Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 8 of 25
Found at i:1297028 original size:18 final size:18
Alignment explanation
Indices: 1296976--1297028 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
1296966 ATATAAATAC
1296976 ATATTTTAAAATTTTATA
1 ATATTTTAAAATTTTATA
*
1296994 ATA---T-AAATTAT-TA
1 ATATTTTAAAATTTTATA
1297007 ATATTTTAAAATTTTATA
1 ATATTTTAAAATTTTATA
1297025 ATAT
1 ATAT
1297029 AAATTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 5 0.18
14 6 0.21
15 1 0.04
16 1 0.04
17 6 0.21
18 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTTAAAATTTTATA
Found at i:1297436 original size:25 final size:23
Alignment explanation
Indices: 1297385--1297438 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
1297375 TTGATTTATT
* * *
1297385 TTATATTATATTTATTTATATTT
1 TTATATTATATTTATTTAAAATA
1297408 TTATATTATAATTATATTTAAAATA
1 TTATATTAT-ATT-TATTTAAAATA
1297433 TTATAT
1 TTATAT
1297439 ATTTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 9 0.35
24 3 0.12
25 14 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATATTATATTTATTTAAAATA
Found at i:1297512 original size:18 final size:19
Alignment explanation
Indices: 1297489--1297533 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1297479 TTCACATGTA
*
1297489 TTTATATTATTTT-TTTAT
1 TTTATATTATTTTAATTAT
1297507 TTTATA-TATTTTAATTAT
1 TTTATATTATTTTAATTAT
*
1297525 ATTATATTA
1 TTTATATTA
1297534 ATATTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATATTATTTTAATTAT
Found at i:1297564 original size:25 final size:26
Alignment explanation
Indices: 1297522--1297571 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1297512 ATATTTTAAT
* *
1297522 TATATTATATTAATATTATATAATCA
1 TATATAATATTAAAATTATATAATCA
*
1297548 TATATAAT-TTAAAATTATCTAATC
1 TATATAATATTAAAATTATATAATC
1297572 TAATGAGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (26 bp):
TATATAATATTAAAATTATATAATCA
Found at i:1297683 original size:2 final size:2
Alignment explanation
Indices: 1297676--1297713 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1297666 AACCTAACAT
1297676 TA TA TA TA 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 TA TA TA TA
1297714 GTTTTAAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1298254 original size:15 final size:15
Alignment explanation
Indices: 1298236--1298265 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1298226 TCAATTGCTT
*
1298236 TTTTTTTTTCTTTTC
1 TTTTTGTTTCTTTTC
1298251 TTTTTGTTTCTTTTC
1 TTTTTGTTTCTTTTC
1298266 ATGTTGCAGG
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:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTGTTTCTTTTC
Found at i:1298974 original size:2 final size:2
Alignment explanation
Indices: 1298967--1299020 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1298957 CATCTTATTT
1298967 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1299009 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1299021 CATACTCTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1299942 original size:13 final size:14
Alignment explanation
Indices: 1299919--1299958 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1299909 TAATATGTTG
1299919 TTTTAACTATTTAT
1 TTTTAACTATTTAT
1299933 TTTTAA-TATTTAT
1 TTTTAACTATTTAT
*
1299946 ATTTAACATATTT
1 TTTTAAC-TATTT
1299959 TTAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 12 0.52
14 6 0.26
15 5 0.22
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAACTATTTAT
Found at i:1301034 original size:14 final size:15
Alignment explanation
Indices: 1301011--1301045 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1301001 TGTTAAGAAA
*
1301011 ATAATTTATTATT-T
1 ATAATATATTATTAT
1301025 ATAATATATTATTAT
1 ATAATATATTATTAT
1301040 ATAATA
1 ATAATA
1301046 ATTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATAATATATTATTAT
Found at i:1301561 original size:27 final size:29
Alignment explanation
Indices: 1301530--1301596 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
1301520 AATTAATTTG
*
1301530 ATTAAATTTTTT-TAA-TATTAAATAA-AT
1 ATTAAATTTTTTATAATTAATAAA-AATAT
1301557 ATTAAATATATTTTATAATTAATAAAAATAT
1 ATTAAAT-T-TTTTATAATTAATAAAAATAT
1301588 ATTAAATTT
1 ATTAAATTT
1301597 AATTTATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 7 0.21
28 1 0.03
29 5 0.15
30 6 0.18
31 15 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTAAATTTTTTATAATTAATAAAAATAT
Found at i:1302545 original size:2 final size:2
Alignment explanation
Indices: 1302538--1302581 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1302528 AGTCCAAGTA
*
1302538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1302580 AT
1 AT
1302582 TCAAACATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1302665 original size:2 final size:2
Alignment explanation
Indices: 1302658--1302700 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1302648 AATCCAAGTA
1302658 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
1302700 A
1 A
1302701 CATGCTATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1306066 original size:35 final size:34
Alignment explanation
Indices: 1306022--1306118 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 34
1306012 ATAATTACGT
*
1306022 TAAACATATACATATTTTATATTAATATTATTAAA
1 TAAATATATA-ATATTTTATATTAATATTATTAAA
* *
1306057 TAAATATATAAT-TTTTAAATATAA-A-T-TTAAT
1 TAAATATATAATATTTTATAT-TAATATTATTAAA
*
1306088 TATAATATATGATATTTT-TATTACATATTAT
1 TA-AATATATAATATTTTATATTA-ATATTAT
1306119 AATTTTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
31 8 0.16
32 13 0.26
33 13 0.26
34 6 0.12
35 10 0.20
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (34 bp):
TAAATATATAATATTTTATATTAATATTATTAAA
Found at i:1306077 original size:15 final size:15
Alignment explanation
Indices: 1306057--1306107 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 15
1306047 TATTATTAAA
1306057 TAAATATATAATTTT
1 TAAATATATAATTTT
1306072 TAAATATA-AATTTAAT
1 TAAATATATAATTT--T
1306088 TATAATATATGATATTTT
1 TA-AATATAT-A-ATTTT
1306106 TA
1 TA
1306108 TTACATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 5 0.17
15 8 0.27
16 3 0.10
17 6 0.20
18 3 0.10
19 1 0.03
20 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TAAATATATAATTTT
Found at i:1306165 original size:22 final size:22
Alignment explanation
Indices: 1306140--1306184 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1306130 ATAGTAATAT
** *
1306140 AATAATATTTTAATTTATTTTA
1 AATAATAAATTAAATTATTTTA
1306162 AATAATAAATTAAATTATTTTA
1 AATAATAAATTAAATTATTTTA
1306184 A
1 A
1306185 GCGTAACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATAATAAATTAAATTATTTTA
Found at i:1306377 original size:12 final size:12
Alignment explanation
Indices: 1306360--1306389 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1306350 TTGATTGATA
1306360 ATAATAATAATT
1 ATAATAATAATT
*
1306372 ATAATAATATTT
1 ATAATAATAATT
1306384 ATAATA
1 ATAATA
1306390 TTTACAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:1308581 original size:35 final size:34
Alignment explanation
Indices: 1308513--1308599 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 34
1308503 CATATTCATG
* *
1308513 TATTTTATA-ATATTATAATTACATTTAAAAATTT
1 TATTTTATATATATTTTAAATACATTTAAAAA-TT
* *
1308547 TATTTTTATATATATTTTAAATATA-TTAATAATT
1 TA-TTTTATATATATTTTAAATACATTTAAAAATT
* *
1308581 TATATTATATAAATTTTAA
1 TATTTTATATATATTTTAA
1308600 GACATTCATA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
33 15 0.33
34 6 0.13
35 13 0.29
36 11 0.24
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (34 bp):
TATTTTATATATATTTTAAATACATTTAAAAATT
Found at i:1312477 original size:3 final size:3
Alignment explanation
Indices: 1312469--1312509 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1312459 ATGCATTTAA
1312469 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1312510 AGGAAGAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1314003 original size:2 final size:2
Alignment explanation
Indices: 1313996--1314055 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1313986 TCAGAACTTC
1313996 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
1314038 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1314056 TTTTATAAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1314924 original size:3 final size:3
Alignment explanation
Indices: 1314916--1314955 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
1314906 AAAATGGAAA
* *
1314916 AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG GAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1314956 TTGTAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1314932 original size:15 final size:15
Alignment explanation
Indices: 1314912--1314955 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1314902 GCTCAAAATG
1314912 GAAAAAGAAGAAGAA
1 GAAAAAGAAGAAGAA
1314927 GAAAAAGAAGAAGAA
1 GAAAAAGAAGAAGAA
**
1314942 GAAGGAGAAGAAGA
1 GAAAAAGAAGAAGA
1314956 TTGTAAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAGAAGAA
Found at i:1315553 original size:2 final size:2
Alignment explanation
Indices: 1315546--1315570 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1315536 AAATAACTCC
1315546 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 A
1315571 CATAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1316193 original size:21 final size:20
Alignment explanation
Indices: 1316167--1316206 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1316157 AATAAGTTAA
* *
1316167 ATTTAAGTATTTTAATATTTG
1 ATTTAAATAATTTAA-ATTTG
1316188 ATTTAAATAATTTAAATTT
1 ATTTAAATAATTTAAATTT
1316207 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTAAATAATTTAAATTTG
Found at i:1316214 original size:36 final size:34
Alignment explanation
Indices: 1316144--1316244 Score: 105
Period size: 36 Copynumber: 2.9 Consensus size: 34
1316134 GTTCGAACAA
*
1316144 TTTAAATTT-TTTAAATAAGTTAAATTTAAGTAT
1 TTTAAATTTGTTTAAATAATTTAAATTTAAGTAT
***
1316177 TTTAATATTTGATTTAAATAATTTAAATTTTTTTAT
1 TTTAA-ATTTG-TTTAAATAATTTAAATTTAAGTAT
* *
1316213 TTTTAATTTGTATTGAATAATCTTAAATTTAA
1 TTTAAATTTGT-TTAAATAAT-TTAAATTTAA
1316245 ATTTAAACTC
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
33 5 0.09
34 5 0.09
35 13 0.24
36 32 0.58
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAAATTTGTTTAAATAATTTAAATTTAAGTAT
Found at i:1322344 original size:2 final size:2
Alignment explanation
Indices: 1322337--1322371 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1322327 ACTTGATCCA
1322337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1322372 CTATGTATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1323914 original size:23 final size:23
Alignment explanation
Indices: 1323884--1323930 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1323874 AAATGAAGAG
1323884 TCAGAGCAACATAGGTTTCAAGT
1 TCAGAGCAACATAGGTTTCAAGT
1323907 TCAGAGCAACATAGGTTTCAAGT
1 TCAGAGCAACATAGGTTTCAAGT
1323930 T
1 T
1323931 TACAAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (23 bp):
TCAGAGCAACATAGGTTTCAAGT
Found at i:1324297 original size:19 final size:19
Alignment explanation
Indices: 1324273--1324310 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1324263 TTGCTTTTAA
1324273 TTGCTTATGCTTATATAAT
1 TTGCTTATGCTTATATAAT
1324292 TTGCTTATGCTTATATAAT
1 TTGCTTATGCTTATATAAT
1324311 CATTTGGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (19 bp):
TTGCTTATGCTTATATAAT
Found at i:1329840 original size:11 final size:11
Alignment explanation
Indices: 1329824--1329856 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1329814 GAGTTTAATA
1329824 TTTTTTTTCTT
1 TTTTTTTTCTT
1329835 TTTTTTTTC-T
1 TTTTTTTTCTT
*
1329845 TCTTTTTTCTT
1 TTTTTTTTCTT
1329856 T
1 T
1329857 AATTTTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:1329841 original size:14 final size:14
Alignment explanation
Indices: 1329824--1329852 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1329814 GAGTTTAATA
1329824 TTTTTT-TTCTTTT
1 TTTTTTCTTCTTTT
1329837 TTTTTTCTTCTTTT
1 TTTTTTCTTCTTTT
1329851 TT
1 TT
1329853 CTTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTCTTCTTTT
Found at i:1330601 original size:34 final size:34
Alignment explanation
Indices: 1330555--1330739 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
1330545 GTAAAAACCA
**
1330555 CCATTTAATCAACAATGACAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1330589 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1330623 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1330657 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1330691 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1330724 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1330740 TCTCCCACTT
Statistics
Matches: 134, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
33 18 0.13
34 112 0.84
35 4 0.03
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1334832 original size:19 final size:19
Alignment explanation
Indices: 1334805--1334867 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1334795 TCACGTGTAC
* *
1334805 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1334824 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1334843 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1334862 AGTACC
1 AGTACC
1334868 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1335221 original size:34 final size:33
Alignment explanation
Indices: 1335175--1335290 Score: 135
Period size: 34 Copynumber: 3.4 Consensus size: 33
1335165 GTAAAAACCA
1335175 CCATTTAATCAACAATGACAACCTACCAAATCTC
1 CCATTTAATCAACAATGA-AACCTACCAAATCTC
* *
1335209 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAAT-G-AAACCTACCAAATCTC
* * *
1335243 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAAT-GAAACCTACCAAATCTC
*
1335277 TCATTTAATCAACA
1 CCATTTAATCAACA
1335291 CCTTGTACCA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
33 3 0.04
34 61 0.87
35 5 0.07
36 1 0.01
ACGTcount: A:0.41, C:0.28, G:0.06, T:0.26
Consensus pattern (33 bp):
CCATTTAATCAACAATGAAACCTACCAAATCTC
Found at i:1335405 original size:4 final size:4
Alignment explanation
Indices: 1335396--1335421 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1335386 ATGGTTAGTA
1335396 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1335422 GTGCTCTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1336298 original size:16 final size:15
Alignment explanation
Indices: 1336279--1336370 Score: 51
Period size: 16 Copynumber: 5.8 Consensus size: 15
1336269 TTGATATAGT
1336279 TTAAAATCAAAATAA
1 TTAAAATCAAAATAA
1336294 CTTAAATAT-AAAATAA
1 -TTAAA-ATCAAAATAA
* * * *
1336310 TTTGAACTCGAAATGA
1 -TTAAAATCAAAATAA
* * *
1336326 TCAAAAACTGAAATAA
1 TTAAAATC-AAAATAA
1336342 TTTAAAATCAAAATAA
1 -TTAAAATCAAAATAA
*
1336358 TTTAAATCTAAAA
1 TTAAAATC-AAAA
1336371 ATAACTTAAC
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
15 12 0.21
16 37 0.65
17 8 0.14
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (15 bp):
TTAAAATCAAAATAA
Found at i:1336374 original size:17 final size:15
Alignment explanation
Indices: 1336336--1336370 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
1336326 TCAAAAACTG
1336336 AAATAATTTAAAATCA
1 AAATAATTT-AAATCA
1336352 AAATAATTTAAATCTA
1 AAATAATTTAAATC-A
1336368 AAA
1 AAA
1336371 ATAACTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATTTAAATCA
Found at i:1336881 original size:17 final size:17
Alignment explanation
Indices: 1336839--1336884 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1336829 TATTTTTATA
1336839 AATTTAAA-TAAA-AAT
1 AATTTAAATTAAATAAT
*
1336854 -ATTTATTATTAAATAAT
1 AATTTA-AATTAAATAAT
1336871 AATTTAAATTAAAT
1 AATTTAAATTAAAT
1336885 TAAATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.20
15 1 0.04
16 4 0.16
17 10 0.40
18 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTAAATTAAATAAT
Found at i:1337050 original size:16 final size:16
Alignment explanation
Indices: 1337026--1337105 Score: 54
Period size: 16 Copynumber: 5.0 Consensus size: 16
1337016 TTTAAGTTAT
*
1337026 TTTCAGGTTCAGGTCA
1 TTTCGGGTTCAGGTCA
*
1337042 TTTCGGGTTTAGGTCA
1 TTTCGGGTTCAGGTCA
* ** *
1337058 CTTT-GGATTTGGGTTA
1 -TTTCGGGTTCAGGTCA
* * *
1337074 TTTCGGGTTCCGATTA
1 TTTCGGGTTCAGGTCA
*
1337090 TTTCGGGTTCGGGTCA
1 TTTCGGGTTCAGGTCA
1337106 ATTGGGTTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
15 3 0.06
16 44 0.88
17 3 0.06
ACGTcount: A:0.12, C:0.15, G:0.30, T:0.42
Consensus pattern (16 bp):
TTTCGGGTTCAGGTCA
Found at i:1337361 original size:23 final size:25
Alignment explanation
Indices: 1337295--1337350 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
1337285 ATCATTATGT
1337295 TCGAATATTGAATTTTCAAAAATTA
1 TCGAATATTGAATTTTCAAAAATTA
1337320 TCGAATATTGAATTTTCAAAAATTA
1 TCGAATATTGAATTTTCAAAAATTA
1337345 TCGAAT
1 TCGAAT
1337351 TGAATTGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (25 bp):
TCGAATATTGAATTTTCAAAAATTA
Found at i:1340929 original size:3 final size:3
Alignment explanation
Indices: 1340921--1340947 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1340911 ACTTATCCAA
1340921 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1340948 TTGAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1343760 original size:2 final size:2
Alignment explanation
Indices: 1343753--1343777 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1343743 ATAACTATTT
1343753 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
1343778 TAGTTAAATT
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:1344610 original size:23 final size:23
Alignment explanation
Indices: 1344579--1344632 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1344569 ATATATTTGA
1344579 TTTACTTATGTATA-ATTTTAAAAT
1 TTTA-TTATGTATATA-TTTAAAAT
*
1344603 TTTATTATTTATATATTTAAAAT
1 TTTATTATGTATATATTTAAAAT
1344626 TTATATT
1 TT-TATT
1344633 TTTATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTATTATGTATATATTTAAAAT
Found at i:1344621 original size:15 final size:14
Alignment explanation
Indices: 1344603--1344645 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1344593 ATTTTAAAAT
1344603 TTTATTATTTATATA
1 TTTA-TATTTATATA
* *
1344618 TTTAAAATTTATATT
1 TTT-ATATTTATATA
1344633 TTTATATTTATAT
1 TTTATATTTATAT
1344646 TTAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 14 0.58
16 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATATTTATATA
Found at i:1344636 original size:23 final size:23
Alignment explanation
Indices: 1344595--1344639 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1344585 TATGTATAAT
1344595 TTTAAAATTTTATTATTTATATA
1 TTTAAAATTTTATTATTTATATA
1344618 TTTAAAATTTATATT-TTTATAT
1 TTTAAAATTT-TATTATTTATAT
1344640 TTATATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTAAAATTTTATTATTTATATA
Found at i:1344653 original size:14 final size:14
Alignment explanation
Indices: 1344614--1344653 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1344604 TTATTATTTA
1344614 TATATTTAAA-ATT
1 TATATTTAAATATT
**
1344627 TATATTTTTATATT
1 TATATTTAAATATT
1344641 TATATTTAAATAT
1 TATATTTAAATAT
1344654 ATAATTTTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTTAAATATT
Found at i:1344908 original size:30 final size:29
Alignment explanation
Indices: 1344881--1344950 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 29
1344871 TTTAAATTGA
*
1344881 ATTAT-TAGATTTGAATTATTAAAAAATTAT
1 ATTATATAAATTT-AATTA-TAAAAAATTAT
1344911 ATTATATAAATTTAATTAT-AAAAATATAT
1 ATTATATAAATTTAATTATAAAAAAT-TAT
1344940 ATTAATATAAA
1 ATT-ATATAAA
1344951 AATAAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 6 0.17
29 7 0.19
30 17 0.47
31 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (29 bp):
ATTATATAAATTTAATTATAAAAAATTAT
Found at i:1344928 original size:14 final size:14
Alignment explanation
Indices: 1344863--1344950 Score: 52
Period size: 14 Copynumber: 6.0 Consensus size: 14
1344853 GAATAAAAAT
* *
1344863 TTTAATAATTTAAA
1 TTTAATTATATAAA
* *
1344877 TTGAATTAT-TAGA
1 TTTAATTATATAAA
*
1344890 TTTGAATTATTAAAAA
1 TTT-AATTA-TATAAA
*
1344906 ATTATATTATATAAA
1 TTTA-ATTATATAAA
*
1344921 TTTAATTATAAAAA
1 TTTAATTATATAAA
*
1344935 TATATATTAATATAAA
1 TTTA-ATT-ATATAAA
1344951 AATAAATTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
13 5 0.09
14 24 0.43
15 13 0.23
16 14 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
TTTAATTATATAAA
Found at i:1351261 original size:28 final size:28
Alignment explanation
Indices: 1351230--1351286 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1351220 AAAAAAAAAT
*
1351230 TATATTTATATAAATTCTA-AAATATTAA
1 TATA-TTATACAAATTCTATAAATATTAA
* *
1351258 TATATTATACAAATTTTATATATATTAA
1 TATATTATACAAATTCTATAAATATTAA
1351286 T
1 T
1351287 TTTATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
TATATTATACAAATTCTATAAATATTAA
Found at i:1351280 original size:20 final size:19
Alignment explanation
Indices: 1351234--1351284 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1351224 AAAAATTATA
* *
1351234 TTTATATAAATTCTAAAAT
1 TTTATATATATTATAAAAT
*
1351253 ATTA-ATATATTATACAAAT
1 TTTATATATATTATA-AAAT
1351272 TTTATATATATTA
1 TTTATATATATTA
1351285 ATTTTATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 8 0.31
19 10 0.38
20 8 0.31
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTATATATATTATAAAAT
Found at i:1353015 original size:3 final size:3
Alignment explanation
Indices: 1353007--1353032 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1352997 AATAAAAAGC
1353007 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1353033 TGTAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1353459 original size:19 final size:20
Alignment explanation
Indices: 1353433--1353484 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1353423 ATAAAAAAAT
* *
1353433 ATAAATATAATATTATATAA
1 ATAAATATAATATAACATAA
1353453 A-AAATATAAATATAACATAA
1 ATAAATAT-AATATAACATAA
1353473 ATAAATA-AATAT
1 ATAAATATAATAT
1353485 CTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 11 0.39
20 12 0.43
21 5 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATATAATATAACATAA
Found at i:1353460 original size:25 final size:24
Alignment explanation
Indices: 1353421--1353484 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
1353411 AATGATCACG
*
1353421 ATATA-AAAAAATATAAATATAAT
1 ATATATAAAAAATATAAATATAAC
1353444 ATTATATAAAAAATATAAATATAAC
1 A-TATATAAAAAATATAAATATAAC
*
1353469 ATAAATAAATAAATAT
1 ATATATAAA-AAATAT
1353485 CTTAAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 1 0.03
24 11 0.31
25 24 0.67
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
ATATATAAAAAATATAAATATAAC
Found at i:1354323 original size:2 final size:2
Alignment explanation
Indices: 1354316--1354353 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1354306 TTTAAACAAA
1354316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1354354 GAGTTGCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1354564 original size:80 final size:80
Alignment explanation
Indices: 1354411--1354566 Score: 222
Period size: 80 Copynumber: 1.9 Consensus size: 80
1354401 CAACGTTATC
* * * *
1354411 TTTTTTCCTCATAATTATTACTTCCCACCGACCCACTTTAAGATGAGTAAAAATTAATTATTAAG
1 TTTTTTCCTCATAATTATTACTCCCCACCGACCCACTTTAAGATAACTAAAAATTAATTATTAAA
*
1354476 TAAAATAAATCTACA
66 CAAAATAAATCTACA
* * * *
1354491 TTTTTTCCTCATAATTATTACTCCCCACCTACCCTCTTTAGGGTAACTAAAAATTAATTATTAAA
1 TTTTTTCCTCATAATTATTACTCCCCACCGACCCACTTTAAGATAACTAAAAATTAATTATTAAA
*
1354556 CAATATAAATC
66 CAAAATAAATC
1354567 CAAGTTGCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (80 bp):
TTTTTTCCTCATAATTATTACTCCCCACCGACCCACTTTAAGATAACTAAAAATTAATTATTAAA
CAAAATAAATCTACA
Found at i:1354609 original size:21 final size:21
Alignment explanation
Indices: 1354585--1354635 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1354575 AAGGCTTATT
1354585 TTTTAAAAAGAAAAATTAT-AA
1 TTTTAAAAA-AAAAATTATAAA
* *
1354606 TTTTGATAAAAATAATTATAAA
1 TTTT-AAAAAAAAAATTATAAA
1354628 TTTTAAAA
1 TTTTAAAA
1354636 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
TTTTAAAAAAAAAATTATAAA
Found at i:1354646 original size:14 final size:15
Alignment explanation
Indices: 1354619--1354687 Score: 58
Period size: 14 Copynumber: 4.9 Consensus size: 15
1354609 TGATAAAAAT
*
1354619 AATTATAAATTTTAA
1 AATTATAAAATTTAA
1354634 AATT-TAAAATTTAA
1 AATTATAAAATTTAA
* *
1354648 AATTAT-TAATATAA
1 AATTATAAAATTTAA
* *
1354662 AATAATTAAA-TTAA
1 AATTATAAAATTTAA
1354676 AATT-T-AAATTTA
1 AATTATAAAATTTA
1354688 TTGAAATACG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
12 3 0.07
13 4 0.09
14 30 0.68
15 7 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTATAAAATTTAA
Found at i:1356456 original size:20 final size:21
Alignment explanation
Indices: 1356425--1356486 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
1356415 AAATTTAACA
*
1356425 AAATTAATAAAAAATCGATTT
1 AAATCAATAAAAAATCGATTT
*
1356446 -AATCGATAAAAAATC-ATCTT
1 AAATCAATAAAAAATCGAT-TT
*
1356466 AAATCAATAAAAAATTGATTT
1 AAATCAATAAAAAATCGATTT
1356487 TTTGTTATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.06
20 15 0.44
21 15 0.44
22 2 0.06
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (21 bp):
AAATCAATAAAAAATCGATTT
Found at i:1357287 original size:2 final size:2
Alignment explanation
Indices: 1357280--1357304 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1357270 TGCATTAATT
1357280 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
1357305 TGTGTATGTA
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:1358727 original size:13 final size:13
Alignment explanation
Indices: 1358706--1358743 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1358696 TTTTGGGGGG
1358706 TAAAACTAAATAA
1 TAAAACTAAATAA
**
1358719 TCCAACTAAAT-A
1 TAAAACTAAATAA
1358731 TAAAACTAAATAA
1 TAAAACTAAATAA
1358744 CCTTAGGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAACTAAATAA
Found at i:1359063 original size:29 final size:31
Alignment explanation
Indices: 1359029--1359098 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
1359019 AATTTTTATG
1359029 TAAATTTTTATATTTTT-A-TTATATCTAAA
1 TAAATTTTTATATTTTTAATTTATATCTAAA
* *
1359058 TAAA-TTATATATTTTTAATTTATATTTAAA
1 TAAATTTTTATATTTTTAATTTATATCTAAA
*
1359088 TAAATATTTAT
1 TAAATTTTTAT
1359099 TTTAAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 11 0.32
29 5 0.15
30 14 0.41
31 4 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
TAAATTTTTATATTTTTAATTTATATCTAAA
Found at i:1359104 original size:17 final size:18
Alignment explanation
Indices: 1359075--1359108 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1359065 TATATTTTTA
1359075 ATTTATATTTAAATAAAT
1 ATTTATATTTAAATAAAT
1359093 ATTTAT-TTTAAATAAA
1 ATTTATATTTAAATAAA
1359109 AAATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTATATTTAAATAAAT
Found at i:1359161 original size:29 final size:29
Alignment explanation
Indices: 1359121--1359226 Score: 90
Period size: 29 Copynumber: 3.7 Consensus size: 29
1359111 ATTAATTACT
* *
1359121 TTAAAATTTTATTTAAATATAACTTAAAA
1 TTAAAAATTTATTTAAATATAAATTAAAA
* * *
1359150 TTATAAAA-TTATTTGAGTATAAATTAAAG
1 TTA-AAAATTTATTTAAATATAAATTAAAA
* * *
1359179 TTAAAAATTTATTT-AATTTTAATAAAAA
1 TTAAAAATTTATTTAAATATAAATTAAAA
* *
1359207 ATAAAAACTTCATTTAAATA
1 TTAAAAA-TTTATTTAAATA
1359227 GAACGATGAA
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
28 19 0.32
29 35 0.58
30 6 0.10
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (29 bp):
TTAAAAATTTATTTAAATATAAATTAAAA
Found at i:1359693 original size:2 final size:2
Alignment explanation
Indices: 1359688--1359733 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1359678 CTAGAAATTT
1359688 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1359730 TA TA
1 TA TA
1359734 CCATTATCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1365248 original size:3 final size:3
Alignment explanation
Indices: 1365234--1365265 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1365224 GAGACGGAAG
*
1365234 CAA CAA CGA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
1365266 CATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.34, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:1365274 original size:2 final size:2
Alignment explanation
Indices: 1365267--1365308 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
1365257 ACAACAACAC
* *
1365267 AT AT AT AT AT AT AT AT AT AC AT AT AT AT -T AT -T GT 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
1365307 AT
1 AT
1365309 TATTTGTAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1365532 original size:17 final size:16
Alignment explanation
Indices: 1365511--1365556 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
1365501 AAATATATAA
1365511 AAATATTAAAATTTTT
1 AAATATTAAAATTTTT
*
1365527 ATAATA-T-AAATTATT
1 A-AATATTAAAATTTTT
1365542 AATATATTAAAATTT
1 AA-ATATTAAAATTT
1365557 ATATCGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
14 1 0.04
15 11 0.46
16 3 0.12
17 9 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATATTAAAATTTTT
Found at i:1365792 original size:47 final size:47
Alignment explanation
Indices: 1365730--1365820 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 47
1365720 TAAAATATTA
* *
1365730 AAAAATATATATATTAA-T-ATTTATATATTTTATAATTAAATTTAAAT
1 AAAAATATATATATTAATTAAATAATA-ATTTTA-AATTAAATTTAAAT
* *
1365777 AAAAATATTTTTATTAATTAAATAATAATTTTAAATTAAATTTA
1 AAAAATATATATATTAATTAAATAATAATTTTAAATTAAATTTA
1365821 TTCGAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 26 0.68
48 7 0.18
49 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (47 bp):
AAAAATATATATATTAATTAAATAATAATTTTAAATTAAATTTAAAT
Found at i:1365798 original size:19 final size:20
Alignment explanation
Indices: 1365771--1365809 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1365761 ATAATTAAAT
*
1365771 TTAAATAAA-AATATTTTTA
1 TTAAATAAATAATAATTTTA
*
1365790 TTAATTAAATAATAATTTTA
1 TTAAATAAATAATAATTTTA
1365810 AATTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATAAATAATAATTTTA
Found at i:1365815 original size:18 final size:18
Alignment explanation
Indices: 1365770--1365817 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1365760 TATAATTAAA
*
1365770 TTTAAA-TAAA-AATATT
1 TTTAAATTAAATAATAAT
1365786 TTTATTAATTAAATAATAAT
1 TTTA--AATTAAATAATAAT
1365806 TTTAAATTAAAT
1 TTTAAATTAAAT
1365818 TTATTCGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.15
18 10 0.37
19 4 0.15
20 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAAATTAAATAATAAT
Found at i:1366277 original size:20 final size:20
Alignment explanation
Indices: 1366238--1366304 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1366228 AAAATATTTT
* *
1366238 AATTTT-AATTTTATTATAA
1 AATTTTAAATATTAATATAA
1366257 AATTTTAAATATTAATATAA
1 AATTTTAAATATTAATATAA
1366277 AA--TTAAATATTTTAATAT--
1 AATTTTAAATA--TTAATATAA
1366295 AATTTTAAAT
1 AATTTTAAAT
1366305 TAAATTACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 9 0.22
19 6 0.15
20 26 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTTAAATATTAATATAA
Found at i:1366284 original size:25 final size:24
Alignment explanation
Indices: 1366256--1366310 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1366246 TTTTATTATA
1366256 AAATTTTAAATATTAATATAAAATT
1 AAATTTTAAATA-TAATATAAAATT
* * *
1366281 AAATATTTTAATATAATTTTAAATT
1 AAAT-TTTAAATATAATATAAAATT
1366306 AAATT
1 AAATT
1366311 ACAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 18 0.69
26 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATTTTAAATATAATATAAAATT
Found at i:1366317 original size:38 final size:36
Alignment explanation
Indices: 1366257--1366327 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 36
1366247 TTTATTATAA
* *
1366257 AATTTTAAATATTAATATAAAATTAAATATTTTAATAT
1 AATTTTAAATATAAATACAAAA-TAAA-ATTTTAATAT
1366295 AATTTTAAAT-TAAATTACAAAATAAAATTTTAA
1 AATTTTAAATATAAA-TACAAAATAAAATTTTAA
1366328 ATCATGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 7 0.23
38 16 0.53
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (36 bp):
AATTTTAAATATAAATACAAAATAAAATTTTAATAT
Found at i:1366739 original size:27 final size:29
Alignment explanation
Indices: 1366709--1366768 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 29
1366699 TTTAATTATA
1366709 AAATATATTTTAA-AATATT-AAT-TTTT
1 AAATATATTTTAATAATATTAAATATTTT
* *
1366735 TAA-ATATTTTAATAATTTTAAATATTTT
1 AAATATATTTTAATAATATTAAATATTTT
1366763 AAATAT
1 AAATAT
1366769 CACAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
25 9 0.33
26 7 0.26
27 3 0.11
28 6 0.22
29 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
AAATATATTTTAATAATATTAAATATTTT
Found at i:1366746 original size:9 final size:9
Alignment explanation
Indices: 1366713--1366768 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
1366703 ATTATAAAAT
1366713 ATATTTTAA
1 ATATTTTAA
*
1366722 A-ATATT-A
1 ATATTTTAA
*
1366729 ATTTTTTAA
1 ATATTTTAA
1366738 ATATTTT-A
1 ATATTTTAA
1366746 ATAATTTTAA
1 AT-ATTTTAA
1366756 ATATTTTAA
1 ATATTTTAA
1366765 ATAT
1 ATAT
1366769 CACAAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 2 0.05
8 10 0.26
9 24 0.62
10 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATATTTTAA
Found at i:1370419 original size:22 final size:22
Alignment explanation
Indices: 1370391--1370438 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1370381 AAAATATTAT
*
1370391 TTTTAT-ATAAATATTTATATAA
1 TTTTATAATAAA-ATTTAAATAA
*
1370413 TTTTATAATTAAATTTAAATAA
1 TTTTATAATAAAATTTAAATAA
1370435 TTTT
1 TTTT
1370439 TTTTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTATAATAAAATTTAAATAA
Found at i:1371367 original size:17 final size:19
Alignment explanation
Indices: 1371335--1371370 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1371325 AAAATTAAAA
1371335 AAATATAAATTATAATAAT
1 AAATATAAATTATAATAAT
1371354 AAATAT-AA-TATAATAAT
1 AAATATAAATTATAATAAT
1371371 TTATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATAAATTATAATAAT
Found at i:1371401 original size:15 final size:17
Alignment explanation
Indices: 1371381--1371412 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1371371 TTATATATTT
1371381 TTTTAT-ATT-TTTTTA
1 TTTTATAATTATTTTTA
1371396 TTTTATAATTATTTTTA
1 TTTTATAATTATTTTTA
1371413 AATTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATAATTATTTTTA
Found at i:1371738 original size:27 final size:27
Alignment explanation
Indices: 1371708--1371760 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1371698 TAATTATATT
* * *
1371708 TAATTTTTTTATATAAATATAAAAATA
1 TAATTTTTCTAAATAAATAAAAAAATA
*
1371735 TAATTTTTCTAAATATATAAAAAAAT
1 TAATTTTTCTAAATAAATAAAAAAAT
1371761 TATATATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TAATTTTTCTAAATAAATAAAAAAATA
Found at i:1372228 original size:3 final size:3
Alignment explanation
Indices: 1372222--1372261 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1372212 TTTTCTTTTA
1372222 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1372262 GCTGAATCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1372248 original size:17 final size:17
Alignment explanation
Indices: 1372226--1372260 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1372216 CTTTTAAATA
1372226 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
1372243 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
1372260 A
1 A
1372261 AGCTGAATCT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:1372248 original size:20 final size:20
Alignment explanation
Indices: 1372223--1372261 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1372213 TTTCTTTTAA
1372223 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
1372243 ATAATAATAATAATAATAA
1 ATAATAATAATAATAATAA
1372262 GCTGAATCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:1372644 original size:58 final size:56
Alignment explanation
Indices: 1372582--1372695 Score: 133
Period size: 62 Copynumber: 2.0 Consensus size: 56
1372572 CCTTAGTATT
*
1372582 TATTAATA-A-AATTTATAATTTTTATATATTTAGATAAGTATTATATTTAAATATGTGA
1 TATTAATATATAATTTATAATTTTTATATATGTA-A-AA-TATTATA-TTAAATATGTGA
* *
1372640 TATTAATATATTTAATTTTTAATTTTTTTATATGTAAAATATTATATTAAATATGT
1 TATTAATATA--TAATTTATAATTTTTATATATGTAAAATATTATATTAAATATGT
1372696 TAAATATCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
58 18 0.37
59 8 0.16
60 2 0.04
61 1 0.02
62 20 0.41
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (56 bp):
TATTAATATATAATTTATAATTTTTATATATGTAAAATATTATATTAAATATGTGA
Found at i:1373292 original size:14 final size:14
Alignment explanation
Indices: 1373239--1373298 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
1373229 AATTTTAAAA
*
1373239 TATATATTTATATT
1 TATATAATTATATT
*
1373253 ATATTTTAATTAT-TT
1 -TA-TATAATTATATT
*
1373268 TATATGTATTATATT
1 TATAT-AATTATATT
*
1373283 TATATAATTATGTT
1 TATATAATTATATT
1373297 TA
1 TA
1373299 AAATTGTCGG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
13 2 0.06
14 16 0.44
15 11 0.31
16 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TATATAATTATATT
Found at i:1373522 original size:24 final size:25
Alignment explanation
Indices: 1373486--1373536 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
1373476 GAATATGTGT
1373486 ATTTATCTGATA-TAATATGTTTAA
1 ATTTATCTGATATTAATATGTTTAA
* * *
1373510 ATTTATTTTATATTTTATATGTTTAA
1 ATTTATCTGATA-TTAATATGTTTAA
1373536 A
1 A
1373537 GAATTATACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 10 0.45
26 12 0.55
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (25 bp):
ATTTATCTGATATTAATATGTTTAA
Found at i:1374882 original size:23 final size:21
Alignment explanation
Indices: 1374833--1374882 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 21
1374823 AAAAAATTAA
*
1374833 TTATTT-ATTACATAATATAT
1 TTATTTAATTAAATAATATAT
*
1374853 GTA-TTAATTAAATAATAAATAT
1 TTATTTAATTAAATAAT--ATAT
1374875 TTATTTAA
1 TTATTTAA
1374883 ATAATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
19 2 0.09
20 11 0.48
22 6 0.26
23 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TTATTTAATTAAATAATATAT
Found at i:1377287 original size:2 final size:2
Alignment explanation
Indices: 1377280--1377321 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1377270 ACCATCACTG
1377280 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
1377322 TCCCATTCCC
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:1378274 original size:2 final size:2
Alignment explanation
Indices: 1378267--1378293 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1378257 ATAGATGTAT
1378267 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1378294 AATCAGTTAT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1379798 original size:129 final size:130
Alignment explanation
Indices: 1379537--1379799 Score: 483
Period size: 130 Copynumber: 2.0 Consensus size: 130
1379527 TGTCAAATAT
*
1379537 AATGTCTATGACAAAAATGCTGCAACGAAGAATGAAGCATTTACAACCATGTACAAATTCCTAAA
1 AATGTCTATGACAAAAATGCTGCAACGAAGAATGAAGCATTTACAACCACGTACAAATTCCTAAA
1379602 AGTGAAGATATTATAGTAGTTTCTAGTGCGATGTGAGATCTCAAATAACAGAATTATTTATAGGA
66 AGTGAAGATATTATAGTAGTTTCTAGTGCGATGTGAGATCTCAAATAACAGAATTATTTATAGGA
* *
1379667 AATGTCTATGACAAAAATGCTGCAACGAGGAATGAAGCATTTACAATCACGTACAAATTCCTAAA
1 AATGTCTATGACAAAAATGCTGCAACGAAGAATGAAGCATTTACAACCACGTACAAATTCCTAAA
*
1379732 AGT-AAGATATTATAGTAGTTTCTAGTGCGATGTGAGATCTCAAATAACAGAATTATTTATTGGA
66 AGTGAAGATATTATAGTAGTTTCTAGTGCGATGTGAGATCTCAAATAACAGAATTATTTATAGGA
1379796 AATG
1 AATG
1379800 GAACTACGAA
Statistics
Matches: 129, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
129 64 0.50
130 65 0.50
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (130 bp):
AATGTCTATGACAAAAATGCTGCAACGAAGAATGAAGCATTTACAACCACGTACAAATTCCTAAA
AGTGAAGATATTATAGTAGTTTCTAGTGCGATGTGAGATCTCAAATAACAGAATTATTTATAGGA
Found at i:1381045 original size:14 final size:14
Alignment explanation
Indices: 1381026--1381055 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1381016 CAAAAGGCAA
1381026 GAAGAATTAGTTAG
1 GAAGAATTAGTTAG
1381040 GAAGAATTAGTTAG
1 GAAGAATTAGTTAG
1381054 GA
1 GA
1381056 CATACTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (14 bp):
GAAGAATTAGTTAG
Found at i:1382302 original size:9 final size:9
Alignment explanation
Indices: 1382281--1382312 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1382271 AAATTATAAA
1382281 ATATTTA-T
1 ATATTTATT
1382289 ATATTTATT
1 ATATTTATT
1382298 ATATTTATT
1 ATATTTATT
1382307 ATATTT
1 ATATTT
1382313 GTATATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATATTTATT
Found at i:1383694 original size:2 final size:2
Alignment explanation
Indices: 1383687--1383723 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1383677 AAGTTGGAAA
1383687 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1383724 ATACTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1388112 original size:2 final size:2
Alignment explanation
Indices: 1388105--1388143 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1388095 GAATCTCCAT
1388105 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1388144 TGCCTTTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1393958 original size:16 final size:16
Alignment explanation
Indices: 1393937--1393967 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1393927 TATAGAATAG
1393937 TTATTCCATTACAGTT
1 TTATTCCATTACAGTT
*
1393953 TTATTCTATTACAGT
1 TTATTCCATTACAGT
1393968 GAACCAAACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (16 bp):
TTATTCCATTACAGTT
Found at i:1397073 original size:118 final size:118
Alignment explanation
Indices: 1396913--1397152 Score: 462
Period size: 118 Copynumber: 2.0 Consensus size: 118
1396903 TCACCTGCTA
1396913 TTTCAAGTAGCAAAGTAAGAAAATTTAAGAGTCAAAAGAACAAAAAAGAGGGAGGAGGCTGTTAG
1 TTTCAAGTAGCAAAGTAAGAAAATTTAAGAGTCAAAAGAACAAAAAAGAGGGAGGAGGCTGTTAG
*
1396978 AAAGAAAATTATATTTTATTTATTTTAAGAGTCTTTAATAAAACAATAATCTT
66 AAAGAAAATTATATTTTATTTATTTTAAGAGTCTTTAATAAAAAAATAATCTT
1397031 TTTCAAGTAGCAAAGTAAGAAAATTTAAGAGTCAAAAGAACAAAAAAGAGGGAGGAGGCTGTTAG
1 TTTCAAGTAGCAAAGTAAGAAAATTTAAGAGTCAAAAGAACAAAAAAGAGGGAGGAGGCTGTTAG
*
1397096 AAAGAAAATTATATTTTATTTATTTTAAGAGTCTTTAATAAAAAAATACTCTT
66 AAAGAAAATTATATTTTATTTATTTTAAGAGTCTTTAATAAAAAAATAATCTT
1397149 TTTC
1 TTTC
1397153 TCCGTGCAGG
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (118 bp):
TTTCAAGTAGCAAAGTAAGAAAATTTAAGAGTCAAAAGAACAAAAAAGAGGGAGGAGGCTGTTAG
AAAGAAAATTATATTTTATTTATTTTAAGAGTCTTTAATAAAAAAATAATCTT
Found at i:1399999 original size:2 final size:2
Alignment explanation
Indices: 1399992--1400034 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1399982 GATCACCTTC
1399992 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1400034 T
1 T
1400035 GTCCAAGACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1406327 original size:27 final size:26
Alignment explanation
Indices: 1406257--1406331 Score: 141
Period size: 26 Copynumber: 2.8 Consensus size: 26
1406247 AAAGTTAATG
1406257 AAAAGTCACAATCATTTGACTTTTTC
1 AAAAGTCACAATCATTTGACTTTTTC
1406283 AAAAGTCACAATCATTTGACTTTTTC
1 AAAAGTCACAATCATTTGACTTTTTC
1406309 AAAAGTCACAATCATTTTGACTT
1 AAAAGTCACAATCA-TTTGACTT
1406332 CTTCTTATAG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 40 0.83
27 8 0.17
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (26 bp):
AAAAGTCACAATCATTTGACTTTTTC
Found at i:1407970 original size:14 final size:14
Alignment explanation
Indices: 1407951--1407977 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1407941 ATTTTTGATA
1407951 CTTATACCCATTAT
1 CTTATACCCATTAT
1407965 CTTATACCCATTA
1 CTTATACCCATTA
1407978 GCATAGGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTATACCCATTAT
Found at i:1412656 original size:12 final size:12
Alignment explanation
Indices: 1412641--1412682 Score: 75
Period size: 12 Copynumber: 3.4 Consensus size: 12
1412631 TAAATTATAA
1412641 AAAATTTAATTT
1 AAAATTTAATTT
1412653 AAAATTTAATTT
1 AAAATTTAATTT
1412665 AAAATTTAATTT
1 AAAATTTAATTT
1412677 ATAAAT
1 A-AAAT
1412683 AAATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 25 0.86
13 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATTTAATTT
Found at i:1412687 original size:24 final size:25
Alignment explanation
Indices: 1412617--1412693 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 25
1412607 AATAAATAAT
* *
1412617 AATTTAAATT-AAATTAAATTATAAAA
1 AATTTAATTTAAAATTAAATT-T-TAA
*
1412643 AATTTAATTTAAAATTTAA-TTTAA
1 AATTTAATTTAAAATTAAATTTTAA
1412667 AATTTAATTTATAAA-TAAATTTTAA
1 AATTTAATTTA-AAATTAAATTTTAA
1412692 AA
1 AA
1412694 AATTTTAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 16 0.36
25 11 0.25
26 10 0.23
27 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTTAATTTAAAATTAAATTTTAA
Found at i:1412698 original size:34 final size:34
Alignment explanation
Indices: 1412660--1412724 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1412650 TTTAAAATTT
1412660 AATTTAAAATTTAATTTAT-AAATA-AATTTTAAAA
1 AATTT-AAA-TTAATTTATGAAATATAATTTTAAAA
* *
1412694 AATTTTAATTATTTTATGAAATATAATTTTA
1 AATTTAAATTAATTTATGAAATATAATTTTA
1412725 TATTTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 8 0.30
33 7 0.26
34 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (34 bp):
AATTTAAATTAATTTATGAAATATAATTTTAAAA
Found at i:1414414 original size:21 final size:20
Alignment explanation
Indices: 1414389--1414434 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1414379 TGTGTTTTAT
1414389 ATTTAAA-AAATTAATTTTAAA
1 ATTTAAATAAA-TAA-TTTAAA
1414410 ATTTAAATTAAATAATTTAAA
1 ATTTAAA-TAAATAATTTAAA
1414431 ATTT
1 ATTT
1414435 TATTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 17 0.74
22 3 0.13
23 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTAAATAAATAATTTAAA
Found at i:1415977 original size:17 final size:16
Alignment explanation
Indices: 1415950--1415984 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1415940 ATAATATATG
1415950 TTATATTTATATCATA
1 TTATATTTATATCATA
*
1415966 TTATAGTTTATATTATA
1 TTATA-TTTATATCATA
1415983 TT
1 TT
1415985 TTATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTATATTTATATCATA
Found at i:1416306 original size:22 final size:22
Alignment explanation
Indices: 1416281--1416322 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1416271 TATTTTTATT
1416281 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1416303 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1416323 ATTTTTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1422497 original size:16 final size:16
Alignment explanation
Indices: 1422442--1422497 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
1422432 ATTTTTGATC
*
1422442 GAGTTA-TTTGAGTTT
1 GAGTTATTTTGATTTT
*
1422457 GAGTTATTTTAATTTT
1 GAGTTATTTTGATTTT
1422473 -AGGTTATTTTGATTTT
1 GA-GTTATTTTGATTTT
*
1422489 GAGTCATTT
1 GAGTTATTT
1422498 CAAATTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.21
16 26 0.76
17 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.20, T:0.57
Consensus pattern (16 bp):
GAGTTATTTTGATTTT
Found at i:1422572 original size:22 final size:23
Alignment explanation
Indices: 1422547--1422619 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 23
1422537 AGTTCAGACC
*
1422547 ATTTTATATTCGAA-TTAA-TTAG
1 ATTTAATATTC-AAGTTAATTTAG
1422569 ATTTAATATTCAAGTTAATTTAG
1 ATTTAATATTCAAGTTAATTTAG
* **
1422592 ATTCAA-A-TCATTTTAAGTTTAG
1 ATTTAATATTCAAGTTAA-TTTAG
1422614 ATTTAA
1 ATTTAA
1422620 ATAAATCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.21
22 25 0.58
23 9 0.21
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.48
Consensus pattern (23 bp):
ATTTAATATTCAAGTTAATTTAG
Found at i:1422818 original size:25 final size:26
Alignment explanation
Indices: 1422776--1422824 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1422766 ATATTTAATT
*
1422776 AAGATTTTATTAAAATATA-AAAATA
1 AAGATATTATTAAAATATATAAAATA
1422801 AAGATATT-TTAAATATATATAAAA
1 AAGATATTATTAAA-ATATATAAAA
1422825 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (26 bp):
AAGATATTATTAAAATATATAAAATA
Found at i:1424156 original size:25 final size:25
Alignment explanation
Indices: 1424128--1424186 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
1424118 TTATATTTAT
1424128 TTAATTAAATTTAAATAAAATATTA
1 TTAATTAAATTTAAATAAAATATTA
* *
1424153 TTAATTAAATTTAAATATAATTTTA
1 TTAATTAAATTTAAATAAAATATTA
1424178 TTAATTAAA
1 TTAATTAAA
1424187 ATATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTAATTAAATTTAAATAAAATATTA
Found at i:1424168 original size:20 final size:19
Alignment explanation
Indices: 1424138--1424204 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
1424128 TTAATTAAAT
*
1424138 TTAAATAAAATATTATTAA
1 TTAAATTAAATATTATTAA
* *
1424157 TTAAATTTAAATATAATTTTA
1 TTAAA-TTAAATATTA-TTAA
*
1424178 TT-AATTAAA-A-TATAAA
1 TTAAATTAAATATTATTAA
1424194 TTAAATTAAAT
1 TTAAATTAAAT
1424205 TATAATAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.11
17 8 0.21
18 1 0.03
19 10 0.26
20 10 0.26
21 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATTAAATATTATTAA
Found at i:1424206 original size:26 final size:25
Alignment explanation
Indices: 1424128--1424206 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 25
1424118 TTATATTTAT
* * *
1424128 TTAATTAAATTTAAATA-AAATATTA
1 TTAATTAAATATAAATATAATTA-AA
* **
1424153 TTAATTAAATTTAAATATAATTTTA
1 TTAATTAAATATAAATATAATTAAA
1424178 TTAATTAAAATATAAAT-TAAATTAAA
1 TTAATT-AAATATAAATAT-AATTAAA
1424204 TTA
1 TTA
1424207 TAATAATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 26 0.57
26 20 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATTAAATATAAATATAATTAAA
Found at i:1424491 original size:19 final size:20
Alignment explanation
Indices: 1424461--1424502 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1424451 TTTAAATATA
*
1424461 AAATCGATTAATTCATTAAT
1 AAATCGATTAATTCATAAAT
1424481 AAATC-ATTAATTCATAAAT
1 AAATCGATTAATTCATAAAT
1424500 AAA
1 AAA
1424503 GTATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATCGATTAATTCATAAAT
Found at i:1426561 original size:7 final size:7
Alignment explanation
Indices: 1426549--1426623 Score: 63
Period size: 7 Copynumber: 11.3 Consensus size: 7
1426539 TTTAAGTTTG
1426549 ATTTAAA
1 ATTTAAA
1426556 ATTTAAA
1 ATTTAAA
1426563 ATTTAAA
1 ATTTAAA
1426570 ATTT--A
1 ATTTAAA
1426575 ATTT-AA
1 ATTTAAA
1426581 ATTTATTAA
1 ATTTA--AA
* *
1426590 ATTTTAT
1 ATTTAAA
*
1426597 TTTTAAA
1 ATTTAAA
1426604 ATTT-AA
1 ATTTAAA
1426610 ATTT--A
1 ATTTAAA
1426615 ATTTAAA
1 ATTTAAA
1426622 AT
1 AT
1426624 AAAAATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
5 10 0.18
6 11 0.20
7 29 0.52
9 6 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATTTAAA
Found at i:1426563 original size:25 final size:25
Alignment explanation
Indices: 1426535--1426585 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1426525 ACTTCGAAAA
* *
1426535 AAAATTT-AAGTTTGATTTAAAATTT
1 AAAATTTAAAATTTAATTT-AAATTT
1426560 AAAATTTAAAATTTAATTTAAATTT
1 AAAATTTAAAATTTAATTTAAATTT
1426585 A
1 A
1426586 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
AAAATTTAAAATTTAATTTAAATTT
Found at i:1426585 original size:6 final size:6
Alignment explanation
Indices: 1426536--1426635 Score: 50
Period size: 6 Copynumber: 16.8 Consensus size: 6
1426526 CTTCGAAAAA
* *
1426536 AAATTT AAGTTT -GATTT AAAATTT AAAATTT AAAATTT -AATTT AAATTT
1 AAATTT AAATTT AAATTT -AAATTT -AAATTT -AAATTT AAATTT AAATTT
** * * *
1426585 --A-TT AAATTTT ATTTTT AAAATTT AAATTT -AATTT AAAATA AAAATT
1 AAATTT AAA-TTT AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT
1426631 AAATT
1 AAATT
1426636 ATTTGATCTT
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
3 2 0.03
4 1 0.01
5 14 0.19
6 31 0.42
7 25 0.34
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:1426638 original size:41 final size:40
Alignment explanation
Indices: 1426557--1426639 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 40
1426547 TGATTTAAAA
**
1426557 TTTAAAATTTAAAATTTAATTTAAATTTATTAAATTTTATT
1 TTTAAAATTTAAAATTTAATTTAAATAAATTAAA-TTTATT
1426598 TTTAAAATTT-AAATTTAATTTAAAATAAAAATTAAA-TTATT
1 TTTAAAATTTAAAATTTAATTT-AAAT--AAATTAAATTTATT
1426639 T
1 T
1426640 GATCTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
40 11 0.30
41 20 0.54
43 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
TTTAAAATTTAAAATTTAATTTAAATAAATTAAATTTATT
Found at i:1426820 original size:19 final size:17
Alignment explanation
Indices: 1426788--1426826 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
1426778 TAAATATTTA
1426788 AATTTAATTTATTTAAT
1 AATTTAATTTATTTAAT
1426805 AATTTAAATATTATTTAAT
1 AATTT-AAT-TTATTTAAT
1426824 AAT
1 AAT
1426827 AATTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 3 0.15
19 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTAATTTATTTAAT
Found at i:1426836 original size:19 final size:17
Alignment explanation
Indices: 1426777--1426836 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 17
1426767 TTTATTTAAA
1426777 TTAAA-TATTT-A-AAT
1 TTAAATTATTTAATAAT
*
1426791 TTAATTTATTTAATAAT
1 TTAAATTATTTAATAAT
1426808 TTAAATATTATTTAATAAT
1 TT-AA-ATTATTTAATAAT
1426827 AATTAAATTA
1 --TTAAATTA
1426837 AATTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 4 0.11
15 5 0.14
16 1 0.03
17 5 0.14
18 2 0.05
19 16 0.43
20 2 0.05
21 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATTATTTAATAAT
Found at i:1430101 original size:20 final size:21
Alignment explanation
Indices: 1430060--1430103 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1430050 CATCCAAAAA
1430060 AAAAAAAATTCAACTTCTCAG
1 AAAAAAAATTCAACTTCTCAG
* *
1430081 AAAATAAATTCATCTTC-CAG
1 AAAAAAAATTCAACTTCTCAG
1430101 AAA
1 AAA
1430104 TCATCTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAAAAAATTCAACTTCTCAG
Found at i:1433693 original size:2 final size:2
Alignment explanation
Indices: 1433686--1433718 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1433676 CAATTCATAA
1433686 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1433719 ATGTATGTAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1433725 original size:4 final size:4
Alignment explanation
Indices: 1433718--1433776 Score: 91
Period size: 4 Copynumber: 14.2 Consensus size: 4
1433708 TCTCTCTCTC
*
1433718 TATG TATG TATG TATG TATG TATG TATG TATG TATAG ATATA TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT-G -TATG TATG TATG
1433768 TATG TATG T
1 TATG TATG T
1433777 GTCAGTTCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
4 47 0.92
5 1 0.02
6 3 0.06
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:1433789 original size:26 final size:26
Alignment explanation
Indices: 1433719--1433776 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 26
1433709 CTCTCTCTCT
*
1433719 ATGTATGTATGTAT-G-TATGTATGT
1 ATGTATGTATGTATAGATATATATGT
1433743 ATG--T--ATGTATAGATATATATGT
1 ATGTATGTATGTATAGATATATATGT
1433765 ATGTATGTATGT
1 ATGTATGTATGT
1433777 GTCAGTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
20 6 0.22
21 1 0.04
22 12 0.44
24 4 0.15
26 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.48
Consensus pattern (26 bp):
ATGTATGTATGTATAGATATATATGT
Found at i:1434893 original size:17 final size:17
Alignment explanation
Indices: 1434842--1434894 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
1434832 TTATTTAGTT
* *
1434842 ATTTTAATTAAATAAATA
1 ATTTT-ATTAATTATATA
*
1434860 ATTTTTATATGATTATATA
1 A-TTTTAT-TAATTATATA
1434879 ATTTTATTAATTATAT
1 ATTTTATTAATTATAT
1434895 TAGATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.28
18 9 0.31
19 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTTATTAATTATATA
Done.