Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004630.1 Kokia drynarioides strain JFW-HI SEQ_118152, 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: 128916
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 54 characters in sequence are not A, C, G, or T
Found at i:541 original size:39 final size:39
Alignment explanation
Indices: 487--567 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
477 CCCTAAATCT
487 ATAAATAGACTCATTTAACACTTATTATGGATAACTTTC
1 ATAAATAGACTCATTTAACACTTATTATGGATAACTTTC
526 ATAAATAGACTCATTTAACACTTATTATGGATAACTTTC
1 ATAAATAGACTCATTTAACACTTATTATGGATAACTTTC
565 ATA
1 ATA
568 CTTTATAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (39 bp):
ATAAATAGACTCATTTAACACTTATTATGGATAACTTTC
Found at i:8142 original size:19 final size:19
Alignment explanation
Indices: 8120--8163 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
8110 TAACACGCAT
**
8120 TTTAAATTGGTCCTCAAAC
1 TTTAAATTCATCCTCAAAC
*
8139 TTTAATTTCATCCTCAAAC
1 TTTAAATTCATCCTCAAAC
8158 TATTAA
1 T-TTAA
8164 TGTTATATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTAAATTCATCCTCAAAC
Found at i:17144 original size:30 final size:30
Alignment explanation
Indices: 17110--17400 Score: 267
Period size: 30 Copynumber: 9.9 Consensus size: 30
17100 AAAATCATGA
* * * *
17110 TTTAGAGAAGTTTAAGGGTCAAAATATAAT
1 TTTAGAAAAGTTTGAGGGTTAAAATGTAAT
* *
17140 TTTAGAAAAGTTTGGGGGGTTAAAATATAA-
1 TTTAGAAAAGTTT-GAGGGTTAAAATGTAAT
*
17170 TTTGGAAAAGTTT-AGGGGTTAAAATGTAAT
1 TTTAGAAAAGTTTGA-GGGTTAAAATGTAAT
* *
17200 TTTAGAAAAGTTT-ATGGGTTAGATTGTAAT
1 TTTAGAAAAGTTTGA-GGGTTAAAATGTAAT
* *
17230 TTTGGAAAAGTTTGAGTGTTAAAATGTAAT
1 TTTAGAAAAGTTTGAGGGTTAAAATGTAAT
* * *
17260 TTTATAGAAGTTCGA-GGTTAAAATGTAA-
1 TTTAGAAAAGTTTGAGGGTTAAAATGTAAT
* * *
17288 TTT-GGAAAGTTTAAGGGTCAAAATGTAAT
1 TTTAGAAAAGTTTGAGGGTTAAAATGTAAT
* * *
17317 TTTAGAGAAGTTTGTGGG-T-CAATGTAAT
1 TTTAGAAAAGTTTGAGGGTTAAAATGTAAT
*
17345 TTTAGAGAAGTTTGAGGGTTAAAATGTAAT
1 TTTAGAAAAGTTTGAGGGTTAAAATGTAAT
* * *
17375 TTT-GTATAAGTTCGGGGGTTAAAATG
1 TTTAG-AAAAGTTTGAGGGTTAAAATG
17401 AGATTTTTCA
Statistics
Matches: 214, Mismatches: 37, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
27 6 0.03
28 40 0.19
29 30 0.14
30 124 0.58
31 14 0.07
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TTTAGAAAAGTTTGAGGGTTAAAATGTAAT
Found at i:20053 original size:39 final size:38
Alignment explanation
Indices: 20009--20173 Score: 145
Period size: 39 Copynumber: 4.3 Consensus size: 38
19999 TTTACCTCAT
*
20009 GCTCGGGGTAAGAGATTGGTTGATGGTAATCTACCCTAA
1 GCTCGGGGTAAGAGATTGGATGATGGTAATCT-CCCTAA
* * * * *
20048 GCTCGGGGTAAGAGATTGGATGGTTGCAATCTGCCTCAG
1 GCTCGGGGTAAGAGATTGGATGATGGTAATCTCCCT-AA
* * * *
20087 GCTCGGGTTAAGAGATT-GACTGATAGTGATCTGCCCTAG
1 GCTCGGGGTAAGAGATTGGA-TGATGGTAATCT-CCCTAA
* * * * *
20126 GCTCAGGGTAAGAGATTGGATGGTTGCAATCTGCC-AA
1 GCTCGGGGTAAGAGATTGGATGATGGTAATCTCCCTAA
20163 GCTCGGGGTAA
1 GCTCGGGGTAA
20174 AATATTGGCT
Statistics
Matches: 101, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
37 11 0.11
38 7 0.07
39 78 0.77
40 5 0.05
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (38 bp):
GCTCGGGGTAAGAGATTGGATGATGGTAATCTCCCTAA
Found at i:20076 original size:78 final size:78
Alignment explanation
Indices: 19994--20173 Score: 229
Period size: 78 Copynumber: 2.3 Consensus size: 78
19984 ATCGATTGGC
* * ** * *
19994 TGCAATTTACCTCATGCTCGGGGTAAGAGATTGGTTGATGGTAATCTACCCTAAGCTCGGGGTAA
1 TGCAATCTACCTCAGGCTCGGGGTAAGAGATTGACTGATAGTAATCTACCCTAAGCTCAGGGTAA
20059 GAGATTGGATGGT
66 GAGATTGGATGGT
* * * * *
20072 TGCAATCTGCCTCAGGCTCGGGTTAAGAGATTGACTGATAGTGATCTGCCCTAGGCTCAGGGTAA
1 TGCAATCTACCTCAGGCTCGGGGTAAGAGATTGACTGATAGTAATCTACCCTAAGCTCAGGGTAA
20137 GAGATTGGATGGT
66 GAGATTGGATGGT
* *
20150 TGCAATCT-GC-CAAGCTCGGGGTAA
1 TGCAATCTACCTCAGGCTCGGGGTAA
20174 AATATTGGCT
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
76 12 0.14
77 1 0.01
78 75 0.85
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (78 bp):
TGCAATCTACCTCAGGCTCGGGGTAAGAGATTGACTGATAGTAATCTACCCTAAGCTCAGGGTAA
GAGATTGGATGGT
Found at i:28407 original size:17 final size:17
Alignment explanation
Indices: 28385--28418 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28375 CAATTTCATT
28385 AGAAAAACTTCTCTACA
1 AGAAAAACTTCTCTACA
*
28402 AGAAAAACTTCTTTACA
1 AGAAAAACTTCTCTACA
28419 TAAAGCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (17 bp):
AGAAAAACTTCTCTACA
Found at i:32392 original size:29 final size:28
Alignment explanation
Indices: 32352--32457 Score: 90
Period size: 29 Copynumber: 3.7 Consensus size: 28
32342 TTTAAGGTTG
*
32352 AAAATGTTATTTTTAGAAATTTGGGGTC
1 AAAATGTAATTTTTAGAAATTTGGGGTC
* ** *
32380 AAAATGGTAATTTTTGGATGTTTGAGTGT-
1 AAAAT-GTAATTTTTAGAAATTTG-GGGTC
* *
32409 AAAATCATAATTTTGAAGAAATTTAGGGGTC
1 AAAAT-GTAATTTT-TAGAAATTT-GGGGTC
32440 AAAATGTAA-TTTTAGAAA
1 AAAATGTAATTTTTAGAAA
32458 AATTTAAAGT
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
28 10 0.17
29 29 0.49
30 14 0.24
31 6 0.10
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.39
Consensus pattern (28 bp):
AAAATGTAATTTTTAGAAATTTGGGGTC
Found at i:32431 original size:88 final size:89
Alignment explanation
Indices: 32260--32457 Score: 201
Period size: 88 Copynumber: 2.2 Consensus size: 89
32250 TAATTCGAGA
* * * *
32260 TGAAAACGTAATTTTTGAGGAATTTAGGGGTCAAAATTGAAACTTTTGGAAAGTTTTGGATTAAA
1 TGAAAATGTTATTTTT-AGAAATTTAGGGGTCAAAATGGAAACTTTTGGAAAGTTTTGGATTAAA
* *
32325 ATCAAACTTTTGGAAAATTTAAGGT
65 ATCAAACTTTTGAAAAATTTAAGGG
* * *
32350 TGAAAATGTTATTTTTAGAAATTT-GGGGTCAAAATGGTAATTTTTGG-ATG-TTT-GAGTGTAA
1 TGAAAATGTTATTTTTAGAAATTTAGGGGTCAAAATGGAAACTTTTGGAAAGTTTTGGA-T-TAA
*
32411 AATCATAA-TTTTGAAGAAATTTAGGGG
64 AATCA-AACTTTTGAA-AAATTTAAGGG
* *
32438 TCAAAATG-TAATTTTAGAAA
1 TGAAAATGTTATTTTTAGAAA
32458 AATTTAAAGT
Statistics
Matches: 92, Mismatches: 12, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
85 2 0.02
86 4 0.04
87 27 0.29
88 38 0.41
89 7 0.08
90 14 0.15
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.37
Consensus pattern (89 bp):
TGAAAATGTTATTTTTAGAAATTTAGGGGTCAAAATGGAAACTTTTGGAAAGTTTTGGATTAAAA
TCAAACTTTTGAAAAATTTAAGGG
Found at i:32451 original size:30 final size:30
Alignment explanation
Indices: 32416--32667 Score: 115
Period size: 30 Copynumber: 8.5 Consensus size: 30
32406 TGTAAAATCA
32416 TAATTTTGAAGAAATTTAGGGGTCAAAATG
1 TAATTTTGAAGAAATTTAGGGGTCAAAATG
** * *
32446 TAATTTTAGAA-AAATTTAAAGTTTAAAATG
1 TAATTTT-GAAGAAATTTAGGGGTCAAAATG
* * * * **
32476 TAATTTGGAA-AAGTTCAGGGGTTATTATG
1 TAATTTTGAAGAAATTTAGGGGTCAAAATG
* * * * **
32505 TAATTTTAAAG-AAGTTCGAGGGTTAAAACA
1 TAATTTTGAAGAAATTTAG-GGGTCAAAATG
* *** *
32535 TAATTTTGGAA-AAGTTTAAAAGTTAAAATG
1 TAATTTT-GAAGAAATTTAGGGGTCAAAATG
* *
32565 TAATTTT-AGAGAAGTTTA-GGGTCACAATG
1 TAATTTTGA-AGAAATTTAGGGGTCAAAATG
* * *
32594 TAATTTTAAAG-AAGTTCGAGGGTCAAAATG
1 TAATTTTGAAGAAATTTAG-GGGTCAAAATG
* *
32624 TAATTTTGGAGAAA-TTCGTGGGTCAAAATG
1 TAATTTTGAAGAAATTTAG-GGGTCAAAATG
** *
32654 GGATTTTTAAGAAA
1 TAATTTTGAAGAAA
32668 ATAAAGGCCT
Statistics
Matches: 165, Mismatches: 46, Indels: 22
0.71 0.20 0.09
Matches are distributed among these distances:
28 4 0.02
29 43 0.26
30 108 0.65
31 10 0.06
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (30 bp):
TAATTTTGAAGAAATTTAGGGGTCAAAATG
Found at i:32510 original size:89 final size:89
Alignment explanation
Indices: 32435--32639 Score: 270
Period size: 89 Copynumber: 2.3 Consensus size: 89
32425 AGAAATTTAG
* *
32435 GGGTCAAAATGTAATTTTAGAAAAATTT-AAAGTTTAAAATGTAA-TTTGGAAAAGTTCAGGGGT
1 GGGTCAAAATGTAATTTTGGAAAAATTTAAAAG-TTAAAATGTAATTTTAGAAAAGTTCA-GGGT
* **
32498 TATTATGTAATTTTAAAGAAGTTCGA
64 CACAATGTAATTTTAAAGAAGTTCGA
* ** * * *
32524 GGGTTAAAACATAATTTTGGAAAAGTTTAAAAGTTAAAATGTAATTTTAGAGAAGTTTAGGGTCA
1 GGGTCAAAATGTAATTTTGGAAAAATTTAAAAGTTAAAATGTAATTTTAGAAAAGTTCAGGGTCA
32589 CAATGTAATTTTAAAGAAGTTCGA
66 CAATGTAATTTTAAAGAAGTTCGA
*
32613 GGGTCAAAATGTAATTTTGGAGAAATT
1 GGGTCAAAATGTAATTTTGGAAAAATT
32640 CGTGGGTCAA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
89 83 0.85
90 15 0.15
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (89 bp):
GGGTCAAAATGTAATTTTGGAAAAATTTAAAAGTTAAAATGTAATTTTAGAAAAGTTCAGGGTCA
CAATGTAATTTTAAAGAAGTTCGA
Found at i:32601 original size:29 final size:30
Alignment explanation
Indices: 32435--32653 Score: 147
Period size: 30 Copynumber: 7.4 Consensus size: 30
32425 AGAAATTTAG
* * **
32435 GGGTCAAAATGTAATTTTAGAAAAATTTAA
1 GGGTCAAAATGTAATTTTAGAGAAGTTCGA
* * * * *
32465 AGTTTAAAATGTAA-TTTGGAAAAGTTC-A
1 GGGTCAAAATGTAATTTTAGAGAAGTTCGA
* ** *
32493 GGGGTTATTATGTAATTTTAAAGAAGTTCGA
1 -GGGTCAAAATGTAATTTTAGAGAAGTTCGA
* ** * * **
32524 GGGTTAAAACATAATTTTGGAAAAGTTTAA
1 GGGTCAAAATGTAATTTTAGAGAAGTTCGA
** * *
32554 AAGTTAAAATGTAATTTTAGAGAAGTT-TA
1 GGGTCAAAATGTAATTTTAGAGAAGTTCGA
* *
32583 GGGTCACAATGTAATTTTAAAGAAGTTCGA
1 GGGTCAAAATGTAATTTTAGAGAAGTTCGA
* * *
32613 GGGTCAAAATGTAATTTTGGAGAAATTCGT
1 GGGTCAAAATGTAATTTTAGAGAAGTTCGA
32643 GGGTCAAAATG
1 GGGTCAAAATG
32654 GGATTTTTAA
Statistics
Matches: 145, Mismatches: 40, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
28 1 0.01
29 43 0.30
30 100 0.69
31 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTAGAGAAGTTCGA
Found at i:35003 original size:11 final size:11
Alignment explanation
Indices: 34969--35003 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
34959 TTTGGTGTTG
*
34969 TTTTGCTATTA
1 TTTTGTTATTA
*
34980 TATTGTTATTA
1 TTTTGTTATTA
34991 TTTTGTTATTA
1 TTTTGTTATTA
35002 TT
1 TT
35004 GTTTGGATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.20, C:0.03, G:0.09, T:0.69
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:36944 original size:29 final size:27
Alignment explanation
Indices: 36911--36993 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 27
36901 TAGAAAATAC
36911 TAAAAATATTAAAAAGTTGTAAAATTATT
1 TAAAAATATTAAAAAGTTGTAAAA--ATT
* * *
36940 TAAAAATTTGTGAAAATGGTT-TAAGAATT
1 TAAAAATAT-T-AAAA-AGTTGTAAAAATT
36969 TAAAAATGATT-AAAAGTTGTAAAAA
1 TAAAAAT-ATTAAAAAGTTGTAAAAA
36994 CTATACTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
26 3 0.07
27 8 0.19
29 19 0.44
30 2 0.05
31 8 0.19
32 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (27 bp):
TAAAAATATTAAAAAGTTGTAAAAATT
Found at i:36962 original size:21 final size:20
Alignment explanation
Indices: 36919--36992 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 20
36909 ACTAAAAATA
* *
36919 TTAAAAAGTTGTAAAATTAT
1 TTAAAAATTTGTAAAATGAT
*
36939 TTAAAAATTTGTGAAAATGGT
1 TTAAAAATTTGT-AAAATGAT
* *
36960 TTAAGAATTT-AAAAATGA-
1 TTAAAAATTTGTAAAATGAT
*
36978 TT-AAAAGTTGTAAAA
1 TTAAAAATTTGTAAAA
36993 ACTATACTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
17 5 0.12
18 6 0.14
19 6 0.14
20 11 0.26
21 15 0.35
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (20 bp):
TTAAAAATTTGTAAAATGAT
Found at i:36991 original size:19 final size:20
Alignment explanation
Indices: 36911--36993 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 20
36901 TAGAAAATAC
36911 TAAAAAT-ATTAAAAAGTTG
1 TAAAAATGATTAAAAAGTTG
* *
36930 T-AAAATTATTTAAAAATTTG
1 TAAAAATGA-TTAAAAAGTTG
* * *
36950 TGAAAATGGTTTAAGAA-TT-
1 TAAAAAT-GATTAAAAAGTTG
36969 TAAAAATGATT-AAAAGTTG
1 TAAAAATGATTAAAAAGTTG
36988 TAAAAA
1 TAAAAA
36994 CTATACTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.06
18 10 0.20
19 14 0.27
20 13 0.25
21 11 0.22
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (20 bp):
TAAAAATGATTAAAAAGTTG
Found at i:39337 original size:3 final size:3
Alignment explanation
Indices: 39329--39353 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39319 TTTTAATCTC
39329 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
39354 TTTTAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42743 original size:31 final size:32
Alignment explanation
Indices: 42702--42769 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
42692 ATTAATAATT
* *
42702 TATAAGAATTAAATC-AAATCAAAATTT-TATA
1 TATAAAAATTAAA-CAAAATAAAAATTTATATA
* *
42733 TATAAAAATTATACAAAATAAAAATTTATATC
1 TATAAAAATTAAACAAAATAAAAATTTATATA
42765 TATAA
1 TATAA
42770 TTACACAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 1 0.03
31 22 0.71
32 8 0.26
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (32 bp):
TATAAAAATTAAACAAAATAAAAATTTATATA
Found at i:42763 original size:30 final size:30
Alignment explanation
Indices: 42717--42780 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
42707 GAATTAAATC
* *
42717 AAATCAAAATTTTATATATAAAAATTATACA
1 AAATCAAAAATTTATATAT-AAAATTACACA
* *
42748 AAAT-AAAAATTTATATCTATAATTACACA
1 AAATCAAAAATTTATATATAAAATTACACA
42777 AAAT
1 AAAT
42781 TTCTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.45
30 12 0.41
31 4 0.14
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (30 bp):
AAATCAAAAATTTATATATAAAATTACACA
Found at i:44415 original size:123 final size:123
Alignment explanation
Indices: 44163--44448 Score: 319
Period size: 123 Copynumber: 2.3 Consensus size: 123
44153 ATGAAGAACC
* *
44163 AACAAA-AACTAAACAAAATCCACACATGAAATATGCACAAGGTGGGATTGGAGACTCAATACAA
1 AACAAAGAACTAAACAAAATCCACACATGAAATATGCACAAAGTGGGATTAGAGACTCAATACAA
* * * *
44227 GTACAAATATACGTTTAACCAATTACAATGTAGAATCAAATCAATATAAAACACAATG
66 GTACAAACATACGTCTAACCAATTACAATGTAAAATCAAATCAATACAAAACACAATG
* * * * * *
44285 GATAAAGAATTAAACAAAACCCACACAT-AGCATATGTACAAAGTGGGATTAGAGACTCAATACA
1 AACAAAGAACTAAACAAAATCCACACATGA-AATATGCACAAAGTGGGATTAGAGACTCAATACA
* ** * * * * * *
44349 AGTACAGACATTTGTCTAACCGATTATAATGTAAAATCAAATCAGTACAAAATATATTG
65 AGTACAAACATACGTCTAACCAATTACAATGTAAAATCAAATCAATACAAAACACAATG
*
44408 AACAAAGAACTAGACAAAATCCAC-CTAT-AAGATATGCACAA
1 AACAAAGAACTAAACAAAATCCACAC-ATGAA-ATATGCACAA
44449 GATAAAATTA
Statistics
Matches: 132, Mismatches: 28, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
122 6 0.05
123 126 0.95
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (123 bp):
AACAAAGAACTAAACAAAATCCACACATGAAATATGCACAAAGTGGGATTAGAGACTCAATACAA
GTACAAACATACGTCTAACCAATTACAATGTAAAATCAAATCAATACAAAACACAATG
Found at i:51761 original size:29 final size:29
Alignment explanation
Indices: 51724--52124 Score: 262
Period size: 29 Copynumber: 13.8 Consensus size: 29
51714 TGGATGCCCG
51724 AGGGTAAAATGGTAA-TTTTGGAAAGTTT
1 AGGGTAAAATGGTAATTTTTGGAAAGTTT
*
51752 AGGGTCAAAAAT-GAAATTTTTGGAAA-TTT
1 AGGGT--AAAATGGTAATTTTTGGAAAGTTT
** * *
51781 -GAATTAAAATGGTAATTTTTGAAAATTTT
1 AG-GGTAAAATGGTAATTTTTGGAAAGTTT
* * * *
51810 GGGGTCAAAATAG-AATTTTTGGAGA-TTCA
1 AGGGT-AAAATGGTAATTTTTGGAAAGTT-T
* * *
51839 AAGGTAAAATGGCAATTTTTTG-AAGTTT
1 AGGGTAAAATGGTAATTTTTGGAAAGTTT
*
51867 GAGGGTAAAATGAG-ATTTTTTGGAAA-TTT
1 -AGGGTAAAATG-GTAATTTTTGGAAAGTTT
* ** *
51896 GGGGTAAAATTATAATTTTTGG-AAGTTCG
1 AGGGTAAAATGGTAATTTTTGGAAAGTT-T
* * *
51925 AGGGAAAAATGGGATTTTTTGG-AAGTTT
1 AGGGTAAAATGGTAATTTTTGGAAAGTTT
*
51953 GGAGGTAAAATGGTAATTTTT-GAAAGTTT
1 AG-GGTAAAATGGTAATTTTTGGAAAGTTT
*
51982 AGGGACAAAAAT-GTAATTTTTGTG-AAGTTT
1 AGGG--TAAAATGGTAATTTTTG-GAAAGTTT
*
52012 AGGGGGAAAATGGTAATTTTTGG-AAGTTT
1 A-GGGTAAAATGGTAATTTTTGGAAAGTTT
* *
52041 AAGGGTTAAAAT-ATGATTTTTGGAAAGTTT
1 -AGGG-TAAAATGGTAATTTTTGGAAAGTTT
*
52071 AAGGGTTAAAAT-GTAATTCTTGGAAAGTTT
1 -AGGG-TAAAATGGTAATTTTTGGAAAGTTT
*
52101 AAGGGACAAAAT-GTAATTTTTGGA
1 -AGGG-TAAAATGGTAATTTTTGGA
52125 TAATTCGAGG
Statistics
Matches: 297, Mismatches: 48, Indels: 54
0.74 0.12 0.14
Matches are distributed among these distances:
27 7 0.02
28 50 0.17
29 130 0.44
30 106 0.36
31 4 0.01
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
AGGGTAAAATGGTAATTTTTGGAAAGTTT
Found at i:51820 original size:57 final size:58
Alignment explanation
Indices: 51726--52129 Score: 278
Period size: 57 Copynumber: 6.9 Consensus size: 58
51716 GATGCCCGAG
* *
51726 GGTAAAATGGTAATTTTGGAAAGTTTAGGGTCAAAAATGA-AATTTTTGGAAATTTGAA
1 GGTAAAATGGTAATTTTTGAAAGTTTGGGGTC-AAAATGAGAATTTTTGGAAATTTGAA
* * * **
51784 -TTAAAATGGTAATTTTTGAAAATTTTGGGGTCAAAAT-AGAATTTTTGGAGATTCAAA
1 GGTAAAATGGTAATTTTTG-AAAGTTTGGGGTCAAAATGAGAATTTTTGGAAATTTGAA
* * *
51841 GGTAAAATGGCAATTTTTTG-AAGTTTGAGGGT-AAAATGAGATTTTTTGGAAATTTG-G
1 GGTAAAATGGTAA-TTTTTGAAAGTTTG-GGGTCAAAATGAGAATTTTTGGAAATTTGAA
** * * * * * * *
51898 GGTAAAATTATAATTTTTGGAAGTTCGAGGG-AAAAATGGGATTTTTTGGAAGTTTGGA
1 GGTAAAATGGTAATTTTTGAAAGTTTG-GGGTCAAAATGAGAATTTTTGGAAATTTGAA
* * * * *
51956 GGTAAAATGGTAATTTTTGAAAGTTTAGGGACAAAAATG-TAATTTTTGTGAAGTTT-AGG
1 GGTAAAATGGTAATTTTTGAAAGTTTGGGGTC-AAAATGAGAATTTTTG-GAAATTTGA-A
* * * *
52015 GGGAAAATGGTAATTTTTGGAAGTTTAAGGGTTAAAAT-ATG-ATTTTTGGAAAGTTT-AA
1 GGTAAAATGGTAATTTTTGAAAGTTT-GGGGTCAAAATGA-GAATTTTTGGAAA-TTTGAA
* * * *
52073 GGGTTAAAAT-GTAATTCTTGGAAAGTTTAAGGGACAAAATG-TAATTTTTGGATAATT
1 -GG-TAAAATGGTAATT-TTTGAAAGTTT-GGGGTCAAAATGAGAATTTTTGGA-AATT
52130 CGAGGTTTAA
Statistics
Matches: 278, Mismatches: 45, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
56 7 0.03
57 92 0.33
58 71 0.26
59 67 0.24
60 39 0.14
61 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTTGAAAGTTTGGGGTCAAAATGAGAATTTTTGGAAATTTGAA
Found at i:51856 original size:86 final size:85
Alignment explanation
Indices: 51758--52040 Score: 252
Period size: 86 Copynumber: 3.3 Consensus size: 85
51748 GTTTAGGGTC
* * **
51758 AAAAAT-GAAATTTTTGGAAATTTGAATTAAAATGGTAATTTTTGAAAATTTTGGGGTCAAAA-T
1 AAAAATGGCAATTTTTGGAAGTTTGAGGTAAAATGGTAATTTTTGAAAA-TTTGGGGT-AAAATT
51821 AGAATTTTTGG-AGATTCAAAGG
64 AGAATTTTTGGAAG-TTCAAAGG
* * * *
51843 TAAAATGGCAATTTTTTGAAGTTTGAGGGTAAAATGAG-ATTTTTTGGAAATTTGGGGTAAAATT
1 AAAAATGGCAATTTTTGGAAGTTTGA-GGTAAAATG-GTAATTTTTGAAAATTTGGGGTAAAATT
* * *
51907 ATAATTTTTGGAAGTTCGAGGG
64 AGAATTTTTGGAAGTTCAAAGG
* * * ** *
51929 AAAAATGGGATTTTTTGGAAGTTTGGAGGTAAAATGGTAATTTTTGAAAGTTTAGGGACAAAAAT
1 AAAAATGGCAATTTTTGGAAGTTT-GAGGTAAAATGGTAATTTTTGAAAATTT-GGGGTAAAATT
* **
51994 -GTAATTTTTGTGAAGTTTAGGGG
64 AG-AATTTTTG-GAAGTTCAAAGG
* *
52017 GAAAATGGTAATTTTTGGAAGTTT
1 AAAAATGGCAATTTTTGGAAGTTT
52041 AAGGGTTAAA
Statistics
Matches: 160, Mismatches: 28, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
85 10 0.06
86 82 0.51
87 37 0.23
88 31 0.19
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (85 bp):
AAAAATGGCAATTTTTGGAAGTTTGAGGTAAAATGGTAATTTTTGAAAATTTGGGGTAAAATTAG
AATTTTTGGAAGTTCAAAGG
Found at i:53209 original size:11 final size:11
Alignment explanation
Indices: 53193--53218 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53183 ATTATTAATA
53193 TTAATATTTAT
1 TTAATATTTAT
53204 TTAATATTTAT
1 TTAATATTTAT
53215 TTAA
1 TTAA
53219 AACATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTAATATTTAT
Found at i:53995 original size:17 final size:17
Alignment explanation
Indices: 53973--54062 Score: 99
Period size: 17 Copynumber: 5.3 Consensus size: 17
53963 TTTTTATTTC
*
53973 AAAATAAATTTAAATTT
1 AAAATAAATTTAAACTT
*
53990 AAAATAAATTTAAACTC
1 AAAATAAATTTAAACTT
* **
54007 CAAATAAGCTTAAACTT
1 AAAATAAATTTAAACTT
*
54024 ACAATAAATTTAAACTT
1 AAAATAAATTTAAACTT
* * *
54041 AAAATGAATTAAAATTT
1 AAAATAAATTTAAACTT
54058 AAAAT
1 AAAAT
54063 CTAAAATTGG
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 59 1.00
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATAAATTTAAACTT
Found at i:59085 original size:169 final size:167
Alignment explanation
Indices: 58791--59099 Score: 483
Period size: 169 Copynumber: 1.8 Consensus size: 167
58781 TCTGAACCGT
*
58791 TTGCTTCCTCATTGTTATTGGGAAAGCTATTACCAAAATTGGTCCAATAATTCTGTCTTAAGCTG
1 TTGCTTCCTCATTGTCATTGGGAAAGCTATTACCAAAATTGGTCCAATAATTCTGTCTTAAGCTG
* * * *
58856 GCTTATATTTGATATTCTGGATGCCAGTAAGAAAGTGTACTTTGTTTTCTTTGCTTAAGGAGAGC
66 CCTTATATTTGATATTCCGGATGCCAGTAAGAAAGTGGACTTTGTTTTCTTTGCTTAAGGAAAGC
58921 CACTTGCTCCAATATCTGTTAGCTTATACTAAATCAA
131 CACTTGCTCCAATATCTGTTAGCTTATACTAAATCAA
* * * *
58958 TTGCTTGCTCATTGTCATTGGGAAAGCTATTGCCAAAATTGGTTCCACTAGTTCTGTCTTAAAGC
1 TTGCTTCCTCATTGTCATTGGGAAAGCTATTACCAAAATTGG-TCCAATAATTCTGTCTT-AAGC
* * *
59023 TGCCTTGTATTTGATATTCCGGATGTCAGTAAGAAAGTGGATTTTGTTTTCTTTGCTTAAGGAAA
64 TGCCTTATATTTGATATTCCGGATGCCAGTAAGAAAGTGGACTTTGTTTTCTTTGCTTAAGGAAA
*
59088 GGCACTTGCTCC
129 GCCACTTGCTCC
59100 GATACCTGAA
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
167 39 0.31
168 15 0.12
169 73 0.57
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (167 bp):
TTGCTTCCTCATTGTCATTGGGAAAGCTATTACCAAAATTGGTCCAATAATTCTGTCTTAAGCTG
CCTTATATTTGATATTCCGGATGCCAGTAAGAAAGTGGACTTTGTTTTCTTTGCTTAAGGAAAGC
CACTTGCTCCAATATCTGTTAGCTTATACTAAATCAA
Found at i:59138 original size:9 final size:9
Alignment explanation
Indices: 59124--59150 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
59114 AAGCAGAGTT
59124 GGAAGAAGA
1 GGAAGAAGA
59133 GGAAGAAGA
1 GGAAGAAGA
59142 GGAAGAAGA
1 GGAAGAAGA
59151 ACATGAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
GGAAGAAGA
Found at i:63434 original size:3 final size:3
Alignment explanation
Indices: 63428--63452 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
63418 CTCATCATTG
63428 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
63453 ATTATATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:69314 original size:16 final size:17
Alignment explanation
Indices: 69290--69322 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
69280 TATTGAATTT
69290 AATTAAA-TTCTTTTTA
1 AATTAAATTTCTTTTTA
*
69306 AATTCAATTTCTTTTTA
1 AATTAAATTTCTTTTTA
69323 TTTTTTTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTAAATTTCTTTTTA
Found at i:74985 original size:23 final size:24
Alignment explanation
Indices: 74945--74991 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
74935 TTAACATCAT
74945 TATAAAAATAAATGATAAA-ATTA
1 TATAAAAATAAATGATAAAGATTA
*
74968 TATAAAATTAAAAT-ATAAAGATTA
1 TATAAAAAT-AAATGATAAAGATTA
74992 AACTTCGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (24 bp):
TATAAAAATAAATGATAAAGATTA
Found at i:75064 original size:10 final size:10
Alignment explanation
Indices: 75049--75079 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
75039 TATAATAACT
75049 AAAAAAAAGA
1 AAAAAAAAGA
75059 AAAAAAAAGA
1 AAAAAAAAGA
*
75069 AAAAAAGAGA
1 AAAAAAAAGA
75079 A
1 A
75080 GAGTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:77725 original size:2 final size:2
Alignment explanation
Indices: 77718--77748 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
77708 GCTCAAAATG
77718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
77749 GAAATCCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:81605 original size:3 final size:3
Alignment explanation
Indices: 81597--81638 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
81587 AGCATCTATC
81597 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
81639 AATTAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:82966 original size:2 final size:2
Alignment explanation
Indices: 82959--82996 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
82949 GTGCCGGTAA
82959 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
82997 TAATGAACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:90638 original size:17 final size:19
Alignment explanation
Indices: 90616--90650 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
90606 CAATTCAAAG
90616 TCAATTT-CA-TATTTTCA
1 TCAATTTGCACTATTTTCA
90633 TCAATTTGCACTATTTTC
1 TCAATTTGCACTATTTTC
90651 TATTTTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.26, C:0.20, G:0.03, T:0.51
Consensus pattern (19 bp):
TCAATTTGCACTATTTTCA
Found at i:90747 original size:12 final size:12
Alignment explanation
Indices: 90727--90758 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
90717 AATAACATAT
*
90727 ACTCACATTGAC
1 ACTCCCATTGAC
90739 ACTCCCATTGAC
1 ACTCCCATTGAC
90751 ACTCCCAT
1 ACTCCCAT
90759 ATGTAGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.41, G:0.06, T:0.25
Consensus pattern (12 bp):
ACTCCCATTGAC
Found at i:98633 original size:2 final size:2
Alignment explanation
Indices: 98621--98654 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
98611 GGATTAAACT
*
98621 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
98655 AAGAGACAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:100217 original size:11 final size:11
Alignment explanation
Indices: 100201--100226 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
100191 TTCTTCTTAC
100201 TTTTTTTGTTT
1 TTTTTTTGTTT
100212 TTTTTTTGTTT
1 TTTTTTTGTTT
100223 TTTT
1 TTTT
100227 GTTTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:109327 original size:26 final size:24
Alignment explanation
Indices: 109277--109332 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
109267 TTTTAATTTA
*
109277 ACTCGAACAATTTCATTCGATTCG
1 ACTCGAACAATTTCATTCGACTCG
**
109301 ACTCGAATCAAATTTCATTTTACTCG
1 ACTCGAA-C-AATTTCATTCGACTCG
109327 ACTCGA
1 ACTCGA
109333 TTCGAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 7 0.26
25 1 0.04
26 19 0.70
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (24 bp):
ACTCGAACAATTTCATTCGACTCG
Found at i:111081 original size:40 final size:40
Alignment explanation
Indices: 110997--111109 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 40
110987 GGTATTATAG
* * * * * * *
110997 TTCATTAACAATCTAACGGTGTTCACAGTGTCACAGCTAG
1 TTCAGTAACAATATTACAGTGTTTACAGTGTCACAGCCAA
* * * *
111037 TTCAGTAGCAATGTTTCAGTGTTTACAGTGTCACTGCCAA
1 TTCAGTAACAATATTACAGTGTTTACAGTGTCACAGCCAA
* *
111077 TTCAGTAATAATATTACAGTGTTTATAGTGTCA
1 TTCAGTAACAATATTACAGTGTTTACAGTGTCA
111110 TTGTCAGTTC
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (40 bp):
TTCAGTAACAATATTACAGTGTTTACAGTGTCACAGCCAA
Found at i:111126 original size:40 final size:40
Alignment explanation
Indices: 111053--111238 Score: 196
Period size: 40 Copynumber: 4.7 Consensus size: 40
111043 AGCAATGTTT
* * * *
111053 CAGTGTTTACAGTGTCACTGCCAATTCAGTAATAATATTA
1 CAGTGTTTACAGTGTCACTGTCAATTCAATAATAACATTG
* * * *
111093 CAGTGTTTATAGTGTCATTGTCAGTTCAATAATAGCATTG
1 CAGTGTTTACAGTGTCACTGTCAATTCAATAATAACATTG
* * * *
111133 TAATGTTTATAGTATCACTG-CAAATTCAATAATAGA-ATTG
1 CAGTGTTTACAGTGTCACTGTC-AATTCAATAATA-ACATTG
* * * *
111173 TAGTGTTTACAGTGTCACTGTCAGTTCAGTAATAGCATTG
1 CAGTGTTTACAGTGTCACTGTCAATTCAATAATAACATTG
111213 CAGTGTTTACAGTGTCACTGTCAATT
1 CAGTGTTTACAGTGTCACTGTCAATT
111239 ATAACCATTC
Statistics
Matches: 120, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 118 0.98
41 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (40 bp):
CAGTGTTTACAGTGTCACTGTCAATTCAATAATAACATTG
Found at i:111151 original size:80 final size:80
Alignment explanation
Indices: 111056--111238 Score: 242
Period size: 80 Copynumber: 2.3 Consensus size: 80
111046 AATGTTTCAG
* * *
111056 TGTTTACAGTGTCACTGCCAATTCAGTAATA-ATATTACAGTGTTTATAGTGTCATTGTCAGTTC
1 TGTTTACAGTGTCACTGCCAATTCAATAATAGA-ATTACAGTGTTTACAGTGTCACTGTCAGTTC
*
111120 AATAATAGCATTGTAA
65 AATAATAGCATTGCAA
* * * **
111136 TGTTTATAGTATCACTGCAAATTCAATAATAGAATTGTAGTGTTTACAGTGTCACTGTCAGTTCA
1 TGTTTACAGTGTCACTGCCAATTCAATAATAGAATTACAGTGTTTACAGTGTCACTGTCAGTTCA
* *
111201 GTAATAGCATTGCAG
66 ATAATAGCATTGCAA
*
111216 TGTTTACAGTGTCACTGTCAATT
1 TGTTTACAGTGTCACTGCCAATT
111239 ATAACCATTC
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 86 0.99
81 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (80 bp):
TGTTTACAGTGTCACTGCCAATTCAATAATAGAATTACAGTGTTTACAGTGTCACTGTCAGTTCA
ATAATAGCATTGCAA
Found at i:115133 original size:2 final size:2
Alignment explanation
Indices: 115126--115156 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
115116 TTACCTAACA
115126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115157 ATAATTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:123034 original size:114 final size:113
Alignment explanation
Indices: 122835--123067 Score: 403
Period size: 114 Copynumber: 2.1 Consensus size: 113
122825 CTGCCTAGTA
* *
122835 ATTTGACATAAAGATGAGAGAAAAAAAAATCAAAATAATGGATAAAATTGCATATAAAGAGATCC
1 ATTTGACATAAAGATGAGAGAAAAAAAAATCAAAATAATGGATAAAATTGCACATAAAGAGATCA
*
122900 GCTACCAGAAGTTTCTATGTTGAATATTTAGATGGGAGATCATTATAT
66 GCTACCAGAAGTTTCTATGTTAAATATTTAGATGGGAGATCATTATAT
* *
122948 ATTTGACATAAAGATGAGAGGAAAAAAAAATCAAAATAATGGTTAAAATTGTACATAAAGAGATC
1 ATTTGACATAAAGATGAGA-GAAAAAAAAATCAAAATAATGGATAAAATTGCACATAAAGAGATC
*
123013 AGCTACCAGAAGTTTCTATGTTAAATATTTAGATGGGAGATCATTATTT
65 AGCTACCAGAAGTTTCTATGTTAAATATTTAGATGGGAGATCATTATAT
123062 ATTTGA
1 ATTTGA
123068 TTAATAAGTC
Statistics
Matches: 113, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 19 0.17
114 94 0.83
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.30
Consensus pattern (113 bp):
ATTTGACATAAAGATGAGAGAAAAAAAAATCAAAATAATGGATAAAATTGCACATAAAGAGATCA
GCTACCAGAAGTTTCTATGTTAAATATTTAGATGGGAGATCATTATAT
Done.