Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004143.1 Hibiscus syriacus cultivar Beakdansim tig00009059_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: 81519
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Found at i:682 original size:21 final size:21
Alignment explanation
Indices: 656--706 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
646 GTTAGGGGAG
* *
656 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGATCGGTACT
677 TTACGTGATGAGATCGGTACT
1 TTACGTGATGAGATCGGTACT
698 TTACGTGAT
1 TTACGTGAT
707 AACAATGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (21 bp):
TTACGTGATGAGATCGGTACT
Found at i:763 original size:21 final size:21
Alignment explanation
Indices: 722--814 Score: 50
Period size: 21 Copynumber: 4.4 Consensus size: 21
712 TGGTGCATGG
*
722 CGTGATGAGGTACTGTCTTTA
1 CGTGATGAGGTAATGTCTTTA
*
743 CGTGGTGAGGTAGATGT-TTTA
1 CGTGATGAGGTA-ATGTCTTTA
* * *
764 TGCGATGA--CAATGGTGCTTTA
1 CGTGATGAGGTAAT-GT-CTTTA
* * *
785 TGTGGTGAGGT-ATCTACTTTA
1 CGTGATGAGGTAATGT-CTTTA
806 CGTGATGAG
1 CGTGATGAG
815 TAGCCGCTCT
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
18 2 0.04
19 3 0.06
21 43 0.81
22 5 0.09
ACGTcount: A:0.20, C:0.11, G:0.32, T:0.37
Consensus pattern (21 bp):
CGTGATGAGGTAATGTCTTTA
Found at i:1147 original size:21 final size:21
Alignment explanation
Indices: 1130--1204 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
1120 TGTCCCTCCT
* *
1130 ATCGTTCAAAAGGACCCTCTC
1 ATCGTTCAAGAGGCCCCTCTC
1151 ATCGTTCAAGAGGCCCCTCTC
1 ATCGTTCAAGAGGCCCCTCTC
*
1172 ATCGTTCAAGAGGCCCCTCCC
1 ATCGTTCAAGAGGCCCCTCTC
*
1193 ACCGTTCAAGAG
1 ATCGTTCAAGAG
1205 CCCGATTCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCTC
Found at i:1169 original size:42 final size:42
Alignment explanation
Indices: 1107--1204 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
1097 GATTCACCTG
* * *
1107 TCATCGTTCAATATGTCCCTC-CTATCGTTCAAAAGGACCCTC
1 TCATCGTTCAAGAGGCCCCTCTC-ATCGTTCAAAAGGACCCTC
* *
1149 TCATCGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCTCATCGTTCAAAAGGACCCTC
* *
1191 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
1205 CCCGATTCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCTCATCGTTCAAAAGGACCCTC
Found at i:2713 original size:20 final size:20
Alignment explanation
Indices: 2697--2736 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2687 CGATTTTTGT
2697 GTTGCGAATTTGATTTTCGC
1 GTTGCGAATTTGATTTTCGC
*
2717 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGATTTTCGC
2737 AACAATTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGATTTTCGC
Found at i:2762 original size:29 final size:29
Alignment explanation
Indices: 2720--2778 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2710 TTTTCGCGTT
*
2720 GCGAATTTGACTTTCGCAACAATTGCAAC
1 GCGAATTTGACTTTCGCAACAATCGCAAC
2749 GCGAATTTGACTTTCGCAACAATCGCAAC
1 GCGAATTTGACTTTCGCAACAATCGCAAC
2778 G
1 G
2779 TTTATATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (29 bp):
GCGAATTTGACTTTCGCAACAATCGCAAC
Found at i:4840 original size:21 final size:20
Alignment explanation
Indices: 4813--4909 Score: 104
Period size: 21 Copynumber: 4.7 Consensus size: 20
4803 AAGCACCTGT
4813 CATCGTTCAAGAGGCCTCTCC
1 CATCGTTCAAGAGGCC-CTCC
*
4834 TATCGTTCAAGAGGCCCTTCC
1 CATCGTTCAAGAGGCCC-TCC
* * *
4855 CACCATTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGG-CCCTCC
*
4876 CATCGTTCAGGAGGTCCCTCC
1 CATCGTTCAAGAGG-CCCTCC
*
4897 CACCGTTCAAGAG
1 CATCGTTCAAGAG
4910 CCCGATTCAC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
20 1 0.02
21 58 0.94
22 3 0.05
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.23
Consensus pattern (20 bp):
CATCGTTCAAGAGGCCCTCC
Found at i:4881 original size:42 final size:42
Alignment explanation
Indices: 4818--4909 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
4808 CCTGTCATCG
*
4818 TTCAAGAGGCCTCTCCTATCGTTCAAGAGG-CCCTTCCCACCA
1 TTCAAGAGGCCCCTCCTATCGTTCAAGAGGTCCC-TCCCACCA
* *
4860 TTCAAGAGGCCCCT-CTCATCGTTCAGGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCCT-ATCGTTCAAGAGGTCCCTCCCACCA
4902 TTCAAGAG
1 TTCAAGAG
4910 CCCGATTCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 2 0.04
42 40 0.89
43 3 0.07
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.23
Consensus pattern (42 bp):
TTCAAGAGGCCCCTCCTATCGTTCAAGAGGTCCCTCCCACCA
Found at i:6064 original size:22 final size:22
Alignment explanation
Indices: 6039--6095 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
6029 AACAGTGAAC
6039 AGTGGGGGAATCGATTCCCTGT
1 AGTGGGGGAATCGATTCCCTGT
6061 AGTGGGGGAATCGATTCCCTGT
1 AGTGGGGGAATCGATTCCCTGT
**
6083 AGCAGGGGAATCG
1 AGTGGGGGAATCG
6096 GTACCCTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.23
Consensus pattern (22 bp):
AGTGGGGGAATCGATTCCCTGT
Found at i:6826 original size:59 final size:59
Alignment explanation
Indices: 6732--6853 Score: 174
Period size: 59 Copynumber: 2.1 Consensus size: 59
6722 CTATCTCGAG
* *
6732 TATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATGTACTAGGTATCCTTAAGTACAGTCCCGAA
* ** *
6791 TATGACACATAAGGTCGTGCCCACCATATAG-ACTAGGTATCCTTTAGTGTATTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATAT-GTACTAGGTATCCTTAAGTACAGTCCCGAA
6850 TATG
1 TATG
6854 CAGCCTGCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 55 0.98
60 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATGTACTAGGTATCCTTAAGTACAGTCCCGAA
Found at i:9531 original size:14 final size:14
Alignment explanation
Indices: 9509--9542 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
9499 TGTTTAATTT
*
9509 ATTTATAAAAGTTG
1 ATTTGTAAAAGTTG
9523 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
9537 ATTTGT
1 ATTTGT
9543 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:0.18, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:9539 original size:78 final size:77
Alignment explanation
Indices: 9442--9605 Score: 240
Period size: 78 Copynumber: 2.1 Consensus size: 77
9432 GCTTGTTTAA
9442 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGA-TTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTT-ACTTGTTTAA
*
9506 TTTATTTATAAAAG
64 TTGATTTATAAAAG
* * ***
9520 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTACTTGTTTAATT
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTACTTGTTTAATT
*
9585 GATTTGTAAAAG
66 GATTTATAAAAG
9597 TTGATTTGT
1 TTGATTTGT
9606 TGTTTTAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
76 1 0.01
77 34 0.44
78 43 0.55
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.51
Consensus pattern (77 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTACTTGTTTAATT
GATTTATAAAAG
Found at i:9730 original size:20 final size:20
Alignment explanation
Indices: 9679--9730 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
9669 CAATGCGATT
*
9679 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGAAAGTCAAA
***
9699 TTCGCAACGCGAAAGTCAAA
1 TTCGCGTTGCGAAAGTCAAA
9719 TTCGCGTTGCGA
1 TTCGCGTTGCGA
9731 TTTTCGCGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (20 bp):
TTCGCGTTGCGAAAGTCAAA
Found at i:12324 original size:24 final size:24
Alignment explanation
Indices: 12290--12343 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
12280 CTGAAACATC
12290 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
12314 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
12338 ATCAAA
1 ATCAAA
12344 TTTCGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:12357 original size:24 final size:24
Alignment explanation
Indices: 12290--12357 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
12280 CTGAAACATC
* * *
12290 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
12314 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
12338 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
12358 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:13356 original size:40 final size:40
Alignment explanation
Indices: 13312--13442 Score: 183
Period size: 40 Copynumber: 3.3 Consensus size: 40
13302 ACTAAAACCT
13312 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
* * *
13352 GTTGCGAAAATAAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
* ** *
13392 GTTGCGAATTTAAAATTCAGTGTTGCGAATTTGAAAATCGT
1 GTTGCGAAATTAAAATTC-GTGTTGCGAATTCAAAAATCGA
13433 GTTGC-AAATT
1 GTTGCGAAATT
13443 TATTGGTCAT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 57 0.72
41 22 0.28
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
Found at i:13443 original size:20 final size:19
Alignment explanation
Indices: 13292--13444 Score: 128
Period size: 20 Copynumber: 7.7 Consensus size: 19
13282 TAAAATATTT
**
13292 GTGTTGCGAAACTAAAA-C
1 GTGTTGCGAATTTAAAATC
* *
13310 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAATTTAAAA-TC
*
13330 GTGTTGCGAATTCAAAAATC
1 GTGTTGCGAATT-TAAAATC
* **
13350 GAGTTGCGAAAATAAAATTC
1 GTGTTGCGAATTTAAAA-TC
* *
13370 GCGTTGCGAATTCAGAAATC
1 GTGTTGCGAATTTA-AAATC
*
13390 GAGTTGCGAATTTAAAATTC
1 GTGTTGCGAATTTAAAA-TC
13410 AGTGTTGCGAATTTGAAAATC
1 -GTGTTGCGAATTT-AAAATC
*
13431 GTGTTGCAAATTTA
1 GTGTTGCGAATTTA
13445 TTGGTCATTT
Statistics
Matches: 110, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
18 15 0.14
19 8 0.07
20 62 0.56
21 21 0.19
22 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (19 bp):
GTGTTGCGAATTTAAAATC
Found at i:19745 original size:18 final size:18
Alignment explanation
Indices: 19718--19768 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
19708 TCATGAGAAT
* *
19718 GTGCACGAAGATTTAAAG
1 GTGCAAGAAGATTCAAAG
19736 GTGCAAGAAGATTCAAAG
1 GTGCAAGAAGATTCAAAG
19754 GTGCAAGAAGATTCA
1 GTGCAAGAAGATTCA
19769 TATTCGCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (18 bp):
GTGCAAGAAGATTCAAAG
Found at i:28564 original size:15 final size:17
Alignment explanation
Indices: 28533--28564 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28523 ATATATTTTT
28533 ATCTATCTTGTAATTTA
1 ATCTATCTTGTAATTTA
28550 ATCTA-CTTG-AATTTA
1 ATCTATCTTGTAATTTA
28565 TTAGATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (17 bp):
ATCTATCTTGTAATTTA
Found at i:28695 original size:25 final size:25
Alignment explanation
Indices: 28666--28714 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
28656 GAAAGAAATA
*
28666 AAAAAAAAGTAAAAAAAACAAAAACT
1 AAAAATAA-TAAAAAAAACAAAAACT
* *
28692 AAAAATCATAAAAATAACAAAAA
1 AAAAATAATAAAAAAAACAAAAA
28715 AAATATAGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.80, C:0.08, G:0.02, T:0.10
Consensus pattern (25 bp):
AAAAATAATAAAAAAAACAAAAACT
Found at i:28868 original size:23 final size:23
Alignment explanation
Indices: 28816--28869 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
28806 TGAAATTCAT
* *
28816 CTCTAAAGTGGAGATTTTCTGTA
1 CTCTAACGTGGAGATTTTCTCTA
*
28839 TTCTAACGTGGAGATTTTCTCTA
1 CTCTAACGTGGAGATTTTCTCTA
28862 CTCTAACG
1 CTCTAACG
28870 ATGCGTTAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (23 bp):
CTCTAACGTGGAGATTTTCTCTA
Found at i:29815 original size:74 final size:74
Alignment explanation
Indices: 29694--29847 Score: 281
Period size: 74 Copynumber: 2.1 Consensus size: 74
29684 GTATTCCTCG
* *
29694 TAATTCTGGATACATAAAAGTTAGATCCTCATAGGCTTCGTCACTTCTAGAGGATTCAATTAAAC
1 TAATTCTGGATACATAAAAGTTAGATCCTCAAAGGCTTAGTCACTTCTAGAGGATTCAATTAAAC
29759 CATTGTTGT
66 CATTGTTGT
*
29768 TAATTCTGGATACATAAAAGTTAGATCCTCAAAGGCTTATTCACTTCTAGAGGATTCAATTAAAC
1 TAATTCTGGATACATAAAAGTTAGATCCTCAAAGGCTTAGTCACTTCTAGAGGATTCAATTAAAC
29833 CATTGTTGT
66 CATTGTTGT
29842 TAATTC
1 TAATTC
29848 CAACGGGATA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (74 bp):
TAATTCTGGATACATAAAAGTTAGATCCTCAAAGGCTTAGTCACTTCTAGAGGATTCAATTAAAC
CATTGTTGT
Found at i:33427 original size:36 final size:36
Alignment explanation
Indices: 33387--33489 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
33377 ACGATGTTGG
33387 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
33423 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
33459 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
33490 ATACTCAACT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:41682 original size:36 final size:36
Alignment explanation
Indices: 41642--41744 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
41632 ACGGTGCTGG
41642 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
41678 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
41714 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
41745 ATACTCAACT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:45864 original size:23 final size:23
Alignment explanation
Indices: 45824--45867 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
45814 GACTTGCGAC
45824 TTTTATTCTAGTTATTTGGATGA
1 TTTTATTCTAGTTATTTGGATGA
*
45847 TTTTATT-TATTTATTTTGGAT
1 TTTTATTCTAGTTA-TTTGGAT
45868 TTGGATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.20, C:0.02, G:0.14, T:0.64
Consensus pattern (23 bp):
TTTTATTCTAGTTATTTGGATGA
Found at i:45910 original size:24 final size:24
Alignment explanation
Indices: 45857--45901 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
45847 TTTTATTTAT
*
45857 TTAT-TTTGGATTTGGATATTTGG
1 TTATCTTTGGATTTGGAAATTTGG
45880 TTATCTTTGGATTTGGAAATTT
1 TTATCTTTGGATTTGGAAATTT
45902 TTTGCTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.56
Consensus pattern (24 bp):
TTATCTTTGGATTTGGAAATTTGG
Found at i:46577 original size:20 final size:20
Alignment explanation
Indices: 46549--46587 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46539 GTAAAAATGC
*
46549 ATAGCAGTACCGTTACTCCA
1 ATAGCAGTACCGATACTCCA
*
46569 ATAGGAGTACCGATACTCC
1 ATAGCAGTACCGATACTCC
46588 CTTTAAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (20 bp):
ATAGCAGTACCGATACTCCA
Found at i:49883 original size:23 final size:23
Alignment explanation
Indices: 49857--49920 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
49847 CAGCTCATAT
49857 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
49880 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
49903 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
49921 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:50110 original size:103 final size:103
Alignment explanation
Indices: 49931--50153 Score: 410
Period size: 103 Copynumber: 2.2 Consensus size: 103
49921 TATAATAATG
* *
49931 TCCCGAAGGACCACATATCACTCCTTAAGTATTATATACACATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACACATACTAGGGATCAAGTATGTGTCT
*
49996 CACCAGACTTCACACATGTTTCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
*
50034 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACACATACTAGGGATCAAGTATGTGTCT
50099 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
50137 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
50154 GACCCTCTAC
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 116 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACACATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:51020 original size:63 final size:63
Alignment explanation
Indices: 50895--51031 Score: 145
Period size: 63 Copynumber: 2.2 Consensus size: 63
50885 TCTTTTAATG
* * *
50895 AAGGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGTATTATT
1 AAGGGATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTGTATTATT
* * * * *
50958 ACGGGATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCCTTAT
1 AAGGGATGCATCGATGCACT-ACTGATGCATCGATGCA-TAAAATGCATTCGATGTTGT-ATTAT
51020 T
63 T
*
51021 AATGGATGCAT
1 AAGGGATGCAT
51032 TGCATTACTT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
62 2 0.03
63 58 0.95
64 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (63 bp):
AAGGGATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTGTATTATT
Found at i:55550 original size:23 final size:23
Alignment explanation
Indices: 55523--55586 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
55513 CAGCTCATAT
*
55523 AATTGCACCAAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
55546 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
55569 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
55587 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:55776 original size:103 final size:103
Alignment explanation
Indices: 55597--55819 Score: 410
Period size: 103 Copynumber: 2.2 Consensus size: 103
55587 TATAATAATG
*
55597 TCCCGAAGGACCACATATCACTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAAGACCACATATCACTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCT
55662 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
* *
55700 TCCCGAAAGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAATTATGTGTCT
1 TCCCGAAAGACCACATATCACTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCT
55765 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
*
55803 TCCCGAAAGATCACATA
1 TCCCGAAAGACCACATA
55820 GACCCTCGAC
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 116 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (103 bp):
TCCCGAAAGACCACATATCACTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:56679 original size:64 final size:63
Alignment explanation
Indices: 56571--56795 Score: 244
Period size: 64 Copynumber: 3.5 Consensus size: 63
56561 TAATGAAGGT
* * * * *
56571 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTATATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTTAT-TTATTAATGGG
*
56635 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTT-TCCTTATTAATGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTAT--TTATTAATGG
56698 G
63 G
* **
56699 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATG-TATTTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTATTTA--TTAATGGG
**
56762 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
56796 CTTCAAACAA
Statistics
Matches: 140, Mismatches: 13, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
62 3 0.02
63 5 0.04
64 130 0.93
65 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTATTTATTAATGGG
Found at i:61079 original size:18 final size:18
Alignment explanation
Indices: 61053--61088 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61043 AAGCAAAAGG
61053 AAATAAAAATCGCAATCA
1 AAATAAAAATCGCAATCA
* *
61071 AAATCAAAATCTCAATCA
1 AAATAAAAATCGCAATCA
61089 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.19, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATAAAAATCGCAATCA
Found at i:61342 original size:29 final size:29
Alignment explanation
Indices: 61300--61381 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
61290 AATTCGCAAC
*
61300 GCGAAAGTCAAATTCACGTTGCGATTGTT
1 GCGAAAGTCAAATTCACATTGCGATTGTT
*
61329 GCGAAAGTCAAATTCGCATTGCGATTGTT
1 GCGAAAGTCAAATTCACATTGCGATTGTT
* * *
61358 GCAAAAGTCAAATTCGCAATGCGA
1 GCGAAAGTCAAATTCACATTGCGA
61382 AAATCAAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (29 bp):
GCGAAAGTCAAATTCACATTGCGATTGTT
Found at i:62925 original size:21 final size:21
Alignment explanation
Indices: 62899--62999 Score: 123
Period size: 21 Copynumber: 4.8 Consensus size: 21
62889 GTGAATCGGG
* * *
62899 CTCTTGAACGGTGGGAGAGAC
1 CTCTTGAACGATGAGAGAGGC
*
62920 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGAGGC
*
62941 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGAGGC
62962 CTCTTGAACGATGAGAGCA-GC
1 CTCTTGAACGATGAGAG-AGGC
* *
62983 CTCTTGAATGATAAGAG
1 CTCTTGAACGATGAGAG
63000 GGATATCTTG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.27, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGAGGC
Found at i:62965 original size:42 final size:42
Alignment explanation
Indices: 62899--63017 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
62889 GTGAATCGGG
* * * **
62899 CTCTTGAACGGTGGGAGAGACCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGACCTCTTGAACGATGAGAGCAGC
*
62941 CTCTTGAACGATGAGAGGGGCCTCTTGAACGATGAGAGCAGC
1 CTCTTGAACGATGAGAGGGACCTCTTGAACGATGAGAGCAGC
* * ** *
62983 CTCTTGAATGATAAGAGGGATATCTTGAATGATGA
1 CTCTTGAACGATGAGAGGGACCTCTTGAACGATGA
63018 CAGGTGAATC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGATGAGAGGGACCTCTTGAACGATGAGAGCAGC
Found at i:63009 original size:63 final size:63
Alignment explanation
Indices: 62899--63017 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 63
62889 GTGAATCGGG
* * * * *
62899 CTCTTGAACGGTGGGAGAGACCTCTTGAACGATGAGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGAGACCTCTTGAACGATAAGAGGGACATCTTGAACGATGAGAGGGGC
* * *
62962 CTCTTGAACGATGAGAGCAG-CCTCTTGAATGATAAGAGGGATATCTTGAATGATGA
1 CTCTTGAACGATGAGAG-AGACCTCTTGAACGATAAGAGGGACATCTTGAACGATGA
63018 CAGGTGAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
63 45 0.96
64 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.23
Consensus pattern (63 bp):
CTCTTGAACGATGAGAGAGACCTCTTGAACGATAAGAGGGACATCTTGAACGATGAGAGGGGC
Found at i:63177 original size:4 final size:4
Alignment explanation
Indices: 63161--63190 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
63151 AGACCGCTAA
*
63161 AAAT AAAT TAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
63191 TGCTGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:63437 original size:21 final size:21
Alignment explanation
Indices: 63413--63462 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
63403 ACCATTGTCG
* *
63413 TCACGTAAAGTACCGACCTTA
1 TCACGTAAAGCACCGACCTCA
* *
63434 TCACGCAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
63455 TCACGTAA
1 TCACGTAA
63463 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:63667 original size:42 final size:42
Alignment explanation
Indices: 63571--63675 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
63561 GATGATGTGA
* * * * * *
63571 TGGAATAGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGGC
1 TGGATTAGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGC
* * * * *
63613 TCGATCAAGTGATGGCTCTGGGTGTCGAGCTGTAGAATCAGT
1 TGGATTAGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGC
63655 TGGATTAGGTGATGGCTCTCG
1 TGGATTAGGTGATGGCTCTCG
63676 AAGTGGGGGT
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.19, C:0.14, G:0.36, T:0.30
Consensus pattern (42 bp):
TGGATTAGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGC
Found at i:65227 original size:20 final size:20
Alignment explanation
Indices: 65202--65240 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
65192 TCGCGTTGCA
65202 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
65222 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
65241 AAGTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:65247 original size:20 final size:20
Alignment explanation
Indices: 65204--65247 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
65194 GCGTTGCAAT
* *
65204 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
65224 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
65244 TTTC
1 TTTC
65248 AAAAACTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:65740 original size:20 final size:20
Alignment explanation
Indices: 65715--65764 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
65705 GTTTCGAATT
65715 CGAAAATAAAATTCGCATTG
1 CGAAAATAAAATTCGCATTG
65735 CGAAAATAAAATTCGCATTG
1 CGAAAATAAAATTCGCATTG
65755 CGAAAATAAA
1 CGAAAATAAA
65765 CGCGCTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (20 bp):
CGAAAATAAAATTCGCATTG
Found at i:65776 original size:19 final size:20
Alignment explanation
Indices: 65715--65777 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
65705 GTTTCGAATT
**
65715 CGAAAATAAAATTCGCATTG
1 CGAAAATAAAACGCGCATTG
**
65735 CGAAAATAAAATTCGCATTG
1 CGAAAATAAAACGCGCATTG
*
65755 CGAAAAT-AAACGCGCTTTG
1 CGAAAATAAAACGCGCATTG
65774 CGAA
1 CGAA
65778 TTTGACTTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (20 bp):
CGAAAATAAAACGCGCATTG
Found at i:69567 original size:3 final size:3
Alignment explanation
Indices: 69559--69614 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
69549 TTTTAGTTTC
*
69559 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
69607 ATT ATT AT
1 ATT ATT AT
69615 GATTTTTTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:71695 original size:18 final size:17
Alignment explanation
Indices: 71672--71710 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
71662 TGTATATATG
*
71672 ATTATCCTCTTCCTTATC
1 ATTATCCTCTT-ATTATC
71690 ATTATCCTCTTATTATC
1 ATTATCCTCTTATTATC
71707 ATTA
1 ATTA
71711 ATACCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATCCTCTTATTATC
Found at i:72068 original size:31 final size:31
Alignment explanation
Indices: 72022--72141 Score: 163
Period size: 31 Copynumber: 3.9 Consensus size: 31
72012 GAAGGACCAG
* * * *
72022 TCCATAGGTTTCGAAGAACCTAGGTAATCAA
1 TCCATATGTTCCGAAGAACATAGGTAAACAA
72053 TCCATATGTTCCGAAGAACATAGGTAAACAA
1 TCCATATGTTCCGAAGAACATAGGTAAACAA
*
72084 TCCATATG-TCCAAAG-ACATAGGTAAACAA
1 TCCATATGTTCCGAAGAACATAGGTAAACAA
* *
72113 TCCATATGTCCCGAAGAACGTAGGTAAAC
1 TCCATATGTTCCGAAGAACATAGGTAAAC
72142 CCTCGACCCT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
29 22 0.28
30 11 0.14
31 46 0.58
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (31 bp):
TCCATATGTTCCGAAGAACATAGGTAAACAA
Found at i:72971 original size:30 final size:30
Alignment explanation
Indices: 72912--72994 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
72902 CCCGAAGGAC
* *
72912 CTATCCAGAGGTCATAAAG-ACCCCGACAA
1 CTATCCATAGGTCATAAAGAACCTCGACAA
72941 CTATCCATAGGTCATAAAGAACCTCGACAA
1 CTATCCATAGGTCATAAAGAACCTCGACAA
* **
72971 CTGTCCATAGGTCCCAAAGAACCT
1 CTATCCATAGGTCATAAAGAACCT
72995 AGGTAAACTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 18 0.38
30 30 0.62
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (30 bp):
CTATCCATAGGTCATAAAGAACCTCGACAA
Found at i:73007 original size:31 final size:31
Alignment explanation
Indices: 72939--73033 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
72929 AGACCCCGAC
* ** *
72939 AACTATCCATAGGTCATAAAGAACCT-CG-A
1 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
72968 CAACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 -AACTGTCCATAGGTCCCAAAGAACCTAGGTA
* * *
73000 AACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATAGGTC-CCAAAGAACCTAGGTA
73031 AAC
1 AAC
73034 CCTCAACTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
30 23 0.42
31 26 0.47
32 6 0.11
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCAAAGAACCTAGGTA
Found at i:78319 original size:21 final size:21
Alignment explanation
Indices: 78295--78338 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
78285 AAGCAAAATT
78295 GTGCATCGATGAACTGCTACA
1 GTGCATCGATGAACTGCTACA
*
78316 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGAACTGCTACA
78337 GT
1 GT
78339 ACTACTACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGAACTGCTACA
Found at i:78782 original size:18 final size:17
Alignment explanation
Indices: 78759--78797 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
78749 TATATATATG
*
78759 ATTATCCTCTTCCTTATC
1 ATTATCCTCTT-ATTATC
78777 ATTATCCTCTTATTATC
1 ATTATCCTCTTATTATC
78794 ATTA
1 ATTA
78798 ATACATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATCCTCTTATTATC
Found at i:79234 original size:31 final size:31
Alignment explanation
Indices: 79112--79235 Score: 176
Period size: 31 Copynumber: 4.0 Consensus size: 31
79102 CCGAAGGACT
* * * * *
79112 AGTCCATAGGTTCTGAAGAACCTAGGTAATC
1 AGTCCATATGTCCCGAAGAACATAGGTAAAC
* *
79143 AGTCCATATGTTCCGAAGAACATAGGTAAAT
1 AGTCCATATGTCCCGAAGAACATAGGTAAAC
79174 AGTCCATATGTCCCGAAGAACATAGGTAAAC
1 AGTCCATATGTCCCGAAGAACATAGGTAAAC
*
79205 AGTCTATATGTCCCGAAGAACATAGGTAAAC
1 AGTCCATATGTCCCGAAGAACATAGGTAAAC
79236 CCTCGACCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (31 bp):
AGTCCATATGTCCCGAAGAACATAGGTAAAC
Found at i:81435 original size:21 final size:20
Alignment explanation
Indices: 81411--81460 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
81401 AACTTTTTGG
81411 GAAACTGTCTTG-GAAAGTTTC
1 GAAACT-TCTTGAGAAA-TTTC
81432 GAAAC-TCTTGTAGAAATTTC
1 GAAACTTCTTG-AGAAATTTC
81452 GAAACTTCT
1 GAAACTTCT
81461 GGTCAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.19
20 9 0.35
21 12 0.46
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
GAAACTTCTTGAGAAATTTC
Done.