Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012551.1 Corchorus capsularis cultivar CVL-1 contig12572, 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: 53750
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1046 original size:323 final size:322
Alignment explanation
Indices: 1--1956 Score: 2211
Period size: 323 Copynumber: 6.0 Consensus size: 322
*
1 ATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCCCAAAACTGTGATAGTTAGTACACG
1 ATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCACAAAACTGTGATAGTTAGTACACG
* *
66 ATTTCGGCTAAAAACTGACCTGAAATTGTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAATTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAAT
131 ATATAATTCAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAACTATCATTTTCCATTTTTT
131 ATATAATTCAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAACTATCATTTTCCATTTTTT
* * * * * *
196 TATAATTAATTTTTAATTAAATAGAAACAAGATTTAGATGCTTGTTAAAGCAAATTCTTAAATCC
196 TATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* *
261 AATGTGGCGGTGATTTGGTTAGATGAATATAGATATTTTAA-AGAGTC-TTCACGCCAAAAATC
261 AATGTGGCGGTGATTTGGTTAGATGAATATAGATATTTCAAGA-AGTCTTTC-TGCCAAAAATC
* * * * ** * * * *
323 ATGCAAAATTGAGCTAGGG-CTCCGGCACGCGTTTTTTG-CAAAAAACCGTGATGGTTAGTACAC
1 ATGCGAAACTGAG-TCGGGACCCCGAAACGCGTTTTTAGCCACAAAACTGTGATAGTTAGTACAC
* * *
386 GATTTCGGCTACAATTTTGCAAAAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATA
65 GATTTCGG---C-----T---AAAAACTGACCCGAAATTTTTTTCCTGAAATTTTTGCCACAATA
* * * * ** *
451 CTGAGAAAAAACTTTATGATTCAACGCCAAAAA-ATTGAAGGGGTTTT-ACGCTTCTAA-TATCG
119 CTCAGAAAAAA-TATATAATTCAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAACTATCA
** * * *
513 TTTTCCCATTTTTATTCGAATTTATTTCTAATAAAATCGAAACAAGATTCAGATGCTCGTAAAAA
183 TTTT-CCATTTTT-TTATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAA
*
578 CAAATCCTTAAATCCAATGTGGCGGTGATTTGGTTAGATTAATATAGATATTTTC-AGAAGTCTT
246 CAAATCCTTAAATCCAATGTGGCGGTGATTTGGTTAGATGAATATAGATA-TTTCAAGAAGTCTT
642 TCTGCCAAAAATC
310 TCTGCCAAAAATC
* *
655 ATGCGAAACTGAGTCGGGACCCCGAAATGCGTTTTTAGCTACAAAACTGTGATAGTTAGTACACG
1 ATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCACAAAACTGTGATAGTTAGTACACG
* *
720 ATTTCGGCTAAAAATTGACCCGAAATTTTTTTCCAGAAATTTTTGCCACAATACTCAGAAAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAATTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAAT
785 ATATAATTCAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAACTATCATTTTCCATTTTTT
131 ATATAATTCAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAACTATCATTTTCCATTTTTT
850 TATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
196 TATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * * * * *
915 AATGTGGCTGTGATTTTGATTATATAAACATAGATAATTCAAGAAGTCTTTCTGCCAAAAATC
261 AATGTGGCGGTGA-TTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATC
* * * * *
978 ATGCGAAACTAAGTCGGGCCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAGTACACG
1 ATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCACAAAACTGTGATAGTTAGTACACG
** *
1043 ATTTCGGCTAAAAACTGAGTCGAAATTTTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAA
66 ATTTCGGCTAAAAACTGACCCGAAA--TTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAA
* * * * *
1108 ATATATAATTCAACGCCAAAAAGATTGTCGAGCTTCTCAGAC-C-TCT-ACT-TCGTTTTTCCAT
129 ATATATAATTCAACGCCAAAAAGATTGACG-GATTTTTA-ACGCTTCTAACTATC-ATTTTCCAT
*** ** * * * * ** *
1169 TTTTTCCCAAAAAATTTCTAATTAAATAGAATCAAGATACAGATACCCGTAAAAA-ATGTCCCTA
191 TTTTTTATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * *
1233 TATCTAA--T-GC--TG--TTGAGTTTGATGCATATTGATATTTTAA-AGAGTC-TTCACGCCAA
256 AATCCAATGTGGCGGTGATTTG-GTTAGATGAATATAGATATTTCAAGA-AGTCTTTC-TGCCAA
1289 AAATC
318 AAATC
* * * ** ** * * * * *
1294 ATGCAAAATTGAGCTAGGG-CTTCGGCACGTGTTTTT-TCTAAAAAACTGTGATGGTTGTTAGTA
1 ATGCGAAACTGAG-TCGGGACCCCGAAACGCGTTTTTAGCCACAAAACTGTGA---TAGTTAGTA
* *
1357 CACGATTTCGGCTATAATTTGGCAAAAAACTGATCCGAAATATTTTTCCT-AAATTTTTTGCCAC
62 CACGATTTCGGC-------T----AAAAACTGACCCGAAATTTTTTTCCTGAAA-TTTTTGCCAC
* * * * ** * *
1421 AATACTGAGAAAAAATTTTATGATTCAACGCCAAAAA-ATTGAAGGGGTTTTCACACTTCTAA-T
115 AATACTCAGAAAAAA-TATATAATTCAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAACT
* ** * *
1484 ATCGTTTTCCCATTTTTATTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
179 ATCATTTT-CCATTTTT-TTATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTA
* * * *
1549 AAAGCAAATCCTTAAATCCAATGTGGAGGTCATTTGGTTAGATGAATATAGATATTTTAAGAAGT
242 AAAACAAATCCTTAAATCCAATGTGGCGGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGT
1614 CTTTCTGCCAAAAATC
307 CTTTCTGCCAAAAATC
*
1630 ATGCGAAACTGAGTCGGAACCCCGAAACGCGTTTTTAGCCACAAAACTGTGATAGTTAGTACACG
1 ATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCACAAAACTGTGATAGTTAGTACACG
*
1695 ATTTCGGCTAAAAACTGACCCGAAATTTTTTTCCTGAAATATTTGCCACAATACTCAGAAAAAAT
66 ATTTCGGCTAAAAACTGACCCGAAATTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAAT
* * *
1760 ATATAATTTAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAAATATCGTTTTTCCATTTTT
131 ATATAATTCAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAACTATC-ATTTTCCA-TTTT
1825 TTTATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
194 TTTATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
* * ** *
1890 CCAATGTGGCTGAGATTTGGTTAGATGAATACGGATATTTCAAGGAGTCTTTCTGCCAAAAATC
259 CCAATGTGGCGGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATC
1954 ATG
1 ATG
1957 TCAAAAACCG
Statistics
Matches: 1357, Mismatches: 204, Indels: 144
0.80 0.12 0.08
Matches are distributed among these distances:
315 17 0.01
316 51 0.04
317 4 0.00
318 22 0.02
320 2 0.00
321 49 0.04
322 180 0.13
323 222 0.16
324 194 0.14
325 81 0.06
326 13 0.01
327 48 0.04
328 30 0.02
329 55 0.04
330 20 0.01
331 22 0.02
332 190 0.14
333 56 0.04
334 20 0.01
335 4 0.00
336 58 0.04
337 19 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (322 bp):
ATGCGAAACTGAGTCGGGACCCCGAAACGCGTTTTTAGCCACAAAACTGTGATAGTTAGTACACG
ATTTCGGCTAAAAACTGACCCGAAATTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAAT
ATATAATTCAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAACTATCATTTTCCATTTTTT
TATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
AATGTGGCGGTGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATC
Found at i:2487 original size:285 final size:284
Alignment explanation
Indices: 1690--2515 Score: 846
Period size: 289 Copynumber: 2.9 Consensus size: 284
1680 GATAGTTAGT
* * ** * *
1690 ACACG-ATTTCGGCTAAAAACTGACCCG-AAATTTTTTTCCTGAAATATTTGCCACAATACTCAG
1 ACACGAATTTCGCCTAAAAAATGACCCGAAAAAGTTTTTCCTGAAATTTTTGCCACAATACT--T
* *
1753 AAAAAATATATAATTTAACGCCAAAAAGATTGACGGATTTTTAACGCTTCTAAATATCGTTTTTC
64 AAAAAATATATAATTCAACGCCAAAAAGATTGA-GGATTTTTCACGCTTCT-AATATCGTTTTTC
* *
1818 CATTTTTTTTATAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATC
127 CA-ATTTTTTATAATTAATTTCTAATTAAATAGAAACAAAATTCAGATGCTCGTAAAAACAAATC
** * *
1883 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATACGGATATTTCAAGGAGTCTTTCTGCCA
191 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTTCTCCCA
* *
1948 AAAATCATGTCAAAAACCGTGATGGTTAGT
256 AAAATCATGTCAAAAACCGTGA-GGTCAGA
* * ** * * *
1978 ACACGATTTTCGCCTAAAAAATGACCCGGAAATTTTTTTTCTCAATTTTTTGCCACAATACTCTA
1 ACACGAATTTCGCCTAAAAAATGACCCGAAAAAGTTTTTCCTGAAATTTTTGCCACAATACT-TA
* * *
2043 AAAAGA-ATAAAATTGAACGCCAAAAATATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTCC
65 AAAA-ATATATAATTCAACGCCAAAAAGATTG-AGGATTTTTCACGCTTCTAATATCGTTTTTCC
* * * * * *
2107 AATTTTTTTTAGAATTAATTTCTAATTAATTCGAAACAACATTTAGATGCTCATAAAAACAAATC
128 AA--TTTTTTATAATTAATTTCTAATTAAATAGAAACAAAATTCAGATGCTCGTAAAAACAAATC
* * *
2172 CTTAAATCCAATATGGCTGAGATTTGGTTAGATAAATATAGATATTTTAAGGTGAT-TTTCTCCC
191 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAG-TCTTTCTCCC
* * * **
2236 AATAATCATGTGAATAGGCG-G-GG-CACCGA
255 AAAAATCATGTCAAAAACCGTGAGGTCA--GA
* *
2265 ATCAC-AATTTCAG-C-AAAAAATTTACCCGAAAAAGTTTTCCCTGAAATTTTTGCCACAATACT
1 A-CACGAATTTC-GCCTAAAAAA-TGACCCGAAAAAGTTTTTCCTGAAATTTTTGCCACAATACT
* * * * * *
2327 TACAAAATTTATATAATTCAACACCAAAAAGATTGATGATTTTTTCACGATCCTATTATCGTTTT
63 TA-AAAA-ATATATAATTCAACGCCAAAAAGATTGAGGA-TTTTTCACGCTTCTAATATCGTTTT
** * * * * *
2392 T-CAATTTTTCCTAATTAAGTTCTAATTAAATAGAATCAAAATTCAAATACTCGTAAAATCAAAT
125 TCCAATTTTTTATAATTAATTTCTAATTAAATAGAAACAAAATTCAGATGCTCGTAAAAACAAAT
* * ** * *
2456 CCTTATATCCAATGCGATTGAGAGTTGGTTAGATGAATATAAATATTTTAAGGAGTCTTT
190 CCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTT
2516 GCGACAAAAA
Statistics
Matches: 447, Mismatches: 75, Indels: 35
0.80 0.13 0.06
Matches are distributed among these distances:
284 1 0.00
285 97 0.22
286 10 0.02
287 51 0.11
288 69 0.15
289 187 0.42
290 32 0.07
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (284 bp):
ACACGAATTTCGCCTAAAAAATGACCCGAAAAAGTTTTTCCTGAAATTTTTGCCACAATACTTAA
AAAATATATAATTCAACGCCAAAAAGATTGAGGATTTTTCACGCTTCTAATATCGTTTTTCCAAT
TTTTTATAATTAATTTCTAATTAAATAGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAA
ATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTTTCTCCCAAAAAT
CATGTCAAAAACCGTGAGGTCAGA
Found at i:3296 original size:331 final size:327
Alignment explanation
Indices: 2822--3981 Score: 1182
Period size: 331 Copynumber: 3.5 Consensus size: 327
2812 ATTTCGGCTA
* *
2822 AAAACTGACCCGAAAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATGATT
1 AAAACTGACCC-AAAA-TGTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATT
* * * * *
2887 CAACGCCAAAAAGATTGATGGGCTTTTCACGCTTTTAATATCCTTTTTCCATTTTTCCCTAATTA
64 CAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTCCCATTTTTTCCTAATTA
* **
2952 ATTTCTAATTAAAT-GAAATCAAGATTTAGATACTCGTAAAAACAAGTCCTTATATCTAATGTTT
129 ATTTCTAATTAAATCGAAAT-AAGATTCAGATACTCGTAAAAACAAGTCCTTATATCTAATGTGA
* * *
3016 TTTAGATTTGGTTATATGAATATAGATATTTTAAGGAGTTTTCGCACCAAAAATCATGCAAAATT
193 TTGAAATTTGGTTAGATGAATATAGATATTTTAAGGAGTTTTCGC-CCAAAAATCATGCAAAATT
*
3081 GAGTCGGGGCTCCGGAATGCGTTTTTCGCCAGAAACCGTGATGGTTAATACACGATTTCGGCTAC
257 GAGTCGGGGCTCCGGAATGCGTTTTACGCCA-AAACC-TGATGGTTAATACACGATTTCGGCTAC
3146 AATTTTGC
320 AATTTTGC
* * * *
3154 AAAGACTGGCCCAAAATGTTTTTCCT-CAATATTTTGCCACAATACTCAGAAAAGACATATAATT
1 AAA-ACTGACCCAAAATGTTTTTCCTGAAAT-TTTTGCCACAATACTCAGAAAAAATATATAATT
** * * * * *
3218 CAATGCCAAAAA-ATTGAAGGATTTTTCATGCTTGTAATATTGTTTTCCCATTTTTATTCGAATT
64 CAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTCCCATTTTT-TCCTAATT
* * * * *
3282 TATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATCTAATGTGA
128 AATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAGTCCTTATATCTAATGTGA
* * * * * * * *
3347 CTGATATTTTGTTAGATGAACATAGATATTTGAAGGAGTTTTTCTG-CCAAAAATTATGCGAAAC
193 TTGAAATTTGGTTAGATGAATATAGATATTTTAAGGAG-TTTTC-GCCCAAAAATCATGCAAAAT
* * * *
3411 TGAGTCGGGGCCCCGAAATGTGCTTTTAGCCCCAAAACCCTGATGGTTAATACACGATTTCGGCT
256 TGAGTCGGGGCTCCGGAATGCG-TTTTA-CGCCAAAA-CCTGATGGTTAATACACGATTTCGGCT
3476 ---A------
318 ACAATTTTGC
3477 AAAACTGACCCGGAAAAT-TTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATT
1 AAAACTGACCC--AAAATGTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATT
* * * * *
3541 CAATGCCAAAAATATTGACGGGCTTTTCACGGTTCTAATATCGTTTTTCCATTTTTTCCTAATTA
64 CAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTCCCATTTTTTCCTAATTA
* * * *
3606 ATTTCTAATTAAATAG-AATCAAGATTCAGATACTCGT-AAAACAAGTCCTTATATCCAATGCGG
129 ATTTCTAATTAAATCGAAAT-AAGATTCAGATACTCGTAAAAACAAGTCCTTATATCTAATGTGA
* * * *
3669 TTGAAATTTGATTAGATGAATATAGTTATTTTAAGGATTTTTCACGCCAAAAATCATGCAAAATT
193 TTGAAATTTGGTTAGATGAATATAGATATTTTAAGGAGTTTTCGC-CCAAAAATCATGCAAAATT
** * * *
3734 GAGTCGGGGCTTTAGGAACGCGTTTTACGTCAAAAACC--AT-G---AT---GGATTTCGGCTAC
257 GAGTCGGGGC-TCCGGAATGCGTTTTACG-CCAAAACCTGATGGTTAATACACGATTTCGGCTAC
3790 AATTTTGC
320 AATTTTGC
* ** * * *
3798 AAAAACTGACCCGAAATGTTTTTTTTTTTAATTTTTTGCCACAATACTCAAAATATATATATATA
1 -AAAACTGACCCAAAATG--TTTTTCCTGAAATTTTTGCCACAATACTC-AGA-A-A-A-A-ATA
* * * * **
3863 TATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCATGCTTTTAATGTCATATTTCTTATTTTTT
57 TATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGT-TTTCCCATTTTTT
* * * *
3928 TCTAAATTAATTTCTAATTAAATGGAAATAAGATTTAGATGCTCGTAAAAACAA
121 CCT-AATTAATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAA
3982 ATTCTTAAAT
Statistics
Matches: 681, Mismatches: 106, Indels: 82
0.78 0.12 0.09
Matches are distributed among these distances:
312 10 0.01
315 3 0.00
318 1 0.00
319 2 0.00
320 4 0.01
321 8 0.01
322 108 0.16
323 120 0.18
324 45 0.07
325 1 0.00
326 1 0.00
327 1 0.00
328 1 0.00
329 47 0.07
330 50 0.07
331 206 0.30
332 59 0.09
333 14 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (327 bp):
AAAACTGACCCAAAATGTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCA
ATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTCCCATTTTTTCCTAATTAAT
TTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAGTCCTTATATCTAATGTGATTG
AAATTTGGTTAGATGAATATAGATATTTTAAGGAGTTTTCGCCCAAAAATCATGCAAAATTGAGT
CGGGGCTCCGGAATGCGTTTTACGCCAAAACCTGATGGTTAATACACGATTTCGGCTACAATTTT
GC
Found at i:3943 original size:654 final size:647
Alignment explanation
Indices: 2567--3998 Score: 1709
Period size: 654 Copynumber: 2.2 Consensus size: 647
2557 CATTTTTAGA
** * * * * * * * *
2567 CAAAAAATTGAAGGGGTTTACACGCTTCTAATCTCGTTTTTCCATTTTTATTCGAATTTAA-TTA
1 CAAAAAATTGAAGGACTTTTCATGCTTGTAATATCATTTTCCCATTTTTATTC-AAATTAATTTC
* *
2631 TAATTAAATCGAAACAAGATTCAGATGCTCT-TAAAAACAAATCCTTAAATCCAATATGGCTAAG
65 TAATTAAATCGAAATAAGATTCAGATGCT-TGTAAAAACAAATCCTTAAATCCAATATGACTAAG
* * *
2695 ATTTAGTTAGATAAATATAGATATTTCAAGGAGTCTTTCTGCCGAAAATCATGTGAAACTGAGCC
129 ATTTAGTTAGATAAACATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTGAGCC
* * * * * * *
2760 GATGCCTCGAAACGCGTTTTCTAATTAAATCGAAAATCATGGTTAGTACACGATTTCGGCTAAAA
194 GAGGCCCCGAAA--C-TGTGCTAATTAAACCCAAAATCATGGTTAATACACGATTTCGGCTAAAA
*
2825 ACTGACCCGAAAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATGATTCAA
256 ACTGACCCGAAAA-TTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAA
* *
2890 CGCCAAAAAGATTGATGGGCTTTTCACGCTTTTAATATCCTTTTTCCATTTTTCCCTAATTAATT
320 CGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCCTTTTTCCATTTTTCCCTAATTAATT
* * *** *
2955 TCTAATTAAATGAAATCAAGATTTAGATACTCGTAAAAACAAGTCCTTATATCTAATGTTTTTTA
385 TCTAATTAAATGAAATCAAGATTCAGATACTCGTAAAAACAAGTCCTTATATCCAATGCGGTTGA
* * * *
3020 GATTTGGTTATATGAATATAGATATTTTAAGGAGTTTTCGCACCAAAAATCATGCAAAATTGAGT
450 AATTTGATTAGATGAATATAGATATTTTAAGGAGTTTTCACACCAAAAATCATGCAAAATTGAGT
* * * *
3085 CGGGGCTCCGGAATGCGTTTTTCGCCAGAAACCGTGATGGTTAATACACGATTTCGGCTACAATT
515 CGGGGCTCAGGAACGCGTTTTACGCCAAAAACC--GATGG-T-AT--ACGATTTCGGCTACAATT
* *
3150 TTGCAAAGACTGGCCCAAAATGTTTTTCCTCAATATTTTGCCACAATACTCAGAAAAGACATATA
574 TTGCAAAAACTGACCCAAAATGTTTTTCCTCAATATTTTGCCACAATACTCAGAAAAGACATATA
3215 ATTCAATGC
639 ATTCAATGC
* ** * *
3224 CAAAAAATTGAAGGATTTTTCATGCTTGTAATATTGTTTTCCCATTTTTATTCGAATTTATTTCT
1 CAAAAAATTGAAGGACTTTTCATGCTTGTAATATCATTTTCCCATTTTTATTCAAATTAATTTCT
* * * *
3289 AATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATCTAATGTGACTGATAT
66 AATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATATGACTAAGAT
* * * * * * *
3354 TTTGTTAGATGAACATAGATATTTGAAGGAGTTTTTCTGCCAAAAATTATGCGAAACTGAGTCGG
131 TTAGTTAGATAAACATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTGAGCCGA
* ** *
3419 GGCCCCGAAA-TGTGCT-TTTAGCCCCAAAACCCTGATGGTTAATACACGATTTCGGCTAAAAAC
196 GGCCCCGAAACTGTGCTAATTAAACCCAAAA---TCATGGTTAATACACGATTTCGGCTAAAAAC
*
3482 TGACCCGGAAAA-TTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAATG
258 TGACCC-GAAAATTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACG
* * * *
3546 CCAAAAATATTGACGGGCTTTTCACGGTTCTAATATCGTTTTTCCATTTTTTCCTAATTAATTTC
322 CCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCCTTTTTCCATTTTTCCCTAATTAATTTC
3611 TAATTAAAT-AGAATCAAGATTCAGATACTCGT-AAAACAAGTCCTTATATCCAATGCGGTTGAA
387 TAATTAAATGA-AATCAAGATTCAGATACTCGTAAAAACAAGTCCTTATATCCAATGCGGTTGAA
* * *
3674 ATTTGATTAGATGAATATAGTTATTTTAAGGATTTTTCACGCCAAAAATCATGCAAAATTGAGTC
451 ATTTGATTAGATGAATATAGATATTTTAAGGAGTTTTCACACCAAAAATCATGCAAAATTGAGTC
* * *
3739 GGGGCTTTAGGAACGCGTTTTACGTCAAAAACC-AT-G-AT-GGATTTCGGCTACAATTTTGCAA
516 GGGGC-TCAGGAACGCGTTTTACGCCAAAAACCGATGGTATACGATTTCGGCTACAATTTTGCAA
* ** * * * * *
3800 AAACTGACCCGAAATGTTTTTTTTTTTAATTTTTTGCCACAATACTCAAAATATATATATATATA
580 AAACTGACCCAAAATG--TTTTTCCTCAATATTTTGCCACAATACTC---AGA-A-A-AGACATA
3865 TAATTCAATGC
637 TAATTCAATGC
* * * * **
3876 CAAAAAGATTGGAGGGCTTTTCATGCTTTTAATGTCATATTTCTTATTTTT-TTCTAAATTAATT
1 CAAAAA-ATTGAAGGACTTTTCATGCTTGTAATATCAT-TTTCCCATTTTTATTC-AAATTAATT
* * * *
3940 TCTAATTAAATGGAAATAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCCAATAT
63 TCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATAT
3999 TGCTGAAGTT
Statistics
Matches: 662, Mismatches: 94, Indels: 41
0.83 0.12 0.05
Matches are distributed among these distances:
644 35 0.05
646 25 0.04
647 2 0.00
649 2 0.00
650 2 0.00
651 3 0.00
652 30 0.05
653 121 0.18
654 229 0.35
655 35 0.05
656 10 0.02
657 168 0.25
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (647 bp):
CAAAAAATTGAAGGACTTTTCATGCTTGTAATATCATTTTCCCATTTTTATTCAAATTAATTTCT
AATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATATGACTAAGAT
TTAGTTAGATAAACATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCGAAACTGAGCCGA
GGCCCCGAAACTGTGCTAATTAAACCCAAAATCATGGTTAATACACGATTTCGGCTAAAAACTGA
CCCGAAAATTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAA
AAAGATTGACGGGCTTTTCACGCTTCTAATATCCTTTTTCCATTTTTCCCTAATTAATTTCTAAT
TAAATGAAATCAAGATTCAGATACTCGTAAAAACAAGTCCTTATATCCAATGCGGTTGAAATTTG
ATTAGATGAATATAGATATTTTAAGGAGTTTTCACACCAAAAATCATGCAAAATTGAGTCGGGGC
TCAGGAACGCGTTTTACGCCAAAAACCGATGGTATACGATTTCGGCTACAATTTTGCAAAAACTG
ACCCAAAATGTTTTTCCTCAATATTTTGCCACAATACTCAGAAAAGACATATAATTCAATGC
Found at i:4017 original size:331 final size:321
Alignment explanation
Indices: 2567--4018 Score: 1181
Period size: 331 Copynumber: 4.4 Consensus size: 321
2557 CATTTTTAGA
* * * * * * *
2567 CAAAAA-ATTGAAGGGGTTTACACGCTTCTAATCTCGTTTTTCCATTTTTATTCGAATTTAA-TT
1 CAAAAAGATTGACGGGCTTTTCACGCTTTTAATATCGTTTTTCCATTTTT-TCCTAA-TTAATTT
* * * * * *
2630 ATAATTAAATCGAAA-CAAGATTCAGATGCTCTTAAAAACAAATCCTTAAATCCAATATGGCTAA
64 CTAATTAAAT-GAAATCAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTTGCTGA
* * * * * * ** * *
2694 GATTTAGTTAGATAAATATAGATATTTCAAGGAGTCTTTCTGCCGAAAATCATGTGAAACTGAGC
128 GATTTGGTTAGATGAATATAGATATTTTAAGGA-TTTTTCCGCCAAAAATCATGCAAAATTGAGT
** * * * * * *
2759 CGATGC-CTCGAAACGCGTTTT---CTAATTAAATCGAAAATCATGG--TT-AG-TACACGATTT
192 CGGGGCTC-CGGAATGCGTTTTACGCCAA--AAA-C---CATGATGGATTTCGGCTACA--ATTT
*
2816 CGGCTAAAAACTGACCCGAAAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATAT
248 -TGC-AAAAACTGACCCG-AAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATAT
* *
2881 ATGATTCAACGC
310 ATAATTCAATGC
* * *
2893 CAAAAAGATTGATGGGCTTTTCACGCTTTTAATATCCTTTTTCCATTTTTCCCTAATTAATTTCT
1 CAAAAAGATTGACGGGCTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTCCTAATTAATTTCT
* * * * ** *
2958 AATTAAATGAAATCAAGATTTAGATACTCGTAAAAACAAGTCCTTATATCTAATGTTTTTTAGAT
66 AATTAAATGAAATCAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTTGCTGAGAT
* * *
3023 TTGGTTATATGAATATAGATATTTTAAGGAGTTTTCGCACCAAAAATCATGCAAAATTGAGTCGG
131 TTGGTTAGATGAATATAGATATTTTAAGGATTTTTC-CGCCAAAAATCATGCAAAATTGAGTCGG
* * *
3088 GGCTCCGGAATGCGTTTTTCGCCAGAAACCGTGATGGTTAATACACGATTTCGGCTACAATTTTG
195 GGCTCCGGAATGCGTTTTACGCCAAAAACC---AT-G---AT---GGATTTCGGCTACAATTTTG
* * * * * * *
3153 CAAAGACTGGCCC-AAAATGTTTTTCCT-CAATATTTTGCCACAATACTCAGAAAAGACATATAA
250 CAAAAACTGACCCGAAATTTTTTTTCCTGAAAT-TTTTGCCACAATACTCAGAAAAAATATATAA
3216 TTCAATGC
314 TTCAATGC
* ** * * * * * * *
3224 CAAAAA-ATTGAAGGATTTTTCATGCTTGTAATATTGTTTTCCCATTTTTATTCGAATTTATTTC
1 CAAAAAGATTGACGGGCTTTTCACGCTTTTAATATCGTTTTTCCATTTTT-TCCTAATTAATTTC
* * *
3288 TAATTAAATCGAAAT-AAGATTCAGATGCTTGTAAAAACAAATCCTTAAATCTAATG-TGACTGA
65 TAATTAAAT-GAAATCAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTTG-CTGA
* * * * * * * *
3351 TATTTTGTTAGATGAACATAGATATTTGAAGGAGTTTTTCTGCCAAAAATTATGCGAAACTGAGT
128 GATTTGGTTAGATGAATATAGATATTTTAAGGA-TTTTTCCGCCAAAAATCATGCAAAATTGAGT
* * * * * **** * *
3416 CGGGGCCCCGAAATGTGCTTTTA-GCCCCAAAACCCTGATGG-TTAATAC-ACGATTTCGGCTAA
192 CGGGGCTCCGGAATGCG-TTTTACG-CCAAAAACCATGATGGATTTCGGCTACAATTT-TGC-AA
*
3478 AAACTGACCCGGAAA-ATTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTC
253 AAACTGACCC-GAAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTC
3542 AATGC
317 AATGC
* * *
3547 CAAAAATATTGACGGGCTTTTCACGGTTCTAATATCGTTTTTCCATTTTTTCCTAATTAATTTCT
1 CAAAAAGATTGACGGGCTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTCCTAATTAATTTCT
* * ** * *
3612 AATTAAAT-AGAATCAAGATTCAGATACTCGT-AAAACAAGTCCTTATATCCAATGCGGTTGAAA
66 AATTAAATGA-AATCAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTTGCTGAGA
* *
3675 TTTGATTAGATGAATATAGTTATTTTAAGGATTTTTCACGCCAAAAATCATGCAAAATTGAGTCG
130 TTTGGTTAGATGAATATAGATATTTTAAGGATTTTTC-CGCCAAAAATCATGCAAAATTGAGTCG
** * *
3740 GGGCTTTAGGAACGCGTTTTACGTCAAAAACCATGATGGATTTCGGCTACAATTTTGCAAAAACT
194 GGGC-TCCGGAATGCGTTTTACGCCAAAAACCATGATGGATTTCGGCTACAATTTTGCAAAAACT
** * * *
3805 GACCCGAAATGTTTTTTTTTTTAATTTTTTGCCACAATACTCAAAATATATATATATATATAATT
258 GACCCGAAAT-TTTTTTTCCTGAAATTTTTGCCACAATACTC-AGA-A-A-A-A-ATATATAATT
3870 CAATGC
316 CAATGC
* * * * * *
3876 CAAAAAGATTGGA-GGGCTTTTCATGCTTTTAATGTCATATTTCTTATTTTTTTCTAAATTAATT
1 CAAAAAGATT-GACGGGCTTTTCACGCTTTTAATATCGTTTTTC-CATTTTTTCCT-AATTAATT
* * * *
3940 TCTAATTAAATGGAAAT-AAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCCAATATTGCTG
63 TCTAATTAAAT-GAAATCAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTTGCTG
*
4004 A-AGTTGGTTAGATGA
127 AGATTTGGTTAGATGA
4019 TGTAAATAGT
Statistics
Matches: 894, Mismatches: 175, Indels: 109
0.76 0.15 0.09
Matches are distributed among these distances:
320 6 0.01
321 16 0.02
322 121 0.14
323 124 0.14
324 49 0.05
325 15 0.02
326 124 0.14
327 42 0.05
328 2 0.00
329 52 0.06
330 52 0.06
331 219 0.24
332 47 0.05
333 12 0.01
334 2 0.00
335 6 0.01
336 1 0.00
337 4 0.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (321 bp):
CAAAAAGATTGACGGGCTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTCCTAATTAATTTCT
AATTAAATGAAATCAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTTGCTGAGAT
TTGGTTAGATGAATATAGATATTTTAAGGATTTTTCCGCCAAAAATCATGCAAAATTGAGTCGGG
GCTCCGGAATGCGTTTTACGCCAAAAACCATGATGGATTTCGGCTACAATTTTGCAAAAACTGAC
CCGAAATTTTTTTTCCTGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGC
Found at i:19620 original size:42 final size:42
Alignment explanation
Indices: 19573--19657 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
19563 ATCATTGGTT
* *
19573 TTCGAATCAAATCCAAAACCAGTAAAAGCTCGACTTGAATGA
1 TTCGAATCAAATCCAAAACCAGTAAAAGCCCGACCTGAATGA
*
19615 TTCGAATCAAATCCAAAACTAGTAAAAGCCCGACCTGAATGA
1 TTCGAATCAAATCCAAAACCAGTAAAAGCCCGACCTGAATGA
19657 T
1 T
19658 AATTACGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.21
Consensus pattern (42 bp):
TTCGAATCAAATCCAAAACCAGTAAAAGCCCGACCTGAATGA
Found at i:20872 original size:1 final size:1
Alignment explanation
Indices: 20866--20895 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
20856 CCATAAAACT
20866 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20896 CTTAGATACC
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:23505 original size:417 final size:403
Alignment explanation
Indices: 22727--23718 Score: 1166
Period size: 417 Copynumber: 2.4 Consensus size: 403
22717 TCAAGGGTTT
* * * *
22727 AATTTCAATAAGATCCACTGTTCAATGAGTTTTGGGTTTTCGGAAGTTTTGATTAAC---CCTTT
1 AATTTCAATAAGATCCACTATTCAATGAGTTTTGGGTTTCCAGAAGTTTTGATTAACTTTCTTTT
* * *
22789 TTCCTCT-CACATGCAGAGTTGATTGACTTCCTC-TACTTCAAAACCGATACCAAATAG-TATCT
66 TTCCCCTCCACATGCAGAGTTGATCGACTTCCTCTTA-TTCAAAACTGATACCAAAT-GTTAT-T
* * *
22851 TTTTTAGTGTGCAATCCGACATTTATTCGAATATCCGAATAAAAAGAAAATTAGAAAAAATTTGG
128 TTTTTAGTGTACAATCCGACATTTATT----TATTCGAATAAAAACAAAATTA-AAAAAATTTGG
* **
22916 ATATCCGATATCCGACATTTAGAAATTTGAAAAATCCAACATTTTTAGGGATATTCGGATATCCG
188 ATATCCGATATCCGACATTTAGAAATTTGAAAAATCCAACATTTTTAGGGATATCCGGATATCAA
* * *
22981 ACATTTTAGGAAAAAAATTATTAAAAGAAAACAATAAAAATAAAAAGAACATTGATTCGATATAT
253 ACATTTTAGGAAAAAAATTATTAAAAGAAAACAACAAAAAGAAAAAGAACATTAATTCGATATAT
* * *
23046 AGGTCCATCTTGATTAAGTATTGGCTAAAGCACAATGTTTGGAATTCCATAAATATTTTTCATTT
318 AGGTCCAACTTGATTAAGTATTGGCTAAAGCACAACGTTTGGAATTCCATAAATA-TTTT--TTA
*
23111 CTGGCATACCAAATTAATCAATGG-TCC
380 CTAGC---CCAAATTAATCAA-GGATCC
* * * *
23138 AATTTTCAATAAGGTCCACTACTAAATGAGTTTTGGGTTTCCAGAAGTTCTGATTAACTTTCTTT
1 AA-TTTCAATAAGATCCACTATTCAATGAGTTTTGGGTTTCCAGAAGTTTTGATTAACTTTC-TT
*
23203 TTTTCCCCTCCACATGCAGAGTTTATCGACTTCCTCTTATTCAAAACTGATACCAAATGTTATTT
64 TTTTCCCCTCCACATGCAGAGTTGATCGACTTCCTCTTATTCAAAACTGATACCAAATGTTATTT
* * * * **
23268 TTTTAGTGTACAATCTGACATTTATTTATTCGGATAATATCTTAA-T-AAAAAATTTAGGCAAAT
129 TTTTAGTGTACAATCCGACATTTATTTATTCGAATAAAAACAAAATTAAAAAAATTT-GG---AT
* **
23331 TTCCGGATATCCGACATTTAGAAATTT-AAAAATCCGGCATTTTTTAGGGATATCCGGATATCAA
190 ATCC-GATATCCGACATTTAGAAATTTGAAAAATCCAACA-TTTTTAGGGATATCCGGATATCAA
*
23395 ACATTTTA-GAAAAAATTTATTAAAAAAGATTAAA-AACAAAAAGAAAAAGAACATTAATTCGGA
253 ACATTTTAGGAAAAAAATTATT--AAAAGA--AAACAACAAAAAGAAAAAGAACATTAATTC-GA
* * *
23458 TATATAGGTCCAACTTGATTAAGTATTGGCTAAAATC-CAACGTTTGGAATTTCATAATTATTTT
313 TATATAGGTCCAACTTGATTAAGTATTGGCT-AAAGCACAACGTTTGGAATTCCATAAATATTTT
* *
23522 TTAGTAGCCCAAATTATTCAAGGATCC
377 TTACTAGCCCAAATTAATCAAGGATCC
* *
23549 AATTTCAATAAGATCCACTATTCAATGAGTTTTGAGTTTCCAAAAGTTTTGATTAACTTTCTTTT
1 AATTTCAATAAGATCCACTATTCAATGAGTTTTGGGTTTCCAGAAGTTTTGATTAACTTTCTTTT
* * *
23614 TTCCCCTCGACATGCAGAGTTGATCAACTTCCT-TTGCTTCAAAACTGATACCAAATGTTATTTT
66 TTCCCCTCCACATGCAGAGTTGATCGACTTCCTCTT-ATTCAAAACTGATACCAAATGTTA-TTT
* *
23678 TTTACTAATGTACAATCCGACATTTATTTATTCAAATAAAA
129 TTT--TAGTGTACAATCCGACATTTATTTATTCGAATAAAA
23719 TCCGAATAAA
Statistics
Matches: 501, Mismatches: 55, Indels: 49
0.83 0.09 0.08
Matches are distributed among these distances:
408 2 0.00
409 66 0.13
410 63 0.13
411 20 0.04
412 91 0.18
413 27 0.05
414 56 0.11
415 7 0.01
416 63 0.13
417 100 0.20
418 6 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (403 bp):
AATTTCAATAAGATCCACTATTCAATGAGTTTTGGGTTTCCAGAAGTTTTGATTAACTTTCTTTT
TTCCCCTCCACATGCAGAGTTGATCGACTTCCTCTTATTCAAAACTGATACCAAATGTTATTTTT
TTAGTGTACAATCCGACATTTATTTATTCGAATAAAAACAAAATTAAAAAAATTTGGATATCCGA
TATCCGACATTTAGAAATTTGAAAAATCCAACATTTTTAGGGATATCCGGATATCAAACATTTTA
GGAAAAAAATTATTAAAAGAAAACAACAAAAAGAAAAAGAACATTAATTCGATATATAGGTCCAA
CTTGATTAAGTATTGGCTAAAGCACAACGTTTGGAATTCCATAAATATTTTTTACTAGCCCAAAT
TAATCAAGGATCC
Found at i:27605 original size:16 final size:16
Alignment explanation
Indices: 27586--27627 Score: 70
Period size: 14 Copynumber: 2.8 Consensus size: 16
27576 ATTCACGAAG
27586 ATACATATATACGAGA
1 ATACATATATACGAGA
27602 ATAC--ATATACGAGA
1 ATACATATATACGAGA
27616 ATACATATATAC
1 ATACATATATAC
27628 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 14 0.58
16 10 0.42
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (16 bp):
ATACATATATACGAGA
Found at i:33578 original size:25 final size:25
Alignment explanation
Indices: 33532--33588 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
33522 TAGTCTGTCG
*
33532 CTTTTCTCTTCGATTATGCTATCTTC
1 CTTTT-TCTTCGATTATACTATCTTC
* *
33558 CTTTTTCTTGGATTCTACTATCTTC
1 CTTTTTCTTCGATTATACTATCTTC
33583 CTTTTT
1 CTTTTT
33589 TCTGCTCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.11, C:0.25, G:0.07, T:0.58
Consensus pattern (25 bp):
CTTTTTCTTCGATTATACTATCTTC
Found at i:34554 original size:6 final size:6
Alignment explanation
Indices: 34543--34569 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34533 TGAGTGAGTA
34543 AACTTC AACTTC AACTTC AACTTC AAC
1 AACTTC AACTTC AACTTC AACTTC AAC
34570 ATTGGGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (6 bp):
AACTTC
Found at i:50997 original size:25 final size:27
Alignment explanation
Indices: 50968--51036 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 27
50958 AGAAAAAAAT
50968 AAATAAAGAGTTTTTTTGGC-C-ATCA
1 AAATAAAGAGTTTTTTTGGCACAATCA
50993 AAATAAAGAGTTTTTTTTTTTGGCACAATCA
1 AAATAAAGAG----TTTTTTTGGCACAATCA
51024 AAATAAAGAGTTT
1 AAATAAAGAGTTT
51037 AATTGGGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
25 10 0.26
27 3 0.08
29 10 0.26
30 1 0.03
31 14 0.37
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (27 bp):
AAATAAAGAGTTTTTTTGGCACAATCA
Found at i:51024 original size:31 final size:29
Alignment explanation
Indices: 50978--51036 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 29
50968 AAATAAAGAG
50978 TTTTTTTGGCCATCAAAATAAAGAGTTTT
1 TTTTTTTGGCCATCAAAATAAAGAGTTTT
51007 TTTTTTTGGCACAATCAAAATAAAGAGTTT
1 TTTTTTTGGC-C-ATCAAAATAAAGAGTTT
51037 AATTGGGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 10 0.36
30 1 0.04
31 17 0.61
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTTTTTGGCCATCAAAATAAAGAGTTTT
Done.