Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015330.1 Corchorus olitorius cultivar O-4 contig15363, 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: 47984
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:9601 original size:19 final size:20
Alignment explanation
Indices: 9571--9674 Score: 95
Period size: 21 Copynumber: 5.2 Consensus size: 20
9561 TTGACATTGT
*
9571 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTATACAGATGAGA
* * *
9592 TTA-CACTGTACATATTAGA
1 TTAGCACTATACAGATGAGA
* *
9611 TTAGGTACTATACAGATAAGA
1 TTA-GCACTATACAGATGAGA
*
9632 TTA-CACTATACAGATTAGA
1 TTAGCACTATACAGATGAGA
*
9651 TTAGGTACTATACAGATGAGA
1 TTA-GCACTATACAGATGAGA
9672 TTA
1 TTA
9675 TTAGAGCAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
19 33 0.48
20 1 0.01
21 35 0.51
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
TTAGCACTATACAGATGAGA
Found at i:9636 original size:40 final size:40
Alignment explanation
Indices: 9581--9674 Score: 161
Period size: 40 Copynumber: 2.4 Consensus size: 40
9571 TTAGCAACTG
* *
9581 TACAGATGAGATTACACTGTACATATTAGATTAGGTACTA
1 TACAGATGAGATTACACTATACAGATTAGATTAGGTACTA
*
9621 TACAGATAAGATTACACTATACAGATTAGATTAGGTACTA
1 TACAGATGAGATTACACTATACAGATTAGATTAGGTACTA
9661 TACAGATGAGATTA
1 TACAGATGAGATTA
9675 TTAGAGCAGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (40 bp):
TACAGATGAGATTACACTATACAGATTAGATTAGGTACTA
Found at i:10969 original size:44 final size:44
Alignment explanation
Indices: 10906--10990 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
10896 ATTTTTTTTA
10906 CAAGTTAACCTTATTCGAGTCGGATTGACCCACTATAGGAGAGC
1 CAAGTTAACCTTATTCGAGTCGGATTGACCCACTATAGGAGAGC
* *
10950 CAAGTTAATCTTATTCGAGTCGGATTGACCCACTATGGGAG
1 CAAGTTAACCTTATTCGAGTCGGATTGACCCACTATAGGAG
10991 TAAAGCTCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
CAAGTTAACCTTATTCGAGTCGGATTGACCCACTATAGGAGAGC
Found at i:19741 original size:18 final size:18
Alignment explanation
Indices: 19718--19760 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
19708 AAAGAGTAAC
19718 ACTTTCCTGGGAAAGTGA
1 ACTTTCCTGGGAAAGTGA
19736 ACTTTCCTGGGAAAGTGA
1 ACTTTCCTGGGAAAGTGA
19754 ACTTTCC
1 ACTTTCC
19761 CACCCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (18 bp):
ACTTTCCTGGGAAAGTGA
Found at i:21414 original size:3 final size:3
Alignment explanation
Indices: 21408--21438 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21398 ATCTCCATCA
21408 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
21439 TATTTTCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:23298 original size:2 final size:2
Alignment explanation
Indices: 23291--23322 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23281 AAACGGGCAC
23291 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
23323 GAAGCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25554 original size:20 final size:20
Alignment explanation
Indices: 25529--25567 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25519 GTCGTGCAAT
25529 TGTGCCCCAAAAGTATGAAA
1 TGTGCCCCAAAAGTATGAAA
*
25549 TGTGCCCTAAAAGTATGAA
1 TGTGCCCCAAAAGTATGAA
25568 TGGTCCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
TGTGCCCCAAAAGTATGAAA
Found at i:27481 original size:20 final size:20
Alignment explanation
Indices: 27444--27482 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27434 ATTGATCATT
* * *
27444 TATAGACTTTTTATATATAA
1 TATAGAATTTATAGATATAA
27464 TATAGAATTTATAGATATA
1 TATAGAATTTATAGATATA
27483 TAATTGCTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
TATAGAATTTATAGATATAA
Found at i:33682 original size:13 final size:13
Alignment explanation
Indices: 33664--33689 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33654 AAAATTCACC
33664 ATCTAGTTAAAAT
1 ATCTAGTTAAAAT
33677 ATCTAGTTAAAAT
1 ATCTAGTTAAAAT
33690 GATTAGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATCTAGTTAAAAT
Found at i:35253 original size:14 final size:14
Alignment explanation
Indices: 35234--35262 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35224 ATACTATACA
35234 GTTACTGTATATAT
1 GTTACTGTATATAT
35248 GTTACTGTATATAT
1 GTTACTGTATATAT
35262 G
1 G
35263 AAATTATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (14 bp):
GTTACTGTATATAT
Found at i:35269 original size:44 final size:44
Alignment explanation
Indices: 35206--35292 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
35196 ACTATTTAGA
* * *
35206 TACTGTATGTATGAAATTATACTATACAGTTACTGTATATATGT
1 TACTGTATATATGAAATTATACTATACAGATACTGTACATATGT
*
35250 TACTGTATATATGAAATTATACTGTACAGATACTGTACATATG
1 TACTGTATATATGAAATTATACTATACAGATACTGTACATATG
35293 AATGAGACTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (44 bp):
TACTGTATATATGAAATTATACTATACAGATACTGTACATATGT
Found at i:35304 original size:18 final size:18
Alignment explanation
Indices: 35281--35317 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
35271 CTGTACAGAT
35281 ACTGTACATATGAATGAG
1 ACTGTACATATGAATGAG
35299 ACTGTACATATGAATGAG
1 ACTGTACATATGAATGAG
35317 A
1 A
35318 TTATACTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (18 bp):
ACTGTACATATGAATGAG
Found at i:35329 original size:23 final size:20
Alignment explanation
Indices: 35277--35318 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
35267 TATACTGTAC
35277 AGATACTGTACATATGAATG
1 AGATACTGTACATATGAATG
35297 AG--ACTGTACATATGAATG
1 AGATACTGTACATATGAATG
35315 AGAT
1 AGAT
35319 TATACTGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 18 0.90
20 2 0.10
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (20 bp):
AGATACTGTACATATGAATG
Found at i:41756 original size:297 final size:300
Alignment explanation
Indices: 41218--41817 Score: 780
Period size: 297 Copynumber: 2.0 Consensus size: 300
41208 TTTTCTTAAG
* * * *
41218 AGTATTTCGGTCAAAAATTGTGGAAAAATATTTCGGGTCAATTTTTACAAAATTTTAGCCGAAAT
1 AGTATTTCGGTCAAAAATTATGGAAAAATATTCCGGGTCAATTTTTACAAAACTATAGCCGAAAT
* *
41283 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACACGTGTTTCAGGGCACCGGCTCAGTTTTGAA
66 CGTGTAC--ACCATCACGGTTTTTGGCTAAAAACACGCGTTCCAGGGCACCGGCTCAGTTTTGAA
* * * *
41348 TGATCTTTGAAGCCAATAGTCATTATAATATCTATATTCATAGAACCAATTCTCAGCCACATTAG
129 TGATCTTTGAAGCCAAGAGTCATTAAAATAACTATATTCATAGAACCAAATCTCAGCCACATTAG
* * * *
41413 ATTTGAGGATTTGTTATTACGAGCATCGATATCTTGTTTCGATTTAATCATAAATTAATTTA-CT
194 ATTTGAGGATTTGTTATTACGAGCATAGAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGCA
* * * *
41477 AAAAAA-TAGGGAATATGATATTAGAAGCGTTAAAAGCCCTTC
259 AAAAAATTA-GAAAAACGATATTAGAAACGTTAAAAGCCCTTC
* * *
41519 AGTATTTTGGTCAAAAATTATGGAAAAATATTCCTGGTCAATTTTTTGCAAAACTATAGCCGAAA
1 AGTATTTCGGTCAAAAATTATGGAAAAATATTCCGGGTCAA-TTTTTACAAAACTATAGCCGAAA
* *
41584 TCGTGTAC-CCATCACGGTTTTTGGC-AAAAA-ACGCGTTCCGGGGCACCGGC-CTAGTTTTGCA
65 TCGTGTACACCATCACGGTTTTTGGCTAAAAACACGCGTTCCAGGGCACCGGCTC-AGTTTTGAA
* ** * * ** * *
41645 TGATTTTTGGCGCCGAGAGTCGTTAAAATAACTATATTCATCTAACCAAATCTCAGCCATATTGG
129 TGATCTTTGAAGCCAAGAGTCATTAAAATAACTATATTCATAGAACCAAATCTCAGCCACATTAG
* * ** *
41710 ATTTGAGGATTTGTTTTTACGAGCATATAAATCTTGTTTCGATTTAATCAGATTTTAATTTAGGA
194 ATTTGAGGATTTGTTATTACGAGCATAGAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGCA
41775 AAAAAATTAGAAAAACGATATTAGAAACGTTAAAAGCCCTTC
259 AAAAAATTAGAAAAACGATATTAGAAACGTTAAAAGCCCTTC
41817 A
1 A
41818 AACTTTTTGG
Statistics
Matches: 258, Mismatches: 37, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
296 1 0.00
297 132 0.51
298 41 0.16
299 19 0.07
301 37 0.14
302 28 0.11
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (300 bp):
AGTATTTCGGTCAAAAATTATGGAAAAATATTCCGGGTCAATTTTTACAAAACTATAGCCGAAAT
CGTGTACACCATCACGGTTTTTGGCTAAAAACACGCGTTCCAGGGCACCGGCTCAGTTTTGAATG
ATCTTTGAAGCCAAGAGTCATTAAAATAACTATATTCATAGAACCAAATCTCAGCCACATTAGAT
TTGAGGATTTGTTATTACGAGCATAGAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGCAAA
AAAATTAGAAAAACGATATTAGAAACGTTAAAAGCCCTTC
Found at i:42616 original size:335 final size:333
Alignment explanation
Indices: 41565--45761 Score: 4647
Period size: 335 Copynumber: 12.6 Consensus size: 333
41555 GTCAATTTTT
* * * * *
41565 TGCAAAACTATAGCCGAAATCGTGTAC---CCATCACGGTTTTTGGCAAAAAACGCGTTCCGGGG
1 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGC
*
41627 CACCGGC-CTAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATAACTATATTCATCTAAC
66 CACCGGCTC-AGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATCTAAC
* * *
41691 CAAATCTCAGCCATATTGGATTTGAGGATTTGTTTTTACGAGCATATAAATCTTGTTTCGATTTA
130 CAAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTA
*
41756 ATCAGATTTTAATTTAGGAAAAAAATTAGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAC
195 ATCAGATTTTAATTTAGG-AAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAC
* * **
41821 TTTTTGGCGTTGAATTATATAATTTTTTAT-CG-A---GGCCAAAAATTTTGGAAAAATAATTCG
259 TTTTTGGCGTTGAATTATATATTTTTTTATGAGTATTTGGCCAAAAATTGAGGAAAAATAATTCG
*
41881 GGTCTATTTT
324 GGTCAATTTT
* *
41891 TGCAAAATTTTAGCCGATATCGTGTACGT---TATCACGGTTTTTGGACTTAAAAACGCGTGTTT
1 TGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTGG-C-TAAAAACGC--GTTT
** * * * *
41953 CAGGTTCACCGGCTCAGTTTTGCATGATTTTTGGAGCCAAGAGTTGTTATAATATCTATATTCAT
61 C-GGGCCACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCAT
* * * * *
42018 CTAA-CATATTCTCAGCCACATTAGATTTGAAGATTTGTGTTTACGAGAATCTGAATCTTGTTTC
125 CTAACCA-AATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTC
* * ** ** * * * * **
42082 GATTGAATCATAAATTAATTTAGGAAAAAAAAGGGAACACGATATTAGAAGCATTAAAAAACCTT
189 GATTTAATCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTT
** * *
42147 CAATGTTTTTGGCGTTGAATTATATA--TTTTTATTAGTATTTTGGTCAAAAATTGAGG-AAAAT
254 CAAACTTTTTGGCGTTGAATTATATATTTTTTTATGAGTA-TTTGGCCAAAAATTGAGGAAAAAT
*
42209 -ATTCCAGGTCAATTTT
318 AATT-CGGGTCAATTTT
* * * ** * *
42225 TGGAAAATTTTAGTCGAAATCGTGTACTAAACATCATAGTTTTTGGCTAGAAACGCGTTCCAGGG
1 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGG
* * * * ** * * * * *
42290 CCA-CGACTTAGTTTTTCTTCTTTTTTTGCGCCGATATTTC-TTGAAATATCAATATTCAT-TAA
65 CCACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGA-GTCGTTAAAATATCTATATTCATCT-A
* * * * *** * *
42352 ATCAAATCTCAGCCACATTACATTTAAGGATATGTTTTTACGAATTTCTGATTCTTGTTTCGATT
128 ACCAAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATT
* **
42417 TAATTAGAAATTAA-TTAGGTAAAAAGCATTGGAAAAACGATATTAGAAACGTTAAAA-CCCTTC
193 TAATCAGATTTTAATTTAGG-AAAAA--ATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTC
* * * * * *
42480 AAAATTTTTGGCATTTAATTATATATTTTCTTAAGAGTATTTCGGTCAAAAATT-ATGGAAAAAT
255 AAACTTTTTGGCGTTGAATTATATATTTTTTTATGAGTATTT-GGCCAAAAATTGA-GGAAAAAT
*
42544 ATTTCGGGTCAATTTT
318 AATTCGGGTCAATTTT
* * *
42560 TGAAAAATTTTAGCCGAAATCGTGAACTAACCATCACGGTTTTTGTCTAAAAACGCGTGTTTCGG
1 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGC--GTTTCGG
* * * * * * *
42625 GGCACCGGCTCAGTTTTGAATGATTTTT-GCAGCCAATAGTCATTATAATATCTATATTCATCAA
64 GCCACCGGCTCAGTTTTGCATGATTTTTGGC-GCCGAGAGTCGTTAAAATATCTATATTCATCTA
* * * *
42689 ACCAATTCTCAGCCACATTAGATTTGAGGTTTTGTTATTACGAGCATCTGAATCTTGTTTCGATT
128 ACCAAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATT
* * ** ** * * * *
42754 TAATTATAAATTAATTTATTAAAAAATTAGGGAACACAATATTA-AAAGCGTTAATAGCCCTTCA
193 TAATCAGATTTTAATTTAGGAAAAAATT-GGAAAAACGATATTAGAAA-CGTTAAAAGCCCTTCA
* * * * *
42818 ATA-TTTTTGGCGTTGAATT-T-TATATTTTTATTAGTATTTTAGTCAAAAAATTGGTGGAAAAA
256 A-ACTTTTTGGCGTTGAATTATATATTTTTTTATGAGTA-TTT-GGCCAAAAATT-GAGGAAAAA
*
42880 -ATATTCCTGGTCAATTTTT
317 TA-ATT-CGGGTCAA-TTTT
* * * * *
42899 TGCAAAACTATAGCCGAAATCGTGTACTGTTAA-CATAACGGTTTTTGGCAAAAAAACGCGTTCC
1 TGCAAAATTTTAGCCGAAATCGTGTAC---TAACCATCACGGTTTTTGGC-TAAAAACGCGTTTC
* * * * *
42963 GGGGCACCGGCCCAGTTTTGCATGATTTTTCGGCACCGATAGTACGTTAAAATAACTATATTCAT
62 GGGCCACCGGCTCAGTTTTGCATGATTTTT-GGCGCCGAGAGT-CGTTAAAATATCTATATTCAT
* * * **
43028 CTAACCAAATCTCAGTCATATTTGATTTGAGGAAGTGTTTTTACGAGCATCTAAATCTTGTTTCG
125 CTAACCAAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCG
*
43093 ATTTAATCAGATTTTAATTTAGGAAAAAAATTGGAAAAACGATATTAGAAACGTTAAAATCCCTT
190 ATTTAATCAGATTTTAATTTAGG-AAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTT
** *
43158 TTAACTTTTTGTG-GTTGAATTAT-TAATTTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAA
254 CAAACTTTTTG-GCGTTGAATTATAT-ATTTTTTTATGAGTAT-TTGGCCAAAAATTGAGGAAAA
43221 ATAATTCGGGTCAATTTT
316 ATAATTCGGGTCAATTTT
* * *
43239 TGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGG-TAAAAAAAGCGTTCCGGG
1 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCT-AAAAACGCGTTTCGGG
* ** * * *
43303 GCTTCGGCCCAGTTTTGCATGATTTTTGGCGCCGAGGGTCGTTAAAATAACTATATTCATCTAAC
65 CCACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATCTAAC
* * *
43368 CAAATCTCAGCCATATT-GAATTGGAGGAATTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT
130 CAAATCTCAGCCACATTAG-ATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT
43432 AATCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAC
194 AATCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAC
* * *
43497 TTTTTGACGTTGAATTATATATTTTTTTATGAGTATCGTGGCCAAAAATTGATGAAAAATAATTC
259 TTTTTGGCGTTGAATTATATATTTTTTTATGAGTAT-TTGGCCAAAAATTGAGGAAAAATAATTC
*
43562 GTGTCAATTTT
323 GGGTCAATTTT
*
43573 TGCAAAATTTTAGCCGAAATCGTGTACGT-----T-ACGGTTTTTGG-TTAAAACGCGTGTTTCG
1 TGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTGGCTAAAAACGC--GTTTCG
* * * * * * *
43631 GGTCACCGACTCAGTTTTGCATGATTTTTGGAGTCAAGAGTCGTTATAATATCTACATTCATCTA
63 GGCCACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATCTA
* *
43696 ACCAATTCTCAGCCACATTAGATTTGAGAATTT-TTTTTACGAGCATCTAAATCTTGTTTCGATT
128 ACCAAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATT
43760 TAATCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAA
193 TAATCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAA
* *
43825 CTTTTTGGCGTTGAATTATATATTTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAACTAATT
258 CTTTTTGGCGTTGAATTATATATTTTTTTATGAGTAT-TTGGCCAAAAATTGAGGAAAAATAATT
43890 CGGGTCAATTTT
322 CGGGTCAATTTT
** * * *
43902 TTAAAAAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTGGGCTAAAAACGCGTTTCGGGG
1 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGC
** * * **
43967 CATAGGCTCAGTTTTGCATGATTTTTGGTGCCGAGGGTCGTTAAAATATCTATATTCATCTTCCC
66 CACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATCTAACC
* *
44032 AATTCTCAGCCACA-TATGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTAA
131 AAATCTCAGCCACATTA-GATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTA
* ** ** * * * *
44096 ATCATAGATTAATTTAATAAAAAAATAGGGAACACGATATTAGAAGCGTTAAAAGCCCTTCAATA
195 ATCAGATTTTAATTT-AGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAA-A
* * * * * *** *
44161 -TTTTCGGTGTTTAATTATATA--TTTTTATTAGTATTTTGCTCAAAAATTTTTGAAATAT-ATT
258 CTTTTTGGCGTTGAATTATATATTTTTTTATGAGTATTTGGC-CAAAAATTGAGGAAAAATAATT
*
44222 CCTGGTCAATTTT
322 -CGGGTCAATTTT
* * * * * * *
44235 T-CCAAACTATAGCCGAAATCGTG---T-A-CGTCACGGTTTTTAGCAAAAAACGCGTTCCGGG-
1 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGC
* * * *
44293 CTCCGGCCCAGTTTTGCATGATTTTCGGCGCCGAGAGTCGTTAAAATAACTATATTCATCTAACC
66 CACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATCTAACC
* * * *
44358 AAATCTTAGCCATATTGGATTGGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAA
131 AAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAA
* *
44423 TCAAATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGTCCTTCAAACTT
196 TCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAACTT
* * * *
44488 TTTGGCGTTGAATTATATATTTTTTTATAAGTATCATGGCCAAAAATTGAGGAAAAATAAATCGT
261 TTTGGCGTTGAATTATATATTTTTTTATGAGTAT-TTGGCCAAAAATTGAGGAAAAATAATTCGG
44553 GTCAATTTT
325 GTCAATTTT
*
44562 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTGTTTCGG
1 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGC--GTTTCGG
** * * * * * *
44627 GTAACAGACTCAGTTTTGCATGATTTTTCGAGCCAAGAGTCGTTATAATATCTATATTCATCTAA
64 GCCACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATCTAA
* * * * * *
44692 CCAAATCTTAGCCATATTGGATTTGAGAATTTGTTTTTACGAGCATCTATATCTTGTTTCAATTT
129 CCAAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT
* * *
44757 AATCAGATTTTCATTTAGGAATAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTT-AAAA
194 AATCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAC
* * *
44821 TTTTTGGCGTTGAATGATATATTTTTTTATGAGTATCGTGGCTAAAAATTGAGGAAAAATAATTC
259 TTTTTGGCGTTGAATTATATATTTTTTTATGAGTAT-TTGGCCAAAAATTGAGGAAAAATAATTC
44886 GGGTCAATTTT
323 GGGTCAATTTT
44897 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGG
1 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGGCTAAAAACGCGTTTCGGG
* *** * *
44962 GCGTAGGCTCAGTTTTGCATGATTTTTGGTGCCGAGAGTCGTTAAAATATCTATATTCA-CATAC
65 CCACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATC-TAA
* * * *
45026 CCAATTCTCAGCCACATAAGATTTGAGGTATTTG-TTTTACGAGCATCTGAATCTTATTTCGATT
129 CCAAATCTCAGCCACATTAGATTTGAGG-ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATT
** * * * * **
45090 TAATCAGAAATTAA-TTAGG-AAAAATAGG-AACACGATATTAGTAGCGTTAAAATACCTTCAAA
193 TAATCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAA
* * *
45152 CTTTTTGGCGTTGAATTATATA--TTTTTAGGAGTATTTTGGTCAAAATTTGAGGAAAAAT-ATT
258 CTTTTTGGCGTTGAATTATATATTTTTTTATGAGTA-TTTGGCCAAAAATTGAGGAAAAATAATT
*
45214 TGCGGTCAATTTT
322 CG-GGTCAATTTT
* * * * * * * *
45227 TGCTAAATTATA-TCGAAATCGTGTACTAACCATCACAGTTTTTGACAAAAAAATGCGTTACAGG
1 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC-TAAAAACGCGTTTC-GG
* * * * * *
45291 G-CACCGGCCCAGTTTTGCATGATTTTCGGCGCCAAGAGTCGTTAAAATAACTATATTCGTCAAA
64 GCCACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATCTAA
* * * * *
45355 CCAAATCTCAGCCATATTGGATTTGAAGATTTGTTTTTACGAACATCTAAATCTTGTTTCAATTT
129 CCAAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT
* * *
45420 AATCTGATTTTAATTTAGGAAAAAATTGTAAAAACGATATTAGAAACGTTAAAAGCCCTTGAAAC
194 AATCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAC
*
45485 TTTTTGGCGTTGAATTATATATTTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAAATAATTC
259 TTTTTGGCGTTGAATTATATATTTTTTTATGAGTAT-TTGGCCAAAAATTGAGGAAAAATAATTC
45550 GGGTCAATTTT
323 GGGTCAATTTT
** * * *
45561 CACAAAATTTTAGCCGAAATCGTTTA-TAAACCATCACGGTTTTTTGGCAAAAAAAGCGTTTCGG
1 TGCAAAATTTTAGCCGAAATCGTGTACT-AACCATCACGG-TTTTTGGCTAAAAACGCGTTTCGG
* ** * * * *
45625 GGCATAGACTCAGTTTTGCATGATTTTTGGTGCCGAGAGTCGTTAAAATATCTATATTCACCTAC
64 GCCACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATCTAA
* * * * * * * *
45690 CCAATTCTCAGCCACATAAAATTTAAGGATTTGTTTTTACGAGAATCTGAATTTTATTTCGATTT
129 CCAAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT
45755 AATCAGA
194 AATCAGA
45762 AAAACGATAT
Statistics
Matches: 3269, Mismatches: 481, Indels: 233
0.82 0.12 0.06
Matches are distributed among these distances:
324 1 0.00
325 58 0.02
326 147 0.04
327 80 0.02
328 45 0.01
329 370 0.11
330 151 0.05
331 206 0.06
332 272 0.08
333 187 0.06
334 435 0.13
335 537 0.16
336 258 0.08
337 189 0.06
338 25 0.01
339 27 0.01
340 60 0.02
341 29 0.01
342 153 0.05
343 25 0.01
344 14 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (333 bp):
TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGC
CACCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGAGTCGTTAAAATATCTATATTCATCTAACC
AAATCTCAGCCACATTAGATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAA
TCAGATTTTAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAACTT
TTTGGCGTTGAATTATATATTTTTTTATGAGTATTTGGCCAAAAATTGAGGAAAAATAATTCGGG
TCAATTTT
Found at i:45575 original size:664 final size:667
Alignment explanation
Indices: 41530--45762 Score: 4744
Period size: 663 Copynumber: 6.4 Consensus size: 667
41520 GTATTTTGGT
* * *
41530 CAAAAATT-ATGGAAAAAT-ATTCCTGGTCAATTTTTTGCAAAACTATAGCCGAAATCGTGTAC-
1 CAAAAATTGA-GGAAAAATAATTCCGGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTACT
* *
41592 -CCATCACGGTTTTTGGCAAAAAACGCGTTCCGGGGCACCGGC-CTAGTTTTGCATGATTTTTGG
64 AACATCACGGTTTTTGGCAAAAAACGCGTTTCGGGGCACCGGCTC-AGTTTTGCATGATTTTTGG
* * *
41655 CGCCGAGAGTCGTTAAAATAACTATATTCATCTAACCAAATCTCAGCCATATTGGATTTGAGGAT
128 CGCCGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTGAGGAT
* * *
41720 TTGTTTTTACGAGCATATAAATCTTGTTTCGATTTAATCAGATTTTAATTTAGGAAAAAAATTAG
193 TTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAATTTAATTTAGG-AAAAAATTGG
* *
41785 AAAAACGATATTAGAAACGTTAAAAGCCCTTCAAACTTTTTGGCGTTGAATTATATA-ATTTT-T
257 AAAAACGATATTAGAAACGTTAAAATCCCTTCAAACTTTTTGGCGTTGAATTATATATTTTTTAT
* ** * *
41848 ---TATCGAGGCCAAAAATTTTGGAAAAATAATTCGGGTCTATTTTTGCAAAATTTTAGCCGATA
322 GAGTATCGTGGCCAAAAATTGAGGAAAAATAATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA
* **
41910 TCGTGTACGT---TATCACGGTTTTTGGACTTAAAAACGCGTGTTTCAGGTTCACCGGCTCAGTT
387 TCGTGTAC-TAACCATCACGGTTTTTGG-C-TAAAAACGCG-GTTTC-GGGGCACCGGCTCAGTT
* * * *
41972 TTGCATGATTTTTGGAGCCAAGAGTTGTTATAATATCTATATTCATCTAA-CATATTCTCAGCCA
447 TTGCATGATTTTTGGCGCCAAGAGTCGTTAAAATATCTATATTCATCTAACCA-AATCTCAGCCA
* * * * * **
42036 CATTAGATTTGAAGATTTGTGTTTACGAGAATCTGAATCTTGTTTCGATTGAATCAT-AAATTAA
511 CATTGGATTTGAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATC-TGATTTTAA
** * * * * ** *
42100 TTTAGGAAAAAAAAGGGAACACGATATTAGAAGCATTAAAAAACCTTCAATGTTTTTGGCGTTGA
575 TTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAA-ATTTTTGGCGTTGA
* ** *
42165 ATTATATA--TTTTTATTAGTATTTTGGT
639 ATTATATATTTTTTTATGAGTATCGTGGC
* * *
42192 CAAAAATTGAGG-AAAAT-ATTCCAGGTCAATTTTTGGAAAATTTTAGTCGAAATCGTGTACTAA
1 CAAAAATTGAGGAAAAATAATTCCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-A
** * * * * * * * * ** *
42255 ACATCATAGTTTTTGGCTAGAAACGCGTTCCAGGGC-CACGACTTAGTTTTTCTTCTTTTTTTGC
65 ACATCACGGTTTTTGGCAAAAAACGCGTTTCGGGGCAC-CGGCTCAGTTTTGCATGATTTTTGGC
* * * * * * *
42319 GCCGATATTTC-TTGAAATATCAATATTCAT-TAAATCAAATCTCAGCCACATTACATTTAAGGA
129 GCCGAGA-GTCGTTAAAATATCTATATTCATCT-AACCAAATCTCAGCCACATTAGATTTGAGGA
* *** * * * *
42382 TATGTTTTTACGAATTTCTGATTCTTGTTTCGATTTAATTAGAAATTAA-TTAGGTAAAAAGCAT
192 TTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAATTTAATTTAGG-AAAAA--AT
* * *
42446 TGGAAAAACGATATTAGAAACGTTAAAA-CCCTTCAAAATTTTTGGCATTTAATTATATATTTTC
254 TGGAAAAACGATATTAGAAACGTTAAAATCCCTTCAAACTTTTTGGCGTTGAATTATATATTTT-
* * * * *
42510 TTAAGAGTAT-TTCGGTCAAAAATT-ATGGAAAAATATTTCGGGTCAATTTTTGAAAAATTTTAG
318 TTATGAGTATCGT-GGCCAAAAATTGA-GGAAAAATAATTCGGGTCAATTTTTGCAAAATTTTAG
* *
42573 CCGAAATCGTGAACTAACCATCACGGTTTTTGTCTAAAAACGCGTGTTTCGGGGCACCGGCTCAG
381 CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCG-GTTTCGGGGCACCGGCTCAG
* * * * * *
42638 TTTTGAATGATTTTT-GCAGCCAATAGTCATTATAATATCTATATTCATCAAACCAATTCTCAGC
445 TTTTGCATGATTTTTGGC-GCCAAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGC
* * * * * *
42702 CACATTAGATTTGAGGTTTTGTTATTACGAGCATCTGAATCTTGTTTCGATTTAAT-T-ATAAAT
509 CACATTGGATTTGAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCTGAT--TT
** * * * *
42765 TAATTTATTAAAAAATTAGGGAACACAATATTA-AAAGCGTTAATAGCCCTTCAATATTTTTGGC
572 TAATTTAGGAAAAAATT-GGAAAAACGATATTAGAAA-CGTTAAAAGCCCTTCAA-ATTTTTGGC
* * ** *
42829 GTTGAATT-T-TATATTTTTATTAGTATTTTAGTC
634 GTTGAATTATATATTTTTTTATGAGTATCGT-GGC
* * * * *
42862 AAAAAATTGGTGGAAAAA-ATATTCCTGGTCAATTTTTTGCAAAACTATAGCCGAAATCGTGTAC
1 CAAAAATT-GAGGAAAAATA-ATTCCGGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * *
42926 TGTTAACATAACGGTTTTTGGCAAAAAAACGCGTTCCGGGGCACCGGCCCAGTTTTGCATGATTT
63 ---TAACATCACGGTTTTTGGC-AAAAAACGCGTTTCGGGGCACCGGCTCAGTTTTGCATGATTT
* * * * * *
42991 TTCGGCACCGATAGTACGTTAAAATAACTATATTCATCTAACCAAATCTCAGTCATATTTGATTT
124 TT-GGCGCCGAGAGT-CGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTT
** *
43056 GAGGAAGTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGATTTTAATTTAGGAAAAA
187 GAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAATTTAATTTAGG-AAAA
**
43121 AATTGGAAAAACGATATTAGAAACGTTAAAATCCCTTTTAACTTTTTGTG-GTTGAATTAT-TAA
251 AATTGGAAAAACGATATTAGAAACGTTAAAATCCCTTCAAACTTTTTG-GCGTTGAATTATAT-A
43184 TTTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAAATAATTCGGGTCAATTTTTGCAAAATTT
314 -TTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAAATAATTCGGGTCAATTTTTGCAAAATTT
* * * ** *
43249 TAGTCGAAATCGTGTACTAACCATCACGGTTTTTGG-TAAAAAAAGC-GTTCCGGGGCTTCGGCC
378 TAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCT-AAAAACGCGGTTTCGGGGCACCGGCT
* * *
43312 CAGTTTTGCATGATTTTTGGCGCCGAGGGTCGTTAAAATAACTATATTCATCTAACCAAATCTCA
442 CAGTTTTGCATGATTTTTGGCGCCAAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCA
* * * * * *
43377 GCCATATTGAATTGGAGGAATTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGATTT
507 GCCACATTGGATTTGAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCTGATTT
*
43442 TAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAACTTTTTGACGT
572 TAATTTAGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAA-TTTTTGGCGT
43507 TGAATTATATATTTTTTTATGAGTATCGTGGC
636 TGAATTATATATTTTTTTATGAGTATCGTGGC
* *
43539 CAAAAATTGATGAAAAATAATT-CGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACGT-
1 CAAAAATTGAGGAAAAATAATTCCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TA
** * *
43602 ---T-ACGGTTTTTGG-TTAAAACGCGTGTTTCGGGTCACCGACTCAGTTTTGCATGATTTTTGG
65 ACATCACGGTTTTTGGCAAAAAACGC--GTTTCGGGGCACCGGCTCAGTTTTGCATGATTTTTGG
* * * * * * *
43662 AGTCAAGAGTCGTTATAATATCTACATTCATCTAACCAATTCTCAGCCACATTAGATTTGAGAAT
128 CGCCGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTGAGGAT
*
43727 TT-TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGATTTTAATTTAGGAAAAAATTGGA
193 TTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAATTTAATTTAGGAAAAAATTGGA
*
43791 AAAACGATATTAGAAACGTTAAAAGCCCTTCAAACTTTTTGGCGTTGAATTATATATTTTTTTAT
258 AAAACGATATTAGAAACGTTAAAATCCCTTCAAACTTTTTGGCGTTGAATTATATA-TTTTTTAT
* ** *
43856 GAGTATCGTGGCCAAAAATTGAGGAAAACTAATTCGGGTCAATTTTTTAAAAAATTTAGCCGAAA
322 GAGTATCGTGGCCAAAAATTGAGGAAAAATAATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA
* **
43921 TCGTGTACTAACCATCACGGTTTTGGGCTAAAAACGC-GTTTCGGGGCATAGGCTCAGTTTTGCA
387 TCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGGTTTCGGGGCACCGGCTCAGTTTTGCA
* * * ** *
43985 TGATTTTTGGTGCCGAGGGTCGTTAAAATATCTATATTCATCTTCCCAATTCTCAGCCACATAT-
452 TGATTTTTGGCGCCAAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACAT-TG
* *
44049 GATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTAAATCATAGA--TTAATTTA
516 GATTTGAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATC-T-GATTTTAATTT-
** * * * * * * *
44112 ATAAAAAAATAGGGAACACGATATTAGAAGCGTTAAAAGCCCTTCAATATTTTCGGTGTTTAATT
578 AGGAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAA-ATTTTTGGCGTTGAATT
* * *
44177 ATATA--TTTTTATTAGTAT-TTTGC
642 ATATATTTTTTTATGAGTATCGTGGC
*** * * * * *
44200 TCAAAAATTTTTGAAATAT-ATTCCTGGTCAATTTTT-CCAAACTATAGCCGAAATCGTG---T-
1 -CAAAAATTGAGGAAAAATAATTCCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTA
* * * * * *
44259 ACGTCACGGTTTTTAGCAAAAAACGCG-TTCCGGGCTCCGGCCCAGTTTTGCATGATTTTCGGCG
65 ACATCACGGTTTTTGGCAAAAAACGCGTTTCGGGGCACCGGCTCAGTTTTGCATGATTTTTGGCG
* * * * *
44323 CCGAGAGTCGTTAAAATAACTATATTCATCTAACCAAATCTTAGCCATATTGGATTGGAGGATTT
130 CCGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTGAGGATTT
44388 GTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCA-AATTTTAATTTAGGAAAAAATTGGAA
195 GTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAA-TTTAATTTAGGAAAAAATTGGAA
44452 AAACGATATTAGAAACGTTAAAAGT-CCTTCAAACTTTTTGGCGTTGAATTATATATTTTTTTAT
259 AAACGATATTAGAAACGTTAAAA-TCCCTTCAAACTTTTTGGCGTTGAATTATATA-TTTTTTAT
* * * *
44516 AAGTATCATGGCCAAAAATTGAGGAAAAATAAATCGTGTCAATTTTTGCAAAATTTTAGCCGAAA
322 GAGTATCGTGGCCAAAAATTGAGGAAAAATAATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA
* ** * *
44581 TCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTGTTTCGGGTAACAGACTCAGTTTTGC
387 TCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCG-GTTTCGGGGCACCGGCTCAGTTTTGC
* * * * *
44646 ATGATTTTTCGAGCCAAGAGTCGTTATAATATCTATATTCATCTAACCAAATCTTAGCCATATTG
451 ATGATTTTTGGCGCCAAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTG
* * * *
44711 GATTTG-AGAATTTGTTTTTACGAGCATCTATATCTTGTTTCAATTTAATCAGATTTTCATTTAG
516 GATTTGAAG-ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCTGATTTTAATTTAG
* * *
44775 GAATAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTAAAATTTTTGGCGTTGAATGATA
580 GAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAATTTTTGGCGTTGAATTATA
44840 TATTTTTTTATGAGTATCGTGGC
645 TATTTTTTTATGAGTATCGTGGC
*
44863 TAAAAATTGAGGAAAAATAATT-CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
1 CAAAAATTGAGGAAAAATAATTCCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
* *** *
44927 CCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGGCGTAGGCTCAGTTTTGCATGATTTTTGGT
66 -CATCACGG-TTTTTGGCAAAAAACGCGTTTCGGGGCACCGGCTCAGTTTTGCATGATTTTTGGC
* * *
44992 GCCGAGAGTCGTTAAAATATCTATATTCA-CATACCCAATTCTCAGCCACATAAGATTTGAGGTA
129 GCCGAGAGTCGTTAAAATATCTATATTCATC-TAACCAAATCTCAGCCACATTAGATTTGAGG-A
* * * *
45056 TTTG-TTTTACGAGCATCTGAATCTTATTTCGATTTAATCAGAAATTAA-TTAGG-AAAAATAGG
192 TTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAATTTAATTTAGGAAAAAATTGG
* * * * *
45118 -AACACGATATTAGTAGCGTTAAAATACCTTCAAACTTTTTGGCGTTGAATTATATA-TTTTTAG
257 AAAAACGATATTAGAAACGTTAAAATCCCTTCAAACTTTTTGGCGTTGAATTATATATTTTTTAT
** * * * * * *
45181 GAGTATTTTGGTCAAAATTTGAGGAAAAAT-ATTTGCGGTCAATTTTTGCTAAATTATA-TCGAA
322 GAGTATCGTGGCCAAAAATTGAGGAAAAATAATTCG-GGTCAATTTTTGCAAAATTTTAGCCGAA
* * * * * * *
45244 ATCGTGTACTAACCATCACAGTTTTTGACAAAAAAATGC-GTTACAGGGCACCGGCCCAGTTTTG
386 ATCGTGTACTAACCATCACGGTTTTTGGC-TAAAAACGCGGTTTCGGGGCACCGGCTCAGTTTTG
* * * * *
45308 CATGATTTTCGGCGCCAAGAGTCGTTAAAATAACTATATTCGTCAAACCAAATCTCAGCCATATT
450 CATGATTTTTGGCGCCAAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATT
* *
45373 GGATTTGAAGATTTGTTTTTACGAACATCTAAATCTTGTTTCAATTTAATCTGATTTTAATTTAG
515 GGATTTGAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCTGATTTTAATTTAG
* *
45438 GAAAAAATTGTAAAAACGATATTAGAAACGTTAAAAGCCCTTGAAACTTTTTGGCGTTGAATTAT
580 GAAAAAATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAA-TTTTTGGCGTTGAATTAT
45503 ATATTTTTTTATGAGTATCGTGGC
644 ATATTTTTTTATGAGTATCGTGGC
** *
45527 CAAAAATTGAGGAAAAATAATT-CGGGTCAATTTTCACAAAATTTTAGCCGAAATCGTTTA-TAA
1 CAAAAATTGAGGAAAAATAATTCCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-A
* ** *
45590 ACCATCACGGTTTTTTGGCAAAAAAAGCGTTTCGGGGCATAGACTCAGTTTTGCATGATTTTTGG
65 A-CATCACGG-TTTTTGGCAAAAAACGCGTTTCGGGGCACCGGCTCAGTTTTGCATGATTTTTGG
* * * * * * *
45655 TGCCGAGAGTCGTTAAAATATCTATATTCACCTACCCAATTCTCAGCCACATAAAATTTAAGGAT
128 CGCCGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTGAGGAT
* * * *
45720 TTGTTTTTACGAGAATCTGAATTTTATTTCGATTTAATCAGAA
193 TTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAA
45763 AAACGATATT
Statistics
Matches: 3057, Mismatches: 405, Indels: 216
0.83 0.11 0.06
Matches are distributed among these distances:
657 1 0.00
659 85 0.03
660 263 0.09
661 92 0.03
662 230 0.08
663 665 0.22
664 435 0.14
665 117 0.04
666 11 0.00
667 97 0.03
668 151 0.05
669 159 0.05
670 128 0.04
671 23 0.01
672 5 0.00
673 11 0.00
674 56 0.02
675 7 0.00
676 68 0.02
677 180 0.06
678 60 0.02
679 195 0.06
680 18 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (667 bp):
CAAAAATTGAGGAAAAATAATTCCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
CATCACGGTTTTTGGCAAAAAACGCGTTTCGGGGCACCGGCTCAGTTTTGCATGATTTTTGGCGC
CGAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTGAGGATTTG
TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCAGAATTTAATTTAGGAAAAAATTGGAAAA
ACGATATTAGAAACGTTAAAATCCCTTCAAACTTTTTGGCGTTGAATTATATATTTTTTATGAGT
ATCGTGGCCAAAAATTGAGGAAAAATAATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
GTACTAACCATCACGGTTTTTGGCTAAAAACGCGGTTTCGGGGCACCGGCTCAGTTTTGCATGAT
TTTTGGCGCCAAGAGTCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTT
GAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATCTGATTTTAATTTAGGAAAAA
ATTGGAAAAACGATATTAGAAACGTTAAAAGCCCTTCAAATTTTTGGCGTTGAATTATATATTTT
TTTATGAGTATCGTGGC
Found at i:46182 original size:19 final size:19
Alignment explanation
Indices: 46133--46174 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
46123 CGTGTACCAT
* *
46133 CACGGTTTTTAGCTAATAA
1 CACGATTTTTGGCTAATAA
46152 CACGATTTTTGGCTAATAA
1 CACGATTTTTGGCTAATAA
46171 CACG
1 CACG
46175 TGTTTTGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (19 bp):
CACGATTTTTGGCTAATAA
Done.