Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013608.1 Kokia drynarioides strain JFW-HI SEQ_128635, 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: 80044
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:2904 original size:30 final size:29
Alignment explanation
Indices: 2868--2927 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 29
2858 CATTTATTCA
2868 ATATATATATTATACTACATTCCTATATAT
1 ATATATATATTATACTACATTCCTAT-TAT
2898 ATATATATATTATACTACATTCCTATTAT
1 ATATATATATTATACTACATTCCTATTAT
2927 A
1 A
2928 AACAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATATATATTATACTACATTCCTATTAT
Found at i:4491 original size:24 final size:24
Alignment explanation
Indices: 4459--4624 Score: 179
Period size: 24 Copynumber: 6.9 Consensus size: 24
4449 GTTCAGTAAA
* *
4459 TTTACGCTCGTCAGCTAAGATACG
1 TTTACGCTCGCCAGCTAATATACG
* *
4483 TTTACGCTCGCCAGCTAATATGCA
1 TTTACGCTCGCCAGCTAATATACG
* * **
4507 TTTACTCTCGCCATCTAATATATA
1 TTTACGCTCGCCAGCTAATATACG
* * *
4531 TTTACGCTCGTCAACTAATATGCG
1 TTTACGCTCGCCAGCTAATATACG
* *
4555 TTTACTCTCGCCATCTAATATACG
1 TTTACGCTCGCCAGCTAATATACG
* *
4579 TTTACGCTCGTCAGCTAATATGCG
1 TTTACGCTCGCCAGCTAATATACG
* *
4603 TTTATGCTGGCCAGCTAATATA
1 TTTACGCTCGCCAGCTAATATA
4625 AGAAACATTG
Statistics
Matches: 116, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 116 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (24 bp):
TTTACGCTCGCCAGCTAATATACG
Found at i:4538 original size:48 final size:48
Alignment explanation
Indices: 4459--4624 Score: 208
Period size: 48 Copynumber: 3.5 Consensus size: 48
4449 GTTCAGTAAA
* * * * * * *
4459 TTTACGCTCGTCAGCTAAGATACGTTTACGCTCGCCAGCTAATATGCA
1 TTTACTCTCGCCATCTAATATACATTTACGCTCGTCAGCTAATATGCG
* *
4507 TTTACTCTCGCCATCTAATATATATTTACGCTCGTCAACTAATATGCG
1 TTTACTCTCGCCATCTAATATACATTTACGCTCGTCAGCTAATATGCG
*
4555 TTTACTCTCGCCATCTAATATACGTTTACGCTCGTCAGCTAATATGCG
1 TTTACTCTCGCCATCTAATATACATTTACGCTCGTCAGCTAATATGCG
* *
4603 TTTA-TGCTGGCCAGCTAATATA
1 TTTACT-CTCGCCATCTAATATA
4625 AGAAACATTG
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
47 1 0.01
48 102 0.99
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (48 bp):
TTTACTCTCGCCATCTAATATACATTTACGCTCGTCAGCTAATATGCG
Found at i:7614 original size:122 final size:124
Alignment explanation
Indices: 7455--7707 Score: 375
Period size: 122 Copynumber: 2.0 Consensus size: 124
7445 TTTAAATTAT
* * *
7455 ATCTTAATATTACTTTTAATACAAATCTAATCATTCAAACAAAAGTATACTATTCAATGTTATAT
1 ATCTTAATATTACTTTCAACACAAATCTAATCATTCAAACAAAAATATACTATTCAATGTTATAT
* *
7520 CTTAAAACATACAATTTATTATTAC-AATAT-AAAAAAAAAACATACACTACCAAACCA
66 CTTAAAACATACAAATTATTATTACAAATATAAAAAAAAAAAAATACACTACCAAACCA
* * *
7577 ATCTTAATATTACTTTCAACACAAATCTAATCATTCAAATAAAAATATAGTGTTCAATGTTATAT
1 ATCTTAATATTACTTTCAACACAAATCTAATCATTCAAACAAAAATATACTATTCAATGTTATAT
* * *
7642 CTTTAAATATACAAATTATTATTACAAATATAAAAAAAAAAAAAAATACACTACCAGACCA
66 CTTAAAACATACAAATTATTATTACAAATAT--AAAAAAAAAAAAATACACTACCAAACCA
7703 ATCTT
1 ATCTT
7708 TTCTTTTTTT
Statistics
Matches: 116, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
122 81 0.70
123 5 0.04
126 30 0.26
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.33
Consensus pattern (124 bp):
ATCTTAATATTACTTTCAACACAAATCTAATCATTCAAACAAAAATATACTATTCAATGTTATAT
CTTAAAACATACAAATTATTATTACAAATATAAAAAAAAAAAAATACACTACCAAACCA
Found at i:8522 original size:40 final size:40
Alignment explanation
Indices: 8470--8555 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
8460 ACCTTAATAT
8470 TAATATATATCAATAAAACTTTAACATAAATCTAATCTAA
1 TAATATATATCAATAAAACTTTAACATAAATCTAATCTAA
8510 TAATATATATCAATAAAACTTTAACATAAATCTAATCTAA
1 TAATATATATCAATAAAACTTTAACATAAATCTAATCTAA
8550 -AATATA
1 TAATATA
8556 AATAATATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 6 0.13
40 40 0.87
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (40 bp):
TAATATATATCAATAAAACTTTAACATAAATCTAATCTAA
Found at i:10280 original size:20 final size:20
Alignment explanation
Indices: 10255--10299 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
10245 ACATATTTTA
10255 ATTTTAAAATTGTCAAATAT
1 ATTTTAAAATTGTCAAATAT
*
10275 ATTTT--AATTGTCAAGTAT
1 ATTTTAAAATTGTCAAATAT
10293 ATTTTAA
1 ATTTTAA
10300 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 17 0.77
20 5 0.23
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTTTAAAATTGTCAAATAT
Found at i:10285 original size:18 final size:18
Alignment explanation
Indices: 10262--10301 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
10252 TTAATTTTAA
10262 AATTGTCAAATATATTTT
1 AATTGTCAAATATATTTT
*
10280 AATTGTCAAGTATATTTT
1 AATTGTCAAATATATTTT
10298 AATT
1 AATT
10302 TTTTAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (18 bp):
AATTGTCAAATATATTTT
Found at i:10405 original size:20 final size:19
Alignment explanation
Indices: 10372--10424 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
10362 ATAAAAGTAG
*
10372 AATATATTAGTTAAAATAAAA
1 AATATA-TATTTAAAAT-AAA
*
10393 AATATATATTT-AAATTAA
1 AATATATATTTAAAATAAA
*
10411 ATTATATATTTAAA
1 AATATATATTTAAA
10425 TATTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 12 0.43
19 6 0.21
20 4 0.14
21 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATATATTTAAAATAAA
Found at i:20513 original size:24 final size:25
Alignment explanation
Indices: 20486--20633 Score: 104
Period size: 24 Copynumber: 5.6 Consensus size: 25
20476 TCCGCCTCCT
**
20486 AACAACATGGGAGGAATGCCCTAC-
1 AACAACATGGGAGGAATGCCCGCCA
* * * *
20510 AACAATAGGGGAGGTATGCCGGCC-
1 AACAACATGGGAGGAATGCCCGCCA
20534 AACAACATGGGAGGAATGCCGCCGCCA
1 AACAACATGGGAGGAATG-C-CCGCCA
* *
20561 AACAACATGGGAGGAGGAATGCCGCCTCCT
1 AACAACAT--G-GGAGGAATG-C-CCGCCA
*
20591 AACAATATGGGAGGAATG-CCGCCA
1 AACAACATGGGAGGAATGCCCGCCA
20615 CCGAACAACATGGGAGGAA
1 ---AACAACATGGGAGGAA
20634 GAATGCCGCC
Statistics
Matches: 99, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
24 37 0.37
25 1 0.01
26 4 0.04
27 32 0.32
28 1 0.01
29 1 0.01
30 23 0.23
ACGTcount: A:0.34, C:0.24, G:0.30, T:0.11
Consensus pattern (25 bp):
AACAACATGGGAGGAATGCCCGCCA
Found at i:20557 original size:27 final size:27
Alignment explanation
Indices: 20477--20788 Score: 156
Period size: 30 Copynumber: 11.2 Consensus size: 27
20467 AGCTGGAGCT
* *
20477 CCGCCTCCTAACAACATGGGAGGAATG
1 CCGCCGCCAAACAACATGGGAGGAATG
** * * *
20504 -C-CCTAC-AACAATAGGGGAGGTATG
1 CCGCCGCCAAACAACATGGGAGGAATG
20528 CCG--GCC-AACAACATGGGAGGAATG
1 CCGCCGCCAAACAACATGGGAGGAATG
20552 CCGCCGCCAAACAACATGGGAGGAGGAATG
1 CCGCCGCCAAACAACAT--G-GGAGGAATG
* * *
20582 CCGCCTCCTAACAATATGGGAGGAATG
1 CCGCCGCCAAACAACATGGGAGGAATG
* *
20609 CCGCCACCGAACAACATGGGAGGAAGAATG
1 CCGCCGCCAAACAACATGGGA-G--GAATG
* * *
20639 CCGCCTCCTAACAATATGGGAGGAGGAATG
1 CCGCCGCCAAACAACAT--G-GGAGGAATG
* * *
20669 CCGCCTCCTAACAATATGGGAGGAGGAATG
1 CCGCCGCCAAACAACAT--G-GGAGGAATG
* * *
20699 CCGCCTCCTAACAATATGGGAGGAGGAATG
1 CCGCCGCCAAACAACAT--G-GGAGGAATG
* * * *
20729 CCGCCTCCTAATAATATGGGAGGAGAAATG
1 CCGCCGCCAAACAACATGGGA-G-G-AATG
* *
20759 CCACCG---AACAACATGAGAGGAATG
1 CCGCCGCCAAACAACATGGGAGGAATG
20783 CCGCCG
1 CCGCCG
20789 AATAACATGG
Statistics
Matches: 243, Mismatches: 25, Indels: 37
0.80 0.08 0.12
Matches are distributed among these distances:
24 43 0.18
25 6 0.02
26 5 0.02
27 47 0.19
28 4 0.02
29 2 0.01
30 131 0.54
32 2 0.01
33 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.29, T:0.13
Consensus pattern (27 bp):
CCGCCGCCAAACAACATGGGAGGAATG
Found at i:20577 original size:30 final size:30
Alignment explanation
Indices: 20543--20760 Score: 334
Period size: 30 Copynumber: 7.4 Consensus size: 30
20533 CAACAACATG
* * *
20543 GGAGGAATGCCGCCGCCAAACAACATGGGA
1 GGAGGAATGCCGCCTCCTAACAATATGGGA
20573 GGAGGAATGCCGCCTCCTAACAATAT--G-
1 GGAGGAATGCCGCCTCCTAACAATATGGGA
* * *
20600 GGAGGAATGCCGCCACCGAACAACATGGGA
1 GGAGGAATGCCGCCTCCTAACAATATGGGA
*
20630 GGAAGAATGCCGCCTCCTAACAATATGGGA
1 GGAGGAATGCCGCCTCCTAACAATATGGGA
20660 GGAGGAATGCCGCCTCCTAACAATATGGGA
1 GGAGGAATGCCGCCTCCTAACAATATGGGA
20690 GGAGGAATGCCGCCTCCTAACAATATGGGA
1 GGAGGAATGCCGCCTCCTAACAATATGGGA
*
20720 GGAGGAATGCCGCCTCCTAATAATATGGGA
1 GGAGGAATGCCGCCTCCTAACAATATGGGA
*
20750 GGAGAAATGCC
1 GGAGGAATGCC
20761 ACCGAACAAC
Statistics
Matches: 172, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
27 23 0.13
28 1 0.01
29 1 0.01
30 147 0.85
ACGTcount: A:0.32, C:0.24, G:0.30, T:0.14
Consensus pattern (30 bp):
GGAGGAATGCCGCCTCCTAACAATATGGGA
Found at i:20783 original size:24 final size:24
Alignment explanation
Indices: 20755--20812 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
20745 TGGGAGGAGA
20755 AATGCCACCGAACAACATGAGAGG
1 AATGCCACCGAACAACATGAGAGG
* * * *
20779 AATGCCGCCGAATAACATGGGTGG
1 AATGCCACCGAACAACATGAGAGG
*
20803 GATGCCACCG
1 AATGCCACCG
20813 GGTCCACCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.29, T:0.12
Consensus pattern (24 bp):
AATGCCACCGAACAACATGAGAGG
Found at i:21688 original size:19 final size:19
Alignment explanation
Indices: 21657--21708 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
21647 TTTAAATTTA
*
21657 AAAAATTAA-AAAATATAT-
1 AAAAATAAATAAAAT-TATC
* *
21675 AAAAATAGATAAAATTTTC
1 AAAAATAAATAAAATTATC
21694 AAAAATAAATAAAAT
1 AAAAATAAATAAAAT
21709 GATTCCTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATAAATAAAATTATC
Found at i:29703 original size:61 final size:61
Alignment explanation
Indices: 29628--29748 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
29618 TCTCCTTCCC
29628 ATCAGTTGCTATCAAAGTTACCCTTTTAGTGGTACAGTCCAAACTTACCTGATGTTCAACT
1 ATCAGTTGCTATCAAAGTTACCCTTTTAGTGGTACAGTCCAAACTTACCTGATGTTCAACT
*
29689 ATCAGTTGCTATCAAAGTTACCCTTTTAGTGGTACAGTCCAGACTTACCTGATGTTCAAC
1 ATCAGTTGCTATCAAAGTTACCCTTTTAGTGGTACAGTCCAAACTTACCTGATGTTCAAC
29749 CAACCAGTCC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (61 bp):
ATCAGTTGCTATCAAAGTTACCCTTTTAGTGGTACAGTCCAAACTTACCTGATGTTCAACT
Found at i:34198 original size:2 final size:2
Alignment explanation
Indices: 34191--34237 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
34181 AAAAATATCA
*
34191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34233 A- AT AT
1 AT AT AT
34238 CCAAACTACT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36177 original size:17 final size:18
Alignment explanation
Indices: 36141--36180 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
36131 TAAACTTCAT
*
36141 ATTTTAAATATATTTTGA
1 ATTTTAAATATATATTGA
*
36159 ATTTTAAATTTA-ATTGA
1 ATTTTAAATATATATTGA
36176 ATTTT
1 ATTTT
36181 TTTTTAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
ATTTTAAATATATATTGA
Found at i:38755 original size:254 final size:254
Alignment explanation
Indices: 38258--38763 Score: 811
Period size: 254 Copynumber: 2.0 Consensus size: 254
38248 TTAGTTGATG
*
38258 ATACTTTCACTCATTGATCCCATTGATAGTCATTCTAAAATGTTGTTGGTAGTCTTATATTGATC
1 ATACTTTCACTCATTGATCCCATTGATAATCATTCTAAAATGTTGTTGGTAGTCTTATATTGATC
* *
38323 ATTTAGCTAGTGTTCGACCCTTTTTAGAGCTCCCAATTCTCGTCTCCAATATTTTTTATGGCAAA
66 ATTTAACTAGTGTTCGACCCTTTTTAGAGCTCCAAATTCTCGTCTCCAATATTTTTTATGGCAAA
* * * *
38388 TCTCTTAAAGCACAATCGTTTAAAAGAGCACAACAATAATATTACTTGATCCTCATCATCAATCT
131 TCTCTTAAAGCACAATCATTTAAAAGAACACAACAATAATATAACTTCATCCTCATCATCAATCT
* * *
38453 GAATCTCAACGTTATTTAAATAATTTAAAAGGGAATGAATTGACTGATGTGATCTCTAA
196 CAATCTCAACGTTATTTAAATAATTTAAAAGGGAATAAATTAACTGATGTGATCTCTAA
*
38512 ATACTTTCACTCATTGATCGCATTGATAATCATT-TCAAAATGTTGTTGGTAGTCTTATATTGAT
1 ATACTTTCACTCATTGATCCCATTGATAATCATTCT-AAAATGTTGTTGGTAGTCTTATATTGAT
*
38576 CATTTAACTAGTGTTCGACCCTTTTTAGAGCTCCAAATTCTTGTCTCCAATA-TTTTTATGGCAA
65 CATTTAACTAGTGTTCGACCCTTTTTAGAGCTCCAAATTCTCGTCTCCAATATTTTTTATGGCAA
* * *
38640 ATCTCTTAATGCACAATCATTTAAAAGAACACAACAATAGTATAA-TCTCATCTTCATCATCAAT
130 ATCTCTTAAAGCACAATCATTTAAAAGAACACAACAATAATATAACT-TCATCCTCATCATCAAT
* *
38704 CTCAATCTCAACTTTATTTAAATAATTTAAAAGAGTAATAAATTAACTGATGTGATCTCT
194 CTCAATCTCAACGTTATTTAAATAATTTAAAAG-GGAATAAATTAACTGATGTGATCTCT
38764 GAGAAGTTCA
Statistics
Matches: 232, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
252 1 0.00
253 99 0.43
254 132 0.57
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (254 bp):
ATACTTTCACTCATTGATCCCATTGATAATCATTCTAAAATGTTGTTGGTAGTCTTATATTGATC
ATTTAACTAGTGTTCGACCCTTTTTAGAGCTCCAAATTCTCGTCTCCAATATTTTTTATGGCAAA
TCTCTTAAAGCACAATCATTTAAAAGAACACAACAATAATATAACTTCATCCTCATCATCAATCT
CAATCTCAACGTTATTTAAATAATTTAAAAGGGAATAAATTAACTGATGTGATCTCTAA
Found at i:41127 original size:30 final size:30
Alignment explanation
Indices: 41093--41154 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
41083 TATTTTATTA
*
41093 TTAATTTTGTTATTATTTTAG-AGACATTTG
1 TTAATTTTGTTACTATTTTAGAAG-CATTTG
41123 TTAATTTTGTTACTATTTTAGAAGCATTTG
1 TTAATTTTGTTACTATTTTAGAAGCATTTG
41153 TT
1 TT
41155 TGTTAAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTAATTTTGTTACTATTTTAGAAGCATTTG
Found at i:43752 original size:2 final size:2
Alignment explanation
Indices: 43745--43789 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
43735 GCTTATTCAA
43745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43787 AT A
1 AT A
43790 CACATTGAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54807 original size:59 final size:58
Alignment explanation
Indices: 54596--54826 Score: 182
Period size: 59 Copynumber: 3.8 Consensus size: 58
54586 GTTTTCTTTA
* * *
54596 AATTTTTGAAATTTAGCCATTCTACTTTTACTTTGA-GAATTTAGCCCTTATTATTTTC
1 AATTTTTGAAATTTAACCATTCTATTTTTACTTTGAGGAATTTAGCCC-TGTTATTTTC
* * * * * * *
54654 AATTTTTGAAATTTAATCC-TCCTACTTTTAATTCGTGGAATTTAACCCTTCACTTGTTTTCTTT
1 AATTTTTGAAATTTAA-CCATTCTATTTTTACTTTGAGGAATTT-A-GC--C-C-TGTTAT-TTT
54718 C
58 C
** * *
54719 AAAATTTGAAATTTAGCCATTCT-TCTTTTA-TTCTGAGGAATTTAGTCCCTGTTCTTTTC
1 AATTTTTGAAATTTAACCATTCTAT-TTTTACTT-TGAGGAATTTAG-CCCTGTTATTTTC
* *
54778 AATTTTTGAAATTTAATCATTCTATTTTTACTTTTAGGAATTTAGCCCT
1 AATTTTTGAAATTTAACCATTCTATTTTTACTTTGAGGAATTTAGCCCT
54827 CCACTTGTTT
Statistics
Matches: 137, Mismatches: 22, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
58 32 0.23
59 47 0.34
60 9 0.07
61 2 0.01
62 1 0.01
63 1 0.01
64 12 0.09
65 33 0.24
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.49
Consensus pattern (58 bp):
AATTTTTGAAATTTAACCATTCTATTTTTACTTTGAGGAATTTAGCCCTGTTATTTTC
Found at i:54820 original size:124 final size:124
Alignment explanation
Indices: 54567--54837 Score: 356
Period size: 124 Copynumber: 2.2 Consensus size: 124
54557 ATTTAGTTCA
* *
54567 AGGAATTT-AGCCTTCACTTGTTTTCTTTAAATTTTTGAAATTTAGCCATTCTACTTTTACTTTG
1 AGGAATTTAACCCTTCACTTGTTTTCTTTAAATATTTGAAATTTAGCCATTCTACTTTTACTTTG
*
54631 AGAATTTAGCCCTTATTATTTTCAATTTTTGAAATTTAATCCTCCTACTTTTAATTCGT
66 AGAATTTAGCCCTTATTATTTTCAATTTTTGAAATTTAATCATCCTACTTTTAATTCGT
*
54690 -GGAATTTAACCCTTCACTTGTTTTCTTTCAAA-ATTTGAAATTTAGCCATTCTTCTTTTA-TTC
1 AGGAATTTAACCCTTCACTTGTTTTCTTT-AAATATTTGAAATTTAGCCATTCTACTTTTACTT-
* * * * * *
54752 TGAGGAATTTAGTCCC-TGTTCTTTTCAATTTTTGAAATTTAATCATTCTATTTTTACTT-TT
64 TGA-GAATTTAG-CCCTTATTATTTTCAATTTTTGAAATTTAATCATCCTACTTTTAATTCGT
* *
54813 AGGAATTTAGCCCTCCACTTGTTTT
1 AGGAATTTAACCCTTCACTTGTTTT
54838 TTCCATTCCA
Statistics
Matches: 130, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
122 9 0.07
123 48 0.37
124 70 0.54
125 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (124 bp):
AGGAATTTAACCCTTCACTTGTTTTCTTTAAATATTTGAAATTTAGCCATTCTACTTTTACTTTG
AGAATTTAGCCCTTATTATTTTCAATTTTTGAAATTTAATCATCCTACTTTTAATTCGT
Found at i:54865 original size:85 final size:87
Alignment explanation
Indices: 54764--54924 Score: 245
Period size: 86 Copynumber: 1.9 Consensus size: 87
54754 AGGAATTTAG
* * ** *
54764 TCCCTGTTCTTTTCAATTTTTGAA-ATTTAATCATTCTATTTTTACTTTTAGGAATTT-AGCCCT
1 TCCCTGTTCTTTTCAATTTTTGAATATTTAATCATTCTACTTTTAATTCAAGGAATTTAACCCCT
*
54827 CCACTTGTTTTTTCCATTCCAA
66 CCACTTATTTTTTCCATTCCAA
*
54849 TCCCTGTTCTTTTCAATTTTTTAATATTTAATCATTCTACTTTTAATTCAAGGAATTTAACCCCT
1 TCCCTGTTCTTTTCAATTTTTGAATATTTAATCATTCTACTTTTAATTCAAGGAATTTAACCCCT
54914 CCACTTATTTT
66 CCACTTATTTT
54925 ATTTTATTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 23 0.34
86 29 0.43
87 15 0.22
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (87 bp):
TCCCTGTTCTTTTCAATTTTTGAATATTTAATCATTCTACTTTTAATTCAAGGAATTTAACCCCT
CCACTTATTTTTTCCATTCCAA
Found at i:57149 original size:18 final size:18
Alignment explanation
Indices: 57114--57153 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
57104 AACTGATATA
**
57114 GAGGATACATTTGAGGTG
1 GAGGATACATCGGAGGTG
*
57132 GAGGATACATCGGTGGTG
1 GAGGATACATCGGAGGTG
57150 GAGG
1 GAGG
57154 TGGGTGATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.45, T:0.23
Consensus pattern (18 bp):
GAGGATACATCGGAGGTG
Found at i:57153 original size:24 final size:24
Alignment explanation
Indices: 57126--57177 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
57116 GGATACATTT
*
57126 GAGGTGGAG-GATACATCGGTGGTG
1 GAGGTGG-GTGATACATCGGGGGTG
*
57150 GAGGTGGGTGATACATTGGGGGTG
1 GAGGTGGGTGATACATCGGGGGTG
57174 GAGG
1 GAGG
57178 ATGCATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.19, C:0.06, G:0.54, T:0.21
Consensus pattern (24 bp):
GAGGTGGGTGATACATCGGGGGTG
Found at i:58099 original size:14 final size:13
Alignment explanation
Indices: 58075--58122 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
58065 TAAAATGTAC
58075 AATATAATTAAAT
1 AATATAATTAAAT
58088 AATATAAATTAAAT
1 AATAT-AATTAAAT
58102 --TA-AATTAAAT
1 AATATAATTAAAT
*
58112 AATTTAATTAA
1 AATATAATTAA
58123 CTATTTACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 8 0.27
12 3 0.10
13 11 0.37
14 8 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATAATTAAAT
Found at i:58113 original size:19 final size:18
Alignment explanation
Indices: 58080--58122 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
58070 TGTACAATAT
58080 AATTAAATAATATAAATTA
1 AATTAAATAATAT-AATTA
*
58099 AATTAAATTAA-ATAATTT
1 AATTAAA-TAATATAATTA
58117 AATTAA
1 AATTAA
58123 CTATTTACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTAAATAATATAATTA
Found at i:67085 original size:43 final size:42
Alignment explanation
Indices: 67015--67133 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 42
67005 CACGAGCTGA
* * * *
67015 GCACACGGGAGTGTGTCAGACTGTGTGTGTATACTATTTTTAG
1 GCACACGGGCGTGTGT-AGACCGTGTGTGCATACTATTTTGAG
* *
67058 GCACACGGGCGTGTGTATGACCATGTGTGCATACTATTTTGGG
1 GCACACGGGCGTGTGTA-GACCGTGTGTGCATACTATTTTGAG
*
67101 GCACACGGGCGTGTGCTAGACCGTGTGTCCATA
1 GCACACGGGCGTGTG-TAGACCGTGTGTGCATA
67134 TTTTTTTTGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.02
43 63 0.95
44 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.29
Consensus pattern (42 bp):
GCACACGGGCGTGTGTAGACCGTGTGTGCATACTATTTTGAG
Found at i:68396 original size:30 final size:29
Alignment explanation
Indices: 68327--68847 Score: 248
Period size: 30 Copynumber: 17.8 Consensus size: 29
68317 TTTGAGGTTA
* * *
68327 AAAATGGAATTTTTAG-AAGTTCAGGG-C
1 AAAATGGAATTTTTGGAAAATTCGGGGTC
* *
68354 AAAATAGTAATTTTTGGAAAAATCGGGGTC
1 AAAAT-GGAATTTTTGGAAAATTCGGGGTC
* *
68384 AAAAATGGAATTTTT-GAAATTTTAGGGGT-
1 -AAAATGGAATTTTTGGAAA-ATTCGGGGTC
* *
68413 AAAATGGTAATTCTTGGAAAAATT-GGTGTC
1 AAAATGG-AATTTTTGG-AAAATTCGGGGTC
* * *
68443 AAAATGGAA-TTTT-CAAAAGTTTAGGCGT-
1 AAAATGGAATTTTTGGAAAA--TTCGGGGTC
68471 AAAATGGTAATTTTTGGAATAA-TCGGGGTC
1 AAAATGG-AATTTTTGGAA-AATTCGGGGTC
* ** *
68501 AAAAATGGATTTTTTGGAATTTTAGAGGG-C
1 -AAAATGGAATTTTTGGAAAATTCG-GGGTC
* ** * *
68531 TAAATGGTAAGATTTGGAAAAATCGAGGTC
1 AAAATGG-AATTTTTGGAAAATTCGGGGTC
* ** *
68561 AAAAATGGAATTTTTGGAAAAATCAAGGTAA
1 -AAAATGGAATTTTTGGAAAATTCGGGGT-C
* * *
68592 AAAATGGAATATTTGG-AAGTTCGAGAG-C
1 AAAATGGAATTTTTGGAAAATTCG-GGGTC
* * * * *
68620 AAAATGTAA-TTTTGTAAAAATCGAGGTTA
1 AAAATGGAATTTTTGGAAAATTCG-GGGTC
* *
68649 AAAATGGAATTTTTGG-AAGTTTGGGAGT-
1 AAAATGGAATTTTTGGAAAATTCGGG-GTC
* *
68677 AAAGTGGTAATTTTTGGAAAAATCGGGGTC
1 AAAATGG-AATTTTTGGAAAATTCGGGGTC
*** *
68707 AAAATGGAATTTTTGGATGTTTAGGGGT-
1 AAAATGGAATTTTTGGAAAATTCGGGGTC
* * * *
68735 AAAATGGTAA-TCTTGGAAAAATCGAGGTG
1 AAAATGG-AATTTTTGGAAAATTCGGGGTC
* * * *
68764 AAAATGGATTTTTTGGAAAGTTTGAGGGTT
1 AAAATGGAATTTTTGGAAAATTCG-GGGTC
* * *
68794 AAAATGTAATTTTTGGAAAGTTTGAGGGTC
1 AAAATGGAATTTTTGGAAAATTCG-GGGTC
* *
68824 AAAATGTAATTTTTGTAAAATTCG
1 AAAATGGAATTTTTGGAAAATTCG
68848 AGGGCTAAAA
Statistics
Matches: 371, Mismatches: 87, Indels: 69
0.70 0.17 0.13
Matches are distributed among these distances:
26 4 0.01
27 9 0.02
28 70 0.19
29 105 0.28
30 155 0.42
31 26 0.07
32 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAATTCGGGGTC
Found at i:68430 original size:59 final size:59
Alignment explanation
Indices: 68326--68576 Score: 294
Period size: 58 Copynumber: 4.3 Consensus size: 59
68316 CTTTGAGGTT
* * *
68326 AAAAATGGAATTTTT-AGAAGTTCA-GGGCAAAATAGTAATTTTTGGAAAAATCGGGGTC
1 AAAAATGGAATTTTTGA-AAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTC
* * * *
68384 AAAAATGGAATTTTTGAAATTTTAGGGGTAAAATGGTAATTCTTGGAAAAATTGGTGTC
1 AAAAATGGAATTTTTGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTC
** * *
68443 -AAAATGGAATTTTCAAAAGTTTAGGCGTAAAATGGTAATTTTTGGAATAATCGGGGTC
1 AAAAATGGAATTTTTGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTC
* * * ** *
68501 AAAAATGGATTTTTTGGAATTTTAGAGGGCT-AAATGGTAAGATTTGGAAAAATCGAGGTC
1 AAAAATGGAATTTTTGAAAGTTTAG-GGG-TAAAATGGTAATTTTTGGAAAAATCGGGGTC
68561 AAAAATGGAATTTTTG
1 AAAAATGGAATTTTTG
68577 GAAAAATCAA
Statistics
Matches: 162, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
58 70 0.43
59 49 0.30
60 42 0.26
61 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (59 bp):
AAAAATGGAATTTTTGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTC
Found at i:68500 original size:117 final size:118
Alignment explanation
Indices: 68320--68574 Score: 340
Period size: 117 Copynumber: 2.2 Consensus size: 118
68310 TGGACACTTT
* * *
68320 GAGGTTAAAAATGGAATTTTTAGAAGTTCAGGGCAAAATAGTAATTTTTGGAAAAATCGGGGTCA
1 GAGGTCAAAAATGGAATTTTCAAAAGTTCAGGGCAAAATAGTAATTTTTGGAAAAATCGGGGTCA
* *
68385 AAAATGGAATTTTTGAAATTTTAG-GGG-TAAAATGGTAA-TTCTTGGAAAAATT
66 AAAATGGAATTTTTGAAATTTTAGAGGGCT-AAATGGTAAGAT-TTGGAAAAATC
* * * *
68437 G-GTGTC-AAAATGGAATTTTCAAAAGTTTAGGCGTAAAATGGTAATTTTTGGAATAATCGGGGT
1 GAG-GTCAAAAATGGAATTTTCAAAAGTTCAGG-GCAAAATAGTAATTTTTGGAAAAATCGGGGT
* *
68500 CAAAAATGGATTTTTTGGAATTTTAGAGGGCTAAATGGTAAGATTTGGAAAAATC
64 CAAAAATGGAATTTTTGAAATTTTAGAGGGCTAAATGGTAAGATTTGGAAAAATC
68555 GAGGTCAAAAATGGAATTTT
1 GAGGTCAAAAATGGAATTTT
68575 TGGAAAAATC
Statistics
Matches: 120, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
116 23 0.19
117 55 0.46
118 26 0.22
119 16 0.13
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (118 bp):
GAGGTCAAAAATGGAATTTTCAAAAGTTCAGGGCAAAATAGTAATTTTTGGAAAAATCGGGGTCA
AAAATGGAATTTTTGAAATTTTAGAGGGCTAAATGGTAAGATTTGGAAAAATC
Found at i:68547 original size:60 final size:58
Alignment explanation
Indices: 68293--68576 Score: 279
Period size: 58 Copynumber: 4.8 Consensus size: 58
68283 TTTTGCCCGA
* * ** * * * * *
68293 GGGTAAAACGGTAATTTTGGACACTTTGAGGTTAAAAATGGAATTTTT-AGAAGTTCA-
1 GGGTAAAATGGTAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGA-AATTTTAG
* *
68350 GGGCAAAATAGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGAAATTTTAG
1 GGGTAAAATGGTAA-TTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGAAATTTTAG
* * ** *
68409 GGGTAAAATGGTAATTCTTGGAAAAATTGGTGTC-AAAATGGAATTTTCAAAAGTTTAG
1 GGGTAAAATGGTAATT-TTGGAAAAATCGGGGTCAAAAATGGAATTTTTGAAATTTTAG
* * * *
68467 GCGTAAAATGGTAATTTTTGGAATAATCGGGGTCAAAAATGGATTTTTTGGAATTTTAG
1 GGGTAAAATGGTAA-TTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGAAATTTTAG
* *
68526 AGGGCT-AAATGGTAAGATTTGGAAAAATCGAGGTCAAAAATGGAATTTTTG
1 -GGG-TAAAATGGTAA-TTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTG
68577 GAAAAATCAA
Statistics
Matches: 186, Mismatches: 33, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
57 11 0.06
58 83 0.45
59 49 0.26
60 42 0.23
61 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.33
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGAAATTTTAG
Found at i:68651 original size:58 final size:56
Alignment explanation
Indices: 68562--68812 Score: 261
Period size: 57 Copynumber: 4.3 Consensus size: 56
68552 ATCGAGGTCA
* * * * *
68562 AAAATGGAATTTTTGGAAAAATCAAGGTAAAAAATGGAATATTTGGAAGTTCGAGAGC
1 AAAATGTAA-TTTTGGAAAAATCGAGGT-AAAAATGGAATTTTTGGAAGTTTGAGAGT
* *
68620 AAAATGTAATTTTGTAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGAGT
1 AAAATGTAATTTTGGAAAAATCGAGG-TAAAAATGGAATTTTTGGAAGTTTGAGAGT
* * * * *
68677 AAAGTGGTAATTTTTGGAAAAATCGGGGTCAAAATGGAATTTTTGGATGTTT-AGGGGT
1 AAAAT-GTAA-TTTTGGAAAAATCGAGGTAAAAATGGAATTTTTGGAAGTTTGA-GAGT
* * * *
68735 AAAATGGTAATCTTGGAAAAATCGAGGTGAAAATGGATTTTTTGGAAAGTTTGAGGGTT
1 AAAAT-GTAATTTTGGAAAAATCGAGGTAAAAATGGAATTTTTGG-AAGTTTGAGAG-T
68794 AAAATGTAATTTTTGGAAA
1 AAAATGTAA-TTTTGGAAA
68813 GTTTGAGGGT
Statistics
Matches: 164, Mismatches: 21, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
57 75 0.46
58 59 0.36
59 30 0.18
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (56 bp):
AAAATGTAATTTTGGAAAAATCGAGGTAAAAATGGAATTTTTGGAAGTTTGAGAGT
Found at i:68700 original size:116 final size:116
Alignment explanation
Indices: 68562--68812 Score: 296
Period size: 116 Copynumber: 2.2 Consensus size: 116
68552 ATCGAGGTCA
*
68562 AAAATGGAATTTTTGGAAAAATCAAGGTAAAAAATGGAATATTTGGAAGTTCGA-GAGCAAAAT-
1 AAAATGTAATTTTTGGAAAAATCAAGGT-AAAAATGGAATATTTGGAAGTT-GAGGAGCAAAATG
* *
68625 GTAATTTTGTAAAAATCGAGGTTAAAAATGGAATTTTTGG-AAGTTTG-GGAG-T
64 GTAATCTTGGAAAAATCGAGG-TAAAAATGGAATTTTTGGAAAGTTTGAGG-GTT
* ** * * * * * *
68677 AAAGTGGTAATTTTTGGAAAAATCGGGGTCAAAATGGAATTTTTGGATGTTTAGGGGTAAAATGG
1 AAAAT-GTAATTTTTGGAAAAATCAAGGTAAAAATGGAATATTTGGAAGTTGAGGAGCAAAATGG
* *
68742 TAATCTTGGAAAAATCGAGGTGAAAATGGATTTTTTGGAAAGTTTGAGGGTT
65 TAATCTTGGAAAAATCGAGGTAAAAATGGAATTTTTGGAAAGTTTGAGGGTT
68794 AAAATGTAATTTTTGGAAA
1 AAAATGTAATTTTTGGAAA
68813 GTTTGAGGGT
Statistics
Matches: 115, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
114 1 0.01
115 46 0.40
116 61 0.53
117 7 0.06
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (116 bp):
AAAATGTAATTTTTGGAAAAATCAAGGTAAAAATGGAATATTTGGAAGTTGAGGAGCAAAATGGT
AATCTTGGAAAAATCGAGGTAAAAATGGAATTTTTGGAAAGTTTGAGGGTT
Found at i:69971 original size:3 final size:3
Alignment explanation
Indices: 69963--70001 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
69953 TGTTCGTTCG
69963 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
70002 TGTTTAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:70693 original size:25 final size:22
Alignment explanation
Indices: 70656--70704 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
70646 TTTGGACATT
70656 ATTTAAATAAATTTATAATTTATA
1 ATTTAAATAAATTTA-AATTT-TA
70680 ATTTATAATAAATTTAAATTTTA
1 ATTTA-AATAAATTTAAATTTTA
70703 AT
1 AT
70705 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 4 0.17
24 10 0.42
25 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAAATAAATTTAAATTTTA
Found at i:70702 original size:7 final size:6
Alignment explanation
Indices: 70663--70749 Score: 51
Period size: 6 Copynumber: 15.0 Consensus size: 6
70653 ATTATTTAAA
*
70663 TAAATT TATAATT TATAATT TATAA-- TAAATT TAAATT TTAA-- TAAATT
1 TAAATT TA-AATT TA-AATT TA-AATT TAAATT TAAATT TAAATT TAAATT
* * * * *
70710 TAAATT TAAA-A TAAACT TAATTT TAAA-A TAATTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
70750 ATGCTGGGCT
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
4 5 0.08
5 9 0.14
6 33 0.52
7 16 0.25
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:70724 original size:17 final size:17
Alignment explanation
Indices: 70672--70749 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
70662 ATAAATTTAT
*
70672 AATTTATAATTTATAATA
1 AATTTA-AATTTAAAATA
*
70690 AATTTAAATTT-TAATA
1 AATTTAAATTTAAAATA
70706 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
70723 AACTTAATTTTAAAATA
1 AATTTAAATTTAAAATA
*
70740 ATTTTAAATT
1 AATTTAAATT
70750 ATGCTGGGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
16 16 0.30
17 31 0.58
18 6 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:71222 original size:50 final size:49
Alignment explanation
Indices: 71164--71535 Score: 378
Period size: 49 Copynumber: 7.6 Consensus size: 49
71154 AGGTGTGAGG
** * * *
71164 TTCGCCATTGCGATTTAAACCTTTCCCTTTCGTGTCCTCGTGATACTGGA
1 TTCGCCATTGCGGCTTAAATCTTTCCC-TTCATGTCCTCGTGGTACTGGA
* * *
71214 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGT-TTCTGAGGTACAAGG-
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCCTC-GTGGTAC-TGGA
* * * * * * *
71263 TTCACCGTTGCGACTTAAACCATTCCCTTTCGTGTCCTCGTGGTACTGAA
1 TTCGCCATTGCGGCTTAAATCTTTCCC-TTCATGTCCTCGTGGTACTGGA
*
71313 TTCGCCATTGCGGCTTAAATTTTTCCCTTCATG-CCTCGTGGTACTGGA
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCCTCGTGGTACTGGA
*
71361 TTCGCCATTGCGGCTGAAATCTTTCCCTTCATGT-CTCGTGGTACTGGA
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCCTCGTGGTACTGGA
** * * *
71409 TTCGCCATTGTAGCTTAAATCTTTCCCTTCATGT-TTCTGAGGTACAAGG-
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCCTC-GTGGTAC-TGGA
* * * * * * *
71458 TTCGCCCTTGCGACTTAAACCTTTCCCTCCATATCTTCGCGGTACTGGA
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCCTCGTGGTACTGGA
*
71507 TTCGCTATTGCGGCTTAAATCTTTCCCTT
1 TTCGCCATTGCGGCTTAAATCTTTCCCTT
71536 TGTGTTTTGC
Statistics
Matches: 264, Mismatches: 48, Indels: 21
0.79 0.14 0.06
Matches are distributed among these distances:
48 96 0.36
49 102 0.39
50 64 0.24
51 2 0.01
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.37
Consensus pattern (49 bp):
TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCCTCGTGGTACTGGA
Found at i:71293 original size:99 final size:98
Alignment explanation
Indices: 71122--71535 Score: 501
Period size: 99 Copynumber: 4.2 Consensus size: 98
71112 AAATTTGCCG
* * * *** *
71122 TTGCGGCTTAAATTTTTCCTTTCATGCATCTGAGGTGTGAGGTTCGCCATTGCGATTTAAACCTT
1 TTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT
* *
71187 TCCCTTTCGTGTCCTCGTGATACTGGATTCGCCA
66 TCCC-TTCATGTCCTCGTGGTACTGGATTCGCCA
* * * *
71221 TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCAT
1 TTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT
* *
71286 TCCCTTTCGTGTCCTCGTGGTACTGAATTCGCCA
66 TCCC-TTCATGTCCTCGTGGTACTGGATTCGCCA
* * * * * * *
71320 TTGCGGCTTAAATTTTTCCCTTCATGCCTC-GTGGTAC-TGGATTCGCCATTGCGGCTGAAATCT
1 TTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG-TTCGCCATTGCGACTTAAACCT
71383 TTCCCTTCATGT-CTCGTGGTACTGGATTCGCCA
65 TTCCCTTCATGTCCTCGTGGTACTGGATTCGCCA
** * *
71416 TTGTAGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCCTTGCGACTTAAACCTT
1 TTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT
* * * * *
71481 TCCCTCCATATCTTCGCGGTACTGGATTCGCTA
66 TCCCTTCATGTCCTCGTGGTACTGGATTCGCCA
71514 TTGCGGCTTAAATCTTTCCCTT
1 TTGCGGCTTAAATCTTTCCCTT
71536 TGTGTTTTGC
Statistics
Matches: 267, Mismatches: 44, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
96 45 0.17
97 42 0.16
98 67 0.25
99 113 0.42
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (98 bp):
TTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTT
TCCCTTCATGTCCTCGTGGTACTGGATTCGCCA
Found at i:71369 original size:48 final size:48
Alignment explanation
Indices: 71122--71535 Score: 357
Period size: 49 Copynumber: 8.5 Consensus size: 48
71112 AAATTTGCCG
* * * * * *
71122 TTGCGGCTTAAATTTTTCCTTTCATGCATCTGAGGT-GTGAGGTTCGCCA
1 TTGCGGCTTAAATCTTTCCCTTCATGCCTC-GTGGTACTG-GATTCGCCA
** * * *
71171 TTGCGATTTAAACCTTTCCCTTTCGTGTCCTCGTGATACTGGATTCGCCA
1 TTGCGGCTTAAATCTTTCCC-TTCATG-CCTCGTGGTACTGGATTCGCCA
** * * * *
71221 TTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGG-TTCACCG
1 TTGCGGCTTAAATCTTTCCCTTCATGCCTC-GTGGTAC-TGGATTCGCCA
* * * * *
71270 TTGCGACTTAAACCATTCCCTTTCGTGTCCTCGTGGTACTGAATTCGCCA
1 TTGCGGCTTAAATCTTTCCC-TTCATG-CCTCGTGGTACTGGATTCGCCA
*
71320 TTGCGGCTTAAATTTTTCCCTTCATGCCTCGTGGTACTGGATTCGCCA
1 TTGCGGCTTAAATCTTTCCCTTCATGCCTCGTGGTACTGGATTCGCCA
* *
71368 TTGCGGCTGAAATCTTTCCCTTCATGTCTCGTGGTACTGGATTCGCCA
1 TTGCGGCTTAAATCTTTCCCTTCATGCCTCGTGGTACTGGATTCGCCA
** ** * * *
71416 TTGTAGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGG-TTCGCCC
1 TTGCGGCTTAAATCTTTCCCTTCATGCCTC-GTGGTAC-TGGATTCGCCA
* * * * * * *
71465 TTGCGACTTAAACCTTTCCCTCCATATCTTCGCGGTACTGGATTCGCTA
1 TTGCGGCTTAAATCTTTCCCTTCAT-GCCTCGTGGTACTGGATTCGCCA
71514 TTGCGGCTTAAATCTTTCCCTT
1 TTGCGGCTTAAATCTTTCCCTT
71536 TGTGTTTTGC
Statistics
Matches: 290, Mismatches: 63, Indels: 24
0.77 0.17 0.06
Matches are distributed among these distances:
48 96 0.33
49 115 0.40
50 72 0.25
51 7 0.02
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (48 bp):
TTGCGGCTTAAATCTTTCCCTTCATGCCTCGTGGTACTGGATTCGCCA
Done.