Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007799.1 Hibiscus syriacus cultivar Beakdansim tig00110109_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1433344
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1332881 original size:20 final size:20
Alignment explanation
Indices: 1332826--1332882 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1332816 ATCTGAGTTA
1332826 ATTATAAAATTATTATTTATTT
1 ATTATAAAATTA-TA-TTATTT
*
1332848 A-TATAAAAAATATATTATTT
1 ATTAT-AAAATTATATTATTT
*
1332868 ATTATAAATTTATAT
1 ATTATAAAATTATAT
1332883 ATATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 15 0.50
21 8 0.27
22 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATAAAATTATATTATTT
Found at i:1333700 original size:42 final size:42
Alignment explanation
Indices: 1333641--1333760 Score: 195
Period size: 42 Copynumber: 2.9 Consensus size: 42
1333631 TTTCCCCGAA
* * *
1333641 TTCCCTTGTTTGTTTCACGTAATTCATTTTCCGGAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
* *
1333683 TTCCCGTGTTTGTTTCACGTAATTTGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
1333725 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1333761 TGTAATTCAT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
Found at i:1333996 original size:22 final size:22
Alignment explanation
Indices: 1333950--1334032 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 22
1333940 AATTATTAAA
* *
1333950 ATATTTAAAAT-ATAT-TTATT
1 ATATTTATAATAATATAATATT
1333970 AATATTTATAATAATATAATATT
1 -ATATTTATAATAATATAATATT
* *
1333993 ATATTTTTAATAATATATTA-T
1 ATATTTATAATAATATAATATT
1334014 AT-TTTAATAATAA-ATAATA
1 ATATTT-ATAATAATATAATA
1334033 AATTTTTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 8 0.15
21 19 0.36
22 22 0.42
23 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTATAATAATATAATATT
Found at i:1333998 original size:43 final size:39
Alignment explanation
Indices: 1333950--1334029 Score: 97
Period size: 43 Copynumber: 1.9 Consensus size: 39
1333940 AATTATTAAA
*
1333950 ATATTTAAAATATATTTATTAATATTTATAATAATATAATATT
1 ATATTTAAAATA-ATATATT-ATATTT-TAATAATA-AATATT
**
1333993 ATATTTTTAATAATATATTATATTTTAATAATAAATA
1 ATATTTAAAATAATATATTATATTTTAATAATAAATA
1334030 ATAAATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 4 0.12
40 8 0.24
41 6 0.18
42 6 0.18
43 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (39 bp):
ATATTTAAAATAATATATTATATTTTAATAATAAATATT
Found at i:1334020 original size:18 final size:19
Alignment explanation
Indices: 1333988--1334025 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1333978 TAATAATATA
1333988 ATATTATATTTTTAATAAT
1 ATATTATATTTTTAATAAT
1334007 ATATTATA-TTTTAATAAT
1 ATATTATATTTTTAATAAT
1334025 A
1 A
1334026 AATAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTATATTTTTAATAAT
Found at i:1334052 original size:30 final size:28
Alignment explanation
Indices: 1334001--1334084 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 28
1333991 TTATATTTTT
1334001 AATAATA-TA-TTATAT-TTTAATAATA
1 AATAATATTATTTATATATTTAATAATA
* *
1334026 AATAATAAATTTTTTATATATTTAATAATG
1 AATAAT--ATTATTTATATATTTAATAATA
1334056 AATAATATTATTTATATATTTCAATAATA
1 AATAATATTATTTATATATTT-AATAATA
1334085 TTTTAGTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
25 6 0.12
27 1 0.02
28 15 0.31
29 12 0.24
30 15 0.31
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
AATAATATTATTTATATATTTAATAATA
Found at i:1334340 original size:20 final size:20
Alignment explanation
Indices: 1334282--1334331 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1334272 TTTTCAGATG
1334282 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1334302 TTTTCTAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1334322 TTTTCCAGAA
1 TTTTCCAGAA
1334332 TTCAAATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1334350 original size:15 final size:15
Alignment explanation
Indices: 1334314--1334393 Score: 81
Period size: 15 Copynumber: 5.4 Consensus size: 15
1334304 TTCTAGAAAT
**
1334314 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1334329 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** **
1334343 GTAATTCATTTTTTA
1 GTAATTCAAATTCCA
* *
1334358 TTAATTCAAATTTCA
1 GTAATTCAAATTCCA
1334373 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1334388 GTAATT
1 GTAATT
1334394 TATTTTTCGA
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
14 12 0.23
15 40 0.77
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1334393 original size:30 final size:30
Alignment explanation
Indices: 1334314--1334393 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
1334304 TTCTAGAAAT
1334314 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
** * *
1334343 GTAATTCATTTTTTATTAATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
1334373 GTAATTCAAATTCCAGTAATT
1 GTAATTCATTTTCCAGTAATT
1334394 TATTTTTCGA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 13 0.32
30 28 0.68
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1338938 original size:27 final size:27
Alignment explanation
Indices: 1338899--1338950 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
1338889 GAATGAAATT
1338899 AAAATTTGAAA-TTCAACTTGAGAGTA
1 AAAATTTGAAATTTCAACTTGAGAGTA
* *
1338925 AAAAGTTTTAAATTTCAATTTGAGAG
1 AAAA-TTTGAAATTTCAACTTGAGAG
1338951 GAGAGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 6 0.27
28 12 0.55
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (27 bp):
AAAATTTGAAATTTCAACTTGAGAGTA
Found at i:1338966 original size:19 final size:19
Alignment explanation
Indices: 1338942--1338980 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1338932 TTAAATTTCA
1338942 ATTTGAGAGGAGAGAATTT
1 ATTTGAGAGGAGAGAATTT
1338961 ATTTGAGAGGAGAGAATTT
1 ATTTGAGAGGAGAGAATTT
1338980 A
1 A
1338981 AATACCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (19 bp):
ATTTGAGAGGAGAGAATTT
Found at i:1345801 original size:22 final size:20
Alignment explanation
Indices: 1345750--1345801 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
1345740 TTGAATTAAT
* *
1345750 AAAAAAATATTATTTTATTT
1 AAAAAAATATTATTTAATTG
1345770 AATAAAAATATTGATTTAATTG
1 AA-AAAAATATT-ATTTAATTG
1345792 AAAAATAATA
1 AAAAA-AATA
1345802 ATATAGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 12 0.44
22 13 0.48
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
AAAAAAATATTATTTAATTG
Found at i:1346168 original size:5 final size:6
Alignment explanation
Indices: 1346154--1346178 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1346144 AATGTAATAA
1346154 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
1346179 AAAATTATTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:1346509 original size:23 final size:24
Alignment explanation
Indices: 1346477--1346521 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1346467 ATGTATTTTT
1346477 ATTTCGTTCTCTA-AAATTTTATA
1 ATTTCGTTCTCTACAAATTTTATA
*
1346500 ATTTCTTTCTCTACAAATTTTA
1 ATTTCGTTCTCTACAAATTTTA
1346522 AAAGTTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.29, C:0.16, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTCGTTCTCTACAAATTTTATA
Found at i:1347128 original size:28 final size:28
Alignment explanation
Indices: 1347062--1347128 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
1347052 TATTTTGTTA
1347062 AATCTCCGACTATTAAAACTTACAAAAT
1 AATCTCCGACTATTAAAACTTACAAAAT
* *
1347090 AATCCCCGACTATTAAAATTTACAAAAT
1 AATCTCCGACTATTAAAACTTACAAAAT
* *
1347118 GATCTCTGACT
1 AATCTCCGACT
1347129 GTAAAGTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (28 bp):
AATCTCCGACTATTAAAACTTACAAAAT
Found at i:1351409 original size:2 final size:2
Alignment explanation
Indices: 1351402--1351426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1351392 ATTCTCTGAC
1351402 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
1351427 AACAAATCTT
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:1354947 original size:38 final size:37
Alignment explanation
Indices: 1354903--1355008 Score: 167
Period size: 38 Copynumber: 2.8 Consensus size: 37
1354893 TCGGGTTGGA
*
1354903 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCAGG
1 TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCAGG
*
1354940 TATTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCGGG
1 T-TTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCAGG
*
1354978 TTTTTTAAAGTGTGATATTCAGGTCGGGTCG
1 TTTTTT-AAGTGTGATATTCGGGTCGGGTCG
1355009 AGTTCGGGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
37 6 0.09
38 58 0.91
ACGTcount: A:0.16, C:0.10, G:0.35, T:0.39
Consensus pattern (37 bp):
TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCAGG
Found at i:1358951 original size:14 final size:14
Alignment explanation
Indices: 1358932--1358958 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1358922 TTATTATTAA
1358932 TTTTTACTAGAGAT
1 TTTTTACTAGAGAT
1358946 TTTTTACTAGAGA
1 TTTTTACTAGAGA
1358959 ATTAGGATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (14 bp):
TTTTTACTAGAGAT
Found at i:1359316 original size:14 final size:14
Alignment explanation
Indices: 1359297--1359330 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1359287 TTAAATGATA
*
1359297 AACGAACACAAATG
1 AACGAACACAAACG
*
1359311 AACGAACATAAACG
1 AACGAACACAAACG
1359325 AACGAA
1 AACGAA
1359331 TGTAAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.21, G:0.15, T:0.06
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:1359326 original size:24 final size:24
Alignment explanation
Indices: 1359294--1359407 Score: 108
Period size: 24 Copynumber: 4.8 Consensus size: 24
1359284 CATTTAAATG
*
1359294 ATAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAAATGAACAAAC
*
1359318 ATAAACG-A-ACGAATGTAAACAAAC
1 ATAAACGAACACAAATG--AACAAAC
* *
1359342 ATAAACGAACACAAACGAACGAAC
1 ATAAACGAACACAAATGAACAAAC
* * *
1359366 GTAAACGAACAC-AATAAATAAAC
1 ATAAACGAACACAAATGAACAAAC
* *
1359389 ATAATCGAACATAAATGAA
1 ATAAACGAACACAAATGAA
1359408 AATATTTTTT
Statistics
Matches: 71, Mismatches: 14, Indels: 10
0.75 0.15 0.11
Matches are distributed among these distances:
22 6 0.08
23 17 0.24
24 42 0.59
25 1 0.01
26 5 0.07
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACAAAC
Found at i:1359349 original size:34 final size:34
Alignment explanation
Indices: 1359311--1359376 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
1359301 AACACAAATG
* *
1359311 AACGAACATAAACGAACGAATGTAAACAAACATA
1 AACGAACACAAACGAACGAACGTAAACAAACATA
*
1359345 AACGAACACAAACGAACGAACGTAAACGAACA
1 AACGAACACAAACGAACGAACGTAAACAAACA
1359377 CAATAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.58, C:0.21, G:0.14, T:0.08
Consensus pattern (34 bp):
AACGAACACAAACGAACGAACGTAAACAAACATA
Found at i:1359586 original size:14 final size:14
Alignment explanation
Indices: 1359569--1359601 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1359559 TGGACTAAAC
1359569 ATAAAGGAAC-ACAT
1 ATAAAGGAACGA-AT
1359583 ATAAAGGAACGAAT
1 ATAAAGGAACGAAT
1359597 ATAAA
1 ATAAA
1359602 CAAACATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.61, C:0.09, G:0.15, T:0.15
Consensus pattern (14 bp):
ATAAAGGAACGAAT
Found at i:1359610 original size:24 final size:24
Alignment explanation
Indices: 1359583--1359644 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1359573 AGGAACACAT
* *
1359583 ATAAAGGAACGAATATAAACAAAC
1 ATAAATGAACGAACATAAACAAAC
** *
1359607 ATAAATGAACGAACATTTACAAAT
1 ATAAATGAACGAACATAAACAAAC
1359631 ATAAATGAACGAAC
1 ATAAATGAACGAAC
1359645 GAACCCTATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (24 bp):
ATAAATGAACGAACATAAACAAAC
Found at i:1362472 original size:29 final size:29
Alignment explanation
Indices: 1362439--1362513 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
1362429 GCCAATGGAG
* ** **
1362439 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCAAGT
1362468 AGGTCGCCATGTAGTCCCGGCGACCAAGT
1 AGGTCGCCATGTAGTCCCGGCGACCAAGT
1362497 AGGTCGCCATGTAGTCC
1 AGGTCGCCATGTAGTCC
1362514 TATCTCACGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.17, C:0.29, G:0.32, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCAAGT
Found at i:1362876 original size:25 final size:26
Alignment explanation
Indices: 1362826--1362876 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1362816 CTTGGTCGCC
* **
1362826 GAGATTGCAGCCGAAGAAAGGGAGAA
1 GAGACTGCAGCCGAAGAAAGAAAGAA
1362852 GAGACTGCAGCCG-AGAAAGAAAGAA
1 GAGACTGCAGCCGAAGAAAGAAAGAA
1362877 AGGGAGAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.45, C:0.14, G:0.35, T:0.06
Consensus pattern (26 bp):
GAGACTGCAGCCGAAGAAAGAAAGAA
Found at i:1363077 original size:41 final size:41
Alignment explanation
Indices: 1363032--1363120 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
1363022 TATATGATTG
* *
1363032 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
1363073 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
1363114 TTAGTTT
1 TTAGTTT
1363121 GTTTTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:1363163 original size:45 final size:45
Alignment explanation
Indices: 1363060--1363191 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
1363050 TACATAAATT
*
1363060 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTAGTTATA-TAA
*
1363102 AAAAA-TAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
*
1363146 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAT
1363192 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 19 0.25
46 5 0.07
47 7 0.09
48 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
Found at i:1363386 original size:16 final size:16
Alignment explanation
Indices: 1363354--1363400 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1363344 TTTAAAAAGT
*
1363354 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
1363370 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
1363386 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
1363401 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:1363395 original size:15 final size:14
Alignment explanation
Indices: 1363375--1363405 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1363365 GTTTATTAGT
1363375 TTATTATATTATAAG
1 TTATTATATTA-AAG
1363390 TTATTATATTAAAG
1 TTATTATATTAAAG
1363404 TT
1 TT
1363406 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:1365576 original size:17 final size:17
Alignment explanation
Indices: 1365554--1365586 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1365544 CAATGATTTT
*
1365554 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
1365571 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
1365587 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:1365603 original size:24 final size:22
Alignment explanation
Indices: 1365571--1365639 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
1365561 AAATCATTAC
1365571 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
1365593 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
1365618 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
1365640 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:1365810 original size:38 final size:38
Alignment explanation
Indices: 1365768--1365864 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 38
1365758 CACTTATTTG
** *
1365768 TTAGTATTCTATAATTATTAGT-AATAATTATTAAATCA
1 TTAGTATTAAATAATTATTA-TAAATAATTACTAAATCA
*
1365806 TTAGTATTAAATCATTATTATAAATAATTACTAAAT-A
1 TTAGTATTAAATAATTATTATAAATAATTACTAAATCA
* *
1365843 ATA--ACTAAATAATTATTATAAA
1 TTAGTATTAAATAATTATTATAAA
1365865 ATCATTATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
35 17 0.33
37 4 0.08
38 30 0.59
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (38 bp):
TTAGTATTAAATAATTATTATAAATAATTACTAAATCA
Found at i:1365885 original size:12 final size:13
Alignment explanation
Indices: 1365794--1366129 Score: 148
Period size: 14 Copynumber: 24.9 Consensus size: 13
1365784 ATTAGTAATA
1365794 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
1365808 AGTATTAAATCATT
1 ATTA-TAAATCATT
1365822 ATTATAAAT-A--
1 ATTATAAATCATT
1365832 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
1365843 ATAACTAAATAATT
1 ATTA-TAAATCATT
1365857 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
1365871 ATTAT-AATGATT
1 ATTATAAATCATT
1365883 ATTATCAAATCATT
1 ATTAT-AAATCATT
1365897 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
1365916 AAATATTTAAATCATT
1 --AT-TATAAATCATT
1365932 A-T-TAAATCATT
1 ATTATAAATCATT
* *
1365943 TTTAT-AATGATT
1 ATTATAAATCATT
1365955 ATTACTAAATCATT
1 ATTA-TAAATCATT
* *
1365969 ATTA-GAATGATT
1 ATTATAAATCATT
1365981 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
1365995 ACTAT-AATGATT
1 ATTATAAATCATT
1366007 ATTATCAAATCATT
1 ATTAT-AAATCATT
1366021 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
1366040 AAATATTTAAATCATT
1 --AT-TATAAATCATT
1366056 A-T-TAAATCATT
1 ATTATAAATCATT
* *
1366067 TTTAT-AATGATT
1 ATTATAAATCATT
1366079 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
1366093 ATTAT-AATGATT
1 ATTATAAATCATT
1366105 ATTATCAAATCATT
1 ATTAT-AAATCATT
*
1366119 ACTAT-AATCAT
1 ATTATAAATCAT
1366130 CAAATCATTA
Statistics
Matches: 259, Mismatches: 28, Indels: 72
0.72 0.08 0.20
Matches are distributed among these distances:
10 4 0.02
11 33 0.13
12 72 0.28
13 11 0.04
14 87 0.34
15 2 0.01
16 16 0.06
17 2 0.01
18 6 0.02
19 22 0.08
20 2 0.01
21 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:1365892 original size:26 final size:26
Alignment explanation
Indices: 1365794--1366126 Score: 218
Period size: 26 Copynumber: 13.4 Consensus size: 26
1365784 ATTAGTAATA
* * *
1365794 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
1365819 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * * *
1365843 ATAACTA-AATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
1365868 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
1365894 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
1365917 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
1365940 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
*
1365966 ATTATTAGAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
1365992 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
1366018 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
1366041 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
1366064 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
1366090 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
1366116 ATTACTATAAT
1 ATTATTATAAT
1366127 CATCAAATCA
Statistics
Matches: 236, Mismatches: 50, Indels: 43
0.72 0.15 0.13
Matches are distributed among these distances:
21 8 0.03
22 4 0.02
23 30 0.13
24 26 0.11
25 34 0.14
26 132 0.56
27 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:1366018 original size:124 final size:123
Alignment explanation
Indices: 1365810--1366126 Score: 530
Period size: 124 Copynumber: 2.6 Consensus size: 123
1365800 AAATCATTAG
* * * * * * * *
1365810 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTAT
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTAAATGATTATTATCAAATCATTAC
1365873 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
1365931 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTAGAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTA-AATGATTATTATCAAATCATTA
1365996 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
65 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
1366055 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTA-AATGATTATTATCAAATCATTA
1366120 CTATAAT
65 CTATAAT
1366127 CATCAAATCA
Statistics
Matches: 184, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
121 18 0.10
123 17 0.09
124 149 0.81
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (123 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTAAATGATTATTATCAAATCATTAC
TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:1366062 original size:98 final size:99
Alignment explanation
Indices: 1365955--1366178 Score: 380
Period size: 98 Copynumber: 2.3 Consensus size: 99
1365945 TATAATGATT
* * *
1365955 ATTACTAAATCATTATTAGAATGATTATTA-TCAAATCATTACTATAATGATTATTATCAAATCA
1 ATTATTAAATCATTTTTATAATGATTATTACT-AAATCATTACTATAATGATTATTATCAAATCA
1366019 TTACTA-AATCATCAAATCATTAAATATTTAAATC
65 TTACTATAATCATCAAATCATTAAATATTTAAATC
*
1366053 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
1366118 TACTATAATCATCAAATCATTAAATATTTAAATC
66 TACTATAATCATCAAATCATTAAATATTTAAATC
*
1366152 ATTATTAAATAATTTTTATAATGATTA
1 ATTATTAAATCATTTTTATAATGATTA
1366179 ATAAATACAT
Statistics
Matches: 119, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
98 64 0.54
99 55 0.46
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (99 bp):
ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
TACTATAATCATCAAATCATTAAATATTTAAATC
Found at i:1366183 original size:23 final size:23
Alignment explanation
Indices: 1366045--1366185 Score: 61
Period size: 26 Copynumber: 5.9 Consensus size: 23
1366035 TCATTAAATA
* *
1366045 TTTA-AATCATTATTAAATCATT
1 TTTATAATCATTAATAAATAATT
* *
1366067 TTTATAATGATTATTACTAAATCATT
1 TTTATAATCATTA--A-TAAATAATT
* * *
1366093 ATTATAATGATTATTATCAAATCATT
1 TTTATAATCATTA--AT-AAATAATT
** * * * *
1366119 ACTATAATCATCAAATCATTAAATA
1 TTTATAATCAT-TAATAAAT-AATT
*
1366144 TTTA-AATCATTATTAAATAATT
1 TTTATAATCATTAATAAATAATT
*
1366166 TTTATAATGATTAATAAATA
1 TTTATAATCATTAATAAATA
1366186 CATAGAAATA
Statistics
Matches: 92, Mismatches: 19, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
22 11 0.12
23 24 0.26
24 8 0.09
25 7 0.08
26 41 0.45
27 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTATAATCATTAATAAATAATT
Found at i:1369082 original size:16 final size:16
Alignment explanation
Indices: 1369036--1369074 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1369026 TATTAATCTA
* *
1369036 ATGATTTAATATTTA-
1 ATGATTTAATAATAAT
1369051 ATGATTTAATAATAAT
1 ATGATTTAATAATAAT
1369067 ATGATTTA
1 ATGATTTA
1369075 GTCATAATCA
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:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (16 bp):
ATGATTTAATAATAAT
Found at i:1369847 original size:42 final size:47
Alignment explanation
Indices: 1369791--1369903 Score: 128
Period size: 50 Copynumber: 2.4 Consensus size: 47
1369781 GTTTAAAGAC
*
1369791 ACTAACAAATTAATTAATATTTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
*
1369833 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-T-ATTTTTTATATAATAT-ATATATAACTTAA
*
1369883 ACTAATAAACTAATATAATAT
1 ACTAACAAACTAAT-TAATAT
1369904 AACTTAAACT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
42 15 0.25
43 1 0.02
44 7 0.12
45 3 0.05
46 2 0.03
47 1 0.02
49 4 0.07
50 23 0.39
51 3 0.05
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.42
Consensus pattern (47 bp):
ACTAACAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
Found at i:1369903 original size:28 final size:30
Alignment explanation
Indices: 1369863--1369925 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
1369853 ATTTTTTATA
*
1369863 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1369893 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1369921 TAATA
1 TAATA
1369926 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1369932 original size:28 final size:28
Alignment explanation
Indices: 1369867--1369932 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
1369857 TTTATATAAT
*
1369867 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
1369895 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
1369923 ATAATTTATA
1 ATAATATATA
1369933 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:1369935 original size:21 final size:21
Alignment explanation
Indices: 1369902--1369950 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1369892 CTAATATAAT
1369902 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1369923 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1369944 ATTAACT
1 A-TAACT
1369951 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1370344 original size:21 final size:21
Alignment explanation
Indices: 1370319--1370390 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
1370309 ACGCAACTAT
1370319 GGATGCAACACATGCAGCTAC
1 GGATGCAACACATGCAGCTAC
* *
1370340 GGATGCAGGA-ATC-TCCCAGCTAT
1 GGATGCA--ACA-CAT-GCAGCTAC
*
1370363 GGATGCAACGCATGCAGCTAC
1 GGATGCAACACATGCAGCTAC
1370384 GGATGCA
1 GGATGCA
1370391 GGAATCTCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 22 0.55
22 3 0.08
23 15 0.38
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.17
Consensus pattern (21 bp):
GGATGCAACACATGCAGCTAC
Found at i:1370365 original size:44 final size:44
Alignment explanation
Indices: 1370315--1370405 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
1370305 AATAACGCAA
1370315 CTATGGATGCAACACATGCAGCTACGGATGCAGGAATCTCCCAG
1 CTATGGATGCAACACATGCAGCTACGGATGCAGGAATCTCCCAG
*
1370359 CTATGGATGCAACGCATGCAGCTACGGATGCAGGAATCTCCCAG
1 CTATGGATGCAACACATGCAGCTACGGATGCAGGAATCTCCCAG
1370403 CTA
1 CTA
1370406 GAATCTAGCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (44 bp):
CTATGGATGCAACACATGCAGCTACGGATGCAGGAATCTCCCAG
Found at i:1370366 original size:23 final size:23
Alignment explanation
Indices: 1370333--1370405 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
1370323 GCAACACATG
1370333 CAGCTACGGATGCAGGAATCTCC
1 CAGCTACGGATGCAGGAATCTCC
* ** *
1370356 CAGCTATGGATGCA--ACGCAT-G
1 CAGCTACGGATGCAGGAATC-TCC
1370377 CAGCTACGGATGCAGGAATCTCC
1 CAGCTACGGATGCAGGAATCTCC
1370400 CAGCTA
1 CAGCTA
1370406 GAATCTAGCT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
21 15 0.39
22 2 0.05
23 21 0.55
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (23 bp):
CAGCTACGGATGCAGGAATCTCC
Found at i:1370528 original size:20 final size:20
Alignment explanation
Indices: 1370503--1370540 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1370493 ACGTGCATGG
*
1370503 CCCATGCACAGTTCCCACGT
1 CCCATGCACAGCTCCCACGT
1370523 CCCATGCACAGCTCCCAC
1 CCCATGCACAGCTCCCAC
1370541 ATGCATCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.50, G:0.13, T:0.16
Consensus pattern (20 bp):
CCCATGCACAGCTCCCACGT
Found at i:1374761 original size:42 final size:42
Alignment explanation
Indices: 1374704--1374786 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
1374694 TCAAAAATGT
* *
1374704 TTTTAATATGTTAGTTTGATTTATTCGTGGATTGTTATTTTG
1 TTTTAATATGTTAGTTTGATATATTCGTAGATTGTTATTTTG
*
1374746 TTTTAATATGTTAGTTTGATATATTTGTAGATTGTTATTTT
1 TTTTAATATGTTAGTTTGATATATTCGTAGATTGTTATTTT
1374787 TGGAGTCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.01, G:0.17, T:0.60
Consensus pattern (42 bp):
TTTTAATATGTTAGTTTGATATATTCGTAGATTGTTATTTTG
Found at i:1379053 original size:2 final size:2
Alignment explanation
Indices: 1379008--1379034 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1378998 TAGTTTAACC
1379008 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1379035 TAATCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1379725 original size:24 final size:25
Alignment explanation
Indices: 1379670--1379725 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1379660 GATTACATGT
* *
1379670 ATTTTTTTTTTGTTTTTTATATCAC
1 ATTTTTTGTTTGTTTTTTAGATCAC
*
1379695 ATCTTTTGTTTGTTTTTATAGAT-A-
1 ATTTTTTGTTTGTTTTT-TAGATCAC
1379719 ATTTTTT
1 ATTTTTT
1379726 CATGTCGCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 6 0.23
25 16 0.62
26 4 0.15
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (25 bp):
ATTTTTTGTTTGTTTTTTAGATCAC
Found at i:1382091 original size:14 final size:14
Alignment explanation
Indices: 1382063--1382099 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1382053 ATAATGATTT
1382063 ATTTTTA-TA-TAA
1 ATTTTTATTATTAA
1382075 ATTTTTATTATTAA
1 ATTTTTATTATTAA
*
1382089 ATTTTAATTAT
1 ATTTTTATTAT
1382100 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 7 0.32
13 2 0.09
14 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTTATTATTAA
Found at i:1401140 original size:2 final size:2
Alignment explanation
Indices: 1401135--1401169 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1401125 TACGTGTGTG
1401135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1401170 TACACGCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1404800 original size:23 final size:23
Alignment explanation
Indices: 1404770--1404819 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1404760 GTGTTCGTTC
1404770 GTTTAGCATTAACGAACATGTTT
1 GTTTAGCATTAACGAACATGTTT
1404793 GTTTAGCATTAACGAACATGTTT
1 GTTTAGCATTAACGAACATGTTT
1404816 GTTT
1 GTTT
1404820 CAACATATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (23 bp):
GTTTAGCATTAACGAACATGTTT
Found at i:1405745 original size:2 final size:2
Alignment explanation
Indices: 1405738--1405763 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1405728 GTCAACCTTC
1405738 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1405764 TGCACGTACA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1409037 original size:28 final size:28
Alignment explanation
Indices: 1409005--1409061 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1408995 TCTATTTCCT
*
1409005 TTATTTTTATTTTATTTGATTTTTTGTG
1 TTATTTTTATTTTATTTCATTTTTTGTG
1409033 TTATTTTTATTTTATTTCATTTTTTGTG
1 TTATTTTTATTTTATTTCATTTTTTGTG
1409061 T
1 T
1409062 GGTTTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.75
Consensus pattern (28 bp):
TTATTTTTATTTTATTTCATTTTTTGTG
Found at i:1420530 original size:45 final size:44
Alignment explanation
Indices: 1420470--1420561 Score: 175
Period size: 45 Copynumber: 2.1 Consensus size: 44
1420460 TCTCCTTAAC
1420470 AATGTTCATATGATACAATTGTTCAAAAGCTCTCCCTCCCTCTT
1 AATGTTCATATGATACAATTGTTCAAAAGCTCTCCCTCCCTCTT
1420514 AATGTTTCATATGATACAATTGTTCAAAAGCTCTCCCTCCCTCTT
1 AATG-TTCATATGATACAATTGTTCAAAAGCTCTCCCTCCCTCTT
1420559 AAT
1 AAT
1420562 AAACAAAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (44 bp):
AATGTTCATATGATACAATTGTTCAAAAGCTCTCCCTCCCTCTT
Found at i:1432883 original size:2 final size:2
Alignment explanation
Indices: 1432876--1432918 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1432866 CCTAAATGAA
*
1432876 AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1432918 A
1 A
1432919 GTTTGAGCAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1433126 original size:16 final size:15
Alignment explanation
Indices: 1433105--1433140 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1433095 TTTATGTAAT
*
1433105 TTTTAAATAAATCATG
1 TTTTAAATAAA-CATA
1433121 TTTTAAATAAACATA
1 TTTTAAATAAACATA
1433136 TTTTA
1 TTTTA
1433141 TTAAGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTTAAATAAACATA
Done.