Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 383 of 410
Found at i:116335407 original size:14 final size:14
Alignment explanation
Indices: 116335390--116335416 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
116335380 TATAATATCC
116335390 AAATAATAACAATA
1 AAATAATAACAATA
116335404 AAATAATAACAAT
1 AAATAATAACAAT
116335417 TAATAGCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:116336854 original size:18 final size:18
Alignment explanation
Indices: 116336827--116336862 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
116336817 TAGAATAAAG
116336827 ATATAAAGAAATCAACAA
1 ATATAAAGAAATCAACAA
*
116336845 ATATACAGAAATCAACAA
1 ATATAAAGAAATCAACAA
116336863 GAAACAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.14, G:0.06, T:0.17
Consensus pattern (18 bp):
ATATAAAGAAATCAACAA
Found at i:116343281 original size:2 final size:2
Alignment explanation
Indices: 116343274--116343298 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
116343264 GCAAAATTTG
116343274 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
116343299 ATGTATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:116345847 original size:23 final size:23
Alignment explanation
Indices: 116345791--116345854 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 23
116345781 ATAGTTTAAG
* *
116345791 AAATATATACATGAAAACAT-TAA
1 AAATATATACAT-AATATATATAA
*
116345814 AAATA-AGTACATAATATATATAT
1 AAATATA-TACATAATATATATAA
116345837 AAATATATAC--AATATATA
1 AAATATATACATAATATATA
116345855 CCTATATTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 8 0.23
22 6 0.17
23 20 0.57
24 1 0.03
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (23 bp):
AAATATATACATAATATATATAA
Found at i:116346077 original size:20 final size:17
Alignment explanation
Indices: 116346052--116346094 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
116346042 GTACGTAATG
116346052 TACATAAATATATATATAT
1 TACATAAATATA-ATAT-T
116346071 ATACAT-AATATAATATT
1 -TACATAAATATAATATT
116346088 TACATAA
1 TACATAA
116346095 TGTATACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 2 0.09
18 4 0.18
19 6 0.27
20 5 0.23
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
TACATAAATATAATATT
Found at i:116346091 original size:16 final size:17
Alignment explanation
Indices: 116346061--116346218 Score: 57
Period size: 17 Copynumber: 9.3 Consensus size: 17
116346051 GTACATAAAT
116346061 ATATATATATATACATA
1 ATATATATATATACATA
*
116346078 ATATA-ATATTTACATA
1 ATATATATATATACATA
* * * * *
116346094 ATGTATACATACAAAAA
1 ATATATATATATACATA
*
116346111 AGGACTATTAATAATACTACATAA
1 A-TA-TA-T-AT-ATA-TACAT-A
* *
116346135 ATATATACGTATATATAAA
1 ATATATA--TATATACATA
116346154 ATATATATATATACAT-
1 ATATATATATATACATA
116346170 ATATA-ATAT-T--A-A
1 ATATATATATATACATA
*
116346182 A-A-ATGTATATACATA
1 ATATATATATATACATA
*
116346197 ATATATATGA-AAACATA
1 ATATATAT-ATATACATA
116346214 ATATA
1 ATATA
116346219 GTATTAGAAA
Statistics
Matches: 101, Mismatches: 21, Indels: 38
0.63 0.13 0.24
Matches are distributed among these distances:
10 1 0.01
11 4 0.04
12 3 0.03
14 2 0.02
15 6 0.06
16 20 0.20
17 33 0.33
18 1 0.01
19 10 0.10
20 5 0.05
21 5 0.05
22 6 0.06
23 3 0.03
24 2 0.02
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (17 bp):
ATATATATATATACATA
Found at i:116346217 original size:26 final size:24
Alignment explanation
Indices: 116346144--116346218 Score: 60
Period size: 26 Copynumber: 2.8 Consensus size: 24
116346134 AATATATACG
116346144 TATATATAAAATATATATATATACATA
1 TATATATAAAA-A-ATA-ATATACATA
* *
116346171 TATAATATTAAAAATGTATATACATAA
1 TAT-ATATAAAAAAT-AATATACAT-A
*
116346198 TATATATGAAAACATAATATA
1 TATATAT-AAAAAATAATATA
116346219 GTATTAGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
26 19 0.49
27 13 0.33
28 7 0.18
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
TATATATAAAAAATAATATACATA
Found at i:116346427 original size:20 final size:21
Alignment explanation
Indices: 116346398--116346436 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
116346388 ACTCACACAC
116346398 ACATATATA-TATATAAAAAAA
1 ACATATATATTAT-TAAAAAAA
116346419 ACATA-ATATTATTAAAAA
1 ACATATATATTATTAAAAA
116346437 TACGTTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
ACATATATATTATTAAAAAAA
Found at i:116346973 original size:20 final size:20
Alignment explanation
Indices: 116346948--116347053 Score: 67
Period size: 21 Copynumber: 5.2 Consensus size: 20
116346938 CTAATAACAT
116346948 TAAAATACATACATAATATA
1 TAAAATACATACATAATATA
116346968 TAAAATACAT--ATAATATA
1 TAAAATACATACATAATATA
* * * * *
116346986 TATATTAGAAATGATAATAATA
1 TAAAATACATA-CATAAT-ATA
* *
116347008 TAAAA-ACTATTCATACGCTATA
1 TAAAATAC-ATACATA--ATATA
116347030 T-AAATACATACATATATATA
1 TAAAATACATACATA-ATATA
116347050 TAAA
1 TAAA
116347054 GTAATGATGT
Statistics
Matches: 63, Mismatches: 14, Indels: 17
0.67 0.15 0.18
Matches are distributed among these distances:
18 14 0.22
20 15 0.24
21 20 0.32
22 13 0.21
23 1 0.02
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAAATACATACATAATATA
Found at i:116346983 original size:18 final size:19
Alignment explanation
Indices: 116346939--116346987 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
116346929 TATATGTAAC
*
116346939 TAATAACAT-TAAAATACA
1 TAATAATATATAAAATACA
116346957 TACATAATATATAAAATACA
1 TA-ATAATATATAAAATACA
116346977 T-ATAATATATA
1 TAATAATATATA
116346988 TATTAGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 12 0.43
19 6 0.21
20 10 0.36
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAATATATAAAATACA
Found at i:116347080 original size:19 final size:19
Alignment explanation
Indices: 116347056--116347092 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
116347046 TATATAAAGT
*
116347056 AATGATGTTAGAAATATAC
1 AATGATATTAGAAATATAC
*
116347075 AATGATATTCGAAATATA
1 AATGATATTAGAAATATA
116347093 TGTAAAATAG
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:0.14, T:0.32
Consensus pattern (19 bp):
AATGATATTAGAAATATAC
Found at i:116347192 original size:24 final size:25
Alignment explanation
Indices: 116347148--116347206 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
116347138 TATAAACAAT
*
116347148 AATATATATAACATACAATAT-TGAA
1 AATATATAT-ACATACAATATACGAA
116347173 AATATATATACATA-ATATATACGAA
1 AATATATATACATACA-ATATACGAA
116347198 AA-ATATATA
1 AATATATATA
116347207 GATATACATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 1 0.03
24 16 0.52
25 14 0.45
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (25 bp):
AATATATATACATACAATATACGAA
Found at i:116347231 original size:30 final size:30
Alignment explanation
Indices: 116347178--116347252 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
116347168 TTGAAAATAT
*
116347178 ATATACATAATATATACGAAAAATATATAG
1 ATATACATAATATATACGAAAAATATATAC
** *
116347208 ATATACATAATATAATA-TTAAAATATTTAC
1 ATATACATAATAT-ATACGAAAAATATATAC
116347238 ATAATACATAA-ATAT
1 AT-ATACATAATATAT
116347253 TAGGAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 26 0.67
31 11 0.28
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.35
Consensus pattern (30 bp):
ATATACATAATATATACGAAAAATATATAC
Found at i:116350672 original size:21 final size:21
Alignment explanation
Indices: 116350646--116350687 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
116350636 CAAACCTAGT
116350646 ATTATTAATTAGGATTGTTTC
1 ATTATTAATTAGGATTGTTTC
116350667 ATTATTAATTAGGATTGTTTC
1 ATTATTAATTAGGATTGTTTC
116350688 CCCCATACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (21 bp):
ATTATTAATTAGGATTGTTTC
Found at i:116352548 original size:113 final size:113
Alignment explanation
Indices: 116352421--116352646 Score: 452
Period size: 113 Copynumber: 2.0 Consensus size: 113
116352411 CATCATAAAA
116352421 ATAATAAGAAATATAAGACATTTTTAAAGAACCTTTACTATATAAGGGATTGATACTGTTGATAT
1 ATAATAAGAAATATAAGACATTTTTAAAGAACCTTTACTATATAAGGGATTGATACTGTTGATAT
116352486 TCAAATTTCAGAATTATTGAGATAGGGGAAATAGCAAGGACTAAAATT
66 TCAAATTTCAGAATTATTGAGATAGGGGAAATAGCAAGGACTAAAATT
116352534 ATAATAAGAAATATAAGACATTTTTAAAGAACCTTTACTATATAAGGGATTGATACTGTTGATAT
1 ATAATAAGAAATATAAGACATTTTTAAAGAACCTTTACTATATAAGGGATTGATACTGTTGATAT
116352599 TCAAATTTCAGAATTATTGAGATAGGGGAAATAGCAAGGACTAAAATT
66 TCAAATTTCAGAATTATTGAGATAGGGGAAATAGCAAGGACTAAAATT
116352647 GTAAATAAAA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (113 bp):
ATAATAAGAAATATAAGACATTTTTAAAGAACCTTTACTATATAAGGGATTGATACTGTTGATAT
TCAAATTTCAGAATTATTGAGATAGGGGAAATAGCAAGGACTAAAATT
Found at i:116354603 original size:2 final size:2
Alignment explanation
Indices: 116354596--116354640 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
116354586 ATCTTTAAAA
116354596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116354638 AT A
1 AT A
116354641 AAGCTAAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:116355247 original size:286 final size:283
Alignment explanation
Indices: 116354735--116355258 Score: 686
Period size: 286 Copynumber: 1.8 Consensus size: 283
116354725 AGTCAAAGAT
116354735 TTTTAAAAATTCTAATTATCTAATTAAAATTATAATAAATTTTAATTATTAAATATAATAATTAC
1 TTTTAAAAATTCTAATTATCTAATTAAAATTATAATAAATTTTAATTATTAAATATAATAATTAC
* *
116354800 CTAAATTATTATATTTCTTATTTAATAAATAAATATTTTTATAAACAAATGGATAATATATAAAA
66 CTAAATTATTATATTTCTTATTTAATAAATAAACACTTTTATAAACAAATGGATAATATATAAAA
*** * * ** *
116354865 TTTTGAAATGTGAATTTTACTTATATTTTAATTTAATTTAAATTATATCCAAATTTGATAATTAG
131 AAATGAAATGTAAATTTTACTTATATATTAATCGAA--TAAA-TATATCCAAATTTGATAATTAA
* *
116354930 TTTTTAAATTTTTATGTTAAAATTAAAATTTAAAATATATAAATGGATATTTATCTAATTATATT
193 TTTTTAAATTTTTATGTTAAAAATAAAATTTAAAATAGATAAATGGATATTTATCTAATTATATT
116354995 TTTATTTAATTAAACATTTATCTAAA
258 TTTATTTAATTAAACATTTATCTAAA
* * *
116355021 TTTTAAAAATT-TAAATTGTCTAATTAGAATTTTAATAAATTTTAATTATTAAATATAATAATTA
1 TTTTAAAAATTCT-AATTATCTAATTAAAATTATAATAAATTTTAATTATTAAATATAATAATTA
* * *
116355085 TCC-AAATTTTTATATTTAATTTTCTTATTTAATTAAATAAACACTTTTATAATCAAATGGGTAA
65 -CCTAAA---TTAT-TAT-A-TTTCTTATTTAA-TAAATAAACACTTTTATAAACAAATGGATAA
* *
116355149 TATATAAAAAAATGAAATGTAAATTTTCCTTA-A-ATT-ATCCGAA-AAA-A-ATCTAAATTTGA
122 TATATAAAAAAATGAAATGTAAATTTTACTTATATATTAAT-CGAATAAATATATCCAAATTTGA
116355208 TAATTAATTTTTAAAATTTTTATGTTAAAAATAAAATTTAAAATAGATAAA
186 TAATTAATTTTT-AAATTTTTATGTTAAAAATAAAATTTAAAATAGATAAA
116355259 AATTATATAT
Statistics
Matches: 207, Mismatches: 20, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
285 23 0.11
286 99 0.48
287 2 0.01
288 3 0.01
289 4 0.02
290 4 0.02
291 5 0.02
292 13 0.06
293 54 0.26
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (283 bp):
TTTTAAAAATTCTAATTATCTAATTAAAATTATAATAAATTTTAATTATTAAATATAATAATTAC
CTAAATTATTATATTTCTTATTTAATAAATAAACACTTTTATAAACAAATGGATAATATATAAAA
AAATGAAATGTAAATTTTACTTATATATTAATCGAATAAATATATCCAAATTTGATAATTAATTT
TTAAATTTTTATGTTAAAAATAAAATTTAAAATAGATAAATGGATATTTATCTAATTATATTTTT
ATTTAATTAAACATTTATCTAAA
Found at i:116356543 original size:57 final size:56
Alignment explanation
Indices: 116356434--116356544 Score: 154
Period size: 57 Copynumber: 1.9 Consensus size: 56
116356424 TTCACACTAG
*
116356434 TTGGTGAATTTAATTGAGTTGTTTTTTTTTTAATTTGCATTAAAGAATTTTAAATTT
1 TTGGTGAATTTAATTGAGTTGTTTTTTTTTTAATTT-CATTAAAGAAATTTAAATTT
*
116356491 TTGGTGAATTTAATTGGGTTGCTTTTTATTTTTAATTT-ATATAAA-AAATTTAAA
1 TTGGTGAATTTAATTGAGTTG-TTTTT-TTTTTAATTTCAT-TAAAGAAATTTAAA
116356545 AAAATTTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
57 30 0.61
58 9 0.18
59 10 0.20
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.54
Consensus pattern (56 bp):
TTGGTGAATTTAATTGAGTTGTTTTTTTTTTAATTTCATTAAAGAAATTTAAATTT
Found at i:116356907 original size:18 final size:18
Alignment explanation
Indices: 116356886--116356935 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
116356876 ATATTTAAAT
*
116356886 TAAAAAAATATGAAATAG
1 TAAAAAAATATAAAATAG
*
116356904 TAAAAAATTATAAAATA-
1 TAAAAAAATATAAAATAG
* *
116356921 TATAGAAATATAAAA
1 TAAAAAAATATAAAA
116356936 AAATATATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
TAAAAAAATATAAAATAG
Found at i:116356918 original size:27 final size:27
Alignment explanation
Indices: 116356863--116356948 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 27
116356853 TAATTTTAAC
* **
116356863 AAAAAATATAAAAATAT-TTAAATTA-
1 AAAAAATATAGAAATATAAAAAATTAT
116356888 AAAAAATAT-GAAATAGTAAAAAATTAT
1 AAAAAATATAGAAATA-TAAAAAATTAT
* *
116356915 AAAATATATAGAAATATAAAAAAATAT
1 AAAAAATATAGAAATATAAAAAATTAT
*
116356942 ATAAAAT
1 AAAAAAT
116356949 TTTATAAGTC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
24 5 0.10
25 10 0.20
26 6 0.12
27 23 0.46
28 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAAATATAGAAATATAAAAAATTAT
Found at i:116357229 original size:10 final size:10
Alignment explanation
Indices: 116357216--116357290 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
116357206 TTTTTTTGGA
116357216 TTTTATTATT
1 TTTTATTATT
* *
116357226 TTTTATAAAT
1 TTTTATTATT
**
116357236 TTTTATTAAA
1 TTTTATTATT
* * *
116357246 ATTTAATAAT
1 TTTTATTATT
*
116357256 TTTTATAATTT
1 TTTTATTA-TT
116357267 TTTTATT-TT
1 TTTTATTATT
116357276 TATTTATTATT
1 T-TTTATTATT
116357287 TTTT
1 TTTT
116357291 TGCCACATGT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
9 3 0.06
10 37 0.74
11 10 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATTATT
Found at i:116357288 original size:30 final size:29
Alignment explanation
Indices: 116357217--116357289 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
116357207 TTTTTTGGAT
116357217 TTTATTATTTTTTATAAATTTTTATTAAAA
1 TTTATTA-TTTTTATAAATTTTTATTAAAA
* * ***
116357247 TTTAATAATTTTTATAATTTTTTTATTTTTA
1 TTT-ATTATTTTTATAA-ATTTTTATTAAAA
116357278 TTTATTATTTTT
1 TTTATTATTTTT
116357290 TTGCCACATG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 20 0.57
31 15 0.43
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTATTATTTTTATAAATTTTTATTAAAA
Found at i:116358704 original size:32 final size:33
Alignment explanation
Indices: 116358639--116358704 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
116358629 CAACCCAATT
* *
116358639 TAAAATTAAATTATACAAAAAATATATATTTTAG
1 TAAAATTAAATTATA-AAAAAATATAAAATTTAG
* *
116358673 TAAAATTGAATTAT-AAATAATATAAAATTTAG
1 TAAAATTAAATTATAAAAAAATATAAAATTTAG
116358705 AGTAAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 15 0.54
34 13 0.46
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (33 bp):
TAAAATTAAATTATAAAAAAATATAAAATTTAG
Found at i:116361377 original size:22 final size:23
Alignment explanation
Indices: 116361347--116361395 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
116361337 GGTAGCTCCG
116361347 TATTACATGCTATATCTTTCCTT
1 TATTACATGCTATATCTTTCCTT
116361370 TATT-CATGCTATATCTTTCCTT
1 TATTACATGCTATATCTTTCCTT
116361392 TATT
1 TATT
116361396 GTTGAATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.55
Consensus pattern (23 bp):
TATTACATGCTATATCTTTCCTT
Found at i:116364200 original size:85 final size:85
Alignment explanation
Indices: 116364057--116364226 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
116364047 CATTTCACTA
116364057 GCTTATAAACATGTCCATGAACCGAGCTGTCCACAAGGCTCACGGGCTAGGCCATTGATAAGGAT
1 GCTTATAAACATGTCCATGAACCGAGCTGTCCACAAGGCTCACGGGCTAGGCCATTGATAAGGAT
116364122 CTTAAAACCCTTGTACTCAT
66 CTTAAAACCCTTGTACTCAT
116364142 GCTTATAAACATGTCCATGAACCGAGCTGTCCACAAGGCTCACGGGCTAGGCCATTGATAAGGAT
1 GCTTATAAACATGTCCATGAACCGAGCTGTCCACAAGGCTCACGGGCTAGGCCATTGATAAGGAT
116364207 CTTAAAACCCTTGTACTCAT
66 CTTAAAACCCTTGTACTCAT
116364227 AGTCACTGGT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (85 bp):
GCTTATAAACATGTCCATGAACCGAGCTGTCCACAAGGCTCACGGGCTAGGCCATTGATAAGGAT
CTTAAAACCCTTGTACTCAT
Found at i:116369034 original size:84 final size:84
Alignment explanation
Indices: 116368893--116369061 Score: 293
Period size: 84 Copynumber: 2.0 Consensus size: 84
116368883 AGTCTTAGTA
* * * *
116368893 TTAGTAATCTAAAGCGCTCTTTCACTCGTTTGCATTCTCTCCCCATTCTTTACTTCCTAAGAAGC
1 TTAGTAATCCAAAGCGCTCTTTCACTCGTTTGCACTCGCTCCCCATTCCTTACTTCCTAAGAAGC
116368958 TCATTATTCAGTGTTGGCT
66 TCATTATTCAGTGTTGGCT
*
116368977 TTAGTAATCCAAAGCGCTCTTTCACTCGTTTGCACTCGCTCCCTATTCCTTACTTCCTAAGAAGC
1 TTAGTAATCCAAAGCGCTCTTTCACTCGTTTGCACTCGCTCCCCATTCCTTACTTCCTAAGAAGC
116369042 TCATTATTCAGTGTTGGCT
66 TCATTATTCAGTGTTGGCT
116369061 T
1 T
116369062 AAGCTAGATC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (84 bp):
TTAGTAATCCAAAGCGCTCTTTCACTCGTTTGCACTCGCTCCCCATTCCTTACTTCCTAAGAAGC
TCATTATTCAGTGTTGGCT
Found at i:116371404 original size:33 final size:33
Alignment explanation
Indices: 116371362--116371428 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
116371352 AGAGTTGTTG
*
116371362 AATTGCACTCGGCAGTACTAACTGCAGATTATC
1 AATTGCACTCGACAGTACTAACTGCAGATTATC
116371395 AATTGCACTCGACAGTACTAACTGCAGATTATC
1 AATTGCACTCGACAGTACTAACTGCAGATTATC
116371428 A
1 A
116371429 CTAAAGTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (33 bp):
AATTGCACTCGACAGTACTAACTGCAGATTATC
Found at i:116372165 original size:22 final size:22
Alignment explanation
Indices: 116372115--116372166 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
116372105 TCTAAATAAT
* * *
116372115 AACAACAAAATAATAGTAATAT
1 AACAGCAAAATAATAGTAAAAC
* *
116372137 AATAGCAAAATGATAGTAAAAC
1 AACAGCAAAATAATAGTAAAAC
116372159 AACAGCAA
1 AACAGCAA
116372167 GAAAAAATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.17
Consensus pattern (22 bp):
AACAGCAAAATAATAGTAAAAC
Found at i:116373143 original size:19 final size:18
Alignment explanation
Indices: 116373119--116373166 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
116373109 ACGTAAAAAG
116373119 TAAAAAGTAAAAGATGAAA
1 TAAAAA-TAAAAGATGAAA
116373138 TAAAAATAAAAAGATGAAA
1 TAAAAAT-AAAAGATGAAA
116373157 TAAAAATAAA
1 TAAAAATAAA
116373167 TAACAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (18 bp):
TAAAAATAAAAGATGAAA
Found at i:116374085 original size:16 final size:16
Alignment explanation
Indices: 116374055--116374102 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
116374045 GAAAATTAAT
116374055 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
116374070 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
116374087 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
116374102 A
1 A
116374103 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:116374101 original size:11 final size:11
Alignment explanation
Indices: 116374046--116374116 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
116374036 ATAGCTTAAG
*
116374046 AAAATTAATAT
1 AAAATTAAAAT
116374057 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
116374069 AATAA-T-AATT
1 AA-AATTAAAAT
*
116374079 AAAAAT-AAAT
1 AAAATTAAAAT
116374089 AAAATTAAAAT
1 AAAATTAAAAT
*
116374100 AAACTTAAAAT
1 AAAATTAAAAT
*
116374111 AGAATT
1 AAAATT
116374117 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:116378977 original size:6 final size:6
Alignment explanation
Indices: 116378958--116379030 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 6
116378948 TATTAGAACT
* * * *
116378958 AGAATC AAAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
*
116379007 AGGTAAT- AGAATC AAAATC AGAAT
1 A-G-AATC AGAATC AGAATC AGAAT
116379031 GTGAATGCAA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
5 4 0.08
6 40 0.78
7 4 0.08
8 3 0.06
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:116378994 original size:25 final size:25
Alignment explanation
Indices: 116378966--116379030 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
116378956 CTAGAATCAA
* *
116378966 AATCAGAATCAGAATTAGGTGACAG
1 AATCAGAATCAGAATCAGGTAACAG
* *
116378991 AATCAGAATCAGTATCAGGTAATAG
1 AATCAGAATCAGAATCAGGTAACAG
*
116379016 AATCAAAATCAGAAT
1 AATCAGAATCAGAAT
116379031 GTGAATGCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (25 bp):
AATCAGAATCAGAATCAGGTAACAG
Found at i:116379255 original size:27 final size:26
Alignment explanation
Indices: 116379162--116379256 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 26
116379152 GCCCAGTTAT
* * *
116379162 CAGATATTGTGACAGAGTCACCTGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
*
116379189 CAGATATTGTGGAAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
116379215 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
*
116379243 CAGATAATGTGGCA
1 CAGATATTGTGGCA
116379257 AAGCTACTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 7 0.12
27 44 0.75
28 8 0.14
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:116379450 original size:22 final size:22
Alignment explanation
Indices: 116379422--116379486 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
116379412 GCAAATACGT
*
116379422 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
116379444 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
116379466 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
116379487 AAGACTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:116379978 original size:27 final size:27
Alignment explanation
Indices: 116379931--116380429 Score: 644
Period size: 27 Copynumber: 18.6 Consensus size: 27
116379921 TGCCCCACAA
* *
116379931 GGTATCTCGGTAATTCCACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* ** *
116379958 GATATTTTAGTAATTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
** * *
116379985 GGTATTTTTGTAATTCTACCTTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * *
116380012 GGTATTGCGATAATTCTACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
116380039 GGTATTTCGGTAATTCTACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
116380066 GGTATTTCGATAATTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
116380093 GGTATTGCGATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
116380120 GGTATTCCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
116380147 GGTATTTCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * * *
116380174 GTTATTGCGATAATTCTACCCTGCAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
116380201 GGTATTTCGGTAATTCTACCCTATA-G
1 GGTATTTCGGTAATTCTACCCTACAGG
116380227 GGTATTTCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
116380254 GGTATTGCGATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
116380281 GGTATTTCGATAATTCTACCCT-CAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
116380307 GGTATTTCGGTAATTTTACCCTAGAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* **
116380334 GGTATTGCAATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
116380361 GGT-GTTCTGGTAATTCTACCCTACAGG
1 GGTATTTC-GGTAATTCTACCCTACAGG
** *
116380388 GGTATTTCGGTTTTTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
116380415 GGTATTTCGGTAATT
1 GGTATTTCGGTAATT
116380430 TTGTAAATCG
Statistics
Matches: 411, Mismatches: 57, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
26 51 0.12
27 357 0.87
28 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCCTACAGG
Found at i:116380443 original size:27 final size:26
Alignment explanation
Indices: 116380413--116380780 Score: 272
Period size: 27 Copynumber: 13.7 Consensus size: 26
116380403 CTACCCTACA
* **
116380413 AGGGTATTTCGGTAATTTTGTAAATC
1 AGGGTATTTTGGTAATTTTACAAATC
*** * ** *
116380439 GAGGGTAAAATGGTAATTCTGTAAGTC
1 -AGGGTATTTTGGTAATTTTACAAATC
* *
116380466 AAGGGTACTTTGGTAATTTTACAAGTC
1 A-GGGTATTTTGGTAATTTTACAAATC
*** **
116380493 GAGGGTATTTCAATAATTTTACAGGTC
1 -AGGGTATTTTGGTAATTTTACAAATC
* ** *
116380520 GAAGGTATTTCAGTAATTTCACAAATC
1 -AGGGTATTTTGGTAATTTTACAAATC
*
116380547 AGGGGTATTTTGGTAATTTCACAAATC
1 A-GGGTATTTTGGTAATTTTACAAATC
*
116380574 AGGGTATTTTGGTAATTTTATAAA-C
1 AGGGTATTTTGGTAATTTTACAAATC
*
116380599 TAGGGGTATTTTGATAATTTTACAAATC
1 -A-GGGTATTTTGGTAATTTTACAAATC
* *
116380627 AGGGGTATTTTGATAATTTTACAAACC
1 A-GGGTATTTTGGTAATTTTACAAATC
** *
116380654 AGGGGTATTTTGGTAATTTTGTAAACC
1 A-GGGTATTTTGGTAATTTTACAAATC
*
116380681 AAGGGTATTTTGATAATTTTACAAA-C
1 -AGGGTATTTTGGTAATTTTACAAATC
* * *
116380707 TAGGGGTATTTTGGTGATTTTATAAACC
1 -A-GGGTATTTTGGTAATTTTACAAATC
* * *
116380735 AAGGGTATTTTAGTGATTTTACAAACC
1 -AGGGTATTTTGGTAATTTTACAAATC
116380762 AGGGATATTTTGGTAATTT
1 AGGG-TATTTTGGTAATTT
116380781 GGTAAACTAA
Statistics
Matches: 286, Mismatches: 45, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.00
26 30 0.10
27 250 0.87
28 5 0.02
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAATC
Found at i:116380787 original size:27 final size:27
Alignment explanation
Indices: 116380523--116380780 Score: 311
Period size: 27 Copynumber: 9.6 Consensus size: 27
116380513 ACAGGTCGAA
** * *
116380523 GGTATTTCAGTAATTTCACAAATCAGG
1 GGTATTTTGGTAATTTTACAAACCAGG
* *
116380550 GGTATTTTGGTAATTTCACAAATCA-G
1 GGTATTTTGGTAATTTTACAAACCAGG
* *
116380576 GGTATTTTGGTAATTTTATAAACTAGG
1 GGTATTTTGGTAATTTTACAAACCAGG
* *
116380603 GGTATTTTGATAATTTTACAAATCAGG
1 GGTATTTTGGTAATTTTACAAACCAGG
*
116380630 GGTATTTTGATAATTTTACAAACCAGG
1 GGTATTTTGGTAATTTTACAAACCAGG
** *
116380657 GGTATTTTGGTAATTTTGTAAACCAAG
1 GGTATTTTGGTAATTTTACAAACCAGG
* *
116380684 GGTATTTTGATAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAACCAGG
* * *
116380711 GGTATTTTGGTGATTTTATAAACCAAG
1 GGTATTTTGGTAATTTTACAAACCAGG
* *
116380738 GGTATTTTAGTGATTTTACAAACCAGG
1 GGTATTTTGGTAATTTTACAAACCAGG
*
116380765 GATATTTTGGTAATTT
1 GGTATTTTGGTAATTT
116380781 GGTAAACTAA
Statistics
Matches: 199, Mismatches: 31, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 22 0.11
27 177 0.89
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAACCAGG
Found at i:116397482 original size:5 final size:5
Alignment explanation
Indices: 116397474--116397510 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
116397464 TTTAGTGCAC
116397474 GAACT GAACT GAACT GAACT GAACT GAACT GAACT GA
1 GAACT GAACT GAACT GAACT GAACT GAACT GAACT GA
116397511 GAGATGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (5 bp):
GAACT
Found at i:116402276 original size:35 final size:33
Alignment explanation
Indices: 116402237--116402330 Score: 100
Period size: 35 Copynumber: 2.8 Consensus size: 33
116402227 TTTAAACTAC
*
116402237 TTTTAAATAATATAATTTTAATTATTATAATTCAT
1 TTTTAAAT-ATATAATTTTAATAATTATAATT-AT
** *
116402272 TTTTATTTTTTATAATTTTAATAATTATAATTAT
1 TTTTA-AATATATAATTTTAATAATTATAATTAT
*
116402306 TCTTAAATATATAATTATT-ATAATT
1 TTTTAAATATATAATT-TTAATAATT
116402331 TCTATTAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
33 14 0.29
34 8 0.16
35 26 0.53
36 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTTAAATATATAATTTTAATAATTATAATTAT
Found at i:116402338 original size:27 final size:26
Alignment explanation
Indices: 116402290--116402350 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
116402280 TTTATAATTT
* * *
116402290 TAATAATTATAATTATTCTTAAATATA
1 TAATTATTATAATTATTATTAAAT-CA
116402317 TAATTATTATAATT-TCTATTAAATCA
1 TAATTATTATAATTAT-TATTAAATCA
116402343 TAATTATT
1 TAATTATT
116402351 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (26 bp):
TAATTATTATAATTATTATTAAATCA
Found at i:116402443 original size:13 final size:12
Alignment explanation
Indices: 116402391--116402445 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
116402381 TATGTCAATC
116402391 TTTTT-AATTAA
1 TTTTTAAATTAA
116402402 TAATTTTAAATTAAA
1 T--TTTTAAATT-AA
*
116402417 TATTTAAATT-A
1 TTTTTAAATTAA
116402428 TTTTTAAATGTAA
1 TTTTTAAAT-TAA
116402441 TTTTT
1 TTTTT
116402446 GGAGTCGGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
11 10 0.28
12 1 0.03
13 18 0.50
14 4 0.11
15 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTTTTAAATTAA
Found at i:116402974 original size:29 final size:30
Alignment explanation
Indices: 116402924--116402985 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
116402914 ACTTATTTTA
*
116402924 TTGTTGATTTTGTTATTATTTTAAAAGCAT
1 TTGTTAATTTTGTTATTATTTTAAAAGCAT
* *
116402954 TTGTTAATTTT-TTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAAGCAT
116402983 TTG
1 TTG
116402986 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAAGCAT
Found at i:116403734 original size:12 final size:11
Alignment explanation
Indices: 116403711--116403739 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
116403701 CACGTGTCTG
116403711 TTTTAATTTTT
1 TTTTAATTTTT
116403722 TTTTAATTTTT
1 TTTTAATTTTT
116403733 TTTTAAT
1 TTTTAAT
116403740 ATATGAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTAATTTTT
Found at i:116404053 original size:2 final size:2
Alignment explanation
Indices: 116404042--116404079 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
116404032 TGGATAGATC
116404042 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
116404080 AAATTAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116408352 original size:21 final size:21
Alignment explanation
Indices: 116408314--116408353 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
116408304 ATTACTCCAA
*
116408314 AGAAGCCGATTGATCCATCTC
1 AGAAGCCGATTCATCCATCTC
116408335 AGAAGCCAGATTCA-CCATC
1 AGAAGCC-GATTCATCCATC
116408354 AAGACTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (21 bp):
AGAAGCCGATTCATCCATCTC
Found at i:116410308 original size:24 final size:24
Alignment explanation
Indices: 116410255--116410354 Score: 92
Period size: 24 Copynumber: 4.1 Consensus size: 24
116410245 AGATGAAGAC
* * *
116410255 GAAGACAAAGACAGAGGGTGGAGAT
1 GAAGATAAAGAC-GAGAGTCGAGAT
116410280 GAAGATAAAGACGAGAGTCGAGAT
1 GAAGATAAAGACGAGAGTCGAGAT
* * * * * *
116410304 AAAGATTAATATGAGGGTGGAGAT
1 GAAGATAAAGACGAGAGTCGAGAT
* *
116410328 GAAGATGAAGACGAGAGTCGATAT
1 GAAGATAAAGACGAGAGTCGAGAT
116410352 GAA
1 GAA
116410355 AATTAATATA
Statistics
Matches: 59, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
24 48 0.81
25 11 0.19
ACGTcount: A:0.44, C:0.06, G:0.35, T:0.15
Consensus pattern (24 bp):
GAAGATAAAGACGAGAGTCGAGAT
Found at i:116410379 original size:48 final size:48
Alignment explanation
Indices: 116410268--116410386 Score: 161
Period size: 48 Copynumber: 2.5 Consensus size: 48
116410258 GACAAAGACA
*
116410268 GAGGGTGGAGATGAAGATAAAGACGAGAGTCGAGATAAAGATTAATAT
1 GAGGGTGGAGATGAAGATGAAGACGAGAGTCGAGATAAAGATTAATAT
*
116410316 GAGGGTGGAGATGAAGATGAAGACGAGAGTCGATATGAAA-ATTAATAT
1 GAGGGTGGAGATGAAGATGAAGACGAGAGTCGAGAT-AAAGATTAATAT
* * *
116410364 -AGGGTTTGAGGTGAAGAAGAAGA
1 GAGGG-TGGAGATGAAGATGAAGA
116410387 TGAAGACGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
47 4 0.06
48 57 0.89
49 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.35, T:0.19
Consensus pattern (48 bp):
GAGGGTGGAGATGAAGATGAAGACGAGAGTCGAGATAAAGATTAATAT
Found at i:116411952 original size:71 final size:71
Alignment explanation
Indices: 116411846--116411991 Score: 292
Period size: 71 Copynumber: 2.1 Consensus size: 71
116411836 GAATTTCCAT
116411846 AGCTACCAAGAGAGAAAAATGTTAAGGAGACTATGGGAAGTTAGAATATCAAGTTGGATTCAAGA
1 AGCTACCAAGAGAGAAAAATGTTAAGGAGACTATGGGAAGTTAGAATATCAAGTTGGATTCAAGA
116411911 AATGGA
66 AATGGA
116411917 AGCTACCAAGAGAGAAAAATGTTAAGGAGACTATGGGAAGTTAGAATATCAAGTTGGATTCAAGA
1 AGCTACCAAGAGAGAAAAATGTTAAGGAGACTATGGGAAGTTAGAATATCAAGTTGGATTCAAGA
116411982 AATGGA
66 AATGGA
116411988 AGCT
1 AGCT
116411992 GAAGGAGAGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.21
Consensus pattern (71 bp):
AGCTACCAAGAGAGAAAAATGTTAAGGAGACTATGGGAAGTTAGAATATCAAGTTGGATTCAAGA
AATGGA
Found at i:116413863 original size:21 final size:21
Alignment explanation
Indices: 116413839--116413909 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
116413829 TTTTTGAAAA
116413839 GAAATGTGTAAGACCATGGTT
1 GAAATGTGTAAGACCATGGTT
* *
116413860 GAAA-G-ATACCATGACAACATGATAT
1 GAAATGTGTA--A-GAC--CATGGT-T
116413885 GAAATGTGTAAGACCATGGTT
1 GAAATGTGTAAGACCATGGTT
116413906 GAAA
1 GAAA
116413910 GATACCATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 10 0.26
22 8 0.21
24 8 0.21
25 6 0.16
26 1 0.03
27 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (21 bp):
GAAATGTGTAAGACCATGGTT
Found at i:116413891 original size:46 final size:46
Alignment explanation
Indices: 116413839--116414156 Score: 431
Period size: 46 Copynumber: 6.9 Consensus size: 46
116413829 TTTTTGAAAA
* * *
116413839 GAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGATAT
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
* * *
116413885 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATAATAT
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
* *
116413931 GAAAT-ATGTAAAACCGTGGTTGAAAGATACCATGGCAACATGACAT
1 GAAATGA-GTAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
** **
116413977 GAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACATGACGG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
* *
116414023 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
* * *
116414069 GAAATGAATAATACCATGGTTGAAAGATACCATGGCAACATGACAA
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
* * * *
116414115 GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
116414157 TCAAAGATAA
Statistics
Matches: 244, Mismatches: 26, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
46 243 1.00
47 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
Found at i:116420713 original size:10 final size:11
Alignment explanation
Indices: 116420686--116420719 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
116420676 ATTTTATTTT
116420686 TATTTTTAATA
1 TATTTTTAATA
*
116420697 AATTTTTAATA
1 TATTTTTAATA
116420708 TA-TTTTAATA
1 TATTTTTAATA
116420718 TA
1 TA
116420720 ACTTTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTTTAATA
Found at i:116425729 original size:7 final size:7
Alignment explanation
Indices: 116425717--116425750 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
116425707 TGTTCTTTTT
116425717 AATTTAA
1 AATTTAA
116425724 AATTTAA
1 AATTTAA
116425731 AATTTAA
1 AATTTAA
116425738 AATTTAA
1 AATTTAA
116425745 AATTTA
1 AATTTA
116425751 TATAAATCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:116430612 original size:25 final size:24
Alignment explanation
Indices: 116430584--116430636 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
116430574 TCTAATCATT
*
116430584 ATTTTTAAATTATCAAAGTTATATA
1 ATTTTTAAATTATCAAAATTAT-TA
** *
116430609 ATTTTTTTATTATTAAAATTATTA
1 ATTTTTAAATTATCAAAATTATTA
116430633 ATTT
1 ATTT
116430637 AACTATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTTTAAATTATCAAAATTATTA
Found at i:116431001 original size:29 final size:29
Alignment explanation
Indices: 116430966--116431023 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
116430956 AGAATGTTTA
*
116430966 AAATTTAGGAACCAATTTAAAATAAAGGT
1 AAATTTAGGAACCAATTCAAAATAAAGGT
116430995 AAATTTAGGAACCAATTCAAAATAAAGGT
1 AAATTTAGGAACCAATTCAAAATAAAGGT
116431024 CATAATTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.26
Consensus pattern (29 bp):
AAATTTAGGAACCAATTCAAAATAAAGGT
Found at i:116431129 original size:2 final size:2
Alignment explanation
Indices: 116431086--116431113 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
116431076 AGTTTTTTAC
116431086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116431114 GTTTAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116433983 original size:24 final size:21
Alignment explanation
Indices: 116433939--116433986 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 21
116433929 TAACATATGA
*
116433939 ATATAATATAAAAAAATTATC
1 ATATAATATAAAAAAAGTATC
116433960 ATATAATATAAATGTAAAAGTATC
1 ATATAATATAAA---AAAAGTATC
116433984 ATA
1 ATA
116433987 ATTTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.52
24 11 0.48
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (21 bp):
ATATAATATAAAAAAAGTATC
Found at i:116436295 original size:66 final size:66
Alignment explanation
Indices: 116436189--116436318 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
116436179 ACCACCCCCA
*
116436189 GCTTTCCAAAATTATCCTAATTAAATGAATTTGAAGAAAAATTAGAA-AACTTACTTTGTATTAT
1 GCTTTCCAAAATTATCCTAATTAAATGAATTTAAAGAAAAATTA-AATAACTTACTTTGTATTAT
116436253 CT
65 CT
116436255 GCTTTCCAAAATTATCCTAATTAAATGAATTTAAAGAAAAATTAAATAACTTACTTTGTATTAT
1 GCTTTCCAAAATTATCCTAATTAAATGAATTTAAAGAAAAATTAAATAACTTACTTTGTATTAT
116436319 ATTCGAATAT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 2 0.03
66 60 0.97
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (66 bp):
GCTTTCCAAAATTATCCTAATTAAATGAATTTAAAGAAAAATTAAATAACTTACTTTGTATTATC
T
Found at i:116445276 original size:14 final size:14
Alignment explanation
Indices: 116445241--116445281 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
116445231 CCTCTGTGAG
116445241 TATTATAT-ATTGTA
1 TATTATATAATT-TA
116445255 T-TTGATATAATTTA
1 TATT-ATATAATTTA
116445269 TATTATATAATTT
1 TATTATATAATTT
116445282 TTGATAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 17 0.71
15 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (14 bp):
TATTATATAATTTA
Found at i:116446183 original size:30 final size:30
Alignment explanation
Indices: 116446138--116446204 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
116446128 AATAATCAGA
* *
116446138 TTTAACTTAATTGAGAA-AAGATAATAAATT
1 TTTATCTTAAATGAGAACAAGATAAT-AATT
116446168 TTTATCTTAAATGAGAACAAGATAATAATT
1 TTTATCTTAAATGAGAACAAGATAATAATT
*
116446198 TCTATCT
1 TTTATCT
116446205 GAGCTTCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 25 0.76
31 8 0.24
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (30 bp):
TTTATCTTAAATGAGAACAAGATAATAATT
Found at i:116447158 original size:31 final size:31
Alignment explanation
Indices: 116447120--116447181 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
116447110 GTAATGGTTA
* *
116447120 ATTTCATTTTTTTAATATTATTTAAT-TTTTT
1 ATTTCATTTTTATAAT-TTAATTAATATTTTT
116447151 ATTTCATTTTTATAATTTAATTAATATTTTT
1 ATTTCATTTTTATAATTTAATTAATATTTTT
116447182 TATAATAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (31 bp):
ATTTCATTTTTATAATTTAATTAATATTTTT
Found at i:116448882 original size:107 final size:107
Alignment explanation
Indices: 116448687--116448883 Score: 254
Period size: 107 Copynumber: 1.8 Consensus size: 107
116448677 TGTTTAAATG
** * * *
116448687 TAAGACCATAGTTGGGCTATGGCATTTTAGTGAAAAGACCATAACTGAGTTATGGCACTGTGAAC
1 TAAGACCATAGCCGGGCTATGGCATTTGAGTGAAAAGACCATAACTGAGTTATGGCAATATGAAC
* *
116448752 GTAAGACCATGGTTAGACTATGGCAGTAGATGTGAATACGTA
66 GTAAGACCATGGTCAGACCATGGCAGTAGATGTGAATACGTA
* * *
116448794 TAAGACCATAGCCGGGCTATGGCATCTTGA-TGATAAGACCATAACTGGGTTATGGCAATATGAG
1 TAAGACCATAGCCGGGCTATGGCAT-TTGAGTGAAAAGACCATAACTGAGTTATGGCAATATGAA
* *
116448858 TGTAAGACCATGG-CAGGGCCATGGCA
65 CGTAAGACCATGGTCA-GACCATGGCA
116448884 ATGTACGTAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
106 1 0.01
107 72 0.95
108 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (107 bp):
TAAGACCATAGCCGGGCTATGGCATTTGAGTGAAAAGACCATAACTGAGTTATGGCAATATGAAC
GTAAGACCATGGTCAGACCATGGCAGTAGATGTGAATACGTA
Found at i:116453624 original size:38 final size:38
Alignment explanation
Indices: 116453549--116453701 Score: 211
Period size: 38 Copynumber: 4.0 Consensus size: 38
116453539 CAAGACACTG
* *
116453549 GAAATGTAACCGGGCTAAAGTCCAGCAGGCTTCGTGCT
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCT
*
116453587 AGAAATGTATCCGGGCTAAAGT-CTGCAGGCTTCGTGCT
1 -GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCT
* * *
116453625 GAAATGTATCTGGGCTAAAGTCCCGTAGGCTTCGTTCT
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCT
*
116453663 GGAAATGTAT-CGGGCTAAAGTCCCGCAGGCTTTGTGCT
1 -GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCT
116453701 G
1 G
116453702 GTAATATAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
37 21 0.21
38 52 0.51
39 29 0.28
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (38 bp):
GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCT
Found at i:116455921 original size:6 final size:6
Alignment explanation
Indices: 116455901--116455944 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
116455891 TCTGTACCTG
* * * *
116455901 ACTGTG ACTGTT ACTGCT ACTGCT ACTGTT ACTGTT ACTCTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT AC
116455945 AGTGTATTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (6 bp):
ACTGTT
Found at i:116467248 original size:121 final size:121
Alignment explanation
Indices: 116467034--116467278 Score: 445
Period size: 121 Copynumber: 2.0 Consensus size: 121
116467024 AAATGTTGTT
*
116467034 CATGGCACTGCAGGGTATGTAATATTCCACTACTTCATAGCTTATTTAGCATTATCCACTCTATA
1 CATGGCACTGCAGGGTATGAAATATTCCACTACTTCATAGCTTATTTAGCATTATCCACTCTATA
116467099 ACGCTCCTCAAACTCTTTAGTTTCCCTAAAGTATCAATGTCCAACACATAATCCAA
66 ACGCTCCTCAAACTCTTTAGTTTCCCTAAAGTATCAATGTCCAACACATAATCCAA
* *
116467155 CATGGCACTGCAGGGTATGAAATATTCCACTACTTCATAGTTTATTTAGCATTATCTACTCTATA
1 CATGGCACTGCAGGGTATGAAATATTCCACTACTTCATAGCTTATTTAGCATTATCCACTCTATA
**
116467220 ACGCTCCTCAAACTCTTTAGTTTCCCTAAAGTATCAATGTCCAACACATTTTCCAA
66 ACGCTCCTCAAACTCTTTAGTTTCCCTAAAGTATCAATGTCCAACACATAATCCAA
116467276 CAT
1 CAT
116467279 AGTTACGAGT
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 119 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (121 bp):
CATGGCACTGCAGGGTATGAAATATTCCACTACTTCATAGCTTATTTAGCATTATCCACTCTATA
ACGCTCCTCAAACTCTTTAGTTTCCCTAAAGTATCAATGTCCAACACATAATCCAA
Found at i:116469753 original size:11 final size:10
Alignment explanation
Indices: 116469727--116469764 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
116469717 GCAATTGACC
116469727 ATTTTT-ATA
1 ATTTTTAATA
*
116469736 GTTTTTAATA
1 ATTTTTAATA
116469746 ACTTTTTAATA
1 A-TTTTTAATA
116469757 ATTTTTAA
1 ATTTTTAA
116469765 AAGAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 5 0.20
10 10 0.40
11 10 0.40
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:116475613 original size:27 final size:27
Alignment explanation
Indices: 116475575--116475629 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
116475565 ATGAAAAACA
116475575 TAACGTCCAAAGGAAAACAAGTAGATT
1 TAACGTCCAAAGGAAAACAAGTAGATT
116475602 TAACGTCCAAAGGAAAACAAGTAGATT
1 TAACGTCCAAAGGAAAACAAGTAGATT
116475629 T
1 T
116475630 GCTTATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (27 bp):
TAACGTCCAAAGGAAAACAAGTAGATT
Found at i:116483286 original size:23 final size:23
Alignment explanation
Indices: 116483228--116483291 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
116483218 AGATTATTTT
*
116483228 TATATAAAAATAAAT-TTTAAAA
1 TATATTAAAATAAATATTTAAAA
* *
116483250 TATAATAAATTAAATATATTAAAA
1 TATATTAAAATAAATAT-TTAAAA
116483274 -ATATTAAAATAAATATTT
1 TATATTAAAATAAATATTT
116483292 TTCAATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 14 0.40
23 15 0.43
24 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TATATTAAAATAAATATTTAAAA
Found at i:116484496 original size:5 final size:5
Alignment explanation
Indices: 116484486--116484514 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
116484476 GTTTTTTGGC
116484486 CCCGG CCCGG CCCGG CCCGG CCCGG CCCG
1 CCCGG CCCGG CCCGG CCCGG CCCGG CCCG
116484515 AATTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.62, G:0.38, T:0.00
Consensus pattern (5 bp):
CCCGG
Found at i:116484652 original size:22 final size:22
Alignment explanation
Indices: 116484613--116484671 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
116484603 GTTTTAAGAA
*
116484613 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
116484634 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
116484656 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
116484672 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:116484688 original size:26 final size:24
Alignment explanation
Indices: 116484642--116484701 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
116484632 ATTTGTTTTA
*
116484642 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
116484666 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
116484692 TTTTTTATTT
1 ATATTTATTT
116484702 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:116488663 original size:14 final size:15
Alignment explanation
Indices: 116488646--116488687 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
116488636 CACCAAAACC
116488646 AAAACCAAAAA-AAT
1 AAAACCAAAAATAAT
116488660 AAAA-CAAAAATAAT
1 AAAACCAAAAATAAT
116488674 AAAACC-AAAATAAT
1 AAAACCAAAAATAAT
116488688 TTAAAGGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.23
14 19 0.73
15 1 0.04
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAACCAAAAATAAT
Found at i:116489984 original size:13 final size:13
Alignment explanation
Indices: 116489968--116489992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
116489958 TTATACATTT
116489968 TAAATTACTTTGA
1 TAAATTACTTTGA
116489981 TAAATTACTTTG
1 TAAATTACTTTG
116489993 TTTTTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
TAAATTACTTTGA
Found at i:116491829 original size:6 final size:6
Alignment explanation
Indices: 116491818--116491844 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
116491808 GAAATGGGAG
116491818 AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
116491845 ATTAGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:116498764 original size:29 final size:30
Alignment explanation
Indices: 116498717--116498784 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
116498707 TGGCCCAAGA
* *
116498717 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
116498747 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
116498777 GCAAATAT
1 GTAAATAT
116498785 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:116501261 original size:46 final size:46
Alignment explanation
Indices: 116501211--116501488 Score: 373
Period size: 46 Copynumber: 6.0 Consensus size: 46
116501201 GTGTGCTCTC
**
116501211 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATC-
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA-CA
** * *
116501257 TGATATGAAATGTGTCAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
116501303 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* *
116501349 TGACA-GAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
*
116501395 TGATATGAAATGAATAAGACTATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * * *
116501441 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
116501487 TG
1 TG
116501489 TCAAAGATAA
Statistics
Matches: 211, Mismatches: 17, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
45 3 0.01
46 207 0.98
47 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:116501369 original size:92 final size:92
Alignment explanation
Indices: 116501211--116501483 Score: 424
Period size: 92 Copynumber: 3.0 Consensus size: 92
116501201 GTGTGCTCTC
** * * *
116501211 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATC-TGATATG-AAATGTGTCA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA-CATGACA-GAAAATGAGTAA
116501274 GACCATGGTTGAAAGATACCATGGCAACG
64 GACCATGGTTGAAAGATACCATGGCAACG
*
116501303 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGA
116501368 CCATGGTTGAAAGATACCATGGCAACG
66 CCATGGTTGAAAGATACCATGGCAACG
*
116501395 TGATATGAAATGAATAAGACTATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGA
* * *
116501460 CCATAGTTGAAAGACACTATGGCA
66 CCATGGTTGAAAGATACCATGGCA
116501484 TCATGTCAAA
Statistics
Matches: 168, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
91 2 0.01
92 166 0.99
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (92 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGA
CCATGGTTGAAAGATACCATGGCAACG
Found at i:116502529 original size:22 final size:22
Alignment explanation
Indices: 116502501--116502545 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
116502491 ATTTAGATTG
116502501 ATTTGGATATTATAAGTGAAGT
1 ATTTGGATATTATAAGTGAAGT
116502523 ATTTGGATATTATAAGTGAAGT
1 ATTTGGATATTATAAGTGAAGT
116502545 A
1 A
116502546 CATGAGGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.40
Consensus pattern (22 bp):
ATTTGGATATTATAAGTGAAGT
Found at i:116506110 original size:20 final size:21
Alignment explanation
Indices: 116506077--116506116 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
116506067 ACACGGCCAA
* *
116506077 GACACACGCTTGTGT-TCTGG
1 GACACACACCTGTGTCTCTGG
116506097 GACACACACCTGTGTCTCTG
1 GACACACACCTGTGTCTCTG
116506117 CCCGTGTGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.17, C:0.30, G:0.25, T:0.28
Consensus pattern (21 bp):
GACACACACCTGTGTCTCTGG
Found at i:116507266 original size:24 final size:24
Alignment explanation
Indices: 116507239--116507284 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
116507229 CAATAATTGG
116507239 GAAGTTCACAAAGAACCATATCGA
1 GAAGTTCACAAAGAACCATATCGA
116507263 GAAGTTCACAAAGAACCATATC
1 GAAGTTCACAAAGAACCATATC
116507285 AGGAAGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.17
Consensus pattern (24 bp):
GAAGTTCACAAAGAACCATATCGA
Found at i:116507290 original size:24 final size:23
Alignment explanation
Indices: 116507238--116507290 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 23
116507228 GCAATAATTG
116507238 GGAAGTTCACAAAGAACCATATC
1 GGAAGTTCACAAAGAACCATATC
116507261 GAGAAGTTCACAAAGAACCATATC
1 G-GAAGTTCACAAAGAACCATATC
116507285 AGGAAG
1 -GGAAG
116507291 CTTTGGATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 1 0.04
24 26 0.93
25 1 0.04
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (23 bp):
GGAAGTTCACAAAGAACCATATC
Found at i:116507500 original size:24 final size:24
Alignment explanation
Indices: 116507455--116507502 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
116507445 CGTTGAACCA
*
116507455 TATAACGGGAAGCTCGAGAGAGCT
1 TATAACGGGAAGCTCGAAAGAGCT
*
116507479 TATAACGGGATGCTC-ATAAGAGCT
1 TATAACGGGAAGCTCGA-AAGAGCT
116507503 ATGGTGTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (24 bp):
TATAACGGGAAGCTCGAAAGAGCT
Found at i:116529410 original size:22 final size:22
Alignment explanation
Indices: 116529385--116529452 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
116529375 GTAAAGTAAA
116529385 AAATATTGAAAGACTTGAAAAT
1 AAATATTGAAAGACTTGAAAAT
* *
116529407 AAATATT-ATTA-ACTT-TAAA-
1 AAATATTGA-AAGACTTGAAAAT
*
116529426 AAATATTGAAGGACTTGAAAAT
1 AAATATTGAAAGACTTGAAAAT
116529448 AAATA
1 AAATA
116529453 CTATTAACTT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
19 7 0.19
20 8 0.22
21 8 0.22
22 13 0.36
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.31
Consensus pattern (22 bp):
AAATATTGAAAGACTTGAAAAT
Found at i:116529426 original size:21 final size:21
Alignment explanation
Indices: 116529397--116529462 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
116529387 ATATTGAAAG
116529397 ACTTGAAAATAAATATTATTA
1 ACTTGAAAATAAATATTATTA
* ***
116529418 ACTT-TAAA-AAATATTGAAGG
1 ACTTGAAAATAAATATT-ATTA
*
116529438 ACTTGAAAATAAATACTATTA
1 ACTTGAAAATAAATATTATTA
116529459 ACTT
1 ACTT
116529463 TATTAAACAA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 7 0.21
20 8 0.24
21 12 0.36
22 6 0.18
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (21 bp):
ACTTGAAAATAAATATTATTA
Found at i:116529441 original size:41 final size:41
Alignment explanation
Indices: 116529381--116529464 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
116529371 CGGTGTAAAG
*
116529381 TAAAAAATATTGAAAGACTTGAAAATAAATATTATTAACTT
1 TAAAAAATATTGAAAGACTTGAAAATAAATACTATTAACTT
*
116529422 TAAAAAATATTGAAGGACTTGAAAATAAATACTATTAACTT
1 TAAAAAATATTGAAAGACTTGAAAATAAATACTATTAACTT
116529463 TA
1 TA
116529465 TTAAACAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (41 bp):
TAAAAAATATTGAAAGACTTGAAAATAAATACTATTAACTT
Found at i:116531153 original size:11 final size:11
Alignment explanation
Indices: 116531136--116531166 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
116531126 TAATAACAAC
116531136 AAAATAATAGT
1 AAAATAATAGT
*
116531147 AACATAATAGT
1 AAAATAATAGT
116531158 AAAATAATA
1 AAAATAATA
116531167 AAAAATAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:116532026 original size:15 final size:17
Alignment explanation
Indices: 116531993--116532027 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
116531983 TTTTGCATAT
116531993 ATAATCTGATTTCTTTA
1 ATAATCTGATTTCTTTA
116532010 ATAAT-TGATTT-TTTA
1 ATAATCTGATTTCTTTA
116532025 ATA
1 ATA
116532028 TAAATTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 6 0.33
17 5 0.28
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (17 bp):
ATAATCTGATTTCTTTA
Found at i:116532030 original size:17 final size:18
Alignment explanation
Indices: 116531990--116532030 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
116531980 TATTTTTGCA
116531990 TATATAATCTGATTTCTT
1 TATATAATCTGATTTCTT
116532008 TA-ATAAT-TGATTT-TT
1 TATATAATCTGATTTCTT
116532023 TAATATAA
1 T-ATATAA
116532031 ATTTATGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 7 0.33
17 9 0.43
18 2 0.10
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
TATATAATCTGATTTCTT
Found at i:116532095 original size:16 final size:16
Alignment explanation
Indices: 116532043--116532097 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
116532033 TTATGTGTAC
116532043 TTATAAAATTCAGTACT
1 TTATAAAATTCAGTA-T
116532060 TATAATATAAATTCAGTAT
1 T-T-ATA-AAATTCAGTAT
*
116532079 TTATAAAATTCAATAT
1 TTATAAAATTCAGTAT
116532095 TTA
1 TTA
116532098 ATTACAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 13 0.38
17 4 0.12
18 2 0.06
19 5 0.15
20 10 0.29
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (16 bp):
TTATAAAATTCAGTAT
Found at i:116544656 original size:30 final size:29
Alignment explanation
Indices: 116544604--116544668 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
116544594 TTTAACATAC
* * *
116544604 AATTGTATACATAAACTTTGATTTTATGT
1 AATTTTATACATAAACTTTGATTTGATCT
*
116544633 AATTTTATACATCAAATTTTGATTTGATCT
1 AATTTTATACAT-AAACTTTGATTTGATCT
116544663 AATTTT
1 AATTTT
116544669 TGTAATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.51
Consensus pattern (29 bp):
AATTTTATACATAAACTTTGATTTGATCT
Found at i:116545980 original size:28 final size:29
Alignment explanation
Indices: 116545949--116546012 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
116545939 AAGAGTTCAA
* * *
116545949 GGTTTAGGA-TTTAGAATCTAGGGTTTAG
1 GGTTTAGGAGTTTAGAATCCAAGGTCTAG
116545977 GGTTTA-GAGTTTAGAATCCAAGGTCTAG
1 GGTTTAGGAGTTTAGAATCCAAGGTCTAG
116546005 GGTTTAGG
1 GGTTTAGG
116546013 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 28 0.90
29 1 0.03
ACGTcount: A:0.25, C:0.06, G:0.33, T:0.36
Consensus pattern (29 bp):
GGTTTAGGAGTTTAGAATCCAAGGTCTAG
Found at i:116548238 original size:12 final size:12
Alignment explanation
Indices: 116548217--116548254 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
116548207 TATATATATA
116548217 TTTTTTTTT-AT
1 TTTTTTTTTAAT
116548228 TTTTTTATTTAAT
1 TTTTTT-TTTAAT
*
116548241 TTTTTTCTTAAT
1 TTTTTTTTTAAT
116548253 TT
1 TT
116548255 AATATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 6 0.25
12 10 0.42
13 8 0.33
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTAAT
Found at i:116548260 original size:24 final size:23
Alignment explanation
Indices: 116548216--116548263 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
116548206 ATATATATAT
* **
116548216 ATTTTTTTTTATTTTTTTATTTA
1 ATTTTTTTTTAATTTAATATTTA
116548239 ATTTTTTTCTTAATTTAATATTTA
1 ATTTTTTT-TTAATTTAATATTTA
116548263 A
1 A
116548264 AATATTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTTTTTTTAATTTAATATTTA
Found at i:116548763 original size:15 final size:15
Alignment explanation
Indices: 116548727--116548766 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
116548717 AAGTCAATTT
*
116548727 TTTAATATTTAAATA
1 TTTAATTTTTAAATA
116548742 TTTAATTTTTAAATA
1 TTTAATTTTTAAATA
116548757 TTTAATTTTT
1 TTTAATTTTT
116548767 TATTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATTTTTAAATA
Found at i:116548768 original size:8 final size:7
Alignment explanation
Indices: 116548727--116548781 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
116548717 AAGTCAATTT
116548727 TTTAATA
1 TTTAATA
116548734 TTTAAATA
1 TTT-AATA
*
116548742 TTTAATT
1 TTTAATA
116548749 TTTAAATA
1 TTT-AATA
116548757 TTTAAT-
1 TTTAATA
*
116548763 TTT-TTA
1 TTTAATA
116548769 TTTAA-A
1 TTTAATA
116548775 TTTAATA
1 TTTAATA
116548782 CTTTTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
5 1 0.03
6 12 0.31
7 13 0.33
8 13 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTAATA
Found at i:116548772 original size:20 final size:22
Alignment explanation
Indices: 116548725--116548796 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 22
116548715 CAAAGTCAAT
* *
116548725 TTTTTAATATTTAAATA-TTTAA
1 TTTTAAATATTT-AATACTTTTA
*
116548747 TTTTTAAATATTTAAT-TTTTTA
1 -TTTTAAATATTTAATACTTTTA
116548769 -TTT-AA-ATTTAATACTTTTA
1 TTTTAAATATTTAATACTTTTA
116548788 TTTTAAATA
1 TTTTAAATA
116548797 AACCTATTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
18 7 0.17
19 7 0.17
20 6 0.15
21 2 0.05
22 8 0.20
23 11 0.27
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTAAATATTTAATACTTTTA
Found at i:116560151 original size:25 final size:27
Alignment explanation
Indices: 116560122--116560190 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 27
116560112 AAATGTGGAC
116560122 AACCATAAAATTATAAAC-AAAA-TAA
1 AACCATAAAATTATAAACTAAAATTAA
116560147 AACCATGAAAA-TATAAACTAAAATTAA
1 AACCAT-AAAATTATAAACTAAAATTAA
116560174 AA--ATAAAA-TA-AAACTAA
1 AACCATAAAATTATAAACTAA
116560191 GAAAAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.17
24 6 0.15
25 15 0.37
26 8 0.20
27 5 0.12
ACGTcount: A:0.68, C:0.10, G:0.01, T:0.20
Consensus pattern (27 bp):
AACCATAAAATTATAAACTAAAATTAA
Found at i:116560185 original size:17 final size:17
Alignment explanation
Indices: 116560126--116560203 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 17
116560116 GTGGACAACC
* *
116560126 ATAAAATTATAAACAAA
1 ATAAAATTAAAAATAAA
*
116560143 ATAAAACCATGAAAATATAAA
1 AT-AAA--ATTAAAA-ATAAA
*
116560164 CTAAAATTAAAAATAAA
1 ATAAAATTAAAAATAAA
* *
116560181 ATAAAACTAAGAAAAAAA
1 ATAAAATTAA-AAATAAA
116560199 ATAAA
1 ATAAA
116560204 TGTTAGAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
17 15 0.31
18 20 0.42
20 8 0.17
21 5 0.10
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (17 bp):
ATAAAATTAAAAATAAA
Found at i:116560189 original size:23 final size:24
Alignment explanation
Indices: 116560154--116560203 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
116560144 TAAAACCATG
*
116560154 AAAATATAAACTAA-AATTAAAAAT
1 AAAATATAAACTAAGAA-AAAAAAT
116560178 AAAATA-AAACTAAGAAAAAAAAT
1 AAAATATAAACTAAGAAAAAAAAT
116560201 AAA
1 AAA
116560204 TGTTAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (24 bp):
AAAATATAAACTAAGAAAAAAAAT
Found at i:116562379 original size:22 final size:22
Alignment explanation
Indices: 116562354--116562397 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
116562344 TTATGGCCAA
116562354 AAAATTTATTATAAAAAATAAT
1 AAAATTTATTATAAAAAATAAT
116562376 AAAATTTATTATAAAAAATAAT
1 AAAATTTATTATAAAAAATAAT
116562398 TTACATGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATTTATTATAAAAAATAAT
Found at i:116573719 original size:42 final size:42
Alignment explanation
Indices: 116573660--116573744 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
116573650 ACCAAGTTGC
116573660 AATAATTTCATTTTGAATGGCCAACTAAATAATTTACCCTAA
1 AATAATTTCATTTTGAATGGCCAACTAAATAATTTACCCTAA
116573702 AATAATTTCATTTTGAATGGCCAACTAAATAATTTACCCTAA
1 AATAATTTCATTTTGAATGGCCAACTAAATAATTTACCCTAA
116573744 A
1 A
116573745 TCTTAAGGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.35
Consensus pattern (42 bp):
AATAATTTCATTTTGAATGGCCAACTAAATAATTTACCCTAA
Found at i:116579249 original size:13 final size:14
Alignment explanation
Indices: 116579233--116579268 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
116579223 CAATCTCATA
116579233 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
116579246 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
116579259 TCTC-ATTTCA
1 TCTCAATTTCA
116579269 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:116579258 original size:18 final size:19
Alignment explanation
Indices: 116579220--116579260 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
116579210 TGGTTCATGT
116579220 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
116579239 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
116579257 TTTC
1 TTTC
116579261 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:116579450 original size:39 final size:38
Alignment explanation
Indices: 116579383--116579517 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
116579373 ACCAATATGG
* * *
116579383 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
116579422 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
116579460 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
116579501 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
116579518 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:116579782 original size:18 final size:19
Alignment explanation
Indices: 116579756--116579794 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
116579746 TTTCAATTCA
116579756 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
116579775 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
116579793 AT
1 AT
116579795 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:116581119 original size:5 final size:5
Alignment explanation
Indices: 116581109--116581161 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
116581099 TTACTTATTT
* *
116581109 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
116581157 ATATA
1 ATATA
116581162 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:116581125 original size:12 final size:12
Alignment explanation
Indices: 116581108--116581163 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
116581098 TTTACTTATT
116581108 TATATAATATAA
1 TATATAATATAA
116581120 TATATAATATAATA
1 TATATAATAT-A-A
116581134 TACTATAATATAA
1 TA-TATAATATAA
*
116581147 TA-ATAATTTAA
1 TATATAATATAA
116581158 TATATA
1 TATATA
116581164 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:116582969 original size:6 final size:6
Alignment explanation
Indices: 116582954--116582994 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
116582944 TACTTCATTT
*
116582954 TTTTTA TTTTTT TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
116582995 TTGCATCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTA
Found at i:116584483 original size:5 final size:5
Alignment explanation
Indices: 116584473--116584508 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
116584463 AATAATTAAG
116584473 TATAT TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
116584509 ATAAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:116584578 original size:31 final size:30
Alignment explanation
Indices: 116584543--116584603 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
116584533 GAAACAGAAT
*
116584543 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
116584574 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
116584604 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:116586179 original size:39 final size:39
Alignment explanation
Indices: 116586072--116586206 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
116586062 GACCTCGAGT
* * *
116586072 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
116586113 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
116586151 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
116586190 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
116586207 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:116592244 original size:5 final size:5
Alignment explanation
Indices: 116592234--116592275 Score: 66
Period size: 5 Copynumber: 8.0 Consensus size: 5
116592224 AATAATTAAG
116592234 TATAT TATAT TATAT TATAT TATAT ATATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT -TATAT TA-TAT TATAT
116592276 ATAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 25 0.71
6 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:116592345 original size:31 final size:30
Alignment explanation
Indices: 116592310--116592370 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
116592300 GAAACAGAAT
*
116592310 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
116592341 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
116592371 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:116593943 original size:39 final size:39
Alignment explanation
Indices: 116593836--116593970 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
116593826 GACCTCGAGT
* * *
116593836 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
116593877 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
116593915 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
116593954 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
116593971 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:116596498 original size:13 final size:14
Alignment explanation
Indices: 116596482--116596517 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
116596472 CAATCTCATA
116596482 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
116596495 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
116596508 TCTC-ATTTCA
1 TCTCAATTTCA
116596518 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:116596507 original size:18 final size:19
Alignment explanation
Indices: 116596469--116596509 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
116596459 TGGTTCATGT
116596469 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
116596488 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
116596506 TTTC
1 TTTC
116596510 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:116596699 original size:39 final size:38
Alignment explanation
Indices: 116596632--116596766 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
116596622 ACCAATATGG
* * *
116596632 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
116596671 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
116596709 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
116596750 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
116596767 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:116597032 original size:18 final size:19
Alignment explanation
Indices: 116597006--116597044 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
116596996 TTTCAATTCA
116597006 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
116597025 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
116597043 AT
1 AT
116597045 ATATCTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:116598374 original size:5 final size:5
Alignment explanation
Indices: 116598364--116598420 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
116598354 TTACTTATTT
* *
116598364 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
116598412 ATAT- ATATA
1 ATATA ATATA
116598421 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:116598380 original size:12 final size:12
Alignment explanation
Indices: 116598363--116598418 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
116598353 TTTACTTATT
116598363 TATATAATATAA
1 TATATAATATAA
116598375 TATATAATATAATA
1 TATATAATAT-A-A
116598389 TACTATAATATAA
1 TA-TATAATATAA
*
116598402 TA-ATAATTTAA
1 TATATAATATAA
116598413 TATATA
1 TATATA
116598419 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Done.