Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020862.1 Corchorus olitorius cultivar O-4 contig20895, 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: 75097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:700 original size:331 final size:330
Alignment explanation
Indices: 1--1430 Score: 1986
Period size: 331 Copynumber: 4.4 Consensus size: 330
*
1 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAA
1 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAA
*
66 TTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATAATCGTAAAAACAAATCCT
66 TTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCT
* ** *
131 TAAATACATTGTCTCTAAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAA
131 TAAATCCATTGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAA
*
196 AATCATGC-AAA-TGAG-C-GGGCCC-GAA-GCG-TTTT-AGCAAAAA-C-TG-TG-ACGTACAC
196 AATCATGCAAAACTGAGCCGGGGCCCGGAACGCGTTTTTAACCAAAAACCGTGATGTAC-TACAC
* * * * * * *
249 GATTTCGGCAAAAATATTGCAGAAATTGACCCGAAAGATATTTCCTCAATTTTTAACCGCAGTAC
260 GATTTCAGCAAAAATTTTGAAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATAC
314 TCGTAA
325 TCGTAA
*
320 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAA
1 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAA
* * * * *
385 TT-TTTCCCGAATTAATTTCTATTTAAATCAAAAAAAGATTCAGATGCTCGTAAAATCAAATCCT
66 TTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCT
* *
449 TAAATCCAATGTGGCTGAGATTTGCGATGATGAATATAGATATTTCAATGAGTCTTGGCG-CAAA
131 TAAATCCATTGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAA
* * *
513 AATCATGCACATCTAAGCCGGGGCCCTGGAACGCGTTTTTAACCAAAAACCGTGATGGTTACTAC
196 AATCATGCAAAACTGAGCCGGGGCCC-GGAACGCGTTTTTAACCAAAAACCGTGAT-G-TACTAC
* * *
578 ACGATTTCAGCAAAAATTTTGAAAAAACTGATCCGAAAGGTTTTTCCTCAATTTTTAACCTCAAT
258 ACGATTTCAGCAAAAATTTTGAAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAAT
643 ACTCGTAA
323 ACTCGTAA
*
651 AAAATATATTATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAA
1 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAA
* * *
716 TT-TTTCCTGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCTT
66 TTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCT
* * * * * *
780 TAAATCCATTGTGGCTGATATTTGGTTAT-ATTAATATAGATTTTTCAATGAGTCTTGGTGTCAA
131 TAAATCCATTGTGGCTGAGATTTGG-GATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAA
* * * ** * *
844 AAATCATGCAAAAGTGAGCCGGGGCACCAGAACGCGTCTTTAGTCAAAAATCGTGA--TAGTACA
195 AAATCATGCAAAACTGAGCCGGGGC-CCGGAACGCGTTTTTAACCAAAAACCGTGATGTACTACA
* *
907 CGATTT-AGACAAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAAT
259 CGATTTCAG-CAAAAATTTTGAAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAAT
*
971 ACTTGTAA
323 ACTCGTAA
* * * *
979 AAAATATATTATTCAACGCCAAAAAGATTGAAAGGTTTTTCACGCTTCTAATACCTTTTTTTCAA
1 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAA
* *
1044 TTCTTTCCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATAATCGTAAAAACAAATCCT
66 TTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCT
* * * *
1109 TAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCATTGAGTCTTGGTGCAAAA
131 TAAATCCATTGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAA
* * * * *
1174 AATCATGCAAAACTGATCCGGGACCCCGAAACACGTTTTTAGCCAAAAACCGTGATGGTTACTAC
196 AATCATGCAAAACTGAGCCGGG-GCCCGGAACGCGTTTTTAACCAAAAACCGTGAT-G-TACTAC
* * * *
1239 ACGATTTCAGCAAAAATTTTGAAAAAACTGATCCGAAAGGTTTTTCCTCAATTTCTAACCTCAAT
258 ACGATTTCAGCAAAAATTTTGAAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAAT
1304 ACTCGTAA
323 ACTCGTAA
*
1312 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGC-T-T-ATATCATTTTTACAA
1 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAA
* *
1374 TTCTTTCCCGATTTAATTTCTAATTAAATCGAAACAAGATTCAGATGATTGTAAAAA
66 TTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAA
1431 TTATATGGGC
Statistics
Matches: 987, Mismatches: 97, Indels: 43
0.88 0.09 0.04
Matches are distributed among these distances:
317 12 0.01
318 111 0.11
319 70 0.07
320 1 0.00
321 6 0.01
323 3 0.00
324 3 0.00
325 4 0.00
326 7 0.01
327 3 0.00
328 137 0.14
329 158 0.16
330 67 0.07
331 238 0.24
332 52 0.05
333 113 0.11
334 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (330 bp):
AAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAA
TTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCT
TAAATCCATTGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAA
AATCATGCAAAACTGAGCCGGGGCCCGGAACGCGTTTTTAACCAAAAACCGTGATGTACTACACG
ATTTCAGCAAAAATTTTGAAAAAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACT
CGTAA
Found at i:1461 original size:26 final size:26
Alignment explanation
Indices: 1432--1634 Score: 250
Period size: 26 Copynumber: 7.9 Consensus size: 26
1422 TTGTAAAAAT
*
1432 TATATGGGCCCTATTGAATATGCAAC
1 TATATGGGCCCTACTGAATATGCAAC
1458 TATATGGGCCCTACTGAATATGCAAC
1 TATATGGGCCCTACTGAATATGCAAC
* * *
1484 TATAAGAGCCCTACTGAATATACAAC
1 TATATGGGCCCTACTGAATATGCAAC
* *
1510 TATATCGGCCCTACTGAATATACAAC
1 TATATGGGCCCTACTGAATATGCAAC
***
1536 TATATGGTTTCTA-TG-A-ATGCAAC
1 TATATGGGCCCTACTGAATATGCAAC
* *
1559 TACATGAGCCCTACTGAATATGCAAC
1 TATATGGGCCCTACTGAATATGCAAC
* * *
1585 TACATGGGCCCTATTAAATATGCAAC
1 TATATGGGCCCTACTGAATATGCAAC
*
1611 TACATGGGCCCTACTGAATATGCA
1 TATATGGGCCCTACTGAATATGCA
1635 CCCCTACTGA
Statistics
Matches: 152, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
23 14 0.09
24 3 0.02
25 3 0.02
26 132 0.87
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (26 bp):
TATATGGGCCCTACTGAATATGCAAC
Found at i:1520 original size:52 final size:50
Alignment explanation
Indices: 1432--2803 Score: 1320
Period size: 52 Copynumber: 26.8 Consensus size: 50
1422 TTGTAAAAAT
*
1432 TATATGGGCCCTATTGAATATGCAACTATATGGGCCCTACTGAATATGCAAC
1 TATAT-GGCCCTACTGAATATGCAACTATAT-GGCCCTACTGAATATGCAAC
* * *
1484 TATAAGAGCCCTACTGAATATACAACTATATCGGCCCTACTGAATATACAAC
1 TATATG-GCCCTACTGAATATGCAACTATAT-GGCCCTACTGAATATGCAAC
** *
1536 TATATGGTTTCTA-TG-A-ATGCAACTACATGAGCCCTACTGAATATGCAAC
1 TATATGG-CCCTACTGAATATGCAACTATATG-GCCCTACTGAATATGCAAC
* * * *
1585 TACATGGGCCCTATTAAATATGCAACTACATGGGCCCTACTGAATATGC-AC
1 TATAT-GGCCCTACTGAATATGCAACTATAT-GGCCCTACTGAATATGCAAC
*
1636 -------CCCTACTGAATATGCAACTACATGGGCCCTACTGAATATGCAAC
1 TATATGGCCCTACTGAATATGCAACTATAT-GGCCCTACTGAATATGCAAC
* * * *
1680 TACATGGGCCCTACTGAATTTGCAACTAGATGGTTCCTACTGAATATGCAAC
1 TATAT-GGCCCTACTGAATATGCAACTATATGG-CCCTACTGAATATGCAAC
* *
1732 TATATGAACCCTATTGAATATGCAACTATATGAGCCCTACTGAATATGCAAC
1 TATATG-GCCCTACTGAATATGCAACTATATG-GCCCTACTGAATATGCAAC
* *
1784 TATATGCCCCGTACTGAATATGCAACTATATGCCCCCTTACTGAATATGCAAC
1 TATATGGCCC-TACTGAATATGCAACTATATG-GCCC-TACTGAATATGCAAC
* * * *
1837 TATATGGTTCCTACTGAATATGCAACTATATAAGACCTACTGAATATTCAAC
1 TATATGG-CCCTACTGAATATGCAACTATAT-GGCCCTACTGAATATGCAAC
*
1889 TATATGAGCCCTACTGAATATGCAACTATATGAACCCTACTGAATATGCAAC
1 TATATG-GCCCTACTGAATATGCAACTATATG-GCCCTACTGAATATGCAAC
* ** * **
1941 TATATAGACCAGACTGAATATACAACTATATACCCCCTACTGAATATGCAAC
1 TATAT-GGCCCTACTGAATATGCAACTATAT-GGCCCTACTGAATATGCAAC
* * * *
1993 TATATGGTTCCC-ACTGAATATGCGACTATATGGTTCCTATTGAATATGCGAC
1 TATATGG--CCCTACTGAATATGCAACTATATGG-CCCTACTGAATATGCAAC
* * * * * * *
2045 TATATCGGCCCAAATGAATGTGCGACTATATGGGCCCTACTGAATTTACGAC
1 TATAT-GGCCCTACTGAATATGCAACTATAT-GGCCCTACTGAATATGCAAC
* * *
2097 TATATGGTTCCTACTGAATATGCGACTATATGGGCCCTATTGAATATGCAAC
1 TATATGG-CCCTACTGAATATGCAACTATAT-GGCCCTACTGAATATGCAAC
* * * *
2149 TATACGAGCCCTACTGAATATACAACTATACGGGCCCTACTGAATATGCCAC
1 TATATG-GCCCTACTGAATATGCAACTATA-TGGCCCTACTGAATATGCAAC
*
2201 TATATAGGCCCTACTGAATATGCAACTATATGAGCACTACTGAATATGCAAC
1 TATAT-GGCCCTACTGAATATGCAACTATATG-GCCCTACTGAATATGCAAC
* * * **
2253 TATATGAGCACTACTGAATAGGCAACTAAATAAACCCTACTGAATATGCAAC
1 TATATG-GCCCTACTGAATATGCAACTATAT-GGCCCTACTGAATATGCAAC
*
2305 TATATGCCCCCTACTGAATATGCAACTATATGAGCCCTAC------T-CAAC
1 TATATG-GCCCTACTGAATATGCAACTATATG-GCCCTACTGAATATGCAAC
* *
2350 TATATGGACCCTACTGAATATGCAAATATATGAGCCATACTGAATATGCAAC
1 TATATGG-CCCTACTGAATATGCAACTATATG-GCCCTACTGAATATGCAAC
* * * *
2402 TATATGGTTCCTATTGAATATGCAATTATATGGTTCCTACTGAATATGCAAC
1 TATATGG-CCCTACTGAATATGCAACTATATGG-CCCTACTGAATATGCAAC
** *
2454 TATATGAGCCCTACTGAATATGCAACTATATGTTTCTTACTGAATATGCAAC
1 TATATG-GCCCTACTGAATATGCAACTATATG-GCCCTACTGAATATGCAAC
* * *
2506 TATCTGGTTCCTACTGAATATGCAACTATATGGTTCCTACTGAATATATGCAAC
1 TATATGG-CCCTACTGAATATGCAACTATATGG-CCCTACTG-A-ATATGCAAC
* * *
2560 TACATGAGCCCTACTGAATATGCAACCACATGAGCCCTACTGAATATGCAAC
1 TATATG-GCCCTACTGAATATGCAACTATATG-GCCCTACTGAATATGCAAC
* *
2612 TATATGGGCCCTACTGAATATGCAAC-------CCGTATTGAATATGCAAC
1 TATAT-GGCCCTACTGAATATGCAACTATATGGCCCTACTGAATATGCAAC
* * *
2656 AATATGGTTCCTACTGAATATGCAACTACATGAGCCCTACTGAATATGCAAC
1 TATATGG-CCCTACTGAATATGCAACTATATG-GCCCTACTGAATATGCAAC
* * *
2708 TATATGAGCCTTACTGAATATGCAACTATATGGTTCTTACTGAATATGCAAC
1 TATATG-GCCCTACTGAATATGCAACTATATGG-CCCTACTGAATATGCAAC
** *
2760 TATATAGTTCCTACTGAATATGCAACTATATGGTTCCTACTGAA
1 TATAT-GGCCCTACTGAATATGCAACTATATGG-CCCTACTGAA
2804 AATTCATTTT
Statistics
Matches: 1112, Mismatches: 136, Indels: 144
0.80 0.10 0.10
Matches are distributed among these distances:
43 41 0.04
44 39 0.04
45 40 0.04
46 1 0.00
48 1 0.00
49 35 0.03
50 4 0.00
51 25 0.02
52 820 0.74
53 61 0.05
54 43 0.04
55 2 0.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (50 bp):
TATATGGCCCTACTGAATATGCAACTATATGGCCCTACTGAATATGCAAC
Found at i:1641 original size:17 final size:17
Alignment explanation
Indices: 1619--1651 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1609 ACTACATGGG
1619 CCCTACTGAATATGCAC
1 CCCTACTGAATATGCAC
1636 CCCTACTGAATATGCA
1 CCCTACTGAATATGCA
1652 ACTACATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.24
Consensus pattern (17 bp):
CCCTACTGAATATGCAC
Found at i:1665 original size:26 final size:26
Alignment explanation
Indices: 1636--2803 Score: 1200
Period size: 26 Copynumber: 45.4 Consensus size: 26
1626 GAATATGCAC
*
1636 CCCTACTGAATATGCAACTACATGGG
1 CCCTACTGAATATGCAACTATATGGG
*
1662 CCCTACTGAATATGCAACTACATGGG
1 CCCTACTGAATATGCAACTATATGGG
* * *
1688 CCCTACTGAATTTGCAACTAGATGGT
1 CCCTACTGAATATGCAACTATATGGG
* **
1714 TCCTACTGAATATGCAACTATATGAA
1 CCCTACTGAATATGCAACTATATGGG
* *
1740 CCCTATTGAATATGCAACTATATGAG
1 CCCTACTGAATATGCAACTATATGGG
*
1766 CCCTACTGAATATGCAACTATAT-GC
1 CCCTACTGAATATGCAACTATATGGG
**
1791 CCCGTACTGAATATGCAACTATATGCC
1 CCC-TACTGAATATGCAACTATATGGG
*
1818 CCCTTACTGAATATGCAACTATATGGT
1 CCC-TACTGAATATGCAACTATATGGG
* **
1845 TCCTACTGAATATGCAACTATATAAG
1 CCCTACTGAATATGCAACTATATGGG
* * *
1871 ACCTACTGAATATTCAACTATATGAG
1 CCCTACTGAATATGCAACTATATGGG
**
1897 CCCTACTGAATATGCAACTATATGAA
1 CCCTACTGAATATGCAACTATATGGG
* *
1923 CCCTACTGAATATGCAACTATATAGA
1 CCCTACTGAATATGCAACTATATGGG
** * ***
1949 CCAGACTGAATATACAACTATATACC
1 CCCTACTGAATATGCAACTATATGGG
*
1975 CCCTACTGAATATGCAACTATATGGTT
1 CCCTACTGAATATGCAACTATATGG-G
* *
2002 CCC-ACTGAATATGCGACTATATGGT
1 CCCTACTGAATATGCAACTATATGGG
* * * *
2027 TCCTATTGAATATGCGACTATATCGG
1 CCCTACTGAATATGCAACTATATGGG
* * * *
2053 CCCAAATGAATGTGCGACTATATGGG
1 CCCTACTGAATATGCAACTATATGGG
* * * *
2079 CCCTACTGAATTTACGACTATATGGT
1 CCCTACTGAATATGCAACTATATGGG
* *
2105 TCCTACTGAATATGCGACTATATGGG
1 CCCTACTGAATATGCAACTATATGGG
* * *
2131 CCCTATTGAATATGCAACTATACGAG
1 CCCTACTGAATATGCAACTATATGGG
* *
2157 CCCTACTGAATATACAACTATACGGG
1 CCCTACTGAATATGCAACTATATGGG
* *
2183 CCCTACTGAATATGCCACTATATAGG
1 CCCTACTGAATATGCAACTATATGGG
*
2209 CCCTACTGAATATGCAACTATATGAG
1 CCCTACTGAATATGCAACTATATGGG
* *
2235 CACTACTGAATATGCAACTATATGAG
1 CCCTACTGAATATGCAACTATATGGG
* * * ***
2261 CACTACTGAATAGGCAACTAAATAAA
1 CCCTACTGAATATGCAACTATATGGG
**
2287 CCCTACTGAATATGCAACTATATGCC
1 CCCTACTGAATATGCAACTATATGGG
*
2313 CCCTACTGAATATGCAACTATATGAG
1 CCCTACTGAATATGCAACTATATGGG
*
2339 CCCTAC------T-CAACTATATGGA
1 CCCTACTGAATATGCAACTATATGGG
* *
2358 CCCTACTGAATATGCAAATATATGAG
1 CCCTACTGAATATGCAACTATATGGG
* *
2384 CCATACTGAATATGCAACTATATGGT
1 CCCTACTGAATATGCAACTATATGGG
* * * *
2410 TCCTATTGAATATGCAATTATATGGT
1 CCCTACTGAATATGCAACTATATGGG
* *
2436 TCCTACTGAATATGCAACTATATGAG
1 CCCTACTGAATATGCAACTATATGGG
**
2462 CCCTACTGAATATGCAACTATATGTT
1 CCCTACTGAATATGCAACTATATGGG
* * * *
2488 TCTTACTGAATATGCAACTATCTGGT
1 CCCTACTGAATATGCAACTATATGGG
* *
2514 TCCTACTGAATATGCAACTATATGGT
1 CCCTACTGAATATGCAACTATATGGG
* * *
2540 TCCTACTGAATATATGCAACTACATGAG
1 CCCTACTG-A-ATATGCAACTATATGGG
* * *
2568 CCCTACTGAATATGCAACCACATGAG
1 CCCTACTGAATATGCAACTATATGGG
2594 CCCTACTGAATATGCAACTATATGGG
1 CCCTACTGAATATGCAACTATATGGG
2620 CCCTACTGAATATGCAAC--------
1 CCCTACTGAATATGCAACTATATGGG
* * * *
2638 CCGTATTGAATATGCAACAATATGGT
1 CCCTACTGAATATGCAACTATATGGG
* * *
2664 TCCTACTGAATATGCAACTACATGAG
1 CCCTACTGAATATGCAACTATATGGG
*
2690 CCCTACTGAATATGCAACTATATGAG
1 CCCTACTGAATATGCAACTATATGGG
* *
2716 CCTTACTGAATATGCAACTATATGGT
1 CCCTACTGAATATGCAACTATATGGG
* * * *
2742 TCTTACTGAATATGCAACTATATAGT
1 CCCTACTGAATATGCAACTATATGGG
* *
2768 TCCTACTGAATATGCAACTATATGGT
1 CCCTACTGAATATGCAACTATATGGG
*
2794 TCCTACTGAA
1 CCCTACTGAA
2804 AATTCATTTT
Statistics
Matches: 981, Mismatches: 140, Indels: 42
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.02
19 16 0.02
20 1 0.00
25 7 0.01
26 888 0.91
27 32 0.03
28 21 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (26 bp):
CCCTACTGAATATGCAACTATATGGG
Found at i:2351 original size:19 final size:19
Alignment explanation
Indices: 2327--2364 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2317 ACTGAATATG
2327 CAACTATAT-GAGCCCTACT
1 CAACTATATGGA-CCCTACT
2346 CAACTATATGGACCCTACT
1 CAACTATATGGACCCTACT
2365 GAATATGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.26
Consensus pattern (19 bp):
CAACTATATGGACCCTACT
Found at i:2365 original size:45 final size:45
Alignment explanation
Indices: 2301--2390 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
2291 ACTGAATATG
* * *
2301 CAACTATATGCCCCCTACTGAATATGCAACTATATGAGCCCTACT
1 CAACTATATGCACCCTACTGAATATGCAAATATATGAGCCATACT
*
2346 CAACTATATGGACCCTACTGAATATGCAAATATATGAGCCATACT
1 CAACTATATGCACCCTACTGAATATGCAAATATATGAGCCATACT
2391 GAATATGCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (45 bp):
CAACTATATGCACCCTACTGAATATGCAAATATATGAGCCATACT
Found at i:3982 original size:20 final size:20
Alignment explanation
Indices: 3957--4072 Score: 88
Period size: 20 Copynumber: 5.5 Consensus size: 20
3947 CGGCGCATTC
*
3957 ACATTGAATTTTCCCAATTG
1 ACATTGAACTTTCCCAATTG
* *
3977 ACATTGAACTTTCCTTAATTCTC
1 ACATTGAACTTTCC-CAA-T-TG
* *
4000 ACATTCAACATTCCCAATTG
1 ACATTGAACTTTCCCAATTG
* * * *
4020 ACATTGAACTTGCCTTATTCTC
1 ACATTGAACTTTCC-CAAT-TG
* *
4042 ACATTCAACTTTCCCAATTA
1 ACATTGAACTTTCCCAATTG
4062 ACATTGAACTT
1 ACATTGAACTT
4073 GCCTTGATTC
Statistics
Matches: 72, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
20 36 0.50
21 7 0.10
22 16 0.22
23 13 0.18
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (20 bp):
ACATTGAACTTTCCCAATTG
Found at i:4130 original size:24 final size:24
Alignment explanation
Indices: 4098--4218 Score: 87
Period size: 24 Copynumber: 5.4 Consensus size: 24
4088 CAATTTTCCC
4098 AATTCACATTGAACTTGCCTTGAT
1 AATTCACATTGAACTTGCCTTGAT
** ***
4122 AATTCACATCCAA-TT---TTCCC
1 AATTCACATTGAACTTGCCTTGAT
*
4142 AATTCACATTGGACTTGCCTTGAT
1 AATTCACATTGAACTTGCCTTGAT
** ***
4166 AATTCACATCCAA-TT---TTCCC
1 AATTCACATTGAACTTGCCTTGAT
4186 AATTCACATTGAACTTGCCTTGAT
1 AATTCACATTGAACTTGCCTTGAT
4210 AATTCACAT
1 AATTCACAT
4219 CCAAATTTCC
Statistics
Matches: 67, Mismatches: 22, Indels: 16
0.64 0.21 0.15
Matches are distributed among these distances:
20 25 0.37
21 4 0.06
23 4 0.06
24 34 0.51
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (24 bp):
AATTCACATTGAACTTGCCTTGAT
Found at i:4142 original size:44 final size:42
Alignment explanation
Indices: 3953--4332 Score: 500
Period size: 44 Copynumber: 9.0 Consensus size: 42
3943 TACGCGGCGC
** * *
3953 ATTCACATTGAATTTTCCCAATTGACATTGAACTTTCCTT-A
1 ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTGA
* ** *
3994 ATTCTCACATTCAACATTCCCAATTGACATTGAACTTGCCTT-A
1 A-T-TCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTGA
* * * *
4037 TTCTCACATTCAACTTTCCCAATTAACATTGAACTTGCCTTG-
1 AT-TCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTGA
*
4079 ATTCAAATCCAATTTTCCCAATTCACATTGAACTTGCCTTGATA
1 ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTG--A
*
4123 ATTCACATCCAATTTTCCCAATTCACATTGGACTTGCCTTGATA
1 ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTG--A
4167 ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTGATA
1 ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTG--A
*
4211 ATTCACATCCAAATTTCCCAATTCACATTGAACTTGCCTTG-
1 ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTGA
4252 ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTG-
1 ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTGA
*
4293 ATTCACCTCCAATTTTCCCAATTCACATTGAACTTGCCTT
1 ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTT
4333 CTCACATTGG
Statistics
Matches: 315, Mismatches: 18, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
41 115 0.37
42 40 0.13
43 35 0.11
44 125 0.40
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (42 bp):
ATTCACATCCAATTTTCCCAATTCACATTGAACTTGCCTTGA
Found at i:4147 original size:20 final size:20
Alignment explanation
Indices: 4122--4320 Score: 83
Period size: 20 Copynumber: 9.4 Consensus size: 20
4112 TTGCCTTGAT
4122 AATTCACATCCAATTTTCCC
1 AATTCACATCCAATTTTCCC
*** * * *
4142 AATTCACATTGGACTTGCCTTG
1 AATTCACATCCAATTTTCC--C
4164 ATAATTCACATCCAATTTTCCC
1 A-A-TTCACATCCAATTTTCCC
** ***
4186 AATTCACATTGAACTTGCCTTGAT
1 AATTCACATCCAA-TT---TTCCC
*
4210 AATTCACATCCAAATTTCCC
1 AATTCACATCCAATTTTCCC
** * * *
4230 AATTCACATTGAACTTGCCTT
1 AATTCACATCCAATTTTCC-C
*
4251 GATTCACATCCAATTTTCCC
1 AATTCACATCCAATTTTCCC
** * * *
4271 AATTCACATTGAACTTGCCTT
1 AATTCACATCCAATTTTCC-C
* *
4292 GATTCACCTCCAATTTTCCC
1 AATTCACATCCAATTTTCCC
4312 AATTCACAT
1 AATTCACAT
4321 TGAACTTGCC
Statistics
Matches: 120, Mismatches: 49, Indels: 20
0.63 0.26 0.11
Matches are distributed among these distances:
20 61 0.51
21 30 0.25
22 2 0.02
23 2 0.02
24 25 0.21
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (20 bp):
AATTCACATCCAATTTTCCC
Found at i:4609 original size:121 final size:121
Alignment explanation
Indices: 4395--4623 Score: 397
Period size: 121 Copynumber: 1.9 Consensus size: 121
4385 CCCACAGCAG
*
4395 GAAGGCAATCCTTGCTGCCACAGGGATATGCTCAGCTCCAATGGGGAGACAACTGCAGAAGAGAA
1 GAAGGCAATCCTTGCTGCCACAGGGATATGCTCAACTCCAATGGGGAGACAACTGCAGAAGAGAA
4460 AAAACATTATAAAGAAACCATCAAAGCAGAAAAAGGAAAATCATACCAGCAAATCC
66 AAAACATTATAAAGAAACCATCAAAGCAGAAAAAGGAAAATCATACCAGCAAATCC
*
4516 GAAGGCAATCCTTGCTGCCACAGGGATATGCTCAACTCCAATGGGGAGATAACTGCAGAAGAGAA
1 GAAGGCAATCCTTGCTGCCACAGGGATATGCTCAACTCCAATGGGGAGACAACTGCAGAAGAGAA
* * *
4581 CAAACATTATCAAA-AAACCATCAGAGCAGAAAAAGGAACATCA
66 AAAACATTAT-AAAGAAACCATCAAAGCAGAAAAAGGAAAATCA
4624 CAGCAAGCAA
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
121 99 0.97
122 3 0.03
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (121 bp):
GAAGGCAATCCTTGCTGCCACAGGGATATGCTCAACTCCAATGGGGAGACAACTGCAGAAGAGAA
AAAACATTATAAAGAAACCATCAAAGCAGAAAAAGGAAAATCATACCAGCAAATCC
Found at i:12207 original size:780 final size:778
Alignment explanation
Indices: 10840--12376 Score: 2975
Period size: 780 Copynumber: 2.0 Consensus size: 778
10830 ATCTCATTTG
10840 TCACATACATTATTTATAAATAGTGATAAACTTATATAAGTAGAGATGAGCTTACTATATTTCCA
1 TCACATACATTATTTATAAATAGTGATAAACTTATATAAGTAGAGATGAGCTTACTATATTTCCA
*
10905 CTCTCATCGCCTTGTCCAAACAAATGCATTTATTCTACAACTCCCCTTTGTTTTCATTTCCCTTT
66 CTCTCATCGCCTTGTCCAAACAAATGCATTTATTCTACAACTCCCCTTCGTTTTCATTTCCCTTT
10970 CCAAAATAGGTTTTCCAGCCGACCTATCTCCAAAAGTTGTCTAAGATTGGTTTTCCCTTCGTTTT
131 CCAAAATAGGTTTTCCAGCCGACCTATCTCCAAAAGTTGTCTAAGATTGGTTTTCCCTTCGTTTT
*
11035 CTTTAAACTCGTTCAAATTGGTTTGTGATCCCACTAACTCTTCTTTCTAGCTACGCCACTGTTGG
196 CTTTAAACTCGTTCAAATTGGTTTGTGACCCCACTAACTCTTCTTTCTAGCTACGCCACTGTTGG
*
11100 AAACCCTAAGCTTTATCAATCTACAACCCCCTCGCTTGCCTCCCTCTAATCCTTCGAGCTTCAAT
261 AAACCCTAAGCTTTATCAATCTACAACCCCCTCGCTTGCCTCCCTCTAATCCTTCGAGCTTCAAC
11165 GACGATCTTCTCCACTTCGATCCTCTCCTCTACGACGTCCCTCTCCAGGTCGAGAGACTGCCGAT
326 GACGATCTTCTCCACTTCGATCCTCTCCTCTACGACGTCCCTCTCCAGGTCGAGAGACTGCCGAT
*
11230 CGATGCCGCTCTCTCCAAGTTCTTGTCCGAAGCAACCCCTCAGTTCATCGATGTCGATTTCGGGT
391 CGATGCCGCTCTCTCCAAGTTCTTGTCCGAAGCAACCCCTCAGTTCATCGATGTCGATTTCGGAT
11295 TTTTCAAGGATACTCAACCTCCTAGTGGTAATGTCGGCGCCAATTTATCTGAGATAGAGTTATGA
456 TTTTCAAGGATACTCAACCTCCTAGTGGTAATGTCGGCGCCAATTTATCTGAGATAGAGTTATGA
11360 GTCCTATTCTCATCAGTTTTCAATTTGAATTTGATAGCTTTGCGTCCATCACATAACCTTGGAGA
521 GTCCTATTCTCATCAGTTTTCAATTTGAATTTGATAGCTTTGCGTCCATCACATAACCTTGGAGA
11425 AGTGATTAAGAAACTTCGCCATGGCAACTGCGCCTTGTTAGTTTCTCTTTTCTTTCACGTTATAT
586 AGTGATTAAGAAACTTCGCCATGGCAACTGCGCCTTGTTAGTTTCTCTTTTCTTTCACGTTATAT
11490 TTCAAAAGGGGGGAAAATGCGATTTATGTTTATCAGTCCAAATGAAACTGCAGTTTTATGAGTGT
651 TTCAAAA-GGGGGAAAATGCGATTTATGTTTATCAGTCCAAATGAAACTGCAGTTTTATGAGTGT
*
11555 TATGATCCGTTTCGGCCCAAATTTAATTGGGCCTTTAAGTTTTATGAGTGTTATTATGTGGTATA
715 TATGATCAGTTTCGGCCCAAATTTAATTGGGCCTTTAA-TTTTATGAGTGTTATTATGTGGTATA
11620 TCACATACATTATTTATAAATAGTGATAAACTTATATAAGTAGAGATGAGCTTACTATATTTCCA
1 TCACATACATTATTTATAAATAGTGATAAACTTATATAAGTAGAGATGAGCTTACTATATTTCCA
11685 CTCTCATCGCCTTGTCCAAACAAATGCATTTATTCTACAACTCCCCTTCGTTTTCATTTCCCTTT
66 CTCTCATCGCCTTGTCCAAACAAATGCATTTATTCTACAACTCCCCTTCGTTTTCATTTCCCTTT
11750 CCAAAATAGGTTTTCCAGCCGACCTATCTCCAAAAGTTGTCTAAGATTGGTTTTCCCTTCGTTTT
131 CCAAAATAGGTTTTCCAGCCGACCTATCTCCAAAAGTTGTCTAAGATTGGTTTTCCCTTCGTTTT
11815 CTTTAAACTCGTTCAAATTGGTTTGTGACCCCACTAACTCTTCTTTCTAGCTACGCCACTGTTGG
196 CTTTAAACTCGTTCAAATTGGTTTGTGACCCCACTAACTCTTCTTTCTAGCTACGCCACTGTTGG
*
11880 AAACCCTAAGCTTTCTCAATCTACAACCCCCTCGCTTGCCTCCCTCTAATCCTTCGAGCTTCAAC
261 AAACCCTAAGCTTTATCAATCTACAACCCCCTCGCTTGCCTCCCTCTAATCCTTCGAGCTTCAAC
11945 GACGATCTTCTCCACTTCGATCCTCTCCTCTACGACGTCCCTCTCCAGGTCGAGAGACTGCCGAT
326 GACGATCTTCTCCACTTCGATCCTCTCCTCTACGACGTCCCTCTCCAGGTCGAGAGACTGCCGAT
12010 CGATGCCGCTCTCTCCAAGTTCTTGTCCGAAGCAACCCCTCAGTTCATCGATGTCGATTTCGGAT
391 CGATGCCGCTCTCTCCAAGTTCTTGTCCGAAGCAACCCCTCAGTTCATCGATGTCGATTTCGGAT
12075 TTTTCAAGGATACTCAACCTCCTAGTGGTAATGTCGGCGCCAATTTATCTGAGATAGAGTTATGA
456 TTTTCAAGGATACTCAACCTCCTAGTGGTAATGTCGGCGCCAATTTATCTGAGATAGAGTTATGA
12140 GTCCTATTCTCATCAGTTTTCAATTTGAATTTGATAGCTTTGCGTCCATCACATAACCTTGGAGA
521 GTCCTATTCTCATCAGTTTTCAATTTGAATTTGATAGCTTTGCGTCCATCACATAACCTTGGAGA
* *
12205 AGTGATTAAGAAACTTCGCCATGGCAATTGCGTCTTGTTAGTTTCTCTTTTCTTTCACGTTATAT
586 AGTGATTAAGAAACTTCGCCATGGCAACTGCGCCTTGTTAGTTTCTCTTTTCTTTCACGTTATAT
12270 TTCAAAAGGGGGAAAATGCGATTTATGTTTATCAGTCCAAATGAAACTGCAGTTTTATGAGTGTT
651 TTCAAAAGGGGGAAAATGCGATTTATGTTTATCAGTCCAAATGAAACTGCAGTTTTATGAGTGTT
*
12335 GTGATCAGTTTCGGCCCAAATTTAATTGGGCCTTTAATTTTA
716 ATGATCAGTTTCGGCCCAAATTTAATTGGGCCTTTAATTTTA
12377 GAAAAATTTC
Statistics
Matches: 748, Mismatches: 9, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
778 5 0.01
779 93 0.12
780 650 0.87
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (778 bp):
TCACATACATTATTTATAAATAGTGATAAACTTATATAAGTAGAGATGAGCTTACTATATTTCCA
CTCTCATCGCCTTGTCCAAACAAATGCATTTATTCTACAACTCCCCTTCGTTTTCATTTCCCTTT
CCAAAATAGGTTTTCCAGCCGACCTATCTCCAAAAGTTGTCTAAGATTGGTTTTCCCTTCGTTTT
CTTTAAACTCGTTCAAATTGGTTTGTGACCCCACTAACTCTTCTTTCTAGCTACGCCACTGTTGG
AAACCCTAAGCTTTATCAATCTACAACCCCCTCGCTTGCCTCCCTCTAATCCTTCGAGCTTCAAC
GACGATCTTCTCCACTTCGATCCTCTCCTCTACGACGTCCCTCTCCAGGTCGAGAGACTGCCGAT
CGATGCCGCTCTCTCCAAGTTCTTGTCCGAAGCAACCCCTCAGTTCATCGATGTCGATTTCGGAT
TTTTCAAGGATACTCAACCTCCTAGTGGTAATGTCGGCGCCAATTTATCTGAGATAGAGTTATGA
GTCCTATTCTCATCAGTTTTCAATTTGAATTTGATAGCTTTGCGTCCATCACATAACCTTGGAGA
AGTGATTAAGAAACTTCGCCATGGCAACTGCGCCTTGTTAGTTTCTCTTTTCTTTCACGTTATAT
TTCAAAAGGGGGAAAATGCGATTTATGTTTATCAGTCCAAATGAAACTGCAGTTTTATGAGTGTT
ATGATCAGTTTCGGCCCAAATTTAATTGGGCCTTTAATTTTATGAGTGTTATTATGTGGTATA
Found at i:13440 original size:2 final size:2
Alignment explanation
Indices: 13433--13466 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13423 AACTATGAAC
13433 TA TA TA TA 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 TA TA TA TA
13467 AATCTTAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18993 original size:29 final size:28
Alignment explanation
Indices: 18960--19030 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
18950 CGTCAGAAAA
**
18960 GGGCTTATTTGGCT-TTTTAAAGAGTTCAG
1 GGGCTTATTTGGCTCAATT-AA-AGTTCAG
18989 GGGCTTATTTGGCTGCAATTAAAGTTCAG
1 GGGCTTATTTGGCT-CAATTAAAGTTCAG
19018 GGGCTTATTTGGC
1 GGGCTTATTTGGC
19031 CATTTTGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 34 0.89
30 2 0.05
31 2 0.05
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.38
Consensus pattern (28 bp):
GGGCTTATTTGGCTCAATTAAAGTTCAG
Found at i:19585 original size:60 final size:60
Alignment explanation
Indices: 19505--19669 Score: 215
Period size: 60 Copynumber: 2.8 Consensus size: 60
19495 GCTAATTGCT
* * * * * *
19505 CAAACAAGGGTCTAAAGTTTGGCAAAATGCTTAAATAAGGGCTTG-ATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATTCTCAAATAAGGGCTTGAAT-TTTTAATTTGAC
** ** *
19565 CAAATAAGGGCCTAACGTTTGCCAAAATTCTCAAATAAGAACCCGAATTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATTCTCAAATAAGGGCTTGAATTTTTAATTTGAC
19625 CAAATAAGGGCCTAACGTTTGCCAAAATTCTCAAATAAGGGCTTG
1 CAAATAAGGGCCTAACGTTTGCCAAAATTCTCAAATAAGGGCTTG
19670 GCATCGAAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 87 0.98
61 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATTCTCAAATAAGGGCTTGAATTTTTAATTTGAC
Found at i:19603 original size:31 final size:31
Alignment explanation
Indices: 19565--19666 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 31
19555 TTAATTTGAC
19565 CAAATAAGGGCCTAACGTTTGCCAAAATTCT
1 CAAATAAGGGCCTAACGTTTGCCAAAATTCT
** * ** *
19596 CAAATAAGAACCCGAA--TTT--TTAATTTGGC-
1 CAAATAAG-GGCCTAACGTTTGCCAAAATT--CT
19625 CAAATAAGGGCCTAACGTTTGCCAAAATTCT
1 CAAATAAGGGCCTAACGTTTGCCAAAATTCT
19656 CAAATAAGGGC
1 CAAATAAGGGC
19667 TTGGCATCGA
Statistics
Matches: 51, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
28 8 0.16
29 8 0.16
30 8 0.16
31 19 0.37
32 8 0.16
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATTCT
Found at i:19810 original size:59 final size:59
Alignment explanation
Indices: 19709--19848 Score: 192
Period size: 59 Copynumber: 2.4 Consensus size: 59
19699 CTGACGTCAA
* *
19709 GCCCTTATTTGAGCATTTTCAATGACATTAGGCCCTTATTT-GGCGAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTT-GATAACATTAGGCCCTTATTTGGGC-AAATTAAAAGATCGG
* * * *
19769 GCCTTTATTTGAGCATTTTGATAACGTTAGGCCTTTATTTGGGCAACTTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTGATAACATTAGGCCCTTATTTGGGCAAATTAAAAGATCGG
*
19828 GCCCTTATTTTAGCATTTTGA
1 GCCCTTATTTGAGCATTTTGA
19849 CAAACGGCCC
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
59 50 0.70
60 21 0.30
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (59 bp):
GCCCTTATTTGAGCATTTTGATAACATTAGGCCCTTATTTGGGCAAATTAAAAGATCGG
Found at i:22601 original size:72 final size:72
Alignment explanation
Indices: 22439--22655 Score: 364
Period size: 72 Copynumber: 3.0 Consensus size: 72
22429 ACACTAACCC
* * *
22439 TCATCCTTTTAATTTATTTAACTCCTCAAAGAATTCCCTACAATTCAGT-AAATGTAAATTACAT
1 TCATCCTTTTAATTTGTTTAACTCCTCCAAGAATTCCCTACAATTCAATAAAATGTAAATTACAT
22503 TGAGATT
66 TGAGATT
*
22510 TCATCCTTTTAATTGGTTTAACTCCTCCAAGAATTCCCTACAATTCAATAAAATGTAAATTACAT
1 TCATCCTTTTAATTTGTTTAACTCCTCCAAGAATTCCCTACAATTCAATAAAATGTAAATTACAT
22575 TGAGATT
66 TGAGATT
* *
22582 TCATCCTTTTTATTTGTTTAACTCCTCCAAGAATTCCCTACAATTCAATAAAATGTAAATTAAAT
1 TCATCCTTTTAATTTGTTTAACTCCTCCAAGAATTCCCTACAATTCAATAAAATGTAAATTACAT
*
22647 TTAGATT
66 TGAGATT
22654 TC
1 TC
22656 GATCACTCCA
Statistics
Matches: 137, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 45 0.33
72 92 0.67
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (72 bp):
TCATCCTTTTAATTTGTTTAACTCCTCCAAGAATTCCCTACAATTCAATAAAATGTAAATTACAT
TGAGATT
Found at i:45638 original size:6 final size:6
Alignment explanation
Indices: 45627--45659 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
45617 TCTCAACGTG
*
45627 AAAACC AAAACC AAAACC AAAGCC AAAACC AAA
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAA
45660 GCTTTCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.67, C:0.30, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:50948 original size:50 final size:49
Alignment explanation
Indices: 50880--51052 Score: 152
Period size: 54 Copynumber: 3.4 Consensus size: 49
50870 AGGGCGACGA
50880 CCAGGACTCCTCCGAGAGAACGTCTCGTCCACGCTAGGATGGACGAGCGT
1 CCAGGACTCCTCCGAGAGAACGTCTCGTCCACGCTAGGA-GGACGAGCGT
** ** * * * *
50930 CCAGGACTCCTCTAAGAGAACGATGC-C-TCCATATTCTAAGGAGCGGGCCAACGA
1 CCAGGACTCCTCCGAGAGAACG-T-CTCGTCC--ACGCT-AGGA--GGACGAGCGT
* *
50984 CCAGGACTCCTCCGGGAGAACGTCTCGTCTACGCTAGGAGGACGAGCGT
1 CCAGGACTCCTCCGAGAGAACGTCTCGTCCACGCTAGGAGGACGAGCGT
* *
51033 CCAGAACTCCTCCGGGAGAA
1 CCAGGACTCCTCCGAGAGAA
51053 TGACGCCTCC
Statistics
Matches: 95, Mismatches: 20, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
49 25 0.26
50 23 0.24
51 6 0.06
52 8 0.08
53 6 0.06
54 27 0.28
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.16
Consensus pattern (49 bp):
CCAGGACTCCTCCGAGAGAACGTCTCGTCCACGCTAGGAGGACGAGCGT
Found at i:51071 original size:103 final size:104
Alignment explanation
Indices: 50876--51126 Score: 380
Period size: 103 Copynumber: 2.4 Consensus size: 104
50866 AAATAGGGCG
* * *
50876 ACGACCAGGACTCCTCCGAGAGAACGTCTCGTCCACGCTAGGATGGACGAGCGTCCAGGACTCCT
1 ACGACCAGGACTCCTCCGGGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGAACTCCT
* *
50941 CTAAGAGAACGATGCCTCCATATTCTAAGGAGCGGGCCA
66 CCAAGAGAACGACGCCTCCATATTCTAAGGAGCGGGCCA
50980 ACGACCAGGACTCCTCCGGGAGAACGTCTCGTCTACGCTAGGA-GGACGAGCGTCCAGAACTCCT
1 ACGACCAGGACTCCTCCGGGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGAACTCCT
** * * *
51044 CCGGGAGAATGACGCCTCCATATTCTAAGGAGCGGGGCG
66 CCAAGAGAACGACGCCTCCATATTCTAAGGAGCGGGCCA
* *
51083 ACG-CCAGGACTCCCCCGGCAGAACGTCTCGTCTACGCTAGGATG
1 ACGACCAGGACTCCTCCGGGAGAACGTCTCGTCTACGCTAGGATG
51127 CAAATGTCCG
Statistics
Matches: 134, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
102 37 0.28
103 56 0.42
104 41 0.31
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.16
Consensus pattern (104 bp):
ACGACCAGGACTCCTCCGGGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGAACTCCT
CCAAGAGAACGACGCCTCCATATTCTAAGGAGCGGGCCA
Found at i:51433 original size:104 final size:102
Alignment explanation
Indices: 51270--51877 Score: 681
Period size: 104 Copynumber: 5.9 Consensus size: 102
51260 TATGAAAATA
* *
51270 GGGCGATGACCAGGACTCCTCCGAGAGAACGTCTCGTCTACGCTAGGATGGACGCGCGTCCAGAA
1 GGGCGACGACCAGGACTCCTCCG-GAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGAA
* * *
51335 GTCCTCCGGGAGAGCGACGCCTCCATATTCTTAGGAGC
65 CTCCTCCGGGAGAACGACGCCTCCATATTCTAAGGAGC
* * *
51373 GGGTCGACGACCAAGACTACC-CCGGTAGAATGTCTCATCTACGCTAGGATGGACGAGCGTCCAG
1 GGG-CGACGACCAGGACT-CCTCCGG-AGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAG
* * * * *
51437 GACTCCTCCAGGAGAACAATGCCTCTATATTCTAAGGAGC
63 AACTCCTCCGGGAGAACGACGCCTCCATATTCTAAGGAGC
* * **
51477 GGG-GAAACGACTAGGACTCCTCCGGGAGAACGTCTCGTCTACGCTGGGATGGATAAGCGTCCAG
1 GGGCG--ACGACCAGGACTCCTCC-GGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAG
* * *
51541 GACTTCTCTGGGAGAACGACGCCTCCATATTCTGAA-GAGC
63 AACTCCTCCGGGAGAACGACGCCTCCATATTCT-AAGGAGC
51581 GGAGCGACGACCAGGACTCCTCCAGGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCA-A
1 GG-GCGACGACCAGGACTCCTCC-GGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGA
* * * **
51645 GACTCCTCCAGGAGAACGATGCCTCCATATTCCAAGGAAA
64 -ACTCCTCCGGGAGAACGACGCCTCCATATTCTAAGGAGC
* * * *
51685 GGG-G-CGAGCAGGACTCCTTCGCGAGAACGTATCGTCTACGCTAGGATGGACGAGCGTCCAGGA
1 GGGCGACGACCAGGACTCCTCCG-GAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGAA
* * *
51748 CTCCTCCGAGAGAACGGCGCCTCCATATTCTAAGGAGG
65 CTCCTCCGGGAGAACGACGCCTCCATATTCTAAGGAGC
* * * * *
51786 GGAGCGATGACCAGGACTCCTCCAGAAGAACGTCTCGTCTAAGCTTGGATGGACGAGCATCCA-A
1 GG-GCGACGACCAGGACTCCTCC-GGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGA
* *
51850 GACTCCTCCGAGTGAACGACGCCTCCAT
64 -ACTCCTCCGGGAGAACGACGCCTCCAT
51878 GGATATGAAT
Statistics
Matches: 425, Mismatches: 61, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
100 1 0.00
101 85 0.20
102 3 0.01
103 10 0.02
104 317 0.75
105 8 0.02
106 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.18
Consensus pattern (102 bp):
GGGCGACGACCAGGACTCCTCCGGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGAAC
TCCTCCGGGAGAACGACGCCTCCATATTCTAAGGAGC
Found at i:51792 original size:205 final size:205
Alignment explanation
Indices: 51280--51877 Score: 767
Period size: 208 Copynumber: 2.9 Consensus size: 205
51270 GGGCGATGAC
* * *
51280 CAGGACTCCTCCGAGAGAACGTCTCGTCTACGCTAGGATGGACGCGCGTCCAGAAGTCCTCCGGG
1 CAGGACTCCTCCGAGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGGACTCCTCCGGG
* * * * *
51345 AGAGCGACGCCTCCATATTCTTAGGAGCGGG-TCGACGACCAAGACTACC-CC-GGTAGAATGTC
66 AGAACGACGCCTCCATATTCTAAGGAG-GGGAGCGACGACCAGGACT-CCTCCAGG-AGAACGTC
* * * * *
51407 TCATCTACGCTAGGATGGACGAGCGTCCAGGACTCCTCCAGGAGAACAATGCCTCTATATTCTAA
128 TCGTCTACGCTAGGATGGACGAGCGTCCAAGACTCCTCCAGGAGAACGATGCCTCCATATTCCAA
**
51472 GGAGCGGGGAAACGA
193 GGAAAGGGG--ACGA
* * ** * *
51487 CTAGGACTCCTCCGGGAGAACGTCTCGTCTACGCTGGGATGGATAAGCGTCCAGGACTTCTCTGG
1 C-AGGACTCCTCCGAGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGGACTCCTCCGG
*
51552 GAGAACGACGCCTCCATATTCTGAA-GAGCGGAGCGACGACCAGGACTCCTCCAGGAGAACGTCT
65 GAGAACGACGCCTCCATATTCT-AAGGAGGGGAGCGACGACCAGGACTCCTCCAGGAGAACGTCT
51616 CGTCTACGCTAGGATGGACGAGCGTCCAAGACTCCTCCAGGAGAACGATGCCTCCATATTCCAAG
129 CGTCTACGCTAGGATGGACGAGCGTCCAAGACTCCTCCAGGAGAACGATGCCTCCATATTCCAAG
51681 GAAAGGGG-CGA
194 GAAAGGGGACGA
* * * *
51692 GCAGGACTCCTTCGCGAGAACGTATCGTCTACGCTAGGATGGACGAGCGTCCAGGACTCCTCCGA
1 -CAGGACTCCTCCGAGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGGACTCCTCCGG
* * *
51757 GAGAACGGCGCCTCCATATTCTAAGGAGGGGAGCGATGACCAGGACTCCTCCAGAAGAACGTCTC
65 GAGAACGACGCCTCCATATTCTAAGGAGGGGAGCGACGACCAGGACTCCTCCAGGAGAACGTCTC
* * * * *
51822 GTCTAAGCTTGGATGGACGAGCATCCAAGACTCCTCC-GAGTGAACGACGCCTCCAT
130 GTCTACGCTAGGATGGACGAGCGTCCAAGACTCCTCCAG-GAGAACGATGCCTCCAT
51878 GGATATGAAT
Statistics
Matches: 343, Mismatches: 40, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
204 3 0.01
205 164 0.48
206 1 0.00
207 5 0.01
208 167 0.49
209 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.18
Consensus pattern (205 bp):
CAGGACTCCTCCGAGAGAACGTCTCGTCTACGCTAGGATGGACGAGCGTCCAGGACTCCTCCGGG
AGAACGACGCCTCCATATTCTAAGGAGGGGAGCGACGACCAGGACTCCTCCAGGAGAACGTCTCG
TCTACGCTAGGATGGACGAGCGTCCAAGACTCCTCCAGGAGAACGATGCCTCCATATTCCAAGGA
AAGGGGACGA
Found at i:54752 original size:10 final size:10
Alignment explanation
Indices: 54737--54800 Score: 101
Period size: 10 Copynumber: 6.4 Consensus size: 10
54727 AATTATTTTT
54737 AAACTAACCC
1 AAACTAACCC
*
54747 AAACTATCCC
1 AAACTAACCC
54757 AAACTAACCC
1 AAACTAACCC
*
54767 AAACTAAGCC
1 AAACTAACCC
54777 AAACTAACCC
1 AAACTAACCC
*
54787 AAACTACCCC
1 AAACTAACCC
54797 AAAC
1 AAAC
54801 ATAAATTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 49 1.00
ACGTcount: A:0.48, C:0.39, G:0.02, T:0.11
Consensus pattern (10 bp):
AAACTAACCC
Found at i:57629 original size:10 final size:10
Alignment explanation
Indices: 57614--57714 Score: 130
Period size: 10 Copynumber: 10.1 Consensus size: 10
57604 AATTATTTTT
57614 AAACTAACCC
1 AAACTAACCC
*
57624 AAACTATCCC
1 AAACTAACCC
* *
57634 AAAATATCCC
1 AAACTAACCC
* *
57644 AAAGTATCCC
1 AAACTAACCC
57654 AAACTAACCC
1 AAACTAACCC
*
57664 AAACTAAGCC
1 AAACTAACCC
57674 AAACTAACCC
1 AAACTAACCC
*
57684 AAACTAACCT
1 AAACTAACCC
57694 AAACTAACCC
1 AAACTAACCC
*
57704 AAACTACCCC
1 AAACTAACCC
57714 A
1 A
57715 GACATAAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 81 1.00
ACGTcount: A:0.48, C:0.37, G:0.02, T:0.14
Consensus pattern (10 bp):
AAACTAACCC
Found at i:60395 original size:11 final size:11
Alignment explanation
Indices: 60379--60413 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
60369 TGATAGTAAG
60379 TATCAATTATA
1 TATCAATTATA
60390 TATCAATTATA
1 TATCAATTATA
60401 TATCAATTATA
1 TATCAATTATA
60412 TA
1 TA
60414 ATTATACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (11 bp):
TATCAATTATA
Found at i:61311 original size:21 final size:21
Alignment explanation
Indices: 61285--61331 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
61275 CATTGTTTGC
61285 TTTTTTT-ATGAGTAGGGTGTTT
1 TTTTTTTAATGAGTA--GTGTTT
61307 TTTTTTTAATGAGTAGTGTTT
1 TTTTTTTAATGAGTAGTGTTT
61328 TTTT
1 TTTT
61332 ACCCCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.42
22 7 0.29
23 7 0.29
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (21 bp):
TTTTTTTAATGAGTAGTGTTT
Found at i:62305 original size:10 final size:10
Alignment explanation
Indices: 62290--62343 Score: 90
Period size: 10 Copynumber: 5.4 Consensus size: 10
62280 AATTATTTTT
62290 AAACTAACCC
1 AAACTAACCC
*
62300 AAACTATCCC
1 AAACTAACCC
62310 AAACTAACCC
1 AAACTAACCC
62320 AAACTAACCC
1 AAACTAACCC
*
62330 AAACTAACAC
1 AAACTAACCC
62340 AAAC
1 AAAC
62344 ATAAATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.52, C:0.37, G:0.00, T:0.11
Consensus pattern (10 bp):
AAACTAACCC
Found at i:68287 original size:15 final size:15
Alignment explanation
Indices: 68267--68296 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
68257 TTGCACATCA
68267 GAATTTGGGTTTGGT
1 GAATTTGGGTTTGGT
68282 GAATTTGGGTTTGGT
1 GAATTTGGGTTTGGT
68297 TAAATTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.40, T:0.47
Consensus pattern (15 bp):
GAATTTGGGTTTGGT
Found at i:70894 original size:12 final size:11
Alignment explanation
Indices: 70874--70918 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
70864 TCAAACCTTT
70874 TTTTTTTTTCG
1 TTTTTTTTTCG
70885 TTTTTGTTTTCG
1 TTTTT-TTTTCG
* *
70897 TTTTTTTGTCC
1 TTTTTTTTTCG
70908 TTTTTTTTTCG
1 TTTTTTTTTCG
70919 CCAGAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (11 bp):
TTTTTTTTTCG
Found at i:70903 original size:22 final size:22
Alignment explanation
Indices: 70874--70918 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
70864 TCAAACCTTT
* *
70874 TTTTTTTTTCGTTTTTGTTTTCG
1 TTTTTTTGTCCTTTTT-TTTTCG
70897 TTTTTTTGTCCTTTTTTTTTCG
1 TTTTTTTGTCCTTTTTTTTTCG
70919 CCAGAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (22 bp):
TTTTTTTGTCCTTTTTTTTTCG
Found at i:74953 original size:25 final size:26
Alignment explanation
Indices: 74925--74975 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
74915 TAGTAGAATA
*
74925 ATTGTAA-A-AATTTATTTCTAAAAAT
1 ATTGTAAGAGAATATATTT-TAAAAAT
74950 ATTGTAAGAGAATATATTTTAAAAAT
1 ATTGTAAGAGAATATATTTTAAAAAT
74976 TCTAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 8 0.35
27 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (26 bp):
ATTGTAAGAGAATATATTTTAAAAAT
Done.