Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 11 of 438
Found at i:3136270 original size:11 final size:11
Alignment explanation
Indices: 3136205--3136271 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
3136195 ACATACAATG
*
3136205 TATATAAAAAA
1 TATATAATAAA
*
3136216 TATATAATATA
1 TATATAATAAA
* *
3136227 TATACAATATA
1 TATATAATAAA
* *
3136238 TACAT-ATCTAA
1 TATATAAT-AAA
3136249 TATAATAATAAA
1 TAT-ATAATAAA
3136261 TATATAATAAA
1 TATATAATAAA
3136272 AACTATTGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 2 0.05
11 33 0.75
12 7 0.16
13 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (11 bp):
TATATAATAAA
Found at i:3136372 original size:21 final size:20
Alignment explanation
Indices: 3136337--3136375 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3136327 AAAAAATATA
*
3136337 GTATTAAAAATATATATAAC
1 GTATAAAAAATATATATAAC
3136357 GTATAAAAATATATATATA
1 GTATAAAAA-ATATATATA
3136376 CATAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (20 bp):
GTATAAAAAATATATATAAC
Found at i:3136488 original size:3 final size:3
Alignment explanation
Indices: 3136480--3136540 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
3136470 ATGACAACAC
3136480 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3136528 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
3136541 AATTAAAGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3137169 original size:21 final size:22
Alignment explanation
Indices: 3137119--3137172 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
3137109 AAAAAAATTC
* *
3137119 TAATTTTTTGTTTTATTTTTTA
1 TAATTTTTTGTGTTATTTGTTA
3137141 TATCATTTTTTGTGTT-TTTGTTA
1 TA--ATTTTTTGTGTTATTTGTTA
3137164 TAATTTTTT
1 TAATTTTTT
3137173 ACTTGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 7 0.25
22 2 0.07
23 8 0.29
24 11 0.39
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (22 bp):
TAATTTTTTGTGTTATTTGTTA
Found at i:3137867 original size:18 final size:17
Alignment explanation
Indices: 3137821--3137879 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 17
3137811 TCACGTGTAA
*
3137821 AAAATTTAGAAAATACTT
1 AAAATTTAAAAAATA-TT
3137839 GAAAA-TTAAAAAGATATT
1 -AAAATTTAAAAA-ATATT
3137857 AAAATTTAAAAAAATATAT
1 AAAATTT-AAAAAATAT-T
3137876 AAAA
1 AAAA
3137880 ACTGTTTCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 4 0.11
18 14 0.40
19 17 0.49
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (17 bp):
AAAATTTAAAAAATATT
Found at i:3141047 original size:5 final size:5
Alignment explanation
Indices: 3141037--3141061 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3141027 AATAAGGAAA
3141037 GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT
3141062 TGTGCTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GATAT
Found at i:3141921 original size:66 final size:66
Alignment explanation
Indices: 3141790--3141927 Score: 204
Period size: 66 Copynumber: 2.1 Consensus size: 66
3141780 TAAAAGCTTG
* * *
3141790 GACAAGGCCCCCAAAAAGGGTTATTAAATCGAGAGGAGGACATCAGAAAACAAAGTAGAACAAGG
1 GACAAGGCCCCCAAAAAGGGTTATTAAATCAAGAGGAGGACATCAAAAAACAAAGCAGAACAAGG
3141855 A
66 A
* * * *
3141856 GACAAGGCCCCCAAAAGGGGTTATTAAATCAAGAGGAGGACATCAAAAAATAGAGCAGAATAAGG
1 GACAAGGCCCCCAAAAAGGGTTATTAAATCAAGAGGAGGACATCAAAAAACAAAGCAGAACAAGG
3141921 A
66 A
3141922 GTACAA
1 G-ACAA
3141928 CGACCAACCA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
66 60 0.94
67 4 0.06
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (66 bp):
GACAAGGCCCCCAAAAAGGGTTATTAAATCAAGAGGAGGACATCAAAAAACAAAGCAGAACAAGG
A
Found at i:3142138 original size:105 final size:109
Alignment explanation
Indices: 3142002--3142300 Score: 356
Period size: 116 Copynumber: 2.7 Consensus size: 109
3141992 AACAGACAAC
** *
3142002 CAAAGCACGGGAAACAAAGGACAAAGCTAGAAACATGACCAAAAGAGTTTAGTCAACAAAGTAGT
1 CAAAGCACGGGAAACAGGGGACAAAGCTAGAAACATGACCAAAAGAGTTTGGTCAACAAAGTAGT
* *
3142067 CAATGACTCAGAAT-G-A-TGA-CTCGGTTTGGACAAAGAAAGA
66 CAATGACTCAGAATAGAATTGAGCTAGGCTTGGACAAAGAAAGA
* * * * *
3142107 CAAAGCACGAGAAATAGGGGACAAAGCTAGAAACAAGACCAAAAGAGTTTGGTCAATAGAGTAGT
1 CAAAGCACGGGAAACAGGGGACAAAGCTAGAAACATGACCAAAAGAGTTTGGTCAACAAAGTAGT
* * *
3142172 TAATGACTCAGAATAGATTAAGTTTGATGGCTAGGCTTGGATAAAGAAAGG
66 CAATGACTCAGAATAG---AA--TTGA--GCTAGGCTTGGACAAAGAAAGA
* *
3142223 CAAAGCACGGGAAACAGAGGG-CAAAGTTAGAAACATGACCAAAAGAGTTTGGTCAACAAAGTAT
1 CAAAGCACGGGAAACAG-GGGACAAAGCTAGAAACATGACCAAAAGAGTTTGGTCAACAAAGTAG
3142287 TCAATGACTCAGAA
65 TCAATGACTCAGAA
3142301 CGGATTGAGT
Statistics
Matches: 161, Mismatches: 21, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
105 70 0.43
106 1 0.01
110 1 0.01
113 3 0.02
116 83 0.52
117 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.17
Consensus pattern (109 bp):
CAAAGCACGGGAAACAGGGGACAAAGCTAGAAACATGACCAAAAGAGTTTGGTCAACAAAGTAGT
CAATGACTCAGAATAGAATTGAGCTAGGCTTGGACAAAGAAAGA
Found at i:3142293 original size:116 final size:116
Alignment explanation
Indices: 3142092--3142343 Score: 337
Period size: 116 Copynumber: 2.2 Consensus size: 116
3142082 ATGACTCGGT
* *
3142092 TTGGACAAAGAAAGACAAAGCACGAGAAATAGGGGACAAAGCTAGAAACAAGACCAAAAGAGTTT
1 TTGGACAAAGAAAGGCAAAGCACGAGAAACAGGGGACAAAGCTAGAAACAAGACCAAAAGAGTTT
* * * *
3142157 GGTCAATAGAGTAGTTAATGACTCAGAATAGATTAAGTTTGATGGCTAGGC
66 GGTCAACAAAGTAGTTAATGACTCAGAACAGATTAAGTATGATGGCTAGGC
* * * *
3142208 TTGGATAAAGAAAGGCAAAGCACGGGAAACAGAGGG-CAAAGTTAGAAACATGACCAAAAGAGTT
1 TTGGACAAAGAAAGGCAAAGCACGAGAAACAG-GGGACAAAGCTAGAAACAAGACCAAAAGAGTT
* * * * *
3142272 TGGTCAACAAAGTA-TTCAATGACTCAGAACGGATTGAGTATGTTGGTTTGGC
65 TGGTCAACAAAGTAGTT-AATGACTCAGAACAGATTAAGTATGATGGCTAGGC
3142324 TTGGACAAAGAAAGGCAAAG
1 TTGGACAAAGAAAGGCAAAG
3142344 TATGGGGGAA
Statistics
Matches: 118, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
115 2 0.02
116 113 0.96
117 3 0.03
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (116 bp):
TTGGACAAAGAAAGGCAAAGCACGAGAAACAGGGGACAAAGCTAGAAACAAGACCAAAAGAGTTT
GGTCAACAAAGTAGTTAATGACTCAGAACAGATTAAGTATGATGGCTAGGC
Found at i:3142403 original size:5 final size:5
Alignment explanation
Indices: 3142393--3142417 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3142383 AAGGGCAAAC
3142393 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
3142418 TGGAGTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:3143088 original size:5 final size:5
Alignment explanation
Indices: 3143078--3143119 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
3143068 ATAAGAATAT
3143078 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
3143120 ACTAAACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:3144329 original size:13 final size:13
Alignment explanation
Indices: 3144304--3144346 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
3144294 AGTGATTTTG
3144304 AATAAGA-ATTAA
1 AATAAGATATTAA
3144316 AATAAGATATTAA
1 AATAAGATATTAA
3144329 AATGAA-ATATTAA
1 AAT-AAGATATTAA
3144342 AATAA
1 AATAA
3144347 TAATAATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.31
13 18 0.62
14 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (13 bp):
AATAAGATATTAA
Found at i:3148250 original size:493 final size:492
Alignment explanation
Indices: 3147322--3148295 Score: 1547
Period size: 493 Copynumber: 2.0 Consensus size: 492
3147312 CCTTTACATC
* *
3147322 CTTCATTGATCCCTCGAGTTTACCCACACATTCCTCTACTGCTAACAGCGTCTCCCTCAAAGAAT
1 CTTCATTGATCCCTCGAGTTTACCCACACATTCCTCTACTGCTAACAACATCTCCCTCAAAGAAT
*
3147387 TTTTGACCCACCTTTGTTCAAAATCTTCTTTTGACATCCCAACGGTTCCTTCGAACCAATAGCTC
66 TTTTGACCCACCTTTGTTCAAAATCTTCTTTCGACATCCCAACGGTTCCTTCGAACCAATAGCTC
* * * *
3147452 GGATACCACTTGTCACGAGGCTAGATCTTTCGTCTTGCGATTCGTGAGGCCTTAGGCGATTCGTT
131 AGATACCACTTGTCACGAGGCTAGATCTTTCGTCTCGCGATCCGTGAGGCCTTAGGCGATCCGTT
* * * *
3147517 CGCCCAAATTCTCCTAAGTCAGCCTTTACCCAAGTGAGGATTTCTTTAAAACTCCTCCAAGGCAC
196 CGCCCAAACTCACCTAAGTCAACCTTTACCCAAGTGAGGATTCCTTTAAAACTCCTCCAAGGCAC
3147582 CAATTTGTATAGTAAAAGTGATTTATGCCAAAAGAAGCAACAAAAGAACAACAGAAAGAACGCAC
261 CAATTTGTATAGTAAAAGTGATTTATGCCAAAAGAAGCAACAAAAGAACAACAGAAAGAACGCAC
* * * * *
3147647 ATAAGGTGTTTGAGTAAATGCTTTCAATATCCTCTTATTGACAAAGATTAATGAAACAATGAATA
326 ACAAGGTGTTTGAGTAAATACTCTCAATATCCTCTTATTCACAAAGAATAATGAAACAATGAATA
*
3147712 GAGTGAGTACAAATGAGGGGGTGGCTCTCTATTTATAGCTGAGCTCCCTTAAAACCAACGGTCAA
391 GAGTGAGTACAAATGAGGGGGTGGCTCTCTATTTATAGCTGAGCTCCC-CAAAACCAACGGTCAA
*
3147777 GATTACAATACATCAAAGGACGAGATTACCTACACGTT
455 GATTAAAATACATCAAAGGACGAGATTACCTACACGTT
*
3147815 CTTCATTGATCCCTCGAGTTTACCCACACATTCCTCTACTGCTGACAACATCTCCCTCAAA-AAC
1 CTTCATTGATCCCTCGAGTTTACCCACACATTCCTCTACTGCTAACAACATCTCCCTCAAAGAA-
* * * *
3147879 TTTTTGGCCCACCTTTTTTCAAACTCTTCTTTCGACATCCCAATGGTTCCTTTC-AACCAATAGC
65 TTTTTGACCCACCTTTGTTCAAAATCTTCTTTCGACATCCCAACGGTTCC-TTCGAACCAATAGC
* * * *
3147943 TCAGATACCACTTGTCACGGGGCTAGATCTTTCGTCTCGCGATCCGTGCGGTCTTAGGTGATCCG
129 TCAGATACCACTTGTCACGAGGCTAGATCTTTCGTCTCGCGATCCGTGAGGCCTTAGGCGATCCG
* * * * * *
3148008 TTCGTCTAAACTCACCTAAGTCAACCTTTACTCAAGTGATGATTCCTTTAGAACTCCTCCAATGC
194 TTCGCCCAAACTCACCTAAGTCAACCTTTACCCAAGTGAGGATTCCTTTAAAACTCCTCCAAGGC
* *
3148073 ACCAATTTGTATAGTAGAAGTGATTTATGCCTAAAGAAGCAACAAAAGAACAACAGAAAGAACGC
259 ACCAATTTGTATAGTAAAAGTGATTTATGCCAAAAGAAGCAACAAAAGAACAACAGAAAGAACGC
3148138 ACACAAGGTGTTTGAGTAAATACTCTCAATATCCTCTTATTCACAAAGAATAATGAAACAATGAA
324 ACACAAGGTGTTTGAGTAAATACTCTCAATATCCTCTTATTCACAAAGAATAATGAAACAATGAA
* * * *
3148203 TGGAGTGAGTACAAATGAGGGGGTGGCTTTCTATTTATAGTTGAGCTCCCCAACACCAACGGTCA
389 TAGAGTGAGTACAAATGAGGGGGTGGCTCTCTATTTATAGCTGAGCTCCCCAAAACCAACGGTCA
*
3148268 AGATTAAAATACATCAACGGACGAGATT
454 AGATTAAAATACATCAAAGGACGAGATT
3148296 TATCCTATCC
Statistics
Matches: 439, Mismatches: 40, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
492 41 0.09
493 395 0.90
494 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (492 bp):
CTTCATTGATCCCTCGAGTTTACCCACACATTCCTCTACTGCTAACAACATCTCCCTCAAAGAAT
TTTTGACCCACCTTTGTTCAAAATCTTCTTTCGACATCCCAACGGTTCCTTCGAACCAATAGCTC
AGATACCACTTGTCACGAGGCTAGATCTTTCGTCTCGCGATCCGTGAGGCCTTAGGCGATCCGTT
CGCCCAAACTCACCTAAGTCAACCTTTACCCAAGTGAGGATTCCTTTAAAACTCCTCCAAGGCAC
CAATTTGTATAGTAAAAGTGATTTATGCCAAAAGAAGCAACAAAAGAACAACAGAAAGAACGCAC
ACAAGGTGTTTGAGTAAATACTCTCAATATCCTCTTATTCACAAAGAATAATGAAACAATGAATA
GAGTGAGTACAAATGAGGGGGTGGCTCTCTATTTATAGCTGAGCTCCCCAAAACCAACGGTCAAG
ATTAAAATACATCAAAGGACGAGATTACCTACACGTT
Found at i:3149797 original size:12 final size:11
Alignment explanation
Indices: 3149773--3149802 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
3149763 CATTTTGTTC
3149773 TTTAGTTTCTTT
1 TTTA-TTTCTTT
3149785 TTTATTTCTTT
1 TTTATTTCTTT
3149796 TTTATTT
1 TTTATTT
3149803 TTGTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTATTTCTTT
Found at i:3150759 original size:2 final size:2
Alignment explanation
Indices: 3150752--3150785 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3150742 TTATCTCTTT
3150752 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3150786 TAGGTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3150882 original size:2 final size:2
Alignment explanation
Indices: 3150875--3150909 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3150865 TTCATTTATG
3150875 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3150910 GTTTGATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3154064 original size:47 final size:47
Alignment explanation
Indices: 3153945--3154064 Score: 125
Period size: 53 Copynumber: 2.4 Consensus size: 47
3153935 AATTCATTTT
* *
3153945 AAATATTAAA-ATTAAAATATTTTAAAAAAAATTTAAAGTTAAATTCA
1 AAATA-TAAATATTAAAATAATTTAAAAAAAATTTAAAGTCAAATTCA
* *
3153992 AAATACAAATAAATATATAAAAATAATTTAAGAAAAATTTGAAGTCAAATTCA
1 AAAT----ATAAATAT-T-AAAATAATTTAAAAAAAATTTAAAGTCAAATTCA
*
3154045 AAATATAAATATTAGAATAA
1 AAATATAAATATTAAAATAA
3154065 CAATAGGATT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
47 10 0.16
48 1 0.02
49 8 0.13
50 4 0.07
51 3 0.05
52 1 0.02
53 34 0.56
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (47 bp):
AAATATAAATATTAAAATAATTTAAAAAAAATTTAAAGTCAAATTCA
Found at i:3158519 original size:22 final size:22
Alignment explanation
Indices: 3158493--3158535 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3158483 TATAATAATA
3158493 AAAAACTTTATAACATATTTTG
1 AAAAACTTTATAACATATTTTG
3158515 AAAAACTTTATAACATATTTT
1 AAAAACTTTATAACATATTTT
3158536 AACTTAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAAACTTTATAACATATTTTG
Found at i:3164050 original size:21 final size:22
Alignment explanation
Indices: 3163988--3164050 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
3163978 ATAATACATT
*
3163988 TAAAATATTAAAAACATT-AAAA
1 TAAAATTTTAAAAA-ATTGAAAA
*
3164010 TAAATATTTTCAATAAATTGAAAA
1 TAAA-ATTTT-AAAAAATTGAAAA
3164034 T-AAATTTTAAAAAATTG
1 TAAAATTTTAAAAAATTG
3164051 TGTATACTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 8 0.23
22 9 0.26
23 9 0.26
24 9 0.26
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (22 bp):
TAAAATTTTAAAAAATTGAAAA
Found at i:3164245 original size:21 final size:21
Alignment explanation
Indices: 3164197--3164247 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3164187 TTATGAAATT
3164197 GTAACAAAATAGTAAAAAACAA
1 GTAA-AAAATAGTAAAAAACAA
**
3164219 CCAAAAAATAGTAAGAAAAC-A
1 GTAAAAAATAGTAA-AAAACAA
3164240 GTAAAAAA
1 GTAAAAAA
3164248 ATAGAAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.12
Consensus pattern (21 bp):
GTAAAAAATAGTAAAAAACAA
Found at i:3164246 original size:22 final size:21
Alignment explanation
Indices: 3164197--3164251 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
3164187 TTATGAAATT
*
3164197 GTAACAAAATAGTAAAAAACA
1 GTAAAAAAATAGTAAAAAACA
***
3164218 ACCAAAAAATAGTAAGAAAACA
1 GTAAAAAAATAGTAA-AAAACA
3164240 GTAAAAAAATAG
1 GTAAAAAAATAG
3164252 AAGTTTCTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (21 bp):
GTAAAAAAATAGTAAAAAACA
Found at i:3164690 original size:18 final size:18
Alignment explanation
Indices: 3164657--3164691 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3164647 ATACAACTTG
*
3164657 TATGCATGCTGTAGCAAT
1 TATGCATGCTGCAGCAAT
*
3164675 TATGCATGTTGCAGCAA
1 TATGCATGCTGCAGCAA
3164692 CATATTTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (18 bp):
TATGCATGCTGCAGCAAT
Found at i:3166196 original size:14 final size:14
Alignment explanation
Indices: 3166157--3166199 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
3166147 CAATTTAATC
*
3166157 ATTTTATTTTTATAA
1 ATTTTAATTTTA-AA
3166172 ATTTTATATTTTAAA
1 ATTTTA-ATTTTAAA
3166187 ATTTTAATTTTAA
1 ATTTTAATTTTAA
3166200 TTCAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.27
15 14 0.54
16 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTAATTTTAAA
Found at i:3168898 original size:14 final size:16
Alignment explanation
Indices: 3168870--3168902 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3168860 TTTAAGGGCA
3168870 AAAAATATATATACAT
1 AAAAATATATATACAT
3168886 AAAAATAT-T-TACAT
1 AAAAATATATATACAT
3168900 AAA
1 AAA
3168903 GCTATATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATATATATACAT
Found at i:3170680 original size:20 final size:18
Alignment explanation
Indices: 3170655--3170691 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
3170645 ATTGCTAAGT
3170655 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
3170675 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
3170692 TAGGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:3171300 original size:46 final size:46
Alignment explanation
Indices: 3171248--3171423 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
3171238 TGGTTGAGCA
*
3171248 TCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
3171294 TTCGAACTCGTTGAGTTGAGTCTGAG-T---TTGTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
* *
3171339 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
3171387 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3171424 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 12, Indels: 22
0.76 0.09 0.16
Matches are distributed among these distances:
42 6 0.06
43 5 0.05
45 2 0.02
46 59 0.55
47 23 0.21
48 2 0.02
50 4 0.04
51 6 0.06
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3171404 original size:93 final size:93
Alignment explanation
Indices: 3171245--3171414 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
3171235 GGATGGTTGA
* **
3171245 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
3171310 TGAGTCTGAGTTTGTGAGATGTAACTAG
66 TGAGTCCGAGTTTGTGAGATGTAACTAG
* * *
3171338 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3171403 TGAGTCCGAGTT
66 TGAGTCCGAGTT
3171415 CACTTATGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTTGTGAGATGTAACTAG
Found at i:3174023 original size:15 final size:16
Alignment explanation
Indices: 3173992--3174041 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
3173982 GGTATTTGGA
3173992 TTTTTATTTGTGTGTT
1 TTTTTATTTGTGTGTT
*
3174008 TTTTTATTTTTG-GTT
1 TTTTTATTTGTGTGTT
* * *
3174023 TTTTAATTTCTATGTT
1 TTTTTATTTGTGTGTT
3174039 TTT
1 TTT
3174042 ATTCTAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.10, C:0.02, G:0.12, T:0.76
Consensus pattern (16 bp):
TTTTTATTTGTGTGTT
Found at i:3174885 original size:18 final size:18
Alignment explanation
Indices: 3174859--3174894 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3174849 CCATTTAGGA
*
3174859 CACTATTCATGTATACAG
1 CACTATTCACGTATACAG
*
3174877 CACTGTTCACGTATACAG
1 CACTATTCACGTATACAG
3174895 TAGTTGGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (18 bp):
CACTATTCACGTATACAG
Found at i:3179684 original size:21 final size:21
Alignment explanation
Indices: 3179660--3179699 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3179650 TGAGAACAAA
3179660 ACGA-AATAAAATGAAATAAAT
1 ACGATAAT-AAATGAAATAAAT
*
3179681 ACGATGATAAATGAAATAA
1 ACGATAATAAATGAAATAA
3179700 TAAAGCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (21 bp):
ACGATAATAAATGAAATAAAT
Found at i:3180190 original size:37 final size:36
Alignment explanation
Indices: 3180149--3180218 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
3180139 TAGTGATAAA
* *
3180149 AATAAAAATAATGACAATGACAATAGAGAGTAATGGC
1 AATAAAAATAATAACAATGAAAATA-AGAGTAATGGC
* *
3180186 AATAATAATAATAATAATGAAAATAAGAGTAAT
1 AATAAAAATAATAACAATGAAAATAAGAGTAAT
3180219 ATTAGTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 8 0.28
37 21 0.72
ACGTcount: A:0.59, C:0.04, G:0.14, T:0.23
Consensus pattern (36 bp):
AATAAAAATAATAACAATGAAAATAAGAGTAATGGC
Found at i:3180194 original size:3 final size:3
Alignment explanation
Indices: 3180186--3180294 Score: 80
Period size: 3 Copynumber: 36.7 Consensus size: 3
3180176 GAGTAATGGC
* * * *
3180186 AAT AAT AAT AAT AAT AAT GAA- AAT AAG AGT AAT ATT AGT AAT ACAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * * * * *
3180232 TA- AAT TAC AAT AGT AA- AGT AGT AGT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3180278 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
3180295 GTTAAATTAA
Statistics
Matches: 84, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
2 4 0.05
3 76 0.90
4 4 0.05
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3180330 original size:8 final size:7
Alignment explanation
Indices: 3180259--3180326 Score: 58
Period size: 6 Copynumber: 10.4 Consensus size: 7
3180249 GTAGTAGTAA
3180259 TAATAA-
1 TAATAAG
3180265 TAATAA-
1 TAATAAG
3180271 TAATAA-
1 TAATAAG
3180277 TAATAA-
1 TAATAAG
3180283 TAATAA-
1 TAATAAG
3180289 TAATAAG
1 TAATAAG
* *
3180296 TTA-AAT
1 TAATAAG
*
3180302 TAATTAG
1 TAATAAG
3180309 TAATGAAG
1 TAAT-AAG
3180317 TAATAAG
1 TAATAAG
3180324 TAA
1 TAA
3180327 ATAAATATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
6 34 0.64
7 13 0.25
8 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (7 bp):
TAATAAG
Found at i:3191153 original size:13 final size:13
Alignment explanation
Indices: 3191130--3191161 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
3191120 CTAATAACAA
3191130 CACCAACTTATAAC
1 CACC-ACTTATAAC
3191144 CACCACTTATAAC
1 CACCACTTATAAC
3191157 CACCA
1 CACCA
3191162 TTAAAGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (13 bp):
CACCACTTATAAC
Found at i:3191817 original size:25 final size:26
Alignment explanation
Indices: 3191773--3191824 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
3191763 AACACTTAAA
*
3191773 AATAATATATATCAATAT-AACTAAC
1 AATAATATAAATCAATATAAACTAAC
3191798 AATAATATAAAT-AATAATAAACTAAC
1 AATAATATAAATCAAT-ATAAACTAAC
3191824 A
1 A
3191825 CTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 3 0.12
25 13 0.54
26 8 0.33
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
AATAATATAAATCAATATAAACTAAC
Found at i:3192715 original size:17 final size:15
Alignment explanation
Indices: 3192680--3192731 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 15
3192670 TTATTTGTAA
3192680 ATTTTAATATATTTTAT
1 ATTTTAA-A-ATTTTAT
3192697 ATTTATAAAATTTTAAT
1 ATTT-TAAAATTTT-AT
*
3192714 ATTTTAAAAATTTAT
1 ATTTTAAAATTTTAT
3192729 ATT
1 ATT
3192732 ACTTTTATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.16
16 13 0.41
17 11 0.34
18 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTAAAATTTTAT
Found at i:3192726 original size:26 final size:26
Alignment explanation
Indices: 3192678--3192729 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3192668 TTTTATTTGT
* *
3192678 AAATTTTAATATATTTTATATTTATA
1 AAATTTTAATATATTTAAAATTTATA
3192704 AAATTTTAATAT-TTTAAAAATTTATA
1 AAATTTTAATATATTT-AAAATTTATA
3192730 TTACTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AAATTTTAATATATTTAAAATTTATA
Found at i:3194377 original size:17 final size:16
Alignment explanation
Indices: 3194344--3194386 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
3194334 TAATTTATTA
3194344 AATAAAA-ATTATCTT
1 AATAAAATATTATCTT
*
3194359 AACTAAAATATTATTTT
1 AA-TAAAATATTATCTT
3194376 AATAAAATATT
1 AATAAAATATT
3194387 TAAATTTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 2 0.08
16 14 0.56
17 9 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAAAATATTATCTT
Found at i:3198986 original size:12 final size:12
Alignment explanation
Indices: 3198971--3199020 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3198961 ATTTAATTTA
3198971 ATATTTATCTAG
1 ATATTTATCTAG
* *
3198983 ATATTAATAT-G
1 ATATTTATCTAG
*
3198994 ATATTTAATTTAG
1 ATATTT-ATCTAG
3199007 -TATTTATCTAG
1 ATATTTATCTAG
3199018 ATA
1 ATA
3199021 ATATTTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
11 11 0.37
12 18 0.60
13 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATTTATCTAG
Found at i:3198992 original size:35 final size:35
Alignment explanation
Indices: 3198951--3199020 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
3198941 TTTAATGAAT
*
3198951 TTAATATTAAATTTAATTTAATATTTATCTAGATA
1 TTAATATGAAATTTAATTTAATATTTATCTAGATA
* *
3198986 TTAATATGATATTTAATTTAGTATTTATCTAGATA
1 TTAATATGAAATTTAATTTAATATTTATCTAGATA
3199021 ATATTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (35 bp):
TTAATATGAAATTTAATTTAATATTTATCTAGATA
Found at i:3199163 original size:13 final size:13
Alignment explanation
Indices: 3199147--3199178 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3199137 AAGTAGAGAG
3199147 AAAATTATTTGAA
1 AAAATTATTTGAA
*
3199160 AAAATTATTTTAA
1 AAAATTATTTGAA
3199173 AAAATT
1 AAAATT
3199179 TCTAAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
AAAATTATTTGAA
Found at i:3199589 original size:38 final size:38
Alignment explanation
Indices: 3199541--3199655 Score: 135
Period size: 38 Copynumber: 3.1 Consensus size: 38
3199531 CAGTCATTTC
* * * * * *
3199541 GAAGATTTGAAATGTTGAACAAATCTTCCCTCTATCTT
1 GAAGCTTTGAAGTGTTGAGCGAATCTTCCCACCATCTT
* *
3199579 GATGCTTTGAAGTGTT-AGGCGAATCTTGCCACCATCTT
1 GAAGCTTTGAAGTGTTGA-GCGAATCTTCCCACCATCTT
3199617 GAAGCTTTGAAGTGTTGAGCGAATCTT-CCACCATCTT
1 GAAGCTTTGAAGTGTTGAGCGAATCTTCCCACCATCTT
3199654 GA
1 GA
3199656 TATGCTACTA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
37 13 0.20
38 52 0.79
39 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (38 bp):
GAAGCTTTGAAGTGTTGAGCGAATCTTCCCACCATCTT
Found at i:3206937 original size:32 final size:32
Alignment explanation
Indices: 3206891--3206956 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
3206881 TAATGTAACA
3206891 TAGCTGCTAAGAATTCAGGGTTTAAATAAGTT
1 TAGCTGCTAAGAATTCAGGGTTTAAATAAGTT
* **
3206923 TAGCTGCTATGAATTTGGGGTTTAAATAAGTT
1 TAGCTGCTAAGAATTCAGGGTTTAAATAAGTT
3206955 TA
1 TA
3206957 TTCATGTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.38
Consensus pattern (32 bp):
TAGCTGCTAAGAATTCAGGGTTTAAATAAGTT
Found at i:3213098 original size:6 final size:6
Alignment explanation
Indices: 3213084--3213120 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
3213074 TGTGTTGTTG
*
3213084 TGTCTT TGTCGT TGTCTT TGTCTT TGTCTT TGTCTT T
1 TGTCTT TGTCTT TGTCTT TGTCTT TGTCTT TGTCTT T
3213121 CACTTTCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.16, G:0.19, T:0.65
Consensus pattern (6 bp):
TGTCTT
Found at i:3213126 original size:18 final size:18
Alignment explanation
Indices: 3213087--3213126 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3213077 GTTGTTGTGT
**
3213087 CTTTGTCGTTGTCTTTGT
1 CTTTGTCGTTGTCTTTCA
*
3213105 CTTTGTCTTTGTCTTTCA
1 CTTTGTCGTTGTCTTTCA
3213123 CTTT
1 CTTT
3213127 CTGACTCTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.20, G:0.15, T:0.62
Consensus pattern (18 bp):
CTTTGTCGTTGTCTTTCA
Found at i:3215317 original size:27 final size:29
Alignment explanation
Indices: 3215276--3215334 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
3215266 CACAATTCTC
*
3215276 TATAACACT-AAAAAAA-AGTAAATAAGT
1 TATAACAATAAAAAAAAGAGTAAATAAGT
3215303 TATAACAATAGAAAAAAAGAGTAAATAAGT
1 TATAACAATA-AAAAAAAGAGTAAATAAGT
3215333 TA
1 TA
3215335 ATTTTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 8 0.29
29 7 0.25
30 13 0.46
ACGTcount: A:0.63, C:0.05, G:0.10, T:0.22
Consensus pattern (29 bp):
TATAACAATAAAAAAAAGAGTAAATAAGT
Found at i:3216767 original size:97 final size:97
Alignment explanation
Indices: 3216595--3216789 Score: 286
Period size: 97 Copynumber: 2.0 Consensus size: 97
3216585 TATGCGGGTG
* * * *
3216595 ACAAGTGATGCTCATTCCATCAATATAAATTACTCATTCAAAAGTAGTGGTTCATGTGTTCTCTA
1 ACAAGTGATGCTCATTCCATCAATATAAATTACTCACTCAAAAATAGCGGTTCACGTGTTCTCTA
3216660 GGTACTGGTTGAATAGTACTATTAATGGAGGT
66 GGTACTGGTTGAATAGTACTATTAATGGAGGT
** *
3216692 ACAAGTGATGCTTGTTCCATCAATATAAATTGC-CTACTCAAAAATAGCGGTTCACGTGTTCTCT
1 ACAAGTGATGCTCATTCCATCAATATAAATTACTC-ACTCAAAAATAGCGGTTCACGTGTTCTCT
*
3216756 AGGTA-TGGGTTGAATAGTACTATTAGTGGAGGT
65 AGGTACT-GGTTGAATAGTACTATTAATGGAGGT
3216789 A
1 A
3216790 TGTTGATGGA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 2 0.02
97 86 0.98
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (97 bp):
ACAAGTGATGCTCATTCCATCAATATAAATTACTCACTCAAAAATAGCGGTTCACGTGTTCTCTA
GGTACTGGTTGAATAGTACTATTAATGGAGGT
Found at i:3222003 original size:39 final size:39
Alignment explanation
Indices: 3221953--3222033 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
3221943 TGTAATTTTT
3221953 AAAAAATTAAATAAAAATTTAATTATTAATCTTAAATGA
1 AAAAAATTAAATAAAAATTTAATTATTAATCTTAAATGA
3221992 AAAAAATTAAATAAAAATTTAATTATTAATCTTAAATGA
1 AAAAAATTAAATAAAAATTTAATTATTAATCTTAAATGA
3222031 AAA
1 AAA
3222034 TTTTTCTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (39 bp):
AAAAAATTAAATAAAAATTTAATTATTAATCTTAAATGA
Found at i:3224881 original size:10 final size:10
Alignment explanation
Indices: 3224858--3224970 Score: 72
Period size: 10 Copynumber: 11.4 Consensus size: 10
3224848 TCATGTGAAA
3224858 AAAAAATTAT
1 AAAAAATTAT
3224868 -AAAAATTAT
1 AAAAAATTAT
**
3224877 AAAAAATCGT
1 AAAAAATTAT
3224887 AAAAAATTAT
1 AAAAAATTAT
*
3224897 GAAAAATATTTT
1 -AAAAA-ATTAT
** *
3224909 TTAAAATCAT
1 AAAAAATTAT
3224919 AAAAAA-TAT
1 AAAAAATTAT
*
3224928 AAAATA-TAT
1 AAAAAATTAT
* *
3224937 -AGAAATATAG
1 AAAAAAT-TAT
3224947 AAAAAATTAT
1 AAAAAATTAT
**
3224957 AAAATTTTAT
1 AAAAAATTAT
3224967 AAAA
1 AAAA
3224971 TCGTAAGAAA
Statistics
Matches: 77, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
8 3 0.04
9 19 0.25
10 38 0.49
11 13 0.17
12 4 0.05
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:3224901 original size:29 final size:28
Alignment explanation
Indices: 3224858--3224986 Score: 100
Period size: 29 Copynumber: 4.4 Consensus size: 28
3224848 TCATGTGAAA
3224858 AAAAAATTATAAAAATTATAAAAAATCGT
1 AAAAAATTAT-AAAATTATAAAAAATCGT
* ** *
3224887 AAAAAATTATGAAAAATATTTTTTAAAATCAT
1 AAAAAATTAT---AAA-ATTATAAAAAATCGT
* *
3224919 AAAAAA-TATAAAATATATAGAAATATAG-
1 AAAAAATTATAAAAT-TATA-AAAAATCGT
* *
3224947 AAAAAATTATAAAATTTTATAAAATCGT
1 AAAAAATTATAAAATTATAAAAAATCGT
3224975 AAGAAAATTATA
1 AA-AAAATTATA
3224987 TAAAATGTAA
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
27 7 0.09
28 16 0.21
29 31 0.40
31 7 0.09
32 17 0.22
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (28 bp):
AAAAAATTATAAAATTATAAAAAATCGT
Found at i:3224982 original size:21 final size:21
Alignment explanation
Indices: 3224957--3225001 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3224947 AAAAAATTAT
*
3224957 AAAATTTTATAAAATCGT-AAG
1 AAAATTATATAAAAT-GTAAAG
3224978 AAAATTATATAAAATGTAAAG
1 AAAATTATATAAAATGTAAAG
3224999 AAA
1 AAA
3225002 CATAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (21 bp):
AAAATTATATAAAATGTAAAG
Found at i:3225031 original size:21 final size:21
Alignment explanation
Indices: 3224973--3225032 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 21
3224963 TTATAAAATC
*
3224973 GTAAGAAAATTATATAAAA-T-
1 GTAAAAAAATTATA-AAAATTA
* *
3224993 GTAAAGAAA-CAT-AAAATTA
1 GTAAAAAAATTATAAAAATTA
3225012 GTAAAAAAATTATAAAAATTA
1 GTAAAAAAATTATAAAAATTA
3225033 TCGTACCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
17 4 0.13
18 1 0.03
19 10 0.32
20 9 0.29
21 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (21 bp):
GTAAAAAAATTATAAAAATTA
Found at i:3225520 original size:51 final size:51
Alignment explanation
Indices: 3225446--3225549 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
3225436 TTTCTTTTTC
* * *
3225446 TTTTTCATTTTAGAATAAACTTTGGCATAATTATTTTCAAATCCCTTGATT
1 TTTTTCATTTTAAAATAAACTTTGACATAAATATTTTCAAATCCCTTGATT
* *
3225497 TTTTTCCTTTTAAAATAAACTTTGATATAAATATTTTCAAATCCCTTGATT
1 TTTTTCATTTTAAAATAAACTTTGACATAAATATTTTCAAATCCCTTGATT
3225548 TT
1 TT
3225550 GATTAAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.50
Consensus pattern (51 bp):
TTTTTCATTTTAAAATAAACTTTGACATAAATATTTTCAAATCCCTTGATT
Found at i:3236823 original size:20 final size:20
Alignment explanation
Indices: 3236786--3236845 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
3236776 CAAATTTAGT
* * *
3236786 ATTTATATTTATATTTTTAGA
1 ATTTAAATTTA-AATTTTAAA
* * *
3236807 ATTTTATTTTAGATTTTAAA
1 ATTTAAATTTAAATTTTAAA
3236827 ATTTAAATTTAAATTTTAA
1 ATTTAAATTTAAATTTTAA
3236846 TATTATTAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTAAATTTAAATTTTAAA
Found at i:3238701 original size:24 final size:24
Alignment explanation
Indices: 3238669--3238716 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3238659 AATGAAGGTG
3238669 AATCAAATCCTGATGGTGCAAGCT
1 AATCAAATCCTGATGGTGCAAGCT
3238693 AATCAAATCCTGATGGTGCAAGCT
1 AATCAAATCCTGATGGTGCAAGCT
3238717 TTCATATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
AATCAAATCCTGATGGTGCAAGCT
Found at i:3246644 original size:47 final size:46
Alignment explanation
Indices: 3246590--3246766 Score: 218
Period size: 47 Copynumber: 3.8 Consensus size: 46
3246580 TGGTTGAGCA
3246590 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGT-GAATG
* *
3246637 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G
* *
3246682 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* *
3246730 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3246767 GCGGGTTACA
Statistics
Matches: 113, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 5 0.04
45 1 0.01
46 37 0.33
47 58 0.51
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
Found at i:3249312 original size:46 final size:45
Alignment explanation
Indices: 3249261--3249427 Score: 203
Period size: 46 Copynumber: 3.7 Consensus size: 45
3249251 GACGAGGGCT
3249261 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGAGCC
* * *
3249307 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGAGAGCC
* * * * * *
3249353 AGTGTCAGACATGTCTGGGACATGCGTCGGCTAC-GA-GATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GAGCC
*
3249397 AGTGTAAGACATGTCTGGGACATGCGTCAGC
1 AGTGTAAGACATGTCTGGGACATGCATCAGC
3249428 ACGGTTACAT
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.02
44 33 0.31
46 70 0.65
47 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGAGAGCC
Found at i:3249357 original size:92 final size:90
Alignment explanation
Indices: 3249210--3249421 Score: 246
Period size: 92 Copynumber: 2.3 Consensus size: 90
3249200 AGATTTGTGT
* * * * *
3249210 GCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGT
3249275 CTGGGACATGCATCAGCCAC-AGTATGAGA
64 CTGGGACATGCATCAGCCACGAG-AT--GA
* * * *
3249304 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCCAGTGTCAGACATGTCT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
* * * *
3249369 GGGACATGCGTCGGCTACGAGATGT
66 GGGACATGCATCAGCCACGAGATGA
*
3249394 GCTAGTGTAAGACATGTCTGGGACATGC
1 GCCAGTGTAAGACATGTCTGGGACATGC
3249422 GTCAGCACGG
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
90 28 0.27
92 49 0.48
93 14 0.14
94 12 0.12
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (90 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCACGAGATGA
Found at i:3249458 original size:46 final size:43
Alignment explanation
Indices: 3249261--3249464 Score: 171
Period size: 46 Copynumber: 4.5 Consensus size: 43
3249251 GACGAGGGCT
* * * *
3249261 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGA-CAT--GTG-C
* * *
3249307 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCGTCAG-CTACGACATG-T-G-C
* * *
3249353 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGTGC
1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC
3249396 TAGTGTAAGACATGTCTGGGACATGCGTCAGC-ACGGTTACATGTGTC
1 -AGTGTAAGACATGTCTGGGACATGCGTCAGCTAC-G--ACATGTG-C
*
3249443 AGTGTAAGACCTGTCTGGGACA
1 AGTGTAAGACATGTCTGGGACA
3249465 CGGCATCGAC
Statistics
Matches: 138, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
43 3 0.02
44 32 0.23
45 3 0.02
46 97 0.70
47 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (43 bp):
AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC
Found at i:3249464 original size:90 final size:91
Alignment explanation
Indices: 3249261--3249427 Score: 221
Period size: 90 Copynumber: 1.8 Consensus size: 91
3249251 GACGAGGGCT
3249261 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCCAGTGTAAGACATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTAT-AGAGCCAGTGTAAGACATGTCTGGG
* *
3249326 ACATGCATCGGCCTCGAGATGATAGCC
65 ACATGCATCAGCCTCGACATGATAGCC
* * * * * *
3249353 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAG-AT-GTGCTAGTGTAAGACATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATAGAGCCAGTGTAAGACATGTCTGGG
*
3249416 ACATGCGTCAGC
65 ACATGCATCAGC
3249428 ACGGTTACAT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 32 0.48
92 32 0.48
93 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (91 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATAGAGCCAGTGTAAGACATGTCTGGGA
CATGCATCAGCCTCGACATGATAGCC
Found at i:3252884 original size:47 final size:46
Alignment explanation
Indices: 3252830--3253006 Score: 218
Period size: 47 Copynumber: 3.8 Consensus size: 46
3252820 TGGTTGAGCA
3252830 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGT-GAATG
* *
3252877 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G
* *
3252922 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* *
3252970 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3253007 GCGGGTTACA
Statistics
Matches: 113, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 5 0.04
45 1 0.01
46 37 0.33
47 58 0.51
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
Found at i:3263999 original size:46 final size:44
Alignment explanation
Indices: 3263940--3264054 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
3263930 ACAGGACAGA
* *
3263940 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
3263986 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
3264030 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
3264055 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:3264035 original size:44 final size:45
Alignment explanation
Indices: 3263940--3264073 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
3263930 ACAGGACAGA
* *
3263940 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
3263986 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
3264030 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
3264074 CAGGATAATA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:3264631 original size:9 final size:9
Alignment explanation
Indices: 3264617--3264641 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3264607 TGATTATCAC
3264617 ATGAAAATT
1 ATGAAAATT
3264626 ATGAAAATT
1 ATGAAAATT
3264635 ATGAAAA
1 ATGAAAA
3264642 ATGTGAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (9 bp):
ATGAAAATT
Found at i:3265283 original size:18 final size:18
Alignment explanation
Indices: 3265250--3265587 Score: 248
Period size: 18 Copynumber: 18.8 Consensus size: 18
3265240 GTGCTAATAG
* * *
3265250 TAAAGATGAAGTTAAAGC
1 TAAAGCTGAAGCTGAAGC
* * *
3265268 TGAAGCCGAAGCTAAAGC
1 TAAAGCTGAAGCTGAAGC
* *
3265286 TAAGGCTGAAGCCGAAGC
1 TAAAGCTGAAGCTGAAGC
*
3265304 TAAAGTTGAAGCTGAAGC
1 TAAAGCTGAAGCTGAAGC
*
3265322 TAAAGCTAAAGCTGAAGC
1 TAAAGCTGAAGCTGAAGC
*
3265340 TAAATCT-AAGGCTGAAGC
1 TAAAGCTGAA-GCTGAAGC
** * * * *
3265358 CGAAGCTAAATCTCATGC
1 TAAAGCTGAAGCTGAAGC
* * *
3265376 TGAAGTTGAAGCTAAAGC
1 TAAAGCTGAAGCTGAAGC
* *
3265394 TAAGGCTGAAGCTAAAGC
1 TAAAGCTGAAGCTGAAGC
* * *
3265412 TGAGGCTGAAACTGAAGC
1 TAAAGCTGAAGCTGAAGC
*
3265430 TAAAGCCGAAGCTGAAGC
1 TAAAGCTGAAGCTGAAGC
*
3265448 TAAAGCTGAAGCCGAAGC
1 TAAAGCTGAAGCTGAAGC
*
3265466 TAAAGCTAAAGCTGAAGC
1 TAAAGCTGAAGCTGAAGC
** ** **
3265484 CGAAGCAAAAGCTGGTGC
1 TAAAGCTGAAGCTGAAGC
* * *
3265502 TGAAGCTAAAGCTAAAGC
1 TAAAGCTGAAGCTGAAGC
* *
3265520 TAAAGCTGAAGCCGAAGG
1 TAAAGCTGAAGCTGAAGC
* *
3265538 AAAAGCTGAAGCTAAAGC
1 TAAAGCTGAAGCTGAAGC
*
3265556 AAAAGCT-AATGCTGAAGC
1 TAAAGCTGAA-GCTGAAGC
* *
3265574 TGAAGCTAAAGCTG
1 TAAAGCTGAAGCTG
3265588 GAATAGGAGG
Statistics
Matches: 253, Mismatches: 63, Indels: 8
0.78 0.19 0.02
Matches are distributed among these distances:
17 4 0.02
18 245 0.97
19 4 0.02
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.16
Consensus pattern (18 bp):
TAAAGCTGAAGCTGAAGC
Found at i:3265288 original size:42 final size:42
Alignment explanation
Indices: 3265256--3265587 Score: 308
Period size: 42 Copynumber: 7.9 Consensus size: 42
3265246 ATAGTAAAGA
* *
3265256 TGAAGTTAAAGCTGAAGCCGAAGCTAAAGCTAAGGCTGAAGC
1 TGAAGCTAAAGCTGAAGCCGAAGCTAAAGCTAAAGCTGAAGC
* * *
3265298 CGAAGCTAAAGTTGAAGCTGAAGCTAAAGCTAAAGCTGAAGC
1 TGAAGCTAAAGCTGAAGCCGAAGCTAAAGCTAAAGCTGAAGC
* * * * * * *
3265340 TAAATCTAAGGCTGAAGCCGAAGCTAAATCTCATGCTGAAGT
1 TGAAGCTAAAGCTGAAGCCGAAGCTAAAGCTAAAGCTGAAGC
* * * *
3265382 TGAAGCTAAAGCT-AAGGCTGAAGCTAAAGCTGAGGCTGAAAC
1 TGAAGCTAAAGCTGAA-GCCGAAGCTAAAGCTAAAGCTGAAGC
* * * *
3265424 TGAAGCTAAAGCCGAAGCTGAAGCTAAAGCTGAAGCCGAAGC
1 TGAAGCTAAAGCTGAAGCCGAAGCTAAAGCTAAAGCTGAAGC
* * ***
3265466 TAAAGCTAAAGCTGAAGCCGAAGCAAAAGCTGGTGCTGAAGC
1 TGAAGCTAAAGCTGAAGCCGAAGCTAAAGCTAAAGCTGAAGC
* * * ** **
3265508 TAAAGCTAAAGCTAAAGCTGAAGCCGAAGGAAAAGCTGAAGC
1 TGAAGCTAAAGCTGAAGCCGAAGCTAAAGCTAAAGCTGAAGC
* * * *
3265550 TAAAGCAAAAGCT-AATGCTGAAGCTGAAGCTAAAGCTG
1 TGAAGCTAAAGCTGAA-GCCGAAGCTAAAGCTAAAGCTG
3265588 GAATAGGAGG
Statistics
Matches: 239, Mismatches: 48, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
41 4 0.02
42 233 0.97
43 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.16
Consensus pattern (42 bp):
TGAAGCTAAAGCTGAAGCCGAAGCTAAAGCTAAAGCTGAAGC
Found at i:3265298 original size:24 final size:24
Alignment explanation
Indices: 3265264--3265579 Score: 252
Period size: 24 Copynumber: 13.4 Consensus size: 24
3265254 GATGAAGTTA
3265264 AAGCTGAAGCCGAAGCTAAAGCT-
1 AAGCTGAAGCCGAAGCTAAAGCTG
*
3265287 AAGGCTGAAGCCGAAGCTAAAGTTG
1 AA-GCTGAAGCCGAAGCTAAAGCTG
**
3265312 AAGCTGAAGCTAAAGCTAAAGCTG
1 AAGCTGAAGCCGAAGCTAAAGCTG
* *
3265336 AAGCT--A----AATCTAAGGCTG
1 AAGCTGAAGCCGAAGCTAAAGCTG
* ** * * *
3265354 AAGCCGAAGCTAAATCTCATGCTG
1 AAGCTGAAGCCGAAGCTAAAGCTG
* ** *
3265378 AAGTTGAAGCTAAAGCTAAGGCTG
1 AAGCTGAAGCCGAAGCTAAAGCTG
* * *
3265402 AAGCTAAAGCTGAGGCTGAAA-CTG
1 AAGCTGAAGCCGAAGCT-AAAGCTG
* * *
3265426 AAGCTAAAGCCGAAGCTGAAGCTA
1 AAGCTGAAGCCGAAGCTAAAGCTG
*
3265450 AAGCTGAAGCCGAAGCTAAAGCTA
1 AAGCTGAAGCCGAAGCTAAAGCTG
*
3265474 AAGCTGAAGCCGAAGCAAAAGCTG
1 AAGCTGAAGCCGAAGCTAAAGCTG
** ** *
3265498 GTGCTGAAGCTAAAGCTAAAGCTA
1 AAGCTGAAGCCGAAGCTAAAGCTG
**
3265522 AAGCTGAAGCCGAAGGAAAAGCTG
1 AAGCTGAAGCCGAAGCTAAAGCTG
* ** *
3265546 AAGCTAAAGCAAAAGCTAATGCTG
1 AAGCTGAAGCCGAAGCTAAAGCTG
3265570 AAGCTGAAGC
1 AAGCTGAAGC
3265580 TAAAGCTGGA
Statistics
Matches: 236, Mismatches: 47, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
18 14 0.06
20 1 0.00
22 1 0.00
23 4 0.02
24 212 0.90
25 4 0.02
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.16
Consensus pattern (24 bp):
AAGCTGAAGCCGAAGCTAAAGCTG
Found at i:3265837 original size:30 final size:30
Alignment explanation
Indices: 3265803--3265873 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
3265793 TAGTGGAGGT
* *
3265803 GGTGGTGGTGGTCACATGCATTTTGGTGGC
1 GGTGGTGGTGGTCACATGCATTTTGCTAGC
* *
3265833 GGTGGTGGTGGTCACATGCGTTTTGCTAGT
1 GGTGGTGGTGGTCACATGCATTTTGCTAGC
3265863 GGTGGTGGTGG
1 GGTGGTGGTGG
3265874 AAGTGGTAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.08, C:0.11, G:0.46, T:0.34
Consensus pattern (30 bp):
GGTGGTGGTGGTCACATGCATTTTGCTAGC
Found at i:3265951 original size:86 final size:87
Alignment explanation
Indices: 3265834--3266040 Score: 274
Period size: 86 Copynumber: 2.4 Consensus size: 87
3265824 TTTGGTGGCG
* * *
3265834 GTGGTGGTGGTCACATGC-GTTTTGCTAGTGGTGGTGGTGGAAGTGGTAGCAGTAGTGTTGATGG
1 GTGGTGGTGGTCACATGCAG-TTTG---GTGGTGGTGGTGGAAATGGTAGCAATACTGTTGATGG
3265898 TGGGGCTAAA-AGCATGGTGGAGAAA
62 TGGGGCTAAAGAGCATGGTGGAGAAA
3265923 GTGGTGGTGGTCACATGCAGTTTGGTGGTGGTGGTGGAAATGGTAGCAATACTGTTGATGGTGGG
1 GTGGTGGTGGTCACATGCAGTTTGGTGGTGGTGGTGGAAATGGTAGCAATACTGTTGATGGTGGG
* ***
3265988 GCTAAAGGGCATGGTGGAGGCG
66 GCTAAAGAGCATGGTGGAGAAA
* * *
3266010 GTGGTGGTGGTCATATGCATTTTGCTGGTGG
1 GTGGTGGTGGTCACATGCAGTTTGGTGGTGG
3266041 CGGCGGTTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
86 44 0.42
87 39 0.37
89 22 0.21
90 1 0.01
ACGTcount: A:0.18, C:0.09, G:0.44, T:0.29
Consensus pattern (87 bp):
GTGGTGGTGGTCACATGCAGTTTGGTGGTGGTGGTGGAAATGGTAGCAATACTGTTGATGGTGGG
GCTAAAGAGCATGGTGGAGAAA
Found at i:3271821 original size:50 final size:50
Alignment explanation
Indices: 3271746--3271841 Score: 183
Period size: 50 Copynumber: 1.9 Consensus size: 50
3271736 TTAATACATT
*
3271746 GTATAATGTCATTCTCACGACCAAGAATAATTATTAACTCCTATTTCCTA
1 GTATAAAGTCATTCTCACGACCAAGAATAATTATTAACTCCTATTTCCTA
3271796 GTATAAAGTCATTCTCACGACCAAGAATAATTATTAACTCCTATTT
1 GTATAAAGTCATTCTCACGACCAAGAATAATTATTAACTCCTATTT
3271842 ACTCAATTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (50 bp):
GTATAAAGTCATTCTCACGACCAAGAATAATTATTAACTCCTATTTCCTA
Found at i:3277820 original size:24 final size:24
Alignment explanation
Indices: 3277786--3277833 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3277776 AAGGTGAAGG
* *
3277786 TTTGTGTATTCTAAATGGAATTCT
1 TTTGTGCATTCTAAAGGGAATTCT
3277810 TTTGTGCATTCTAAAGGGAATTCT
1 TTTGTGCATTCTAAAGGGAATTCT
3277834 ACCTAGCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (24 bp):
TTTGTGCATTCTAAAGGGAATTCT
Found at i:3282194 original size:16 final size:16
Alignment explanation
Indices: 3282173--3282212 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
3282163 CACTAGGATG
3282173 GTTGAGTTCCGAACTC
1 GTTGAGTTCCGAACTC
*
3282189 GTTGAGTTTCGAACTC
1 GTTGAGTTCCGAACTC
3282205 GTTGAGTT
1 GTTGAGTT
3282213 GAGTCTGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (16 bp):
GTTGAGTTCCGAACTC
Found at i:3285942 original size:3 final size:3
Alignment explanation
Indices: 3285928--3285973 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
3285918 TTATCTCAAT
3285928 TAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3285974 GTAAATATCT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3287050 original size:15 final size:15
Alignment explanation
Indices: 3287030--3287059 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3287020 CCAAATTATA
3287030 TACCCTATTTGGCAG
1 TACCCTATTTGGCAG
3287045 TACCCTATTTGGCAG
1 TACCCTATTTGGCAG
3287060 GAGTTTCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
TACCCTATTTGGCAG
Found at i:3291385 original size:10 final size:10
Alignment explanation
Indices: 3291334--3291387 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
3291324 TTAGTTGCTG
*
3291334 TTATTATTTCT
1 TTATT-TTTTT
3291345 TTATTTTTGTT
1 TTATTTTT-TT
3291356 TATATTTTTATT
1 T-TATTTTT-TT
*
3291368 TTGTTTTTTT
1 TTATTTTTTT
3291378 TTATTTTTTT
1 TTATTTTTTT
3291388 CGGTCATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 14 0.38
11 13 0.35
12 10 0.27
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:3291420 original size:3 final size:3
Alignment explanation
Indices: 3291412--3291445 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3291402 TTTATTTCAT
3291412 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3291446 ATTTATGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3294374 original size:12 final size:12
Alignment explanation
Indices: 3294357--3294472 Score: 126
Period size: 12 Copynumber: 9.7 Consensus size: 12
3294347 GTCCTCCTAT
3294357 TTCGGCTTTTGC
1 TTCGGCTTTTGC
*
3294369 TTCGGCCTTTGC
1 TTCGGCTTTTGC
* *
3294381 TTCAGCCTTTGC
1 TTCGGCTTTTGC
*
3294393 TTTGGCTTTTGC
1 TTCGGCTTTTGC
3294405 TTCGG-TGTTTGC
1 TTCGGCT-TTTGC
**
3294417 TTCGGCTTCAGC
1 TTCGGCTTTTGC
3294429 TTCGGCTTTTGC
1 TTCGGCTTTTGC
* **
3294441 TTCAGCTTCAGC
1 TTCGGCTTTTGC
3294453 TTCGGCTTTTGC
1 TTCGGCTTTTGC
*
3294465 TTCCGCTT
1 TTCGGCTT
3294473 CAGCTTTGGC
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
11 1 0.01
12 83 0.98
13 1 0.01
ACGTcount: A:0.03, C:0.28, G:0.23, T:0.46
Consensus pattern (12 bp):
TTCGGCTTTTGC
Found at i:3294424 original size:6 final size:6
Alignment explanation
Indices: 3294415--3294540 Score: 94
Period size: 6 Copynumber: 21.0 Consensus size: 6
3294405 TTCGGTGTTT
* * ** * **
3294415 GCTTCG GCTTCA GCTTCG GCTTTT GCTTCA GCTTCA GCTTCG GCTTTT
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
* ** *
3294463 GCTTCC GCTTCA GCTTTG GCTTCA GCTTCA GCTTTA GCCTTTC- -CTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA G-C-TTCA GCTTCA
* * *
3294511 GCTTTA GCTTTA GCTTCA GCTTCG GCTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
3294541 CCACCACCAC
Statistics
Matches: 94, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
4 3 0.03
5 1 0.01
6 87 0.93
7 1 0.01
8 2 0.02
ACGTcount: A:0.10, C:0.30, G:0.20, T:0.40
Consensus pattern (6 bp):
GCTTCA
Found at i:3294473 original size:24 final size:24
Alignment explanation
Indices: 3294357--3294484 Score: 143
Period size: 24 Copynumber: 5.3 Consensus size: 24
3294347 GTCCTCCTAT
*
3294357 TTCGGCTTTTGCTTCGGCCTT-TGC
1 TTCGGCTTTTGCTTCGG-CTTCAGC
* * * **
3294381 TTCAGCCTTTGCTTTGGCTTTTGC
1 TTCGGCTTTTGCTTCGGCTTCAGC
3294405 TTCGG-TGTTTGCTTCGGCTTCAGC
1 TTCGGCT-TTTGCTTCGGCTTCAGC
*
3294429 TTCGGCTTTTGCTTCAGCTTCAGC
1 TTCGGCTTTTGCTTCGGCTTCAGC
*
3294453 TTCGGCTTTTGCTTCCGCTTCAGC
1 TTCGGCTTTTGCTTCGGCTTCAGC
*
3294477 TTTGGCTT
1 TTCGGCTT
3294485 CAGCTTCAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.03
24 86 0.96
25 1 0.01
ACGTcount: A:0.04, C:0.27, G:0.23, T:0.45
Consensus pattern (24 bp):
TTCGGCTTTTGCTTCGGCTTCAGC
Found at i:3294490 original size:24 final size:24
Alignment explanation
Indices: 3294415--3294540 Score: 112
Period size: 24 Copynumber: 5.2 Consensus size: 24
3294405 TTCGGTGTTT
* **
3294415 GCTTCGGCTTCAGCTTCGGCTTTT
1 GCTTCAGCTTCAGCTTCGGCTTCA
**
3294439 GCTTCAGCTTCAGCTTCGGCTTTT
1 GCTTCAGCTTCAGCTTCGGCTTCA
* *
3294463 GCTTCCGCTTCAGCTTTGGCTTCA
1 GCTTCAGCTTCAGCTTCGGCTTCA
*
3294487 GCTTCAGCTTTAGCCTTTC--CTTCA
1 GCTTCAGCTTCAG-C-TTCGGCTTCA
* * * *
3294511 GCTTTAGCTTTAGCTTCAGCTTCG
1 GCTTCAGCTTCAGCTTCGGCTTCA
3294535 GCTTCA
1 GCTTCA
3294541 CCACCACCAC
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
22 3 0.03
23 1 0.01
24 80 0.92
25 1 0.01
26 2 0.02
ACGTcount: A:0.10, C:0.30, G:0.20, T:0.40
Consensus pattern (24 bp):
GCTTCAGCTTCAGCTTCGGCTTCA
Found at i:3294645 original size:6 final size:6
Alignment explanation
Indices: 3294622--3294867 Score: 138
Period size: 6 Copynumber: 41.0 Consensus size: 6
3294612 TTCAGCCTTT
** *
3294622 GCTTCA GCTTTT GCTTCA GTTTCA GCTTCA GCTTCA GCCTTTC- -CTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA G-C-TTCA GCTTCA
* * * * * *
3294670 GCTTTA GCTTTA GCTTCA TCTTCG GCTTCA -CTTTTA GCTTCA GCTTTA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GC-TTCA GCTTCA GCTTCA
* * * * * * * * *
3294718 GCTTTA GCTTCA ACTTTA GCTTCT TCTTTA GATTTA GCTTTA GCTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
* * * * * * * *
3294766 GATTCA GCTTTA GCTTCA TCTTTA ACTTTA GCTTGA GCTTCA TCTTCA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
* * ** * * * *
3294814 GCTTTA ACTTCA TTTTTA GCTTTA GCTTGA GCTTCA GCTTCA GCTTTA
1 GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA GCTTCA
3294862 GCTTCA
1 GCTTCA
3294868 TCTTTACCAC
Statistics
Matches: 182, Mismatches: 52, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
4 3 0.02
5 2 0.01
6 172 0.95
7 2 0.01
8 3 0.02
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.45
Consensus pattern (6 bp):
GCTTCA
Found at i:3294646 original size:30 final size:30
Alignment explanation
Indices: 3294612--3294687 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
3294602 CAGTGTTTGC
* *
3294612 TTCAGCCTTTGCTTCAGCTTTTGCTTCAG-T
1 TTCAG-CTTTGCTTCAGCCTTTCCTTCAGCT
*
3294642 TTCAGCTTCAGCTTCAGCCTTTCCTTCAGCT
1 TTCAGCTT-TGCTTCAGCCTTTCCTTCAGCT
3294673 TT-AGCTTTAGCTTCA
1 TTCAGCTTT-GCTTCA
3294688 TCTTCGGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 3 0.08
30 33 0.85
31 3 0.08
ACGTcount: A:0.13, C:0.29, G:0.14, T:0.43
Consensus pattern (30 bp):
TTCAGCTTTGCTTCAGCCTTTCCTTCAGCT
Found at i:3294646 original size:42 final size:42
Alignment explanation
Indices: 3294582--3294859 Score: 144
Period size: 42 Copynumber: 6.8 Consensus size: 42
3294572 GTCCTCCTAT
** ** *
3294582 TTCAGCTTTTGCTTTTGCTTCAG-TGTTTGCTTCAGCCTTTGC
1 TTCAGCTTTTGCTTCAGCTTCAGCT-TCAGCTTCAGCCTTTCC
*
3294624 TTCAGCTTTTGCTTCAGTTTCAGCTTCAGCTTCAGCCTTTCC
1 TTCAGCTTTTGCTTCAGCTTCAGCTTCAGCTTCAGCCTTTCC
* * * * * *
3294666 TTCAGCTTTAGCTTTAGCTTCATCTTCGGCTTCA-CTTTTAGC
1 TTCAGCTTTTGCTTCAGCTTCAGCTTCAGCTTCAGCCTTT-CC
* * * * ** **
3294708 TTCAGCTTTAGCTTTAGCTTCAACTTTAGCTTC-TTCTTTAGA
1 TTCAGCTTTTGCTTCAGCTTCAGCTTCAGCTTCAGCCTTT-CC
* * * * * *
3294750 TTTAGCTTTAGCTTCAGATTCAGCTTTAGCTTCA-TCTTTAAC
1 TTCAGCTTTTGCTTCAGCTTCAGCTTCAGCTTCAGCCTTT-CC
* ** * * *
3294792 TTTAGCTTGAGCTTCATCTTCAGCTTTAACTTCA---TTT--
1 TTCAGCTTTTGCTTCAGCTTCAGCTTCAGCTTCAGCCTTTCC
* *
3294829 TT-AGCTTTAGCTTGAGCTTCAGCTTCAGCTT
1 TTCAGCTTTTGCTTCAGCTTCAGCTTCAGCTT
3294860 TAGCTTCATC
Statistics
Matches: 198, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
36 24 0.12
37 2 0.01
40 3 0.02
41 4 0.02
42 164 0.83
43 1 0.01
ACGTcount: A:0.15, C:0.24, G:0.14, T:0.46
Consensus pattern (42 bp):
TTCAGCTTTTGCTTCAGCTTCAGCTTCAGCTTCAGCCTTTCC
Found at i:3294860 original size:42 final size:42
Alignment explanation
Indices: 3294694--3294873 Score: 225
Period size: 42 Copynumber: 4.3 Consensus size: 42
3294684 TTCATCTTCG
* * * * *
3294694 GCTTCACTTTTAGCTTCAGCTTTAGCTTTAGCTTCAACTTTA
1 GCTTCATTTTTAGCTTTAGCTTGAGCTTCAGCTTCAGCTTTA
* * * * *
3294736 GCTTCTTCTTTAGATTTAGCTTTAGCTTCAGATTCAGCTTTA
1 GCTTCATTTTTAGCTTTAGCTTGAGCTTCAGCTTCAGCTTTA
* * *
3294778 GCTTCATCTTTAACTTTAGCTTGAGCTTCATCTTCAGCTTTA
1 GCTTCATTTTTAGCTTTAGCTTGAGCTTCAGCTTCAGCTTTA
*
3294820 ACTTCATTTTTAGCTTTAGCTTGAGCTTCAGCTTCAGCTTTA
1 GCTTCATTTTTAGCTTTAGCTTGAGCTTCAGCTTCAGCTTTA
*
3294862 GCTTCATCTTTA
1 GCTTCATTTTTA
3294874 CCACTTGCAC
Statistics
Matches: 118, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 118 1.00
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (42 bp):
GCTTCATTTTTAGCTTTAGCTTGAGCTTCAGCTTCAGCTTTA
Found at i:3294872 original size:12 final size:12
Alignment explanation
Indices: 3294592--3294873 Score: 146
Period size: 12 Copynumber: 23.5 Consensus size: 12
3294582 TTCAGCTTTT
*
3294592 GCTTTTGCTTCA
1 GCTTTAGCTTCA
*
3294604 G-TGTTTGCTTCA
1 GCT-TTAGCTTCA
3294616 GCCTTT-GCTTCA
1 G-CTTTAGCTTCA
*
3294628 GCTTTTGCTTCA
1 GCTTTAGCTTCA
3294640 G-TTTCAGCTTCA
1 GCTTT-AGCTTCA
*
3294652 GCTTCAGCCTTTC-
1 GCTTTAG-C-TTCA
* *
3294665 -CTTCAGCTTTA
1 GCTTTAGCTTCA
3294676 GCTTTAGCTTCA
1 GCTTTAGCTTCA
* **
3294688 TCTTCGGCTTCA
1 GCTTTAGCTTCA
3294700 -CTTTTAGCTTCA
1 GC-TTTAGCTTCA
*
3294712 GCTTTAGCTTTA
1 GCTTTAGCTTCA
* * *
3294724 GCTTCAACTTTA
1 GCTTTAGCTTCA
* *
3294736 GCTTCT-TCTTTA
1 GCTT-TAGCTTCA
* *
3294748 GATTTAGCTTTA
1 GCTTTAGCTTCA
* *
3294760 GCTTCAGATTCA
1 GCTTTAGCTTCA
3294772 GCTTTAGCTTCA
1 GCTTTAGCTTCA
* * *
3294784 TCTTTAACTTTA
1 GCTTTAGCTTCA
*
3294796 GCTTGAGCTTCA
1 GCTTTAGCTTCA
* * *
3294808 TCTTCAGCTTTA
1 GCTTTAGCTTCA
* * ** *
3294820 ACTTCATTTTTA
1 GCTTTAGCTTCA
*
3294832 GCTTTAGCTTGA
1 GCTTTAGCTTCA
*
3294844 GCTTCAGCTTCA
1 GCTTTAGCTTCA
3294856 GCTTTAGCTTCA
1 GCTTTAGCTTCA
*
3294868 TCTTTA
1 GCTTTA
3294874 CCACTTGCAC
Statistics
Matches: 211, Mismatches: 45, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
10 2 0.01
11 11 0.05
12 188 0.89
13 6 0.03
14 4 0.02
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (12 bp):
GCTTTAGCTTCA
Found at i:3295099 original size:54 final size:54
Alignment explanation
Indices: 3295024--3295131 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
3295014 TTTAGCTTCA
* * * *
3295024 TCTTTACCACTTGCATTTGTATTACCACTACCATATCCTCCATCTTGTCCTTTT
1 TCTTTACCACTTACATCTGTATCACCACTACCATATCCTCCACCTTGTCCTTTT
*
3295078 TCTTTACCACTTACATCTGTATCACCACTACCATCTCCTCCACCTTGTCCTTTT
1 TCTTTACCACTTACATCTGTATCACCACTACCATATCCTCCACCTTGTCCTTTT
3295132 ACCCTACCGG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.19, C:0.35, G:0.05, T:0.42
Consensus pattern (54 bp):
TCTTTACCACTTACATCTGTATCACCACTACCATATCCTCCACCTTGTCCTTTT
Found at i:3295230 original size:210 final size:210
Alignment explanation
Indices: 3294868--3295839 Score: 1527
Period size: 210 Copynumber: 4.6 Consensus size: 210
3294858 TTTAGCTTCA
3294868 TCTTTACCACTTGCA-CTTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGG
1 TCTTTACCACTTGCATC-TGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGG
* *
3294932 AATCATTAGAGCTATCAGTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCT
65 AATCATTAGAGCTGTCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCT
* *
3294997 TCAACTTCATCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATATCC
130 TCAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATCTCC
*
3295062 TCCATCTTGTCCTTTT
195 TCCACCTTGTCCTTTT
* * *
3295078 TCTTTACCACTTACATCTGTATCACCACTACCATCTCCTCCACCTTGTCCTTTTACCCTACCGGA
1 TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
*
3295143 ATCATTAGAGCCGTCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCTT
66 ATCATTAGAGCTGTCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCTT
*
3295208 CAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACTATCTCCT
131 CAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATCTCCT
*
3295273 CGACCTTGTCCTTTT
196 CCACCTTGTCCTTTT
* *
3295288 TCTTTACCACTTGCATCTGTGTCACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
1 TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
* * * * *
3295353 ATCATTAGAGCTGTTATTTCCACCATTATTTTCATCAACCTTTCCCT-TCCCTCCAAATTTTCCT
66 ATCATTAGAGCTGTCACTTCCACCACTATTTCCATCGACCTTTCCCTGT-CCTCCAAATTTTCCT
* *
3295417 TCAACTTCAGCTTTATCTTTAGCTTCATCTTTACCTCTTGCATTTGTATTACCATTACCATCTCC
130 TCAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATCTCC
*
3295482 TTCACCTTGTCCTTTT
195 TCCACCTTGTCCTTTT
* *
3295498 TTTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCAGA
1 TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
* * * * *
3295563 ATCACTAGAGCTGTCACTTCCACCAATATTTCCATCGACCTTTCCCTGTCCTTCAAAATTTCCTC
66 ATCATTAGAGCTGTCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCTT
* * * *
3295628 CAGCTTCAGCTTTAGCTTTAGCTTCATCTTTACCACTTGCATCTATATTACCACTACCATCTCCT
131 CAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATCTCCT
*
3295693 CCATCTTGT-CTCTTT
196 CCACCTTGTCCT-TTT
* * * *
3295708 TCTCTACCACTGGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCTCACCAGA
1 TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
* * * *
3295773 ATAACTAGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCTCTGTCCTCCAAATTTTCCTT
66 ATCATTAGAGCTGTCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCTT
3295838 CA
131 CA
3295840 TCTTTACCAC
Statistics
Matches: 701, Mismatches: 57, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
209 3 0.00
210 696 0.99
211 2 0.00
ACGTcount: A:0.20, C:0.35, G:0.07, T:0.38
Consensus pattern (210 bp):
TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
ATCATTAGAGCTGTCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCTT
CAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATCTCCT
CCACCTTGTCCTTTT
Found at i:3295316 original size:54 final size:54
Alignment explanation
Indices: 3295234--3295341 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
3295224 TTTAGCTTCA
* * * *
3295234 TCTTTACCACTTGCATTTGTATTACCACTACTATCTCCTCGACCTTGTCCTTTT
1 TCTTTACCACTTGCATCTGTATCACCACTACCATCTCCTCCACCTTGTCCTTTT
*
3295288 TCTTTACCACTTGCATCTGTGTCACCACTACCATCTCCTCCACCTTGTCCTTTT
1 TCTTTACCACTTGCATCTGTATCACCACTACCATCTCCTCCACCTTGTCCTTTT
3295342 ACCCCACCGG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.16, C:0.35, G:0.07, T:0.42
Consensus pattern (54 bp):
TCTTTACCACTTGCATCTGTATCACCACTACCATCTCCTCCACCTTGTCCTTTT
Found at i:3295530 original size:54 final size:54
Alignment explanation
Indices: 3295446--3295551 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
3295436 TAGCTTCATC
* * * *
3295446 TTTACCTCTTGCATTTGTATTACCATTACCATCTCCTTCACCTTGTCCTTTTTT
1 TTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTTT
3295500 TTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTT
1 TTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTT
3295552 ACCCCACCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.16, C:0.33, G:0.06, T:0.45
Consensus pattern (54 bp):
TTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTTT
Found at i:3295649 original size:420 final size:420
Alignment explanation
Indices: 3294868--3296097 Score: 1691
Period size: 420 Copynumber: 3.0 Consensus size: 420
3294858 TTTAGCTTCA
3294868 TCTTTACCACTTGCA-CTTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGG
1 TCTTTACCACTTGCATC-TGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGG
*
3294932 AATCATTAGAGCTATCAGTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCT
65 AATCATTAGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCT
*
3294997 TCAACTTCATCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATATCC
130 TCAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATATCC
*
3295062 TCCATCTTGTCCTTTTTCTTTACCACTTACATCTGTATCACCACTACCATCTCCTCCACCTTGTC
195 TCCACCTTGTCCTTTTTCTTTACCACTTACATCTGTATCACCACTACCATCTCCTCCACCTTGTC
* * * *
3295127 CTTTTACCCTACCGGAATCATTAGAGCCGTCACTTCCACCACTATTTCCATCGACCTTTCCCTGT
260 CTTTTACCCCACCAGAATCACTAGAGCCGTCACTTCCACCAATATTTCCATCGACCTTTCCCTGT
* * * * *
3295192 CCTCCAAATTTTCCTTCAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATT
325 CCTCCAAAATTTCCTCCAACTTCAGCTTTAGCTTTAGCTTCATCTTTACCACTTGCATCTATATT
* *
3295257 ACCACTACTATCTCCTCGACCTTGTC-CTTTT
390 ACCACTACCATCTCCTCCACCTTGTCTC-TTT
* *
3295288 TCTTTACCACTTGCATCTGTGTCACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
1 TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
* * * * * *
3295353 ATCATTAGAGCTGTTATTTCCACCATTATTTTCATCAACCTTTCCCT-TCCCTCCAAATTTTCCT
66 ATCATTAGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCCCTGT-CCTCCAAATTTTCCT
* * *
3295417 TCAACTTCAGCTTTATCTTTAGCTTCATCTTTACCTCTTGCATTTGTATTACCATTACCATCTCC
130 TCAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATATCC
* * * *
3295482 TTCACCTTGTCCTTTTTTTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTC
195 TCCACCTTGTCCTTTTTCTTTACCACTTACATCTGTATCACCACTACCATCTCCTCCACCTTGTC
*
3295547 CTTTTACCCCACCAGAATCACTAGAGCTGTCACTTCCACCAATATTTCCATCGACCTTTCCCTGT
260 CTTTTACCCCACCAGAATCACTAGAGCCGTCACTTCCACCAATATTTCCATCGACCTTTCCCTGT
* *
3295612 CCTTCAAAATTTCCTCCAGCTTCAGCTTTAGCTTTAGCTTCATCTTTACCACTTGCATCTATATT
325 CCTCCAAAATTTCCTCCAACTTCAGCTTTAGCTTTAGCTTCATCTTTACCACTTGCATCTATATT
*
3295677 ACCACTACCATCTCCTCCATCTTGTCTCTTT
390 ACCACTACCATCTCCTCCACCTTGTCTCTTT
* * * *
3295708 TCTCTACCACTGGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCTCACCAGA
1 TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
* * *
3295773 ATAACTAGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCTCTG---TCC------T-C--
66 ATCATTAGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCTT
* * *
3295826 CAA----A--TTT-TC-----CTTCATCTTTACCACTTGCATCTATATTACCACTACCATCTCCT
131 CAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATATCCT
* * * * *
3295879 CTACCTTGTCCTTTTTCTTTACCACTGACGTCTATATTACCACTACCATCTCCTCCACCTTGTCC
196 CCACCTTGTCCTTTTTCTTTACCACTTACATCTGTATCACCACTACCATCTCCTCCACCTTGTCC
* * ** * *
3295944 TTTTACCCTACCAGAATAACTAGAGCTATCACTTCTACCACTATTTCCATCGACCTTTCCCTGTC
261 TTTTACCCCACCAGAATCACTAGAGCCGTCACTTCCACCAATATTTCCATCGACCTTTCCCTGTC
* *
3296009 CTCC-AAATTT--T-C--CTTCAACTTTAGCTTTAGTTTCATCTTTACCACTTGCATCTATATTA
326 CTCCAAAATTTCCTCCAACTTCAGCTTTAGCTTTAGCTTCATCTTTACCACTTGCATCTATATTA
3296068 CCACTACCATCTCCTCCACCTTGT-TCTTT
391 CCACTACCATCTCCTCCACCTTGTCTCTTT
3296097 T
1 T
3296098 ACCCCACTAG
Statistics
Matches: 739, Mismatches: 67, Indels: 39
0.87 0.08 0.05
Matches are distributed among these distances:
389 6 0.01
390 68 0.09
392 1 0.00
393 1 0.00
395 6 0.01
396 161 0.22
401 2 0.00
402 3 0.00
404 1 0.00
408 3 0.00
410 1 0.00
411 1 0.00
417 3 0.00
419 1 0.00
420 479 0.65
421 2 0.00
ACGTcount: A:0.20, C:0.35, G:0.07, T:0.38
Consensus pattern (420 bp):
TCTTTACCACTTGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCCCACCGGA
ATCATTAGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTCCTT
CAACTTCAGCTTTATCTTTAGCTTCATCTTTACCACTTGCATTTGTATTACCACTACCATATCCT
CCACCTTGTCCTTTTTCTTTACCACTTACATCTGTATCACCACTACCATCTCCTCCACCTTGTCC
TTTTACCCCACCAGAATCACTAGAGCCGTCACTTCCACCAATATTTCCATCGACCTTTCCCTGTC
CTCCAAAATTTCCTCCAACTTCAGCTTTAGCTTTAGCTTCATCTTTACCACTTGCATCTATATTA
CCACTACCATCTCCTCCACCTTGTCTCTTT
Found at i:3295731 original size:54 final size:53
Alignment explanation
Indices: 3295658--3295761 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 53
3295648 GCTTCATCTT
* *
3295658 TACCACTTGCATCTATATTACCACTACCATCTCCTCCATCTTGTCTCTTTTCTC
1 TACCACTGGCATCTATATTACCACTACCATCTCCTCCACCTTGTC-CTTTTCTC
*
3295712 TACCACTGGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTT
1 TACCACTGGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTT
3295762 ACCTCACCAG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 5 0.11
54 42 0.89
ACGTcount: A:0.18, C:0.38, G:0.06, T:0.38
Consensus pattern (53 bp):
TACCACTGGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTCTC
Found at i:3295946 original size:54 final size:54
Alignment explanation
Indices: 3295840--3295947 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
3295830 TTTTCCTTCA
*
3295840 TCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCTACCTTGTCCTTTT
1 TCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTT
*
3295894 TCTTTACCAC-TGACGTCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTT
1 TCTTTACCACTTG-CATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTT
3295948 ACCCTACCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 2 0.04
54 49 0.96
ACGTcount: A:0.19, C:0.36, G:0.05, T:0.41
Consensus pattern (54 bp):
TCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTT
Found at i:3295963 original size:186 final size:186
Alignment explanation
Indices: 3295649--3296031 Score: 653
Period size: 186 Copynumber: 2.1 Consensus size: 186
3295639 TTAGCTTTAG
*
3295649 CTTCATCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCATCTTGTCTCTTTTCTCTA
1 CTTCATCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTCTCTTTTCTCTA
* *
3295714 CCACTGGCATCTGTATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCTCACCAGAATAACT
66 CCACTGACATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCTCACCAGAATAACT
*
3295779 AGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCTCTGTCCTCCAAATTTTC
131 AGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTC
* *
3295835 CTTCATCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCTACCTTGTC-CTTTTTCTTT
1 CTTCATCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTCTC-TTTTCTCT
*
3295899 ACCACTGACGTCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTACC-CTACCAGAATAA
65 ACCACTGACATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCTC-ACCAGAATAA
*
3295963 CTAGAGCTATCACTTCTACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTC
129 CTAGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTC
*
3296021 CTTCAACTTTA
1 CTTCATCTTTA
3296032 GCTTTAGTTT
Statistics
Matches: 186, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
185 2 0.01
186 184 0.99
ACGTcount: A:0.21, C:0.36, G:0.05, T:0.37
Consensus pattern (186 bp):
CTTCATCTTTACCACTTGCATCTATATTACCACTACCATCTCCTCCACCTTGTCTCTTTTCTCTA
CCACTGACATCTATATTACCACTACCATCTCCTCCACCTTGTCCTTTTACCTCACCAGAATAACT
AGAGCTATCACTTCCACCACTATTTCCATCGACCTTTCCCTGTCCTCCAAATTTTC
Found at i:3296972 original size:3 final size:3
Alignment explanation
Indices: 3296964--3297001 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
3296954 GCTACCACTT
* *
3296964 CCA CCA CCA CCA CCA TCA CCA CTA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
3297002 TCCTCCTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.63, G:0.00, T:0.05
Consensus pattern (3 bp):
CCA
Found at i:3303688 original size:327 final size:325
Alignment explanation
Indices: 3303156--3303742 Score: 782
Period size: 327 Copynumber: 1.8 Consensus size: 325
3303146 AATGACTTTT
* * * * * *
3303156 GTAACACACTTATGACAAAATCATTGGACGACTACGTATTAAGTAGCTTTTGTAATGTATATATT
1 GTAACACACTTATGACAAAAGCATTGGACGACTAAGTATTAAATAACTTTTATAATGTATATAAT
* * * * *
3303221 AAGTGAGAGCTCAATCATGATATTTTAGTAGAATAATTTTGTGACTAAATAATGTTATAACTAAT
66 AAGGGAGAACTCAATCACGATACTTTAGTAGAATAATTCTGTGACTAAATAATGTTATAACTAAT
** * * * *
3303286 AGGAGACAAGTTGAAACTTAATTATAAATTATTTTAGCCATGATTATATATGTTCAATCAGTCCC
131 AGGAGACAAGCCGAAACTTAATTATAAATTATTTAAGCCATAATTATACATGTCCAATCAGTCCC
* ** *
3303351 TCTACTAGCTCGACATAACCAAAAACGGATTGTATGTAGAATCAATGAATAGAAATGAATGAAAA
196 TCTACTAGCTCGACATAACCAAAAACGAATTACATGTAGAACCAATGAATAGAAATGAATGAAAA
3303416 AAAGAAGTAAGAGAAATAGATTGCATATATCACTATCCTAAAGAGATTAAGGATATCTCATGAGG
261 AAAGAAGTAAGAGAAATAGATTGCATATATCACTATCCTAAAGAGATTAAGGATATCTCATGAGG
* * *
3303481 GTAACAGACTTATGACAATAGCATTGGACGAGTAAGTATTAAATAACTTTTATAATGGTATATAA
1 GTAACACACTTATGACAAAAGCATTGGACGACTAAGTATTAAATAACTTTTATAAT-GTATATAA
* * * *
3303546 TATGGGAGAACTC-AGCTACGATACTTTAGTTGAA-AGACTTCTGTGACTAAATAATGTTATAAT
65 TAAGGGAGAACTCAATC-ACGATACTTTAGTAGAATA-A-TTCTGTGACTAAATAATGTTATAAC
* * * *
3303609 TAATAGGCGACGAGCCGAAACTTAATTATAAATTATTTAAGCCTTAATTATACATGTCCAATTAG
127 TAATAGGAGACAAGCCGAAACTTAATTATAAATTATTTAAGCCATAATTATACATGTCCAATCAG
* * * * * *
3303674 TCCCTCTGCTAGCTCGACATAACTAGAAATGAATTACATGTAGAACCAGTGATTAGAAATGAATG
192 TCCCTCTACTAGCTCGACATAACCAAAAACGAATTACATGTAGAACCAATGAATAGAAATGAATG
3303739 AAAA
257 AAAA
3303743 TGATGAAGTA
Statistics
Matches: 220, Mismatches: 38, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
325 51 0.23
326 32 0.15
327 137 0.62
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.31
Consensus pattern (325 bp):
GTAACACACTTATGACAAAAGCATTGGACGACTAAGTATTAAATAACTTTTATAATGTATATAAT
AAGGGAGAACTCAATCACGATACTTTAGTAGAATAATTCTGTGACTAAATAATGTTATAACTAAT
AGGAGACAAGCCGAAACTTAATTATAAATTATTTAAGCCATAATTATACATGTCCAATCAGTCCC
TCTACTAGCTCGACATAACCAAAAACGAATTACATGTAGAACCAATGAATAGAAATGAATGAAAA
AAAGAAGTAAGAGAAATAGATTGCATATATCACTATCCTAAAGAGATTAAGGATATCTCATGAGG
Found at i:3303979 original size:16 final size:17
Alignment explanation
Indices: 3303952--3303986 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3303942 TTCAGGTGGG
*
3303952 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
3303969 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
3303985 TT
1 TT
3303987 AAATTAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:3304579 original size:20 final size:20
Alignment explanation
Indices: 3304554--3304600 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3304544 CACACGCCCA
*
3304554 TGTGGCCTGGGACATGGCCG
1 TGTGGCCTGGAACATGGCCG
3304574 TGTGGCCTGGAACATGGCCG
1 TGTGGCCTGGAACATGGCCG
3304594 TGTGGCC
1 TGTGGCC
3304601 AGGCCATGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.11, C:0.26, G:0.43, T:0.21
Consensus pattern (20 bp):
TGTGGCCTGGAACATGGCCG
Found at i:3315038 original size:33 final size:30
Alignment explanation
Indices: 3314986--3315054 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 30
3314976 TTTGGTCATA
*
3314986 TAATACATTATTAATATTTCAATTTATTATTT
1 TAATAAATTATTAATATTTCAA-TT-TTATTT
3315018 TAATAAATTATTTAATATTTCAATTTTATTT
1 TAATAAATTA-TTAATATTTCAATTTTATTT
3315049 TAATAA
1 TAATAA
3315055 TAAATTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 12 0.34
32 11 0.31
33 12 0.34
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (30 bp):
TAATAAATTATTAATATTTCAATTTTATTT
Found at i:3315061 original size:13 final size:14
Alignment explanation
Indices: 3315045--3315086 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
3315035 TTTCAATTTT
3315045 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
3315058 ATTTTAAAAATGATA
1 ATTTTAATAAT-ATA
3315073 ATTTTAAATAATAT
1 ATTTT-AATAATAT
3315087 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:3315147 original size:19 final size:19
Alignment explanation
Indices: 3315120--3315156 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3315110 TCAACATTAA
*
3315120 TATTTCAATAATAAATATT
1 TATTACAATAATAAATATT
*
3315139 TATTACAATTATAAATAT
1 TATTACAATAATAAATAT
3315157 ATTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTACAATAATAAATATT
Found at i:3315289 original size:30 final size:29
Alignment explanation
Indices: 3315228--3315289 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3315218 ACAGATTTGT
** *
3315228 AATTTAGTCTTTTTACTTTTATTTCTAAA
1 AATTTAGTCCATTTACTTTTAATTCTAAA
3315257 AATTTAGTCCATTTACTTTTCAAATT-TAAA
1 AATTTAGTCCATTTACTTTT--AATTCTAAA
3315287 AAT
1 AAT
3315290 CAAATCCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 18 0.64
30 7 0.25
31 3 0.11
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.52
Consensus pattern (29 bp):
AATTTAGTCCATTTACTTTTAATTCTAAA
Found at i:3315645 original size:14 final size:14
Alignment explanation
Indices: 3315626--3315664 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3315616 CCAGAAAAGT
3315626 AAATCATTTTCTAG
1 AAATCATTTTCTAG
* *
3315640 AAATCATTTTTTGG
1 AAATCATTTTCTAG
*
3315654 AAGTCATTTTC
1 AAATCATTTTC
3315665 AGTGAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (14 bp):
AAATCATTTTCTAG
Found at i:3319260 original size:66 final size:66
Alignment explanation
Indices: 3319181--3319327 Score: 206
Period size: 66 Copynumber: 2.2 Consensus size: 66
3319171 CAAGTCACCT
* *
3319181 CTACCAGTTCCACCACCTTTTCCACCAAACCCTCCTTGGCCTCCTACTCCA-CTAGCAACATTAG
1 CTACCACTTCCACCACCTTTTCCACCAAACCCACCTTGGCCTCCTACTCCACCTA-CAACATTAG
3319245 CG
65 CG
** * * * *
3319247 CTACCACTTCCACCACCTTTTCCACCAAACTGACCTTGTCCTCTTACTCCACCTATAACATTAGT
1 CTACCACTTCCACCACCTTTTCCACCAAACCCACCTTGGCCTCCTACTCCACCTACAACATTAGC
3319312 G
66 G
3319313 CTACCACTTCCACCA
1 CTACCACTTCCACCA
3319328 AACCCTCCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 69 0.96
67 3 0.04
ACGTcount: A:0.24, C:0.43, G:0.07, T:0.27
Consensus pattern (66 bp):
CTACCACTTCCACCACCTTTTCCACCAAACCCACCTTGGCCTCCTACTCCACCTACAACATTAGC
G
Found at i:3319390 original size:66 final size:66
Alignment explanation
Indices: 3319320--3320153 Score: 1039
Period size: 66 Copynumber: 12.4 Consensus size: 66
3319310 GTGCTACCAC
* * * *
3319320 TTCCACCAAACCCTCCTTTCCCTCCTATTCCACCAGCAACATTAGCGTTGCCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
3319385 T
66 T
* * *
3319386 TTCCACCAAACCCTCCTTGCCCTCCTACTCCATCAGCAGCATTAGCACTACCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
3319451 T
66 T
* * * * *
3319452 TTCCACCAAACCCTTCTTTCCCTCCTACTCCACCAGCAGCATTAGCACTACCGCTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
3319517 T
66 T
* * * * *
3319518 TTCCACCAAACCCTTCTTTCCCTCCTACTCCACCCGCAGCATTAGCACTACCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
3319583 T
66 T
3319584 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCTCTATCACTTGCGCTACCA
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAAC---A----T-T-A---GCGCTACCA
3319649 CTTCCACCACCTT
54 CTTCCACCACCTT
* * * *
3319662 TTCCACCAAACCCTCCTTGCCCACCAAATCCACCAGCAACATTAGCGCTACCAGTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
3319727 T
66 T
** * * * * *
3319728 TTCCACCAAATTCTCCTTTCCCTCCAAATCCACCAGCAACATTACCACTACCACCTCCACTTCCA
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCT---A---CCACTTCCA
3319793 CCACCTT
60 CCACCTT
* * * * * *
3319800 TACCACCAAACCCTTCTTGCCCTCCTACTCCACGAGCAATATTAGTGCTACCACTTCCACTACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
3319865 T
66 T
* * * * *
3319866 TTCCATCAAACCCTCCTTGCCCTCCTACTCCACCAACAACATTAACGCTACTACTTCTACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
3319931 T
66 T
*
3319932 TTCCACCAAATCCC-CCTTGCCCTCCTACTCCACCAGCAACATTAGTGCTACCACTTCCACCACC
1 TTCCACCAAA-CCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACC
3319996 TT
65 TT
* *
3319998 TTCCACCAAAACCTCCTTG---TCCTACTCCACCATCAACATTAGCGCTACCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
3320060 T
66 T
* * *
3320061 TTCCTCCAAATCCTCCTTGCCCTCCTACTCCACCAGCAATATTA-CTGCTACCACTTCCACCACC
1 TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGC-GCTACCACTTCCACCACC
3320125 TT
65 TT
*
3320127 TTCCACCAAACCCTCCTTGTCCTCCTA
1 TTCCACCAAACCCTCCTTGCCCTCCTA
3320154 TGTTACCTCC
Statistics
Matches: 675, Mismatches: 69, Indels: 48
0.85 0.09 0.06
Matches are distributed among these distances:
63 59 0.09
65 3 0.00
66 490 0.73
67 3 0.00
69 4 0.01
70 1 0.00
71 1 0.00
72 52 0.08
73 1 0.00
74 1 0.00
75 2 0.00
78 58 0.09
ACGTcount: A:0.23, C:0.46, G:0.05, T:0.26
Consensus pattern (66 bp):
TTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
T
Found at i:3319404 original size:120 final size:119
Alignment explanation
Indices: 3319200--3320122 Score: 515
Period size: 132 Copynumber: 7.1 Consensus size: 119
3319190 CCACCACCTT
** *
3319200 TTCCACCAAACCCTCCTTGGCCTCCTACTCCACTAGCAACATTAGCGCTACCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
*** * * * *
3319265 TTTCCACCAAACTGACCTTGTCCTCTTACTCCACCTATAACATTAGTGCTACCAC
66 TTTCCACCAAACCCTCCTTGTCCTCCTACTCCACC-ACAGCATTAGTACTACCAC
* * *
3319320 TTCCACCAAACCCTCCTTTCCCTCCTATTCCACCAGCAACATTAGCGTTGCCACTTCCACCACCT
1 TTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
* *
3319385 TTTCCACCAAACCCTCCTTGCCCTCCTACTCCATCAGCAGCATTAGCACTACCACTTCCACCACC
66 TTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCA-CAGCATTAG---T---AC-T--ACCA-C
* * * *
3319450 TTTTCCACCAAACCCTTCTTTCCCTCCTACTCCACCAGCAGCATTAGCACTACCGCTTCCACCAC
1 --TTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCAC
* *
3319515 CTTTTCCACCAAACCCTTCTT-TCCCTCCTACTCCACCCGCAGCATTAGCACTACCACTTCCACC
64 CTTTTCCACCAAACCCTCCTTGT-CCTCCTACTCCA-CCACAGCATTAG---T---AC-T--ACC
3319579 ACC
118 A-C
*
3319582 TTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCTCTATCACTTGCGCTAC
1 --TTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAAC---A----T-T-A---GCGCTAC
* * * * *
3319647 CACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCACCAAATCCACCAGCAACATTAGCGCTA
52 CACTTCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCA-CAGCATTA--G-TA
3319712 CCAGTTCCACCACC
113 -C---T--ACCA-C
** * * * *
3319726 TTTTCCACCAAATTCTCCTTTCCCTCCAAATCCACCAGCAACATTACCACTACCACCTCCACTTC
1 --TTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTAGCGCT---A---CCACTTC
* * * * ** *
3319791 CACCACCTTTACCACCAAACCCTTCTTGCCCTCCTACTCCACGAGCAATATTAGTGCTACCAC
58 CACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCA-CAGCATTAGTACTACCAC
* * * *
3319854 TTCCACTACCTTTTCCATCAAACCCTCCTTGCCCTCCTACTCCACCAACAACATTAACGCTACTA
1 TT-C-C-A-------C--CAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTAGCGCTACCA
* * *
3319919 CTTCTACCACCTTTTCCACCAAATCCC-CCTTGCCCTCCTACTCCACCAGCAACATTAGTGCTAC
54 CTTCCACCACCTTTTCCACCAAA-CCCTCCTTGTCCTCCTACTCCACCA-CAGCATTA--G-T--
3319983 CACTTCCACCACC
112 -AC-T--ACCA-C
* * *
3319996 TTTTCCACCAAAACCTCC-TT--GTCCTACTCCACCATCAACATTAGCGCTACCACTTCCACCAC
1 --TTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCAC
* * * ** * *
3320058 CTTTTCCTCCAAATCCTCCTTGCCCTCCTACTCCACCAGCAATATTACTGCTACCAC
64 CTTTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCA-CAGCATTAGTACTACCAC
3320115 TTCCACCA
1 TTCCACCA
3320123 CCTTTTCCAC
Statistics
Matches: 657, Mismatches: 80, Indels: 135
0.75 0.09 0.15
Matches are distributed among these distances:
117 8 0.01
119 2 0.00
120 99 0.15
122 1 0.00
123 2 0.00
126 4 0.01
127 2 0.00
128 4 0.01
129 87 0.13
130 1 0.00
131 2 0.00
132 217 0.33
133 4 0.01
134 3 0.00
135 6 0.01
136 3 0.00
137 1 0.00
138 89 0.14
139 2 0.00
140 1 0.00
141 8 0.01
142 3 0.00
143 3 0.00
144 104 0.16
146 1 0.00
ACGTcount: A:0.24, C:0.45, G:0.06, T:0.26
Consensus pattern (119 bp):
TTCCACCAAACCCTCCTTTCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCT
TTTCCACCAAACCCTCCTTGTCCTCCTACTCCACCACAGCATTAGTACTACCAC
Found at i:3320184 original size:129 final size:127
Alignment explanation
Indices: 3319790--3320185 Score: 435
Period size: 129 Copynumber: 3.0 Consensus size: 127
3319780 ACCTCCACTT
* * * *
3319790 CCACCACCTTTACCACCAAACCCTTCTTGCCCTCCTACTCCACGAGCAATATTAGTGCTACCACT
1 CCACCACCTTTTCCACCAAATCCTCCTTGCCCTCCTACTCCACCAGCAATATTAGTGCTACCACT
* * * * * * *
3319855 TCCACTACCTTTTCCATCAAACCCTCCTTGCCCTCCTACTCCACCAACAACAT-TAACGCTACTA
66 TCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTA-TCCACC-TCAACATCCAACACT-TTA
* *
3319919 CTTCTACCACCTTTTCCACCAAATCCCCCTTGCCCTCCTACTCCACCAGCAACATTAGTGCTACC
1 C--C-ACCACCTTTTCCACCAAATCCTCCTTGCCCTCCTACTCCACCAGCAATATTAGTGCTACC
* * *
3319984 ACTTCCACCACCTTTTCCACCAAAACCTCCTTGTCCTAC--TCCACCATCAACATTAGCGCTACC
63 ACTTCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTATCCACC-TCAACA-T--C-C-AAC
3320047 AC-TT-
122 ACTTTA
* *
3320051 CCACCACCTTTTCCTCCAAATCCTCCTTGCCCTCCTACTCCACCAGCAATATTACTGCTACCACT
1 CCACCACCTTTTCCACCAAATCCTCCTTGCCCTCCTACTCCACCAGCAATATTAGTGCTACCACT
**
3320116 TCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTATGTTACCTCCAA-ATCCAACACTTTTA
66 TCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTAT-CCACCT-CAACATCCAACAC-TTTA
3320180 CCACCA
1 CCACCA
3320186 GCAATATTAC
Statistics
Matches: 226, Mismatches: 25, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
126 4 0.02
127 1 0.00
128 3 0.01
129 112 0.50
130 3 0.01
131 4 0.02
132 95 0.42
133 1 0.00
135 3 0.01
ACGTcount: A:0.24, C:0.44, G:0.05, T:0.27
Consensus pattern (127 bp):
CCACCACCTTTTCCACCAAATCCTCCTTGCCCTCCTACTCCACCAGCAATATTAGTGCTACCACT
TCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTATCCACCTCAACATCCAACACTTTA
Found at i:3320195 original size:90 final size:90
Alignment explanation
Indices: 3320090--3320365 Score: 435
Period size: 90 Copynumber: 3.1 Consensus size: 90
3320080 CCCTCCTACT
*
3320090 CCACCAGCAATATTACTGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTAT
1 CCACCAGCAATATTACCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTAT
*
3320155 GTTACCTCCAAATCCAACACTTTTA
66 ATTACCTCCAAATCCAACACTTTTA
* * ** ** *
3320180 CCACCAGCAATATTACCGCTACTACTTGCTTCACCTTTTTGACCAAATCCTCCTTGTCCTCCTAT
1 CCACCAGCAATATTACCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTAT
3320245 ATTACCTCCAAATCCAACACTTTTA
66 ATTACCTCCAAATCCAACACTTTTA
* *
3320270 CCACCAGCAATATTACCGCTGCCACTTCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCAAT
1 CCACCAGCAATATTACCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTAT
* *
3320335 ATTACCTCCAACTCCAACACCTTTA
66 ATTACCTCCAAATCCAACACTTTTA
3320360 CCACCA
1 CCACCA
3320366 CCTCTTGCTA
Statistics
Matches: 166, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 166 1.00
ACGTcount: A:0.26, C:0.41, G:0.05, T:0.29
Consensus pattern (90 bp):
CCACCAGCAATATTACCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGTCCTCCTAT
ATTACCTCCAAATCCAACACTTTTA
Found at i:3321666 original size:6 final size:6
Alignment explanation
Indices: 3321655--3321686 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3321645 ATTAAGCCTT
*
3321655 TTTTCC TTTTCC TTTTCC TTTTCA TTTTCC TT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TT
3321687 CTAAGGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTCC
Found at i:3322683 original size:11 final size:11
Alignment explanation
Indices: 3322667--3322694 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3322657 CAAAAAACGA
3322667 AGTCCAAGTTC
1 AGTCCAAGTTC
3322678 AGTCCAAGTTC
1 AGTCCAAGTTC
3322689 AGTCCA
1 AGTCCA
3322695 GAATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (11 bp):
AGTCCAAGTTC
Found at i:3322818 original size:19 final size:19
Alignment explanation
Indices: 3322793--3322883 Score: 134
Period size: 19 Copynumber: 4.9 Consensus size: 19
3322783 ATAATCTTCA
3322793 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
3322812 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3322831 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
3322848 ATGAT-TGCAATGTTAGAT
1 ATGATATGCAATCTTAGAT
*
3322866 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
3322884 AGATATGATT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
17 16 0.25
18 15 0.23
19 33 0.52
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:3322833 original size:14 final size:15
Alignment explanation
Indices: 3322814--3322851 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
3322804 TCTTAGATGT
3322814 GATATG-CAATCTTA
1 GATATGACAATCTTA
3322828 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
3322845 GATATGA
1 GATATGA
3322852 TTGCAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:3322864 original size:35 final size:37
Alignment explanation
Indices: 3322801--3322890 Score: 125
Period size: 35 Copynumber: 2.5 Consensus size: 37
3322791 CAATGATATG
*
3322801 CAATCTTAGATGTGATATGCAATCTTAGATATG-ATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGAATA
*
3322837 CAATCTTAGATATGAT-TGCAATGTTAGATATGATATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGA-ATA
3322874 CAATCTTAGA-A-GATATG
1 CAATCTTAGATATGATATG
3322891 ATTTTGTAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
35 18 0.37
36 18 0.37
37 13 0.27
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (37 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGAATA
Found at i:3323392 original size:17 final size:17
Alignment explanation
Indices: 3323372--3323431 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
3323362 CCAATAAATT
3323372 TTATATTTTTTATATAA
1 TTATATTTTTTATATAA
*
3323389 TTAT-TATTCTTATA-AA
1 TTATAT-TTTTTATATAA
3323405 -TATATTTTTTATTATATA
1 TTATATTTTTTA-TATA-A
3323423 TTATATTTT
1 TTATATTTT
3323432 AAATTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 8 0.23
16 6 0.17
17 12 0.34
18 1 0.03
19 8 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTTTTTATATAA
Found at i:3323416 original size:15 final size:16
Alignment explanation
Indices: 3323373--3323431 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
3323363 CAATAAATTT
3323373 TATATTTTTTATATAA
1 TATATTTTTTATATAA
3323389 T-TATTATTCTTATA-AA
1 TATATT-TT-TTATATAA
3323405 TATATTTTTTATTATATA
1 TATATTTTTTA-TATA-A
3323423 TTATATTTT
1 -TATATTTT
3323432 AAATTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.19
16 10 0.28
17 10 0.28
18 1 0.03
19 8 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTTTTATATAA
Found at i:3323456 original size:26 final size:26
Alignment explanation
Indices: 3323408--3323457 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3323398 TTATAAATAT
* * * *
3323408 ATTTTTTATTATATATTATATTTTAA
1 ATTTATTATTAAATATCACATTTTAA
3323434 ATTTATTATTAAATATCACATTTT
1 ATTTATTATTAAATATCACATTTT
3323458 TTTATATGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATTATTAAATATCACATTTTAA
Found at i:3328947 original size:66 final size:66
Alignment explanation
Indices: 3328827--3329009 Score: 150
Period size: 66 Copynumber: 2.8 Consensus size: 66
3328817 TCAACTAGAA
* * * *** * * * **
3328827 CCTCCTTACCCTACTACTCTACCAGCAACATTAATACTACCACTGCCACTACCTTCTCCACCTTA
1 CCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAA
*
3328892 T
66 C
* * * *
3328893 CCTCTTTGTCCTTCTACTCCACCAACAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAA
1 CCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAA
3328958 C
66 C
* ** ** ** *
3328959 CCTCTTTGTTCTCCTACTCCACCAATAACATTAGTACTACCACTTCTACCA
1 CCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCA
3329010 AACCCTCCTT
Statistics
Matches: 96, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 96 1.00
ACGTcount: A:0.25, C:0.42, G:0.04, T:0.30
Consensus pattern (66 bp):
CCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAA
C
Found at i:3329123 original size:120 final size:120
Alignment explanation
Indices: 3328910--3329391 Score: 347
Period size: 132 Copynumber: 3.8 Consensus size: 120
3328900 GTCCTTCTAC
* **
3328910 TCCACCAACAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCTTTGTTCTCCTA
1 TCCACCAACAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTA
* * * *
3328975 CTCCACCAATAACATTAGTACTACCACTTCTACCAAACCCTCCTTTCCCTCCTAT
66 CTCCACCAACAAAATTAGCACTACCACTTCCACCAAACCCTCCTTTCCCTCCTAT
* * * *
3329030 TCCACCAGCAACATTAGCGTTGCCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCTTA
1 TCCACCAACAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTA
* * * * *
3329095 CTCCACTAGCAAAATTTGCGCTACCACTTCCACCACATTTTCCACCAAACCCTCCTTGCCCTGCT
66 CTCCACCAACAAAA--T----TAGCAC-T--ACCAC---TTCCACCAAACCCTCCTTTCCCTCCT
*
3329160 AC
119 AT
* * * * *
3329162 TCCA-CAAGCAAAATTTGTGCTACCACTTCCACCACATTTTCCACCAAACCCTCATTGCCCTCCT
1 TCCACCAA-CAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCT
* * * * *
3329226 ATTCCACCACCAACATTAGCGCTACTAGTTCCACCACTTTTTCCACCAAACTCTCTTTTCCCTCC
65 ACTCCACCAACAAAATTA--GC-AC----T--ACCAC---TTCCACCAAACCCTCCTTTCCCTCC
*
3329291 TAA
118 TAT
** * * * * * *
3329294 TCCACCAGTAACATTAACACTACCACTTCTACCACC-TTTCTCACCCAATCCTCCTTGCCCTTCT
1 TCCACCAACAACATTAGCGCTACCACTTCCACCACCTTTTC-CACCAAACCCTCCTTGCCCTCCT
* * * **
3329358 ACTCCGCCAGCAACATTAGTGCTACCACTTCCAC
65 ACTCCACCAACAAAATTAGCACTACCACTTCCAC
3329392 TACCGTTTCC
Statistics
Matches: 286, Mismatches: 55, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
120 74 0.26
122 1 0.00
123 5 0.02
125 1 0.00
126 6 0.02
127 1 0.00
128 1 0.00
129 8 0.03
130 2 0.01
131 6 0.02
132 179 0.63
133 2 0.01
ACGTcount: A:0.25, C:0.42, G:0.06, T:0.27
Consensus pattern (120 bp):
TCCACCAACAACATTAGCGCTACCACTTCCACCACCTTTTCCACCAAACCCTCCTTGCCCTCCTA
CTCCACCAACAAAATTAGCACTACCACTTCCACCAAACCCTCCTTTCCCTCCTAT
Found at i:3329459 original size:66 final size:66
Alignment explanation
Indices: 3329006--3329457 Score: 537
Period size: 66 Copynumber: 6.8 Consensus size: 66
3328996 TACCACTTCT
* * * *
3329006 ACCAAACCCTCCTTTCCCTCCTATTCCACCAGCAACATTAGCGTTGCCACTTCCACCACCTTTTC
1 ACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTC
3329071 C
66 C
* * * * *
3329072 ACCAAACCCTCCTTGCCCTCTTACTCCACTAGCAAAATTTGCGCTACCACTTCCACCACATTTTC
1 ACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTC
3329137 C
66 C
* * * * * *
3329138 ACCAAACCCTCCTTGCCCTGCTACTCCACAAGCAAAATTTGTGCTACCACTTCCACCACATTTTC
1 ACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTC
3329203 C
66 C
* * * * * *
3329204 ACCAAACCCTCATTGCCCTCCTATTCCACCACCAACATTAGCGCTACTAGTTCCACCACTTTTTC
1 ACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTC
3329269 C
66 C
* * * * * * * *
3329270 ACCAAACTCTCTTTTCCCTCCTAATCCACCAGTAACATTAACACTACCACTTCTACCACC-TTTC
1 ACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTC
3329334 TC
66 -C
* * * * * * *
3329336 ACCCAATCCTCCTTGCCCTTCTACTCCGCCAGCAACATTAGTGCTACCACTTCCACTACCGTTTC
1 ACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTC
3329401 C
66 C
* **
3329402 ACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAATATTAGCATTACCACTTCCAC
1 ACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCAC
3329458 TATGTGAAAA
Statistics
Matches: 326, Mismatches: 58, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
65 4 0.01
66 318 0.98
67 4 0.01
ACGTcount: A:0.24, C:0.43, G:0.06, T:0.27
Consensus pattern (66 bp):
ACCAAACCCTCCTTGCCCTCCTACTCCACCAGCAACATTAGCGCTACCACTTCCACCACCTTTTC
C
Found at i:3334492 original size:132 final size:132
Alignment explanation
Indices: 3334247--3334534 Score: 409
Period size: 132 Copynumber: 2.2 Consensus size: 132
3334237 CTAACACACT
* * * * *
3334247 ACCTTTTCCACCAAACCCTCCTTACGCTCTTACTCTACCAGCAACATTAACATTAACACTTCTAC
1 ACCTTTTCCACCAAACCCTCCTTGCCCTCTTACTCCACCAACAACATTAACATTAACACTTCCAC
** * *
3334312 CATTTTTTCCACCAAACCCCCATTGCCCTCCTACTCTACCAACGACATTAG-CACTACCACTTCC
66 CACATTTTCCACCAAACCCCCATTGCCCTCCTACTCCACCAACAACATT-GCCACTACCACTTCC
3334376 ACC
130 ACC
* * *
3334379 ACCTTTTCCACCAAACCCTCCTTGCCCTCTTACTCCACCAACAACATTAGCGTTACCACTTCCAC
1 ACCTTTTCCACCAAACCCTCCTTGCCCTCTTACTCCACCAACAACATTAACATTAACACTTCCAC
* * *
3334444 CACATTTTCCTCCAAACCCTCC-TTGCCTTCCTACTCCACCAGCAACATTGCCACTACCACTTCC
66 CACATTTTCCACCAAACCC-CCATTGCCCTCCTACTCCACCAACAACATTGCCACTACCACTTCC
3334508 ACC
130 ACC
3334511 ACCTTTTCCACCAAACCCTCCTTG
1 ACCTTTTCCACCAAACCCTCCTTG
3334535 TCTTCCTATA
Statistics
Matches: 139, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
131 1 0.01
132 136 0.98
133 2 0.01
ACGTcount: A:0.25, C:0.44, G:0.04, T:0.27
Consensus pattern (132 bp):
ACCTTTTCCACCAAACCCTCCTTGCCCTCTTACTCCACCAACAACATTAACATTAACACTTCCAC
CACATTTTCCACCAAACCCCCATTGCCCTCCTACTCCACCAACAACATTGCCACTACCACTTCCA
CC
Found at i:3334542 original size:66 final size:66
Alignment explanation
Indices: 3334247--3334534 Score: 364
Period size: 66 Copynumber: 4.4 Consensus size: 66
3334237 CTAACACACT
* * * * * * * * *
3334247 ACCTTTTCCACCAAACCCTCCTTACGCTCTTACTCTACCAGCAACATTAACATTAACACTTCTAC
1 ACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAACAACATTAGCACTACCACTTCCAC
3334312 C
66 C
** * *
3334313 ATTTTTTCCACCAAACCC-CCATTGCCCTCCTACTCTACCAACGACATTAGCACTACCACTTCCA
1 ACCTTTTCCACCAAACCCTCC-TTGCCCTCCTACTCCACCAACAACATTAGCACTACCACTTCCA
3334377 CC
65 CC
* **
3334379 ACCTTTTCCACCAAACCCTCCTTGCCCTCTTACTCCACCAACAACATTAGCGTTACCACTTCCAC
1 ACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAACAACATTAGCACTACCACTTCCAC
3334444 C
66 C
* * * *
3334445 ACATTTTCCTCCAAACCCTCCTTGCCTTCCTACTCCACCAGCAACATT-GCCACTACCACTTCCA
1 ACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAACAACATTAG-CACTACCACTTCCA
3334509 CC
65 CC
3334511 ACCTTTTCCACCAAACCCTCCTTG
1 ACCTTTTCCACCAAACCCTCCTTG
3334535 TCTTCCTATA
Statistics
Matches: 192, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
65 3 0.02
66 187 0.97
67 2 0.01
ACGTcount: A:0.25, C:0.44, G:0.04, T:0.27
Consensus pattern (66 bp):
ACCTTTTCCACCAAACCCTCCTTGCCCTCCTACTCCACCAACAACATTAGCACTACCACTTCCAC
C
Done.