Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018369.1 Corchorus olitorius cultivar O-4 contig18402, 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: 131528
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:756 original size:333 final size:332
Alignment explanation
Indices: 1--759 Score: 1042
Period size: 333 Copynumber: 2.3 Consensus size: 332
* * *
1 TGATGGTTATTACACGATTTTGGCTAAAATTTTGGAAAAAATAACCGCGAAAAATTTTTCCTCAG
1 TGATAGTTAGTACACGATTTTGGCTAAAATTTT-GAAAAAA-AACCGCGAAAAATTTTTCCTCAA
* * *
66 TTTTTGTATAAAATACTCATAAAATATATATAACTTAACGCCAAAAAGATTGGAGGACTTTTCAC
64 TTTTTGGATAAAATACTCATAAAATATAAATAACTTAACGCCAAAAACATTGGAGGACTTTTCAC
*
131 GCTTTTAATATTCGTTTTTCATATTTTTCCAGAATTAATTTCTAATTAAATCGAAACAAGATTTA
129 GCTTTTAATATTCGTTTTTCATATTTTTCCAGAATTAATTTCTAATTAAATCGAAACAAGATTCA
**
196 AATGCTCGTAAAAACAATCCTCAAATGAAATGTGGCTAAGTTTTTATTAGATGAATATAGATATT
194 AATGCTCGTAAAAACAATCCTCAAATGAAACATGGCTAAGTTTTTATTAGATGAATATAGATATT
* * * * * ** *
261 TCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGTCCCCGAAACGCCTTTTTTTGC
259 TCAAGGAGTCTTGACACCAAAAATCATACAAAACTGAGACAGGACCCCGAAACGCCGATTTTAGC
326 CAAAAACCG
324 CAAAAACCG
* **
335 TGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAATGACCGCGAAAAATTTTTCCTCAAT
1 TGATAGTTAGTACACGATTTTGGCTAAAATTTTG-AAAAAAAACCGCGAAAAATTTTTCCTCAAT
* * *
400 TTTTGGATAAAATACTCATAAAATATAAATAATTTAACGCCAAAAACATTGGATGACTTTTCATG
65 TTTTGGATAAAATACTCATAAAATATAAATAACTTAACGCCAAAAACATTGGAGGACTTTTCACG
** *
465 CTTTTAATA-TCGTTTTTCATATTTTTTTAGAATTAATTTTTAATTAAATCGAAACAAGATTCAA
130 CTTTTAATATTCGTTTTTCATATTTTTCCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAA
*
529 ATGCTCGTAAAAACAAATCCTCAAAT-ACTACATGGCTAAGTTTTTATTAGATGAATATAGATAT
195 ATGCTCGTAAAAAC-AATCCTCAAATGA-AACATGGCTAAGTTTTTATTAGATGAATATAGATAT
* * * *
593 TAT-AAGGAGTCTTGACACCGAAAATCATACAAAATTGCGACAGGACCTCGAAACG-CGATTTTA
258 T-TCAAGGAGTCTTGACACCAAAAATCATACAAAACTGAGACAGGACCCCGAAACGCCGATTTTA
*
656 GCCAAAACCCG
322 GCCAAAAACCG
* ***** * *
667 TGATAGTTAGTATACGATTTTGGCTAAAA-TTTGAAAAAAAAAAAAAAAAAAGTTTTTCCTGAAA
1 TGATAGTTAGTACACGATTTTGGCTAAAATTTTGAAAAAAAACCGCGAAAAA-TTTTTCCTCAAT
731 TTTTGGATAAAATACTCCTATAAAATATA
65 TTTTGGATAAAATACT-C-ATAAAATATA
760 TAAAAATATA
Statistics
Matches: 377, Mismatches: 41, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
330 11 0.03
331 30 0.08
332 109 0.29
333 189 0.50
334 38 0.10
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (332 bp):
TGATAGTTAGTACACGATTTTGGCTAAAATTTTGAAAAAAAACCGCGAAAAATTTTTCCTCAATT
TTTGGATAAAATACTCATAAAATATAAATAACTTAACGCCAAAAACATTGGAGGACTTTTCACGC
TTTTAATATTCGTTTTTCATATTTTTCCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAAA
TGCTCGTAAAAACAATCCTCAAATGAAACATGGCTAAGTTTTTATTAGATGAATATAGATATTTC
AAGGAGTCTTGACACCAAAAATCATACAAAACTGAGACAGGACCCCGAAACGCCGATTTTAGCCA
AAAACCG
Found at i:767 original size:10 final size:10
Alignment explanation
Indices: 752--784 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
742 ATACTCCTAT
752 AAAATATATA
1 AAAATATATA
762 AAAATATAT-
1 AAAATATATA
771 -AAATATATA
1 AAAATATATA
780 AAAAT
1 AAAAT
785 GACAGACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAATATATA
Found at i:11291 original size:18 final size:19
Alignment explanation
Indices: 11242--11291 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
11232 AAATATAATA
*
11242 ATTATTAGTGTTA-TTATT
1 ATTATTAGTATTATTTATT
*
11260 AATATTAGTATTATTTATT
1 ATTATTAGTATTATTTATT
*
11279 ATTACTAGT-TTAT
1 ATTATTAGTATTAT
11292 ATTTCTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTATTAGTATTATTTATT
Found at i:11493 original size:13 final size:13
Alignment explanation
Indices: 11475--11500 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11465 TACAAAAGTT
11475 AAAAAAACAAAAA
1 AAAAAAACAAAAA
11488 AAAAAAACAAAAA
1 AAAAAAACAAAAA
11501 CAAGCGGGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:20571 original size:198 final size:199
Alignment explanation
Indices: 20177--20554 Score: 517
Period size: 199 Copynumber: 1.9 Consensus size: 199
20167 ATAGTATGGG
20177 TAATTATTTGATATAAACTGACGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGATAC
1 TAATTATTTGA-ATAAACTGACGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGATAC
*
20242 ATGTCCATTTTCTAAATTAATTAAATTTTAAATATTTCAATCTAGTTCCTAAGGAACACATGTCA
65 ATGTCCATTTTCTAAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAAGGAACACATGTCA
* * * * ** * * *
20307 CCCTTTAAAACCCGTTTGTGCAGTCTGCTAGATTCCACTTATGGTGTCTTTATAGTATTTTGTTT
130 CCCTTCAAAACCCGCTTGTGCAGTCTGCTAAACTCCACCGACGGTGTATTTATAGTACTTTGTTT
20372 TTGGA
195 TTGGA
* * *
20377 TAATTATTTG-ATACACTGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGATATA
1 TAATTATTTGAATAAACTGACGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGATACA
* * * * *
20441 TGTCCATTTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGG-ACATATGTT
66 TGTCCA-TTTTCTAAATTAATTAAATTTTAAATATTTCAATCTAGTCCCT-AAGGAACACATGTC
** * *
20505 ACCCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGGTGTAT
129 ACCCTTCAAAACCCGCTTGTGCAGTCTGCTAAACTCCACCGACGGTGTAT
20555 AATTTGCCTT
Statistics
Matches: 155, Mismatches: 21, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
198 57 0.37
199 84 0.54
200 14 0.09
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (199 bp):
TAATTATTTGAATAAACTGACGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGATACA
TGTCCATTTTCTAAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAAGGAACACATGTCAC
CCTTCAAAACCCGCTTGTGCAGTCTGCTAAACTCCACCGACGGTGTATTTATAGTACTTTGTTTT
TGGA
Found at i:28832 original size:19 final size:19
Alignment explanation
Indices: 28808--28845 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28798 CTTAATTAAA
28808 ATTAAATTGAGATGTCTAT
1 ATTAAATTGAGATGTCTAT
28827 ATTAAATTGAGATGTCTAT
1 ATTAAATTGAGATGTCTAT
28846 TGCCACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTAAATTGAGATGTCTAT
Found at i:36475 original size:21 final size:21
Alignment explanation
Indices: 36438--36480 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
36428 TATGTTTCAC
*
36438 ATTAAAATATCAATTTAATTT
1 ATTAAAATATAAATTTAATTT
*
36459 ATTAAAATA-AAAGTTTAGTTT
1 ATTAAAATATAAA-TTTAATTT
36480 A
1 A
36481 ACTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTAAAATATAAATTTAATTT
Found at i:37393 original size:25 final size:25
Alignment explanation
Indices: 37364--37448 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 25
37354 CAATTTTCGG
37364 ATTCATAAACCAACTCAAAGCCCAT
1 ATTCATAAACCAACTCAAAGCCCAT
* ** *
37389 ATTCATCTAAA--AATTCAGACATTTCCAA
1 ATTCA--TAAACCAACTCA-A-A-GCCCAT
37417 ATCTCATAAACCAACTCAAAGCCCAT
1 AT-TCATAAACCAACTCAAAGCCCAT
37443 ATTCAT
1 ATTCAT
37449 CTAAATATTC
Statistics
Matches: 44, Mismatches: 8, Indels: 16
0.65 0.12 0.24
Matches are distributed among these distances:
25 14 0.32
26 6 0.14
27 10 0.23
28 6 0.14
29 8 0.18
ACGTcount: A:0.42, C:0.28, G:0.04, T:0.26
Consensus pattern (25 bp):
ATTCATAAACCAACTCAAAGCCCAT
Found at i:37430 original size:54 final size:54
Alignment explanation
Indices: 37366--37477 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
37356 ATTTTCGGAT
37366 TCATAAACCAACTCAAAGCCCATATTCATCTAAAAATTCAGACATTTCCAAATC
1 TCATAAACCAACTCAAAGCCCATATTCATCTAAAAATTCAGACATTTCCAAATC
*
37420 TCATAAACCAACTCAAAGCCCATATTCATCTAAATATTCAGACATTTCCAAATC
1 TCATAAACCAACTCAAAGCCCATATTCATCTAAAAATTCAGACATTTCCAAATC
37474 TCAT
1 TCAT
37478 TCAAGAATTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.41, C:0.28, G:0.04, T:0.28
Consensus pattern (54 bp):
TCATAAACCAACTCAAAGCCCATATTCATCTAAAAATTCAGACATTTCCAAATC
Found at i:78452 original size:2 final size:2
Alignment explanation
Indices: 78445--78471 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
78435 TTAATTATTG
78445 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 T
78472 TGATTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90082 original size:24 final size:24
Alignment explanation
Indices: 90052--90143 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
90042 TCCAGGCATC
*
90052 CCACCAGGCATACCACCAGGGAAA
1 CCACCAGGCATACCTCCAGGGAAA
* * *
90076 CCTCCAGCCATTCCTCCAGGGAAA
1 CCACCAGGCATACCTCCAGGGAAA
90100 CCACCAGGCATACCTCCAGGGAAA
1 CCACCAGGCATACCTCCAGGGAAA
*
90124 CCACCAGGCATTCCTCCAGG
1 CCACCAGGCATACCTCCAGG
90144 CATACCTCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.29, C:0.40, G:0.20, T:0.11
Consensus pattern (24 bp):
CCACCAGGCATACCTCCAGGGAAA
Found at i:90155 original size:48 final size:48
Alignment explanation
Indices: 90042--90155 Score: 165
Period size: 48 Copynumber: 2.4 Consensus size: 48
90032 AATCAACATT
* *
90042 TCCAGGCATCCCACCAGGCATACCACCAGGGAAACCTCCAGCCATTCC
1 TCCAGGCATACCACCAGGCATACCACCAGGGAAACCACCAGCCATTCC
* * * *
90090 TCCAGGGAAACCACCAGGCATACCTCCAGGGAAACCACCAGGCATTCC
1 TCCAGGCATACCACCAGGCATACCACCAGGGAAACCACCAGCCATTCC
*
90138 TCCAGGCATACCTCCAGG
1 TCCAGGCATACCACCAGG
90156 AAAACCGCCA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.28, C:0.40, G:0.19, T:0.12
Consensus pattern (48 bp):
TCCAGGCATACCACCAGGCATACCACCAGGGAAACCACCAGCCATTCC
Found at i:90170 original size:36 final size:36
Alignment explanation
Indices: 90103--90179 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
90093 AGGGAAACCA
* *
90103 CCAGGCATACCTCCAGGGAAACCACCAGGCATTCCT
1 CCAGGCATACCTCCAGGAAAACCACCAGGCATGCCT
*
90139 CCAGGCATACCTCCAGGAAAACCGCCAGGCATGCCT
1 CCAGGCATACCTCCAGGAAAACCACCAGGCATGCCT
90175 CCAGG
1 CCAGG
90180 TCTTCTACTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.27, C:0.39, G:0.22, T:0.12
Consensus pattern (36 bp):
CCAGGCATACCTCCAGGAAAACCACCAGGCATGCCT
Found at i:90178 original size:12 final size:12
Alignment explanation
Indices: 90042--90179 Score: 114
Period size: 12 Copynumber: 11.5 Consensus size: 12
90032 AATCAACATT
*
90042 TCCAGGCATCCC
1 TCCAGGCATACC
*
90054 ACCAGGCATACC
1 TCCAGGCATACC
* * *
90066 ACCAGGGAAACC
1 TCCAGGCATACC
* *
90078 TCCAGCCATTCC
1 TCCAGGCATACC
* *
90090 TCCAGGGAAACC
1 TCCAGGCATACC
*
90102 ACCAGGCATACC
1 TCCAGGCATACC
* *
90114 TCCAGGGAAACC
1 TCCAGGCATACC
* *
90126 ACCAGGCATTCC
1 TCCAGGCATACC
90138 TCCAGGCATACC
1 TCCAGGCATACC
* *
90150 TCCAGGAAAACC
1 TCCAGGCATACC
* *
90162 GCCAGGCATGCC
1 TCCAGGCATACC
90174 TCCAGG
1 TCCAGG
90180 TCTTCTACTG
Statistics
Matches: 94, Mismatches: 32, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 94 1.00
ACGTcount: A:0.28, C:0.40, G:0.20, T:0.12
Consensus pattern (12 bp):
TCCAGGCATACC
Found at i:95451 original size:45 final size:45
Alignment explanation
Indices: 95400--95487 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
95390 CCTAAATTTA
* * *
95400 ACTCCTCCATCTCTAGGCAATTCATCAAAATAAAGCTAATATTCT
1 ACTCCTCCATCTCTAGACAAGTCATCAAAAAAAAGCTAATATTCT
* * *
95445 ACTCCTCCATCTCTATATAAGTCATCAAAAAAAAGTTAATATT
1 ACTCCTCCATCTCTAGACAAGTCATCAAAAAAAAGCTAATATT
95488 AATTGTTGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (45 bp):
ACTCCTCCATCTCTAGACAAGTCATCAAAAAAAAGCTAATATTCT
Found at i:99639 original size:19 final size:19
Alignment explanation
Indices: 99615--99651 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
99605 CTAATTTGTA
*
99615 ACCGTTTCACCATCGTTTG
1 ACCGTTTCACCACCGTTTG
99634 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
99652 TGGGACCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.35, G:0.14, T:0.35
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:99747 original size:19 final size:19
Alignment explanation
Indices: 99723--99759 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
99713 GTACAGTACC
99723 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
99742 TAATCTTATCTGTACAGT
1 TAATCTAATCTGTACAGT
99760 TGCCAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:107594 original size:10 final size:10
Alignment explanation
Indices: 107579--107603 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
107569 GTACATACTA
107579 CCATTTTCTC
1 CCATTTTCTC
107589 CCATTTTCTC
1 CCATTTTCTC
107599 CCATT
1 CCATT
107604 AAGGCCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.40, G:0.00, T:0.48
Consensus pattern (10 bp):
CCATTTTCTC
Found at i:113536 original size:27 final size:27
Alignment explanation
Indices: 113506--113592 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
113496 GGAGCATGGC
113506 ATCTCATTATGTATTTTGCCTTACAAG
1 ATCTCATTATGTATTTTGCCTTACAAG
** * ** **
113533 ATCTCA-TGCGTGACTATT-AATTAC-CC
1 ATCTCATTATGT-A-TTTTGCCTTACAAG
113559 ATCTCATTATGTATTTTGCCTTACAAG
1 ATCTCATTATGTATTTTGCCTTACAAG
113586 ATCTCAT
1 ATCTCAT
113593 GCCTAGACAG
Statistics
Matches: 41, Mismatches: 14, Indels: 10
0.63 0.22 0.15
Matches are distributed among these distances:
25 3 0.07
26 14 0.34
27 21 0.51
28 3 0.07
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (27 bp):
ATCTCATTATGTATTTTGCCTTACAAG
Found at i:116684 original size:3 final size:3
Alignment explanation
Indices: 116676--116702 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
116666 GTGTATGCGT
116676 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
116703 TACGCAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:122769 original size:60 final size:60
Alignment explanation
Indices: 122705--122833 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 60
122695 TTAAATAGGC
* * * *
122705 CCCTAACATATGTAAAAATGCTCAATTTAGGATTCATACTTTTAATTTAGTTAAATAAAG-
1 CCCTAACATATGCAAAAATGCTCAAATTAGGATACATACTTTGAATTTAGTTAAA-AAAGA
** * * * * * *
122765 CCCTAATGTATGCGAAAATGTTCAAATTAGGGTACATGCTTTGAATTTGGTTAAAAAGGA
1 CCCTAACATATGCAAAAATGCTCAAATTAGGATACATACTTTGAATTTAGTTAAAAAAGA
122825 CCCTAACAT
1 CCCTAACAT
122834 TATCGTATGC
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
59 3 0.06
60 51 0.94
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (60 bp):
CCCTAACATATGCAAAAATGCTCAAATTAGGATACATACTTTGAATTTAGTTAAAAAAGA
Found at i:123072 original size:60 final size:60
Alignment explanation
Indices: 122945--123072 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
122935 TAAATTAAGA
* * * * *
122945 TCCTAATTAACCAAATTAAAAGCATGAGGCATAAATTGAGCATTTCCATATACGTTAGGG
1 TCCTATTTAACCAAATGAAAAGCATGAGCCATAAATTGAGCATTTCCACATACGTTAGAG
** *
123005 TTGTATTTAACCAAATGAAAAGCATGAGCCTTAAATTGAGCATATT-CACATACGTTA-AG
1 TCCTATTTAACCAAATGAAAAGCATGAGCCATAAATTGAGCAT-TTCCACATACGTTAGAG
123064 TACCTATTT
1 T-CCTATTT
123073 GAGCAATTAG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 2 0.04
60 52 0.93
61 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (60 bp):
TCCTATTTAACCAAATGAAAAGCATGAGCCATAAATTGAGCATTTCCACATACGTTAGAG
Found at i:129583 original size:11 final size:11
Alignment explanation
Indices: 129567--129598 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
129557 GCGAAATTAA
129567 TATTCGTTTAG
1 TATTCGTTTAG
*
129578 TATTCGTTTAT
1 TATTCGTTTAG
129589 TATTCGTTTA
1 TATTCGTTTA
129599 ATAGCACGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.09, G:0.12, T:0.59
Consensus pattern (11 bp):
TATTCGTTTAG
Found at i:129635 original size:6 final size:6
Alignment explanation
Indices: 129624--129663 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
129614 TCGTTAATTA
129624 ATCTAT ATCTAT A-CTAT -T-TAT ATCTAT ATCTAT A-CTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
129664 ATAAAAGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 3 0.10
5 10 0.33
6 17 0.57
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:129650 original size:21 final size:21
Alignment explanation
Indices: 129624--129666 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
129614 TCGTTAATTA
*
129624 ATCTATATCTATACTATTTAT
1 ATCTATATCTATACTATATAT
129645 ATCTATATCTATACTATATAT
1 ATCTATATCTATACTATATAT
129666 A
1 A
129667 AAAGTACGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (21 bp):
ATCTATATCTATACTATATAT
Found at i:129666 original size:15 final size:17
Alignment explanation
Indices: 129626--129663 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
129616 GTTAATTAAT
129626 CTATATCTATA-CTAT-
1 CTATATCTATATCTATA
*
129641 TTATATCTATATCTATA
1 CTATATCTATATCTATA
129658 CTATAT
1 CTATAT
129664 ATAAAAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.53
16 4 0.21
17 5 0.26
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (17 bp):
CTATATCTATATCTATA
Found at i:129874 original size:23 final size:23
Alignment explanation
Indices: 129848--130099 Score: 116
Period size: 22 Copynumber: 11.3 Consensus size: 23
129838 TTTACCATCT
*
129848 AAATTTTATAGGGAGGTTTATCA
1 AAATTTCATAGGGAGGTTTATCA
* *
129871 AAATTTTATAGGAATGGTTTATCA
1 AAATTTCATAGGGA-GGTTTATCA
*
129895 AAATTTCATAGCGAGG-TTATCA
1 AAATTTCATAGGGAGGTTTATCA
* * * *
129917 CAATTTCATAGTG-TGATTATCA
1 AAATTTCATAGGGAGGTTTATCA
*
129939 AAATTTC--AGGG-TGTAATTA-CTA
1 AAATTTCATAGGGAGGT--TTATC-A
* *
129961 ACAA-TTCATATGGAGGTTT-TTA
1 A-AATTTCATAGGGAGGTTTATCA
* ** *
129983 AATTTTCATAACGTGG-TTATCA
1 AAATTTCATAGGGAGGTTTATCA
* * *
130005 ATATATCATATGGAGG-TTATCA
1 AAATTTCATAGGGAGGTTTATCA
* * **
130027 ACATCTCATAGTGTTGG-TTATCA
1 AAATTTCATAG-GGAGGTTTATCA
* **
130050 AAATTTCATTGGGA-AATTATCA
1 AAATTTCATAGGGAGGTTTATCA
* *
130072 AAATTTCATAGTGAGGTCTA-CA
1 AAATTTCATAGGGAGGTTTATCA
130094 AAATTT
1 AAATTT
130100 TATAAGAAGG
Statistics
Matches: 174, Mismatches: 40, Indels: 31
0.71 0.16 0.13
Matches are distributed among these distances:
20 5 0.03
21 5 0.03
22 101 0.58
23 38 0.22
24 23 0.13
25 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (23 bp):
AAATTTCATAGGGAGGTTTATCA
Found at i:129894 original size:24 final size:23
Alignment explanation
Indices: 129848--129927 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 23
129838 TTTACCATCT
*
129848 AAATTTTATAGGGAGGTTTATCA
1 AAATTTTATAGGAAGGTTTATCA
129871 AAATTTTATAGGAATGGTTTATCA
1 AAATTTTATAGGAA-GGTTTATCA
*
129895 AAATTTCATAGCG-AGG-TTATCA
1 AAATTTTATAG-GAAGGTTTATCA
* *
129917 CAATTTCATAG
1 AAATTTTATAG
129928 TGTGATTATC
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
22 16 0.31
23 15 0.29
24 20 0.38
25 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (23 bp):
AAATTTTATAGGAAGGTTTATCA
Found at i:130112 original size:111 final size:109
Alignment explanation
Indices: 129848--130112 Score: 238
Period size: 111 Copynumber: 2.4 Consensus size: 109
129838 TTTACCATCT
* * * *
129848 AAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAATGGTTTATCAAAATTTCATAGCGAGGTT
1 AAATTTCATAGTGAGG-TTA-CAAAATTTTATAAGAA-GG-TTATCAAAATATCATAGCGAGGTT
* *
129913 ATCACAATTTCATAGTGTGATTATCAAAATTTCAGGGTGTAATTACTA
62 ATCACAATCTCATAGTGTGATTATCAAAATTTCAGGGTGAAATTACTA
*** * *
129961 ACAA-TTCATA-TGGAGGTTTTTAAATTTTCATAACG-TGGTTATCAATATATCATATG-GAGGT
1 A-AATTTCATAGT-GAGGTTACAAAATTTT-ATAA-GAAGGTTATCAAAATATCATA-GCGAGGT
* *
130022 TATCA-ACATCTCATAGTGTTGGTTATCAAAATTTCATTGG-GAAATTA-TCA
61 TATCACA-ATCTCATAGTG-TGATTATCAAAATTTCA-GGGTGAAATTACT-A
130072 AAATTTCATAGTGAGGTCTACAAAATTTTATAAGAAGGTTA
1 AAATTTCATAGTGAGGT-TACAAAATTTTATAAGAAGGTTA
130113 AAATAAAATT
Statistics
Matches: 122, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
109 1 0.01
110 38 0.31
111 54 0.44
112 16 0.13
113 11 0.09
114 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (109 bp):
AAATTTCATAGTGAGGTTACAAAATTTTATAAGAAGGTTATCAAAATATCATAGCGAGGTTATCA
CAATCTCATAGTGTGATTATCAAAATTTCAGGGTGAAATTACTA
Found at i:130179 original size:22 final size:22
Alignment explanation
Indices: 130154--130206 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
130144 CCATAGTATC
*
130154 GTTATTAAAATTTC-ATAGGAAG
1 GTTATTAAAATTTCAAAAGG-AG
*
130176 GTTA-TCAAATTTCAAAAGGAG
1 GTTATTAAAATTTCAAAAGGAG
*
130197 GTTATCAAAA
1 GTTATTAAAA
130207 ATAGTGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (22 bp):
GTTATTAAAATTTCAAAAGGAG
Found at i:131020 original size:333 final size:331
Alignment explanation
Indices: 130329--131503 Score: 1235
Period size: 333 Copynumber: 3.5 Consensus size: 331
130319 ATTATAATAA
* * * * * *
130329 TAACCATCATAGG-TTTTGGCTAAAAACGCGTTCCGCAGCTC-CGACT-AAGTTTTTAATGACTT
1 TAACCATCA-CGGTTTTTTGCTAAAAACGCGTTCCGGAGC-CACGACTCAA-TTTTTCATCATTT
* * *
130391 TTGGC-CACCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGACAAATTGGATTT
63 TTGGCGC-CC-AGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCAAATTGGATTT
* * * * *
130455 AAGGA-ATTGATTTTGCGATCATCAAAATCATGTTTCGATTTAACCAGAAATTAATTCGGAAACA
126 AAGGATA-TAATTTTACGAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACA
* *
130519 TATAGGAAAATCGATATTAGAAGTGTGAAAAACCCTTCAATCATTTAGACGTTGAATTAAATATA
190 TATAGGAAAATCGATATTAGAAGCGT-AAAAACCCTTCAAT-ATTTAGGCGTTGAATT-AATATA
* *
130584 TTCA-ATAAGTGTTTTGGCCAAAGATTGTGGAAAAAA-CTTCCGGGTCAATTTTTGCAAAATTTT
252 TT-ATATTAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTT
*
130647 AGCCGAAATCATGTAC
316 AGCCGAAATCGTGTAC
* * * * * * *
130663 TAACCAT-AGCGGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTCCATGATTTAT
1 TAACCATCA-CGGTTTTTTGCTAAAAACGCGTTCCGGAGCCACGACTCAATTTTTCATCATTTTT
* *
130727 GGC-CCCATGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAG
65 GGCGCCCA-GACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCAAATTGGATTTAAG
* * * *
130791 GATTTAATTTTACAAGCATCAGAATCATGTTTTGATTTAATCAGAAATTAATTCGGAAAGATATA
129 GATATAATTTTACGAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATA
* * *
130856 GGAAAATCGATATTCGAAGCCTAAAAACCCTTCAATATTTTAGGCGTTGAATTACACATATTATA
194 GGAAAATCGATATTAGAAGCGTAAAAACCCTTCAATA-TTTAGGCGTTGAATTA-ATATATTATA
* *
130921 TTAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGGCGA
257 TTAGTGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGA
*
130986 AAACGTGTAC
322 AATCGTGTAC
* * * *
130996 TAACCATCAC-GTTTTTTGGCTAAAAACGCGTTCCGGGGCCACGACTCAGTTTTTCTTCTTTTTT
1 TAACCATCACGGTTTTTT-GCTAAAAACGCGTTCCGGAGCCACGACTCAATTTTTCATCATTTTT
* * * * * * *
131060 GGCGCCGAGGCTCCTTGAAATATCTACATTCATCAAATCAAATGTCAGTC-ACTATGGATTTAAG
65 GGCGCCCAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCAAAT-TGGATTTAAG
* * * * * * * * * *
131124 GATATATTTTTATGAGCTTCTGATTCTTGTTTCGGTTTAATCAGAAATTAATTAGTAAAACACAT
129 GATATAATTTTACGAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCG-GAAACATAT
* * * * * * * * * *
131189 TGGAAAAACGATATTAGAAACGTTAAACCCCTTCAAAATTTAAGCATTGAATT-ATAT-TTTTTT
193 AGGAAAATCGATATTAGAAGCGTAAAAACCCTTCAATATTTAGGCGTTGAATTAATATATTATAT
* * * * * * *
131252 TAGAGTATTTCGGCCAAAAATTGAGG-AAAATTATTTCGGGTCAATTTTTACAAAATTATAGCCG
258 TAGTGT-TTT-GGCCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
131316 AAATCGTGTAC
321 AAATCGTGTAC
* * *
131327 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGCCACGACTCTATTTTTCTTCTTTTTTG
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGCCACGACTCAATTTTTCATCATTTTTG
* * * * * ** * *
131392 GCGCCGAGACTCCTTGAAAAATCTGTATTCATCAAATCAAATGTCAGCCACTTTGGATTTAATGC
66 GCGCCCAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCAAATTGGATTTAAGGA
* * * * * *
131457 TATATTTTTATGAGCTTCTGATTCTTGTTTCGATTTAATCAGAAATT
131 TATAATTTTACGAGCATCAGAATCATGTTTCGATTTAATCAGAAATT
131504 TATTAGTAAA
Statistics
Matches: 723, Mismatches: 100, Indels: 39
0.84 0.12 0.05
Matches are distributed among these distances:
330 9 0.01
331 205 0.28
332 96 0.13
333 323 0.45
334 88 0.12
335 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (331 bp):
TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGCCACGACTCAATTTTTCATCATTTTTG
GCGCCCAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCAAATTGGATTTAAGGA
TATAATTTTACGAGCATCAGAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAACATATAGG
AAAATCGATATTAGAAGCGTAAAAACCCTTCAATATTTAGGCGTTGAATTAATATATTATATTAG
TGTTTTGGCCAAAGATTGTGGAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC
GTGTAC
Done.