Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007980.1 Hibiscus syriacus cultivar Beakdansim tig00110419_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: 1499237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1414580 original size:13 final size:14
Alignment explanation
Indices: 1414557--1414598 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
1414547 AACTATAATA
1414557 AAAATATAAAAAAT
1 AAAATATAAAAAAT
1414571 AAAA-ATAAAAAAT
1 AAAATATAAAAAAT
*
1414584 ATAATTATAATAAAA
1 A-AAATATAA-AAAA
1414599 ATATAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.42
14 6 0.25
15 4 0.17
16 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATATAAAAAAT
Found at i:1415231 original size:23 final size:23
Alignment explanation
Indices: 1415188--1415232 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1415178 ATTTGGTTGG
*
1415188 TAAATATTTCTAATCCCTGATAA
1 TAAATATTTCTAATCACTGATAA
*
1415211 TAAATTATTTCTAA-CAGTGATA
1 TAAA-TATTTCTAATCACTGATA
1415233 TTTTGAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (23 bp):
TAAATATTTCTAATCACTGATAA
Found at i:1415514 original size:2 final size:2
Alignment explanation
Indices: 1415507--1415532 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1415497 TAATTTTGTA
1415507 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
1415533 TTATGAATTT
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:1419085 original size:22 final size:23
Alignment explanation
Indices: 1419060--1419104 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1419050 TTTTAAATTA
*
1419060 ATATTTTTTTA-AAATAGTTTTT
1 ATATTTTTTTATAAATAATTTTT
1419082 ATATTTTTTTATAAATAATTTTT
1 ATATTTTTTTATAAATAATTTTT
1419105 TTAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATATTTTTTTATAAATAATTTTT
Found at i:1419103 original size:37 final size:34
Alignment explanation
Indices: 1419062--1419133 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 34
1419052 TTAAATTAAT
1419062 ATTTTTTTAAAATAGTTTTTATATTTTT-TTATAAATA
1 ATTTTTTTAAAATA--TTTTAT-TTTTTGTTA-AAATA
1419099 ATTTTTTTAAAATATTTTATTTTTTGTTAAAATA
1 ATTTTTTTAAAATATTTTATTTTTTGTTAAAATA
1419133 A
1 A
1419134 GATTTATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
34 11 0.32
35 9 0.26
37 14 0.41
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (34 bp):
ATTTTTTTAAAATATTTTATTTTTTGTTAAAATA
Found at i:1419175 original size:25 final size:24
Alignment explanation
Indices: 1419135--1419181 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
1419125 TTAAAATAAG
1419135 ATTTATATAATTATTATTTATTTAA
1 ATTTATATAATTATTA-TTATTTAA
1419160 ATTTAT-TAATTAATTATTATTT
1 ATTTATATAATT-ATTATTATTT
1419182 GTGCTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTATATAATTATTATTATTTAA
Found at i:1420973 original size:42 final size:42
Alignment explanation
Indices: 1420905--1421010 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
1420895 GATGATGCAA
* *
1420905 CAAGGGTACATGCCCAGCCCACCAGTTCAAATGTCATCTCCG
1 CAAGGTTACATGCCAAGCCCACCAGTTCAAATGTCATCTCCG
* * * *
1420947 CAATGTTATATGCCAAGCCCACCAGTTCATATGTCATCTCCT
1 CAAGGTTACATGCCAAGCCCACCAGTTCAAATGTCATCTCCG
* *
1420989 CAAGGTTACATTCCTAGCCCAC
1 CAAGGTTACATGCCAAGCCCAC
1421011 AGGGGTACAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (42 bp):
CAAGGTTACATGCCAAGCCCACCAGTTCAAATGTCATCTCCG
Found at i:1421058 original size:21 final size:21
Alignment explanation
Indices: 1420992--1421058 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
1420982 ATCTCCTCAA
* *
1420992 GGTTACATTCCTAGCCCACAG
1 GGTTACATACCCAGCCCACAG
* *
1421013 GGGTACATACCCAGCCCACAA
1 GGTTACATACCCAGCCCACAG
* * *
1421034 GGTTACATGCCCAGCTCGCAG
1 GGTTACATACCCAGCCCACAG
1421055 GGTT
1 GGTT
1421059 TTATGACACC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (21 bp):
GGTTACATACCCAGCCCACAG
Found at i:1422069 original size:20 final size:21
Alignment explanation
Indices: 1422024--1422070 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1422014 AAAATAACCC
*
1422024 AATTTC-ACATTCTAACATCA
1 AATTTCAACAATCTAACATCA
1422044 AA-TTCAACAATCTAACAT-A
1 AATTTCAACAATCTAACATCA
1422063 AATTTCAA
1 AATTTCAA
1422071 GAATAATAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTTCAACAATCTAACATCA
Found at i:1422605 original size:139 final size:139
Alignment explanation
Indices: 1422073--1422697 Score: 754
Period size: 139 Copynumber: 4.5 Consensus size: 139
1422063 AATTTCAAGA
* * * **
1422073 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAGGGAAGACGTGCCCCCTGAAACGTACT
1 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGGCGCGCCCCCTGAAACGCGCT
* * * * *
1422138 TTCACCACTTTGTTGTGTCCTCTCAAACATGATAGATACTGACATGAATAGTGCCCCGCC-AGGA
66 TTCACCACTTTGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCGGGGA
*
1422202 GACATTACAC
131 -ACATCACAC
*** * * **
1422212 ATAATAAAACAATTATAACCTATTCTCTG--ATAAAAAAGGAAGGCACGCCCCCTGAAACGCATT
1 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGGCGCGCCCCCTGAAACGCGCT
* * * * *
1422275 TTCACTACTTTACTACGTCCCCTCAAACATTATAGGTACTGACATGAATAGTGCCCCACCGTGGG
66 TTCACCACTTTGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCG-GGG
1422340 -ACATCACAC
130 AACATCACAC
* * * *
1422349 ATAATAGGGTAATTATAACATATTCTCTGACACAAAAAAAAAGAAGGCGCACCCCCTGAAACGCG
1 ATAATAGGGCAATTATAACCTATTCTCTG--ACAAAAAAAAGGAAGGCGCGCCCCCTGAAACGCG
* * * * *
1422414 CTTTCATCACTTTGCTGCGTCCACACAAACATGATATGTACTGACATAAATAGTGCCCCGCCGGG
64 CTTTCACCACTTTGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCGGG
1422479 GAACATCACAC
129 GAACATCACAC
* * * *
1422490 ATAATAGGGTAATTATAACCTATTCTCTAACAAAAAAAGGGAAGGCGCGCGCCCTGAAACGCGCT
1 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGGCGCGCCCCCTGAAACGCGCT
* * ** * * * *
1422555 TTCACCAATTTGTTGTATCCCCTCAAACATGATAGGTACTGATATGAATAGTACCCTGCCGGGGG
66 TTCACCACTTTGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCGGGGA
*
1422620 ACATCGCAC
131 ACATCACAC
* * *
1422629 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGACGCGCCCCTTGAAACGCGTT
1 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGGCGCGCCCCCTGAAACGCGCT
1422694 TTCA
66 TTCA
1422698 TATGAATAGT
Statistics
Matches: 410, Mismatches: 69, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
137 110 0.27
139 182 0.44
140 3 0.01
141 115 0.28
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (139 bp):
ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGGCGCGCCCCCTGAAACGCGCT
TTCACCACTTTGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCGGGGA
ACATCACAC
Found at i:1428022 original size:20 final size:20
Alignment explanation
Indices: 1427992--1428044 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1427982 CTGATTCAGT
* * *
1427992 AGGTATGGATACCTAAGTGGG
1 AGGTATCGATACCGAAG-GGA
1428013 A-GTATCGATACCGAAGGGA
1 AGGTATCGATACCGAAGGGA
1428032 AGGTATCGATACC
1 AGGTATCGATACC
1428045 ATTTCAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 24 0.86
21 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.21
Consensus pattern (20 bp):
AGGTATCGATACCGAAGGGA
Found at i:1428093 original size:19 final size:20
Alignment explanation
Indices: 1428069--1428122 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
1428059 TGCAAAATCG
1428069 GTATCGATACCATAGCA-TA
1 GTATCGATACCATAGCAGTA
* *
1428088 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGCA--GTA
1428110 GTATCGATACCAT
1 GTATCGATACCAT
1428123 GGTATGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 15 0.52
22 14 0.48
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (20 bp):
GTATCGATACCATAGCAGTA
Found at i:1428114 original size:22 final size:22
Alignment explanation
Indices: 1428069--1428139 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
1428059 TGCAAAATCG
*
1428069 GTATCGATACCATAGCA---TA
1 GTATCGATACCATAGTATGGTA
*
1428088 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
*
1428110 GTATCGATACCATGGTATGG--
1 GTATCGATACCATAGTATGGTA
1428130 GTATCGATAC
1 GTATCGATAC
1428140 TGAAGTGCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 15 0.33
20 10 0.22
22 20 0.44
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:1428760 original size:54 final size:54
Alignment explanation
Indices: 1428462--1428745 Score: 451
Period size: 54 Copynumber: 5.3 Consensus size: 54
1428452 TACCAAATAA
*
1428462 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
*
1428516 GCACTAAGTGTGCATTTTACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
*
1428570 GCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * * * **
1428624 GTATTAAGTGTGCATTTCATGGAATTCATTCTATGTGGATGAATAATTGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* *
1428678 GCTCTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* *
1428732 ACACTATGTGTGCA
1 GCACTAAGTGTGCA
1428746 AAACACAAAA
Statistics
Matches: 212, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 212 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
Found at i:1428801 original size:162 final size:162
Alignment explanation
Indices: 1428462--1428801 Score: 428
Period size: 162 Copynumber: 2.1 Consensus size: 162
1428452 TACCAAATAA
1428462 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGT
1 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGT
* * *** ***
1428527 GCATTTTACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCATGG
66 GCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCAAAACACAA
** *
1428592 AATTCATCCTATGTGGATGAATAACCGTTTCG
131 AATTCATAATATGTGGATGAATAACCGTATCG
* * * * * ** *
1428624 GTATTAAGTGTGCATTTCATGGAATTCATTCTATGTGGATGAATAATTGTTTCGGCTCTAAGTGT
1 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGT
* *
1428689 GCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTCGACACTATGTGTGCAAAACACAA
66 GCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCAAAACACAA
* ** * *
1428754 AATTCATAATTTGTTTATGAATGACCGTATGG
131 AATTCATAATATGTGGATGAATAACCGTATCG
* *
1428786 GCACTACGGGTGCATT
1 GCACTAAGTGTGCATT
1428802 ACAAAGAAAT
Statistics
Matches: 148, Mismatches: 30, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
162 148 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (162 bp):
GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGT
GCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCAAAACACAA
AATTCATAATATGTGGATGAATAACCGTATCG
Found at i:1434839 original size:20 final size:19
Alignment explanation
Indices: 1434794--1434845 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1434784 CTGATTCAAT
* *
1434794 AGGTATCGATAACTAAGGG
1 AGGTATCGATACCGAAGGG
*
1434813 GGGTATCGATACCGAAGGG
1 AGGTATCGATACCGAAGGG
1434832 AAGGTATCGATACC
1 -AGGTATCGATACC
1434846 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (19 bp):
AGGTATCGATACCGAAGGG
Found at i:1434921 original size:22 final size:22
Alignment explanation
Indices: 1434870--1434929 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
1434860 TGCAAAAATG
*
1434870 GTATCGATACCATAGCA---TA
1 GTATCGATACCATAGTATGGTA
*
1434889 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
* *
1434911 GTATTGATACCATGGTATG
1 GTATCGATACCATAGTATG
1434930 CATATCGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 15 0.45
22 18 0.55
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:1435331 original size:54 final size:54
Alignment explanation
Indices: 1435265--1435658 Score: 459
Period size: 54 Copynumber: 7.3 Consensus size: 54
1435255 TTACCAAATA
* *
1435265 GGCACTAAGTGTGCATTT-ATCGGAATCCATCCTATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCA-CGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
1435319 GGAACTAAGTGTGTATTTCACGGAATTTATTCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1435373 GGCACTACGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * * ***
1435427 GGCATTAAGTGTGCATTTCACGAAATTTATCATATGTGCATGAATAATTATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1435481 GGCACTAAGTGTACATTTCACGGAATTCATTCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
1435535 GACACTTAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *** ** ** * *
1435589 GGCACTATGTGTGCAAAGCACGGAATTCATAATATGTTTATGAATGACCGTAT-
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
1435642 GGCACTACGGGTGCATT
1 GGCACTAAGTGTGCATT
1435659 ACAACGAAAT
Statistics
Matches: 288, Mismatches: 51, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
53 13 0.05
54 274 0.95
55 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:1443401 original size:3 final size:3
Alignment explanation
Indices: 1443393--1443476 Score: 150
Period size: 3 Copynumber: 28.0 Consensus size: 3
1443383 CCATATTGAT
*
1443393 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1443441 TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1443477 AATATATTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1444024 original size:15 final size:15
Alignment explanation
Indices: 1444004--1444045 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1443994 TCTCAGCAGC
1444004 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1444019 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
1444034 AAAGAAGAGAAA
1 AAAGAAAAGAAA
1444046 CTTACCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1444029 original size:20 final size:20
Alignment explanation
Indices: 1444004--1444045 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1443994 TCTCAGCAGC
*
1444004 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
1444024 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
1444044 AA
1 AA
1444046 CTTACCGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:1444235 original size:13 final size:13
Alignment explanation
Indices: 1444217--1444247 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1444207 GGCCACCAAA
1444217 GGCGGTGGCCGGC
1 GGCGGTGGCCGGC
*
1444230 GGCGGTGGCTGGC
1 GGCGGTGGCCGGC
1444243 GGCGG
1 GGCGG
1444248 ACGAACACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.65, T:0.10
Consensus pattern (13 bp):
GGCGGTGGCCGGC
Found at i:1445647 original size:24 final size:23
Alignment explanation
Indices: 1445607--1445656 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1445597 TTAATTTATA
*
1445607 ATTTTTTTATATATATACATATT
1 ATTTTTATATATATATACATATT
* *
1445630 ATTTTTATAGTATTTATATATATT
1 ATTTTTATA-TATATATACATATT
1445654 ATT
1 ATT
1445657 AATATTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTTTATATATATATACATATT
Found at i:1448963 original size:15 final size:15
Alignment explanation
Indices: 1448943--1448974 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1448933 ATCAATACCT
1448943 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1448958 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1448973 TT
1 TT
1448975 ATTCATTTCA
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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1456310 original size:9 final size:9
Alignment explanation
Indices: 1456296--1456343 Score: 78
Period size: 9 Copynumber: 5.1 Consensus size: 9
1456286 TGCTTGAAGG
1456296 GAAAAAAAA
1 GAAAAAAAA
1456305 GAAAAAAAAA
1 G-AAAAAAAA
1456315 GAAAAAAAA
1 GAAAAAAAA
1456324 GAAAAAAAGA
1 GAAAAAAA-A
1456334 GAAAAAAAA
1 GAAAAAAAA
1456343 G
1 G
1456344 GGGGGTCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 19 0.51
10 18 0.49
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:1456312 original size:10 final size:10
Alignment explanation
Indices: 1456297--1456342 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
1456287 GCTTGAAGGG
1456297 AAAAAAAAGA
1 AAAAAAAAGA
1456307 AAAAAAAAG-
1 AAAAAAAAGA
1456316 AAAAAAAAGA
1 AAAAAAAAGA
*
1456326 AAAAAAGAGA
1 AAAAAAAAGA
1456336 AAAAAAA
1 AAAAAAA
1456343 GGGGGGTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 9 0.27
10 24 0.73
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:1456318 original size:19 final size:19
Alignment explanation
Indices: 1456296--1456343 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1456286 TGCTTGAAGG
1456296 GAAAAAAAAGAAAAAAAAA
1 GAAAAAAAAGAAAAAAAAA
*
1456315 GAAAAAAAAGAAAAAAAGA
1 GAAAAAAAAGAAAAAAAAA
1456334 GAAAAAAAAG
1 GAAAAAAAAG
1456344 GGGGGTCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
GAAAAAAAAGAAAAAAAAA
Found at i:1457820 original size:83 final size:83
Alignment explanation
Indices: 1457637--1458508 Score: 1480
Period size: 83 Copynumber: 10.6 Consensus size: 83
1457627 TAAAGCAATG
*
1457637 TGCTCATAGCATCTTCTGGAAGTTTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1457702 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
1457720 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTTGGCAGAACCAATCAT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTTGGCAGAACCAATCAT
*
1457785 TGAATTTGGAAGATG-ATT
65 TGAATTTAGAAGATGAATT
1457803 GTGCTCATAGCAT-TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 -TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
*
1457867 TGAATTTGGAAGATGAA-T
65 TGAATTTAGAAGATGAATT
1457885 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1457949 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
*
1457967 TGCTCATCGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1458031 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
*
1458049 TGCTCATAG-AGCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC-ATCA-T
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1458111 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
1458129 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1458194 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
* * * *
1458212 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTAAAACCAGTCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
*
1458277 GAATTT-GAAAGATGAATG
66 GAATTTAG-AAGATGAATT
* *
1458295 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
1458360 GAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
* *
1458378 TGCTCATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCA-T
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
* *
1458442 GGATTTAAAAGATGAA-T
66 GAATTTAGAAGATGAATT
*
1458459 TGCTCATAGCATCTTCTGGAAGTGATCTTTGAGTTAT-TGATCTGGTTTGG
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1458509 TAGGAACTAC
Statistics
Matches: 756, Mismatches: 21, Indels: 27
0.94 0.03 0.03
Matches are distributed among these distances:
80 41 0.05
81 166 0.22
82 188 0.25
83 316 0.42
84 45 0.06
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (83 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
GAATTTAGAAGATGAATT
Found at i:1459398 original size:113 final size:111
Alignment explanation
Indices: 1459218--1459769 Score: 734
Period size: 113 Copynumber: 5.0 Consensus size: 111
1459208 TAGCAAAGAT
* *
1459218 TCAAATCTATCATTTGATGGATTGA-CATTTCCA-GAAAGTTCAT-A--AGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGA-TCATCATTTCCAGGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
1459278 AGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTGC
** * * * *
1459326 TTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCATTTCCAGG-AAAGTTCATAATGAGAAGAACTCATCTGA
1459391 AGAAGGAAGAAGAAGTTCATAATGAG-A-AATTGTTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTGC
*
1459436 TCAAATCCATCATTTGATGGATCATC-TTTCCAGAGAAAGTTCATAATAAG-AGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCATTTCCAG-GAAAGTTCATAATGAGAAGAACTCATCTGA
1459499 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTGC
*
1459547 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCATTTCCAG-GAAAGTTCATAATGAGAAGAACTCATCTGA
*
1459612 AGAAGGAAGAAGAAGTTCATAATGAGAAGAAATTTGTTCAACCTTTTAC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAG-AA-TTGTTCAACCTTTTGC
* * * * *
1459661 -CTGAATTCATCAATTGATGGATTATCTTTTCCA-GAGAAGTTCATAATGAGAAGAACTCATCTG
1 TC-AAATCCATCATTTGATGGATCATCATTTCCAGGA-AAGTTCATAATGAGAAGAACTCATCTG
* *
1459724 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAA--GTTCAACTTTTTGC
64 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTGC
1459770 ATATTCTATC
Statistics
Matches: 403, Mismatches: 26, Indels: 29
0.88 0.06 0.06
Matches are distributed among these distances:
107 2 0.00
108 63 0.16
109 33 0.08
110 47 0.12
111 45 0.11
112 28 0.07
113 140 0.35
114 45 0.11
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (111 bp):
TCAAATCCATCATTTGATGGATCATCATTTCCAGGAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTGC
Found at i:1459623 original size:221 final size:225
Alignment explanation
Indices: 1459218--1459755 Score: 758
Period size: 221 Copynumber: 2.4 Consensus size: 225
1459208 TAGCAAAGAT
* *
1459218 TCAAATCTATCATTTGATGGATTGA-CATTTCC--AGAAAGTTCATAA-GA-AGAACTCATCTGA
1 TCAAATCCATCATTTGATGGA-TCATCATTTCCAGAGAAAGTTCATAATGAGAGAACTCATCTGA
* * * ** *
1459278 AGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGA
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTTGA
*
1459343 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
130 TGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
*
1459408 CATAAT-G-AGAAA-TTGTTCAACCTTTTGC
195 CATAATAGAAGAAATTTGTTCAACCTTTTAC
*
1459436 TCAAATCCATCATTTGATGGATCATC-TTTCCAGAGAAAGTTCATAATAAGAGAACTCATCTGAA
1 TCAAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAGAACTCATCTGAA
*
1459500 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTTGAT
* * *
1459565 GGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
131 GGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1459629 CATAATGAGAAGAAATTTGTTCAACCTTTTAC
195 CATAAT-AGAAGAAATTTGTTCAACCTTTTAC
* * * * *
1459661 -CTGAATTCATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTG
1 TC-AAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAG-AGAACTCATCTG
*
1459724 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAA
64 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1459756 GTTCAACTTT
Statistics
Matches: 286, Mismatches: 21, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
217 7 0.02
218 21 0.07
219 13 0.05
220 1 0.00
221 136 0.48
222 1 0.00
223 1 0.00
224 6 0.02
225 48 0.17
226 52 0.18
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (225 bp):
TCAAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTTGAT
GGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
ATAATAGAAGAAATTTGTTCAACCTTTTAC
Found at i:1460092 original size:3 final size:3
Alignment explanation
Indices: 1460084--1460169 Score: 127
Period size: 3 Copynumber: 28.7 Consensus size: 3
1460074 CCATATTGAT
* * * *
1460084 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TAA TTA TAA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1460132 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1460170 TAAATATATT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1460503 original size:13 final size:13
Alignment explanation
Indices: 1460485--1460524 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1460475 TCTCAGCAGC
*
1460485 AAAGAAACAGAAA
1 AAAGAAAAAGAAA
1460498 AAAGAAAGAA-AAA
1 AAAGAAA-AAGAAA
1460511 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
1460524 A
1 A
1460525 CTTACGAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.08
13 21 0.88
14 1 0.04
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:1463546 original size:169 final size:170
Alignment explanation
Indices: 1463267--1463596 Score: 511
Period size: 169 Copynumber: 1.9 Consensus size: 170
1463257 ATTTATTAAA
* *
1463267 TTATCTAATAAATACATGAAATTTTAAATAGAAAATAATAAGAAATTTTATTAAACATCAAATTG
1 TTATCTAATAAATACATGAAATTTTAAATAGAAAATAATAAGAAATTTTATTAAACACCAAATTA
* * * * *
1463332 CTCACACAAAACAAGCATGGTCCTTTTTTAAAGAGGTACATGTTAGA-TTTAACCTTCTTCATCT
66 CTCACACAAAACAAGCATGATCCTCTTTTAAAGAGGTAAATGTTAGATTTTAACATTCTTCATCG
*
1463396 TATCAAGAATAATAAAAGAATAATAAAATGATACACTTAG
131 TATCAAAAATAATAAAAGAATAATAAAATGATACACTTAG
* *
1463436 TTATCTAATAAATACATTAAATTTTAAATAGAAAATTATAAGAAATTTTATTAAACACCAAATTA
1 TTATCTAATAAATACATGAAATTTTAAATAGAAAATAATAAGAAATTTTATTAAACACCAAATTA
* *
1463501 CTCACACAAAACAAGCATGATCCTCTTTT-AAGAGGATAAATGTTAGATTTTAATATTTTTCATC
66 CTCACACAAAACAAGCATGATCCTCTTTTAAAGAGG-TAAATGTTAGATTTTAACATTCTTCATC
* *
1463565 GTGTCAAAAATAATAAAAGAATAATTAAATGA
130 GTATCAAAAATAATAAAAGAATAATAAAATGA
1463597 AAAGTAAAAA
Statistics
Matches: 145, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
168 6 0.04
169 98 0.68
170 41 0.28
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (170 bp):
TTATCTAATAAATACATGAAATTTTAAATAGAAAATAATAAGAAATTTTATTAAACACCAAATTA
CTCACACAAAACAAGCATGATCCTCTTTTAAAGAGGTAAATGTTAGATTTTAACATTCTTCATCG
TATCAAAAATAATAAAAGAATAATAAAATGATACACTTAG
Found at i:1464136 original size:41 final size:40
Alignment explanation
Indices: 1464091--1464174 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
1464081 ATTAGCGGCA
*
1464091 TTTGTATAAAAAACGCCGCCAAAGAATGTACTTTAGTGGAG
1 TTTGTAT-AAAAACGCCGCCAAAGAATATACTTTAGTGGAG
* * * *
1464132 TTTGTATAAAACCGCCGCTAAAGACTATACTTTAGTGGCG
1 TTTGTATAAAAACGCCGCCAAAGAATATACTTTAGTGGAG
1464172 TTT
1 TTT
1464175 TTAGACAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
40 31 0.82
41 7 0.18
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (40 bp):
TTTGTATAAAAACGCCGCCAAAGAATATACTTTAGTGGAG
Found at i:1464209 original size:41 final size:41
Alignment explanation
Indices: 1464101--1464422 Score: 389
Period size: 41 Copynumber: 7.9 Consensus size: 41
1464091 TTTGTATAAA
* * * * *
1464101 AAACGCCGCCAAAGAAT-GTACTTTAGTGGAGTTTGTATA-
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
1464140 AAACCGCCGCTAAAGACT-ATACTTTAGTGGCGTTTTTAGAC
1 AAA-CGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
** *
1464181 AAACGCTACTATAGACTCGTACTTTAGTGGCGTTTTTAGAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
1464222 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
1464263 AAACGTCGATATAGACTCGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
1464304 AAACGCCTCTACAGACTCGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
1464345 AAACGCCGCTAAAGACTCGTACTTTAATGGCGTTTGTGTTTAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT-T-TATAC
* * *
1464388 AAACGCCGCTAAAGACTTGTATTTTAGTGGCGTTT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT
1464423 GTAATAGACT
Statistics
Matches: 250, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
39 3 0.01
40 41 0.16
41 169 0.68
42 1 0.00
43 36 0.14
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:1468110 original size:42 final size:42
Alignment explanation
Indices: 1467992--1468321 Score: 347
Period size: 43 Copynumber: 7.7 Consensus size: 42
1467982 TAATGAGCTT
* * * * * *
1467992 TTTTGCGGCCTTTGTATCAAAAAACGCCGCTACATATATGAGC
1 TTTTGCGGCGTTTAT-TCCAAAAACGCCGCTATAGATATGACC
1468035 TTTTGCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACC
1 TTTTGCGGCGTTTAT-TCCAAAAACGCCGCTATAGATATGACC
* * * *
1468078 ATTTGCGGTGTTTATTCCAAAAATGCCGCTATAGATCTGACC
1 TTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATATGACC
* *
1468120 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACC
1 TTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATATGACC
* * * *
1468162 TTTTGGCGGCGTTTCTTCCAAAAACGCTGCTATAGATCTGACA
1 TTTT-GCGGCGTTTATTCCAAAAACGCCGCTATAGATATGACC
*
1468205 TTTTGCGGCGTTT-TTCCAGAAACGCCGCTATAGATATCGACC
1 TTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATAT-GACC
* * * * * * * *
1468247 TTTTGCGACGTTTTTTTCTAGAAACACCGCGATAGGTCTTGACC
1 TTTTGCGGCG-TTTATTCCAAAAACGCCGCTATAGAT-ATGACC
* * *
1468291 TATTGTGGCGTTTGTTCCAAAAACGCCGCTA
1 TTTTGCGGCGTTTATTCCAAAAACGCCGCTA
1468322 ACTTTAGCGG
Statistics
Matches: 247, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
41 21 0.09
42 88 0.36
43 108 0.44
44 29 0.12
45 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (42 bp):
TTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATATGACC
Found at i:1468123 original size:85 final size:84
Alignment explanation
Indices: 1468011--1468321 Score: 365
Period size: 85 Copynumber: 3.7 Consensus size: 84
1468001 CTTTGTATCA
* * * * *
1468011 AAAAACGCCGCTACATATATGAGCTTTTGCGGCGTTTATATCCAAAAACGCCGCTATAGATATGA
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGA
*
1468076 CCATTTGCGGTGTTTATTCC
65 CCTTTTGCGGTGTTTATTCC
* *
1468096 AAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGAC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGAC
* *
1468161 CTTTTGGCGGCGTTTCTTCC
66 CTTTT-GCGGTGTTTATTCC
* * *
1468181 AAAAACGCTGCTATAGATCTGACATTTTGCGGCGTTT-TTCCAGAAACGCCGCTATAGATATCGA
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GA
* *
1468245 CCTTTTGCGACGT-TTTTTTCT
65 CCTTTTGCG--GTGTTTATTCC
* * * * * *
1468266 AGAAACACCGCGATAGGTCTTGACCTATTGTGGCGTTTGTTCCAAAAACGCCGCTA
1 AAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTA
1468322 ACTTTAGCGG
Statistics
Matches: 193, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
84 54 0.28
85 107 0.55
86 16 0.08
87 16 0.08
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (84 bp):
AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGAC
CTTTTGCGGTGTTTATTCC
Found at i:1471934 original size:23 final size:22
Alignment explanation
Indices: 1471907--1471951 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1471897 ATAATCAATA
*
1471907 ATATAAAGTAAAACATATTGATG
1 ATATAAAATAAAACATA-TGATG
*
1471930 ATATAAAATAAATCATATGATG
1 ATATAAAATAAAACATATGATG
1471952 GAAATACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (22 bp):
ATATAAAATAAAACATATGATG
Found at i:1473071 original size:51 final size:51
Alignment explanation
Indices: 1473007--1473118 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
1472997 AGCAGTAAAA
* **
1473007 CGCGCCCCATGCA-CCGCACTATACGATGATTTGGCGCCACGTGGGGTATAG
1 CGCGCCCCCTGCACCCGCACTATACGATGAGCTGGCGCCACGT-GGGTATAG
* *
1473058 CGCGCCCCCTGCACCCGCGCTATACGGTGAGCTGGCGCCACGTGGGTATAG
1 CGCGCCCCCTGCACCCGCACTATACGATGAGCTGGCGCCACGTGGGTATAG
* *
1473109 CACGGCCCCT
1 CGCGCCCCCT
1473119 ATAGCGCGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 28 0.53
52 25 0.47
ACGTcount: A:0.16, C:0.37, G:0.30, T:0.17
Consensus pattern (51 bp):
CGCGCCCCCTGCACCCGCACTATACGATGAGCTGGCGCCACGTGGGTATAG
Found at i:1473294 original size:12 final size:10
Alignment explanation
Indices: 1473252--1473293 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
1473242 TTTTATCACA
1473252 TCAAATTCTC
1 TCAAATTCTC
1473262 TCAAATTCTC
1 TCAAATTCTC
1473272 T-AAATTTCTC
1 TCAAA-TTCTC
*
1473282 TCAAATACTC
1 TCAAATTCTC
1473292 TC
1 TC
1473294 TTTTTAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.10
10 23 0.79
11 3 0.10
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:1473557 original size:110 final size:111
Alignment explanation
Indices: 1473417--1473637 Score: 372
Period size: 110 Copynumber: 2.0 Consensus size: 111
1473407 TAGAAATCAT
* *
1473417 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * * *
1473482 TATTTAGTT-ATTTATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
1473527 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1473592 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
1473638 TTTTTGTAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 70 0.68
111 33 0.32
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1476344 original size:51 final size:46
Alignment explanation
Indices: 1476234--1476349 Score: 135
Period size: 51 Copynumber: 2.4 Consensus size: 46
1476224 ACAAAACGCG
* *
1476234 GTACCTGATCCGCGCTATATAAAATTATGTTTAAAGGTATGTCGCG
1 GTACCTGATCCGCGCTATATAAAATTATGTGTAAAGGTATGTCGCA
**
1476280 GTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAG-CGCA
1 GTACCTGATCCGCGCTATATAAAATTATGT-----GTAAAGGTAT-GTCGCA
1476331 GTACCTGATCCGCGCTATA
1 GTACCTGATCCGCGCTATA
1476350 CCCCTACGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
46 28 0.48
51 29 0.50
52 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (46 bp):
GTACCTGATCCGCGCTATATAAAATTATGTGTAAAGGTATGTCGCA
Found at i:1479675 original size:23 final size:23
Alignment explanation
Indices: 1479645--1479693 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1479635 TGAGAAAAAA
*
1479645 GATGAGTGAAATGTGAACATTTT
1 GATGAGTGAAATATGAACATTTT
*
1479668 GATGAGTGGAATATGAACATTTT
1 GATGAGTGAAATATGAACATTTT
1479691 GAT
1 GAT
1479694 ATCGATATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (23 bp):
GATGAGTGAAATATGAACATTTT
Found at i:1480939 original size:32 final size:32
Alignment explanation
Indices: 1480903--1480975 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1480893 TATCGGATCG
1480903 GTTGATTTTTAGGTCAGGTCAAGATTGGATAT
1 GTTGATTTTTAGGTCAGGTCAAGATTGGATAT
*
1480935 GTTGATTTTTAGGTCGGGTCAAGATTGGATAT
1 GTTGATTTTTAGGTCAGGTCAAGATTGGATAT
1480967 GTTGATTTT
1 GTTGATTTT
1480976 CGAGTCGGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (32 bp):
GTTGATTTTTAGGTCAGGTCAAGATTGGATAT
Found at i:1480983 original size:32 final size:32
Alignment explanation
Indices: 1480903--1480985 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
1480893 TATCGGATCG
* *
1480903 GTTGATTTTTAGGTCAGGTCAAGATTGGATAT
1 GTTGATTTTGAGGTCGGGTCAAGATTGGATAT
*
1480935 GTTGATTTTTAGGTCGGGTCAAGATTGGATAT
1 GTTGATTTTGAGGTCGGGTCAAGATTGGATAT
1480967 GTTGATTTTCGA-GTCGGGT
1 GTTGATTTT-GAGGTCGGGT
1480986 TAATACTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 47 0.98
33 1 0.02
ACGTcount: A:0.20, C:0.07, G:0.31, T:0.41
Consensus pattern (32 bp):
GTTGATTTTGAGGTCGGGTCAAGATTGGATAT
Found at i:1484783 original size:28 final size:27
Alignment explanation
Indices: 1484752--1484811 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 27
1484742 ATACTGACAC
* *
1484752 AAAATTTTATGTTATATGATAATT-TTAT
1 AAAATTATATATTATA-GA-AATTATTAT
1484780 AAAATTATATATTATAGAAATTAATTAT
1 AAAATTATATATTATAGAAATT-ATTAT
1484808 AAAA
1 AAAA
1484812 AAAATCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 2 0.07
28 22 0.79
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (27 bp):
AAAATTATATATTATAGAAATTATTAT
Done.