Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007429.1 Hibiscus syriacus cultivar Beakdansim tig00020141_pilon, 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: 139381
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1362 original size:41 final size:41
Alignment explanation
Indices: 1275--1362 Score: 92
Period size: 41 Copynumber: 2.1 Consensus size: 41
1265 TGTGATCGAT
* * *
1275 AATTCGCAACGCGATCTCTGATATCGCAAATCAGTTTTTCA
1 AATTCGCAACGCGAACACTGATATCGCAAATCAGTTTTCCA
*
1316 GATTCGCAACGCGAACAC-GACTATCGC-AATGC-GATTTTCCA
1 AATTCGCAACGCGAACACTGA-TATCGCAAAT-CAG-TTTTCCA
1357 AATTCG
1 AATTCG
1363 TTGCGATAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
40 6 0.15
41 33 0.85
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (41 bp):
AATTCGCAACGCGAACACTGATATCGCAAATCAGTTTTCCA
Found at i:1406 original size:21 final size:21
Alignment explanation
Indices: 1361--1985 Score: 402
Period size: 21 Copynumber: 30.1 Consensus size: 21
1351 TTTCCAAATT
1361 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
1380 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1401 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
1422 CGTTGCG--AGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * **
1441 TGTTGCGATTGTTGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1462 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
1483 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1504 TGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
1525 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1546 CGTTGCGATTTTATTCCAA-TT--
1 CGTTGCGA---TAGTCCAAGTTCG
1567 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1588 CGTTGCGATTTATTCCAAATTCG
1 CGTTGCGA--TAGTCCAAGTTCG
*
1611 TGTTGCGATAG-CCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
**
1629 CGTTGCGATAGTTGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1650 CGTTGCGATTTA-TCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
1670 CGTTGC--TGGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1689 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1710 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
1731 CATTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1752 CG-TGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
1772 CGTTGCGATTTATTCC-AGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
1792 CGTTGTGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
1813 CGTTGCGATTTATTCTAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
1834 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1855 CGTTGCGATTTATTCCAAATTCG
1 CGTTGCGA--TAGTCCAAGTTCG
*
1878 TGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
1897 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
1918 CGTTACGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
1939 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1960 CGTTGCGATTTATTCCAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCG
1983 CGT
1 CGT
1986 CCAAATATTG
Statistics
Matches: 472, Mismatches: 76, Indels: 112
0.72 0.12 0.17
Matches are distributed among these distances:
16 1 0.00
17 15 0.03
18 21 0.04
19 101 0.21
20 30 0.06
21 181 0.38
22 14 0.03
23 103 0.22
24 6 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:1424 original size:42 final size:40
Alignment explanation
Indices: 1372--1450 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
1362 GTTGCGATAG
* *
1372 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCG--AGTCCAAGTTCGCGTTGCGATTTAT
*
1414 TCCAAATTCGTTGCGAGTCCAAGTTCGTGTTGCGATT
1 TCCAAATTCGTTGCGAGTCCAAGTTCGCGTTGCGATT
1451 GTTGAAGTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 20 0.59
42 14 0.41
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (40 bp):
TCCAAATTCGTTGCGAGTCCAAGTTCGCGTTGCGATTTAT
Found at i:1446 original size:61 final size:61
Alignment explanation
Indices: 1345--1982 Score: 448
Period size: 61 Copynumber: 10.3 Consensus size: 61
1335 ACTATCGCAA
1345 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTC-GTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCG-TAGTCCAAGTTCGGTTGCGATAGTCGAAGTTCGCGT
* *
1404 TGCGATTTATTCCAAATTCGTTGCG-AGTCCAAGTTCGTGTTGCGATTGTTGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGTAGTCCAAGTTCG-GTTGCGATAGTCGAAGTTCGCGT
* * * *
1465 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAGTT--CGT
1 TGCGATTTATTCCAAATTCGTTGCG-TAGTCCAAGTTCG-GTTGCGA--TAGTCGAAGTTCGCGT
* * * * *
1528 TGCGA--TAGTCGAAGTTCGCGTTGCGATTTTATTCCAA-TTC-GTTGCGATAGTCCAAGTTCGC
1 TGCGATTTATTCCAAATT--CGTTGCG----TAGTCCAAGTTCGGTTGCGATAGTCGAAGTTCGC
1589 GT
60 GT
*
1591 TGCGATTTATTCCAAATTCGTGTTGCGATAG-CCAAGTTC-GTTGCGATAGTTGAAGTTCGCGT
1 TGCGATTTATTCCAAATTC--GTTGCG-TAGTCCAAGTTCGGTTGCGATAGTCGAAGTTCGCGT
*
1653 TGCGATTTA-TCCAAATTCGTTGC-TGGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGTAGTCCAAGTTCG-GTTGCGATAGTCGAAGTTCGCGT
* * * * *
1713 TGCGATTTATTCCAAGTTCATTGCGATAGTCGAAGTTCGCG-TGCGATTTATTCCAAGTT--CGT
1 TGCGATTTATTCCAAATTCGTTGCG-TAGTCCAAGTTCG-GTTGCGA--TAGTCGAAGTTCGCGT
* * * * * *
1775 TGCGATTTATTCC-AGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATT--CGT
1 TGCGATTTATTCCAAATTCGTTGCG-TAGTCCAAGTTCG-GTTGCGA--TAGTCGAAGTTCGCGT
* * * * *
1837 TGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTGTTGCGATAGTCCAAGTT--C
1 TGCGATTTATTCCAAATT--CGTTGCG---TAGTCCAAGTTCG-GTTGCGATAGTCGAAGTTCGC
1898 GT
60 GT
* * * * * *
1900 TGCGA--TAGTCGAAGTTCGCGTTACGATTTATTCCAAATTC-GTTGCGATAGTCGAAGTTCGCG
1 TGCGATTTATTCCAAATT--CGTTGCG---TAGTCCAAGTTCGGTTGCGATAGTCGAAGTTCGCG
1962 T
61 T
*
1963 TGCGATTTATTCCAAGTTCG
1 TGCGATTTATTCCAAATTCG
1983 CGTCCAAATA
Statistics
Matches: 493, Mismatches: 48, Indels: 72
0.80 0.08 0.12
Matches are distributed among these distances:
57 2 0.00
58 8 0.02
59 21 0.04
60 38 0.08
61 151 0.31
62 80 0.16
63 128 0.26
64 9 0.02
65 50 0.10
66 6 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (61 bp):
TGCGATTTATTCCAAATTCGTTGCGTAGTCCAAGTTCGGTTGCGATAGTCGAAGTTCGCGT
Found at i:1500 original size:42 final size:42
Alignment explanation
Indices: 1431--1982 Score: 472
Period size: 42 Copynumber: 13.2 Consensus size: 42
1421 TCGTTGCGAG
* *
1431 TCCAAGTTCGTGTTGCGATTGTTGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTC--GTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
1475 TCCAAGTTCGTTGCGATAGTCGAAGTTCGTGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1517 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTTAT
*
1560 TCCAA-TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
1601 TCCAAATTCGTGTTGCGATAG-CCAAGTT--CGTTGCGA--TAGT
1 TCCAAGTTC--GTTGCGATAGTCGAAGTTCGCGTTGCGATTTA-T
* * * **
1641 T-GAAGTTCGCGTTGCGATTTA-TCCAAATT--CGTTGC----TGG
1 TCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTAT
1679 TCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
1723 TCCAAGTTCATTGCGATAGTCGAAGTTCGCG-TGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * * *
1764 TCCAAGTTCGTTGCGATTTATTC-CAGTT--CGTTGTGA--TAG
1 TCCAAGTTCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTAT
* * * * *
1803 TCGAAGTTCGCGTTGCGATTTATTCTAAATT--CGTTGCGA--TAG
1 TCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTAT
* * * * *
1845 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTGTTGCGA--TAG
1 TCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTAT
*
1889 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTACGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
1931 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1973 TCCAAGTTCG
1 TCCAAGTTCG
1983 CGTCCAAATA
Statistics
Matches: 443, Mismatches: 37, Indels: 58
0.82 0.07 0.11
Matches are distributed among these distances:
37 2 0.00
38 7 0.02
39 38 0.09
40 26 0.06
41 77 0.17
42 226 0.51
43 21 0.05
44 46 0.10
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:2367 original size:21 final size:21
Alignment explanation
Indices: 2338--2402 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2328 TTCAAGATTG
*
2338 CCCAAGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
2359 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATTCCCC
*
2380 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
2401 CC
1 CC
2403 TGTATAAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.20, C:0.42, G:0.26, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:2466 original size:19 final size:20
Alignment explanation
Indices: 2427--2468 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2417 AACAGAATGT
2427 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACCGATTCCCC
2447 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACCGATTCCCC
2467 CC
1 CC
2469 CTGTTCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (20 bp):
CCAGGGGGTACCGATTCCCC
Found at i:2531 original size:21 final size:21
Alignment explanation
Indices: 2505--2546 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2495 ATTTGAATAT
*
2505 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2526 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2547 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2609 original size:21 final size:21
Alignment explanation
Indices: 2575--2614 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2565 TTTGAGTAGA
*
2575 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2597 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2615 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3300 original size:21 final size:19
Alignment explanation
Indices: 3261--3313 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 19
3251 CGTTGCGATT
*
3261 TTGGACTATCGCAGCGAAC
1 TTGGACTATCGAAGCGAAC
3280 TTGGACTATCGTAACGCGAAC
1 TTGGACTATCG-AA-GCGAAC
*
3301 TTAGACTATCGAA
1 TTGGACTATCGAA
3314 CAATTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 3 0.10
21 16 0.53
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (19 bp):
TTGGACTATCGAAGCGAAC
Found at i:3411 original size:19 final size:19
Alignment explanation
Indices: 3384--3426 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
3374 CGATACCGGA
*
3384 GATCACGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
3403 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
3422 GATCG
1 GATCG
3427 TATTGCGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (19 bp):
GATCGCGTTGCGAATTATC
Found at i:3432 original size:19 final size:19
Alignment explanation
Indices: 3391--3434 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3381 GGAGATCACG
*
3391 TTGCGAATTATCGATCGCG
1 TTGCGAATTATCGATCGCA
*
3410 TTGCGAATTATCGATCGTA
1 TTGCGAATTATCGATCGCA
3429 TTGCGA
1 TTGCGA
3435 TTTAGTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (19 bp):
TTGCGAATTATCGATCGCA
Found at i:9174 original size:19 final size:19
Alignment explanation
Indices: 9129--9175 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
9119 AAACCTTTGA
*
9129 ATAACACGACATCGAATGC
1 ATAACACTACATCGAATGC
9148 ATAACACTACATCGAATGC
1 ATAACACTACATCGAATGC
9167 ATAACACTA
1 ATAACACTA
9176 ACGATTCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.19
Consensus pattern (19 bp):
ATAACACTACATCGAATGC
Found at i:9446 original size:14 final size:14
Alignment explanation
Indices: 9427--9456 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9417 CTACATTCGA
9427 CTGCTATCGAACCT
1 CTGCTATCGAACCT
9441 CTGCTATCGAACCT
1 CTGCTATCGAACCT
9455 CT
1 CT
9457 CATACCGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (14 bp):
CTGCTATCGAACCT
Found at i:17892 original size:13 final size:13
Alignment explanation
Indices: 17874--17898 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17864 TCTTCGGTGA
17874 TTAATTAATTAAT
1 TTAATTAATTAAT
17887 TTAATTAATTAA
1 TTAATTAATTAA
17899 ACATAAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAATTAATTAAT
Found at i:18304 original size:33 final size:33
Alignment explanation
Indices: 18242--18311 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
18232 ACTAGCCATC
* *
18242 CGAGAGCATCCGAGGCCATCCGAACGAGCTGTG
1 CGAGAGCATCCGAGGCCAACCGAACGAGCTATG
* **
18275 CGAGAGCATCCGAGGGCAACCGAGTGAGCTATG
1 CGAGAGCATCCGAGGCCAACCGAACGAGCTATG
18308 CGAG
1 CGAG
18312 GGAATTCGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.26, C:0.27, G:0.36, T:0.11
Consensus pattern (33 bp):
CGAGAGCATCCGAGGCCAACCGAACGAGCTATG
Found at i:18372 original size:29 final size:29
Alignment explanation
Indices: 18339--18394 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
18329 GAGCGAGGGT
* *
18339 AGGTCGCCCGGAGTGTATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
18368 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
18395 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:19664 original size:21 final size:21
Alignment explanation
Indices: 19595--19664 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
19585 ACTAAATATT
*
19595 TTTTTCTTAATATTTCTATAA
1 TTTTTCGTAATATTTCTATAA
** **
19616 TTTATACTACGTAA-ATCACTATTT
1 TTT-T--T-CGTAATATTTCTATAA
19640 TTTTTCGTAATATTTCTATAA
1 TTTTTCGTAATATTTCTATAA
19661 TTTT
1 TTTT
19665 ACCTTATTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 5 0.14
21 14 0.40
22 1 0.03
23 1 0.03
24 10 0.29
25 4 0.11
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTTCGTAATATTTCTATAA
Found at i:19725 original size:15 final size:16
Alignment explanation
Indices: 19705--19738 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
19695 TAATTCACTA
19705 AATATTTTTTTTC-AT
1 AATATTTTTTTTCTAT
19720 AATATTTTTTTTCTAT
1 AATATTTTTTTTCTAT
19736 AAT
1 AAT
19739 TCACAGAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
AATATTTTTTTTCTAT
Found at i:19857 original size:3 final size:3
Alignment explanation
Indices: 19849--19885 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
19839 CACAAAGCAA
19849 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19886 TGTTAATCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23505 original size:34 final size:37
Alignment explanation
Indices: 23461--23562 Score: 149
Period size: 34 Copynumber: 2.8 Consensus size: 37
23451 TTTCGTCCTA
23461 CTAGGATTCAAACTCCTAAAAATAAGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAAGATAGACATTTT
*
23496 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAAGATAGACATTTT
*
23531 GCTAGGATTCAAACTCCTAAAAATATGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAAGATAGA
23563 GTTCTACTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.47
35 3 0.05
37 27 0.45
38 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAAGATAGACATTTT
Found at i:23586 original size:37 final size:37
Alignment explanation
Indices: 23458--23588 Score: 153
Period size: 37 Copynumber: 3.6 Consensus size: 37
23448 ATTTTTCGTC
23458 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
*
23495 -T--TAGGATTCAAACTCCTAAAAATAGGATA-ACATT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGA-ATT
* * * *
23529 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
* * *
23566 CTACTAAGATTTAAATTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
23589 TATAGGATCC
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.01
34 30 0.37
35 1 0.01
36 1 0.01
37 47 0.58
38 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
Found at i:24326 original size:19 final size:21
Alignment explanation
Indices: 24290--24338 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
24280 ATATTACATT
*
24290 ATTATTATTTTACTTTATTAA
1 ATTATTATTTTACGTTATTAA
24311 ATTATT-TTTT-CGTTATTATA
1 ATTATTATTTTACGTTATTA-A
*
24331 TTTATTAT
1 ATTATTAT
24339 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 7 0.29
20 10 0.42
21 7 0.29
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTATTATTTTACGTTATTAA
Found at i:27150 original size:8 final size:8
Alignment explanation
Indices: 27137--27175 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
27127 GAACATTTCA
*
27137 TGCATTCT
1 TGCATTTT
27145 TGCA-TTT
1 TGCATTTT
27152 TGCATTTT
1 TGCATTTT
*
27160 TGCCTTTT
1 TGCATTTT
27168 TGCATTTT
1 TGCATTTT
27176 CATCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:28365 original size:9 final size:9
Alignment explanation
Indices: 28353--28405 Score: 52
Period size: 9 Copynumber: 5.3 Consensus size: 9
28343 TAAAAAGGGC
28353 AAAAAGAAA
1 AAAAAGAAA
28362 AAAAAGCAAAAAA
1 AAAAAG----AAA
28375 AAAAAGCAAA
1 AAAAAG-AAA
*
28385 AAAAAGAAC
1 AAAAAGAAA
28394 AAAAAGAAA
1 AAAAAGAAA
28403 AAA
1 AAA
28406 GAAAAAGGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 19 0.51
10 9 0.24
13 9 0.24
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:28365 original size:18 final size:16
Alignment explanation
Indices: 28351--28411 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
28341 AATAAAAAGG
28351 GCAAAAAGAAAAAAAA
1 GCAAAAAGAAAAAAAA
28367 GCAAAAA-AAAAAAGCAA
1 GCAAAAAGAAAAAA--AA
* *
28384 -AAAAAAGAACAAAAA
1 GCAAAAAGAAAAAAAA
*
28399 GAAAAAAGAAAAA
1 GCAAAAAGAAAAA
28412 GGGACAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 8 0.21
16 23 0.61
17 7 0.18
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (16 bp):
GCAAAAAGAAAAAAAA
Found at i:28387 original size:25 final size:25
Alignment explanation
Indices: 28353--28411 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
28343 TAAAAAGGGC
28353 AAAAAGAAAAAAAAG--CAAAAA-A
1 AAAAAGAAAAAAAAGAACAAAAAGA
28375 AAAAAGCAAAAAAAAGAACAAAAAGA
1 AAAAAG-AAAAAAAAGAACAAAAAGA
28401 AAAAAGAAAAA
1 AAAAAGAAAAA
28412 GGGACAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.18
23 9 0.27
25 11 0.33
26 7 0.21
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (25 bp):
AAAAAGAAAAAAAAGAACAAAAAGA
Found at i:28410 original size:12 final size:12
Alignment explanation
Indices: 28359--28404 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
28349 GGGCAAAAAG
28359 AAAAAAAAGCAAA
1 AAAAAAAAGC-AA
28372 AAAAAAAAGCAA
1 AAAAAAAAGCAA
28384 AAAAAAGAA-CAA
1 AAAAAA-AAGCAA
28396 AAAGAAAAA
1 AAA-AAAAA
28405 AGAAAAAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 16 0.52
13 15 0.48
ACGTcount: A:0.85, C:0.07, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGCAA
Found at i:28412 original size:13 final size:13
Alignment explanation
Indices: 28359--28411 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
28349 GGGCAAAAAG
28359 AAAAAAAAGCAAA
1 AAAAAAAAGCAAA
28372 AAAAAAAAGCAAA
1 AAAAAAAAGCAAA
*
28385 AAAAAGAA-CAAA
1 AAAAAAAAGCAAA
28397 AAGAAAAAAG-AAA
1 AA-AAAAAAGCAAA
28410 AA
1 AA
28412 GGGACAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 6 0.17
13 30 0.83
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGCAAA
Found at i:28421 original size:32 final size:32
Alignment explanation
Indices: 28344--28421 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
28334 TAATCAGAAT
28344 AAAAAGGG-CAAAAAGAAAAAAAAGCAAAAAA
1 AAAAAGGGACAAAAAGAAAAAAAAGCAAAAAA
** * *
28375 AAAAAGCAAAAAAAAGAACAAAAAG-AAAAAA
1 AAAAAGGGACAAAAAGAAAAAAAAGCAAAAAA
28406 GAAAAAGGGACAAAAA
1 -AAAAAGGGACAAAAA
28422 ACACATGCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 12 0.32
32 26 0.68
ACGTcount: A:0.78, C:0.06, G:0.15, T:0.00
Consensus pattern (32 bp):
AAAAAGGGACAAAAAGAAAAAAAAGCAAAAAA
Found at i:30122 original size:36 final size:36
Alignment explanation
Indices: 30014--30137 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
30004 ATTGAAAACA
* * *
30014 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
30050 TTTCCCTTGGAACTAAGTTTT-GTCTCTCTTAAGACAG
1 TTTCCCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
* *
30087 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
30123 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
30138 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:30231 original size:67 final size:67
Alignment explanation
Indices: 30113--30268 Score: 201
Period size: 67 Copynumber: 2.4 Consensus size: 67
30103 TTTCGTCTAT
* ** *
30113 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTTTTC
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTGTT-
30175 TCC
65 TCC
* * *
30178 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTGTTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTGTTT
30243 CC
66 CC
* *
30245 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
30269 ACAGATATCT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 52 0.67
68 7 0.09
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (67 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTGTTT
CC
Found at i:31031 original size:106 final size:105
Alignment explanation
Indices: 30872--31532 Score: 902
Period size: 106 Copynumber: 6.3 Consensus size: 105
30862 GCCATCCGCG
* * * * *
30872 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACAACGAA
* * *
30937 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGGTTGTCAACAAA-AATTTCCCAATTTCAGAGCCA
* * *
30981 ATTTCAACTTCACATCGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
* * *
31046 ACCGCTGGTTGTCAATAAAAAAATTCCCAATTTTAGAGCCA
66 ACCGCTGGTTGTCAA-CAAAAATTTCCCAATTTCAGAGCCA
* *
31087 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
* *
31152 ACCGCTGGTTGTCAACAAATATTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAAAATTTCCCAATTTCAGAGCCA
* * * * *
31192 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGTATGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
* *
31257 ACCGCTGGTTGTCAAC-AAATTTTCCCGATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAAAATTTCCCAATTTCAGAGCCA
31296 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
* **
31361 ACCGCTGCTTGTCAAC-AAAATTT--C-A-TTCAGATTCA
66 ACCGCTGGTTGTCAACAAAAATTTCCCAATTTCAGAGCCA
* *
31396 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
* ** *
31461 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGGTTGTCAACAAA-AATTTCCCAATTTCAGAGCCA
* *
31502 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
31533 TGGAACAATG
Statistics
Matches: 499, Mismatches: 46, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
100 85 0.17
101 3 0.01
102 6 0.01
104 101 0.20
105 98 0.20
106 179 0.36
107 6 0.01
109 21 0.04
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
ACCGCTGGTTGTCAACAAAAATTTCCCAATTTCAGAGCCA
Found at i:32124 original size:34 final size:37
Alignment explanation
Indices: 32080--32181 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
32070 TTTCGTCCTA
32080 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
32115 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
*
32150 GCTAGGATTCAAACTCCTAAAAATATGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
32182 GTTCTACTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.48
35 3 0.05
37 27 0.44
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:32165 original size:37 final size:35
Alignment explanation
Indices: 32080--32215 Score: 159
Period size: 37 Copynumber: 3.8 Consensus size: 35
32070 TTTCGTCCTA
32080 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
32115 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
* *
32150 GCTAGGATTCAAACTCCTAAAAATATGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
32187 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
32216 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 51 0.59
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:32701 original size:2 final size:2
Alignment explanation
Indices: 32694--32726 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
32684 TTAAAGTTAT
32694 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32727 ACTATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32813 original size:22 final size:21
Alignment explanation
Indices: 32788--32832 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
32778 TTTGCTACTA
32788 TTATTATCA-TTATATGTATATT
1 TTATTAT-ATTTATAT-TATATT
*
32810 TTATTATATTTATATTTTATT
1 TTATTATATTTATATTATATT
32831 TT
1 TT
32833 TACTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTATATTTATATTATATT
Found at i:32817 original size:16 final size:16
Alignment explanation
Indices: 32796--32830 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
32786 TATTATTATC
32796 ATTATATGTATATTTT
1 ATTATATGTATATTTT
*
32812 ATTATATTTATATTTT
1 ATTATATGTATATTTT
32828 ATT
1 ATT
32831 TTTACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
ATTATATGTATATTTT
Found at i:32941 original size:16 final size:16
Alignment explanation
Indices: 32920--32953 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
32910 CATGTATTTA
32920 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
32936 TATTATTTTACTTTAT
1 TATTATATTACATTAT
32952 TA
1 TA
32954 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:32958 original size:21 final size:22
Alignment explanation
Indices: 32934--32984 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
32924 ATATTACATT
*
32934 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
32955 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
32977 TTTATTAT
1 ATTATTAT
32985 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:37392 original size:60 final size:60
Alignment explanation
Indices: 37315--37464 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 60
37305 TGTGTGTTCT
* * * *
37315 TAAACTATGACCCTCATTTTAAATTAGTCCTTAAAATT-TTAAATATTCTAAATTCAT-CC
1 TAAACTATAACTCTCATTCTAAATTAGTCCTTAAAATTATGAAA-ATTCTAAATTCATCCC
* * * * *
37374 TCAAACTATAATTGTCATTCTAAATTGGTCTTTAAACTTATGAAAATTCTAAATTCATCCC
1 T-AAACTATAACTCTCATTCTAAATTAGTCCTTAAAATTATGAAAATTCTAAATTCATCCC
*
37435 TAAACTATGACTCTCATTCTAAATTAGTCC
1 TAAACTATAACTCTCATTCTAAATTAGTCC
37465 AAAACTTTTG
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 1 0.01
60 66 0.89
61 7 0.09
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.39
Consensus pattern (60 bp):
TAAACTATAACTCTCATTCTAAATTAGTCCTTAAAATTATGAAAATTCTAAATTCATCCC
Found at i:38374 original size:13 final size:13
Alignment explanation
Indices: 38339--38375 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
38329 AAATATCAAG
38339 ATAAAAAACA-TA
1 ATAAAAAACATTA
*
38351 A-ATAAAACATTA
1 ATAAAAAACATTA
38363 ATAAAAAACATTA
1 ATAAAAAACATTA
38376 CGAAAATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 7 0.33
12 4 0.19
13 10 0.48
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAAAAAACATTA
Found at i:42739 original size:4 final size:4
Alignment explanation
Indices: 42707--42746 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
42697 TAATTTGCCC
* * *
42707 TAAA TAAA TCAA TAAA CAAA TATA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
42747 GTTTCTTGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:43035 original size:2 final size:2
Alignment explanation
Indices: 43028--43057 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43018 CCACTTATGT
43028 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
43058 AAGTACCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46928 original size:12 final size:11
Alignment explanation
Indices: 46905--46937 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
46895 ATTATCAGTG
46905 ATCGATTAATA
1 ATCGATTAATA
46916 ATCGATATAATA
1 ATCGAT-TAATA
46928 ATCGATTAAT
1 ATCGATTAAT
46938 TAACTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (11 bp):
ATCGATTAATA
Found at i:47872 original size:16 final size:17
Alignment explanation
Indices: 47822--47873 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
47812 ATAAAAAACA
47822 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
47839 GA-TT-AAA-TTATGAGT
1 AATTTGAAAGTTA-GAGT
47854 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
47870 AATT
1 AATT
47874 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:48203 original size:21 final size:21
Alignment explanation
Indices: 48165--48204 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48155 ATTGACATGG
*
48165 TCACTTTTATTTCATAAATAT
1 TCACTTTTATGTCATAAATAT
48186 TCACTTTTA-GTCATTAAAT
1 TCACTTTTATGTCA-TAAAT
48205 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.50
Consensus pattern (21 bp):
TCACTTTTATGTCATAAATAT
Found at i:53697 original size:60 final size:60
Alignment explanation
Indices: 53623--53754 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
53613 AGTATAGGGT
* *
53623 AAAA-TATAAAATGAT-TTTCTGACTATA-ATGTATTGTTTTATTAAATCTTTCAACTATTA
1 AAAATTATAAAATGATCTTT-TAACTATAGA-GTATTGTTTTATTAAATCATTCAACTATTA
* * * * *
53682 AAAATTATAAAATGATCTTTTAACTATAGAGTGTTGTTTTGTTGAGTCATTCGACTATTA
1 AAAATTATAAAATGATCTTTTAACTATAGAGTATTGTTTTATTAAATCATTCAACTATTA
*
53742 AAAATTACAAAAT
1 AAAATTATAAAAT
53755 ATCACCTAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
59 4 0.06
60 54 0.87
61 4 0.06
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (60 bp):
AAAATTATAAAATGATCTTTTAACTATAGAGTATTGTTTTATTAAATCATTCAACTATTA
Found at i:54897 original size:336 final size:336
Alignment explanation
Indices: 54297--54945 Score: 1007
Period size: 336 Copynumber: 1.9 Consensus size: 336
54287 ACTTAGCGTG
* *
54297 TTAGTACCTAAATTTTCAATTTTGGTCAATTTTAATACCTAAACTTTCAAAAAAAAATCAAAACT
1 TTAGTACCTAAATTATCAATTTTGCTCAATTTTAATACCTAAACTTTCAAAAAAAAATCAAAACT
* * *
54362 TAATGTTAAATTTTGAACAATGATACTAAAATGAAACAACAACTAAACTTTAGATATGATTTTTT
66 TAATGTTAAATTTTGAACAATGATACTAAAATGAAAAAAAAACTAAACTTTAGATATGATTTTTA
* * *
54427 AAAAATTCAAAGTTTAGGTACTAAAAGAGACCAAAATTGAAGTTTGGGTACTAAACACGTAATTT
131 AAAAATTCAAAGTTTAGGTACTAAAAGAGACCAAAATTGAAATTTGAGTACTAAACACATAATTT
* * *
54492 ACCCAAATTTTTAACTATTGTGTTAGCGATCAGATGATTCGATCGTCCAATCATTAAAATTTAAG
196 ACCCAAATTTTTAACTATTGTGTTAGCGATCAGAAGATTCGATCCTCCAATCATTAAAATTCAAG
*
54557 GTTATAAGTTTTGCTTGTACGTATACATACATACAACAAAATTTGGCAAACTTAACACGTTATAA
261 GTTATAAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTTAACACGTTATAA
54622 ACTTAAATCAT
326 ACTTAAATCAT
* * *
54633 TTAGTACTTAAATTATCAATTTTGCTCTATTTTAATACCTAAACTTTC-AAAAAATATCAAAACT
1 TTAGTACCTAAATTATCAATTTTGCTCAATTTTAATACCTAAACTTTCAAAAAAAAATCAAAACT
* * * *
54697 TAATGTTAAATTTTGAACAATGGTACTAAAATGAAAAAAAAATTGAACTTTAGATATGGTTTTTA
66 TAATGTTAAATTTTGAACAATGATACTAAAATGAAAAAAAAACTAAACTTTAGATATGATTTTTA
* * * * *
54762 AAAACATTCAAAGTTTAGGTACTGAAAGGGATCAAAATTGATAATTTTAGTACTAAACGCATAAT
131 AAAA-ATTCAAAGTTTAGGTACTAAAAGAGACCAAAATTGA-AATTTGAGTACTAAACACATAAT
* *
54827 TTA-CTATAATTTTTAACTATTGTGTTAGCGAT-AGAAGATTCGATCCTCCAGTCATTAAAATTC
194 TTACCCA-AATTTTTAACTATTGTGTTAGCGATCAGAAGATTCGATCCTCCAATCATTAAAATTC
*
54890 GAGGTTATAAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTT
258 AAGGTTATAAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTT
54946 TTCGCCAGAT
Statistics
Matches: 283, Mismatches: 27, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
335 77 0.27
336 160 0.57
337 46 0.16
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (336 bp):
TTAGTACCTAAATTATCAATTTTGCTCAATTTTAATACCTAAACTTTCAAAAAAAAATCAAAACT
TAATGTTAAATTTTGAACAATGATACTAAAATGAAAAAAAAACTAAACTTTAGATATGATTTTTA
AAAAATTCAAAGTTTAGGTACTAAAAGAGACCAAAATTGAAATTTGAGTACTAAACACATAATTT
ACCCAAATTTTTAACTATTGTGTTAGCGATCAGAAGATTCGATCCTCCAATCATTAAAATTCAAG
GTTATAAGTTTTGCCTGTACGTATACATACATACAACAAAATTTGGCAAACTTAACACGTTATAA
ACTTAAATCAT
Found at i:58925 original size:21 final size:21
Alignment explanation
Indices: 58901--58941 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58891 AAAGCTCGTT
* *
58901 AAAAGTTGAAAATTTTATTAA
1 AAAACTTGAAAATATTATTAA
*
58922 AAAACTTTAAAATATTATTA
1 AAAACTTGAAAATATTATTA
58942 TATTAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAACTTGAAAATATTATTAA
Found at i:60354 original size:2 final size:2
Alignment explanation
Indices: 60347--60406 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
60337 TAATTTAATG
60347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60389 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
60407 TCACGTATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60714 original size:24 final size:24
Alignment explanation
Indices: 60687--60766 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 24
60677 CACCGAAGTG
60687 TCACGTAGAATTTGTCCCAAAGGA
1 TCACGTAGAATTTGTCCCAAAGGA
*
60711 TCACGTAGAA-TTGTCCCAAAGTA
1 TCACGTAGAATTTGTCCCAAAGGA
* * * *
60734 CCACATAG-ATTTATCCCGAAGGA
1 TCACGTAGAATTTGTCCCAAAGGA
*
60757 TCGCGTAGAA
1 TCACGTAGAA
60767 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
22 1 0.02
23 33 0.73
24 11 0.24
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (24 bp):
TCACGTAGAATTTGTCCCAAAGGA
Found at i:60863 original size:15 final size:15
Alignment explanation
Indices: 60840--60893 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
60830 GTAGAGCACA
60840 TTCACATAAAACATT
1 TTCACATAAAACATT
* *
60855 TTCATATAAAACATA
1 TTCACATAAAACATT
*
60870 TTCACATATAACATTT
1 TTCACATAAAACA-TT
60886 TTCACATA
1 TTCACATA
60894 CCAATAAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
15 24 0.73
16 9 0.27
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (15 bp):
TTCACATAAAACATT
Found at i:63967 original size:98 final size:93
Alignment explanation
Indices: 63773--64047 Score: 334
Period size: 98 Copynumber: 2.9 Consensus size: 93
63763 TTGAGGGAGA
*
63773 AAAAAAACTCAATCTTTGGCTCATTTTATTACAACAAAACACCTTTTCCCTTGTTTTTTATCTGT
1 AAAAAAACTCAATCTTTGGCTCATTTTATT-CAA-AAAACACCTTTCCCCTTGTTTTTTATCTGT
*
63838 TTAGAGCCATCTTCAAGCTTGGGTTCTGAG
64 TTAGAGCCATCTTCAAGCTTGGGTTATGAG
* * *
63868 AAAAATACTCAAGCTTTGGCTCATTTTATTCAAAGAAAGCACCTTTGCCCTTGTTTTTTTTTATC
1 AAAAAAACTCAATCTTTGGCTCATTTTATTCAAA-AAA-CACCTTTCCCCTTG---TTTTTTATC
*
63933 TGTTTTGAGCCATCTTCAAGCTTGGGTTATGAG
61 TGTTTAGAGCCATCTTCAAGCTTGGGTTATGAG
* * * * * ***
63966 AAAAAAACTCAATATTTGGCTCATTTTCTTCAAACAAAATACCTTTCCCCTTGCTCTGCCTCTGT
1 AAAAAAACTCAATCTTTGGCTCATTTTATTC-AA-AAAACACCTTTCCCCTTGTTTTTTATCTGT
*
64031 TTTGAGCCATCTTCAAG
64 TTAGAGCCATCTTCAAG
64048 GTAGGGTTCT
Statistics
Matches: 157, Mismatches: 16, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
93 1 0.01
94 6 0.04
95 65 0.41
98 79 0.50
99 5 0.03
100 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (93 bp):
AAAAAAACTCAATCTTTGGCTCATTTTATTCAAAAAACACCTTTCCCCTTGTTTTTTATCTGTTT
AGAGCCATCTTCAAGCTTGGGTTATGAG
Found at i:65026 original size:37 final size:39
Alignment explanation
Indices: 64985--65062 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
64975 ATTTAACGTT
*
64985 AAATTTTGAATGA-A-ATACTAAAATAAAACAGAAACTA
1 AAATTTTGAATGACATATACTAAAATAAAACAAAAACTA
* * *
65022 AAATTTTTAATGACATGTACTAAAATGAAACAAAAACTA
1 AAATTTTGAATGACATATACTAAAATAAAACAAAAACTA
65061 AA
1 AA
65063 CTTTAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 12 0.34
38 1 0.03
39 22 0.63
ACGTcount: A:0.58, C:0.09, G:0.08, T:0.26
Consensus pattern (39 bp):
AAATTTTGAATGACATATACTAAAATAAAACAAAAACTA
Found at i:65078 original size:11 final size:11
Alignment explanation
Indices: 65064--65097 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
65054 AAAACTAAAC
*
65064 TTTAAATTTAA
1 TTTAAAATTAA
65075 TTTAAAATTAA
1 TTTAAAATTAA
65086 TTTAAAAGTTAA
1 TTTAAAA-TTAA
65098 ATACTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TTTAAAATTAA
Found at i:67501 original size:31 final size:31
Alignment explanation
Indices: 67458--67518 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
67448 CCTTCCAAAT
*
67458 GTTACAGAATGATCATTAAATTTATCAAACA
1 GTTACAGAATGATCATTAAACTTATCAAACA
* * *
67489 GTTACAGGATGATCTTTCAACTTATCAAAC
1 GTTACAGAATGATCATTAAACTTATCAAAC
67519 TGATACAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (31 bp):
GTTACAGAATGATCATTAAACTTATCAAACA
Found at i:69199 original size:21 final size:21
Alignment explanation
Indices: 69173--69215 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
69163 TAATCCGGAT
69173 CAGATATTACAGTGGTAAGGG
1 CAGATATTACAGTGGTAAGGG
69194 CAGATATTACAGTGGTAAGGG
1 CAGATATTACAGTGGTAAGGG
69215 C
1 C
69216 GACCCTCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.23
Consensus pattern (21 bp):
CAGATATTACAGTGGTAAGGG
Found at i:70502 original size:3 final size:3
Alignment explanation
Indices: 70494--70518 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
70484 AGAGAAGGAA
70494 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
70519 GATCAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:89784 original size:2 final size:2
Alignment explanation
Indices: 89777--89823 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
89767 ATTTAATAAT
89777 TA TA TA TA 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 TA TA TA TA
89819 TA TA T
1 TA TA T
89824 GGTATGTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:98665 original size:12 final size:12
Alignment explanation
Indices: 98633--98694 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
98623 TGCGGGAAAA
98633 TTAAAA-TTA-T
1 TTAAAATTTATT
*
98643 TT-AAATCTATT
1 TTAAAATTTATT
98654 TTAAAATTTATT
1 TTAAAATTTATT
* **
98666 TTAAAATATAGA
1 TTAAAATTTATT
98678 TT--AATTTATT
1 TTAAAATTTATT
98688 TTAAAAT
1 TTAAAAT
98695 ATAGATTGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
9 3 0.08
10 11 0.28
11 3 0.08
12 22 0.56
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:98683 original size:22 final size:22
Alignment explanation
Indices: 98659--99023 Score: 606
Period size: 22 Copynumber: 16.6 Consensus size: 22
98649 CTATTTTAAA
* *
98659 ATTTATTTTAAAATATAGATTA
1 ATTTATTTTAAAATATGGATTG
*
98681 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
***
98703 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
98725 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
98747 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
98769 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
98791 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
98813 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
98835 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
98857 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
98879 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
98901 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
98922 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
98945 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
98967 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
98989 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
99011 ATTTATTTTAAAA
1 ATTTATTTTAAAA
99024 AATTTATTAT
Statistics
Matches: 324, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
21 3 0.01
22 318 0.98
23 3 0.01
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:99616 original size:35 final size:34
Alignment explanation
Indices: 99576--99646 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
99566 TTGACATAAC
*
99576 ATATAAAATT-AAGTACTTATTTTGACAAAAAAGTA
1 ATAT-AAATTAAAG-ACTTATTTTGACAAAAAACTA
* *
99611 ATATAATTTAAAGACTTATTTTGACCAAAAACTA
1 ATATAAATTAAAGACTTATTTTGACAAAAAACTA
99645 AT
1 AT
99647 TTAAGGTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 25 0.78
35 7 0.22
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.35
Consensus pattern (34 bp):
ATATAAATTAAAGACTTATTTTGACAAAAAACTA
Found at i:99793 original size:21 final size:19
Alignment explanation
Indices: 99769--99824 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
99759 CCTATAAAGT
99769 ATTACAAATAATTAATAAAA
1 ATTA-AAATAATTAATAAAA
* *
99789 CATTAAATATTATAAATAAAA
1 -ATTAAA-ATAATTAATAAAA
*
99810 ATTAAAAAAATTAAT
1 ATTAAAATAATTAAT
99825 TTTAATATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 6 0.21
20 8 0.28
21 15 0.52
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTAAAATAATTAATAAAA
Found at i:100436 original size:15 final size:15
Alignment explanation
Indices: 100418--100470 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
100408 AAAATAAATT
100418 TTAAATTTAGAGTAA
1 TTAAATTTAGAGTAA
100433 TTAAA-TTAGGAGTAA
1 TTAAATTTA-GAGTAA
*
100448 TTTGAAAGTTA-AGTAA
1 -TT-AAATTTAGAGTAA
100464 TTAAATT
1 TTAAATT
100471 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 7 0.21
15 13 0.39
16 7 0.21
17 3 0.09
18 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (15 bp):
TTAAATTTAGAGTAA
Found at i:101185 original size:14 final size:14
Alignment explanation
Indices: 101166--101195 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
101156 TTTTTCAATT
101166 TCGAGTTATTCAAG
1 TCGAGTTATTCAAG
101180 TCGAGTTATTCAAG
1 TCGAGTTATTCAAG
101194 TC
1 TC
101196 AACTCGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (14 bp):
TCGAGTTATTCAAG
Found at i:101776 original size:20 final size:21
Alignment explanation
Indices: 101737--101781 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
101727 TTCTTTAATA
101737 TATAATATTATGAATATATTT
1 TATAATATTATGAATATATTT
* *
101758 TATAATTTTA-GATTATATTT
1 TATAATATTATGAATATATTT
101778 TATA
1 TATA
101782 TGTTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TATAATATTATGAATATATTT
Found at i:102627 original size:25 final size:25
Alignment explanation
Indices: 102545--102627 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 25
102535 AAAATTAAAT
102545 TAATTAAATTAAAATTTTAAAATTA
1 TAATTAAATTAAAATTTTAAAATTA
* * *
102570 TATTTAAATAAAAAAATATTCCCAAAATTA
1 TAATTAAAT--TAAAAT-TT--TAAAATTA
*
102600 TAATTAAATTTAAATTTTAAAATTA
1 TAATTAAATTAAAATTTTAAAATTA
102625 TAA
1 TAA
102628 ACTCTCGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
25 18 0.39
27 7 0.15
28 6 0.13
30 15 0.33
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATTAAATTAAAATTTTAAAATTA
Found at i:105635 original size:60 final size:60
Alignment explanation
Indices: 105513--105638 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
105503 AACATAATGA
* * *
105513 ATAGTCAAATGACCATTTTATAACTTTTAATAGTTGAATGACTTAATAAAACAACATTCT
1 ATAGTCAAATGACCATTTTATAACTTTTAATAGTCGAATAACTTAATAAAACAACATCCT
* * * * * ** *
105573 ATAGTCAGATGATCGTTTTATAACTTTTGATAGTCGAATAACTTAATGAAGTAGCATCCT
1 ATAGTCAAATGACCATTTTATAACTTTTAATAGTCGAATAACTTAATAAAACAACATCCT
105633 ATAGTC
1 ATAGTC
105639 GAGGACCGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (60 bp):
ATAGTCAAATGACCATTTTATAACTTTTAATAGTCGAATAACTTAATAAAACAACATCCT
Found at i:109950 original size:15 final size:16
Alignment explanation
Indices: 109918--109950 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
109908 AAAATCTTTC
109918 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
109934 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
109949 TT
1 TT
109951 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:110720 original size:16 final size:16
Alignment explanation
Indices: 110696--110729 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
110686 TATCGCCGAC
*
110696 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
110712 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
110728 CG
1 CG
110730 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:115097 original size:29 final size:29
Alignment explanation
Indices: 115060--115116 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
115050 AACTTTTCTA
* *
115060 TTTGGTTAAAATAGGAATCTAAAGTATTT
1 TTTGATTAAAATAAGAATCTAAAGTATTT
*
115089 TTTGATTAAAATAAGTATCTAAAGTATT
1 TTTGATTAAAATAAGAATCTAAAGTATT
115117 CAACTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTGATTAAAATAAGAATCTAAAGTATTT
Found at i:116073 original size:20 final size:21
Alignment explanation
Indices: 116036--116074 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
116026 TACTTTAGAG
*
116036 AAATACTAAAACATAATATGA
1 AAATACTAAAACAAAATATGA
*
116057 AAATA-TAAAATAAAATAT
1 AAATACTAAAACAAAATAT
116075 TTACAGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (21 bp):
AAATACTAAAACAAAATATGA
Found at i:119931 original size:20 final size:19
Alignment explanation
Indices: 119884--119928 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
119874 ATAATATTAG
119884 TTAATGTAAAAAATAAATAT
1 TTAAT-TAAAAAATAAATAT
119904 TTAAATTAAAAAATATAATAAT
1 TT-AATTAAAAAATA-AAT-AT
119926 TTA
1 TTA
119929 TTAGATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 11 0.50
21 7 0.32
22 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TTAATTAAAAAATAAATAT
Found at i:120749 original size:147 final size:147
Alignment explanation
Indices: 120407--120978 Score: 832
Period size: 147 Copynumber: 3.9 Consensus size: 147
120397 TTAAAAACGA
* * * * *
120407 CTAATAATGTAAATGGT-AAAAAAATAGGTGTTACCTATTACATTAAACTACCTACTGGTTTTTT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
* * * *
120471 TAAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTATATTAAAATACCTAC
66 TTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGACGCTACCTATTACATTAAAATACCTAC
* *
120536 CGGTTTATTTAAAGATTA
131 C-GTTTTTTTAAAGATTG
* *
120554 CTAACAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAATACCTACTGGTTTTT
1 CTAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTT
120619 TTTAAGGTTGCTAATAATGTAAACGGT-AAAAAAATAGACGCTACCTATTACATTAAAATACCTA
65 TTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGACGCTACCTATTACATTAAAATACCTA
120683 -CGTTTTGTTTAAAGATTG
130 CCGTTTT-TTTAAAGATTG
* *
120701 CTAATAATGTAAACGATAAAATAAAATAGGAGCTACCTATTACATTAAAATACCTACCGGTTTTT
1 CTAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTT
* * *
120766 TTTAAGGTTGTTAATATTGTAAACGGT-AAAAAAATAGACACTACCTATTACATTAAAATACCTA
65 TTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGACGCTACCTATTACATTAAAATACCTA
*
120830 CCGGTTTTTTT-AAGGTTG
130 CC-GTTTTTTTAAAGATTG
*
120848 TTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGG-TTTTT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
* ** * *
120912 TGAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGTGCTACCTATTACATTAAACTACTTAC
66 TTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGACGCTACCTATTACATTAAAATACCTAC
120977 CG
131 CG
120979 GATATATTGA
Statistics
Matches: 389, Mismatches: 30, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
145 29 0.07
146 75 0.19
147 173 0.44
148 41 0.11
149 71 0.18
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (147 bp):
CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
TTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGACGCTACCTATTACATTAAAATACCTAC
CGTTTTTTTAAAGATTG
Found at i:120793 original size:222 final size:217
Alignment explanation
Indices: 120407--120979 Score: 831
Period size: 222 Copynumber: 2.6 Consensus size: 217
120397 TTAAAAACGA
* * * *
120407 CTAATAATGTAAATGGTAAAAAAATAGGTGTTACCTATTACATTAAACTACCTACTGGTTTTTTT
1 CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTAC--GTTTTTTT
* * *
120472 AAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTATATTAAAATACCTACC
64 AAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACC
* *
120537 GGTTTATTTAAAGATTACTAACAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAA
129 GGTTTATTTAAAGATTACTAACAATGTAAACGGT-AAA-AAAATAGACACTACCTATTACATTAA
*
120602 AATACCTACTGGTTTTTTTTAAGGTTG
192 AATACCTACCGG-TTTTTTTAAGGTTG
*
120629 CTAATAATGTAAACGGTAAAAAAATAGACGCTACCTATTACATTAAAATACCTACGTTTTGTTTA
1 CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACGTTTT-TTTA
* *
120694 AAGATTGCTAATAATGTAAACGATAAAATAAAATAGGAGCTACCTATTACATTAAAATACCTACC
65 AAGGTTGCTAATAATGTAAACGGTAAAA-AAAATAGGAGCTACCTATTACATTAAAATACCTACC
* * * ** * *
120759 GGTTTTTTTTAAGGTTGTTAATATTGTAAACGGTAAAAAAATAGACACTACCTATTACATTAAAA
129 GGTTTATTTAAAGATTACTAACAATGTAAACGGTAAAAAAATAGACACTACCTATTACATTAAAA
120824 TACCTACCGGTTTTTTTAAGGTTG
194 TACCTACCGGTTTTTTTAAGGTTG
* *
120848 TTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
1 CTAATAATGTAAACGGT-AAAAAAATAGGCGCTACCTATTACATTAAAATACCTA-CGTTTTTTT
* * * *
120913 GAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGTGCTACCTATTACATTAAACTACTTACC
64 AAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACC
120978 GG
129 GG
120980 ATATATTGAA
Statistics
Matches: 318, Mismatches: 29, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
219 65 0.20
220 105 0.33
221 38 0.12
222 110 0.35
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (217 bp):
CTAATAATGTAAACGGTAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACGTTTTTTTAA
AGGTTGCTAATAATGTAAACGGTAAAAAAAATAGGAGCTACCTATTACATTAAAATACCTACCGG
TTTATTTAAAGATTACTAACAATGTAAACGGTAAAAAAATAGACACTACCTATTACATTAAAATA
CCTACCGGTTTTTTTAAGGTTG
Found at i:120989 original size:74 final size:74
Alignment explanation
Indices: 120407--120979 Score: 827
Period size: 73 Copynumber: 7.8 Consensus size: 74
120397 TTAAAAACGA
* * * * *
120407 CTAATAATGTAAATGGT-AAAAAAATAGGTGTTACCTATTACATTAAACTACCTACTGGTTTTTT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
120471 TAAAGGTTG
66 TAAAGGTTG
* * *
120480 CTAATAATGTAAACGGTAAAAAAAATAGGCGTTACCTATTATATTAAAATACCTACCGGTTTATT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
* *
120545 TAAAGATTA
66 TAAAGGTTG
* *
120554 CTAACAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACATTAAAATACCTACTGGTTTTT
1 CTAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTT
*
120619 TTTAAGGTTG
65 TTAAAGGTTG
*
120629 CTAATAATGTAAACGGT-AAAAAAATAGACGCTACCTATTACATTAAAATACCTA-C-GTTTTGT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTT-T
*
120691 TTAAAGATTG
65 TTAAAGGTTG
* *
120701 CTAATAATGTAAACGATAAAATAAAATAGGAGCTACCTATTACATTAAAATACCTACCGGTTTTT
1 CTAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTT
*
120766 TTTAAGGTTG
65 TTAAAGGTTG
* * * *
120776 TTAATATTGTAAACGGT-AAAAAAATAGACACTACCTATTACATTAAAATACCTACCGGTTTTTT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
120840 T-AAGGTTG
66 TAAAGGTTG
*
120848 TTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGG-TTTTT
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
*
120912 TGAAGGTTG
66 TAAAGGTTG
* * *
120921 CTAATAATGTAAACGGTAAAAAAAATAGGTGCTACCTATTACATTAAACTACTTACCGG
1 CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGG
120980 ATATATTGAA
Statistics
Matches: 452, Mismatches: 39, Indels: 18
0.89 0.08 0.04
Matches are distributed among these distances:
71 5 0.01
72 54 0.12
73 195 0.43
74 107 0.24
75 86 0.19
76 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (74 bp):
CTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCGGTTTTTT
TAAAGGTTG
Found at i:121261 original size:112 final size:113
Alignment explanation
Indices: 121059--121288 Score: 390
Period size: 112 Copynumber: 2.0 Consensus size: 113
121049 TAGCGCCTAT
121059 AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAATTAATATAACAGGTAAAAACATGA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACATAAC-A--AATATAACAGGTAAAAACATGA
*
121124 CAAAACCAGTTTTATTATGACAAAACCGGTAAAGAGCTACCGGATATGTTG
63 CAAAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCGGATATGTTG
*
121175 AAAGTATCGATACTTTATAAAAATGTATCGATACATAAC-AATATAACAGGTAAAAATATGACAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAAATATAACAGGTAAAAACATGACAA
* *
121239 AACCAGTTTCATTATGATAAAACTGGTAAAGAGCTACCGGATATGTTG
66 AACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCGGATATGTTG
121287 AA
1 AA
121289 GGGTCATCAT
Statistics
Matches: 110, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
112 71 0.65
116 39 0.35
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (113 bp):
AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAAATATAACAGGTAAAAACATGACAA
AACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCGGATATGTTG
Found at i:130145 original size:2 final size:2
Alignment explanation
Indices: 130138--130178 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
130128 AATAGATTCT
130138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
130179 TAAATTAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:130592 original size:33 final size:33
Alignment explanation
Indices: 130550--130670 Score: 224
Period size: 33 Copynumber: 3.7 Consensus size: 33
130540 TTCAATCCCT
*
130550 ACCCATTGGCAGATATATAGAGAGATGGATCGA
1 ACCCATTGGCATATATATAGAGAGATGGATCGA
130583 ACCCATTGGCATATATATAGAGAGATGGATCGA
1 ACCCATTGGCATATATATAGAGAGATGGATCGA
*
130616 ACCCATTGGCATATATATAGAGAGATGGACCGA
1 ACCCATTGGCATATATATAGAGAGATGGATCGA
130649 ACCCATTGGCATATATATAGAG
1 ACCCATTGGCATATATATAGAG
130671 GACGAATCAC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (33 bp):
ACCCATTGGCATATATATAGAGAGATGGATCGA
Found at i:131483 original size:4 final size:4
Alignment explanation
Indices: 131469--131500 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
131459 GACTGTATAA
*
131469 TTAT ATAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
131501 ACATGCATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:132435 original size:22 final size:22
Alignment explanation
Indices: 132404--132447 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
132394 CACCCCTATG
132404 GTAGGAGAGCAGTGATACAGGC
1 GTAGGAGAGCAGTGATACAGGC
* * *
132426 GTAGGGGAGCGGTGATGCAGGC
1 GTAGGAGAGCAGTGATACAGGC
132448 CGGGGTAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.14, G:0.48, T:0.14
Consensus pattern (22 bp):
GTAGGAGAGCAGTGATACAGGC
Found at i:132935 original size:13 final size:13
Alignment explanation
Indices: 132904--132937 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
132894 GGACCTGAAC
132904 TTGTTTAAATTAA
1 TTGTTTAAATTAA
*
132917 -TGTTTAGATTAA
1 TTGTTTAAATTAA
132929 TTGTTTAAA
1 TTGTTTAAA
132938 CCCCTGACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (13 bp):
TTGTTTAAATTAA
Done.