Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008017.1 Hibiscus syriacus cultivar Beakdansim tig00110483_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: 3132588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 15
Found at i:1768661 original size:5 final size:5
Alignment explanation
Indices: 1768651--1768699 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
1768641 ATAGATAGAT
1768651 ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA ATGA
1 ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA ATGA
1768700 CTTATATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.59, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
ATGAA
Found at i:1768760 original size:2 final size:2
Alignment explanation
Indices: 1768753--1768824 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1768743 GAACATGTGA
1768753 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
1768795 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
1768825 GTCTAAGAGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1769200 original size:14 final size:14
Alignment explanation
Indices: 1769181--1769208 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1769171 GAAAAGAAGC
1769181 TATGTGATACGTGA
1 TATGTGATACGTGA
1769195 TATGTGATACGTGA
1 TATGTGATACGTGA
1769209 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:1769579 original size:149 final size:149
Alignment explanation
Indices: 1769309--1770068 Score: 1472
Period size: 149 Copynumber: 5.1 Consensus size: 149
1769299 GAGTCGAGGG
1769309 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1769374 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1769439 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1769458 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1769523 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1769588 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1769607 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1769672 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1769737 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1769756 TCTACGCGGTCCTTCGGGACATATGTATA-T-TTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1769819 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1769884 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
1769903 TTTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
1769968 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1770033 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1770052 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1770069 TGCAATTATA
Statistics
Matches: 605, Mismatches: 3, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
147 145 0.24
148 3 0.00
149 457 0.76
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1769966 original size:296 final size:298
Alignment explanation
Indices: 1769309--1770068 Score: 1472
Period size: 296 Copynumber: 2.6 Consensus size: 298
1769299 GAGTCGAGGG
1769309 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1769374 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1769439 TATGGCACTACGGTGCAATTCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGT
131 TATGGCACTACGGTGCAATTCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGT
1769504 GAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTG
196 GAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTG
1769569 GTCCTTATGGACATCATTATATGGCACTACGGTGCAAT
261 GTCCTTATGGACATCATTATATGGCACTACGGTGCAAT
1769607 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1769672 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1769737 TATGGCACTACGGTGCAATTCTACGCGGTCCTTCGGGACATATGTATA-T-TTTGGAACATGTGT
131 TATGGCACTACGGTGCAATTCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGT
1769800 GAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTG
196 GAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTG
1769865 GTCCTTATGGACATCATTATATGGCACTACGGTGCAAT
261 GTCCTTATGGACATCATTATATGGCACTACGGTGCAAT
*
1769903 TTTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
1769968 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1770033 TATGGCACTACGGTGCAATTCTACGCGG-CACTTCGG
131 TATGGCACTACGGTGCAATTCTACGCGGTC-CTTCGG
1770069 TGCAATTATA
Statistics
Matches: 459, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
295 1 0.00
296 279 0.61
297 1 0.00
298 178 0.39
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (298 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAATTCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGT
GAAGTCTTGAAAGACACATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTG
GTCCTTATGGACATCATTATATGGCACTACGGTGCAAT
Found at i:1770069 original size:23 final size:23
Alignment explanation
Indices: 1770036--1770080 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1770026 ATCATTATAT
*
1770036 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1770059 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1770081 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1783075 original size:10 final size:10
Alignment explanation
Indices: 1783060--1783106 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
1783050 GTCCTAAGTT
1783060 GAAAAAAAAA
1 GAAAAAAAAA
1783070 GAAAAAAAAA
1 GAAAAAAAAA
1783080 GAAAAAAAAA
1 GAAAAAAAAA
*
1783090 AAAAAAAAAA
1 GAAAAAAAAA
*
1783100 GGAAAAA
1 GAAAAAA
1783107 GAACAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:1783076 original size:8 final size:8
Alignment explanation
Indices: 1783063--1783117 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
1783053 CTAAGTTGAA
1783063 AAAAAAAG
1 AAAAAAAG
1783071 AAAAAAA-
1 AAAAAAAG
1783078 AAGAAAAA-
1 AA-AAAAAG
1783086 AAAAAAA-
1 AAAAAAAG
1783093 AAAAAAAG
1 AAAAAAAG
*
1783101 -GAAAAAG
1 AAAAAAAG
*
1783108 AACAAAAG
1 AAAAAAAG
1783116 AA
1 AA
1783118 GAGAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 20 0.49
8 21 0.51
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1783106 original size:1 final size:1
Alignment explanation
Indices: 1783061--1783099 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
1783051 TCCTAAGTTG
* *
1783061 AAAAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1783100 GGAAAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1784031 original size:105 final size:105
Alignment explanation
Indices: 1783844--1784986 Score: 1866
Period size: 105 Copynumber: 11.0 Consensus size: 105
1783834 GGTTTTACCA
** *
1783844 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1783909 AAGGGACCGCTGGTTGTCAACAAACGTTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* *
1783949 AGCCAATTTCTGCTTCACAATGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1784014 AAGGGACCGCTGATTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
** *
1784054 AGCTTATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1784119 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAA-TTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
**
1784158 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1784223 AAGGGACCG-TGGTTGTCAACAAACATTTCTCAA-TTCAT
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
1784261 AGCCAA-TTCTGCTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1784325 AAGGGACCGCTGGTTGTCAACAAACA-TTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
1784364 AGCCTATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAA--CAAGTTCAACTTCACGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
1784427 AAGGGACCGCTGGTTGTCTACAAATATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
**
1784467 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1784532 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
1784572 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1784637 AAGGGACCGCTGGTTGTC-ACAAACA-TTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* * *
1784675 AGCCAATTTCTACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCATGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1784740 AAGGGGACCGCTGGTTTGTCAACAAACA-TTCTCAATTTCAG
66 AA-GGGACCGCTGG-TTGTCAACAAACATTTCTCAATTTCAG
** * *
1784781 AGCCAATTTCAAC-TCACAACGAAGGATATTGGACTCCAGGCAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1784845 AAGGGACCG-TGGTTGTCAAACAAACA-TTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTC-AACAAACATTTCTCAATTTCAG
* * *
1784884 AGCCAATTTCCGCTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTTACGACG
1 AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
1784949 AA-GGACCGCTGGTTGTCAATAAACAATTAC-CAATTTCA
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCA
1784987 ATTACACGAT
Statistics
Matches: 976, Mismatches: 48, Indels: 29
0.93 0.05 0.03
Matches are distributed among these distances:
102 119 0.12
103 237 0.24
104 201 0.21
105 387 0.40
106 32 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
AGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
Found at i:1790120 original size:13 final size:14
Alignment explanation
Indices: 1790086--1790120 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1790076 TACTAGCTGG
1790086 GGCAAATCTTCAGA
1 GGCAAATCTTCAGA
1790100 GTGCAAATCTTCA-A
1 G-GCAAATCTTCAGA
1790114 GGCAAAT
1 GGCAAAT
1790121 ACTTACAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 3 0.15
15 11 0.55
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (14 bp):
GGCAAATCTTCAGA
Found at i:1792592 original size:20 final size:21
Alignment explanation
Indices: 1792551--1792592 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1792541 TATAATCAAA
**
1792551 ACATAATTTGTTTTTAGTTTG
1 ACATAATTTGTTTTTAAATTG
1792572 ACATAATTTG-TTTTAAATTG
1 ACATAATTTGTTTTTAAATTG
1792592 A
1 A
1792593 ATTACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (21 bp):
ACATAATTTGTTTTTAAATTG
Found at i:1793211 original size:21 final size:20
Alignment explanation
Indices: 1793187--1793301 Score: 99
Period size: 21 Copynumber: 5.5 Consensus size: 20
1793177 CATATTCGCA
1793187 TTGCGATAGTCCAAGTTCGAG
1 TTGCGATAGTCCAAGTTC-AG
*
1793208 TTGCGATTTATTCCAAGTTC-G
1 TTGCGA--TAGTCCAAGTTCAG
*
1793229 TTGCGATAGTCGAAGTTCACG
1 TTGCGATAGTCCAAGTTCA-G
* *
1793250 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-AG
* *
1793271 TTGCGATTTATTCCAAATTC-G
1 TTGCGA--TAGTCCAAGTTCAG
1793292 TTGCGATAGT
1 TTGCGATAGT
1793302 ATTCGCGCGG
Statistics
Matches: 79, Mismatches: 8, Indels: 16
0.77 0.08 0.16
Matches are distributed among these distances:
19 13 0.16
21 46 0.58
23 20 0.25
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCAG
Found at i:1793273 original size:42 final size:43
Alignment explanation
Indices: 1793181--1793277 Score: 112
Period size: 42 Copynumber: 2.3 Consensus size: 43
1793171 GATTTACATA
* *
1793181 TTCGCATTGCGATAGTCCAAGTTCGAGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGATAGTCCAAGTTCGAGTTGCGA-TTAGTCCAAG
* *
1793225 TT--CGTTGCGATAGTCGAAGTTC-ACGTTGCGA-TAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAGTTCGA-GTTGCGATTAGTCCAAG
1793265 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1793278 TTATTCCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
40 9 0.20
41 1 0.02
42 34 0.74
44 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.33
Consensus pattern (43 bp):
TTCGCGTTGCGATAGTCCAAGTTCGAGTTGCGATTAGTCCAAG
Found at i:1793756 original size:12 final size:12
Alignment explanation
Indices: 1793739--1793780 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1793729 TTCCACATAG
1793739 TATTGGAAACAC
1 TATTGGAAACAC
* * *
1793751 TATTGGGAATAG
1 TATTGGAAACAC
1793763 TATTGGAAACAC
1 TATTGGAAACAC
1793775 TATTGG
1 TATTGG
1793781 GAATGATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.31
Consensus pattern (12 bp):
TATTGGAAACAC
Found at i:1793790 original size:24 final size:24
Alignment explanation
Indices: 1793735--1793784 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1793725 TCAATTCCAC
1793735 ATAGTATTGGAAACACTATTGGGA
1 ATAGTATTGGAAACACTATTGGGA
1793759 ATAGTATTGGAAACACTATTGGGA
1 ATAGTATTGGAAACACTATTGGGA
1793783 AT
1 AT
1793785 GATATTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (24 bp):
ATAGTATTGGAAACACTATTGGGA
Found at i:1794076 original size:21 final size:21
Alignment explanation
Indices: 1794042--1794159 Score: 152
Period size: 21 Copynumber: 5.7 Consensus size: 21
1794032 GCGAATATGT
*
1794042 AAGTT-GCAATGCGATAGTCC
1 AAGTTCGCATTGCGATAGTCC
* *
1794062 AAGTTCGCATTGCGAT-TTAC
1 AAGTTCGCATTGCGATAGTCC
*
1794082 ATA-TTCGCATTGCGATAATCC
1 A-AGTTCGCATTGCGATAGTCC
1794103 AAGTTCGCATTGCGATAGTCC
1 AAGTTCGCATTGCGATAGTCC
*
1794124 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCC
*
1794145 AAGTTCGCGTTGCGA
1 AAGTTCGCATTGCGA
1794160 ATCTGGAAAC
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
20 22 0.26
21 64 0.74
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (21 bp):
AAGTTCGCATTGCGATAGTCC
Found at i:1794076 original size:41 final size:41
Alignment explanation
Indices: 1794025--1794159 Score: 143
Period size: 41 Copynumber: 3.3 Consensus size: 41
1794015 ACTTGGACTA
* *
1794025 TCGCAATGCGAATATGTAAGTT-GCAATGCGATAGTCCAAGT
1 TCGCATTGCG-ATATGTAAGTTCGCATTGCGATAGTCCAAGT
* *
1794066 TCGCATTGCGAT-T-TACATATTCGCATTGCGATAATCCAAGT
1 TCGCATTGCGATATGTA-A-GTTCGCATTGCGATAGTCCAAGT
*
1794107 TCGCATTGCGATA-GTCCAAGTTCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATATGT--AAGTTCGCATTGCGATAGTCCAAGT
*
1794149 TCGCGTTGCGA
1 TCGCATTGCGA
1794160 ATCTGGAAAC
Statistics
Matches: 79, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 4 0.05
41 38 0.48
42 31 0.39
43 1 0.01
44 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (41 bp):
TCGCATTGCGATATGTAAGTTCGCATTGCGATAGTCCAAGT
Found at i:1794547 original size:16 final size:16
Alignment explanation
Indices: 1794526--1794556 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1794516 TGACCGGCTC
1794526 TTCTTCTTCTTCACTT
1 TTCTTCTTCTTCACTT
*
1794542 TTCTTCTTTTTCACT
1 TTCTTCTTCTTCACT
1794557 CGAAGCATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (16 bp):
TTCTTCTTCTTCACTT
Found at i:1795894 original size:16 final size:17
Alignment explanation
Indices: 1795863--1795896 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1795853 TAAATATTTG
1795863 ATAAATTCTAATAAATA
1 ATAAATTCTAATAAATA
*
1795880 ATAATTTCTAA-AAATA
1 ATAAATTCTAATAAATA
1795896 A
1 A
1795897 ACACGTTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAATTCTAATAAATA
Found at i:1796408 original size:54 final size:57
Alignment explanation
Indices: 1796297--1796424 Score: 219
Period size: 54 Copynumber: 2.3 Consensus size: 57
1796287 GAGAAGGTCA
*
1796297 TTATGGCACGGGCATGACCGGAACAGAATACAAGGGAGAGACCGGTCATGGCCATGG
1 TTATGGCACGGGCATGACCGGAACAGAATACAAGGGAGAGACCGGTCATGACCATGG
1796354 TTATGGCACGGGCATGACC-GAACAGAATACAA-GG-GAGACCGGTCATGACCATGG
1 TTATGGCACGGGCATGACCGGAACAGAATACAAGGGAGAGACCGGTCATGACCATGG
1796408 TTAT-GCACGGGCATGAC
1 TTATGGCACGGGCATGAC
1796425 AGGGGCAACG
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
53 13 0.19
54 23 0.33
55 2 0.03
56 13 0.19
57 19 0.27
ACGTcount: A:0.30, C:0.22, G:0.33, T:0.16
Consensus pattern (57 bp):
TTATGGCACGGGCATGACCGGAACAGAATACAAGGGAGAGACCGGTCATGACCATGG
Found at i:1798126 original size:12 final size:13
Alignment explanation
Indices: 1798109--1798160 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
1798099 ATTTAATCTC
1798109 TTTAT-TTATTTA
1 TTTATGTTATTTA
*
1798121 TTTATTTTA-TTA
1 TTTATGTTATTTA
*
1798133 TTTAATGCTATTT-
1 TTT-ATGTTATTTA
1798146 TTTATGTTATTTA
1 TTTATGTTATTTA
1798159 TT
1 TT
1798161 GTTGTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 19 0.58
13 12 0.36
14 2 0.06
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (13 bp):
TTTATGTTATTTA
Found at i:1798273 original size:9 final size:9
Alignment explanation
Indices: 1798243--1798397 Score: 81
Period size: 9 Copynumber: 17.1 Consensus size: 9
1798233 TTATTATTTC
1798243 TTTTT-TTA
1 TTTTTATTA
1798251 -TTTTATTCA
1 TTTTTATT-A
1798260 TTTTTTATTA
1 -TTTTTATTA
1798270 TTTTTATTTA
1 TTTTTA-TTA
1798280 TTTTT-TTCA
1 TTTTTATT-A
*
1798289 TTTTCATTTTCA
1 TTTT--TATT-A
*
1798301 TTTTT-TCA
1 TTTTTATTA
1798309 TTTTTA-TA
1 TTTTTATTA
*
1798317 TCTTTATT-
1 TTTTTATTA
* *
1798325 TATCTATGT-
1 TTTTTAT-TA
*
1798334 TCTTTATTA
1 TTTTTATTA
*
1798343 TTATTATTA
1 TTTTTATTA
*
1798352 TTATTATTA
1 TTTTTATTA
*
1798361 TTATTATTA
1 TTTTTATTA
*
1798370 TTATTATTA
1 TTTTTATTA
*
1798379 TTATTATTA
1 TTTTTATTA
*
1798388 TTATTATTA
1 TTTTTATTA
1798397 T
1 T
1798398 ATTAACATTT
Statistics
Matches: 125, Mismatches: 9, Indels: 25
0.79 0.06 0.16
Matches are distributed among these distances:
7 4 0.03
8 22 0.18
9 73 0.58
10 10 0.08
11 8 0.06
12 8 0.06
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (9 bp):
TTTTTATTA
Found at i:1798278 original size:6 final size:6
Alignment explanation
Indices: 1798236--1798395 Score: 58
Period size: 6 Copynumber: 24.8 Consensus size: 6
1798226 AATTTTGTTA
1798236 TTATTT CTT-TTT TTA-TT TTATTCAT TT-TTT ATTATTT TTATTT ATT-TTT
1 TTATTT -TTATTT TTATTT TTATT--T TTATTT -TTATTT TTATTT -TTATTT
* *
1798285 TTCATTT TCATTT TCATTTT TTCATTT TTATATCT TTATTT ATCTATGTTCT
1 TT-ATTT TTATTT TTA-TTT TT-ATTT TTAT-T-T TTATTT -T-TA--TT-T
* * * * * * * *
1798337 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
*
1798385 TTATTA TTATT
1 TTATTT TTATT
1798396 ATATTAACAT
Statistics
Matches: 132, Mismatches: 3, Indels: 37
0.77 0.02 0.22
Matches are distributed among these distances:
5 10 0.08
6 78 0.59
7 27 0.20
8 11 0.08
9 2 0.02
10 3 0.02
11 1 0.01
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.71
Consensus pattern (6 bp):
TTATTT
Found at i:1798345 original size:3 final size:3
Alignment explanation
Indices: 1798337--1798401 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
1798327 TCTATGTTCT
1798337 TTA TTA TTA TTA TTA TTA TTA TTA 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
1798385 TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA
1798402 ACATTTTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1801217 original size:96 final size:97
Alignment explanation
Indices: 1801046--1801243 Score: 285
Period size: 96 Copynumber: 2.1 Consensus size: 97
1801036 TATATATATA
* *
1801046 TATATATACAATAAAACTTGAGCTGTCCCTCTAAAGCAATTAGTTAAACGCCTCGACTTTATGGA
1 TATATATACAATAAAACTTGAGCTATCCCTCTAAAGCAATTAGTTAAACGCCTCGACTTTATAGA
*
1801111 TAAGATTCAGCTAGCCTGATAAAGGTGATTAT
66 TAAGAGTCAGCTAGCCTGATAAAGGTGATTAT
* * * *
1801143 TATA-ATACAATAAAGCTTGAGCTATCCCTCTAAATCAATTGGTTAAATTC-CCT-GGCTTTATA
1 TATATATACAATAAAACTTGAGCTATCCCTCTAAAGCAATTAGTTAAA--CGCCTCGACTTTATA
1801205 GATAAGAGTCAGCTAGCCTGATAAAGGTGATTAT
64 GATAAGAGTCAGCTAGCCTGATAAAGGTGATTAT
*
1801239 AATAT
1 TATAT
1801244 TGAGTTGTCC
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
96 82 0.91
97 7 0.08
98 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (97 bp):
TATATATACAATAAAACTTGAGCTATCCCTCTAAAGCAATTAGTTAAACGCCTCGACTTTATAGA
TAAGAGTCAGCTAGCCTGATAAAGGTGATTAT
Found at i:1808973 original size:84 final size:84
Alignment explanation
Indices: 1808826--1809821 Score: 1323
Period size: 84 Copynumber: 11.9 Consensus size: 84
1808816 TCCAGTACAT
* * * * * * * *
1808826 CATAACTCAAAGCGAGAAAGGTTATATGTCAACCAAA-ACCTTCGAGTTCGATTACATTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * *
1808890 AAAGGCACATAATTTACAA
66 AAAGGCACATCATTTGCAG
* * *
1808909 CATAGCTCAAGGAGAGAAGAGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTTAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
1808974 AAAGGCACATCATTTGTAG
66 AAAGGCACATCATTTGCAG
* * * * * * *
1808993 CAGAGCACAAGGAGAGAAGGGTTATCTGCCAATAAAATACCTTTGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1809058 AAAGGCACATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* *
1809077 CATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAAACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* **
1809142 AAAAGCACATCATTTATAG
66 AAAGGCACATCATTTGCAG
*
1809161 CATAGCTCAAGGCGAGAAGGGCTATCTGCTAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
1809226 AAAGGCACATCATTTACAA
66 AAAGGCACATCATTTGCAG
* *
1809245 TATAGCTCAAGGCGAAAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
1809310 AAAGGAACATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* * * * *
1809329 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACATTCGAGTTCGATTAGACTCAACTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
1809394 AAAGACACATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* * *
1809413 CATAGCTCAAGGCGAGAAGGGTTATCTGGCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
1809478 AAAGGAACATCATTTGTAG
66 AAAGGCACATCATTTGCAG
* * * * *
1809497 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACATTCGAGTTCGATTAGACTCAACTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
1809562 AAAGACACATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* * * * *
1809581 TATAGCTCAAGGCGAGAAGGGATATCTGGCAACAAAAGACCTTCGAGTTCAATTACACTCATCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1809646 AAAGGCACATCATTTGCAG
66 AAAGGCACATCATTTGCAG
* *
1809665 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGATTTCGATTAAACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
1809730 AAAGGCACATCCAATTTACAA
66 AAAGGCACAT-C-ATTTGCAG
* * *** * * * *
1809751 CAT-GTCTCAAGGCAAGAAGAGCTATCTGTTGAC-AAATACCTTCGAGTTCAATTCCATTCAGCT
1 CATAG-CTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCT
*
1809814 CAAGGGCA
65 CAAAGGCA
1809822 TGTCAAATTC
Statistics
Matches: 808, Mismatches: 101, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
83 28 0.03
84 715 0.88
85 33 0.04
86 32 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (84 bp):
CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTGCAG
Found at i:1811049 original size:20 final size:18
Alignment explanation
Indices: 1811022--1811065 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1811012 ATTTATTTTA
*
1811022 TTATTTAATGATTTTTTGT
1 TTATTTAATGA-TTATTGT
*
1811041 TTATGTTAATTATTATTGT
1 TTAT-TTAATGATTATTGT
1811060 TTATTT
1 TTATTT
1811066 CACGCATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 6 0.27
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (18 bp):
TTATTTAATGATTATTGT
Found at i:1811194 original size:20 final size:21
Alignment explanation
Indices: 1811154--1811195 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
1811144 ATTTTTTTAC
1811154 TTTATTTCATTTTTTCATTTT
1 TTTATTTCATTTTTTCATTTT
1811175 TTTATTT-ATTTTTT-ATTTT
1 TTTATTTCATTTTTTCATTTT
1811194 TT
1 TT
1811196 ATATCTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 7 0.33
21 7 0.33
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTATTTCATTTTTTCATTTT
Found at i:1811194 original size:26 final size:26
Alignment explanation
Indices: 1811130--1811209 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
1811120 ATTTAACCTT
*
1811130 TTTTGTTATTATTCATTTTTTTACTTTA
1 TTTT-TTATTTTTCATTTTTTTA-TTTA
**
1811158 TTTCAT-TTTTTCATTTTTTTATTTA
1 TTTTTTATTTTTCATTTTTTTATTTA
* * *
1811183 TTTTTTATTTTTTATATCTTTATTTA
1 TTTTTTATTTTTCATTTTTTTATTTA
1811209 T
1 T
1811210 CCATGTTCTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
25 8 0.19
26 31 0.72
27 1 0.02
28 3 0.07
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.75
Consensus pattern (26 bp):
TTTTTTATTTTTCATTTTTTTATTTA
Found at i:1813153 original size:12 final size:12
Alignment explanation
Indices: 1813136--1813169 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1813126 TAGTTTATAA
1813136 ATTATTATTTAT
1 ATTATTATTTAT
1813148 ATTATTATTTA-
1 ATTATTATTTAT
1813159 ATTATT-TTTAT
1 ATTATTATTTAT
1813170 TCAACTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTATTATTTAT
Found at i:1815197 original size:6 final size:6
Alignment explanation
Indices: 1815188--1815216 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1815178 TTTTTCCGGT
1815188 TCTGTC TCTGTC TCTGTC TCTGTC TCTGT
1 TCTGTC TCTGTC TCTGTC TCTGTC TCTGT
1815217 TCGCAGGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.17, T:0.52
Consensus pattern (6 bp):
TCTGTC
Found at i:1815656 original size:3 final size:3
Alignment explanation
Indices: 1815648--1815731 Score: 100
Period size: 3 Copynumber: 27.7 Consensus size: 3
1815638 TTTAAATATT
*
1815648 TAA TAA TAAA TAA TAA TATA TAA -AA -AA TAA TAA TAA TAA TAT TAA
1 TAA TAA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1815693 TAA TGA TAA TAA TAA TAT TAA TAA TATA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA
1815732 TGGATAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 4 0.06
3 58 0.82
4 9 0.13
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1816083 original size:116 final size:116
Alignment explanation
Indices: 1815881--1816398 Score: 758
Period size: 116 Copynumber: 4.4 Consensus size: 116
1815871 TTCTCCAGAT
* ** *
1815881 GAGTTCTTCTCATTACGAACTTTCTGCTGGGGATGATGTTCCATCAAATGATGAATTCAAGCAAG
1 GAGTTCTTCTCATTATGAACTTTCT-CTGGAAATGATGATCCATCAAATGATGAATTCAAGC-A-
1815946 AAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
63 AAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
1816000 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATTATGATCCATCAAGTGATGAATTCAAGCAAAA
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAAAA
*
1816065 GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 GATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* * ** *
1816116 GAGTTCTTCTCATTATGAACTCTTTCTCTGGAAATGATGATCCATCAAGTGATGGATTTGAGCTA
1 GAGTTCTTCTCATTATGAA--CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAA
1816181 AAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
64 AAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
1816234 GAGTTCTTCTCATTATGAACTCTAC-CTGGTAAA-GTTGATCCATCAAATGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACT-TTCTCTGG-AAATGATGATCCATCAAATGATGAATTCAAGCAA
1816297 AAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---
64 AAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* ** * * *
1816347 GAGTTCTTCTCATTATGAACTCTAACTGGAAAAGATGATCCACCAGATGATG
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATG
1816399 GATTTGAGTC
Statistics
Matches: 367, Mismatches: 26, Indels: 18
0.89 0.06 0.04
Matches are distributed among these distances:
112 3 0.01
113 41 0.11
116 152 0.41
117 6 0.02
118 141 0.38
119 24 0.07
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (116 bp):
GAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAAAA
GATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:1817090 original size:47 final size:49
Alignment explanation
Indices: 1817020--1817124 Score: 137
Period size: 52 Copynumber: 2.1 Consensus size: 49
1817010 TCTAAATTCA
*
1817020 ATGCT-TGATTCTGTCCAA--TCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGATTCTGTCCAACCACAGATAACTCAAAGAACACTTCC-GAAG
1817067 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCGAAG
1 ATGCTATGATTCTGTCCAACC--A-CAGATAACTCAAAGAACACTTCCGAAG
1817118 ATGCTAT
1 ATGCTAT
1817125 TGGCATATTC
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
47 15 0.29
48 2 0.04
51 11 0.22
52 23 0.45
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (49 bp):
ATGCTATGATTCTGTCCAACCACAGATAACTCAAAGAACACTTCCGAAG
Found at i:1818287 original size:16 final size:14
Alignment explanation
Indices: 1818279--1818342 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
1818269 TTTTCTATTA
1818279 TTTTTTTTTCTTCTTC
1 TTTTTTTTT-TT-TTC
*
1818295 TTTTTTTTTTTTCCC
1 TTTTTTTTTTTT-TC
*
1818310 TTTCTTTTTTTTTC
1 TTTTTTTTTTTTTC
*
1818324 TTTCTTTTTTTTTC
1 TTTTTTTTTTTTTC
1818338 TTTTT
1 TTTTT
1818343 CTCTTCTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
14 20 0.47
15 14 0.33
16 9 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:1818287 original size:21 final size:19
Alignment explanation
Indices: 1818263--1818359 Score: 97
Period size: 19 Copynumber: 4.8 Consensus size: 19
1818253 ACCTTGACCC
1818263 TTTTCTTTTTCTATTATTTTT
1 TTTTCTTTTTCT-TT-TTTTT
*
1818284 TTTTCTTCTTCTTTTTTTT
1 TTTTCTTTTTCTTTTTTTT
**
1818303 TTTTCCCTTTCTTTTTTTT
1 TTTTCTTTTTCTTTTTTTT
1818322 TCTTTCTTTTT-TTTTCTTTT
1 T-TTTCTTTTTCTTTT-TTTT
1818342 TCTCTTCTTCTTTCTTTT
1 T-T-TTCTT-TTTCTTTT
1818360 CTTCAAGCAT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
19 26 0.40
20 16 0.25
21 16 0.25
22 3 0.05
23 4 0.06
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTTCTTTTTTTT
Found at i:1818298 original size:14 final size:14
Alignment explanation
Indices: 1818284--1818359 Score: 66
Period size: 14 Copynumber: 5.3 Consensus size: 14
1818274 TATTATTTTT
1818284 TTTTCTTCTTCTTT-
1 TTTT-TTCTTCTTTC
*
1818298 TTTTTTTTTCCCTTTC
1 TTTTTTCTT--CTTTC
*
1818314 TTTTTTTTTCTTTC
1 TTTTTTCTTCTTTC
*
1818328 TTTTTTTTTCTTT-
1 TTTTTTCTTCTTTC
*
1818341 TTCTCTTCTTCTTTC
1 TT-TTTTCTTCTTTC
1818356 TTTT
1 TTTT
1818360 CTTCAAGCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 6 0.11
14 32 0.60
15 6 0.11
16 9 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTCTTTC
Found at i:1818319 original size:36 final size:34
Alignment explanation
Indices: 1818263--1818363 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 34
1818253 ACCTTGACCC
** *
1818263 TTTTCTTTTTCTATTATTTTTTTTTCTTCTTCTTT
1 TTTTCTTTTTCCCTTCTTTTTTTTTCTTCTT-TTT
1818298 TTTT-TTTTTCCCTTTCTTTTTTTTTCTTTCTTTTT
1 TTTTCTTTTTCCC-TTCTTTTTTTTTC-TTCTTTTT
*
1818333 TTTTCTTTTTCTCTTCTTCTTTCTTTTCTTC
1 TTTTCTTTTTCCCTTCTT-TTT-TTTTCTTC
1818364 AAGCATAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
34 6 0.11
35 28 0.49
36 18 0.32
37 5 0.09
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (34 bp):
TTTTCTTTTTCCCTTCTTTTTTTTTCTTCTTTTT
Found at i:1818347 original size:18 final size:17
Alignment explanation
Indices: 1818279--1818361 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 17
1818269 TTTTCTATTA
1818279 TTTTTTTTTCTTCTTCTTT
1 TTTTTTTTTC-TCTT-TTT
*
1818298 TTTTTTTTTCCCTTTCTT
1 TTTTTTTTTCTCTTT-TT
1818316 TTTTTTTCTT-TCTTTTT
1 TTTTTTT-TTCTCTTTTT
*
1818333 TTTTCTTTTTCTCTTCTT
1 TTTT-TTTTTCTCTTTTT
* *
1818351 CTTTCTTTTCT
1 TTTTTTTTTCT
1818362 TCAAGCATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 15 0.27
18 28 0.51
19 12 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTTTCTCTTTTT
Found at i:1818359 original size:24 final size:24
Alignment explanation
Indices: 1818310--1818359 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1818300 TTTTTTTCCC
* *
1818310 TTTCTTTTTTTTTCTTTCTTTTTT
1 TTTCTTTTTTCTTCTTTCTTTCTT
1818334 TTTCTTTTTCTCTTC-TTCTTTCTT
1 TTTCTTTTT-TCTTCTTTCTTTCTT
1818358 TT
1 TT
1818360 CTTCAAGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTCTTTCTT
Found at i:1829685 original size:24 final size:22
Alignment explanation
Indices: 1829653--1829701 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1829643 TTACTATTAT
* *
1829653 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
1829677 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
1829699 ATA
1 ATA
1829702 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:1830613 original size:21 final size:21
Alignment explanation
Indices: 1830574--1830613 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1830564 GTTGGTATTA
**
1830574 GTTTGTTTTTTTCTTTTCTCT
1 GTTTGTTTTTTTCGGTTCTCT
*
1830595 GTTTTTTTTTTTCGGTTCT
1 GTTTGTTTTTTTCGGTTCT
1830614 ATCTCTGTCT
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:0.00, C:0.12, G:0.12, T:0.75
Consensus pattern (21 bp):
GTTTGTTTTTTTCGGTTCTCT
Found at i:1831107 original size:3 final size:3
Alignment explanation
Indices: 1831099--1831154 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1831089 TAATATAAAT
1831099 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1831147 TAA TAA TA
1 TAA TAA TA
1831155 TGGATAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1836797 original size:20 final size:20
Alignment explanation
Indices: 1836772--1836821 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1836762 AATCAAAATA
1836772 ATCGCAACGTGATTCTGACT
1 ATCGCAACGTGATTCTGACT
*
1836792 ATCGCAACGCGATTCTGACT
1 ATCGCAACGTGATTCTGACT
*
1836812 GTCGCAACGT
1 ATCGCAACGT
1836822 TGAATTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (20 bp):
ATCGCAACGTGATTCTGACT
Found at i:1837667 original size:24 final size:24
Alignment explanation
Indices: 1837640--1837693 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1837630 GTATTCGAAA
1837640 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
1837664 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1837688 TTTGAT
1 TTTGAT
1837694 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1840286 original size:140 final size:140
Alignment explanation
Indices: 1840034--1840316 Score: 548
Period size: 140 Copynumber: 2.0 Consensus size: 140
1840024 GCAAACGTTG
1840034 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1840099 TTGAACATTGCTATAATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATAATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1840164 CGAATTTGAC
131 CGAATTTGAC
1840174 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1840239 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATAATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
1840304 GGAATTTGAC
131 CGAATTTGAC
1840314 TAT
1 TAT
1840317 CGCAACTCAA
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATAATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:1840312 original size:20 final size:20
Alignment explanation
Indices: 1840287--1840455 Score: 215
Period size: 20 Copynumber: 8.8 Consensus size: 20
1840277 TTACACATTC
* *
1840287 ATTTGAATATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1840307 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
1840326 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1840341 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1840361 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1840381 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1840401 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1840421 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
1840441 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
1840456 TGAGAAAATC
Statistics
Matches: 129, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
14 9 0.07
15 3 0.02
19 3 0.02
20 114 0.88
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1840559 original size:20 final size:20
Alignment explanation
Indices: 1840499--1840573 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1840489 ACGCGAATTA
*
1840499 ACTTTCGCGTTGCGATTTTG
1 ACTTTCGCATTGCGATTTTG
* *
1840519 GCTTTCGCATTGCAATTTTG
1 ACTTTCGCATTGCGATTTTG
1840539 ACTTTCGCATTGCGATTTTG
1 ACTTTCGCATTGCGATTTTG
* * *
1840559 AGTTTAGCGTTGCGA
1 ACTTTCGCATTGCGA
1840574 AAGTGTACCT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
ACTTTCGCATTGCGATTTTG
Found at i:1840689 original size:36 final size:36
Alignment explanation
Indices: 1840648--1840777 Score: 118
Period size: 36 Copynumber: 3.4 Consensus size: 36
1840638 TTACATTTCA
* *
1840648 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAAAAATCACAAATAAGAATTATTTACAC
** * * *
1840684 ATCAATTAAACAAATCAACTTTTACAAGTCAACT-TTTACAA
1 ATCAATTAAA-AAATC-AC--AAATAAG--AATTATTTACAC
*
1840725 ATCAATTAAACAATCACAAATAAGAATTATTTACAC
1 ATCAATTAAAAAATCACAAATAAGAATTATTTACAC
1840761 ATCAATTAAACAAATCA
1 ATCAATTAAA-AAATCA
1840778 ACTTTTACAA
Statistics
Matches: 72, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
35 3 0.04
36 26 0.36
37 12 0.17
38 2 0.03
39 2 0.03
40 8 0.11
41 16 0.22
42 3 0.04
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (36 bp):
ATCAATTAAAAAATCACAAATAAGAATTATTTACAC
Found at i:1840709 original size:27 final size:26
Alignment explanation
Indices: 1840677--1840800 Score: 87
Period size: 27 Copynumber: 4.7 Consensus size: 26
1840667 ATAAGAATTA
1840677 TTTACACATCAATTAAACAAATCAACT
1 TTTACA-ATCAATTAAACAAATCAACT
**
1840704 TTTACAAGTCAACTTTTACAAATCAA-T
1 TTTACAA-TCAA-TTAAACAAATCAACT
** * * * *
1840731 TAAACAATC-A-CAAA-TAA-GAATT
1 TTTACAATCAATTAAACAAATCAACT
1840753 ATTTACACATCAATTAAACAAATCAACT
1 -TTTACA-ATCAATTAAACAAATCAACT
1840781 TTTACAAATCAATTAAACAA
1 TTTAC-AATCAATTAAACAA
1840801 GCAAAAAATG
Statistics
Matches: 72, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
21 2 0.03
22 3 0.04
23 5 0.07
24 3 0.04
25 2 0.03
26 6 0.08
27 36 0.50
28 15 0.21
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.30
Consensus pattern (26 bp):
TTTACAATCAATTAAACAAATCAACT
Found at i:1840715 original size:14 final size:14
Alignment explanation
Indices: 1840693--1840729 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1840683 CATCAATTAA
1840693 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1840707 ACAAGTCAACTTTT
1 ACAAATCAACTTTT
1840721 ACAAATCAA
1 ACAAATCAA
1840730 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1840722 original size:41 final size:42
Alignment explanation
Indices: 1840675--1840792 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 42
1840665 AAATAAGAAT
1840675 TATTTACACATCAATTAAACAAATCAACTTTTACAAGTCAAC
1 TATTTACACATCAATTAAACAAATCAACTTTTACAAGTCAAC
* ** * *
1840717 T-TTTACAAATCAATTAAAC-AATC-AC--AAATAAG--AAT
1 TATTTACACATCAATTAAACAAATCAACTTTTACAAGTCAAC
*
1840752 TATTTACACATCAATTAAACAAATCAACTTTTACAAATCAA
1 TATTTACACATCAATTAAACAAATCAACTTTTACAAGTCAA
1840793 TTAAACAAGC
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
35 3 0.05
36 17 0.29
37 8 0.14
38 2 0.03
39 2 0.03
40 7 0.12
41 17 0.29
42 3 0.05
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.31
Consensus pattern (42 bp):
TATTTACACATCAATTAAACAAATCAACTTTTACAAGTCAAC
Found at i:1840744 original size:77 final size:77
Alignment explanation
Indices: 1840626--1840792 Score: 271
Period size: 77 Copynumber: 2.1 Consensus size: 77
1840616 ATTGAAATCA
*
1840626 ACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAATT
1 ACAAATCAACTTTTACA----AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATT
1840691 AAACAAATCAACTTTT
62 AAACAAATCAACTTTT
* *
1840707 ACAAGTCAACTTTTACAAATCAATTAAACAATCACAAATAAGAATTATTTACACATCAATTAAAC
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAAC
1840772 AAATCAACTTTT
66 AAATCAACTTTT
1840784 ACAAATCAA
1 ACAAATCAA
1840793 TTAAACAAGC
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
77 66 0.80
81 16 0.20
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (77 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAAC
AAATCAACTTTT
Found at i:1840785 original size:63 final size:66
Alignment explanation
Indices: 1840707--1840879 Score: 201
Period size: 63 Copynumber: 2.6 Consensus size: 66
1840697 ATCAACTTTT
* *
1840707 ACAAGTCAACTTTTACAAATCAATTAAACAATCACAAA-TAAGAA-TTA-TTTACACATCAATTA
1 ACAAATCAACTTTTACAAATCAATTAAACAATCAAAAACTAAGAATTTATTTTACACATCAATTA
1840769 A
66 A
* * * *
1840770 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATGCTAATAATTCTTATTTTCCTCATC
1 ACAAATCAACTTTTACAAATCAATTAAACAATC-AAAAA--CTAAGAA-T-TTATTTTACACATC
1840835 AATTAA
61 AATTAA
1840841 ACAAATCAGACTTTTA-AGAATCAATTAAACAATCAAAAA
1 ACAAATCA-ACTTTTACA-AATCAATTAAACAATCAAAAA
1840880 AAGTGTACCC
Statistics
Matches: 93, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
63 31 0.33
64 4 0.04
67 5 0.05
70 3 0.03
71 28 0.30
72 22 0.24
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.29
Consensus pattern (66 bp):
ACAAATCAACTTTTACAAATCAATTAAACAATCAAAAACTAAGAATTTATTTTACACATCAATTA
A
Found at i:1842227 original size:21 final size:21
Alignment explanation
Indices: 1842203--1842296 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 21
1842193 GGACCTTTTC
1842203 AACGATGACAGGGGCCTCTTG
1 AACGATGACAGGGGCCTCTTG
* *
1842224 AACGGTAGA-AGGGGACTCTTG
1 AACGAT-GACAGGGGCCTCTTG
** * *
1842245 AGGGATGATAGGGGCATCTTG
1 AACGATGACAGGGGCCTCTTG
* * *
1842266 AACGAT-AGGAGAGGCCTTTTG
1 AACGATGA-CAGGGGCCTCTTG
1842287 AACGATGACA
1 AACGATGACA
1842297 TGTGAGTCGG
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
20 3 0.05
21 49 0.89
22 3 0.05
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.20
Consensus pattern (21 bp):
AACGATGACAGGGGCCTCTTG
Found at i:1842294 original size:42 final size:42
Alignment explanation
Indices: 1842196--1842296 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
1842186 GTGGGAGGGA
* * * *
1842196 CCTTTTCAACGATGACAGGGGCCTCTTGAACGGTAGAAGGGG
1 CCTTTTGAACGATGACAGGGGCATCTTGAACGATAGAAGAGG
* * ** * *
1842238 ACTCTTGAGGGATGATAGGGGCATCTTGAACGATAGGAGAGG
1 CCTTTTGAACGATGACAGGGGCATCTTGAACGATAGAAGAGG
1842280 CCTTTTGAACGATGACA
1 CCTTTTGAACGATGACA
1842297 TGTGAGTCGG
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.23
Consensus pattern (42 bp):
CCTTTTGAACGATGACAGGGGCATCTTGAACGATAGAAGAGG
Found at i:1843120 original size:21 final size:21
Alignment explanation
Indices: 1843093--1843145 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1843083 TGCACCATTG
*
1843093 TCATCACGTAAAGTACTGACC
1 TCATCACGTAAAGCACTGACC
* * * *
1843114 TCCTCACGCAAGGCATTGACC
1 TCATCACGTAAAGCACTGACC
1843135 TCATCACGTAA
1 TCATCACGTAA
1843146 CTCCCATAAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (21 bp):
TCATCACGTAAAGCACTGACC
Found at i:1844792 original size:73 final size:74
Alignment explanation
Indices: 1844672--1844809 Score: 233
Period size: 73 Copynumber: 1.9 Consensus size: 74
1844662 CGAAACTTAA
*
1844672 AATCGCAACACGAAAATGAAAATCACAACACAAAAATGACTATCGCAACGCAAATTTGACTATCG
1 AATCGCAACACGAAAATGAAAATCACAACACAAAAATGACTATCGCAACACAAATTTGACTATCG
1844737 CAACGAGAT
66 CAACGAGAT
* * *
1844746 AATCGCAACGCG-AAATGAAAATCGCAACACAAAAATGACTATCGCAACATAAATTTGACTATCG
1 AATCGCAACACGAAAATGAAAATCACAACACAAAAATGACTATCGCAACACAAATTTGACTATCG
1844810 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
73 49 0.82
74 11 0.18
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.17
Consensus pattern (74 bp):
AATCGCAACACGAAAATGAAAATCACAACACAAAAATGACTATCGCAACACAAATTTGACTATCG
CAACGAGAT
Found at i:1844804 original size:20 final size:20
Alignment explanation
Indices: 1844673--1844809 Score: 81
Period size: 20 Copynumber: 7.2 Consensus size: 20
1844663 GAAACTTAAA
* **
1844673 ATCGCAACACGAAAATGAAA
1 ATCGCAACACAAAAATGACT
*
1844693 ATCACAACACAAAAATGACT
1 ATCGCAACACAAAAATGACT
* **
1844713 ATCGCAACGCAAATTTGACT
1 ATCGCAACACAAAAATGACT
* *
1844733 ATCGC-A-AC-GAGAT-A--
1 ATCGCAACACAAAAATGACT
* * **
1844747 ATCGCAACGC-GAAATGAAA
1 ATCGCAACACAAAAATGACT
1844766 ATCGCAACACAAAAATGACT
1 ATCGCAACACAAAAATGACT
* **
1844786 ATCGCAACATAAATTTGACT
1 ATCGCAACACAAAAATGACT
1844806 ATCG
1 ATCG
1844810 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
14 5 0.06
15 1 0.01
16 6 0.07
17 3 0.03
18 1 0.01
19 10 0.11
20 64 0.71
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.18
Consensus pattern (20 bp):
ATCGCAACACAAAAATGACT
Found at i:1845202 original size:20 final size:21
Alignment explanation
Indices: 1845177--1845241 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
1845167 TCTGAGAGAT
1845177 GGAGAT-AGACGGATTTCGTC
1 GGAGATGAGACGGATTTCGTC
*
1845197 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGTC
* * *
1845219 AGAGATGGGGACGGATGTCGTC
1 GGAGAT-GAGACGGATTTCGTC
1845241 G
1 G
1845242 TAGAGAGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.15
22 33 0.85
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGTC
Found at i:1845211 original size:22 final size:22
Alignment explanation
Indices: 1845184--1845241 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1845174 GATGGAGATA
1845184 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
1845206 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
1845228 GACGGATGTCGTCG
1 GACGGATTTCGTCG
1845242 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.19, C:0.16, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1845432 original size:20 final size:20
Alignment explanation
Indices: 1845409--1845452 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1845399 TATCGCAACA
*
1845409 CGATAGTCAGAATCGCGTTG
1 CGATAGTAAGAATCGCGTTG
1845429 CGATAGTAAGAATCGCGTTG
1 CGATAGTAAGAATCGCGTTG
1845449 CGAT
1 CGAT
1845453 TTACATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (20 bp):
CGATAGTAAGAATCGCGTTG
Found at i:1845541 original size:19 final size:19
Alignment explanation
Indices: 1845517--1845553 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1845507 TGCGATACTG
* *
1845517 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
1845536 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
1845554 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:1845911 original size:24 final size:25
Alignment explanation
Indices: 1845884--1845930 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1845874 ACTAAACATG
1845884 TATTCAAC-CATT-AATATATTTTTA
1 TATT-AACTCATTAAATATATTTTTA
*
1845908 TATTAACTTATTAAATATATTTT
1 TATTAACTCATTAAATATATTTT
1845931 ATTACTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 7 0.35
25 10 0.50
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTAACTCATTAAATATATTTTTA
Found at i:1845939 original size:25 final size:27
Alignment explanation
Indices: 1845896--1845961 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 27
1845886 TTCAACCATT
*
1845896 AATATATTTT-TATATTAACTT-A-TTA
1 AATATATTTTAT-TACTAACTTAATTTA
1845921 AATATATTTTATTACTAACTTAATTTA
1 AATATATTTTATTACTAACTTAATTTA
*
1845948 AAAATATCTTTATT
1 AATATAT-TTTATT
1845962 TTTATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 18 0.51
26 2 0.06
27 9 0.26
28 6 0.17
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (27 bp):
AATATATTTTATTACTAACTTAATTTA
Found at i:1846149 original size:31 final size:31
Alignment explanation
Indices: 1846114--1846184 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1846104 CCGTGATAAT
*
1846114 CATATCTTAATTAAATAAAAACGAAAGTGAC
1 CATATCTTAATTAAATAAAAACAAAAGTGAC
* * *
1846145 CATATATTAATTAAATAAAAATAAAAGTGAT
1 CATATCTTAATTAAATAAAAACAAAAGTGAC
1846176 CATATCTTA
1 CATATCTTA
1846185 TGTTTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (31 bp):
CATATCTTAATTAAATAAAAACAAAAGTGAC
Found at i:1849535 original size:48 final size:48
Alignment explanation
Indices: 1849479--1849589 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 48
1849469 AAATATTTTA
1849479 TCTGATTTCCGACT-TGAATTCTGTTATGATATATGACCTGAATTCTGT
1 TCTGATTTCCGA-TATGAATTCTGTTATGATATATGACCTGAATTCTGT
** * * * **
1849527 TCTGATTTCTTATATGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATATGAATTCTGTTATGATATATGACCTGAATTCTGT
* * *
1849575 TTTAATTTCTGATAT
1 TCTGATTTCCGATAT
1849590 CTCCGTTTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 51 0.98
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (48 bp):
TCTGATTTCCGATATGAATTCTGTTATGATATATGACCTGAATTCTGT
Found at i:1849536 original size:12 final size:12
Alignment explanation
Indices: 1849516--1849585 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1849506 GATATATGAC
*
1849516 CTGAATTCTGTT
1 CTGATTTCTGTT
1849528 CTGATTTCT-TAT
1 CTGATTTCTGT-T
*
1849540 ATGGA-TTCTGTT
1 CT-GATTTCTGTT
*
1849552 CTGATATCTGTT
1 CTGATTTCTGTT
*
1849564 CTGAATTCTGTT
1 CTGATTTCTGTT
* *
1849576 TTAATTTCTG
1 CTGATTTCTG
1849586 ATATCTCCGT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 3 0.07
12 39 0.87
13 3 0.07
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.53
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:1849585 original size:24 final size:25
Alignment explanation
Indices: 1849493--1849591 Score: 87
Period size: 24 Copynumber: 4.0 Consensus size: 25
1849483 ATTTCCGACT
* * * *
1849493 TGAATTCTGTTATGATATATG-ACC
1 TGAATTCTGTTCTGATTTCTGTATC
*
1849517 TGAATTCTGTTCTGATTTCT-TATA
1 TGAATTCTGTTCTGATTTCTGTATC
* *
1849541 TGGATTCTGTTCTGATATCTGT-TC
1 TGAATTCTGTTCTGATTTCTGTATC
* *
1849565 TGAATTCTGTTTTAATTTCTGATATC
1 TGAATTCTGTTCTGATTTCTG-TATC
1849591 T
1 T
1849592 CCGTTTAACG
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
24 54 0.92
25 2 0.03
26 3 0.05
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (25 bp):
TGAATTCTGTTCTGATTTCTGTATC
Found at i:1849754 original size:2 final size:2
Alignment explanation
Indices: 1849747--1849775 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1849737 GGGATGGGGG
1849747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1849776 GTTTTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1851700 original size:18 final size:18
Alignment explanation
Indices: 1851679--1851720 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1851669 ACCCATTTTT
1851679 CTGACCCGACCCGTTCAC
1 CTGACCCGACCCGTTCAC
* *
1851697 CTGACCCGACCTGTTGAC
1 CTGACCCGACCCGTTCAC
1851715 C-GACCC
1 CTGACCC
1851721 ATTGACCGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.17, C:0.48, G:0.19, T:0.17
Consensus pattern (18 bp):
CTGACCCGACCCGTTCAC
Found at i:1854255 original size:48 final size:48
Alignment explanation
Indices: 1854199--1854309 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
1854189 AAATATTTTA
1854199 TCTGATTTCCGACT-TGAATTCTGTTATGATATATGACCAGAATTCTGT
1 TCTGATTTCCGA-TATGAATTCTGTTATGATATATGACCAGAATTCTGT
* * * * ** *
1854247 TCTGATTTCTGATATGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATATGAATTCTGTTATGATATATGACCAGAATTCTGT
* *
1854295 TTTGATTTCTGATAT
1 TCTGATTTCCGATAT
1854310 CTCCGTTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
47 1 0.02
48 53 0.98
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCGATATGAATTCTGTTATGATATATGACCAGAATTCTGT
Found at i:1854267 original size:24 final size:24
Alignment explanation
Indices: 1854199--1854309 Score: 100
Period size: 24 Copynumber: 4.6 Consensus size: 24
1854189 AAATATTTTA
*
1854199 TCTGATTTCCGACT-TGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGT
* * * *
1854223 TATGATATATGACCA-GAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGT
*
1854247 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * *
1854271 TCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
1854295 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
1854310 CTCCGTTTAA
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
23 1 0.01
24 66 0.99
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:1854281 original size:12 final size:12
Alignment explanation
Indices: 1854242--1854305 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
1854232 TGACCAGAAT
*
1854242 TCTGTTCTGATT
1 TCTGTTCTGATA
* *
1854254 TCTGATATGGAT-
1 TCTGTTCT-GATA
1854266 TCTGTTCTGATA
1 TCTGTTCTGATA
1854278 TCTGTTCTGA-A
1 TCTGTTCTGATA
* *
1854289 TTCTGTTTTGATT
1 -TCTGTTCTGATA
1854302 TCTG
1 TCTG
1854306 ATATCTCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 4 0.10
12 35 0.83
13 3 0.07
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (12 bp):
TCTGTTCTGATA
Found at i:1854285 original size:17 final size:18
Alignment explanation
Indices: 1854242--1854293 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
1854232 TGACCAGAAT
1854242 TCTGTTCTGATTTCTGATA
1 TCTGTTCTGA-TTCTGATA
*
1854261 T-GGATTCTG-TTCTGATA
1 TCTG-TTCTGATTCTGATA
1854278 TCTGTTCTGAATTCTG
1 TCTGTTCTG-ATTCTG
1854294 TTTTGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 11 0.41
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.50
Consensus pattern (18 bp):
TCTGTTCTGATTCTGATA
Found at i:1854474 original size:2 final size:2
Alignment explanation
Indices: 1854467--1854499 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1854457 GGGATGGGGG
1854467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1854500 GTTTTAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1863392 original size:21 final size:21
Alignment explanation
Indices: 1863366--1863405 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1863356 TTACATAGTA
*
1863366 AAAGGATCGATCCCTTTGACC
1 AAAGGATCGATCCCCTTGACC
1863387 AAAGGATCGATCCCCTTGA
1 AAAGGATCGATCCCCTTGA
1863406 AAACATATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (21 bp):
AAAGGATCGATCCCCTTGACC
Found at i:1863463 original size:20 final size:21
Alignment explanation
Indices: 1863440--1863493 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1863430 AGTGACTTTG
* *
1863440 GGATCGATCTCTTGACAAAA-
1 GGATCGATCCCTTCACAAAAT
* *
1863460 GGATCAATCCCTTCCCAAAAT
1 GGATCGATCCCTTCACAAAAT
1863481 GGATCGATCCCTT
1 GGATCGATCCCTT
1863494 TGGTATAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (21 bp):
GGATCGATCCCTTCACAAAAT
Found at i:1863485 original size:21 final size:20
Alignment explanation
Indices: 1863455--1863493 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1863445 GATCTCTTGA
1863455 CAAAAGGATCAATCCCTTCC
1 CAAAAGGATCAATCCCTTCC
*
1863475 CAAAATGGATCGATCCCTT
1 CAAAA-GGATCAATCCCTT
1863494 TGGTATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.23
Consensus pattern (20 bp):
CAAAAGGATCAATCCCTTCC
Found at i:1865141 original size:18 final size:18
Alignment explanation
Indices: 1865120--1865201 Score: 139
Period size: 18 Copynumber: 4.6 Consensus size: 18
1865110 ATTTGTCCCA
1865120 AAGGACCACTATGTCCTG
1 AAGGACCACTATGTCCTG
1865138 AAGGACCACTATGTCCTG
1 AAGGACCACTATGTCCTG
*
1865156 AAGGACCACTATGTCCCG
1 AAGGACCACTATGTCCTG
1865174 AAGGACCACTATGT-CTCG
1 AAGGACCACTATGTCCT-G
1865192 AAGGACCACT
1 AAGGACCACT
1865202 GATAATCCCT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
17 1 0.02
18 60 0.98
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (18 bp):
AAGGACCACTATGTCCTG
Found at i:1866021 original size:21 final size:21
Alignment explanation
Indices: 1865997--1866052 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1865987 TATTTGAGAG
1865997 TGCATCGATACACATTGAAGA
1 TGCATCGATACACATTGAAGA
1866018 TGCATCGATACACATTGAAGA
1 TGCATCGATACACATTGAAGA
*
1866039 TGCATCGATGCACA
1 TGCATCGATACACA
1866053 CAACCCAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (21 bp):
TGCATCGATACACATTGAAGA
Found at i:1867378 original size:20 final size:20
Alignment explanation
Indices: 1867339--1867378 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1867329 ATAACTTTAA
**
1867339 GGTGTATCGATACATTCAGG
1 GGTGTATCGATACACACAGG
1867359 GGTGTATCGATACACACAGG
1 GGTGTATCGATACACACAGG
1867379 AAGGCATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (20 bp):
GGTGTATCGATACACACAGG
Found at i:1868549 original size:21 final size:21
Alignment explanation
Indices: 1868523--1868566 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1868513 TGATGAAATT
*
1868523 ACTGTAGCAGTGCATCGATAC
1 ACTGTAGCAATGCATCGATAC
1868544 ACTGTAGCAATGCATCGATAC
1 ACTGTAGCAATGCATCGATAC
1868565 AC
1 AC
1868567 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAATGCATCGATAC
Found at i:1869636 original size:21 final size:21
Alignment explanation
Indices: 1869612--1869656 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1869602 AAGAGAGAAG
1869612 AAATAATTTCAACTCAATGCT
1 AAATAATTTCAACTCAATGCT
1869633 AAATAATTTCAACTCAATGCT
1 AAATAATTTCAACTCAATGCT
1869654 AAA
1 AAA
1869657 GTCATGCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (21 bp):
AAATAATTTCAACTCAATGCT
Found at i:1874293 original size:230 final size:230
Alignment explanation
Indices: 1873891--1874965 Score: 1700
Period size: 230 Copynumber: 4.7 Consensus size: 230
1873881 CTTTGTATTC
* * *
1873891 TTTTATCAAACTATCTTAAAGTTGGTGTTG-CC-CGTGTAAAATGTGGAATAGACATTTTGTCGG
1 TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACA-TTTGTTGG
* * * *
1873954 GGAGGCAGCTTTGCCGAGGTGATCATTTTCTTGCGATCTTCTCTTTTCCATGTTGCCAATATTTT
65 TGAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTT
*
1874019 AGTTGGTCATGCTAGGCTGCATTAGGGTGATGCATCTTTTTCTGGATTATACCTATTGCCTAAGT
130 AGTTGGTCATGCTAGGCTGCATTAGGGTGATACATCTTTTTCTGGATTATACCTATTGCCTAAGT
1874084 GGACCTACATGTTCTTTAAAACTACCTTATGATTGT
195 GGACCTACATGTTCTTTAAAACTACCTTATGATTGT
*
1874120 TTTTATCAAACTACCTTAAGGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGT
1 TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGT
1874185 GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
66 GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
*
1874250 GTTGGTCATGCTAGGCTGCGTTAGGGTGATACATCTTTTTCTGGATTATACCTATTGCCTAAGTG
131 GTTGGTCATGCTAGGCTGCATTAGGGTGATACATCTTTTTCTGGATTATACCTATTGCCTAAGTG
1874315 GACCTACATGTTCTTTAAAACTACCTTATGATTGT
196 GACCTACATGTTCTTTAAAACTACCTTATGATTGT
*
1874350 TTTTATCAAACTACCTTAAGGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGT
1 TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGT
1874415 GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
66 GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
* * *
1874480 GTTGGCCATGCTAGGCTGCATTAGGGTGATACATCTTTTTTTGGATTATACCTATTGCCTGAGTG
131 GTTGGTCATGCTAGGCTGCATTAGGGTGATACATCTTTTTCTGGATTATACCTATTGCCTAAGTG
*
1874545 GACCTACATGTTCTTTAATACTACCTTATGATTGT
196 GACCTACATGTTCTTTAAAACTACCTTATGATTGT
*
1874580 TTCTATCAAACTACC----------TG--G-CCTCGTGTAAGATGTGGAATAGACATTTGTTGGT
1 TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGT
1874632 GAGGCAACTTTGCCGAGGTGATCATTTTCTT-CTGATCTCCTCTTTTCCCTGTTGCCAATATTTT
66 GAGGCAACTTTGCCGAGGTGATCATTTTCTTGC-GATCTCCTCTTTTCCCTGTTGCCAATATTTT
** * * *
1874696 AGTTGGTCATGCTAGAATGCATTAGGGTGATCCATCATTTTT-TAGATGATACCTATTGCCTAAG
130 AGTTGGTCATGCTAGGCTGCATTAGGGTGATACATC-TTTTTCTGGATTATACCTATTGCCTAAG
1874760 TGGACCTACATGTTCTTTAAAACTACCTTATGATTGT
194 TGGACCTACATGTTCTTTAAAACTACCTTATGATTGT
* * * * * *
1874797 TTTTATCAAACTACCTTAAAGTTGCTGCTGCCCTTGTGTAAGATGTAGAATATACATTT-TTGGG
1 TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGT
* *
1874861 GAGGCAACTTTGCTGAGGTGATCATTTTCTTGCGATCTCCTCTTTCCCCTGTTGCCAATATTTTA
66 GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
* ** *
1874926 GTTGGTCATGCAAGGCTGTTTTACGGTGATACATCTTTTT
131 GTTGGTCATGCTAGGCTGCATTAGGGTGATACATCTTTTT
1874966 TATACCAATT
Statistics
Matches: 790, Mismatches: 38, Indels: 37
0.91 0.04 0.04
Matches are distributed among these distances:
216 1 0.00
217 197 0.25
218 6 0.01
220 2 0.00
227 2 0.00
228 5 0.01
229 122 0.15
230 434 0.55
231 21 0.03
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (230 bp):
TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGT
GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
GTTGGTCATGCTAGGCTGCATTAGGGTGATACATCTTTTTCTGGATTATACCTATTGCCTAAGTG
GACCTACATGTTCTTTAAAACTACCTTATGATTGT
Found at i:1874809 original size:447 final size:450
Alignment explanation
Indices: 1873891--1874966 Score: 1700
Period size: 447 Copynumber: 2.4 Consensus size: 450
1873881 CTTTGTATTC
* * *
1873891 TTTTATCAAACTATCTTAAAGTTGGTGTTG-CC-CGTGTAAAATGTGGAATAGACATTTTGTCGG
1 TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACA-TTTGTTGG
* * *
1873954 GGAGGCAGCTTTGCCGAGGTGATCATTTTCTTGCGATCTTCTCTTTTCCATGTTGCCAATATTTT
65 GGAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTT
* *
1874019 AGTTGGTCATGCTAGGCTGCATTAGGGTGATGCATCTTTTTCTGGATTATACCTATTGCCTAAGT
130 AGTTGGTCATGCTAGGCTGCATTAGGGTGATACATCTTTTTTTGGATTATACCTATTGCCTAAGT
*
1874084 GGACCTACATGTTCTTTAAAACTACCTTATGATTGTTTTTATCAAACTACCTTAAGGTTGGTGTT
195 GGACCTACATGTTCTTTAAAACTACCTTATGATTGTTTCTATCAAACTACC---------GTG-T
1874149 GCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGTGAGGCAACTTTGCCGAGGTGATCATTTTC
250 GCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGTGAGGCAACTTTGCCGAGGTGATCATTTTC
** *
1874214 TTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTAGTTGGTCATGCTAGGCTGCGTTAGGGTGA
315 TTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTAGTTGGTCATGCTAGAATGCATTAGGGTGA
* *
1874279 TACATCTTTTTCTGGATTATACCTATTGCCTAAGTGGACCTACATGTTCTTTAAAACTACCTTAT
380 TACATCTTTTTCTAGATGATACCTATTGCCTAAGTGGACCTACATGTTCTTTAAAACTACCTTAT
1874344 GATTGT
445 GATTGT
* *
1874350 TTTTATCAAACTACCTTAAGGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGT
1 TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGG
1874415 GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
66 GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
* *
1874480 GTTGGCCATGCTAGGCTGCATTAGGGTGATACATCTTTTTTTGGATTATACCTATTGCCTGAGTG
131 GTTGGTCATGCTAGGCTGCATTAGGGTGATACATCTTTTTTTGGATTATACCTATTGCCTAAGTG
*
1874545 GACCTACATGTTCTTTAATACTACCTTATGATTGTTTCTATCAAACTACC-TG-G-CCTCGTGTA
196 GACCTACATGTTCTTTAAAACTACCTTATGATTGTTTCTATCAAACTACCGTGTGCCCTCGTGTA
1874607 AGATGTGGAATAGACATTTGTTGGTGAGGCAACTTTGCCGAGGTGATCATTTTCTT-CTGATCTC
261 AGATGTGGAATAGACATTTGTTGGTGAGGCAACTTTGCCGAGGTGATCATTTTCTTGC-GATCTC
*
1874671 CTCTTTTCCCTGTTGCCAATATTTTAGTTGGTCATGCTAGAATGCATTAGGGTGATCCATCATTT
325 CTCTTTTCCCTGTTGCCAATATTTTAGTTGGTCATGCTAGAATGCATTAGGGTGATACATC-TTT
1874736 TT-TAGATGATACCTATTGCCTAAGTGGACCTACATGTTCTTTAAAACTACCTTATGATTGT
389 TTCTAGATGATACCTATTGCCTAAGTGGACCTACATGTTCTTTAAAACTACCTTATGATTGT
* * * * *
1874797 TTTTATCAAACTACCTTAAAGTTGCTGCTGCCCTTGTGTAAGATGTAGAATATACATTT-TTGGG
1 TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGG
* *
1874861 GAGGCAACTTTGCTGAGGTGATCATTTTCTTGCGATCTCCTCTTTCCCCTGTTGCCAATATTTTA
66 GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
* ** *
1874926 GTTGGTCATGCAAGGCTGTTTTACGGTGATACATCTTTTTT
131 GTTGGTCATGCTAGGCTGCATTAGGGTGATACATCTTTTTT
1874967 ATACCAATTG
Statistics
Matches: 579, Mismatches: 34, Indels: 21
0.91 0.05 0.03
Matches are distributed among these distances:
446 104 0.18
447 238 0.41
448 6 0.01
450 2 0.00
459 28 0.05
460 180 0.31
461 21 0.04
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (450 bp):
TTTTATCAAACTACCTTAAAGTTGGTGTTGCCCTCGTGTAAGATGTGGAATAGACATTTGTTGGG
GAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCCTCTTTTCCCTGTTGCCAATATTTTA
GTTGGTCATGCTAGGCTGCATTAGGGTGATACATCTTTTTTTGGATTATACCTATTGCCTAAGTG
GACCTACATGTTCTTTAAAACTACCTTATGATTGTTTCTATCAAACTACCGTGTGCCCTCGTGTA
AGATGTGGAATAGACATTTGTTGGTGAGGCAACTTTGCCGAGGTGATCATTTTCTTGCGATCTCC
TCTTTTCCCTGTTGCCAATATTTTAGTTGGTCATGCTAGAATGCATTAGGGTGATACATCTTTTT
CTAGATGATACCTATTGCCTAAGTGGACCTACATGTTCTTTAAAACTACCTTATGATTGT
Found at i:1878965 original size:25 final size:25
Alignment explanation
Indices: 1878903--1878965 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 25
1878893 ATTGACGCTG
*
1878903 TTATCAATCCTTA-TTTTCTAAGACAA
1 TTAT-AAT-CTTATTTTTCTAAAACAA
* *
1878929 TCT-TATTTTTATTTTTCTAAAACAA
1 T-TATAATCTTATTTTTCTAAAACAA
1878954 TTATAATCTTAT
1 TTATAATCTTAT
1878966 CTTAATGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
24 4 0.14
25 22 0.76
26 2 0.07
27 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (25 bp):
TTATAATCTTATTTTTCTAAAACAA
Found at i:1879116 original size:31 final size:31
Alignment explanation
Indices: 1879078--1879136 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1879068 ATAACACATA
1879078 CCATATATACAAAAACAATGATATAACATTG
1 CCATATATACAAAAACAATGATATAACATTG
* * *
1879109 CCATATATTCATAAGCAATGATATAACA
1 CCATATATACAAAAACAATGATATAACA
1879137 CGTCATATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (31 bp):
CCATATATACAAAAACAATGATATAACATTG
Found at i:1883087 original size:14 final size:14
Alignment explanation
Indices: 1883068--1883095 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1883058 TAACAGACTT
1883068 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1883082 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1883096 TGGTATCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:1884928 original size:51 final size:51
Alignment explanation
Indices: 1884852--1884950 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
1884842 AGGGGGAGAT
* *
1884852 TTACAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATTAG
1 TTACAAGGAATTTCAACCTGCTCAAACCGATATTTCTTTACAGCCTATTAG
1884903 TTACAAGGAATTTCAACCTGCTCAAACCGATATTTCTTTACAGCCTAT
1 TTACAAGGAATTTCAACCTGCTCAAACCGATATTTCTTTACAGCCTAT
1884951 CCTTTCCTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (51 bp):
TTACAAGGAATTTCAACCTGCTCAAACCGATATTTCTTTACAGCCTATTAG
Found at i:1887191 original size:16 final size:16
Alignment explanation
Indices: 1887170--1887200 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1887160 TAACAGACTT
1887170 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
1887186 GTCTGTTTTCTACAC
1 GTCTGTTTTCTACAC
1887201 TAACCTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.45
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:1896868 original size:12 final size:12
Alignment explanation
Indices: 1896851--1896876 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1896841 ATTATAAAGT
1896851 AATATATGTTTG
1 AATATATGTTTG
1896863 AATATATGTTTG
1 AATATATGTTTG
1896875 AA
1 AA
1896877 AGACTCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
AATATATGTTTG
Found at i:1898807 original size:24 final size:24
Alignment explanation
Indices: 1898775--1898821 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1898765 TGTTGCACTG
*
1898775 ATACAGATACGGGGATGGGGACGT
1 ATACAGATACGGGGACGGGGACGT
*
1898799 ATACGGATACGGGGACGGGGACG
1 ATACAGATACGGGGACGGGGACG
1898822 GAAAATGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.45, T:0.13
Consensus pattern (24 bp):
ATACAGATACGGGGACGGGGACGT
Found at i:1899020 original size:13 final size:13
Alignment explanation
Indices: 1899002--1899032 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1898992 AACAAAGCAT
1899002 GCGAATATAAAAG
1 GCGAATATAAAAG
1899015 GCGAATATAAAAG
1 GCGAATATAAAAG
1899028 GCGAA
1 GCGAA
1899033 AAGAGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.26, T:0.13
Consensus pattern (13 bp):
GCGAATATAAAAG
Found at i:1914381 original size:39 final size:39
Alignment explanation
Indices: 1914338--1914456 Score: 220
Period size: 39 Copynumber: 3.1 Consensus size: 39
1914328 CAAATTTAAT
*
1914338 ACGAATTATAATATAAAAAACTGCATCAGATTTTTCTAA
1 ACGAATTCTAATATAAAAAACTGCATCAGATTTTTCTAA
1914377 ACGAATTCTAATATAAAAAACTGCATCAGATTTTTCTAA
1 ACGAATTCTAATATAAAAAACTGCATCAGATTTTTCTAA
*
1914416 ACGAATTCTAATATAAAAAACTGCATCAGATTTGTCTAA
1 ACGAATTCTAATATAAAAAACTGCATCAGATTTTTCTAA
1914455 AC
1 AC
1914457 TCAAATCAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (39 bp):
ACGAATTCTAATATAAAAAACTGCATCAGATTTTTCTAA
Found at i:1917023 original size:14 final size:14
Alignment explanation
Indices: 1917004--1917062 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
1916994 GTAATTGATT
*
1917004 TTCTGAAAATTGAA
1 TTCTGAAAAATGAA
1917018 TTCTGAAAAATGAA
1 TTCTGAAAAATGAA
* * **
1917032 TTATTGGAATTTGAA
1 TT-CTGAAAAATGAA
1917047 TTCTGAAAAATGAA
1 TTCTGAAAAATGAA
1917061 TT
1 TT
1917063 ACGTTTTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 25 0.71
15 10 0.29
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.37
Consensus pattern (14 bp):
TTCTGAAAAATGAA
Found at i:1917134 original size:22 final size:22
Alignment explanation
Indices: 1917106--1917168 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
1917096 TATTAATAAT
1917106 TTAATAAATTATTTATATGAAA
1 TTAATAAATTATTTATATGAAA
* * * **
1917128 TTAATAAATAATATAAATGTTA
1 TTAATAAATTATTTATATGAAA
*
1917150 TTAATAATTTATTATATAT
1 TTAATAAATTATT-TATAT
1917169 TATTAAAATA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (22 bp):
TTAATAAATTATTTATATGAAA
Found at i:1917271 original size:30 final size:29
Alignment explanation
Indices: 1917214--1917275 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
1917204 AATATAATTG
* *
1917214 ATTATTTTATTATAATATTAAAAAAATAAT
1 ATTATATTATTAAAATATTAAAAAAAT-AT
*
1917244 ATTATATTATTAGAAATATT-AATAAATAT
1 ATTATATTATTA-AAATATTAAAAAAATAT
1917273 ATT
1 ATT
1917276 TTAAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.18
30 17 0.61
31 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
ATTATATTATTAAAATATTAAAAAAATAT
Found at i:1917556 original size:41 final size:41
Alignment explanation
Indices: 1917511--1917589 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
1917501 CACTGGAAAT
** ** *
1917511 ATTTTCCGGAAAACAAATTACGTGAAACAAATACGAAAAAA
1 ATTTTCCAAAAAACAAATTACGAAAAACAAACACGAAAAAA
* *
1917552 ATTTTCTAAAAAATAAATTACGAAAAACAAACACGAAA
1 ATTTTCCAAAAAACAAATTACGAAAAACAAACACGAAA
1917590 TTTCAGGAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20
Consensus pattern (41 bp):
ATTTTCCAAAAAACAAATTACGAAAAACAAACACGAAAAAA
Found at i:1918642 original size:3 final size:3
Alignment explanation
Indices: 1918634--1918675 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1918624 ATTTGCAATA
1918634 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1918676 AAACATATAC
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:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1918943 original size:17 final size:16
Alignment explanation
Indices: 1918923--1918963 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1918913 ATAAATATCC
1918923 TATTTTTATATATATAT
1 TATTTTTATATATA-AT
*
1918940 TA-TTTTAT-TTTAAT
1 TATTTTTATATATAAT
1918954 TATTTTTATA
1 TATTTTTATA
1918964 GAAATGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 6 0.29
17 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTATATATAAT
Found at i:1919097 original size:22 final size:22
Alignment explanation
Indices: 1919055--1919097 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1919045 ATTTCTAAGT
* * *
1919055 AAATAAATATCTTTATTTATAA
1 AAATAAATATATATATATATAA
1919077 AAATAAATATATATATATATA
1 AAATAAATATATATATATATA
1919098 TATTAATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAAATATATATATATATAA
Found at i:1919623 original size:29 final size:29
Alignment explanation
Indices: 1919591--1919647 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1919581 TAATTCTTTC
*
1919591 TTTTCAAAAT-TTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATATA-TTATTA
* *
1919620 TTTTCATAATATTTATATGTATATTATT
1 TTTTCAAAATATTTATATATATATTATT
1919648 TTATTAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTCAAAATATTTATATATATATTATTA
Found at i:1924143 original size:2 final size:2
Alignment explanation
Indices: 1924131--1924168 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1924121 ATCCTTTAAA
*
1924131 AT AT AT GT 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
1924169 CCCTTGTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1927383 original size:75 final size:74
Alignment explanation
Indices: 1927163--1927407 Score: 260
Period size: 75 Copynumber: 3.3 Consensus size: 74
1927153 ATCAACAAGA
* * * * *
1927163 AGCAAATGTTGGGGTATGCTGAAAACCTATTTCAATCATAATCAGGAACATTGACGCATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCA-AATCAAGAATATTGACACATTTTGAA
* * * *
1927228 TGTTTATGTC
65 CGTTTGTATT
* * * * * ** *
1927238 AACAAATGTTGGGGCTTACTGCAAGCCCATTTCAATC-AATTGA-AATATTGGCACATTTTGAAC
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAAATCAAGAATATTGACACATTTTGAAC
1927301 GTTTGTATT
66 GTTTGTATT
* * * *
1927310 AGCTAATGTTGGGGCATGCTGAAATCCCCTTTCAATCAGAATCAAGAATGTTGACACATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCA-AATCAAGAATATTGACACATTTTGAA
1927375 CGTTTGTATT
65 CGTTTGTATT
*
1927385 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
1927408 GGCCCACATC
Statistics
Matches: 138, Mismatches: 29, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
72 52 0.38
73 3 0.02
74 4 0.03
75 79 0.57
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (74 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAAATCAAGAATATTGACACATTTTGAAC
GTTTGTATT
Found at i:1928600 original size:22 final size:22
Alignment explanation
Indices: 1928575--1928651 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
1928565 ATCTACACTT
1928575 TTCAAAGATGATAGATTCTTTC
1 TTCAAAGATGATAGATTCTTTC
*
1928597 TTCAAAGATGATATCATATC--TC
1 TTCAAAGATGATA-GAT-TCTTTC
* *
1928619 TTTAAAGATGATAGGTTCTCTT-
1 TTCAAAGATGATAGATTCT-TTC
1928641 TTCAAAGATGA
1 TTCAAAGATGA
1928652 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 2 0.04
21 1 0.02
22 37 0.82
23 3 0.07
24 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTTTC
Found at i:1929246 original size:124 final size:122
Alignment explanation
Indices: 1929026--1929727 Score: 751
Period size: 124 Copynumber: 5.9 Consensus size: 122
1929016 CACTTGATGG
*
1929026 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
1929091 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAA-AAGATAGATCAGC
*
1929150 ATCAACTTTTCCAGAGAAAGTCCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
* *
1929215 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAA-AAGATAGATCAGC
* * * *
1929274 GTCAACTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAAGAATAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGA-GGAAGAAGAAGTTCAT
* * * * * ** *
1929339 AATGAGAAGAGCTTGTTCAACATTTTGCTTCAAT-TCATCAC----TCGATGGATC-G-
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCT-ATCACAGAAAAGATAGATCAGC
* * * *
1929391 -GC-A--TTGCCATGTAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCA
1 ATCAACTTTTCCA-G-AGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
* * * * * * *
1929451 TAATGAGAATAATTTGTTCAACATTTTGCTTGAAT-TCATCAC--------TCGAT--GG
64 TAATGAGAAGAACTTGTTCAACCTTTTGCATGACTCT-ATCACAGAAAAGATAGATCAGC
*
1929500 ATCAACTTTTCCAGAG--AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
1929563 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATTACGGAAAGAGATAGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAA-AGATAGATCAGC
* * *
1929621 ATCAACTTTTCCACAGAAAGTTCATAATGAA-AAGAACTTATCTGAAGAGGAAGGAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAAT-AAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
** * *
1929685 -CCGAGAAGAACTTGTTCAGCC-TTTGCATGATTAC-ATCACAGAA
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACT-CTATCACAGAA
1929728 TGAGATAAAT
Statistics
Matches: 503, Mismatches: 50, Indels: 53
0.83 0.08 0.09
Matches are distributed among these distances:
108 1 0.00
109 4 0.01
110 79 0.16
111 4 0.01
112 1 0.00
113 61 0.12
114 31 0.06
115 3 0.01
116 1 0.00
119 11 0.02
121 32 0.06
122 19 0.04
123 43 0.09
124 213 0.42
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (122 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAAAGATAGATCAGC
Found at i:1929490 original size:113 final size:111
Alignment explanation
Indices: 1929291--1929589 Score: 465
Period size: 110 Copynumber: 2.7 Consensus size: 111
1929281 TTTCCAAAGA
* *
1929291 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAAGAATAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGA-GGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
**
1929356 CAACATTTTGCTTCAATTCATCACTCGATGGATCGGCATTGCCATGTAG
65 CAACATTTTGCTTCAATTCATCACTCGATGGATCAACATTGCCA-G-AG
* * *
1929405 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAATAATTTGTTC
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *
1929470 AACATTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAG
66 AACATTTTGCTTCAATTCATCACTCGATGGATCAACATTGCCAGAG
1929516 -AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
1929580 AACCTTTTGC
66 AACATTTTGC
1929590 ATGACTCTAT
Statistics
Matches: 171, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
110 70 0.41
111 2 0.01
112 1 0.01
113 67 0.39
114 31 0.18
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (111 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACATTTTGCTTCAATTCATCACTCGATGGATCAACATTGCCAGAG
Found at i:1929578 original size:110 final size:110
Alignment explanation
Indices: 1929275--1929589 Score: 468
Period size: 113 Copynumber: 2.8 Consensus size: 110
1929265 TAGATCAACG
* *
1929275 TCAACTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAAGAATAAGTTCATA
1 TCAACTTTTCC--AGAGAGTTCATAATGAGAAGAACTCATCTGAAGA-GGAAGAAGAAGTTCATA
*
1929340 ATGAGAAGAGCTTGTTCAACATTTTGCTTCAATTCATCACTCGATGGA
63 ATGAGAAGAACTTGTTCAACATTTTGCTTCAATTCATCACTCGATGGA
** * * *
1929388 TCGGCATTGCCATGTAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATA
1 TCAACTTTTCCA-G-AG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
1929453 ATGAGAATAATTTGTTCAACATTTTGCTTGAATTCATCACTCGATGGA
63 ATGAGAAGAACTTGTTCAACATTTTGCTTCAATTCATCACTCGATGGA
1929501 TCAACTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
1 TCAACTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
*
1929566 AGAAGAACTTGTTCAACCTTTTGC
66 AGAAGAACTTGTTCAACATTTTGC
1929590 ATGACTCTAT
Statistics
Matches: 180, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
110 70 0.39
111 3 0.02
112 2 0.01
113 75 0.42
114 30 0.17
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (110 bp):
TCAACTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACATTTTGCTTCAATTCATCACTCGATGGA
Found at i:1931101 original size:23 final size:23
Alignment explanation
Indices: 1931074--1931119 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1931064 CCCTTTCTGA
* *
1931074 TATTTCTAAGTAAATAAATATAT
1 TATTTATAAATAAATAAATATAT
* *
1931097 TATTTATAAATATATATATATAT
1 TATTTATAAATAAATAAATATAT
1931120 ATATATTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATAT
Found at i:1932470 original size:3 final size:3
Alignment explanation
Indices: 1932462--1932498 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
1932452 GTAAATCAGA
1932462 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C-AT CAT CAT
1932499 TATTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1934393 original size:16 final size:15
Alignment explanation
Indices: 1934368--1934397 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1934358 TCGTTTTCAT
1934368 TTAAAAAATAAAATA
1 TTAAAAAATAAAATA
1934383 TTAAGAAAATAAAAT
1 TTAA-AAAATAAAAT
1934398 TCTTTAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
TTAAAAAATAAAATA
Found at i:1935064 original size:20 final size:20
Alignment explanation
Indices: 1935041--1935105 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
1935031 TTGCGATTTT
*
1935041 TCAAATTCGCCACGCGAAAG
1 TCAAATTCGCAACGCGAAAG
*
1935061 TCAAA-TCGCAACAC-AGAAG
1 TCAAATTCGCAACGCGA-AAG
*
1935080 TCAAATTCGTAACGCGAAAG
1 TCAAATTCGCAACGCGAAAG
1935100 TCAAAT
1 TCAAAT
1935106 GTTTTTACGC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.39
20 21 0.55
21 1 0.03
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.17
Consensus pattern (20 bp):
TCAAATTCGCAACGCGAAAG
Found at i:1935259 original size:22 final size:22
Alignment explanation
Indices: 1935233--1935283 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1935223 CTACGGCGGC
1935233 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
1935255 ATCCGTCCCTATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1935277 ATCCGTC
1 ATCCGTC
1935284 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1935599 original size:20 final size:20
Alignment explanation
Indices: 1935558--1935599 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1935548 GAAACTAAAA
* * *
1935558 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
1935578 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
1935598 TC
1 TC
1935600 AGAAACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:1937439 original size:21 final size:22
Alignment explanation
Indices: 1937407--1937505 Score: 100
Period size: 21 Copynumber: 4.7 Consensus size: 22
1937397 GATGCACCTA
* *
1937407 TCATCATTCAAGAGGCGCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
1937429 T-ATCGTTCAAGAGGCCCCT-C
1 TCATCGTTCAAGAGGCCCCTCC
* *
1937449 TCATC-ATCGAAGAAGCCCCTCC
1 TCATCGTTC-AAGAGGCCCCTCC
* *
1937471 T-ACCGTTCAAGAGGCCCC-CG
1 TCATCGTTCAAGAGGCCCCTCC
1937491 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
1937506 TCTCGCCCGC
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 6 0.10
21 52 0.83
22 5 0.08
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.21
Consensus pattern (22 bp):
TCATCGTTCAAGAGGCCCCTCC
Found at i:1937454 original size:42 final size:42
Alignment explanation
Indices: 1937407--1937505 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
1937397 GATGCACCTA
* *
1937407 TCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTC-
1 TCATCATTCAAGAGGCCCCTCCTACCGTTCAAGAGGCCCC-CG
*
1937449 TCATCA-TCGAAGAAGCCCCTCCTACCGTTCAAGAGGCCCCCG
1 TCATCATTC-AAGAGGCCCCTCCTACCGTTCAAGAGGCCCCCG
*
1937491 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
1937506 TCTCGCCCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
41 3 0.06
42 44 0.90
43 2 0.04
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.21
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCTACCGTTCAAGAGGCCCCCG
Found at i:1938939 original size:14 final size:14
Alignment explanation
Indices: 1938920--1938959 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1938910 TTTTGATTAA
1938920 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
1938934 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
1938948 TTGATTTGTAAA
1 TTGATTTGTAAA
1938960 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1938971 original size:61 final size:62
Alignment explanation
Indices: 1938870--1939008 Score: 183
Period size: 65 Copynumber: 2.2 Consensus size: 62
1938860 TTTTACATTG
*
1938870 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
** * *
1938930 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTT-CTTGATTAATTGATTTGTA
*
1938995 AAAGTTGAATTGTT
1 AAAGTTGATTTGTT
1939009 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 17 0.25
61 17 0.25
63 4 0.06
65 30 0.44
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.50
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Done.