Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 131 of 211
Found at i:41508512 original size:9 final size:9
Alignment explanation
Indices: 41508494--41508535 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
41508484 ATTCTCAAAT
41508494 AATA-TCAA
1 AATATTCAA
41508502 AATATTCAA
1 AATATTCAA
41508511 AATATTCAA
1 AATATTCAA
41508520 AATATTCAA
1 AATATTCAA
*
41508529 AAAATTC
1 AATATTC
41508536 TATTTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 4 0.12
9 28 0.88
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (9 bp):
AATATTCAA
Found at i:41508562 original size:25 final size:24
Alignment explanation
Indices: 41508525--41508649 Score: 136
Period size: 25 Copynumber: 5.3 Consensus size: 24
41508515 TTCAAAATAT
41508525 TCAAA-AAATTCTATTTTATTACA
1 TCAAATAAATTCTATTTTATTACA
41508548 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAA-TTCTATTTTATTACA
** *
41508573 TCAAAT-AATATC-A--AAATAAC-
1 TCAAATAAAT-TCTATTTTATTACA
* *
41508593 TAAAAAAAATTCTATTTTATTACA
1 TCAAATAAATTCTATTTTATTACA
41508617 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAA-TTCTATTTTATTACA
41508642 TCAAATAA
1 TCAAATAA
41508650 TATCAAAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.07
21 8 0.10
23 11 0.13
24 14 0.17
25 44 0.53
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (24 bp):
TCAAATAAATTCTATTTTATTACA
Found at i:41508609 original size:69 final size:69
Alignment explanation
Indices: 41508527--41508659 Score: 266
Period size: 69 Copynumber: 1.9 Consensus size: 69
41508517 CAAAATATTC
41508527 AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
1 AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
41508592 CTAA
66 CTAA
41508596 AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
1 AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
41508660 TTCAAAATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (69 bp):
AAAAAATTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
CTAA
Found at i:41509101 original size:18 final size:18
Alignment explanation
Indices: 41509078--41509117 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41509068 GACTCGGAAA
*
41509078 AGGATACAAATAAGGGTT
1 AGGATACAAATAAGGGCT
*
41509096 AGGATACATATAAGGGCT
1 AGGATACAAATAAGGGCT
41509114 AGGA
1 AGGA
41509118 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.30, T:0.20
Consensus pattern (18 bp):
AGGATACAAATAAGGGCT
Found at i:41509778 original size:7 final size:7
Alignment explanation
Indices: 41509768--41509792 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41509758 TTATATACAT
41509768 AATACTA
1 AATACTA
41509775 AATACTA
1 AATACTA
41509782 AATACTA
1 AATACTA
41509789 AATA
1 AATA
41509793 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:41510000 original size:20 final size:20
Alignment explanation
Indices: 41509963--41510000 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41509953 TTTATTTTTA
*
41509963 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
41509983 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
41510001 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:41510918 original size:12 final size:12
Alignment explanation
Indices: 41510894--41510936 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
41510884 ATTTTTACGG
41510894 TTTAAAAAA-AT
1 TTTAAAAAATAT
41510905 TTTAAAAAATAT
1 TTTAAAAAATAT
* *
41510917 TTTTAAAATTA-
1 TTTAAAAAATAT
41510928 TTTAAAAAA
1 TTTAAAAAA
41510937 AGGGAGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTAAAAAATAT
Found at i:41513526 original size:44 final size:44
Alignment explanation
Indices: 41513463--41513568 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
41513453 TGTAGGCTTT
* * * *
41513463 CAAAAAATGCTCAAATCACCTAAACTCGAAATACTGAGTCATCC
1 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
41513507 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
1 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
41513551 CAAAACATGCTCAATATC
1 CAAAACATGCTC-ATATC
41513569 TCTACTTCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 52 0.91
45 5 0.09
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (44 bp):
CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
Found at i:41513856 original size:14 final size:14
Alignment explanation
Indices: 41513839--41513882 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
41513829 GGTGCAGGAC
*
41513839 TGGAGGTGGACCGG
1 TGGAGGTGGATCGG
*
41513853 TGGAGGTGGATCAG
1 TGGAGGTGGATCGG
41513867 TGGAGGTGGATCGG
1 TGGAGGTGGATCGG
41513881 TG
1 TG
41513883 CTCGGTGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.16, C:0.09, G:0.55, T:0.20
Consensus pattern (14 bp):
TGGAGGTGGATCGG
Found at i:41533009 original size:9 final size:9
Alignment explanation
Indices: 41532997--41533036 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
41532987 ATTCGGTCGG
41532997 TTAACCGAA
1 TTAACCGAA
*
41533006 TTAACCTAA
1 TTAACCGAA
*
41533015 TTACCCGAA
1 TTAACCGAA
*
41533024 TTACCCGAA
1 TTAACCGAA
41533033 TTAA
1 TTAA
41533037 TCAATTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (9 bp):
TTAACCGAA
Found at i:41533188 original size:18 final size:18
Alignment explanation
Indices: 41533165--41533208 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
41533155 AATTTTTATG
*
41533165 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
41533183 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
41533201 GTTGGGTT
1 ATTGGGTT
41533209 TGGATTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.00, G:0.48, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:41535666 original size:178 final size:177
Alignment explanation
Indices: 41535367--41535717 Score: 639
Period size: 178 Copynumber: 2.0 Consensus size: 177
41535357 CAATGGTAAC
* *
41535367 AATGAGATAAAATAGGATTGTATTGAGTGAACGGATTTAACTCAAAGGAATCAAGGATATCATAT
1 AATGAGATAAAATAGGATTGTATTGAGTGAACAGATTTAACTCAAAAGAATCAAGGATATCATAT
*
41535432 GAGGGTAACACACACATGACGAGATTAGTGGACAAAGCAGTTGGATGAATTGCTTTCATAAAGAG
66 GAGGGTAACACACACATGACGAGATCAGTGGACAAAGCAGTTGGATGAATTGCTTTCATAAAGAG
*
41535497 TATACAATGAGGAGTTTTCAATCATGGTACTTCTTGTGGACTGATGAT
131 TATACAAT-AAGAGTTTTCAATCATGGTACTTCTTGTGGACTGATGAT
41535545 AATGAGATAAAATAGGATTGTATTGAGTGAACAGATTTAACTCAAAAGAATCAAGGATATCATAT
1 AATGAGATAAAATAGGATTGTATTGAGTGAACAGATTTAACTCAAAAGAATCAAGGATATCATAT
* *
41535610 GAGGGTAACACACACATGACGAGATCATTGGACAAAGCAGTTGGATGAATTGCTTTCGTAAAGAG
66 GAGGGTAACACACACATGACGAGATCAGTGGACAAAGCAGTTGGATGAATTGCTTTCATAAAGAG
41535675 TATACAATAAGAGTTTTCAATCATGGTACTTCTTGTGGACTGA
131 TATACAATAAGAGTTTTCAATCATGGTACTTCTTGTGGACTGA
41535718 CTCCATGATT
Statistics
Matches: 167, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
177 34 0.20
178 133 0.80
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (177 bp):
AATGAGATAAAATAGGATTGTATTGAGTGAACAGATTTAACTCAAAAGAATCAAGGATATCATAT
GAGGGTAACACACACATGACGAGATCAGTGGACAAAGCAGTTGGATGAATTGCTTTCATAAAGAG
TATACAATAAGAGTTTTCAATCATGGTACTTCTTGTGGACTGATGAT
Found at i:41538705 original size:25 final size:26
Alignment explanation
Indices: 41538655--41538707 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
41538645 AGTTGTAGAG
41538655 AGAAAATTCTCTAAAGAGATTATTCT
1 AGAAAATTCTCTAAAGAGATTATTCT
* * *
41538681 AGAAAATT-TCTAGAGATATTTTTCT
1 AGAAAATTCTCTAAAGAGATTATTCT
41538706 AG
1 AG
41538708 TTTACAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTCT
Found at i:41542503 original size:26 final size:26
Alignment explanation
Indices: 41542469--41542529 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
41542459 TATCCGAAGC
* *
41542469 TCCTGATTAAATGCTCTTTGTGAGCT
1 TCCTGATTAAAAGCTCTTTGTGAACT
* *
41542495 TCCTAATTAAAAGTTCTTTGTGAACT
1 TCCTGATTAAAAGCTCTTTGTGAACT
41542521 TCCTGATTA
1 TCCTGATTA
41542530 TGGCTCTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (26 bp):
TCCTGATTAAAAGCTCTTTGTGAACT
Found at i:41542590 original size:25 final size:25
Alignment explanation
Indices: 41542543--41542599 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
41542533 CTCTTATGAG
* *
41542543 CTTCTTGTTATATAGCCCGGATAAA
1 CTTCCTGTTATATAGCCCAGATAAA
* *
41542568 CTTCCTGTTATATAGCTCAGATAAG
1 CTTCCTGTTATATAGCCCAGATAAA
41542593 CTTCCTG
1 CTTCCTG
41542600 ATAGGCTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (25 bp):
CTTCCTGTTATATAGCCCAGATAAA
Found at i:41542658 original size:26 final size:26
Alignment explanation
Indices: 41542481--41542658 Score: 63
Period size: 25 Copynumber: 7.1 Consensus size: 26
41542471 CTGATTAAAT
* **
41542481 GCTCTTTGTGAGCTTCCTAATTA-AAA
1 GCTCTTTGTGAGCTTCCT-GTTATATG
* * *
41542507 GTTCTTTGTGAACTTCCTGAT-TATG
1 GCTCTTTGTGAGCTTCCTGTTATATG
* * *
41542532 GCTC-TTATGAGCTTCTTGTTATATA
1 GCTCTTTGTGAGCTTCCTGTTATATG
** * * *
41542557 GC-C-CGGATAAACTTCCTGTTATATA
1 GCTCTTTG-TGAGCTTCCTGTTATATG
* *
41542582 GCTC--AGATAAGCTTCCTG--ATA-G
1 GCTCTTTG-TGAGCTTCCTGTTATATG
* ** *
41542604 GCTCTTTGTGAGCTTTTCAATTA-AAG
1 GCTCTTTGTGAGC-TTCCTGTTATATG
41542630 GCTCTTTGTGAGCTTCCTGTTATATG
1 GCTCTTTGTGAGCTTCCTGTTATATG
41542656 GCT
1 GCT
41542659 TGAGAGAGGA
Statistics
Matches: 111, Mismatches: 30, Indels: 22
0.68 0.18 0.13
Matches are distributed among these distances:
22 4 0.04
23 7 0.06
24 17 0.15
25 46 0.41
26 37 0.33
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (26 bp):
GCTCTTTGTGAGCTTCCTGTTATATG
Found at i:41555635 original size:22 final size:22
Alignment explanation
Indices: 41555581--41555641 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
41555571 ATAATTATTT
* *
41555581 TTTATAA-ATATATATTTAATG
1 TTTATAATATAAATATTTAATA
*
41555602 TTT-TAATGATAAATATTTACTA
1 TTTATAAT-ATAAATATTTAATA
41555624 TTTATAATATAAAATATT
1 TTTATAATAT-AAATATT
41555642 AAACAATGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.09
21 3 0.09
22 16 0.48
23 11 0.33
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTATAATATAAATATTTAATA
Found at i:41557420 original size:17 final size:17
Alignment explanation
Indices: 41557395--41557443 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
41557385 ATTGATTCTT
*
41557395 AAAATTTTAAAAATTAA
1 AAAAATTTAAAAATTAA
41557412 AAAAATTT-AAAA-TAA
1 AAAAATTTAAAAATTAA
41557427 AAAATTATTTAAAAATT
1 AAAA--ATTTAAAAATT
41557444 TATTTTTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 7 0.26
16 4 0.15
17 11 0.41
18 4 0.15
19 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAATTTAAAAATTAA
Found at i:41558081 original size:17 final size:18
Alignment explanation
Indices: 41558042--41558084 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
41558032 TGTGGTGTTT
41558042 TAAAAATATTATTTTATGTA
1 TAAAAATATTATTTTA--TA
*
41558062 TAAAATTATTATTTTA-A
1 TAAAAATATTATTTTATA
41558079 TAAAAA
1 TAAAAA
41558085 AATTTCGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
20 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAAAAATATTATTTTATA
Found at i:41570777 original size:52 final size:50
Alignment explanation
Indices: 41570632--41570843 Score: 229
Period size: 52 Copynumber: 4.3 Consensus size: 50
41570622 ATAGTAAAAT
* * *
41570632 TATGGTCTTACACA-TAGTCACATATCACAT-ACCGAGGCCATAGCCCAGC
1 TATGGTCTTATACAGTAG-CACATATCACATCTCCGAAGCCATAGCCCAGC
* * * * * *
41570681 CATGGTCTTATAC-GGATCACATATCACA-CT--GATGCCATATCCCAGA
1 TATGGTCTTATACAGTAGCACATATCACATCTCCGAAGCCATAGCCCAGC
41570727 TATGGTCTTATACAGTAGCACATATCACATTTCTCCGAAGCCATAGCCCAGC
1 TATGGTCTTATACAGTAGCACATATCACA--TCTCCGAAGCCATAGCCCAGC
* * *
41570779 TATGGTCTTATACGGAAGCACAAATCACATTTCTCCGAAGCCATAGCCCAGC
1 TATGGTCTTATACAGTAGCACATATCACA--TCTCCGAAGCCATAGCCCAGC
41570831 TATGGTCTTATAC
1 TATGGTCTTATAC
41570844 GGAAATCACA
Statistics
Matches: 138, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
46 25 0.18
47 13 0.09
48 11 0.08
49 12 0.09
50 2 0.01
52 75 0.54
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (50 bp):
TATGGTCTTATACAGTAGCACATATCACATCTCCGAAGCCATAGCCCAGC
Found at i:41574721 original size:4 final size:4
Alignment explanation
Indices: 41574712--41574750 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
41574702 CTAAGAAGTA
*
41574712 TATG TATG TATA TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
41574751 TGAAGTGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:41583597 original size:28 final size:27
Alignment explanation
Indices: 41583545--41583597 Score: 63
Period size: 26 Copynumber: 1.9 Consensus size: 27
41583535 AATTAATTCA
* *
41583545 AAATCTATATTTCAGCATCCTAATATC
1 AAATCTATATGTCAGCATCCAAATATC
41583572 AAAT-TATATGTCATGCATGCCAAATA
1 AAATCTATATGTCA-GCAT-CCAAATA
41583598 AACCTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 8 0.36
27 8 0.36
28 6 0.27
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (27 bp):
AAATCTATATGTCAGCATCCAAATATC
Found at i:41584783 original size:17 final size:17
Alignment explanation
Indices: 41584761--41584805 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
41584751 ATTTCAGGGG
41584761 CACATGGTCGTATGGTC
1 CACATGGTCGTATGGTC
41584778 CACATGGTCGTATGGTC
1 CACATGGTCGTATGGTC
*
41584795 CACATGCTCGT
1 CACATGGTCGT
41584806 GTGAAAGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (17 bp):
CACATGGTCGTATGGTC
Found at i:41595299 original size:18 final size:18
Alignment explanation
Indices: 41595284--41595318 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41595274 CAGCCCAATA
*
41595284 CCATCATTTGGCCCAAAG
1 CCATCAATTGGCCCAAAG
41595302 CCATCAATTGGCCCAAA
1 CCATCAATTGGCCCAAA
41595319 ATTACGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.34, G:0.14, T:0.20
Consensus pattern (18 bp):
CCATCAATTGGCCCAAAG
Found at i:41595351 original size:15 final size:15
Alignment explanation
Indices: 41595331--41595360 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41595321 TACGAGTAAG
41595331 TCCACCATTAGGCCC
1 TCCACCATTAGGCCC
*
41595346 TCCACCATTCGGCCC
1 TCCACCATTAGGCCC
41595361 ACTTGATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.50, G:0.13, T:0.20
Consensus pattern (15 bp):
TCCACCATTAGGCCC
Found at i:41595477 original size:63 final size:62
Alignment explanation
Indices: 41595341--41595486 Score: 152
Period size: 63 Copynumber: 2.3 Consensus size: 62
41595331 TCCACCATTA
* * *
41595341 GGCCCTCCACCATTCGGCCCACTTGATTGTGGCCTATACACATTATTGTCAAAAGTCGGCCT
1 GGCCCCCCACCATTCGGCCCACTTGATTGTGGCCTATACACATTATTGTCAAAACTCGACCT
* * * * * *
41595403 GACCCCTCCACCATTTGGCCCACTTGGTTGTGGCCTATACGCA-TGTTGCTCAACAC-CTGACCT
1 GGCCCC-CCACCATTCGGCCCACTTGATTGTGGCCTATACACATTATTG-TCAAAACTC-GACCT
*
41595466 GGGCCCCCCACCAATCGGCCC
1 -GGCCCCCCACCATTCGGCCC
41595487 TGCATACTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
62 9 0.13
63 54 0.79
64 5 0.07
ACGTcount: A:0.18, C:0.38, G:0.20, T:0.24
Consensus pattern (62 bp):
GGCCCCCCACCATTCGGCCCACTTGATTGTGGCCTATACACATTATTGTCAAAACTCGACCT
Found at i:41603870 original size:31 final size:32
Alignment explanation
Indices: 41603829--41603890 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
41603819 TAAACATTAA
*
41603829 AAAATTATTTTAAAAATAAAAAAA-ATATTTT
1 AAAAGTATTTTAAAAATAAAAAAATATATTTT
*
41603860 AAAAGTATTTTAAAATTAAAAAAATATATTT
1 AAAAGTATTTTAAAAATAAAAAAATATATTT
41603891 ATTATATTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (32 bp):
AAAAGTATTTTAAAAATAAAAAAATATATTTT
Found at i:41607869 original size:5 final size:5
Alignment explanation
Indices: 41607859--41607889 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
41607849 TATATTTTTT
*
41607859 TATTA TATTA TATTA TATCA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA T
41607890 TCCTTTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:41612759 original size:56 final size:57
Alignment explanation
Indices: 41612689--41612800 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 57
41612679 ACACTAAAGC
* *
41612689 ATGAAAATGATCAATTTGAAACACTAAAACAGCAG-CTTGATTCAATTTAAGACAGT
1 ATGAAAATGATCAATTTGAAACACTAAAACAACAGTCTTAATTCAATTTAAGACAGT
* * * *
41612745 ATGAAAATGCTCAATTTGAAACACTCAAACAACAGTTTTAATTCAATTTATGACAG
1 ATGAAAATGATCAATTTGAAACACTAAAACAACAGTCTTAATTCAATTTAAGACAG
41612801 CAAGCAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
56 32 0.65
57 17 0.35
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (57 bp):
ATGAAAATGATCAATTTGAAACACTAAAACAACAGTCTTAATTCAATTTAAGACAGT
Found at i:41613645 original size:18 final size:18
Alignment explanation
Indices: 41613602--41613636 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41613592 AATTTTTATG
*
41613602 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
41613620 ATTGGGTTGGGTTGGAT
1 ATTGGGTTGGGTTGGAT
41613637 GCTTGGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.49, T:0.40
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:41613978 original size:24 final size:25
Alignment explanation
Indices: 41613934--41614050 Score: 71
Period size: 24 Copynumber: 4.5 Consensus size: 25
41613924 TTTTGGATTC
41613934 AAATTATAAAAATTAAAAAAAATTA
1 AAATTATAAAAATTAAAAAAAATTA
*
41613959 AAATTA-AAAAA-TATAGAAAAATT-
1 AAATTATAAAAATTA-AAAAAAATTA
* *
41613982 AAATATATATATAATTCAAAAAACATATCA
1 AAAT-TATA-AAAATT-AAAAAA-A-ATTA
* * *
41614012 AAATTTTAAAATTTCAAAATAAAAATA
1 AAATTATAAAAATT-AAAA-AAAATTA
*
41614039 AAAATA-AAAAAT
1 AAATTATAAAAAT
41614051 ATAGAAAACT
Statistics
Matches: 70, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
23 6 0.09
24 15 0.21
25 7 0.10
26 8 0.11
27 11 0.16
28 12 0.17
29 7 0.10
30 4 0.06
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (25 bp):
AAATTATAAAAATTAAAAAAAATTA
Found at i:41615101 original size:20 final size:20
Alignment explanation
Indices: 41615072--41615109 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41615062 TAAATTCGTA
* *
41615072 TTAAAGCATTTTTGATATTT
1 TTAAAACATTTTTAATATTT
41615092 TTAAAACATTTTTAATAT
1 TTAAAACATTTTTAATAT
41615110 ATTAAATGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
TTAAAACATTTTTAATATTT
Found at i:41624762 original size:46 final size:46
Alignment explanation
Indices: 41624688--41625172 Score: 767
Period size: 46 Copynumber: 10.6 Consensus size: 46
41624678 TACTTATGAT
* * **
41624688 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAAACTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
* **
41624732 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAACTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
* * * **
41624778 CACTTATCACTTTGTCACTTGACCAGATAAGTGTAGTTAAAACTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
* * *
41624824 CACTTATCACTTTGTCACTTGACCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
41624870 CACTTATCACTTTATCACTTGATCAGATAAGTGCAGCTAATGCTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
* *
41624916 CACTTATCACTTTCTCACTTGATCAGATAAGTGCAGCTAATGCTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
41624962 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
* *
41625008 CACTTATCACTTTCTCACTTGATCAGATAAGTGCAGCTAATGCTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
41625054 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
41625100 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
41625146 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTATCACTTGATCAGA
41625173 AGTACTCAAA
Statistics
Matches: 424, Mismatches: 15, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
44 10 0.02
45 5 0.01
46 409 0.96
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
Found at i:41626937 original size:11 final size:13
Alignment explanation
Indices: 41626917--41626948 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41626907 AATAAATTAA
41626917 TAAAATATCAT-T
1 TAAAATATCATAT
41626929 TAAAA-ATCATAT
1 TAAAATATCATAT
41626941 TAAAATAT
1 TAAAATAT
41626949 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:41630850 original size:4 final size:4
Alignment explanation
Indices: 41630841--41631053 Score: 426
Period size: 4 Copynumber: 53.2 Consensus size: 4
41630831 ACTTCAATAC
41630841 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
41630889 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
41630937 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
41630985 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
41631033 ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT A
41631054 GAACTCCTCA
Statistics
Matches: 209, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 209 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:41638409 original size:140 final size:140
Alignment explanation
Indices: 41638157--41638436 Score: 490
Period size: 140 Copynumber: 2.0 Consensus size: 140
41638147 AATTTAATTG
*
41638157 TTATTTTTTTCTAACTAAATTTGACCCTCAACCTTTAAAAAAAGTCTAATTTAATCATTAATCTT
1 TTATTTTTTTCTAACTAAATTTGACCCTCAACCTTTAAAAAAAGTATAATTTAATCATTAATCTT
* *
41638222 TGAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACTGACTAAGGGTCCCTTTGAATGGGAG
66 TCAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACCGACTAAGGGTCCCTTTGAATGGGAG
41638287 ATGCAATTAC
131 ATGCAATTAC
*
41638297 TTATTTTATTT-TAACTAAATTTGACCCTCAACCTTTAAAAAAATTATAATTTAATCATTAATCT
1 TTATTTT-TTTCTAACTAAATTTGACCCTCAACCTTTAAAAAAAGTATAATTTAATCATTAATCT
*
41638361 TTCAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACCGACTAAGGGTCCCTTTGGATGGGA
65 TTCAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACCGACTAAGGGTCCCTTTGAATGGGA
*
41638426 GATGCATTTAC
130 GATGCAATTAC
41638437 CTGCAGTTAG
Statistics
Matches: 133, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
140 130 0.98
141 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (140 bp):
TTATTTTTTTCTAACTAAATTTGACCCTCAACCTTTAAAAAAAGTATAATTTAATCATTAATCTT
TCAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACCGACTAAGGGTCCCTTTGAATGGGAG
ATGCAATTAC
Found at i:41638642 original size:19 final size:19
Alignment explanation
Indices: 41638615--41638652 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41638605 CGAATTTGTA
41638615 TGAAC-TTTTTATTATTTTT
1 TGAACTTTTTTA-TATTTTT
*
41638634 TGAATTTTTTTATATTTTT
1 TGAACTTTTTTATATTTTT
41638653 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (19 bp):
TGAACTTTTTTATATTTTT
Found at i:41638893 original size:27 final size:27
Alignment explanation
Indices: 41638855--41638910 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
41638845 GTTGATCTAA
41638855 GAAACTGTAGCCTTCATTTAATTTCGG
1 GAAACTGTAGCCTTCATTTAATTTCGG
41638882 GAAACTGTAGCCTTCATTTAATTTCGG
1 GAAACTGTAGCCTTCATTTAATTTCGG
41638909 GA
1 GA
41638911 CTTTTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (27 bp):
GAAACTGTAGCCTTCATTTAATTTCGG
Found at i:41639077 original size:27 final size:27
Alignment explanation
Indices: 41639039--41639107 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
41639029 GAGGAGGGTA
*
41639039 TCCCATGGGCGGCACCAAAGGTGCCTT
1 TCCCATGGGCGGCACCAAAGGTGCCAT
* * * *
41639066 TCCCATAGGCGGGACCGATGGTGCCAT
1 TCCCATGGGCGGCACCAAAGGTGCCAT
41639093 TCCCATGGGCGGCAC
1 TCCCATGGGCGGCAC
41639108 TGCCCATATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.33, G:0.32, T:0.17
Consensus pattern (27 bp):
TCCCATGGGCGGCACCAAAGGTGCCAT
Found at i:41639191 original size:28 final size:28
Alignment explanation
Indices: 41639159--41639243 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 28
41639149 AGAAGGAGAG
41639159 GGAAAGAAGAAGAAAGAAAGAAAGAAAA
1 GGAAAGAAGAAGAAAGAAAGAAAGAAAA
* * *
41639187 TGAAAGGAGAGGAAAGAAAGAAA-AAGAA
1 GGAAAGAAGAAGAAAGAAAGAAAGAA-AA
41639215 GGAAAGAA-AAGGAAAGGAGAAG-AAGAAAA
1 GGAAAGAAGAA-GAAA-GA-AAGAAAGAAAA
41639244 AAGAAGGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
27 3 0.07
28 32 0.70
29 6 0.13
30 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (28 bp):
GGAAAGAAGAAGAAAGAAAGAAAGAAAA
Found at i:41639213 original size:38 final size:37
Alignment explanation
Indices: 41639151--41639283 Score: 161
Period size: 34 Copynumber: 3.7 Consensus size: 37
41639141 GGGTGAAGAG
*
41639151 AAGGAGAGGGAAAGAAGAAGAAAGAAAGAAAGAAAATGA
1 AAGGAGA-GGAAAGAAGAA-AAAGAAGGAAAGAAAATGA
*
41639190 AAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGA
1 AAGGAGAGGAAAG-AAGAAAAAGAAGGAAAGAAAATGA
*
41639228 AAGGAGAAG-AAG-A-AAAAAGAAGGAAAGAAAATGA
1 AAGGAGAGGAAAGAAGAAAAAGAAGGAAAGAAAATGA
*
41639262 AAGGAGA--AGAGAA-AAAAAGAAG
1 AAGGAGAGGAAAGAAGAAAAAGAAG
41639284 AGAAGAATTA
Statistics
Matches: 86, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
33 2 0.02
34 37 0.43
35 1 0.01
37 3 0.03
38 31 0.36
39 12 0.14
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (37 bp):
AAGGAGAGGAAAGAAGAAAAAGAAGGAAAGAAAATGA
Found at i:41639271 original size:24 final size:23
Alignment explanation
Indices: 41639161--41639271 Score: 84
Period size: 24 Copynumber: 4.6 Consensus size: 23
41639151 AAGGAGAGGG
*
41639161 AAAGAAGAAGAAAGAAAGAAAGAA
1 AAAGAA-AGGAAAGAAAGAAAGAA
* *
41639185 AATGAAAGGAGAGGAAAGAAAGAA
1 AAAGAAAGGA-AAGAAAGAAAGAA
41639209 AAAG-AAGGAAAGAAAAGGAAAGGAGA
1 AAAGAAAGGAAAG-AAA-GAAA-GA-A
*
41639235 AGAAGAAA--AAAGAAGGAAAGAA
1 A-AAGAAAGGAAAGAAAGAAAGAA
*
41639257 AATGAAAGGAGAAGA
1 AAAGAAAGGA-AAGA
41639272 GAAAAAAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
21 5 0.07
22 4 0.06
23 14 0.20
24 32 0.46
25 4 0.06
26 6 0.09
27 3 0.04
28 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.02
Consensus pattern (23 bp):
AAAGAAAGGAAAGAAAGAAAGAA
Found at i:41640114 original size:158 final size:151
Alignment explanation
Indices: 41639608--41640384 Score: 629
Period size: 159 Copynumber: 4.9 Consensus size: 151
41639598 AATGATATAT
*
41639608 TTAATAAATTTCAAACATAATGCT-CTGAAATAAAGTAAAATTATAAAAATAGAAATTATGATA-
1 TTAATAAATTTCAAACATAATG-TACTGAAATAATGTAAAATTAT-AAAATAGAAATTATGATAT
* *
41639671 TTTTTAAAATAATAAAATGCTGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACT
64 TTTTTAAAGTAATAAAATTC-GAGAAAAAAATACGAACAAATGGCCGAAGTAAGA--G--TT--T
*
41639736 TTTACTAA-CTTTTTAAAAATTCAAAA-ATAA
122 TTTACTAATTTTTTTAAAAA-TCAAAATA-AA
* * * * * *
41639766 TTAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACAAA-AATAAT
1 TTAAT---AA-ATTTCAAACATAATGTACTGAAATAATGTAAAATTATAAAATAGAAATTATGAT
* * * * * * *
41639830 ATTTTTTATTACGAGTAATAAAATTCGGGAAAATAATACGAGCAGAGGGCAGGAA-TAAGGGTTT
62 ATTTTTTA--A--AGTAATAAAATTCGAGAAAAAAATACGAACAAATGGC-CGAAGTAAGAG--T
** * * *
41639894 TTTTTACACTAAATTAATTTAAAAAACACACTAAA
120 TTTTT--ACT-AATTTTTTTAAAAATCAAAATAAA
41639929 TTAATAAATTTCAAACATAAT-TAACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATAT
1 TTAATAAATTTCAAACATAATGT-ACTGAAATAATGTAAAATTATAAAA-TAGAAATTATGATAT
* ** * **
41639993 TTTCTAAAACAATAAAATGTAGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGCTTTACT
64 TTTTTAAAGTAATAAAAT-TCGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACT
41640058 AATTTTTTTAAAAATTCAGAAATAAA
128 AATTTTTTTAAAAA-TCA-AAATAAA
* * * * * *
41640084 -TAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACAAA-AATAAT
1 TTAAT---AA-ATTTCAAACATAATGTACTGAAATAATGTAAAATTATAAAATAGAAATTATGAT
* * * * * * *
41640147 ATTTTTTATTGTGAGTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAA-TAAGGGGTT
62 ATTTTTTA----AAGTAATAAAATTCGAGAAAAAAATACGAACAAATGGC-CGAAGTAA-GAG-T
** * * *
41640211 TTTTTACACTAAATTAATTTAAAAAGCACACTAAA
120 TTTTT--ACT-AATTTTTTTAAAAATCAAAATAAA
*
41640246 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATTATAAAA-TAGAAATTATGATATT
*
41640311 TTTTAAAGTAATAAAATACGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTA
65 TTTTAAAGTAATAAAATTC-GAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTA
41640376 ACTTTTTTT
129 A-TTTTTTT
41640385 TCAACATGCA
Statistics
Matches: 488, Mismatches: 87, Indels: 92
0.73 0.13 0.14
Matches are distributed among these distances:
153 14 0.03
154 17 0.03
155 5 0.01
156 21 0.04
157 36 0.07
158 90 0.18
159 99 0.20
160 37 0.08
161 45 0.09
162 44 0.09
163 22 0.05
164 44 0.09
165 14 0.03
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (151 bp):
TTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATTATAAAATAGAAATTATGATATTT
TTTAAAGTAATAAAATTCGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTAAT
TTTTTTAAAAATCAAAATAAA
Found at i:41640187 original size:317 final size:315
Alignment explanation
Indices: 41639608--41640384 Score: 1270
Period size: 317 Copynumber: 2.4 Consensus size: 315
41639598 AATGATATAT
* * *
41639608 TTAATAAATTTCAAACATAATGCTCTGAAATAAAGTAAAATTATAAAAATAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
41639673 TTTAAAATAATAAAATGCTGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTTT
66 TTTAAAATAATAAAATG-TGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTG-----C-TT
* *
41639738 TACTAA-CTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACAAAATGTACTGAAATA
124 TACTAATTTTTTTAAAAATTCAAAAATAAATAATACAAATATTTCAAACAAAATGTACTGAAATA
41639802 ATATAAAATAATAAAATACAAAAATAATATTTTTTATTACGAGTAATAAAATTCGGGAAAATAAT
189 ATATAAAATAATAAAATACAAAAATAATATTTTTTATTACGAGTAATAAAATTCGGGAAAATAAT
* *
41639867 ACGAGCAGAGGGCAGGAATAAGGGTTTTTTTTACACTAAATTAATTTAAAAAACACACTAAA
254 ACGAGCAAAGGGCAGGAATAAGGGGTTTTTTTACACTAAATTAATTTAAAAAACACACTAAA
**
41639929 TTAATAAATTTCAAACATAATTAACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
*
41639994 TTCTAAAACAATAAAATGTAGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGCTTTACTA
66 TT-TAAAATAATAAAATGT-GAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGCTTTACTA
*
41640059 ATTTTTTTAAAAATTCAGAAATAAATAATACAAATATTTCAAACAAAATGTACTGAAATAATATA
129 ATTTTTTTAAAAATTCAAAAATAAATAATACAAATATTTCAAACAAAATGTACTGAAATAATATA
**
41640124 AAATAATAAAATACAAAAATAATATTTTTTATTGTGAGTAATAAAATTCGGGAAAATAATACGAG
194 AAATAATAAAATACAAAAATAATATTTTTTATTACGAGTAATAAAATTCGGGAAAATAATACGAG
*
41640189 CAAAGGGCAGGAATAAGGGGTTTTTTTACACTAAATTAATTTAAAAAGCACACTAAA
259 CAAAGGGCAGGAATAAGGGGTTTTTTTACACTAAATTAATTTAAAAAACACACTAAA
41640246 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATA-T
* **
41640311 TTTTAAAGTAATAAAATACG-GAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACT
65 TTTTAAAATAATAAAAT--GTGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGCTTTACT
41640375 AACTTTTTTT
128 AA-TTTTTTT
41640385 TCAACATGCA
Statistics
Matches: 429, Mismatches: 20, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
316 8 0.02
317 295 0.69
318 11 0.03
319 1 0.00
321 63 0.15
322 51 0.12
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (315 bp):
TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
TTTAAAATAATAAAATGTGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGCTTTACTAAT
TTTTTTAAAAATTCAAAAATAAATAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAA
ATAATAAAATACAAAAATAATATTTTTTATTACGAGTAATAAAATTCGGGAAAATAATACGAGCA
AAGGGCAGGAATAAGGGGTTTTTTTACACTAAATTAATTTAAAAAACACACTAAA
Found at i:41645563 original size:3 final size:3
Alignment explanation
Indices: 41645555--41645600 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
41645545 TAACTAACAC
41645555 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
41645601 GTTTTATACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41646044 original size:27 final size:27
Alignment explanation
Indices: 41645983--41646047 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
41645973 ACACAAGTGA
*
41645983 TGCCGCCAATGGGAAAGGCACCTTCGG
1 TGCCGCCTATGGGAAAGGCACCTTCGG
*
41646010 TGCCGCCTATGGGAAAGGCACCTTTGG
1 TGCCGCCTATGGGAAAGGCACCTTCGG
41646037 TGCCGCCTATG
1 TGCCGCCTATG
41646048 AGATACCCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.18, C:0.29, G:0.32, T:0.20
Consensus pattern (27 bp):
TGCCGCCTATGGGAAAGGCACCTTCGG
Found at i:41649794 original size:18 final size:18
Alignment explanation
Indices: 41649725--41649795 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
41649715 CAAAGTTTAT
41649725 AAAA-AATAGAAAATTGAA
1 AAAATAATAGAAAATT-AA
* * *
41649743 AAAATATTA-AAACTTATT
1 AAAATAATAGAAAATTA-A
*
41649761 AAAATAATAGAGAATTAA
1 AAAATAATAGAAAATTAA
*
41649779 AAAATAATATAAAATTA
1 AAAATAATAGAAAATTA
41649796 TGAACAATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 1 0.02
18 32 0.78
19 8 0.20
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAATAATAGAAAATTAA
Found at i:41655592 original size:51 final size:51
Alignment explanation
Indices: 41655512--41655650 Score: 147
Period size: 51 Copynumber: 2.7 Consensus size: 51
41655502 TATGCCGGTT
* * * *
41655512 CACATAGTAGCATGCACATAGTACTACACAGGTGAACATCA-CTATCCGATA
1 CACATAGTAGCCTTCACATAGTACTACACATGTGACCAT-AGCTATCCGATA
* * * *
41655563 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCGA-AGCTATCCGGTA
1 CACATAGTAGCCTTCACATAGTACTACACATGTGA-CCATAGCTATCCGATA
* * *
41655614 CGCATAGTAGCCTGCACATAGTACTACACATGCGACC
1 CACATAGTAGCCTTCACATAGTACTACACATGTGACC
41655651 TATCATTCTG
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
50 2 0.03
51 70 0.96
52 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (51 bp):
CACATAGTAGCCTTCACATAGTACTACACATGTGACCATAGCTATCCGATA
Found at i:41655758 original size:87 final size:87
Alignment explanation
Indices: 41655577--41655759 Score: 194
Period size: 86 Copynumber: 2.1 Consensus size: 87
41655567 TAGTAGCCTT
*
41655577 CACATAGTACTACACACGTGATCGAAGCTATCCGGTACGCATAGTAGCCTGCACATAGTACTACA
1 CACATAGTACTACACACGTGATCGAAGCTATACGGTACGCATAGTAGCCTGCACATAGTACTACA
* ** *
41655642 CATGCGACCTATCATTCTGATA
66 CACGCGACAAAGCATTCTGATA
* * * *
41655664 CATATAGTACTACACACGTGATC-AAGTTTTACGGTTCACG-A-AGTAGCCTTCACATAGTACTA
1 CACATAGTACTACACACGTGATCGAAGCTATACGG-T-ACGCATAGTAGCCTGCACATAGTACTA
* * *
41655726 CACACGTGATCAAAGC-TTTTCGGTA
64 CACACGCGA-CAAAGCATTCT-GATA
41655751 CACATAGTA
1 CACATAGTA
41655760 GCCTTCACTT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
86 38 0.48
87 38 0.48
88 3 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (87 bp):
CACATAGTACTACACACGTGATCGAAGCTATACGGTACGCATAGTAGCCTGCACATAGTACTACA
CACGCGACAAAGCATTCTGATA
Found at i:41655778 original size:51 final size:50
Alignment explanation
Indices: 41655667--41655937 Score: 280
Period size: 51 Copynumber: 5.3 Consensus size: 50
41655657 TCTGATACAT
* *
41655667 ATAGTACTACACACGTGATC-AAGTTTTACGGTTCACGA-AGTAGCCTTCAC
1 ATAGTACTACACACGTGACCAAAGTTTT-CGGTACAC-ATAGTAGCCTTCAC
*
41655717 ATAGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCCTTCAC
1 ATAGTACTACACACGTGACCAAAG-TTTTCGGTACACATAGTAGCCTTCAC
* * * * *
41655768 TTAGTACTACACATGTGACCATTA-TTTATCGATACACGTAGTAGCCTTCAC
1 ATAGTACTACACACGTGACCA-AAGTTT-TCGGTACACATAGTAGCCTTCAC
* * * *
41655819 ACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCAC
1 ATAGTACTACACACGTGACCAAAG-TTTTCGGTACACATAGTAGCCTTCAC
* * * * *
41655870 TTAGTACTACACATGTGACCATTA-TTTATCGATACACGTAGTAGCCTTCAC
1 ATAGTACTACACACGTGACCA-AAGTTT-TCGGTACACATAGTAGCCTTCAC
*
41655921 ACAGTACTACACACGTG
1 ATAGTACTACACACGTG
41655938 TTCATTGATA
Statistics
Matches: 186, Mismatches: 26, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
50 27 0.15
51 151 0.81
52 8 0.04
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (50 bp):
ATAGTACTACACACGTGACCAAAGTTTTCGGTACACATAGTAGCCTTCAC
Found at i:41655843 original size:102 final size:102
Alignment explanation
Indices: 41655700--41655933 Score: 414
Period size: 102 Copynumber: 2.3 Consensus size: 102
41655690 TTTTACGGTT
* * * * *
41655700 CACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCCTT
1 CACGTAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTT
41655765 CACTTAGTACTACACATGTGACCATTATTTATCGATA
66 CACTTAGTACTACACATGTGACCATTATTTATCGATA
*
41655802 CACGTAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATTGTAGCCTT
1 CACGTAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTT
41655867 CACTTAGTACTACACATGTGACCATTATTTATCGATA
66 CACTTAGTACTACACATGTGACCATTATTTATCGATA
41655904 CACGTAGTAGCCTTCACACAGTACTACACA
1 CACGTAGTAGCCTTCACACAGTACTACACA
41655934 CGTGTTCATT
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 126 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (102 bp):
CACGTAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTT
CACTTAGTACTACACATGTGACCATTATTTATCGATA
Found at i:41660537 original size:4 final size:4
Alignment explanation
Indices: 41660530--41660555 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41660520 TGTGTATTTA
41660530 TTGT TTGT TTGT TTGT TTGT TTGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TT
41660556 ATTATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:41660621 original size:23 final size:23
Alignment explanation
Indices: 41660577--41660622 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41660567 ACATTGTTCG
* *
41660577 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
41660600 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
41660623 CAAATAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:41674470 original size:35 final size:35
Alignment explanation
Indices: 41674431--41674505 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
41674421 TGTGAAGGGT
* *
41674431 ATGGATGAATTGGTATGTTTTGCATGTGTAAAAGG
1 ATGGATGAATTGGTATGCTTGGCATGTGTAAAAGG
41674466 ATGGATGAATTGGTATGCTTGGCATGTGTAAAAGG
1 ATGGATGAATTGGTATGCTTGGCATGTGTAAAAGG
*
41674501 TTGGA
1 ATGGA
41674506 ACTTCTTGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.35
Consensus pattern (35 bp):
ATGGATGAATTGGTATGCTTGGCATGTGTAAAAGG
Found at i:41676172 original size:13 final size:13
Alignment explanation
Indices: 41676154--41676185 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41676144 TTTCCAGCAA
41676154 TTATGAATTTATT
1 TTATGAATTTATT
41676167 TTATGAATTTATT
1 TTATGAATTTATT
*
41676180 TGATGA
1 TTATGA
41676186 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:41676393 original size:50 final size:50
Alignment explanation
Indices: 41676280--41676521 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
41676270 ATTTGGGTAA
* * *
41676280 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
41676336 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41676386 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41676436 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
41676486 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
41676522 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:41676469 original size:100 final size:103
Alignment explanation
Indices: 41676280--41676529 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
41676270 ATTTGGGTAA
41676280 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
41676345 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
41676386 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
41676448 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
41676486 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
41676530 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:41677967 original size:28 final size:28
Alignment explanation
Indices: 41677936--41678019 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 28
41677926 CATGACAGTT
*
41677936 AAGAAAAGCCTTTGTGGTGAACTCTGAA
1 AAGAAAAGCCTTTGTGGCGAACTCTGAA
*
41677964 AAGAATAA-CCTTTGTGGCGAATTCTGAA
1 AAGAA-AAGCCTTTGTGGCGAACTCTGAA
* * *
41677992 AAGAATAGCCTATGTGGCAAACTCTGAA
1 AAGAAAAGCCTTTGTGGCGAACTCTGAA
41678020 TGGATCGCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.02
28 45 0.94
29 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (28 bp):
AAGAAAAGCCTTTGTGGCGAACTCTGAA
Found at i:41680770 original size:72 final size:68
Alignment explanation
Indices: 41680694--41680831 Score: 188
Period size: 68 Copynumber: 2.0 Consensus size: 68
41680684 TGATTAAACT
* *
41680694 TAATCACTTTAATATTAAATTAATATA-ATATTTATCTAAAAGATAAACATTAAATTAAATTTAA
1 TAATCACTTTAATATTAAATTAATA-ACATA-CTAT-T--AAGATAAACACTAAATTAAATTTAA
41680758 TATTAAGA
61 TATTAAGA
* *
41680766 TAATCACTTTAATATTAAATTAATAACATACTATTAATATAAGCACTAAATTAAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAACATACTATTAAGATAAACACTAAATTAAATTTAATATTA
41680831 A
66 A
41680832 ACTATTAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
68 28 0.46
70 1 0.02
71 4 0.07
72 28 0.46
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAACATACTATTAAGATAAACACTAAATTAAATTTAATATTA
AGA
Found at i:41680789 original size:20 final size:18
Alignment explanation
Indices: 41680686--41680790 Score: 58
Period size: 20 Copynumber: 5.7 Consensus size: 18
41680676 TTCAACTGTG
41680686 ATTAAACTTAATCACTTTAAT
1 ATTAAA-TTAAT-A-TTTAAT
41680707 ATTAAATTAATA--TAAT
1 ATTAAATTAATATTTAAT
* * * * *
41680723 ATT-TATCTAAAAGATAAAC
1 ATTAAAT-TAATA-TTTAAT
41680742 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
41680759 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
41680779 ATTAAATTAATA
1 ATTAAATTAATA
41680791 ACATACTATT
Statistics
Matches: 66, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
15 2 0.03
16 11 0.17
17 11 0.17
18 2 0.03
19 12 0.18
20 22 0.33
21 6 0.09
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:41691554 original size:22 final size:22
Alignment explanation
Indices: 41691518--41691562 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
41691508 TTGATGTTCT
41691518 AGTTGGAATTGTAATGTGTCTAA
1 AGTTGGAATTGTAATGTGT-TAA
*
41691541 AGTTGGTA-TGTAATGTGTTAA
1 AGTTGGAATTGTAATGTGTTAA
41691562 A
1 A
41691563 TTTAATGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 10 0.48
23 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.40
Consensus pattern (22 bp):
AGTTGGAATTGTAATGTGTTAA
Found at i:41696494 original size:22 final size:21
Alignment explanation
Indices: 41696466--41696510 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
41696456 ACAAATAATT
41696466 AAAAGAA-CTTAGAAATTTATAA
1 AAAAGAATCTTA-AAA-TTATAA
*
41696488 AAAAGAATTTTAAAATTATAA
1 AAAAGAATCTTAAAATTATAA
41696509 AA
1 AA
41696511 GAACTCAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 10 0.48
23 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAGAATCTTAAAATTATAA
Found at i:41696975 original size:18 final size:18
Alignment explanation
Indices: 41696954--41697000 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
41696944 TTTTTAATAA
*
41696954 TTTTTTTATTTTTAAATT
1 TTTTTTTAATTTTAAATT
* *
41696972 TTTTATGAATTTTAAATT
1 TTTTTTTAATTTTAAATT
*
41696990 TTTATTTAATT
1 TTTTTTTAATT
41697001 ATTATTGATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTTTAATTTTAAATT
Found at i:41699545 original size:108 final size:109
Alignment explanation
Indices: 41699347--41699765 Score: 677
Period size: 108 Copynumber: 3.9 Consensus size: 109
41699337 AAATTGTTCC
*
41699347 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTTGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
41699412 TCTCGTTCGACCAAATAGCTAAATATCC-TTTAAAAACTTTTCA
66 TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
*
41699455 AAAATAATGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
* *
41699520 TCTCGTTCCACCAAAT-GACTTAATATCCTTTTCAAAAA-TTTTC-
66 TCTCGTTCGACCAAATAG-CTAAATATCCTTTT-AAAAACTTTTCA
*
41699563 AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
41699628 TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
66 TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
* *
41699672 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGTTTCGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
* * * *
41699737 TCACGTT-TAGGCAAATTGCTAAATATCCT
66 TCTCGTTCGA-CCAAATAGCTAAATATCCT
41699766 CTTGAATTTT
Statistics
Matches: 289, Mismatches: 15, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
107 6 0.02
108 184 0.64
109 94 0.33
110 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (109 bp):
AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
Found at i:41703794 original size:23 final size:22
Alignment explanation
Indices: 41703768--41703837 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
41703758 AAAAAAAAGG
41703768 AAAATGAAAAGAGAGAAAAAATC
1 AAAATGAAAA-AGAGAAAAAATC
* *
41703791 AAAATCAAAATA-A-AAAAAAAC
1 AAAATGAAAA-AGAGAAAAAATC
* *
41703812 AAAAAGAAAAAGAGAAATCAATC
1 AAAATGAAAAAGAGAAA-AAATC
41703835 AAA
1 AAA
41703838 GTCAAAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.43
22 4 0.11
23 16 0.43
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.09
Consensus pattern (22 bp):
AAAATGAAAAAGAGAAAAAATC
Found at i:41703821 original size:44 final size:45
Alignment explanation
Indices: 41703756--41703850 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
41703746 AGATCCGATT
* *
41703756 TAAAAAAAAAGGAAAATGAAAAGAGAGAAA-AAATCAAAATCAAAA
1 TAAAAAAAAAGCAAAAAGAAAA-AGAGAAATAAATCAAAATCAAAA
* *
41703801 TAAAAAAAAA-CAAAAAGAAAAAGAGAAATCAATCAAAGTCAAAA
1 TAAAAAAAAAGCAAAAAGAAAAAGAGAAATAAATCAAAATCAAAA
41703845 TAAAAA
1 TAAAAA
41703851 TATGAAAAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 7 0.16
44 28 0.62
45 10 0.22
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (45 bp):
TAAAAAAAAAGCAAAAAGAAAAAGAGAAATAAATCAAAATCAAAA
Found at i:41705651 original size:86 final size:86
Alignment explanation
Indices: 41705506--41706351 Score: 1188
Period size: 86 Copynumber: 9.8 Consensus size: 86
41705496 GTGAAAATAA
*
41705506 AAAACAAAGCCTTGCCTTCATTAGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
41705571 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
41705592 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
41705657 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
*
41705678 AAAACAAAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
41705743 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
*
41705764 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAAAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
41705829 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
* *
41705850 AAAACAAAGCCTTGCCTTCATTGTTTGCAGTGGAGCTGGTTAAAGAAGCAGATTTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
41705915 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
* *
41705936 AAAACAAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTA
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
41706001 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
41706022 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
*
41706087 CGTTAACAACGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
* * * **
41706108 AAGACACAAA-CCTTGCCTCTC-TCGGTTG-TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCT
1 AA-A-ACAAAGCCTTGCCT-TCATTGGTTGCAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCT
** ** * *
41706170 TTTTGTATTGACAGCGAAGCAGGTCG
61 TCCTGCGTTAACAGCGAAGCAGATCG
* * * **
41706196 AAGACACAAA-CCTTGCCTCTC-TCGGTTG-TGATGGAGCTGGTTGAAGACAATAGATCTTGCCT
1 AA-A-ACAAAGCCTTGCCT-TCATTGGTTGCAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCT
* * *
41706258 TCCTGCATTGACAGCGAAGCAGGTCG
61 TCCTGCGTTAACAGCGAAGCAGATCG
* * * * * **
41706284 AAGACGCAAA-TCTTGCCCCTC-TTGGTTG-TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCT
1 AA-A-ACAAAGCCTTG-CCTTCATTGGTTGCAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCT
41706346 TCCTGC
61 TCCTGC
41706352 ATTGATAACG
Statistics
Matches: 719, Mismatches: 35, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
86 505 0.70
87 30 0.04
88 182 0.25
89 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (86 bp):
AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
CGTTAACAGCGAAGCAGATCG
Found at i:41705792 original size:172 final size:171
Alignment explanation
Indices: 41705506--41706743 Score: 1255
Period size: 172 Copynumber: 7.2 Consensus size: 171
41705496 GTGAAAATAA
* *
41705506 AAAACAAAGCCTTGCCTTCATTAGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTC-TTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
41705571 CGTTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCCTTCATTGGTTGCAG-TGGAGCTGGTTA
65 CGTTAACAGCGAAGCAGATCGAAACACAAA-CCTTGCCTTC-TTGGTTG-AGATGGAGCTGGTTA
* * * *
41705634 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
127 AAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCG
41705678 AAAACAAAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTC-TTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
41705743 CGTTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCCTTCATTGGTTGCAG-TGGAGCTGGTTA
65 CGTTAACAGCGAAGCAGATCGAAACACAAA-CCTTGCCTTC-TTGGTTG-AGATGGAGCTGGTTA
* * *
41705806 AA-A-AAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
127 AAGACAA-CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCG
* * *
41705850 AAAACAAAGCCTTGCCTTCATTGTTTGCAGTGGAGCTGGTTAAAGAAGCAGATTTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTC-TTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
*
41705915 CGTTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCCTTCATTGGTT-ACAGTGGAGCTGGTTA
65 CGTTAACAGCGAAGCAGATCGAAACACAAA-CCTTGCCTTC-TTGGTTGAGA-TGGAGCTGGTTA
* * * * *
41705978 AAGA-AGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCG
127 AAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCG
*
41706022 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTC-TTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
* * * *
41706087 CGTTAACAACGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGA
65 CGTTAACAGCGAAGCAGATCGAA-ACACAAACCTTGCCT-TCTTGGTTGAGATGGAGCTGGTTAA
* ** *
41706152 AGACAAAAGATCTTGCCTTTTTGTATTGACAGCGAAGCAGGTCG
128 AGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCG
* * **
41706196 AAGACACAAA-CCTTGCCTCTCTCGGTTGT-GATGGAGCTGGTTGAAGACAATAGATCTTGCCTT
1 AA-A-ACAAAGCCTTGCCT-TCTTGGTTGTAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCTT
* * * * * * *
41706259 CCTGCATTGACAGCGAAGCAGGTCGAAGACGCAAATCTTGCCCCTCTTGGTTGTGATGGAGCTGG
61 CCTGCGTTAACAGCGAAGCAGATCGAA-ACACAAACCTTG-CCTTCTTGGTTGAGATGGAGCTGG
* * * *
41706324 TTGAAGACAAAAGATCTTGCCTTCCTGCATTGATAACGAAGCAGGTC-
124 TTAAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCG
* * * *
41706371 AAAGACACAAACTTTGCC-TC-TGGTTG-A----A----G--ACA-AA--AGATCTTGACTTCCT
1 AAA-ACA-AAGCCTTGCCTTCTTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCT
* * * * * * *
41706420 GCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTAGTTA
64 GCGTTAACAGCGAAGCAGATCGAA-ACACAAACCTTGCCT-TCTTGGTTGAGATGGAGCTGGTTA
* * * *
41706485 AAGACAAAAGATCTTGCCTTCCTACATTGACGGCGAAGCAGGT-T
127 AAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCG
* * * **
41706529 AAAGACACAAACCTTGCCTCTCTCGGTTGT-GATGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
1 AAA-ACA-AAGCCTTGCCT-TCTTGGTTGTAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCTT
* * * * * *
41706593 CCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTT-ATGATGGATCTG
61 CCTGCGTTAACAGCGAAGCAGATCGAA-ACACAAACCTTGCCT-TCTTGGTTGA-GATGGAGCTG
* *
41706657 GTTGAAGACAACAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGGTCG
123 GTTAAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCG
* * * *
41706706 AAGACGAA-CCTTACCTTTCTCGGTTGTAGTGGAGCTGG
1 AAAACAAAGCCTTGCC-TTCTTGGTTGTAGTGGAGCTGG
41706744 CTGAAGAATT
Statistics
Matches: 944, Mismatches: 79, Indels: 84
0.85 0.07 0.08
Matches are distributed among these distances:
157 2 0.00
158 125 0.13
160 3 0.00
161 6 0.01
162 1 0.00
164 1 0.00
166 1 0.00
168 1 0.00
170 2 0.00
171 2 0.00
172 412 0.44
173 37 0.04
174 74 0.08
175 38 0.04
176 235 0.25
177 4 0.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (171 bp):
AAAACAAAGCCTTGCCTTCTTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTGC
GTTAACAGCGAAGCAGATCGAAACACAAACCTTGCCTTCTTGGTTGAGATGGAGCTGGTTAAAGA
CAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCG
Found at i:41706167 original size:44 final size:44
Alignment explanation
Indices: 41706119--41706345 Score: 173
Period size: 44 Copynumber: 5.2 Consensus size: 44
41706109 AGACACAAAC
41706119 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
** * * * * *
41706163 CTTGCCT-T-TTTGTAT-TGACAGCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCTCTCGGT-TGTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
*
41706207 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAATAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
** * * * **
41706251 CTTGCCT-TC-CTGCAT-TGACAGCGAAGCAGGTCGAAGACGCAA-AT
1 CTTGCCTCTCTC-GGTTGTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
* *
41706295 CTTGCCCCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
41706339 CTTGCCT
1 CTTGCCT
41706346 TCCTGCATTG
Statistics
Matches: 134, Mismatches: 33, Indels: 32
0.67 0.17 0.16
Matches are distributed among these distances:
42 10 0.07
43 36 0.27
44 43 0.32
45 36 0.27
46 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (44 bp):
CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
Found at i:41706201 original size:45 final size:45
Alignment explanation
Indices: 41706150--41706377 Score: 134
Period size: 45 Copynumber: 5.2 Consensus size: 45
41706140 GGAGCTGGTT
*
41706150 GAAGACAAAAGATCTTGCCTTTTTGTATTGACAGCGAAGCAGGTC
1 GAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTC
* * * * * *
41706195 GAAGACACAA-ACCTTGCCTCTCTCGGT-TGTGA-TG-G-AGCTGGTT
1 GAAGACAAAAGATCTTGCCT-T-TCTGTAT-TGACAGCGAAGCAGGTC
* * *
41706238 GAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTC
1 GAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTC
** ** * * *
41706283 GAAGACGCAA-ATCTTGCCCCTCTTGGT-TGTGA-TG-G-AGCTGGTT
1 GAAGACAAAAGATCTTGCCTTTC-T-GTAT-TGACAGCGAAGCAGGTC
* * * *
41706326 GAAGACAAAAGATCTTGCCTTCCTGCATTGATAACGAAGCAGGTC
1 GAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTC
*
41706371 AAAGACA
1 GAAGACA
41706378 CAAACTTTGC
Statistics
Matches: 130, Mismatches: 37, Indels: 32
0.65 0.19 0.16
Matches are distributed among these distances:
42 9 0.07
43 33 0.25
44 38 0.29
45 40 0.31
46 10 0.08
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (45 bp):
GAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTC
Found at i:41706434 original size:70 final size:70
Alignment explanation
Indices: 41706320--41706461 Score: 248
Period size: 70 Copynumber: 2.0 Consensus size: 70
41706310 TGTGATGGAG
* * *
41706320 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGATAACGAAGCAGGTCAAAGACACAAACTT
1 CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAACGAAGCAGGTCAAAGACACAAACCT
41706385 TGCCT
66 TGCCT
*
41706390 CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAACGAAGCAGGTCAAAGACACAAACCT
41706455 TGCCT
66 TGCCT
41706460 CT
1 CT
41706462 CTCGGTTGTG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (70 bp):
CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAACGAAGCAGGTCAAAGACACAAACCT
TGCCT
Found at i:41706451 original size:334 final size:334
Alignment explanation
Indices: 41706071--41706710 Score: 1030
Period size: 334 Copynumber: 1.9 Consensus size: 334
41706061 TTAAAGAAGC
* * *
41706071 AGATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGACTTCCTGCATTAACAACGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTTG
* * ** ** *
41706136 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTTTGTATTGACAGCGAAGCAGGTCGAAGAC
66 TGATGGAGCTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCAAAGAC
*
41706201 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAATAGATCTTGCCTTCCTGCAT
131 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCAT
* * * *
41706266 TGACAGCGAAGCAGGTCGAAGACGCAAATCTTGCC-CCTCTTGGTTGTGATGGAGCTGGTTGAAG
196 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCC-CTCGGTTATGATGGAGCTGGTTGAAG
*
41706330 ACAAAAGATCTTGCCTTCCTGCATTGATAACGAAGCAGGTCAAAGACACAAACTTTGCCTCTGGT
260 ACAAAAGATCTTGCCTTCCTGCATTGACAACGAAGCAGGTCAAAGACACAAACTTTGCCTCTGGT
41706395 TGAAGACAAA
325 TGAAGACAAA
* * *
41706405 AGATCTTGACTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGACTTCCTGCATTAACAACGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTTG
* *
41706470 TGATGGAGCTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACGGCGAAGCAGGTTAAAGAC
66 TGATGGAGCTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCAAAGAC
41706535 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCAT
131 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCAT
*
41706600 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTATGATGGATCTGGTTGAAGA
196 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTATGATGGAGCTGGTTGAAGA
* * * *
41706665 CAACAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGGTCGAAGAC
261 CAAAAGATCTTGCCTTCCTGCATTGACAACGAAGCAGGTCAAAGAC
41706711 GAACCTTACC
Statistics
Matches: 279, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
334 277 0.99
335 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (334 bp):
AGATCTTGACTTCCTGCATTAACAACGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCAAAGAC
ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCAT
TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTATGATGGAGCTGGTTGAAGA
CAAAAGATCTTGCCTTCCTGCATTGACAACGAAGCAGGTCAAAGACACAAACTTTGCCTCTGGTT
GAAGACAAA
Found at i:41706522 original size:158 final size:164
Alignment explanation
Indices: 41706231--41706710 Score: 621
Period size: 158 Copynumber: 2.9 Consensus size: 164
41706221 TTGTGATGGA
* * *
41706231 GCTGGTTGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACGCAAATC
1 GCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACC
* * * *
41706296 TTGCCCCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGATAAC
66 TTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC
41706361 GAAGCAGGTCAAAGACACAAA-CTT-T-GC-C-T
131 GAAGCAGGTCAAAGACACAAACCTTCTCGCTCGT
* *
41706390 -CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACC
1 GCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACC
* * * *
41706454 TTGCCTCTCTCGGTTGTGATGGAGCTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACGGC
66 TTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC
* *
41706519 GAAGCAGGTTAAAGACACAAACCTTGCCTCTCTCGGTTGTGAT
131 GAAGCAGGTCAAAGACACAAACCTT--CTCGCTC------G-T
41706562 GGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAA
1 ---GCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAA
* * * * *
41706627 ACCTTGCCTCCCTCGGTTATGATGGATCTGGTTGAAGACAACAGATCTTGCCTTCTTGCATTGAC
63 ACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGAC
*
41706692 AGCGAAGCAGGTCGAAGAC
128 AGCGAAGCAGGTCAAAGAC
41706711 GAACCTTACC
Statistics
Matches: 275, Mismatches: 28, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
158 136 0.49
159 3 0.01
162 1 0.00
163 1 0.00
164 1 0.00
172 1 0.00
176 132 0.48
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24
Consensus pattern (164 bp):
GCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACC
TTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC
GAAGCAGGTCAAAGACACAAACCTTCTCGCTCGT
Found at i:41706546 original size:88 final size:88
Alignment explanation
Indices: 41706390--41706750 Score: 539
Period size: 88 Copynumber: 4.1 Consensus size: 88
41706380 AACTTTGCCT
*
41706390 CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
41706455 TGCCTCTCTCGGTTGTGATGGAG
66 TGCCTCTCTCGGTTGTGATGGAG
* * * * *
41706478 CTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACGGCGAAGCAGGTTAAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
41706543 TGCCTCTCTCGGTTGTGATGGAG
66 TGCCTCTCTCGGTTGTGATGGAG
*
41706566 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
* * *
41706631 TGCCTCCCTCGGTTATGATGGAT
66 TGCCTCTCTCGGTTGTGATGGAG
* * * *
41706654 CTGGTTGAAGACAACAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGGTCGAAG--ACGAACCT
1 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
* *
41706717 TACCTTTCTCGGTTGT-AGTGGAG
66 TGCCTCTCTCGGTTGTGA-TGGAG
*
41706740 CTGGCTGAAGA
1 CTGGTTGAAGA
41706751 ATTTCAGATC
Statistics
Matches: 248, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
85 1 0.00
86 33 0.13
88 214 0.86
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (88 bp):
CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
TGCCTCTCTCGGTTGTGATGGAG
Found at i:41706578 original size:246 final size:246
Alignment explanation
Indices: 41706144--41706636 Score: 806
Period size: 246 Copynumber: 2.0 Consensus size: 246
41706134 TGTGATGGAG
* ** * *
41706144 CTGGTTGAAGACAAAAGATCTTGCCTTTTTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
* * * *
41706209 TGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCG
66 TGCCTCTCTCGGTTGTGATGGAGCTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACAGCG
* * * *
41706274 AAGCAGGTCGAAGACGCAAATCTTGCCCCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
131 AAGCAGGTCAAAGACACAAACCTTGCCCCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
* *
41706339 CTTGCCTTCCTGCATTGATAACGAAGCAGGTCAAAGACACAAACTTTGCCT
196 CTTGCCTTCCTGCATTGACAACGAAGCAGGTCAAAGACACAAACCTTGCCT
41706390 CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
*
41706455 TGCCTCTCTCGGTTGTGATGGAGCTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACGGCG
66 TGCCTCTCTCGGTTGTGATGGAGCTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACAGCG
* *
41706520 AAGCAGGTTAAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
131 AAGCAGGTCAAAGACACAAACCTTGCCCCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
* *
41706585 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
196 CTTGCCTTCCTGCATTGACAACGAAGCAGGTCAAAGACACAAACCTTGCCT
41706636 C
1 C
41706637 CCTCGGTTAT
Statistics
Matches: 227, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
246 227 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (246 bp):
CTGGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
TGCCTCTCTCGGTTGTGATGGAGCTAGTTAAAGACAAAAGATCTTGCCTTCCTACATTGACAGCG
AAGCAGGTCAAAGACACAAACCTTGCCCCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
CTTGCCTTCCTGCATTGACAACGAAGCAGGTCAAAGACACAAACCTTGCCT
Found at i:41706633 original size:44 final size:44
Alignment explanation
Indices: 41706392--41706710 Score: 158
Period size: 44 Copynumber: 7.2 Consensus size: 44
41706382 CTTTGCCTCT
* * *
41706392 GGTTGAAGACAAAAGATCTTGACTTCCTGCATTGACAGCGAAGCA
1 GGTTGAAGACACAA-ACCTTGCCTTCCTGCATTGACAGCGAAGCA
** ** *
41706437 GGTCAAAGACACAAACCTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTA
1 GGTTGAAGACACAAACCTTGCCTTC-CT-GCAT-TGACAGCGAAGC-A
* * * * *
41706481 -GTTAAAGACAAAAGATCTTGCCTTCCTACATTGACGGCGAAGCA
1 GGTTGAAGACACAA-ACCTTGCCTTCCTGCATTGACAGCGAAGCA
* ** * *
41706525 GGTTAAAGACACAAACCTTGCC-TCTCTCGGTTGTGA-TG-G-AGCT
1 GGTTGAAGACACAAACCTTGCCTTC-CT-GCAT-TGACAGCGAAGCA
* *
41706568 GGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCA
1 GGTTGAAGACACAA-ACCTTGCCTTCCTGCATTGACAGCGAAGCA
* * ** * * *
41706613 GGTCGAAGACACAAACCTTGCCTCCCTCGGTTATGA-TG-G-ATCT
1 GGTTGAAGACACAAACCTTGCCTTCCT-GCAT-TGACAGCGAAGCA
* * *
41706656 GGTTGAAGACAACAGATCTTGCCTTCTTGCATTGACAGCGAAGCA
1 GGTTGAAGAC-ACAAACCTTGCCTTCCTGCATTGACAGCGAAGCA
*
41706701 GGTCGAAGAC
1 GGTTGAAGAC
41706711 GAACCTTACC
Statistics
Matches: 201, Mismatches: 49, Indels: 48
0.67 0.16 0.16
Matches are distributed among these distances:
42 9 0.04
43 52 0.26
44 67 0.33
45 64 0.32
46 9 0.04
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (44 bp):
GGTTGAAGACACAAACCTTGCCTTCCTGCATTGACAGCGAAGCA
Found at i:41706854 original size:44 final size:45
Alignment explanation
Indices: 41706756--41706875 Score: 120
Period size: 44 Copynumber: 2.7 Consensus size: 45
41706746 GAAGAATTTC
* * * *
41706756 AGATCTTATCTCCCTGAGATTACAGCGGAGTAAATTGAAGTTAGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGTAAATTAAAATGAGA
* * **
41706801 A-ATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATGA-A
1 AGATCTTATCTCCCTGAGATTACAGCGGAGTAAATTAAAATGAGA
* *
41706844 AGATCTTATCTCTCTGA-AGTTACAGCAGAGTA
1 AGATCTTATCTCCCTGAGA-TTACAGCGGAGTA
41706876 GATCGCATCA
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
43 2 0.03
44 57 0.95
45 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (45 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGTAAATTAAAATGAGA
Found at i:41709438 original size:109 final size:109
Alignment explanation
Indices: 41709049--41709467 Score: 659
Period size: 108 Copynumber: 3.9 Consensus size: 109
41709039 AAATTGTTCC
* *
41709049 AAAATAAGGCAATGTTTTGCTTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTTGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
41709114 TCTCGTTCGACCAAATAGCTAAATATCC-TTTAAAAACTTTTCA
66 TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
*
41709157 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAATGTGCCCTAAGGTACTGGGTTTCGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
* *
41709222 TCTCGTTCCACCAAAT-GACTTAATATCCTTTTCAAAAA-TTTTC-
66 TCTCGTTCGACCAAATAG-CTAAATATCCTTTT-AAAAACTTTTCA
*
41709265 AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
41709330 TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
66 TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
* **
41709374 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGTTGGGTTTCGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
* * * *
41709439 TCACGTT-TAGGCAAATTGCTAAATATCCT
66 TCTCGTTCGA-CCAAATAGCTAAATATCCT
41709468 CTTGAATTTT
Statistics
Matches: 287, Mismatches: 17, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
107 6 0.02
108 183 0.64
109 93 0.32
110 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (109 bp):
AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
Found at i:41709940 original size:22 final size:22
Alignment explanation
Indices: 41709897--41709940 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
41709887 TAAACTATTA
* *
41709897 AAAATTTTCATTCATTTCATTT
1 AAAATTTTCAATCATTTAATTT
* *
41709919 AAAATTTTTAATCCTTTAATTT
1 AAAATTTTCAATCATTTAATTT
41709941 TCTAAACGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (22 bp):
AAAATTTTCAATCATTTAATTT
Found at i:41711636 original size:60 final size:60
Alignment explanation
Indices: 41711569--41711700 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
41711559 AAAACTTTGA
*
41711569 CAAGTACCAAATCCAACAAAAAAAAAGATTAAGTACCAAATTAGGAAAAAGAGTCAAGTT
1 CAAGTACCAAATCCAACAAAAAAAAAGATTAAGTACCAAATTAAGAAAAAGAGTCAAGTT
** **** * * * *
41711629 CAAGTACCAAATTGAACCCTCAAAAAGTTTAAGTACCAACTTAAGAAAAAGTGTTAAGTT
1 CAAGTACCAAATCCAACAAAAAAAAAGATTAAGTACCAAATTAAGAAAAAGAGTCAAGTT
* *
41711689 TAGGTACCAAAT
1 CAAGTACCAAAT
41711701 TAGGAAAAAG
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (60 bp):
CAAGTACCAAATCCAACAAAAAAAAAGATTAAGTACCAAATTAAGAAAAAGAGTCAAGTT
Found at i:41711637 original size:31 final size:31
Alignment explanation
Indices: 41711599--41711731 Score: 101
Period size: 31 Copynumber: 4.4 Consensus size: 31
41711589 AAAAAAGATT
41711599 AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
1 AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
**** ** *
41711630 AAGTACCAAATT--GAACCCTCA-AAAAGTTT
1 AAGTACCAAATTAGGAA-AAAGAGTCAAGTTC
* * * * *
41711659 AAGTACCAACTTAAGAAAAAGTGTTAAGTTT
1 AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
* *
41711690 AGGTACCAAATTAGGAAAAAGTGTCAAGTTC
1 AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
*
41711721 AGGTACCAAAT
1 AAGTACCAAAT
41711732 GTTATATTAA
Statistics
Matches: 78, Mismatches: 20, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
29 19 0.24
30 1 0.01
31 58 0.74
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.23
Consensus pattern (31 bp):
AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
Found at i:41719340 original size:3 final size:3
Alignment explanation
Indices: 41719332--41719404 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
41719322 TTTCATTCTG
*
41719332 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41719380 ATA ATA AT- ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
41719405 TCTGCATTCC
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:41720560 original size:19 final size:19
Alignment explanation
Indices: 41720536--41720576 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
41720526 TGATTTATTC
41720536 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
*
41720555 TAAGATTTATCTACTTAAA
1 TAAGATTTATCTACCTAAA
41720574 TAA
1 TAA
41720577 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:41724330 original size:42 final size:43
Alignment explanation
Indices: 41724243--41724335 Score: 131
Period size: 42 Copynumber: 2.2 Consensus size: 43
41724233 AACTGAATTT
* *
41724243 AAATAATTC-CTTTATTCTAATAAACTACTAAAAAGATGAGAA
1 AAATAATTCTCTTTATTCTAATAAACTACTAAAAAGATAAAAA
41724285 AAATAATTCTC-TTATTCTAATAAACTACT-AAAAGATAAAATA
1 AAATAATTCTCTTTATTCTAATAAACTACTAAAAAGATAAAA-A
41724327 AAAT-ATTCT
1 AAATAATTCT
41724336 TAGAATATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
41 14 0.30
42 32 0.68
43 1 0.02
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (43 bp):
AAATAATTCTCTTTATTCTAATAAACTACTAAAAAGATAAAAA
Found at i:41724388 original size:23 final size:24
Alignment explanation
Indices: 41724362--41724409 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
41724352 ATTTATTCTA
41724362 AGATTTATCTAC-TAAATAAATTT
1 AGATTTATCTACTTAAATAAATTT
*
41724385 AGATTTATCTACTTAAATAACTTT
1 AGATTTATCTACTTAAATAAATTT
41724409 A
1 A
41724410 AAATATATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (24 bp):
AGATTTATCTACTTAAATAAATTT
Found at i:41725218 original size:2 final size:2
Alignment explanation
Indices: 41725211--41725235 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41725201 ATTGATTATA
41725211 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
41725236 GAAGCAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:41725482 original size:7 final size:7
Alignment explanation
Indices: 41725470--41725496 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
41725460 TTTCTGAAGT
41725470 AAAAATA
1 AAAAATA
41725477 AAAAATA
1 AAAAATA
41725484 AAAAATA
1 AAAAATA
41725491 AAAAAT
1 AAAAAT
41725497 GTAATATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:41733046 original size:20 final size:18
Alignment explanation
Indices: 41732999--41733047 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
41732989 CAAGATAAAC
41732999 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
41733016 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
41733036 ATTAAATTAATA
1 ATTAAATTAATA
41733048 AAATACTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:41742587 original size:25 final size:26
Alignment explanation
Indices: 41742559--41742608 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
41742549 GTTTTTAAGT
41742559 TTTTA-TATATTTTTTATG-TTATTTA
1 TTTTACTATA-TTTTTATGTTTATTTA
*
41742584 TTTTACTTTATTTTTATGTTTATTT
1 TTTTACTATATTTTTATGTTTATTT
41742609 TTGAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (26 bp):
TTTTACTATATTTTTATGTTTATTTA
Found at i:41747647 original size:38 final size:37
Alignment explanation
Indices: 41747559--41747649 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 37
41747549 GACCCATTAC
* *
41747559 GTGGTGTGTAGGGTGGATGGGCCTATCATGGTCCTAT
1 GTGGTGTGTAGGGTGGATAGGCCTATCATAGTCCTAT
* *
41747596 GTGGTGTGTAGGGTTGATAGGCTTATCATAG-CCTAT
1 GTGGTGTGTAGGGTGGATAGGCCTATCATAGTCCTAT
*
41747632 AAGTGGTGTGCAGGGTGG
1 --GTGGTGTGTAGGGTGG
41747650 TCGGAGTGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 5 0.11
37 27 0.59
38 14 0.30
ACGTcount: A:0.16, C:0.11, G:0.41, T:0.32
Consensus pattern (37 bp):
GTGGTGTGTAGGGTGGATAGGCCTATCATAGTCCTAT
Found at i:41750345 original size:28 final size:27
Alignment explanation
Indices: 41750313--41750384 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 27
41750303 ATTATTAATA
41750313 TTGAATTGAGGATATTAATTG-TTTACGG
1 TTGAATTGAGGATATTAA--GATTTACGG
* * *
41750341 TTGAATGTAAGG-TGAGTGAGATTTACGG
1 TTGAAT-TGAGGAT-ATTAAGATTTACGG
41750369 TTGAATTGAGGATATT
1 TTGAATTGAGGATATT
41750385 GTGGAAGTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
27 7 0.20
28 21 0.60
29 7 0.20
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (27 bp):
TTGAATTGAGGATATTAAGATTTACGG
Found at i:41750524 original size:20 final size:20
Alignment explanation
Indices: 41750499--41750601 Score: 89
Period size: 20 Copynumber: 5.2 Consensus size: 20
41750489 GCTTGTATGG
*
41750499 GTTTGCACTTCGGTGTCTCT
1 GTTTGCACTTCGGTGCCTCT
41750519 GTTTGCACTTCGGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
* * **
41750539 GATTGCAGTTCTATGCCTCT
1 GTTTGCACTTCGGTGCCTCT
* * ** *
41750559 GATTCCACTTCAATGCCCCT
1 GTTTGCACTTCGGTGCCTCT
** *
41750579 AATTGCACTTCGGTGCCTTT
1 GTTTGCACTTCGGTGCCTCT
41750599 GTT
1 GTT
41750602 ATTATTTCGA
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.12, C:0.28, G:0.20, T:0.40
Consensus pattern (20 bp):
GTTTGCACTTCGGTGCCTCT
Found at i:41750545 original size:40 final size:40
Alignment explanation
Indices: 41750501--41750596 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
41750491 TTGTATGGGT
* * * ** * *
41750501 TTGCACTTCGGTGTCTCTGTTTGCACTTCGGTGCCTCTGA
1 TTGCACTTCGGTGCCTCTGATTCCACTTCAATGCCCCTAA
* **
41750541 TTGCAGTTCTATGCCTCTGATTCCACTTCAATGCCCCTAA
1 TTGCACTTCGGTGCCTCTGATTCCACTTCAATGCCCCTAA
41750581 TTGCACTTCGGTGCCT
1 TTGCACTTCGGTGCCT
41750597 TTGTTATTAT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.12, C:0.30, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCACTTCGGTGCCTCTGATTCCACTTCAATGCCCCTAA
Found at i:41759523 original size:32 final size:32
Alignment explanation
Indices: 41759447--41759524 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
41759437 AATTATTTAT
* *
41759447 TGAAAACATTTTCTGGTGTTTGGATGAATCTG
1 TGAAAATATTTTCTGGTGTTTGGATGAATCTC
* * *
41759479 TGTAAAATATTTTCTGTTGTTTGGCA-GATTTTC
1 TG-AAAATATTTTCTGGTGTTTGG-ATGAATCTC
41759512 TGAAAATATTTTC
1 TGAAAATATTTTC
41759525 CGGAAAAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
32 13 0.33
33 25 0.64
34 1 0.03
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.46
Consensus pattern (32 bp):
TGAAAATATTTTCTGGTGTTTGGATGAATCTC
Found at i:41768949 original size:16 final size:15
Alignment explanation
Indices: 41768923--41768983 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 15
41768913 GCAACCCAAT
41768923 TTTTA-TTTTATTTA
1 TTTTATTTTTATTTA
41768937 TTATTATTTTTATTTA
1 TT-TTATTTTTATTTA
*
41768953 CTTTATTTATTACTTTA
1 TTTTATTT-TTA-TTTA
41768970 TTTTATTATTTATT
1 TTTTATT-TTTATT
41768984 ACTTATTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 2 0.05
15 9 0.22
16 15 0.38
17 13 0.32
18 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTTTTATTTA
Found at i:41768957 original size:25 final size:26
Alignment explanation
Indices: 41768924--41768973 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
41768914 CAACCCAATT
*
41768924 TTTATTTTATTTATTA-TTATTTTTA
1 TTTACTTTATTTATTACTTATTTTTA
41768949 TTTACTTTATTTATTACTTTATTTT
1 TTTACTTTATTTATTAC-TTATTTT
41768974 ATTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
27 7 0.32
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTACTTTATTTATTACTTATTTTTA
Found at i:41768971 original size:8 final size:7
Alignment explanation
Indices: 41768937--41768990 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
41768927 ATTTTATTTA
41768937 TTATTAT
1 TTATTAT
41768944 TT-TTAT
1 TTATTAT
41768950 TTACTTTAT
1 TTA--TTAT
41768959 TTATTACT
1 TTATTA-T
41768967 TTA-T-T
1 TTATTAT
41768972 TTATTAT
1 TTATTAT
*
41768979 TTATTAC
1 TTATTAT
41768986 TTATT
1 TTATT
41768991 TGGATATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
5 4 0.10
6 7 0.17
7 18 0.45
8 4 0.10
9 7 0.17
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTAT
Found at i:41770007 original size:102 final size:102
Alignment explanation
Indices: 41769823--41770009 Score: 286
Period size: 102 Copynumber: 1.8 Consensus size: 102
41769813 TTTAAGAACA
*
41769823 TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGTGTCAAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
* * *
41769888 GTGTTCTTAAGAAAAAAATTATAATAAATTAGGAGTC
66 ATGTCCTAAAGAAAAAAATTATAATAAATTAGGAGTC
* *
41769925 TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGTTGTCATCTCTCTTCGCGTCAAAAGGTTCAGT
1 TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGCGTCAAAAGGTTC-G-
41769990 ATAT-TCCTAAAGTAAAAAAA
64 ATATGTCCTAAAG-AAAAAAA
41770010 AAAGAAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
102 59 0.78
103 7 0.09
104 10 0.13
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.32
Consensus pattern (102 bp):
TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
ATGTCCTAAAGAAAAAAATTATAATAAATTAGGAGTC
Found at i:41775257 original size:25 final size:25
Alignment explanation
Indices: 41775229--41775276 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41775219 AGATAGTACG
*
41775229 CCAAAAAGGCTTTTCAGAGAATTTT
1 CCAAAAAGGCTTCTCAGAGAATTTT
* *
41775254 CCAAAAAGTCTTCTGAGAGAATT
1 CCAAAAAGGCTTCTCAGAGAATT
41775277 CACCACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (25 bp):
CCAAAAAGGCTTCTCAGAGAATTTT
Found at i:41779961 original size:12 final size:12
Alignment explanation
Indices: 41779944--41779969 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41779934 TGATATTATA
41779944 TTTTAAAATATT
1 TTTTAAAATATT
41779956 TTTTAAAATATT
1 TTTTAAAATATT
41779968 TT
1 TT
41779970 ATATAAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAAAATATT
Found at i:41784714 original size:16 final size:16
Alignment explanation
Indices: 41784693--41784761 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
41784683 GATTAGCTAT
*
41784693 TACACCACTAATCCAA
1 TACACCTCTAATCCAA
41784709 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
41784726 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
41784742 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
41784758 TACA
1 TACA
41784762 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 35 0.69
17 16 0.31
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:41784737 original size:33 final size:32
Alignment explanation
Indices: 41784693--41784761 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
41784683 GATTAGCTAT
41784693 TACACCACTAATCCAATACACCTCTAATCCCAA
1 TACACCACTAATCCAATACACCTCTAAT-CCAA
*
41784726 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCACTAATCCAATACACCTCTAATCCAA
41784758 TACA
1 TACA
41784762 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (32 bp):
TACACCACTAATCCAATACACCTCTAATCCAA
Found at i:41785446 original size:21 final size:22
Alignment explanation
Indices: 41785420--41785460 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
41785410 AATATAAACA
41785420 TATACTATATT-A-TAAAAATAG
1 TATACT-TATTCATTAAAAATAG
41785441 TATACTTATTCATTAAAAAT
1 TATACTTATTCATTAAAAAT
41785461 TGTTATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (22 bp):
TATACTTATTCATTAAAAATAG
Found at i:41787277 original size:18 final size:18
Alignment explanation
Indices: 41787238--41787280 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
41787228 GTTATTTCAT
* *
41787238 TTATACAATTTCTTTTTT
1 TTATTCAATTTCTTTTTG
41787256 TTATTCAATTT-TTTTTGG
1 TTATTCAATTTCTTTTT-G
41787274 TTATTCA
1 TTATTCA
41787281 CCCATGTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (18 bp):
TTATTCAATTTCTTTTTG
Found at i:41791730 original size:13 final size:13
Alignment explanation
Indices: 41791712--41791744 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
41791702 AATAAATATA
41791712 TATTTTTTATTTT
1 TATTTTTTATTTT
41791725 TATTTTTTTATTTT
1 TA-TTTTTTATTTT
41791739 TATTTT
1 TATTTT
41791745 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:41791999 original size:17 final size:18
Alignment explanation
Indices: 41791968--41792009 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
41791958 TAGCCTAGAA
*
41791968 TATTTG-GATAAATTA-T
1 TATTTGAGAAAAATTAGT
41791984 TATTTGAGAAAAATTAGT
1 TATTTGAGAAAAATTAGT
41792002 TGATTTGA
1 T-ATTTGA
41792010 TAGAGTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
18 2 0.09
19 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (18 bp):
TATTTGAGAAAAATTAGT
Found at i:41792599 original size:42 final size:42
Alignment explanation
Indices: 41792540--41792622 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
41792530 AAGTTTCCGT
* * **
41792540 TTAACCATTATAGGTTTCCGTTCAGTTCTTTTGAGCTTCTGA
1 TTAACCATTATAGGTTTCCATTCAGCTCTGATGAGCTTCTGA
*
41792582 TTAACCCTTAT-GAGTTTCCATTCAGCTCTGATGAGCTTCTG
1 TTAACCATTATAG-GTTTCCATTCAGCTCTGATGAGCTTCTG
41792623 TTCAACCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (42 bp):
TTAACCATTATAGGTTTCCATTCAGCTCTGATGAGCTTCTGA
Found at i:41799349 original size:25 final size:24
Alignment explanation
Indices: 41799296--41799350 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
41799286 TATTTACTTT
* *
41799296 AATATTTAAAAATTTTAAATGAAT
1 AATATTAAAAAATTTTAAATGAAA
*
41799320 GATATTAAATAAATTTTAAAT-ATAA
1 AATATTAAA-AAATTTTAAATGA-AA
41799345 AATATT
1 AATATT
41799351 TATCAATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AATATTAAAAAATTTTAAATGAAA
Found at i:41801795 original size:9 final size:9
Alignment explanation
Indices: 41801776--41801818 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
41801766 CAAAGTAAAT
41801776 ATTAA-TTA
1 ATTAATTTA
41801784 ATTAATTTA
1 ATTAATTTA
*
41801793 ATTAATCTA
1 ATTAATTTA
* *
41801802 ATTAACTAA
1 ATTAATTTA
41801811 ATTAATTT
1 ATTAATTT
41801819 CTCAATTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (9 bp):
ATTAATTTA
Found at i:41801795 original size:13 final size:13
Alignment explanation
Indices: 41801777--41801818 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
41801767 AAAGTAAATA
41801777 TTAATTAATTAAT
1 TTAATTAATTAAT
41801790 TTAATTAATCTAA-
1 TTAATTAAT-TAAT
*
41801803 TTAACTAAATTAAT
1 TTAA-TTAATTAAT
41801817 TT
1 TT
41801819 CTCAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTAATTAAT
Found at i:41804501 original size:23 final size:21
Alignment explanation
Indices: 41804475--41804518 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
41804465 CTAATTATTT
*
41804475 TAAAAGGTTAATTAGTAATTAAA
1 TAAAAGGTAAATTA--AATTAAA
*
41804498 TAAATGGTAAATTAAATTAAA
1 TAAAAGGTAAATTAAATTAAA
41804519 GGATGGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (21 bp):
TAAAAGGTAAATTAAATTAAA
Found at i:41805110 original size:30 final size:30
Alignment explanation
Indices: 41805044--41805111 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
41805034 ACGGGTTGTC
* *
41805044 ACACGGCCGTGTACTACACACGGTATCTAT
1 ACACGGTCGTGTACTACACACGATATCTAT
* *
41805074 ACACGGTCGTGTACTACACACGATCTCTGT
1 ACACGGTCGTGTACTACACACGATATCTAT
41805104 ACACGGTC
1 ACACGGTC
41805112 TTGTGATCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.24
Consensus pattern (30 bp):
ACACGGTCGTGTACTACACACGATATCTAT
Found at i:41815126 original size:23 final size:24
Alignment explanation
Indices: 41815100--41815151 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
41815090 TTAAAATGAC
*
41815100 TAAATATCATAAAGAAG-ATAA-AA
1 TAAAAATCA-AAAGAAGCATAATAA
*
41815123 TAAAAATCAAATGAAGCATAATAA
1 TAAAAATCAAAAGAAGCATAATAA
41815147 TAAAA
1 TAAAA
41815152 TAAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 12 0.48
24 7 0.28
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (24 bp):
TAAAAATCAAAAGAAGCATAATAA
Found at i:41815127 original size:5 final size:5
Alignment explanation
Indices: 41815117--41815213 Score: 72
Period size: 5 Copynumber: 18.0 Consensus size: 5
41815107 CATAAAGAAG
* *
41815117 ATAAA ATAAAA ATCAA ATGAAGC ATAATA ATAAA AT-AA ATAAA ATAAAA
1 ATAAA AT-AAA ATAAA AT-AA-A ATAA-A ATAAA ATAAA ATAAA AT-AAA
*
41815166 ATAATTA ATAAA ATACTAA AT-AA ATAAA ATAGA ATAAA ATAAA ATAAA
1 ATAA--A ATAAA ATA--AA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
41815214 TGAAGGCAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 20
0.74 0.07 0.20
Matches are distributed among these distances:
4 8 0.11
5 39 0.52
6 17 0.23
7 11 0.15
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:41815156 original size:22 final size:21
Alignment explanation
Indices: 41815108--41815165 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 21
41815098 ACTAAATATC
41815108 ATAAA-GAAGATAAAATAAAA
1 ATAAATGAAGATAAAATAAAA
41815128 ATCAAATGAAGCATAATAAT-AAA
1 AT-AAATGAAG-ATAA-AATAAAA
*
41815151 ATAAAT-AAAATAAAA
1 ATAAATGAAGATAAAA
41815166 ATAATTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 2 0.06
20 6 0.18
21 5 0.15
22 8 0.24
23 9 0.27
24 3 0.09
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (21 bp):
ATAAATGAAGATAAAATAAAA
Found at i:41815166 original size:15 final size:13
Alignment explanation
Indices: 41815145--41815214 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 13
41815135 GAAGCATAAT
41815145 AATAAAATAAATAA
1 AATAAAATAAAT-A
*
41815159 AATAAAA-ATAATT
1 AATAAAATA-AATA
41815172 AATAAAATACTAAATA
1 AAT-AAA-A-TAAATA
41815188 AATAAAATAGAATAA
1 AATAAAATA-AAT-A
41815203 AATAAAATAAAT
1 AATAAAATAAAT
41815215 GAAGGCAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
13 6 0.13
14 20 0.43
15 14 0.30
16 6 0.13
17 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:41815187 original size:34 final size:31
Alignment explanation
Indices: 41815149--41815211 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 31
41815139 CATAATAATA
41815149 AAATAAATAAAATAAAAATAATTAATAAAATACT
1 AAATAAATAAAAT-AAAATAA--AATAAAATACT
*
41815183 AAATAAATAAAATAGAATAAAATAAAATA
1 AAATAAATAAAATAAAATAAAATAAAATA
41815212 AATGAAGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.32
33 6 0.21
34 13 0.46
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (31 bp):
AAATAAATAAAATAAAATAAAATAAAATACT
Found at i:41819691 original size:37 final size:37
Alignment explanation
Indices: 41819641--41819716 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
41819631 AACATGGTGA
* *
41819641 CTGCATCTAAATTAAAGACACCGGTTGTTTTCATTGG
1 CTGCATCTAAATTAAAGACACCGGCTGTTTTCATCGG
*
41819678 CTGCATCTAAATTAAAGACACTGGCTGTTTTCATCGG
1 CTGCATCTAAATTAAAGACACCGGCTGTTTTCATCGG
41819715 CT
1 CT
41819717 TCGTCCTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (37 bp):
CTGCATCTAAATTAAAGACACCGGCTGTTTTCATCGG
Found at i:41825486 original size:16 final size:16
Alignment explanation
Indices: 41825465--41825508 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
41825455 AATGAAAAGG
*
41825465 TTGAAAAGGATGCCAA
1 TTGAAAAGGATACCAA
41825481 TTGAAAAGGATACCAA
1 TTGAAAAGGATACCAA
*
41825497 ATGAAAAGGATA
1 TTGAAAAGGATA
41825509 TCATTGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18
Consensus pattern (16 bp):
TTGAAAAGGATACCAA
Found at i:41829178 original size:22 final size:22
Alignment explanation
Indices: 41829123--41829175 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
41829113 ATTTTATGAA
*
41829123 AATTATGTGTGAATTAATTAGTT
1 AATTAAGT-TGAATTAATTAGTT
* *
41829146 AATTGAGTTGAATTTATTAGTT
1 AATTAAGTTGAATTAATTAGTT
41829168 AA-TAAGTT
1 AATTAAGTT
41829176 TGAGTTGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 5 0.19
22 15 0.58
23 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (22 bp):
AATTAAGTTGAATTAATTAGTT
Done.