Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 129 of 187
Found at i:39160245 original size:26 final size:26
Alignment explanation
Indices: 39160213--39160274 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
39160203 TTTGGCAATA
39160213 CTTTTGAAAAGTG-ATGTGAAAAAGTG
1 CTTTTGAAAAGTGCATGTG-AAAAGTG
* * * *
39160239 CTTTTGAGAAGTGCTTTTGAGAAGTG
1 CTTTTGAAAAGTGCATGTGAAAAGTG
39160265 CTTTTGAAAA
1 CTTTTGAAAA
39160275 ATTTGAGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 27 0.90
27 3 0.10
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (26 bp):
CTTTTGAAAAGTGCATGTGAAAAGTG
Found at i:39160250 original size:13 final size:13
Alignment explanation
Indices: 39160234--39160271 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
39160224 TGATGTGAAA
39160234 AAGTGCTTTTGAG
1 AAGTGCTTTTGAG
39160247 AAGTGCTTTTGAG
1 AAGTGCTTTTGAG
39160260 AAGTGCTTTTGA
1 AAGTGCTTTTGA
39160272 AAAATTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (13 bp):
AAGTGCTTTTGAG
Found at i:39167632 original size:46 final size:47
Alignment explanation
Indices: 39167581--39167748 Score: 189
Period size: 46 Copynumber: 3.6 Consensus size: 47
39167571 TAAGCTCATT
* *
39167581 CATATGTTGCAGACTCGAGATTACAGGAA-TAGGTTTCGAGCTCCTA
1 CATATGTTGCAGACTCGAGAATACAGGAATTAGGTTTCGAGCTCCTG
* * * *
39167627 CATATGTTGTAGACTCGAGAATATA-GAATTAGGTTCCAAGCTCCTG
1 CATATGTTGCAGACTCGAGAATACAGGAATTAGGTTTCGAGCTCCTG
* * * * *
39167673 CATATGTTGCGGACTTGAGAATAC-GGAATTAGGTTTTGTGTTCCTG
1 CATATGTTGCAGACTCGAGAATACAGGAATTAGGTTTCGAGCTCCTG
* * *
39167719 TATCTGTTGCAGACTCGAGAATACAAGAAT
1 CATATGTTGCAGACTCGAGAATACAGGAAT
39167749 ATTAAGCCTT
Statistics
Matches: 99, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
45 3 0.03
46 92 0.93
47 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (47 bp):
CATATGTTGCAGACTCGAGAATACAGGAATTAGGTTTCGAGCTCCTG
Found at i:39167727 original size:92 final size:92
Alignment explanation
Indices: 39167565--39167741 Score: 221
Period size: 92 Copynumber: 1.9 Consensus size: 92
39167555 GAGTTTGCCC
* * *
39167565 AGGTTCTAAGCTCATTCATATGTTGCAGACTCGAGATTACAGGAATAGGTTTCGAGCTCCTACAT
1 AGGTTCCAAGCTCATGCATATGTTGCAGACTCGAGAATACAGGAATAGGTTTCGAGCTCCTACAT
*
39167630 ATGTTGTAGACTCGAGAATATAGAATT
66 ATGTTGCAGACTCGAGAATATAGAATT
* * * * * * **
39167657 AGGTTCCAAGCTCCTGCATATGTTGCGGACTTGAGAATAC-GGAATTAGGTTTTGTGTTCCTGTA
1 AGGTTCCAAGCTCATGCATATGTTGCAGACTCGAGAATACAGGAA-TAGGTTTCGAGCTCCTACA
*
39167721 TCTGTTGCAGACTCGAGAATA
65 TATGTTGCAGACTCGAGAATA
39167742 CAAGAATATT
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
91 4 0.06
92 67 0.94
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (92 bp):
AGGTTCCAAGCTCATGCATATGTTGCAGACTCGAGAATACAGGAATAGGTTTCGAGCTCCTACAT
ATGTTGCAGACTCGAGAATATAGAATT
Found at i:39178266 original size:75 final size:75
Alignment explanation
Indices: 39178128--39178268 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 75
39178118 GACTTACTAG
* * *
39178128 TTAACATTCAACCTTTCTTTTCTACCAACAAATTTACATATCAAACAACCTATATAGATTCATAT
1 TTAACATTCAACCTTTCTTTTCTACCAACAAATTTACATATCAAACAACCTATACAAAGTCATAT
39178193 TACTCATTAC
66 TACTCATTAC
* * ** *
39178203 TTAATATTCAACCTTTCTTTTCTATCAGTAGATTTACATATCAAACAACCTATACAAAGTCATAT
1 TTAACATTCAACCTTTCTTTTCTACCAACAAATTTACATATCAAACAACCTATACAAAGTCATAT
39178268 T
66 T
39178269 TGCTTATTCG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (75 bp):
TTAACATTCAACCTTTCTTTTCTACCAACAAATTTACATATCAAACAACCTATACAAAGTCATAT
TACTCATTAC
Found at i:39181946 original size:10 final size:10
Alignment explanation
Indices: 39181899--39181946 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
39181889 CCATTACGTA
39181899 TTTAATTGTGT
1 TTTAATT-TGT
*
39181910 GTTTATTTTGT
1 -TTTAATTTGT
*
39181921 TTTAAGTTGT
1 TTTAATTTGT
39181931 TTTAATTTGT
1 TTTAATTTGT
*
39181941 CTTAAT
1 TTTAAT
39181947 AGATTTAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 22 0.71
11 3 0.10
12 6 0.19
ACGTcount: A:0.19, C:0.02, G:0.15, T:0.65
Consensus pattern (10 bp):
TTTAATTTGT
Found at i:39191212 original size:49 final size:50
Alignment explanation
Indices: 39191132--39191370 Score: 142
Period size: 50 Copynumber: 4.7 Consensus size: 50
39191122 GATAATAACA
* * * * *
39191132 TGCCAAAGCCATGTCCCAGACATGGTATTACATGAGATGTT-TCATGT-AC
1 TGCCAATGCCATGTCCTAGATATGGTCTTACATGAGA-GTTCTCATATCAC
* * * * *
39191181 TGCCAATGCCATATCCTAGATATGATCTTACATGGGAGTTCTTATATCAG
1 TGCCAATGCCATGTCCTAGATATGGTCTTACATGAGAGTTCTCATATCAC
* ** * ** * *
39191231 TGCCCATGCCATGTCCTAGATATGGTCTTACGGGGGACCTCTCATCTTGA-
1 TGCCAATGCCATGTCCTAGATATGGTCTTACATGAGAGTTCTCAT-ATCAC
* * * * ** *
39191281 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCTAGATATGGTCTTACATGAGAGTTCTCAT-A--TC---AC
* *
39191337 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCTAGATATGGTCTTACATG
39191371 GGATCTCATT
Statistics
Matches: 151, Mismatches: 30, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
48 3 0.02
49 34 0.23
50 77 0.51
51 2 0.01
52 1 0.01
55 1 0.01
56 33 0.22
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGATATGGTCTTACATGAGAGTTCTCATATCAC
Found at i:39192522 original size:46 final size:47
Alignment explanation
Indices: 39192342--39192559 Score: 307
Period size: 47 Copynumber: 4.6 Consensus size: 47
39192332 TCAATTAGGG
* * *
39192342 CAGCATATATATACAACAATTTGGGTAGCATTTAAGCATCAAAATTGGA
1 CAGCATATATGT--AACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
* *
39192391 CAGCATATATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAA
1 CAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
*
39192438 CAGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
1 CAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
*
39192485 CAGCAT-TATGTAACAAATTGGGCAGCATTT-AGACATCAAAATTGGG
1 CAGCATATATGTAACAAATTGGGCAGCATTTAAG-CATCAAAATTGGA
* *
39192531 TAGCAT-TATGTAACAAATTGGGTAGCATT
1 CAGCATATATGTAACAAATTGGGCAGCATT
39192560 ATGTAACAAA
Statistics
Matches: 156, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
45 2 0.01
46 62 0.40
47 81 0.52
49 11 0.07
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (47 bp):
CAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
Found at i:39192576 original size:114 final size:115
Alignment explanation
Indices: 39192439--39192666 Score: 361
Period size: 114 Copynumber: 2.0 Consensus size: 115
39192429 AAAATTGAAC
*
39192439 AGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATT
1 AGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAACATTATGTAACAAATT
* **
39192504 GGGCAGCATTT-AGACATCAAAATTGGGTAGCATTATGTAACAAATTGGGT
66 GGGCAGCATTTAAG-CATCAAAATTCGACAGCATTATGTAACAAATTGGGT
* * *
39192554 AGCAT-TATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGGACAACATTATGTAACAATTT
1 AGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAACATTATGTAACAAATT
*
39192618 GGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACATATTGGG
66 GGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACAAATTGGG
39192667 CGGCATTTAG
Statistics
Matches: 104, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
114 97 0.93
115 7 0.07
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (115 bp):
AGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAACATTATGTAACAAATT
GGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACAAATTGGGT
Found at i:39192595 original size:46 final size:46
Alignment explanation
Indices: 39192545--39192822 Score: 448
Period size: 46 Copynumber: 6.0 Consensus size: 46
39192535 ATTATGTAAC
**
39192545 AAATTGGGTAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
* * *
39192591 AAATTGGACAACATTATGTAACAATTTGGGCAGCATTTAAGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
* * *
39192637 AAATTCGACAGCATTATGTAACATATTGGGCGGCATTTAGGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
*
39192683 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAAGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
*
39192729 AAATTGGACAGCATTATGTAACAAATTGGGCAACATTTAGGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
* *
39192775 AAATTGGACAGCATTATGCAACAAATTGGGCAGCATTTATGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
39192821 AA
1 AA
39192823 TCAATCCATC
Statistics
Matches: 212, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 212 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (46 bp):
AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
Found at i:39192667 original size:160 final size:161
Alignment explanation
Indices: 39192383--39192719 Score: 550
Period size: 160 Copynumber: 2.1 Consensus size: 161
39192373 TTAAGCATCA
* *
39192383 AAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAACAGCATATAT
1 AAATTGGGCAGCAT-TATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAACAACATATAT
*
39192448 ATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCAT
65 ATAACAAATTGGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACAAATTGGGCAGCAT
**
39192513 TTAGACATCAAAATTGGGTAGCATTATGTAAC
130 TTAGACATCAAAATTGGACAGCATTATGTAAC
* * *
39192545 AAATTGGGTAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGGACAACAT-TATG
1 AAATTGGGCAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAACAACATATATA
* * *
39192609 TAACAATTTGGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACATATTGGGCGGCATT
66 TAACAAATTGGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACAAATTGGGCAGCATT
*
39192674 TAGGCATCAAAATTGGACAGCATTATGTAAC
131 TAGACATCAAAATTGGACAGCATTATGTAAC
39192705 AAATTGGGCAGCATT
1 AAATTGGGCAGCATT
39192720 TAAGCATCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
160 106 0.65
161 44 0.27
162 12 0.07
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (161 bp):
AAATTGGGCAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAACAACATATATA
TAACAAATTGGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACAAATTGGGCAGCATT
TAGACATCAAAATTGGACAGCATTATGTAAC
Found at i:39192711 original size:114 final size:114
Alignment explanation
Indices: 39192450--39192697 Score: 318
Period size: 114 Copynumber: 2.2 Consensus size: 114
39192440 GCATATATAT
* * * *
39192450 AACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCATTT
1 AACAAATTGGACAGCATTTAGGCAACAAAATTGGACAACATTATGTAACAAATTGGGCAGCATTT
* ** * * *
39192515 AGACATCAAAATTGGGTAGCATTATGTAACAAATTGGGTAGCATTATGT
66 AGACATCAAAATTCGACAGCATTATGTAACAAATTGGGCAGCATTAGGC
* * *
39192564 AACAAATTGGGCAGCATTTAGGCATCAAAATTGGACAACATTATGTAACAATTTGGGCAGCATTT
1 AACAAATTGGACAGCATTTAGGCAACAAAATTGGACAACATTATGTAACAAATTGGGCAGCATTT
* *
39192629 A-AGCATCAAAATTCGACAGCATTATGTAACATATTGGGCGGCATTTAGGC
66 AGA-CATCAAAATTCGACAGCATTATGTAACAAATTGGGCAGCA-TTAGGC
*
39192679 ATCAAAATTGGACAGCATT
1 AAC-AAATTGGACAGCATT
39192698 ATGTAACAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
113 1 0.01
114 97 0.82
115 6 0.05
116 14 0.12
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (114 bp):
AACAAATTGGACAGCATTTAGGCAACAAAATTGGACAACATTATGTAACAAATTGGGCAGCATTT
AGACATCAAAATTCGACAGCATTATGTAACAAATTGGGCAGCATTAGGC
Found at i:39192757 original size:160 final size:160
Alignment explanation
Indices: 39192383--39192765 Score: 500
Period size: 160 Copynumber: 2.4 Consensus size: 160
39192373 TTAAGCATCA
* * * * * * *
39192383 AAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAACAGCATATAT
1 AAATTGGGCAGCAT-TAAGCAACAAATTGGACAGCATTTAGGCAACAAAATTGGACAACAT-TAT
*
39192448 ATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCAT
64 ATAACAAATTGGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACAAATTGGGCAGCAT
**
39192513 TTAGACATCAAAATTGGGTAGCATTATGTAAC
129 TTAGACATCAAAATTGGACAGCATTATGTAAC
* * * * * *
39192545 AAATTGGGTAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGGACAACATTATGT
1 AAATTGGGCAGCATTAAGCAACAAATTGGACAGCATTTAGGCAACAAAATTGGACAACATTATAT
* * *
39192610 AACAATTTGGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACATATTGGGCGGCATTT
66 AACAAATTGGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACAAATTGGGCAGCATTT
*
39192675 AGGCATCAAAATTGGACAGCATTATGTAAC
131 AGACATCAAAATTGGACAGCATTATGTAAC
* * * *
39192705 AAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCA-TTATGTAAC-AAATTGGGCAACATT
1 AAATTGGGCAGCA-TTAAGCAAC-AAATTGGACAGCATTTAGGCAACAAAATTGGACAACATT
39192766 TAGGCATCAA
Statistics
Matches: 198, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
160 118 0.60
161 56 0.28
162 24 0.12
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (160 bp):
AAATTGGGCAGCATTAAGCAACAAATTGGACAGCATTTAGGCAACAAAATTGGACAACATTATAT
AACAAATTGGGCAGCATTTAAGCATCAAAATTCGACAGCATTATGTAACAAATTGGGCAGCATTT
AGACATCAAAATTGGACAGCATTATGTAAC
Found at i:39193710 original size:43 final size:43
Alignment explanation
Indices: 39193644--39193767 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 43
39193634 AACTCGTACA
* *
39193644 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCACATA-CCG
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGTAAACACA-AGCCG
*
39193687 ATGCCACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCACTGTCCCAGAC-GTGGTCTTACACGTAAACACAAGCCG
* *
39193730 ATGCCAATGTCCCAGATGTGGTCTTACACG-ATAACACA
1 ATGCCACTGTCCCAGACGTGGTCTTACACGTA-AACACA
39193768 TATCGAAAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
42 5 0.07
43 65 0.92
44 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACGTGGTCTTACACGTAAACACAAGCCG
Found at i:39194025 original size:8 final size:8
Alignment explanation
Indices: 39194012--39194036 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39194002 ACGGACACAG
39194012 TCGACTAC
1 TCGACTAC
39194020 TCGACTAC
1 TCGACTAC
39194028 TCGACTAC
1 TCGACTAC
39194036 T
1 T
39194037 TTTGACTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.28
Consensus pattern (8 bp):
TCGACTAC
Found at i:39200823 original size:46 final size:47
Alignment explanation
Indices: 39200643--39200860 Score: 325
Period size: 47 Copynumber: 4.6 Consensus size: 47
39200633 TCAATTAGGG
* * *
39200643 CAGCATATATATACAACAATTTGGGTAGCATTTAAGCATCAAAATTGGA
1 CAGCATATATGT--AACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
* *
39200692 CAGCATATATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAA
1 CAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
*
39200739 CAGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
1 CAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
39200786 CAGCAT-TATGTAACAAATTGGGCAGCATTT-AGACATCAAAATTGGA
1 CAGCATATATGTAACAAATTGGGCAGCATTTAAG-CATCAAAATTGGA
*
39200832 CAGCAT-TATGTAACAAATTGGGTAGCATT
1 CAGCATATATGTAACAAATTGGGCAGCATT
39200861 ATGTAACATA
Statistics
Matches: 158, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
45 2 0.01
46 64 0.41
47 81 0.51
49 11 0.07
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (47 bp):
CAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
Found at i:39200878 original size:114 final size:115
Alignment explanation
Indices: 39200740--39200967 Score: 370
Period size: 114 Copynumber: 2.0 Consensus size: 115
39200730 AAAATTGAAC
39200740 AGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATT
1 AGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATT
* *
39200805 GGGCAGCATTT-AGACATCAAAATTGGACAGCATTATGTAACAAATTGGGT
66 GGGCAGCATTTAAG-CATCAAAATTCGACAACATTATGTAACAAATTGGGT
* * * *
39200855 AGCAT-TATGTAACATATTGGGCAGCATTTAGGCATCAAAATTGGACAGCATTATGTAACAATTT
1 AGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATT
*
39200919 GGGCAGCATTTAAGCATCAAAATTCGACAACATTATGTAACATATTGGG
66 GGGCAGCATTTAAGCATCAAAATTCGACAACATTATGTAACAAATTGGG
39200968 CGGCATTTAG
Statistics
Matches: 105, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
114 98 0.93
115 7 0.07
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (115 bp):
AGCATATATATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATT
GGGCAGCATTTAAGCATCAAAATTCGACAACATTATGTAACAAATTGGGT
Found at i:39200896 original size:46 final size:46
Alignment explanation
Indices: 39200846--39201123 Score: 430
Period size: 46 Copynumber: 6.0 Consensus size: 46
39200836 ATTATGTAAC
** *
39200846 AAATTGGGTAGCATTATGTAACATATTGGGCAGCATTTAGGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
* *
39200892 AAATTGGACAGCATTATGTAACAATTTGGGCAGCATTTAAGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
* * * *
39200938 AAATTCGACAACATTATGTAACATATTGGGCGGCATTTAGGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
*
39200984 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAAGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
* *
39201030 AAATTGGATAGCATTATGTAACAAATTGGGCAGCGTTTAGGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
* *
39201076 AAATTGGACAGCATTATGCAACAAATTGGGCAGCATTTATGCATCA
1 AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
39201122 AA
1 AA
39201124 TCAATCCATC
Statistics
Matches: 209, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 209 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (46 bp):
AAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCA
Found at i:39200968 original size:160 final size:161
Alignment explanation
Indices: 39200684--39201020 Score: 559
Period size: 160 Copynumber: 2.1 Consensus size: 161
39200674 TTAAGCATCA
*
39200684 AAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAACAGCATATAT
1 AAATTGGGCAGCAT-TATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAACAGCATATAT
* *
39200749 ATAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCAT
65 ATAACAAATTGGGCAGCATTTAAGCATCAAAATTCGACAACATTATGTAACAAATTGGGCAGCAT
39200814 TTAGACATCAAAATTGGACAGCATTATGTAAC
130 TTAGACATCAAAATTGGACAGCATTATGTAAC
* * * *
39200846 AAATTGGGTAGCATTATGTAACATATTGGGCAGCATTTAGGCATCAAAATTGGACAGCAT-TATG
1 AAATTGGGCAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAACAGCATATATA
* * *
39200910 TAACAATTTGGGCAGCATTTAAGCATCAAAATTCGACAACATTATGTAACATATTGGGCGGCATT
66 TAACAAATTGGGCAGCATTTAAGCATCAAAATTCGACAACATTATGTAACAAATTGGGCAGCATT
*
39200975 TAGGCATCAAAATTGGACAGCATTATGTAAC
131 TAGACATCAAAATTGGACAGCATTATGTAAC
39201006 AAATTGGGCAGCATT
1 AAATTGGGCAGCATT
39201021 TAAGCATCAA
Statistics
Matches: 163, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
160 107 0.66
161 44 0.27
162 12 0.07
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (161 bp):
AAATTGGGCAGCATTATGTAACAAATTGGGCAGCATTTAGGCATCAAAATTGAACAGCATATATA
TAACAAATTGGGCAGCATTTAAGCATCAAAATTCGACAACATTATGTAACAAATTGGGCAGCATT
TAGACATCAAAATTGGACAGCATTATGTAAC
Found at i:39207218 original size:50 final size:49
Alignment explanation
Indices: 39207128--39207248 Score: 116
Period size: 50 Copynumber: 2.4 Consensus size: 49
39207118 TTATGTACAT
* * * *
39207128 GTATGCTCATACGAGCTATGAATCGGTATGCTCACTCGAGCCATAGATTA
1 GTATGCTCTTACGAGCTAT-AATCAGTATGCTCACACGAGCCATAAATTA
* ** * *
39207178 GTATGCTCTTAGGAGCTATAATTCAGTATGCTTTCACGAGCTATAAATTG
1 GTATGCTCTTACGAGCTATAA-TCAGTATGCTCACACGAGCCATAAATTA
* * *
39207228 GCATGCTCTCATGAGCTATAA
1 GTATGCTCTTACGAGCTATAA
39207249 ATTGGTATAC
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
49 2 0.03
50 56 0.97
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (49 bp):
GTATGCTCTTACGAGCTATAATCAGTATGCTCACACGAGCCATAAATTA
Found at i:39207233 original size:25 final size:25
Alignment explanation
Indices: 39207130--39207269 Score: 95
Period size: 25 Copynumber: 5.6 Consensus size: 25
39207120 ATGTACATGT
* * *
39207130 ATGCTCAT-ACGAGCTATGAATCGGT
1 ATGCTC-TCACGAGCTATAAATTGGC
* * * * * *
39207155 ATGCTCACTCGAGCCATAGATTAGT
1 ATGCTCTCACGAGCTATAAATTGGC
* * * *
39207180 ATGCTCTTAGGAGCTAT-AATTCAGT
1 ATGCTCTCACGAGCTATAAATT-GGC
*
39207205 ATGCTTTCACGAGCTATAAATTGGC
1 ATGCTCTCACGAGCTATAAATTGGC
* *
39207230 ATGCTCTCATGAGCTATAAATTGGT
1 ATGCTCTCACGAGCTATAAATTGGC
*
39207255 ATACTCTCACGAGCT
1 ATGCTCTCACGAGCT
39207270 GTGGATTATC
Statistics
Matches: 89, Mismatches: 23, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
24 3 0.03
25 82 0.92
26 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (25 bp):
ATGCTCTCACGAGCTATAAATTGGC
Found at i:39213208 original size:23 final size:23
Alignment explanation
Indices: 39213165--39213217 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
39213155 GATTGTATAA
*
39213165 TTTTCTCTTTAGATTTAGTTTTAT
1 TTTTCTCTTTA-ACTTAGTTTTAT
39213189 TTTTCTCTTT-ACTTAGGTTTTAT
1 TTTTCTCTTTAACTTA-GTTTTAT
*
39213212 ATTTCT
1 TTTTCT
39213218 ATTCTTATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 4 0.15
23 12 0.46
24 10 0.38
ACGTcount: A:0.15, C:0.11, G:0.08, T:0.66
Consensus pattern (23 bp):
TTTTCTCTTTAACTTAGTTTTAT
Found at i:39214630 original size:17 final size:17
Alignment explanation
Indices: 39214610--39214643 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39214600 ATCTAACTAA
* *
39214610 TATAATGAAACATATAT
1 TATAATAAAACAAATAT
39214627 TATAATAAAACAAATAT
1 TATAATAAAACAAATAT
39214644 AGTAGAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (17 bp):
TATAATAAAACAAATAT
Found at i:39214880 original size:18 final size:18
Alignment explanation
Indices: 39214853--39214887 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39214843 CATTTGGTAT
39214853 CGATACTTCTATGAGTAC
1 CGATACTTCTATGAGTAC
*
39214871 CGATATTTCTATGAGTA
1 CGATACTTCTATGAGTA
39214888 TCAATACTAT
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:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (18 bp):
CGATACTTCTATGAGTAC
Found at i:39218048 original size:18 final size:19
Alignment explanation
Indices: 39218025--39218065 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
39218015 AATATTACAC
39218025 ATTTCAATTTT-ACATTAA
1 ATTTCAATTTTCACATTAA
*
39218043 ATTTCAATTTTCACATTAT
1 ATTTCAATTTTCACATTAA
39218062 ATTT
1 ATTT
39218066 TGCTTATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTCAATTTTCACATTAA
Found at i:39223235 original size:25 final size:24
Alignment explanation
Indices: 39223204--39223254 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
39223194 ATGGTTTTAA
39223204 TTAATTTTTAAATTTTTTATAAATT
1 TTAA-TTTTAAATTTTTTATAAATT
** *
39223229 TTAATTTTATGTTTTTTATATATT
1 TTAATTTTAAATTTTTTATAAATT
39223253 TT
1 TT
39223255 TAAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTAATTTTAAATTTTTTATAAATT
Found at i:39229876 original size:94 final size:94
Alignment explanation
Indices: 39229746--39229993 Score: 289
Period size: 94 Copynumber: 2.6 Consensus size: 94
39229736 GAGTTTGCCG
* * * *
39229746 AGACAGTAAACACGAGGTAGTCTACCATGACGTTAAACATGGGGTTACATGTGTAAGACCTTATC
1 AGACAGTAAACACGGGGTAGTCTACCAGGACATTAAACATGGGGTTACATGTGTAAGACCTTAGC
* * *
39229811 TCAACTATGGCAATATAAGGAGTCCATCA
66 TCAACTATGGCAACATAAGGAGCCCACCA
* ** * *
39229840 AGACAGCAAACACGGGGTAGTCTGTCAGGATATTAAACATGGGGATACATGTGTAAGACCTTAGC
1 AGACAGTAAACACGGGGTAGTCTACCAGGACATTAAACATGGGGTTACATGTGTAAGACCTTAGC
*** * ** *
39229905 TTGGCTATGGGAACATGGGGAGCCCACCG
66 TCAACTATGGCAACATAAGGAGCCCACCA
* * * *
39229934 GGATAGTAAACATGGGGTAGTCCACCAGGACATTAAACATGGGGTTACATGTGTAAGACC
1 AGACAGTAAACACGGGGTAGTCTACCAGGACATTAAACATGGGGTTACATGTGTAAGACC
39229994 ATAGTTTGGT
Statistics
Matches: 126, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
94 126 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.22
Consensus pattern (94 bp):
AGACAGTAAACACGGGGTAGTCTACCAGGACATTAAACATGGGGTTACATGTGTAAGACCTTAGC
TCAACTATGGCAACATAAGGAGCCCACCA
Found at i:39229970 original size:27 final size:27
Alignment explanation
Indices: 39229916--39229978 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
39229906 TGGCTATGGG
* *
39229916 AACATGGGG-AGCCCACCGGGATAGTA
1 AACATGGGGTAGCCCACCAGGACAGTA
* *
39229942 AACATGGGGTAGTCCACCAGGACATTA
1 AACATGGGGTAGCCCACCAGGACAGTA
39229969 AACATGGGGT
1 AACATGGGGT
39229979 TACATGTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.32, C:0.21, G:0.32, T:0.16
Consensus pattern (27 bp):
AACATGGGGTAGCCCACCAGGACAGTA
Found at i:39231848 original size:27 final size:29
Alignment explanation
Indices: 39231817--39231871 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
39231807 TTAGGACTTA
39231817 TCTTTT-AATT-T-CTTGCTGTCAATTTTT
1 TCTTTTAAATTCTGCTTG-TGTCAATTTTT
39231844 TCTTTTAAATTCTGCTTGTGTCAATTTT
1 TCTTTTAAATTCTGCTTGTGTCAATTTT
39231872 ATTTAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.24
28 4 0.16
29 11 0.44
30 4 0.16
ACGTcount: A:0.16, C:0.15, G:0.09, T:0.60
Consensus pattern (29 bp):
TCTTTTAAATTCTGCTTGTGTCAATTTTT
Found at i:39240110 original size:20 final size:21
Alignment explanation
Indices: 39240085--39240123 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39240075 ATAATGTTAT
*
39240085 AAAATTT-TAACAATATAATG
1 AAAATTTATAACAAAATAATG
39240105 AAAATTTATAACAAAATAA
1 AAAATTTATAACAAAATAA
39240124 CATAAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAATTTATAACAAAATAATG
Found at i:39247234 original size:39 final size:38
Alignment explanation
Indices: 39247176--39247249 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
39247166 CTAACACTCA
**
39247176 CACCAACTAGTTAGTAACTAACATAG-CCTACCAGTGGC
1 CACCAACTAGTTAACAACTAACAT-GTCCTACCAGTGGC
39247214 CACCAAACTAGTTAACAACTAACATGTCCTACCAGT
1 CACC-AACTAGTTAACAACTAACATGTCCTACCAGT
39247250 TGCCTATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
38 5 0.16
39 27 0.84
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (38 bp):
CACCAACTAGTTAACAACTAACATGTCCTACCAGTGGC
Found at i:39251638 original size:40 final size:40
Alignment explanation
Indices: 39251578--39251677 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
39251568 TCGAAATGCT
* * *
39251578 AACAAAGGCACCGAAGTGCATACAAAGGTACCGAAGTGCA
1 AACAGAGGCACCAAAGTGCATACAAAGGTACCAAAGTGCA
* * *
39251618 AACAGAGGCACTAAAGTGCATACAGAGGTACTAAAGTGCA
1 AACAGAGGCACCAAAGTGCATACAAAGGTACCAAAGTGCA
*
39251658 CACAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
39251678 AAAAGAGGCA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (40 bp):
AACAGAGGCACCAAAGTGCATACAAAGGTACCAAAGTGCA
Found at i:39251684 original size:20 final size:20
Alignment explanation
Indices: 39251578--39251687 Score: 112
Period size: 20 Copynumber: 5.5 Consensus size: 20
39251568 TCGAAATGCT
* *
39251578 AACAAAGGCACCGAAGTGCA
1 AACAGAGGCACCAAAGTGCA
* * * *
39251598 TACAAAGGTACCGAAGTGCA
1 AACAGAGGCACCAAAGTGCA
*
39251618 AACAGAGGCACTAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
* * *
39251638 TACAGAGGTACTAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
*
39251658 CACAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
*
39251678 AAAAGAGGCA
1 AACAGAGGCA
39251688 TCGAAGTGTA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGCA
Found at i:39251695 original size:40 final size:39
Alignment explanation
Indices: 39251560--39251695 Score: 105
Period size: 40 Copynumber: 3.4 Consensus size: 39
39251550 CAATCGCACC
* * * *
39251560 AGAGAGCATCGAAATGCTAACAAAGGCACCGAAGTGCATACA
1 AGAG-GCATCGAAGTGC-AACAGAGGCACCAAAGTGCA-AAA
* * * * *
39251602 A-AGGTACCGAAGTGCAAACAGAGGCACTAAAGTGCATAC
1 AGAGGCATCGAAGTGC-AACAGAGGCACCAAAGTGCAAAA
* *
39251641 AGAGGTA-CTAAAGTGCACACAGAGGCACCAAAGTGCAAAA
1 AGAGGCATC-GAAGTGCA-ACAGAGGCACCAAAGTGCAAAA
39251681 AGAGGCATCGAAGTG
1 AGAGGCATCGAAGTG
39251696 TAAATCCCGT
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
39 3 0.04
40 67 0.91
41 3 0.04
42 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (39 bp):
AGAGGCATCGAAGTGCAACAGAGGCACCAAAGTGCAAAA
Found at i:39252703 original size:69 final size:70
Alignment explanation
Indices: 39252619--39252755 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 70
39252609 AAGAATTTTT
*
39252619 TTTTAATGTTTTTATGTTTTAACTAATGTTTATAATTTTAATTAATTAACAAATACATTACTTTA
1 TTTTAATGTTTTTATGTTTTAACTAATGTTTATAATTTTAATTAACTAACAAATACATTACTTTA
39252684 ATTTG
66 ATTTG
* * *
39252689 TTTT-ATGTTTTTATGTTTTAACTCATGTTTATAATTTTAGTTAACTAACAAATACATTATTTTA
1 TTTTAATGTTTTTATGTTTTAACTAATGTTTATAATTTTAATTAACTAACAAATACATTACTTTA
39252753 ATT
66 ATT
39252756 AAAACAACCT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 59 0.94
70 4 0.06
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.55
Consensus pattern (70 bp):
TTTTAATGTTTTTATGTTTTAACTAATGTTTATAATTTTAATTAACTAACAAATACATTACTTTA
ATTTG
Found at i:39262173 original size:58 final size:58
Alignment explanation
Indices: 39262104--39262284 Score: 269
Period size: 57 Copynumber: 3.1 Consensus size: 58
39262094 TTTTCCAAAT
*
39262104 CATTTTCATTTTTCATTTAGGAGAAAACCGTATTCATTTCCAAATGTTTTCATTTCTC
1 CATTTTCATTTTTCATTTAGGAGAAAACCATATTCATTTCCAAATGTTTTCATTTCTC
*
39262162 CATTTTCA-TTTTCATTTAGGAGAAAACCATATTCATTTCCAAATGTTTCCATTTCTC
1 CATTTTCATTTTTCATTTAGGAGAAAACCATATTCATTTCCAAATGTTTTCATTTCTC
* * * *
39262219 CATTTTCATTTTCCTTTTA-GAGAAAACCATA-ACAATTTTCAAATGTTTCTCATTTCTC
1 CATTTTCATTTTTCATTTAGGAGAAAACCATATTC-ATTTCCAAATGTTT-TCATTTCTC
39262277 CATTTTCA
1 CATTTTCA
39262285 CAATCTCTAT
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
56 1 0.01
57 80 0.71
58 32 0.28
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (58 bp):
CATTTTCATTTTTCATTTAGGAGAAAACCATATTCATTTCCAAATGTTTTCATTTCTC
Found at i:39264257 original size:40 final size:39
Alignment explanation
Indices: 39264213--39264315 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 39
39264203 TGATATCAAT
39264213 TATGTCCGTTTGAGCCATACCTAGTGAATCTACTAAAACG
1 TATGTCC-TTTGAGCCATACCTAGTGAATCTACTAAAACG
* * *
39264253 TATGTGCTTTCGAGCCATACCTAGTGAATCTACTGAAATG
1 TATGTCCTTT-GAGCCATACCTAGTGAATCTACTAAAACG
*
39264293 AATG-CGCTTTTGAGCCATACCTA
1 TATGTC-C-TTTGAGCCATACCTA
39264316 CCGATTCCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
39 3 0.05
40 49 0.89
41 3 0.05
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (39 bp):
TATGTCCTTTGAGCCATACCTAGTGAATCTACTAAAACG
Found at i:39264328 original size:40 final size:40
Alignment explanation
Indices: 39264224--39264403 Score: 184
Period size: 40 Copynumber: 4.5 Consensus size: 40
39264214 ATGTCCGTTT
* * *
39264224 GAGCCATACCTAGTGAATCTACTAAAACGTATGTGCTTTC
1 GAGCCATACCTACTGAATCTACTGAAACGTATGCGCTTTC
* * * *
39264264 GAGCCATACCTAGTGAATCTACTGAAATGAATGCGCTTTT
1 GAGCCATACCTACTGAATCTACTGAAACGTATGCGCTTTC
* * * *
39264304 GAGCCATACCTACCGATTCCACTGAAACGTATGCGCTATC
1 GAGCCATACCTACTGAATCTACTGAAACGTATGCGCTTTC
* * *
39264344 GAGCCTTACCTACTGATTCTACTGAAA-GTATGC-TTTATC
1 GAGCCATACCTACTGAATCTACTGAAACGTATGCGCTT-TC
* * *
39264383 GATCCATACCTAATGATTCTA
1 GAGCCATACCTACTGAATCTA
39264404 GTGGAAGTTG
Statistics
Matches: 118, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
38 1 0.01
39 26 0.22
40 91 0.77
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (40 bp):
GAGCCATACCTACTGAATCTACTGAAACGTATGCGCTTTC
Found at i:39264354 original size:80 final size:80
Alignment explanation
Indices: 39264221--39264370 Score: 210
Period size: 80 Copynumber: 1.9 Consensus size: 80
39264211 ATTATGTCCG
** * * * *
39264221 TTTGAGCCATACCTAGTGAATCTACTAAAACGTATGTGCTTTCGAGCCATACCTAGTGAATCTAC
1 TTTGAGCCATACCTACCGAATCCACTAAAACGTATGCGCTATCGAGCCATACCTACTGAATCTAC
39264286 TGAAATGAATGCGCT
66 TGAAATGAATGCGCT
* * * *
39264301 TTTGAGCCATACCTACCGATTCCACTGAAACGTATGCGCTATCGAGCCTTACCTACTGATTCTAC
1 TTTGAGCCATACCTACCGAATCCACTAAAACGTATGCGCTATCGAGCCATACCTACTGAATCTAC
39264366 TGAAA
66 TGAAA
39264371 GTATGCTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 60 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (80 bp):
TTTGAGCCATACCTACCGAATCCACTAAAACGTATGCGCTATCGAGCCATACCTACTGAATCTAC
TGAAATGAATGCGCT
Found at i:39270215 original size:74 final size:74
Alignment explanation
Indices: 39270119--39270268 Score: 228
Period size: 74 Copynumber: 2.0 Consensus size: 74
39270109 AGTGGGCCAT
* * *
39270119 GGCCTCCCAAGGTTTAAAATTTTTTCAATTTAGCCCTTTGTAGATATACTATGGCCCTCCCAAAA
1 GGCCCCCCAAGGTTTAAAATTTTTGCAATTTAGCCCTTTGTAGATATACTATAGCCCTCCCAAAA
*
39270184 ATATAAGTA
66 ATACAAGTA
* ** *
39270193 GGCCCCCCAAGGTTTAAGATTTTTGCAATTTTTCCCTTTGTATATATACTATAGCCCTCCCAAAA
1 GGCCCCCCAAGGTTTAAAATTTTTGCAATTTAGCCCTTTGTAGATATACTATAGCCCTCCCAAAA
39270258 ATACAAGTA
66 ATACAAGTA
39270267 GG
1 GG
39270269 GCCTTCCAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (74 bp):
GGCCCCCCAAGGTTTAAAATTTTTGCAATTTAGCCCTTTGTAGATATACTATAGCCCTCCCAAAA
ATACAAGTA
Found at i:39270671 original size:18 final size:18
Alignment explanation
Indices: 39270644--39270682 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
39270634 TTCTAAATGT
*
39270644 AAAAGAAAAAT-CAAACA
1 AAAAGAAAAATAAAAACA
39270661 AAAATGAAAAATAAAAACA
1 AAAA-GAAAAATAAAAACA
39270680 AAA
1 AAA
39270683 GCAACCCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.79, C:0.08, G:0.05, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAATAAAAACA
Found at i:39277985 original size:22 final size:21
Alignment explanation
Indices: 39277933--39277999 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
39277923 CTGTTACGTT
39277933 TTTTCC-TTCTTCTCTTCTTC
1 TTTTCCTTTCTTCTCTTCTTC
** *
39277953 TTATTTTTTTCTTTTCTTCATTC
1 TT-TTCCTTTCTTCTCTTC-TTC
* *
39277976 TTTTCCTTTCCTCGTGTTCTTC
1 TTTTCCTTTCTTC-TCTTCTTC
39277998 TT
1 TT
39278000 CCTGTTCTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 22 0.63
23 9 0.26
ACGTcount: A:0.03, C:0.27, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTTCCTTTCTTCTCTTCTTC
Found at i:39281353 original size:18 final size:18
Alignment explanation
Indices: 39281330--39281365 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39281320 TGTATAATAT
* *
39281330 TATATCATGTTATTTTTA
1 TATATCAAGTAATTTTTA
39281348 TATATCAAGTAATTTTTA
1 TATATCAAGTAATTTTTA
39281366 ACACATAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (18 bp):
TATATCAAGTAATTTTTA
Found at i:39283929 original size:19 final size:19
Alignment explanation
Indices: 39283905--39283943 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39283895 CAAAATGTAC
39283905 AATATAATTAAATAAATTA
1 AATATAATTAAATAAATTA
*
39283924 AATATAATTAAATAATTTA
1 AATATAATTAAATAAATTA
39283943 A
1 A
39283944 TTAACTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATAATTAAATAAATTA
Found at i:39283932 original size:10 final size:10
Alignment explanation
Indices: 39283905--39283937 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
39283895 CAAAATGTAC
39283905 AATATAATTA
1 AATATAATTA
39283915 AATA-AATTA
1 AATATAATTA
39283924 AATATAATTA
1 AATATAATTA
39283934 AATA
1 AATA
39283938 ATTTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATATAATTA
Found at i:39283943 original size:9 final size:9
Alignment explanation
Indices: 39283905--39283943 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
39283895 CAAAATGTAC
39283905 AATATAATTA
1 AATA-AATTA
39283915 AATAAATTA
1 AATAAATTA
39283924 AATATAATTA
1 AATA-AATTA
*
39283934 AATAATTTA
1 AATAAATTA
39283943 A
1 A
39283944 TTAACTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 14 0.52
10 13 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AATAAATTA
Found at i:39286422 original size:30 final size:30
Alignment explanation
Indices: 39286378--39286435 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39286368 CTAGGCCTTC
* * *
39286378 CCACACGGGTTGGACACACGGCCATGTGAG
1 CCACACAGGATGGACACACAGCCATGTGAG
39286408 CCACACAGGATGGACACACAGCCATGTG
1 CCACACAGGATGGACACACAGCCATGTG
39286436 CCACACCGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.31, G:0.29, T:0.12
Consensus pattern (30 bp):
CCACACAGGATGGACACACAGCCATGTGAG
Found at i:39289036 original size:13 final size:14
Alignment explanation
Indices: 39289018--39289049 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
39289008 GTCAATATTT
39289018 TATAATTACTT-AA
1 TATAATTACTTCAA
39289031 TATAATTACTTCAA
1 TATAATTACTTCAA
39289045 TATAA
1 TATAA
39289050 CAACCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
TATAATTACTTCAA
Found at i:39293749 original size:25 final size:25
Alignment explanation
Indices: 39293714--39293763 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
39293704 ATACACTCAA
*
39293714 AAAATATAACGTAAACTTAAATCTT
1 AAAATAAAACGTAAACTTAAATCTT
*
39293739 AAAATAAAACGTAAATTTAAATCTT
1 AAAATAAAACGTAAACTTAAATCTT
39293764 GAAGATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (25 bp):
AAAATAAAACGTAAACTTAAATCTT
Found at i:39302540 original size:32 final size:32
Alignment explanation
Indices: 39302504--39302566 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
39302494 AACAACATGT
39302504 TGTTATAAAGATATAATCTTTATAATCTTACG
1 TGTTATAAAGATATAATCTTTATAATCTTACG
39302536 TGTTATAAAGATATAATCTTTATAATCTTAC
1 TGTTATAAAGATATAATCTTTATAATCTTAC
39302567 TATAGAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (32 bp):
TGTTATAAAGATATAATCTTTATAATCTTACG
Found at i:39308740 original size:6 final size:6
Alignment explanation
Indices: 39308731--39308783 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
39308721 TCTCCCATGA
*
39308731 ACATGT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
39308779 ACATA
1 ACATA
39308784 AACTTTCTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:39311254 original size:2 final size:2
Alignment explanation
Indices: 39311247--39311295 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
39311237 GATACTACAT
39311247 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39311289 TC TC TC T
1 TC TC TC T
39311296 TTATTCTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:39314489 original size:86 final size:83
Alignment explanation
Indices: 39314394--39314782 Score: 350
Period size: 81 Copynumber: 4.7 Consensus size: 83
39314384 ATTAAATCAA
* * * * * *
39314394 AATAAAATTTGTTAAACAGCGAGAATAAATTCCAAAACAGAATTATTTGA-TTAATTCTTTTTGT
1 AATAAAATCTGTTAAACAGAGAGAATAAATCCCGAAACAG-ATT-TTTAATTTAATTCTTTAT-T
*
39314458 TTGGAAAACAAAATCAAAATCG
63 TTGG-AAACAAAATTAAAATCG
* * *
39314480 AATAAAATTTGTTAAACAGAGGGAATAAATCTCGAAACAG-TTTTTCAATTTAATTC--TATTTT
1 AATAAAATCTGTTAAACAGAGAGAATAAATCCCGAAACAGATTTTT-AATTTAATTCTTTATTTT
39314542 GGAAACAAAATTAAAATCG
65 GGAAACAAAATTAAAATCG
* * *
39314561 AATAAAATCTGTTAAAC-GATAGGAATAAATCCCGAAACAGATTTTCAATTTAA-T-TTTATATT
1 AATAAAATCTGTTAAACAGAGA-GAATAAATCCCGAAACAGATTTTTAATTTAATTCTTTATTTT
39314623 GGAAACAAAATTAAAATCG
65 GGAAACAAAATTAAAATCG
* * **
39314642 AATAAAATCTGTTAAACGGAGAGAATAAATCCCGAAACATATTTTATTTAATTTTAATT-TCTCG
1 AATAAAATCTGTTAAACAGAGAGAATAAATCCCGAAACAGA--TT-TTTAA-TTTAATTCT-TTA
* * * *
39314706 TTTTAGCAACAAAATAGAAAATGG
61 TTTTGGAAACAAAAT-TAAAATCG
* * * **
39314730 AATAAAATCTATTAAA-TGACAAGAATAAATCTTGAAACAGA-TTTT-ATTTAATT
1 AATAAAATCTGTTAAACAGA-GAGAATAAATCCCGAAACAGATTTTTAATTTAATT
39314783 TTAATACTCG
Statistics
Matches: 258, Mismatches: 30, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
80 3 0.01
81 115 0.45
82 19 0.07
83 8 0.03
84 10 0.04
85 13 0.05
86 37 0.14
87 15 0.06
88 38 0.15
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (83 bp):
AATAAAATCTGTTAAACAGAGAGAATAAATCCCGAAACAGATTTTTAATTTAATTCTTTATTTTG
GAAACAAAATTAAAATCG
Found at i:39314944 original size:166 final size:167
Alignment explanation
Indices: 39314479--39314950 Score: 437
Period size: 166 Copynumber: 2.9 Consensus size: 167
39314469 AATCAAAATC
* * * * * *
39314479 GAATAAAATTTGTTAAACAGAGGGAATAAATCTCGAAACAG--TTT-TTCAA-TTTAATT-CT-A
1 GAATAAAATCTGTTAAACGGAGAGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTACTCG
* * * * * * * * *
39314538 TTTTGGAAACAAAAT-TAAAATCGAATAAAATCTGTTAAACGATAGGAATAAATCCCGAAACAGA
66 TTTTAGAAACAAAATAAAAAATGGAATAAAATCTATTAAATGACAAGAATAAATCCTGAAACAAA
* * ***** **
39314602 TTTTCAATTTAATTTT-ATA-TTGGAAACAAAATTAAAATC
131 ATTT--ATTTAATTTTAATACTCGTTTGGAAAA--AAAAAG
* *
39314641 GAATAAAATCTGTTAAACGGAGAGAATAAATCCCGAAACATATTTTATTTAATTTTAATTTCTCG
1 GAATAAAATCTGTTAAACGGAGAGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTACTCG
* * * *
39314706 TTTTAGCAACAAAATAGAAAATGGAATAAAATCTATTAAATGACAAGAATAAATCTTGAAACAGA
66 TTTTAGAAACAAAATAAAAAATGGAATAAAATCTATTAAATGACAAGAATAAATCCTGAAACAAA
*
39314771 TTTTATTTAATTTTAATACTCGTTTGGAAAAAAAAAG
131 ATTTATTTAATTTTAATACTCGTTTGGAAAAAAAAAG
* * * * *
39314808 GAATAAAATCTGTTGAATGGCTG-GAATAAATCCTGGAACAGATTTTATTTAAATTTTAA-TACT
1 GAATAAAATCTGTTAAACGG-AGAGAATAAATCCCGAAACAGATTTTATTT-AATTTTAATTACT
* * * * *
39314871 TG-TTTGGAAACAAAATAAAAAATGGAATAAAATCTGTTGAATGACGAGAATAAATCCTGAAACA
64 CGTTTTAGAAACAAAATAAAAAATGGAATAAAATCTATTAAATGACAAGAATAAATCCTGAAACA
39314935 AAATTTATTTAATTTT
129 AAATTTATTTAATTTT
39314951 TATTTTCAAA
Statistics
Matches: 257, Mismatches: 42, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
162 36 0.14
164 3 0.01
165 4 0.02
166 76 0.30
167 62 0.24
168 25 0.10
169 51 0.20
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (167 bp):
GAATAAAATCTGTTAAACGGAGAGAATAAATCCCGAAACAGATTTTATTTAATTTTAATTACTCG
TTTTAGAAACAAAATAAAAAATGGAATAAAATCTATTAAATGACAAGAATAAATCCTGAAACAAA
ATTTATTTAATTTTAATACTCGTTTGGAAAAAAAAAG
Found at i:39314952 original size:87 final size:86
Alignment explanation
Indices: 39314456--39314950 Score: 419
Period size: 81 Copynumber: 5.9 Consensus size: 86
39314446 AATTCTTTTT
* * * * *
39314456 GTTTGGAAAACAAAAT-CAAAATCGAATAAAATTTGTTAAACAGA-GGGAATAAAT-CTCGAAAC
1 GTTTGG-AAACAAAATAAAAAATGGAATAAAATCTGTTAAA-TGACGAGAATAAATCCT-GAAAC
* * *
39314518 AG--TTT-TTCAA-TTTAATTCTA
63 AGATTTTATTTAATTTTAATACTC
* * * * * *
39314538 TTTTGGAAACAAAAT-TAAAATCGAATAAAATCTGTTAAACGA-TAGGAATAAATCCCGAAACAG
1 GTTTGGAAACAAAATAAAAAATGGAATAAAATCTGTTAAATGACGA-GAATAAATCCTGAAACAG
39314601 ATTTTCAATTTAATTTT-ATA---
65 ATTTT--ATTTAATTTTAATACTC
* * * * *
39314621 --TTGGAAACAAAAT-TAAAATCGAATAAAATCTGTTAAACGGA-GAGAATAAATCCCGAAACAT
1 GTTTGGAAACAAAATAAAAAATGGAATAAAATCTGTTAAA-TGACGAGAATAAATCCTGAAACAG
*
39314682 ATTTTATTTAATTTTAATTTCTC
65 ATTTTATTTAATTTTAA-TACTC
* * * * * *
39314705 GTTTTAGCAACAAAATAGAAAATGGAATAAAATCTATTAAATGACAAGAATAAATCTTGAAACAG
1 G-TTTGGAAACAAAATAAAAAATGGAATAAAATCTGTTAAATGACGAGAATAAATCCTGAAACAG
39314770 ATTTTATTTAATTTTAATACTC
65 ATTTTATTTAATTTTAATACTC
* * *
39314792 GTTTGG-----AAA-AAAAAA-GGAATAAAATCTGTTGAATGGCTG-GAATAAATCCTGGAACAG
1 GTTTGGAAACAAAATAAAAAATGGAATAAAATCTGTTAAATGAC-GAGAATAAATCCTGAAACAG
*
39314849 ATTTTATTTAAATTTTAATACTT
65 ATTTTATTT-AATTTTAATACTC
* *
39314872 GTTTGGAAACAAAATAAAAAATGGAATAAAATCTGTTGAATGACGAGAATAAATCCTGAAACAAA
1 GTTTGGAAACAAAATAAAAAATGGAATAAAATCTGTTAAATGACGAGAATAAATCCTGAAACAGA
*
39314937 ATTTATTTAATTTT
66 TTTTATTTAATTTT
39314951 TATTTTCAAA
Statistics
Matches: 347, Mismatches: 37, Indels: 54
0.79 0.08 0.12
Matches are distributed among these distances:
79 54 0.16
80 26 0.07
81 109 0.31
82 9 0.03
83 3 0.01
85 3 0.01
86 23 0.07
87 66 0.19
88 54 0.16
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (86 bp):
GTTTGGAAACAAAATAAAAAATGGAATAAAATCTGTTAAATGACGAGAATAAATCCTGAAACAGA
TTTTATTTAATTTTAATACTC
Found at i:39315582 original size:20 final size:20
Alignment explanation
Indices: 39315557--39315605 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
39315547 AGGGGCAATT
* *
39315557 AAATCAATTTGATTAAAATC
1 AAATCAAATTGACTAAAATC
39315577 AAATCAAATTGACTAAAATC
1 AAATCAAATTGACTAAAATC
*
39315597 AAATAAAAT
1 AAATCAAAT
39315606 CAGGATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (20 bp):
AAATCAAATTGACTAAAATC
Found at i:39320527 original size:21 final size:21
Alignment explanation
Indices: 39320497--39320562 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
39320487 GTGCTAAACT
* *
39320497 GAAACCCATAAGGGTTGAA-T
1 GAAAGCCATAAGGGTTGAACA
*
39320517 GGAAGCTCAT-AGGAGTTGAACA
1 GAAAGC-CATAAGG-GTTGAACA
*
39320539 GAAAGCCATAAGGGTTAAAC-
1 GAAAGCCATAAGGGTTGAACA
39320559 GAAA
1 GAAA
39320563 ACTCATATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 11 0.30
21 18 0.49
22 8 0.22
ACGTcount: A:0.42, C:0.14, G:0.27, T:0.17
Consensus pattern (21 bp):
GAAAGCCATAAGGGTTGAACA
Found at i:39320548 original size:42 final size:41
Alignment explanation
Indices: 39320497--39320582 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 41
39320487 GTGCTAAACT
* * * *
39320497 GAAACCCATAAGGGTTGAATGGAAGCTCATAGGAGTTGAACA
1 GAAACCCATAAGGGTTAAACGAAAACTCATAGGAGTT-AACA
* *
39320539 GAAAGCCATAAGGGTTAAACGAAAACTCATATGAGTTAACA
1 GAAACCCATAAGGGTTAAACGAAAACTCATAGGAGTTAACA
39320580 GAA
1 GAA
39320583 GCTCGTGAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 7 0.18
42 31 0.82
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (41 bp):
GAAACCCATAAGGGTTAAACGAAAACTCATAGGAGTTAACA
Found at i:39325641 original size:67 final size:67
Alignment explanation
Indices: 39325533--39325661 Score: 213
Period size: 67 Copynumber: 1.9 Consensus size: 67
39325523 TATATTACAA
*
39325533 GGGATTTAGCCTGGACTGGTAATCCCGTTGTAAAAAATGAGGTTCGCAGGAGTGTGCTCTCTTGC
1 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAAAATGAGGTTCGCAGGAGTGTGCTCTCTTGC
39325598 AG
66 AG
** **
39325600 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAGGAAATGAGGTTCGTGGGAGTGTGCTCTCT
1 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAAAATGAGGTTCGCAGGAGTGTGCTCTCT
39325662 GAATTGGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (67 bp):
GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAAAATGAGGTTCGCAGGAGTGTGCTCTCTTGC
AG
Found at i:39339764 original size:13 final size:13
Alignment explanation
Indices: 39339746--39339770 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39339736 TGATTTATAT
39339746 GTGTGAAAATTTC
1 GTGTGAAAATTTC
39339759 GTGTGAAAATTT
1 GTGTGAAAATTT
39339771 TATCATTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:39341921 original size:13 final size:13
Alignment explanation
Indices: 39341903--39341932 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39341893 TCTATGAGGT
*
39341903 TTTTGGTTGATTG
1 TTTTGGTTGATTA
39341916 TTTTGGTTGATTA
1 TTTTGGTTGATTA
39341929 TTTT
1 TTTT
39341933 TGGAGGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.23, T:0.67
Consensus pattern (13 bp):
TTTTGGTTGATTA
Found at i:39341933 original size:14 final size:13
Alignment explanation
Indices: 39341902--39341935 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
39341892 TTCTATGAGG
39341902 TTTTTGGTTGATT
1 TTTTTGGTTGATT
*
39341915 GTTTTGGTTGATT
1 TTTTTGGTTGATT
39341928 ATTTTTGG
1 -TTTTTGG
39341936 AGGTTGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.09, C:0.00, G:0.26, T:0.65
Consensus pattern (13 bp):
TTTTTGGTTGATT
Found at i:39344112 original size:21 final size:20
Alignment explanation
Indices: 39344088--39344131 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
39344078 GAGCTGAATG
*
39344088 GAAACCCATAAGGGTTAAACA
1 GAAACCCATAAGAGTT-AACA
* *
39344109 GAAACTCATATGAGTTAACA
1 GAAACCCATAAGAGTTAACA
39344129 GAA
1 GAA
39344132 GCTTGTGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (20 bp):
GAAACCCATAAGAGTTAACA
Found at i:39345654 original size:24 final size:23
Alignment explanation
Indices: 39345627--39345672 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
39345617 CTATTTTATT
*
39345627 TTCCCCAAAATAAATAAATAAAAA
1 TTCCACAAAATAAAT-AATAAAAA
* *
39345651 TTCCATAAATTAAATAATAAAA
1 TTCCACAAAATAAATAATAAAA
39345673 CCACCTCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (23 bp):
TTCCACAAAATAAATAATAAAAA
Found at i:39345926 original size:5 final size:5
Alignment explanation
Indices: 39345918--39345943 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39345908 GAGATGAAAT
39345918 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
39345944 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:39346499 original size:16 final size:16
Alignment explanation
Indices: 39346449--39346500 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 16
39346439 GGGTAAGAAG
39346449 TAAAAGTTTAGAGGGAAAA
1 TAAAAGTTT-GAGGG--AA
39346468 TAAAAAGTTTTG-GGGAA
1 T-AAAAG-TTTGAGGGAA
39346485 TAAAAGTTTGAGGGAA
1 TAAAAGTTTGAGGGAA
39346501 AATAAATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 3 0.10
19 4 0.13
20 6 0.20
21 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (16 bp):
TAAAAGTTTGAGGGAA
Found at i:39346520 original size:31 final size:33
Alignment explanation
Indices: 39346447--39346536 Score: 103
Period size: 35 Copynumber: 2.7 Consensus size: 33
39346437 AAGGGTAAGA
39346447 AGTAAAAGTTTAGAGGGAAAATAAAAAGTTTTGGGG
1 AGTAAAAGTTTAGAGGGAAAATAAAAAG---TGGGG
* *
39346483 AATAAAAGTTT-GAGGGAAAATAAATAG-GGGG
1 AGTAAAAGTTTAGAGGGAAAATAAAAAGTGGGG
* *
39346514 AGTAAAATTTTGGAGGGAAAATA
1 AGTAAAAGTTTAGAGGGAAAATA
39346537 TTAAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 13 0.27
32 11 0.22
35 15 0.31
36 10 0.20
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (33 bp):
AGTAAAAGTTTAGAGGGAAAATAAAAAGTGGGG
Found at i:39346622 original size:31 final size:29
Alignment explanation
Indices: 39346587--39346645 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
39346577 GGAGGTGGGA
*
39346587 TGGGAAGAGAATAAAAGTTTTAGGGGGAAAT
1 TGGG-AGAGAATAAAAATTTT-GGGGGAAAT
* *
39346618 TGGGAGGGAGTAAAAATTTTGGGGGAAA
1 TGGGAGAGAATAAAAATTTTGGGGGAAA
39346646 ATAAAAGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 13 0.52
31 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.22
Consensus pattern (29 bp):
TGGGAGAGAATAAAAATTTTGGGGGAAAT
Found at i:39346956 original size:9 final size:9
Alignment explanation
Indices: 39346942--39346969 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
39346932 AGTTGATTCA
39346942 AATAACTCG
1 AATAACTCG
39346951 AATAACTCG
1 AATAACTCG
39346960 AATAACTCG
1 AATAACTCG
39346969 A
1 A
39346970 TTCGTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (9 bp):
AATAACTCG
Found at i:39352747 original size:16 final size:16
Alignment explanation
Indices: 39352713--39352750 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
39352703 TTAAAATCTA
39352713 TAAAAA-AAGATAATT
1 TAAAAATAAGATAATT
39352728 TAAAAATAA-ATAATT
1 TAAAAATAAGATAATT
39352743 GTAAAAAT
1 -TAAAAAT
39352751 TATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (16 bp):
TAAAAATAAGATAATT
Found at i:39352771 original size:22 final size:23
Alignment explanation
Indices: 39352724--39352772 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
39352714 AAAAAAAGAT
39352724 AATTTAAAAATAAATAATTGTAAA
1 AATTTAAAAATAAATAA-TGTAAA
39352748 AATTATAAAAATAAAT-A-GTAAA
1 AATT-TAAAAATAAATAATGTAAA
39352770 AAT
1 AAT
39352773 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.33
24 5 0.21
25 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
AATTTAAAAATAAATAATGTAAA
Found at i:39352799 original size:19 final size:18
Alignment explanation
Indices: 39352768--39352821 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
39352758 ATAAATAGTA
39352768 AAAATATTTTAAAAATATAT
1 AAAATA-TTTAAAAATAT-T
39352788 AAAATATTTAAAAATATT
1 AAAATATTTAAAAATATT
*
39352806 AAAATGTTGTAAAAAT
1 AAAATATT-TAAAAAT
39352822 CTTTAAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 8 0.25
19 18 0.56
20 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (18 bp):
AAAATATTTAAAAATATT
Found at i:39352979 original size:29 final size:27
Alignment explanation
Indices: 39352935--39352996 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
39352925 ATTTGTTTAC
* * *
39352935 ATTTTTTTACATTTATACAAAATTTTAA
1 ATTTTTTAACAGTTATA-AAAATTGTAA
39352963 TATTTTTTAACAGTTATAAAAATTGTAA
1 -ATTTTTTAACAGTTATAAAAATTGTAA
39352991 ATTTTT
1 ATTTTT
39352997 AAAATGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 6 0.20
28 9 0.30
29 15 0.50
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTTTTTAACAGTTATAAAAATTGTAA
Found at i:39353402 original size:18 final size:17
Alignment explanation
Indices: 39353381--39353429 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
39353371 AAAAAAAATA
39353381 TAATTTTTAAAATTTTAT
1 TAATTTTTAAAATTTT-T
39353399 TAATTTTTACAAA-TTTT
1 TAATTTTTA-AAATTTTT
39353416 TAATATTTTAAAAT
1 TAAT-TTTTAAAAT
39353430 AAATTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.29
18 17 0.61
19 3 0.11
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATTTTTAAAATTTTT
Found at i:39357544 original size:21 final size:21
Alignment explanation
Indices: 39357520--39357569 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
39357510 TGCTCATCAA
39357520 ACTTATTTATCAAATATATAT
1 ACTTATTTATCAAATATATAT
*
39357541 ACTTGATCT-TCAAATATATAT
1 ACTT-ATTTATCAAATATATAT
39357562 A-TTATTTA
1 ACTTATTTA
39357570 CATATCACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 17 0.68
22 3 0.12
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (21 bp):
ACTTATTTATCAAATATATAT
Found at i:39357745 original size:41 final size:40
Alignment explanation
Indices: 39357655--39357774 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 40
39357645 TGATTTAATA
* * * * * *
39357655 CACCGGCTTTTAGCCTGCTAGACTTATAGTCCGAATAATTT
1 CACCGGCATTAAGCCTGCTAGAC-AATAGTCTGAATTATAT
*
39357696 CACTGGCATTAAGCCTGCTAGACAATGAGTCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGACAAT-AGTCTGAATTATAT
* *
39357737 CACCGGCATCAAGCCTGCTAGATAATAAGTCTGAATTA
1 CACCGGCATTAAGCCTGCTAGACAAT-AGTCTGAATTA
39357775 CATTCGATCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
40 2 0.03
41 65 0.97
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACAATAGTCTGAATTATAT
Found at i:39365935 original size:50 final size:50
Alignment explanation
Indices: 39365826--39366060 Score: 272
Period size: 50 Copynumber: 4.6 Consensus size: 50
39365816 GGTAAAGAGA
* * *
39365826 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGATATCATGAGAGG
1 TCCCATATAAGACCATGTCTGGGACATGGCATGGGCA-CC--G--A-CATGAGAAG
* * * *
39365882 TCCCCTATAAGACCATGTCTGGAACATGGCATGGGCATCGAGATGAGAAG
1 TCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAG
* * *
39365932 TCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAG
*** *
39365982 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAAA
1 TCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAG-AAG
*
39366033 TCCCATGTAAGACCATGTCTGGGACATG
1 TCCCATATAAGACCATGTCTGGGACATG
39366061 ACTTTGGCAT
Statistics
Matches: 157, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
50 94 0.60
51 28 0.18
53 1 0.01
55 1 0.01
56 33 0.21
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (50 bp):
TCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAG
Found at i:39366009 original size:100 final size:105
Alignment explanation
Indices: 39365825--39366070 Score: 349
Period size: 100 Copynumber: 2.4 Consensus size: 105
39365815 GGGTAAAGAG
*
39365825 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGATATCATGAGAGGTCCCCTAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGA-ATCATGAGAGGTCCCCCAT
* *
39365890 AAGACCATGTCTGGAACATGGCATGGGCATCGAGATGAG-AA
64 AAGACCATGTCTGGAACATGGCATGGGCACCGACATGAGAAA
* * * *
39365931 GTCCCATATAAGACCATGTCTGGGACATGGCATTGGCA-CC-G-A-GATGAGAGGTCCCCCGTAA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAATCATGAGAGGTCCCCCATAA
*
39365992 GACCATGTCTGGGACATGGCATGGGCACCGACATGAGAAA
66 GACCATGTCTGGAACATGGCATGGGCACCGACATGAGAAA
* *
39366032 ATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
39366071 GTTTTTACCA
Statistics
Matches: 126, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
100 50 0.40
101 37 0.29
103 1 0.01
105 2 0.02
106 36 0.29
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (105 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAATCATGAGAGGTCCCCCATAA
GACCATGTCTGGAACATGGCATGGGCACCGACATGAGAAA
Found at i:39367773 original size:21 final size:21
Alignment explanation
Indices: 39367747--39367809 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
39367737 TACACCATCC
*
39367747 CAGGGAACACCGTAGTGAT-AA
1 CAGGGAACACCGAAGTG-TGAA
*
39367768 CAGGGAA-ACCAAAGTGTGAA
1 CAGGGAACACCGAAGTGTGAA
*
39367788 CAGGG-ACACCGAAGTGTAAA
1 CAGGGAACACCGAAGTGTGAA
39367808 CA
1 CA
39367810 TATAGGCATC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.06
20 27 0.75
21 7 0.19
ACGTcount: A:0.41, C:0.19, G:0.29, T:0.11
Consensus pattern (21 bp):
CAGGGAACACCGAAGTGTGAA
Found at i:39373870 original size:21 final size:21
Alignment explanation
Indices: 39373846--39373905 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 21
39373836 CCCTTCCCTC
39373846 TTTT-TATTTATTTATTTATTCT
1 TTTTATATTTA-TTA-TTATTCT
39373868 TTTTATATTTATTATTATTCT
1 TTTTATATTTATTATTATTCT
* *
39373889 TGTT-T-GTTATTATTATT
1 TTTTATATTTATTATTATT
39373906 TGTTTTAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 11 0.31
20 1 0.03
21 10 0.29
22 7 0.20
23 6 0.17
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (21 bp):
TTTTATATTTATTATTATTCT
Found at i:39374037 original size:14 final size:14
Alignment explanation
Indices: 39374018--39374056 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
39374008 TTGTTTCATT
*
39374018 GAAAATGGCTTCTG
1 GAAAATGACTTCTG
*
39374032 GAAAATGATTTCTG
1 GAAAATGACTTCTG
39374046 GAAAATGACTT
1 GAAAATGACTT
39374057 ACTTTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (14 bp):
GAAAATGACTTCTG
Found at i:39374670 original size:18 final size:18
Alignment explanation
Indices: 39374632--39374667 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39374622 TTATTATTTT
*
39374632 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
39374650 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
39374668 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:39374812 original size:10 final size:9
Alignment explanation
Indices: 39374783--39374808 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39374773 ATTTTATATT
39374783 AATATTTTA
1 AATATTTTA
39374792 AATATTTTA
1 AATATTTTA
39374801 AATATTTT
1 AATATTTT
39374809 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:39378955 original size:25 final size:26
Alignment explanation
Indices: 39378927--39378998 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 26
39378917 ATTTTCACCA
*
39378927 CTCGTGTGAGTGC-TT-TGATTCATAG
1 CTCGTGTGAG-GCATTCTGATTCACAG
39378952 CTCGTGTGA-GCATTCTGATTCACAG
1 CTCGTGTGAGGCATTCTGATTCACAG
*
39378977 GTCGTGTGA-GCATTCTGATTCA
1 CTCGTGTGAGGCATTCTGATTCA
39378999 GGAATTGACG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 39 0.91
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.36
Consensus pattern (26 bp):
CTCGTGTGAGGCATTCTGATTCACAG
Found at i:39379338 original size:188 final size:188
Alignment explanation
Indices: 39379016--39379399 Score: 651
Period size: 188 Copynumber: 2.0 Consensus size: 188
39379006 ACGGATTACA
* * * *
39379016 GTTATATGAGCTAGCACACTATGTGTGAGTTATCCCGGGTATCCAACGGTATTCTAAATGGTTTA
1 GTTACATGAGCTAGCACACAATGTGTGAGCTATCCCGGGTATCCAACGGTATTCTAAATGGTTCA
* * * * *
39379081 TTGGACATGATTTGAAAGGAAATGGTAAGAGTTAGATATGAACTAAGATATGTTCATATATGAAT
66 ATGGACAAGATTTGAAAGAAAATGGTAAGAGTTAGATAAGAACTAAGATATGTTCACATATGAAT
*
39379146 TGCATTGGATGGGTGATATATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
131 TGCATTGGATGGGTGATACATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
39379204 GTTACATGAGCTAGCACACAATGTGTGAGCTATCCCGGGTATCCAACGGTATTCTAAATGGTTCA
1 GTTACATGAGCTAGCACACAATGTGTGAGCTATCCCGGGTATCCAACGGTATTCTAAATGGTTCA
* *
39379269 ATGGGCAAGATTTGAAAGAAAATGGTAAGAGTTCGATAAGAACTAAGATATGTTCACATATGAAT
66 ATGGACAAGATTTGAAAGAAAATGGTAAGAGTTAGATAAGAACTAAGATATGTTCACATATGAAT
*
39379334 TGCATTGGATTGGTGATACATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
131 TGCATTGGATGGGTGATACATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
39379392 GTTACATG
1 GTTACATG
39379400 CTTAAATGTT
Statistics
Matches: 183, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
188 183 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (188 bp):
GTTACATGAGCTAGCACACAATGTGTGAGCTATCCCGGGTATCCAACGGTATTCTAAATGGTTCA
ATGGACAAGATTTGAAAGAAAATGGTAAGAGTTAGATAAGAACTAAGATATGTTCACATATGAAT
TGCATTGGATGGGTGATACATGGATAAATGTAAGTTGAGATGGATGATATATTCATAT
Found at i:39379544 original size:15 final size:15
Alignment explanation
Indices: 39379524--39379553 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39379514 CTTACTTATA
39379524 TAAGTGCCCAAATGG
1 TAAGTGCCCAAATGG
39379539 TAAGTGCCCAAATGG
1 TAAGTGCCCAAATGG
39379554 AAATATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (15 bp):
TAAGTGCCCAAATGG
Found at i:39379843 original size:20 final size:19
Alignment explanation
Indices: 39379820--39379861 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
39379810 TAAAGAAAGT
39379820 AAATAC-AATGGAAAGTAATG
1 AAATACAAAT-GAAAGTAA-G
*
39379840 AAATGCAAATGAAAGTAAG
1 AAATACAAATGAAAGTAAG
39379859 AAA
1 AAA
39379862 ATTTGAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.60, C:0.05, G:0.19, T:0.17
Consensus pattern (19 bp):
AAATACAAATGAAAGTAAG
Found at i:39383654 original size:2 final size:2
Alignment explanation
Indices: 39383647--39383675 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39383637 TGAACCATGA
39383647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39383676 GAATAATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39384725 original size:23 final size:23
Alignment explanation
Indices: 39384699--39384818 Score: 127
Period size: 23 Copynumber: 5.3 Consensus size: 23
39384689 ATAAGTGCCA
*
39384699 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
39384722 CACT--TACGTAACCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
39384743 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* ** *
39384766 CACTGATATATAGCCTTATCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
39384789 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
39384812 CACTGAT
1 CACTGAT
39384819 CAATAACACT
Statistics
Matches: 75, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
21 17 0.23
23 58 0.77
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:39384801 original size:46 final size:46
Alignment explanation
Indices: 39384699--39384818 Score: 154
Period size: 46 Copynumber: 2.7 Consensus size: 46
39384689 ATAAGTGCCA
* * *
39384699 CACTGATATGTAGCCAAAGCTACCACT--TACGTAACCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACATAACCGTAGCTAC
* * * *
39384743 CACTGAAATGTAGCCGAAGCTACCACTGATATATAGCCTTATCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACATAACCGTAGCTAC
*
39384789 CACTGAAATGTAGTCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
39384819 CAATAACACT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
44 25 0.38
46 41 0.62
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACATAACCGTAGCTAC
Found at i:39385070 original size:18 final size:17
Alignment explanation
Indices: 39385044--39385082 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39385034 ATTTTCCTTC
39385044 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
39385061 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
39385079 CACA
1 CACA
39385083 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:39402181 original size:17 final size:16
Alignment explanation
Indices: 39402159--39402192 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39402149 GAGGATGGCG
39402159 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
39402176 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
39402192 T
1 T
39402193 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:39409677 original size:29 final size:29
Alignment explanation
Indices: 39409604--39409815 Score: 201
Period size: 29 Copynumber: 7.2 Consensus size: 29
39409594 GTGTGTTAAA
* * *
39409604 CGATGGTCGAAATCATCCCTTTTCTTTAAT
1 CGATGGTCGAAACCATCCCTTTTC-ATATT
*
39409634 CGATGGTC-ATCACCATCCCTTTTCATATT
1 CGATGGTCGA-AACCATCCCTTTTCATATT
**
39409663 CGATGGTCGAAACCATCCCTTTTCATTAAA
1 CGATGGTCGAAACCATCCCTTTTCA-TATT
** ***
39409693 CGATGACCTTCACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * *
39409722 CGATAGTTGAAACTATCTCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
** *
39409751 CGATGGTCGTCACCATCCCTTTTCATAGT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* *
39409780 CGATAGTCGAAACTATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
39409809 CAATGGT
1 CGATGGT
39409816 TGTCGATTCG
Statistics
Matches: 142, Mismatches: 37, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
29 99 0.70
30 43 0.30
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.37
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:39409783 original size:58 final size:58
Alignment explanation
Indices: 39409604--39409815 Score: 255
Period size: 59 Copynumber: 3.6 Consensus size: 58
39409594 GTGTGTTAAA
* * *
39409604 CGATGGTCGAAA-TCATCCCTTTTCTTTAATCGATGGTCATCACCATCCCTTTTCATATT
1 CGATAGTCGAAACT-ATCCCTTTTC-ATATTCGATGGTCATCACCATCCCTTTTCATATT
* * ** ** *
39409663 CGATGGTCGAAACCATCCCTTTTCATTAAACGATGACCTTCACCATCCCTTTTCATATT
1 CGATAGTCGAAACTATCCCTTTTCA-TATTCGATGGTCATCACCATCCCTTTTCATATT
* * * *
39409722 CGATAGTTGAAACTATCTCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAGT
1 CGATAGTCGAAACTATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATATT
*
39409780 CGATAGTCGAAACTATCCCTTTTCATATTCAATGGT
1 CGATAGTCGAAACTATCCCTTTTCATATTCGATGGT
39409816 TGTCGATTCG
Statistics
Matches: 132, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
58 60 0.45
59 72 0.55
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.37
Consensus pattern (58 bp):
CGATAGTCGAAACTATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATATT
Found at i:39415696 original size:111 final size:111
Alignment explanation
Indices: 39415502--39415720 Score: 429
Period size: 111 Copynumber: 2.0 Consensus size: 111
39415492 CATTTACAAC
39415502 ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
1 ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
39415567 CCTTAGAAACAATTCGGGACTAAATCAAAAACATTTAAAACTTAAG
66 CCTTAGAAACAATTCGGGACTAAATCAAAAACATTTAAAACTTAAG
39415613 ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
1 ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
*
39415678 CCTTAGAAACAATTCGGGACTAAATTAAAAACATTTAAAACTT
66 CCTTAGAAACAATTCGGGACTAAATCAAAAACATTTAAAACTT
39415721 TATGGAAAAA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.29
Consensus pattern (111 bp):
ATTTCATATTCGTTGTAAAATCCAATCAAACACATGCATAACGTCCCTTTTTCGAGCCATCGAGG
CCTTAGAAACAATTCGGGACTAAATCAAAAACATTTAAAACTTAAG
Found at i:39417540 original size:32 final size:32
Alignment explanation
Indices: 39417504--39417568 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
39417494 CATCAACAAC
39417504 ACATGTTACTTCATTTAAACATGATTCATATG
1 ACATGTTACTTCATTTAAACATGATTCATATG
* *
39417536 ACATGTTAGTTCATTTAAACATGATTTATATG
1 ACATGTTACTTCATTTAAACATGATTCATATG
39417568 A
1 A
39417569 ATTTGACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (32 bp):
ACATGTTACTTCATTTAAACATGATTCATATG
Found at i:39418132 original size:28 final size:29
Alignment explanation
Indices: 39417955--39418239 Score: 252
Period size: 29 Copynumber: 9.8 Consensus size: 29
39417945 TGGTCGAAAT
* *
39417955 CATCCCTTTTCTTTAATTGATGGTTGTCAC
1 CATCCCTTTTC-ATAGTTGATGGTTGTCAC
* * * * **
39417985 CATCCCATTTCATATTTGATGATCGAAAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
* *
39418014 CATCCCTTTTCATTAATTGAT-GTCCGTCAC
1 CATCCCTTTTCA-TAGTTGATGGT-TGTCAC
* * * * **
39418044 CATCCATTTTCTTATTTGATGGTCGAAAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
**
39418073 CATCCCTTTTCATTAGTCAATGGTTGTCAC
1 CATCCCTTTTCA-TAGTTGATGGTTGTCAC
*
39418103 CATCCCTTTTCA-AGTTCATGGTTGTCAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
* * **
39418131 CAT-CCTTTTCATAGCTGATAGTTGAAAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
* * * **
39418159 TATCCATTTTCATATTTGATGGTCATCAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
*
39418188 CATCCCTTTTCATAGTTGATGGTCGTCAC
1 CATCCCTTTTCATAGTTGATGGTTGTCAC
39418217 CATCCCTTTTCATAGTTGATGGT
1 CATCCCTTTTCATAGTTGATGGT
39418240 CAAAACTACC
Statistics
Matches: 204, Mismatches: 45, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
27 8 0.04
28 30 0.15
29 110 0.54
30 56 0.27
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (29 bp):
CATCCCTTTTCATAGTTGATGGTTGTCAC
Found at i:39418169 original size:86 final size:86
Alignment explanation
Indices: 39418012--39418269 Score: 252
Period size: 87 Copynumber: 3.0 Consensus size: 86
39418002 GATGATCGAA
* * * * *
39418012 ACCATCCCTTTTCATTAATTGAT-GTCCGTCACCATCCATTTTCTTATTTGATGGTCGAAACCAT
1 ACCATCCCTTTTCA-TAGTTCATGGT-CGTCACCATCC-TTTTCATAGTTGATAGTCGAAACCAT
* **
39418076 CCCTTTTCATTAGTCAATGGTTGTC
63 CCATTTTCA-TAGTCAATGGTCATC
* * * *
39418101 ACCATCCCTTTTCA-AGTTCATGGTTGTCACCATCCTTTTCATAGCTGATAGTTGAAACTATCCA
1 ACCATCCCTTTTCATAGTTCATGGTCGTCACCATCCTTTTCATAGTTGATAGTCGAAACCATCCA
* **
39418165 TTTTCATATTTGATGGTCATC
66 TTTTCATAGTCAATGGTCATC
* * * *
39418186 ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTTGATGGTCAAAACTA-CC
1 ACCATCCCTTTTCATAGTTCATGGTCGTCACCAT-CCTTTTCATAGTTGATAGTCGAAACCATCC
* *
39418250 TTTTTTCATATTCAATGGTC
65 -ATTTTCATAGTCAATGGTC
39418270 GTCGATTCGT
Statistics
Matches: 141, Mismatches: 24, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
85 24 0.17
86 47 0.33
87 54 0.38
88 2 0.01
89 14 0.10
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (86 bp):
ACCATCCCTTTTCATAGTTCATGGTCGTCACCATCCTTTTCATAGTTGATAGTCGAAACCATCCA
TTTTCATAGTCAATGGTCATC
Found at i:39418259 original size:58 final size:58
Alignment explanation
Indices: 39417943--39418245 Score: 290
Period size: 59 Copynumber: 5.2 Consensus size: 58
39417933 TGTGCTAAAC
* * * * *
39417943 GATGGTCGAAATCATCCCTTTTCTTTAATTGATGGTTGTCACCATCCCATTTCATATTT
1 GATGGTCGAAACCATCCCTTTTC-ATAGTTGATGGTCGTCACCATCCCTTTTCATATTT
* * * *
39418002 GATGATCGAAACCATCCCTTTTCATTAATTGAT-GTCCGTCACCATCCATTTTCTTATTT
1 GATGGTCGAAACCATCCCTTTTCA-TAGTTGATGGT-CGTCACCATCCCTTTTCATATTT
** * *
39418061 GATGGTCGAAACCATCCCTTTTCATTAGTCAATGGTTGTCACCATCCCTTTTCA-AGTT
1 GATGGTCGAAACCATCCCTTTTCA-TAGTTGATGGTCGTCACCATCCCTTTTCATATTT
* * ** * * * ** * *
39418119 CATGGTTGTCACCAT-CCTTTTCATAGCTGATAGTTGAAACTATCCATTTTCATATTT
1 GATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATATTT
* *
39418176 GATGGTC-ATCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTT
1 GATGGTCGA-AACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATATTT
*
39418234 GATGGTCAAAAC
1 GATGGTCGAAAC
39418246 TACCTTTTTT
Statistics
Matches: 197, Mismatches: 40, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
56 21 0.11
57 22 0.11
58 59 0.30
59 93 0.47
60 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (58 bp):
GATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATATTT
Found at i:39422305 original size:42 final size:43
Alignment explanation
Indices: 39422186--39422352 Score: 196
Period size: 43 Copynumber: 3.9 Consensus size: 43
39422176 CGTTTATGTG
* * *
39422186 AAAAACGCTGCTAAAGAACATGACCTTTGGCGACACTTTACCG
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTACCC
* * *
39422229 AAAAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCC
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTACCC
* * *
39422272 AAAAACGCTGCTAAAG-ACATGATCTTTAGCGGCGCTTGTA-TC
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTT-TACCC
* *
39422314 ACAAAC-CTTGCTAAAGATCATGACCTTTAGCGGCACTTT
1 AAAAACGC-TGCTAAAGAACATGACCTTTAGCGGCACTTT
39422353 TACAAACGCC
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 35 0.33
43 71 0.66
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
AAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTACCC
Found at i:39422340 original size:85 final size:86
Alignment explanation
Indices: 39422186--39422352 Score: 214
Period size: 85 Copynumber: 2.0 Consensus size: 86
39422176 CGTTTATGTG
*
39422186 AAAAACGCTGCTAAAGAACATGACCTTTGGCGACACTTTACCGAAAAACACCGCTAAAGAACATG
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGACACTTTACCGAAAAACACCGCTAAAGAACATG
*
39422251 ACCTTTAGCGGCGCTTTACCC
66 ACCTTTAGCGGCACTTTACCC
* * * * * * *
39422272 AAAAACGCTGCTAAAG-ACATGATCTTTAGCGGCGCTTGTATC-ACAAAC-CTTGCTAAAGATCA
1 AAAAACGCTGCTAAAGAACATGACCTTTAGCGACACTT-TACCGAAAAACAC-CGCTAAAGAACA
39422334 TGACCTTTAGCGGCACTTT
64 TGACCTTTAGCGGCACTTT
39422353 TACAAACGCC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 1 0.01
85 50 0.71
86 19 0.27
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (86 bp):
AAAAACGCTGCTAAAGAACATGACCTTTAGCGACACTTTACCGAAAAACACCGCTAAAGAACATG
ACCTTTAGCGGCACTTTACCC
Found at i:39422410 original size:83 final size:81
Alignment explanation
Indices: 39422235--39422411 Score: 196
Period size: 83 Copynumber: 2.1 Consensus size: 81
39422225 ACCGAAAAAC
* ***
39422235 ACCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAAAAACGCTGCTAAAGACATGATCTTTA
1 ACCGCTAAAGAACATGACCTTTAGCGGCACTTTA-CC-AAAACGCCAATAAAGACATGATCTTTA
39422300 GCGGCGCTTGTATCACAA
64 GCGGCGCTTGTATCACAA
* *
39422318 ACCTTGCTAAAGATCATGACCTTTAGCGGCACTTTTA-C-AAACGCCAATATAGAACATGATCTT
1 ACC--GCTAAAGAACATGACCTTTAGCGGCAC-TTTACCAAAACGCCAATAAAG-ACATGATCTT
* *
39422381 TAGCGGCGTTTTTATCACAA
62 TAGCGGCGCTTGTATCACAA
39422401 ATGCCGCTAAA
1 A--CCGCTAAA
39422412 AGTACCATTC
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
82 10 0.12
83 38 0.47
84 1 0.01
85 27 0.34
86 4 0.05
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (81 bp):
ACCGCTAAAGAACATGACCTTTAGCGGCACTTTACCAAAACGCCAATAAAGACATGATCTTTAGC
GGCGCTTGTATCACAA
Found at i:39426399 original size:14 final size:14
Alignment explanation
Indices: 39426382--39426428 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
39426372 AAATCTGAGT
39426382 AATGAACACAACAA
1 AATGAACACAACAA
39426396 AATGAAACACACACACA
1 AATG-AACACA-ACA-A
*
39426413 AATAAACA-AACAA
1 AATGAACACAACAA
39426426 AAT
1 AAT
39426429 AATAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 4 0.14
14 7 0.24
15 7 0.24
16 7 0.24
17 4 0.14
ACGTcount: A:0.66, C:0.21, G:0.04, T:0.09
Consensus pattern (14 bp):
AATGAACACAACAA
Found at i:39427083 original size:14 final size:14
Alignment explanation
Indices: 39427066--39427109 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
39427056 ATAAACCCTA
39427066 AACCCCTAACACTT
1 AACCCCTAACACTT
* *
39427080 AACCCCTAACTCCT
1 AACCCCTAACACTT
*
39427094 AACCCCTAACCCTT
1 AACCCCTAACACTT
39427108 AA
1 AA
39427110 ACCATAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCCCTAACACTT
Found at i:39427083 original size:21 final size:21
Alignment explanation
Indices: 39427059--39427112 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
39427049 ATAAATAATA
*
39427059 AACCCTAAACCCCTAACACTT
1 AACCCTAAACCCCTAACACCT
* *
39427080 AACCCCT-AACTCCTAACCCCT
1 AA-CCCTAAACCCCTAACACCT
39427101 AACCCTTAAACC
1 AACCC-TAAACC
39427113 ATAAATCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
20 3 0.12
21 16 0.62
22 7 0.27
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCTAAACCCCTAACACCT
Found at i:39427195 original size:14 final size:14
Alignment explanation
Indices: 39427163--39427215 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
39427153 AATGGTAACA
*
39427163 CCTAAACTTTAAAC
1 CCTAAACTATAAAC
* *
39427177 TCTAAACTATATAC
1 CCTAAACTATAAAC
* *
39427191 CCTAAACCAAAAAC
1 CCTAAACTATAAAC
*
39427205 CCTAAATTATA
1 CCTAAACTATA
39427216 GTGATAATTA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (14 bp):
CCTAAACTATAAAC
Found at i:39427609 original size:41 final size:41
Alignment explanation
Indices: 39427536--39427616 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
39427526 AAAAATAGAG
*
39427536 CATTAGCGGCGCTTTTTCAAAAACGCCCCTAAAGTCCCGAC
1 CATTAGCGGCGCTTTTTCAAAAACGCCCCTAAAGCCCCGAC
* * * *
39427577 CATTAGCGGCGCTTTTTTAAAAATGTCGCTAAAGCCCCGA
1 CATTAGCGGCGCTTTTTCAAAAACGCCCCTAAAGCCCCGA
39427617 AAGCTCAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (41 bp):
CATTAGCGGCGCTTTTTCAAAAACGCCCCTAAAGCCCCGAC
Found at i:39428314 original size:20 final size:19
Alignment explanation
Indices: 39428250--39428315 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
39428240 CAGAAGCACT
*
39428250 GAAGTGAAA-ATGAAGGCGTC
1 GAAGTGAAATA-G-AGGCATC
* *
39428270 GAAGTGAAATCAAAGGCACC
1 GAAGTGAAAT-AGAGGCATC
*
39428290 AAAGTGAAAGTAGAGGCATC
1 GAAGTGAAA-TAGAGGCATC
39428310 GAAGTG
1 GAAGTG
39428316 CAAACTCGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
20 34 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.32, T:0.14
Consensus pattern (19 bp):
GAAGTGAAATAGAGGCATC
Found at i:39435201 original size:25 final size:25
Alignment explanation
Indices: 39435168--39435229 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
39435158 ACGAGCTGTA
39435168 AACGGTAAGCTCCTCCAAGCTGAAT
1 AACGGTAAGCTCCTCCAAGCTGAAT
**
39435193 AACGGTAAGCTCCTCTGAGCTGAAT
1 AACGGTAAGCTCCTCCAAGCTGAAT
**
39435218 AATTGTAAGCTC
1 AACGGTAAGCTC
39435230 ATGCAAGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (25 bp):
AACGGTAAGCTCCTCCAAGCTGAAT
Found at i:39435237 original size:50 final size:49
Alignment explanation
Indices: 39435152--39435274 Score: 122
Period size: 50 Copynumber: 2.5 Consensus size: 49
39435142 GTACAAGTAT
* * ** * *
39435152 GCTCATACGAGCTGTAAACGGTAAGCTCCTCCAAGCTGA-ATAACGGTAA
1 GCTCATATGAGCTGAAAATTGTAAGCTCATCCAAGCAGAGA-AACGGTAA
* * * *
39435201 GCTCCTCTGAGCTGAATAATTGTAAGCTCATGCAAGCAGAGAACCGGTAA
1 GCTCATATGAGCTGAA-AATTGTAAGCTCATCCAAGCAGAGAAACGGTAA
*
39435251 GCTCATATGAGCTGAAATTTGTAA
1 GCTCATATGAGCTGAAAATTGTAA
39435275 CCCTAATGAC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
49 19 0.32
50 39 0.66
51 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (49 bp):
GCTCATATGAGCTGAAAATTGTAAGCTCATCCAAGCAGAGAAACGGTAA
Found at i:39445703 original size:22 final size:24
Alignment explanation
Indices: 39445658--39445704 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
39445648 ATGAACTTAA
*
39445658 GACATATTTAAAATGCTCAGATTAT
1 GACATATTTAAAA-GCTCAAATTAT
39445683 GACATATTT-AAA-CTCAAATTAT
1 GACATATTTAAAAGCTCAAATTAT
39445705 TGATGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
24 3 0.14
25 9 0.43
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (24 bp):
GACATATTTAAAAGCTCAAATTAT
Found at i:39450624 original size:13 final size:13
Alignment explanation
Indices: 39450606--39450650 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
39450596 CTATAAACTC
39450606 TGTTTTCAAGTTA
1 TGTTTTCAAGTTA
*
39450619 TGTTTTCAAGTCA
1 TGTTTTCAAGTTA
39450632 TGTTTTCAAGTTA
1 TGTTTTCAAGTTA
39450645 TGTTTT
1 TGTTTT
39450651 ACATGAGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.56
Consensus pattern (13 bp):
TGTTTTCAAGTTA
Found at i:39451888 original size:17 final size:18
Alignment explanation
Indices: 39451855--39451890 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
39451845 AGTCATGTCT
39451855 TATGTTGTTATGCGAACC
1 TATGTTGTTATGCGAACC
*
39451873 TATGTTG-TATGTGAACC
1 TATGTTGTTATGCGAACC
39451890 T
1 T
39451891 TTATAACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (18 bp):
TATGTTGTTATGCGAACC
Found at i:39454278 original size:16 final size:16
Alignment explanation
Indices: 39454257--39454291 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
39454247 TGAAAAGGTA
39454257 TGAGTTGATGATGATT
1 TGAGTTGATGATGATT
*
39454273 TGAGTTGATGATGTTT
1 TGAGTTGATGATGATT
39454289 TGA
1 TGA
39454292 ATATGTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (16 bp):
TGAGTTGATGATGATT
Found at i:39460199 original size:37 final size:37
Alignment explanation
Indices: 39460158--39460231 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
39460148 TTTAATAAAA
39460158 TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
1 TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
39460195 TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
1 TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
39460232 ACATCTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (37 bp):
TAATTAGACCATTAATTTTAATAGTGGACAAAGATGG
Found at i:39467220 original size:14 final size:13
Alignment explanation
Indices: 39467202--39467235 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
39467192 TAAATAATTA
39467202 ATTTTTTAATATT
1 ATTTTTTAATATT
39467215 ATTTTTTAATATT
1 ATTTTTTAATATT
39467228 ATTTTTTA
1 ATTTTTTA
39467236 TAAAAACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTTTAATATT
Found at i:39467477 original size:20 final size:20
Alignment explanation
Indices: 39467423--39467477 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
39467413 TCTAATGTTT
39467423 TTTTTAGT-AATTTTTTATA
1 TTTTTAGTAAATTTTTTATA
* * *
39467442 TTTTTCTGCAATTTTTTTATA
1 TTTTT-AGTAAATTTTTTATA
39467463 TTTTTAGTAAATTTT
1 TTTTTAGTAAATTTT
39467478 ATAATGATAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.18
20 8 0.29
21 15 0.54
ACGTcount: A:0.24, C:0.04, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTAGTAAATTTTTTATA
Found at i:39468399 original size:33 final size:33
Alignment explanation
Indices: 39468354--39468420 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
39468344 TAATTATTTT
39468354 AATTAATTAAATTTTATTAAAAT-TATATTTAAA
1 AATTAATTAAATTTT-TTAAAATATATATTTAAA
*
39468387 AATT-ATTGAAATTTTTTATAATATATATTTAAA
1 AATTAATT-AAATTTTTTAAAATATATATTTAAA
39468420 A
1 A
39468421 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
AATTAATTAAATTTTTTAAAATATATATTTAAA
Found at i:39471419 original size:13 final size:13
Alignment explanation
Indices: 39471386--39471411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39471376 GGGTTCTTAG
39471386 GCCTAATTTTCAA
1 GCCTAATTTTCAA
39471399 GCCTAATTTTCAA
1 GCCTAATTTTCAA
39471412 TCTCAATTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
GCCTAATTTTCAA
Found at i:39486311 original size:2 final size:2
Alignment explanation
Indices: 39486301--39486339 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
39486291 TAAATTGGTG
* *
39486301 AT AT A- AT AT AT AT AC AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39486340 TCCATTGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Done.