Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 15 of 352
Found at i:4698125 original size:33 final size:33
Alignment explanation
Indices: 4698056--4698153 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
4698046 CTATACCCAT
* * *
4698056 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
4698093 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
4698126 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
4698154 ACATATCTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:4698413 original size:41 final size:41
Alignment explanation
Indices: 4698368--4698523 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
4698358 ACCGGCTCTT
*
4698368 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
4698409 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
4698450 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
4698491 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
4698524 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:4699030 original size:21 final size:23
Alignment explanation
Indices: 4699006--4699053 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
4698996 AATATATATA
4699006 TATTTC-AC-TCATACTTTTAAT
1 TATTTCAACATCATACTTTTAAT
*
4699027 TATTTCAACTATCATATTTTTAAT
1 TATTTCAAC-ATCATACTTTTAAT
4699051 TAT
1 TAT
4699054 ATTTCATCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
24 15 0.65
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTCAACATCATACTTTTAAT
Found at i:4707354 original size:27 final size:24
Alignment explanation
Indices: 4707314--4707380 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 24
4707304 TGATTTTTTA
**
4707314 ATATTTTAAAAATTTTCTATATATTT
1 ATATTTTTTAAATTTTCTATA-A-TT
* *
4707340 ATTATTTTTTTAATTTTGTATAATT
1 A-TATTTTTTAAATTTTCTATAATT
4707365 ATATTTTTTAAATTTT
1 ATATTTTTTAAATTTT
4707381 AGAAGAATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 14 0.40
25 3 0.09
26 2 0.06
27 16 0.46
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (24 bp):
ATATTTTTTAAATTTTCTATAATT
Found at i:4708572 original size:29 final size:28
Alignment explanation
Indices: 4708509--4708571 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 28
4708499 CAAATACTTA
4708509 TTTTTGTAATTAATTTATTTTTCATATAT
1 TTTTTGTAATTAATTTATTTTT-ATATAT
*
4708538 TTTTTGTAATTAATTATTACTTTTATATTAT
1 TTTTTGTAATTAA-T-TTATTTTTATA-TAT
4708569 TTT
1 TTT
4708572 GATAAAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 13 0.43
30 4 0.13
31 13 0.43
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTTTGTAATTAATTTATTTTTATATAT
Found at i:4708696 original size:20 final size:18
Alignment explanation
Indices: 4708658--4708698 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
4708648 AAATATATCA
4708658 TAATCTTATAAACAAAAT
1 TAATCTTATAAACAAAAT
*
4708676 TAATCATTATAAAACATAAT
1 TAATC-TTAT-AAACAAAAT
4708696 TAA
1 TAA
4708699 ATATCTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 4 0.20
20 11 0.55
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATCTTATAAACAAAAT
Found at i:4711526 original size:26 final size:25
Alignment explanation
Indices: 4711470--4711530 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
4711460 AATTGTTTTA
*
4711470 ATATTTGTTT-TTATGTTTTTAAAT
1 ATATTTATTTATTATGTTTTTAAAT
*
4711494 ATATTTAATTTATTATTTTTTTAAAT
1 ATATTT-ATTTATTATGTTTTTAAAT
* *
4711520 TTTTTTATTTA
1 ATATTTATTTA
4711531 ATGAAATAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (25 bp):
ATATTTATTTATTATGTTTTTAAAT
Found at i:4711958 original size:45 final size:44
Alignment explanation
Indices: 4711892--4711978 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 44
4711882 TGGCTAGATC
4711892 TAAAGAAAAATTTTACATTTCAAAATTAGT-GCAAAGCATAACAAA
1 TAAAGAAAAATTTTACATTTCAAAA-TAGTAG-AAAGCATAACAAA
* *
4711937 TAAAGTAAAAA-TTTACTTTTCAAAATAGTAGAAATCATAACA
1 TAAAG-AAAAATTTTACATTTCAAAATAGTAGAAAGCATAACA
4711979 TTTAATCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
44 14 0.37
45 19 0.50
46 5 0.13
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (44 bp):
TAAAGAAAAATTTTACATTTCAAAATAGTAGAAAGCATAACAAA
Found at i:4715325 original size:2 final size:2
Alignment explanation
Indices: 4715320--4715345 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4715310 ATATATACAT
4715320 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
4715346 CAAAGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4718628 original size:16 final size:17
Alignment explanation
Indices: 4718596--4718628 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4718586 TAATTTAGTA
*
4718596 AAATCCAAATAATTTAC
1 AAATACAAATAATTTAC
4718613 AAATACAAAT-ATTTAC
1 AAATACAAATAATTTAC
4718629 CGATTGCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATACAAATAATTTAC
Found at i:4721009 original size:27 final size:26
Alignment explanation
Indices: 4720929--4721014 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 26
4720919 ATCGTCGTCG
*
4720929 TCATCTGCAGCAGCACCAACACAATCA
1 TCATCTGCAACAG-ACCAACACAATCA
* * * *
4720956 GCAGCTGCAAC-GACACCACTACCATCA
1 TCATCTGCAACAGAC-CAAC-ACAATCA
*
4720983 TCATCTGCACCAGTACCAACACAATCA
1 TCATCTGCAACAG-ACCAACACAATCA
*
4721010 CCATC
1 TCATC
4721015 ACAATCAGCA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
25 2 0.05
26 4 0.09
27 32 0.73
28 4 0.09
29 2 0.05
ACGTcount: A:0.35, C:0.40, G:0.10, T:0.15
Consensus pattern (26 bp):
TCATCTGCAACAGACCAACACAATCA
Found at i:4721048 original size:27 final size:29
Alignment explanation
Indices: 4720970--4721048 Score: 74
Period size: 33 Copynumber: 2.6 Consensus size: 29
4720960 CTGCAACGAC
*
4720970 ACCACTACCATCATCATCTGCACCAGTACCA
1 ACCA-TACCATCATCATCAGCACCA-TACCA
4721001 ACACAATCACCATCA-CAATCAGCACC-TA-CA
1 AC-C-AT-ACCATCATC-ATCAGCACCATACCA
4721031 ACCATACCATCATCATCA
1 ACCATACCATCATCATCA
4721049 TCTGCAACAA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
27 11 0.26
28 3 0.07
29 1 0.02
30 4 0.10
31 4 0.10
32 3 0.07
33 16 0.38
ACGTcount: A:0.38, C:0.41, G:0.04, T:0.18
Consensus pattern (29 bp):
ACCATACCATCATCATCAGCACCATACCA
Found at i:4721092 original size:30 final size:30
Alignment explanation
Indices: 4721011--4721099 Score: 76
Period size: 30 Copynumber: 3.0 Consensus size: 30
4721001 ACACAATCAC
* * *
4721011 CATCACAATCAGCACCTACAACCAT-ACCAT
1 CATCACAATCATCAACTACAA-CATCAACAT
*
4721041 CATCATC-ATC-TGCAACAACAACATCAACAT
1 CATCA-CAATCAT-CAACTACAACATCAACAT
* *
4721071 CATCACAATCATCATCTACAACAGCAACA
1 CATCACAATCATCAACTACAACATCAACA
4721100 CCAGCTCCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
29 4 0.09
30 41 0.87
31 2 0.04
ACGTcount: A:0.43, C:0.36, G:0.03, T:0.18
Consensus pattern (30 bp):
CATCACAATCATCAACTACAACATCAACAT
Found at i:4721114 original size:36 final size:36
Alignment explanation
Indices: 4721042--4721117 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
4721032 CCATACCATC
* * *
4721042 ATCATCATCTGCAACAACAACATCAACATCATCACA
1 ATCATCATCTACAACAACAACACCAACATCAACACA
* *
4721078 ATCATCATCTACAACAGCAACACCAGC-TCCAACACA
1 ATCATCATCTACAACAACAACACCAACAT-CAACACA
4721114 ATCA
1 ATCA
4721118 GCGGCTACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.43, C:0.36, G:0.04, T:0.17
Consensus pattern (36 bp):
ATCATCATCTACAACAACAACACCAACATCAACACA
Found at i:4721415 original size:15 final size:15
Alignment explanation
Indices: 4721395--4721426 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4721385 TCACCGTCGC
4721395 CATCACCAGCACCAG
1 CATCACCAGCACCAG
*
4721410 CATCACCAGTACCAG
1 CATCACCAGCACCAG
4721425 CA
1 CA
4721427 ACGACAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.44, G:0.12, T:0.09
Consensus pattern (15 bp):
CATCACCAGCACCAG
Found at i:4722825 original size:16 final size:16
Alignment explanation
Indices: 4722804--4722838 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4722794 TAAATAAATT
4722804 ATTAAAAAT-TTATAAA
1 ATTAAAAATATTA-AAA
4722820 ATTAAAAATATTAAAA
1 ATTAAAAATATTAAAA
4722836 ATT
1 ATT
4722839 CGATTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTAAAAATATTAAAA
Found at i:4723688 original size:18 final size:19
Alignment explanation
Indices: 4723653--4723692 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
4723643 AAAATTAAGA
4723653 AAAAATATATTATAAAAAT
1 AAAAATATATTATAAAAAT
4723672 AAAAATAT-TTA-ATAAAAT
1 AAAAATATATTATA-AAAAT
4723690 AAA
1 AAA
4723693 TTTTGAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.05
18 11 0.55
19 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATATATTATAAAAAT
Found at i:4724681 original size:59 final size:59
Alignment explanation
Indices: 4724543--4724696 Score: 163
Period size: 59 Copynumber: 2.6 Consensus size: 59
4724533 TTTCACATTT
* * *
4724543 TTTTTTAATTTAGTACCTAA-TTTTTTTTTTCTAATTTTGATACTTGAACTTGACACAA
1 TTTTCTAATCTAGTACCTAAGTTTTTTTTTTCTAATTTTGATAATTGAACTTGACACAA
* * * *
4724601 TTTTCTAATCTAGTGCTTAAGTTTTTTTTTGTCTAA-TTTGATAATTGAACTTGGCAC-T
1 TTTTCTAATCTAGTACCTAAGTTTTTTTTT-TCTAATTTTGATAATTGAACTTGACACAA
* * *
4724659 TTTTCCT-ATTTTGATACCTAAGTTTTTTTTTTCAAATT
1 TTTT-CTAATCTAG-TACCTAAGTTTTTTTTTTCTAATT
4724697 ACTCCATAAC
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
58 28 0.35
59 46 0.58
60 5 0.06
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (59 bp):
TTTTCTAATCTAGTACCTAAGTTTTTTTTTTCTAATTTTGATAATTGAACTTGACACAA
Found at i:4724685 original size:58 final size:59
Alignment explanation
Indices: 4724543--4724688 Score: 147
Period size: 58 Copynumber: 2.5 Consensus size: 59
4724533 TTTCACATTT
* * * *
4724543 TTTTTTAATTTAGTACCTAA-TTTTTTTTTTCTAATTTTGATACTTGAACTTGACACAA
1 TTTTCTAATCTAGTACCTAAGTTTTTTTTGTCTAATTTTGATAATTGAACTTGACACAA
* * * *
4724601 TTTTCTAATCTAGTGCTTAAGTTTTTTTTTGTCTAA-TTTGATAATTGAACTTGGCAC-T
1 TTTTCTAATCTAGTACCTAAG-TTTTTTTTGTCTAATTTTGATAATTGAACTTGACACAA
* *
4724659 TTTTCCT-ATTTTGATACCTAAGTTTTTTTT
1 TTTT-CTAATCTAG-TACCTAAGTTTTTTTT
4724689 TTCAAATTAC
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
58 32 0.44
59 27 0.38
60 13 0.18
ACGTcount: A:0.23, C:0.12, G:0.10, T:0.55
Consensus pattern (59 bp):
TTTTCTAATCTAGTACCTAAGTTTTTTTTGTCTAATTTTGATAATTGAACTTGACACAA
Found at i:4725311 original size:28 final size:28
Alignment explanation
Indices: 4725269--4725339 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
4725259 GTTCATATAT
* * * *
4725269 CAAATTAAGAAAAAATTTAAGTTTAGATAC
1 CAAATTAGGAAAAAA-TAAACTTAAG-TAC
4725299 CAAATT-GGAAAAAATAAACTTAAGTAC
1 CAAATTAGGAAAAAATAAACTTAAGTAC
4725326 CAAATTAGGAAAAA
1 CAAATTAGGAAAAA
4725340 GTATCATGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.25
28 14 0.39
29 7 0.19
30 6 0.17
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.24
Consensus pattern (28 bp):
CAAATTAGGAAAAAATAAACTTAAGTAC
Found at i:4730667 original size:23 final size:20
Alignment explanation
Indices: 4730640--4730688 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
4730630 AATATTTTTT
*
4730640 ATTTATTTTTATGAATTTAATTA
1 ATTTATTTTT-TGAAATTAA--A
*
4730663 ATTTACTTTTTGAAATTAAA
1 ATTTATTTTTTGAAATTAAA
4730683 ATTTAT
1 ATTTAT
4730689 GTCTATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.26
22 8 0.35
23 9 0.39
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTTATTTTTTGAAATTAAA
Found at i:4739985 original size:19 final size:19
Alignment explanation
Indices: 4739961--4740001 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4739951 TAGAAAATTA
4739961 TATTTTTACAAAGAT-TTTT
1 TATTTTT-CAAAGATATTTT
*
4739980 TATTTTTTAAAGATATTTT
1 TATTTTTCAAAGATATTTT
4739999 TAT
1 TAT
4740002 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
TATTTTTCAAAGATATTTT
Found at i:4741388 original size:24 final size:24
Alignment explanation
Indices: 4741361--4741441 Score: 60
Period size: 24 Copynumber: 3.5 Consensus size: 24
4741351 AATACAAATC
4741361 AATATAATTTTATTAATATATACT
1 AATATAATTTTATTAATATATACT
* * * * **
4741385 AATA-AA-ATAATAAACA-AGTTTT
1 AATATAATTTTATTAATATA-TACT
*
4741407 AAGATAATTTTATTAATATATACT
1 AATATAATTTTATTAATATATACT
*
4741431 AATAGAATTTT
1 AATATAATTTT
4741442 TATGAGAAGA
Statistics
Matches: 38, Mismatches: 15, Indels: 8
0.62 0.25 0.13
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 4 0.11
24 21 0.55
25 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
AATATAATTTTATTAATATATACT
Found at i:4741737 original size:15 final size:16
Alignment explanation
Indices: 4741717--4741758 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
4741707 GATAACAATA
*
4741717 TTAATATTAATTGAG-
1 TTAATATTAATCGAGC
4741732 TTAATATTCAATCGAGC
1 TTAATATT-AATCGAGC
4741749 TTAATTATTA
1 TTAA-TATTA
4741759 TTATTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 6 0.26
17 5 0.22
18 4 0.17
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (16 bp):
TTAATATTAATCGAGC
Found at i:4753923 original size:27 final size:28
Alignment explanation
Indices: 4753884--4753939 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
4753874 TAAAAAACAA
* *
4753884 ATATATACTTAAGG-TGGAATGATATAT
1 ATATATACTTAAGGATGAAATGAAATAT
4753911 ATATATA-TATAAGGATGAAATGAAATAT
1 ATATATACT-TAAGGATGAAATGAAATAT
4753939 A
1 A
4753940 ACGTAGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.04
27 12 0.48
28 12 0.48
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (28 bp):
ATATATACTTAAGGATGAAATGAAATAT
Found at i:4759223 original size:19 final size:18
Alignment explanation
Indices: 4759200--4759254 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
4759190 ATTTTAAATG
4759200 ATTTAAACACTTTTTAAT
1 ATTTAAACACTTTTTAAT
* *
4759218 ATTTTAATATA-TATTTTATT
1 A-TTTAA-ACACT-TTTTAAT
4759238 ATTTAAACACTTTTTAA
1 ATTTAAACACTTTTTAA
4759255 CATTCACACA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
18 8 0.28
19 12 0.41
20 9 0.31
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTAAACACTTTTTAAT
Found at i:4759827 original size:19 final size:19
Alignment explanation
Indices: 4759805--4759859 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
4759795 AAATTTATGA
4759805 TAATTATTTATTATTATTT
1 TAATTATTTATTATTATTT
**
4759824 TAATTA-AAATTCATTATTT
1 TAATTATTTATT-ATTATTT
*
4759843 TTATTATTTGATTATTA
1 TAATTATTT-ATTATTA
4759860 ATATATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.11
19 18 0.64
20 4 0.14
21 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TAATTATTTATTATTATTT
Found at i:4763056 original size:2 final size:2
Alignment explanation
Indices: 4763051--4763093 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4763041 TTTTTGTTTT
4763051 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
4763093 T
1 T
4763094 TGGGTTTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:4771001 original size:19 final size:19
Alignment explanation
Indices: 4770962--4771001 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4770952 GTGTAAGGTG
*
4770962 ATAATAATATACAAATGTA
1 ATAATAATATACAAATATA
* *
4770981 ATAATAATATATATATATA
1 ATAATAATATACAAATATA
4771000 AT
1 AT
4771002 TGTAAAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAATAATATACAAATATA
Found at i:4771061 original size:27 final size:27
Alignment explanation
Indices: 4771009--4771066 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
4770999 AATTGTAAAA
* *
4771009 TAAATAATTAATTACTTTGTATTTAAG
1 TAAATAATTAATTACTTTGAAATTAAG
*
4771036 TAAATAATTATTTA-TTTGAAAATTAAG
1 TAAATAATTAATTACTTTG-AAATTAAG
4771063 TAAA
1 TAAA
4771067 ATATAATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (27 bp):
TAAATAATTAATTACTTTGAAATTAAG
Found at i:4773493 original size:18 final size:17
Alignment explanation
Indices: 4773467--4773520 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
4773457 AAAAATTCAA
*
4773467 TTTTTATTCAAAAATAC
1 TTTTAATTCAAAAATAC
*
4773484 TTTATAATTCAAAAATAA
1 TTT-TAATTCAAAAATAC
4773502 TTTTAA-T-AAACAATAC
1 TTTTAATTCAAA-AATAC
4773518 TTT
1 TTT
4773521 CAAATAACGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 3 0.09
16 8 0.25
17 6 0.19
18 15 0.47
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTAATTCAAAAATAC
Found at i:4773508 original size:17 final size:17
Alignment explanation
Indices: 4773465--4773508 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
4773455 AGAAAAATTC
*
4773465 AATTTTTATTCAAAAAT
1 AATTTTAATTCAAAAAT
*
4773482 ACTTTATAATTCAAAAAT
1 AATTT-TAATTCAAAAAT
4773500 AATTTTAAT
1 AATTTTAAT
4773509 AAACAATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTTAATTCAAAAAT
Found at i:4778262 original size:23 final size:23
Alignment explanation
Indices: 4778220--4778282 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
4778210 TAAAATAATG
* *
4778220 AAATTATAAATT-AATATAT-AAT
1 AAATTAT-AATTAAATTTATAAAA
*
4778242 AAATCTATATTTAAATTTATAAAA
1 AAAT-TATAATTAAATTTATAAAA
4778266 AAATTATAATTAAATTT
1 AAATTATAATTAAATTT
4778283 TCACTTTCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.21
23 21 0.62
24 6 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATTATAATTAAATTTATAAAA
Found at i:4778280 original size:11 final size:11
Alignment explanation
Indices: 4778214--4778281 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
4778204 TCCCTTTAAA
*
4778214 ATAATGAAATT
1 ATAATTAAATT
4778225 ATAAATT-AATAT
1 AT-AATTAAAT-T
4778237 ATAA-TAAATCT
1 ATAATTAAAT-T
*
4778248 ATATTTAAATTT
1 ATAATTAAA-TT
**
4778260 ATAAAAAAATT
1 ATAATTAAATT
4778271 ATAATTAAATT
1 ATAATTAAATT
4778282 TTCACTTTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
10 1 0.02
11 25 0.57
12 17 0.39
13 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
ATAATTAAATT
Found at i:4787867 original size:29 final size:27
Alignment explanation
Indices: 4787835--4787893 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
4787825 ATTTAATTAA
4787835 TATTTTAAAATTTAGAAAT-ATATAAAAAT
1 TATTTTAAAATTTA-AAATCAT-T-AAAAT
4787864 TATTTTAAAATTTAAAATCATTAAAAT
1 TATTTTAAAATTTAAAATCATTAAAAT
4787891 TAT
1 TAT
4787894 AAAAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 8 0.28
28 5 0.17
29 16 0.55
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
TATTTTAAAATTTAAAATCATTAAAAT
Found at i:4787879 original size:36 final size:35
Alignment explanation
Indices: 4787827--4787912 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 35
4787817 ACATTCGTAT
*
4787827 TTAATTAATATTTTAAAAT-TTAGAAA-TATATAAAAA
1 TTAATTAA-AATTTAAAATATTA-AAATTATA-AAAAA
*
4787863 TTATTTTAAAATTTAAAATCATTAAAATTATAAAAAA
1 TTA-ATTAAAATTTAAAAT-ATTAAAATTATAAAAAA
4787900 TTAATTAAAATTT
1 TTAATTAAAATTT
4787913 GACATGTCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
36 21 0.49
37 15 0.35
38 7 0.16
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
TTAATTAAAATTTAAAATATTAAAATTATAAAAAA
Found at i:4792186 original size:23 final size:22
Alignment explanation
Indices: 4792153--4792209 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
4792143 TTTTATGAAA
*
4792153 TAAAAAT-TAAA-TTATGAAAAC
1 TAAAAATATAAAGTCAT-AAAAC
4792174 TATAAAATATAAAGTCATAAAAC
1 TA-AAAATATAAAGTCATAAAAC
4792197 TAAAATATATAAA
1 TAAAA-ATATAAA
4792210 ATTAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 2 0.06
22 8 0.26
23 18 0.58
24 3 0.10
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (22 bp):
TAAAAATATAAAGTCATAAAAC
Found at i:4792215 original size:21 final size:22
Alignment explanation
Indices: 4792155--4792216 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
4792145 TTATGAAATA
*
4792155 AAAAT-TAAATTATGAAAACTAT
1 AAAATATAAAATAT-AAAACTAT
*
4792177 AAAATATAAAGTCATAAAACTA-
1 AAAATATAAAAT-ATAAAACTAT
4792199 AAATATATAAAAT-TAAAA
1 AAA-ATATAAAATATAAAA
4792217 AAATAAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 5 0.14
22 8 0.23
23 20 0.57
24 2 0.06
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (22 bp):
AAAATATAAAATATAAAACTAT
Found at i:4792218 original size:23 final size:22
Alignment explanation
Indices: 4792169--4792223 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4792159 TTAAATTATG
* *
4792169 AAAACTATAAAATATAAAGTCAT
1 AAAACTA-AAAATATAAAATCAA
*
4792192 AAAACTAAAATATATAAAATTAA
1 AAAACTAAAA-ATATAAAATCAA
*
4792215 AAAAATAAA
1 AAAACTAAA
4792224 TGTGAAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAACTAAAAATATAAAATCAA
Found at i:4792307 original size:15 final size:16
Alignment explanation
Indices: 4792271--4792315 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 16
4792261 CCTTTTTTGA
*
4792271 ATTAAAATATTATTTT
1 ATTAAAATATAATTTT
4792287 -TT-AAAT-TAATTTT
1 ATTAAAATATAATTTT
*
4792300 ATTAAAATATTATTTT
1 ATTAAAATATAATTTT
4792316 TATAGGTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 6 0.25
16 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTAAAATATAATTTT
Found at i:4796273 original size:5 final size:5
Alignment explanation
Indices: 4796265--4796297 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
4796255 TCCTCTCCAT
4796265 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
4796298 GGTATGCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:4803535 original size:15 final size:15
Alignment explanation
Indices: 4803515--4803560 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
4803505 ATGCTAAAGT
4803515 AAAATTAATTATAAA
1 AAAATTAATTATAAA
*
4803530 AAAATT-ATTTTAAA
1 AAAATTAATTATAAA
*
4803544 AAAATTATTTATAAA
1 AAAATTAATTATAAA
4803559 AA
1 AA
4803561 TATATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATTAATTATAAA
Found at i:4803543 original size:14 final size:14
Alignment explanation
Indices: 4803515--4803580 Score: 73
Period size: 14 Copynumber: 4.7 Consensus size: 14
4803505 ATGCTAAAGT
*
4803515 AAAATTAATTATAAA
1 AAAATT-ATTTTAAA
4803530 AAAATTATTTTAAA
1 AAAATTATTTTAAA
*
4803544 AAAATTA-TTTATA
1 AAAATTATTTTAAA
*
4803557 AAAATATATTTTAAT
1 AAAAT-TATTTTAAA
4803572 AAAA-TATTT
1 AAAATTATTT
4803581 ATCTTTGAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
13 15 0.33
14 16 0.36
15 14 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTATTTTAAA
Found at i:4803544 original size:13 final size:13
Alignment explanation
Indices: 4803528--4803580 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 13
4803518 ATTAATTATA
4803528 AAAAAATTATTTT
1 AAAAAATTATTTT
4803541 AAAAAAATTA-TTT
1 -AAAAAATTATTTT
4803554 ATAAAAATATATTTT
1 A-AAAAAT-TATTTT
4803569 AATAAAA-TATTT
1 AA-AAAATTATTT
4803581 ATCTTTGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 14 0.40
14 12 0.34
15 8 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAAAATTATTTT
Found at i:4803569 original size:15 final size:15
Alignment explanation
Indices: 4803523--4803575 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
4803513 GTAAAATTAA
*
4803523 TTATAAAAAAATTATT
1 TTATAAAAATA-TATT
*
4803539 TTAAAAAAAT-TA-T
1 TTATAAAAATATATT
4803552 TTATAAAAATATATT
1 TTATAAAAATATATT
4803567 TTAATAAAA
1 TT-ATAAAA
4803576 TATTTATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 10 0.32
14 4 0.13
15 3 0.10
16 14 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTATAAAAATATATT
Found at i:4815029 original size:20 final size:20
Alignment explanation
Indices: 4815004--4815044 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4814994 TCGATTGATT
4815004 TTTGTTTTACCTAGTAACGG
1 TTTGTTTTACCTAGTAACGG
4815024 TTTGTTTTACCTAGTAACGG
1 TTTGTTTTACCTAGTAACGG
4815044 T
1 T
4815045 GTCGTCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (20 bp):
TTTGTTTTACCTAGTAACGG
Found at i:4816953 original size:13 final size:14
Alignment explanation
Indices: 4816937--4816972 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
4816927 CAATCTCATA
4816937 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
4816950 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
4816963 TCTC-ATTTCA
1 TCTCAATTTCA
4816973 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:4816962 original size:18 final size:19
Alignment explanation
Indices: 4816924--4816964 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
4816914 TGGTTCATGT
4816924 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
4816943 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
4816961 TTTC
1 TTTC
4816965 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:4817140 original size:29 final size:27
Alignment explanation
Indices: 4817065--4817161 Score: 89
Period size: 27 Copynumber: 3.6 Consensus size: 27
4817055 ATATGCGGAT
4817065 TCCTCCCAAACACACCAGAATATCCA-A
1 TCCTCCCAAACACACCAGAATAT-CATA
*
4817092 ----CCCAAACACACCCAGAATATTATAAA
1 TCCTCCCAAACACA-CCAGAATATCAT--A
*
4817118 TCCT-CCATAACACACCAGTATATCATA
1 TCCTCCCA-AACACACCAGAATATCATA
4817145 TCCTCCCAAACACACCA
1 TCCTCCCAAACACACCA
4817162 ATAAGGCATT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
23 11 0.19
24 9 0.16
26 1 0.02
27 14 0.25
28 3 0.05
29 13 0.23
30 6 0.11
ACGTcount: A:0.41, C:0.38, G:0.03, T:0.18
Consensus pattern (27 bp):
TCCTCCCAAACACACCAGAATATCATA
Found at i:4817635 original size:15 final size:15
Alignment explanation
Indices: 4817615--4817658 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4817605 TATTATATTT
4817615 CAATCAATATAAATC
1 CAATCAATATAAATC
* * * *
4817630 CAATCAAAATGATTT
1 CAATCAATATAAATC
4817645 CAATCAATATAAAT
1 CAATCAATATAAAT
4817659 TTGATAAATT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (15 bp):
CAATCAATATAAATC
Found at i:4819587 original size:16 final size:17
Alignment explanation
Indices: 4819568--4819606 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
4819558 TATTTTTATT
4819568 AAATTATTA--TATAATA
1 AAATTATTAGTTAT-ATA
4819584 AAATTATTAGTTATATA
1 AAATTATTAGTTATATA
4819601 AAATTA
1 AAATTA
4819607 AAATTATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 9 0.43
18 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AAATTATTAGTTATATA
Found at i:4823894 original size:51 final size:51
Alignment explanation
Indices: 4823831--4823933 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
4823821 GAAACTCTGT
* * *
4823831 CGGATCCGATTTCTCGTCAAACGTATGATTATGAATTGG-GCTTGGTTAATC
1 CGGATCCGATTTCTCATCAAAAGTATGATTATGAAATGGAG-TTGGTTAATC
4823882 CGGATCCGATTTCTCATCAAAAGTATGATTATGAAATGGAGTTGGTTAATC
1 CGGATCCGATTTCTCATCAAAAGTATGATTATGAAATGGAGTTGGTTAATC
4823933 C
1 C
4823934 AATGGGGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (51 bp):
CGGATCCGATTTCTCATCAAAAGTATGATTATGAAATGGAGTTGGTTAATC
Found at i:4828011 original size:21 final size:21
Alignment explanation
Indices: 4827987--4828042 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
4827977 AATAAAATTG
4827987 ATTTTTTATTTAATATGAT-TA
1 ATTTTTTATTTAAT-TGATATA
** *
4828008 ATTTTAAAATTTTATTGATATA
1 ATTTT-TTATTTAATTGATATA
4828030 ATTTTTTATTTAA
1 ATTTTTTATTTAA
4828043 AATAAATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
ATTTTTTATTTAATTGATATA
Found at i:4830939 original size:111 final size:111
Alignment explanation
Indices: 4830745--4830963 Score: 438
Period size: 111 Copynumber: 2.0 Consensus size: 111
4830735 TTGGGTAAGG
4830745 AATTTGTATTAAAAATATATACGGGCAGGGCCAGGCACCAGTGTTAATGAGAGAACACTCTTTAA
1 AATTTGTATTAAAAATATATACGGGCAGGGCCAGGCACCAGTGTTAATGAGAGAACACTCTTTAA
4830810 GTGTCATTTCATCCAACAATAAGTGAGCATAAGAAATGGCCTACTT
66 GTGTCATTTCATCCAACAATAAGTGAGCATAAGAAATGGCCTACTT
4830856 AATTTGTATTAAAAATATATACGGGCAGGGCCAGGCACCAGTGTTAATGAGAGAACACTCTTTAA
1 AATTTGTATTAAAAATATATACGGGCAGGGCCAGGCACCAGTGTTAATGAGAGAACACTCTTTAA
4830921 GTGTCATTTCATCCAACAATAAGTGAGCATAAGAAATGGCCTA
66 GTGTCATTTCATCCAACAATAAGTGAGCATAAGAAATGGCCTA
4830964 GTTTCCTAGT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (111 bp):
AATTTGTATTAAAAATATATACGGGCAGGGCCAGGCACCAGTGTTAATGAGAGAACACTCTTTAA
GTGTCATTTCATCCAACAATAAGTGAGCATAAGAAATGGCCTACTT
Found at i:4838360 original size:15 final size:16
Alignment explanation
Indices: 4838340--4838369 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4838330 TGAAATAACT
4838340 ATTTTGTAA-TTTTTC
1 ATTTTGTAAGTTTTTC
4838355 ATTTTGTAAGTTTTT
1 ATTTTGTAAGTTTTT
4838370 ATAATGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.03, G:0.10, T:0.67
Consensus pattern (16 bp):
ATTTTGTAAGTTTTTC
Found at i:4838449 original size:17 final size:16
Alignment explanation
Indices: 4838421--4838473 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
4838411 TTTGGTTTGC
4838421 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
4838437 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
4838454 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
4838470 TGTA
1 TGTA
4838474 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:4838538 original size:44 final size:45
Alignment explanation
Indices: 4838454--4838544 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
4838444 GGATTAGAGG
* * *
4838454 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
4838499 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
4838543 TG
1 TG
4838545 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:4838887 original size:15 final size:16
Alignment explanation
Indices: 4838823--4838887 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 16
4838813 GAAATAATTA
*
4838823 ATATTAAATATATTTT
1 ATATTAAATATATCTT
*
4838839 A-ATTAAATATATGATT
1 ATATTAAATATAT-CTT
*
4838855 -TAATAAA-AT-TCTT
1 ATATTAAATATATCTT
4838868 AATATTAAATAT-TCTT
1 -ATATTAAATATATCTT
4838884 ATAT
1 ATAT
4838888 GAATTTTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
13 2 0.05
14 1 0.03
15 23 0.57
16 14 0.35
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATTAAATATATCTT
Found at i:4838908 original size:119 final size:119
Alignment explanation
Indices: 4838689--4838976 Score: 418
Period size: 119 Copynumber: 2.4 Consensus size: 119
4838679 TTAATCATAT
*
4838689 TTTAACATAATTATTATTAAATAT-TTATAATTAAAATATATAATTTATAATAAAATTCTTAATA
1 TTTAACATAATTATTATTAAATATATTTTAATT-AAATATATAA-TT-TAATAAAATTCTTAATA
* * *
4838753 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
63 ATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * *
4838810 TTTGAA-ATAATTAATATTAAATATATTTTAATTAAATATATGATTTAATAAAATTCTTAATATT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAATATATAATTTAATAAAATTCTTAATAAT
*
4838874 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
** *
4838929 TTTAACATAATTATTATTAAATATAAGTTAATAAAAATATATAATTTA
1 TTTAACATAATTATTATTAAATATATTTTAAT-TAAATATATAATTTA
4838977 TCATCATACT
Statistics
Matches: 150, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
118 2 0.01
119 95 0.63
120 15 0.10
121 29 0.19
122 9 0.06
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (119 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAATATATAATTTAATAAAATTCTTAATAATA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:4871674 original size:5 final size:6
Alignment explanation
Indices: 4871657--4871681 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4871647 TGTCGATTTC
4871657 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
4871682 TTCTCGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:4872450 original size:26 final size:26
Alignment explanation
Indices: 4872384--4872451 Score: 66
Period size: 31 Copynumber: 2.4 Consensus size: 26
4872374 TAGATGAAAA
*
4872384 TTTTAATATAATGATTAAATTATATTTT
1 TTTTATTATAATGATTAAATTATA--TT
4872412 TTCTTATCATATAATGATTAAATTATCA-T
1 TT-TTAT--TATAATGATTAAATTAT-ATT
4872441 TTTTATTATAA
1 TTTTATTATAA
4872452 ATAATAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
26 5 0.14
28 6 0.17
29 6 0.17
31 17 0.49
32 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (26 bp):
TTTTATTATAATGATTAAATTATATT
Found at i:4874695 original size:20 final size:20
Alignment explanation
Indices: 4874666--4874709 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4874656 TGTAAACAAT
4874666 CCAAACCAAGTTTAATTGTA
1 CCAAACCAAGTTTAATTGTA
* *
4874686 CCAAATCAAGTTTAATTGTG
1 CCAAACCAAGTTTAATTGTA
4874706 CCAA
1 CCAA
4874710 TTAAATGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (20 bp):
CCAAACCAAGTTTAATTGTA
Found at i:4875517 original size:21 final size:20
Alignment explanation
Indices: 4875492--4875560 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
4875482 TATAATGATT
4875492 ATTATTATGGTTTTATATTAA
1 ATTATTAT-GTTTTATATTAA
*
4875513 ATTATTATAATTATTA-ATTAA
1 ATTATTAT-GTT-TTATATTAA
*
4875534 CATTA-TA-GTTTTATATTAG
1 -ATTATTATGTTTTATATTAA
4875553 ATTATTAT
1 ATTATTAT
4875561 TATTAGCATT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
18 7 0.18
19 8 0.21
21 17 0.44
22 7 0.18
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (20 bp):
ATTATTATGTTTTATATTAA
Found at i:4875573 original size:15 final size:14
Alignment explanation
Indices: 4875547--4875577 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4875537 TATAGTTTTA
4875547 TATTAGATTATTAT
1 TATTAGATTATTAT
4875561 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
4875576 TA
1 TA
4875578 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:4875805 original size:24 final size:23
Alignment explanation
Indices: 4875743--4875814 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 23
4875733 GTTTGAGAAA
*
4875743 TAAATTAAATA-ATG-ACAAATG
1 TAAATTAAATATTTGTACAAATG
* *
4875764 T-AATAAAATTATTGGTACAAATG
1 TAAATTAAA-TATTTGTACAAATG
*
4875787 TAGAATTAAATATTTGTACAATTG
1 TA-AATTAAATATTTGTACAAATG
4875811 TAAA
1 TAAA
4875815 ATATGTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 6 0.15
21 3 0.08
22 1 0.03
23 10 0.25
24 14 0.35
25 6 0.15
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (23 bp):
TAAATTAAATATTTGTACAAATG
Found at i:4876714 original size:12 final size:12
Alignment explanation
Indices: 4876697--4876739 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
4876687 AGAAAGAATG
4876697 TATGAACTAAAT
1 TATGAACTAAAT
* *
4876709 TATGAATTGAAT
1 TATGAACTAAAT
4876721 GTATGAACTAAAT
1 -TATGAACTAAAT
4876734 TATGAA
1 TATGAA
4876740 TTGAGTTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.35
Consensus pattern (12 bp):
TATGAACTAAAT
Found at i:4876720 original size:25 final size:25
Alignment explanation
Indices: 4876692--4876743 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
4876682 GTACGAGAAA
4876692 GAATGTATGAACTAAATTATGAATT
1 GAATGTATGAACTAAATTATGAATT
4876717 GAATGTATGAACTAAATTATGAATT
1 GAATGTATGAACTAAATTATGAATT
4876742 GA
1 GA
4876744 GTTAGTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (25 bp):
GAATGTATGAACTAAATTATGAATT
Found at i:4876727 original size:13 final size:12
Alignment explanation
Indices: 4876692--4876739 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
4876682 GTACGAGAAA
4876692 GAATGTATGAACT
1 GAAT-TATGAACT
* *
4876705 AAATTATGAATT
1 GAATTATGAACT
4876717 GAATGTATGAACT
1 GAAT-TATGAACT
*
4876730 AAATTATGAA
1 GAATTATGAA
4876740 TTGAGTTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 16 0.55
13 13 0.45
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (12 bp):
GAATTATGAACT
Found at i:4882373 original size:21 final size:21
Alignment explanation
Indices: 4882348--4882416 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4882338 TATAATGATT
*
4882348 ATTATTATGGTTTTATATTAA
1 ATTATTATGATTTTATATTAA
*
4882369 ATTATTATAATTATTA-ATT-A
1 ATTATTATGATT-TTATATTAA
* *
4882389 A-CATTATGATTTTATATTAG
1 ATTATTATGATTTTATATTAA
4882409 ATTATTAT
1 ATTATTAT
4882417 TATTAGCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 3 0.08
21 18 0.47
22 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTATGATTTTATATTAA
Found at i:4882429 original size:15 final size:14
Alignment explanation
Indices: 4882345--4882433 Score: 55
Period size: 13 Copynumber: 6.5 Consensus size: 14
4882335 TATTATAATG
*
4882345 ATTATTATTATGGTT
1 ATTATTATTA-GATT
*
4882360 -TTA-TATTAAATT
1 ATTATTATTAGATT
*
4882372 ATTATAATT--ATT
1 ATTATTATTAGATT
**
4882384 AATTAACATTATGATT
1 -ATTATTATTA-GATT
4882400 -TTA-TATTAGATT
1 ATTATTATTAGATT
4882412 ATTATTATTAGCATT
1 ATTATTATTAG-ATT
4882427 ATTATTA
1 ATTATTA
4882434 AATAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
12 9 0.15
13 22 0.37
14 15 0.25
15 10 0.17
16 3 0.05
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (14 bp):
ATTATTATTAGATT
Found at i:4883492 original size:12 final size:12
Alignment explanation
Indices: 4883475--4883517 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
4883465 AGAAAGAATG
4883475 TATGAACTAAAT
1 TATGAACTAAAT
* *
4883487 TATGAATTGAAT
1 TATGAACTAAAT
4883499 GTATGAACTAAAT
1 -TATGAACTAAAT
4883512 TATGAA
1 TATGAA
4883518 TTGAGTTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.35
Consensus pattern (12 bp):
TATGAACTAAAT
Found at i:4883498 original size:25 final size:25
Alignment explanation
Indices: 4883470--4883521 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
4883460 GTACGAGAAA
4883470 GAATGTATGAACTAAATTATGAATT
1 GAATGTATGAACTAAATTATGAATT
4883495 GAATGTATGAACTAAATTATGAATT
1 GAATGTATGAACTAAATTATGAATT
4883520 GA
1 GA
4883522 GTTAGTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (25 bp):
GAATGTATGAACTAAATTATGAATT
Found at i:4883505 original size:13 final size:12
Alignment explanation
Indices: 4883470--4883517 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
4883460 GTACGAGAAA
4883470 GAATGTATGAACT
1 GAAT-TATGAACT
* *
4883483 AAATTATGAATT
1 GAATTATGAACT
4883495 GAATGTATGAACT
1 GAAT-TATGAACT
*
4883508 AAATTATGAA
1 GAATTATGAA
4883518 TTGAGTTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 16 0.55
13 13 0.45
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (12 bp):
GAATTATGAACT
Found at i:4887044 original size:19 final size:19
Alignment explanation
Indices: 4887020--4887057 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4887010 CCTAAATGGA
4887020 TCAATGATATGTTATAAGG
1 TCAATGATATGTTATAAGG
*
4887039 TCAATGATATGTTGTAAGG
1 TCAATGATATGTTATAAGG
4887058 GTAACACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (19 bp):
TCAATGATATGTTATAAGG
Found at i:4894708 original size:27 final size:27
Alignment explanation
Indices: 4894657--4894708 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
4894647 CCTACAGCTG
*
4894657 TTAAAATATAATTTTTTATTAACTTTA
1 TTAAAATATAATTTTTTAATAACTTTA
* *
4894684 TTAATATATAATTTTTTAATGACTT
1 TTAAAATATAATTTTTTAATAACTT
4894709 AAATTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAAAATATAATTTTTTAATAACTTTA
Found at i:4894717 original size:27 final size:27
Alignment explanation
Indices: 4894657--4894718 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
4894647 CCTACAGCTG
* * *
4894657 TTAAAATATAATTTTTTATTAACTTTA
1 TTAATATATAATTTTTTAATAACTTAA
*
4894684 TTAATATATAATTTTTTAATGACTTAAA
1 TTAATATATAATTTTTTAATAACTT-AA
4894712 TT-ATATA
1 TTAATATA
4894719 AATAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (27 bp):
TTAATATATAATTTTTTAATAACTTAA
Found at i:4902021 original size:14 final size:14
Alignment explanation
Indices: 4901992--4902020 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4901982 TTCTTTCTTC
4901992 TTCTTCTTTTTTTT
1 TTCTTCTTTTTTTT
4902006 TTCTT-TTTTTTTT
1 TTCTTCTTTTTTTT
4902019 TT
1 TT
4902021 TAAGTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTCTTCTTTTTTTT
Found at i:4902441 original size:15 final size:15
Alignment explanation
Indices: 4902421--4902458 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4902411 TTGAGAGAGG
*
4902421 AAAATTAACGATTAA
1 AAAATTAAAGATTAA
*
4902436 AAAATTAAATATTAA
1 AAAATTAAAGATTAA
4902451 AAAATTAA
1 AAAATTAA
4902459 GTACATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAATTAAAGATTAA
Found at i:4919674 original size:26 final size:26
Alignment explanation
Indices: 4919616--4919677 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
4919606 TTGGTCATTA
*
4919616 ACTTTTAGATTTTAATTAATTTACTT
1 ACTTTTGGATTTTAATTAATTTACTT
4919642 ACTTTTGGATTTTAATTAATTTACTT
1 ACTTTTGGATTTTAATTAATTTACTT
4919668 ACTTTTGGAT
1 ACTTTTGGAT
4919678 GGTAAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.56
Consensus pattern (26 bp):
ACTTTTGGATTTTAATTAATTTACTT
Found at i:4919800 original size:17 final size:17
Alignment explanation
Indices: 4919754--4919801 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
4919744 ATATAATTCA
*
4919754 TAAAAAAAATA-AAAAT
1 TAAAAAAATTATAAAAT
*
4919770 T-AAAAATTTAATAAAAT
1 TAAAAAAATT-ATAAAAT
4919787 TAAAAAAATTATAAA
1 TAAAAAAATTATAAA
4919802 TTTTTTAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 6 0.23
16 2 0.08
17 11 0.42
18 7 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAAAATTATAAAAT
Found at i:4922247 original size:15 final size:16
Alignment explanation
Indices: 4922217--4922255 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4922207 GAGCCGTAAT
*
4922217 TTTATTAATATTTTAA
1 TTTATAAATATTTTAA
4922233 TTTATAAAT-TTTTAA
1 TTTATAAATATTTTAA
*
4922248 TTTTTAAA
1 TTTATAAA
4922256 AGGTCTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATAAATATTTTAA
Found at i:4930909 original size:11 final size:12
Alignment explanation
Indices: 4930888--4930914 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4930878 CTCCATCGAC
4930888 AAAAAGAAAAAA
1 AAAAAGAAAAAA
4930900 AAAAAGAAAAAA
1 AAAAAGAAAAAA
4930912 AAA
1 AAA
4930915 GAACGACCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:4931183 original size:5 final size:5
Alignment explanation
Indices: 4931175--4931202 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4931165 ATCTGATTGG
4931175 AAGAA AAGAA AAGAA AAGAA AAGAA AAG
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAG
4931203 GGTGAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:4937981 original size:65 final size:64
Alignment explanation
Indices: 4937876--4938014 Score: 251
Period size: 65 Copynumber: 2.2 Consensus size: 64
4937866 GGTCAAAGTG
*
4937876 CAATTTACCATCAAATTGAAATAAAGCATTATGATTCTCTCTCTTTTATTGTATAAAAAAAAATA
1 CAATTTACCATCAAATTGAAATAAAGCATTATGATCCTCTCTCTTTTATTGTAT-AAAAAAAATA
*
4937941 CAATTTACCATCAAATTGAAATAAAGCATTATGATCCTCTCTCTTTTCTTGTATAAAAAAAATA
1 CAATTTACCATCAAATTGAAATAAAGCATTATGATCCTCTCTCTTTTATTGTATAAAAAAAATA
4938005 CAATTTACCA
1 CAATTTACCA
4938015 ATATATAAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 20 0.28
65 52 0.72
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36
Consensus pattern (64 bp):
CAATTTACCATCAAATTGAAATAAAGCATTATGATCCTCTCTCTTTTATTGTATAAAAAAAATA
Found at i:4939989 original size:14 final size:16
Alignment explanation
Indices: 4939970--4940004 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4939960 AAATTAATTA
4939970 TAAAATA-TACA-AAT
1 TAAAATATTACATAAT
4939984 TAAAATATTACATAAT
1 TAAAATATTACATAAT
4940000 TAAAA
1 TAAAA
4940005 ATGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 4 0.21
16 8 0.42
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAATATTACATAAT
Found at i:4941538 original size:18 final size:18
Alignment explanation
Indices: 4941515--4941551 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4941505 ATTAATGTTC
4941515 ATCTATTAGTGGTAGTTT
1 ATCTATTAGTGGTAGTTT
4941533 ATCTATTAGTGGTAGTTT
1 ATCTATTAGTGGTAGTTT
4941551 A
1 A
4941552 ATTCCTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (18 bp):
ATCTATTAGTGGTAGTTT
Found at i:4944896 original size:20 final size:19
Alignment explanation
Indices: 4944862--4944910 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
4944852 TTATTTAGTG
4944862 TTTTATTTTTTAAAAAATA
1 TTTTATTTTTTAAAAAATA
4944881 TTTTATTTTTTAAAAAATA
1 TTTTATTTTTTAAAAAATA
4944900 TTTTATTTTTT
1 TTTTATTTTTT
4944911 GTCTTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATTTTTTAAAAAATA
Found at i:4946412 original size:10 final size:10
Alignment explanation
Indices: 4946375--4946413 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
4946365 CAAATATATA
4946375 ATATAAAATT
1 ATATAAAATT
4946385 ATTATAAAA-T
1 A-TATAAAATT
*
4946395 ATAAAAAATT
1 ATATAAAATT
4946405 ATATAAAAT
1 ATATAAAAT
4946414 ATAAAATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 6 0.24
10 12 0.48
11 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATATAAAATT
Found at i:4946428 original size:19 final size:18
Alignment explanation
Indices: 4946369--4946430 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
4946359 TTAAACCAAA
*
4946369 TATATAATATAAAATTAT
1 TATAAAATATAAAATTAT
4946387 TATAAAATATAAAAAATTA-
1 TATAAAATAT--AAAATTAT
4946406 TATAAAATATAAAATTAGT
1 TATAAAATATAAAATTA-T
4946425 TATAAA
1 TATAAA
4946431 GTTAAAAGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 7 0.18
18 9 0.23
19 16 0.41
20 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
TATAAAATATAAAATTAT
Found at i:4947108 original size:11 final size:11
Alignment explanation
Indices: 4947094--4947120 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4947084 TAAAAGGTAA
4947094 AAAAAAATTAT
1 AAAAAAATTAT
4947105 AAAAAAATTAT
1 AAAAAAATTAT
4947116 AAAAA
1 AAAAA
4947121 TTAATTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:4947290 original size:10 final size:10
Alignment explanation
Indices: 4947277--4947319 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
4947267 TCATATTAAC
4947277 AAATATAAAA
1 AAATATAAAA
4947287 AAATATAATAA
1 AAATATAA-AA
*
4947298 AAATATATAA
1 AAATATAAAA
4947308 AAATATAAAA
1 AAATATAAAA
4947318 AA
1 AA
4947320 GGTTACACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATATAAAA
Found at i:4947301 original size:21 final size:20
Alignment explanation
Indices: 4947277--4947319 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
4947267 TCATATTAAC
4947277 AAATATAAAAAAATATAATAA
1 AAATATAAAAAAATATAA-AA
*
4947298 AAATATATAAAAATATAAAA
1 AAATATAAAAAAATATAAAA
4947318 AA
1 AA
4947320 GGTTACACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAATATAAAAAAATATAAAA
Found at i:4948998 original size:2 final size:2
Alignment explanation
Indices: 4948991--4949019 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4948981 TTCTAAAATT
4948991 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4949020 GTGTGTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4949276 original size:19 final size:19
Alignment explanation
Indices: 4949252--4949291 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4949242 TATTTTGAAT
4949252 TTCAATTTCTCTTCATACC
1 TTCAATTTCTCTTCATACC
4949271 TTCAATTTCTCTTCATACC
1 TTCAATTTCTCTTCATACC
4949290 TT
1 TT
4949292 TTAACTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCAATTTCTCTTCATACC
Found at i:4954798 original size:8 final size:8
Alignment explanation
Indices: 4954781--4954820 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
4954771 TAGTTTCTCT
*
4954781 AAATAGAA
1 AAATAAAA
4954789 AAATAAAA
1 AAATAAAA
*
4954797 AAATAGAA
1 AAATAAAA
4954805 AAAT-AAA
1 AAATAAAA
4954812 AAATAAAA
1 AAATAAAA
4954820 A
1 A
4954821 CAGAAACACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:4954802 original size:16 final size:16
Alignment explanation
Indices: 4954781--4954814 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4954771 TAGTTTCTCT
4954781 AAATAGAAAAATAAAA
1 AAATAGAAAAATAAAA
4954797 AAATAGAAAAATAAAA
1 AAATAGAAAAATAAAA
4954813 AA
1 AA
4954815 TAAAAACAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAATAGAAAAATAAAA
Found at i:4954871 original size:13 final size:13
Alignment explanation
Indices: 4954853--4954882 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4954843 GTTTGCCAGT
4954853 AAAATAATTTCGA
1 AAAATAATTTCGA
*
4954866 AAAATAATTTCTA
1 AAAATAATTTCGA
4954879 AAAA
1 AAAA
4954883 ATGATTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAATAATTTCGA
Found at i:4954902 original size:20 final size:19
Alignment explanation
Indices: 4954873--4954914 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
4954863 CGAAAAATAA
4954873 TTTCTAAAAAATGATTTACT
1 TTTCT-AAAAATGATTTACT
*
4954893 TTTCTGAAAATGATTTACT
1 TTTCTAAAAATGATTTACT
4954912 TTT
1 TTT
4954915 TTAGTGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCTAAAAATGATTTACT
Found at i:4963106 original size:15 final size:16
Alignment explanation
Indices: 4963070--4963104 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4963060 TTAAAAAGTT
4963070 TTTTAAAATCTTAATA
1 TTTTAAAATCTTAATA
4963086 TTTTAAAAT-TTAATTA
1 TTTTAAAATCTTAA-TA
4963102 TTT
1 TTT
4963105 AAGGCAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATCTTAATA
Found at i:4963317 original size:28 final size:27
Alignment explanation
Indices: 4963286--4963346 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
4963276 ATAAAAATAA
*
4963286 AAAAAATCAAATA-CGAAATTTGAAATCC
1 AAAAAATCAAA-ACCAAAATTTGAAA-CC
**
4963314 AAAACCTCAAAACCAAAATTTGAAACC
1 AAAAAATCAAAACCAAAATTTGAAACC
4963341 AAAAAA
1 AAAAAA
4963347 ATTAAACCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.61, C:0.18, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAAAATCAAAACCAAAATTTGAAACC
Found at i:4963423 original size:24 final size:23
Alignment explanation
Indices: 4963381--4963428 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
4963371 AATAACAAAT
4963381 ATAATTAATACTTAATTATGTTTA
1 ATAATTAATACTTAATTAT-TTTA
*
4963405 ATAAGTTAATA-TTATTTATTTTA
1 ATAA-TTAATACTTAATTATTTTA
4963428 A
1 A
4963429 AGTCTTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
ATAATTAATACTTAATTATTTTA
Found at i:4968334 original size:16 final size:16
Alignment explanation
Indices: 4968307--4968341 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4968297 GAAAAGTTGT
4968307 TTTAAGAAATTTATATA
1 TTTAAGAAATTTAT-TA
4968324 TTTAA-AAATTTATTA
1 TTTAAGAAATTTATTA
4968339 TTT
1 TTT
4968342 TTTCATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 8 0.44
17 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAAGAAATTTATTA
Found at i:4969895 original size:20 final size:20
Alignment explanation
Indices: 4969870--4969909 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4969860 CGTAAAATGA
*
4969870 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
4969890 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
4969910 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:4969899 original size:34 final size:35
Alignment explanation
Indices: 4969855--4969921 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
4969845 CAGTAAAATA
*
4969855 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
4969889 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
4969922 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:4969925 original size:14 final size:15
Alignment explanation
Indices: 4969849--4969925 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
4969839 GTTTGGCAGT
* *
4969849 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
4969863 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
4969877 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
4969897 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
4969912 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
4969926 TGTTTGGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:4971360 original size:35 final size:37
Alignment explanation
Indices: 4971309--4971379 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 37
4971299 AAATTCAACC
4971309 ATTTCAATATCCAACAAGCTTAAAACATAAT-AATAA
1 ATTTCAATATCCAACAAGCTTAAAACATAATCAATAA
4971345 ATTT-AATATCCAACAAGCTTAAAACATAATCAATA
1 ATTTCAATATCCAACAAGCTTAAAACATAATCAATA
4971380 TCTAACAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 26 0.76
36 8 0.24
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (37 bp):
ATTTCAATATCCAACAAGCTTAAAACATAATCAATAA
Found at i:4971379 original size:27 final size:28
Alignment explanation
Indices: 4971349--4971416 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
4971339 TAATAAATTT
*
4971349 AATATCCAACAAGCTT-AAAACATA-ATC
1 AATATCCAACAA-ATTCAAAACATATATC
* *
4971376 AATATCTAACAAATTCAAGACATATATC
1 AATATCCAACAAATTCAAAACATATATC
*
4971404 AAAATCCAACAAA
1 AATATCCAACAAA
4971417 CTAAAATTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.06
27 18 0.53
28 14 0.41
ACGTcount: A:0.54, C:0.21, G:0.03, T:0.22
Consensus pattern (28 bp):
AATATCCAACAAATTCAAAACATATATC
Found at i:4972930 original size:15 final size:16
Alignment explanation
Indices: 4972910--4972942 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
4972900 AGTACCACTT
4972910 AAAATGAAAGCA-TGA
1 AAAATGAAAGCATTGA
4972925 AAAATGAAAGCATTGA
1 AAAATGAAAGCATTGA
4972941 AA
1 AA
4972943 GTTCAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAATGAAAGCATTGA
Found at i:4975382 original size:25 final size:25
Alignment explanation
Indices: 4975343--4975394 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
4975333 AAAATGTCTG
4975343 CTGCTTAGAAGAGAACAGAAAATGT
1 CTGCTTAGAAGAGAACAGAAAATGT
**
4975368 CTGCTTAG-AGAAGAATGGAAAATGT
1 CTGCTTAGAAG-AGAACAGAAAATGT
4975393 CT
1 CT
4975395 TACCAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (25 bp):
CTGCTTAGAAGAGAACAGAAAATGT
Found at i:4982189 original size:15 final size:16
Alignment explanation
Indices: 4982153--4982187 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4982143 TTAAAAAGTT
4982153 TTTTAAAATCTTAATA
1 TTTTAAAATCTTAATA
4982169 TTTTAAAAT-TTAATTA
1 TTTTAAAATCTTAA-TA
4982185 TTT
1 TTT
4982188 AAGGCAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATCTTAATA
Found at i:4982400 original size:28 final size:27
Alignment explanation
Indices: 4982369--4982429 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
4982359 ATAAAAATAA
*
4982369 AAAAAATCAAATA-CGAAATTTGAAATCC
1 AAAAAATCAAA-ACCAAAATTTGAAA-CC
**
4982397 AAAACCTCAAAACCAAAATTTGAAACC
1 AAAAAATCAAAACCAAAATTTGAAACC
4982424 AAAAAA
1 AAAAAA
4982430 ATTAAACCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.61, C:0.18, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAAAATCAAAACCAAAATTTGAAACC
Found at i:4982506 original size:24 final size:23
Alignment explanation
Indices: 4982464--4982511 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
4982454 AATAACAAAT
4982464 ATAATTAATACTTAATTATGTTTA
1 ATAATTAATACTTAATTAT-TTTA
*
4982488 ATAAGTTAATA-TTATTTATTTTA
1 ATAA-TTAATACTTAATTATTTTA
4982511 A
1 A
4982512 AGTCTTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
ATAATTAATACTTAATTATTTTA
Found at i:4993755 original size:37 final size:37
Alignment explanation
Indices: 4993705--4993778 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
4993695 AAGGACATAT
*
4993705 ACAGAGACTGAGCAAATCATACAATCCAAACAGCAAA
1 ACAGAGACTGAGCAAATCATACAATCCAAACAACAAA
4993742 ACAGAGACTGAGCAAATCATACAATCCAAACAACAAA
1 ACAGAGACTGAGCAAATCATACAATCCAAACAACAAA
4993779 TAAAGGAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.11
Consensus pattern (37 bp):
ACAGAGACTGAGCAAATCATACAATCCAAACAACAAA
Found at i:4993983 original size:61 final size:61
Alignment explanation
Indices: 4993888--4994015 Score: 238
Period size: 61 Copynumber: 2.1 Consensus size: 61
4993878 ACATGGTAGG
4993888 AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGGTTCATGCCAACTTCCAA
1 AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGGTTCATGCCAACTTCCAA
*
4993949 AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGTTTCATGCCAACTTCCAA
1 AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGGTTCATGCCAACTTCCAA
4994010 ATAAAC
1 A-AAAC
4994016 TTCCGAATCA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
61 61 0.94
62 4 0.06
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (61 bp):
AAAACAATAAAGATAATTTGCAGGAACTGCAAAATGACAATGGGTTCATGCCAACTTCCAA
Found at i:4993989 original size:33 final size:33
Alignment explanation
Indices: 4993891--4993989 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 33
4993881 TGGTAGGAAA
4993891 ACAATAAAGATAATTTGCAGGAACTGCAAAATG
1 ACAATAAAGATAATTTGCAGGAACTGCAAAATG
** * * * * *
4993924 ACAAT-GGGTTCA--TGC--CAACTTCCAAAA-A
1 ACAATAAAGATAATTTGCAGGAAC-TGCAAAATG
4993952 ACAATAAAGATAATTTGCAGGAACTGCAAAATG
1 ACAATAAAGATAATTTGCAGGAACTGCAAAATG
4993985 ACAAT
1 ACAAT
4993990 GGTTTCATGC
Statistics
Matches: 45, Mismatches: 14, Indels: 14
0.62 0.19 0.19
Matches are distributed among these distances:
28 8 0.18
29 9 0.20
30 3 0.07
31 3 0.07
32 9 0.20
33 13 0.29
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.21
Consensus pattern (33 bp):
ACAATAAAGATAATTTGCAGGAACTGCAAAATG
Found at i:4997222 original size:24 final size:24
Alignment explanation
Indices: 4997190--4997243 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4997180 TTGGTAAATT
*
4997190 TCAATACAATAGCAATAAATTTCA
1 TCAATACAATAGCAATAAACTTCA
*
4997214 TCAATACAATAGCAATCAACTTCA
1 TCAATACAATAGCAATAAACTTCA
*
4997238 TTAATA
1 TCAATA
4997244 TTTTAATACG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.30
Consensus pattern (24 bp):
TCAATACAATAGCAATAAACTTCA
Found at i:4998958 original size:29 final size:30
Alignment explanation
Indices: 4998911--4998968 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
4998901 TGATTATTTT
4998911 ATATTATTTTTTTATTTTT-TTAAAATAAA
1 ATATTATTTTTTTATTTTTATTAAAATAAA
4998940 ATATTATTTTTTTTATTTTTATTAAAATA
1 ATATTA-TTTTTTTATTTTTATTAAAATA
4998969 TTTAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.22
30 13 0.48
31 8 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
ATATTATTTTTTTATTTTTATTAAAATAAA
Found at i:4998965 original size:26 final size:28
Alignment explanation
Indices: 4998911--4998970 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
4998901 TGATTATTTT
*
4998911 ATATTATTTTTTTATTTTTTTAAAATAAA
1 ATATTATTTTTTTATATTTTT-AAATAAA
*
4998940 ATATTATTTTTTT-TATTTTT-ATTAAA
1 ATATTATTTTTTTATATTTTTAAATAAA
4998966 ATATT
1 ATATT
4998971 TAAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 10 0.34
28 6 0.21
29 13 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
ATATTATTTTTTTATATTTTTAAATAAA
Found at i:4999297 original size:15 final size:14
Alignment explanation
Indices: 4999273--4999362 Score: 81
Period size: 15 Copynumber: 5.9 Consensus size: 14
4999263 GTCCACACCG
4999273 AAAGAAAGAAAAAAA
1 AAAG-AAGAAAAAAA
*
4999288 AAAGAGAGAAAGAAA
1 AAAGA-AGAAAAAAA
**
4999303 GGAGAAGAAAAAAA
1 AAAGAAGAAAAAAA
4999317 AAAGAAGAATAAGAAGAA
1 AAAGAAG-A-AA-AA-AA
4999335 AAAGAAGAAAAAGAA
1 AAAGAAGAAAAA-AA
*
4999350 GAAGAAGAAAAAA
1 AAAGAAGAAAAAA
4999363 GGTAATGTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
14 15 0.24
15 32 0.51
16 4 0.06
17 3 0.05
18 9 0.14
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (14 bp):
AAAGAAGAAAAAAA
Found at i:4999313 original size:27 final size:25
Alignment explanation
Indices: 4999272--4999362 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 25
4999262 CGTCCACACC
4999272 GAAAG-AA-AGAA-AAAAAAAAGAGA
1 GAAAGAAAGAGAAGAAAAAAAAGA-A
4999295 GAAAGAAAGGAGAAGAAAAAAAA-AA
1 GAAAGAAA-GAGAAGAAAAAAAAGAA
*
4999320 G-AAGAATA-AGAAGAAAAAGAAGAA
1 GAAAGAA-AGAGAAGAAAAAAAAGAA
4999344 -AAAG-AAGAAGAAGAAAAAA
1 GAAAGAAAG-AGAAGAAAAAA
4999363 GGTAATGTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
22 1 0.02
23 18 0.32
24 22 0.39
25 3 0.05
26 5 0.09
27 8 0.14
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (25 bp):
GAAAGAAAGAGAAGAAAAAAAAGAA
Done.