Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011576.1 Kokia drynarioides strain JFW-HI SEQ_126565, 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: 148175
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1247 original size:30 final size:30
Alignment explanation
Indices: 1180--1468 Score: 270
Period size: 30 Copynumber: 9.7 Consensus size: 30
1170 GGAGGTCCCT
*** *
1180 AAACTATCCAAAAATTTTGTTTTT-ACCCCC
1 AAACT-TCCAAAAATTCCATTTTTAACCCCA
* * *
1210 GAACTTCCAAAAATCCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
*
1240 AAACTTCCAAAAATTCCATTTTT-ACCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
* *
1269 GAACTTCCAAAAA-TCCTATTTTTACCCCCA
1 AAACTTCCAAAAATTCC-ATTTTTAACCCCA
*
1299 AAACTTCCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
* * * *
1328 AAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
* * *
1358 AAACTTCCAAAAAAT--ATGTTTTTACCCCC
1 AAACTTCCAAAAATTCCAT-TTTTAACCCCA
* **
1387 AAACTTCCAAAAATTCCATTTTTTACCCTG
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
*
1417 AAACTTCCCAAAATTCCATTTTT-ACCCTC-
1 AAACTTCCAAAAATTCCATTTTTAACCC-CA
*
1446 GAACTTCCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
1469 ATCCCCGGAT
Statistics
Matches: 217, Mismatches: 32, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
28 5 0.02
29 101 0.47
30 106 0.49
31 5 0.02
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCA
Found at i:1278 original size:59 final size:59
Alignment explanation
Indices: 1180--1468 Score: 355
Period size: 59 Copynumber: 4.9 Consensus size: 59
1170 GGAGGTCCCT
***
1180 AAACTATCCAAAAATTTTGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
* * * *
1240 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCTATTTTTACCCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
* * *
1299 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
* *** * * * *
1358 AAACTTCCAAAAAATATGTTTTTACCCCCAAACTTCCAAAAATTCCATTTTTTACC-CTG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTC-A
* * *
1417 AAACTTCCCAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTACCATTTT
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAA-TCCCATTTT
1469 ATCCCCGGAT
Statistics
Matches: 199, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
58 1 0.01
59 185 0.93
60 13 0.07
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
Found at i:1568 original size:28 final size:29
Alignment explanation
Indices: 1514--1573 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
1504 GAATTTTCCC
1514 AAATTACCATTTTAGCCCCGAGAATCC-A
1 AAATTACCATTTTAGCCCCGAGAATCCGA
** * *
1542 AAATTACCATTTTCTCCCCGGGTATCCGA
1 AAATTACCATTTTAGCCCCGAGAATCCGA
1571 AAA
1 AAA
1574 GTCTCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (29 bp):
AAATTACCATTTTAGCCCCGAGAATCCGA
Found at i:11517 original size:16 final size:16
Alignment explanation
Indices: 11496--11528 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11486 CGTGCCTCGC
11496 ATAATTCTTATGCTCT
1 ATAATTCTTATGCTCT
11512 ATAATTCTTATGCTCT
1 ATAATTCTTATGCTCT
11528 A
1 A
11529 CCCTTGATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (16 bp):
ATAATTCTTATGCTCT
Found at i:12891 original size:33 final size:31
Alignment explanation
Indices: 12854--12987 Score: 110
Period size: 33 Copynumber: 4.1 Consensus size: 31
12844 CCCTTTCCAA
*
12854 ATCACCTTCACTATCAAATTCTACCTCTTCATC
1 ATCACCTTC-CCATCAAATTCTACC-CTTCATC
* * *
12887 ATCACCCTCCCCATCAGATTTTACCCCTTCATC
1 ATCA-CCTTCCCATCAAATTCTA-CCCTTCATC
*
12920 ATCACCCTTCCCATCAACTTCTAGCCCTTCATC
1 ATCA-CCTTCCCATCAAATTCTA-CCCTTCATC
* *
12953 ATCA-CTCCCCCAT-AAACTTCTACCCCTTTATC
1 ATCACCT-TCCCATCAAA-TTCTA-CCCTTCATC
12985 ATC
1 ATC
12988 GCCCTCCCCA
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
31 4 0.05
32 21 0.25
33 53 0.63
34 6 0.07
ACGTcount: A:0.24, C:0.43, G:0.01, T:0.32
Consensus pattern (31 bp):
ATCACCTTCCCATCAAATTCTACCCTTCATC
Found at i:12912 original size:66 final size:66
Alignment explanation
Indices: 12811--12980 Score: 161
Period size: 66 Copynumber: 2.6 Consensus size: 66
12801 TCAGCTTGTA
* ** * * *
12811 CCCTTCCTACATCACCCTCATCATCAGCTTCTACCCTTTCCA-AATCA-CCTTCACTATCAAATT
1 CCCTTCAT-CATCACCCTCCCCATCAGATTCTACCCCTT-CATAATCACCCTTC-CCATCAAATT
12874 CTA-
63 CTAG
* * *
12877 CCTCTTCATCATCACCCTCCCCATCAGATTTTACCCCTTCATCATCACCCTTCCCATCAACTTCT
1 CC-CTTCATCATCACCCTCCCCATCAGATTCTACCCCTTCATAATCACCCTTCCCATCAAATTCT
12942 AG
65 AG
* *
12944 CCCTTCATCATCACTC-CCCCAT-AAACTTCTACCCCTT
1 CCCTTCATCATCACCCTCCCCATCAGA-TTCTACCCCTT
12981 TATCATCGCC
Statistics
Matches: 87, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
64 2 0.02
65 18 0.21
66 55 0.63
67 12 0.14
ACGTcount: A:0.23, C:0.44, G:0.02, T:0.31
Consensus pattern (66 bp):
CCCTTCATCATCACCCTCCCCATCAGATTCTACCCCTTCATAATCACCCTTCCCATCAAATTCTA
G
Found at i:12971 original size:32 final size:31
Alignment explanation
Indices: 12872--12987 Score: 117
Period size: 33 Copynumber: 3.6 Consensus size: 31
12862 CACTATCAAA
* *
12872 TTCTACCTCTTCATCATCACCCTCCCCATCAGA-
1 TTCTACCCCTTCATCATCA-CC-CCCCAT-AAAC
* *
12905 TTTTACCCCTTCATCATCACCCTTCCCATCAAC
1 TTCTACCCCTTCATCATCACCC--CCCATAAAC
*
12938 TTCTAGCCCTTCATCATCACTCCCCCATAAAC
1 TTCTACCCCTTCATCATCAC-CCCCCATAAAC
*
12970 TTCTACCCCTTTATCATC
1 TTCTACCCCTTCATCATC
12988 GCCCTCCCCA
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
31 1 0.01
32 27 0.39
33 40 0.57
34 2 0.03
ACGTcount: A:0.22, C:0.44, G:0.02, T:0.33
Consensus pattern (31 bp):
TTCTACCCCTTCATCATCACCCCCCATAAAC
Found at i:14019 original size:16 final size:16
Alignment explanation
Indices: 14000--14061 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
13990 ATATGTCGTG
14000 GATTTGAGGATTTCAC
1 GATTTGAGGATTTCAC
* * *
14016 GATTTGGGGGTTTCAT
1 GATTTGAGGATTTCAC
*
14032 GATTTGAGGAATTTGAC
1 GATTTGAGG-ATTTCAC
*
14049 GAGTTGAGGATTT
1 GATTTGAGGATTT
14062 TAGAATTTGG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
16 25 0.68
17 12 0.32
ACGTcount: A:0.23, C:0.06, G:0.32, T:0.39
Consensus pattern (16 bp):
GATTTGAGGATTTCAC
Found at i:16755 original size:21 final size:21
Alignment explanation
Indices: 16729--16781 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
16719 TTTTAACTTG
*
16729 AATCCTAGACCTTGGATCCTA
1 AATCCTAGACCTTGGACCCTA
*
16750 AATCCTAGACCTTGGACCCTG
1 AATCCTAGACCTTGGACCCTA
*
16771 AATCTTAGACC
1 AATCCTAGACC
16782 CTAGAACCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (21 bp):
AATCCTAGACCTTGGACCCTA
Found at i:21210 original size:25 final size:26
Alignment explanation
Indices: 21171--21219 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
21161 TACTTATATC
21171 ATATAAAATATAAAAAATATATTATA
1 ATATAAAATATAAAAAATATATTATA
21197 ATAT-AAATATAAAAAATATATTA
1 ATATAAAATATAAAAAATATATTA
21220 AATTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATAAAATATAAAAAATATATTATA
Found at i:21476 original size:21 final size:21
Alignment explanation
Indices: 21451--21490 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21441 TAATCTTAGT
21451 AAAATTATTAACTTTAAAATA
1 AAAATTATTAACTTTAAAATA
*
21472 AAAATTATTAATTTTAAAA
1 AAAATTATTAACTTTAAAA
21491 AATTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTATTAACTTTAAAATA
Found at i:21492 original size:18 final size:20
Alignment explanation
Indices: 21451--21502 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
21441 TAATCTTAGT
21451 AAAATTATTAACTTTAAAATA
1 AAAATTATTAA-TTTAAAATA
*
21472 AAAATTATTAATTT-TAA-A
1 AAAATTATTAATTTAAAATA
*
21490 AAATTTATTAATT
1 AAAATTATTAATT
21503 AAATTCAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 13 0.45
19 2 0.07
20 3 0.10
21 11 0.38
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATTATTAATTTAAAATA
Found at i:25707 original size:16 final size:18
Alignment explanation
Indices: 25686--25724 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
25676 TTTCACGTTA
*
25686 TTTATTTTA-TTT-TCGT
1 TTTATTTTAGTTTAACGT
25702 TTTATTTTAGTTTAACGT
1 TTTATTTTAGTTTAACGT
25720 TTTAT
1 TTTAT
25725 CTCTAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 3 0.15
18 8 0.40
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTATTTTAGTTTAACGT
Found at i:31535 original size:16 final size:18
Alignment explanation
Indices: 31514--31552 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
31504 TTTCACTTTA
*
31514 TTTATTTTA-TTT-TCGT
1 TTTATTTTAGTTTAACGT
31530 TTTATTTTAGTTTAACGT
1 TTTATTTTAGTTTAACGT
31548 TTTAT
1 TTTAT
31553 CTCTAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 3 0.15
18 8 0.40
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTATTTTAGTTTAACGT
Found at i:33145 original size:18 final size:18
Alignment explanation
Indices: 33044--33218 Score: 63
Period size: 18 Copynumber: 9.9 Consensus size: 18
33034 AAAAAAACAT
33044 ATTT-AAAGAATAAATCA
1 ATTTAAAAGAATAAATCA
* *
33061 ATTTAAAACAATAAATTAA
1 ATTTAAAAGAATAAA-TCA
33080 ATTT-AAA-AATAGAAT--
1 ATTTAAAAGAATA-AATCA
*
33095 -TTTATTAAA-AATACAT--
1 ATTTA--AAAGAATAAATCA
*
33111 ATTTAAAGAATAATAAATCA
1 ATTT-AA-AAGAATAAATCA
*
33131 ATTTAAAAGAATAAATTAA
1 ATTTAAAAGAATAAA-TCA
*
33150 ATTTTAAAAAAATATAATCTA
1 A-TTTAAAAGAATA-AATC-A
* * * *
33171 AATTGAAA-AAGACATC-
1 ATTTAAAAGAATAAATCA
33187 -TTT-AAAGAATAAATCA
1 ATTTAAAAGAATAAATCA
33203 ATTT-AAAGTAATAAAT
1 ATTTAAAAG-AATAAAT
33219 TAAAATTTAA
Statistics
Matches: 123, Mismatches: 15, Indels: 39
0.69 0.08 0.22
Matches are distributed among these distances:
14 6 0.05
15 8 0.07
16 3 0.02
17 28 0.23
18 39 0.32
19 14 0.11
20 21 0.17
21 4 0.03
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (18 bp):
ATTTAAAAGAATAAATCA
Found at i:33155 original size:20 final size:22
Alignment explanation
Indices: 33132--33174 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
33122 AATAAATCAA
*
33132 TTTAAAAGAATA-AAT-TAAAT
1 TTTAAAAAAATATAATCTAAAT
33152 TTTAAAAAAATATAATCTAAAT
1 TTTAAAAAAATATAATCTAAAT
33174 T
1 T
33175 GAAAAAGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 3 0.15
22 6 0.30
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTAAAAAAATATAATCTAAAT
Found at i:33159 original size:21 final size:22
Alignment explanation
Indices: 33135--33182 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
33125 AAATCAATTT
*
33135 AAAAGAATA-AAT-TAAATTTTA
1 AAAAGAATATAATCTAAA-TTGA
33156 AAAA-AATATAATCTAAATTGA
1 AAAAGAATATAATCTAAATTGA
33177 AAAAGA
1 AAAAGA
33183 CATCTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 14 0.61
22 5 0.22
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (22 bp):
AAAAGAATATAATCTAAATTGA
Found at i:33233 original size:18 final size:19
Alignment explanation
Indices: 33187--33241 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
33177 AAAAGACATC
*
33187 TTTAAAGAATAAA-T-CAA
1 TTTAAAGAATAAATTAAAA
33204 TTTAAAGTAATAAATTAAAA
1 TTTAAAG-AATAAATTAAAA
*
33224 TTTAAA-AATAGATTAAAA
1 TTTAAAGAATAAATTAAAA
33242 ATACATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 7 0.21
18 17 0.52
19 1 0.03
20 8 0.24
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
TTTAAAGAATAAATTAAAA
Found at i:33267 original size:137 final size:134
Alignment explanation
Indices: 33029--33297 Score: 396
Period size: 137 Copynumber: 1.9 Consensus size: 134
33019 AAATATCGAA
33029 AAATTAAAAAAACATATTTAAAGAATAAATCAATTTAAAACAATAAATTAAATTTAAAAATAGAA
1 AAATTAAAAAAACATATTTAAAGAATAAATCAATTTAAAACAATAAATTAAATTTAAAAATAG--
* *
33094 TTTTATTAAAAATACATATTTAAAGAATAATAAATCAATTTAAAAGAATAAATTAAATTTTAAAA
64 ---TATTAAAAATACATATTTAAAGAATAATAAATCAACTTAAAACAATAAATTAAA--TTAAAA
33159 AAATATAATCT
124 AAATATAATCT
* * **
33170 AAATTGAAAAAGACATCTTTAAAGAATAAATCAATTTAAAGTAATAAATTAAAATTTAAAAATAG
1 AAATT-AAAAAAACATATTTAAAGAATAAATCAATTTAAAACAATAAATT-AAATTTAAAAATAG
33235 -ATTAAAAATACATATTTAAAGAATAATAAATCAACTTAAAACAATAAATTAAATTAAAAAAAT
64 TATTAAAAATACATATTTAAAGAATAATAAATCAACTTAAAACAATAAATTAAATTAAAAAAAT
33298 TTATTTCTAA
Statistics
Matches: 120, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
135 10 0.08
137 51 0.43
141 5 0.04
142 40 0.33
143 14 0.12
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.31
Consensus pattern (134 bp):
AAATTAAAAAAACATATTTAAAGAATAAATCAATTTAAAACAATAAATTAAATTTAAAAATAGTA
TTAAAAATACATATTTAAAGAATAATAAATCAACTTAAAACAATAAATTAAATTAAAAAAATATA
ATCT
Found at i:33280 original size:18 final size:18
Alignment explanation
Indices: 33259--33293 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33249 TTTAAAGAAT
*
33259 AATAAATCAACTTAAAAC
1 AATAAATCAAATTAAAAC
*
33277 AATAAATTAAATTAAAA
1 AATAAATCAAATTAAAA
33294 AAATTTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAATCAAATTAAAAC
Found at i:37627 original size:25 final size:23
Alignment explanation
Indices: 37599--37644 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
37589 GTTGGATCAA
37599 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
37624 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
37645 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:38692 original size:10 final size:10
Alignment explanation
Indices: 38677--38730 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
38667 TTTCTTCTTC
*
38677 TTTTTTCCAA
1 TTTTTTTCAA
**
38687 TTTTTTTCTT
1 TTTTTTTCAA
38697 TTTTTTTCAA
1 TTTTTTTCAA
*
38707 TTTTTTTCGA
1 TTTTTTTCAA
38717 TTTTTTTC-A
1 TTTTTTTCAA
38726 TTTTT
1 TTTTT
38731 CTAAATAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
9 6 0.16
10 32 0.84
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:38700 original size:20 final size:20
Alignment explanation
Indices: 38666--38724 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
38656 CATTTTTATC
*
38666 TTTTCTTCTTCTTTTTTCCAA
1 TTTTTTTCTT-TTTTTTCCAA
*
38687 TTTTTTTCTTTTTTTTTCAA
1 TTTTTTTCTTTTTTTTCCAA
*
38707 TTTTTTTCGATTTTTTTC
1 TTTTTTTC-TTTTTTTTC
38725 ATTTTTCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTTCCAA
Found at i:38725 original size:20 final size:20
Alignment explanation
Indices: 38677--38730 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
38667 TTTCTTCTTC
* **
38677 TTTTTTCCAATTTTTTTCTT
1 TTTTTTTCAATTTTTTTCGA
38697 TTTTTTTCAATTTTTTTCGA
1 TTTTTTTCAATTTTTTTCGA
38717 TTTTTTTC-ATTTTT
1 TTTTTTTCAATTTTT
38731 CTAAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTTTCAATTTTTTTCGA
Found at i:39660 original size:6 final size:6
Alignment explanation
Indices: 39651--39676 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39641 AATGCATAAC
39651 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
39677 TGTACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:45125 original size:29 final size:28
Alignment explanation
Indices: 45067--45212 Score: 222
Period size: 29 Copynumber: 5.1 Consensus size: 28
45057 CTTTGTATAT
*
45067 GATATTATTGAAAAGGTATATCCGAAAG
1 GATATTATTGAAAAGTTATATCCGAAAG
* *
45095 GATATTATTAAAAATGTTATATCTGAAAG
1 GATATTATTGAAAA-GTTATATCCGAAAG
45124 GATATTATTGAAAAG-TATATCCGAAAG
1 GATATTATTGAAAAGTTATATCCGAAAG
*
45151 GATATTATTGGAAAGATTATATCCGAAAG
1 GATATTATTGAAAAG-TTATATCCGAAAG
45180 GATATTATTGAAAAGGTTATATCCGAAAG
1 GATATTATTGAAAA-GTTATATCCGAAAG
45209 GATA
1 GATA
45213 GGGATTGTCT
Statistics
Matches: 107, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.23
28 14 0.13
29 67 0.63
30 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (28 bp):
GATATTATTGAAAAGTTATATCCGAAAG
Found at i:45143 original size:15 final size:15
Alignment explanation
Indices: 45067--45195 Score: 66
Period size: 15 Copynumber: 9.1 Consensus size: 15
45057 CTTTGTATAT
45067 GATATTATTGAAAAG
1 GATATTATTGAAAAG
*
45082 G-TA-TATCCG-AAAG
1 GATATTAT-TGAAAAG
* *
45095 GATATTATTAAAAAT
1 GATATTATTGAAAAG
*
45110 GTTA-TATCTG-AAAG
1 GATATTAT-TGAAAAG
45124 GATATTATTGAAAA-
1 GATATTATTGAAAAG
*
45138 G-TA-TATCCG-AAAG
1 GATATTAT-TGAAAAG
*
45151 GATATTATTGGAAA-
1 GATATTATTGAAAAG
*
45165 GAT-TATATCCG-AAAG
1 GATAT-TAT-TGAAAAG
45180 GATATTATTGAAAAG
1 GATATTATTGAAAAG
45195 G
1 G
45196 TTATATCCGA
Statistics
Matches: 85, Mismatches: 12, Indels: 34
0.65 0.09 0.26
Matches are distributed among these distances:
12 6 0.07
13 13 0.15
14 30 0.35
15 35 0.41
16 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (15 bp):
GATATTATTGAAAAG
Found at i:45152 original size:56 final size:57
Alignment explanation
Indices: 45067--45212 Score: 233
Period size: 56 Copynumber: 2.6 Consensus size: 57
45057 CTTTGTATAT
*
45067 GATATTATTGAAAAGGTATATCCGAAAGGATATTATTAAAAATG-TTATATCTGAAAG
1 GATATTATTGAAAAGGTATATCCGAAAGGATATTATTAAAAA-GATTATATCCGAAAG
**
45124 GATATTATTGAAAA-GTATATCCGAAAGGATATTATTGGAAAGATTATATCCGAAAG
1 GATATTATTGAAAAGGTATATCCGAAAGGATATTATTAAAAAGATTATATCCGAAAG
45180 GATATTATTGAAAAGGTTATATCCGAAAGGATA
1 GATATTATTGAAAAGG-TATATCCGAAAGGATA
45213 GGGATTGTCT
Statistics
Matches: 83, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
55 1 0.01
56 51 0.61
57 15 0.18
58 16 0.19
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (57 bp):
GATATTATTGAAAAGGTATATCCGAAAGGATATTATTAAAAAGATTATATCCGAAAG
Found at i:45192 original size:14 final size:14
Alignment explanation
Indices: 45067--45192 Score: 68
Period size: 14 Copynumber: 8.9 Consensus size: 14
45057 CTTTGTATAT
45067 GATATTATTGAAAAG
1 GATATTATTG-AAAG
*
45082 G-TA-TATCCGAAAG
1 GATATTAT-TGAAAG
* *
45095 GATATTATTAAAAAT
1 GATATTATT-GAAAG
*
45110 GTTA-TATCTGAAAG
1 GATATTAT-TGAAAG
*
45124 GATATTATTGAAAA
1 GATATTATTGAAAG
*
45138 G-TA-TATCCGAAAG
1 GATATTAT-TGAAAG
45151 GATATTATTGGAAA-
1 GATATTATT-GAAAG
*
45165 GAT-TATATCCGAAAG
1 GATAT-TAT-TGAAAG
45180 GATATTATTGAAA
1 GATATTATTGAAA
45193 AGGTTATATC
Statistics
Matches: 83, Mismatches: 14, Indels: 29
0.66 0.11 0.23
Matches are distributed among these distances:
12 3 0.04
13 16 0.19
14 36 0.43
15 27 0.33
16 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.33
Consensus pattern (14 bp):
GATATTATTGAAAG
Found at i:49838 original size:14 final size:14
Alignment explanation
Indices: 49819--49845 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49809 ATTAATTAAA
49819 TATAAATTTATATC
1 TATAAATTTATATC
49833 TATAAATTTATAT
1 TATAAATTTATAT
49846 TCTTTAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
TATAAATTTATATC
Found at i:50614 original size:26 final size:26
Alignment explanation
Indices: 50575--50704 Score: 125
Period size: 26 Copynumber: 5.0 Consensus size: 26
50565 GCATTAGATT
* * * *
50575 GGTTGACTTAGAAAGCAGTATAGACC
1 GGTTGACCTGGAAACCAATATAGACC
*
50601 GGTTGACCTGGAAACCAAATATAAACC
1 GGTTGACCTGGAAACC-AATATAGACC
**
50628 GGTTGACCTAAAAACCAATATAGACC
1 GGTTGACCTGGAAACCAATATAGACC
* * * *
50654 GGATGACTTGGAAACCAGTATAGATC
1 GGTTGACCTGGAAACCAATATAGACC
* * *
50680 GGATGACCTGAAAACTAATATAGAC
1 GGTTGACCTGGAAACCAATATAGAC
50705 TGATTGGTTG
Statistics
Matches: 84, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
26 62 0.74
27 22 0.26
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (26 bp):
GGTTGACCTGGAAACCAATATAGACC
Found at i:50655 original size:53 final size:52
Alignment explanation
Indices: 50575--50704 Score: 143
Period size: 53 Copynumber: 2.5 Consensus size: 52
50565 GCATTAGATT
* * * * *
50575 GGTTGACTTAGAAAGCAGTATAGACCGGTTGACCTGGAAACCAAATATAAACC
1 GGTTGACCTAAAAACCAATATAGACCGGATGACCTGGAAACC-AATATAAACC
* * * *
50628 GGTTGACCTAAAAACCAATATAGACCGGATGACTTGGAAACCAGTATAGATC
1 GGTTGACCTAAAAACCAATATAGACCGGATGACCTGGAAACCAATATAAACC
* * *
50680 GGATGACCTGAAAACTAATATAGAC
1 GGTTGACCTAAAAACCAATATAGAC
50705 TGATTGGTTG
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
52 29 0.45
53 36 0.55
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (52 bp):
GGTTGACCTAAAAACCAATATAGACCGGATGACCTGGAAACCAATATAAACC
Found at i:50703 original size:52 final size:53
Alignment explanation
Indices: 50593--50704 Score: 145
Period size: 52 Copynumber: 2.1 Consensus size: 53
50583 TAGAAAGCAG
* *
50593 TATAGACCGGTTGACCTGGAAACCAAATATAAACCGGTTGACCTAAAAACCAA
1 TATAGACCGGATGACCTGGAAACCAAATATAAACCGGATGACCTAAAAACCAA
* * * * * *
50646 TATAGACCGGATGACTTGGAAACC-AGTATAGATCGGATGACCTGAAAACTAA
1 TATAGACCGGATGACCTGGAAACCAAATATAAACCGGATGACCTAAAAACCAA
50698 TATAGAC
1 TATAGAC
50705 TGATTGGTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 29 0.57
53 22 0.43
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (53 bp):
TATAGACCGGATGACCTGGAAACCAAATATAAACCGGATGACCTAAAAACCAA
Found at i:58191 original size:28 final size:28
Alignment explanation
Indices: 58145--58201 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
58135 TCACTTGGTT
*
58145 AGCCTTTGAAATTAGTAAAGCTTCAGTC
1 AGCCTTTGAAAATAGTAAAGCTTCAGTC
* *
58173 AGCCTTTGAAAATATTAAAGCTTTAGTC
1 AGCCTTTGAAAATAGTAAAGCTTCAGTC
58201 A
1 A
58202 ATTGGGCGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (28 bp):
AGCCTTTGAAAATAGTAAAGCTTCAGTC
Found at i:76001 original size:227 final size:227
Alignment explanation
Indices: 75606--76060 Score: 910
Period size: 227 Copynumber: 2.0 Consensus size: 227
75596 AAGCAGTATG
75606 ACCATCAATTCAGAGGTAACTGGTCACTCAACTTCTGATTTTGGTTCATCGGCTACTCCTACTGC
1 ACCATCAATTCAGAGGTAACTGGTCACTCAACTTCTGATTTTGGTTCATCGGCTACTCCTACTGC
75671 TTTGTCTTCATCGGTATTCACGGCTGACCAATACAACTAAATTCTGAGTCTCATCAACAAGGCTC
66 TTTGTCTTCATCGGTATTCACGGCTGACCAATACAACTAAATTCTGAGTCTCATCAACAAGGCTC
75736 CTTCGAAAGATTCCACTATGAATCTTGTAGGTATGGTTTCTGGATGTTTACTTGCTACTAATGTA
131 CTTCGAAAGATTCCACTATGAATCTTGTAGGTATGGTTTCTGGATGTTTACTTGCTACTAATGTA
75801 TCTCTTCACTGTATTTTGGATACAGGGGCGAC
196 TCTCTTCACTGTATTTTGGATACAGGGGCGAC
75833 ACCATCAATTCAGAGGTAACTGGTCACTCAACTTCTGATTTTGGTTCATCGGCTACTCCTACTGC
1 ACCATCAATTCAGAGGTAACTGGTCACTCAACTTCTGATTTTGGTTCATCGGCTACTCCTACTGC
75898 TTTGTCTTCATCGGTATTCACGGCTGACCAATACAACTAAATTCTGAGTCTCATCAACAAGGCTC
66 TTTGTCTTCATCGGTATTCACGGCTGACCAATACAACTAAATTCTGAGTCTCATCAACAAGGCTC
75963 CTTCGAAAGATTCCACTATGAATCTTGTAGGTATGGTTTCTGGATGTTTACTTGCTACTAATGTA
131 CTTCGAAAGATTCCACTATGAATCTTGTAGGTATGGTTTCTGGATGTTTACTTGCTACTAATGTA
76028 TCTCTTCACTGTATTTTGGATACAGGGGCGAC
196 TCTCTTCACTGTATTTTGGATACAGGGGCGAC
76060 A
1 A
76061 GATCATATCT
Statistics
Matches: 228, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 228 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (227 bp):
ACCATCAATTCAGAGGTAACTGGTCACTCAACTTCTGATTTTGGTTCATCGGCTACTCCTACTGC
TTTGTCTTCATCGGTATTCACGGCTGACCAATACAACTAAATTCTGAGTCTCATCAACAAGGCTC
CTTCGAAAGATTCCACTATGAATCTTGTAGGTATGGTTTCTGGATGTTTACTTGCTACTAATGTA
TCTCTTCACTGTATTTTGGATACAGGGGCGAC
Found at i:77278 original size:20 final size:21
Alignment explanation
Indices: 77253--77293 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
77243 CATTTTTATA
77253 ATATATAAAAACT-AAAAAAT
1 ATATATAAAAACTCAAAAAAT
* *
77273 ATATATTAAAATTCAAAAAAT
1 ATATATAAAAACTCAAAAAAT
77294 TGAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (21 bp):
ATATATAAAAACTCAAAAAAT
Found at i:77582 original size:13 final size:13
Alignment explanation
Indices: 77564--77591 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
77554 TATTGTAAAA
77564 GATTGCTATCGAT
1 GATTGCTATCGAT
77577 GATTGCTATCGAT
1 GATTGCTATCGAT
77590 GA
1 GA
77592 ATAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (13 bp):
GATTGCTATCGAT
Found at i:79515 original size:19 final size:19
Alignment explanation
Indices: 79491--79528 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
79481 CACATTTGCT
79491 TTAAGA-TATCAATATCCTA
1 TTAAGAGTATCAATA-CCTA
79510 TTAAGAGTATCAATACCTA
1 TTAAGAGTATCAATACCTA
79529 GAATTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (19 bp):
TTAAGAGTATCAATACCTA
Found at i:83475 original size:192 final size:192
Alignment explanation
Indices: 83146--83531 Score: 508
Period size: 192 Copynumber: 2.0 Consensus size: 192
83136 ACCAAACAAC
* * ***
83146 ACCCCAAACACCAAACACTCCTTACGAAAGCCTAGAACGGCTCAAAACGGCGGAGGAAAGTTGGT
1 ACCCCAAACACCAAACACTACTTACGAAAGCCTAGAACGGCTCAAAACGGCGGAGGAAAGGTAAA
** * * *
83211 AAAGTTAAAGGTTGAAAGAGGGGTCCTTGTGCCGATTTCGTAACGACGACAATGATGGAGGTTCG
66 AAAGTTAAAGGCCGAAAGAGGGGTCCTTGTGCCGATTTCGTAACGACAACAACGAGGGAGGTTCG
*
83276 ATGGTGTGGGTGAGATCGCT-AAGTGACAAGAAGAATGATGGTAAGGGC-AGTGTAATGCATGG
131 ATGGTGTGGGTGAGATC-CTGAAGTGACAAGAAGAATGATGGTAAGGGCGA-TGTAATGCACGG
** ** *
83338 ACCCCAAACACCAAACACTACTTA-GCAACTCCTAGAACGGCTCAAAACGTTGTAGGAAAGGTAA
1 ACCCCAAACACCAAACACTACTTACG-AAAGCCTAGAACGGCTCAAAACGGCGGAGGAAAGGTAA
* * * * **
83402 AAAAGTTAAAGGCCGAAAGAGGGGTTCTTGTGCCGATTTCTTAATGGCAATGACGAGGGAGGTTC
65 AAAAGTTAAAGGCCGAAAGAGGGGTCCTTGTGCCGATTTCGTAACGACAACAACGAGGGAGGTTC
* *
83467 GGTGGTGTGGGTGAGATCTTGAAGTGACAAGAAGAATGATGGTAAGGGCGATGTAATGCACGG
130 GATGGTGTGGGTGAGATCCTGAAGTGACAAGAAGAATGATGGTAAGGGCGATGTAATGCACGG
83530 AC
1 AC
83532 AATGGTATGG
Statistics
Matches: 167, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
191 2 0.01
192 164 0.98
193 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (192 bp):
ACCCCAAACACCAAACACTACTTACGAAAGCCTAGAACGGCTCAAAACGGCGGAGGAAAGGTAAA
AAAGTTAAAGGCCGAAAGAGGGGTCCTTGTGCCGATTTCGTAACGACAACAACGAGGGAGGTTCG
ATGGTGTGGGTGAGATCCTGAAGTGACAAGAAGAATGATGGTAAGGGCGATGTAATGCACGG
Found at i:89743 original size:23 final size:23
Alignment explanation
Indices: 89629--89738 Score: 130
Period size: 23 Copynumber: 4.8 Consensus size: 23
89619 CAACGGTAGG
** *
89629 TCAAAGTCAACAGTTCGGTTCGA
1 TCAAAGTCAATGGTTTGGTTCGA
89652 TCAAAGTCAATGGTTTGGTTCGA
1 TCAAAGTCAATGGTTTGGTTCGA
* *
89675 TCAAAGTCAATGATTTAGTTCGA
1 TCAAAGTCAATGGTTTGGTTCGA
* * *
89698 TCAAAGTTAATAGTTTGGTTCGG
1 TCAAAGTCAATGGTTTGGTTCGA
* *
89721 TCAAAGTTAACGGTTTGG
1 TCAAAGTCAATGGTTTGG
89739 GTCGGGTTGG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (23 bp):
TCAAAGTCAATGGTTTGGTTCGA
Found at i:100225 original size:24 final size:24
Alignment explanation
Indices: 100198--100285 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
100188 AACTATTTAG
100198 GGCTCGTAAGAGCTAACCATTCTA
1 GGCTCGTAAGAGCTAACCATTCTA
*
100222 GGCTCGTAAGAGCTAACCATTCTG
1 GGCTCGTAAGAGCTAACCATTCTA
* *
100246 GGCTCGTAAGAGTTGACCA-TCTTA
1 GGCTCGTAAGAGCTAACCATTC-TA
* *
100270 GGCTCATAAGATCTAA
1 GGCTCGTAAGAGCTAA
100286 TGTTGTCTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 2 0.04
24 53 0.96
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCATTCTA
Found at i:100826 original size:276 final size:276
Alignment explanation
Indices: 100326--100885 Score: 1050
Period size: 276 Copynumber: 2.0 Consensus size: 276
100316 GGAGGACTGA
100326 AAATGATATTTGTGAACTTACTAAGCTTAATAAGCTTACCCATGTATCTATTGTTGTTTTGTAGA
1 AAATGA-ATTTGTGAACTTACTAAGCTTAATAAGCTTACCCATGTATCTATTGTTGTTTTGTAGA
** *
100391 TATATTTTGTTGTTTGAAGATCGAATCATCTCAAAGAAATCACACTATTACGGAGCTCGTTTAGT
65 TATATTTTACTGTCTGAAGATCGAATCATCTCAAAGAAATCACACTATTACGGAGCTCGTTTAGT
100456 AGTTTTTACATCACTTGATTTTATGGCATGTACTAGGATGAAATTATTATATAACTCTAGAATTT
130 AGTTTTTACATCACTTGATTTTATGGCATGTACTAGGATGAAATTATTATATAACTCTAGAATTT
*
100521 GGATGCTGGTTCATTGTTGTAACCTTGGTTAGGTAGTTATCATACCTTGCATGGTACTACGGGTG
195 GGATGCTGGTTCATTGTTGTAACCTTGGTTAGGTAGTTATCATACCTTGCATGATACTACGGGTG
100586 AAAGTAGGCTTACAATG
260 AAAGTAGGCTTACAATG
100603 AAATGAATTTGTGAACTTACTAAGCTTAATAAGCTTACCCATGTATCTATTGTTGTTTTGTAGAT
1 AAATGAATTTGTGAACTTACTAAGCTTAATAAGCTTACCCATGTATCTATTGTTGTTTTGTAGAT
100668 ATATTTTACTGTCTGAAGATCGAATCATCTCAAAGAAATCACACTATTACGGAGCTCGTTT-GAT
66 ATATTTTACTGTCTGAAGATCGAATCATCTCAAAGAAATCACACTATTACGGAGCTCGTTTAG-T
*
100732 AGTTTTTACATCACTTGATTTTATGGCATGTACTAGGATGAAATTATTATATAACTCTGGAATTT
130 AGTTTTTACATCACTTGATTTTATGGCATGTACTAGGATGAAATTATTATATAACTCTAGAATTT
100797 GGATGCTGGTTCATTGTTGTAACCTTGGTTAGGTAGTTATCATACCTTGCATGATACTACGGGTG
195 GGATGCTGGTTCATTGTTGTAACCTTGGTTAGGTAGTTATCATACCTTGCATGATACTACGGGTG
100862 AAAGTAGGCTTACAATG
260 AAAGTAGGCTTACAATG
100879 AAATGAA
1 AAATGAA
100886 CTATATTATC
Statistics
Matches: 277, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
275 1 0.00
276 270 0.97
277 6 0.02
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (276 bp):
AAATGAATTTGTGAACTTACTAAGCTTAATAAGCTTACCCATGTATCTATTGTTGTTTTGTAGAT
ATATTTTACTGTCTGAAGATCGAATCATCTCAAAGAAATCACACTATTACGGAGCTCGTTTAGTA
GTTTTTACATCACTTGATTTTATGGCATGTACTAGGATGAAATTATTATATAACTCTAGAATTTG
GATGCTGGTTCATTGTTGTAACCTTGGTTAGGTAGTTATCATACCTTGCATGATACTACGGGTGA
AAGTAGGCTTACAATG
Found at i:102693 original size:57 final size:57
Alignment explanation
Indices: 102605--102724 Score: 213
Period size: 57 Copynumber: 2.1 Consensus size: 57
102595 CCTAACAAAG
* *
102605 TTCGACTAGCATAGTAGATGGGATGAAAAATTTATTCCTTTGTTGGCCCATCACAAT
1 TTCGACTAACATAGTAGATGGGATGAAAAATTTATTCCTTTGTTGGCCCATCACAAC
*
102662 TTCGACTAACATATTAGATGGGATGAAAAATTTATTCCTTTGTTGGCCCATCACAAC
1 TTCGACTAACATAGTAGATGGGATGAAAAATTTATTCCTTTGTTGGCCCATCACAAC
102719 TTCGAC
1 TTCGAC
102725 CGCTAAGTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (57 bp):
TTCGACTAACATAGTAGATGGGATGAAAAATTTATTCCTTTGTTGGCCCATCACAAC
Found at i:109856 original size:22 final size:22
Alignment explanation
Indices: 109831--109872 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
109821 GAATATTGCC
* *
109831 AGAGAATCTTAGTGTTCATGCT
1 AGAGAATCTCACTGTTCATGCT
109853 AGAGAATCTCACTGTTCATG
1 AGAGAATCTCACTGTTCATG
109873 TTGTATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (22 bp):
AGAGAATCTCACTGTTCATGCT
Found at i:119755 original size:17 final size:17
Alignment explanation
Indices: 119724--119765 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
119714 AATATATACG
*
119724 AAAATGCAACTAC-AAT
1 AAAATGCAACGACAAAT
*
119740 ACAAATGCATCGACAAAT
1 A-AAATGCAACGACAAAT
119758 AAAATGCA
1 AAAATGCA
119766 GGGATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 17 0.77
18 4 0.18
ACGTcount: A:0.55, C:0.19, G:0.10, T:0.17
Consensus pattern (17 bp):
AAAATGCAACGACAAAT
Found at i:126260 original size:12 final size:12
Alignment explanation
Indices: 126245--126270 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
126235 TGGTTGAGAA
126245 TGTTGTTGTTGC
1 TGTTGTTGTTGC
126257 TGTTGTTGTTGC
1 TGTTGTTGTTGC
126269 TG
1 TG
126271 ATGATGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.35, T:0.58
Consensus pattern (12 bp):
TGTTGTTGTTGC
Found at i:129537 original size:22 final size:22
Alignment explanation
Indices: 129509--129550 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
129499 CAGAGAATAT
129509 TGCCAGAGAATCTAACTGTTAA
1 TGCCAGAGAATCTAACTGTTAA
*
129531 TGCCAGAGAATCTCACTGTT
1 TGCCAGAGAATCTAACTGTT
129551 CATTTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (22 bp):
TGCCAGAGAATCTAACTGTTAA
Found at i:141784 original size:15 final size:15
Alignment explanation
Indices: 141764--141797 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
141754 TCGCAGCTCC
141764 CGCAACA-TGAGTGCT
1 CGCAACACT-AGTGCT
141779 CGCAACACTAGTGCT
1 CGCAACACTAGTGCT
141794 CGCA
1 CGCA
141798 TCTTTCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.94
16 1 0.06
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (15 bp):
CGCAACACTAGTGCT
Found at i:148005 original size:15 final size:15
Alignment explanation
Indices: 147985--148044 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
147975 ATATTTTAAT
147985 TATTTTAATATAAAA
1 TATTTTAATATAAAA
*
148000 TATTTT-ATTTCAAAA
1 TATTTTAATAT-AAAA
*
148015 TATAATTTAAAATAAAA
1 TAT--TTTAATATAAAA
*
148032 TATTTTAACATAA
1 TATTTTAATATAA
148045 TTTAATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 3 0.08
15 22 0.59
17 10 0.27
18 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTTAATATAAAA
Done.