Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019233.1 Corchorus olitorius cultivar O-4 contig19266, 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: 93527
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1814 original size:21 final size:21
Alignment explanation
Indices: 1765--1805 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1755 ATTCTTTCAG
1765 CAACATCACTTGACTCTTCCA
1 CAACATCACTTGACTCTTCCA
*
1786 CAACATCACTTGATTCTTCC
1 CAACATCACTTGACTCTTCC
1806 TTAATATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.37, G:0.05, T:0.32
Consensus pattern (21 bp):
CAACATCACTTGACTCTTCCA
Found at i:5622 original size:11 final size:12
Alignment explanation
Indices: 5592--5624 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5582 CTTATAATTA
*
5592 ATTTTAATTATT
1 ATTTTAATTTTT
5604 ATTTTAATTTTT
1 ATTTTAATTTTT
5616 A-TTTAATTT
1 ATTTTAATTT
5625 AGACACAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTAATTTTT
Found at i:6839 original size:121 final size:122
Alignment explanation
Indices: 6640--6887 Score: 399
Period size: 121 Copynumber: 2.0 Consensus size: 122
6630 TAAAACCATG
* *
6640 AATAAGACTACAAGAAACAAGAGTACAGACTACAAACAGAATTAGAAACATCAAACATACATGCC
1 AATAAGACTACAAGAAACAAGAGTACAAACTACAAAC---A--AGAAACATCAAACATACATACC
*
6705 ACCTCAGTCTTGATTCCCAATTCGCACAAAATCAAACCCATAAACTTTGAAGCTTTGAAGTT
61 ACCACAGTCTTGATTCCCAATTCGCACAAAATCAAACCCATAAACTTTGAAGCTTTGAAGTT
*
6767 AATAAGACTACAAGAGACAAGAGTACAAACTACAAAC-AGAAACATCAAACATACATACCACCAC
1 AATAAGACTACAAGAAACAAGAGTACAAACTACAAACAAGAAACATCAAACATACATACCACCAC
*
6831 AGTCTTGATTCCCAATTCGCACAAAATCAAACCCATAAACTTTGAAGCTTTTAAGTT
66 AGTCTTGATTCCCAATTCGCACAAAATCAAACCCATAAACTTTGAAGCTTTGAAGTT
6888 TAGGGTTTAT
Statistics
Matches: 116, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
121 81 0.70
127 35 0.30
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.21
Consensus pattern (122 bp):
AATAAGACTACAAGAAACAAGAGTACAAACTACAAACAAGAAACATCAAACATACATACCACCAC
AGTCTTGATTCCCAATTCGCACAAAATCAAACCCATAAACTTTGAAGCTTTGAAGTT
Found at i:7290 original size:12 final size:12
Alignment explanation
Indices: 7273--7304 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7263 TAAATTATAT
7273 TAATATATAATA
1 TAATATATAATA
7285 TAATATAT-ATA
1 TAATATATAATA
7296 T-ATATATAA
1 TAATATATAA
7305 CTAAGGGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.32
11 5 0.26
12 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATATATAATA
Found at i:15008 original size:24 final size:24
Alignment explanation
Indices: 14943--15001 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
14933 TTCTTAGGGA
*
14943 TTTTTTTTTTTAAAGAAGAGAGTT
1 TTTTTTTTTTTAGAGAAGAGAGTT
* * *
14967 GTTTGTTTTTCAGAGAAGAGAGTT
1 TTTTTTTTTTTAGAGAAGAGAGTT
14991 TTTTTTTTTTT
1 TTTTTTTTTTT
15002 TGGGAAGGCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.02, G:0.19, T:0.58
Consensus pattern (24 bp):
TTTTTTTTTTTAGAGAAGAGAGTT
Found at i:16636 original size:2 final size:2
Alignment explanation
Indices: 16624--16677 Score: 90
Period size: 2 Copynumber: 26.0 Consensus size: 2
16614 ATTCGACTCG
16624 AT AT GAT AT AT AT AT AT AT AT GAT 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
16668 AT AT AT AT AT
1 AT AT AT AT AT
16678 CATGAGAAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 46 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31418 original size:179 final size:178
Alignment explanation
Indices: 31095--31420 Score: 433
Period size: 179 Copynumber: 1.8 Consensus size: 178
31085 CCGATTAAGG
*
31095 TGATTTAAGTGTCTATTAAAAGACTGTTCCATGATCTACAACTTTAATGAAAGACTCAAAAACTA
1 TGATTCAAGTGTCTATTAAAAGACTGTTCCATGATCTACAACTTTAATGAAAGACTCAAAAACTA
* * * * * * * * *
31160 AATTTAATGTTTCAAGTATCAAATATGCTTTCGAAAAATTTATTGTTTTGGTTAACGGGATTAGA
66 AATTTAATGTTTCAAGTATAAAAAATACTTTCCAAAAATTTATTGTTTCGGTTAAAGGAAATAAA
*
31225 CGGTCTACTTAATATTATCAAACTTTTATTTCAGATGTCTTATTGAGA
131 CAGTCTACTTAATATTATCAAACTTTTATTTCAGATGTCTTATTGAGA
* * * * * * *
31273 TGATTCAAGTTTCTCTTGAAAGATTGTTCCATGATCTACAACTTTCATGTAAGACTCGGAAAACT
1 TGATTCAAGTGTCTATTAAAAGACTGTTCCATGATCTACAACTTTAATGAAAGACTC-AAAAACT
31338 AAATTTAATGTTT-AAGGTATAAAAAATAC-TTCCAAAGAA-TTAGTTGTTTCGGTTAAAGGAAA
65 AAATTTAATGTTTCAA-GTATAAAAAATACTTTCCAAA-AATTTA-TTGTTTCGGTTAAAGGAAA
31400 TAAACAGTCTACTTAATATTA
127 TAAACAGTCTACTTAATATTA
31421 CATAATTTGT
Statistics
Matches: 126, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
178 61 0.48
179 65 0.52
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGACTGTTCCATGATCTACAACTTTAATGAAAGACTCAAAAACTA
AATTTAATGTTTCAAGTATAAAAAATACTTTCCAAAAATTTATTGTTTCGGTTAAAGGAAATAAA
CAGTCTACTTAATATTATCAAACTTTTATTTCAGATGTCTTATTGAGA
Found at i:42815 original size:15 final size:15
Alignment explanation
Indices: 42795--42826 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
42785 GGATAGATTG
42795 AAAGAGGGTACATGA
1 AAAGAGGGTACATGA
42810 AAAGAGGGTACATGA
1 AAAGAGGGTACATGA
42825 AA
1 AA
42827 CACATTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.31, T:0.12
Consensus pattern (15 bp):
AAAGAGGGTACATGA
Found at i:54546 original size:9 final size:8
Alignment explanation
Indices: 54529--54555 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
54519 GCGGCATCAG
54529 TTATTTTT
1 TTATTTTT
54537 TTATTTTT
1 TTATTTTT
54545 TTATTTTT
1 TTATTTTT
54553 TTA
1 TTA
54556 ATTATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TTATTTTT
Found at i:57223 original size:4 final size:4
Alignment explanation
Indices: 57214--57238 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
57204 ATTTCAAGAA
57214 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
57239 TTAGTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:60677 original size:15 final size:15
Alignment explanation
Indices: 60646--60694 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
60636 TTTACTTCTA
*
60646 ATAATTTTTTTAGATT
1 ATAATATTTTTA-ATT
60662 ATAATATTTTTAATT
1 ATAATATTTTTAATT
* *
60677 ATAATATTGTTATTT
1 ATAATATTTTTAATT
60692 ATA
1 ATA
60695 GTCATGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (15 bp):
ATAATATTTTTAATT
Found at i:62067 original size:331 final size:330
Alignment explanation
Indices: 61038--66158 Score: 4254
Period size: 331 Copynumber: 15.6 Consensus size: 330
61028 TACTTTACAA
* * * *
61038 CATCTAAGCAAATCTCAGCAACATTGGATTTAAGAATTT-TTTTTACGAGCATCTGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * *
61102 TCGATTTAATTAGAAATTAATTTAGAAAAAAATAAGAAATACGATATTAAAAGCGT-ACAAAGCC
66 TCGATTTAATTAGAAATTAATTCAG--AAAAATATGAAAAACGATATTAAAAGCGTGA-AAAGTC
* * * * * *
61166 CTCCACTCTTTTTGGCGTTGAATTATATA-CTTTTATGAGTATTTTAGCCAAAAATTAAGGAGAA
128 CTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
** * * *
61230 ATCTTTT--ATGTCAATTTTTGTAAAATTTTAGCCGAAATCATGTATAAACAAACCATCACGGTT
193 AAATTTTCGA-GTCAATTTTTGCAAAATTTTAGCCGAAAT--TGCAT--ACTAACCATCACGG--
* * ** * *
61293 TTTTGGCTAAAAACGCGTTCCGGGGACCCGACTCAATTTTGCATGATTTTTGGCTTCAAGACTAC
251 TTTTGGCTAAAAACGCATTCCGGGG-CCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCC
61358 TTGAAATATCTATATT
315 TTGAAATATCTATATT
* * *
61374 CATCTAATCAAATCTCAGCCACATTGGATTTATGGATTTGTTTTTACGAGAATCTGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * * * *
61439 TCGATTTGATTAAAAATTAATTTGAAAAAAATAAGAAAAACGATATTATAAA-CGTCAAAAG-CG
66 TCGATTTAATTAGAAATTAA-TTCAGAAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGTC-
* * * * *
61502 CTTCAATC-TTTTG--GTTGAATTATATA-ATTTTTATAAGCATGTGAGCTAAAAATTGA-GAAA
128 CTTCAATCTTTTTGACGTTGAATTATATATA-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * * * * * ** * * *
61562 ATATTTTTCTAATCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATAACAGTTTTTG
192 AAAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCATACTAACCATCAC-GGTTTTG
* * * ** *
61627 GCTAAAAAAGCATTCTGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGCTAAGACTCCTTGAG
256 GCTAAAAACGCATTCCGGGG-CCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAA
*
61692 ATATCCATATT
320 ATATCTATATT
* * * * * *
61703 CATCTAATCAAATATCAGCCAAATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCGTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * * * *
61768 TCGATTTAATTAGAAACTAATTCAGAAAGATATGAAAAACGCTATTAAAATCGTGAAAAGTTCTC
66 TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTT
* * * * * *
61833 CAATCTTTTTTACGTTAAATTATATATATTTTATGAGTATTTTATCCATAAATAGGGGAAAAAAA
131 CAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAAA
* * * *
61898 TTTTCGAGTCATTTTTTGCAAAGTTTTGGCCAAAATTGCATACTAACCATCACGGTTTTGGCTAA
196 TTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCATACTAACCATCACGGTTTTGGCTAA
* * * * * *
61963 AAATGCATTTCGGGGCCCCGACTCAGTTTTCCATGGTTTTTAGCGCCGACACTCCTTGAAATATC
261 AAACGCATTCCGGGG-CCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATC
62028 TATATT
325 TATATT
* * * *
62034 AATCTAATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCT-AACTCTTGT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAA-TCTTGT
* **
62098 TTCGATTTAATTAGAATTTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAACCCT
65 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * * * *
62163 TCAATCTTTTTGGCATTGAATTATATATTTTTTGTGAGTATTAT-GACTAAAAATTGAGG--AAA
130 TCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAG-CCAAAAATTGAGGAAAAA
* * * * * ** * *
62225 TATCTTTCGAGTTAATTCTTGCAAAATTTTAGCTGAAATCGTGTAATAATCATCACGGTTTTTGG
194 AAT-TTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCATACTAACCATCACGG-TTTTGG
* * * * *
62290 CTAAAAACGCGA-TCCAGGGCCC-AGTTCAATTTTGAATGATTTTTGGCGCCGAAACTCCTTGAA
257 CTAAAAACGC-ATTCCGGGGCCCGA-CTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAA
*
62353 ATACCTATATT
320 ATATCTATATT
* * * * *
62364 AATCTAACCAAATCTCA---AC------------CA-TTGTTTTTACAAACATCTGAATCATT-T
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATC-TTGT
* * * * * *
62412 TT--TTTATAATTAGAAATAAACTCGGTAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAA
65 TTCGATT-TAATTAGAAATTAA-T---TCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
** * * * * * * *
62475 ACCCTTCAATTTTTTTGGCGTTGAATTATACAGTTTTTTTATGAGTATTGTGGCTAAAAATTGA-
125 GTCCTTCAATCTTTTTGACGTTGAATTATATA--TATTTTATGAGTATTTTAGCCAAAAATTGAG
* * * * * * *
62539 GAGAATATTTTTCTG-GTCATTTTTCTGTAAAATTTTAGCCAAAATCGTGC--ACTAACCATCAT
188 GAAAAAAATTTTC-GAGTCAATTTT-TGCAAAATTTTAGCCGAAAT--TGCATACTAACCATCAC
* * * * *
62601 GGTTTTTATTATTATTATTTTTGTTAAAAACGCGTTTCGAGGTCCCGACTCAGTTTTGCATGATT
249 GG---------------TTTTGGCTAAAAACGCATTCCG-GGGCCCGACTCAGTTTTGCATGATT
* *
62666 TTTGGCGTCGAGACTCCTCGAAATATC--TA-T
298 TTTGGCGCCGAGACTCCTTGAAATATCTATATT
* * * *
62696 -A--T--T-AAATCTCAACCACATTGCATTTAAGGATTTATTTTTACAAGCATCTGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * * * *
62755 TCGATTTAATTAGAAATTGATTCAGAAAAATATGAAAAATGATTTTAAAGGCGAGAAAAGTCCTC
66 TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTT
* * *
62820 CAATCTTTTTGGA-GTTGAATTATATAAATTTTATGAGTATTTTAGACAAAAATTGAGGAAAAAT
131 CAATCTTTTT-GACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAA
* * * *
62884 A-TTTCTG-TTCAATTTTTGCAAAATATTAGCCGAAA-T-CATGTACGTTAATCGAAATTACGGT
195 ATTTTC-GAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCA--TAC--TAA-C--CATCACGG-
* * ** ** ** * *
62945 TTTTTGCTAAAAACGCGTTCCGAGACCCCGGTTCAGCGTTGCATGATTTTTTGCTCCGAGACTCC
251 TTTTGGCTAAAAACGCATTCCG-GGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCC
*
63010 TTGAAATATCTACATT
315 TTGAAATATCTATATT
* * * *** * *
63026 CACCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG-TACAACAAGCATCTGAATCATGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * **
63090 TCGATTTAATTAGAAATTAATTC-GAAAAATAATAGGAAAAACGATATTAGAAGCATTAAAAACC
66 TCGATTTAATTAGAAATTAATTCAGAAAAAT-AT--GAAAAACGATATTAAAAGCGTGAAAAGTC
*** **
63154 CTTCAATCTTTTTGGA-GTTGAATTATATA-ATTTTTATGAGTATTGCGGATAAAAATTGAGG-A
128 CTTCAATCTTTTT-GACGTTGAATTATATATA-TTTTATGAGTATTTTAGCCAAAAATTGAGGAA
* * * * * ** * *
63216 TATAATTTTTGAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAATCATCACGGTTTTT
191 AAAAATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCATACTAACCATCACGG-TTTT
* * * * * * * * *
63281 GGCTAAAAGCGCGTTTCGCGACCCAACTAAGTTTTGCATGATTTTTGGCGTCAAGAC-CCTTTGA
255 GGCTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCC-TTGA
* *
63345 GATATCCATATT
319 AATATCTATATT
* * * * * * *
63357 CATTTAATCTAATCTCAGCTACTTTGGATTGAAGAATTTGTTTTTACGAGCATCTGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * * *
63422 TCAATTTAACTACAAAGTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTC
66 TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTT
* * * *
63487 CATTCTTTTTGGCGTT-ACACTATATATATTTTATGAGTATTTTAGCCAAAAATTGTCGG--AAA
131 CAATCTTTTTGACGTTGA-ATTATATATATTTTATGAGTATTTTAGCCAAAAATTG-AGGAAAAA
* * **
63549 AATCTTTCGGGTCAATTTTTGCAAAATTTTAG-C-------CA-A-TAACGAT-----TTTCAGC
194 AAT-TTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCATACTAACCATCACGGTTTTGGC
* *
63599 TAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCGAGCCTCCTTGAAATA
258 TAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATA
* *
63664 CCAATATT
323 TCTATATT
* *
63672 CAACTAATCAAATCTCAGCCACATTGAACTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * * *
63737 TCAATTTAATTAGAAATTAATTCAGGAAAATATGAAAAATGATATTAAAAGCGTGAAAAAGGCTT
66 TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTG-AAAAGTCCT
* * * * * *** ** *
63802 TCAAT-TTTTTGGCATTGAATTATATATTTTTTATGAATATTTTCGCTTGAAATCAAGGAAAAAT
130 TCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAA
* * * *
63866 CTTTT-GAGTCAATTTTTGCAATATTTTAGCCGAAA-T-CATGTACTAACTATCGCGGTTTTCGG
195 ATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCA--TACTAACCATCACGGTTTT-GG
* * * * *** *
63928 CTAAAACCGCATTCCGGGTCCCGACTCAGTTTTGGATTATTTTTGATTCCAAGACTCCTTGAAAT
257 CTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAAT
63993 ATCTATATT
322 ATCTATATT
* * * * *
64002 CATCTAATCATATCTCAGCCACATTAAATTTAAGAATTTGCTTTTACGAGCATCTAAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * * * *
64067 TCAATTTAATTAGAAATTAATT-TGAAAAA-ATAGAAAAAACAATATTAGAAGTGTCAAAAGTCC
66 TCGATTTAATTAGAAATTAATTCAGAAAAATAT-G-AAAAACGATATTAAAAGCGTGAAAAGTCC
* ** * *
64130 ATCAATCTTTTTGATATTGAATTATATATTTTTTATGAGTATTTTACCCAAAAATTGAGG----A
129 TTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
** * * * * *
64191 TCTTTT-GGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTATA-TAAACCATCACAGTTTTTGG
194 AATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCATACT-AACCATCAC-GGTTTTGG
* * * *
64254 CTAAAAACGCATTCCGGGGTCCAACTCAGTTTTGCATGATTTTTGGTGCCGAGCCTCCTTGAAAT
257 CTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAAT
*
64319 ACCTATATT
322 ATCTATATT
* * * * * *
64328 CAACTGATCAAATCTCAGCCACATTTAACTGAAGGATTTGTTTTTACGAGCATCTGGATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * *
64393 TCGACTTAATTAGAAATTAATTCAGGAAAATATGAAAAACAATATTAAAAGCGTGAAAAG----T
66 TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTT
* ** *
64454 CAA---TGTTGGTGTT-ACATTATATATATCTTATGAGTATTTTAGCCAAAAATTGTACGG--AA
131 CAATCTTTTTGACGTTGA-ATTATATATATTTTATGAGTATTTTAGCCAAAAATTG-A-GGAAAA
* * * **
64513 AAATCTTTCGGGTCAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCATCACGGTTTTCG
193 AAAT-TTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCATACTAACCATCACGGTTTT-G
* * * *
64578 GCTAAAAACACATTCCGGGGCCCGACTCAGTTTTACATGATTTTTGGTGCCGAGCCTCCTTGAAA
256 GCTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAA
* *
64643 TACCAATATT
321 TATCTATATT
* * *
64653 CAACTAATCAAATCTCAACCACATTGAACTTAAGGATTTGTTTTTACGAGCATCTGAAATCTTGT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTG-AATCTTGT
* * * *
64718 TTCGATTTAATTAGAAATTAATTCAGGAAAATATGAAAAACGATATTAAAAGTGTGAAAAAGGCT
65 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTG-AAAAGTCC
* * * * *** **
64783 TTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCGCTTGAAATCAAGGAAAAA
129 TTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
* * *
64848 TATTTT-GAGTCAATTTTTGCAATATTTTAGCCGAAA-T-CATGTACTAACCATCGCGGTTTTCG
194 AATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCA--TACTAACCATCACGGTTTT-G
* * * * * * * *
64910 GCTAAAACCGCGTTTCGGGGCCCGGCTCAATTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAC
256 GCTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAA
64975 TATCTATATT
321 TATCTATATT
* * * *
64985 CATCTAACCAAATCGCAGCCACATT-AGATTTAAGAATTTGTTTTTTCGAGCATCTGAATCTTGT
1 CATCTAATCAAATCTCAGCCACATTGA-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
** * * * * * *
65049 TTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACAATATTAGAAGGGTCAAAAGCCC
65 TTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * * *
65114 TTCAATCTTTTTGATGTCGAATTATATAT-TTTAATGAGTATTTTAGCCAAAATTTGTGGAAATA
129 TTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
** * * * * *
65178 TCTTTT-GGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTATACTAACCATCACGGTTTTCAGC
194 AATTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCATACTAACCATCACGGTTTT-GGC
** * * * *
65242 TAAAAACG-AGTTCCATGACCACGGCTCAATTTTGCATTATTTTTGGCGCCGAGACTCCTTGAAA
258 TAAAAACGCA-TTCCGGGGCC-CGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAA
*
65306 TATCTTTATT
321 TATCTATATT
* * ** * * * *
65316 CATCTAATCAAATCTTAGGCACATT-AGATTTAAAAATTTGTTTTTATGTGCATTTGAATTTTGT
1 CATCTAATCAAATCTCAGCCACATTGA-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
65380 TTCGATTTAATTAGAAATTAATTCAAAATAAATATGAAAAACGATATTAAAAGCGTGAAAAGTAC
65 TTCGATTTAATTAGAAATTAATTCAGAA-AAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * * * *
65445 TGCAATCCTTTTGACGTTGAATTATATAT-TTTTATGAGTATTTTCGCTAGAAATCGTGG--AAA
129 TTCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
*
65507 AATCTTTCG-GCTCAATTTTTGCAAAAGTTTAGCCGAAA-T-CAGTACTAACCATCACGGTTTTC
194 AAT-TTTCGAG-TCAATTTTTGCAAAATTTTAGCCGAAATTGCA-TACTAACCATCACGGTTTT-
* * * * * * * *
65569 GGCTAAAACCGCGTTCCGGGGTCCGGCTCTGTTTTGCATGATTTTCGGTGCCAAGACTCCTTGAA
255 GGCTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAA
65634 ATATCTATATT
320 ATATCTATATT
* * * * *
65645 CATCTAACCAAATCTCAGCCACATTAAATTTAACGATTTGCTTTTACGACCATCTGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * * * * * *
65710 TCGA--T--TT---AA-T--TTGA-AAAAATAGGAAAAACAATATTAGAAGCTTTAAAAGCCCTT
66 TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTT
* * ** * * **
65764 CAATGTTTTTGATGTCAAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATC
131 CAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAAA
* ** ** *
65829 TTTT-GGGTCAATTTTTGCAAAATTTTAGTTGAAATCGTGC--ACTAACCATCACATTTTTTTCG
196 TTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAAT--TGCATACTAACCATCAC--GGTTTTGG
* * * * * * * * *
65891 CTAAAAACGCCTTCCAGGGCACGGCTCTGTTTTGCATGATTCTTGGCACCAAGACTTCTTGAAAT
257 CTAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAAT
* * *
65956 ATTTTTTTT
322 ATCTATATT
* * * * ** * *
65965 CATCTATTCAAATTTCAGGCACATTGGATTTAAGGATTTGTTTTTGTGTGCATCCGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* *
66030 TCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAAACGTGAAAAGTCCT
66 TCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * * * *
66095 CCAATCCTGTTGGCGTTGAATTATATATAATTTATGAGTATTTTTGCCAAAAATTGAGGAAAAA
130 TCAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
66159 TCTTTCGGGT
Statistics
Matches: 3870, Mismatches: 717, Indels: 400
0.78 0.14 0.08
Matches are distributed among these distances:
312 2 0.00
313 12 0.00
314 46 0.01
315 214 0.06
316 17 0.00
317 115 0.03
318 54 0.01
319 96 0.02
320 157 0.04
321 13 0.00
322 10 0.00
323 3 0.00
324 16 0.00
325 169 0.04
326 275 0.07
327 87 0.02
328 43 0.01
329 286 0.07
330 527 0.14
331 673 0.17
332 388 0.10
333 36 0.01
334 113 0.03
335 97 0.03
336 121 0.03
337 187 0.05
338 10 0.00
339 55 0.01
340 1 0.00
341 8 0.00
342 25 0.01
343 12 0.00
344 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (330 bp):
CATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTT
CAATCTTTTTGACGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAAA
TTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATTGCATACTAACCATCACGGTTTTGGCTAA
AAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCT
ATATT
Found at i:62782 original size:656 final size:646
Alignment explanation
Indices: 61085--66165 Score: 2217
Period size: 656 Copynumber: 7.7 Consensus size: 646
61075 TTTTTTTACG
* * ** * *
61085 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTTAGAAAAAAATAAGAAATACGATAT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATAAACTCGA-AAAAAAATAGGAAAAACGATAT
* * * * * * * * ***
61149 TAAAAGCGT-ACAAAGCCCTCCACTCTTTTTGGCGTTGAATTATA-TACTTTTATGAGTATTTTA
65 TAGAAGCATGA-AAAACCCTTCAATCTTTTTGGAGTTGAATTATACAATTTTTATGAGTATTGCG
** * * * * * *
61212 GCCAAAAATTAAGGAGA-AATCTTTT-ATGTCAATTTTTGTAAAATTTTAGCCGAAATCATGTAT
129 GATAAAAATTGAGGATATAAT-TTTTGA-GTCAATTTTTGCAAAATTCTAGCCAAAATC--GT-G
* * * * *
61275 AAACAAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGGACCCGACTCAA-TTTTGCATGA
189 CAA-TAACCATCACGG-TTTTTGGCTAAAAACGCGTTTC-GCGACCCAACT-AAGTTTTGCATGA
* * * *
61339 TTTTTGGCTTCAAGACTACTT-GAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGAT
250 TTTTTGGCGTCAAGAC-CCTTCGAAATATC--TA-T-A--T--T-AAATCT-AACCACATTGCAT
* * * * * *
61403 TTATGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTGATTAAAAATTAATTTGAAAAA
304 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCAGAAA
* * *
61468 AATAAGAAAAACGATATTATAAA-CGTCAAAAG-CGCTTCAATC-TTTTGG--TTGAATTATATA
368 AATATGAAAAACGATATTA-AAAGCGTGAAAAGTC-CTCCAATCTTTTTGGCATTGAATTATATA
* * * * * * * *
61528 -ATTTTTATAAGCATGTGAGCTAAAAATTGA-GAAAATATTTTTCTAATCAATTTTTACAAAATT
431 TA-TTTTATGAGTATTTGA-C-AAAAATTGAGGAAAA-ATCTTTCGAGTTAATTTTTGCAAAATT
* * * * * * * ** *
61591 TTAGCCGAAATCGTGTA-ATAA-CCATAACAGTTTTTGGCTAAAAAAGC-ATTCTGGGGTCCCGG
492 TTAGCCGAAATCATGTACATAATCAATCACGGTTTTTGGCTAAAAACGCGA-TCCGAGACCCCAG
* *** * * * * * * *
61653 CTCAGTTTTGCATGATTTTTGGCG-CTAAGACTCCTTGAGATATCC-ATATTCATCTAATCAAAT
556 TTCAACGTTGAATGATTTTTGGCGCCGAA-ACTCCTTGAAATA-CCTACATTAACCTAACCAAAT
* * * ***
61716 ATCAGCCAAATTGGATTTAAGAATTTGTTTTTACA
619 CTCAGACACATTGG--TT----ATTTG-TACAACA
* * * * * *
61751 AGCATCTGAATCGTGTTTCGATTTAATTAGAAACT-AATTC--AGAAAGATATGAAAAACGCTAT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAA-TAAACTCGAAAAAAAATAGGAAAAACGATAT
* * * *** * * * *
61813 TAAAATCGTGAAAAGTTCTCCAATCTTTTT-TACGTTAAATTATA-TATATTTTATGAGTATT--
65 TAGAAGCATGAAAAACCCTTCAATCTTTTTGGA-GTTGAATTATACAAT-TTTTATGAGTATTGC
** * * * * * * * * * *
61874 TTATCCATAAATAGGGGAAAAAAATTTTCGAGTCATTTTTTGCAAAGTTTTGGCCAAAAT--TGC
128 GGAT--AAAAATTGAGG-ATATAATTTTTGAGTCAATTTTTGCAAAATTCTAGCCAAAATCGTGC
* * * * * * * *
61937 ATACTAACCATCACGG-TTTTGGCTAAAAATGCATTTCGGGGCCCCGACTCAGTTTTCCATGGTT
190 A-A-TAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GCGACCCAACTAAGTTTTGCATGATT
* * * * *
62001 TTTAGCGCCGACACTCCTT-GAAATATCTATATTAATCTAATAAAATCTTAGCCACATTGCATTT
252 TTTGGCGTCAAGAC-CCTTCGAAATATC--TA-T-A--T--T-AAATC-TAACCACATTGCATTT
*
62065 AAGGATTTGTTTTTACGAGCATCT-AACTCTTGTTTCGATTTAATTAGAATTTAATTCAGAAAAA
306 AAGGATTTGTTTTTACGAGCATCTGAA-TCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAA
** * *
62129 TATGAAAAACGATATTAAAAGCGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATATATTTT
370 TATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATT
* * * *
62194 TTGTGAGTATTATGACTAAAAATTGAGGAAATATCTTTCGAGTTAATTCTTGCAAAATTTTAGCT
435 TTATGAGTATT-TGAC-AAAAATTGAGGAAAAATCTTTCGAGTTAATTTTTGCAAAATTTTAGCC
* ** **
62259 GAAATCGTGTA-ATAATC-ATCACGGTTTTTGGCTAAAAACGCGATCC-AGGGCCCAGTTCAATT
498 GAAATCATGTACATAATCAATCACGGTTTTTGGCTAAAAACGCGATCCGAGACCCCAGTTCAACG
* *
62321 TTGAATGATTTTTGGCGCCGAAACTCCTTGAAATACCTATATTAATCTAACCAAATCTCA-AC-C
563 TTGAATGATTTTTGGCGCCGAAACTCCTTGAAATACCTACATTAACCTAACCAAATCTCAGACAC
62384 ATT-G-T-TTT-TAC-A-A
628 ATTGGTTATTTGTACAACA
**
62397 A-CATCTGAATCAT-TTT-TTTTATAATTAGAAATAAACTCGGTAAAAAAAATAGGAAAAACGAT
1 AGCATCTGAATCATGTTTCGATT-TAATTAGAAATAAACTC-G-AAAAAAAATAGGAAAAACGAT
* * * *
62459 ATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATACAGTTTTTTTATGAGTATT
63 ATTAGAAGCATGAAAAACCCTTCAATCTTTTTGGAGTTGAATTATACA--ATTTTTATGAGTATT
* * * * * *
62524 GTGGCTAAAAATTGAGAGA-ATATTTTTCTG-GTCATTTTTCTGTAAAATTTTAGCCAAAATCGT
126 GCGGATAAAAATTGAG-GATATAATTTT-TGAGTCAATTTT-TGCAAAATTCTAGCCAAAATCGT
* * * * * * * *
62587 GCACTAACCATCATGGTTTTTATTATTATTATTTTTGTTAAAAACGCGTTTCGAGGTCCCGACTC
188 GCAATAACCATCACGG-------------T-TTTTGGCTAAAAACGCGTTTCG-CGACCCAACTA
*
62652 AGTTTTGCATGATTTTTGGCGTCGAGACTCC-TCGAAATATCTATATTAAATCTCAACCACATTG
238 AGTTTTGCATGATTTTTGGCGTCAAGAC-CCTTCGAAATATCTATATTAAATCT-AACCACATTG
* * *
62716 CATTTAAGGATTTATTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTGATTCAGA
301 CATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGA
* * * *
62781 AAAATATGAAAAATGATTTTAAAGGCGAGAAAAGTCCTCCAATCTTTTTGG-AGTTGAATTATAT
366 AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCA-TTGAATTATAT
* * * *
62845 AAATTTTATGAGTATTTTAGACAAAAATTGAGGAAAAATATTTC-TGTTCAATTTTTGCAAAATA
430 ATATTTTATGAGTA-TTT-GACAAAAATTGAGGAAAAATCTTTCGAGTT-AATTTTTGCAAAATT
* * * *
62909 TTAGCCGAAATCATGTACGTTAATCGAAATTACGGTTTTTTGCTAAAAACGCGTTCCGAGACCCC
492 TTAGCCGAAATCATGTAC-ATAATC--AATCACGGTTTTTGGCTAAAAACGCGATCCGAGACCCC
* * * * * * * *
62974 GGTTCAGCGTTGCATGATTTTTTGCTCCGAGACTCCTTGAAATATCTACATTCACCTAACCAAAT
554 AGTTCAACGTTGAATGATTTTTGGCGCCGAAACTCCTTGAAATACCTACATTAACCTAACCAAAT
*
63039 CTCAGCCACATTGGATTTAAGGATTTGTACAACA
619 CTCAGACACATTGG--TT----ATTTGTACAACA
* * *
63073 AGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGAAAAATAATAGGAAAAACGATATT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATAAACTCGAAAAAAAATAGGAAAAACGATATT
* *
63138 AGAAGCATTAAAAACCCTTCAATCTTTTTGGAGTTGAATTATATAATTTTTATGAGTATTGCGGA
66 AGAAGCATGAAAAACCCTTCAATCTTTTTGGAGTTGAATTATACAATTTTTATGAGTATTGCGGA
* * *
63203 TAAAAATTGAGGATATAATTTTTGAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAAT
131 TAAAAATTGAGGATATAATTTTTGAGTCAATTTTTGCAAAATTCTAGCCAAAATCGTGCAATAAC
*
63268 CATCACGGTTTTTGGCTAAAAGCGCGTTTCGCGACCCAACTAAGTTTTGCATGATTTTTGGCGTC
196 CATCACGGTTTTTGGCTAAAAACGCGTTTCGCGACCCAACTAAGTTTTGCATGATTTTTGGCGTC
* * * * * *
63333 AAGACCCTTTGAGATATCCATATTCATTTAATCTAATCTCAGCTACTTTGGATTGAAGAATTTGT
261 AAGACCCTTCGAAATAT-C-TA-T-ATTAAATCTAA-C-CA-C-A--TTGCATTTAAGGATTTGT
* * * *
63398 TTTTACGAGCATCTGAATCTTGTTTCAATTTAACTACAAAGTAATTCAGAAAAATATGAAAAACG
316 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACG
* * *
63463 ATATTAAAAGCGTGAAAAGTCCTCCATTCTTTTTGGCGTT-ACACTATATATATTTTATGAGTAT
381 ATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTGA-ATTATATATATTTTATGAGTA-
* * * *
63527 TTTAGCCAAAAATTGTCGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC--AAT-A--
444 TTT-GACAAAAATTG-AGGAAAAATCTTTCGAGTTAATTTTTGCAAAATTTTAGCCGAAATCATG
* * * * * *** *
63587 -ACGAT--T--TTCA---------GCTAAAAACGC-ATTCCGGGGCCCGA-CTCAGTTTTGCATG
507 TAC-ATAATCAATCACGGTTTTTGGCTAAAAACGCGA-TCCGAGACCCCAGTTCAACGTTGAATG
* ** * * * *
63636 ATTTTTGGTGCCGAGCCTCCTTGAAATACCAATATTCAA-CTAATCAAATCTCAGCCACATTGAA
570 ATTTTTGGCGCCGAAACTCCTTGAAATACCTACATT-AACCTAACCAAATCTCAGACACATTG--
* *** *
63700 CTTAAGGATTTGTTTTTACG
632 GTT----ATTTG-TACAACA
* * * * ** * *
63720 AGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTC--AGGAAAATATGAAAAATGATATT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATAAACTCGAAAAAAAATAGGAAAAACGATATT
* * * * * * * *
63783 AAAAGCGTGAAAAAGGCTTTCAAT-TTTTTGGCA-TTGAATTATATATTTTTTATGAATATTTTC
66 AGAAGCATGAAAAA-CCCTTCAATCTTTTTGG-AGTTGAATTATACAATTTTTATGAGTA-TTGC
* ** ** * * * * * * *
63846 -GCTTGAAATCAAGGA-AAAATCTTTTGAGTCAATTTTTGCAATATTTTAGCCGAAATCATGTAC
128 GGATAAAAATTGAGGATATAAT-TTTTGAGTCAATTTTTGCAAAATTCTAGCCAAAATCGTGCAA
* * * * * * * * * * * *
63909 TAACTATCGCGGTTTTCGGCTAAAACCGCATTCCGGGTCCCGACTCAGTTTTGGATTATTTTT-G
192 TAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGCGACCCAACTAAGTTTTGCATGATTTTTGG
** ** *
63973 ATTCCAAGACTCCTT-GAAATATCTATATTCATCTAATCATATCTCAGCCACATTAAATTTAAGA
257 CGT-CAAGAC-CCTTCGAAATATCTATATT-A---AATC-TA----A-CCACATTGCATTTAAGG
* * * *
64037 ATTTGCTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAGAAATTAATT-TGAAAAA-ATAG
310 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAT-G
* * * * ** *
64100 AAAAAACAATATTAGAAGTGTCAAAAGTCCAT-CAATCTTTTTGATATTGAATTATATATTTTTT
374 -AAAAACGATATTAAAAGCGTGAAAAGTCC-TCCAATCTTTTTGGCATTGAATTATATATATTTT
* * * * *
64164 ATGAGTATTTTACCCAAAAATTGAGG----ATCTTTTGGGTCAATTTTTGTAAAATTTTAGCCGA
437 ATGAGTATTTGA--CAAAAATTGAGGAAAAATCTTTCGAGTTAATTTTTGCAAAATTTTAGCCGA
* * * * *** ** ***
64225 AATC--GTATATAAACCATCACAGTTTTTGGCTAAAAACGC-ATTCCG-GGGTCCAACTCAGTTT
500 AATCATGTACATAATCAATCACGGTTTTTGGCTAAAAACGCGA-TCCGAGACCCCAGTTCAACGT
* * ** * * * *
64286 TGCATGATTTTTGGTGCCGAGCCTCCTTGAAATACCTATATTCAA-CTGATCAAATCTCAGCCAC
564 TGAATGATTTTTGGCGCCGAAACTCCTTGAAATACCTACATT-AACCTAACCAAATCTCAGACAC
* *** *
64350 ATTTAACTGAAG-GATTTGTTTTTACG
628 A--T---TG--GTTATTTG-TACAACA
* * * * * ** * *
64376 AGCATCTGGATCTTGTTTCGACTTAATTAGAAATTAATTC--AGGAAAATATGAAAAACAATATT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATAAACTCGAAAAAAAATAGGAAAAACGATATT
* * * * * * * ***
64439 AAAAGCGTG-AAAA---GTCAA---TGTTGGTGTT-ACATTATA-TATATCTTATGAGTATTTTA
66 AGAAGCATGAAAAACCCTTCAATCTTTTTGGAGTTGA-ATTATACAAT-TTTTATGAGTATTGCG
** * * * * *
64495 GCCAAAAATTGTACGGA-AAAATCTTTCGGGTCAATTTTTGCAAAATT-TCAGCCGAAATCGTGT
129 GATAAAAATTG-A-GGATATAAT-TTTTGAGTCAATTTTTGCAAAATTCT-AGCCAAAATCGTGC
* * * * * * * * * *
64558 ACTAACCATCACGGTTTTCGGCTAAAAACACATTCCGGGGCCCGACTCAGTTTTACATGATTTTT
190 AATAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGCGACCCAACTAAGTTTTGCATGATTTTT
* * * * * * *
64623 GGTGCCGAGCCTCCTT-GAAATACCAATATTCAACTAATCAAATCTCAACCACATTGAACTTAAG
255 GGCGTCAAGAC-CCTTCGAAATATC--TA-T--A-T--T-AAATCT-AACCACATTGCATTTAAG
*
64687 GATTTGTTTTTACGAGCATCTGAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGGAAAATAT
309 GATTTGTTTTTACGAGCATCTG-AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAT
* * * * * * *
64752 GAAAAACGATATTAAAAGTGTGAAAAAGGCTTTCAATTTTTTTGGCGTTGAATTATATATTTTTT
373 GAAAAACGATATTAAAAGCGTG-AAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATTTT
** ** * * * *
64817 ATGAGTATTTTCG-CTTGAAATCAAGGAAAAATATTTTGAGTCAATTTTTGCAATATTTTAGCCG
437 ATGAGTA-TTT-GAC-AAAAATTGAGGAAAAATCTTTCGAGTTAATTTTTGCAAAATTTTAGCCG
* * * * * * ** * * **
64881 AAATCATGTAC-TAA-CCATCGCGGTTTTCGGCTAAAACCGCGTTTCG-GGGCCCGGCTCAATTT
499 AAATCATGTACATAATCAATCACGGTTTTTGGCTAAAAACGCGATCCGAGACCCCAGTTCAACGT
* * * * * * * * *
64943 TGCATGATTTTTGGTGCC-AAGACTCCTTGAACTATCTATATTCATCTAACCAAATCGCAGCCAC
564 TGAATGATTTTTGGCGCCGAA-ACTCCTTGAAATACCTACATTAACCTAACCAAATCTCAGACAC
* **** *
65007 ATTAGATTTAAGAATTTGTTTTTTCG
628 ATT-G-GTT----ATTTG-TACAACA
* * * * * *
65033 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTG-GAAAAAATAGGAAAAACAATATT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATAAACTCGAAAAAAAATAGGAAAAACGATATT
** * * * * * ***
65097 AGAAGGGTCAAAAGCCCTTCAATCTTTTT-GATGTCGAATTATA-TATTTTAATGAGTATTTTAG
66 AGAAGCATGAAAAACCCTTCAATCTTTTTGGA-GTTGAATTATACAATTTTTATGAGTATTGCGG
** * * * * * * * ** *
65160 CCAAAATTTGTGGAAAT-ATCTTTTGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTATACTA
130 ATAAAAATTGAGGATATAAT-TTTTGAGTCAATTTTTGCAAAATTCTAGCCAAAATCGTGCAATA
** * * ** ** *
65224 ACCATCACGGTTTTCAGCTAAAAACGAGTTCCATGACCACGGCTCAA-TTTTGCATTATTTTTGG
194 ACCATCACGGTTTTTGGCTAAAAACGCGTTTCGCGACC-CAACT-AAGTTTTGCATGATTTTTGG
* * ** **
65288 CGCCGAGACTCCTT-GAAATATCTTTATTCATCTAATCAAATCTTAGGCACATTAG-ATTTAAAA
257 CGTCAAGAC-CCTTCGAAATATC--TA-T-A--T--T-AAATC-TAACCACATT-GCATTTAAGG
* * * * *
65351 ATTTGTTTTTATGTGCATTTGAATTTTGTTTCGATTTAATTAGAAATTAATTCAAAATAAATATG
310 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA-AAATATG
* * * * *
65416 AAAAACGATATTAAAAGCGTGAAAAGTACTGCAATCCTTTTGACGTTGAATTATATAT-TTTTAT
374 AAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATTTTAT
* * * * *
65480 GAGTATTTTCG-CTAGAAATCGTGGAAAAATCTTTCG-GCTCAATTTTTGCAAAAGTTTAGCCGA
439 GAGTA-TTT-GAC-AAAAATTGAGGAAAAATCTTTCGAG-TTAATTTTTGCAAAATTTTAGCCGA
* * * * *** * * ****
65543 AATCA-GTAC-TAA-CCATCACGGTTTTCGGCTAAAACCGCGTTCCG-GGGTCCGGCTCTGTTTT
500 AATCATGTACATAATCAATCACGGTTTTTGGCTAAAAACGCGATCCGAGACCCCAGTTCAACGTT
* * * * * * * *
65604 GCATGATTTTCGGTGCC-AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACA
565 GAATGATTTTTGGCGCCGAA-ACTCCTTGAAATACCTACATTAACCTAACCAAATCTCAGACACA
** *** *
65668 TTAAATTTAACGATTTGCTTTTACG
629 TT--GGTT----ATTTG-TACAACA
* * *
65693 ACCATCTGAATCTTGTTTCGATTTAA-T-----T----T-G--AAAAAATAGGAAAAACAATATT
1 AGCATCTGAATCATGTTTCGATTTAATTAGAAATAAACTCGAAAAAAAATAGGAAAAACGATATT
* * * * ** * * ***
65745 AGAAGCTTTAAAAGCCCTTCAATGTTTTT-GATGTCAAATTATATATTTTTTATGAGTATTTTAG
66 AGAAGCATGAAAAACCCTTCAATCTTTTTGGA-GTTGAATTATACAATTTTTATGAGTATTGCGG
** * * * *** *
65809 CCAAAAATTGAGGAAAT-ATCTTTTGGGTCAATTTTTGCAAAATTTTAGTTGAAATCGTGCACTA
130 ATAAAAATTGAGGATATAAT-TTTTGAGTCAATTTTTGCAAAATTCTAGCCAAAATCGTGCAATA
** * * * * * ** ** *
65873 ACCATCACATTTTTTTCGCTAAAAACGCCTTCCAG-GGCACGGCTCTGTTTTGCATGATTCTTGG
194 ACCATCAC-GGTTTTTGGCTAAAAACGCGTTTC-GCGACCCAACTAAGTTTTGCATGATTTTTGG
** * * * ** *
65937 CACCAAGACTTCTT-GAAATATTTTTTTTCATCTATTCAAATTTCAGGCACATTGGATTTAAGGA
257 CGTCAAGAC-CCTTCGAAATA-------TC-TATATT-AAATCT-AACCACATTGCATTTAAGGA
** * * *
66001 TTTGTTTTTGTGTGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGA
311 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGA
* * * * *
66066 AAAACGATATTAAAAACGTGAAAAGTCCTCCAATCCTGTTGGCGTTGAATTATATATAATTTATG
375 AAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATTTTATG
*
66131 AGTATTTTTGCCAAAAATTGAGGAAAAATCTTTCG
440 AGTA--TTTGACAAAAATTGAGGAAAAATCTTTCG
66166 GGTCATTTTT
Statistics
Matches: 3632, Mismatches: 550, Indels: 482
0.78 0.12 0.10
Matches are distributed among these distances:
640 31 0.01
641 3 0.00
642 4 0.00
643 9 0.00
644 37 0.01
645 305 0.08
646 94 0.03
647 66 0.02
648 120 0.03
649 295 0.08
650 111 0.03
651 161 0.04
652 59 0.02
653 58 0.02
654 8 0.00
655 17 0.00
656 367 0.10
657 185 0.05
658 79 0.02
659 76 0.02
660 308 0.08
661 160 0.04
662 333 0.09
663 126 0.03
664 88 0.02
665 99 0.03
666 68 0.02
667 146 0.04
668 33 0.01
669 2 0.00
673 39 0.01
674 46 0.01
675 1 0.00
676 65 0.02
677 13 0.00
678 18 0.00
679 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (646 bp):
AGCATCTGAATCATGTTTCGATTTAATTAGAAATAAACTCGAAAAAAAATAGGAAAAACGATATT
AGAAGCATGAAAAACCCTTCAATCTTTTTGGAGTTGAATTATACAATTTTTATGAGTATTGCGGA
TAAAAATTGAGGATATAATTTTTGAGTCAATTTTTGCAAAATTCTAGCCAAAATCGTGCAATAAC
CATCACGGTTTTTGGCTAAAAACGCGTTTCGCGACCCAACTAAGTTTTGCATGATTTTTGGCGTC
AAGACCCTTCGAAATATCTATATTAAATCTAACCACATTGCATTTAAGGATTTGTTTTTACGAGC
ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAG
CGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATTTTATGAGTATTTGACAAAAAT
TGAGGAAAAATCTTTCGAGTTAATTTTTGCAAAATTTTAGCCGAAATCATGTACATAATCAATCA
CGGTTTTTGGCTAAAAACGCGATCCGAGACCCCAGTTCAACGTTGAATGATTTTTGGCGCCGAAA
CTCCTTGAAATACCTACATTAACCTAACCAAATCTCAGACACATTGGTTATTTGTACAACA
Found at i:63540 original size:330 final size:330
Alignment explanation
Indices: 62625--66175 Score: 3548
Period size: 330 Copynumber: 10.9 Consensus size: 330
62615 TTATTTTTGT
* * * * * *
62625 TAAAAACGCGTTTCGAGGTCCCGACTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTCGAAAT
1 TAAAAACGCGTTCCG-GGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAAT
* * * *
62690 ATC--TA-T-A--T--T-AAATCTCAACCACATTGCATTTAAGGATTTATTTTTACAAGCATCTG
65 ATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTG
* * * * *
62746 AATCTTGTTTCGATTTAATTAGAAATTGATTCAGAAAAATATGAAAAATGATTTTAAAGGCGAGA
130 AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGA
* * *
62811 AAAGTCCTCCAATCTTTTTGGAGTTGAATTATATAAATTTTATGAGTATTTTAGACAAAAATTGA
195 AAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGA
* * * * * *
62876 GGAAAAATATTTCT-GTTCAATTTTTGCAAAATATTAGCCGAAATCATGTACGTTAATCGAAATT
260 GGAAAAATCTTT-TGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TAA-C--CATC
**
62940 ACGGTTTTTTGC
319 ACGGTTTTCGGC
** ** ** * *
62952 TAAAAACGCGTTCCGAGACCCCGGTTCAGCGTTGCATGATTTTTTGCT-CCGAGACTCCTTGAAA
1 TAAAAACGCGTTCCG-GGGCCCGACTCAGTTTTGCATGA-TTTTTGGTGCCAAGACTCCTTGAAA
* * * * *** *
63016 TATCTACATTCACCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG-TACAACAAGCATCT
64 TATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCT
* *
63080 GAATCATGTTTCGATTTAATTAGAAATTAATTC-GAAAAATAATAGGAAAAACGATATTAGAAGC
129 GAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAT-AT--GAAAAACGATATTAAAAGC
* * ** * * *** **
63144 ATTAAAAACCCTTCAATCTTTTTGGAGTTGAATTATATA-ATTTTTATGAGTATTGCGGATAAAA
191 GTGAAAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTTTAGCCAAAA
* * * * *
63208 ATTGAGGATATAAT-TTTTGAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAATCATC
255 ATTGAGGA-AAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
*
63272 ACGGTTTTTGGC
319 ACGGTTTTCGGC
* * * * * * * * *
63284 TAAAAGCGCGTTTCGCGACCCAACTAAGTTTTGCATGATTTTTGGCGTCAAGAC-CCTTTGAGAT
1 TAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCC-TTGAAAT
* * * * * * * *
63348 ATCCATATTCATTTAATCTAATCTCAGCTACTTTGGATTGAAGAATTTGTTTTTACGAGCATCTG
65 ATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTG
* * * *
63413 AATCTTGTTTCAATTTAACTACAAAGTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGA
130 AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGA
* *
63478 AAAGTCCTCCATTCTTTTTGGCGTT-ACACTATATATATTTTATGAGTATTTTAGCCAAAAATTG
195 AAAGTCCTCCAATCTTTTTGGCGTTGA-ATTATATATATTTTATGAGTATTTTAGCCAAAAATTG
* * *
63542 TCGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC---A------A-T----A--ACGA
259 -AGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG
*
63591 TTTTCAGC
323 TTTTCGGC
* * *
63599 TAAAAACGCATTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCGAGCCTCCTTGAAATA
1 TAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATA
* * * *
63664 CCAATATTCAACTAATCAAATCTCAGCCACATTGAACTTAAGGATTTGTTTTTACGAGCATCTGA
66 TCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGA
* * *
63729 ATCTTGTTTCAATTTAATTAGAAATTAATTCAGGAAAATATGAAAAATGATATTAAAAGCGTGAA
131 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTG-A
* * * * * * * *** **
63794 AAAGGCTTTCAAT-TTTTTGGCATTGAATTATATATTTTTTATGAATATTTTCGCTTGAAATCAA
195 AAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGA
* * * * *
63858 GGAAAAATCTTTTGAGTCAATTTTTGCAATATTTTAGCCGAAATCATGTACTAACTATCGCGGTT
260 GGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTT
63923 TTCGGC
325 TTCGGC
* * * * * * *
63929 TAAAACCGCATTCCGGGTCCCGACTCAGTTTTGGATTATTTTTGATTCCAAGACTCCTTGAAATA
1 TAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATA
* * * * *
63994 TCTATATTCATCTAATCATATCTCAGCCACATTAAATTTAAGAATTTGCTTTTACGAGCATCTAA
66 TCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGA
* * * * * *
64059 ATCTTGTTTCAATTTAATTAGAAATTAATT-TGAAAAA-ATAGAAAAAACAATATTAGAAGTGTC
131 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAT-G-AAAAACGATATTAAAAGCGTG
*** * *
64122 AAAAGTCCAT-CAATCTTTTTGATATTGAATTATATATTTTTTATGAGTATTTTACCCAAAAATT
194 AAAAGTCC-TCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATT
* * *
64186 GAGG----ATCTTTTGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTATA-TAAACCATCACA
258 GAGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-AACCATCACG
*
64246 GTTTTTGGC
322 GTTTTCGGC
* * * * *
64255 TAAAAACGCATTCCGGGGTCCAACTCAGTTTTGCATGATTTTTGGTGCCGAGCCTCCTTGAAATA
1 TAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATA
* * * * * * *
64320 CCTATATTCAACTGATCAAATCTCAGCCACATTTAACTGAAGGATTTGTTTTTACGAGCATCTGG
66 TCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGA
* * *
64385 ATCTTGTTTCGACTTAATTAGAAATTAATTCAGGAAAATATGAAAAACAATATTAAAAGCGTGAA
131 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
* * *
64450 AAG---T-CAA---TGTTGGTGTT-ACATTATATATATCTTATGAGTATTTTAGCCAAAAATTGT
196 AAGTCCTCCAATCTTTTTGGCGTTGA-ATTATATATATTTTATGAGTATTTTAGCCAAAAATTG-
* *
64507 ACGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCATCACGG
259 A-GGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG
64572 TTTTCGGC
323 TTTTCGGC
* * * * *
64580 TAAAAACACATTCCGGGGCCCGACTCAGTTTTACATGATTTTTGGTGCCGAGCCTCCTTGAAATA
1 TAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATA
* * * * *
64645 CCAATATTCAACTAATCAAATCTCAACCACATTGAACTTAAGGATTTGTTTTTACGAGCATCTGA
66 TCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTG-
* *
64710 AATCTTGTTTCGATTTAATTAGAAATTAATTCAGGAAAATATGAAAAACGATATTAAAAGTGTGA
130 AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTG-
* * * * * * *** **
64775 AAAAGGCTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCGCTTGAAATCA
194 AAAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTG
* * * * *
64840 AGGAAAAATATTTTGAGTCAATTTTTGCAATATTTTAGCCGAAATCATGTACTAACCATCGCGGT
259 AGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
64905 TTTCGGC
324 TTTCGGC
* * * * *
64912 TAAAACCGCGTTTCGGGGCCCGGCTCAATTTTGCATGATTTTTGGTGCCAAGACTCCTTGAACTA
1 TAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATA
* * * *
64977 TCTATATTCATCTAACCAAATCGCAGCCACATT-AGATTTAAGAATTTGTTTTTTCGAGCATCTG
66 TCTATATTCATCTAATCAAATCTCAGCCACATTGA-ATTTAAGGATTTGTTTTTACGAGCATCTG
** * * * * *
65041 AATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACAATATTAGAAGGGTC
130 AATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTG
* * ** * * *
65106 AAAAGCCCTTCAATCTTTTTGATGTCGAATTATATAT-TTTAATGAGTATTTTAGCCAAAATTTG
194 AAAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTG
* * * *
65170 TGGAAATATCTTTTGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTATACTAACCATCACGGT
259 AGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
*
65235 TTTCAGC
324 TTTCGGC
* ** * * * * * *
65242 TAAAAACGAGTTCCATGACCACGGCTCAATTTTGCATTATTTTTGGCGCCGAGACTCCTTGAAAT
1 TAAAAACGCGTTCCGGGGCC-CGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAAT
* * * ** * * *
65307 ATCTTTATTCATCTAATCAAATCTTAGGCACATT-AGATTTAAAAATTTGTTTTTATGTGCATTT
65 ATCTATATTCATCTAATCAAATCTCAGCCACATTGA-ATTTAAGGATTTGTTTTTACGAGCATCT
* *
65371 GAATTTTGTTTCGATTTAATTAGAAATTAATTCAAAATAAATATGAAAAACGATATTAAAAGCGT
129 GAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA-AAATATGAAAAACGATATTAAAAGCGT
* * * * * * * *
65436 GAAAAGTACTGCAATCCTTTTGACGTTGAATTATATAT-TTTTATGAGTATTTTCGCTAGAAATC
193 GAAAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATT
* * * * *
65500 GTGGAAAAATCTTTCGGCTCAATTTTTGCAAAAGTTTAGCCGAAATC-AGTACTAACCATCACGG
258 GAGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG
65564 TTTTCGGC
323 TTTTCGGC
* * * * *
65572 TAAAACCGCGTTCCGGGGTCCGGCTCTGTTTTGCATGATTTTCGGTGCCAAGACTCCTTGAAATA
1 TAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATA
* * * * *
65637 TCTATATTCATCTAACCAAATCTCAGCCACATTAAATTTAACGATTTGCTTTTACGACCATCTGA
66 TCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGA
* * * * * *
65702 ATCTTGTTTCGA--T--TT---AA-T--TTGA-AAAAATAGGAAAAACAATATTAGAAGCTTTAA
131 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
* * * ** ** *
65756 AAGCCCTTCAATGTTTTTGATGTCAAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAG
196 AAGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAG
* ** * **
65821 GAAATATCTTTTGGGTCAATTTTTGCAAAATTTTAGTTGAAATCGTGCACTAACCATCACATTTT
261 GAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC--GGT
65886 TTTC-GC
324 TTTCGGC
* * * * * * ** *
65892 TAAAAACGCCTTCCAGGGCACGGCTCTGTTTTGCATGATTCTTGGCACCAAGACTTCTTGAAATA
1 TAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATA
* * * * * * * ** * *
65957 TTTTTTTTCATCTATTCAAATTTCAGGCACATTGGATTTAAGGATTTGTTTTTGTGTGCATCCGA
66 TCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGA
* *
66022 ATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAAACGTGA
131 ATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGA
* * * *
66087 AAAGTCCTCCAATCCTGTTGGCGTTGAATTATATATAATTTATGAGTATTTTTGCCAAAAATTGA
195 AAAGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGA
*
66152 GGAAAAATCTTTCGGGTC-ATTTTT
260 GGAAAAATCTTTTGGGTCAATTTTT
66176 AGCATCATGG
Statistics
Matches: 2668, Mismatches: 467, Indels: 174
0.81 0.14 0.05
Matches are distributed among these distances:
314 36 0.01
315 209 0.08
316 13 0.00
317 54 0.02
318 65 0.02
319 57 0.02
320 119 0.04
321 9 0.00
322 8 0.00
323 1 0.00
324 3 0.00
325 180 0.07
326 275 0.10
327 64 0.02
328 13 0.00
329 120 0.04
330 432 0.16
331 410 0.15
332 356 0.13
333 9 0.00
334 44 0.02
335 48 0.02
336 30 0.01
337 109 0.04
338 4 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (330 bp):
TAAAAACGCGTTCCGGGGCCCGACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATA
TCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGA
ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
AAGTCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAG
GAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
TCGGC
Found at i:67120 original size:117 final size:113
Alignment explanation
Indices: 66972--67197 Score: 321
Period size: 117 Copynumber: 2.0 Consensus size: 113
66962 TTACAAAAAA
* * * *
66972 GGTAGCAGGAAACGGAATGTGGGAAATTCATAGAGGGGA-TTTTTAGTCATCCGAAAAGTGAGAA
1 GGTAGCAGGAAAAGGAAGGGGGGAAACTCATAGA-GGGACTTTTTAGTCATCCGAAAAGTGA-AA
*
67036 AA-GACAAAAAAAAAAGGTCAAAATGTGGCACCACATTAATCATCAATTTAAAG
64 AAGGAC---AAAAAAA-GCCAAAATGTGGCACCACATTAATCATCAATTTAAAG
67089 GGTAGCAGGAAAAGGAAGGGGGGAAACTCATAGAGGGACTTTTTAGTCATCCGAAAAGTGAAAAA
1 GGTAGCAGGAAAAGGAAGGGGGGAAACTCATAGAGGGACTTTTTAGTCATCCGAAAAGTGAAAAA
* *
67154 GGACCAAAAAAGCCAAAATGTGGCACCACATTAATCCTCAATTT
66 GGACAAAAAAAGCCAAAATGTGGCACCACATTAATCATCAATTT
67198 GGCCTTTTAG
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
113 31 0.31
114 6 0.06
116 8 0.08
117 55 0.55
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.19
Consensus pattern (113 bp):
GGTAGCAGGAAAAGGAAGGGGGGAAACTCATAGAGGGACTTTTTAGTCATCCGAAAAGTGAAAAA
GGACAAAAAAAGCCAAAATGTGGCACCACATTAATCATCAATTTAAAG
Found at i:67938 original size:2 final size:2
Alignment explanation
Indices: 67931--67956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
67921 ATGTTTATTT
67931 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
67957 ACAACAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:68672 original size:15 final size:15
Alignment explanation
Indices: 68648--68682 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
68638 GTTTTTGATT
68648 TCTA-CATGTATATA
1 TCTATCATGTATATA
68662 TCTATCATGTATATA
1 TCTATCATGTATATA
68677 TCTATC
1 TCTATC
68683 CTGTCAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (15 bp):
TCTATCATGTATATA
Found at i:69637 original size:10 final size:10
Alignment explanation
Indices: 69622--69647 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
69612 TAATTGCAGG
69622 AAAAAAAATA
1 AAAAAAAATA
69632 AAAAAAAATA
1 AAAAAAAATA
69642 AAAAAA
1 AAAAAA
69648 CTAGTTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:70088 original size:23 final size:23
Alignment explanation
Indices: 70058--70109 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
70048 TCATCACAAG
* *
70058 TTTATTTGTAAAGATTATGATTA
1 TTTATTTGTAAAAATTATGAGTA
70081 TTTATTTGTAAAAATTATGAGTA
1 TTTATTTGTAAAAATTATGAGTA
*
70104 ATTATT
1 TTTATT
70110 AAGCATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (23 bp):
TTTATTTGTAAAAATTATGAGTA
Found at i:75730 original size:21 final size:21
Alignment explanation
Indices: 75701--75741 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
75691 ATTGGATTCC
*
75701 TAATGATTCAGAATCGAGTTT
1 TAATAATTCAGAATCGAGTTT
*
75722 TAATAATTCAGAGTCGAGTT
1 TAATAATTCAGAATCGAGTT
75742 AGACCCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (21 bp):
TAATAATTCAGAATCGAGTTT
Found at i:76050 original size:33 final size:33
Alignment explanation
Indices: 75997--76059 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
75987 TTGAGTCAGG
* *
75997 TCGGATTAAATTTGGGTCAGGTTGATTCGGAAT
1 TCGGATTAAATTTGGATCAGGTTAATTCGGAAT
* *
76030 TCGGGTTAATTTTGGATCAGGTTAATTCGG
1 TCGGATTAAATTTGGATCAGGTTAATTCGG
76060 GTTCGGACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.22, C:0.10, G:0.30, T:0.38
Consensus pattern (33 bp):
TCGGATTAAATTTGGATCAGGTTAATTCGGAAT
Found at i:76219 original size:20 final size:20
Alignment explanation
Indices: 76194--76232 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
76184 TATACACCAA
*
76194 ATTTTCAGAA-ATTATTATTT
1 ATTTTC-GAATATTAGTATTT
76214 ATTTTCGAATATTAGTATT
1 ATTTTCGAATATTAGTATT
76233 GAATTCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTTTCGAATATTAGTATTT
Found at i:90005 original size:10 final size:10
Alignment explanation
Indices: 89990--90032 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
89980 AAAATGTATT
*
89990 GAAAAACAAA
1 GAAAAAAAAA
90000 GAAAAAAAAA
1 GAAAAAAAAA
90010 G--AAAAAAA
1 GAAAAAAAAA
90018 GAAAAGAAAAA
1 GAAAA-AAAAA
90029 GAAA
1 GAAA
90033 GCTCTCATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.28
10 12 0.41
11 9 0.31
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:90014 original size:19 final size:19
Alignment explanation
Indices: 89992--90032 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
89982 AATGTATTGA
89992 AAAACAAAGAAAA-AAAAAG
1 AAAA-AAAGAAAAGAAAAAG
90011 AAAAAAAGAAAAGAAAAAG
1 AAAAAAAGAAAAGAAAAAG
90030 AAA
1 AAA
90033 GCTCTCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAGAAAAAG
Done.