Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014353.1 Corchorus olitorius cultivar O-4 contig14386, 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: 37341
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1257 original size:632 final size:630
Alignment explanation
Indices: 1--1265 Score: 2440
Period size: 632 Copynumber: 2.0 Consensus size: 630
1 ATATTTGAATACTTGTTTCTTTTTAGAAAAGTCTAGGTTGAACTTGGACTACAAAAAAAAAAAAA
1 ATATTTGAATACTTGTTTCTTTTTAGAAAAGTCTAGGTTGAACTTGGACTACAAAAAAAAAAAAA
66 ATCTCAAACTACCATTAAAATATTAAAAATTGTAAATAATAATTAGTTATAAAAATAAGCATTTA
66 ATCTCAAACTACCATTAAAATATTAAAAATTGTAAATAATAATTAGTTATAAAAATAAGCATTTA
131 TTTACTTACCTTAACAATTCTCCATATTTCGTCCTTTTTTTCTATAGGCATAAGTCTCCAATCAT
131 TTTACTTACCTTAACAATTCTCCATATTTCGTCCTTTTTTTCTATAGGCATAAGTCTCCAATCAT
196 CAAACTCCAACAGAGTTATATCTTTATTTCTGGCAACAGTACCGCAAAAGTACTCTAGCTGACCA
196 CAAACTCCAACAGAGTTATATCTTTATTTCTGGCAACAGTACCGCAAAAGTACTCTAGCTGACCA
*
261 TCATCTACACATTGATTGTAGATGTTAAACTCGGAAGACAACTCTTGCCAAGGACCAAGATTCCA
261 TCATCTACACATTAATTGTAGATGTTAAACTCGGAAGACAACTCTTGCCAAGGACCAAGATTCCA
326 CATATCTTTAAGTTCAGTACGCCCTCGAGTTTTTCTTGGTAAAATAGGCGCAACTACAAAATAAA
326 CATATCTTTAAGTTCAGTACGCCCTCGAGTTTTTCTTGGTAAAATAGGCGCAACTACAAAATAAA
*
391 TAATTTTAAGAAGAGTTAAACCAATTCAGTATCCTTAAGAATAAATATCCAATCAATCAATAAGT
391 TAATTTTAAGAAGAGTTAAACCAATTCAGTATCCTTAAGAATAAATATCCAATCAATCAATAACT
456 TACACTGGTCAAGATTATCCTCATCGTCACTAGTATCATTCTCATGATTCGTCACAATCTCAATG
456 TACACTGGTCAAGATTATCCTCATCGTCACTAGTATCATTCTCATGATTCGTCACAATCTCAATG
521 TCATGCATATTGAGAAAAATGTTTATGACAACATCATGGGAACATTGTTAGATGTTGATGGGAAG
521 TCATGCATATTGAGAAAAATGTTTATGACAACATCATGGGAACATTGTTAGATGTTGATGGGAAG
586 ACTAAAGACAACTTGAAGTCCCGTCTTGACCTTCAAAGGTTGGGC
586 ACTAAAGACAACTTGAAGTCCCGTCTTGACCTTCAAAGGTTGGGC
631 ATATTTGAATACTTGTTTCTTTTTAGAAAAGTCTAGGTTGAACTTGGACTACAAAAAAAAAAAAA
1 ATATTTGAATACTTGTTTCTTTTTAGAAAAGTCTAGGTTGAACTTGGACTAC-AAAAAAAAAAAA
696 AATCTCAAACTACCATTAAAATATTAAAAATTGTAAATAATAATTAGTTATAAAAATAAGCATTT
65 AATCTCAAACTACCATTAAAATATTAAAAATTGTAAATAATAATTAGTTATAAAAATAAGCATTT
761 ATTTACTTACCTTAACAATTCTCCATATTTCGTCCTTTTTTTTCTATAGGCATAAGTCTCCAATC
130 ATTTACTTACCTTAACAATTCTCCATATTTCGTCC-TTTTTTTCTATAGGCATAAGTCTCCAATC
826 ATCAAACTCCAACAGAGTTATATCTTTATTTCTGGCAACAGTACCGCAAAAGTACTCTAGCTGAC
194 ATCAAACTCCAACAGAGTTATATCTTTATTTCTGGCAACAGTACCGCAAAAGTACTCTAGCTGAC
891 CATCATCTACACATTAATTGTAGATGTTAAACTCGGAAGACAACTCTTGCCAAGGACCAAGATTC
259 CATCATCTACACATTAATTGTAGATGTTAAACTCGGAAGACAACTCTTGCCAAGGACCAAGATTC
* *
956 CACATATCTTTGAGTTCAGTACGCCCTCGAGTTTTTCTTGGTAAAATAGGCGCCACTACAAAATA
324 CACATATCTTTAAGTTCAGTACGCCCTCGAGTTTTTCTTGGTAAAATAGGCGCAACTACAAAATA
*
1021 AATATTTTTAAGAAGAGTTAAACCAATTCAGTATCCTTAAGAATAAATATCCAATCAATCAATAA
389 AATAATTTTAAGAAGAGTTAAACCAATTCAGTATCCTTAAGAATAAATATCCAATCAATCAATAA
* *
1086 CTTACACTGGTCAGGATTATCCTCATCGTCACTAGTATCATTCTCATGATTCGTCACAATCTCGA
454 CTTACACTGGTCAAGATTATCCTCATCGTCACTAGTATCATTCTCATGATTCGTCACAATCTCAA
1151 TGTCATGCATATTGAGAAAAATGTTTATGACAACATCATGGGAACATTGTTAGATGTTGATGGGA
519 TGTCATGCATATTGAGAAAAATGTTTATGACAACATCATGGGAACATTGTTAGATGTTGATGGGA
*
1216 AGACTAAAGACAACTTGAAGTCCTGTCTTGACCTTCAAAGGTTGGGC
584 AGACTAAAGACAACTTGAAGTCCCGTCTTGACCTTCAAAGGTTGGGC
1263 ATA
1 ATA
1266 AGAAGTGAAC
Statistics
Matches: 625, Mismatches: 8, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
630 52 0.08
631 112 0.18
632 461 0.74
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (630 bp):
ATATTTGAATACTTGTTTCTTTTTAGAAAAGTCTAGGTTGAACTTGGACTACAAAAAAAAAAAAA
ATCTCAAACTACCATTAAAATATTAAAAATTGTAAATAATAATTAGTTATAAAAATAAGCATTTA
TTTACTTACCTTAACAATTCTCCATATTTCGTCCTTTTTTTCTATAGGCATAAGTCTCCAATCAT
CAAACTCCAACAGAGTTATATCTTTATTTCTGGCAACAGTACCGCAAAAGTACTCTAGCTGACCA
TCATCTACACATTAATTGTAGATGTTAAACTCGGAAGACAACTCTTGCCAAGGACCAAGATTCCA
CATATCTTTAAGTTCAGTACGCCCTCGAGTTTTTCTTGGTAAAATAGGCGCAACTACAAAATAAA
TAATTTTAAGAAGAGTTAAACCAATTCAGTATCCTTAAGAATAAATATCCAATCAATCAATAACT
TACACTGGTCAAGATTATCCTCATCGTCACTAGTATCATTCTCATGATTCGTCACAATCTCAATG
TCATGCATATTGAGAAAAATGTTTATGACAACATCATGGGAACATTGTTAGATGTTGATGGGAAG
ACTAAAGACAACTTGAAGTCCCGTCTTGACCTTCAAAGGTTGGGC
Found at i:4285 original size:214 final size:211
Alignment explanation
Indices: 3386--4704 Score: 1342
Period size: 214 Copynumber: 6.2 Consensus size: 211
3376 CAAAAAACGT
* * * * * * * *
3386 TAAA-AAGAGCAACGTTATTAGAAAACATTATTAAAATTTAGAAAGAGTCGCAAGGTACTGCGAC
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTTAAAAAGAGTCGCAAGGTA-TGCGAC
* * * * * * ** * * *
3450 GTTTATTAAAAAAGACACATATTTAAGCGACGTTTACCCTAAACTTTGTCATAAATGTCGGAGAA
65 ATTTATT-AAAATGTCATATATTAAAACGACGTTT-CCAAAAACGTTGTTATAAATGTCGGAAAA
* * *
3515 GTCTATTTTAAAGAGACGTTTGTTAAAAATGTCGCATGATTGAACAACGTTTGAGATAAACGTCT
128 GTCTATCTTAAAGCGACGTTTGTTAAAAATGTCGCATGATTGAACGACGTTTGAGA-AAACGTCT
*
3580 CAACAAACGTCGCAAAAGCA
192 CTACAAACGTCGCAAAAGCA
* * * *
3600 TAAACAAGAGCGACGTTATTAAAAAAAGTCACTCAGTTTAAAAAAGAGTCGCAATGTACTGCGAC
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTTAAAAAGAGTCGCAAGGTA-TGCGAC
* * * * *
3665 ATTTATTAAAATGTCATATTTTAAAACGATGTTT-TATAACAACGTTCTTATAAATGTTGGAAAA
65 ATTTATTAAAATGTCATATATTAAAACGACGTTTCCA-AA-AACGTTGTTATAAATGTCGGAAAA
* * ** * * *
3729 GTCTATCTTAAAGCAATGTTTGTTGATTAATGTCACTTGATTGAACGACATTTGAGAAACACGT-
128 GTCTATCTTAAAGCGACGTTTGTT-AAAAATGTCGCATGATTGAACGACGTTTGAGAAA-ACGTC
* *
3793 TGCTTCAAACGTTGCAAAAGCA
191 T-CTACAAACGTCGCAAAAGCA
* ** *
3815 TAAACTAGAGCGACGTTATTAAAAAACGTCACTCAAATTAAAAAAAGAGTCGTAAGGTATTGCGA
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTC-AATTTTAAAAAGAGTCGCAAGGTA-TGCGA
* * * ** * *
3880 CATTTATCAAAATGTCATAT-TTCATAACGATGTTTCCCTAAACGTTGTTATAAATGTCAGAGAA
64 CATTTATTAAAATGTCATATATT-AAAACGACGTTTCCAAAAACGTTGTTATAAATGTCGGAAAA
* * * * * * *
3944 GTATGTCCTAAAGCGACATTTGTTAAAAAATGTCGCAAGATTGAATGACGTTTGAGAAAAATGTC
128 GTCTATCTTAAAGCGACGTTTGTT-AAAAATGTCGCATGATTGAACGACGTTTGAG-AAAACGTC
*
4009 GT-TACAATCGTCGCACAAA-CA
191 -TCTACAAACGTCGCA-AAAGCA
* * *
4030 TAAACTAGAGCGACATTATTAAAAAACGTCACTCAATTTTAAAAAGTGTCGCAAGGTGATGCGAC
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTTAAAAAGAGTCGCAAGGT-ATGCGAC
* *
4095 ATTTATTAAAATGTCATATATTAAAACGACGTTTCGGAAAAACGTTGCTATAAATGTCGGAAAAG
65 ATTTATTAAAATGTCATATATTAAAACGACGTTTC-CAAAAACGTTGTTATAAATGTCGGAAAAG
*
4160 TCTATCTTAAAGCGACGCTTGTTAAAAAATGTCGCATGATTGAACGACGTTTGAGAAAACGTCTC
129 TCTATCTTAAAGCGACGTTTGTT-AAAAATGTCGCATGATTGAACGACGTTTGAGAAAACGTCTC
*
4225 TACAAACGTCGCAAAAGTA
193 TACAAACGTCGCAAAAGCA
* **** * * *
4244 TTAACAAGAGCGATACAATTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATTTCACGA
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTT-AAAAAGAGTCGCAAGGTAT-GCGA
* * * * * *
4309 CGTTTAATAAAATGTCATTTATT-AAATGACGCTTCTGAAAAACGTTGTTATAAATGTCGGAAAA
64 CATTTATTAAAATGTCATATATTAAAACGACGTTTC-CAAAAACGTTGTTATAAATGTCGGAAAA
* *
4373 GACTATCTTAAAGCGACGTTTGTTCAAAAATGTTGCATGATTGAACGACGTTTGAGAAAACGTCT
128 GTCTATCTTAAAGCGACGTTTGTT-AAAAATGTCGCATGATTGAACGACGTTTGAGAAAACGTCT
*
4438 CTACAAACGTCGCAAAAGTA
192 CTACAAACGTCGCAAAAGCA
** * * *
4458 TAAACAAGAGCGACGCAATTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATTTTACGA
1 TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTT-AAAAAGAGTCGCAAG-GTATGCGA
* * * * *
4523 TATTTATTAAAATGTCATTTATT-AAATGACGTTTCCCTAAAATGTTGTTATAAATGTCGGAAAA
64 CATTTATTAAAATGTCATATATTAAAACGACGTTT-CCAAAAACGTTGTTATAAATGTCGGAAAA
* * * * * *
4587 GTCTATCTTAAAGCGAGGTTTGTTAAAAATGCCACATGATTGAACGACGTTAGACAAAAATGTCT
128 GTCTATCTTAAAGCGACGTTTGTTAAAAATGTCGCATGATTGAACGACGTTTGA-GAAAACGTCT
* **
4652 CTACAAATGTCGTTAAAGCA
192 CTACAAACGTCGCAAAAGCA
* * * * *
4672 TGAGCAATAGCGACCTT-TTATAAAAATGTCACT
1 TAAACAAGAGCGACGTTATTA-AAAAACGTCACT
4705 TAAGTTAAGA
Statistics
Matches: 932, Mismatches: 149, Indels: 48
0.83 0.13 0.04
Matches are distributed among these distances:
213 34 0.04
214 474 0.51
215 361 0.39
216 62 0.07
217 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (211 bp):
TAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTTAAAAAGAGTCGCAAGGTATGCGACA
TTTATTAAAATGTCATATATTAAAACGACGTTTCCAAAAACGTTGTTATAAATGTCGGAAAAGTC
TATCTTAAAGCGACGTTTGTTAAAAATGTCGCATGATTGAACGACGTTTGAGAAAACGTCTCTAC
AAACGTCGCAAAAGCA
Found at i:4512 original size:429 final size:426
Alignment explanation
Indices: 3490--4672 Score: 1364
Period size: 429 Copynumber: 2.8 Consensus size: 426
3480 CGTTTACCCT
* * * * *
3490 AAACTTTGTCATAAATGTCGGAGAAGTCTATTTTAAAGAGACGTTTGTTAAAAATGTCGCATGAT
1 AAACGTTGTTATAAATGTCGGAGAAGACTATCTTAAAGCGACGTTTGTTAAAAATGTCGCATGAT
* *
3555 TGAACAACGTTTGAGATAAACGTCTCAACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTATT
66 TGAACGACGTTTGAGA-AAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTATT
* * *
3620 AAAAAAAGTCACTC-AGTTTAAAAAAGAGTCGCAATGTACTGCGACATTTATTAAAATGTCATAT
130 AAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGGTA-TGCGACATTTATTAAAATGTCATAT
* * * * * * * *
3684 TTTAAAACGATGTTTTATAACAACGTT-CTTATAAATGTTGGAAAAGTCTATCTTAAAGCAATGT
194 ATTAAAACGACGTTTCACAAAAACGTTGC-TATAAATGTCGGAAAAGTCTATCTTAAAGCGACGT
** * * * *
3748 TTGTTGATTAATGTCACTTGATTGAACGACATTTGAGAAACACGT-TGCTTCAAACGTTGCAAAA
258 TTGTT-AAAAATGTCACATGATTGAACGACGTTTGAGAAA-ACGTCT-CTACAAACGTCGCAAAA
* *** * * *
3812 GCATAAACTAGAGCGACGTTATTAAAAAACGTCACTCAAATTAAAAAAAGAGTCGTAAGGTATTG
320 GCATAAACAAGAGCGACACAATTAAAAAACGTCACTCAAATTAAAAAAAGAGTCGCAAGATATTA
* * **
3877 CGACATTTATCAAAATGTCATATTTCATAACGATGTTTCCCT
385 CGACATTTATCAAAATGTCATATTTCATAACGACGCTTCCAA
* * * * *
3919 AAACGTTGTTATAAATGTCAGAGAAGTA-TGTCCTAAAGCGACATTTGTTAAAAAATGTCGCAAG
1 AAACGTTGTTATAAATGTCGGAGAAG-ACTATCTTAAAGCGACGTTTGTT-AAAAATGTCGCATG
* * * * *
3983 ATTGAATGACGTTTGAGAAAAATGTCGT-TACAATCGTCGCACAAA-CATAAACTAGAGCGACAT
64 ATTGAACGACGTTTGAG-AAAACGTC-TCTACAAACGTCGCA-AAAGCATAAACAAGAGCGACGT
*
4046 TATTAAAAAACGTCACTCAATTTT-AAAAAGTGTCGCAAGGTGATGCGACATTTATTAAAATGTC
126 TATTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGGT-ATGCGACATTTATTAAAATGTC
**
4110 ATATATTAAAACGACGTTTCGGAAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGA
190 ATATATTAAAACGACGTTTCACAAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGA
* *
4175 CGCTTGTTAAAAAATGTCGCATGATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAA
255 CGTTTGTT-AAAAATGTCACATGATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAA
* * * * *
4240 AGTATTAACAAGAGCGATACAATTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGAT-TT
319 AGCATAAACAAGAGCGACACAATTAAAAAACGTCACTCAAATTAAAAAAAGAGTCGCAAGATATT
* * * *
4304 CACGACGTTTAAT-AAAATGTCAT-TTATTA-AATGACGCTTCTGAA
384 -ACGACATTT-ATCAAAATGTCATATT-TCATAACGACGCTTC-CAA
* *
4348 AAACGTTGTTATAAATGTCGGAAAAGACTATCTTAAAGCGACGTTTGTTCAAAAATGTTGCATGA
1 AAACGTTGTTATAAATGTCGGAGAAGACTATCTTAAAGCGACGTTTGTT-AAAAATGTCGCATGA
* **
4413 TTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGTATAAACAAGAGCGACGCAATT
65 TTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTATT
* * * * *
4478 AAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATTTTACGATATTTATTAAAATGTCATTT
130 AAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAG-GTATGCGACATTTATTAAAATGTCATAT
* * * * * *
4543 ATT-AAATGACGTTTCCCTAAAATGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCGAGGTT
194 ATTAAAACGACGTTTCACAAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTT
* * * * * **
4607 TGTTAAAAATGCCACATGATTGAACGACGTTAGACAAAAATGTCTCTACAAATGTCGTTAAAGCA
259 TGTTAAAAATGTCACATGATTGAACGACGTTTGA-GAAAACGTCTCTACAAACGTCGCAAAAGCA
4672 T
323 T
4673 GAGCAATAGC
Statistics
Matches: 637, Mismatches: 98, Indels: 39
0.82 0.13 0.05
Matches are distributed among these distances:
427 31 0.05
428 151 0.24
429 236 0.37
430 208 0.33
431 11 0.02
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (426 bp):
AAACGTTGTTATAAATGTCGGAGAAGACTATCTTAAAGCGACGTTTGTTAAAAATGTCGCATGAT
TGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACGTTATTA
AAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGGTATGCGACATTTATTAAAATGTCATATAT
TAAAACGACGTTTCACAAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTG
TTAAAAATGTCACATGATTGAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAA
ACAAGAGCGACACAATTAAAAAACGTCACTCAAATTAAAAAAAGAGTCGCAAGATATTACGACAT
TTATCAAAATGTCATATTTCATAACGACGCTTCCAA
Found at i:6085 original size:17 final size:17
Alignment explanation
Indices: 6037--6085 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
6027 ATAGCGCATC
*
6037 CATTTTA-TTGG-TAGG
1 CATTTTATTTGGTTAGA
*
6052 CATTTTAATTTGTTTAGA
1 CATTTT-ATTTGGTTAGA
6070 CATTTTATTTGGTTAG
1 CATTTTATTTGGTTAG
6086 TTTTGCATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 6 0.21
16 1 0.04
17 12 0.43
18 9 0.32
ACGTcount: A:0.22, C:0.06, G:0.18, T:0.53
Consensus pattern (17 bp):
CATTTTATTTGGTTAGA
Found at i:23294 original size:2 final size:2
Alignment explanation
Indices: 23287--23311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23277 CTGAACCAAA
23287 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
23312 TTTTTAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:24467 original size:39 final size:39
Alignment explanation
Indices: 24424--24714 Score: 432
Period size: 39 Copynumber: 7.6 Consensus size: 39
24414 TTCTGATCAA
* *
24424 GAGACTGCAGAAGAAGAAAATGATCAAGATGACACTGCT
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
*
24463 GAGACTGCAGAAGAAGAAAGTGATCAAGATG--A-TGCT
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
24499 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
* *
24538 GAGACTGTAGAAGAAAAAAGTGATAAAGATGACACTGCT
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
* *
24577 GAGACTGCAGAAGAAGAAAGTGATCAAGATG--A-TGTT
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
* *
24613 GAGACTGCAAAAGAAGAAAGTGATAAAGATGACACTGTT
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
*
24652 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGTT
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
* *
24691 GAGACTCCAGAAGAAGAAAATGAT
1 GAGACTGCAGAAGAAGAAAGTGAT
24715 GAAGCTTGTT
Statistics
Matches: 233, Mismatches: 13, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
36 66 0.28
37 2 0.01
38 2 0.01
39 163 0.70
ACGTcount: A:0.44, C:0.11, G:0.27, T:0.17
Consensus pattern (39 bp):
GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
Found at i:24550 original size:75 final size:77
Alignment explanation
Indices: 24424--24714 Score: 421
Period size: 75 Copynumber: 3.8 Consensus size: 77
24414 TTCTGATCAA
* * *
24424 GAGACTGCAGAAGAAGAAAATGATCAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATCA
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATAA
24489 AGATG-A-TGCT
66 AGATGAACTGCT
* *
24499 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCTGAGACTGTAGAAGAAAAAAGTGATAA
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATAA
24564 AGATGACACTGCT
66 AGATGA-ACTGCT
* * *
24577 GAGACTGCAGAAGAAGAAAGTGATCAAGATG--A-TGTTGAGACTGCAAAAGAAGAAAGTGATAA
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATAA
*
24639 AGATGACACTGTT
66 AGATGA-ACTGCT
* * *
24652 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGTTGAGACTCCAGAAGAAGAAAATGAT
1 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGAT
24715 GAAGCTTGTT
Statistics
Matches: 195, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
75 133 0.68
76 1 0.01
77 2 0.01
78 59 0.30
ACGTcount: A:0.44, C:0.11, G:0.27, T:0.17
Consensus pattern (77 bp):
GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATAA
AGATGAACTGCT
Found at i:24605 original size:114 final size:114
Alignment explanation
Indices: 24424--24714 Score: 485
Period size: 114 Copynumber: 2.6 Consensus size: 114
24414 TTCTGATCAA
*
24424 GAGACTGCAGAAGAAGAAAA-TGATCAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATC
1 GAGACTGCAGAAGAA-AAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATC
*
24488 AAGATGATGCTGAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGCT
65 AAGATGATGCTGAGACTGCAAAAGAAGAAAGTGATAAAGATGACACTGCT
*
24538 GAGACTGTAGAAGAAAAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATCA
1 GAGACTGCAGAAGAAAAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATCA
* *
24603 AGATGATGTTGAGACTGCAAAAGAAGAAAGTGATAAAGATGACACTGTT
66 AGATGATGCTGAGACTGCAAAAGAAGAAAGTGATAAAGATGACACTGCT
* * * *
24652 GAGACTGCAGAAGAAGAAAGTGATAAAGATGACACTGTTGAGACTCCAGAAGAAGAAAATGAT
1 GAGACTGCAGAAGAAAAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGAT
24715 GAAGCTTGTT
Statistics
Matches: 166, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 4 0.02
114 162 0.98
ACGTcount: A:0.44, C:0.11, G:0.27, T:0.17
Consensus pattern (114 bp):
GAGACTGCAGAAGAAAAAAGTGATAAAGATGACACTGCTGAGACTGCAGAAGAAGAAAGTGATCA
AGATGATGCTGAGACTGCAAAAGAAGAAAGTGATAAAGATGACACTGCT
Found at i:28350 original size:38 final size:38
Alignment explanation
Indices: 28307--28381 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
28297 AGTTTACCAG
28307 TATACGAGATTTCTCTCTTTTTGTGCAAATTAAGCAAC
1 TATACGAGATTTCTCTCTTTTTGTGCAAATTAAGCAAC
28345 TATACGAGATTTCTCTCTTTTTGTGCAAATTAAGCAA
1 TATACGAGATTTCTCTCTTTTTGTGCAAATTAAGCAA
28382 ACTACAGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (38 bp):
TATACGAGATTTCTCTCTTTTTGTGCAAATTAAGCAAC
Found at i:34747 original size:28 final size:28
Alignment explanation
Indices: 34716--34776 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
34706 CTTTGTTTCG
34716 ATTTTGCTTTT--AATGAACAAACCAATCA
1 ATTTTGCTTTTGAAAT--ACAAACCAATCA
**
34744 ATTTTTTTTTTGAAATACAAACCAATCA
1 ATTTTGCTTTTGAAATACAAACCAATCA
34772 ATTTT
1 ATTTT
34777 CAATATTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 26 0.90
30 3 0.10
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.43
Consensus pattern (28 bp):
ATTTTGCTTTTGAAATACAAACCAATCA
Found at i:36284 original size:203 final size:204
Alignment explanation
Indices: 35883--36294 Score: 740
Period size: 203 Copynumber: 2.0 Consensus size: 204
35873 TTCCTTAATA
35883 ATAAATAAATCGGATCTTTAATATCTTTAATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTAATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
35948 AATTTAATAAATCAGCCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAA
*
36013 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATTTTAGACTTAAAAAATTAATAACAT
131 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
36078 TCACCATTG
196 TCACCATTG
* *
36087 ATAAATAAATCGGATCTTTAATGTCTTTTATAATTTTGAAAATTTTGTTTGACATTGATCTAATT
1 ATAAATAAATCGGATCTTTAATATCTTTAATAATTTTG-AAATTTTGTTTGACATTGATCTAATT
36152 TAATTTAATAAATCAACCACTAATGTTCAACTACATTTTTTTT-GTATAG-T-TATATATATAAT
65 TAATTTAATAAATCAACCACTAATGTTCAACTA-ATTTTTTTTGGTATAGTTCTATATATATAAT
36214 AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
129 AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
36279 ATTCACCATTG
194 ATTCACCATTG
36290 ATAAA
1 ATAAA
36295 GTTATTAAGC
Statistics
Matches: 201, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
203 91 0.45
204 37 0.18
205 64 0.32
206 9 0.04
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (204 bp):
ATAAATAAATCGGATCTTTAATATCTTTAATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAA
TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
TCACCATTG
Found at i:37104 original size:36 final size:36
Alignment explanation
Indices: 37050--37119 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
37040 GAGATTTTGG
* *
37050 AGAAATATAATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAATA
* *
37086 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAA
37120 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (36 bp):
AGAAATATAATAACCAAAATCACAAAAAATGTAATA
Done.