Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009268.1 Hibiscus syriacus cultivar Beakdansim tig00112926_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: 304330
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:1046 original size:15 final size:15
Alignment explanation
Indices: 1026--1055 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1016 TACGGATAAG
*
1026 TAATTAAATAGTTAA
1 TAATTAAATAATTAA
1041 TAATTAAATAATTAA
1 TAATTAAATAATTAA
1056 ATATATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TAATTAAATAATTAA
Found at i:1050 original size:8 final size:8
Alignment explanation
Indices: 1026--1058 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1016 TACGGATAAG
1026 TAATTAAA
1 TAATTAAA
*
1034 TAGTT-AA
1 TAATTAAA
1041 TAATTAAA
1 TAATTAAA
1049 TAATTAAA
1 TAATTAAA
1057 TA
1 TA
1059 TATAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
TAATTAAA
Found at i:8235 original size:27 final size:27
Alignment explanation
Indices: 8205--8260 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
8195 GAGAATGATC
8205 GAAATGGCGATCAAAAGCGGGAAGCTT
1 GAAATGGCGATCAAAAGCGGGAAGCTT
8232 GAAATGGCGATCAAAAGCGGGAAGCTT
1 GAAATGGCGATCAAAAGCGGGAAGCTT
8259 GA
1 GA
8261 GGGAGGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.34, T:0.14
Consensus pattern (27 bp):
GAAATGGCGATCAAAAGCGGGAAGCTT
Found at i:14286 original size:23 final size:22
Alignment explanation
Indices: 14260--14317 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 22
14250 AAAATGAGTG
14260 AAAATGAAAAAATAAAAAAATAAA
1 AAAATGAAAAAAT--AAAAATAAA
*
14284 AAAAT-AAAAAATAAAAATGAA
1 AAAATGAAAAAATAAAAATAAA
14305 AAAATGGAAAAAA
1 AAAAT-GAAAAAA
14318 GAAGGGTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 13 0.42
23 13 0.42
24 5 0.16
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAATGAAAAAATAAAAATAAA
Found at i:14307 original size:8 final size:8
Alignment explanation
Indices: 14260--14317 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
14250 AAAATGAGTG
14260 AAAATGAA
1 AAAATGAA
*
14268 AAAATAAA
1 AAAATGAA
*
14276 AAAATAAA
1 AAAATGAA
14284 AAAAT-AA
1 AAAATGAA
14291 AAAAT--A
1 AAAATGAA
14297 AAAATGAA
1 AAAATGAA
14305 AAAATGGAA
1 AAAAT-GAA
14314 AAAA
1 AAAA
14318 GAAGGGTTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
6 6 0.13
7 7 0.15
8 26 0.57
9 7 0.15
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:14307 original size:15 final size:14
Alignment explanation
Indices: 14267--14309 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
14257 GTGAAAATGA
14267 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
*
14281 AAAAAAATAAAAAAT
1 AAAAATA-AAAAAAT
*
14296 AAAAATGAAAAAAT
1 AAAAATAAAAAAAT
14310 GGAAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:15378 original size:55 final size:55
Alignment explanation
Indices: 15230--15470 Score: 326
Period size: 55 Copynumber: 4.4 Consensus size: 55
15220 CAGATTCCCA
*
15230 ACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACAATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * *
15285 GCAATTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGATATAGGGGGCAGAC
1 ACAATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
15338 ACAATCGTTGAAGATCGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 ACAATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
15393 GCGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACAATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
15448 ACGATTGTTGAAGA-TATTCGAGT
1 ACAATTGTTGAAGATTGTTCGAGT
15471 TCTATTCTCC
Statistics
Matches: 163, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
53 44 0.27
54 10 0.06
55 109 0.67
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (55 bp):
ACAATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:15495 original size:54 final size:54
Alignment explanation
Indices: 15237--15702 Score: 312
Period size: 54 Copynumber: 8.6 Consensus size: 54
15227 CCAACAATTA
* * * * *
15237 TTGAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTG
1 TTGAAGA-TATTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAGACACGATTG
* * * * * * * *
15292 ATGAAGAT-TGT-G-GGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATCG
1 TTGAAGATAT-TCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCAGACACGATTG
* * * * *
15345 TTGAAGATCGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTG
1 TTGAAGAT-ATTCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCAGACACGATTG
* * *
15400 TTGAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGA-TATTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCAGACACGATTG
* * * *
15455 TTGAAGATATTCGAGTTCTATTCTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTG
1 TTGAAGATATTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCAGACACGATTG
** * *
15509 AAGAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGC-GA-ACCTGTTTG
1 TTGAAGATATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACA-C-GATTG
** *
15563 AAGAAGATATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGC-GA-ACCAGTTAG
1 TTGAAGATATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACACGA-TT-G
** * * * * *
15617 CAGAAGAT-TCTTGAGTTCTATACTCCCTGAA-ACAATAGGGGGCGGACTCG-TTAG
1 TTGAAGATAT-TCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCAGACACGATT-G
**
15671 CAGAAGATTATTCGAGTTCTATACTCCCTGAA
1 TTGAAGA-TATTCGAGTTCTATACTCCCTGAA
15703 ACAATAGGGA
Statistics
Matches: 356, Mismatches: 33, Indels: 44
0.82 0.08 0.10
Matches are distributed among these distances:
52 1 0.00
53 50 0.14
54 175 0.49
55 126 0.35
56 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (54 bp):
TTGAAGATATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAGACACGATTG
Found at i:15524 original size:163 final size:163
Alignment explanation
Indices: 15237--15548 Score: 364
Period size: 163 Copynumber: 1.9 Consensus size: 163
15227 CCAACAATTA
*
15237 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGATGAAGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTG
* * * * * ** *
15302 TGGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACAATCGTTGAAGATCGTTCGAG-TCTTA
66 TGGGTCTTATACTCCCTGAAGAAAGAGGGAGCAAACACAATCGAAGAAGATCATTCGAGTTC-TA
* *
15366 TACTCTCTGAAGAAATAGGGGGCAGACGCGATTG
130 TACTCCCTGAAGAAAGAGGGGGCAGACGCGATTG
* *
15400 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATAT
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGAT-T
* * * ** *
15465 -TCGAGT-TCTATTCTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTGAAGAAGAT-ATTCGAGTT
65 GT-GGGTCT-TATACTCCCTGA-AGAAAGAGGGAGCAAACACAATCGAAGAAGATCATTCGAGTT
*
15526 CTATTCTCCCTGAAGAAAGAGGG
127 CTATACTCCCTGAAGAAAGAGGG
15549 AGCGAACCTG
Statistics
Matches: 124, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
163 88 0.71
164 36 0.29
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (163 bp):
TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACAATTGATGAAGATTG
TGGGTCTTATACTCCCTGAAGAAAGAGGGAGCAAACACAATCGAAGAAGATCATTCGAGTTCTAT
ACTCCCTGAAGAAAGAGGGGGCAGACGCGATTG
Found at i:15701 original size:55 final size:53
Alignment explanation
Indices: 15355--15774 Score: 324
Period size: 54 Copynumber: 7.7 Consensus size: 53
15345 TTGAAGATCG
* * ** *
15355 TTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCGATTGTTGAAGATTG
1 TTCGAGTTC-TATACTCCCTGAAGAAATAGGGAGCGA-AC-CG-TTGCAGAAGATTA
* **
15410 TTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGC-AGACACGATTGTTGAAGA-TA
1 TTCGAGTTCT-ATACTCCCTGAAGAAATAGGGAGCGA-AC-CG-TTGCAGAAGATTA
* * * *
15464 TTCGAGTTCTATTCTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTGAAGAAGA-TA
1 TTCGAGTTCTATACTCCCTGA-AGAAATAGGGAGCGAA-CCG-TTGCAGAAGATTA
* * *
15518 TTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCGAACCTGTTTGAAGAAGA-TA
1 TTCGAGTTCTATACTCCCTGAAGAAATAGGGAGCGAACC-G-TTGCAGAAGATTA
* *
15572 TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCAGTTAGCAGAAGATTC
1 TTCGAGTTCTATACTCCCTGAAGAAATAGGGAGCGAACC-GTT-GCAGAAGATTA
* *
15627 TT-GAGTTCTATACTCCCTGAA-ACAATAGGGGGCGGACTCGTTAGCAGAAGATTA
1 TTCGAGTTCTATACTCCCTGAAGA-AATAGGGAGCGAAC-CGTT-GCAGAAGATTA
** *
15681 TTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCGTCCCCAGAAGATTC
1 TTCGAGTTCTATACTCCCTGAAGA-AATAGGGAGCGAA-CCGT-TGCAGAAGATTA
* ** *
15736 TTCAAGTTCTATGTTCCCTGAA-ACGATAGGGAGCGAACC
1 TTCGAGTTCTATACTCCCTGAAGA-AATAGGGAGCGAACC
15775 CGATTTTGAA
Statistics
Matches: 324, Mismatches: 27, Indels: 29
0.85 0.07 0.08
Matches are distributed among these distances:
53 6 0.02
54 182 0.56
55 135 0.42
56 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (53 bp):
TTCGAGTTCTATACTCCCTGAAGAAATAGGGAGCGAACCGTTGCAGAAGATTA
Found at i:16071 original size:8 final size:8
Alignment explanation
Indices: 16055--16087 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
16045 TACGGATAAG
16055 TAATTAAA
1 TAATTAAA
*
16063 TAGTTAAA
1 TAATTAAA
16071 TAATTAAA
1 TAATTAAA
16079 TAA-TAAA
1 TAATTAAA
16086 TA
1 TA
16088 TATAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (8 bp):
TAATTAAA
Found at i:19675 original size:12 final size:12
Alignment explanation
Indices: 19649--19681 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19639 CGGCGCAAAT
19649 GGAGAGGAGGAA
1 GGAGAGGAGGAA
19661 GGAGATGGAGG-A
1 GGAGA-GGAGGAA
19673 GGAGAGGAG
1 GGAGAGGAG
19682 AGCGAAGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 11 0.55
13 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.03
Consensus pattern (12 bp):
GGAGAGGAGGAA
Found at i:20638 original size:23 final size:22
Alignment explanation
Indices: 20612--20666 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
20602 GAAAAATGTG
* *
20612 TCACAAAAGAAGAGAGGAACATA
1 TCACAAAAG-ACAGAGGAAAATA
20635 TCAC-AAAGACAGAGGAAAATA
1 TCACAAAAGACAGAGGAAAATA
20656 TCAC-AAAGACA
1 TCACAAAAGACA
20667 TAATTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 22 0.73
22 4 0.13
23 4 0.13
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.09
Consensus pattern (22 bp):
TCACAAAAGACAGAGGAAAATA
Found at i:20650 original size:21 final size:21
Alignment explanation
Indices: 20624--20666 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
20614 ACAAAAGAAG
*
20624 AGAGGAACATATCACAAAGAC
1 AGAGGAAAATATCACAAAGAC
20645 AGAGGAAAATATCACAAAGAC
1 AGAGGAAAATATCACAAAGAC
20666 A
1 A
20667 TAATTATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.16, G:0.19, T:0.09
Consensus pattern (21 bp):
AGAGGAAAATATCACAAAGAC
Found at i:24385 original size:24 final size:24
Alignment explanation
Indices: 24337--24402 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
24327 CAATCTTATA
* *
24337 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
24360 TGGCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
24384 TGGCA-TTACGGTGCAAATT
1 TGGCACTT-CGGTGCAAATT
24403 TATACGAGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
23 15 0.38
24 24 0.62
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:27816 original size:34 final size:30
Alignment explanation
Indices: 27778--27846 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
27768 TTGATATAAC
27778 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
*
27812 AATTT-ACAAAATGTTTTTTGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
27841 AATTTA
1 AATTTA
27847 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:27830 original size:31 final size:29
Alignment explanation
Indices: 27787--27846 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 29
27777 CAATTTAAGG
27787 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTT-GACTT-AATTGAATTTA
*
27818 CAAAATGTTTTTTGACTTAATTGAATTTA
1 CAAAATGGTTTTTGACTTAATTGAATTTA
27847 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 5 0.18
31 12 0.43
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (29 bp):
CAAAATGGTTTTTGACTTAATTGAATTTA
Found at i:27857 original size:29 final size:30
Alignment explanation
Indices: 27787--27846 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
27777 CAATTTAAGG
27787 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
27818 CAAAATGTTTTTTGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
27847 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:27941 original size:8 final size:8
Alignment explanation
Indices: 27928--28027 Score: 55
Period size: 8 Copynumber: 14.0 Consensus size: 8
27918 GGTGTCAAAG
27928 TGCATCCA
1 TGCATCCA
*
27936 TGCATCCC
1 TGCATCCA
*
27944 TGCA---G
1 TGCATCCA
27949 TGCATCCA
1 TGCATCCA
*
27957 TGCATCCC
1 TGCATCCA
27965 TGCA---A
1 TGCATCCA
27970 TGCATCCA
1 TGCATCCA
27978 TGCAT-C-
1 TGCATCCA
*
27984 TGCA-CTAA
1 TGCATC-CA
*
27992 TGCATCGA
1 TGCATCCA
28000 TGCAT-CA
1 TGCATCCA
28007 TGCA---A
1 TGCATCCA
28012 TGCATCCA
1 TGCATCCA
28020 TGCATCCA
1 TGCATCCA
28028 AACATCGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 26
0.68 0.08 0.25
Matches are distributed among these distances:
5 13 0.18
6 4 0.06
7 6 0.08
8 47 0.66
9 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:27952 original size:21 final size:21
Alignment explanation
Indices: 27928--28026 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
27918 GGTGTCAAAG
*
27928 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCATCCCTGCAA
27949 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAA
27970 TGCATCCATGCAT--CTGCACTAA
1 TGCATCCATGCATCCCTG--C-AA
* *
27992 TGCATCGATGCAT-CATGCAA
1 TGCATCCATGCATCCCTGCAA
28012 TGCATCCATGCATCC
1 TGCATCCATGCATCC
28027 AAACATCGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.20
21 36 0.52
22 14 0.20
23 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.25
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAA
Found at i:27972 original size:13 final size:13
Alignment explanation
Indices: 27956--28023 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
27946 CAGTGCATCC
*
27956 ATGCATCCCTGCA
1 ATGCATCCATGCA
27969 ATGCATCCATGCA
1 ATGCATCCATGCA
* *
27982 TCTGCA-CTAATGCA
1 -ATGCATC-CATGCA
27996 TCGATGCAT-CATGCA
1 ---ATGCATCCATGCA
28011 ATGCATCCATGCA
1 ATGCATCCATGCA
28024 TCCAAACATC
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
12 6 0.14
13 19 0.44
14 9 0.21
15 5 0.12
16 4 0.09
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (13 bp):
ATGCATCCATGCA
Found at i:27996 original size:22 final size:20
Alignment explanation
Indices: 27928--28121 Score: 116
Period size: 21 Copynumber: 9.8 Consensus size: 20
27918 GGTGTCAAAG
* *
27928 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCAT-CATGCAA
*
27949 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCAT-CATGCAA
27970 TGCATCCATGCATC-TGCACTAA
1 TGCATCCATGCATCATG--C-AA
*
27992 TGCATCGATGCATCATGCAA
1 TGCATCCATGCATCATGCAA
28012 TGCATCCATGCATC---CAA
1 TGCATCCATGCATCATGCAA
* * * *
28029 -ACATCGAATGCA--AT-TAG
1 TGCATC-CATGCATCATGCAA
* * *
28046 TGCATCGATGCATCTTGCTA
1 TGCATCCATGCATCATGCAA
* * *
28066 TGCATCGATGCATCCTTGCCA
1 TGCATCCATGCAT-CATGCAA
* * *
28087 TGCATCGATGCATCCTGCCA
1 TGCATCCATGCATCATGCAA
28107 TGCATCCATGCATCA
1 TGCATCCATGCATCA
28122 AGGCTGCAAC
Statistics
Matches: 144, Mismatches: 17, Indels: 25
0.77 0.09 0.13
Matches are distributed among these distances:
16 4 0.03
17 14 0.10
18 4 0.03
19 3 0.02
20 48 0.33
21 54 0.38
22 15 0.10
23 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (20 bp):
TGCATCCATGCATCATGCAA
Found at i:28999 original size:34 final size:30
Alignment explanation
Indices: 28961--29029 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
28951 TTGATATAAC
28961 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
28995 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
29024 AATTTA
1 AATTTA
29030 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:29040 original size:29 final size:30
Alignment explanation
Indices: 28970--29029 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
28960 CAATTTAAGG
28970 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
29001 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
29030 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:29124 original size:8 final size:8
Alignment explanation
Indices: 29111--29197 Score: 59
Period size: 8 Copynumber: 12.0 Consensus size: 8
29101 GGTGTCAAAG
29111 TGCATCCA
1 TGCATCCA
*
29119 TGCATCCC
1 TGCATCCA
*
29127 TGCA---G
1 TGCATCCA
29132 TGCATCCA
1 TGCATCCA
29140 TGCATCCA
1 TGCATCCA
29148 TGCAT-C-
1 TGCATCCA
*
29154 TGCA-CTAA
1 TGCATC-CA
*
29162 TGCATCGA
1 TGCATCCA
29170 TGCAT-CA
1 TGCATCCA
29177 TGCA---A
1 TGCATCCA
29182 TGCATCCA
1 TGCATCCA
29190 TGCATCCA
1 TGCATCCA
29198 AACATCGAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
5 9 0.14
6 4 0.06
7 6 0.10
8 43 0.68
9 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:29135 original size:21 final size:21
Alignment explanation
Indices: 29109--29290 Score: 78
Period size: 21 Copynumber: 8.8 Consensus size: 21
29099 AGGGTGTCAA
*
29109 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCATGC
29130 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCATCCATGC
* * *
29151 ATCTGCA-CTAATGCATCGATGC
1 A-GTGCATC-CATGCATCCATGC
*
29173 A-T-CATGCAATGCATCCATGC
1 AGTGCAT-CCATGCATCCATGC
* ** * * *
29193 A-TCCAAACATCGAATGCAAT-T
1 AGTGCATCCAT-GCAT-CCATGC
* *
29214 AGTGCATCGATGCAT-CTTGC
1 AGTGCATCCATGCATCCATGC
* *
29234 TA-TGCATCGATGCATCCTTGCC
1 -AGTGCATCCATGCATCCATG-C
*
29256 A-TGCATCGATGCATCC-TGCC
1 AGTGCATCCATGCATCCATG-C
29276 A-TGCATCCATGCATC
1 AGTGCATCCATGCATC
29291 AAGGCTGCAA
Statistics
Matches: 129, Mismatches: 20, Indels: 25
0.74 0.11 0.14
Matches are distributed among these distances:
19 3 0.02
20 48 0.37
21 53 0.41
22 25 0.19
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCATGC
Found at i:29185 original size:20 final size:20
Alignment explanation
Indices: 29160--29291 Score: 98
Period size: 20 Copynumber: 6.8 Consensus size: 20
29150 CATCTGCACT
29160 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATCATGC
*
29180 AATGCATCCATGCATC---C
1 AATGCATCGATGCATCATGC
* *
29197 AA-ACATCGAATGCA--AT-T
1 AATGCATCG-ATGCATCATGC
* *
29214 AGTGCATCGATGCATCTTGC
1 AATGCATCGATGCATCATGC
* *
29234 TATGCATCGATGCATCCTTGC
1 AATGCATCGATGCAT-CATGC
* *
29255 CATGCATCGATGCATCCTGC
1 AATGCATCGATGCATCATGC
* *
29275 CATGCATCCATGCATCA
1 AATGCATCGATGCATCA
29292 AGGCTGCAAC
Statistics
Matches: 90, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
16 4 0.04
17 14 0.16
18 5 0.06
19 1 0.01
20 47 0.52
21 19 0.21
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (20 bp):
AATGCATCGATGCATCATGC
Found at i:30168 original size:34 final size:30
Alignment explanation
Indices: 30130--30198 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
30120 TTGATATAAC
30130 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
30164 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
30193 AATTTA
1 AATTTA
30199 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:30209 original size:29 final size:30
Alignment explanation
Indices: 30139--30198 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
30129 CAATTTAAGG
30139 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
30170 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
30199 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:30293 original size:8 final size:8
Alignment explanation
Indices: 30280--30379 Score: 55
Period size: 8 Copynumber: 14.0 Consensus size: 8
30270 GGTGTCAAAG
30280 TGCATCCA
1 TGCATCCA
*
30288 TGCATCCC
1 TGCATCCA
*
30296 TGCA---G
1 TGCATCCA
30301 TGCATCCA
1 TGCATCCA
*
30309 TGCATCCC
1 TGCATCCA
30317 TGCA---A
1 TGCATCCA
30322 TGCATCCA
1 TGCATCCA
30330 TGCAT-C-
1 TGCATCCA
*
30336 TGCA-CTAA
1 TGCATC-CA
*
30344 TGCATCGA
1 TGCATCCA
30352 TGCAT-CA
1 TGCATCCA
30359 TGCA---A
1 TGCATCCA
30364 TGCATCCA
1 TGCATCCA
30372 TGCATCCA
1 TGCATCCA
30380 AACATCGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 26
0.68 0.08 0.25
Matches are distributed among these distances:
5 13 0.18
6 4 0.06
7 6 0.08
8 47 0.66
9 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:30304 original size:21 final size:21
Alignment explanation
Indices: 30280--30378 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
30270 GGTGTCAAAG
*
30280 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCATCCCTGCAA
30301 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAA
30322 TGCATCCATGCAT--CTGCACTAA
1 TGCATCCATGCATCCCTG--C-AA
* *
30344 TGCATCGATGCAT-CATGCAA
1 TGCATCCATGCATCCCTGCAA
30364 TGCATCCATGCATCC
1 TGCATCCATGCATCC
30379 AAACATCGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.20
21 36 0.52
22 14 0.20
23 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.25
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAA
Found at i:30324 original size:13 final size:13
Alignment explanation
Indices: 30308--30375 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
30298 CAGTGCATCC
*
30308 ATGCATCCCTGCA
1 ATGCATCCATGCA
30321 ATGCATCCATGCA
1 ATGCATCCATGCA
* *
30334 TCTGCA-CTAATGCA
1 -ATGCATC-CATGCA
30348 TCGATGCAT-CATGCA
1 ---ATGCATCCATGCA
30363 ATGCATCCATGCA
1 ATGCATCCATGCA
30376 TCCAAACATC
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
12 6 0.14
13 19 0.44
14 9 0.21
15 5 0.12
16 4 0.09
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (13 bp):
ATGCATCCATGCA
Found at i:30348 original size:22 final size:20
Alignment explanation
Indices: 30280--30473 Score: 116
Period size: 21 Copynumber: 9.8 Consensus size: 20
30270 GGTGTCAAAG
* *
30280 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCAT-CATGCAA
*
30301 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCAT-CATGCAA
30322 TGCATCCATGCATC-TGCACTAA
1 TGCATCCATGCATCATG--C-AA
*
30344 TGCATCGATGCATCATGCAA
1 TGCATCCATGCATCATGCAA
30364 TGCATCCATGCATC---CAA
1 TGCATCCATGCATCATGCAA
* * * *
30381 -ACATCGAATGCA--AT-TAG
1 TGCATC-CATGCATCATGCAA
* * *
30398 TGCATCGATGCATCTTGCTA
1 TGCATCCATGCATCATGCAA
* * *
30418 TGCATCGATGCATCCTTGCCA
1 TGCATCCATGCAT-CATGCAA
* * *
30439 TGCATCGATGCATCCTGCCA
1 TGCATCCATGCATCATGCAA
30459 TGCATCCATGCATCA
1 TGCATCCATGCATCA
30474 AGGCTGCAAC
Statistics
Matches: 144, Mismatches: 17, Indels: 25
0.77 0.09 0.13
Matches are distributed among these distances:
16 4 0.03
17 14 0.10
18 4 0.03
19 3 0.02
20 48 0.33
21 54 0.38
22 15 0.10
23 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (20 bp):
TGCATCCATGCATCATGCAA
Found at i:31295 original size:2 final size:2
Alignment explanation
Indices: 31288--31312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31278 ATGATTGGAA
31288 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 A
31313 AAATTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34759 original size:21 final size:21
Alignment explanation
Indices: 34733--34773 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
34723 TATAGCAGGA
34733 TAGCA-GGATATCGATTCCCTG
1 TAGCAGGGA-ATCGATTCCCTG
34754 TAGCAGGGGAATCGATTCCC
1 TAGCA-GGGAATCGATTCCC
34774 CTCTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
TAGCAGGGAATCGATTCCCTG
Found at i:38230 original size:30 final size:30
Alignment explanation
Indices: 38194--38255 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
38184 TGCTTTCATG
38194 TGTTATTTACTTCTTTCTCTAGGCAGCAAC
1 TGTTATTTACTTCTTTCTCTAGGCAGCAAC
38224 TGTTATTTACTTCTTTCTCTAGGCAGCAAC
1 TGTTATTTACTTCTTTCTCTAGGCAGCAAC
38254 TG
1 TG
38256 CTTTGGCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.44
Consensus pattern (30 bp):
TGTTATTTACTTCTTTCTCTAGGCAGCAAC
Found at i:40832 original size:147 final size:146
Alignment explanation
Indices: 40623--40910 Score: 468
Period size: 147 Copynumber: 2.0 Consensus size: 146
40613 GTTTTAACCG
*
40623 AATTAATTACCAACCAAATTAATTGAAAATATAAATATTTAATATATAATATGTATTATTTATAA
1 AATTAATTACCAACCAAATTAACTGAAAATATAAATATTTAATATATAATATGTATTATTTATAA
* * * * * *
40688 ATTTTGGTTAATTCGGTTAATTGACCAATTAAATGAATTTTGTTCGGTTTGGTTAGTTAATTTCG
66 ATTTCGGTTAATTCGGTTAATTGACCAATTAAATGAACTTTGTTCGGTTCGATTAATTAATTTCA
*
40753 AAAAAATTTCAGTTCT
131 AAAAAAATTCAGTTCT
*
40769 AATTAATTACCAACCAAATTAACTGGAAATATAAAATATTTAATATATAATATGTATTATTTATA
1 AATTAATTACCAACCAAATTAACTGAAAATAT-AAATATTTAATATATAATATGTATTATTTATA
* *
40834 AATTTCGGTTAATTCGGTTAATTGACCGATTAAATGAACTTTGTTCGGTTCGATTAATTATTTTC
65 AATTTCGGTTAATTCGGTTAATTGACCAATTAAATGAACTTTGTTCGGTTCGATTAATTAATTTC
40899 AAAAAAAATTCA
130 AAAAAAAATTCA
40911 ATTCGATTAA
Statistics
Matches: 130, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
146 30 0.23
147 100 0.77
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (146 bp):
AATTAATTACCAACCAAATTAACTGAAAATATAAATATTTAATATATAATATGTATTATTTATAA
ATTTCGGTTAATTCGGTTAATTGACCAATTAAATGAACTTTGTTCGGTTCGATTAATTAATTTCA
AAAAAAATTCAGTTCT
Found at i:41158 original size:3 final size:3
Alignment explanation
Indices: 41152--41185 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
41142 TTATAATAAT
41152 TTA TTA TTA TTA TTAA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA T
41186 ATATATTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41170 original size:13 final size:13
Alignment explanation
Indices: 41154--41179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41144 ATAATAATTT
41154 ATTATTATTATTA
1 ATTATTATTATTA
41167 ATTATTATTATTA
1 ATTATTATTATTA
41180 TTTTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:44285 original size:28 final size:27
Alignment explanation
Indices: 44258--44319 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
44248 AAATTGAAAT
* *
44258 TATAAAATTAAAGGTCTTAATTATAAA
1 TATAAAATTAAAGGCCCTAATTATAAA
**
44285 TATAAAAATTGGAGGCCCTAATTATAAA
1 TAT-AAAATTAAAGGCCCTAATTATAAA
44313 TATAAAA
1 TATAAAA
44320 AAATTGGGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (27 bp):
TATAAAATTAAAGGCCCTAATTATAAA
Found at i:47622 original size:20 final size:21
Alignment explanation
Indices: 47571--47624 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
47561 AAATTTAATG
*
47571 AGTAAAATAAAA-AAAATAAA
1 AGTACAATAAAATAAAATAAA
*
47591 AGTACAAT-AAATAAAATAAG
1 AGTACAATAAAATAAAATAAA
*
47611 AG-ATAATAAAATAA
1 AGTACAATAAAATAA
47625 GAGGAATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (21 bp):
AGTACAATAAAATAAAATAAA
Found at i:59221 original size:6 final size:6
Alignment explanation
Indices: 59213--59254 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
59203 ATCCTGGGCT
* *
59213 GAAGCT GAAGCT GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA
1 GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA
59255 CATGCCTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.33, T:0.05
Consensus pattern (6 bp):
GAAGCA
Found at i:60724 original size:2 final size:2
Alignment explanation
Indices: 60717--60747 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60707 CTACCATTAA
60717 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 A
60748 GATAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63793 original size:19 final size:19
Alignment explanation
Indices: 63769--63806 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
63759 AAAGTGAAAC
63769 AAGAAACAGAAAACCCTAG
1 AAGAAACAGAAAACCCTAG
63788 AAGAAACAGAAAACCCTAG
1 AAGAAACAGAAAACCCTAG
63807 GAATAGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.21, G:0.16, T:0.05
Consensus pattern (19 bp):
AAGAAACAGAAAACCCTAG
Found at i:64858 original size:7 final size:7
Alignment explanation
Indices: 64846--64872 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
64836 TATATTAGAT
64846 TAGATTC
1 TAGATTC
64853 TAGATTC
1 TAGATTC
64860 TAGATTC
1 TAGATTC
64867 TAGATT
1 TAGATT
64873 TTTTCTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (7 bp):
TAGATTC
Found at i:67109 original size:16 final size:16
Alignment explanation
Indices: 67088--67124 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
67078 GTAAAATATA
67088 TATTCCAGTAATATTT
1 TATTCCAGTAATATTT
*
67104 TATTCCAGTAATCTTT
1 TATTCCAGTAATATTT
67120 TATTC
1 TATTC
67125 TTTCAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (16 bp):
TATTCCAGTAATATTT
Found at i:69667 original size:29 final size:29
Alignment explanation
Indices: 69623--69679 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
69613 AGTGTTGGTC
69623 GTAGGTCGCCAGGCACTCCGGACGACCTT
1 GTAGGTCGCCAGGCACTCCGGACGACCTT
* *
69652 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCAGGCACTCCGGACGACCT
69680 ACCCTTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.18
Consensus pattern (29 bp):
GTAGGTCGCCAGGCACTCCGGACGACCTT
Found at i:69714 original size:12 final size:12
Alignment explanation
Indices: 69697--69721 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
69687 CTCAAACAGA
69697 GAGAATGAACGT
1 GAGAATGAACGT
69709 GAGAATGAACGT
1 GAGAATGAACGT
69721 G
1 G
69722 TTGCATGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:69784 original size:29 final size:29
Alignment explanation
Indices: 69750--69863 Score: 122
Period size: 29 Copynumber: 3.9 Consensus size: 29
69740 TCCCAACACA
* * * *
69750 TAGGTCGCCATTCCCTCCGGGCAACTTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
* * **
69779 TAGGTCGCCAT-AACCTCCTGGCGACCTAC
1 TAGGTCGCCATGCA-CTCCGGGCGACCTTG
* *
69808 AAGGTCGCCATGCACTCCGGGTGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
69837 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
69864 ACCCTCGCTC
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
29 67 0.99
30 1 0.01
ACGTcount: A:0.17, C:0.35, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:69841 original size:58 final size:58
Alignment explanation
Indices: 69751--69865 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 58
69741 CCCAACACAT
* * * *
69751 AGGTCGCCATTCCCTCCGGGCAACTTTGTAGGTCGCCATA-ACCTCCTGGCGACCTACA
1 AGGTCGCCATGCACTCCGGGCAACCTTGTAGGTCGCCATACA-CTCCGGGCGACCTACA
** *
69809 AGGTCGCCATGCACTCCGGGTGACCTTGTAGGTCGCCATGCACTCCGGGCGACCTAC
1 AGGTCGCCATGCACTCCGGGCAACCTTGTAGGTCGCCATACACTCCGGGCGACCTAC
69866 CCTCGCTCGG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
58 48 0.98
59 1 0.02
ACGTcount: A:0.17, C:0.36, G:0.26, T:0.21
Consensus pattern (58 bp):
AGGTCGCCATGCACTCCGGGCAACCTTGTAGGTCGCCATACACTCCGGGCGACCTACA
Found at i:69940 original size:33 final size:33
Alignment explanation
Indices: 69879--69941 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
69869 CGCTCGGCTT
*
69879 CCCTCGCATAGCTCGCACGGTTGCCCTCGGATG
1 CCCTCGCATAGCTCGCACGGATGCCCTCGGATG
** *
69912 CCCTCGCATAGCTCGTTCGGATGGCCTCGG
1 CCCTCGCATAGCTCGCACGGATGCCCTCGG
69942 TCGGATGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.11, C:0.38, G:0.29, T:0.22
Consensus pattern (33 bp):
CCCTCGCATAGCTCGCACGGATGCCCTCGGATG
Found at i:69945 original size:14 final size:14
Alignment explanation
Indices: 69923--69993 Score: 80
Period size: 14 Copynumber: 5.4 Consensus size: 14
69913 CCTCGCATAG
*
69923 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
69937 CTCGGTCGGAT-G-
1 CTCGGTCGGATGGC
*
69949 TTC--TCGGATGGC
1 CTCGGTCGGATGGC
69961 CTCGGAT-GGATGGC
1 CTCGG-TCGGATGGC
69975 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
69989 CTCGG
1 CTCGG
69994 ATGCCCAGCG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
10 6 0.12
11 1 0.02
12 4 0.08
13 2 0.04
14 34 0.71
15 1 0.02
ACGTcount: A:0.08, C:0.27, G:0.39, T:0.25
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:69971 original size:24 final size:27
Alignment explanation
Indices: 69923--69996 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 27
69913 CCTCGCATAG
69923 CTCGTTCGGATGGCCTCGG-TCGGAT-G-
1 CTCG-TCGGATGGCCTCGGAT-GGATGGC
*
69949 TTC-TCGGATGGCCTCGGATGGATGGC
1 CTCGTCGGATGGCCTCGGATGGATGGC
69975 CTCGGTCGGATGGCCTCGGATG
1 CTC-GTCGGATGGCCTCGGATG
69997 CCCAGCGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 18 0.44
25 2 0.05
26 4 0.10
28 17 0.41
ACGTcount: A:0.09, C:0.26, G:0.39, T:0.26
Consensus pattern (27 bp):
CTCGTCGGATGGCCTCGGATGGATGGC
Found at i:70073 original size:29 final size:29
Alignment explanation
Indices: 70036--70093 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
70026 GCAATCTCTT
*
70036 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
70065 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
70094 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:70679 original size:16 final size:15
Alignment explanation
Indices: 70608--70694 Score: 64
Period size: 13 Copynumber: 6.3 Consensus size: 15
70598 AAATAAATAT
70608 TATAATAATA-ATAA
1 TATAATAATATATAA
70622 T-TAATAATAT-TAA
1 TATAATAATATATAA
* *
70635 T-TATTAA-ATGTAA
1 TATAATAATATATAA
*
70648 TA-AATAAT-TAAAA
1 TATAATAATATATAA
70661 TATAATAATATATAAA
1 TATAATAATATAT-AA
* *
70677 TATAGTAAT-TAAAA
1 TATAATAATATATAA
70691 TATA
1 TATA
70695 TATTTTATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
12 2 0.03
13 30 0.51
14 13 0.22
15 4 0.07
16 10 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TATAATAATATATAA
Found at i:70695 original size:16 final size:15
Alignment explanation
Indices: 70651--70697 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
70641 AATGTAATAA
70651 ATAATTAAAATATA-
1 ATAATTAAAATATAT
70665 ATAATATATAAATATA-
1 ATAAT-TA-AAATATAT
*
70681 GTAATTAAAATATAT
1 ATAATTAAAATATAT
70696 AT
1 AT
70698 TTTATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 12 0.43
15 5 0.18
16 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAATTAAAATATAT
Found at i:71365 original size:23 final size:23
Alignment explanation
Indices: 71339--71384 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
71329 AGACAATCAT
71339 TACCCTGCAAGATGTTGCATTTC
1 TACCCTGCAAGATGTTGCATTTC
71362 TACCCTGCAAGATGTTGCATTTC
1 TACCCTGCAAGATGTTGCATTTC
71385 ATCTGTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (23 bp):
TACCCTGCAAGATGTTGCATTTC
Found at i:77152 original size:17 final size:17
Alignment explanation
Indices: 77130--77168 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
77120 TGTGCCGAAT
*
77130 GAGATTTCTGTTAAGAG
1 GAGATTGCTGTTAAGAG
*
77147 GAGATTGCTGTTAAGGG
1 GAGATTGCTGTTAAGAG
77164 GAGAT
1 GAGAT
77169 CGCTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (17 bp):
GAGATTGCTGTTAAGAG
Found at i:79325 original size:28 final size:28
Alignment explanation
Indices: 79293--79351 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
79283 TTTCTGACCC
*
79293 CTAGCATGACTAATGCTCCTATGAAATG
1 CTAGCATGACTAATGCTCCTATCAAATG
79321 CTAGCATGACTAATGCTCCTATCAAATG
1 CTAGCATGACTAATGCTCCTATCAAATG
79349 CTA
1 CTA
79352 TAAATAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (28 bp):
CTAGCATGACTAATGCTCCTATCAAATG
Found at i:79335 original size:15 final size:15
Alignment explanation
Indices: 79293--79337 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
79283 TTTCTGACCC
79293 CTAGCATGACTAATG
1 CTAGCATGACTAATG
*
79308 CT-CCTATGA--AATG
1 CTAGC-ATGACTAATG
79321 CTAGCATGACTAATG
1 CTAGCATGACTAATG
79336 CT
1 CT
79338 CCTATCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (15 bp):
CTAGCATGACTAATG
Found at i:81087 original size:87 final size:87
Alignment explanation
Indices: 80971--81146 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
80961 ATGTCTGAAT
*
80971 CTCGATATGAAACAGAAACCGAATTGCCTTTTTGTCTGGTTTTGTTCTAGTGATTTTGACTCCAT
1 CTCGATATGAAACAGAAACCGAATCGCCTTTTTGTCTGGTTTTGTTCTAGTGATTTTGACTCCAT
81036 GTTTCTTGTGGGACAGGTTTGG
66 GTTTCTTGTGGGACAGGTTTGG
81058 CTCGATATGAAACAGAAACCGAATCGCCTTTTTGTCTGGTTTTGTTCTAGTGATTTTGACTCCAT
1 CTCGATATGAAACAGAAACCGAATCGCCTTTTTGTCTGGTTTTGTTCTAGTGATTTTGACTCCAT
81123 GTTTCTTGTGGGACAGGTTTGG
66 GTTTCTTGTGGGACAGGTTTGG
81145 CT
1 CT
81147 GTTATAACTG
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (87 bp):
CTCGATATGAAACAGAAACCGAATCGCCTTTTTGTCTGGTTTTGTTCTAGTGATTTTGACTCCAT
GTTTCTTGTGGGACAGGTTTGG
Found at i:92046 original size:43 final size:43
Alignment explanation
Indices: 91967--92051 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
91957 GAAGCACATG
* * *
91967 AAAGTAACAATTCATAAATATACCAAACTAATATATTACAACC
1 AAAGTAACAATTCACAAACATACCAAACTAACATATTACAACC
**
92010 AAAGTAACAATTCACAAACATATTAAA-TGAACATATTACAAC
1 AAAGTAACAATTCACAAACATACCAAACT-AACATATTACAAC
92052 TATTCTTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.54, C:0.18, G:0.04, T:0.25
Consensus pattern (43 bp):
AAAGTAACAATTCACAAACATACCAAACTAACATATTACAACC
Found at i:98072 original size:2 final size:2
Alignment explanation
Indices: 98065--98102 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
98055 ATGGAAAATA
98065 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
98103 TCCCCAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110665 original size:4 final size:4
Alignment explanation
Indices: 110656--110686 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
110646 ATTTTTTCTC
*
110656 TTAT TTAT TTAT TTAT TTAT TTAT TTTT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
110687 ATAAGAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:112934 original size:22 final size:21
Alignment explanation
Indices: 112900--112943 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
112890 AGAATGATTT
112900 ATTTATTATTTTA-AAATAAA
1 ATTTATTATTTTATAAATAAA
*
112920 ATTTATATAATTTTATTAATAAA
1 ATTTAT-T-ATTTTATAAATAAA
112943 A
1 A
112944 ATATTAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 6 0.30
23 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTATTATTTTATAAATAAA
Found at i:113121 original size:27 final size:27
Alignment explanation
Indices: 113091--113182 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 27
113081 ATTAAATAAA
113091 AATAATATTATTTATTATTAATAATTT
1 AATAATATTATTTATTATTAATAATTT
*
113118 AATAATATTATTTA-TATGAAATTAA-TT
1 AATAATATTATTTATTAT-TAA-TAATTT
*
113145 AATAATATAATTT-TT-TTAATAATTT
1 AATAATATTATTTATTATTAATAATTT
*
113170 ATTATATATTATT
1 AATA-ATATTATT
113183 AAAATAAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
24 3 0.05
25 7 0.13
26 11 0.20
27 31 0.56
28 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
AATAATATTATTTATTATTAATAATTT
Found at i:113316 original size:12 final size:12
Alignment explanation
Indices: 113282--113330 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
113272 ATTAATAAAT
113282 ATATTTTAAT-A
1 ATATTTTAATAA
* *
113293 AT-TATAAATAA
1 ATATTTTAATAA
113304 ATATTTTAATAA
1 ATATTTTAATAA
113316 AT-TTTTAATGAA
1 ATATTTTAAT-AA
113328 ATA
1 ATA
113331 CTAAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 5 0.17
11 12 0.40
12 13 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
ATATTTTAATAA
Found at i:113329 original size:24 final size:22
Alignment explanation
Indices: 113271--113330 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
113261 TTATTAGAAA
113271 TATTAATAAATATATTTTAATAAT
1 TATTAAT-AA-ATATTTTAATAAT
*
113295 TATAAATAAATATTTTAATAAAT
1 TATTAATAAATATTTTAAT-AAT
*
113318 TTTTAATGAAATA
1 TATTAAT-AAATA
113331 CTAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 10 0.32
23 10 0.32
24 11 0.35
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTAATAAATATTTTAATAAT
Found at i:115994 original size:15 final size:15
Alignment explanation
Indices: 115974--116002 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
115964 CCTCAAAGCA
115974 TTTAAAAAAATATAG
1 TTTAAAAAAATATAG
115989 TTTAAAAAAATATA
1 TTTAAAAAAATATA
116003 TGGACTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
TTTAAAAAAATATAG
Found at i:121469 original size:212 final size:213
Alignment explanation
Indices: 121075--121482 Score: 764
Period size: 212 Copynumber: 1.9 Consensus size: 213
121065 TGATGTAAAT
121075 TTACAGCTTGTTCCTTATATGACTCCTTTTATCAAACCAATAGACAGTCCATGCAAAAATCTTTG
1 TTACAGCTTGTTCCTTATATGACTCCTTTTATCAAACCAATAGACAGTCCATGCAAAAATCTTTG
*
121140 CATCTGATCTCATATCAGCAAAAGAACAACTTATCAGCTGCTATATGACTGCCATACATTAACAT
66 CATCTGATATCATATCAGCAAAAG-A-AACTTATCAGCTGCTATATGACTGCCATACATTAACAT
121205 CCTCGTTCCCTAAATAAAGAAGTCATTCATCACAAGAATCTAACATTGAAGATTCATGAATTCCA
129 CCTCGTTCCCTAAATAAAGAAGTCATTCATCACAAGAATCTAACATTGAAGATTCATGAATTCCA
121270 TGGAAACTCAAAAGGAATGC
194 TGGAAACTCAAAAGGAATGC
*
121290 TTACAGCTTGTTCCTTATATGACTCCTTTTATCATACCAATAGACAGTCCATGCAAAAATCTTTG
1 TTACAGCTTGTTCCTTATATGACTCCTTTTATCAAACCAATAGACAGTCCATGCAAAAATCTTTG
*
121355 CATCTGATATCATATCAGCAAAAG-AACTTATCAGCTGCTATATGACTGTCATACATTAACATCC
66 CATCTGATATCATATCAGCAAAAGAAACTTATCAGCTGCTATATGACTGCCATACATTAACATCC
121419 TCGTTCCCTAAATAAAGAAGTCATTCATCACAAGAATCTAACATTGAAGATTCATGAATTCCAT
131 TCGTTCCCTAAATAAAGAAGTCATTCATCACAAGAATCTAACATTGAAGATTCATGAATTCCAT
121483 AAAACATGAG
Statistics
Matches: 190, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
212 103 0.54
215 87 0.46
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.30
Consensus pattern (213 bp):
TTACAGCTTGTTCCTTATATGACTCCTTTTATCAAACCAATAGACAGTCCATGCAAAAATCTTTG
CATCTGATATCATATCAGCAAAAGAAACTTATCAGCTGCTATATGACTGCCATACATTAACATCC
TCGTTCCCTAAATAAAGAAGTCATTCATCACAAGAATCTAACATTGAAGATTCATGAATTCCATG
GAAACTCAAAAGGAATGC
Found at i:125759 original size:26 final size:28
Alignment explanation
Indices: 125699--125761 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 28
125689 CGGGGTGACC
125699 ATATCTTAACTAAATAAAAACGAAAGTGATT
1 ATATCTTAACTAAATAAAAACGAAAG-G--T
* *
125730 ATATCTTAATTAAATAAAAACGAAAGAT
1 ATATCTTAACTAAATAAAAACGAAAGGT
125758 ATAT
1 ATAT
125762 TATCTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
31 25 0.83
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (28 bp):
ATATCTTAACTAAATAAAAACGAAAGGT
Found at i:131407 original size:20 final size:21
Alignment explanation
Indices: 131372--131410 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
131362 TAAATGCAAT
131372 GTTTTCATACTTATTTTTATA
1 GTTTTCATACTTATTTTTATA
*
131393 GTTTT-ATATTTATTTTTA
1 GTTTTCATACTTATTTTTA
131411 GAAATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (21 bp):
GTTTTCATACTTATTTTTATA
Found at i:137165 original size:15 final size:15
Alignment explanation
Indices: 137145--137174 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
137135 TGAAAATACA
*
137145 AAAATTTAAATAAAT
1 AAAATTAAAATAAAT
137160 AAAATTAAAATAAAT
1 AAAATTAAAATAAAT
137175 TAATTTGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATTAAAATAAAT
Found at i:137718 original size:18 final size:19
Alignment explanation
Indices: 137686--137729 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
137676 TTATATTTTT
*
137686 AAAATTTTTTAAAAATAAA
1 AAAATTTTTTAAAAAGAAA
*
137705 AATATTTTTT-AAAAGAAA
1 AAAATTTTTTAAAAAGAAA
137723 AAAATTT
1 AAAATTT
137730 AAAAAACTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAATTTTTTAAAAAGAAA
Found at i:137724 original size:19 final size:18
Alignment explanation
Indices: 137686--137729 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
137676 TTATATTTTT
137686 AAAATTTTTTAAAAATAA
1 AAAATTTTTTAAAAATAA
137704 AAATATTTTTTAAAAGA-AA
1 AAA-ATTTTTTAAAA-ATAA
137723 AAAATTT
1 AAAATTT
137730 AAAAAACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.29
19 16 0.67
20 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTTTTTAAAAATAA
Found at i:138653 original size:31 final size:31
Alignment explanation
Indices: 138615--138726 Score: 188
Period size: 31 Copynumber: 3.6 Consensus size: 31
138605 TCCATAGATT
*
138615 CCGAAGAACCTAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
*
138646 CCAAAGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
* *
138677 CCGAAGAACATAGGTAAACAGTCCATATGCC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
138708 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
138727 CTTCGACCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAATCCATATGTC
Found at i:140686 original size:98 final size:98
Alignment explanation
Indices: 140517--140696 Score: 333
Period size: 98 Copynumber: 1.8 Consensus size: 98
140507 CTGCACCTAT
* *
140517 TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGAAGTAGTTTAGGTACTAAAAAGTG
1 TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGAAGTAATTTAGGCACTAAAAAGTG
140582 TATTAAGCCTTTATTTTGAGATCTAGATTATAG
66 TATTAAGCCTTTATTTTGAGATCTAGATTATAG
*
140615 TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGATGTAATTTAGGCACTAAAAAGTG
1 TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGAAGTAATTTAGGCACTAAAAAGTG
140680 TATTAAGCCTTTATTTT
66 TATTAAGCCTTTATTTT
140697 AATATTTATG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 79 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (98 bp):
TGTTAGCAAAAACTTCTTTAGGATCTAGATTGTATTTTGAGAAGTAATTTAGGCACTAAAAAGTG
TATTAAGCCTTTATTTTGAGATCTAGATTATAG
Found at i:147725 original size:21 final size:21
Alignment explanation
Indices: 147701--147743 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
147691 TGATATGAAT
*
147701 TGTAACGAACATGAATGGTAA
1 TGTAACGAACATGAATGATAA
* *
147722 TGTAATGAAGATGAATGATAA
1 TGTAACGAACATGAATGATAA
147743 T
1 T
147744 ACAGCGTGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (21 bp):
TGTAACGAACATGAATGATAA
Found at i:148122 original size:21 final size:21
Alignment explanation
Indices: 148096--148136 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
148086 AAATTAAAAC
*
148096 AAATATAAATAACAATACAAT
1 AAATATAAATAACAAAACAAT
* *
148117 AAATATTAATGACAAAACAA
1 AAATATAAATAACAAAACAA
148137 CAAAATCAAA
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:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (21 bp):
AAATATAAATAACAAAACAAT
Found at i:149662 original size:31 final size:31
Alignment explanation
Indices: 149639--149841 Score: 352
Period size: 31 Copynumber: 6.5 Consensus size: 31
149629 CATAGATTCT
* *
149639 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
149670 GAAGAACATAGTTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
149701 AAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
149732 GAAGAACATAGGTAAACAGTCCATATGTCTC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
149763 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
149794 GAAGAACATAGGTAAACAGTCCATATATCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
149825 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
149842 CCTCAACCCT
Statistics
Matches: 163, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 163 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:152619 original size:21 final size:21
Alignment explanation
Indices: 152595--152655 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
152585 AACTTTGAAA
152595 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
152616 AAAT-G-TTT---A-TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
152630 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
152651 AAATG
1 AAATG
152656 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:152686 original size:37 final size:37
Alignment explanation
Indices: 152587--152705 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 37
152577 TGGTAACCAA
152587 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
*
152624 ATTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
152659 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
152696 -GTTGAAAAAT
1 CTTTGAAAAAT
152706 GATAATGGGA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
35 29 0.39
36 18 0.24
37 27 0.36
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:157243 original size:21 final size:21
Alignment explanation
Indices: 157219--157279 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
157209 AACTTTGAAA
157219 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
157240 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
157254 AAATAGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
157275 AAATG
1 AAATG
157280 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:157325 original size:36 final size:36
Alignment explanation
Indices: 157211--157329 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
157201 TGGTAACCAA
*
157211 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
157248 CTTTG-AAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
157283 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
157320 -GTTGAAAAAT
1 CTTTGAAAAAT
157330 GATAATGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 34 0.44
36 16 0.21
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:164878 original size:2 final size:2
Alignment explanation
Indices: 164871--164910 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
164861 TTACCCATCT
164871 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
164911 CAATTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:171525 original size:14 final size:15
Alignment explanation
Indices: 171506--171534 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
171496 GAACTAGACA
171506 GGAGGGGGGG-GGGG
1 GGAGGGGGGGAGGGG
171520 GGAGGGGGGGAGGGG
1 GGAGGGGGGGAGGGG
171535 CAATTGACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.10, C:0.00, G:0.90, T:0.00
Consensus pattern (15 bp):
GGAGGGGGGGAGGGG
Found at i:175168 original size:23 final size:24
Alignment explanation
Indices: 175127--175175 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
175117 ATCTTTGATG
175127 TAACATGGAAGGTGGTAACAAAAA
1 TAACATGGAAGGTGGTAACAAAAA
175151 TAACATGGAA-GTGGTAACAAAAA
1 TAACATGGAAGGTGGTAACAAAAA
175174 TA
1 TA
175176 TTTAATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.18
Consensus pattern (24 bp):
TAACATGGAAGGTGGTAACAAAAA
Found at i:175526 original size:213 final size:211
Alignment explanation
Indices: 175155--175578 Score: 814
Period size: 213 Copynumber: 2.0 Consensus size: 211
175145 CAAAAATAAC
175155 ATGGAAGTGGTAACAAAAATATTTAATTTACAACTCTAAAAGAAAGGTGTAAAATTAACTTCTTC
1 ATGGAAGTGGTAACAAAAATATTTAATTTACAACTCTAAAAGAAAGGTGTAAAATTAACTTCTTC
175220 ACAAAAACCAATGATTAGCAAAGAATAGATACAATACCTCCACTGTGTTCCCAAACCATGCCTGT
66 ACAAAAACCAATGATTAGCAAAGAATAGATACAATACCTCCACTGTGTTCCCAAACCATGCCTGT
175285 TCTGGTATGGAAAAGAACAACCATATCCATGGAGTAAATTCATACAAGTTAT-CCATCTATTTGA
131 TCTGGTATGGAAAAGAACAACCATATCCATGGAGTAAATTCATACAAGTTATACCATCTATTTGA
175349 TTAGCTTTCTAGAAAA
196 TTAGCTTTCTAGAAAA
175365 ATGGAAGGTGGTAACAAAAATATTTAATTTACAACTCTAAAAGAAAAGGTGTAAAATTAACTTCT
1 ATGGAA-GTGGTAACAAAAATATTTAATTTACAACTCTAAAAG-AAAGGTGTAAAATTAACTTCT
175430 TCACAAAAACCAATGATTTAGCAAAGAATAGATACAATACCTCCACTGTGTTCCCAAACCATGCC
64 TCACAAAAACCAATGA-TTAGCAAAGAATAGATACAATACCTCCACTGTGTTCCCAAACCATGCC
175495 TGTTCTGGTATGGAAAAGAACAACCATATCCATGGAGTAAATTCATACAAGTTATACCATCTATT
128 TGTTCTGGTATGGAAAAGAACAACCATATCCATGGAGTAAATTCATACAAGTTATACCATCTATT
175560 TGATTAGCTTTCTAGAAAA
193 TGATTAGCTTTCTAGAAAA
175579 CCAATAACTA
Statistics
Matches: 210, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
210 6 0.03
211 36 0.17
212 37 0.18
213 103 0.49
214 28 0.13
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (211 bp):
ATGGAAGTGGTAACAAAAATATTTAATTTACAACTCTAAAAGAAAGGTGTAAAATTAACTTCTTC
ACAAAAACCAATGATTAGCAAAGAATAGATACAATACCTCCACTGTGTTCCCAAACCATGCCTGT
TCTGGTATGGAAAAGAACAACCATATCCATGGAGTAAATTCATACAAGTTATACCATCTATTTGA
TTAGCTTTCTAGAAAA
Found at i:176455 original size:20 final size:21
Alignment explanation
Indices: 176417--176465 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
176407 TCATATTAAT
* **
176417 ATATAATATAATAAATAAATG
1 ATATCATATAATAAATAAAAA
*
176438 ATATCATAT-ATAACTAAAAA
1 ATATCATATAATAAATAAAAA
176458 ATATCATA
1 ATATCATA
176466 AATGTATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATCATATAATAAATAAAAA
Found at i:188441 original size:14 final size:14
Alignment explanation
Indices: 188424--188475 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
188414 CGTTCATTTA
188424 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
188438 CGTTCAGTTATGTT
1 CGTTCGGTTATGTT
*
188452 AG-T---TTATGTT
1 CGTTCGGTTATGTT
188462 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
188476 TGTTTATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
13 1 0.03
14 21 0.68
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:188500 original size:24 final size:24
Alignment explanation
Indices: 188411--188500 Score: 108
Period size: 24 Copynumber: 3.8 Consensus size: 24
188401 CATAGGTCTC
* * * *
188411 GTTCGTTCATTTACGTTCGGTTAT
1 GTTCGTTCAGTTATGTTTGTTTAT
*
188435 GTTCGTTCAGTTATGTTAGTTTAT
1 GTTCGTTCAGTTATGTTTGTTTAT
*
188459 GTTCGTTCGGTTATGTTTGTTTAT
1 GTTCGTTCAGTTATGTTTGTTTAT
* *
188483 GTTCATTCATTTATGTTT
1 GTTCGTTCAGTTATGTTT
188501 AACTCAATCT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGTTCAGTTATGTTTGTTTAT
Found at i:189316 original size:12 final size:11
Alignment explanation
Indices: 189299--189389 Score: 92
Period size: 12 Copynumber: 7.9 Consensus size: 11
189289 TGTCATGCTT
189299 GAATCGAGCTCA
1 GAATCGAGCT-A
*
189311 GAATCGAGCTT
1 GAATCGAGCTA
189322 GAATCGAGCTCA
1 GAATCGAGCT-A
* * *
189334 TAATCGATCTT
1 GAATCGAGCTA
189345 GAATCGAGCTCA
1 GAATCGAGCT-A
* *
189357 GAATCGATCTT
1 GAATCGAGCTA
189368 GAATCGAGCTGA
1 GAATCGAGCT-A
189380 GAATCGAGCT
1 GAATCGAGCT
189390 TCAATTGAGC
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
11 27 0.42
12 37 0.58
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (11 bp):
GAATCGAGCTA
Found at i:189325 original size:23 final size:23
Alignment explanation
Indices: 189295--189425 Score: 163
Period size: 23 Copynumber: 5.7 Consensus size: 23
189285 GCAATGTCAT
189295 GCTTGAATCGAGCTCAGAATCGA
1 GCTTGAATCGAGCTCAGAATCGA
*
189318 GCTTGAATCGAGCTCATAATCGA
1 GCTTGAATCGAGCTCAGAATCGA
*
189341 TCTTGAATCGAGCTCAGAATCGA
1 GCTTGAATCGAGCTCAGAATCGA
* *
189364 TCTTGAATCGAGCTGAGAATCGA
1 GCTTGAATCGAGCTCAGAATCGA
* * **
189387 GCTTCAATTGAGCTCGAGTCTCGA
1 GCTTGAATCGAGCTC-AGAATCGA
* *
189411 GTTTTAATCGAGCTC
1 GCTTGAATCGAGCTC
189426 TTAATTTTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 76 0.81
24 18 0.19
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (23 bp):
GCTTGAATCGAGCTCAGAATCGA
Found at i:189680 original size:16 final size:16
Alignment explanation
Indices: 189629--189687 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
189619 GGGTCTCCAA
189629 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
189645 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
**
189661 CGTTTATGTTCGTGCG
1 CGTTTATGTTCGTGTT
189677 CGTTTATGTTC
1 CGTTTATGTTC
189688 ATTTATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.08, C:0.15, G:0.24, T:0.53
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:190606 original size:12 final size:10
Alignment explanation
Indices: 190574--190604 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
190564 TTTATCCCAC
190574 CAAATTCTCT
1 CAAATTCTCT
190584 CAAATTCTCT
1 CAAATTCTCT
*
190594 CAAATACTCT
1 CAAATTCTCT
190604 C
1 C
190605 TCTTTTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:190683 original size:17 final size:18
Alignment explanation
Indices: 190646--190686 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
190636 ATATTATGTA
*
190646 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
190664 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
190681 TTTACT
1 TTTACT
190687 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:190942 original size:111 final size:111
Alignment explanation
Indices: 190748--190969 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
190738 TGGAAATCAT
* * *
190748 ATATCTCTACACTTTACTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
190813 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
190859 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
190924 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
190970 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:192987 original size:26 final size:25
Alignment explanation
Indices: 192960--193028 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 25
192950 ATATTTGTAT
192960 TTACTTTATTTTGTTAAATTAAAAA
1 TTACTTTATTTTGTTAAATTAAAAA
* * * *
192985 TT--TTTATTATT-TATCATTTAATAC
1 TTACTTTATT-TTGT-TAAATTAAAAA
193009 TTACTTTATTTTGTTAAATT
1 TTACTTTATTTTGTTAAATT
193029 TGTTGGACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
23 7 0.21
24 11 0.33
25 8 0.24
26 7 0.21
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (25 bp):
TTACTTTATTTTGTTAAATTAAAAA
Found at i:193029 original size:26 final size:26
Alignment explanation
Indices: 192960--193029 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
192950 ATATTTGTAT
192960 TTACTTTATTTTGTTAAA-TTAAAAA
1 TTACTTTATTTTGTTAAATTTAAAAA
* * * *
192985 TT--TTTATTAT-TTATCATTTAATAC
1 TTACTTTATTTTGTTA-AATTTAAAAA
193009 TTACTTTATTTTGTTAAATTT
1 TTACTTTATTTTGTTAAATTT
193030 GTTGGACTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
22 3 0.09
23 8 0.24
24 7 0.21
25 2 0.06
26 11 0.32
27 3 0.09
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (26 bp):
TTACTTTATTTTGTTAAATTTAAAAA
Found at i:193096 original size:35 final size:33
Alignment explanation
Indices: 193057--193141 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
193047 GTATTTCAGT
193057 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
193092 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
193127 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
193142 TAAAATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:196392 original size:21 final size:20
Alignment explanation
Indices: 196368--196485 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 20
196358 AAGTTCCCAG
196368 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
196388 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
196409 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
196431 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
196451 AATCGCAACGCGAAAAT-ATA
1 AATCGCAACGCGATTATGA-A
196471 AATCGCAACGCGATT
1 AATCGCAACGCGATT
196486 TTAACTATCG
Statistics
Matches: 76, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
19 2 0.03
20 36 0.47
21 34 0.45
22 3 0.04
23 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:196456 original size:20 final size:20
Alignment explanation
Indices: 196431--196686 Score: 135
Period size: 20 Copynumber: 12.7 Consensus size: 20
196421 GATTTTCCAG
*
196431 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
**
196451 AATCGCAACGCGAA-AATATA
1 AATCGCAACGCGAATACGA-A
***
196471 AATCGCAACGCG-ATTTTAA
1 AATCGCAACGCGAATACGAA
* * * *
196490 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACG-AA
* * * * *
196512 AATCGTAACACGTATCCGTA
1 AATCGCAACGCGAATACGAA
196532 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * * *
196553 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
196573 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
196593 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
196613 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * * *
196633 AATCGTAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
196653 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
196674 AATCGCAACGCGA
1 AATCGCAACGCGA
196687 TCTCTGGTAT
Statistics
Matches: 182, Mismatches: 41, Indels: 25
0.73 0.17 0.10
Matches are distributed among these distances:
19 5 0.03
20 130 0.71
21 45 0.25
22 2 0.01
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:196607 original size:40 final size:41
Alignment explanation
Indices: 196492--196685 Score: 284
Period size: 40 Copynumber: 4.8 Consensus size: 41
196482 GATTTTAACT
* * * *
196492 ATCGCAACGAGTATCCGTAAAATCGTAACACGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
196533 ATCGCAACGACAATACGTAAAATCACAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
196574 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
196614 ATCGCAACGAGAATACGT-AAATCGTAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
196654 ATCGCAACGACAATACGTAAAATCGCAACGCG
1 ATCGCAACGAGAATACGTAAAATCGCAACGCG
196686 ATCTCTGGTA
Statistics
Matches: 137, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 74 0.54
41 63 0.46
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:196803 original size:20 final size:20
Alignment explanation
Indices: 196778--196865 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
196768 TTTTCCTAAT
196778 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
196798 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
**
196818 TCGCAATTCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
**
196838 TCGCAATACGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
196858 TCGCAACG
1 TCGCAACG
196866 AGAAATGGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 1 0.02
20 59 0.98
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:197369 original size:24 final size:24
Alignment explanation
Indices: 197342--197395 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
197332 GTATTCGAAA
197342 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
197366 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
197390 TTTGAT
1 TTTGAT
197396 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:197597 original size:14 final size:14
Alignment explanation
Indices: 197578--197614 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
197568 TATCAATTAA
197578 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
197592 ACAAATCATCTTTT
1 ACAAATCAACATTT
197606 ACAAATCAA
1 ACAAATCAA
197615 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:199072 original size:42 final size:42
Alignment explanation
Indices: 198965--199072 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
198955 TCTAGAATGT
* * *
198965 TGGGAG-GGACCTCTTCAACGATGATAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGATAGGGGCCTCTTGAACGA
* * **
199007 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
199049 TAGGG-GAGGCCTCTTGAACGATGA
1 T-GGGAGAGGCCTCTTGAACGATGA
199073 CAGGTGAGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 49 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:199579 original size:20 final size:20
Alignment explanation
Indices: 199556--199624 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
199546 GAAACTTAAA
199556 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
199576 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
199596 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
199616 ATCGCAACG
1 ATCGCAACG
199625 AGAGAATCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:199701 original size:19 final size:19
Alignment explanation
Indices: 199656--199703 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
199646 AAAATCGCAA
* * *
199656 TGCGATTATAGTTTCGCGT
1 TGCGATTTTGGTTTCACGT
*
199675 TGTGATTTTGGTTTCACGT
1 TGCGATTTTGGTTTCACGT
199694 TGCGATTTTG
1 TGCGATTTTG
199704 TCGTTGCGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCACGT
Found at i:199715 original size:33 final size:33
Alignment explanation
Indices: 199672--199796 Score: 146
Period size: 33 Copynumber: 3.8 Consensus size: 33
199662 TATAGTTTCG
* ** * *
199672 CGTTGTGATTTTGGTTTCACGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCACGTTGCGATTCTCT
*
199705 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCACGTTGCGATTCTCT
*
199738 CGTTGCGATTTTCATTTCTCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCACGTTGCGATTCTCT
* * *
199771 TGTTACGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCACGTTGCGAT
199797 AGTCATTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 17 0.21
33 65 0.79
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCACGTTGCGATTCTCT
Found at i:199729 original size:19 final size:19
Alignment explanation
Indices: 199705--199836 Score: 72
Period size: 19 Copynumber: 7.4 Consensus size: 19
199695 GCGATTTTGT
199705 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
199724 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
199738 CGTTGCGATTTTCATTTCT
1 CGTTGCGATTTTCATTTCG
*
199757 CGTTGCGATTCTC--TT--
1 CGTTGCGATTTTCATTTCG
*
199772 -GTTACGA--TTCATTTCG
1 CGTTGCGATTTTCATTTCG
** *
199788 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCG
*
199809 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
199829 TGTTGCGA
1 CGTTGCGA
199837 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 27
0.68 0.10 0.21
Matches are distributed among these distances:
12 2 0.02
14 18 0.21
16 3 0.03
17 11 0.13
19 26 0.30
20 11 0.13
21 15 0.17
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:199743 original size:14 final size:14
Alignment explanation
Indices: 199724--199781 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
199714 TTTCATTTCG
199724 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
199738 CGTTGCGATTTTCATTTCT
1 CGTTGCGA--TTC---TCT
199757 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
199771 TGTTACGATTC
1 CGTTGCGATTC
199782 ATTTCGCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 20 0.54
16 3 0.08
17 3 0.08
19 11 0.30
ACGTcount: A:0.10, C:0.24, G:0.19, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:200058 original size:94 final size:93
Alignment explanation
Indices: 199884--200171 Score: 450
Period size: 94 Copynumber: 3.1 Consensus size: 93
199874 ATGGATTGCA
* * *
199884 TTACTTCAACTAAAAGACAAAACAAAGACAAATACTAACTCTTCAGAGTATTAAAGAATACACAG
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAA--CTTCACAGTGTTAAAGAATACACAG
* * *
199949 TTTAGCATAATTGGCAGCAAACGAACAAAT
64 TTTAGCAGAATTGGCAGCAACCGAATAAAT
199979 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
200044 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
* *
200073 TTACTTCAACCAAAAGACAAAACAAAAGACATATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
200138 TTAGCAGTATTGGTAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
200167 TTACT
1 TTACT
200172 AAGCAATCTA
Statistics
Matches: 181, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
93 19 0.10
94 125 0.69
95 4 0.02
96 33 0.18
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:201885 original size:39 final size:35
Alignment explanation
Indices: 201842--201931 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 35
201832 TCTTTTGGTT
*
201842 GAAATGAAAATCGCAATGAGAGAATGACTATCGTAACGC
1 GAAATGAAAATCGCAATGAGAG-A-GA--ATCGCAACGC
*
201881 GAAATGAAAATCGCAA--CGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAATGAGAGAGAATCGCAACGC
201914 GAAATGAAAATCGCAATG
1 GAAATGAAAATCGCAATG
201932 CGATTTTGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
33 25 0.53
35 2 0.04
36 1 0.02
37 3 0.06
39 16 0.34
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (35 bp):
GAAATGAAAATCGCAATGAGAGAGAATCGCAACGC
Found at i:201893 original size:19 final size:19
Alignment explanation
Indices: 201842--201934 Score: 79
Period size: 19 Copynumber: 5.1 Consensus size: 19
201832 TCTTTTGGTT
* *
201842 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
** *
201861 GAGAATGACTATCGTAACGC
1 GA-AATGAAAATCGCAACGC
201881 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
201898 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
201914 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
201933 GA
1 GA
201935 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 27 0.47
20 14 0.25
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:201963 original size:19 final size:20
Alignment explanation
Indices: 201941--202037 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
201931 GCGATTTTGG
201941 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
*
201960 TTTCGCGTTGCAATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
* * **
201980 TTCTCTCGTTGTGATAGTCAT
1 TT-TCGCGTTGCGATTTTCAT
* *
202001 TTTCGTGTTGCAATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
**
202021 TTTCATGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
202038 AAGTTTAGAA
Statistics
Matches: 62, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
19 18 0.29
20 29 0.47
21 15 0.24
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:201990 original size:40 final size:41
Alignment explanation
Indices: 201946--202037 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
201936 TTTGGTTTCG
201946 CGTTGCGATTTTCA-TTTCGCGTTGCAATTTTCATTTCTC-T
1 CGTTGCGATTTTCATTTTCGCGTTGCAATTTTCATTT-TCAT
* ** *
201986 CGTTGTGATAGTCATTTTCGTGTTGCAATTTTCATTTTCAT
1 CGTTGCGATTTTCATTTTCGCGTTGCAATTTTCATTTTCAT
202027 -GTTGCGATTTT
1 CGTTGCGATTTT
202038 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 21 0.49
41 22 0.51
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.51
Consensus pattern (41 bp):
CGTTGCGATTTTCATTTTCGCGTTGCAATTTTCATTTTCAT
Found at i:202620 original size:20 final size:20
Alignment explanation
Indices: 202595--202767 Score: 204
Period size: 20 Copynumber: 8.6 Consensus size: 20
202585 CTTTAAAAAT
202595 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
202615 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
202635 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
202656 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
202676 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
202696 CGTGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
202716 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
202736 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
202757 CTCGTTGCGAT
1 CGCGTTGCGAT
202768 AGTCAGAATC
Statistics
Matches: 126, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
20 90 0.71
21 36 0.29
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:202681 original size:40 final size:41
Alignment explanation
Indices: 202597--202767 Score: 274
Period size: 40 Copynumber: 4.2 Consensus size: 41
202587 TTAAAAATCG
*
202597 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
202638 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
202678 CGTTGCGATTTACAGATACGTGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
202718 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
202759 CGTTGCGAT
1 CGTTGCGAT
202768 AGTCAGAATC
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 74 0.62
41 46 0.38
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:202799 original size:20 final size:20
Alignment explanation
Indices: 202776--202828 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
202766 ATAGTCAGAA
*
202776 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
202796 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
202816 CCGCGTTGCGATT
1 TCGCGTTGCGATT
202829 CTGGAAAATC
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:0.13, C:0.21, G:0.25, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Done.