Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 45 of 93
Found at i:17246761 original size:32 final size:31
Alignment explanation
Indices: 17246698--17246771 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
17246688 ATAAGGATTT
*
17246698 AATTGAATAAAATTCTATAGTAAAGGGACTA
1 AATTGAACAAAATTCTATAGTAAAGGGACTA
* *
17246729 AATTGAACACAATTTTATAAGTAGAA-GGACTA
1 AATTGAACAAAATTCTAT-AGTA-AAGGGACTA
*
17246761 AATCGAACAAA
1 AATTGAACAAA
17246772 GCCCTATTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 15 0.42
32 19 0.53
33 2 0.06
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (31 bp):
AATTGAACAAAATTCTATAGTAAAGGGACTA
Found at i:17247809 original size:30 final size:31
Alignment explanation
Indices: 17247743--17247818 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
17247733 ACGACAAAAA
* *
17247743 TTTGTTCAATTTAGTTCTTGTATTATAGATT
1 TTTGTTCAATTTAGTTCATGTATTATAGACT
*
17247774 TTTGTTCAATTTAGTTCATGTATT-TGGACT
1 TTTGTTCAATTTAGTTCATGTATTATAGACT
17247804 TTTGTTCAATTTAGT
1 TTTGTTCAATTTAGT
17247819 CCATATACTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 19 0.45
31 23 0.55
ACGTcount: A:0.21, C:0.08, G:0.14, T:0.57
Consensus pattern (31 bp):
TTTGTTCAATTTAGTTCATGTATTATAGACT
Found at i:17254260 original size:2 final size:2
Alignment explanation
Indices: 17254248--17254288 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
17254238 CAATGGAAAA
17254248 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17254289 GTACACATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17255153 original size:3 final size:3
Alignment explanation
Indices: 17255145--17255194 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
17255135 AAGCTTGCGN
* *
17255145 ATA ATA ATA AAA ATA ATA ATA A-A ATGA A-A ATA ATA ATT A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
17255188 ATA ATA A
1 ATA ATA A
17255195 ATGAGAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 5 0.13
3 32 0.82
4 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:17255193 original size:17 final size:16
Alignment explanation
Indices: 17255145--17255194 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
17255135 AAGCTTGCGN
*
17255145 ATAATAATA-AAAATA
1 ATAATAAAATAAAATA
17255160 ATAATAAAATGAAAATA
1 ATAATAAAAT-AAAATA
*
17255177 ATAATTAAATAATAATA
1 ATAATAAAATAA-AATA
17255194 A
1 A
17255195 ATGAGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 8 0.27
16 2 0.07
17 20 0.67
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
ATAATAAAATAAAATA
Found at i:17256174 original size:14 final size:15
Alignment explanation
Indices: 17256146--17256175 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17256136 TTTTGCTTAG
17256146 TGCATTTGTTTATTT
1 TGCATTTGTTTATTT
17256161 TGCATTTG-TTATTT
1 TGCATTTGTTTATTT
17256175 T
1 T
17256176 ATTGCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (15 bp):
TGCATTTGTTTATTT
Found at i:17267234 original size:38 final size:38
Alignment explanation
Indices: 17267171--17267504 Score: 487
Period size: 38 Copynumber: 8.8 Consensus size: 38
17267161 TCAAAAAAAA
* * *
17267171 AAAAGGTTTTGTTACCTCAGTTTTGAGGAGTTCATTTTT
1 AAAA-GTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
*
17267210 AAAAGTTTCGTTGCCTTAGCTTTGAGGAGTTCA-TTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
*
17267247 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
** * *
17267285 AAAAGTTTCGTTGCCTTGGCTTTGAGAAGTTCATTTTA
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
*
17267323 AAAAGTTTCGTTGCCTCGGCTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
17267361 AAAAGTCTT-GTTGCCTCAGCTTTGAGGAGTTCATTTTT
1 AAAAGT-TTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
*
17267399 AAAAGTTTCGTTGCCTCAGCTTTGAAGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
*
17267437 AAAAGTCTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
1 AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
* *
17267475 -AAAGTTTCATTGCCTCA-ATCTTGAGGAGTT
1 AAAAGTTTCGTTGCCTCAGCT-TTGAGGAGTT
17267505 TTTTTCTTAA
Statistics
Matches: 270, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
36 1 0.00
37 62 0.23
38 201 0.74
39 6 0.02
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (38 bp):
AAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT
Found at i:17267538 original size:76 final size:76
Alignment explanation
Indices: 17267185--17267547 Score: 356
Period size: 76 Copynumber: 4.8 Consensus size: 76
17267175 GGTTTTGTTA
* * * * * * *
17267185 CCTCAGTTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTTAGCTTTGAGGAGTTCA-TTTTAA
1 CCTCAGCTTTGAAGAGTTCATTTTTAAAAATCTCATTACCTAAGCTTTGAGGAGTTCATTTTTAA
17267249 AAGTTTCATTG
66 AAGTTTCATTG
* * * * * ** * *
17267260 CCTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTTGGCTTTGAGAAGTTCATTTTAAA
1 CCTCAGCTTTGAAGAGTTCATTTTTAAAAATCTCATTACCTAAGCTTTGAGGAGTTCATTTTTAA
*
17267325 AAGTTTCGTTG
66 AAGTTTCATTG
* * * ** * *
17267336 CCTCGGCTTTGAGGAGTTCATTTTTAAAAGTCTTGTTGCCTCAGCTTTGAGGAGTTCATTTTTAA
1 CCTCAGCTTTGAAGAGTTCATTTTTAAAAATCTCATTACCTAAGCTTTGAGGAGTTCATTTTTAA
*
17267401 AAGTTTCGTTG
66 AAGTTTCATTG
* * * *
17267412 CCTCAGCTTTGAAGAGTTCATTTTTAAAAGTCTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT-A
1 CCTCAGCTTTGAAGAGTTCATTTTTAAAAATCTCATTACCTAAGCTTTGAGGAGTTCATTTTTAA
17267476 AAGTTTCATTG
66 AAGTTTCATTG
* * ** * *
17267487 CCTCA-ATCTTGAGGAGTTTTTTTCTTAAAAATGTCATTACCTTAATC-TTGAGGAGTTCATT
1 CCTCAGCT-TTGAAGAGTTCATTT-TTAAAAATCTCATTACC-TAAGCTTTGAGGAGTTCATT
17267548 AAAAAAAAAA
Statistics
Matches: 258, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
74 1 0.00
75 83 0.32
76 171 0.66
77 3 0.01
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (76 bp):
CCTCAGCTTTGAAGAGTTCATTTTTAAAAATCTCATTACCTAAGCTTTGAGGAGTTCATTTTTAA
AAGTTTCATTG
Found at i:17267563 original size:7 final size:7
Alignment explanation
Indices: 17267548--17267577 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
17267538 GGAGTTCATT
17267548 AAAAA-A
1 AAAAACA
17267554 AAAAACA
1 AAAAACA
17267561 AAAAACA
1 AAAAACA
17267568 AAAAACA
1 AAAAACA
17267575 AAA
1 AAA
17267578 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:17269096 original size:3 final size:3
Alignment explanation
Indices: 17269083--17269145 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
17269073 AAAAATAAAA
* *
17269083 AAT AGT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17269131 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
17269146 GTATAGGTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17269477 original size:10 final size:10
Alignment explanation
Indices: 17269458--17269486 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
17269448 TTTTAATTTT
17269458 AAAT-AAAAA
1 AAATAAAAAA
17269467 AAATAAAAAA
1 AAATAAAAAA
17269477 AAATAAAAAA
1 AAATAAAAAA
17269487 TGATAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAATAAAAAA
Found at i:17270828 original size:20 final size:20
Alignment explanation
Indices: 17270803--17270842 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17270793 CTCCACATGC
* *
17270803 ATGTATCGATACATTTTTAA
1 ATGTATCAATACATTCTTAA
17270823 ATGTATCAATACATTCTTAA
1 ATGTATCAATACATTCTTAA
17270843 GAATTTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (20 bp):
ATGTATCAATACATTCTTAA
Found at i:17272731 original size:19 final size:20
Alignment explanation
Indices: 17272707--17272745 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17272697 TAAATTAAAA
17272707 GTAA-TTAT-TCATCAAATTT
1 GTAATTTATATCAT-AAATTT
17272726 GTAATTTATATCATAAATTT
1 GTAATTTATATCATAAATTT
17272746 ATTAAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (20 bp):
GTAATTTATATCATAAATTT
Found at i:17276694 original size:20 final size:20
Alignment explanation
Indices: 17276669--17276714 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
17276659 CTTATAAACC
17276669 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
17276689 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
17276709 TCAAAT
1 TCAAAT
17276715 GAGGACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:17280557 original size:43 final size:43
Alignment explanation
Indices: 17280445--17280731 Score: 213
Period size: 44 Copynumber: 6.6 Consensus size: 43
17280435 TTCAAAGAAA
* * * * * *
17280445 AAGCTTTTCATCTAAAATAAGACTACGTAACTTT-AAAGAAGAA
1 AAGCTCTTCATCTAGAATAAGGCTACATAACTTTGAAATAA-AT
* * * *
17280488 ATAGCTCCGT-ATCTAAAATAAAGCTACATGACTTTGAAATAAAT
1 A-AGCT-CTTCATCTAGAATAAGGCTACATAACTTTGAAATAAAT
* * *
17280532 AATCTTCTT-ATCTAGATTAAGGCTACATAACTTTGAAAATGAAT
1 AAGC-TCTTCATCTAGAATAAGGCTACATAACTTTG-AAATAAAT
* * *
17280576 AAGCTCTTCATCTGGAATAAGGCTACGTAACTTTGAAAATGAAT
1 AAGCTCTTCATCTAGAATAAGGCTACATAACTTTG-AAATAAAT
* * * * * * *
17280620 AAACTCCTCATCTGGAATGAGGCTACGTAACTTTAAAAATGAAT
1 AAGCTCTTCATCTAGAATAAGGCTACATAACTTT-GAAATAAAT
* * * *
17280664 AAGCGCCTCATCTAGAATGAGGCTACATAACTTT-AGAATGAAT
1 AAGCTCTTCATCTAGAATAAGGCTACATAACTTTGA-AATAAAT
* *
17280707 AAGCTCTTTATCTGGAATAAGGCTA
1 AAGCTCTTCATCTAGAATAAGGCTA
17280732 AGCTCTTTAT
Statistics
Matches: 204, Mismatches: 32, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.00
43 58 0.28
44 139 0.68
45 6 0.03
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (43 bp):
AAGCTCTTCATCTAGAATAAGGCTACATAACTTTGAAATAAAT
Found at i:17280599 original size:44 final size:44
Alignment explanation
Indices: 17280504--17280731 Score: 264
Period size: 44 Copynumber: 5.2 Consensus size: 44
17280494 CCGTATCTAA
* * * * *
17280504 AATAAAGCTACATGACTTTG-AAATAAATAATCTTCTT-ATCTAG
1 AATAAGGCTACATAACTTTGAAAATGAATAAGC-TCTTCATCTGG
*
17280547 ATTAAGGCTACATAACTTTGAAAATGAATAAGCTCTTCATCTGG
1 AATAAGGCTACATAACTTTGAAAATGAATAAGCTCTTCATCTGG
* * *
17280591 AATAAGGCTACGTAACTTTGAAAATGAATAAACTCCTCATCTGG
1 AATAAGGCTACATAACTTTGAAAATGAATAAGCTCTTCATCTGG
* * * * * *
17280635 AATGAGGCTACGTAACTTTAAAAATGAATAAGCGCCTCATCTAG
1 AATAAGGCTACATAACTTTGAAAATGAATAAGCTCTTCATCTGG
* * *
17280679 AATGAGGCTACATAACTTT-AGAATGAATAAGCTCTTTATCTGG
1 AATAAGGCTACATAACTTTGAAAATGAATAAGCTCTTCATCTGG
17280722 AATAAGGCTA
1 AATAAGGCTA
17280732 AGCTCTTTAT
Statistics
Matches: 161, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
43 49 0.30
44 112 0.70
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (44 bp):
AATAAGGCTACATAACTTTGAAAATGAATAAGCTCTTCATCTGG
Found at i:17280659 original size:88 final size:87
Alignment explanation
Indices: 17280460--17280731 Score: 262
Period size: 87 Copynumber: 3.1 Consensus size: 87
17280450 TTTCATCTAA
* * * * * *
17280460 AATAAGACTACGTAACTTTAAAGAA-GAA-ATAGCTCCGT-ATCTAAAATAAAGCTACATGACTT
1 AATAAGGCTACATAACTTTAAA-AATGAATA-AGCGCC-TCATCTAGAATAAGGCTACATAACTT
* * * * * *
17280522 TGAAATAAATAATCTTCTTATCTAG
63 TAAAATGAATAAACTCCTCATCTGG
* * * * * *
17280547 ATTAAGGCTACATAACTTTGAAAATGAATAAGCTCTTCATCTGGAATAAGGCTACGTAACTTTGA
1 AATAAGGCTACATAACTTTAAAAATGAATAAGCGCCTCATCTAGAATAAGGCTACATAACTTT-A
17280612 AAATGAATAAACTCCTCATCTGG
65 AAATGAATAAACTCCTCATCTGG
* * * *
17280635 AATGAGGCTACGTAACTTTAAAAATGAATAAGCGCCTCATCTAGAATGAGGCTACATAACTTTAG
1 AATAAGGCTACATAACTTTAAAAATGAATAAGCGCCTCATCTAGAATAAGGCTACATAACTTTAA
* * *
17280700 AATGAATAAGCTCTTTATCTGG
66 AATGAATAAACTCCTCATCTGG
17280722 AATAAGGCTA
1 AATAAGGCTA
17280732 AGCTCTTTAT
Statistics
Matches: 151, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
86 3 0.02
87 75 0.50
88 73 0.48
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (87 bp):
AATAAGGCTACATAACTTTAAAAATGAATAAGCGCCTCATCTAGAATAAGGCTACATAACTTTAA
AATGAATAAACTCCTCATCTGG
Found at i:17280733 original size:24 final size:24
Alignment explanation
Indices: 17280706--17280755 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
17280696 TTAGAATGAA
17280706 TAAGCTCTTTATCTGGAATAAGGC
1 TAAGCTCTTTATCTGGAATAAGGC
*
17280730 TAAGCTCTTTATTTGGAATAAGGC
1 TAAGCTCTTTATCTGGAATAAGGC
17280754 TA
1 TA
17280756 TGTAACTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (24 bp):
TAAGCTCTTTATCTGGAATAAGGC
Found at i:17283002 original size:23 final size:23
Alignment explanation
Indices: 17282976--17283038 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
17282966 TGTGGCATGC
*
17282976 CATGGTGTGCATATGTGAGACGA
1 CATGGTGAGCATATGTGAGACGA
** *
17282999 CATGGTGAAAATATGTGAGACGG
1 CATGGTGAGCATATGTGAGACGA
*
17283022 CATGGTAAGCATATGTG
1 CATGGTGAGCATATGTG
17283039 GCACGACTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.11, G:0.33, T:0.25
Consensus pattern (23 bp):
CATGGTGAGCATATGTGAGACGA
Found at i:17283119 original size:47 final size:47
Alignment explanation
Indices: 17283046--17283273 Score: 276
Period size: 47 Copynumber: 4.8 Consensus size: 47
17283036 GTGGCACGAC
* * * *
17283046 TGTGACATGGCAGGGTTCAAAATTTGTGACACGCCATGAAGGGAATT
1 TGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATT
*
17283093 TGTGACATGGCAGGGTTCAGAGTTTGTGACACGCCATGGGAGGGAATT
1 TGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCAT-GGAGGGAATT
* * *
17283141 TGTGACACGTCAAGGTTCAGAGTTTGTGACACGCTATGGAGGGAATT
1 TGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATT
* * * ** *
17283188 TGTGACGCGGTAGGGTTCAGAGTTTGTGACACGACATGGAGAAAATC
1 TGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATT
** * * *
17283235 TGTGACACGATAGGGTTTAGAGTGTGTGACACGACATGG
1 TGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATGG
17283274 CTTGAACATG
Statistics
Matches: 160, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
47 118 0.74
48 42 0.26
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.25
Consensus pattern (47 bp):
TGTGACACGGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATT
Found at i:17283142 original size:24 final size:24
Alignment explanation
Indices: 17283066--17283193 Score: 91
Period size: 24 Copynumber: 5.4 Consensus size: 24
17283056 CAGGGTTCAA
*
17283066 AATTTGTGACACGCCAT-GAAGGG
1 AATTTGTGACACGCCATGGGAGGG
* * ***
17283089 AATTTGTGACATGGCA-GGGTTCAG
1 AATTTGTGACACGCCATGGG-AGGG
*
17283113 AGTTTGTGACACGCCATGGGAGGG
1 AATTTGTGACACGCCATGGGAGGG
* * ****
17283137 AATTTGTGACACGTCAAGGTTCAG
1 AATTTGTGACACGCCATGGGAGGG
* *
17283161 AGTTTGTGACACGCTAT-GGAGGG
1 AATTTGTGACACGCCATGGGAGGG
17283184 AATTTGTGAC
1 AATTTGTGAC
17283194 GCGGTAGGGT
Statistics
Matches: 74, Mismatches: 28, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
23 26 0.35
24 45 0.61
25 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.27
Consensus pattern (24 bp):
AATTTGTGACACGCCATGGGAGGG
Found at i:17283209 original size:95 final size:94
Alignment explanation
Indices: 17283059--17283272 Score: 268
Period size: 95 Copynumber: 2.3 Consensus size: 94
17283049 GACATGGCAG
* * *
17283059 GGTTCAAAATTTGTGACACGCCATGAAGGGAATTTGTGACATGGCAGGGTTCAGAGTTTGTGACA
1 GGTTCAGAGTTTGTGACACGCCATGAAGGGAATTTGTGACACGGCAGGGTTCAGAGTTTGTGACA
* ** *
17283124 CGCCATGGGAGGGAATTTGTGACACG-TCAA
66 CGACAT-GGAGAAAATCTGTGACACGAT-AA
* * * *
17283154 GGTTCAGAGTTTGTGACACGCTATGGAGGGAATTTGTGACGCGGTAGGGTTCAGAGTTTGTGACA
1 GGTTCAGAGTTTGTGACACGCCATGAAGGGAATTTGTGACACGGCAGGGTTCAGAGTTTGTGACA
*
17283219 CGACATGGAGAAAATCTGTGACACGATAG
66 CGACATGGAGAAAATCTGTGACACGATAA
* * *
17283248 GGTTTAGAGTGTGTGACACGACATG
1 GGTTCAGAGTTTGTGACACGCCATG
17283273 GCTTGAACAT
Statistics
Matches: 102, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
94 38 0.37
95 64 0.63
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.26
Consensus pattern (94 bp):
GGTTCAGAGTTTGTGACACGCCATGAAGGGAATTTGTGACACGGCAGGGTTCAGAGTTTGTGACA
CGACATGGAGAAAATCTGTGACACGATAA
Found at i:17283293 original size:23 final size:23
Alignment explanation
Indices: 17283259--17283302 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17283249 GTTTAGAGTG
17283259 TGTGACACGACATGGCTTGAACA
1 TGTGACACGACATGGCTTGAACA
* *
17283282 TGTGACATGACATGGTTTGAA
1 TGTGACACGACATGGCTTGAA
17283303 ATAGGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (23 bp):
TGTGACACGACATGGCTTGAACA
Found at i:17283372 original size:8 final size:8
Alignment explanation
Indices: 17283353--17283385 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
17283343 ACGTCCACTG
17283353 AATGAATGA
1 AATGAAT-A
17283362 AATGAATA
1 AATGAATA
17283370 AATGAATA
1 AATGAATA
17283378 AATGAATA
1 AATGAATA
17283386 TTATAAGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (8 bp):
AATGAATA
Found at i:17283956 original size:31 final size:31
Alignment explanation
Indices: 17283916--17284150 Score: 344
Period size: 31 Copynumber: 7.6 Consensus size: 31
17283906 GTGTTAGTGT
*
17283916 TGGCGTGTAACAACATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
17283947 TGGCATGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* * *
17283978 TGGCTTGTAACAACATTTGACTTGATACGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
17284009 TGGCGTGTAACAACATTTTACATGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
17284040 TGGAGTGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* * *
17284071 TAGCGTGTAACAATATTTTACTTTATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* **
17284102 TGGTGTGTAACAACATTTTACTTGATATGTG
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
17284133 TGGGGTGTAACAACATTT
1 TGGCGTGTAACAACATTT
17284151 ATTTCTTTCT
Statistics
Matches: 182, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 182 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTTACTTGATATGCA
Found at i:17285798 original size:145 final size:146
Alignment explanation
Indices: 17285564--17285872 Score: 390
Period size: 145 Copynumber: 2.1 Consensus size: 146
17285554 TGGTTCTAAC
* * *
17285564 GGTTTGTGTTCAACAATTTCTTATGTGATTATCGAATAACATATTTGTGTTTGCAGTTGGACCAT
1 GGTTTGTGTTCAACAATTTCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTAGACCAT
** * * *
17285629 GCGACGACAACTCCACAATGACCGAAAGGTCCTCCTCAGATGCACAATGCTAACGAGGTGTTGGT
66 GCGACGACAACTCCACAACCACCGAAAGGTCCTCCTCAGACGCACAATGCTAACGAGGTATCGGT
*
17285694 AAGATCAATTTTAA-A
131 AAGATCAATTCTAATA
* *
17285709 GGTTTGTGTTCAACAATTTCATATGTGATTATCGTATAACATATCTGTGTTTGTAGTTAGACCAT
1 GGTTTGTGTTCAACAATTTCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTAGACCAT
* * * * ** * * * * *
17285774 GCGACGATAGCTCCATAACCACCGAGAGGTTTTCTTCAGACGTATAGTGCTAACGAGTTATCGGT
66 GCGACGACAACTCCACAACCACCGAAAGGTCCTCCTCAGACGCACAATGCTAACGAGGTATCGGT
*
17285839 AAGATCAGTTCTAATA
131 AAGATCAATTCTAATA
17285855 -GTTTGTGTTCAAC-ATTTC
1 GGTTTGTGTTCAACAATTTC
17285873 CACATGTTTG
Statistics
Matches: 140, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
144 5 0.04
145 134 0.96
146 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (146 bp):
GGTTTGTGTTCAACAATTTCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTAGACCAT
GCGACGACAACTCCACAACCACCGAAAGGTCCTCCTCAGACGCACAATGCTAACGAGGTATCGGT
AAGATCAATTCTAATA
Found at i:17288008 original size:31 final size:31
Alignment explanation
Indices: 17287973--17288243 Score: 172
Period size: 31 Copynumber: 8.7 Consensus size: 31
17287963 CTGCAACAAG
* *
17287973 TCAGCGTGTCATGCCATAAATTTTCTTGCAC
1 TCAGCGTGTCATGCCATAAATCTGCTTGCAC
* * * ** *
17288004 TCAGCGTGTCACGCCTTAAATATGC-AACAAG
1 TCAGCGTGTCATGCCATAAATCTGCTTGC-AC
* * *
17288035 TCAGCGTGTCATGTCATAAATTTGCTTGAAC
1 TCAGCGTGTCATGCCATAAATCTGCTTGCAC
* * ** *
17288066 TCAGCGTGTCATGTCATAAATATGC-AACAAG
1 TCAGCGTGTCATGCCATAAATCTGCTTGC-AC
* * * *
17288097 TTAGCGTGTCATACCATAAATCTAC-TACAAC
1 TCAGCGTGTCATGCCATAAATCTGCTTGC-AC
* * *
17288128 ACAGTGTGTCACGCCATAAATCTGCTTGCAC
1 TCAGCGTGTCATGCCATAAATCTGCTTGCAC
* ** **
17288159 TCAACGTGTCACCCCATAAATCTGCTACCAC
1 TCAGCGTGTCATGCCATAAATCTGCTTGCAC
* * * * *
17288190 ACAGTGTGTCATGCAAAAAATCTACTTGCAC
1 TCAGCGTGTCATGCCATAAATCTGCTTGCAC
*
17288221 TAAGCGTGTCACT-CCATAAATCT
1 TCAGCGTGTCA-TGCCATAAATCT
17288244 ACTACCAATG
Statistics
Matches: 180, Mismatches: 55, Indels: 10
0.73 0.22 0.04
Matches are distributed among these distances:
30 1 0.01
31 176 0.98
32 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (31 bp):
TCAGCGTGTCATGCCATAAATCTGCTTGCAC
Found at i:17288045 original size:62 final size:62
Alignment explanation
Indices: 17287959--17288148 Score: 245
Period size: 62 Copynumber: 3.0 Consensus size: 62
17287949 GTCACCCCTG
* * *
17287959 AATACTGCAACAAGTCAGCGTGTCATGCCATAAATTTTCTTGCACTCAGCGTGTCACGCCTTA
1 AATA-TGCAACAAGTCAGCGTGTCATGCCATAAATTTGCTTGAACTCAGCGTGTCACGCCATA
* * *
17288022 AATATGCAACAAGTCAGCGTGTCATGTCATAAATTTGCTTGAACTCAGCGTGTCATGTCATA
1 AATATGCAACAAGTCAGCGTGTCATGCCATAAATTTGCTTGAACTCAGCGTGTCACGCCATA
* * * * ** * *
17288084 AATATGCAACAAGTTAGCGTGTCATACCATAAATCTACTACAACACAGTGTGTCACGCCATA
1 AATATGCAACAAGTCAGCGTGTCATGCCATAAATTTGCTTGAACTCAGCGTGTCACGCCATA
17288146 AAT
1 AAT
17288149 CTGCTTGCAC
Statistics
Matches: 110, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
62 106 0.96
63 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (62 bp):
AATATGCAACAAGTCAGCGTGTCATGCCATAAATTTGCTTGAACTCAGCGTGTCACGCCATA
Found at i:17288249 original size:62 final size:63
Alignment explanation
Indices: 17288099--17288250 Score: 211
Period size: 62 Copynumber: 2.4 Consensus size: 63
17288089 GCAACAAGTT
* * * *
17288099 AGCGTGTCA-TACCATAAATCTACTACAACACAGTGTGTCACGCCATAAATCTGCTTGCACTCA
1 AGCGTGTCACT-CCATAAATCTACTACCACACAGTGTGTCACGCAAAAAATCTACTTGCACTCA
* * *
17288162 A-CGTGTCACCCCATAAATCTGCTACCACACAGTGTGTCATGCAAAAAATCTACTTGCACT-A
1 AGCGTGTCACTCCATAAATCTACTACCACACAGTGTGTCACGCAAAAAATCTACTTGCACTCA
17288223 AGCGTGTCACTCCATAAATCTACTACCA
1 AGCGTGTCACTCCATAAATCTACTACCA
17288251 ATGAAAGTGT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
61 2 0.03
62 75 0.96
63 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.25
Consensus pattern (63 bp):
AGCGTGTCACTCCATAAATCTACTACCACACAGTGTGTCACGCAAAAAATCTACTTGCACTCA
Found at i:17288273 original size:62 final size:62
Alignment explanation
Indices: 17288099--17288274 Score: 189
Period size: 62 Copynumber: 2.8 Consensus size: 62
17288089 GCAACAAGTT
* *
17288099 AGCGTGTCA-TACCATAAATCTACTA-CAACACAGTGTGTCACGCCATAAATCTGCTTGCACTCA
1 AGCGTGTCACT-CCATAAATCTACTACCAACA-A-TGTGTCATGCCATAAATCTACTTGCACTCA
* * * * *
17288162 A-CGTGTCACCCCATAAATCTGCTACCACACAGTGTGTCATGCAAAAAATCTACTTGCACT-A
1 AGCGTGTCACTCCATAAATCTACTACCA-ACAATGTGTCATGCCATAAATCTACTTGCACTCA
* * *
17288223 AGCGTGTCACTCCATAAATCTACTACCAATGAAAGTGTCATGCCTTAAATCT
1 AGCGTGTCACTCCATAAATCTACTACCAA-CAATGTGTCATGCCATAAATCT
17288275 GCTACCAGTC
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
61 3 0.03
62 84 0.90
63 3 0.03
64 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (62 bp):
AGCGTGTCACTCCATAAATCTACTACCAACAATGTGTCATGCCATAAATCTACTTGCACTCA
Found at i:17289785 original size:43 final size:43
Alignment explanation
Indices: 17289738--17289852 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
17289728 TAGCTCATGT
** * *
17289738 GCACTCCCTACTCGCACATGGCTGGGTCATCAC-C-AGGTTATGC
1 GCACTCCCTACTCGCACATAACCGGGTCATC-CTCGA-CTTATGC
*
17289781 GCACTCCCTACTCGCACGTAACCGGGTCATCCTCGACTTATGC
1 GCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTTATGC
* * *
17289824 GCACTCCTTACTCGCACATAGCCGAGTCA
1 GCACTCCCTACTCGCACATAACCGGGTCA
17289853 ATATAATTAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 1 0.02
43 59 0.97
44 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTTATGC
Found at i:17291310 original size:24 final size:24
Alignment explanation
Indices: 17291278--17291329 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
17291268 AAAGTGCACT
17291278 TGCAACAGCAATAGCTTCACTTGG
1 TGCAACAGCAATAGCTTCACTTGG
* *
17291302 TGCAGCAGCAGTAGCTTCACTTGG
1 TGCAACAGCAATAGCTTCACTTGG
17291326 TGCA
1 TGCA
17291330 CCATTAGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (24 bp):
TGCAACAGCAATAGCTTCACTTGG
Found at i:17293760 original size:21 final size:21
Alignment explanation
Indices: 17293696--17293760 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
17293686 CCTCCATCAT
* * *
17293696 CTCCAACAGCTTTGTATGGGC
1 CTCCACCAGCTTCGGATGGGC
* * *
17293717 CACCACCAACTTCAGATGGGC
1 CTCCACCAGCTTCGGATGGGC
17293738 CTCCACCAGCTTCGGATGGGC
1 CTCCACCAGCTTCGGATGGGC
17293759 CT
1 CT
17293761 TTAGTAGCCT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.20, C:0.35, G:0.23, T:0.22
Consensus pattern (21 bp):
CTCCACCAGCTTCGGATGGGC
Found at i:17296197 original size:15 final size:15
Alignment explanation
Indices: 17296177--17296206 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17296167 AATATTCAAC
17296177 AAAATGAAAAAATAA
1 AAAATGAAAAAATAA
*
17296192 AAAATGAATAAATAA
1 AAAATGAAAAAATAA
17296207 TTGCAAGCGT
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:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAATGAAAAAATAA
Found at i:17300047 original size:22 final size:22
Alignment explanation
Indices: 17300022--17300168 Score: 95
Period size: 22 Copynumber: 6.6 Consensus size: 22
17300012 AGCCATGTCC
*
17300022 AAAAATATTACACGTAAGTTCA
1 AAAAATGTTACACGTAAGTTCA
*
17300044 AAAAATGTTACACGCCT-TGTTC-
1 AAAAATGTTACACG--TAAGTTCA
* *
17300066 AAAAATGTTACACGCAAATTCA
1 AAAAATGTTACACGTAAGTTCA
* *
17300088 AAAATTGTTACACGCCT-TGTTC-
1 AAAAATGTTACACG--TAAGTTCA
* * *
17300110 CAAAATGTTACATGCAAGTTCA
1 AAAAATGTTACACGTAAGTTCA
* * *
17300132 AAAATTGTTACACGCCATGTTCA
1 AAAAATGTTACACG-TAAGTTCA
* *
17300155 CAACATGTTACACG
1 AAAAATGTTACACG
17300169 CCATATGTTA
Statistics
Matches: 95, Mismatches: 21, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
21 7 0.07
22 62 0.65
23 25 0.26
24 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (22 bp):
AAAAATGTTACACGTAAGTTCA
Found at i:17300051 original size:44 final size:44
Alignment explanation
Indices: 17299982--17300169 Score: 207
Period size: 44 Copynumber: 4.2 Consensus size: 44
17299972 TCAATCATGT
* * * *
17299982 TGTTACACGCCATGTTTAGAAAATGTTACAAGCCATGTCCAAAAA
1 TGTTACACG-CAAGTTCAAAAAATGTTACACGCCATGTCCAAAAA
* * * *
17300027 TATTACACGTAAGTTCAAAAAATGTTACACGCCTTGTTCAAAAA
1 TGTTACACGCAAGTTCAAAAAATGTTACACGCCATGTCCAAAAA
* * *
17300071 TGTTACACGCAAATTCAAAAATTGTTACACGCCTTGTTCC-AAAA
1 TGTTACACGCAAGTTCAAAAAATGTTACACGCCATG-TCCAAAAA
* * * *
17300115 TGTTACATGCAAGTTCAAAAATTGTTACACGCCATGTTCACAACA
1 TGTTACACGCAAGTTCAAAAAATGTTACACGCCATGTCCA-AAAA
17300160 TGTTACACGC
1 TGTTACACGC
17300170 CATATGTTAA
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
43 2 0.02
44 97 0.80
45 22 0.18
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (44 bp):
TGTTACACGCAAGTTCAAAAAATGTTACACGCCATGTCCAAAAA
Found at i:17300099 original size:88 final size:88
Alignment explanation
Indices: 17300001--17300169 Score: 234
Period size: 88 Copynumber: 1.9 Consensus size: 88
17299991 CCATGTTTAG
* *
17300001 AAAATGTTACAAGCCATG-TCCAAAAATATTACACGTAAGTTCAAAAAATGTTACACGCCTTGTT
1 AAAATGTTACAAGCCATGTTCC-AAAATATTACACGCAAGTTCAAAAAATGTTACACGCCATGTT
17300065 CA-AAAATGTTACACGCAAATTCA
65 CACAAAATGTTACACGCAAATTCA
* * * * *
17300088 AAAATTGTTACACGCCTTGTTCCAAAATGTTACATGCAAGTTCAAAAATTGTTACACGCCATGTT
1 AAAA-TGTTACAAGCCATGTTCCAAAATATTACACGCAAGTTCAAAAAATGTTACACGCCATGTT
*
17300153 CACAACATGTTACACGC
65 CACAAAATGTTACACGC
17300170 CATATGTTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
87 4 0.06
88 51 0.72
89 16 0.23
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.28
Consensus pattern (88 bp):
AAAATGTTACAAGCCATGTTCCAAAATATTACACGCAAGTTCAAAAAATGTTACACGCCATGTTC
ACAAAATGTTACACGCAAATTCA
Found at i:17310591 original size:29 final size:28
Alignment explanation
Indices: 17310549--17310610 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
17310539 TGGATTGTGT
* * * *
17310549 ATGGGTTTGTGGTGAGCTTGTTAACAATC
1 ATGGGTTTGAGGTGAACTTATTAA-AACC
17310578 ATGGGTTTGAGGTGAACTTATTAAAACC
1 ATGGGTTTGAGGTGAACTTATTAAAACC
17310606 ATGGG
1 ATGGG
17310611 CTATTGCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.26, C:0.10, G:0.31, T:0.34
Consensus pattern (28 bp):
ATGGGTTTGAGGTGAACTTATTAAAACC
Found at i:17317812 original size:20 final size:20
Alignment explanation
Indices: 17317787--17317826 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17317777 TCACTAATCC
*
17317787 TTTCCTTTCAACAACGTCAA
1 TTTCCTTTCAACAAAGTCAA
17317807 TTTCCTTTCAACAAAGTCAA
1 TTTCCTTTCAACAAAGTCAA
17317827 GACAAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (20 bp):
TTTCCTTTCAACAAAGTCAA
Found at i:17322623 original size:21 final size:22
Alignment explanation
Indices: 17322590--17322630 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
17322580 TACATTTTTT
*
17322590 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
*
17322612 CACTT-TTCCCTTGATTTTT
1 CACTTGTTCCCTTGAATTTT
17322631 TCTACCTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.15, C:0.24, G:0.07, T:0.54
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:17333982 original size:43 final size:43
Alignment explanation
Indices: 17333934--17334049 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
17333924 TCTTTAGTAG
*
17333934 AAGGTAAAAGAGAAGAAGTATACGTAAAAAGGTACACAAGAAC
1 AAGGTAAAAGAGAAGAAGTATACATAAAAAGGTACACAAGAAC
* * *
17333977 AAGGTAAAAGAGAA-AAGGCATACATGAAAAGGTACACGAGAAC
1 AAGGTAAAAGAGAAGAA-GTATACATAAAAAGGTACACAAGAAC
** * *
17334020 AAGGTACGAGAGAAGAGGTATACATGAAAA
1 AAGGTAAAAGAGAAGAAGTATACATAAAAA
17334050 TGTATAAAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 2 0.03
43 60 0.95
44 1 0.02
ACGTcount: A:0.53, C:0.09, G:0.26, T:0.11
Consensus pattern (43 bp):
AAGGTAAAAGAGAAGAAGTATACATAAAAAGGTACACAAGAAC
Found at i:17334033 original size:15 final size:15
Alignment explanation
Indices: 17333962--17334026 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 15
17333952 TATACGTAAA
*
17333962 AAGGTACACAAGAAC
1 AAGGTACACGAGAAC
* *
17333977 AAGGTAAAAGAGAA-
1 AAGGTACACGAGAAC
* *
17333991 AAGGCATAC-ATGAA-
1 AAGGTACACGA-GAAC
17334005 AAGGTACACGAGAAC
1 AAGGTACACGAGAAC
17334020 AAGGTAC
1 AAGGTAC
17334027 GAGAGAAGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
13 1 0.03
14 19 0.49
15 19 0.49
ACGTcount: A:0.52, C:0.14, G:0.25, T:0.09
Consensus pattern (15 bp):
AAGGTACACGAGAAC
Found at i:17334363 original size:18 final size:18
Alignment explanation
Indices: 17334276--17334416 Score: 67
Period size: 18 Copynumber: 7.9 Consensus size: 18
17334266 ACTATCACGT
17334276 GAAGTAGTTGTTCCA-TGC
1 GAAGTAGTTGTTCCACT-C
* *
17334294 AAAGTAGTTGTTCCACTT
1 GAAGTAGTTGTTCCACTC
* * **
17334312 GTATTAGTTGTTTTACAT-
1 GAAGTAGTTGTTCCAC-TC
* *
17334330 GAAGTA-CTGCTCCACTC
1 GAAGTAGTTGTTCCACTC
* *
17334347 AAAGTAGTTGTTCCACTT
1 GAAGTAGTTGTTCCACTC
* * * **
17334365 GTATTAATTGTTTTACAT-
1 GAAGTAGTTGTTCCAC-TC
*
17334383 GAAGTAG-TGCTCCACTC
1 GAAGTAGTTGTTCCACTC
*
17334400 AAAGTAGTTGTTCCACT
1 GAAGTAGTTGTTCCACT
17334417 TGTATTAATT
Statistics
Matches: 85, Mismatches: 31, Indels: 14
0.65 0.24 0.11
Matches are distributed among these distances:
16 2 0.02
17 21 0.25
18 59 0.69
19 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (18 bp):
GAAGTAGTTGTTCCACTC
Found at i:17334464 original size:35 final size:35
Alignment explanation
Indices: 17334413--17334569 Score: 135
Period size: 35 Copynumber: 4.5 Consensus size: 35
17334403 GTAGTTGTTC
*
17334413 CACTTGTAT-TAATTGTTTTACATG-AAATAGTGCTC
1 CACTTGT-TCTAATTGTTTT-CATGTAAATAGTGCTT
* *
17334448 CACTTGTTCTACTTGTTTT-GTGTAAAGTAGTGCTT
1 CACTTGTTCTAATTGTTTTCATGTAAA-TAGTGCTT
* * * *
17334483 CACTTGTTCTATTTG-TTCCATGTACAGTAGTGTTT
1 CACTTGTTCTAATTGTTTTCATGTA-AATAGTGCTT
* **
17334518 CACTTGTTCTAATTGTTCTGCGCG-AAATAGTGCTT
1 CACTTGTTCTAATTGTT-TTCATGTAAATAGTGCTT
*
17334553 CACTTGTTCTAGTTGTT
1 CACTTGTTCTAATTGTT
17334570 CTTATTATCC
Statistics
Matches: 100, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
33 2 0.02
34 6 0.06
35 86 0.86
36 3 0.03
37 3 0.03
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.46
Consensus pattern (35 bp):
CACTTGTTCTAATTGTTTTCATGTAAATAGTGCTT
Found at i:17334464 original size:53 final size:53
Alignment explanation
Indices: 17334275--17334451 Score: 293
Period size: 53 Copynumber: 3.3 Consensus size: 53
17334265 TACTATCACG
* *
17334275 TGAAGTAGTTGTTCCA-TGCAAAGTAGTTGTTCCACTTGTATTAGTTGTTTTACA
1 TGAAGTAG-TGCTCCACT-CAAAGTAGTTGTTCCACTTGTATTAATTGTTTTACA
*
17334329 TGAAGTACTGCTCCACTCAAAGTAGTTGTTCCACTTGTATTAATTGTTTTACA
1 TGAAGTAGTGCTCCACTCAAAGTAGTTGTTCCACTTGTATTAATTGTTTTACA
17334382 TGAAGTAGTGCTCCACTCAAAGTAGTTGTTCCACTTGTATTAATTGTTTTACA
1 TGAAGTAGTGCTCCACTCAAAGTAGTTGTTCCACTTGTATTAATTGTTTTACA
*
17334435 TGAAATAGTGCTCCACT
1 TGAAGTAGTGCTCCACT
17334452 TGTTCTACTT
Statistics
Matches: 117, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
53 109 0.93
54 8 0.07
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (53 bp):
TGAAGTAGTGCTCCACTCAAAGTAGTTGTTCCACTTGTATTAATTGTTTTACA
Found at i:17334514 original size:70 final size:70
Alignment explanation
Indices: 17334440--17334570 Score: 183
Period size: 70 Copynumber: 1.9 Consensus size: 70
17334430 TTACATGAAA
* * * * *
17334440 TAGTGCTCCACTTGTTCTACTTGTTTTGTG-TAAAGTAGTGCTTCACTTGTTCTATTTGTTCCAT
1 TAGTGCTCCACTTGTTCTAATTGTTCTGCGCGAAA-TAGTGCTTCACTTGTTCTAGTTGTTCCAT
17334504 GTACAG
65 GTACAG
* *
17334510 TAGTGTTTCACTTGTTCTAATTGTTCTGCGCGAAATAGTGCTTCACTTGTTCTAGTTGTTC
1 TAGTGCTCCACTTGTTCTAATTGTTCTGCGCGAAATAGTGCTTCACTTGTTCTAGTTGTTC
17334571 TTATTATCCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
70 50 0.94
71 3 0.06
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.46
Consensus pattern (70 bp):
TAGTGCTCCACTTGTTCTAATTGTTCTGCGCGAAATAGTGCTTCACTTGTTCTAGTTGTTCCATG
TACAG
Found at i:17334685 original size:19 final size:20
Alignment explanation
Indices: 17334661--17334698 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17334651 TGTGATGCCG
*
17334661 AGGCGTTGT-AAAGACACCT
1 AGGCGTGGTGAAAGACACCT
17334680 AGGCGTGGTGAAAGACACC
1 AGGCGTGGTGAAAGACACC
17334699 AATCGTGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.21, G:0.32, T:0.16
Consensus pattern (20 bp):
AGGCGTGGTGAAAGACACCT
Found at i:17335486 original size:22 final size:22
Alignment explanation
Indices: 17335457--17335502 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
17335447 CAAAAATGTT
*
17335457 AAAACCAAGAATT-AATTTTGA
1 AAAACCAAAAATTAAATTTTGA
17335478 AAAATCCAAAAATTAAAATTTTGA
1 AAAA-CCAAAAATT-AAATTTTGA
17335502 A
1 A
17335503 GAATATTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 8 0.38
24 9 0.43
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.28
Consensus pattern (22 bp):
AAAACCAAAAATTAAATTTTGA
Found at i:17346083 original size:26 final size:27
Alignment explanation
Indices: 17346047--17346116 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 27
17346037 ACTTTTCGTT
* *
17346047 GAAAA-TCCGTTGGAAA-TTTTCAACA
1 GAAAATTCCGTTGGAAACATTCCAACA
17346072 GAAAATTCCGTTGGAAAAACATTCCAACA
1 GAAAATTCCGTTGG--AAACATTCCAACA
*
17346101 GAAAATTTCGTTGGAA
1 GAAAATTCCGTTGGAA
17346117 TTGTTTTTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 5 0.13
26 8 0.21
27 2 0.05
28 3 0.08
29 20 0.53
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (27 bp):
GAAAATTCCGTTGGAAACATTCCAACA
Found at i:17346146 original size:15 final size:15
Alignment explanation
Indices: 17346126--17346155 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17346116 ATTGTTTTTC
17346126 CGTTGGAAATAATTT
1 CGTTGGAAATAATTT
*
17346141 CGTTGGAAATGATTT
1 CGTTGGAAATAATTT
17346156 TCCAACGGAA
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:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (15 bp):
CGTTGGAAATAATTT
Found at i:17346212 original size:30 final size:30
Alignment explanation
Indices: 17346178--17346244 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
17346168 CCGTTGAAAA
17346178 TTTCCAAAGGAATTTTCCGGTAG-AAATGCT
1 TTTCCAAAGGAATTTTCC-GTAGAAAATGCT
* *
17346208 TTTCCAAAGGAATTTTTCGTTGAAAATGCT
1 TTTCCAAAGGAATTTTCCGTAGAAAATGCT
17346238 TTTCCAA
1 TTTCCAA
17346245 TGAAAAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 3 0.09
30 31 0.91
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (30 bp):
TTTCCAAAGGAATTTTCCGTAGAAAATGCT
Found at i:17346289 original size:54 final size:54
Alignment explanation
Indices: 17346208--17346329 Score: 163
Period size: 54 Copynumber: 2.3 Consensus size: 54
17346198 TAGAAATGCT
* * * *
17346208 TTTCCAAAGGAATTTTTCGTTGAAAATGCTTTTCCAATGAAAAAACATTGAATA
1 TTTCCAACGAAATTTTTAGTTGAAAATGCTTTTCCAATGAAAAAACATTGAAAA
* * * *
17346262 TTTCTAACGAAATTTTTAGTTGGAAATGCTTTTCCAATGGAAAAACGTTGAAAA
1 TTTCCAACGAAATTTTTAGTTGAAAATGCTTTTCCAATGAAAAAACATTGAAAA
*
17346316 TTTCCAACGGAATT
1 TTTCCAACGAAATT
17346330 CATTTATATT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (54 bp):
TTTCCAACGAAATTTTTAGTTGAAAATGCTTTTCCAATGAAAAAACATTGAAAA
Found at i:17346842 original size:12 final size:13
Alignment explanation
Indices: 17346822--17346858 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
17346812 GCATTCTTAA
*
17346822 TTTCTTCACGTAT
1 TTTCATCACGTAT
17346835 TTTC-TCACGTA-
1 TTTCATCACGTAT
17346846 TTTCATCACGTAT
1 TTTCATCACGTAT
17346859 CTTACCCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.18
12 14 0.64
13 4 0.18
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49
Consensus pattern (13 bp):
TTTCATCACGTAT
Found at i:17348826 original size:18 final size:18
Alignment explanation
Indices: 17348803--17348838 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17348793 TTCACAGTCG
17348803 TCATCTTCAAGTTCATCT
1 TCATCTTCAAGTTCATCT
*
17348821 TCATCTTCAATTTCATCT
1 TCATCTTCAAGTTCATCT
17348839 CCTTCCATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.28, G:0.03, T:0.47
Consensus pattern (18 bp):
TCATCTTCAAGTTCATCT
Found at i:17351102 original size:25 final size:26
Alignment explanation
Indices: 17351074--17351127 Score: 92
Period size: 25 Copynumber: 2.1 Consensus size: 26
17351064 TTACAATTTG
17351074 GAATATGCAAATTTTATGGAAAT-AT
1 GAATATGCAAATTTTATGGAAATAAT
*
17351099 GAATATTCAAATTTTATGGAAATAAT
1 GAATATGCAAATTTTATGGAAATAAT
17351125 GAA
1 GAA
17351128 ACTCTCTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (26 bp):
GAATATGCAAATTTTATGGAAATAAT
Found at i:17352432 original size:19 final size:19
Alignment explanation
Indices: 17352404--17352441 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17352394 CCATTTAACT
* *
17352404 TATTGTAGTATGATTTGAG
1 TATTGCAGTATAATTTGAG
17352423 TATTGCAGTATAATTTGAG
1 TATTGCAGTATAATTTGAG
17352442 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.45
Consensus pattern (19 bp):
TATTGCAGTATAATTTGAG
Found at i:17353826 original size:13 final size:13
Alignment explanation
Indices: 17353808--17353832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17353798 AGAGAAATTG
17353808 TGATTTTATAAAA
1 TGATTTTATAAAA
17353821 TGATTTTATAAA
1 TGATTTTATAAA
17353833 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:17354764 original size:28 final size:29
Alignment explanation
Indices: 17354723--17354782 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
17354713 GTCTATAGGC
* *
17354723 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
17354751 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
17354781 AA
1 AA
17354783 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:17357360 original size:15 final size:16
Alignment explanation
Indices: 17357340--17357380 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
17357330 AAGATATTTT
17357340 GATTTTAAAG-CTTTG
1 GATTTTAAAGTCTTTG
*
17357355 GATTTTAAAGTTTTTG
1 GATTTTAAAGTCTTTG
17357371 G-TTTTAAAGT
1 GATTTTAAAGT
17357381 TGTTTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (16 bp):
GATTTTAAAGTCTTTG
Found at i:17357381 original size:15 final size:15
Alignment explanation
Indices: 17357336--17357381 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
17357326 AGATAAGATA
*
17357336 TTTTGATTTTAAAG-
1 TTTTGGTTTTAAAGT
*
17357350 CTTTGGATTTTAAAGT
1 TTTTGG-TTTTAAAGT
17357366 TTTTGGTTTTAAAGT
1 TTTTGGTTTTAAAGT
17357381 T
1 T
17357382 GTTTTAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 18 0.67
16 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (15 bp):
TTTTGGTTTTAAAGT
Found at i:17357426 original size:5 final size:5
Alignment explanation
Indices: 17357416--17357448 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
17357406 TGTGTGGCCC
17357416 AAGTT AAGTT AAGTT AAGTT -AGTT AAGTT AAGT
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGT
17357449 CAGGTTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (5 bp):
AAGTT
Found at i:17357441 original size:14 final size:15
Alignment explanation
Indices: 17357416--17357448 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
17357406 TGTGTGGCCC
17357416 AAGTTAAGTTAAGTT
1 AAGTTAAGTTAAGTT
17357431 AAGTT-AGTTAAGTT
1 AAGTTAAGTTAAGTT
17357445 AAGT
1 AAGT
17357449 CAGGTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (15 bp):
AAGTTAAGTTAAGTT
Found at i:17357455 original size:19 final size:19
Alignment explanation
Indices: 17357417--17357456 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
17357407 GTGTGGCCCA
*
17357417 AGTTAAGTTAAGTTAAGTT
1 AGTTAAGTTAAGTCAAGTT
*
17357436 AGTTAAGTTAAGTCAGGTT
1 AGTTAAGTTAAGTCAAGTT
17357455 AG
1 AG
17357457 ATAGAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (19 bp):
AGTTAAGTTAAGTCAAGTT
Found at i:17421833 original size:50 final size:50
Alignment explanation
Indices: 17421767--17421927 Score: 222
Period size: 50 Copynumber: 3.3 Consensus size: 50
17421757 TAAGATTTAC
17421767 AAAATAAACAACTCCTCATCCGAGGCTTAACCACTTCAACATCAATTTGA
1 AAAATAAACAACTCCTCATCCGAGGCTTAACCACTTCAACATCAATTTGA
** * *
17421817 AAAATAAACAACTCCTCATTTGAGGCCTAACCATTTCAACATCAATTTGA
1 AAAATAAACAACTCCTCATCCGAGGCTTAACCACTTCAACATCAATTTGA
* ** *
17421867 AAAATAACCAACTCCTCATCCGAGGCTCCACCACTT-TA-A--AATTTGA
1 AAAATAAACAACTCCTCATCCGAGGCTTAACCACTTCAACATCAATTTGA
17421913 AAAATAAACAACTCC
1 AAAATAAACAACTCC
17421928 CCCTTCGAGG
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
46 21 0.21
48 1 0.01
49 1 0.01
50 75 0.77
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.24
Consensus pattern (50 bp):
AAAATAAACAACTCCTCATCCGAGGCTTAACCACTTCAACATCAATTTGA
Found at i:17421874 original size:27 final size:27
Alignment explanation
Indices: 17421794--17421877 Score: 68
Period size: 27 Copynumber: 3.3 Consensus size: 27
17421784 ATCCGAGGCT
*
17421794 TAACCACTTCAACATCAATTTGAAAAA
1 TAACCAATTCAACATCAATTTGAAAAA
* * ****
17421821 TAAACAACTC--C-TC-ATTTGAGGCC
1 TAACCAATTCAACATCAATTTGAAAAA
*
17421844 TAACCATTTCAACATCAATTTGAAAAA
1 TAACCAATTCAACATCAATTTGAAAAA
17421871 TAACCAA
1 TAACCAA
17421878 CTCCTCATCC
Statistics
Matches: 38, Mismatches: 15, Indels: 8
0.62 0.25 0.13
Matches are distributed among these distances:
23 13 0.34
24 2 0.05
25 2 0.05
26 2 0.05
27 19 0.50
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (27 bp):
TAACCAATTCAACATCAATTTGAAAAA
Found at i:17421925 original size:46 final size:46
Alignment explanation
Indices: 17421725--17421964 Score: 193
Period size: 46 Copynumber: 5.0 Consensus size: 46
17421715 TCGAAGAAGC
* *
17421725 TAAACAACTCCTCATCCAAGGCTCTATA-C-CTTTAAGATTT-ACAAAA
1 TAAACAACTCCTCATCCGAGGCTC-A-ACCACTTTAAAATTTGA-AAAA
* *
17421771 TAAACAACTCCTCATCCGAGGCTTAACCACTTCAACATCAATTTGAAAAA
1 TAAACAACTCCTCATCCGAGGCTCAACCACTT-TA-A--AATTTGAAAAA
**
17421821 TAAACAACTCCTCATTTGAGGC-CTAACCA-TTTCAACATCAATTTGAAAAA
1 TAAACAACTCCTCATCCGAGGCTC-AACCACTTT--A-A--AATTTGAAAAA
* *
17421871 TAACCAACTCCTCATCCGAGGCTCCACCACTTTAAAATTTGAAAAA
1 TAAACAACTCCTCATCCGAGGCTCAACCACTTTAAAATTTGAAAAA
* * * * ** *
17421917 TAAACAACTCCCCCTTCGAGGCTCCATAACTTTGAAATTTGAAAAA
1 TAAACAACTCCTCATCCGAGGCTCAACCACTTTAAAATTTGAAAAA
17421963 TA
1 TA
17421965 GGCTCCATAA
Statistics
Matches: 163, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 77 0.47
47 1 0.01
48 2 0.01
49 3 0.02
50 72 0.44
51 5 0.03
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.26
Consensus pattern (46 bp):
TAAACAACTCCTCATCCGAGGCTCAACCACTTTAAAATTTGAAAAA
Found at i:17421968 original size:29 final size:29
Alignment explanation
Indices: 17421935--17421993 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
17421925 TCCCCCTTCG
17421935 AGGCTCCATAACTTTGAAATTTGAAAAAT
1 AGGCTCCATAACTTTGAAATTTGAAAAAT
17421964 AGGCTCCATAACTTTGAAATTTGAAAAAT
1 AGGCTCCATAACTTTGAAATTTGAAAAAT
17421993 A
1 A
17421994 AACAACTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (29 bp):
AGGCTCCATAACTTTGAAATTTGAAAAAT
Found at i:17422081 original size:126 final size:121
Alignment explanation
Indices: 17421860--17422090 Score: 318
Period size: 126 Copynumber: 1.9 Consensus size: 121
17421850 TTTCAACATC
* * **
17421860 AATTTGAAAAATAACCAACTCCTCATCCGAGGCTCCACCACTTTAAAATTTGAAAAATAAACAAC
1 AATTTGAAAAATAAACAACTCCTCATACGAGGCTAAACCACTTTAAAATTTGAAAAATAAACAAC
* * * *
17421925 TCCCCCTTCGAGGCTCCATAACTTTGAAATTTGAAAAATAGGCTCCATAACTTTGA
66 TCCCCATCCGAGGCTCCACAACTTTAAAATTTGAAAAATAGGCTCCATAACTTTGA
*
17421981 AATTTGAAAAATAAACAACTCCTCATACGAGGCTTAAACCACTTTAAAATCAATTTGAAAAGTAA
1 AATTTGAAAAATAAACAACTCCTCATACGAGGC-TAAACCACTTT--AA--AATTTGAAAAATAA
* *
17422046 ACAACTCCTCATCCGAGGCTCCACCACTTTAAAATTTGAAAAATA
61 ACAACTCCCCATCCGAGGCTCCACAACTTTAAAATTTGAAAAATA
17422091 AATAACTCCT
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
121 31 0.33
122 9 0.10
124 2 0.02
126 52 0.55
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (121 bp):
AATTTGAAAAATAAACAACTCCTCATACGAGGCTAAACCACTTTAAAATTTGAAAAATAAACAAC
TCCCCATCCGAGGCTCCACAACTTTAAAATTTGAAAAATAGGCTCCATAACTTTGA
Found at i:17422098 original size:46 final size:46
Alignment explanation
Indices: 17421964--17422157 Score: 235
Period size: 46 Copynumber: 4.1 Consensus size: 46
17421954 TTTGAAAAAT
* *
17421964 AGGCTCCATAACTTTGAAATTTGAAAAATAAACAACTCCTCATACG
1 AGGCTCCACAACTTTAAAATTTGAAAAATAAACAACTCCTCATACG
** * * *
17422010 AGGCTTAAACCACTTTAAAATCAATTTGAAAAGTAAACAACTCCTCATCCG
1 AGGC-TCCACAACTTT--AA--AATTTGAAAAATAAACAACTCCTCATACG
* * * *
17422061 AGGCTCCACCACTTTAAAATTTGAAAAATAAATAACTCCTCCTCCG
1 AGGCTCCACAACTTTAAAATTTGAAAAATAAACAACTCCTCATACG
*
17422107 AGGCTCCACAACTTTGAAATTTGAAAAATAAACAACTCCTCATACG
1 AGGCTCCACAACTTTAAAATTTGAAAAATAAACAACTCCTCATACG
17422153 AGGCT
1 AGGCT
17422158 TAAACCATTT
Statistics
Matches: 126, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
46 76 0.60
47 7 0.06
48 2 0.02
49 1 0.01
50 9 0.07
51 31 0.25
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (46 bp):
AGGCTCCACAACTTTAAAATTTGAAAAATAAACAACTCCTCATACG
Found at i:17422111 original size:172 final size:171
Alignment explanation
Indices: 17421810--17422136 Score: 539
Period size: 172 Copynumber: 1.9 Consensus size: 171
17421800 CTTCAACATC
** * *
17421810 AATTTGAAAAATAAACAACTCCTCATTTGAGGCCTAACCATTTCAACATCAATTTGAAAAATAAC
1 AATTTGAAAAATAAACAACTCCTCATACGAGGCCTAACCATTTCAAAATCAATTTGAAAAATAAA
*
17421875 CAACTCCTCATCCGAGGCTCCACCACTTTAAAATTTGAAAAATAAACAACTCCCCCTTCGAGGCT
66 CAACTCCTCATCCGAGGCTCCACCACTTTAAAATTTGAAAAATAAACAACTCCCCCTCCGAGGCT
*
17421940 CCATAACTTTGAAATTTGAAAAATAGGCTCCATAACTTTGA
131 CCACAACTTTGAAATTTGAAAAATAGGCTCCATAACTTTGA
* *
17421981 AATTTGAAAAATAAACAACTCCTCATACGAGGCTTAAACCACTTT-AAAATCAATTTGAAAAGTA
1 AATTTGAAAAATAAACAACTCCTCATACGAGGCCT-AACCA-TTTCAAAATCAATTTGAAAAATA
* *
17422045 AACAACTCCTCATCCGAGGCTCCACCACTTTAAAATTTGAAAAATAAATAACTCCTCCTCCGAGG
64 AACAACTCCTCATCCGAGGCTCCACCACTTTAAAATTTGAAAAATAAACAACTCCCCCTCCGAGG
17422110 CTCCACAACTTTGAAATTTGAAAAATA
129 CTCCACAACTTTGAAATTTGAAAAATA
17422137 AACAACTCCT
Statistics
Matches: 144, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
171 32 0.22
172 109 0.76
173 3 0.02
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (171 bp):
AATTTGAAAAATAAACAACTCCTCATACGAGGCCTAACCATTTCAAAATCAATTTGAAAAATAAA
CAACTCCTCATCCGAGGCTCCACCACTTTAAAATTTGAAAAATAAACAACTCCCCCTCCGAGGCT
CCACAACTTTGAAATTTGAAAAATAGGCTCCATAACTTTGA
Found at i:17434927 original size:18 final size:18
Alignment explanation
Indices: 17434890--17434928 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17434880 TTATGAGAAT
* * *
17434890 TTTATGAAATAAATTGAA
1 TTTATAAAATAAACTAAA
17434908 TTTATAAAATAAACTAAA
1 TTTATAAAATAAACTAAA
17434926 TTT
1 TTT
17434929 TTATAAGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (18 bp):
TTTATAAAATAAACTAAA
Found at i:17437225 original size:10 final size:10
Alignment explanation
Indices: 17437210--17437245 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
17437200 TGAATCCCAT
17437210 TTTTTTTCTC
1 TTTTTTTCTC
17437220 TTTTTTTCT-
1 TTTTTTTCTC
17437229 TATTTTTTCTC
1 T-TTTTTTCTC
17437240 TTTTTT
1 TTTTTT
17437246 AGGCATAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 22 0.92
11 1 0.04
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:17445513 original size:12 final size:12
Alignment explanation
Indices: 17445496--17445520 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17445486 TGGACTTCAT
17445496 TTGAATAATTAA
1 TTGAATAATTAA
17445508 TTGAATAATTAA
1 TTGAATAATTAA
17445520 T
1 T
17445521 ATAAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TTGAATAATTAA
Found at i:17449140 original size:15 final size:15
Alignment explanation
Indices: 17449120--17449156 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
17449110 AATTACTATT
*
17449120 ATATATATACTTTTA
1 ATATATATACTTTAA
17449135 ATATATATACTTTAA
1 ATATATATACTTTAA
17449150 ATATATA
1 ATATATA
17449157 AAGATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATACTTTAA
Found at i:17449207 original size:16 final size:17
Alignment explanation
Indices: 17449179--17449223 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
17449169 TTCTACTTTC
17449179 TATTAATCTTATAAAAAT
1 TATTAA-CTTATAAAAAT
17449197 TA-TAACTTAT-AAAAT
1 TATTAACTTATAAAAAT
17449212 TATTAA-TTATAA
1 TATTAACTTATAA
17449224 TATATATACC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.44
16 9 0.36
17 3 0.12
18 2 0.08
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTAACTTATAAAAAT
Found at i:17484207 original size:21 final size:19
Alignment explanation
Indices: 17484181--17484221 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
17484171 AATTTAAAAC
17484181 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
17484202 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
17484221 A
1 A
17484222 TTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:17494610 original size:25 final size:25
Alignment explanation
Indices: 17494557--17494615 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
17494547 TTTTCATAGT
* * *
17494557 TAAATCATTTTAAAAGTATCAATTA
1 TAAATTATTTTAAAAGTATAAATCA
* *
17494582 TAAATTATTTTTAAAGTATAAATCC
1 TAAATTATTTTAAAAGTATAAATCA
*
17494607 TAAAGTATT
1 TAAATTATT
17494616 CAAATTATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (25 bp):
TAAATTATTTTAAAAGTATAAATCA
Found at i:17494763 original size:2 final size:2
Alignment explanation
Indices: 17494758--17494828 Score: 84
Period size: 2 Copynumber: 39.0 Consensus size: 2
17494748 GAGATTTCAC
17494758 AT AT AT -T AT AT -T AT AT AT -T AT AT -T AT AT 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 AT
*
17494796 AT TT AT AT AT AT AT AT -T AT AT AT A- AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17494829 TGCTTGTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
1 7 0.12
2 53 0.88
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:17494775 original size:12 final size:12
Alignment explanation
Indices: 17494758--17494829 Score: 95
Period size: 10 Copynumber: 6.6 Consensus size: 12
17494748 GAGATTTCAC
17494758 ATATATTATATT
1 ATATATTATATT
17494770 ATATATTATATT
1 ATATATTATATT
17494782 ATATA-TATA-T
1 ATATATTATATT
17494792 ATATATT-TA-T
1 ATATATTATATT
17494802 ATATA-TATATT
1 ATATATTATATT
17494813 ATATA-TA-ATT
1 ATATATTATATT
17494823 ATATATT
1 ATATATT
17494830 GCTTGTTTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.02
10 24 0.43
11 14 0.25
12 17 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATATTATATT
Found at i:17497817 original size:22 final size:22
Alignment explanation
Indices: 17497779--17497821 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17497769 TATTTTTTAA
*
17497779 AAAATTATATAATAATAATTTTT
1 AAAATTATATAAAAAT-ATTTTT
17497802 AAAATTA-ATAAAAATATTTT
1 AAAATTATATAAAAATATTTT
17497822 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATTATATAAAAATATTTTT
Found at i:17498402 original size:23 final size:23
Alignment explanation
Indices: 17498376--17498423 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
17498366 TCTTGTTTGC
*
17498376 ATTTGTCTTTT-AAAAGGGGAAGA
1 ATTTG-CTTTTCAAAAAGGGAAGA
17498399 ATTTGCTTTTCAAAAAGGGAAGA
1 ATTTGCTTTTCAAAAAGGGAAGA
17498422 AT
1 AT
17498424 GGGTCTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTTGCTTTTCAAAAAGGGAAGA
Found at i:17499386 original size:30 final size:31
Alignment explanation
Indices: 17499341--17499410 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
17499331 TTATTATGTT
*
17499341 AAATCAAATTTTTATA-TTTTTATTTTGAATC
1 AAAT-AAACTTTTATACTTTTTATTTTGAATC
* *
17499372 AAATAAACTTTTATACTTTTTATTTTGAGTT
1 AAATAAACTTTTATACTTTTTATTTTGAATC
17499403 AAATAAAC
1 AAATAAAC
17499411 CTTTGTAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (31 bp):
AAATAAACTTTTATACTTTTTATTTTGAATC
Found at i:17508368 original size:13 final size:11
Alignment explanation
Indices: 17508338--17508378 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
17508328 TTGACTTTTT
17508338 TAAAAATTTAA
1 TAAAAATTTAA
17508349 TAAAAATATTAA
1 TAAAAAT-TTAA
17508361 TCAAAAA-TTAA
1 T-AAAAATTTAA
17508372 -AAAAATT
1 TAAAAATT
17508379 ATATGATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.19
10 1 0.04
11 11 0.41
12 5 0.19
13 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTTAA
Found at i:17527477 original size:13 final size:13
Alignment explanation
Indices: 17527461--17527485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17527451 GAACCAATTT
17527461 AGTCGACCAAGTC
1 AGTCGACCAAGTC
17527474 AGTCGACCAAGT
1 AGTCGACCAAGT
17527486 GCTCTCTGCC
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:0.28, G:0.24, T:0.16
Consensus pattern (13 bp):
AGTCGACCAAGTC
Found at i:17528052 original size:67 final size:67
Alignment explanation
Indices: 17527973--17528158 Score: 232
Period size: 67 Copynumber: 2.8 Consensus size: 67
17527963 AAGTTGGTTG
* * *
17527973 TTGGGTTTTGGTTGATCCCAGT-AAAAACCATTGTTG-TAGGTTGTGGTTGAGCCCTTGAAAAAC
1 TTGGGTTTTGGTTAAGCCC-GTGAAAAACCATTG-TGAAAGGTTGTGGTTGAGCCCTTGAAAAAC
17528036 CACT
64 CACT
*
17528040 TTGGGTTTTGGTTAAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTAAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCCTTGAAAAACCA
17528105 CT
66 CT
* * * * * * * *
17528107 TTGGGTTTTAGTTTAGCTCGTGAAAAACTAGTGTAAAAGGTTTTGGCTGAGC
1 TTGGGTTTTGGTTAAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGC
17528159 TTGTAAAAGC
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
66 4 0.04
67 101 0.96
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (67 bp):
TTGGGTTTTGGTTAAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCCTTGAAAAACCA
CT
Found at i:17528058 original size:32 final size:32
Alignment explanation
Indices: 17527973--17528134 Score: 130
Period size: 35 Copynumber: 4.9 Consensus size: 32
17527963 AAGTTGGTTG
* * *
17527973 TTGGGTTTTGGTTGATCCCAGT-AAAAACCATT
1 TTGGGTTGTGGTTGAGCCC-GTGAAAAACCACT
*
17528005 GTTGTAGGTTGTGGTTGAGCCCTTGAAAAACCACT
1 -TTG--GGTTGTGGTTGAGCCCGTGAAAAACCACT
* *
17528040 TTGGGTTTTGGTTAAGCCCGTGAAAAACCA-T
1 TTGGGTTGTGGTTGAGCCCGTGAAAAACCACT
**
17528071 TGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCACT
1 T-TG---GGTTGTGGTTGAGCCCGTGAAAAACCACT
* * * *
17528107 TTGGGTTTTAGTTTAGCTCGTGAAAAAC
1 TTGGGTTGTGGTTGAGCCCGTGAAAAAC
17528135 TAGTGTAAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 17
0.75 0.12 0.12
Matches are distributed among these distances:
31 2 0.02
32 45 0.43
33 3 0.03
34 4 0.04
35 48 0.46
36 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (32 bp):
TTGGGTTGTGGTTGAGCCCGTGAAAAACCACT
Found at i:17535787 original size:27 final size:26
Alignment explanation
Indices: 17535750--17535801 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
17535740 CTACTAAATG
*
17535750 TTTTTGTTGAATGCTTATATTTATGC
1 TTTTTGTTGAATGCTTATATCTATGC
*
17535776 TTTTATGTTGAATGTTTATATCTATG
1 TTTT-TGTTGAATGCTTATATCTATG
17535802 TGATTAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.58
Consensus pattern (26 bp):
TTTTTGTTGAATGCTTATATCTATGC
Found at i:17535790 original size:40 final size:39
Alignment explanation
Indices: 17535700--17535792 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 39
17535690 GGGATGTTTC
* *
17535700 TATGCTGAATGTTTTTTTGAATGTTTATATCTATGTTTT
1 TATGCTGAATGTTTTTTTGAATGCTTATATCTATGCTTT
* * * *
17535739 TCTACTAAATGTTTTTGTTGAATGCTTATATTTATGCTTT
1 TATGCTGAATGTTTTT-TTGAATGCTTATATCTATGCTTT
*
17535779 TATGTTGAATGTTT
1 TATGCTGAATGTTT
17535793 ATATCTATGT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
39 13 0.30
40 30 0.70
ACGTcount: A:0.22, C:0.06, G:0.15, T:0.57
Consensus pattern (39 bp):
TATGCTGAATGTTTTTTTGAATGCTTATATCTATGCTTT
Found at i:17539751 original size:27 final size:26
Alignment explanation
Indices: 17539715--17539765 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
17539705 TATATTGTGA
*
17539715 TTTAGAATTTTATATTTAATTTGTTTG
1 TTTAGAATTTTACATTT-ATTTGTTTG
* *
17539742 TTTAGCATTTTCCATTTATTTGTT
1 TTTAGAATTTTACATTTATTTGTT
17539766 ATAAATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.22, C:0.06, G:0.10, T:0.63
Consensus pattern (26 bp):
TTTAGAATTTTACATTTATTTGTTTG
Found at i:17549556 original size:71 final size:71
Alignment explanation
Indices: 17549477--17549695 Score: 250
Period size: 71 Copynumber: 3.1 Consensus size: 71
17549467 AATTGTTTAA
* *
17549477 TTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATCAAGCCCAACAATTTAATTA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATCAAGCCCAACAACTTAATTA
17549542 AACAAT
66 AACAAT
* * * **
17549548 TTTAATCAATTAGGCCCAATGACTTAATTAAACTATTTTAATCAA-CTAGGCCCAATGACTTAAT
1 TTTAATCAATTAGGCCCAATGACTTAATTAAAC-AATTTAATTAATC-AAGCCCAACAACTTAAT
17549612 TAAACAA-
64 TAAACAAT
* * * * * * * *
17549619 TTTAATTAATTAGACTCGATGACTTAATTAAATAATTTAATTTAT-TAG-GC-ACAACTTAATTA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATCAAGCCCAACAACTTAATTA
17549681 AACAAT
66 AACAAT
17549687 TTTAATCAA
1 TTTAATCAA
17549696 GTGCCTGAGA
Statistics
Matches: 123, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
67 15 0.12
68 9 0.07
69 1 0.01
70 8 0.07
71 61 0.50
72 29 0.24
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.35
Consensus pattern (71 bp):
TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATCAAGCCCAACAACTTAATTA
AACAAT
Found at i:17549565 original size:36 final size:35
Alignment explanation
Indices: 17549475--17549695 Score: 232
Period size: 35 Copynumber: 6.3 Consensus size: 35
17549465 TTAATTGTTT
17549475 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * * *
17549510 AATTTAATTAATCAAGCCCAACAATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
*
17549545 AATTTTAATCAATTAGGCCCAATGACTTAATTAAAC
1 AA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
17549581 TATTTTAATCAACTAGGCCCAATGACTTAATTAAAC
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * * * *
17549617 AATTTAATTAATTAGACTCGATGACTTAATTAAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
** *
17549652 AATTTAATTTATTAGG--C-ACAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
17549684 AATTTTAATCAA
1 AA-TTTAATCAA
17549696 GTGCCTGAGA
Statistics
Matches: 156, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
32 14 0.09
33 8 0.05
35 74 0.47
36 59 0.38
37 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:17550544 original size:73 final size:73
Alignment explanation
Indices: 17550466--17550661 Score: 261
Period size: 73 Copynumber: 2.7 Consensus size: 73
17550456 GAGTTCATAA
* *
17550466 ACAGAGACGACTTAATCGACTAAGAAGCATAGTTAGTCGTCTAAGAGCTGACTGCTAGAAACTGG
1 ACAGAGACGACTTAATCGACTAAGAAGCAT-GTTAGTCGACTAAGAGCTCACTGCTAGAAACTGG
*
17550531 GTTCAG-AG
65 GATCAGAAG
* * *
17550539 ACAGAGACGACTTAATCGACTAAGAAACATTGTTAGTCGACTAAGAGCTCACTGTTTGAAACTGG
1 ACAGAGACGACTTAATCGACTAAGAAGCA-TGTTAGTCGACTAAGAGCTCACTGCTAGAAACTGG
17550604 GATCAGAAG
65 GATCAGAAG
* * * *
17550613 ACAGA-ATCAACTTAATCGACTAAAAAGTATGTTAGTCAACTAAGAGCTC
1 ACAGAGA-CGACTTAATCGACTAAGAAGCATGTTAGTCGACTAAGAGCTC
17550662 TTTGTCTGCC
Statistics
Matches: 109, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
73 83 0.76
74 26 0.24
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (73 bp):
ACAGAGACGACTTAATCGACTAAGAAGCATGTTAGTCGACTAAGAGCTCACTGCTAGAAACTGGG
ATCAGAAG
Found at i:17563318 original size:42 final size:42
Alignment explanation
Indices: 17563271--17563386 Score: 142
Period size: 42 Copynumber: 2.8 Consensus size: 42
17563261 GGACCCGGCT
* * * *
17563271 ATGTGCGAGTAGGAGTGCACATATGTCGTTGCTGACCAGACC
1 ATGTGCGAGTGGGAGTGCACATAAGCCATTGCTGACCAGACC
* * ***
17563313 ATGTGCGAGTGGGAGTGCACGTAAGCCATTGCTGACCCGGTT
1 ATGTGCGAGTGGGAGTGCACATAAGCCATTGCTGACCAGACC
*
17563355 ATGTGCGAGTGGGAGTGCGCATAAGCCATTGC
1 ATGTGCGAGTGGGAGTGCACATAAGCCATTGC
17563387 ATATGAGATG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.23
Consensus pattern (42 bp):
ATGTGCGAGTGGGAGTGCACATAAGCCATTGCTGACCAGACC
Found at i:17563805 original size:60 final size:60
Alignment explanation
Indices: 17563705--17563866 Score: 193
Period size: 60 Copynumber: 2.7 Consensus size: 60
17563695 CATCTTGTTG
* * * * *
17563705 CAGCGA-ATTTCATTCTTGCTGTAGCGAGAAACTTTCTGTTTTTGGGTTACAATTTCGCTG
1 CAGCGAGA-TTCAATCTTGCTGCAGCGAGAAACTTTCTGTTTTTGGGTCACAATTTCACTA
* * * *
17563765 TAGCGAGATTCAATCTTGCTACAGCGAGAAACATTT-TGTTTCTGGGTCACAATTTCATTA
1 CAGCGAGATTCAATCTTGCTGCAGCGAGAAAC-TTTCTGTTTTTGGGTCACAATTTCACTA
* *
17563825 CAGCGAGATTCAATCTCGCTGCAGCGAAAAACTTTCTGTTTT
1 CAGCGAGATTCAATCTTGCTGCAGCGAGAAACTTTCTGTTTT
17563867 GGTCTCCTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 3 0.04
60 78 0.92
61 4 0.05
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (60 bp):
CAGCGAGATTCAATCTTGCTGCAGCGAGAAACTTTCTGTTTTTGGGTCACAATTTCACTA
Found at i:17573718 original size:41 final size:41
Alignment explanation
Indices: 17573671--17573777 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 41
17573661 ATATTGCCCG
*
17573671 TGTGCACGATGTGGGGGGATGCAC-ACGATGATGATATCCCT
1 TGTGCACGATGTGGGGGGATGCACAAAG-TGATGATATCCCT
* * **
17573712 TGTGCACGATGTGAGGGGATGCATAAAGTGATGATATTGCT
1 TGTGCACGATGTGGGGGGATGCACAAAGTGATGATATCCCT
* *
17573753 TCTGCATGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
17573778 TGAGCTGGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 54 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (41 bp):
TGTGCACGATGTGGGGGGATGCACAAAGTGATGATATCCCT
Found at i:17580937 original size:41 final size:41
Alignment explanation
Indices: 17580880--17580984 Score: 138
Period size: 41 Copynumber: 2.6 Consensus size: 41
17580870 GCATTAGCTG
* *
17580880 TGCATGATGTGAGGGGATGCACAAAATGATGATATCGCTTA
1 TGCATGATGTGGGGGGATGCACAAAATGATGATATCACTTA
* * * *
17580921 TGCATGATGTGGGGGGATGCATAAAGTGATGATATTACTTG
1 TGCATGATGTGGGGGGATGCACAAAATGATGATATCACTTA
* *
17580962 TGCACGATATGGGGGGATGCACA
1 TGCATGATGTGGGGGGATGCACA
17580985 CGTTGACTCC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (41 bp):
TGCATGATGTGGGGGGATGCACAAAATGATGATATCACTTA
Found at i:17599605 original size:14 final size:14
Alignment explanation
Indices: 17599586--17599612 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17599576 TTGGTTTTAA
17599586 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
17599600 TTTTAGTTAATTA
1 TTTTAGTTAATTA
17599613 ATAAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:17610622 original size:20 final size:20
Alignment explanation
Indices: 17610580--17610622 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
17610570 GAAAGAGAGC
**
17610580 TCTTAGTCGACTAACTTTTT
1 TCTTAGTCGACTAACTTGGT
* *
17610600 TCTTGGTCGACTAAGTTGGT
1 TCTTAGTCGACTAACTTGGT
17610620 TCT
1 TCT
17610623 GTCTTCTGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.47
Consensus pattern (20 bp):
TCTTAGTCGACTAACTTGGT
Found at i:17610741 original size:72 final size:73
Alignment explanation
Indices: 17610573--17610767 Score: 272
Period size: 72 Copynumber: 2.7 Consensus size: 73
17610563 AATTGCAGAA
**
17610573 AGAGAGC-TCTTAGTCGACTAACTTTTTTCTTGGTCGACTAAGTTGGTTCTGTCTTCTGATCACA
1 AGAGAGCAT-TTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGGTTCTGTCTTCTGATCACA
17610637 GATTCTGGC
65 GATTCTGGC
* *
17610646 AGAGAGCATTTAATCGACGAACTCATTTCTTGGTCGACTAAGTTGGTTCTGTC-T-TGAAGTC-C
1 AGAGAGCATTTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGGTTCTGTCTTCTG-A-TCAC
*
17610708 AGATTTTGGC
64 AGATTCTGGC
**
17610718 AGAGAGCATTTAGTCGACTAACTCACATCTTGGTCGACTAAGTTGGTTCT
1 AGAGAGCATTTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGGTTCT
17610768 ATTTCTCAAT
Statistics
Matches: 110, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
71 2 0.02
72 58 0.53
73 49 0.45
74 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (73 bp):
AGAGAGCATTTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGGTTCTGTCTTCTGATCACAG
ATTCTGGC
Found at i:17612175 original size:23 final size:23
Alignment explanation
Indices: 17612149--17612192 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
17612139 TTCTCTTCAT
17612149 TTTTCAATTTCAA-TTTTAAGCTC
1 TTTTCAATTT-AAGTTTTAAGCTC
*
17612172 TTTTCCATTTAAGTTTTAAGC
1 TTTTCAATTTAAGTTTTAAGC
17612193 AACATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTTCAATTTAAGTTTTAAGCTC
Found at i:17612937 original size:19 final size:19
Alignment explanation
Indices: 17612888--17612937 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
17612878 ATAACAACAT
17612888 TTTTCTT-TTTTTCTTTGGC
1 TTTTCTTCTTTTTCTTT-GC
17612907 TTTTC-TC-TTTTCTTT-C
1 TTTTCTTCTTTTTCTTTGC
17612923 TTTTCTTCTTCTTTC
1 TTTTCTTCTT-TTTC
17612938 ATCTCAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 6 0.22
17 2 0.07
18 10 0.37
19 9 0.33
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTCTTCTTTTTCTTTGC
Found at i:17613762 original size:6 final size:6
Alignment explanation
Indices: 17613751--17613807 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
17613741 CACTTTTTTC
* *
17613751 TTCTTT TTCTTT TTCTTT TTCTCTT TT-TTT ATGTCTTT TTATTT TTATTT
1 TTCTTT TTCTTT TTCTTT TTCT-TT TTCTTT -T-TCTTT TTCTTT TTCTTT
*
17613801 CTCTTT T
1 TTCTTT T
17613808 CTCACAACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 2 0.05
6 32 0.74
7 6 0.14
8 3 0.07
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:17613787 original size:20 final size:21
Alignment explanation
Indices: 17613745--17613790 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
17613735 TCTTTACACT
*
17613745 TTTTTCTTCTTTTTCTTTTTC
1 TTTTTCTTCTTTTTCTTTGTC
17613766 TTTTTC-TCTTTTT-TTATGTC
1 TTTTTCTTCTTTTTCTT-TGTC
17613786 TTTTT
1 TTTTT
17613791 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 15 0.65
21 6 0.26
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTCTTCTTTTTCTTTGTC
Found at i:17617055 original size:21 final size:21
Alignment explanation
Indices: 17617025--17617067 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17617015 AAGCACATAT
*
17617025 GTTGTCTTAATTAAGGCTAGA
1 GTTGTCTTAATTAAGGCAAGA
* *
17617046 GTTGTTTTAATTTAGGCAAGA
1 GTTGTCTTAATTAAGGCAAGA
17617067 G
1 G
17617068 CGTATTTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.40
Consensus pattern (21 bp):
GTTGTCTTAATTAAGGCAAGA
Found at i:17621926 original size:23 final size:24
Alignment explanation
Indices: 17621889--17621934 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
17621879 TGGCTAGAAA
17621889 AAAAAATGAATTAAAAAAATATTC
1 AAAAAATGAATTAAAAAAATATTC
* *
17621913 AAAATATGAA-TAAAATAATATT
1 AAAAAATGAATTAAAAAAATATT
17621935 ATTCTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAAAATGAATTAAAAAAATATTC
Found at i:17624898 original size:15 final size:15
Alignment explanation
Indices: 17624874--17624908 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17624864 TTGCAGGGAT
*
17624874 TGTGATTACAAGGAA
1 TGTGAATACAAGGAA
*
17624889 TGTGAATACAAGGAT
1 TGTGAATACAAGGAA
17624904 TGTGA
1 TGTGA
17624909 TTTCTAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (15 bp):
TGTGAATACAAGGAA
Found at i:17625547 original size:30 final size:30
Alignment explanation
Indices: 17625513--17625572 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
17625503 TTTAGCTCAA
* * *
17625513 ATACAAAGATTTTCATACATTTAATTGAAT
1 ATACAAAGAATTTCATACATTCAATAGAAT
17625543 ATACAAAGAATTTCATACATTCAATAGAAT
1 ATACAAAGAATTTCATACATTCAATAGAAT
17625573 CTGAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (30 bp):
ATACAAAGAATTTCATACATTCAATAGAAT
Found at i:17626137 original size:17 final size:17
Alignment explanation
Indices: 17626111--17626146 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17626101 GAAGATGCCA
* *
17626111 TGCTCTTAAAATATCTG
1 TGCTCCTAAAATAACTG
17626128 TGCTCCTAAAATAACTG
1 TGCTCCTAAAATAACTG
17626145 TG
1 TG
17626147 AAGGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (17 bp):
TGCTCCTAAAATAACTG
Found at i:17627535 original size:6 final size:6
Alignment explanation
Indices: 17627526--17627573 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
17627516 ATTAAATTTA
* * *
17627526 AAAAAT AAAAAT AAAAAAT ATAATAT TATAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT -AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAA
17627574 TATATAACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 24 0.71
7 10 0.29
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:17627591 original size:27 final size:25
Alignment explanation
Indices: 17627529--17627580 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
17627519 AAATTTAAAA
*
17627529 AATAAAAATAAAAAATATAATATTAT
1 AATAAAAAT-AAAAATAAAATATTAT
17627555 AATAAAAATAAAAATAAAATA-TAT
1 AATAAAAATAAAAATAAAATATTAT
17627579 AA
1 AA
17627581 CATTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 11 0.44
26 9 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AATAAAAATAAAAATAAAATATTAT
Found at i:17627813 original size:15 final size:15
Alignment explanation
Indices: 17627793--17627849 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
17627783 TTATTTTCCC
* *
17627793 TGCAATCACTTTGCT
1 TGCAATCACATTACT
17627808 TGCAATCACATTACT
1 TGCAATCACATTACT
* *
17627823 TACAATCACATTACC
1 TGCAATCACATTACT
*
17627838 TGTAATCACATT
1 TGCAATCACATT
17627850 GCATTCTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (15 bp):
TGCAATCACATTACT
Found at i:17630063 original size:41 final size:41
Alignment explanation
Indices: 17630006--17630087 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
17629996 AATAGAAGAA
17630006 AGAAAAACATAACATCCATTTTAGCCACACATGCGTTCCTT
1 AGAAAAACATAACATCCATTTTAGCCACACATGCGTTCCTT
17630047 AGAAAAACATAACATCCATTTTAGCCACACATGCGTTCCTT
1 AGAAAAACATAACATCCATTTTAGCCACACATGCGTTCCTT
17630088 CATACACCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (41 bp):
AGAAAAACATAACATCCATTTTAGCCACACATGCGTTCCTT
Found at i:17630440 original size:150 final size:154
Alignment explanation
Indices: 17630262--17630560 Score: 408
Period size: 150 Copynumber: 1.9 Consensus size: 154
17630252 GACAAGTGTC
* *** * *
17630262 AACACTTGGTAGAAGAAGGGGAAAAGGCACGAGGAGAGCATTGGCCACTTCCCCTGCCCAAAACT
1 AACACTTGGTAAAAGAAAAAGAAAAGGCACGAGGAGAGCATTAGCAACTTCCCCTGCCCAAAACT
* * * *
17630327 AATTCCCAAAGGCAACC-AAGT-T-TCCCAAACCCGC-AAGAAAAACCTTCCCAACACCACATGG
66 AATTCCCAAAGGCAACCAAAATCTCTCCCAAACCCACAAAAAAAAACCTCCCCAACACCACATGG
17630388 CAACCAAACACAAAGCTACGTGCT
131 CAACCAAACACAAAGCTACGTGCT
* * *
17630412 AACACTTGGTAAAAGAAAAAGAAAAGGCATGGGGGGAGCATTAGCAACTTCCCCTGCCCAAAACT
1 AACACTTGGTAAAAGAAAAAGAAAAGGCACGAGGAGAGCATTAGCAACTTCCCCTGCCCAAAACT
*
17630477 AATTCCCAAAGGCAGCCAAAATACCCCTCTCCCAAACCCACAAAAAAAAACCTCCCCAACACCAC
66 AATTCCCAAAGGCAACCAAAAT----CTCTCCCAAACCCACAAAAAAAAACCTCCCCAACACCAC
17630542 ATGGCAACCAAACACAAAG
127 ATGGCAACCAAACACAAAG
17630561 TCACATGTCA
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
150 72 0.57
151 3 0.02
156 1 0.01
157 11 0.09
158 40 0.31
ACGTcount: A:0.40, C:0.31, G:0.16, T:0.12
Consensus pattern (154 bp):
AACACTTGGTAAAAGAAAAAGAAAAGGCACGAGGAGAGCATTAGCAACTTCCCCTGCCCAAAACT
AATTCCCAAAGGCAACCAAAATCTCTCCCAAACCCACAAAAAAAAACCTCCCCAACACCACATGG
CAACCAAACACAAAGCTACGTGCT
Found at i:17631083 original size:11 final size:11
Alignment explanation
Indices: 17631064--17631138 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
17631054 TTATTATTTT
*
17631064 AAAATATTTCA
1 AAAAAATTTCA
*
17631075 AAAAAATTTTTA
1 AAAAAA-TTTCA
**
17631087 AAAAAATTGAA
1 AAAAAATTTCA
**
17631098 AAAAAAACTCAA
1 AAAAAATTTC-A
17631110 AAAATAATTTTCA
1 AAAA-AA-TTTCA
*
17631123 AAAAAAATTCA
1 AAAAAATTTCA
17631134 AAAAA
1 AAAAA
17631139 TAAAAGTGGT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
11 23 0.47
12 17 0.35
13 7 0.14
14 2 0.04
ACGTcount: A:0.67, C:0.07, G:0.01, T:0.25
Consensus pattern (11 bp):
AAAAAATTTCA
Found at i:17631099 original size:22 final size:22
Alignment explanation
Indices: 17631060--17631102 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17631050 GTTATTATTA
* *
17631060 TTTTAAAATATTTCAAAAAAAT
1 TTTTAAAAAAATTCAAAAAAAT
*
17631082 TTTTAAAAAAATTGAAAAAAA
1 TTTTAAAAAAATTCAAAAAAA
17631103 AACTCAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTTAAAAAAATTCAAAAAAAT
Found at i:17631530 original size:23 final size:22
Alignment explanation
Indices: 17631485--17631531 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
17631475 TATTTTTATG
* * *
17631485 TTTTCAAAATTTATAGATTTTT
1 TTTTCAAAATTTAGAAATATTT
17631507 TTTTCAAAAATTTAGAAATATTT
1 TTTTC-AAAATTTAGAAATATTT
17631530 TT
1 TT
17631532 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTTCAAAATTTAGAAATATTT
Found at i:17632361 original size:18 final size:19
Alignment explanation
Indices: 17632333--17632380 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
17632323 AGAATAGGGG
*
17632333 AAAAAAATATTTTA-GAAT
1 AAAATAATATTTTATGAAT
*
17632351 AAAATATTATTTTATGAAT
1 AAAATAATATTTTATGAAT
17632370 AAAATAATATT
1 AAAATAATATT
17632381 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATGAAT
Found at i:17634466 original size:19 final size:19
Alignment explanation
Indices: 17634435--17634480 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
17634425 TTTTGACCCC
17634435 ATTTGACGTATTGGAGTATG
1 ATTTGA-GTATTGGAGTATG
17634455 ATTTGAGTATTGGAGTATG
1 ATTTGAGTATTGGAGTATG
17634474 ATTTGAG
1 ATTTGAG
17634481 GTAAAGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.41
Consensus pattern (19 bp):
ATTTGAGTATTGGAGTATG
Found at i:17634996 original size:19 final size:19
Alignment explanation
Indices: 17634972--17635009 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17634962 CCATTTGACT
*
17634972 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
17634991 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
17635010 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:17640250 original size:22 final size:23
Alignment explanation
Indices: 17640216--17640261 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
17640206 TTAGATTGGT
*
17640216 ATCAGAGCATTTGG-TTTTAAAG
1 ATCAGAACATTTGGTTTTTAAAG
*
17640238 ATCAGAACTTTTGGTTTTTAAAG
1 ATCAGAACATTTGGTTTTTAAAG
17640261 A
1 A
17640262 AAAAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (23 bp):
ATCAGAACATTTGGTTTTTAAAG
Done.