Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007684.1 Corchorus capsularis cultivar CVL-1 contig07705, 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: 70313
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:6745 original size:213 final size:213
Alignment explanation
Indices: 6258--6966 Score: 1122
Period size: 213 Copynumber: 3.3 Consensus size: 213
6248 AAGTACATGC
6258 TAGTCCATCTTGGCAAAGCTAAATA-GCCCCACT-GGCAATGTTTAGTTTTGAATGCTAATGGAC
1 TAGTCCATCTTGGCAAAGCTAAA-ACGCCCCA-TAGGCAATGTTTAGTTTTGAATGCTAATGGAC
* * *
6321 TTACATTAATGTCTCTTTCAATTTCAATAGCTCTGTGCTTCTTTTCTTAGATGGAGTTCAGATCA
64 TTATATTAATG--TC--TC--TTTCAATAGTTCTGTGCTTCTTTTCTTAGATGGAGCTCAGATCA
* * * * ** *
6386 GTAGGGGGAAGACATTGGTATATTGTTAATTGCACTAGGAAAATTGGACTGTTTTGGCTATTTAA
123 GTAGGGAGAAGACATTAGTATTTTGTT-ATTGCACTAGTAAAAAAGGACTGTTTTGGGTATTTAA
6451 TCCTTTTTGTTTG--ACAAA-GTATTT
187 TCCTTTTTGTTTGACACAAAGGTATTT
* * *
6475 TAGTCCATCTTGGCAAAGCTAAAAAGCCCCCTGGGCAATGTTTAGTTTTGAATGCTAATGGACTT
1 TAGTCCATCTTGGCAAAGCTAAAACGCCCCATAGGCAATGTTTAGTTTTGAATGCTAATGGACTT
*
6540 ATATTAATGTCTCTTTCAATAGTTTTGTGCTTCTTTTCTTAGATGGAGCTCAGATCAGTAGGGAG
66 ATATTAATGTCTCTTTCAATAGTTCTGTGCTTCTTTTCTTAGATGGAGCTCAGATCAGTAGGGAG
6605 AAGACATTAGTATTTTGTTATTGCACTAGTAAAAAAGGACTGTTTTGGGTATTTAATCCTTTTTG
131 AAGACATTAGTATTTTGTTATTGCACTAGTAAAAAAGGACTGTTTTGGGTATTTAATCCTTTTTG
6670 TTTGACACAAAGGTATTT
196 TTTGACACAAAGGTATTT
* **
6688 TAGTCCATCTTGGCAAAGCTAAAACGTCTTATAGGCAATGTTTAGTTTTGAATGCTAATGGACTT
1 TAGTCCATCTTGGCAAAGCTAAAACGCCCCATAGGCAATGTTTAGTTTTGAATGCTAATGGACTT
6753 ATATTAATGTCTCTTTCAATAGTTCTGTGCTTCTTTTCTTAGATGGAGCTCAGATCAGTAGGGAG
66 ATATTAATGTCTCTTTCAATAGTTCTGTGCTTCTTTTCTTAGATGGAGCTCAGATCAGTAGGGAG
6818 AAGACATTAGTATTTTGTTATTGCACTAGTAAAAAAGGACTGTTTTGGGTATTTAATCCTTTTTG
131 AAGACATTAGTATTTTGTTATTGCACTAGTAAAAAAGGACTGTTTTGGGTATTTAATCCTTTTTG
6883 TTTGACACAAAGGTATTT
196 TTTGACACAAAGGTATTT
* **
6901 TAGTCCATCTTGGCAAAGCTAAAACGTCTTATAGGCAATGTTTAGTTTTGAATGCTAATGGACTT
1 TAGTCCATCTTGGCAAAGCTAAAACGCCCCATAGGCAATGTTTAGTTTTGAATGCTAATGGACTT
6966 A
66 A
6967 GATCAAATGC
Statistics
Matches: 468, Mismatches: 19, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
210 46 0.10
211 65 0.14
212 5 0.01
213 280 0.60
215 2 0.00
216 2 0.00
217 68 0.15
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (213 bp):
TAGTCCATCTTGGCAAAGCTAAAACGCCCCATAGGCAATGTTTAGTTTTGAATGCTAATGGACTT
ATATTAATGTCTCTTTCAATAGTTCTGTGCTTCTTTTCTTAGATGGAGCTCAGATCAGTAGGGAG
AAGACATTAGTATTTTGTTATTGCACTAGTAAAAAAGGACTGTTTTGGGTATTTAATCCTTTTTG
TTTGACACAAAGGTATTT
Found at i:12255 original size:205 final size:206
Alignment explanation
Indices: 11897--12311 Score: 778
Period size: 205 Copynumber: 2.0 Consensus size: 206
11887 TTTATATTAC
11897 GGGTAAATATTCAAATTAGGACTAAAAGTTTGAGGAAGTGCTAAATTTGGGCCTAATTCTTCAGA
1 GGGTAAATATTCAAATTAGGACTAAAAGTTTGAGGAAGTGCTAAATTTGGGCCTAATTCTTCAGA
* *
11962 TTGAATTTAATTAGGCGTAAACGTTTGGGTCATCAACCAAATTAGGCCTTTTTCTGACGGGACCC
66 TTGAATTTAATTAGGCCTAAACGTTTGGGTCATCAACCAAATTAGGCCGTTTTCTGACGGGACCC
12027 GCATGTGTAATGCACGCGCCGTTAAGTTTTACG-TTTTTTTTTTAATGTGGTAACGGCGCGTGCA
131 GCATGTGTAATGCACGCGCCGTTAAGTTTTACGTTTTTTTTTTTAATGTGGTAACGGCGCGTGCA
12091 CGACACGCAAG
196 CGACACGCAAG
12102 GGGTAAATATTCAAATTAGGACTAAAAGTTTGAGGAAGTGCTAAATTTGGGCCTAATTCTTCAGA
1 GGGTAAATATTCAAATTAGGACTAAAAGTTTGAGGAAGTGCTAAATTTGGGCCTAATTCTTCAGA
12167 TTGAATTTAATTAGGCCTAAACGTTTGGGTCATCAACCAAATTAGGCCGTTTTCTGACGGGACCC
66 TTGAATTTAATTAGGCCTAAACGTTTGGGTCATCAACCAAATTAGGCCGTTTTCTGACGGGACCC
* * *
12232 GCATGTGTAATGCACGTGCCGTTAAGTTTTACGTTTTTTTTTTTTATGTGGTAACGGCGTGTGCA
131 GCATGTGTAATGCACGCGCCGTTAAGTTTTACGTTTTTTTTTTTAATGTGGTAACGGCGCGTGCA
12297 CGACACGCAAG
196 CGACACGCAAG
12308 GGGT
1 GGGT
12312 TCTGTCAAAA
Statistics
Matches: 204, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
205 160 0.78
206 44 0.22
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (206 bp):
GGGTAAATATTCAAATTAGGACTAAAAGTTTGAGGAAGTGCTAAATTTGGGCCTAATTCTTCAGA
TTGAATTTAATTAGGCCTAAACGTTTGGGTCATCAACCAAATTAGGCCGTTTTCTGACGGGACCC
GCATGTGTAATGCACGCGCCGTTAAGTTTTACGTTTTTTTTTTTAATGTGGTAACGGCGCGTGCA
CGACACGCAAG
Found at i:26307 original size:30 final size:30
Alignment explanation
Indices: 26268--26328 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
26258 GAATCACCAC
* *
26268 CACCTCTAGATCCTGCTTCACCGCCGCCAG
1 CACCACTAGATCCTCCTTCACCGCCGCCAG
*
26298 CACCACTAGATCCTCCTTCACTGCCGCCAG
1 CACCACTAGATCCTCCTTCACCGCCGCCAG
26328 C
1 C
26329 TTTACCAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.48, G:0.15, T:0.20
Consensus pattern (30 bp):
CACCACTAGATCCTCCTTCACCGCCGCCAG
Found at i:26749 original size:144 final size:144
Alignment explanation
Indices: 26370--26739 Score: 632
Period size: 144 Copynumber: 2.6 Consensus size: 144
26360 CCACCTTTCT
* * * * *
26370 CAATTCCTCCACCCTTTCCAATGCCACCTCCAATTCCTCCACCACTGCCTCCTTCATTGCCACCA
1 CAATTCCACCACCCTTTCCAATGCCACCTTCAGTTCCACCACCACTACCTCCTTCATTGCCACCA
26435 CCTTTACCAGAATCACCCTCACCACCATTGCCACCACCTTTCCCAATTCCACCACCAATGCCTCC
66 CCTTTACCAGAATCACCCTCACCACCATTGCCACCACCTTTCCCAATTCCACCACCAATGCCTCC
*
26500 CCAGTGCCAGTGAC
131 CCAATGCCAGTGAC
* **
26514 CAATTCCACCACCCTTTCCAATGCCGCCTTCAGTTCCACCACCACTACCTTTTTCATTGCCACCA
1 CAATTCCACCACCCTTTCCAATGCCACCTTCAGTTCCACCACCACTACCTCCTTCATTGCCACCA
26579 CCTTTACCAGAATCACCCTCACCACCATTGCCACCACCTTTCCCAATTCCACCACCAATGCCTCC
66 CCTTTACCAGAATCACCCTCACCACCATTGCCACCACCTTTCCCAATTCCACCACCAATGCCTCC
*
26644 CCAATGCCAGTGGC
131 CCAATGCCAGTGAC
* *
26658 CAATTCCACCACCCTTTCCAATGCCACCTTCAGCTCCACCACCACTACCTCCTTCATTGCCACCT
1 CAATTCCACCACCCTTTCCAATGCCACCTTCAGTTCCACCACCACTACCTCCTTCATTGCCACCA
26723 CCTTTACCAGAATCACC
66 CCTTTACCAGAATCACC
26740 ATTGCCACCA
Statistics
Matches: 211, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 211 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.24
Consensus pattern (144 bp):
CAATTCCACCACCCTTTCCAATGCCACCTTCAGTTCCACCACCACTACCTCCTTCATTGCCACCA
CCTTTACCAGAATCACCCTCACCACCATTGCCACCACCTTTCCCAATTCCACCACCAATGCCTCC
CCAATGCCAGTGAC
Found at i:28474 original size:34 final size:34
Alignment explanation
Indices: 28431--28500 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
28421 TCCTTATAAG
28431 TGCACTATCAAACATGTCTACCGAGAAGCTAACA
1 TGCACTATCAAACATGTCTACCGAGAAGCTAACA
28465 TGCACTATCAAACATGTCTACCGAGAAGCTAACA
1 TGCACTATCAAACATGTCTACCGAGAAGCTAACA
28499 TG
1 TG
28501 TGTGCAGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (34 bp):
TGCACTATCAAACATGTCTACCGAGAAGCTAACA
Found at i:33572 original size:11 final size:11
Alignment explanation
Indices: 33551--33579 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
33541 AATAATATTA
33551 ATATA-TATAT
1 ATATATTATAT
33561 ATATATTATAT
1 ATATATTATAT
33572 ATATATTA
1 ATATATTA
33580 ATAGTAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATTATAT
Found at i:33610 original size:22 final size:21
Alignment explanation
Indices: 33585--33637 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
33575 TATTAATAGT
*
33585 AATACAATCAATTATTTTTGAG
1 AATACAATCAATTATATTT-AG
* *
33607 AATATATTCAATTATATTTAG
1 AATACAATCAATTATATTTAG
33628 -ATACAATCAA
1 AATACAATCAA
33638 ATTTTCCAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 8 0.31
21 2 0.08
22 16 0.62
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (21 bp):
AATACAATCAATTATATTTAG
Found at i:35643 original size:18 final size:18
Alignment explanation
Indices: 35622--35656 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35612 ACCACCTCCG
35622 CCACCTCCAAAACCACCT
1 CCACCTCCAAAACCACCT
*
35640 CCACCTCCAAATCCACC
1 CCACCTCCAAAACCACC
35657 ACCTGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.57, G:0.00, T:0.11
Consensus pattern (18 bp):
CCACCTCCAAAACCACCT
Found at i:35712 original size:24 final size:24
Alignment explanation
Indices: 35680--35725 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35670 CCTGCTCCTC
* *
35680 CTCCACCTCCGAATCCACCACCTG
1 CTCCACCTCCAAAACCACCACCTG
*
35704 CTCCTCCTCCAAAACCACCACC
1 CTCCACCTCCAAAACCACCACC
35726 ACCACCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.57, G:0.04, T:0.15
Consensus pattern (24 bp):
CTCCACCTCCAAAACCACCACCTG
Found at i:35733 original size:18 final size:18
Alignment explanation
Indices: 35712--35746 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35702 TGCTCCTCCT
35712 CCAAAACCACCACCACCA
1 CCAAAACCACCACCACCA
*
35730 CCAAAACCACCGCCACC
1 CCAAAACCACCACCACC
35747 GCCACTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.57, G:0.03, T:0.00
Consensus pattern (18 bp):
CCAAAACCACCACCACCA
Found at i:35740 original size:42 final size:42
Alignment explanation
Indices: 35609--35740 Score: 138
Period size: 42 Copynumber: 3.1 Consensus size: 42
35599 GGTGTCCGAT
* * *
35609 TCCACCACCTCCGCCACCTCCAAAACCACCTCCACCTCCAAA
1 TCCACCACCTGCACCTCCTCCAAAACCACCTCCACCTCCAAA
* **** * *
35651 TCCACCACCTGCACCTCCGCCTGCTCCTCCTCCACCTCCGAA
1 TCCACCACCTGCACCTCCTCCAAAACCACCTCCACCTCCAAA
* * *
35693 TCCACCACCTGCTCCTCCTCCAAAACCACCACCACCACCAAA
1 TCCACCACCTGCACCTCCTCCAAAACCACCTCCACCTCCAAA
*
35735 ACCACC
1 TCCACC
35741 GCCACCGCCA
Statistics
Matches: 69, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.25, C:0.57, G:0.05, T:0.14
Consensus pattern (42 bp):
TCCACCACCTGCACCTCCTCCAAAACCACCTCCACCTCCAAA
Found at i:35876 original size:36 final size:36
Alignment explanation
Indices: 35793--35876 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
35783 ACCTTTGCCG
* * * * * *
35793 AATCCACCTCCAGCACCTCCTCCGGCGCCGCCGCCA
1 AATCCACCACCTGCACCACCTCCAGCACCGCCACCA
*
35829 ATTCCACCACCTGCACCACCTCCAGCACCGCCACCA
1 AATCCACCACCTGCACCACCTCCAGCACCGCCACCA
35865 AATCCACCACCT
1 AATCCACCACCT
35877 TTTCCAATCC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.23, C:0.55, G:0.11, T:0.12
Consensus pattern (36 bp):
AATCCACCACCTGCACCACCTCCAGCACCGCCACCA
Found at i:35892 original size:30 final size:31
Alignment explanation
Indices: 35859--36459 Score: 398
Period size: 30 Copynumber: 19.8 Consensus size: 31
35849 TCCAGCACCG
* *
35859 CCACCAAAT-CCACCACCTTTTCCAATCCCG
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* **
35889 CCACC-AATGCCACCACCTTTACCAAAACCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * *
35919 CCTCCACCACCGATGCCACCACCCTTCCCAATTCCA
1 ---CCACCA--AATGCCACCACCTTTTCCAATTCCA
* * *
35955 CCACC-AATGCCTCCACCTTTGCCAATTCCG
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * *
35985 CCACC-AATTCCACCACCCTTTCCAATGCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* ** *
36015 CCTCCGTAT-CCACCACCCTTTCCAATTCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * * *
36045 CCACC-GATGCCTCCTCCTTTTCCAATGCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * *
36075 CCTCCATAT-CCACCACCCTTTCCAATTCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * * *
36105 CCACC-GATGCCTCCTCCTTTTCCAATGCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * * *
36135 CCTCCATAT-CCACCACCCTTTCCTATTCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * *
36165 CCACC-AATGCCCCCTCCTTTCCCAATTCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* *
36195 CCACCATAA--CCACCTCCTTTTCCTATTCCA
1 CCACCA-AATGCCACCACCTTTTCCAATTCCA
* * * *
36225 CCACC-AATGCCTCCACCCTTACCAATCCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* *
36255 CCACCAAAT-CCACCTCCTTTTCCTATTCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * * * *
36285 CCACC-AATACCTCCTCCTTTGCCAATGCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * *
36315 CCTCCATAA--CCACCACCCTTTCCTATTCCA
1 CCACCA-AATGCCACCACCTTTTCCAATTCCA
* * * *
36345 CCACC-TATGCCTCCACCCTTACCAATTCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * * *
36375 CCACCATAT-CCGCCACCTTTTCCTACTCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* * * *
36405 CCACC-AATGCCTCCACCCTTACCAATCCCA
1 CCACCAAATGCCACCACCTTTTCCAATTCCA
* *
36435 CCACCAAAT-CCACCTCCTTTACCAA
1 CCACCAAATGCCACCACCTTTTCCAA
36460 AGCCTCCACC
Statistics
Matches: 444, Mismatches: 101, Indels: 52
0.74 0.17 0.09
Matches are distributed among these distances:
28 3 0.01
29 14 0.03
30 378 0.85
31 15 0.03
32 4 0.01
33 10 0.02
36 20 0.05
ACGTcount: A:0.23, C:0.50, G:0.04, T:0.23
Consensus pattern (31 bp):
CCACCAAATGCCACCACCTTTTCCAATTCCA
Found at i:35912 original size:18 final size:18
Alignment explanation
Indices: 35891--35960 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 18
35881 CAATCCCGCC
*
35891 ACCAATGCCACCACCTTT
1 ACCAATGCCACCACCATT
** * **
35909 ACCAAAACCACCTCCACC
1 ACCAATGCCACCACCATT
* *
35927 ACCGATGCCACCACCCTT
1 ACCAATGCCACCACCATT
* *
35945 CCCAATTCCACCACCA
1 ACCAATGCCACCACCA
35961 ATGCCTCCAC
Statistics
Matches: 35, Mismatches: 17, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.30, C:0.51, G:0.04, T:0.14
Consensus pattern (18 bp):
ACCAATGCCACCACCATT
Found at i:36001 original size:60 final size:58
Alignment explanation
Indices: 35921--36454 Score: 516
Period size: 60 Copynumber: 8.9 Consensus size: 58
35911 CAAAACCACC
* * * * * *
35921 TCCACCACCGATGCCACCACCCTTCCCAATTCCACCACCAATGCCTCCACCTTTGCCAAT
1 TCCACCACCAATGCCTCCACCCTTTCCAATGCCACCACCAAT-CCACCACCTTT-CCTAT
* * * * * *
35981 TCCGCCACCAATTCCACCACCCTTTCCAATGCCACCTCCGTATCCACCACCCTTTCCAAT
1 TCCACCACCAATGCCTCCACCCTTTCCAATGCCACCACC-AATCCACCA-CCTTTCCTAT
* * * * *
36041 TCCACCACCGATGCCTCCTCCTTTTCCAATGCCACCTCCATATCCACCACCCTTTCCAAT
1 TCCACCACCAATGCCTCCACCCTTTCCAATGCCACCACCA-ATCCACCA-CCTTTCCTAT
* * * *
36101 TCCACCACCGATGCCTCCTCCTTTTCCAATGCCACCTCCATATCCACCACCCTTTCCTAT
1 TCCACCACCAATGCCTCCACCCTTTCCAATGCCACCACCA-ATCCACCA-CCTTTCCTAT
* * *
36161 TCCACCACCAATGCC-CC-CTCCTTTCCCAATTCCACCACCATAACCACCTCCTTTTCCTAT
1 TCCACCACCAATGCCTCCAC-CCTTT-CCAATGCCACCACCA-ATCCACCACC-TTTCCTAT
* * *
36221 TCCACCACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACCTCCTTTTCCTAT
1 TCCACCACCAATGCCTCCACCCTTTCCAATGCCACCACC-AATCCACCACC-TTTCCTAT
* * * *
36281 TCCACCACCAATACCTCC-TCCTTTGCCAATGCCACCTCCATAACCACCACCCTTTCCTAT
1 TCCACCACCAATGCCTCCACCCTTT-CCAATGCCACCACCA-ATCCACCA-CCTTTCCTAT
* * * * *
36341 TCCACCACCTATGCCTCCACCCTTACCAATTCCACCACCATATCCGCCACCTTTTCCTAC
1 TCCACCACCAATGCCTCCACCCTTTCCAATGCCACCACCA-ATCCACCACC-TTTCCTAT
* * *
36401 TCCACCACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACCTCCTTT
1 TCCACCACCAATGCCTCCACCCTTTCCAATGCCACCACC-AATCCACCACCTTT
36455 ACCAAAGCCT
Statistics
Matches: 414, Mismatches: 45, Indels: 31
0.84 0.09 0.06
Matches are distributed among these distances:
58 1 0.00
59 18 0.04
60 373 0.90
61 21 0.05
62 1 0.00
ACGTcount: A:0.22, C:0.50, G:0.04, T:0.24
Consensus pattern (58 bp):
TCCACCACCAATGCCTCCACCCTTTCCAATGCCACCACCAATCCACCACCTTTCCTAT
Found at i:36109 original size:120 final size:120
Alignment explanation
Indices: 35921--36448 Score: 610
Period size: 120 Copynumber: 4.4 Consensus size: 120
35911 CAAAACCACC
* * * * * *
35921 TCCACCACCGATGCCACCACCCTTCCCAATTCCACCACCA-ATGCCTCCA-CCTTTGCCAATTCC
1 TCCACCACCAATGCCTCCTCCTTTCCCAATGCCACCACCATAT-CCACCACCCTTT-CCAATTCC
* * * * * * *
35984 GCCACCAATTCCACCACCCTTTCCAATGCCACCTCCGTATCCACCACCCTTTCCAAT
64 ACCACCAATGCCTCCACCCTTACCAATGCCACCACCATATCCACCACCCTTTCCTAT
* * *
36041 TCCACCACCGATGCCTCCTCCTTTTCCAATGCCACCTCCATATCCACCACCCTTTCCAATTCCAC
1 TCCACCACCAATGCCTCCTCCTTTCCCAATGCCACCACCATATCCACCACCCTTTCCAATTCCAC
* * * * *
36106 CACCGATGCCTCCTCCTTTTCCAATGCCACCTCCATATCCACCACCCTTTCCTAT
66 CACCAATGCCTCCACCCTTACCAATGCCACCACCATATCCACCACCCTTTCCTAT
* * * * * *
36161 TCCACCACCAATGCCCCCTCCTTTCCCAATTCCACCACCATAACCACCTCCTTTTCCTATTCCAC
1 TCCACCACCAATGCCTCCTCCTTTCCCAATGCCACCACCATATCCACCACCCTTTCCAATTCCAC
* * * *
36226 CACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACCTCCTTTTCCTAT
66 CACCAATGCCTCCACCCTTACCAATGCCACCACCATATCCACCACCCTTTCCTAT
* * * * *
36281 TCCACCACCAATACCTCCTCCTTTGCCAATGCCACCTCCATAACCACCACCCTTTCCTATTCCAC
1 TCCACCACCAATGCCTCCTCCTTTCCCAATGCCACCACCATATCCACCACCCTTTCCAATTCCAC
* * * * *
36346 CACCTATGCCTCCACCCTTACCAATTCCACCACCATATCCGCCACCTTTTCCTAC
66 CACCAATGCCTCCACCCTTACCAATGCCACCACCATATCCACCACCCTTTCCTAT
* * * * *
36401 TCCACCACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACC
1 TCCACCACCAATGCCTCCTCCTTTCCCAATGCCACCACCATATCCACC
36449 TCCTTTACCA
Statistics
Matches: 352, Mismatches: 54, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
120 345 0.98
121 7 0.02
ACGTcount: A:0.23, C:0.50, G:0.04, T:0.24
Consensus pattern (120 bp):
TCCACCACCAATGCCTCCTCCTTTCCCAATGCCACCACCATATCCACCACCCTTTCCAATTCCAC
CACCAATGCCTCCACCCTTACCAATGCCACCACCATATCCACCACCCTTTCCTAT
Found at i:36449 original size:180 final size:180
Alignment explanation
Indices: 35970--36459 Score: 665
Period size: 180 Copynumber: 2.7 Consensus size: 180
35960 AATGCCTCCA
* * * * * * * *
35970 CCTTTGCCAATTCCGCCACCAATTCCACCACCCTTTCCAATGCCACCTCCGTATCCACCACCCTT
1 CCTTT-CCTATTCCACCACCAATGCCACCACCCTTACCAATTCCACCACCATATCCACCACCTTT
* * * * * * * * * *
36035 TCCAATTCCACCACCGATGCCTCCTCCTTTTCCAATGCCACCTCCATATCCACCACCCTTTCCAA
65 TCCTATTCCACCACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACCTCCTTTTCCAA
* * * *
36100 TTCCACCACCGATGCCTCCTCCTTTTCCAATGCCACCTCCATATCCACCAC
130 TTCCACCACCAATACCTCCTCCTTTGCCAATGCCACCTCCATAACCACCAC
* * * * * *
36151 CCTTTCCTATTCCACCACCAATGCCCCCTCCTTTCCCAATTCCACCACCATAACCACCTCCTTTT
1 CCTTTCCTATTCCACCACCAATGCCACCACCCTTACCAATTCCACCACCATATCCACCACCTTTT
*
36216 CCTATTCCACCACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACCTCCTTTTCCTAT
66 CCTATTCCACCACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACCTCCTTTTCCAAT
36281 TCCACCACCAATACCTCCTCCTTTGCCAATGCCACCTCCATAACCACCAC
131 TCCACCACCAATACCTCCTCCTTTGCCAATGCCACCTCCATAACCACCAC
* * *
36331 CCTTTCCTATTCCACCACCTATGCCTCCACCCTTACCAATTCCACCACCATATCCGCCACCTTTT
1 CCTTTCCTATTCCACCACCAATGCCACCACCCTTACCAATTCCACCACCATATCCACCACCTTTT
* *
36396 CCTACTCCACCACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACCTCCTTTACCAA
66 CCTATTCCACCACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACCTCCTTTTCCAA
36460 AGCCTCCACC
Statistics
Matches: 270, Mismatches: 39, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
180 265 0.98
181 5 0.02
ACGTcount: A:0.22, C:0.49, G:0.03, T:0.25
Consensus pattern (180 bp):
CCTTTCCTATTCCACCACCAATGCCACCACCCTTACCAATTCCACCACCATATCCACCACCTTTT
CCTATTCCACCACCAATGCCTCCACCCTTACCAATCCCACCACCAAATCCACCTCCTTTTCCAAT
TCCACCACCAATACCTCCTCCTTTGCCAATGCCACCTCCATAACCACCAC
Found at i:36528 original size:18 final size:17
Alignment explanation
Indices: 36486--36541 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
36476 ACCCCCGTGC
*
36486 CCACCTCCTAAACCACCA
1 CCACCTCC-AAACCACCT
*
36504 CCGCCTCCAAAGCCACCT
1 CCACCTCCAAA-CCACCT
*
36522 CCACCTCCGAATCCACCT
1 CCACCTCC-AAACCACCT
36540 CC
1 CC
36542 TCCACCACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.09
18 27 0.84
19 2 0.06
ACGTcount: A:0.25, C:0.57, G:0.05, T:0.12
Consensus pattern (17 bp):
CCACCTCCAAACCACCT
Found at i:36597 original size:18 final size:18
Alignment explanation
Indices: 36570--36604 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36560 TCCACCAAAT
36570 CCGCCCCCAGCCCCACCA
1 CCGCCCCCAGCCCCACCA
* *
36588 CCGCCTCCAGCTCCACC
1 CCGCCCCCAGCCCCACC
36605 GCCAAAACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.69, G:0.11, T:0.06
Consensus pattern (18 bp):
CCGCCCCCAGCCCCACCA
Found at i:36619 original size:24 final size:24
Alignment explanation
Indices: 36591--36643 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
36581 CCCACCACCG
* *
36591 CCTCCAGCTCCACCGCCAAAACCA
1 CCTCCACCTCCACCACCAAAACCA
* **
36615 GCTCCACCTCCGGCACCAAAACCA
1 CCTCCACCTCCACCACCAAAACCA
36639 CCTCC
1 CCTCC
36644 CTTAGTTAGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.55, G:0.09, T:0.09
Consensus pattern (24 bp):
CCTCCACCTCCACCACCAAAACCA
Found at i:38308 original size:16 final size:15
Alignment explanation
Indices: 38287--38316 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
38277 ATTTTATTGC
38287 GAAGAAAAAGAAAAAA
1 GAAGAAAAA-AAAAAA
38303 GAAGAAAAAAAAAA
1 GAAGAAAAAAAAAA
38317 CATGTCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAAAAAAA
Found at i:40149 original size:15 final size:17
Alignment explanation
Indices: 40129--40169 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
40119 TATAATTAGT
40129 TACTAGTACTAG-TAG-
1 TACTAGTACTAGCTAGC
40144 TACTAGTACTAGCTAGC
1 TACTAGTACTAGCTAGC
40161 TAGCTAGTA
1 TA-CTAGTA
40170 TATAATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.52
16 3 0.13
17 2 0.09
18 6 0.26
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (17 bp):
TACTAGTACTAGCTAGC
Found at i:40735 original size:2 final size:2
Alignment explanation
Indices: 40728--40761 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40718 CTTACAAATN
40728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40762 AACATAGTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42094 original size:28 final size:28
Alignment explanation
Indices: 42054--42112 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
42044 TTACCCTTAT
42054 AAATATATTAATTTTTTCTTTTTGAATG
1 AAATATATTAATTTTTTCTTTTTGAATG
42082 AAATATATTAATTTTTTCTTTTTGAATG
1 AAATATATTAATTTTTTCTTTTTGAATG
42110 AAA
1 AAA
42113 GTTTAGAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (28 bp):
AAATATATTAATTTTTTCTTTTTGAATG
Found at i:44018 original size:27 final size:26
Alignment explanation
Indices: 43980--44032 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
43970 ATCTCCCCTA
43980 CTCTAAACTTTTGTGTCCCTATAAAAT
1 CTCTAAACTTTTGTGTCCCTA-AAAAT
*
44007 CTCTAAATTTTTGTGTCCCTAAAAAT
1 CTCTAAACTTTTGTGTCCCTAAAAAT
44033 AGAAGATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.42
Consensus pattern (26 bp):
CTCTAAACTTTTGTGTCCCTAAAAAT
Found at i:44984 original size:94 final size:91
Alignment explanation
Indices: 44882--45059 Score: 329
Period size: 94 Copynumber: 1.9 Consensus size: 91
44872 GACAAAAAAA
44882 ATTTGTAAGTTGGAACAGCTTAAAAAAAAATCCGTAAATAGTTTAGGTTAATGTCTTAATATTGA
1 ATTTGTAAGTTGGAACAGCTTAAAAAAAAATCCGTAAATAGTTTAGGTTAATGTCTT-A-A-TGA
44947 TTTGCCCAAATATTATAAATATTTGTAAT
63 TTTGCCCAAATATTATAAATATTTGTAAT
44976 ATTTGTAAGTTGGAACAGCTTAAAAAAAAATCCGTAAATAGTTTAGGTTAATGTCTTAATGATTT
1 ATTTGTAAGTTGGAACAGCTTAAAAAAAAATCCGTAAATAGTTTAGGTTAATGTCTTAATGATTT
45041 GCCCAAATATTATAAATAT
66 GCCCAAATATTATAAATAT
45060 ATGCATTTTC
Statistics
Matches: 84, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
91 25 0.30
92 1 0.01
93 1 0.01
94 57 0.68
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (91 bp):
ATTTGTAAGTTGGAACAGCTTAAAAAAAAATCCGTAAATAGTTTAGGTTAATGTCTTAATGATTT
GCCCAAATATTATAAATATTTGTAAT
Found at i:47281 original size:13 final size:14
Alignment explanation
Indices: 47265--47294 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47255 TTTATATTTA
47265 TTAAT-AAATTATT
1 TTAATAAAATTATT
47278 TTAATAAAATTATT
1 TTAATAAAATTATT
47292 TTA
1 TTA
47295 TGTTTTACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAATAAAATTATT
Found at i:48238 original size:6 final size:6
Alignment explanation
Indices: 48229--48262 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
48219 TTTCTTTTTT
*
48229 TGTTAA TGTTAA CGTTAA TGTTAA TGTTAA TGTT
1 TGTTAA TGTTAA TGTTAA TGTTAA TGTTAA TGTT
48263 GTTCTAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (6 bp):
TGTTAA
Found at i:49629 original size:2 final size:2
Alignment explanation
Indices: 49624--49656 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49614 AAAAACAGTG
49624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49657 TCAAGTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62414 original size:2 final size:2
Alignment explanation
Indices: 62407--62491 Score: 76
Period size: 2 Copynumber: 45.0 Consensus size: 2
62397 AATTGATGAC
* * *
62407 AT AT AT AT AT AT AT AT AT AT AT AT AA AT A- AT TT GT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62446 AT -T AT AT AT A- AT AT A- ACT A- AGT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT
62486 AT AT AT
1 AT AT AT
62492 GTAATAATTC
Statistics
Matches: 70, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
1 7 0.10
2 61 0.87
3 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64065 original size:60 final size:61
Alignment explanation
Indices: 63995--64157 Score: 219
Period size: 60 Copynumber: 2.7 Consensus size: 61
63985 GGTAATTGCT
* * *
63995 CAAATAAGGGCCTAACGTTTGTC-AAAATGTTCAAATAAGGGTCCGATCTTTTAATTT-GA
1 CAAATAAGGGCCTAACGTTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGA
* *
64054 CACAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAAGGCCCGATCTTTTAATTTGGT
1 CA-AATAAGGGCCTAACGTTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGA
*
64115 CAAATAAGGGCTTAA--TATTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGT-TTATCGAAAATGCTCAAATAAGGGCC
64158 TGGTATCAGT
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
59 6 0.07
60 83 0.90
61 3 0.03
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (61 bp):
CAAATAAGGGCCTAACGTTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGA
Found at i:64266 original size:60 final size:60
Alignment explanation
Indices: 64191--64304 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
64181 GAGACAGACC
* * *
64191 CTTATTTGAGCATTTTGGCAAACGTTAGTCCCTTATTTGGCCAAATTCAAAGATGGGGCT
1 CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGACCAAATTCAAAGATGGGGCT
* * * * *
64251 CTTATTTGAGTATTTTGGTAAATATTAGGCCCTTATTTGATCAAATTGAAAGAT
1 CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGACCAAATTCAAAGAT
64305 TACCCTTATT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (60 bp):
CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGACCAAATTCAAAGATGGGGCT
Found at i:64655 original size:17 final size:18
Alignment explanation
Indices: 64633--64669 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
64623 CATATTAATT
64633 ATTAATATAT-TATATAA
1 ATTAATATATATATATAA
*
64650 ATTAATATATATGTATAA
1 ATTAATATATATATATAA
64668 AT
1 AT
64670 AGGGTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTAATATATATATATAA
Found at i:65790 original size:2 final size:2
Alignment explanation
Indices: 65783--65808 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65773 GAGTTAGCAA
65783 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
65809 TGAAAAATAT
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):
AT
Found at i:66222 original size:2 final size:2
Alignment explanation
Indices: 66211--66248 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
66201 ACTGGCCACC
66211 AT AT AT -T AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66249 TTGTTTAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Done.