Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_pilon, whole genome shotgun sequence
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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 23
Found at i:1160343 original size:20 final size:20
Alignment explanation
Indices: 1160318--1160386 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
1160308 GCGATTCTCT
*
1160318 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
1160338 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1160358 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
1160378 TGTTGCGAT
1 CGTTGCGAT
1160387 TTTCATTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1160392 original size:20 final size:20
Alignment explanation
Indices: 1160318--1160396 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
1160308 GCGATTCTCT
*
1160318 CGTTGCGATAGTCAAATTT-G
1 CGTTGCGATAGTC-ATTTTCG
**
1160338 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1160358 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1160378 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1160397 AGAAACTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.08
20 48 0.92
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1160587 original size:25 final size:24
Alignment explanation
Indices: 1160533--1160587 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1160523 TGTTTATTAT
* *
1160533 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1160557 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1160583 TGTTT
1 TGTTT
1160588 ATTGTGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1161369 original size:15 final size:16
Alignment explanation
Indices: 1161344--1161373 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1161334 TTATTTAACA
1161344 ATTACTAATGTTTGTT
1 ATTACTAATGTTTGTT
1161360 ATTA-TAATGTTTGT
1 ATTACTAATGTTTGT
1161374 AGATTTGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (16 bp):
ATTACTAATGTTTGTT
Found at i:1161738 original size:18 final size:18
Alignment explanation
Indices: 1161717--1161761 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1161707 TCCACTTCGG
*
1161717 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1161735 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1161753 GAGCCATCA
1 GAGCCATCA
1161762 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1162297 original size:19 final size:20
Alignment explanation
Indices: 1162243--1162309 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1162233 TAGTTTACTT
* *
1162243 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1162263 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1162283 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1162302 TCGCAACG
1 TCGCAACG
1162310 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1162355 original size:19 final size:19
Alignment explanation
Indices: 1162243--1162363 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
1162233 TAGTTTACTT
* **
1162243 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1162263 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1162283 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1162302 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
1162316 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
1162334 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1162353 TCGCAATGCGA
1 TCGCAACGCGA
1162364 TTTGTGTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.21
19 26 0.31
20 24 0.29
21 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1162394 original size:14 final size:14
Alignment explanation
Indices: 1162375--1162432 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1162365 TTGTGTTTCG
1162375 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1162389 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1162405 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1162421 CGTTGTGATTTT
1 CGTTGCGATTTT
1162433 AATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1162413 original size:32 final size:33
Alignment explanation
Indices: 1162370--1162448 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
1162360 GCGATTTGTG
* *
1162370 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTAA
*
1162402 TTTCGCATTGCGATTTTGTCGTTGTGATTTTAA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTAA
1162435 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1162449 AGCCATTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 25 0.58
33 18 0.42
ACGTcount: A:0.13, C:0.16, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTAA
Found at i:1162467 original size:20 final size:20
Alignment explanation
Indices: 1162435--1162488 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1162425 GTGATTTTAA
*
1162435 TTTCGCATTGCGATAGCCA-
1 TTTCGCGTTGCGATAGCCAT
*
1162454 TTTCTGCGTTGCGATAGTCAT
1 TTTC-GCGTTGCGATAGCCAT
1162475 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1162489 TTTAAGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.13
20 23 0.74
21 4 0.13
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:1162937 original size:40 final size:42
Alignment explanation
Indices: 1162857--1162937 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 42
1162847 TCACCGGTCA
* * *
1162857 TCCCTCAAGAGTCCCCTCCAATCGTTCAATAGGCCCCTATCC
1 TCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTATCC
*
1162899 TCCCTCAAGATTCCCC-CC-ACCGTTCAAGAGGCCACTATC
1 TCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTATC
1162938 ATCGTTGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 18 0.51
41 2 0.06
42 15 0.43
ACGTcount: A:0.22, C:0.43, G:0.12, T:0.22
Consensus pattern (42 bp):
TCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTATCC
Found at i:1164364 original size:14 final size:14
Alignment explanation
Indices: 1164345--1164380 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1164335 ATTGTTTAAT
1164345 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1164359 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1164373 TGATTTGT
1 TGATTTGT
1164381 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1164488 original size:20 final size:20
Alignment explanation
Indices: 1164463--1164501 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1164453 ATGTTGAAGG
1164463 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
1164483 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
1164502 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:1164531 original size:19 final size:19
Alignment explanation
Indices: 1164507--1164571 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
1164497 GCAACGAGAG
1164507 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1164526 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1164545 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
1164559 AATCGCAATGCGA
1 AATCGCAATGCGA
1164572 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1164636 original size:20 final size:20
Alignment explanation
Indices: 1164597--1164665 Score: 115
Period size: 19 Copynumber: 3.5 Consensus size: 20
1164587 GCGATTTTGT
1164597 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
*
1164616 CGTTGCGATAGCTATTTTCG
1 CGTTGCGATAGCCATTTTCG
1164636 CGTTGCGA-AGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1164655 CGTTGCGATAG
1 CGTTGCGATAG
1164666 TCAAATGAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
19 31 0.67
20 15 0.33
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:1164903 original size:20 final size:20
Alignment explanation
Indices: 1164878--1164928 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1164868 AAATGATTGC
1164878 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
1164898 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
*
1164918 CTTTCGTAACG
1 CTTTCGCAACG
1164929 AGATAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:1165918 original size:12 final size:12
Alignment explanation
Indices: 1165901--1165925 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1165891 ATATAATCCT
1165901 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1165913 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1165925 G
1 G
1165926 TCCCCAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1168238 original size:19 final size:19
Alignment explanation
Indices: 1168216--1168313 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1168206 GGAAATTACT
1168216 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1168235 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1168249 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* **
1168268 ATTGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1168282 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1168301 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1168314 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.50
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1168258 original size:33 final size:33
Alignment explanation
Indices: 1168216--1168309 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1168206 GGAAATTACT
1168216 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1168249 ATCGCAATGCGAAATGAAAATTGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1168282 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1168310 CGAATTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1168341 original size:14 final size:14
Alignment explanation
Indices: 1168324--1168380 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1168314 TTTAATTTCG
1168324 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1168338 CGTTGCGATTTTTATTT
1 CGTTGCGA---TTCTCT
1168355 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
1168371 CGTTGCGATT
1 CGTTGCGATT
1168381 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 16 0.47
16 6 0.18
17 6 0.18
19 6 0.18
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1168363 original size:33 final size:33
Alignment explanation
Indices: 1168309--1168398 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
1168299 AAATCGCAAC
* *
1168309 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
*
1168342 GCGATTTTTATTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
*
1168375 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTAATTTCGCATTGCGAT
1168399 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.44
Consensus pattern (33 bp):
GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
Found at i:1168364 original size:19 final size:19
Alignment explanation
Indices: 1168340--1168398 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
1168330 GATTCTCTCG
1168340 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTTATTTCGCA
* *
1168359 TTGCGA---TTCTCTCG--
1 TTGCGATTTTTATTTCGCA
*
1168373 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTTATTTCGCA
1168392 TTGCGAT
1 TTGCGAT
1168399 AGTACTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 6 0.20
16 6 0.20
17 5 0.17
19 13 0.43
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTTATTTCGCA
Found at i:1168524 original size:14 final size:14
Alignment explanation
Indices: 1168505--1168541 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1168495 CATCAATTAA
1168505 ACAAATCAACTGTT
1 ACAAATCAACTGTT
* *
1168519 ACAAATCACCTTTT
1 ACAAATCAACTGTT
1168533 ACAAATCAA
1 ACAAATCAA
1168542 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.27
Consensus pattern (14 bp):
ACAAATCAACTGTT
Found at i:1169983 original size:42 final size:42
Alignment explanation
Indices: 1169898--1169991 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
1169888 GTGAATCGGG
* *
1169898 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* * *
1169940 CTCTTGAACGGTGGGATGGGA-CTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTCAACG-ATGACAGGGGC
*
1169982 CTCTTCAACG
1 CTCTTGAACG
1169992 ATAGGAGTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 36 0.82
43 4 0.09
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:1170412 original size:91 final size:90
Alignment explanation
Indices: 1170237--1170421 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 90
1170227 ATTTCAAACT
* *
1170237 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
1170302 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
1170330 TTCAACCAAAAGAAAAAACAAAAAGACAAATACTAACTTCATAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGAAAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
**
1170394 GTTTTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1170421 T
1 T
1170422 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 41 0.48
93 18 0.21
95 26 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1172158 original size:19 final size:19
Alignment explanation
Indices: 1172094--1172225 Score: 121
Period size: 19 Copynumber: 7.1 Consensus size: 19
1172084 TCTTTTGGTT
*
1172094 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
1172113 GATAATGAGAATCGCAACAC
1 GA-AATGAAAATCGCAACGC
**
1172133 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** *
1172153 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
1172170 G--AT-AGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1172186 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1172205 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1172224 GA
1 GA
1172226 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 7 0.07
15 2 0.02
16 2 0.02
17 2 0.02
18 2 0.02
19 49 0.52
20 28 0.30
21 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1172243 original size:19 final size:19
Alignment explanation
Indices: 1172221--1172264 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1172211 AAAATCGCAA
*
1172221 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCACGT
**
1172240 TGCG-TTTTTTTTTCACGT
1 TGCGATTTTGGTTTCACGT
1172258 TGCGATT
1 TGCGATT
1172265 CTCTCGTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.07, C:0.16, G:0.25, T:0.52
Consensus pattern (19 bp):
TGCGATTTTGGTTTCACGT
Found at i:1172880 original size:20 final size:20
Alignment explanation
Indices: 1172855--1172908 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1172845 GATTTTGTAT
1172855 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1172875 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1172895 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1172909 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1175027 original size:12 final size:13
Alignment explanation
Indices: 1175010--1175038 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1175000 CTTAATTGCG
1175010 AAAATTAAAA-TT
1 AAAATTAAAATTT
1175022 AAAATTAAAATTT
1 AAAATTAAAATTT
1175035 AAAA
1 AAAA
1175039 CATTCGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:1175188 original size:27 final size:26
Alignment explanation
Indices: 1175135--1175201 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
1175125 AACGAATATT
1175135 AAATAAACCAAAAAAAATGAAACTAAAA
1 AAATAAA--AAAAAAAATGAAACTAAAA
1175163 AAATAGAATAAAAAAAAT-AAGA-TAAAA
1 AAATA-AA-AAAAAAAATGAA-ACTAAAA
1175190 AAATAAAAAAAA
1 AAATAAAAAAAA
1175202 TGTTAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 5 0.14
26 2 0.06
27 12 0.33
28 15 0.42
29 2 0.06
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.12
Consensus pattern (26 bp):
AAATAAAAAAAAAAATGAAACTAAAA
Found at i:1175195 original size:13 final size:13
Alignment explanation
Indices: 1175145--1175195 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
1175135 AAATAAACCA
1175145 AAAAAAATGAA-ACT
1 AAAAAAAT-AAGA-T
1175159 AAAAAAAT-AGAAT
1 AAAAAAATAAG-AT
1175172 AAAAAAAATAAGAT
1 -AAAAAAATAAGAT
1175186 AAAAAAATAA
1 AAAAAAATAA
1175196 AAAAAATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.03
13 11 0.33
14 19 0.58
15 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (13 bp):
AAAAAAATAAGAT
Found at i:1177303 original size:36 final size:31
Alignment explanation
Indices: 1177217--1177282 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
1177207 CTCGAAGGTC
*
1177217 TTTTGTGTTTCAAGATAAACATTTTCAAAGG
1 TTTTGTGTTTCAAGAGAAACATTTTCAAAGG
1177248 TTTTGTGTTTCAAGAGAAACGA-TTTCAAAGG
1 TTTTGTGTTTCAAGAGAAAC-ATTTTCAAAGG
1177279 TTTT
1 TTTT
1177283 TTTTTGTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (31 bp):
TTTTGTGTTTCAAGAGAAACATTTTCAAAGG
Found at i:1177340 original size:37 final size:36
Alignment explanation
Indices: 1177289--1177375 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
1177279 TTTTTTTTTG
* * * *
1177289 TGTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1177326 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
1177362 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
1177376 TGTTTTCAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 14 0.32
37 30 0.68
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:1177450 original size:102 final size:100
Alignment explanation
Indices: 1177289--1177527 Score: 230
Period size: 102 Copynumber: 2.4 Consensus size: 100
1177279 TTTTTTTTTG
* * ** * * ** ** * *
1177289 TGTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTAGTACCAAAAGAAAATGTCTCAAGAGAG
* *
1177354 ACAAAATTCATTTCAAGGGAA-ATGTTTTCAATG-TTT
66 ACAAAATTCATTTC-AGGGAAGA--TATTCAAAGATTT
* *
1177390 ATGTTTCAAGAGAAACTATTTCAAGAGAGAAAAAACTTAGTACCAAAAGAAAATGTCTCAAGGGA
1 -TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTAGTACCAAAAGAAAATGTCTCAAGAGA
* * *
1177455 GACGAAATTTATTTCATGGAAGATATTCAAAGATTT
65 GACAAAATTCATTTCAGGGAAGATATTCAAAGATTT
* * *
1177491 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTT
1177528 GGAAACTGTC
Statistics
Matches: 112, Mismatches: 23, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
100 40 0.36
101 8 0.07
102 64 0.57
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (100 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTAGTACCAAAAGAAAATGTCTCAAGAGAG
ACAAAATTCATTTCAGGGAAGATATTCAAAGATTT
Found at i:1177531 original size:28 final size:28
Alignment explanation
Indices: 1177500--1177578 Score: 158
Period size: 28 Copynumber: 2.8 Consensus size: 28
1177490 TTGTTTCAAG
1177500 GGAAACTGTCTCAAGAGAGACAAAACTT
1 GGAAACTGTCTCAAGAGAGACAAAACTT
1177528 GGAAACTGTCTCAAGAGAGACAAAACTT
1 GGAAACTGTCTCAAGAGAGACAAAACTT
1177556 GGAAACTGTCTCAAGAGAGACAA
1 GGAAACTGTCTCAAGAGAGACAA
1177579 TGGTGAGCAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (28 bp):
GGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:1178140 original size:217 final size:211
Alignment explanation
Indices: 1177702--1178176 Score: 592
Period size: 217 Copynumber: 2.2 Consensus size: 211
1177692 TGTATTGTTC
* * * *
1177702 TGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTTG-AACTGGGAAATTGTTTGTTACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAATTGTTTGTTACA
* * * * *
1177766 ACCAACCGTCCCTTCGCTATGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGTTGTAA
65 ACCAACCGCCCCTTCGCTATAAAGTTGAACTTGTGCTGTCTCAAGTCTAATATCATTCGTTGTAA
* * ** ** * *
1177831 AGTTGAAATTGGTTTTGAAACAGGGAAATTGTTTGTTGACAACCAGCAGTCCCTTCGCTGTGAAG
130 AGTTGAAATTGCTTATGAAACAGAAAAATTGTTTGTCAACAACCAGCAGCCCCTTCACTGTGAAG
1177896 TTGAACTTGTGTTGCCT
195 TTGAACTTGTGTTGCCT
* *
1177913 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTT-ACA
** * * * * *
1177978 GTCAGCCGCCCCTTTGCTGTAAAGTTGAGCTTGTGCTGTCTCAAGTCTAATATCATTCGTTGTGA
65 ACCAACCGCCCCTTCGCTATAAAGTTGAACTTGTGCTGTCTCAAGTCTAATATCATTCGTTGTAA
* * * *
1178043 AGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTTTGTCAACAATCAGCCGCCCCTTCATTG
130 AGTTGAAATTG-CT-T--ATGAAACAGAAAAA-TTGTTTGTCAACAACCAGCAGCCCCTTCACTG
* *
1178108 TGAAGTTGAGCTTGTGTTGTCT
190 TGAAGTTGAACTTGTGTTGCCT
1178130 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
1178177 GGAAGCCCAT
Statistics
Matches: 223, Mismatches: 34, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
210 2 0.01
211 52 0.23
212 67 0.30
213 1 0.00
214 1 0.00
216 10 0.04
217 90 0.40
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (211 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTACAA
CCAACCGCCCCTTCGCTATAAAGTTGAACTTGTGCTGTCTCAAGTCTAATATCATTCGTTGTAAA
GTTGAAATTGCTTATGAAACAGAAAAATTGTTTGTCAACAACCAGCAGCCCCTTCACTGTGAAGT
TGAACTTGTGTTGCCT
Found at i:1178170 original size:111 final size:107
Alignment explanation
Indices: 1177703--1178173 Score: 556
Period size: 106 Copynumber: 4.4 Consensus size: 107
1177693 GTATTGTTCT
* ** *
1177703 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTTG-AACTGGGAAATTGTTTGTT-ACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAACTGAGAAATTGTTTGTTGACA
* * *
1177766 ACCAACCGTCCCTTCGCTATGAAGTTGAACTTGTGTTGTCTC
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
* * * * *
1177808 GAGTCTAATATCCTTCGTTGTAAAGTTGAAATTGG-TTTTGAAACAGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAACTGAGAAATTGTTTGTTGACA
* * *
1177872 ACCAGCAGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGCCTC
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
*
1177914 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAACTGAGAAATTGTTTGTTGACA
** * * * *
1177978 GTCAGCCGCCCCTTTGCTGTAAAGTTGAGCTTGTGCTGTCTC
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
* * * * * *
1178020 AAGTCTAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAGTTGTTTGTC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT---TGAAACTGAGAAA-TTGTTTGTT
* * ** * *
1178085 AACAATCAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTGTCTT
62 GACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
*
1178131 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC-TGAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAA
1178174 TTGGGAAGCC
Statistics
Matches: 312, Mismatches: 46, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
104 4 0.01
105 48 0.15
106 164 0.53
107 6 0.02
110 11 0.04
111 79 0.25
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (107 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAACTGAGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:1178890 original size:32 final size:32
Alignment explanation
Indices: 1178843--1178929 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
1178833 CCCAAAGATG
* *
1178843 CCCCAAAATTCGATGTTAAATCTCAAAAAATA
1 CCCCAACATTTGATGTTAAATCTCAAAAAATA
*
1178875 CCCCAACATTTGATGTTAAATCTCAAAAAATG
1 CCCCAACATTTGATGTTAAATCTCAAAAAATA
* *
1178907 CCCCAGCATTTGATGTTGAATCT
1 CCCCAACATTTGATGTTAAATCT
1178930 TTAATTATAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CCCCAACATTTGATGTTAAATCTCAAAAAATA
Found at i:1180017 original size:26 final size:26
Alignment explanation
Indices: 1179982--1180042 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1179972 ATGCGTCTTG
* *
1179982 TTTTCTTTTTTTCCTTTGTTTTTGC-T
1 TTTTC-TTTTTTACTTTCTTTTTGCGT
*
1180008 TTTTGCTTTTTTATTTTCTTTTTGCGT
1 TTTT-CTTTTTTACTTTCTTTTTGCGT
1180035 TTTTCTTT
1 TTTTCTTT
1180043 GTTTTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.02, C:0.13, G:0.08, T:0.77
Consensus pattern (26 bp):
TTTTCTTTTTTACTTTCTTTTTGCGT
Found at i:1180048 original size:19 final size:19
Alignment explanation
Indices: 1180002--1180048 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1179992 TTCCTTTGTT
* *
1180002 TTTGCTTTTTGCTTTTTTA
1 TTTGTTTTTTGCGTTTTTA
*
1180021 TTT-TCTTTTTGCGTTTTTC
1 TTTGT-TTTTTGCGTTTTTA
1180040 TTTGTTTTT
1 TTTGTTTTT
1180049 CTCTTTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.02, C:0.11, G:0.11, T:0.77
Consensus pattern (19 bp):
TTTGTTTTTTGCGTTTTTA
Found at i:1180053 original size:26 final size:26
Alignment explanation
Indices: 1180000--1180056 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1179990 TTTTCCTTTG
*
1180000 TTTTTGCTTTTTGCTTTTTTATTTTC
1 TTTTTGCTTTTTGCTTTTTTATTCTC
1180026 TTTTTGCGTTTTT-CTTTGTTT-TTCTC
1 TTTTTGC-TTTTTGCTTT-TTTATTCTC
1180052 TTTTT
1 TTTTT
1180057 TCTTCTTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.02, C:0.12, G:0.09, T:0.77
Consensus pattern (26 bp):
TTTTTGCTTTTTGCTTTTTTATTCTC
Found at i:1181661 original size:52 final size:52
Alignment explanation
Indices: 1181582--1181685 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
1181572 CGAATGAATG
* *
1181582 CATCTCTGGATTTCATCATTTATTGAACCTGTTCTATAACGGAAATGCCATT
1 CATCTCTGGATTTCATCATTTACTGAACCTGTTCTATAACGGAAACGCCATT
* * * *
1181634 CATCTCTGGCTTTTATCCTTTGCTGAACCTGTTCTATAACGGAAACGCCATT
1 CATCTCTGGATTTCATCATTTACTGAACCTGTTCTATAACGGAAACGCCATT
1181686 GAAATCCTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (52 bp):
CATCTCTGGATTTCATCATTTACTGAACCTGTTCTATAACGGAAACGCCATT
Found at i:1183231 original size:23 final size:22
Alignment explanation
Indices: 1183190--1183243 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1183180 AAACGAATAT
* *
1183190 TAAATAAACCAAAAAAAATGAAAC
1 TAAA-AAAACAAAAAAAAT-AAAA
*
1183214 TAAAAAAACAAAATAAATAAAA
1 TAAAAAAACAAAAAAAATAAAA
1183236 TAAAAAAA
1 TAAAAAAA
1183244 TGTTAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 11 0.41
23 12 0.44
24 4 0.15
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (22 bp):
TAAAAAAACAAAAAAAATAAAA
Found at i:1183275 original size:25 final size:24
Alignment explanation
Indices: 1183224--1183275 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
1183214 TAAAAAAACA
*
1183224 AAATAAATAAAATAAAAAAATGTT
1 AAATAAATAAAATAAAAAAATGCT
1183248 AAATAAACT-AAATAAAAAAAGTGCT
1 AAATAAA-TAAAATAAAAAAA-TGCT
1183273 AAA
1 AAA
1183276 ATTTAAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
AAATAAATAAAATAAAAAAATGCT
Found at i:1184578 original size:2 final size:2
Alignment explanation
Indices: 1184571--1184612 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1184561 TGTAAATAAC
1184571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1184612 A
1 A
1184613 ATCACATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1186105 original size:2 final size:2
Alignment explanation
Indices: 1186098--1186135 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1186088 ATATTTATTC
1186098 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
1186136 GATTGTATGA
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):
AT
Found at i:1187040 original size:20 final size:20
Alignment explanation
Indices: 1187015--1187054 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1187005 AATTCACAAT
1187015 GCGAATCTGTAAATCGCAAC
1 GCGAATCTGTAAATCGCAAC
*
1187035 GCGAATTTGTAAATCGCAAC
1 GCGAATCTGTAAATCGCAAC
1187055 ACAGAAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
GCGAATCTGTAAATCGCAAC
Found at i:1187071 original size:20 final size:19
Alignment explanation
Indices: 1187048--1187294 Score: 219
Period size: 20 Copynumber: 12.3 Consensus size: 19
1187038 AATTTGTAAA
1187048 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
1187068 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* *
1187088 TCACTACACTGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
1187108 TCGCAACGCGAA-TCTGTAAA-
1 TCGCAACACGAAGTC---AAAT
* * *
1187128 TCGTAATATAGAAGTCAAAT
1 TCGCAACA-CGAAGTCAAAT
1187148 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
1187168 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
1187188 TCGCAACACTGAATTTCAAAT
1 TCGCAACAC-GAA-GTCAAAT
*
1187209 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
1187229 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* *
1187249 TCGCAACGCAATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
1187269 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACG-AAGTCAAAT
1187289 TCGCAA
1 TCGCAA
1187295 AGCTTGTTTA
Statistics
Matches: 189, Mismatches: 24, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.01
19 11 0.06
20 146 0.77
21 28 0.15
22 2 0.01
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:1187102 original size:40 final size:39
Alignment explanation
Indices: 1187048--1187294 Score: 241
Period size: 40 Copynumber: 6.2 Consensus size: 39
1187038 AATTTGTAAA
1187048 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACAC-GAAGTCAAATTCGCAACGCGATAGTCAAAT
* * *
1187088 TCACTACACTGAAGTCAAATTCGCAACGCGAATCTGT-AAA-
1 TCGCAACAC-GAAGTCAAATTCGCAACGCG-AT-AGTCAAAT
* * * *
1187128 TCGTAATATAGAAGTCAAATTCGCAACACAGA-AGTCAAAT
1 TCGCAACA-CGAAGTCAAATTCGCAACGC-GATAGTCAAAT
* * *
1187168 TCGCAACGCGATAGTCAAATTCGCAACACTGA-ATTTCAAAT
1 TCGCAACACGA-AGTCAAATTCGCAACGC-GATA-GTCAAAT
*
1187209 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACAC-GAAGTCAAATTCGCAACGCGATAGTCAAAT
* * *
1187249 TCGCAACGCAATAGTCAAATTCGCAACGCGAAAGTCAAAT
1 TCGCAACACGA-AGTCAAATTCGCAACGCGATAGTCAAAT
1187289 TCGCAA
1 TCGCAA
1187295 AGCTTGTTTA
Statistics
Matches: 173, Mismatches: 23, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
38 2 0.01
39 7 0.04
40 124 0.72
41 37 0.21
42 3 0.02
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (39 bp):
TCGCAACACGAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:1187224 original size:61 final size:60
Alignment explanation
Indices: 1187060--1187294 Score: 262
Period size: 60 Copynumber: 3.9 Consensus size: 60
1187050 GCAACACAGA
* * * * **
1187060 AGTCAAATTCGCAACGCGATAGTCAAATTCACTACACTGAAGTCAAATTCGCAACGCGAAT
1 AGTCAAATTCGCAACACAATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCG-AT
* * * * *
1187121 CTGT-AAA-TCGTAATATAGA-AGTCAAATTCGCAACACAGAAGTCAAATTCGCAACGCGAT
1 -AGTCAAATTCGCAACACA-ATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
*
1187180 AGTCAAATTCGCAACACTGAAT-TTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACAC--AATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
* * *
1187241 AGTCAAATTCGCAACGCAATAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAA
1 AGTCAAATTCGCAACACAATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAA
1187295 AGCTTGTTTA
Statistics
Matches: 147, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
58 2 0.01
59 8 0.05
60 76 0.52
61 58 0.39
62 3 0.02
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (60 bp):
AGTCAAATTCGCAACACAATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
Found at i:1188631 original size:20 final size:20
Alignment explanation
Indices: 1188577--1188632 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
1188567 CGGTTTGCGA
1188577 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
1188597 TTTCG-GTTTGTGAATTTGAC
1 TTTCGCG-TTGCGAATTTGAC
1188617 TTTCGCGTTGCGAATT
1 TTTCGCGTTGCGAATT
1188633 CAAGGAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:1188857 original size:18 final size:18
Alignment explanation
Indices: 1188834--1188870 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1188824 AAGCCGGTTG
*
1188834 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1188852 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1188870 T
1 T
1188871 CTTTTGCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.24, T:0.57
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1194928 original size:24 final size:24
Alignment explanation
Indices: 1194901--1194960 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1194891 CTGAAACATC
1194901 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* *
1194925 ATC-AAAGTCTGGGTATTGACCAAG
1 ATCAAAATTC-GAGTATTGACCAAG
*
1194949 ATCAAATTTCGA
1 ATCAAAATTCGA
1194961 ATACTGACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 5 0.17
24 20 0.69
25 4 0.14
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:1195914 original size:19 final size:20
Alignment explanation
Indices: 1195890--1195982 Score: 93
Period size: 19 Copynumber: 4.7 Consensus size: 20
1195880 AACTAAAACA
1195890 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
*
1195909 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT-GAAATTCG
* *
1195929 AGTTGCGAATTTGAAATTC-
1 TGTTGCGAAATTGAAATTCG
* *
1195948 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
*
1195969 TGTTGCGAATTTGA
1 TGTTGCGAAATTGA
1195983 CTATCGCGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
18 4 0.06
19 26 0.41
20 18 0.28
21 16 0.25
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:1195935 original size:20 final size:20
Alignment explanation
Indices: 1195891--1196201 Score: 128
Period size: 20 Copynumber: 15.6 Consensus size: 20
1195881 ACTAAAACAT
* *
1195891 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* *
1195910 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGA
1195930 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
*
1195949 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTC-GA
* *
1195970 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
* * *
1195990 GTTACGAATTTG-ACTTCTGT
1 GTTGCGAATTTGAAATTC-GA
* *
1196010 GTTGCG-ATTTACAAATTCGC
1 GTTGCGAATTT-GAAATTCGA
* *
1196030 GTTGCG-ATTT-ACAGATTTGC
1 GTTGCGAATTTGA-A-ATTCGA
* *
1196050 GTTGCGAATTTG-ACTTCAGT
1 GTTGCGAATTTGAAATTC-GA
* *
1196070 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
* *
1196090 GTTGCGAATTTG-ACTTCCGT
1 GTTGCGAATTTGAAATT-CGA
* * * *
1196110 GTTACGAATTTG-ACTTATGT
1 GTTGCGAATTTGAAATT-CGA
*
1196130 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGA-A-ATTCGA
* *
1196150 GTTGCGAATTTGGAAACT-GG
1 GTTGCGAATTT-GAAATTCGA
* * * *
1196170 GTTGCGAAATTGTAGTTCGC
1 GTTGCGAATTTGAAATTCGA
1196190 GTTGCGAATTTG
1 GTTGCGAATTTG
1196202 TTGGTCATTT
Statistics
Matches: 235, Mismatches: 36, Indels: 41
0.75 0.12 0.13
Matches are distributed among these distances:
18 1 0.00
19 45 0.19
20 155 0.66
21 32 0.14
22 1 0.00
23 1 0.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:1195953 original size:39 final size:41
Alignment explanation
Indices: 1195891--1195982 Score: 118
Period size: 39 Copynumber: 2.3 Consensus size: 41
1195881 ACTAAAACAT
* *
1195891 GTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATC-GA
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAGA
* * *
1195930 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAGA
1195970 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1195983 CTATCGCGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 26 0.57
40 20 0.43
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (41 bp):
GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAGA
Found at i:1195975 original size:60 final size:58
Alignment explanation
Indices: 1195891--1196002 Score: 152
Period size: 60 Copynumber: 1.9 Consensus size: 58
1195881 ACTAAAACAT
*
1195891 GTTGCGAAATTAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCA
1 GTTGCGAAATTAAATTCGTGTTGCGAATTCGAAAATCGAGTTACGAATTTGAAATTCA
* * ** *
1195949 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTACGAATTTGA
1 GTTGCGAAATT-AAATTC-GTGTTGCGAATTCGAAAATCGAGTTACGAATTTGA
1196003 CTTCTGTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 10 0.22
59 6 0.13
60 30 0.65
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.35
Consensus pattern (58 bp):
GTTGCGAAATTAAATTCGTGTTGCGAATTCGAAAATCGAGTTACGAATTTGAAATTCA
Found at i:1196034 original size:60 final size:60
Alignment explanation
Indices: 1195961--1196161 Score: 232
Period size: 60 Copynumber: 3.3 Consensus size: 60
1195951 TGCGAATTTG
*
1195961 AAATTCAGTGTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCGATTTAC
1 AAATTC-GCGTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCGATTTAC
* * * *
1196022 AAATTCGCGTTGCG-ATTT-ACAGATTTGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGAC
1 AAATTCGCGTTGCGAATTTGAC-TA-TCGCGTTACGAATTTGACTTCTGTGTTGCG-ATTT-AC
* * *
1196084 -TA-TCGCGTTGCGAATTTGACT-TCCGTGTTACGAATTTGACTTATGTGTTGCGATTTAC
1 AAATTCGCGTTGCGAATTTGACTAT-CGCGTTACGAATTTGACTTCTGTGTTGCGATTTAC
*
1196142 AGATTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
1196162 GAAACTGGGT
Statistics
Matches: 118, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
58 4 0.03
59 11 0.09
60 84 0.71
61 15 0.13
62 4 0.03
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.39
Consensus pattern (60 bp):
AAATTCGCGTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCGATTTAC
Found at i:1196174 original size:100 final size:100
Alignment explanation
Indices: 1195949--1196201 Score: 291
Period size: 100 Copynumber: 2.5 Consensus size: 100
1195939 TTGAAATTCA
* * *
1195949 GTTGCGAATTTGA-AATTCAGTGTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGTGTT
1 GTTGCGAATTTGACAA--CAGGGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCCGTGTT
* *
1196013 GCGATTTACAAATTCGCGTTGCGATTTACAGATTTGC
64 ACGATTTACAAATTCGCGTTGCGATTTACAGATTCGC
** *
1196050 GTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCCGTGTTAC
1 GTTGCGAATTTGACAACAGGGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCCGTGTTAC
** *
1196115 GAATTTGACTTA-T-GTGTTGCGATTTACAGATTCGC
66 G-ATTT-ACAAATTCGCGTTGCGATTTACAGATTCGC
* * *
1196150 GTTGCGAATTTGGA-AACTGGGTTGCGAAATTGTAGT-TCGCGTTGCGAATTTG
1 GTTGCGAATTT-GACAACAGGGTTGCGAATTTG-ACTATCGCGTTGCGAATTTG
1196202 TTGGTCATTT
Statistics
Matches: 132, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
100 107 0.81
101 22 0.17
102 3 0.02
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.38
Consensus pattern (100 bp):
GTTGCGAATTTGACAACAGGGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCCGTGTTAC
GATTTACAAATTCGCGTTGCGATTTACAGATTCGC
Found at i:1196202 original size:20 final size:19
Alignment explanation
Indices: 1195930--1196201 Score: 148
Period size: 20 Copynumber: 13.6 Consensus size: 19
1195920 CGAAAATCGA
* *
1195930 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTG-ACTTCGC
* *
1195949 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTC-GC
1195970 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
* *
1195990 GTTACGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GC
1196010 GTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC---TTCGC
*
1196030 GTTGCG-ATTT-ACAGATTTGC
1 GTTGCGAATTTGAC---TTCGC
*
1196050 GTTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACTTC-GC
1196070 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
*
1196090 GTTGCGAATTTGACTTCCGT
1 GTTGCGAATTTGACTT-CGC
* * *
1196110 GTTACGAATTTGACTTATGT
1 GTTGCGAATTTGACTT-CGC
1196130 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC---TTCGC
*
1196150 GTTGCGAATTTGGAAAC-T-GG
1 GTTGCGAATTT-G--ACTTCGC
* *
1196170 GTTGCGAAATTGTAGTTCGC
1 GTTGCGAATTTG-ACTTCGC
1196190 GTTGCGAATTTG
1 GTTGCGAATTTG
1196202 TTGGTCATTT
Statistics
Matches: 206, Mismatches: 25, Indels: 43
0.75 0.09 0.16
Matches are distributed among these distances:
18 5 0.02
19 33 0.16
20 134 0.65
21 30 0.15
22 2 0.01
25 2 0.01
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTGACTTCGC
Found at i:1197277 original size:31 final size:31
Alignment explanation
Indices: 1197226--1197302 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
1197216 CTTTTAAAAC
* * *
1197226 TTGCAATACAATC-CCCAACATTTAGTCTGT
1 TTGCAATATAGTCTCCCAACATTTAGTCCGT
1197256 TTGCAATATAGTCTCCCAACATTTAGTCCGT
1 TTGCAATATAGTCTCCCAACATTTAGTCCGT
*
1197287 TTGCAATATGGTCTCC
1 TTGCAATATAGTCTCC
1197303 AACGTAACTG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 11 0.26
31 31 0.74
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (31 bp):
TTGCAATATAGTCTCCCAACATTTAGTCCGT
Found at i:1202598 original size:39 final size:39
Alignment explanation
Indices: 1202553--1202628 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
1202543 TAAATTAACA
*
1202553 TTAGCACTTTCATTAGAATTTTCAATTAACATTAAATGT
1 TTAGCACTTTCATTAGAATTTTCAATTAACATGAAATGT
1202592 TTAGCACTTTCATTAGAATTTTCAATTAACATGAAAT
1 TTAGCACTTTCATTAGAATTTTCAATTAACATGAAAT
1202629 TCTATTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (39 bp):
TTAGCACTTTCATTAGAATTTTCAATTAACATGAAATGT
Found at i:1202721 original size:40 final size:40
Alignment explanation
Indices: 1202677--1202754 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
1202667 TATCTGTTAA
*
1202677 TCACTTCTATTTCTTGGATAAAACCTTTCAACATGCGAAG
1 TCACTTCTATTGCTTGGATAAAACCTTTCAACATGCGAAG
*
1202717 TCACTTCTATTGCTTGGATAAAACCTTTTAACATGCGA
1 TCACTTCTATTGCTTGGATAAAACCTTTCAACATGCGA
1202755 TTTTAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (40 bp):
TCACTTCTATTGCTTGGATAAAACCTTTCAACATGCGAAG
Found at i:1203534 original size:29 final size:30
Alignment explanation
Indices: 1203483--1203549 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
1203473 TAATTAACAA
1203483 GGACGGGGAAAAATCGAATTTTTTAAACGG
1 GGACGGGGAAAAATCGAATTTTTTAAACGG
*
1203513 GGACGGGGAAAAATTGAATTTTTTAAACGG
1 GGACGGGGAAAAATCGAATTTTTTAAACGG
*
1203543 AGACGGG
1 GGACGGG
1203550 TTTAGTATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.36, C:0.09, G:0.33, T:0.22
Consensus pattern (30 bp):
GGACGGGGAAAAATCGAATTTTTTAAACGG
Found at i:1203889 original size:29 final size:29
Alignment explanation
Indices: 1203847--1203905 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1203837 TGACTTCTAG
1203847 TGGTTTCTAATTTGTATCTTGTATTTATT
1 TGGTTTCTAATTTGTATCTTGTATTTATT
*
1203876 TGGTTTCTAATTTGTATGTTGTATTTATT
1 TGGTTTCTAATTTGTATCTTGTATTTATT
1203905 T
1 T
1203906 CAGTCTATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.63
Consensus pattern (29 bp):
TGGTTTCTAATTTGTATCTTGTATTTATT
Found at i:1205870 original size:16 final size:16
Alignment explanation
Indices: 1205849--1205888 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1205839 CCAGATCTGC
*
1205849 AATAATATATAATAAT
1 AATAATATATAACAAT
*
1205865 AATAATAAATAACAAT
1 AATAATATATAACAAT
*
1205881 AAAAATAT
1 AATAATAT
1205889 TATTATAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATATATAACAAT
Found at i:1206047 original size:2 final size:2
Alignment explanation
Indices: 1206040--1206078 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1206030 TAATTTTCCA
*
1206040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1206079 GAGAGAGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1211678 original size:12 final size:12
Alignment explanation
Indices: 1211661--1211726 Score: 56
Period size: 12 Copynumber: 6.1 Consensus size: 12
1211651 AAAAAAATTA
1211661 ATTAAATAAAAT
1 ATTAAATAAAAT
*
1211673 ATTAAA-ATAAT
1 ATTAAATAAAAT
1211684 -TTAAAT---A-
1 ATTAAATAAAAT
1211691 ATTAAATAAAAT
1 ATTAAATAAAAT
*
1211703 ACT-AATAAAAT
1 ATTAAATAAAAT
*
1211714 ATAAAATAAAAT
1 ATTAAATAAAAT
1211726 A
1 A
1211727 AAATATACCT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
8 7 0.16
10 5 0.12
11 14 0.33
12 17 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:1211695 original size:30 final size:29
Alignment explanation
Indices: 1211659--1211732 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
1211649 GTAAAAAAAT
*
1211659 TAATTAAATAAAATATTAA-AATAATTTAAA
1 TAATTAAATAAAATATTAATAA-AATAT-AA
*
1211689 TAATTAAATAAAATACTAATAAAATATAA
1 TAATTAAATAAAATATTAATAAAATATAA
*
1211718 -AATAAAATAAAATAT
1 TAATTAAATAAAATAT
1211733 ACCTTAAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 13 0.33
29 2 0.05
30 22 0.56
31 2 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (29 bp):
TAATTAAATAAAATATTAATAAAATATAA
Found at i:1211728 original size:17 final size:18
Alignment explanation
Indices: 1211696--1211733 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1211686 AAATAATTAA
*
1211696 ATAAAATACTAATAAAAT
1 ATAAAATACAAATAAAAT
1211714 ATAAAATA-AAATAAAAT
1 ATAAAATACAAATAAAAT
1211731 ATA
1 ATA
1211734 CCTTAAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAATACAAATAAAAT
Found at i:1211991 original size:13 final size:14
Alignment explanation
Indices: 1211961--1211994 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1211951 ATCAGCGTAA
1211961 GGCGCGCTTCAGGG
1 GGCGCGCTTCAGGG
1211975 GGCGCGCTTCA-GG
1 GGCGCGCTTCAGGG
1211988 GGCGCGC
1 GGCGCGC
1211995 CTTACCCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.06, C:0.32, G:0.50, T:0.12
Consensus pattern (14 bp):
GGCGCGCTTCAGGG
Found at i:1213468 original size:24 final size:24
Alignment explanation
Indices: 1213439--1213519 Score: 112
Period size: 24 Copynumber: 3.4 Consensus size: 24
1213429 CATAATAATC
1213439 GTGCCACAAGAGTAGAGAAAACGT
1 GTGCCACAAGAGTAGAGAAAACGT
1213463 GTGCCACAAGAGTAGAGAAAACGT
1 GTGCCACAAGAGTAGAGAAAACGT
* * *
1213487 GTGACACAAGAATA-ATGAAAA-GC
1 GTGCCACAAGAGTAGA-GAAAACGT
1213510 GTGCCACAAG
1 GTGCCACAAG
1213520 GACAAAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 11 0.21
24 41 0.79
ACGTcount: A:0.43, C:0.17, G:0.27, T:0.12
Consensus pattern (24 bp):
GTGCCACAAGAGTAGAGAAAACGT
Found at i:1213856 original size:19 final size:19
Alignment explanation
Indices: 1213824--1213884 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
1213814 GTTTATAATT
*
1213824 TTTTTGATATTTTTACAATA
1 TTTTT-ATAATTTTACAATA
1213844 TTTTTATAATTTTACATATA
1 TTTTTATAATTTTACA-ATA
*
1213864 GTTTTTAT-ATTTTATAATA
1 -TTTTTATAATTTTACAATA
1213883 TT
1 TT
1213885 ATATATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 2 0.05
19 13 0.35
20 15 0.41
21 7 0.19
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTTATAATTTTACAATA
Found at i:1213883 original size:21 final size:20
Alignment explanation
Indices: 1213815--1213883 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
1213805 TCTGTGAAAG
1213815 TTTATAAT-T-TTTTTGATAT
1 TTTATAATATATTTTT-ATAT
1213834 TTT-TACA-ATATTTTTATAAT
1 TTTATA-ATATATTTTTAT-AT
*
1213854 TTTA-CATATAGTTTTTATAT
1 TTTATAATATA-TTTTTATAT
1213874 TTTATAATAT
1 TTTATAATAT
1213884 TATATATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
18 2 0.05
19 8 0.20
20 19 0.47
21 11 0.28
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTATAATATATTTTTATAT
Found at i:1222075 original size:39 final size:39
Alignment explanation
Indices: 1222030--1222108 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1222020 TAAATTAACA
1222030 TTAGCACTTTCATTAGAATTTTCAATTAACATTAAATGC
1 TTAGCACTTTCATTAGAATTTTCAATTAACATTAAATGC
1222069 TTAGCACTTTCATTAGAATTTTCAATTAACATTAAATGC
1 TTAGCACTTTCATTAGAATTTTCAATTAACATTAAATGC
1222108 T
1 T
1222109 ATTTAATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (39 bp):
TTAGCACTTTCATTAGAATTTTCAATTAACATTAAATGC
Found at i:1222198 original size:40 final size:40
Alignment explanation
Indices: 1222154--1222231 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
1222144 TATCTGCTAA
*
1222154 TCACTTCTATTTCTTGGATAAAACCTTTCAACATGCGAAG
1 TCACTTCTATTGCTTGGATAAAACCTTTCAACATGCGAAG
*
1222194 TCACTTCTATTGCTTGGATAAAACCTTTTAACATGCGA
1 TCACTTCTATTGCTTGGATAAAACCTTTCAACATGCGA
1222232 TTTTAATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (40 bp):
TCACTTCTATTGCTTGGATAAAACCTTTCAACATGCGAAG
Found at i:1222389 original size:2 final size:2
Alignment explanation
Indices: 1222382--1222407 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1222372 AGAGAATAAC
1222382 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
1222408 TATTGAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1226753 original size:17 final size:17
Alignment explanation
Indices: 1226727--1226771 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1226717 TATATTGTTG
* *
1226727 ATCAAAGAATCACTATC
1 ATCAAGGAATCACCATC
*
1226744 ATCAAGGAATCACCGTC
1 ATCAAGGAATCACCATC
1226761 ATTCAAGGAAT
1 A-TCAAGGAAT
1226772 TCCAACATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.22
Consensus pattern (17 bp):
ATCAAGGAATCACCATC
Found at i:1236484 original size:30 final size:30
Alignment explanation
Indices: 1236445--1236519 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
1236435 AACAACATCT
* * *
1236445 TAAATGACTAAAATAGTACAAACAAGAAT-G
1 TAAAGGACTAAAATAGAAAAAAC-AGAATCG
* *
1236475 TAAAGGACTAACATAGAAAAAACAGAATCT
1 TAAAGGACTAAAATAGAAAAAACAGAATCG
*
1236505 TAAAGGGCTAAAATA
1 TAAAGGACTAAAATA
1236520 ATTAAAACAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.19
Consensus pattern (30 bp):
TAAAGGACTAAAATAGAAAAAACAGAATCG
Found at i:1237744 original size:3 final size:3
Alignment explanation
Indices: 1237736--1237774 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
1237726 AGTAAAAACA
*
1237736 AAT AAT AAT ATAT AAT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
1237775 CATAATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1238154 original size:40 final size:40
Alignment explanation
Indices: 1238108--1238195 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
1238098 GGTTATCTGA
*
1238108 GTTGACACATCTCCTACATAATGAGGAGATCTGATCATGT
1 GTTGACACAACTCCTACATAATGAGGAGATCTGATCATGT
*
1238148 GTTGACACAACTCCTACATAATGAGGAGTTCTGATCATGT
1 GTTGACACAACTCCTACATAATGAGGAGATCTGATCATGT
*
1238188 GATGACAC
1 GTTGACAC
1238196 TGTTCATCTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (40 bp):
GTTGACACAACTCCTACATAATGAGGAGATCTGATCATGT
Found at i:1238268 original size:166 final size:166
Alignment explanation
Indices: 1238020--1238320 Score: 462
Period size: 166 Copynumber: 1.8 Consensus size: 166
1238010 ATGTAGTCAG
* *
1238020 GTGATGAAACTGCTCATCTGTTCATGAGTCTTGGTCATCTAAGGGTGATAACACTGTTCCAACGT
1 GTGATGAAACTGCTCATCTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCAACGT
* * * *
1238085 GATGAGGACGTCTGGTTATCTGAGTTGACACATCTCCTACATAATGAGGAGATCTGATCATGTGT
66 GATGAGGACGACTGGTTATCTGAGTTGACACAACTCCTACATAATGAGGAGATATGATCATGTGA
1238150 TGACACAACTCCTACATAATGAGGAGTTCTGATCAT
131 TGACACAACTCCTACATAATGAGGAGTTCTGATCAT
* * *
1238186 GTGATGACACTGTTCATCTGTTTATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCC-AC-T
1 GTGATGAAACTGCTCATCTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCAACGT
* * *
1238249 CTACTGGGGACGACTGGTTATCTGAGTTGACACAACTCCTATATAATGAGGAGATATGATCATGT
66 -GA-TGAGGACGACTGGTTATCTGAGTTGACACAACTCCTACATAATGAGGAGATATGATCATGT
1238314 GATGACA
129 GATGACA
1238321 TTGCTCATCT
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
164 1 0.01
165 3 0.02
166 117 0.97
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (166 bp):
GTGATGAAACTGCTCATCTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCAACGT
GATGAGGACGACTGGTTATCTGAGTTGACACAACTCCTACATAATGAGGAGATATGATCATGTGA
TGACACAACTCCTACATAATGAGGAGTTCTGATCAT
Found at i:1238309 original size:126 final size:126
Alignment explanation
Indices: 1238148--1238705 Score: 850
Period size: 126 Copynumber: 4.4 Consensus size: 126
1238138 CTGATCATGT
* * *
1238148 GTTGACACAACTCCTACATAATGAGGAGTTCTGATCATGTGATGACACTGTTCATCTGTTTATGA
1 GTTGACACAACTCCTACATAATGAGGAGATCTGATCATGTGATGACACTGCTCATCTGTTCATGA
*
1238213 GTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTACTGGGGACGACTGGTTATCTGA
66 GTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGCTGGGGACGACTGGTTATCTGA
* * *
1238274 GTTGACACAACTCCTATATAATGAGGAGATATGATCATGTGATGACATTGCTCATCTGTTCATGA
1 GTTGACACAACTCCTACATAATGAGGAGATCTGATCATGTGATGACACTGCTCATCTGTTCATGA
*
1238339 GTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGCTGGGGAC-AGTTGGTTATCTGA
66 GTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGCTGGGGACGA-CTGGTTATCTGA
* * * * * *
1238400 GTTGACACAGCTCCTACATAATGAGGAAATTTGATCATGTGATGACACTTCTCATATGTTTATGA
1 GTTGACACAACTCCTACATAATGAGGAGATCTGATCATGTGATGACACTGCTCATCTGTTCATGA
* * * *
1238465 GTCTTGGCCATCTAAGGGTGATAACATGGTTCCAATCTGCTGGGGACGGCTGGTTATATGA
66 GTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGCTGGGGACGACTGGTTATCTGA
* * * *
1238526 GTTGACACAATTCGTACATAATGAGGAGATCTAATCATGTGATGACACTACTCATCTGTTCATGA
1 GTTGACACAACTCCTACATAATGAGGAGATCTGATCATGTGATGACACTGCTCATCTGTTCATGA
* * *
1238591 GTCTTGGTCATCTAAGGATGATAACACGGTTCCACTCTGCTAGGGACGACTGGTTATCTGA
66 GTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGCTGGGGACGACTGGTTATCTGA
* *
1238652 GTTGGCATAACT-CTACATAATGAGGAGATCTGATCATGTGATGACACTGCTCAT
1 GTTGACACAACTCCTACATAATGAGGAGATCTGATCATGTGATGACACTGCTCAT
1238706 ACTATGATGA
Statistics
Matches: 387, Mismatches: 43, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
125 40 0.10
126 347 0.90
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (126 bp):
GTTGACACAACTCCTACATAATGAGGAGATCTGATCATGTGATGACACTGCTCATCTGTTCATGA
GTCTTGGCCATCTAAGGGTGATAACACGGTTCCACTCTGCTGGGGACGACTGGTTATCTGA
Found at i:1239057 original size:32 final size:33
Alignment explanation
Indices: 1238995--1239083 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 33
1238985 CACATCAGGG
* * * * *
1238995 TGTTAAATCCCCAAATATGACC-CAATATTTGA
1 TGTTGAATCTCCAAAAATGTCCTCAACATTTGA
* *
1239027 TGTTGGATCTCCAAAAATG-CCTCAACATTTGT
1 TGTTGAATCTCCAAAAATGTCCTCAACATTTGA
* *
1239059 TGTTGAATCTTCAAAGATGTCCTCA
1 TGTTGAATCTCCAAAAATGTCCTCA
1239084 TTATTCCTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 2 0.04
32 39 0.85
33 5 0.11
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (33 bp):
TGTTGAATCTCCAAAAATGTCCTCAACATTTGA
Found at i:1242312 original size:63 final size:63
Alignment explanation
Indices: 1242209--1242339 Score: 192
Period size: 63 Copynumber: 2.1 Consensus size: 63
1242199 TTTTATTTAG
** * *
1242209 AATG-ATCATGCAGAATTTGAAGATGCAAATACAGATGTAAAAGTGATGATCCTCTGAAATGT
1 AATGCATCATGCAGAATGCGAAAATGCAAATACAGATGTAAAAGTGATGATCCTCTGAAATGC
* * *
1242271 AATGCATCATGCATAATGCGAAAATGCAAATGCAGATGTAAAATTGATGATCCTCTGAAATGC
1 AATGCATCATGCAGAATGCGAAAATGCAAATACAGATGTAAAAGTGATGATCCTCTGAAATGC
1242334 AATGCA
1 AATGCA
1242340 ACAAGGGATG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
62 4 0.07
63 57 0.93
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (63 bp):
AATGCATCATGCAGAATGCGAAAATGCAAATACAGATGTAAAAGTGATGATCCTCTGAAATGC
Found at i:1244208 original size:30 final size:30
Alignment explanation
Indices: 1244163--1244249 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
1244153 TTTACAACCC
* * * *
1244163 AAAACAACAACTTAAATGACTAAAATAGTA
1 AAAACAAGAATTTAAAGGACTAAAATAGAA
* *
1244193 TAAACAAGAATTTAAAGGACTAACATAGAA
1 AAAACAAGAATTTAAAGGACTAAAATAGAA
*
1244223 AAAAC-AGAATCTTAAAGGGCTAAAATA
1 AAAACAAGAAT-TTAAAGGACTAAAATA
1244250 ATTAAAACAG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 5 0.11
30 42 0.89
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (30 bp):
AAAACAAGAATTTAAAGGACTAAAATAGAA
Found at i:1245542 original size:32 final size:34
Alignment explanation
Indices: 1245480--1245543 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
1245470 TTTCCTCTTG
*
1245480 ATTGATTGGAGTAGGTAGGGAACAAATTTCCTAT
1 ATTGATTAGAGTAGGTAGGGAACAAATTTCCTAT
1245514 ATTGATTAGAGTAGGTA-GG-ACAAATTTCCT
1 ATTGATTAGAGTAGGTAGGGAACAAATTTCCT
1245544 CTCCTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 11 0.38
33 2 0.07
34 16 0.55
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (34 bp):
ATTGATTAGAGTAGGTAGGGAACAAATTTCCTAT
Found at i:1245690 original size:3 final size:3
Alignment explanation
Indices: 1245672--1245730 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
1245662 AACACATATT
* * * *
1245672 ATA AGTA ATAA ATA ATA ATA ATA ATA AT- TTC ATA ATA ATA TTT ATA
1 ATA A-TA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1245718 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
1245731 CATAATATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 1 0.02
3 39 0.85
4 6 0.13
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:1245728 original size:29 final size:28
Alignment explanation
Indices: 1245686--1245743 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
1245676 GTAATAAATA
**
1245686 ATAATAATAATAATTTCATAATAATATTT
1 ATAATAATAATAATAACATAAT-ATATTT
1245715 ATAATAATAATAATAACATAATATATTT
1 ATAATAATAATAATAACATAATATATTT
1245743 A
1 A
1245744 ATATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAATAATAATAATAACATAATATATTT
Found at i:1253713 original size:19 final size:19
Alignment explanation
Indices: 1253689--1253735 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1253679 TATGAATGAA
1253689 TAAAATGCAATGTGAAAAG
1 TAAAATGCAATGTGAAAAG
*
1253708 TAAAATGCAGTGTGAAAAG
1 TAAAATGCAATGTGAAAAG
1253727 TAAAATGCA
1 TAAAATGCA
1253736 TATGCAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.21
Consensus pattern (19 bp):
TAAAATGCAATGTGAAAAG
Found at i:1253744 original size:19 final size:18
Alignment explanation
Indices: 1253689--1253744 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
1253679 TATGAATGAA
*
1253689 TAAAATGCAATGTGAAAAG
1 TAAAATGC-ATATGAAAAG
*
1253708 TAAAATGCAGTGTGAAAAG
1 TAAAATGCA-TATGAAAAG
1253727 TAAAATGCATATGCAAAA
1 TAAAATGCATATG-AAAA
1253745 TGCAAGGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.12
19 30 0.88
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (18 bp):
TAAAATGCATATGAAAAG
Found at i:1255101 original size:439 final size:439
Alignment explanation
Indices: 1254283--1255161 Score: 1537
Period size: 439 Copynumber: 2.0 Consensus size: 439
1254273 CTCTAATGCA
* * *
1254283 CTCTTTTCTTTTGAAAGTATCTTCGCCTGATGTCTGCTATGCTTGAGCTCTTCTTTACTTTCTCT
1 CTCTTTTCTTTTAAAAGTATCTTCGCCTGATGTCTGCTATGCTTGAGCTCTTCTTTAATTTCTCC
* * * * *
1254348 AACTTCTTCTTTAGTTTGCTCATATCGTTTTGGCGGACATTAATGTAGGTGTAACCAGTTATATC
66 AACTTCTTCTTTAGCTTCCTCATATCATTTTGACGGACATTAATGTAGGTGTAACCAGTCATATC
* *
1254413 TGACACGAATCCAGGCGGTAAGCTATCTCTATTGGTGATTTGGGACTGCTCAGACCATCTCATAA
131 TGACACAAATCCAGGCGGTAAGCTATCGCTATTGGTGATTTGGGACTGCTCAGACCATCTCATAA
* * * * * *
1254478 CATTTGCATTGTCTTCTTCCTATTTTTGGACTATTCGTTCCATATTACTAGCCTTCTATATGGAC
196 CATCTGCATTATCTTATTCCTATTTTTGGACCATTCGTTCCATATTACTAGCATTCTATATGGAA
1254543 ATTGATCACGGATCAACACCATGGAATGAGTAGTGCAATGCAAAAAACATAAATAAAATAAAAAG
261 ATTGATCACGGATCAACACCATGGAATGAGTAGTGCAATGCAAAAAACATAAATAAAATAAAAAG
1254608 ACAAAAGAAAATCAGTCAGTAATCATAAATAAATCAATCAAGAATAATATAATTTGTCAATAAAA
326 ACAAAAGAAAATCAGTCAGTAATCATAAATAAATCAATCAAGAATAATATAATTTGTCAATAAAA
1254673 CCTACCCTCACATGTCGACTACCCAATCATGCTTTA-ACAGTATCCTACC
391 CCTACCCTCACATGTCGACTACCCAATCATGCTTTAGA-AGTATCCTACC
1254722 CTCTTTTCTTTTAAAAGTATCTTCGCCTGATGTCTGCTATGCTTGAGCTCTTCTTTAATTTCTCC
1 CTCTTTTCTTTTAAAAGTATCTTCGCCTGATGTCTGCTATGCTTGAGCTCTTCTTTAATTTCTCC
1254787 AACTTCTTCTTTAGCTTCCTCATATCATTTTGACGGACATTAATGTAGGTGTAACCAGTCATATC
66 AACTTCTTCTTTAGCTTCCTCATATCATTTTGACGGACATTAATGTAGGTGTAACCAGTCATATC
* *
1254852 TGACACAAATCTAGGCGGTAAGCTATCGCTATTGGTGATTTGGGACTGCTCGGACCATCTC-TGA
131 TGACACAAATCCAGGCGGTAAGCTATCGCTATTGGTGATTTGGGACTGCTCAGACCATCTCAT-A
1254916 ACATCTGCATTATCTTATTCCTATTTTTGGACCATTCGTTCCATATTACTAGCATTCTATATGGA
195 ACATCTGCATTATCTTATTCCTATTTTTGGACCATTCGTTCCATATTACTAGCATTCTATATGGA
1254981 AATTGATCACGGATCAACACCATGGAATGAGTAGTGCAATGCAAAAAACATAAATAAAATAAAAA
260 AATTGATCACGGATCAACACCATGGAATGAGTAGTGCAATGCAAAAAACATAAATAAAATAAAAA
1255046 GACAAAAGAAAATCAGTCAGTAATCATAAATAAATCAATCAAGAATAATATAATTTGTCAATAAA
325 GACAAAAGAAAATCAGTCAGTAATCATAAATAAATCAATCAAGAATAATATAATTTGTCAATAAA
** *
1255111 ACCTACCCTCACATGTCGGTTACCCAGTCATGCTTTAGAAGTATCCTACC
390 ACCTACCCTCACATGTCGACTACCCAATCATGCTTTAGAAGTATCCTACC
1255161 C
1 C
1255162 CAAACATGAT
Statistics
Matches: 417, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
438 1 0.00
439 415 1.00
440 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (439 bp):
CTCTTTTCTTTTAAAAGTATCTTCGCCTGATGTCTGCTATGCTTGAGCTCTTCTTTAATTTCTCC
AACTTCTTCTTTAGCTTCCTCATATCATTTTGACGGACATTAATGTAGGTGTAACCAGTCATATC
TGACACAAATCCAGGCGGTAAGCTATCGCTATTGGTGATTTGGGACTGCTCAGACCATCTCATAA
CATCTGCATTATCTTATTCCTATTTTTGGACCATTCGTTCCATATTACTAGCATTCTATATGGAA
ATTGATCACGGATCAACACCATGGAATGAGTAGTGCAATGCAAAAAACATAAATAAAATAAAAAG
ACAAAAGAAAATCAGTCAGTAATCATAAATAAATCAATCAAGAATAATATAATTTGTCAATAAAA
CCTACCCTCACATGTCGACTACCCAATCATGCTTTAGAAGTATCCTACC
Found at i:1257029 original size:16 final size:17
Alignment explanation
Indices: 1257008--1257044 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1256998 AGTATATGAT
1257008 ATATAAA-ATAATAT-TA
1 ATATAAATAT-ATATGTA
1257024 ATATAAATATATATGTA
1 ATATAAATATATATGTA
1257041 ATAT
1 ATAT
1257045 TTACATACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATATAAATATATATGTA
Found at i:1258851 original size:3 final size:3
Alignment explanation
Indices: 1258830--1258893 Score: 92
Period size: 3 Copynumber: 20.7 Consensus size: 3
1258820 CCGGATCTAC
* *
1258830 AAT AAT ATAT AAT ATT AAT AAT AAT AAGT AAC AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
1258877 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
1258894 ATTATAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1264722 original size:18 final size:18
Alignment explanation
Indices: 1264695--1264735 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1264685 TGAAGATCAG
* *
1264695 TTTTCTTTTTATCATTCT
1 TTTTCCTTTTATAATTCT
1264713 TTTTCCTTTTATAATTCT
1 TTTTCCTTTTATAATTCT
*
1264731 ATTTC
1 TTTTC
1264736 TGCTTTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCCTTTTATAATTCT
Found at i:1268370 original size:30 final size:31
Alignment explanation
Indices: 1268305--1268381 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
1268295 AAAACAACAA
* * *
1268305 CTTAAATGACTAAAATAGTACAAACAGGAAT
1 CTTAAAGGACTAAAATAGAAAAAACAGGAAT
* *
1268336 -TTAAAGGACTAACATAGAAAAAATA-GAAT
1 CTTAAAGGACTAAAATAGAAAAAACAGGAAT
*
1268365 CTTAAAGGGCTAAAATA
1 CTTAAAGGACTAAAATA
1268382 ATTAAAACAG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.22
Consensus pattern (31 bp):
CTTAAAGGACTAAAATAGAAAAAACAGGAAT
Found at i:1270792 original size:32 final size:34
Alignment explanation
Indices: 1270721--1270797 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
1270711 CTTTATGTTG
*
1270721 ATTTCCTCTTGATTGATTGGATTAGGTAGGGGACAA
1 ATTTCCTC-TGATTGATTGGAGTAGGTA-GGGACAA
1270757 ATTTCCTCT-ATTGATTGGAGTAGGTA-GGACAA
1 ATTTCCTCTGATTGATTGGAGTAGGTAGGGACAA
1270789 ATTTCCTCT
1 ATTTCCTCT
1270798 CATTTTTTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 15 0.38
34 16 0.40
35 1 0.03
36 8 0.20
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (34 bp):
ATTTCCTCTGATTGATTGGAGTAGGTAGGGACAA
Found at i:1271245 original size:43 final size:43
Alignment explanation
Indices: 1271193--1271298 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 43
1271183 TGATTTATAG
* *
1271193 TGGCATTTTTGTTCGA-AAATGCCACTAATTATTATGTCTTTAA
1 TGGCATTTTT-TGCGACAAACGCCACTAATTATTATGTCTTTAA
* * * *
1271236 TGTCATTTTTTGCTACAAACGCCGCTAATTATTCTGTCTTTAA
1 TGGCATTTTTTGCGACAAACGCCACTAATTATTATGTCTTTAA
*
1271279 TGGCATTTTTTTGCTACAAA
1 TGGCA-TTTTTTGCGACAAA
1271299 ACGCGGCTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 3 0.06
43 37 0.69
44 14 0.26
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.44
Consensus pattern (43 bp):
TGGCATTTTTTGCGACAAACGCCACTAATTATTATGTCTTTAA
Found at i:1271290 original size:44 final size:44
Alignment explanation
Indices: 1271208--1271310 Score: 145
Period size: 43 Copynumber: 2.3 Consensus size: 44
1271198 TTTTTGTTCG
* * *
1271208 AAAATGCCACTAATTATTATGTCTTTAATGTCATTTTTTGCTAC
1 AAAACGCCGCTAATTATTATGTCTTTAATGGCATTTTTTGCTAC
*
1271252 -AAACGCCGCTAATTATTCTGTCTTTAATGGCATTTTTTTGCTAC
1 AAAACGCCGCTAATTATTATGTCTTTAATGGCA-TTTTTTGCTAC
*
1271296 AAAACGCGGCTAATT
1 AAAACGCCGCTAATT
1271311 CTTTTGTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
43 28 0.54
44 11 0.21
45 13 0.25
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (44 bp):
AAAACGCCGCTAATTATTATGTCTTTAATGGCATTTTTTGCTAC
Found at i:1271333 original size:45 final size:44
Alignment explanation
Indices: 1271217--1271333 Score: 119
Period size: 45 Copynumber: 2.7 Consensus size: 44
1271207 GAAAATGCCA
* * *
1271217 CTAATTATTATGTCTTTAATGTCA-TTTTTTGCTACAAACGCCG
1 CTAATTATTCTGTCTTTAACGACATTTTTTTGCTACAAACGCCG
* * *
1271260 CTAATTATTCTGTCTTTAATGGCATTTTTTTGCTACAAAACGCGG
1 CTAATTATTCTGTCTTTAACGACATTTTTTTGCTAC-AAACGCCG
* * * * *
1271305 CTAATTCTTTTGTTTTTAGCGACGTTTTT
1 CTAATTATTCTGTCTTTAACGACATTTTT
1271334 AATGCAAAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 22 0.35
44 11 0.18
45 29 0.47
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (44 bp):
CTAATTATTCTGTCTTTAACGACATTTTTTTGCTACAAACGCCG
Found at i:1277884 original size:13 final size:13
Alignment explanation
Indices: 1277866--1277893 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1277856 ATTGAAGTCA
1277866 TATTTCCTCACAT
1 TATTTCCTCACAT
1277879 TATTTCCTCACAT
1 TATTTCCTCACAT
1277892 TA
1 TA
1277894 GCTCCAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTTCCTCACAT
Found at i:1278352 original size:19 final size:19
Alignment explanation
Indices: 1278297--1278340 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1278287 TATGAATGGA
* *
1278297 TAAACTACAATGTGAAAAG
1 TAAAATACAATGCGAAAAG
*
1278316 TAAAATACAGTGCGAAAAG
1 TAAAATACAATGCGAAAAG
1278335 TAAAAT
1 TAAAAT
1278341 GCATATGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.20
Consensus pattern (19 bp):
TAAAATACAATGCGAAAAG
Found at i:1285723 original size:3 final size:3
Alignment explanation
Indices: 1285702--1285758 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
1285692 CCGGATCGAC
* *
1285702 AAT AAT ATAT AAT ATT AAT AAT AAT AAGT AA- AAT AAT AAA AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
1285748 AAT AAT AAT AA
1 AAT AAT AAT AA
1285759 AATTATAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1285769 original size:9 final size:9
Alignment explanation
Indices: 1285717--1285770 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
1285707 TATATAATAT
*
1285717 TAATAATAA
1 TAATAAAAA
1285726 TAAGT-AAAA
1 TAA-TAAAAA
1285735 TAATAAAAA
1 TAATAAAAA
*
1285744 TAATAATAA
1 TAATAAAAA
1285753 TAAT-AAAA
1 TAATAAAAA
*
1285761 TTATAAAAA
1 TAATAAAAA
1285770 T
1 T
1285771 GAAAAGTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
8 7 0.18
9 30 0.79
10 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
TAATAAAAA
Found at i:1290065 original size:27 final size:30
Alignment explanation
Indices: 1290003--1290072 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1289993 AAAAATTATT
*
1290003 AAATTACAATAAAAGTCTAAATATTTATAA
1 AAATTATAATAAAAGTCTAAATATTTATAA
*
1290033 AAATTATTATAAAAGTCT-AAT-TTT-TAA
1 AAATTATAATAAAAGTCTAAATATTTATAA
*
1290060 ATATTATAATAAA
1 AAATTATAATAAA
1290073 TGCCAAAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 14 0.39
28 3 0.08
29 3 0.08
30 16 0.44
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (30 bp):
AAATTATAATAAAAGTCTAAATATTTATAA
Found at i:1290086 original size:29 final size:29
Alignment explanation
Indices: 1290053--1290216 Score: 172
Period size: 29 Copynumber: 5.7 Consensus size: 29
1290043 AAAAGTCTAA
* *
1290053 TTTTTA-AATATTATAATAAATGCCAAAAC
1 TTTTTATAA-ATTACAATAAATACCAAAAC
* **
1290082 TTTTTATAAATTACAATAAATATCACAATT
1 TTTTTATAAATTACAATAAATACCA-AAAC
*
1290112 TTTTTATAAATTACAATAAATACCATAAC
1 TTTTTATAAATTACAATAAATACCAAAAC
*
1290141 TTTTTATAAATTACAATAAACACCAAAAC
1 TTTTTATAAATTACAATAAATACCAAAAC
* *
1290170 TATTTATAAATTACAATCAAAGA--AAAAC
1 TTTTTATAAATTACAAT-AAATACCAAAAC
***
1290198 TTACCATAAATTACAATAA
1 TTTTTATAAATTACAATAA
1290217 TGGCTTATAA
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.02
28 18 0.16
29 63 0.55
30 32 0.28
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.35
Consensus pattern (29 bp):
TTTTTATAAATTACAATAAATACCAAAAC
Found at i:1290132 original size:59 final size:58
Alignment explanation
Indices: 1290053--1290216 Score: 172
Period size: 59 Copynumber: 2.8 Consensus size: 58
1290043 AAAAGTCTAA
* * * **
1290053 TTTTTA-AATATTATAATAAATGCCAAAACTTTTTATAAATTACAATAAATATCACAATT
1 TTTTTATAA-ATTACAATAAATGCCAAAACTTTTTATAAATTACAATAAACACCA-AAAC
* *
1290112 TTTTTATAAATTACAATAAATACCATAACTTTTTATAAATTACAATAAACACCAAAAC
1 TTTTTATAAATTACAATAAATGCCAAAACTTTTTATAAATTACAATAAACACCAAAAC
* * ***
1290170 TATTTATAAATTACAATCAAA-G-AAAAACTTACCATAAATTACAATAA
1 TTTTTATAAATTACAAT-AAATGCCAAAACTTTTTATAAATTACAATAA
1290217 TGGCTTATAA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
57 20 0.22
58 18 0.20
59 49 0.55
60 2 0.02
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.35
Consensus pattern (58 bp):
TTTTTATAAATTACAATAAATGCCAAAACTTTTTATAAATTACAATAAACACCAAAAC
Found at i:1291399 original size:18 final size:19
Alignment explanation
Indices: 1291378--1291422 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1291368 TTTTCAAACG
* *
1291378 TTTTTTATATTTCTTA-AA
1 TTTTTAATATTTATTATAA
1291396 TTTTTAATATTTATTATAA
1 TTTTTAATATTTATTATAA
1291415 -TTTTAATA
1 TTTTTAATA
1291423 ACATTTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTAATATTTATTATAA
Found at i:1293595 original size:2 final size:2
Alignment explanation
Indices: 1293588--1293620 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1293578 AAAATATCTA
1293588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1293621 CTAAAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1306329 original size:19 final size:19
Alignment explanation
Indices: 1306305--1306352 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1306295 ACCTGAATCT
* *
1306305 ATAATAATATATAATATTA
1 ATAATAATATATAAAAATA
*
1306324 ATAATAATAAATAAAAATA
1 ATAATAATATATAAAAATA
*
1306343 AAAATAATAT
1 ATAATAATAT
1306353 TATTATTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATAATATATAAAAATA
Found at i:1306428 original size:2 final size:2
Alignment explanation
Indices: 1306423--1306447 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1306413 TCTTAAAAAC
1306423 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
1306448 TAACCTAACA
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:1308507 original size:8 final size:8
Alignment explanation
Indices: 1308453--1308543 Score: 51
Period size: 8 Copynumber: 11.2 Consensus size: 8
1308443 GTGTTAGAGG
*
1308453 AAAAAATG
1 AAAAAATA
* *
1308461 AATAAATG
1 AAAAAATA
*
1308469 AAAAAAGA
1 AAAAAATA
*
1308477 AGAAGAATA
1 A-AAAAATA
1308486 AAAATAAGTA
1 AAAA-AA-TA
1308496 AAAAAAT-
1 AAAAAATA
1308503 -AAAAATA
1 AAAAAATA
**
1308510 AAAGGATA
1 AAAAAATA
*
1308518 AATAAATA
1 AAAAAATA
*
1308526 AATAAATA
1 AAAAAATA
*
1308534 AATAAATA
1 AAAAAATA
1308542 AA
1 AA
1308544 TGAAATATTA
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
6 6 0.09
8 44 0.67
9 10 0.15
10 6 0.09
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (8 bp):
AAAAAATA
Found at i:1308524 original size:4 final size:4
Alignment explanation
Indices: 1308515--1308550 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
1308505 AAATAAAAGG
1308515 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATGAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATA
1308551 TTAATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:1308561 original size:2 final size:2
Alignment explanation
Indices: 1308554--1308590 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1308544 TGAAATATTA
1308554 AT 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 AT A
1308591 AATGAGTAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1308672 original size:18 final size:17
Alignment explanation
Indices: 1308651--1308706 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
1308641 AAAATATAAT
1308651 ATAATATAATATAAACAA
1 ATAA-ATAATATAAACAA
* * *
1308669 ATAAAAAAATAAAAAAAA
1 AT-AAATAATATAAACAA
1308687 ATAAAT-ATATAAATCAA
1 ATAAATAATATAAA-CAA
1308704 ATA
1 ATA
1308707 TAAAAGTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 6 0.20
17 8 0.27
18 14 0.47
19 2 0.07
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAATAATATAAACAA
Found at i:1308984 original size:63 final size:61
Alignment explanation
Indices: 1308842--1309008 Score: 151
Period size: 65 Copynumber: 2.6 Consensus size: 61
1308832 GCTTATAAGT
*
1308842 AAAATATTTAAAAAAAGTATGTATATATATATAAATAATAATATTAAAAAATAACCAAATG
1 AAAATATTTAAAAAAAATATGTATATATATATAAATAATAATATTAAAAAATAACCAAATG
** * *
1308903 AATATAAATAAATAAAAAATATATGTATATATA-AT-AATAATATATAGTGTAAAAAAT-ATCAA
1 ---A-AAATATTTAAAAAAAATATGTATATATATATAAATAATA-ATA-T-TAAAAAATAACCAA
*
1308965 TTG
59 ATG
* * *
1308968 AAAATCATTTAAAAAAACATACGTATATATATTTATATAAT
1 AAAAT-ATTTAAAAAAA-ATATGTATATATATATAAATAAT
1309009 GACAATAATG
Statistics
Matches: 83, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
61 4 0.05
62 9 0.11
63 19 0.23
64 7 0.08
65 36 0.43
66 8 0.10
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.34
Consensus pattern (61 bp):
AAAATATTTAAAAAAAATATGTATATATATATAAATAATAATATTAAAAAATAACCAAATG
Found at i:1309469 original size:37 final size:37
Alignment explanation
Indices: 1309428--1309524 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
1309418 GGATCATATC
* * *
1309428 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTACT
* *
1309465 TTTAGGAGTTTGAATCCTAGTAAAATTCTATCCTACT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTACT
1309502 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCCTAGTAG
1309525 GACGAAAAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTACT
Found at i:1310439 original size:106 final size:106
Alignment explanation
Indices: 1310255--1311938 Score: 2643
Period size: 106 Copynumber: 15.9 Consensus size: 106
1310245 GCATTGTTCC
* * ** * * *
1310255 GAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGAACCT-GGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTATTGACA
* * * *
1310319 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1310361 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1310426 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1310467 GAGTCCAATATCCATCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAACTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1310532 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1310573 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1310638 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1310679 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1310744 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1310785 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTAGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
1310850 CCAGCGGT-CCTTCGTCGTGAAGTTGAACTTGTGATGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1310890 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1310955 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1310996 GAGTCCAATATCCTTCGTTGTGAACTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1311061 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1311102 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTCGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
1311167 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1311208 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGTAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
1311273 CCATCGGTCCCTTTGTCGTAAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1311314 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1311379 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1311420 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1311485 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1311526 CAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1311591 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1311632 GAGTCCAATATACTTCGCTGTGAAGTTGAAATTGACTCTGAAATTAGGAAGTTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
1311697 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1311738 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1311803 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1311844 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
** * *
1311909 CCAGCCATTCCTTCGTTGTGAAGTTGAACT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT
1311939 CCACTCTCGA
Statistics
Matches: 1464, Mismatches: 112, Indels: 4
0.93 0.07 0.00
Matches are distributed among these distances:
105 101 0.07
106 1363 0.93
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1312697 original size:22 final size:22
Alignment explanation
Indices: 1312671--1312725 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1312661 TTATGTTTGG
1312671 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1312693 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1312715 TCAAAGGTTTG
1 TCAAAGGTTTG
1312726 ATGGGGTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1313341 original size:11 final size:11
Alignment explanation
Indices: 1313320--1313386 Score: 56
Period size: 10 Copynumber: 6.5 Consensus size: 11
1313310 TCTTTTTGAT
1313320 TTTTGTTCTTTC
1 TTTT-TTCTTTC
1313332 TTTTTTCTTT-
1 TTTTTTCTTTC
*
1313342 TGTTTTC-TTC
1 TTTTTTCTTTC
1313352 TTTTTTGC-TTC
1 TTTTTT-CTTTC
1313363 TTTTTT-TTT-
1 TTTTTTCTTTC
*
1313372 GTTTTT-TTTC
1 TTTTTTCTTTC
1313382 TTTTT
1 TTTTT
1313387 GTTCTGATTG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
9 10 0.21
10 17 0.36
11 16 0.34
12 4 0.09
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTC
Done.