Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006380.1 Kokia drynarioides strain JFW-HI SEQ_120957, 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: 85501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2783 original size:41 final size:41
Alignment explanation
Indices: 2706--2923 Score: 258
Period size: 41 Copynumber: 5.2 Consensus size: 41
2696 TCGAGTCGTA
* *
2706 AGTCTTCCTTTAACCATATTCTCATTCTCATCTCGAGACATG
1 AGTCTTCC-TTAATCATAGTCTCATTCTCATCTCGAGACATG
* * *
2748 AGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGACATG
1 AGTCTTCCTTAATCATAGTCTCATTCTCATCTCGAGACATG
* *
2789 AGTCTTCCTTATTCATAGTCTCATTCTCATCTAGAGACATG
1 AGTCTTCCTTAATCATAGTCTCATTCTCATCTCGAGACATG
* * *
2830 AGTCTTCCTTATTTATAGTCTCATTCTCATCTCGACACATG
1 AGTCTTCCTTAATCATAGTCTCATTCTCATCTCGAGACATG
* * * * *
2871 AGTCTTCCATTTATACA-ATTTCTCATGCTCAACCCGAGACATG
1 AGTCTTCC-TTAAT-CATA-GTCTCATTCTCATCTCGAGACATG
2914 AGTCTTCCTT
1 AGTCTTCCTT
2924 TTTATACACC
Statistics
Matches: 153, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
41 111 0.73
42 14 0.09
43 28 0.18
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.38
Consensus pattern (41 bp):
AGTCTTCCTTAATCATAGTCTCATTCTCATCTCGAGACATG
Found at i:13010 original size:44 final size:43
Alignment explanation
Indices: 12850--13060 Score: 154
Period size: 43 Copynumber: 4.9 Consensus size: 43
12840 GTTTATGAGG
* * ** * * *
12850 AAAAACGCCGCTATAGAACATGAACTTTAGCGACGCTTCTCCC
1 AAAAATGCCGCTAAAGAACATGGTCTTTAGCGGCACTTCTACC
* * * * * * * *
12893 ACAAACGCCACTAAAGAACATGGTCATTAGTGACGCTTCTCCC
1 AAAAATGCCGCTAAAGAACATGGTCTTTAGCGGCACTTCTACC
* * * * *
12936 ACAAACGCTGCTAAAGAACATGGTCATTAGCGGCACTTAC-CCC
1 AAAAATGCCGCTAAAGAACATGGTCTTTAGCGGCACTT-CTACC
* * **
12979 AAAAAATGCCGTTAAAGAACATGGTTTTTAGCGGTGCTTCTACC
1 -AAAAATGCCGCTAAAGAACATGGTCTTTAGCGGCACTTCTACC
* * *
13023 AAAAATGTCGCTAATGAACATGGTCTTTAGCAGCACTT
1 AAAAATGCCGCTAAAGAACATGGTCTTTAGCGGCACTT
13061 TTCTCACAAA
Statistics
Matches: 137, Mismatches: 28, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
43 104 0.76
44 33 0.24
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAAATGCCGCTAAAGAACATGGTCTTTAGCGGCACTTCTACC
Found at i:18994 original size:26 final size:26
Alignment explanation
Indices: 18958--19019 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
18948 AAAATTTATG
18958 CCTATAGTGTCATATGACACCTCTAA
1 CCTATAGTGTCATATGACACCTCTAA
* * * *
18984 CCTATAGTGTCATATGGCATCTTTAG
1 CCTATAGTGTCATATGACACCTCTAA
19010 CCTATAGTGT
1 CCTATAGTGT
19020 TGACAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (26 bp):
CCTATAGTGTCATATGACACCTCTAA
Found at i:19119 original size:43 final size:46
Alignment explanation
Indices: 19058--19159 Score: 138
Period size: 43 Copynumber: 2.3 Consensus size: 46
19048 GCATTAATTA
*
19058 AATAATTAAATATTTGGGTT-ATTTT-TTAA-TAAATAACTAACTG
1 AATAATTAAATATTTGGGTTCATTTTAATAATTAAATAACTAACTG
** *
19101 AATAATTAAATATTTGGGTTCATTTTAATAATTAAATATTTAATTG
1 AATAATTAAATATTTGGGTTCATTTTAATAATTAAATAACTAACTG
19147 AATATATTAAATA
1 AATA-ATTAAATA
19160 ATTAAATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
43 20 0.39
44 5 0.10
45 3 0.06
46 15 0.29
47 8 0.16
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (46 bp):
AATAATTAAATATTTGGGTTCATTTTAATAATTAAATAACTAACTG
Found at i:19179 original size:14 final size:14
Alignment explanation
Indices: 19160--19190 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19150 ATATTAAATA
*
19160 ATTAAATATTTTGG
1 ATTAAATATTTTCG
19174 ATTAAATATTTTCG
1 ATTAAATATTTTCG
19188 ATT
1 ATT
19191 GTTATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (14 bp):
ATTAAATATTTTCG
Found at i:19182 original size:29 final size:28
Alignment explanation
Indices: 19101--19183 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 28
19091 TAACTAACTG
* * *
19101 AATAATTAAATATTTGGGTT-CAT-TTT
1 AATAATTAAATATTTGGATTAAATATTA
*
19127 AATAATTAAATATTT-AATTGAATATATTA
1 AATAATTAAATATTTGGATT-AA-ATATTA
19156 AATAATTAAATATTTTGGATTAAATATT
1 AATAATTAAATA-TTTGGATTAAATATT
19184 TTCGATTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
25 2 0.04
26 15 0.33
28 2 0.04
29 19 0.41
30 5 0.11
31 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (28 bp):
AATAATTAAATATTTGGATTAAATATTA
Found at i:19235 original size:42 final size:43
Alignment explanation
Indices: 19174--19258 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 43
19164 AATATTTTGG
*
19174 ATTAAATATTTTCGATTGTTATTAATAAATAGCTAATTAAATA
1 ATTAAATATTTTCGATTGTTATTAATAAATAACTAATTAAATA
* * * *
19217 ATTAAATA-TTTGGGTTGTTTTTAATAATTAACTAATTAAATA
1 ATTAAATATTTTCGATTGTTATTAATAAATAACTAATTAAATA
19259 TCTTGAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 29 0.78
43 8 0.22
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (43 bp):
ATTAAATATTTTCGATTGTTATTAATAAATAACTAATTAAATA
Found at i:19279 original size:34 final size:32
Alignment explanation
Indices: 19240--19324 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
19230 GTTGTTTTTA
19240 ATAATTAACTAATTAAATATCTT-GAATTAAAT
1 ATAATTAACTAATTAAATAT-TTAGAATTAAAT
* *
19272 ATTTAATTAACTAA-T-AATGTTTATAATTAAAT
1 A--TAATTAACTAATTAAATATTTAGAATTAAAT
*
19304 ATAATTAAATAATTAAATATT
1 ATAATTAACTAATTAAATATT
19325 GTATTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
30 10 0.23
31 3 0.07
32 19 0.43
33 1 0.02
34 11 0.25
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (32 bp):
ATAATTAACTAATTAAATATTTAGAATTAAAT
Found at i:19538 original size:22 final size:22
Alignment explanation
Indices: 19510--19600 Score: 85
Period size: 22 Copynumber: 4.0 Consensus size: 22
19500 CTAAACTGTT
19510 TATAATTAAATATTTAATTAAA
1 TATAATTAAATATTTAATTAAA
*
19532 TATAATTAAGTAATTAAATAATTAAA
1 TATAATTAAAT-ATT---TAATTAAA
* * *
19558 TATAATTAAATAATTAAAT-AT
1 TATAATTAAATATTTAATTAAA
*
19579 TTTGAATTAAATATTTAATTAA
1 TAT-AATTAAATATTTAATTAA
19601 CTAATATTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
21 3 0.05
22 28 0.51
23 4 0.07
25 2 0.04
26 18 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATAATTAAATATTTAATTAAA
Found at i:19553 original size:26 final size:26
Alignment explanation
Indices: 19510--19577 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
19500 CTAAACTGTT
19510 TATAATTAAAT-ATT---TAATTAAA
1 TATAATTAAATAATTAAATAATTAAA
*
19532 TATAATTAAGTAATTAAATAATTAAA
1 TATAATTAAATAATTAAATAATTAAA
19558 TATAATTAAATAATTAAATA
1 TATAATTAAATAATTAAATA
19578 TTTTGAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.25
23 3 0.08
26 27 0.68
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
TATAATTAAATAATTAAATAATTAAA
Found at i:19563 original size:18 final size:18
Alignment explanation
Indices: 19511--19578 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
19501 TAAACTGTTT
19511 ATAATTAAATATTTAATTAAA
1 ATAATTAAATA--TAATT-AA
*
19532 TATAATT-AA-GTAATTAA
1 -ATAATTAAATATAATTAA
19549 ATAATTAAATATAATTAA
1 ATAATTAAATATAATTAA
19567 ATAATTAAATAT
1 ATAATTAAATAT
19579 TTTGAATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.14
17 4 0.10
18 24 0.57
21 2 0.05
22 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (18 bp):
ATAATTAAATATAATTAA
Found at i:19596 original size:8 final size:8
Alignment explanation
Indices: 19511--19577 Score: 66
Period size: 8 Copynumber: 8.4 Consensus size: 8
19501 TAAACTGTTT
19511 ATAATTAA
1 ATAATTAA
*
19519 ATATTTAA
1 ATAATTAA
* *
19527 TTAA--AT
1 ATAATTAA
19533 ATAATTAA
1 ATAATTAA
*
19541 GTAATTAA
1 ATAATTAA
19549 ATAATTAAA
1 ATAATT-AA
19558 TATAATTAA
1 -ATAATTAA
19567 ATAATTAA
1 ATAATTAA
19575 ATA
1 ATA
19578 TTTTGAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
6 4 0.09
8 33 0.70
9 4 0.09
10 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (8 bp):
ATAATTAA
Found at i:19754 original size:31 final size:28
Alignment explanation
Indices: 19693--19754 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
19683 GGAATTTGTA
**
19693 TATATTATTAATTTATAATAAATTATTG
1 TATATTATTAATTTATAATAAACCATTG
*
19721 TATATTATTAATTTGTAATAGAAACCATATG
1 TATATTATTAATTTATAAT--AAACCAT-TG
19752 TAT
1 TAT
19755 TCTAAACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.64
30 5 0.18
31 5 0.18
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (28 bp):
TATATTATTAATTTATAATAAACCATTG
Found at i:22496 original size:41 final size:41
Alignment explanation
Indices: 22449--22617 Score: 207
Period size: 41 Copynumber: 4.1 Consensus size: 41
22439 TAATGCTCTG
* *
22449 GACCTTTTGCGGCATTTTTTACATAAACGCCGCTATTGCTT
1 GACCTTTAGCGGCATTTTTTACATAAACGCCGCTATTGATT
* * *
22490 GACCTTTAGCAGCATTTTTTCCATAAACACCGCTATTGATT
1 GACCTTTAGCGGCATTTTTTACATAAACGCCGCTATTGATT
**
22531 GACCTTTAGCGG-GGTTTTTACCATAAACGCCGCTATTGATT
1 GACCTTTAGCGGCATTTTTTA-CATAAACGCCGCTATTGATT
* * * *
22572 AATCTTTAGCGGCGTTTTTCT-CATAAATGCCGCTATTGATT
1 GACCTTTAGCGGCATTTTT-TACATAAACGCCGCTATTGATT
22613 GACCT
1 GACCT
22618 CTAATTTTTT
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
40 5 0.05
41 98 0.90
42 5 0.05
43 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.37
Consensus pattern (41 bp):
GACCTTTAGCGGCATTTTTTACATAAACGCCGCTATTGATT
Found at i:22688 original size:22 final size:21
Alignment explanation
Indices: 22657--22698 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
22647 CCTTAGAATT
22657 TTTAGAAATTTTATAATATTTAA
1 TTTAGAAATTTTA-AA-ATTTAA
22680 TTTA-AAATTTTAAAATTTA
1 TTTAGAAATTTTAAAATTTA
22699 TAAAAGTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 8 0.42
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAGAAATTTTAAAATTTAA
Found at i:23003 original size:12 final size:12
Alignment explanation
Indices: 22986--23012 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
22976 TTTCTGAAAG
22986 AATAAAAATAGT
1 AATAAAAATAGT
22998 AATAAAAATAGT
1 AATAAAAATAGT
23010 AAT
1 AAT
23013 TTTTCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (12 bp):
AATAAAAATAGT
Found at i:24417 original size:41 final size:41
Alignment explanation
Indices: 24372--24933 Score: 304
Period size: 41 Copynumber: 13.7 Consensus size: 41
24362 TAAATGTAAA
* *
24372 TTAGCGGCGTTTATTGTA-AAACGCCGCTAATGCTCCGACCT
1 TTAGCGGCGTTT-TTATATAAACGCCGCTAATGCTCTGACCT
* * *
24413 TTAGCGGCG-CTTCATCATAAATGCCGCTAATGCTCTGACCT
1 TTAGCGGCGTTTTTAT-ATAAACGCCGCTAATGCTCTGACCT
* * *
24454 TTAGCGGC-TCTTCTT-CATAAATGCCGCTAATGCT-TCAACCT
1 TTAGCGGCGT-TT-TTATATAAACGCCGCTAATGCTCT-GACCT
** * * * * * *
24495 TTAGCGG-AATTTTATAATAAATGCTGCTACTGCTCCGAGCA
1 TTAGCGGCGTTTTTAT-ATAAACGCCGCTAATGCTCTGACCT
* * * *
24536 TTAGCGGGGCTTTTCTATAAACGCCACTAATGCTCTGACCT
1 TTAGCGGCGTTTTTATATAAACGCCGCTAATGCTCTGACCT
* * *
24577 TTAGCGGCATTTTTTTATAAATGCCGCTAATGCTCTGACCT
1 TTAGCGGCGTTTTTATATAAACGCCGCTAATGCTCTGACCT
** * * * * *
24618 TTAGCGATGCTTTTCTATAAACGCCGCTAATACTCTAACCA
1 TTAGCGGCGTTTTTATATAAACGCCGCTAATGCTCTGACCT
* * * *
24659 TTAGCGGCGCTTTTCTATAAACACCGCTAATGCTCCGACCT
1 TTAGCGGCGTTTTTATATAAACGCCGCTAATGCTCTGACCT
* * * * * *
24700 TTAGCAGCGCTTTCT-CATAAACGTCGCTAATGCTTTGGCCT
1 TTAGCGGCG-TTTTTATATAAACGCCGCTAATGCTCTGACCT
* * * * **
24741 TTAGCGGTGCTTTTGTATAAACGCCGCTAATGTTCAAACCT
1 TTAGCGGCGTTTTTATATAAACGCCGCTAATGCTCTGACCT
* * **** *
24782 TTA-CTAGCGCTTTGCCCTAAACGTCGCTAATGCTCTGACCT
1 TTAGC-GGCGTTTTTATATAAACGCCGCTAATGCTCTGACCT
** * * * * *
24823 TTAATGGTGTGTTTTCCTATAAACACCGCTAGTGCT-TTACCT
1 TTAGCGGCGT-TTTT-ATATAAACGCCGCTAATGCTCTGACCT
* * ** * *
24865 TTTGCGGTGTTTATGGT-TAAACGCCTCTAATGCT-TTACCGT
1 TTAGCGGCGTTT-TTATATAAACGCCGCTAATGCTCTGACC-T
* *
24906 TT-GTGGCGTTTTTGA-AAAAACGCCGCTA
1 TTAGCGGCGTTTTT-ATATAAACGCCGCTA
24934 TTACTTTACC
Statistics
Matches: 396, Mismatches: 104, Indels: 43
0.73 0.19 0.08
Matches are distributed among these distances:
39 5 0.01
40 45 0.11
41 305 0.77
42 25 0.06
43 16 0.04
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (41 bp):
TTAGCGGCGTTTTTATATAAACGCCGCTAATGCTCTGACCT
Found at i:24597 original size:123 final size:122
Alignment explanation
Indices: 24390--24825 Score: 409
Period size: 123 Copynumber: 3.5 Consensus size: 122
24380 GTTTATTGTA
* * *
24390 AAACGCCGCTAATGCTCCGACCTTTAGCGGCGCTTCATC-ATAAATGCCGCTAATGCTCTGACCT
1 AAACGCCGCTAATGCTCCGACCATTAGCGGCGCTT-TTCTATAAACGCCGCTAATGCTCTGACCT
24454 TTAGCGGCTCTTCTTCATAAATGCCGCTAATGCT-TCAACCTTTAGCG-GAATTTTATAAT
65 TTAGCGGCTCTTCTTCATAAATGCCGCTAATGCTCT-AACCTTTAGCGAG-ATTTTAT-AT
* * * * * *
24513 AAATGCTGCTACTGCTCCGAGCATTAGCGGGGCTTTTCTATAAACGCCACTAATGCTCTGACCTT
1 AAACGCCGCTAATGCTCCGACCATTAGCGGCGCTTTTCTATAAACGCCGCTAATGCTCTGACCTT
* * * * *
24578 TAGCGGCAT-TTTTTTATAAATGCCGCTAATGCTCTGACCTTTAGCGATGCTTTTCTAT
66 TAGCGGC-TCTTCTTCATAAATGCCGCTAATGCTCTAACCTTTAGCGA-GATTTTATAT
* ** * *
24636 AAACGCCGCTAATACTCTAACCATTAGCGGCGCTTTTCTATAAACACCGCTAATGCTCCGACCTT
1 AAACGCCGCTAATGCTCCGACCATTAGCGGCGCTTTTCTATAAACGCCGCTAATGCTCTGACCTT
* * * ** * * *
24701 TAGCAGCGCT-TTC-TCATAAACGTCGCTAATGCTTTGGCCTTTAGCGGTGCTTTTGTAT
66 TAGC-G-GCTCTTCTTCATAAATGCCGCTAATGCTCTAACCTTTAGC-GAGATTTTATAT
* ** * * * ** *
24759 AAACGCCGCTAATGTTCAAACCTTTA-CTAGCGCTTTGCCCTAAACGTCGCTAATGCTCTGACCT
1 AAACGCCGCTAATGCTCCGACCATTAGC-GGCGCTTTTCTATAAACGCCGCTAATGCTCTGACCT
24823 TTA
65 TTA
24826 ATGGTGTGTT
Statistics
Matches: 260, Mismatches: 44, Indels: 18
0.81 0.14 0.06
Matches are distributed among these distances:
122 3 0.01
123 242 0.93
124 12 0.05
125 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.32
Consensus pattern (122 bp):
AAACGCCGCTAATGCTCCGACCATTAGCGGCGCTTTTCTATAAACGCCGCTAATGCTCTGACCTT
TAGCGGCTCTTCTTCATAAATGCCGCTAATGCTCTAACCTTTAGCGAGATTTTATAT
Found at i:24782 original size:82 final size:82
Alignment explanation
Indices: 24390--24825 Score: 370
Period size: 82 Copynumber: 5.3 Consensus size: 82
24380 GTTTATTGTA
* * * *
24390 AAACGCCGCTAATGCTCCGACCTTTAGCGGCGCTTCATC-ATAAATGCCGCTAATGCTCTGACCT
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTT-TTCTATAAACGCCGCTAATGCTCAGACCT
24454 TTAGC-G-GCTCTTCTTCAT
65 TTAGCAGCGCT-TTC-TCAT
* * ** * * * * * *
24472 AAATGCCGCTAATGCT-TCAACCTTTAGCGG-AATTTTATAATAAATGCTGCTACTGCTCCGAGC
1 AAACGCCGCTAATGCTCT-GACCTTTAGCGGCGCTTTTCT-ATAAACGCCGCTAATGCTCAGACC
* * *
24535 ATTAGCGGGGCTTT-TCTAT
64 TTTAGCAGCGCTTTCTC-AT
* ** * * *
24554 AAACGCCACTAATGCTCTGACCTTTAGCGGCATTTTTTTATAAATGCCGCTAATGCTCTGACCTT
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTTCTATAAACGCCGCTAATGCTCAGACCTT
*
24619 TAGC-GATGCTTT-TCTAT
66 TAGCAG-CGCTTTCTC-AT
* * * * *
24636 AAACGCCGCTAATACTCTAACCATTAGCGGCGCTTTTCTATAAACACCGCTAATGCTCCGACCTT
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTTCTATAAACGCCGCTAATGCTCAGACCTT
24701 TAGCAGCGCTTTCTCAT
66 TAGCAGCGCTTTCTCAT
* * * * * * *
24718 AAACGTCGCTAATGCTTTGGCCTTTAGCGGTGCTTTTGTATAAACGCCGCTAATGTTCAAACCTT
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTTCTATAAACGCCGCTAATGCTCAGACCTT
*
24783 TA-CTAGCGCTTTGC-CCT
66 TAGC-AGCGCTTT-CTCAT
*
24800 AAACGTCGCTAATGCTCTGACCTTTA
1 AAACGCCGCTAATGCTCTGACCTTTA
24826 ATGGTGTGTT
Statistics
Matches: 292, Mismatches: 49, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
80 1 0.00
81 6 0.02
82 268 0.92
83 14 0.05
84 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.32
Consensus pattern (82 bp):
AAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTTCTATAAACGCCGCTAATGCTCAGACCTT
TAGCAGCGCTTTCTCAT
Found at i:24886 original size:40 final size:40
Alignment explanation
Indices: 24841--24949 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 40
24831 GTGTTTTCCT
* * * *
24841 ATAAACACCGCTAGTGCTTTACCTTTTGCGGTGTTTATGG
1 ATAAACGCCGCTAATGCTTTACCTTTTGCGGCGTTTATGA
* * * * *
24881 TTAAACGCCTCTAATGCTTTACCGTTTGTGGCGTTTTTGA
1 ATAAACGCCGCTAATGCTTTACCTTTTGCGGCGTTTATGA
* * *
24921 AAAAACGCCGCTATTACTTTACCTTTTGC
1 ATAAACGCCGCTAATGCTTTACCTTTTGC
24950 AGCATTTTCT
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (40 bp):
ATAAACGCCGCTAATGCTTTACCTTTTGCGGCGTTTATGA
Found at i:32547 original size:21 final size:21
Alignment explanation
Indices: 32522--32566 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
32512 TTAGTTTAGC
*
32522 AAAAACAAGAAAA-ATAGAGAA
1 AAAAACAA-AAAAGAAAGAGAA
*
32543 AAAAATAAAAAAGAAAGAGAA
1 AAAAACAAAAAAGAAAGAGAA
32564 AAA
1 AAA
32567 TGAGTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAACAAAAAAGAAAGAGAA
Found at i:34698 original size:74 final size:74
Alignment explanation
Indices: 34606--34754 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
34596 TATGTGTTCC
34606 GTTGTAAATACACTATATTTACAACCTAACCTGTATAGTTACGGAAAAGTCTACATCGAATGAGA
1 GTTGTAAATACACTATATTTACAACCTAACCTGTATAGTTACGGAAAAGTCTACATCGAATGAGA
34671 GTACGTTTG
66 GTACGTTTG
34680 GTTGTAAATACACTATATTTACAACCTAACCTGTATAGTTACGGAAAAGTCTACATCGAATGAGA
1 GTTGTAAATACACTATATTTACAACCTAACCTGTATAGTTACGGAAAAGTCTACATCGAATGAGA
34745 GTACGTTTG
66 GTACGTTTG
34754 G
1 G
34755 GGGCGGTCAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (74 bp):
GTTGTAAATACACTATATTTACAACCTAACCTGTATAGTTACGGAAAAGTCTACATCGAATGAGA
GTACGTTTG
Found at i:36632 original size:133 final size:135
Alignment explanation
Indices: 36383--36644 Score: 334
Period size: 133 Copynumber: 2.0 Consensus size: 135
36373 ATCGCTTACA
* * * *
36383 CCTCCTTTGGGTACGATCCTCGAAATACTACCAAGTGTTCCATTGTAACACACTACATTTACAAC
1 CCTCCTTTGGATACGATCCTAGAAATACTACCAAGTATTCCATTGTAACAAACTACATTTACAAC
* * ** * * *
36448 CTGACCCGTATACTTGTGGAAGTCGAAAACCTTCACAGAATGGGAGCACGTTCGAAGGTGGTCAC
66 CTAACCCGTATACCTACGGAAGTCGAAAACCATCACAGAATAGGAGCACGTTCGAAGGCGGTCAC
36513 TAAAG
131 TAAAG
* * *
36518 CCTCCTTTGGATACGATCCTTAG-AATACTACCAAGTATTTCGTTGT-ACAAACTATA-TTACAA
1 CCTCCTTTGGATACGATCC-TAGAAATACTACCAAGTATTCCATTGTAACAAACTACATTTACAA
* *
36580 CCTAACCCGTATACCTACGGAAGTCGAAAACACAT-ACCGAATAGGAGTACGTTCGAAGGCGGTC
65 CCTAACCCGTATACCTACGGAAGTCGAAAAC-CATCACAGAATAGGAGCACGTTCGAAGGCGGTC
36644 A
129 A
36645 AGTTGTTGGC
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
133 59 0.54
134 10 0.09
135 38 0.35
136 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (135 bp):
CCTCCTTTGGATACGATCCTAGAAATACTACCAAGTATTCCATTGTAACAAACTACATTTACAAC
CTAACCCGTATACCTACGGAAGTCGAAAACCATCACAGAATAGGAGCACGTTCGAAGGCGGTCAC
TAAAG
Found at i:37943 original size:22 final size:20
Alignment explanation
Indices: 37905--37945 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
37895 TGACAAGTAT
*
37905 TATATATATTACTACTTTAA
1 TATATATATCACTACTTTAA
37925 TATATATACTCACTAACTTTA
1 TATATATA-TCACT-ACTTTA
37946 TTATGTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATATATCACTACTTTAA
Found at i:47604 original size:19 final size:19
Alignment explanation
Indices: 47565--47602 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
47555 CTAAAAATCG
47565 ATAAATAATATTTCAGAAA
1 ATAAATAATATTTCAGAAA
*
47584 ATAAA-AATATTTTAGAAA
1 ATAAATAATATTTCAGAAA
47602 A
1 A
47603 ATTAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
ATAAATAATATTTCAGAAA
Found at i:49309 original size:28 final size:28
Alignment explanation
Indices: 49282--49400 Score: 105
Period size: 28 Copynumber: 4.2 Consensus size: 28
49272 CCTCTATGGT
*
49282 GAACCTCTAAAAGGAAAACCTTTTTGGT
1 GAACCTCTAAAAGGAAAACCTTTTTGGC
* * *
49310 AAACCTCTAAAAGGAAAACATTTATGGC
1 GAACCTCTAAAAGGAAAACCTTTTTGGC
* * * * * *
49338 GAACATTTGTAAA-GAAAGCCTCTGTGGC
1 GAACCTCT-AAAAGGAAAACCTTTTTGGC
* * *
49366 AAACATCTAAAAGGAAAGCCTTTTTGGC
1 GAACCTCTAAAAGGAAAACCTTTTTGGC
49394 GAACCTC
1 GAACCTC
49401 AGGAAAGGAA
Statistics
Matches: 70, Mismatches: 19, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
27 3 0.04
28 64 0.91
29 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.24
Consensus pattern (28 bp):
GAACCTCTAAAAGGAAAACCTTTTTGGC
Found at i:55347 original size:56 final size:56
Alignment explanation
Indices: 55286--55430 Score: 164
Period size: 56 Copynumber: 2.6 Consensus size: 56
55276 GAATCAGTCT
* * **
55286 TGCGACCTAAGGCAAACCCTGTTCTTGTATTCTGATAAGCATGTACGAATTGGTCC
1 TGCGACCTAAGGCAAACCCTGTTCGTGTATTCTGATAAGCATGTACAAACCGGTCC
* * * * * **
55342 TGCGACCTAAAGCAGACCTTGTTCGTGTTTTCTGATAAGCATGTGCAAACCGGTTT
1 TGCGACCTAAGGCAAACCCTGTTCGTGTATTCTGATAAGCATGTACAAACCGGTCC
* * *
55398 TGTGACCTAAGGCAAACCCTATTCGTGTTTTCT
1 TGCGACCTAAGGCAAACCCTGTTCGTGTATTCT
55431 TAAAAGTATG
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (56 bp):
TGCGACCTAAGGCAAACCCTGTTCGTGTATTCTGATAAGCATGTACAAACCGGTCC
Found at i:57836 original size:31 final size:30
Alignment explanation
Indices: 57792--57893 Score: 77
Period size: 31 Copynumber: 3.4 Consensus size: 30
57782 TTAATATAAC
* *
57792 ATTTGGTATCTAAATTTGACACTTTTTATTA
1 ATTTGATACCTAAATTTGACA-TTTTTATTA
**
57823 ATTTGATACCTAAACTTT----TTTTTACCCA
1 ATTTGATACCTAAA-TTTGACATTTTTA-TTA
* * *
57851 ATTTGATACCTGAACTTGACATTTTTTCTTA
1 ATTTGATACCTAAATTTGACA-TTTTTATTA
57882 ATTTGATACCTA
1 ATTTGATACCTA
57894 CACTTTTTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
27 8 0.15
28 14 0.26
31 24 0.44
32 8 0.15
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (30 bp):
ATTTGATACCTAAATTTGACATTTTTATTA
Found at i:57854 original size:28 final size:28
Alignment explanation
Indices: 57821--57961 Score: 122
Period size: 31 Copynumber: 4.8 Consensus size: 28
57811 CACTTTTTAT
57821 TAATTTGATACCTAAACTTTTTTTTACC
1 TAATTTGATACCTAAACTTTTTTTTACC
* * *
57849 CAATTTGATACCTGAACTTGACATTTTTT-CT
1 TAATTTGATACCTAAACTT----TTTTTTACC
* **
57880 TAATTTGATACCTACACTTTTTTGGACC
1 TAATTTGATACCTAAACTTTTTTTTACC
* * *
57908 TAATTTGGTACTTAAACTTGATTTTTTTTCC
1 TAATTTGATACCTAAAC-T--TTTTTTTACC
*
57939 TAATTTGGTACCTAAACTTTTTT
1 TAATTTGATACCTAAACTTTTTT
57962 AAAAAAATTT
Statistics
Matches: 89, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
27 4 0.04
28 37 0.42
29 1 0.01
30 1 0.01
31 40 0.45
32 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (28 bp):
TAATTTGATACCTAAACTTTTTTTTACC
Found at i:57884 original size:59 final size:59
Alignment explanation
Indices: 57792--57961 Score: 196
Period size: 59 Copynumber: 2.9 Consensus size: 59
57782 TTAATATAAC
* * * * * **
57792 ATTTGGTATCTAAATTTGACACTTTTTATTAATTTGATACCTAAACTTTTTTTTACCCA
1 ATTTGATACCTAAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTGGACCCA
* * *
57851 ATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTACACTTTTTTGGACCTA
1 ATTTGATACCTAAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTGGACCCA
* * ** * *
57910 ATTTGGTACTTAAACTTGATTTTTTTTCCTAATTTGGTACCTAAACTTTTTT
1 ATTTGATACCTAAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTT
57962 AAAAAAATTT
Statistics
Matches: 93, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 93 1.00
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (59 bp):
ATTTGATACCTAAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTGGACCCA
Found at i:66473 original size:21 final size:21
Alignment explanation
Indices: 66447--66516 Score: 140
Period size: 21 Copynumber: 3.3 Consensus size: 21
66437 CCTCTTCTTT
66447 TTCTTCTTCCTCCAGAATAAA
1 TTCTTCTTCCTCCAGAATAAA
66468 TTCTTCTTCCTCCAGAATAAA
1 TTCTTCTTCCTCCAGAATAAA
66489 TTCTTCTTCCTCCAGAATAAA
1 TTCTTCTTCCTCCAGAATAAA
66510 TTCTTCT
1 TTCTTCT
66517 CCAGATGACG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.26, C:0.29, G:0.04, T:0.41
Consensus pattern (21 bp):
TTCTTCTTCCTCCAGAATAAA
Found at i:81274 original size:23 final size:25
Alignment explanation
Indices: 81243--81292 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
81233 ATCTCATTTC
*
81243 AAAAGCTGAAAAATAAATAA-AAAT
1 AAAAGCTGAAAAATAAAGAATAAAT
*
81267 AAAA-CTGAAAACTAAAGAATAAAT
1 AAAAGCTGAAAAATAAAGAATAAAT
81291 AA
1 AA
81293 TGGTGTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.70, C:0.06, G:0.08, T:0.16
Consensus pattern (25 bp):
AAAAGCTGAAAAATAAAGAATAAAT
Found at i:85316 original size:23 final size:23
Alignment explanation
Indices: 85286--85331 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
85276 CGACAAAGGA
85286 GTCAGTCTTTGAAATCCTCAAGT
1 GTCAGTCTTTGAAATCCTCAAGT
85309 GTCAGTCTTTGAAATCCTCAAGT
1 GTCAGTCTTTGAAATCCTCAAGT
85332 CTAGTCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (23 bp):
GTCAGTCTTTGAAATCCTCAAGT
Done.