Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_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: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 12
Found at i:703726 original size:41 final size:41
Alignment explanation
Indices: 703665--703746 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
703655 ACTAACGGTG
703665 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
1 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
* *
703706 CTGAACATTGTTACATGAATGTACCAAAGCTGAACTGATAA
1 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
703747 GTACTCACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (41 bp):
CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
Found at i:703882 original size:18 final size:17
Alignment explanation
Indices: 703823--703892 Score: 86
Period size: 18 Copynumber: 4.0 Consensus size: 17
703813 TATTGATCTG
703823 TATCTAATAACTGTAAAA
1 TATCTAATAACTGT-AAA
* ** *
703841 TATCTGATATTTGTAAT
1 TATCTAATAACTGTAAA
703858 TATCTAATAACTGTAAA
1 TATCTAATAACTGTAAA
703875 TCATCTAATAACTGTAAA
1 T-ATCTAATAACTGTAAA
703893 CATTTAGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
17 16 0.37
18 27 0.63
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (17 bp):
TATCTAATAACTGTAAA
Found at i:703891 original size:35 final size:35
Alignment explanation
Indices: 703823--703891 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
703813 TATTGATCTG
* **
703823 TATCTAATAACTGTAAAATATCTGATATTTGTAAT
1 TATCTAATAACTGTAAAATATCTAATAACTGTAAT
703858 TATCTAATAACTGT-AAATCATCTAATAACTGTAA
1 TATCTAATAACTGTAAAAT-ATCTAATAACTGTAA
703892 ACATTTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 4 0.13
35 26 0.87
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (35 bp):
TATCTAATAACTGTAAAATATCTAATAACTGTAAT
Found at i:710464 original size:5 final size:5
Alignment explanation
Indices: 710456--710511 Score: 112
Period size: 5 Copynumber: 11.2 Consensus size: 5
710446 CGTCTCGTCT
710456 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA
1 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA
710506 CGGCA C
1 CGGCA C
710512 TGTACGTGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.20, C:0.41, G:0.39, T:0.00
Consensus pattern (5 bp):
CGGCA
Found at i:716504 original size:22 final size:22
Alignment explanation
Indices: 716479--716520 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
716469 AAGAGTTATT
* *
716479 TGATTTAATTCCAGGTGTTACA
1 TGATATAATTCCAGGAGTTACA
*
716501 TGATATAATTTCAGGAGTTA
1 TGATATAATTCCAGGAGTTA
716521 TAAAAGCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (22 bp):
TGATATAATTCCAGGAGTTACA
Found at i:718546 original size:31 final size:31
Alignment explanation
Indices: 718508--718630 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
718498 CCCGAAGGAC
* *
718508 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
718539 CAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
718570 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
718601 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
718631 CCCTCGACCC
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:722649 original size:31 final size:31
Alignment explanation
Indices: 722611--722733 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
722601 CCCGAAGGAC
* *
722611 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
722642 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
722673 CAATCCATATGTCCCGAAGAGCATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
722704 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
722734 CCCTCGACCC
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:726177 original size:25 final size:25
Alignment explanation
Indices: 726149--726210 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
726139 ATAAAAAAAC
*
726149 AAAAATATTAAA-TAAATCAAAAGGA
1 AAAAATATTAAAGAAAATCAAAA-GA
* *
726174 AAAAATAATAAAGAAAATGAAAAGA
1 AAAAATATTAAAGAAAATCAAAAGA
726199 AAACAA-ATTAAA
1 AAA-AATATTAAA
726211 ATTACGAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (25 bp):
AAAAATATTAAAGAAAATCAAAAGA
Found at i:726191 original size:26 final size:24
Alignment explanation
Indices: 726134--726201 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
726124 ATAATAAAAT
* * *
726134 AAAAAATAAAAAAACAAAAATATTA
1 AAAAAATCAAAAGA-AAAAATAATA
*
726159 AATAAATCAAAAGGAAAAAATAATA
1 AAAAAATCAAAA-GAAAAAATAATA
*
726184 AAGAAAATGAAAAGAAAA
1 AA-AAAATCAAAAGAAAA
726202 CAAATTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 26 0.74
26 9 0.26
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.13
Consensus pattern (24 bp):
AAAAAATCAAAAGAAAAAATAATA
Found at i:727338 original size:35 final size:34
Alignment explanation
Indices: 727259--727527 Score: 152
Period size: 36 Copynumber: 7.4 Consensus size: 34
727249 AATTAAATGA
* * * *
727259 AAAATCATTTTTAAACTATATATTATGTTTTTTTT
1 AAAAT-ATTTTTAAACCATATATTATATATATTTT
*
727294 AAAATTATTTTCTAAACCATATAATATATATATTTT
1 AAAA-TATTTT-TAAACCATATATTATATATATTTT
*
727330 AAAATATTTTAAAAACCTATATATTATATATATTTT
1 AAAATATTTT-TAAACC-ATATATTATATATATTTT
* * * *
727366 -CAATTTTTTTATAACTATATATTATATAGT-TTTC
1 AAAATATTTTTA-AACCATATATTATATA-TATTTT
* *
727400 AAAATGTTTTTAAAAAACCATATACTATATA-AGTTTTT
1 AAAATATTTTT---AAACCATATATTATATATA--TTTT
* * *
727438 AAAATGTTCTTAAAAACCATGTATTATATA-AGTTTT
1 AAAATATT-TT-TAAACCATATATTATATATA-TTTT
*
727474 CAAAATGTTTTTAAGAAAACCATATATTATATA-AGTTTT
1 -AAAATATTTTT----AAACCATATATTATATATA-TTTT
*
727513 CAAAATCTTTTTAAA
1 -AAAATATTTTTAAA
727528 AAATTATGTA
Statistics
Matches: 190, Mismatches: 25, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
34 16 0.08
35 42 0.22
36 47 0.25
37 38 0.20
38 12 0.06
39 35 0.18
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.47
Consensus pattern (34 bp):
AAAATATTTTTAAACCATATATTATATATATTTT
Found at i:727504 original size:39 final size:37
Alignment explanation
Indices: 727307--727529 Score: 246
Period size: 37 Copynumber: 6.1 Consensus size: 37
727297 ATTATTTTCT
* *
727307 AAACCATATAATATATATA-TTTT-AAAAT-ATTTTAA
1 AAACCATATATTATATA-AGTTTTCAAAATGTTTTTAA
*
727342 AAACCTATATATTATATATA-TTTTC--AAT-TTTTTTA
1 AAACC-ATATATTATATA-AGTTTTCAAAATGTTTTTAA
* *
727377 TAACTATATATTATAT-AGTTTTCAAAATGTTTTTAAA
1 AAACCATATATTATATAAGTTTTCAAAATGTTTTT-AA
* * *
727414 AAACCATATACTATATAAGTTTTTAAAATGTTCTTAA
1 AAACCATATATTATATAAGTTTTCAAAATGTTTTTAA
*
727451 AAACCATGTATTATATAAGTTTTCAAAATGTTTTTAAGA
1 AAACCATATATTATATAAGTTTTCAAAATGTTTTT-A-A
*
727490 AAACCATATATTATATAAGTTTTCAAAATCTTTTTAA
1 AAACCATATATTATATAAGTTTTCAAAATGTTTTTAA
727527 AAA
1 AAA
727530 ATTATGTAAT
Statistics
Matches: 161, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
32 1 0.01
33 5 0.03
34 11 0.07
35 19 0.12
36 22 0.14
37 51 0.32
38 18 0.11
39 34 0.21
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
AAACCATATATTATATAAGTTTTCAAAATGTTTTTAA
Found at i:727509 original size:76 final size:76
Alignment explanation
Indices: 727385--727555 Score: 240
Period size: 76 Copynumber: 2.3 Consensus size: 76
727375 TATAACTATA
* *
727385 TATTATAT-AGTTTTCAAAATGTTTTTAAAAAACCATATACTATATAAGTTTTTAAAATGTTCTT
1 TATTATATAAGTTTTCAAAATGTTTTTAAAAAACCATATACTATATAAGTTTTCAAAATCTTCTT
727449 -AAAAACCATG
66 AAAAAACCATG
* *
727459 TATTATATAAGTTTTCAAAATGTTTTTAAGAAAACCATATATTATATAAGTTTTCAAAATCTTTT
1 TATTATATAAGTTTTCAAAATGTTTTTAA-AAAACCATATACTATATAAGTTTTCAAAATCTTCT
**
727524 TAAAAAATTATG
65 TAAAAAACCATG
*
727536 TAATATATACA-TTTTCAAAA
1 TATTATATA-AGTTTTCAAAA
727556 GTATATATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
74 8 0.09
75 20 0.23
76 32 0.37
77 25 0.29
78 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (76 bp):
TATTATATAAGTTTTCAAAATGTTTTTAAAAAACCATATACTATATAAGTTTTCAAAATCTTCTT
AAAAAACCATG
Found at i:737243 original size:11 final size:11
Alignment explanation
Indices: 737226--737267 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
737216 ATATTTGAAC
737226 AATATAAACAA
1 AATATAAACAA
* *
737237 AAGATAAAGAA
1 AATATAAACAA
737248 CAATATAAACAA
1 -AATATAAACAA
737260 AATATAAA
1 AATATAAA
737268 GAACTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (11 bp):
AATATAAACAA
Found at i:737248 original size:23 final size:23
Alignment explanation
Indices: 737222--737271 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
737212 AATAATATTT
737222 GAACAATATAAACAAAAGATAAA
1 GAACAATATAAACAAAAGATAAA
*
737245 GAACAATATAAACAAAATATAAA
1 GAACAATATAAACAAAAGATAAA
737268 GAAC
1 GAAC
737272 TTAAAAGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.68, C:0.10, G:0.08, T:0.14
Consensus pattern (23 bp):
GAACAATATAAACAAAAGATAAA
Found at i:756540 original size:78 final size:78
Alignment explanation
Indices: 756441--756598 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 78
756431 AGCGTTCTGC
* *
756441 CAAGTGCTGTTGGTTTTAATCCTATGATCATTATCATGACCACTGCTTATTGTATCTCGAAGGGA
1 CAAGTGCTGTTGGTTTTAATCCTATGATCATTATCATGACCACTGCTTATTGTATCTCAAAGGAA
756506 ATAGCAGTTAGAA
66 ATAGCAGTTAGAA
756519 CAAGTGCTGTTGGTTTTAATCCTATGATCATTATCATGACCACTGCTTATTGTATCTCAAAGGAA
1 CAAGTGCTGTTGGTTTTAATCCTATGATCATTATCATGACCACTGCTTATTGTATCTCAAAGGAA
756584 ATAGCAGTTAGAA
66 ATAGCAGTTAGAA
756597 CA
1 CA
756599 CCAAAAAATA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (78 bp):
CAAGTGCTGTTGGTTTTAATCCTATGATCATTATCATGACCACTGCTTATTGTATCTCAAAGGAA
ATAGCAGTTAGAA
Found at i:758454 original size:31 final size:32
Alignment explanation
Indices: 758419--758494 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
758409 TTGAGGCCAT
* **
758419 AGAGCCTACCCAAATGTGTA-CTTGGGGCCTA
1 AGAGCCTACCCAAAGGAATACCTTGGGGCCTA
* *
758450 AGAGCCTACCCAAGGGAATACCTTGGGGCCTT
1 AGAGCCTACCCAAAGGAATACCTTGGGGCCTA
758482 AGAGCCTACCCAA
1 AGAGCCTACCCAA
758495 GTCTCACCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 16 0.41
32 23 0.59
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (32 bp):
AGAGCCTACCCAAAGGAATACCTTGGGGCCTA
Found at i:792675 original size:14 final size:15
Alignment explanation
Indices: 792644--792678 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
792634 GCATGCCTAC
792644 AATAAAGGAAATAGA
1 AATAAAGGAAATAGA
*
792659 AATAAAGTAAA-AGA
1 AATAAAGGAAATAGA
792673 AATAAA
1 AATAAA
792679 TAGTGCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AATAAAGGAAATAGA
Found at i:801976 original size:19 final size:19
Alignment explanation
Indices: 801952--801988 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
801942 TTGGTTGCAC
801952 TTTTTTTAATTTTTTTGTT
1 TTTTTTTAATTTTTTTGTT
**
801971 TTTTTTTCGTTTTTTTGT
1 TTTTTTTAATTTTTTTGT
801989 GTGTGCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.03, G:0.08, T:0.84
Consensus pattern (19 bp):
TTTTTTTAATTTTTTTGTT
Found at i:806999 original size:2 final size:2
Alignment explanation
Indices: 806992--807025 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
806982 CAGTATAAAC
806992 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
807026 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:807030 original size:2 final size:2
Alignment explanation
Indices: 807025--807113 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
807015 TATATATATA
807025 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
807067 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
807109 TG TG T
1 TG TG T
807114 TAAGTAAAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:809674 original size:31 final size:31
Alignment explanation
Indices: 809639--809706 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
809629 TTAAAACTAT
809639 AAAATAATTTATAGA-T-AAAATATAAGTTCA
1 AAAATAATTTATAGATTAAAAATATAA-TTCA
* *
809669 GAAAATCATTTATATATTAAAAATATAATTCA
1 -AAAATAATTTATAGATTAAAAATATAATTCA
809701 AAAATA
1 AAAATA
809707 TCCTGTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 18 0.56
32 5 0.16
33 9 0.28
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (31 bp):
AAAATAATTTATAGATTAAAAATATAATTCA
Found at i:810338 original size:32 final size:31
Alignment explanation
Indices: 810284--810393 Score: 105
Period size: 32 Copynumber: 3.5 Consensus size: 31
810274 TTGGGACATG
**
810284 AGAGCCTACCCAAGAGTGTACCTTGGGGACCTA
1 AGAGCCTACCCAAG-GAATACCTTGGGG-CCTA
*
810317 AGAGCCTACCCATGGAATACCTTGGGGCCTTA
1 AGAGCCTACCCAAGGAATACCTTGGGGCC-TA
* * ** *
810349 A-AGCATACCTAAGGAAATATATTGGGGCCTT
1 AGAGCCTACCCAAGG-AATACCTTGGGGCCTA
810380 AGAGCCTACCCAAG
1 AGAGCCTACCCAAG
810394 TGTCACCTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
31 14 0.22
32 36 0.57
33 13 0.21
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (31 bp):
AGAGCCTACCCAAGGAATACCTTGGGGCCTA
Found at i:811534 original size:26 final size:26
Alignment explanation
Indices: 811481--811553 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 26
811471 TCAAGGCTTG
* *
811481 GGGGTATTTTAGGTTATTTTATACTTCA
1 GGGGTATTTT-GG-TCTTTTATAATTCA
811509 GGGGTATTTTGGTCTTTTATAATTCA
1 GGGGTATTTTGGTCTTTTATAATTCA
* * *
811535 AGGGTATTTTAGTCCTTTA
1 GGGGTATTTTGGTCTTTTA
811554 CTTCTGTCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 28 0.70
27 2 0.05
28 10 0.25
ACGTcount: A:0.21, C:0.08, G:0.22, T:0.49
Consensus pattern (26 bp):
GGGGTATTTTGGTCTTTTATAATTCA
Found at i:816017 original size:15 final size:17
Alignment explanation
Indices: 815985--816017 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
815975 TAGAGGATTG
815985 AGAGTTTTGAGAAATTT
1 AGAGTTTTGAGAAATTT
816002 AGAG-TTTGAG-AATTT
1 AGAGTTTTGAGAAATTT
816017 A
1 A
816018 AAAGCTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (17 bp):
AGAGTTTTGAGAAATTT
Found at i:816303 original size:117 final size:117
Alignment explanation
Indices: 816098--816797 Score: 723
Period size: 117 Copynumber: 5.8 Consensus size: 117
816088 TACTATTCAC
* * * * *
816098 GTGAAAGCGTGTTCCTGGGGG-GCGCCTTCCATTATTTTATCAGATAATATGTTATAATTGCCCT
1 GTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * * *
816162 ATTATGTCACTCATATCCCTCGGGGGCACTATTAATGTCAATACCTAAAATG
66 ATTATGTCACTCATGTCCCTCGGGGGAACTATTCATGTCAGTACCTAAAATG
* * * *
816214 GTGAAAGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCAGATAATATATTATCATTTCCCT
1 GTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * * *
816279 GTTATGTCACTCATGTCCCTCGGGGGCACTATTCATATCAGTACCCAAAATG
66 ATTATGTCACTCATGTCCCTCGGGGGAACTATTCATGTCAGTACCTAAAATG
* * * * *
816331 GTGAAAGCGCATTCCCGAGGGCGAGCCTTCCATTATTTTATCAGAAAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* *
816396 ATTATGTCACTCATGTCCCTCGGGGGAACTATTCATGTCAGTAACAAAAATG
66 ATTATGTCACTCATGTCCCTCGGGGGAACTATTCATGTCAGTACCTAAAATG
* *
816448 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTA-AGAATATGTTATCATTGCCC
1 GTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGT-CAGAGAATATGTTATCATTGCCC
* * **
816512 TATTATGTCACTCATGT-CCTCCGGGGAACTAATT-ATATCAGTACCTATTATTTCTGAGGG
65 TATTATGTCACTCATGTCCCTCGGGGGAACT-ATTCATGTCAGTACCTA--A------AATG
* * * *
816572 GACTTGAAGGCGCATTCCCGGGGGTGCGCCTTCCATTATTTTGTGTA-AGAATATGTTATCATTG
1 G---TGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGT-CAGAGAATATGTTATCATTG
* * *
816636 CCCTATAATGTCACTCATATCCC-CCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGA-G
62 CCCTATTATGTCACTCATGTCCCTCGGGGGAACTATTCATGTCAGTACCTA--A------A-ATG
* ** * *
816699 GACTTGAAGGCGCGTTCTTGGGGGGGCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTGC
1 G---TGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGC
*
816764 CCTATTATGTCACTCATGTCCC-CCGGGGAACTAT
63 CCTATTATGTCACTCATGTCCCTCGGGGGAACTAT
816798 AGATGGATCG
Statistics
Matches: 516, Mismatches: 50, Indels: 25
0.87 0.08 0.04
Matches are distributed among these distances:
116 41 0.08
117 264 0.51
118 2 0.00
124 3 0.01
126 5 0.01
127 199 0.39
128 2 0.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (117 bp):
GTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTCATGTCCCTCGGGGGAACTATTCATGTCAGTACCTAAAATG
Found at i:816680 original size:127 final size:126
Alignment explanation
Indices: 816449--816797 Score: 574
Period size: 127 Copynumber: 2.8 Consensus size: 126
816439 ACAAAAATGG
816449 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTAAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTAAGAATATGTTATCATTGCCCTA
* *
816514 TTATGTCACTCATGTCCTCCGGGGAACTAATTATATCAGTACCTATTATTTCTGAGGGGACT
66 TTATGTCACTCATGTCCCCCGGGGAACT-ATTATATCAGTACCTATTATTTCTGAGAGGACT
* *
816576 TGAAGGCGCATTCCCGGGGGTGCGCCTTCCATTATTTTGTGTAAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTAAGAATATGTTATCATTGCCCTA
* * *
816641 TAATGTCACTCATATCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGAGGACT
66 TTATGTCACTCATGTCCCCCGGGGAACTATT-ATATCAGTACCTATTATTTCTGAGAGGACT
** *
816703 TGAAGGCGCGTTCTTGGGGGGGCGCCTTCCATTATTTTGT-TAGAGAATATGTTATCATTGCCCT
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTA-AGAATATGTTATCATTGCCCT
816767 ATTATGTCACTCATGTCCCCCGGGGAACTAT
65 ATTATGTCACTCATGTCCCCCGGGGAACTAT
816798 AGATGGATCG
Statistics
Matches: 207, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
126 5 0.02
127 202 0.98
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (126 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGTAAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCCCGGGGAACTATTATATCAGTACCTATTATTTCTGAGAGGACT
Found at i:816957 original size:23 final size:23
Alignment explanation
Indices: 816931--817029 Score: 70
Period size: 23 Copynumber: 4.6 Consensus size: 23
816921 TGAAGTTTGA
816931 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGGATAAAATGTTATGG
* *
816954 ATAAATT-GAT-AAATGTAAAGTG
1 ATAAATTGGATAAAATGTTATG-G
* * *
816976 ATCAGTTGG-T----TGTT-TGA
1 ATAAATTGGATAAAATGTTATGG
*
816993 ATAAATTGGATAAAATGTTATAG
1 ATAAATTGGATAAAATGTTATGG
*
817016 ATAAATTGAATAAA
1 ATAAATTGGATAAA
817030 TGTGAAGTGA
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
17 7 0.12
18 2 0.04
19 3 0.05
21 8 0.14
22 14 0.25
23 22 0.39
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAAATTGGATAAAATGTTATGG
Found at i:816996 original size:62 final size:63
Alignment explanation
Indices: 816925--817051 Score: 220
Period size: 62 Copynumber: 2.0 Consensus size: 63
816915 ATTATGTGAA
* *
816925 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTG-ATAAATGTAAAGTGATCAGTTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATAGATAAATTGAATAAATGTAAAGTGATAAGTTGGTT
*
816987 GTTTGAATAAATTGGATAAAATGTTATAGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATAGATAAATTGAATAAATGTAAAGTGATAAGTTGGTT
817050 GT
1 GT
817052 GACATTGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
62 36 0.59
63 25 0.41
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (63 bp):
GTTTGAATAAATTGGATAAAATGTTATAGATAAATTGAATAAATGTAAAGTGATAAGTTGGTT
Found at i:817188 original size:57 final size:57
Alignment explanation
Indices: 817066--817205 Score: 183
Period size: 57 Copynumber: 2.5 Consensus size: 57
817056 TTGAAATTGT
* * *
817066 ATGGAATAAGCATCGACATGATTTTACGAATAAATGTGATGTGATAAGTACTTGGGA
1 ATGGAATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAGTACTTGGGA
* * ** **
817123 CTGAAATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAGTTGGTT-TTA
1 ATGGAATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAG-TACTTGGGA
817180 ATGGAATGAGCATCGACATGTTTTTA
1 ATGGAATGAGCATCGACATGTTTTTA
817206 TGTATGGATA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
57 68 0.96
58 3 0.04
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (57 bp):
ATGGAATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAGTACTTGGGA
Found at i:819746 original size:3 final size:3
Alignment explanation
Indices: 819738--819770 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
819728 AATAAATTTA
819738 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
819771 TTTGCTAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:823557 original size:2 final size:2
Alignment explanation
Indices: 823550--823583 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
823540 TCATTTGGGT
823550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
823584 ATTAGTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:823727 original size:2 final size:2
Alignment explanation
Indices: 823722--823791 Score: 79
Period size: 2 Copynumber: 35.5 Consensus size: 2
823712 TGTGCGCATT
* * *
823722 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
823764 TG TA TG TA TA TA TA CA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
823792 TATTAATGTT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:833546 original size:43 final size:45
Alignment explanation
Indices: 833454--833838 Score: 199
Period size: 45 Copynumber: 8.7 Consensus size: 45
833444 GAATCTTCAA
* * *
833454 CTTGACTCTCTCGTGAAGAGGAGTAAATCTTTCA--A-TGTTATT
1 CTTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGTATTGTCATT
*
833496 CTTGACTTTCTCGTGAAGA-AAGTCAATC-TTCAGTATTGTCATT
1 CTTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGTATTGTCATT
* *
833539 CTTGACTTTCTCGTGAAGAGAAGTTAATCTTTTAGTATTGTC-TT
1 CTTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGTATTGTCATT
* * * * * * * *
833583 CCTTAATTTTTCTCGAGTAA-AGGAGTCAGTCTTTTAGTGTTGTC-TT
1 -CTTGA-CTTTCTCGTG-AAGAGAAGTAAATCTTTCAGTATTGTCATT
*** * * * * *
833629 CCTTGACTTTCTTACGAAGAGGAGTAGATCTTTTAGTGA-TGTCCTA
1 -CTTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGT-ATTGTCATT
* ** * * ** * ** *
833675 CTTGACTATCTCACGAGGAGGAGTCTATC-TTC-CTGGTGTCCTT
1 CTTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGTATTGTCATT
* * * *
833718 CTTGACTTTCTCGTGAAGAGGAGTAAACCTTTTAGTGA-TGTAATT
1 CTTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGT-ATTGTCATT
* *
833763 CTTGACTTTCTCGCGAAGAGGAGTCAACAT-TTT-AGTGA-TGTCATT
1 CTTGACTTTCTCGTGAAGAGAAGT-AA-ATCTTTCAGT-ATTGTCATT
* * *
833808 CTTAAATTTCTCGTG-AGAGGAGTAAATCTTT
1 CTTGACTTTCTCGTGAAGAGAAGTAAATCTTT
833839 TAGTGATGTT
Statistics
Matches: 275, Mismatches: 50, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
40 4 0.01
41 7 0.03
42 21 0.08
43 59 0.21
44 24 0.09
45 116 0.42
46 41 0.15
47 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (45 bp):
CTTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGTATTGTCATT
Found at i:833661 original size:45 final size:45
Alignment explanation
Indices: 833603--833995 Score: 256
Period size: 45 Copynumber: 8.8 Consensus size: 45
833593 TCTCGAGTAA
* *
833603 AGGAGTCAG-TCTTTTAGTGTTGT-CTTCCTTGACTTTCTTACGAAG
1 AGGAGT-AGATCTTTTAGTGATGTACTT-CTTGACTTTCTCACGAAG
* * * *
833648 AGGAGTAGATCTTTTAGTGATGTCCTACTTGACTATCTCACGAGG
1 AGGAGTAGATCTTTTAGTGATGTACTTCTTGACTTTCTCACGAAG
** * * **
833693 AGGAGTCTATCTTCCT-G-G-TGTCCTTCTTGACTTTCTCGTGAAG
1 AGGAGTAGATCTT-TTAGTGATGTACTTCTTGACTTTCTCACGAAG
* * * *
833736 AGGAGTAAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAG
1 AGGAGTAGATCTTTTAGTGATGTACTTCTTGACTTTCTCACGAAG
* * **
833781 AGGAGTCA-A-CATTTTAGTGATGT-CATTCTTAAATTTCTCGTG-AG
1 AGGAGT-AGATC-TTTTAGTGATGTAC-TTCTTGACTTTCTCACGAAG
* * * * **
833825 AGGAGTAAATCTTTTAGTGATGTTA-TTTTTTATTTTCTTGCGAAG
1 AGGAGTAGATCTTTTAGTGATG-TACTTCTTGACTTTCTCACGAAG
* * * * * *
833870 AGGACTCA-ACCTTTTGGTTAAGTTA-TTCTTGACTTTCTCTCGAAG
1 AGGAGT-AGATCTTTTAGTGATG-TACTTCTTGACTTTCTCACGAAG
* * *
833915 AGGAGTCA-ACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAG
1 AGGAGT-AGATCTTTTAGTGATGTACTTCTTGACTTTCTCACGAAG
* * *
833960 AGGAGT-CATCTTTTAGTGATATAATTCTTGACTTTC
1 AGGAGTAGATCTTTTAGTGATGTACTTCTTGACTTTC
833996 AACCTTTTAG
Statistics
Matches: 285, Mismatches: 46, Indels: 35
0.78 0.13 0.10
Matches are distributed among these distances:
42 1 0.00
43 32 0.11
44 66 0.23
45 181 0.64
46 5 0.02
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (45 bp):
AGGAGTAGATCTTTTAGTGATGTACTTCTTGACTTTCTCACGAAG
Found at i:833736 original size:88 final size:89
Alignment explanation
Indices: 833454--833995 Score: 286
Period size: 89 Copynumber: 6.1 Consensus size: 89
833444 GAATCTTCAA
* * * * * **
833454 CTTGACTCTCTCGTGAAGAGGAGTAAATCTTTCA---ATGTTATTCTTGACTTTCTCGTGAAGA-
1 CTTGACTTTCTCGTGAAGAGGAGTAAATCTTTTAGTGATGTAATACTTGACTATCTCACGAAGAG
* *
833515 AAGTCA-ATCTT-CAGTATTGTCATT
66 GAGTCACATCTTACTG-A-TGTCATT
* * ** * * * *
833539 CTTGACTTTCTCGTGAAGAGAAGTTAATCTTTTAGT-ATTGTCTTCCTTAATTTTTCTCGA-GTA
1 CTTGACTTTCTCGTGAAGAGGAGTAAATCTTTTAGTGA-TGTAATACTTGA-CTATCTC-ACG-A
* * *
833602 A-AGGAGTCAGTC-TTTTAGTGTTGTC-TT
62 AGAGGAGTCA--CATCTTACTGATGTCATT
*** * ** *
833629 CCTTGACTTTCTTACGAAGAGGAGTAGATCTTTTAGTGATGTCCTACTTGACTATCTCACGAGGA
1 -CTTGACTTTCTCGTGAAGAGGAGTAAATCTTTTAGTGATGTAATACTTGACTATCTCACGAAGA
* * * *
833694 GGAGTC-TATCTTCCTGGTGTCCTT
65 GGAGTCACATCTTACTGATGTCATT
* * * *
833718 CTTGACTTTCTCGTGAAGAGGAGTAAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAG
1 CTTGACTTTCTCGTGAAGAGGAGTAAATCTTTTAGTGATGTAATACTTGACTATCTCACGAAGAG
* *
833783 GAGTCAACATTTTAGTGATGTCATT
66 GAGTC-ACATCTTACTGATGTCATT
* * * ** * * * **
833808 CTTAAATTTCTCGTG-AGAGGAGTAAATCTTTTAGTGATGTTATTTTTTATTTTCTTGCGAAGAG
1 CTTGACTTTCTCGTGAAGAGGAGTAAATCTTTTAGTGATGTAATACTTGACTATCTCACGAAGAG
* * * ** * * *
833872 GACTCAACCTTTTGGTTAAGTTATT
66 GAGTC-ACATCTTACTGATGTCATT
* * * * *
833897 CTTGACTTTCTC-TCGAAGAGGAGTCAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGA
1 CTTGACTTTCTCGT-GAAGAGGAGTAAATCTTTTAGTGATGTAATACTTGACTATCTCACGAAGA
* * * *
833961 GGAGTCATC-TTTTAGTGATATAATT
65 GGAGTCA-CATCTTACTGATGTCATT
833986 CTTGACTTTC
1 CTTGACTTTC
833996 AACCTTTTAG
Statistics
Matches: 357, Mismatches: 78, Indels: 40
0.75 0.16 0.08
Matches are distributed among these distances:
85 30 0.08
87 1 0.00
88 77 0.22
89 107 0.30
90 94 0.26
91 43 0.12
92 4 0.01
93 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.40
Consensus pattern (89 bp):
CTTGACTTTCTCGTGAAGAGGAGTAAATCTTTTAGTGATGTAATACTTGACTATCTCACGAAGAG
GAGTCACATCTTACTGATGTCATT
Found at i:833906 original size:134 final size:134
Alignment explanation
Indices: 833732--833979 Score: 363
Period size: 134 Copynumber: 1.9 Consensus size: 134
833722 ACTTTCTCGT
* *
833732 GAAGAGGAGTAAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACATTTTA
1 GAAGAGGACTAAACCTTTTAGTGAAGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACATTTTA
* *
833797 GTGATGTCATTCTTAAATTTCTCGTG-AGAGGAGTAAATCTTTTAGTGATGTTATTTTTTATTTT
66 GTGATGTAATTCTTAAATTTCTCGCGAAGAGGAGT-AATCTTTTAGTGATGTTATTTTTTATTTT
833861 CTTGC
130 CTTGC
* * * * * *
833866 GAAGAGGACTCAACCTTTTGGTTAAGTTATTCTTGACTTTCTCTCGAAGAGGAGTCAACCTTTTA
1 GAAGAGGACTAAACCTTTTAGTGAAGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACATTTTA
* * *
833931 GTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCATCTTTTAGTGAT
66 GTGATGTAATTCTTAAATTTCTCGCGAAGAGGAGTAATCTTTTAGTGAT
833980 ATAATTCTTG
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
134 92 0.92
135 8 0.08
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (134 bp):
GAAGAGGACTAAACCTTTTAGTGAAGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACATTTTA
GTGATGTAATTCTTAAATTTCTCGCGAAGAGGAGTAATCTTTTAGTGATGTTATTTTTTATTTTC
TTGC
Found at i:834005 original size:30 final size:30
Alignment explanation
Indices: 833969--834025 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
833959 GAGGAGTCAT
833969 CTTTTAGTGATATAATTCTTGACTTTCAAC
1 CTTTTAGTGATATAATTCTTGACTTTCAAC
*
833999 CTTTTAGTGATGTAATTCTTGACTTTC
1 CTTTTAGTGATATAATTCTTGACTTTC
834026 TCGCGAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (30 bp):
CTTTTAGTGATATAATTCTTGACTTTCAAC
Found at i:834041 original size:74 final size:75
Alignment explanation
Indices: 833920--834070 Score: 268
Period size: 74 Copynumber: 2.0 Consensus size: 75
833910 CGAAGAGGAG
*
833920 TCAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTC-ATCTTTTAGTGATATAA
1 TCAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATATAA
833984 TTCTTGACTT
66 TTCTTGACTT
* *
833994 TCAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGTTGTAA
1 TCAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATATAA
834059 TTCTTGACTT
66 TTCTTGACTT
834069 TC
1 TC
834071 TCATGAAGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 47 0.64
75 26 0.36
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (75 bp):
TCAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATATAA
TTCTTGACTT
Found at i:834058 original size:45 final size:45
Alignment explanation
Indices: 833994--834113 Score: 168
Period size: 45 Copynumber: 2.7 Consensus size: 45
833984 TTCTTGACTT
* *
833994 TCAACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAG
1 TCAACCTTTTAGTGATGTAATTCTTGACTTTCTCACGAAGAAGAG
* *
834039 TCAACCTTTTAGTGTTGTAATTCTTGACTTTCTCATGAAGAAGAG
1 TCAACCTTTTAGTGATGTAATTCTTGACTTTCTCACGAAGAAGAG
* * * *
834084 TAAACCTTTTAGAGATGTCATTCTTTACTT
1 TCAACCTTTTAGTGATGTAATTCTTGACTT
834114 GACTTTCTAG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (45 bp):
TCAACCTTTTAGTGATGTAATTCTTGACTTTCTCACGAAGAAGAG
Found at i:834381 original size:43 final size:45
Alignment explanation
Indices: 834279--834405 Score: 122
Period size: 43 Copynumber: 2.9 Consensus size: 45
834269 GAAGCTTTAA
* * *
834279 CTTGAC-TCTCTCATGAAGAGGAGTAAATCTTTCA--A-TGTTATT
1 CTTGACTTC-CTCATGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* *
834321 TTTGACTTTCTCATGAAGA-AAGTCAATC-TTCAGTATTGTCATT
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTCAGTATTGTCATT
* * * *
834364 CTTGACTTCCTCGTGAAGAGTAGTTAATCTTTTAGTATTGTC
1 CTTGACTTCCTCATGAAGAGAAGTCAATCTTTCAGTATTGTC
834406 TTCCTTAATT
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
40 4 0.06
41 7 0.10
42 16 0.24
43 23 0.34
44 7 0.10
45 11 0.16
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (45 bp):
CTTGACTTCCTCATGAAGAGAAGTCAATCTTTCAGTATTGTCATT
Found at i:834486 original size:45 final size:45
Alignment explanation
Indices: 834279--834530 Score: 164
Period size: 45 Copynumber: 5.7 Consensus size: 45
834269 GAAGCTTTAA
* * * * * * *
834279 CTTGACTCTCTCATGAAGAGGAGTAAATCTTTCAATGTTAT-TT-
1 CTTGACTTTCTCACGAAGAGGAGTAGATCTTTTAGTATTGTCTTC
* * *
834322 -TTGACTTTCTCATGAAGA-AAGTCA-ATC-TTCAGTATTGTCATT-
1 CTTGACTTTCTCACGAAGAGGAGT-AGATCTTTTAGTATTGTC-TTC
* ** *
834364 CTTGACTTCCTCGTGAAGAGTAGTTA-ATCTTTTAGTATTGTCTTC
1 CTTGACTTTCTCACGAAGAGGAG-TAGATCTTTTAGTATTGTCTTC
* * * *
834409 CTTAATTTTTCTCGA-GAAAAGGAGTCAG-TCTTTTAGTGTTGTCTTC
1 CTTGA-CTTTCTC-ACGAAGAGGAGT-AGATCTTTTAGTATTGTCTTC
* * * *
834455 CTTGACTTTCTTACGAAGAGGAGTAGATCTTTTAGTCTTGTCCTA
1 CTTGACTTTCTCACGAAGAGGAGTAGATCTTTTAGTATTGTCTTC
* *
834500 CTTGACTTTCTCACGAGGAGGAGTCGATCTT
1 CTTGACTTTCTCACGAAGAGGAGTAGATCTT
834531 CGCGGTGTCC
Statistics
Matches: 169, Mismatches: 26, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
40 8 0.05
41 6 0.04
42 20 0.12
43 16 0.09
44 11 0.07
45 74 0.44
46 34 0.20
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (45 bp):
CTTGACTTTCTCACGAAGAGGAGTAGATCTTTTAGTATTGTCTTC
Found at i:834598 original size:45 final size:45
Alignment explanation
Indices: 834541--834941 Score: 520
Period size: 45 Copynumber: 9.0 Consensus size: 45
834531 CGCGGTGTCC
* ** *
834541 TTCTTTACTTTCTCGTAAAGAGGAGTAAACCTTTTAGTGATGTAA
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAA
* * *
834586 TTCTCGACTTTCTCGCGAAGAGGAGTCAAACTTTTAGTGATGTCA
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAA
* * * * *
834631 TTCTTAAATTTCTCGTG-AGAGGAGTCAATCTTTTAGTGATGTTAT
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATG-TAA
* ** * * * * *
834676 TTTTTG-CTTTCTTACGAACAGGACTCAACCTTTTGGTTATGTTA
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAA
834720 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAA
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAA
* * * *
834765 TTATTGACTTTCTTGCAAAGAGGAGTC-ACCTTTTAGTGATATAA
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAA
*
834809 TTCTTGACTTTCTCGCGAAGAGGAATCAACCTTTTAGTGATGTAA
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAA
*
834854 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGTTGTAA
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAA
* *
834899 TTCTTGACTTTCTCGTGAAGAAGAGTCAACCTTTTAGTGATGT
1 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGT
834942 CATTTTCTAC
Statistics
Matches: 303, Mismatches: 49, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
44 74 0.24
45 229 0.76
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (45 bp):
TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAA
Found at i:834731 original size:134 final size:135
Alignment explanation
Indices: 834568--834947 Score: 514
Period size: 134 Copynumber: 2.8 Consensus size: 135
834558 AAGAGGAGTA
* * *
834568 AACCTTTTAGTGATGTAATTCTCGACTTTCTCGCGAAGAGGAGTCAAACTTTTAGTGATGTCATT
1 AACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAATT
* * * *
834633 CTTAAATTTCTCGTGAGAGGAGTCAATCTTTTAGTGATGTTATTTTTTG-CTTTCTTACGAACAG
66 CTTGACTTTCTCGTGAGAGGAGTCAACCTTTTAGTGATGTTATTTTTTGACTTTCTCACGAACAG
*
834697 GACTC
131 GAATC
* * *
834702 AACCTTTTGGTTATGTTATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAATT
1 AACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAATT
* * ** * * * * *
834767 ATTGACTTTCTTGCAAAGAGGAGTC-ACCTTTTAGTGAT-ATAATTCTTGACTTTCTCGCGAAGA
66 CTTGACTTTCTCG-TGAGAGGAGTCAACCTTTTAGTGATGTTATTTTTTGACTTTCTCACGAACA
834830 GGAATC
130 GGAATC
*
834836 AACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGTTGTAATT
1 AACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAATT
* *
834901 CTTGACTTTCTCGTGAAGAAGAGTCAACCTTTTAGTGATGTCATTTT
66 CTTGACTTTCTCGTG-AGAGGAGTCAACCTTTTAGTGATGTTATTTT
834948 CTACTTGACT
Statistics
Matches: 208, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
133 7 0.03
134 176 0.85
135 22 0.11
136 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (135 bp):
AACCTTTTAGTGATGTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAATT
CTTGACTTTCTCGTGAGAGGAGTCAACCTTTTAGTGATGTTATTTTTTGACTTTCTCACGAACAG
GAATC
Found at i:834743 original size:179 final size:179
Alignment explanation
Indices: 834541--834941 Score: 529
Period size: 179 Copynumber: 2.2 Consensus size: 179
834531 CGCGGTGTCC
* * * * *
834541 TTCTTTACTTTCTCGTAAAGAGGAGTAAACCTTTTAGTGATGTAATTCTCGACTTTCTCGCGAAG
1 TTCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTAATTATCGACTTTCTCGCAAAG
* * * * *
834606 AGGAGTCAAACTTTTAGTGATGTCATTCTTAAATTTCTCGTG-AGAGGAGTCAATCTTTTAGTGA
66 AGGAGTC-AACTTTTAGTGATATAATTCTTAAATTTCTCGCGAAGAGGAATCAACCTTTTAGTGA
* * * * *
834670 TGTTATTTTTTG-CTTTCTTACGAACAGGACTCAACCTTTTGGT-TATGTTA
130 TG-TAATTCTTGACTTTCTCACGAACAGGACTCAACCTTTTAGTGT-TGTAA
* * *
834720 TTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTAATTATTGACTTTCTTGCAAAG
1 TTCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTAATTATCGACTTTCTCGCAAAG
* * *
834785 AGGAGTCACCTTTTAGTGATATAATTCTTGACTTTCTCGCGAAGAGGAATCAACCTTTTAGTGAT
66 AGGAGTCAACTTTTAGTGATATAATTCTTAAATTTCTCGCGAAGAGGAATCAACCTTTTAGTGAT
* * *
834850 GTAATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGTTGTAA
131 GTAATTCTTGACTTTCTCACGAACAGGACTCAACCTTTTAGTGTTGTAA
*
834899 TTCTTGACTTTCTCGTGAAGAAGAGTCAACCTTTTAGTGATGT
1 TTCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGT
834942 CATTTTCTAC
Statistics
Matches: 193, Mismatches: 26, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
178 35 0.18
179 157 0.81
180 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (179 bp):
TTCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTAATTATCGACTTTCTCGCAAAG
AGGAGTCAACTTTTAGTGATATAATTCTTAAATTTCTCGCGAAGAGGAATCAACCTTTTAGTGAT
GTAATTCTTGACTTTCTCACGAACAGGACTCAACCTTTTAGTGTTGTAA
Found at i:836222 original size:10 final size:10
Alignment explanation
Indices: 836207--836231 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
836197 TGCATTTACG
836207 TATATATACA
1 TATATATACA
836217 TATATATACA
1 TATATATACA
836227 TATAT
1 TATAT
836232 TATATATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATATACA
Found at i:840402 original size:27 final size:27
Alignment explanation
Indices: 840362--840419 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
840352 GAGTTTGAAA
*
840362 TTAAGGTTTTC-AAAGTTTAGGGATTTT
1 TTAAGGTTTTCAAAAATTT-GGGATTTT
*
840389 TTAA-GTTTTACAAAAATTTTGGATTTT
1 TTAAGGTTTT-CAAAAATTTGGGATTTT
840416 TTAA
1 TTAA
840420 AATATTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 5 0.19
27 16 0.59
28 6 0.22
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.50
Consensus pattern (27 bp):
TTAAGGTTTTCAAAAATTTGGGATTTT
Found at i:840434 original size:15 final size:15
Alignment explanation
Indices: 840414--840450 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
840404 ATTTTGGATT
840414 TTTTAAAATATTTAA
1 TTTTAAAATATTTAA
* *
840429 TTTTAAAATTTTTTA
1 TTTTAAAATATTTAA
840444 TTTTAAA
1 TTTTAAA
840451 TAAAATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTAAAATATTTAA
Found at i:840929 original size:28 final size:28
Alignment explanation
Indices: 840892--840952 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
840882 TTCCAATCCT
*
840892 AAAACATAAACACTAAACTATAAATTTA
1 AAAAAATAAACACTAAACTATAAATTTA
** * *
840920 AAAAAATAAACTTTAAACTATACATTTT
1 AAAAAATAAACACTAAACTATAAATTTA
840948 AAAAA
1 AAAAA
840953 GACAAGATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAAATAAACACTAAACTATAAATTTA
Found at i:846934 original size:3 final size:3
Alignment explanation
Indices: 846920--846959 Score: 62
Period size: 3 Copynumber: 12.7 Consensus size: 3
846910 TTAAATAAAT
846920 ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
846960 TAAAACGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:847451 original size:114 final size:115
Alignment explanation
Indices: 847243--847466 Score: 281
Period size: 114 Copynumber: 1.9 Consensus size: 115
847233 GCTTCACTGC
* *
847243 TCTTTAGGGAAGATCAAATTTGATAAAAAAAAGGATCTGCTCCGCTGCACTACAGGGCAAACCAG
1 TCTTTAGGGAAGATCAAA-TTGATAAAAAAAAGGATATGCTCCACTGCACTACAGGGCAAACCAG
* * *
847308 ATCTGGAGACTTTGATTCATTTCATTGCTCTTCAGGGAAGATTGAATTTGT
65 ATATGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATTTGT
* * * * * * *
847359 TCTTTAGGGAAGATCAAA-T-ATAAGAAAAATGGATATGTTCCACTGTATTCCAGGGTAAATCAG
1 TCTTTAGGGAAGATCAAATTGATAA-AAAAAAGGATATGCTCCACTGCACTACAGGGCAAACCAG
* * *
847422 ATATGGAGACTTTGATTGACTTCACTGCTCTTTAGGGAATATTGA
65 ATATGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGA
847467 GCTAGGGTTG
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
113 4 0.04
114 70 0.76
116 18 0.20
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (115 bp):
TCTTTAGGGAAGATCAAATTGATAAAAAAAAGGATATGCTCCACTGCACTACAGGGCAAACCAGA
TATGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATTTGT
Found at i:847553 original size:131 final size:129
Alignment explanation
Indices: 847359--847780 Score: 429
Period size: 131 Copynumber: 3.2 Consensus size: 129
847349 TTGAATTTGT
* * *
847359 TCTTTAGGGAAGATCAAATATAAGAAAAATGGATATGTTCCACTGT-ATTCCAGGGTAAATCAGA
1 TCTTAAGGGAAGATCAAATAT--GAAAAAAGGATAT-TTCCACTGTGCTTCC-GGGTAAATCAGA
* * * * * *
847423 TATGGAGACTTTGATTGACTTCACTGCTCTTTAGGGAATATTGAGCTAG-GGTTGATTTGCTTAA
62 TCTGGAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGA-ATAGAGGTTGATTTGCTTAA
847487 CTAC
126 CTAC
* * * *
847491 TCTTCAGGGAAGATCAAATCTGGAAAAAAGGATCTTCTCCACTGTGCTTCCGGGTATATCAGATC
1 TCTTAAGGGAAGATCAAATAT-GAAAAAAGGATATT-TCCACTGTGCTTCCGGGTAAATCAGATC
* * * *
847556 TGGAAACGTTGATTCACTTCACTGCTCTACAGGGAAGATTGAATTGAGGTTGATTTGCTTTACTA
64 TGGAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATAGAGGTTGATTTGCTTAACTA
847621 C
129 C
* * * *
847622 TCTTAAGAGAAGATCAAATATGAAAAAAGTGATATGATCCACTGCTGC-TCAGGGTAGATCAGAT
1 TCTTAAGGGAAGATCAAATATGAAAAAAG-GATAT-TTCCACTG-TGCTTCCGGGTAAATCAGAT
* * ** * ** *
847686 CTGGAAACTTTGATTCACTTTACTGCTCTTCAGGAAAGATTGAATCCCA-GTAGATTTGCTCCAT
63 CTGGAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAAT-AGAGGTTGATTTGCTTAAC
847750 TAC
127 TAC
* * *
847753 TCTTTAGGGAAGATCAAATCTAAAAAAA
1 TCTTAAGGGAAGATCAAATATGAAAAAA
847781 TTATATGTTT
Statistics
Matches: 245, Mismatches: 38, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
130 11 0.04
131 207 0.84
132 27 0.11
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (129 bp):
TCTTAAGGGAAGATCAAATATGAAAAAAGGATATTTCCACTGTGCTTCCGGGTAAATCAGATCTG
GAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATAGAGGTTGATTTGCTTAACTAC
Found at i:848918 original size:17 final size:17
Alignment explanation
Indices: 848896--848937 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
848886 AGTCACGTTG
*
848896 AGAATGACATCATTAAA
1 AGAATGACATAATTAAA
848913 AGAATGACATAATTAAA
1 AGAATGACATAATTAAA
*
848930 AGATTGAC
1 AGAATGAC
848938 TCCTCTCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (17 bp):
AGAATGACATAATTAAA
Found at i:848999 original size:45 final size:45
Alignment explanation
Indices: 848912--849165 Score: 278
Period size: 45 Copynumber: 5.7 Consensus size: 45
848902 ACATCATTAA
* * * * * *
848912 AAGAATGACATAATTAAAAGATTGACTCCTCTCCTCGAGAAAGTT
1 AAGAATGACATCACTAAAAGATTGACTCTTCTTCACGAGAAAGTC
* * *
848957 AATAATGACATCA-TAAAAATATTGACTCTTCTTCACGGGAAAGTC
1 AAGAATGACATCACT-AAAAGATTGACTCTTCTTCACGAGAAAGTC
* * * * *
849002 AAGTATGATAACACT-AAAGATTGACTCTTATTCAAGAGAAAGTC
1 AAGAATGACATCACTAAAAGATTGACTCTTCTTCACGAGAAAGTC
* * * *
849046 AAGAATGACAACACTAAAAGATTGACTATTCTTCATGATAAAGTC
1 AAGAATGACATCACTAAAAGATTGACTCTTCTTCACGAGAAAGTC
*
849091 AAGAATGACATCACTAAAAGATTGACTCTTCTTCAGGAGAAAGTC
1 AAGAATGACATCACTAAAAGATTGACTCTTCTTCACGAGAAAGTC
* * * *
849136 AAGAATGACAACATTGAAAGATTAACTCTT
1 AAGAATGACATCACTAAAAGATTGACTCTT
849166 TTTTATAAGA
Statistics
Matches: 176, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
44 39 0.22
45 136 0.77
46 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (45 bp):
AAGAATGACATCACTAAAAGATTGACTCTTCTTCACGAGAAAGTC
Found at i:849079 original size:89 final size:89
Alignment explanation
Indices: 848912--849158 Score: 264
Period size: 89 Copynumber: 2.8 Consensus size: 89
848902 ACATCATTAA
* * * * ** * * *
848912 AAGAATGACATA-ATTAAAAGATTGACTCCTCTCCTCGAGAAAGTTAATAATGACATCATAAAAA
1 AAGAATGACA-ACACTAAAAGATTGACTCTTATTCAAGAGAAAGTCAAGAATGACAACAT-AAAA
* * *
848976 TATTGACTCTTCTTCACGGGAAAGTC
64 GATTGACTATTCTTCACGAGAAAGTC
* *
849002 AAGTATGATAACACT-AAAGATTGACTCTTATTCAAGAGAAAGTCAAGAATGACAACACTAAAAG
1 AAGAATGACAACACTAAAAGATTGACTCTTATTCAAGAGAAAGTCAAGAATGACAACA-TAAAAG
* *
849066 ATTGACTATTCTTCATGATAAAGTC
65 ATTGACTATTCTTCACGAGAAAGTC
* * * *
849091 AAGAATGACATCACTAAAAGATTGACTCTTCTTCAGGAGAAAGTCAAGAATGACAACATTGAAAG
1 AAGAATGACAACACTAAAAGATTGACTCTTATTCAAGAGAAAGTCAAGAATGACAACA-TAAAAG
849156 ATT
65 ATT
849159 AACTCTTTTT
Statistics
Matches: 131, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
89 72 0.55
90 59 0.45
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (89 bp):
AAGAATGACAACACTAAAAGATTGACTCTTATTCAAGAGAAAGTCAAGAATGACAACATAAAAGA
TTGACTATTCTTCACGAGAAAGTC
Found at i:849239 original size:37 final size:36
Alignment explanation
Indices: 849198--849326 Score: 116
Period size: 37 Copynumber: 3.5 Consensus size: 36
849188 GGTTTCTAGG
849198 GAAACAATCCTAAGAATGACTAAAATAATTTTTTAGA
1 GAAACAATCCTAAGAA-GACTAAAATAATTTTTTAGA
* ** * * *
849235 GAAACAATCATAAGAAGGACTCTAACAAATTTCTAGA
1 GAAACAATCCTAAGAA-GACTAAAATAATTTTTTAGA
* * * *
849272 GAAACGATCCTAAGAAGTA-TAAAAATGATATTTTACA
1 GAAACAATCCTAAGAAG-ACT-AAAATAATTTTTTAGA
*
849309 GAAACCATCCTAAGAAGA
1 GAAACAATCCTAAGAAGA
849327 ACTAGAGTGA
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
36 3 0.04
37 69 0.96
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (36 bp):
GAAACAATCCTAAGAAGACTAAAATAATTTTTTAGA
Found at i:855987 original size:24 final size:24
Alignment explanation
Indices: 855960--856045 Score: 127
Period size: 24 Copynumber: 3.6 Consensus size: 24
855950 CCAGGTCAAG
*
855960 TATCAGATCAGAATCTATTTCAGA
1 TATCAGATCAGAATCTATGTCAGA
*
855984 TATCAGATCATAATCTATGTCAGA
1 TATCAGATCAGAATCTATGTCAGA
* *
856008 TATCAGATCAGAATCCATGTCAGG
1 TATCAGATCAGAATCTATGTCAGA
*
856032 TATCATATCAGAAT
1 TATCAGATCAGAAT
856046 TCAAATCGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (24 bp):
TATCAGATCAGAATCTATGTCAGA
Found at i:858523 original size:13 final size:13
Alignment explanation
Indices: 858490--858566 Score: 64
Period size: 13 Copynumber: 5.4 Consensus size: 13
858480 GCCGGTCAAC
858490 GGTCAACGGGTCAG
1 GGTCAACGGGTC-G
858504 CGGTCAACGGGTCG
1 -GGTCAACGGGTCG
*
858518 GGTCAAAGGGTCTGG
1 GGTCAACGGGTC--G
858533 TCAGGTCAACGGGTCG
1 ---GGTCAACGGGTCG
*
858549 GGTAAACGGGTCG
1 GGTCAACGGGTCG
*
858562 AGTCA
1 GGTCA
858567 GGTCGGGTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
13 26 0.50
14 1 0.02
15 13 0.25
16 1 0.02
18 11 0.21
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:858539 original size:18 final size:18
Alignment explanation
Indices: 858513--858547 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
858503 GCGGTCAACG
*
858513 GGTCGGGTCAAAGGGTCT
1 GGTCAGGTCAAAGGGTCT
*
858531 GGTCAGGTCAACGGGTC
1 GGTCAGGTCAAAGGGTC
858548 GGGTAAACGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.20, G:0.43, T:0.20
Consensus pattern (18 bp):
GGTCAGGTCAAAGGGTCT
Found at i:858543 original size:31 final size:31
Alignment explanation
Indices: 858494--858570 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
858484 GTCAACGGTC
858494 AACGGGTC-AG-C-GGTCAACGGGTCGGGTCA
1 AACGGGTCGAGTCAGGTCAACGGGTCGGGT-A
858523 AA-GGGTCTG-GTCAGGTCAACGGGTCGGGTA
1 AACGGGTC-GAGTCAGGTCAACGGGTCGGGTA
858553 AACGGGTCGAGTCAGGTC
1 AACGGGTCGAGTCAGGTC
858571 GGGTTATGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
28 5 0.12
29 3 0.07
30 5 0.12
31 29 0.69
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.17
Consensus pattern (31 bp):
AACGGGTCGAGTCAGGTCAACGGGTCGGGTA
Found at i:867597 original size:3 final size:3
Alignment explanation
Indices: 867591--867630 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
867581 AAGTATTAAT
* *
867591 TAA TAA TAA TAA TAA TAA TAA -CA TAA TAA TGA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
867631 TAAAACGTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:867618 original size:17 final size:17
Alignment explanation
Indices: 867596--867633 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
867586 TTAATTAATA
867596 ATAATAATAATAATAAC
1 ATAATAATAATAATAAC
* *
867613 ATAATAATGATAATAAT
1 ATAATAATAATAATAAC
867630 ATAA
1 ATAA
867634 AACGTCGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
ATAATAATAATAATAAC
Found at i:867618 original size:20 final size:20
Alignment explanation
Indices: 867593--867630 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
867583 GTATTAATTA
867593 ATAATAATAATAATAATAAC
1 ATAATAATAATAATAATAAC
*
867613 ATAATAATGATAATAATA
1 ATAATAATAATAATAATA
867631 TAAAACGTCG
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:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
ATAATAATAATAATAATAAC
Found at i:873175 original size:27 final size:29
Alignment explanation
Indices: 873145--873217 Score: 114
Period size: 27 Copynumber: 2.6 Consensus size: 29
873135 GGGGAAGTTC
873145 AGATTTCTTTTTCATATTTAAT-A-AAAA
1 AGATTTCTTTTTCATATTTAATAAGAAAA
873172 AGATTTCTTTTTCATATTTAATAAGAAAA
1 AGATTTCTTTTTCATATTTAATAAGAAAA
* *
873201 ATATTTCTATTTCATAT
1 AGATTTCTTTTTCATAT
873218 AGGTTCCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 22 0.52
28 1 0.02
29 19 0.45
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.49
Consensus pattern (29 bp):
AGATTTCTTTTTCATATTTAATAAGAAAA
Found at i:879598 original size:6 final size:6
Alignment explanation
Indices: 879587--879616 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
879577 TTAACAGACA
879587 AATATT AATATT AATATT AATATT AATATT
1 AATATT AATATT AATATT AATATT AATATT
879617 TTTTCCTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATATT
Found at i:880630 original size:19 final size:18
Alignment explanation
Indices: 880606--880661 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
880596 GTCAGACCGA
880606 TCAAAGTCAACGAGTCAGG
1 TCAAAGTCAACGAGTC-GG
* *
880625 TCAAAGTCATCGGGTCGG
1 TCAAAGTCAACGAGTCGG
*
880643 ATCAAAGTCAAAGAGTCGG
1 -TCAAAGTCAACGAGTCGG
880662 GTCGGGTTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 2 0.06
19 29 0.94
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.18
Consensus pattern (18 bp):
TCAAAGTCAACGAGTCGG
Found at i:882584 original size:3 final size:3
Alignment explanation
Indices: 882576--882625 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
882566 TCCCATTCGA
882576 TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
882622 TAT T
1 TAT T
882626 CAGATCCAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:882949 original size:14 final size:13
Alignment explanation
Indices: 882932--882963 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
882922 AAAATATCAT
882932 AGCAAAAAGCAAAA
1 AGCAAAAAG-AAAA
882946 AGCAAAAAGAAAA
1 AGCAAAAAGAAAA
882959 AGCAA
1 AGCAA
882964 GTAATATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (13 bp):
AGCAAAAAGAAAA
Found at i:882953 original size:8 final size:7
Alignment explanation
Indices: 882932--882963 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
882922 AAAATATCAT
882932 AGCAAAA
1 AGCAAAA
882939 AGCAAAA
1 AGCAAAA
882946 AGCAAAA
1 AGCAAAA
882953 AG-AAAA
1 AGCAAAA
882959 AGCAA
1 AGCAA
882964 GTAATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (7 bp):
AGCAAAA
Found at i:887603 original size:19 final size:20
Alignment explanation
Indices: 887579--887628 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
887569 AATGGAGTGC
887579 ATGGATGCACTACA-GGAGA
1 ATGGATGCACTACAGGGAGA
* * * *
887598 ATGGATGAACTATAGGGTGC
1 ATGGATGCACTACAGGGAGA
887618 ATGGATGCACT
1 ATGGATGCACT
887629 TTGACACCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.22
Consensus pattern (20 bp):
ATGGATGCACTACAGGGAGA
Found at i:887865 original size:21 final size:21
Alignment explanation
Indices: 887841--887880 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
887831 ATGTTTAATG
887841 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
887862 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
887881 CCAACTGTTG
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:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:890130 original size:20 final size:19
Alignment explanation
Indices: 890105--890193 Score: 105
Period size: 20 Copynumber: 4.8 Consensus size: 19
890095 TCGAAATGGA
890105 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACA-G
*
890125 GTGCATTGATG--C-ACA-
1 GTGCATGGATGCACTACAG
*
890140 GTGCACGGATGCACTACAG
1 GTGCATGGATGCACTACAG
*
890159 GTCCATGGATGCACTACAGG
1 GTGCATGGATGCACTACA-G
890179 GTGCATGGATGCACT
1 GTGCATGGATGCACT
890194 TTGATACCCT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
15 9 0.16
17 4 0.07
18 4 0.07
19 16 0.28
20 25 0.43
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.22
Consensus pattern (19 bp):
GTGCATGGATGCACTACAG
Found at i:890150 original size:35 final size:34
Alignment explanation
Indices: 890104--890172 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
890094 TTCGAAATGG
* * *
890104 AGTGCATGGATGCACTACATGGTGCATTGATGCAC
1 AGTGCACGGATGCACTACA-GGTCCATGGATGCAC
890139 AGTGCACGGATGCACTACAGGTCCATGGATGCAC
1 AGTGCACGGATGCACTACAGGTCCATGGATGCAC
890173 TACAGGGTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 13 0.42
35 18 0.58
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (34 bp):
AGTGCACGGATGCACTACAGGTCCATGGATGCAC
Found at i:890440 original size:21 final size:21
Alignment explanation
Indices: 890416--890455 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
890406 ATGTTTAATG
*
890416 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAACTGTTAAC
*
890437 AAAATGATATCAACTGTTA
1 AAAAAGATATCAACTGTTA
890456 GAAAATATAT
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:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATATCAACTGTTAAC
Found at i:892924 original size:20 final size:21
Alignment explanation
Indices: 892894--892935 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
892884 ACTAGCCGTT
*
892894 ACAGCCAGGGTGCATGGATGC
1 ACAGCCAGGGTGCATCGATGC
892915 ACAG-CAGGGTGCATCGATGC
1 ACAGCCAGGGTGCATCGATGC
892935 A
1 A
892936 TTAATTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.26, C:0.24, G:0.36, T:0.14
Consensus pattern (21 bp):
ACAGCCAGGGTGCATCGATGC
Found at i:892979 original size:19 final size:18
Alignment explanation
Indices: 892955--893008 Score: 81
Period size: 19 Copynumber: 2.9 Consensus size: 18
892945 TTCAAAATGG
892955 AGTGCATGGATGCACTGCA
1 AGTGCATGGATGCACTG-A
*
892974 AGTGCATGGATGCACTGT
1 AGTGCATGGATGCACTGA
892992 AGTTGCATGGATGCACT
1 AG-TGCATGGATGCACT
893009 TTGACACCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 2 0.06
19 31 0.94
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGCATGGATGCACTGA
Found at i:894511 original size:24 final size:24
Alignment explanation
Indices: 894484--894557 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
894474 CATATCAAAA
* *
894484 ATCAAAACATAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
*
894508 ATCAAATTAAAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAGGTCAAGT
** * *
894532 ATCCGATCAGAATCCAGGTCAGGT
1 ATCAAATCAAAATCCAGGTCAAGT
894556 AT
1 AT
894558 TATAACAGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (24 bp):
ATCAAATCAAAATCCAGGTCAAGT
Found at i:898156 original size:24 final size:24
Alignment explanation
Indices: 898127--898172 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
898117 GCATGACATG
*
898127 GTACATAGATGTTTTATGCATCGT
1 GTACATAGATGTTTTATACATCGT
898151 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
898173 ATATGGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:905661 original size:24 final size:24
Alignment explanation
Indices: 905634--905679 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
905624 GCATGACATG
905634 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
905658 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
905680 ATATGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:908238 original size:33 final size:33
Alignment explanation
Indices: 908201--908266 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
908191 AAAATTAAAG
908201 ATAATCATGCTTTG-AATA-AATACTTTTAGGATC
1 ATAATCATG-TTTGTAA-AGAATACTTTTAGGATC
908234 ATAATCATGTTTGTAAAGAATACTTTTAGGATC
1 ATAATCATGTTTGTAAAGAATACTTTTAGGATC
908267 TTCTTGGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (33 bp):
ATAATCATGTTTGTAAAGAATACTTTTAGGATC
Found at i:914419 original size:23 final size:23
Alignment explanation
Indices: 914364--914419 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
914354 ATGTAATCGA
* *
914364 TCAACGA-TCAGATCGGACAATG
1 TCAACGAGTCAGACCGGACAAAG
* *
914386 TCAA-TAGTCAGACCGGTCAAAG
1 TCAACGAGTCAGACCGGACAAAG
914408 TCAACGAGTCAG
1 TCAACGAGTCAG
914420 GTCAAAGTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.04
22 20 0.74
23 6 0.22
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (23 bp):
TCAACGAGTCAGACCGGACAAAG
Found at i:914424 original size:19 final size:18
Alignment explanation
Indices: 914399--914457 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 18
914389 ATAGTCAGAC
914399 CGGTCAAAGTCAACGAGT
1 CGGTCAAAGTCAACGAGT
* *
914417 CAGGTCAAAGTCATCGGGT
1 C-GGTCAAAGTCAACGAGT
*
914436 CGGATCAAAGTCAAAGAGT
1 CGG-TCAAAGTCAACGAGT
914455 CGG
1 CGG
914458 GTCGGGTTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 3 0.09
19 31 0.91
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (18 bp):
CGGTCAAAGTCAACGAGT
Found at i:916376 original size:3 final size:3
Alignment explanation
Indices: 916368--916454 Score: 167
Period size: 3 Copynumber: 29.3 Consensus size: 3
916358 TCTCATTCGA
916368 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
916415 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
916455 CAGATCCAAG
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:920285 original size:26 final size:27
Alignment explanation
Indices: 920201--920350 Score: 193
Period size: 29 Copynumber: 5.6 Consensus size: 27
920191 AATGAAACCT
920201 ATATGAAAAAGAAATATTTTTTTATTAA
1 ATATGAAAAAGAAATA-TTTTTTATTAA
920229 ATATGAAAAAAGAAATATTTTTTTATTAA
1 ATATG-AAAAAGAAATA-TTTTTTATTAA
* *
920258 ATATGAAAAAGAAA-ACTTTTTATGAA
1 ATATGAAAAAGAAATATTTTTTATTAA
920284 ATATGAAAAAGAAATATTTTTTATTAA
1 ATATGAAAAAGAAATATTTTTTATTAA
*
920311 ATAT---AAA-AAATGAATTTTTATTAA
1 ATATGAAAAAGAAAT-ATTTTTTATTAA
920335 ATATGAAAAAAGAAAT
1 ATATG-AAAAAGAAAT
920351 CTTAACTCCC
Statistics
Matches: 109, Mismatches: 5, Indels: 15
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.04
24 18 0.17
26 23 0.21
27 15 0.14
28 17 0.16
29 32 0.29
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (27 bp):
ATATGAAAAAGAAATATTTTTTATTAA
Found at i:921636 original size:2 final size:2
Alignment explanation
Indices: 921629--921674 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
921619 TGATTTAGTC
921629 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
921671 AT AT
1 AT AT
921675 CTCAATTCCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:921899 original size:20 final size:20
Alignment explanation
Indices: 921874--921912 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
921864 GATTAGGTAC
*
921874 CGATTTTCAGACCTTCCAAT
1 CGATTTACAGACCTTCCAAT
*
921894 CGATTTACAGATCTTCCAA
1 CGATTTACAGACCTTCCAA
921913 ACAAGTCAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (20 bp):
CGATTTACAGACCTTCCAAT
Found at i:923040 original size:22 final size:22
Alignment explanation
Indices: 923014--923077 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
923004 TTTGGTCATA
923014 GTCAAAGTCAACGGTCAGACAG
1 GTCAAAGTCAACGGTCAGACAG
** * *
923036 GTCAAAGTCAACAATCATACCG
1 GTCAAAGTCAACGGTCAGACAG
923058 GTCAAAGTCAACGGGTCAGA
1 GTCAAAGTCAAC-GGTCAGA
923078 TCAAAGTCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 30 0.88
23 4 0.12
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (22 bp):
GTCAAAGTCAACGGTCAGACAG
Found at i:924294 original size:3 final size:3
Alignment explanation
Indices: 924286--924342 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
924276 TGGAAGCTTA
* * * *
924286 TCT TCT TCT CCT TCT TCT TCT CCT TCT TCT TCT CCT TCT TCT TCT CCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
924334 TCT TCT TCT
1 TCT TCT TCT
924343 CCCCGTAGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:924301 original size:12 final size:12
Alignment explanation
Indices: 924286--924344 Score: 118
Period size: 12 Copynumber: 4.9 Consensus size: 12
924276 TGGAAGCTTA
924286 TCTTCTTCTCCT
1 TCTTCTTCTCCT
924298 TCTTCTTCTCCT
1 TCTTCTTCTCCT
924310 TCTTCTTCTCCT
1 TCTTCTTCTCCT
924322 TCTTCTTCTCCT
1 TCTTCTTCTCCT
924334 TCTTCTTCTCC
1 TCTTCTTCTCC
924345 CCGTAGGTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTTCTTCTCCT
Found at i:927394 original size:2 final size:2
Alignment explanation
Indices: 927387--927428 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
927377 TTTTATCTTT
* *
927387 TA TA TA TA TA TA TA TT TA TA TT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
927429 AATTAAAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:927843 original size:6 final size:6
Alignment explanation
Indices: 927832--927859 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
927822 AATGAAAAAT
927832 TATTAA TATTAA TATTAA TATTAA TATT
1 TATTAA TATTAA TATTAA TATTAA TATT
927860 TTTCTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TATTAA
Found at i:928557 original size:33 final size:33
Alignment explanation
Indices: 928520--928583 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
928510 AATTAAAGAG
928520 AATCATGCTT-TGAATAAATACTTTTAGGATCAT
1 AATCATGCTTGTGAA-AAATACTTTTAGGATCAT
* *
928553 AATCATGTTTGTGAAGAATACTTTTAGGATC
1 AATCATGCTTGTGAAAAATACTTTTAGGATC
928584 TTCTTGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (33 bp):
AATCATGCTTGTGAAAAATACTTTTAGGATCAT
Found at i:929804 original size:23 final size:23
Alignment explanation
Indices: 929755--929812 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
929745 AAACAACTGA
*
929755 AAAACATGCCA-AAAAATAAAAG
1 AAAACGTGCCATAAAAATAAAAG
*
929777 AAAACGTGCCATAAAAATAAATG
1 AAAACGTGCCATAAAAATAAAAG
*
929800 AAAACGTGTCATA
1 AAAACGTGCCATA
929813 TATGCAGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.16
Consensus pattern (23 bp):
AAAACGTGCCATAAAAATAAAAG
Found at i:929975 original size:15 final size:15
Alignment explanation
Indices: 929955--929984 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
929945 AGAAAAAACG
*
929955 ATGAACGATTTACCA
1 ATGAACGACTTACCA
929970 ATGAACGACTTACCA
1 ATGAACGACTTACCA
929985 TAATATTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
ATGAACGACTTACCA
Found at i:930504 original size:22 final size:23
Alignment explanation
Indices: 930462--930505 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
930452 TGCAATTAAA
*
930462 AAAAGAAAATAAAGATTTAATAT
1 AAAAGAAAATAAAGATATAATAT
930485 AAAA-AAAATAAA-ATGATAATA
1 AAAAGAAAATAAAGAT-ATAATA
930506 AAGAATGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.11
22 13 0.68
23 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (23 bp):
AAAAGAAAATAAAGATATAATAT
Found at i:931652 original size:16 final size:16
Alignment explanation
Indices: 931631--931718 Score: 176
Period size: 16 Copynumber: 5.5 Consensus size: 16
931621 ACAAAACCTC
931631 TGAATCATTCAACATT
1 TGAATCATTCAACATT
931647 TGAATCATTCAACATT
1 TGAATCATTCAACATT
931663 TGAATCATTCAACATT
1 TGAATCATTCAACATT
931679 TGAATCATTCAACATT
1 TGAATCATTCAACATT
931695 TGAATCATTCAACATT
1 TGAATCATTCAACATT
931711 TGAATCAT
1 TGAATCAT
931719 ACAGCACTTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 72 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:931668 original size:32 final size:32
Alignment explanation
Indices: 931631--931735 Score: 176
Period size: 32 Copynumber: 3.3 Consensus size: 32
931621 ACAAAACCTC
931631 TGAATCATTCAACATTTGAATCATTCAACATT
1 TGAATCATTCAACATTTGAATCATTCAACATT
931663 TGAATCATTCAACATTTGAATCATTCAACATT
1 TGAATCATTCAACATTTGAATCATTCAACATT
* * *
931695 TGAATCATTCAACATTTGAATCATACAGCACT
1 TGAATCATTCAACATTTGAATCATTCAACATT
931727 T-AATCATTC
1 TGAATCATTC
931736 TGAAGTAAAC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
31 8 0.11
32 62 0.89
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (32 bp):
TGAATCATTCAACATTTGAATCATTCAACATT
Found at i:931686 original size:48 final size:48
Alignment explanation
Indices: 931617--931735 Score: 177
Period size: 48 Copynumber: 2.5 Consensus size: 48
931607 CAGAGCTAAT
*
931617 TCATACAAAACCTCTGAATCATTCAACATTTGAATCATTCAACATTTGAA
1 TCATACAACA-CT-TGAATCATTCAACATTTGAATCATTCAACATTTGAA
* *
931667 TCATTCAACATTTGAATCATTCAACATTTGAATCATTCAACATTTGAA
1 TCATACAACACTTGAATCATTCAACATTTGAATCATTCAACATTTGAA
*
931715 TCATACAGCACTT-AATCATTC
1 TCATACAACACTTGAATCATTC
931736 TGAAGTAAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
47 8 0.13
48 46 0.73
49 1 0.02
50 8 0.13
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (48 bp):
TCATACAACACTTGAATCATTCAACATTTGAATCATTCAACATTTGAA
Found at i:931939 original size:53 final size:53
Alignment explanation
Indices: 931859--931972 Score: 228
Period size: 53 Copynumber: 2.2 Consensus size: 53
931849 TGCGTCCACA
931859 ACTATTAATTTTAATCCATCGGGACCTCCTAGAGAGAACAATATTCTTTTTTT
1 ACTATTAATTTTAATCCATCGGGACCTCCTAGAGAGAACAATATTCTTTTTTT
931912 ACTATTAATTTTAATCCATCGGGACCTCCTAGAGAGAACAATATTCTTTTTTT
1 ACTATTAATTTTAATCCATCGGGACCTCCTAGAGAGAACAATATTCTTTTTTT
931965 ACTATTAA
1 ACTATTAA
931973 GCTCACTCAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (53 bp):
ACTATTAATTTTAATCCATCGGGACCTCCTAGAGAGAACAATATTCTTTTTTT
Found at i:932622 original size:27 final size:26
Alignment explanation
Indices: 932577--932695 Score: 170
Period size: 26 Copynumber: 4.6 Consensus size: 26
932567 AATGGAACCT
* *
932577 ATATGAAAAAGAATTTTTTTTATTAA
1 ATATGAAAAAGAAATATTTTTATTAA
*
932603 ATATGAAAAAGAAATATTTTTATGAA
1 ATATGAAAAAGAAATATTTTTATTAA
932629 ATATGAAAAAGAAATATTTTTTATTAA
1 ATATGAAAAAGAAATA-TTTTTATTAA
*
932656 ATATGAAAAAG-GA-ATTTTTATTAA
1 ATATGAAAAAGAAATATTTTTATTAA
932680 ATATGAAAAAAGAAAT
1 ATATG-AAAAAGAAAT
932696 CTTAACTCCC
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
24 15 0.18
25 7 0.08
26 41 0.49
27 20 0.24
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (26 bp):
ATATGAAAAAGAAATATTTTTATTAA
Found at i:932662 original size:53 final size:51
Alignment explanation
Indices: 932577--932695 Score: 177
Period size: 53 Copynumber: 2.3 Consensus size: 51
932567 AATGGAACCT
*
932577 ATATGAAAAAG-AATTTTTTTTATTAAATATGAAAAAGAAATATTTTTATGAA
1 ATATGAAAAAGAAATATTTTTTATTAAATATGAAAAAG-AA-ATTTTTATGAA
* *
932629 ATATGAAAAAGAAATATTTTTTATTAAATATGAAAAAGGAATTTTTATTAA
1 ATATGAAAAAGAAATATTTTTTATTAAATATGAAAAAGAAATTTTTATGAA
932680 ATATGAAAAAAGAAAT
1 ATATG-AAAAAGAAAT
932696 CTTAACTCCC
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
51 15 0.24
52 22 0.35
53 25 0.40
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (51 bp):
ATATGAAAAAGAAATATTTTTTATTAAATATGAAAAAGAAATTTTTATGAA
Found at i:943239 original size:3 final size:3
Alignment explanation
Indices: 943231--943290 Score: 61
Period size: 3 Copynumber: 19.7 Consensus size: 3
943221 TCATTTCGTT
* *
943231 TTA TTA TTA -AA TTTA TTA TTA TTA TTA ATA TTA -TA TATA TATA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA
943277 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
943291 TAATAAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 3 0.06
3 37 0.76
4 9 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:944403 original size:2 final size:2
Alignment explanation
Indices: 944396--944462 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
944386 CTGATTGTTT
944396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
944438 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
944463 TAGGTTAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:944927 original size:20 final size:21
Alignment explanation
Indices: 944902--944951 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
944892 TCATTTTCTG
944902 ATATTATTAAATAAA-TATAT
1 ATATTATTAAATAAATTATAT
**
944922 ATATTATTTTTATAAATTATAT
1 ATATTA-TTAAATAAATTATAT
944944 ATATTATT
1 ATATTATT
944952 TTATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 11 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTATTAAATAAATTATAT
Found at i:944945 original size:22 final size:21
Alignment explanation
Indices: 944912--944953 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
944902 ATATTATTAA
944912 ATAAATATATATATTATTTTT
1 ATAAATATATATATTATTTTT
944933 ATAAATTATATATATTATTTT
1 ATAAA-TATATATATTATTTT
944954 ATTTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAAATATATATATTATTTTT
Found at i:945152 original size:148 final size:148
Alignment explanation
Indices: 944853--945152 Score: 306
Period size: 148 Copynumber: 2.0 Consensus size: 148
944843 TATTTATTTT
* *
944853 TTAATATTAAGAACTAAGTTGTCTTAAAGCACTTAGAAGTCATTTTCTGATATTATTAAATAAAT
1 TTAATATTAAGAAATAAGTTGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTATTAAATAAAT
* * * * * * *
944918 ATATATATTATTTTTATAAATTATATATATTATTTTATTTTAATTATTTTTATAAAAGTGTTTTA
66 AAATATATTATTTATATAAAATATATATATTATTATATATTAATTATTTTTATAAAAGTATTTAA
* * ** * **
944983 TTAGTATTTATTTATTTA
131 TAAATATACAATTATGAA
* * * *
945001 TTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCTTTTTTTGATATT-TCTAAGTAAA
1 TTAATATTAAGAAATAAGTTGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTAT-TAAATAAA
* *
945065 TAAATATCTTATTTATA-AAAATATATATA-TA-TATATATTAATATATTTTCT-TAAAATTATA
65 TAAATATATTATTTATATAAAATATATATATTATTATATATTAAT-TATTTT-TATAAAAGTAT-
945126 TTAATAAATA-ACAGGATTATGAA
127 TTAATAAATATACA--ATTATGAA
945149 TTAA
1 TTAA
945153 ATATATTTTT
Statistics
Matches: 124, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
145 9 0.07
146 16 0.13
147 20 0.16
148 79 0.64
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (148 bp):
TTAATATTAAGAAATAAGTTGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTATTAAATAAAT
AAATATATTATTTATATAAAATATATATATTATTATATATTAATTATTTTTATAAAAGTATTTAA
TAAATATACAATTATGAA
Found at i:950607 original size:65 final size:65
Alignment explanation
Indices: 950488--950699 Score: 222
Period size: 65 Copynumber: 3.3 Consensus size: 65
950478 TTTATCAAAG
* * * *
950488 TGATGCACCGATGCAC-CAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATG
1 TGATGCATCGATGCACTC-AGCCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATG
*
950549 AATT
62 CATT
* * *
950553 TCATGCATCGATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
950616 TT
64 TT
* * *
950618 TGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
950682 TGATGCATCGATGCACTC
1 TGATGCATCGATGCACTC
950700 TTAGTGCACC
Statistics
Matches: 125, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 47 0.38
65 72 0.58
66 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (65 bp):
TGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:950697 original size:17 final size:19
Alignment explanation
Indices: 950669--950717 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
950659 TATTTTGAAA
950669 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
950687 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
950706 CACCGATGCACT
1 CATCGATGCACT
950718 AAGGGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:958766 original size:45 final size:45
Alignment explanation
Indices: 958714--958805 Score: 136
Period size: 45 Copynumber: 2.0 Consensus size: 45
958704 AAAAAATGAG
958714 AAATGAAAAATG-AAAATGAAAAAAAATG-AAAATG-AAAATGAAAAA
1 AAATGAAAAATGAAAAATG---AAAAATGAAAAATGAAAAATGAAAAA
958759 AAATGAAAAATGAAAAATGAAAAATGAAAAATGAAAAATGAAAAA
1 AAATGAAAAATGAAAAATGAAAAATGAAAAATGAAAAATGAAAAA
958804 AA
1 AA
958806 GAAAAAAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
43 7 0.16
44 6 0.14
45 25 0.57
46 6 0.14
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (45 bp):
AAATGAAAAATGAAAAATGAAAAATGAAAAATGAAAAATGAAAAA
Found at i:958811 original size:52 final size:51
Alignment explanation
Indices: 958690--958818 Score: 163
Period size: 52 Copynumber: 2.5 Consensus size: 51
958680 GCCTGAAAAG
* *
958690 AAATGAAAAAAGGAAAAAAATGAGAAATGAAAAATGAAAATGAAAAAAAATGA
1 AAATGAAAAAAAGAAAAAAATGAAAAATGAAAAATGAAAATG--AAAAAATGA
**
958743 AAATGAAAATGA-AAAAAAATGAAAAATGAAAAATGAAAAATG-AAAAATGAA
1 AAATGAAAAAAAGAAAAAAATGAAAAATGAAAAATG-AAAATGAAAAAATG-A
*
958794 AAATGAAAAAAAGAAAAAAAAGAAA
1 AAATGAAAAAAAGAAAAAAATGAAA
958819 TAAAAGGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
50 7 0.11
51 11 0.17
52 33 0.50
53 15 0.23
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (51 bp):
AAATGAAAAAAAGAAAAAAATGAAAAATGAAAAATGAAAATGAAAAAATGA
Found at i:958812 original size:7 final size:7
Alignment explanation
Indices: 958705--958803 Score: 114
Period size: 7 Copynumber: 13.7 Consensus size: 7
958695 AAAAAAGGAA
958705 AAAAATG
1 AAAAATG
*
958712 AGAAATG
1 AAAAATG
958719 AAAAATG
1 AAAAATG
958726 -AAAATG
1 AAAAATG
958732 AAAAAAAATG
1 ---AAAAATG
958742 -AAAATG
1 AAAAATG
958748 -AAAATG
1 AAAAATG
958754 AAAAAAAATG
1 ---AAAAATG
958764 AAAAATG
1 AAAAATG
958771 AAAAATG
1 AAAAATG
958778 AAAAATG
1 AAAAATG
958785 AAAAATG
1 AAAAATG
958792 AAAAATG
1 AAAAATG
958799 AAAAA
1 AAAAA
958804 AAGAAAAAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 16
0.82 0.02 0.16
Matches are distributed among these distances:
6 18 0.22
7 52 0.63
10 12 0.15
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:958823 original size:21 final size:21
Alignment explanation
Indices: 958718--958811 Score: 86
Period size: 22 Copynumber: 4.3 Consensus size: 21
958708 AATGAGAAAT
958718 GAAAAATG-AAAATGAAAAAAA
1 GAAAAATGAAAAAT-AAAAAAA
958739 -ATGAAAATG-AAAATGAAAAAAAA
1 GA--AAAATGAAAAAT--AAAAAAA
* *
958762 TGAAAAATGAAAAATGAAAAAT
1 -GAAAAATGAAAAATAAAAAAA
958784 GAAAAATGAAAAATGAAAAAAA
1 GAAAAATGAAAAAT-AAAAAAA
958806 GAAAAA
1 GAAAAA
958812 AAAGAAATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
20 1 0.02
21 14 0.23
22 27 0.44
23 13 0.21
24 5 0.08
25 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (21 bp):
GAAAAATGAAAAATAAAAAAA
Found at i:960244 original size:55 final size:54
Alignment explanation
Indices: 960176--960838 Score: 735
Period size: 55 Copynumber: 12.1 Consensus size: 54
960166 GAAGCAAACT
* * *
960176 CGTTTATTGAAGATTGTTCGAGTTCTATACTCTTTGAAGGAATAAAGAGCGGACC
1 CGTTT-TTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
*
960231 CGTTTTATAAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAG-AGGACC
1 CGTTTT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCA-GACC
* *
960286 CGTTTTACGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACT
1 CGTTTT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
* * *
960341 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACC
1 CGTTT-TTGAAGATTGTTCGAGTTCTATACTCTCTGAA-GGAATAGAGAGCAGACC
* * * *
960396 CGTTTTACGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAAAGAGCGGACT
1 CGTTTT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
* * * * * *
960451 CGTTTGTTGAAGATTGATCGAGTCCTATACTCTCTGAAGAAATAGGGACCAGACA
1 CGTTT-TTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
** * * * * *
960506 CGATAGTTGAAGATTGTTCGAG-TCTTATACTCCCTGAATGAATAGGGACCAGACA
1 CG-TTTTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCAGACC
** ** * * * *
960561 TATTCGATGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCATACC
1 CGTT-TTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
* * * *
960616 CATTTGTTGAAGATTATTCGAGTACTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTT-TTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
* *
960671 CGTTTTATGAAGATTGTTTGAGTCCTATACTCTCTGAAGGAATAGAGAGCAGACC
1 CGTTTT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
*
960726 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTATGAAGGAATAGAGAGC-GAACC
1 CGTTT-TTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAG-ACC
* *
960781 CGTTTGGTGAAGATTGTTCGAG-TCTTATACTCCCTGAAGGAATATG-GAGCAGACC
1 CGTTT-TTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATA-GAGAGCAGACC
960836 CGT
1 CGT
960839 CATTCGAAAA
Statistics
Matches: 527, Mismatches: 62, Indels: 38
0.84 0.10 0.06
Matches are distributed among these distances:
54 10 0.02
55 506 0.96
56 11 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (54 bp):
CGTTTTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
Found at i:962003 original size:14 final size:14
Alignment explanation
Indices: 961984--962017 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
961974 GCGTGGGTTT
961984 GGAGAAGAGATAGG
1 GGAGAAGAGATAGG
961998 GGAGAAGAGATAGG
1 GGAGAAGAGATAGG
962012 GGAGAA
1 GGAGAA
962018 TGGAGACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.50, T:0.06
Consensus pattern (14 bp):
GGAGAAGAGATAGG
Found at i:963497 original size:20 final size:21
Alignment explanation
Indices: 963472--963515 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
963462 CGACATATAA
963472 TATTAATTA-TTATATAATTT
1 TATTAATTATTTATATAATTT
*
963492 TATTAATTATTTTTATAATTT
1 TATTAATTATTTATATAATTT
963513 TAT
1 TAT
963516 ATTTGTAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTAATTATTTATATAATTT
Found at i:963518 original size:23 final size:21
Alignment explanation
Indices: 963471--963518 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
963461 TCGACATATA
963471 ATATTAATTATTATATAATTT
1 ATATTAATTATTATATAATTT
*
963492 -TATTAATTATTTTTATAATTTT
1 ATATTAATTA-TTATATAA-TTT
963514 ATATT
1 ATATT
963519 TGTAGCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 7 0.30
22 3 0.13
23 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTAATTATTATATAATTT
Found at i:966868 original size:36 final size:36
Alignment explanation
Indices: 966821--966890 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
966811 GACATTCAAA
*
966821 GGGTATCGATACATGAA-GAACTGTATCGATACCAAG
1 GGGTATCGATACATGAAGGAA-GGTATCGATACCAAG
* * *
966857 GGGTATTGATACCTTAAGGAAGGTATCGATACCA
1 GGGTATCGATACATGAAGGAAGGTATCGATACCA
966891 TCTAAAACGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 26 0.90
37 3 0.10
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (36 bp):
GGGTATCGATACATGAAGGAAGGTATCGATACCAAG
Found at i:966887 original size:20 final size:16
Alignment explanation
Indices: 966843--966890 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 16
966833 ATGAAGAACT
966843 GTATCGATACCAAGGG
1 GTATCGATACCAAGGG
*
966859 GTATTGATACCTTAAGGAAG
1 GTATCGATACC--AAGG--G
966879 GTATCGATACCA
1 GTATCGATACCA
966891 TCTAAAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 10 0.38
18 5 0.19
20 11 0.42
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (16 bp):
GTATCGATACCAAGGG
Found at i:969993 original size:54 final size:54
Alignment explanation
Indices: 969924--970085 Score: 209
Period size: 54 Copynumber: 3.0 Consensus size: 54
969914 CTAACCAGAA
* *
969924 ATCTGTGCATAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
* * *
969978 ATCTGGGCAGAAGCCACAGGAAAGAATGAATATGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
* ** * * *
970032 ATCTAAGCAGAAATCACATGAGATG-ATGAATGTGTTGTAAAATGTTTTATGAAC
1 ATCTGAGCAGAAGCCACATGA-AAGAATGAATGTGTTGTCAAATGTTTTACGAAC
970086 CAGTAAATAT
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 92 0.98
55 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:970484 original size:22 final size:22
Alignment explanation
Indices: 970450--970529 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
970440 ACATCTACAT
970450 TCTTCAAAAGATGATAGATTCTC
1 TCTTC-AAAGATGATAGATTCTC
970473 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
970495 TTTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
970517 TTTTCAAAGATGA
1 TCTTCAAAGATGA
970530 AAGCTTTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 51 0.91
23 5 0.09
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:971321 original size:76 final size:76
Alignment explanation
Indices: 971195--971381 Score: 293
Period size: 76 Copynumber: 2.5 Consensus size: 76
971185 CTATTTCCCA
* * *
971195 CATCTGTAAGTCGTACAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
*
971260 AGCCTTCGGGT
66 AACCTTCGGGT
*
971271 CATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
971336 AACCTTCGGGT
66 AACCTTCGGGT
* * * *
971347 CATCTGTAAGCCCTTCAGTGCATGTTGTTTTCAAA
1 CATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAA
971382 GCCTTCGGGT
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 102 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
AACCTTCGGGT
Done.