Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013556.1 Corchorus olitorius cultivar O-4 contig13589, 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: 49634
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1423 original size:323 final size:322
Alignment explanation
Indices: 355--1592 Score: 1791
Period size: 323 Copynumber: 3.9 Consensus size: 322
345 TGAGCTGGGA
355 CCGCTAAAAACAGACCCGAAATTTTTTTTCTTGAAT-TTTTTGCCACAATACTCAGAAAAAATAT
1 CCGCTAAAAACAGACCCGAAA-TTTTTTTCTT-AATGTTTTTGCCACAATACTCAGAAAAAATAT
* * *
419 ATAATTCAACGCCAAAAAGATTATAGGGTTTTTCAAGCTTCTAATATCGTTTTTTCATTTTTCCC
64 ATAATTCAACGCCAAAAAGATTGTAGGGTTTTTCACGCTTCTAATATCGTTTTATCATTTTTCCC
* * * *
484 GAAATAATTTCTAACTAAAT-GAAA-AATGATTCAGATGGTCGTAAAA-ACAAATCCATAAATAG
129 GAAATAATTTCTAATTAAATCGAAACAA-GATTCAGATGCTTGTAAAAGA-AAATCCATAAATCG
* * * *
546 AATGCGACTAGGAATTGGTTCCATGACTATAGATATTTCGAAGAGACTTTCTGCTAAAAATCATG
192 AATGTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTTCTGCTAAAAATCATG
* * * *
611 CAAATCTTAAGCTGGGACCCCGAAATGCGTTTTTGATCCAAAAACCGTGATGGTTAGTACACAAT
257 CAAA-CCTGAGCTGGGACCCCGAAACGCGTTTTTGATCCAAAAACCGTGATGGTTAGTACACGAT
676 TT
321 TT
* * * * * *
678 CCGTTAAAAACAGACCCGAAATTTTTTTTTTTGAGGATTTTGCCACAATACTCTGAAAAAATATA
1 CCGCTAAAAACAGACCCGAAA-TTTTTTTCTTAATGTTTTTGCCACAATACTCAGAAAAAATATA
* * *
743 TAATTCAACGCCAAAAAGATTGTAAGGTTTTTCACGCTTCTAATATCGTTTT-TCATATTTCCCA
65 TAATTCAACGCCAAAAAGATTGTAGGGTTTTTCACGCTTCTAATATCGTTTTATCATTTTTCCCG
*
807 AAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAGCAAATCCATAAATCGAAT
130 AAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAGAAAATCCATAAATCGAAT
*
872 GTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTTC-CCTAAAAATCATGCAA
195 GTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTTCTGCTAAAAATCATGCAA
* * *
936 ATCTTAGCTGGGACCCCAAAACGCGTTTTTGATCCAAAAACCGTGA---TTAGTACACGATTT
260 ACCTGAGCTGGGACCCCGAAACGCGTTTTTGATCCAAAAACCGTGATGGTTAGTACACGATTT
* *
996 CCGCTAAAAACAGACCCGAAATTTTTTCCTTGA-GATTTTTGCCACAATACTCAGAAAAAATATA
1 CCGCTAAAAACAGACCCGAAATTTTTTTCTTAATG-TTTTTGCCACAATACTCAGAAAAAATATA
* * *
1060 TAATTCAACGCCAATAAGATTGTCGGGTTTTTCACGCTTCTCATATCGTTTTATCATTTTTCCCG
65 TAATTCAACGCCAAAAAGATTGTAGGGTTTTTCACGCTTCTAATATCGTTTTATCATTTTTCCCG
* * * *
1125 AAATAATTTCTAATTAAATCGAAACAAGGTACAGATGGTTGCAAAA-AAAATCCATAAATCGAAT
130 AAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAGAAAATCCATAAATCGAAT
* * * *
1189 GTAAATAGGAATTGGTTCGATAAATATAGATATTTCAAAGAGACTTTCTGCTAAAAATCTTGCAA
195 GTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTTCTGCTAAAAATCATGCAA
* *
1254 ACCTGAGCTGGAACCCCGAAACGCGTTTTT-AGCCCAAAAACCGTGATGGTTAGTACACGATTT
260 ACCTGAGCTGGGACCCCGAAACGCGTTTTTGA-TCCAAAAACCGTGATGGTTAGTACACGATTT
* * *
1317 CCGCTCAAAATAGACCCGAGAATTTTTTTCTTAAATGTTTTTGCCACAATACTCAGAAAAAGTAT
1 CCGCTAAAAACAGACCCGA-AATTTTTTTCTT-AATGTTTTTGCCACAATACTCAGAAAAAATAT
* *
1382 ATAATTCAACGCCAATAAGATTGTAGGGATTTTCACGCTTCTAATATC-TATTTATCATTTTTCC
64 ATAATTCAACGCCAAAAAGATTGTAGGGTTTTTCACGCTTCTAATATCGT-TTTATCATTTTTCC
* * * *
1446 CGAAATAATTTATAATTAAATCGAAACAAGATTCAGATTCATGTAAAAGCAAATCCATAAATCGA
128 CGAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAGAAAATCCATAAATCGA
*
1511 ATGTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTGCTGCTAAAAATCATGC
193 ATGTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTTCTGCTAAAAATCATGC
*
1576 AAAACTGAGCTGGGACC
258 AAACCTGAGCTGGGACC
1593 GCTAAAAACA
Statistics
Matches: 823, Mismatches: 76, Indels: 31
0.88 0.08 0.03
Matches are distributed among these distances:
316 1 0.00
317 148 0.18
318 138 0.17
321 71 0.09
322 57 0.07
323 315 0.38
324 93 0.11
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (322 bp):
CCGCTAAAAACAGACCCGAAATTTTTTTCTTAATGTTTTTGCCACAATACTCAGAAAAAATATAT
AATTCAACGCCAAAAAGATTGTAGGGTTTTTCACGCTTCTAATATCGTTTTATCATTTTTCCCGA
AATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAGAAAATCCATAAATCGAATG
TGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTTCTGCTAAAAATCATGCAAA
CCTGAGCTGGGACCCCGAAACGCGTTTTTGATCCAAAAACCGTGATGGTTAGTACACGATTT
Found at i:1820 original size:275 final size:274
Alignment explanation
Indices: 1317--1867 Score: 831
Period size: 275 Copynumber: 2.0 Consensus size: 274
1307 TACACGATTT
* * *
1317 CCGCTCAAAATAGACCCGAGAATTTTTTTCTTAAATGTTTTTGCCACAATACTCAGAAAAAGTAT
1 CCGCTAAAAACAGACCCGAGAATTTTTTTCTTAAATGTTTTTGCCACAATACTCAGAAAAAATAT
* *
1382 ATAATTCAACGCCAATAAGATTGTAGGGATTTTCACGCTTCTAATATCTATTTATCATTTTTCCC
66 ATAATTCAACGCCAAAAAGATTATAGGGATTTTCACGCTTCTAATATCTATTTATCATTTTTCCC
* * * * *
1447 GAAATAATTTATAATTAAATCGAAACAAGATTCAGATTCATGTAAAAGCAAATCCATAAATCGAA
131 GAAATAATTTATAATTAAATCAAAACAAGATTCAAATGCATGTAAAAACAAATCCATAAATAGAA
*
1512 TGTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTGCTGCTAAAAATCATGCA
196 TGTAACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTGCTGCTAAAAATCATGCA
*
1577 AAACTGAGCTGGGA
261 AAACTGAGCTAGGA
*
1591 CCGCTAAAAACAGACCCGA-AATTTTTTTTTCTTGAAT-TTTTTGCCACAATACTCAGAAAAAAT
1 CCGCTAAAAACAGACCCGAGAA--TTTTTTTCTTAAATGTTTTTGCCACAATACTCAGAAAAAAT
* *
1654 ATATAATTCAACGCCAAAAAGATTATAGGGTTTTTCACGCTTCTAATATCGT-TTTTTCATTTTT
64 ATATAATTCAACGCCAAAAAGATTATAGGGATTTTCACGCTTCTAATATC-TATTTATCA-TTTT
* * *
1718 TCCCGAATTAATTTCTAATTAAATTAAAACAAGATTCAAATGC-TCGTAAAAACAAATCCATAAA
127 TCCCGAAATAATTTATAATTAAATCAAAACAAGATTCAAATGCAT-GTAAAAACAAATCCATAAA
* * *
1782 TAGAATGTAACTAGGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCTAAAAATC
191 TAGAATGTAACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTGCTGCTAAAAATC
*
1847 TTGCAAAACTGAGCTAGGA
256 ATGCAAAACTGAGCTAGGA
1866 CC
1 CC
1868 CTGAAACTCG
Statistics
Matches: 250, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
273 2 0.01
274 96 0.38
275 152 0.61
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (274 bp):
CCGCTAAAAACAGACCCGAGAATTTTTTTCTTAAATGTTTTTGCCACAATACTCAGAAAAAATAT
ATAATTCAACGCCAAAAAGATTATAGGGATTTTCACGCTTCTAATATCTATTTATCATTTTTCCC
GAAATAATTTATAATTAAATCAAAACAAGATTCAAATGCATGTAAAAACAAATCCATAAATAGAA
TGTAACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGACTTGCTGCTAAAAATCATGCA
AAACTGAGCTAGGA
Found at i:2646 original size:515 final size:516
Alignment explanation
Indices: 1591--2666 Score: 1638
Period size: 515 Copynumber: 2.1 Consensus size: 516
1581 TGAGCTGGGA
* * *
1591 CCGCTAAAAACAGACCCGAAATTTTTTTTTCTTGAATTTTTTGCCACAATACTCAGAAAAAATAT
1 CCGCTAAAAACTGACCCGAAAATTTTTTTTCTTGAATTTTTTGCCACAATACTCAAAAAAAATAT
* * * *
1656 ATAATTCAACGCCAAAAAGATTATAGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTCC
66 ATAATTCAACGACAAAAAAATTATAGGGTTTTTCACGCTTCTAATACCGTTTTTTCATTTTTTCA
* *
1721 CGAATTAATTTCTAATTAAATTAAAACAAGATTCAAATGCTCGTAAAAACAAATCCATAAATAGA
131 CGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCAATAAATAGA
*
1786 ATGTAACTAGGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCTAAAAATCTTGC
196 ATGTAACTAGGATTTGGTTCGATGAATATAAATATTTCAAAGAGTCTTTCTGCTAAAAATCTTGC
* *
1851 AAAACTGAGCTAGGACCCTGAAACTCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTC
261 AAAACTGAGCCAGGACCCTGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTC
1916 CGCTATAAACAGACCCGAAAATTTATCTGAATTTTTCGCCACAAAACAAATCCTTAAATTGAATG
326 CGCTATAAACAGACCCGAAAATTTATCTGAATTTTTCGCCACAAAACAAATCCTTAAATTGAATG
*
1981 TCACTGGCTTTCATTTGATGAACATGGATATTTCAAAGAGTCTTTCTGCGTAAAATCTTGCGTAA
391 TCACTGGCTTTCATTTGATGAACATGGATATTTCAAAGAGTCTTTCTGCGTAAAATCTTGCGAAA
*
2046 CTGAGCTGGAACCCCGAAACGCGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTT
456 CTGAGCTGGAACCCCGAAACACGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTT
* *
2107 CCACTAAAAA-T-ACATCCGAAAATTTTTTTTCTTGAATTTTTTTGCTACAATACTCAAAAAAAA
1 CCGCTAAAAACTGAC--CCGAAAATTTTTTTTCTTGAA-TTTTTTGCCACAATACTCAAAAAAAA
* * *
2170 GTATATAATTCAAC-ATAAAAAAATTTGTAGGGTTTTTCACGCTTCTATTACCGTTTTTTCATTT
63 -TATATAATTCAACGACAAAAAAA-TTATAGGGTTTTTCACGCTTCTAATACCGTTTTTTCATTT
* * * * * *
2234 TTTTAGGAA-TAATTTCTGATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCAATAA
126 TTTCACGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCAATAA
*
2298 ATAGAATGTAACTAGGATTTTGTTCGATGAATATAAATATTTCAAAGAGTCTTT-TGCTAAAAAT
191 ATAGAATGTAACTAGGATTTGGTTCGATGAATATAAATATTTCAAAGAGTCTTTCTGCTAAAAAT
* *
2362 CTTGCAAAACTGAGCCGGGACCC-GAAACGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACG
256 CTTGCAAAACTGAGCCAGGACCCTGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACG
* *
2426 ATTTCCGCTATAAACAGACCCGAAACTTTATCTGAATTTTTTGCCACAAAA-AAATCCTTAAATT
321 ATTTCCGCTATAAACAGACCCGAAAATTTATCTGAATTTTTCGCCACAAAACAAATCCTTAAATT
* *
2490 GAATGTCATTAGGCTTTCGTTTGATGAACATGGATATTTCAAAGAGTCTTTCTGC-TAAAAAT-T
386 GAATGTCACT-GGCTTTCATTTGATGAACATGGATATTTCAAAGAGTCTTTCTGCGT-AAAATCT
* * *
2553 TG-GAAAACTGAGCTGGGACCCCGAAACACGTTTTTAGCCCAAAAACTGTGATGGTTATTACACG
449 TGCG-AAACTGAGCTGGAACCCCGAAACACGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACG
2617 ATTT
513 ATTT
* * * *
2621 CGGCTAAAAACTGACCTGAAAA--ATTTATC-TGAATTTTTTGCCACAA
1 CCGCTAAAAACTGACCCGAAAATTTTTTTTCTTGAATTTTTTGCCACAA
2667 AACAAATCCT
Statistics
Matches: 509, Mismatches: 41, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
510 12 0.02
511 4 0.01
512 5 0.01
513 1 0.00
514 101 0.20
515 137 0.27
516 62 0.12
517 131 0.26
518 56 0.11
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (516 bp):
CCGCTAAAAACTGACCCGAAAATTTTTTTTCTTGAATTTTTTGCCACAATACTCAAAAAAAATAT
ATAATTCAACGACAAAAAAATTATAGGGTTTTTCACGCTTCTAATACCGTTTTTTCATTTTTTCA
CGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCAATAAATAGA
ATGTAACTAGGATTTGGTTCGATGAATATAAATATTTCAAAGAGTCTTTCTGCTAAAAATCTTGC
AAAACTGAGCCAGGACCCTGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTC
CGCTATAAACAGACCCGAAAATTTATCTGAATTTTTCGCCACAAAACAAATCCTTAAATTGAATG
TCACTGGCTTTCATTTGATGAACATGGATATTTCAAAGAGTCTTTCTGCGTAAAATCTTGCGAAA
CTGAGCTGGAACCCCGAAACACGTTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTT
Found at i:2823 original size:194 final size:194
Alignment explanation
Indices: 2283--3065 Score: 896
Period size: 194 Copynumber: 4.0 Consensus size: 194
2273 GATGCTCGTA
** * * * * *
2283 AAAACAAATCAATAAATAGAATGTAACTAGGATTTTGTTCGATGAATATAAATATTTCAAAGAGT
1 AAAACAAATCCTTAAATCGAATGTGACTAGGATTTGGTTTGATGAATATAGATATTTCAAAGAGT
* * *
2348 CTTT-TGCTAAAAATCTTGCAAAACTGAGCCGGGA-CCCGAAACGCGTTTTTAG-CCTAAAACCG
66 CTTTCTGCTAAAAATCTTGCAAAACTGAGCTGGGACCCCGAAACGCGTTTTTAGCCCAAAAACTG
* * * *
2410 TGATGGTTAGTACACGATTTCCGCTATAAACAGACCCG-AAACTTTATCTGAATTTTTTGCCAC
131 TGATGGTTATTACACGATTTCCGCTAAAAACTGACCCGAAAAATTTATCTGAATTTTTTGCCAC
* * * * * * *
2473 AAAA-AAATCCTTAAATTGAATGTCATTAGGCTTTCGTTTGATGAACATGGATATTTCAAAGAGT
1 AAAACAAATCCTTAAATCGAATGTGACTAGGATTTGGTTTGATGAATATAGATATTTCAAAGAGT
* *
2537 CTTTCTGCTAAAAAT-TTGGAAAACTGAGCTGGGACCCCGAAACACGTTTTTAGCCCAAAAACTG
66 CTTTCTGCTAAAAATCTTGCAAAACTGAGCTGGGACCCCGAAACGCGTTTTTAGCCCAAAAACTG
* *
2601 TGATGGTTATTACACGATTTCGGCTAAAAACTGACCTGAAAAATTTATCTGAATTTTTTGCCAC
131 TGATGGTTATTACACGATTTCCGCTAAAAACTGACCCGAAAAATTTATCTGAATTTTTTGCCAC
* *
2665 AAAACAAATCCTTAAATCGAATGTGACTGGGATTTGGTTTGATGAATATAGATATTTCAAAGGGT
1 AAAACAAATCCTTAAATCGAATGTGACTAGGATTTGGTTTGATGAATATAGATATTTCAAAGAGT
** * * *
2730 CTTTCTAATAAAAATCTTCCAAAACTGAGCTGGAACCCCAAAACGCGTTTTTAGCCCAAAAACTG
66 CTTTCTGCTAAAAATCTTGCAAAACTGAGCTGGGACCCCGAAACGCGTTTTTAGCCCAAAAACTG
* ** * **
2795 TGATGGTTATTACACAATTTTTGCTAAAAACTTACCCGAAAAATTTATCTGAATTTTTTGAAAC
131 TGATGGTTATTACACGATTTCCGCTAAAAACTGACCCGAAAAATTTATCTGAATTTTTTGCCAC
* * * * * * * * *
2859 AAAAAAAAATCCTTAAGTCGAATCTGACTGGGATTTGATTTGTTGTATATAGTTATTTCAAATAG
1 -AAAACAAATCCTTAAATCGAATGTGACTAGGATTTGGTTTGATGAATATAGATATTTCAAAGAG
* * * * *
2924 TCTTTCTGCTAAAAATCTTGTAAAACTGAGCTGGGACCACGAAAGCCGAATCGCGTGTTTAGGCT
65 TCTTTCTGCTAAAAATCTTGCAAAACTGAGCTGGGA-C-C-----CCGAAACGCGTTTTTAGCCC
** ** *
2989 AAAAACCATGATGGTT-TGTACACGATTTCCGCTAAAAACTGACCCGGAAATTTTTTTCTTGAAT
123 AAAAACTGTGATGGTTAT-TACACGATTTCCGCTAAAAACTGACCC-GAAAAATTTATC-TGAA-
3053 TTTTTTGCCAC
184 TTTTTTGCCAC
3064 AA
1 AA
3066 TACTCCAGAA
Statistics
Matches: 500, Mismatches: 75, Indels: 22
0.84 0.13 0.04
Matches are distributed among these distances:
189 70 0.14
190 31 0.06
191 41 0.08
192 28 0.06
193 64 0.13
194 101 0.20
195 86 0.17
196 1 0.00
197 1 0.00
201 1 0.00
202 52 0.10
203 9 0.02
204 6 0.01
205 9 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (194 bp):
AAAACAAATCCTTAAATCGAATGTGACTAGGATTTGGTTTGATGAATATAGATATTTCAAAGAGT
CTTTCTGCTAAAAATCTTGCAAAACTGAGCTGGGACCCCGAAACGCGTTTTTAGCCCAAAAACTG
TGATGGTTATTACACGATTTCCGCTAAAAACTGACCCGAAAAATTTATCTGAATTTTTTGCCAC
Found at i:3653 original size:324 final size:324
Alignment explanation
Indices: 2997--4036 Score: 1402
Period size: 323 Copynumber: 3.2 Consensus size: 324
2987 CTAAAAACCA
* * *
2997 TGATGGTTTGTACACGATTTCCGCTAAAAACTGACCCGGAAATTTTT-TTCTTGAATTTTTTTGC
1 TGATGGTTAGTACACGATTTCCGCTAAAAACAGACCC-GAAATTTTTATTCTTG-AGTTTTTTGC
**** *
3061 CACAATACTCCAG-AAAAATATATAATTCAATATGAAAAAGATTGTAGGGTTTTTCACGCTTCTA
64 CACAATACT-CAGAAAAAATATATAATTCAACGCCAAAAAGATTATAGGGTTTTTCACGCTTCTA
* * * * *
3125 ATATCATTTTTT-TCATTTTTTTGCCGAAATAATTTCTAATTGAATCGAAACAACATTCAGATGC
128 ATATCGTTTTTTCT-ATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
* ** *
3189 TTGTAAAAACAAATCCATAAATCTAATGTGACTAGGAATTGGTTCGATGAATATAGATATTTCAA
192 TCGT-AAAACAAATCCATAAATAGAATGCGACTAGGAATTGGTTCGATGAATATAGATATTTCAA
* * * * *
3254 ATAGACTTTCTGCGAAAACTCATGCAAATCTAAGCT-AGGTCCCCGAAACGCGTTTTTGCCCCAA
256 ATAGACTTTCTGCTAAAAATCATGCAAATCTGAGCTGAGAT-CCCGAAACGCGTTTTTGGCCCAA
3318 AAACCG
320 AAA-CG
3324 TGATGGTTAGTACACGATTTCCGCTAAAAACAGACCCGAAATTTTTATTCTTGAGTTTTTTGCCA
1 TGATGGTTAGTACACGATTTCCGCTAAAAACAGACCCGAAATTTTTATTCTTGAGTTTTTTGCCA
* * *
3389 CAATAGTCAGAAAAAATATATGATTCAACGCCAAAAAGATTATAGGGTTTTTCAAGCTTCTAATA
66 CAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTATAGGGTTTTTCACGCTTCTAATA
*
3454 TCGTTTTTTCATATTTTTTTCCCGAATTAATTTCTAAGTT-TATCGAAACAAGATTCAGATGCTC
131 TCGTTTTTTC-TATTTTTTTCCCGAATTAATTTCTAA-TTAAATCGAAACAAGATTCAGATGCTC
* * *
3518 GT-AAA-AAATCCATAAATAGAATGCGGCTAGGAATTGGTTCGATGAATATAGGTATTTCAAAGA
194 GTAAAACAAATCCATAAATAGAATGCGACTAGGAATTGGTTCGATGAATATAGATATTTCAAATA
* * *
3581 GACTTTCTGCTAAAAATCATGCAAATCTGAGCTGAGATCCCGAAATGTGTTTTTGGCCCAAATAC
259 GACTTTCTGCTAAAAATCATGCAAATCTGAGCTGAGATCCCGAAACGCGTTTTTGGCCCAAAAAC
3646 AG
324 -G
* *
3648 TGATGGTTAGTACACGATTTCCGCTAAAAATAGACCCGAAATTTTTCTTCTTGAGTTTTTT-CCA
1 TGATGGTTAGTACACGATTTCCGCTAAAAACAGACCCGAAATTTTTATTCTTGAGTTTTTTGCCA
* * *
3712 TAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATTATAGGGGTTTTCACGCTTCTAATA
66 CAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTATAGGGTTTTTCACGCTTCTAATA
**
3777 TCGTTTTTTC-A-TTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCATTTGCTCGT
131 TCGTTTTTTCTATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
*
3840 AAAAACAAATCCATAAATAGAATGCGACTAGGATTTGGTTCGATGAATATAGATATTTCAAATAG
196 -AAAACAAATCCATAAATAGAATGCGACTAGGAATTGGTTCGATGAATATAGATATTTCAAATAG
* * * * * * *
3905 ACTTTCTGCTAAAAATCTTGCAAAACTGAGATGGGACCCCGAAGCGCGTTTTTAGCCCAAAAATC
260 ACTTTCTGCTAAAAATCATGCAAATCTGAGCTGAGATCCCGAAACGCGTTTTTGGCCCAAAAA-C
3970 G
324 G
* * * * ** *
3971 TGATGGTTATTACACGATTTCGGCTAAAAACTGACCTGAAAAATTTA-TC-TGAATTTTTTGCCA
1 TGATGGTTAGTACACGATTTCCGCTAAAAACAGACCCGAAATTTTTATTCTTGAGTTTTTTGCCA
4034 CAA
66 CAA
4037 AACAAATCCT
Statistics
Matches: 634, Mismatches: 66, Indels: 31
0.87 0.09 0.04
Matches are distributed among these distances:
319 2 0.00
320 46 0.07
321 10 0.02
322 10 0.02
323 221 0.35
324 165 0.26
325 9 0.01
326 81 0.13
327 87 0.14
328 3 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (324 bp):
TGATGGTTAGTACACGATTTCCGCTAAAAACAGACCCGAAATTTTTATTCTTGAGTTTTTTGCCA
CAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTATAGGGTTTTTCACGCTTCTAATA
TCGTTTTTTCTATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
AAAACAAATCCATAAATAGAATGCGACTAGGAATTGGTTCGATGAATATAGATATTTCAAATAGA
CTTTCTGCTAAAAATCATGCAAATCTGAGCTGAGATCCCGAAACGCGTTTTTGGCCCAAAAACG
Found at i:4170 original size:194 final size:192
Alignment explanation
Indices: 3841--4228 Score: 530
Period size: 194 Copynumber: 2.0 Consensus size: 192
3831 TTTGCTCGTA
*
3841 AAAACAAATCCATAAATAGAATGCGACTAGGATTTGGTTCGATGAATATAGATATTTCAAATAGA
1 AAAACAAATCCATAAATAGAATGCGACTAGGATTTGGTTCGATGAATATAGATATTTCAAAGAGA
* * *
3906 CTTTCTGCTAAAAATCTTGCAAAACTGAGATGGGACCCCGAAGCGCGTTTTTAGCCCAAAAATCG
66 CTTTCTGCTAAAAATCTTGCAAAACTGAGATGGAACCCCGAAACGCGTTTTTAGCCCAAAAACCG
* *
3971 TGATGGTTATTACACGATTTCGGCTAAAAACT-GACCTGAAAAATTTATC-TGAATTTTT-TGCC
131 TGATGG----TACACGATTTCCGCTAAAAA-TAGACCCGAAAAATTTATCTTGAATTTTTCTGCC
4033 AC
191 AC
* * * * * * *
4035 AAAACAAATCCTTAAATCGAATGTGACTGGGATTTGGTTTGATGAATATAGATATTTTAAAGAGT
1 AAAACAAATCCATAAATAGAATGCGACTAGGATTTGGTTCGATGAATATAGATATTTCAAAGAGA
* * * *
4100 CTTTTTGCTAAAAATCTTGCATAACTGAGCTGGAACCCCGAAACGCGTTTTTAGCCCAAAAGCCG
66 CTTTCTGCTAAAAATCTTGCAAAACTGAGATGGAACCCCGAAACGCGTTTTTAGCCCAAAAACCG
** *
4165 TGATGGTACACGATTTCCGCTAAAAATAGACCCGAAATTTTTTTCTTGAATTTTTCTGCCAC
131 TGATGGTACACGATTTCCGCTAAAAATAGACCCGAAAAATTTATCTTGAATTTTTCTGCCAC
4227 AA
1 AA
4229 TACTCAGAAA
Statistics
Matches: 171, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
189 1 0.01
190 32 0.19
191 9 0.05
192 8 0.05
194 121 0.71
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (192 bp):
AAAACAAATCCATAAATAGAATGCGACTAGGATTTGGTTCGATGAATATAGATATTTCAAAGAGA
CTTTCTGCTAAAAATCTTGCAAAACTGAGATGGAACCCCGAAACGCGTTTTTAGCCCAAAAACCG
TGATGGTACACGATTTCCGCTAAAAATAGACCCGAAAAATTTATCTTGAATTTTTCTGCCAC
Found at i:4405 original size:837 final size:840
Alignment explanation
Indices: 3194--4777 Score: 2037
Period size: 837 Copynumber: 1.9 Consensus size: 840
3184 GATGCTTGTA
* *
3194 AAAACAAATCCATAAATCTAATGTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAATAGA
1 AAAACAAATCCATAAATCGAATGTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGA
* *
3259 CTTTCTGCGAAAACTCATGCAAATCTAAGCTAGGTCCCCGAAACGCGTTTTTGCCCCAAAAACCG
66 CTTTCTGCGAAAAATCATGCAAATCTAAGCTAGGACCCCGAAACGCGTTTTTGCCCCAAAAACCG
*
3324 TGATGGTTAGTACACGATTTCCGCTAAAAACAGACCCGAAATTTTTATTCTTGAGTTTTTTGCCA
131 TGATGG-T-GTACACGATTTCCGCTAAAAACAGACCCGAAATTTTTATTCTTGAATTTTTTGCCA
* * *
3389 CAATAGTCAGAAAAAATATATGATTCAACGCCAAAAAGATTATAGGGTTTTTCAAGCTTCTAATA
194 CAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTATAGGGTTTTTCAAGCTTATAATA
* * *
3454 TCGTTTTTTCATATTTTTTTCCCGAATTAATTTCTAAGTTTATCGAAACAAGATTCAGATGCTCG
259 TCGTTTTTTCACATTTTTTTCCCGAATTAACTTCTAAGTTAATCGAAACAAGATTCAGATGCTCG
* * * *
3519 TAAAAAATCCATAAATAGAATGCGGCTAGGAATTGGTTCGATGAATATAGGTATTTCAAAGAGAC
324 TAAAAAATCCATAAATACAATGCGGCTAGGAATTAGTTAGATGAATATAGATATTTCAAAGAGAC
* * * * * * * * *
3584 TTTCTGCTAAAAATCATGCAAATCTGAGCTGAGATCC-CGAAATGTGTTTTTGGCCCAAATA-CA
389 TTTCTGCCAAAAATCATGCAAAACTGAGC-CAGAGCCTCAAAACGCGTTTTTAGCCCAAAAATC-
* * * * *
3647 GTGATGGTTA-GTACACGATTTCCGCTAAAAA-TAGACCCG-AAATTTTTCTTCTTGAGTTTTTT
452 GTGAT-G-AACGTACACGATTTCCGCTAAAAACT-GACACGAAAATGTTT-TTCCTGAATTTTTT
* * *
3709 -CCATAATACTCA-AAAAAAATATATAATTCAACGCCAAAAAGATT-ATAGGGGTTTTCACGCTT
513 GCCACAATACTCAGAAAAAAATATATAATTCAAAGCCAAAAAGATTGA-AGGGCTTTTCACGCTT
* * **
3771 CTAATATCGTTTTTTCATTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCATTTGC
577 CTAATATCATTTTTCCATTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
* *
3836 TCGTAAAAACAAATCCATAAATAGAATGCGACTAGG-ATTTGGTTCGATGAATATAGATATTTCA
642 TCGTAAAAACAAATCCATAAATACAATGCGACT-GGAATTTCGTTCGATGAATATAGATATTTCA
* *
3900 A-ATAGA-CTTT-CTGCTAAAAATCTTGCAAAACTGAGATGGGACCCCGAAGCGCGTTTTTAGCC
706 AGA-A-ATCTTTAC-GCCAAAAATCATGCAAAACTGAGATGGGACCCCGAAGCGCGTTTTTAGCC
3962 CAAAAATCGTGATGGTTATTACACGATTTCGGCTAAAAACTGACCTGAAAAATTTATCTGAATTT
768 CAAAAATCGTGATGGTTATTACACGATTTCGGCTAAAAACTGACCTGAAAAATTTATCTGAATTT
4027 TTTGCCAC
833 TTTGCCAC
* * * * * *
4035 AAAACAAATCCTTAAATCGAATGTGACTGGGATTTGGTTTGATGAATATAGATATTTTAAAGAGT
1 AAAACAAATCCATAAATCGAATGTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGA
* * * * *
4100 CTTTTTGCTAAAAATCTTGCATAA-CTGAGCT-GGAACCCCGAAACGCGTTTTTAG-CCCAAAAG
66 CTTTCTGCGAAAAATCATGCA-AATCTAAGCTAGG-ACCCCGAAACGCGTTTTT-GCCCCAAAAA
*
4162 CCGTGAT-G-GTACACGATTTCCGCTAAAAATAGACCCGAAATTTTT-TTCTTGAATTTTTCTGC
128 CCGTGATGGTGTACACGATTTCCGCTAAAAACAGACCCGAAATTTTTATTCTTGAATTTTT-TGC
* * *
4224 CACAATACTCAGAAAAAGTATATAATTCAACGCCAAAAAGATTGTAGGGTTTTTCATGCTTATAA
192 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTATAGGGTTTTTCAAGCTTATAA
* * *
4289 TATC-TTTTTTC-CCTTTTTTT-CCGAATTTACTTGTAA-TTAAATCGAAACAAGATTCTA-ATG
257 TATCGTTTTTTCACATTTTTTTCCCGAATTAACTTCTAAGTT-AATCGAAACAAGATTC-AGATG
* * * * *
4349 CTCGTAAAAGCAAATCCTTAAATCCAATGTGGCT-GAGATTTAGTTAGATTAATATAGATATTTC
320 CTCGT-AAA--AAATCCATAAATACAATGCGGCTAG-GAATTAGTTAGATGAATATAGATATTTC
* ** ** *
4413 AATGATTCTTTCTGCCGGAAATCATGCAAAACTGAGCCAGGGCCTCAAAACGCGTTTTTAGCCCA
381 AAAGAGACTTTCTGCCAAAAATCATGCAAAACTGAGCCAGAGCCTCAAAACGCGTTTTTAGCCCA
4478 AAAATCGTGATGAACGTACACGATTTCCGCTAAAAACTGACACGAAAATGTTTTTCCTGAATTTT
446 AAAATCGTGATGAACGTACACGATTTCCGCTAAAAACTGACACGAAAATGTTTTTCCTGAATTTT
* * * *
4543 TTGCCACAATACTCAGAAGAAAATATATAATTCAAAGCCAAAAAGATTGACGTGCTTTTCACTCT
511 TTGCCACAATACTCAGAAAAAAATATATAATTCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCT
* * *
4608 TCTAATATCATTTTTCCATTTTTTTCCTAATTAGTTTCTAATTAAATCGAAACAAGATTCAGATG
576 TCTAATATCATTTTTCCATTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
** * * * * *
4673 CTCGTAAAAGGAAATCCTTAAATCCAATGTGGCTGGAATTTCGTTCGATGAATCTAGATATTTCA
641 CTCGTAAAAACAAATCCATAAATACAATGCGACTGGAATTTCGTTCGATGAATATAGATATTTCA
*
4738 AGAAATCTTTACGCCAAAAATCATGCAAAACTTAGATGGG
706 AGAAATCTTTACGCCAAAAATCATGCAAAACTGAGATGGG
4778 GTCTTGGAAC
Statistics
Matches: 637, Mismatches: 84, Indels: 47
0.83 0.11 0.06
Matches are distributed among these distances:
833 2 0.00
834 36 0.06
835 12 0.02
836 63 0.10
837 220 0.35
838 184 0.29
839 3 0.00
840 3 0.00
841 111 0.17
842 3 0.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (840 bp):
AAAACAAATCCATAAATCGAATGTGACTAGGAATTGGTTCGATGAATATAGATATTTCAAAGAGA
CTTTCTGCGAAAAATCATGCAAATCTAAGCTAGGACCCCGAAACGCGTTTTTGCCCCAAAAACCG
TGATGGTGTACACGATTTCCGCTAAAAACAGACCCGAAATTTTTATTCTTGAATTTTTTGCCACA
ATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTATAGGGTTTTTCAAGCTTATAATATC
GTTTTTTCACATTTTTTTCCCGAATTAACTTCTAAGTTAATCGAAACAAGATTCAGATGCTCGTA
AAAAATCCATAAATACAATGCGGCTAGGAATTAGTTAGATGAATATAGATATTTCAAAGAGACTT
TCTGCCAAAAATCATGCAAAACTGAGCCAGAGCCTCAAAACGCGTTTTTAGCCCAAAAATCGTGA
TGAACGTACACGATTTCCGCTAAAAACTGACACGAAAATGTTTTTCCTGAATTTTTTGCCACAAT
ACTCAGAAAAAAATATATAATTCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCA
TTTTTCCATTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
CAAATCCATAAATACAATGCGACTGGAATTTCGTTCGATGAATATAGATATTTCAAGAAATCTTT
ACGCCAAAAATCATGCAAAACTGAGATGGGACCCCGAAGCGCGTTTTTAGCCCAAAAATCGTGAT
GGTTATTACACGATTTCGGCTAAAAACTGACCTGAAAAATTTATCTGAATTTTTTGCCAC
Found at i:4652 original size:324 final size:318
Alignment explanation
Indices: 4035--5142 Score: 1044
Period size: 324 Copynumber: 3.4 Consensus size: 318
4025 TTTTTGCCAC
* * * * * *
4035 AAAA-CAAATCCTTAAATCGAATGTGACTGGGATTTGGTTTGATGAATATAGATATTTTAAAGAG
1 AAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTT-GTTAGATGAATATAGATA-TTTCAAGAA
* * * * * * * *
4099 TCTTTTTGCTAAAAATCTTGCATAACTGAGCTGGAACCCCGAAACGCGTTTTTAGCCCAAAAGCC
64 TCTTTCTGCCAAAAATCATGCAAAACTGAGCAGG-GCCTCGAAACGCGTTTTTAGCCCAAAAACC
* *
4164 GTGATG---GTACACGATTTCCGCTAAAAA-TAGACCCG-AAATTTTTTTCTTGAATTTTTCTGC
128 GTGATGAACGTACACGATTTCCGCTAAAAACT-GA-CCGAAAATATTTTTCCTGAATTTTT-TGC
* *
4224 CACAATACTCAGAAAAAGTATATAATTCAACGCCAAAAAGATTGTAGGGTTTTTCA-TGCTTATA
190 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTG-AGGGTTTTTCACT-CTTCTA
* * * *
4288 ATATCTTTTTTCCCTTTTTTTCCGAATTTACTTGTAATTAAATCGAAACAAGATTCTA-ATGCTC
253 ATATCTTTTTTCCATTTTTTTCCTAATTTAATTCTAATTAAATCGAAACAAGATTC-AGATGCTC
4352 GT
317 GT
* *
4354 AAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATTAATATAGATATTTCAATGAT
1 AAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTT-GTTAGATGAATATAGATATTTCAA-GAA
** * *
4419 TCTTTCTGCCGGAAATCATGCAAAACTGAGCCAGGGCCTCAAAACGCGTTTTTAGCCCAAAAATC
64 TCTTTCTGCCAAAAATCATGCAAAACTGAG-CAGGGCCTCGAAACGCGTTTTTAGCCCAAAAACC
*
4484 GTGATGAACGTACACGATTTCCGCTAAAAACTGACACGAAAATGTTTTTCCTGAATTTTTTGCCA
128 GTGATGAACGTACACGATTTCCGCTAAAAACTGAC-CGAAAATATTTTTCCTGAATTTTTTGCCA
* * *
4549 CAATACTCAGAAGAAAATATATAATTCAAAGCCAAAAAGATTGACGTGCTTTTCACTCTTCTAAT
192 CAATACTCAGAA-AAAATATATAATTCAACGCCAAAAAGATTGA-GGGTTTTTCACTCTTCTAAT
* *
4614 ATCATTTTTCCATTTTTTTCCTAA-TTAGTTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
255 ATCTTTTTTCCATTTTTTTCCTAATTTA-ATTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * *
4678 AAAAGGAAATCCTTAAATCCAATGTGGCTG-GAATTTCGTTCGATGAATCTAGATATTTCAAGAA
1 AAAAGCAAATCCTTAAATCCAATGTGGCTGAG-ATTT-GTTAGATGAATATAGATATTTCAAG-A
* * * * *
4742 ATCTTTAC-GCCAAAAATCATGCAAAACTTAG-ATGGGGTCTTGGAACACGTTTTTAG-CCAAAA
63 ATCTTT-CTGCCAAAAATCATGCAAAACTGAGCA--GGGCCTCGAAACGCGTTTTTAGCCCAAAA
* * ** * * **
4804 ACCGTGATGGTACACGATTTCAGCTAAATTTTTGC-AAAAAGCTGACCCAAAAAATTTTTCCTCC
125 ACCGTGAT-G-A-ACG--TACA-C--GATTTCCGCTAAAAA-CTGACCGAAAATATTTTTCCTGA
* * * * * * **
4868 ATTCTCTGTCACATTACTTAGAAAAAATATGTAATTCAACGCCAAAAATTTTGAAGGGTTTTTCA
181 ATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTG-AGGGTTTTTCA
* *
4933 CTGTTCTAGTATCGTTTTTTCCA-TTTTTT-CTGAATTTAATTCTAATTAAATCGAAACAAGATT
245 CTCTTCTAATATC-TTTTTTCCATTTTTTTCCT-AATTTAATTCTAATTAAATCGAAACAAGATT
*
4996 CAGATGCTGGT
308 CAGATGCTCGT
** * * * * *
5007 AAAAATAAATCCTTAAATCAAATTTTGCCTTAGATTTGATTACATGAATATAGATATTTCAAGTA
1 AAAAGCAAATCCTTAAATCCAA-TGTGGCTGAGATTTG-TTAGATGAATATAGATATTTCAAG-A
* *** * * ** * * *
5072 GTCTTGGAGTCAAAAATCATGCAAAATTGAGGTGAGTCCTCGGAACGCGTTTTTAG-CGAAAAAC
63 ATCTTTCTGCCAAAAATCATGCAAAACTGAGCAG-GGCCTCGAAACGCGTTTTTAGCCCAAAAAC
5136 CGTGATG
127 CGTGATG
5143 GTTAGTATAC
Statistics
Matches: 657, Mismatches: 94, Indels: 66
0.80 0.12 0.08
Matches are distributed among these distances:
319 9 0.01
320 101 0.15
321 3 0.00
322 2 0.00
323 62 0.09
324 214 0.33
325 3 0.00
326 3 0.00
328 5 0.01
329 110 0.17
330 133 0.20
331 12 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (318 bp):
AAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTTGTTAGATGAATATAGATATTTCAAGAATC
TTTCTGCCAAAAATCATGCAAAACTGAGCAGGGCCTCGAAACGCGTTTTTAGCCCAAAAACCGTG
ATGAACGTACACGATTTCCGCTAAAAACTGACCGAAAATATTTTTCCTGAATTTTTTGCCACAAT
ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAGGGTTTTTCACTCTTCTAATATCTTT
TTTCCATTTTTTTCCTAATTTAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
Found at i:19573 original size:31 final size:32
Alignment explanation
Indices: 19535--19607 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
19525 TAAAAAGCGA
*
19535 TCAATTTAATCA-ATGTACTCAAAAGATTGGG
1 TCAATTTAATCATATATACTCAAAAGATTGGG
* * *
19566 TCAATTTAAT-ATCTATACTCACAAGATTGTG
1 TCAATTTAATCATATATACTCAAAAGATTGGG
*
19597 TCAATTGAATC
1 TCAATTTAATC
19608 CAACTGATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (32 bp):
TCAATTTAATCATATATACTCAAAAGATTGGG
Found at i:19849 original size:17 final size:18
Alignment explanation
Indices: 19824--19859 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
19814 TAAAAAGCTA
*
19824 TTATTTTAAAATA-TATT
1 TTATATTAAAATACTATT
19841 TTATATTAAAATACTATT
1 TTATATTAAAATACTATT
19859 T
1 T
19860 AAACTCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATATTAAAATACTATT
Found at i:26905 original size:21 final size:19
Alignment explanation
Indices: 26880--26937 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
26870 GCTGCTCTAA
*
26880 TAATCTCATATGTACAATACC
1 TAATCTCATTTGTACAAT--C
* * *
26901 TAATCTAATTTGTACAGTG
1 TAATCTCATTTGTACAATC
26920 TAATCTCATTTGTACAAT
1 TAATCTCATTTGTACAAT
26938 TGCTAAATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (19 bp):
TAATCTCATTTGTACAATC
Found at i:39374 original size:11 final size:11
Alignment explanation
Indices: 39358--39398 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
39348 CTGTTTCCTC
39358 TCTTTTTTTTT
1 TCTTTTTTTTT
*
39369 TCTTTTTTTTC
1 TCTTTTTTTTT
*
39380 TCTTTTTCATTT
1 TCTTTTT-TTTT
39392 TCTTTTT
1 TCTTTTT
39399 GGATAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:39382 original size:22 final size:23
Alignment explanation
Indices: 39356--39398 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39346 ATCTGTTTCC
*
39356 TCTCTTTTT-TTTTTCTTTTTTT
1 TCTCTTTTTCATTTTCTTTTTTT
39378 TCTCTTTTTCATTTTCTTTTT
1 TCTCTTTTTCATTTTCTTTTT
39399 GGATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (23 bp):
TCTCTTTTTCATTTTCTTTTTTT
Found at i:40986 original size:2 final size:2
Alignment explanation
Indices: 40979--41028 Score: 75
Period size: 2 Copynumber: 24.5 Consensus size: 2
40969 GTGGTAGAAT
40979 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA
41023 TA -A TA T
1 TA TA TA T
41029 TAAAAAGATA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.02
2 40 0.89
3 4 0.09
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:41323 original size:21 final size:19
Alignment explanation
Indices: 41278--41335 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
41268 CTGTTTAGCA
41278 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
41297 ACTGTACAGATTAGAATATAT
1 ACTGTACAGATGAG-AT-TAC
* *
41318 ACTGTACAAATAAGATTA
1 ACTGTACAGATGAGATTA
41336 TTAGAGTAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.45
20 4 0.12
21 14 0.42
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:45734 original size:3 final size:3
Alignment explanation
Indices: 45726--45752 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
45716 CACAATTATA
45726 TGC TGC TGC TGC TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC
45753 AAGTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
TGC
Found at i:48807 original size:178 final size:179
Alignment explanation
Indices: 48474--48827 Score: 579
Period size: 179 Copynumber: 2.0 Consensus size: 179
48464 TAATATCATT
* *
48474 TAAGAAATATATTTAAAAAATTTTAATATATCTGATTTTTTAATTAAAATAGTAAAATGGTAAAA
1 TAAGAAATATATTTAAAAAATTATAATATATCTAATTTTTTAATTAAAATAGTAAAATGGTAAAA
** *
48539 ATAAAATAGTTATAAATATATTAGATTTGATTAAATAAAAATAGAGTTTTTAATTGAGTAAAATT
66 ATAAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACT
* *
48604 GTAAAAGTTTAAACAATGACATTTAAGAAA-ATATAT-GAAAAATAAGGG
131 GAAAAAATTTAAACAATGACATTTAAGAAATATA-ATCGAAAAATAAGGG
48652 TAAGAAATATATTTAAAAAATTATAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAAA
1 TAAGAAATATATTTAAAAAATTATAATATATCTAA-TTTTTTAATTAAAATAGTAAAATGGTAAA
* *
48717 AATAAAATATTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAC
65 AATAAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAAC
*
48782 T-AAAAAATTTAAACAATGGCATTTAAGAAATATAATCGAAAAATAA
130 TGAAAAAATTTAAACAATGACATTTAAGAAATATAATCGAAAAATAA
48828 TCGTCAATTC
Statistics
Matches: 163, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
178 61 0.37
179 102 0.63
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (179 bp):
TAAGAAATATATTTAAAAAATTATAATATATCTAATTTTTTAATTAAAATAGTAAAATGGTAAAA
ATAAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACT
GAAAAAATTTAAACAATGACATTTAAGAAATATAATCGAAAAATAAGGG
Found at i:49293 original size:29 final size:31
Alignment explanation
Indices: 49235--49307 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
49225 TAAATATAAA
* * *
49235 AAAAAAATCTCTTATGTTTTTCTTTTGGGAC
1 AAAATAATCCCTTATGTTTTTCTTATGGGAC
49266 AAAATAATCCCTTATG-TTTT-TTATGGGAC
1 AAAATAATCCCTTATGTTTTTCTTATGGGAC
* *
49295 AAATTAGTCCCTT
1 AAAATAATCCCTT
49308 GCTTCCACGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.51
30 4 0.11
31 14 0.38
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (31 bp):
AAAATAATCCCTTATGTTTTTCTTATGGGAC
Done.