Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 103 of 208
Found at i:31187918 original size:137 final size:137
Alignment explanation
Indices: 31187672--31187946 Score: 514
Period size: 137 Copynumber: 2.0 Consensus size: 137
31187662 TAAGAAAAAG
* *
31187672 AAGAATTATGAATCAAGAATGATTCTTGATGCCCAAGACTAGTGCCGAACAGATTCTTGAAGATT
1 AAGAATTATGAATCAAGAACGATTCCTGATGCCCAAGACTAGTGCCGAACAGATTCTTGAAGATT
31187737 GAAAGGGCTGGAAACGCAACAAGAGAGATTAAAGCAATTTAATCAATGAATCGGCACAAGCAGAA
66 GAAAGGGCTGGAAACGCAACAAGAGAGATTAAAGCAATTTAATCAATGAATCGGCACAAGCAGAA
31187802 AAATTAA
131 AAATTAA
* *
31187809 AAGAATTATGAATCAAGAACGATTCCTGATGCCCAAGACTGGTGCCGAATAGATTCTTGAAGATT
1 AAGAATTATGAATCAAGAACGATTCCTGATGCCCAAGACTAGTGCCGAACAGATTCTTGAAGATT
31187874 GAAAGGGCTGGAAACGCAACAAGAGAGATTAAAGCAATTTAATCAATGAATCGGCACAAGCAGAA
66 GAAAGGGCTGGAAACGCAACAAGAGAGATTAAAGCAATTTAATCAATGAATCGGCACAAGCAGAA
31187939 AAATTAA
131 AAATTAA
31187946 A
1 A
31187947 GAGGAATAAA
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (137 bp):
AAGAATTATGAATCAAGAACGATTCCTGATGCCCAAGACTAGTGCCGAACAGATTCTTGAAGATT
GAAAGGGCTGGAAACGCAACAAGAGAGATTAAAGCAATTTAATCAATGAATCGGCACAAGCAGAA
AAATTAA
Found at i:31219550 original size:12 final size:12
Alignment explanation
Indices: 31219533--31219561 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31219523 CCACATTTAG
31219533 CCAACAACTCTT
1 CCAACAACTCTT
31219545 CCAACAACTCTT
1 CCAACAACTCTT
31219557 CCAAC
1 CCAAC
31219562 CATCCTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (12 bp):
CCAACAACTCTT
Found at i:31234710 original size:24 final size:24
Alignment explanation
Indices: 31234682--31234734 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
31234672 GGTTTTAGGG
**
31234682 TTTAGGGTTTAGGCCATACCAATT
1 TTTAGGGAATAGGCCATACCAATT
31234706 TTTAGGGAATAGGCCATACCAATT
1 TTTAGGGAATAGGCCATACCAATT
31234730 TTTAG
1 TTTAG
31234735 TTAACACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTAGGGAATAGGCCATACCAATT
Found at i:31236172 original size:13 final size:13
Alignment explanation
Indices: 31236154--31236179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31236144 TGAAATCATA
31236154 ATTATAATAATTT
1 ATTATAATAATTT
31236167 ATTATAATAATTT
1 ATTATAATAATTT
31236180 CAGTAAAAAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATAATAATTT
Found at i:31238212 original size:7 final size:8
Alignment explanation
Indices: 31238196--31238220 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31238186 CTCGTTTTGA
31238196 TTTTATTT
1 TTTTATTT
31238204 TTTTATTT
1 TTTTATTT
31238212 TTTTATTT
1 TTTTATTT
31238220 T
1 T
31238221 GTTGCACGTA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:31251230 original size:18 final size:18
Alignment explanation
Indices: 31251191--31251233 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
31251181 ATTTGAATTT
31251191 AAAAGAAAAACATGTACTC
1 AAAAGAAAAACATGTAC-C
*
31251210 AAAAGAAAATAGATGTA-C
1 AAAAGAAAA-ACATGTACC
31251228 AAAAGA
1 AAAAGA
31251234 GCATGTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 9 0.41
20 6 0.27
ACGTcount: A:0.63, C:0.09, G:0.14, T:0.14
Consensus pattern (18 bp):
AAAAGAAAAACATGTACC
Found at i:31251877 original size:19 final size:18
Alignment explanation
Indices: 31251836--31251878 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
31251826 AATTTTTGTC
* *
31251836 ATAAAATAATTAATTTTT
1 ATAAAATAATTAAATTCT
31251854 ATAAAATAATTAAATTCT
1 ATAAAATAATTAAATTCT
31251872 ATTAAAA
1 A-TAAAA
31251879 ATTTGAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAAATAATTAAATTCT
Found at i:31251937 original size:20 final size:21
Alignment explanation
Indices: 31251893--31251940 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
31251883 GAACATGTTC
31251893 ATTTTTAGTCAATTTTACAATT
1 ATTTTTAGTCAATTTTA-AATT
* *
31251915 ATTTTTAGTGAATTTT-GATT
1 ATTTTTAGTCAATTTTAAATT
31251935 ATTTTT
1 ATTTTT
31251941 GACAAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
22 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (21 bp):
ATTTTTAGTCAATTTTAAATT
Found at i:31256412 original size:24 final size:25
Alignment explanation
Indices: 31256378--31256426 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
31256368 TACATGTATA
*
31256378 CTCATACGAGCT-ATAAATGGTAAG
1 CTCATAAGAGCTAATAAATGGTAAG
31256402 CTCATAAGAGCTGAATAAATGGTAA
1 CTCATAAGAGCT-AATAAATGGTAA
31256427 CACTAATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
26 11 0.50
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (25 bp):
CTCATAAGAGCTAATAAATGGTAAG
Found at i:31274323 original size:21 final size:22
Alignment explanation
Indices: 31274278--31274323 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
31274268 AGAGAAAAAT
*
31274278 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
31274300 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
31274321 AAA
1 AAA
31274324 GCGAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:31278245 original size:119 final size:120
Alignment explanation
Indices: 31278043--31278317 Score: 344
Period size: 119 Copynumber: 2.3 Consensus size: 120
31278033 TTAGGGATAG
* * * ** **
31278043 CGAAGTACAAACAAGGGCACGTATGTGCATTCAGGGATATCGAAGTACAAATAGGGGCACGTATG
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAGGGATATCAAAGTACAAACAGGGGCAAATACA
* *
31278108 TGTATTCAGGGGTATTAAAGTACAAATAGGGGCA-GTATATGCATTTAGAGG-TAC
66 TGCATTCAGGGGTATTAAAGTACAAATAGGGGCATGTATATGCATTCAG-GGCTAC
*
31278162 CGAAGTACAAACAGGGGCACGTATGTTCATTCAGAGG-TAAT-AAAGTACAAACAGGGGCAAATA
1 CGAAGTACAAACAGGGGCACGTATGTGCATTCAG-GGAT-ATCAAAGTACAAACAGGGGCAAATA
* *
31278225 CATGCATTCAGGGGTTTTAAAGTACAAATAGGGGCATGTATGTGCATTCAGGGCTAC
64 CATGCATTCAGGGGTATTAAAGTACAAATAGGGGCATGTATATGCATTCAGGGCTAC
** *
31278282 TAAAGTGA-AAACAGGGGCATGTATGTGCATTCAGGG
1 CGAAGT-ACAAACAGGGGCACGTATGTGCATTCAGGG
31278318 GTGCCGAAGT
Statistics
Matches: 135, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
119 87 0.64
120 47 0.35
121 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (120 bp):
CGAAGTACAAACAGGGGCACGTATGTGCATTCAGGGATATCAAAGTACAAACAGGGGCAAATACA
TGCATTCAGGGGTATTAAAGTACAAATAGGGGCATGTATATGCATTCAGGGCTAC
Found at i:31278277 original size:20 final size:20
Alignment explanation
Indices: 31278254--31278318 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
31278244 AAGTACAAAT
31278254 AGGGGCATGTATGTGCATTC
1 AGGGGCATGTATGTGCATTC
* * * **
31278274 A-GGGCTACT-AAAGTGAAAAC
1 AGGGGC-A-TGTATGTGCATTC
31278294 AGGGGCATGTATGTGCATTC
1 AGGGGCATGTATGTGCATTC
31278314 AGGGG
1 AGGGG
31278319 TGCCGAAGTG
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
19 5 0.16
20 21 0.68
21 5 0.16
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (20 bp):
AGGGGCATGTATGTGCATTC
Found at i:31278334 original size:40 final size:40
Alignment explanation
Indices: 31278045--31278319 Score: 266
Period size: 40 Copynumber: 6.9 Consensus size: 40
31278035 AGGGATAGCG
* * * *
31278045 AAGTACAAACAAGGGCACGTATGTGCATTCAGGGATATCG
1 AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCA
* * **
31278085 AAGTACAAATAGGGGCACGTATGTGTATTCAGGGGTATTA
1 AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCA
* * * * *
31278125 AAGTACAAATAGGGGCA-GTATATGCATTTAGAGGTACCG
1 AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCA
* * **
31278164 AAGTACAAACAGGGGCACGTATGTTCATTCAGAGGTAATA
1 AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCA
** ** ***
31278204 AAGTACAAACAGGGGCAAATACATGCATTCAGGGGTTTTA
1 AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCA
* * * *
31278244 AAGTACAAATAGGGGCATGTATGTGCATTCAGGGCTACTA
1 AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCA
*
31278284 AAGTGA-AAACAGGGGCATGTATGTGCATTCAGGGGT
1 AAGT-ACAAACAGGGGCACGTATGTGCATTCAGGGGT
31278320 GCCGAAGTGA
Statistics
Matches: 195, Mismatches: 38, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
39 31 0.16
40 163 0.84
41 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCA
Found at i:31282059 original size:3 final size:3
Alignment explanation
Indices: 31282051--31282080 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31282041 GGTTAAATTG
31282051 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31282081 GATGATGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31282085 original size:3 final size:3
Alignment explanation
Indices: 31282079--31282149 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
31282069 AATAATAATA
31282079 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
31282127 ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG AT
31282150 AACAAAGTCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:31289924 original size:25 final size:25
Alignment explanation
Indices: 31289896--31289944 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
31289886 CCACAACTGG
*
31289896 TGAGAGCATACCGATTTATAGCTCT
1 TGAGAGCATACCGATCTATAGCTCT
31289921 TGAGAGCATACCGATCTATAGCTC
1 TGAGAGCATACCGATCTATAGCTC
31289945 GAGTGAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
TGAGAGCATACCGATCTATAGCTCT
Found at i:31289952 original size:25 final size:25
Alignment explanation
Indices: 31289897--31289957 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
31289887 CACAACTGGT
* **
31289897 GAGAGCATACCGATTTATAGCTCTT
1 GAGAGCATACCGATCTATAGCTCGA
31289922 GAGAGCATACCGATCTATAGCTCGA
1 GAGAGCATACCGATCTATAGCTCGA
*
31289947 GTGAGCATACC
1 GAGAGCATACC
31289958 AATTCACAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (25 bp):
GAGAGCATACCGATCTATAGCTCGA
Found at i:31294162 original size:25 final size:25
Alignment explanation
Indices: 31294134--31294183 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
31294124 TTCAAGGTAG
31294134 AATATCATAAAATCAAATTCTTACT
1 AATATCATAAAATCAAATTCTTACT
31294159 AATATCATAAAATCAAATTCTTACT
1 AATATCATAAAATCAAATTCTTACT
31294184 TACTCTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (25 bp):
AATATCATAAAATCAAATTCTTACT
Found at i:31302535 original size:15 final size:15
Alignment explanation
Indices: 31302500--31302528 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31302490 TGTAAGGAGG
31302500 AAGAAATACAGTGTA
1 AAGAAATACAGTGTA
31302515 AAGAAATACAGTGT
1 AAGAAATACAGTGT
31302529 GAGGAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (15 bp):
AAGAAATACAGTGTA
Found at i:31306805 original size:2 final size:2
Alignment explanation
Indices: 31306798--31306826 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31306788 AAATATGAGG
31306798 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
31306827 GCAGGAAAGA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:31307288 original size:14 final size:14
Alignment explanation
Indices: 31307269--31307295 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31307259 ATAGACATGG
31307269 CTATTTTAAATATT
1 CTATTTTAAATATT
31307283 CTATTTTAAATAT
1 CTATTTTAAATAT
31307296 AAAAAATAAA
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:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (14 bp):
CTATTTTAAATATT
Found at i:31309651 original size:2 final size:2
Alignment explanation
Indices: 31309644--31309682 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31309634 TGTTTCCTCC
31309644 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
31309683 AAGTCTCAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:31309774 original size:5 final size:5
Alignment explanation
Indices: 31309764--31309810 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
31309754 TACGGTTGCA
* * * *
31309764 CACCT CACCT CAACT CACCT CAACT CACCT CACCT TACCT CATCT CA
1 CACCT CACCT CACCT CACCT CACCT CACCT CACCT CACCT CACCT CA
31309811 TTATTTTCTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.26, C:0.51, G:0.00, T:0.23
Consensus pattern (5 bp):
CACCT
Found at i:31310603 original size:13 final size:14
Alignment explanation
Indices: 31310585--31310613 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31310575 AATTCGAATC
31310585 AGCTAGCTA-ACTT
1 AGCTAGCTAGACTT
31310598 AGCTAGCTAGACTT
1 AGCTAGCTAGACTT
31310612 AG
1 AG
31310614 ACATCTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (14 bp):
AGCTAGCTAGACTT
Found at i:31314950 original size:21 final size:21
Alignment explanation
Indices: 31314905--31314950 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31314895 CTAAGATGTG
*
31314905 AATTGGATTAAATTGAATATG
1 AATTGGATTAAATTGAATATA
*
31314926 AATTGTATTAAATTG-ATATTA
1 AATTGGATTAAATTGAATA-TA
31314947 AATT
1 AATT
31314951 CATTAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (21 bp):
AATTGGATTAAATTGAATATA
Found at i:31315292 original size:24 final size:24
Alignment explanation
Indices: 31315265--31315329 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 24
31315255 CGAAAGAGTG
*
31315265 TCCCATTATTAGCTCTCATGAGCT
1 TCCCATTATTAGCTCTCACGAGCT
* * * **
31315289 TCCCGTTATATGGTTCTTGCGAGCT
1 TCCCATTAT-TAGCTCTCACGAGCT
*
31315314 TCCCATTAATAGCTCT
1 TCCCATTATTAGCTCT
31315330 TTGGAGCATC
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.38
Consensus pattern (24 bp):
TCCCATTATTAGCTCTCACGAGCT
Found at i:31315336 original size:24 final size:24
Alignment explanation
Indices: 31315265--31315341 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
31315255 CGAAAGAGTG
* *
31315265 TCCCATTATTAGCTCTCAT-GAGCT
1 TCCCATTAATAGCTCT-TTGGAGCT
* * *
31315289 TCCCGTTATATGGTTC-TTGCGAGCT
1 TCCCATTA-ATAGCTCTTTG-GAGCT
*
31315314 TCCCATTAATAGCTCTTTGGAGCA
1 TCCCATTAATAGCTCTTTGGAGCT
31315338 TCCC
1 TCCC
31315342 GATTGGTTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
23 1 0.03
24 20 0.50
25 19 0.47
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (24 bp):
TCCCATTAATAGCTCTTTGGAGCT
Found at i:31315476 original size:25 final size:27
Alignment explanation
Indices: 31315403--31315485 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 27
31315393 GTCCCGATAT
* *
31315403 ATGGCTCTTCGA--AGCTTCCTGGTTA
1 ATGGCTCTTCCATGAGCTTCCTGATTA
* * *
31315428 AAGGCTCTTTCATGAGCTTTCTGATTA
1 ATGGCTCTTCCATGAGCTTCCTGATTA
31315455 ATGGCTC-TCCA-GAGCTTCCTGA-TA
1 ATGGCTCTTCCATGAGCTTCCTGATTA
*
31315479 TTGGCTC
1 ATGGCTC
31315486 ACTTGAACTT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 8 0.17
25 19 0.40
26 3 0.06
27 17 0.36
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
ATGGCTCTTCCATGAGCTTCCTGATTA
Found at i:31323328 original size:50 final size:48
Alignment explanation
Indices: 31323274--31323395 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 48
31323264 AGGTCTCCCA
*
31323274 TAAGACCATGTCTGGGACATGGCATGGGCACTAATATGAGAAAC-CCCATG
1 TAAGACCATGTCTGGGACATGGCATGGGCACT-ACA-G-GAAACACCCATG
* * * * * *
31323324 TAAGACCATATCTAGGATATGGCATTGGTAGTACAGGAAACATCCCATG
1 TAAGACCATGTCTGGGACATGGCATGGGCACTACAGGAAACA-CCCATG
31323373 TAAGACCATGTCTGGGACATGGC
1 TAAGACCATGTCTGGGACATGGC
31323396 TTTGGCATGT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
47 5 0.08
48 1 0.02
49 28 0.47
50 26 0.43
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATGGGCACTACAGGAAACACCCATG
Found at i:31323395 original size:49 final size:50
Alignment explanation
Indices: 31323162--31323402 Score: 150
Period size: 50 Copynumber: 4.7 Consensus size: 50
31323152 GTAAAGAGAT
* ** ***
31323162 CCCATGTAAGACCATGTCTGGGACTTGGCATTGGCATCATTGAGGTTATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--T-A--ACATGAGAAAC
* * * * ** * **
31323218 CCCATGTAAGACGATGTCTTGAACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTAACATGAGA-AAC
* *
31323269 TCCCA--TAAGACCATGTCTGGGACATGGCATGGGCACTAATATGAGAAAC
1 -CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTAACATGAGAAAC
* * * * *
31323318 CCCATGTAAGACCATATCTAGGATATGGCATTGGTAGT-ACA-G-GAAAC
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTAACATGAGAAAC
*
31323365 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 --CCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
31323403 TGTTATTATC
Statistics
Matches: 146, Mismatches: 33, Indels: 19
0.74 0.17 0.10
Matches are distributed among these distances:
47 5 0.03
48 5 0.03
49 34 0.23
50 65 0.45
51 1 0.01
52 4 0.03
55 1 0.01
56 31 0.21
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTAACATGAGAAAC
Found at i:31325060 original size:15 final size:15
Alignment explanation
Indices: 31325040--31325071 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31325030 CATTTCACTA
*
31325040 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
31325055 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
31325070 TT
1 TT
31325072 TGCATACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:31329080 original size:48 final size:48
Alignment explanation
Indices: 31329009--31329106 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
31328999 TATTCCAAAA
* * *
31329009 TAATATTATTTTAATAATTTAATATTAAATTTAATTTAATACTTATCT
1 TAATAGTAGTTTAATAATTTAATATTAAATTGAATTTAATACTTATCT
* **
31329057 TAATAGTAGTTTATTAATTTAATATTAAATTGAATTTAATGTTTATCT
1 TAATAGTAGTTTAATAATTTAATATTAAATTGAATTTAATACTTATCT
31329105 TA
1 TA
31329107 TAGATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (48 bp):
TAATAGTAGTTTAATAATTTAATATTAAATTGAATTTAATACTTATCT
Found at i:31331894 original size:170 final size:171
Alignment explanation
Indices: 31331605--31331944 Score: 655
Period size: 170 Copynumber: 2.0 Consensus size: 171
31331595 GTGAACCCAG
*
31331605 TTCGCAGTTTAGTGACCTTGCCAAAGCTTTTGTTTAACTTATATTTTGGGCACTTTGTGTTTTTC
1 TTCGCAATTTAGTGACCTTGCCAAAGCTTTTGTTTAACTTATATTTTGGGCACTTTGTGTTTTTC
*
31331670 TTTCTTGTATATTCTTTAAGTTCGCAAGAGCTCACACACACCTTTCTAAACAATGTACATAGTTA
66 TTTCTTGTATATTCTTTAAGTTCGCAAGAGCTCACACACACCTTTCTAAACAATGCACATAGTTA
31331735 GATTGCACGGTATGTAATGGCGAGGCGA-CGATCTAGACGT
131 GATTGCACGGTATGTAATGGCGAGGCGAGCGATCTAGACGT
31331775 TTCGCAATTTAGTGACCTTGCCAAAGCTTTTGTTTAACTTATATTTTGGGCACTTTGTGTTTTTC
1 TTCGCAATTTAGTGACCTTGCCAAAGCTTTTGTTTAACTTATATTTTGGGCACTTTGTGTTTTTC
31331840 TTTCTTGTATATTCTTTAAGTTCGCAAGAGCTCACACACACCTTTCTAAACAATGCACATAGTTA
66 TTTCTTGTATATTCTTTAAGTTCGCAAGAGCTCACACACACCTTTCTAAACAATGCACATAGTTA
31331905 GATTGCACGGTATGTAATGGCGAGGCGAGCGATCTAGACG
131 GATTGCACGGTATGTAATGGCGAGGCGAGCGATCTAGACG
31331945 AAGAATAAAC
Statistics
Matches: 167, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
170 156 0.93
171 11 0.07
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (171 bp):
TTCGCAATTTAGTGACCTTGCCAAAGCTTTTGTTTAACTTATATTTTGGGCACTTTGTGTTTTTC
TTTCTTGTATATTCTTTAAGTTCGCAAGAGCTCACACACACCTTTCTAAACAATGCACATAGTTA
GATTGCACGGTATGTAATGGCGAGGCGAGCGATCTAGACGT
Found at i:31341737 original size:27 final size:27
Alignment explanation
Indices: 31341699--31341790 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
31341689 GCTGTGCTTG
*
31341699 CAGATTTGTTTTGGTGAACTATGTTCA
1 CAGATGTGTTTTGGTGAACTATGTTCA
*
31341726 CAGATGTGTTTTGATGAACTATGTTCA
1 CAGATGTGTTTTGGTGAACTATGTTCA
* *
31341753 CAGATGTGTTTTTGTGAACTACGTTCA
1 CAGATGTGTTTTGGTGAACTATGTTCA
*
31341780 CAAATGTGTTT
1 CAGATGTGTTT
31341791 GTTAAGCTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (27 bp):
CAGATGTGTTTTGGTGAACTATGTTCA
Found at i:31350002 original size:25 final size:25
Alignment explanation
Indices: 31349968--31350019 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
31349958 GATCTTGAGT
31349968 TAGCTTTAGAGCTTTCATAAGCTCG
1 TAGCTTTAGAGCTTTCATAAGCTCG
31349993 TAGCTTTAGAGCTTTCATAAGCTCG
1 TAGCTTTAGAGCTTTCATAAGCTCG
31350018 TA
1 TA
31350020 TAAGACCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (25 bp):
TAGCTTTAGAGCTTTCATAAGCTCG
Found at i:31350852 original size:43 final size:42
Alignment explanation
Indices: 31350805--31350909 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 42
31350795 AAATATGCTT
*
31350805 GCACACATAGTGCATCATCAG-GCAAGTCGAAGAAATTATACTG
1 GCACACATAGTGCATCATCAGAG-AACT-GAAGAAATTATACTG
* *
31350848 GCACACGA-CGTGCATCATCAGATGAACTGAAGCAATTATACTG
1 GCACAC-ATAGTGCATCATCAGA-GAACTGAAGAAATTATACTG
**
31350891 GCACATGTAGTGCATCATC
1 GCACACATAGTGCATCATC
31350910 TGTAACAGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
43 47 0.90
44 4 0.08
45 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (42 bp):
GCACACATAGTGCATCATCAGAGAACTGAAGAAATTATACTG
Found at i:31352177 original size:25 final size:24
Alignment explanation
Indices: 31352137--31352284 Score: 125
Period size: 25 Copynumber: 6.0 Consensus size: 24
31352127 GGACACACCA
* * *
31352137 CAGCTCGTACGGGCTTACCGATTT
1 CAGCTCGTAAGAGCTTACCAATTT
* *
31352161 GCAGGTCGTAAGAGCTTACTAATTCT
1 -CAGCTCGTAAGAGCTTACCAATT-T
*
31352187 CAGCTCGTATGAGCTTACCAATTT
1 CAGCTCGTAAGAGCTTACCAATTT
* *
31352211 ACAGCTCGTGAGAGTTTACCAATTCT
1 -CAGCTCGTAAGAGCTTACCAATT-T
* * **
31352237 CAACTCGTATGAGCTTACTGATTT
1 CAGCTCGTAAGAGCTTACCAATTT
* *
31352261 ACAGCTCGTACGAGCATACCAATT
1 -CAGCTCGTAAGAGCTTACCAATT
31352285 CATATCTCAT
Statistics
Matches: 97, Mismatches: 22, Indels: 8
0.76 0.17 0.06
Matches are distributed among these distances:
24 2 0.02
25 93 0.96
26 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (24 bp):
CAGCTCGTAAGAGCTTACCAATTT
Found at i:31352203 original size:50 final size:50
Alignment explanation
Indices: 31352137--31352285 Score: 190
Period size: 50 Copynumber: 3.0 Consensus size: 50
31352127 GGACACACCA
* * * * *
31352137 CAGCTCGTACGGGCTTACCGATTTGCAGGTCGTAAGAGCTTACTAATTCT
1 CAGCTCGTATGAGCTTACCGATTTACAGCTCGTAAGAGCTTACCAATTCT
* * *
31352187 CAGCTCGTATGAGCTTACCAATTTACAGCTCGTGAGAGTTTACCAATTCT
1 CAGCTCGTATGAGCTTACCGATTTACAGCTCGTAAGAGCTTACCAATTCT
* * * *
31352237 CAACTCGTATGAGCTTACTGATTTACAGCTCGTACGAGCATACCAATTC
1 CAGCTCGTATGAGCTTACCGATTTACAGCTCGTAAGAGCTTACCAATTC
31352286 ATATCTCATA
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTACCGATTTACAGCTCGTAAGAGCTTACCAATTCT
Found at i:31354546 original size:23 final size:23
Alignment explanation
Indices: 31354494--31354591 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
31354484 AGTGTTATTG
31354494 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
**
31354517 -TCAGTGGTAGCTTCAACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
31354539 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
31354562 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
31354585 ATCAGTG
1 ATCAGTG
31354592 TGGCACTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 20 0.30
23 47 0.70
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:31356653 original size:42 final size:42
Alignment explanation
Indices: 31356521--31356666 Score: 168
Period size: 42 Copynumber: 3.5 Consensus size: 42
31356511 AGGGGTGTTA
* * *
31356521 CATCATCGGATAAACGAAAGCAATCATACCAGCACATAAATG
1 CATCATCGGATAAACCAAAGCAATCATACTAGCACATAAGTG
** * * * *
31356563 CATCATTAGATAAATCGAAGTAATCATACTAGCACATAAGTT
1 CATCATCGGATAAACCAAAGCAATCATACTAGCACATAAGTG
* *
31356605 CATCATCGGATAAACCAAAGCGAA-CAAACTAGCACGTAAGTG
1 CATCATCGGATAAACCAAAGC-AATCATACTAGCACATAAGTG
*
31356647 CATCATCGGCTAAACCAAAG
1 CATCATCGGATAAACCAAAG
31356667 TATAAACCCT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 83 0.98
43 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (42 bp):
CATCATCGGATAAACCAAAGCAATCATACTAGCACATAAGTG
Found at i:31358886 original size:20 final size:20
Alignment explanation
Indices: 31358861--31358901 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
31358851 CATATCACAC
*
31358861 CAGAGGCACCGAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAA
*
31358881 CAGAGGCACTAAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAA
31358901 C
1 C
31358902 CCGTACATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.07
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGCAAA
Found at i:31364477 original size:20 final size:18
Alignment explanation
Indices: 31364407--31364477 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 18
31364397 AAATATTCTA
*
31364407 AAAAATTAAAATTATTAAG
1 AAAAATTAAAATTATT-AT
31364426 AATAAATTAAAATTAATTAT
1 AA-AAATTAAAATT-ATTAT
*
31364446 GAAAATTGTAAATAATTATTAT
1 -AAAAAT-T-AA-AATTATTAT
31364468 AAAAATTAAA
1 AAAAATTAAA
31364478 TTAAATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
18 1 0.02
19 4 0.09
20 16 0.37
21 11 0.26
22 7 0.16
23 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AAAAATTAAAATTATTAT
Found at i:31364484 original size:22 final size:23
Alignment explanation
Indices: 31364428--31364490 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 23
31364418 TTATTAAGAA
*
31364428 TAAATTAAAATTAATTATGAAAATTG
1 TAAATT-AAATT-ATTAT-AAAAATG
31364454 TAAA-T-AATTATTATAAAAAT-
1 TAAATTAAATTATTATAAAAATG
*
31364474 TAAATTAAATTTTTATA
1 TAAATTAAATTATTATA
31364491 TTTTTATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 4 0.12
21 6 0.18
22 14 0.42
23 4 0.12
25 1 0.03
26 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (23 bp):
TAAATTAAATTATTATAAAAATG
Found at i:31365172 original size:21 final size:21
Alignment explanation
Indices: 31365122--31365177 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
31365112 TTTGAATAGT
31365122 AAATTTTAATTATTTATATAATA
1 AAATTTT-A-TATTTATATAATA
31365145 ATTAATTTTATATTTCATAT-ATA
1 A--AATTTTATATTT-ATATAATA
31365168 AAATTTTATA
1 AAATTTTATA
31365178 AATAATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 9 0.30
23 10 0.33
24 5 0.17
25 6 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATTTTATATTTATATAATA
Found at i:31366363 original size:18 final size:19
Alignment explanation
Indices: 31366329--31366366 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
31366319 AATTCAATAC
*
31366329 TTTCAATTCAACTAATAAT
1 TTTCAATTCAACAAATAAT
31366348 TTTCAATTC-ACAAATAAT
1 TTTCAATTCAACAAATAAT
31366366 T
1 T
31366367 AAATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTCAATTCAACAAATAAT
Found at i:31371889 original size:26 final size:26
Alignment explanation
Indices: 31371853--31371904 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
31371843 TGTTTGGATG
31371853 CCGTAAGGGTGTTGGAGTTCCAAATT
1 CCGTAAGGGTGTTGGAGTTCCAAATT
31371879 CCGTAAGGGTGTTGGAGTTCCAAATT
1 CCGTAAGGGTGTTGGAGTTCCAAATT
31371905 AACTGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (26 bp):
CCGTAAGGGTGTTGGAGTTCCAAATT
Found at i:31375949 original size:14 final size:14
Alignment explanation
Indices: 31375941--31375970 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
31375931 ATTTTTATAT
31375941 TTTGGTTTTAATAC
1 TTTGGTTTTAATAC
31375955 TTTGGTTTTAATAC
1 TTTGGTTTTAATAC
31375969 TT
1 TT
31375971 GGGCTCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (14 bp):
TTTGGTTTTAATAC
Found at i:31378963 original size:14 final size:14
Alignment explanation
Indices: 31378925--31378979 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
31378915 AATTTGGTTC
31378925 ATTTATTTTTTTATTT
1 ATTTA-TTTTTTA-TT
*
31378941 AATTAATTTTTTATT
1 -ATTTATTTTTTATT
* *
31378956 CTTTATTTTTTGTT
1 ATTTATTTTTTATT
31378970 ATTTATTTTT
1 ATTTATTTTT
31378980 AGGTGTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 20 0.61
15 2 0.06
16 7 0.21
17 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (14 bp):
ATTTATTTTTTATT
Found at i:31382005 original size:6 final size:6
Alignment explanation
Indices: 31381989--31382031 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
31381979 CCCAAAAGAA
* *
31381989 AATTTT CATTTT AATTTT AATTTT -ATTTCC AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT AATTT-T AATTTT AATTTT A
31382032 TTATTTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 4 0.13
6 23 0.74
7 4 0.13
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:31383027 original size:64 final size:64
Alignment explanation
Indices: 31382948--31383073 Score: 252
Period size: 64 Copynumber: 2.0 Consensus size: 64
31382938 TTATGATGTC
31382948 TGTGCCTCAATCGTTCATGCTTTCAATTAAACTCATGCATGTATTTCATTCATTAAAATGTGTT
1 TGTGCCTCAATCGTTCATGCTTTCAATTAAACTCATGCATGTATTTCATTCATTAAAATGTGTT
31383012 TGTGCCTCAATCGTTCATGCTTTCAATTAAACTCATGCATGTATTTCATTCATTAAAATGTG
1 TGTGCCTCAATCGTTCATGCTTTCAATTAAACTCATGCATGTATTTCATTCATTAAAATGTG
31383074 ATTGAATGCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (64 bp):
TGTGCCTCAATCGTTCATGCTTTCAATTAAACTCATGCATGTATTTCATTCATTAAAATGTGTT
Found at i:31383542 original size:19 final size:19
Alignment explanation
Indices: 31383518--31383557 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
31383508 ATCTCATCTC
31383518 ATTCA-TTGCATTTAGATTA
1 ATTCATTTGCATTTAG-TTA
31383537 ATTCATTTGCATTTAGTTA
1 ATTCATTTGCATTTAGTTA
31383556 AT
1 AT
31383558 AATAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (19 bp):
ATTCATTTGCATTTAGTTA
Found at i:31390537 original size:14 final size:14
Alignment explanation
Indices: 31390518--31390548 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31390508 CCCCAAAAGA
*
31390518 GCGTCCACGTCAGC
1 GCGTCCACATCAGC
31390532 GCGTCCACATCAGC
1 GCGTCCACATCAGC
31390546 GCG
1 GCG
31390549 ATGTCAGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.42, G:0.29, T:0.13
Consensus pattern (14 bp):
GCGTCCACATCAGC
Found at i:31390818 original size:11 final size:10
Alignment explanation
Indices: 31390779--31390849 Score: 88
Period size: 11 Copynumber: 6.5 Consensus size: 10
31390769 AACTAAATCC
31390779 TTTCTCTCAA
1 TTTCTCTCAA
31390789 TTTCTCTCTAA
1 TTTCTCTC-AA
31390800 TATTCTCTCAAA
1 T-TTCTCTC-AA
31390812 TTTCTCTCAA
1 TTTCTCTCAA
31390822 TTTCCTCTCAA
1 TTT-CTCTCAA
31390833 TTTCCTCTCAAA
1 TTT-CTCTC-AA
31390845 TTTCT
1 TTTCT
31390850 ATTTAAAATA
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
10 13 0.23
11 28 0.50
12 15 0.27
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:31390821 original size:33 final size:33
Alignment explanation
Indices: 31390779--31390849 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
31390769 AACTAAATCC
31390779 TTTCTCTCAATTT-CTCTCTAATATT-CTCTCAAA
1 TTTCTCTCAATTTCCTCTC-AAT-TTCCTCTCAAA
31390812 TTTCTCTCAATTTCCTCTCAATTTCCTCTCAAA
1 TTTCTCTCAATTTCCTCTCAATTTCCTCTCAAA
31390845 TTTCT
1 TTTCT
31390850 ATTTAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
32 2 0.06
33 29 0.81
34 5 0.14
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (33 bp):
TTTCTCTCAATTTCCTCTCAATTTCCTCTCAAA
Found at i:31394954 original size:18 final size:18
Alignment explanation
Indices: 31394917--31394960 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
31394907 TTGGTGCTGT
*
31394917 TGTATCCTAGTCCCTTTA
1 TGTATCCTAGACCCTTTA
31394935 TGTATCCTA-ACCCTTATA
1 TGTATCCTAGACCCTT-TA
*
31394953 TGTTTCCT
1 TGTATCCT
31394961 TTTTCTAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (18 bp):
TGTATCCTAGACCCTTTA
Found at i:31395227 original size:21 final size:20
Alignment explanation
Indices: 31395201--31395260 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
31395191 CCAACACCGA
*
31395201 CAACCAGATCCCCTACCGGAG
1 CAACCAAATCCCC-ACCGGAG
*
31395222 GAACCAAAATCCCCACCGGAG
1 CAACC-AAATCCCCACCGGAG
*
31395243 CAACCACAACCCCCACCG
1 CAACCA-AATCCCCACCG
31395261 AAGGCTAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 25 0.76
22 7 0.21
ACGTcount: A:0.33, C:0.47, G:0.15, T:0.05
Consensus pattern (20 bp):
CAACCAAATCCCCACCGGAG
Found at i:31395234 original size:22 final size:21
Alignment explanation
Indices: 31395208--31395260 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
31395198 CGACAACCAG
*
31395208 ATCCCCTACCGGAGGAACCAAA
1 ATCCCC-ACCGGAGCAACCAAA
*
31395230 ATCCCCACCGGAGCAACCACA
1 ATCCCCACCGGAGCAACCAAA
*
31395251 ACCCCCACCG
1 ATCCCCACCG
31395261 AAGGCTAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.32, C:0.47, G:0.15, T:0.06
Consensus pattern (21 bp):
ATCCCCACCGGAGCAACCAAA
Found at i:31398748 original size:126 final size:126
Alignment explanation
Indices: 31398517--31398933 Score: 681
Period size: 126 Copynumber: 3.3 Consensus size: 126
31398507 CCAAACATGT
* * *
31398517 GCTATTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTACTGGCAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * *
31398582 GCTTAAAGCGTTTTTGACACAATTTGCTTAGAAACCTCTACTCGAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
*
31398643 GCTACTGTAGCAAAAGCCCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * * *
31398708 ACGTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
*
31398769 GCTACTGTAGCAAAAGCGCGTCCACGTGGTAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* *
31398834 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATATTTTCAAGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* * *
31398895 GCTACTATAGCAAGAGTGCGTCCACGTGGGAGCTTCTTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
31398934 AAATTAACAA
Statistics
Matches: 268, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 268 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (126 bp):
GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
Found at i:31399115 original size:96 final size:96
Alignment explanation
Indices: 31398966--31399270 Score: 321
Period size: 96 Copynumber: 3.2 Consensus size: 96
31398956 AGTAACTCTA
* *
31398966 AACCCCAAACCCTAATTTATTTGAGTTTTTACTTAAAAACACTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTT-AATTTTTACTTAAAAACACTAAACACTAAACCCTAATCTAAT
31399031 TTTATAAA-AATTTATAATTAATTTACTCAAGT
65 TTT-TAAATAATTTATAATTAATTTACTCAAGT
* * * * * * * *
31399063 AACCCTGAACCCTAATTTATTTAATTTTTCCTTAAAAACTCTTAACTCTAAACCTTTATCTGATT
1 AACCCTAAACCCTAATTTATTTAATTTTTACTTAAAAACACTAAACACTAAACCCTAATCTAATT
*
31399128 TTTAAATAATTTTTAATTAATTTACTCAAGT
66 TTTAAATAATTTATAATTAATTTACTCAAGT
* * * * * * *
31399159 AACCTTAAACCCTAATTTAATTGATTTTTTCTTAAAAAAACAATAAACACGAAA-CCTAATCCAA
1 AACCCTAAACCCTAATTTATTTAATTTTTACTT--AAAAACACTAAACACTAAACCCTAATCTAA
* * ** **
31399223 -TTTTGAA-AATTTGATAATTAATTTAATTGACA
64 TTTTTAAATAATTT-ATAATTAATTTACTCAAGT
31399255 AACCCTAAACCCTAAT
1 AACCCTAAACCCTAAT
31399271 CACTTATTTA
Statistics
Matches: 171, Mismatches: 33, Indels: 9
0.80 0.15 0.04
Matches are distributed among these distances:
95 9 0.05
96 122 0.71
97 26 0.15
98 14 0.08
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.38
Consensus pattern (96 bp):
AACCCTAAACCCTAATTTATTTAATTTTTACTTAAAAACACTAAACACTAAACCCTAATCTAATT
TTTAAATAATTTATAATTAATTTACTCAAGT
Found at i:31401458 original size:10 final size:10
Alignment explanation
Indices: 31401445--31401531 Score: 63
Period size: 10 Copynumber: 8.7 Consensus size: 10
31401435 TATATATATA
31401445 TATTTTCCTT
1 TATTTTCCTT
31401455 TATTTTCCTT
1 TATTTTCCTT
* *
31401465 TATTTTCATAAA
1 TATTTTCCT--T
31401477 TATTTTCCTT
1 TATTTTCCTT
*
31401487 TATTTT--AT
1 TATTTTCCTT
* * * *
31401495 AATATAT-ATA
1 TAT-TTTCCTT
31401505 TATTTTCCTT
1 TATTTTCCTT
31401515 TATTTTCCTT
1 TATTTTCCTT
31401525 TATTTTC
1 TATTTTC
31401532 ATAAATATGT
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
8 3 0.05
9 4 0.07
10 44 0.75
12 8 0.14
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.64
Consensus pattern (10 bp):
TATTTTCCTT
Found at i:31401481 original size:32 final size:32
Alignment explanation
Indices: 31401444--31401539 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
31401434 ATATATATAT
31401444 ATATTTTCCTTTATTTTCCTTTATTTTCATAA
1 ATATTTTCCTTTATTTTCCTTTATTTTCATAA
* * * *
31401476 ATATTTTCCTTTA-TTT--TATAATAT-ATAT
1 ATATTTTCCTTTATTTTCCTTTATTTTCATAA
31401504 ATATTTTCCTTTATTTTCCTTTATTTTCATAA
1 ATATTTTCCTTTATTTTCCTTTATTTTCATAA
31401536 ATAT
1 ATAT
31401540 GTTATGTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
28 16 0.31
29 8 0.15
31 8 0.15
32 20 0.38
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.61
Consensus pattern (32 bp):
ATATTTTCCTTTATTTTCCTTTATTTTCATAA
Found at i:31401483 original size:22 final size:22
Alignment explanation
Indices: 31401455--31401501 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
31401445 TATTTTCCTT
31401455 TATTTTCCTTTATTTTCATAA-A
1 TATTTTCCTTTATTTT-ATAATA
31401477 TATTTTCCTTTATTTTATAATA
1 TATTTTCCTTTATTTTATAATA
31401499 TAT
1 TAT
31401502 ATATATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTCCTTTATTTTATAATA
Found at i:31401753 original size:13 final size:12
Alignment explanation
Indices: 31401729--31401767 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
31401719 TCATGGATTA
31401729 TTGTTT-TTTAT
1 TTGTTTATTTAT
31401740 TTCGTTTATTTAT
1 TT-GTTTATTTAT
31401753 TTGTTTATATTAT
1 TTGTTTAT-TTAT
31401766 TT
1 TT
31401768 TTATGCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 10 0.40
13 13 0.52
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (12 bp):
TTGTTTATTTAT
Found at i:31401798 original size:15 final size:15
Alignment explanation
Indices: 31401775--31401807 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
31401765 TTTTTATGCC
31401775 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
31401790 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
31401805 ATT
1 ATT
31401808 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:31403976 original size:3 final size:3
Alignment explanation
Indices: 31403968--31404005 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
31403958 CATATCTAGT
31403968 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31404006 GGGTTAAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:31404476 original size:21 final size:21
Alignment explanation
Indices: 31404450--31404497 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
31404440 TCTATTTTTA
31404450 TATTTTTA-T-ATGTTTATATAT
1 TATTTTTATTAAT-TTTATA-AT
31404471 TATTTTTATTAATTTTATAAT
1 TATTTTTATTAATTTTATAAT
31404492 TATTTT
1 TATTTT
31404498 ACAACTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 16 0.64
22 7 0.28
23 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTTTATTAATTTTATAAT
Found at i:31404485 original size:10 final size:9
Alignment explanation
Indices: 31404442--31404545 Score: 59
Period size: 10 Copynumber: 10.9 Consensus size: 9
31404432 TTTATAATTC
31404442 TATTTTTA-
1 TATTTTTAT
31404450 TATTTTTAT
1 TATTTTTAT
*
31404459 ATGTTTATATAT
1 -TATTT-T-TAT
31404471 TATTTTTAT
1 TATTTTTAT
31404480 TAATTTTATAAT
1 T-ATTTT-T-AT
*
31404492 TA-TTTTAC
1 TATTTTTAT
* *
31404500 AACTTTTAT
1 TATTTTTAT
* *
31404509 GATTTTTTAA
1 TA-TTTTTAT
*
31404519 TATTTTTAC
1 TATTTTTAT
31404528 TATTTTTCAT
1 TATTTTT-AT
31404538 TATTTTTA
1 TATTTTTA
31404546 AATTTAAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
8 10 0.13
9 25 0.33
10 27 0.36
11 7 0.09
12 6 0.08
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (9 bp):
TATTTTTAT
Found at i:31408552 original size:24 final size:24
Alignment explanation
Indices: 31408502--31408554 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
31408492 GTATTGAAAT
* *
31408502 TTAAAAATTTTAAAAATATAAAGA
1 TTAAAAATATCAAAAATATAAAGA
*
31408526 TTAAAAATATCAAATAATATCAA-A
1 TTAAAAATATCAAA-AATATAAAGA
31408550 TTAAA
1 TTAAA
31408555 TAACAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
TTAAAAATATCAAAAATATAAAGA
Found at i:31410217 original size:116 final size:116
Alignment explanation
Indices: 31409977--31410232 Score: 302
Period size: 116 Copynumber: 2.2 Consensus size: 116
31409967 GTTCTGTTCA
* * * * *
31409977 TGTTTTCTGTTTCCATTTCATTGTACATTTTGCATTTTCCATCTATTGAATGGACTGATGTTTTC
1 TGTTTTCTGTTTCCATTTCATTTTACACTTTGCATTTTCCATCGATTGAATGAACTGATGTTTCC
* * * *
31410042 GGGTTTCCATTTCATTTCTTTCAAGTGTCTGGTCTTTATAATGTCCGATCG
66 AGGTTTCCATTTCACTGCTTTCAAGTGTCTGGCCTTTATAATGTCCGATCG
* * * * * * *
31410093 TATCTTCTGTTTCCATTTCATTTTACGCTTTGTATTTTCCATGGGTTGAATGAAGTGACT-TTTC
1 TGTTTTCTGTTTCCATTTCATTTTACACTTTGCATTTTCCATCGATTGAATGAACTGA-TGTTTC
* *
31410157 CAGGTTTCCATTTCACTGCTTTCAAGTGTCTGGCCTTTATAA-GTTTCG-TTG
65 CAGGTTTCCATTTCACTGCTTTCAAGTGTCTGGCCTTTATAATG-TCCGATCG
31410208 TTGTTTTCTGTTTCCATTTCATTTT
1 -TGTTTTCTGTTTCCATTTCATTTT
31410233 GCGTTTTCCA
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
115 3 0.03
116 113 0.97
117 1 0.01
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.50
Consensus pattern (116 bp):
TGTTTTCTGTTTCCATTTCATTTTACACTTTGCATTTTCCATCGATTGAATGAACTGATGTTTCC
AGGTTTCCATTTCACTGCTTTCAAGTGTCTGGCCTTTATAATGTCCGATCG
Found at i:31417232 original size:30 final size:31
Alignment explanation
Indices: 31417164--31417233 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
31417154 TTAATATGCT
* *
31417164 ATTTGGTACCTGAGTTTCACTTTAATGTTCA
1 ATTTGGTACCTGAGTTTCACTTCAATATTCA
**
31417195 ATTTGGTACCTGAGTTTGGCTTCAATATT-A
1 ATTTGGTACCTGAGTTTCACTTCAATATTCA
*
31417225 TTTTGGTAC
1 ATTTGGTAC
31417234 TTGATTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 9 0.26
31 25 0.74
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (31 bp):
ATTTGGTACCTGAGTTTCACTTCAATATTCA
Found at i:31418411 original size:11 final size:11
Alignment explanation
Indices: 31418397--31418422 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31418387 TTTATTTTAT
31418397 TTTTAAAATAC
1 TTTTAAAATAC
31418408 TTTTAAAATAC
1 TTTTAAAATAC
31418419 TTTT
1 TTTT
31418423 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:31418458 original size:26 final size:26
Alignment explanation
Indices: 31418408--31418460 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
31418398 TTTAAAATAC
* * *
31418408 TTTTAAAATACTTTTTTATTTTTTAT
1 TTTTAAAATAATTTTTTAGTGTTTAT
*
31418434 TTTTAAAATAATTTTTTGGTGTTTAT
1 TTTTAAAATAATTTTTTAGTGTTTAT
31418460 T
1 T
31418461 AAAAAAATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (26 bp):
TTTTAAAATAATTTTTTAGTGTTTAT
Found at i:31420837 original size:46 final size:44
Alignment explanation
Indices: 31420768--31420856 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 44
31420758 ATGTGAACCA
* *
31420768 ATATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCCACCGG
1 ATATCATTAATTAAAAGGTGGTTGCTATATGCTGAAT-CCACCGG
* *
31420812 ATATCATTGATTACAAAGGGTGGTTGCTGTATGCTGAATCCACCG
1 ATATCATTAATTA-AAA-GGTGGTTGCTATATGCTGAATCCACCG
31420857 TGTATCTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 12 0.32
45 2 0.05
46 22 0.58
47 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (44 bp):
ATATCATTAATTAAAAGGTGGTTGCTATATGCTGAATCCACCGG
Found at i:31425094 original size:41 final size:42
Alignment explanation
Indices: 31425027--31425109 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 42
31425017 ATGGATACGG
*
31425027 GTTAGGGGTGTTACACAACACATTGACTTTGAATCTAGATGA
1 GTTAGGGGTGTTACACAACACATTGACTTTGAATCTAAATGA
*
31425069 GTTAGGGGTGTT-CACAACACCTTGACTTTGAATCTAAATGA
1 GTTAGGGGTGTTACACAACACATTGACTTTGAATCTAAATGA
31425110 TGGGGACCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 27 0.69
42 12 0.31
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (42 bp):
GTTAGGGGTGTTACACAACACATTGACTTTGAATCTAAATGA
Found at i:31426970 original size:51 final size:49
Alignment explanation
Indices: 31426912--31427036 Score: 121
Period size: 50 Copynumber: 2.5 Consensus size: 49
31426902 ATGAGTTACT
*
31426912 TAATGCATGACTTTATTTAAGATGCAAACTTTAACTATCATG-GTAGTTAAA
1 TAATGCAT-ACTTTATTTAAGATGCAAAC-TTAACTAACATGAG-AGTTAAA
* * * * **
31426963 TAATGCATATCATAATTTATGATGCAATCTTAACTAACATGAGAGTTTCA
1 TAATGCATA-CTTTATTTAAGATGCAAACTTAACTAACATGAGAGTTAAA
31427013 TAATGCATAACTTTA-TTAA-ATGCA
1 TAATGCAT-ACTTTATTTAAGATGCA
31427037 GAACACATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
48 5 0.08
49 3 0.05
50 28 0.46
51 25 0.41
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (49 bp):
TAATGCATACTTTATTTAAGATGCAAACTTAACTAACATGAGAGTTAAA
Found at i:31427019 original size:50 final size:51
Alignment explanation
Indices: 31426926--31427021 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 51
31426916 GCATGACTTT
*
31426926 ATTTAAGATGCAAACTTTAACTATCATGGTAGTTAAATAATGCATATCATA
1 ATTTAAGATGCAAACTTTAACTAACATGGTAGTTAAATAATGCATATCATA
* * **
31426977 ATTTATGATGCAATC-TTAACTAACATGAG-AGTTTCATAATGCATA
1 ATTTAAGATGCAAACTTTAACTAACATG-GTAGTTAAATAATGCATA
31427022 ACTTTATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 25 0.64
51 14 0.36
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (51 bp):
ATTTAAGATGCAAACTTTAACTAACATGGTAGTTAAATAATGCATATCATA
Found at i:31442611 original size:24 final size:24
Alignment explanation
Indices: 31442536--31442599 Score: 128
Period size: 24 Copynumber: 2.7 Consensus size: 24
31442526 TTTCTAGAAG
31442536 ATTTAGCATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
31442560 ATTTAGCATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
31442584 ATTTAGCATTTATTAG
1 ATTTAGCATTTATTAG
31442600 CATAGTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:31446210 original size:53 final size:53
Alignment explanation
Indices: 31446121--31446279 Score: 219
Period size: 53 Copynumber: 3.0 Consensus size: 53
31446111 CTTAGTTTTC
* * *
31446121 CCATATAATGTCATAACCCACCAATTATGGTCTTACACGATATGATCTTCTTT
1 CCATATGATGTCATAACCCACCAGTTACGGTCTTACACGATATGATCTTCTTT
* * *
31446174 CCATATGATGCCATAACCCACCAGTTACGGTTTTACATGATATGATCTTCTTT
1 CCATATGATGTCATAACCCACCAGTTACGGTCTTACACGATATGATCTTCTTT
* * * * *
31446227 CCATATGATGTCATAACCCACCAGTTACGATCTTGCAGGACATGGTCTTCTTT
1 CCATATGATGTCATAACCCACCAGTTACGGTCTTACACGATATGATCTTCTTT
31446280 AGTGCCATGG
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 93 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (53 bp):
CCATATGATGTCATAACCCACCAGTTACGGTCTTACACGATATGATCTTCTTT
Found at i:31448074 original size:41 final size:41
Alignment explanation
Indices: 31448010--31448128 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 41
31448000 TACCTAATAT
* * * *
31448010 AATACACCGGCACAAAGCCTGCTAGGCTTAAAACCTGATAC
1 AATACACTGACACGAAGCCTGCTAGGCTTAAAGCCTGATAC
* * * *
31448051 GATACA-TCGACACGAAGCTTGCTAGGCTCAAGGCCTGATAC
1 AATACACT-GACACGAAGCCTGCTAGGCTTAAAGCCTGATAC
* *
31448092 AATACACTGGCACGAAGCCTGCTAGGCATAAAGCCTG
1 AATACACTGACACGAAGCCTGCTAGGCTTAAAGCCTG
31448129 CTAGGCATAA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
41 61 0.98
42 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.18
Consensus pattern (41 bp):
AATACACTGACACGAAGCCTGCTAGGCTTAAAGCCTGATAC
Found at i:31448125 original size:16 final size:16
Alignment explanation
Indices: 31448106--31448141 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
31448096 CACTGGCACG
31448106 AAGCCTGCTAGGCATA
1 AAGCCTGCTAGGCATA
31448122 AAGCCTGCTAGGCATA
1 AAGCCTGCTAGGCATA
31448138 AAGC
1 AAGC
31448142 TTGAACAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (16 bp):
AAGCCTGCTAGGCATA
Found at i:31448192 original size:97 final size:98
Alignment explanation
Indices: 31448018--31448225 Score: 267
Period size: 97 Copynumber: 2.1 Consensus size: 98
31448008 ATAATACACC
* * * * * *
31448018 GGCACAAAGCCTGCTAGGCTTAAAACCTGATACGATACATCGACACGAAGCTTGCTAGGCTCAAG
1 GGCACAAAGCCTGCTAGGCATAAAACCTGATACAATACACCGACACGAAGCCTGCTAGGCACAAA
* *
31448083 GCCTGATACAATACACTGGCACGAAGCCTGCTA
66 GCCTGATACAATACACTAGCACGAAGCCTACTA
* * * *
31448116 GGCATAAAGCCTGCTAGGCATAAAGCTTGA-ACAATACACCGACACTAAGCCTGCTAGGCACAAA
1 GGCACAAAGCCTGCTAGGCATAAAACCTGATACAATACACCGACACGAAGCCTGCTAGGCACAAA
*
31448180 GCCTGA-ATCAATACACTAGCACTAAGCCTACTA
66 GCCTGATA-CAATACACTAGCACGAAGCCTACTA
*
31448213 GGAACAAAGCCTG
1 GGCACAAAGCCTG
31448226 AATCAATACA
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
96 1 0.01
97 67 0.71
98 26 0.28
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (98 bp):
GGCACAAAGCCTGCTAGGCATAAAACCTGATACAATACACCGACACGAAGCCTGCTAGGCACAAA
GCCTGATACAATACACTAGCACGAAGCCTACTA
Found at i:31448204 original size:41 final size:41
Alignment explanation
Indices: 31448122--31448284 Score: 222
Period size: 41 Copynumber: 4.0 Consensus size: 41
31448112 GCTAGGCATA
* * *
31448122 AAGCCTGCTAGGCATAAAGCTTGAA-CAATACACC-GACACT
1 AAGCCTACTAGGCACAAAGCCTGAATCAATACACCAG-CACT
* *
31448162 AAGCCTGCTAGGCACAAAGCCTGAATCAATACACTAGCACT
1 AAGCCTACTAGGCACAAAGCCTGAATCAATACACCAGCACT
* *
31448203 AAGCCTACTAGGAACAAAGCCTGAATCAATACACCAACACT
1 AAGCCTACTAGGCACAAAGCCTGAATCAATACACCAGCACT
* *
31448244 AAGCCTACTAAGCACAAATCCTGAATCAATACACCAGCACT
1 AAGCCTACTAGGCACAAAGCCTGAATCAATACACCAGCACT
31448285 CCGGCGAGAC
Statistics
Matches: 110, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 23 0.21
41 86 0.78
42 1 0.01
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (41 bp):
AAGCCTACTAGGCACAAAGCCTGAATCAATACACCAGCACT
Found at i:31448809 original size:41 final size:41
Alignment explanation
Indices: 31448736--31448997 Score: 167
Period size: 41 Copynumber: 6.4 Consensus size: 41
31448726 AGTACAAGTT
* *
31448736 ACCTGATACAATACACCGGCACAAAGCCTGCTAGGCTTAAA
1 ACCTGATACAATACACCGACACAAAGCCTGCTAGGCTCAAA
* * * * * *
31448777 ACCTGATACGATACATCGACACGAATCTTGCTAGGCTCAAG
1 ACCTGATACAATACACCGACACAAAGCCTGCTAGGCTCAAA
* * * * *
31448818 GCCTGATACAATACACTGGCACAAAGCTTGCTAGGCACAAA
1 ACCTGATACAATACACCGACACAAAGCCTGCTAGGCTCAAA
* * * * *
31448859 GCTTGA-ATCAATACACCGACACTAAGCCTACTAGGCACAAA
1 ACCTGATA-CAATACACCGACACAAAGCCTGCTAGGCTCAAA
* * * * * *
31448900 GCCTGA-ATCAATACA-CAAGCACTAAGTCTGCTAGACACAAA
1 ACCTGATA-CAATACACCGA-CACAAAGCCTGCTAGGCTCAAA
* * * *
31448941 GCCTGA-ATCAATACA-CTAGCACTAAGCCTGCTAGGCACAAA
1 ACCTGATA-CAATACACCGA-CACAAAGCCTGCTAGGCTCAAA
*
31448982 GCCTGAATA-AATACAC
1 ACCTG-ATACAATACAC
31448998 TAGCACTAAG
Statistics
Matches: 185, Mismatches: 31, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.02
41 180 0.97
42 1 0.01
43 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (41 bp):
ACCTGATACAATACACCGACACAAAGCCTGCTAGGCTCAAA
Found at i:31448879 original size:82 final size:81
Alignment explanation
Indices: 31448737--31449032 Score: 301
Period size: 82 Copynumber: 3.6 Consensus size: 81
31448727 GTACAAGTTA
** ** * * *
31448737 CCTGATACAATACACCGGCACAAAGCCTGCTAGGCTTAAAACCTG-ATACGATACATCGACACGA
1 CCTGATACAATACACTAGCACAAAGCCTGCTAGGCACAAAGCCTGAAT-CAATACA-CGACACTA
* * * *
31448801 ATCTTGCTAGGCTCAAGG
64 AGCCTGCTAGGCACAAAG
* * *
31448819 CCTGATACAATACACTGGCACAAAGCTTGCTAGGCACAAAGCTTGAATCAATACACCGACACTAA
1 CCTGATACAATACACTAGCACAAAGCCTGCTAGGCACAAAGCCTGAATCAATACA-CGACACTAA
*
31448884 GCCTACTAGGCACAAAG
65 GCCTGCTAGGCACAAAG
* * * * *
31448901 CCTGA-ATCAATACACAAGCACTAAGTCTGCTAGACACAAAGCCTGAATCAATACACTAGCACTA
1 CCTGATA-CAATACACTAGCACAAAGCCTGCTAGGCACAAAGCCTGAATCAATACACGA-CACTA
31448965 AGCCTGCTAGGCACAAAG
64 AGCCTGCTAGGCACAAAG
* * * *
31448983 CCTGAATA-AATACACTAGCACTAAGCCTACTAAGTACAAAGCCTGAATCA
1 CCTG-ATACAATACACTAGCACAAAGCCTGCTAGGCACAAAGCCTGAATCA
31449033 TTATTTCCAA
Statistics
Matches: 180, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
81 3 0.02
82 173 0.96
83 3 0.02
84 1 0.01
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.18
Consensus pattern (81 bp):
CCTGATACAATACACTAGCACAAAGCCTGCTAGGCACAAAGCCTGAATCAATACACGACACTAAG
CCTGCTAGGCACAAAG
Found at i:31448998 original size:41 final size:41
Alignment explanation
Indices: 31448805--31449032 Score: 289
Period size: 41 Copynumber: 5.6 Consensus size: 41
31448795 ACACGAATCT
* * * * *
31448805 TGCTAGGCTCAAGGCCTG-ATACAATACACTGGCACAAAGCT
1 TGCTAGGCACAAAGCCTGAAT-CAATACACTAGCACTAAGCC
* *
31448846 TGCTAGGCACAAAGCTTGAATCAATACAC-CGACACTAAGCC
1 TGCTAGGCACAAAGCCTGAATCAATACACTAG-CACTAAGCC
* * *
31448887 TACTAGGCACAAAGCCTGAATCAATACACAAGCACTAAGTC
1 TGCTAGGCACAAAGCCTGAATCAATACACTAGCACTAAGCC
*
31448928 TGCTAGACACAAAGCCTGAATCAATACACTAGCACTAAGCC
1 TGCTAGGCACAAAGCCTGAATCAATACACTAGCACTAAGCC
*
31448969 TGCTAGGCACAAAGCCTGAATAAATACACTAGCACTAAGCC
1 TGCTAGGCACAAAGCCTGAATCAATACACTAGCACTAAGCC
* * *
31449010 TACTAAGTACAAAGCCTGAATCA
1 TGCTAGGCACAAAGCCTGAATCA
31449033 TTATTTCCAA
Statistics
Matches: 164, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.01
41 160 0.98
42 3 0.02
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (41 bp):
TGCTAGGCACAAAGCCTGAATCAATACACTAGCACTAAGCC
Found at i:31458371 original size:5 final size:5
Alignment explanation
Indices: 31458361--31458387 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
31458351 TTTGACATAG
31458361 AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AA
31458388 CACGAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:31461246 original size:3 final size:3
Alignment explanation
Indices: 31461238--31461334 Score: 194
Period size: 3 Copynumber: 32.3 Consensus size: 3
31461228 TCAAAGGAAG
31461238 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
31461286 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
31461334 C
1 C
31461335 NNNNNNNNNN
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:31461443 original size:3 final size:3
Alignment explanation
Indices: 31461435--31461494 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
31461425 NNNNNNNNNN
31461435 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
31461483 CTT CTT CTT CTT
1 CTT CTT CTT CTT
31461495 TTTGAGTTAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:31462414 original size:21 final size:22
Alignment explanation
Indices: 31462389--31462430 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31462379 CCATATATAT
31462389 TACTT-ATATTCA-TATTATTTA
1 TACTTAATA-TCATTATTATTTA
31462410 TACTTAATATCATTATTATTT
1 TACTTAATATCATTATTATTT
31462431 TTATAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (22 bp):
TACTTAATATCATTATTATTTA
Found at i:31462426 original size:22 final size:21
Alignment explanation
Indices: 31462389--31462430 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31462379 CCATATATAT
31462389 TACTTATATTCATATTATTTA
1 TACTTATATTCATATTATTTA
31462410 TACTTA-ATATCATTATTATTT
1 TACTTATAT-TCA-TATTATTT
31462431 TTATAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 9 0.47
22 8 0.42
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
TACTTATATTCATATTATTTA
Found at i:31463245 original size:119 final size:119
Alignment explanation
Indices: 31463034--31463276 Score: 398
Period size: 119 Copynumber: 2.0 Consensus size: 119
31463024 TTAGAAACAG
* * *
31463034 GGGTCACACAGCTGTATGGTCAGGCCGTGTGACATAGCCCAAATTGTGTGAGCATTCGAAGTATG
1 GGGTCACACAGCTGTATGGCCAGGCCGTGTGACATAGCCCAAACTGTGTGAGCATTCGAAGTATA
*
31463099 GGACACACGGCTGTGTCACAGCCCGTGTGTCTGCCAGTGTGGGTATTCGAAATA
66 GGACACACGGCTGTGTCACAGCCCGTGTGTCTGCCAATGTGGGTATTCGAAATA
*
31463153 GGGTCACACAGCTGTATGGCCAGGTCGTGTGACATAGCCCAAACCT-TGTGAGCATTCGAAGTAT
1 GGGTCACACAGCTGTATGGCCAGGCCGTGTGACATAGCCCAAA-CTGTGTGAGCATTCGAAGTAT
* **
31463217 AGGACACATGGCTGTGTTGCAGCCCGTGTGTCTGCCAATGTGGGTATTCGAAATA
65 AGGACACACGGCTGTGTCACAGCCCGTGTGTCTGCCAATGTGGGTATTCGAAATA
31463272 GGGTC
1 GGGTC
31463277 GCACGGTTGT
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
119 114 0.99
120 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.25
Consensus pattern (119 bp):
GGGTCACACAGCTGTATGGCCAGGCCGTGTGACATAGCCCAAACTGTGTGAGCATTCGAAGTATA
GGACACACGGCTGTGTCACAGCCCGTGTGTCTGCCAATGTGGGTATTCGAAATA
Found at i:31463294 original size:55 final size:54
Alignment explanation
Indices: 31463206--31463392 Score: 185
Period size: 55 Copynumber: 3.4 Consensus size: 54
31463196 CCTTGTGAGC
* * * * * * *
31463206 ATTCGAAGTATAGGACACATGGCTGTGTTGCAGCCCGTGTGTCTGCCAATGTGGGT
1 ATTCGAAATAT-GGTCACACGGTTGTGTCGCAGCTCGTGTGTCTGCC-GTGTGGGT
* * *
31463262 ATTCGAAATAGGGTCGCACGGTTGTGTCGCAGCTCGTGTGTCTGCTCGTGTGTGT
1 ATTCGAAATATGGTCACACGGTTGTGTCGCAGCTCGTGTGTCTGC-CGTGTGGGT
* * * * * *
31463317 ATTCGAAATATGGTCACACAGTCGTGTCGTAACTCATGTGTCTGCTTGTGTGGGT
1 ATTCGAAATATGGTCACACGGTTGTGTCGCAGCTCGTGTGTCTGC-CGTGTGGGT
*
31463372 ATTTGAAATATGGTCACACGG
1 ATTCGAAATATGGTCACACGG
31463393 CCATGTGAAA
Statistics
Matches: 109, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
55 99 0.91
56 10 0.09
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (54 bp):
ATTCGAAATATGGTCACACGGTTGTGTCGCAGCTCGTGTGTCTGCCGTGTGGGT
Found at i:31472277 original size:21 final size:22
Alignment explanation
Indices: 31472248--31472298 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
31472238 TCTCTCTCGC
*
31472248 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
31472269 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
31472291 TTT-ATTTT
1 TTTCATTTT
31472299 TCTCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:31498993 original size:16 final size:16
Alignment explanation
Indices: 31498969--31498999 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31498959 TTTATGTTAT
31498969 AAAAATTACAAAAACC
1 AAAAATTACAAAAACC
*
31498985 AAAATTTACAAAAAC
1 AAAAATTACAAAAAC
31499000 TATTAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATTACAAAAACC
Found at i:31499187 original size:27 final size:27
Alignment explanation
Indices: 31499152--31499242 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
31499142 TCATTATATG
31499152 ATTTTTATAAAATTTTATATTTTTATC
1 ATTTTTATAAAATTTTATATTTTTATC
*** * *
31499179 ATTTTTATAATAA-AAAATCA-TTATATG
1 ATTTTTATAA-AATTTTAT-ATTTTTATC
31499206 ATTTTTATAAAATTTTATATTTTTATC
1 ATTTTTATAAAATTTTATATTTTTATC
31499233 ATTTTTATAA
1 ATTTTTATAA
31499243 TTATTTTTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
26 3 0.06
27 44 0.88
28 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (27 bp):
ATTTTTATAAAATTTTATATTTTTATC
Found at i:31499202 original size:54 final size:54
Alignment explanation
Indices: 31499136--31499243 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
31499126 AAAATTTATA
31499136 AAAAAATCATTATATGATTTTTATAAAATTTTATATTTTTATCATTTTTATAAT
1 AAAAAATCATTATATGATTTTTATAAAATTTTATATTTTTATCATTTTTATAAT
31499190 AAAAAATCATTATATGATTTTTATAAAATTTTATATTTTTATCATTTTTATAAT
1 AAAAAATCATTATATGATTTTTATAAAATTTTATATTTTTATCATTTTTATAAT
31499244 TATTTTTATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (54 bp):
AAAAAATCATTATATGATTTTTATAAAATTTTATATTTTTATCATTTTTATAAT
Found at i:31500846 original size:26 final size:26
Alignment explanation
Indices: 31500817--31500880 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
31500807 CTGTACTACT
31500817 TTTATAATTTTTAA-AATTTTAAATTA
1 TTTATAATTTTTAATAATTTT-AATTA
* *
31500843 TTTAT-ATTTTATAATAATTTTATTTT
1 TTTATAATTTT-TAATAATTTTAATTA
31500869 TTTATAATTTTT
1 TTTATAATTTTT
31500881 TGACTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 5 0.15
26 17 0.52
27 11 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTATAATTTTTAATAATTTTAATTA
Found at i:31500870 original size:18 final size:19
Alignment explanation
Indices: 31500849--31500908 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 19
31500839 ATTATTTATA
* *
31500849 TTTTATAATAATTTTATTT
1 TTTTATAATATTTTTAATT
* *
31500868 TTTTATAAT-TTTTTGACT
1 TTTTATAATATTTTTAATT
31500886 TTTTATAA-ATTTTTAATT
1 TTTTATAATATTTTTAATT
31500904 TTTTA
1 TTTTA
31500909 AAATGTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 25 0.74
19 9 0.26
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTATAATATTTTTAATT
Found at i:31500898 original size:10 final size:9
Alignment explanation
Indices: 31500816--31500906 Score: 61
Period size: 8 Copynumber: 10.4 Consensus size: 9
31500806 GCTGTACTAC
31500816 TTTTATAAT
1 TTTTATAAT
*
31500825 TTTTA-AAA
1 TTTTATAAT
31500833 TTTTA-AAT
1 TTTTATAAT
31500841 TATTTAT-A-
1 T-TTTATAAT
31500849 TTTTATAAT
1 TTTTATAAT
*
31500858 AATTTTAT-TT
1 --TTTTATAAT
31500868 TTTTATAAT
1 TTTTATAAT
*
31500877 TTTT-TGACT
1 TTTTAT-AAT
*
31500886 TTTTATAAA
1 TTTTATAAT
31500895 TTTT-TAAT
1 TTTTATAAT
31500903 TTTT
1 TTTT
31500907 TAAAATGTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
7 5 0.08
8 26 0.40
9 26 0.40
10 2 0.03
11 6 0.09
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:31500910 original size:16 final size:16
Alignment explanation
Indices: 31500816--31500910 Score: 64
Period size: 17 Copynumber: 5.4 Consensus size: 16
31500806 GCTGTACTAC
**
31500816 TTTTATAATTTTTAAAA
1 TTTTA-AATTTTTAATT
31500833 TTTTAAATTATTTATATT
1 TTTTAAATT-TTTA-ATT
* * *
31500851 TTATAATAATTTTATTT
1 TTTTAA-ATTTTTAATT
*
31500868 TTTTATAATTTTTTGACTT
1 TTTTA-AA-TTTTT-AATT
31500887 TTTATAAATTTTTAATT
1 TTT-TAAATTTTTAATT
31500904 TTTTAAA
1 TTTTAAA
31500911 ATGTCAAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
16 8 0.13
17 22 0.35
18 20 0.32
19 10 0.16
20 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (16 bp):
TTTTAAATTTTTAATT
Found at i:31500955 original size:21 final size:21
Alignment explanation
Indices: 31500914--31500956 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
31500904 TTTTAAAATG
* *
31500914 TCAAAATATTTTTTTTATTTT
1 TCAAAAAATTTTATTTATTTT
31500935 TCAAAAAATTTTGATTT-TTTT
1 TCAAAAAATTTT-ATTTATTTT
31500956 T
1 T
31500957 AATTTTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
TCAAAAAATTTTATTTATTTT
Found at i:31511081 original size:40 final size:40
Alignment explanation
Indices: 31511040--31511396 Score: 468
Period size: 40 Copynumber: 8.9 Consensus size: 40
31511030 ACACAGACAA
* *
31511040 AAGCTCATAAGAGCTAATCCAATCGAAACACGCCAAACAA
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
* *
31511080 AAGCTCATAAGAGCTGATCCAA-CTGAAACATGCCAAATAG
1 AAGCTCATAAGAGCTGATCCAATC-GAAACACGCCAAACAG
* *
31511120 AAGCTCATAAGAGTTGATCCAATCGAAACA-GACCAAATAG
1 AAGCTCATAAGAGCTGATCCAATCGAAACACG-CCAAACAG
* * *
31511160 AAGCTCATAAGAGCTGATCCAACCAAAACACGCCAAATAG
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
** * *
31511200 AAGCTCATAATCGCTGATCCAGTCGAAACACGCCACACAG
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
* *
31511240 AAGCTCATAAGAGCTGATCCAATCGAAACACACCAAACAA
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
* *
31511280 AAGCTCATAAGAGCTGATCC-AGCTGAAACACGCCGAACAG
1 AAGCTCATAAGAGCTGATCCAATC-GAAACACGCCAAACAG
* * * *
31511320 AATCTTATAAGAGCTTATCCAATCGAAACACGCCAAATAG
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
*
31511360 AAGCTCATAAGAGCTTATCCAATCGAAACACGCCAAA
1 AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAA
31511397 AGAGAGTATA
Statistics
Matches: 278, Mismatches: 33, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
39 4 0.01
40 270 0.97
41 4 0.01
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.15
Consensus pattern (40 bp):
AAGCTCATAAGAGCTGATCCAATCGAAACACGCCAAACAG
Found at i:31511982 original size:20 final size:20
Alignment explanation
Indices: 31511954--31511998 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
31511944 TAATGTGTCT
* *
31511954 TGTCCTAACCGAATTAGTTG
1 TGTCTTAACCGAATTAATTG
**
31511974 TGTCTTAACTTAATTAATTG
1 TGTCTTAACCGAATTAATTG
31511994 TGTCT
1 TGTCT
31511999 AGTTTTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (20 bp):
TGTCTTAACCGAATTAATTG
Found at i:31514721 original size:12 final size:12
Alignment explanation
Indices: 31514689--31514713 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31514679 TCATCCTGAT
31514689 TCAGAACTTATA
1 TCAGAACTTATA
31514701 TCAGAACTTATA
1 TCAGAACTTATA
31514713 T
1 T
31514714 TATAACTTGA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCAGAACTTATA
Found at i:31520836 original size:20 final size:20
Alignment explanation
Indices: 31520813--31520888 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
31520803 TGCATGCAGT
*
31520813 CAGGAGCACCGAAGTGCAAA
1 CAGGGGCACCGAAGTGCAAA
* * **
31520833 CAGGGGCACGGATGTGTGAA
1 CAGGGGCACCGAAGTGCAAA
* *
31520853 TAGGGGCACCAAAGTGCAAA
1 CAGGGGCACCGAAGTGCAAA
* *
31520873 CAGGGACATCGAAGTG
1 CAGGGGCACCGAAGTG
31520889 TAGTCTGGGG
Statistics
Matches: 41, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.36, T:0.11
Consensus pattern (20 bp):
CAGGGGCACCGAAGTGCAAA
Found at i:31527033 original size:102 final size:102
Alignment explanation
Indices: 31526895--31527090 Score: 331
Period size: 102 Copynumber: 1.9 Consensus size: 102
31526885 GAACGTGTTC
*
31526895 TTTTTAGGATAATCAGTGTCTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTATAGAAGTGCTGA
1 TTTTTAGGATAATCAGTGTCTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTACAGAAGTGCTGA
* *
31526960 TCTTGACCTTGC-CAGAATCAGGAAAGGAAAGTGTTTT
66 TCCTGACCTTGCTC-GAATCAAGAAAGGAAAGTGTTTT
* *
31526997 TTTTTGGGATAATCAGTGTTTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTACAGAAGTGCTGA
1 TTTTTAGGATAATCAGTGTCTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTACAGAAGTGCTGA
31527062 TCCTGACCTTGCTCGAATCAAGAAAGGAA
66 TCCTGACCTTGCTCGAATCAAGAAAGGAA
31527091 TTTATGGTAT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 87 0.99
103 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.33
Consensus pattern (102 bp):
TTTTTAGGATAATCAGTGTCTGGAAAGTTTTGAGAAGTTGAAAGTCATGTTTACAGAAGTGCTGA
TCCTGACCTTGCTCGAATCAAGAAAGGAAAGTGTTTT
Found at i:31528566 original size:104 final size:104
Alignment explanation
Indices: 31528379--31528749 Score: 595
Period size: 104 Copynumber: 3.6 Consensus size: 104
31528369 TGTATATAAA
** * * **
31528379 AGGGGTTGCTGTGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAGGTGCG-TGATCCACCATACC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTATT
* *
31528442 TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCTCG
65 TTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
31528483 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTT
31528548 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
31528587 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTT
31528652 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * **
31528691 AAGGGTTGCTAAGTGCTGATTCCCCGATTT-AGTGGTGGTGCTAAGTGCGGGATCCACCG
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCG
31528750 ATAACGGTTA
Statistics
Matches: 253, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
103 26 0.10
104 187 0.74
105 39 0.15
106 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTT
TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:31546101 original size:3 final size:3
Alignment explanation
Indices: 31546093--31546144 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
31546083 AAATTAGTTA
*
31546093 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31546141 AAT A
1 AAT A
31546145 GAAAAAAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31551340 original size:48 final size:49
Alignment explanation
Indices: 31551276--31551370 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
31551266 AAGGTGGAAG
* *
31551276 TATGTGACAGTTTATCTGC-ATTAAT-GTGACACTGTTCACAATTTTGAT
1 TATGTGACAGTATATCTGCGATT-ATGGTGACACTGTTCACAAATTTGAT
* *
31551324 TATGTGGCAGTATATCTGCGATTTTGGTGACACTGTTCACAAATTTG
1 TATGTGACAGTATATCTGCGATTATGGTGACACTGTTCACAAATTTG
31551371 GTGTGTTGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
48 18 0.44
49 23 0.56
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (49 bp):
TATGTGACAGTATATCTGCGATTATGGTGACACTGTTCACAAATTTGAT
Found at i:31553372 original size:27 final size:27
Alignment explanation
Indices: 31553313--31553378 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
31553303 CCTAAACTGA
*
31553313 TATAAAATGGCTGTTATGCCCCCACGT
1 TATAAAATGACTGTTATGCCCCCACGT
** * *
31553340 GGTAAAATGACTGTTATGCCCCTATGT
1 TATAAAATGACTGTTATGCCCCCACGT
31553367 TATAAAATGACT
1 TATAAAATGACT
31553379 ACATGCTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (27 bp):
TATAAAATGACTGTTATGCCCCCACGT
Found at i:31555527 original size:3 final size:3
Alignment explanation
Indices: 31555519--31555572 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
31555509 AAGGGCTCAA
* * * *
31555519 ATT ATT ATT ATC ATT ATC ATT ACT ATT ATT ATT AAAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
31555565 ATT ATT AT
1 ATT ATT AT
31555573 CTTTTTTACA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:31555686 original size:3 final size:3
Alignment explanation
Indices: 31555678--31555703 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31555668 AAAAGAGTAA
31555678 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
31555704 GCATTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:31556060 original size:144 final size:145
Alignment explanation
Indices: 31555905--31556181 Score: 427
Period size: 144 Copynumber: 1.9 Consensus size: 145
31555895 TCTTGGGAAT
* *
31555905 TTTTTTTAAAAAAATG-GAAAGTTTAGATTTTAAAAATAAAAATATATTTTTTTAGTCATTTCAA
1 TTTTTTTAAAAAAAAGAGAAAGTTTAGATTTTAAAAATAAAAATAT-GTTTTTTAGTCATTTCAA
* *
31555969 AGG-AAATTTTAAA-ATTTTAAAACAAAGTTATGAT-TTTTTTAACTATTTCGAAATAAAAGCTT
65 AGGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAA-CTT
31556031 TGATTTAAAAAAAAATA
129 TGATTTAAAAAAAAATA
* **
31556048 TTTTTTTAAAAAAAAGAGAAAGTTTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATTTTTAA
1 TTTTTTTAAAAAAAAGAGAAAGTTTAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTCAAA
* *
31556113 GGAAAAATTTAAATTTTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCGAAATAAAACTTTG
66 GGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAACTTTG
31556178 ATTT
131 ATTT
31556182 TTAAAGAAAG
Statistics
Matches: 121, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
143 33 0.27
144 37 0.31
145 28 0.23
146 23 0.19
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.43
Consensus pattern (145 bp):
TTTTTTTAAAAAAAAGAGAAAGTTTAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTCAAA
GGAAAAATTTAAATATTTTAAAACAAAGTTATGATCTTTTTCAACTATTTCGAAATAAAACTTTG
ATTTAAAAAAAAATA
Found at i:31556219 original size:21 final size:20
Alignment explanation
Indices: 31556169--31556220 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
31556159 ATTTCGAAAT
31556169 AAAACTTTGA-TTTTTAAAG
1 AAAACTTTGATTTTTTAAAG
* *
31556188 -AAAGTAGTGATTTTTTAAAAG
1 AAAACT-TTGATTTTTT-AAAG
31556209 AAAACTTTGATT
1 AAAACTTTGATT
31556221 CTACAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 5 0.20
21 9 0.36
22 4 0.16
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (20 bp):
AAAACTTTGATTTTTTAAAG
Found at i:31558273 original size:20 final size:21
Alignment explanation
Indices: 31558243--31558281 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
31558233 ATTTTTGCAT
*
31558243 ATTAGATTTATTTATTTGTGC
1 ATTAGATTTATTTAATTGTGC
31558264 ATTA-ATTTATTTAATTGT
1 ATTAGATTTATTTAATTGT
31558282 CTAATGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (21 bp):
ATTAGATTTATTTAATTGTGC
Found at i:31566174 original size:20 final size:20
Alignment explanation
Indices: 31566146--31566212 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
31566136 GCAAGTTAAG
31566146 ATGAGCTAAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
* * *** *
31566166 ATAAGCTAAGGACAAGCTCA
1 ATGAGCTAAAGTTGAGCTGA
31566186 ATGAGCTAAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTGA
31566206 ATGAGCT
1 ATGAGCT
31566213 TCAAGTAGAG
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.22
Consensus pattern (20 bp):
ATGAGCTAAAGTTGAGCTGA
Found at i:31571754 original size:20 final size:20
Alignment explanation
Indices: 31571697--31571763 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
31571687 GCAAGTTAAG
* *
31571697 ATGAGCTGAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAGCTAA
* * *** *
31571717 ATAAGCTAAGGACAAGCTCA
1 ATGAGCTAAAGTTGAGCTAA
31571737 ATGAGCTAAAGTTGAGCTAA
1 ATGAGCTAAAGTTGAGCTAA
31571757 ATGAGCT
1 ATGAGCT
31571764 TGAAGTAGAG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.22
Consensus pattern (20 bp):
ATGAGCTAAAGTTGAGCTAA
Found at i:31578609 original size:17 final size:18
Alignment explanation
Indices: 31578587--31578623 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31578577 CCCACTCTGA
*
31578587 CTTCCCT-TTTCCCCTTT
1 CTTCCCTATTTCCACTTT
31578604 CTTCCCTATTTCCACTTT
1 CTTCCCTATTTCCACTTT
31578622 CT
1 CT
31578624 CCCATTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (18 bp):
CTTCCCTATTTCCACTTT
Found at i:31578787 original size:17 final size:17
Alignment explanation
Indices: 31578765--31578801 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
31578755 CACACTTCCC
*
31578765 TTCTTCCCCTTTCCTTT
1 TTCTTCCCCCTTCCTTT
31578782 TTCTTCCCCCTTCCTTT
1 TTCTTCCCCCTTCCTTT
31578799 TTC
1 TTC
31578802 CCCCTCCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (17 bp):
TTCTTCCCCCTTCCTTT
Found at i:31579000 original size:3 final size:3
Alignment explanation
Indices: 31578992--31579055 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
31578982 TTTTTCTTTT
* * *
31578992 TTA TTA TTA -TA TTA TTA TTT TTA TTA TTCC TTA TTT TTA TTTA CTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA -TTA
31579039 TTA TTA TTTA TT- TTA TT
1 TTA TTA -TTA TTA TTA TT
31579056 TTTACTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
2 4 0.08
3 34 0.69
4 11 0.22
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Done.