Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008961.1 Hibiscus syriacus cultivar Beakdansim tig00112295_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: 183149
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:444 original size:14 final size:15
Alignment explanation
Indices: 406--446 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
396 ATAAAAGTCT
406 TACCCTACATGATATC
1 TACCC-ACATGATATC
422 TACCCCACATGATA-C
1 TA-CCCACATGATATC
437 TACCCACATG
1 TACCCACATG
447 CTTAAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 10 0.42
17 3 0.12
ACGTcount: A:0.32, C:0.37, G:0.07, T:0.24
Consensus pattern (15 bp):
TACCCACATGATATC
Found at i:1429 original size:24 final size:23
Alignment explanation
Indices: 1402--1491 Score: 76
Period size: 24 Copynumber: 3.9 Consensus size: 23
1392 GAAAAAAGTG
*
1402 AAAATGAATAAATAAAGAAAATA
1 AAAAAGAATAAATAAAGAAAATA
* *
1425 AAAAACAAATAAATAAAGCAAAAGA
1 AAAAA-GAATAAATAAAG-AAAATA
* * *
1450 ACAAAGAATAAAAAAATAAAATA
1 AAAAAGAATAAATAAAGAAAATA
* *
1473 AAATA-AATAAA-AAATAAAA
1 AAAAAGAATAAATAAAGAAAA
1492 AAGGTAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
21 8 0.15
22 6 0.11
23 12 0.22
24 20 0.36
25 9 0.16
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.13
Consensus pattern (23 bp):
AAAAAGAATAAATAAAGAAAATA
Found at i:1472 original size:5 final size:5
Alignment explanation
Indices: 1462--1528 Score: 59
Period size: 5 Copynumber: 13.6 Consensus size: 5
1452 AAAGAATAAA
* ** *
1462 AAAAT AAAAT AAAAT AAATAA AAAAT AAAA- AAGGT AAAA- ATAAT AATAAT
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT
1512 AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAA
1529 GACATAATGA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
4 9 0.18
5 31 0.63
6 9 0.18
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1475 original size:28 final size:29
Alignment explanation
Indices: 1424--1528 Score: 72
Period size: 29 Copynumber: 3.6 Consensus size: 29
1414 TAAAGAAAAT
* * * *
1424 AAAAAACAAATAAATAAAGCAAAA-GAAC
1 AAAAAATAAAAAAATAAAACAAAATAAAC
* * *
1452 AAAGAATAAAAAAATAAAATAAAATAAAT
1 AAAAAATAAAAAAATAAAACAAAATAAAC
* *
1481 AAAAAATAAAAAAGGTAAAA-ATAATAATA-
1 AAAAAATAAAAAA-ATAAAACAAAATAA-AC
*
1510 ATAAAATAAATAAAATAAA
1 AAAAAATAAA-AAAATAAA
1529 GACATAATGA
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
28 19 0.31
29 33 0.54
30 9 0.15
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (29 bp):
AAAAAATAAAAAAATAAAACAAAATAAAC
Found at i:1482 original size:9 final size:9
Alignment explanation
Indices: 1402--1528 Score: 55
Period size: 9 Copynumber: 14.9 Consensus size: 9
1392 GAAAAAAGTG
*
1402 AAAATGAAT
1 AAAATAAAT
*
1411 -AAATAAAG
1 AAAATAAAT
1419 AAAAT-AA-
1 AAAATAAAT
*
1426 AAAACAAAT
1 AAAATAAAT
*
1435 -AAATAAAGC
1 AAAATAAA-T
*
1444 AAAAGAACA-
1 AAAATAA-AT
1453 AAGAATAAA-
1 AA-AATAAAT
1462 AAAATAAAAT
1 AAAAT-AAAT
1472 AAAATAAAT
1 AAAATAAAT
1481 -AAA-AAAT
1 AAAATAAAT
*
1488 AAAA-AAGGT
1 AAAATAA-AT
1497 --AA-AAAT
1 AAAATAAAT
1503 AATAAT-AAT
1 AA-AATAAAT
1512 AAAATAAAT
1 AAAATAAAT
1521 AAAATAAA
1 AAAATAAA
1529 GACATAATGA
Statistics
Matches: 93, Mismatches: 9, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
6 1 0.01
7 12 0.13
8 30 0.32
9 35 0.38
10 14 0.15
11 1 0.01
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1506 original size:29 final size:29
Alignment explanation
Indices: 1456--1528 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
1446 AAGAACAAAG
1456 AATAAAAAAATAAAATAAAATAAATAA-AA
1 AATAAAAAAATAAAATAAAAT-AATAATAA
* *
1485 AATAAAAAAGGTAAAA-ATAATAATAATAA
1 AATAAAAAA-ATAAAATAAAATAATAATAA
1514 AATAAATAAAATAAA
1 AATAAA-AAAATAAA
1529 GACATAATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 5 0.13
29 25 0.66
30 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (29 bp):
AATAAAAAAATAAAATAAAATAATAATAA
Found at i:1536 original size:28 final size:28
Alignment explanation
Indices: 1408--1532 Score: 74
Period size: 24 Copynumber: 4.7 Consensus size: 28
1398 AGTGAAAATG
* *
1408 AATAAATAAAGA-AAATA-AAA-AA-CA
1 AATAAATAAAGATAAAGACAAATAATAA
*
1432 AATAAATAAAGCA-AAAGAACAAAGAATAA
1 AATAAATAAAG-ATAAAG-ACAAATAATAA
*
1461 AA-AAATAAA-ATAAA-ATAAATAA-AA
1 AATAAATAAAGATAAAGACAAATAATAA
* * *
1485 AATAAA-AAAGGTAAAAATAATAATAATAA
1 AATAAATAAAGATAAAGA-CA-AATAATAA
1514 AATAAATAAA-ATAAAGACA
1 AATAAATAAAGATAAAGACA
1533 TAATGACGCA
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
24 18 0.23
25 17 0.22
26 3 0.04
27 7 0.09
28 15 0.19
29 16 0.20
30 3 0.04
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (28 bp):
AATAAATAAAGATAAAGACAAATAATAA
Found at i:1580 original size:19 final size:18
Alignment explanation
Indices: 1558--1594 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1548 AATAATGCAG
*
1558 AAAATAAATAAAAATATAA
1 AAAACAAATAAAAA-ATAA
1577 AAAACAAATAAAAAATAA
1 AAAACAAATAAAAAATAA
1595 GTAAGTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAACAAATAAAAAATAA
Found at i:1664 original size:3 final size:3
Alignment explanation
Indices: 1651--1705 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
1641 AAGTATAAAG
1651 AAT ATAT AAT AAT -AT AAT AAT AAT AA- AAT -AT ATAT AAT AACT -AT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AA-T AAT
1695 AAT AAT AAT AA
1 AAT AAT AAT AA
1706 GAAGAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
2 7 0.16
3 31 0.69
4 7 0.16
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1670 original size:11 final size:11
Alignment explanation
Indices: 1651--1704 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
1641 AAGTATAAAG
1651 AATAT-ATAAT
1 AATATAATAAT
1661 AATATAATAAT
1 AATATAATAAT
1672 -A-ATAA-AAT
1 AATATAATAAT
1680 -ATAT-ATAAT
1 AATATAATAAT
1689 AACTATAATAAT
1 AA-TATAATAAT
1701 AATA
1 AATA
1705 AGAAGAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
8 5 0.13
9 9 0.24
10 7 0.18
11 10 0.26
12 7 0.18
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATAATAAT
Found at i:1842 original size:145 final size:145
Alignment explanation
Indices: 1675--1975 Score: 385
Period size: 141 Copynumber: 2.1 Consensus size: 145
1665 TAATAATAAT
*
1675 AAAATATATATAATAACTATAATAATAATAAGAAGAAAAAAAGAGTATAAAAAACAAAAAACTTA
1 AAAATATATATAATACCTATAAT-ATAATAAGAAG-AAAAAAGA--ATAAAAAA-AAAAAACTTA
*
1740 -CT-CT-T-ATTAATGCA-AA-AATGATTAAATTTGGGTGGAG-AC-AAAAACGGGA-GGG-CCT
61 CCTACTATAATTAATGCAGAAGAATGATT-AATTTGGGTGGAGAACAAAAAAAGGGAGGGGACCT
1795 A-GAAGAAAAAAAGGTGAG-AGA
125 ATG-AG-AAAAAAGGTGAGAAGA
* * *
1816 AAATTATATATAATA-CTATAATATAATAAGAAGAAAAAATAATAAAAAAATAAAACTTAGCCTA
1 AAAATATATATAATACCTATAATATAATAAGAAGAAAAAAGAATAAAAAAAAAAAACTTA-CCTA
1880 CTATAATTAATGCAGAAGAATGATTAATTTGGGTGGAGAACAAAAAAAGGGAGGGGACCTATGAG
65 CTATAATTAATGCAGAAGAATGATTAATTTGGGTGGAGAACAAAAAAAGGGAGGGGACCTATGAG
1945 AAAAAAGGTGAGAAGA
130 AAAAAAGGTGAGAAGA
1961 AAAATATATATAATA
1 AAAATATATATAATA
1976 TGGAATAAAG
Statistics
Matches: 142, Mismatches: 5, Indels: 22
0.84 0.03 0.13
Matches are distributed among these distances:
135 9 0.06
136 8 0.06
137 2 0.01
138 9 0.06
139 12 0.08
140 16 0.11
141 29 0.20
142 9 0.06
143 9 0.06
144 15 0.11
145 23 0.16
146 1 0.01
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.22
Consensus pattern (145 bp):
AAAATATATATAATACCTATAATATAATAAGAAGAAAAAAGAATAAAAAAAAAAAACTTACCTAC
TATAATTAATGCAGAAGAATGATTAATTTGGGTGGAGAACAAAAAAAGGGAGGGGACCTATGAGA
AAAAAGGTGAGAAGA
Found at i:4356 original size:21 final size:21
Alignment explanation
Indices: 4313--4357 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4303 ACGAGGATTG
** *
4313 ATCCTCCTTTACGAGGGACCA
1 ATCCTCCTTTACGAAAGAACA
*
4334 ATCCTCCTTTAGGAAAGAACA
1 ATCCTCCTTTACGAAAGAACA
4355 ATC
1 ATC
4358 TTAAAGGGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (21 bp):
ATCCTCCTTTACGAAAGAACA
Found at i:8046 original size:3 final size:3
Alignment explanation
Indices: 8038--8084 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
8028 TAATGGTGAT
8038 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
8085 TTCTGATGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9172 original size:43 final size:43
Alignment explanation
Indices: 9106--9324 Score: 144
Period size: 43 Copynumber: 5.1 Consensus size: 43
9096 ATGCTAATTA
* * * *
9106 GCGGCGTTTGTATCAAAATATGCCGTTATAGATATAACTTTTT
1 GCGGCGTTTGTATAAAAAAATGCCGCTATAGATATAACCTTTT
* *
9149 GCGGCGTTTGTATAAAAAAATGCCGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTATAAAAAAATGCCGCTATAGATATAACCTTTT
** ** * * * * *
9192 GCGGTTTTTGTAT-TTAAAACGTCGCTATAGATCTGATCTTTT
1 GCGGCGTTTGTATAAAAAAATGCCGCTATAGATATAACCTTTT
* * * * *
9234 GCGGTGTTTGT-TCCAAAAACAT--CGCTATAGGTCTGACCTTTT
1 GCGGCGTTTGTAT--AAAAAAATGCCGCTATAGATATAACCTTTT
* * * *
9276 GCGGTGTTTGTATCCAAAAACAT--CGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTAT--AAAAAAATGCCGCTATAGATATAACCTTTT
9319 GCGGCG
1 GCGGCG
9325 CTATAGATCT
Statistics
Matches: 148, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 62 0.42
43 82 0.55
44 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (43 bp):
GCGGCGTTTGTATAAAAAAATGCCGCTATAGATATAACCTTTT
Found at i:9233 original size:42 final size:43
Alignment explanation
Indices: 9145--9322 Score: 220
Period size: 42 Copynumber: 4.2 Consensus size: 43
9135 AGATATAACT
* * *
9145 TTTTGCGGCGTTTGTAT--AAAAAAATGCCGCTATAGATTTGACC
1 TTTTGCGGTGTTTGTATCCAAAAACAT--CGCTATAGATCTGACC
* ** * *
9188 TTTTGCGGTTTTTGTAT-TTAAAACGTCGCTATAGATCTGATC
1 TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATCTGACC
*
9230 TTTTGCGGTGTTTGT-TCCAAAAACATCGCTATAGGTCTGACC
1 TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATCTGACC
*
9272 TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATTTGACC
1 TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATCTGACC
9315 TTTTGCGG
1 TTTTGCGG
9323 CGCTATAGAT
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.01
42 63 0.54
43 48 0.41
44 5 0.04
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (43 bp):
TTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATCTGACC
Found at i:9326 original size:24 final size:25
Alignment explanation
Indices: 9299--9349 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
9289 CCAAAAACAT
*
9299 CGCTATAGAT-TTGACCTTTTGCGG
1 CGCTATAGATCTTGACCTTTAGCGG
9323 CGCTATAGATCTTGACCTTTAGCGG
1 CGCTATAGATCTTGACCTTTAGCGG
9348 CG
1 CG
9350 TTTGTATCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (25 bp):
CGCTATAGATCTTGACCTTTAGCGG
Found at i:9386 original size:68 final size:67
Alignment explanation
Indices: 9256--9391 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 67
9246 CCAAAAACAT
* * * * * *
9256 CGCTATAGGTCTGACCTTTTGCGGTGTTTGTATCCAAAAACATCGCTATAGATTTGACCTTTTGC
1 CGCTATAGATCTGACCTTTAGCGGCGTTTGTATCCAAAAACATCGCTATAAATCTAACCTTTTGC
9321 GG
66 GG
** * *
9323 CGCTATAGATCTTGACCTTTAGCGGCGTTTGTATCCAAAAATGTCGGTATAAATCTAATCTTTTG
1 CGCTATAGATC-TGACCTTTAGCGGCGTTTGTATCCAAAAACATCGCTATAAATCTAACCTTTTG
9388 CGG
65 CGG
9391 C
1 C
9392 ATTTGTTTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
67 10 0.17
68 48 0.83
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (67 bp):
CGCTATAGATCTGACCTTTAGCGGCGTTTGTATCCAAAAACATCGCTATAAATCTAACCTTTTGC
GG
Found at i:11043 original size:51 final size:50
Alignment explanation
Indices: 10988--11099 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 50
10978 CTTGCCCCGT
** * *
10988 GCTATATGCTGATTTGGCGTCACAT-TGAGTATAGCGCGCCTCCTGTACTGC
1 GCTATA-GCTGACATGGC-TCACATGTGAGTATAGCGCGCCCCCTGTACCGC
* * *
11039 GCTATACGCTGACATGGCTTACATGTGGGTATAGCGCGCCCCCTGTTCCGC
1 GCTATA-GCTGACATGGCTCACATGTGAGTATAGCGCGCCCCCTGTACCGC
11090 GCTATAGCTG
1 GCTATAGCTG
11100 TTTATCTGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
50 9 0.17
51 43 0.83
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.29
Consensus pattern (50 bp):
GCTATAGCTGACATGGCTCACATGTGAGTATAGCGCGCCCCCTGTACCGC
Found at i:16939 original size:11 final size:12
Alignment explanation
Indices: 16923--16952 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16913 AAGTATAATA
16923 AACAAAA-TTAT
1 AACAAAATTTAT
16934 AACAAAATTTAT
1 AACAAAATTTAT
16946 AACAAAA
1 AACAAAA
16953 AATCGCACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (12 bp):
AACAAAATTTAT
Found at i:18188 original size:39 final size:39
Alignment explanation
Indices: 18145--18228 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
18135 AACGGTGAAG
*
18145 TAGGGAGTG-AGATGCGA-AGGAGAAATGAAAAAGGGGAAT
1 TAGGGAGTGAAG-GGCGAGAGGA-AAATGAAAAAGGGGAAT
* * **
18184 TAGGGATTGAAGGGCGAGAGGAAAATGAGATTGGGGAAT
1 TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
18223 TAGGGA
1 TAGGGA
18229 TTATGGCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 32 0.84
40 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.43, T:0.15
Consensus pattern (39 bp):
TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
Found at i:23412 original size:39 final size:39
Alignment explanation
Indices: 23369--23452 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
23359 AACGGTGAAG
*
23369 TAGGGAGTG-AGATGCGA-AGGAGAAATGAAAAAGGGGAAT
1 TAGGGAGTGAAG-GGCGAGAGGA-AAATGAAAAAGGGGAAT
* * **
23408 TAGGGATTGAAGGGCGAGAGGAAAATGAGATTGGGGAAT
1 TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
23447 TAGGGA
1 TAGGGA
23453 TTATGGCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 32 0.84
40 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.43, T:0.15
Consensus pattern (39 bp):
TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
Found at i:23859 original size:17 final size:17
Alignment explanation
Indices: 23837--23872 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
23827 TAGATCGTCA
23837 CATCAACTCTCTAATGG
1 CATCAACTCTCTAATGG
23854 CATCAACTCTCTAATGG
1 CATCAACTCTCTAATGG
23871 CA
1 CA
23873 GCTTTTTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.28
Consensus pattern (17 bp):
CATCAACTCTCTAATGG
Found at i:29898 original size:12 final size:12
Alignment explanation
Indices: 29881--29906 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29871 AAACAAGGTT
29881 AAAAAAAAGATA
1 AAAAAAAAGATA
29893 AAAAAAAAGATA
1 AAAAAAAAGATA
29905 AA
1 AA
29907 GAAATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAAAGATA
Found at i:34997 original size:21 final size:22
Alignment explanation
Indices: 34962--35007 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
34952 AATAAAATGT
34962 TTAATGAAAAAGATACCAATTG
1 TTAATGAAAAAGATACCAATTG
* *
34984 TTAAT-AAAATGATATCAATTG
1 TTAATGAAAAAGATACCAATTG
35005 TTA
1 TTA
35008 CCAATTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (22 bp):
TTAATGAAAAAGATACCAATTG
Found at i:37547 original size:21 final size:21
Alignment explanation
Indices: 37518--37567 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
37508 ACTGGTGGCA
*
37518 GATGTACTGCAGGGGTGCATG
1 GATGCACTGCAGGGGTGCATG
37539 GATGCACTGCAGGGGTGCATG
1 GATGCACTGCAGGGGTGCATG
37560 GATGCACT
1 GATGCACT
37568 TTGACACCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (21 bp):
GATGCACTGCAGGGGTGCATG
Found at i:37814 original size:21 final size:21
Alignment explanation
Indices: 37790--37829 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
37780 ATGTTTAATG
37790 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
37811 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
37830 TCGATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:39839 original size:2 final size:2
Alignment explanation
Indices: 39832--39865 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
39822 CTCATAATAC
39832 TA TA TA TA TA TA TA TA TA TA TCA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
39866 AGCAATCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41488 original size:20 final size:22
Alignment explanation
Indices: 41463--41502 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
41453 TGTCGTATAT
41463 AACCATT-GGGGATG-TTTTGA
1 AACCATTAGGGGATGATTTTGA
41483 AACCATTAGGGGATGATTTT
1 AACCATTAGGGGATGATTTT
41503 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (22 bp):
AACCATTAGGGGATGATTTTGA
Found at i:41753 original size:21 final size:21
Alignment explanation
Indices: 41656--41743 Score: 142
Period size: 21 Copynumber: 4.2 Consensus size: 21
41646 TCGAAATGGA
* *
41656 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTGCAGGG
*
41676 GTGCATCGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
41697 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
41718 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
41739 GTGCA
1 GTGCA
41744 CAAATGCACT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
20 16 0.25
21 47 0.75
ACGTcount: A:0.20, C:0.20, G:0.39, T:0.20
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:52092 original size:30 final size:30
Alignment explanation
Indices: 52056--52129 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
52046 TTTTAGACAT
52056 AATATTAATTTAA-TCTTAAACTTTAAATAA
1 AATATTAATTTAACT-TTAAACTTTAAATAA
**
52086 AATATTAATTTAACTTTAAACTTTACGTAA
1 AATATTAATTTAACTTTAAACTTTAAATAA
52116 AATATTAATTTAAC
1 AATATTAATTTAAC
52130 CACTGTGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 40 0.98
31 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.43
Consensus pattern (30 bp):
AATATTAATTTAACTTTAAACTTTAAATAA
Found at i:54262 original size:72 final size:72
Alignment explanation
Indices: 54171--54314 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
54161 ACATAAAATA
*
54171 TATTAACCAAATGATAAATAGGAAGTTACTTGGAAAATAATACTCTTGGCTTTGTTTAATAAGGT
1 TATTAACCAAATGATAAATAGGAAGTTACTTGGAAAATAATACTCTTGGCTCTGTTTAATAAGGT
54236 GGTTCAG
66 GGTTCAG
* *
54243 TATTAACCTAATGATAAATATGAAGTTACTTGGAAAATAATACTCTTGGCTCTGTTTAATAAGGT
1 TATTAACCAAATGATAAATAGGAAGTTACTTGGAAAATAATACTCTTGGCTCTGTTTAATAAGGT
54308 GGTTCAG
66 GGTTCAG
54315 GCCTAGCTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (72 bp):
TATTAACCAAATGATAAATAGGAAGTTACTTGGAAAATAATACTCTTGGCTCTGTTTAATAAGGT
GGTTCAG
Found at i:54411 original size:67 final size:67
Alignment explanation
Indices: 54329--54461 Score: 230
Period size: 67 Copynumber: 2.0 Consensus size: 67
54319 AGCTTTGGAC
* *
54329 GTTATGTCTGGTCTGCACTAAGTGGAACTTGGTATTCTTAGCTCTGTTTAATTATCATCTGCCCT
1 GTTATGTCTGGTCTGCACCAAGTGGAACTTAGTATTCTTAGCTCTGTTTAATTATCATCTGCCCT
54394 GG
66 GG
* *
54396 GTTATGTCTGGTCTGCACCATGTGGAGCTTAGTATTCTTAGCTCTGTTTAATTATCATCTGCCCT
1 GTTATGTCTGGTCTGCACCAAGTGGAACTTAGTATTCTTAGCTCTGTTTAATTATCATCTGCCCT
54461 G
66 G
54462 CCTTCTATCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (67 bp):
GTTATGTCTGGTCTGCACCAAGTGGAACTTAGTATTCTTAGCTCTGTTTAATTATCATCTGCCCT
GG
Found at i:57283 original size:129 final size:129
Alignment explanation
Indices: 57053--57289 Score: 422
Period size: 129 Copynumber: 1.8 Consensus size: 129
57043 AAATATATAT
* **
57053 ATAATCAAACAAATTTGATAATGCAGATCATAGGATGCAAAATCAAAGCAATCGTTTGCCCAACA
1 ATAATCAAACAAATTTGAAAATGCAGATCATAGGATGCAAAATCAAAGCAATCGTTCACCCAACA
57118 GTACATACAAATTCAAAACCCAACATCAAAACAATTCATCGCTATAAGATAGAAAGTAAAACTA
66 GTACATACAAATTCAAAACCCAACATCAAAACAATTCATCGCTATAAGATAGAAAGTAAAACTA
*
57182 ATAATCAAACAAATTTGAAAATGCAGATCATAGGAAT-CAAAATCAAAGGAATCGTTCACCCAAC
1 ATAATCAAACAAATTTGAAAATGCAGATCATAGG-ATGCAAAATCAAAGCAATCGTTCACCCAAC
57246 AGTACATACAAATTCAAAACCCAACATCAAAACAATTCATCGCT
65 AGTACATACAAATTCAAAACCCAACATCAAAACAATTCATCGCT
57290 TCACATAAAA
Statistics
Matches: 103, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
129 101 0.98
130 2 0.02
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (129 bp):
ATAATCAAACAAATTTGAAAATGCAGATCATAGGATGCAAAATCAAAGCAATCGTTCACCCAACA
GTACATACAAATTCAAAACCCAACATCAAAACAATTCATCGCTATAAGATAGAAAGTAAAACTA
Found at i:58833 original size:28 final size:27
Alignment explanation
Indices: 58797--58851 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
58787 TAATATATTA
*
58797 TTTTATAATTTTTGATA-TATTTTTAAT
1 TTTTATAA-TATTGATAGTATTTTTAAT
*
58824 TTTTAATAATATTGTTAGTATTTTTAAT
1 TTTT-ATAATATTGATAGTATTTTTAAT
58852 ATATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (27 bp):
TTTTATAATATTGATAGTATTTTTAAT
Found at i:58867 original size:21 final size:20
Alignment explanation
Indices: 58787--58867 Score: 78
Period size: 19 Copynumber: 4.0 Consensus size: 20
58777 TAATAATTAA
58787 TAATATATTATTTTATAATTTT
1 TAATATA-TATTTT-TAATTTT
*
58809 T--GATATATTTTTAATTTT
1 TAATATATATTTTTAATTTT
*
58827 TAATA-ATATTGTTAGTATTTT
1 TAATATATATTTTTA--ATTTT
58848 TAATATATATTTTTTAATTT
1 TAATATATA-TTTTTAATTT
58868 CATTAGTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
18 8 0.16
19 14 0.29
20 4 0.08
21 14 0.29
22 4 0.08
23 5 0.10
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
TAATATATATTTTTAATTTT
Found at i:58917 original size:17 final size:17
Alignment explanation
Indices: 58895--58930 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
58885 ATTATAAGTG
*
58895 TTTTATATTTTAAATAA
1 TTTTATATTTTAAAAAA
58912 TTTTATATTTTAAAAAA
1 TTTTATATTTTAAAAAA
58929 TT
1 TT
58931 AAATATGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATATTTTAAAAAA
Found at i:76279 original size:194 final size:188
Alignment explanation
Indices: 75947--76322 Score: 682
Period size: 194 Copynumber: 2.0 Consensus size: 188
75937 TGTTTGAGAG
75947 AACTTGGGAAGGATTACATAAGCAATGGGATAGTTAATCACTATAACCTAATCCCTTTTACTTCA
1 AACTTGGGAAGGATTACATAAGCAATGGGATAGTTAATCACTATAACCTAATCCCTTTTACTTCA
76012 GAGATACTAAGCTAGGATTTCAAACTATGAGGGTAGTGTGTCATCAATATTGTAGGCTACCATAG
66 GAGATACTAAGCTAGGATTTCAAACTATGAGGGTAGTGTGTCATCAATATTGTAGGCTACCATAG
76077 TTGAGACTGAGAGGTTGCCATAGTTGATATTGAGAGGAGATATGGT-GCATTTTTTTAGA
131 TTGAGACTGAGAGGTTGCCATAGTTGATATTGAGA-G-GATATGGTGGCATTTTTTTAGA
76136 AACTTGGGAAGGATTAACATAAGCAATGGGATAGTTAATCACTATAACCTAATCCCTTTTTACTT
1 AACTTGGGAAGGATT-ACATAAGCAATGGGATAGTTAATCACTATAACCTAATCCC-TTTTACTT
76201 CAGAGATACTAAGCTAGGATTTCAAAGACTATGAGGGGTAGTGTGTCATCAATATTGTAGGCTAC
64 CAGAGATACTAAGCTAGGATTTC-AA-ACTATGA-GGGTAGTGTGTCATCAATATTGTAGGCTAC
76266 CATAGTTGAGACTGAGAGGTTGCCATAGTTGATATTGAGAGGATATGGTGGCATTTT
126 CATAGTTGAGACTGAGAGGTTGCCATAGTTGATATTGAGAGGATATGGTGGCATTTT
76323 ATTTTGTTAG
Statistics
Matches: 181, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
189 15 0.08
190 40 0.22
191 31 0.17
192 10 0.06
193 15 0.08
194 70 0.39
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (188 bp):
AACTTGGGAAGGATTACATAAGCAATGGGATAGTTAATCACTATAACCTAATCCCTTTTACTTCA
GAGATACTAAGCTAGGATTTCAAACTATGAGGGTAGTGTGTCATCAATATTGTAGGCTACCATAG
TTGAGACTGAGAGGTTGCCATAGTTGATATTGAGAGGATATGGTGGCATTTTTTTAGA
Found at i:77285 original size:9 final size:10
Alignment explanation
Indices: 77257--77287 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
77247 ACAAAATCCC
77257 TTTTATTTAT
1 TTTTATTTAT
77267 TTTTATTTAT
1 TTTTATTTAT
77277 TTTTA-TTAT
1 TTTTATTTAT
77286 TT
1 TT
77288 CAAACCAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:80401 original size:23 final size:23
Alignment explanation
Indices: 80371--80419 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
80361 TCAATAGTGT
80371 AGGTTGCCATAGTTAAGACTGAG
1 AGGTTGCCATAGTTAAGACTGAG
* *
80394 AGGTTGCCATAGTTGAGGCTGAG
1 AGGTTGCCATAGTTAAGACTGAG
80417 AGG
1 AGG
80420 AGATACGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.37, T:0.24
Consensus pattern (23 bp):
AGGTTGCCATAGTTAAGACTGAG
Found at i:81511 original size:10 final size:10
Alignment explanation
Indices: 81496--81522 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
81486 ACAAAATACC
81496 TTTTATTTCT
1 TTTTATTTCT
81506 TTTTATTTCT
1 TTTTATTTCT
81516 TTTTATT
1 TTTTATT
81523 ATTTCAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTATTTCT
Found at i:87731 original size:20 final size:20
Alignment explanation
Indices: 87681--87744 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
87671 AACCAATCCA
* *
87681 TCTAGTATGGATAGCAGCCT
1 TCTAGTATGGATACCAACCT
87701 TCTAG-AGTGGATACCAACCT
1 TCTAGTA-TGGATACCAACCT
*
87721 TCTGGTATGGATACCAACCT
1 TCTAGTATGGATACCAACCT
87741 TCTA
1 TCTA
87745 ATATCAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
TCTAGTATGGATACCAACCT
Found at i:87754 original size:20 final size:20
Alignment explanation
Indices: 87711--87757 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
87701 TCTAGAGTGG
** **
87711 ATACCAACCTTCTGGTATGG
1 ATACCAACCTTCTAATATCA
87731 ATACCAACCTTCTAATATCA
1 ATACCAACCTTCTAATATCA
87751 ATACCAA
1 ATACCAA
87758 ACATTCAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.28, G:0.09, T:0.28
Consensus pattern (20 bp):
ATACCAACCTTCTAATATCA
Found at i:89195 original size:23 final size:21
Alignment explanation
Indices: 89169--89212 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
89159 TCATACCCGG
89169 AATATCATTCATGATAAATATCA
1 AATAT-ATTCATGATAAA-ATCA
*
89192 AATATGTTCATGATAAAATCA
1 AATATATTCATGATAAAATCA
89213 TATGTAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (21 bp):
AATATATTCATGATAAAATCA
Found at i:89217 original size:19 final size:21
Alignment explanation
Indices: 89176--89217 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
89166 CGGAATATCA
89176 TTCATGATAAATATCAAATATG
1 TTCATGATAAATATC-AATATG
89198 TTCATGATAAA-ATC-ATATG
1 TTCATGATAAATATCAATATG
89217 T
1 T
89218 AACAATCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
21 3 0.15
22 11 0.55
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
TTCATGATAAATATCAATATG
Found at i:90118 original size:15 final size:15
Alignment explanation
Indices: 90098--90135 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
90088 AGGTCATCCC
90098 CTCACTCGATATTAT
1 CTCACTCGATATTAT
90113 CTCACTCGATATTAT
1 CTCACTCGATATTAT
90128 CTCACTCG
1 CTCACTCG
90136 TTCTCTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.37
Consensus pattern (15 bp):
CTCACTCGATATTAT
Found at i:90817 original size:20 final size:20
Alignment explanation
Indices: 90744--90831 Score: 63
Period size: 20 Copynumber: 4.3 Consensus size: 20
90734 TCTTATATAT
* *
90744 ATACCAATCCATCTAGTATGG
1 ATACCAA-CCTTCTAATATGG
* *
90765 ATATCAGCCTTCT-ATAGTGG
1 ATACCAACCTTCTAATA-TGG
* **
90785 ATTCC-ACCTTTCTGGTATGG
1 ATACCAACC-TTCTAATATGG
*
90805 ATACCAACCTTCTAATATCG
1 ATACCAACCTTCTAATATGG
90825 ATACCAA
1 ATACCAA
90832 GCATTCAGTA
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
19 4 0.08
20 37 0.73
21 10 0.20
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (20 bp):
ATACCAACCTTCTAATATGG
Found at i:92307 original size:23 final size:21
Alignment explanation
Indices: 92281--92325 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
92271 TTCATACCCG
92281 AAATATCATTCATGATAAATATC
1 AAATAT-ATTCATGATAAA-ATC
*
92304 AAATATGTTCATGATAAAATC
1 AAATATATTCATGATAAAATC
92325 A
1 A
92326 TATGTAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 11 0.52
23 6 0.29
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (21 bp):
AAATATATTCATGATAAAATC
Found at i:92330 original size:19 final size:21
Alignment explanation
Indices: 92289--92330 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
92279 CGAAATATCA
92289 TTCATGATAAATATCAAATATG
1 TTCATGATAAATATC-AATATG
92311 TTCATGATAAA-ATC-ATATG
1 TTCATGATAAATATCAATATG
92330 T
1 T
92331 AACAATCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
21 3 0.15
22 11 0.55
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
TTCATGATAAATATCAATATG
Found at i:96095 original size:19 final size:19
Alignment explanation
Indices: 96071--96116 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
96061 CTCCTTGTGT
96071 AATTCTTTTTATTCTTAGC
1 AATTCTTTTTATTCTTAGC
96090 AATTCTTTTTATTCTTAGC
1 AATTCTTTTTATTCTTAGC
*
96109 ATTTCTTT
1 AATTCTTT
96117 CTAACATGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.20, C:0.15, G:0.04, T:0.61
Consensus pattern (19 bp):
AATTCTTTTTATTCTTAGC
Found at i:96715 original size:39 final size:39
Alignment explanation
Indices: 96635--96715 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
96625 CCTGTACATC
* * *
96635 CAGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGCGTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTG
96674 CAGTAAGGACTTACCCTGAGCACAAAGTCA-AAGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAG-CAGAAGAGCCTG
96713 CAG
1 CAG
96716 AAAGCTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 36 0.95
40 2 0.05
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTG
Found at i:96773 original size:44 final size:43
Alignment explanation
Indices: 96721--96835 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 43
96711 TGCAGAAAGC
* * **
96721 TATAAGGTCTTACCCTTGCACATAGTAGAGGAGCATGCGCAAA
1 TATAAGGTCTTACCCTTGCACATAGCAGAGAAGCATGCAAAAA
* *
96764 TGATAAGGTCTTACCC-TGTCACATAGCAGAGAAGCCTTCAAAAA
1 T-ATAAGGTCTTACCCTTG-CACATAGCAGAGAAGCATGCAAAAA
*
96808 TAGTAAGGTCTTACCCTTGTACATAGCA
1 TA-TAAGGTCTTACCCTTGCACATAGCA
96836 AATGAGCCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
43 4 0.07
44 55 0.90
45 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (43 bp):
TATAAGGTCTTACCCTTGCACATAGCAGAGAAGCATGCAAAAA
Found at i:100829 original size:22 final size:22
Alignment explanation
Indices: 100781--100830 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
100771 CAAAGAGATA
*
100781 TGGGCTCCCCACGGTGATACAC
1 TGGGTTCCCCACGGTGATACAC
*
100803 TGGGTTCCCTACGGTGATACAC
1 TGGGTTCCCCACGGTGATACAC
100825 TGGGTT
1 TGGGTT
100831 GAATAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (22 bp):
TGGGTTCCCCACGGTGATACAC
Found at i:102570 original size:15 final size:15
Alignment explanation
Indices: 102550--102581 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
102540 ATAGCATACA
102550 TATTACCAGGGACTC
1 TATTACCAGGGACTC
102565 TATTACCAGGGACTC
1 TATTACCAGGGACTC
102580 TA
1 TA
102582 GCAGCTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (15 bp):
TATTACCAGGGACTC
Found at i:103184 original size:38 final size:38
Alignment explanation
Indices: 103113--103185 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
103103 ATACATATTT
* *
103113 CAGAAAACTGCATAAAACATATACATATCAAAATACAG
1 CAGAAAACCGCATAAAACATATACAAATCAAAATACAG
* *
103151 CAGAAAACCGTATAAAACATTTACAGAAT-AAAATA
1 CAGAAAACCGCATAAAACATATACA-AATCAAAATA
103186 TCGGTAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 28 0.93
39 2 0.07
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.19
Consensus pattern (38 bp):
CAGAAAACCGCATAAAACATATACAAATCAAAATACAG
Found at i:103203 original size:2 final size:2
Alignment explanation
Indices: 103196--103241 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
103186 TCGGTAATAA
103196 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
103238 AT AT
1 AT AT
103242 CAAGACGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103643 original size:43 final size:43
Alignment explanation
Indices: 103568--103707 Score: 149
Period size: 43 Copynumber: 3.2 Consensus size: 43
103558 CACAAAACCG
* * *
103568 AGGAGCCTGTGGAAAGTTGTAAGGTATTACCCTTGCAAATAGCAT
1 AGGAGCCTGTGGAAAG--GTAAGGTCTTACCCTTGCACATAGCAA
* *
103613 ATGAGCCTGTGGAAAGGTAAGGTCTTACCC-TGACACATAGCAG
1 AGGAGCCTGTGGAAAGGTAAGGTCTTACCCTTG-CACATAGCAA
** *
103656 AGGAGTCCT-CCGAAATAGTAAGGTCTTACCCTTGCACATAGCAA
1 AGGAG-CCTGTGGAAA-GGTAAGGTCTTACCCTTGCACATAGCAA
103700 AGGAGCCT
1 AGGAGCCT
103708 TCAGAAACTT
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.02
43 32 0.39
44 31 0.38
45 17 0.21
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (43 bp):
AGGAGCCTGTGGAAAGGTAAGGTCTTACCCTTGCACATAGCAA
Found at i:105703 original size:17 final size:19
Alignment explanation
Indices: 105668--105708 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
105658 ATTGAATACT
105668 TTTAATAATATACTAACAA
1 TTTAATAATATACTAACAA
105687 TTTAATAAT-TA-TAACAA
1 TTTAATAATATACTAACAA
*
105704 ATTAA
1 TTTAA
105709 AAGGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTAATAATATACTAACAA
Found at i:110485 original size:25 final size:23
Alignment explanation
Indices: 110437--110520 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 23
110427 TTTAATTCAT
110437 AATATTTTTATATATTAATT-TTAA
1 AATA-TTTT-TATATTAATTATTAA
110461 AAGTATTTTTATATTAACTTATT-A
1 AA-TATTTTTATATTAA-TTATTAA
110485 AATATATTTTATCATTAAATTAATTTAA
1 AATAT-TTTTAT-ATT-AATT-A-TTAA
110513 AATATTTT
1 AATATTTT
110521 ATCTTTATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
23 11 0.22
24 17 0.33
25 9 0.18
26 3 0.06
27 5 0.10
28 6 0.12
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (23 bp):
AATATTTTTATATTAATTATTAA
Found at i:110519 original size:26 final size:26
Alignment explanation
Indices: 110450--110523 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 26
110440 ATTTTTATAT
110450 ATTAATTTTAAAAGTATTTTTAT-ATTAA
1 ATTAA-TTTAAAA-TA-TTTTATCATTAA
*
110478 CTT-A-TTAAATATATTTTATCATTAA
1 ATTAATTTAAA-ATATTTTATCATTAA
110503 ATTAATTTAAAATATTTTATC
1 ATTAATTTAAAATATTTTATC
110524 TTTATTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
24 6 0.15
25 14 0.35
26 12 0.30
27 6 0.15
28 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (26 bp):
ATTAATTTAAAATATTTTATCATTAA
Found at i:111617 original size:4 final size:4
Alignment explanation
Indices: 111618--111682 Score: 58
Period size: 4 Copynumber: 15.8 Consensus size: 4
111608 ATATATATAT
* * * * *
111618 ATAC ATAC ATAC ATAC ATAT ATAC ATGC ATGC ATAG ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
111666 ATAT ATTTAC ATAC ATA
1 ATAC A--TAC ATAC ATA
111683 TATCAGAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
4 46 0.94
6 3 0.06
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:111643 original size:16 final size:16
Alignment explanation
Indices: 111622--111685 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
111612 ATATATATAC
111622 ATACATACATACATAT
1 ATACATACATACATAT
* * *
111638 ATACATGCATGCATAG
1 ATACATACATACATAT
*
111654 ATACATGCATACATAT
1 ATACATACATACATAT
*
111670 AT--TTACATACATAT
1 ATACATACATACATAT
111684 AT
1 AT
111686 CAGAAAACCA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
14 12 0.29
16 29 0.71
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (16 bp):
ATACATACATACATAT
Found at i:111810 original size:4 final size:4
Alignment explanation
Indices: 111803--111868 Score: 78
Period size: 4 Copynumber: 15.8 Consensus size: 4
111793 TATATATATA
* *
111803 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAGAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT--AC ATAC
*
111853 ATAT ATTAC ATAC ATA
1 ATAC A-TAC ATAC ATA
111869 TATCAGAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
4 47 0.89
5 3 0.06
6 3 0.06
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:111937 original size:187 final size:184
Alignment explanation
Indices: 111596--111966 Score: 627
Period size: 187 Copynumber: 2.0 Consensus size: 184
111586 ATAAGAAATG
* * * *
111596 TTCATACGATAAATATATATATATACATACATACATACATATATACATGCATGCATAGATACATG
1 TTCATACGATAAATATATATATATACATACATACATACATACATACATACATACATACATACATG
111661 CATACATATATTTACATACATATATCAGAAAACCAAATAAAATATATACAAATAAAATATCGGTA
66 CATACATATATTTACATACATATATCAGAAAACCAAATAAAATATATACAAATAAAATATCGGTA
*
111726 ATACAGATATATCGAGGCAGTAGCAAAAATAAGTGTCACCAATTATAACAAAAA
131 ATACAGATATATCGAGGCAGTAGCAAAAATAAGTGTCACCAAATATAACAAAAA
* *
111780 TTCATATGATAAATATATATATAATACATACATACATACATACATACATACATACATACATGCAT
1 TTCATACGATAAATATATATAT-ATACATACATACATACATACATACATACATACATACATACAT
*
111845 AGACATGCATATA-TTACATACATATATCAGAAAACCAAATAAAATATATACAGAATAAAATATC
65 -G-CATACATATATTTACATACATATATCAGAAAACCAAATAAAATATATACA-AATAAAATATC
111909 GGTAATACAGATATATCGAGGCAGTAGCAAAAATAAGTGTCACCAAATATAACAAAAA
127 GGTAATACAGATATATCGAGGCAGTAGCAAAAATAAGTGTCACCAAATATAACAAAAA
111967 AGGCATATAA
Statistics
Matches: 175, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
184 21 0.12
185 37 0.21
186 40 0.23
187 77 0.44
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (184 bp):
TTCATACGATAAATATATATATATACATACATACATACATACATACATACATACATACATACATG
CATACATATATTTACATACATATATCAGAAAACCAAATAAAATATATACAAATAAAATATCGGTA
ATACAGATATATCGAGGCAGTAGCAAAAATAAGTGTCACCAAATATAACAAAAA
Found at i:117392 original size:23 final size:23
Alignment explanation
Indices: 117361--117431 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 23
117351 CACTGAAGTG
*
117361 CCACGTATAAATGTCCCGAATGA
1 CCACGTATAAATGTCCCGAAGGA
* *
117384 CCACATATATATGTCCCGAAGGA
1 CCACGTATAAATGTCCCGAAGGA
* * *
117407 CCGCGTAGAAATGTCCCAAAGGA
1 CCACGTATAAATGTCCCGAAGGA
117430 CC
1 CC
117432 GTGTAGAACC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (23 bp):
CCACGTATAAATGTCCCGAAGGA
Found at i:117432 original size:23 final size:23
Alignment explanation
Indices: 117394--117439 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
117384 CCACATATAT
*
117394 ATGTCCCGAAGGACCGCGTAGAA
1 ATGTCCCAAAGGACCGCGTAGAA
*
117417 ATGTCCCAAAGGACCGTGTAGAA
1 ATGTCCCAAAGGACCGCGTAGAA
117440 CCCTCGACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.28, T:0.15
Consensus pattern (23 bp):
ATGTCCCAAAGGACCGCGTAGAA
Found at i:120786 original size:8 final size:7
Alignment explanation
Indices: 120738--120792 Score: 59
Period size: 6 Copynumber: 8.6 Consensus size: 7
120728 GTACGATAAA
120738 CATATAT
1 CATATAT
120745 -ATATAT
1 CATATAT
120751 -ATATAT
1 CATATAT
120757 -ATATAT
1 CATATAT
120763 -ATATAT
1 CATATAT
120769 -ATATAT
1 CATATAT
120775 -ATATATT
1 CATATA-T
120782 CATATAT
1 CATATAT
120789 CATA
1 CATA
120793 AAACTGTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
6 35 0.76
7 6 0.13
8 5 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (7 bp):
CATATAT
Found at i:120788 original size:2 final size:2
Alignment explanation
Indices: 120739--120780 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
120729 TACGATAAAC
120739 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
120781 TCATATATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:122515 original size:18 final size:20
Alignment explanation
Indices: 122475--122523 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
122465 TTTATTATAT
122475 GAGAGAAAAGGTTGAAAATA
1 GAGAGAAAAGGTTGAAAATA
*
122495 GAGAGAAAAGGTTGAAAAGA
1 GAGAGAAAAGGTTGAAAATA
122515 GAGAGAAAA
1 GAGAGAAAA
122524 AGAGGGTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (20 bp):
GAGAGAAAAGGTTGAAAATA
Found at i:122991 original size:43 final size:41
Alignment explanation
Indices: 122924--123018 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 41
122914 ATTTATTCTA
* *
122924 TAAATAAA-AATATAATTAATTGAAATAATGAGTAGAACCT
1 TAAATAAATAATATAATTAATTGAAATAATGAATAGAACAT
* *
122964 TAAATAAATAATAATAATTTAATTGAAATAGTGAATATAACAT
1 TAAATAAATAAT-ATAA-TTAATTGAAATAATGAATAGAACAT
*
123007 TAAATAAGTAAT
1 TAAATAAATAAT
123019 GAGTTTAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
40 8 0.17
41 3 0.06
42 4 0.09
43 32 0.68
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (41 bp):
TAAATAAATAATATAATTAATTGAAATAATGAATAGAACAT
Found at i:123673 original size:19 final size:18
Alignment explanation
Indices: 123637--123679 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
123627 TAACAAATAG
*
123637 AATAATTTAACAAAATTT
1 AATAATTGAACAAAATTT
* *
123655 CAATAATTGAATAATATTT
1 -AATAATTGAACAAAATTT
123674 AATAAT
1 AATAAT
123680 ATTTTAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (18 bp):
AATAATTGAACAAAATTT
Found at i:124249 original size:79 final size:78
Alignment explanation
Indices: 124136--124343 Score: 321
Period size: 79 Copynumber: 2.7 Consensus size: 78
124126 AAATAAATAA
*
124136 TATTTAAATAAAAA-ATACGATTTAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAAT
1 TATTTAAATAAAAAGATA-GATTAAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAAT
124200 TTAAATCAAACTAT
65 TTAAATCAAACTAT
* * *
124214 TGA-TTAAATAAAAAGATGGGGTTAAAGTAAAAGTAGTAAATAGAATTTGAATAAATACTAGTAA
1 T-ATTTAAATAAAAAGAT-AGATTAAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAA
124278 TTTAAATCAAACTAT
64 TTTAAATCAAACTAT
* *
124293 TATTTAAATAGAAAGATAGATTTAAGTAAAAGTAGTAAATAGAATTTAAAT
1 TATTTAAATAAAAAGATAGATTAAAGTAAAAGTAGTAAATAGAATTTAAAT
124344 CAAACAATGC
Statistics
Matches: 117, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
78 43 0.37
79 74 0.63
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.32
Consensus pattern (78 bp):
TATTTAAATAAAAAGATAGATTAAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAATT
TAAATCAAACTAT
Found at i:127842 original size:31 final size:31
Alignment explanation
Indices: 127778--127847 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
127768 AAACTGCGCA
* **
127778 TTTAGTACCTAAGCTATCAGTTATGATTTGT
1 TTTAGTACCTAAACTATCAGTTATGATCCGT
* * *
127809 TTTAGTATCTAAACTATCAGTTTTGGTCCGT
1 TTTAGTACCTAAACTATCAGTTATGATCCGT
127840 TTTAGTAC
1 TTTAGTAC
127848 TTATTAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (31 bp):
TTTAGTACCTAAACTATCAGTTATGATCCGT
Found at i:128765 original size:13 final size:13
Alignment explanation
Indices: 128747--128792 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
128737 ATTATAAAAC
128747 ATATTTTAATTAT
1 ATATTTTAATTAT
128760 ATA-TTTAATTTAT
1 ATATTTTAA-TTAT
*
128773 AAATTTT-ATTAT
1 ATATTTTAATTAT
128785 A-ATTTTAA
1 ATATTTTAA
128793 GAGAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 10 0.34
14 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTTAATTAT
Found at i:129048 original size:20 final size:20
Alignment explanation
Indices: 128999--129051 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
128989 GATTTTCCAG
* *
128999 AATCGCAACACGAATATGAA
1 AATCGCAACGCGAACATGAA
129019 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAACATGA-A
129039 AATCGCAACGCGA
1 AATCGCAACGCGA
129052 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATGAA
Found at i:129087 original size:41 final size:41
Alignment explanation
Indices: 129038--129256 Score: 227
Period size: 41 Copynumber: 5.4 Consensus size: 41
129028 GCGAACATAT
* * * *
129038 AAATCGCAACGCGATTCTG-ACTATCGCAACGAGTATCCGTA
1 AAATCGCAACGCGATTCCGTA-AATCGCAACGAGAATACGTA
*
129079 AAATCGCAACGCGTATT-CGTAAATCGCAACGACAATACGTA
1 AAATCGCAACGCG-ATTCCGTAAATCGCAACGAGAATACGTA
* *
129120 AAATCGCAACGCG-TATCCGTAAATCGCAAC-AGGTATCCGT-
1 AAATCGCAACGCGAT-TCCGTAAATCGCAACGA-GAATACGTA
* * * *
129160 AAATCGCAATGCGAATACATAAATCGCAACGAGAATACGT-
1 AAATCGCAACGCGATTCCGTAAATCGCAACGAGAATACGTA
* *
129200 AAATCGCAATGCG-TATCCGTAAATCGCAACGACAATACGTA
1 AAATCGCAACGCGAT-TCCGTAAATCGCAACGAGAATACGTA
129241 AAATCGCAACGCGATT
1 AAATCGCAACGCGATT
129257 TTTAAAGCGG
Statistics
Matches: 149, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
39 1 0.01
40 68 0.46
41 75 0.50
42 5 0.03
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (41 bp):
AAATCGCAACGCGATTCCGTAAATCGCAACGAGAATACGTA
Found at i:129104 original size:20 final size:20
Alignment explanation
Indices: 129060--129253 Score: 187
Period size: 20 Copynumber: 9.6 Consensus size: 20
129050 GATTCTGACT
* *
129060 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATACGT-AA
*
129081 ATCGCAACGCGTATTCGTAA
1 ATCGCAACGCGTATACGTAA
*
129101 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATACGT-AA
*
129122 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
*
129142 ATCGCAACAG-GTATCCGTAA
1 ATCGCAAC-GCGTATACGTAA
* * *
129162 ATCGCAATGCGAATACATAA
1 ATCGCAACGCGTATACGTAA
* *
129182 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATACGTAA
* *
129202 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
*
129222 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATACGT-AA
129243 ATCGCAACGCG
1 ATCGCAACGCG
129254 ATTTTTAAAG
Statistics
Matches: 145, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.01
20 98 0.68
21 46 0.32
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATACGTAA
Found at i:129183 original size:40 final size:41
Alignment explanation
Indices: 129060--129253 Score: 250
Period size: 40 Copynumber: 4.8 Consensus size: 41
129050 GATTCTGACT
* * *
129060 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATTCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
129101 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * * * * *
129142 ATCGCAAC-AGGTATCCGT-AAATCGCAATGCGAATACATAA
1 ATCGCAACGA-GAATACGTAAAATCGCAACGCGTATCCGTAA
*
129182 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
129222 ATCGCAACGACAATACGTAAAATCGCAACGCG
1 ATCGCAACGAGAATACGTAAAATCGCAACGCG
129254 ATTTTTAAAG
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
40 69 0.52
41 63 0.48
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:129837 original size:20 final size:19
Alignment explanation
Indices: 129812--129883 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
129802 TTCTAAACTT
129812 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
129832 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
129852 ACTACCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
129873 AAAATCGCAAC
1 AAAATCGCAAC
129884 GAGAGGAATC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.51, C:0.21, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:129873 original size:21 final size:21
Alignment explanation
Indices: 129827--129888 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
129817 CGCAACATGA
*
129827 AAATGAAAATCGCAAC-ACGA-
1 AAATGAAAACCGCAACGA-GAG
**
129847 AAATGACTACCGCAACGAGAG
1 AAATGAAAACCGCAACGAGAG
*
129868 AAATGAAAATCGCAACGAGAG
1 AAATGAAAACCGCAACGAGAG
129889 GAATCGCAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.50, C:0.19, G:0.21, T:0.10
Consensus pattern (21 bp):
AAATGAAAACCGCAACGAGAG
Found at i:129933 original size:19 final size:19
Alignment explanation
Indices: 129911--130037 Score: 85
Period size: 20 Copynumber: 7.1 Consensus size: 19
129901 GAAACCAAAA
*
129911 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
129930 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
129944 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
129963 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
129977 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
129996 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
130016 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
130036 TC
1 TC
130038 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.24
16 4 0.05
17 5 0.06
19 23 0.27
20 32 0.38
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:129958 original size:33 final size:33
Alignment explanation
Indices: 129916--130037 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
129906 CAAAATCGCA
129916 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
129949 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
129982 TTGCGATAGTCATTTCCGCGTTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGC----G--ATTCTCTCG
130022 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
130038 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
33 44 0.58
34 8 0.11
38 1 0.01
39 1 0.01
40 22 0.29
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:130035 original size:20 final size:20
Alignment explanation
Indices: 129973--130028 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
129963 TCGCGTTGCG
129973 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
129993 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
130013 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
130029 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:131864 original size:94 final size:94
Alignment explanation
Indices: 131703--132082 Score: 665
Period size: 94 Copynumber: 4.1 Consensus size: 94
131693 TAGATTGCTT
*
131703 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
131768 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
131797 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
131862 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
131891 AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
131956 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
131985 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
132050 ATTTGTATTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
132078 AGTAA
1 AGTAA
132083 TGCAATCCAT
Statistics
Matches: 276, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 250 0.91
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:132186 original size:19 final size:17
Alignment explanation
Indices: 132170--132252 Score: 82
Period size: 19 Copynumber: 4.8 Consensus size: 17
132160 AAAAATGACT
132170 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
*
132187 ATCGCAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
132201 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
**
132220 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAA--TGA
132239 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
132253 CTATAATCGC
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 9 0.16
15 4 0.07
16 4 0.07
17 8 0.15
19 30 0.55
ACGTcount: A:0.45, C:0.25, G:0.22, T:0.08
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:132260 original size:19 final size:19
Alignment explanation
Indices: 132200--132262 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
132190 GCAACGAGAG
132200 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
*
132219 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACTAA
*
132238 AATCGCAACGCGAAACTAT
1 AATCGCAACGCGAAACTAA
132257 AATCGC
1 AATCGC
132263 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.44, C:0.27, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:132281 original size:19 final size:19
Alignment explanation
Indices: 132259--132365 Score: 89
Period size: 19 Copynumber: 5.8 Consensus size: 19
132249 GAAACTATAA
132259 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
132278 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
132292 TCTCGTTGCGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
*
132311 TCGCGTTGCGATTTACATT
1 TCGCGTTGCGATTTTCATT
* **
132330 TCGCCTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
132351 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
132366 AAGTTCCAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
14 9 0.13
16 3 0.04
17 3 0.04
19 39 0.58
21 13 0.19
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:132839 original size:21 final size:21
Alignment explanation
Indices: 132815--132884 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
132805 CTATCATTCC
132815 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * ** *
132836 TCAAGAGGCCACTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
132857 TGAAGAAGT-CCCTCCCACCAT
1 TCAAG-AGTCCCCTCCCACCGT
132878 TCAAGAG
1 TCAAGAG
132885 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:132842 original size:42 final size:42
Alignment explanation
Indices: 132766--132884 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
132756 GACTCACCTG
* * * * * *
132766 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
132808 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
132850 TCA-TCGTTGAAGAAGT-CCCTCCCACCATTCAAGAG
1 TCATTC-CTCAAG-AGTCCCCTCCCACCGTTCAAGAG
132885 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 60 0.92
43 3 0.05
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:134253 original size:14 final size:14
Alignment explanation
Indices: 134234--134267 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
134224 TGTTTAATTA
134234 ATTTGTAAAAGATG
1 ATTTGTAAAAGATG
*
134248 ATTTGTAAAAGTTG
1 ATTTGTAAAAGATG
134262 ATTTGT
1 ATTTGT
134268 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGATG
Found at i:134390 original size:19 final size:19
Alignment explanation
Indices: 134366--134434 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
134356 TTGAAGGCAA
*
134366 AAATGAATATCGCAATGCG
1 AAATGAAAATCGCAATGCG
134385 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAATGCG
* *
134402 --A-GAGAATCGCAATACG
1 AAATGAAAATCGCAATGCG
134418 AAATGAAAATCGCAATG
1 AAATGAAAATCGCAATG
134435 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 25 0.61
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (19 bp):
AAATGAAAATCGCAATGCG
Found at i:134420 original size:33 final size:33
Alignment explanation
Indices: 134374--134446 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
134364 AAAAATGAAT
* * *
134374 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGACAAA
*
134407 ATCGCAATACGAAATGAAAATCGCAATGACAAA
1 ATCGCAATACGAAATGAAAATCGCAACGACAAA
134440 ATCGCAA
1 ATCGCAA
134447 CGTGAAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGACAAA
Found at i:134461 original size:19 final size:19
Alignment explanation
Indices: 134437--134482 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
134427 TCGCAATGAC
*
134437 AAAATCGCAACGTGAAACT
1 AAAATCGCAACGCGAAACT
134456 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
134475 AAATTCGC
1 AAAATCGC
134483 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:134524 original size:33 final size:34
Alignment explanation
Indices: 134482--134648 Score: 178
Period size: 33 Copynumber: 4.8 Consensus size: 34
134472 ACTAAATTCG
* *
134482 CGTTGCGATTTTCATTTTGCTTTGCG-TTTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTCTCT
*
134515 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCT
1 CGTTGCGATTTTCATTTCGCATTGCGAT--T--TCTCT
* * *
134553 GCGTTGCGATATTCATATTCGCGTTGCGATTT-TCA
1 -CGTTGCGATTTTCAT-TTCGCATTGCGATTTCTCT
* *
134588 CGCTGCGATTTTCATTTAGCATTGCGA-TTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTCTCT
*
134621 CGTTGCGATTTTCATTTCGTATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
134649 AGACATTAAG
Statistics
Matches: 111, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
32 2 0.02
33 60 0.54
34 14 0.13
35 2 0.02
36 2 0.02
38 5 0.05
39 14 0.13
40 12 0.11
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTCTCT
Found at i:134561 original size:20 final size:19
Alignment explanation
Indices: 134478--134587 Score: 95
Period size: 20 Copynumber: 5.9 Consensus size: 19
134468 CGAAACTAAA
*
134478 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
* *
134497 TTTGCTTTGCG-T-TTC--
1 TTCGCGTTGCGATATTCAT
* *
134512 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
* *
134530 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATATTCAT
134549 TTCTGCGTTGCGATATTCAT
1 TTC-GCGTTGCGATATTCAT
*
134569 ATTCGCGTTGCGATTTTCA
1 -TTCGCGTTGCGATATTCA
134588 CGCTGCGATT
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
14 7 0.10
15 1 0.01
16 3 0.04
17 3 0.04
18 1 0.01
19 26 0.36
20 28 0.39
21 3 0.04
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATATTCAT
Found at i:134600 original size:73 final size:72
Alignment explanation
Indices: 134481--134615 Score: 191
Period size: 73 Copynumber: 1.9 Consensus size: 72
134471 AACTAAATTC
* * * * * *
134481 GCGTTGCGATTTTCATTTTGCTTTGCGTTTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGT
1 GCGTTGCGATATTCATTTCGCGTTGCGTTTCTCACGCTGCGATTTTCATTTAGCATTGCGATAGT
134546 CATTTCT
66 CATTTCT
134553 GCGTTGCGATATTCATATTCGCGTTGCGATTT-TCACGCTGCGATTTTCATTTAGCATTGCGAT
1 GCGTTGCGATATTCAT-TTCGCGTTGCG-TTTCTCACGCTGCGATTTTCATTTAGCATTGCGAT
134616 TCTCTCGTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
72 15 0.27
73 37 0.67
74 3 0.05
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (72 bp):
GCGTTGCGATATTCATTTCGCGTTGCGTTTCTCACGCTGCGATTTTCATTTAGCATTGCGATAGT
CATTTCT
Found at i:134615 original size:19 final size:19
Alignment explanation
Indices: 134478--134648 Score: 111
Period size: 19 Copynumber: 9.7 Consensus size: 19
134468 CGAAACTAAA
*
134478 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
134497 TTTGCTTTGCG--TTTC-T
1 TTCGCATTGCGATTTTCAT
*
134513 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
134530 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
* *
134549 TTCTGCGTTGCGATATTCAT
1 TTC-GCATTGCGATTTTCAT
*
134569 ATTCGCGTTGCGATTTTCA-
1 -TTCGCATTGCGATTTTCAT
134588 --CGC--TGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
134603 TTAGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
134619 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
134636 TTCGTATTGCGAT
1 TTCGCATTGCGAT
134649 AGACATTAAG
Statistics
Matches: 121, Mismatches: 14, Indels: 34
0.72 0.08 0.20
Matches are distributed among these distances:
14 22 0.18
16 16 0.13
17 17 0.14
19 35 0.29
20 28 0.23
21 3 0.02
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:137218 original size:24 final size:24
Alignment explanation
Indices: 137151--137206 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
137141 CTGAAAAATC
137151 ATCAAATTCCGAGTATTGACCAAG
1 ATCAAATTCCGAGTATTGACCAAG
* *
137175 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAATTCCGAGTATTGACCAAG
137199 ATCAAATT
1 ATCAAATT
137207 TCGAATACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAATTCCGAGTATTGACCAAG
Found at i:138090 original size:20 final size:20
Alignment explanation
Indices: 138067--138108 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
138057 GAATCTCGTT
138067 GCGATTTAC-TAAATCGCAAC
1 GCGA-TTACGTAAATCGCAAC
138087 GCGATTACGTAAATCGCAAC
1 GCGATTACGTAAATCGCAAC
138107 GC
1 GC
138109 AAATTGCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
GCGATTACGTAAATCGCAAC
Found at i:138136 original size:20 final size:20
Alignment explanation
Indices: 138112--138221 Score: 114
Period size: 20 Copynumber: 5.4 Consensus size: 20
138102 GCAACGCAAA
* *
138112 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATACGCG
*
138132 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATACGCG
* *
138152 TTTCGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGTATACG-CG
*
138173 TTGCGATTTACGAATACGCG
1 TTGCGATTTACGTATACGCG
* *
138193 TTGCGATTTTACGGATACTCG
1 TTGCGA-TTTACGTATACGCG
138214 TTGCGATT
1 TTGCGATT
138222 CTGGAAAATC
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
20 41 0.55
21 34 0.45
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATACGCG
Found at i:138177 original size:41 final size:41
Alignment explanation
Indices: 138112--138221 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
138102 GCAACGCAAA
* *
138112 TTGCGA-TTTACGTATTCG-CATTGCGATTTACGGATACGCG
1 TTGCGATTTTACGTATT-GTCGTTGCGATTTACGAATACGCG
*
138152 TTTCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCG
1 TTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCG
* **
138193 TTGCGATTTTACGGATACTCGTTGCGATT
1 TTGCGATTTTACGTATTGTCGTTGCGATT
138222 CTGGAAAATC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 6 0.10
41 55 0.90
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (41 bp):
TTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCG
Found at i:138320 original size:20 final size:19
Alignment explanation
Indices: 138271--138324 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
138261 ATTCTTCATA
138271 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
138290 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
138311 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
138325 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:138679 original size:2 final size:2
Alignment explanation
Indices: 138672--138698 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
138662 GTGGCCACCG
138672 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
138699 GGGTAAACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:139190 original size:2 final size:2
Alignment explanation
Indices: 139183--139219 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
139173 AACAAATTTA
139183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
139220 CTTTAGATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:143962 original size:3 final size:3
Alignment explanation
Indices: 143954--143981 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
143944 ATTAAAATCC
143954 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
143982 CTCTATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:144777 original size:18 final size:20
Alignment explanation
Indices: 144737--144785 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
144727 TTTATTATAT
144737 GAGAGAAAAGGTTGAAAATA
1 GAGAGAAAAGGTTGAAAATA
*
144757 GAGAGAAAAGGTTGAAAAGA
1 GAGAGAAAAGGTTGAAAATA
144777 GAGAGAAAA
1 GAGAGAAAA
144786 AGAGGGTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (20 bp):
GAGAGAAAAGGTTGAAAATA
Found at i:144945 original size:30 final size:30
Alignment explanation
Indices: 144911--144967 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
144901 TTTAGATCTG
* *
144911 AATTTAATCAAAATTTCATTTTGGTCCCAA
1 AATTTAATCAAAATTTCAATTTAGTCCCAA
*
144941 AATTTAATTAAAATTTCAATTTAGTCC
1 AATTTAATCAAAATTTCAATTTAGTCC
144968 TCGAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (30 bp):
AATTTAATCAAAATTTCAATTTAGTCCCAA
Found at i:145232 original size:40 final size:40
Alignment explanation
Indices: 145187--145278 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
145177 ATTTATTCTA
* *
145187 TAAATAAA-AATATAATTAATTGAAATAATGAGTAGAACCT
1 TAAATAAATAATA-AATTAATTGAAATAATGAATAGAACAT
* * *
145227 TAAATAAATAATAATTTAATTGAAATAGTGAATATAACAT
1 TAAATAAATAATAAATTAATTGAAATAATGAATAGAACAT
*
145267 TAAATAAGTAAT
1 TAAATAAATAAT
145279 GAGTTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 41 0.91
41 4 0.09
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (40 bp):
TAAATAAATAATAAATTAATTGAAATAATGAATAGAACAT
Found at i:145934 original size:19 final size:18
Alignment explanation
Indices: 145898--145940 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
145888 TAACAAATAG
*
145898 AATAATTTAACAAAATTT
1 AATAATTGAACAAAATTT
* *
145916 CAATAATTGAATAATATTT
1 -AATAATTGAACAAAATTT
145935 AATAAT
1 AATAAT
145941 ATTTTAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (18 bp):
AATAATTGAACAAAATTT
Found at i:146482 original size:78 final size:78
Alignment explanation
Indices: 146397--146603 Score: 328
Period size: 77 Copynumber: 2.7 Consensus size: 78
146387 AAATAAATAA
* *
146397 TATTTAAATAAAAAATACGATTTAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAATT
1 TATTTAAATAAAAGATAGGATTTAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAATT
146462 TAAATCAAACTAT
66 TAAATCAAACTAT
* * * *
146475 TGA-TTAAATAAAAGATGGGGTTAAAGT-AAAGTAGTAAATAGAATTTGAATAAATACTAGTAAT
1 T-ATTTAAATAAAAGATAGGATTTAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAAT
146538 TTAAATCAAACTAT
65 TTAAATCAAACTAT
146552 TATTTAAATAGAAAGATAGGATTTAAGTAAAAGTAGTAAATAGAATTTAAAT
1 TATTTAAATA-AAAGATAGGATTTAAGTAAAAGTAGTAAATAGAATTTAAAT
146604 CAAACAATGC
Statistics
Matches: 115, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
76 1 0.01
77 57 0.50
78 34 0.30
79 23 0.20
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (78 bp):
TATTTAAATAAAAGATAGGATTTAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAATT
TAAATCAAACTAT
Found at i:151015 original size:13 final size:13
Alignment explanation
Indices: 150997--151042 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
150987 ATTATAAAAC
150997 ATATTTTAATTAT
1 ATATTTTAATTAT
151010 ATA-TTTAATTTAT
1 ATATTTTAA-TTAT
*
151023 AAATTTT-ATTAT
1 ATATTTTAATTAT
151035 A-ATTTTAA
1 ATATTTTAA
151043 GAGAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 10 0.34
14 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTTAATTAT
Found at i:151274 original size:20 final size:20
Alignment explanation
Indices: 151249--151423 Score: 122
Period size: 20 Copynumber: 8.7 Consensus size: 20
151239 GATTTTCCAG
*
151249 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
151269 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
151289 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
151309 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
151330 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
151350 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
151370 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
151390 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
151411 AATCGCAACGCGA
1 AATCGCAACGCGA
151424 TTTTTAAAGC
Statistics
Matches: 123, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.02
20 87 0.71
21 34 0.28
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:151336 original size:21 final size:20
Alignment explanation
Indices: 151310--151420 Score: 132
Period size: 20 Copynumber: 5.5 Consensus size: 20
151300 GATTCTGACT
151310 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
151331 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
151351 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* *
151371 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
151391 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
151412 ATCGCAACG
1 ATCGCAACG
151421 CGATTTTTAA
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 48 0.63
21 28 0.37
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:151353 original size:81 final size:81
Alignment explanation
Indices: 151249--151423 Score: 192
Period size: 81 Copynumber: 2.2 Consensus size: 81
151239 GATTTTCCAG
* * * * *
151249 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGT-A-AAT
** *
151312 CGCAACGAGTATCCGTAA
64 CGCAACGACAATACGTAA
* * * * * *
151330 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATCG
151395 CAACGACAATACGTAA
66 CAACGACAATACGTAA
151411 AATCGCAACGCGA
1 AATCGCAACGCGA
151424 TTTTTAAAGC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
81 72 0.94
82 4 0.05
83 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (81 bp):
AATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATCG
CAACGACAATACGTAA
Found at i:151384 original size:40 final size:41
Alignment explanation
Indices: 151310--151422 Score: 183
Period size: 40 Copynumber: 2.8 Consensus size: 41
151300 GATTCTGACT
* *
151310 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
151351 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
151391 ATCGCAACGACAATACGTAAAATCGCAACGCG
1 ATCGCAACGAGAATACGTAAAATCGCAACGCG
151423 ATTTTTAAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 38 0.58
41 28 0.42
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:152005 original size:20 final size:19
Alignment explanation
Indices: 151980--152051 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
151970 TTCTAAACTT
151980 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
152000 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
152020 ACTACCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
152041 AAAATCGCAAC
1 AAAATCGCAAC
152052 GCGAAACCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.51, C:0.21, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:152086 original size:19 final size:19
Alignment explanation
Indices: 152064--152195 Score: 121
Period size: 19 Copynumber: 7.1 Consensus size: 19
152054 GAAACCAAAA
*
152064 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
152083 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
152097 TCTCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
152116 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
152135 TTGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
152154 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
152174 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
152194 TC
1 TC
152196 AACCAAAAGA
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
14 9 0.10
16 2 0.02
17 3 0.03
19 45 0.49
20 32 0.35
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:152162 original size:20 final size:19
Alignment explanation
Indices: 152113--152186 Score: 94
Period size: 20 Copynumber: 3.8 Consensus size: 19
152103 TGCGATTTTA
**
152113 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATAGTC
*
152132 ATTTTGCGTTGCGATAGTC
1 ATTTCGCGTTGCGATAGTC
152151 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGATAGTC
*
152171 ATTCTCTCGTTGCGAT
1 ATT-TCGCGTTGCGAT
152187 TTTCATTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 20 0.42
20 27 0.56
21 1 0.02
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.42
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGTC
Found at i:154052 original size:94 final size:94
Alignment explanation
Indices: 153891--154270 Score: 656
Period size: 94 Copynumber: 4.1 Consensus size: 94
153881 TAGATTGCTT
*
153891 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
153956 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
153985 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
154050 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
154079 AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
154144 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
154173 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAACTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
154238 ATTTGTATTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
154266 AGTAA
1 AGTAA
154271 TGCAATCCAT
Statistics
Matches: 275, Mismatches: 10, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 249 0.91
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:154383 original size:17 final size:17
Alignment explanation
Indices: 154358--154468 Score: 71
Period size: 14 Copynumber: 6.8 Consensus size: 17
154348 AAAAATGACT
154358 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
* *
154375 ATCG-AA-ACGAGA-GA
1 ATCGCAACGCGAAATGA
154389 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
* *
154408 ATCTCAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
154422 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
154441 ATCGCAA--CGACAA--A
1 ATCGCAACGCGA-AATGA
154455 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
154469 CCAAAATCGC
Statistics
Matches: 73, Mismatches: 8, Indels: 28
0.67 0.07 0.26
Matches are distributed among these distances:
14 21 0.29
15 8 0.11
16 14 0.19
17 13 0.18
18 2 0.03
19 15 0.21
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.10
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:154415 original size:19 final size:19
Alignment explanation
Indices: 154388--154487 Score: 76
Period size: 19 Copynumber: 5.8 Consensus size: 19
154378 GAAACGAGAG
154388 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
154407 AATCTCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
154421 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
154440 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAATGAA
**
154454 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATGAA
*
154473 AATCGCAACGTGAAA
1 AATCGCAACGCGAAA
154488 CTATAATCGC
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 19 0.29
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 34 0.52
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Done.