Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 7 of 15
Found at i:1289959 original size:21 final size:22
Alignment explanation
Indices: 1289935--1289980 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1289925 AAATAAAAAA
1289935 TTTAATGAAAA-AAAT-TTTTAC
1 TTTAAT-AAAATAAATGTTTTAC
1289956 TTTAATAAAATTAAATGTTTTAC
1 TTTAATAAAA-TAAATGTTTTAC
1289979 TT
1 TT
1289981 CCGTATAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 4 0.18
23 8 0.36
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
TTTAATAAAATAAATGTTTTAC
Found at i:1290146 original size:24 final size:23
Alignment explanation
Indices: 1290118--1290162 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1290108 TAAAAATTTT
1290118 TAATT-TCATTATAAATATATTAAA
1 TAATTATC-TTATAAAT-TATTAAA
*
1290142 TAATTATCTTATATATTATTA
1 TAATTATCTTATAAATTATTA
1290163 TAATTTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATTATCTTATAAATTATTAAA
Found at i:1296771 original size:28 final size:23
Alignment explanation
Indices: 1296721--1296764 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1296711 TTTTTAATTT
1296721 TTAATTTTTATTTTAGCTTTCTA
1 TTAATTTTTATTTTAGCTTTCTA
1296744 TTAATTTTTATTTTAGCTTTC
1 TTAATTTTTATTTTAGCTTTC
1296765 CAATCTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.05, T:0.66
Consensus pattern (23 bp):
TTAATTTTTATTTTAGCTTTCTA
Found at i:1300292 original size:23 final size:25
Alignment explanation
Indices: 1300243--1300293 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1300233 AATAGTATTT
*
1300243 TAATATTTTATTTAAATAAAAATTA
1 TAATATTTTATTTAAATAAAAAGTA
*
1300268 TAATA-TTTATTTACAT-AAAAGTA
1 TAATATTTTATTTAAATAAAAAGTA
1300291 TAA
1 TAA
1300294 GATGCTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATATTTTATTTAAATAAAAAGTA
Found at i:1300423 original size:17 final size:18
Alignment explanation
Indices: 1300389--1300436 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
1300379 TAATAACTTA
*
1300389 TATTATTAAAAATTAATAT
1 TATTATT-AAATTTAATAT
1300408 T-TTATTAAATTTAATAT
1 TATTATTAAATTTAATAT
1300425 TATATATTAAAT
1 TAT-TATTAAAT
1300437 AATAACAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 11 0.42
18 6 0.23
19 9 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTATTAAATTTAATAT
Found at i:1300451 original size:15 final size:15
Alignment explanation
Indices: 1300431--1300461 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1300421 ATATTATATA
*
1300431 TTAAATAATAACAAT
1 TTAAATAATAAAAAT
1300446 TTAAATAATAAAAAT
1 TTAAATAATAAAAAT
1300461 T
1 T
1300462 AAAAAAATTA
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:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAATAATAAAAAT
Found at i:1301365 original size:44 final size:44
Alignment explanation
Indices: 1301310--1301400 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
1301300 TTGTCCTGCT
*
1301310 TGTCTTCAAGTTTGAGAAGTCTCTTCATGTGTTATCTTGTCTTG
1 TGTCTTCAAGTTTGAGAAGTCTCTTCATGTGTTATCCTGTCTTG
* *
1301354 TGTCTTCAAGTTTGAGAAGTCTCTTCATGTGTTTTCCTGTGTTG
1 TGTCTTCAAGTTTGAGAAGTCTCTTCATGTGTTATCCTGTCTTG
1301398 TGT
1 TGT
1301401 AAGTGATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.14, C:0.15, G:0.22, T:0.48
Consensus pattern (44 bp):
TGTCTTCAAGTTTGAGAAGTCTCTTCATGTGTTATCCTGTCTTG
Found at i:1303125 original size:88 final size:88
Alignment explanation
Indices: 1302976--1303152 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
1302966 AGGTAGGGGA
1302976 TACTTAGATTCGTGCTGGTTCCATGTCCATTTGAGGGAGACATGAATCTTTAATGTTTCAGCGTG
1 TACTTAGATTCGTGCTGGTTCCATGTCCATTTGAGGGAGACATGAATCTTTAATGTTTCAGCGTG
1303041 GCACCCTTCTTCACGCTAATGGC
66 GCACCCTTCTTCACGCTAATGGC
1303064 TACTTAGATTCGTGCTGGTTCCATGTCCATTTGAGGGAGACATGAATCTTTAATGTTTCAGCGTG
1 TACTTAGATTCGTGCTGGTTCCATGTCCATTTGAGGGAGACATGAATCTTTAATGTTTCAGCGTG
1303129 GCACCCTTCTTCACGCTAATGGC
66 GCACCCTTCTTCACGCTAATGGC
1303152 T
1 T
1303153 TCACAGTTGC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (88 bp):
TACTTAGATTCGTGCTGGTTCCATGTCCATTTGAGGGAGACATGAATCTTTAATGTTTCAGCGTG
GCACCCTTCTTCACGCTAATGGC
Found at i:1303889 original size:79 final size:78
Alignment explanation
Indices: 1303671--1303908 Score: 323
Period size: 78 Copynumber: 3.0 Consensus size: 78
1303661 TCATTGGCAC
* *
1303671 AGTTACAACTCATAAGAGCAGTGCAAAGTTCCTGTCTTTCCCATAGGCCGTATCCATGCTATTGT
1 AGTTACAACTCACAAGAGCAATGCAAAGTTCCTGTCTTTCCCATAGGCCGTATCCATGCTATTGT
*
1303736 TCCGAATACCTCT
66 TCCGAATGCCTCT
* ** * * *
1303749 AGTTACAACTCGCAAGAGCAATGCAAAGTTCCCATCATTCCTATAGGCCGTCTCCATGCTATTGT
1 AGTTACAACTCACAAGAGCAATGCAAAGTTCCTGTCTTTCCCATAGGCCGTATCCATGCTATTGT
*
1303814 TCCAAATGCCTCT
66 TCCGAATGCCTCT
* * * * *
1303827 GGTTACAACTCACAAAGAGCAATGCAAAGGTCCTGTCTTTCCGATCGGCCGTTTCCATGCTATTG
1 AGTTACAACTCAC-AAGAGCAATGCAAAGTTCCTGTCTTTCCCATAGGCCGTATCCATGCTATTG
*
1303892 TTCCGAATGCCTTT
65 TTCCGAATGCCTCT
1303906 AGT
1 AGT
1303909 GACTAGTAGT
Statistics
Matches: 137, Mismatches: 22, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
78 79 0.58
79 58 0.42
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (78 bp):
AGTTACAACTCACAAGAGCAATGCAAAGTTCCTGTCTTTCCCATAGGCCGTATCCATGCTATTGT
TCCGAATGCCTCT
Found at i:1305920 original size:22 final size:22
Alignment explanation
Indices: 1305894--1305935 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1305884 ATTAAAAAAT
1305894 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1305916 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1305936 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1306223 original size:11 final size:11
Alignment explanation
Indices: 1306201--1306230 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1306191 TAAGATCTAT
1306201 AAATATAAAAAA
1 AAATA-AAAAAA
1306213 AAATAAAAAAA
1 AAATAAAAAAA
1306224 AAATAAA
1 AAATAAA
1306231 TATTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:1306267 original size:19 final size:19
Alignment explanation
Indices: 1306224--1306260 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1306214 AATAAAAAAA
* *
1306224 AAATAAATATTTTTATATC
1 AAATATATATATTTATATC
1306243 AAATATATATATTTATAT
1 AAATATATATATTTATAT
1306261 TTAATATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATATATATTTATATC
Found at i:1306748 original size:21 final size:21
Alignment explanation
Indices: 1306706--1306759 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1306696 TGTAATTATT
* *
1306706 TATTTAATTTTAATTAATTAA
1 TATTTAATTTTAATAAAATAA
1306727 TATTTAAATTTTAA-AAAATAA
1 TATTT-AATTTTAATAAAATAA
* *
1306748 TTTTTTATTTTA
1 TATTTAATTTTA
1306760 TTTTCTCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 6 0.21
21 14 0.50
22 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTAATTTTAATAAAATAA
Found at i:1307507 original size:2 final size:2
Alignment explanation
Indices: 1307500--1307541 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1307490 AACTGCTTGA
1307500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1307542 GAGTAATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1311276 original size:13 final size:13
Alignment explanation
Indices: 1311258--1311286 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1311248 AATTTTTGCC
1311258 AAAAGAAAAAGGA
1 AAAAGAAAAAGGA
1311271 AAAAGAAAAAGGA
1 AAAAGAAAAAGGA
1311284 AAA
1 AAA
1311287 CTACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGGA
Found at i:1311799 original size:13 final size:13
Alignment explanation
Indices: 1311766--1311801 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1311756 TTATAATTTG
*
1311766 ATATTTAAAATAA
1 ATATTTAAATTAA
1311779 AT-TTTAAATTAA
1 ATATTTAAATTAA
1311791 ATATTTAAATT
1 ATATTTAAATT
1311802 TTACTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATTTAAATTAA
Found at i:1312294 original size:30 final size:31
Alignment explanation
Indices: 1312242--1312308 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
1312232 TCGAATAGTT
* **
1312242 TTTTAGTTTTAAATTTTTATTTAAGAAA-A-A
1 TTTTAATTTTAAATTTAAATTTAA-AAACATA
*
1312272 TTTTAATTTTTAATTTAAATTTAAAAACATA
1 TTTTAATTTTAAATTTAAATTTAAAAACATA
1312303 TTTTAA
1 TTTTAA
1312309 CATAAAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 3 0.10
30 21 0.68
31 7 0.23
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTTAATTTTAAATTTAAATTTAAAAACATA
Found at i:1312558 original size:30 final size:28
Alignment explanation
Indices: 1312522--1312588 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 28
1312512 CATTTGAAAC
1312522 AAAAATTTATTTAAATTAAAATTAAAAGAT-
1 AAAAATTTATTTAAA-TAAAA-TAAAA-ATA
* *
1312552 AAAAATTTATTTACATATAATAAAAATA
1 AAAAATTTATTTAAATAAAATAAAAATA
1312580 AAAAATTTA
1 AAAAATTTA
1312589 ATTTTTCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 14 0.41
29 4 0.12
30 14 0.41
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAAATTTATTTAAATAAAATAAAAATA
Found at i:1321459 original size:2 final size:2
Alignment explanation
Indices: 1321452--1321490 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
1321442 TAAATATACC
1321452 TA TA TA TA TA TA TA TA CTA 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 TA TA TA TA
1321491 CCCATCAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1323243 original size:21 final size:21
Alignment explanation
Indices: 1323207--1323266 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
1323197 TTAATTTTAT
1323207 ATTTAATTATTAAAATAAATAA
1 ATTTAATTA-TAAAATAAATAA
*
1323229 ATTTAATTATAAAATATATAA
1 ATTTAATTATAAAATAAATAA
1323250 ATATTAA-TATAAAATAA
1 AT-TTAATTATAAAATAA
1323267 TTTTTATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTAATTATAAAATAAATAA
Found at i:1323269 original size:37 final size:35
Alignment explanation
Indices: 1323205--1323276 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 35
1323195 ATTTAATTTT
* *
1323205 ATATTTAATTATTAAAATAAATAAATTTAATTATAAA
1 ATATATAAATATTAAAATAAATAAATTT--TTATAAA
*
1323242 ATATATAAATATTAATATAAA-ATAATTTTTATAAA
1 ATATATAAATATTAAAATAAATA-AATTTTTATAAA
1323277 TTATTGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 7 0.23
36 1 0.03
37 23 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (35 bp):
ATATATAAATATTAAAATAAATAAATTTTTATAAA
Found at i:1323303 original size:29 final size:27
Alignment explanation
Indices: 1323244--1323314 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 27
1323234 ATTATAAAAT
*
1323244 ATATAAA-TATTAATATAAAATAATTT
1 ATATAAATTATTAATATAAAATAATTA
* *
1323270 TTATAAATTATTGATAATAAATATAATTA
1 ATATAAATTATTAAT-ATAAA-ATAATTA
1323299 ATATAAATTAATTAAT
1 ATATAAATT-ATTAAT
1323315 TTAATTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 6 0.17
27 6 0.17
28 5 0.14
29 14 0.39
30 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
ATATAAATTATTAATATAAAATAATTA
Found at i:1323310 original size:14 final size:14
Alignment explanation
Indices: 1323244--1323327 Score: 75
Period size: 14 Copynumber: 6.1 Consensus size: 14
1323234 ATTATAAAAT
1323244 ATATAAA-T-ATTA
1 ATATAAATTAATTA
* *
1323256 ATATAAAATAATTT
1 ATATAAATTAATTA
* *
1323270 TTATAAATT-ATTG
1 ATATAAATTAATTA
1323283 ATAATAAATATAATTA
1 AT-ATAAAT-TAATTA
1323299 ATATAAATTAATTA
1 ATATAAATTAATTA
* *
1323313 ATTTAATTTAATTA
1 ATATAAATTAATTA
1323327 A
1 A
1323328 AATTTTTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
12 7 0.12
13 5 0.08
14 35 0.59
15 7 0.12
16 5 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (14 bp):
ATATAAATTAATTA
Found at i:1323498 original size:22 final size:22
Alignment explanation
Indices: 1323452--1323502 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1323442 TTAACTTAAA
1323452 TATTTTAAGATTATATATTACT
1 TATTTTAAGATTATATATTACT
*
1323474 TATTTTTA-ATTATATAATATA-T
1 TATTTTAAGATTATAT-AT-TACT
1323496 TATTTTA
1 TATTTTA
1323503 TATTTGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTTTAAGATTATATATTACT
Found at i:1323501 original size:21 final size:21
Alignment explanation
Indices: 1323452--1323502 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 21
1323442 TTAACTTAAA
1323452 TATTTTAAGATTATATATTACT
1 TATTTT-AGATTATATATTACT
1323474 TATTTTTA-ATTATATAATATA-T
1 TA-TTTTAGATTATAT-AT-TACT
1323496 TATTTTA
1 TATTTTA
1323503 TATTTGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 12 0.46
22 8 0.31
23 6 0.23
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTTTAGATTATATATTACT
Found at i:1323752 original size:9 final size:10
Alignment explanation
Indices: 1323729--1323800 Score: 53
Period size: 10 Copynumber: 7.1 Consensus size: 10
1323719 TTTTTGGAAT
1323729 TAAAATTATCA
1 TAAAATTAT-A
1323740 -AAAATTAT-
1 TAAAATTATA
1323748 TAAAATTATA
1 TAAAATTATA
*
1323758 TAAAAAGTTAGA
1 T-AAAA-TTATA
1323770 -AAAATTATA
1 TAAAATTATA
1323779 TTAAAAGTTAT-
1 -TAAAA-TTATA
*
1323790 TGAAATTATA
1 TAAAATTATA
1323800 T
1 T
1323801 CTAAAAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 17
0.71 0.04 0.24
Matches are distributed among these distances:
9 16 0.32
10 18 0.36
11 8 0.16
12 8 0.16
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.38
Consensus pattern (10 bp):
TAAAATTATA
Found at i:1323789 original size:12 final size:11
Alignment explanation
Indices: 1323745--1323818 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 11
1323735 TATCAAAAAT
1323745 TATTAAAATTA
1 TATTAAAATTA
*
1323756 TATAAAAAGTTA
1 TATTAAAA-TTA
*
1323768 GA--AAAATTA
1 TATTAAAATTA
*
1323777 TATTAAAAGT-
1 TATTAAAATTA
*
1323787 TATTGAAATTA
1 TATTAAAATTA
*
1323798 TATCTAAAA-AA
1 TAT-TAAAATTA
1323809 T-TTAAAATTA
1 TATTAAAATTA
1323819 CATAAAAGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 13
0.69 0.13 0.19
Matches are distributed among these distances:
9 9 0.19
10 14 0.29
11 17 0.35
12 8 0.17
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.38
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:1323795 original size:21 final size:21
Alignment explanation
Indices: 1323727--1323837 Score: 88
Period size: 21 Copynumber: 5.4 Consensus size: 21
1323717 TATTTTTGGA
1323727 ATTAAAATTATCA--AAAA-TT
1 ATTAAAATTAT-ATTAAAAGTT
*
1323746 ATTAAAATTATATAAAAAGTT
1 ATTAAAATTATATTAAAAGTT
**
1323767 AGAAAAATTATATTAAAAGTT
1 ATTAAAATTATATTAAAAGTT
* **
1323788 ATTGAAATTATATCTAAAAAAT
1 ATTAAAATTATAT-TAAAAGTT
*
1323810 -TTAAAATTACA-TAAAAGATT
1 ATTAAAATTATATTAAAAG-TT
*
1323830 ATCAAAAT
1 ATTAAAAT
1323838 CAAAATTATA
Statistics
Matches: 73, Mismatches: 13, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
18 1 0.01
19 16 0.22
20 5 0.07
21 45 0.62
22 6 0.08
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.35
Consensus pattern (21 bp):
ATTAAAATTATATTAAAAGTT
Found at i:1323946 original size:33 final size:32
Alignment explanation
Indices: 1323876--1324013 Score: 83
Period size: 33 Copynumber: 4.3 Consensus size: 32
1323866 AAATAAAATT
* *
1323876 TTATCAAAATTATATAAAAAA-TA-ACTAA-CA
1 TTATCAAAATTATA-AAAAAATTATATTAATGA
1323906 CTATATCAAAGATTATAAAAAAATTATATTAATGA
1 -T-TATCAAA-ATTATAAAAAAATTATATTAATGA
* * * *
1323941 TTATCAAAATTACATAAAATATTATGA-AAATTA
1 TTATCAAAATTATA-AAAAAATTAT-ATTAATGA
* * *
1323974 -TATCAAAAATTAT--TAAAATCATATTAAAGA
1 TTATC-AAAATTATAAAAAAATTATATTAATGA
1324004 TTATCAAAAT
1 TTATCAAAAT
1324014 CATATTAAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
29 1 0.01
30 14 0.17
31 5 0.06
32 22 0.26
33 35 0.42
34 6 0.07
35 1 0.01
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (32 bp):
TTATCAAAATTATAAAAAAATTATATTAATGA
Found at i:1323951 original size:21 final size:21
Alignment explanation
Indices: 1323876--1324022 Score: 107
Period size: 21 Copynumber: 6.9 Consensus size: 21
1323866 AAATAAAATT
*
1323876 TTATCAAAATTATA-TAAAAA
1 TTATCAAAATTATATTAAAGA
* * * * *
1323896 ATAACTAACACTATATCAAAGA
1 TTATC-AAAATTATATTAAAGA
* *
1323918 TTATAAAAAAATTATATTAATGA
1 TTAT--CAAAATTATATTAAAGA
* * *
1323941 TTATCAAAATTACATAAAATA
1 TTATCAAAATTATATTAAAGA
* * *
1323962 TTATGAAAATTATATCAAAAA
1 TTATCAAAATTATATTAAAGA
* *
1323983 TTATTAAAATCATATTAAAGA
1 TTATCAAAATTATATTAAAGA
*
1324004 TTATCAAAATCATATTAAA
1 TTATCAAAATTATATTAAA
1324023 TGCTATATTA
Statistics
Matches: 96, Mismatches: 27, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
20 3 0.03
21 71 0.74
22 6 0.06
23 16 0.17
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTATATTAAAGA
Found at i:1324003 original size:86 final size:86
Alignment explanation
Indices: 1323792--1324012 Score: 207
Period size: 86 Copynumber: 2.5 Consensus size: 86
1323782 AAAGTTATTG
* * *
1323792 AAATTATATCTAAAAAAT-TTAAAATTACATAAAAGATTATCAAAATCAAAATTATACTGAATGT
1 AAATTATATC-AAAAATTATTAAAATCATATAAAAGATTAT--AAA--AAAATTATACTGAATGT
*
1323856 TAAAAGAATTAAATAAAATTTTATCA
61 TAAAAGAATTAAATAAAATATTATCA
* * * * * *
1323882 AAATTATATAAAAAATAACTAACA-CTATATCAAAGATTATAAAAAAATTATA-TTAATGATTAT
1 AAATTATATCAAAAATTATTAAAATC-ATATAAAAGATTATAAAAAAATTATACTGAATG-TTA-
* * *
1323945 CAA-AATTACATAAAATATTATGA
63 AAAGAATTAAATAAAATATTATCA
* *
1323968 AAATTATATCAAAAATTATTAAAATCATATTAAAGATTATCAAAA
1 AAATTATATCAAAAATTATTAAAATCATATAAAAGATTATAAAAA
1324013 TCATATTAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
85 5 0.05
86 66 0.62
87 3 0.03
88 3 0.03
89 5 0.05
90 25 0.23
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (86 bp):
AAATTATATCAAAAATTATTAAAATCATATAAAAGATTATAAAAAAATTATACTGAATGTTAAAA
GAATTAAATAAAATATTATCA
Found at i:1325483 original size:20 final size:19
Alignment explanation
Indices: 1325451--1325519 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
1325441 TTTGAGTATA
*
1325451 AAAATTATCAAAAGTTATT
1 AAAATTATAAAAAGTTATT
**
1325470 AAAATTAATAAAAAGTTACA
1 AAAATT-ATAAAAAGTTATT
** *
1325490 AAAATCATATTGAAAGTTACT
1 AAAAT--TATAAAAAGTTATT
1325511 AAAATTATA
1 AAAATTATA
1325520 TTAAGGTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 9 0.22
20 15 0.38
21 15 0.38
22 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.32
Consensus pattern (19 bp):
AAAATTATAAAAAGTTATT
Found at i:1325507 original size:21 final size:21
Alignment explanation
Indices: 1325481--1325521 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1325471 AAATTAATAA
1325481 AAAGTTACAAAAATCATATTG
1 AAAGTTACAAAAATCATATTG
* *
1325502 AAAGTTACTAAAATTATATT
1 AAAGTTACAAAAATCATATT
1325522 AAGGTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (21 bp):
AAAGTTACAAAAATCATATTG
Found at i:1325610 original size:21 final size:21
Alignment explanation
Indices: 1325584--1325632 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1325574 TATTACTATA
*
1325584 AAAATTATATTAAAAATTATC
1 AAAATTATATCAAAAATTATC
* *
1325605 AAAATTATATCAAATATTATT
1 AAAATTATATCAAAAATTATC
1325626 AAAATTA
1 AAAATTA
1325633 AGATAATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATTATATCAAAAATTATC
Found at i:1325881 original size:21 final size:20
Alignment explanation
Indices: 1325850--1325915 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
1325840 AATTATATAA
1325850 ATCAAATATTACGATAAAAAAT
1 ATCAAA-ATTAC-ATAAAAAAT
* *
1325872 ATTAAAATTACATAAAAAGTT
1 ATCAAAATTACATAAAAA-AT
*
1325893 ATCAAAATTATATAAAAAAT
1 ATCAAAATTACATAAAAAAT
1325913 ATC
1 ATC
1325916 TTTATAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 11 0.29
21 22 0.58
22 5 0.13
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (20 bp):
ATCAAAATTACATAAAAAAT
Found at i:1326418 original size:3 final size:3
Alignment explanation
Indices: 1326410--1326453 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1326400 TTTGAAAACC
1326410 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1326454 ACAATACGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1330625 original size:34 final size:34
Alignment explanation
Indices: 1330558--1330628 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
1330548 TATTTGTATT
* *
1330558 TATTTTTTATATTTAAAATATTATATTTTTTATA
1 TATTTTTGATATTTAAAATATTATATTTATTATA
1330592 TATTTTTGATATGTTAATAAT-TTAT-TTTATTATA
1 TATTTTTGATAT-TTAA-AATATTATATTTATTATA
1330626 TAT
1 TAT
1330629 ATATATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 22 0.67
35 8 0.24
36 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (34 bp):
TATTTTTGATATTTAAAATATTATATTTATTATA
Found at i:1330742 original size:19 final size:18
Alignment explanation
Indices: 1330712--1330773 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
1330702 TATTATTTAA
1330712 AATATTATAAATTTATGT
1 AATATTATAAATTTATGT
1330730 AATATTAATAAATATT-TGT
1 AATATT-ATAAAT-TTATGT
* * *
1330749 TATATTTGTATATTTATGT
1 AATA-TTATAAATTTATGT
*
1330768 CATATT
1 AATATT
1330774 TATTTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 10 0.28
19 22 0.61
20 4 0.11
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (18 bp):
AATATTATAAATTTATGT
Found at i:1330804 original size:24 final size:25
Alignment explanation
Indices: 1330777--1330833 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 25
1330767 TCATATTTAT
1330777 TTTTTTATATTATGTTTTAAT-TAA
1 TTTTTTATATTATGTTTTAATGTAA
* * *
1330801 -TTTTTA-ATTTTGTTTTCATGTTA
1 TTTTTTATATTATGTTTTAATGTAA
1330824 TTTTTTATAT
1 TTTTTTATAT
1330834 ATTTAAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 11 0.41
23 8 0.30
24 6 0.22
25 2 0.07
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (25 bp):
TTTTTTATATTATGTTTTAATGTAA
Found at i:1330938 original size:10 final size:10
Alignment explanation
Indices: 1330923--1330953 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1330913 GTATCATATA
1330923 TATTTTTTAT
1 TATTTTTTAT
1330933 TATTTTTTAT
1 TATTTTTTAT
1330943 TATTTTTTAT
1 TATTTTTTAT
1330953 T
1 T
1330954 TATATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:1330964 original size:21 final size:20
Alignment explanation
Indices: 1330918--1330964 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1330908 TATTCGTATC
*
1330918 ATATATATTTTTTATTATTTT
1 ATAT-TATTTTTTATTATATT
*
1330939 TTATTATTTTTTATTTATATT
1 ATATTATTTTTTA-TTATATT
1330960 ATATT
1 ATATT
1330965 CATATCGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
ATATTATTTTTTATTATATT
Found at i:1331203 original size:29 final size:26
Alignment explanation
Indices: 1331151--1331203 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
1331141 TGTATTTAAA
*
1331151 ATATTATATTTTTATATATTTTTTTC
1 ATATTATATTTTTATATATATTTTTC
1331177 ATATTAATAATTTATTATATATATTTT
1 ATATT-AT-ATTT-TTATATATATTTT
1331204 ATATTTACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 2 0.09
28 4 0.17
29 12 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
ATATTATATTTTTATATATATTTTTC
Found at i:1331709 original size:15 final size:16
Alignment explanation
Indices: 1331673--1331712 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1331663 TTTAATATTT
*
1331673 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
1331690 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1331705 ATAAAATT
1 ATAAAATT
1331713 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1331715 original size:16 final size:17
Alignment explanation
Indices: 1331673--1331715 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1331663 TTTAATATTT
*
1331673 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
1331690 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
1331705 ATAAAATTTAT
1 ATAAAATTTAT
1331716 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1332782 original size:28 final size:27
Alignment explanation
Indices: 1332715--1332785 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 27
1332705 TTTTTATTAA
* *
1332715 AAATAATTAAATATTAAAAATATAGTG
1 AAATAATTAATTTTTAAAAATATAGTG
* * * * *
1332742 AATTATTTTATTTTTAAATAATATATTT
1 AAATAATTAATTTTTAAA-AATATAGTG
1332770 AAATAATTAATTTTTA
1 AAATAATTAATTTTTA
1332786 CATTAACTTA
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
27 13 0.39
28 20 0.61
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (27 bp):
AAATAATTAATTTTTAAAAATATAGTG
Found at i:1332900 original size:18 final size:21
Alignment explanation
Indices: 1332859--1332901 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1332849 AATTTATTTT
*
1332859 ATAATTAAATTTTTATTAATA
1 ATAATTAAATATTTATTAATA
1332880 ATAATTAAA-ATTTA-TAA-A
1 ATAATTAAATATTTATTAATA
1332898 ATAA
1 ATAA
1332902 AAAAAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 4 0.19
21 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATTAAATATTTATTAATA
Found at i:1336541 original size:9 final size:9
Alignment explanation
Indices: 1336513--1336544 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
1336503 TTTGATATCG
1336513 TATTT-TAA
1 TATTTATAA
1336521 TATTTA-AA
1 TATTTATAA
1336529 TATTTATAA
1 TATTTATAA
1336538 TATTTAT
1 TATTTAT
1336545 TTATAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 13 0.59
9 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTTATAA
Found at i:1336545 original size:29 final size:30
Alignment explanation
Indices: 1336491--1336554 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
1336481 TTTAAAAAAT
* *
1336491 ATATTTATATATTTTGATATCGTATTT-TA
1 ATATTTAAATATTTTAATATCGTATTTATA
*
1336520 ATATTTAAATATTTATAATAT-TTATTTATA
1 ATATTTAAATATTT-TAATATCGTATTTATA
1336550 A-ATTT
1 ATATTT
1336555 TATTTAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (30 bp):
ATATTTAAATATTTTAATATCGTATTTATA
Found at i:1336574 original size:24 final size:24
Alignment explanation
Indices: 1336547--1336593 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1336537 ATATTTATTT
1336547 ATAAAT-TTTATTTAATTTATAAAA
1 ATAAATATTTA-TTAATTTATAAAA
*
1336571 ATAAATATTTATTATTTTATAAA
1 ATAAATATTTATTAATTTATAAA
1336594 TAATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATAAATATTTATTAATTTATAAAA
Found at i:1336594 original size:18 final size:17
Alignment explanation
Indices: 1336571--1336611 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1336561 ATTTATAAAA
*
1336571 ATAAATATTTATTATTTT
1 ATAAATAATTATT-TTTT
1336589 ATAAATAATTATTTTTT
1 ATAAATAATTATTTTTT
*
1336606 AAAAAT
1 ATAAAT
1336612 GTAATACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAAATAATTATTTTTT
Found at i:1339792 original size:12 final size:12
Alignment explanation
Indices: 1339775--1339809 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1339765 AAATATGAAT
1339775 AATTAAATTTAA
1 AATTAAATTTAA
*
1339787 AATTAAATATAA
1 AATTAAATTTAA
*
1339799 AAATAAATTTA
1 AATTAAATTTA
1339810 TTTTTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AATTAAATTTAA
Found at i:1340166 original size:20 final size:21
Alignment explanation
Indices: 1340141--1340180 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1340131 ATTATAAATT
*
1340141 TTAAAT-TAATTTATTATTTG
1 TTAAATATAATTTAATATTTG
*
1340161 TTAAATATACTTTAATATTT
1 TTAAATATAATTTAATATTT
1340181 ATACCCTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTAAATATAATTTAATATTTG
Found at i:1340945 original size:14 final size:14
Alignment explanation
Indices: 1340915--1340956 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1340905 AAATATTATT
*
1340915 ATTAAAAAATTAA-A
1 ATTATAAAA-TAATA
1340929 ATTATAAAATAATA
1 ATTATAAAATAATA
*
1340943 ATTATAATATAATA
1 ATTATAAAATAATA
1340957 TCATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 3 0.12
14 22 0.88
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTATAAAATAATA
Found at i:1341219 original size:6 final size:6
Alignment explanation
Indices: 1341208--1341239 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1341198 GGGCGAGTTG
*
1341208 AGAACC AGAACC AGAACC AGAACC AGAGCC AG
1 AGAACC AGAACC AGAACC AGAACC AGAACC AG
1341240 GCCAGGCCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.47, C:0.31, G:0.22, T:0.00
Consensus pattern (6 bp):
AGAACC
Found at i:1344185 original size:22 final size:22
Alignment explanation
Indices: 1344139--1344201 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 22
1344129 AAACATTAAG
* *
1344139 ATAATTAAATTTAACTTACTCA
1 ATAATCAAATTTAACTTAATCA
*
1344161 ATAACTCAAATTTTACTTAAT-A
1 ATAA-TCAAATTTAACTTAATCA
* *
1344183 ATAATTAAATTTAAATTAA
1 ATAATCAAATTTAACTTAA
1344202 ATTTTTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 12 0.35
22 9 0.26
23 13 0.38
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAATCAAATTTAACTTAATCA
Found at i:1344891 original size:22 final size:21
Alignment explanation
Indices: 1344849--1344911 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
1344839 TTGTATAAAA
1344849 ATATTAAA-TTAT-TA-TTTT
1 ATATTAAATTTATATATTTTT
1344867 ATATTAATATTTATATATTTTT
1 ATATTAA-ATTTATATATTTTT
* *
1344889 ATAAATAAATTTAAATATTTTT
1 AT-ATTAAATTTATATATTTTT
1344911 A
1 A
1344912 AAATAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 7 0.18
19 1 0.03
20 4 0.11
21 2 0.05
22 20 0.53
23 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTAAATTTATATATTTTT
Found at i:1344915 original size:21 final size:22
Alignment explanation
Indices: 1344875--1344919 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1344865 TTATATTAAT
*
1344875 ATTTATATATTTTTATAAATAA
1 ATTTAAATATTTTTATAAATAA
1344897 ATTTAAATATTTTTA-AAATAA
1 ATTTAAATATTTTTATAAATAA
1344918 AT
1 AT
1344920 AATAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAAATATTTTTATAAATAA
Found at i:1344930 original size:27 final size:25
Alignment explanation
Indices: 1344889--1344940 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
1344879 ATATATTTTT
*
1344889 ATAAATAAATTTAAATATTTTTAAA
1 ATAAATAAATTTAAATAATTTTAAA
1344914 ATAAATAATAATTTAAATAATTTTAAA
1 ATAAAT-A-AATTTAAATAATTTTAAA
1344941 TCATAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.25
26 1 0.04
27 17 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAAATAAATTTAAATAATTTTAAA
Found at i:1352213 original size:17 final size:17
Alignment explanation
Indices: 1352191--1352225 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1352181 CGGGACCGTT
1352191 CCTACTCTCCTGATGAC
1 CCTACTCTCCTGATGAC
1352208 CCTACTCTCCTGATGAC
1 CCTACTCTCCTGATGAC
1352225 C
1 C
1352226 GATACTACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.43, G:0.11, T:0.29
Consensus pattern (17 bp):
CCTACTCTCCTGATGAC
Found at i:1352254 original size:42 final size:42
Alignment explanation
Indices: 1352208--1352493 Score: 165
Period size: 42 Copynumber: 6.8 Consensus size: 42
1352198 TCCTGATGAC
* * *
1352208 CCTACTCTCCTGATGACCGATACTACAGAAGGCGTGAAAGGC
1 CCTACTCACCTGATGACAGATACTACAGAAGGCGTGAAAGGT
* * * ** * * * * ** *
1352250 CCTACTCACCAGATTATATTTACTACCGTAGGTGGGATTGTT
1 CCTACTCACCTGATGACAGATACTACAGAAGGCGTGAAAGGT
* *
1352292 CCTACTCACCTGATGATC-GATACTATA-ACAGGCATGAAAGGT
1 CCTACTCACCTGATGA-CAGATACTACAGA-AGGCGTGAAAGGT
* * * ** *
1352334 CCTACTCACCAGATGACAGTTACTATCA-TAGGCGTGACTGTT
1 CCTACTCACCTGATGACAGATACTA-CAGAAGGCGTGAAAGGT
* *
1352376 CCTATTCACCTGATGATC-GATACTACAGAAGGCATGAAAGGT
1 CCTACTCACCTGATGA-CAGATACTACAGAAGGCGTGAAAGGT
* * * * *
1352418 CCTACTC-CCTAGATGACAGTTACTACCA-TAGGCGGGACCA-TT
1 CCTACTCACCT-GATGACAGATACTA-CAGAAGGCGTGA-AAGGT
*
1352460 CCTATTCACCTGATGATC-GATACTACAGAAGGCG
1 CCTACTCACCTGATGA-CAGATACTACAGAAGGCG
1352494 GGATCGGTAC
Statistics
Matches: 176, Mismatches: 55, Indels: 26
0.68 0.21 0.10
Matches are distributed among these distances:
41 9 0.05
42 158 0.90
43 9 0.05
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (42 bp):
CCTACTCACCTGATGACAGATACTACAGAAGGCGTGAAAGGT
Found at i:1352357 original size:84 final size:84
Alignment explanation
Indices: 1352208--1352492 Score: 385
Period size: 84 Copynumber: 3.4 Consensus size: 84
1352198 TCCTGATGAC
* * * * * * *
1352208 CCTACTCTCCTGATGACCGATACTACAGAAGGCGTGAAAGGCCCTACTCACCAGATTATATTTAC
1 CCTACTCACCTGATGATCGATACTACAGAAGGCATGAAAGGTCCTACTCACCAGATGACAGTTAC
* * *
1352273 TACCGTAGGTGGGATTGTT
66 TACCATAGGCGGGACTGTT
*
1352292 CCTACTCACCTGATGATCGATACTATA-ACAGGCATGAAAGGTCCTACTCACCAGATGACAGTTA
1 CCTACTCACCTGATGATCGATACTACAGA-AGGCATGAAAGGTCCTACTCACCAGATGACAGTTA
* *
1352356 CTATCATAGGCGTGACTGTT
65 CTACCATAGGCGGGACTGTT
*
1352376 CCTATTCACCTGATGATCGATACTACAGAAGGCATGAAAGGTCCTACTC-CCTAGATGACAGTTA
1 CCTACTCACCTGATGATCGATACTACAGAAGGCATGAAAGGTCCTACTCACC-AGATGACAGTTA
**
1352440 CTACCATAGGCGGGACCATT
65 CTACCATAGGCGGGACTGTT
*
1352460 CCTATTCACCTGATGATCGATACTACAGAAGGC
1 CCTACTCACCTGATGATCGATACTACAGAAGGC
1352493 GGGATCGGTA
Statistics
Matches: 179, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
83 3 0.02
84 175 0.98
85 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (84 bp):
CCTACTCACCTGATGATCGATACTACAGAAGGCATGAAAGGTCCTACTCACCAGATGACAGTTAC
TACCATAGGCGGGACTGTT
Found at i:1357452 original size:45 final size:44
Alignment explanation
Indices: 1357365--1357460 Score: 120
Period size: 47 Copynumber: 2.1 Consensus size: 44
1357355 ATATAATCTA
** *
1357365 ATATTATCTGACACAGGTATGTTAATTTTTTGAAAGTTTTTTTTC
1 ATATTATCTGACACAGGTATGAAAATTTTTTCAAAG-TTTTTTTC
*
1357410 ATATTATCTGACACAGTTATGCAAAATTGTTTTCAAAGTTTTTTTTC
1 ATATTATCTGACACAGGTATG-AAAATT-TTTTCAAAG-TTTTTTTC
1357457 ATAT
1 ATAT
1357461 ATTTGGAGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 20 0.44
46 4 0.09
47 21 0.47
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.49
Consensus pattern (44 bp):
ATATTATCTGACACAGGTATGAAAATTTTTTCAAAGTTTTTTTC
Found at i:1358055 original size:62 final size:62
Alignment explanation
Indices: 1357958--1358081 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 62
1357948 AGTTCATTGG
* *
1357958 ATTATTCAACTAGGAAATAAATGAAACCAGGAAAAACTTACAGGAAATCCTTCTAACTAGAT
1 ATTATTCAACTAGAAAATAAATGAAACCAGGAAAAACTTACAGGAAACCCTTCTAACTAGAT
1358020 ATTATTCAACTAGAAAATAAATGAAACCAGGAAAAACTTACAGGAAACCCTTCTAACTAGAT
1 ATTATTCAACTAGAAAATAAATGAAACCAGGAAAAACTTACAGGAAACCCTTCTAACTAGAT
1358082 TGTTGTTAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (62 bp):
ATTATTCAACTAGAAAATAAATGAAACCAGGAAAAACTTACAGGAAACCCTTCTAACTAGAT
Found at i:1361834 original size:12 final size:14
Alignment explanation
Indices: 1361819--1361850 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1361809 TTAAAATAAA
1361819 AATTAAA-TT-TTT
1 AATTAAATTTATTT
1361831 AATTAAATTTATTT
1 AATTAAATTTATTT
1361845 AATTAA
1 AATTAA
1361851 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 2 0.11
14 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTAAATTTATTT
Found at i:1362081 original size:8 final size:8
Alignment explanation
Indices: 1362070--1362126 Score: 61
Period size: 7 Copynumber: 7.8 Consensus size: 8
1362060 CTACATTACT
1362070 TTTAAATA
1 TTTAAATA
1362078 TTT-AATA
1 TTTAAATA
*
1362085 -TTAACT-
1 TTTAAATA
1362091 TTTAAATA
1 TTTAAATA
1362099 TTT-AATA
1 TTTAAATA
*
1362106 TTTTAATA
1 TTTAAATA
1362114 -TTAAATA
1 TTTAAATA
1362121 TTTAAA
1 TTTAAA
1362127 AGTAATCTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
6 2 0.05
7 24 0.59
8 15 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAATA
Found at i:1362092 original size:21 final size:22
Alignment explanation
Indices: 1362067--1362125 Score: 86
Period size: 21 Copynumber: 2.7 Consensus size: 22
1362057 ATACTACATT
1362067 ACTTTTAAATATTTAATA-TTA
1 ACTTTTAAATATTTAATATTTA
1362088 ACTTTTAAATATTTAATATTTTA
1 ACTTTTAAATATTTAATA-TTTA
*
1362111 A-TATTAAATATTTAA
1 ACTTTTAAATATTTAA
1362126 AAGTAATCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 18 0.51
22 13 0.37
23 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
ACTTTTAAATATTTAATATTTA
Found at i:1362113 original size:15 final size:15
Alignment explanation
Indices: 1362074--1362123 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1362064 ATTACTTTTA
1362074 AATA-TTTAATA-TT
1 AATATTTTAATATTT
*
1362087 AACT-TTTAAATATTT
1 AA-TATTTTAATATTT
*
1362102 AATATTTTAATATTA
1 AATATTTTAATATTT
1362117 AATATTT
1 AATATTT
1362124 AAAAGTAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.27
15 20 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
AATATTTTAATATTT
Found at i:1362355 original size:20 final size:20
Alignment explanation
Indices: 1362310--1362361 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
1362300 ATATGAATAT
1362310 AATTTTAAATAATGAAATGA
1 AATTTTAAATAATGAAATGA
** *
1362330 TTTTTTAAATCAAT-AAATTA
1 AATTTTAAAT-AATGAAATGA
*
1362350 AATTTTAGATAA
1 AATTTTAAATAA
1362362 ATAATTTGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (20 bp):
AATTTTAAATAATGAAATGA
Found at i:1365800 original size:20 final size:20
Alignment explanation
Indices: 1365762--1365800 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1365752 TATTTTTATT
*
1365762 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
1365782 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
1365801 TTAGGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:1365868 original size:11 final size:11
Alignment explanation
Indices: 1365834--1365868 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1365824 TAATTTATTT
1365834 TTATATTTATA
1 TTATATTTATA
*
1365845 TAATATTTATA
1 TTATATTTATA
*
1365856 TTATTTTTATA
1 TTATATTTATA
1365867 TT
1 TT
1365869 TTAATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1372058 original size:30 final size:30
Alignment explanation
Indices: 1372022--1372106 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
1372012 TTTGAAATGT
*
1372022 TTTAATTTTTATTTAAATAAATTTTTAATA
1 TTTAATTTTTATCTAAATAAATTTTTAATA
* * * *
1372052 TTTAA---TT-TGT--ATAAACTCTTAATT
1 TTTAATTTTTATCTAAATAAATTTTTAATA
1372076 TTTAATTTTTATCTAAATAAATTTTTAATA
1 TTTAATTTTTATCTAAATAAATTTTTAATA
1372106 T
1 T
1372107 AAAATTAACT
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
24 16 0.39
26 2 0.05
27 4 0.10
28 2 0.05
30 17 0.41
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTAATTTTTATCTAAATAAATTTTTAATA
Found at i:1372059 original size:24 final size:23
Alignment explanation
Indices: 1372016--1372083 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
1372006 AATAAGTTTG
*
1372016 AAATGTTTTAATTTTTATTTAAAT
1 AAAT-TTTTAATTTTAATTTAAAT
**
1372040 AAATTTTTAATATTTAATTTGTAT
1 AAATTTTTAAT-TTTAATTTAAAT
* *
1372064 AAACTCTTAATTTTTAATTT
1 AAATTTTTAA-TTTTAATTT
1372084 TTATCTAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 7 0.19
24 29 0.78
25 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (23 bp):
AAATTTTTAATTTTAATTTAAAT
Found at i:1373452 original size:2 final size:2
Alignment explanation
Indices: 1373445--1373484 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1373435 TGATTCCCGA
1373445 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1373485 ATATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1373489 original size:2 final size:2
Alignment explanation
Indices: 1373484--1373511 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1373474 TCTCTCTCTC
1373484 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
1373512 ATAGTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1376701 original size:17 final size:18
Alignment explanation
Indices: 1376681--1376716 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1376671 TCGTAGAAAT
1376681 ATATTTAATAT-TTTAAA
1 ATATTTAATATATTTAAA
*
1376698 ATATTTTATATATTTAAA
1 ATATTTAATATATTTAAA
1376716 A
1 A
1376717 AAAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTAATATATTTAAA
Found at i:1376717 original size:19 final size:19
Alignment explanation
Indices: 1376677--1376717 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1376667 TGTATCGTAG
*
1376677 AAATATATTTAATATTTTA
1 AAATATATTTAATATTTAA
1376696 AAATAT-TTTATATATTTAA
1 AAATATATTTA-ATATTTAA
1376715 AAA
1 AAA
1376718 AAATTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATATTTAATATTTAA
Found at i:1377346 original size:29 final size:31
Alignment explanation
Indices: 1377312--1377388 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 31
1377302 TTATATTCGA
1377312 ATATATATATATAATATTTTAT-AAATTT-T
1 ATATATATATATAATATTTTATCAAATTTAT
* * * *
1377341 TTATATATTTA-AAAATTTTTATCATATTTAT
1 ATATATATATATAATA-TTTTATCAAATTTAT
*
1377372 ATATATATATATTATAT
1 ATATATATATATAATAT
1377389 ATACGAGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
28 3 0.08
29 15 0.42
30 5 0.14
31 11 0.31
32 2 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
ATATATATATATAATATTTTATCAAATTTAT
Found at i:1377356 original size:19 final size:18
Alignment explanation
Indices: 1377325--1377370 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1377315 TATATATATA
*
1377325 ATAT-TTTATAAATTTTTT
1 ATATATTTA-AAAATTTTT
1377343 ATATATTTAAAAATTTTT
1 ATATATTTAAAAATTTTT
1377361 ATCATATTTA
1 AT-ATATTTA
1377371 TATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATATTTAAAAATTTTT
Found at i:1377650 original size:19 final size:19
Alignment explanation
Indices: 1377601--1377652 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 19
1377591 AATATTTTAA
1377601 ATTTTATATATTTAAA--AT
1 ATTTT-TATATTTAAATTAT
*
1377619 ATTATTATA---AAATTAT
1 ATTTTTATATTTAAATTAT
1377635 ATTTTTATATTTAAATTA
1 ATTTTTATATTTAAATTA
1377653 AAATATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.11
16 10 0.37
17 4 0.15
18 4 0.15
19 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTATATTTAAATTAT
Found at i:1378091 original size:16 final size:16
Alignment explanation
Indices: 1378070--1378105 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1378060 TTTAAACCAG
* *
1378070 ACAAGAGCTTAAGTTC
1 ACAAGAACTTAAATTC
1378086 ACAAGAACTTAAATTC
1 ACAAGAACTTAAATTC
1378102 ACAA
1 ACAA
1378106 CCAAACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.22
Consensus pattern (16 bp):
ACAAGAACTTAAATTC
Found at i:1383638 original size:7 final size:7
Alignment explanation
Indices: 1383622--1383672 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
1383612 TATAATTATT
*
1383622 TTTAAAA
1 TTTAATA
1383629 TTTAATA
1 TTTAATA
1383636 TTTAATAAA
1 TTTAAT--A
1383645 TTTAATA
1 TTTAATA
*
1383652 TTTAAAA
1 TTTAATA
1383659 TTTTAATA
1 -TTTAATA
1383667 -TTAATA
1 TTTAATA
1383673 ATTATTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
6 6 0.16
7 19 0.50
8 6 0.16
9 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
TTTAATA
Found at i:1383645 original size:16 final size:16
Alignment explanation
Indices: 1383626--1383673 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
1383616 ATTATTTTTA
1383626 AAATTTAATATTTAAT
1 AAATTTAATATTTAAT
1383642 AAATTTAATATTTAA-
1 AAATTTAATATTTAAT
*
1383657 AATTTTAATA-TTAAT
1 AAATTTAATATTTAAT
1383672 AA
1 AA
1383674 TTATTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 4 0.13
15 11 0.37
16 15 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTAATATTTAAT
Found at i:1383654 original size:23 final size:24
Alignment explanation
Indices: 1383622--1383666 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1383612 TATAATTATT
*
1383622 TTTAAAATTTAATA-TTTAATAAA
1 TTTAAAATTTAAAATTTTAATAAA
*
1383645 TTTAATATTTAAAATTTTAATA
1 TTTAAAATTTAAAATTTTAATA
1383667 TTAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAAAATTTAAAATTTTAATAAA
Found at i:1383675 original size:15 final size:16
Alignment explanation
Indices: 1383629--1383675 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 16
1383619 ATTTTTAAAA
*
1383629 TTTAATATTTAATAAA
1 TTTAATATTTAATAAT
1383645 TTTAATATTTAA-AAT
1 TTTAATATTTAATAAT
1383660 TTTAATA-TTAATAAT
1 TTTAATATTTAATAAT
1383675 T
1 T
1383676 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 4 0.14
15 13 0.45
16 12 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATATTTAATAAT
Found at i:1383684 original size:30 final size:29
Alignment explanation
Indices: 1383608--1383673 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
1383598 ATCGAATTAA
*
1383608 TTAATATAA-TTATTTTTAAAATTTAATAT
1 TTAATA-AATTTATATTTAAAATTTAATAT
1383637 TTAATAAATTTAATATTTAAAATTTTAATA-
1 TTAATAAATTT-ATATTTAAAA-TTTAATAT
1383667 TTAATAA
1 TTAATAA
1383674 TTATTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 2 0.06
29 8 0.24
30 16 0.48
31 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTAATAAATTTATATTTAAAATTTAATAT
Found at i:1384381 original size:14 final size:15
Alignment explanation
Indices: 1384364--1384398 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
1384354 ATTGATTTAA
1384364 TTTTTATTT-TGATT
1 TTTTTATTTATGATT
1384378 TTTTTATTTATGATT
1 TTTTTATTTATGATT
1384393 TATTTT
1 T-TTTT
1384399 TGGATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 6 0.32
16 4 0.21
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (15 bp):
TTTTTATTTATGATT
Found at i:1384670 original size:19 final size:19
Alignment explanation
Indices: 1384646--1384694 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1384636 AGTTAATTCG
*
1384646 TTTTAATTTAAAATTATAT
1 TTTTAATTTAAAATAATAT
*
1384665 TTTTAAATTAAAATAATAT
1 TTTTAATTTAAAATAATAT
1384684 TTTT-ATTTAAA
1 TTTTAATTTAAA
1384695 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTAATTTAAAATAATAT
Found at i:1384700 original size:19 final size:18
Alignment explanation
Indices: 1384646--1384696 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1384636 AGTTAATTCG
*
1384646 TTTTAATTTAAAATT-ATA
1 TTTTTATTT-AAATTAATA
* *
1384664 TTTTTAAATTAAAATAATA
1 TTTTT-ATTTAAATTAATA
1384683 TTTTTATTTAAATT
1 TTTTTATTTAAATT
1384697 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTATTTAAATTAATA
Found at i:1384735 original size:21 final size:21
Alignment explanation
Indices: 1384687--1384740 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1384677 ATAATATTTT
1384687 TATTTAAAT-TTAATTAAAAA
1 TATTTAAATATTAATTAAAAA
*
1384707 TATATAAATATTAA-TATAAAA
1 TATTTAAATATTAATTA-AAAA
*
1384728 TTTTTAAACTATT
1 TATTTAAA-TATT
1384741 TTTAACAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.36
21 14 0.50
22 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTAAATATTAATTAAAAA
Found at i:1385372 original size:16 final size:16
Alignment explanation
Indices: 1385351--1385384 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1385341 CTATATAAAT
*
1385351 ATTAAATTTAATCTAA
1 ATTAAATTAAATCTAA
*
1385367 ATTAAATTAAATTTAA
1 ATTAAATTAAATCTAA
1385383 AT
1 AT
1385385 ATTTTAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAATTAAATCTAA
Found at i:1385966 original size:2 final size:2
Alignment explanation
Indices: 1385959--1385986 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1385949 TTTATTAATT
1385959 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
1385987 AATTTTAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1387556 original size:31 final size:32
Alignment explanation
Indices: 1387476--1387542 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
1387466 ATAATAAGAT
* *
1387476 ATAAATAAATAAATATTTTTAAATTTATATTAA
1 ATAAAT-AATTAATATATTTAAATTTATATTAA
1387509 ATAAATAATTAATATATTTAAATTTATA-TAA
1 ATAAATAATTAATATATTTAAATTTATATTAA
1387540 ATA
1 ATA
1387543 TAAAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 6 0.19
32 20 0.62
33 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
ATAAATAATTAATATATTTAAATTTATATTAA
Found at i:1387594 original size:28 final size:28
Alignment explanation
Indices: 1387563--1387616 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1387553 ATATATAATT
1387563 ATAATATATAAA-AATATAAAAATTAAAA
1 ATAA-ATATAAATAATATAAAAATTAAAA
* * *
1387591 ATAAATTTAAATAATATTAAATTTAA
1 ATAAATATAAATAATATAAAAATTAA
1387617 CTGCTACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
ATAAATATAAATAATATAAAAATTAAAA
Found at i:1387883 original size:20 final size:21
Alignment explanation
Indices: 1387858--1387896 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1387848 TAATTAAATA
*
1387858 TTAAATATATAAT-TTTAATG
1 TTAAATAAATAATATTTAATG
1387878 TTAAATAAATAATATTTAA
1 TTAAATAAATAATATTTAA
1387897 CATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TTAAATAAATAATATTTAATG
Found at i:1388491 original size:32 final size:32
Alignment explanation
Indices: 1388455--1388515 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1388445 TTTCTTTTAT
*
1388455 TTTTAAAATTGATTTTATAGTTTTTTTAATTG
1 TTTTAAAATTGATTTTATAGTTATTTTAATTG
*
1388487 TTTTAAAGTTGATTTTATAGTTATTTTAA
1 TTTTAAAATTGATTTTATAGTTATTTTAA
1388516 AAAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.61
Consensus pattern (32 bp):
TTTTAAAATTGATTTTATAGTTATTTTAATTG
Found at i:1388502 original size:12 final size:12
Alignment explanation
Indices: 1388455--1388516 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
1388445 TTTCTTTTAT
*
1388455 TTTTAAAATTGA
1 TTTTAAAGTTGA
*
1388467 TTTTATAGTT--
1 TTTTAAAGTTGA
*
1388477 TTTTTAA-TTG-
1 TTTTAAAGTTGA
1388487 TTTTAAAGTTGA
1 TTTTAAAGTTGA
*
1388499 TTTTATAGTT-A
1 TTTTAAAGTTGA
1388510 TTTTAAA
1 TTTTAAA
1388517 AAATAATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
9 2 0.05
10 11 0.28
11 10 0.25
12 17 0.43
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (12 bp):
TTTTAAAGTTGA
Found at i:1388502 original size:21 final size:21
Alignment explanation
Indices: 1388461--1388516 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
1388451 TTATTTTTAA
* *
1388461 AATTGATTTTATAGTTTTTTT
1 AATTGATTTTAAAGTTATTTT
1388482 AATTG-TTTTAAAGTTGATTTT
1 AATTGATTTTAAAGTT-ATTTT
1388503 ATAGTT-ATTTTAAA
1 A-A-TTGATTTTAAA
1388517 AAATAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 9 0.31
21 10 0.34
22 1 0.03
23 9 0.31
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
AATTGATTTTAAAGTTATTTT
Found at i:1390357 original size:12 final size:12
Alignment explanation
Indices: 1390310--1390359 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 12
1390300 TAATCTAATC
1390310 TAATTTATCAAAT
1 TAATTTA-CAAAT
*
1390323 AGTAATTAACAAAT
1 --TAATTTACAAAT
1390337 TAATGTTACAAAT
1 TAAT-TTACAAAT
1390350 TAATTTACAA
1 TAATTTACAA
1390360 TGATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 10 0.31
13 11 0.34
14 5 0.16
15 6 0.19
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (12 bp):
TAATTTACAAAT
Found at i:1393743 original size:20 final size:20
Alignment explanation
Indices: 1393718--1393760 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1393708 AATTTCTTGC
1393718 TATTTTATCTAA-ATTATAAT
1 TATTTTATC-AATATTATAAT
*
1393738 TATTTTTTCAATATTATAAT
1 TATTTTATCAATATTATAAT
1393758 TAT
1 TAT
1393761 ATATATGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTATCAATATTATAAT
Found at i:1395163 original size:2 final size:2
Alignment explanation
Indices: 1395156--1395184 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1395146 TCCAAAAGAA
1395156 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 A
1395185 CAATATAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1397464 original size:2 final size:2
Alignment explanation
Indices: 1397452--1397480 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1397442 TAAATAATTC
1397452 AT AT A- 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
1397481 GAAGATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1398197 original size:11 final size:11
Alignment explanation
Indices: 1398168--1398210 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1398158 AAATTAACTA
*
1398168 TATAAATTAAT
1 TATAATTTAAT
1398179 TA-AATTTAAT
1 TATAATTTAAT
*
1398189 TATAATTTAAA
1 TATAATTTAAT
1398200 TATAATTTAAT
1 TATAATTTAAT
1398211 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATAATTTAAT
Found at i:1398198 original size:17 final size:16
Alignment explanation
Indices: 1398167--1398210 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
1398157 AAAATTAACT
*
1398167 ATATAAATTAA-TTAA
1 ATATAATTTAATTTAA
*
1398182 ATTTAATTATAATTTAA
1 ATATAATT-TAATTTAA
1398199 ATATAATTTAAT
1 ATATAATTTAAT
1398211 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAATTTAATTTAA
Found at i:1398204 original size:32 final size:31
Alignment explanation
Indices: 1398167--1398256 Score: 79
Period size: 32 Copynumber: 3.1 Consensus size: 31
1398157 AAAATTAACT
1398167 ATATAAATTAATTAAATTTAATTATAATTTAA
1 ATATAAATTAATTAAA-TTAATTATAATTTAA
*
1398199 ATATAATTTAA-TAAA--AA-TA-AA-TT--
1 ATATAAATTAATTAAATTAATTATAATTTAA
* *
1398222 ATGTAAATTAATTAAATTAAATTATGATTTAA
1 ATATAAATTAATTAAATT-AATTATAATTTAA
1398254 ATA
1 ATA
1398257 AGCTCATCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 18
0.66 0.07 0.27
Matches are distributed among these distances:
23 9 0.20
24 4 0.09
25 2 0.05
26 2 0.05
27 4 0.09
28 4 0.09
29 1 0.02
30 2 0.05
31 4 0.09
32 12 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (31 bp):
ATATAAATTAATTAAATTAATTATAATTTAA
Found at i:1398244 original size:14 final size:14
Alignment explanation
Indices: 1398170--1398245 Score: 52
Period size: 14 Copynumber: 5.5 Consensus size: 14
1398160 ATTAACTATA
1398170 TAAATTAATTAAAT
1 TAAATTAATTAAAT
* *
1398184 TTAATT-A-TAATT
1 TAAATTAATTAAAT
*
1398196 TAAATATAATTTAAT
1 TAAAT-TAATTAAAT
* *
1398211 AAAAATAAATT--AT
1 -TAAATTAATTAAAT
1398224 GTAAATTAATTAAAT
1 -TAAATTAATTAAAT
1398239 TAAATTA
1 TAAATTA
1398246 TGATTTAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
12 8 0.17
13 12 0.26
14 13 0.28
15 9 0.20
16 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (14 bp):
TAAATTAATTAAAT
Found at i:1399039 original size:2 final size:2
Alignment explanation
Indices: 1399032--1399082 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
1399022 CTAAATTTAA
* *
1399032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AC AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1399073 AT TT AT AT AT
1 AT AT AT AT AT
1399083 TCATACAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1399156 original size:2 final size:2
Alignment explanation
Indices: 1399149--1399179 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1399139 TAATAGATTC
1399149 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 A
1399180 AACACACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1399426 original size:166 final size:167
Alignment explanation
Indices: 1399163--1399513 Score: 623
Period size: 166 Copynumber: 2.1 Consensus size: 167
1399153 ATATATATAT
* *
1399163 ATATATATATATATATAAACACACATGTACATGTTCTTTTTTCTATTTTCTTTGGGTTTGGCAAA
1 ATATATATATATATAT-AACACACATATACATGTTCCTTTTTCTATTTTCTTTGGGTTTGGCAAA
* *
1399228 ATTAATTATCAAAGAAATAATAACATATAGAAAATCAAGAAAGCAAGATGGAGGTTGGTTGAAAT
65 ATTAATTATCAAAGAAATAATAAAATATAGAAAATCAAGAAAGCAAGATGGAGGATGGTTGAAAT
1399293 TAAGGGCATGAGGCAATAGTAAAAGTAGAGACATGAGG
130 TAAGGGCATGAGGCAATAGTAAAAGTAGAGACATGAGG
1399331 ATATATATATATATATAA-ACACATATACATGTTCCTTTTTCTATTTTCTTTGGGTTTGGCAAAA
1 ATATATATATATATATAACACACATATACATGTTCCTTTTTCTATTTTCTTTGGGTTTGGCAAAA
*
1399395 TTAATTATTAAAGAAATAATAAAATATAGAAAATCAAGAAAGCAAGATGGAGGATGGTTGAAATT
66 TTAATTATCAAAGAAATAATAAAATATAGAAAATCAAGAAAGCAAGATGGAGGATGGTTGAAATT
* *
1399460 AAGGGCATGGGGCAATAGTAAAAGTAGAGATATGAGG
131 AAGGGCATGAGGCAATAGTAAAAGTAGAGACATGAGG
1399497 ATATATATATATATATA
1 ATATATATATATATATA
1399514 TATATATATA
Statistics
Matches: 176, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
166 158 0.90
167 2 0.01
168 16 0.09
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (167 bp):
ATATATATATATATATAACACACATATACATGTTCCTTTTTCTATTTTCTTTGGGTTTGGCAAAA
TTAATTATCAAAGAAATAATAAAATATAGAAAATCAAGAAAGCAAGATGGAGGATGGTTGAAATT
AAGGGCATGAGGCAATAGTAAAAGTAGAGACATGAGG
Found at i:1399504 original size:2 final size:2
Alignment explanation
Indices: 1399497--1399524 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1399487 AGATATGAGG
1399497 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
1399525 TGATATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1401154 original size:18 final size:18
Alignment explanation
Indices: 1401131--1401169 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1401121 TGCTTTATTA
*
1401131 ATATATTACATTTAAAAT
1 ATATATAACATTTAAAAT
*
1401149 ATATATAATATTTAAAAT
1 ATATATAACATTTAAAAT
1401167 ATA
1 ATA
1401170 ATTGATTTTA
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:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATAACATTTAAAAT
Found at i:1401385 original size:13 final size:13
Alignment explanation
Indices: 1401363--1401393 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1401353 ATCATCCCTC
*
1401363 AAGTCCAAGTCCA
1 AAGTCAAAGTCCA
1401376 AAGTCAAAGTCCA
1 AAGTCAAAGTCCA
1401389 AAGTC
1 AAGTC
1401394 TACACGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (13 bp):
AAGTCAAAGTCCA
Found at i:1405344 original size:20 final size:20
Alignment explanation
Indices: 1405321--1405390 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1405311 AAAAGCTACT
* *
1405321 TTTTTAAAATAAGTATATAG
1 TTTTTAAAATAAATAAATAG
* **
1405341 TTTTAAAAATAAATCGATAG
1 TTTTTAAAATAAATAAATAG
* *
1405361 TTTTTAAATATAATTAAATAT
1 TTTTTAAA-ATAAATAAATAG
1405382 TTTTTAAAA
1 TTTTTAAAA
1405391 AATTATTAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 24 0.60
21 16 0.40
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (20 bp):
TTTTTAAAATAAATAAATAG
Found at i:1405367 original size:21 final size:21
Alignment explanation
Indices: 1405320--1405391 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
1405310 AAAAAGCTAC
* * *
1405320 TTTTTTAAAATAAGTATATAG
1 TTTTTAAAAATAAATAAATAG
**
1405341 -TTTTAAAAATAAATCGATAG
1 TTTTTAAAAATAAATAAATAG
* * *
1405361 TTTTTAAATATAATTAAATAT
1 TTTTTAAAAATAAATAAATAG
1405382 TTTTTAAAAA
1 TTTTTAAAAA
1405392 ATTATTAATT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (21 bp):
TTTTTAAAAATAAATAAATAG
Found at i:1405405 original size:21 final size:20
Alignment explanation
Indices: 1405361--1405421 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
1405351 AAATCGATAG
*
1405361 TTTTTAAATATAATTA-AATAT
1 TTTTTAAAAAT-ATTATAAT-T
1405382 TTTTTAAAAA-ATTATTAATT
1 TTTTTAAAAATATTA-TAATT
1405402 TTTTTAAAAATATTATAATT
1 TTTTTAAAAATATTATAATT
1405422 AAAAATTAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 4 0.11
20 16 0.44
21 16 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTAAAAATATTATAATT
Found at i:1407229 original size:23 final size:23
Alignment explanation
Indices: 1407203--1407249 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1407193 TTTAATATGA
* *
1407203 ATTTATATTTATATATTATTAAT
1 ATTTAAATTTAAATATTATTAAT
1407226 ATTTAAATTTAAATATTATTAAT
1 ATTTAAATTTAAATATTATTAAT
1407249 A
1 A
1407250 AATTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTAAATTTAAATATTATTAAT
Found at i:1407259 original size:23 final size:22
Alignment explanation
Indices: 1407205--1407259 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1407195 TAATATGAAT
* *
1407205 TTATATTTATATATTATTAATAT
1 TTAT-TTTAAATATTATTAATAA
*
1407228 TTAAATTTAAATATTATTAATAAA
1 TT-ATTTTAAATATTATTAAT-AA
1407252 TTATTTTA
1 TTATTTTA
1407260 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTTTAAATATTATTAATAA
Found at i:1407300 original size:32 final size:33
Alignment explanation
Indices: 1407259--1407340 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
1407249 AAATTATTTT
*
1407259 ATTTTATTTTATTAATAAATATAAATGT-AA-A
1 ATTTTATTTTATTAATAAATATAAATATAAATA
*
1407290 ATTTTAATTTTTTTAA-AAA-ATAAATATAAATA
1 ATTTT-ATTTTATTAATAAATATAAATATAAATA
1407322 ATTTTA-TTTATTAATAAAT
1 ATTTTATTTTATTAATAAAT
1407341 TATATTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
30 14 0.33
31 14 0.33
32 15 0.35
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (33 bp):
ATTTTATTTTATTAATAAATATAAATATAAATA
Found at i:1407350 original size:25 final size:26
Alignment explanation
Indices: 1407308--1407371 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
1407298 TTTTTTAAAA
*
1407308 AATAAATATAAATAATTTTATTTATT
1 AATAAATATAAATAATTTAATTTATT
* *
1407334 AATAAAT-TATATTATTTAATTTATT
1 AATAAATATAAATAATTTAATTTATT
1407359 AATAATATATAAA
1 AATAA-ATATAAA
1407372 ATTATATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 20 0.62
26 9 0.28
27 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAAATATAAATAATTTAATTTATT
Found at i:1409917 original size:15 final size:16
Alignment explanation
Indices: 1409897--1409929 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1409887 TATTATTTAA
*
1409897 ATTTAATTA-TAAAAT
1 ATTTAAATATTAAAAT
1409912 ATTTAAATATTAAAAT
1 ATTTAAATATTAAAAT
1409928 AT
1 AT
1409930 ATTTATATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAAATATTAAAAT
Found at i:1410459 original size:18 final size:21
Alignment explanation
Indices: 1410417--1410459 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 21
1410407 ATTTTTATTT
*
1410417 AAATCTTTTAAAATATTAAAT
1 AAATCTTTTAAAATATTAAAC
1410438 AAAT-TTTT-AAAT-TTAAAC
1 AAATCTTTTAAAATATTAAAC
1410456 AAAT
1 AAAT
1410460 AATTAACTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 4 0.19
20 4 0.19
21 4 0.19
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATCTTTTAAAATATTAAAC
Done.