Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008925.1 Hibiscus syriacus cultivar Beakdansim tig00112230_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: 2702387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1426804 original size:21 final size:21
Alignment explanation
Indices: 1426766--1426805 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1426756 TAATTCAAAT
* **
1426766 TCCATTAATTCATTTTCCAGA
1 TCCAGTAATTCAAATTCCAGA
1426787 TCCAGTAATTCAAATTCCA
1 TCCAGTAATTCAAATTCCA
1426806 ATAATTCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (21 bp):
TCCAGTAATTCAAATTCCAGA
Found at i:1426946 original size:55 final size:55
Alignment explanation
Indices: 1426852--1427151 Score: 347
Period size: 55 Copynumber: 5.5 Consensus size: 55
1426842 AAACAGACCA
* ** **
1426852 TAAGTCTGATTTTCAGAAGTTTCTTGATGGTA-TTT-AAATGAAATTTTAAAGAAAC
1 TAAGTTTGATTTTCAGAAGTTTCTT-AACG-ACTTTCAAATGAGTTTTTAAAGAAAC
*
1426907 TAAGTTTGATTTTCAAAAGTTTCTTAACGACTTTCAAATGAGTTTTTAAAGAAAC
1 TAAGTTTGATTTTCAGAAGTTTCTTAACGACTTTCAAATGAGTTTTTAAAGAAAC
* * * *
1426962 TAAGTTTGATTTTTAGAACTTTCTTAATGACTTCCAAATGAGTTTTTAAAGAAAC
1 TAAGTTTGATTTTCAGAAGTTTCTTAACGACTTTCAAATGAGTTTTTAAAGAAAC
* *
1427017 TACA-TTTGATTTTTAGAAGTTTCTTAACGACTTTCAAATGAGTTATTAAA-AAACC
1 TA-AGTTTGATTTTCAGAAGTTTCTTAACGACTTTCAAATGAGTTTTTAAAGAAA-C
* * * * * * * *
1427072 TAAGTATGGTTTTCATAAGTTTCTTAATGATTTTTAAATGAGCTTTCAAAGAAAC
1 TAAGTTTGATTTTCAGAAGTTTCTTAACGACTTTCAAATGAGTTTTTAAAGAAAC
*
1427127 TAAGTTTGATTTTCAGAGGTTTCTT
1 TAAGTTTGATTTTCAGAAGTTTCTT
1427152 GACATGATGA
Statistics
Matches: 210, Mismatches: 29, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
53 1 0.00
54 9 0.04
55 196 0.93
56 4 0.02
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (55 bp):
TAAGTTTGATTTTCAGAAGTTTCTTAACGACTTTCAAATGAGTTTTTAAAGAAAC
Found at i:1427799 original size:42 final size:41
Alignment explanation
Indices: 1427738--1427840 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 41
1427728 ACTTAGTAAG
* * * ** * *
1427738 TCCTTCGGGCCATCAATAAGTCTTTTGAGCATGATGCCTAAA
1 TCCTTCAGGTCATCTATAAGTCTTTCAAGCAAGATG-ATAAA
*
1427780 TCCTTCAGGTCATCTATAAGTCTTTCAAGCAAGATGATAAG
1 TCCTTCAGGTCATCTATAAGTCTTTCAAGCAAGATGATAAA
* *
1427821 TCCTTTAAGTCATCTATAAG
1 TCCTTCAGGTCATCTATAAG
1427841 ACCTTCGGGC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 21 0.41
42 30 0.59
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (41 bp):
TCCTTCAGGTCATCTATAAGTCTTTCAAGCAAGATGATAAA
Found at i:1427882 original size:241 final size:237
Alignment explanation
Indices: 1427278--1428141 Score: 1095
Period size: 238 Copynumber: 3.7 Consensus size: 237
1427268 TCATTTGGGG
* * * *
1427278 CATCAGTAAGTCTTTCGAGCGTGATGCTTAAATGCTTCGGGTCATGTGTAAGTCTTTCGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAG
*
1427343 ATGATAAGTCCTTCAGGCCATCCATAAGA-------CATGATGTTTTCATATGA-TTTAAAAAAA
66 ATGATAAGTCCTTCAGGCCATCCATAAGACCTTCGGCATGATGTTTTCACATGATTTTAAAAAAA
*
1427400 TGAGAAA-ACGATTTCCAAAGTTTCTCATTTAAATCTTTTCTAAAAATTGATTTTTGAAAAGTAA
131 TGAGAAAGA-GATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTGAAAAGTAA
* * *
1427464 GAAAACGATTTCCAAAGTTTCTTACATAGTAAGTCCTTCGAGC
195 GAAAAAGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGC
* * * *
1427507 CATCAGTAAGTCTTTCAAGCATGGTGCTTAAATCCTTCGGGTCATCTGTAAGT-TTTTGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAG
* * * * * *
1427571 ATGTTAAGTCCTTCGGGCTATCCATAAGACCCTCAAGCATGATGATTTCACATGATTTTAAAAAA
66 ATGATAAGTCCTTCAGGCCATCCATAAGACCTTC-GGCATGATGTTTTCACATGATTTT-AAAAA
* * *
1427636 AATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCTTCTCTGGAAATTGATTTTTCTTAAAAA
129 AATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGA--TTT-TT-GAAA
* *
1427701 AATAAGAAAATGATTTCCAAAG-TTCTTACTTAGTAAGTCCTTCGGGC
190 AGTAAGAAAAAGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGC
* * * * *
1427748 CATCAATAAGTCTTTTGAGCATGATGCCTAAATCCTTCAGGTCATCTATAAGTCTTTCAAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAG
* * * * * *
1427813 ATGATAAGTCCTTTAAGTCATCTATAAGACCTTCGGGCATGATGTTTTTACATGATTTTCAAAAA
66 ATGATAAGTCCTTCAGGCCATCCATAAGACCTTC-GGCATGATGTTTTCACATGATTTTAAAAAA
* *
1427878 ATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTAATTTTTGAAAAGTAA
130 ATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTGAAAAGTAA
* * *
1427943 GAAAAAGATTTCCAAAGTTTCTTACTTAATAAGTCATTTGGGC
195 GAAAAAGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGC
* * * * * *
1427986 CATCAGTAAGTATTTCGAGCATGGTACTTAAATCCTTTGTGTCATCTATAAGTTTTTCGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAG
* * **
1428051 ATGATAAGCCCTTCGGGCCATCCATAAGACCTTCTGGC-TGGATGTTTTCACATGATTTTTGAAA
66 ATGATAAGTCCTTCAGGCCATCCATAAGACCTTC-GGCAT-GATGTTTTCACATGATTTTAAAAA
*
1428115 AATGAGAAAGCGATTTCCAAAGTTTCT
129 AATGAGAAAGAGATTTCCAAAGTTTCT
1428142 TACTTAGTAA
Statistics
Matches: 545, Mismatches: 72, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
228 36 0.07
229 48 0.09
236 16 0.03
237 27 0.05
238 209 0.38
239 4 0.01
240 3 0.01
241 123 0.23
242 79 0.14
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (237 bp):
CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAG
ATGATAAGTCCTTCAGGCCATCCATAAGACCTTCGGCATGATGTTTTCACATGATTTTAAAAAAA
TGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTGAAAAGTAAG
AAAAAGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGC
Found at i:1439510 original size:32 final size:31
Alignment explanation
Indices: 1439442--1439511 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1439432 TAAGGCGATC
* * * *
1439442 CTTGGGT-AGGCTTTTTGGCCCTGAGATTTT
1 CTTGGGTAAGCCTTTATGGCCCCGAGATTGT
*
1439472 TTTGGGTAAGCCTTTATGGCCCCGAGAATTGT
1 CTTGGGTAAGCCTTTATGGCCCCGAG-ATTGT
1439504 CTTGGGTA
1 CTTGGGTA
1439512 GGCTCACAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 6 0.19
31 15 0.47
32 11 0.34
ACGTcount: A:0.14, C:0.17, G:0.30, T:0.39
Consensus pattern (31 bp):
CTTGGGTAAGCCTTTATGGCCCCGAGATTGT
Found at i:1447618 original size:18 final size:18
Alignment explanation
Indices: 1447578--1447619 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1447568 CATTTTGATC
1447578 CTTTTTATTACTTTCTGT
1 CTTTTTATTACTTTCTGT
* *
1447596 TTTTTTATTA-TTTGTGT
1 CTTTTTATTACTTTCTGT
1447613 ACTTTTT
1 -CTTTTT
1447620 TTGTCATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTATTACTTTCTGT
Found at i:1448070 original size:19 final size:19
Alignment explanation
Indices: 1448041--1448079 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1448031 CAGCATTGAA
1448041 TTGCATTTAATTTCCATTTT
1 TTGCATTTAATTTCC-TTTT
1448061 TTGC-TTTAATTTCCTTTT
1 TTGCATTTAATTTCCTTTT
1448079 T
1 T
1448080 ATTTGTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 10 0.53
20 4 0.21
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.64
Consensus pattern (19 bp):
TTGCATTTAATTTCCTTTT
Found at i:1449286 original size:23 final size:23
Alignment explanation
Indices: 1449254--1449310 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
1449244 TTTCTTCCCT
*
1449254 TTCTCTTCTTCTCCGCTCAACTC
1 TTCTCCTCTTCTCCGCTCAACTC
1449277 TTCTCCTCTTCTCCGCTCAACTC
1 TTCTCCTCTTCTCCGCTCAACTC
1449300 TTCTCCTCTTC
1 TTCTCCTCTTC
1449311 CCCTCCTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.07, C:0.46, G:0.04, T:0.44
Consensus pattern (23 bp):
TTCTCCTCTTCTCCGCTCAACTC
Found at i:1450622 original size:15 final size:17
Alignment explanation
Indices: 1450590--1450641 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1450580 ATTTACCCTT
*
1450590 TAATTAA-ATTATTGTTA
1 TAATTAATATAATT-TTA
1450607 TAA-TAAT-TAATTTTA
1 TAATTAATATAATTTTA
*
1450622 TAATTAATATATTTTTA
1 TAATTAATATAATTTTA
1450639 TAA
1 TAA
1450642 AATAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 6 0.20
16 11 0.37
17 13 0.43
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TAATTAATATAATTTTA
Found at i:1450982 original size:22 final size:22
Alignment explanation
Indices: 1450952--1450996 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1450942 CCACTATGTT
*
1450952 TTTTTCTTAACAACCAGAAATA
1 TTTTCCTTAACAACCAGAAATA
1450974 TTTTCCTTAACAACCAGAAATA
1 TTTTCCTTAACAACCAGAAATA
1450996 T
1 T
1450997 AATGTCTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (22 bp):
TTTTCCTTAACAACCAGAAATA
Found at i:1458988 original size:24 final size:25
Alignment explanation
Indices: 1458929--1458988 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 25
1458919 ATATAACTCT
*
1458929 ACGGCGGTGGTGGCATCTGATATGG
1 ACGGCGGTGGCGGCATCTGATATGG
*
1458954 AAACGGTGGTGGCGGCATCTGATATGG
1 --ACGGCGGTGGCGGCATCTGATATGG
*
1458981 -CTGCGGTG
1 ACGGCGGTG
1458989 CCATTTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 6 0.21
27 23 0.79
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.23
Consensus pattern (25 bp):
ACGGCGGTGGCGGCATCTGATATGG
Found at i:1458988 original size:27 final size:27
Alignment explanation
Indices: 1458929--1458980 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1458919 ATATAACTCT
* *
1458929 ACGGCGGTGGTGGCATCTGATATGGAA
1 ACGGTGGTGGCGGCATCTGATATGGAA
1458956 ACGGTGGTGGCGGCATCTGATATGG
1 ACGGTGGTGGCGGCATCTGATATGG
1458981 CTGCGGTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.42, T:0.23
Consensus pattern (27 bp):
ACGGTGGTGGCGGCATCTGATATGGAA
Found at i:1460797 original size:17 final size:17
Alignment explanation
Indices: 1460775--1460814 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1460765 GAATTTGACC
1460775 GGGTTTGAGCTTTAAGA
1 GGGTTTGAGCTTTAAGA
*
1460792 GGGTTTGAGCTTTGAGA
1 GGGTTTGAGCTTTAAGA
1460809 GGGTTT
1 GGGTTT
1460815 TAGAGCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.40, T:0.38
Consensus pattern (17 bp):
GGGTTTGAGCTTTAAGA
Found at i:1463373 original size:10 final size:10
Alignment explanation
Indices: 1463346--1463444 Score: 58
Period size: 11 Copynumber: 9.6 Consensus size: 10
1463336 ACTAGATTAT
1463346 AAAATAAAAA
1 AAAATAAAAA
1463356 AGAAATAAAAA
1 A-AAATAAAAA
*
1463367 AAGATAAAAAA
1 AAAAT-AAAAA
* *
1463378 AAAATATTAAT
1 AAAATA-AAAA
* *
1463389 ATAAT-AATA
1 AAAATAAAAA
* *
1463398 ATAATAAAAT
1 AAAATAAAAA
*
1463408 AAAATAGATAA
1 AAAATA-AAAA
1463419 AAAAT-AAAA
1 AAAATAAAAA
*
1463428 ATAATAAAAA
1 AAAATAAAAA
1463438 TAAAATA
1 -AAAATA
1463445 GGATCAAAAT
Statistics
Matches: 66, Mismatches: 16, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
9 13 0.20
10 16 0.24
11 37 0.56
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:1463392 original size:45 final size:42
Alignment explanation
Indices: 1463343--1463442 Score: 114
Period size: 45 Copynumber: 2.3 Consensus size: 42
1463333 ATTACTAGAT
1463343 TATAAAATAAAAAAGAAATAAAAAAAGATAAAAAA-AAAATATTAA
1 TATAAAATAAAAAA-AAAT-AAAAAAGATAAAAAATAAAA-A-TAA
* *
1463388 TATAATAATAATAATAAAATAAAATAGATAAAAAATAAAAATAA
1 TATAA-AATAA-AAAAAAATAAAAAAGATAAAAAATAAAAATAA
1463432 TA-AAAATAAAA
1 TATAAAATAAAA
1463443 TAGGATCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
41 2 0.04
42 5 0.10
43 2 0.04
44 5 0.10
45 20 0.40
46 13 0.26
47 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (42 bp):
TATAAAATAAAAAAAAATAAAAAAGATAAAAAATAAAAATAA
Found at i:1463401 original size:6 final size:6
Alignment explanation
Indices: 1463380--1463444 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
1463370 ATAAAAAAAA
*
1463380 AATATT AAT-AT AATAAT AATAAT AA-AAT AA-AAT AGATAA- AA-AAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT A-ATAAT AATAAT
* *
1463424 AAAAAT AATAAA AATAA- AATA
1 AATAAT AATAAT AATAAT AATA
1463445 GGATCAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
4 2 0.04
5 20 0.39
6 27 0.53
7 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (6 bp):
AATAAT
Found at i:1463454 original size:16 final size:15
Alignment explanation
Indices: 1463346--1463445 Score: 70
Period size: 14 Copynumber: 6.8 Consensus size: 15
1463336 ACTAGATTAT
*
1463346 AAAATAAAAAAGA-A
1 AAAATAAAATAGATA
*
1463360 ATAA-AAAA-AGATA
1 AAAATAAAATAGATA
* *
1463373 AAAAAAAAATA-TTA
1 AAAATAAAATAGATA
1463387 ATATAATAATAATA-AT-
1 A-A-AATAA-AATAGATA
1463403 AAAATAAAATAGATAA
1 AAAATAAAATAGAT-A
1463419 AAAATAAAAATA-ATA
1 AAAAT-AAAATAGATA
1463434 AAAATAAAATAG
1 AAAATAAAATAG
1463446 GATCAAAATG
Statistics
Matches: 70, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
12 3 0.04
13 12 0.17
14 23 0.33
15 9 0.13
16 12 0.17
17 11 0.16
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (15 bp):
AAAATAAAATAGATA
Found at i:1468952 original size:37 final size:37
Alignment explanation
Indices: 1468860--1468961 Score: 172
Period size: 36 Copynumber: 2.8 Consensus size: 37
1468850 GTAATATAGT
*
1468860 TTTTTAAAAACATTTTGAAAA-TATATATAATATATAG
1 TTTTTAAAAACATTTTGAAAACT-TATATAATATATAA
1468897 TTTTT-AAAACATTTTGAAAACTTATATAATATATAA
1 TTTTTAAAAACATTTTGAAAACTTATATAATATATAA
1468933 TTTTTAAAAACATTTTGAAAACTTATATA
1 TTTTTAAAAACATTTTGAAAACTTATATA
1468962 TAGTTTTTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
36 33 0.53
37 29 0.47
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (37 bp):
TTTTTAAAAACATTTTGAAAACTTATATAATATATAA
Found at i:1470893 original size:2 final size:2
Alignment explanation
Indices: 1470882--1470914 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1470872 AAGACCTATT
1470882 TA TA -A 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
1470915 AAAGATTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1474022 original size:5 final size:5
Alignment explanation
Indices: 1474009--1474057 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
1473999 CCCCCTTTTA
* *
1474009 TTCTG TTCTT TTCTT TTCTT TTCTT TT-TG TTCTT TT-TT GTTC-T TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT -TTCTT TTCTT
1474057 T
1 T
1474058 CAAGAAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
4 8 0.22
5 29 0.78
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:1474041 original size:24 final size:23
Alignment explanation
Indices: 1474012--1474057 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1474002 CCTTTTATTC
1474012 TGTTCTTTTCTT-TTCTTTTCTTTT
1 TGTTCTTTT-TTGTTC-TTTCTTTT
1474036 TGTTCTTTTTTGTTCTTTCTTT
1 TGTTCTTTTTTGTTCTTTCTTT
1474058 CAAGAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (23 bp):
TGTTCTTTTTTGTTCTTTCTTTT
Found at i:1474200 original size:19 final size:19
Alignment explanation
Indices: 1474176--1474212 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1474166 TACAATCCTT
1474176 TTTATTT-AACATTAATTAA
1 TTTATTTCAA-ATTAATTAA
1474195 TTTATTTCAAATTAATTA
1 TTTATTTCAAATTAATTA
1474213 TTAGGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTTCAAATTAATTAA
Found at i:1474461 original size:17 final size:17
Alignment explanation
Indices: 1474439--1474473 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1474429 AAACATAATG
*
1474439 AAAATAAAATAACATAA
1 AAAATAAAATAAAATAA
*
1474456 AAAATAGAATAAAATAA
1 AAAATAAAATAAAATAA
1474473 A
1 A
1474474 GATATTACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAATAAAATAAAATAA
Found at i:1474687 original size:8 final size:8
Alignment explanation
Indices: 1474677--1474736 Score: 111
Period size: 8 Copynumber: 7.5 Consensus size: 8
1474667 TGAATCGATA
*
1474677 TATATATA
1 TATATATC
1474685 TATATATC
1 TATATATC
1474693 TATATATC
1 TATATATC
1474701 TATATATC
1 TATATATC
1474709 TATATATC
1 TATATATC
1474717 TATATATC
1 TATATATC
1474725 TATATATC
1 TATATATC
1474733 TATA
1 TATA
1474737 AATGAAAGAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 51 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATATC
Found at i:1476093 original size:3 final size:3
Alignment explanation
Indices: 1476065--1476166 Score: 161
Period size: 3 Copynumber: 34.3 Consensus size: 3
1476055 TTTGTAAAAA
* * * *
1476065 AAT AAA AAT ATT ATT AAT AA- AGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1476112 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1476160 AAT AAT A
1 AAT AAT A
1476167 GTAGGGCAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
2 1 0.01
3 91 0.99
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1476497 original size:103 final size:104
Alignment explanation
Indices: 1476298--1476529 Score: 267
Period size: 103 Copynumber: 2.2 Consensus size: 104
1476288 GAAGATGAAA
* * *
1476298 TTGTTCCTTCTC-TCTAAGGAAATC-AGTTCAATCTTGGAAATAATTTGGTGTTGAAAACAAAAT
1 TTGTTCCTTCTCAT-TGAGGAAGTCGAG-TCAATCTTGGAAATAATATGGTGTTGAAAACAAAAT
*
1476361 TGCTCATCCATGTTGAAGAGTTCTGGCCACTTTCATATGACCC
64 T-CTCATCCATGTTGAAGAGTTCTGCCCACTTTCATATGA-CC
* * * *
1476404 TT-TTCCTTCTCGTTGAGGAAGTCGAGTCAATC-TGGAGATAATATGGTGTTGAAGACAACACTT
1 TTGTTCCTTCTCATTGAGGAAGTCGAGTCAATCTTGGAAATAATATGGTGTTGAAAACAA-AATT
* * * *
1476467 -TCGTCCATGTTGAATAGTTCTGCCCGCTTTCATATGACG
65 CTCATCCATGTTGAAGAGTTCTGCCCACTTTCATATGACC
*
1476506 TTGTTCCTTCTCATTTAGGAAGTC
1 TTGTTCCTTCTCATTGAGGAAGTC
1476530 AGGTAAATAT
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
102 3 0.03
103 52 0.48
104 23 0.21
105 26 0.24
106 5 0.05
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (104 bp):
TTGTTCCTTCTCATTGAGGAAGTCGAGTCAATCTTGGAAATAATATGGTGTTGAAAACAAAATTC
TCATCCATGTTGAAGAGTTCTGCCCACTTTCATATGACC
Found at i:1482837 original size:22 final size:23
Alignment explanation
Indices: 1482807--1482861 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1482797 CAGAGAGAAT
*
1482807 CGATACCCCC-TTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
1482829 CGATTCCCCCTTTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
1482852 CGATTCCCCC
1 CGATTCCCCC
1482862 CTGTAGGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 9 0.29
23 22 0.71
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGGGAAC
Found at i:1482869 original size:22 final size:22
Alignment explanation
Indices: 1482807--1482885 Score: 88
Period size: 23 Copynumber: 3.6 Consensus size: 22
1482797 CAGAGAGAAT
*
1482807 CGATACCCCCTTGAAGGGGAAC
1 CGATACCCCCCTGAAGGGGAAC
* *
1482829 CGATTCCCCCTTTGAAGGGGAAC
1 CGATACCCCC-CTGAAGGGGAAC
* * *
1482852 CGATTCCCCCCTGTA-GGGAAT
1 CGATACCCCCCTGAAGGGGAAC
1482873 CGATACCCCCCTG
1 CGATACCCCCCTG
1482886 GGGTTCTGGT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
21 17 0.33
22 12 0.24
23 22 0.43
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.19
Consensus pattern (22 bp):
CGATACCCCCCTGAAGGGGAAC
Found at i:1484800 original size:17 final size:17
Alignment explanation
Indices: 1484771--1484808 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1484761 CATTTTGGAT
1484771 ATTT-TGGAATGTTTGA
1 ATTTGTGGAATGTTTGA
*
1484787 ATTTGTGGATTGTTTGA
1 ATTTGTGGAATGTTTGA
*
1484804 CTTTG
1 ATTTG
1484809 AATTTGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (17 bp):
ATTTGTGGAATGTTTGA
Found at i:1485159 original size:23 final size:23
Alignment explanation
Indices: 1485129--1485174 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1485119 TTAGAGTAAG
1485129 GGGGAGTAATTTCAAAACTTGAT
1 GGGGAGTAATTTCAAAACTTGAT
1485152 GGGGAGTAATTTCAAAACTTGAT
1 GGGGAGTAATTTCAAAACTTGAT
1485175 TTCAAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (23 bp):
GGGGAGTAATTTCAAAACTTGAT
Found at i:1485250 original size:8 final size:8
Alignment explanation
Indices: 1485237--1485262 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1485227 TGTTGAAAAC
1485237 ATTTTGAT
1 ATTTTGAT
1485245 ATTTTGAT
1 ATTTTGAT
1485253 ATTTTGAT
1 ATTTTGAT
1485261 AT
1 AT
1485263 AACAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
ATTTTGAT
Found at i:1487189 original size:72 final size:72
Alignment explanation
Indices: 1487103--1487312 Score: 195
Period size: 67 Copynumber: 3.0 Consensus size: 72
1487093 GTCTGAAGTG
* * *
1487103 AGACAAAACTTTGTTTTGACATAAACAATCTC-AAATTCTTATGTTTCAAGA-AAAACTATCTCA
1 AGACAAAACTTTGTTTGGACAGAAACAATCTCTAAAGT-TTATGTTTCAAGAGAAAA-TATCTCA
1487166 AGCGAGACC
64 AGCGAGACC
* * * *
1487175 AGACCAAACTTTGTTTGGAGAGAAACAATCTCTAAGGTTTATGTTTCAAGAGAAAATGTCTC-A-
1 AGACAAAACTTTGTTTGGACAGAAACAATCTCTAAAGTTTATGTTTCAAGAGAAAATATCTCAAG
*
1487238 --A-ACA
66 CGAGACC
* * * * *
1487242 AGACGAGACTTTGGTTT-GAGAGAAACAATCT-TAAAGGTTTATGTTTCAATAGAAAATGTCTCA
1 AGACAAAACTTT-GTTTGGACAGAAACAATCTCTAAA-GTTTATGTTTCAAGAGAAAATATCTCA
*
1487305 AGTGAGAC
64 AGCGAGAC
1487313 AAAAATTGTT
Statistics
Matches: 117, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
66 3 0.03
67 51 0.44
68 6 0.05
71 2 0.02
72 48 0.41
73 7 0.06
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (72 bp):
AGACAAAACTTTGTTTGGACAGAAACAATCTCTAAAGTTTATGTTTCAAGAGAAAATATCTCAAG
CGAGACC
Found at i:1489705 original size:8 final size:8
Alignment explanation
Indices: 1489687--1489760 Score: 51
Period size: 8 Copynumber: 8.4 Consensus size: 8
1489677 ATCTGTTCTC
1489687 TTTCTTTTT
1 TTTC-TTTT
1489696 TTTCTTTT
1 TTTCTTTT
1489704 TTT-TTCTCT
1 TTTCTT-T-T
1489713 TTTCCTCTTT
1 TTT-CT-TTT
*
1489723 GTTTCTCTT
1 -TTTCTTTT
1489732 TTTCTTTT
1 TTTCTTTT
*
1489740 TTTCCTCTT
1 TTT-CTTTT
1489749 TTTCTTTAT
1 TTTCTTT-T
1489758 TTT
1 TTT
1489761 TTATTTATCT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
7 2 0.04
8 21 0.40
9 21 0.40
10 3 0.06
11 5 0.09
12 1 0.02
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1489708 original size:12 final size:12
Alignment explanation
Indices: 1489682--1489715 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1489672 ACTTAATCTG
1489682 TTCTCTTTCTTTT
1 TTCTCTTT-TTTT
*
1489695 TTTTCTTTTTTT
1 TTCTCTTTTTTT
1489707 TTCTCTTTT
1 TTCTCTTTT
1489716 CCTCTTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTCTTTTTTT
Found at i:1489727 original size:18 final size:16
Alignment explanation
Indices: 1489706--1489755 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 16
1489696 TTTCTTTTTT
1489706 TTTCTCTTTTCCTCTTTG
1 TTTCTCTTTT--TCTTTG
*
1489724 TTTCTCTTTTTCTTTT
1 TTTCTCTTTTTCTTTG
1489740 TTTCCTCTTTTTCTTT
1 TTT-CTCTTTTTCTTT
1489756 ATTTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 8 0.27
17 12 0.40
18 10 0.33
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTCTCTTTTTCTTTG
Found at i:1489760 original size:18 final size:16
Alignment explanation
Indices: 1489702--1489760 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 16
1489692 TTTTTTTCTT
1489702 TTTTTTTCTCTTTTCCTC
1 TTTTTTTCTCTTTT--TC
*
1489720 TTTGTTTCTCTTTTTC
1 TTTTTTTCTCTTTTTC
1489736 TTTTTTTCCTCTTTTTC
1 TTTTTTT-CTCTTTTTC
1489753 TTTATTTT
1 TTT-TTTT
1489761 TTATTTATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.22
17 12 0.32
18 17 0.46
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTTTTCTCTTTTTC
Found at i:1492904 original size:18 final size:18
Alignment explanation
Indices: 1492868--1492906 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1492858 AACATGTTTT
*
1492868 AAACAATTTTAAGAAAAA
1 AAACAATTTTAACAAAAA
*
1492886 AAACATTTTTAACACAAAA
1 AAACAATTTTAACA-AAAA
1492905 AA
1 AA
1492907 TTGTTCTGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (18 bp):
AAACAATTTTAACAAAAA
Found at i:1493551 original size:2 final size:2
Alignment explanation
Indices: 1493544--1493596 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1493534 ATATGAATCG
1493544 AT AT AT AT AT AT AT AT 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
1493586 AT AT AT AT AT A
1 AT AT AT AT AT A
1493597 CATACACATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1495200 original size:3 final size:3
Alignment explanation
Indices: 1495187--1495223 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1495177 AAAAATAAAA
*
1495187 AAT ATT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1495224 ACAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1506273 original size:31 final size:32
Alignment explanation
Indices: 1506220--1506294 Score: 118
Period size: 31 Copynumber: 2.4 Consensus size: 32
1506210 TGTTGATATG
*
1506220 TGTTGTTTTAATTCTTTTTTCATGCAACAACT
1 TGTTTTTTTAATTCTTTTTTCATGCAACAACT
1506252 TGTTTTTTTAATTC-TTTTTCATGCAACAACT
1 TGTTTTTTTAATTCTTTTTTCATGCAACAACT
*
1506283 T-ATTTTTTAATT
1 TGTTTTTTTAATT
1506295 TGTTTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 10 0.24
31 18 0.44
32 13 0.32
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (32 bp):
TGTTTTTTTAATTCTTTTTTCATGCAACAACT
Found at i:1506474 original size:22 final size:22
Alignment explanation
Indices: 1506448--1506492 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1506438 TTGAAACAAA
*
1506448 TATTT-GAGATTTATCTTGTTAT
1 TATTTGGA-ATTTATATTGTTAT
*
1506470 TATTTGGAATTTTTATTGTTAT
1 TATTTGGAATTTATATTGTTAT
1506492 T
1 T
1506493 TTTATGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.62
Consensus pattern (22 bp):
TATTTGGAATTTATATTGTTAT
Found at i:1511361 original size:29 final size:31
Alignment explanation
Indices: 1511326--1511386 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1511316 TTATTTCATC
*
1511326 ACTAAAT-ATTT-TTATAACTTT-TTATTGTG
1 ACTAAATAATTTGTTACAA-TTTGTTATTGTG
1511355 ACTAAATAATTTGTTACAATTTGTTATTGTG
1 ACTAAATAATTTGTTACAATTTGTTATTGTG
1511386 A
1 A
1511387 AAACTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.25
30 7 0.25
31 14 0.50
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (31 bp):
ACTAAATAATTTGTTACAATTTGTTATTGTG
Found at i:1511394 original size:47 final size:47
Alignment explanation
Indices: 1511341--1511435 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1511331 ATATTTTTAT
1511341 AACTTTTTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAA
1 AACTTTTTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAA
1511388 AACTTTTTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAA
1 AACTTTTTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAA
1511435 A
1 A
1511436 GAATATTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (47 bp):
AACTTTTTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAA
Found at i:1511445 original size:47 final size:47
Alignment explanation
Indices: 1511347--1511445 Score: 164
Period size: 47 Copynumber: 2.1 Consensus size: 47
1511337 TTATAACTTT
* *
1511347 TTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAAACTTT
1 TTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAAACATA
1511394 TTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAAGA-ATA
1 TTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAA-ACATA
1511441 TTATT
1 TTATT
1511446 TGTCACAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 48 0.98
48 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.48
Consensus pattern (47 bp):
TTATTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAAACATA
Found at i:1511488 original size:17 final size:17
Alignment explanation
Indices: 1511468--1511505 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1511458 TTATAATGAG
1511468 AAATTAATATTTGTTA-T
1 AAATTAATATTT-TTATT
*
1511485 AAATTATTATTTTTATT
1 AAATTAATATTTTTATT
1511502 AAAT
1 AAAT
1511506 AAATTTATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AAATTAATATTTTTATT
Found at i:1515345 original size:16 final size:15
Alignment explanation
Indices: 1515324--1515366 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1515314 TGAAAATAAA
1515324 TAAAAACTAAAGAAAG
1 TAAAAACTAAA-AAAG
1515340 TAAAAACTCAAAAAAG
1 TAAAAACT-AAAAAAG
*
1515356 -AAAAAGTAAAA
1 TAAAAACTAAAA
1515367 CTTTATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 12 0.48
17 3 0.12
ACGTcount: A:0.72, C:0.07, G:0.09, T:0.12
Consensus pattern (15 bp):
TAAAAACTAAAAAAG
Found at i:1540295 original size:44 final size:43
Alignment explanation
Indices: 1540245--1540347 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 43
1540235 TGTTGGATTT
* * *
1540245 CCAACTTATTTCTATCACTGTGTTGGAGCTATAACCATCATTAC
1 CCAACTTATTTCTA-AACTATGTTGGAGCTATAACCAACATTAC
*
1540289 CCAACTTATTTCCTAAACTATGTTGGAGCTATTACCAACATTAC
1 CCAACTTATTT-CTAAACTATGTTGGAGCTATAACCAACATTAC
* *
1540333 CTAACTTAATTCTAA
1 CCAACTTATTTCTAA
1540348 GATTTCTCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 4 0.08
44 45 0.87
45 3 0.06
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (43 bp):
CCAACTTATTTCTAAACTATGTTGGAGCTATAACCAACATTAC
Found at i:1546508 original size:33 final size:33
Alignment explanation
Indices: 1546471--1546538 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1546461 GCCATTTCTT
1546471 TGGTT-AACTAGTTAGTGTTCGAGAGAAACTAGG
1 TGGTTCAA-TAGTTAGTGTTCGAGAGAAACTAGG
*
1546504 TGGTTCGATAGTTAGTGTTCGAGAGAAACTAGG
1 TGGTTCAATAGTTAGTGTTCGAGAGAAACTAGG
1546537 TG
1 TG
1546539 AAGATCAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.32, T:0.31
Consensus pattern (33 bp):
TGGTTCAATAGTTAGTGTTCGAGAGAAACTAGG
Found at i:1546511 original size:19 final size:19
Alignment explanation
Indices: 1546487--1546538 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 19
1546477 ACTAGTTAGT
1546487 GTTCGAGAGAAACTAGGTG
1 GTTCGAGAGAAACTAGGTG
* *
1546506 GTTCGATAG---TTA-GT-
1 GTTCGAGAGAAACTAGGTG
1546520 GTTCGAGAGAAACTAGGTG
1 GTTCGAGAGAAACTAGGTG
1546539 AAGATCAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 10
0.63 0.11 0.26
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 2 0.08
17 2 0.08
18 2 0.08
19 8 0.33
ACGTcount: A:0.29, C:0.10, G:0.35, T:0.27
Consensus pattern (19 bp):
GTTCGAGAGAAACTAGGTG
Found at i:1549567 original size:12 final size:13
Alignment explanation
Indices: 1549545--1549576 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1549535 GTAATTTTTA
1549545 TTTGTTTTGTTTG
1 TTTGTTTTGTTTG
1549558 TTTG-TTTGTTTG
1 TTTGTTTTGTTTG
1549570 TTT-TTTT
1 TTTGTTTT
1549577 CTTTACTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (13 bp):
TTTGTTTTGTTTG
Found at i:1557254 original size:20 final size:20
Alignment explanation
Indices: 1557229--1557274 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1557219 AGATTAATTC
* *
1557229 ATAATTTTATCAATCAACAT
1 ATAATTTCAACAATCAACAT
*
1557249 ATAATTTCAACAATTAACAT
1 ATAATTTCAACAATCAACAT
*
1557269 GTAATT
1 ATAATT
1557275 CTAGTAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (20 bp):
ATAATTTCAACAATCAACAT
Found at i:1557309 original size:37 final size:36
Alignment explanation
Indices: 1557268--1557343 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
1557258 ACAATTAACA
*
1557268 TGTAATTCTAGT-AAATAAATACACCGGTTAAAATATT
1 TGTAATTCTA-TCAAATAAATACACC-ATTAAAATATT
* *
1557305 TGTAATTGTATCAAGTAAATACACCATTAAAATATT
1 TGTAATTCTATCAAATAAATACACCATTAAAATATT
1557341 TGT
1 TGT
1557344 TTTGTCTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 14 0.40
37 21 0.60
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (36 bp):
TGTAATTCTATCAAATAAATACACCATTAAAATATT
Found at i:1558830 original size:43 final size:43
Alignment explanation
Indices: 1558761--1559106 Score: 273
Period size: 42 Copynumber: 8.1 Consensus size: 43
1558751 GGGCTTAAAC
* *
1558761 TATAAA-GT-AAAAGT-ATGATTGAAAAAATTAAGGACCACAAT
1 TATAAATGTAAAAAGTGA-GATTGAAAAAATTAAGGGCCTCAAT
* *
1558802 TATAAATGTAAAAAGTGAGATTTAAAAAATTAAGGGTCTCAAT
1 TATAAATGTAAAAAGTGAGATTGAAAAAATTAAGGGCCTCAAT
* * * * * *
1558845 TTTAAAGGTAAAAAGTGTGATTGAAAAAAATTAGGGGCTTAAAT
1 TATAAATGTAAAAAGTGAGATTG-AAAAAATTAAGGGCCTCAAT
*
1558889 TGTATAA-GTAAAATA-TGAGATT-AAAAAAGTT-AGGGCCTCAAT
1 TATA-AATGTAAAA-AGTGAGATTGAAAAAA-TTAAGGGCCTCAAT
* * *
1558931 TATAAATGTAAAATGTTAGATT-AAAAAATT-AGGAGCCTCGAT
1 TATAAATGTAAAAAGTGAGATTGAAAAAATTAAGG-GCCTCAAT
* * * * *
1558973 TATAAAGGTAGAAAGTGAGATTGAAAATAA-TATGAG-TTCAAT
1 TATAAATGTAAAAAGTGAGATTGAAAA-AATTAAGGGCCTCAAT
* * * * * * *
1559015 TGTAAATGTATAAAGTGGGATTGAAAAACTTAAGGTCATAAAT
1 TATAAATGTAAAAAGTGAGATTGAAAAAATTAAGGGCCTCAAT
* * * *
1559058 TCTAAATATAAAAAAGTAAGATTGAAAATATTAAGGGCCTCAAT
1 TATAAATGT-AAAAAGTGAGATTGAAAAAATTAAGGGCCTCAAT
1559102 TATAA
1 TATAA
1559107 CGATGAAAAA
Statistics
Matches: 239, Mismatches: 50, Indels: 29
0.75 0.16 0.09
Matches are distributed among these distances:
41 14 0.06
42 92 0.38
43 65 0.27
44 65 0.27
45 3 0.01
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (43 bp):
TATAAATGTAAAAAGTGAGATTGAAAAAATTAAGGGCCTCAAT
Found at i:1558867 original size:86 final size:86
Alignment explanation
Indices: 1558761--1559106 Score: 268
Period size: 86 Copynumber: 4.1 Consensus size: 86
1558751 GGGCTTAAAC
*
1558761 TATAAA-GT-AAAAGTATGATTGAAAAAATTAAGGACCACAATTATAAATGTAAAAAGTGAGATT
1 TATAAATGTAAAAAGTGTGATTGAAAAAATTAAGGACCACAATTATAAATGTAAAAAGTGAGATT
* *
1558824 TAAAAAATTAAGGGTCTCAAT
66 GAAAAAATTAAGGGCCTCAAT
* * * * * *
1558845 TTTAAAGGTAAAAAGTGTGATTGAAAAAAATTAGGGGCTTA-AATTGTATAA-GTAAAATA-TGA
1 TATAAATGTAAAAAGTGTGATTG-AAAAAATTAAGGAC-CACAATTATA-AATGTAAAA-AGTGA
1558907 GATT-AAAAAAGTT-AGGGCCTCAAT
62 GATTGAAAAAA-TTAAGGGCCTCAAT
* * * * *
1558931 TATAAATGTAAAATGT-TAGATT-AAAAAATT-AGGAGCCTCGATTATAAAGGTAGAAAGTGAGA
1 TATAAATGTAAAAAGTGT-GATTGAAAAAATTAAGGA-CCACAATTATAAATGTAAAAAGTGAGA
* * *
1558993 TTGAAAATAA-TATGAG-TTCAAT
64 TTGAAAA-AATTAAGGGCCTCAAT
* * * * * * * * *
1559015 TGTAAATGTATAAAGTGGGATTGAAAAACTTAAGG-TCATAAATTCTAAATATAAAAAAGTAAGA
1 TATAAATGTAAAAAGTGTGATTGAAAAAATTAAGGACCA-CAATTATAAATGT-AAAAAGTGAGA
*
1559079 TTGAAAATATTAAGGGCCTCAAT
64 TTGAAAAAATTAAGGGCCTCAAT
1559102 TATAA
1 TATAA
1559107 CGATGAAAAA
Statistics
Matches: 201, Mismatches: 39, Indels: 41
0.72 0.14 0.15
Matches are distributed among these distances:
83 5 0.02
84 55 0.27
85 25 0.12
86 70 0.35
87 42 0.21
88 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (86 bp):
TATAAATGTAAAAAGTGTGATTGAAAAAATTAAGGACCACAATTATAAATGTAAAAAGTGAGATT
GAAAAAATTAAGGGCCTCAAT
Found at i:1558883 original size:128 final size:127
Alignment explanation
Indices: 1558744--1558999 Score: 331
Period size: 128 Copynumber: 2.0 Consensus size: 127
1558734 AAAAATAATT
1558744 AAATTAGGGGCTTAAACTATA-AAGTAAAAGTAT-GATTGAAAAAA-TTAAGGACCACAATTATA
1 AAATTAGGGGCTTAAACTATATAAGTAAAA-TATAGATT-AAAAAAGTT-AGGACCACAATTATA
* * *
1558806 AATGTAAAAAGTGAGATTTAAAAAATTAAGG-GTCTCAATTTTAAAGGTAAAAAGTGTGATTGAA
63 AATGTAAAAAGTGAGA-TTAAAAAATT-AGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTGAA
1558870 AA
126 AA
* * * *
1558872 AAATTAGGGGCTTAAATTGTATAAGTAAAATATGAGATTAAAAAAGTTAGGGCCTCAATTATAAA
1 AAATTAGGGGCTTAAACTATATAAGTAAAATAT-AGATTAAAAAAGTTAGGACCACAATTATAAA
* * * *
1558937 TGTAAAATGTTAGATTAAAAAATTAGGAGCCTCGATTATAAAGGTAGAAAGTGAGATTGAAAA
65 TGTAAAAAGTGAGATTAAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAA
1559000 TAATATGAGT
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
127 3 0.03
128 62 0.55
129 41 0.37
130 6 0.05
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (127 bp):
AAATTAGGGGCTTAAACTATATAAGTAAAATATAGATTAAAAAAGTTAGGACCACAATTATAAAT
GTAAAAAGTGAGATTAAAAAATTAGGAGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAA
Found at i:1558900 original size:44 final size:43
Alignment explanation
Indices: 1558744--1558999 Score: 179
Period size: 43 Copynumber: 6.0 Consensus size: 43
1558734 AAAAATAATT
* *
1558744 AAATTAGGGGCTTAAACTATAAA-GT-AAAAGT-ATGATTGAAA
1 AAATTAGGGGCTTAAATTATAAAGGTAAAAAGTGA-GATTAAAA
* * * * *
1558785 AAATTAAGGAC-CACAATTATAAATGTAAAAAGTGAGATTTAAA
1 AAATTAGGGGCTTA-AATTATAAAGGTAAAAAGTGAGATTAAAA
* * * *
1558828 AAATTAAGGG-TCTCAATTTTAAAGGTAAAAAGTGTGATTGAAAA
1 AAATTAGGGGCT-TAAATTATAAAGGTAAAAAGTGAGATT-AAAA
*
1558872 AAATTAGGGGCTTAAATTGTATAA-GTAAAATA-TGAGATTAAAA
1 AAATTAGGGGCTTAAATTATA-AAGGTAAAA-AGTGAGATTAAAA
* * * * * *
1558915 AAGTTA-GGGCCTCAATTATAAATGTAAAATGTTAGATT-AAA
1 AAATTAGGGGCTTAAATTATAAAGGTAAAAAGTGAGATTAAAA
* * ** * *
1558956 AAATTAGGAGCCTCGATTATAAAGGTAGAAAGTGAGATTGAAA
1 AAATTAGGGGCTTAAATTATAAAGGTAAAAAGTGAGATTAAAA
1558999 A
1 A
1559000 TAATATGAGT
Statistics
Matches: 172, Mismatches: 29, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
40 1 0.01
41 27 0.16
42 51 0.30
43 57 0.33
44 32 0.19
45 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (43 bp):
AAATTAGGGGCTTAAATTATAAAGGTAAAAAGTGAGATTAAAA
Found at i:1562324 original size:20 final size:20
Alignment explanation
Indices: 1562299--1562339 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1562289 TATAGCATTT
1562299 CAAGCACTTTAAAACTCAAG
1 CAAGCACTTTAAAACTCAAG
*
1562319 CAAGCACTTTAAAATTCAAG
1 CAAGCACTTTAAAACTCAAG
1562339 C
1 C
1562340 TTTTAGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.22
Consensus pattern (20 bp):
CAAGCACTTTAAAACTCAAG
Found at i:1565214 original size:2 final size:2
Alignment explanation
Indices: 1565207--1565241 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1565197 TTATAATTCG
1565207 AT AT AT AT AT 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 AT AT AT AT AT A
1565242 GTGTTATTTG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1585847 original size:19 final size:19
Alignment explanation
Indices: 1585814--1585869 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
1585804 GCCATCTCTA
*
1585814 TCATTTCTT-TATTTCATT
1 TCATTACTTATATTTCATT
1585832 TCATT-CTTAATATTTCATT
1 TCATTACTT-ATATTTCATT
1585851 TCATTACTTATATTATCAT
1 TCATTACTTATATT-TCAT
1585870 CCCCTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.09
18 5 0.15
19 19 0.56
20 7 0.21
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (19 bp):
TCATTACTTATATTTCATT
Found at i:1586158 original size:8 final size:8
Alignment explanation
Indices: 1586147--1586171 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1586137 GCGAAAAATT
1586147 AGAAAAGA
1 AGAAAAGA
1586155 AGAAAAGA
1 AGAAAAGA
1586163 AGAAAAGA
1 AGAAAAGA
1586171 A
1 A
1586172 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:1591444 original size:19 final size:19
Alignment explanation
Indices: 1591420--1591461 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
1591410 ATCCTTTCTT
1591420 TATTTCATTTCATT-CTTAA
1 TATTTCATTTCATTACTT-A
1591439 TATTTCATTTCATTACTTA
1 TATTTCATTTCATTACTTA
1591458 TATT
1 TATT
1591462 ATTATCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTCATTTCATTACTTA
Found at i:1607289 original size:20 final size:20
Alignment explanation
Indices: 1607260--1607297 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1607250 TCTGCACCAC
*
1607260 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
1607280 ATGCATCTATATGATCCT
1 ATGCAACTATATGATCCT
1607298 GTATGAGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1607641 original size:15 final size:16
Alignment explanation
Indices: 1607618--1607651 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1607608 AAACTTTCAT
*
1607618 TTTCACTTTCAAATTC
1 TTTCACTTTCAAATAC
1607634 TTTC-CTTTCAAATAC
1 TTTCACTTTCAAATAC
1607649 TTT
1 TTT
1607652 TCTTAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTCACTTTCAAATAC
Found at i:1618521 original size:17 final size:17
Alignment explanation
Indices: 1618499--1618568 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
1618489 AATTAAGAGT
*
1618499 TAGTTTGATTAATGCAC
1 TAGTTTGATTAATGAAC
* *
1618516 TAGTTTAATAAATGAAC
1 TAGTTTGATTAATGAAC
*
1618533 TAGTTTGATTAATGAAG
1 TAGTTTGATTAATGAAC
*
1618550 TAACTTT-ATTAATGAAC
1 T-AGTTTGATTAATGAAC
1618567 TA
1 TA
1618569 AATGCATGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
16 1 0.02
17 39 0.89
18 4 0.09
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (17 bp):
TAGTTTGATTAATGAAC
Found at i:1618564 original size:34 final size:34
Alignment explanation
Indices: 1618499--1618568 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
1618489 AATTAAGAGT
* *
1618499 TAGTTTGATTAATGCACTAGTTTAATAAATGAAC
1 TAGTTTGATTAATGAACTACTTTAATAAATGAAC
* *
1618533 TAGTTTGATTAATGAAGTAACTTT-ATTAATGAAC
1 TAGTTTGATTAATGAACT-ACTTTAATAAATGAAC
1618567 TA
1 TA
1618569 AATGCATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
TAGTTTGATTAATGAACTACTTTAATAAATGAAC
Found at i:1618598 original size:34 final size:34
Alignment explanation
Indices: 1618516--1618598 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 34
1618506 ATTAATGCAC
* ** *
1618516 TAGTTTAATAAATGAACTAGTTTGATTAATGAAG
1 TAGTTTATTAAATGAACTAGAATGATGAATGAAG
*
1618550 TAACTTTATT-AATGAACTA-AATGCATGAATGAAG
1 T-AGTTTATTAAATGAACTAGAATG-ATGAATGAAG
1618584 TAGTTTATTAAATGA
1 TAGTTTATTAAATGA
1618599 CTGGATGCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
33 9 0.22
34 25 0.62
35 6 0.15
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (34 bp):
TAGTTTATTAAATGAACTAGAATGATGAATGAAG
Found at i:1618637 original size:17 final size:17
Alignment explanation
Indices: 1618608--1618651 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1618598 ACTGGATGCA
1618608 TAAAT-AAACTACTTCCC
1 TAAATGAAA-TACTTCCC
* *
1618625 TAAATGAAATACTTGCT
1 TAAATGAAATACTTCCC
1618642 TAAATGAAAT
1 TAAATGAAAT
1618652 GCATGCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (17 bp):
TAAATGAAATACTTCCC
Found at i:1618658 original size:17 final size:17
Alignment explanation
Indices: 1618625--1618666 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1618615 ACTACTTCCC
*
1618625 TAAATGAAATACTTGCT
1 TAAATGAAATACATGCT
*
1618642 TAAATGAAATGCATGCT
1 TAAATGAAATACATGCT
*
1618659 TTAATGAA
1 TAAATGAA
1618667 CAACATACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:1622859 original size:109 final size:110
Alignment explanation
Indices: 1622655--1622864 Score: 307
Period size: 109 Copynumber: 1.9 Consensus size: 110
1622645 GTATATTTCA
* *
1622655 AGAACATCTATCATAGAATAGGCATGGAAAGCGTTACTTTATAGAAGTAGTGCAATTCGATACAT
1 AGAACATCTATCATAGAATAGGCATGAAAAGCGTTACTTTATAGAAGTAGTGCAATTCGATACAA
*
1622720 CATTCGAACAAAAAGAGAACTTGAAATAAATTGAGTCTAGTTTAT
66 AATTCGAACAAAAAGAGAACTTGAAATAAATTGAGTCTAGTTTAT
* * * **
1622765 AGAACATCTATC-TAGAATGGGCGTGAAAAGTGTTACTTTATAGAAGTAGTGTGATTCGATACAA
1 AGAACATCTATCATAGAATAGGCATGAAAAGCGTTACTTTATAGAAGTAGTGCAATTCGATACAA
* *
1622829 AATTCGAACGAAAAGTA-AACTTTAAATAAATTGAGT
66 AATTCGAACAAAAAG-AGAACTTGAAATAAATTGAGT
1622865 ACATTTTGAG
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
109 76 0.85
110 13 0.15
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (110 bp):
AGAACATCTATCATAGAATAGGCATGAAAAGCGTTACTTTATAGAAGTAGTGCAATTCGATACAA
AATTCGAACAAAAAGAGAACTTGAAATAAATTGAGTCTAGTTTAT
Found at i:1625401 original size:18 final size:18
Alignment explanation
Indices: 1625378--1625420 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1625368 TCTTAGATTA
*
1625378 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
1625396 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATCT
1625414 TTTATTT
1 TTTATTT
1625421 CAAAAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1625478 original size:15 final size:14
Alignment explanation
Indices: 1625462--1625520 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
1625452 TTTATTACTA
1625462 TTATTTATTATTTT
1 TTATTTATTATTTT
***
1625476 ATTATTT-TCCCTTT
1 -TTATTTATTATTTT
*
1625490 TTATTTATTATTAT
1 TTATTTATTATTTT
1625504 TTATTTTATTATTTT
1 TTA-TTTATTATTTT
1625519 TT
1 TT
1625521 TCTTTTAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 6 0.18
14 10 0.29
15 18 0.53
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTATTATTTT
Found at i:1625516 original size:38 final size:35
Alignment explanation
Indices: 1625452--1625555 Score: 97
Period size: 37 Copynumber: 2.9 Consensus size: 35
1625442 CCTTTTTATC
*
1625452 TTTATTACTATTATTTATTATT-TTATTATTTTCCCTT
1 TTTATTATTATTATTTATT-TTATTATT-TTTT-CCTT
*
1625489 TTTATTTATTATTATTTATTTTATTATTTTTTTCTT
1 TTTA-TTATTATTATTTATTTTATTATTTTTTCCTT
* *
1625525 TTAAAATTATAATTATTTATTTTA--ATTTTTT
1 TT--TATTATTATTATTTATTTTATTATTTTTT
1625556 ATATCTTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
35 7 0.12
36 5 0.08
37 27 0.46
38 20 0.34
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (35 bp):
TTTATTATTATTATTTATTTTATTATTTTTTCCTT
Found at i:1625527 original size:35 final size:37
Alignment explanation
Indices: 1625460--1625555 Score: 103
Period size: 35 Copynumber: 2.7 Consensus size: 37
1625450 TCTTTATTAC
* *
1625460 TATTATT-TATTATTTTATTA-TTTTCCCTTTTT-ATT
1 TATTATTAT-TTATTTTATTATTTTTTCCTTTTTAAAT
* *
1625495 TATTATTATTTATTTTATTATTTTTTTCTTTTAAAAT
1 TATTATTATTTATTTTATTATTTTTTCCTTTTTAAAT
*
1625532 TATAATTATTTATTTTA--ATTTTTT
1 TATTATTATTTATTTTATTATTTTTT
1625556 ATATCTTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
35 25 0.47
36 10 0.19
37 18 0.34
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (37 bp):
TATTATTATTTATTTTATTATTTTTTCCTTTTTAAAT
Found at i:1630526 original size:5 final size:5
Alignment explanation
Indices: 1630518--1630618 Score: 69
Period size: 5 Copynumber: 19.8 Consensus size: 5
1630508 CATTCTATTT
* * * ****
1630518 TTTTA TTTTG TTTCA TTTTA TTTTG TTTTA TTTTTA TTTTA TTTTTA GCAAA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA -TTTTA TTTTA
* * * *
1630570 CTTTA TTTTCA TTCTA -TTTA TTTTA TTTTA ATTTA TTTTA TTCTA TTTT
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1630619 TCTCTGAACA
Statistics
Matches: 71, Mismatches: 21, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
4 3 0.04
5 54 0.76
6 14 0.20
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (5 bp):
TTTTA
Found at i:1632472 original size:72 final size:75
Alignment explanation
Indices: 1632289--1632479 Score: 246
Period size: 76 Copynumber: 2.6 Consensus size: 75
1632279 TTTTATCTTT
* * * * *
1632289 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTAT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATTATATTTAAATATTA-
*
1632354 CTTTGTTTTAG
65 CTTTGTTATAG
* *
1632365 GTATTTTAGTTTAAATAGGTTTTAGTATTTAAATTAGGATTTAGAATATTA-ATTTAAATATTA-
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATTATATTTAAATATTAC
1632428 TTT-TTATAG
66 TTTGTTATAG
* *
1632437 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTATGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTTA
1632480 AGATGTTTTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
71 5 0.05
72 39 0.38
73 3 0.03
75 9 0.09
76 47 0.46
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (75 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATTATATTTAAATATTAC
TTTGTTATAG
Found at i:1633095 original size:18 final size:18
Alignment explanation
Indices: 1633072--1633114 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1633062 TCTTAGATTA
1633072 TTTATTTAATTATTT-TCT
1 TTTATTTAATT-TTTATCT
*
1633090 TTTATTTAGTTTTTATCT
1 TTTATTTAATTTTTATCT
1633108 TTTATTT
1 TTTATTT
1633115 CAAAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTTTTATCT
Found at i:1633163 original size:7 final size:7
Alignment explanation
Indices: 1633153--1633210 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
1633143 TATCTTTTCT
1633153 TTTATTA
1 TTTATTA
1633160 TTTATTA
1 TTTATTA
1633167 TTTATTA
1 TTTATTA
**
1633174 TTT-TCC
1 TTTATTA
*
1633180 CTT-TTA
1 TTTATTA
1633186 TTTATTA
1 TTTATTA
1633193 -TTATTTA
1 TTTA-TTA
1633200 TTTTATTA
1 -TTTATTA
1633208 TTT
1 TTT
1633211 TTTGTTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
6 9 0.22
7 26 0.63
8 3 0.07
9 3 0.07
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:1633177 original size:22 final size:23
Alignment explanation
Indices: 1633152--1633210 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 23
1633142 TTATCTTTTC
1633152 TTTTATTATTTATTATT-TATTAT
1 TTTTATTATTTATTATTAT-TTAT
*
1633175 TTTCCCTTTTATTTATTATTATTTA-
1 TTT---TATTATTTATTATTATTTAT
1633200 TTTTATTATTT
1 TTTTATTATTT
1633211 TTTGTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
22 7 0.23
23 3 0.10
25 3 0.10
26 16 0.53
27 1 0.03
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTATTATTTATTATTATTTAT
Found at i:1633204 original size:15 final size:14
Alignment explanation
Indices: 1633182--1633249 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 14
1633172 TATTTTCCCT
1633182 TTTATTTATTATTA
1 TTTATTTATTATTA
*
1633196 TTTATTTTATTATTT
1 TTTA-TTTATTATTA
*
1633211 TTTGTTT-TTAAATTA
1 TTTATTTATT--ATTA
1633226 TAATTATTTATT-TTA
1 T--TTATTTATTATTA
*
1633241 TTTTTTTAT
1 TTTATTTAT
1633250 ATCTTTTCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
13 9 0.21
14 7 0.16
15 20 0.47
17 5 0.12
18 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:1637726 original size:36 final size:36
Alignment explanation
Indices: 1637677--1637745 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
1637667 AAGCATATTG
* *
1637677 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAT
1 TTTGTCTCCCTTGAGACAGCTCCTCTTGAAACAAAT
**
1637713 TTTGTCTTGCTTGAGACAGCTCCTCTTGAAACA
1 TTTGTCTCCCTTGAGACAGCTCCTCTTGAAACA
1637746 TAAATCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (36 bp):
TTTGTCTCCCTTGAGACAGCTCCTCTTGAAACAAAT
Found at i:1637807 original size:66 final size:67
Alignment explanation
Indices: 1637695--1637943 Score: 288
Period size: 66 Copynumber: 3.7 Consensus size: 67
1637685 CCTTGAGACA
* * * * *
1637695 GTTTCTCTTGAAACAAA-TTTTGTCTTGCTTGAGACAGC-TCCTCTTGAAACATAAATCTTTTAG
1 GTTTCTCTTGAAACAAAGTTTCGTCTCGCTTGAGATAGCTTCC-CTTGAAACATAAACCTTTGAG
1637758 ATT
65 ATT
* * *
1637761 GTTTCTCTTGAAACAAA-TTTTGTCTCGCTTAAAATAGCTTCCCTTGAAACATAAACCTTTGAGA
1 GTTTCTCTTGAAACAAAGTTTCGTCTCGCTTGAGATAGCTTCCCTTGAAACATAAACCTTTGAGA
1637825 TT
66 TT
* * * * ** *
1637827 GTTTCTATCGAAACAAAAGTTTCGTCTTGCTTGAGATAGTTTCTTTTAAAACATAAACCTTTGAG
1 GTTTCTCTTGAAAC-AAAGTTTCGTCTCGCTTGAGATAGCTTCCCTTGAAACATAAACCTTTGAG
1637892 ATT
65 ATT
* * * *
1637895 GTTTCTCTGGAAACAAAGTTTCGTCTCGTTTGAGACAGTTTCCCTTGAA
1 GTTTCTCTTGAAACAAAGTTTCGTCTCGCTTGAGATAGCTTCCCTTGAA
1637944 GCCCAAATTT
Statistics
Matches: 156, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
66 68 0.44
67 35 0.22
68 53 0.34
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (67 bp):
GTTTCTCTTGAAACAAAGTTTCGTCTCGCTTGAGATAGCTTCCCTTGAAACATAAACCTTTGAGA
TT
Found at i:1637963 original size:134 final size:132
Alignment explanation
Indices: 1637695--1637980 Score: 310
Period size: 134 Copynumber: 2.2 Consensus size: 132
1637685 CCTTGAGACA
* * * * *
1637695 GTTTCTCTTGAAAC-AAATTTTGTCTTGCTTGAGACAGCTCCTCTTGAAACATAAATCTTTTAGA
1 GTTTCTATTGAAACAAAATTTCGTCTTGCTTGAGACAGCTCCTCTTAAAACATAAACCTTTGAGA
* * * *
1637759 TTGTTTCTCTTGAAACAAATTTTGTCTCGCTTAAAATAGCTTCCCTTGAAACATAAACCTTTGAG
66 TTGTTTCTCTGGAAACAAATTTCGTCTCGCTTAAAACAGCTTCCCTTGAAACACAAA-CTTTGAG
1637824 ATT
130 ATT
* * * * *
1637827 GTTTCTATCGAAACAAAAGTTTCGTCTTGCTTGAGATAGTTTCTTTTAAAACATAAACCTTTGAG
1 GTTTCTATTGAAACAAAA-TTTCGTCTTGCTTGAGACAGCTCCTCTTAAAACATAAACCTTTGAG
* * * * * *
1637892 ATTGTTTCTCTGGAAACAAAGTTTCGTCTCGTTTGAGACAGTTTCCCTTGAAGCCCAAA-TTTCG
65 ATTGTTTCTCTGGAAACAAA-TTTCGTCTCGCTTAAAACAGCTTCCCTTGAAACACAAACTTT-G
1637956 A-AGTT
128 AGA-TT
1637961 GTTTC-ACTTGAAACAAAATT
1 GTTTCTA-TTGAAACAAAATT
1637981 GATCTGATTT
Statistics
Matches: 127, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
132 12 0.09
133 10 0.08
134 76 0.60
135 29 0.23
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (132 bp):
GTTTCTATTGAAACAAAATTTCGTCTTGCTTGAGACAGCTCCTCTTAAAACATAAACCTTTGAGA
TTGTTTCTCTGGAAACAAATTTCGTCTCGCTTAAAACAGCTTCCCTTGAAACACAAACTTTGAGA
TT
Found at i:1638053 original size:102 final size:101
Alignment explanation
Indices: 1637887--1638221 Score: 334
Period size: 102 Copynumber: 3.3 Consensus size: 101
1637877 ACATAAACCT
* * * ** * *
1637887 TTGAGATTG-TTTCTCTGGAAACAAAGTTTCGTCTCGTTTGAGACAGTTTCCCTTGAAGCCCAAA
1 TTGAGATTGTTTTC-CTGAAAACAAA-TTTCATATCACTTGAGACAGTTTCCCTTGAAACACAAA
* * * * *
1637951 TTTCGAAGTTGTTTCACTTGAAACAAAATTGATCTGAT
64 TTTTGAAATTGTTTCACTTAAAACAAAATTGATCTCAC
* *
1637989 TTGAGATTGTTTTCCT-AAAACCAAATTTCATATCGCTTGAGACAGCTTTCCCTCGAAACACAAA
1 TTGAGATTGTTTTCCTGAAAA-CAAATTTCATATCACTTGAGACAG-TTTCCCTTGAAACACAAA
*
1638053 TTTTGAAATTGTTTCACTTAAAACAAAATTGGTCTCAC
64 TTTTGAAATTGTTTCACTTAAAACAAAATTGATCTCAC
* * * * **
1638091 TTGAGATTGTTTTCCTGAAAACAAATTTCGTCTCACTTGAGATAGTTTTCCCTTGGAACGTAAAT
1 TTGAGATTGTTTTCCTGAAAACAAATTTCATATCACTTGAGACAG-TTTCCCTTGAAACACAAAT
* * **
1638156 TTTGAAATTTTTTCACTAAAAACAAAATTTTTCTCAC
65 TTTGAAATTGTTTCACTTAAAACAAAATTGATCTCAC
* * * *
1638193 CTGAGATAGCTTCTCTTG-AAACAAATTTC
1 TTGAGATTG-TTTTCCTGAAAACAAATTTC
1638222 TTTGCACTCA
Statistics
Matches: 198, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
101 20 0.10
102 164 0.83
103 14 0.07
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (101 bp):
TTGAGATTGTTTTCCTGAAAACAAATTTCATATCACTTGAGACAGTTTCCCTTGAAACACAAATT
TTGAAATTGTTTCACTTAAAACAAAATTGATCTCAC
Found at i:1638112 original size:36 final size:36
Alignment explanation
Indices: 1638055--1638141 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
1638045 AACACAAATT
* * *
1638055 TTGAAATTG-TTTCACTTAAAACAAAATTGGTCTCAC
1 TTGAGATTGTTTTC-CTGAAAACAAAATTCGTCTCAC
*
1638091 TTGAGATTGTTTTCCTGAAAACAAATTTCGTCTCAC
1 TTGAGATTGTTTTCCTGAAAACAAAATTCGTCTCAC
*
1638127 TTGAGATAGTTTTCC
1 TTGAGATTGTTTTCC
1638142 CTTGGAACGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
36 41 0.91
37 4 0.09
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAGATTGTTTTCCTGAAAACAAAATTCGTCTCAC
Found at i:1644954 original size:66 final size:66
Alignment explanation
Indices: 1644856--1645196 Score: 456
Period size: 66 Copynumber: 5.2 Consensus size: 66
1644846 CCTTGAGACA
* * *
1644856 GTTTCTCTTGAAACAAGTTTTGTCTT-GCTTGAGACAGCTTCTCTTGAAACATAAACCTTTGAGA
1 GTTTCTCTTGAAACAAATTTTGT-TTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
1644920 TT
65 TT
* *
1644922 GTTTCTCTTGAAACAAATTTTGTTTCACTTGAGATAGTTTCTCATGAAACATAAA-CTATTGAGA
1 GTTTCTCTTGAAACAAATTTTGTTTCGCTTGAGATAGTTTCTCTTGAAACATAAACCT-TTGAGA
1644986 TT
65 TT
* * * *
1644988 GTTACTCTTGAAAC-AATTTTTTTCTCGCTAGAGACAGTTTCTCTTGAAACATAAACCTTTGAGA
1 GTTTCTCTTGAAACAAATTTTGTT-TCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
1645052 TT
65 TT
* *
1645054 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTGTTTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGAT
1645119 T
66 T
* * * * * *
1645120 GTTTTTCTCGAAACAAAGTTTAGTCTT-GCATGAGATAATATCTCTTGAAACATAAACCTTTGAG
1 GTTTCTCTTGAAACAAA-TTTTGT-TTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAG
1645184 ATT
64 ATT
1645187 GTTTCTCTTG
1 GTTTCTCTTG
1645197 GAAAAAAAAA
Statistics
Matches: 242, Mismatches: 26, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
65 12 0.05
66 171 0.71
67 58 0.24
68 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (66 bp):
GTTTCTCTTGAAACAAATTTTGTTTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGAT
T
Found at i:1645094 original size:36 final size:35
Alignment explanation
Indices: 1644846--1645104 Score: 149
Period size: 36 Copynumber: 7.7 Consensus size: 35
1644836 TGTCTGTCTC
* * *
1644846 CCTTGAGACAGTTTCTCTTGAAACAAGTTTTGTCTT
1 CCTTGAGATAGTTTCTCTTGAAACAAATTTTATC-T
* * *
1644882 GCTTGAGACAGCTTCTCTTGAAACATAA----A-C-
1 CCTTGAGATAGTTTCTCTTGAAACA-AATTTTATCT
* * * *
1644912 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTTT
1 CCTTGAGATAGTTTCTCTTGAAACAAATTTTATCT
*
1644947 CACTTGAGATAGTTTCTCATGAAACATAA----A-CT
1 C-CTTGAGATAGTTTCTCTTGAAACA-AATTTTATCT
* * * * *
1644979 -ATTGAGATTGTTACTCTTGAAACAATTTTTTTCT
1 CCTTGAGATAGTTTCTCTTGAAACAAATTTTATCT
* *
1645013 CGCTAGAGACAGTTTCTCTTGAAACATAA----A-C-
1 C-CTTGAGATAGTTTCTCTTGAAACA-AATTTTATCT
* *
1645044 CTTTGAGATTGTTTCTCTTGAAACAAATTTTATCT
1 CCTTGAGATAGTTTCTCTTGAAACAAATTTTATCT
1645079 CGCTTGAGATAGTTTCTCTTGAAACA
1 C-CTTGAGATAGTTTCTCTTGAAACA
1645105 TAAACCTTTG
Statistics
Matches: 164, Mismatches: 35, Indels: 48
0.66 0.14 0.19
Matches are distributed among these distances:
29 5 0.03
30 60 0.37
31 1 0.01
32 3 0.02
33 1 0.01
34 3 0.02
35 2 0.01
36 85 0.52
37 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (35 bp):
CCTTGAGATAGTTTCTCTTGAAACAAATTTTATCT
Found at i:1645348 original size:101 final size:101
Alignment explanation
Indices: 1645178--1645483 Score: 398
Period size: 102 Copynumber: 3.0 Consensus size: 101
1645168 AACATAAACC
* * * * * * *
1645178 TTTGAGATTGTTTCTCTTGGAAAAAAAAATTCGTCTCACTTGAGATTG-TTTCCCTTGAAGCCCA
1 TTTGAGATTGTTT-TCCT--AAAAAAAATTTCATCTCACTTGAGATAGTTTTCCCTCGAAACTCA
*
1645242 AATTTTGAAGTTGTTTCACTTGAAACAAAATTGATCTCA
63 AATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCA
* *
1645281 TTTGAGATTGTTTTCCTAAAAAAAATTTCATCTCACTTGAGACAGTTTTCCATCGAAACTCAAAT
1 TTTGAGATTGTTTTCCTAAAAAAAATTTCATCTCACTTGAGATAGTTTTCCCTCGAAACTCAAAT
* *
1645346 TTTGAAATTGTTTTAGTTGAAACAAAATTGATCTCA
66 TTTGAAATTGTTTCACTTGAAACAAAATTGATCTCA
* * * ** *
1645382 CTTGAGATTATTTTCCTAAAAACAAATTTCTTCTTGCTTGAGATAGTTTTCCCTCGGAACTCAAA
1 TTTGAGATTGTTTTCCTAAAAA-AAATTTCATCTCACTTGAGATAGTTTTCCCTCGAAACTCAAA
*
1645447 TTTTGAAATTGTTTCACTTGAAACAAAATTTATCTCA
65 TTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCA
1645484 CCTGAGATAG
Statistics
Matches: 178, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
100 24 0.13
101 68 0.38
102 73 0.41
103 13 0.07
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (101 bp):
TTTGAGATTGTTTTCCTAAAAAAAATTTCATCTCACTTGAGATAGTTTTCCCTCGAAACTCAAAT
TTTGAAATTGTTTCACTTGAAACAAAATTGATCTCA
Found at i:1645507 original size:102 final size:101
Alignment explanation
Indices: 1645240--1645515 Score: 347
Period size: 102 Copynumber: 2.7 Consensus size: 101
1645230 CCTTGAAGCC
* * * * * *
1645240 CAAATTTTGAAGTTGTTTCACTTGAAACAAAATTGATCTCATTTGAGATTGTTTTCCTAAAAAAA
1 CAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATAGTTCTCTTAAAACAA
*
1645305 ATTTCATCTCACTTGAGACAGTTTTCCATCGAAACT
66 ATTTCTTCTCACTTGAGACAGTTTTCCATCGAAACT
* * * *
1645341 CAAATTTTGAAATTGTTTTAGTTGAAACAAAATTGATCTCACTTGAGATTA-TTTTCCTAAAAAC
1 CAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGA-TAGTTCT-CTTAAAAC
** * * *
1645405 AAATTTCTTCTTGCTTGAGATAGTTTTCCCTCGGAACT
64 AAATTTCTTCTCACTTGAGACAGTTTTCCATCGAAACT
* * *
1645443 CAAATTTTGAAATTGTTTCACTTGAAACAAAATTTATCTCACCTGAGATAGCTTCTCTTGAAACA
1 CAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATAG-TTCTCTTAAAACA
1645508 AATTTCTT
65 AATTTCTT
1645516 TCCACTCATT
Statistics
Matches: 150, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
101 50 0.33
102 97 0.65
103 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (101 bp):
CAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATAGTTCTCTTAAAACAA
ATTTCTTCTCACTTGAGACAGTTTTCCATCGAAACT
Found at i:1646004 original size:21 final size:22
Alignment explanation
Indices: 1645978--1646021 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1645968 ACCATCCACT
*
1645978 ACCCCTAACAA-CAACCATAAA
1 ACCCCTAACAACCAAACATAAA
*
1645999 ACCCCTCACAACCAAACATAAA
1 ACCCCTAACAACCAAACATAAA
1646021 A
1 A
1646022 AAAATGAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.52, C:0.39, G:0.00, T:0.09
Consensus pattern (22 bp):
ACCCCTAACAACCAAACATAAA
Found at i:1648101 original size:12 final size:12
Alignment explanation
Indices: 1648084--1648108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1648074 TTTTGTTTTC
1648084 TCTGGATTTTAG
1 TCTGGATTTTAG
1648096 TCTGGATTTTAG
1 TCTGGATTTTAG
1648108 T
1 T
1648109 GTGGGTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (12 bp):
TCTGGATTTTAG
Found at i:1649390 original size:30 final size:30
Alignment explanation
Indices: 1649342--1649404 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1649332 TCAAACATAT
** **
1649342 AAAGATTAAAATGTTTTTTTCTATAATA-A
1 AAAGATTAAAATACTTTTTAATATAATAGA
1649371 AAAGATTAAAATAACTTTTTAATATAATAGA
1 AAAGATTAAAAT-ACTTTTTAATATAATAGA
1649402 AAA
1 AAA
1649405 ACGTATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.43
30 12 0.43
31 4 0.14
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (30 bp):
AAAGATTAAAATACTTTTTAATATAATAGA
Found at i:1650151 original size:36 final size:36
Alignment explanation
Indices: 1650111--1650212 Score: 156
Period size: 35 Copynumber: 2.9 Consensus size: 36
1650101 CAAATTGTAA
1650111 AATATTTATATATTTTCTTTAAAAAATTAAATTCAT
1 AATATTTATATATTTTCTTTAAAAAATTAAATTCAT
1650147 AATA-TT-TATATTTTCTTTAAAAAAATTAAATTCAT
1 AATATTTATATATTTTCTTT-AAAAAATTAAATTCAT
*
1650182 AATATTTATATAATTTT-TTTACAAAATTAAA
1 AATATTTATAT-ATTTTCTTTAAAAAATTAAA
1650213 AATATAAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 8
0.87 0.01 0.11
Matches are distributed among these distances:
34 12 0.20
35 22 0.36
36 16 0.26
37 6 0.10
38 5 0.08
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (36 bp):
AATATTTATATATTTTCTTTAAAAAATTAAATTCAT
Found at i:1652316 original size:17 final size:17
Alignment explanation
Indices: 1652296--1652334 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1652286 ATTTTCAATA
1652296 AAAATACATAAAAAATT
1 AAAATACATAAAAAATT
* * *
1652313 AAAATATATAATAATTT
1 AAAATACATAAAAAATT
1652330 AAAAT
1 AAAAT
1652335 TTTTTAAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATACATAAAAAATT
Found at i:1655271 original size:18 final size:17
Alignment explanation
Indices: 1655216--1655271 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1655206 ACAATAAAAA
1655216 TATAATAAATAAATAATT
1 TATAA-AAATAAATAATT
* * *
1655234 TCTAAAATTATAATGA-T
1 TATAAAAATA-AATAATT
1655251 TATAAAAATAAATTAATT
1 TATAAAAATAAA-TAATT
1655269 TAT
1 TAT
1655272 TTTGTTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 2 0.07
17 15 0.52
18 12 0.41
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TATAAAAATAAATAATT
Found at i:1661076 original size:108 final size:110
Alignment explanation
Indices: 1660854--1661084 Score: 281
Period size: 108 Copynumber: 2.1 Consensus size: 110
1660844 TTCATTTAAG
* * * ** *
1660854 TAAAAAATATTAATTTAATTTATGACGGGACAATGATTCTGTCGGAAATTATGTTCAACTTTAAT
1 TAAAAAATATCAATTTAATTTATAACGGGACAATAATTCTGTAAGAAATTATATT--A-TTTAAT
* * *
1660919 TAAAATATACCAATTTAATTTGTGATAGAATAATCATTCCGTCGGAAA
63 TAAAATATAACAATTTAATTTGTGATAGAATAATCATTACGTCGAAAA
*
1660967 TAAAAAATATCAATTTAATTTATAATGGGACAATAATTCTGTAAGAAATT-TATT-TTTAATTAA
1 TAAAAAATATCAATTTAATTTATAACGGGACAATAATTCTGTAAGAAATTATATTATTTAATTAA
* *
1661030 AATATAATAATTTAATTTCG-GAT-GAAATAATCATTATGTCGAAAA
66 AATATAACAATTTAATTT-GTGATAG-AATAATCATTACGTCGAAAA
1661075 TAAAAAATAT
1 TAAAAAATAT
1661085 AGCTACCCGT
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
107 1 0.01
108 55 0.53
109 1 0.01
112 3 0.03
113 44 0.42
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (110 bp):
TAAAAAATATCAATTTAATTTATAACGGGACAATAATTCTGTAAGAAATTATATTATTTAATTAA
AATATAACAATTTAATTTGTGATAGAATAATCATTACGTCGAAAA
Found at i:1663396 original size:38 final size:38
Alignment explanation
Indices: 1663345--1663417 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
1663335 ATTTTTTTAA
* *
1663345 ATTTGTGATGGAATATGTGTATCCATCACAAATTTGTG
1 ATTTGTGACGGAATATGTGGATCCATCACAAATTTGTG
*
1663383 ATTTGTGACGGAATATGTGGATCCGTCACAAATTT
1 ATTTGTGACGGAATATGTGGATCCATCACAAATTT
1663418 CTGACAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (38 bp):
ATTTGTGACGGAATATGTGGATCCATCACAAATTTGTG
Found at i:1668727 original size:2 final size:2
Alignment explanation
Indices: 1668720--1668746 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1668710 ATGATGGCTT
1668720 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
1668747 TGGTGATATT
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:1671421 original size:3 final size:3
Alignment explanation
Indices: 1671413--1671450 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1671403 AGTCAAAGAA
* *
1671413 CAT CAT CAT CGT CAT CAC CAT CA- CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1671451 AACAATAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:1672238 original size:64 final size:64
Alignment explanation
Indices: 1672159--1672278 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
1672149 CTGACCTTAA
* * *
1672159 TCCAAAGAAAGTATATGATCAAAAGAAACCCAAAATATTACTTACCTATGAGTTGTGTCTTTAG
1 TCCAAAGAAAGTATATGACCAAAAGAAACCCAAAACATTACTTACCTAGGAGTTGTGTCTTTAG
1672223 TCCAAAGAAAGTATATGACCAAAAGAAACCCAAAACATTACTTACCTAGGAGTTGT
1 TCCAAAGAAAGTATATGACCAAAAGAAACCCAAAACATTACTTACCTAGGAGTTGT
1672279 ATGGCCATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.26
Consensus pattern (64 bp):
TCCAAAGAAAGTATATGACCAAAAGAAACCCAAAACATTACTTACCTAGGAGTTGTGTCTTTAG
Found at i:1675387 original size:30 final size:28
Alignment explanation
Indices: 1675318--1675388 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 28
1675308 AGGGTCATCT
* ***
1675318 AATTAATTTTAATATAACATTATTGTTG
1 AATTAATTTTGATATAACATTATTGAAA
1675346 AATTAATATTTTGATATAACATTAAATTGAAA
1 AATT-A-ATTTTGATATAACATT--ATTGAAA
1675378 AATTAATTTTG
1 AATTAATTTTG
1675389 GACTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 4 0.11
29 1 0.03
30 21 0.60
31 1 0.03
32 8 0.23
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (28 bp):
AATTAATTTTGATATAACATTATTGAAA
Found at i:1675828 original size:15 final size:15
Alignment explanation
Indices: 1675808--1675844 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1675798 AATCCTTAGT
1675808 GTGGATGATAAGGTA
1 GTGGATGATAAGGTA
1675823 GTGGATGATAAGGTA
1 GTGGATGATAAGGTA
1675838 GTGGATG
1 GTGGATG
1675845 TAGACTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.27
Consensus pattern (15 bp):
GTGGATGATAAGGTA
Found at i:1677223 original size:41 final size:41
Alignment explanation
Indices: 1677163--1677271 Score: 155
Period size: 41 Copynumber: 2.7 Consensus size: 41
1677153 TGTCTAAAAA
*
1677163 CTTAACATCATGCTTGAAAGACTTACTAATGGCTCAAAGGT
1 CTTAACATCATGCTTGAAAGACTTACTAATGACTCAAAGGT
** * * *
1677204 CTTAACATCACACTCGAAAGACTTATTGATGACTCAAAGGT
1 CTTAACATCATGCTTGAAAGACTTACTAATGACTCAAAGGT
*
1677245 CTAAACATCATGCTTGAAAGACTTACT
1 CTTAACATCATGCTTGAAAGACTTACT
1677272 GATTTCCTGA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (41 bp):
CTTAACATCATGCTTGAAAGACTTACTAATGACTCAAAGGT
Found at i:1680499 original size:18 final size:17
Alignment explanation
Indices: 1680445--1680493 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1680435 TTGGAATCCT
* *
1680445 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
1680463 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
1680481 AGTGCATTCGATG
1 AGTGCA-TCGATG
1680494 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:1680534 original size:64 final size:62
Alignment explanation
Indices: 1680445--1680624 Score: 195
Period size: 64 Copynumber: 2.8 Consensus size: 62
1680435 TTGGAATCCT
* *
1680445 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAA-TAG
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATTAG
* ** * *
1680506 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATT
1 ---AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATT
1680571 AG
61 AG
*
1680573 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
1680625 CAATTTATTC
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
63 1 0.01
64 89 0.91
65 2 0.02
66 3 0.03
67 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (62 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATTAG
Found at i:1680595 original size:19 final size:19
Alignment explanation
Indices: 1680571--1680621 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1680561 TAATTAAATT
1680571 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1680590 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1680609 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1680622 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1680659 original size:21 final size:21
Alignment explanation
Indices: 1680635--1680674 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1680625 CAATTTATTC
1680635 ATTGATGAATCGATGCATGGT
1 ATTGATGAATCGATGCATGGT
* *
1680656 ATTGATGCATCGGTGCATG
1 ATTGATGAATCGATGCATG
1680675 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGAATCGATGCATGGT
Found at i:1683258 original size:24 final size:23
Alignment explanation
Indices: 1683185--1683264 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
1683175 CATGATCTTG
*
1683185 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
1683208 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
*
1683229 TACATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
1683253 TGCATCGATGCA
1 TGCATCGATGCA
1683265 TTGTTAAGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
23 11 0.24
24 16 0.36
25 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:1683279 original size:44 final size:44
Alignment explanation
Indices: 1683184--1683284 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 44
1683174 GCATGATCTT
* *
1683184 GTGCATCGATGCACATTCAAGGCATGCATCGGTGCATCATGCGGA
1 GTGCATCGATGCACATTCAAGGCATGCATCGATGCAT-ATGCGAA
* * **
1683229 -TACATCGATGCACATTCAAAGGGATGCATCGATGCAT-TGTTAA
1 GTGCATCGATGCACATTC-AAGGCATGCATCGATGCATATGCGAA
*
1683272 GTGCATCGGTGCA
1 GTGCATCGATGCA
1683285 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 3 0.07
44 26 0.57
45 17 0.37
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (44 bp):
GTGCATCGATGCACATTCAAGGCATGCATCGATGCATATGCGAA
Found at i:1689134 original size:64 final size:62
Alignment explanation
Indices: 1689045--1689224 Score: 186
Period size: 64 Copynumber: 2.8 Consensus size: 62
1689035 TTGGACTCCT
* * *
1689045 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGAATTCGATGTTTGAA-AAA-TAG
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATTAG
* ** * *
1689106 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATT
1 ---AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATT
1689171 AG
61 AG
*
1689173 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
1689225 CAATTTATTC
Statistics
Matches: 97, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
63 1 0.01
64 88 0.91
65 2 0.02
66 3 0.03
67 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (62 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATTAG
Found at i:1689195 original size:19 final size:19
Alignment explanation
Indices: 1689171--1689221 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1689161 TAATTAAATT
1689171 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1689190 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1689209 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1689222 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1689259 original size:21 final size:21
Alignment explanation
Indices: 1689235--1689274 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1689225 CAATTTATTC
1689235 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1689256 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1689275 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1690528 original size:29 final size:30
Alignment explanation
Indices: 1690474--1690534 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
1690464 TTTTTATCCT
* *
1690474 TAAACTTTTCAAAATTTATACTTTGGCCAC
1 TAAACTTTTCAAAACTTACACTTTGGCCAC
* *
1690504 TAAACTTTT-AAAACTTACATTTTGGTCAC
1 TAAACTTTTCAAAACTTACACTTTGGCCAC
1690533 TA
1 TA
1690535 CCCAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTACACTTTGGCCAC
Found at i:1691901 original size:45 final size:49
Alignment explanation
Indices: 1691826--1691936 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 49
1691816 AGGATTAGAT
1691826 TTATTATTTTATTAGGAATTAAGGATGAGTTAAAACAT-TATT-TTTAG-TTA
1 TTATTATTTTATTAGGAATT-A--ATGAGTTAAAACATGT-TTATTTAGTTTA
*
1691876 TTATTATTTTATTAGGAATT-A-GAGTTAAGACATGTTTAGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAATGAGTTAAAACATGTTTA-TTTAGTTTA
1691924 TTATTATTTTATT
1 TTATTATTTTATT
1691937 CATTAGTTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
45 13 0.23
46 2 0.04
47 5 0.09
48 16 0.29
50 20 0.36
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (49 bp):
TTATTATTTTATTAGGAATTAATGAGTTAAAACATGTTTATTTAGTTTA
Found at i:1701013 original size:54 final size:54
Alignment explanation
Indices: 1700954--1701674 Score: 964
Period size: 54 Copynumber: 13.4 Consensus size: 54
1700944 TTCATTGAGA
* * ** * * *
1700954 TGCACACATAGTGCCTATACAGTCATTCATAAACATATTATGAATTATGT-GGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
* ** *
1701007 TCGCACA-TATAATGTATATATGGTTGTTCATCAACATATGATGAATTCTGTGGGT
1 T-GCACACT-TAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
1701062 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
* * * * * *
1701116 TTCGCACTTAGTGCCTATTCGGTTGTTTATCAATATATGATGAATTTTGT-GGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
*
1701169 TCGCACACTTAGTGCCTATACTGTTGTTCATCAACATATGATGAATTCTGTGGGT
1 T-GCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
* * * *
1701224 TGCACACTTAGTACCTATACGGTTATTCATCAACATATGATGAATTCCGTAGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
* * *
1701278 TGCACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCGTGGTT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
*
1701332 TGTACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
* * *
1701386 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGTTGAATTATTTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
** * * * *
1701440 TGCACACTTAGTGCCTATATTGTTGTTCATCAACCTATGATTAATTCCGTGGTT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
* * *
1701494 TGCACATTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCGTGGTT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
* ** *
1701548 TGCACATTTAGTAACTATACGGTTGTTCATCAATATATGATGAATT-TCGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCT-GTGGGT
* * *
1701602 TCCGCACTTAGTGCCTATACGGTTGTTCATTAACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
*
1701656 TACACACTTAGTGCCTATA
1 TGCACACTTAGTGCCTATA
1701675 GTACACATAG
Statistics
Matches: 586, Mismatches: 74, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
53 5 0.01
54 571 0.97
55 10 0.02
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
Found at i:1702069 original size:18 final size:18
Alignment explanation
Indices: 1702036--1702087 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
1702026 AGATATATTA
1702036 AAATAA-AATA-AATAAT
1 AAATAATAATATAATAAT
1702052 AAATAATAATATAATAAT
1 AAATAATAATATAATAAT
*
1702070 AAATATTAATAGTAATAA
1 AAATAATAATA-TAATAA
1702088 ATATAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 6 0.19
17 4 0.12
18 16 0.50
19 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATAATAATATAATAAT
Found at i:1702090 original size:10 final size:11
Alignment explanation
Indices: 1702028--1702090 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 11
1702018 AGTTGAAAAG
*
1702028 ATATATTAA-A
1 ATATAATAATA
*
1702038 ATAAAATAAATA
1 ATATAAT-AATA
1702050 ATA-AATAATA
1 ATATAATAATA
1702060 ATATAATAATAA
1 ATATAATAAT-A
*
1702072 ATATTAATAGTA
1 ATA-TAATAATA
1702084 ATA-AATA
1 ATATAATA
1702091 TAAAAGGGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
10 16 0.36
11 11 0.24
12 12 0.27
13 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
ATATAATAATA
Found at i:1702093 original size:22 final size:23
Alignment explanation
Indices: 1702037--1702094 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
1702027 GATATATTAA
1702037 AATAAA-ATAAATAATAAATAAT
1 AATAAATATAAATAATAAATAAT
* *
1702059 AATATAATAATAAAT-ATTAATAGT
1 AATA-AAT-ATAAATAATAAATAAT
1702083 AATAAATATAAA
1 AATAAATATAAA
1702095 AGGGGGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 9 0.29
23 5 0.16
24 11 0.35
25 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AATAAATATAAATAATAAATAAT
Found at i:1702880 original size:75 final size:76
Alignment explanation
Indices: 1702813--1702976 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 76
1702803 AAAAAATAAT
* * *
1702813 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATAAAGAT
1702877 AAAATATAAAA
66 AAAATATAAAA
*
1702888 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATAAAGAT
* * *
1702952 ATAATGTTTAAA
66 AAAAT-ATAAAA
*
1702964 ATATTATCCTAAA
1 ATAATATCCTAAA
1702977 TTTGAGTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 32 0.41
76 47 0.59
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATAAAGAT
AAAATATAAAA
Found at i:1704721 original size:11 final size:11
Alignment explanation
Indices: 1704704--1704743 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1704694 AGTTCGCTAA
1704704 AAAAATAAAAC
1 AAAAATAAAAC
*
1704715 GAAAATAAAA-
1 AAAAATAAAAC
1704725 AAAAATAAAAAC
1 AAAAAT-AAAAC
1704737 AAAAATA
1 AAAAATA
1704744 TAACGAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 5 0.20
11 14 0.56
12 6 0.24
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:1704728 original size:21 final size:22
Alignment explanation
Indices: 1704702--1704743 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1704692 AAAGTTCGCT
*
1704702 AAAAAAAT-AAAACGAAAATAA
1 AAAAAAATAAAAACAAAAATAA
1704723 AAAAAAATAAAAACAAAAATA
1 AAAAAAATAAAAACAAAAATA
1704744 TAACGAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAAAAATAAAAACAAAAATAA
Done.