Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold163
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: 1788591
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.32
Warning! 179834 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:1701611 original size:26 final size:27
Alignment explanation
Indices: 1701582--1701632 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1701572 TAAGTAATTT
*
1701582 TTTTTAA-AATAAATGGGTAGTTTTAA
1 TTTTTAATAATAAATGAGTAGTTTTAA
*
1701608 TTTTTAATATTAAATGAGTAGTTTT
1 TTTTTAATAATAAATGAGTAGTTTT
1701633 GAAATGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (27 bp):
TTTTTAATAATAAATGAGTAGTTTTAA
Found at i:1703403 original size:22 final size:22
Alignment explanation
Indices: 1703378--1703423 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1703368 TATAATATGT
*
1703378 TATATATTTATTTTTTATATAA
1 TATATATTTATTTTTTACATAA
1703400 TATATATTTATTTTTTACATAA
1 TATATATTTATTTTTTACATAA
1703422 TA
1 TA
1703424 AAACTTACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TATATATTTATTTTTTACATAA
Found at i:1703568 original size:14 final size:14
Alignment explanation
Indices: 1703544--1703577 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1703534 GTCTAATTTT
1703544 TTTTGTCAAATCATA
1 TTTT-TCAAATCATA
1703559 TTTTTCAAATCATA
1 TTTTTCAAATCATA
1703573 TTTTT
1 TTTTT
1703578 TGCTCAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (14 bp):
TTTTTCAAATCATA
Found at i:1703703 original size:13 final size:13
Alignment explanation
Indices: 1703685--1703711 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1703675 AATCAGCAAC
1703685 TACATCACATAAT
1 TACATCACATAAT
1703698 TACATCACATAAT
1 TACATCACATAAT
1703711 T
1 T
1703712 GCAACTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (13 bp):
TACATCACATAAT
Found at i:1706437 original size:21 final size:19
Alignment explanation
Indices: 1706411--1706463 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
1706401 TTTTTTTACT
1706411 TTTAATTTTATTATTATAATA
1 TTTAATTTTATTATTA-AA-A
*
1706432 TTTAATCTTATTATTAAAA
1 TTTAATTTTATTATTAAAA
1706451 TTAATAATTTTAT
1 TT--TAATTTTAT
1706464 CCTAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 2 0.07
21 23 0.82
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATTTTATTATTAAAA
Found at i:1716506 original size:19 final size:19
Alignment explanation
Indices: 1716478--1716536 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
1716468 TTGGATCGAT
*
1716478 ACATTATATCGATACAT-A
1 ACATTGTATCGATACATGA
*
1716496 TTCATTGTATCGATACATGA
1 -ACATTGTATCGATACATGA
1716516 ACAATTGTATCGATACATGA
1 AC-ATTGTATCGATACATGA
1716536 A
1 A
1716537 ACTGGCAGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:1716524 original size:20 final size:20
Alignment explanation
Indices: 1716499--1716536 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1716489 ATACATATTC
1716499 ATTGTATCGATACATGAACA
1 ATTGTATCGATACATGAACA
1716519 ATTGTATCGATACATGAA
1 ATTGTATCGATACATGAA
1716537 ACTGGCAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGAACA
Found at i:1723473 original size:20 final size:20
Alignment explanation
Indices: 1723448--1723493 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1723438 AACTCAAGCC
*
1723448 AACCTTAAACACTTTAACTG
1 AACCTTAAACACTTTAACCG
*
1723468 AACCTTGAACACTTTAACCG
1 AACCTTAAACACTTTAACCG
1723488 AACCTT
1 AACCTT
1723494 CTCTCGGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.28, G:0.07, T:0.28
Consensus pattern (20 bp):
AACCTTAAACACTTTAACCG
Found at i:1724725 original size:22 final size:22
Alignment explanation
Indices: 1724694--1724735 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1724684 TTTTTTAAGA
*
1724694 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGAGAGAAATGC
*
1724716 TTTGATAAAGGGAGAGAAAT
1 TTTGACAAAGGGAGAGAAAT
1724736 ATGTTTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.21
Consensus pattern (22 bp):
TTTGACAAAGGGAGAGAAATGC
Found at i:1725345 original size:13 final size:13
Alignment explanation
Indices: 1725327--1725351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1725317 CATTATGCTT
1725327 TGTATCGATACAA
1 TGTATCGATACAA
1725340 TGTATCGATACA
1 TGTATCGATACA
1725352 TTTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1725348 original size:33 final size:32
Alignment explanation
Indices: 1725306--1725370 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1725296 ACACACCCAG
*
1725306 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCGATACATT-TGCATTGTATCGATACA
*
1725339 ATGTATCGATACATTTTCATTGTATCGATACA
1 ATGTATCGATACATTTGCATTGTATCGATACA
1725371 TGGACAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (32 bp):
ATGTATCGATACATTTGCATTGTATCGATACA
Found at i:1725382 original size:20 final size:20
Alignment explanation
Indices: 1725336--1725394 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1725326 TTGTATCGAT
**
1725336 ACAA-TGTATCGATACATTT
1 ACAATTGTATCGATACATGG
*
1725355 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
1725374 ACAATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
1725394 A
1 A
1725395 AACTGGCAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 1 0.03
19 15 0.44
20 18 0.53
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:1726964 original size:25 final size:25
Alignment explanation
Indices: 1726934--1726987 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
1726924 TTTTAAATTT
*
1726934 TATTAATAAAATTAAGAGATTTTTA
1 TATTAACAAAATTAAGAGATTTTTA
1726959 TATTAACAAAATTAAGAGATTTTTA
1 TATTAACAAAATTAAGAGATTTTTA
1726984 TATT
1 TATT
1726988 CTTTGTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (25 bp):
TATTAACAAAATTAAGAGATTTTTA
Found at i:1729626 original size:26 final size:24
Alignment explanation
Indices: 1729592--1729655 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
1729582 ATTTGCCATG
*
1729592 TAAACTAAAAAATGTGTTATATTTTTT
1 TAAA-TAAAAAAT-TGTTAT-TTTTTA
*
1729619 TAATTAAAAAGGATTGTTATTTTTTA
1 TAAATAAAAA--ATTGTTATTTTTTA
1729645 TAAATAAAAAA
1 TAAATAAAAAA
1729656 AGCTTGGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.03
26 20 0.62
27 9 0.28
28 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (24 bp):
TAAATAAAAAATTGTTATTTTTTA
Found at i:1731245 original size:2 final size:2
Alignment explanation
Indices: 1731206--1731230 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1731196 ATAATATACA
1731206 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1731231 AGAGTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1739444 original size:16 final size:16
Alignment explanation
Indices: 1739416--1739461 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1739406 TTTTTTTTTT
1739416 AAATAGATT-TTATTCA
1 AAATA-ATTCTTATTCA
1739432 AAATAATTCTTATTCA
1 AAATAATTCTTATTCA
*
1739448 AGATAATTCTTATT
1 AAATAATTCTTATT
1739462 TGAAGCAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 3 0.11
16 25 0.89
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (16 bp):
AAATAATTCTTATTCA
Found at i:1741139 original size:15 final size:15
Alignment explanation
Indices: 1741121--1741153 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1741111 GATTTTAAGC
1741121 TTTTTTT-TTTTTAA
1 TTTTTTTATTTTTAA
1741135 TTTTTTTATTTTTAA
1 TTTTTTTATTTTTAA
1741150 TTTT
1 TTTT
1741154 ATTCATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTATTTTTAA
Found at i:1741576 original size:3 final size:3
Alignment explanation
Indices: 1741568--1741596 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1741558 TTGATGAAAT
1741568 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1741597 TTGAGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1742187 original size:2 final size:2
Alignment explanation
Indices: 1742180--1742204 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1742170 AAATTGATTT
1742180 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1742205 TTGTAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1748406 original size:8 final size:8
Alignment explanation
Indices: 1748394--1748427 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1748384 ATATATAAAC
1748394 TTTAATAA
1 TTTAATAA
*
1748402 ATTAAT-A
1 TTTAATAA
1748409 TTTAATAA
1 TTTAATAA
1748417 TTTAATAA
1 TTTAATAA
1748425 TTT
1 TTT
1748428 TAAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAATAA
Found at i:1748415 original size:7 final size:7
Alignment explanation
Indices: 1748403--1748464 Score: 52
Period size: 7 Copynumber: 8.0 Consensus size: 7
1748393 CTTTAATAAA
1748403 TTAATAT
1 TTAATAT
1748410 TTAATAAT
1 TTAAT-AT
1748418 TTAATAATT
1 TTAAT-A-T
1748427 TTAAAATAT
1 TT--AATAT
1748436 TTATATAT
1 TTA-ATAT
*
1748444 TTATTAT
1 TTAATAT
*
1748451 TTTATAT
1 TTAATAT
1748458 TTAATAT
1 TTAATAT
1748465 ATTTTATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
7 20 0.43
8 16 0.35
9 6 0.13
10 1 0.02
11 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTAATAT
Found at i:1748434 original size:26 final size:25
Alignment explanation
Indices: 1748405--1748454 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
1748395 TTAATAAATT
1748405 AATATTTA-ATAATTTAATAATTTTAA
1 AATATTTATAT-ATTT-ATAATTTTAA
*
1748431 AATATTTATATATTTATTATTTTA
1 AATATTTATATATTTATAATTTTA
1748455 TATTTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 12 0.55
27 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AATATTTATATATTTATAATTTTAA
Found at i:1748456 original size:16 final size:16
Alignment explanation
Indices: 1748368--1748474 Score: 73
Period size: 15 Copynumber: 6.8 Consensus size: 16
1748358 TTGCGTTTGT
*
1748368 TATATTTTATATAT-A
1 TATATTTTATATTTAA
* *
1748383 TATA-TATAAACTTTAA
1 TATATTTTATA-TTTAA
* *
1748399 TA-AATTAATATTTAA
1 TATATTTTATATTTAA
*
1748414 TA-ATTTAATAATTTTAA
1 TATATTTTAT-A-TTTAA
*
1748431 AATATTTATATATTT-A
1 TATATTT-TATATTTAA
1748447 T-TATTTTATATTTAA
1 TATATTTTATATTTAA
1748462 TATATTTTATATT
1 TATATTTTATATT
1748475 ATATTTATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
14 11 0.15
15 27 0.37
16 19 0.26
17 9 0.12
18 5 0.07
19 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTTTATATTTAA
Found at i:1748467 original size:9 final size:9
Alignment explanation
Indices: 1748406--1748473 Score: 60
Period size: 9 Copynumber: 8.2 Consensus size: 9
1748396 TAATAAATTA
1748406 ATATTTAAT
1 ATATTTAAT
1748415 A-ATTTAAT
1 ATATTTAAT
*
1748423 A-ATTTTAAA
1 ATA-TTTAAT
1748432 ATATTT-AT
1 ATATTTAAT
1748440 ATATTT-AT
1 ATATTTAAT
1748448 -TATTT--T
1 ATATTTAAT
1748454 ATATTTAAT
1 ATATTTAAT
*
1748463 ATATTTTAT
1 ATATTTAAT
1748472 AT
1 AT
1748474 TATATTTATA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
6 1 0.02
7 10 0.20
8 18 0.35
9 21 0.41
10 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTTAAT
Found at i:1748488 original size:23 final size:23
Alignment explanation
Indices: 1748432--1748489 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 23
1748422 TAATTTTAAA
*
1748432 ATATTTATATAT-TTATTATTTT
1 ATATTTATATATATTATTATATT
1748454 ATATTTA-ATATATT-TTATATT
1 ATATTTATATATATTATTATATT
1748475 ATATTTATATTATAT
1 ATATTTATA-TATAT
1748490 AATCATAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 17 0.53
22 10 0.31
23 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATTTATATATATTATTATATT
Found at i:1748489 original size:16 final size:15
Alignment explanation
Indices: 1748439--1748485 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
1748429 AAAATATTTA
1748439 TATATTTATTAT-TT
1 TATATTTATTATATT
*
1748453 TATATTTAATATATT
1 TATATTTATTATATT
1748468 T-TA--TATTATATT
1 TATATTTATTATATT
1748480 TATATT
1 TATATT
1748486 ATATAATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 13 0.48
15 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATATTTATTATATT
Found at i:1748855 original size:16 final size:17
Alignment explanation
Indices: 1748830--1748866 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1748820 TTATTAAAGG
1748830 ATTT-TAAATTTTTTAT
1 ATTTATAAATTTTTTAT
1748846 -TTTATAAATTTTTTAT
1 ATTTATAAATTTTTTAT
1748862 ATTTA
1 ATTTA
1748867 ATCAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTATAAATTTTTTAT
Found at i:1753112 original size:2 final size:2
Alignment explanation
Indices: 1753107--1753149 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1753097 CTCTCTCTCT
1753107 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1753149 T
1 T
1753150 TACAAGTTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1755303 original size:22 final size:21
Alignment explanation
Indices: 1755278--1755321 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1755268 TTTTTGATAC
*
1755278 ATATTTTTTAATAAATTTAAAA
1 ATATTTTTT-ATAAAATTAAAA
*
1755300 ATATTTTTTTTAAAATTAAAA
1 ATATTTTTTATAAAATTAAAA
1755321 A
1 A
1755322 ATAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTTTTTATAAAATTAAAA
Found at i:1755322 original size:22 final size:23
Alignment explanation
Indices: 1755281--1755324 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1755271 TTGATACATA
*
1755281 TTTTTTAATAAATTTAAAAATAT
1 TTTTTTAATAAATTAAAAAATAT
*
1755304 TTTTTTTA-AAATTAAAAAATA
1 TTTTTTAATAAATTAAAAAATA
1755325 AAATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTTTAATAAATTAAAAAATAT
Found at i:1755451 original size:18 final size:20
Alignment explanation
Indices: 1755428--1755471 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1755418 ATATAGTTTA
1755428 TTAAAAA-A-GATATTAATC
1 TTAAAAATATGATATTAATC
* *
1755446 TTAAAAATATGATTTTAATT
1 TTAAAAATATGATATTAATC
1755466 TTAAAA
1 TTAAAA
1755472 TATAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 1 0.05
20 14 0.64
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (20 bp):
TTAAAAATATGATATTAATC
Found at i:1755469 original size:20 final size:20
Alignment explanation
Indices: 1755428--1755484 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
1755418 ATATAGTTTA
* *
1755428 TTAAAAA-A-GATATTAATC
1 TTAAAAATATGATTTTAATT
1755446 TTAAAAATATGATTTTAATT
1 TTAAAAATATGATTTTAATT
* *
1755466 TT-AAAATATAATTTAAATT
1 TTAAAAATATGATTTTAATT
1755485 ATGTTTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 7 0.21
19 16 0.48
20 10 0.30
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
TTAAAAATATGATTTTAATT
Found at i:1755523 original size:26 final size:26
Alignment explanation
Indices: 1755494--1755551 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
1755484 TATGTTTTTG
1755494 AAAATTA-ATAAATGA-TTTAAAAATTT
1 AAAATTACA-AAATGATTTTAAAAA-TT
* *
1755520 AAAACTACAAAATTATTTTAAAAATT
1 AAAATTACAAAATGATTTTAAAAATT
1755546 AAAATT
1 AAAATT
1755552 TTAAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAATTACAAAATGATTTTAAAAATT
Found at i:1755677 original size:12 final size:12
Alignment explanation
Indices: 1755626--1755683 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1755616 AAAAAATTAA
1755626 AAAATTTAATTT
1 AAAATTTAATTT
* *
1755638 TAAACTTAATTT
1 AAAATTTAATTT
**
1755650 AAAATTATTTTTT
1 AAAATT-TAATTT
*
1755663 AAAATTTCATTT
1 AAAATTTAATTT
*
1755675 AAAAATTAA
1 AAAATTTAA
1755684 CTTTTTTTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
12 25 0.71
13 10 0.29
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATTTAATTT
Found at i:1755733 original size:13 final size:13
Alignment explanation
Indices: 1755626--1755733 Score: 53
Period size: 13 Copynumber: 8.3 Consensus size: 13
1755616 AAAAAATTAA
*
1755626 AAAATTTAATTTT
1 AAAATTAAATTTT
*
1755639 AAACTT-AA-TTT
1 AAAATTAAATTTT
**
1755650 AAAATTATTTTTT
1 AAAATTAAATTTT
** *
1755663 AAAATTTCATTTA
1 AAAATTAAATTTT
*
1755676 AAAATTAACTTTTTT
1 AAAATTAA--ATTTT
*
1755691 TAAA--AAATTTT
1 AAAATTAAATTTT
* *
1755702 AAAATCTTAAGTTTA
1 AAAA--TTAAATTTT
1755717 AAAATTAAATTTT
1 AAAATTAAATTTT
1755730 AAAA
1 AAAA
1755734 CTTTTAAATA
Statistics
Matches: 68, Mismatches: 19, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
11 15 0.22
12 2 0.03
13 36 0.53
15 15 0.22
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (13 bp):
AAAATTAAATTTT
Found at i:1756086 original size:21 final size:21
Alignment explanation
Indices: 1756053--1756109 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1756043 AAATATGAAA
* **
1756053 TTTAAATATTTTATTTTATTT
1 TTTAAATTTTTTATAATATTT
* *
1756074 TTTTAATTTTTTAAAATATTT
1 TTTAAATTTTTTATAATATTT
1756095 TTTAAATTTATTTAT
1 TTTAAATTT-TTTAT
1756110 CAAAAAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTAAATTTTTTATAATATTT
Found at i:1756361 original size:22 final size:23
Alignment explanation
Indices: 1756319--1756362 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1756309 AACAAACAAA
* *
1756319 TTAAAATTTTAAATATTATATTT
1 TTAAAATTTTAAAAATCATATTT
1756342 TTAAAA-TTTAAAAATCATATT
1 TTAAAATTTTAAAAATCATATT
1756363 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAAAATTTTAAAAATCATATTT
Found at i:1757954 original size:24 final size:23
Alignment explanation
Indices: 1757902--1757956 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1757892 ATCCATGTAA
1757902 TTCATGTATAAAATTAATTAGGG
1 TTCATGTATAAAATTAATTAGGG
* *
1757925 TACATGTATAGATATTTAA-TAGGG
1 TTCATGTATA-A-AATTAATTAGGG
1757949 TTCATGTA
1 TTCATGTA
1757957 ACAAGTCACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.33
24 13 0.48
25 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.40
Consensus pattern (23 bp):
TTCATGTATAAAATTAATTAGGG
Found at i:1762425 original size:24 final size:23
Alignment explanation
Indices: 1762373--1762427 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1762363 ATCCATGTAA
1762373 TTCATGTATAAAATTAATTAGGG
1 TTCATGTATAAAATTAATTAGGG
* *
1762396 TACATGTATAGATATTTAA-TAGGG
1 TTCATGTATA-A-AATTAATTAGGG
1762420 TTCATGTA
1 TTCATGTA
1762428 ACAAGTCACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.33
24 13 0.48
25 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.40
Consensus pattern (23 bp):
TTCATGTATAAAATTAATTAGGG
Found at i:1769081 original size:21 final size:21
Alignment explanation
Indices: 1769052--1769094 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1769042 TTAATTACTA
*
1769052 TTTTATTAAGAAAT-TATTAAT
1 TTTTATTAA-AAATATAATAAT
*
1769073 TTTTTTTAAAAATATAATAAT
1 TTTTATTAAAAATATAATAAT
1769094 T
1 T
1769095 ATAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTATTAAAAATATAATAAT
Found at i:1770123 original size:12 final size:12
Alignment explanation
Indices: 1770106--1770131 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1770096 TATAGAAATT
1770106 ATTTTATGTCTC
1 ATTTTATGTCTC
1770118 ATTTTATGTCTC
1 ATTTTATGTCTC
1770130 AT
1 AT
1770132 ATCATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (12 bp):
ATTTTATGTCTC
Found at i:1770221 original size:22 final size:22
Alignment explanation
Indices: 1770161--1770222 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
1770151 CAAATAATTA
*
1770161 ATTA-ATTATTTATTTAAAAAT
1 ATTATATTATTTATTAAAAAAT
*
1770182 ATTTTATTATAATT-TTAAAAAAT
1 ATTATATTAT--TTATTAAAAAAT
1770205 A-TATATTATTCTATTAAA
1 ATTATATTATT-TATTAAA
1770223 TTTACGAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 1 0.03
21 4 0.12
22 17 0.52
23 9 0.27
24 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTATATTATTTATTAAAAAAT
Found at i:1770763 original size:13 final size:13
Alignment explanation
Indices: 1770747--1770821 Score: 71
Period size: 13 Copynumber: 5.6 Consensus size: 13
1770737 TCATTATTAA
1770747 AATTTTTAAAAAT
1 AATTTTTAAAAAT
1770760 AATTTTTAAAAAT
1 AATTTTTAAAAAT
* *
1770773 AACTATTAAAAAT
1 AATTTTTAAAAAT
* **
1770786 AATATTTTATACTT
1 AAT-TTTTAAAAAT
1770800 AATATTTT-AAAAT
1 AAT-TTTTAAAAAT
1770813 AATTCTTTA
1 AATT-TTTA
1770822 TTTATTAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
12 1 0.02
13 34 0.69
14 14 0.29
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:1770805 original size:26 final size:27
Alignment explanation
Indices: 1770751--1770821 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
1770741 TATTAAAATT
1770751 TTTAAAAATAATTTTTAAAAATAACTA
1 TTTAAAAATAATTTTTAAAAATAACTA
* **
1770778 -TTAAAAATAATATTTTATACTTAA-TA
1 TTTAAAAATAAT-TTTTAAAAATAACTA
*
1770804 TTTTAAAATAATTCTTTA
1 TTTAAAAATAATT-TTTA
1770822 TTTATTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 14 0.38
27 23 0.62
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTAAAAATAATTTTTAAAAATAACTA
Found at i:1773892 original size:15 final size:15
Alignment explanation
Indices: 1773874--1773903 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1773864 ATATAAACCT
*
1773874 AATATTTATAAAAAA
1 AATACTTATAAAAAA
1773889 AATACTTATAAAAAA
1 AATACTTATAAAAAA
1773904 TAAAATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AATACTTATAAAAAA
Found at i:1775538 original size:20 final size:20
Alignment explanation
Indices: 1775509--1775548 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1775499 AATAAGCAAT
*
1775509 AATAAAAAATTAAA-TAAAA
1 AATAAAAAATCAAATTAAAA
1775528 AATATAAAAATCAAATTAAAA
1 AATA-AAAAATCAAATTAAAA
1775549 GTTGAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (20 bp):
AATAAAAAATCAAATTAAAA
Found at i:1776873 original size:2 final size:2
Alignment explanation
Indices: 1776864--1776892 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1776854 TCATATATGC
1776864 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1776893 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:1778154 original size:29 final size:30
Alignment explanation
Indices: 1778120--1778183 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1778110 GATAAGTGAG
* *
1778120 TATTTTTTA-AACATTAAAAGA-ATAAATG
1 TATTTTTTATAAAATTAAAAGAGATAAATA
**
1778148 TATTTTTTATAAAATTTTAAGAGATAAATA
1 TATTTTTTATAAAATTAAAAGAGATAAATA
1778178 TATTTT
1 TATTTT
1778184 ATTTTTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 9 0.30
29 9 0.30
30 12 0.40
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (30 bp):
TATTTTTTATAAAATTAAAAGAGATAAATA
Found at i:1779181 original size:23 final size:23
Alignment explanation
Indices: 1779147--1779191 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1779137 AAATTGTAAA
1779147 TATTAAAATTTAAAATTTAAAAT
1 TATTAAAATTTAAAATTTAAAAT
* **
1779170 TATTAAATTTTAATTTTTAAAA
1 TATTAAAATTTAAAATTTAAAA
1779192 AATAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTAAAATTTAAAATTTAAAAT
Found at i:1779368 original size:22 final size:23
Alignment explanation
Indices: 1779334--1779376 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
1779324 TTTAGATTCT
1779334 TATTTTTAATTT-ATAATATATGA
1 TATTTTTAATTTAAT-ATATATGA
*
1779357 TATTTTT-GTTTAATATATAT
1 TATTTTTAATTTAATATATAT
1779377 TTAAATATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (23 bp):
TATTTTTAATTTAATATATATGA
Found at i:1780732 original size:2 final size:2
Alignment explanation
Indices: 1780725--1780754 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1780715 CTTTTGATAC
*
1780725 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1780755 TCGAGGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1781217 original size:14 final size:14
Alignment explanation
Indices: 1781193--1781229 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1781183 TTAAATATAA
1781193 ATATT-TTTTAATG
1 ATATTATTTTAATG
1781206 ATATTATTTTAATG
1 ATATTATTTTAATG
*
1781220 ATATAATTTT
1 ATATTATTTT
1781230 TGATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (14 bp):
ATATTATTTTAATG
Found at i:1781351 original size:11 final size:11
Alignment explanation
Indices: 1781325--1781367 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
1781315 ATAAAATTAA
1781325 TTTTTATCAA-
1 TTTTTATCAAT
1781335 -TTTTATCAAT
1 TTTTTATCAAT
* *
1781345 TTTTTATTAAA
1 TTTTTATCAAT
1781356 TTTTTATCAAT
1 TTTTTATCAAT
1781367 T
1 T
1781368 AAATTAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTTATCAAT
Found at i:1781837 original size:19 final size:19
Alignment explanation
Indices: 1781813--1781849 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1781803 TTATTTTTAG
*
1781813 ATAATAATTTATGTAATTA
1 ATAATAATTTATATAATTA
*
1781832 ATAATATTTTATATAATT
1 ATAATAATTTATATAATT
1781850 TTGTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
ATAATAATTTATATAATTA
Found at i:1781967 original size:20 final size:19
Alignment explanation
Indices: 1781942--1782001 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
1781932 ATTATTTTAA
*
1781942 AGTAATGTTTTATGTATATT
1 AGTAATATTTTATGTA-ATT
1781962 AGTAATATTTTTATGTAATT
1 AGTAATA-TTTTATGTAATT
*
1781982 AGGTAATATTTTATATAATT
1 A-GTAATATTTTATGTAATT
1782002 TGATTGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (19 bp):
AGTAATATTTTATGTAATT
Found at i:1782328 original size:77 final size:75
Alignment explanation
Indices: 1782047--1782342 Score: 224
Period size: 77 Copynumber: 3.9 Consensus size: 75
1782037 GGTGATGTTT
* * * * * *
1782047 TTATTTATAAATAATATTTTATGTAACT-TAATATTTTTATGTAATAGGGTAATGTTTAATATAA
1 TTATTTTTAAGTAATATTTTATGTAACTATAATATTTTTATGTAATTGAGTAATATTT-ATGTAA
*
1782111 TTTTAATAAAAA
65 -TTTATTAAAAA
* * * * * * *
1782123 TTATTTTTTAGTAATGTTTTATGTTAGTA-AAT-TTTTTATATAATT-AGATAATATTTTACGTG
1 TTATTTTTAAGTAATATTTTATGTAACTATAATATTTTTATGTAATTGAG-TAATA-TTTATGTA
* *
1782185 ATTT-TGATGAAA
64 ATTTATTA-AAAA
* * * * * * * * *
1782197 TTATTTTTAGGTAATATATTATATAGCAGATAATATTTATATGTAAGTGGGTAATATTTATGCAA
1 TTATTTTTAAGTAATATTTTATGTAAC-TATAATATTTTTATGTAATTGAGTAATATTTATGTAA
1782262 TTCTATTAAAAA
65 TT-TATTAAAAA
* * *
1782274 TTATTCTTAAGTAATATTTTATGTAACTAATAATATTTTTATGTAATTTAGTAATATTTTATTTA
1 TTATTTTTAAGTAATATTTTATGTAACT-ATAATATTTTTATGTAATTGAGTAATA-TTTATGTA
1782339 ATTT
64 ATTT
1782343 GGTAATATTT
Statistics
Matches: 162, Mismatches: 46, Indels: 23
0.70 0.20 0.10
Matches are distributed among these distances:
73 1 0.01
74 26 0.16
75 19 0.12
76 39 0.24
77 65 0.40
78 12 0.07
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (75 bp):
TTATTTTTAAGTAATATTTTATGTAACTATAATATTTTTATGTAATTGAGTAATATTTATGTAAT
TTATTAAAAA
Found at i:1782361 original size:20 final size:20
Alignment explanation
Indices: 1782283--1782380 Score: 110
Period size: 20 Copynumber: 5.0 Consensus size: 20
1782273 ATTATTCTTA
*
1782283 AGTAATATTTTATGTAA-CT
1 AGTAATATTTTATGTAATTT
*
1782302 AATAATATTTTTATGTAATTT
1 AGTAATA-TTTTATGTAATTT
*
1782323 AGTAATATTTTATTTAATTT
1 AGTAATATTTTATGTAATTT
* *
1782343 GGTAATATTTTATGTAATTC
1 AGTAATATTTTATGTAATTT
* *
1782363 GGTAATATTAT-TGTAATT
1 AGTAATATTTTATGTAATT
1782381 CTAATGAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.19
20 49 0.71
21 7 0.10
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (20 bp):
AGTAATATTTTATGTAATTT
Found at i:1782435 original size:76 final size:76
Alignment explanation
Indices: 1782350--1782546 Score: 218
Period size: 77 Copynumber: 2.6 Consensus size: 76
1782340 TTTGGTAATA
* *
1782350 TTTTATGTAATTCGGTAATATTATTGTAATTCTAATGAAAAGTTTTTAGGTAATGCTTT-ACATA
1 TTTTATGTAATTCGATAATATTATTGTAATTCTAATGAAAAGTTTTTAAGTAATG-TTTGACATA
** *
1782414 ATTGGGTATTGT
65 ATTGAATAATGT
* * * * * *
1782426 TTTTATGTAATTTGATAATGTTTTATGTAATTATGATGAAAAGTTTTTAAGTAATGTTTGACCTA
1 TTTTATGTAATTCGATAATATTAT-TGTAATTCTAATGAAAAGTTTTTAAGTAATGTTTGACATA
1782491 ATTGAATAATGT
65 ATTGAATAATGT
** * *
1782503 TCATATGTAATTCGATAATATTCA-AGTAATTCTAATGGAAAGTT
1 TTTTATGTAATTCGATAATATT-ATTGTAATTCTAATGAAAAGTT
1782547 CTTTGAATGT
Statistics
Matches: 98, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
76 39 0.40
77 59 0.60
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.46
Consensus pattern (76 bp):
TTTTATGTAATTCGATAATATTATTGTAATTCTAATGAAAAGTTTTTAAGTAATGTTTGACATAA
TTGAATAATGT
Found at i:1782436 original size:21 final size:20
Alignment explanation
Indices: 1782412--1782457 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1782402 ATGCTTTACA
* *
1782412 TAATTGGGTATTGTTTTTATG
1 TAATTGGATAATG-TTTTATG
*
1782433 TAATTTGATAATGTTTTATG
1 TAATTGGATAATGTTTTATG
1782453 TAATT
1 TAATT
1782458 ATGATGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (20 bp):
TAATTGGATAATGTTTTATG
Found at i:1782474 original size:24 final size:21
Alignment explanation
Indices: 1782424--1782480 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 21
1782414 ATTGGGTATT
*
1782424 GTTTTTATGTAATTTGATAAT
1 GTTTTTATGTAATTTGATAAA
1782445 G-TTTTATGTAATTATGATGAAAA
1 GTTTTTATGTAATT-TGAT--AAA
*
1782468 GTTTTTAAGTAAT
1 GTTTTTATGTAAT
1782481 GTTTGACCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 12 0.40
21 5 0.17
23 3 0.10
24 10 0.33
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
GTTTTTATGTAATTTGATAAA
Found at i:1782716 original size:20 final size:21
Alignment explanation
Indices: 1782677--1782740 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 21
1782667 AATGTTCTAC
*
1782677 GTAATTTGATAATGATTTTAT
1 GTAATTTCATAATGATTTTAT
*
1782698 GTAATTTCATAGT-ATTTTAT
1 GTAATTTCATAATGATTTTAT
*
1782718 GTAATTTTGA-AAT-ATTTTAT
1 GTAA-TTTCATAATGATTTTAT
1782738 GTA
1 GTA
1782741 TTTGGACAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (21 bp):
GTAATTTCATAATGATTTTAT
Found at i:1782751 original size:20 final size:20
Alignment explanation
Indices: 1782677--1782751 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
1782667 AATGTTCTAC
1782677 GTAATTT-GATAATGATTTTAT
1 GTAATTTGGA-AAT-ATTTTAT
* *
1782698 GTAATTT-CATAGTATTTTAT
1 GTAATTTGGA-AATATTTTAT
*
1782718 GTAATTTTGAAATATTTTAT
1 GTAATTTGGAAATATTTTAT
1782738 GT-ATTTGGACAATA
1 GTAATTTGGA-AATA
1782752 GTATGTTTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.13
20 29 0.62
21 12 0.26
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (20 bp):
GTAATTTGGAAATATTTTAT
Found at i:1783155 original size:54 final size:55
Alignment explanation
Indices: 1783039--1783157 Score: 131
Period size: 54 Copynumber: 2.2 Consensus size: 55
1783029 ATATAACTTG
* * * *
1783039 TAATG-TTTAT-ATAGGTAATGTTTTATGTATTTTTTATGAAAATTATTCTTTGG
1 TAATGTTTTATAATAGGTAATATTTTATGTATTTCTGATGAAAATTATTCTTTGA
* *
1783092 TAATATTTTATAATTAGGTAATATTTTATGTA-TTCTGAT-TAAATTATT-TTTAGA
1 TAATGTTTTATAA-TAGGTAATATTTTATGTATTTCTGATGAAAATTATTCTTT-GA
1783146 TAATGTTTTATA
1 TAATGTTTTATA
1783158 TAACGAGTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
53 7 0.13
54 25 0.45
55 6 0.11
56 17 0.31
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.55
Consensus pattern (55 bp):
TAATGTTTTATAATAGGTAATATTTTATGTATTTCTGATGAAAATTATTCTTTGA
Found at i:1783264 original size:30 final size:31
Alignment explanation
Indices: 1783202--1783280 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 31
1783192 TAATAAAAAT
*
1783202 TATTTTTAGGTAATGTATTATGTAACTAGTAA
1 TATTTTTA-GTAATGTATTATATAACTAGTAA
*
1783234 TATTTTTA-TAATAGT-TTATATAACTTGTAA
1 TATTTTTAGTAAT-GTATTATATAACTAGTAA
*
1783264 TATTTGTATGTAATGTA
1 TATTTTTA-GTAATGTA
1783281 GTAATATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 24 0.60
31 4 0.10
32 12 0.30
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.51
Consensus pattern (31 bp):
TATTTTTAGTAATGTATTATATAACTAGTAA
Found at i:1784488 original size:17 final size:17
Alignment explanation
Indices: 1784450--1784489 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1784440 GGGTGAGGGG
*
1784450 AAAGGAGGGGGAAGAGG
1 AAAGGAGGGGGAAGAGA
* *
1784467 GAAGGATGGGGAAGAGA
1 AAAGGAGGGGGAAGAGA
1784484 AAAGGA
1 AAAGGA
1784490 AAAGAATGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.53, T:0.03
Consensus pattern (17 bp):
AAAGGAGGGGGAAGAGA
Done.