Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014571.1 Corchorus capsularis cultivar CVL-1 contig14592, 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: 51701
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:15780 original size:18 final size:17
Alignment explanation
Indices: 15753--15787 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
15743 TCCAACCCTA
15753 GATTTCTGCCTTTCTTT
1 GATTTCTGCCTTTCTTT
15770 GATTCTCTGCCTTTCTTT
1 GATT-TCTGCCTTTCTTT
15788 TTAATCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.06, C:0.26, G:0.11, T:0.57
Consensus pattern (17 bp):
GATTTCTGCCTTTCTTT
Found at i:25991 original size:12 final size:12
Alignment explanation
Indices: 25974--25998 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25964 AAGTGTCGCC
25974 TTAAATAATCCT
1 TTAAATAATCCT
25986 TTAAATAATCCT
1 TTAAATAATCCT
25998 T
1 T
25999 ATTAAAGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAATAATCCT
Found at i:27881 original size:179 final size:179
Alignment explanation
Indices: 27581--27905 Score: 580
Period size: 179 Copynumber: 1.8 Consensus size: 179
27571 CAAGGGTTAA
*
27581 AAGAAACTTTCATTGTAAGATACGATATCTGTTAGACTTGACTGAGACTGTTTAAAGTTTTCACA
1 AAGAAACTTTCATTGTAAGATACGATATCTCTTAGACTTGACTGAGACTGTTTAAAGTTTTCACA
* *
27646 AGGGTTAAAGACATGGTTGTCAGATCCGGACCGACCCGACCGGGTCACCCGGTTAGCCCGGGACC
66 AGGGTTAAAGACATGGTTGTCAGACCCGGACCGACCCGACCGGGTCACCCGGTTAGCCCCGGACC
27711 CAGTGGCCTCTCCGGGTCGAAGAGGGGTGGCATCCGGGGGTATGTTGGC
131 CAGTGGCCTCTCCGGGTCGAAGAGGGGTGGCATCCGGGGGTATGTTGGC
*
27760 AAGAAACTTTCGTTGTAAGATACGATATCTCTTAGACTTGACTGAGACTGTTTAAAGTTTTCACA
1 AAGAAACTTTCATTGTAAGATACGATATCTCTTAGACTTGACTGAGACTGTTTAAAGTTTTCACA
* *
27825 AGGGTTGAAGACATGGTTGTCAGACCCGGACC-AGCCCGGCCGGGTCACCCGGTTAGCCCCGGAC
66 AGGGTTAAAGACATGGTTGTCAGACCCGGACCGA-CCCGACCGGGTCACCCGGTTAGCCCCGGAC
27889 CCAGTGGCCTCTCCGGG
130 CCAGTGGCCTCTCCGGG
27906 CCGGCATGTT
Statistics
Matches: 139, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
178 1 0.01
179 138 0.99
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (179 bp):
AAGAAACTTTCATTGTAAGATACGATATCTCTTAGACTTGACTGAGACTGTTTAAAGTTTTCACA
AGGGTTAAAGACATGGTTGTCAGACCCGGACCGACCCGACCGGGTCACCCGGTTAGCCCCGGACC
CAGTGGCCTCTCCGGGTCGAAGAGGGGTGGCATCCGGGGGTATGTTGGC
Found at i:45322 original size:29 final size:30
Alignment explanation
Indices: 45268--45347 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
45258 CGGAGCCGTT
* *
45268 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTA
*
45298 AAGTTCAGGGGGCAAAATGT-CCAAAATTA
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTA
* * *
45327 AAGTTTATGAGGCAAAACGTC
1 AAGTTCAGGGGGCAAAACGTC
45348 TAAACACTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 24 0.57
30 18 0.43
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCCCAAAATTA
Found at i:48749 original size:335 final size:332
Alignment explanation
Indices: 46309--49843 Score: 4453
Period size: 335 Copynumber: 10.7 Consensus size: 332
46299 GGTTTCGAGA
* * * * *
46309 CAGTTTTTTCAAAAATTTAGCCGAAATCGTGTACTTTA-CATCACGGTATTTGGCTAAAAATGCG
1 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTGGCTAAAAACGCG
** ** ** * * ** * * *
46373 TTCTAGGACCCCAACTCAGTTTTGCGTGATTTTTTTTTGCACCGAGACTCATTGAAATATCTATA
65 TTCCGGGGTCCCGGCTTAGTTTTCCACGA---TTTTTGGCGCCGAGACTCCTTGAAATATCTATA
* * * * ** * * * * *
46438 TTCATCTAATCAAATCTCAGCCACATTGGGTTTAAAAATATGTTTTTACGAGCATCTAAATCCTG
127 TTCATCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAAT-TTT
* * * *
46503 TTTCGATTTAAACAGAAATTAATTT-G------AAGGAAAAACGATATTGGAAGCTTGAAAAGCC
191 TTTCGATTTAATCAGAAATTAATTTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAG-C
* * * * * * *
46561 ATCCAATCTATCCAACCTTTTTGGTGTTGAATTATATACTTTTAATGAGTATTTTGGCCTAAAAT
255 --CC-A--TA---AATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAAT
* * **
46626 TGAGGAAACA-TATTTTAGATT
312 TGAGGAAAAAGT-TTTTCGGGT
* * ** * * * * *
46647 CATTTTTTGCAAAAATTTAATCGAAATCGTGTATGTTA-CATCACGGTATTTAGCTAAAAACGTG
1 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA-CTAACCATCACGGTTTTTGGCTAAAAACGCG
* * * ** *
46711 TTCCGTGG-CCCGG-TTCAGTTTTGCATGATTTCAGGCACCGAGACTCCTTGAAATATCTATATT
65 TTCCGGGGTCCCGGCTT-AGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATT
* * * * * * *
46774 CATCTAATAAAAT-ATCAGACACATTAGG-TTTAAGGATATACTT-TTACGAGCATCTAAATTTT
129 CATCTATTCAAATCA-CAGCCACACT-GGATTTAAGGATAT-GTTCTTGCGAGCATCTGAATTTT
* * * * * * *
46836 GTTTTGATTTAATCTA-AAATTAATTTGGAAAAAATAGGAAAAA-AAAATTTAAAAGCGTGAAAA
191 -TTTCGATTTAATC-AGAAATTAATTTCGAAAAAAAAAGAAAAACGATA-TTAGAAGCGTGAAAA
* * * * * * * * *
46899 ACCCTTCAATCTTTTTGGTGTTGAGA-AATATATTTTTTATAAGTACTATGGTA-AAAAATT-AT
253 GCCCATAAATCTTTTTGGGGTTGA-ATTATATAATTTTTATGAGTATTGTGG-ACAAAAATTGA-
*** *
46961 GCTGAAATTTTTTCGGGT
315 GGAAAAAGTTTTTCGGGT
* * * * **
46979 AAGTTTTTACAAAATTTTAGCCGAAATCGTGTACTAATCATCACGATTTTCAGCTAAAAACGCGT
1 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
* * * * * *
47044 TCAC-GGGCCCCGGCTCAGTTTTGCATGATTTTTGACGCCAAGACTCCTTG-AA-A--TATATTC
66 TC-CGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTC
* * * * * * *
47104 ATCTAATCAATTCTCAACCACATTGGA-TTATAGGATATGTTCTTACGAGCATCTGAATCTTGTT
130 ATCTATTCAAATCACAGCCACACTGGATTTA-AGGATATGTTCTTGCGAGCATCTGAAT-TTTTT
* * *
47168 TCCATTTTATCAGAAATTAATTTGGTAAAAAAAAAAACAGAAAAACGATATTAGAAGCGTGAAAA
193 TCGATTTAATCAGAAATTAATTTCG----AAAAAAAA-AGAAAAACGATATTAGAAGCGTGAAAA
* * * * *
47233 ACCCTTCAATCTTTTTGGTGTTGAATTATATAATTTTTATAAGTATTGT-GACAAAAATTGAGGA
253 GCCCATAAATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGA
47297 AAAAGTTTTTCGGGT
318 AAAAGTTTTTCGGGT
*
47312 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGCTTTTGGCTAAAAACGCGT
1 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
* *
47377 TACGGGGTCCCGGCTTAGTTTTCCACGA--TTTGGCGCCGAGACTCCTTGAAATATCTATATCCA
66 TCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
*
47440 TCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCAGAATTTTTTTCG
131 TCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTCG
* *
47505 ATTTAATCAGAAATTAATTTCG-AAAAAAAAGGAAAACGATATTAGAAGCGTGAAAGGCCCATAA
196 ATTTAATCAGAAATTAATTTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATAA
47569 ATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAG-TT
261 ATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAGTTT
47633 TTCGGGT
326 TTCGGGT
* * *
47640 CAGTTTTTACAAAATTTTAGCTGAAATCGTG---T-A-CGTCACGGTTTTTGGCTAAAAACGCGT
1 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
*
47700 TCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTTTGCGCCGAGACTCCTTGAAATATCTATATTC
66 TCCGGGGTCCCGGCTTAGTTTTCCACGA-TTTTTGGCGCCGAGACTCCTTGAAATATCTATATTC
47765 ATCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTT
130 ATCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAA--TTTTTT
* * *
47830 TCGATTTAATCAGAAATGAATTTCGAAAAAAAAGGAAAAACGATATTAGATGCGTGAAAAGCCCA
193 TCGATTTAATCAGAAATTAATTTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCA
*
47895 TAAATCTTTTTGGGGTTAAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAG
258 TAAATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAG
47960 TTTTTCGGGT
323 TTTTTCGGGT
* * *
47970 CAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACACGT
1 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
* * *
48035 TCCGGGGTCCCGGCTTCGTTTTCCACGATTTTGGGCGCCGAGACTTCTTGAAATATCTATATTCA
66 TCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
* * *
48100 TCTATTCAAAT-AGCAACCACACTGGATTTAAGGATATGTTCTTGCGTGCATCTGAACTTTTTTC
131 TCTATTCAAATCA-CAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTC
*
48164 GATTTAATCAGAAATTAATTTCG-AAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATA
195 GATTTAATCAGAAATTAATTTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATA
*
48228 AATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTAGACAAAAATTGA-GAGAAAAGT
260 AATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGA-AAAAGT
48292 TTTTCGGGT
324 TTTTCGGGT
48301 CAGTTTTTGCAAAATTTTAGCCGAAAATCGTGTACGT-----T-ACGGTTTTT-GCTAAAAACGC
1 CAGTTTTTGCAAAATTTTAGCCG-AAATCGTGTAC-TAACCATCACGGTTTTTGGCTAAAAACGC
* * * * * *
48359 GTTCCAGGGACCCGACTTAGTATTCCATGATTTTTGGCGCCGAAACTCCTTGAAATATCTATATT
64 GTTCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATT
* * *
48424 CATCTATTCAAA-CTCAGCCACATTGGATTTAATGATATGTTCTTGCGAGCATCTGAATTTTTTT
129 CATCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAA--TTTTT
*
48488 TTCCGATTTAATCAGAAAATTAATTTGGAAAAAAAAAGAAAAACGATATTAGAAGCGTG-AAAGC
192 TT-CGATTTAATCAG-AAATTAATTTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGC
* * * * * * *
48552 CCTTAGATCTTTTTGGTGATGAATTATAT-ATTTTTAATAAGTATTGTTGACAACAATTGAGGAA
255 CCATAAATCTTTTTGGGGTTGAATTATATAATTTTT-ATGAGTATTGTGGACAAAAATTGAGGAA
* *
48616 AATGTTTTTCAGGT
319 AAAGTTTTTCGGGT
* * * * *
48630 AAGTGTTCGCAAAATTTTAGCCGAAAATCATGTACTAACCATCACGGTTTTCGGCTAAAAACGCG
1 CAGTTTTTGCAAAATTTTAGCCG-AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCG
*
48695 TTCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCGTTGAAATATCTATATTC
65 TTCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTC
* * *
48760 ATCTATTCAAATCACAGGCACACTAGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTATTTC
130 ATCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTC
*
48825 GATTTAATCAGAAATTAATTTCAAAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCAT
195 GATTTAATCAGAAATTAATTTC-GAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCAT
* *
48890 AAATTTTTTTGGGGTTGAATTATATAATTTATATGAGTATTGTGGACAAAAATTGAGGAAAAAGT
259 AAATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAGT
48955 TTTTCGGGT
324 TTTTCGGGT
* * * *
48964 CTGTTTTTGCAAAATTTAAGCCGAAATCGTGTACTAGCCATCACGGTTTTTGGCTAAAAATGCGT
1 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
* *
49029 TCCGGGGTCCCGGCTTAGTTTTCCACCATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTAA
66 TCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
49094 TCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTCG
131 TCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTCG
* * * *
49159 ATTTAATCAGAAATTAATTACGAAAAAAAAGAAAGAAAAACGATAATGGAAGTGTGAAAAGCCCA
196 ATTTAATCAGAAATTAATTTCG--AAAAAA-AAAGAAAAACGATATTAGAAGCGTGAAAAGCCCA
*
49224 TAAATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAAGAAAAAG
258 TAAATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAG
49289 TTTTTCGGGT
323 TTTTTCGGGT
*
49299 CAGTTTTTGCAAAATTTAAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
1 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
* *
49364 TCCGGGGTCCCGGCTTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCA
66 TCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
* * *
49429 TCTATTCAAATCAAAGCTACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGGATTTTTTTTC
131 TCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCT-GAATTTTTTTC
*
49494 GATTTAATCAGAAATTAATTTCG-AAAAAAAAGAAAAACGATATTAGAATCGTGAAAAGCCCATA
195 GATTTAATCAGAAATTAATTTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATA
* *
49558 AATATTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTT
260 AATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAGTT
49623 TTTCGGGT
325 TTTCGGGT
* * *
49631 CAGTTTTTGGAAAATTTAAGCCGAAATCGTG---T-A-CATCACTGTTTTTGGCTAAAAACGCGT
1 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
* *
49691 TCCGGGGTCCCGGCTTTGTTTTCCACGATTTTTGGCGCCGAGAGTCCTTGAAATATCTATATTCA
66 TCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
* *
49756 TCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAACATATGAATTTTTTTCG
131 TCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTCG
49821 ATTTAATCAGAAATTAATTTCGA
196 ATTTAATCAGAAATTAATTTCGA
49844 CGATTTTTGT
Statistics
Matches: 2842, Mismatches: 270, Indels: 181
0.86 0.08 0.05
Matches are distributed among these distances:
323 52 0.02
324 1 0.00
325 40 0.01
326 199 0.07
327 153 0.05
328 166 0.06
329 302 0.11
330 73 0.03
331 151 0.05
332 292 0.10
333 382 0.13
334 380 0.13
335 477 0.17
336 76 0.03
337 14 0.00
338 61 0.02
340 3 0.00
341 20 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (332 bp):
CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGT
TCCGGGGTCCCGGCTTAGTTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
TCTATTCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTCG
ATTTAATCAGAAATTAATTTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATAA
ATCTTTTTGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAGTTT
TTCGGGT
Found at i:49857 original size:16 final size:16
Alignment explanation
Indices: 49838--49868 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49828 CAGAAATTAA
*
49838 TTTCGACGATTTTTGT
1 TTTCCACGATTTTTGT
49854 TTTCCACGATTTTTG
1 TTTCCACGATTTTTG
49869 GCGCCGAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.16, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTCCACGATTTTTGT
Found at i:50542 original size:328 final size:328
Alignment explanation
Indices: 49852--51701 Score: 1822
Period size: 328 Copynumber: 5.6 Consensus size: 328
49842 GACGATTTTT
* * *
49852 GTTTTCCACGATTTTTGGCGCCGAGAGTCCTTGAAATATCTATATTCATCTATTCAAATCACAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* * * *
49917 CACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCGATTTAATCAGAAATGA
66 CACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTTAATTAGAAATTA
* *
49982 ATTTCGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTGA
131 ATTTCG--AGAAAA--TAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTGA
50047 ATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGG-AAAAGTTTTTCGGGTCAGTTTTT
192 ATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAAGTTTTTCGGGTCAGTTTTT
*
50111 GCAAAATTTAAGCCGAAATCGTGTACGCT-ACCATCACGATTTTTGGCTAAAAACGCGTTCCGGT
257 GCAAAATTTAAGCCGAAATCGTGTA--CTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGT
* *
50175 GTACCGGCTTT
320 -T-CCCGCTTA
* * * *
50186 GTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATTTATATTCATCTATTCAAATCACAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* * * *
50251 CACACTGGGTTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTCAATCAGAAATTA
66 CACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTTAATTAGAAATTA
* *
50316 ATTT-G-GAAAATAAAATGATATTAGAAGCGTGAAAAGCCCATAAATCTCTTTGGGGTTGAATTA
131 ATTTCGAGAAAATAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTGAATTA
*
50379 TATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAAGTTTTTCGGGGTCTGTTTTTGCA
196 TATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAAGTTTTTC-GGGTCAGTTTTTGCA
* * *
50444 AAATATAAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGCTAAAAACGCATTCCGGTTCCCG
260 AAATTTAAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGTTCCCG
50509 ACTTA
325 -CTTA
* * * * * * *
50514 ATTTTGCTTGATTTTTGGTGCTGAGACTCCTTGTAATATCTATATTCATCTAATCAAATCTCAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* * ** **
50579 CACATTGGATTTGAGGATATATTCTTGCGATTATCT-AAACTTTTTTCAATTTAATTAGAAATTA
66 CACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTTAATTAGAAATTA
* * * * **
50643 ATTTGGAAAAAAATGAAAAACAATATTAGAAGCGTGAAAAG-CCATTAAATCGTTTTGCTGTTGA
131 ATTTCG-AGAAAAT--AAAACGATATTAGAAGCGTGAAAAGCCCA-TAAATCTTTTTGGGGTTGA
* * * *
50707 ATTATATAATTTTTAAGATTATTGTGGACAAAAATTGA-GGATATAGTTTTTCGGGTCAGTTTTT
192 ATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAAGTTTTTCGGGTCAGTTTTT
** * *
50771 GCAAAATTTTTGCCGAAATAGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGAT
257 GCAAAATTTAAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCC-GG-T
*
50836 T-CCGTGTTA
320 TCCCG-CTTA
* * * * ** * *
50845 GTTTTCCATGATATTTGGCTCCAAGACTCCTTGAAGTATCTATATTCAAGTAATCAAGTCTCAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* * * * *
50910 CACATTGAATTTAAGGATATGATCTTAC-ATGCATCTGAATCTTTCTTTCGATTTAATTAGAAAT
66 CACATTGGATTTAAGGATATGTTCTTGCGA-GCATCTGAAT-TTTTTTTCAATTTAATTAGAAAT
* * * ** * * *
50974 TAATTTGGAAGAAAATAGGGAAAACGATATTAGAACCGTTAAAAGCCTTTCAATGTTTTTGGTGT
129 TAATTTCG-AGAAAAT----AAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGT
* * ** *** ** ** *
51039 TGAATTATAT-ATTTTATATAAGCATTGTGTCCAAAAATTTTGAAAAAAAAAG-AATTCTAGTTA
189 TGAATTATATAATTTT-TATGAGTATTGTGGACAAAAA--TTGAGGGAAAAAGTTTTTCGGGTCA
** * *
51102 GTTTTTTTTGCAAAAATTT-AGCTAAAATCGTGTA-TAAACCATCACGGTTTTT-TCTAAAAATG
251 G---TTTTTGC-AAAATTTAAGCCGAAATCGTGTACT-AACCATCACGGTTTTTGGCTAAAAACG
* * *
51164 CGTTTCGGGGTCCTGCTTTA
311 CG-TTCCGGTTCCCGC-TTA
* * * *
51184 GTTTTCCATGATTTTTTGCGCCTAGACTACTTGAAAT-TACTATTTTCATCTATTCAAATCTCAG
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATAT-CTATATTCATCTATTCAAATCTCAG
* * * * *
51248 CCACATTGGATTTAAGGATATGTTCTTACGAGCATCTAAATCTTGTTTCAATGTAATTAGAAATT
65 CCACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTTAATTAGAAATT
* * * *
51313 CATTTCGAAAAAAAGAAAGA-AAAACGATATTAGAAGCGTGAAAGGCCCATAAATATTTTTGCGG
130 AATTTCG------AGAAA-ATAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGG
*
51377 TTGAATTATATAGTTTTTATGAGTATTGTGGACAAAAATTGAGGG-AAAAGTTTTTCGGGTCAGT
188 TTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAAGTTTTTCGGGTCAGT
*
51441 TTTTGCAAAATTTAAGCCGAATTCGTG---------T-AC-G----T---T----ACGCGTTCCG
253 TTTTGCAAAATTTAAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCC-
*
51484 GGGTCCCGGCTTTA
317 GGTTCCC-GC-TTA
* * * * * *
51498 -TTTTCCACGATTTTTGGCGCAGAGACTCCTTGTAATATCTATATTTATGTATTCAAATCACAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* *
51562 CAC-TCTGGATTTAAGGATATGTTCTTGCGAGCATCTGAA-TTTTTTTCGATTTAATCAGAAATT
66 CACAT-TGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTTAATTAGAAA-T
* * *
51625 TAATTTCAGAAAAAAAAAAAGAAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATATTTTTGG
129 TAATTTC-G------AGAAA-ATAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGG
51690 GGTTGAATTATA
186 GGTTGAATTATA
Statistics
Matches: 1280, Mismatches: 188, Indels: 115
0.81 0.12 0.07
Matches are distributed among these distances:
312 21 0.02
313 104 0.08
314 20 0.02
315 52 0.04
317 1 0.00
319 1 0.00
323 1 0.00
324 2 0.00
325 1 0.00
327 31 0.02
328 179 0.14
329 43 0.03
330 109 0.09
331 102 0.08
332 78 0.06
333 43 0.03
334 149 0.12
335 60 0.05
336 6 0.00
337 22 0.02
338 31 0.02
339 168 0.13
340 42 0.03
341 7 0.01
343 6 0.00
344 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (328 bp):
GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
CACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTTAATTAGAAATTA
ATTTCGAGAAAATAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTGAATTA
TATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAAGTTTTTCGGGTCAGTTTTTGCAA
AATTTAAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGTTCCCGC
TTA
Found at i:50581 original size:806 final size:802
Alignment explanation
Indices: 49046--50646 Score: 2548
Period size: 806 Copynumber: 2.0 Consensus size: 802
49036 TCCCGGCTTA
49046 GTTTTCCACCATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTAATCTATTCAAATCACAGC
1 GTTTTCCACCATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTAATCTATTCAAATCACAGC
*
49111 CACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTCGATTTAATCAGAAATTAA
66 CACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTCGATTTAATCAGAAATGAA
* *
49176 TTACGAAAAAAAAGAAAGAAAAACGATAATGGAAGTGTGAAAAGCCCATAAATCTTTTTGGGGTT
131 TTACGAAAAAAAAG--AGAAAAACGATAATAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTT
49241 GAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAAGAAAAAGTTTTTCGGGTCAGTTTT
194 GAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAAGAAAAAGTTTTTCGGGTCAGTTTT
*
49306 TGCAAAATTTAAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGG
259 TGCAAAATTTAAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGGG
*
49371 TCCCGGCTTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATCTATTC
324 TACCGGCTTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATCTATTC
* * * *
49436 AAATCAAAGCTACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGGATTTTTTTTCGATTTAA
389 AAATCAAAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTCAA
* *
49501 TCAGAAATTAATTTCGAAAAAAAAGAAAAACGATATTAGAATCGTGAAAAGCCCATAAATATTTT
454 TCAGAAATTAATTTCG--AAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATATCTT
49566 TGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGT
517 TGGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGT
* * * *
49631 CAGTTTTTGGAAAATTTAAGCCGAAATCGTGTACATCACTGTTTTTGGCTAAAAACGCGTTCCGG
582 CAGTTTTTGCAAAATATAAGCCGAAATCGTGTACACCACTGTTTTTGGCTAAAAACGCATTCCGG
* ** * *
49696 GGTCCCGGCTTTGTTTTCCACGATTTTTGGCGCCGAGAGTCCTTGAAATATCTATATTCATCTAT
647 GGTCCCGACTTAATTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAA
* * * *
49761 TCAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAACATATGAATTTTTTTCGATTTA
712 TCAAATCACAGCCACACTGGATTTAAGGATATATTCTTGCGAACATATAAACTTTTTTCAATTTA
49826 ATCAGAAATTAATTTCGACGATTTTT
777 ATCAGAAATTAATTTCGACGATTTTT
* * *
49852 GTTTTCCACGATTTTTGGCGCCGAGAGTCCTTGAAATATCTATATTCATCTATTCAAATCACAGC
1 GTTTTCCACCATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTAATCTATTCAAATCACAGC
49917 CACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCGATTTAATCAGAAATGA
66 CACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAA-TTTTTTTCGATTTAATCAGAAATGA
* *
49982 ATTTCGAAAAAAAAG-GAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTG
130 ATTACGAAAAAAAAGAGAAAAACGATAATAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTG
* *
50046 AATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGTCAGTTTTT
195 AATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAAGAAAAAGTTTTTCGGGTCAGTTTTT
*
50111 GCAAAATTTAAGCCGAAATCGTGTACGCT-ACCATCACGATTTTTGGCTAAAAACGCGTTCCGGT
260 GCAAAATTTAAGCCGAAATCGTGTA--CTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGG
*
50175 GTACCGGCTTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATTTATATTCATCTATT
323 GTACCGGCTTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATCTATT
* *
50240 CAAATCACAGCCACACTGGGTTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTCA
388 CAAATCAAAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTCA
* * * *
50305 ATCAGAAATTAATTT-G-GAAAA-TAAAATGATATTAGAAGCGTGAAAAGCCCATAAATCTCTTT
453 ATCAGAAATTAATTTCGAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATATCTTT
50367 GGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAAGTTTTTCGGGG
518 GGGGTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGG-AAAAGTTTTTC-GGG
*
50432 TCTGTTTTTGCAAAATATAAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGCTAAAAACGCA
581 TCAGTTTTTGCAAAATATAAGCCGAAATCGTGTAC--ACCA-C-T-GTTTTTGGCTAAAAACGCA
* * ** * * *
50497 TTCC-GGTTCCCGACTTAATTTTGCTTGATTTTTGGTGCTGAGACTCCTTGTAATATCTATATTC
641 TTCCGGGGTCCCGACTTAATTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTC
* * * ** *
50561 ATCTAATCAAATCTCAGCCACATTGGATTTGAGGATATATTCTTGCGATTATCTAAACTTTTTTC
706 ATCTAATCAAATCACAGCCACACTGGATTTAAGGATATATTCTTGCGAACATATAAACTTTTTTC
*
50626 AATTTAATTAGAAATTAATTT
771 AATTTAATCAGAAATTAATTT
50647 GGAAAAAAAT
Statistics
Matches: 731, Mismatches: 54, Indels: 20
0.91 0.07 0.02
Matches are distributed among these distances:
800 85 0.12
801 15 0.02
802 35 0.05
804 138 0.19
805 171 0.23
806 227 0.31
807 60 0.08
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (802 bp):
GTTTTCCACCATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTAATCTATTCAAATCACAGC
CACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTCGATTTAATCAGAAATGAA
TTACGAAAAAAAAGAGAAAAACGATAATAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTGA
ATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAAGAAAAAGTTTTTCGGGTCAGTTTTTG
CAAAATTTAAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGGGTA
CCGGCTTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATCTATTCAA
ATCAAAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTCAATC
AGAAATTAATTTCGAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATATCTTTGGG
GTTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGTCAGT
TTTTGCAAAATATAAGCCGAAATCGTGTACACCACTGTTTTTGGCTAAAAACGCATTCCGGGGTC
CCGACTTAATTTTCCACGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAA
ATCACAGCCACACTGGATTTAAGGATATATTCTTGCGAACATATAAACTTTTTTCAATTTAATCA
GAAATTAATTTCGACGATTTTT
Found at i:50779 original size:660 final size:661
Alignment explanation
Indices: 49853--51701 Score: 2086
Period size: 660 Copynumber: 2.8 Consensus size: 661
49843 ACGATTTTTG
* * * *
49853 TTTTCCACGATTTTTGGCGCCGAGAGTCCTTGAAATATCTATATTCATCTATTCAAATCACAGCC
1 TTTTCCATGATTTTTGGCGCTGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGCC
* ** * * *
49918 ACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCGATTTAATCAGAAATGAA
66 ACATTGGATTTAAGGATATGTTCTTGCGAGCATCT-AAACTTTTTTCAATTTAATTAGAAATTAA
* *
49983 TTTCGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTGAA
130 TTTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGCGGTTGAA
50048 TTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGTCAGTTTTTGC
195 TTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGTCAGTTTTTGC
50113 AAAATTTAAGCCGAAATCGTGTACGCTACCATCACGATTTTTGGCTAAAAACGCGTTCCGGTGTA
260 AAAATTTAAGCCGAAAT-GTGTACG-TACCATCACG-TTTTTGGCTAAAAACGCGTTCCGG-GTA
* *
50178 CCGGCTTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATTTATATTCATCTATTCAA
321 CCGGCTTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATGTATTCAA
* * *
50243 ATCACAGCCACACTGGGTTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCAATTCAATC
386 ATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCGATTTAATC
* * *
50308 AGAAATTAATTT-G-GAAAATAAAATGATATTAGAAGCGTGAAAAGCCCATAAATCTCTTTGGGG
451 AGAAATTAATTTAGAGAAAATAAAACGATATTAGAAGCGTGAAAAGCCCATAAATATTTTTGGGG
* * *** * * * *
50371 TTGAATTATATAATTTT-TATGAGTATTGTGGACAAAAA-TTGAGGGAAAAAG-TTTTTCG-GGG
516 TTGAATTATAT-ATTTTATATAAGCATTGTGGACAAAAATTTGAAAAAAAAAGAATTCTAGTGAG
* *
50432 TCTGTTTTTGC-AAAATATAAGCCGAAATCGTGTACT-AACCATCATGGTTTTTGGCTAAAAACG
580 T-TGTTTTTGCAAAAAT-TAAGCCAAAATCGTGTA-TAAACCATCACGGTTTTT-GCTAAAAACG
*
50495 C-ATTCCGGTTCCCGAC-TTAA
641 CGATTCCGGGTCCCG-CTTTAA
* * * * *
50515 TTTTGCTTGATTTTTGGTGCTGAGACTCCTTGTAATATCTATATTCATCTAATCAAATCTCAGCC
1 TTTTCCATGATTTTTGGCGCTGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGCC
* * **
50580 ACATTGGATTTGAGGATATATTCTTGCGATTATCTAAACTTTTTTCAATTTAATTAGAAATTAAT
66 ACATTGGATTTAAGGATATGTTCTTGCGAGCATCTAAACTTTTTTCAATTTAATTAGAAATTAAT
* * * * *
50645 TT-GGAAAAAAATGAAAAACAATATTAGAAGCGTGAAAAG-CCATTAAATCGTTTTGCTGTTGAA
131 TTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCA-TAAATCTTTTTGCGGTTGAA
* * *
50708 TTATATAATTTTTAAGATTATTGTGGACAAAAATTGA-GGATATAGTTTTTCGGGTCAGTTTTTG
195 TTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGA-AAAGTTTTTCGGGTCAGTTTTTG
** *
50772 CAAAATTTTTGCCGAAATAGTGTA-ATAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGAT
259 CAAAATTTAAGCCGAAAT-GTGTACGT-ACCATCAC-GTTTTTGGCTAAAAACGCGTTCCGGG-T
* * * * * * * *
50836 TCCGTG-TTAGTTTTCCATGATATTTGGCTCCA-AGACTCCTTGAAGTATCTATATTCAAGTAAT
320 ACCG-GCTTTGTTTTCCACGATTTTTGGC-GCAGAGACTCCTTGAAATATCTATATTCATGTATT
* * * * * * *
50899 CAAGTCTCAGCCACATTGAATTTAAGGATATGATCTTAC-ATGCATCTGAATCTTTCTTTCGATT
383 CAAATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGA-GCATCTGAAT-TTTTTTTCGATT
* * * * ** *
50963 TAATTAGAAATTAATTTGGAAGAAAATAGGGAAAACGATATTAGAACCGTTAAAAGCCTTTCAAT
446 TAATCAGAAATTAATTTAG-AGAAAAT----AAAACGATATTAGAAGCGTGAAAAGCCCATAAAT
* * **
51028 GTTTTTGGTGTTGAATTATATATTTTATATAAGCATTGTGTCCAAAAATTTTGAAAAAAAAAGAA
506 ATTTTTGGGGTTGAATTATATATTTTATATAAGCATTGTGGACAAAAA-TTTGAAAAAAAAAGAA
* * * * *
51093 TTCTAGTTAGTTTTTTTTGCAAAAATTTAGCTAAAATCGTGTATAAACCATCACGGTTTTTTCTA
570 TTCTAGTGAGTTGTTTTTGCAAAAATTAAGCCAAAATCGTGTATAAACCATCACGGTTTTTGCTA
* * * * *
51158 AAAATGCGTTTCGGGGTCCTGCTTTAG
635 AAAACGCGATTCCGGGTCCCGCTTTAA
* * *
51185 TTTTCCATGATTTTTTGCGCCT-AGACTACTTGAAAT-TACTATTTTCATCTATTCAAATCTCAG
1 TTTTCCATGATTTTTGGCG-CTGAGACTCCTTGAAATAT-CTATATTCATCTATTCAAATCTCAG
* * *
51248 CCACATTGGATTTAAGGATATGTTCTTACGAGCATCTAAATCTTGTTTCAATGTAATTAGAAATT
64 CCACATTGGATTTAAGGATATGTTCTTGCGAGCATCTAAA-CTTTTTTCAATTTAATTAGAAATT
* * *
51313 CATTTCGAAAAAAAGAAAGAAAAACGATATTAGAAGCGTGAAAGGCCCATAAATATTTTTGCGGT
128 AATTTCG-AAAAAA-AAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGCGGT
*
51378 TGAATTATATAGTTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGTCAGTTT
191 TGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGTCAGTTT
*
51443 TTGCAAAATTTAAGCCG-AA--T-T-CGT---GT-ACG----T---T----ACGCGTTCCGGGGT
256 TTGCAAAATTTAAGCCGAAATGTGTACGTACCATCACGTTTTTGGCTAAAAACGCGTTCC-GGGT
* * * *
51488 CCCGGCTTTATTTTCCACGATTTTTGGCGCAGAGACTCCTTGTAATATCTATATTTATGTATTCA
320 ACCGGCTTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATGTATTCA
*
51553 AATCACAGCCACTCTGGATTTAAGGATATGTTCTTGCGAGCATCTGAA-TTTTTTTCGATTTAAT
385 AATCACAGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCGATTTAAT
* *
51617 CAGAAATTTAATTTCAGAAAAAAAAAAAGAAAAAACGATATTAGAAGCGTGAAAAGCCCATAAAT
450 CAGAAA-TTAATTT-AG------AGAAA-ATAAAACGATATTAGAAGCGTGAAAAGCCCATAAAT
51682 ATTTTTGGGGTTGAATTATA
506 ATTTTTGGGGTTGAATTATA
Statistics
Matches: 994, Mismatches: 147, Indels: 100
0.80 0.12 0.08
Matches are distributed among these distances:
650 20 0.02
651 10 0.01
652 99 0.10
653 4 0.00
654 47 0.05
656 1 0.00
657 5 0.01
658 4 0.00
659 130 0.13
660 158 0.16
661 28 0.03
662 86 0.09
663 7 0.01
664 2 0.00
665 1 0.00
666 5 0.01
667 63 0.06
669 24 0.02
670 139 0.14
671 35 0.04
672 1 0.00
673 7 0.01
674 112 0.11
675 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (661 bp):
TTTTCCATGATTTTTGGCGCTGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGCC
ACATTGGATTTAAGGATATGTTCTTGCGAGCATCTAAACTTTTTTCAATTTAATTAGAAATTAAT
TTCGAAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGCGGTTGAAT
TATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGTCAGTTTTTGCA
AAATTTAAGCCGAAATGTGTACGTACCATCACGTTTTTGGCTAAAAACGCGTTCCGGGTACCGGC
TTTGTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATGTATTCAAATCAC
AGCCACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATTTTTTTTCGATTTAATCAGAAA
TTAATTTAGAGAAAATAAAACGATATTAGAAGCGTGAAAAGCCCATAAATATTTTTGGGGTTGAA
TTATATATTTTATATAAGCATTGTGGACAAAAATTTGAAAAAAAAAGAATTCTAGTGAGTTGTTT
TTGCAAAAATTAAGCCAAAATCGTGTATAAACCATCACGGTTTTTGCTAAAAACGCGATTCCGGG
TCCCGCTTTAA
Found at i:51263 original size:339 final size:333
Alignment explanation
Indices: 49852--51701 Score: 1932
Period size: 339 Copynumber: 5.6 Consensus size: 333
49842 GACGATTTTT
* * *
49852 GTTTTCCACGATTTTTGGCGCCGAGAGTCCTTGAAATATCTATATTCATCTATTCAAATCACAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* * * *
49917 CACACTGGATTTAAGGATATGTTCTTGCGAGCATCTGAAT-TTTTTTTCGATTTAATCAGAAATG
66 CACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATCTTTTTTTCAATTTAATTAGAAATT
49981 AATTTCGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTG
131 AATTTCGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTG
*
50046 AATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGTCAGTTTTT
196 AATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAGTTTTTCGGGTCAGTTTTT
*** * *
50111 GCAAAATTTAAGCCGAAATCGTGTACGCTACCATCACGATTTTTGGCTAAAAACGCGTTCCGGTG
261 GCAAAATTT-AGCCGAAATCGTGTACTAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGG
50176 TACCGGCTTT-
325 T-CC-GCTTTA
* * * *
50186 GTTTTCCACGATTTTTGGCGCAGAGACTCCTTGAAATATTTATATTCATCTATTCAAATCACAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* * * *
50251 CACACTGGGTTTAAGGATATGTTCTTGCGAGCATCTGAAT-TTTTTTTCAATTCAATCAGAAATT
66 CACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATCTTTTTTTCAATTTAATTAGAAATT
* * * *
50315 AATTT-G---GAAAA--TAAAATGATATTAGAAGCGTGAAAAGCCCATAAATCTCTTTGGGGTTG
131 AATTTCGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTG
*
50374 AATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAAGTTTTTCGGGGTCTGTTT
196 AATTATATAATTTTTATGAGTATTGTGGACAAAAATTGA-GGAAAAAGTTTTTC-GGGTCAGTTT
* * *
50439 TTGCAAAATATAAGCCGAAATCGTGTACT-AACCATCATGGTTTTTGGCTAAAAACGCATTCC-G
259 TTGCAAAAT-TTAGCCGAAATCGTGTACTAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGG
*
50502 GTTCCCGAC-TTA
323 GGT-CCG-CTTTA
* * * * * * *
50514 ATTTTGCTTGATTTTTGGTGCTGAGACTCCTTGTAATATCTATATTCATCTAATCAAATCTCAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* * ** *
50579 CACATTGGATTTGAGGATATATTCTTGCGATTATCT-AAAC-TTTTTTCAATTTAATTAGAAATT
66 CACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATCTTTTTTTCAATTTAATTAGAAATT
* * * * **
50642 AATTT-GGAAAAAAATGAAAAACAATATTAGAAGCGTGAAAAG-CCATTAAATCGTTTTGCTGTT
131 AATTTCGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCA-TAAATCTTTTTGGGGTT
* * * *
50705 GAATTATATAATTTTTAAGATTATTGTGGACAAAAATTGAGGATATAGTTTTTCGGGTCAGTTTT
195 GAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAGTTTTTCGGGTCAGTTTT
* * *
50770 TGCAAAATTTTTGCCGAAATAGTGTAAT-AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGG
260 TGCAAAA-TTTAGCCGAAATCGTGTACTAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGG
*
50834 ATTCCG-TGTTA
324 -GTCCGCT-TTA
* * * * ** * *
50845 GTTTTCCATGATATTTGGCTCCAAGACTCCTTGAAGTATCTATATTCAAGTAATCAAGTCTCAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* * * * *
50910 CACATTGAATTTAAGGATATGATCTTAC-ATGCATCTGAATCTTTCTTTCGATTTAATTAGAAAT
66 CACATTGGATTTAAGGATATGTTCTTGCGA-GCATCTGAATCTTTTTTTCAATTTAATTAGAAAT
* * * * * ** * * *
50974 TAATTTGGAAGAAAATAGGGAAAACGATATTAGAACCGTTAAAAGCCTTTCAATGTTTTTGGTGT
130 TAATTTCGAA-AAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGT
* * ** ** ** ** *
51039 TGAATTATAT-ATTTTATATAAGCATTGTGTCCAAAAATTTTGAAAAAAAAAG-AATTCTAGTTA
194 TGAATTATATAATTTT-TATGAGTATTGTGGACAAAAA--TTG-AGGAAAAAGTTTTTCGGGTCA
** * *
51102 GTTTTTTTTGCAAAAATTTAGCTAAAATCGTGTA-TAAACCATCACGGTTTTT-TCTAAAAATGC
255 G---TTTTTGC-AAAATTTAGCCGAAATCGTGTACTAAACCATCACGGTTTTTGGCTAAAAACGC
*
51165 GTTTCGGGGTCCTGCTTTA
316 GTTCCGGGGTCC-GCTTTA
* * * *
51184 GTTTTCCATGATTTTTTGCGCCTAGACTACTTGAAAT-TACTATTTTCATCTATTCAAATCTCAG
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATAT-CTATATTCATCTATTCAAATCTCAG
* * * *
51248 CCACATTGGATTTAAGGATATGTTCTTACGAGCATCTAAATC-TTGTTTCAATGTAATTAGAAAT
65 CCACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATCTTTTTTTCAATTTAATTAGAAAT
* * * * *
51312 TCATTTCGAAAAAAAGAAAGAAAAACGATATTAGAAGCGTGAAAGGCCCATAAATATTTTTGCGG
130 TAATTTCG-AAAAAA-AAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGG
* *
51377 TTGAATTATATAGTTTTTATGAGTATTGTGGACAAAAATTGAGGGAAAAGTTTTTCGGGTCAGTT
193 TTGAATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAGTTTTTCGGGTCAGTT
*
51442 TTTGCAAAATTTAAGCCGAATTCGTG----------T-AC-G----T---T----ACGCGTTCCG
258 TTTGCAAAATTT-AGCCGAAATCGTGTACTAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCG
51484 GGGTCCCGGCTTTA
322 GGGT-CC-GCTTTA
* * * * * *
51498 -TTTTCCACGATTTTTGGCGCAGAGACTCCTTGTAATATCTATATTTATGTATTCAAATCACAGC
1 GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
* *
51562 CAC-TCTGGATTTAAGGATATGTTCTTGCGAGCATCTGAA--TTTTTTTCGATTTAATCAGAAAT
66 CACAT-TGGATTTAAGGATATGTTCTTGCGAGCATCTGAATCTTTTTTTCAATTTAATTAGAAA-
* *
51624 TTAATTTCAGAAAAAAAAAAAGAAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATATTTTTG
129 TTAATTTC-G---AAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTG
51689 GGGTTGAATTATA
190 GGGTTGAATTATA
Statistics
Matches: 1277, Mismatches: 190, Indels: 117
0.81 0.12 0.07
Matches are distributed among these distances:
312 18 0.01
313 106 0.08
314 10 0.01
315 55 0.04
316 7 0.01
317 1 0.00
319 1 0.00
323 1 0.00
324 2 0.00
325 1 0.00
327 32 0.03
328 174 0.14
329 42 0.03
330 106 0.08
331 104 0.08
332 79 0.06
333 34 0.03
334 151 0.12
335 65 0.05
336 7 0.01
337 20 0.02
338 38 0.03
339 176 0.14
340 43 0.03
341 4 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (333 bp):
GTTTTCCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTATTCAAATCTCAGC
CACATTGGATTTAAGGATATGTTCTTGCGAGCATCTGAATCTTTTTTTCAATTTAATTAGAAATT
AATTTCGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCCATAAATCTTTTTGGGGTTG
AATTATATAATTTTTATGAGTATTGTGGACAAAAATTGAGGAAAAAGTTTTTCGGGTCAGTTTTT
GCAAAATTTAGCCGAAATCGTGTACTAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGT
CCGCTTTA
Done.