Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024775.1 Corchorus olitorius cultivar O-4 contig24808, 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: 55341
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:9780 original size:332 final size:327
Alignment explanation
Indices: 7974--9896 Score: 1720
Period size: 332 Copynumber: 5.9 Consensus size: 327
7964 AACTCGAAAG
* *
7974 ATTTTTCCTCAATTTTT-GGCAAAAGTACTCATAAAATATATATAATTCAATGCCAAAAAGATTG
1 ATTTTTCCTCAATTTTTAGCCAAAA-TACTCATAAAAT-TATATAATTCAACGCCAAAAAGATTG
* *
8038 GAGGA-TTTTCATG-TTTTAATATCGTTTTT-ATATTTTTTCTA-AATTAA-TTC-AATTAAATC
64 AAGGACTTTTCATGCTTCTAATATCGTTTTTCATATTTTTT-TAGAATTAATTTCTAATTAAATC
* * * *
8097 GAAACAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGCGGCTAAGATTTTATTAGA
128 GAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGA
* * * * * * * *
8162 AGAATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAAATCATGCAAAACAGAGTCGTGGCCCTGT
192 TGAATATAGATATTTCAAGGAGTCTTGGCGCC-AAAAATCATGCAAAACTGAGCCGGGGCCCCGG
* * * * * ** *
8227 AACGCGTTTTTAACCAAAAACTGTGATGGTTAGTACATGATTTCAACTAAAATTTTACAAAAATT
256 AACGCGTTTTTAGCAAAAAACCGTGATGATTA-TACACGATTTCGGCTAAAATTTTGCAAAAATT
*
8292 GATCCGAAA
320 GA-CCCAAA
* * * * ** *** *
8301 GA-TATTCTCTCAATTTTTAGCTAAAATATTCATAAAAAATATATAATTCGGCATAAAAAATATT
1 -ATTTTTC-CTCAATTTTTAGCCAAAATACTCAT-AAAATTATATAATTCAACGCCAAAAAGATT
* * * * * *
8365 GAAGGACTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTTCCGAATGAATTTCTAATTAAAT
63 GAAGGACTTTTCATGCTTCTAATATCGTTTTTCATATTTTTTT-AGAATTAATTTCTAATTAAAT
* * *
8430 CGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCTAATGT-GCTAAGATTTGGTTAG
127 CGAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAG
* * * *
8494 ATGAATATAGATATTTCAAGGAGTCTTGACACCAGAAATCATGCAAAACTGGGCC-GGGCCCCGG
191 ATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGG
** ** * *
8558 AAAACGTTTTTAGCTGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATT
256 AACGCGTTTTTAGCAAAAAACCGTGATGATTA-TACACGATTTCGGCTAAAATTTTGCAAAAATT
*
8623 GACCCGGAA
320 GACCC-AAA
* * * * *
8632 TTTTTTTCTTAATTTTTAGCCACAATACTCATAAAAGATATATAATTCAACGCCAAAAAGATTGA
1 ATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAA-TTATATAATTCAACGCCAAAAAGATTGA
* * * * ** *
8697 AGGGCGTCTCACGCTTCTAATATAATTTTTCCTATTTTCTTTCA-AATTAATTT-TAATTAAGA-
65 AGGACTTTTCATGCTTCTAATATCGTTTTTCATATTTT-TTT-AGAATTAATTTCTAATTAA-AT
* * * * * * * *
8759 CGAAACATGTTTTCAAATGCTCGTAAAAACAAATCTTTAAATCAAATGCGGCTAAGATTTGGTCA
127 CGAAACAAG-ATTCAGATGCTCGT-AAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTA
* * ** * * * *
8824 GATAAATATAGATATTTTAAGGAGT-TTTCCACAAAAAAT-ATTGCAAAACTGACCCGGGGCGCC
190 GATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCA-TGCAAAACTGAGCCGGGGCCCC
** *
8887 GGAACGCGTTTTTAGCCAAAAAA-C-T-ATGATGGTACACGATTTCGGCTAAAATTTTGTAAAAA
254 GGAACGCGTTTTTAG-CAAAAAACCGTGATGATTATACACGATTTCGGCTAAAATTTTGCAAAAA
8949 TTGACCCGAAA
318 TTGACCC-AAA
* * * * * * *
8960 TATTTTCCCTCAATATTTAGCCACAATACTCAT-AGA--ACAT-ATTAAACGCCAAAAAGATTGG
1 -ATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAATTATATAATTCAACGCCAAAAAGATTGA
* * * * * *
9021 AGAACTTTTTATACTTTTATTATCGTGTTTCATA-TTTTTT-GAATTAATTTCTAATTAAATCGA
65 AGGACTTTTCATGCTTCTAATATCGTTTTTCATATTTTTTTAGAATTAATTTCTAATTAAATCGA
* * * *
9084 AACAAAATTCAGATACCCGTAAAA-ATGAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGAT
130 AACAAGATTCAGATGCTCGTAAAACA--AATCCTTAAATCCAATGTGGCTAAGATTTGATTAGAT
** * * * * *
9148 GAATATCTATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGCC-GGGCCCATTGA
193 GAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCC--CGG
* * * * * *
9212 AACACGTTTTTAGCCAAAAACCGTGATGTAATATACACGATTTTGGATAAAATTTTGCAAAAAAT
256 AACGCGTTTTTAGCAAAAAACCGTGATG-ATTATACACGATTTCGGCTAAAATTTTGCAAAAATT
9277 GACCCGACAA
320 GACCC-A-AA
* *
9287 ATTTTTCCGTCAA--GTT----AAAATACTCATAAAATATATATAATTTAACGCCAAAAAGATTG
1 ATTTTTCC-TCAATTTTTAGCCAAAATACTCATAAAAT-TATATAATTCAACGCCAAAAAGATTG
* * * *
9346 AAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTCT-GATTTAATTTCTAATTAAAGCG
64 AAGGACTTTTCATGCTTCTAATATCGTTTTTCATATTTTTTTAGAATTAATTTCTAATTAAATCG
* * * * *
9410 AAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTAGCTGAGATTTTATTAGAT
129 AAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGAT
* * * * * *
9475 GAATATGGATATCTCAAAGAGTCTTGGCGCCAATAATGATGCAAAACTTAGCCGGGGCCCCGGAA
193 GAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAA
* * * * *
9540 CGCATTCTTAGCAAAAAACCGTGATAATTATAACACGATTTCGGCTAGAATATTGCAAAAATTG-
258 CGCGTTTTTAGCAAAAAACCGTGATGATTAT-ACACGATTTCGGCTAAAATTTTGCAAAAATTGA
9604 CCTCAAA
322 CC-CAAA
* *
9611 AGTTATTTCCTCAATTTTTAGCCACAAATACTCATAAAAATTATACAATTCAACGCTAAAAAGAT
1 A-TT-TTTCCTCAATTTTTAGCCA-AAATACTCAT-AAAATTATATAATTCAACGCCAAAAAGAT
* * * *
9676 TGAAGGGCTTTTCATGCTTCTAATATCGTATTTCCTATTATTTTAGAATTAATTTCTAATTAAAT
62 TGAAGGACTTTTCATGCTTCTAATATCGTTTTTCATATTTTTTTAGAATTAATTTCTAATTAAAT
* * * * ** * * *
9741 CGAAACATGATTCAGGTGTTTGGT-TTACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAG
127 CGAAACAAGATTCAGATG-CTCGTAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAG
* * * ** * * * * *
9805 ATGAATATAAATATTTGAAGGAGTATTGGCATCAAAAATCATTCAACACTGAACTGGAGCCCCGG
191 ATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGG
** * * *
9870 AACATGTTTTTAACCAAAAATCGTGAT
256 AACGCGTTTTTAGCAAAAAACCGTGAT
9897 TTCGACTAAG
Statistics
Matches: 1289, Mismatches: 247, Indels: 114
0.78 0.15 0.07
Matches are distributed among these distances:
319 1 0.00
320 4 0.00
321 84 0.07
322 45 0.03
323 18 0.01
324 44 0.03
325 24 0.02
326 148 0.11
327 132 0.10
328 92 0.07
329 67 0.05
330 157 0.12
331 137 0.11
332 199 0.15
333 83 0.06
334 54 0.04
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (327 bp):
ATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAATTATATAATTCAACGCCAAAAAGATTGAA
GGACTTTTCATGCTTCTAATATCGTTTTTCATATTTTTTTAGAATTAATTTCTAATTAAATCGAA
ACAAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAA
TATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGC
GTTTTTAGCAAAAAACCGTGATGATTATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCA
AA
Found at i:18951 original size:29 final size:31
Alignment explanation
Indices: 18912--18983 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
18902 ATTTGTAGCG
* *
18912 TTTGGACATTTTGTCCC-C-AGAA-TTTCAAT
1 TTTGGACATTTTGACCCTCTA-AACTCTCAAT
18941 TTTGGACATTTT-ACCCTCTAAACTCTCAAT
1 TTTGGACATTTTGACCCTCTAAACTCTCAAT
18971 TTTGGACATTTTG
1 TTTGGACATTTTG
18984 CCATTTCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 3 0.08
29 15 0.41
30 19 0.51
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (31 bp):
TTTGGACATTTTGACCCTCTAAACTCTCAAT
Found at i:19075 original size:33 final size:33
Alignment explanation
Indices: 19037--19099 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
19027 GGCCAAAATG
19037 ATGACGTAGCATTGCCACGTCGAACCAAAACCA
1 ATGACGTAGCATTGCCACGTCGAACCAAAACCA
*
19070 ATGACGTGGCATTGCCACGTCGAACCAAAA
1 ATGACGTAGCATTGCCACGTCGAACCAAAA
19100 GTGCCACGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.16
Consensus pattern (33 bp):
ATGACGTAGCATTGCCACGTCGAACCAAAACCA
Found at i:19114 original size:32 final size:32
Alignment explanation
Indices: 19037--19121 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 32
19027 GGCCAAAATG
*
19037 ATGACGTAGCATTGCCACGTCGAACCAAAACCA
1 ATGACGTGGCATTGCCACGTCGAACCAAAA-CA
19070 ATGACGTGGCATTGCCACGTCGAACC-AAA-A
1 ATGACGTGGCATTGCCACGTCGAACCAAAACA
*
19100 GTGCCACGTGGCATTGCCACGT
1 ATG--ACGTGGCATTGCCACGT
19122 TGGCGACATG
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
30 3 0.06
32 20 0.42
33 25 0.52
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (32 bp):
ATGACGTGGCATTGCCACGTCGAACCAAAACA
Found at i:19216 original size:29 final size:30
Alignment explanation
Indices: 19159--19236 Score: 113
Period size: 29 Copynumber: 2.6 Consensus size: 30
19149 ATCGCTTGAA
*
19159 AGGGGGCAAAACGTCCAAAATTGAAAGTTC
1 AGGGGGCAAAATGTCCAAAATTGAAAGTTC
*
19189 AGGGGGTAAAATGTCCAAAATTG-AAGTTC
1 AGGGGGCAAAATGTCCAAAATTGAAAGTTC
* *
19218 AGAGAGCAAAATGTCCAAA
1 AGGGGGCAAAATGTCCAAA
19237 TACTACAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (30 bp):
AGGGGGCAAAATGTCCAAAATTGAAAGTTC
Found at i:20159 original size:13 final size:13
Alignment explanation
Indices: 20141--20170 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20131 TATCTTTATC
*
20141 CTATCTTATTTTA
1 CTATCTTATCTTA
20154 CTATCTTATCTTA
1 CTATCTTATCTTA
20167 CTAT
1 CTAT
20171 ATACTATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (13 bp):
CTATCTTATCTTA
Found at i:20178 original size:5 final size:5
Alignment explanation
Indices: 20170--20208 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
20160 TATCTTACTA
20170 TATAC TATAC TATAC TATAC TATAC TATATAC TATAC TA
1 TATAC TATAC TATAC TATAC TATAC --TATAC TATAC TA
20209 CTATATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 27 0.84
7 5 0.16
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAC
Found at i:20190 original size:15 final size:16
Alignment explanation
Indices: 20170--20208 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
20160 TATCTTACTA
20170 TATACTATAC-TATAC
1 TATACTATACATATAC
20185 TATACTATACTATATAC
1 TATACTATAC-ATATAC
20202 TATACTA
1 TATACTA
20209 CTATATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 10 0.45
17 12 0.55
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (16 bp):
TATACTATACATATAC
Found at i:20210 original size:15 final size:15
Alignment explanation
Indices: 20165--20215 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
20155 TATCTTATCT
20165 TACTATATACTATAC
1 TACTATATACTATAC
20180 TA-TACTATAC--TA-
1 TACTA-TATACTATAC
20192 TACTATATACTATAC
1 TACTATATACTATAC
20207 TACTATATA
1 TACTATATA
20216 AAATCACGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.23
13 4 0.13
14 4 0.13
15 16 0.52
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (15 bp):
TACTATATACTATAC
Found at i:24085 original size:33 final size:33
Alignment explanation
Indices: 24032--24125 Score: 145
Period size: 33 Copynumber: 2.9 Consensus size: 33
24022 CTCTTACAAC
* *
24032 CAATGAAGTT-GCGGGCCTTCATCACGTCGTTT
1 CAATGAAGTTCACGGGCCTTCATCACGCCGTTT
*
24064 CAATGAAGTTCACGGGCCTTCATCATGCCGTTT
1 CAATGAAGTTCACGGGCCTTCATCACGCCGTTT
*
24097 CAATGAAGTTCACGAGCCTTCATCACGCC
1 CAATGAAGTTCACGGGCCTTCATCACGCC
24126 TTTACATGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 10 0.18
33 46 0.82
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (33 bp):
CAATGAAGTTCACGGGCCTTCATCACGCCGTTT
Found at i:32163 original size:23 final size:21
Alignment explanation
Indices: 32116--32187 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
32106 CTTTTTTGGC
* * *
32116 CTTATAAAGTTTTTTACTCAC
1 CTTATTAAGTTTTTTACTAAT
32137 CTTATTAAGTGTTTTTACCTAAT
1 CTTATTAAGT-TTTTTA-CTAAT
* *
32160 CTTATTAAGATTTTTAGTAAT
1 CTTATTAAGTTTTTTACTAAT
32181 CTTATTA
1 CTTATTA
32188 TGGATTTTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
21 20 0.45
22 12 0.27
23 12 0.27
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.51
Consensus pattern (21 bp):
CTTATTAAGTTTTTTACTAAT
Found at i:32553 original size:86 final size:86
Alignment explanation
Indices: 32448--32626 Score: 313
Period size: 86 Copynumber: 2.1 Consensus size: 86
32438 AACCTTGTAA
* *
32448 ATTTTCTTAGTAAGCTTATAAATTTTTTATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAAT
1 ATTTT-TTAGTAAGCTTATAAATTTTTCACTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAAT
32513 TTATTCAATCACCTCATTTAAG
65 TTATTCAATCACCTCATTTAAG
*
32535 ATTTTTTGGTAAGCTTATAAATTTTTCACTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATT
1 ATTTTTTAGTAAGCTTATAAATTTTTCACTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATT
*
32600 TATTCAATCACCTCGTTTAAG
66 TATTCAATCACCTCATTTAAG
32621 ATTTTT
1 ATTTTT
32627 AGTGATCTTA
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 83 0.94
87 5 0.06
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (86 bp):
ATTTTTTAGTAAGCTTATAAATTTTTCACTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATT
TATTCAATCACCTCATTTAAG
Found at i:32640 original size:21 final size:22
Alignment explanation
Indices: 32616--32668 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
32606 ATCACCTCGT
* *
32616 TTAAGATTTTTAGTGATCTTA-
1 TTAAGATTTTTAGAGACCTTAC
*
32637 TTAACATGTTTTAGAGACCTTAC
1 TTAAGAT-TTTTAGAGACCTTAC
32660 TTAAG-TTTT
1 TTAAGATTTT
32669 ATTTAGTGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.49
Consensus pattern (22 bp):
TTAAGATTTTTAGAGACCTTAC
Found at i:32711 original size:20 final size:21
Alignment explanation
Indices: 32688--32731 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
32678 CCTTGTAATA
32688 TTTATAGTTAA-CTTATGAA-T
1 TTTATAG-TAACCTTATGAAGT
32708 TTTATAGTAACCTTATGAAGT
1 TTTATAGTAACCTTATGAAGT
32729 TTT
1 TTT
32732 TTTTAGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (21 bp):
TTTATAGTAACCTTATGAAGT
Found at i:32756 original size:23 final size:23
Alignment explanation
Indices: 32707--32757 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
32697 AACTTATGAA
* *
32707 TTTTATAGTAACCTTATGAAGTT
1 TTTTATAGTAACCATATGAAGTG
*
32730 TTTTTTAGTAACCATATTG-AGTG
1 TTTTATAGTAACCATA-TGAAGTG
32753 TTTTA
1 TTTTA
32758 GAAATCTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (23 bp):
TTTTATAGTAACCATATGAAGTG
Found at i:33385 original size:21 final size:21
Alignment explanation
Indices: 33331--33385 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
33321 CAATATATAA
*
33331 CTTAGTAAGTATTTTAGTAAC
1 CTTAGTAAGTTTTTTAGTAAC
* *
33352 CTTATTAATTTTTTTAGTAAC
1 CTTAGTAAGTTTTTTAGTAAC
*
33373 CTTAGAAAGTTTT
1 CTTAGTAAGTTTT
33386 ATATACTCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (21 bp):
CTTAGTAAGTTTTTTAGTAAC
Found at i:34577 original size:12 final size:12
Alignment explanation
Indices: 34560--34639 Score: 60
Period size: 12 Copynumber: 7.0 Consensus size: 12
34550 TCTCGAACCC
34560 GCCCGAACCCGA
1 GCCCGAACCCGA
***
34572 GCCCGAA-AATA
1 GCCCGAACCCGA
*
34583 -CCCGAACCTGA
1 GCCCGAACCCGA
*
34594 ACCCG-ACCCGA
1 GCCCGAACCCGA
* *
34605 GACCGAGCCCGA
1 GCCCGAACCCGA
34617 GCCCG-ACCCGA
1 GCCCGAACCCGA
*
34628 GCCCGAATCCGA
1 GCCCGAACCCGA
34640 AATAATTTGA
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
10 6 0.12
11 20 0.39
12 25 0.49
ACGTcount: A:0.28, C:0.45, G:0.24, T:0.04
Consensus pattern (12 bp):
GCCCGAACCCGA
Found at i:34610 original size:6 final size:6
Alignment explanation
Indices: 34595--34633 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
34585 CGAACCTGAA
*
34595 CCCGA- CCCGAG ACCGAG CCCGAG CCCGA- CCCGAG CCCGA
1 CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGA
34634 ATCCGAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.21, C:0.51, G:0.28, T:0.00
Consensus pattern (6 bp):
CCCGAG
Found at i:34626 original size:11 final size:11
Alignment explanation
Indices: 34595--34633 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
34585 CGAACCTGAA
34595 CCCGACCCGAG
1 CCCGACCCGAG
*
34606 ACCGAGCCCGAG
1 CCCGA-CCCGAG
34618 CCCGACCCGAG
1 CCCGACCCGAG
34629 CCCGA
1 CCCGA
34634 ATCCGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.21, C:0.51, G:0.28, T:0.00
Consensus pattern (11 bp):
CCCGACCCGAG
Found at i:34639 original size:23 final size:23
Alignment explanation
Indices: 34584--34639 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
34574 CCGAAAATAC
* *
34584 CCGAACCTGAACCCGACCCGAGA
1 CCGAACCCGAGCCCGACCCGAGA
* *
34607 CCGAGCCCGAGCCCGACCCGAGC
1 CCGAACCCGAGCCCGACCCGAGA
*
34630 CCGAATCCGA
1 CCGAACCCGA
34640 AATAATTTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.46, G:0.25, T:0.04
Consensus pattern (23 bp):
CCGAACCCGAGCCCGACCCGAGA
Found at i:35515 original size:32 final size:32
Alignment explanation
Indices: 35466--35553 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
35456 TACCCGAGCT
** *
35466 CGAACCCGGTAATACCCGAACTCGACATAACC
1 CGAACCCGAAAATACCCGAACCCGACATAACC
* * *
35498 TGAGCCCGAAAATACCCGAACCCGACTTAACC
1 CGAACCCGAAAATACCCGAACCCGACATAACC
35530 CGAACCCGAAAATACCCGAACCCG
1 CGAACCCGAAAATACCCGAACCCG
35554 CCCGAGCCCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.35, C:0.39, G:0.16, T:0.10
Consensus pattern (32 bp):
CGAACCCGAAAATACCCGAACCCGACATAACC
Found at i:35546 original size:16 final size:15
Alignment explanation
Indices: 35466--35553 Score: 68
Period size: 16 Copynumber: 5.5 Consensus size: 15
35456 TACCCGAGCT
*
35466 CGAACCCGGTAATACC
1 CGAACCC-GAAATACC
* *
35482 CGAACTCGACATAACC
1 CGAACCCGAAAT-ACC
* *
35498 TGAGCCCGAAAATACC
1 CGAACCCG-AAATACC
**
35514 CGAACCCGACTTAACC
1 CGAACCCGAAAT-ACC
35530 CGAACCCGAAAATACC
1 CGAACCCG-AAATACC
35546 CGAACCCG
1 CGAACCCG
35554 CCCGAGCCCG
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
15 5 0.09
16 45 0.82
17 5 0.09
ACGTcount: A:0.35, C:0.39, G:0.16, T:0.10
Consensus pattern (15 bp):
CGAACCCGAAATACC
Found at i:36096 original size:1 final size:1
Alignment explanation
Indices: 36090--36126 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
36080 ACCCGGCGTT
*
36090 AAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
36127 CTCAGGACGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:39291 original size:21 final size:21
Alignment explanation
Indices: 39267--39321 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
39257 GGCTTGGAAT
* *
39267 GGTGATGGCACGGGCAGAGCC
1 GGTGGTGGCACGGGCAGAACC
* **
39288 GGTGGTAGCACGGGCTTAACC
1 GGTGGTGGCACGGGCAGAACC
39309 GGTGGTGGCACGG
1 GGTGGTGGCACGG
39322 TGAATGGGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.22, G:0.47, T:0.15
Consensus pattern (21 bp):
GGTGGTGGCACGGGCAGAACC
Found at i:41688 original size:19 final size:19
Alignment explanation
Indices: 41664--41701 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41654 AAAACAAATT
41664 TTTTTTATGTCGCAAAAAC
1 TTTTTTATGTCGCAAAAAC
* *
41683 TTTTTTTTTTCGCAAAAAC
1 TTTTTTATGTCGCAAAAAC
41702 GAAAACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (19 bp):
TTTTTTATGTCGCAAAAAC
Found at i:41706 original size:25 final size:24
Alignment explanation
Indices: 41678--41732 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
41668 TTATGTCGCA
41678 AAAACTTTTTTTTTTCGCAAAAACG
1 AAAACTTTTTTTTTT-GCAAAAACG
*
41703 AAAACTTTTTTTTTTTCAAAAACG
1 AAAACTTTTTTTTTTGCAAAAACG
*
41727 CAAACT
1 AAAACT
41733 AAAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (24 bp):
AAAACTTTTTTTTTTGCAAAAACG
Found at i:41711 original size:24 final size:24
Alignment explanation
Indices: 41678--41732 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
41668 TTATGTCGCA
41678 AAAACTTTTTTTTTTCGCAAAAACG
1 AAAAC-TTTTTTTTTCGCAAAAACG
**
41703 AAAACTTTTTTTTTTTCAAAAACG
1 AAAACTTTTTTTTTCGCAAAAACG
*
41727 CAAACT
1 AAAACT
41733 AAAAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (24 bp):
AAAACTTTTTTTTTCGCAAAAACG
Found at i:43914 original size:2 final size:2
Alignment explanation
Indices: 43907--43946 Score: 53
Period size: 2 Copynumber: 18.5 Consensus size: 2
43897 CTCTTTGAGA
43907 TC TC TC TC TC TC TC TC TC TC TC TC ATGC TGC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC -T-C T-C TC TC TC TC T
43947 AGAAACCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 30 0.83
3 5 0.14
4 1 0.03
ACGTcount: A:0.03, C:0.45, G:0.05, T:0.47
Consensus pattern (2 bp):
TC
Found at i:47573 original size:15 final size:14
Alignment explanation
Indices: 47550--47609 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
47540 TTTTTTTTAA
47550 TTTAAAAAATATTT
1 TTTAAAAAATATTT
47564 TTTCAAAAAATAATTT
1 TTT-AAAAAAT-ATTT
47580 CTTTAAAAAA-A-TT
1 -TTTAAAAAATATTT
*
47593 TTGAAAAAATTATTT
1 TTTAAAAAA-TATTT
47608 TT
1 TT
47610 GAATAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
12 8 0.21
13 2 0.05
14 5 0.13
15 11 0.28
16 10 0.26
17 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (14 bp):
TTTAAAAAATATTT
Found at i:47579 original size:16 final size:16
Alignment explanation
Indices: 47553--47591 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
47543 TTTTTAATTT
*
47553 AAAAAATATTT-TTTC
1 AAAAAATATTTCTTTA
47568 AAAAAATAATTTCTTTA
1 AAAAAAT-ATTTCTTTA
47585 AAAAAAT
1 AAAAAAT
47592 TTTGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 10 0.48
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAAATATTTCTTTA
Found at i:47611 original size:15 final size:14
Alignment explanation
Indices: 47553--47617 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 14
47543 TTTTTAATTT
*
47553 AAAAAATATTTTTTC
1 AAAAAATA-TTTTTG
*
47568 AAAAAATAATTTCTTT
1 AAAAAAT-ATTT-TTG
47584 AAAAAA-A-TTTTG
1 AAAAAATATTTTTG
47596 AAAAAATTATTTTTG
1 AAAAAA-TATTTTTG
47611 AATAAAA
1 AA-AAAA
47618 AAAAACAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 8 0.19
13 2 0.05
14 2 0.05
15 17 0.40
16 13 0.31
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (14 bp):
AAAAAATATTTTTG
Found at i:47617 original size:28 final size:28
Alignment explanation
Indices: 47563--47618 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
47553 AAAAAATATT
*
47563 TTTTCAAAAAATAATTTCTTTAAAAAAA
1 TTTTCAAAAAATAATTTCTTGAAAAAAA
* *
47591 TTTTGAAAAAATTATTT-TTGAATAAAAA
1 TTTTCAAAAAATAATTTCTTGAA-AAAAA
47619 AAAACAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (28 bp):
TTTTCAAAAAATAATTTCTTGAAAAAAA
Found at i:48015 original size:16 final size:16
Alignment explanation
Indices: 47974--48018 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
47964 TAATAATTTT
* *
47974 TATTTTCAA-AAAACA
1 TATTTTTAATAAAAAA
47989 TATTTTT--TAAAAAA
1 TATTTTTAATAAAAAA
48003 TATTTTTAATAAAAAA
1 TATTTTTAATAAAAAA
48019 AGATGACGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
16 7 0.28
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTTTTAATAAAAAA
Found at i:48016 original size:15 final size:14
Alignment explanation
Indices: 47974--48017 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
47964 TAATAATTTT
*
47974 TATTTTCAAAAAACA
1 TATTTTTAAAAAA-A
*
47989 TATTTTTTAAAAAA
1 TATTTTTAAAAAAA
48003 TATTTTTAATAAAAA
1 TATTTTTAA-AAAAA
48018 AAGATGACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTTTTAAAAAAA
Found at i:53593 original size:2 final size:2
Alignment explanation
Indices: 53543--53584 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
53533 GAATCAAGTT
*
53543 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
53585 CCCCTCTCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:55311 original size:3 final size:3
Alignment explanation
Indices: 55303--55341 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
55293 CATGTTGTCT
55303 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.