Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014111.1 Corchorus olitorius cultivar O-4 contig14144, 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: 5588
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Found at i:1074 original size:334 final size:334
Alignment explanation
Indices: 1--2610 Score: 3704
Period size: 334 Copynumber: 7.8 Consensus size: 334
* *
1 AAAATTTTGCAAAAAACTGACCCGAAAA-ATTTTTCCCTAATTTTTTGCCACAATACTCAGTAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGA-TTTTCCCCAATTTTTTGCCACAATACTCAGAAAA
** * * * * *
65 ATCATATAATTCAACGCCAAAAGTATTATAGTGTTTTTCACGTTTCTAATATCATTTTTCCATTT
65 ATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT
* * * * * * * * *
130 ACTGCTACAACACATTTCTAATTAAATCAAAACAAGATTAAAATGCTCGTAAAAACAAATTTGTA
130 TCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCTGTA
* * * * *
195 AATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTGTTTCTACCGAAAT
195 AATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTCTGCCAAAAA
* * * * * *
260 TCAAGCAAAACCGAGTCACGGCCCCGAAACGCGTTTTCAGCCAAAAACCATGTTGGTTAGTAGAC
260 TCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACAC
*
325 GATTTCGGCT
325 GATTTCGGAT
* * * *
335 AACATTTTGCAAAAAACTGACCCGAAATGTTTTTCCCCAATTTTTTGCCACAATACTAAGAAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
* *
400 TAATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGTTTCTAATATCGTTTTTCCATTTT
66 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* * * **
465 CTGCCACAATACAATTCTTATTAAATCGAAACAAGATTTAGATACTCGTAAAAATAAATCCATAA
131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCTGTAA
** * * * **
530 ATCCATTGTGGCTGAGAGATTTGATTAGATGAATATATATATTTCG-AGAAGTCTTAGTGCCAAA
196 ATCCAACGTGGCT--GAGATTTGGTTAGATGAATACAGATATTTCGAAG-AGTCTTTCTGCCAAA
* * *
594 AATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACGGTGATGGTTAGTAC
258 AATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTAC
* *
659 ACGATTTTGGCT
323 ACGATTTCGGAT
* *
671 AAAATTTAGCAAAAAACTGACCCGAAAA-AGTATTTCTCCAATTTTTTGCCACAATACTCAGAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGA-T-TTTCCCCAATTTTTTGCCACAATACTCAGAAA
*** **
735 AATCATATAATTCTACGCCCAAAAA-ATTTTAATGTTTTTCACGCTTCTAATATCGTTTTTCCAT
64 AATCATATAATTC-AATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-
* * * ** ** *
799 TTTTTTTCC-GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGGTCGTAAAAACAAATCT
127 TTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCT
* * *
863 GTAAATCCAACGTGGCTGAGATTTGGTTAGATGAAAACAGATATTTCGAAGAGACTTTCAGCCAA
192 GTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTCTGCCAA
* * * *
928 AAATAATGCAAAACTGAGTC-TGGCCCCGAAACGCGATTTCAGCCAAAAACCGTCATGGTTAGTA
257 AAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTA
**
992 CAAAATTTCGGAT
322 CACGATTTCGGAT
*
1005 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTTGCCACAATACTCTGAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAA-TTTTTTGCCACAATACTCAGAAAA
*
1070 ATCATATAATTTAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT
65 ATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT
* * * *
1135 TCTGCCATAATACATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAATGAATCCGTA
130 TCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCTGTA
** * * * * * *
1200 AATCCATTGTGGCTGAGAAATTTGATTAGATAAATATAGATATTTCGAGGAGTTTTTCTGCCGAA
195 AATCCAACGTGGCTGAG--ATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTCTGCCAAA
*
1265 AATCATGCAAAATTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACC--G-T-G--A-T-C
258 AATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTAC
1322 ACGATTTCGGAT
323 ACGATTTCGGAT
*
1334 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCACTTTTTTGCCACAATACTCAGAAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
*
1399 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTT
66 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* *
1464 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAATAAATCGGTAA
131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCTGTAA
* * * *
1529 ATTCAACGTGGCTAAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCGAAAAT
196 ATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTCTGCCAAAAAT
* *
1594 CATGCAAAACTTAGTCATGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
261 CATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
1659 ATTTCGGAT
326 ATTTCGGAT
* * *
1668 AAAATTTTGCAAAAAACTGAGCCGAAAAGATTTTCCCCAATTTTTTGCCAAAATACGCAGAAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
* * *
1733 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGTTTATAATATCGTTCTTCCATTTT
66 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* * *
1798 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAACTCTGTAA
131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCTGTAA
* * *
1863 ATCCAACGTGGCTGAGATTTGGTTAGATGAATACATATATTTCGAGGAGTTTTTCTGCCAAAAAT
196 ATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTCTGCCAAAAAT
*
1928 CATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAA-CGTGATGGTTAGTATACG
261 CATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
1992 ATTTCGGAT
326 ATTTCGGAT
* * * *
2001 AAAATTATGCAAAAAACTGACCTGAAAAGATTTTCCCCAATTTTTTGCCAAAATACACAGAAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
*
2066 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTT
66 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* *
2131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAATAAATCCGTAA
131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCTGTAA
* *
2196 ATTCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCAAAAAT
196 ATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTCTGCCAAAAAT
* **
2261 CATGCAAAACTTAGTCAGCACCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
261 CATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
2326 ATTTCGGAT
326 ATTTCGGAT
* * * *
2335 AAAATTTTGCAAAAAACTGACCTGAAATGATTTTTCCCAATTTTTTGCCACAATTCTCAGAAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
2400 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
66 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* * * * **
2465 CTACCATAATACATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAATGAATCAATAA
131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCTGTAA
** * * *
2530 ATCCATGGTGGCTGAGAGATTTGATTAGATGAATATAGATATTTCG-AGAAGTTTTTCTGCCAAA
196 ATCCAACGTGGCT--GAGATTTGGTTAGATGAATACAGATATTTCGAAG-AGTCTTTCTGCCAAA
2594 AATCATGCAAAACTGAG
258 AATCATGCAAAACTGAG
2611 CCAATTATAT
Statistics
Matches: 2034, Mismatches: 214, Indels: 54
0.88 0.09 0.02
Matches are distributed among these distances:
326 88 0.04
328 160 0.08
329 51 0.03
330 2 0.00
331 1 0.00
332 1 0.00
333 340 0.17
334 907 0.45
335 60 0.03
336 244 0.12
337 165 0.08
338 15 0.01
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (334 bp):
AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCTGTAA
ATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTCTGCCAAAAAT
CATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
ATTTCGGAT
Found at i:2198 original size:667 final size:664
Alignment explanation
Indices: 1--3463 Score: 4589
Period size: 667 Copynumber: 5.3 Consensus size: 664
* *
1 AAAATTTTGCAAAAAACTGACCCGAAAA-ATTTTTCCCTAATTTTTTGCCACAATACTCAGTAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGA-TTTTCCCCAATTTTTTGCCACAATACTCAGAAAA
* * * * *
65 ATCATATAATTCAACGCCAAAAGTATTATAGTGTTTTTCACGTTTCTAATATCATTTTTCCATTT
65 ATCATATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT
* * * * * *
130 ACTGCTACAACACATTTCTAATTAAATCAAAACAAGATTAAAATGCTCGTAAAAACAAATTTGTA
130 TCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCTGTA
* * * * * *
195 AATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAGGAGTGTTTCTACCGAAAT
195 AATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCAAAAA
* * * * *
260 TCAAGCAAAACCGAGTCACGGCCCCGAAACGCGTTTTCAGCCAAAAACCATGTTGGTTAGTAGAC
260 TCATGCAAAACTGAGTCA-GGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACAC
* * * *
325 GATTTCGGCTAACATTTTGCAAAAAACTGACCCGAAATGTTTTTCCCCAATTTTTTGCCACAATA
324 GATTTCGGATAAAATTTTGCAAAAAACTGA-CCGAAAAGATTTTCCCCAATTTTTTGCCACAATA
* * *
390 CTAAGAAAAATAATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGTTTCTAATATCGTT
388 CTCAGAAAAATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTT
* * *
455 TTTCCATTTTCTGCCACAATACAATTCTTATTAAATCGAAACAAGATTTAGATACTCGTAAAAAT
453 TTTCCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA-
* *
520 AAATCCATAAATCCATTGTGGCTGAGAGATTTGATTAGATGAATATATATATTTCGAGAAGTCTT
517 GAATCCATAAATCCATTGTGGCT-AGAGATTTGATTAGATGAATATATATATTTCGAGAAGTTTT
** * *
585 AGTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACGGTGAT
581 TCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAAC--TGAT
* *
650 GGTTAGTACACGATTTTGGCT
644 GGTTAGTACACGATTTCGGAT
* *
671 AAAATTTAGCAAAAAACTGACCCGAAAA-AGTATTTCTCCAATTTTTTGCCACAATACTCAGAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGA-T-TTTCCCCAATTTTTTGCCACAATACTCAGAAA
* **
735 AATCATATAATTCTACGCCCAAAAA-ATTTTAATGTTTTTCACGCTTCTAATATCGTTTTTCCAT
64 AATCATATAATTCAACG-CCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-
* * * ** * *
799 TTTTTTTCC-GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGGTCGTAAAAACAAATCT
127 TTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCT
* *
863 GTAAATCCAACGTGGCTGAGATTTGGTTAGATGAAAACAGATATTTCGAAGAGACTTTCA-GCCA
192 GTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTT-ATGCCA
* * * *
927 AAAATAATGCAAAACTGAGTCTGGCCCCGAAACGCGATTTCAGCCAAAAACCGTCATGGTTAGTA
256 AAAATCATGCAAAACTGAGTCAGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTA
**
992 CAAAATTTCGGATAAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTTGCCAC
321 CACGATTTCGGATAAAATTTTGCAAAAAACTGA-CCGAAAAGATTTTCCCCAA-TTTTTTGCCAC
* *
1057 AATACTCTGAAAAATCATATAATTTAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATAT
384 AATACTCAGAAAAATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATAT
* *
1122 CGTTTTTCCATTTTCTGCCATAATACATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAA
449 CGTTTTTCCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAA
* * * * *
1187 AAATGAATCCGTAAATCCATTGTGGCTGAGAAATTTGATTAGATAAATATAGATATTTCGAGGAG
514 AAA-GAATCCATAAATCCATTGTGGCT-AGAGATTTGATTAGATGAATATATATATTTCGAGAAG
* * *
1252 TTTTTCTGCCGAAAATCATGCAAAATTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACCG
577 TTTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACTG
1317 -T-G--A-T-CACGATTTCGGAT
642 ATGGTTAGTACACGATTTCGGAT
*
1334 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCACTTTTTTGCCACAATACTCAGAAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
** *
1399 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTT
66 TCATATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* * *
1464 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAATAAATCGGTAA
131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCTGTAA
* * *
1529 ATTCAACGTGGCTAAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCGAAAAT
196 ATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCAAAAAT
*
1594 CATGCAAAACTTAGTCATGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
261 CATGCAAAACTGAGTCA-GGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
*
1659 ATTTCGGATAAAATTTTGCAAAAAACTGAGCCGAAAAGATTTTCCCCAATTTTTTGCCAAAATAC
325 ATTTCGGATAAAATTTTGCAAAAAACTGA-CCGAAAAGATTTTCCCCAATTTTTTGCCACAATAC
* * * *
1724 GCAGAAAAATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGTTTATAATATCGTTC
389 TCAGAAAAATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTT
* *
1789 TTCCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACA
454 TTCCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAGA
** ** * * *
1854 ACTCTGTAAATCCAACGTGGCT-GAGATTTGGTTAGATGAATACATATATTTCGAGGAGTTTTTC
519 A-TCCATAAATCCATTGTGGCTAGAGATTTGATTAGATGAATATATATATTTCGAGAAGTTTTTC
1918 TGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACGTGATGGT
583 TGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAAC-TGATGGT
*
1983 TAGTATACGATTTCGGAT
647 TAGTACACGATTTCGGAT
* * * *
2001 AAAATTATGCAAAAAACTGACCTGAAAAGATTTTCCCCAATTTTTTGCCAAAATACACAGAAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
** *
2066 TCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTCTTCCATTTT
66 TCATATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* * *
2131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAATAAATCCGTAA
131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCTGTAA
*
2196 ATTCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCAAAAAT
196 ATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCAAAAAT
* *
2261 CATGCAAAACTTAGTCAGCACCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
261 CATGCAAAACTGAGTCAG-GCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACG
* * *
2326 ATTTCGGATAAAATTTTGCAAAAAACTGACCTGAAATGATTTTTCCCAATTTTTTGCCACAATTC
325 ATTTCGGATAAAATTTTGCAAAAAACTGACC-GAAAAGATTTTCCCCAATTTTTTGCCACAATAC
2391 TCAGAAAAATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTT
389 TCAGAAAAATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTT
* * *
2456 TTCCATTTTCTACCATAATACATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAATG
454 TTCCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA-G
* * *
2521 AATCAATAAATCCATGGTGGCTGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTTTTT
518 AATCCATAAATCCATTGTGGCT-AGAGATTTGATTAGATGAATATATATATTTCGAGAAGTTTTT
* * * * *
2586 CTGCCAAAAATCATGCAAAACT--G--A--G--CC--AA----TTAT-A--TAGATA-T-TTGGT
582 CTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACTGATGGT
* *
2632 TAGTACACGATTTCAGCT
647 TAGTACACGATTTCGGAT
* * * *
2650 AAAATTTTGCAAAAATCTGACCCGAAAAGTTTTTCCCCAATTTTTTGCCACAGTACTCAGTAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
* * ** *
2715 TCATATAATTCAACGCCAAAAGTATTATAGAATTTTTCACACTTCTAATATCGTTTTTCCATTTT
66 TCATATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
* *
2780 CTGCCACAATACATTTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTGTAA
131 CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCTGTAA
* * * *
2845 ATCCAACGTGGCTGAAATTTGGTTAGATGAATACAGATATTTCGAGGAGTCTTTCTGCTAAAAAT
196 ATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCAAAAAT
* * *
2910 CATGCAAAACTGAGTCAGAACCTCGAAACGCGTTTTCAG-CAAAAAGCTGTGATGGTTAGTACAC
261 CATGCAAAACTGAGTCAG-GCCCCGAAACGCGTTTTCAGCCAAAAA-CCGTGATGGTTAGTACAC
* *
2974 GATTTCGGCTAAAATTTTGCAAAAAACTGACCGGAAAAGTTTTTCCCCAATTTTTTGCCACAATA
324 GATTTCGGATAAAATTTTGCAAAAAACTGACC-GAAAAGATTTTCCCCAATTTTTTGCCACAATA
* *
3039 CTCAGAAAAATCATATAATTCAATTCCAAAAATATTTAAGGGCTTTTCACGCTTCTAATATCGTT
388 CTCAGAAAAATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTT
* * *
3104 TTTCCATTTTCCGCAACAATACATTTCTAATTAAATCGAAACAAGATTTAGATACTCGT---AA-
453 TTTCCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAG
* * *
3165 AA---ATAAATCAATTGTGGCTAAGAGATTTGATTATATGAATAT-TGATATTTCGAGAAGTCTT
518 AATCCATAAATCCATTGTGGCT-AGAGATTTGATTAGATGAATATAT-ATATTTCGAGAAGTTTT
* * * * *
3226 TCTGCCAAAAATCATGCAAAACT--G--A--G--CC--AA----TTAT-A--TAGATA-T-TTGG
581 TCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACTGATGG
* *
3272 TTAGTACATGATTTCGGCT
646 TTAGTACACGATTTCGGAT
** * *
3291 AAAATTTTGCAAAAAACTGACCCGAAAATTTTTTTCCCCAATTTTTTGCAACAATACTCATAAAA
1 AAAATTTTGCAAAAAACTGACCCGAAAA-GATTTTCCCCAATTTTTTGCCACAATACTCAGAAAA
* * * * ** * *
3356 TTCATATAATTCAACGACAAAAACAATGAAGGGTTTTTCGCGTTTCTAATATCGTTTTTCCATTT
65 ATCATATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT
** ** ** *
3421 T-TTTCTGAATTTATTTCTAATTAAATCGAAATAAGATTCAAAT
130 TCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAAT
3464 ACCAGTAACA
Statistics
Matches: 2522, Mismatches: 245, Indels: 81
0.89 0.09 0.03
Matches are distributed among these distances:
641 175 0.07
642 85 0.03
644 2 0.00
646 2 0.00
648 6 0.00
649 481 0.19
650 1 0.00
652 3 0.00
654 1 0.00
655 3 0.00
659 2 0.00
660 92 0.04
661 20 0.01
662 354 0.14
663 132 0.05
664 2 0.00
665 3 0.00
666 4 0.00
667 522 0.21
668 3 0.00
669 60 0.02
670 114 0.05
671 444 0.18
672 11 0.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (664 bp):
AAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTCAGAAAAA
TCATATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTT
CTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCTGTAA
ATCCAACGTGGCTGAGATTTGGTTAGATGAATACAGATATTTCGAAGAGTCTTTATGCCAAAAAT
CATGCAAAACTGAGTCAGGCCCCGAAACGCGTTTTCAGCCAAAAACCGTGATGGTTAGTACACGA
TTTCGGATAAAATTTTGCAAAAAACTGACCGAAAAGATTTTCCCCAATTTTTTGCCACAATACTC
AGAAAAATCATATAATTCAATTCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCGTTTTT
CCATTTTCTGCCACAATACATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAAGAAT
CCATAAATCCATTGTGGCTAGAGATTTGATTAGATGAATATATATATTTCGAGAAGTTTTTCTGC
CAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCGTTTTCAGCCAAAAACTGATGGTTAGT
ACACGATTTCGGAT
Found at i:3622 original size:48 final size:47
Alignment explanation
Indices: 3532--3640 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 47
3522 TAAGCCATTC
** * * *
3532 CATTTTTGGCACCTAAAAGTCGTGATAGATAGTCTTTGGATTTTAAGT
1 CATTTTTGGCACC-AAAAGTCACGACAGATAGCCTTTAGATTTTAAGT
* *
3580 CATTTTTGGCACACAAAAGTCACGACAGTTAGCCTTTAGATTTTATGT
1 CATTTTTGGCAC-CAAAAGTCACGACAGATAGCCTTTAGATTTTAAGT
*
3628 CATTTTTAGCACC
1 CATTTTTGGCACC
3641 TCAAAAGTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
47 1 0.02
48 50 0.96
49 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (47 bp):
CATTTTTGGCACCAAAAGTCACGACAGATAGCCTTTAGATTTTAAGT
Found at i:5301 original size:21 final size:21
Alignment explanation
Indices: 5277--5336 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 21
5267 ATAAACATTG
5277 AACTTGCCTTGATTCACATCC
1 AACTTGCCTTGATTCACATCC
* * * **
5298 AACTTTACC--AATTGACATTG
1 AAC-TTGCCTTGATTCACATCC
5318 AACTTGCCTTGATTCACAT
1 AACTTGCCTTGATTCACAT
5337 TCAAATTTTC
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
19 4 0.14
20 10 0.36
21 10 0.36
22 4 0.14
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (21 bp):
AACTTGCCTTGATTCACATCC
Found at i:5408 original size:81 final size:82
Alignment explanation
Indices: 5247--5577 Score: 435
Period size: 81 Copynumber: 4.1 Consensus size: 82
5237 TACGCGGCAC
* * * * *
5247 ATTCACATTTAACTTTCCCAATAAACATTGAACTTGCCTTGATTCACATCCAACTTTACCAATTG
1 ATTCACATTCAAATTTCCCAATTAACATTGAACTTGCCTTCATTCACATCCAACTTTCCCAATTG
5312 ACATTGAACTTGCCTTG
66 ACATTGAACTTGCCTTG
* * *
5329 ATTCACATTCAAATTTTCCAATTAACATTGAACTTGCCTT-ATTCACATCTGAA-TTTTCCAATT
1 ATTCACATTCAAATTTCCCAATTAACATTGAACTTGCCTTCATTCACATC-CAACTTTCCCAATT
*
5392 GACATTGAACTAGCCTTG
65 GACATTGAACTTGCCTTG
* * *
5410 ATTCACATCCAAATTTTCCAATCAACATTGAACTTGCCTT-ATTCACATCCAACTTTCCCTAA-T
1 ATTCACATTCAAATTTCCCAATTAACATTGAACTTGCCTTCATTCACATCCAACTTTCCC-AATT
5473 GACATTGAACTTGCCTT-
65 GACATTGAACTTGCCTTG
* * * *
5490 ATTCACATTC-AA--TCCCAAATGACATTGAACTTGCCTTCATTCACATTCAAATTTCCCAATTG
1 ATTCACATTCAAATTTCCCAATTAACATTGAACTTGCCTTCATTCACATCCAACTTTCCCAATTG
*
5552 ACATTGAACTTGCCTTA
66 ACATTGAACTTGCCTTG
5569 ATTCACATT
1 ATTCACATT
5578 GGCCCTCAAT
Statistics
Matches: 224, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
77 23 0.10
78 35 0.16
79 11 0.05
80 11 0.05
81 104 0.46
82 40 0.18
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.36
Consensus pattern (82 bp):
ATTCACATTCAAATTTCCCAATTAACATTGAACTTGCCTTCATTCACATCCAACTTTCCCAATTG
ACATTGAACTTGCCTTG
Found at i:5463 original size:20 final size:20
Alignment explanation
Indices: 5440--5497 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
5430 ATCAACATTG
5440 AACTTGCCTTATTCACATCC
1 AACTTGCCTTATTCACATCC
* * * * **
5460 AACTTTCCCTAATGACATTG
1 AACTTGCCTTATTCACATCC
5480 AACTTGCCTTATTCACAT
1 AACTTGCCTTATTCACAT
5498 TCAATCCCAA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.29, G:0.07, T:0.36
Consensus pattern (20 bp):
AACTTGCCTTATTCACATCC
Found at i:5577 original size:41 final size:40
Alignment explanation
Indices: 5247--5577 Score: 393
Period size: 41 Copynumber: 8.2 Consensus size: 40
5237 TACGCGGCAC
* * **
5247 ATTCACATTTAACTTTCCCAATAAACATTGAACTTGCCTT
1 ATTCACATTCAAATTTCCCAATTGACATTGAACTTGCCTT
* * *
5287 GATTCACATCCAACTTTACCAATTGACATTGAACTTGCCTT
1 -ATTCACATTCAAATTTCCCAATTGACATTGAACTTGCCTT
* *
5328 GATTCACATTCAAATTTTCCAATTAACATTGAACTTGCCTT
1 -ATTCACATTCAAATTTCCCAATTGACATTGAACTTGCCTT
* * *
5369 ATTCACA-TCTGAATTTTCCAATTGACATTGAACTAGCCTT
1 ATTCACATTC-AAATTTCCCAATTGACATTGAACTTGCCTT
* * **
5409 GATTCACATCCAAATTTTCCAATCAACATTGAACTTGCCTT
1 -ATTCACATTCAAATTTCCCAATTGACATTGAACTTGCCTT
* *
5450 ATTCACATCCAACTTTCCCTAA-TGACATTGAACTTGCCTT
1 ATTCACATTCAAATTTCCC-AATTGACATTGAACTTGCCTT
*
5490 ATTCACATTC-AA--TCCCAAATGACATTGAACTTGCCTT
1 ATTCACATTCAAATTTCCCAATTGACATTGAACTTGCCTT
5527 CATTCACATTCAAATTTCCCAATTGACATTGAACTTGCCTT
1 -ATTCACATTCAAATTTCCCAATTGACATTGAACTTGCCTT
5568 AATTCACATT
1 -ATTCACATT
5578 GGCCCTCAAT
Statistics
Matches: 256, Mismatches: 25, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
36 2 0.01
37 22 0.09
38 10 0.04
39 5 0.02
40 76 0.30
41 140 0.55
42 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.36
Consensus pattern (40 bp):
ATTCACATTCAAATTTCCCAATTGACATTGAACTTGCCTT
Done.