Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009000.1 Hibiscus syriacus cultivar Beakdansim tig00112382_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: 1742898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1633340 original size:35 final size:35
Alignment explanation
Indices: 1633287--1633632 Score: 424
Period size: 35 Copynumber: 9.9 Consensus size: 35
1633277 CAGATTCTTC
* *
1633287 TCAATTTAACCTTCACGTAAGAGTTGTGAAGTGAT
1 TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
*
1633322 TCGATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
1 TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
** * *
1633357 TTGATTCAACCTTCACGGAAGAGTAGTGAAGTAAT
1 TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
* *
1633392 TAAATTCAACCTTCACATAAGAGTAGTGAAGTGAT
1 TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
* * * * * *
1633427 TTAATCCAACCTTCATGCAAGAGTAGTGAAATAAT
1 TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
* **
1633462 TCAATTTAACAATCACGTAAGAGTAGTGAAGTGAT
1 TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
*
1633497 TCGATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
1 TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
* * * * **
1633532 TCGATTCAGCCTTCACGGAAGAGTAGTAAAGCAAT
1 TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
*
1633567 TCAATTCAACCTTCATGTAAGAGTAGTGAAGTGAT
1 TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
* *
1633602 TCAA-TCTAGCCTTCACGGAAGAGTAGTGAAG
1 TCAATTC-AACCTTCACGTAAGAGTAGTGAAG
1633633 CAAGATCAGA
Statistics
Matches: 264, Mismatches: 46, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
34 2 0.01
35 262 0.99
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (35 bp):
TCAATTCAACCTTCACGTAAGAGTAGTGAAGTGAT
Found at i:1633832 original size:3 final size:3
Alignment explanation
Indices: 1633826--1633869 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
1633816 TATATAATAA
*
1633826 TAT TAT TA- TAT GAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1633870 CAAGACCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1633834 original size:18 final size:18
Alignment explanation
Indices: 1633811--1633852 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1633801 GTGACGTATC
1633811 TATTATAT-ATAATAATAT
1 TATTATATGAT-ATAATAT
*
1633829 TATTATATGATATATTAT
1 TATTATATGATATAATAT
1633847 TATTAT
1 TATTAT
1633853 TATTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TATTATATGATATAATAT
Found at i:1633859 original size:15 final size:16
Alignment explanation
Indices: 1633811--1633869 Score: 68
Period size: 15 Copynumber: 3.7 Consensus size: 16
1633801 GTGACGTATC
*
1633811 TATTATATATAATAATAT
1 TATTAT-TATTAT-ATAT
*
1633829 TATTA-TATGATATAT
1 TATTATTATTATATAT
1633844 TATTATTATTAT-TAT
1 TATTATTATTATATAT
1633859 TATTATTATTA
1 TATTATTATTA
1633870 CAAGACCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
15 23 0.61
16 10 0.26
18 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TATTATTATTATATAT
Found at i:1635101 original size:22 final size:23
Alignment explanation
Indices: 1635073--1635116 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1635063 TATTATAAAT
*
1635073 CTATAT-ATTTTTATAATTTAAC
1 CTATATAATTTTAATAATTTAAC
*
1635095 CTATATAATTTTAATATTTTAA
1 CTATATAATTTTAATAATTTAA
1635117 ATAAATATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (23 bp):
CTATATAATTTTAATAATTTAAC
Found at i:1637426 original size:6 final size:6
Alignment explanation
Indices: 1637417--1637451 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
1637407 TTTTTCATTT
1637417 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1637452 TTTCTATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:1640296 original size:24 final size:24
Alignment explanation
Indices: 1640252--1640298 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1640242 ATAAAGAACC
1640252 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAATATACCATTA
*
1640276 AAAATAAAGTTTAAATA-ACCATT
1 AAAATAAA-CTTAAATATACCATT
1640299 CAACCAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAATAAACTTAAATATACCATTA
Found at i:1650428 original size:24 final size:24
Alignment explanation
Indices: 1650384--1650430 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1650374 ATAAATAACC
*
1650384 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1650408 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
1650431 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1653349 original size:15 final size:15
Alignment explanation
Indices: 1653329--1653358 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1653319 CTACGAATAA
1653329 CTGGGTACTGCATCG
1 CTGGGTACTGCATCG
1653344 CTGGGTACTGCATCG
1 CTGGGTACTGCATCG
1653359 TCTTCAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
CTGGGTACTGCATCG
Found at i:1657058 original size:2 final size:2
Alignment explanation
Indices: 1657053--1657112 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1657043 CACACAACTT
1657053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1657095 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1657113 AGTATGTATC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1657154 original size:43 final size:43
Alignment explanation
Indices: 1657093--1657182 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
1657083 TATATATATA
1657093 TATATATATATATATATATAAGTATGTATCAACCTTTGATTAT
1 TATATATATATATATATATAAGTATGTATCAACCTTTGATTAT
* *
1657136 TATATGTATATATATATATATGTATGTATCAACCTTTGATTAT
1 TATATATATATATATATATAAGTATGTATCAACCTTTGATTAT
1657179 TATA
1 TATA
1657183 AATCAAATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (43 bp):
TATATATATATATATATATAAGTATGTATCAACCTTTGATTAT
Found at i:1669202 original size:38 final size:38
Alignment explanation
Indices: 1669144--1669222 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
1669134 ATTAGGGTTA
*
1669144 AAATAAAGCAAATAAATAATTAAAATAAAATATAAA-AT
1 AAATAAAACAAATAAATAATTAAAATAAAATA-AAATAT
* * *
1669182 AAATAAAACAATTAATTAATTAAAATCAAATAAAATAT
1 AAATAAAACAAATAAATAATTAAAATAAAATAAAATAT
1669220 AAA
1 AAA
1669223 AGAAATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 3 0.08
38 33 0.92
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (38 bp):
AAATAAAACAAATAAATAATTAAAATAAAATAAAATAT
Found at i:1674894 original size:68 final size:68
Alignment explanation
Indices: 1674145--1674876 Score: 1027
Period size: 68 Copynumber: 10.8 Consensus size: 68
1674135 AAATATTAAT
* * * * *
1674145 AGGCCTAACTGCGCATTTAACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTACCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1674210 TTG
66 TTG
* * * * *
1674213 AGGCCTAACTTTGCATTTGACAGAAATGTGTCATTTGTACCAGTTAGATTAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1674278 TTG
66 TTG
* ** *
1674281 AGGCCTAACTATGCATTTGACAGAAAAATGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1674346 TTG
66 TTG
* *
1674349 AGGCCTAACTGTGCATTTGACAGAAAGTTGTCATTTGA-GTCAGTTAGATGAAAGGCTAAGTGCC
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTT-ATGCCAGTTAGATGAAAGGCTAAGTGCC
1674413 TTTG
65 TTTG
* * * * *
1674417 AGGCCTAACTGTGCATTTGACAGAAAGGTGTGATTTGTTCTAATTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1674482 TTG
66 TTG
* * * * * **
1674485 AGGCCTAAATGTGTATTTGACAAAAAGGTGTCAATTATGCTAGTTAGATGAAAGGAGAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1674550 TTG
66 TTG
* * * * * *
1674553 AGGCCTAACTGTACATTTGATAAAAATGTGTCATTTATGTCAATTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1674618 TTG
66 TTG
* *
1674621 AGGCCTAAATGTACATTTGACTA-AAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 AGGCCTAACTGTGCATTTGAC-AGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
1674685 TTTG
65 TTTG
* * * *
1674689 AGGCCTAACTGTGCATTTGACATAAAGGTGACATTTGTTCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1674754 TTG
66 TTG
* *
1674757 AGGCCTAACTGTGCATTTTACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1674822 TTG
66 TTG
* * *
1674825 AGGCCTAATTGTGCATTTGGCAGAAAGATGTCATTTATGCCAGTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
1674877 CGGTTAAATA
Statistics
Matches: 593, Mismatches: 67, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
67 1 0.00
68 590 0.99
69 2 0.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:1674968 original size:81 final size:79
Alignment explanation
Indices: 1674826--1675465 Score: 692
Period size: 81 Copynumber: 7.9 Consensus size: 79
1674816 GTGCCTTTGA
* * *
1674826 GGCCTAATTGTGCATTTGGCAGAAAGATGTCATTTATGCCAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1674891 TGAGTAATATAATAAT
66 TGAGTAA-A-AATAAT
* * * *
1674907 GGTCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATACCAGTTTGATGAACGATTAAATACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1674972 TGAGTAAAAGAATAAT
66 TGAGT-AAA-AATAAT
** * * * * * *
1674988 GGCCTAACTGTGAATTTGGCAAAAATGTGCCAATTATACCAGTTAGATGAACGGTTAAATACCAT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1675053 TGAGTAAAAGATGAAT
66 TGAGTAAAA-AT-AAT
* * * * * * *
1675069 GGCCTAGTTGTGCATTCGGTAGAAAGATATCAATTATGCCAGTTGGATGAATGGTTAAATACAGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1675134 TGAGTAAAACAATAAT
66 TGAGT-AAA-AATAAT
* * * * *
1675150 GGACTAGTTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAATGGGTAAATACCTT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
1675215 TGAGTAAATGATGAAT
66 TGAGTAAA-AAT-AAT
* * ** * * *
1675231 GGCCTAGTTATGCATTTGGGAGAAATATGTCAGTTATGCTAGTTAGATGAAAGGTTAAATACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1675296 TGAGTAAAAGATGAAT
66 TGAGTAAAA-AT-AAT
* * * **
1675312 GGCCTAGTTGTGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAACATTGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1675377 TGAGTAAAAAAATAAT
66 TGAGT--AAAAATAAT
* * * * *
1675393 GGACTAGATGTGCATTTGACAGAAA-GTGTCAAATT-TG-CAGGTTAGATGAAAGGCTAAATACC
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTC-AATTATGCCA-GTTAGATGAACGGTTAAATACC
* *
1675455 TTTGGGTAAAA
64 GTTGAGTAAAA
1675466 GAATAAAAGA
Statistics
Matches: 471, Mismatches: 77, Indels: 25
0.82 0.13 0.04
Matches are distributed among these distances:
78 4 0.01
79 3 0.01
80 39 0.08
81 411 0.87
82 9 0.02
83 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (79 bp):
GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
TGAGTAAAAATAAT
Found at i:1675277 original size:243 final size:243
Alignment explanation
Indices: 1674826--1675471 Score: 852
Period size: 243 Copynumber: 2.7 Consensus size: 243
1674816 GTGCCTTTGA
* * * *
1674826 GGCCTAATTGTGCATTTGGCAGAAAGATGTCATTTATGCCAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAGTTGTGCATTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAATACAGT
* * * * *
1674891 TGAGTAATATAATAATGGTCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATACCAGTTTGATG
66 TGAGTAAAAAAATAATGGACTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATG
* ** * * *
1674956 AACGATTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTGTGAATTTGGCAAAAATGTGCCAA
131 AAAGGCTAAATACCTTTGAGTAAAAGAATAATGGCCTAACTATGAATTTGGCAAAAATATGCCAA
*
1675021 TTATACCAGTTAGATGAACGGTTAAATACCATTGAGTAAAAGATGAAT
196 TTATACCAGTTAGATGAAAGGTTAAATACCATTGAGTAAAAGATGAAT
* * * *
1675069 GGCCTAGTTGTGCATTCGGTAGAAAGATATCAATTATGCCAGTTGGATGAATGGTTAAATACAGT
1 GGCCTAGTTGTGCATTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAATACAGT
* *
1675134 TGAGTAAAACAATAATGGACTAGTTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATG
66 TGAGTAAAAAAATAATGGACTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATG
* * * ** * * * *
1675199 AATGGGTAAATACCTTTGAGTAAATG-ATGAATGGCCTAGTTATGCATTTGGGAGAAATATGTCA
131 AAAGGCTAAATACCTTTGAGTAAAAGAAT-AATGGCCTAACTATGAATTTGGCAAAAATATGCCA
* * * *
1675263 GTTATGCTAGTTAGATGAAAGGTTAAATACCGTTGAGTAAAAGATGAAT
195 ATTATACCAGTTAGATGAAAGGTTAAATACCATTGAGTAAAAGATGAAT
* **
1675312 GGCCTAGTTGTGCATTTGGTAGAAATG-TGTCAATTATGCCAGTTAGATGAACGGTTAAACATTG
1 GGCCTAGTTGTGCATTTGGTAGAAA-GATGTCAATTATGCCAGTTAGATGAACGGTTAAATACAG
* *
1675376 TTGAGTAAAAAAATAATGGACTAGATGTGCATTTGACAGAAA-GTGTCAAATT-TG-CAGGTTAG
65 TTGAGTAAAAAAATAATGGACTAGTTGTGCATTTGGCAGAAAGGTGTC-AATTATGCCA-GTTAG
*
1675438 ATGAAAGGCTAAATACCTTTGGGTAAAAGAATAA
128 ATGAAAGGCTAAATACCTTTGAGTAAAAGAATAA
1675472 AAGAATTATA
Statistics
Matches: 351, Mismatches: 47, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
241 2 0.01
242 41 0.12
243 307 0.87
244 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (243 bp):
GGCCTAGTTGTGCATTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAATACAGT
TGAGTAAAAAAATAATGGACTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATG
AAAGGCTAAATACCTTTGAGTAAAAGAATAATGGCCTAACTATGAATTTGGCAAAAATATGCCAA
TTATACCAGTTAGATGAAAGGTTAAATACCATTGAGTAAAAGATGAAT
Found at i:1679085 original size:81 final size:79
Alignment explanation
Indices: 1678992--1679529 Score: 675
Period size: 81 Copynumber: 6.7 Consensus size: 79
1678982 GTAAAGGGGG
* * *
1678992 AAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAATATCATTGAGTAAAAGATGAATGGCATTA
1 AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-CGTTGAGTAAAAGAT-AATGGC-CTA
1679057 -CTGTGCATTTGGCAGA
63 GCTGTGCATTTGGCAGA
*
1679073 AAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAATACTGTTGAGTAAAAGAATAATGGCCTAG
1 AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAC-GTTGAGTAAAAG-ATAATGGCCTAG
* *
1679138 TTTTGCATTTGGCAGA
64 CTGTGCATTTGGCAGA
* * *
1679154 AATGTGTCAATTATACTAGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGAATAATGGCCTAG
1 AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-CGTTGAGTAAAAG-ATAATGGCCTAG
*
1679219 CTGTGCATTTGACAGA
64 CTGTGCATTTGGCAGA
* * * *
1679235 AATGTGTCAATTATGCCAGTTAGATGAACGATTAAATACCGTTGACTAAAAGATGAATGGTCTAG
1 AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-CGTTGAGTAAAAGAT-AATGGCCTAG
*
1679300 CTGTGTATTTGGCAGA
64 CTGTGCATTTGGCAGA
* * *
1679316 ACGGTGTCGATTATGCCAGTTAGATGAACGGTTAAATACTGTTGAGTAAAAGATGAATAGCCTAG
1 AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAC-GTTGAGTAAAAGAT-AATGGCCTAG
1679381 CTGTGCATTTGGCAGA
64 CTGTGCATTTGGCAGA
* * * *
1679397 AAGGTGTCAATTATGGCAATTAGATGAACGGTTAAACACTGTTGAGTAAAAGAATAATGGACTAG
1 AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAC-GTTGAGTAAAAG-ATAATGGCCTAG
*
1679462 CTGTGCATTTGACAGA
64 CTGTGCATTTGGCAGA
* * * * * *
1679478 AA-GTGTCAAATATGCAAGTTAGATGAAAGGCTAAATACCTTTGGGTAAAAGA
1 AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-CGTTGAGTAAAAGA
1679530 ATAAAGAAAT
Statistics
Matches: 403, Mismatches: 46, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
79 1 0.00
80 44 0.11
81 353 0.88
82 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.29
Consensus pattern (79 bp):
AAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACGTTGAGTAAAAGATAATGGCCTAGCT
GTGCATTTGGCAGA
Found at i:1679423 original size:243 final size:241
Alignment explanation
Indices: 1678995--1679504 Score: 758
Period size: 243 Copynumber: 2.1 Consensus size: 241
1678985 AAGGGGGAAG
* * * *
1678995 GTGTCAATTATGTCAGTTAGATGAACGGTTAAATATCATTGAGTAAAAGATGAATGGCATTACTG
1 GTGTCAATTATGCCAGTTAGATGAACGATTAAATACCATTGACTAAAAGATGAATGGCA-TACTG
1679060 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAATACTGTTGAGTAAAAG
65 TGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAATACTGTTGAGTAAAAG
* * * * *
1679125 AATAATGGCCTAGTTTTGCATTTGGCAGAAATGTGTCAATTATACTAGTTAGATGAACGGTTAAA
130 AATAATAGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATACTAATTAGATGAACGGTTAAA
* *
1679190 TA-TCGTTGAGTAAAAGAATAATGGCCTAGCTGTGCATTTGACAGAAA
195 CACT-GTTGAGTAAAAGAATAATGGACTAGCTGTGCATTTGACAGAAA
*
1679237 TGTGTCAATTATGCCAGTTAGATGAACGATTAAATACCGTTGACTAAAAGATGAATGGTC-TAGC
1 -GTGTCAATTATGCCAGTTAGATGAACGATTAAATACCATTGACTAAAAGATGAATGG-CATA-C
* * * *
1679301 TGTGTATTTGGCAGAACGGTGTCGATTATGCCAGTTAGATGAACGGTTAAATACTGTTGAGTAAA
63 TGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAATACTGTTGAGTAAA
*
1679366 AG-ATGAATAGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGGC-AATTAGATGAACGGT
128 AGAAT-AATAGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTAT-ACTAATTAGATGAACGGT
1679429 TAAACACTGTTGAGTAAAAGAATAATGGACTAGCTGTGCATTTGACAGAAA
191 TAAACACTGTTGAGTAAAAGAATAATGGACTAGCTGTGCATTTGACAGAAA
* *
1679480 GTGTCAAATATGCAAGTTAGATGAA
1 GTGTCAATTATGCCAGTTAGATGAA
1679505 AGGCTAAATA
Statistics
Matches: 243, Mismatches: 19, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
242 27 0.11
243 213 0.88
244 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (241 bp):
GTGTCAATTATGCCAGTTAGATGAACGATTAAATACCATTGACTAAAAGATGAATGGCATACTGT
GCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAATACTGTTGAGTAAAAGA
ATAATAGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATACTAATTAGATGAACGGTTAAAC
ACTGTTGAGTAAAAGAATAATGGACTAGCTGTGCATTTGACAGAAA
Found at i:1680500 original size:19 final size:20
Alignment explanation
Indices: 1680469--1680511 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1680459 CCACTAAAAT
1680469 TTTAGTTCGAT-CCCTGTAA
1 TTTAGTTCGATCCCCTGTAA
*
1680488 TTTATGTTC-ATCCCCTTTAA
1 TTTA-GTTCGATCCCCTGTAA
1680508 TTTA
1 TTTA
1680512 AATTCGCTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTAGTTCGATCCCCTGTAA
Found at i:1683654 original size:12 final size:12
Alignment explanation
Indices: 1683622--1683675 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
1683612 TATACAAATG
1683622 CCTAACTC-TCA
1 CCTAACTCTTCA
*
1683633 ACTAACTCTTCA
1 CCTAACTCTTCA
*
1683645 CCTAATTCTTCA
1 CCTAACTCTTCA
*
1683657 CATAACTCTTCA
1 CCTAACTCTTCA
1683669 CCTAACT
1 CCTAACT
1683676 AAATTGATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
11 7 0.19
12 29 0.81
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (12 bp):
CCTAACTCTTCA
Found at i:1687084 original size:24 final size:24
Alignment explanation
Indices: 1687052--1687137 Score: 118
Period size: 24 Copynumber: 3.6 Consensus size: 24
1687042 GTAATTACAG
*
1687052 CCTCGTCCATGACCGTGACTTCCA
1 CCTCGTCCACGACCGTGACTTCCA
*
1687076 CCTCGTCCACGACCGTGACTTTCA
1 CCTCGTCCACGACCGTGACTTCCA
* *
1687100 CCTCGTCCACGACTGCGACTTCCA
1 CCTCGTCCACGACCGTGACTTCCA
* *
1687124 CCTTGTCCATGACC
1 CCTCGTCCACGACC
1687138 TCTACCTCTG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.16, C:0.43, G:0.16, T:0.24
Consensus pattern (24 bp):
CCTCGTCCACGACCGTGACTTCCA
Found at i:1688396 original size:12 final size:12
Alignment explanation
Indices: 1688362--1688415 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
1688352 ATATACAAAT
1688362 ACCTAACTC-TC
1 ACCTAACTCTTC
1688373 A-CTAACTCTTC
1 ACCTAACTCTTC
* *
1688384 ACTTAATTCTTC
1 ACCTAACTCTTC
1688396 ACCTAACTCTTC
1 ACCTAACTCTTC
1688408 ACCTAACT
1 ACCTAACT
1688416 AAATTGATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
10 7 0.19
11 4 0.11
12 26 0.70
ACGTcount: A:0.28, C:0.37, G:0.00, T:0.35
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:1688493 original size:41 final size:40
Alignment explanation
Indices: 1688436--1688526 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 40
1688426 AAGCAATTAC
1688436 ATCAATTTAGTTTGAGTTTGGGTTTAGGCTCTCATAATCG
1 ATCAATTTAGTTTGAGTTTGGGTTTAGGCTCTCATAATCG
1688476 AATCAATTTAGTTTGAGTTTGGGTTTAGGCTCTCATAATCG
1 -ATCAATTTAGTTTGAGTTTGGGTTTAGGCTCTCATAATCG
1688517 ATCAAATTTA
1 ATC-AATTTA
1688527 TGATCCAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 3 0.06
41 46 0.94
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (40 bp):
ATCAATTTAGTTTGAGTTTGGGTTTAGGCTCTCATAATCG
Found at i:1690960 original size:36 final size:36
Alignment explanation
Indices: 1690872--1690978 Score: 189
Period size: 35 Copynumber: 3.0 Consensus size: 36
1690862 TTTGTTGATA
1690872 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
1690908 ATGCT-AAATTAGGTTATCCCACTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
* *
1690943 ATGCTCAAATTAGGTTATCCCATTAGTATTGGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
1690979 GACGATTTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 35 0.51
36 33 0.49
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (36 bp):
ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
Found at i:1692504 original size:19 final size:19
Alignment explanation
Indices: 1692480--1692518 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1692470 TTCAGTCTTG
1692480 AATAGTAAGTTGAAAATAA
1 AATAGTAAGTTGAAAATAA
1692499 AATAGTAAGTTGAAAATAA
1 AATAGTAAGTTGAAAATAA
1692518 A
1 A
1692519 TGTCAGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (19 bp):
AATAGTAAGTTGAAAATAA
Found at i:1695643 original size:31 final size:31
Alignment explanation
Indices: 1695605--1695696 Score: 166
Period size: 31 Copynumber: 3.0 Consensus size: 31
1695595 CAAGAGTTTG
1695605 GGAGTTCCTAGTGAGAATGACATATTGAATA
1 GGAGTTCCTAGTGAGAATGACATATTGAATA
* *
1695636 GGAGTTCCTAGTGAGAAGGACATATTGAATG
1 GGAGTTCCTAGTGAGAATGACATATTGAATA
1695667 GGAGTTCCTAGTGAGAATGACATATTGAAT
1 GGAGTTCCTAGTGAGAATGACATATTGAAT
1695697 TCACCGAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (31 bp):
GGAGTTCCTAGTGAGAATGACATATTGAATA
Found at i:1696297 original size:35 final size:36
Alignment explanation
Indices: 1696252--1696358 Score: 189
Period size: 35 Copynumber: 3.0 Consensus size: 36
1696242 AATGTTGATA
1696252 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
1696288 ATGCT-AAATTAGGTTATCCCACTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
* *
1696323 ATGCTCAAATTAGGTTATCCCATTAGTATTGGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
1696359 GACTATTTTC
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 35 0.51
36 33 0.49
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (36 bp):
ATGCTCAAATTAGGTTATCCCACTAGTATTAGAAAT
Found at i:1700553 original size:26 final size:26
Alignment explanation
Indices: 1700524--1700596 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
1700514 GCACTTTTTA
1700524 TACAACACTTTTCAAAAGCTAGTTTC
1 TACAACACTTTTCAAAAGCTAGTTTC
1700550 TACAACACTTTTCAAAAGCTAGTTTC
1 TACAACACTTTTCAAAAGCTAGTTTC
*
1700576 TACAATACTTTTCAAAAGCTA
1 TACAACACTTTTCAAAAGCTA
1700597 TACCAAACTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (26 bp):
TACAACACTTTTCAAAAGCTAGTTTC
Found at i:1701367 original size:29 final size:29
Alignment explanation
Indices: 1701306--1701367 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1701296 GGTTAGTGAC
* * *
1701306 TAAATTATAAGTTTTGAAAGTTTAGTGGT
1 TAAAGTATAAGTTTTGAAAGTCTAGTGGA
*
1701335 TAAAGTATAATTTTTGAAAAGTCTAG-GGA
1 TAAAGTATAAGTTTTG-AAAGTCTAGTGGA
1701364 TAAA
1 TAAA
1701368 AAGGTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.39
Consensus pattern (29 bp):
TAAAGTATAAGTTTTGAAAGTCTAGTGGA
Found at i:1703134 original size:14 final size:16
Alignment explanation
Indices: 1703109--1703146 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1703099 TTTTATATCG
*
1703109 ATTATGTTTTAT-AGA
1 ATTATATTTTATCAGA
1703124 ATT-TATTTTATCAGA
1 ATTATATTTTATCAGA
1703139 ATTATATT
1 ATTATATT
1703147 ATGTTAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 9 0.45
16 4 0.20
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (16 bp):
ATTATATTTTATCAGA
Found at i:1705756 original size:77 final size:78
Alignment explanation
Indices: 1705631--1705819 Score: 224
Period size: 78 Copynumber: 2.4 Consensus size: 78
1705621 TTTTAGGCGT
* ** * * * *
1705631 AACCCATTTTATTAATTAAAATATTAACATTTTAGATCGCAACATA-TTTCTTAGTGAGCCATGA
1 AACCCATTTTATTAATAAAAATATTAACATTCCAAATCACAACATATTTTCTTAGTGAACAATGA
*
1705695 CATTTTCTT-ACGC-
66 CA--TTCTTGACACA
* *
1705708 AACCCATTTTATTAATAAAAATATTAACATTCCAAATCATAACCTATTTTCTTAGTGAACAATGA
1 AACCCATTTTATTAATAAAAATATTAACATTCCAAATCACAACATATTTTCTTAGTGAACAATGA
*
1705773 CATTCTTGGCACA
66 CATTCTTGACACA
1705786 AACCCATTTTATTAATAAAAATATTATA-ATTCCA
1 AACCCATTTTATTAATAAAAATATTA-ACATTCCA
1705820 TATCCCAATT
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
76 5 0.05
77 41 0.42
78 50 0.52
79 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (78 bp):
AACCCATTTTATTAATAAAAATATTAACATTCCAAATCACAACATATTTTCTTAGTGAACAATGA
CATTCTTGACACA
Found at i:1707833 original size:16 final size:16
Alignment explanation
Indices: 1707812--1707846 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1707802 TGCACAAATG
* *
1707812 TAATAATATTAATTAA
1 TAATAATAATAATAAA
1707828 TAATAATAATAATAAA
1 TAATAATAATAATAAA
1707844 TAA
1 TAA
1707847 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAATAATAATAAA
Found at i:1708808 original size:236 final size:237
Alignment explanation
Indices: 1708235--1709015 Score: 1131
Period size: 236 Copynumber: 3.3 Consensus size: 237
1708225 TTCATCGTGA
* * *
1708235 AGTTGAAA-CTGTGGATGGCCCCTCCGTCGTGAAGTTGAGCCTTGAATTTGATATCCTTCGTCAT
1 AGTTGAAATC-GTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTG-ACTTGATATCCTTCGTCGT
* *
1708299 GAAGTTG-AATCCAATTAA-TTATATTGTTTCGA-TTCTAATATCC-CCGCCGTGAAGTTGAAAT
64 GAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTT-TAATATCCTCCGCCGTGAAGTTGAAAT
* * * *
1708360 TGGCTCTGAAATTGGGAAGCCC--CTTCGTGAATTTAAGCCTCAAATGGCACG--ATCCT-CATC
128 TGGCTCTGAAACTGGGAAGCCCTTCATCGTGAAATTGAGCCTCAAATGGCACGATATCCTCCATC
*
1708420 GTGGAGTTGAAATCGTGGATGTGTGGTACGATATCCTCCGTCGTGG
193 GTGGAGTTGAAATCGTGGA-GTGTGGTACGATATCCTCCGTTGTGG
1708466 AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGA-ATCCTTCGTCGTGA
1 AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGATATCCTTCGTCGTGA
**
1708530 AGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGG
66 AGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTTTAATATCCTCCGCCGTGAAGTTGAAATTGG
* * *
1708595 CTCTGAAACTGGGAAGCCCTTTCATCATGAAGTTGAGCCTCAAATAGCACGATATCCTCCATCGT
131 CTCTGAAACTGGGAAGCCC-TTCATCGTGAAATTGAGCCTCAAATGGCACGATATCCTCCATCGT
*
1708660 GGAGTTGAAATCGT-GA-TATGGTACGATATCCTCCGTTGTGG
195 GGAGTTGAAATCGTGGAGTGTGGTACGATATCCTCCGTTGTGG
**
1708701 AGTTGAAATTATGGAT-GCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTG
1 AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTG-ATATCCTTCGTCGTG
* *
1708765 AAGTTGAAATCCAAGTAAGTTGTATTGTTTAGAGTTTAATATCCTCCACCGTGAAGTTGAAATTG
65 AAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTTTAATATCCTCCGCCGTGAAGTTGAAATTG
* * * * *
1708830 GCTCTGAAACTGGAAAGCTCCTTCGTCGTGAAATTGAGCCTCAAATGGCATGATATCCTCCGTTG
130 GCTCTGAAACTGGGAAGC-CCTTCATCGTGAAATTGAGCCTCAAATGGCACGATATCCTCCATCG
*
1708895 TGGAGTTGAAATCGTGGATGTGTGGATACGATATCCTCTGTTGTGG
194 TGGAGTTGAAATCGTGGA-GTGTGG-TACGATATCCTCCGTTGTGG
*
1708941 ATTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTG
1 AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTG-ATATCCTTCGTCGTG
1709006 AAGTTGAAAT
65 AAGTTGAAAT
1709016 GTATTGTTTC
Statistics
Matches: 497, Mismatches: 34, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
229 18 0.04
230 15 0.03
231 61 0.12
232 41 0.08
234 32 0.06
235 62 0.12
236 143 0.29
237 11 0.02
238 20 0.04
239 4 0.01
240 32 0.06
241 58 0.12
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (237 bp):
AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGATATCCTTCGTCGTGA
AGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTTTAATATCCTCCGCCGTGAAGTTGAAATTGG
CTCTGAAACTGGGAAGCCCTTCATCGTGAAATTGAGCCTCAAATGGCACGATATCCTCCATCGTG
GAGTTGAAATCGTGGAGTGTGGTACGATATCCTCCGTTGTGG
Found at i:1718875 original size:20 final size:20
Alignment explanation
Indices: 1718833--1718881 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1718823 TAACTTTTTC
*
1718833 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
1718853 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
*
1718872 TTTTACCTTT
1 TTTTATCTTT
1718882 TCTCTTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Found at i:1731658 original size:9 final size:9
Alignment explanation
Indices: 1731644--1731690 Score: 55
Period size: 8 Copynumber: 5.6 Consensus size: 9
1731634 CCTAAATTAA
*
1731644 AAAAAAGGG
1 AAAAAAGAG
1731653 AAAAAAGAG
1 AAAAAAGAG
1731662 -AAAAAGAG
1 AAAAAAGAG
1731670 AAAAAAGA-
1 AAAAAAGAG
*
1731678 ACAAAAG-G
1 AAAAAAGAG
1731686 AAAAA
1 AAAAA
1731691 GAAAAAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
8 18 0.55
9 15 0.45
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:1731665 original size:8 final size:8
Alignment explanation
Indices: 1731654--1731698 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1731644 AAAAAAGGGA
1731654 AAAAAGAG
1 AAAAAGAG
1731662 AAAAAGAG
1 AAAAAGAG
1731670 AAAAA-AG
1 AAAAAGAG
1731677 AACAAA-AGG
1 AA-AAAGA-G
1731686 AAAAAGA-
1 AAAAAGAG
1731693 AAAAAG
1 AAAAAG
1731699 GTTCAAGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 10 0.29
8 20 0.59
9 4 0.12
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:1731667 original size:17 final size:16
Alignment explanation
Indices: 1731644--1731699 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 16
1731634 CCTAAATTAA
1731644 AAAAAAGGGAAAAAAG
1 AAAAAAGGGAAAAAAG
*
1731660 AGAAAAAGAGAAAAAAG
1 A-AAAAAGGGAAAAAAG
1731677 AACAAAA-GG-AAAAAG
1 AA-AAAAGGGAAAAAAG
1731692 AAAAAAGG
1 AAAAAAGG
1731700 TTCAAGATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 4 0.11
15 9 0.26
16 3 0.09
17 19 0.54
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAAGGGAAAAAAG
Found at i:1731678 original size:15 final size:14
Alignment explanation
Indices: 1731654--1731698 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
1731644 AAAAAAGGGA
1731654 AAAAAGAGAAAAAGAG
1 AAAAA-AGAAAAA-AG
1731670 AAAAAAGAACAAAAG
1 AAAAAAGAA-AAAAG
*
1731685 GAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
1731699 GTTCAAGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 5 0.19
15 14 0.52
16 8 0.30
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:1735093 original size:2 final size:2
Alignment explanation
Indices: 1735086--1735123 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1735076 TATTTTACCT
1735086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1735124 CTTTTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1735174 original size:21 final size:21
Alignment explanation
Indices: 1735150--1735204 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1735140 TACTTATTTA
1735150 TCTATTTTATTTTTTTTATTC
1 TCTATTTTATTTTTTTTATTC
* *
1735171 TCTATTTT-TATCTTTTTATTT
1 TCTATTTTAT-TTTTTTTATTC
*
1735192 TC-CTTTTATTTTT
1 TCTATTTTATTTTT
1735205 ACTTATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (21 bp):
TCTATTTTATTTTTTTTATTC
Found at i:1735212 original size:35 final size:34
Alignment explanation
Indices: 1735125--1735212 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 34
1735115 ATATATATAC
*
1735125 TTTTTATATTTTATTTACTTATTTATCTATTTTATTT
1 TTTTTAT-TTTTACTTA-TT-TTTATCTATTTTATTT
*
1735162 TTTTTA-TTCT-C-TATTTTTATCT-TTTTATTT
1 TTTTTATTTTTACTTATTTTTATCTATTTTATTT
1735192 TCCTTTTATTTTTACTTATTT
1 T--TTTTATTTTTACTTATTT
1735213 ATTTATCTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
30 9 0.21
31 7 0.16
32 7 0.16
33 5 0.12
34 1 0.02
35 8 0.19
37 6 0.14
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (34 bp):
TTTTTATTTTTACTTATTTTTATCTATTTTATTT
Found at i:1735297 original size:25 final size:24
Alignment explanation
Indices: 1735269--1735346 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
1735259 ATTAGTATTA
1735269 TTATTTTCTTCATTTATTTATTTAT
1 TTATTTT-TTCATTTATTTATTTAT
*
1735294 TTATTCTATTCATTT-TTATATTTACT
1 TTATT-TTTTCATTTATT-TATTTA-T
1735320 TTA-TTTTT-ATCTTATTTATTT-T
1 TTATTTTTTCAT-TTATTTATTTAT
1735342 TTATT
1 TTATT
1735347 ACTTTCCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 12 0.27
25 21 0.47
26 5 0.11
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (24 bp):
TTATTTTTTCATTTATTTATTTAT
Found at i:1735334 original size:5 final size:4
Alignment explanation
Indices: 1735280--1735346 Score: 61
Period size: 4 Copynumber: 16.8 Consensus size: 4
1735270 TATTTTCTTC
*
1735280 ATTT ATTT ATTT ATTT ATTCT ATTC ATTT -TTAT ATTT ACTTT A-TT -TTT
1 ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATT-T ATTT A-TTT ATTT ATTT
1735328 ATCTT ATTT ATTT -TTT ATT
1 AT-TT ATTT ATTT ATTT ATT
1735347 ACTTTCCTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
3 9 0.17
4 30 0.57
5 14 0.26
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1738382 original size:241 final size:239
Alignment explanation
Indices: 1737946--1738797 Score: 1225
Period size: 241 Copynumber: 3.6 Consensus size: 239
1737936 ATTCCCTTCA
* * *
1737946 TCGTGAAGTTGAAA-CTGTGGATGGCCCCTCCGTCGTGAAGTTGAGCCTTGAATTTGATATCCTT
1 TCGTGGAGTTGAAATC-GTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTG-ACTTGATATCCTT
* * * * *
1738010 CGTCATGAAGTTGAAATCCAATTAAGTTATATTGTTTCGATTCTAATATCCTCCGCCGTGAAGTT
64 CGTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTT
* * *
1738075 GAAATTGGCTCTGAAATTGGGAAGCCCCTTCGTCATGAATTTAAGCCTCAAATGGCACGGTATCC
129 GAAATTGGCTCTGAAACTGGGAAGCCCCTTCGTCATGAA-TTGAGCCTCAAATGGCACGATATCC
*
1738140 TCTATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
193 TCCATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
1738187 TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTC
1 TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTG-ATATCCTTC
1738252 GTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTG
65 GTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTG
* *
1738317 AAATTGGCTCTGAAACT-GGAAGCCCCTTTCATCATGAAGTTGAGCCTCAAATAGCACGATATCC
130 AAATTGGCTCTGAAACTGGGAAGCCCC-TTCGTCATGAA-TTGAGCCTCAAATGGCACGATATCC
* *
1738381 TCCATCGTGGACTTGAAATCGTGGATATGTGGGTACGATATCCTCCG
193 TCCATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
* ** * *
1738428 TTGTGGAGTTGAAATTATGGATGGCCCCTTCGTCGTGAAATTGAGCCTTGACTTGATATCTTTCG
1 TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGATATCCTTCG
* ** *
1738493 TCGTGAAGTTTGAAATCCAAGTAAGTTGTATTGTTTAGAGTTTAATATCCTCCACCGTGAAGTTG
66 TCGTGAAG-TTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTG
* * *
1738558 AAATTGGCTCTGAAACTGGGAAGCTCCTTCGTCGTGAATTGAGCCTCAAATGGCATGATATCCTC
130 AAATTGGCTCTGAAACTGGGAAGCCCCTTCGTCATGAATTGAGCCTCAAATGGCACGATATCCTC
* * * *
1738623 CGTTG-GGAGTTGAAATCGTGGATGTGTGGATACGATATCCTCTG
195 CATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
* *
1738667 TTGTGGATTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAG-CTTGACTTGAATATCC-TC
1 TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTG-ATATCCTTC
* * * **
1738730 GTCGTGAAGTTGAAATCCAAGT-A--TGTATTGTTTCAAGCCCAATATCCTTCGTTGTGAAGTTG
65 GTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTG
1738792 AAATTG
130 AAATTG
1738798 ACTTTGAACG
Statistics
Matches: 554, Mismatches: 51, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
234 36 0.06
236 1 0.00
237 13 0.02
238 20 0.04
239 81 0.15
240 58 0.10
241 336 0.61
242 9 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (239 bp):
TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGATATCCTTCG
TCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTGA
AATTGGCTCTGAAACTGGGAAGCCCCTTCGTCATGAATTGAGCCTCAAATGGCACGATATCCTCC
ATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
Done.