Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010319.1 Corchorus capsularis cultivar CVL-1 contig10340, 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: 194590
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1135 original size:296 final size:303
Alignment explanation
Indices: 250--1157 Score: 1248
Period size: 302 Copynumber: 3.0 Consensus size: 303
240 CAGATGCACG
* *
250 TAAAAACAAATCCATAAATCCATTCTGGCTGAGATTTAGTTAGATGAAAATAGATATTTCAAGGA
1 TAAAAAAAAATACATAAATCCATTCTGGCTGAGATTTAGTTAGATGAAAATAGATATTTCAAGGA
* *
315 GTCTTTCTGCCAAAAATCTTG-AAAACTGAGCCGGGGCCCCGGAATGCGTTTTTAGCCCAAAAAT
66 GTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCCAAAAAT
*
379 CGTGATGGTTAGTACACGATTTAGGAAAAAAATTGACCCGAATTTTTTTTTGAAATTTTTTCCAT
131 CG-GAT-G-TAGTACACGATTTAGGAAAAAAATTGACCCGAATTTTTTTTAGAAA-TTTTTCCAT
* *
444 AATACTC--AAAAAATATATAACTCAATGCCAGAACATTGACGGGCTTTTCACTCTTCTAATATC
192 AATACTCAGAAAAAATATATAATTCAATGCCAAAACATTGACGGGCTTTTCACTCTTCTAATATC
507 ATTTTTCCAATTTTTTTTCGAATTTATTTCTAATTAAATTGAAACAAGATTCAGATGCAC
257 ATTTTTCC-A-TTTTTTTCGAATTTATTTC----T-AA-T-AAACAAGATTC--A--CAC
* * *
567 GTTAAAAAAAAATCCATAAAGCCATTATGGCTGAGATTTAGTTAGATGAAAATAGATATTTCAAG
1 --TAAAAAAAAATACATAAATCCATTCTGGCTGAGATTTAGTTAGATGAAAATAGATATTTCAAG
632 GAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCCAAAA
64 GAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCCAAAA
*
697 ATCGTGATTGTTAGTACACGATTTAGGAAAAAAATTGACCCAAAATTTTTTTTAGAAATTGTTTC
129 ATCG-GA-TG-TAGTACACGATTTAGGAAAAAAATTGACCC-GAATTTTTTTTAGAAATT-TTTC
* *
762 CATAATACTCAGAAAAAATATATAATTCAATGCCAAAAGATTGACGGGCTTTTCACTCATCTAAT
189 CATAATACTCAGAAAAAATATATAATTCAATGCCAAAACATTGACGGGCTTTTCACTCTTCTAAT
827 ATCATTTTTCCATTTTTTTCGAATTTATTTCTAA-AAACAA-A-TC-CA-
254 ATCATTTTTCCATTTTTTTCGAATTTATTTCTAATAAACAAGATTCACAC
* * * *
872 T-AAAAATAATACATAAATCCATTCTGGCTGAGATTTGGTTATATGAAAATAGATATTTCAATGA
1 TAAAAAAAAATACATAAATCCATTCTGGCTGAGATTTAGTTAGATGAAAATAGATATTTCAAGGA
* * *
936 GTCTTTCTGCCAAAAATCATGCAAAACTAAGCTGGGGCGCCGGAACGCGTTTTTAGCCCAAAAAT
66 GTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCCAAAAAT
* * *
1001 C-G-TG-A-CACACGATTTTGGAAAAAAAAAATTGACCCGAATTTTTTTTAGAAAATTTTCCATA
131 CGGATGTAGTACACGATTTAGG---AAAAAAATTGACCCGAATTTTTTTTAGAAATTTTTCCATA
* * *
1062 ATACTCAGAAAAAATATATAATTTAATGCCAAAATATTGACGGGATTTTCACTCTTCTAATATCA
193 ATACTCAGAAAAAATATATAATTCAATGCCAAAACATTGACGGGCTTTTCACTCTTCTAATATCA
1127 TTTTTCCATTTTTTTCGAATTTATTTCTAAT
258 TTTTTCCATTTTTTTCGAATTTATTTCTAAT
1158 TAAATCGAGA
Statistics
Matches: 550, Mismatches: 29, Indels: 42
0.89 0.05 0.07
Matches are distributed among these distances:
295 11 0.02
296 100 0.18
297 16 0.03
298 16 0.03
300 1 0.00
302 119 0.22
303 1 0.00
306 2 0.00
311 2 0.00
312 1 0.00
313 6 0.01
316 2 0.00
317 1 0.00
319 82 0.15
320 81 0.15
321 48 0.09
322 1 0.00
323 60 0.11
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (303 bp):
TAAAAAAAAATACATAAATCCATTCTGGCTGAGATTTAGTTAGATGAAAATAGATATTTCAAGGA
GTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCCAAAAAT
CGGATGTAGTACACGATTTAGGAAAAAAATTGACCCGAATTTTTTTTAGAAATTTTTCCATAATA
CTCAGAAAAAATATATAATTCAATGCCAAAACATTGACGGGCTTTTCACTCTTCTAATATCATTT
TTCCATTTTTTTCGAATTTATTTCTAATAAACAAGATTCACAC
Found at i:4364 original size:650 final size:640
Alignment explanation
Indices: 1518--4745 Score: 3384
Period size: 650 Copynumber: 5.0 Consensus size: 640
1508 CTGAGATTTG
* * * * * *
1518 GTTTTTAGACCAAAAACCGTGATGGTCAGTACACGATTACGACTAAAAATTGACCCGAATTTTTT
1 GTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTT
* * * * *
1583 TTTA-AAATCTTT-TCTACAATACGCAAAAAAAATATGTAATTCAATGCCAAAAATATTCACAGG
66 TTTAGAAATTTTTGTC-ACAATACTCAAAAAAAATATATAATTCAATGCCAAAAAGATTGAC-GG
* * * * *
1646 G-TTTTCACACTTCTAATAT--TTTTTCCATTTTTTTTCAAATTAATTTTTAATTAAATTGAGAC
129 GCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAGAC
1708 AAGATTCAGATGCTCGTAAAAACAAATCCTTATAT-CAATTGTGGCTGAGATTTGGTTCGATGAA
194 AAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAA-TGTGGCTGAGATTTGGTTCGATGAA
* * * * * * * *
1772 AATAAATATTTCAAGGAGTCATTGCGCCAAATATCATGCAAAATTGAGCCGGTTACCC-GAAATG
258 TATAGATATTTCAAGGAGTCTTTGCACCAAAAATTATGCAAAATTGAGCCGG-TGCCCAG-AACG
* * *
1836 CGTTTTTAGC----AAAAAACAGTGATTTCGGCTAAAATTTTGCAAAAACCGAACCGAAAATTTT
321 CGTTTTTAGCAAAAAAAAAACCGTGATTTCGGCTAAAATTTTGCAAAAACTGAACCGAAAAATTT
** * ** * *
1897 TTCCTC-AATTTTTCT-CCATAATTTTC-GGAAAAATATATAATAAAATGAAAAAAAAATTGAAG
386 TTCCTCAAATTTTT-TGCCATAATAGTCAGAAAAAATATATAATTCAACG-CAAAAAAATTGAAG
* * *
1959 TGTTTTTCATGTTTCTAATATCAGTTTTCCATTTTTTCCAAATTTATTTCTAATTAAATCGAAAC
449 -GTTTTTCACGTTTCTAATATCATTTTTCCATTTTTT-CGAATTTATTTCTAATTAAATCGAAAC
* * * *
2024 AAGATTCAGATACTCGTAAAAACAAATCCATAAATCCATTGTGGCTCAGATTTGGTTAGATGATA
512 AAGATTCAGATGCTCGTAAAAACAAATCCATAAATCCAATGTGGCTAAGATTTGGTTAGATGAAA
* * *
2089 ATAGATATTTCAAGGAGTCTTTCTGCCAAAAATTATACAAAACTGAGCCGGGG-CCTCGGAACGC
577 ATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATACAAAACTGAGCGGGGGCCCT-GAAACGC
** * *
2153 GTTTTT-GCCCAAAAATTGTGATGGTTAATACATGATTTCGG-TAAAAAACTGACCCG--ATTTT
1 GTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT-AAAAACTGACCCGAAATTTT
* * *
2214 TTTTTGAAATTTTT-TCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAATGATTGACGG
65 TTTTAGAAATTTTTGT-CACAATACTCAAAAAAAATATATAATTCAATGCCAAAAAGATTGACGG
*
2278 GCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTT-CGAATTTATTTCTAATTAAATCGAGAC
129 GCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAGAC
* * ** *
2342 AAGATTCAGATGCTCGTAAAAAAAAAATCCTTATGTAAAATGTGGCTGAGATTTGCTTCG-TAGA
194 AAGATTCAGATGCTCGT-AAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGAT-GA
* ** * *
2406 ATACAGATATTTCAAAAAGTCTATGCACC-AAATTTCATGCAAAATTGAGCCGGTGCCTCAGAAC
257 ATATAGATATTTCAAGGAGTCTTTGCACCAAAAATT-ATGCAAAATTGAGCCGGTGCC-CAGAAC
* *
2470 GCGTTTTTTAGAGAAAGAAAAAAAAACCGTGATGGTTAGTACATTATTTCGGATAAAATTTTGAA
320 GCG-TTTTT--AG-CA-AAAAAAAAACC------G-T-G------ATTTCGGCTAAAATTTTG--
* * * * * *
2535 AAAAAAAATTATCTGAAAAATATTTT-CTCATATTTTTTGCAGCCATAATAGTCAGAAAAAATAT
364 -CAAAAACTGAACCGAAAAAT-TTTTCCTCAAATTTTTT---GCCATAATAGTCAGAAAAAATAT
* * * *
2599 ATAATTCAACTCAAAAAAATTGAAAGGTTTTTTACGCTTT-TAATATCGTTTTTCTAATTTTTTT
424 ATAATTCAACGCAAAAAAATTG-AAGGTTTTTCACG-TTTCTAATATCATTTTTC-CA--TTTTT
** * ** * *
2663 TCGAACGTATTTCTAATTAAATCGTAACAAGATTCAGATATTCGTAAAAACAAATCTATAATTCC
484 TCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCATAAATCC
* * * * *
2728 AATGTGGCTGAGATTTGGTTAGATAAAAATAGATATTTCAAGGAGACTTTCAGCCAAAAAATTCT
549 AATGTGGCTAAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCTTTCTGCC-AAAAA-TCA
* *
2793 TACAAAACTGAGCGGGTGTCCC-GGAACGC
612 TACAAAACTGAGCGGG-GGCCCTGAAACGC
* * * * **
2822 GTTTTTAGCCCAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAAACTGGCCGGATTTTTTT
1 GTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGA-AATTTT
* * * * *
2887 TTTTTGAAATTTTTGCCACAATAGT-AAAAAAATATATATAATTCAATGCCAAAAAGATTGATGT
65 TTTTAGAAATTTTTGTCACAATACTCAAAAAAA-ATATATAATTCAATGCCAAAAAGATTGACGG
* * * *
2951 GCTTTTCACGATTCTAATACCATTTTTCCATTTTTTTCCAAAAATTAATTTCTAATTAAATCGAG
129 GCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCC--GAATTAATTTCTAATTAAATCGAG
* * *
3016 ACAAGATTCAGATGTTCGTAAAAACAAATACTTATATCCAATGTAGCTGAGATTTGGTTCGATGA
192 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGA
* * *
3081 ATATAGATATTTCAAGGAGTCTTTGCTCC-GAAATTCATGCAAAATTGAGTCGG-GTCCCAAGAA
257 ATATAGATATTTCAAGGAGTCTTTGCACCAAAAATT-ATGCAAAATTGAGCCGGTG-CCC-AGAA
** * * * *
3144 CATGTTTTTAGCAAAAACAGTGATGGTTAGTA-CATGATTTCGGTTAAAATTTTGCAAAAATTGA
319 CGCGTTTTTAGCAAAAA-A---A-----A-AACCGTGATTTCGGCTAAAATTTTGCAAAAACTGA
* * * *
3208 TCCGAAAAATTTTTCCTTAAATTTTTTGTCATAATAGTCA-AAAAAATTATATAATTCAACTCAA
374 ACCGAAAAATTTTTCCTCAAATTTTTTGCCATAATAGTCAGAAAAAA-TATATAATTCAACGC-A
* * * *
3272 AAAAAATTGAAGGGTTTTTTA-GCTTCTAATATCGTTTTTCCTTTTTTTTTCCGAATTTATTTCT
437 AAAAAATTGAA-GGTTTTTCACGTTTCTAATATCATTTTTCC--ATTTTTT-CGAATTTATTTCT
* * *
3336 AATTAATTCGAAACAAGAATCAGATGCTTGTAAAAACAAATCCATAAATCCAATGTGGCTAAGAT
498 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCATAAATCCAATGTGGCTAAGAT
* * * * * *
3401 TTGGTTAGATGAAAAAATATATTTTAAGGAGTTTTTCTGCCAAAAATCATGCAAAACTGAGCCGA
563 TTGGTTAGATGAAAATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATACAAAACTGAG-CGG
* *
3466 GGGCCCCGAAACAC
627 GGGCCCTGAAACGC
* *
3480 GTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAGCTGACCCGAAAATAAA
1 GTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCG-AAAT---
* ** * * * * ** * *
3545 ATTTTACAAAAAATTTTGCCATAATACTCTGAAAAAATATATAATTCAAAGCCAAAAAAAATTGA
62 TTTTTTTAGAAATTTTTGTCACAATACTCAAAAAAAATATATAATTCAATGCC-AAAAAGATTGA
* * * * *
3610 CAGGCTTTTCACACTTCTAATATCGCTTTTCCTTTTTTTTCGGAATTAATTTCTAATTAAATCGA
126 CGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * **
3675 GACAAGATTCAGATGTTCGTAAAAACAAATCCTTATATCCAATTTGGCTGAGATTTGGTTTTATG
191 GACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATG
* *
3740 AATATAGATATTTTAAGGAGTCTTTGCACCAAAAATTATGC-AAATCTGAGCCGGTGCCCTGTAA
256 AATATAGATATTTCAAGGAGTCTTTGCACCAAAAATTATGCAAAAT-TGAGCCGGTGCCCAG-AA
* * * *
3804 CACGTTTTTA-CAAAAAAAAAACCGTGATTTCGGCAAAAAGTTTTTCAAAAACTGAACTGAAAAA
319 CGCGTTTTTAGCAAAAAAAAAACCGTGATTTCGGCTAAAA-TTTTGCAAAAACTGAACCGAAAAA
*
3868 TTCTTT-CTCAAATTTTTTGCCACAATAGTCAGAAAAGAAATATATAATTCAACGCAAAAAAATT
383 TT-TTTCCTCAAATTTTTTGCCATAATAGTCAG-AAA-AAATATATAATTCAACGCAAAAAAATT
*
3932 GAAGGATTTTTCACGCTTCTAATCTAATATTATTTTTCCATTTTTTCGAATTTATTTCTAATTAA
445 GAAGG-TTTTTCACG--T-T--TCTAATATCATTTTTCCATTTTTTCGAATTTATTTCTAATTAA
* * * *
3997 ATCGAAACAAGATTCATATGCTCGTAAAAA-AAATCCATAAATCTAATATGGCTAAAATTTGGTT
504 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCATAAATCCAATGTGGCTAAGATTTGGTT
* *
4061 AGATGAAAATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC-AAACTCAGCGGGGGCCCT
569 AGATGAAAATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATACAAAACTGAGCGGGGGCCCT
*
4125 GAAACGT
634 GAAACGC
* **
4132 GTTTTTAGCCCAAAAACCGTGATGGTTAGTACACAATTTTCGGCTAAAAACTGACCCGAAAAATT
1 GTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGA-TTTCGGCTAAAAACTGACCCGAAATTTT
* * * * *
4197 TTTCAGAAATTTTTGTCACAATACTAAAAAAATATATATATAATTCAATGTCAAAAAGATTTATG
65 TTTTAGAAATTTTTGTCACAATACTCAAAAAA-A-ATATATAATTCAATGCCAAAAAGATTGACG
*** * *
4262 GGCTTTTTGTGCTGCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATTGAGA
128 GGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAGA
* *
4327 CAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAAATTTAGTTCGATGAA
193 CAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAA
* ** ** *
4392 TATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATTTAAAATTGAGTTGGTGCCCCGGAACGC
258 TATAGATATTTCAAGGAGTCTTTGCACCAAAAATTATGCAAAATTGAGCCGGTG-CCCAGAACGC
* * * * *
4457 GTTTTTAGCAAAAAAAAAACTGTGATTTCGGTTAAAATTTGGTAAAAACTGAACCGAAAAGTTTT
322 GTTTTTAGCAAAAAAAAAACCGTGATTTCGGCTAAAATTTTGCAAAAACTGAACCGAAAAATTTT
* * * *
4522 TCCTTAATTTTTTTGCCACAATAGTCAGAAAAAATATATAATT-AACACCAAAAAAATTGAAGGG
387 TCCTCAAATTTTTTGCCATAATAGTCAGAAAAAATATATAATTCAAC-GCAAAAAAATTGAA-GG
* *
4586 TTTTTCACGATTCTAATATC-GTTTTCCATATTTTTTCGAATTTATTTCTAATTAAATCGAAACA
450 TTTTTCACGTTTCTAATATCATTTTTCC--ATTTTTTCGAATTTATTTCTAATTAAATCGAAACA
* * * * * *
4650 AGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAAATGAATA
513 AGATTCAGATGCTCGTAAAAACAAATCCATAAATCCAATGTGGCTAAGATTTGGTTAGATGAAAA
* * *
4715 TAGATATTTCAAGGAGTTTTTATGCAAAAAA
578 TAGATATTTCAAGGAGTCTTTCTGCCAAAAA
4746 AAATCATGAT
Statistics
Matches: 2173, Mismatches: 298, Indels: 234
0.80 0.11 0.09
Matches are distributed among these distances:
632 11 0.01
633 65 0.03
634 87 0.04
635 102 0.05
636 8 0.00
638 2 0.00
642 6 0.00
643 8 0.00
644 61 0.03
645 64 0.03
647 3 0.00
648 34 0.02
649 36 0.02
650 240 0.11
651 96 0.04
652 73 0.03
653 44 0.02
654 76 0.03
655 46 0.02
656 7 0.00
657 17 0.01
658 112 0.05
659 157 0.07
660 154 0.07
661 63 0.03
662 83 0.04
665 56 0.03
666 23 0.01
667 106 0.05
668 11 0.01
669 29 0.01
670 47 0.02
671 6 0.00
672 9 0.00
673 88 0.04
674 9 0.00
675 90 0.04
676 41 0.02
679 2 0.00
680 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (640 bp):
GTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATTTTT
TTTAGAAATTTTTGTCACAATACTCAAAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGC
TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAGACAA
GATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATAT
AGATATTTCAAGGAGTCTTTGCACCAAAAATTATGCAAAATTGAGCCGGTGCCCAGAACGCGTTT
TTAGCAAAAAAAAAACCGTGATTTCGGCTAAAATTTTGCAAAAACTGAACCGAAAAATTTTTCCT
CAAATTTTTTGCCATAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAATTGAAGGTTTTTC
ACGTTTCTAATATCATTTTTCCATTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAG
ATGCTCGTAAAAACAAATCCATAAATCCAATGTGGCTAAGATTTGGTTAGATGAAAATAGATATT
TCAAGGAGTCTTTCTGCCAAAAATCATACAAAACTGAGCGGGGGCCCTGAAACGC
Found at i:9408 original size:4 final size:4
Alignment explanation
Indices: 9401--9446 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
9391 CAAAAAAAAA
* *
9401 AAAC AAAC CAAC AAAC CAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
9447 CAACAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:21510 original size:26 final size:26
Alignment explanation
Indices: 21481--21530 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
21471 TGTATTGGAA
*
21481 GGTGACGAATAAAAATGACA-ATAATT
1 GGTGACAAATAAAAA-GACACATAATT
*
21507 GGTGACAAATATAAAGACACATAA
1 GGTGACAAATAAAAAGACACATAA
21531 GGAGTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.52, C:0.10, G:0.18, T:0.20
Consensus pattern (26 bp):
GGTGACAAATAAAAAGACACATAATT
Found at i:25319 original size:2 final size:2
Alignment explanation
Indices: 25312--25337 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25302 AATGTTCTTT
25312 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
25338 GTTGATTTGC
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):
TA
Found at i:27918 original size:11 final size:11
Alignment explanation
Indices: 27872--27912 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
27862 CCCTTTCCTA
*
27872 TATAAAATAAT
1 TATAAATTAAT
27883 TATCAAA-TAAT
1 TAT-AAATTAAT
27894 TATAAATTAAT
1 TATAAATTAAT
27905 TATAAATT
1 TATAAATT
27913 TGTTATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.11
11 22 0.79
12 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:34946 original size:29 final size:29
Alignment explanation
Indices: 34904--34963 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
34894 CGATACGAAG
34904 GAAAGGTGGGAAAGGAAAGCCAACATGTA
1 GAAAGGTGGGAAAGGAAAGCCAACATGTA
34933 GAAAGGTGGGAAAGGAAAGCCAACATGTA
1 GAAAGGTGGGAAAGGAAAGCCAACATGTA
34962 GA
1 GA
34964 TATTCGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.10, G:0.35, T:0.10
Consensus pattern (29 bp):
GAAAGGTGGGAAAGGAAAGCCAACATGTA
Found at i:36662 original size:1 final size:1
Alignment explanation
Indices: 36656--36685 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
36646 ATCCCTACTG
36656 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
36686 GAGAGAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:36884 original size:22 final size:22
Alignment explanation
Indices: 36856--36901 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
36846 TCCTTAAAGC
*
36856 ATCCAAGAATCAATGGAAAACT
1 ATCCAAGAATCAAAGGAAAACT
36878 ATCCAAGAATCAAAGGAAAACT
1 ATCCAAGAATCAAAGGAAAACT
36900 AT
1 AT
36902 GGGGTACAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.17
Consensus pattern (22 bp):
ATCCAAGAATCAAAGGAAAACT
Found at i:38398 original size:35 final size:35
Alignment explanation
Indices: 38352--38418 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
38342 CTGCAAATTT
38352 GATGTGTTTAATCAATAAGTAATCAATATTTTACA
1 GATGTGTTTAATCAATAAGTAATCAATATTTTACA
38387 GATGTGTTTAATCAATAAGTAATCAATATTTT
1 GATGTGTTTAATCAATAAGTAATCAATATTTT
38419 GCATGTCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (35 bp):
GATGTGTTTAATCAATAAGTAATCAATATTTTACA
Found at i:42618 original size:28 final size:29
Alignment explanation
Indices: 42564--42619 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
42554 TGTGTTGGTT
*
42564 AAATTGTTAAAGAAAAATTTCACCAAAAAA
1 AAATTGTTAAAG-AAAATTACACCAAAAAA
42594 AAATTGTTAAAG-AAATTACACCAAAA
1 AAATTGTTAAAGAAAATTACACCAAAA
42620 TAGAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 13 0.52
30 12 0.48
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.23
Consensus pattern (29 bp):
AAATTGTTAAAGAAAATTACACCAAAAAA
Found at i:46775 original size:2 final size:2
Alignment explanation
Indices: 46768--46817 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
46758 TGAAGCAATG
* *
46768 TA TA TA TA TA TA TA T- TA TA TA -A TT TC TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46807 TA TA TA TA TA T
1 TA TA TA TA TA T
46818 TCTTTTCGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57465 original size:13 final size:13
Alignment explanation
Indices: 57447--57478 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
57437 TCTTTCCTCT
*
57447 GCAAAAAGACAGA
1 GCAAAAAAACAGA
57460 GCAAAAAAACAGA
1 GCAAAAAAACAGA
57473 GCAAAA
1 GCAAAA
57479 CCTTCAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.16, G:0.19, T:0.00
Consensus pattern (13 bp):
GCAAAAAAACAGA
Found at i:65846 original size:31 final size:31
Alignment explanation
Indices: 65808--65867 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
65798 ATATGTTAGA
65808 TAAATAAGGATATAATT-GATGTTTCAAAAAT
1 TAAATAAGGATAT-ATTAGATGTTTCAAAAAT
* *
65839 TAAATAAGGGTATATTAGGTGTTTCAAAA
1 TAAATAAGGATATATTAGATGTTTCAAAA
65868 GTTTTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (31 bp):
TAAATAAGGATATATTAGATGTTTCAAAAAT
Found at i:71870 original size:33 final size:33
Alignment explanation
Indices: 71802--71870 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
71792 AAACTTAATT
* ** **
71802 ATAACCCTAAAATTAGTTTTTTTTTTGGCACAA
1 ATAACCCTAAAATTAGTTTCTTAATTAACACAA
71835 ATAACCCTAAAATTAGTTTACTTAATTAACA-AA
1 ATAACCCTAAAATTAGTTT-CTTAATTAACACAA
71868 ATA
1 ATA
71871 TATGTGGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 24 0.80
34 6 0.20
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (33 bp):
ATAACCCTAAAATTAGTTTCTTAATTAACACAA
Found at i:93786 original size:72 final size:72
Alignment explanation
Indices: 93609--93786 Score: 302
Period size: 72 Copynumber: 2.5 Consensus size: 72
93599 ATGCAAACAG
* *
93609 TGGCATTCCTATTATACATAATGGTATAGTAGTGTCAGTTAAAATTGAATAGTTTTGTACTTGGC
1 TGGCATTCCTATTATACATAATGGTATAGTGGTGTCAGTTAAAATTGAATACTTTTGTACTTGGC
*
93674 ACAGTGA
66 ACAATGA
*
93681 TGGCATTCCTATTATACATAATGGTATAGTGGTGTCAGTTAAAGTTGAATACTTTTGTACTTGGC
1 TGGCATTCCTATTATACATAATGGTATAGTGGTGTCAGTTAAAATTGAATACTTTTGTACTTGGC
93746 ACAATGA
66 ACAATGA
* *
93753 TGGCATTCCTATTATACATCATGGTATAATGGTG
1 TGGCATTCCTATTATACATAATGGTATAGTGGTG
93787 CTTCCAAATA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 100 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (72 bp):
TGGCATTCCTATTATACATAATGGTATAGTGGTGTCAGTTAAAATTGAATACTTTTGTACTTGGC
ACAATGA
Found at i:94007 original size:91 final size:91
Alignment explanation
Indices: 93898--94190 Score: 287
Period size: 91 Copynumber: 3.2 Consensus size: 91
93888 ATGAAAAACG
* *
93898 GTGGCATTCCTACTATACATAAAGGTATAGTGGTGTCAATTCAAATAAGATAAATGCATGGCATT
1 GTGGCATTCCTATTATACATAAAGGTATAGTGGTGTCAATTCAAATAAGATAGATGCATGGCATT
93963 CTTATTGAATGCTAAAAGGCACAATA
66 CTTATTGAATGCTAAAAGGCACAATA
* * * *
93989 GTGGCATTCCTATTATACATCAAGGTATAATGGTG-C-A-TCGAAATAA-A-AGTTGGTAATGGG
1 GTGGCATTCCTATTATACATAAAGGTATAGTGGTGTCAATTC-AAATAAGATAGAT-G-CAT-GG
* * **
94049 AATTCTTAAT--ATGCAGTAAAAGACGCA-AACG
62 CATTCTTATTGAATGC--TAAAAG--GCACAATA
* *
94080 GTGGCATTCCTATTATACATAAAGGTATAGTGGTGTCAATTCTAATAAGATACTTTGATACATGG
1 GTGGCATTCCTATTATACATAAAGGTATAGTGGTGTCAATTCAAATAAGATA----GATGCATGG
* *
94145 CATTCTTATTGAATGCTAAAGGGCACAATT
62 CATTCTTATTGAATGCTAAAAGGCACAATA
*
94175 GTGGCATTGCTATTAT
1 GTGGCATTCCTATTAT
94191 CATTTGATGA
Statistics
Matches: 160, Mismatches: 22, Indels: 36
0.73 0.10 0.17
Matches are distributed among these distances:
87 2 0.01
88 8 0.05
89 9 0.06
90 17 0.11
91 67 0.42
92 4 0.03
93 6 0.04
94 6 0.04
95 18 0.11
96 15 0.09
97 2 0.01
98 4 0.03
99 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (91 bp):
GTGGCATTCCTATTATACATAAAGGTATAGTGGTGTCAATTCAAATAAGATAGATGCATGGCATT
CTTATTGAATGCTAAAAGGCACAATA
Found at i:95412 original size:146 final size:146
Alignment explanation
Indices: 94951--95428 Score: 418
Period size: 146 Copynumber: 3.2 Consensus size: 146
94941 GAACATAGTT
94951 GCATTCCTATTATATACAT-AAGGTATAATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAG
1 GCATTCCTA-T-TATACATCAAGGTATAATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAG
* *
95015 ACGCAAACAGTGGCATTCCTATTATACATAATGGTATAGTGGTGTCAGTTAAAATTGAATACATT
64 ACGGAAACAATGGCATTCCTATTATACATAATGGTATAGTGGTGTCAGTTAAAATTGAATAC-TT
*
95080 TGTACTTGGCACAGTGATG
128 TGTACATGGCACAGTGATG
* * *
95099 GCATTCCTATTATACATCATGGTATAATGGTGCTTCCAAATAAAAGTTGG-TG-ACGGTAGTTCT
1 GCATTCCTATTATACATCAAGGTATAATGGTG----C-AATAAAAGTTGGTTGCA-GG-AATT-G
* * * * *
95162 TATTATG-CGGTAAAAAGCTCAATGGAGGCATTCCTATTAATACAGCAA-GTTCTTA-T--TGT-
58 TA-AAAGACGG---AAA---CAAT---GGCATTCCTATT-ATACA-TAATGGT-ATAGTGGTGTC
* ** * * *
95221 ATGCTAAAA--G-GCAC--AGT--A-GGAACA-T-AGTT
110 A-GTTAAAATTGAATACTTTGTACATGGCACAGTGA-TG
*
95250 GCATTCCTATTATACATTAAGGTATAATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAGAC
1 GCATTCCTATTATACATCAAGGTATAATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAGAC
95315 GGAAACAATGGCATTCCTATTATACATAATGGTATAGTGGTGTCAGTTAAAATTGAATACTTTGT
66 GGAAACAATGGCATTCCTATTATACATAATGGTATAGTGGTGTCAGTTAAAATTGAATACTTTGT
95380 ACATGGCACAGTGATG
131 ACATGGCACAGTGATG
*
95396 GCATTCCTATTATACATCATGGTATAATGGTGC
1 GCATTCCTATTATACATCAAGGTATAATGGTGC
95429 TTCCAAATAA
Statistics
Matches: 254, Mismatches: 34, Indels: 86
0.68 0.09 0.23
Matches are distributed among these distances:
134 4 0.02
135 8 0.03
136 12 0.05
137 9 0.04
138 1 0.00
139 5 0.02
140 2 0.01
142 5 0.02
144 3 0.01
145 10 0.04
146 55 0.22
147 20 0.08
148 10 0.04
150 2 0.01
151 37 0.15
152 20 0.08
153 4 0.02
154 2 0.01
155 2 0.01
156 3 0.01
158 2 0.01
159 4 0.02
160 1 0.00
161 9 0.04
162 12 0.05
163 8 0.03
164 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32
Consensus pattern (146 bp):
GCATTCCTATTATACATCAAGGTATAATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAGAC
GGAAACAATGGCATTCCTATTATACATAATGGTATAGTGGTGTCAGTTAAAATTGAATACTTTGT
ACATGGCACAGTGATG
Found at i:95483 original size:297 final size:299
Alignment explanation
Indices: 94912--95509 Score: 1094
Period size: 297 Copynumber: 2.0 Consensus size: 299
94902 ATAAATGGCA
*
94912 TTCTTATTGTATGCTATAAGGCACAGTAGGAACATAGTTGCATTCCTATTATATACATAAGGTAT
1 TTCTTATTGTATGCTAAAAGGCACAGTAGGAACATAGTTGCATTCCTATTATATACATAAGGTAT
*
94977 AATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAGACGCAAACAGTGGCATTCCTATTATAC
66 AATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAGACGCAAACAATGGCATTCCTATTATAC
*
95042 ATAATGGTATAGTGGTGTCAGTTAAAATTGAATACATTTGTACTTGGCACAGTGATGGCATTCCT
131 ATAATGGTATAGTGGTGTCAGTTAAAATTGAATACATTTGTACATGGCACAGTGATGGCATTCCT
* *
95107 ATTATACATCATGGTATAATGGTGCTTCCAAATAAAAGTTGGTGACGGTAGTTCTTATTATGCGG
196 ATTATACATCATGGTATAATGGTGCTTCCAAATAAAAGTTGGTGACGGTAGCTCTTATTATGCAG
95172 TAAAAAGCTCAATGGAGGCATTCCTATTAATACAGCAAG
261 TAAAAAGCTCAATGGAGGCATTCCTATTAATACAGCAAG
95211 TTCTTATTGTATGCTAAAAGGCACAGTAGGAACATAGTTGCATTCCTA-T-TATACATTAAGGTA
1 TTCTTATTGTATGCTAAAAGGCACAGTAGGAACATAGTTGCATTCCTATTATATACA-TAAGGTA
*
95274 TAATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAGACGGAAACAATGGCATTCCTATTATA
65 TAATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAGACGCAAACAATGGCATTCCTATTATA
95339 CATAATGGTATAGTGGTGTCAGTTAAAATTGAATAC-TTTGTACATGGCACAGTGATGGCATTCC
130 CATAATGGTATAGTGGTGTCAGTTAAAATTGAATACATTTGTACATGGCACAGTGATGGCATTCC
*
95403 TATTATACATCATGGTATAATGGTGCTTCCAAATAAAAGTTGGTGACTGTAGCTCTTATTATGCA
195 TATTATACATCATGGTATAATGGTGCTTCCAAATAAAAGTTGGTGACGGTAGCTCTTATTATGCA
*
95468 GTAAAAGGCTCAATGGAGGCATTCCTATTAATACAGCAAG
260 GTAAAAAGCTCAATGGAGGCATTCCTATTAATACAGCAAG
95508 TT
1 TT
95510 ATAATGGTGC
Statistics
Matches: 290, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
297 136 0.47
298 107 0.37
299 47 0.16
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (299 bp):
TTCTTATTGTATGCTAAAAGGCACAGTAGGAACATAGTTGCATTCCTATTATATACATAAGGTAT
AATGGTGCAATAAAAGTTGGTTGCAGGAATTGTAAAAGACGCAAACAATGGCATTCCTATTATAC
ATAATGGTATAGTGGTGTCAGTTAAAATTGAATACATTTGTACATGGCACAGTGATGGCATTCCT
ATTATACATCATGGTATAATGGTGCTTCCAAATAAAAGTTGGTGACGGTAGCTCTTATTATGCAG
TAAAAAGCTCAATGGAGGCATTCCTATTAATACAGCAAG
Found at i:102266 original size:17 final size:17
Alignment explanation
Indices: 102236--102268 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
102226 AATGATGACT
102236 AAAATATTTCCTCCCTG
1 AAAATATTTCCTCCCTG
102253 AAAA-ATTTCTCTCCCT
1 AAAATATTTC-CTCCCT
102269 TTTGAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.36
Consensus pattern (17 bp):
AAAATATTTCCTCCCTG
Found at i:105192 original size:20 final size:21
Alignment explanation
Indices: 105161--105201 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
105151 ACAAAGAAAC
105161 CTCACAATTCCGTGAGAGTAA
1 CTCACAATTCCGTGAGAGTAA
105182 CTCAC-ATTCCGTGAGAGTAA
1 CTCACAATTCCGTGAGAGTAA
105202 AACCCAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
CTCACAATTCCGTGAGAGTAA
Found at i:107296 original size:13 final size:13
Alignment explanation
Indices: 107275--107307 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
107265 TTTGCACCTG
*
107275 TTTTGTTTTGTTT
1 TTTTTTTTTGTTT
107288 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
107301 TTTTTTT
1 TTTTTTT
107308 CACTTTATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:119382 original size:2 final size:2
Alignment explanation
Indices: 119375--119400 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
119365 CGTTATATGC
119375 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
119401 GACGCTTTTT
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
Found at i:147278 original size:17 final size:17
Alignment explanation
Indices: 147230--147279 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
147220 CACCCACATG
*
147230 CCACATGTCAAGAAAAA
1 CCACATGTCAAGCAAAA
* *
147247 TCA-ATG-CAACCCAAAA
1 CCACATGTCAA-GCAAAA
147263 CCACATGTCAAGCAAAA
1 CCACATGTCAAGCAAAA
147280 AATTAATGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
15 3 0.12
16 9 0.36
17 10 0.40
18 3 0.12
ACGTcount: A:0.50, C:0.28, G:0.10, T:0.12
Consensus pattern (17 bp):
CCACATGTCAAGCAAAA
Found at i:147676 original size:23 final size:24
Alignment explanation
Indices: 147644--147706 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 24
147634 GTGGCATGCC
147644 ACATGTCACCTTTTGGAACATATG
1 ACATGTCACCTTTTGGAACATATG
* *
147668 A-ATGTCACCTTTTGGTACATGTG
1 ACATGTCACCTTTTGGAACATATG
* *
147691 ACGTGCCACCTTTTGG
1 ACATGTCACCTTTTGG
147707 TACACGTGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (24 bp):
ACATGTCACCTTTTGGAACATATG
Found at i:147705 original size:24 final size:24
Alignment explanation
Indices: 147673--147747 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
147663 ATATGAATGT
*
147673 CACCTTTTGGTACATGTGACGTGC
1 CACCTTTTGGTACACGTGACGTGC
*
147697 CACCTTTTGGTACACGTGGCGTGC
1 CACCTTTTGGTACACGTGACGTGC
147721 CACCTTTTGGTACACGT-AGCGTGC
1 CACCTTTTGGTACACGTGA-CGTGC
147745 CAC
1 CAC
147748 GTGTCATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.29
Consensus pattern (24 bp):
CACCTTTTGGTACACGTGACGTGC
Found at i:166504 original size:23 final size:23
Alignment explanation
Indices: 166478--166523 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
166468 CTACTGATGA
*
166478 TTGCTTTTACCAACATCTAGATT
1 TTGCTTTTACCAACAGCTAGATT
166501 TTGCTTTTACCAACAGCTAGATT
1 TTGCTTTTACCAACAGCTAGATT
166524 GGATCTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (23 bp):
TTGCTTTTACCAACAGCTAGATT
Found at i:167130 original size:153 final size:154
Alignment explanation
Indices: 166851--167155 Score: 481
Period size: 153 Copynumber: 2.0 Consensus size: 154
166841 TTTTGCACCA
* * **
166851 TACTTTTTTATTTTGATCAAAACACATCCTAATGTTTTATTTTTTGTTCCACGTTGCACCCTCTG
1 TACTTTTTTATTTCGATCAAAACACATCCTAATATTTTATTTTTTGGCCCACGTTGCACCCTCTG
* *
166916 TTACGGTGAACTAACGGCACCGTCACGGAGTCCTATGTGGCATGCTGACATGGCAAAAATGTATT
66 TTACGGTGAACTAACGGCACCGTCACGAAGTCCTATGTGGCATGCTGACATGCCAAAAATGTATT
*
166981 ATTTCATCATCACGTCGCCGTCCC
131 ATTTCATCATAACGTCGCCGTCCC
167005 TACTTTTTTATTTCGATCAAAACACA-CCATAATATTTTA-TTTTTGGCCCACGTTGCACCCTCT
1 TACTTTTTTATTTCGATCAAAACACATCC-TAATATTTTATTTTTTGGCCCACGTTGCACCCTCT
* * *
167068 GTTACGGTGAACTAATGGCACCGTCAC-AAGTTCTTATGTGGCATGCTGACGTGCCAAAAATGTA
65 GTTACGGTGAACTAACGGCACCGTCACGAAG-TCCTATGTGGCATGCTGACATGCCAAAAATGTA
167132 TTATTTCATCATAACGTCGCCGTC
129 TTATTTCATCATAACGTCGCCGTC
167156 GAAACTTAAT
Statistics
Matches: 139, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
152 2 0.01
153 103 0.74
154 34 0.24
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (154 bp):
TACTTTTTTATTTCGATCAAAACACATCCTAATATTTTATTTTTTGGCCCACGTTGCACCCTCTG
TTACGGTGAACTAACGGCACCGTCACGAAGTCCTATGTGGCATGCTGACATGCCAAAAATGTATT
ATTTCATCATAACGTCGCCGTCCC
Found at i:170219 original size:9 final size:9
Alignment explanation
Indices: 170186--170224 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
170176 CATATTTTGA
170186 AGGAAGAGGG
1 AGGAAG-GGG
*
170196 -GGAAGAGG
1 AGGAAGGGG
170204 AGGAAGGGG
1 AGGAAGGGG
170213 AGGAAGGGG
1 AGGAAGGGG
170222 AGG
1 AGG
170225 GGAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 2 0.08
9 24 0.92
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (9 bp):
AGGAAGGGG
Found at i:172663 original size:3 final size:3
Alignment explanation
Indices: 172655--172683 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
172645 TGGCCTGAAA
172655 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
172684 CTTACCGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:187004 original size:107 final size:106
Alignment explanation
Indices: 186818--187082 Score: 415
Period size: 107 Copynumber: 2.5 Consensus size: 106
186808 AATTTTTCTA
* **
186818 ACCCTTAAAATAAAATTTTAATTTTAATTTGGACTAAACTTAGTG-AATTAATTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGACTAAACTTAGTGAAATTAATTATATATTTTAT
*
186882 TTCTAAAACCCTATAACAATAAATTATTAATTATGGAATTT
66 TTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
* * * *
186923 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAACTAAACTTAATGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGG-ACTAAACTTAGTGAAATTAATTATATATTTTA
*
186988 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
*
187030 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTT-GGACTAAACTTAGTGAAATTAA
187083 GGCTAAACTT
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
105 29 0.20
106 12 0.08
107 102 0.70
108 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGACTAAACTTAGTGAAATTAATTATATATTTTAT
TTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
Found at i:193308 original size:13 final size:16
Alignment explanation
Indices: 193278--193310 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
193268 TAACGACAGC
193278 AATAATGATAATTAAT
1 AATAATGATAATTAAT
193294 AATAAT-ATAATATAAT
1 AATAATGATAAT-TAAT
193310 A
1 A
193311 CTCACCAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATAATGATAATTAAT
Done.