Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008111.1 Hibiscus syriacus cultivar Beakdansim tig00110647_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: 1666726
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
File 9 of 9
Found at i:1581366 original size:16 final size:17
Alignment explanation
Indices: 1581332--1581369 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
1581322 TAATATAAAA
1581332 TAAACACTAAATATTTT
1 TAAACACTAAATATTTT
1581349 TAAACAC--AATATTTTT
1 TAAACACTAAATA-TTTT
1581365 TAAAC
1 TAAAC
1581370 GGGAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 9 0.45
17 7 0.35
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAACACTAAATATTTT
Found at i:1581387 original size:82 final size:83
Alignment explanation
Indices: 1581251--1581412 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 83
1581241 TTTTTAAAAC
* *
1581251 AACACTAAATATTTTTAAACACAATATTTTTTTAAACTGTAATAAATTAAACAAATTAATTTTAT
1 AACACTAAATATTTTTAAACACAATATTTTTTTAAACGGGAATAAATTAAACAAATTAATTTTAT
1581316 ATAATCTAATATAAAATA
66 ATAATCTAATATAAAATA
1581334 AACACTAAATATTTTTAAACACAATA-TTTTTTAAACGGGAATAAATTAAACAAATTAATTTTAT
1 AACACTAAATATTTTTAAACACAATATTTTTTTAAACGGGAATAAATTAAACAAATTAATTTTAT
*
1581398 ATACTCTAATATAAA
66 ATAATCTAATATAAA
1581413 CTAACTAATT
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 50 0.66
83 26 0.34
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.38
Consensus pattern (83 bp):
AACACTAAATATTTTTAAACACAATATTTTTTTAAACGGGAATAAATTAAACAAATTAATTTTAT
ATAATCTAATATAAAATA
Found at i:1581453 original size:14 final size:14
Alignment explanation
Indices: 1581434--1581460 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1581424 ACACATACAC
1581434 AACAACAAAAAATG
1 AACAACAAAAAATG
1581448 AACAACAAAAAAT
1 AACAACAAAAAAT
1581461 AATAAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
AACAACAAAAAATG
Found at i:1581858 original size:21 final size:21
Alignment explanation
Indices: 1581834--1581877 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1581824 TTAATATATT
1581834 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1581855 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1581876 AT
1 AT
1581878 TAACAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1581863 original size:28 final size:28
Alignment explanation
Indices: 1581800--1581864 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
1581790 TTATATAATC
* *
1581800 TAATATATAACTTAAACTAACAAATTAA
1 TAATTTATAACTTAAACTAACAAACTAA
1581828 T-ATATTATAACTTAAACTAACAAACTAA
1 TAAT-TTATAACTTAAACTAACAAACTAA
1581856 TAATTTATA
1 TAATTTATA
1581865 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (28 bp):
TAATTTATAACTTAAACTAACAAACTAA
Found at i:1582522 original size:29 final size:29
Alignment explanation
Indices: 1582480--1582547 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
1582470 GAGGACTGTA
*
1582480 TGGCGACCTACAAGGTCGCCCGGAGTGCT
1 TGGCGACCTACAAGGTCGCCCGGAGTACT
*
1582509 TGGCGACCTACAAGGTCGCCTGGAGTACT
1 TGGCGACCTACAAGGTCGCCCGGAGTACT
1582538 TGGCGACCTA
1 TGGCGACCTA
1582548 TGCTTGGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.32, T:0.19
Consensus pattern (29 bp):
TGGCGACCTACAAGGTCGCCCGGAGTACT
Found at i:1582686 original size:29 final size:29
Alignment explanation
Indices: 1582652--1582711 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
1582642 CATGCAGAGA
1582652 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1 CTCCAAGCTCGCCCGGATGCCATGGCGAC
* *
1582681 CTCCAAGGTCGCCCGGATGGCATGGCGAC
1 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1582710 CT
1 CT
1582712 ACGACAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.38, G:0.30, T:0.15
Consensus pattern (29 bp):
CTCCAAGCTCGCCCGGATGCCATGGCGAC
Found at i:1584456 original size:31 final size:31
Alignment explanation
Indices: 1584421--1584492 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
1584411 ATCCAAAGTT
1584421 TTACACAAATGAGATACTTTTCATTTAGTAC
1 TTACACAAATGAGATACTTTTCATTTAGTAC
*
1584452 TTACACAAATGAGATAGTTTTCATTTAGTAC
1 TTACACAAATGAGATACTTTTCATTTAGTAC
*
1584483 TTGCACAAAT
1 TTACACAAAT
1584493 AACAATTCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (31 bp):
TTACACAAATGAGATACTTTTCATTTAGTAC
Found at i:1587069 original size:43 final size:43
Alignment explanation
Indices: 1587022--1587380 Score: 327
Period size: 43 Copynumber: 8.4 Consensus size: 43
1587012 TATGTACTTA
* * * * *
1587022 AATTATAAAAGTAAAAA-TTATGATTTAAAAAATTAGTGAACTC
1 AATTATAAAGGTAAAAAGTGA-GATTAAAAAAATTAGAGACCTC
*
1587065 AATTATAAAGGTAAAGAGTGAGATTAAAAAAATTAGAGACCTC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGACCTC
* * * *
1587108 AATTTTAAAGGTAAAAAGTGAGATTGAAAAACATTAGGGACCTA
1 AATTATAAAGGTAAAAAGTGAGATT-AAAAAAATTAGAGACCTC
*
1587152 AATTATATAA-GTAAAAAGTGAGATTAAAAAAATTA-AGAGCTTC
1 AATTATA-AAGGTAAAAAGTGAGATTAAAAAAATTAGAGA-CCTC
* *
1587195 AATTATAAAGGTAAAAAGTGAGATT-AAAAAATT-GGGGCCTC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGACCTC
* * * * **
1587236 AATTATAAAGGTAGAAACTGAAATT-AAAAAATTTG-GAGTTC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGACCTC
* * * * * ***
1587277 AATTATAAAAGTACAAAGTGAGTTTAAAAAACTTAGGGTTATC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGACCTC
* * * * *
1587320 AATTATAAATGTAAAAAAATGAGATTAAAAAAATTAAAGTCATC
1 AATTATAAAGGT-AAAAAGTGAGATTAAAAAAATTAGAGACCTC
*
1587364 AATTATAAAGATAAAAA
1 AATTATAAAGGTAAAAA
1587381 ATATGATTAC
Statistics
Matches: 261, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
41 56 0.21
42 22 0.08
43 109 0.42
44 72 0.28
45 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (43 bp):
AATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGACCTC
Found at i:1587172 original size:87 final size:85
Alignment explanation
Indices: 1587017--1587420 Score: 376
Period size: 87 Copynumber: 4.8 Consensus size: 85
1587007 TAAATTATGT
* * * * * *
1587017 ACTTAAATTATAAAAGTAAAAA-TTATGATTTAAAAAATTAGTGAACTCAATTATAAAGGTAAAG
1 ACTTCAATTATAAAGGTAAAAAGTGA-GA-TTAAAAAATTAGGGACCTCAATTATAAAGGTAAAA
1587081 AGTGAGATTAAAAAAATTAGAG
64 AGTGAGATTAAAAAAATTAGAG
* * *
1587103 ACCTCAATTTTAAAGGTAAAAAGTGAGATTGAAAAACATTAGGGACCTAAATTATATAA-GTAAA
1 ACTTCAATTATAAAGGTAAAAAGTGAGATT-AAAAA-ATTAGGGACCTCAATTATA-AAGGTAAA
1587167 AAGTGAGATTAAAAAAATTA-AG
63 AAGTGAGATTAAAAAAATTAGAG
* *
1587189 AGCTTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATT-GGGGCCTCAATTATAAAGGTAGAAA
1 A-CTTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGGGACCTCAATTATAAAGGTAAAAA
* * *
1587253 CTGAAATT-AAAAAATTTG-G
65 GTGAGATTAAAAAAATTAGAG
* * * * *** *
1587272 AGTTCAATTATAAAAGTACAAAGTGAGTTTAAAAAACTTAGGGTTATCAATTATAAATGTAAAAA
1 ACTTCAATTATAAAGGTAAAAAGTGAGATTAAAAAA-TTAGGGACCTCAATTATAAAGGT-AAAA
* *
1587337 AATGAGATTAAAAAAATTAAAG
64 AGTGAGATTAAAAAAATTAGAG
* * * * * * * *
1587359 TCATCAATTATAAAGATAAAAAAT-ATGATTACAAAA--AGGAAACTCAATTATAAAGATAAAAA
1 ACTTCAATTATAAAGGTAAAAAGTGA-GATTAAAAAATTAGGGACCTCAATTATAAAGGTAAAAA
1587421 AAAGTTGAAG
Statistics
Matches: 260, Mismatches: 45, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
82 31 0.12
83 19 0.07
84 56 0.22
85 15 0.06
86 42 0.16
87 95 0.37
88 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (85 bp):
ACTTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGGGACCTCAATTATAAAGGTAAAAAG
TGAGATTAAAAAAATTAGAG
Found at i:1587381 original size:43 final size:43
Alignment explanation
Indices: 1587063--1587479 Score: 247
Period size: 43 Copynumber: 9.9 Consensus size: 43
1587053 ATTAGTGAAC
* * * * *
1587063 TCAATTATAAAGGTAAAGAGTGAGATTAAAAAAATTAGAGACC
1 TCAATTATAAAGATAAAAAGTGAGATTAAAAAAATTAAAGTCA
* * * ** * *
1587106 TCAATTTTAAAGGTAAAAAGTGAGATTGAAAAACATTAGGGACC
1 TCAATTATAAAGATAAAAAGTGAGATT-AAAAAAATTAAAGTCA
* *
1587150 TAAATTATATAAG-TAAAAAGTGAGATTAAAAAAATTAAGAG-CT
1 TCAATTATA-AAGATAAAAAGTGAGATTAAAAAAATTAA-AGTCA
* ** * *
1587193 TCAATTATAAAGGTAAAAAGTGAGATT-AAAAAATT-GGGGCC
1 TCAATTATAAAGATAAAAAGTGAGATTAAAAAAATTAAAGTCA
* * * * * **
1587234 TCAATTATAAAGGTAGAAACTGAAATTAAAAAATTTGGAGT--
1 TCAATTATAAAGATAAAAAGTGAGATTAAAAAAATTAAAGTCA
* * * ** *
1587275 TCAATTATAAA-AGTACAAAGTGAGTTTAAAAAACTTAGGGTTA
1 TCAATTATAAAGA-TAAAAAGTGAGATTAAAAAAATTAAAGTCA
*
1587318 TCAATTATAAATG-TAAAAAAATGAGATTAAAAAAATTAAAGTCA
1 TCAATTATAAA-GAT-AAAAAGTGAGATTAAAAAAATTAAAGTCA
* * **
1587362 TCAATTATAAAGATAAAAAAT-ATGATTACAAAAAGGAAA--C-
1 TCAATTATAAAGATAAAAAGTGA-GATTAAAAAAATTAAAGTCA
** *
1587402 TCAATTATAAAGATAAAAA-AAAG-TTGAAGAAAATTAAAGT-A
1 TCAATTATAAAGATAAAAAGTGAGATT-AAAAAAATTAAAGTCA
* * *
1587443 TTCAATTATAAAAATAAAAA-T-ATAATAAAAAAATTAA
1 -TCAATTATAAAGATAAAAAGTGAGATTAAAAAAATTAA
1587480 GAATTTTATA
Statistics
Matches: 304, Mismatches: 48, Indels: 46
0.76 0.12 0.12
Matches are distributed among these distances:
38 2 0.01
39 9 0.03
40 21 0.07
41 69 0.23
42 38 0.12
43 92 0.30
44 70 0.23
45 3 0.01
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (43 bp):
TCAATTATAAAGATAAAAAGTGAGATTAAAAAAATTAAAGTCA
Found at i:1587675 original size:31 final size:30
Alignment explanation
Indices: 1587601--1587709 Score: 116
Period size: 30 Copynumber: 3.6 Consensus size: 30
1587591 TAGAAAATAA
1587601 TTTACGTAAAAT-AGATTACTTGAAAACTGT
1 TTTACGTAAAATGA-ATTACTTGAAAACTGT
* * * *
1587631 TTTATGTAGAATGAATTA-TATGAAAATTATT
1 TTTACGTAAAATGAATTACT-TGAAAACT-GT
*
1587662 TTTACGTAAAATGAATTACCT-AAAACTGT
1 TTTACGTAAAATGAATTACTTGAAAACTGT
*
1587691 TTTACATAAAATGAATTAC
1 TTTACGTAAAATGAATTAC
1587710 ATTTTCTAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
29 20 0.31
30 26 0.40
31 19 0.29
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACTTGAAAACTGT
Found at i:1587685 original size:14 final size:14
Alignment explanation
Indices: 1587663--1587711 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1587653 AAAATTATTT
*
1587663 TTACGTAAAATGAA
1 TTACATAAAATGAA
* **
1587677 TTACCTAAAACTGTT
1 TTACATAAAA-TGAA
1587692 TTACATAAAATGAA
1 TTACATAAAATGAA
1587706 TTACAT
1 TTACAT
1587712 TTTCTAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (14 bp):
TTACATAAAATGAA
Found at i:1591838 original size:15 final size:15
Alignment explanation
Indices: 1591818--1591882 Score: 130
Period size: 15 Copynumber: 4.3 Consensus size: 15
1591808 CCGTAGGACC
1591818 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1591833 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1591848 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1591863 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1591878 ACTAC
1 ACTAC
1591883 AATACCCTCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.28, C:0.34, G:0.25, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:1593616 original size:4 final size:4
Alignment explanation
Indices: 1593607--1593643 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
1593597 TTTTATTCAA
1593607 TATT TATT TATT TATT TATT TATT TATT TATT ATATT
1 TATT TATT TATT TATT TATT TATT TATT TATT -TATT
1593644 CATTCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1595805 original size:13 final size:13
Alignment explanation
Indices: 1595783--1595820 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1595773 AGCATTCTAA
*
1595783 TTTTAGTTTTATT
1 TTTTAATTTTATT
1595796 TTTTAATTTTATT
1 TTTTAATTTTATT
1595809 TTTTAATTTTAT
1 TTTTAATTTTAT
1595821 CTTTGAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTAATTTTATT
Found at i:1595931 original size:17 final size:17
Alignment explanation
Indices: 1595909--1595943 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1595899 ATTTTAATTT
*
1595909 ATTTTTCTAAATTTTAA
1 ATTTTTATAAATTTTAA
*
1595926 ATTTTTATATATTTTAA
1 ATTTTTATAAATTTTAA
1595943 A
1 A
1595944 AATATACTTT
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:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTATAAATTTTAA
Found at i:1596302 original size:2 final size:2
Alignment explanation
Indices: 1596295--1596319 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1596285 AAATTACTAT
1596295 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1596320 GATGTCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1599650 original size:54 final size:54
Alignment explanation
Indices: 1599516--1599945 Score: 535
Period size: 54 Copynumber: 8.0 Consensus size: 54
1599506 ACCAAATAGA
* ** *
1599516 CACTAAGTGTGCAAAGTAC-ATAATTCATCATATGTTGATGAATAATTGTTTTTGG
1 CACTAAGTGTGCAAAGCACGA-AATTCATCATATGTTGATGAATAACCG-TTTCGG
* *
1599571 CACTAAGTGTGCAAAGCAAGGAATTCATCATATGTTGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATGAATAACCGTTTCGG
*
1599625 CACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATAAATAACCGTTTCGG
1 CACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATGAATAACCGTTTCGG
** ** * * *
1599679 CACTAAGTGCACAATTCAC-ATAATTCATCATATGTTGATGAATAACTGTTTTGA
1 CACTAAGTGTGCAAAGCACGA-AATTCATCATATGTTGATGAATAACCGTTTCGG
* * * *
1599733 CACTAAATGTGCAAAGCATGGAATTCATCATATGTTGATGAATAACCGTTTTGG
1 CACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATGAATAACCGTTTCGG
* **
1599787 CACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTCAA
1 CACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
1599841 CACTAAGTGTGCAAAGCAC-AGAATTCATCATATGTTGATGAATAACCG-TTAGA
1 CACTAAGTGTGCAAAGCACGA-AATTCATCATATGTTGATGAATAACCGTTTCGG
* * ** * *
1599894 TACTAAGTGTGTAATTCACAAAATTCATCATATGTTGATGAATAACCATTTC
1 CACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATGAATAACCGTTTC
1599946 AGTATTATGT
Statistics
Matches: 327, Mismatches: 42, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
53 46 0.14
54 239 0.73
55 42 0.13
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (54 bp):
CACTAAGTGTGCAAAGCACGAAATTCATCATATGTTGATGAATAACCGTTTCGG
Found at i:1599791 original size:162 final size:162
Alignment explanation
Indices: 1599515--1599945 Score: 605
Period size: 162 Copynumber: 2.7 Consensus size: 162
1599505 TACCAAATAG
** * * *
1599515 ACACTAAGTGTGCAAAGTACATAATTCATCATATGTTGATGAATAATTGTTTTTGGCACTAAGTG
1 ACACTAAGTGCACAAAGCACATAATTCATCATATGTTGATGAATAACTG-TTTTGACACTAAGTG
1599580 TGCAAAGCAAGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGCACG
65 TGCAAAGCAAGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGCACG
*
1599645 AAATTCATCATATGTTGATAAATAACCGTTTCG
130 AAATTCATCATATGTTGATAAATAACCGTTTCA
* ** *
1599678 GCACTAAGTGCACAATTCACATAATTCATCATATGTTGATGAATAACTGTTTTGACACTAAATGT
1 ACACTAAGTGCACAAAGCACATAATTCATCATATGTTGATGAATAACTGTTTTGACACTAAGTGT
* * *
1599743 GCAAAGCATGGAATTCATCATATGTTGATGAATAACCGTTTTGGCACTAAGTGTGCAAATCACGA
66 GCAAAGCAAGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGCACGA
*
1599808 AATTCATCATATGTTGATGAATAACCGTTTCA
131 AATTCATCATATGTTGATAAATAACCGTTTCA
** * * * *
1599840 ACACTAAGTGTGCAAAGCACAGAATTCATCATATGTTGATGAATAACCG-TTAGATACTAAGTGT
1 ACACTAAGTGCACAAAGCACATAATTCATCATATGTTGATGAATAACTGTTTTGACACTAAGTGT
* ** * *
1599904 GTAATTCACA-AAATTCATCATATGTTGATGAATAACCATTTC
66 GCAAAGCA-AGGAATTCATCATATGTTGATGAATAACCGTTTC
1599946 AGTATTATGT
Statistics
Matches: 236, Mismatches: 31, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
161 46 0.19
162 148 0.63
163 42 0.18
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (162 bp):
ACACTAAGTGCACAAAGCACATAATTCATCATATGTTGATGAATAACTGTTTTGACACTAAGTGT
GCAAAGCAAGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGCACGA
AATTCATCATATGTTGATAAATAACCGTTTCA
Found at i:1600014 original size:161 final size:162
Alignment explanation
Indices: 1599515--1599998 Score: 499
Period size: 162 Copynumber: 3.0 Consensus size: 162
1599505 TACCAAATAG
* * ** * * *
1599515 ACACTAAGTGTGCAAAGTACATAATTCATCATATGTTGATGAATAATTGTTTTTGGCACTAAGTG
1 ACACTAAGTGTGCAAAGCACAGAATTCATCATATGTTGATGAATAACCG-TTTAGACACTAAATG
* * * * *
1599580 TGCAAAGCA-AGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGCAC
65 TGCAAAGCACA-AAATTCATCATATGTTGATGAATAACCATTTCAGCACTAAGTGTGCAAACCAA
* * * *
1599644 GAAATTCATCATATGTTGATAAATAACCGTTTCG
129 GAAATTCATAATATGTTGATGAATAACCGTATCA
* ** ** * * *
1599678 GCACTAAGTGCACAATTCACATAATTCATCATATGTTGATGAATAACTGTTTTGACACTAAATGT
1 ACACTAAGTGTGCAAAGCACAGAATTCATCATATGTTGATGAATAACCGTTTAGACACTAAATGT
*** * ** * *
1599743 GCAAAGCATGGAATTCATCATATGTTGATGAATAACCGTTTTGGCACTAAGTGTGCAAATCACGA
66 GCAAAGCACAAAATTCATCATATGTTGATGAATAACCATTTCAGCACTAAGTGTGCAAACCAAGA
* *
1599808 AATTCATCATATGTTGATGAATAACCGTTTCA
131 AATTCATAATATGTTGATGAATAACCGTATCA
* *
1599840 ACACTAAGTGTGCAAAGCACAGAATTCATCATATGTTGATGAATAACCG-TTAGATACTAAGTGT
1 ACACTAAGTGTGCAAAGCACAGAATTCATCATATGTTGATGAATAACCGTTTAGACACTAAATGT
* ** * * * *
1599904 GTAATTCACAAAATTCATCATATGTTGATGAATAACCATTTCAGTATTATGTGTGCAACCCATAG
66 GCAAAGCACAAAATTCATCATATGTTGATGAATAACCATTTCAGCACTAAGTGTGCAAACCA-AG
* *
1599969 -AATTCATAATGA-GTTTATGAATGACCGTAT
130 AAATTCATAAT-ATGTTGATGAATAACCGTAT
1599999 AGATACTACG
Statistics
Matches: 275, Mismatches: 43, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
161 84 0.31
162 149 0.54
163 42 0.15
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (162 bp):
ACACTAAGTGTGCAAAGCACAGAATTCATCATATGTTGATGAATAACCGTTTAGACACTAAATGT
GCAAAGCACAAAATTCATCATATGTTGATGAATAACCATTTCAGCACTAAGTGTGCAAACCAAGA
AATTCATAATATGTTGATGAATAACCGTATCA
Found at i:1601298 original size:15 final size:15
Alignment explanation
Indices: 1601274--1601313 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1601264 TGGTTATGTC
1601274 TATT-ATGTGTCCTT
1 TATTGATGTGTCCTT
1601288 TATTGATGTGTCCTT
1 TATTGATGTGTCCTT
1601303 TATTGATGTGT
1 TATTGATGTGT
1601314 TTAGCAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.15, C:0.10, G:0.20, T:0.55
Consensus pattern (15 bp):
TATTGATGTGTCCTT
Found at i:1607330 original size:16 final size:15
Alignment explanation
Indices: 1607306--1607347 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1607296 TTCATATTTA
*
1607306 TTTATTTTTCAAATAT
1 TTTAATTTT-AAATAT
*
1607322 TTTAATTTTTAATAT
1 TTTAATTTTAAATAT
1607337 TTTAATTTTAA
1 TTTAATTTTAA
1607348 TCAAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATTTTAAATAT
Found at i:1607335 original size:15 final size:15
Alignment explanation
Indices: 1607317--1607345 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1607307 TTATTTTTCA
1607317 AATATTTTAATTTTT
1 AATATTTTAATTTTT
1607332 AATATTTTAATTTT
1 AATATTTTAATTTT
1607346 AATCAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATATTTTAATTTTT
Found at i:1608255 original size:28 final size:28
Alignment explanation
Indices: 1608217--1608270 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1608207 AAAAATAATA
*
1608217 ATTATTAATTA-ATAATTTAATATATTTT
1 ATTATTAATTAGA-AAATTAATATATTTT
*
1608245 ATTATTTATTAGAAAATTAATATATT
1 ATTATTAATTAGAAAATTAATATATT
1608271 AGTCATTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTATTAATTAGAAAATTAATATATTTT
Found at i:1608984 original size:59 final size:60
Alignment explanation
Indices: 1608885--1609002 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 60
1608875 TATTCAGATG
* * *
1608885 ACCATTTTGAAACTTTTAATAGTCAAGGGACTTAACAAAAC-ATGCTC-TATAATAAAGGA
1 ACCATTTTGAAACTTTTAATAGTCAAAGAACTCAACAAAACAATG-TCATATAATAAAGGA
* * * *
1608944 ACCATTTT-ATAACTTTTAATAGTCAAATAACTCGATAAAACAATGTCATATAATCAAGG
1 ACCATTTTGA-AACTTTTAATAGTCAAAGAACTCAACAAAACAATGTCATATAATAAAGG
1609003 GATCATTTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
58 1 0.02
59 35 0.71
60 13 0.27
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (60 bp):
ACCATTTTGAAACTTTTAATAGTCAAAGAACTCAACAAAACAATGTCATATAATAAAGGA
Found at i:1617168 original size:2 final size:2
Alignment explanation
Indices: 1617161--1617187 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1617151 TTTATTCACC
1617161 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
1617188 TATTGATTCA
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:1617227 original size:20 final size:21
Alignment explanation
Indices: 1617204--1617242 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1617194 TTCATTCTTT
1617204 TTATTTT-ATAAAAAATATCA
1 TTATTTTAATAAAAAATATCA
*
1617224 TTATTTTAATTAAAAATAT
1 TTATTTTAATAAAAAATAT
1617243 TTTACAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATTTTAATAAAAAATATCA
Found at i:1618235 original size:65 final size:62
Alignment explanation
Indices: 1618165--1618323 Score: 221
Period size: 65 Copynumber: 2.5 Consensus size: 62
1618155 GAATAAATTG
* *
1618165 AACATCGAATGCATTTCATGCATCGATGCACATACTATGCATCGATGCACTCAGAGT-TTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-CTATTT-TG-
1618229 A
62 A
* *
1618230 AACATCGAATGCATTTGATGCATCGATGCACCAACCATGCATCGATGCACTCTGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCA-CAACCATGCATCGATGCACTCAGCTATTTTGA
*
1618293 AACATCGAATGCATTTCATGCATCAATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
1618324 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
62 1 0.01
63 29 0.34
64 3 0.03
65 51 0.59
66 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (62 bp):
AACATCGAATGCATTTCATGCATCGATGCACAACCATGCATCGATGCACTCAGCTATTTTGA
Found at i:1624201 original size:44 final size:44
Alignment explanation
Indices: 1624115--1624212 Score: 137
Period size: 44 Copynumber: 2.2 Consensus size: 44
1624105 TTCGTGCTTC
*
1624115 ATGCATCGATACACTTAACAGTGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATACACATAACAGTGCATCGATGCATCCCTTTGAAT
*
1624159 ATGCATCGATACACCATAA-AGGTGCATCGATGCATGCC-TTGAAT
1 ATGCATCGATACA-CATAACA-GTGCATCGATGCATCCCTTTGAAT
*
1624203 GTGCATCGAT
1 ATGCATCGAT
1624213 GCATCCATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 29 0.59
45 20 0.41
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (44 bp):
ATGCATCGATACACATAACAGTGCATCGATGCATCCCTTTGAAT
Found at i:1624210 original size:23 final size:22
Alignment explanation
Indices: 1624135--1624218 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 22
1624125 ACACTTAACA
1624135 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
* * * * *
1624159 ATGCATCGATACA-CCATAAAG
1 GTGCATCGATGCATCCTTGAAT
1624180 GTGCATCGATGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
1624203 GTGCATCGATGCATCC
1 GTGCATCGATGCATCC
1624219 ATTGGGTTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
21 14 0.29
22 4 0.08
23 19 0.40
24 11 0.23
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:1626306 original size:13 final size:13
Alignment explanation
Indices: 1626288--1626324 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1626278 CATTTCACAT
1626288 TTGATTATGAATA
1 TTGATTATGAATA
1626301 TTGATTATGAATA
1 TTGATTATGAATA
1626314 TTGATTATGAA
1 TTGATTATGAA
1626325 ACTAATGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (13 bp):
TTGATTATGAATA
Found at i:1627014 original size:45 final size:46
Alignment explanation
Indices: 1626919--1627026 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 46
1626909 TGCACATACT
* * *
1626919 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCTGAGTTTTATGAAAACATAGAATGCATTTC
1626965 ATGCATCGATGCACTCTG-GCTATTT-TG-AAACATAGAATGCATTTC
1 ATGCATCGATGCACTCTGAG-T-TTTATGAAAACATAGAATGCATTTC
1627010 ATGCATCGATGCACTCT
1 ATGCATCGATGCACTCT
1627027 TAGTGCACCG
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 34 0.60
46 20 0.35
47 3 0.05
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACTCTGAGTTTTATGAAAACATAGAATGCATTTC
Found at i:1628248 original size:31 final size:31
Alignment explanation
Indices: 1628210--1628279 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
1628200 CTTTTAAAAC
*
1628210 TTGCAATACAATCCCTTAATATTTAGTCTAT
1 TTGCAATACAATCCCCTAATATTTAGTCTAT
* *** *
1628241 TTTCAATATGGTCCCCTAATATTTAGTCTGT
1 TTGCAATACAATCCCCTAATATTTAGTCTAT
1628272 TTGCAATA
1 TTGCAATA
1628280 TGGTCCCCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (31 bp):
TTGCAATACAATCCCCTAATATTTAGTCTAT
Found at i:1628280 original size:31 final size:31
Alignment explanation
Indices: 1628221--1628287 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1628211 TGCAATACAA
* *
1628221 TCCCTTAATATTTAGTCTATTTTCAATATGG
1 TCCCCTAATATTTAGTCTATTTGCAATATGG
*
1628252 TCCCCTAATATTTAGTCTGTTTGCAATATGG
1 TCCCCTAATATTTAGTCTATTTGCAATATGG
1628283 TCCCC
1 TCCCC
1628288 AAAATAACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (31 bp):
TCCCCTAATATTTAGTCTATTTGCAATATGG
Found at i:1630735 original size:29 final size:29
Alignment explanation
Indices: 1630693--1630775 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
1630683 GGATAGAAGA
1630693 TTTAGATGAATCTAACCTTATCAAGGATG
1 TTTAGATGAATCTAACCTTATCAAGGATG
1630722 TTTAGATGAATCTAACCTTATCAAGGATG
1 TTTAGATGAATCTAACCTTATCAAGGATG
*
1630751 TTTAGATGAATCTAACGTTAATCAA
1 TTTAGATGAATCTAACCTT-ATCAA
1630776 CACTAAACGC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 47 0.90
30 5 0.10
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (29 bp):
TTTAGATGAATCTAACCTTATCAAGGATG
Found at i:1632097 original size:31 final size:31
Alignment explanation
Indices: 1632059--1632126 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1632049 CAGTTATGTC
* *
1632059 GGGGACCATATTGCAAACTGACTAAATATTG
1 GGGGACCATATTGAAAACAGACTAAATATTG
* *
1632090 GGGGACCATATTGAAAACAGATTAAATGTTG
1 GGGGACCATATTGAAAACAGACTAAATATTG
1632121 GGGGAC
1 GGGGAC
1632127 TGTATTACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGAAAACAGACTAAATATTG
Found at i:1634403 original size:3 final size:3
Alignment explanation
Indices: 1634395--1634438 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1634385 CCCATTATCC
1634395 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1634439 AATAATAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1634449 original size:23 final size:23
Alignment explanation
Indices: 1634397--1634463 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
1634387 CATTATCCTT
* *
1634397 ATTATTATTATTATTATATTATTATT
1 ATTATTATTATTATTA-A--ATAATA
1634423 ATTATTATTATTATTAAATAATA
1 ATTATTATTATTATTAAATAATA
** *
1634446 ATTACAAATATTATTAAA
1 ATTATTATTATTATTAAA
1634464 GGCCCAGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.53
25 1 0.03
26 16 0.44
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTATTATTATTATTAAATAATA
Found at i:1635212 original size:20 final size:20
Alignment explanation
Indices: 1635187--1635229 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1635177 TTTGGCCACC
1635187 GTGAATAGTGACCGGCGGTG
1 GTGAATAGTGACCGGCGGTG
* *
1635207 GTGAATAGTGATCGGTGGTG
1 GTGAATAGTGACCGGCGGTG
1635227 GTG
1 GTG
1635230 GTGGTGGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.09, G:0.47, T:0.26
Consensus pattern (20 bp):
GTGAATAGTGACCGGCGGTG
Found at i:1635283 original size:30 final size:30
Alignment explanation
Indices: 1635247--1635369 Score: 228
Period size: 30 Copynumber: 4.1 Consensus size: 30
1635237 TGGTGGTAGT
1635247 GAAGGGAGAGATTCTCTCTCCTTAGAGAGA
1 GAAGGGAGAGATTCTCTCTCCTTAGAGAGA
1635277 GAAGGGAGAGATTCTCTCTCCTTAGAGAGA
1 GAAGGGAGAGATTCTCTCTCCTTAGAGAGA
*
1635307 GAAGGGAGAGCTTCTCTCTCCTTAGAGAGA
1 GAAGGGAGAGATTCTCTCTCCTTAGAGAGA
*
1635337 GAAGGGAGAGCTTCTCTCTCCTTAGAGAGA
1 GAAGGGAGAGATTCTCTCTCCTTAGAGAGA
1635367 GAA
1 GAA
1635370 CCAAAATGAA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 92 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (30 bp):
GAAGGGAGAGATTCTCTCTCCTTAGAGAGA
Found at i:1635908 original size:2 final size:2
Alignment explanation
Indices: 1635901--1635928 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1635891 ATTCATATTA
1635901 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
1635929 GAAATATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1636271 original size:26 final size:24
Alignment explanation
Indices: 1636225--1636272 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1636215 CCCTAAGTAT
*
1636225 ATATATATTTTCTTTAATATTTTA
1 ATATATATTTTCTTGAATATTTTA
*
1636249 ATATATGTTTTCTTAGAATTATTT
1 ATATATATTTTCTT-GAA-TATTT
1636273 GATTGAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 2 0.10
26 5 0.25
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
ATATATATTTTCTTGAATATTTTA
Found at i:1644651 original size:54 final size:55
Alignment explanation
Indices: 1644562--1644672 Score: 179
Period size: 54 Copynumber: 2.0 Consensus size: 55
1644552 AGCTTTACTG
* *
1644562 ACAAGAAATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTCTCAAATGTTTT
1 ACAAGAAATCTGGGCAGAAGCCACAAGAAAGGATGAATGTATTCTCAAATGTTTT
* *
1644617 ACAA-AAATCTGGGCAGAAGCCACAAGAAATGATGAATGTATTGTCAAATGTTTT
1 ACAAGAAATCTGGGCAGAAGCCACAAGAAAGGATGAATGTATTCTCAAATGTTTT
1644671 AC
1 AC
1644673 GAACCAGTGA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 48 0.92
55 4 0.08
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (55 bp):
ACAAGAAATCTGGGCAGAAGCCACAAGAAAGGATGAATGTATTCTCAAATGTTTT
Found at i:1645957 original size:9 final size:9
Alignment explanation
Indices: 1645943--1645976 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1645933 GAAATCGGTT
1645943 AATTAACTG
1 AATTAACTG
*
1645952 AATTAACCG
1 AATTAACTG
1645961 AATTAACTG
1 AATTAACTG
1645970 AATTAAC
1 AATTAAC
1645977 CTTTAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (9 bp):
AATTAACTG
Found at i:1645966 original size:18 final size:18
Alignment explanation
Indices: 1645943--1645977 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1645933 GAAATCGGTT
1645943 AATTAACTGAATTAACCG
1 AATTAACTGAATTAACCG
1645961 AATTAACTGAATTAACC
1 AATTAACTGAATTAACC
1645978 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (18 bp):
AATTAACTGAATTAACCG
Found at i:1646639 original size:177 final size:177
Alignment explanation
Indices: 1646339--1648255 Score: 2985
Period size: 177 Copynumber: 10.8 Consensus size: 177
1646329 AATACCCCTA
* *
1646339 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTCAGGGGTTTCCTAATTATCTCAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
* *
1646404 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGATAACTAAAAAACTAAGCCTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
* *
1646469 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCGTCCATAAAACCTTC
131 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
* *
1646516 AGCGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGAGGGTTTCCTAATTATCTCAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
*
1646581 AAGAGTTGTTAAAGGAAGCTAATCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
*
1646646 GGGGGTTTCTTGATTTGTAAGTCCTTCAGGCCATCCATAAGACCTTC
131 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
* *
1646693 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGAGATTCCTAATTATCTCAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
*
1646758 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGAGGTTCCTTGACAACTAAGAAACTAAGCCTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
1646823 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
131 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
* * *
1646870 AGTGCAGGATATTTTCAAATGAGATTTTAGAAACTAATCCTTCGGGGGTTTCCAAATTATCTCAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
* * * *
1646935 AAGAGTTGTTAAAGAAAACTAAGCCTAACAAAGTGGTTCCTTTACAACTAAGAAACTAAGCCTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
1647000 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
131 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
* *
1647047 AGTGCAGAATGTTTTCAAATGAGATTTTAGAAACTAAGGCTTCGGGGGTTTCCTAATTATCTCAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
* * *
1647112 AAGAGTTGTTAAAAGAAGCTAAGCCTAACAAAGAGGTTTCTTGACAACTAAGAAACTAAGCCTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
** *
1647177 GGGGGTTTCTTGATTTGTAAGTCCTTAAGGCCATCCATAAAACCTTC
131 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
* * * **
1647224 AGTGTAGGATGTTTTTAAATGATATTTTAGAAACTAAGCCTTATGGGGTTTCCTAATTATCTCAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
* ***
1647289 AAGAGTTATTAAAGGAAGCTAAGCCTAACAAATTAGTTCCTTGACAACTAAGAAACTAAGCCTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
*
1647354 GGGGGTTTCTTGATTTGTAAGTCCTTCAGGCCATCCATAAGACCTTC
131 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
* * * *
1647401 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCAAGACTTCAGGGGTTTACTAATTATCTCAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
* * * *
1647466 AAGAGCTGTTATAGGAAGCTAATCCTAATAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
* * * * *
1647531 GGGAGTTTCTTGATTTTTAAGTCATACGGGCCATCTATAAGACC-TC
131 GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
* * ** *
1647577 AGTGCATGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTCGGGGGTTTATTAATTATCTAAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
* * * * *
1647642 AAGAGCTATTAAAGGAAGATAAGCCTAACAAAGGAGTTCTTTGACAACTAAGAAACTAAGCCTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
* * *
1647707 AGGGGGTTTCTTGATTTGAAAGTCCTACGGGCCATCCATAAGACCTTT
131 -GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
* * * * **
1647755 AGTGCAAGATTTTTTCAAATGACATTTTAGAAACCAAGCCTTCGGGGGTTTATTAATTATCTCAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTC-A
* * * *
1647820 AAAAAGTTGTTAAATGAAGCTAAGCCTAATAAAGGGGTTCCTTAACAACTAAGAAACTAAGCCTT
65 AAAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTT
* *
1647885 CAGGGGTTTCTTGATTTGTAAGTCCTACGGGCCATCCATAAGACCTTC
130 CGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
* ** * *
1647933 AGTGCATGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCAAGGGTTTCCTAATTATTTTAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
* **
1647998 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAA-GGGTTCCTTGACAACTAAGAAGCTAAGATTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
* *
1648062 AGGGGTTTCTTGATTTGTAAGTCC-TCTGGGACATCCATAAGACCTTC
131 GGGGGTTTCTTGATTTGTAAGTCCTTC-GGGCCATCCATAAGACCTTC
1648109 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
1 AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
* * *
1648174 AAGAGTTGTTAAAGGAAGTTAATCCTAATAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
66 AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
1648239 GGGGGTTTCTTGATTTG
131 GGGGGTTTCTTGATTTG
1648256 AATTTCAAAG
Statistics
Matches: 1593, Mismatches: 142, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
175 1 0.00
176 280 0.18
177 1097 0.69
178 157 0.10
179 58 0.04
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (177 bp):
AGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAA
AAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTC
GGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTC
Found at i:1648353 original size:73 final size:73
Alignment explanation
Indices: 1648276--1648453 Score: 311
Period size: 73 Copynumber: 2.4 Consensus size: 73
1648266 ATTAGCAAAG
* *
1648276 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTTTTTCTCTAGAGAAAGTTTCACTTG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTTTCTCTCTAGAGAAAGTTTCACTCG
*
1648341 AAATAGCA
66 AAATAACA
*
1648349 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTTTCTCTCTTGAGAAAGTTTCACTCG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTTTCTCTCTAGAGAAAGTTTCACTCG
*
1648414 AAATAACG
66 AAATAACA
1648422 ATTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAA
1648454 TATATCTTGA
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 100 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (73 bp):
ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTTTCTCTCTAGAGAAAGTTTCACTCG
AAATAACA
Found at i:1648455 original size:37 final size:35
Alignment explanation
Indices: 1648276--1648455 Score: 135
Period size: 36 Copynumber: 5.0 Consensus size: 35
1648266 ATTAGCAAAG
*
1648276 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAATAA
* * * * ** ** *
1648311 ACTTTTTTTCTCTAGAGAAAGTTTCACTTGAAATAGCA
1 A-TTTATCTCACTTGAGATTGTTTTTCTTAAAATA--A
*
1648349 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAATAA
* * ** ** **
1648384 ACTTTTTCTCTCTTGAGAAAGTTTCACTCGAAATAA
1 A-TTTATCTCACTTGAGATTGTTTTTCTTAAAATAA
1648420 CGATTTATCTCACTTGAGATTGTTTTTCTTAAAATA
1 --ATTTATCTCACTTGAGATTGTTTTTCTTAAAATA
1648456 TATCTTGATA
Statistics
Matches: 102, Mismatches: 37, Indels: 10
0.68 0.25 0.07
Matches are distributed among these distances:
35 3 0.03
36 48 0.47
37 48 0.47
38 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.43
Consensus pattern (35 bp):
ATTTATCTCACTTGAGATTGTTTTTCTTAAAATAA
Found at i:1648780 original size:125 final size:125
Alignment explanation
Indices: 1648466--1649055 Score: 802
Period size: 125 Copynumber: 4.8 Consensus size: 125
1648456 TATCTTGATA
* * *
1648466 GAGTTCAAAATATGAAGAACTCCTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAAAACTTATTC
1 GAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
* * *
1648531 AACATTTTT-CTTGACTCTATCGCAGAAGGAGATAGAGAAACAGAGCCATTTCCAGATA-
66 AACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCAGACAG
* * *
1648589 GAGTTCGT-A-AT-AAGAACTCATCTGAAGATGAAGAAGACGTTCATAGTCTGAAGAACTTATTC
1 GAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
* *
1648651 AACCTTTTTTCTTGACTCTATCGCAGAAGGAGATAGAGCAACAGAGTCATTTCCAGACAG
66 AACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCAGACAG
* *
1648711 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACGTT-TT
1 GAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAAC-TTATT
** * * *
1648775 CAACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGTATCA-TCTTTTCCAGA-AG
65 CAACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACA-GAGCCATTTCCAGACAG
* * *
1648835 GAGTTCGTAATAAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
1 GAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
* * *
1648900 AACATTTTTGCTTGACTCTATCGCAGAATGAGATAGAGCAACAGAGCCATTTCTAGACAG
66 AACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCAGACAG
* * * *
1648960 AAGTTCATAATCTGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATAATCTGAAGAACCTTATT
1 GAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAA-CTTATT
* * * *
1649025 CAACC-TTTTGATCGATTCTATCGTAGAAGGA
65 CAACCTTTTTGCTTGACTCTATCGCAGAAGGA
1649056 AATAAAACAA
Statistics
Matches: 410, Mismatches: 46, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
120 55 0.13
121 48 0.12
122 8 0.02
123 10 0.02
124 107 0.26
125 169 0.41
126 13 0.03
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (125 bp):
GAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
AACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCAGACAG
Found at i:1648916 original size:249 final size:244
Alignment explanation
Indices: 1648466--1649087 Score: 858
Period size: 249 Copynumber: 2.5 Consensus size: 244
1648456 TATCTTGATA
* * * * *
1648466 GAGTTCAAAATATGAAGAACTCCTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAAAACTTATTC
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTC
* *
1648531 AACATTTTT-CTTGACTCTATCGCAGAAGGAGATAGAGAAACAGAGC-CATTTCCAGATA-GAGT
66 AACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAG---CAGATCACATTTCCAGA-AGGAGT
* * *
1648593 TCGTAATAAGAACTCATCTGAAGATGAAGAAGACGTTCATAGTCTGAAGAACTTATTCAACCTTT
127 TCGTAATAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACATTT
* *
1648658 TTTCTTGACTCTATCGCAGAAGGAGATAGAGCAACAGAGTCATTTCCAGACAG
192 TTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCAGACAG
1648711 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACGTT-TT
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAAC-TTATT
*
1648775 CAACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGTATCATCTTTTCCAGAAGGAGTT
65 CAACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAG-ATCA-CATTTCCAGAAGGAGTT
*
1648840 CGTAATAAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACAT
128 CGTAAT---AAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACAT
* *
1648905 TTTTGCTTGACTCTATCGCAGAATGAGATAGAGCAACAGAGCCATTTCTAGACAG
190 TTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCAGACAG
* *
1648960 AAGTTCATAATCTGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATAATCTGAAGAACCTTATT
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAA-CTTATT
* * * * * * * *
1649025 CAACC-TTTTGATCGATTCTATCGTAGAAGGAAATAAAACAACATCAACATTTCCAGAAGGAGT
65 CAACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGC-AGATC-ACATTTCCAGAAGGAGT
1649088 ATAACACCCC
Statistics
Matches: 337, Mismatches: 27, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
243 3 0.01
244 2 0.01
245 66 0.20
246 50 0.15
249 206 0.61
250 10 0.03
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (244 bp):
GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTC
AACCTTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGATCACATTTCCAGAAGGAGTTCGT
AATAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACATTTTTGC
TTGACTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCAGACAG
Found at i:1649900 original size:23 final size:23
Alignment explanation
Indices: 1649874--1649934 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1649864 CTCGTATAAA
*
1649874 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
* *
1649897 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
*
1649920 TGTACCAAAGTGCCA
1 TGCACCAAAGTGCCA
1649935 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCAAAGTGCCACGTAGAAT
Found at i:1653795 original size:2 final size:2
Alignment explanation
Indices: 1653784--1653827 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1653774 ATATCATGCT
1653784 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1653825 TA T
1 TA T
1653828 TCACTTCATT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1664325 original size:14 final size:14
Alignment explanation
Indices: 1664306--1664372 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
1664296 TATATTTACT
1664306 TTTTATTTTTCTTA
1 TTTTATTTTTCTTA
*
1664320 TTTTATTTGT-TT-
1 TTTTATTTTTCTTA
*
1664332 TTTT-CTTTTCATT-
1 TTTTATTTTTC-TTA
1664345 TTTT-TCTTTTCTTA
1 TTTTAT-TTTTCTTA
1664359 TTTTATTTTT-TTA
1 TTTTATTTTTCTTA
1664372 T
1 T
1664373 ATTAGTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
11 3 0.07
12 4 0.09
13 14 0.32
14 22 0.50
15 1 0.02
ACGTcount: A:0.10, C:0.07, G:0.01, T:0.81
Consensus pattern (14 bp):
TTTTATTTTTCTTA
Found at i:1664356 original size:19 final size:17
Alignment explanation
Indices: 1664320--1664370 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1664310 ATTTTTCTTA
1664320 TTTTATTTGTTTTTTTC
1 TTTTATTTGTTTTTTTC
*
1664337 TTTTCATTTTTTTCTTTTC
1 TTTT-ATTTGTTT-TTTTC
* *
1664356 TTAT-TTTATTTTTTT
1 TTTTATTTGTTTTTTT
1664371 ATATTAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.14
17 10 0.34
18 7 0.24
19 8 0.28
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTATTTGTTTTTTTC
Found at i:1664503 original size:9 final size:9
Alignment explanation
Indices: 1664488--1664647 Score: 68
Period size: 9 Copynumber: 17.6 Consensus size: 9
1664478 GCTCGTTATC
1664488 TTTATTTTGA
1 TTTATTTT-A
1664498 -TTATTTTA
1 TTTATTTTA
1664506 TTTATTTT-
1 TTTATTTTA
1664514 TCTTCATTTT-
1 T-TT-ATTTTA
1664524 TTTATTTCT-
1 TTTATTT-TA
1664533 TTTA-TTT-
1 TTTATTTTA
* *
1664540 TTTATGTTC
1 TTTATTTTA
1664549 TTTATTTTA
1 TTTATTTTA
*
1664558 TTTAGTTT-
1 TTTATTTTA
1664566 TTTATCTTTA
1 TTTAT-TTTA
1664576 TTTTATTTTTA
1 -TTTA-TTTTA
* * *
1664587 TGTCTTTTC
1 TTTATTTTA
1664596 TTT-TTCTTA
1 TTTATT-TTA
*
1664605 TTT-TTCTTT
1 TTTATT-TTA
*
1664614 TTTCATTTATT
1 TTT-ATTT-TA
**
1664625 TTTATTTCC
1 TTTATTTTA
1664634 TTTATTTTA
1 TTTATTTTA
1664643 TTTAT
1 TTTAT
1664648 CTTCATTGCC
Statistics
Matches: 121, Mismatches: 15, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
7 5 0.04
8 16 0.13
9 71 0.59
10 13 0.11
11 15 0.12
12 1 0.01
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1664509 original size:18 final size:17
Alignment explanation
Indices: 1664488--1664585 Score: 85
Period size: 18 Copynumber: 5.5 Consensus size: 17
1664478 GCTCGTTATC
*
1664488 TTTATTTTGATTATTTTA
1 TTTATTTT-TTTATTTTA
1664506 TTTATTTTTCTTCATTTT-
1 TTTATTTTT-TT-ATTTTA
1664524 TTTATTTCTTTTA-TTT-
1 TTTATTT-TTTTATTTTA
*
1664540 TTTATGTTCTTTATTTTA
1 TTTAT-TTTTTTATTTTA
*
1664558 TTTAGTTTTTTATCTTTA
1 TTTATTTTTTTAT-TTTA
1664576 TTTTATTTTT
1 -TTTATTTTT
1664586 ATGTCTTTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
16 12 0.18
17 13 0.19
18 27 0.40
19 15 0.22
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTATTTTTTTATTTTA
Found at i:1664533 original size:16 final size:15
Alignment explanation
Indices: 1664498--1664647 Score: 61
Period size: 16 Copynumber: 8.8 Consensus size: 15
1664488 TTTATTTTGA
1664498 TTATTTTATTTATTTTTC
1 TTATTTT-TTTA--TTTC
1664516 TTCATTTTTTTATTTC
1 TT-ATTTTTTTATTTC
*
1664532 TTTTATTTTTTATGTTC
1 TTAT-TTTTTTAT-TTC
*
1664549 TTTATTTTATTTAGTTTT
1 -TTATTTT-TTTA-TTTC
1664567 TTATCTTTATTTTATTT-
1 TTA--TTT-TTTTATTTC
*
1664584 TTATGTCTTTTCTTTTTC
1 TTAT-T-TTTT-TATTTC
*
1664602 TTATTTTTCTTTTTTC
1 TTATTTTT-TTATTTC
*
1664618 ATT-TATTTTTATTTCC
1 -TTATTTTTTTATTT-C
1664634 TTTATTTTATTTAT
1 -TTATTTT-TTTAT
1664648 CTTCATTGCC
Statistics
Matches: 106, Mismatches: 8, Indels: 36
0.71 0.05 0.24
Matches are distributed among these distances:
15 7 0.07
16 34 0.32
17 24 0.23
18 27 0.25
19 13 0.12
20 1 0.01
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (15 bp):
TTATTTTTTTATTTC
Found at i:1664659 original size:24 final size:25
Alignment explanation
Indices: 1664613--1664665 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
1664603 TATTTTTCTT
* * *
1664613 TTTTCATTTATTTTTATTTCCTTTA
1 TTTTCATTTATCTTCATTGCCTTTA
*
1664638 TTTT-ATTTATCTTCATTGCCTTTT
1 TTTTCATTTATCTTCATTGCCTTTA
1664662 TTTT
1 TTTT
1664666 TCTAACATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTTCATTTATCTTCATTGCCTTTA
Found at i:1665248 original size:17 final size:18
Alignment explanation
Indices: 1665226--1665274 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
1665216 GTTTCAGATT
*
1665226 CAGATTTCAATTCC-TGA
1 CAGATTTCAATTCCTTCA
*
1665243 CAGATTCCAATTCCTTCA
1 CAGATTTCAATTCCTTCA
1665261 CAGATTTCAATTCC
1 CAGATTTCAATTCC
1665275 CTCAGAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35
Consensus pattern (18 bp):
CAGATTTCAATTCCTTCA
Found at i:1665911 original size:3 final size:3
Alignment explanation
Indices: 1665903--1666701 Score: 715
Period size: 3 Copynumber: 269.0 Consensus size: 3
1665893 GTGATGACCT
1665903 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GGAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA
* * *
1665949 -AA GAA GAA GAA GGA GAA GAA GAA GAA GGA GAA GAA GAA GAA GGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
1665996 GAA GAA GGA GAA GAA GAA GAA G-A GAA GAA G-A GAA G-A GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * *
1666041 GAA GAA GAA G-A GAA GAA GGA GAA G-A GAA GAA GGA GAA GAG GAT GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
1666087 AAA GAA GAA GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * * * *
1666135 GAA -AGA GGA GAA GAA GGA GGA GGA GGA GAA GAA GAA GAA GGA GAA
1 GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
1666180 GAA TAA GAA GAA GAA GGAA G-A GGA GGA GAA GAA GAA GAA TG-A GAA
1 GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA
* * * * *
1666225 GAA GAA GAA GAA GGA GGA GGA GGA GAA GAA GAA CAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * *
1666273 -AGA GGA GGA GAA GAA GGA GAA GAA GGA GAA GAA GAA GAA GAA GAA
1 GA-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1666318 TG-A GAA GAA GAA GAA GAA GAA TG-A GAA GAA GAA GAA GAA GAA GAA
1 -GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
* * * *
1666363 GAA GAA GAA GAA GAA GAA GAA GAA GGA GCA GAA GAA GAA GGAG GAG
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA
* * * * * * *
1666409 GAG GAG GAA -AA GAA GAA GAA GAA -AA GGA GAG GAGA GGA GGA GGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA
* * * * * * *
1666453 GAA GAG GAG GAG GAG GAG GAG GAGA GAA TAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA
* * * *
1666499 GAAA GGA GAA G-A GGA GAA GAA GGA GAA GAA GGA GAA GAA G-A GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
1666543 GAA GGAA GAA GGA GAA GAA GGA GAA GAA G-A GAA GAA GAA GGA GAA
1 GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * * * * *
1666588 -AA GGA GGA G-A GGA GAA GAA GGA GAA TGAG GAA GGAG GAA GAA GGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA -GAA GAA GAA GAA
* * * * *
1666633 GAA G-A GGA GAA GAA GAT G-A GCA GAA GAG GAA GAA GAA GGA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
1666679 GGA GAA GAA GAA G-A GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA
1666702 TGAGCGAAGG
Statistics
Matches: 672, Mismatches: 88, Indels: 72
0.81 0.11 0.09
Matches are distributed among these distances:
2 38 0.06
3 610 0.91
4 24 0.04
ACGTcount: A:0.58, C:0.00, G:0.41, T:0.01
Consensus pattern (3 bp):
GAA
Done.