Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007932.1 Hibiscus syriacus cultivar Beakdansim tig00110342_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: 1116633
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:513145 original size:83 final size:83
Alignment explanation
Indices: 512974--513172 Score: 244
Period size: 83 Copynumber: 2.4 Consensus size: 83
512964 GAATATGTAA
* * *
512974 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTC
1 ATCGCATTGCGATAGTCGACTATCGCATTGCG-ATATGTAAATCGCAATGCGATAGTCCAAGTTC
*
513039 GCATTGCGATAGTCCAAGT
65 GCATTGCGATAGTCCAACT
* *
513058 -TCGCATTACGATAGTCGACTATCGCATTGCGAT-T-TACATATTCGCATTGCGATAGTCCAAGT
1 ATCGCATTGCGATAGTCGACTATCGCATTGCGATATGTA-A-A-TCGCAATGCGATAGTCCAAGT
*
513120 TCGCATTGCGATAGT-CGACT
63 TCGCATTGCGATAGTCCAACT
* **
513140 ATCGCATTGCGATAGTCCAAAATCGCATTGCGA
1 ATCGCATTGCGATAGTCGACTATCGCATTGCGA
513173 ATCTGGAAAC
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
80 2 0.02
81 2 0.02
82 6 0.06
83 90 0.90
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (83 bp):
ATCGCATTGCGATAGTCGACTATCGCATTGCGATATGTAAATCGCAATGCGATAGTCCAAGTTCG
CATTGCGATAGTCCAACT
Found at i:516598 original size:5 final size:5
Alignment explanation
Indices: 516583--516615 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
516573 ACTTAATTAA
516583 AAAAT -AAAT AAAAT AAACAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAA
516616 TCTAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:516604 original size:11 final size:10
Alignment explanation
Indices: 516583--516615 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
516573 ACTTAATTAA
516583 AAAAT-AAAT
1 AAAATAAAAT
516592 AAAATAAACAT
1 AAAATAAA-AT
516603 AAAATAAAAT
1 AAAATAAAAT
516613 AAA
1 AAA
516616 TCTAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 7 0.32
11 10 0.45
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:517817 original size:14 final size:15
Alignment explanation
Indices: 517800--517832 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
517790 ATTGATTGGG
*
517800 GGTTTGGG-TGGTTT
1 GGTTTGGGTTGGTTC
517814 GGTTTGGGTTGGTTC
1 GGTTTGGGTTGGTTC
517829 GGTT
1 GGTT
517833 CGGTTCGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (15 bp):
GGTTTGGGTTGGTTC
Found at i:518278 original size:136 final size:136
Alignment explanation
Indices: 518029--518410 Score: 568
Period size: 136 Copynumber: 2.8 Consensus size: 136
518019 CCCCTCAATT
* *
518029 GAGCAATAGGGCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGG-TGAGTTCAT
1 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTC-GGATGAGTTCTT
* * * *
518093 CTCATTATGAACTCTCTATTAAAAATGTCAATCCCTCAAGCAAGACGTTGCTAATTCGAAGTGTT
65 CTCATTATAAACTCTCCATCAAAAATGTCAATCCCTCAAGCAAGGCGTTGCTAATTCGAAGTGTT
518158 GTGAATC
130 GTGAATC
* *
518165 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTGTCGGATGAGTTCTTA
1 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
* * * * * *
518230 TCATTATCAACTCTCCATCAAAAATGTCATTCTCTCAAGCGAGGCGTTGCTGATTTGAAGTGTTG
66 TCATTATAAACTCTCCATCAAAAATGTCAATCCCTCAAGCAAGGCGTTGCTAATTCGAAGTGTTG
518295 TGAATC
131 TGAATC
* * *
518301 GAGCAATAGGTCGAACAAGTTCTTTTCATTATGAACTTTTTCTCCCTCTGTCGGATAAGTTCTTC
1 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
* **
518366 TCATTATAAATTCTCCATCGGAAATGTCAATCCCTCAAGCAAGGC
66 TCATTATAAACTCTCCATCAAAAATGTCAATCCCTCAAGCAAGGC
518411 ATAGTTTGTT
Statistics
Matches: 220, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
135 2 0.01
136 218 0.99
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (136 bp):
GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
TCATTATAAACTCTCCATCAAAAATGTCAATCCCTCAAGCAAGGCGTTGCTAATTCGAAGTGTTG
TGAATC
Found at i:518501 original size:39 final size:39
Alignment explanation
Indices: 518433--518749 Score: 487
Period size: 39 Copynumber: 8.2 Consensus size: 39
518423 AAGAAAAATA
* *
518433 ATCTCAAGTGAGAT-AAATCTTCTATTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
518471 ATCTCAAGCGAGATAAAATCTTGTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
518510 ATCTCAAGCGAGAT-GAATCTTTTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
518548 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
518587 ATCTCAAGCAAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
518626 ATCTCAAGCGAGATAAAATCTTATGTTTCAAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * * * *
518665 ATCTCAAGCAAGATAAAATTTTCTATTTCAAGTGATACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
518704 ATCTCAAGCGAGAT-AAATCTTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
518742 ATCTCAAG
1 ATCTCAAG
518750 TGAGGCATTA
Statistics
Matches: 255, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
38 76 0.30
39 179 0.70
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (39 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
Found at i:518523 original size:77 final size:78
Alignment explanation
Indices: 518433--518749 Score: 496
Period size: 77 Copynumber: 4.1 Consensus size: 78
518423 AAGAAAAATA
** *
518433 ATCTCAAGTGAGAT-AAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTGTGT
1 ATCTCAAGCAAGATAAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGT
518497 TTCGAGTGAAACT
66 TTCGAGTGAAACT
* * * * *
518510 ATCTCAAGCGAGAT-GAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
1 ATCTCAAGCAAGATAAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGT
518574 TTCGAGTGAAACT
66 TTCGAGTGAAACT
*
518587 ATCTCAAGCAAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGT
1 ATCTCAAGCAAGATAAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGT
*
518652 TTCAAGTGAAACT
66 TTCGAGTGAAACT
* * *
518665 ATCTCAAGCAAGATAAAATTTTCTATTTCAAGTGATACTATCTCAAGCGAGAT-AAATCTTATGT
1 ATCTCAAGCAAGATAAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGT
518729 TTCGAGTGAAACT
66 TTCGAGTGAAACT
518742 ATCTCAAG
1 ATCTCAAG
518750 TGAGGCATTA
Statistics
Matches: 224, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
77 116 0.52
78 108 0.48
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (78 bp):
ATCTCAAGCAAGATAAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGT
TTCGAGTGAAACT
Found at i:518988 original size:136 final size:136
Alignment explanation
Indices: 518761--519010 Score: 446
Period size: 136 Copynumber: 1.8 Consensus size: 136
518751 GAGGCATTAC
*
518761 TGATTCAAATTGTTGTGAATCGAGCAATAGGTCAAACAAGTTCTTCTCATTATGAACTTCCTCTC
1 TGATTCAAAGTGTTGTGAATCGAGCAATAGGTCAAACAAGTTCTTCTCATTATGAACTTCCTCTC
* *
518826 CCTCCGTCGGATGAGCTCTTCTCATTATGAACTCTTCATTTGAAATGTTAATCCCTCAAGCAAGG
66 CCTCCGTCGGATGAGCTATTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTCAAGCAAGG
518891 TGTTTA
131 TGTTTA
*
518897 TGATTCGAAGTGTTGTGAATCGAGCAATAGGTCAAACAAGTTCTTCTCATTATGAACTTCCTCTC
1 TGATTCAAAGTGTTGTGAATCGAGCAATAGGTCAAACAAGTTCTTCTCATTATGAACTTCCTCTC
**
518962 CCTCTTTCGGATGAGCTATTCTCATTATGAACTCTCCATTTGAAATGTT
66 CCTCCGTCGGATGAGCTATTCTCATTATGAACTCTCCATTTGAAATGTT
519011 GATCGGTTCA
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 108 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (136 bp):
TGATTCAAAGTGTTGTGAATCGAGCAATAGGTCAAACAAGTTCTTCTCATTATGAACTTCCTCTC
CCTCCGTCGGATGAGCTATTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTCAAGCAAGG
TGTTTA
Found at i:520611 original size:23 final size:24
Alignment explanation
Indices: 520557--520609 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 24
520547 TTAGGCTGAC
520557 TTGGGAAGGTAATGTGTTTCAGGTTAAT
1 TTGGGAAGGTAATGTGTTTCAGG----T
*
520585 TTGGGTAGGTAATGTGTTTCAGGT
1 TTGGGAAGGTAATGTGTTTCAGGT
520609 T
1 T
520610 GGCTTCTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.08
28 22 0.92
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.42
Consensus pattern (24 bp):
TTGGGAAGGTAATGTGTTTCAGGT
Found at i:523535 original size:28 final size:29
Alignment explanation
Indices: 523490--523544 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
523480 AACTTTGTTC
**
523490 GGTTCGGTTAATTATTAAAA-AAAAAATT
1 GGTTCGGTTAACGATTAAAACAAAAAATT
*
523518 GGTTCGGTTAACGGTTAAAACAAAAAA
1 GGTTCGGTTAACGATTAAAACAAAAAA
523545 AGTTTCTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.29
Consensus pattern (29 bp):
GGTTCGGTTAACGATTAAAACAAAAAATT
Found at i:529425 original size:3 final size:3
Alignment explanation
Indices: 529417--529513 Score: 160
Period size: 3 Copynumber: 32.7 Consensus size: 3
529407 CCTGCAAATG
* * *
529417 TAA TAA TAA TAA TAT TAA TAA TAG T-A TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
529464 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
529512 TA
1 TA
529514 TAAACCCAGA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
2 1 0.01
3 86 0.99
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:529992 original size:129 final size:129
Alignment explanation
Indices: 529848--530349 Score: 607
Period size: 129 Copynumber: 3.9 Consensus size: 129
529838 TTAACACGAT
* * * * * *
529848 TCCTACATAATGAGGAAATCTA-GTCGGGTGATGACACGTTTCCTACGTGATAAGGACGGCAGGC
1 TCCTACGTGATGAGGAAATC-AGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGC
* * * * *
529912 CATCTATAGATGATAACACAGTTCCTACATGATGAGGACGATTGGTTATCTGGGGTTGACACGGC
65 CATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCTGGGTTTGACACGGC
* * * * * *
529977 TCCTACTTGATGAGGAGATCAGGTC-AGGTGATGACACGGTACCTACGCGATGAGGAAGACTA-G
1 TCCTACGTGATGAGGAAATCAGGTCGA-GTGATGACACGGTTCCTACGTGATGAGGACGTC-AGG
* *
530040 CCATCTA-AGGGTGATAACACGGTTCCTACGTGATGAGGACGGTTAGTTATCTGGGTTTGACATG
64 CCATCTATA-GGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCTGGGTTTGACACG
530104 GC
128 GC
* * * * * * * *
530106 TCCTGCGTGATGAGGAGATCAGGTTGAGTGATGACAAGGTTCCTACATGATGAGGACATCAAGTC
1 TCCTACGTGATGAGGAAATCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGCC
** * *
530171 ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTTGACACAGC
66 ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCTGGGTTTGACACGGC
* ** * **
530235 TCCTACGTGATGAAGAAGCCAGGTTGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTT
1 TCCTACGTGATGAGGAAATCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGCC
530300 ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCT
66 ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCT
530350 AGAGTGACAA
Statistics
Matches: 321, Mismatches: 45, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
128 3 0.01
129 315 0.98
130 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (129 bp):
TCCTACGTGATGAGGAAATCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGCC
ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCTGGGTTTGACACGGC
Found at i:530338 original size:46 final size:45
Alignment explanation
Indices: 529874--530338 Score: 253
Period size: 46 Copynumber: 10.7 Consensus size: 45
529864 AATCTAGTCG
* * * **
529874 GGTGATGACACGTTTCCTACGTGATAAGGACGGCAGGCCATCTATA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCT-TA
* * * * *
529920 GATGATAACACAGTTCCTACATGATGAGGACGAT-TGGTTATC-T-
1 GGTGATGACACGGTTCCTACGTGATGAGGACG-TCAGGTTATCTTA
* * * *
529963 GGGGTTGACACGGCTCCTACTTGATGAGGA-GATCAGG---TC--A
1 GGTGATGACACGGTTCCTACGTGATGAGGACG-TCAGGTTATCTTA
* * * * ** *
530003 GGTGATGACACGGTACCTACGCGATGAGGAAGACTA-GCCATCTAA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTC-AGGTTATCTTA
* * *
530048 GGGTGATAACACGGTTCCTACGTGATGAGGACGGTTA-GTTATC-TG
1 -GGTGATGACACGGTTCCTACGTGATGAGGAC-GTCAGGTTATCTTA
* * * * *
530093 GGT-TTGACATGGCTCCTGCGTGATGAGGA-GATCAGG---T-TGA
1 GGTGATGACACGGTTCCTACGTGATGAGGACG-TCAGGTTATCTTA
* * * * *
530133 -GTGATGACAAGGTTCCTACATGATGAGGACATCAAGTCATCTATA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCT-TA
* * * *
530178 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATC-TG
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCTTA
* * * * * * *
530222 GGT-TTGACACAGCTCCTACGTGATGAAGAAGCCAGG---T-TGA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCTTA
530262 -GTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCTATA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCT-TA
*
530307 GGTGATAACACGGTTCCTACGTGATGAGGACG
1 GGTGATGACACGGTTCCTACGTGATGAGGACG
530339 ATTAGTTATC
Statistics
Matches: 310, Mismatches: 78, Indels: 62
0.69 0.17 0.14
Matches are distributed among these distances:
39 4 0.01
40 82 0.26
41 3 0.01
42 5 0.02
43 76 0.25
44 10 0.03
45 3 0.01
46 126 0.41
47 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (45 bp):
GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCTTA
Found at i:530441 original size:32 final size:33
Alignment explanation
Indices: 530399--530484 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
530389 GCACAATAGT
* *
530399 CTTCTTCGTGAAGTTGAAATTGTG-GGTGG-CTC
1 CTTCGTCGTGAAGTTGAAATT-TGAGGTGGAATC
* *
530431 CTTCGTCGTGAAGTTGAACTTTGAGTTGGATATC
1 CTTCGTCGTGAAGTTGAAATTTGAGGTGGA-ATC
*
530465 CTTCGTTGTGAAGTTGAAAT
1 CTTCGTCGTGAAGTTGAAAT
530485 CCAATCTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.04
32 23 0.51
34 20 0.44
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (33 bp):
CTTCGTCGTGAAGTTGAAATTTGAGGTGGAATC
Found at i:532701 original size:51 final size:52
Alignment explanation
Indices: 532573--532715 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 52
532563 TATTCCAACA
* *
532573 TTTTCATGTTGGA-GTGAGCCTTCAAGATGCCCCACATGGATTACTTCTGTATT
1 TTTTCATGAT-GATGTGAGCCTTCAAGATACCCCACATGGATTACTTC-GTATT
* * * *
532626 TTTT-ATGCTGATGTGAACCCTCAAGATACCCCATATGGATTACTTC-TATT
1 TTTTCATGATGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCGTATT
*
532676 TTTTCATGATGATGTGAGCCTTCAAGATA-CCTACATGGAT
1 TTTTCATGATGATGTGAGCCTTCAAGATACCCCACATGGAT
532716 AATATGGACC
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
50 17 0.22
51 23 0.29
52 34 0.44
53 4 0.05
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (52 bp):
TTTTCATGATGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCGTATT
Found at i:534224 original size:12 final size:12
Alignment explanation
Indices: 534207--534239 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
534197 TGATTCAATT
534207 TCTTTTTTTATA
1 TCTTTTTTTATA
534219 TCTTTTTTTATA
1 TCTTTTTTTATA
534231 TCTTTTTTT
1 TCTTTTTTT
534240 CTTTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (12 bp):
TCTTTTTTTATA
Found at i:534246 original size:5 final size:5
Alignment explanation
Indices: 534236--534329 Score: 96
Period size: 5 Copynumber: 19.8 Consensus size: 5
534226 TTATATCTTT
534236 TTTTC TTTTC TTTTC TTTTC -TTT- TTTTC TTTT- TTCTT- TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC
*
534283 TTTTC TTTT- TTTTC -TCTC TTTTC TTTT- TTCTCTC TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-T-TC TTTTC TTTTC TTTT
534330 TTATAGATGA
Statistics
Matches: 77, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
4 23 0.30
5 50 0.65
6 2 0.03
7 2 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:534246 original size:37 final size:37
Alignment explanation
Indices: 534231--534331 Score: 79
Period size: 37 Copynumber: 2.8 Consensus size: 37
534221 TTTTTTTATA
* * *
534231 TCTTTTTT-TCTTTTCTTTTCTTTTCTTTTTTTCTTTTT
1 TCTTTTTTCT-TTT-CTTTTCTTTTCTTTTTTTCATATC
* *
534269 TCTTTTTTCTTTTCTTTTCTTTT-TTTTCTCTC-T-TT
1 TCTTTTTTCTTTTCTTTTCTTTTCTTTT-TTTCATATC
*
534304 TCTTTTTTC-TCTCTTTTC-TTTCTTTTTT
1 TCTTTTTTCTTTTCTTTTCTTTTCTTTTTT
534332 ATAGATGAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
33 4 0.07
34 12 0.21
35 11 0.19
36 5 0.09
37 13 0.23
38 11 0.19
39 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (37 bp):
TCTTTTTTCTTTTCTTTTCTTTTCTTTTTTTCATATC
Found at i:534249 original size:23 final size:22
Alignment explanation
Indices: 534222--534309 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 22
534212 TTTTATATCT
*
534222 TTTTTTATATCTTTTTTTCTTTTC
1 TTTTTT-T-TCTTCTTTTCTTTTC
*
534246 TTTTCTTTTCTTTTTTTC-TTT-
1 TTTT-TTTTCTTCTTTTCTTTTC
*
534267 TTTCTTTT-TTCTTTTCTTTTC
1 TTTTTTTTCTTCTTTTCTTTTC
534288 TTTTTTTTCTCTCTTTTCTTTT
1 TTTTTTTTCT-TCTTTTCTTTT
534310 TTCTCTCTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
19 7 0.12
20 7 0.12
21 10 0.18
22 4 0.07
23 21 0.38
24 5 0.09
25 2 0.04
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTTTCTTCTTTTCTTTTC
Found at i:534252 original size:18 final size:18
Alignment explanation
Indices: 534231--534331 Score: 109
Period size: 18 Copynumber: 5.4 Consensus size: 18
534221 TTTTTTTATA
534231 TCTTTTTTTCTTTTCTTT
1 TCTTTTTTTCTTTTCTTT
534249 TCTTTTCTTT-TTTTCTTT
1 TCTTTT-TTTCTTTTCTTT
*
534267 TTTCTTTTTTCTTTTCTTT
1 TCT-TTTTTTCTTTTCTTT
*
534286 TCTTTTTTT-TCTCTCTTT
1 TCTTTTTTTCT-TTTCTTT
534304 TCTTTTTTCTCTCTTT-TCTT
1 TCTTTTTT-TCT-TTTCT-TT
534324 TCTTTTTT
1 TCTTTTTT
534332 ATAGATGAGT
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
17 1 0.01
18 39 0.54
19 18 0.25
20 14 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TCTTTTTTTCTTTTCTTT
Found at i:534260 original size:16 final size:15
Alignment explanation
Indices: 534236--534331 Score: 95
Period size: 16 Copynumber: 5.9 Consensus size: 15
534226 TTATATCTTT
*
534236 TTTTCTTTTCTTTTC
1 TTTTCTTTTTTTTTC
534251 TTTTCTTTTTTTCTT-
1 TTTTCTTTTTTT-TTC
534266 TTTTCTTTTTTCTTTTC
1 TTTTC-TTTTT-TTTTC
534283 TTTTCTTTTTTTTCTCTC
1 TTTTC-TTTTTTT-T-TC
*
534301 TTTTCTTTTTTCTCTC
1 TTTTCTTTTTT-TTTC
534317 TTTTCTTTCTTTTTT
1 TTTTCTTT-TTTTTT
534332 ATAGATGAGT
Statistics
Matches: 70, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
15 16 0.23
16 23 0.33
17 23 0.33
18 8 0.11
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTTTTTC
Found at i:534268 original size:42 final size:41
Alignment explanation
Indices: 534205--534329 Score: 137
Period size: 42 Copynumber: 3.0 Consensus size: 41
534195 CTTGATTCAA
* * *
534205 TTTCTTTT-TTTATATCTTTTTTTATATCTTTTTTTCTTTTCT
1 TTTCTTTTCTTTTTTTC-TTTTTTCT-TCTTTTTTTCTTTTCT
*
534247 TTTCTTTTCTTTTTTTCTTTTTTCTTTTTTCTTTTCTTTTCT
1 TTTCTTTTCTTTTTTTCTTTTTTCTTCTTT-TTTTCTTTTCT
*
534289 TTT-TTTTCTCTCTTTTCTTTTTTCTCTCTTTTCTTTCTTTT
1 TTTCTTTTCT-TTTTTTCTTTTTTCT-TCTTTT-TTTCTTTT
534330 TTATAGATGA
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
41 10 0.14
42 44 0.61
43 18 0.25
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (41 bp):
TTTCTTTTCTTTTTTTCTTTTTTCTTCTTTTTTTCTTTTCT
Found at i:540451 original size:3 final size:3
Alignment explanation
Indices: 540443--540528 Score: 136
Period size: 3 Copynumber: 28.7 Consensus size: 3
540433 CCTGCAAATG
* * * *
540443 TAA TAA TAA TAA TAT TAA TAA TAG TAT TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
540491 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
540529 TAAACCCGGA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:543053 original size:6 final size:6
Alignment explanation
Indices: 543042--543563 Score: 961
Period size: 6 Copynumber: 88.0 Consensus size: 6
543032 TAAAATTAGA
543042 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
543090 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
543138 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
543186 ATGTAT ATG--T ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
543232 ATG--T ATGTAT ATGTAT ATGTAT ATGTATAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATG--TAT ATGTAT ATGTAT ATGTAT
543280 ATGTAT ATG--T ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
543326 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
543374 ATG--T ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
543420 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
543468 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
*
543516 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ACGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
543564 TCATGTGGAC
Statistics
Matches: 505, Mismatches: 1, Indels: 20
0.96 0.00 0.04
Matches are distributed among these distances:
4 16 0.03
6 483 0.96
8 6 0.01
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:565809 original size:57 final size:57
Alignment explanation
Indices: 565715--565824 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 57
565705 CTCGGAATAA
*
565715 CACTCCTTTGCATAGTGCCCATGCTTGCCACAATTATAGCACTCGACATTTGATTTG
1 CACTCCTTTGCATAGTGCCCATGCTTGCCACAATTATAGCACTCAACATTTGATTTG
* * *
565772 CACTCTTTTGCATAGTGCCCATGCTTGCCGCAGTTATAGCACTCAACATTTGA
1 CACTCCTTTGCATAGTGCCCATGCTTGCCACAATTATAGCACTCAACATTTGA
565825 ATGATTTGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (57 bp):
CACTCCTTTGCATAGTGCCCATGCTTGCCACAATTATAGCACTCAACATTTGATTTG
Found at i:569916 original size:39 final size:39
Alignment explanation
Indices: 569833--569909 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
569823 CTTGTAAGAC
* * * **
569833 CTTATCGCAGGCTCTTTTACTTTGTGTTCAGGGTAAGTT
1 CTTACCGCAGGCTCCTCTACTTTGTGCACAGGGTAAGTT
569872 CTTACCGCAGGCTCCTCTACTTTGTGCACAGGGTAAGT
1 CTTACCGCAGGCTCCTCTACTTTGTGCACAGGGTAAGT
569910 CTTTACCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (39 bp):
CTTACCGCAGGCTCCTCTACTTTGTGCACAGGGTAAGTT
Found at i:580218 original size:17 final size:18
Alignment explanation
Indices: 580196--580229 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
580186 TTGAAAGGTC
*
580196 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
580213 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
580230 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:583066 original size:795 final size:794
Alignment explanation
Indices: 581532--583125 Score: 3010
Period size: 795 Copynumber: 2.0 Consensus size: 794
581522 TAATAAACAG
*
581532 AATG-GGCCTAATGTGACTCTTGGGGCCCCAAGATACATTAGGTTGGCTTCCCTTGCTGTGTGCT
1 AATGTGGCCTAATATGACTCTTGGGGCCCCAAGATACATTAGGTTGGCTTCCCTTGCTGTGTGCT
581596 TAGGGTAAGCTATATGGACTTGGACTTACGGGCTTAAGGATACAAGCTCTAAAGCTTATCCTTAG
66 TAGGGTAAGCTATATGGACTTGGACTTACGGGCTTAAGGATACAAGCTCTAAAGCTTATCCTTAG
*
581661 GTTGGCTTTCTTTTTACTGTGTGCTTAGAGTAAGCTATATGGAAAATAGTTTTGGAAATTACTGA
131 GTTGGCTTTCTTTTTACTGTGTGCTTAGAGTAAGCTATATGGAAAATAGTTTTAGAAATTACTGA
581726 TGGTGTACAAGAAAAGAGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTATGAATTTATGAG
196 TGGTGTACAAGAAAAGAGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTATGAATTTATGAG
581791 ATTTACTGGACTATGATTTGTTTATTGTACCTATTATGATTTTATTGTATTGTTGGAACACACTA
261 ATTTACTGGACTATGATTTGTTTATTGTACCTATTATGATTTTATTGTATTGTTGGAACACACTA
* *
581856 GACATCCTATTTGATATCCTAAAAACGTGATACTATGAATGCTTCCTATGAACTGAGATATTCAT
326 GACATCATATTCGATATCCTAAAAACGTGATACTATGAATGCTTCCTATGAACTGAGATATTCAT
*
581921 GGATTCTATTAGATGAACTACCAGTGGAACCTCAGATTATTCTGAAAATTTGTATATGTCTGATT
391 GGATTCTATTAGATGAACTACCAGTGGAACCTCAGATTATTCTGAAAATTTGTATACGTCTGATT
* *
581986 CAATAAGAAAATTATGACTTTTCATTTATCTACATGTCCTTTAGCATCATCAGGTAGTTCTGTAT
456 CAATAAGAAAATTATGACTTTCCATTTATCTACATGTCCTTTAGCATCATCAAGTAGTTCTGTAT
582051 TACTGAGCTTTCCGAAGCTCACTCTATTACTCATCATTGCAGGTTAAAAGAATTGTATCAGTGCA
521 TACTGAGCTTTCCGAAGCTCACTCTATTACTCATCATTGCAGGTTAAAAGAATTGTATCAGTGCA
582116 GTTATCGATATCAATAAGGGAGTTCTTCCGGCGTTGCTTACAGAGTATGGTACATGTGATTAGGG
586 GTTATCGATATCAATAAGGGAGTTCTTCCGGCGTTGCTTACAGAGTATGGTACATGTGATTAGGG
*
582181 GGCATATAATTGTATTTTGTTTTATATACGCGTATGAAAACATGTTTTATTTCCGAACAATGATA
651 GGCATATAATTGTATTTTATTTTATATACGCGTATGAAAACATGTTTTATTTCCGAACAATGATA
*
582246 AATCAATTTGTTAGTTACATGTTTTAATAAAAGTTTTAAATTTTCTGAGATTTTTACAGTGGGTC
716 AATCAATTTGTTAGTTACATGTTTTAATAAAAGTTTTAAATTTTCTGAGATTTTTACAGTGAGTC
582311 ACTCCGGTGGCCCT
781 ACTCCGGTGGCCCT
582325 AAATGTGGCCTAATATGACTCTTGGGGCCCCAAGATACATTAGGTTGGCTTCCCTTGCTGTGTGC
1 -AATGTGGCCTAATATGACTCTTGGGGCCCCAAGATACATTAGGTTGGCTTCCCTTGCTGTGTGC
*
582390 TTAGGGTAAGCTATATGGACTTGGACTTACGGGCTTAAGGATACAATCTCTAAAGCTTATCCTTA
65 TTAGGGTAAGCTATATGGACTTGGACTTACGGGCTTAAGGATACAAGCTCTAAAGCTTATCCTTA
* **
582455 TGTTGGCTTTCTTTTTGTTGTGTGCTTAGAGTAAGCTATATGGAAAATAGTTTTAGAAATTACTG
130 GGTTGGCTTTCTTTTTACTGTGTGCTTAGAGTAAGCTATATGGAAAATAGTTTTAGAAATTACTG
582520 ATGGTGTACAAGAAAAGAGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTATGAATTTATGA
195 ATGGTGTACAAGAAAAGAGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTATGAATTTATGA
582585 GATTTACTGGACTATGATTTGTTTATTGTACCTATTATGATTTTATTGTATTGTTGGAACACACT
260 GATTTACTGGACTATGATTTGTTTATTGTACCTATTATGATTTTATTGTATTGTTGGAACACACT
* *
582650 AGATATTATATTCGATATCCTAAAAACGTGATACTATGAATGCTTCCTATGAACTGAGATATTCA
325 AGACATCATATTCGATATCCTAAAAACGTGATACTATGAATGCTTCCTATGAACTGAGATATTCA
*
582715 TGGATTCTATTCGATGAACTACCAGTGGAACCTCAGATTATTCTGAAAATTTGTATACGTCTGAT
390 TGGATTCTATTAGATGAACTACCAGTGGAACCTCAGATTATTCTGAAAATTTGTATACGTCTGAT
*
582780 TCAATAAGAAAATTATGACTTTCCATTTATCTGCATGTCCTTTAGCATCATCAAGTAGTTCTGTA
455 TCAATAAGAAAATTATGACTTTCCATTTATCTACATGTCCTTTAGCATCATCAAGTAGTTCTGTA
582845 TTACTGAGCTTTCCGAAGCTCACTCTATTACTCATCATTGCAGGTTAAAAGAATTGTATCAGTGC
520 TTACTGAGCTTTCCGAAGCTCACTCTATTACTCATCATTGCAGGTTAAAAGAATTGTATCAGTGC
582910 AGTTATCGATATCAATAAGGGAGTTCTTCCGGCGTTGCTTACAGAGTATGGTACATGTGATTAGG
585 AGTTATCGATATCAATAAGGGAGTTCTTCCGGCGTTGCTTACAGAGTATGGTACATGTGATTAGG
*
582975 GGGCATGTAATTGTATTTTATTTTATATACGCGTATGAAAACATGTTTTATTTCCGAACAATGAT
650 GGGCATATAATTGTATTTTATTTTATATACGCGTATGAAAACATGTTTTATTTCCGAACAATGAT
583040 AAATCAATTTGTTAGTTACATGTTTTAATAAAAGTTTTAAATTTTCTGAGATTTTTACAGTGAGT
715 AAATCAATTTGTTAGTTACATGTTTTAATAAAAGTTTTAAATTTTCTGAGATTTTTACAGTGAGT
583105 CACTCCGGTGGCCCT
780 CACTCCGGTGGCCCT
583120 AATGTG
1 AATGTG
583126 ACACTCCAGA
Statistics
Matches: 781, Mismatches: 18, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
794 10 0.01
795 771 0.99
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (794 bp):
AATGTGGCCTAATATGACTCTTGGGGCCCCAAGATACATTAGGTTGGCTTCCCTTGCTGTGTGCT
TAGGGTAAGCTATATGGACTTGGACTTACGGGCTTAAGGATACAAGCTCTAAAGCTTATCCTTAG
GTTGGCTTTCTTTTTACTGTGTGCTTAGAGTAAGCTATATGGAAAATAGTTTTAGAAATTACTGA
TGGTGTACAAGAAAAGAGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTATGAATTTATGAG
ATTTACTGGACTATGATTTGTTTATTGTACCTATTATGATTTTATTGTATTGTTGGAACACACTA
GACATCATATTCGATATCCTAAAAACGTGATACTATGAATGCTTCCTATGAACTGAGATATTCAT
GGATTCTATTAGATGAACTACCAGTGGAACCTCAGATTATTCTGAAAATTTGTATACGTCTGATT
CAATAAGAAAATTATGACTTTCCATTTATCTACATGTCCTTTAGCATCATCAAGTAGTTCTGTAT
TACTGAGCTTTCCGAAGCTCACTCTATTACTCATCATTGCAGGTTAAAAGAATTGTATCAGTGCA
GTTATCGATATCAATAAGGGAGTTCTTCCGGCGTTGCTTACAGAGTATGGTACATGTGATTAGGG
GGCATATAATTGTATTTTATTTTATATACGCGTATGAAAACATGTTTTATTTCCGAACAATGATA
AATCAATTTGTTAGTTACATGTTTTAATAAAAGTTTTAAATTTTCTGAGATTTTTACAGTGAGTC
ACTCCGGTGGCCCT
Found at i:584497 original size:17 final size:18
Alignment explanation
Indices: 584464--584497 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
584454 TTAATTCTGT
*
584464 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
584482 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
584498 GACATTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:590339 original size:12 final size:12
Alignment explanation
Indices: 590322--590356 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
590312 GTGTGGTAAG
590322 CTTCTCCTTCCT
1 CTTCTCCTTCCT
590334 CTTCTCCTTCCT
1 CTTCTCCTTCCT
*
590346 GTTCTCCTTCC
1 CTTCTCCTTCC
590357 CTTTTTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (12 bp):
CTTCTCCTTCCT
Found at i:590929 original size:3 final size:3
Alignment explanation
Indices: 590921--591000 Score: 108
Period size: 3 Copynumber: 26.7 Consensus size: 3
590911 CCTGCAAACA
* * * *
590921 AAT AAT AAT AAT AAA AAT ATT AAT AAAT AAT GAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
590967 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
591001 AAATGGATGT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 62 0.93
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:591127 original size:21 final size:20
Alignment explanation
Indices: 591103--591164 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
591093 TTGAGTATCT
591103 TATAAGTTAAAAAATTTAATA
1 TATAA-TTAAAAAATTTAATA
* * *
591124 TATAATTTAAGAATTTCATA
1 TATAATTAAAAAATTTAATA
* *
591144 T-TAATTTAAAATTTGTAATA
1 TATAATTAAAAAATT-TAATA
591164 T
1 T
591165 CATCTGTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 11 0.32
20 18 0.53
21 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
TATAATTAAAAAATTTAATA
Found at i:591144 original size:20 final size:18
Alignment explanation
Indices: 591113--591157 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
591103 TATAAGTTAA
591113 AAAATTTAATATATAATTT
1 AAAATTTAATAT-TAATTT
*
591132 AAGAATTTCATATTAATTT
1 AA-AATTTAATATTAATTT
591151 AAAATTT
1 AAAATTT
591158 GTAATATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
AAAATTTAATATTAATTT
Found at i:600039 original size:6 final size:6
Alignment explanation
Indices: 600023--600068 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
600013 AATAAAATTT
600023 AAAAT- AAAATG AAAATG AAAATG AAAACTTG AAAA-G AAAA-G AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAA--TG AAAATG AAAATG AAAAT
600069 AGAGAACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 15 0.41
6 16 0.43
8 6 0.16
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:600062 original size:25 final size:26
Alignment explanation
Indices: 600028--600077 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
600018 AATTTAAAAT
600028 AAAATGAAAATGAAAAT-GAAAACTTG
1 AAAATGAAAA-GAAAATAGAAAACTTG
*
600054 AAAA-GAAAAGAAAATAGAGAACTT
1 AAAATGAAAAGAAAATAGAAAACTT
600078 TATAAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 12 0.55
26 4 0.18
ACGTcount: A:0.64, C:0.04, G:0.16, T:0.16
Consensus pattern (26 bp):
AAAATGAAAAGAAAATAGAAAACTTG
Found at i:601627 original size:25 final size:25
Alignment explanation
Indices: 601593--601650 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
601583 CCAAGACGAA
601593 TTTTCGTGGAGTCTAGGATTCAAAC
1 TTTTCGTGGAGTCTAGGATTCAAAC
601618 TTTTCGTGGAGTCTAGGATTCAAAC
1 TTTTCGTGGAGTCTAGGATTCAAAC
601643 TTTTCGTG
1 TTTTCGTG
601651 ATTTCCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.40
Consensus pattern (25 bp):
TTTTCGTGGAGTCTAGGATTCAAAC
Found at i:607440 original size:14 final size:16
Alignment explanation
Indices: 607421--607457 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
607411 TCGTTCCGGT
607421 GTATAAAAA-AATTCA
1 GTATAAAAATAATTCA
*
607436 G-ATAAAAATACTTCA
1 GTATAAAAATAATTCA
607451 GTATAAA
1 GTATAAA
607458 TCAGTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 7 0.37
15 7 0.37
16 5 0.26
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (16 bp):
GTATAAAAATAATTCA
Found at i:608667 original size:14 final size:15
Alignment explanation
Indices: 608643--608675 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
608633 CTTCTGGTCT
608643 TTCCAACTTCTTAAA
1 TTCCAACTTCTTAAA
*
608658 TTCC-ACTTCTTGAA
1 TTCCAACTTCTTAAA
608672 TTCC
1 TTCC
608676 GATTCTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.24, C:0.30, G:0.03, T:0.42
Consensus pattern (15 bp):
TTCCAACTTCTTAAA
Found at i:610585 original size:31 final size:32
Alignment explanation
Indices: 610550--610624 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 32
610540 CTAAGGTGAC
* *
610550 TCTTGGGTAGGCACCGAGGCCCCGAG-ATCTT
1 TCTTGGGTAGGCACCGAGGCCCCGAGTAACCT
* * *
610581 TCTTGGGTAGGCCCCGTGGCCTCGAGTAACCT
1 TCTTGGGTAGGCACCGAGGCCCCGAGTAACCT
*
610613 ACTTGGGTAGGC
1 TCTTGGGTAGGC
610625 TCTCGGGCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.24
Consensus pattern (32 bp):
TCTTGGGTAGGCACCGAGGCCCCGAGTAACCT
Found at i:613541 original size:4 final size:4
Alignment explanation
Indices: 613532--613567 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
613522 GCACCAAACC
613532 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -TTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
613568 CATTTCCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:614551 original size:21 final size:21
Alignment explanation
Indices: 614503--614552 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
614493 GTTTCCAGAT
*
614503 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
614524 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
614545 TCGCAATG
1 TCGCAATG
614553 TGAATATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:614610 original size:21 final size:21
Alignment explanation
Indices: 614565--614653 Score: 76
Period size: 21 Copynumber: 4.2 Consensus size: 21
614555 AATATGTAAA
* *
614565 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAAT
*
614585 ATCGCATTGCGATAGTCCAAGT
1 -TCGCATTGCGATAGTCCAAAT
* *
614607 TCGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
*
614630 TCG--TTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
614649 TCGCA
1 TCGCA
614654 ACGACTGGTG
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
19 11 0.20
21 31 0.55
22 3 0.05
23 11 0.20
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:615267 original size:6 final size:6
Alignment explanation
Indices: 615259--615309 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
615249 GCCCGTCTCG
* *
615259 GGTCGG GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
615307 GGT
1 GGT
615310 AATACGTGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.00, C:0.16, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:615421 original size:21 final size:21
Alignment explanation
Indices: 615395--615476 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 21
615385 CGTTGCGATT
*
615395 TTGGACTATCGCAACGTGAAC
1 TTGGACTATCGCAACGCGAAC
*
615416 TTGGACTATCGCAATGCGAA-
1 TTGGACTATCGCAACGCGAAC
* *
615436 TATGTA-AATCGCAACGCGAAC
1 T-TGGACTATCGCAACGCGAAC
*
615457 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
615477 TATGTAAATC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
20 16 0.32
21 34 0.68
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:615447 original size:41 final size:41
Alignment explanation
Indices: 615402--615495 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
615392 ATTTTGGACT
*
615402 ATCGCAACGTGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAA
615443 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAA
*
615484 ATCGCAATGCGA
1 ATCGCAACGCGA
615496 TAGTCGAAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAA
Found at i:615448 original size:20 final size:20
Alignment explanation
Indices: 615423--615495 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
615413 AACTTGGACT
615423 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* * *
615443 ATCGCAACGCGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTA-A
615464 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
615484 ATCGCAATGCGA
1 ATCGCAATGCGA
615496 TAGTCGAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:620956 original size:13 final size:13
Alignment explanation
Indices: 620938--620974 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
620928 GATCAAAGTC
620938 AATGAGTTGACCT
1 AATGAGTTGACCT
620951 AATGAGTTGACCT
1 AATGAGTTGACCT
*
620964 AGTGAGTTGAC
1 AATGAGTTGAC
620975 TCAGTCGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (13 bp):
AATGAGTTGACCT
Found at i:622363 original size:20 final size:19
Alignment explanation
Indices: 622314--622351 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
622304 ATTAAATTAT
622314 TAATAATTTAA-TTAAAAA
1 TAATAATTTAATTTAAAAA
622332 TAATAATTTAATTTAAAAA
1 TAATAATTTAATTTAAAAA
622351 T
1 T
622352 TAAAAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAATTTAATTTAAAAA
Found at i:622528 original size:21 final size:21
Alignment explanation
Indices: 622502--622542 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
622492 TAAAAAAAAT
*
622502 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
622523 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
622543 TTTAACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:625517 original size:12 final size:11
Alignment explanation
Indices: 625481--625511 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
625471 ATTTTTACAA
625481 TTTTTTAATAT
1 TTTTTTAATAT
625492 TTTTTTGAATAT
1 TTTTTT-AATAT
625504 TTTTTTAA
1 TTTTTTAA
625512 AAATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TTTTTTAATAT
Found at i:631234 original size:15 final size:15
Alignment explanation
Indices: 631214--631244 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
631204 CAACAGATAG
631214 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
631229 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
631244 A
1 A
631245 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:632942 original size:22 final size:22
Alignment explanation
Indices: 632884--632944 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
632874 CGCCTTGCAC
* * *
632884 TGATACGAAAGTGCATTCGCAT
1 TGATACTAAAGTGCCTTCACAT
632906 TGATACTAAAGTGCCTTCACAT
1 TGATACTAAAGTGCCTTCACAT
632928 TGATACTAAAGTGCCTT
1 TGATACTAAAGTGCCTT
632945 AAAACTGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (22 bp):
TGATACTAAAGTGCCTTCACAT
Found at i:634590 original size:29 final size:29
Alignment explanation
Indices: 634557--634617 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
634547 AGGAAAAATC
*
634557 CAAGACTTTGATTTTTTAAAACTATATTG
1 CAAGACTTTGATTCTTTAAAACTATATTG
*
634586 CAAGACTTTGATTCTTTAAAACTATGTTG
1 CAAGACTTTGATTCTTTAAAACTATATTG
634615 CAA
1 CAA
634618 AGGGGATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (29 bp):
CAAGACTTTGATTCTTTAAAACTATATTG
Found at i:634726 original size:15 final size:15
Alignment explanation
Indices: 634702--634738 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
634692 ATAAAGGAAC
634702 AAGAAATGAAGA-AA
1 AAGAAATGAAGAGAA
634716 AAGAGAATGAAGAGAA
1 AAGA-AATGAAGAGAA
634732 AAGAAAT
1 AAGAAAT
634739 ATGATGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 11 0.52
16 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (15 bp):
AAGAAATGAAGAGAA
Found at i:634742 original size:17 final size:16
Alignment explanation
Indices: 634705--634747 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
634695 AAGGAACAAG
634705 AAATGAAGA-AAAAGA
1 AAATGAAGAGAAAAGA
*
634720 GAATGAAGAGAAAAGA
1 AAATGAAGAGAAAAGA
*
634736 AATATGATGAGA
1 AA-ATGAAGAGA
634748 TAAAAAACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 7 0.30
17 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.12
Consensus pattern (16 bp):
AAATGAAGAGAAAAGA
Found at i:637484 original size:30 final size:30
Alignment explanation
Indices: 637445--637525 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
637435 AAAAAAATAA
* * *
637445 TTTACATAAAATAAATTACCTGAAAATTGT
1 TTTACATAAAATGAATTACATGAAAAATGT
*
637475 TTTATATAAAATGAATTACATGAAAAATGT
1 TTTACATAAAATGAATTACATGAAAAATGT
*
637505 TTTACGTAAAATGAATTACAT
1 TTTACATAAAATGAATTACAT
637526 TTTCTGGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (30 bp):
TTTACATAAAATGAATTACATGAAAAATGT
Found at i:637673 original size:76 final size:76
Alignment explanation
Indices: 637593--637745 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
637583 TCATTTTCAC
*
637593 TAATTGTTTGATACACTATAATTAATTTTATAGAAAATGATTTACATAAAATGAATAAAGTTTGG
1 TAATTGTGTGATACACTATAATTAATTTTATAGAAAATGATTTACATAAAATGAATAAAGTTTGG
**
637658 TTCGGTTAATA
66 TTCAATTAATA
637669 TAATTGTGTGATACACTATAATTAATTTTATAGAAAATGATTTACATAAAATGAATAAAGTTTGG
1 TAATTGTGTGATACACTATAATTAATTTTATAGAAAATGATTTACATAAAATGAATAAAGTTTGG
637734 TTCAATTAATA
66 TTCAATTAATA
637745 T
1 T
637746 TTAAAAAAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (76 bp):
TAATTGTGTGATACACTATAATTAATTTTATAGAAAATGATTTACATAAAATGAATAAAGTTTGG
TTCAATTAATA
Found at i:637900 original size:19 final size:19
Alignment explanation
Indices: 637878--637920 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
637868 TTTATTAACA
*
637878 TAATACTAAAT-TATTATAT
1 TAATACTAAATATA-TAAAT
*
637897 TAATATTAAATATATAAAT
1 TAATACTAAATATATAAAT
637916 TAATA
1 TAATA
637921 TTACTCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATACTAAATATATAAAT
Found at i:640500 original size:26 final size:26
Alignment explanation
Indices: 640471--640532 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
640461 ACATAGATTT
*
640471 ATTAAAAACTAAAAAATTAAAA-AAAA
1 ATTAAAAA-TAAAAAAATAAAATAAAA
*
640497 ATTAAAGATAAAAAAATAAAATAAAA
1 ATTAAAAATAAAAAAATAAAATAAAA
*
640523 AATAAAAATA
1 ATTAAAAATA
640533 TCGAAGATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 12 0.39
26 19 0.61
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (26 bp):
ATTAAAAATAAAAAAATAAAATAAAA
Found at i:640509 original size:15 final size:13
Alignment explanation
Indices: 640481--640529 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
640471 ATTAAAAACT
*
640481 AAAAAATTAAA-A
1 AAAAAATAAAATA
*
640493 AAAAATTAAAGATA
1 AAAAAATAAA-ATA
640507 AAAAAATAAAAT-
1 AAAAAATAAAATA
640519 AAAAAATAAAA
1 AAAAAATAAAA
640530 ATATCGAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 19 0.59
13 3 0.09
14 10 0.31
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:640512 original size:20 final size:20
Alignment explanation
Indices: 640489--640530 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
640479 CTAAAAAATT
* *
640489 AAAAAAAAATTAAAGATAAA
1 AAAAAAAAATAAAAAATAAA
*
640509 AAAATAAAATAAAAAATAAA
1 AAAAAAAAATAAAAAATAAA
640529 AA
1 AA
640531 TATCGAAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAAAAAATAAAAAATAAA
Found at i:647069 original size:22 final size:22
Alignment explanation
Indices: 647038--647079 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
647028 GATGTACCGA
647038 ATCGCAATTTTGAAACGATCCG
1 ATCGCAATTTTGAAACGATCCG
*
647060 ATCGCGATTTTGAAACGATC
1 ATCGCAATTTTGAAACGATC
647080 TGAACGCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (22 bp):
ATCGCAATTTTGAAACGATCCG
Found at i:647087 original size:22 final size:22
Alignment explanation
Indices: 647034--647087 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
647024 CTACGATGTA
*
647034 CCGAATCGCAATTTTGAAACGAT
1 CCGAA-CGCGATTTTGAAACGAT
*
647057 CCGATCGCGATTTTGAAACGAT
1 CCGAACGCGATTTTGAAACGAT
*
647079 CTGAACGCG
1 CCGAACGCG
647088 TTCGTACTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
CCGAACGCGATTTTGAAACGAT
Found at i:648623 original size:2 final size:2
Alignment explanation
Indices: 648616--648642 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
648606 CGTTCATTAC
648616 TA 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 TA T
648643 TATTTCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:648810 original size:12 final size:12
Alignment explanation
Indices: 648793--648817 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
648783 ACTTTATCTA
648793 TTTTTTTTATTT
1 TTTTTTTTATTT
648805 TTTTTTTTATTT
1 TTTTTTTTATTT
648817 T
1 T
648818 AATTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTATTT
Found at i:651647 original size:21 final size:21
Alignment explanation
Indices: 651621--651753 Score: 82
Period size: 20 Copynumber: 6.5 Consensus size: 21
651611 CAGTTCCCAG
651621 AATCGCAACGCGATTATGAAT
1 AATCGCAACGCGATTATGAAT
*
651642 AATCGCAATGCGA-TA-GTACA-
1 AATCGCAACGCGATTATG-A-AT
** * **
651662 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTATGAAT
*
651684 AATCGCAACGCGAATATGAA-
1 AATCGCAACGCGATTATGAAT
**
651704 AATCGCAACGCGAACAT--AT
1 AATCGCAACGCGATTATGAAT
* *
651723 AAATCGCAACGCGATTCTGACT
1 -AATCGCAACGCGATTATGAAT
651745 -ATCGCAACG
1 AATCGCAACG
651754 AGTATTCGTA
Statistics
Matches: 86, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 44 0.51
21 36 0.42
22 4 0.05
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (21 bp):
AATCGCAACGCGATTATGAAT
Found at i:651709 original size:20 final size:20
Alignment explanation
Indices: 651684--651969 Score: 194
Period size: 20 Copynumber: 14.5 Consensus size: 20
651674 GATTTTCCAT
*
651684 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATATGTA
* *
651704 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATATGTA
* *
651724 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATATGTA
* * *
651743 CTATCGCAACGAGTAT-TCGTAA
1 -AATCGCAACGCGAATAT-GT-A
* **
651765 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGTA
* *
651785 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATATGT-A
* *
651806 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGTA
* **
651826 AATCGCAACGAGAATACATA
1 AATCGCAACGCGAATATGTA
*
651846 AATCGTAACGCG-----G-A
1 AATCGCAACGCGAATATGTA
* *
651860 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGTA
* * *
651880 AATCGCAATGCGTATCCT-TA
1 AATCGCAACGCGAAT-ATGTA
* *
651900 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATATGTA
* *
651920 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATATGTA
* *
651940 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATATGTA
651960 AATCGCAACG
1 AATCGCAACG
651970 AGATTCTAAC
Statistics
Matches: 210, Mismatches: 42, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
14 11 0.05
19 3 0.01
20 164 0.78
21 31 0.15
22 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATATGTA
Found at i:651776 original size:41 final size:41
Alignment explanation
Indices: 651745--651969 Score: 238
Period size: 40 Copynumber: 5.7 Consensus size: 41
651735 GATTCTGACT
* *
651745 ATCGCAACGAGTATTCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
651786 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
651827 ATCGCAACGAGAATACAT-AAATCGTAACGCG-----G-AA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
651861 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCTTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * * * *
651901 ATCGCAATGCGAATACGT-AAATCGCAATGCGAATACGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
651941 ATCGCAATGCGAAT-CTGT-AAATCGCAACG
1 ATCGCAACGAGAATAC-GTAAAATCGCAACG
651970 AGATTCTAAC
Statistics
Matches: 162, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
34 30 0.19
35 1 0.01
39 1 0.01
40 75 0.46
41 55 0.34
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:651906 original size:74 final size:75
Alignment explanation
Indices: 651784--651924 Score: 223
Period size: 74 Copynumber: 1.9 Consensus size: 75
651774 GCGTATCCGT
651784 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACATAAAT
1 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACATAAAT
651849 CGTAACGCGG
66 CGTAACGCGG
* * * *
651859 AAATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCT-TAAATCGCAATGCGAATACGTAAA
1 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTAT-CTGTAAATCGCAACGAGAATACATAAA
651922 TCG
65 TCG
651925 CAATGCGAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
74 39 0.64
75 22 0.36
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (75 bp):
AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACATAAAT
CGTAACGCGG
Found at i:652855 original size:24 final size:24
Alignment explanation
Indices: 652828--652881 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
652818 GTATTCGAAA
652828 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
652852 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
652876 TTTGAT
1 TTTGAT
652882 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:654177 original size:30 final size:30
Alignment explanation
Indices: 654136--654194 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
654126 CCCCGCATCC
* *
654136 GCACCGCATCCACCCGCCCCTCATCCGCCT
1 GCACCGCATCCACCCACCCCACATCCGCCT
*
654166 GCACTGCATCCACCCACCCCACATCCGCC
1 GCACCGCATCCACCCACCCCACATCCGCC
654195 CGCCCAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.17, C:0.59, G:0.12, T:0.12
Consensus pattern (30 bp):
GCACCGCATCCACCCACCCCACATCCGCCT
Found at i:656685 original size:20 final size:20
Alignment explanation
Indices: 656655--656762 Score: 88
Period size: 19 Copynumber: 5.8 Consensus size: 20
656645 CAATCATCTT
*
656655 AATGTCTATCGCAACGTGGA
1 AATGACTATCGCAACGTGGA
* *
656675 AATTACTATCGCAACG-CGA
1 AATGACTATCGCAACGTGGA
**
656694 AATGAAAATCGCAACGT-G-
1 AATGACTATCGCAACGTGGA
656712 AA--A--ATCGCAACGTGGA
1 AATGACTATCGCAACGTGGA
*
656728 AATGACTATCGCAATGT-GA
1 AATGACTATCGCAACGTGGA
**
656747 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
656763 AGAGAATCGC
Statistics
Matches: 71, Mismatches: 10, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 3 0.04
18 3 0.04
19 31 0.44
20 23 0.32
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
AATGACTATCGCAACGTGGA
Found at i:656704 original size:19 final size:18
Alignment explanation
Indices: 656682--656832 Score: 92
Period size: 19 Copynumber: 8.7 Consensus size: 18
656672 GGAAATTACT
656682 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
656701 ATCGCAA-CG---TGAAA
1 ATCGCAAGCGAAATGAAA
* **
656715 ATCGCAACGTGGAAATGACT
1 ATCGCAA-G-CGAAATGAAA
*
656735 ATCGCAATGTGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
656754 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
656768 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
656787 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
656801 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
656820 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
656833 TTTAGTTTCG
Statistics
Matches: 101, Mismatches: 15, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
14 31 0.31
15 2 0.02
16 4 0.04
17 6 0.06
18 2 0.02
19 45 0.45
20 11 0.11
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:656715 original size:14 final size:14
Alignment explanation
Indices: 656696--656730 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
656686 CAACGCGAAA
656696 TGAAAATCGCAACG
1 TGAAAATCGCAACG
656710 TGAAAATCGCAACG
1 TGAAAATCGCAACG
*
656724 TGGAAAT
1 TGAAAAT
656731 GACTATCGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:656739 original size:34 final size:33
Alignment explanation
Indices: 656682--656748 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
656672 GGAAATTACT
656682 ATCGCAACGCGAAATGAAAATCGCAACGTGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGTGAAA
* ** *
656715 ATCGCAACGTGGAAATGACTATCGCAATGTGAAA
1 ATCGCAACG-CGAAATGAAAATCGCAACGTGAAA
656749 TGAAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 9 0.31
34 20 0.69
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGTGAAA
Found at i:656749 original size:53 final size:53
Alignment explanation
Indices: 656662--656795 Score: 182
Period size: 53 Copynumber: 2.5 Consensus size: 53
656652 CTTAATGTCT
* *
656662 ATCGCAACGTGGAAATTACTATCGCAACGCGAAATGAAAATCGCAACGTGAAA
1 ATCGCAACGTGGAAATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAAA
* * *
656715 ATCGCAACGTGGAAATGACTATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGTGGAAATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAAA
**
656768 ATCGCAA--TGCGAAATGAAAATCGCAACG
1 ATCGCAACGTG-GAAATGACTATCGCAACG
656796 AGGGAATCGC
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
51 2 0.03
52 15 0.21
53 55 0.76
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (53 bp):
ATCGCAACGTGGAAATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAAA
Found at i:656775 original size:33 final size:33
Alignment explanation
Indices: 656735--656828 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
656725 GGAAATGACT
*
656735 ATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
656768 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
656801 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
656829 CGAATTTAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:656882 original size:33 final size:33
Alignment explanation
Indices: 656828--656917 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
656818 AAATCGCAAC
* * * * *
656828 GCGAATTTAGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
656861 GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
* *
656894 GCGATTTTCATTTTGCATTGCGAT
1 GCGATTTTAATTTCGCATTGCGAT
656918 AGTCATTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (33 bp):
GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
Found at i:657043 original size:14 final size:14
Alignment explanation
Indices: 657024--657060 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
657014 CATCAATTAA
657024 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
657038 ACAAATCATCTTTT
1 ACAAATCAACTTTT
657052 ACAAATCAA
1 ACAAATCAA
657061 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:658495 original size:42 final size:42
Alignment explanation
Indices: 658410--658503 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
658400 GTGAATCGGG
* *
658410 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* * *
658452 CTCTTGAACGGTGGGAGGAGA-CTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGG-GACCTCTTCAACG-ATGACAGGGGC
*
658494 CTCTTCAACG
1 CTCTTGAACG
658504 ATAGGAGTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:658517 original size:42 final size:42
Alignment explanation
Indices: 658449--658528 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
658439 CGATGACAGT
* * *
658449 GGCCTCTTGAACGGTGGGAGGAGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGAGACTCTCGAGGAATGATAGG
* *
658491 GGCCTCTTCAACGATAGGAGTG-GACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAG-GAGACTCTCGAGGAATGA
658529 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 31 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGAGACTCTCGAGGAATGATAGG
Found at i:660524 original size:20 final size:20
Alignment explanation
Indices: 660499--660595 Score: 84
Period size: 20 Copynumber: 5.2 Consensus size: 20
660489 CTTTTGGTTG
660499 GAATGAAAATCGCAACGAGA
1 GAATGAAAATCGCAACGAGA
*
660519 GAATGAAAATCGCAACGCG-
1 GAATGAAAATCGCAACGAGA
** *
660538 GAAATGACTATCGTAAC--GA
1 G-AATGAAAATCGCAACGAGA
*
660557 G-A-G--AATCGCAACGCGA
1 GAATGAAAATCGCAACGAGA
660573 -AATGAAAATCGCAACGAGA
1 GAATGAAAATCGCAACGAGA
660592 GAAT
1 GAAT
660596 CACAACGCGA
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
14 7 0.11
16 4 0.07
17 2 0.03
18 1 0.02
19 14 0.23
20 33 0.54
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
GAATGAAAATCGCAACGAGA
Found at i:660584 original size:19 final size:19
Alignment explanation
Indices: 660500--660638 Score: 118
Period size: 19 Copynumber: 7.7 Consensus size: 19
660490 TTTTGGTTGG
*
660500 AATGAAAATCGCAACGAGA
1 AATGAAAATCGCAACGCGA
660519 GAATGAAAATCGCAACGCGGA
1 -AATGAAAATCGCAACGC-GA
** *
660540 AATGACTATCGTAA--CG-
1 AATGAAAATCGCAACGCGA
*
660556 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
660573 AATGAAAATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
* *
660589 -A-GAGAATCACAACGCGA
1 AATGAAAATCGCAACGCGA
*
660606 AATTAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
660625 AATGAAAATCGCAA
1 AATGAAAATCGCAA
660639 TACGATTTTG
Statistics
Matches: 94, Mismatches: 14, Indels: 23
0.72 0.11 0.18
Matches are distributed among these distances:
14 17 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 36 0.38
20 27 0.29
21 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:660589 original size:33 final size:33
Alignment explanation
Indices: 660526--660621 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
660516 AGAGAATGAA
** *
660526 AATCGCAACGCGGAAATGACTATCGTAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
660560 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
660593 AATCACAACGCGAAATTAAAATCGCAACG
1 AATCGCAACGCGAAATGAAAATCGCAACG
660622 CGAAATGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 46 0.81
34 11 0.19
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:660674 original size:14 final size:14
Alignment explanation
Indices: 660655--660692 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
660645 TTTGGTTTCG
660655 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
660669 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
660683 CGTTGCGATT
1 CGTTGCGATT
660693 TTCATTTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:660753 original size:20 final size:20
Alignment explanation
Indices: 660684--660755 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
660674 CGATTCTCTC
660684 GTTGCGATTTTCA-TTTCGCT
1 GTTGCGATTTTCATTTTC-CT
**
660704 CGTTGCGATAGTCATTTTCCT
1 -GTTGCGATTTTCATTTTCCT
*
660725 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCCT
660745 GTTGCGATTTT
1 GTTGCGATTTT
660756 AAATTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 28 0.62
21 13 0.29
22 4 0.09
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCCT
Found at i:661396 original size:74 final size:75
Alignment explanation
Indices: 661292--661441 Score: 230
Period size: 74 Copynumber: 2.0 Consensus size: 75
661282 GATTTACGTA
* *
661292 TTCGCATTGCGATTTACGTATTCGCATTGCGATTTACTGATACGCATTGTGA-TTTACATATTCT
1 TTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTGCGATTTTACATATTCT
661356 CGTTGCGATT
66 CGTTGCGATT
* * * * *
661366 TTCGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
1 TTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTGCGATTTTACATATTCT
661431 CGTTGCGATT
66 CGTTGCGATT
661441 T
1 T
661442 ACGGATACGC
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
74 46 0.68
75 22 0.32
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.42
Consensus pattern (75 bp):
TTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTGCGATTTTACATATTCT
CGTTGCGATT
Found at i:661424 original size:21 final size:20
Alignment explanation
Indices: 661258--661480 Score: 188
Period size: 20 Copynumber: 11.3 Consensus size: 20
661248 AAAAATCGTA
*
661258 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGGATACGCG
* * *
661278 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGGATACGCG
* * *
661298 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGGATACGCG
* *
661318 TTGCGATTTACTGATACGCA
1 TTGCGATTTACGGATACGCG
* ** * *
661338 TTGTGATTTACATATTCTCG
1 TTGCGATTTACGGATACGCG
661358 TTGCGATTT-----T-CGCG
1 TTGCGATTTACGGATACGCG
* * *
661372 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
661392 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* * *
661412 TTGCGATTTTACGTATTCTCG
1 TTGCGA-TTTACGGATACGCG
661433 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
661453 TTGCAATTTTACGGATACTCG
1 TTGCGA-TTTACGGATACGCG
661474 TTGCGAT
1 TTGCGAT
661481 AGTCAGTATC
Statistics
Matches: 169, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.07
15 1 0.01
19 1 0.01
20 120 0.71
21 35 0.21
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:661431 original size:41 final size:40
Alignment explanation
Indices: 661258--661480 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
661248 AAAAATCGTA
* * * * * * *
661258 TTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
* * * *
661298 TTGCGATTTACGTATTCGCATTGCGATTTACTGATACGCA
1 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
* *
661338 TTGTGATTTACATATTCTCGTTGCGATTT-----T-CGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
661372 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
661412 TTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCG
1 TTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCG
* * *
661453 TTGCAATTTTACGGATACTCGTTGCGAT
1 TTGCGA-TTTACGTATTCTCGTTGCGAT
661481 AGTCAGTATC
Statistics
Matches: 161, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
34 30 0.19
35 1 0.01
39 1 0.01
40 70 0.43
41 59 0.37
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
Found at i:661494 original size:41 final size:41
Alignment explanation
Indices: 661368--661502 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
661358 TTGCGATTTT
* * *
661368 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGGATA
* * *
661408 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGGATA
* *
661449 CGCGTTGCAATTTTACGGATACTCGTTGCGATAGTCA-GTAT-
1 CGCGTTGCGATTTTACGGATACTCGTTGCGAT--TCACGGATA
661490 CGCGTTGCGATTT
1 CGCGTTGCGATTT
661503 ATATGTTCGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
40 10 0.12
41 71 0.83
42 3 0.03
43 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGGATA
Found at i:661496 original size:61 final size:61
Alignment explanation
Indices: 661366--661503 Score: 172
Period size: 61 Copynumber: 2.3 Consensus size: 61
661356 CGTTGCGATT
* * * * * *
661366 TTCGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTA
1 TTCGCGTTGCGATTTACGGATACGCGTTGCAATTTACGGATACGCGTTGCGATGTCACGTA
* *
661427 TTCTCGTTGCGATTTACGGATACGCGTTGCAATTTTACGGATACTCGTTGCGATAGTCA-GTA
1 TTCGCGTTGCGATTTACGGATACGCGTTGCAA-TTTACGGATACGCGTTGCGAT-GTCACGTA
661489 -TCGCGTTGCGATTTA
1 TTCGCGTTGCGATTTA
661504 TATGTTCGCG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
61 41 0.62
62 23 0.35
63 2 0.03
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.38
Consensus pattern (61 bp):
TTCGCGTTGCGATTTACGGATACGCGTTGCAATTTACGGATACGCGTTGCGATGTCACGTA
Found at i:661582 original size:42 final size:42
Alignment explanation
Indices: 661488--661582 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
661478 GATAGTCAGT
* * *
661488 ATCGCGTTGCG-ATTTATATGTTCGCGTTGCGATTATGGAAA
1 ATCGCGTTGCGAATTTATATGATCGCATTGCGATTATGCAAA
** * * *
661529 ATCGCAATGCGAATTTGTACT-ATCGCATTGCGATTATTCATA
1 ATCGCGTTGCGAATTTATA-TGATCGCATTGCGATTATGCAAA
661571 ATCGCGTTGCGA
1 ATCGCGTTGCGA
661583 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
41 9 0.21
42 32 0.76
43 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (42 bp):
ATCGCGTTGCGAATTTATATGATCGCATTGCGATTATGCAAA
Found at i:661620 original size:20 final size:19
Alignment explanation
Indices: 661571--661624 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
661561 ATTATTCATA
661571 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
661590 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
661611 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
661625 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:662555 original size:26 final size:27
Alignment explanation
Indices: 662511--662586 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
662501 TTAATTTATC
*
662511 AAAAATATTTTATTATTAA-CTTAATTT
1 AAAAATAATTTATT-TTAATCTTAATTT
*
662538 AAAAATAATTTATTTTAATTTTAATTT
1 AAAAATAATTTATTTTAATCTTAATTT
* *
662565 AAAAAT-ATATATTTTATTCTTA
1 AAAAATAATTTATTTTAATCTTA
662587 TCTAAACTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 17 0.40
27 26 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
AAAAATAATTTATTTTAATCTTAATTT
Found at i:662562 original size:57 final size:61
Alignment explanation
Indices: 662494--662745 Score: 188
Period size: 63 Copynumber: 4.2 Consensus size: 61
662484 TAAGAAATAT
* * *
662494 TTTTATATTAATTTATCAAA-A-ATATTTTATTATTAACTTAA-T-TTAAAAATA-A-TTTA
1 TTTTATTTTAATTTA-AAAATATATATTTTATTATTAACTAAACTATTAAAAATATATTTTA
* *
662550 TTTTAATTTTAATTTAAAAATATATATTTTATTCTTATCTAAACTATTAAAAATATATTTTA
1 TTTT-ATTTTAATTTAAAAATATATATTTTATTATTAACTAAACTATTAAAAATATATTTTA
* * *
662612 TTATTATTTTAACTATTTAAAGTATATATATTTTA-TATTAA-T---TTATT--AAATATATTAT
1 TT-TTATTTT-A--ATTTAAA-AATATATATTTTATTATTAACTAAACTATTAAAAATATATTTT
662670 A
61 A
* * * * ** *
662671 TTATTACTTTAAATTATTAAATATATATTTTATTCTTTTCTAAACTTTTAAAAATATATTTTA
1 TT-TTATTTTAATTTA-AAAATATATATTTTATTATTAACTAAACTATTAAAAATATATTTTA
662734 TTATTATTTTAA
1 TT-TTATTTTAA
662746 CTTTTCAAAG
Statistics
Matches: 155, Mismatches: 21, Indels: 33
0.74 0.10 0.16
Matches are distributed among these distances:
56 23 0.15
57 15 0.10
58 19 0.12
59 21 0.14
60 9 0.06
61 8 0.05
62 11 0.07
63 25 0.16
64 1 0.01
65 11 0.07
66 12 0.08
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (61 bp):
TTTTATTTTAATTTAAAAATATATATTTTATTATTAACTAAACTATTAAAAATATATTTTA
Found at i:662690 original size:30 final size:29
Alignment explanation
Indices: 662571--662817 Score: 143
Period size: 30 Copynumber: 8.2 Consensus size: 29
662561 ATTTAAAAAT
* * * *
662571 ATATATTTTATTCTTATCTAAACTATTAAAA
1 ATATATTATATTATTATTTAAATTATT--AA
* * *
662602 ATATATTTTATTATTATTTTAACTATTTAA
1 ATATATTATATTATTATTTAAATTA-TTAA
*
662632 AGTATA-TATATT-TTATATTAATTTATTAA
1 A-TATATTATATTATTAT-TTAAATTATTAA
662661 ATATATTATATTATTACTTTAAATTATTAA
1 ATATATTATATTATTA-TTTAAATTATTAA
* *
662691 ATATA-TATTTTATTCTTTTCTAAACTT-TTAAAA
1 ATATATTATATTA-T-TATT-TAAA-TTATT--AA
* *
662724 ATATATTTTATTATTATTTTAACTT-TTCAA
1 ATATATTATATTATTA-TTTAAATTATT-AA
* * *
662754 A-GT-TTACATT-TTATATT-AATTCAGTAA
1 ATATATTATATTATTAT-TTAAATT-ATTAA
662781 ATATATTATATTATTACTTTAAATTATTAA
1 ATATATTATATTATTA-TTTAAATTATTAA
662811 ATATATT
1 ATATATT
662818 TTTATTCTTA
Statistics
Matches: 171, Mismatches: 23, Indels: 45
0.72 0.10 0.19
Matches are distributed among these distances:
26 4 0.02
27 8 0.05
28 11 0.06
29 28 0.16
30 54 0.32
31 43 0.25
32 8 0.05
33 10 0.06
34 5 0.03
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (29 bp):
ATATATTATATTATTATTTAAATTATTAA
Found at i:662729 original size:91 final size:93
Alignment explanation
Indices: 662534--662729 Score: 224
Period size: 91 Copynumber: 2.2 Consensus size: 93
662524 TATTAACTTA
* * * *
662534 ATTTAAAAATA-ATTTATTTTAATTTTAATTTAAAAATATATATTTTATTCTTATCTAAACTATT
1 ATTTAAAAATATATATATTTTAATATTAATTTAAAAATATATATTATATTATTATCTAAACTATT
*
662598 AAAAATATATTTTATTATTATTTTAACT
66 AAAAATATATTTTATTATTATTTAAACT
* ** * *
662626 ATTT-AAAGTATATATATTTT-ATATTAATTTATTAA-ATATATTATATTATTACTTTAAATTAT
1 ATTTAAAAATATATATATTTTAATATTAATTTAAAAATATATATTATATTATTA-TCTAAACTAT
* *
662688 TAAATATATATTTTATTCTT-TTCTAAACT
65 TAAAAATATATTTTATTATTATT-TAAACT
662717 -TTTAAAAATATAT
1 ATTTAAAAATATAT
662730 TTTATTATTA
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
90 19 0.22
91 56 0.64
92 12 0.14
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.54
Consensus pattern (93 bp):
ATTTAAAAATATATATATTTTAATATTAATTTAAAAATATATATTATATTATTATCTAAACTATT
AAAAATATATTTTATTATTATTTAAACT
Found at i:662748 original size:31 final size:31
Alignment explanation
Indices: 662511--662750 Score: 182
Period size: 31 Copynumber: 8.0 Consensus size: 31
662501 TTAATTTATC
**
662511 AAAA-ATATTTTATTATTAACTTAA--TTTA
1 AAAATATATTTTATTATTATTTTAACTTTTA
*
662539 AAAATA-A-TTTATT-TTAATTTTAA-TTTAA
1 AAAATATATTTTATTATT-ATTTTAACTTTTA
* * * *
662567 AAATATATATTTTATTCTTATCTAAACTATTA
1 AAA-ATATATTTTATTATTATTTTAACTTTTA
662599 AAAATATATTTTATTATTATTTTAACTATTT-
1 AAAATATATTTTATTATTATTTTAACT-TTTA
* * *
662630 AAAGTATA-TATATT-TTATATTAA--TTTA
1 AAAATATATTTTATTATTATTTTAACTTTTA
* * * *
662657 TTAAATATATTATATTATTACTTTAAATTATTA
1 -AAAATATATTTTATTATTATTTTAACTT-TTA
* * *
662690 AATATATATTTTATTCTT-TTCTAAACTTTTA
1 AAAATATATTTTATTATTATT-TTAACTTTTA
662721 AAAATATATTTTATTATTATTTTAACTTTT
1 AAAATATATTTTATTATTATTTTAACTTTT
662751 CAAAGTTTAC
Statistics
Matches: 166, Mismatches: 28, Indels: 33
0.73 0.12 0.15
Matches are distributed among these distances:
26 5 0.03
27 11 0.07
28 17 0.10
29 18 0.11
30 13 0.08
31 67 0.40
32 32 0.19
33 3 0.02
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (31 bp):
AAAATATATTTTATTATTATTTTAACTTTTA
Found at i:662806 original size:120 final size:122
Alignment explanation
Indices: 662567--662829 Score: 444
Period size: 122 Copynumber: 2.2 Consensus size: 122
662557 TTTAATTTAA
662567 AAATATATATTTTATTCTTATCTAAACTATTAAAAATATATTTTATTATTATTTTAACTATTTAA
1 AAATATATATTTTATTCTTATCTAAACTATTAAAAATATATTTTATTATTATTTTAACTATTTAA
* * *
662632 AGTATATATATTTTATATTAATTTATTAAATATATTATATTATTACTTTAAATTATT
66 AGTATATACATTTTATATTAATTCAGTAAATATATTATATTATTACTTTAAATTATT
* *
662689 AAATATATATTTTATTCTTTTCTAAACTTTTAAAAATATATTTTATTATTATTTTAACT-TTTCA
1 AAATATATATTTTATTCTTATCTAAACTATTAAAAATATATTTTATTATTATTTTAACTATTT-A
662753 AAGT-T-TACATTTTATATTAATTCAGTAAATATATTATATTATTACTTTAAATTATT
65 AAGTATATACATTTTATATTAATTCAGTAAATATATTATATTATTACTTTAAATTATT
662809 AAATATAT-TTTTATTCTTATC
1 AAATATATATTTTATTCTTATC
662830 CTAAGTTCAA
Statistics
Matches: 134, Mismatches: 6, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
119 12 0.09
120 56 0.42
121 4 0.03
122 62 0.46
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (122 bp):
AAATATATATTTTATTCTTATCTAAACTATTAAAAATATATTTTATTATTATTTTAACTATTTAA
AGTATATACATTTTATATTAATTCAGTAAATATATTATATTATTACTTTAAATTATT
Found at i:662877 original size:18 final size:19
Alignment explanation
Indices: 662841--662902 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
662831 TAAGTTCAAA
662841 ATATTTTAACATAAAATAT
1 ATATTTTAACATAAAATAT
662860 ATATTTTAACAT--AA-AT
1 ATATTTTAACATAAAATAT
662876 ATATTTT-ACAATAAAATAT
1 ATATTTTAAC-ATAAAATAT
*
662895 ATAATTTA
1 ATATTTTA
662903 TTAAAAGTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
15 2 0.05
16 11 0.30
17 2 0.05
18 2 0.05
19 20 0.54
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTTTAACATAAAATAT
Found at i:669917 original size:13 final size:13
Alignment explanation
Indices: 669895--669927 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
669885 AAAGAAAAGG
669895 AAAAAA-AAAATA
1 AAAAAATAAAATA
*
669907 ACAAAATAAAATA
1 AAAAAATAAAATA
669920 AAAAAATA
1 AAAAAATA
669928 TGTAGCTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:670960 original size:15 final size:14
Alignment explanation
Indices: 670875--670961 Score: 56
Period size: 15 Copynumber: 6.2 Consensus size: 14
670865 TCGGGCCGGG
670875 TATATATATTTAAAT
1 TATATATA-TTAAAT
* *
670890 TAAATATATATATAT
1 TATATATAT-TAAAT
*
670905 TATATATATT--TT
1 TATATATATTAAAT
*
670917 TTTA-AT-TTAAAT
1 TATATATATTAAAT
* *
670929 TAAATTTATTAATAT
1 TATATATATTAA-AT
670944 TATATATATATAAAT
1 TATATATAT-TAAAT
670959 TAT
1 TAT
670962 TTTTAATATT
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
10 2 0.04
11 2 0.04
12 7 0.13
13 1 0.02
14 6 0.11
15 33 0.61
16 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATATATTAAAT
Found at i:671072 original size:36 final size:36
Alignment explanation
Indices: 671019--671132 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
671009 TTACTAAACT
* * *
671019 CGTCCCCATCCCTGTTTAACATAAACGGTTTTTCCT
1 CGTCCCCGTCCCCGTTTAACATAAACGGTTTTTCCC
* *
671055 CGTTCCCGTCTCCGTTTAACATAAACGGTTTTTCCC
1 CGTCCCCGTCCCCGTTTAACATAAACGGTTTTTCCC
*
671091 CGTCCCCGTCCCCGTTTAACATAAACGATTTTTCCC
1 CGTCCCCGTCCCCGTTTAACATAAACGGTTTTTCCC
*
671127 CATCCC
1 CGTCCC
671133 GCTTAATTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.18, C:0.37, G:0.11, T:0.33
Consensus pattern (36 bp):
CGTCCCCGTCCCCGTTTAACATAAACGGTTTTTCCC
Found at i:672865 original size:33 final size:33
Alignment explanation
Indices: 672823--672934 Score: 188
Period size: 33 Copynumber: 3.4 Consensus size: 33
672813 ATAAACAAGT
*
672823 CATGATGGATGGATCTATGCATGTAACGTATGG
1 CATGATGGATGGATCTATGCATGTGACGTATGG
*
672856 CATGATGGATGGATCTATGCATGTGACGTATGA
1 CATGATGGATGGATCTATGCATGTGACGTATGG
*
672889 CATGATGGATGAATCTATGCATGTGACGTATGG
1 CATGATGGATGGATCTATGCATGTGACGTATGG
*
672922 CATGATGCATGGA
1 CATGATGGATGGA
672935 AACAAAAACA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.29
Consensus pattern (33 bp):
CATGATGGATGGATCTATGCATGTGACGTATGG
Found at i:673321 original size:33 final size:33
Alignment explanation
Indices: 673281--673346 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
673271 ATTTGAAAGA
673281 ATAATAATTACTAAGGTCAATTAATAAGATTTT
1 ATAATAATTACTAAGGTCAATTAATAAGATTTT
673314 ATAATAATTACTAAGGTCAATTAATAAGATTTT
1 ATAATAATTACTAAGGTCAATTAATAAGATTTT
673347 CAGCCCATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (33 bp):
ATAATAATTACTAAGGTCAATTAATAAGATTTT
Found at i:689825 original size:16 final size:16
Alignment explanation
Indices: 689804--689836 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
689794 TAATAAATAA
689804 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
689820 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
689836 A
1 A
689837 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:689918 original size:13 final size:13
Alignment explanation
Indices: 689900--689940 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
689890 TCATTTAATA
689900 AATAAACGAAAAC
1 AATAAACGAAAAC
**
689913 AATAAACGAACTC
1 AATAAACGAAAAC
689926 AATAAACGAACAAC
1 AATAAACGAA-AAC
689940 A
1 A
689941 CAAAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 21 0.91
14 2 0.09
ACGTcount: A:0.63, C:0.20, G:0.07, T:0.10
Consensus pattern (13 bp):
AATAAACGAAAAC
Found at i:715871 original size:21 final size:23
Alignment explanation
Indices: 715846--715901 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 23
715836 GACCCAACAC
715846 AAAATAATATATTTTT-TT-AA-A
1 AAAATAAT-TATTTTTATTCAATA
715867 AAAAT-ATTATTTTTATTCAATA
1 AAAATAATTATTTTTATTCAATA
*
715889 AAAATAAGTATTT
1 AAAATAATTATTT
715902 AATTCAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 7 0.23
22 6 0.20
23 6 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
AAAATAATTATTTTTATTCAATA
Found at i:721673 original size:37 final size:38
Alignment explanation
Indices: 721621--721706 Score: 140
Period size: 38 Copynumber: 2.3 Consensus size: 38
721611 TTTATTTTGT
721621 TCGGGTC-GGTCGGG-TTTTTTAAGTATGATATTCGGG
1 TCGGGTCGGGTCGGGTTTTTTTAAGTATGATATTCGGG
*
721657 TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGTCGGGTTTTTTTAAGTATGATATTCGGG
721695 TCGGGTTCGGGT
1 TCGGG-TCGGGT
721707 TTAGGGTGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 7 0.15
37 7 0.15
38 26 0.57
39 6 0.13
ACGTcount: A:0.10, C:0.12, G:0.40, T:0.38
Consensus pattern (38 bp):
TCGGGTCGGGTCGGGTTTTTTTAAGTATGATATTCGGG
Found at i:721815 original size:253 final size:253
Alignment explanation
Indices: 721398--722014 Score: 950
Period size: 253 Copynumber: 2.4 Consensus size: 253
721388 ACTTTATTTT
*
721398 GGTCGGGTCGGATCAGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTG
1 GGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTC--G--G-GTTCGGGTTTAGGGTG
*
721463 -AAAAAACTGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTT
61 AAAAAAACCGGACCGA-CCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTT
* *
721527 ATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTT
125 ATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGAATTTCTAATTCATATATTC
* * *
721592 GGGTTGGGTCGGATGAAACTTTATTTTGTTCGGGTC-GGTCGGGTTTTTTAAGTATGATATTCG
190 GGGTCGGGTCGGATGAAACCTTATTTTGTTCGAGTCGGGTCGGGTTTTTTAAGTATGATATTCG
*
721655 GGTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAA
1 GGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAA
721720 AACCGGACCGACCTGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAA
66 AACCGGACCGACC-GAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAA
721785 ATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGAATTTCTAATTCATATATTCGGGTC
130 ATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGAATTTCTAATTCATATATTCGGGTC
*
721850 GGGTCGGATGAAACCTTATTTTGTTCGAGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
195 GGGTCGGATGAAACCTTATTTTGTTCGAGTCGGGTCGGGTTTTTTAAGTATGATATTCG
*
721909 GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTCAGGTCAGGTCGGGTCGGGTTCGGGTTTA
1 GGTCGGGTCGGATCGGGTTTTTTTAAGTGTG--A-T-A--T----TCGGGTCGGGTTCGGGTTTA
*
721974 GGGTGAAAAAACCCGGACCGATCCGAAAAATATATATAATT
56 GGGTGAAAAAAACCGGACCGA-CCG-AAAATATATATAATT
722015 TTACCTTATA
Statistics
Matches: 333, Mismatches: 12, Indels: 22
0.91 0.03 0.06
Matches are distributed among these distances:
252 18 0.05
253 157 0.47
254 55 0.17
255 1 0.00
256 1 0.00
257 41 0.12
258 1 0.00
260 1 0.00
264 41 0.12
265 17 0.05
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.35
Consensus pattern (253 bp):
GGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAA
AACCGGACCGACCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAA
TAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGAATTTCTAATTCATATATTCGGGTCG
GGTCGGATGAAACCTTATTTTGTTCGAGTCGGGTCGGGTTTTTTAAGTATGATATTCG
Found at i:721940 original size:38 final size:38
Alignment explanation
Indices: 721874--721965 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 38
721864 CTTATTTTGT
*
721874 TCGAGTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGG
1 TCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGG
*
721911 TCGAGTCGGATCGGGTTTTTTTAAGTGTGATATTCAGG
1 TCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGG
721949 TC-AGGTCGGGTCGGGTT
1 TCGA-GTCGGGTCGGGTT
721966 CGGGTTTAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
37 15 0.30
38 35 0.70
ACGTcount: A:0.14, C:0.12, G:0.37, T:0.37
Consensus pattern (38 bp):
TCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGG
Found at i:722569 original size:16 final size:18
Alignment explanation
Indices: 722543--722587 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
722533 TATGGAATTG
*
722543 GATTACAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
*
722559 TATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
722577 GATTCCAATTC
1 GATTCCAATTC
722588 TCTCATAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 1 0.04
18 13 0.54
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:723770 original size:45 final size:45
Alignment explanation
Indices: 723705--723818 Score: 165
Period size: 45 Copynumber: 2.5 Consensus size: 45
723695 AGTCATAAAT
723705 AATATATATATATAGTTTTGAAAATATGGTTTTTGAAAATAATATA
1 AATATAT-TATATAGTTTTGAAAATATGGTTTTTGAAAATAATATA
* * *
723751 AATATATTATATAGTTTTGAAATTTTGGTTTTTGAAAGTAATATA
1 AATATATTATATAGTTTTGAAAATATGGTTTTTGAAAATAATATA
* *
723796 AATATTATTGTATAGTTTGGAAA
1 AATA-TATTATATAGTTTTGAAA
723819 TCAAGGTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 39 0.63
46 23 0.37
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (45 bp):
AATATATTATATAGTTTTGAAAATATGGTTTTTGAAAATAATATA
Found at i:723901 original size:7 final size:7
Alignment explanation
Indices: 723891--723927 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
723881 AAGTATTAAG
723891 TATATGT
1 TATATGT
723898 TATATGT
1 TATATGT
723905 TATATG-
1 TATATGT
723911 T-T-TGT
1 TATATGT
723916 TATATGT
1 TATATGT
723923 TATAT
1 TATAT
723928 TTAATTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 2 0.07
5 2 0.07
6 2 0.07
7 21 0.78
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (7 bp):
TATATGT
Found at i:737059 original size:23 final size:23
Alignment explanation
Indices: 737029--737073 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
737019 GAATGACCAC
737029 ATAGGTTTGCACTGAAGTGCCAA
1 ATAGGTTTGCACTGAAGTGCCAA
737052 ATAGGTTTGCACTGAAGTGCCA
1 ATAGGTTTGCACTGAAGTGCCA
737074 CATAATTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (23 bp):
ATAGGTTTGCACTGAAGTGCCAA
Found at i:737097 original size:21 final size:21
Alignment explanation
Indices: 737071--737120 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
737061 CACTGAAGTG
*
737071 CCACATAATTGTCCCAAAGGA
1 CCACATAATTATCCCAAAGGA
* *
737092 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCAAAGGA
737113 CCACATAA
1 CCACATAA
737121 ACCATCAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (21 bp):
CCACATAATTATCCCAAAGGA
Found at i:737619 original size:160 final size:163
Alignment explanation
Indices: 737421--737745 Score: 588
Period size: 160 Copynumber: 2.0 Consensus size: 163
737411 TCAGATTAAA
737421 ACATTTATTCATGGCATCTTTTCACAAAGCATTAATCATTATTTTCATTTAATCACATATATAAT
1 ACATTTATTCATGGCATCTTTTCACAAAGCATTAATCATTATTTTCATTTAATCACATATATAAT
737486 AAA-TCATAGTGA-TTACATAATTATTTCATATTACATATCATTATTCAACATATTCATTTAC-T
66 AAATTCATAGTGATTTACATAATTATTTCATATTACATATCATTATTCAACATATTCATTTACTT
737548 GTAT-AAACATAATC-ATAGAAAATCTTCACAT
131 GTATAAAACATAATCAATAGAAAATCTTCACAT
737579 ACATTTATTCATGGCATCTTGTTTCACAAAGCATTAATCATTATTTTCATTTAATCACATATATA
1 ACATTTATTCATGGCATC-T-TTTCACAAAGCATTAATCATTATTTTCATTTAATCACATATATA
737644 ATAAATTCATAGTGATTTACATAATTATTTCATATTACATATCATTATTCAACATATTCATTTAC
64 ATAAATTCATAGTGATTTACATAATTATTTCATATTACATATCATTATTCAACATATTCATTTAC
737709 TTGTATAAAACATAATCATATAGAAAATCTTCACAT
129 TTGTATAAAACATAATCA-ATAGAAAATCTTCACAT
737745 A
1 A
737746 TAATCATATC
Statistics
Matches: 159, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
158 18 0.11
159 1 0.01
160 49 0.31
161 9 0.06
162 49 0.31
163 5 0.03
164 10 0.06
166 18 0.11
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (163 bp):
ACATTTATTCATGGCATCTTTTCACAAAGCATTAATCATTATTTTCATTTAATCACATATATAAT
AAATTCATAGTGATTTACATAATTATTTCATATTACATATCATTATTCAACATATTCATTTACTT
GTATAAAACATAATCAATAGAAAATCTTCACAT
Found at i:744719 original size:13 final size:13
Alignment explanation
Indices: 744703--744737 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
744693 TAAGATTTTC
744703 TTTTTGAAAATCA
1 TTTTTGAAAATCA
744716 TTTTTG-AAATCA
1 TTTTTGAAAATCA
744728 TTTTTGAAAA
1 TTTTTGAAAA
744738 ATTACTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:745046 original size:15 final size:15
Alignment explanation
Indices: 745021--745063 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
745011 TCAAACCATT
745021 CAAATCCAAAACAAA
1 CAAATCCAAAACAAA
* * *
745036 CATATCTAAAACACA
1 CAAATCCAAAACAAA
745051 CAAATCCAAAACA
1 CAAATCCAAAACA
745064 TTCAAAATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (15 bp):
CAAATCCAAAACAAA
Found at i:745069 original size:15 final size:15
Alignment explanation
Indices: 745021--745069 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
745011 TCAAACCATT
*
745021 CAAATCCAAAACAAA
1 CAAATCCAAAACATA
* * *
745036 CATATCTAAAACACA
1 CAAATCCAAAACATA
*
745051 CAAATCCAAAACATT
1 CAAATCCAAAACATA
745066 CAAA
1 CAAA
745070 ATGTTTTAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (15 bp):
CAAATCCAAAACATA
Done.