Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011506.1 Kokia drynarioides strain JFW-HI SEQ_126491, 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: 26104
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Warning! 140 characters in sequence are not A, C, G, or T
Found at i:1636 original size:10 final size:9
Alignment explanation
Indices: 1611--1851 Score: 58
Period size: 10 Copynumber: 24.8 Consensus size: 9
1601 AAATTGAAAA
*
1611 ATAAAAATCA
1 ATAAAAAT-T
*
1621 ATAAAAGTT
1 ATAAAAATT
1630 ATAAAAATT
1 ATAAAAATT
**
1639 ATTAAATTTT
1 A-TAAAAATT
1649 AATAAAAATAT
1 -ATAAAAAT-T
* **
1660 TTAAACTTT
1 ATAAAAATT
1669 ATTAAAAATT
1 A-TAAAAATT
*
1679 AGGGAAAAATT
1 A--TAAAAATT
*
1690 ATATAAATCGT
1 ATAAAAAT--T
*
1701 AAAAAAATT
1 ATAAAAATT
1710 ATTAAAAATT
1 A-TAAAAATT
* **
1720 GTAAATTTT
1 ATAAAAATT
*
1729 ATAAAAGTT
1 ATAAAAATT
*
1738 GTAAAAAATT
1 AT-AAAAATT
1748 AT-AAAA-T
1 ATAAAAATT
1755 ATACAGAAATAT
1 ATA-A-AAAT-T
*
1767 AGAAAAAATT
1 A-TAAAAATT
1777 AT-AAAATT
1 ATAAAAATT
* *
1785 TTATAAATTT
1 ATA-AAAATT
*
1795 GTAATAAAATT
1 AT-A-AAAATT
**
1806 ATAAAAAAA
1 ATAAAAATT
*
1815 AGTAAAGAAAT
1 A-TAAA-AATT
1826 AT-AAAATT
1 ATAAAAATT
1834 AGTAAAAAATT
1 A-T-AAAAATT
1845 ATAAAAA
1 ATAAAAA
1852 CTATCCTACC
Statistics
Matches: 168, Mismatches: 40, Indels: 47
0.66 0.16 0.18
Matches are distributed among these distances:
7 3 0.02
8 15 0.09
9 44 0.26
10 62 0.37
11 40 0.24
12 3 0.02
13 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:1653 original size:20 final size:21
Alignment explanation
Indices: 1630--1679 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1620 AATAAAAGTT
*
1630 ATAAAAATTA-TTAAATTTTA
1 ATAAAAATTATTTAAACTTTA
1650 ATAAAAA-TATTTAAACTTTA
1 ATAAAAATTATTTAAACTTTA
*
1670 TTAAAAATTA
1 ATAAAAATTA
1680 GGGAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAAATTATTTAAACTTTA
Found at i:1734 original size:17 final size:18
Alignment explanation
Indices: 1705--1742 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1695 AATCGTAAAA
1705 AAATTATTAAAAA-TTGT
1 AAATTATTAAAAAGTTGT
1722 AAATT-TTATAAAAGTTGT
1 AAATTATTA-AAAAGTTGT
1740 AAA
1 AAA
1743 AAATTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 9 0.47
18 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
AAATTATTAAAAAGTTGT
Found at i:1749 original size:19 final size:18
Alignment explanation
Indices: 1683--1850 Score: 81
Period size: 19 Copynumber: 8.7 Consensus size: 18
1673 AAAATTAGGG
*
1683 AAAAATTATATAAATCGTAA
1 AAAAATTATA-AAATTGT-A
1703 AAAAATTATTAAAAATTGT-
1 AAAAATTA-T-AAAATTGTA
**
1722 AAATTTTATAAAAGTTGTA
1 AAAAATTATAAAA-TTGTA
*
1741 AAAAATTATAAAA-TATA
1 AAAAATTATAAAATTGTA
* * *
1758 CAGAAATATAGAAAAAATTATA
1 -A-AAA-AT-TATAAAATTGTA
** *
1780 AAATTTTATAAATTTGTA
1 AAAAATTATAAAATTGTA
**
1798 ATAAAATTATAAAAAAAAGTA
1 A-AAAATTAT--AAAATTGTA
1819 AAGAAA-TATAAAATTAGTA
1 AA-AAATTATAAAATT-GTA
1838 AAAAATTATAAAA
1 AAAAATTATAAAA
1851 ACTATCCTAC
Statistics
Matches: 112, Mismatches: 21, Indels: 31
0.68 0.13 0.19
Matches are distributed among these distances:
17 7 0.06
18 22 0.20
19 39 0.35
20 16 0.14
21 23 0.21
22 5 0.04
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (18 bp):
AAAAATTATAAAATTGTA
Found at i:1750 original size:58 final size:57
Alignment explanation
Indices: 1683--1811 Score: 145
Period size: 58 Copynumber: 2.2 Consensus size: 57
1673 AAAATTAGGG
* ** *
1683 AAAAATTATATAAATCGTAAAAAAAT-TATTAAAAATTGT-AAATTTTATAAAAGTTGTA
1 AAAAATTATA-AAAT-ATAAAAAAATATAGAAAAAATTATAAAATTTTAT-AAAGTTGTA
* * *
1741 AAAAATTATAAAATATACAGAAATATAGAAAAAATTATAAAATTTTATAAATTTGTA
1 AAAAATTATAAAATATAAAAAAATATAGAAAAAATTATAAAATTTTATAAAGTTGTA
1798 ATAAAATTATAAAA
1 A-AAAATTATAAAA
1812 AAAAGTAAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
56 7 0.11
57 23 0.38
58 31 0.51
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (57 bp):
AAAAATTATAAAATATAAAAAAATATAGAAAAAATTATAAAATTTTATAAAGTTGTA
Found at i:1754 original size:29 final size:28
Alignment explanation
Indices: 1704--1811 Score: 96
Period size: 29 Copynumber: 3.8 Consensus size: 28
1694 AAATCGTAAA
* * *
1704 AAAATTATTAAAAATTGT-AAATTTTAT
1 AAAATTGTAAAAAATTATAAAATTTTAT
* *
1731 AAAAGTTGTAAAAAATTATAAAA-TATAC
1 AAAA-TTGTAAAAAATTATAAAATTTTAT
1759 AGAAATATAG-AAAAAATTATAAAATTTTAT
1 A-AAAT-T-GTAAAAAATTATAAAATTTTAT
*
1789 AAATTTGTAATAAAATTATAAAA
1 AAAATTGTAA-AAAATTATAAAA
1812 AAAAGTAAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
27 5 0.08
28 19 0.29
29 36 0.55
30 5 0.08
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (28 bp):
AAAATTGTAAAAAATTATAAAATTTTAT
Found at i:2408 original size:92 final size:87
Alignment explanation
Indices: 2259--2474 Score: 220
Period size: 91 Copynumber: 2.4 Consensus size: 87
2249 ATTATGGCAA
* *
2259 TTCAAGTATCCAATTGAGTGCAAAAAAAAGTAAGGGCCTAATTACTTTTCTTG-AAAAAGTTTGA
1 TTCAAGTACCCAATTGAGTGCAAAAAAAA-TAA-GTCCTAATTACTTTTCTTGAAAAAAGTTTGA
**
2323 GGGTCTTTTTTTTTATGCATTTTGATAG
64 -GGT-TTTTTTGATAT--ATTTTGATAG
* * * * * *
2351 TTTAAGTACCCAATTTAGTGCAAAAAAAATAAGTCTTAATTGCTTCTTTTTTTAAAAAAAAGTTT
1 TTCAAGTACCCAATTGAGTGCAAAAAAAATAAGTCCTAA-T--TACTTTTCTT-GAAAAAAGTTT
2416 GAGGTTTTTTTGATATATTTTGATAG
62 GAGGTTTTTTTGATATATTTTGATAG
* *
2442 TTCAAGTACCTAATTGAGTG-AAAAAAAAAAAGT
1 TTCAAGTACCCAATTGAGTGCAAAAAAAATAAGT
2475 AGGAACTTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
90 17 0.16
91 31 0.30
92 26 0.25
93 17 0.16
94 3 0.03
95 11 0.10
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (87 bp):
TTCAAGTACCCAATTGAGTGCAAAAAAAATAAGTCCTAATTACTTTTCTTGAAAAAAGTTTGAGG
TTTTTTTGATATATTTTGATAG
Found at i:2493 original size:91 final size:93
Alignment explanation
Indices: 2312--2516 Score: 233
Period size: 91 Copynumber: 2.2 Consensus size: 93
2302 ACTTTTCTTG
** * *
2312 AAAAAGTTTGAGGGTCTTTTTTTTTATGCATTTTGATAGTTTAAGTACCCAATTTAGTGCAAAAA
1 AAAAAGTTTGAGGGT-TTTTTTGATAT-CATTTTGATAGTTCAAGTACCCAATTGAGTGCAAAAA
* *** **
2377 AAATAAGTCTTAATTGCTTCTTTTTTTAAA
64 AAAAAAGTAGGAATTAATTCTTTTTTTAAA
*
2407 AAAAAGTTTGA-GGTTTTTTTGATAT-ATTTTGATAGTTCAAGTACCTAATTGAGTG-AAAAAAA
1 AAAAAGTTTGAGGGTTTTTTTGATATCATTTTGATAGTTCAAGTACCCAATTGAGTGCAAAAAAA
2469 AAAAGTAGGAACTTAATTGCTTTTTTT-AA
66 AAAAGTAGGAA-TTAATT-CTTTTTTTAAA
2498 AAAAA--TTGAGGGTTTTTTT
1 AAAAAGTTTGAGGGTTTTTTT
2517 ACACCCATAA
Statistics
Matches: 96, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
89 4 0.04
90 23 0.24
91 38 0.40
92 8 0.08
93 9 0.09
94 3 0.03
95 11 0.11
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (93 bp):
AAAAAGTTTGAGGGTTTTTTTGATATCATTTTGATAGTTCAAGTACCCAATTGAGTGCAAAAAAA
AAAAGTAGGAATTAATTCTTTTTTTAAA
Found at i:2516 original size:92 final size:90
Alignment explanation
Indices: 2259--2516 Score: 206
Period size: 91 Copynumber: 2.8 Consensus size: 90
2249 ATTATGGCAA
* * * * **
2259 TTCAAGTATCCAATTGAGTG--CAAAAAAAAGTAAGG-GCCTAATTACTTTTCTTGAAAAAGTTT
1 TTCAAGTA-CCAATTGAGTGAAAAAAAAAAAGT-AGGAACTTAATT-CTTTT-TTTAAAAAAATT
* *
2321 GAGGGTCTTTTTTTTTATGCATTTTGATAG
62 GAGGGT-TTTTTTTTGATACATTTTGATAG
* * * *** **
2351 TTTAAGTACCCAATTTAGTGCAAAAAAAATAAGTCTTAA-TTGCTTCTTTTTTTAAAAAAAAGTT
1 TTCAAGTA-CCAATTGAGTG-AAAAAAAAAAAGTAGGAACTTAATTCTTTTTTT-AAAAAAA--T
*
2415 TGA-GG--TTTTTTTGATATATTTTGATAG
61 TGAGGGTTTTTTTTTGATACATTTTGATAG
2442 TTCAAGTACCTAATTGAGTGAAAAAAAAAAAGTAGGAACTTAATTGCTTTTTTTAAAAAAATTGA
1 TTCAAGTACC-AATTGAGTGAAAAAAAAAAAGTAGGAACTTAATT-CTTTTTTTAAAAAAATTGA
2507 GGGTTTTTTT
64 GGGTTTTTTT
2517 ACACCCATAA
Statistics
Matches: 127, Mismatches: 26, Indels: 26
0.71 0.15 0.15
Matches are distributed among these distances:
89 4 0.03
90 18 0.14
91 45 0.35
92 32 0.25
93 10 0.08
94 5 0.04
95 13 0.10
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (90 bp):
TTCAAGTACCAATTGAGTGAAAAAAAAAAAGTAGGAACTTAATTCTTTTTTTAAAAAAATTGAGG
GTTTTTTTTTGATACATTTTGATAG
Found at i:3560 original size:9 final size:9
Alignment explanation
Indices: 3546--3583 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
3536 AAATAAAAAC
3546 AAATCTTTT
1 AAATCTTTT
3555 AAATCTTTT
1 AAATCTTTT
*
3564 AAATTCTTTA
1 AAA-TCTTTT
3574 AAAT-TTTT
1 AAATCTTTT
3582 AA
1 AA
3584 GTATATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 5 0.19
9 13 0.50
10 8 0.31
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (9 bp):
AAATCTTTT
Found at i:5494 original size:19 final size:20
Alignment explanation
Indices: 5457--5494 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5447 TTTAACGAGG
* *
5457 TTAAAAATTGGAATTGAAAT
1 TTAAAAAGTGGAATGGAAAT
5477 TTAAAAAGTGGAA-GGAAA
1 TTAAAAAGTGGAATGGAAA
5495 AAGTTCTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (20 bp):
TTAAAAAGTGGAATGGAAAT
Found at i:12006 original size:157 final size:155
Alignment explanation
Indices: 11714--12547 Score: 949
Period size: 157 Copynumber: 5.4 Consensus size: 155
11704 TGATTAAAAC
* * * * *
11714 AAAATCACCACTTTACTTCAAAAA-TCAAAAATTTTATTTCAAAATAG-TTAAAAAAAGCAAAAC
1 AAAATCACTATTTTACTT-AAAAACT-AAAACTTTTATTTCGAAATAGTTTAAAAAAATCAAAAC
* * *
11777 TTTGTTTAAAAATTTGAACTTTTTCTTTAAAAAAACTAAAAAATAGTTTTTTATTTTTTTAAAAA
64 TTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTA--TTTTTAAAAA
* *
11842 TCTAAACTTTCTTTTTTTTTTTTTTAATG
127 TATAAACTTTCTTTTTTTTTTTTTTAAAG
* **** *
11871 AAAATCACTACTTTACTTAAAAACCTAAAAAAAAT-TTTCGAAATAGTTTTAAAAAAATCAAAAT
1 AAAATCACTATTTTACTTAAAAA-CTAAAACTTTTATTTCGAAATAG-TTTAAAAAAATCAAAAC
* * * *
11935 TTTATTTAAAATTTTAAACTTTTTCTTTAAAATAATTAAAAGAACAGATTTTTATTTTTAAAAAT
64 TTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAA-AATAGATTTTTATTTTTAAAAAT
*
12000 ATAAA----C-TTTTTCTTTTTTTAAAG
128 ATAAACTTTCTTTTTTTTTTTTTTAAAG
* * * *
12023 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAACTAAAACTTTTATTTCGAAATAGTTTAAAAAAATCAAAACTT
* *
12088 TGTTTAAAAATTTAAAATTTTTCTTTAAAATAACT-AAAAA-AGATTTTTATTTTTAAAAAATGT
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTT-AAAAATAT
*
12151 AAACTTTC----TATTTTTTTTAAAG
130 AAACTTTCTTTTTTTTTTTTTTAAAG
* *
12173 AAAAAT-A-TATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAAACT
1 -AAAATCACTATTTTACTTAAAAACTAAAACTTTTATTTCGAAATAGTTTAAAAAAATCAAAACT
12235 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTA-TTTTAAAAATAT
65 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATAT
* *
12299 AAATTTTCTCTTCTTTTTTTTTTAAAG
130 AAACTTTCT-TTTTTTTTTTTTTAAAG
* * * *
12326 AAAATCACTATTTTTCTTAAAAA-TCCAAACTTTTATTTCGAAATTGTTTAAAAAAAATCAAAAT
1 AAAATCACTATTTTACTTAAAAACT-AAAACTTTTATTTCGAAATAGTTT-AAAAAAATCAAAAC
* * *
12390 TTTGTTTAAAAATTTAAACATTTTCTTTAAAATAACTAAAAAAATTGATTTTTATTTTTAAAAGT
64 TTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAATAGATTTTTATTTTTAAAAAT
* * *
12455 TTGAACTTT-TTATTTTTATTTTTTTTAA-
128 ATAAACTTTCTT-TTTTT-TTTTTTTAAAG
* * * *
12483 AAAATCACTATTTTTCTTAAAAA-TCAAAACTTTTATTTCAAAATTGTTT-AAAAAACCAAAACT
1 AAAATCACTATTTTACTTAAAAACT-AAAACTTTTATTTCGAAATAGTTTAAAAAAATCAAAACT
12546 TT
65 TT
12548 TCCCAAAATC
Statistics
Matches: 594, Mismatches: 55, Indels: 58
0.84 0.08 0.08
Matches are distributed among these distances:
148 79 0.13
149 58 0.10
150 25 0.04
151 58 0.10
152 52 0.09
153 17 0.03
154 34 0.06
155 16 0.03
156 65 0.11
157 105 0.18
158 75 0.13
159 10 0.02
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (155 bp):
AAAATCACTATTTTACTTAAAAACTAAAACTTTTATTTCGAAATAGTTTAAAAAAATCAAAACTT
TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATA
AACTTTCTTTTTTTTTTTTTTAAAG
Found at i:12400 original size:20 final size:21
Alignment explanation
Indices: 12377--12421 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
12367 AATTGTTTAA
*
12377 AAAAAATCAAA-ATTTTGTTT
1 AAAAAATCAAACATTTTCTTT
* *
12397 AAAAATTTAAACATTTTCTTT
1 AAAAAATCAAACATTTTCTTT
12418 AAAA
1 AAAA
12422 TAACTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAAATCAAACATTTTCTTT
Found at i:12957 original size:3 final size:3
Alignment explanation
Indices: 12949--12977 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12939 CATGAGACCC
12949 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12978 TGAGCCCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:21187 original size:20 final size:19
Alignment explanation
Indices: 21158--21196 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
21148 ACAATTAAAC
21158 AAAAATAAAATAAAATAAT
1 AAAAATAAAATAAAATAAT
*
21177 AAAAATAAAAATAATATAAT
1 AAAAAT-AAAATAAAATAAT
21197 TTATATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATAAAATAAAATAAT
Found at i:21282 original size:12 final size:13
Alignment explanation
Indices: 21249--21311 Score: 58
Period size: 13 Copynumber: 4.7 Consensus size: 13
21239 AAATCATGAT
21249 ATAATTAAAAATA
1 ATAATTAAAAATA
*
21262 ACAAATTAAAAA-A
1 A-TAATTAAAAATA
21275 ATAATTAAAAGATA
1 ATAATTAAAA-ATA
*
21289 A-AATAAAAAATGA
1 ATAATTAAAAAT-A
21302 CATAATTAAA
1 -ATAATTAAA
21312 GAGGCAAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 10 0.25
13 12 0.30
14 12 0.30
15 6 0.15
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (13 bp):
ATAATTAAAAATA
Found at i:21599 original size:21 final size:22
Alignment explanation
Indices: 21573--21622 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
21563 ATTAAAGGTT
*
21573 AAAATTAAAAAAAAAGAATA-A
1 AAAATTAAAAAAAAACAATATA
**
21594 AAAATTAAATTAAAACAATATA
1 AAAATTAAAAAAAAACAATATA
21616 AAAATTA
1 AAAATTA
21623 TAGGGACTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAATTAAAAAAAAACAATATA
Found at i:22898 original size:30 final size:28
Alignment explanation
Indices: 22826--22917 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 28
22816 ATTCAAGGTC
* *
22826 AAAAATGGGATTGTTGGAAGTTTGGGGGT
1 AAAAATGGGATT-TTAGAAGTTAGGGGGT
* *
22855 -AAAATGGTAATTTTAAGAAGGTTAGGGGTT
1 AAAAATGG-GATTTT-AGAA-GTTAGGGGGT
*
22885 AAAAATGGGATTTTTGGAAGTTCA-GGGGT
1 AAAAATGGGA-TTTTAGAAGTT-AGGGGGT
22914 AAAA
1 AAAA
22918 TAGTAATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
28 9 0.18
29 17 0.34
30 13 0.26
31 11 0.22
ACGTcount: A:0.35, C:0.01, G:0.34, T:0.30
Consensus pattern (28 bp):
AAAAATGGGATTTTAGAAGTTAGGGGGT
Found at i:22957 original size:89 final size:88
Alignment explanation
Indices: 22855--23045 Score: 244
Period size: 89 Copynumber: 2.1 Consensus size: 88
22845 GTTTGGGGGT
*
22855 AAAATGGTAATTTTA-AGAAGGTTAGGGG-TTAAAAATGGGATTTTTGGAAGTTC-AGGGGTAAA
1 AAAATGG-AATTTTAGAG-A-GTTAGGGGATCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAA
* *
22917 ATAGTAATTTTTGGACGGTTCGGGATCA
62 ATAGTAA-TTTTGGAAGATTCGGGATCA
* * *
22945 AAAATGGGATTTTTGAGAGTTTGGGGATCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAG
1 AAAATGGAATTTTAGAGAGTTAGGGGATCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAG
*
23010 TAATTTTGGAAGATTCGGGGTCA
66 TAATTTTGGAAGATTCGGGATCA
*
23033 AAATTGGAATTTT
1 AAAATGGAATTTT
23046 TGGAAGTTCG
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
88 35 0.39
89 44 0.49
90 10 0.11
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (88 bp):
AAAATGGAATTTTAGAGAGTTAGGGGATCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAG
TAATTTTGGAAGATTCGGGATCA
Found at i:22959 original size:30 final size:29
Alignment explanation
Indices: 22720--23117 Score: 255
Period size: 30 Copynumber: 13.6 Consensus size: 29
22710 AGAATGGTAG
** *
22720 TTTTGGAATGTTCGGAATCAAAAATAGGAT
1 TTTTGGAA-GTTCGGGGTCAAAAATGGGAT
* * *
22750 CTTTGAAAGTTCGAGGGT--AAAATGGTAAT
1 TTTTGGAAGTTCG-GGGTCAAAAATGG-GAT
* * **
22779 TTTTGGAAATTCGAGG--AAAAATAGTAAT
1 TTTTGGAAGTTCGGGGTCAAAAAT-GGGAT
**
22807 TTTTGGAAGATTCAAGGTCAAAAATGGGAT
1 TTTTGGAAG-TTCGGGGTCAAAAATGGGAT
* * *
22837 TGTTGGAAGTTTGGGGGT--AAAATGGTAAT
1 TTTTGGAAG-TTCGGGGTCAAAAATGG-GAT
** * *
22866 TTTAAGAAGGTTAGGGGTTAAAAATGGGAT
1 TTTTGGAA-GTTCGGGGTCAAAAATGGGAT
**
22896 TTTTGGAAGTTCAGGGGT--AAAATAGTAAT
1 TTTTGGAAGTTC-GGGGTCAAAAAT-GGGAT
* *
22925 TTTTGGACGGTTCGGGATCAAAAATGGGAT
1 TTTTGGA-AGTTCGGGGTCAAAAATGGGAT
*
22955 TTTT-GAGAGTTTGGGGATCAAAAATGGGAT
1 TTTTGGA-AGTTCGGGG-TCAAAAATGGGAT
* * *
22985 TTTTGGAAGTTCGAGGGT--AAAATAGTAA
1 TTTTGGAAGTTCG-GGGTCAAAAATGGGAT
* *
23013 TTTTGGAAGATTCGGGGTCAAAATTGGAAT
1 TTTTGGAAG-TTCGGGGTCAAAAATGGGAT
**
23043 TTTTGGAAGTTCGGGGGT--AAAATAGTAAT
1 TTTTGGAAGTTC-GGGGTCAAAAAT-GGGAT
*
23072 TTTTGGAAGATTCGAGGTCAAAAATGGGAT
1 TTTTGGAAG-TTCGGGGTCAAAAATGGGAT
23102 TTTTGGAAGTTCGGGG
1 TTTTGGAAGTTCGGGG
23118 GTAAAATAGT
Statistics
Matches: 288, Mismatches: 53, Indels: 55
0.73 0.13 0.14
Matches are distributed among these distances:
28 60 0.21
29 93 0.32
30 107 0.37
31 28 0.10
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (29 bp):
TTTTGGAAGTTCGGGGTCAAAAATGGGAT
Found at i:22997 original size:59 final size:57
Alignment explanation
Indices: 22720--23123 Score: 272
Period size: 59 Copynumber: 6.9 Consensus size: 57
22710 AGAATGGTAG
** * * *
22720 TTTTGGAATGTTCGGAATCAAAAATAGG-ATCTTTGAAAGTTCGAGGGT-AAAATGGTAAT
1 TTTTGGAA-GTTCGGGGTCAAAAAT-GGAATTTTTGGAAGTTCG-GGGTAAAAATGG-GAT
* * * **
22779 TTTTGGAAATTCGAGG--AAAAATAGTAATTTTTGGAAGATTCAAGGTCAAAAATGGGAT
1 TTTTGGAAGTTCGGGGTCAAAAAT-GGAATTTTTGGAAG-TTCGGGGT-AAAAATGGGAT
* * ** *
22837 TGTTGGAAGTTTGGGGGT--AAAATGGTAATTTTAAGAAGGTTAGGGGTTAAAAATGGGAT
1 TTTTGGAAG-TTCGGGGTCAAAAATGG-AATTTTTGGAA-GTTCGGGG-TAAAAATGGGAT
* * *
22896 TTTTGGAAGTTCAGGGGT--AAAATAGTAATTTTTGGACGGTTCGGGATCAAAAATGGGAT
1 TTTTGGAAGTTC-GGGGTCAAAAAT-GGAATTTTTGGA-AGTTCGGGGT-AAAAATGGGAT
* * * * *
22955 TTTT-GAGAGTTTGGGGATCAAAAATGGGATTTTTGGAAGTTCGAGGGT-AAAATAGTAA
1 TTTTGGA-AGTTCGGGG-TCAAAAATGGAATTTTTGGAAGTTCG-GGGTAAAAATGGGAT
* **
23013 TTTTGGAAGATTCGGGGTCAAAATTGGAATTTTTGGAAGTTCGGGGGT-AAAATAGTAAT
1 TTTTGGAAG-TTCGGGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGTAAAAAT-GGGAT
* *
23072 TTTTGGAAGATTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAA
1 TTTTGGAAG-TTCGGGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGTAAAA
23124 TAGTANNNNN
Statistics
Matches: 276, Mismatches: 46, Indels: 45
0.75 0.13 0.12
Matches are distributed among these distances:
56 8 0.03
57 12 0.04
58 71 0.26
59 161 0.58
60 19 0.07
61 5 0.02
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (57 bp):
TTTTGGAAGTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGTAAAAATGGGAT
Found at i:23276 original size:21 final size:22
Alignment explanation
Indices: 23250--23299 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
23240 ATTAAAGGTT
*
23250 AAAATTAAAAAAAAAGAATA-A
1 AAAATTAAAAAAAAACAATATA
**
23271 AAAATTAAATTAAAACAATATA
1 AAAATTAAAAAAAAACAATATA
23293 AAAATTA
1 AAAATTA
23300 TAGGGACTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAATTAAAAAAAAACAATATA
Found at i:24575 original size:30 final size:28
Alignment explanation
Indices: 24503--24594 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 28
24493 ATTCAAGGTC
* *
24503 AAAAATGGGATTGTTGGAAGTTTGGGGGT
1 AAAAATGGGATT-TTAGAAGTTAGGGGGT
* *
24532 -AAAATGGTAATTTTAAGAAGGTTAGGGGTT
1 AAAAATGG-GATTTT-AGAA-GTTAGGGGGT
*
24562 AAAAATGGGATTTTTGGAAGTTCA-GGGGT
1 AAAAATGGGA-TTTTAGAAGTT-AGGGGGT
24591 AAAA
1 AAAA
24595 TAGTAATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
28 9 0.18
29 17 0.34
30 13 0.26
31 11 0.22
ACGTcount: A:0.35, C:0.01, G:0.34, T:0.30
Consensus pattern (28 bp):
AAAAATGGGATTTTAGAAGTTAGGGGGT
Found at i:24674 original size:59 final size:57
Alignment explanation
Indices: 24397--24875 Score: 334
Period size: 59 Copynumber: 8.2 Consensus size: 57
24387 AGAATGGTAG
** * * *
24397 TTTTGGAATG-TTCGGAATCAAAAATAGG-ATCTTTGAAAGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAA-GATTCGGGGTCAAAAAT-GGAATTTTTGGAAGTTCG-GGGTAAAATGG-GAT
* * **
24456 TTTTGGAA-ATTCGAGG--AAAAATAGTAATTTTTGGAAGATTCAAGGTCAAAAATGGGAT
1 TTTTGGAAGATTCGGGGTCAAAAAT-GGAATTTTTGGAAG-TTCGGGGT--AAAATGGGAT
* * * ** *
24514 TGTTGGAAGTTTGGGGGT--AAAATGGTAATTTTAAGAAGGTTAGGGGTTAAAAATGGGAT
1 TTTTGGAAGATTCGGGGTCAAAAATGG-AATTTTTGGAA-GTTCGGGG-T-AAAATGGGAT
* * *
24573 TTTTGGAAG-TTCAGGGGT--AAAATAGTAATTTTTGGACGGTTCGGGATCAAAAATGGGAT
1 TTTTGGAAGATTC-GGGGTCAAAAAT-GGAATTTTTGGA-AGTTCGGGGT--AAAATGGGAT
* * * * *
24632 TTTT-G-AGAGTTTGGGGATCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAA
1 TTTTGGAAGA-TTCGGGG-TCAAAAATGGAATTTTTGGAAGTTCG-GGGTAAAATGGGAT
* **
24690 TTTTGGAAGATTCGGGGTCAAAATTGGAATTTTTGGAAGTTCGGGGGTAAAATAGTAAT
1 TTTTGGAAGATTCGGGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGTAAAAT-GGGAT
* * * *
24749 TTTTGGAAGATTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTATT
1 TTTTGGAAGATTCGGGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGTAAAATGGGA-T
** * *
24808 TTTTGGAAGATTCGGGGTTTAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAAT
1 TTTTGGAAGATTCGGGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGTAAAATGG-GAT
24867 TTTTGGAAG
1 TTTTGGAAG
24876 GTTTAGGGAC
Statistics
Matches: 341, Mismatches: 53, Indels: 52
0.76 0.12 0.12
Matches are distributed among these distances:
56 8 0.02
57 14 0.04
58 69 0.20
59 225 0.66
60 20 0.06
61 5 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.33
Consensus pattern (57 bp):
TTTTGGAAGATTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGTAAAATGGGAT
Found at i:24866 original size:118 final size:117
Alignment explanation
Indices: 24649--24875 Score: 384
Period size: 118 Copynumber: 1.9 Consensus size: 117
24639 AGTTTGGGGA
24649 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTGGAAGATTCGGGGTCAAAAT
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTGGAAGATTCGGGGTCAAAAT
24714 TGGAATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAAGATTCGAGG
66 TGGAATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAAGATTCGAGG
* * *
24766 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTATTTTTTGGAAGATTCGGGGTTTAAA
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTA-ATTTTGGAAGATTCGGGG-TCAAA
* *
24831 A-TGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAG
64 ATTGGAATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAAG
24876 GTTTAGGGAC
Statistics
Matches: 103, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
117 39 0.38
118 59 0.57
119 5 0.05
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (117 bp):
TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTGGAAGATTCGGGGTCAAAAT
TGGAATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAAGATTCGAGG
Found at i:24872 original size:29 final size:29
Alignment explanation
Indices: 24428--24875 Score: 330
Period size: 30 Copynumber: 15.3 Consensus size: 29
24418 AAATAGGATC
* *
24428 TTTGAAAGTTCGAGGGTAAAATGGTAATT
1 TTTGGAAGTTCGGGGGTAAAATGGTAATT
* * * *
24457 TTTGGAAATTC-GAGGAAAAATAGTAATT
1 TTTGGAAGTTCGGGGGTAAAATGGTAATT
** *
24485 TTTGGAAGATTC-AAGGTCAAAAATGG-GATT
1 TTTGGAAG-TTCGGGGGT--AAAATGGTAATT
* *
24515 GTTGGAAGTTTGGGGGTAAAATGGTAATT
1 TTTGGAAGTTCGGGGGTAAAATGGTAATT
** * * *
24544 TTAAGAAGGTTAGGGGTTAAAAATGG-GATT
1 TTTGGAA-GTTCGGGGGT-AAAATGGTAATT
* *
24574 TTTGGAAGTTCAGGGGTAAAATAGTAATT
1 TTTGGAAGTTCGGGGGTAAAATGGTAATT
* * *
24603 TTTGGACGGTTC-GGGATCAAAAATGG-GATT
1 TTTGGA-AGTTCGGGGGT--AAAATGGTAATT
* * *
24633 TTT-GAGAGTTTGGGGATCAAAAATGG-GATT
1 TTTGGA-AGTTCGGGGGT--AAAATGGTAATT
* *
24663 TTTGGAAGTTCGAGGGTAAAATAGTAA-T
1 TTTGGAAGTTCGGGGGTAAAATGGTAATT
24691 TTTGGAAGATTC-GGGGTCAAAATTGG-AATT
1 TTTGGAAG-TTCGGGGGT-AAAA-TGGTAATT
*
24721 TTTGGAAGTTCGGGGGTAAAATAGTAATT
1 TTTGGAAGTTCGGGGGTAAAATGGTAATT
* *
24750 TTTGGAAGATTC-GAGGTCAAAAATGG-GATT
1 TTTGGAAG-TTCGGGGGT--AAAATGGTAATT
* *
24780 TTTGGAAGTTCGGGGGTAAAATAGTATTT
1 TTTGGAAGTTCGGGGGTAAAATGGTAATT
* *
24809 TTTGGAAGATTCGGGGTTTAAAATGG-GATT
1 TTTGGAAG-TTCGGGG-GTAAAATGGTAATT
24839 TTTGGAAGTTCGGGGGTAAAATGGTAATT
1 TTTGGAAGTTCGGGGGTAAAATGGTAATT
24868 TTTGGAAG
1 TTTGGAAG
24876 GTTTAGGGAC
Statistics
Matches: 334, Mismatches: 57, Indels: 56
0.75 0.13 0.13
Matches are distributed among these distances:
28 68 0.20
29 113 0.34
30 119 0.36
31 34 0.10
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (29 bp):
TTTGGAAGTTCGGGGGTAAAATGGTAATT
Done.