TTGACTTCTCTTTACGAGAAAGTCAAAAATTGACTCTACTGAGGAGTCAGAAATAATAAAGATTG
ACTTCTCTTCACGAGGAAGTCAAAGATTGACTATACTGAGGAGTCAGGATAACAAAGATTGACTT
CTCTTTTCAAGGAAGTAAAAGATTGACTATACTGAGGAGTCAGGGAATAATAAAGG
Found at i:2142260 original size:17 final size:17
Alignment explanation
Indices: 2142238--2142276 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2142228 CGGAGAAAGG
2142238 AACAAAAAACATGTTCA
1 AACAAAAAACATGTTCA
2142255 AACAAAAAACATGTTCA
1 AACAAAAAACATGTTCA
2142272 AACAA
1 AACAA
2142277 GATGCTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.62, C:0.18, G:0.05, T:0.15
Consensus pattern (17 bp):
AACAAAAAACATGTTCA
Found at i:2144248 original size:24 final size:25
Alignment explanation
Indices: 2144212--2144274 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
2144202 TATAAATACA
* *
2144212 AATGCAAAGATGCAAAAATACGTAAAT
1 AATG-AAA-ATGCAAAAATAAGCAAAT
*
2144239 -ATGAAAATGCAGAAATAAGCAAAT
1 AATGAAAATGCAAAAATAAGCAAAT
*
2144263 AATGCAAATGCA
1 AATGAAAATGCA
2144275 TGTATGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 15 0.48
25 13 0.42
26 3 0.10
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.17
Consensus pattern (25 bp):
AATGAAAATGCAAAAATAAGCAAAT
Found at i:2146931 original size:18 final size:18
Alignment explanation
Indices: 2146908--2146952 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2146898 GGCTTAGTCT
* * *
2146908 GGTTCTGGGTCTTGATCG
1 GGTTCTGGATCTGGACCG
2146926 GGTTCTGGATCTGGACCG
1 GGTTCTGGATCTGGACCG
2146944 GGTTCTGGA
1 GGTTCTGGA
2146953 CATGTTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.40, T:0.33
Consensus pattern (18 bp):
GGTTCTGGATCTGGACCG
Found at i:2147095 original size:17 final size:17
Alignment explanation
Indices: 2147064--2147098 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2147054 CAAGAATTAT
*
2147064 ATAATAATAGGTATATA
1 ATAATAATAAGTATATA
*
2147081 ATAATAATAATTATATA
1 ATAATAATAAGTATATA
2147098 A
1 A
2147099 AAACGCAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
ATAATAATAAGTATATA
Found at i:2149999 original size:75 final size:75
Alignment explanation
Indices: 2149909--2150057 Score: 210
Period size: 75 Copynumber: 2.0 Consensus size: 75
2149899 TATCCTAGAA
* * * * *
2149909 TTTGAATTATAATATTATGAAT-AGAGTGAATTAAATTGAAAGGGTTGTCTATGTTGTAAACTTT
1 TTTGAATTATAATATTATGAATGA-AATGAATTAAATTGAAAGGATTGTCTATCTTATAAACTTG
2149973 TACAATATATG
65 TACAATATATG
* * *
2149984 TTTGAATTATAATATTATGAATGAAATGGATTAAATTGAAAGGATTGTTTCTCTTATAAACTTGT
1 TTTGAATTATAATATTATGAATGAAATGAATTAAATTGAAAGGATTGTCTATCTTATAAACTTGT
2150049 ACAATATAT
66 ACAATATAT
2150058 TATATAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
75 64 0.98
76 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (75 bp):
TTTGAATTATAATATTATGAATGAAATGAATTAAATTGAAAGGATTGTCTATCTTATAAACTTGT
ACAATATATG
Found at i:2156044 original size:21 final size:20
Alignment explanation
Indices: 2156026--2156065 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2156016 CAAAATATCA
*
2156026 TTCATGATAAATATCATATATG
1 TTCATGAT-AACATCATATA-G
2156048 TTCATGATAACATCATAT
1 TTCATGATAACATCATAT
2156066 GTAACGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (20 bp):
TTCATGATAACATCATATAG
Found at i:2160266 original size:67 final size:66
Alignment explanation
Indices: 2160127--2160273 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 66
2160117 TTATGGTCAT
* * * *
2160127 AGGGTACCGAGACCCTATGAAGGGGTATCGATACCCCTCTTGAACAAAAAATTACAGAATGTAAG
1 AGGGTATCGATACCCTATGAAGGGGTATCGATACCCCTCCTGAACAAAAAATTACAGAATGTAAC
*
2160192 T
66 C
* * * *
2160193 ATGGTATCGATACCCTAT-AGGGGGTATCGATACCCC-CCTGAAGATGAAAAATTTCTAGAATGT
1 AGGGTATCGATACCCTATGAAGGGGTATCGATACCCCTCCTGAACA--AAAAATTAC-AGAATGT
*
2160256 TACC
63 AACC
*
2160260 AGGGTATCTATACC
1 AGGGTATCGATACC
2160274 ATAGACAGGG
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
64 6 0.09
65 17 0.26
66 23 0.35
67 20 0.30
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (66 bp):
AGGGTATCGATACCCTATGAAGGGGTATCGATACCCCTCCTGAACAAAAAATTACAGAATGTAAC
C
Found at i:2163361 original size:32 final size:28
Alignment explanation
Indices: 2163300--2163354 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
2163290 CTATTATTTT
2163300 TATTATTTTAATATTATTAAATAAAATA
1 TATTATTTTAATATTATTAAATAAAATA
*
2163328 TATTATTATTATTATTATTAAATAAAA
1 TATTATT-TTAATATTATTAAATAAAA
2163355 AAATATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TATTATTTTAATATTATTAAATAAAATA
Found at i:2163812 original size:12 final size:12
Alignment explanation
Indices: 2163793--2163822 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2163783 GCAAAACACC
2163793 AACAAACAACAA
1 AACAAACAACAA
*
2163805 AGCAAACAACAA
1 AACAAACAACAA
2163817 AACAAA
1 AACAAA
2163823 AAAGAGAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.73, C:0.23, G:0.03, T:0.00
Consensus pattern (12 bp):
AACAAACAACAA
Found at i:2164752 original size:22 final size:18
Alignment explanation
Indices: 2164737--2164772 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2164727 TTATTTAGCC
*
2164737 ATAAATATATATTTATATA
1 ATAAATA-ATATTTATTTA
2164756 ATAAATAATATTTATTT
1 ATAAATAATATTTATTT
2164773 TATTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAAATAATATTTATTTA
Found at i:2164942 original size:117 final size:116
Alignment explanation
Indices: 2164803--2165036 Score: 294
Period size: 117 Copynumber: 2.0 Consensus size: 116
2164793 ATTTTAATCC
* * * * *
2164803 TGTTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCC
1 TGTTTTAATATTTATTTATTTTT-AACATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-C
* *
2164866 ATTTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAAT-TATATTAAT
64 ATTTTCTGATATTTCTAAATAAATAAATATCTTA-TTTATAAATATATATAAAT
* ** *
2164919 TGTTTTAATTATTTATTTATTTTTAACATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCA
1 TGTTTTAA-TATTTATTTATTTTTAACATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
* *
2164984 TTTTCTGATATTTCTAAATAAATAAATATTTTATTTATACATATATATAAAT
65 TTTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAAT
2165036 T
1 T
2165037 AATATATTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
116 20 0.20
117 60 0.59
118 21 0.21
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (116 bp):
TGTTTTAATATTTATTTATTTTTAACATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
TTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAAT
Found at i:2167104 original size:8 final size:7
Alignment explanation
Indices: 2167080--2167121 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2167070 TTTTCATACA
2167080 TGCA-TT
1 TGCATTT
2167086 TGCATTT
1 TGCATTT
2167093 TGCATCTT
1 TGCAT-TT
2167101 TGCATTT
1 TGCATTT
* *
2167108 TTCATTG
1 TGCATTT
2167115 TGCATTT
1 TGCATTT
2167122 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:2167104 original size:15 final size:14
Alignment explanation
Indices: 2167080--2167121 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2167070 TTTTCATACA
2167080 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
2167093 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
2167108 TTCATTGTGCATTT
1 TGCATTTTGCATTT
2167122 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:2167198 original size:14 final size:14
Alignment explanation
Indices: 2167178--2167223 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2167168 TTACATTCAT
2167178 ATATTTACATTTGC
1 ATATTTACATTTGC
* *
2167192 ATTTTTACGTTTG-
1 ATATTTACATTTGC
2167205 -TATTTACATTTGC
1 ATATTTACATTTGC
2167218 ATATTT
1 ATATTT
2167224 CCATAATTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.38
14 16 0.62
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.57
Consensus pattern (14 bp):
ATATTTACATTTGC
Found at i:2172396 original size:114 final size:113
Alignment explanation
Indices: 2172196--2172418 Score: 347
Period size: 114 Copynumber: 2.0 Consensus size: 113
2172186 GTGTCACGTT
* *
2172196 CTCATAGTAGAAATAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 CTCATAGTAGAAATAAGAGACCCAATAGCATATTCTGGAAGTGATCTTTGAGTTATCTGATCTGA
* * * * *
2172261 TTTGGTATGAACCCCAAAACCAATTATTGGATTTGAAAGATGAATTTG
66 TTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
*
2172309 CTCATAGTAGAAATAAGAAGACCCAATAGCATATTTTGGAAGTGATCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAG-AGACCCAATAGCATATTCTGGAAGTGATCTTTGAGTTATCTGATCTG
* *
2172374 GTTCGGTAGGAACCCCAGAACCAATCATTAGAATTGAAAGATGAA
65 ATTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
2172419 CTGCATATTA
Statistics
Matches: 99, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
113 17 0.17
114 82 0.83
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (113 bp):
CTCATAGTAGAAATAAGAGACCCAATAGCATATTCTGGAAGTGATCTTTGAGTTATCTGATCTGA
TTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
Found at i:2175445 original size:22 final size:22
Alignment explanation
Indices: 2175416--2175470 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2175406 ATCTACACTC
*
2175416 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTATT
*
2175438 TTTAAAGATGATAGATTCTATT
1 TTCAAAGATGATAGATTCTATT
2175460 TTCAAAGATGA
1 TTCAAAGATGA
2175471 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTATT
Found at i:2176416 original size:76 final size:76
Alignment explanation
Indices: 2176316--2177040 Score: 1229
Period size: 76 Copynumber: 9.6 Consensus size: 76
2176306 CTATTTCCTA
* *
2176316 CATCTGTAAGTCCTACAGTACATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2176381 AACCTTAGGGT
66 AACCTTAGGGT
*
2176392 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2176457 AGCCTTAGGGT
66 AACCTTAGGGT
* *
2176468 CATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2176533 AACCTTAGGGT
66 AACCTTAGGGT
* *
2176544 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2176609 AACCTTAGGGT
66 AACCTTAGGGT
2176620 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2176685 AGA-CTTAGGGT
66 A-ACCTTAGGGT
* * * *
2176696 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGTTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2176761 AGCCTTAGGGT
66 AACCTTAGGGT
**
2176772 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGATATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2176837 AGCCTTAGGGT
66 AACCTTAGGGT
2176848 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2176913 AACCTTAGGGT
66 AACCTTAGGGT
*
2176924 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2176989 AGCCTTAGGGT
66 AACCTTAGGGT
* * * *
2177000 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAA-CCTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
2177041 TGGGTCATCT
Statistics
Matches: 614, Mismatches: 33, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
75 4 0.01
76 609 0.99
77 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGT
Found at i:2177055 original size:46 final size:46
Alignment explanation
Indices: 2176976--2177079 Score: 174
Period size: 46 Copynumber: 2.3 Consensus size: 46
2176966 CGGGAGCTTT
*
2176976 TTGATGTTTTC-AAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGC
1 TTGATGTTTTCAAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGC
* *
2177021 TTGATGTTTTCAAAAACCTTTGGGTCATCTGTAAGCCCTTTAGTGC
1 TTGATGTTTTCAAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGC
2177067 TTGATGTTTTCAA
1 TTGATGTTTTCAA
2177080 CATTTCAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 11 0.20
46 44 0.80
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (46 bp):
TTGATGTTTTCAAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGC
Found at i:2177199 original size:3 final size:3
Alignment explanation
Indices: 2177185--2177249 Score: 67
Period size: 3 Copynumber: 20.7 Consensus size: 3
2177175 ATAATTTTTC
* * * *
2177185 TAT TAT TTT TAT TAT TAT TAAA TAA AAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT TAT
2177232 ATAT TAT TAT TAT TAT TA
1 -TAT TAT TAT TAT TAT TA
2177250 AATAAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
3 46 0.87
4 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2177235 original size:19 final size:19
Alignment explanation
Indices: 2177211--2177249 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2177201 ATTAAATAAA
2177211 ATATATTATTATTATTATT
1 ATATATTATTATTATTATT
2177230 ATATATTATTATTATTATT
1 ATATATTATTATTATTATT
2177249 A
1 A
2177250 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATATTATTATTATTATT
Found at i:2177713 original size:12 final size:12
Alignment explanation
Indices: 2177694--2177723 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2177684 GCAAAACACC
2177694 AACAAACAACAA
1 AACAAACAACAA
*
2177706 AGCAAACAACAA
1 AACAAACAACAA
2177718 AACAAA
1 AACAAA
2177724 AAGAGAAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.73, C:0.23, G:0.03, T:0.00
Consensus pattern (12 bp):
AACAAACAACAA
Found at i:2178655 original size:18 final size:18
Alignment explanation
Indices: 2178634--2178676 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2178624 TTATTATTAT
*
2178634 TATTTATCT-ATAAATATA
1 TATTTATATAATAAATA-A
2178652 TATTTATATAATAAATAA
1 TATTTATATAATAAATAA
2178670 TATTTAT
1 TATTTAT
2178677 TTTATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTATATAATAAATAA
Found at i:2178836 original size:179 final size:182
Alignment explanation
Indices: 2178642--2179004 Score: 696
Period size: 179 Copynumber: 2.0 Consensus size: 182
2178632 ATTATTTATC
2178642 TATAAATATATATTTATATAATAAATAATATTTATTTTATTTAATTACTTTTAACTTTTTTTAAT
1 TATAAATATATATTTATATAATAAATAATATTTATTTTATTTAATTACTTTTAACTTTTTTTAAT
2178707 CTTGTTTTAATATTTATTTATTTTTCAATATTAA-AAAGGGCAGTCTTAAAACAACTGG-GTCCA
66 CTTGTTTTAATATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAACAACTGGAGTCCA
2178770 TTTTCTGATATTTTTAAAT-AATAAATATCCTATTTTATAAATTATATTAAT
131 TTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATTAAT
2178821 TATAAATATATATTTATATAATAAATAATATTTATTTTATTTAATTACTTTTAACTTTTTTTAAT
1 TATAAATATATATTTATATAATAAATAATATTTATTTTATTTAATTACTTTTAACTTTTTTTAAT
2178886 CTTGTTTTAATATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAACAACTGGATGTCC
66 CTTGTTTTAATATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAACAACTGGA-GTCC
2178951 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATTAAT
130 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATTAAT
2179004 T
1 T
2179005 TTTTAATTAT
Statistics
Matches: 180, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
179 99 0.55
180 24 0.13
182 24 0.13
183 33 0.18
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.50
Consensus pattern (182 bp):
TATAAATATATATTTATATAATAAATAATATTTATTTTATTTAATTACTTTTAACTTTTTTTAAT
CTTGTTTTAATATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAACAACTGGAGTCCA
TTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATTAAT
Found at i:2178840 original size:16 final size:17
Alignment explanation
Indices: 2178790--2178855 Score: 50
Period size: 16 Copynumber: 4.0 Consensus size: 17
2178780 TTTTTAAATA
**
2178790 ATAAATATCCTATTT-T
1 ATAAATATAATATTTAT
*
2178806 ATAAAT-T-ATATTAATT
1 ATAAATATAATATTTA-T
2178822 ATAAATAT-ATATTTAT
1 ATAAATATAATATTTAT
*
2178838 ATAATAAATAATATTTAT
1 ATAA-ATATAATATTTAT
2178856 TTTATTTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 4 0.10
15 1 0.02
16 18 0.44
17 10 0.24
18 8 0.20
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAATATAATATTTAT
Found at i:2179073 original size:116 final size:115
Alignment explanation
Indices: 2178890--2179120 Score: 306
Period size: 116 Copynumber: 2.0 Consensus size: 115
2178880 TTTAATCTTG
* * * *
2178890 TTTTAATATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAACAACTGGATGTCCATTT
1 TTTTAATATTTATTTATTTTTCAATATGAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCATTT
* *
2178955 TCTGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATTAATT
66 TCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATATAAATT
* * *
2179005 TTTTAATTATTTATTTATTTTT-AATATCGAAGAAAAGAGCTGTCTTAAGACACCTAGAAGT-CA
1 TTTTAA-TATTTATTTATTTTTCAATAT-GAAG-AAAGAGCAGTCTTAAAACAACTAGAAGTCCA
**
2179068 TTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATT
63 TTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAATT
2179121 AATATATTTT
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
115 20 0.20
116 59 0.58
117 22 0.22
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (115 bp):
TTTTAATATTTATTTATTTTTCAATATGAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCATTT
TCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAATT
Found at i:2182733 original size:21 final size:20
Alignment explanation
Indices: 2182708--2182754 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
2182698 AGGTTATTCG
*
2182708 GGACAATACAGTGATCCTTC
1 GGACAATACAATGATCCTTC
*
2182728 GAGACAATACAATGGTCCTTC
1 G-GACAATACAATGATCCTTC
2182749 GGACAA
1 GGACAA
2182755 ATTTCATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
GGACAATACAATGATCCTTC
Found at i:2182891 original size:2 final size:2
Alignment explanation
Indices: 2182884--2182909 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2182874 ATCAAATACA
2182884 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2182910 GATGTATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2187503 original size:3 final size:3
Alignment explanation
Indices: 2187497--2187530 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
2187487 TAAATCAAAA
2187497 ATT ATT ATT ATT ATT ATT ATT A-T ATT ATTT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A
2187531 AAAATTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2188219 original size:14 final size:14
Alignment explanation
Indices: 2188200--2188226 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2188190 ACCGTTACGG
2188200 TGGCCGGCGGCGGT
1 TGGCCGGCGGCGGT
2188214 TGGCCGGCGGCGG
1 TGGCCGGCGGCGG
2188227 AGTACGGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.30, G:0.59, T:0.11
Consensus pattern (14 bp):
TGGCCGGCGGCGGT
Found at i:2189728 original size:20 final size:21
Alignment explanation
Indices: 2189705--2189756 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
2189695 AGAAATTAAA
2189705 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
2189725 AATTCTTTTCTTTAAAATTTTT
1 AATTCATTTATTT-AAATTTTT
2189747 -ATT-ATTTATT
1 AATTCATTTATT
2189757 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:2189767 original size:15 final size:15
Alignment explanation
Indices: 2189735--2189782 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
2189725 AATTCTTTTC
*
2189735 TTTAAAATTTTTATTA
1 TTTAATATTTTTA-TA
*
2189751 TTTATTATTTTTATA
1 TTTAATATTTTTATA
2189766 -TTAATATTGTTTATA
1 TTTAATATT-TTTATA
2189781 TT
1 TT
2189783 CAAATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 7 0.26
15 8 0.30
16 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTAATATTTTTATA
Found at i:2199408 original size:19 final size:19
Alignment explanation
Indices: 2199348--2199408 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
2199338 ATCTACACTT
*
2199348 TTAAAGATGATAGATTTCAC
1 TTAAAGATGATAGA-TTCTC
* * *
2199368 TTCAGAA-ATGACAAATTTTC
1 TT-A-AAGATGATAGATTCTC
2199388 TTAAAGATGATAGATTCTC
1 TTAAAGATGATAGATTCTC
2199407 TT
1 TT
2199409 TTCAAAGATG
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 7 0.23
21 7 0.23
22 2 0.06
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (19 bp):
TTAAAGATGATAGATTCTC
Found at i:2200334 original size:75 final size:76
Alignment explanation
Indices: 2200056--2201203 Score: 2030
Period size: 75 Copynumber: 15.5 Consensus size: 76
2200046 CTATTTCTCA
*
2200056 CATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200121 AGCCTTCGGGT
66 AGCCTTCGGGT
2200132 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200196 AGCCTTCGGG-
66 AGCCTTCGGGT
2200206 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200270 AGCCTTCGGGT
66 AGCCTTCGGGT
2200281 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200345 AGCCTTCGGGT
66 AGCCTTCGGGT
2200356 CATCTGTAAGTCCTTCAGTGC-TGATGTTTCC-AAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200419 AGCCTTCGGGT
66 AGCCTTCGGGT
2200430 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGTCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200493 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2200504 CATCTGTAAGTCCTTCAGTGTATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200569 AGCC-TCGGGT
66 AGCCTTCGGGT
2200579 CATCTGTAAG----TCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200639 AGCCTTCGGGT
66 AGCCTTCGGGT
2200650 CATCTGTAAGT-CTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200713 AGCCTTCGGGT
66 AGCCTTCGGGT
2200724 CATCTGTAAGTCCTTCAG-G--TGCATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATG-ATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCA
2200786 AAGCCTTCGGG-
65 AAGCCTTCGGGT
2200797 --TCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200859 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2200870 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTACGGGAGCTTTTTGATG-TTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200933 AGCCTTCGGGT
66 AGCCTTCGGGT
2200944 CATCTGTAAGTCCTTC-GTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2201008 AGCCTTC-GGT
66 AGCCTTCGGGT
2201018 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2201083 AGCCTTC-GGT
66 AGCCTTCGGGT
* *
2201093 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
*
2201158 AGCCTTAGGGT
66 AGCCTTCGGGT
2201169 CATCTGTAAGTCCTTCAGTGCATGATGTTT-CAAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAA
2201204 CCTTCGGGTC
Statistics
Matches: 1039, Mismatches: 8, Indels: 51
0.95 0.01 0.05
Matches are distributed among these distances:
70 10 0.01
71 75 0.07
72 28 0.03
73 112 0.11
74 335 0.32
75 371 0.36
76 108 0.10
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:2200343 original size:149 final size:151
Alignment explanation
Indices: 2200056--2201203 Score: 2031
Period size: 149 Copynumber: 7.7 Consensus size: 151
2200046 CTATTTCTCA
*
2200056 CATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200121 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
2200186 GATGTTTCAAAGCCTTCGGG-
131 GATGTTTCAAAGCCTTCGGGT
2200206 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200270 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGTCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
2200334 GATGTTTTCAAAGCCTTCGGGT
131 GATG-TTTCAAAGCCTTCGGGT
2200356 CATCTGTAAGTCCTTCAGTGC-TGATGTTTCC-AAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200419 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGTCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
2200483 GATGTTTCAAAGCCTTCGGGT
131 GATGTTTCAAAGCCTTCGGGT
*
2200504 CATCTGTAAGTCCTTCAGTGTATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200569 AGCC-TCGGGTCATCTGTAAG----TCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
2200629 GATGTTTCAAAGCCTTCGGGT
131 GATGTTTCAAAGCCTTCGGGT
2200650 CATCTGTAAGT-CTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2200713 AGCCTTCGGGTCATCTGTAAGTCCTTCAG-G--TGCATGTTTCCAAAAAGTCTTCGGGAGCTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATG-ATGTTTCCAAAAAGTCTTCGGGAGCTTTT
2200775 TGATGTTTTCAAAGCCTTCGGG-
130 TGATG-TTTCAAAGCCTTCGGGT
2200797 --TCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
*
2200859 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTACGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
2200924 GATGTTTC-AAGCCTTCGGGT
131 GATGTTTCAAAGCCTTCGGGT
2200944 CATCTGTAAGTCCTTC-GTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
2201008 AGCCTTC-GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
2201072 GATGTTTTCAAAGCCTTC-GGT
131 GATG-TTTCAAAGCCTTCGGGT
* *
2201093 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
*
2201158 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT-CAAAA
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAA
2201204 CCTTCGGGTC
Statistics
Matches: 964, Mismatches: 8, Indels: 52
0.94 0.01 0.05
Matches are distributed among these distances:
144 5 0.01
145 106 0.11
146 133 0.14
147 39 0.04
148 220 0.23
149 258 0.27
150 170 0.18
151 33 0.03
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (151 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTT
GATGTTTCAAAGCCTTCGGGT
Found at i:2201263 original size:45 final size:45
Alignment explanation
Indices: 2201146--2201291 Score: 240
Period size: 45 Copynumber: 3.3 Consensus size: 45
2201136 GGTAGCTTTT
* *
2201146 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
2201191 TGATG-TTTCAAAACCTTCGGGTCATCTGTAAGTCCTTTAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
2201235 TGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
2201280 TGATGTTTTCAA
1 TGATGTTTTCAA
2201292 CATTCCTCCT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 41 0.44
45 53 0.56
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:2201439 original size:3 final size:3
Alignment explanation
Indices: 2201433--2201460 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2201423 AAAATCAAAA
2201433 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2201461 TATATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2201475 original size:9 final size:10
Alignment explanation
Indices: 2201433--2201476 Score: 56
Period size: 9 Copynumber: 4.5 Consensus size: 10
2201423 AAAATCAAAA
2201433 TATTATTA-T
1 TATTATTATT
2201442 TATTATTA-T
1 TATTATTATT
2201451 TATTATTATT
1 TATTATTATT
*
2201461 TATATTTTATT
1 TAT-TATTATT
2201472 TATTA
1 TATTA
2201477 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 17 0.55
10 5 0.16
11 9 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTATTATT
Found at i:2202172 original size:14 final size:14
Alignment explanation
Indices: 2202153--2202179 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2202143 ACCGTTACGG
2202153 TGGCCGGCGGCGGT
1 TGGCCGGCGGCGGT
2202167 TGGCCGGCGGCGG
1 TGGCCGGCGGCGG
2202180 AGTACGGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.30, G:0.59, T:0.11
Consensus pattern (14 bp):
TGGCCGGCGGCGGT
Found at i:2203167 original size:108 final size:110
Alignment explanation
Indices: 2202969--2203167 Score: 285
Period size: 109 Copynumber: 1.8 Consensus size: 110
2202959 TATTTGATAT
* * * *
2202969 TATTTATTTTTAATATCAAAGAAAAAAGTTGTCTTAAGGTACCTAGAAGCTCTTTTCTGATATTT
1 TATTTATTTTAAATATCAAAGAAAAAAGCTGTCTTAAAGTACCTAGAAGCTCCTTTCTGATATTT
* * *
2203034 TTGAATAAATAAATATCTTACTATATTAAAATAAAAGGTTTTTGA
66 CTAAATAAATAAATATATTACTATATTAAAATAAAAGGTTTTTGA
* *
2203079 TATTTA-TTTAAATATTAAAGAAAAGAGCTGTCTTAAAGTACCTAGAAGC-CCTTTCTGATATTT
1 TATTTATTTTAAATATCAAAGAAAAAAGCTGTCTTAAAGTACCTAGAAGCTCCTTTCTGATATTT
* *
2203142 CTAAATAAGTAAATATATTATTATAT
66 CTAAATAAATAAATATATTACTATAT
2203168 ATTAATATAT
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
108 34 0.44
109 38 0.49
110 6 0.08
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (110 bp):
TATTTATTTTAAATATCAAAGAAAAAAGCTGTCTTAAAGTACCTAGAAGCTCCTTTCTGATATTT
CTAAATAAATAAATATATTACTATATTAAAATAAAAGGTTTTTGA
Found at i:2206419 original size:107 final size:106
Alignment explanation
Indices: 2206226--2206442 Score: 418
Period size: 107 Copynumber: 2.0 Consensus size: 106
2206216 ATTTTTACCC
2206226 GAAG-AAAAATGCAAACTAAACCAATTTGGACTATTAACAAGCTGTTCTCTACTTGATATATTAA
1 GAAGAAAAAATGCAAACTAAACCAATTTGGACTATTAACAAGCTGTTCTCTACTTGATATATTAA
2206290 TGTAATGCTCCAAGGTACTATAGCAAAGTCGAGTGGCTTAA
66 TGTAATGCTCCAAGGTACTATAGCAAAGTCGAGTGGCTTAA
2206331 GAAGAAAATAATGCAAACTAAACCAATTTGGACTATTAACAAGCTGTTCTCTACTTGATATATTA
1 GAAGAAAA-AATGCAAACTAAACCAATTTGGACTATTAACAAGCTGTTCTCTACTTGATATATTA
2206396 ATGTAATGCTCCAAGGTACTATAGCAAAGTCGAGTGGCTTAA
65 ATGTAATGCTCCAAGGTACTATAGCAAAGTCGAGTGGCTTAA
2206438 GAAGA
1 GAAGA
2206443 TACTAATTCA
Statistics
Matches: 110, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
105 4 0.04
106 3 0.03
107 103 0.94
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (106 bp):
GAAGAAAAAATGCAAACTAAACCAATTTGGACTATTAACAAGCTGTTCTCTACTTGATATATTAA
TGTAATGCTCCAAGGTACTATAGCAAAGTCGAGTGGCTTAA
Found at i:2211847 original size:41 final size:40
Alignment explanation
Indices: 2211796--2211933 Score: 136
Period size: 41 Copynumber: 3.4 Consensus size: 40
2211786 TTTATAGCTA
*
2211796 AAACGCCGCAATAGAGATGTTTATAGTGGCGTTTTTTCAAC
1 AAACGTCGCAATAGAG-TGTTTATAGTGGCGTTTTTTCAAC
* *
2211837 AAACGTCGCAATAGAGTGGTAATT-TAGCGGCGTTTTTAC-AC
1 AAACGTCGCAATAGAGT-GT--TTATAGTGGCGTTTTTTCAAC
* * * *
2211878 AAACGTCGCGATAGTGTTGTTTATATTGGCGTTTGTTCAAC
1 AAACGTCGCAATAGAG-TGTTTATAGTGGCGTTTTTTCAAC
* *
2211919 AAACGACGCTATAGA
1 AAACGTCGCAATAGA
2211934 TAAGTAATTT
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
39 2 0.03
40 12 0.15
41 49 0.62
42 14 0.18
43 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (40 bp):
AAACGTCGCAATAGAGTGTTTATAGTGGCGTTTTTTCAAC
Found at i:2218151 original size:44 final size:44
Alignment explanation
Indices: 2218087--2218200 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 44
2218077 GTGTTATTTA
***
2218087 GCGGCGTTTGTATAAAAAAAACGCCGCTATATAT-AAGACCTATC
1 GCGGCGTTTGTATCCTAAAAACGCCGCTATAT-TCAAGACCTATC
* * * *
2218131 GCGGCGTTTGTATCCTAAAAACGGCACTATATTCCAGTCCTATC
1 GCGGCGTTTGTATCCTAAAAACGCCGCTATATTCAAGACCTATC
*
2218175 GCGGCGTTTGTACCCTAAAAACGCCG
1 GCGGCGTTTGTATCCTAAAAACGCCG
2218201 TTAAATACCA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.02
44 58 0.98
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (44 bp):
GCGGCGTTTGTATCCTAAAAACGCCGCTATATTCAAGACCTATC
Found at i:2218217 original size:44 final size:44
Alignment explanation
Indices: 2218124--2218227 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 44
2218114 TATATATAAG
* * * * *
2218124 ACCTATCGCGGCGTTTGTATCCTAAAAACGGCACTATATTCCAG
1 ACCTATCGCGGCGTTTGTACCCTAAAAACGCCACTAAATACCAA
* **
2218168 TCCTATCGCGGCGTTTGTACCCTAAAAACGCCGTTAAATACCAA
1 ACCTATCGCGGCGTTTGTACCCTAAAAACGCCACTAAATACCAA
* *
2218212 ACCTATTGCGCCGTTT
1 ACCTATCGCGGCGTTT
2218228 TCATAAAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (44 bp):
ACCTATCGCGGCGTTTGTACCCTAAAAACGCCACTAAATACCAA
Found at i:2218388 original size:43 final size:43
Alignment explanation
Indices: 2218279--2218418 Score: 156
Period size: 43 Copynumber: 3.2 Consensus size: 43
2218269 TTTGTGATAA
* * * * *
2218279 AAACGCCGCTAAATATTGACACCAATTGCGGCATTT-TTAAGAC
1 AAACGCCGCTAAATATCGATACCTATTGCGGCGTTTGTTTA-AC
*
2218322 AAACGCCGCTAAATATCGGTACCTATTGCGGCGTTTGTTTAAC
1 AAACGCCGCTAAATATCGATACCTATTGCGGCGTTTGTTTAAC
* * * *
2218365 AAACGCCGCTATATATCGTTACCTATTGTGGCGTTTTTGGTTAAC
1 AAACGCCGCTAAATATCGATACCTATTGCGGCG--TTTGTTTAAC
2218410 AAACGCCGC
1 AAACGCCGC
2218419 GAACTTTAGC
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
43 63 0.75
44 3 0.04
45 18 0.21
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAATATCGATACCTATTGCGGCGTTTGTTTAAC
Found at i:2219381 original size:20 final size:20
Alignment explanation
Indices: 2219382--2219432 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2219372 TTCGGGTCAA
*
2219382 TTCGGGTCAACGTTTAGATT
1 TTCGGGTCAACCTTTAGATT
*
2219402 TTCGAGTCAACCTTTAGATT
1 TTCGGGTCAACCTTTAGATT
*
2219422 TTCAGGTCAAC
1 TTCGGGTCAAC
2219433 TGGTGTCGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
TTCGGGTCAACCTTTAGATT
Found at i:2219897 original size:23 final size:23
Alignment explanation
Indices: 2219871--2219934 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
2219861 TAATTTCGGT
*
2219871 TTGGGTTGCTTTCGGTTCGACTA
1 TTGGGTTACTTTCGGTTCGACTA
* * * *
2219894 TTGGGTTACTCTCTGTTCGAGTT
1 TTGGGTTACTTTCGGTTCGACTA
2219917 TTGGGTTACTTTCGGTTC
1 TTGGGTTACTTTCGGTTC
2219935 AGATTGATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (23 bp):
TTGGGTTACTTTCGGTTCGACTA
Found at i:2221327 original size:31 final size:31
Alignment explanation
Indices: 2221289--2221465 Score: 115
Period size: 31 Copynumber: 5.3 Consensus size: 31
2221279 ATAATAATCG
*
2221289 AGTGACCAAAACATAAATTAGATGATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
* ** * *
2221320 AGTGACCAAATA-AGCAGTTTAGCCTAAATAATAATCG
1 AGTGACCAAA-ACA-TAAATTAG-AT-AAT-AT-AT-A
2221357 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
** * *
2221388 AGTGACCAAATAGGCAGTTTACCTTAAATAATA-ATCG
1 AGTGACCAAA-A--CA---TAAATTAGATAATATAT-A
*
2221425 AGTGACCAAAACATAAATTAGATAATATAAA
1 AGTGACCAAAACATAAATTAGATAATATATA
2221456 AGTGACCAAA
1 AGTGACCAAA
2221466 TAGGTAGTTT
Statistics
Matches: 110, Mismatches: 20, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
31 42 0.38
32 10 0.09
33 3 0.03
34 9 0.08
35 3 0.03
36 11 0.10
37 32 0.29
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (31 bp):
AGTGACCAAAACATAAATTAGATAATATATA
Found at i:2221346 original size:68 final size:68
Alignment explanation
Indices: 2221184--2221548 Score: 526
Period size: 68 Copynumber: 5.4 Consensus size: 68
2221174 TGACCAAAAC
* * * * *
2221184 ATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAAAAT--A-T-A-TATGAA-TTATATTAGA
1 ATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCA-AAACATAAATTAGA
2221243 TAAT
65 TAAT
2221247 ATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCAAAACATAAATTAGAT
1 ATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCAAAACATAAATTAGAT
*
2221312 GAT
66 AAT
* * *
2221315 ATATAAGTGACCAAATAAGCAGTTTAGCCTAAATAATAATCGAGTGACCAAAACATAAATTAGAT
1 ATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCAAAACATAAATTAGAT
2221380 AAT
66 AAT
* *
2221383 ATATAAGTGACCAAATAGGCAGTTTACCTTAAATAATAATCGAGTGACCAAAACATAAATTAGAT
1 ATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCAAAACATAAATTAGAT
2221448 AAT
66 AAT
* * * *
2221451 ATAAAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACAAAAATAGAAATTAGAT
1 ATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCAAAACATAAATTAGAT
2221516 AAT
66 AAT
* *
2221519 ATATAAGTGATCAAATAAGTAGTTTACCCT
1 ATATAAGTGACCAAATAGGTAGTTTACCCT
2221549 TAAAAAAATC
Statistics
Matches: 274, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
63 39 0.14
65 1 0.00
66 1 0.00
67 3 0.01
68 230 0.84
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (68 bp):
ATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCAAAACATAAATTAGAT
AAT
Found at i:2222118 original size:22 final size:22
Alignment explanation
Indices: 2222059--2222118 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
2222049 TTTTTTTCTA
2222059 CTTTTATGGCATGTTTCCTATG
1 CTTTTATGGCATGTTTCCTATG
* * *
2222081 CCTTTATGACATGTTTCTTATG
1 CTTTTATGGCATGTTTCCTATG
*
2222103 CTTTTATGGCACGTTT
1 CTTTTATGGCATGTTT
2222119 TTGGTCATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.15, C:0.18, G:0.17, T:0.50
Consensus pattern (22 bp):
CTTTTATGGCATGTTTCCTATG
Found at i:2223331 original size:20 final size:21
Alignment explanation
Indices: 2223289--2223333 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2223279 AAATGGAAAC
2223289 TCGCAACGCGATTTTCAACTA
1 TCGCAACGCGATTTTCAACTA
2223310 TCGCAACGCGATTTTC-ACTA
1 TCGCAACGCGATTTTCAACTA
2223330 TCGC
1 TCGC
2223334 GATAGTGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (21 bp):
TCGCAACGCGATTTTCAACTA
Found at i:2224170 original size:22 final size:22
Alignment explanation
Indices: 2224140--2224261 Score: 217
Period size: 22 Copynumber: 5.5 Consensus size: 22
2224130 TAATTATTAT
*
2224140 TTTTTAATTTTTCAATGAATGG
1 TTTTTAATTTTTCAATGAATGC
*
2224162 TGTTTAATTTTTCAATGAATGC
1 TTTTTAATTTTTCAATGAATGC
2224184 TTTTTAATTTTTCAATGAATGC
1 TTTTTAATTTTTCAATGAATGC
2224206 TTTTTAATTTTTCAATGAATGC
1 TTTTTAATTTTTCAATGAATGC
*
2224228 TTATTAATTTTTCAATGAATGC
1 TTTTTAATTTTTCAATGAATGC
2224250 TTTTTAATTTTT
1 TTTTTAATTTTT
2224262 TTACCAAACG
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 95 1.00
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTTTAATTTTTCAATGAATGC
Found at i:2224815 original size:25 final size:25
Alignment explanation
Indices: 2224787--2224842 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
2224777 TTAGAAAAGT
2224787 ATTATACCCAATTCATATTAAGATA
1 ATTATACCCAATTCATATTAAGATA
2224812 ATTATACCCAATTCATATTAAGATA
1 ATTATACCCAATTCATATTAAGATA
2224837 ATTATA
1 ATTATA
2224843 ATTTTCTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.38
Consensus pattern (25 bp):
ATTATACCCAATTCATATTAAGATA
Found at i:2224953 original size:24 final size:24
Alignment explanation
Indices: 2224936--2224984 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
2224926 AAAATGAGTT
2224936 ATTATAAAT-TATTAAAAATAAATA
1 ATTA-AAATATATTAAAAATAAATA
2224960 ATTAAAATATATTAAAAATTAAATA
1 ATTAAAATATATTAAAAA-TAAATA
2224985 TTTTCATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 13 0.57
25 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
ATTAAAATATATTAAAAATAAATA
Found at i:2228841 original size:21 final size:21
Alignment explanation
Indices: 2228817--2228856 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2228807 AAGACTATTT
2228817 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTGAAACA
**
2228838 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
2228857 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAACA
Found at i:2240824 original size:23 final size:22
Alignment explanation
Indices: 2240789--2240842 Score: 90
Period size: 23 Copynumber: 2.4 Consensus size: 22
2240779 ATTTTGATTC
2240789 GATTCAAACATGAAATCAACTTT
1 GATTC-AACATGAAATCAACTTT
2240812 GATTCAACGATGAAATCAACTTT
1 GATTCAAC-ATGAAATCAACTTT
2240835 GATTCAAC
1 GATTCAAC
2240843 CTTATACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (22 bp):
GATTCAACATGAAATCAACTTT
Found at i:2245777 original size:22 final size:22
Alignment explanation
Indices: 2245746--2245795 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2245736 CATACCCGAA
**
2245746 ATATA-ATTCATGATAAGTATC
1 ATATATATTCATGATAAACATC
2245767 ATATATATTCATGATAAACATC
1 ATATATATTCATGATAAACATC
2245789 ATATATA
1 ATATATA
2245796 ATGATAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (22 bp):
ATATATATTCATGATAAACATC
Found at i:2248850 original size:25 final size:25
Alignment explanation
Indices: 2248822--2248875 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
2248812 TATATTTAGG
*
2248822 TTTATCTTAAAATATATTATTTTTA
1 TTTATCATAAAATATATTATTTTTA
*
2248847 TTTA-GATAAAATATATTATTTTTA
1 TTTATCATAAAATATATTATTTTTA
2248871 TTTAT
1 TTTAT
2248876 ATATTTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTATCATAAAATATATTATTTTTA
Found at i:2248856 original size:24 final size:24
Alignment explanation
Indices: 2248829--2248874 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2248819 AGGTTTATCT
2248829 TAAAATATATTATTTTTATTTAGA
1 TAAAATATATTATTTTTATTTAGA
2248853 TAAAATATATTATTTTTATTTA
1 TAAAATATATTATTTTTATTTA
2248875 TATATTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TAAAATATATTATTTTTATTTAGA
Found at i:2257512 original size:23 final size:23
Alignment explanation
Indices: 2257486--2257534 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2257476 AGCATCGAGC
2257486 TGCCTTTGGTCCAAGTGTTGAGA
1 TGCCTTTGGTCCAAGTGTTGAGA
2257509 TGCCTTTGGTCCAAGTGTTGAGA
1 TGCCTTTGGTCCAAGTGTTGAGA
2257532 TGC
1 TGC
2257535 ATCCACCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.35
Consensus pattern (23 bp):
TGCCTTTGGTCCAAGTGTTGAGA
Found at i:2259889 original size:2 final size:2
Alignment explanation
Indices: 2259884--2259909 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2259874 ATTATATAGC
2259884 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2259910 GCTAAGTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2260075 original size:48 final size:48
Alignment explanation
Indices: 2260016--2260111 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
2260006 TCTATATAGA
2260016 TACATCATACATTGGATATAAAAAATGAAAAGCAAATCACGGTATACT
1 TACATCATACATTGGATATAAAAAATGAAAAGCAAATCACGGTATACT
*
2260064 TACATCGTACATTGGATATAAAAAATGAAAAGCAAATCACGGTATACT
1 TACATCATACATTGGATATAAAAAATGAAAAGCAAATCACGGTATACT
2260112 GAGTTCAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.25
Consensus pattern (48 bp):
TACATCATACATTGGATATAAAAAATGAAAAGCAAATCACGGTATACT
Found at i:2261461 original size:39 final size:39
Alignment explanation
Indices: 2261221--2261810 Score: 749
Period size: 39 Copynumber: 15.1 Consensus size: 39
2261211 TGACAAAATT
* * * *
2261221 TGTTTCAAGGGAAACTGTCTCAAGAGAGAGAAAA--TT-
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
2261257 TGTTTCGAGGG-AACTTGTCTCAAGCGAGATAAAATCTTC
1 TGTTTCGAGGGAAAC-TATCTCAAGCGAGATAAAATCTTC
* *
2261296 TGTTTCGAGGGAAACATGTCTCAAGCGAGATAAAATCATC
1 TGTTTCGAGGGAAAC-TATCTCAAGCGAGATAAAATCTTC
*
2261336 TGTTTCGAGGGAAACATGTCTCAAGCGAGATAAAATCTTC
1 TGTTTCGAGGGAAAC-TATCTCAAGCGAGATAAAATCTTC
* * * * *
2261376 TGTTTCGAGGGAAACATGTCTCAAGTGAGACAATATCTTT
1 TGTTTCGAGGGAAAC-TATCTCAAGCGAGATAAAATCTTC
* *
2261416 TGTTTCGAGGGAAACTATCTTAAGCGAGACAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
2261455 TATTTCGAGGGAAACTATCTCAAGCGAGAAAAAATCTTT
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
2261494 TGTTTCGAGGAAAACTATCTCAAGAGAGACAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * * *
2261533 TGTTTCAAGGAAAACTATCTCAAGAGAGACAAAATATTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
2261572 TTTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
2261611 TGTTTCAAGGGAAACTATCTCAAGCAAGACAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
2261650 TGTTT-GAAGGGAAACTATCTCAAACGAGATAAAATCTTC
1 TGTTTCG-AGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
2261689 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATATTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
2261728 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
2261767 TATTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
2261806 TGTTT
1 TGTTT
2261811 AAAGGAAAAA
Statistics
Matches: 504, Mismatches: 43, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
35 3 0.01
36 27 0.05
38 2 0.00
39 356 0.71
40 116 0.23
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (39 bp):
TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
Found at i:2262026 original size:77 final size:76
Alignment explanation
Indices: 2261900--2262046 Score: 215
Period size: 77 Copynumber: 1.9 Consensus size: 76
2261890 ACATGTAGTG
* * * *
2261900 AAATGAAATGTCTTGTTTTGAATAAAATCCGTTTCAAGCGAGACAAATCTTGTATTAAGAAAAAT
1 AAATGAAATGTCTTCTTTCGAATAAAATCCGTCTCAAGCGAGACAAATCTTGTATTAAGAAAAAC
2261965 AATCTTGAGTC
66 AATCTTGAGTC
* *
2261976 AAATGAAATGTTCTTCTTTCGAGTAAAAAT-CGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAA
1 AAATGAAATG-TCTTCTTTCGAAT-AAAATCCGTCTCAAGCGAGACAAATCTTGTATTAAGAAAA
2262040 ACAATCT
64 ACAATCT
2262047 CCAGTGAGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 10 0.16
77 48 0.76
78 5 0.08
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (76 bp):
AAATGAAATGTCTTCTTTCGAATAAAATCCGTCTCAAGCGAGACAAATCTTGTATTAAGAAAAAC
AATCTTGAGTC
Done.