Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000017.1 Hibiscus syriacus cultivar Beakdansim tig00000032_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: 94146
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2844 original size:23 final size:23
Alignment explanation
Indices: 2762--2840 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
2752 TTAGTACAGA
*
2762 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
*
2785 GGGAACTGATACCCCCCTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
* * *
2808 GGGAATCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCCCTTGAAG
2831 GGGAACCGAT
1 GGGAACCGAT
2841 TCCCACCCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (23 bp):
GGGAACCGATACCCCCCTTGAAG
Found at i:4465 original size:18 final size:18
Alignment explanation
Indices: 4444--4484 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4434 AGAACAACAC
4444 GAGGAACAAGAACGAG-CA
1 GAGGAACAAGAAC-AGCCA
*
4462 GAGGAACAAGCACAGCCA
1 GAGGAACAAGAACAGCCA
4480 GAGGA
1 GAGGA
4485 TCAAATTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.46, C:0.20, G:0.34, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGAACAGCCA
Found at i:10870 original size:20 final size:20
Alignment explanation
Indices: 10845--10887 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
10835 TCTAAAAGCC
*
10845 CATTTAGGATCATATAGATG
1 CATTTAGGAACATATAGATG
*
10865 CATTTAGGAACATATAGTTG
1 CATTTAGGAACATATAGATG
10885 CAT
1 CAT
10888 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (20 bp):
CATTTAGGAACATATAGATG
Found at i:16482 original size:6 final size:6
Alignment explanation
Indices: 16467--16502 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
16457 ACTTTGTAAA
*
16467 AAAAAG AAAAGAA AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAA
16503 ATGAAGCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:16483 original size:13 final size:12
Alignment explanation
Indices: 16464--16503 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
16454 CCCACTTTGT
16464 AAAAAAAAGAAA
1 AAAAAAAAGAAA
16476 AGAAAAAAAGAAA
1 A-AAAAAAAGAAA
*
16489 AAGAAAAAGAAA
1 AAAAAAAAGAAA
16501 AAA
1 AAA
16504 TGAAGCTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:16503 original size:14 final size:13
Alignment explanation
Indices: 16465--16501 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
16455 CCACTTTGTA
16465 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
16478 AAAAAAAGAAAA-
1 AAAAAAAGAAAAG
*
16490 AGAAAAAGAAAA
1 AAAAAAAGAAAA
16502 AATGAAGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:17140 original size:20 final size:20
Alignment explanation
Indices: 17115--17157 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17105 TCTAAAAGTC
*
17115 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
17135 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
17155 CAT
1 CAT
17158 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:18768 original size:24 final size:23
Alignment explanation
Indices: 18715--18791 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 23
18705 CACATATTTG
*
18715 TCCCGAAGGACAGCGTA-GTTTTA
1 TCCCGAAGGACA-CATAGGTTTTA
* *
18738 TCTCGAAGGATCACATAGGTTTTG
1 TCCCGAAGGA-CACATAGGTTTTA
18762 TCCCGAAGGACCACATAGG-TTTA
1 TCCCGAAGGA-CACATAGGTTTTA
18785 TCCCGAA
1 TCCCGAA
18792 TGACCAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.48
24 24 0.52
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (23 bp):
TCCCGAAGGACACATAGGTTTTA
Found at i:18796 original size:23 final size:24
Alignment explanation
Indices: 18715--18802 Score: 92
Period size: 23 Copynumber: 3.8 Consensus size: 24
18705 CACATATTTG
*
18715 TCCCGAAGGA-CAGCGTA-GTTTTA
1 TCCCGAAGGACCA-CATAGGTTTTA
* * *
18738 TCTCGAAGGATCACATAGGTTTTG
1 TCCCGAAGGACCACATAGGTTTTA
18762 TCCCGAAGGACCACATAGG-TTTA
1 TCCCGAAGGACCACATAGGTTTTA
* *
18785 TCCCGAATGACCAAATAG
1 TCCCGAAGGACCACATAG
18803 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 31 0.56
24 24 0.44
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (24 bp):
TCCCGAAGGACCACATAGGTTTTA
Found at i:18967 original size:19 final size:20
Alignment explanation
Indices: 18943--18980 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
18933 TTTTCGTATA
*
18943 CACATATTCATAT-CACATT
1 CACATAATCATATACACATT
18962 CACATAATCATATACACAT
1 CACATAATCATATACACAT
18981 AACCATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (20 bp):
CACATAATCATATACACATT
Found at i:21089 original size:19 final size:19
Alignment explanation
Indices: 21065--21111 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
21055 AATGATTTTC
* * *
21065 TTTGAAATCAAAATTAGAT
1 TTTGAAAACAAAATGAAAT
21084 TTTGAAAAACAAAATGAAAT
1 TTTG-AAAACAAAATGAAAT
21104 TTTGAAAA
1 TTTGAAAA
21112 ATGATTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (19 bp):
TTTGAAAACAAAATGAAAT
Found at i:22856 original size:17 final size:17
Alignment explanation
Indices: 22834--22878 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
22824 ATTTGGTTTT
22834 TTTTTTAT-TAAATTCAG
1 TTTTTTATGTAAATT-AG
22851 TTTTTTATGTAAATTAG
1 TTTTTTATGTAAATTAG
*
22868 TTTGTTATGTA
1 TTTTTTATGTA
22879 TCCGATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (17 bp):
TTTTTTATGTAAATTAG
Found at i:26369 original size:2 final size:2
Alignment explanation
Indices: 26362--26396 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
26352 TTAATTGCTT
26362 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26397 GAAATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27586 original size:10 final size:10
Alignment explanation
Indices: 27572--27638 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
27562 CGACTCGACC
27572 CGTTGACCAG
1 CGTTGACCAG
*
27582 TGTTGA-C--
1 CGTTGACCAG
27589 CGTTGACCAG
1 CGTTGACCAG
* *
27599 CGTTAACCAC
1 CGTTGACCAG
27609 CGTTGACCAG
1 CGTTGACCAG
* *
27619 AACTTTGACCGG
1 --CGTTGACCAG
27631 CGTTGACC
1 CGTTGACC
27639 GACCCTTGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
7 5 0.12
8 1 0.02
9 1 0.02
10 28 0.65
12 8 0.19
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.24
Consensus pattern (10 bp):
CGTTGACCAG
Found at i:29807 original size:24 final size:24
Alignment explanation
Indices: 29777--29845 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
29767 TACATGACCT
29777 GATTCTGTTCTGATTTTTGATCTG
1 GATTCTGTTCTGATTTTTGATCTG
*
29801 GATTCTGTTCTGATATCTT-ATCTG
1 GATTCTGTTCTGAT-TTTTGATCTG
* * *
29825 AATTCTGTTTTGATTTCTGAT
1 GATTCTGTTCTGATTTTTGAT
29846 ATCTTCGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 2 0.05
24 33 0.87
25 3 0.08
ACGTcount: A:0.16, C:0.13, G:0.17, T:0.54
Consensus pattern (24 bp):
GATTCTGTTCTGATTTTTGATCTG
Found at i:29812 original size:12 final size:11
Alignment explanation
Indices: 29775--29839 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 11
29765 GATACATGAC
29775 CTGATTCTGTT
1 CTGATTCTGTT
* *
29786 CTGATTTTTGAT
1 CTGA-TTCTGTT
29798 CTGGATTCTGTT
1 CT-GATTCTGTT
29810 CTGATATCT-TAT
1 CTGAT-TCTGT-T
29822 CTGAATTCTGTT
1 CTG-ATTCTGTT
*
29834 TTGATT
1 CTGATT
29840 TCTGATATCT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
11 11 0.26
12 27 0.63
13 5 0.12
ACGTcount: A:0.15, C:0.14, G:0.17, T:0.54
Consensus pattern (11 bp):
CTGATTCTGTT
Found at i:32924 original size:23 final size:24
Alignment explanation
Indices: 32897--32955 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
32887 CCACGAGCAA
*
32897 AAGAGAAGAAAATT-ATCAATATT
1 AAGAGAAGAAAATTCATCAATATC
* *
32920 GAGAGAAGAAAATTCATCAATGTC
1 AAGAGAAGAAAATTCATCAATATC
32944 AAGAGAAGAAAA
1 AAGAGAAGAAAA
32956 ATACAAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (24 bp):
AAGAGAAGAAAATTCATCAATATC
Found at i:45862 original size:128 final size:127
Alignment explanation
Indices: 45548--46052 Score: 498
Period size: 127 Copynumber: 3.9 Consensus size: 127
45538 GATGACAAAG
* * * ** *
45548 CTCCTACATAATGAGGAGATCTAGTCAGG-GAATAACACTTCTTATACATGATGAAGAGTTCTTG
1 CTCCTACATAATGAGGAGATATGGTCAGGTG-ATGACACGGCTCATACATGATGAAGAGTTC-TG
* * *
45612 GCCATCTTTATGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTATCAAAGGTTG
64 GCCATC--TA--AA-GGTGATAACACGGTTCCTACATGATGAGGACGA-TGGTTATC-AGGGTTG
*
45677 ACACGA
122 ACATGA
* * * *
45683 CTCCTACATAATAAGAAGATCA-GGTCGGGTGATGACACGGCTCATACATGATGAAGATTTCTGG
1 CTCCTACATAATGAGGAGAT-ATGGTCAGGTGATGACACGGCTCATACATGATGAAGAGTTCTGG
* * * *
45747 CCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGGATGGCTATCTGGGTTTACATAA
65 CCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGAC-GATGGTTATCAGGGTTGACATGA
* * *
45811 CTCCTACATAATGAGGAGATATGGTCAGTTGATTACACGACTCATACATGATGAAGAGTTCTGGC
1 CTCCTACATAATGAGGAGATATGGTCAGGTGATGACACGGCTCATACATGATGAAGAGTTCTGGC
* * * *
45876 CATCTAAAGGTGATAACACTGCTCATACTATGATGA--ATC-TTGGTTATCCAGGGTTGACATGA
66 CATCTAAAGGTGATAACACGGTTCCTAC-ATGATGAGGA-CGATGGTTAT-CAGGGTTGACATGA
* * * * * * *
45938 CTCCTACGTGATGAGGAGATCTGGTCGGGTGATGACACGGTTCATACGTGATGAAGAGTTTTGGC
1 CTCCTACATAATGAGGAGATATGGTCAGGTGATGACACGGCTCATACATGATGAAGAGTTCTGGC
* * ** * *
46003 CATCTAAGGGTGATAACACTGTTCCTATGTGATAAGGACTACTGGTTATC
66 CATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGA-TGGTTATC
46053 TAAAGTTGAC
Statistics
Matches: 309, Mismatches: 50, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
126 11 0.04
127 93 0.30
128 92 0.30
129 50 0.16
130 4 0.01
132 2 0.01
134 8 0.03
135 48 0.16
136 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (127 bp):
CTCCTACATAATGAGGAGATATGGTCAGGTGATGACACGGCTCATACATGATGAAGAGTTCTGGC
CATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGATGGTTATCAGGGTTGACATGA
Found at i:45990 original size:127 final size:127
Alignment explanation
Indices: 45548--46023 Score: 474
Period size: 128 Copynumber: 3.7 Consensus size: 127
45538 GATGACAAAG
* * * ** *
45548 CTCCTACATAATGAGGAGATCTAGTCAGGG-AATAACACTTCTTATACATGATGAAGAGTTCTTG
1 CTCCTACATAATGAGGAGATCTGGTC-GGGTGATGACACGGCTCATACATGATGAAGAGTTC-TG
* * * * * * *
45612 GCCATCTTTATGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTATCAAAGGTTG
64 GCCATC--TA--AA-GGTGATAACACTGCTCATACATGATGA-GACGA-TGGTTATCCAGGGTTG
*
45677 ACACGA
122 ACATGA
* * * *
45683 CTCCTACATAATAAGAAGATCAGGTCGGGTGATGACACGGCTCATACATGATGAAGATTTCTGGC
1 CTCCTACATAATGAGGAGATCTGGTCGGGTGATGACACGGCTCATACATGATGAAGAGTTCTGGC
* * * * * * *
45748 CATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGGATGGCTAT-CTGGGTTTACATAA
66 CATCTAAAGGTGATAACACTGCTCATACATGATGA-GAC-GATGGTTATCCAGGGTTGACATGA
* * * * *
45811 CTCCTACATAATGAGGAGATATGGTCAGTTGATTACACGACTCATACATGATGAAGAGTTCTGGC
1 CTCCTACATAATGAGGAGATCTGGTCGGGTGATGACACGGCTCATACATGATGAAGAGTTCTGGC
*
45876 CATCTAAAGGTGATAACACTGCTCATACTATGATGA-ATC-TTGGTTATCCAGGGTTGACATGA
66 CATCTAAAGGTGATAACACTGCTCATAC-ATGATGAGA-CGATGGTTATCCAGGGTTGACATGA
* * * * *
45938 CTCCTACGTGATGAGGAGATCTGGTCGGGTGATGACACGGTTCATACGTGATGAAGAGTTTTGGC
1 CTCCTACATAATGAGGAGATCTGGTCGGGTGATGACACGGCTCATACATGATGAAGAGTTCTGGC
*
46003 CATCTAAGGGTGATAACACTG
66 CATCTAAAGGTGATAACACTG
46024 TTCCTATGTG
Statistics
Matches: 289, Mismatches: 47, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
126 6 0.02
127 87 0.30
128 90 0.31
129 42 0.15
130 4 0.01
132 2 0.01
134 11 0.04
135 47 0.16
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (127 bp):
CTCCTACATAATGAGGAGATCTGGTCGGGTGATGACACGGCTCATACATGATGAAGAGTTCTGGC
CATCTAAAGGTGATAACACTGCTCATACATGATGAGACGATGGTTATCCAGGGTTGACATGA
Found at i:46103 original size:129 final size:130
Alignment explanation
Indices: 45540--46103 Score: 471
Period size: 129 Copynumber: 4.4 Consensus size: 130
45530 CGTCTAAGGA
* * * * ** *
45540 TGACAAAG-CTCCTACATAATGAGGAGATCTA-GTCAGGG-AATAACACTTCTTATACATGATGA
1 TGACACAGACTCCTACATAATGAAGAGATC-AGGTC-GGGTGATGACACGGCTCATACATGATGA
* *
45602 AGAGTTCTTGGCCATCTTTATGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTA
64 AGAGTT-TTGGCCATC--TA--AA-GGTGATAACACGGTTCCTACATGATGAGGACGACTGGTTA
45667 TC-AAAGGT
123 TCTAAA-GT
45675 TGACAC-GACTCCTACATAAT-AAGAAGATCAGGTCGGGTGATGACACGGCTCATACATGATGAA
1 TGACACAGACTCCTACATAATGAAG-AGATCAGGTCGGGTGATGACACGGCTCATACATGATGAA
* *
45738 GA-TTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGGA-TGGCTATCT-G
65 GAGTTT-TGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGAC-GACTGGTTATCTAA
*
45800 GGT
128 AGT
* * * * * * *
45803 TTACATA-ACTCCTACATAATGAGGAGAT-ATGGTCAGTTGATTACACGACTCATACATGATGAA
1 TGACACAGACTCCTACATAATGAAGAGATCA-GGTCGGGTGATGACACGGCTCATACATGATGAA
* * * * * * *
45866 GAGTTCTGGCCATCTAAAGGTGATAACACTGCTCATACTATGATGA--ATC--TTGGTTATCCAG
65 GAGTTTTGGCCATCTAAAGGTGATAACACGGTTCCTAC-ATGATGAGGA-CGACTGGTTATCTAA
*
45927 GGT
128 AGT
* * * * * * *
45930 TGACA-TGACTCCTACGTGATGAGGAGATCTGGTCGGGTGATGACACGGTTCATACGTGATGAAG
1 TGACACAGACTCCTACATAATGAAGAGATCAGGTCGGGTGATGACACGGCTCATACATGATGAAG
* * ** * *
45994 AGTTTTGGCCATCTAAGGGTGATAACACTGTTCCTATGTGATAAGGACTACTGGTTATCTAAAGT
66 AGTTTTGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGACTGGTTATCTAAAGT
* * *
46059 TGACACAG-CTCCAACGTGATGAAGAGATCAGGTC-GGTGGATGACA
1 TGACACAGACTCCTACATAATGAAGAGATCAGGTCGGGT-GATGACA
46104 AATTGTTGTG
Statistics
Matches: 355, Mismatches: 51, Indels: 52
0.78 0.11 0.11
Matches are distributed among these distances:
126 12 0.03
127 90 0.25
128 88 0.25
129 93 0.26
130 5 0.01
132 2 0.01
133 1 0.00
134 17 0.05
135 47 0.13
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (130 bp):
TGACACAGACTCCTACATAATGAAGAGATCAGGTCGGGTGATGACACGGCTCATACATGATGAAG
AGTTTTGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGACTGGTTATCTAAAGT
Found at i:47155 original size:32 final size:32
Alignment explanation
Indices: 47111--47193 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
47101 TATCAGGATG
*
47111 TTGAATCCCCAAAGATGCCCCAACATTCAATA
1 TTGAATCTCCAAAGATGCCCCAACATTCAATA
* * * *
47143 TTGAATCTCCAAAAATACCCCAACATTTAATG
1 TTGAATCTCCAAAGATGCCCCAACATTCAATA
*
47175 TTGAATCTTCAAAGATGCC
1 TTGAATCTCCAAAGATGCC
47194 ATCTATTGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (32 bp):
TTGAATCTCCAAAGATGCCCCAACATTCAATA
Found at i:48249 original size:10 final size:9
Alignment explanation
Indices: 48234--48281 Score: 51
Period size: 10 Copynumber: 4.9 Consensus size: 9
48224 TTGCCTTTTC
48234 TTTTTCTTCT
1 TTTTTCTT-T
48244 TTTTTCTTT
1 TTTTTCTTT
48253 TCTTTTCTTTT
1 T-TTTTC-TTT
48264 CTTTTTCTTT
1 -TTTTTCTTT
*
48274 TTATTCTT
1 TTTTTCTT
48282 CTTCAAGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 9 0.26
10 16 0.47
11 8 0.24
12 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:48253 original size:5 final size:5
Alignment explanation
Indices: 48228--48274 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
48218 TTGCCTTTGC
48228 CTTTT CTTTTT CTTCTT -TTTT CTTTT CTTTT CTTTT CTTTTT CTTTT
1 CTTTT C-TTTT CTT-TT CTTTT CTTTT CTTTT CTTTT C-TTTT CTTTT
48275 TATTCTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 2 0.05
5 24 0.63
6 12 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
CTTTT
Found at i:48253 original size:15 final size:15
Alignment explanation
Indices: 48229--48281 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
48219 TGCCTTTGCC
48229 TTTTCTTTTTCTTCTT
1 TTTTCTTTTTCTT-TT
48245 TTTTC-TTTTCTTTT
1 TTTTCTTTTTCTTTT
48259 CTTTTCTTTTTCTTTT
1 -TTTTCTTTTTCTTTT
*
48275 TATTCTT
1 TTTTCTT
48282 CTTCAAGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
14 2 0.06
15 18 0.53
16 14 0.41
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:48254 original size:21 final size:21
Alignment explanation
Indices: 48228--48283 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
48218 TTGCCTTTGC
48228 CTTTTCTTTTTCTTCT-TTTTT
1 CTTTTC-TTTTCTTCTCTTTTT
*
48249 CTTTTCTTTTCTTTTCTTTTT
1 CTTTTCTTTTCTTCTCTTTTT
*
48270 CTTTT-TATTCTTCT
1 CTTTTCTTTTCTTCT
48284 TCAAGTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (21 bp):
CTTTTCTTTTCTTCTCTTTTT
Found at i:52216 original size:27 final size:25
Alignment explanation
Indices: 52179--52228 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 25
52169 GAAAATGCTT
52179 AAAAATGAAATGCATATGCAAAATG
1 AAAAATGAAATGCATATGCAAAATG
52204 AAAAGATGCAAATGCATATGCAAAA
1 AAAA-ATG-AAATGCATATGCAAAA
52229 ATGTTGATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 16 0.70
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.18
Consensus pattern (25 bp):
AAAAATGAAATGCATATGCAAAATG
Found at i:54412 original size:30 final size:29
Alignment explanation
Indices: 54339--54493 Score: 87
Period size: 30 Copynumber: 5.2 Consensus size: 29
54329 TGTAAAGGAT
* * * **
54339 TAAAATAGTATAAACAAAAATTTAAAGGTT
1 TAAAATAGTAAAAAC-AAAACTTAAAAGAC
** *
54369 TAAAATAACAAAAATCACAACTTAAAAGAC
1 TAAAATAGTAAAAA-CAAAACTTAAAAGAC
* * *
54399 TAAAATAGTAAAAA-ATGAACCTTAAGATAC
1 TAAAATAGTAAAAACA--AAACTTAAAAGAC
* * **
54429 TAAAATGGTAAAAACAAAAATTTAATGGAC
1 TAAAATAGTAAAAAC-AAAACTTAAAAGAC
* * *
54459 AAAAATAGTAAAAACTAGAATTTAAAAGAC
1 TAAAATAGTAAAAAC-AAAACTTAAAAGAC
54489 TAAAA
1 TAAAA
54494 AAATTTAAGG
Statistics
Matches: 93, Mismatches: 27, Indels: 10
0.72 0.21 0.08
Matches are distributed among these distances:
28 1 0.01
30 90 0.97
31 1 0.01
32 1 0.01
ACGTcount: A:0.60, C:0.08, G:0.09, T:0.23
Consensus pattern (29 bp):
TAAAATAGTAAAAACAAAACTTAAAAGAC
Found at i:55223 original size:14 final size:14
Alignment explanation
Indices: 55204--55232 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55194 TAAATCGGTG
55204 GTTTTTGCTATCTC
1 GTTTTTGCTATCTC
55218 GTTTTTGCTATCTC
1 GTTTTTGCTATCTC
55232 G
1 G
55233 GCCACCACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.17, T:0.55
Consensus pattern (14 bp):
GTTTTTGCTATCTC
Found at i:56096 original size:3 final size:3
Alignment explanation
Indices: 56075--56125 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
56065 TGCAAATATT
* *
56075 ATA AT- ATA ATT AGA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
56120 ATA ATA
1 ATA ATA
56126 TTTTTTTGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:59742 original size:50 final size:51
Alignment explanation
Indices: 59616--59750 Score: 182
Period size: 51 Copynumber: 2.7 Consensus size: 51
59606 TTCATACTAC
* *
59616 AAAAAGTGTAACACTTAACACATATTTACACCGGTGTAAGTGAATAAAATA
1 AAAAAGTGTAACACTTAACACATACTTACACTGGTGTAAGTGAATAAAATA
*** ** *
59667 AAAAAACATAACACTTAATGCATACTTACACTGGTGTGAGTGAATAAAAT-
1 AAAAAGTGTAACACTTAACACATACTTACACTGGTGTAAGTGAATAAAATA
*
59717 AAAAAGTGTAGCACTTAACACATACTTACACTGG
1 AAAAAGTGTAACACTTAACACATACTTACACTGG
59751 CATAAGTATG
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
50 28 0.40
51 42 0.60
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (51 bp):
AAAAAGTGTAACACTTAACACATACTTACACTGGTGTAAGTGAATAAAATA
Found at i:60492 original size:25 final size:25
Alignment explanation
Indices: 60464--60534 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
60454 AAAATGGAGT
60464 AAAAATA-TATTGATATTTTTTCAAC
1 AAAAATAGTA-TGATATTTTTTCAAC
60489 -AAAATAGGTATGATATTTTTTCAAC
1 AAAAATA-GTATGATATTTTTTCAAC
*
60514 -AAAATAGGTATGATTTTTTTT
1 AAAAATA-GTATGATATTTTTT
60535 ATTTTTAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
24 6 0.14
25 35 0.81
26 2 0.05
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (25 bp):
AAAAATAGTATGATATTTTTTCAAC
Found at i:60529 original size:23 final size:24
Alignment explanation
Indices: 60478--60533 Score: 94
Period size: 25 Copynumber: 2.3 Consensus size: 24
60468 ATATATTGAT
60478 ATTTTTTCAACAAAATAGGTATGA
1 ATTTTTTCAACAAAATAGGTATGA
60502 TATTTTTTCAACAAAATAGGTATGA
1 -ATTTTTTCAACAAAATAGGTATGA
*
60527 TTTTTTT
1 ATTTTTT
60534 TATTTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 6 0.20
25 24 0.80
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (24 bp):
ATTTTTTCAACAAAATAGGTATGA
Found at i:62717 original size:27 final size:27
Alignment explanation
Indices: 62686--62742 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
62676 ATCTGCTGGA
* *
62686 CTTCTCGGGTCTGGGCCTCCGA-TTTAT
1 CTTCTCAGGTCTGGACCTCC-ATTTTAT
*
62713 CTTCTCAGGTCTTGACCTCCATTTTAT
1 CTTCTCAGGTCTGGACCTCCATTTTAT
62740 CTT
1 CTT
62743 TGGGTTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.11, C:0.30, G:0.18, T:0.42
Consensus pattern (27 bp):
CTTCTCAGGTCTGGACCTCCATTTTAT
Found at i:63218 original size:9 final size:9
Alignment explanation
Indices: 63201--63309 Score: 56
Period size: 10 Copynumber: 12.4 Consensus size: 9
63191 ATGAAAAAAG
63201 AATAATAAA
1 AATAATAAA
*
63210 AAT-ATTAA
1 AATAATAAA
*
63218 AATAATAAT
1 AATAATAAA
*
63227 AGTAAT-AA
1 AATAATAAA
63235 AATAAATAAA
1 AAT-AATAAA
63245 AATAAATAAA
1 AAT-AATAAA
* *
63255 ATTGAGTAAA
1 AAT-AATAAA
63265 AATAA-AATA
1 AATAATAA-A
63274 AAT-A-AAA
1 AATAATAAA
63281 AATGAA-ATAA
1 AAT-AATA-AA
63291 AAT-A-AAA
1 AATAATAAA
63298 AATAA-AAA
1 AATAATAAA
63306 AATA
1 AATA
63310 TGGTTAAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
7 9 0.11
8 25 0.31
9 21 0.26
10 26 0.32
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (9 bp):
AATAATAAA
Found at i:63221 original size:17 final size:17
Alignment explanation
Indices: 63201--63309 Score: 73
Period size: 17 Copynumber: 6.2 Consensus size: 17
63191 ATGAAAAAAG
*
63201 AATAATAAAAATATTAA
1 AATAATAAAAATAATAA
* *
63218 AATAATAATAGTAATAA
1 AATAATAAAAATAATAA
63235 AATAAATAAAAATAAATAA
1 AAT-AATAAAAAT-AATAA
*
63254 AATTGAGTAAAAATAA-AA
1 AA-T-AATAAAAATAATAA
*
63272 TA-AATAAAAAATGAAATAA
1 AATAAT-AAAAAT--AATAA
*
63291 AAT-A-AAAAATAAAAA
1 AATAATAAAAATAATAA
63306 AATA
1 AATA
63310 TGGTTAAATT
Statistics
Matches: 72, Mismatches: 11, Indels: 19
0.71 0.11 0.19
Matches are distributed among these distances:
15 9 0.12
16 6 0.08
17 23 0.32
18 12 0.17
19 13 0.18
20 9 0.12
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AATAATAAAAATAATAA
Found at i:63281 original size:16 final size:16
Alignment explanation
Indices: 63230--63309 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 16
63220 TAATAATAGT
63230 AATAAAATAAAT-AAA
1 AATAAAATAAATAAAA
63245 AAT-AAATAAAATTGAGTAAA
1 AATAAAAT-AAA-T-A--AAA
63265 AATAAAATAAATAAAA
1 AATAAAATAAATAAAA
*
63281 AATGAAATAAAATAAAA
1 AATAAAAT-AAATAAAA
63298 AATAAAA-AAATA
1 AATAAAATAAATA
63310 TGGTTAAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
14 4 0.07
15 11 0.20
16 11 0.20
17 14 0.25
18 1 0.02
19 1 0.02
20 9 0.16
21 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (16 bp):
AATAAAATAAATAAAA
Found at i:63281 original size:26 final size:27
Alignment explanation
Indices: 63234--63306 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 27
63224 AATAGTAATA
* *
63234 AAATAAATA-AAAATAAAT-AAAATTG
1 AAATAAAAATAAAATAAATAAAAAATG
*
63259 -AGTAAAAATAAAATAAATAAAAAATG
1 AAATAAAAATAAAATAAATAAAAAATG
63285 AAAT-AAAAT-AAA-AAATAAAAAA
1 AAATAAAAATAAAATAAATAAAAAA
63307 ATATGGTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 16 0.39
25 12 0.29
26 11 0.27
27 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (27 bp):
AAATAAAAATAAAATAAATAAAAAATG
Found at i:63290 original size:12 final size:11
Alignment explanation
Indices: 63233--63306 Score: 62
Period size: 12 Copynumber: 6.4 Consensus size: 11
63223 TAATAGTAAT
63233 AAAATAAAT-A
1 AAAATAAATAA
63243 AAAATAAATAA
1 AAAATAAATAA
*
63254 AATTGAGTAAA-AA
1 AA---AATAAATAA
63267 TAAAATAAATAA
1 -AAAATAAATAA
63279 AAAATGAAATAA
1 AAAAT-AAATAA
*
63291 AATAAAAAATAA
1 AA-AATAAATAA
63303 AAAA
1 AAAA
63307 ATATGGTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
10 9 0.17
11 15 0.28
12 18 0.34
13 4 0.08
14 7 0.13
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:63307 original size:26 final size:26
Alignment explanation
Indices: 63234--63307 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
63224 AATAGTAATA
*
63234 AAAT-AAAT-AAAAATAAATAAAATTG
1 AAATAAAATAAAAAATAAA-AAAAATG
* *
63259 -AGTAAAAATAAAATAA-ATAAAAAATG
1 AAAT-AAAATAAAA-AATAAAAAAAATG
63285 AAATAAAATAAAAAATAAAAAAA
1 AAATAAAATAAAAAATAAAAAAA
63308 TATGGTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
24 2 0.05
25 2 0.05
26 25 0.66
27 7 0.18
28 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (26 bp):
AAATAAAATAAAAAATAAAAAAAATG
Found at i:63317 original size:26 final size:27
Alignment explanation
Indices: 63238--63311 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 27
63228 GTAATAAAAT
63238 AAAT-AAAAATAAATAAAAT-TGAGTA
1 AAATAAAAAATAAATAAAATATGAGTA
* * *
63263 AAA-ATAAAATAAATAAAAAATGAAATA
1 AAATAAAAAATAAATAAAATATG-AGTA
63290 AAATAAAAAATAAA-AAAATATG
1 AAATAAAAAATAAATAAAATATG
63312 GTTAAATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 16 0.40
26 2 0.05
27 13 0.32
28 9 0.22
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.20
Consensus pattern (27 bp):
AAATAAAAAATAAATAAAATATGAGTA
Found at i:63379 original size:4 final size:4
Alignment explanation
Indices: 63372--63406 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
63362 AAGAAAGGAA
63372 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
63407 AGGACCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:64569 original size:15 final size:13
Alignment explanation
Indices: 64541--64605 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 13
64531 AAAAGGAATT
64541 AAAAAAATAAAATA
1 AAAAAAAT-AAATA
64555 AAAAAACATATAATA
1 AAAAAA-ATA-AATA
64570 AATAAAAATAAATA
1 AA-AAAAATAAATA
**
64584 AAATGAATAAA-A
1 AAAAAAATAAATA
*
64596 AAAGAAATAA
1 AAAAAAATAA
64606 TAATAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
12 9 0.20
13 7 0.16
14 13 0.30
15 11 0.25
16 4 0.09
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAAAAATAAATA
Found at i:64574 original size:19 final size:18
Alignment explanation
Indices: 64550--64608 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
64540 TAAAAAAATA
64550 AAATAAAAAAACATATAAT
1 AAATAAAAAAA-ATATAAT
*
64569 AAATAAAAATAAATAAAAT
1 AAATAAAAA-AAATATAAT
* *
64588 GAATAAAAAAAGAAATAAT
1 AAATAAAAAAA-ATATAAT
64607 AA
1 AA
64609 TAATATTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 2 0.06
19 29 0.88
20 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATAAAAAAAATATAAT
Found at i:64592 original size:9 final size:9
Alignment explanation
Indices: 64540--64595 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
64530 AAAAAGGAAT
64540 TAAA-AAAA
1 TAAATAAAA
64548 TAAAATAAAA
1 T-AAATAAAA
* *
64558 AAACATATAA
1 TAA-ATAAAA
64568 TAAATAAAAA
1 TAAAT-AAAA
64578 TAAATAAAA
1 TAAATAAAA
*
64587 TGAATAAAA
1 TAAATAAAA
64596 AAAGAAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 19 0.49
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (9 bp):
TAAATAAAA
Found at i:64596 original size:10 final size:10
Alignment explanation
Indices: 64543--64596 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
64533 AAGGAATTAA
64543 AAAAATAAAAT
1 AAAAAT-AAAT
64554 AAAAA-AACAT
1 AAAAATAA-AT
*
64564 -ATAATAAAT
1 AAAAATAAAT
64573 AAAAATAAAT
1 AAAAATAAAT
*
64583 -AAAATGAAT
1 AAAAATAAAT
64592 AAAAA
1 AAAAA
64597 AAGAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
9 15 0.42
10 16 0.44
11 5 0.14
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:64603 original size:21 final size:21
Alignment explanation
Indices: 64546--64613 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
64536 GAATTAAAAA
* *
64546 AATAAAATAAAAAAACATATAAT
1 AATAAAA-AAAGAAATA-ATAAT
* *
64569 AA-ATAAAAATAAATAA-AAT
1 AATAAAAAAAGAAATAATAAT
64588 GAATAAAAAAAGAAATAATAAT
1 -AATAAAAAAAGAAATAATAAT
64610 AATA
1 AATA
64614 TTATATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 23 0.62
22 6 0.16
23 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (21 bp):
AATAAAAAAAGAAATAATAAT
Found at i:64608 original size:34 final size:34
Alignment explanation
Indices: 64541--64613 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
64531 AAAAGGAATT
* *
64541 AAAA-AAATAAAATAAAAAAACATATAATAAATA
1 AAAATAAATAAAATAAAAAAAAAGATAATAAATA
64574 AAAATAAATAAAATGAATAAAAAAAGA-AAT-AATA
1 AAAATAAATAAAAT-AA-AAAAAAAGATAATAAATA
*
64608 ATAATA
1 AAAATA
64614 TTATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 4 0.12
34 18 0.53
35 5 0.15
36 7 0.21
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (34 bp):
AAAATAAATAAAATAAAAAAAAAGATAATAAATA
Found at i:64769 original size:49 final size:47
Alignment explanation
Indices: 64716--64907 Score: 162
Period size: 46 Copynumber: 4.1 Consensus size: 47
64706 CAAAAAAATC
*
64716 ATATAT-TATGTA-ATTCTCAAAATATTTTCAAAAACTATAATATATAT
1 ATATATATATATATATTCTCAAAATATTTT-AAAAACTAT-ATATATAT
* * *
64763 ATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATATATAT
1 ATATATATATATATATTCTCAAAATATTTTAAAAACTATATATATAT
* * * * * * * * *
64810 ATATAT-TTTCA-AAATGTTTTAAAAAACTATATATA-TATATATATAT
1 ATATATATAT-ATATAT-TCTCAAAATATTTTAAAAACTATATATATAT
* * *
64856 ATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATA-ATAT
1 ATATATATATATATATTCTCAAAATATTTTAAAAACTATATATATAT
64902 ATATAT
1 ATATAT
64908 GTTTTCAAAA
Statistics
Matches: 114, Mismatches: 24, Indels: 15
0.75 0.16 0.10
Matches are distributed among these distances:
46 44 0.39
47 43 0.38
48 14 0.12
49 13 0.11
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (47 bp):
ATATATATATATATATTCTCAAAATATTTTAAAAACTATATATATAT
Found at i:64807 original size:37 final size:37
Alignment explanation
Indices: 64762--65137 Score: 275
Period size: 37 Copynumber: 9.5 Consensus size: 37
64752 ATAATATATA
*
64762 TATATATATATATATGTTTTCAAAATGTTTTAAAAAC
1 TATATATATATATATATTTTCAAAATGTTTTAAAAAC
64799 TATATATATATATATATTTTCAAAATGTTTTAAAAAAC
1 TATATATATATATATATTTTCAAAATGTTTT-AAAAAC
*
64837 TATATATATATATATATATATATATATATATATGTTTTCAAAATGTTTTAAAAAC
1 TATATATATATATATAT-T-T-T-CA-A-A-A-----------TGTTTTAAAAAC
64892 TATATA-ATATATATATGTTTTCAAAATGTTTTAAAAAAC
1 TATATATATATATATAT-TTT-CAAAATGTTTT-AAAAAC
*
64931 TATATAATATATATATATTTTCAAAATGTTTTAGAAAC
1 TATAT-ATATATATATATTTTCAAAATGTTTTAAAAAC
*
64969 -ATATATTTATTATATATTTTCAAAATGTTTTTAAAAAC
1 TATATATATA-TATATATTTTCAAAATG-TTTTAAAAAC
****
65007 TATATAT-TATATA-ATTTTCAAAAAAAAAATTAAAAA-
1 TATATATATATATATATTTTC--AAAATGTTTTAAAAAC
* *
65043 TCATATAT-TATATA-AGTTTTCAAAAATGATTT-CAAAC
1 T-ATATATATATATATA-TTTTC-AAAATGTTTTAAAAAC
*
65080 TATATA-ATATATACATTTTCAAAAAAATCGTTTTAAAAAC
1 TATATATATATATATATTTTC---AAAAT-GTTTTAAAAAC
65120 TATATTATATATATATAT
1 TATA-TATATATATATAT
65138 ATATATATAA
Statistics
Matches: 282, Mismatches: 19, Indels: 71
0.76 0.05 0.19
Matches are distributed among these distances:
36 30 0.11
37 85 0.30
38 60 0.21
39 33 0.12
40 13 0.05
41 13 0.05
42 10 0.04
43 1 0.00
44 1 0.00
45 1 0.00
49 1 0.00
50 1 0.00
51 1 0.00
52 2 0.01
53 1 0.00
54 11 0.04
55 12 0.04
56 6 0.02
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (37 bp):
TATATATATATATATATTTTCAAAATGTTTTAAAAAC
Found at i:64842 original size:2 final size:2
Alignment explanation
Indices: 64837--64869 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
64827 TTTAAAAAAC
64837 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64870 GTTTTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64875 original size:93 final size:94
Alignment explanation
Indices: 64751--64948 Score: 366
Period size: 93 Copynumber: 2.1 Consensus size: 94
64741 TTTCAAAAAC
64751 TATA-ATATATATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATAT-ATATATATAT
1 TATATATATATATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATATAT
64814 ATTTTCAAAATGTTTTAAAAAACTATATA
66 ATTTTCAAAATGTTTTAAAAAACTATATA
64843 TATATATATATATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATATAT
1 TATATATATATATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATATAT
*
64908 GTTTTCAAAATGTTTTAAAAAACTATATA
66 ATTTTCAAAATGTTTTAAAAAACTATATA
64937 -ATATATATATAT
1 TATATATATATAT
64949 TTTCAAAATG
Statistics
Matches: 103, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
92 4 0.04
93 61 0.59
94 38 0.37
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (94 bp):
TATATATATATATATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATATAT
ATTTTCAAAATGTTTTAAAAAACTATATA
Found at i:64881 original size:56 final size:54
Alignment explanation
Indices: 64799--64907 Score: 191
Period size: 56 Copynumber: 2.0 Consensus size: 54
64789 TTTTAAAAAC
64799 TATATATATATATATATTTTCAAAATGTTTTAAAAAACTATATATATATATATATA
1 TATATATATATATATATTTTCAAAATGTTTT-AAAAACTATATA-ATATATATATA
*
64855 TATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATATAT
1 TATATATATATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATAT
64908 GTTTTCAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
54 10 0.19
55 12 0.23
56 30 0.58
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (54 bp):
TATATATATATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATATA
Found at i:65982 original size:69 final size:69
Alignment explanation
Indices: 65871--66003 Score: 187
Period size: 69 Copynumber: 1.9 Consensus size: 69
65861 ATGTGTCATC
* * * *
65871 GAGCTGAATAAAATCGAACTCGACAATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGT
1 GAGCTGAATAAAATCGAACTCGACAATCTTTGCTGACAGATAGCCCTCCTCGCCTTGAGCTATGT
65936 CTTT
66 CTTT
** *
65940 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGCTGACAGATAGCCCTCCTCGCCTTGAGCTATG
1 GAGCTGAATAAAATCGAACTCGACA-ATCTTTGCTGACAGATAGCCCTCCTCGCCTTGAGCTATG
66004 CTGTAAATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 1 0.02
69 55 0.98
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (69 bp):
GAGCTGAATAAAATCGAACTCGACAATCTTTGCTGACAGATAGCCCTCCTCGCCTTGAGCTATGT
CTTT
Found at i:66077 original size:84 final size:84
Alignment explanation
Indices: 65936--66095 Score: 275
Period size: 84 Copynumber: 1.9 Consensus size: 84
65926 TGAGCTATGT
* *
65936 CTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGCTGACAGATAGCCCTCCTCGCCTTGAGCT
1 CTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTACTGACAAATAGCCCTCCTCGCCTTGAGCT
66001 ATGCTGTAAATTTGAATGC
66 ATGCTGTAAATTTGAATGC
* * *
66020 CTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTATTGACAAATATCCCTTCTCGCCTTGAGCT
1 CTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTACTGACAAATAGCCCTCCTCGCCTTGAGCT
66085 ATGCTGTAAAT
66 ATGCTGTAAAT
66096 AGGCTGGGAG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (84 bp):
CTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTACTGACAAATAGCCCTCCTCGCCTTGAGCT
ATGCTGTAAATTTGAATGC
Found at i:71722 original size:42 final size:41
Alignment explanation
Indices: 71705--71825 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 41
71695 AAAAAAGAAT
*
71705 AATAAAAAAAATTAAAATAATAATAGTAATAAAAAATAAAAA
1 AATAAAAAAAA-TAAAATAATAATAGAAATAAAAAATAAAAA
* * *
71747 AATAAAAAAAATAAAAT-AGAGTAAAAATAAAGTAAATAAAAA
1 AATAAAAAAAATAAAATAATAATAGAAATAAA--AAATAAAAA
* * *
71789 ATAAAAAAAACAATGAAATAA-AATAAAAATAATAAAA
1 A-ATAAAAAA-AATAAAATAATAATAGAAATAA-AAAA
71826 AATAGGGTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
40 10 0.15
41 6 0.09
42 21 0.32
43 10 0.15
44 17 0.26
45 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (41 bp):
AATAAAAAAAATAAAATAATAATAGAAATAAAAAATAAAAA
Found at i:71729 original size:24 final size:23
Alignment explanation
Indices: 71702--71827 Score: 77
Period size: 25 Copynumber: 5.5 Consensus size: 23
71692 TGAAAAAAAG
71702 AATAATAAAAAAAATTAAAATAAT
1 AATAATAAAAAAAA-TAAAATAAT
*
71726 AATAGTAATAAAAAAT---A-AA-
1 AATAATAA-AAAAAATAAAATAAT
71745 AA-AATAAAAAAAATAAAATAGAGT
1 AATAATAAAAAAAATAAAATA-A-T
* **
71769 AAAAATAAAGTAAATAAAA-AAT
1 AATAATAAAAAAAATAAAATAAT
* * * *
71791 AAAAAAAACAATGAAATAAAATAAA
1 AATAATAA-AA-AAAATAAAATAAT
71816 AATAATAAAAAA
1 AATAATAAAAAA
71828 TAGGGTTAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 25
0.69 0.10 0.22
Matches are distributed among these distances:
17 7 0.09
18 4 0.05
19 2 0.03
20 3 0.04
21 2 0.03
22 9 0.11
23 3 0.04
24 21 0.27
25 28 0.35
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (23 bp):
AATAATAAAAAAAATAAAATAAT
Found at i:71747 original size:9 final size:9
Alignment explanation
Indices: 71705--71827 Score: 63
Period size: 9 Copynumber: 13.0 Consensus size: 9
71695 AAAAAAGAAT
71705 AATAAAAAA
1 AATAAAAAA
* *
71714 AATTAAAAT
1 AATAAAAAA
* **
71723 AATAATAGT
1 AATAAAAAA
71732 AAT--AAAA
1 AATAAAAAA
71739 AAT-AAAAA
1 AATAAAAAA
71747 AATAAAAAA
1 AATAAAAAA
*
71756 AATAAAATAG
1 AATAAAA-AA
*
71766 AGTAAAAATA
1 AATAAAAA-A
71776 AAGTAAATAAAA
1 AA-T-AA-AAAA
71788 AATAAAAAAAA
1 AAT--AAAAAA
*
71799 CAATGAAATAA
1 -AAT-AAAAAA
*
71810 AATAAAAAT
1 AATAAAAAA
71819 AATAAAAAA
1 AATAAAAAA
71828 TAGGGTTAAA
Statistics
Matches: 88, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
7 4 0.05
8 7 0.08
9 41 0.47
10 11 0.12
11 11 0.12
12 11 0.12
13 3 0.03
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (9 bp):
AATAAAAAA
Found at i:71754 original size:16 final size:17
Alignment explanation
Indices: 71695--71827 Score: 74
Period size: 18 Copynumber: 7.4 Consensus size: 17
71685 ATAAACATGA
71695 AAAAAAGAATAATAAAAA-
1 AAAAAA-AATAA-AAAAAT
* * *
71713 AAATTAAAATAATAATAGT
1 AAA-AAAAATAA-AAAAAT
71732 AATAAAAAATAAAAAAAT
1 AA-AAAAAATAAAAAAAT
*
71750 AAAAAAAATAAAATAGAGT
1 AAAAAAAATAAAA-A-AAT
*
71769 AAAAATAAAGTAAATAAA-
1 AAAAA-AAA-TAAAAAAAT
* *
71787 AAATAAAA-AAAACAAT
1 AAAAAAAATAAAAAAAT
*
71803 GAAATAAAATAAAAATAAT
1 -AAAAAAAATAAAAA-AAT
71822 AAAAAA
1 AAAAAA
71828 TAGGGTTAAA
Statistics
Matches: 90, Mismatches: 14, Indels: 22
0.71 0.11 0.17
Matches are distributed among these distances:
15 5 0.06
17 22 0.24
18 32 0.36
19 22 0.24
20 5 0.06
21 4 0.04
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAT
Found at i:71754 original size:41 final size:40
Alignment explanation
Indices: 71705--71798 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 40
71695 AAAAAAGAAT
71705 AATAAAAAAAATTAAAATA-A-TAATAGTAATAAA-AAATAAAAA
1 AATAAAAAAAA-TAAAATAGAGTAA-A--AATAAAGAAAT-AAAA
71747 AATAAAAAAAATAAAATAGAGTAAAAATAAAGTAAATAAAA
1 AATAAAAAAAATAAAATAGAGTAAAAATAAAG-AAATAAAA
71788 AATAAAAAAAA
1 AATAAAAAAAA
71799 CAATGAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
40 6 0.12
41 22 0.46
42 17 0.35
43 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (40 bp):
AATAAAAAAAATAAAATAGAGTAAAAATAAAGAAATAAAA
Found at i:71773 original size:33 final size:37
Alignment explanation
Indices: 71718--71789 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 37
71708 AAAAAAAATT
71718 AAAATAATAATAGTAATAAAAAATAAA-AAAATAAAA
1 AAAATAATAATAGTAATAAAAAATAAAGAAAATAAAA
* *
71754 AAAATAA-AATAG-AGT-AAAAATAAAGTAAATAAAA
1 AAAATAATAATAGTAATAAAAAATAAAGAAAATAAAA
71788 AA
1 AA
71790 TAAAAAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 9 0.27
34 12 0.36
35 5 0.15
36 7 0.21
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (37 bp):
AAAATAATAATAGTAATAAAAAATAAAGAAAATAAAA
Found at i:73081 original size:23 final size:25
Alignment explanation
Indices: 73055--73116 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
73045 AAAGGAATTA
73055 AAAAAATAAAATAAA-AAAAT--AT
1 AAAAAATAAAATAAATAAAATGAAT
*
73077 TAAAAATAAAAATAAATAAAATGAAT
1 AAAAAAT-AAAATAAATAAAATGAAT
73103 AAAAAATAATAATA
1 AAAAAATAA-AATA
73117 TTATTATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 6 0.18
23 8 0.24
24 5 0.15
25 2 0.06
26 12 0.36
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (25 bp):
AAAAAATAAAATAAATAAAATGAAT
Found at i:73109 original size:16 final size:14
Alignment explanation
Indices: 73054--73116 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 14
73044 AAAAGGAATT
73054 AAAAAAATAAAATA
1 AAAAAAATAAAATA
73068 AAAAAATATTAAAAATA
1 AAAAAA-A-T-AAAATA
73085 AAAATAAATAAAATGA
1 AAAA-AAATAAAAT-A
73101 ATAAAAAATAATAATA
1 A-AAAAAATAA-AATA
73117 TTATTATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
14 6 0.14
15 6 0.14
16 11 0.26
17 17 0.40
18 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAAAAAATAAAATA
Found at i:73182 original size:38 final size:36
Alignment explanation
Indices: 73140--73668 Score: 258
Period size: 38 Copynumber: 14.8 Consensus size: 36
73130 ATATATATAT
*
73140 AAATATTTTTAAAAACTACATAATATATATAATTTCAA
1 AAATA-TTTTAAAAACTATATAATATATATAATTTC-A
* *
73178 AAATATTTT-GAAACTATAT-AT-TATAT-ATTTAAA
1 AAATATTTTAAAAACTATATAATATATATAATTT-CA
* * *
73211 AAACAATTTCAAAAA-AATCAT-ATATTATATAATTTTCA
1 AAA-TATTTTAAAAACTAT-ATAATA-TATATAA-TTTCA
* * *
73249 AAATGTTTTCAAAACCTATATAATATATATATTTTCA
1 AAATATTTT-AAAAACTATATAATATATATAATTTCA
* *
73286 AAATATTTTCAAAACTATATAATATATATATGTTTTCA
1 AAATATTTTAAAAACTATATAATATATATA--ATTTCA
*
73324 AAATATTTTAAAAACTATATAATATATAT-ATAT--
1 AAATATTTTAAAAACTATATAATATATATAATTTCA
* * * * *
73357 ATATA-TATATATA-TATAT-ATATATAT-ATAT-A
1 AAATATTTTAAAAACTATATAATATATATAATTTCA
* * * *
73388 TATATATATATATATA-TATATATATATATATATATTTC-
1 -AAATAT-TTTAAAAACTATATA-ATATATATA-ATTTCA
** *
73426 -AATGGTTTAAAAACTATAT-ATATATATATTTTCA
1 AAATATTTTAAAAACTATATAATATATATAATTTCA
*
73460 AAATGTTTTAAAAACTATAT--TATATAT--TTTCA
1 AAATATTTTAAAAACTATATAATATATATAATTTCA
* *
73492 AAATGTTTTAGAAAA--ATAT-ATATATA-AATTTTTA
1 AAATATTTTA-AAAACTATATAATATATATAA-TTTCA
*
73526 AAATGTTTTTTAAAAA-TCATAT-AT-TATATAAGTTTTCAA
1 AAA--TATTTTAAAAACT-ATATAATATATATAA--TTTC-A
* * *
73565 AAATGTTTTTAAAAACCATATATTATATA-AATTTTCA
1 AAAT-ATTTTAAAAACTATATAATATATATAA-TTTCA
* * * *
73602 AAATGA-TTT-CAAACTATATAATATATACATTTTAAA
1 AAAT-ATTTTAAAAACTATATAATATATATAATTT-CA
* *
73638 AAATCGTTTTCAAAACTATATAATATATATA
1 AAAT-ATTTTAAAAACTATATAATATATATA
73669 TATAAATAAA
Statistics
Matches: 398, Mismatches: 48, Indels: 90
0.74 0.09 0.17
Matches are distributed among these distances:
30 12 0.03
31 9 0.02
32 31 0.08
33 20 0.05
34 47 0.12
35 56 0.14
36 61 0.15
37 43 0.11
38 100 0.25
39 15 0.04
40 4 0.01
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (36 bp):
AAATATTTTAAAAACTATATAATATATATAATTTCA
Found at i:73350 original size:2 final size:2
Alignment explanation
Indices: 73339--73422 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
73329 TTTTAAAAAC
73339 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73422 T
1 T
73423 TTCAATGGTT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 80 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:73444 original size:32 final size:33
Alignment explanation
Indices: 73408--73669 Score: 176
Period size: 35 Copynumber: 7.5 Consensus size: 33
73398 TATATATATA
*
73408 TATATATATATATATTTC-AATGGTTTAAAAAC
1 TATATATATATATATTTCAAATGTTTTAAAAAC
73440 TATATATATATATATTTTCAAAATGTTTTAAAAAC
1 TATATATATATATA-TTTC-AAATGTTTTAAAAAC
*
73475 TATAT-TATATAT-TTTCAAAATGTTTTAGAAAAA
1 TATATATATATATATTTC-AAATGTTTTA-AAAAC
* * *
73508 TATATATATAAATTTTTAAAATGTTTTTTAAAAA-
1 TATATATATATATATTTCAAATG--TTTTAAAAAC
73542 TCATATAT-TATATAAGTTTTCAAAAATGTTTTTAAAAAC
1 T-ATATATATATAT-A--TTTC--AAATG-TTTTAAAAAC
* * * *
73581 CATATATTATATAAATTTTCAAAATGATTT-CAAAC
1 TATATA-TATATATA-TTTC-AAATGTTTTAAAAAC
* * *
73616 TATATAATATATACATTTTAAAAAATCGTTTTCAAAAC
1 TATAT-ATATATATA-TTT--CAAAT-GTTTTAAAAAC
73654 TATATAATATATATAT
1 TATAT-ATATATATAT
73670 ATAAATAAAT
Statistics
Matches: 191, Mismatches: 17, Indels: 39
0.77 0.07 0.16
Matches are distributed among these distances:
32 29 0.15
33 13 0.07
34 23 0.12
35 50 0.26
36 13 0.07
37 14 0.07
38 38 0.20
39 7 0.04
40 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (33 bp):
TATATATATATATATTTCAAATGTTTTAAAAAC
Found at i:73484 original size:66 final size:66
Alignment explanation
Indices: 73408--73628 Score: 218
Period size: 66 Copynumber: 3.2 Consensus size: 66
73398 TATATATATA
* *
73408 TATATATATATATATTTC-AATGGTTTAAAAACTATATATATATATATTTTCAAAATGTTTTAAA
1 TATAT-TATATATATTTCAAATGTTTTAAAAAC-ATATATATATAAATTTTCAAAATGTTTTAAA
73472 AAC
64 AAC
*
73475 TATATTATATAT-TTTCAAAATGTTTTAGAAAA-ATATATATATAAATTTTTAAAATGTTTTTTA
1 TATATTATATATATTTC-AAATGTTTTA-AAAACATATATATATAAATTTTCAAAATG--TTTTA
73538 AAAATC
62 AAAA-C
*
73544 ATATATTATATA-AGTTTTCAAAAATGTTTTTAAAAACCATATATTATATAAATTTTCAAAATGA
1 -TATATTATATATA--TTTC--AAATG-TTTTAAAAA-CATATA-TATATAAATTTTCAAAATGT
*
73608 TTT-CAAAC
58 TTTAAAAAC
*
73616 TATATAATATATA
1 TATATTATATATA
73629 CATTTTAAAA
Statistics
Matches: 131, Mismatches: 7, Indels: 27
0.79 0.04 0.16
Matches are distributed among these distances:
65 4 0.03
66 29 0.22
67 13 0.10
68 13 0.10
69 1 0.01
70 11 0.08
71 10 0.08
72 6 0.05
73 13 0.10
74 8 0.06
75 5 0.04
76 18 0.14
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (66 bp):
TATATTATATATATTTCAAATGTTTTAAAAACATATATATATAAATTTTCAAAATGTTTTAAAAA
C
Found at i:73710 original size:3 final size:3
Alignment explanation
Indices: 73702--73760 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
73692 TAGTGTCTAC
73702 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
73750 AAT AAT AAT AA
1 AAT AAT AAT AA
73761 GAACTCGAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:74533 original size:38 final size:38
Alignment explanation
Indices: 74482--74558 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
74472 CCTAGGATTC
74482 GGATTAATATTTCAATCTAAATATTCTAATTGCTATTT
1 GGATTAATATTTCAATCTAAATATTCTAATTGCTATTT
74520 GGATTAATATTTCAATCTAAATATTCTAATTGCTATTT
1 GGATTAATATTTCAATCTAAATATTCTAATTGCTATTT
74558 G
1 G
74559 CAATGGATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (38 bp):
GGATTAATATTTCAATCTAAATATTCTAATTGCTATTT
Found at i:74957 original size:28 final size:28
Alignment explanation
Indices: 74925--74990 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
74915 AGTTCCTAGA
*
74925 CTTTTGTTTCTTGGTACTGATGCTGTTG
1 CTTTTGTTTCTTGGTACTGATACTGTTG
74953 CTTTTGTTTCTTGGTACTGATACTGTTG
1 CTTTTGTTTCTTGGTACTGATACTGTTG
74981 CTTTTGTTTC
1 CTTTTGTTTC
74991 AGACCGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.08, C:0.15, G:0.21, T:0.56
Consensus pattern (28 bp):
CTTTTGTTTCTTGGTACTGATACTGTTG
Found at i:75933 original size:23 final size:23
Alignment explanation
Indices: 75903--75953 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
75893 CTGAAAGATC
75903 ATATGCTTGACTTGCTGCACTTA
1 ATATGCTTGACTTGCTGCACTTA
* *
75926 ATATGCTTGATTTGCTGTACTTA
1 ATATGCTTGACTTGCTGCACTTA
75949 ATATG
1 ATATG
75954 GTAATGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (23 bp):
ATATGCTTGACTTGCTGCACTTA
Found at i:81994 original size:143 final size:151
Alignment explanation
Indices: 81646--82031 Score: 402
Period size: 143 Copynumber: 2.5 Consensus size: 151
81636 TAAATAGAAC
* * * *
81646 ATTTATTTATTTAAAAATATCAGAAAAT-GACATCTAGTTGTTTTAAGATAGCATTTTTTTAATA
1 ATTTATTTATTT-AAAATATCA-AAAATAGACATCTAGTTATTTTAAGACAGC-CTTTCTTAATA
* *
81710 TTAATAAATAAATAAATATTAATAATAATATAATAATTTTTCCTAAAAAATAATAAAAACTAAGT
63 TTAAAAAATAAATAAATATT-AGAATAATATAATAATTTTTCCTAAAAAATAATAAAAACTAAG-
81775 AAATATATATACATTTATAAGCAATAT
126 AAATATATATACATTTATAA-CAATAT
* *
81802 ATTTATTTATTTTTTAAAATATC-ATAATAGA-ATGTCTAGTTATTTTAAGACCGTCCTTTCTTA
1 ATTTATTTA---TTTAAAATATCAAAAATAGACA--TCTAGTTATTTTAAGACAG-CCTTTCTTA
* * * **
81865 ATATTAAGAAATAAATAAATATT-GAA-AATGTGATAATTTTTCCTAAAAAATAATTGAAA-T-A
60 ATATTAAAAAATAAATAAATATTAGAATAATATAATAATTTTTCCTAAAAAATAATAAAAACTAA
* *
81926 -AAATATATATA-ATTT-TTA-TA-AT
125 GAAATATATATACATTTATAACAATAT
* *
81948 ATTTATTTATTTAAAATA-CAAAAATAAGACATCTAGTTATATTAAGACTGCCCTTTCTTAATAT
1 ATTTATTTATTTAAAATATCAAAAAT-AGACATCTAGTTATTTTAAGACAG-CCTTTCTTAATAT
82012 TAAAAAATAAATAAATATTA
64 TAAAAAATAAATAAATATTA
82032 TTATTTAAAC
Statistics
Matches: 200, Mismatches: 19, Indels: 34
0.79 0.08 0.13
Matches are distributed among these distances:
142 1 0.00
143 61 0.31
144 3 0.01
145 1 0.00
146 11 0.05
147 1 0.00
149 2 0.01
150 4 0.02
151 11 0.05
153 1 0.00
154 1 0.00
155 29 0.14
156 16 0.08
157 2 0.01
158 52 0.26
159 4 0.02
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.41
Consensus pattern (151 bp):
ATTTATTTATTTAAAATATCAAAAATAGACATCTAGTTATTTTAAGACAGCCTTTCTTAATATTA
AAAAATAAATAAATATTAGAATAATATAATAATTTTTCCTAAAAAATAATAAAAACTAAGAAATA
TATATACATTTATAACAATAT
Found at i:82046 original size:26 final size:25
Alignment explanation
Indices: 82011--82064 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
82001 TTTCTTAATA
82011 TTAAAAAATAAATAAATAT-TATTAT
1 TTAAAAAATAAATAAATATATA-TAT
* *
82036 TTAAACAAATATATATATATATATAT
1 TTAAA-AAATAAATAAATATATATAT
82062 TTA
1 TTA
82065 TATGACTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 18 0.72
27 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAAAAATAAATAAATATATATAT
Found at i:82094 original size:11 final size:11
Alignment explanation
Indices: 82078--82143 Score: 64
Period size: 11 Copynumber: 5.8 Consensus size: 11
82068 GACTAAGATG
82078 AAAATAATAAT
1 AAAATAATAAT
82089 AAAATAATAAT
1 AAAATAATAAT
*
82100 GAAAGTAATAATT
1 -AAAATAATAA-T
*
82113 TAAAT-AT-AT
1 AAAATAATAAT
82122 CAAAAGTAATAAT
1 -AAAA-TAATAAT
82135 AAAATAATA
1 AAAATAATA
82144 TTGTAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
9 1 0.02
10 4 0.09
11 19 0.42
12 18 0.40
13 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:82108 original size:23 final size:23
Alignment explanation
Indices: 82075--82143 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
82065 TATGACTAAG
*
82075 ATGAAAATAATAATAAAATAATA
1 ATGAAAGTAATAATAAAATAATA
*
82098 ATGAAAGTAATAATTTAAAT-AT-
1 ATGAAAGTAATAA-TAAAATAATA
*
82120 ATCAAAAGTAATAATAAAATAATA
1 AT-GAAAGTAATAATAAAATAATA
82144 TTGTAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.18
23 26 0.68
24 5 0.13
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (23 bp):
ATGAAAGTAATAATAAAATAATA
Found at i:82196 original size:21 final size:22
Alignment explanation
Indices: 82172--82212 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
82162 AAAAGAAATT
*
82172 AAAAT-TATAAAATTAAAATGC
1 AAAATATATAAAATAAAAATGC
*
82193 AAAATATATTAAATAAAAAT
1 AAAATATATAAAATAAAAAT
82213 TATCAAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATATATAAAATAAAAATGC
Found at i:83386 original size:3 final size:3
Alignment explanation
Indices: 83378--83445 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
83368 ATTATTTATT
* *
83378 TAA TAA TAA TAA TAA TAA TATA TTA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
83424 TAA TATT TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
83446 GGGTAAAGTA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 53 0.93
4 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:83413 original size:31 final size:31
Alignment explanation
Indices: 83378--83445 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
83368 ATTATTTATT
83378 TAATAATAATAATAATAATATATT-ATAATAA
1 TAATAATAATAATAATAATAT-TTAATAATAA
*
83409 TAATATTAATAATAATAATATTTAATAATAA
1 TAATAATAATAATAATAATATTTAATAATAA
83440 TAATAA
1 TAATAA
83446 GGGTAAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
TAATAATAATAATAATAATATTTAATAATAA
Found at i:83716 original size:35 final size:35
Alignment explanation
Indices: 83669--83754 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
83659 AAAACAGTCA
* * *
83669 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
83704 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
83739 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
83755 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:83748 original size:21 final size:21
Alignment explanation
Indices: 83723--83765 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
83713 TTCTAAACCC
83723 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
83744 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
83765 T
1 T
83766 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:83924 original size:14 final size:16
Alignment explanation
Indices: 83888--83924 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
83878 TATTAATGTA
83888 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
83905 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
83920 T-AATA
1 TGAATA
83925 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:84589 original size:130 final size:130
Alignment explanation
Indices: 84386--84633 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
84376 AATTTTCTTC
* * *
84386 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
84451 CCTGATTAAATGATTAATTTATTAAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
84516 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* *
84581 CCTAATTAAATGATTAATTTATTAGATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAAATTTATTTAATTTAGGACCAAATTGAT
84634 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:89126 original size:4 final size:4
Alignment explanation
Indices: 89117--89143 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
89107 TTCAACTATG
89117 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
89144 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Done.