Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015825.1 Corchorus olitorius cultivar O-4 contig15858, 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: 43372
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:14 original size:2 final size:2
Alignment explanation
Indices: 8--44 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 AGTTAGT
8 TA TA 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 TA TA T
45 TCAATTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4821 original size:12 final size:12
Alignment explanation
Indices: 4804--4828 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4794 TTTTAGTAGA
4804 TTCTTCTTCTTT
1 TTCTTCTTCTTT
4816 TTCTTCTTCTTT
1 TTCTTCTTCTTT
4828 T
1 T
4829 GGCCAGTGTA
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:5532 original size:21 final size:22
Alignment explanation
Indices: 5507--5549 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
5497 CATCGCATAC
*
5507 ATCTC-GCGTCATGACAAGTTA
1 ATCTCTGCATCATGACAAGTTA
5528 ATCTCTTGCATCATGACAAGTT
1 ATCTC-TGCATCATGACAAGTT
5550 TCTAACATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (22 bp):
ATCTCTGCATCATGACAAGTTA
Found at i:5946 original size:29 final size:30
Alignment explanation
Indices: 5913--5979 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
5903 CAATGGTCAA
* *
5913 ATAAGCCCCTAAACTTC-AATTTTGGCCAG
1 ATAAGCCCCTAAACTACTAATTTTGACCAG
* *
5942 ATAAGCCCCTGAACTACTAATTTTTACCAG
1 ATAAGCCCCTAAACTACTAATTTTGACCAG
5972 ATAAGCCC
1 ATAAGCCC
5980 TTCTGCTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (30 bp):
ATAAGCCCCTAAACTACTAATTTTGACCAG
Found at i:6298 original size:29 final size:30
Alignment explanation
Indices: 6230--6301 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
6220 CTCATAACCA
* *
6230 AAGG-GTTTATCTGGCCAAAATTGGTAGTT
1 AAGGAGTTTATTTGGCCAAAATTGGAAGTT
6259 AAGGAGTTTATTTGGCCAAAATT-GAAGTT
1 AAGGAGTTTATTTGGCCAAAATTGGAAGTT
*
6288 TAGGA-TCTTATTTG
1 AAGGAGT-TTATTTG
6302 ACCATTGACA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 1 0.03
29 20 0.53
30 17 0.45
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (30 bp):
AAGGAGTTTATTTGGCCAAAATTGGAAGTT
Found at i:6809 original size:9 final size:8
Alignment explanation
Indices: 6793--6835 Score: 50
Period size: 9 Copynumber: 4.9 Consensus size: 8
6783 ACCTTTTCCC
6793 TCTCTTCT
1 TCTCTTCT
6801 TCTTCTTCT
1 TC-TCTTCT
6810 TCTCTTCTT
1 TCTCTTC-T
6819 TCTCTCTCT
1 TCTCT-TCT
6828 CTCTCTTC
1 -TCTCTTC
6836 AATATTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.23
9 17 0.55
10 7 0.23
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (8 bp):
TCTCTTCT
Found at i:6830 original size:17 final size:17
Alignment explanation
Indices: 6787--6831 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 17
6777 GGTCCCACCT
*
6787 TTTCCCTCTCT-TCTTC
1 TTTCTCTCTCTCTCTTC
6803 -TTCT-TCT-TCTCTTC
1 TTTCTCTCTCTCTCTTC
6817 TTTCTCTCTCTCTCT
1 TTTCTCTCTCTCTCT
6832 CTTCAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
13 1 0.04
14 8 0.33
15 7 0.29
16 3 0.12
17 5 0.21
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTCTCTCTCTCTCTTC
Found at i:12992 original size:85 final size:84
Alignment explanation
Indices: 12852--13102 Score: 371
Period size: 85 Copynumber: 3.0 Consensus size: 84
12842 CACACTTCCT
* *
12852 CTATTCTTTAATTTGGTATAAAT-CC-TATCTGGTTATTACATTAAATCGATCGGAAATCTAATC
1 CTATTCTTTAATTTGGTATAAATCCCATATCTGGTAATTACATTAGATCGATCGGAAATCTAATC
12915 CGGAATCAAAATTACATCC
66 CGGAATCAAAATTACATCC
* *
12934 CTATTCTTTAATTTGATATAAATCCCATTATCTAGTAATTACATTAGATCGATCGGAAATCTAAT
1 CTATTCTTTAATTTGGTATAAATCCCA-TATCTGGTAATTACATTAGATCGATCGGAAATCTAAT
** *
12999 CTAGAATCAAAATTACATCT
65 CCGGAATCAAAATTACATCC
** *
13019 CTATTCTTTAATTTGGTATAAATCCCAGTATCTGGTAATTACATTAGATCGATTAGACATCTAAT
1 CTATTCTTTAATTTGGTATAAATCCCA-TATCTGGTAATTACATTAGATCGATCGGAAATCTAAT
*
13084 CCGTAATCAAAATTACATC
65 CCGGAATCAAAATTACATC
13103 ACTAAATGAA
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
82 22 0.15
83 2 0.01
85 126 0.84
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (84 bp):
CTATTCTTTAATTTGGTATAAATCCCATATCTGGTAATTACATTAGATCGATCGGAAATCTAATC
CGGAATCAAAATTACATCC
Found at i:20224 original size:178 final size:178
Alignment explanation
Indices: 19911--20235 Score: 476
Period size: 178 Copynumber: 1.8 Consensus size: 178
19901 ACAAACTATG
* * * *
19911 TAATATTAAGTAGACCATCTATTTCTGTTAACCGAAACAACTAATTCTTTGGAAGCATTTTTTAT
1 TAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGAT
* ** *
19976 ACCTTGAATATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAAAAACCTTTT
66 ACCTTGAACATTAAATTTAGTTTTCGAACCCTTCATAAAAGTTGTAGATCATGGAAAAACCTTCT
*
20041 AATAGACACTTGAATCATCTCAATCAGACCTCTGGAACAAAAGTTATA
131 AATAGACACTTAAATCATCTCAATCAGACCTCTGGAACAAAAGTTATA
* *
20089 TAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAGCATTTTTGA
1 TAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTT-GGAAGCATTTTTGA
* * *
20153 TA-CTTGAAACATTAAATTTAGTTTTCTAACCCTTCATGAAAGTTGTAGATCAT-GAAACAATCT
65 TACCTTG-AACATTAAATTTAGTTTTCGAACCCTTCATAAAAGTTGTAGATCATGGAAA-AACCT
20216 TCTAATAGACACTTAAATCA
128 TCTAATAGACACTTAAATCA
20236 CCTTAATTGG
Statistics
Matches: 130, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
177 11 0.08
178 119 0.92
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (178 bp):
TAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGAT
ACCTTGAACATTAAATTTAGTTTTCGAACCCTTCATAAAAGTTGTAGATCATGGAAAAACCTTCT
AATAGACACTTAAATCATCTCAATCAGACCTCTGGAACAAAAGTTATA
Found at i:20268 original size:178 final size:178
Alignment explanation
Indices: 19911--20275 Score: 450
Period size: 178 Copynumber: 2.1 Consensus size: 178
19901 ACAAACTATG
* * * *
19911 TAATATTAAGTAGACCATCTATTTCTGTTAACCGAAACAACTAATTCTTTGGAAGCATTTTTTAT
1 TAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGAT
* ** *
19976 ACCTTGAATATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAAAAACCTTTT
66 ACCTTGAACATTAAATTTAGTTTTCGAACCCTTCATAAAAGTTGTAGATCATGGAAAAACCTTCT
* * ** *
20041 AATAGACACTTGAATCATCTCAATCAGACCTCTGGAACAAAAGTTATA
131 AATAGACACTTAAATCACCTCAATCAGACAACCGGAACAAAAGTTATA
* *
20089 TAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAGCATTTTTGA
1 TAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTT-GGAAGCATTTTTGA
* * *
20153 TA-CTTGAAACATTAAATTTAGTTTTCTAACCCTTCATGAAAGTTGTAGATCAT-GAAACAATCT
65 TACCTTG-AACATTAAATTTAGTTTTCGAACCCTTCATAAAAGTTGTAGATCATGGAAA-AACCT
* ** * *
20216 TCTAATAGACACTTAAATCACCTTAATTGGATAACCGGAGAGAAAA-TTATA
128 TCTAATAGACACTTAAATCACCTCAATCAGACAACCGGA-ACAAAAGTTATA
*
20267 TAATGTTAA
1 TAATATTAA
20276 ATACACCGTT
Statistics
Matches: 159, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
177 11 0.07
178 143 0.90
179 5 0.03
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (178 bp):
TAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTTTTGAT
ACCTTGAACATTAAATTTAGTTTTCGAACCCTTCATAAAAGTTGTAGATCATGGAAAAACCTTCT
AATAGACACTTAAATCACCTCAATCAGACAACCGGAACAAAAGTTATA
Found at i:20986 original size:17 final size:17
Alignment explanation
Indices: 20964--20998 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20954 ATCAGTGGTG
*
20964 GTCGGTTATCGGTCAGT
1 GTCGGTTATCGATCAGT
*
20981 GTCGGTTTTCGATCAGT
1 GTCGGTTATCGATCAGT
20998 G
1 G
20999 CAACAAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.17, G:0.34, T:0.37
Consensus pattern (17 bp):
GTCGGTTATCGATCAGT
Found at i:22554 original size:22 final size:23
Alignment explanation
Indices: 22521--22563 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
22511 TATTAAAAGA
*
22521 TAAAAAGAAATTAAAAGAAAATC
1 TAAAAAGAAATTAAAAAAAAATC
22544 TAAAAAG-AATTAAAAAAAAA
1 TAAAAAGAAATTAAAAAAAAA
22564 CGCAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (23 bp):
TAAAAAGAAATTAAAAAAAAATC
Found at i:24794 original size:332 final size:330
Alignment explanation
Indices: 24019--26544 Score: 2382
Period size: 332 Copynumber: 7.6 Consensus size: 330
24009 GATCTCGGCT
* * * * *
24019 AAAATTGACCCGAAATATTTTTCCTCAAATTTTAGCCACAATACTTATAAAATATATATAATTCA
1 AAAATTGACCCGAAA-AATTTTCCTCAAATTTTGGCTAAAATACTTATAAAAAATATATAATTCA
* *
24084 ACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTCCATA-TTTTTCTGAATTAA
65 ACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAA
* * * * * *
24148 TTTTTAATTAACTTAAAACAAGATTTAGATGCTCGTAAAAACAAATCATTAAATTCAATGTGGCT
130 TTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * *
24213 GAGATTTGATTAGATGAGTATAGATATTTCAAGGAGTCTCGGCGTCAAAAATCATGCAAAACTAA
195 GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGA
* * * * **
24278 GCCGGGGTCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG-TAGTACACGATTCCAACTAAAA
260 GCC-GGGCCCCGAAACGCGTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
24342 TTTTGCA
324 TTTTGCA
* *
24349 GAAAA-TGACCTGAAAAAAATTTCCT-AAATTTTTGGCTAAAATACTTATAAAAAATATATAATT
1 -AAAATTGACCCG-AAAAATTTTCCTCAAA-TTTTGGCTAAAATACTTATAAAAAATATATAATT
* **
24412 TAACGCCAAAAATTTTGGAGGACTTTTCACGCTTTTAATATCGTTTTTTCATA-TTTTTCTGAAA
63 CAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG-TTTTTCATATTTTTTCTG-AA
* * * *
24476 TTAATTTTTAAATAAATCGAAACAAGATTCAGATGCTCGTATAAACAAATCCTTAAATGCAATGT
126 TTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGT
* * * *
24541 GACTGATATTTGATTAGATGAATATAGATTTTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAA
191 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
** *
24606 CTGAGCCACAGCCCCGAAACACGTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCT
256 CTGAGCC-GGGCCCCGAAACGCGTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCT
24671 AAAATTTTGCA
320 AAAATTTTGCA
* * * * *
24682 AAAAATGGCCCGAAAAACTTTTCCTCAAATTTTGGCTAAAATA-TTAATGAAATATATATAATTT
1 AAAATTGACCCGAAAAA-TTTTCCTCAAATTTTGGCTAAAATACTT-ATAAAAAATATATAATTC
* *
24746 AACGCCAAAAAGGTTGGAGGACTTTTCGA-GCTTTTCATATCGTTTTTCATATTTTTTCTGAATT
64 AACGCCAAAAAGATTGGAGGACTTTTC-ACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATT
* * * * * *
24810 AATTGCTAATTAAATCGAAACAAGATTTAGATACTCATAAAAACAAATCTTTAAATGCAATGTGG
128 AATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGG
* * * * * *
24875 CCGAGATTTGATTAGATGAATATGGATATTTCAAGGAGTCTTGGCGGCAAAAAACATACAAAACT
193 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
*** * ** * * * ** *
24940 GA-CCTAGGGCTTTGGAACGCGTTTTTTTCCAAAAACCGTGATGAATATTTTACACGATTTTGGC
258 GAGCC--GGGCCCCGAAACGCGTTTTTAGCAAAAAACTGTGATG-GT-TAGTACACGATTTCGGC
*
25004 TAACATTTTGCA
319 TAAAATTTTGCA
** * ** * *
25016 AAAATTGACTGGAAAGATATTTCCTC-AATTTTTACTTAAATACTCATAAAAAATATATAATTCA
1 AAAATTGACCCGAAAAAT-TTTCCTCAAATTTTGGCTAAAATACTTATAAAAAATATATAATTCA
* * * * * * * * **
25080 ACACCAAAAATATTGAACGGA-TTTTTAAGCTTCTAATATCGTTTTTCCTACTTTTTCCAAATTA
65 ACGCCAAAAAGATTGGA-GGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTA
* * *
25144 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGC
129 ATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGC
* * * *
25209 TGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTTGGCG-CAAGAAATCATTCGAAACT
194 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAA-AAATCATGCAAAACT
* * ** * * * * *
25273 GACCCGAGACCATGGAATGCTTTTTTACCCAAAAAAACTGTGATGG-TA-T--ACGATTTCGGCG
258 GAGCCG-GGCCCCGAAACGCGTTTTTA-GC-AAAAAACTGTGATGGTTAGTACACGATTTCGGCT
*
25334 AATATTTTGCA
320 AAAATTTTGCA
* * * * * * *
25345 AAAATTGACCCGAAATATGTTTCCTCAATTTTTAGCCACAATACTTATAAAAAA-AAAAAATTCA
1 AAAATTGACCCGAAAAAT-TTTCCTCAAATTTTGGCTAAAATACTTATAAAAAATATATAATTCA
* * * * * *
25409 AAGCCAAAAAGATTGAAGGGCTTTTCACACTTTT-AGATCGTTTTATC-TATTTTTTCTGAACTA
65 ACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTT-TCATATTTTTTCTGAATTA
* * * * *
25472 ATTTCTAATTAAATCAAAATATGAATT-AGATTCTTGTAAAAAC-AA----T---GGC----T-G
129 ATTTCTAATTAAATCAAAACAAG-ATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGG
** *
25523 -TGATTTTTG--TAGATGAATATAGATATTTCAAGGTGTCTCGGCGCCAAAAATCATGCAAAACT
193 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * * * * * ** * * * *
25585 GAACCTGGCCCCGCAACGCTTTTTTAGCCAAAAACTGTAATAATTATTATACAATTTCGGCTTAA
258 GAGCCGGGCCCCGAAACGCGTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAA
*
25650 ATTTTGTA
323 ATTTTGCA
* * * * * *
25658 AAAATTGACCCGAAAGATATATT-CTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTC
1 AAAATTGACCCGAAA-A-ATTTTCCTCAAATTTTGGCTAAAATACTTATAAAAAATATATAATTC
** * * * * * * * *
25722 TGCACCATAAAGATTGAAGGGCTTTTCACGCTTTCAATATCGTTTTTTATATTTTTCCTCAATTA
64 AACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTA
* * * *
25787 ATTTCTAATTAAATAAAAACAAGATTCAGATGCTCGAAAAAACAAATCTTTAAATGAAATGTGGC
129 ATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGC
* * * ** *
25852 TAAGATTTTATTAGATGAATATATATATTTCAAGGAGTCTCGAAGCCAAAAATCATGGAAAACTG
194 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTG
* * *** * *
25917 AGCCGGGGTCCCGAAACACGTTTTTAGCCAAAAAAAAAATGATGGTTAGTACACAATTTTGGCTA
259 AGCC-GGGCCCCGAAACGCGTTTTTAG-C-AAAAAACTGTGATGGTTAGTACACGATTTCGGCTA
25982 AAATTTTGCTAAA
321 AAATTTTGC---A
*** * * * * *
25995 AAAAAAAACCGGAAAAATTTTCCTCAATTTTTGGATAAAATACTTATAAAATATATATAATTTAA
1 AAAATTGACCCGAAAAATTTTCCTCAAATTTTGGCTAAAATACTTATAAAAAATATATAATTCAA
* * * *
26060 CACCAAAAAGATTGGAGGACTTTTCACGCTTTAAATATCATTTTTTCAAATTTTTTTTTCTGAAT
66 CGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATC-GTTTTTC--A-TATTTTTTCTGAAT
* * * * *
26125 TAATTTCT-ATTAAATCGAAATAAGATTAAGATGCTCGTAAAAACAAATCCTTAAAT-CTTATAT
127 TAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGC-AATGT
* * * * * *
26188 GGTTGAGATTTGACTAGATGAATATAGATATTTCAAGTAGTCTCGGAGTCAAGAATCATGCAAAA
191 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
* * * * *
26253 TTGAGGCGGGTCCCTGGAATGCGTTTTTAGCAAAAAA-TCGTGATGGTTACTTAGTACACGATTT
256 CTGAGCCGGG-CCCCGAAACGCGTTTTTAGCAAAAAACT-GTGATGG----TTAGTACACGATTT
* *
26317 TGGCTAAATTTTTGCA
315 CGGCTAAAATTTTGCA
* * * * *
26333 AAAATTGACACGAAAGATTTCTCTTCAATTTTTGGCTAAAA-ATCTCAT-AAAAATATATAATTC
1 AAAATTGACCCGAAAAATTT-TCCTCAAATTTTGGCTAAAATA-CTTATAAAAAATATATAATTC
* * * *
26396 AACGCCAAAAAGATTGGGGGCACTTTTCACGCTTTTAATATCGTATTCCTTATTTTTTCT-ATAT
64 AACGCCAAAAAGATTGGAGG-ACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGA-AT
* * * * * *
26460 TAATTTCTAATTAAATCAAAACAAGATTCATATGCTCGTAAGAACAAATTCTTAAATCCAATCTT
127 TAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTG
*
26525 GCTGAGATTTGGTTAGATGA
192 GCTGAGATTTGATTAGATGA
26545 TGTAAAGTAT
Statistics
Matches: 1797, Mismatches: 320, Indels: 151
0.79 0.14 0.07
Matches are distributed among these distances:
309 11 0.01
310 3 0.00
311 16 0.01
312 48 0.03
313 66 0.04
314 48 0.03
315 58 0.03
316 3 0.00
320 2 0.00
323 2 0.00
327 3 0.00
328 58 0.03
329 86 0.05
330 102 0.06
331 78 0.04
332 344 0.19
333 321 0.18
334 88 0.05
335 35 0.02
336 132 0.07
337 30 0.02
338 55 0.03
339 162 0.09
340 19 0.01
341 27 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (330 bp):
AAAATTGACCCGAAAAATTTTCCTCAAATTTTGGCTAAAATACTTATAAAAAATATATAATTCAA
CGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAAT
TTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTG
AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG
CCGGGCCCCGAAACGCGTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATT
TTGCA
Found at i:25941 original size:976 final size:986
Alignment explanation
Indices: 24058--26252 Score: 2383
Period size: 976 Copynumber: 2.2 Consensus size: 986
24048 TTTTAGCCAC
*
24058 AATACTTATAAAATATATATAATTCAACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATAT
1 AATACTTATAAAATATATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGC-TTTAATAT
* * **
24123 CG-TTTTCCATATTTTTCTGAATTAATTTTTAATTAACTTAAAACAAGATTTAGATGCTCGTAAA
65 CGTTTTTCC-TATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAA
* *
24187 AACAAATCATTAAATTCAATGTGGCTGAGATTTGATTAGATGAGTATAGATATTTCAAGGAGTCT
129 AACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
* * * *
24252 CGGCGTCAAAAATCATGCAAAACTAAGCCGGGGTCCCGAAACGCGTTTTTAGCCAAAAACCGTGA
194 CGGCGTCAAAAATCATGCAAAACTAAGCCCGAGACCCGAAACGCGTTTTTACCCAAAAACCGTGA
* *
24317 TGGTAGTACACGATTCCAACTAAAATTTTGCAGAAAATGACCTGAAAAAAATTTCCTAAATTTTT
259 TGGTAGTA-ACGATTCCAACGAAAATTTTGCAGAAAATGACCCGAAAAAAATTTCCTAAATTTTT
* * * * * * ** * *
24382 GGCTAAAATACTTATAAAAAATATATAATTTAACGCCAAAAATTTTGGAGGACTTTTCACGCTTT
323 AGCCAAAATACTTATAAAAAATAAAAAATTCAAAGCCAAAAAGATTGAAGGACTTTTCACACTTT
* * * * *
24447 TAATATCGTTTTTTCATATTTTTCTGAAATTAATTTTTAAATAAATCGAAACAAGATTCAGATGC
388 TAAGATCGTTTTATCATATTTTTCTGAAACTAATTTCTAAATAAATCAAAACAAGATTCAGAT-C
*
24512 TCGTATAAACAAATCCTTAAATGCAATGTGACTGATATTTGATTAGATGAATATAGATTTTTCAA
452 TCGTATAAACAAA-CC-T-AATGC-ATGTGACT-ATATTTGA-TAGATGAATATAGATATTTCAA
*
24577 GGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCCACAGCCCCGAAACACGTTTTTAGCAAAAA
511 GGAGTCTCGACGCCAAAAATCATGCAAAACTGAACCACAGCCCCGAAACACGTTTTTAGCAAAAA
* ** * * *
24642 ACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGGCCCGAAAAACTTTTCCT
576 ACTGTAATAATTAGTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAACTATTCCT
* * * * * * * *
24707 CAAATTTTGGCTAAAATATTAATGAAATATATATAATTTAACGCCAAAAAGGTTGGAGGACTTTT
641 CAAATTTTAGCCAAAATACTAATAAAAAATATATAATTTAACACCAAAAAGATTGAAGGACTTTT
* * **
24772 CGAGCTTTTCATATCGTTTTTCATATTTTTTCTGAATTAATTGCTAATTAAATCGAAACAAGATT
706 CGAGCTTTTCATATCGTTTTTCATATTTTTCCTCAATTAATTGCTAATTAAATAAAAACAAGATT
* * * *
24837 TAGATACTCATAAAAACAAATCTTTAAATGCAATGTGGCCGAGATTTGATTAGATGAATATGGAT
771 CAGATACTCATAAAAACAAATCTTTAAATGAAATGTGGCCAAGATTTGATTAGATGAATATAGAT
* ** * ** * * *
24902 ATTTCAAGGAGTCTTGGCGGCAAAAAACATACAAAACTGACCTAGGGCTTTGGAACGCGTTTTTT
836 ATTTCAAGGAGTCTCGAAGCCAAAAAACATACAAAACTGACCTAGGGCTCCGAAACACGTTTTTA
* *** ** * * *** *
24967 TCC-AAAAACCGTGATGAATATTTTACACGATTTTGGCTAACATTTTGC-AAAAATTGACTGGAA
901 GCCAAAAAAAAATGATG-AT-TAGTACACAATTTTGGCTAAAATTTTGCAAAAAAAAAACCGGAA
* *
25030 AGATATTTCCTCAATTTTT-ACTTA
964 AAAT-TTTCCTCAATTTTTGA-TAA
* * * * * *
25054 AATACTCATAAAAAATATATAATTCAACACCAAAAATATTGAACGGA-TTTTTAAGCTTCTAATA
1 AATACTTATAAAATATATATAATTCAACACCAAAAAGATTGGA-GGACTTTTCACGCTT-TAATA
**
25118 TCGTTTTTCCTACTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAA
64 TCGTTTTTCCTA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAA
*
25183 AAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTC
128 AAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* * * * * * * *
25248 TTGGCG-CAAGAAATCATTCGAAACTGA-CCCGAGACCATGGAATGCTTTTTTACCCAAAAAAAC
193 TCGGCGTCAA-AAATCATGCAAAACTAAGCCCGAGACC-CGAAACGCGTTTTTACCC--AAAAAC
* * ** * * ** *
25311 TGTGATGGTA-T-ACGATTTCGGCGAATATTTTGCA-AAAATTGACCCGAAATATGTTTCCTCAA
254 CGTGATGGTAGTAACGATTCCAACGAAAATTTTGCAGAAAA-TGACCCGAAAAAAATTTCCTAAA
* *
25373 TTTTTAGCCACAATACTTATAAAAAA-AAAAAATTCAAAGCCAAAAAGATTGAAGGGCTTTTCAC
318 TTTTTAGCCAAAATACTTATAAAAAATAAAAAATTCAAAGCCAAAAAGATTGAAGGACTTTTCAC
* * *
25437 ACTTTT-AGATCGTTTTATC-TATTTTTTCTG-AACTAATTTCTAATTAAATCAAAATATGAATT
383 ACTTTTAAGATCGTTTTATCATA-TTTTTCTGAAACTAATTTCTAAATAAATCAAAACAAG-ATT
* *
25499 -AGAT-TCTTGT-AA-AAA-C-AATGGC-TGTGA-T-T-TTTG-TAGATGAATATAGATATTTCA
446 CAGATCTCGTATAAACAAACCTAAT-GCATGTGACTATATTTGATAGATGAATATAGATATTTCA
* * ** * * * *
25553 AGGTGTCTCGGCGCCAAAAATCATGCAAAACTGAACC-TGGCCCCGCAACGCTTTTTTAGCCAAA
510 AGGAGTCTCGACGCCAAAAATCATGCAAAACTGAACCACAGCCCCGAAACACGTTTTTAGCAAAA
* * * * *
25617 AACTGTAATAATTATTATACAATTTCGGCTTAAATTTTGTAAAAATTGACCCGAAAGATA-TATT
575 AACTGTAATAATTAGTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAA-A-ACTATT
* * * * * *
25681 -CTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCT-GCACCATAAAGATTGAAGGGC
638 CCTCAAATTTTAGCCAAAATACTAATAAAAAATATATAATT-TAACACCAAAAAGATTGAAGGAC
* *
25744 TTTTC-ACGC-TTTCAATATCGTTTTTTATATTTTTCCTCAATTAATTTCTAATTAAATAAAAAC
702 TTTTCGA-GCTTTTC-ATATCGTTTTTCATATTTTTCCTCAATTAATTGCTAATTAAATAAAAAC
* * *
25807 AAGATTCAGATGCTCGA-AAAAACAAATCTTTAAATGAAATGTGGCTAAGATTTTATTAGATGAA
765 AAGATTCAGATACTC-ATAAAAACAAATCTTTAAATGAAATGTGGCCAAGATTTGATTAGATGAA
* * ** *
25871 TATATATATTTCAAGGAGTCTCGAAGCCAAAAATCATGGAAAACTGAGCC--GGGGTCCCGAAAC
829 TATAGATATTTCAAGGAGTCTCGAAGCCAAAAAACATACAAAACTGA-CCTAGGGCT-CCGAAAC
*
25934 ACGTTTTTAGCCAAAAAAAAAATGATGGTTAGTACACAATTTTGGCTAAAATTTTGCTAAAAAAA
892 ACGTTTTTAGCC-AAAAAAAAATGATGATTAGTACACAATTTTGGCTAAAATTTTGC--AAAAAA
25999 AAAACCGGAAAAATTTTCCTCAATTTTTGGATAA
954 AAAACCGGAAAAATTTTCCTCAATTTTT-GATAA
*
26033 AATACTTATAAAATATATATAATTTAACACCAAAAAGATTGGAGGACTTTTCACGCTTTAAATAT
1 AATACTTATAAAATATATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTT-AATAT
* * * * *
26098 CATTTTTTCAAATTTTTTTTTCTGAATTAATTTCT-ATTAAATCGAAATAAGATTAAGATGCTCG
65 C-GTTTTTC----CTATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG
* * * * *
26162 TAAAAACAAATCCTTAAA-TCTTATATGGTTGAGATTTGACTAGATGAATATAGATATTTCAAGT
125 TAAAAACAAATCCTTAAATTC-AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGG
* *
26226 AGTCTCGGAGTCAAGAATCATGCAAAA
189 AGTCTCGGCGTCAAAAATCATGCAAAA
26253 TTGAGGCGGG
Statistics
Matches: 1000, Mismatches: 163, Indels: 86
0.80 0.13 0.07
Matches are distributed among these distances:
975 9 0.01
976 295 0.29
977 63 0.06
978 29 0.03
979 73 0.07
980 8 0.01
981 2 0.00
982 101 0.10
983 25 0.03
984 4 0.00
985 2 0.00
987 1 0.00
989 3 0.00
990 2 0.00
991 4 0.00
993 28 0.03
994 22 0.02
995 41 0.04
996 123 0.12
997 149 0.15
998 1 0.00
999 15 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (986 bp):
AATACTTATAAAATATATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTAATATC
GTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA
CAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCG
GCGTCAAAAATCATGCAAAACTAAGCCCGAGACCCGAAACGCGTTTTTACCCAAAAACCGTGATG
GTAGTAACGATTCCAACGAAAATTTTGCAGAAAATGACCCGAAAAAAATTTCCTAAATTTTTAGC
CAAAATACTTATAAAAAATAAAAAATTCAAAGCCAAAAAGATTGAAGGACTTTTCACACTTTTAA
GATCGTTTTATCATATTTTTCTGAAACTAATTTCTAAATAAATCAAAACAAGATTCAGATCTCGT
ATAAACAAACCTAATGCATGTGACTATATTTGATAGATGAATATAGATATTTCAAGGAGTCTCGA
CGCCAAAAATCATGCAAAACTGAACCACAGCCCCGAAACACGTTTTTAGCAAAAAACTGTAATAA
TTAGTACACAATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAACTATTCCTCAAATTTTAG
CCAAAATACTAATAAAAAATATATAATTTAACACCAAAAAGATTGAAGGACTTTTCGAGCTTTTC
ATATCGTTTTTCATATTTTTCCTCAATTAATTGCTAATTAAATAAAAACAAGATTCAGATACTCA
TAAAAACAAATCTTTAAATGAAATGTGGCCAAGATTTGATTAGATGAATATAGATATTTCAAGGA
GTCTCGAAGCCAAAAAACATACAAAACTGACCTAGGGCTCCGAAACACGTTTTTAGCCAAAAAAA
AATGATGATTAGTACACAATTTTGGCTAAAATTTTGCAAAAAAAAAACCGGAAAAATTTTCCTCA
ATTTTTGATAA
Found at i:29004 original size:122 final size:127
Alignment explanation
Indices: 28760--29013 Score: 419
Period size: 130 Copynumber: 2.0 Consensus size: 127
28750 ATTTAAGAAA
28760 TATATTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAAT
1 TATATTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---AT
* *
28825 AGGTAAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGT-AAAA
63 A-GTAAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATCAAAA
28889 G
127 G
28890 TATATTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-T
1 TATATTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGT
28953 -AAA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATCAAAAG
66 AAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATCAAAAG
29013 T
1 T
29014 TTAAACAATG
Statistics
Matches: 121, Mismatches: 2, Indels: 9
0.92 0.02 0.07
Matches are distributed among these distances:
122 49 0.40
123 9 0.07
124 1 0.01
126 2 0.02
130 60 0.50
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGT
AAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATCAAAAG
Found at i:42207 original size:2 final size:2
Alignment explanation
Indices: 42200--42244 Score: 54
Period size: 2 Copynumber: 21.0 Consensus size: 2
42190 AGAAGGAAAG
*
42200 GA GA GA GA GA AA TGA GA TGA GA TGA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA -GA GA -GA GA -GA GA GA GA GA GA GA GA GA GA
42243 GA
1 GA
42245 AAGGAAAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 33 0.87
3 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.07
Consensus pattern (2 bp):
GA
Found at i:42942 original size:21 final size:21
Alignment explanation
Indices: 42910--42959 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
42900 TTCAAATCAT
42910 ATATAA-ATAACTTTTAATTA
1 ATATAAGATAACTTTTAATTA
42930 ATATAAGATAACTTTTAATTA
1 ATATAAGATAACTTTTAATTA
42951 ATATAAGAT
1 ATATAAGAT
42960 TCGACGCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (21 bp):
ATATAAGATAACTTTTAATTA
Found at i:43274 original size:2 final size:2
Alignment explanation
Indices: 43269--43294 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43259 TGAGGTAATA
43269 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
43295 TATGTAATAT
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
Done.