Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008661.1 Hibiscus syriacus cultivar Beakdansim tig00111659_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: 1762280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:520122 original size:20 final size:21
Alignment explanation
Indices: 520084--520122 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
520074 AAAATTTATC
*
520084 TAAAATATTAATATTTTTACT
1 TAAAATATCAATATTTTTACT
520105 TAAAATATCAAT-TTTTTA
1 TAAAATATCAATATTTTTA
520123 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAATATCAATATTTTTACT
Found at i:520174 original size:23 final size:21
Alignment explanation
Indices: 520147--520197 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
520137 AATATCAAAT
520147 AATAATAAAATCGATAGAAAAAA
1 AATAATAAAATC-A-AGAAAAAA
* *
520170 AATAATAAAATCAATAAAAAT
1 AATAATAAAATCAAGAAAAAA
520191 AATAATA
1 AATAATA
520198 TTTCCGGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 13 0.50
22 1 0.04
23 12 0.46
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (21 bp):
AATAATAAAATCAAGAAAAAA
Found at i:522824 original size:15 final size:15
Alignment explanation
Indices: 522799--522876 Score: 56
Period size: 14 Copynumber: 5.3 Consensus size: 15
522789 TCCTTAAGCT
522799 TTAAA-TTTAGATCC
1 TTAAATTTTAGATCC
*
522813 TTAAATTTTAGA-CTT
1 TTAAATTTTAGATC-C
*
522828 TTACA-TTTAGATCC
1 TTAAATTTTAGATCC
** *
522842 TTGGATTTTAGCTCTC
1 TTAAATTTTAGATC-C
*
522858 TTACATTTTAG-TCC
1 TTAAATTTTAGATCC
522872 TTAAA
1 TTAAA
522877 ACTTCAATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
14 20 0.40
15 20 0.40
16 10 0.20
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (15 bp):
TTAAATTTTAGATCC
Found at i:522838 original size:29 final size:29
Alignment explanation
Indices: 522797--522876 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
522787 AATCCTTAAG
*
522797 CTTTAAATTTAGATCCTTAAATTTTAGACT
1 CTTTACATTTAGATCCTTAAATTTTAG-CT
**
522827 -TTTACATTTAGATCCTTGGATTTTAGCT
1 CTTTACATTTAGATCCTTAAATTTTAGCT
522855 CTCTTACATTTTAG-TCCTTAAA
1 CT-TTACA-TTTAGATCCTTAAA
522877 ACTTCAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 11 0.26
31 5 0.12
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (29 bp):
CTTTACATTTAGATCCTTAAATTTTAGCT
Found at i:524280 original size:2 final size:2
Alignment explanation
Indices: 524273--524297 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
524263 TTTTTATTTT
524273 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
524298 GTAATTTTTC
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:527002 original size:135 final size:136
Alignment explanation
Indices: 526829--527095 Score: 527
Period size: 135 Copynumber: 2.0 Consensus size: 136
526819 ACATGGCACT
526829 CTTACCATCCGGATTCGCAATCCTTCTGTATACTTCACCGAGTTACCATGGTGGACGAAGTGACT
1 CTTACCATCCGGATTCGCAATCCTTCTGTATACTTCACCGAGTTACCATGGTGGACGAAGTGACT
526894 CCAACGGACCTTTGGTTAAAAATGAGTTCGATGGGAGTATAAGTGGTGGATGCCTAC-TACAGTA
66 CCAACGGACCTTTGGTTAAAAATGAGTTCGATGGGAGTATAAGTGGTGGATGCCTACTTACAGTA
526958 GGGGCA
131 GGGGCA
526964 CTTACCATCCGGATTCGCAATCCTTCTGTATACTTCACCGAGTTACCATGGTGGACGAAGTGACT
1 CTTACCATCCGGATTCGCAATCCTTCTGTATACTTCACCGAGTTACCATGGTGGACGAAGTGACT
527029 CCAACGGACCTTTGGTTAAAAATGAGTTCGATGGGAGTATAAGTGGTGGATGCCTACTTACAGTA
66 CCAACGGACCTTTGGTTAAAAATGAGTTCGATGGGAGTATAAGTGGTGGATGCCTACTTACAGTA
527094 GG
131 GG
527096 ATTTCAGATT
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
135 122 0.93
136 9 0.07
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (136 bp):
CTTACCATCCGGATTCGCAATCCTTCTGTATACTTCACCGAGTTACCATGGTGGACGAAGTGACT
CCAACGGACCTTTGGTTAAAAATGAGTTCGATGGGAGTATAAGTGGTGGATGCCTACTTACAGTA
GGGGCA
Found at i:528685 original size:20 final size:19
Alignment explanation
Indices: 528638--528714 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
528628 TGCGATTTTC
528638 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCG-ATAT
*
528658 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGA-TAT
* *
528678 GACTATCGCAACGCGATGCT
1 GACTATCGCAATGCGAT-AT
528698 GACTATCGCAATGCGAT
1 GACTATCGCAATGCGAT
528715 TTTCAAAGCG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.06
20 44 0.92
21 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (19 bp):
GACTATCGCAATGCGATAT
Found at i:528910 original size:22 final size:22
Alignment explanation
Indices: 528882--528936 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
528872 CTCTCTAAGG
*
528882 CGAAATCCGTCCCCATCTTCGA
1 CGAAATCCGTCCCCATCTCCGA
* *
528904 CGAAATCAGTCCCCATCTCCGG
1 CGAAATCCGTCCCCATCTCCGA
528926 CGAAATCCGTC
1 CGAAATCCGTC
528937 TATCTCCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (22 bp):
CGAAATCCGTCCCCATCTCCGA
Found at i:529338 original size:19 final size:19
Alignment explanation
Indices: 529316--529360 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
529306 ATAATCGCAA
529316 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
529335 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
529354 TGCGATT
1 TGCGATT
529361 CTCGCATTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:529409 original size:20 final size:20
Alignment explanation
Indices: 529367--529433 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
529357 GATTCTCGCA
** * *
529367 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTTGTG
529387 TTGCGATAGTCATTTTTGTG
1 TTGCGATAGTCATTTTTGTG
**
529407 TTGCGATTTTCATTTTTGTG
1 TTGCGATAGTCATTTTTGTG
529427 TTGCGAT
1 TTGCGAT
529434 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.16, C:0.13, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGCGATAGTCATTTTTGTG
Found at i:529434 original size:20 final size:20
Alignment explanation
Indices: 529386--529436 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
529376 TCAAATTCGC
**
529386 GTTGCGATAGTCATTTTTGT
1 GTTGCGATTTTCATTTTTGT
529406 GTTGCGATTTTCATTTTTGT
1 GTTGCGATTTTCATTTTTGT
529426 GTTGCGATTTT
1 GTTGCGATTTT
529437 AAGTTTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.10, G:0.24, T:0.55
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTTGT
Found at i:531182 original size:18 final size:18
Alignment explanation
Indices: 531159--531208 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
531149 TTTACTCGTA
531159 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
531177 ATTTCACTAAGATTAACC
1 ATTTCACTTAGATTAACC
531195 ATTTCACTTAGATT
1 ATTTCACTTAGATT
531209 GCTTAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:531382 original size:20 final size:20
Alignment explanation
Indices: 531357--531403 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
531347 AGTTTACTTC
531357 CGCAACGCGAAAATGACTAT
1 CGCAACGCGAAAATGACTAT
**
531377 CGCAACGCGAATTTGACTAT
1 CGCAACGCGAAAATGACTAT
531397 CGCAACG
1 CGCAACG
531404 AAAGAATCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (20 bp):
CGCAACGCGAAAATGACTAT
Found at i:531471 original size:20 final size:21
Alignment explanation
Indices: 531446--531501 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
531436 GCGATTCTCT
*
531446 CGTTGCAATAGTCA-AATTCG
1 CGTTGCGATAGTCATAATTCG
**
531466 CGTTGCGATAGTCATTTTTCG
1 CGTTGCGATAGTCATAATTCG
531487 CGTTGCGATAGTCAT
1 CGTTGCGATAGTCAT
531502 TCGTGTTGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCATAATTCG
Found at i:531488 original size:21 final size:21
Alignment explanation
Indices: 531462--531502 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
531452 AATAGTCAAA
531462 TTCGCGTTGCGATAGTCATTT
1 TTCGCGTTGCGATAGTCATTT
531483 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
531503 CGTGTTGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCATTT
Found at i:531810 original size:21 final size:21
Alignment explanation
Indices: 531787--531862 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
531777 GGCTTCCCCT
*
531787 ATCGTTCAAGAGGCCACTATT
1 ATCGTTCAAGAGGCCACTATC
** * * **
531808 ATCCCTCAAGAGTCCCCTCCC
1 ATCGTTCAAGAGGCCACTATC
*
531829 ACCGTTCAAGAGGCCACTATC
1 ATCGTTCAAGAGGCCACTATC
*
531850 ATCGTTGAAGAGG
1 ATCGTTCAAGAGG
531863 TCCCTCCCAA
Statistics
Matches: 39, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCACTATC
Found at i:531861 original size:42 final size:42
Alignment explanation
Indices: 531789--531871 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
531779 CTTCCCCTAT
*
531789 CGTTCAAGAGGCCACTATTATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
** *
531831 CGTTCAAGAGGCCACTATCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
531872 ACATTCTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:533311 original size:14 final size:14
Alignment explanation
Indices: 533277--533338 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
533267 TTGCTTGTTT
*
533277 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
533291 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
533305 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
533320 TATTGATGTGTAAA
1 AATTGATTTGTAAA
533334 TAATT
1 -AATT
533339 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:533475 original size:20 final size:20
Alignment explanation
Indices: 533452--533490 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
533442 ACGCTAAACT
*
533452 CAAAATCGCAATGCGAAAGA
1 CAAAATCGCAACGCGAAAGA
533472 CAAAATCGCAACGCGAAAG
1 CAAAATCGCAACGCGAAAG
533491 TCAATTCGCG
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:0.49, C:0.23, G:0.21, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACGCGAAAGA
Found at i:533526 original size:20 final size:20
Alignment explanation
Indices: 533484--533763 Score: 291
Period size: 20 Copynumber: 14.7 Consensus size: 20
533474 AAATCGCAAC
*
533484 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
533503 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
533523 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
533537 ACGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
*
533557 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
533577 GCGATACTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
533597 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
533617 GCGATAGTCAAA-TAGCCGTT
1 GCGATAGTCAAATTCG-CGTT
533637 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
533657 GCGATAGTCATATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
*
533677 GTGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
533697 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
*
533711 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
533731 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
533751 GCGATATTCAAAT
1 GCGATAGTCAAAT
533764 GAATGTGTAA
Statistics
Matches: 217, Mismatches: 29, Indels: 29
0.79 0.11 0.11
Matches are distributed among these distances:
14 20 0.09
16 2 0.01
18 2 0.01
19 10 0.05
20 181 0.83
21 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:534082 original size:18 final size:18
Alignment explanation
Indices: 534059--534093 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
534049 AAGCCGGTTG
*
534059 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
534077 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
534094 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:536147 original size:14 final size:14
Alignment explanation
Indices: 536128--536154 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
536118 TCCCGTGGCA
536128 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
536142 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
536155 TTTCTTCTTT
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:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:536160 original size:12 final size:13
Alignment explanation
Indices: 536129--536161 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
536119 CCCGTGGCAT
536129 TTTCTTCGGGGAC
1 TTTCTTCGGGGAC
536142 TTTTCTTCGGGGA-
1 -TTTCTTCGGGGAC
536155 TTTCTTC
1 TTTCTTC
536162 TTTTTCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.06, C:0.21, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTCTTCGGGGAC
Found at i:536388 original size:24 final size:24
Alignment explanation
Indices: 536354--536407 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
536344 CTGAAACATC
536354 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
536378 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
536402 ATCAAA
1 ATCAAA
536408 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:537264 original size:20 final size:20
Alignment explanation
Indices: 537228--537349 Score: 129
Period size: 20 Copynumber: 6.0 Consensus size: 20
537218 AAATTCAGTG
* * *
537228 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAAAATCGCA
* *
537248 TTACGATAGTCAAAATCGTA
1 TTGCGATAGTCAAAATCGCA
537268 TTGCGATAGTCAAAATCGCA
1 TTGCGATAGTCAAAATCGCA
*
537288 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAAAATCGCA
* * *
537308 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAAAATCGCA
537328 TTGCGATAGTCGGAAAATCGCA
1 TTGCGATAGTC--AAAATCGCA
537350 ACGCGAATTT
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 76 0.89
21 1 0.01
22 7 0.08
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCAAAATCGCA
Found at i:538646 original size:60 final size:60
Alignment explanation
Indices: 538521--538639 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 60
538511 GCTATTTTAA
* * *
538521 AACTTTTAATAGTCAAGGGACTAAACAAAACAACTCTCTATAGTCAGGGGACCATGTTGT
1 AACTTTTAATAGTCAAAGGACTAAACAAAACAAATCTCTAGAGTCAGGGGACCATGTTGT
* * * * *
538581 AACTTTTAATAGTCAAATGACTCAATAAAGCAAAATC-CTAGAGTTAGGGGACCAT-TTGT
1 AACTTTTAATAGTCAAAGGACTAAACAAAAC-AAATCTCTAGAGTCAGGGGACCATGTTGT
538640 GTACTTTACC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 4 0.08
60 42 0.84
61 4 0.08
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (60 bp):
AACTTTTAATAGTCAAAGGACTAAACAAAACAAATCTCTAGAGTCAGGGGACCATGTTGT
Found at i:552273 original size:55 final size:55
Alignment explanation
Indices: 552203--552339 Score: 213
Period size: 55 Copynumber: 2.5 Consensus size: 55
552193 ATGAGAAATC
* * **
552203 TAAGGTACATGAGTCATATGAGTAACAGTGTCAGGTTACTCCTCCTCGGTACCA-
1 TAAGGTACACGAGTCATATGAGTAACAGTGTCAGGTTACTCCACCTCGACACCAT
*
552257 TAGTGGTACACGAGTCATATGAGTAACAGTGTCAGGTTACTCCACCTCGACACCAT
1 TA-AGGTACACGAGTCATATGAGTAACAGTGTCAGGTTACTCCACCTCGACACCAT
552313 TAAGGTACACGAGTCATATGAGTAACA
1 TAAGGTACACGAGTCATATGAGTAACA
552340 ATATCATATC
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
54 2 0.03
55 71 0.95
56 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (55 bp):
TAAGGTACACGAGTCATATGAGTAACAGTGTCAGGTTACTCCACCTCGACACCAT
Found at i:558039 original size:19 final size:19
Alignment explanation
Indices: 558001--558045 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
557991 AACAAGTATG
*
558001 CTTTGA-CCAAACTGTTGA
1 CTTTGACCCAAACTATTGA
*
558019 CTTTGACCCATACTATTGA
1 CTTTGACCCAAACTATTGA
558038 CTTTGACC
1 CTTTGACC
558046 AGAGTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (19 bp):
CTTTGACCCAAACTATTGA
Found at i:562784 original size:15 final size:16
Alignment explanation
Indices: 562764--562794 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
562754 CGTAAATGAT
562764 AATAA-TAAAATATCA
1 AATAATTAAAATATCA
562779 AATAATTAAAATATCA
1 AATAATTAAAATATCA
562795 TGTCTATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATTAAAATATCA
Found at i:563283 original size:21 final size:20
Alignment explanation
Indices: 563234--563286 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
563224 CAACCACTTT
*
563234 TATGTTATTATGTGTGATGT
1 TATGTTATTATGTGTGATGA
*
563254 TCATATTATTA-GTGATGCATGA
1 T-ATGTTATTATGTG-TG-ATGA
563276 TATGTTATTAT
1 TATGTTATTAT
563287 CATGACTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.15
21 18 0.69
22 4 0.15
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (20 bp):
TATGTTATTATGTGTGATGA
Found at i:567181 original size:21 final size:21
Alignment explanation
Indices: 567133--567186 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
567123 GTTTCCAGAT
*
567133 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
567154 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
567175 TCGCAATACGAA
1 TCGCAATGCGAA
567187 TATGTAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:567222 original size:20 final size:20
Alignment explanation
Indices: 567174--567222 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
567164 AACTTGGACT
**
567174 ATCGCAATACGAATATGTAA
1 ATCGCAATGTGAATATGTAA
567194 ATCGCAATGTGAATATGTAA
1 ATCGCAATGTGAATATGTAA
*
567214 ATTGCAATG
1 ATCGCAATG
567223 CGATAGTCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (20 bp):
ATCGCAATGTGAATATGTAA
Found at i:567258 original size:7 final size:7
Alignment explanation
Indices: 567246--567303 Score: 80
Period size: 7 Copynumber: 8.3 Consensus size: 7
567236 TCGCAATGCG
567246 AACCCTA
1 AACCCTA
567253 AACCCTA
1 AACCCTA
567260 AACCCTA
1 AACCCTA
*
567267 AATCCTA
1 AACCCTA
*
567274 AATCCTA
1 AACCCTA
*
567281 AATCCTA
1 AACCCTA
*
567288 AATCCTA
1 AACCCTA
567295 AACCCTA
1 AACCCTA
567302 AA
1 AA
567304 TTATACTTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (7 bp):
AACCCTA
Found at i:567304 original size:21 final size:21
Alignment explanation
Indices: 567249--567304 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
567239 CAATGCGAAC
*
567249 CCTAAACCCTAAACCCTAAAT
1 CCTAAACCCTAAATCCTAAAT
*
567270 CCTAAATCCTAAATCCTAAAT
1 CCTAAACCCTAAATCCTAAAT
567291 CCTAAACCCTAAAT
1 CCTAAACCCTAAAT
567305 TATACTTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (21 bp):
CCTAAACCCTAAATCCTAAAT
Found at i:567394 original size:14 final size:14
Alignment explanation
Indices: 567384--567433 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
567374 TACAAACTCT
567384 AAACCCTAAACTAC
1 AAACCCTAAACTAC
*
567398 AAACCTTAAACTAC
1 AAACCCTAAACTAC
567412 AAACCCT-AACTA-
1 AAACCCTAAACTAC
*
567424 TAACCCTAAA
1 AAACCCTAAA
567434 ACTTAATCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 6 0.19
13 7 0.22
14 19 0.59
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACCCTAAACTAC
Found at i:567408 original size:21 final size:21
Alignment explanation
Indices: 567362--567401 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
567352 ATCTTTGCAA
567362 TAAACCCTAAACTACAAACTC
1 TAAACCCTAAACTACAAACTC
567383 TAAACCCTAAACTACAAAC
1 TAAACCCTAAACTACAAAC
567402 CTTAAACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACCCTAAACTACAAACTC
Found at i:567435 original size:27 final size:28
Alignment explanation
Indices: 567384--567436 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
567374 TACAAACTCT
*
567384 AAACCCTAAACTACAAACCTTAAACTAC
1 AAACCCTAAACTACAAACCTAAAACTAC
* *
567412 AAACCCT-AACTATAACCCTAAAACT
1 AAACCCTAAACTACAAACCTAAAACT
567437 TAATCTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (28 bp):
AAACCCTAAACTACAAACCTAAAACTAC
Found at i:568172 original size:66 final size:64
Alignment explanation
Indices: 568095--568224 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 64
568085 CCTTCATAAT
568095 AAAACTATTCTATTATAGTAATTTGTAATGC-AACTGTTATAAAACTATTCTATTATCAATCAAT
1 AAAACTATTCTATTATAGTAATTTGTAATGCAAACTGTT-T-AAACTATTCTATTATC-ATCAAT
568159 TA
63 TA
568161 AAAACTATTCTATTATAGTAATTTGTAATGCAAACTGTTTAAACTATTCTATTATCATCAATTA
1 AAAACTATTCTATTATAGTAATTTGTAATGCAAACTGTTTAAACTATTCTATTATCATCAATTA
568225 TAGTAAAACA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
64 8 0.13
65 16 0.25
66 32 0.51
67 7 0.11
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (64 bp):
AAAACTATTCTATTATAGTAATTTGTAATGCAAACTGTTTAAACTATTCTATTATCATCAATTA
Found at i:569362 original size:11 final size:11
Alignment explanation
Indices: 569342--569373 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
569332 TGGTGAGCAC
*
569342 TTGAGCTTGAA
1 TTGAGTTTGAA
569353 TTGAGTTTGAA
1 TTGAGTTTGAA
569364 TTGAGTTTGA
1 TTGAGTTTGA
569374 GTCTCAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.03, G:0.28, T:0.44
Consensus pattern (11 bp):
TTGAGTTTGAA
Found at i:572372 original size:13 final size:13
Alignment explanation
Indices: 572354--572405 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
572344 GTCATAAATC
*
572354 TATGACGCGCATT
1 TATGACACGCATT
**
572367 TATGACATACATT
1 TATGACACGCATT
*
572380 TATGACATGCATT
1 TATGACACGCATT
*
572393 TATGACGCGCATT
1 TATGACACGCATT
572406 GCGCGTCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:573630 original size:12 final size:12
Alignment explanation
Indices: 573613--573643 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
573603 ATATATTGAT
573613 AATCAAATGAAA
1 AATCAAATGAAA
573625 AATCAAATGAAA
1 AATCAAATGAAA
*
573637 AAACAAA
1 AATCAAA
573644 CCCGGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:580148 original size:15 final size:15
Alignment explanation
Indices: 580109--580140 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
580099 ACTATTGTGA
*
580109 CAAATTTAATTTTGT
1 CAAAATTAATTTTGT
580124 CAAAATTAATTTTGT
1 CAAAATTAATTTTGT
580139 CA
1 CA
580141 CTATTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (15 bp):
CAAAATTAATTTTGT
Found at i:582420 original size:21 final size:19
Alignment explanation
Indices: 582396--582438 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
582386 TTGATGTTAT
582396 AATTTAACTTAATTGTGACAA
1 AATTT-ACTT-ATTGTGACAA
* *
582417 AATTTACTTTTTGTGATAA
1 AATTTACTTATTGTGACAA
582436 AAT
1 AAT
582439 AATTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (19 bp):
AATTTACTTATTGTGACAA
Found at i:596746 original size:30 final size:32
Alignment explanation
Indices: 596711--596793 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 32
596701 GACATGTCAT
*
596711 ATATCACGTCATCATCTTAAGTGAT-T-GTAC
1 ATATCACATCATCATCTTAAGTGATGTGGTAC
*
596741 ATATCACATCATCGTCTTAAGTGATGTGGTAC
1 ATATCACATCATCATCTTAAGTGATGTGGTAC
* *
596773 ATACCACATCAACATCTTAAG
1 ATATCACATCATCATCTTAAG
596794 AGACATGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 23 0.50
31 1 0.02
32 22 0.48
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (32 bp):
ATATCACATCATCATCTTAAGTGATGTGGTAC
Found at i:598510 original size:31 final size:30
Alignment explanation
Indices: 598461--598518 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
598451 ATTTGAATAT
598461 AGATCAAATGAACCTTTATTTGAAAAATCAA
1 AGATCAAATGAACCTTTATTT-AAAAATCAA
***
598492 AGATCAAATGAGTTTTTATTTAAAAAT
1 AGATCAAATGAACCTTTATTTAAAAAT
598519 TTCAATCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (30 bp):
AGATCAAATGAACCTTTATTTAAAAATCAA
Found at i:600481 original size:42 final size:43
Alignment explanation
Indices: 600394--600482 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 43
600384 ATGAAATTGT
* * * *
600394 AAAAAATAGATGCCTTAATTGTAAAGGTAGAAATCAATATTGA
1 AAAAAATAGATGCCTCAATTATAAAGGTAGAAATCAAGATCGA
* * **
600437 AAAAAATAGATGCCTCAATTATAATGGTA-TAATTGAGATCGA
1 AAAAAATAGATGCCTCAATTATAAAGGTAGAAATCAAGATCGA
600479 AAAA
1 AAAA
600483 CCTTAAGGGC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 12 0.32
43 26 0.68
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (43 bp):
AAAAAATAGATGCCTCAATTATAAAGGTAGAAATCAAGATCGA
Found at i:600829 original size:51 final size:51
Alignment explanation
Indices: 600774--600926 Score: 272
Period size: 50 Copynumber: 3.0 Consensus size: 51
600764 AAATTCGTAC
* * *
600774 CCTTAAATTTATAATATAAATTTATAAGTCCATACCCCTAACATAAAACTA
1 CCTTAAATTTACAATATAAATTTATAAGTTCATACCCCTAATATAAAACTA
600825 CCTTAAATTTACAATATAAATTTATAAGTTCATACCCCTAATATAAAACTA
1 CCTTAAATTTACAATATAAATTTATAAGTTCATACCCCTAATATAAAACTA
600876 -CTTAAATTTACAATATAAATTTATAAGTTCATACCCCTAATATAAAACTA
1 CCTTAAATTTACAATATAAATTTATAAGTTCATACCCCTAATATAAAACTA
600926 C
1 C
600927 ATATATGTTT
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
50 50 0.51
51 48 0.49
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (51 bp):
CCTTAAATTTACAATATAAATTTATAAGTTCATACCCCTAATATAAAACTA
Found at i:602595 original size:18 final size:19
Alignment explanation
Indices: 602572--602615 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
602562 TCAGTAATCC
*
602572 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
602590 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
602610 TATTCC
1 TATTCC
602616 GTAAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:602603 original size:20 final size:20
Alignment explanation
Indices: 602578--602615 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
602568 ATCCTATTCC
*
602578 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
602598 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
602616 GTAAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:602765 original size:18 final size:16
Alignment explanation
Indices: 602721--602765 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
602711 ATAATTGTCC
*
602721 ATTAAAATTTTAAATT
1 ATTATAATTTTAAATT
602737 ATTATATATTTTAAATTT
1 ATTATA-ATTTTAAA-TT
602755 ATTTATAATTT
1 A-TTATAATTT
602766 CTATCAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 5 0.20
17 8 0.32
18 7 0.28
19 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATAATTTTAAATT
Found at i:604447 original size:7 final size:7
Alignment explanation
Indices: 604428--604460 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
604418 AAATATATAT
604428 AGAGAGAG
1 AGAGAG-G
604436 AGAGAGG
1 AGAGAGG
604443 AGAGAGG
1 AGAGAGG
604450 AGAGAGG
1 AGAGAGG
604457 AGAG
1 AGAG
604461 GACATTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (7 bp):
AGAGAGG
Found at i:605958 original size:4 final size:4
Alignment explanation
Indices: 605949--606068 Score: 69
Period size: 4 Copynumber: 28.0 Consensus size: 4
605939 AGAGGTAATT
* * *
605949 TTTA TTTA TTTA TTTA CTTTGA ATTA TTTA TTTA TTTCAA ATAA TTTA
1 TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTT--A TTTA TTTA
* * * * * * *
605997 TTTA TTTA TGTA TTCA TTTA TTTTGA ATAA ATTA GTGA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA TTTA
*
606047 TTTCAA ATTA TTTA TTTA TTTA
1 TTT--A TTTA TTTA TTTA TTTA
606069 ATTGAAATGG
Statistics
Matches: 89, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
4 73 0.82
5 9 0.10
6 7 0.08
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (4 bp):
TTTA
Found at i:605977 original size:18 final size:17
Alignment explanation
Indices: 605954--606071 Score: 72
Period size: 18 Copynumber: 7.1 Consensus size: 17
605944 TAATTTTTAT
605954 TTATTTATTTACTTTGAA
1 TTATTTATTTA-TTTGAA
*
605972 TTATTTATTTATTTCAAA
1 TTATTTATTTATTT-GAA
*
605990 TAATTTATTTATTT--A
1 TTATTTATTTATTTGAA
*
606005 TGTATTCATTTATTTTGAA
1 T-TATTTATTTA-TTTGAA
* * *
606024 -TA---AATTA-GTGAT
1 TTATTTATTTATTTGAA
*
606036 TTATTTATTTATTTCAAA
1 TTATTTATTTATTT-GAA
606054 TTATTTATTTATTT-AA
1 TTATTTATTTATTTGAA
606070 TT
1 TT
606072 GAAATGGTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
12 3 0.04
13 2 0.03
14 4 0.05
15 2 0.03
16 16 0.21
17 9 0.12
18 41 0.53
19 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (17 bp):
TTATTTATTTATTTGAA
Found at i:605979 original size:26 final size:25
Alignment explanation
Indices: 605945--606068 Score: 90
Period size: 26 Copynumber: 4.7 Consensus size: 25
605935 ATACAGAGGT
605945 AATT-TTTATTTATTTATTTACTTTG
1 AATTATTTATTTATTTATTTA-TTTG
* *
605970 AATTATTTATTTATTTCAAATAATTT-
1 AATTATTTATTTATTT--ATTTATTTG
* * *
605996 ATTTATTTATGTATTCATTTATTTTG
1 AATTATTTATTTATTTATTTA-TTTG
* *
606022 AATAAATTAGTGATTTATTTATTTATTTCA
1 AAT-TATT--T-ATTTATTTATTTATTT-G
606052 AATTATTTATTTATTTA
1 AATTATTTATTTATTTA
606069 ATTGAAATGG
Statistics
Matches: 76, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
24 3 0.04
25 7 0.09
26 35 0.46
27 7 0.09
28 3 0.04
29 7 0.09
30 14 0.18
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (25 bp):
AATTATTTATTTATTTATTTATTTG
Found at i:606076 original size:22 final size:22
Alignment explanation
Indices: 606034--606076 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
606024 TAAATTAGTG
*
606034 ATTTATTTATTTATTTCAAATT
1 ATTTATTTATTTAATTCAAATT
*
606056 ATTTATTTATTTAATTGAAAT
1 ATTTATTTATTTAATTCAAAT
606077 GGTATGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTATTTATTTAATTCAAATT
Found at i:609848 original size:16 final size:15
Alignment explanation
Indices: 609818--609858 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
609808 CTACAAAAAC
609818 ATTTTA-TTA-TATT
1 ATTTTATTTATTATT
609831 ATATTTATTTATTATT
1 AT-TTTATTTATTATT
*
609847 ATTTTTTTTATT
1 ATTTTATTTATT
609859 TTTTTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.08
14 4 0.17
15 12 0.50
16 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTATTTATTATT
Found at i:609849 original size:19 final size:18
Alignment explanation
Indices: 609820--609859 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
609810 ACAAAAACAT
609820 TTTATTATATTATATTTA
1 TTTATTATATTATATTTA
* *
609838 TTTATTATTATTTTTTTTA
1 TTTATTA-TATTATATTTA
609857 TTT
1 TTT
609860 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTATATTATATTTA
Found at i:609957 original size:33 final size:34
Alignment explanation
Indices: 609919--610000 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 34
609909 AAAAAATAAA
*
609919 TCAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 TCAACGTATTTGAGTCCTATTAAAACACTAAAAC
*
609953 -CAACGTATTTGAGTCTTATTAAAACACTAAAAC
1 TCAACGTATTTGAGTCCTATTAAAACACTAAAAC
*
609986 TGAA-GTATTTGAGTC
1 TCAACGTATTTGAGTC
610001 TAAGTAGGAC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 42 0.95
34 2 0.05
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (34 bp):
TCAACGTATTTGAGTCCTATTAAAACACTAAAAC
Found at i:614572 original size:32 final size:33
Alignment explanation
Indices: 614524--614618 Score: 104
Period size: 32 Copynumber: 2.9 Consensus size: 33
614514 TGCGGGCATC
*
614524 TTTGAAGATTCAACATCAAATGTTGGGGTATTT
1 TTTGAAGATTCAACATCAAATGTTGGGGCATTT
* * *
614557 TTTGAA-ATTTAACATCAAATTTTTGGGCATTT
1 TTTGAAGATTCAACATCAAATGTTGGGGCATTT
* * * *
614589 TTT-TAGATTCAACATCGAATATTAGGGCAT
1 TTTGAAGATTCAACATCAAATGTTGGGGCAT
614619 CTTTGGGAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 1 0.02
32 45 0.87
33 6 0.12
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (33 bp):
TTTGAAGATTCAACATCAAATGTTGGGGCATTT
Found at i:615884 original size:37 final size:37
Alignment explanation
Indices: 615834--615942 Score: 184
Period size: 37 Copynumber: 3.0 Consensus size: 37
615824 TTTCCAAGTT
615834 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
* *
615871 TTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
*
615907 TTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
615943 ATTTGAATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 33 0.49
37 34 0.51
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
Found at i:615921 original size:36 final size:36
Alignment explanation
Indices: 615832--615940 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
615822 AATTTCCAAG
615832 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
615869 TCTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
615905 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
615941 ATATTTGAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 36 0.54
37 31 0.46
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:616131 original size:31 final size:31
Alignment explanation
Indices: 616073--616137 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
616063 CTTGAAACAC
* *
616073 AAAAAAAAAACCCTCGAAATTATTTCTCTTG
1 AAAAAAAAAACCCTCGAAAATACTTCTCTTG
* * *
616104 AAAAAAAAAACCTTTGAAAATGCTTCTCTTG
1 AAAAAAAAAACCCTCGAAAATACTTCTCTTG
616135 AAA
1 AAA
616138 CATCAAACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.28
Consensus pattern (31 bp):
AAAAAAAAAACCCTCGAAAATACTTCTCTTG
Found at i:616284 original size:83 final size:82
Alignment explanation
Indices: 616144--616401 Score: 349
Period size: 83 Copynumber: 3.1 Consensus size: 82
616134 GAAACATCAA
* * *
616144 ACCTTCGAGTTCGACTACGCTCAACTTCAAGACACATCATTTACAGCATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
616209 GGTTATCTGCCAACAAAG
66 GGTTATCTG-CAACAAAG
*
616227 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACCCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
*
616292 GGTTATCTGTCAACAAGG
66 GGTTATCTG-CAACAAAG
* * * * * * * * *
616310 ACCTCCGAGTTCGACTCCACTCAGCTCAAAAGCACCATCATTTGCAGCATAGCTCAAGGCAATAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTACAGCATAACTCAAGGCTAGAA
616375 GGGTTATCTGC--CAAAG
65 GGGTTATCTGCAACAAAG
616391 ACCTTCGAGTT
1 ACCTTCGAGTT
616402 TGATTACATT
Statistics
Matches: 156, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
81 14 0.09
83 107 0.69
84 35 0.22
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (82 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
GGTTATCTGCAACAAAG
Found at i:616770 original size:3 final size:3
Alignment explanation
Indices: 616750--616800 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
616740 CAAAAACATT
616750 TTA TTA -TA TTA -TA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
616794 TT- TTA TT
1 TTA TTA TT
616801 TTTGCAAGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.14
3 36 0.82
4 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:616891 original size:33 final size:33
Alignment explanation
Indices: 616854--616919 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
616844 GAAAATAAAT
* *
616854 CAACGTATTTGAGTCCTATTGAAATACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
616887 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
616920 TGAAGCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAAAC
Found at i:616930 original size:33 final size:33
Alignment explanation
Indices: 616854--616935 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
616844 GAAAATAAAT
* * *
616854 CAACGTATTTGAGTCCTATTGAAATACTAAAAC
1 CAACGCATTTGAGTCCTATTAAAACACTAAAAC
*
616887 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGCATTTGAGTCCTATTAAAACACTAAAAC
*
616920 TGAA-GCATTTGAGTCC
1 -CAACGCATTTGAGTCC
616936 AAGTAGGACT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 42 0.95
34 2 0.05
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (33 bp):
CAACGCATTTGAGTCCTATTAAAACACTAAAAC
Found at i:617458 original size:12 final size:13
Alignment explanation
Indices: 617436--617464 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
617426 TGGATTGAAT
617436 TTTTGAATTTTAA
1 TTTTGAATTTTAA
617449 TTTT-AATTTTAA
1 TTTTGAATTTTAA
617461 TTTT
1 TTTT
617465 CGCAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:621422 original size:15 final size:14
Alignment explanation
Indices: 621376--621433 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 14
621366 ACTTATACAC
621376 TATTATTAA-ATTA
1 TATTATTAAGATTA
*
621389 TATTAGGTTAATATT-
1 TATTA--TTAAGATTA
621404 TATTATTAAGGATTA
1 TATTATTAA-GATTA
621419 TATTAATTAAGATTA
1 TATT-ATTAAGATTA
621434 GATATTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 9 0.24
14 3 0.08
15 18 0.47
16 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (14 bp):
TATTATTAAGATTA
Found at i:623139 original size:18 final size:16
Alignment explanation
Indices: 623116--623161 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
623106 TGTTTATGAG
623116 GGAATTGGAATCTGTAAA
1 GGAATTGGAATCTGT--A
*
623134 GGAATTAGAATCTGTA
1 GGAATTGGAATCTGTA
623150 GGAATTGGAATC
1 GGAATTGGAATC
623162 CAATTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (16 bp):
GGAATTGGAATCTGTA
Found at i:623958 original size:37 final size:38
Alignment explanation
Indices: 623888--623960 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
623878 AACCTGAACC
*
623888 CGACCCGAATATCGCACTTAAAAAAACCCGACCCGACT
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
623926 CGACCCGAATATCACACTT-AAAAAACCCGACCCGA
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGA
623961 ACAAAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 16 0.47
38 18 0.53
ACGTcount: A:0.38, C:0.37, G:0.12, T:0.12
Consensus pattern (38 bp):
CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
Found at i:624200 original size:5 final size:5
Alignment explanation
Indices: 624190--624215 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
624180 ATAAAGTTTC
624190 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
624216 ATATATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:634038 original size:18 final size:18
Alignment explanation
Indices: 634017--634062 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
634007 GTAAAAATAT
*
634017 ATTAAAAT-AATAAAAGCG
1 ATTAAAATAAAT-AAAGCA
634035 ATT-AAATAAATAAAGCA
1 ATTAAAATAAATAAAGCA
*
634052 ATTAAAGTAAA
1 ATTAAAATAAA
634063 AATAAGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.24
Consensus pattern (18 bp):
ATTAAAATAAATAAAGCA
Found at i:636054 original size:32 final size:32
Alignment explanation
Indices: 635984--636056 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
635974 CCTAAGGTGA
*
635984 CCCTTGGGTAGGCTCTAAGGCCCCGAGAAACT
1 CCCTTGGGTAGGCTCTAAGGCCCCAAGAAACT
** * *
636016 TTCTTGGGTAGGCTCTCAGGCCCCAAGGAACT
1 CCCTTGGGTAGGCTCTAAGGCCCCAAGAAACT
636048 CCCTTGGGT
1 CCCTTGGGT
636057 TAATCATGGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.18, C:0.30, G:0.29, T:0.23
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTAAGGCCCCAAGAAACT
Found at i:644258 original size:24 final size:24
Alignment explanation
Indices: 644225--644271 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
644215 TTTATTAGTT
*
644225 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
* *
644249 TAATTAAATATGTAATATTATTA
1 TAATTAAATATATAAAATTATTA
644272 TATCTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:644676 original size:24 final size:25
Alignment explanation
Indices: 644644--644704 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
644634 TAGTAATCCA
644644 TTCGTTTATATTTC-TTCAT-TTATG
1 TTCGTTTATATTTCTTTCATATT-TG
*
644668 TTCGTTTATA-TTCTTTTATATTTG
1 TTCGTTTATATTTCTTTCATATTTG
644692 TTCGTTTATATTT
1 TTCGTTTATATTT
644705 TGTCCAATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 3 0.09
24 26 0.79
25 4 0.12
ACGTcount: A:0.16, C:0.10, G:0.08, T:0.66
Consensus pattern (25 bp):
TTCGTTTATATTTCTTTCATATTTG
Found at i:651751 original size:2 final size:2
Alignment explanation
Indices: 651746--651803 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
651736 GATCCCACTA
651746 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
651788 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
651804 TTAACGAGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:652025 original size:29 final size:29
Alignment explanation
Indices: 651991--652049 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
651981 CCTAAATTAA
*
651991 TTTGATGGCATTGTTTACATCAATTTAGT
1 TTTGATGGCATTGCTTACATCAATTTAGT
*
652020 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGGCATTGCTTACATCAATTTAGT
652049 T
1 T
652050 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (29 bp):
TTTGATGGCATTGCTTACATCAATTTAGT
Found at i:656705 original size:29 final size:29
Alignment explanation
Indices: 656669--656727 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
656659 CATAAATTAA
656669 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
656698 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
656727 T
1 T
656728 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:668668 original size:65 final size:65
Alignment explanation
Indices: 668550--668716 Score: 164
Period size: 65 Copynumber: 2.6 Consensus size: 65
668540 TTTTCAGGTA
* * * * *
668550 AGTGTACTGATGCATAAATCAATGCATCGATGTACCCTTGTTTTAATTGAACATCGAATAGCTTT
1 AGTGTACTGATGCACAAATCAATGCATCGATGCACCCATGTATTAATTAAACATCGAATAGCTTT
* * * *
668615 AGTGTATTGATGCACATA-CAATGCATCGATGCACTCCATGTATT-ATTAAAACATCGAATTGAT
1 AGTGTACTGATGCACAAATCAATGCATCGATGCAC-CCATGTATTAATT-AAACATCGAATAG-C
668678 TTT
63 TTT
* *
668681 A-TGCACCGATGCACAAGA-C-ATGCATCGATGCACCCA
1 AGTGTACTGATGCACAA-ATCAATGCATCGATGCACCCA
668717 GGCTTTTTCA
Statistics
Matches: 85, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
64 21 0.25
65 58 0.68
66 6 0.07
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (65 bp):
AGTGTACTGATGCACAAATCAATGCATCGATGCACCCATGTATTAATTAAACATCGAATAGCTTT
Found at i:668755 original size:64 final size:64
Alignment explanation
Indices: 668635--668758 Score: 157
Period size: 64 Copynumber: 1.9 Consensus size: 64
668625 TGCACATACA
*
668635 ATGCATCGATGCACTCCATGTATTATTAAAACATCGAATTGATTTTATGCACCGATGCACAAGAC
1 ATGCATCGATGCACTCCAGGTATTATTAAAACATCGAA-TGATTTTATGCACCGATGCACAAGAC
*
668700 ATGCATCGATGCAC-CCAGGCT-TT-TTCAAAACATCGAA-GCATATTTATGCATCGATGCAC
1 ATGCATCGATGCACTCCAGG-TATTATT-AAAACATCGAATG-AT-TTTATGCACCGATGCAC
668759 TCTTAGTGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
62 1 0.02
63 4 0.08
64 33 0.62
65 15 0.28
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACTCCAGGTATTATTAAAACATCGAATGATTTTATGCACCGATGCACAAGAC
Found at i:669246 original size:17 final size:17
Alignment explanation
Indices: 669224--669259 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
669214 TCAAGAATTT
669224 GGGGTATAATTCTTGAG
1 GGGGTATAATTCTTGAG
669241 GGGGTATAATTCTTGAG
1 GGGGTATAATTCTTGAG
669258 GG
1 GG
669260 AGTTGTAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.06, G:0.39, T:0.33
Consensus pattern (17 bp):
GGGGTATAATTCTTGAG
Found at i:674419 original size:29 final size:30
Alignment explanation
Indices: 674377--674448 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
674367 CTCGAATGAC
*
674377 CTATCCAAAGGTCACAAAG-ACCTCGGTAA
1 CTATCCAAAGGTCACAAAGAACCTCGGCAA
* *
674406 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAAAGGTCACAAAGAACCTCGGCAA
* *
674436 CTGTCCATAGGTC
1 CTATCCAAAGGTC
674449 TCGACGAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
CTATCCAAAGGTCACAAAGAACCTCGGCAA
Found at i:674475 original size:31 final size:31
Alignment explanation
Indices: 674434--674506 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
674424 GAACCTCGGC
* *
674434 AACTGTCCATAGGTCTCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
* *
674465 AACTGACCATAGGTCCCGAAGAACTTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
674496 AACTGTCCATA
1 AACTGTCCATA
674507 TGTATCGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:674525 original size:31 final size:31
Alignment explanation
Indices: 674434--674529 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
674424 GAACCTCGGC
* * *
674434 AACTGTCCATAGGT-CTCGACGAACCTAGGTA
1 AACTGACCATAGGTAC-CGAAGAACATAGGTA
* *
674465 AACTGACCATAGGTCCCGAAGAACTTAGGTA
1 AACTGACCATAGGTACCGAAGAACATAGGTA
* * *
674496 AACTGTCCATATGTATCGAA-AGACATAGGTA
1 AACTGACCATAGGTACCGAAGA-ACATAGGTA
674527 AAC
1 AAC
674530 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.02
31 53 0.96
32 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (31 bp):
AACTGACCATAGGTACCGAAGAACATAGGTA
Found at i:675586 original size:21 final size:21
Alignment explanation
Indices: 675554--675596 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
675544 TGTTTGTTTA
675554 ATTGAGAGTGCATCAATGCAC
1 ATTGAGAGTGCATCAATGCAC
*
675575 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCAATGCAC
675596 A
1 A
675597 CGACCCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCAATGCAC
Found at i:676072 original size:14 final size:15
Alignment explanation
Indices: 676053--676082 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
676043 GCTCACGATG
676053 AAGAAGAAGAA-ATA
1 AAGAAGAAGAAGATA
676067 AAGAAGAAGAAGATA
1 AAGAAGAAGAAGATA
676082 A
1 A
676083 CTTCCCCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (15 bp):
AAGAAGAAGAAGATA
Found at i:678579 original size:29 final size:30
Alignment explanation
Indices: 678537--678608 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
678527 CCCGAAAGAC
*
678537 CTATCCAAAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAAAGGTCACAAAGAACCCCGGCAA
* * *
678566 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAAAGGTCACAAAGAACCCCGGCAA
* *
678596 CTGTCCATAGGTC
1 CTATCCAAAGGTC
678609 CCGACGAACC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.18
Consensus pattern (30 bp):
CTATCCAAAGGTCACAAAGAACCCCGGCAA
Found at i:678632 original size:31 final size:31
Alignment explanation
Indices: 678594--678666 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
678584 GAACCTCGGC
*
678594 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
678625 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
678656 AACTGTCCATA
1 AACTGTCCATA
678667 TGTCTTGAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:678685 original size:31 final size:31
Alignment explanation
Indices: 678594--678689 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
678584 GAACCTCGGC
* *
678594 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
*
678625 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* **
678656 AACTGTCCATATGTCTTGAA-AGACATAGGTA
1 AACTGTCCATAGGTCCCGAAGA-ACATAGGTA
678687 AAC
1 AAC
678690 CCTAGACTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 1 0.02
31 58 0.98
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:685158 original size:14 final size:14
Alignment explanation
Indices: 685139--685166 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
685129 CTTGCTCACG
685139 ATGAAGAAGAAGAA
1 ATGAAGAAGAAGAA
685153 ATGAAGAAGAAGAA
1 ATGAAGAAGAAGAA
685167 GATAACTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
ATGAAGAAGAAGAA
Found at i:691011 original size:18 final size:18
Alignment explanation
Indices: 690990--691029 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
690980 GTAGTATCAG
690990 TACCCCATTTGATATCGA
1 TACCCCATTTGATATCGA
691008 TACCCCATTTGATATCGA
1 TACCCCATTTGATATCGA
691026 TACC
1 TACC
691030 ATTTTTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (18 bp):
TACCCCATTTGATATCGA
Found at i:691719 original size:30 final size:30
Alignment explanation
Indices: 691684--691757 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 30
691674 TATACGATAT
691684 ATAAAATATATTTTCTAAAG-TAAAATAAGA
1 ATAAAATATATTTT-TAAAGTTAAAATAAGA
*
691714 ATAAAATATA-TTTTAAAGTTAAGATAAGA
1 ATAAAATATATTTTTAAAGTTAAAATAAGA
691743 ATAAAATATATTTTT
1 ATAAAATATATTTTT
691758 TAATGTTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 5 0.12
29 22 0.54
30 14 0.34
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (30 bp):
ATAAAATATATTTTTAAAGTTAAAATAAGA
Found at i:692876 original size:31 final size:31
Alignment explanation
Indices: 692838--692907 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
692828 GTTTCAAAAT
* * *
692838 TAACAAATT-AGTCATTAACGTTATTGATATA
1 TAACAAATTGA-TCATCAACATTATCGATATA
*
692869 TAACAAATTGATCATCAACATTATCGATTTA
1 TAACAAATTGATCATCAACATTATCGATATA
692900 TAACAAAT
1 TAACAAAT
692908 CGGTCGCTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (31 bp):
TAACAAATTGATCATCAACATTATCGATATA
Found at i:695372 original size:24 final size:24
Alignment explanation
Indices: 695345--695410 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
695335 AAACGGAGAT
* *
695345 ATCAGAAATTAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
* *
695369 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATCCAG
*
695393 ATCAG-AATCAGAACAGAA
1 ATCAGAAATCAAAACAGAA
695411 CTCATGTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 12 0.32
24 25 0.68
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:695374 original size:12 final size:12
Alignment explanation
Indices: 695357--695438 Score: 64
Period size: 12 Copynumber: 6.9 Consensus size: 12
695347 CAGAAATTAA
695357 AACAGAATTCAG
1 AACAGAATTCAG
*
695369 ATCAG-ATATCAG
1 AACAGAAT-TCAG
*
695381 AACAGAATCCAG
1 AACAGAATTCAG
*
695393 ATCAGAA-TCAG
1 AACAGAATTCAG
*
695404 AACAGAACTCATG
1 AACAGAATTCA-G
*
695417 TAAC-GTA-TCAG
1 -AACAGAATTCAG
695428 AACAGAATTCA
1 AACAGAATTCA
695439 ATTCTGAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
10 3 0.05
11 14 0.25
12 30 0.55
13 5 0.09
14 3 0.05
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:697890 original size:14 final size:16
Alignment explanation
Indices: 697871--697903 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
697861 GTCAACGTCG
697871 GTCAAC-GGTCAAC-A
1 GTCAACGGGTCAACGA
697885 GTCAACGGGTCAACGA
1 GTCAACGGGTCAACGA
697901 GTC
1 GTC
697904 GGGTCGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 7 0.41
16 4 0.24
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.15
Consensus pattern (16 bp):
GTCAACGGGTCAACGA
Found at i:697953 original size:13 final size:13
Alignment explanation
Indices: 697921--697955 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
697911 GTCAACGGGT
* *
697921 CGGGTCAGGTCAA
1 CGGGTCGGGTAAA
697934 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
697947 CGGGTCGGG
1 CGGGTCGGG
697956 CCGGGTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.49, T:0.14
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:697955 original size:18 final size:18
Alignment explanation
Indices: 697890--697943 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
697880 CAACAGTCAA
*
697890 CGGGTCAACGAGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
697908 CGAGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
697926 CAGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
697944 AAACGGGTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.17
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:698965 original size:31 final size:31
Alignment explanation
Indices: 698922--698999 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
698912 GTTAACGTAG
* *
698922 AGTGACCGATTTGTTATAAATCGATAATGTT
1 AGTGACCAATTTGTTATAAATCGATAACGTT
* **
698953 AGTGACCAATTTGTCATTTATCGATAACGTT
1 AGTGACCAATTTGTTATAAATCGATAACGTT
* *
698984 AATGACTAATTTGTTA
1 AGTGACCAATTTGTTA
699000 CTTTTAAAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (31 bp):
AGTGACCAATTTGTTATAAATCGATAACGTT
Found at i:700205 original size:37 final size:39
Alignment explanation
Indices: 700161--700244 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 39
700151 ACTTTATTTT
700161 GTTCGGGTCGGG-TTTTTTAAGTATGATATTCGGGTCGA
1 GTTCGGGTCGGGTTTTTTTAAGTATGATATTCGGGTCGA
* *
700199 G-TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTTCGGGTCGGGTTTTTTTAAGTATGATATTCGGGTCGA
700237 GTTCGGGT
1 GTTCGGGT
700245 TTAGGGTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
37 10 0.24
38 26 0.62
39 6 0.14
ACGTcount: A:0.12, C:0.11, G:0.38, T:0.39
Consensus pattern (39 bp):
GTTCGGGTCGGGTTTTTTTAAGTATGATATTCGGGTCGA
Found at i:700454 original size:249 final size:244
Alignment explanation
Indices: 699939--700455 Score: 774
Period size: 249 Copynumber: 2.1 Consensus size: 244
699929 ACTTTATTTT
*
699939 GGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCAGGTCGGGTCGGGTTCGAGTTTAGGGTG
1 GGTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATT---GTCGGGTCGGGTTCGAGTTTAGGGTG
*
700004 AAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTT
63 AAAAAAACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTT
700069 ATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTTGGATTTCTAATACATATATTC
128 ATTAAATAAAAATAATTTTTTATTATTT---GTCGGGTC--G--GGATTTCTAATACATATATTC
700134 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTATGATATTCG
186 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTATGATATTCG
* *
700193 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATA-T-TCGGGTCGGGTTCGGGTTTAGGGTGAAA
1 GGTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTGTCGGGTCGGGTTCGAGTTTAGGGTGAAA
* *
700256 AAAATCAGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATT
66 AAAACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATT
*
700321 AAATAAAAATAATTTTTTATTA-TT-TCGGGTC-GGATTTCTAATTCATATATTCGGGTCGGGTC
131 AAATAAAAATAATTTTTTATTATTTGTCGGGTCGGGATTTCTAATACATATATTCGGGTCGGGTC
* *
700383 GGATGAAACTTTATTTTGTTCGGGTTGGGTTGGGTTTTTTAAGTGTGATATTCG
196 GGATGAAACTTTATTTTGTTC-----GGGTCGGGTTTTTTAAGTATGATATTCG
*
700437 GGTCAGGTCGGGTCGGGTT
1 GGTCGGGTCGGGTCGGGTT
700456 CGAGTTTAGG
Statistics
Matches: 247, Mismatches: 11, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
239 51 0.21
244 50 0.20
248 2 0.01
249 111 0.45
253 1 0.00
254 32 0.13
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (244 bp):
GGTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTGTCGGGTCGGGTTCGAGTTTAGGGTGAAA
AAAACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATT
AAATAAAAATAATTTTTTATTATTTGTCGGGTCGGGATTTCTAATACATATATTCGGGTCGGGTC
GGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTATGATATTCG
Found at i:701060 original size:16 final size:18
Alignment explanation
Indices: 701035--701079 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
701025 TATGAAATTG
*
701035 GATTCCAATTCC-T-ACA
1 GATTTCAATTCCTTCACA
*
701051 GATTTTAATTCCTTCACA
1 GATTTCAATTCCTTCACA
701069 GATTTCAATTC
1 GATTTCAATTC
701080 TCTCATAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 1 0.04
18 13 0.54
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:705008 original size:73 final size:73
Alignment explanation
Indices: 704910--705063 Score: 299
Period size: 73 Copynumber: 2.1 Consensus size: 73
704900 GGTACAAATA
704910 AAAAATTTCAGGGTGGGACGATCCGTAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAGA
1 AAAAATTTCAGGGTGGGACGATCCGTAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAGA
704975 TGGACATC
66 TGGACATC
*
704983 AAAAATTTCAGGGTGGGACGATCCGTAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAGG
1 AAAAATTTCAGGGTGGGACGATCCGTAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAGA
705048 TGGACATC
66 TGGACATC
705056 AAAAATTT
1 AAAAATTT
705064 TAAGGTGTAC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (73 bp):
AAAAATTTCAGGGTGGGACGATCCGTAAAATAAGTAACTAATCGAAGAAAACTTAAATTTCAAGA
TGGACATC
Found at i:705082 original size:21 final size:21
Alignment explanation
Indices: 705036--705082 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
705026 GAAGAAAACT
*
705036 TAAATTTCAAGGTGGACATCA
1 TAAATTTCAAGGTGGACACCA
* * *
705057 AAAATTTTAAGGTGTACACCA
1 TAAATTTCAAGGTGGACACCA
705078 TAAAT
1 TAAAT
705083 AAAATCAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
TAAATTTCAAGGTGGACACCA
Found at i:712088 original size:2 final size:2
Alignment explanation
Indices: 712081--712113 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
712071 GTGAGTTTAA
712081 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
712114 GATTATTTTT
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:712351 original size:127 final size:128
Alignment explanation
Indices: 712209--712460 Score: 452
Period size: 128 Copynumber: 2.0 Consensus size: 128
712199 AAAAATTATA
* *
712209 TAATATATATACACCTACCTAAAACATGTTTCCAATATATGTTGGCATGCAAGATAGGTC-TTTA
1 TAATATATATACACCTACCTAAAACATGTTTCCAAGATATGTTGCCATGCAAGATAGGTCTTTTA
* *
712273 ACATCTTTGACATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTTCTTGAGCAACATAAT
66 ACACCTTTGACATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTCCTTGAGCAACATAAT
712336 TAATATATATACACCTACCTAAAACATGTTTCCAAGATATGTTGCCATGCAAGATAGGTCTTTTA
1 TAATATATATACACCTACCTAAAACATGTTTCCAAGATATGTTGCCATGCAAGATAGGTCTTTTA
*
712401 ACACCTTTGATATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTCCTTGAGCAACAT
66 ACACCTTTGACATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTCCTTGAGCAACAT
712461 TTCTTTTATT
Statistics
Matches: 119, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
127 58 0.49
128 61 0.51
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (128 bp):
TAATATATATACACCTACCTAAAACATGTTTCCAAGATATGTTGCCATGCAAGATAGGTCTTTTA
ACACCTTTGACATCATTCTTTTTAAGATCAAGTCTAAATATACTCCTCCTTGAGCAACATAAT
Found at i:713635 original size:17 final size:17
Alignment explanation
Indices: 713606--713648 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
713596 TTTTTTAAAT
*
713606 TATTA-ATTTTTAAAAA
1 TATTATATTATTAAAAA
713622 -ACTTATATTATTAAAAA
1 TA-TTATATTATTAAAAA
713639 TATTATATTA
1 TATTATATTA
713649 GTTATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 3 0.13
17 18 0.78
18 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTATATTATTAAAAA
Found at i:713715 original size:23 final size:23
Alignment explanation
Indices: 713688--713735 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
713678 AGGATTTTTT
*
713688 TAATTTAATATATAA-ATTATTAA
1 TAATTAAATATATAATATTA-TAA
*
713711 TAATTAAATATGTAATATTATAA
1 TAATTAAATATATAATATTATAA
713734 TA
1 TA
713736 TATATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TAATTAAATATATAATATTATAA
Found at i:715226 original size:64 final size:64
Alignment explanation
Indices: 715113--715236 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
715103 GTGAACCAAG
* * * * *
715113 TGTGCATCGATGCATAAAATGCATTTGATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTACT
1 TGTGCATCGATGCATAAAATACATTCGATGTTTGAAAATAACCTAAGTGCATCGATGCATTACT
* *
715177 TGTGCATCGATGCATGAAATACATTCGATGTTTTAATAA-AACCTAAGTGCATCGATGCAT
1 TGTGCATCGATGCATAAAATACATTCGATGTTTGAA-AATAACCTAAGTGCATCGATGCAT
715237 AGAGAGTGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
64 50 0.96
65 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATACATTCGATGTTTGAAAATAACCTAAGTGCATCGATGCATTACT
Found at i:715246 original size:19 final size:19
Alignment explanation
Indices: 715222--715274 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
715212 ATAAAACCTA
715222 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
715241 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
715260 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
715275 GAAATGCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (19 bp):
AGTGCATCGATGCATAGAG
Found at i:715246 original size:64 final size:64
Alignment explanation
Indices: 715114--715256 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 64
715104 TGAACCAAGT
* * * * * ***
715114 GTGCATCGATGCATAAAATGCATTTGATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTACTT
1 GTGCATCGATGCATAAAATACATTCGATGTTTGAAAATAACCTAAGTGCATCGATGCATTAAGA
* *
715178 GTGCATCGATGCATGAAATACATTCGATGTTTTAATAA-AACCTAAGTGCATCGATGCA-TAGAG
1 GTGCATCGATGCATAAAATACATTCGATGTTTGAA-AATAACCTAAGTGCATCGATGCATTA-AG
715241 A
64 A
715242 GTGCATCGATGCATA
1 GTGCATCGATGCATA
715257 GAGAGTGCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 2 0.03
64 62 0.94
65 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATACATTCGATGTTTGAAAATAACCTAAGTGCATCGATGCATTAAGA
Found at i:715310 original size:83 final size:83
Alignment explanation
Indices: 715178--715339 Score: 204
Period size: 83 Copynumber: 1.9 Consensus size: 83
715168 TGCATTACTT
*
715178 GTGCATCGATGCATGAAATACATTCGATGTTTTAATAAAACCTAAGTGCATCGATGCATAGA-GA
1 GTGCATCGATGCATGAAATACATTCGATGTTTCAATAAAACCTAAGTGCATCGATGCATAGATGA
715242 GTGCATCGATGCATAGAGA
66 -TGCATCGATGCATAGAGA
* ** ** *
715261 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTC-AATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATACATTCGATGTTTCAATAAAACCTAA--GTGCATCGATGCATAGA-
715324 TGATGCATCGATGCAT
63 TGATGCATCGATGCAT
715340 GCCTTTGAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
81 2 0.03
82 7 0.10
83 44 0.65
84 13 0.19
85 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (83 bp):
GTGCATCGATGCATGAAATACATTCGATGTTTCAATAAAACCTAAGTGCATCGATGCATAGATGA
TGCATCGATGCATAGAGA
Found at i:721705 original size:21 final size:21
Alignment explanation
Indices: 721681--721730 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
721671 GAAGTTTTAA
721681 GATCATCAATATTCTTTTGAT
1 GATCATCAATATTCTTTTGAT
*
721702 GATCATTAATATTCTTTTGAT
1 GATCATCAATATTCTTTTGAT
721723 GATCATCA
1 GATCATCA
721731 TGAACTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (21 bp):
GATCATCAATATTCTTTTGAT
Found at i:721722 original size:18 final size:20
Alignment explanation
Indices: 721675--721730 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
721665 TTAAAAGAAG
*
721675 TTTTAAGATCATCAATATTC
1 TTTTATGATCATCAATATTC
*
721695 TTTTGATGATCATTAATATTC
1 TTTT-ATGATCATCAATATTC
721716 TTTTGATGATCATCA
1 TTTT-ATGATCATCA
721731 TGAACTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (20 bp):
TTTTATGATCATCAATATTC
Found at i:721894 original size:22 final size:21
Alignment explanation
Indices: 721851--721890 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
721841 AAGACTATTT
721851 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
721872 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
721891 ATATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:723897 original size:45 final size:45
Alignment explanation
Indices: 723833--723936 Score: 181
Period size: 45 Copynumber: 2.3 Consensus size: 45
723823 TGCACCAAGT
* * *
723833 GTGCATCGATGCATAAAATGCATTTGATGTTTGAAAATAGCCTGA
1 GTGCATCGGTGCATAAAATGCATTCGATGTTTAAAAATAGCCTGA
723878 GTGCATCGGTGCATAAAATGCATTCGATGTTTAAAAATAGCCTGA
1 GTGCATCGGTGCATAAAATGCATTCGATGTTTAAAAATAGCCTGA
723923 GTGCATCGGTGCAT
1 GTGCATCGGTGCAT
723937 TGCTTGTGTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (45 bp):
GTGCATCGGTGCATAAAATGCATTCGATGTTTAAAAATAGCCTGA
Found at i:742286 original size:37 final size:36
Alignment explanation
Indices: 742189--742305 Score: 159
Period size: 34 Copynumber: 3.3 Consensus size: 36
742179 GGCAACCAAC
742189 TTTGAAAAAATA-ATTTTCAAAGTTTGGTAAATGTTT
1 TTTG-AAAAATAGATTTTCAAAGTTTGGTAAATGTTT
*
742225 TTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 TTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
* *
742259 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 -TTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
*
742296 GTTGAAAAAT
1 TTTGAAAAAT
742306 GATAATGACA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
34 28 0.38
35 4 0.05
36 18 0.25
37 23 0.32
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.44
Consensus pattern (36 bp):
TTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
Found at i:747795 original size:21 final size:20
Alignment explanation
Indices: 747771--747834 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
747761 AACTTTGAAA
747771 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
747792 AAATGTTTT-----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
747806 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
747827 AAATGTTT
1 AAATGTTT
747835 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
20 11 0.32
21 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:747809 original size:35 final size:36
Alignment explanation
Indices: 747764--747884 Score: 165
Period size: 35 Copynumber: 3.4 Consensus size: 36
747754 GGCAACCAAC
747764 TTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
1 TTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTTT
* *
747801 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
* *
747836 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATG-TTT
1 TTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTTT
*
747872 CTTGAAAAATGAT
1 TTTGAAAAATGAT
747885 AATGGGATAA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 35 0.47
36 16 0.21
37 24 0.32
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (36 bp):
TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
Found at i:756839 original size:21 final size:20
Alignment explanation
Indices: 756807--756845 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
756797 ATTGTTATTA
756807 TTTTTTTGTATTCATGTTTT
1 TTTTTTTGTATTCATGTTTT
*
756827 TTTTTGTTTTATTCATGTT
1 TTTTT-TTGTATTCATGTT
756846 GGATCAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.05, G:0.10, T:0.74
Consensus pattern (20 bp):
TTTTTTTGTATTCATGTTTT
Done.