Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008161.1 Hibiscus syriacus cultivar Beakdansim tig00110730_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: 673301
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 4
Found at i:491545 original size:31 final size:31
Alignment explanation
Indices: 491509--491586 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
491499 AATAAACCAA
* *
491509 AAAATAAT-ATTAATAATA-ATATAATAAATAT
1 AAAATAATAAATAATAATATAAATAAT--ATAT
*
491540 AAAATAATAAATAATACTATAAATAATATAT
1 AAAATAATAAATAATAATATAAATAATATAT
*
491571 AATATAATAAATAATA
1 AAAATAATAAATAATA
491587 TGTACACTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 27 0.66
32 8 0.20
33 6 0.15
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAATAATAAATAATAATATAAATAATATAT
Found at i:491547 original size:19 final size:19
Alignment explanation
Indices: 491523--491587 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 19
491513 TAATATTAAT
491523 AATAATATAATAA-ATATAA
1 AATAATATAATAATATAT-A
491542 AATAATA-AATAATACTATA
1 AATAATATAATAATA-TATA
491561 AATAATAT-ATAATATAATA
1 AATAATATAATAATAT-ATA
491580 AATAATAT
1 AATAATAT
491588 GTACACTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.14
19 33 0.79
20 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAATATAATAATATATA
Found at i:491552 original size:38 final size:38
Alignment explanation
Indices: 491511--491586 Score: 98
Period size: 41 Copynumber: 1.9 Consensus size: 38
491501 TAAACCAAAA
* * *
491511 AATAATATTAATAATAATATAATAAATATAAAATAATAAAT
1 AATACTATAAATAAT-ATATAATATA-AT-AAATAATAAAT
491552 AATACTATAAATAATATATAATATAATAAATAATA
1 AATACTATAAATAATATATAATATAATAAATAATA
491587 TGTACACTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 8 0.25
39 2 0.06
40 9 0.28
41 13 0.41
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (38 bp):
AATACTATAAATAATATATAATATAATAAATAATAAAT
Found at i:491646 original size:22 final size:22
Alignment explanation
Indices: 491620--491669 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
491610 ACTATATAGC
491620 ATATATTATATTTTCAAAAACT
1 ATATATTATATTTTCAAAAACT
* *
491642 ATATAATATGTTTTCAAAAACT
1 ATATATTATATTTTCAAAAACT
491664 ATATAT
1 ATATAT
491670 ACTATATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATATTATATTTTCAAAAACT
Found at i:491650 original size:27 final size:26
Alignment explanation
Indices: 491589--491650 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
491579 AAATAATATG
491589 TACACTATATTTAATTTAAAAACTATA
1 TACA-TATATTTAATTTAAAAACTATA
*
491616 TAGCATATATTATATTTTCAAAAACTATA
1 TA-CATATATT-TAATTT-AAAAACTATA
491645 TA-ATAT
1 TACATAT
491651 GTTTTCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 12 0.39
28 7 0.23
29 12 0.39
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.42
Consensus pattern (26 bp):
TACATATATTTAATTTAAAAACTATA
Found at i:491754 original size:22 final size:21
Alignment explanation
Indices: 491692--491761 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
491682 TTTTTTAAAC
* **
491692 TATTTTCAAAAGCCATTTTTTA
1 TATTTTCAAAA-CCATATAATA
*
491714 TATGCTTTCAAAACTATATAATA
1 TAT--TTTCAAAACCATATAATA
*
491737 TATTTTCTAAAACCATATATTA
1 TATTTTC-AAAACCATATAATA
491759 TAT
1 TAT
491762 ACATTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.10
22 18 0.46
23 9 0.23
24 8 0.21
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.46
Consensus pattern (21 bp):
TATTTTCAAAACCATATAATA
Found at i:499436 original size:16 final size:16
Alignment explanation
Indices: 499415--499455 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
499405 GATTGGACAC
499415 CATCTTACCTGATCTG
1 CATCTTACCTGATCTG
499431 CATCTTACCTGATCTG
1 CATCTTACCTGATCTG
499447 CATCTTACC
1 CATCTTACC
499456 AAATATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.20, C:0.34, G:0.10, T:0.37
Consensus pattern (16 bp):
CATCTTACCTGATCTG
Found at i:499840 original size:21 final size:19
Alignment explanation
Indices: 499816--499882 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
499806 CTAATCTCAA
*
499816 AAAAAGAAAAAATTATAAAAT
1 AAAAA-AAAAAA-TAAAAAAT
*
499837 AAAAAAATAAAGTAAAAAAT
1 AAAAAAA-AAAATAAAAAAT
499857 AAATAAAACAAAATAAAAAAT
1 AAA-AAAA-AAAATAAAAAAT
499878 AAAAA
1 AAAAA
499883 TAATGAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.81, C:0.01, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAAAAAAAAATAAAAAAT
Found at i:499842 original size:7 final size:7
Alignment explanation
Indices: 499815--499882 Score: 59
Period size: 7 Copynumber: 9.7 Consensus size: 7
499805 ACTAATCTCA
*
499815 AAAAAAG
1 AAAAAAT
499822 AAAAAATT
1 AAAAAA-T
*
499830 ATAAAAT
1 AAAAAAT
499837 AAAAAA-
1 AAAAAAT
* *
499843 ATAAAGT
1 AAAAAAT
499850 AAAAAAT
1 AAAAAAT
499857 AAATAAA-
1 AAA-AAAT
*
499864 ACAAAAT
1 AAAAAAT
499871 AAAAAAT
1 AAAAAAT
499878 AAAAA
1 AAAAA
499883 TAATGAAGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
6 7 0.15
7 33 0.69
8 8 0.17
ACGTcount: A:0.81, C:0.01, G:0.03, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:499846 original size:13 final size:13
Alignment explanation
Indices: 499830--499885 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
499820 AGAAAAAATT
499830 ATAAAATAAAAAA
1 ATAAAATAAAAAA
*
499843 ATAAAGT-AAAAA
1 ATAAAATAAAAAA
499855 AT-AAATAAAACAAA
1 ATAAAAT-AAA-AAA
499869 ATAAAA-AATAAAA
1 ATAAAATAA-AAAA
499882 ATAA
1 ATAA
499886 TGAAGAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
11 3 0.08
12 7 0.19
13 17 0.47
14 6 0.17
15 3 0.08
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (13 bp):
ATAAAATAAAAAA
Found at i:499855 original size:12 final size:11
Alignment explanation
Indices: 499833--499880 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
499823 AAAAATTATA
499833 AAATAAAAAAAT
1 AAAT-AAAAAAT
499845 AAAGTAAAAAAT
1 AAA-TAAAAAAT
*
499857 AAATAAAACA-
1 AAATAAAAAAT
499867 AAATAAAAAAT
1 AAATAAAAAAT
499878 AAA
1 AAA
499881 AATAATGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 9 0.28
11 9 0.28
12 13 0.41
13 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:509358 original size:17 final size:17
Alignment explanation
Indices: 509338--509394 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
509328 TTGTGAATTT
509338 GTTTGGATTTATGGATG
1 GTTTGGATTTATGGATG
* * *
509355 GTTTGAACTTATAT-GTTT
1 GTTTGGA-TT-TATGGATG
509373 GTTTGGATTTATGGATG
1 GTTTGGATTTATGGATG
509390 GTTTG
1 GTTTG
509395 AACTTATATG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
16 3 0.10
17 15 0.48
18 10 0.32
19 3 0.10
ACGTcount: A:0.18, C:0.02, G:0.30, T:0.51
Consensus pattern (17 bp):
GTTTGGATTTATGGATG
Found at i:509375 original size:35 final size:35
Alignment explanation
Indices: 509335--509408 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
509325 GGATTGTGAA
509335 TTTGTTTGGATTTATGGATGGTTTGAACTTATATG
1 TTTGTTTGGATTTATGGATGGTTTGAACTTATATG
509370 TTTGTTTGGATTTATGGATGGTTTGAACTTATATG
1 TTTGTTTGGATTTATGGATGGTTTGAACTTATATG
509405 TTTG
1 TTTG
509409 GTGTGATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.53
Consensus pattern (35 bp):
TTTGTTTGGATTTATGGATGGTTTGAACTTATATG
Found at i:509401 original size:17 final size:17
Alignment explanation
Indices: 509346--509401 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
509336 TTGTTTGGAT
509346 TTATGGATGGTTTGAAC
1 TTATGGATGGTTTGAAC
* * * * *
509363 TTATATGTTTGTTTGGAT
1 TTAT-GGATGGTTTGAAC
509381 TTATGGATGGTTTGAAC
1 TTATGGATGGTTTGAAC
509398 TTAT
1 TTAT
509402 ATGTTTGGTG
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.50
Consensus pattern (17 bp):
TTATGGATGGTTTGAAC
Found at i:509410 original size:19 final size:19
Alignment explanation
Indices: 509353--509410 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
509343 GATTTATGGA
509353 TGGTTTGAACTTATATGTT
1 TGGTTTGAACTTATATGTT
* **
509372 T-GTTTGGA-TT-TATGGA
1 TGGTTTGAACTTATATGTT
509388 TGGTTTGAACTTATATGTT
1 TGGTTTGAACTTATATGTT
509407 TGGT
1 TGGT
509411 GTGATTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 5 0.17
17 8 0.27
18 8 0.27
19 9 0.30
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.52
Consensus pattern (19 bp):
TGGTTTGAACTTATATGTT
Found at i:509417 original size:35 final size:35
Alignment explanation
Indices: 509335--509419 Score: 136
Period size: 35 Copynumber: 2.4 Consensus size: 35
509325 GGATTGTGAA
*
509335 TTTGTTTGGATTTATGGATGGTTTGAACTTATATG
1 TTTGTGTGGATTTATGGATGGTTTGAACTTATATG
*
509370 TTTGTTTGGATTTATGGATGGTTTGAACTTATATG
1 TTTGTGTGGATTTATGGATGGTTTGAACTTATATG
509405 TTTG-GTGTGATTTAT
1 TTTGTGTG-GATTTAT
509420 TTATTATTGC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
34 2 0.04
35 46 0.96
ACGTcount: A:0.19, C:0.02, G:0.26, T:0.53
Consensus pattern (35 bp):
TTTGTGTGGATTTATGGATGGTTTGAACTTATATG
Found at i:519816 original size:14 final size:16
Alignment explanation
Indices: 519779--519831 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 16
519769 TGCAATCACC
*
519779 CATATCACACATATAT
1 CATATCATACATATAT
*
519795 CATGTCATACA-AT-T
1 CATATCATACATATAT
519809 CATATCATACATCATAT
1 CATATCATACAT-ATAT
519826 ACATAT
1 -CATAT
519832 ATTACATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 11 0.37
15 2 0.07
16 11 0.37
17 1 0.03
18 5 0.17
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (16 bp):
CATATCATACATATAT
Found at i:519992 original size:23 final size:23
Alignment explanation
Indices: 519946--520007 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
519936 CAGCTCGTAT
* * *
519946 AAATGCACCAAAGTGCCACGTAG
1 AAATACACCGAAGTGCCACATAG
* * * *
519969 AATTGCACCGTAGTGCCGCATAG
1 AAATACACCGAAGTGCCACATAG
519992 AAATACACCGAAGTGC
1 AAATACACCGAAGTGC
520008 TATATCAGGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACATAG
Found at i:521588 original size:20 final size:20
Alignment explanation
Indices: 521565--521616 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
521555 AATAAACGTA
521565 TGCATCGATGCACTCTACAG
1 TGCATCGATGCACTCTACAG
521585 TGCATCGATGCACTCTACAG
1 TGCATCGATGCACTCTACAG
*
521605 TGTATCGATGCA
1 TGCATCGATGCA
521617 TTCTTTAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCACTCTACAG
Found at i:523112 original size:24 final size:24
Alignment explanation
Indices: 523085--523143 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
523075 CTTATCTTCA
*
523085 CAGCAGATGAGGCTTTCTCTTTTG
1 CAGCAGATGAGGCTTTATCTTTTG
523109 CAGCAGATGAGGCTTTATCTTTTG
1 CAGCAGATGAGGCTTTATCTTTTG
523133 CAGCAGATGAG
1 CAGCAGATGAG
523144 TCCCCTTGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (24 bp):
CAGCAGATGAGGCTTTATCTTTTG
Found at i:528821 original size:20 final size:20
Alignment explanation
Indices: 528744--528829 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
528734 ATAACCAGAA
*
528744 CCCTCA-GGGGGTATCGATT
1 CCCTCATGGGGGAATCGATT
*
528763 CCC-C-TAGGGGGAATCGGATC
1 CCCTCAT-GGGGGAATC-GATT
* *
528783 CCCTTCAAAGGGGGAATCGGTT
1 CCC-TC-ATGGGGGAATCGATT
*
528805 CCCTCATGGGGGTATCGATT
1 CCCTCATGGGGGAATCGATT
528825 CCCTC
1 CCCTC
528830 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
18 1 0.02
19 11 0.21
20 23 0.44
21 2 0.04
22 6 0.12
23 9 0.17
ACGTcount: A:0.17, C:0.29, G:0.30, T:0.23
Consensus pattern (20 bp):
CCCTCATGGGGGAATCGATT
Found at i:529549 original size:19 final size:18
Alignment explanation
Indices: 529525--529562 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
529515 TCTAATTTGC
529525 ATCCTCCATAATCCGCATT
1 ATCCTCCATAAT-CGCATT
529544 ATCCTCCATAATCGCATT
1 ATCCTCCATAATCGCATT
529562 A
1 A
529563 GAAAAAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (18 bp):
ATCCTCCATAATCGCATT
Found at i:532643 original size:21 final size:22
Alignment explanation
Indices: 532600--532643 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
532590 TTATTTTCAA
* *
532600 TTTTTAATTTTGAAACATCATT
1 TTTTTAATTTTGAAAAATAATT
*
532622 TTTTTTATTTT-AAAAATAATT
1 TTTTTAATTTTGAAAAATAATT
532643 T
1 T
532644 CTCATAATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTAATTTTGAAAAATAATT
Found at i:536264 original size:23 final size:23
Alignment explanation
Indices: 536205--536264 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
536195 AAAAAAAAGG
*
536205 AAAAATAAAAA-AA-ACGAAACA
1 AAAAATAAAAATAAGACAAAACA
*
536226 AATAAA-ACAAAATAAGACAAAATA
1 AA-AAATA-AAAATAAGACAAAACA
536250 AAAAATAAAAATAAG
1 AAAAATAAAAATAAG
536265 GAATAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 3 0.09
22 7 0.22
23 13 0.41
24 9 0.28
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.10
Consensus pattern (23 bp):
AAAAATAAAAATAAGACAAAACA
Found at i:536364 original size:17 final size:17
Alignment explanation
Indices: 536344--536382 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
536334 TGTAGTATTT
*
536344 AATAAATAAAGTAAAAA-
1 AATAAA-AAAGGAAAAAC
536361 AATAAAAAAGGAAAAAC
1 AATAAAAAAGGAAAAAC
536378 AATAA
1 AATAA
536383 CGAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (17 bp):
AATAAAAAAGGAAAAAC
Found at i:536535 original size:3 final size:3
Alignment explanation
Indices: 536527--536565 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
536517 ATGAAAAATA
536527 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
536566 GTAAAAGGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:537113 original size:8 final size:9
Alignment explanation
Indices: 537077--537112 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
537067 TTCGAACCCA
537077 AAAAAAAGAGG
1 AAAAAAA-A-G
537088 AAAAAAAAG
1 AAAAAAAAG
537097 AAAAAAAAG
1 AAAAAAAAG
537106 AAAAAAA
1 AAAAAAA
537113 GCTACATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.68
10 1 0.04
11 7 0.28
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:537817 original size:13 final size:12
Alignment explanation
Indices: 537787--537892 Score: 58
Period size: 12 Copynumber: 8.4 Consensus size: 12
537777 AATTAATATG
537787 TATAATATATGCTA
1 TATAATATA-G-TA
537801 TATAATTATAGTA
1 TATAA-TATAGTA
537814 TATAATATAGTA
1 TATAATATAGTA
*
537826 TGTACATATTATGTAA
1 TATA-ATA-TA-GT-A
*
537842 TATAATACA-TA
1 TATAATATAGTA
* *
537853 TACACTATA-TA
1 TATAATATAGTA
537864 CTATAATAATAGTA
1 -TATAAT-ATAGTA
*
537878 TA-AAT-TAATA
1 TATAATATAGTA
537888 TATAA
1 TATAA
537893 ATATTATGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
10 6 0.08
11 11 0.15
12 18 0.24
13 15 0.20
14 11 0.15
15 9 0.12
16 4 0.05
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (12 bp):
TATAATATAGTA
Found at i:538680 original size:21 final size:21
Alignment explanation
Indices: 538656--538698 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
538646 GTATTGTGAG
*
538656 GATGAGGTGTGTCCAGTACTT
1 GATGAAGTGTGTCCAGTACTT
*
538677 GATGAAGTGTGTCCAGTGCTT
1 GATGAAGTGTGTCCAGTACTT
538698 G
1 G
538699 TTCCTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.35, T:0.33
Consensus pattern (21 bp):
GATGAAGTGTGTCCAGTACTT
Found at i:542596 original size:21 final size:21
Alignment explanation
Indices: 542570--542647 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
542560 CATATGAAAT
542570 TTGTCCCGAATGACCATTGTA
1 TTGTCCCGAATGACCATTGTA
* *
542591 TTGTCCCGAATGACCACTATA
1 TTGTCCCGAATGACCATTGTA
*
542612 TTATCCC-AACTGACCATTGTA
1 TTGTCCCGAA-TGACCATTGTA
542633 TTGTCCCGAATGACC
1 TTGTCCCGAATGACC
542648 TATGAAACCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.04
21 45 0.92
22 2 0.04
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (21 bp):
TTGTCCCGAATGACCATTGTA
Found at i:543337 original size:177 final size:176
Alignment explanation
Indices: 543042--543394 Score: 679
Period size: 177 Copynumber: 2.0 Consensus size: 176
543032 CATATAAGCA
*
543042 TATATCAGTTCATATAATCAAGTATACATACATTTCATGTATTCACATCCTTATAATCAATACTC
1 TATATCAGTTCATATAATCAAGTATACATACATTTCATGTATTCACATCCTTATAAGCAATACTC
543107 TATACACTATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATCCTATAAACTAA
66 TATACACTATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATCCTATAAACTAA
543172 AATGCACTCATAAGAATCATATAACACTTTAGGAGTCACTTCTTAC
131 AATGCACTCATAAGAATCATATAACACTTTAGGAGTCACTTCTTAC
543218 TATATCAGTTCATATAATCAAGTATACATACATTTCATGTCATTCACATCCTTATAAGCAATACT
1 TATATCAGTTCATATAATCAAGTATACATACATTTCATGT-ATTCACATCCTTATAAGCAATACT
*
543283 TTATACACTATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATCCTATAAACTA
65 CTATACACTATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATCCTATAAACTA
543348 AAATGCACTCATAAGAATCATATAACACTTTAGGAGTCACTTCTTAC
130 AAATGCACTCATAAGAATCATATAACACTTTAGGAGTCACTTCTTAC
543395 CATAGTAACT
Statistics
Matches: 174, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
176 40 0.23
177 134 0.77
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (176 bp):
TATATCAGTTCATATAATCAAGTATACATACATTTCATGTATTCACATCCTTATAAGCAATACTC
TATACACTATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATCCTATAAACTAA
AATGCACTCATAAGAATCATATAACACTTTAGGAGTCACTTCTTAC
Found at i:548572 original size:21 final size:20
Alignment explanation
Indices: 548537--548626 Score: 108
Period size: 21 Copynumber: 4.3 Consensus size: 20
548527 CATACGAAAT
*
548537 TTGTCCAGAAGGACCACTGTA
1 TTGTCC-GAAAGACCACTGTA
*
548558 TTGTACCGAAAGACCACTATA
1 TTGT-CCGAAAGACCACTGTA
*
548579 TTGTCCCAAAGGACCACTGTA
1 TTGTCCGAAA-GACCACTGTA
*
548600 TTGTCCTGAAGGACCACTGTA
1 TTGTCC-GAAAGACCACTGTA
548621 TTGTCC
1 TTGTCC
548627 CCAAGAACCT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.08
21 51 0.85
22 4 0.07
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (20 bp):
TTGTCCGAAAGACCACTGTA
Found at i:548596 original size:42 final size:43
Alignment explanation
Indices: 548537--548627 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 43
548527 CATACGAAAT
548537 TTGT-CCAGAAGGACCACTGTATTGTACC-GAAAGACCACTATA
1 TTGTCCCAGAAGGACCACTGTATTGT-CCTGAAAGACCACTATA
* *
548579 TTGTCCCA-AAGGACCACTGTATTGTCCTGAAGGACCACTGTA
1 TTGTCCCAGAAGGACCACTGTATTGTCCTGAAAGACCACTATA
548621 TTGTCCC
1 TTGTCCC
548628 CAAGAACCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 2 0.04
42 40 0.89
43 3 0.07
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (43 bp):
TTGTCCCAGAAGGACCACTGTATTGTCCTGAAAGACCACTATA
Found at i:549340 original size:177 final size:177
Alignment explanation
Indices: 549037--549390 Score: 645
Period size: 177 Copynumber: 2.0 Consensus size: 177
549027 CATATAAGCA
*
549037 TATATCAGTTCATATAATCAAGTATACATACATTTCATGTAATTCACATCCTTATAATCAATACT
1 TATATCAGTTCATATAATCAAGTATACATACATTTCATGTAATTCACATCCTTATAAGCAATACT
*
549102 TTATATACCATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATCCTATAAACTA
66 TTATACACCATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATCCTATAAACTA
*
549167 AAATGCACTCATAAGAATCATATAACACTTTAGGAGTCATTTCTTAC
131 AAATGCACTCATAAGAATCATATAACACTTTAGGAGTCACTTCTTAC
*
549214 TATATCAGTTCATATAATCAAGTATACATACATTTCATGTCATTCACATCCTTATAAGCAATACT
1 TATATCAGTTCATATAATCAAGTATACATACATTTCATGTAATTCACATCCTTATAAGCAATACT
* *
549279 TTATACACTATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATTCTATAAACTA
66 TTATACACCATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATCCTATAAACTA
*
549344 AAATGCACTCATAAGAATCATATAACACTTTATGAGTCACTTCTTAC
131 AAATGCACTCATAAGAATCATATAACACTTTAGGAGTCACTTCTTAC
549391 CATAGTAACT
Statistics
Matches: 170, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
177 170 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (177 bp):
TATATCAGTTCATATAATCAAGTATACATACATTTCATGTAATTCACATCCTTATAAGCAATACT
TTATACACCATAACTATTGGAAATAGACTTATCACAAGTCCAATTCCTTATAATCCTATAAACTA
AAATGCACTCATAAGAATCATATAACACTTTAGGAGTCACTTCTTAC
Found at i:552148 original size:12 final size:11
Alignment explanation
Indices: 552131--552207 Score: 76
Period size: 10 Copynumber: 7.4 Consensus size: 11
552121 AAACCGAAAA
552131 AATAATATTAAT
1 AATAATA-TAAT
552143 AATAATATAAT
1 AATAATATAAT
552154 -ATAATATAA-
1 AATAATATAAT
552163 AATAATA-AAT
1 AATAATATAAT
*
552173 AATACTATAAAT
1 AATAATAT-AAT
552185 AAT-ATATAAT
1 AATAATATAAT
*
552195 -ACAATA-AAT
1 AATAATATAAT
552204 AATA
1 AATA
552208 TGTACAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
9 6 0.11
10 29 0.53
11 7 0.13
12 13 0.24
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAATATAAT
Found at i:552184 original size:19 final size:19
Alignment explanation
Indices: 552130--552207 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
552120 TAAACCGAAA
*
552130 AAATAATATTA-ATAATAAT
1 AAATAATACTATA-AATAAT
*
552149 ATAAT-ATAATATAAAATAAT
1 A-AATAATACTAT-AAATAAT
552169 AAATAATACTATAAATAAT
1 AAATAATACTATAAATAAT
* *
552188 ATATAATACAATAAATAAT
1 AAATAATACTATAAATAAT
552207 A
1 A
552208 TGTACAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 34 0.67
20 16 0.31
21 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATACTATAAATAAT
Found at i:552207 original size:3 final size:3
Alignment explanation
Indices: 552131--552195 Score: 50
Period size: 3 Copynumber: 22.3 Consensus size: 3
552121 AAACCGAAAA
*
552131 AAT AAT ATT AAT AAT AAT -AT AAT -AT AAT -AT AA- AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
552173 AAT ACT -AT AAAT AAT ATAT AAT A
1 AAT AAT AAT -AAT AAT A-AT AAT A
552196 CAATAAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
2 9 0.18
3 33 0.66
4 8 0.16
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:552244 original size:27 final size:29
Alignment explanation
Indices: 552214--552268 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
552204 AATATGTACA
552214 ATATATT-TATTTT-AAAAACTATATAAC
1 ATATATTATATTTTCAAAAACTATATAAC
*
552241 ATATATTATATTTTCAAAAATTATATAA
1 ATATATTATATTTTCAAAAACTATATAA
552269 TATGTTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.28
28 6 0.24
29 12 0.48
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATATTATATTTTCAAAAACTATATAAC
Found at i:552267 original size:22 final size:22
Alignment explanation
Indices: 552241--552311 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
552231 ACTATATAAC
*
552241 ATATATTATATTTTCAAAAATT
1 ATATAATATATTTTCAAAAATT
* *
552263 ATATAATATGTTTTCAAAAACT
1 ATATAATATATTTTCAAAAATT
* *
552285 ATATAATATGTTTTCAAAAACT
1 ATATAATATATTTTCAAAAATT
552307 ATATA
1 ATATA
552312 TATTATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (22 bp):
ATATAATATATTTTCAAAAATT
Found at i:552400 original size:22 final size:21
Alignment explanation
Indices: 552359--552407 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
552349 CATATTTTTT
* *
552359 ATATGTTTTCAAAACTATATA
1 ATATATTTTCAAAACCATATA
552380 ATATATTTTCAAAAACCATATA
1 ATATATTTTC-AAAACCATATA
*
552402 TTATAT
1 ATATAT
552408 ATGTTCCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATATTTTCAAAACCATATA
Found at i:553844 original size:50 final size:50
Alignment explanation
Indices: 553764--553862 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
553754 CCAATATATC
* *
553764 TTTATCAGTAAAATCCAGCAAGTCGATTGGATTAGTGGTTTCAATAGCAA
1 TTTATCAGTAAAATCCAGCAAATCGATTGGATTAGTGGTTTCAACAGCAA
* * *
553814 TTTATCAGTAAAATCTAGTAAATCGGTTGGATTAGTGGTTTCAACAGCA
1 TTTATCAGTAAAATCCAGCAAATCGATTGGATTAGTGGTTTCAACAGCA
553863 GTGGTTTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (50 bp):
TTTATCAGTAAAATCCAGCAAATCGATTGGATTAGTGGTTTCAACAGCAA
Found at i:562386 original size:25 final size:25
Alignment explanation
Indices: 562352--562410 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
562342 CAATTGAACG
562352 ACACTTTATTCTGGATGTGCATCAA
1 ACACTTTATTCTGGATGTGCATCAA
562377 ACACTTTATTCTGGATGTGCATCAA
1 ACACTTTATTCTGGATGTGCATCAA
562402 ACACTTTAT
1 ACACTTTAT
562411 GAACTGTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (25 bp):
ACACTTTATTCTGGATGTGCATCAA
Found at i:569579 original size:21 final size:21
Alignment explanation
Indices: 569553--569711 Score: 191
Period size: 21 Copynumber: 7.6 Consensus size: 21
569543 AACTTGGACA
569553 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
* *
569574 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCAT
569595 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
* *
569616 TGCGAT-TTACATA-TTCGCAT
1 TGCGATAGTCCA-AGTTCGCAT
569636 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
* *
569657 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCAT
* *
569678 TGCGATTTATTCCAAATTCG--T
1 TGCGA--TAGTCCAAGTTCGCAT
569699 TGCGATAGTCCAA
1 TGCGATAGTCCAA
569712 AATCGCAACG
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
19 7 0.06
20 17 0.14
21 85 0.71
23 10 0.08
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.31
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCGCAT
Found at i:569664 original size:62 final size:63
Alignment explanation
Indices: 569567--569711 Score: 206
Period size: 62 Copynumber: 2.3 Consensus size: 63
569557 ATAGTCCAAG
* * *
569567 TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATTTA-CATA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTATCAAA
* *
569629 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTA-T-CAAA
569694 TTCG--TTGCGATAGTCCAA
1 TTCGCATTGCGATAGTCCAA
569712 AATCGCAACG
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
62 54 0.72
63 14 0.19
65 7 0.09
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (63 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTATCAAA
Found at i:570484 original size:21 final size:20
Alignment explanation
Indices: 570426--570577 Score: 103
Period size: 21 Copynumber: 7.2 Consensus size: 20
570416 TATCGTCGTT
*
570426 GCGAACTTGGACTATCTCAA
1 GCGAACTTGGACTATCGCAA
* *
570446 -CGAATTTGGAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
570467 CGCGAACTTGGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
* * *
570488 -CGAATTTGGAATAAATCGCAGC
1 GCGAACTTGGACT--ATCGCA-A
*
570510 GCGAACTTCGACTATCGCAA
1 GCGAACTTGGACTATCGCAA
* *
570530 -CGAATTTGGAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
*
570551 CGCGAACTTCGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
570572 TGCGAA
1 -GCGAA
570578 TATGTAAATC
Statistics
Matches: 101, Mismatches: 19, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
19 29 0.29
21 44 0.44
23 28 0.28
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (20 bp):
GCGAACTTGGACTATCGCAA
Found at i:570489 original size:42 final size:42
Alignment explanation
Indices: 570426--570571 Score: 256
Period size: 42 Copynumber: 3.5 Consensus size: 42
570416 TATCGTCGTT
* *
570426 GCGAACTTGGACTATCTCAACGAATTTGGAATAAATCGCAAC
1 GCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAAC
* *
570468 GCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAGC
1 GCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAAC
570510 GCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAAC
1 GCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAAC
570552 GCGAACTTCGACTATCGCAA
1 GCGAACTTCGACTATCGCAA
570572 TGCGAATATG
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 100 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (42 bp):
GCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAAC
Found at i:572869 original size:9 final size:9
Alignment explanation
Indices: 572855--572879 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
572845 GAGTAAATGC
572855 AGAAGAGAA
1 AGAAGAGAA
572864 AGAAGAGAA
1 AGAAGAGAA
572873 AGAAGAG
1 AGAAGAG
572880 CATAGCTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (9 bp):
AGAAGAGAA
Found at i:574080 original size:16 final size:15
Alignment explanation
Indices: 574061--574142 Score: 55
Period size: 16 Copynumber: 5.5 Consensus size: 15
574051 AAAAATATAA
*
574061 AAATATAAAATTATT
1 AAATATAAAATAATT
*
574076 CAAATATTAAAAAAATT
1 -AAATA-TAAAATAATT
* *
574093 AAATATAAAATACTG
1 AAATATAAAATAATT
574108 AAA-AT-AAA-AATT
1 AAATATAAAATAATT
574120 AAATTACTAAAA-AATT
1 AAA-TA-TAAAATAATT
*
574136 GAATATA
1 AAATATA
574143 CATATTAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
12 5 0.09
13 3 0.06
14 5 0.09
15 13 0.25
16 19 0.36
17 8 0.15
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (15 bp):
AAATATAAAATAATT
Found at i:576296 original size:20 final size:20
Alignment explanation
Indices: 576271--576322 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
576261 ATAAAAATGT
*
576271 ATAAAATCGGTACCACGATG
1 ATAAAACCGGTACCACGATG
576291 ATAAAACCGGTACCACGATG
1 ATAAAACCGGTACCACGATG
576311 ATAAAACCGGTA
1 ATAAAACCGGTA
576323 AAGCGCTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.17
Consensus pattern (20 bp):
ATAAAACCGGTACCACGATG
Found at i:578995 original size:18 final size:18
Alignment explanation
Indices: 578972--579010 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
578962 GAAAAAATAT
578972 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
*
578990 GAAGAATAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
579008 GAA
1 GAA
579011 ATGAGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:580542 original size:18 final size:19
Alignment explanation
Indices: 580499--580546 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
580489 AATGTAGGGT
*
580499 TAATTTTGTATAAGGTTTA
1 TAATTTTGTATAAGATTTA
*
580518 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
580537 -AATTTTGTAT
1 TAATTTTGTAT
580547 GTGAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:581889 original size:200 final size:200
Alignment explanation
Indices: 580994--581961 Score: 1272
Period size: 201 Copynumber: 4.8 Consensus size: 200
580984 GGTAACAGAT
* * *
580994 GTGTCGATACATTTATACAAAGCATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
** * * * *
581059 GGTAATTTTTTAATGTAACATGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTTAATGTAACCGGTATAAATATACTGGTTTTATTAGAAAAGAGGTCAACATAATGT
* * * * *
581124 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCTCAAAAGCGGTACACG
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGC-CAAACGAGGTGCACG
581189 CATAAA
195 CATAAA
*
581195 GTGTCGATACATTTATAAAAAGTCTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * * *
581260 GGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATGT-GAGAATATGTCAATATAATG
66 GGTAATTTTTTAATGTAACCGGTATAAATATACTGGTTTTAT-TAGAAAAGAGGTCAACATAATG
* * * * *
581324 TATTGACACTTTTGAAATTTGTGTTGATACGTTTTGTCCAGAATGAATGTCCAAACTAGCTGCAC
130 TATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGAGGTGCAC
581389 GCATAAA
194 GCATAAA
* * *
581396 GTTTCGATACATTTATACAAAGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * ** *
581461 GGTAATTTTTTAATGTAATCAGTATAAATATACTGGTTTTATGAGAGAATATATCTACATAATGT
66 GGTAATTTTTTAATGTAACCGGTATAAATATACTGGTTTTATTAGAAAAGAGGTCAACATAATGT
* * *
581526 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGAGGTGCACG
*
581591 AATAAA
195 CATAAA
* * * *
581597 GTGTCGATACATTTATAAAAAGTATCGATCTCAAAAACATCAAAACCTATAATTATAATGTATTA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * *
581662 GGTAACTTTTCAATGTAACCTGTATAAATATACCGGTTTAATTAGAAAAGCGGTCAACATAATGT
66 GGTAATTTTTTAATGTAACCGGTATAAATATACTGGTTTTATTAGAAAAGAGGTCAACATAATGT
* * *
581727 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCATGC
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGC
581792 ATAAA
196 ATAAA
* *
581797 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATTGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* ** * * * * * * *
581862 GGTAAATTTACAATATAACCGGTATAAATACATTGGTTTAACTAGAAAAGCGTTCAACATAATGT
66 GGTAATTTTTTAATGTAACCGGTATAAATATACTGGTTTTATTAGAAAAGAGGTCAACATAATGT
*
581927 ATCGACACTTTTTAAATTTGTGTCGATACCTTTTT
131 ATCGACACTTTTGAAATTTGTGTCGATA-CTTTTT
581962 AAATTTCGCA
Statistics
Matches: 680, Mismatches: 83, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
200 162 0.24
201 517 0.76
202 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTTAATGTAACCGGTATAAATATACTGGTTTTATTAGAAAAGAGGTCAACATAATGT
ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGC
ATAAA
Found at i:582272 original size:15 final size:15
Alignment explanation
Indices: 582252--582280 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
582242 ATCTTTCTCA
582252 AAGCTCTTCTCAACC
1 AAGCTCTTCTCAACC
582267 AAGCTCTTCTCAAC
1 AAGCTCTTCTCAAC
582281 GACAATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.38, G:0.07, T:0.28
Consensus pattern (15 bp):
AAGCTCTTCTCAACC
Found at i:583582 original size:18 final size:18
Alignment explanation
Indices: 583559--583610 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
583549 ACAACACTTA
583559 CCACGACAACACCATTTG
1 CCACGACAACACCATTTG
583577 CCACGACAACACCATTTG
1 CCACGACAACACCATTTG
*
583595 CCACGACAACGCCATT
1 CCACGACAACACCATT
583611 CATACTTCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.33, C:0.40, G:0.12, T:0.15
Consensus pattern (18 bp):
CCACGACAACACCATTTG
Found at i:586776 original size:200 final size:200
Alignment explanation
Indices: 586338--587048 Score: 911
Period size: 200 Copynumber: 3.6 Consensus size: 200
586328 GTAAATAGAT
* ** *
586338 GTGTCGATACATTTTATAAA-AGTATCGACCCCAAAAACATCGAAACTAATGATTATAATGTAAT
1 GTGTCGATACA-TTTATAAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* * *
586402 AGGTAAATTAACAATATAACCGGTATAAAAATACCGG-TTAATTACAAAA-C-ATGTCAACATAA
65 AGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGAAAAGCGA--TCAACATAA
* ** * *
586464 TGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATACCCAACCGAGGTGC
128 TGTATCGACACTTTTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCCAAACGAGGTGC
586529 ACGCATAAA
192 ACGCATAAA
* * *
586538 GTGTCGATATATTTATAAAAAGTATCCATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
*
586603 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAAGCGATCAACATAATGT
66 GGTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGAAAAGCGATCAACATAATGT
* ** * * *
586668 ATCGATACTTTTTAAATTTGTGTTAATACTTGTTGTCCAGAATCAATGCCCAAACGAGGTGTATG
131 ATCGACACTTTTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAATGCCCAAACGAGGTGCACG
586733 CATAAA
195 CATAAA
* * * *
586739 GTGTCGATACATTTA-AAATTGTATCGATCCTAAAAACATCAAAACCGATAATTATAATGTAGTA
1 GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * *
586803 GGTAAATTTGCAATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATAG-G-TCAACATAAT
66 GGTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGA-AA-AGCGATCAACATAAT
*
586866 GTATCGACACTTTTTAAATTTGTGTCGATACTTTT-TTCAGAATGAATGCCC-AACGAGGTGCAC
129 GTATCGACACTTTTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCCAAACGAGGTGCAC
*
586929 ACATAAA
194 GCATAAA
* *
586936 GTGTCGATATATTTA-AAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * * * *
587000 TGTAAATTTGCATTATTACCGGTATAAATAAATCGGTTTAGTTAGAAAA
66 GGTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGAAAA
587049 TAGGTCAATA
Statistics
Matches: 450, Mismatches: 54, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
195 1 0.00
196 2 0.00
197 112 0.25
198 14 0.03
199 10 0.02
200 210 0.47
201 97 0.22
202 3 0.01
203 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (200 bp):
GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGAAAAGCGATCAACATAATGT
ATCGACACTTTTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACGC
ATAAA
Found at i:587162 original size:87 final size:88
Alignment explanation
Indices: 587056--587219 Score: 276
Period size: 87 Copynumber: 1.9 Consensus size: 88
587046 AAATAGGTCA
* * *
587056 ATATAAACGTTATCTATTACATTATATAAGCGCCACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCACCACCTAATATGTTATTGTACTTGATAATATTT
*
587121 CTG-GTTAAATGCCTATTTTATT
66 CCGTGTTAAATGCCTATTTTATT
*
587143 ATATAAACGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCACCACCTAATATGTTATTGTACTTGATAATATTT
587208 CCGTGTTAAATG
66 CCGTGTTAAATG
587220 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
87 63 0.89
88 8 0.11
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (88 bp):
ATATAAACGCTACCTATTACATTATATAAGCACCACCTAATATGTTATTGTACTTGATAATATTT
CCGTGTTAAATGCCTATTTTATT
Found at i:587190 original size:23 final size:23
Alignment explanation
Indices: 587140--587184 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
587130 TGCCTATTTT
* *
587140 ATTATATAAACGCTACCTATTAC
1 ATTATATAAACACTACCTAATAC
*
587163 ATTATATAAGCACTACCTAATA
1 ATTATATAAACACTACCTAATA
587185 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (23 bp):
ATTATATAAACACTACCTAATAC
Found at i:588613 original size:23 final size:26
Alignment explanation
Indices: 588569--588618 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
588559 TGTGAAATCC
588569 AACCTAAAAAAAGATAACAAAAATGT
1 AACCTAAAAAAAGATAACAAAAATGT
*
588595 AACC-AAAAATAGA-AA-AAAAATGT
1 AACCTAAAAAAAGATAACAAAAATGT
588618 A
1 A
588619 TAAAAACGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 2 0.09
25 8 0.35
26 4 0.17
ACGTcount: A:0.68, C:0.10, G:0.08, T:0.14
Consensus pattern (26 bp):
AACCTAAAAAAAGATAACAAAAATGT
Found at i:592650 original size:20 final size:21
Alignment explanation
Indices: 592625--592676 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
592615 TTTTCCCAAT
*
592625 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* *
592645 TCGCAACGCGAATTAGGAAAA
1 TCGCAATGCGAATTAAGAAAA
592666 TCGCAATGCGA
1 TCGCAATGCGA
592677 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:592689 original size:41 final size:40
Alignment explanation
Indices: 592644--592731 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
592634 GAATAAGTAA
592644 ATCGCAACGCGAATTA-GGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCG-A-TACGGAAAATCGCAATGCGATACTGACT
* * ** * *
592685 ATCGCAATGCGATACTGACTATCGCAATGTGATACTTACT
1 ATCGCAACGCGATACGGAAAATCGCAATGCGATACTGACT
592725 ATCGCAA
1 ATCGCAA
592732 TGCAACGCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.05
40 28 0.70
41 10 0.25
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (40 bp):
ATCGCAACGCGATACGGAAAATCGCAATGCGATACTGACT
Found at i:592690 original size:20 final size:20
Alignment explanation
Indices: 592665--592734 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
592655 AATTAGGAAA
592665 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
592685 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
592705 ATCGCAATGTGATACTTACT
1 ATCGCAATGCGATACTGACT
592725 ATCGCAATGC
1 ATCGCAATGC
592735 AACGCAATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:592758 original size:20 final size:21
Alignment explanation
Indices: 592666--592779 Score: 74
Period size: 20 Copynumber: 5.4 Consensus size: 21
592656 ATTAGGAAAA
* *
592666 TCGCAATGC-GATACTGACTA
1 TCGCAACGCAGATACTGACTT
* *
592686 TCGCAATGC-GATACTGACTA
1 TCGCAACGCAGATACTGACTT
* * * *
592706 TCGCAATG-TGATACTTACTA
1 TCGCAACGCAGATACTGACTT
*
592726 TCGCAATGCAACGCAATACTGACTT
1 TCGCAACGC-A-G--ATACTGACTT
*
592751 TCGCAACG-AGATTCTGACTT
1 TCGCAACGCAGATACTGACTT
592771 TCGCAACGC
1 TCGCAACGC
592780 GATTTACATA
Statistics
Matches: 81, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
20 63 0.78
22 1 0.01
23 2 0.02
25 15 0.19
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (21 bp):
TCGCAACGCAGATACTGACTT
Found at i:592783 original size:20 final size:20
Alignment explanation
Indices: 592733--592783 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
592723 CTATCGCAAT
* *
592733 GCAACGCAATACTGACTTTC
1 GCAACGCGATTCTGACTTTC
*
592753 GCAACGAGATTCTGACTTTC
1 GCAACGCGATTCTGACTTTC
592773 GCAACGCGATT
1 GCAACGCGATT
592784 TACATAGCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (20 bp):
GCAACGCGATTCTGACTTTC
Found at i:593366 original size:19 final size:19
Alignment explanation
Indices: 593344--593489 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
593334 GAAACCAAAA
*
593344 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
593363 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
593382 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
593396 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
593415 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
593429 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
593448 TCCGCGTTGTGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
593468 ATCCCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
593488 TC
1 TC
593490 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 20 0.20
16 4 0.04
17 5 0.05
19 42 0.42
20 29 0.29
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:593404 original size:14 final size:14
Alignment explanation
Indices: 593385--593440 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
593375 TTTCATTTCG
593385 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
593399 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
593418 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
593432 CGTTGCGAT
1 CGTTGCGAT
593441 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:593414 original size:33 final size:33
Alignment explanation
Indices: 593366--593464 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
593356 TTTCATTTCG
**
593366 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
593399 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
*
593432 CGTTGCGATAGTCATTTCCGCGTTGTGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
593465 ATTATCCCGT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 48 0.77
34 14 0.23
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.41
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:595655 original size:21 final size:21
Alignment explanation
Indices: 595631--595697 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
595621 TCATTCCTCG
595631 AGAGTCCCCTCCCATCGTTCA
1 AGAGTCCCCTCCCATCGTTCA
* * ** *
595652 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCATCGTTCA
* *
595673 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCATCGTTCA
595694 AGAG
1 AGAG
595698 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCATCGTTCA
Found at i:595655 original size:42 final size:42
Alignment explanation
Indices: 595579--595697 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
595569 GACTCGCCTG
* *
595579 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTA
* * * * * *
595621 TCATTCCTCGAGAGTCCCCTCCCATCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTA
** * *
595663 TCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 TCATCCCTCAAGA-GTCCACTCCCATCATTCAAGAG
595698 CCCGATTCAC
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 57 0.93
43 4 0.07
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTA
Found at i:597073 original size:14 final size:14
Alignment explanation
Indices: 597054--597089 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
597044 ATTGTTTAAT
597054 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
597068 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
597082 TGATTTGT
1 TGATTTGT
597090 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:597288 original size:33 final size:33
Alignment explanation
Indices: 597245--597344 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
597235 ACGCGAAATT
*
597245 AAATTCGCGTTGCAATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
597278 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
* *
597311 -ATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAAT-TCGCGTTGCGATTTTCATTTCGCATTGCG
597344 A
1 A
597345 TAGTAATTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
32 2 0.03
33 58 0.97
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (33 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:597311 original size:19 final size:19
Alignment explanation
Indices: 597287--597345 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
597277 GAAATTAGCG
597287 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
597306 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
597320 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
597339 TTGCGAT
1 TTGCGAT
597346 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:599858 original size:24 final size:24
Alignment explanation
Indices: 599824--599877 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
599814 CTGAAACATC
*
599824 ATCAAAATCCGAG-TATTGACCAAT
1 ATCAAAATCCG-GTTATTGACCAAG
*
599848 ATCAAAGTCCGGTTATTGACCAAG
1 ATCAAAATCCGGTTATTGACCAAG
599872 ATCAAA
1 ATCAAA
599878 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGTTATTGACCAAG
Found at i:600688 original size:20 final size:21
Alignment explanation
Indices: 600663--600714 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
600653 TTTTCCTAAT
*
600663 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
600683 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
600704 TCGCAATGCGA
1 TCGCAATGCGA
600715 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:600736 original size:20 final size:20
Alignment explanation
Indices: 600703--600763 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
600693 AATTTGGAAA
* *
600703 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
600723 ATCGCAACGAGATAATTCTGACT
1 ATCGCAACGAGAT-A--CTGACT
* *
600746 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
600764 AAATCGTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 15 0.44
21 1 0.03
23 18 0.53
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:601011 original size:20 final size:20
Alignment explanation
Indices: 600986--601073 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
600976 CAACGGGGAA
600986 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
601006 ATCGCAACGCGAAACTGGCT
1 ATCGCAACGCGAAAATGGCT
* ** ***
601026 ATTGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
601046 ATTGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
601066 ATCGCAAC
1 ATCGCAAC
601074 TAGAAAATCG
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
19 4 0.08
20 43 0.83
21 5 0.10
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:601145 original size:19 final size:19
Alignment explanation
Indices: 601123--601167 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
601113 TTCTCGTTGT
601123 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
601142 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
601161 GATTTTC
1 GATTTTC
601168 TCGTTGCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:601323 original size:14 final size:14
Alignment explanation
Indices: 601304--601340 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
601294 CATCAATTAA
601304 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
601318 ACAAATCATCTTTT
1 ACAAATCAACATTT
601332 ACAAATCAA
1 ACAAATCAA
601341 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:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:602807 original size:21 final size:20
Alignment explanation
Indices: 602783--602842 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
602773 AACGGTGAGG
602783 GGGGACTCTTGAGGGA-GGATA
1 GGGGACTCTTGAGGGATGG--A
* **
602804 GGGGCCTCTTGAACGATTGGA
1 GGGGACTCTTGAGGGA-TGGA
602825 GGGGACTCTTGAGGGATG
1 GGGGACTCTTGAGGGATG
602843 ACAGGTGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
23 2 0.06
ACGTcount: A:0.20, C:0.13, G:0.45, T:0.22
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGGA
Found at i:603235 original size:20 final size:20
Alignment explanation
Indices: 603209--603275 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
603199 GAAACTTAAA
603209 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
603229 ATTGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
* *
603249 ATCGCAATGCG-AAATGA-A
1 ATCGCAACGCGAAAATGACT
603267 ATCGCAACG
1 ATCGCAACG
603276 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 8 0.21
19 5 0.13
20 26 0.67
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:603331 original size:19 final size:19
Alignment explanation
Indices: 603303--603383 Score: 91
Period size: 19 Copynumber: 4.5 Consensus size: 19
603293 AACACAAATT
* *
603303 GCATTACGATTTTCATTTT
1 GCATTGCGATTTTCATTTC
*
603322 GCGTTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
*
603341 GCATTGCGA-TTT--TGTC
1 GCATTGCGATTTTCATTTC
603357 G--TTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
603374 GCATTGCGAT
1 GCATTGCGAT
603384 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 31 0.61
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
GCATTGCGATTTTCATTTC
Found at i:603361 original size:33 final size:32
Alignment explanation
Indices: 603317--603383 Score: 125
Period size: 33 Copynumber: 2.1 Consensus size: 32
603307 TACGATTTTC
603317 ATTTTGCGTTGCGATTTTCATTTCGCATTGCG
1 ATTTTGCGTTGCGATTTTCATTTCGCATTGCG
603349 ATTTTGTCGTTGCGATTTTCATTTCGCATTGCG
1 ATTTTG-CGTTGCGATTTTCATTTCGCATTGCG
603382 AT
1 AT
603384 AGCCATTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (32 bp):
ATTTTGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:603390 original size:19 final size:20
Alignment explanation
Indices: 603368--603405 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
603358 TTGCGATTTT
603368 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
603387 CATTTCCGCGTTGCGATAG
1 CATTTCCGCATTGCGATAG
603406 TTATTTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:603411 original size:20 final size:19
Alignment explanation
Indices: 603356--603422 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
603346 GCGATTTTGT
*
603356 CGTTGCGAT-TTTCATTTCG
1 CGTTGCGATAGTT-ATTTCG
* **
603375 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTTATTT-CG
603395 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTTA-TTTCG
*
603415 TGTTGCGA
1 CGTTGCGA
603423 AAGTAAACTA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
19 12 0.32
20 22 0.59
21 3 0.08
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTTATTTCG
Found at i:603930 original size:18 final size:18
Alignment explanation
Indices: 603904--603948 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
603894 GTCGATCAGA
*
603904 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
603922 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
603940 TGATGGCTC
1 TGATGGCTC
603949 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:605315 original size:20 final size:20
Alignment explanation
Indices: 605267--605325 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
605257 AATAGTTTCT
** *
605267 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
605287 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
605307 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
605326 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:605606 original size:20 final size:20
Alignment explanation
Indices: 605581--605633 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
605571 TTTGAGAGAT
605581 GGAGATAGATGGATTTCGTC
1 GGAGATAGATGGATTTCGTC
*
605601 GGAGATAGGGACGGATTTCGTC
1 GGAGATA--GATGGATTTCGTC
*
605623 GGAGATGGATG
1 GGAGATAGATG
605634 AGAGAGTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.36
22 18 0.64
ACGTcount: A:0.25, C:0.09, G:0.42, T:0.25
Consensus pattern (20 bp):
GGAGATAGATGGATTTCGTC
Found at i:605845 original size:20 final size:20
Alignment explanation
Indices: 605799--605953 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
605789 CGCTTTGAAA
* * *
605799 ATCGCATTGCGATTATTTATT
1 ATCGCATTGCGA-TAGTCAGT
* * *
605820 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
605840 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
605860 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
605881 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
605901 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
605921 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
605941 ATCGCATTGCGAT
1 ATCGCATTGCGAT
605954 TTTCCCAATT
Statistics
Matches: 115, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 87 0.76
21 23 0.20
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:605905 original size:61 final size:61
Alignment explanation
Indices: 605799--605952 Score: 186
Period size: 61 Copynumber: 2.5 Consensus size: 61
605789 CGCTTTGAAA
* * *
605799 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATTTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
605860 ATCTCGTTGCGATT-TTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATT-TATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * *
605921 ATCGCATTGCGA-TAGTCAGTATCGCATTGCGA
1 ATCGCATTGCGATTATTTATTATCGCATTGCGA
605953 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
60 17 0.22
61 61 0.78
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGATTATTTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:605938 original size:81 final size:82
Alignment explanation
Indices: 605799--605956 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 82
605789 CGCTTTGAAA
* * * * * *
605799 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCT
1 ATCGCATTGCGATTAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCG
*
605864 CGTTGCGATTTTGTATT
66 CATTGCGATTTTGTATT
* * *
605881 ATCGCATTGCGA-TAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCG
1 ATCGCATTGCGATTAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCG
605945 CATTGCGATTTT
66 CATTGCGATTTT
605957 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 54 0.82
82 12 0.18
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (82 bp):
ATCGCATTGCGATTAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCG
CATTGCGATTTTGTATT
Found at i:605972 original size:81 final size:81
Alignment explanation
Indices: 605799--605974 Score: 201
Period size: 81 Copynumber: 2.2 Consensus size: 81
605789 CGCTTTGAAA
* * * * * *
605799 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCT
1 ATCGCATTGCGA-TAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCG
* ** *
605864 CGTTGCGATTTTGTATT
65 CATTGCGATTTTCCAAT
* * *
605881 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGC
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGC
605946 ATTGCGATTTTCCCAAT
66 ATTGCGATTTT-CCAAT
*
605963 -TCGCGTTGCGAT
1 ATCGCATTGCGAT
605975 TTACTTATTC
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 65 0.82
82 14 0.18
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (81 bp):
ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGC
ATTGCGATTTTCCAAT
Found at i:605987 original size:81 final size:79
Alignment explanation
Indices: 605799--605994 Score: 196
Period size: 81 Copynumber: 2.4 Consensus size: 79
605789 CGCTTTGAAA
* * *
605799 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCT
1 ATCGCATTGCG---ATTTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCG
* ** *
605864 CGTTGCGATTTTGTATT
63 CATTGCGATTTTCCAAT
* * * * *
605881 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGC
1 ATCGCATTGCGAT--TTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGC
605946 ATTGCGATTTTCCCAAT
64 ATTGCGATTTT-CCAAT
*
605963 -TCGCGTTGCGATTTACTTATTCGCATTGCGAA
1 ATCGCATTGCGATTTA-TTA-TCGCATTGCGAA
605995 TTGGGAAAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
79 4 0.04
80 2 0.02
81 74 0.80
82 13 0.14
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (79 bp):
ATCGCATTGCGATTTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCAT
TGCGATTTTCCAAT
Found at i:606064 original size:21 final size:21
Alignment explanation
Indices: 606024--606064 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
606014 ACTGTAGACA
** *
606024 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
606045 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
606065 GCGAATTTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:606504 original size:36 final size:38
Alignment explanation
Indices: 606455--606527 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
606445 ATAATATTAC
606455 AAATTGTAAAATATTTATATA-TTTTCTTTAAAAAATT
1 AAATTGTAAAATATTTATATAGTTTTCTTTAAAAAATT
* * *
606492 AAATT-TATAATATTTATATAGTTTTTTTTACAAAAT
1 AAATTGTAAAATATTTATATAGTTTTCTTTAAAAAAT
606528 AAAAAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 14 0.44
37 18 0.56
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (38 bp):
AAATTGTAAAATATTTATATAGTTTTCTTTAAAAAATT
Found at i:606538 original size:37 final size:36
Alignment explanation
Indices: 606464--606538 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
606454 CAAATTGTAA
* **
606464 AATATTTATATATTTTCTTTAAAAAATTAAATTTAT
1 AATATTTATATATTTTCTTTAAAAAATAAAAAATAT
* *
606500 AATATTTATATAGTTTTTTTTACAAAATAAAAAATAT
1 AATATTTATATA-TTTTCTTTAAAAAATAAAAAATAT
606537 AA
1 AA
606539 AAAAGGTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
36 12 0.36
37 21 0.64
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (36 bp):
AATATTTATATATTTTCTTTAAAAAATAAAAAATAT
Found at i:607970 original size:17 final size:17
Alignment explanation
Indices: 607944--607986 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
607934 GCAATTTTTT
607944 TAAA-AATAATTAATAA
1 TAAATAATAATTAATAA
**
607960 TAAATAATAATTTTTAA
1 TAAATAATAATTAATAA
607977 TAAATTAATA
1 TAAA-TAATA
607987 GCAACGAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 14 0.61
18 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATAATAATTAATAA
Found at i:610846 original size:22 final size:22
Alignment explanation
Indices: 610784--610843 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
610774 ATGTATATAA
* *
610784 AATTTTTATAAATGGTATATTTT
1 AATTTATATAAAT-TTATATTTT
610807 AATTTATATAAATTTATATTTT
1 AATTTATATAAATTTATATTTT
610829 AACTTTGATA-AAATT
1 AA-TTT-ATATAAATT
610844 ATAATATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 10 0.30
23 20 0.61
24 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
AATTTATATAAATTTATATTTT
Found at i:611516 original size:2 final size:2
Alignment explanation
Indices: 611509--611540 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
611499 AACTTCTTCC
611509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
611541 GTTGTTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:615230 original size:3 final size:3
Alignment explanation
Indices: 615222--615324 Score: 84
Period size: 3 Copynumber: 34.7 Consensus size: 3
615212 CTGTAATATG
* * * *
615222 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
615267 TTA TAA TAA TTA TAA CAA TTA TAA TAA TAA AAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
615315 AAA TAA -AA TA
1 TAA TAA TAA TA
615325 GGAAAAAATT
Statistics
Matches: 77, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
2 4 0.05
3 71 0.92
4 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:615690 original size:58 final size:58
Alignment explanation
Indices: 615595--615711 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
615585 TCTGAAAATG
* *
615595 TTGATGCTAATCTATTTCCTTCTATGATAGATTATACAAAAGGTTGAACAAGCTCTTC
1 TTGATGCTAATCTATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAGCTCTTC
* *
615653 TTGATGCTAATCTATCTCCTTCTGTGATAGATCATACAAAAGGTTGAGCAAGCTCTTC
1 TTGATGCTAATCTATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAGCTCTTC
615711 T
1 T
615712 CATTATGAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (58 bp):
TTGATGCTAATCTATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAGCTCTTC
Found at i:615982 original size:24 final size:23
Alignment explanation
Indices: 615955--616000 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
615945 TGAACAAGAT
615955 CTTC-TCATTATGAACTTCTTCTTC
1 CTTCTTCA-TATG-ACTTCTTCTTC
*
615979 CTTCTTCATATGAGTTCTTCTT
1 CTTCTTCATATGACTTCTTCTT
616001 ATTATGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 8 0.40
25 3 0.15
ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52
Consensus pattern (23 bp):
CTTCTTCATATGACTTCTTCTTC
Found at i:616001 original size:123 final size:123
Alignment explanation
Indices: 615653--616276 Score: 1034
Period size: 123 Copynumber: 5.0 Consensus size: 123
615643 CAAGCTCTTC
* * * *
615653 TTGATGCTAATCTATCTCCTTCTGTGATAGA-TCATACAAAAGGTTGAGCAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
*
615717 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAG
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAG
* * *
615776 TTGATGCTGATCTATCTCATTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATT
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGC-AAAAGGTTGAACAAGCTCTTCTCATT
*
615841 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTTTGAACTTCTCTGGAAAAG
65 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
*
615900 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGATCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
* * *
615965 TGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAA
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAG
616024 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATT
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGC-AAAAGGTTGAACAAGCTCTTCTCATT
*
616089 ATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
65 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
*
616148 TTGATGTTGATCTATCTGCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
* * *
616213 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTGGAAATG
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT-TCTCTGGAAAAG
616272 TTGAT
1 TTGAT
616277 CCATCGAATG
Statistics
Matches: 473, Mismatches: 23, Indels: 9
0.94 0.05 0.02
Matches are distributed among these distances:
123 169 0.36
124 165 0.35
125 139 0.29
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
Found at i:616127 original size:248 final size:248
Alignment explanation
Indices: 615653--616258 Score: 1079
Period size: 248 Copynumber: 2.4 Consensus size: 248
615643 CAAGCTCTTC
* * * *
615653 TTGATGCTAATCTATCTCCTTCTGTGATAGA-TCATACAAAAGGTTGAGCAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
*
615717 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAGTTGATG
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAATTGATG
615782 CTGATCTATCTCATTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
131 CTGATCTATCTCATTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* *
615847 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTTTGAACTTCTCTGGAAAAG
196 TTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
*
615900 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGATCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
*
615965 TGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAATTGATG
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAATTGATG
* * *
616030 TTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
131 CTGATCTATCTCATTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
616095 TTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
196 TTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
*
616148 TTGATGTTGATCTATCTGCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
*
616213 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT
616259 CTTTCTGGAA
Statistics
Matches: 342, Mismatches: 16, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
247 29 0.08
248 313 0.92
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (248 bp):
TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAATTGATG
CTGATCTATCTCATTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
TTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
Found at i:617473 original size:18 final size:18
Alignment explanation
Indices: 617450--617484 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
617440 TATATGAAAC
617450 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
617468 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
617485 GATAAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:617872 original size:11 final size:11
Alignment explanation
Indices: 617858--617911 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
617848 TTTTTCAACA
617858 TTTTTTCTCTT
1 TTTTTTCTCTT
*
617869 TTTTTTCTTTT
1 TTTTTTCTCTT
* *
617880 TTTCTTTATTTTT
1 TTT-TTT-CTCTT
617893 TCTTTTTCTCTT
1 T-TTTTTCTCTT
617905 TTTTTTC
1 TTTTTTC
617912 CAACATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 19 0.53
12 7 0.19
13 8 0.22
14 2 0.06
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:617880 original size:19 final size:18
Alignment explanation
Indices: 617858--617911 Score: 76
Period size: 18 Copynumber: 3.0 Consensus size: 18
617848 TTTTTCAACA
617858 TTTTTTCTCTTTTTTTTC
1 TTTTTTCTCTTTTTTTTC
617876 TTTTTT-TCTTTATTTTT-
1 TTTTTTCTCTTT-TTTTTC
617893 TCTTTTTCTCTTTTTTTTC
1 T-TTTTTCTCTTTTTTTTC
617912 CAACATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.19
18 21 0.66
19 5 0.16
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTCTCTTTTTTTTC
Found at i:625258 original size:15 final size:15
Alignment explanation
Indices: 625235--625266 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
625225 TGCAATGAAT
625235 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
625250 AATGCATGTATGCAA
1 AATGAATGTATGCAA
625265 AA
1 AA
625267 GGTATTGATC
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:630539 original size:16 final size:16
Alignment explanation
Indices: 630514--630554 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
630504 GGCTGCGTGT
*
630514 CCCTATGGTATCATAA
1 CCCTAGGGTATCATAA
630530 CCCTAGGGTATCATAA
1 CCCTAGGGTATCATAA
630546 CCCTAGGGT
1 CCCTAGGGT
630555 TTCAGCTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (16 bp):
CCCTAGGGTATCATAA
Found at i:630764 original size:3 final size:3
Alignment explanation
Indices: 630756--630849 Score: 75
Period size: 3 Copynumber: 31.7 Consensus size: 3
630746 CTGTAATATG
* * * *
630756 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
630801 TTA TAA TAA TTA TAA CAA TTA TAA TAA TTA TAA TAA TAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
630848 TA
1 TA
630850 GGTAAAAATT
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
2 4 0.06
3 64 0.91
4 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:637782 original size:19 final size:20
Alignment explanation
Indices: 637745--637784 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
637735 ACTCTTTAAG
637745 TTATTATAATAACAATTGTA
1 TTATTATAATAACAATTGTA
637765 TTATTA-AATTAA-AATTGTA
1 TTATTATAA-TAACAATTGTA
637784 T
1 T
637785 ATACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TTATTATAATAACAATTGTA
Found at i:642590 original size:10 final size:10
Alignment explanation
Indices: 642570--642620 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
642560 TTTCATCACA
*
642570 TCAAATCCTC
1 TCAAATACTC
* *
642580 TAAAATTCTC
1 TCAAATACTC
642590 TCAAATACTC
1 TCAAATACTC
* *
642600 TCAATTTCTC
1 TCAAATACTC
642610 TCAAATACTC
1 TCAAATACTC
642620 T
1 T
642621 TATATTCTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.37
Consensus pattern (10 bp):
TCAAATACTC
Found at i:642595 original size:20 final size:20
Alignment explanation
Indices: 642570--642620 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
642560 TTTCATCACA
*
642570 TCAAATCCTCTAAAATTCTC
1 TCAAATACTCTAAAATTCTC
* *
642590 TCAAATACTCTCAATTTCTC
1 TCAAATACTCTAAAATTCTC
642610 TCAAATACTCT
1 TCAAATACTCT
642621 TATATTCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.37
Consensus pattern (20 bp):
TCAAATACTCTAAAATTCTC
Found at i:642684 original size:23 final size:26
Alignment explanation
Indices: 642650--642704 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
642640 TTAAGGTATA
*
642650 TTTT-ATTATATTTAA-TATTT-TAT
1 TTTTAATTATATTTAAGTATTTAAAT
642673 TTTTAATT-TATTTAAGTATTTAAAT
1 TTTTAATTATATTTAAGTATTTAAAT
642698 TTTTAAT
1 TTTTAAT
642705 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.39
24 8 0.29
25 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTAATTATATTTAAGTATTTAAAT
Found at i:642700 original size:24 final size:23
Alignment explanation
Indices: 642649--642715 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
642639 TTTAAGGTAT
*
642649 ATTTTATTATATTTAATATTTTA
1 ATTTTATTATATTTAATATTTAA
*
642672 TTTTTAATT-TATTTAAGTATTTAA
1 ATTTT-ATTATATTTAA-TATTTAA
*
642696 ATTTT-TAATATTT--TATTTAA
1 ATTTTATTATATTTAATATTTAA
642716 TTAATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.19
22 1 0.03
23 16 0.43
24 13 0.35
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (23 bp):
ATTTTATTATATTTAATATTTAA
Found at i:643845 original size:19 final size:20
Alignment explanation
Indices: 643812--643850 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
643802 AAAATCGATT
643812 TTAGATTATAGTTTT-ATAA
1 TTAGATTATAGTTTTGATAA
643831 TTAGATTATTA-TTTTGATAA
1 TTAGATTA-TAGTTTTGATAA
643851 AAATTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (20 bp):
TTAGATTATAGTTTTGATAA
Found at i:644548 original size:21 final size:21
Alignment explanation
Indices: 644518--644557 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
644508 AGAATGCTCG
644518 GAGGGAACCGATTCCCCCCAA
1 GAGGGAACCGATTCCCCCCAA
*
644539 GAGGGTACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
644558 TGTTCAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.40, G:0.25, T:0.12
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAA
Found at i:650339 original size:20 final size:21
Alignment explanation
Indices: 650316--650398 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
650306 TTGGTGCAGA
*
650316 GGGAATCGATTCCCCCCTGA-
1 GGGAACCGATTCCCCCCTGAG
*
650336 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-CTG-AG
**
650359 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCTGAG
* *
650380 GGGAATCGATACCCCCCTG
1 GGGAACCGATTCCCCCCTG
650399 GGGTTCTGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.29
21 19 0.37
22 1 0.02
23 16 0.31
ACGTcount: A:0.22, C:0.36, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCTGAG
Found at i:653124 original size:21 final size:21
Alignment explanation
Indices: 653094--653133 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
653084 AGAATGCTCG
653094 GAGGGAACCGATTCCCCCCAA
1 GAGGGAACCGATTCCCCCCAA
*
653115 GAGGGTACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
653134 TGTTCAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.40, G:0.25, T:0.12
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAA
Found at i:654424 original size:18 final size:18
Alignment explanation
Indices: 654401--654437 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
654391 AGCTGCTCAC
654401 GACGACGACGATGACGAT
1 GACGACGACGATGACGAT
* *
654419 GACGACTACGATGATGAT
1 GACGACGACGATGACGAT
654437 G
1 G
654438 GTGATGACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16
Consensus pattern (18 bp):
GACGACGACGATGACGAT
Found at i:654593 original size:14 final size:14
Alignment explanation
Indices: 654574--654607 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
654564 TATTTAGTTG
*
654574 TTTATTGGACTTTT
1 TTTATTGGAATTTT
*
654588 TTTATTGTAATTTT
1 TTTATTGGAATTTT
654602 TTTATT
1 TTTATT
654608 ATTTATCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.71
Consensus pattern (14 bp):
TTTATTGGAATTTT
Found at i:654665 original size:33 final size:34
Alignment explanation
Indices: 654628--654701 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
654618 TAATACTTAC
654628 TTTATTTCATT-AATTTGGTTGGA-TTTATT-TTAA
1 TTTATTTCATTAAATTT-GTTGGACTTT-TTGTTAA
**
654661 TTTATTTTGTTAAATTTGTTGGACTTTTTGTTAA
1 TTTATTTCATTAAATTTGTTGGACTTTTTGTTAA
*
654695 TGTATTT
1 TTTATTT
654702 TGGTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 17 0.49
34 18 0.51
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.62
Consensus pattern (34 bp):
TTTATTTCATTAAATTTGTTGGACTTTTTGTTAA
Done.