Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008958.1 Hibiscus syriacus cultivar Beakdansim tig00112289_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: 2490255
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1681130 original size:26 final size:27
Alignment explanation
Indices: 1681100--1681157 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
1681090 ATTTTTTATT
*
1681100 TTTATTTGTATCT-TTTTTTCCTTTGA
1 TTTATTTATATCTCTTTTTTCCTTTGA
* *
1681126 TTTATTTATTTTTCTTTTTTCCTTTGA
1 TTTATTTATATCTCTTTTTTCCTTTGA
1681153 TTTAT
1 TTTAT
1681158 ATAATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.72
Consensus pattern (27 bp):
TTTATTTATATCTCTTTTTTCCTTTGA
Found at i:1681605 original size:21 final size:21
Alignment explanation
Indices: 1681574--1681652 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
1681564 CTAAACCCCA
* *
1681574 AAATCTCAAACCCTAAAACCT
1 AAATCTTAAACCCTAAAATCT
* *
1681595 ATATCTTAAACCATAAATATC-
1 AAATCTTAAACCCTAAA-ATCT
* *
1681616 AAATCATAAACCCTAAAATAT
1 AAATCTTAAACCCTAAAATCT
1681637 AAAT-TTAAACCCTAAA
1 AAATCTTAAACCCTAAA
1681653 TCATAAGCCC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 13 0.28
21 32 0.68
22 2 0.04
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (21 bp):
AAATCTTAAACCCTAAAATCT
Found at i:1682332 original size:20 final size:20
Alignment explanation
Indices: 1682309--1682352 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1682299 AAGTTGTGAT
1682309 ACTTT-CACAATAGTTTCAAA
1 ACTTTCCACAA-AGTTTCAAA
* *
1682329 ACTTTCCCCAAAGTTTCGAA
1 ACTTTCCACAAAGTTTCAAA
1682349 ACTT
1 ACTT
1682353 CATGTGCAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (20 bp):
ACTTTCCACAAAGTTTCAAA
Found at i:1684694 original size:18 final size:18
Alignment explanation
Indices: 1684671--1684710 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1684661 AGGCATTTGA
1684671 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTCGTGCTTGT
1684689 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
1684707 TCCT
1 TCCT
1684711 TGTGCTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.00, C:0.33, G:0.23, T:0.45
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:1685907 original size:10 final size:9
Alignment explanation
Indices: 1685883--1685921 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
1685873 ATATTTTTTT
*
1685883 ATTTCGAAA
1 ATTTCAAAA
1685892 ATTTCAAAA
1 ATTTCAAAA
1685901 CATTTCAAAAA
1 -ATTTC-AAAA
1685912 ATTTCAAAA
1 ATTTCAAAA
1685921 A
1 A
1685922 CTTCTTGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 13 0.48
10 10 0.37
11 4 0.15
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (9 bp):
ATTTCAAAA
Found at i:1694336 original size:23 final size:22
Alignment explanation
Indices: 1694293--1694336 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1694283 ACAACTCCTT
*
1694293 TTGGATAGGAAATATAATATCC
1 TTGGATAGGAAATACAATATCC
* *
1694315 TTGGTTAGGATAATACATTATC
1 TTGGATAGGA-AATACAATATC
1694337 AGAGGTTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
TTGGATAGGAAATACAATATCC
Found at i:1697600 original size:21 final size:21
Alignment explanation
Indices: 1697576--1697618 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1697566 TTCATATTCA
* *
1697576 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1697597 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1697618 T
1 T
1697619 AGCCCGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1704342 original size:19 final size:20
Alignment explanation
Indices: 1704305--1704342 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1704295 TTTTTTTATG
*
1704305 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1704325 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1704343 TCTAGCATTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1704392 original size:21 final size:21
Alignment explanation
Indices: 1704368--1704407 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1704358 ATTATATTCG
* *
1704368 TTGAGGGGGTATCGATTCCTC
1 TTGAAGGGGTACCGATTCCTC
*
1704389 TTGAATGGGTACCGATTCC
1 TTGAAGGGGTACCGATTCC
1704408 CCTAGTCCAG
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:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCTC
Found at i:1709227 original size:36 final size:36
Alignment explanation
Indices: 1709170--1709476 Score: 320
Period size: 36 Copynumber: 8.6 Consensus size: 36
1709160 TCAAATCTGA
* * *
1709170 TTACAACCTAAAA-ACGTGTTACAAGCTAAAAATAGG
1 TTACAACCTAAAATATG-GTTACAACCTAAAAATATG
* * *
1709206 TCACAACCTAAAATATGGTTACAACCTAAAAACATA
1 TTACAACCTAAAATATGGTTACAACCTAAAAATATG
* *
1709242 TTACAACCTAAAAACAT-ATTACAACCT-AAAATATGG
1 TTACAACCT-AAAATATGGTTACAACCTAAAAATAT-G
* * * *
1709278 TCACAACCGAAAAACAT-GTTACAACCT-AAAATACGG
1 TTACAACC-TAAAATATGGTTACAACCTAAAAATA-TG
* * *
1709314 TTACAACCTAAAATATGGTTATAATCT-AAAACATG
1 TTACAACCTAAAATATGGTTACAACCTAAAAATATG
* *
1709349 TTACAACCTAAAATATGGTCACAACCTAAAAACATG
1 TTACAACCTAAAATATGGTTACAACCTAAAAATATG
*
1709385 TTACAACCTAAAATATGGTTACAACCTAAAAATATC
1 TTACAACCTAAAATATGGTTACAACCTAAAAATATG
* * * * *
1709421 TCATAACCTAAAATATGGTTACAACTTAAAAACATA
1 TTACAACCTAAAATATGGTTACAACCTAAAAATATG
1709457 TTACAACCTAAAATATGGTT
1 TTACAACCTAAAATATGGTT
1709477 CTTAACACAA
Statistics
Matches: 229, Mismatches: 35, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
35 37 0.16
36 184 0.80
37 8 0.03
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (36 bp):
TTACAACCTAAAATATGGTTACAACCTAAAAATATG
Found at i:1709253 original size:54 final size:54
Alignment explanation
Indices: 1709170--1709469 Score: 358
Period size: 54 Copynumber: 5.6 Consensus size: 54
1709160 TCAAATCTGA
* *
1709170 TTACAACCTAAAAACGTGTTACAAGCTAAAAATAGGTCACAACCTAAAATATGG
1 TTACAACCTAAAAACATGTTACAACCTAAAAATAGGTCACAACCTAAAATATGG
* * ** *
1709224 TTACAACCTAAAAACATATTACAACCTAAAAACATATTACAACCTAAAATATGG
1 TTACAACCTAAAAACATGTTACAACCTAAAAATAGGTCACAACCTAAAATATGG
* * *
1709278 TCACAACCGAAAAACATGTTACAACCT-AAAATACGGTTACAACCTAAAATATGG
1 TTACAACCTAAAAACATGTTACAACCTAAAAATA-GGTCACAACCTAAAATATGG
* * *
1709332 TTATAATCT-AAAACATGTTACAACCT-AAAATATGGTCACAACCTAAAAACAT-G
1 TTACAACCTAAAAACATGTTACAACCTAAAAATA-GGTCACAACCT-AAAATATGG
* ** *
1709385 TTACAACCT-AAAATATGGTTACAACCTAAAAATATCTCATAACCTAAAATATGG
1 TTACAACCTAAAAACAT-GTTACAACCTAAAAATAGGTCACAACCTAAAATATGG
* *
1709439 TTACAACTTAAAAACATATTACAACCTAAAA
1 TTACAACCTAAAAACATGTTACAACCTAAAA
1709470 TATGGTTCTT
Statistics
Matches: 210, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
53 58 0.28
54 140 0.67
55 12 0.06
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (54 bp):
TTACAACCTAAAAACATGTTACAACCTAAAAATAGGTCACAACCTAAAATATGG
Found at i:1709450 original size:18 final size:18
Alignment explanation
Indices: 1709170--1709476 Score: 281
Period size: 18 Copynumber: 17.1 Consensus size: 18
1709160 TCAAATCTGA
*
1709170 TTACAACCTAAAA-ACGTG
1 TTACAACCTAAAATATG-G
*
1709188 TTACAAGCTAAAA-ATAGG
1 TTACAACCTAAAATAT-GG
*
1709206 TCACAACCTAAAATATGG
1 TTACAACCTAAAATATGG
* *
1709224 TTACAACCTAAAAACAT-A
1 TTACAACCT-AAAATATGG
* *
1709242 TTACAACCTAAAAACAT-A
1 TTACAACCT-AAAATATGG
1709260 TTACAACCTAAAATATGG
1 TTACAACCTAAAATATGG
* * *
1709278 TCACAACCGAAAAACAT-G
1 TTACAACC-TAAAATATGG
*
1709296 TTACAACCTAAAATACGG
1 TTACAACCTAAAATATGG
1709314 TTACAACCTAAAATATGG
1 TTACAACCTAAAATATGG
* * *
1709332 TTATAATCTAAAACAT-G
1 TTACAACCTAAAATATGG
1709349 TTACAACCTAAAATATGG
1 TTACAACCTAAAATATGG
* *
1709367 TCACAACCTAAAAACAT-G
1 TTACAACCT-AAAATATGG
1709385 TTACAACCTAAAATATGG
1 TTACAACCTAAAATATGG
*
1709403 TTACAACCTAAAAATAT-C
1 TTACAACCT-AAAATATGG
* *
1709421 TCATAACCTAAAATATGG
1 TTACAACCTAAAATATGG
* * *
1709439 TTACAACTTAAAAACAT-A
1 TTACAACCT-AAAATATGG
1709457 TTACAACCTAAAATATGG
1 TTACAACCTAAAATATGG
1709475 TT
1 TT
1709477 CTTAACACAA
Statistics
Matches: 237, Mismatches: 39, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
17 44 0.19
18 159 0.67
19 34 0.14
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (18 bp):
TTACAACCTAAAATATGG
Found at i:1712524 original size:24 final size:24
Alignment explanation
Indices: 1712497--1712596 Score: 76
Period size: 24 Copynumber: 4.2 Consensus size: 24
1712487 GATATCAAAA
*
1712497 ATCAAAACATAATTCAAATCAGAT
1 ATCAAAACAGAATTCAAATCAGAT
* * ** *
1712521 ATCATAACAGAATCCAGGTTATGA-
1 ATCAAAACAGAATTCAAATCA-GAT
* * *
1712545 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAAATCAGAT
* * *
1712569 GTCAAAATAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAAATCAGAT
1712593 ATCA
1 ATCA
1712597 GATAAAATAT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAAATCAGAT
Found at i:1713762 original size:18 final size:18
Alignment explanation
Indices: 1713739--1713774 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1713729 TTTCCATCAG
*
1713739 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1713757 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1713775 GTCATTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1715099 original size:15 final size:15
Alignment explanation
Indices: 1715069--1715124 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
1715059 GGTCAACACT
1715069 GGTCAATGCCGGTCAAC
1 GGTCAATG--GGTCAAC
1715086 GGTCAATGGGTCAAC
1 GGTCAATGGGTCAAC
* * *
1715101 AGTCAACGGGTC--G
1 GGTCAATGGGTCAAC
1715114 GGTCAATGGGT
1 GGTCAATGGGT
1715125 TGGGTCAACG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.26
15 17 0.50
17 8 0.24
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.20
Consensus pattern (15 bp):
GGTCAATGGGTCAAC
Found at i:1715124 original size:13 final size:13
Alignment explanation
Indices: 1715102--1715143 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1715092 TGGGTCAACA
1715102 GTCAACGGGTCGG
1 GTCAACGGGTCGG
* *
1715115 GTCAATGGGTTGG
1 GTCAACGGGTCGG
1715128 GTCAACGGGTCGG
1 GTCAACGGGTCGG
1715141 GTC
1 GTC
1715144 GGGTAAACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.14, C:0.19, G:0.45, T:0.21
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:1715145 original size:31 final size:31
Alignment explanation
Indices: 1715107--1715179 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
1715097 CAACAGTCAA
** *
1715107 CGGGTCGGGTCAATGGGTTGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGTTGGGTAAACGGGT
*
1715138 CGGGTCGGGTAAACAGGTTGGGTAAACGGGT
1 CGGGTCGGGTCAACAGGTTGGGTAAACGGGT
*
1715169 CGGGTTGGGTC
1 CGGGTCGGGTC
1715180 GGGTTATGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.15, C:0.15, G:0.48, T:0.22
Consensus pattern (31 bp):
CGGGTCGGGTCAACAGGTTGGGTAAACGGGT
Found at i:1715173 original size:13 final size:13
Alignment explanation
Indices: 1715138--1715173 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1715128 GTCAACGGGT
1715138 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
* *
1715151 CAGGTTGGGTAAA
1 CGGGTCGGGTAAA
1715164 CGGGTCGGGT
1 CGGGTCGGGT
1715174 TGGGTCGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1718509 original size:18 final size:18
Alignment explanation
Indices: 1718486--1718520 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1718476 TTCCATCCGG
*
1718486 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1718504 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1718521 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1719913 original size:13 final size:13
Alignment explanation
Indices: 1719895--1719928 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1719885 TCACGGGTCG
1719895 GGTCGGGTAAACA
1 GGTCGGGTAAACA
**
1719908 GGTCGGGTAAATG
1 GGTCGGGTAAACA
1719921 GGTCGGGT
1 GGTCGGGT
1719929 TGGGTCGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.47, T:0.21
Consensus pattern (13 bp):
GGTCGGGTAAACA
Found at i:1722080 original size:6 final size:6
Alignment explanation
Indices: 1722069--1722112 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
1722059 CGTTTTCAAG
* *
1722069 CTCTCC CTCTCC CTCTCT CTCTCT CTCTCTC C-CTCC CTCTCC CT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTC-C CTCTCC CTCTCC CT
1722113 AGCATCCGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 2 0.06
6 31 0.91
7 1 0.03
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
CTCTCC
Found at i:1722110 original size:10 final size:10
Alignment explanation
Indices: 1722071--1722112 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
1722061 TTTTCAAGCT
1722071 CTCCCTCTCC
1 CTCCCTCTCC
* *
1722081 CTCTCTCTCT
1 CTCCCTCTCC
*
1722091 CTCTCTCTCC
1 CTCCCTCTCC
1722101 CTCCCTCTCC
1 CTCCCTCTCC
1722111 CT
1 CT
1722113 AGCATCCGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (10 bp):
CTCCCTCTCC
Found at i:1727882 original size:32 final size:32
Alignment explanation
Indices: 1727846--1727907 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
1727836 CCCGAAGGAC
*
1727846 CTGTCCATATGT-CCAGAAGGACATAGGTAAAA
1 CTGTCCATATGTGCC-GAAGAACATAGGTAAAA
1727878 CTGTCCATATGTGCCGAAGAACATAGGTAA
1 CTGTCCATATGTGCCGAAGAACATAGGTAA
1727908 CCCTCGACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (32 bp):
CTGTCCATATGTGCCGAAGAACATAGGTAAAA
Found at i:1730080 original size:22 final size:23
Alignment explanation
Indices: 1730054--1730097 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1730044 GAGAAATATG
1730054 TGGCACTTAAGTGC-AACCTATA
1 TGGCACTTAAGTGCAAACCTATA
**
1730076 TGGCACTTCGGTGCAAACCTAT
1 TGGCACTTAAGTGCAAACCTAT
1730098 GTGGTCATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (23 bp):
TGGCACTTAAGTGCAAACCTATA
Found at i:1732238 original size:449 final size:441
Alignment explanation
Indices: 1731357--1732367 Score: 1188
Period size: 449 Copynumber: 2.3 Consensus size: 441
1731347 AGGGCGTTAT
* *
1731357 ATATTCACT-AAAAAACAA-GTAGTTAATCTCAACCTTTGATTTTCCAT-AATCCAACGATCATT
1 ATATTCACTGAAAAAA-AACG-AGTTAATCTCAACCTTTGA-TTTCCCTCAATCCAACGATCCTT
* *
1731419 AAAAGGTGT--AATACGAAAAGAGTTTTACACAATGTAAGTGGATCCTAACCCATATAGAGGTAG
63 AAAAGGTGTAAAATA-GAAAA-AATTTTACACAATGTAAGTGGATCCTAACCCATATAGAGGAAG
* * * *
1731482 GTTCCAATTACACTGTGCTCTTTTAGTTTTACATCTTTTTAGGATCATTGGATGAGAGAAATTAA
126 GATCCAATTACACTGTGCTCTTTTAGTTTTACACCTTTCTAGGACCATTGGATGAGAGAAATTAA
* * * * * * * *
1731547 AGGCTGATATTAATAGTAAAAATTATAAGATATTCGCTAAAAAAACAAGGAGTTAATCTCAGTCT
191 AGGCTGAGATTAACAGCAAAAATGAAAAGATATTCACTAAAAAAACAAGGAATTAATCTCAGCCT
*
1731612 TTGATTTCCCTCAATCCAACAATCGTAAAAAGGTGTAAAATCAAAAGAGTTTTACAAAGTGTAAG
256 TTGATTTCCCTCAATCCAACAATCCTAAAAAGGTGTAAAATCAAAAGAGTTTT--AAAG-GT-AG
* *
1731677 TGAATCATAACCCATATAGGGGTAGGATCCAATTACACTATGTAAAAGTCTTTTAGTTTTACACA
317 TGAATCATAACCCATATAGGGGCAGGATCCAATTACACTATGTAAAACTCTTTTAGTTTTACACA
* * *
1731742 TTTTTAGGACCATCGGATGAGAGAAATCAAAGACCGATATCAATAGTAGAAAATGAATAAG
382 TTTTTAGGACCATCGGATGAGAGAAATCAAAGACCAAGATCAATAGTAGAAAATG-AGAAG
** * *
1731803 ATATTCACTGAAAAAATAACGAGTTAATCTCGGCCTTTGATGTCCCTCAATCCAACGATCCTTGA
1 ATATTCACTGAAAAAA-AACGAGTTAATCTCAACCTTTGATTTCCCTCAATCCAACGATCCTTAA
* *
1731868 AAGGTGTAAAACTAGGAAAAAATTTTACACAATGTAAGTAGATCCTAACCCATTTAG-GAGAAGG
65 AAGGTGTAAAA-TA-GAAAAAATTTTACACAATGTAAGTGGATCCTAACCCATATAGAG-GAAGG
* * * *
1731932 ATCCAATTACATTGTGTAAAATTTTTTCCTAGTTTTACACCTTTCTAGGACCATTGGATGATAGA
127 ATCCAATTACACTGTG-----CTCTTT--TAGTTTTACACCTTTCTAGGACCATTGGATGAGAGA
*
1731997 AATTAAAGGCTGAGATTAACAGCAGAAAATGAAAAGATATTCACTAGAAAAAAATAAGGAATTAA
185 AATTAAAGGCTGAGATTAACAGCA-AAAATGAAAAGATATTCACT--AAAAAAACAAGGAATTAA
* * * *
1732062 TTTCAGCCTTTGATTTCCCTCAATCCAACGATCCTAAAAAGGTGTGAAAT-TAAAGAGTTTT-AA
247 TCTCAGCCTTTGATTTCCCTCAATCCAACAATCCTAAAAAGGTGTAAAATCAAAAGAGTTTTAAA
* * * * * *
1732125 -GT-G-G-ATCCTTACCCATATTGGGGCAGGATCCAATTACGCTGTGTAAAACTTTTTTAGTTTT
312 GGTAGTGAATCATAACCCATATAGGGGCAGGATCCAATTACACTATGTAAAACTCTTTTAGTTTT
* * * * * * *
1732186 ACACCTTTTTAGGACTATTGGATGAGTGAAATTAAAGACTAAGATTAATAGTAGAAAATGAGAAG
377 ACACATTTTTAGGACCATCGGATGAGAGAAATCAAAGACCAAGATCAATAGTAGAAAATGAGAAG
* * *
1732251 ATACTCACTG-GAAAAAACAGAGTTAATCTCAACCTTTGATTTCCCTCAATCCAACGATCCTAAA
1 ATATTCACTGAAAAAAAAC-GAGTTAATCTCAACCTTTGATTTCCCTCAATCCAACGATCCTTAA
* *
1732315 AAGATGTAAAATTA-AAAAAA-TTTACACAATGTAAGTGGATCCTAACCCCTATA
65 AAGGTGTAAAA-TAGAAAAAATTTTACACAATGTAAGTGGATCCTAACCCATATA
1732368 TATATATCAT
Statistics
Matches: 483, Mismatches: 64, Indels: 38
0.83 0.11 0.06
Matches are distributed among these distances:
444 30 0.06
445 6 0.01
446 17 0.04
447 103 0.21
448 15 0.03
449 154 0.32
450 8 0.02
451 1 0.00
453 2 0.00
454 4 0.01
455 2 0.00
456 53 0.11
457 17 0.04
458 10 0.02
459 61 0.13
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (441 bp):
ATATTCACTGAAAAAAAACGAGTTAATCTCAACCTTTGATTTCCCTCAATCCAACGATCCTTAAA
AGGTGTAAAATAGAAAAAATTTTACACAATGTAAGTGGATCCTAACCCATATAGAGGAAGGATCC
AATTACACTGTGCTCTTTTAGTTTTACACCTTTCTAGGACCATTGGATGAGAGAAATTAAAGGCT
GAGATTAACAGCAAAAATGAAAAGATATTCACTAAAAAAACAAGGAATTAATCTCAGCCTTTGAT
TTCCCTCAATCCAACAATCCTAAAAAGGTGTAAAATCAAAAGAGTTTTAAAGGTAGTGAATCATA
ACCCATATAGGGGCAGGATCCAATTACACTATGTAAAACTCTTTTAGTTTTACACATTTTTAGGA
CCATCGGATGAGAGAAATCAAAGACCAAGATCAATAGTAGAAAATGAGAAG
Found at i:1740339 original size:22 final size:22
Alignment explanation
Indices: 1740308--1740379 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
1740298 CTGAGTGGCA
1740308 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
1740331 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
1740353 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
1740374 TATGAA
1 TATGAA
1740380 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:1740364 original size:21 final size:21
Alignment explanation
Indices: 1740316--1740378 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1740306 CATATGAAAT
* *
1740316 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
1740338 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
1740359 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
1740379 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:1746652 original size:21 final size:21
Alignment explanation
Indices: 1746623--1746665 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1746613 TTACAAATAG
*
1746623 GGAATCGATTCCCCTGCTACA
1 GGAACCGATTCCCCTGCTACA
1746644 GGAACCGATTCCCCTGCTACA
1 GGAACCGATTCCCCTGCTACA
1746665 G
1 G
1746666 TACTTCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (21 bp):
GGAACCGATTCCCCTGCTACA
Found at i:1747201 original size:22 final size:22
Alignment explanation
Indices: 1747170--1747241 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
1747160 CTGAGTGGCA
1747170 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
1747193 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
* *
1747215 TATG-AGTTGTCCTGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
1747236 TATGAA
1 TATGAA
1747242 ACCCTCGACT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 19 0.43
22 22 0.50
23 3 0.07
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:1747226 original size:21 final size:21
Alignment explanation
Indices: 1747178--1747240 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1747168 CATATGAAAT
* *
1747178 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
1747200 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
*
1747221 TTGTCCTGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
1747241 AACCCTCGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:1750838 original size:26 final size:26
Alignment explanation
Indices: 1750809--1750864 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
1750799 AAGTAGATAA
* *
1750809 ATCGAAAAGCGAGTTGCTGCGTCTGC
1 ATCGAAAAGCGAATCGCTGCGTCTGC
* *
1750835 ATCGGAAAGCGAATCGCTGCGTTTGC
1 ATCGAAAAGCGAATCGCTGCGTCTGC
1750861 ATCG
1 ATCG
1750865 CTGCACGGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (26 bp):
ATCGAAAAGCGAATCGCTGCGTCTGC
Found at i:1756149 original size:17 final size:18
Alignment explanation
Indices: 1756123--1756161 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1756113 TATTCCAAAC
*
1756123 AAAAATTTGACT-TTAAA
1 AAAAACTTGACTCTTAAA
1756140 AAAAACTTGACTCTTAAA
1 AAAAACTTGACTCTTAAA
1756158 AAAA
1 AAAA
1756162 TATAATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAACTTGACTCTTAAA
Found at i:1756942 original size:21 final size:23
Alignment explanation
Indices: 1756918--1756959 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1756908 CTTAAATTTA
1756918 AAATCA-TGATTTT-ATTTTTCC
1 AAATCATTGATTTTGATTTTTCC
1756939 AAATCATTGATTTTGATTTTT
1 AAATCATTGATTTTGATTTTT
1756960 GAAAGCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.55
Consensus pattern (23 bp):
AAATCATTGATTTTGATTTTTCC
Found at i:1757021 original size:19 final size:20
Alignment explanation
Indices: 1756976--1757023 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1756966 TCAAAATCAT
**
1756976 TTTTCAAAATTTAATTTTGC
1 TTTTCAAAATCCAATTTTGC
1756996 TTTTCAAAATCCAATTTTGC
1 TTTTCAAAATCCAATTTTGC
1757016 -TTTCAAAA
1 TTTTCAAAA
1757024 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATCCAATTTTGC
Found at i:1758229 original size:21 final size:22
Alignment explanation
Indices: 1758203--1758243 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1758193 TCAGGACATG
1758203 GAGTATCGGTAC-TCCTTTAAT
1 GAGTATCGGTACTTCCTTTAAT
*
1758224 GAGTATTGGTACTTCCTTTA
1 GAGTATCGGTACTTCCTTTA
1758244 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (22 bp):
GAGTATCGGTACTTCCTTTAAT
Found at i:1761164 original size:16 final size:16
Alignment explanation
Indices: 1761143--1761176 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1761133 AATATGGTTT
* *
1761143 TTTCTTTCTTCCTTCA
1 TTTCTTTCATCATTCA
1761159 TTTCTTTCATCATTCA
1 TTTCTTTCATCATTCA
1761175 TT
1 TT
1761177 CTCCTTTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTCTTTCATCATTCA
Found at i:1764532 original size:19 final size:19
Alignment explanation
Indices: 1764497--1764534 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1764487 TCCTTATTAT
*
1764497 TCTTTTTTTTTTCTCTTCA
1 TCTTTTTTTCTTCTCTTCA
1764516 TCTTTTTCTTCTT-TCTTCA
1 TCTTTTT-TTCTTCTCTTCA
1764535 CATATCTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (19 bp):
TCTTTTTTTCTTCTCTTCA
Found at i:1769803 original size:27 final size:27
Alignment explanation
Indices: 1769772--1769837 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
1769762 GATAATGGCT
1769772 CTGAATCATTCAGAATGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
1769799 CTGAATCATTCAGAATGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
1769826 CTGAATCATTCA
1 CTGAATCATTCA
1769838 TCACTGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTATG
Found at i:1771033 original size:18 final size:18
Alignment explanation
Indices: 1771002--1771037 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1770992 CATATGAATT
*
1771002 TGTCCAGAAGGACCACTA
1 TGTCCAGAAAGACCACTA
*
1771020 TGTCCCGAAAGACCACTA
1 TGTCCAGAAAGACCACTA
1771038 AAAATCCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (18 bp):
TGTCCAGAAAGACCACTA
Found at i:1771422 original size:13 final size:15
Alignment explanation
Indices: 1771390--1771426 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
1771380 TTATATCATA
1771390 TTATCATGTGTACAT
1 TTATCATGTGTACAT
*
1771405 ATATCATG-G-ACAT
1 TTATCATGTGTACAT
1771418 TTATCATGT
1 TTATCATGT
1771427 ATCATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 11 0.58
14 1 0.05
15 7 0.37
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (15 bp):
TTATCATGTGTACAT
Found at i:1775511 original size:13 final size:15
Alignment explanation
Indices: 1775479--1775515 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
1775469 TTATATCATA
1775479 TTATCATGTGTACAT
1 TTATCATGTGTACAT
*
1775494 ATATCATG-G-ACAT
1 TTATCATGTGTACAT
1775507 TTATCATGT
1 TTATCATGT
1775516 ATCATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 11 0.58
14 1 0.05
15 7 0.37
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (15 bp):
TTATCATGTGTACAT
Found at i:1778653 original size:21 final size:21
Alignment explanation
Indices: 1778628--1778667 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1778618 AAGACTCTAT
1778628 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
1778649 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
1778668 AAATAGTCTT
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:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:1782520 original size:23 final size:22
Alignment explanation
Indices: 1782478--1782561 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 22
1782468 ATAGGGCAGA
1782478 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
*
1782500 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
* * * * *
1782523 GAGAACCGATTCCTCCAT-ATAG
1 GGGAATCGATACCCCCTTGA-AG
1782545 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
1782562 GGAGGTTCTG
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 1 0.02
22 30 0.60
23 19 0.38
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:1784177 original size:18 final size:18
Alignment explanation
Indices: 1784139--1784179 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1784129 AGAACAACAC
* **
1784139 GAGGAACAAGCACGAGTA
1 GAGGAACAAGCACAACCA
1784157 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
1784175 GAGGA
1 GAGGA
1784180 TCAAATGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.20, G:0.32, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:1792932 original size:51 final size:47
Alignment explanation
Indices: 1792828--1792948 Score: 120
Period size: 51 Copynumber: 2.5 Consensus size: 47
1792818 GTAACCATGC
*
1792828 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAAATA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTG---AAAATA
* * **
1792878 ATAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTA-A
1 A-AATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAATA
1792927 AAATAAGCTTATGAGCTTATGG
1 AAATAAGCTTATGAGCTTATGG
1792949 GATGAAAGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
48 21 0.34
49 2 0.03
50 2 0.03
51 22 0.35
53 1 0.02
54 14 0.23
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAATA
Found at i:1794712 original size:3 final size:3
Alignment explanation
Indices: 1794699--1794765 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
1794689 CTGCAAAAAG
* * * *
1794699 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA CAA CAG TAG TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1794745 TAA TAA TAA TCA T-A TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
1794766 CTAATATTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1796340 original size:30 final size:30
Alignment explanation
Indices: 1796306--1796374 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
1796296 AAAGTGAGAT
*
1796306 GACATCAAAATCATTAAGAAGACAACAAAG
1 GACATCAAAATCATTAACAAGACAACAAAG
* *
1796336 GACATCAAAATCATTAACATGGCAACAAAG
1 GACATCAAAATCATTAACAAGACAACAAAG
1796366 GACATCAAA
1 GACATCAAA
1796375 GAACAACGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.54, C:0.19, G:0.13, T:0.14
Consensus pattern (30 bp):
GACATCAAAATCATTAACAAGACAACAAAG
Found at i:1798437 original size:67 final size:64
Alignment explanation
Indices: 1798306--1798438 Score: 151
Period size: 67 Copynumber: 2.0 Consensus size: 64
1798296 ACACAACATG
* * * * * *
1798306 AAAAATAACTAAAACATGAGATGCGAACACAGCTTATGCAGATATGCCTCAAAACATATCTCAT
1 AAAAATAACTAAAACATGAGATGCGAACACAACTCATACAGAAATGCATCAAAACATATATCAT
* *
1798370 AAAAATAACTAAAGCACGATGAGATGCGTACACAACTCATACATAAATGCATCAAAA-ACTATAT
1 AAAAATAACTAAA--AC-ATGAGATGCGAACACAACTCATACAGAAATGCATCAAAACA-TATAT
1798434 CAT
62 CAT
1798437 AA
1 AA
1798439 GAATCATTAG
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
64 13 0.23
66 3 0.05
67 41 0.72
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (64 bp):
AAAAATAACTAAAACATGAGATGCGAACACAACTCATACAGAAATGCATCAAAACATATATCAT
Found at i:1806800 original size:34 final size:34
Alignment explanation
Indices: 1806762--1806874 Score: 147
Period size: 34 Copynumber: 3.3 Consensus size: 34
1806752 TTAATATGTG
1806762 TCTGATAACTGTAAAACATTTGATATCTG-AAATA
1 TCTGATAACTGT-AAACATTTGATATCTGTAAATA
* *
1806796 TCTGATAACTGTAATCATTGGATATCTGTAAATA
1 TCTGATAACTGTAAACATTTGATATCTGTAAATA
* * * *
1806830 TCTGATAAATATAATCATCTGATATCTGTAAATA
1 TCTGATAACTGTAAACATTTGATATCTGTAAATA
*
1806864 TCAGATAACTG
1 TCTGATAACTG
1806875 AAAATCATCT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 14 0.20
34 55 0.80
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (34 bp):
TCTGATAACTGTAAACATTTGATATCTGTAAATA
Found at i:1806870 original size:17 final size:17
Alignment explanation
Indices: 1806762--1806884 Score: 83
Period size: 17 Copynumber: 7.2 Consensus size: 17
1806752 TTAATATGTG
* *
1806762 TCTGATAACTGTAAAACA
1 TCTGATATCTGT-AAATA
*
1806780 TTTGATATCTG-AAATA
1 TCTGATATCTGTAAATA
*
1806796 TCTGATAACTGT-AATCA
1 TCTGATATCTGTAAAT-A
1806813 T-TGGATATCTGTAAATA
1 TCT-GATATCTGTAAATA
** *
1806830 TCTGATAAATAT-AATCA
1 TCTGATATCTGTAAAT-A
1806847 TCTGATATCTGTAAATA
1 TCTGATATCTGTAAATA
* * *
1806864 TCAGATAACTGAAAATCA
1 TCTGATATCTGTAAAT-A
1806882 TCT
1 TCT
1806885 AATAATTGTT
Statistics
Matches: 81, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
16 20 0.25
17 42 0.52
18 19 0.23
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (17 bp):
TCTGATATCTGTAAATA
Found at i:1812762 original size:22 final size:22
Alignment explanation
Indices: 1812737--1812810 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
1812727 GTGATAAGGA
1812737 ACTTTAGTATCAGTGCTAATGC
1 ACTTTAGTATCAGTGCTAATGC
* * *
1812759 ACTTCCA-TATTAGTGCT-TTGGC
1 ACTT-TAGTATCAGTGCTAAT-GC
*
1812781 ACTTTAGTA-CTAGTGCTAAGGC
1 ACTTTAGTATC-AGTGCTAATGC
1812803 ACTTTAGT
1 ACTTTAGT
1812811 TAATCAATGG
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
21 2 0.05
22 37 0.93
23 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (22 bp):
ACTTTAGTATCAGTGCTAATGC
Found at i:1813267 original size:16 final size:16
Alignment explanation
Indices: 1813246--1813278 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1813236 AATAAGATAT
*
1813246 AATAAATGTCTATGTG
1 AATAAATGTCTACGTG
1813262 AATAAATGTCTACGTG
1 AATAAATGTCTACGTG
1813278 A
1 A
1813279 TAAGCTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (16 bp):
AATAAATGTCTACGTG
Found at i:1813422 original size:46 final size:42
Alignment explanation
Indices: 1813366--1813460 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 42
1813356 GACTCGAGGG
* *
1813366 TTCTAGGCGGTCCTTCGGGATAATTCTACGTGGTCCTTCGGGACA
1 TTCTATGCGGTCCTTCGGGA-AA-TCTACGT-GTCATTCGGGACA
* *
1813411 TTTCTATGCGGTCCTTCGGGACATCTATGTGTCATTCGGGACA
1 -TTCTATGCGGTCCTTCGGGAAATCTACGTGTCATTCGGGACA
1813454 TTCTATG
1 TTCTATG
1813461 TGGAACTTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
42 7 0.16
43 12 0.27
44 6 0.13
45 1 0.02
46 19 0.42
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (42 bp):
TTCTATGCGGTCCTTCGGGAAATCTACGTGTCATTCGGGACA
Found at i:1813434 original size:23 final size:22
Alignment explanation
Indices: 1813366--1813460 Score: 104
Period size: 23 Copynumber: 4.3 Consensus size: 22
1813356 GACTCGAGGG
* *
1813366 TTCTAGGCGGTCCTTCGGGATAA
1 TTCTATGCGGTCCTTCGGGA-CA
* *
1813389 TTCTACGTGGTCCTTCGGGACA
1 TTCTATGCGGTCCTTCGGGACA
1813411 TTTCTATGCGGTCCTTCGGGACA
1 -TTCTATGCGGTCCTTCGGGACA
* *
1813434 -TCTATG-TGTCATTCGGGACA
1 TTCTATGCGGTCCTTCGGGACA
1813454 TTCTATG
1 TTCTATG
1813461 TGGAACTTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
20 12 0.19
21 12 0.19
22 1 0.02
23 38 0.60
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (22 bp):
TTCTATGCGGTCCTTCGGGACA
Found at i:1815551 original size:64 final size:64
Alignment explanation
Indices: 1815481--1815623 Score: 184
Period size: 64 Copynumber: 2.2 Consensus size: 64
1815471 GAATGTCATC
* *
1815481 AGTGCATCGATGCACCCCCTTAA-AATATAAACATCGAATGCCA-TCAGTGCATCGATGCATAAG
1 AGTGCATCGATGCACCCCCTTAAGAAGA-AAACATCGAATGCAATTC-GTGCATCGATGCA-AAG
1815544 G-
63 GT
* * * *
1815545 AGTGCATCGATGCACCCCCTTAAGAAGAAAACATCGAATGTAATTCTTGTATCGATGCACAGGT
1 AGTGCATCGATGCACCCCCTTAAGAAGAAAACATCGAATGCAATTCGTGCATCGATGCAAAGGT
1815609 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
1815624 ACGTTAAAGG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
63 3 0.04
64 62 0.89
65 5 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (64 bp):
AGTGCATCGATGCACCCCCTTAAGAAGAAAACATCGAATGCAATTCGTGCATCGATGCAAAGGT
Found at i:1816401 original size:18 final size:18
Alignment explanation
Indices: 1816376--1816470 Score: 73
Period size: 18 Copynumber: 5.1 Consensus size: 18
1816366 CGAGGGATAA
1816376 ACAGTGGTCCTTCGGGAC
1 ACAGTGGTCCTTCGGGAC
* * * *
1816394 ATAGTGGTTCTTCAGAAC
1 ACAGTGGTCCTTCGGGAC
*
1816412 AAACAATGGTCCTTCGGGAC
1 --ACAGTGGTCCTTCGGGAC
* * * *
1816432 ATAATGGTTCTTCGGAAC
1 ACAGTGGTCCTTCGGGAC
1816450 AAACAGTGGTCCTTCGGGAC
1 --ACAGTGGTCCTTCGGGAC
1816470 A
1 A
1816471 AATATTCAGT
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
18 30 0.53
20 27 0.47
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (18 bp):
ACAGTGGTCCTTCGGGAC
Found at i:1816425 original size:38 final size:38
Alignment explanation
Indices: 1816374--1816470 Score: 167
Period size: 38 Copynumber: 2.6 Consensus size: 38
1816364 GTCGAGGGAT
*
1816374 AAACAGTGGTCCTTCGGGACATAGTGGTTCTTCAGAAC
1 AAACAGTGGTCCTTCGGGACATAATGGTTCTTCAGAAC
* *
1816412 AAACAATGGTCCTTCGGGACATAATGGTTCTTCGGAAC
1 AAACAGTGGTCCTTCGGGACATAATGGTTCTTCAGAAC
1816450 AAACAGTGGTCCTTCGGGACA
1 AAACAGTGGTCCTTCGGGACA
1816471 AATATTCAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.25
Consensus pattern (38 bp):
AAACAGTGGTCCTTCGGGACATAATGGTTCTTCAGAAC
Found at i:1816426 original size:20 final size:20
Alignment explanation
Indices: 1816398--1816472 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 20
1816388 CGGGACATAG
* *
1816398 TGGTTCTTCAGAACAAACAA
1 TGGTCCTTCGGAACAAACAA
* *
1816418 TGGTCCTTCGGGAC--ATAA
1 TGGTCCTTCGGAACAAACAA
* *
1816436 TGGTTCTTCGGAACAAACAG
1 TGGTCCTTCGGAACAAACAA
*
1816456 TGGTCCTTCGGGACAAA
1 TGGTCCTTCGGAACAAA
1816473 TATTCAGTGC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 15 0.35
20 28 0.65
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (20 bp):
TGGTCCTTCGGAACAAACAA
Found at i:1818737 original size:25 final size:24
Alignment explanation
Indices: 1818686--1818738 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
1818676 ATACAAAAAC
* * *
1818686 AAAACGGGGAATTAATCTCATGCA
1 AAAAAGGGGAATTAATCCCATACA
*
1818710 AAAAAGGGGAAATTAATCCCATATA
1 AAAAAGGGG-AATTAATCCCATACA
1818735 AAAA
1 AAAA
1818739 TGGAAGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.19
Consensus pattern (24 bp):
AAAAAGGGGAATTAATCCCATACA
Found at i:1822126 original size:22 final size:21
Alignment explanation
Indices: 1822082--1822126 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1822072 TTAAAAATAT
*
1822082 AATTAATATAATTAAAGTTTA
1 AATTAATATAATTAAAGTATA
1822103 AATTCAATAT-ATTAAAGTCATA
1 AATT-AATATAATTAAAGT-ATA
1822125 AA
1 AA
1822127 AATAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (21 bp):
AATTAATATAATTAAAGTATA
Found at i:1823562 original size:19 final size:19
Alignment explanation
Indices: 1823530--1823579 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1823520 GACCAGTTCG
** *
1823530 GGTTGACTTAGTTCAGTTT
1 GGTTGACTCGGTTCAGTCT
*
1823549 GGTTGACTCGGTTCTGTCT
1 GGTTGACTCGGTTCAGTCT
1823568 GAGTTGACTCGG
1 G-GTTGACTCGG
1823580 ATCGGTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.12, C:0.16, G:0.32, T:0.40
Consensus pattern (19 bp):
GGTTGACTCGGTTCAGTCT
Found at i:1831500 original size:29 final size:29
Alignment explanation
Indices: 1831468--1831536 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
1831458 TAGAACAAGG
* **
1831468 AATTAATCCCATACAGAGTTAGAATGGAA
1 AATTAATCCCATACAAAAATAGAATGGAA
* **
1831497 AATTAATCCCATGCAAAAATAGAATGGGG
1 AATTAATCCCATACAAAAATAGAATGGAA
1831526 AATTAATCCCA
1 AATTAATCCCA
1831537 CGCAGATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (29 bp):
AATTAATCCCATACAAAAATAGAATGGAA
Found at i:1831999 original size:7 final size:7
Alignment explanation
Indices: 1831976--1832033 Score: 93
Period size: 7 Copynumber: 8.4 Consensus size: 7
1831966 CGAGGGAAAA
1831976 AAAGAAGG
1 AAAG-AGG
1831984 AAA-AGG
1 AAAGAGG
1831990 AAAGAGG
1 AAAGAGG
1831997 AAAGAGG
1 AAAGAGG
1832004 AAAGAGG
1 AAAGAGG
1832011 AAAGAGG
1 AAAGAGG
1832018 -AAGAGG
1 AAAGAGG
1832024 AAAGAGG
1 AAAGAGG
1832031 AAA
1 AAA
1832034 AAGTTCTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.25
7 33 0.69
8 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (7 bp):
AAAGAGG
Found at i:1832006 original size:20 final size:20
Alignment explanation
Indices: 1831980--1832033 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1831970 GGAAAAAAAG
1831980 AAGGAAA-AGGAAAGAGGAA
1 AAGGAAAGAGGAAAGAGGAA
1831999 AGAGGAAAGAGGAAAGAGGAA
1 A-AGGAAAGAGGAAAGAGGAA
*
1832020 GAGGAAAGAGGAAA
1 AAGGAAAGAGGAAA
1832034 AAGTTCTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 19 0.59
21 12 0.38
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (20 bp):
AAGGAAAGAGGAAAGAGGAA
Found at i:1832012 original size:27 final size:28
Alignment explanation
Indices: 1831976--1832033 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
1831966 CGAGGGAAAA
1831976 AAAGAAGGAAA-AGGAAAGAGGAAAGAGG
1 AAAGAAGGAAAGAGG-AAGAGGAAAGAGG
1832004 AAAG-AGGAAAGAGGAAGAGGAAAGAGG
1 AAAGAAGGAAAGAGGAAGAGGAAAGAGG
1832031 AAA
1 AAA
1832034 AAGTTCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (28 bp):
AAAGAAGGAAAGAGGAAGAGGAAAGAGG
Found at i:1840943 original size:3 final size:3
Alignment explanation
Indices: 1840935--1840969 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1840925 ATGCTGCAAG
1840935 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1840970 GTAGTAGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1840974 original size:3 final size:3
Alignment explanation
Indices: 1840968--1841009 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1840958 TTATTATTAT
1840968 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1841010 CAGCATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:1841510 original size:20 final size:20
Alignment explanation
Indices: 1841485--1841531 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1841475 TCATGGTGTT
*
1841485 AGCATCAATATTGGAAGGTG
1 AGCATCAATACTGGAAGGTG
*
1841505 AGCATCAATACTGGATGGTG
1 AGCATCAATACTGGAAGGTG
*
1841525 AGTATCA
1 AGCATCA
1841532 CGATTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (20 bp):
AGCATCAATACTGGAAGGTG
Found at i:1847887 original size:44 final size:45
Alignment explanation
Indices: 1847823--1847919 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 45
1847813 ATTTATTTTC
1847823 ATTTTTCGAACAAGCATGCGAACTAGATATCATGCGGTTAGG-TTT
1 ATTTTT-GAACAAGCATGCGAACTAGATATCATGCGGTTAGGATTT
* *
1847868 ATTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTAGGATTT
1 ATTTTTGAACAAGCATGCGAACTAGATATCATGCGGTTAGGATTT
*
1847913 CTTTTTG
1 ATTTTTG
1847920 TGGATAACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
44 33 0.69
45 15 0.31
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (45 bp):
ATTTTTGAACAAGCATGCGAACTAGATATCATGCGGTTAGGATTT
Found at i:1857577 original size:11 final size:11
Alignment explanation
Indices: 1857558--1857660 Score: 52
Period size: 12 Copynumber: 9.2 Consensus size: 11
1857548 TATTTCGCTT
1857558 AAAGAAGAAATA
1 AAAGAAGAAA-A
1857570 AAAG-AGAAAA
1 AAAGAAGAAAA
*
1857580 AAA-ACGAAAA
1 AAAGAAGAAAA
*
1857590 AATGAA-AAAA
1 AAAGAAGAAAA
* *
1857600 ATAATAATAAAA
1 A-AAGAAGAAAA
* *
1857612 ATGAGAAAAAGAA
1 A-AAGAAGAA-AA
1857625 AAAGAAGAAAA
1 AAAGAAGAAAA
*
1857636 GAAGAAAAGAAAA
1 -AA-AGAAGAAAA
*
1857649 AATG-AGAAAA
1 AAAGAAGAAAA
1857659 AA
1 AA
1857661 TAAAAATGAG
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
10 24 0.34
11 11 0.15
12 25 0.35
13 11 0.15
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.07
Consensus pattern (11 bp):
AAAGAAGAAAA
Found at i:1857599 original size:16 final size:16
Alignment explanation
Indices: 1857578--1857722 Score: 98
Period size: 16 Copynumber: 9.4 Consensus size: 16
1857568 TAAAAGAGAA
1857578 AAAAAACGA-AAAAATG
1 AAAAAA-GATAAAAATG
*
1857594 AAAAAA-ATAATAAT-
1 AAAAAAGATAAAAATG
* *
1857608 AAAAATGAGAAAAA-G
1 AAAAAAGATAAAAATG
1857623 -AAAAAGA-AGAAAA-G
1 AAAAAAGATA-AAAATG
1857637 AAGAAAAGA-AAAAATG
1 AA-AAAAGATAAAAATG
1857653 AGAAAAA-ATAAAAATG
1 A-AAAAAGATAAAAATG
1857669 AGAAAAA-ATAAAAATG
1 A-AAAAAGATAAAAATG
*
1857685 AAAAAAGA-AAGAAA-A
1 AAAAAAGATAA-AAATG
*
1857700 ATAAAAAGAGAAAAATG
1 A-AAAAAGATAAAAATG
1857717 AAAAAA
1 AAAAAA
1857723 AGAGAAATAA
Statistics
Matches: 108, Mismatches: 7, Indels: 28
0.76 0.05 0.20
Matches are distributed among these distances:
13 1 0.01
14 17 0.16
15 24 0.22
16 62 0.57
17 4 0.04
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (16 bp):
AAAAAAGATAAAAATG
Found at i:1857721 original size:8 final size:7
Alignment explanation
Indices: 1857578--1857722 Score: 78
Period size: 8 Copynumber: 18.9 Consensus size: 7
1857568 TAAAAGAGAA
1857578 AAAAAACG
1 AAAAAA-G
1857586 AAAAAATG
1 AAAAAA-G
1857594 AAAAAA-
1 AAAAAAG
* *
1857600 ATAATAAT
1 A-AAAAAG
*
1857608 AAAAATG
1 AAAAAAG
1857615 AGAAAAAG
1 A-AAAAAG
1857623 -AAAAAG
1 AAAAAAG
1857629 AAGAAAAG
1 AA-AAAAG
1857637 AAGAAAAG
1 AA-AAAAG
1857645 AAAAAATGAG
1 -AAAAA--AG
*
1857655 AAAAAAT
1 AAAAAAG
1857662 AAAAATGAG
1 AAAAA--AG
*
1857671 AAAAAAT
1 AAAAAAG
*
1857678 AAAAATG
1 AAAAAAG
1857685 AAAAAAG
1 AAAAAAG
*
1857692 AAAGAAAA
1 AAA-AAAG
1857700 ATAAAAAG
1 A-AAAAAG
1857708 AGAAAAATG
1 A-AAAAA-G
1857717 AAAAAA
1 AAAAAA
1857723 AGAGAAATAA
Statistics
Matches: 109, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
6 7 0.06
7 30 0.28
8 53 0.49
9 17 0.16
10 2 0.02
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (7 bp):
AAAAAAG
Found at i:1857721 original size:39 final size:40
Alignment explanation
Indices: 1857608--1857722 Score: 118
Period size: 40 Copynumber: 3.0 Consensus size: 40
1857598 AAATAATAAT
*
1857608 AAAAATG--AGAAAAAGAAAAAGA-AGAAAA-GAAGAAAAGA
1 AAAAATGAAAGAAAAATAAAAAGAGA-AAAATGAA-AAAAGA
* *
1857646 AAAAATGAGA-AAAAATAAAAATGAGAAAAAAT-AAAAATGA
1 AAAAATGAAAGAAAAATAAAAA-GAG-AAAAATGAAAAAAGA
1857686 AAAAA-GAAAGAAAAATAAAAAGAGAAAAATGAAAAAA
1 AAAAATGAAAGAAAAATAAAAAGAGAAAAATGAAAAAA
1857723 AGAGAAATAA
Statistics
Matches: 65, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
38 13 0.20
39 21 0.32
40 24 0.37
41 6 0.09
42 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (40 bp):
AAAAATGAAAGAAAAATAAAAAGAGAAAAATGAAAAAAGA
Found at i:1859096 original size:36 final size:37
Alignment explanation
Indices: 1859007--1859116 Score: 159
Period size: 36 Copynumber: 3.0 Consensus size: 37
1858997 TCAAAACAGG
* * * * *
1859007 TCAATCTTAAGCTTTCATGAAAGAGCAGTGAAGCAAT
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
*
1859044 TCAAACTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1859081 TC-ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1859117 CTCGTTTGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
36 33 0.50
37 33 0.50
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
Found at i:1859179 original size:51 final size:51
Alignment explanation
Indices: 1859124--1859479 Score: 541
Period size: 51 Copynumber: 6.9 Consensus size: 51
1859114 AAACTCGTTT
*
1859124 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1859175 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1859226 ATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1859277 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
1859328 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * * ** *
1859379 ATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * *
1859430 GTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 GTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1859480 CGTTTGCCAA
Statistics
Matches: 284, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
51 252 0.89
55 32 0.11
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:1868544 original size:21 final size:21
Alignment explanation
Indices: 1868502--1868545 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1868492 TTTCTGGGCT
* *
1868502 AGGGGAATCGATACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1868523 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1868544 AG
1 AG
1868546 CGAACCAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.25, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1868617 original size:23 final size:22
Alignment explanation
Indices: 1868573--1868617 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1868563 AATGTCATGG
*
1868573 GGGAACCGATACCCCCATAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1868595 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1868618 AGAAATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1870178 original size:23 final size:23
Alignment explanation
Indices: 1870145--1870207 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1870135 ATTATTATAT
1870145 GGCACTACGATGCAATTCTACGC
1 GGCACTACGATGCAATTCTACGC
* *
1870168 GGCACTCCGATGCAATTCTACGT
1 GGCACTACGATGCAATTCTACGC
* *
1870191 GGCACTTCGGTGCAATT
1 GGCACTACGATGCAATT
1870208 ATACAAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (23 bp):
GGCACTACGATGCAATTCTACGC
Found at i:1875447 original size:23 final size:23
Alignment explanation
Indices: 1875414--1875476 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1875404 ATTATTATAT
1875414 GGCACTACGATGCAATTCTACGC
1 GGCACTACGATGCAATTCTACGC
* * *
1875437 GGCACTCCGATGCAATTCTTCGT
1 GGCACTACGATGCAATTCTACGC
* *
1875460 GGCACTTCGGTGCAATT
1 GGCACTACGATGCAATT
1875477 ATACAAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACGATGCAATTCTACGC
Found at i:1882751 original size:18 final size:18
Alignment explanation
Indices: 1882728--1882764 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1882718 TATATGTATG
1882728 ATCCTCAAACTTGAGATC
1 ATCCTCAAACTTGAGATC
1882746 ATCCTCAAACTTGAGATC
1 ATCCTCAAACTTGAGATC
1882764 A
1 A
1882765 ATGTTATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (18 bp):
ATCCTCAAACTTGAGATC
Found at i:1883509 original size:77 final size:79
Alignment explanation
Indices: 1883377--1883535 Score: 207
Period size: 77 Copynumber: 2.0 Consensus size: 79
1883367 CCAAATATAG
** *
1883377 TAAATAAACATTACAAGAATGTAATTTTGATTACAACTCTTTTAATGGAAATTTAATTTGGAA-T
1 TAAATAAACATTACAAGAATGTAATTCGGAATACAACTCTTTTAATGGAAATTTAATTT-GAATT
*
1883441 AATTAAATAAGAGTT
65 AATTAAATAAGAATT
* * * * *
1883456 TAAATAAACATTA-AAGAGTGTAATTCGGAATATAAGTC-TTTAATGTATATTTAATTTGAATTA
1 TAAATAAACATTACAAGAATGTAATTCGGAATACAACTCTTTTAATGGAAATTTAATTTGAATTA
1883519 ATTAAATAAGAATT
66 ATTAAATAAGAATT
1883533 TAA
1 TAA
1883536 TTAATTCAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
76 3 0.04
77 35 0.50
78 19 0.27
79 13 0.19
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.38
Consensus pattern (79 bp):
TAAATAAACATTACAAGAATGTAATTCGGAATACAACTCTTTTAATGGAAATTTAATTTGAATTA
ATTAAATAAGAATT
Found at i:1887530 original size:17 final size:17
Alignment explanation
Indices: 1887493--1887535 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1887483 AGTCTTTGTT
* * *
1887493 TCTCGAATGAGAGTTTT
1 TCTCGAAAGAGAATTTC
1887510 TCTCGAAAGAGAATTTC
1 TCTCGAAAGAGAATTTC
1887527 TCTC-AAAGA
1 TCTCGAAAGA
1887536 AAGGGAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (17 bp):
TCTCGAAAGAGAATTTC
Found at i:1888099 original size:22 final size:23
Alignment explanation
Indices: 1888074--1888117 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1888064 AATTAAGTTT
1888074 TAATCTTA-AAAAAATTTCAAAA
1 TAATCTTACAAAAAATTTCAAAA
* **
1888096 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAAAAATTTCAAA
1888118 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAAAAATTTCAAAA
Found at i:1893919 original size:22 final size:22
Alignment explanation
Indices: 1893894--1893974 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
1893884 CCATCGGATA
1893894 ACTAAAGTGCCTTAGCACT-AGT
1 ACTAAAGTGCCTTAGCACTGA-T
* * *
1893916 ACTAAAGTGGCTCAACACTGAT
1 ACTAAAGTGCCTTAGCACTGAT
* * * *
1893938 ACGAAAGTGCATTTGCAGTGAT
1 ACTAAAGTGCCTTAGCACTGAT
1893960 ACTAAAGTGCCTTAG
1 ACTAAAGTGCCTTAG
1893975 AATTATTGAG
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (22 bp):
ACTAAAGTGCCTTAGCACTGAT
Found at i:1895302 original size:31 final size:31
Alignment explanation
Indices: 1895227--1895304 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
1895217 TTTAAAAACA
* *
1895227 TAAGTTTTAATCACTTACGTGATCGTTTTAT
1 TAAGTTTTAGTCACTTACGTGATCATTTTAT
*
1895258 TAAGTTTTTGTCACTTACGTGATCATTTTAT
1 TAAGTTTTAGTCACTTACGTGATCATTTTAT
*
1895289 TAAGTTTTGGTCACTT
1 TAAGTTTTAGTCACTT
1895305 GGACATTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.50
Consensus pattern (31 bp):
TAAGTTTTAGTCACTTACGTGATCATTTTAT
Found at i:1896872 original size:18 final size:18
Alignment explanation
Indices: 1896849--1896890 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1896839 GTTAGCAAAC
*
1896849 CGTTAAATATTTAACGAT
1 CGTTAAAGATTTAACGAT
1896867 CGTTAAAGATTTAACGAT
1 CGTTAAAGATTTAACGAT
1896885 CGTTAA
1 CGTTAA
1896891 TCTTCAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
CGTTAAAGATTTAACGAT
Found at i:1896940 original size:31 final size:31
Alignment explanation
Indices: 1896896--1896960 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1896886 GTTAATCTTC
* *
1896896 AGTGACCACATCTTAATTAAAGCGAAACGAA
1 AGTGACCAAATCTTAATTAAAACGAAACGAA
* *
1896927 AGTGACTAAATCTTAATTAAAACGAAATGAA
1 AGTGACCAAATCTTAATTAAAACGAAACGAA
1896958 AGT
1 AGT
1896961 TACATATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (31 bp):
AGTGACCAAATCTTAATTAAAACGAAACGAA
Found at i:1897468 original size:3 final size:3
Alignment explanation
Indices: 1897460--1897508 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1897450 GTAACCTTGG
1897460 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1897508 C
1 C
1897509 TCCTTCTTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1900480 original size:15 final size:17
Alignment explanation
Indices: 1900450--1900482 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1900440 TCATAACCAT
1900450 TTTTTATAAATAAATTA
1 TTTTTATAAATAAATTA
1900467 TTTTTA-AAAT-AATTA
1 TTTTTATAAATAAATTA
1900482 T
1 T
1900483 GACTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTATAAATAAATTA
Found at i:1901076 original size:273 final size:273
Alignment explanation
Indices: 1900629--1901174 Score: 1076
Period size: 273 Copynumber: 2.0 Consensus size: 273
1900619 GATCTGCATG
1900629 TTATCGTAAATTCGTTTTAATGATTCGGGAGGTAATTACGCGTGAGGAAAGGTGAGCACCCCACA
1 TTATCGTAAATTCGTTTTAATGATTCGGGAGGTAATTACGCGTGAGGAAAGGTGAGCACCCCACA
1900694 ACGCCCATAATTGGTGCCGTCGATTATATGTTGTCTAAAATGATGGAATTCTACATATTTGAACT
66 ACGCCCATAATTGGTGCCGTCGATTATATGTTGTCTAAAATGATGGAATTCTACATATTTGAACT
1900759 CGAAATTTGAGTTGTGATTCTTTTATTTCGATAAGTTTTTTTAAATGAGTGAATTTATTAAAAAA
131 CGAAATTTGAGTTGTGATTCTTTTATTTCGATAAGTTTTTTTAAATGAGTGAATTTATTAAAAAA
1900824 TAATCGACTCGATAAATGATTTAATCAACTCGGCTTCATTTAAGAATTATGTCCTCTCACTACGT
196 TAATCGACTCGATAAATGATTTAATCAACTCGGCTTCATTTAAGAATTATGTCCTCTCACTACGT
1900889 GAATTAACAAAAA
261 GAATTAACAAAAA
1900902 TTATCGTAAATTCGTTTTAATGATTCGGGAGGTAATTACGCGTGAGGAAAGGTGAGCACCCCCAC
1 TTATCGTAAATTCGTTTTAATGATTCGGGAGGTAATTACGCGTGAGGAAAGGTGAGCA-CCCCAC
1900967 AACGCCCATAATTGGTGCCGTCGATTATATGTTGTCTAAAATGATGGAATTCTACATATTTGAAC
65 AACGCCCATAATTGGTGCCGTCGATTATATGTTGTCTAAAATGATGGAATTCTACATATTTGAAC
1901032 TCG-AATTTGAGTTGTGATTCTTTTATTTCGATAAGTTTTTTTAAATGAGTGAATTTATTAAAAA
130 TCGAAATTTGAGTTGTGATTCTTTTATTTCGATAAGTTTTTTTAAATGAGTGAATTTATTAAAAA
1901096 ATAATCGACTCGATAAATGATTTAATCAACTCGGCTTCATTTAAGAATTATGTCCTCTCACTACG
195 ATAATCGACTCGATAAATGATTTAATCAACTCGGCTTCATTTAAGAATTATGTCCTCTCACTACG
1901161 TGAATTAACAAAAA
260 TGAATTAACAAAAA
1901175 ATTGAAATTC
Statistics
Matches: 272, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
273 198 0.73
274 74 0.27
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (273 bp):
TTATCGTAAATTCGTTTTAATGATTCGGGAGGTAATTACGCGTGAGGAAAGGTGAGCACCCCACA
ACGCCCATAATTGGTGCCGTCGATTATATGTTGTCTAAAATGATGGAATTCTACATATTTGAACT
CGAAATTTGAGTTGTGATTCTTTTATTTCGATAAGTTTTTTTAAATGAGTGAATTTATTAAAAAA
TAATCGACTCGATAAATGATTTAATCAACTCGGCTTCATTTAAGAATTATGTCCTCTCACTACGT
GAATTAACAAAAA
Found at i:1901378 original size:16 final size:17
Alignment explanation
Indices: 1901341--1901382 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1901331 ACAAGTAAAT
1901341 AAACAAATAAAATACTA
1 AAACAAATAAAATACTA
1901358 AAACAAATAAAATAC-A
1 AAACAAATAAAATACTA
*
1901374 CAACAAATA
1 AAACAAATA
1901383 TTTATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (17 bp):
AAACAAATAAAATACTA
Found at i:1906390 original size:14 final size:15
Alignment explanation
Indices: 1906371--1906400 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1906361 TTGCATAATA
1906371 TATATTTATAT-ATT
1 TATATTTATATGATT
1906385 TATATTTATATGATT
1 TATATTTATATGATT
1906400 T
1 T
1906401 GGTATATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TATATTTATATGATT
Found at i:1906993 original size:23 final size:23
Alignment explanation
Indices: 1906912--1907002 Score: 119
Period size: 23 Copynumber: 4.0 Consensus size: 23
1906902 GACATTATAT
* *
1906912 GGCACTACGGTGAATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
1906935 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
1906958 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
1906981 GGCACTTCAGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1907003 AGCTGTGGTG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1912074 original size:110 final size:107
Alignment explanation
Indices: 1911884--1912097 Score: 401
Period size: 110 Copynumber: 2.0 Consensus size: 107
1911874 TGGAATTTAT
1911884 AGGTCTTTGAGACACATATTTGGTCCTTGGTATATGTATATTCTTAAGGAATTTCTATGTGGTCC
1 AGGTCTTTGAGACACATATTTGGTCCTTGGTATATGTATATTCTTAAGGAATTTCTATGTGGTCC
1911949 TTATAGACATTATATGGCACTACGGTGCATTTCTATGCGATA
66 TTATAGACATTATATGGCACTACGGTGCATTTCTATGCGATA
1911991 AGGTCTTTGAGACACATATTTGGTCCTTGGTATATGTATATGATTCTTAAGGAATTTCTATGTGG
1 AGGTCTTTGAGACACATATTTGGTCCTTGGTATATG--TAT-ATTCTTAAGGAATTTCTATGTGG
1912056 TCCTTATAGACATTATATGGCACTACGGTGCATTTCTATGCG
63 TCCTTATAGACATTATATGGCACTACGGTGCATTTCTATGCG
1912098 GCACTTCGGT
Statistics
Matches: 104, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
107 36 0.35
109 3 0.03
110 65 0.62
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (107 bp):
AGGTCTTTGAGACACATATTTGGTCCTTGGTATATGTATATTCTTAAGGAATTTCTATGTGGTCC
TTATAGACATTATATGGCACTACGGTGCATTTCTATGCGATA
Found at i:1912100 original size:23 final size:23
Alignment explanation
Indices: 1912073--1912164 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
1912063 AGACATTATA
*
1912073 TGGCACTACGGTGCATTTCTATG
1 TGGCACTACGGTGCATTTCTACG
* * *
1912096 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTACGGTGCATTTCTACG
*
1912119 TGGCACTACGGTTCATTTCTACG
1 TGGCACTACGGTGCATTTCTACG
* * *
1912142 TAGCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCATTTCTACG
1912165 AGCTGTGGTG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTCTACG
Found at i:1919368 original size:44 final size:46
Alignment explanation
Indices: 1919303--1919393 Score: 168
Period size: 44 Copynumber: 2.0 Consensus size: 46
1919293 AGCGCCGGTG
1919303 ATGGTTATAAAACCATCAACCGAACCTGCAAGAACACCACGAGAGC
1 ATGGTTATAAAACCATCAACCGAACCTGCAAGAACACCACGAGAGC
1919349 ATGGTT-T-AAACCATCAACCGAACCTGCAAGAACACCACGAGAGC
1 ATGGTTATAAAACCATCAACCGAACCTGCAAGAACACCACGAGAGC
1919393 A
1 A
1919394 ACCACAGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 38 0.84
45 1 0.02
46 6 0.13
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.13
Consensus pattern (46 bp):
ATGGTTATAAAACCATCAACCGAACCTGCAAGAACACCACGAGAGC
Found at i:1921237 original size:22 final size:23
Alignment explanation
Indices: 1921208--1921273 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
1921198 TCAACATTTC
1921208 TATATATACTTATTATTTTCA-TAA
1 TATATATA--TATTATTTTCATTAA
*
1921232 TATATATATATTATTTTTATTAA
1 TATATATATATTATTTTCATTAA
* * *
1921255 TATTTTTATTTTATTTTCA
1 TATATATATATTATTTTCA
1921274 AGTATTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.28
23 18 0.50
24 8 0.22
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TATATATATATTATTTTCATTAA
Found at i:1924564 original size:14 final size:14
Alignment explanation
Indices: 1924545--1924578 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1924535 GTCAATACCT
1924545 TTTGCATACATTCA
1 TTTGCATACATTCA
1924559 TTTGCATACATTCA
1 TTTGCATACATTCA
1924573 -TTGCAT
1 TTTGCAT
1924579 TATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (14 bp):
TTTGCATACATTCA
Found at i:1933011 original size:25 final size:22
Alignment explanation
Indices: 1932955--1933008 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1932945 ACATCTACAT
1932955 TCTTCAAAGATAATAGATTCTC
1 TCTTCAAAGATAATAGATTCTC
*
1932977 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATAATAGATTCTC
*
1932999 TTTTCAAAGA
1 TCTTCAAAGA
1933009 AGAAAGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATAATAGATTCTC
Found at i:1933016 original size:22 final size:22
Alignment explanation
Indices: 1932955--1933017 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
1932945 ACATCTACAT
*
1932955 TCTTCAAAGATA-ATAGATTCTC
1 TCTTCAAAGA-AGAAAGATTCTC
* *
1932977 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGAAGAAAGATTCTC
*
1932999 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGAAGAAAGATT
1933018 TATTGGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGAAGAAAGATTCTC
Found at i:1933280 original size:40 final size:40
Alignment explanation
Indices: 1933225--1933321 Score: 167
Period size: 40 Copynumber: 2.4 Consensus size: 40
1933215 CAGGTAGAGC
*
1933225 TCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGT
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
1933265 TCATAATGAGAAGAACTCGTCTGAAGAATGAAGAAGAAGT
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1933305 TCATAATGAGAAGAACT
1 TCATAATGAGAAGAACT
1933322 TGTTCAGCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (40 bp):
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
Found at i:1933326 original size:20 final size:19
Alignment explanation
Indices: 1933263--1933327 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
1933253 GGAATAAGAA
1933263 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* *
1933282 CGTCTGAAGAATGAAGAAGAA--
1 -GT-T-CATAATG-AGAAGAACT
1933303 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
1933323 GTTCA
1 GTTCA
1933328 GCCTTTTGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
17 7 0.20
18 5 0.14
19 1 0.03
20 9 0.26
21 1 0.03
22 5 0.14
23 7 0.20
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:1933496 original size:122 final size:122
Alignment explanation
Indices: 1933261--1933526 Score: 367
Period size: 122 Copynumber: 2.2 Consensus size: 122
1933251 AAGGAATAAG
* * *
1933261 AAGTTCATAATGAGAAGAACTCGTCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTT
* * * *
1933326 CAGCCTTTTGCTCTACTCTATCGCAGAAGGAGATAGATCATCATCAACATTTCCAGAGA
66 CAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCA-A-A
*
1933385 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAAAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTT
* * *
1933449 TAACC-TTTGCAT-GACTCTATTATAGAAGGAGATAGATCAACATCAACATTTCCAAA
66 CAACCTTTTGC-TCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAAA
*
1933505 AGTGTTCATAATGAGAAGAACT
1 A-AGTTCATAATGAGAAGAACT
1933527 AATCCCAAAA
Statistics
Matches: 128, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
120 2 0.02
121 20 0.16
122 42 0.33
123 36 0.28
124 28 0.22
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (122 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTGTT
CAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAAA
Found at i:1933677 original size:17 final size:17
Alignment explanation
Indices: 1933619--1933678 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
1933609 CAGCATTTCT
*
1933619 AGAAGGAGTTCATAATG
1 AGAAGAAGTTCATAATG
* **
1933636 AGAAGAACTCGTC-TAAAAA
1 AGAAGAAGT--TCAT-AATG
1933655 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
1933672 AGAAGAA
1 AGAAGAA
1933679 TTTGTTCAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
17 18 0.56
18 2 0.06
19 12 0.38
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.18
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:1933928 original size:3 final size:3
Alignment explanation
Indices: 1933920--1933978 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
1933910 TCCATTTGAT
* *
1933920 TTA TTA TTA TTA TTA TTA TGA TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1933968 TTA TTA TTA TT
1 TTA TTA TTA TT
1933979 TACATTACAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1935764 original size:148 final size:148
Alignment explanation
Indices: 1935475--1935750 Score: 382
Period size: 148 Copynumber: 1.9 Consensus size: 148
1935465 AAAAATAATC
* *
1935475 ATATTTTTTTATTTTTTAATATTAAGAAATTGGTTGTCTTAAAGCACCTAGAAGTCCTTTTATGA
1 ATATTTATTTATTTTTTAATATTAAGAAATTGGATGTCTTAAAGCACCTAGAAGTCCTTTTATGA
* * * * * *
1935540 TATTCTCAAATAAATAAATATCCTATTTTTATAAATTATATATATTAATTTATTTTAATTATTTT
66 TATTCTCAAATAAATAAATATCCTATTTATATAAAATAAAGATATTAATATATATTAATTATTTT
1935605 TAGAAAAATATTTTATTA
131 TAGAAAAATATTTTATTA
* *
1935623 ATATTTATTTATTTTTTAATATTAAGAAA-TGAGATGTCTTAAAGCACCTAGAAGTCCTTTTCTT
1 ATATTTATTTATTTTTTAATATTAAGAAATTG-GATGTCTTAAAGCACCTAGAAGTCCTTTTATG
* *
1935687 ATATT-TATAAATAAATAAATATCTTATTTATA-AAAATAAAGATA-T-ATATATATTAATATAT
65 ATATTCT-CAAATAAATAAATATCCTATTTATATAAAATAAAGATATTAATATATATTAAT-TAT
1935748 TTT
128 TTT
1935751 CTTAAAATTA
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
145 10 0.09
146 7 0.06
147 12 0.11
148 84 0.74
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (148 bp):
ATATTTATTTATTTTTTAATATTAAGAAATTGGATGTCTTAAAGCACCTAGAAGTCCTTTTATGA
TATTCTCAAATAAATAAATATCCTATTTATATAAAATAAAGATATTAATATATATTAATTATTTT
TAGAAAAATATTTTATTA
Found at i:1942212 original size:2 final size:2
Alignment explanation
Indices: 1942205--1942254 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1942195 TCTAAAAATA
1942205 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
1942247 AT AT AT AT
1 AT AT AT AT
1942255 CCAAGGCATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1943256 original size:15 final size:15
Alignment explanation
Indices: 1943236--1943267 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1943226 GTTGGGTCGG
*
1943236 GTCGTGGTCGTGGTC
1 GTCGTGGTCGTGATC
1943251 GTCGTGGTCGTGATC
1 GTCGTGGTCGTGATC
1943266 GT
1 GT
1943268 GGTAATGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.03, C:0.19, G:0.44, T:0.34
Consensus pattern (15 bp):
GTCGTGGTCGTGATC
Found at i:1943401 original size:21 final size:21
Alignment explanation
Indices: 1943375--1943600 Score: 371
Period size: 21 Copynumber: 10.8 Consensus size: 21
1943365 TGCAATTTTG
1943375 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
* *
1943396 GACTATCGCAATGAATTTGGA
1 GACTATCGCAACGAACTTGGA
* *
1943417 GACTACCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
1943438 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
1943459 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
1943480 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
1943501 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
1943522 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
* *
1943543 GACTACCGCAACGAACTTAGA
1 GACTATCGCAACGAACTTGGA
*
1943564 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
1943585 GACTATCGCAACGAAC
1 GACTATCGCAACGAAC
1943601 GAACTTGGAG
Statistics
Matches: 189, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 189 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
GACTATCGCAACGAACTTGGA
Found at i:1943682 original size:21 final size:19
Alignment explanation
Indices: 1943371--1943725 Score: 197
Period size: 21 Copynumber: 16.9 Consensus size: 19
1943361 TCGTTGCAAT
*
1943371 TTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
* *
1943390 CTTGGAGACTATCGCAATGAA
1 TTTGGA-A-TATCGCAACGAA
*
1943411 TTTGGAGACTACCGCAACGAA
1 TTTGGA-A-TATCGCAACGAA
1943432 TTTGGAGACTATCGCAACGAA
1 TTTGGA-A-TATCGCAACGAA
*
1943453 CTTGGAGACTATCGCAACGAA
1 TTTGGA-A-TATCGCAACGAA
*
1943474 CTTGGAGACTATCGCAACGAA
1 TTTGGA-A-TATCGCAACGAA
1943495 TTTGGAGACTATCGCAACGAA
1 TTTGGA-A-TATCGCAACGAA
*
1943516 CTTGGAGACTATCGCAACGAA
1 TTTGGA-A-TATCGCAACGAA
*
1943537 TTTGGAGACTACCGCAACGAA
1 TTTGGA-A-TATCGCAACGAA
* *
1943558 CTTAGAGACTATCGCAACGAA
1 -TTTG-GAATATCGCAACGAA
1943579 TTTGGAGACTATCGCAACGAACGAA
1 TTTGGA-A-TATCG---C-AACGAA
* * *
1943604 CTTGGAGACTAGCGCAACAAA
1 TTTGGA-A-TATCGCAACGAA
* * *
1943625 TTTGTAATAAATCGTGACGCGAA
1 TTTGGAAT--ATCG-CA-ACGAA
* *
1943648 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
1943667 TTTGGAATAAATCGCAACGCAAA
1 TTTGGAAT--ATCGCAACG--AA
* * *
1943690 CTTGGACTATCGCAATGAA
1 TTTGGAATATCGCAACGAA
* *
1943709 TTTGGAAAATCACAACG
1 TTTGGAATATCGCAACG
1943726 CGAACTTCAA
Statistics
Matches: 277, Mismatches: 41, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
19 32 0.12
20 5 0.02
21 198 0.71
22 5 0.02
23 18 0.06
24 1 0.00
25 18 0.06
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:1943715 original size:42 final size:42
Alignment explanation
Indices: 1943375--1943714 Score: 408
Period size: 42 Copynumber: 8.0 Consensus size: 42
1943365 TGCAATTTTG
*
1943375 GACTATCGCAACGAACTTGGAGACTATCGCAATGAATTTGGA
1 GACTATCGCAACGAACTTGGAGACTATCGCAACGAATTTGGA
* * *
1943417 GACTACCGCAACGAATTTGGAGACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGAGACTATCGCAACGAATTTGGA
1943459 GACTATCGCAACGAACTTGGAGACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGAGACTATCGCAACGAATTTGGA
1943501 GACTATCGCAACGAACTTGGAGACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGAGACTATCGCAACGAATTTGGA
* *
1943543 GACTACCGCAACGAACTTAGAGACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGAGACTATCGCAACGAATTTGGA
* * *
1943585 GACTATCGCAACGAACGAACTTGGAGACTAGCGCAACAAATTTGTA
1 GACTATCG---C-AACGAACTTGGAGACTATCGCAACGAATTTGGA
* *
1943631 -A-TAAATCGTGACGCGAACTT-G-GACTATCGCAACGAATTTGGA
1 GACT--ATCG-CA-ACGAACTTGGAGACTATCGCAACGAATTTGGA
*
1943673 -A-TAAATCGCAACGCAAACTT-G-GACTATCGCAATGAATTTGGA
1 GACT--ATCGCAACG--AACTTGGAGACTATCGCAACGAATTTGGA
1943715 AAATCACAAC
Statistics
Matches: 266, Mismatches: 23, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
40 2 0.01
41 1 0.00
42 218 0.82
43 2 0.01
44 8 0.03
45 2 0.01
46 33 0.12
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAGACTATCGCAACGAATTTGGA
Found at i:1943750 original size:21 final size:21
Alignment explanation
Indices: 1943721--1943765 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1943711 TGGAAAATCA
*
1943721 CAACGCGAACTTCAACTATCG
1 CAACACGAACTTCAACTATCG
**
1943742 CAACACGAACTTGGACTATCG
1 CAACACGAACTTCAACTATCG
1943763 CAA
1 CAA
1943766 TGCGAATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.31, G:0.16, T:0.18
Consensus pattern (21 bp):
CAACACGAACTTCAACTATCG
Found at i:1944267 original size:19 final size:21
Alignment explanation
Indices: 1944209--1944267 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 21
1944199 TCAATGGATT
1944209 TAATTTTAAAGATTTTTTTAAACA
1 TAATTTTAAAGA---TTTTAAACA
*
1944233 TAATTTTAAAGGTTTTAAA-A
1 TAATTTTAAAGATTTTAAACA
*
1944253 -AATTTTAAATATTTT
1 TAATTTTAAAGATTTT
1944268 CAAATATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 13 0.41
20 1 0.03
21 7 0.22
24 11 0.34
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TAATTTTAAAGATTTTAAACA
Found at i:1952227 original size:19 final size:19
Alignment explanation
Indices: 1952203--1952251 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1952193 AAGGTGATTT
1952203 GTGTATCGATGCATGGGTA
1 GTGTATCGATGCATGGGTA
1952222 GTGTATCGATGCATGGGTA
1 GTGTATCGATGCATGGGTA
1952241 GTGTATCGATG
1 GTGTATCGATG
1952252 TACATGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.10, G:0.37, T:0.33
Consensus pattern (19 bp):
GTGTATCGATGCATGGGTA
Found at i:1953219 original size:2 final size:2
Alignment explanation
Indices: 1953212--1953257 Score: 60
Period size: 2 Copynumber: 23.0 Consensus size: 2
1953202 GTATTTGCGG
1953212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AT A- AT AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT -AT
1953254 AT AT
1 AT AT
1953258 GTTTATGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 2 0.05
2 35 0.88
3 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1953772 original size:23 final size:23
Alignment explanation
Indices: 1953739--1953798 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
1953729 CATTTTATAT
*
1953739 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACAC
* *
1953762 GGTACTTCGGTGCAATTCTACAT
1 GGCACTTCGGTGCAATTCTACAC
1953785 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1953799 TTTATACGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:1954229 original size:12 final size:12
Alignment explanation
Indices: 1954194--1954232 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 12
1954184 GAGATTTAAA
1954194 ATAATGTGTGATAT
1 ATAATGT-T-ATAT
1954208 ATATATGTTATAT
1 ATA-ATGTTATAT
1954221 ATAATGTTATAT
1 ATAATGTTATAT
1954233 TGTTTTGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.38
13 7 0.29
14 4 0.17
15 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (12 bp):
ATAATGTTATAT
Found at i:1955738 original size:13 final size:13
Alignment explanation
Indices: 1955700--1955742 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1955690 ATTTTAAAAA
*
1955700 ATAATTAAAAAAT
1 ATAATTAAAATAT
*
1955713 -TAATATTAAATAT
1 ATAAT-TAAAATAT
1955726 ATAATTAAAATAT
1 ATAATTAAAATAT
1955739 ATAA
1 ATAA
1955743 CATTCAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATTAAAATAT
Found at i:1955843 original size:20 final size:20
Alignment explanation
Indices: 1955818--1955859 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1955808 ATAATTTTCC
*
1955818 ATTAAATATAATATAAAAAT
1 ATTAAACATAATATAAAAAT
*
1955838 ATTAAACATTATATAAAAAT
1 ATTAAACATAATATAAAAAT
1955858 AT
1 AT
1955860 AGGGTAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAACATAATATAAAAAT
Found at i:1956742 original size:20 final size:20
Alignment explanation
Indices: 1956717--1956788 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1956707 ACCCAAAAAT
1956717 ATAATATAAAAACATTAAAC
1 ATAATATAAAAACATTAAAC
1956737 ATAATATAAAAACA-TAAA-
1 ATAATATAAAAACATTAAAC
* *
1956755 A-ACTA-AATAACATTAAAC
1 ATAATATAAAAACATTAAAC
1956773 ATAAATATAAAAACAT
1 AT-AATATAAAAACAT
1956789 CACATCTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 6 0.14
17 7 0.16
18 2 0.05
19 4 0.09
20 17 0.40
21 7 0.16
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
ATAATATAAAAACATTAAAC
Done.