Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 4 of 226
Found at i:1295338 original size:7 final size:7
Alignment explanation
Indices: 1295328--1295359 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1295318 TTATATACAT
1295328 AATACTA
1 AATACTA
1295335 AATACTA
1 AATACTA
1295342 AATACTA
1 AATACTA
1295349 AATACTA
1 AATACTA
1295356 AATA
1 AATA
1295360 TGAAACGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:1295824 original size:27 final size:27
Alignment explanation
Indices: 1295786--1295837 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1295776 AAATATATAT
*
1295786 TTTTTATTTTTTTAATTTTAAAATACA
1 TTTTAATTTTTTTAATTTTAAAATACA
*
1295813 TTTTAATTTTTTTATTTTTAAAATA
1 TTTTAATTTTTTTAATTTTAAAATA
1295838 AAATTTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTAATTTTTTTAATTTTAAAATACA
Found at i:1296595 original size:20 final size:19
Alignment explanation
Indices: 1296545--1296597 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
1296535 AATAAAAATT
1296545 AATTAAAATTACATAATAAA
1 AATTAAAATTA-ATAATAAA
* * *
1296565 AAATATTAATTAATATTCAAA
1 AATTA-AAATTAATAAT-AAA
1296586 AATTAAAATTAA
1 AATTAAAATTAA
1296598 CCCGACCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTAAAATTAATAATAAA
Found at i:1299247 original size:14 final size:14
Alignment explanation
Indices: 1299224--1299253 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1299214 TTTGATGTAT
*
1299224 TATATTTATAAAAA
1 TATATATATAAAAA
1299238 TATATATATAAAAA
1 TATATATATAAAAA
1299252 TA
1 TA
1299254 AAAAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATATATAAAAA
Found at i:1299876 original size:24 final size:24
Alignment explanation
Indices: 1299849--1299897 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1299839 ATGGTAAAAC
*
1299849 ATAATGCTAAAATCATAATATATT
1 ATAATACTAAAATCATAATATATT
* *
1299873 ATAATACTAAAATCTTAGTATATT
1 ATAATACTAAAATCATAATATATT
1299897 A
1 A
1299898 CTTTAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (24 bp):
ATAATACTAAAATCATAATATATT
Found at i:1318151 original size:2 final size:2
Alignment explanation
Indices: 1318144--1318176 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1318134 TTGGTTCCTA
*
1318144 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1318177 TTCCTTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:1331398 original size:3 final size:3
Alignment explanation
Indices: 1331390--1331414 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1331380 TTTTCCCTTA
1331390 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1331415 AGCATCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1348017 original size:16 final size:16
Alignment explanation
Indices: 1347987--1348026 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1347977 ATATTTCATG
*
1347987 CATTTCAT-CAATAAT
1 CATTTCATAAAATAAT
1348002 CATTTCATAAAATAAT
1 CATTTCATAAAATAAT
*
1348018 TATTTCATA
1 CATTTCATA
1348027 TATTTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
CATTTCATAAAATAAT
Found at i:1348573 original size:45 final size:45
Alignment explanation
Indices: 1348510--1348688 Score: 261
Period size: 45 Copynumber: 4.0 Consensus size: 45
1348500 TAACGGCAGT
* * * *
1348510 AGTAACAGTAACAGTATTCAACACACAAAATGCTGAATCTGTAAC
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAAC
*
1348555 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAC
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAAC
1348600 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAATC
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAA-C
* * * *
1348646 AGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTAATCAGTAA
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAA
1348689 GCCAGCAAAT
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 100 0.81
46 24 0.19
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAAC
Found at i:1349225 original size:2 final size:2
Alignment explanation
Indices: 1349218--1349247 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1349208 CATTCAATTC
1349218 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
1349248 TTATTTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1358917 original size:2 final size:2
Alignment explanation
Indices: 1358910--1358936 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1358900 CTTCTTTTAC
1358910 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 A
1358937 AAGTTGAGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1384224 original size:25 final size:25
Alignment explanation
Indices: 1384190--1384239 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1384180 TAAATCTTAC
*
1384190 CTTAGTTTTTTATTTTATTGAAAAT
1 CTTACTTTTTTATTTTATTGAAAAT
1384215 CTTACTTTTTTATTTTATTGAAAAT
1 CTTACTTTTTTATTTTATTGAAAAT
1384240 TTTGGAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (25 bp):
CTTACTTTTTTATTTTATTGAAAAT
Found at i:1384967 original size:24 final size:24
Alignment explanation
Indices: 1384919--1384968 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1384909 AGATTCCCAT
* *
1384919 TATTAGCTCTCATGAGCATCTCGA
1 TATTAGCTCTCATGAGCAACCCGA
1384943 TATTAGCTCT-ATTGAGCAACCCGA
1 TATTAGCTCTCA-TGAGCAACCCGA
1384967 TA
1 TA
1384969 CATGGCTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (24 bp):
TATTAGCTCTCATGAGCAACCCGA
Found at i:1385305 original size:11 final size:11
Alignment explanation
Indices: 1385291--1385316 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1385281 AGACCAAATT
1385291 GAATAGGTGAA
1 GAATAGGTGAA
1385302 GAATAGGTGAA
1 GAATAGGTGAA
1385313 GAAT
1 GAAT
1385317 TGACGGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (11 bp):
GAATAGGTGAA
Found at i:1385885 original size:33 final size:33
Alignment explanation
Indices: 1385843--1385979 Score: 105
Period size: 33 Copynumber: 4.1 Consensus size: 33
1385833 AATTGATGGA
* *
1385843 TAAGACCATAACTGGGTTATGGCACTATGAACG
1 TAAGACCATAACTGGGCTATGGCACTATGAATG
** * * * * *
1385876 TAAGACCATAGTTGGACCATGGCAGTTTTTACATG
1 TAAGACCATAACTGGGCTATGGCA-CTATGA-ATG
* * *
1385911 TAAGACCATAGCTGGGCTATGGCATTCTG-ATG
1 TAAGACCATAACTGGGCTATGGCACTATGAATG
* * *
1385943 ATAAGACCATAACTTGGTTATGGCACTACGAATG
1 -TAAGACCATAACTGGGCTATGGCACTATGAATG
1385977 TAA
1 TAA
1385980 AGGATGAATG
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
32 3 0.04
33 45 0.56
34 9 0.11
35 23 0.29
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (33 bp):
TAAGACCATAACTGGGCTATGGCACTATGAATG
Found at i:1387260 original size:27 final size:26
Alignment explanation
Indices: 1387230--1387318 Score: 119
Period size: 25 Copynumber: 3.5 Consensus size: 26
1387220 TGGATCTCTA
* *
1387230 GAGCTTCCCGATTAAAGGCTCTTTTAT
1 GAGCTTCCCGATTAATGGCTCTTTT-G
1387257 GAGCTTCCCGATTAATGGCT-TTTTG
1 GAGCTTCCCGATTAATGGCTCTTTTG
*
1387282 GAGCTTCCCGATTAATGGCTC-TCTG
1 GAGCTTCCCGATTAATGGCTCTTTTG
*
1387307 GAGCTTTCCGAT
1 GAGCTTCCCGAT
1387319 ATTTGGCTCG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
25 34 0.60
26 4 0.07
27 19 0.33
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (26 bp):
GAGCTTCCCGATTAATGGCTCTTTTG
Found at i:1387327 original size:25 final size:25
Alignment explanation
Indices: 1387219--1387318 Score: 110
Period size: 25 Copynumber: 3.9 Consensus size: 25
1387209 GTCTCGATAT
* *
1387219 ATGGATCTCTAGAGCTTCCCGATTA
1 ATGGCTCTCTGGAGCTTCCCGATTA
* * *
1387244 AAGGCTCTTTTATGAGCTTCCCGATTA
1 ATGGCTC-TCT-GGAGCTTCCCGATTA
* *
1387271 ATGGCTTTTTGGAGCTTCCCGATTA
1 ATGGCTCTCTGGAGCTTCCCGATTA
*
1387296 ATGGCTCTCTGGAGCTTTCCGAT
1 ATGGCTCTCTGGAGCTTCCCGAT
1387319 ATTTGGCTCG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 39 0.62
26 5 0.08
27 19 0.30
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (25 bp):
ATGGCTCTCTGGAGCTTCCCGATTA
Found at i:1387336 original size:50 final size:51
Alignment explanation
Indices: 1387282--1387395 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 51
1387272 TGGCTTTTTG
* * * *
1387282 GAGCTTCCCGATTA-ATGGCTCTC-TGGAGCTTTCC-GATATTTGGCTCGCAA
1 GAGCTTCCCGATTACATAGCTCACAT-GAGC-TTCCTGATATATGGCTCGAAA
* *
1387332 GAGCTTCTCG-TTACATAGCTCACATGAGCTTCCTGTTATATGGCTCGAAA
1 GAGCTTCCCGATTACATAGCTCACATGAGCTTCCTGATATATGGCTCGAAA
*
1387382 GAGCTTCCTGATTA
1 GAGCTTCCCGATTA
1387396 TATGCTCGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
49 7 0.13
50 41 0.79
51 4 0.08
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (51 bp):
GAGCTTCCCGATTACATAGCTCACATGAGCTTCCTGATATATGGCTCGAAA
Found at i:1387402 original size:25 final size:25
Alignment explanation
Indices: 1387322--1387404 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 25
1387312 TTCCGATATT
* *
1387322 TGGCTCGCAAGAGCTT-CTCGTTACA
1 TGGCTCGAAAGAGCTTCCT-GTTATA
* *
1387347 TAGCTC-ACATGAGCTTCCTGTTATA
1 TGGCTCGA-AAGAGCTTCCTGTTATA
1387372 TGGCTCGAAAGAGCTTCCTGATTATA
1 TGGCTCGAAAGAGCTTCCTG-TTATA
1387398 T-GCTCGA
1 TGGCTCGA
1387405 TTTGGCATAC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 39 0.81
26 9 0.19
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (25 bp):
TGGCTCGAAAGAGCTTCCTGTTATA
Found at i:1387877 original size:11 final size:11
Alignment explanation
Indices: 1387861--1387885 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1387851 CGTAAAGGTT
1387861 GGAAGCTGGTC
1 GGAAGCTGGTC
1387872 GGAAGCTGGTC
1 GGAAGCTGGTC
1387883 GGA
1 GGA
1387886 GCTACATCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (11 bp):
GGAAGCTGGTC
Found at i:1390187 original size:22 final size:20
Alignment explanation
Indices: 1390141--1390187 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
1390131 TTATTAATTG
* *
1390141 TGAATATTAAAAATATATGT
1 TGAAAATTAAAAATATATAT
1390161 T-AAAATTAAACAATATATAT
1 TGAAAATTAAA-AATATATAT
1390181 ATGAAAA
1 -TGAAAA
1390188 AAGGGGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.36
20 9 0.41
21 1 0.05
22 4 0.18
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (20 bp):
TGAAAATTAAAAATATATAT
Found at i:1392288 original size:13 final size:14
Alignment explanation
Indices: 1392266--1392294 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1392256 TATTTTTGTT
1392266 TTTTACTAATATAA
1 TTTTACTAATATAA
1392280 TTTTA-TAATATAA
1 TTTTACTAATATAA
1392293 TT
1 TT
1392295 GTTCAAACTT
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:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTACTAATATAA
Found at i:1392814 original size:18 final size:20
Alignment explanation
Indices: 1392779--1392815 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
1392769 ATATAATTTT
*
1392779 AAAATATATATAATACATCA
1 AAAATATATATAAAACATCA
1392799 AAAATAT-TA-AAAACATC
1 AAAATATATATAAAACATC
1392816 GAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 2 0.12
20 7 0.44
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATATATATAAAACATCA
Found at i:1393056 original size:61 final size:61
Alignment explanation
Indices: 1392990--1393113 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
1392980 AACAACAAAA
1392990 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAACAATAAGAAAATAATAT
1 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAACAATAAGAAAATAATAT
*
1393051 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGTGAGAAAACAATAAGAAAATAATAT
1 TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAACAATAAGAAAATAATAT
1393112 TA
1 TA
1393114 AAAACAAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (61 bp):
TAGTAGCAACATAATAGTAAAATGGTAGCAAAATAGGGAGAAAACAATAAGAAAATAATAT
Found at i:1401925 original size:37 final size:37
Alignment explanation
Indices: 1401883--1401957 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1401873 AGCAAAAAAA
1401883 ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
1 ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
1401920 ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
1 ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
1401957 A
1 A
1401958 GTTAGAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.45
Consensus pattern (37 bp):
ACTTGGTTTAAGGTTGTCTTTAACTGAGACTTGGTTT
Found at i:1403489 original size:29 final size:29
Alignment explanation
Indices: 1403434--1403489 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1403424 GTTTAATGGG
* *
1403434 CAATTGTATACATGAACTTTGGTTTTGTA
1 CAATTGTATACATGAAATTTGGATTTGTA
* * *
1403463 CAATTTTATACATTAAATTTTGATTTG
1 CAATTGTATACATGAAATTTGGATTTG
1403490 ATCCAATTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (29 bp):
CAATTGTATACATGAAATTTGGATTTGTA
Found at i:1406532 original size:30 final size:30
Alignment explanation
Indices: 1406498--1406560 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1406488 ACTTATTTTA
1406498 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
1406528 TTGTTAATTTTGTTATTATTTTAGAGCCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
1406558 TTG
1 TTG
1406561 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:1410001 original size:11 final size:12
Alignment explanation
Indices: 1409984--1410015 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1409974 GTCCATTATA
1409984 CTTTCTTTTTCT
1 CTTTCTTTTTCT
1409996 -TTTC-TTTTCT
1 CTTTCTTTTTCT
1410006 CTTTCTTTTT
1 CTTTCTTTTT
1410016 TTTGCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 6 0.33
11 8 0.44
12 4 0.22
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
CTTTCTTTTTCT
Found at i:1410010 original size:16 final size:15
Alignment explanation
Indices: 1409985--1410018 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1409975 TCCATTATAC
*
1409985 TTTCTTTTTCTTTTCT
1 TTTCTCTTTCTTTT-T
1410001 TTTCTCTTTCTTTTT
1 TTTCTCTTTCTTTTT
1410016 TTT
1 TTT
1410019 GCTTATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTCTTTCTTTTT
Found at i:1411809 original size:15 final size:15
Alignment explanation
Indices: 1411791--1411820 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1411781 TAATTATTTA
*
1411791 ATTTTAAATTAAAAT
1 ATTTTAAATAAAAAT
1411806 ATTTTAAATAAAAAT
1 ATTTTAAATAAAAAT
1411821 TTAATAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTTTAAATAAAAAT
Found at i:1412649 original size:6 final size:6
Alignment explanation
Indices: 1412595--1412630 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1412585 TTAATAAATT
*
1412595 TATTTA TATTTA TATTTA TATTTA TATTTA TTTTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1412631 ATTCCTGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATTTA
Found at i:1414936 original size:14 final size:15
Alignment explanation
Indices: 1414917--1414949 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
1414907 AGAATAGATT
1414917 TTTAATTAA-ATAAA
1 TTTAATTAATATAAA
1414931 TTTAATTAATTATAAA
1 TTTAATTAA-TATAAA
1414947 TTT
1 TTT
1414950 TAAACCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAATTAATATAAA
Found at i:1419413 original size:2 final size:2
Alignment explanation
Indices: 1419406--1419435 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1419396 AAAAAGCAAT
1419406 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1419436 ATAAGTAAGN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1419572 original size:2 final size:2
Alignment explanation
Indices: 1419565--1419597 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1419555 AATAAAGAAC
1419565 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 A
1419598 AGAAATGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1421257 original size:20 final size:20
Alignment explanation
Indices: 1421217--1421277 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
1421207 TACTCCAATC
* *
1421217 TATTTTT-TAAATTTTGAAT
1 TATTTTTATAATTTTTAAAT
1421236 T-TCTTTTAT--TTTTTAAA-
1 TAT-TTTTATAATTTTTAAAT
1421253 TATTTTTATAATTTTTAAAT
1 TATTTTTATAATTTTTAAAT
1421273 TATTT
1 TATTT
1421278 ATTAATATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
17 7 0.21
18 8 0.24
19 13 0.38
20 6 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTTTATAATTTTTAAAT
Found at i:1421283 original size:19 final size:19
Alignment explanation
Indices: 1421245--1421283 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1421235 TTTCTTTTAT
*
1421245 TTTTTAAATATTTTTATAA
1 TTTTTAAATATTTATATAA
1421264 TTTTTAAATTATTTAT-TAA
1 TTTTTAAA-TATTTATATAA
1421283 T
1 T
1421284 ATAGCATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTAAATATTTATATAA
Found at i:1432917 original size:15 final size:16
Alignment explanation
Indices: 1432892--1432925 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1432882 AAATTGTAAT
1432892 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
1432908 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
1432923 TTT
1 TTT
1432926 TTTCTTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:1435977 original size:22 final size:22
Alignment explanation
Indices: 1435952--1435995 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1435942 ACCAGCGAGG
1435952 ATTTGATAGTACTAGAATACGT
1 ATTTGATAGTACTAGAATACGT
1435974 ATTTGATAGTACTAGAATACGT
1 ATTTGATAGTACTAGAATACGT
1435996 TGTTTGGTAT
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:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
ATTTGATAGTACTAGAATACGT
Found at i:1436055 original size:21 final size:22
Alignment explanation
Indices: 1436045--1436087 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
1436035 TCTTTAATTA
1436045 TAAAAT-ATTATTTTATACATT
1 TAAAATAATTATTTTATACATT
1436066 TAAAATAATTATATTTAATACA
1 TAAAATAATTAT-TTT-ATACA
1436088 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 3 0.16
24 5 0.26
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAATAATTATTTTATACATT
Found at i:1436125 original size:22 final size:23
Alignment explanation
Indices: 1436080--1436126 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1436070 ATAATTATAT
* *
1436080 TTAATACAAATATATAAATTAAA
1 TTAATAAAAATATATAAATAAAA
*
1436103 TTAATAAAAAT-TATATATAAAA
1 TTAATAAAAATATATAAATAAAA
1436125 TT
1 TT
1436127 TGATGATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAATAAAAATATATAAATAAAA
Found at i:1436767 original size:24 final size:24
Alignment explanation
Indices: 1436740--1436791 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1436730 TTAGTAAGTC
*
1436740 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1436764 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1436788 AAAT
1 AAAT
1436792 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1438726 original size:24 final size:24
Alignment explanation
Indices: 1438699--1438750 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1438689 TTAGTAAGTC
*
1438699 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1438723 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1438747 AAAT
1 AAAT
1438751 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1446506 original size:13 final size:12
Alignment explanation
Indices: 1446484--1446514 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1446474 TGCAATTCTC
1446484 AAAAAAAAAAGA
1 AAAAAAAAAAGA
1446496 AAAAGAAAAAAGA
1 AAAA-AAAAAAGA
1446509 AAAAAA
1 AAAAAA
1446515 CAGTAGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1452617 original size:6 final size:6
Alignment explanation
Indices: 1452603--1452642 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
1452593 TTCCAGAACA
*
1452603 AGAAGGG AGAAGG AGAAGG AGAAGG AGAAGA AGAAGG AGA
1 AGAA-GG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGA
1452643 TGGATGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:1465921 original size:22 final size:22
Alignment explanation
Indices: 1465893--1465976 Score: 132
Period size: 22 Copynumber: 3.8 Consensus size: 22
1465883 TGTTGATAGT
*
1465893 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
1465915 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
1465937 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * *
1465959 ACGAACTAAACCCTCATG
1 ACGTACTAAGCTCTCATG
1465977 GAGCTACAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:1469151 original size:30 final size:30
Alignment explanation
Indices: 1469117--1469178 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1469107 TAGACTACTA
1469117 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
1469147 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
1469177 CA
1 CA
1469179 AACCTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.37, G:0.06, T:0.19
Consensus pattern (30 bp):
CATAGCCTTTCATACTCAAAACCGCAACAC
Found at i:1470107 original size:50 final size:50
Alignment explanation
Indices: 1470025--1470205 Score: 236
Period size: 50 Copynumber: 3.5 Consensus size: 50
1470015 AGGCTATTAC
* *
1470025 ATGCCATGTCCCAGACATGGTCGTATAGGGGACCTCTCATCTCGGTGCCA
1 ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCA
* * * *
1470075 ACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCC
1 ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCA
*
1470125 ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG-TGCCA
*
1470181 ATGTCATGTCCCAGACATGGTCTTA
1 ATGCCATGTCCCAGACATGGTCTTA
1470206 TATGGGATCT
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
50 80 0.71
53 2 0.02
54 1 0.01
55 2 0.02
56 28 0.25
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCA
Found at i:1470333 original size:13 final size:13
Alignment explanation
Indices: 1470312--1470343 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1470302 GCTTGGATCA
*
1470312 TCATCAAATAAAT
1 TCATAAAATAAAT
1470325 TCATAAAATAAAT
1 TCATAAAATAAAT
1470338 TCATAA
1 TCATAA
1470344 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1470590 original size:30 final size:30
Alignment explanation
Indices: 1470555--1470612 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1470545 CCTCGACTCT
*
1470555 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1470585 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1470613 AAGGCTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:1472943 original size:50 final size:51
Alignment explanation
Indices: 1472879--1473013 Score: 166
Period size: 51 Copynumber: 2.7 Consensus size: 51
1472869 CCGACACATT
* * ** * *
1472879 TAGTAGCCTACACATAGTACTACACACGTGATCAA-GCTTTCCT-GTTCACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCAT-CTGGTACACA
*
1472929 TAGTAACCTGCACATAGTACTACACACGTGACCAAGGCCATCTGGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCATCTGGTACACA
* *
1472980 TAGTAGCCTGCATATAGTACTACACATGTGACCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA
1473014 TTATCTATCG
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
50 34 0.47
51 39 0.53
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCATCTGGTACACA
Found at i:1473002 original size:51 final size:50
Alignment explanation
Indices: 1472836--1473013 Score: 164
Period size: 51 Copynumber: 3.5 Consensus size: 50
1472826 TTCAGTGGTT
* * * * *
1472836 TGCACATAGTACCACCCATGTGACCATTGTCATCC-G-ACACATTTAGTAGCC
1 TGCACATAGTACTACACACGTGACCA-AGCCATCCTGTACACA--TAGTAGCC
* * ** * * *
1472887 TACACATAGTACTACACACGTGATCAAGCTTTCCTGTTCACGTAGTAACC
1 TGCACATAGTACTACACACGTGACCAAGCCATCCTGTACACATAGTAGCC
1472937 TGCACATAGTACTACACACGTGACCAAGGCCAT-CTGGTACACATAGTAGCC
1 TGCACATAGTACTACACACGTGACCAA-GCCATCCT-GTACACATAGTAGCC
* *
1472988 TGCATATAGTACTACACATGTGACCA
1 TGCACATAGTACTACACACGTGACCA
1473014 TTATCTATCG
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
50 38 0.37
51 61 0.60
52 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (50 bp):
TGCACATAGTACTACACACGTGACCAAGCCATCCTGTACACATAGTAGCC
Found at i:1473029 original size:51 final size:51
Alignment explanation
Indices: 1472879--1473060 Score: 165
Period size: 51 Copynumber: 3.6 Consensus size: 51
1472869 CCGACACATT
* * ** * *
1472879 TAGTAGCCTACACATAGTACTACACACGTGATCAA-GCTTTCCTG-TTCACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCAT-CTGATACACA
* *
1472929 TAGTAACCTGCACATAGTACTACACACGTGACCAAGGCCATCTGGTACACA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCATCTGATACACA
* * * * *
1472980 TAGTAGCCTGCATATAGTACTACACATGTGACCATTA-TCTATC-GATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA--AGGCCATCTGATACACA
* * *
1473031 TAGTAGCCTGCACTTTGTACTACATACGTG
1 TAGTAGCCTGCACATAGTACTACACACGTG
1473061 CTCATAGGTA
Statistics
Matches: 109, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 35 0.32
51 69 0.63
52 4 0.04
53 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCCATCTGATACACA
Found at i:1473880 original size:43 final size:43
Alignment explanation
Indices: 1473791--1473880 Score: 155
Period size: 43 Copynumber: 2.1 Consensus size: 43
1473781 TTCATAAATA
*
1473791 TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAGGCTAT
1 TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAGCCTAT
1473834 TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAGTCCT-T
1 TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAG-CCTAT
1473877 TTTA
1 TTTA
1473881 ACTAATTAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 43 0.96
44 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (43 bp):
TTTATCACTCTGGCAAGTTTTACACCTTTTCAATTTAGCCTAT
Found at i:1474220 original size:54 final size:54
Alignment explanation
Indices: 1474118--1474221 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
1474108 TCATCGAATT
* * **
1474118 TAGTGGTCTTGAACCACTATTTCTGACACTACTAAAAATTGGGTTGTTACTTAC
1 TAGTGGTCTTGAACCACTATTTCTGACACCACTAAAAATTAGACTGTTACTTAC
* * *
1474172 TAGTGGTCTTGAACCACTGTTTTTGACACCACTGAAAATTAGACTGTTAC
1 TAGTGGTCTTGAACCACTATTTCTGACACCACTAAAAATTAGACTGTTAC
1474222 AGTAAGTGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (54 bp):
TAGTGGTCTTGAACCACTATTTCTGACACCACTAAAAATTAGACTGTTACTTAC
Found at i:1478258 original size:22 final size:24
Alignment explanation
Indices: 1478212--1478258 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1478202 AAGATTATAG
* *
1478212 ATAAGTTATCAAACTTTTAAATAA
1 ATAAGTTAACAAACTTTCAAATAA
1478236 ATAAGTTAAC-AA-TTTCAAATAA
1 ATAAGTTAACAAACTTTCAAATAA
1478258 A
1 A
1478259 CAAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 9 0.43
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
ATAAGTTAACAAACTTTCAAATAA
Found at i:1478875 original size:25 final size:26
Alignment explanation
Indices: 1478807--1478878 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
1478797 GATGTTCATG
* *
1478807 TTATTAAT-TTTTACATTTTTATAAA
1 TTATTAATAATTTAAATTTTTATAAA
**
1478832 TTATTAATAATTTTTATTTTT-TAAA
1 TTATTAATAATTTAAATTTTTATAAA
*
1478857 TTTTTAA-AATTATAAATTTTTA
1 TTATTAATAATT-TAAATTTTTA
1478879 GTATTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 4 0.11
25 25 0.66
26 9 0.24
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTAATAATTTAAATTTTTATAAA
Found at i:1478894 original size:21 final size:23
Alignment explanation
Indices: 1478868--1478910 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1478858 TTTTAAAATT
*
1478868 ATAAATTT-TTAG-TATTTTTTA
1 ATAAATTTATAAGTTATTTTTTA
1478889 ATAAATTTATAAGTTATTTTTT
1 ATAAATTTATAAGTTATTTTTT
1478911 TTATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (23 bp):
ATAAATTTATAAGTTATTTTTTA
Found at i:1479081 original size:19 final size:19
Alignment explanation
Indices: 1479057--1479098 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1479047 ATAAAAATAA
1479057 AAATAA-AATATTAAATATT
1 AAATAATAATATTAAAT-TT
*
1479076 AAATAATAATATTTAATTT
1 AAATAATAATATTAAATTT
1479095 AAAT
1 AAAT
1479099 TTAGTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATAATAATATTAAATTT
Found at i:1485775 original size:24 final size:23
Alignment explanation
Indices: 1485737--1485783 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1485727 ATTCACTAAA
*
1485737 AAAATTTAAACCCTAAATCACTT
1 AAAATTTAAACCCTAAACCACTT
*
1485760 AAAATTTCAAATCCTAAACCACTT
1 AAAATTT-AAACCCTAAACCACTT
1485784 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAATTTAAACCCTAAACCACTT
Found at i:1489868 original size:29 final size:29
Alignment explanation
Indices: 1489826--1489883 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1489816 TTCCTCATTA
1489826 ACCATTTGACTAGCATTACTACAAGTTTT
1 ACCATTTGACTAGCATTACTACAAGTTTT
1489855 ACCATTTGACTAGCATTACTACAAGTTTT
1 ACCATTTGACTAGCATTACTACAAGTTTT
1489884 CTTTGGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (29 bp):
ACCATTTGACTAGCATTACTACAAGTTTT
Found at i:1508057 original size:41 final size:41
Alignment explanation
Indices: 1508000--1508090 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
1507990 AAATGGGGTA
1508000 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
*
1508041 TGGGAGTGGCTTAGATACAAAAGGGTCTGTGCCTCAGGTGT
1 TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
*
1508082 TGGGGGTGG
1 TGGGAGTGG
1508091 AGAGTTTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.21, C:0.13, G:0.41, T:0.25
Consensus pattern (41 bp):
TGGGAGTGGCTTAGATACAAAAGGGACTGTGCCTCAGGTGT
Found at i:1516915 original size:29 final size:31
Alignment explanation
Indices: 1516841--1516924 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 31
1516831 ATTAAATCAA
* * * **
1516841 AATTAAAGTTTCAAGTATACATTTAAACCAC
1 AATTAAAGTTTCATGTATATAATTGCACCAC
* *
1516872 AATTAGAGTTTCATGTGTATAATTGCACCA-
1 AATTAAAGTTTCATGTATATAATTGCACCAC
1516902 AATTAAAG-TTCATGTATATAATT
1 AATTAAAGTTTCATGTATATAATT
1516925 TTACATTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 14 0.32
30 7 0.16
31 23 0.52
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (31 bp):
AATTAAAGTTTCATGTATATAATTGCACCAC
Found at i:1533191 original size:2 final size:2
Alignment explanation
Indices: 1533184--1533208 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1533174 TAATTGGTAT
1533184 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1533209 TCTATTTTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1533473 original size:21 final size:21
Alignment explanation
Indices: 1533413--1533539 Score: 141
Period size: 21 Copynumber: 6.0 Consensus size: 21
1533403 TTTGGGTGGA
* *
1533413 TCAGCTCTCACAAGCTTC-GAT
1 TCAGCTCTTACGAGCTTCTG-T
* * **
1533434 TTAGCTCTCACGATATTCTGT
1 TCAGCTCTTACGAGCTTCTGT
* *
1533455 TTAGCTCGTT-TGAGCTTCTGT
1 TCAGCTC-TTACGAGCTTCTGT
1533476 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
1533497 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
1533518 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
1533539 T
1 T
1533540 AACGATGTAC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.02
21 88 0.96
22 2 0.02
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:1533492 original size:63 final size:63
Alignment explanation
Indices: 1533413--1533539 Score: 159
Period size: 63 Copynumber: 2.0 Consensus size: 63
1533403 TTTGGGTGGA
* * *
1533413 TCAGCTCTCACAAGCTTC-GATTTAGCTCTCACGATATTCTGTTTAGCTCGTT-TGAGCTTCTGT
1 TCAGCTCTCACAAGCTTCTG-TTCAGCTCTCACGAGATTCTGTTCAGCTC-TTATGAGCTTCTGT
* * * *
1533476 TCAGCTCTTACGAGCTTCTGTTCAGCTCTTACGAGCTTCTGTTCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTCACAAGCTTCTGTTCAGCTCTCACGAGATTCTGTTCAGCTCTTATGAGCTTCTGT
1533539 T
1 T
1533540 AACGATGTAC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 52 0.95
64 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (63 bp):
TCAGCTCTCACAAGCTTCTGTTCAGCTCTCACGAGATTCTGTTCAGCTCTTATGAGCTTCTGT
Found at i:1535225 original size:31 final size:31
Alignment explanation
Indices: 1535184--1535249 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1535174 ACAGGCTGAG
* *
1535184 ACACGACCGTGTGTTCTTATTTCGAATGTCC
1 ACACGACCGTGTGTTCCTATTTCAAATGTCC
*
1535215 ACACGGCCGTGTGTTCCTATTTCAAATGTCC
1 ACACGACCGTGTGTTCCTATTTCAAATGTCC
1535246 ACAC
1 ACAC
1535250 CGCCTAAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (31 bp):
ACACGACCGTGTGTTCCTATTTCAAATGTCC
Found at i:1537126 original size:2 final size:2
Alignment explanation
Indices: 1537119--1537144 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1537109 TATGTTCATA
1537119 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1537145 CGCGCTCGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1542635 original size:18 final size:18
Alignment explanation
Indices: 1542596--1542636 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1542586 TTAGCAGTCT
*
1542596 AATTATAATTTTTTATTT
1 AATTATAATTTTTTATTA
1542614 AATTATTAATTTTTT-TTA
1 AATTA-TAATTTTTTATTA
1542632 AATTA
1 AATTA
1542637 GGTTTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTATAATTTTTTATTA
Found at i:1551122 original size:32 final size:32
Alignment explanation
Indices: 1551064--1551128 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1551054 CACTTTTCAT
** *
1551064 GCTTCTGGTTTAGACCTGGACTATCTTTTTAG
1 GCTTCTGGTTTAGACCTAAACCATCTTTTTAG
1551096 GCTTCTGGTTTAGACCTAAACCATCTTTTTAG
1 GCTTCTGGTTTAGACCTAAACCATCTTTTTAG
1551128 G
1 G
1551129 TTTGAAGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (32 bp):
GCTTCTGGTTTAGACCTAAACCATCTTTTTAG
Found at i:1556551 original size:63 final size:63
Alignment explanation
Indices: 1556473--1556599 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
1556463 TATCTGCAAG
1556473 TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
1 TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
1556536 TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
1 TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
1556599 T
1 T
1556600 TCATTCTGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (63 bp):
TGAGTTCTAAAATTCTCTGATGCCTTGGTGCCATTTATAATTGTTGTTTTCAGTTTATTGCCT
Found at i:1584105 original size:18 final size:18
Alignment explanation
Indices: 1584082--1584116 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1584072 ATACATTTGT
* *
1584082 AGTGAAGAATATGAGAAG
1 AGTGAAAAATAAGAGAAG
1584100 AGTGAAAAATAAGAGAA
1 AGTGAAAAATAAGAGAA
1584117 TGAAAAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (18 bp):
AGTGAAAAATAAGAGAAG
Found at i:1586549 original size:16 final size:16
Alignment explanation
Indices: 1586515--1586548 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1586505 AATATTTTAT
1586515 AAAGAATTTTATATTA
1 AAAGAATTTTATATTA
1586531 AAAGAATTTT-TATTA
1 AAAGAATTTTATATTA
1586546 AAA
1 AAA
1586549 ATAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AAAGAATTTTATATTA
Found at i:1588739 original size:41 final size:40
Alignment explanation
Indices: 1588692--1588816 Score: 196
Period size: 40 Copynumber: 3.1 Consensus size: 40
1588682 AATATATTTA
* *
1588692 TTTTTTAATTTTAAAATACTTTTAGAATACTTTTTTCAAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT-AAAT
* *
1588733 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAAA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAAT
*
1588773 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAAT
1588813 TTTT
1 TTTT
1588817 AAAATAAATT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 44 0.57
41 33 0.43
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAAT
Found at i:1588828 original size:21 final size:21
Alignment explanation
Indices: 1588790--1588829 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1588780 ATTTTAAAAT
**
1588790 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
1588811 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
1588830 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:1588836 original size:22 final size:20
Alignment explanation
Indices: 1588789--1588836 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
1588779 AATTTTAAAA
* *
1588789 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
1588809 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
1588832 TATTT
1 TATTT
1588837 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 11 0.48
22 10 0.43
23 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:1598774 original size:27 final size:27
Alignment explanation
Indices: 1598740--1598798 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1598730 AACTTGAGGT
* *
1598740 GGCACCAAAGGTGCTAAAGTGATTGGC
1 GGCACCAAAGGTGCCAAAGAGATTGGC
*
1598767 GGCACCAAATGTGCCAAAGAGATTGGC
1 GGCACCAAAGGTGCCAAAGAGATTGGC
1598794 GGCAC
1 GGCAC
1598799 TGGATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.32, T:0.15
Consensus pattern (27 bp):
GGCACCAAAGGTGCCAAAGAGATTGGC
Found at i:1599290 original size:19 final size:19
Alignment explanation
Indices: 1599266--1599328 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1599256 TCTAATTAAG
1599266 TAATAATTCTATTTTACTT
1 TAATAATTCTATTTTACTT
** ***
1599285 TAATAAGTT-TATTAAAAAG
1 TAATAA-TTCTATTTTACTT
*
1599304 TAATAACTCTATTTTACTT
1 TAATAATTCTATTTTACTT
1599323 TAATAA
1 TAATAA
1599329 ACTATTGCTT
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
18 1 0.03
19 28 0.90
20 2 0.06
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (19 bp):
TAATAATTCTATTTTACTT
Found at i:1599392 original size:18 final size:17
Alignment explanation
Indices: 1599363--1599397 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1599353 GTAATGTTTC
*
1599363 AAAAAATGTTTTTAGGA
1 AAAAAATGTTTTAAGGA
1599380 AAAAAATGTTTTTAAGGA
1 AAAAAATG-TTTTAAGGA
1599398 GAAGTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
AAAAAATGTTTTAAGGA
Found at i:1600494 original size:27 final size:27
Alignment explanation
Indices: 1600452--1600540 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
1600442 TTTAGTCCTA
1600452 TGCCGCCAATCTCTTTGGCACCTTTGG
1 TGCCGCCAATCTCTTTGGCACCTTTGG
*
1600479 T-CGGGCCAATCTCTTTGGCACCTTTGG
1 TGC-CGCCAATCTCTTTGGCACCTTTGG
*
1600506 TGCCGCCAATCACTTTGGCACCTTTGG
1 TGCCGCCAATCTCTTTGGCACCTTTGG
1600533 TGCCGCCA
1 TGCCGCCA
1600541 CAGGTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.12, C:0.34, G:0.24, T:0.30
Consensus pattern (27 bp):
TGCCGCCAATCTCTTTGGCACCTTTGG
Found at i:1601448 original size:26 final size:26
Alignment explanation
Indices: 1601418--1601469 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1601408 AGTAAAAAAG
1601418 AATGTTCTAATGTTTTCTCATAACAC
1 AATGTTCTAATGTTTTCTCATAACAC
1601444 AATGTTCTAATGTTTTCTCATAACAC
1 AATGTTCTAATGTTTTCTCATAACAC
1601470 CCTCGAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (26 bp):
AATGTTCTAATGTTTTCTCATAACAC
Found at i:1603303 original size:22 final size:23
Alignment explanation
Indices: 1603278--1603320 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1603268 AATAAGTAGG
* *
1603278 CTTTCAA-AGGTGAAGTTTATCC
1 CTTTCAAGAGATGAACTTTATCC
1603300 CTTTCAAGAGATGAACTTTAT
1 CTTTCAAGAGATGAACTTTAT
1603321 GGCTAGTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (23 bp):
CTTTCAAGAGATGAACTTTATCC
Found at i:1609722 original size:21 final size:22
Alignment explanation
Indices: 1609698--1609742 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1609688 AAATTTAGTG
1609698 TTAAGATAAAATAT-TGTTTAA
1 TTAAGATAAAATATGTGTTTAA
* * *
1609719 TTAATATAAATTTTGTGTTTAA
1 TTAAGATAAAATATGTGTTTAA
1609741 TT
1 TT
1609743 TTAAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTAAGATAAAATATGTGTTTAA
Found at i:1622798 original size:33 final size:33
Alignment explanation
Indices: 1622758--1623021 Score: 106
Period size: 33 Copynumber: 7.8 Consensus size: 33
1622748 GTTTAATGAA
*
1622758 AAGACCATAACTGGGTTATGACACTTTGAATGT
1 AAGACCATAACTGGGCTATGACACTTTGAATGT
*** * * * * *
1622791 AAGACCATGGTTGGACCATGGA-AATGTTTAATGAA
1 AAGACCATAACTGGGCTAT-GACACT-TTGAATG-T
*
1622826 AAGACCATAACTGGGTTATGACACTTTGAATGT
1 AAGACCATAACTGGGCTATGACACTTTGAATGT
*** * * * * *
1622859 AAGACCATGGTTGGACCATGGCAGTATAGATACATGTGT
1 AAGACCATAACTGGGCTATGACACT-TTG--A-A--TGT
* *
1622898 AAGACCATAACTGGGCTATGGCA-TTCTG-ATAAT
1 AAGACCATAACTGGGCTATGACACTT-TGAAT-GT
* * * ***
1622931 AAGACCATAATTGGGTTATGGCACTACAAATGT
1 AAGACCATAACTGGGCTATGACACTTTGAATGT
* *
1622964 AAGAACATAACTGGGCTATGGCA-TTCTG-ATGAT
1 AAGACCATAACTGGGCTATGACACTT-TGAATG-T
* *
1622997 AAGACCATAACTGGGTTGTGACACT
1 AAGACCATAACTGGGCTATGACACT
1623022 ACAAATGTAA
Statistics
Matches: 164, Mismatches: 50, Indels: 33
0.66 0.20 0.13
Matches are distributed among these distances:
32 5 0.03
33 95 0.58
34 23 0.14
35 15 0.09
36 1 0.01
37 2 0.01
38 2 0.01
39 21 0.13
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (33 bp):
AAGACCATAACTGGGCTATGACACTTTGAATGT
Found at i:1622831 original size:68 final size:68
Alignment explanation
Indices: 1622722--1622879 Score: 316
Period size: 68 Copynumber: 2.3 Consensus size: 68
1622712 AATTGACGAA
1622722 TAAGACCATGGTTGGACCATGGAAATGTTTAATGAAAAGACCATAACTGGGTTATGACACTTTGA
1 TAAGACCATGGTTGGACCATGGAAATGTTTAATGAAAAGACCATAACTGGGTTATGACACTTTGA
1622787 ATG
66 ATG
1622790 TAAGACCATGGTTGGACCATGGAAATGTTTAATGAAAAGACCATAACTGGGTTATGACACTTTGA
1 TAAGACCATGGTTGGACCATGGAAATGTTTAATGAAAAGACCATAACTGGGTTATGACACTTTGA
1622855 ATG
66 ATG
1622858 TAAGACCATGGTTGGACCATGG
1 TAAGACCATGGTTGGACCATGG
1622880 CAGTATAGAT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 90 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (68 bp):
TAAGACCATGGTTGGACCATGGAAATGTTTAATGAAAAGACCATAACTGGGTTATGACACTTTGA
ATG
Found at i:1622977 original size:66 final size:66
Alignment explanation
Indices: 1622895--1623033 Score: 233
Period size: 66 Copynumber: 2.1 Consensus size: 66
1622885 TAGATACATG
* * *
1622895 TGTAAGACCATAACTGGGCTATGGCATTCTGATAATAAGACCATAATTGGGTTATGGCACTACAA
1 TGTAAGAACATAACTGGGCTATGGCATTCTGATAATAAGACCATAACTGGGTTATGACACTACAA
1622960 A
66 A
* *
1622961 TGTAAGAACATAACTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTGTGACACTACAA
1 TGTAAGAACATAACTGGGCTATGGCATTCTGATAATAAGACCATAACTGGGTTATGACACTACAA
1623026 A
66 A
1623027 TGTAAGA
1 TGTAAGA
1623034 TCATGGCAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (66 bp):
TGTAAGAACATAACTGGGCTATGGCATTCTGATAATAAGACCATAACTGGGTTATGACACTACAA
A
Found at i:1623033 original size:33 final size:33
Alignment explanation
Indices: 1622895--1623033 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
1622885 TAGATACATG
* * **
1622895 TGTAAGACCATAACTGGGCTATGGCA-TTCTGA
1 TGTAAGACCATAACTGGGTTATGGCACTACAAA
* *
1622927 TAATAAGACCATAATTGGGTTATGGCACTACAAA
1 T-GTAAGACCATAACTGGGTTATGGCACTACAAA
* * * **
1622961 TGTAAGAACATAACTGGGCTATGGCA-TTCTGA
1 TGTAAGACCATAACTGGGTTATGGCACTACAAA
* *
1622993 TGATAAGACCATAACTGGGTTGTGACACTACAAA
1 TG-TAAGACCATAACTGGGTTATGGCACTACAAA
1623027 TGTAAGA
1 TGTAAGA
1623034 TCATGGCAGG
Statistics
Matches: 83, Mismatches: 20, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
32 6 0.07
33 68 0.82
34 9 0.11
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (33 bp):
TGTAAGACCATAACTGGGTTATGGCACTACAAA
Found at i:1623066 original size:66 final size:66
Alignment explanation
Indices: 1622895--1623071 Score: 198
Period size: 66 Copynumber: 2.7 Consensus size: 66
1622885 TAGATACATG
* * * * * *
1622895 TGTAAGACCATAACTGGGCTATGGCATTCTGATAATAAGACCATAATTGGGTTATGGCACTACAA
1 TGTAAGAACATAACAGGGCTATGGCATGCTGATGATAAGACCATAACTGGGTTATGACACTACAA
1622960 A
66 A
* * *
1622961 TGTAAGAACATAACTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTGTGACACTACAA
1 TGTAAGAACATAACAGGGCTATGGCATGCTGATGATAAGACCATAACTGGGTTATGACACTACAA
1623026 A
66 A
* **
1623027 TGTAAGATCATGGCAGGGAC-ATGGCAATGCATG-TG-TAAGACCATA
1 TGTAAGAACATAACAGGG-CTATGGC-ATGC-TGATGATAAGACCATA
1623072 GTTGGACTAT
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
66 90 0.92
67 6 0.06
68 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (66 bp):
TGTAAGAACATAACAGGGCTATGGCATGCTGATGATAAGACCATAACTGGGTTATGACACTACAA
A
Found at i:1632613 original size:42 final size:42
Alignment explanation
Indices: 1632548--1632629 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1632538 TAATAATATA
* *
1632548 TAATATAAACATTAAAAAAATTAAGATAACTATATATTAAAT
1 TAATATAAACATTAAAAAAATTAAAATAAATATATATTAAAT
* * *
1632590 TAATATAAA-ATTATTAAATATTAAAATAAATATATTTTAA
1 TAATATAAACATTA-AAAAAATTAAAATAAATATATATTAA
1632630 TAAATAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (42 bp):
TAATATAAACATTAAAAAAATTAAAATAAATATATATTAAAT
Found at i:1632625 original size:21 final size:19
Alignment explanation
Indices: 1632565--1632625 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 19
1632555 AACATTAAAA
*
1632565 AAATTAAGATAACTATATATT
1 AAATTAAAATAA--ATATATT
*
1632586 AAATTAATATAAA-ATTATT
1 AAATTAAAATAAATA-TATT
1632605 AAATATTAAAATAAATATATT
1 -AA-ATTAAAATAAATATATT
1632626 TTAATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 1 0.03
19 5 0.15
20 2 0.06
21 25 0.74
22 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
AAATTAAAATAAATATATT
Found at i:1636603 original size:51 final size:51
Alignment explanation
Indices: 1636542--1636641 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
1636532 CTCAATTTCC
*
1636542 TCTCATTTTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* *
1636593 TCTCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
1636642 TTAATTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:1636628 original size:11 final size:11
Alignment explanation
Indices: 1636530--1636625 Score: 60
Period size: 11 Copynumber: 9.0 Consensus size: 11
1636520 CTAAATTATT
1636530 CTCTCAATTTC
1 CTCTCAATTTC
* *
1636541 CTCTCATTTTG
1 CTCTCAATTTC
1636552 CTCTCAATTTC
1 CTCTCAATTTC
1636563 CT-TCCAAATTT-
1 CTCT-C-AATTTC
*
1636574 CTCTCAA-ATC
1 CTCTCAATTTC
* *
1636584 C-AT--ATTTA
1 CTCTCAATTTC
* *
1636592 ATCTCAATTTG
1 CTCTCAATTTC
1636603 CTCTCAATTTC
1 CTCTCAATTTC
1636614 CTCTCAAATTTC
1 CTCTC-AATTTC
1636626 TCTTAAATCC
Statistics
Matches: 63, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.06
11 42 0.67
12 12 0.19
ACGTcount: A:0.23, C:0.30, G:0.02, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:1636660 original size:15 final size:15
Alignment explanation
Indices: 1636640--1636673 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1636630 AAATCCCTAT
1636640 TTTTAATTTTTTTAA
1 TTTTAATTTTTTTAA
1636655 TTTTAATTTTTTTAA
1 TTTTAATTTTTTTAA
1636670 TTTT
1 TTTT
1636674 TTTTAAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTAATTTTTTTAA
Found at i:1636679 original size:10 final size:9
Alignment explanation
Indices: 1636639--1636676 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
1636629 TAAATCCCTA
1636639 TTTTTAATT
1 TTTTTAATT
1636648 TTTTTAA--
1 TTTTTAATT
1636655 -TTTTAATT
1 TTTTTAATT
1636663 TTTTTAATT
1 TTTTTAATT
1636672 TTTTT
1 TTTTT
1636677 TAAATCGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 6 0.23
9 20 0.77
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTAATT
Found at i:1636788 original size:11 final size:11
Alignment explanation
Indices: 1636772--1636801 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1636762 CCAGAGAATT
1636772 TATTTTTTAAA
1 TATTTTTTAAA
1636783 TATTTTTT-AA
1 TATTTTTTAAA
1636793 TATTTTTTA
1 TATTTTTTA
1636802 TTTATGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTTTTAAA
Found at i:1637748 original size:7 final size:7
Alignment explanation
Indices: 1637736--1637761 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1637726 TAGTCGATTG
1637736 GTATTTA
1 GTATTTA
1637743 GTATTTA
1 GTATTTA
1637750 GTATTTA
1 GTATTTA
1637757 GTATT
1 GTATT
1637762 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:1638431 original size:18 final size:18
Alignment explanation
Indices: 1638408--1638450 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1638398 TGCCAAGTGC
* *
1638408 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
1638426 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
1638444 GTTTCCT
1 GTATCCT
1638451 TTTCCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:1640001 original size:37 final size:38
Alignment explanation
Indices: 1639950--1640024 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
1639940 TATAATAAAT
1639950 AAATATTTTTTATTC-TTTAATTTTAAAAT-ATTTTTA
1 AAATATTTTTTATTCTTTTAATTTTAAAATAATTTTTA
*
1639986 AAATACTTTTTTATTCTTTTTATTTTTAAAATAATTTTT
1 AAATA-TTTTTTATTC-TTTTAATTTTAAAATAATTTTT
1640025 TCGATGTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 5 0.15
37 10 0.29
39 13 0.38
40 6 0.18
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (38 bp):
AAATATTTTTTATTCTTTTAATTTTAAAATAATTTTTA
Found at i:1640248 original size:14 final size:14
Alignment explanation
Indices: 1640229--1640273 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
1640219 TTTAATTTTT
*
1640229 AACCTTAAATCCTA
1 AACCTTAAACCCTA
1640243 AACCTTAAAACCCTA
1 AACCTT-AAACCCTA
*
1640258 AACCTTAAACCTTA
1 AACCTTAAACCCTA
1640272 AA
1 AA
1640274 AGTAGTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:1640251 original size:7 final size:7
Alignment explanation
Indices: 1640229--1640273 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
1640219 TTTAATTTTT
1640229 AACCTTA
1 AACCTTA
1640236 AATCC-TA
1 AA-CCTTA
1640243 AACCTTAA
1 AACCTT-A
*
1640251 AACCCTA
1 AACCTTA
1640258 AACCTTA
1 AACCTTA
1640265 AACCTTA
1 AACCTTA
1640272 AA
1 AA
1640274 AGTAGTGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 2 0.06
7 23 0.70
8 8 0.24
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (7 bp):
AACCTTA
Found at i:1640259 original size:15 final size:15
Alignment explanation
Indices: 1640229--1640266 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1640219 TTTAATTTTT
*
1640229 AACCTT-AAATCCTA
1 AACCTTAAAACCCTA
1640243 AACCTTAAAACCCTA
1 AACCTTAAAACCCTA
1640258 AACCTTAAA
1 AACCTTAAA
1640267 CCTTAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (15 bp):
AACCTTAAAACCCTA
Found at i:1644644 original size:12 final size:12
Alignment explanation
Indices: 1644627--1644651 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1644617 TCTCTGCCTA
1644627 CACTCGCTCGCT
1 CACTCGCTCGCT
1644639 CACTCGCTCGCT
1 CACTCGCTCGCT
1644651 C
1 C
1644652 TCTTTCTCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.52, G:0.16, T:0.24
Consensus pattern (12 bp):
CACTCGCTCGCT
Found at i:1666250 original size:19 final size:20
Alignment explanation
Indices: 1666207--1666250 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1666197 TTAAAATACT
* *
1666207 TTTAAAATAAATTTTTTTATT
1 TTTAAAAT-AATTTTTTAATG
1666228 TTTAAAAT-ATTTTTTAATG
1 TTTAAAATAATTTTTTAATG
1666247 TTTA
1 TTTA
1666251 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
21 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTAAAATAATTTTTTAATG
Found at i:1674291 original size:32 final size:30
Alignment explanation
Indices: 1674227--1674291 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
1674217 AAGTTCTGAA
* * *
1674227 TTTTTATTAAATTTTGCAATCAATTTTTAT
1 TTTTTATTAAATTTTCCAATCAATATTAAT
*
1674257 TTTTTAATTAAATTTTACCACTCAATATTAAT
1 TTTTT-ATTAAATTTT-CCAATCAATATTAAT
1674289 TTT
1 TTT
1674292 GATGATTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.17
31 10 0.34
32 14 0.48
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTTATTAAATTTTCCAATCAATATTAAT
Found at i:1680278 original size:22 final size:24
Alignment explanation
Indices: 1680230--1680278 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
1680220 GAGCTTCTTA
* *
1680230 TATATTTTTCTTGAATTTTTCATT
1 TATATTTTTCTTGAATTTTTAAAT
1680254 TATATTTTT-TTGAA-TTTTAAAT
1 TATATTTTTCTTGAATTTTTAAAT
1680276 TAT
1 TAT
1680279 TTGTTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 5 0.22
24 9 0.39
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TATATTTTTCTTGAATTTTTAAAT
Found at i:1699203 original size:18 final size:18
Alignment explanation
Indices: 1699180--1699218 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1699170 CCTAGAAATA
*
1699180 GGACGACATAAATCTATT
1 GGACGACATAAATCTACT
*
1699198 GGACGATATAAATCTACT
1 GGACGACATAAATCTACT
1699216 GGA
1 GGA
1699219 TTAGAGTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (18 bp):
GGACGACATAAATCTACT
Found at i:1717175 original size:23 final size:23
Alignment explanation
Indices: 1717144--1717189 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1717134 AGTCAAAAAG
1717144 ATTGATTCATAGATGCTATTAAC
1 ATTGATTCATAGATGCTATTAAC
* *
1717167 ATTGTTTCATAGATTCTATTAAC
1 ATTGATTCATAGATGCTATTAAC
1717190 TTAGCTTAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (23 bp):
ATTGATTCATAGATGCTATTAAC
Found at i:1718830 original size:12 final size:12
Alignment explanation
Indices: 1718811--1718841 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1718801 ATATGGTTAT
1718811 TTTG-TTAATAG
1 TTTGATTAATAG
1718822 TTTGATTAATAG
1 TTTGATTAATAG
1718834 TTTGATTA
1 TTTGATTA
1718842 GAATTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (12 bp):
TTTGATTAATAG
Found at i:1721738 original size:20 final size:20
Alignment explanation
Indices: 1721693--1721740 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1721683 TACGTTTTTA
*
1721693 ATTATCATTTATAAATTAATT
1 ATTA-CATTTATAAATTAAGT
*
1721714 CTTACATTTGATAAA-TAAGT
1 ATTACATTT-ATAAATTAAGT
1721734 ATTACAT
1 ATTACAT
1721741 ATTTAAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (20 bp):
ATTACATTTATAAATTAAGT
Found at i:1721796 original size:15 final size:15
Alignment explanation
Indices: 1721759--1721797 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1721749 GGTGATAATT
* *
1721759 AATATTAATTTTTTA
1 AATATTAATATATTA
1721774 AA-ATTAATATATTA
1 AATATTAATATATTA
1721788 AATATTAATA
1 AATATTAATA
1721798 GATGAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATATTAATATATTA
Found at i:1722761 original size:133 final size:134
Alignment explanation
Indices: 1722575--1722991 Score: 497
Period size: 135 Copynumber: 3.1 Consensus size: 134
1722565 CGCTTCCACG
* * * *
1722575 AAAACGCCGCAAAAAATTGGAATATAGCGGCGTTTTCTGAGAAACGCCGGTAAAGATAACGAATT
1 AAAACGCCGGAAAAAATTGGAATATAGCGGCGTTTTCAGAGAAACGCCGGTAAAGATATCTAATT
* * *
1722640 TGAGGAAAAAATCTGAGCAAAACAGTACCGTTTTATGGTTTCATTTTATTTCTTTAGTGGCGCAT
66 TGAGGAAAAATTTTGAGCAAAAC-GTACCGTTTTATTGTTTCATTTTATTTCTTTAGTGGCGCAT
1722705 TGTAA
130 TGTAA
* *
1722710 AAAACGCCGGAAAAGATT-GAAT-TGGCGGCGTTTTCAGAGAAACGCCGGTAAAGATATCTAATT
1 AAAACGCCGGAAAAAATTGGAATATAGCGGCGTTTTCAGAGAAACGCCGGTAAAGATATCTAATT
* *
1722773 TGAGGAAAAATTTTG-GACAAAACGCTACCGTTTTATTGCTTCGTTTTATTTCTTTAGTGGCGCA
66 TGAGGAAAAATTTTGAG-CAAAACG-TACCGTTTTATTGTTTCATTTTATTTCTTTAGTGGCGCA
1722837 TTGTAAA
129 TTGT-AA
* * * * *
1722844 AAAACGCC--ACAAATATTGGGATATAGTGGCGTTATT-GGAGAAACGCCGGTAAGGATATCTAA
1 AAAACGCCGGA-AAAAATTGGAATATAGCGGCGTT-TTCAGAGAAACGCCGGTAAAGATATCTAA
* * * * *
1722906 TTTGAGGAAAAATTTTGAGCAACACGGTACTGTTTTGTTGTTTCCTTTT-TATGCTTTAGTGGCG
64 TTTGAGGAAAAATTTTGAGCAAAAC-GTACCGTTTTATTGTTTCATTTTAT-TTCTTTAGTGGCG
* *
1722970 AAATGTTAA
127 CATTG-TAA
1722979 AAAACGCCGGAAA
1 AAAACGCCGGAAA
1722992 CGGTTCGGAT
Statistics
Matches: 244, Mismatches: 25, Indels: 25
0.83 0.09 0.09
Matches are distributed among these distances:
132 3 0.01
133 102 0.42
134 18 0.07
135 113 0.46
136 7 0.03
137 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (134 bp):
AAAACGCCGGAAAAAATTGGAATATAGCGGCGTTTTCAGAGAAACGCCGGTAAAGATATCTAATT
TGAGGAAAAATTTTGAGCAAAACGTACCGTTTTATTGTTTCATTTTATTTCTTTAGTGGCGCATT
GTAA
Found at i:1723376 original size:21 final size:20
Alignment explanation
Indices: 1723337--1723377 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1723327 TTTGTGTTCT
*
1723337 GGGCTTAGAGTTTAGGTTTA
1 GGGCTTAGAGTTGAGGTTTA
*
1723357 GGGCTTGGAGATTGAGGTTTA
1 GGGCTTAGAG-TTGAGGTTTA
1723378 AGGTTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.20, C:0.05, G:0.39, T:0.37
Consensus pattern (20 bp):
GGGCTTAGAGTTGAGGTTTA
Found at i:1726200 original size:15 final size:15
Alignment explanation
Indices: 1726165--1726203 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1726155 ATAAGTTTTC
*
1726165 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
1726180 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
1726196 TAAATTTA
1 TAAATTTA
1726204 GTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:1726229 original size:62 final size:61
Alignment explanation
Indices: 1726150--1726283 Score: 178
Period size: 62 Copynumber: 2.2 Consensus size: 61
1726140 TGTTTTAATA
* * * * **
1726150 TCTATATAAGTTTTCTAAATTTATTTGTATTAAAATTTATTAGTATTAAATTTAGTTCGTTT
1 TCTAAATAAGTGTTCTAAATTTATTAGTAATAAAATTTATTAGTATTAAATTTA-TAAGTTT
* *
1726212 TCTAAATAAGTGTTCTAAATTTGTTAGTAATAAAATTTATTAGTATTAATTTTATAAGTTT
1 TCTAAATAAGTGTTCTAAATTTATTAGTAATAAAATTTATTAGTATTAAATTTATAAGTTT
*
1726273 TCTACATAAGT
1 TCTAAATAAGT
1726284 TACATAATAC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
61 15 0.24
62 48 0.76
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (61 bp):
TCTAAATAAGTGTTCTAAATTTATTAGTAATAAAATTTATTAGTATTAAATTTATAAGTTT
Found at i:1726309 original size:9 final size:9
Alignment explanation
Indices: 1726275--1726377 Score: 61
Period size: 9 Copynumber: 11.2 Consensus size: 9
1726265 ATAAGTTTTC
*
1726275 TACATAAGT
1 TACATAACT
1726284 TACATAA--
1 TACATAACT
**
1726291 TACACCACT
1 TACATAACT
1726300 TACATAACT
1 TACATAACT
*
1726309 TACAAAACT
1 TACATAACT
*
1726318 TATATAA--
1 TACATAACT
1726325 TACATAACT
1 TACATAACT
*
1726334 TATATTTAAGCT
1 TACA--TAA-CT
*
1726346 TGCATAACT
1 TACATAACT
1726355 TACATAATAACT
1 TAC---ATAACT
1726367 TACATAACT
1 TACATAACT
1726376 TA
1 TA
1726378 TATATAATAA
Statistics
Matches: 72, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
7 11 0.15
9 42 0.58
10 3 0.04
11 3 0.04
12 13 0.18
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (9 bp):
TACATAACT
Found at i:1726338 original size:16 final size:16
Alignment explanation
Indices: 1726275--1726335 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
1726265 ATAAGTTTTC
*
1726275 TACATAAGTTACATAA
1 TACATAACTTACATAA
**
1726291 TACACCACTTACATAA
1 TACATAACTTACATAA
* *
1726307 CTTACAAAACTTATATAA
1 --TACATAACTTACATAA
1726325 TACATAACTTA
1 TACATAACTTA
1726336 TATTTAAGCT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
16 23 0.64
18 13 0.36
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:1726353 original size:21 final size:21
Alignment explanation
Indices: 1726303--1726381 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
1726293 CACCACTTAC
*
1726303 ATAACTTACAAAAC-T-TAT-
1 ATAACTTACATAACTTATATA
1726321 ATAA--TACATAACTTATAT-
1 ATAACTTACATAACTTATATA
* * *
1726339 TTAAGCTTGCATAACTTACATA
1 ATAA-CTTACATAACTTATATA
1726361 ATAACTTACATAACTTATATA
1 ATAACTTACATAACTTATATA
1726382 TAATAACATA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
16 7 0.15
17 1 0.02
18 10 0.21
21 27 0.56
22 3 0.06
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.37
Consensus pattern (21 bp):
ATAACTTACATAACTTATATA
Found at i:1726366 original size:12 final size:12
Alignment explanation
Indices: 1726349--1726535 Score: 64
Period size: 12 Copynumber: 17.4 Consensus size: 12
1726339 TTAAGCTTGC
1726349 ATAACTTACATA
1 ATAACTTACATA
1726361 ATAACTTAC---
1 ATAACTTACATA
*
1726370 ATAACTTATAT-
1 ATAACTTACATA
*
1726381 ATAA-TAACATA
1 ATAACTTACATA
*
1726392 ATAAATTACATA
1 ATAACTTACATA
*
1726404 AT-ACTT-TAT-
1 ATAACTTACATA
* *
1726413 GTTA--TA-ATA
1 ATAACTTACATA
*
1726422 CATAACTTATAT-
1 -ATAACTTACATA
*
1726434 ATAAGCTTGCAT-
1 ATAA-CTTACATA
1726446 A--ACTTACATA
1 ATAACTTACATA
1726456 ATAACTTAC---
1 ATAACTTACATA
1726465 ATAACTTACAT-
1 ATAACTTACATA
1726476 ATAA--TAGCATA
1 ATAACTTA-CATA
*
1726487 ATAAATTACATA
1 ATAACTTACATA
*
1726499 AT-ACTT-TAT-
1 ATAACTTACATA
*
1726508 ATAA-TAACATA
1 ATAACTTACATA
*
1726519 ATAACTTATATA
1 ATAACTTACATA
1726531 ATAAC
1 ATAAC
1726536 ATAATAACTA
Statistics
Matches: 132, Mismatches: 18, Indels: 50
0.66 0.09 0.25
Matches are distributed among these distances:
8 3 0.02
9 29 0.22
10 19 0.14
11 30 0.23
12 47 0.36
13 4 0.03
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:1726394 original size:31 final size:30
Alignment explanation
Indices: 1726356--1726531 Score: 133
Period size: 31 Copynumber: 5.6 Consensus size: 30
1726346 TGCATAACTT
1726356 ACATAATAACTTACATAACTTATATATAATA
1 ACATAATAACTTACATAACTT-TATATAATA
* * *
1726387 ACATAATAAATTACATAATACTTTATGTTAT-
1 ACATAATAACTTACAT-A-ACTTTATATAATA
* * * *
1726418 A-ATACATAACTTATATATAAGCTTGCATA-ACTT
1 ACATA-ATAAC-T-TACATAA-CTT-TATATAATA
*
1726451 ACATAATAACTTACATAACTTACATATAATA
1 ACATAATAACTTACATAACTT-TATATAATA
* *
1726482 GCATAATAAATTACATAATACTTTATATAATA
1 ACATAATAACTTACAT-A-ACTTTATATAATA
*
1726514 ACATAATAACTTATATAA
1 ACATAATAACTTACATAA
1726532 TAACATAATA
Statistics
Matches: 114, Mismatches: 19, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
30 11 0.10
31 44 0.39
32 36 0.32
33 20 0.18
34 3 0.03
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.36
Consensus pattern (30 bp):
ACATAATAACTTACATAACTTTATATAATA
Found at i:1726422 original size:95 final size:95
Alignment explanation
Indices: 1726320--1726530 Score: 352
Period size: 95 Copynumber: 2.2 Consensus size: 95
1726310 ACAAAACTTA
* *
1726320 TATAATACATAACTTATATTTAAGCTTGCATAACTTACATAATAACTTACATAACTTATATATAA
1 TATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACTTACATAACTTACATATAA
*
1726385 TAACATAATAAATTACATAATACTTTATGT
66 TAACATAATAAATTACATAATACTTTATAT
1726415 TATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACTTACATAACTTACATATAA
1 TATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACTTACATAACTTACATATAA
*
1726480 TAGCATAATAAATTACATAATACTTTATAT
66 TAACATAATAAATTACATAATACTTTATAT
*
1726510 AATAACATA-ATAACTTATATA
1 TAT-A-ATACATAACTTATATA
1726531 ATAACATAAT
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
95 93 0.85
96 13 0.12
97 3 0.03
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (95 bp):
TATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACTTACATAACTTACATATAA
TAACATAATAAATTACATAATACTTTATAT
Found at i:1726448 original size:21 final size:20
Alignment explanation
Indices: 1726420--1727062 Score: 354
Period size: 18 Copynumber: 34.7 Consensus size: 20
1726410 TATGTTATAA
*
1726420 TACATAACTTATATATAAGCT
1 TACATAACTTACATATAA-CT
*
1726441 TGCATAACTTACATAATAACT
1 TACATAACTTACAT-ATAACT
1726462 TACATAACTTACATATAA--
1 TACATAACTTACATATAACT
* *
1726480 TAGCATAA--TA-A-ATTACA
1 TA-CATAACTTACATATAACT
* *
1726497 TA-AT-ACTTTATATAATAACA
1 TACATAAC-TTACAT-ATAACT
* *
1726517 TA-ATAACTTATATAATAACA
1 TACATAACTTACAT-ATAACT
* *
1726537 TA-ATAACTAACATACAA--
1 TACATAACTTACATATAACT
* * * *
1726554 TATATAAACATATATAGAAACT
1 TACAT-AACTTACATA-TAACT
* * *
1726576 TGCATAACTTATATAATAACA
1 TACATAACTTACAT-ATAACT
*
1726597 TA-ATAAC-TA-ACATAA--
1 TACATAACTTACATATAACT
*
1726612 TACATAACCTA-A-ATAACT
1 TACATAACTTACATATAACT
1726630 TACATAACTTAC--ATAACT
1 TACATAACTTACATATAACT
* *
1726648 TACATTA--TAC--ACAACT
1 TACATAACTTACATATAACT
*
1726664 TACATAAATTA-A-ATAACT
1 TACATAACTTACATATAACT
*
1726682 TACATAACTTACATA-CA-T
1 TACATAACTTACATATAACT
*
1726700 TAAATAACTTAC--ATAACT
1 TACATAACTTACATATAACT
1726718 TACATAACTTACATTATACACAACT
1 TACATAACTTACA-TAT----AACT
*
1726743 TACATAAATTA-A-ATAACT
1 TACATAACTTACATATAACT
*
1726761 TACATAACTTAC--ATAAGT
1 TACATAACTTACATATAACT
*
1726779 TACATAAATTA-A-ATAACT
1 TACATAACTTACATATAACT
1726797 TACATAACTTACATA-AA-T
1 TACATAACTTACATATAACT
*
1726815 TAAATAACTTAC--ATAACT
1 TACATAACTTACATATAACT
*
1726833 TACATAAATTA-A-ATAACT
1 TACATAACTTACATATAACT
1726851 TACATAACTTAC--ATAACT
1 TACATAACTTACATATAACT
*
1726869 TACATAAATTA-A-ATAACT
1 TACATAACTTACATATAACT
1726887 TACATAACTTAC--ATAACT
1 TACATAACTTACATATAACT
*
1726905 TACATAAATTA-A-ATAACT
1 TACATAACTTACATATAACT
*
1726923 TACATAAGTTACATA-AA-T
1 TACATAACTTACATATAACT
* *
1726941 TAAATAACTTTC--ATAACT
1 TACATAACTTACATATAACT
*
1726959 TACATAAGTTACATA-AA-T
1 TACATAACTTACATATAACT
* *
1726977 TAAATAACTTTC--ATAACT
1 TACATAACTTACATATAACT
1726995 TACATAACTTACATA-AA-T
1 TACATAACTTACATATAACT
*
1727013 TAAATAACTTAC--ATAACT
1 TACATAACTTACATATAACT
*
1727031 TACATAAATTA-A-ATAACT
1 TACATAACTTACATATAACT
1727049 TACATAACTTACAT
1 TACATAACTTACAT
1727063 TATACATAAC
Statistics
Matches: 502, Mismatches: 58, Indels: 125
0.73 0.08 0.18
Matches are distributed among these distances:
14 1 0.00
15 7 0.01
16 29 0.06
17 24 0.05
18 294 0.59
19 30 0.06
20 49 0.10
21 43 0.09
22 10 0.02
24 1 0.00
25 14 0.03
ACGTcount: A:0.50, C:0.16, G:0.01, T:0.33
Consensus pattern (20 bp):
TACATAACTTACATATAACT
Done.