Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold19
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: 2266706
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17655 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1017439 original size:16 final size:17
Alignment explanation
Indices: 1017391--1017440 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1017381 ATAATGAATG
1017391 TATA-AAAATTTATATA
1 TATATAAAATTTATATA
1017407 -ATATAAAATATTA-ATA
1 TATATAAAAT-TTATATA
1017423 TAT-TAAAATTTATATA
1 TATATAAAATTTATATA
1017439 TA
1 TA
1017441 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.20
16 19 0.63
17 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATAAAATTTATATA
Found at i:1017441 original size:46 final size:48
Alignment explanation
Indices: 1017367--1017466 Score: 114
Period size: 46 Copynumber: 2.1 Consensus size: 48
1017357 ATTATAAAAT
* *
1017367 AATATTAATATAATATAATGAATGTATAAAAATTT-ATATAA-TATAA
1 AATATTAATATAATAAAATGAATATATAAAAATTTAATATAATTATAA
* ** * *
1017413 AATATTAATATATTAAAATTTATATATAATATTTTAAATATAATTATAA
1 AATATTAATATAATAAAATGAATATATAAAAATTT-AATATAATTATAA
1017462 AATAT
1 AATAT
1017467 AAAAATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
46 28 0.64
48 6 0.14
49 10 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (48 bp):
AATATTAATATAATAAAATGAATATATAAAAATTTAATATAATTATAA
Found at i:1017466 original size:27 final size:27
Alignment explanation
Indices: 1017402--1017468 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 27
1017392 ATAAAAATTT
1017402 ATATAA-TATAAAATATTAATATATTAA
1 ATATAATTATAAAATA-TAATATATTAA
*
1017429 A-AT--TTAT---ATATAATATTTTAA
1 ATATAATTATAAAATATAATATATTAA
1017450 ATATAATTATAAAATATAA
1 ATATAATTATAAAATATAA
1017469 AAATATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
21 11 0.34
22 5 0.16
24 4 0.12
25 3 0.09
26 2 0.06
27 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATATAATTATAAAATATAATATATTAA
Found at i:1018245 original size:18 final size:18
Alignment explanation
Indices: 1018187--1018248 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
1018177 AAAACTTTTT
*
1018187 ATTAGAATTACATAAAAC
1 ATTATAATTACATAAAAC
*
1018205 ATTATCTACTTACATATAAAC
1 ATTA--TAATTACATA-AAAC
1018226 ATTATAATTACATAAAAC
1 ATTATAATTACATAAAAC
1018244 ATTAT
1 ATTAT
1018249 TAGTTATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 13 0.34
19 9 0.24
20 8 0.21
21 8 0.21
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (18 bp):
ATTATAATTACATAAAAC
Found at i:1018261 original size:19 final size:19
Alignment explanation
Indices: 1018192--1018266 Score: 89
Period size: 19 Copynumber: 3.9 Consensus size: 19
1018182 TTTTTATTAG
1018192 AATTACATAAAACATTATCT
1 AATTACATAAAACATTAT-T
*
1018212 ACTTACATATAAACATTA-T
1 AATTACATA-AAACATTATT
1018231 AATTACATAAAACATTATT
1 AATTACATAAAACATTATT
* * *
1018250 AGTTATATAAAATATTA
1 AATTACATAAAACATTA
1018267 CTAAAAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.17
19 24 0.50
20 8 0.17
21 8 0.17
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (19 bp):
AATTACATAAAACATTATT
Found at i:1018320 original size:96 final size:96
Alignment explanation
Indices: 1018133--1018325 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
1018123 AAATACTATC
* * * *
1018133 TAATTACATAACAACATTATCAGCTACATAAAATATTACTTAAGAAAACTTTTTATTAGAATTAC
1 TAATTACATAACAACATTATCAGCTACATAAAATATTACTTAAAAAAAATTTTAATCAGAATTAC
* * *
1018198 ATAAAACATTATCTACTTACATATAAACATTA
66 ACAAAACATTACCTACATACA-ATAAACATTA
* * *
1018230 TAATTACATAA-AACATTATTAGTTATATAAAATATTAC-TAAAAAATAATTTTAATCAGAATTA
1 TAATTACATAACAACATTATCAGCTACATAAAATATTACTTAAAAAA-AATTTTAATCAGAATTA
* *
1018293 CACAAGATATTACCCTATCATAC-ATAAACATTA
65 CACAAAACATTA-CCTA-CATACAATAAACATTA
1018326 CTCAAAAATA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
95 6 0.07
96 57 0.70
97 14 0.17
98 4 0.05
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (96 bp):
TAATTACATAACAACATTATCAGCTACATAAAATATTACTTAAAAAAAATTTTAATCAGAATTAC
ACAAAACATTACCTACATACAATAAACATTA
Found at i:1018670 original size:21 final size:20
Alignment explanation
Indices: 1018605--1018681 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
1018595 TAGAAATACT
* * *
1018605 ATTATCAAAATATATAAAAT
1 ATTATCAAATTACATAAAAC
*
1018625 ATTA-CAAAATTATATAAAAC
1 ATTATC-AAATTACATAAAAC
* *
1018645 ATTATGAAATTGCATAAAATC
1 ATTATCAAATTACATAAAA-C
1018666 ATTATCAAATTACATA
1 ATTATCAAATTACATA
1018682 GGACATTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 31 0.66
21 15 0.32
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.34
Consensus pattern (20 bp):
ATTATCAAATTACATAAAAC
Found at i:1019011 original size:21 final size:20
Alignment explanation
Indices: 1018977--1019039 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
1018967 TTTTCGTCAA
* *
1018977 AATTACATAAAATATTATCT
1 AATTATATAAAATATTACCT
1018997 AATTATATATAAATATTACCT
1 AATTATATA-AAATATTACCT
*
1019018 AATTATAT-AAACATTACCT
1 AATTATATAAAATATTACCT
1019037 AAT
1 AAT
1019040 AATTTTCATC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 13 0.33
20 8 0.21
21 18 0.46
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTATATAAAATATTACCT
Found at i:1019025 original size:77 final size:76
Alignment explanation
Indices: 1018786--1019050 Score: 241
Period size: 77 Copynumber: 3.5 Consensus size: 76
1018776 AACATTATAA
* * * * * * * * *
1018786 AATTATGTAAAATATTACCTAAGAACTTTTCATCAGAATTGCTTAAAAATATTACCCAATTATAT
1 AATTATATAAAACATTACTTAAGAAATTTTCATCAAAATTACAT-AAAATATTATCTAATTATAT
*
1018851 ATAAAAACTACT
65 ATAAAAATTACT
* * *
1018863 CAATTATATAAAATATTACTTAAGAAATTTTCATCATAATTACATAAAATATTAT-TGAATTACA
1 -AATTATATAAAACATTACTTAAGAAATTTTCATCAAAATTACATAAAATATTATCT-AATTATA
* * *
1018927 AACAAACATTAACT
64 TATAAAAATT-ACT
* * * *
1018941 GAGTATATAAAACATTA-TTAAAGAATTTTTCGTCAAAATTACATAAAATATTATCTAATTATAT
1 AATTATATAAAACATTACTT-AAGAAATTTTCATCAAAATTACATAAAATATTATCTAATTATAT
*
1019005 ATAAATATTACCT
65 ATAAAAATTA-CT
* *
1019018 AATTATAT-AAACATTACCTAA-TAATTTTCATCA
1 AATTATATAAAACATTACTTAAGAAATTTTCATCA
1019051 GACATATTAT
Statistics
Matches: 152, Mismatches: 29, Indels: 15
0.78 0.15 0.08
Matches are distributed among these distances:
75 9 0.06
76 13 0.09
77 88 0.58
78 42 0.28
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (76 bp):
AATTATATAAAACATTACTTAAGAAATTTTCATCAAAATTACATAAAATATTATCTAATTATATA
TAAAAATTACT
Found at i:1019026 original size:19 final size:20
Alignment explanation
Indices: 1018986--1019040 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1018976 AAATTACATA
*
1018986 AAATATTATCTAATTATATAT
1 AAATATTACCTAA-TATATAT
1019007 AAATATTACCTAAT-TATAT
1 AAATATTACCTAATATATAT
*
1019026 AAACATTACCTAATA
1 AAATATTACCTAATA
1019041 ATTTTCATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 18 0.58
20 1 0.03
21 12 0.39
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATATTACCTAATATATAT
Found at i:1019262 original size:20 final size:20
Alignment explanation
Indices: 1019237--1019295 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1019227 CTTTTCATTA
*
1019237 AAATTACATATAACATTACC
1 AAATTATATATAACATTACC
* * *
1019257 AAATTATGTAAAATATTACC
1 AAATTATATATAACATTACC
* *
1019277 TAATTATATATAACGTTAC
1 AAATTATATATAACATTAC
1019296 TAATTTAATA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (20 bp):
AAATTATATATAACATTACC
Found at i:1019262 original size:77 final size:74
Alignment explanation
Indices: 1019088--1019262 Score: 172
Period size: 77 Copynumber: 2.3 Consensus size: 74
1019078 TATTTAAAAG
* * ** *
1019088 ATTACATATAATATTATCAAATTAAATAAAATATTATAAATTATGTAAATTATTACCAAGAACTT
1 ATTACATATAACATTATCAAATTAAATAAAACATTATAAATTACATAAAATATTACCAAGAACTT
* *
1019153 TTTATCATA
66 TTCATCAAA
* * * * * *
1019162 ATTACATA-ACACGTTATCGAATTACATATGAACATTAATCAATTACATAAAATATTAACTAAGA
1 ATTACATATA-ACATTATCAAATTAAATA-AAACATT-ATAAATTACATAAAATATT-ACCAAGA
*
1019226 ACTTTTCATTAAA
62 ACTTTTCATCAAA
*
1019239 ATTACATATAACATTACCAAATTA
1 ATTACATATAACATTATCAAATTA
1019263 TGTAAAATAT
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
73 1 0.01
74 22 0.28
75 5 0.06
76 15 0.19
77 35 0.44
78 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (74 bp):
ATTACATATAACATTATCAAATTAAATAAAACATTATAAATTACATAAAATATTACCAAGAACTT
TTCATCAAA
Found at i:1019314 original size:19 final size:19
Alignment explanation
Indices: 1019258--1019314 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
1019248 AACATTACCA
*
1019258 AATTATGTAAAATATTACCT
1 AATTATATAAAATATTA-CT
* **
1019278 AATTATATATAACGTTACT
1 AATTATATAAAATATTACT
1019297 AATT-TAATAAAATATTAC
1 AATTAT-ATAAAATATTAC
1019315 CTAAAAATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 13 0.45
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (19 bp):
AATTATATAAAATATTACT
Found at i:1019315 original size:39 final size:40
Alignment explanation
Indices: 1019238--1019318 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
1019228 TTTTCATTAA
*
1019238 AATTACATATAACATTACCAAATTATGTAAAATATTACCT
1 AATTACATATAACATTACCAAATTATATAAAATATTACCT
* * * *
1019278 AATTATATATAACGTTACTAATTTA-ATAAAATATTACCT
1 AATTACATATAACATTACCAAATTATATAAAATATTACCT
1019317 AA
1 AA
1019319 AAATAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.37
Consensus pattern (40 bp):
AATTACATATAACATTACCAAATTATATAAAATATTACCT
Found at i:1020168 original size:16 final size:17
Alignment explanation
Indices: 1020139--1020178 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1020129 TTTTTTTAAT
1020139 TATTTA-TTATATATAA
1 TATTTATTTATATATAA
*
1020155 TATTTATTTA-ATATTA
1 TATTTATTTATATATAA
1020171 -ATTTATTT
1 TATTTATTT
1020179 TTAAATATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTATTTATATATAA
Found at i:1021517 original size:2 final size:2
Alignment explanation
Indices: 1021510--1021540 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1021500 CCATCATCTC
1021510 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1021541 TAATTCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1021690 original size:23 final size:22
Alignment explanation
Indices: 1021647--1021690 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1021637 AGTTATCACT
* *
1021647 TTTTTTTAAAAAAAATAATTTA
1 TTTTTTCAAAAAAAAAAATTTA
1021669 TTTTTTCAAAAAAAAAACATTT
1 TTTTTTCAAAAAAAAAA-ATTT
1021691 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTTTCAAAAAAAAAAATTTA
Found at i:1021710 original size:16 final size:15
Alignment explanation
Indices: 1021679--1021707 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1021669 TTTTTTCAAA
1021679 AAAAAAACATTTTTT
1 AAAAAAACATTTTTT
1021694 AAAAAAAC-TTTTTT
1 AAAAAAACATTTTTT
1021708 TTACACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAAAACATTTTTT
Found at i:1021998 original size:16 final size:16
Alignment explanation
Indices: 1021977--1022007 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1021967 AGGATCATTC
*
1021977 AAAGAAGAAAAAGAAA
1 AAAGAAAAAAAAGAAA
1021993 AAAGAAAAAAAAGAA
1 AAAGAAAAAAAAGAA
1022008 GGTTATTAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAGAAA
Found at i:1022417 original size:16 final size:16
Alignment explanation
Indices: 1022396--1022432 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1022386 TTAGATGTTA
*
1022396 TATATTTTCATATATT
1 TATATTTTAATATATT
1022412 TATATTTTAATATATT
1 TATATTTTAATATATT
1022428 TATAT
1 TATAT
1022433 AAATATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTTTAATATATT
Found at i:1030523 original size:2 final size:2
Alignment explanation
Indices: 1030518--1030551 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1030508 TTTCTTCTGA
*
1030518 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1030552 TTGTTATTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1031210 original size:19 final size:21
Alignment explanation
Indices: 1031186--1031230 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1031176 TTAGAGATGC
1031186 AATTATA-TTTTTATTT-TTT
1 AATTATATTTTTTATTTATTT
1031205 AATTATATTTTTTATTTATTT
1 AATTATATTTTTTATTTATTT
1031226 -ATTAT
1 AATTAT
1031231 TTATTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
AATTATATTTTTTATTTATTT
Found at i:1031224 original size:11 final size:11
Alignment explanation
Indices: 1031195--1031235 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
1031185 CAATTATATT
1031195 TTTATTTTTTAA
1 TTTATTTTTT-A
1031207 TTATATTTTTTA
1 TT-TATTTTTTA
*
1031219 TTTATTTATTA
1 TTTATTTTTTA
1031230 TTTATT
1 TTTATT
1031236 AATATTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 14 0.52
12 5 0.19
13 8 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:1031241 original size:17 final size:17
Alignment explanation
Indices: 1031190--1031243 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 17
1031180 AGATGCAATT
*
1031190 ATATTT-TTATTTTTTA
1 ATATTTATTATTTATTA
* *
1031206 AT-TATATTTTTTATT-
1 ATATTTATTATTTATTA
1031221 -TATTTATTATTTATTA
1 ATATTTATTATTTATTA
1031237 ATATTTA
1 ATATTTA
1031244 ATTCAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
14 1 0.03
15 13 0.45
16 9 0.31
17 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATATTTATTATTTATTA
Found at i:1031827 original size:6 final size:6
Alignment explanation
Indices: 1031816--1031854 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1031806 TCCATTAATT
1031816 TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTA
1 TTACTA TTACTA TTACTA TTACTA TTACTA TTACTA TTA
1031855 TATAGTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (6 bp):
TTACTA
Found at i:1035291 original size:13 final size:13
Alignment explanation
Indices: 1035272--1035302 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1035262 TTAATTTACT
1035272 AAAATGAAATAAA
1 AAAATGAAATAAA
*
1035285 CAAATGAAATAAA
1 AAAATGAAATAAA
1035298 AAAAT
1 AAAAT
1035303 AATAGATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAATGAAATAAA
Found at i:1035549 original size:25 final size:25
Alignment explanation
Indices: 1035521--1035616 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 25
1035511 TAAAAATAAA
*
1035521 TTAATAAAATTATTTTTAAAATATT
1 TTAATAAAATTATATTTAAAATATT
*
1035546 TTAAT--AATAATATTTATAAATATT
1 TTAATAAAATTATATTTA-AAATATT
* * *
1035570 TTAA-CAAACTATACTTAAAA-ATT
1 TTAATAAAATTATATTTAAAATATT
* *
1035593 TTATTTAGAATTATATTTAAAATA
1 TTA-ATAAAATTATATTTAAAATA
1035617 ATATTATTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
23 15 0.27
24 14 0.25
25 25 0.45
26 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (25 bp):
TTAATAAAATTATATTTAAAATATT
Found at i:1035609 original size:12 final size:12
Alignment explanation
Indices: 1035525--1035621 Score: 58
Period size: 12 Copynumber: 8.0 Consensus size: 12
1035515 AATAAATTAA
*
1035525 TAAAATTATTTT
1 TAAAATTATATT
1035537 TAAAA-TAT-TT
1 TAAAATTATATT
*
1035547 TAATAATAATATT
1 TAA-AATTATATT
1035560 TATAAA-TAT-TT
1 TA-AAATTATATT
*
1035571 TAACAAACTATACTT
1 T-A-AAATTATA-TT
* *
1035586 AAAAATTTTATT
1 TAAAATTATATT
*
1035598 TAGAATTATATT
1 TAAAATTATATT
*
1035610 TAAAATAATATT
1 TAAAATTATATT
1035622 ATTTAATATA
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
10 5 0.08
11 8 0.12
12 34 0.52
13 15 0.23
14 2 0.03
15 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (12 bp):
TAAAATTATATT
Found at i:1035686 original size:15 final size:15
Alignment explanation
Indices: 1035605--1035698 Score: 59
Period size: 15 Copynumber: 6.1 Consensus size: 15
1035595 ATTTAGAATT
1035605 ATATTTAAA-ATAATA
1 ATATTTAAATATAA-A
*
1035620 TTATTT-AATATATAA
1 ATATTTAAATATA-AA
*
1035635 ATATTT-TATATAAA
1 ATATTTAAATATAAA
* * *
1035649 AGATTAAAACTAAAAATA
1 ATATTTAAA-T-ATAA-A
1035667 ATATTTAAATATAAA
1 ATATTTAAATATAAA
*
1035682 ATATTTATATAATAAA
1 ATATTTAAAT-ATAAA
1035698 A
1 A
1035699 AAGTATTTAT
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
14 8 0.13
15 30 0.49
16 11 0.18
17 4 0.07
18 8 0.13
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (15 bp):
ATATTTAAATATAAA
Found at i:1035707 original size:19 final size:19
Alignment explanation
Indices: 1035674--1035713 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
1035664 ATAATATTTA
*
1035674 AATATAAAATATTTAT-AT
1 AATAAAAAATATTTATGAT
1035692 AATAAAAAAGTATTTATGAT
1 AATAAAAAA-TATTTATGAT
1035712 AA
1 AA
1035714 CATTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AATAAAAAATATTTATGAT
Found at i:1037532 original size:21 final size:21
Alignment explanation
Indices: 1037497--1037536 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1037487 TTTTATGTAT
1037497 TATAATTTTATTTAATATTATG
1 TATAATTTTATTTAA-ATTATG
*
1037519 TATATTTTTA-TTAAATTA
1 TATAATTTTATTTAAATTA
1037537 ATAATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TATAATTTTATTTAAATTATG
Found at i:1037580 original size:21 final size:21
Alignment explanation
Indices: 1037555--1037621 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
1037545 TATTCTGTAA
1037555 ATTTTAATATATTTATATTAT
1 ATTTTAATATATTTATATTAT
* * *
1037576 TTTTTATTATTTTTATATTAT
1 ATTTTAATATATTTATATTAT
*
1037597 ATTTTAATTATATATATATATAT
1 ATTTTAA-TATATTTATAT-TAT
1037620 AT
1 AT
1037622 ATATGTAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 23 0.62
22 9 0.24
23 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTAATATATTTATATTAT
Found at i:1037594 original size:11 final size:11
Alignment explanation
Indices: 1037566--1037607 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
1037556 TTTTAATATA
1037566 TTTATATTATT
1 TTTATATTATT
1037577 TTT-TATTATT
1 TTTATATTATT
1037587 TTTATATTATAT
1 TTTATATTAT-T
1037599 TTTA-ATTAT
1 TTTATATTAT
1037608 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.34
11 14 0.48
12 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATATTATT
Found at i:1037608 original size:11 final size:11
Alignment explanation
Indices: 1037555--1037609 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
1037545 TATTCTGTAA
1037555 ATTTTAA-TAT
1 ATTTTAATTAT
1037565 A-TTTATATTAT
1 ATTTTA-ATTAT
*
1037576 -TTTTTATTAT
1 ATTTTAATTAT
1037586 -TTTTATATTAT
1 ATTTTA-ATTAT
1037597 ATTTTAATTAT
1 ATTTTAATTAT
1037608 AT
1 AT
1037610 ATATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 4 0.11
10 11 0.29
11 18 0.47
12 5 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTAATTAT
Found at i:1037951 original size:29 final size:29
Alignment explanation
Indices: 1037888--1037967 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
1037878 AAGTTTATTA
*
1037888 AAAATTTATGTATTA-TAATAAATAATATT
1 AAAATTTATGTATTATTAA-AAATAAAATT
** *
1037917 TTAATTTATGTATTATTAAAATTAAAATT
1 AAAATTTATGTATTATTAAAAATAAAATT
* *
1037946 AAAATTTTTATATT-TTAAAAAT
1 AAAATTTATGTATTATTAAAAAT
1037968 TATAATAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 7 0.17
29 31 0.76
30 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
AAAATTTATGTATTATTAAAAATAAAATT
Found at i:1038025 original size:19 final size:18
Alignment explanation
Indices: 1038004--1038069 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
1037994 CTTTAAATTT
1038004 TTTTAAATATTAATAAAA
1 TTTTAAATATTAATAAAA
* *
1038022 TTTT-TATA-TATCTAAAA
1 TTTTAAATATTA-ATAAAA
*
1038039 TTTTAAATTTTATATAAAA
1 TTTTAAATATTA-ATAAAA
*
1038058 ATTTAAAT-TTAA
1 TTTTAAATATTAA
1038070 CTTACAATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
16 2 0.05
17 13 0.33
18 9 0.23
19 15 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAAATATTAATAAAA
Found at i:1039337 original size:30 final size:31
Alignment explanation
Indices: 1039282--1039340 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
1039272 ATAACAATAA
*
1039282 TAATTTTATATTATAATATTATTTAAAATTTT
1 TAATTTTATATTAT-ATAATATTTAAAATTTT
*
1039314 TAATTTTTTATTAT-TAATATTTAAAAT
1 TAATTTTATATTATATAATATTTAAAAT
1039341 CTATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.48
32 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TAATTTTATATTATATAATATTTAAAATTTT
Found at i:1041784 original size:6 final size:6
Alignment explanation
Indices: 1041749--1041776 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1041739 TTAAAACCAG
1041749 AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1041777 AAAGAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:1044631 original size:14 final size:15
Alignment explanation
Indices: 1044612--1044640 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1044602 TATTAACGTG
1044612 TAAAATTT-TATAAT
1 TAAAATTTATATAAT
1044626 TAAAATTTATATAAT
1 TAAAATTTATATAAT
1044641 ATTTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTTATATAAT
Found at i:1044735 original size:11 final size:11
Alignment explanation
Indices: 1044721--1044770 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
1044711 TTTTTCATTC
1044721 TCTTTTCTTTT
1 TCTTTTCTTTT
1044732 TCTTTT-TTTT
1 TCTTTTCTTTT
*
1044742 TCCTTTCTCTTT
1 TCTTTTCT-TTT
* *
1044754 TC-CTTCTTTC
1 TCTTTTCTTTT
1044764 TCTTTTC
1 TCTTTTC
1044771 CCTTCTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 13 0.41
11 14 0.44
12 5 0.16
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:1044747 original size:17 final size:16
Alignment explanation
Indices: 1044723--1044769 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1044713 TTTCATTCTC
*
1044723 TTTTCTTTTTCTTTTT
1 TTTTCTTTCTCTTTTT
1044739 TTTTCCTTTCTC-TTTT
1 TTTT-CTTTCTCTTTTT
**
1044755 CCTTCTTTCTCTTTT
1 TTTTCTTTCTCTTTT
1044770 CCCTTCTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.27
16 13 0.50
17 6 0.23
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTCTCTTTTT
Found at i:1044750 original size:28 final size:29
Alignment explanation
Indices: 1044706--1044769 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
1044696 TTCTACTGCA
1044706 TCTC-TTTTTTCATTCTCTTTT-CTT-TT
1 TCTCTTTTTTTCATTCTCTTTTCCTTCTT
* *
1044732 TCTTTTTTTTTCCTTTCTCTTTTCCTTCTT
1 TCTCTTTTTTT-CATTCTCTTTTCCTTCTT
1044762 TCTCTTTT
1 TCTCTTTT
1044770 CCCTTCTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 3 0.10
27 6 0.19
28 10 0.32
29 3 0.10
30 9 0.29
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (29 bp):
TCTCTTTTTTTCATTCTCTTTTCCTTCTT
Found at i:1044771 original size:15 final size:14
Alignment explanation
Indices: 1044706--1044770 Score: 71
Period size: 15 Copynumber: 4.6 Consensus size: 14
1044696 TTCTACTGCA
*
1044706 TCTCTTTT-TTCAT
1 TCTCTTTTCTTCTT
1044719 TCTCTTTTCTT-TT
1 TCTCTTTTCTTCTT
* *
1044732 TCTTTTTTTTTCCTT
1 TCTCTTTTCTT-CTT
1044747 TCTCTTTTCCTTCTT
1 TCTCTTTT-CTTCTT
1044762 TCTCTTTTC
1 TCTCTTTTC
1044771 CCTTCTTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
13 18 0.42
14 3 0.07
15 20 0.47
16 2 0.05
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTCTTTTCTTCTT
Found at i:1045692 original size:12 final size:12
Alignment explanation
Indices: 1045677--1045703 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1045667 ATGGTTGACT
1045677 CAACAAAATGAG
1 CAACAAAATGAG
1045689 CAACAAAATGAG
1 CAACAAAATGAG
1045701 CAA
1 CAA
1045704 GACTTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.19, G:0.15, T:0.07
Consensus pattern (12 bp):
CAACAAAATGAG
Found at i:1046569 original size:18 final size:18
Alignment explanation
Indices: 1046548--1046595 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1046538 ATTAAAAAAT
1046548 AAAATAAAATAAAAATAA
1 AAAATAAAATAAAAATAA
*
1046566 AAAATTAAATAAAAATAA
1 AAAATAAAATAAAAATAA
**
1046584 CTAATAAAATAA
1 AAAATAAAATAA
1046596 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAATAAAATAAAAATAA
Found at i:1046734 original size:11 final size:11
Alignment explanation
Indices: 1046720--1046767 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
1046710 ATTAAATACG
1046720 AATTATAAATT
1 AATTATAAATT
1046731 AATTTATAAATT
1 AA-TTATAAATT
*
1046743 -ATCATAAATT
1 AATTATAAATT
*
1046753 AATCATAAATT
1 AATTATAAATT
1046764 AATT
1 AATT
1046768 TATGAGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 8 0.24
11 16 0.48
12 9 0.27
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTATAAATT
Found at i:1046749 original size:22 final size:21
Alignment explanation
Indices: 1046724--1046764 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1046714 AATACGAATT
*
1046724 ATAAATTAATTTATAAATTATC
1 ATAAATTAA-TCATAAATTATC
1046746 ATAAATTAATCATAAATTA
1 ATAAATTAATCATAAATTA
1046765 ATTTATGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAATTAATCATAAATTATC
Found at i:1046797 original size:20 final size:21
Alignment explanation
Indices: 1046752--1046797 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1046742 TATCATAAAT
*
1046752 TAATCATAAATTAATTTATGAG
1 TAATCATAAATT-ATTTATAAG
*
1046774 TAATCATAAATT-TTTTTAAG
1 TAATCATAAATTATTTATAAG
1046794 TAAT
1 TAAT
1046798 GTTATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (21 bp):
TAATCATAAATTATTTATAAG
Found at i:1047110 original size:2 final size:2
Alignment explanation
Indices: 1047103--1047138 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1047093 ATATGGGCGG
1047103 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1047139 TTGTTGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1047218 original size:16 final size:17
Alignment explanation
Indices: 1047193--1047232 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1047183 TTTTAAAATT
*
1047193 TAAATATTAATATAATA
1 TAAATATTAAAATAATA
*
1047210 -AAATTTTAAAATAATA
1 TAAATATTAAAATAATA
1047226 TAAATAT
1 TAAATAT
1047233 ATACATGTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATTAAAATAATA
Found at i:1047231 original size:22 final size:22
Alignment explanation
Indices: 1047186--1047228 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1047176 CCATCAATTT
1047186 TAAAATTTAAATATTAATATAA
1 TAAAATTTAAATATTAATATAA
1047208 TAAAATTTTAAA-A-TAATATAA
1 TAAAA-TTTAAATATTAATATAA
1047229 ATATATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAATTTAAATATTAATATAA
Found at i:1047705 original size:20 final size:20
Alignment explanation
Indices: 1047680--1047784 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
1047670 TTTTACCTAG
1047680 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1047700 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1047720 ATGTATTGATACATTCTGTCTTTTTTCCCA
1 ATGTATCGATACA--------TTTTT--CA
1047750 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
1047771 ATGTATCGATACAT
1 ATGTATCGATACAT
1047785 CTAGTTAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
20 43 0.65
21 2 0.03
23 5 0.08
28 3 0.05
30 1 0.02
31 12 0.18
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1049165 original size:302 final size:302
Alignment explanation
Indices: 1048619--1049223 Score: 1210
Period size: 302 Copynumber: 2.0 Consensus size: 302
1048609 CTAAAATGCC
1048619 ATGTTCATTCTAGTAGCCTTTGACCATACATTTTTTTTATTATGTTTCATGCATTTTTAATATGT
1 ATGTTCATTCTAGTAGCCTTTGACCATACATTTTTTTTATTATGTTTCATGCATTTTTAATATGT
1048684 CCAGCATCTCATTGAATGTTATCCATCAGTTCATTGTATGATTATCACATTTTCCAAGTCAAGAT
66 CCAGCATCTCATTGAATGTTATCCATCAGTTCATTGTATGATTATCACATTTTCCAAGTCAAGAT
1048749 GCGTGCTTGTTTGCATTTGAAAATTGATTTTCCAAAAACCTCTCCTAAGTTAAGCATATTAGCCT
131 GCGTGCTTGTTTGCATTTGAAAATTGATTTTCCAAAAACCTCTCCTAAGTTAAGCATATTAGCCT
1048814 CAATCAATGAGGATTAACATAAGCTTAAGATTTTTACCAAGAAAATATCATAATCTTGGGGTAAA
196 CAATCAATGAGGATTAACATAAGCTTAAGATTTTTACCAAGAAAATATCATAATCTTGGGGTAAA
1048879 GTTAATTTTCAGGTCTGGATTCGTGATTAAATGAGTTCAAAT
261 GTTAATTTTCAGGTCTGGATTCGTGATTAAATGAGTTCAAAT
1048921 ATGTTCATTCTAGTAGCCTTTGACCATACATTTTTTTTATTATGTTTCATGCATTTTTAATATGT
1 ATGTTCATTCTAGTAGCCTTTGACCATACATTTTTTTTATTATGTTTCATGCATTTTTAATATGT
1048986 CCAGCATCTCATTGAATGTTATCCATCAGTTCATTGTATGATTATCACATTTTCCAAGTCAAGAT
66 CCAGCATCTCATTGAATGTTATCCATCAGTTCATTGTATGATTATCACATTTTCCAAGTCAAGAT
1049051 GCGTGCTTGTTTGCATTTGAAAATTGATTTTCCAAAAACCTCTCCTAAGTTAAGCATATTAGCCT
131 GCGTGCTTGTTTGCATTTGAAAATTGATTTTCCAAAAACCTCTCCTAAGTTAAGCATATTAGCCT
1049116 CAATCAATGAGGATTAACATAAGCTTAAGATTTTTACCAAGAAAATATCATAATCTTGGGGTAAA
196 CAATCAATGAGGATTAACATAAGCTTAAGATTTTTACCAAGAAAATATCATAATCTTGGGGTAAA
1049181 GTTAATTTTCAGGTCTGGATTCGTGATTAAATGAGTTCAAAT
261 GTTAATTTTCAGGTCTGGATTCGTGATTAAATGAGTTCAAAT
1049223 A
1 A
1049224 CATGATTTTT
Statistics
Matches: 303, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
302 303 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (302 bp):
ATGTTCATTCTAGTAGCCTTTGACCATACATTTTTTTTATTATGTTTCATGCATTTTTAATATGT
CCAGCATCTCATTGAATGTTATCCATCAGTTCATTGTATGATTATCACATTTTCCAAGTCAAGAT
GCGTGCTTGTTTGCATTTGAAAATTGATTTTCCAAAAACCTCTCCTAAGTTAAGCATATTAGCCT
CAATCAATGAGGATTAACATAAGCTTAAGATTTTTACCAAGAAAATATCATAATCTTGGGGTAAA
GTTAATTTTCAGGTCTGGATTCGTGATTAAATGAGTTCAAAT
Found at i:1052333 original size:22 final size:23
Alignment explanation
Indices: 1052290--1052333 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1052280 GGGGCCACTC
*
1052290 TTTTTTTGATTGATGTTCATTCT
1 TTTTTTTGATTGATATTCATTCT
* *
1052313 TTTTTTTG-TTGCTATTTATTC
1 TTTTTTTGATTGATATTCATTC
1052334 CCATTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.11, C:0.09, G:0.11, T:0.68
Consensus pattern (23 bp):
TTTTTTTGATTGATATTCATTCT
Found at i:1064780 original size:20 final size:20
Alignment explanation
Indices: 1064733--1064807 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1064723 AAAAAGACAT
*
1064733 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1064752 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1064773 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1064793 AATGTATCGATACAT
1 AATGTATCGATACAT
1064808 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1064801 original size:40 final size:39
Alignment explanation
Indices: 1064730--1064807 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1064720 GGTAAAAAGA
* *
1064730 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1064769 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1064808 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1066133 original size:29 final size:29
Alignment explanation
Indices: 1065339--1066134 Score: 1057
Period size: 28 Copynumber: 27.7 Consensus size: 29
1065329 GGGTTGTCAT
*
1065339 TGACTTGCATGGGCTTTAAAAGG-GTGCCAC
1 TGACTTG--TGGGCTTTGAAAGGAGTGCCAC
*
1065369 TGACTTGCGTGGGCTTTGAAA-GAATGCCAC
1 TGACTT--GTGGGCTTTGAAAGGAGTGCCAC
* *
1065399 TAACTCGTGGGCTTTGAAAGGA-TGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
*
1065427 TGACTTGTGGGCTTTGAAA-GAGTTCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* *
1065455 TGACTTGTGGGCTTTGAAAAG-GTACCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* *
1065483 TGACTTGCTTGAGCTTTAAAAGGAGTGCCAC
1 TGACTTG--TGGGCTTTGAAAGGAGTGCCAC
*
1065514 TGACTTGTGTGGGCTTTAAAAGG-GTGCCAC
1 TGAC-T-TGTGGGCTTTGAAAGGAGTGCCAC
1065544 TGACTTGTGGGCTTTGAAA-GAGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* * * **
1065572 TGAATTGTGGGCTTCGCAA-TTGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* *
1065600 TAACTTGTGGGCTTCGAAAGG-GTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
*
1065628 TGACTTGTGGGCTCTGAAAGG-GTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
*
1065656 TAACTTGTGGGCTTTGAAAGG-GTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* * *
1065684 TGACTTGTGAGCTTTGAAAAGAATGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* **
1065713 TGATTTGTGGGCTTTGAAAAAAGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
1065742 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
1065771 TGACTTGTGGGCTTTGAAAGG-GTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* *
1065799 TAACTTGTGGGCTTTGAAAAGAGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* *
1065828 TGATTTGTGGGCTTTGAAAAGAGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
1065857 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
*
1065886 TAACTTGTGGGCTTTGAAAGG-GTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* *
1065914 TAACTTGTGGGCTTTAAAAGGAGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
1065943 TGACTTGTGGGCTTTGAAAGG-GTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* * *
1065971 TGACTTATGGGCTTTGAAAAGAGTGTCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
1066000 TGACTTGTGGGCTTTGAAAGG-GTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
* *
1066028 TGAGTTATGGGCTTTGAAAGG-GTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
*
1066056 TGACTTGTGGGCTTTGAAAAGAGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
*
1066085 TGATTTGTGGGCTTTGAAAGGAGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGAGTGCCAC
1066114 TGACTTGTGGGCTTTGAAAGG
1 TGACTTGTGGGCTTTGAAAGG
1066135 GATGAACATT
Statistics
Matches: 685, Mismatches: 63, Indels: 37
0.87 0.08 0.05
Matches are distributed among these distances:
27 3 0.00
28 337 0.49
29 269 0.39
30 49 0.07
31 23 0.03
32 2 0.00
33 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
TGACTTGTGGGCTTTGAAAGGAGTGCCAC
Found at i:1067367 original size:1 final size:1
Alignment explanation
Indices: 1067363--1067420 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
1067353 TTTTTTGCTA
* * * * * *
1067363 TTTTTTCTTTTTTTTTTGTTTTTTTGTTTTATTTTTTTTGTTTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1067421 GGGTGTAAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.03, C:0.02, G:0.05, T:0.90
Consensus pattern (1 bp):
T
Found at i:1067385 original size:19 final size:20
Alignment explanation
Indices: 1067353--1067421 Score: 79
Period size: 19 Copynumber: 3.4 Consensus size: 20
1067343 GACCCTTCTA
1067353 TTTTTTGCTATTTTTTCTT-TT
1 TTTTTTGCT-TTTTTT-TTATT
*
1067374 TTTTTTGTTTTTTTGTTTTATT
1 TTTTTTG-CTTTTT-TTTTATT
1067396 TTTTTTG-TTTTTTTTTATT
1 TTTTTTGCTTTTTTTTTATT
1067415 TTTTTTG
1 TTTTTTG
1067422 GGTGTAAAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
19 14 0.32
20 5 0.11
21 13 0.30
22 12 0.27
ACGTcount: A:0.04, C:0.03, G:0.07, T:0.86
Consensus pattern (20 bp):
TTTTTTGCTTTTTTTTTATT
Found at i:1073448 original size:13 final size:13
Alignment explanation
Indices: 1073430--1073455 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1073420 TACAGCAAGT
1073430 ATGTATCGATACA
1 ATGTATCGATACA
1073443 ATGTATCGATACA
1 ATGTATCGATACA
1073456 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1075705 original size:21 final size:21
Alignment explanation
Indices: 1075672--1075716 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1075662 TTGCAAGTTG
*
1075672 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1075694 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1075714 AAA
1 AAA
1075717 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1077540 original size:15 final size:15
Alignment explanation
Indices: 1077520--1077550 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1077510 TAAAAATGTC
*
1077520 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1077535 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1077550 C
1 C
1077551 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1079646 original size:13 final size:13
Alignment explanation
Indices: 1079628--1079653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1079618 ACATTTTCCT
1079628 TTGTATCGATACA
1 TTGTATCGATACA
1079641 TTGTATCGATACA
1 TTGTATCGATACA
1079654 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1082222 original size:13 final size:13
Alignment explanation
Indices: 1082204--1082229 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1082194 TACAGCAAGT
1082204 ATGTATCGATACA
1 ATGTATCGATACA
1082217 ATGTATCGATACA
1 ATGTATCGATACA
1082230 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1091398 original size:20 final size:20
Alignment explanation
Indices: 1091351--1091425 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1091341 AAAAAGACAT
*
1091351 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1091370 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1091391 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1091411 AATGTATCGATACAT
1 AATGTATCGATACAT
1091426 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1091419 original size:40 final size:39
Alignment explanation
Indices: 1091348--1091425 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1091338 GGTAAAAAGA
* *
1091348 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1091387 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1091426 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1092107 original size:1 final size:1
Alignment explanation
Indices: 1092101--1092191 Score: 56
Period size: 1 Copynumber: 91.0 Consensus size: 1
1092091 TTTCGTACCT
* ** * * ** * **
1092101 AAAAAAACAAAAAAAAAAAAACCAAGAAAAAAAACAAAAAAAACCAAAAAAATAAACCAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
1092166 AAAACAAAAAACAAACAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1092192 GGGGTTCAGA
Statistics
Matches: 68, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.85, C:0.13, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:1092139 original size:22 final size:21
Alignment explanation
Indices: 1092102--1092180 Score: 90
Period size: 22 Copynumber: 3.7 Consensus size: 21
1092092 TTCGTACCTA
*
1092102 AAAAAACAAAAAAAAAAAAACC
1 AAAAAA-AAAACAAAAAAAACC
1092124 AAGAAAAAAAACAAAAAAAACC
1 AA-AAAAAAAACAAAAAAAACC
1092146 AAAAAAATAAACCAAAAAAAA--
1 AAAAAAA-AAA-CAAAAAAAACC
*
1092167 AAACAAAAAACAAA
1 AAAAAAAAAACAAA
1092181 CAAACAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.08
20 3 0.06
21 11 0.21
22 21 0.40
23 13 0.25
ACGTcount: A:0.85, C:0.13, G:0.01, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAACAAAAAAAACC
Found at i:1092141 original size:35 final size:35
Alignment explanation
Indices: 1092101--1092191 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 35
1092091 TTTCGTACCT
*
1092101 AAAAAAACAAAAAAAAAAAAACCAAGAAAAAAAAC
1 AAAAAAACAAAAAAAAAAAAACCAAAAAAAAAAAC
* *
1092136 AAAAAAA-ACCAAAAAAATAAACCAAAAAAAAAAAC
1 AAAAAAACA-AAAAAAAAAAAACCAAAAAAAAAAAC
*
1092171 -AAAAAACAAACAAACAAAAAA
1 AAAAAAACAAA-AAAAAAAAAA
1092192 GGGGTTCAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
34 8 0.17
35 39 0.83
ACGTcount: A:0.85, C:0.13, G:0.01, T:0.01
Consensus pattern (35 bp):
AAAAAAACAAAAAAAAAAAAACCAAAAAAAAAAAC
Found at i:1093473 original size:28 final size:28
Alignment explanation
Indices: 1093435--1093534 Score: 146
Period size: 28 Copynumber: 3.6 Consensus size: 28
1093425 CTACAACGTT
* *
1093435 CATCTCTTCAAAGCCCACAGGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * *
1093463 CATATTTTCAAAGCCTACAAGTTAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
1093491 CATCTTTTCAAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
1093519 CATCCTTTCAAAGCCC
1 CATCTTTTCAAAGCCC
1093535 TTCAAAGCCC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (28 bp):
CATCTTTTCAAAGCCCACAAGTCAGTGG
Found at i:1093501 original size:56 final size:56
Alignment explanation
Indices: 1093441--1094048 Score: 644
Period size: 56 Copynumber: 10.4 Consensus size: 56
1093431 CGTTCATCTC
* *** * * *
1093441 TTCAAAGCCCACAGGTCAGTGGCATATTTTCAAAGCCTACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1093497 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCTTCAAAGCCCACAAGTTAGTGGTATCC
1 TTCAAAGCCCACAAGTCAGTGGCA------C----CCTTTCAAAGCCCACAAGTCAGTGGCATCC
1093562 T
56 T
* * * *
1093563 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
1093619 TTCAAAGCCCACAAGTCAGTGGTACCCCTTCAAAGCTCACAAGTCAGCGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAT--CCT
* * * *
1093677 TTCAAAGCCCATAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAAATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGC--ATCCT
* * * *
1093737 TTCAAAGCCCACAAGTTAGTGGCA-TCTCTTCAAAAGACCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT-TTC-AAAGCCCACAAGTCAGTGGCATCCT
1093794 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAT--CCT
* * * *
1093852 TTCAAAGCCCACACAAATCAGTGGCACCCTTCCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1093910 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1093966 TTCAAAGCCCACAAGTCAGTAGTA-CCTCTTCAAAGCCCACAAGTCAGTGGCTTCCCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT-TTCAAAGCCCACAAGTCAGTGGCAT--CCT
1094024 TTCAAAGCCCACATAAGTCAGTGGC
1 TTCAAAGCCCAC--AAGTCAGTGGC
1094049 TTCAAAGCCC
Statistics
Matches: 468, Mismatches: 56, Indels: 52
0.81 0.10 0.09
Matches are distributed among these distances:
55 3 0.01
56 204 0.44
57 32 0.07
58 70 0.15
59 17 0.04
60 88 0.19
61 4 0.01
62 2 0.00
66 48 0.10
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (56 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1093548 original size:38 final size:38
Alignment explanation
Indices: 1093497--1093572 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
1093487 GTGGCATCTT
1093497 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCC
* *
1093535 TTCAAAGCCCACAAGTTAGTGGTATCCTTTCAAAGCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCC
1093573 ACAAGTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.24
Consensus pattern (38 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCC
Found at i:1093572 original size:28 final size:28
Alignment explanation
Indices: 1093535--1094048 Score: 600
Period size: 28 Copynumber: 17.8 Consensus size: 28
1093525 TTCAAAGCCC
* * *
1093535 TTCAAAGCCCACAAGTTAGTGGTATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1093563 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1093591 TTCAAAGCCCACAAGTCAATGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1093619 TTCAAAGCCCACAAGTCAGTGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1093647 TTCAAAGCTCACAAGTCAGCGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGC--ACCCT
* *
1093677 TTCAAAGCCCATAAGTCGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1093705 TTCAAAGCCCACACAAGTCGGTGGCAAATCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC--ACCCT
* *
1093737 TTCAAAGCCCACAAGTTAGTGGCA-TCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1093764 CTTCAAAAGACCACAAGTTAGTGGCATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCACCCT
1093794 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
1093822 TTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGC--ACCCT
*
1093852 TTCAAAGCCCACACAAATCAGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCT
* *
1093882 TCCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
1093910 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1093938 TTCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1093966 TTCAAAGCCCACAAGTCAGTAGTA-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1093993 CTTCAAAGCCCACAAGTCAGTGGCTTCCCCT
1 -TTCAAAGCCCACAAGTCAGTGGC--ACCCT
1094024 TTCAAAGCCCACATAAGTCAGTGGC
1 TTCAAAGCCCAC--AAGTCAGTGGC
1094049 TTCAAAGCCC
Statistics
Matches: 425, Mismatches: 42, Indels: 34
0.85 0.08 0.07
Matches are distributed among these distances:
27 4 0.01
28 269 0.63
29 26 0.06
30 85 0.20
31 7 0.02
32 34 0.08
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:1094058 original size:25 final size:25
Alignment explanation
Indices: 1094024--1094073 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1094014 GGCTTCCCCT
1094024 TTCAAAGCCCACATAAGTCAGTGGC
1 TTCAAAGCCCACATAAGTCAGTGGC
* *
1094049 TTCAAAGCCCATATAAGTTAGTGGC
1 TTCAAAGCCCACATAAGTCAGTGGC
1094074 ACCTTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (25 bp):
TTCAAAGCCCACATAAGTCAGTGGC
Found at i:1094313 original size:48 final size:48
Alignment explanation
Indices: 1094184--1094315 Score: 219
Period size: 48 Copynumber: 2.8 Consensus size: 48
1094174 GGCACCTTTA
* *
1094184 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACAATGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACCTTTCCC
* *
1094232 TTAGCTTAATGTCGCTGGCCTTGAATCAGCACATTGTCCACCTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACCTTTCCC
*
1094280 TTAGCTCAATGTCGCTGGCCTTGAATTGGCACATTG
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTG
1094316 GCACTCCTCT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACCTTTCCC
Found at i:1095075 original size:19 final size:19
Alignment explanation
Indices: 1095051--1095104 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
1095041 TTTTACCTAG
*
1095051 ATGTATCGATACATTTTCA
1 ATGTATCGATACATTATCA
*
1095070 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TATCA
*
1095090 ATGCATCGATACATT
1 ATGTATCGATACATT
1095105 CTGTCTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:1095607 original size:14 final size:14
Alignment explanation
Indices: 1095579--1095607 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1095569 ATATCGTAGC
1095579 AAAACATCAACAAA
1 AAAACATCAACAAA
1095593 AAAAC-TCAACAAA
1 AAAACATCAACAAA
1095606 AA
1 AA
1095608 GTCCATTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.72, C:0.21, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAACATCAACAAA
Found at i:1102801 original size:31 final size:31
Alignment explanation
Indices: 1102763--1102839 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
1102753 TACATTGAAA
* *
1102763 AATGTATCGATACATCTGGGAAAAAAGATAG
1 AATGTATCGATACATCTAGGAAAAAAGACAG
1102794 AATGTATCGATACATCTAGGAAAAAAGACAG
1 AATGTATCGATACATCTAGGAAAAAAGACAG
1102825 AATGTATCGATACAT
1 AATGTATCGATACAT
1102840 TCATACATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.23
Consensus pattern (31 bp):
AATGTATCGATACATCTAGGAAAAAAGACAG
Found at i:1107280 original size:52 final size:52
Alignment explanation
Indices: 1107207--1107392 Score: 209
Period size: 52 Copynumber: 3.6 Consensus size: 52
1107197 TAACTAGATG
* *
1107207 TATCGATACATTGAAGAATGTATCGATACATTTGGTTCAAAAACTCAGAATA
1 TATCGATACAATGAAAAATGTATCGATACATTTGGTTCAAAAACTCAGAATA
* * * * *
1107259 TATCGTTACAATGAATAATGTATCGATACATTCGGGTT-AAAAACTCATAATG
1 TATCGATACAATGAAAAATGTATCGATACATT-TGGTTCAAAAACTCAGAATA
* * * * *
1107311 TATCGATACAATAAAAAATGTATCGATATATTTGG-AC-CAAACTCAGAATC
1 TATCGATACAATGAAAAATGTATCGATACATTTGGTTCAAAAACTCAGAATA
* *
1107361 TATCGATACAAT-AAAAATGTATTGATATATTT
1 TATCGATACAATGAAAAATGTATCGATACATTT
1107393 TCTTTCCAGA
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
49 19 0.16
50 22 0.19
51 2 0.02
52 69 0.59
53 4 0.03
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (52 bp):
TATCGATACAATGAAAAATGTATCGATACATTTGGTTCAAAAACTCAGAATA
Found at i:1107474 original size:20 final size:21
Alignment explanation
Indices: 1107449--1107502 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1107439 CATTTTAAAA
*
1107449 ATGTATCAATACATTCTCTT-
1 ATGTATCAATACATTCACTTG
*
1107469 ATGTATCGATACATTCACTTG
1 ATGTATCAATACATTCACTTG
*
1107490 TTGTATCAATACA
1 ATGTATCAATACA
1107503 AATTGCTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGTATCAATACATTCACTTG
Found at i:1110162 original size:51 final size:51
Alignment explanation
Indices: 1110012--1110232 Score: 264
Period size: 51 Copynumber: 4.3 Consensus size: 51
1110002 GAAATAATGA
* * * * * *
1110012 GGTTGGAGTATCCTCGATTGTGAAAATTTGGTGTTTTTAGAAATAAAATCTG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTAGAAATAAAACCGG
* * *
1110064 AGTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTT-GAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTAG-AAATAAAACCGG
*
1110116 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
* * * * * *
1110167 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
1110218 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1110233 TCGGAGGTAA
Statistics
Matches: 148, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
51 87 0.59
52 50 0.34
53 11 0.07
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:1110292 original size:27 final size:28
Alignment explanation
Indices: 1110215--1110293 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 28
1110205 GAAATAAAGC
***
1110215 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCAATGAGGTAA
* ** *
1110243 CGGGGTTGGAGTATCTCTGATGA-TTAA
1 CGGGGTTGGAGTATCCCCAATGAGGTAA
*
1110270 TGGGGTTGGAGTATCCCCAATGAG
1 CGGGGTTGGAGTATCCCCAATGAG
1110294 AAATTGATGT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.20, C:0.16, G:0.37, T:0.27
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCAATGAGGTAA
Found at i:1110321 original size:103 final size:105
Alignment explanation
Indices: 1110165--1110360 Score: 279
Period size: 103 Copynumber: 1.9 Consensus size: 105
1110155 AAATAAAACC
* *
1110165 GGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGA-TATGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATC
* ** *
1110230 CCCTCGGAGGTAACGGGGTTGGAGTATCTCTGATGATTAAT
65 CCCTCAGAAATAACGGGGTTGGAATATCTCTGATGATTAAT
** * *
1110271 GGGGTTGGAGTATCCCC-A-ATGAGAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTGTCC
1 GGGGTTGGAGTATCCCCGATATGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
1110334 CCTCAGAAATAACGGGGTTGGAATATC
66 CCTCAGAAATAACGGGGTTGGAATATC
1110361 CCCGATTGTG
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
103 62 0.77
105 1 0.01
106 17 0.21
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (105 bp):
GGGGTTGGAGTATCCCCGATATGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
CCTCAGAAATAACGGGGTTGGAATATCTCTGATGATTAAT
Found at i:1110363 original size:182 final size:182
Alignment explanation
Indices: 1110164--1110651 Score: 456
Period size: 182 Copynumber: 2.7 Consensus size: 182
1110154 GAAATAAAAC
1110164 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
*
1110229 CCCCTCGGAGGTAACGGGGTTGGAGTATCTCTGATGATTAATGGGGTTGGAGTATCCCCA-ATGA
66 CCCCTCGGA--TAACGGGGTTGGAGTATCTCTGATGATTAATGGGGTTGGAGTATCCCCATAAGA
* * * *
1110293 GAAATTGATGTTTTAGAAATAAAACC-GGGGTTGGAGTGTCCCCTCAGAAATAA
129 GAAATTGATATTTTAGAAATAAAACCTGGGATTGGAGTATCCACTCAGAAATAA
* * ** ** ** *
1110346 CGGGGTTGGAATATCCCCGATTGTGA-AAAGTCGGTGCTTTGGAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAGAAA-TCAATATTTTGGAAATAAAGCCGGGGTTGGAGTA
* * *** * * * * * *
1110410 T-CCC-C-GATTATGGAAAATGG-GTGT-TTTAGA-AATAAAATCGGAGTTGGAGTATCCTCGAT
65 TCCCCTCGGATAACGG-GGTTGGAGTATCTCT-GATGAT-TAAT-GGGGTTGGAGTATCC-CCA-
* * * * *
1110469 TAAGAGAAATTGATATTTTGGAAATGAAACCTGGGATTTGAGTATCCATTCGGAAATAA
124 TAAGAGAAATTGATATTTTAGAAATAAAACCTGGGATTGGAGTATCCACTCAGAAATAA
* *
1110528 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTT-AAGAATAAAGCAGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGA-AATAAAGCCGGGGTTGGAGTA
* * * * * *
1110592 TCCCTTTGGAAATAGCGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCC
65 TCCCCTCGG--ATAACGGGGTTGGAGTATCTCTGATGATTAATGGGGTTGGAGTATCCCC
1110652 GATTGTGAAA
Statistics
Matches: 229, Mismatches: 58, Indels: 35
0.71 0.18 0.11
Matches are distributed among these distances:
176 4 0.02
177 12 0.05
178 17 0.07
179 4 0.02
180 1 0.00
181 33 0.14
182 121 0.53
183 5 0.02
185 2 0.01
186 17 0.07
187 11 0.05
188 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.28
Consensus pattern (182 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGATAACGGGGTTGGAGTATCTCTGATGATTAATGGGGTTGGAGTATCCCCATAAGAGA
AATTGATATTTTAGAAATAAAACCTGGGATTGGAGTATCCACTCAGAAATAA
Found at i:1110412 original size:51 final size:51
Alignment explanation
Indices: 1110350--1110470 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
1110340 AAATAACGGG
* * *
1110350 GTTGGAATATCCCCGATTGT-GAAAAGTCGGTGCTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAA-TCGGTGCTTTAGAAATAAAATCGGA
* *
1110401 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATCGGTGCTTTAGAAATAAAATCGGA
*
1110452 GTTGGAGTATCCTCGATTA
1 GTTGGAGTATCCCCGATTA
1110471 AGAGAAATTG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 58 0.92
52 5 0.08
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATCGGTGCTTTAGAAATAAAATCGGA
Found at i:1110493 original size:51 final size:51
Alignment explanation
Indices: 1110383--1110493 Score: 152
Period size: 51 Copynumber: 2.2 Consensus size: 51
1110373 AAGTCGGTGC
* * *
1110383 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATGGAAAATGGGTGT
1 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGGAAAATGGATAT
* * *
1110434 TTTAGAAATAAAATCGGAGTTGGAGTATCCTCGATTAA-GAGAAATTGATAT
1 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGGA-AAATGGATAT
1110485 TTTGGAAAT
1 TTTGGAAAT
1110494 GAAACCTGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
50 2 0.04
51 50 0.96
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.32
Consensus pattern (51 bp):
TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGGAAAATGGATAT
Found at i:1110623 original size:79 final size:80
Alignment explanation
Indices: 1110452--1110627 Score: 221
Period size: 79 Copynumber: 2.2 Consensus size: 80
1110442 TAAAATCGGA
* ** * * *
1110452 GTTGGAGTATCCTCGATTAAGAGAAATTGATATTTTGGAAATGAAACCTGGGATTTGAGTATCCA
1 GTTGGAGTATCCCCGATTAAGAGAAATCAATATTTTAGAAATGAAACCAGGGATTGGAGTATCCA
1110517 TTCGGAAATAACGGG
66 TTCGGAAATAACGGG
* * *
1110532 GTTGGAGTATCCCCGATTATGAGAAATCAATATTTTA-AGAAT-AAAGCAGGGGTTGGAGTATCC
1 GTTGGAGTATCCCCGATTAAGAGAAATCAATATTTTAGA-AATGAAACCAGGGATTGGAGTATCC
* * *
1110595 CTTTGGAAATAGCGGG
65 ATTCGGAAATAACGGG
1110611 GTTGGAGTATCCCCGAT
1 GTTGGAGTATCCCCGAT
1110628 GATTAACGGG
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
79 48 0.58
80 35 0.42
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (80 bp):
GTTGGAGTATCCCCGATTAAGAGAAATCAATATTTTAGAAATGAAACCAGGGATTGGAGTATCCA
TTCGGAAATAACGGG
Found at i:1110821 original size:51 final size:51
Alignment explanation
Indices: 1110672--1110810 Score: 226
Period size: 51 Copynumber: 2.7 Consensus size: 51
1110662 AATTGGTGTT
* * *
1110672 TTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTATAGAAAATTAGTG
1 TTTTGAAAATAAAATCGGAGTTGAAATATCCTCGATTATAGAAAATTAGTG
*
1110723 TTTTGAAAATAAAATCGGAGTTGAAATAT-TTCCGATTATAGAAAATTAGTG
1 TTTTGAAAATAAAATCGGAGTTGAAATATCCT-CGATTATAGAAAATTAGTG
1110774 TTTTGAAAATAAAATCGGAGTTGAAATATCCTCGATT
1 TTTTGAAAATAAAATCGGAGTTGAAATATCCTCGATT
1110811 GTGGAGAATT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
50 1 0.01
51 79 0.98
52 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (51 bp):
TTTTGAAAATAAAATCGGAGTTGAAATATCCTCGATTATAGAAAATTAGTG
Found at i:1113228 original size:21 final size:21
Alignment explanation
Indices: 1113202--1113243 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1113192 GTATCAATAC
1113202 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1113223 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1113244 GGCAGTAGCT
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:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:1113321 original size:32 final size:31
Alignment explanation
Indices: 1113280--1113343 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 31
1113270 TATCGATACA
*
1113280 ATACAACACTTATGTATCGATACATTGTATTG
1 ATACAACACTTATGTATCGATACACT-TATTG
1113312 ATACAACACTTATGTATCGATACACTTATTG
1 ATACAACACTTATGTATCGATACACTTATTG
1113343 A
1 A
1113344 ATGTATCGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 6 0.19
32 25 0.81
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (31 bp):
ATACAACACTTATGTATCGATACACTTATTG
Found at i:1113333 original size:19 final size:19
Alignment explanation
Indices: 1113280--1113335 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
1113270 TATCGATACA
1113280 ATACAACACTTATGTATCG
1 ATACAACACTTATGTATCG
*
1113299 AT---ACA--T-TGTATTG
1 ATACAACACTTATGTATCG
1113312 ATACAACACTTATGTATCG
1 ATACAACACTTATGTATCG
1113331 ATACA
1 ATACA
1113336 CTTATTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
13 8 0.28
14 1 0.03
16 6 0.21
18 1 0.03
19 13 0.45
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
ATACAACACTTATGTATCG
Found at i:1113338 original size:16 final size:16
Alignment explanation
Indices: 1113285--1113340 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
1113275 ATACAATACA
1113285 ACACTTATGTATCGAT
1 ACACTTATGTATCGAT
*
1113301 ACA--T-TGTATTGAT
1 ACACTTATGTATCGAT
1113314 ACAACACTTATGTATCGAT
1 ---ACACTTATGTATCGAT
1113333 ACACTTAT
1 ACACTTAT
1113341 TGAATGTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 8 0.25
14 1 0.03
16 14 0.44
18 1 0.03
19 8 0.25
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (16 bp):
ACACTTATGTATCGAT
Found at i:1113349 original size:21 final size:22
Alignment explanation
Indices: 1113323--1113366 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1113313 TACAACACTT
*
1113323 ATGTATCGATACA-CTTATTGA
1 ATGTATCGATACAGATTATTGA
1113344 ATGTATCGATACAGATTATTGA
1 ATGTATCGATACAGATTATTGA
1113366 A
1 A
1113367 AATAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
ATGTATCGATACAGATTATTGA
Found at i:1117835 original size:20 final size:20
Alignment explanation
Indices: 1117791--1117848 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1117781 ATTTCAACGA
***
1117791 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
1117811 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
1117831 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
1117849 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:1117905 original size:13 final size:13
Alignment explanation
Indices: 1117887--1117911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1117877 ATCACTTAAA
1117887 TGTATCGATACAT
1 TGTATCGATACAT
1117900 TGTATCGATACA
1 TGTATCGATACA
1117912 CTGATATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1117976 original size:52 final size:52
Alignment explanation
Indices: 1117900--1118048 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 52
1117890 ATCGATACAT
** *
1117900 TGTATCGATACACTGAT-ATTTGTATCGATACATGTAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
1117952 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
**
1118004 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
1118049 TCATATTTCG
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (52 bp):
TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1123342 original size:14 final size:15
Alignment explanation
Indices: 1123319--1123360 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1123309 ATGGTGAAAT
*
1123319 AATTTTTTTA-AAAA
1 AATTTCTTTACAAAA
1123333 AATTTCTTTAACTAAAA
1 AATTTCTTT-AC-AAAA
1123350 AATTTCTTTAC
1 AATTTCTTTAC
1123361 TCAATAGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.33
15 1 0.04
16 2 0.08
17 13 0.54
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTCTTTACAAAA
Found at i:1124563 original size:130 final size:130
Alignment explanation
Indices: 1124330--1124587 Score: 299
Period size: 130 Copynumber: 2.0 Consensus size: 130
1124320 TCATTCATGT
* * * *
1124330 TTTTATTTCTAAAATACCAATTTTTCACCATCGGTGATACTCCAACTCTATTATTCTAGAAGGGA
1 TTTTATTTCTAAAACACCAATTTTTCACCATCGGTGATACTCCAACCCTATAATTCTAGAAGAGA
** ** * * *
1124395 TACTCCAACCTCGGTTGTATTTTTGAAATACTGATTTTCCACCATCGGGGATACTACAACCCCAA
66 TACTCCAACCTCAATTGTATTTTCCAAATACTAATTTTCCACAATCGAGGATACTACAACCCCAA
* **
1124460 TTTTATTTCTAAAACATCAATTTTTCACCATCGAG-GATACTTTAACCCTATAATTTCTA-AAGA
1 TTTTATTTCTAAAACACCAATTTTTCACCATCG-GTGATACTCCAACCCTATAA-TTCTAGAAGA
* * *
1124523 GATACTCCAACCTCAATTTTA-TTTCCAAA-ACATCAATTTTCCATAATCGAGGATACTCCAACC
64 GATACTCCAACCTCAATTGTATTTTCCAAATAC-T-AATTTTCCACAATCGAGGATACTACAACC
1124586 CC
127 CC
1124588 GTTACTTCGA
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
128 2 0.02
129 7 0.07
130 92 0.86
131 6 0.06
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.34
Consensus pattern (130 bp):
TTTTATTTCTAAAACACCAATTTTTCACCATCGGTGATACTCCAACCCTATAATTCTAGAAGAGA
TACTCCAACCTCAATTGTATTTTCCAAATACTAATTTTCCACAATCGAGGATACTACAACCCCAA
Found at i:1124575 original size:79 final size:79
Alignment explanation
Indices: 1124441--1125025 Score: 414
Period size: 79 Copynumber: 7.4 Consensus size: 79
1124431 TTCCACCATC
* * * *
1124441 GGGGATACTACAACCCCAATTTTATTTCTAAAACATCAATTTTTCACCATCGAGGATACTTTAAC
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGATACTTCAAC
* * *
1124506 CCTATAATTTCTAA
66 CCCATTATTTCTGA
* * * * * *
1124520 AGAGATACTCCAACCTCAATTTTATTTCCAAAACATCAATTTTCCATAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGATACTTCAAC
* *
1124585 CCCGTTACTTC-GA
66 CCCATTATTTCTGA
* * * *
1124598 GGGGATACTCCAACCTCGATTTTATTTCCAAAACATCGATTTTTCACCATCGAGGATA-TTCCAA
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGATACTT-CAA
1124662 CCCCATTATTT-TCGA
65 CCCCATTATTTCT-GA
* ** * *
1124677 GGGGATACTCCAACCCCGATTTTCATTTATAAAACATCAATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCAATTTT-ATTTCCAAAACATCAATTTTTCACAATCGAGGATACTTCAA
* * *
1124742 CCTCGTTATTTCCGA
65 CCCCATTATTTCTGA
* * ** * * * *
1124757 GGGGATGC-CTCAACCCTAGCTTTATTTCTAAAACATCGATTTTTCATAATC-AGGGATACTCCA
1 GGGGATACTC-CAACCCCAATTTTATTTCCAAAACATCAATTTTTCACAATCGA-GGATACTTCA
** *
1124820 ACCCTGTTATTTTTGA
64 ACCCCATTATTTCTGA
** * ***** * * * * *
1124836 AAGGATACTCTAACTTTGGTTTTATTTCCCAAACGTCAA-TTTTCTACCAT-AAGGGATACTTTA
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTTC-ACAATCGA-GGATACTTCA
*
1124899 ACCCTATTATTT-TCGA
64 ACCCCATTATTTCT-GA
* * * ** * * * * *
1124915 GGGGATATTCCAACCCCGATTTTATTTTCAAAATGTCGATTTTCCACCATCG-GGGTACTCCAAC
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGATACTTCAAC
* **
1124979 CCTATTATTTCCAA
66 CCCATTATTTCTGA
* * * *
1124993 AGGGATACTCCAACCCTATTTTTATCTCCAAAA
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAA
1125026 TACTGATTTT
Statistics
Matches: 400, Mismatches: 91, Indels: 31
0.77 0.17 0.06
Matches are distributed among these distances:
77 1 0.00
78 116 0.29
79 217 0.54
80 65 0.16
81 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTTCACAATCGAGGATACTTCAAC
CCCATTATTTCTGA
Found at i:1124807 original size:237 final size:236
Alignment explanation
Indices: 1124441--1125007 Score: 614
Period size: 237 Copynumber: 2.4 Consensus size: 236
1124431 TTCCACCATC
* * * **
1124441 GGGGATACTACAACCCCAATTTTATTTCTAAAACATCAATTTTTCACCATCGAGGATACTTTAAC
1 GGGGATACTCCAACCCCGATTTTATTT-TAAAACATCAATTTTTCACCATCGGGGATACTCCAAC
* *
1124506 CCTATAATTTCTAAAGAGATACTCCAACCTCAATTTTATTTCCAAAACATCAATTTTCCATAATC
65 CCTATAATTTCCAAAGAGATACTCCAACCTCAACTTTATTTCCAAAACATCAATTTTCCATAATC
**
1124571 -GAGGATACTCCAACCCCGTTA-CTTCGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACAT
130 AG-GGATACTCCAACCCCGTTATCTTCGAAAGGATACTCCAACCTCGATTTTATTTCCAAAACAT
* *
1124634 CGATTTT-TCACCAT-CGAGGATA-TTCCAACCCCATTATTTTCGA
194 CAATTTTCT-ACCATAAG-GGATACTT-CAACCCCATTATTTTCGA
*
1124677 GGGGATACTCCAACCCCGATTTTCATTTATAAAACATCAATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTT-ATTT-TAAAACATCAATTTTTCACCATCGGGGATACTCCAA
* * * * * * * *
1124742 CCTCGT-T-ATTTCCGAGGGGATGC-CTCAACC-CTAGCTTTATTTCTAAAACATCGATTTTTCA
64 CC-C-TATAATTTCCAAAGAGATACTC-CAACCTC-AACTTTATTTCCAAAACATCAATTTTCCA
* * * * * * * *
1124803 TAATCAGGGATACTCCAACCCTGTTATTTTTGAAAGGATACTCTAACTTTGGTTTTATTTCCCAA
125 TAATCAGGGATACTCCAACCCCGTTATCTTCGAAAGGATACTCCAACCTCGATTTTATTTCCAAA
* * *
1124868 ACGTCAATTTTCTACCATAAGGGATACTTTAACCCTATTATTTTCGA
190 ACATCAATTTTCTACCATAAGGGATACTTCAACCCCATTATTTTCGA
* ** * *
1124915 GGGGATATTCCAACCCCGATTTTATTTTCAAAATGTCGATTTTCCACCATCGGGG-TACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTT-AAAACATCAATTTTTCACCATCGGGGATACTCCAAC
* *
1124979 CCTATTATTTCCAAAGGGATACTCCAACC
65 CCTATAATTTCCAAAGAGATACTCCAACC
1125008 CTATTTTTAT
Statistics
Matches: 276, Mismatches: 41, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
234 1 0.00
235 2 0.01
236 52 0.19
237 127 0.46
238 89 0.32
239 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (236 bp):
GGGGATACTCCAACCCCGATTTTATTTTAAAACATCAATTTTTCACCATCGGGGATACTCCAACC
CTATAATTTCCAAAGAGATACTCCAACCTCAACTTTATTTCCAAAACATCAATTTTCCATAATCA
GGGATACTCCAACCCCGTTATCTTCGAAAGGATACTCCAACCTCGATTTTATTTCCAAAACATCA
ATTTTCTACCATAAGGGATACTTCAACCCCATTATTTTCGA
Found at i:1126332 original size:20 final size:20
Alignment explanation
Indices: 1126280--1126361 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 20
1126270 AAAAAAAAAA
1126280 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
1126299 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
1126320 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
1126340 ATTCTACAAATGTATCGATAC
1 ATTC-ACAAATGTATCGATAC
1126361 A
1 A
1126362 GGGTCCCAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.05
20 18 0.33
21 34 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:1126341 original size:41 final size:40
Alignment explanation
Indices: 1126280--1126361 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
1126270 AAAAAAAAAA
* *
1126280 ATTCCAAATGTATCGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAAATGTATCGATAC
1126320 ATTCACAAATGTATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAAATGTATCGATAC
1126361 A
1 A
1126362 GGGTCCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAAATGTATCGATAC
Found at i:1126421 original size:19 final size:19
Alignment explanation
Indices: 1126397--1126464 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1126387 AATTCAACGA
1126397 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1126416 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1126431 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1126448 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1126465 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1126435 original size:32 final size:32
Alignment explanation
Indices: 1126399--1126461 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1126389 TTCAACGATT
*
1126399 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1126431 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1126462 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1126436 original size:13 final size:13
Alignment explanation
Indices: 1126418--1126442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1126408 ACATAAGTTT
1126418 TGTATCGATACAA
1 TGTATCGATACAA
1126431 TGTATCGATACA
1 TGTATCGATACA
1126443 TAAGTATTGT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1126522 original size:13 final size:13
Alignment explanation
Indices: 1126504--1126529 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1126494 CATTTTTCTG
1126504 TGTATCGATACAT
1 TGTATCGATACAT
1126517 TGTATCGATACAT
1 TGTATCGATACAT
1126530 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1126526 original size:33 final size:33
Alignment explanation
Indices: 1126484--1126550 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1126474 GCCAAGGAAA
***
1126484 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1126517 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1126550 T
1 T
1126551 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1129062 original size:28 final size:27
Alignment explanation
Indices: 1128995--1129065 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1128985 CTTCACAATC
* *
1128995 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1129022 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1129050 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1129066 TGACTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1129110 original size:51 final size:50
Alignment explanation
Indices: 1129050--1129220 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 50
1129040 TTATTTCTGA
* * *
1129050 GGGGATACTCCAACCCTGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCC-GATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1129101 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAA-CCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
* * *
1129154 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAA-CCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1129206 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1129221 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
51 33 0.34
52 21 0.22
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1129213 original size:105 final size:104
Alignment explanation
Indices: 1128883--1129220 Score: 269
Period size: 105 Copynumber: 3.2 Consensus size: 104
1128873 CTCAATTCTC
* * * * ** *
1128883 CACAATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACATTAATTT-T-CTATAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
1128946 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
66 TACTCCAA-TCCGATTTTATTTCC-AAAAATACCAATTT-TT
* * * ** * * * * * *
1128988 CACAATCGGGGACACTCCAACCCC-G-TTAATCATCGGGGATACTCCAA---CCCCGTTATTTCT
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTC---AAAACACCAATTTCTCCTTTA-ATC-
* * * * *
1129048 GAGGGGATACTCCAACCCTGACTTTATTTTC-AAAATATCGATTTTT
61 --GGGGATACTCCAATCC-GATTTTATTTCCAAAAATACCAATTTTT
* * *
1129094 CATAATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
1129159 TACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTT
66 TACTCCAA-TCCGATTTTATTTCCAAAAATACCAATTTTT
1129199 CACAATCGAGGATACTCCAACC
1 CACAATCGAGGATACTCCAACC
1129221 TCGTTATTTC
Statistics
Matches: 173, Mismatches: 43, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
103 5 0.03
104 23 0.13
105 64 0.37
106 31 0.18
107 13 0.08
108 14 0.08
109 23 0.13
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (104 bp):
CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
TACTCCAATCCGATTTTATTTCCAAAAATACCAATTTTT
Found at i:1129239 original size:28 final size:28
Alignment explanation
Indices: 1129203--1129284 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1129193 ATTTTTCACA
*
1129203 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1129231 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
1129259 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
1129285 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:1134371 original size:23 final size:23
Alignment explanation
Indices: 1134344--1134392 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1134334 GCATGTGCTT
*
1134344 TCATCGACCAATATAAACATGTA
1 TCATCGACCAACATAAACATGTA
1134367 TCATCGACCAACATAAACATGTA
1 TCATCGACCAACATAAACATGTA
1134390 TCA
1 TCA
1134393 GATTGGGTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (23 bp):
TCATCGACCAACATAAACATGTA
Found at i:1142714 original size:61 final size:60
Alignment explanation
Indices: 1142530--1143103 Score: 634
Period size: 61 Copynumber: 9.4 Consensus size: 60
1142520 AGCCTTTTAT
* * *
1142530 CCTTTCAGTCCTTAAAGAGCAAGACGTTTTTCCTTTTAAAGCCCACACAAGTTGTTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * ** * * *
1142590 CCTTTTAGTCTTTGAAGAGCAGGACACTTCTTT-TTTGTTAAAGTCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGAC-GTT-TTTCCTT-TTAAAGCCCACACAAGTTGGTGGCA
** * *
1142652 CCTTTCAGTCCTCAAAGAGCAAAACGCTTTTTTCTTTTAAAGCCTACACGAA-TTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACG-TTTTTCCTTTTAAAGCCCACAC-AAGTTGGTGGCA
* * * * * *
1142713 CCTTTCAATCCTCAAAGAACAAGACATCATTTCCTTTTAAAGCCCACACAAGTTGGTGGTA
1 CCTTTCAGTCCTCAAAGAGCAGGACGT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1142774 CCTTTCAGTCCCCAAAGAGCAGGACGTCTTTTCCTTTTAAAACCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
1142835 CCTTTCAGTCCCCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
1142896 CCTTTCAATCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAGGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACG-TTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * **
1142957 CCTTTCAATCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCTCACATAAGTTTATGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACG-TTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1143018 CCTTTCAGTCCTCAAAGAACAGGACGTCTTTT-CTTTTCAAAGCCCACATAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGT-TTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* * *
1143079 TCTTTTAGTCC-CTAAAGAGCTGGAC
1 CCTTTCAGTCCTC-AAAGAGCAGGAC
1143104 ACTTTTTTTA
Statistics
Matches: 442, Mismatches: 60, Indels: 23
0.84 0.11 0.04
Matches are distributed among these distances:
60 30 0.07
61 361 0.82
62 51 0.12
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (60 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1143739 original size:49 final size:51
Alignment explanation
Indices: 1143685--1143797 Score: 176
Period size: 49 Copynumber: 2.3 Consensus size: 51
1143675 TTTCATAATT
1143685 TGTATCGATACATCCTTCATTGTATCGATACATTCT-GGTTTT-ACCTAAA
1 TGTATCGATACATCCTTCATTGTATCGATACATTCTAGGTTTTAACCTAAA
** * *
1143734 TGTATCGATACATTTTTCATTGTATCGATACATTTTAGGTTTTAACGTAAA
1 TGTATCGATACATCCTTCATTGTATCGATACATTCTAGGTTTTAACCTAAA
1143785 TGTATCGATACAT
1 TGTATCGATACAT
1143798 TCAGGTACTT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
49 33 0.57
50 6 0.10
51 19 0.33
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.42
Consensus pattern (51 bp):
TGTATCGATACATCCTTCATTGTATCGATACATTCTAGGTTTTAACCTAAA
Found at i:1146412 original size:78 final size:78
Alignment explanation
Indices: 1146076--1146781 Score: 404
Period size: 79 Copynumber: 9.0 Consensus size: 78
1146066 TCATTCATGT
* * * * *
1146076 TTTTATTTCTAAAATACTGATTTTTCACCATCGGGGATACTCCAA-TTCTGTTATTCTCGAGGGA
1 TTTTATTTCTAAAACACTGATTTTTCACAATCGGGGATACTCCAACCTC-ATTATT-TCGAGGGG
* *
1146140 ATACTCGAATCTCGA
64 ATACTCCAACCTCGA
* * * * * *
1146155 TTTT-TTTC-GAAACACT-AATTTTCTACGATCGAGGATACTCTAACCTTATTATTTCCGAGGGG
1 TTTTATTTCTAAAACACTGATTTTTC-ACAATCGGGGATACTCCAACCTCATTATTT-CGAGGGG
*
1146217 ATAGTCCAACCTCGA
64 ATACTCCAACCTCGA
* * * * * *
1146232 TTTTATTT-TCAAAACACCGATTTTCCACCATCGGGGATACTCTAACC-CTATTATTTTCGAAGA
1 TTTTATTTCT-AAAACACTGATTTTTCACAATCGGGGATACTCCAACCTC-ATTA-TTTCGAGGG
*
1146295 GATACTCCAACCCCGA
63 GATACTCCAACCTCGA
* *
1146311 TTTTATTT-TCAGAACACTAATTTTTCACAATCGGGGATACTCCAACCTCATTACTTT-GAGGGG
1 TTTTATTTCT-AAAACACTGATTTTTCACAATCGGGGATACTCCAACCTCATTA-TTTCGAGGGG
*
1146374 ATACTCCAACC-CCA
64 ATACTCCAACCTCGA
* * * * * *
1146388 GTTTTATTTCTAAAATACTGATTTTTCACTATCGGGGATATTTCAACCCCGTTATTTTCGAGGGG
1 -TTTTATTTCTAAAACACTGATTTTTCACAATCGGGGATACTCCAACCTCATTA-TTTCGAGGGG
*
1146453 ATACTACAACCAT-GA
64 ATACTCCAACC-TCGA
* * * * * * * * *
1146468 TTTTTACTTATAAAATA-TCAATTTTTCACAATCGGGGATATTTCAACC-CTATTATGTCCAAAG
1 -TTTTATTTCTAAAACACT-GATTTTTCACAATCGGGGATACTCCAACCTC-ATTAT-TTCGAGG
* * *
1146531 GGATGCTCTAACCTTGA
62 GGATACTCCAACCTCGA
* * * * * * **
1146548 CTTTATTTCTAAAACA-TCAATTTTTCACAATCGAGGATACTTCAACCCCGTTATTTCTGAAAGG
1 TTTTATTTCTAAAACACT-GATTTTTCACAATCGGGGATACTCCAACCTCATTATTTC-GAGGGG
* *
1146612 ATACTCTAACCCCGA
64 ATACTCCAACCTCGA
* * * * ** * **
1146627 TTTTATTTCCAAAAC-GTCAATTTTTCACCATCGAAGATACTCCAACC-CTGTTATTTTTTAGGG
1 TTTTATTTCTAAAACACT-GATTTTTCACAATCGGGGATACTCCAACCTC-ATTA-TTTCGAGGG
* *
1146690 GATACTTCAACC-CTA
63 GATACTCCAACCTCGA
* *** * * * * * *
1146705 GTTTTATTTCCAAAATGTTGATTTTCCACCATC-AGGATACTCCAATCCT-GTTATTTCCATAGG
1 -TTTTATTTCTAAAACACTGATTTTTCACAATCGGGGATACTCCAA-CCTCATTATTTCGA-GGG
1146768 GATACTCCAACCTC
63 GATACTCCAACCTC
1146782 TTTTTTATCT
Statistics
Matches: 506, Mismatches: 91, Indels: 60
0.77 0.14 0.09
Matches are distributed among these distances:
76 7 0.01
77 55 0.11
78 102 0.20
79 267 0.53
80 75 0.15
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (78 bp):
TTTTATTTCTAAAACACTGATTTTTCACAATCGGGGATACTCCAACCTCATTATTTCGAGGGGAT
ACTCCAACCTCGA
Found at i:1146414 original size:158 final size:158
Alignment explanation
Indices: 1146076--1146779 Score: 518
Period size: 158 Copynumber: 4.5 Consensus size: 158
1146066 TCATTCATGT
* ** *
1146076 TTTTATTTCTAAAATACTGATTTTTCACCATCGGGGATACTCCAATTCTGTTATTCTCG-AGGGA
1 TTTTATTTCTAAAATACTGATTTTTCACCATCGGGGATACTCTAACCCTGTTATTTTCGAAGGG-
* * * * *
1146140 ATACTCGAATCTCGA-TTT-TTTTC-GAAACACT-AA-TTTTCTACGATCGAGGATACTCTAACC
65 ATACTCCAACCCCGATTTTATTTTCAG-AACACTCAATTTTTC-ACAATCGAGGATACTCCAACC
* * *
1146200 TTATTATTTCCGAGGGGATAGTCCAACCTC-GA
128 CTATTATTT--GAGGGGATACTCCAACCCCAGA
* * * * *
1146232 TTTTATTT-TCAAAACACCGATTTTCCACCATCGGGGATACTCTAACCCTATTATTTTCGAAGAG
1 TTTTATTTCT-AAAATACTGATTTTTCACCATCGGGGATACTCTAACCCTGTTATTTTCGAAGGG
*
1146296 ATACTCCAACCCCGATTTTATTTTCAGAACACT-AATTTTTCACAATCGGGGATACTCCAA-CCT
65 ATACTCCAACCCCGATTTTATTTTCAGAACACTCAATTTTTCACAATCGAGGATACTCCAACCCT
1146359 CATTACTTTGAGGGGATACTCCAACCCCAG-
130 -ATTA-TTTGAGGGGATACTCCAACCCCAGA
* * * *
1146389 TTTTATTTCTAAAATACTGATTTTTCACTATCGGGGATA-TTTCAACCCCGTTATTTTCGAGGGG
1 TTTTATTTCTAAAATACTGATTTTTCACCATCGGGGATACTCT-AACCCTGTTATTTTCGAAGGG
* ** * * * * * *
1146453 ATACTACAACCATGATTTTTACTTAT-AAAATA-TCAATTTTTCACAATCGGGGATATTTCAACC
65 ATACTCCAACCCCGA-TTTTA-TTTTCAGAACACTCAATTTTTCACAATCGAGGATACTCCAACC
** * * * **
1146516 CTATTATGTCCAAAGGGATGCTCTAA-CCTTGA
128 CTATTAT-T-TGAGGGGATACTCCAACCCCAGA
* * * * * * *
1146548 CTTTATTTCTAAAACA-TCAATTTTTCACAATCGAGGATACT-TCAACCCCGTTA-TTTCTGAAA
1 TTTTATTTCTAAAATACT-GATTTTTCACCATCGGGGATACTCT-AACCCTGTTATTTTC-GAAG
* * * *
1146610 GGATACTCTAACCCCGATTTTATTTCCA-AA-ACGTCAATTTTTCACCATCGAAGATACTCCAAC
63 GGATACTCCAACCCCGATTTTATTTTCAGAACAC-TCAATTTTTCACAATCGAGGATACTCCAAC
* * * *
1146673 CCTGTTATTTTTTAGGGGATACTTCAACCCTAG-
127 CCTATTA--TTTGAGGGGATACTCCAACCCCAGA
* ** * * * * *
1146706 TTTTATTTCCAAAATGTTGATTTTCCACCATC-AGGATACTCCAATCCTGTTA-TTTCCATAGGG
1 TTTTATTTCTAAAATACTGATTTTTCACCATCGGGGATACTCTAACCCTGTTATTTTCGA-AGGG
1146769 ATACTCCAACC
65 ATACTCCAACC
1146780 TCTTTTTTAT
Statistics
Matches: 437, Mismatches: 81, Indels: 59
0.76 0.14 0.10
Matches are distributed among these distances:
155 1 0.00
156 65 0.15
157 126 0.29
158 152 0.35
159 91 0.21
160 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (158 bp):
TTTTATTTCTAAAATACTGATTTTTCACCATCGGGGATACTCTAACCCTGTTATTTTCGAAGGGA
TACTCCAACCCCGATTTTATTTTCAGAACACTCAATTTTTCACAATCGAGGATACTCCAACCCTA
TTATTTGAGGGGATACTCCAACCCCAGA
Found at i:1146788 original size:78 final size:79
Alignment explanation
Indices: 1146566--1146807 Score: 224
Period size: 79 Copynumber: 3.1 Consensus size: 79
1146556 CTAAAACATC
* * * * * ** * *
1146566 AATTTTTCACAATCGAGGATACTTCAACCCCGTTATTTC-TGAAAGGATACTCTAACCC-CGATT
1 AATTTTCCACCATCGAAGATACTCCAACCCTGTTATTTCAT-AGGGGATACTCCAACCCTAG-TT
* *
1146629 TTATTTCCAAAACGTC
64 TTATTTCCAAAATGTT
* ** *
1146645 AATTTTTCACCATCGAAGATACTCCAACCCTGTTATTTTTTAGGGGATACTTCAACCCTAGTTTT
1 AATTTTCCACCATCGAAGATACTCCAACCCTGTTATTTCATAGGGGATACTCCAACCCTAGTTTT
1146710 ATTTCCAAAATGTT
66 ATTTCCAAAATGTT
* * * *
1146724 GATTTTCCACCATC-AGGATACTCCAATCCTGTTATTTCCATA-GGGATACTCCAACCTCT-TTT
1 AATTTTCCACCATCGAAGATACTCCAACCCTGTTATTT-CATAGGGGATACTCCAACC-CTAGTT
* *
1146786 TTATCTCCAAAATATT
64 TTATTTCCAAAATGTT
1146802 AATTTT
1 AATTTT
1146808 TTTCATCGTG
Statistics
Matches: 136, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
78 55 0.40
79 79 0.58
80 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (79 bp):
AATTTTCCACCATCGAAGATACTCCAACCCTGTTATTTCATAGGGGATACTCCAACCCTAGTTTT
ATTTCCAAAATGTT
Found at i:1147028 original size:24 final size:20
Alignment explanation
Indices: 1146980--1147020 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1146970 TACCTCATTA
1146980 ATCGAAAACAATTATTAGAC
1 ATCGAAAACAATTATTAGAC
1147000 ATCGAAAACAATTATTAGAC
1 ATCGAAAACAATTATTAGAC
1147020 A
1 A
1147021 CACTTCGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (20 bp):
ATCGAAAACAATTATTAGAC
Found at i:1148254 original size:20 final size:20
Alignment explanation
Indices: 1148217--1148255 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1148207 CAATCTTTTA
*
1148217 AATCAAGAATGTATATAACG
1 AATCAAGAATGTACATAACG
1148237 AATCAAGAAT-TCACATAAC
1 AATCAAGAATGT-ACATAAC
1148256 TCAGCCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (20 bp):
AATCAAGAATGTACATAACG
Found at i:1149100 original size:32 final size:32
Alignment explanation
Indices: 1149059--1149136 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
1149049 ACAAACAGTA
1149059 AATGTATCGATACATAAGTTTTGTACCGATAC
1 AATGTATCGATACATAAGTTTTGTACCGATAC
* *
1149091 AATGTATCGATGCATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTTTTGTACCGATAC
1149123 AATGTATCGATACA
1 AATGTATCGATACA
1149137 AAGCTACCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (32 bp):
AATGTATCGATACATAAGTTTTGTACCGATAC
Done.