Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010465.1 Kokia drynarioides strain JFW-HI SEQ_125363, 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: 78396
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 79 characters in sequence are not A, C, G, or T
Found at i:32 original size:11 final size:12
Alignment explanation
Indices: 16--45 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6 TTTATTTATT
16 TAATAAAT-AAA
1 TAATAAATAAAA
27 TAATAAATAAAA
1 TAATAAATAAAA
39 TAATAAA
1 TAATAAA
46 ATTTGGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAATAAATAAAA
Found at i:2606 original size:15 final size:14
Alignment explanation
Indices: 2582--2693 Score: 116
Period size: 15 Copynumber: 7.4 Consensus size: 14
2572 TTCACCTAAC
2582 AAAAAGAGAAGAAAAG
1 AAAAA-AGAA-AAAAG
2598 AAAAAAGAAAAAAGG
1 AAAAAAGAAAAAA-G
*
2613 AAAAAAGAAAAAGGAA
1 AAAAAAGAAAAA--AG
*
2629 AAAAAAGGAAAAAGG
1 AAAAAA-GAAAAAAG
*
2644 AAAAAAGGAAAAAGG
1 AAAAAA-GAAAAAAG
2659 AAAAAAGGAAAAAAGG
1 AAAAAA-GAAAAAA-G
2675 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
2689 AAAAA
1 AAAAA
2694 TGAGAGGTTG
Statistics
Matches: 87, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
14 10 0.11
15 52 0.60
16 18 0.21
17 7 0.08
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:2609 original size:8 final size:7
Alignment explanation
Indices: 2582--2693 Score: 116
Period size: 7 Copynumber: 14.7 Consensus size: 7
2572 TTCACCTAAC
2582 AAAAAGAG
1 AAAAA-AG
2590 AAGAAAAG
1 AA-AAAAG
2598 AAAAAAG
1 AAAAAAG
2605 AAAAAAGG
1 AAAAAA-G
2613 AAAAAAG
1 AAAAAAG
*
2620 AAAAAGGAA
1 AAAAA--AG
2629 AAAAAAGG
1 AAAAAA-G
*
2637 AAAAAGG
1 AAAAAAG
2644 AAAAAAGG
1 AAAAAA-G
*
2652 AAAAAGG
1 AAAAAAG
2659 AAAAAAGG
1 AAAAAA-G
2667 AAAAAAGG
1 AAAAAA-G
2675 AAAAAAG
1 AAAAAAG
2682 AAAAAAG
1 AAAAAAG
2689 AAAAA
1 AAAAA
2694 TGAGAGGTTG
Statistics
Matches: 91, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
7 43 0.47
8 39 0.43
9 9 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:4215 original size:40 final size:40
Alignment explanation
Indices: 4135--4310 Score: 158
Period size: 40 Copynumber: 4.3 Consensus size: 40
4125 GCCACGATTT
* ** *
4135 AATCTTTTACCCTAACTAGAGGGTAAATTGTAGACTATCC
1 AATCTTTTACCCTAACTAGAGGGCAAATTAAAGACCATCC
* * * *
4175 AATCTTCTACCCTAACTAGAAGGCAGATTAAAGTCCATCC
1 AATCTTTTACCCTAACTAGAGGGCAAATTAAAGACCATCC
* * *
4215 AA--TTTTACCCCTAAACCAAGAGGGACAGATTGAAGACACCATCC
1 AATCTTTTA-CCCT-AA-CTAGAGGG-CAAATT-AA-AGACCATCC
* * *
4259 AATCTTTTACCCTAACCAGAGGGCAAATTAAAGACCTTCT
1 AATCTTTTACCCTAACTAGAGGGCAAATTAAAGACCATCC
4299 AATCTTTTACCC
1 AATCTTTTACCC
4311 GAGCCATGGG
Statistics
Matches: 110, Mismatches: 18, Indels: 16
0.76 0.12 0.11
Matches are distributed among these distances:
38 4 0.04
39 4 0.04
40 54 0.49
41 8 0.07
42 11 0.10
43 9 0.08
44 11 0.10
45 4 0.04
46 5 0.05
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.27
Consensus pattern (40 bp):
AATCTTTTACCCTAACTAGAGGGCAAATTAAAGACCATCC
Found at i:4233 original size:124 final size:129
Alignment explanation
Indices: 4040--4287 Score: 301
Period size: 124 Copynumber: 1.9 Consensus size: 129
4030 ACATCATCCC
* * *
4040 ATCCAATCTTTTACCCCTAAGTCAAGAAAGGCAGATTGAAGTCATCATTCCATCTTTACCCTTAA
1 ATCCAATCTTCTACCCCTAAG-CAAGAAAGGCAGATTAAAGTCA-CATTCCATCTTTACCCCTAA
** * * ** * *
4105 ACCAAAAGGGGTAAATTGAAGCCACGATTTAATCTTTTACCCTAACTAGAGGGTAAATTGTAGAC
64 ACCAAAAGGGACAAATTGAAGACACCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGTAGAC
4170 T
129 T
*
4171 ATCCAATCTTCTA-CCCTAA-CTAG-AAGGCAGATTAAAGTC-CA-TCCAAT-TTTACCCCTAAA
1 ATCCAATCTTCTACCCCTAAGCAAGAAAGGCAGATTAAAGTCACATTCC-ATCTTTACCCCTAAA
* *
4230 CCAAGAGGGACAGATTGAAGACACCATCCAATCTTTTACCCTAACCAGAGGGCAAATT
65 CCAAAAGGGACAAATTGAAGACACCATCCAATCTTTTACCCTAACCAGAGGGCAAATT
4288 AAAGACCTTC
Statistics
Matches: 102, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
124 62 0.61
125 4 0.04
127 15 0.15
128 3 0.03
130 6 0.06
131 12 0.12
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (129 bp):
ATCCAATCTTCTACCCCTAAGCAAGAAAGGCAGATTAAAGTCACATTCCATCTTTACCCCTAAAC
CAAAAGGGACAAATTGAAGACACCATCCAATCTTTTACCCTAACCAGAGGGCAAATTGTAGACT
Found at i:4345 original size:38 final size:35
Alignment explanation
Indices: 4314--4380 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
4304 TTTACCCGAG
*
4314 CCATG-GGCAGATTGAAGTCATCCAATTTTTTACC
1 CCATGTGGCAGATTGAAGTCATCCAATCTTTTACC
*
4348 CCATGTGGCAGATTGAAGTCATTCAATCTTTTA
1 CCATGTGGCAGATTGAAGTCATCCAATCTTTTA
4381 TACCTAAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (35 bp):
CCATGTGGCAGATTGAAGTCATCCAATCTTTTACC
Found at i:4345 original size:124 final size:124
Alignment explanation
Indices: 4068--4349 Score: 279
Period size: 124 Copynumber: 2.3 Consensus size: 124
4058 AAGTCAAGAA
* ** * *
4068 AGGCAGATTGAAGTCAT-C-ATTCCATCTTTACCCTTAAACCAAAAGGGGTAAATTGAAGCCACG
1 AGGCAGATTGAAGTCATCCAATT---T-TTTACCCCTAAACCAAAAGGGACAAATTGAAGACACC
** * * ** * *
4131 ATTTAATCTTTTACCCTAACTAGAGGGTAAATTGTAGACTATCCAATCTTCTACCCTAACTAG
62 ATCCAATCTTTTACCCTAACCAGAGGGCAAATTAAAGACTATCCAATCTTCTACCCGAACCAG
* * *
4194 AAGGCAGATTAAAGTCCATCCAA--TTTTACCCCTAAACCAAGAGGGACAGATTGAAGACACCAT
1 -AGGCAGATTGAAGT-CATCCAATTTTTTACCCCTAAACCAAAAGGGACAAATTGAAGACACCAT
* * *
4257 CCAATCTTTTACCCTAACCAGAGGGCAAATTAAAGACCT-TCTAATCTTTTACCCGAGCCATG
64 CCAATCTTTTACCCTAACCAGAGGGCAAATTAAAGA-CTATCCAATCTTCTACCCGAACCA-G
4319 -GGCAGATTGAAGTCATCCAATTTTTTACCCC
1 AGGCAGATTGAAGTCATCCAATTTTTTACCCC
4350 ATGTGGCAGA
Statistics
Matches: 128, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
122 7 0.05
123 12 0.09
124 87 0.68
125 4 0.03
127 13 0.10
128 3 0.02
129 1 0.01
130 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (124 bp):
AGGCAGATTGAAGTCATCCAATTTTTTACCCCTAAACCAAAAGGGACAAATTGAAGACACCATCC
AATCTTTTACCCTAACCAGAGGGCAAATTAAAGACTATCCAATCTTCTACCCGAACCAG
Found at i:4440 original size:45 final size:45
Alignment explanation
Indices: 4371--4673 Score: 214
Period size: 45 Copynumber: 6.6 Consensus size: 45
4361 TGAAGTCATT
* *
4371 CAATCTTTTATACCTAAGTCAAGAGGGGCAAATTAAAACTACTATC
1 CAATCTTTTATACCT-AGTCAAGAGGGGCAAATTAAAACCACCATC
* * * **
4417 TAATCTTTTACT-CCTAGTCAAGAGGGGCAGATTGAGGCCACCATC
1 CAATCTTTTA-TACCTAGTCAAGAGGGGCAAATTAAAACCACCATC
* * * * *
4462 CAATCTTTTATCCCTAGTCAAGAGGGGCAGATTTAAGCCACCATA
1 CAATCTTTTATACCTAGTCAAGAGGGGCAAATTAAAACCACCATC
* * * * ** * * *
4507 CAATCTTTTA-CCTCTAATCAAGAGAGACAGGTTGAAGCCATCATC
1 CAATCTTTTATAC-CTAGTCAAGAGGGGCAAATTAAAACCACCATC
** * * * * *
4552 CAAATCTTTTACCCCTAATCAATAGGGGCAGATTGAAGCCACCATC
1 C-AATCTTTTATACCTAGTCAAGAGGGGCAAATTAAAACCACCATC
** * * *
4598 CAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCACCATC
1 CAATCTTTTATACCT-AGTCAAGAGGGGCAAATTAAAACCACCATC
* * *
4644 CAATCTTTTATGCCTAAATCAAGAGAGGCA
1 CAATCTTTTATACCT-AGTCAAGAGGGGCA
4674 GATTGAAGCT
Statistics
Matches: 222, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
44 3 0.01
45 113 0.51
46 103 0.46
47 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
CAATCTTTTATACCTAGTCAAGAGGGGCAAATTAAAACCACCATC
Found at i:4570 original size:46 final size:45
Alignment explanation
Indices: 4371--4688 Score: 375
Period size: 46 Copynumber: 7.0 Consensus size: 45
4361 TGAAGTCATT
** * * * * *
4371 CAATCTTTTATACCTAAGTCAAGAGGGGCAAATTAAAACTACTATC
1 CAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCCACCATC
* * * *
4417 TAATCTTTTACTCCTAGTCAAGAGGGGCAGATTGAGGCCACCATC
1 CAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATC
* * * *
4462 CAATCTTTTATCCCTAGTCAAGAGGGGCAGATTTAAGCCACCATA
1 CAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATC
* * * * *
4507 CAATCTTTTACCTCTAATCAAGAGAGACAGGTTGAAGCCATCATC
1 CAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATC
*
4552 CAAATCTTTTACCCCTAATCAATAGGGGCAGATTGAAGCCACCATC
1 C-AATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATC
4598 CAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCACCATC
1 CAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCCACCATC
** * *
4644 CAATCTTTTATGCCTAAATCAAGAGAGGCAGATTGAAGCTACCAT
1 CAATCTTTTACCCCT-AATCAAGAGGGGCAGATTGAAGCCACCAT
4689 ATCACAGAAG
Statistics
Matches: 233, Mismatches: 36, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
45 114 0.49
46 117 0.50
47 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
CAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATC
Found at i:4584 original size:91 final size:90
Alignment explanation
Indices: 4371--4689 Score: 381
Period size: 91 Copynumber: 3.5 Consensus size: 90
4361 TGAAGTCATT
* * * * * * *
4371 CAATCTTTTATACCTAAGTCAAGAGGGGCAAATTAAAACTACTAT-CTAATCTTTTA-CTCCTAG
1 CAATCTTTTATCCCTAA-TCAAGAGGGGCAGATTGAAGCCACCATAC-AATCTTTTACCT-CTAA
*
4434 TCAAGAGGGGCAGATTGAGGCCACCATC
63 TCAAGAGGGGCAGATTGAAGCCACCATC
* *
4462 CAATCTTTTATCCCTAGTCAAGAGGGGCAGATTTAAGCCACCATACAATCTTTTACCTCTAATCA
1 CAATCTTTTATCCCTAATCAAGAGGGGCAGATTGAAGCCACCATACAATCTTTTACCTCTAATCA
* * * *
4527 AGAGAGACAGGTTGAAGCCATCATC
66 AGAGGGGCAGATTGAAGCCACCATC
* * * *
4552 CAAATCTTTTACCCCTAATCAATAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAGT
1 C-AATCTTTTATCCCTAATCAAGAGGGGCAGATTGAAGCCACCATACAATCTTTTACCTCTAA-T
4617 CAAGAGGGGCAGATTGAAGCCACCATC
64 CAAGAGGGGCAGATTGAAGCCACCATC
* * *
4644 CAATCTTTTATGCCTAAATCAAGAGAGGCAGATTGAAGCTACCATA
1 CAATCTTTTATCCCT-AATCAAGAGGGGCAGATTGAAGCCACCATA
4690 TCACAGAAGC
Statistics
Matches: 194, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
90 58 0.30
91 85 0.44
92 51 0.26
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (90 bp):
CAATCTTTTATCCCTAATCAAGAGGGGCAGATTGAAGCCACCATACAATCTTTTACCTCTAATCA
AGAGGGGCAGATTGAAGCCACCATC
Found at i:6226 original size:30 final size:29
Alignment explanation
Indices: 6168--6257 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 29
6158 ATTTTACGTA
* * *
6168 TTTATTCTA-TTTTTT-AAATTAAATCTT
1 TTTATTTTATTTTTTTAAAATTTAACCTT
6195 TTTATTTTATTTTTGTTAAAATTTAACCTT
1 TTTATTTTATTTTT-TTAAAATTTAACCTT
*
6225 TTTATTTTTATTTCTTTTAAAA-TTACCCTT
1 TTTA-TTTTATTT-TTTTAAAATTTAACCTT
6255 TTT
1 TTT
6258 TCTGTTTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
27 8 0.15
28 4 0.07
29 2 0.04
30 24 0.44
31 14 0.26
32 2 0.04
ACGTcount: A:0.26, C:0.09, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTATTTTATTTTTTTAAAATTTAACCTT
Found at i:6237 original size:31 final size:30
Alignment explanation
Indices: 6150--6257 Score: 93
Period size: 30 Copynumber: 3.7 Consensus size: 30
6140 GTTGTTTCTC
* * * *
6150 TCTTTT-AAATTTTACGTATTTATTCTA-T
1 TCTTTTAAAATTTAACCTTTTTATTTTATT
* *
6178 T-TTTT-AAATTAAATCTTTTTATTTTATT
1 TCTTTTAAAATTTAACCTTTTTATTTTATT
6206 T-TTGTTAAAATTTAACCTTTTTATTTTTATT
1 TCTT-TTAAAATTTAACCTTTTTA-TTTTATT
*
6237 TCTTTTAAAA-TTACCCTTTTT
1 TCTTTTAAAATTTAACCTTTTT
6258 TCTGTTTCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
27 19 0.29
28 5 0.08
29 2 0.03
30 24 0.36
31 14 0.21
32 2 0.03
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (30 bp):
TCTTTTAAAATTTAACCTTTTTATTTTATT
Found at i:6555 original size:24 final size:24
Alignment explanation
Indices: 6504--6563 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
6494 TCATTTAGTT
* * *
6504 AAACTTTGTTTATTTGTTTCAATT
1 AAACTCTGATTATTTGTTTCAATA
* *
6528 AAACTCTGATTATTTGTTTGAGTA
1 AAACTCTGATTATTTGTTTCAATA
*
6552 AAACTCTTATTA
1 AAACTCTGATTA
6564 GTCTAGATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (24 bp):
AAACTCTGATTATTTGTTTCAATA
Found at i:14898 original size:19 final size:19
Alignment explanation
Indices: 14871--14914 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
14861 CAAGGCTTGA
* *
14871 TGGATAGAAACAAACTGCT
1 TGGAAAGAAACAAACTGAT
14890 TGGAAAGAAACAAACTGAT
1 TGGAAAGAAACAAACTGAT
14909 TGGAAA
1 TGGAAA
14915 AGTGATGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (19 bp):
TGGAAAGAAACAAACTGAT
Found at i:16726 original size:24 final size:24
Alignment explanation
Indices: 16650--16714 Score: 130
Period size: 24 Copynumber: 2.7 Consensus size: 24
16640 TATTTTTATC
16650 ACTCTGTTTATTTGTTTCAATTAA
1 ACTCTGTTTATTTGTTTCAATTAA
16674 ACTCTGTTTATTTGTTTCAATTAA
1 ACTCTGTTTATTTGTTTCAATTAA
16698 ACTCTGTTTATTTGTTT
1 ACTCTGTTTATTTGTTT
16715 GAGTCAAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (24 bp):
ACTCTGTTTATTTGTTTCAATTAA
Found at i:16901 original size:22 final size:23
Alignment explanation
Indices: 16845--16901 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
16835 TTTTGGAGAA
* * *
16845 TTTAGTGTTTACGTTTTGAGGGT
1 TTTAGTTTTTAAGTTTTCAGGGT
*
16868 TCTTTGTTTTTAAGTTTTCAGGG-
1 T-TTAGTTTTTAAGTTTTCAGGGT
16891 TTTAGTTTTTA
1 TTTAGTTTTTA
16902 TCTTCATCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 9 0.32
23 2 0.07
24 17 0.61
ACGTcount: A:0.14, C:0.05, G:0.23, T:0.58
Consensus pattern (23 bp):
TTTAGTTTTTAAGTTTTCAGGGT
Found at i:17021 original size:8 final size:8
Alignment explanation
Indices: 17008--17032 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16998 ATTTGTGTGT
17008 TCAATTTC
1 TCAATTTC
17016 TCAATTTC
1 TCAATTTC
17024 TCAATTTC
1 TCAATTTC
17032 T
1 T
17033 TCCACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAATTTC
Found at i:18459 original size:26 final size:26
Alignment explanation
Indices: 18420--18470 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
18410 CCATTCTTTT
18420 GAAAGTCATAAGTG-GGAAAGACATTC
1 GAAAGTCATAAGTGAGG-AAGACATTC
*
18446 GAAAGTCATGAGTGAGGAAGACATT
1 GAAAGTCATAAGTGAGGAAGACATT
18471 TAAAGAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.41, C:0.10, G:0.29, T:0.20
Consensus pattern (26 bp):
GAAAGTCATAAGTGAGGAAGACATTC
Found at i:20379 original size:86 final size:86
Alignment explanation
Indices: 20277--20494 Score: 305
Period size: 86 Copynumber: 2.5 Consensus size: 86
20267 TGTTTCTTCA
* * * * *
20277 GATAAAAATATATTAGCTTTTTTAGAGCCTTGAATTAATTTTGTTCTATGAAATATTAATATGTT
1 GATAACAATATATTAGCTCTTTTAGAGCCCT-AATTAATTTTGTACTATGAAATATTAACATGTT
20342 CCATTACCACATTGAACAT-AG
65 CCATTACCACATTGAACATAAG
* *
20363 GATAACAATATATTAGCTCTTTTAGAGCCCTAAATTAATTTTGTACTGTGAACTATTAACATGTT
1 GATAACAATATATTAGCTCTTTTAGAGCCCT-AATTAATTTTGTACTATGAAATATTAACATGTT
* *
20428 CCATTATCACATTGAACTTAAG
65 CCATTACCACATTGAACATAAG
*
20450 G-TAACAATATATTAGCTCTTCTAGAGCCCTAAGTTAATTTTGTAC
1 GATAACAATATATTAGCTCTTTTAGAGCCCTAA-TTAATTTTGTAC
20495 CCCCAAAGAT
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
85 2 0.02
86 114 0.96
87 3 0.03
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (86 bp):
GATAACAATATATTAGCTCTTTTAGAGCCCTAATTAATTTTGTACTATGAAATATTAACATGTTC
CATTACCACATTGAACATAAG
Found at i:24989 original size:26 final size:26
Alignment explanation
Indices: 24953--25007 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
24943 CATAAGACAG
24953 AATGATTAGTAATAATTAAAGTTCTC
1 AATGATTAGTAATAATTAAAGTTCTC
24979 AATGATTAGTAATAATTAAAGTTCTC
1 AATGATTAGTAATAATTAAAGTTCTC
25005 AAT
1 AAT
25008 TTTTGTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (26 bp):
AATGATTAGTAATAATTAAAGTTCTC
Found at i:26310 original size:23 final size:25
Alignment explanation
Indices: 26284--26331 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
26274 TTTTTAAAAA
26284 AATATTT-AT-ATTATATTTA-TTTT
1 AATATTTAATAATTA-ATTTAGTTTT
26307 AATATTTAATAATTAATTTAGTTTT
1 AATATTTAATAATTAATTTAGTTTT
26332 TATTATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
AATATTTAATAATTAATTTAGTTTT
Found at i:33451 original size:301 final size:298
Alignment explanation
Indices: 32835--33519 Score: 765
Period size: 301 Copynumber: 2.3 Consensus size: 298
32825 ATATGCATAA
*
32835 ATTAGATTAGTAAAA-TCTTAAATTTACCACTAAATCAAAGTTTCATTTAAACATATTTTATACA
1 ATTAGATTAGTAAAACT-TTAAATTTACCACTAAATCAAAGTTTCATTTTAACATATTTTATACA
* * * * *
32899 ATTTTATTTTAATATGCATAATTTATTATCTCCATCAGTTGTATATTTATACTATTAATAAAGCT
65 ATTTTATTTTAATACGCACAATTTATGATCTCCATAAATTGTATATTTATACTATTAATAAAGCT
** * *
32964 CCTGATTGAATTGATGTCACGAGTTAATCGAACACCAACTCGGTTAAAAAAATTATGAAAATGTT
130 CCTGATTGAATTGATGTCACGAGTTAATCGAACACCAACTCAATTAAAAAAATTATGAAAATATC
* * *
33029 CATCCGTAATTAAAATAAATTGTATTATTTGAAAGTATTTTAGTATTTTCATTTTAAAAAAAACG
195 CATCCGTAATTAAAATAAACTATATTATTTGAAAGTATTTTAATATTTTCATTTTAAAAAAAACG
* ** **
33094 AATAAAAATATATATATTGTGAGATTTGAATTCATGTTC
260 AATAAAAATATATATATTGTGAGAGTTGAACACACATTC
* * ** * ** **
33133 ATTGGATTATTAAAACTTTAAATTTACTTCTAAACCAAAACTTCATTTTAACATATTTTATATTA
1 ATTAGATTAGTAAAACTTTAAATTTACCACTAAATCAAAGTTTCATTTTAACATATTTTATACAA
33198 TTTTATTTTAATACGCACAATTTATGATCTCCATAAATTGTATACTTATACTTACTATTAATAAA
66 TTTTATTTTAATACGCACAATTTATGATCTCCATAAATTGTATA-TT-TA--TACTATTAATAAA
* * * * * * * *
33263 -ATCTTTGATTGAGTT-AGTGTTATGAGTTAATTG-GCACCAACTCAATTAAGAAAATTATGAAA
127 GCTC-CTGATTGAATTGA-TGTCACGAGTTAATCGAACACCAACTCAATTAAAAAAATTATGAAA
* * * *
33325 ATATCCTTCTGTAATTAAAATAAACTATATTATTTGAGAA-TATTTTAATCTTTTTA-TTTAAAT
190 ATATCCATCCGTAATTAAAATAAACTATATTATTTGA-AAGTATTTTAATATTTTCATTTTAAA-
* * * * *
33388 AAAAATC-AATAAAAATATGTTTATTTTTTA-AGTTGAACACACATTG
253 AAAAA-CGAATAAAAATATATATA-TTGTGAGAGTTGAACACACATTC
* * *
33434 ATTAGATTAGTAAAACTTTAAATTTACCACTAAATCAAAGTTTCATTTTAATATGTTTTATACAT
1 ATTAGATTAGTAAAACTTTAAATTTACCACTAAATCAAAGTTTCATTTTAACATATTTTATACAA
* * *
33499 TTTTATTATAAAATGCACAAT
66 TTTTATTTTAATACGCACAAT
33520 ATCATTTTCA
Statistics
Matches: 317, Mismatches: 59, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
298 92 0.29
299 3 0.01
300 8 0.03
301 172 0.54
302 42 0.13
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (298 bp):
ATTAGATTAGTAAAACTTTAAATTTACCACTAAATCAAAGTTTCATTTTAACATATTTTATACAA
TTTTATTTTAATACGCACAATTTATGATCTCCATAAATTGTATATTTATACTATTAATAAAGCTC
CTGATTGAATTGATGTCACGAGTTAATCGAACACCAACTCAATTAAAAAAATTATGAAAATATCC
ATCCGTAATTAAAATAAACTATATTATTTGAAAGTATTTTAATATTTTCATTTTAAAAAAAACGA
ATAAAAATATATATATTGTGAGAGTTGAACACACATTC
Found at i:40601 original size:29 final size:29
Alignment explanation
Indices: 40569--40625 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
40559 GTCATGTCAT
*
40569 AGATACAATTAC-GAATGCAGACATGATAC
1 AGATACAATTACAG-ATGCAAACATGATAC
* *
40598 AGATATAGTTACAGATGCAAACATGATA
1 AGATACAATTACAGATGCAAACATGATA
40626 ACCCCTATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.23
Consensus pattern (29 bp):
AGATACAATTACAGATGCAAACATGATAC
Found at i:40810 original size:64 final size:64
Alignment explanation
Indices: 40709--40830 Score: 199
Period size: 64 Copynumber: 1.9 Consensus size: 64
40699 ATGACACATC
* * *
40709 GCAGTGTTTACAGTGTCACTGTCAGTTTAATTGTAATCTTGTAGTGTTTACAGTGTCACTTGTT
1 GCAGTGTTAACAGTGTCACTGTCAGTTCAATTGTAATCTTGCAGTGTTTACAGTGTCACTTGTT
* *
40773 GCAGTGTTAACAGTGTCATTGTCAGTTCAGTTGTAATCTTGCAGTGTTTACAGTGTCA
1 GCAGTGTTAACAGTGTCACTGTCAGTTCAATTGTAATCTTGCAGTGTTTACAGTGTCA
40831 TTACCGGTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (64 bp):
GCAGTGTTAACAGTGTCACTGTCAGTTCAATTGTAATCTTGCAGTGTTTACAGTGTCACTTGTT
Found at i:41349 original size:53 final size:53
Alignment explanation
Indices: 41269--41389 Score: 152
Period size: 53 Copynumber: 2.3 Consensus size: 53
41259 AAAACAATAT
* * ** *
41269 ACACACACCCATGTGTCAGCCAATGTGCCCCAGAACAATATGCACACACCTTA
1 ACACACGCCCATGTGTCAGCCAATGTGCCCCAAAACAATACACACACACCCTA
** * *
41322 ACACACGCCCATGTGTCAGCCCGTGTGCCTCAAAACAATACACACACACCCTG
1 ACACACGCCCATGTGTCAGCCAATGTGCCCCAAAACAATACACACACACCCTA
*
41375 ACACACGCCCGTGTG
1 ACACACGCCCATGTG
41390 CCTCCAAACA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.31, C:0.38, G:0.16, T:0.16
Consensus pattern (53 bp):
ACACACGCCCATGTGTCAGCCAATGTGCCCCAAAACAATACACACACACCCTA
Found at i:41367 original size:41 final size:42
Alignment explanation
Indices: 41340--41421 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 42
41330 CCATGTGTCA
41340 GCCCGTGTGCCTCAAAACA-ATACACACACACCCTGACACAC
1 GCCCGTGTGCCTCAAAACAGATACACACACACCCTGACACAC
* *
41381 GCCCGTGTGCCTCCAAACAGTTACACACACA-CCTGACACAC
1 GCCCGTGTGCCTCAAAACAGATACACACACACCCTGACACAC
41422 ATCTGTGTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 28 0.74
42 10 0.26
ACGTcount: A:0.32, C:0.41, G:0.13, T:0.13
Consensus pattern (42 bp):
GCCCGTGTGCCTCAAAACAGATACACACACACCCTGACACAC
Found at i:41430 original size:41 final size:41
Alignment explanation
Indices: 41341--41435 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
41331 CATGTGTCAG
* *
41341 CCCGTGTGCCTCAAAACAATACACACACACCCTGACACACG
1 CCCGTGTGCCTCCAAACAATACACACACACCCTGACACACA
*
41382 CCCGTGTGCCTCCAAACAGTTACACACACA-CCTGACACACA
1 CCCGTGTGCCTCCAAACA-ATACACACACACCCTGACACACA
* *
41423 TCTGTGTGCCTCC
1 CCCGTGTGCCTCC
41436 TATAACTCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 38 0.79
42 10 0.21
ACGTcount: A:0.28, C:0.41, G:0.14, T:0.17
Consensus pattern (41 bp):
CCCGTGTGCCTCCAAACAATACACACACACCCTGACACACA
Found at i:42563 original size:21 final size:21
Alignment explanation
Indices: 42537--42579 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
42527 TTAGGGATCC
* *
42537 TTAATTTTAATGG-TCAATGG
1 TTAAATTTAATGGTTAAATGG
42557 TTAAATTTAATGGTTAAATGG
1 TTAAATTTAATGGTTAAATGG
42578 TT
1 TT
42580 TTTTGATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (21 bp):
TTAAATTTAATGGTTAAATGG
Found at i:42996 original size:88 final size:88
Alignment explanation
Indices: 42839--43109 Score: 348
Period size: 89 Copynumber: 3.1 Consensus size: 88
42829 GTCAAAAGAC
* * * * * *
42839 CTTTTTGATGCA-TTTGACGGTTTAAGTACTCAATTGAGTGGAAAAAAATTAGCGGCTTAATTGC
1 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAAATAGGGGCTTAATTGC
**
42903 TTTTTTTGAAAAAGTTTGTGGGT
66 TTTTTTTGAAAAAGTTTAAGGGT
* * * *
42926 CTTTTTGATGCATTTTGAAAGTTCAAGCACCCAATTGAGTACAAAAAAAGACAGGGGCTTAATTG
1 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAA-ATAGGGGCTTAATTG
42991 CTTTTTTTGAAAAAGTTTAAGGGT
65 CTTTTTTTGAAAAAGTTTAAGGGT
* *
43015 CTTTTTGATACATTTTGGCAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGTAGGGGCTTAATT
1 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGC-AAAAAAAA-TAGGGGCTTAATT
* * *
43080 GCATTTTTTAAAAAAGTTTTAGGG-
64 GCTTTTTTTGAAAAAGTTTAAGGGT
43104 CTTTTT
1 CTTTTT
43110 ATACCCTTAA
Statistics
Matches: 159, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
87 12 0.08
88 29 0.18
89 78 0.49
90 40 0.25
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (88 bp):
CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAAATAGGGGCTTAATTGC
TTTTTTTGAAAAAGTTTAAGGGT
Found at i:46386 original size:12 final size:11
Alignment explanation
Indices: 46365--46456 Score: 67
Period size: 12 Copynumber: 7.9 Consensus size: 11
46355 ATAACATCCA
46365 AACAACCAAAAT
1 AACAA-CAAAAT
*
46377 AACAATCAAAAC
1 AACAA-CAAAAT
*
46389 AGCAACAAAAAT
1 AACAAC-AAAAT
46401 AACAACAAAAAT
1 AACAAC-AAAAT
* *
46413 AACAATAAAAAC
1 AACAA-CAAAAT
*
46425 AACACCAAAAT
1 AACAACAAAAT
* *
46436 AATAAAAAAAT
1 AACAACAAAAT
*
46447 AACACCAAAA
1 AACAACAAAA
46457 CAATAACCAA
Statistics
Matches: 62, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
11 20 0.32
12 42 0.68
ACGTcount: A:0.71, C:0.20, G:0.01, T:0.09
Consensus pattern (11 bp):
AACAACAAAAT
Found at i:46405 original size:36 final size:35
Alignment explanation
Indices: 46365--46459 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 35
46355 ATAACATCCA
* *
46365 AACAACCAAAATAACAATCAAAACAGCAACAAAAAT
1 AACAACAAAAATAACAATCAAAACAAC-ACAAAAAT
* *
46401 AACAACAAAAATAACAATAAAAACAACACCAAAAT
1 AACAACAAAAATAACAATCAAAACAACACAAAAAT
* *
46436 AATAA-AAAAATAAC-ACCAAAACAA
1 AACAACAAAAATAACAATCAAAACAA
46460 TAACCAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 8 0.15
34 9 0.17
35 11 0.21
36 24 0.46
ACGTcount: A:0.71, C:0.20, G:0.01, T:0.08
Consensus pattern (35 bp):
AACAACAAAAATAACAATCAAAACAACACAAAAAT
Found at i:46425 original size:21 final size:21
Alignment explanation
Indices: 46392--46456 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
46382 TCAAAACAGC
46392 AACAAAAATAACAACA-AAAAT
1 AACAAAAA-AACAACACAAAAT
46413 AACAATAAAAACAACACCAAAAT
1 AACAA-AAAAACAACA-CAAAAT
* *
46436 AATAAAAAAATAACACCAAAA
1 AACAAAAAAACAACA-CAAAA
46457 CAATAACCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.31
22 18 0.46
23 9 0.23
ACGTcount: A:0.74, C:0.17, G:0.00, T:0.09
Consensus pattern (21 bp):
AACAAAAAAACAACACAAAAT
Found at i:46450 original size:22 final size:22
Alignment explanation
Indices: 46419--46501 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
46409 AAATAACAAT
*
46419 AAAAACAACACCAAAATAATAA
1 AAAAACAACACCAAAACAATAA
*
46441 AAAAATAACACCAAAACAATAA
1 AAAAACAACACCAAAACAATAA
** * *
46463 CCAAA-AGCACCAAAACAGTAA
1 AAAAACAACACCAAAACAATAA
*
46484 AAACACAACACCAAAACA
1 AAAAACAACACCAAAACA
46502 GCACCAAAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.32
22 34 0.68
ACGTcount: A:0.67, C:0.24, G:0.02, T:0.06
Consensus pattern (22 bp):
AAAAACAACACCAAAACAATAA
Found at i:46515 original size:22 final size:22
Alignment explanation
Indices: 46442--46515 Score: 57
Period size: 22 Copynumber: 3.4 Consensus size: 22
46432 AAATAATAAA
* *
46442 AAAATAACACCAAAACAATAACC
1 AAAAGAACACCAAAAC-AGAACC
46465 AAAAG--CACCAAAACAGTAA--
1 AAAAGAACACCAAAACAG-AACC
* *
46484 AAACACAACACCAAAACAGCACC
1 AAA-AGAACACCAAAACAGAACC
46507 AAAAGAACA
1 AAAAGAACA
46516 ATATAATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
19 3 0.08
20 2 0.05
21 12 0.30
22 16 0.40
23 7 0.17
ACGTcount: A:0.64, C:0.27, G:0.05, T:0.04
Consensus pattern (22 bp):
AAAAGAACACCAAAACAGAACC
Found at i:47356 original size:57 final size:56
Alignment explanation
Indices: 47237--47357 Score: 145
Period size: 57 Copynumber: 2.1 Consensus size: 56
47227 ATTGTTATTA
* * ** *
47237 AATTTTAATAGGATTATTATTAAATGTAATTTAATAAAAAAATAAAAAATTTAATT
1 AATTTTAATAGAATTATTATTAAATATAATTTAATAAAAAAATAAAAAAAATAAAT
* *
47293 ATATTTTAATATAATTATTATTAAATATAATTTGATAAAAATAA-AAATAAAAATAAAT
1 A-ATTTTAATAGAATTATTATTAAATATAATTTAATAAAAA-AATAAA-AAAAATAAAT
47351 AATTTTA
1 AATTTTA
47358 TAACATTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
56 1 0.02
57 44 0.80
58 10 0.18
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (56 bp):
AATTTTAATAGAATTATTATTAAATATAATTTAATAAAAAAATAAAAAAAATAAAT
Found at i:47374 original size:68 final size:68
Alignment explanation
Indices: 47274--47405 Score: 187
Period size: 67 Copynumber: 1.9 Consensus size: 68
47264 AATTTAATAA
* * *
47274 AAAAATAAAAAATTTAATTATATTTTAATATAATTATTATT-AAATAT-AATTTGATAAAAATAA
1 AAAAATAAAAAATTTAATAACATTTTAATATAATTATTATTAAAATATGAA-TTAATAAAAATAA
47337 AAAT
65 AAAT
* *
47341 AAAAATAAATAATTTTATAACATTATTAATATAATTATTATTAAAATATGAATTAATAAAAATAA
1 AAAAATAAAAAATTTAATAACATT-TTAATATAATTATTATTAAAATATGAATTAATAAAAATAA
47406 TAGTATATAG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 20 0.35
68 17 0.30
69 18 0.32
70 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (68 bp):
AAAAATAAAAAATTTAATAACATTTTAATATAATTATTATTAAAATATGAATTAATAAAAATAAA
AAT
Found at i:50615 original size:30 final size:29
Alignment explanation
Indices: 50497--50831 Score: 141
Period size: 29 Copynumber: 11.4 Consensus size: 29
50487 ATTTTATTTA
* *
50497 AAAATTATATTTTGACCCGTAAAC--CTCT
1 AAAATTACATTTTAACCC-TAAACTTCTCT
* * *
50525 AAAATCACATTTTAACCCCCAAACCTTTTC-
1 AAAATTACATTTTAA-CCCTAAA-CTTCTCT
* * * ** * * *
50555 ATAATCATATTTTCTCCCCAAGCTTTTCT
1 AAAATTACATTTTAACCCTAAACTTCTCT
*
50584 AAAATTGCATTTTAACCCTTAAACTTCTCT
1 AAAATTACATTTTAACCC-TAAACTTCTCT
* * *
50614 AAAA-TATA-TTTGACTCCCAAACTTCT-T
1 AAAATTACATTTTAAC-CCTAAACTTCTCT
* * * * * *
50641 CAAAATTTCATTTTGACCCCAAAATTTTCA
1 -AAAATTACATTTTAACCCTAAACTTCTCT
* * * *
50671 AAAATTTCATTTTGACCCCTAAA-TTTTCC
1 AAAATTACATTTT-AACCCTAAACTTCTCT
* * *
50700 AAAATCACATTTTAACCCCTTAAATTTCTTT
1 AAAATTACATTTTAA-CCC-TAAACTTCTCT
* *
50731 AAAATTACATTTTGACCCTTAAA-TTTTCT
1 AAAATTACATTTTAACCC-TAAACTTCTCT
* * *
50760 CAAAATCACGTTTTAACCCTAAACCTTC-CA
1 -AAAATTACATTTTAACCCTAAA-CTTCTCT
* *
50790 AAAATCACATTTTAACTCTAAACTT-TCAT
1 AAAATTACATTTTAACCCTAAACTTCTC-T
*
50819 AAAATTACCTTTT
1 AAAATTACATTTT
50832 GCTTCCAAAA
Statistics
Matches: 235, Mismatches: 52, Indels: 39
0.72 0.16 0.12
Matches are distributed among these distances:
27 1 0.00
28 43 0.18
29 108 0.46
30 63 0.27
31 20 0.09
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTCTCT
Found at i:50755 original size:89 final size:90
Alignment explanation
Indices: 50636--50805 Score: 218
Period size: 89 Copynumber: 1.9 Consensus size: 90
50626 ACTCCCAAAC
* ** * **
50636 TTCTTCAAAATTTCATTTTGACCCCAAAATTTTC-AAAAATTTCATTTTGACCCCTAAATTTTCC
1 TTCTTCAAAATTACATTTTGACCCCAAAATTTTCTAAAAATCACATTTT-AACCCTAAACCTTCC
50700 -AAAATCACATTTTAACCCCTTAAAT
65 AAAAATCACATTTTAACCCCTTAAAT
* ** * *
50725 TTCTTTAAAATTACATTTTGACCCTTAAATTTTCTCAAAATCACGTTTTAACCCTAAACCTTCCA
1 TTCTTCAAAATTACATTTTGACCCCAAAATTTTCTAAAAATCACATTTTAACCCTAAACCTTCCA
50790 AAAATCACATTTTAAC
66 AAAATCACATTTTAAC
50806 TCTAAACTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
89 42 0.62
90 26 0.38
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (90 bp):
TTCTTCAAAATTACATTTTGACCCCAAAATTTTCTAAAAATCACATTTTAACCCTAAACCTTCCA
AAAATCACATTTTAACCCCTTAAAT
Found at i:50900 original size:12 final size:12
Alignment explanation
Indices: 50883--50909 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
50873 CATTTTTGAC
50883 CTTTTTTATTTT
1 CTTTTTTATTTT
50895 CTTTTTTATTTT
1 CTTTTTTATTTT
50907 CTT
1 CTT
50910 CGATATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (12 bp):
CTTTTTTATTTT
Found at i:61635 original size:15 final size:16
Alignment explanation
Indices: 61606--61635 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61596 AACAACACGA
61606 TGAAAAGTGAAATAAC
1 TGAAAAGTGAAATAAC
61622 TGAAAAGT-AAATAA
1 TGAAAAGTGAAATAA
61636 AAAAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (16 bp):
TGAAAAGTGAAATAAC
Found at i:71671 original size:76 final size:75
Alignment explanation
Indices: 71545--71714 Score: 223
Period size: 76 Copynumber: 2.3 Consensus size: 75
71535 ATGAAGCGGT
* * ** *
71545 CATCTTCCTGATGAAATACACAGAAGTAGACCAATTCAATAAAACAAAGCTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACACAGAAGTAGACCAAATCAATAAAACAAAGCTCAATACGAATGAAA
71610 CATCCAAACCC
66 C-TCCAAACCC
* * * * * *
71621 CATCTTTCTGATGAGATACAGAGAAGTAGACTAAATCAATGAAGCAAAGCTCAATACGAATGAGA
1 CATCTTCCTGATGAGATACACAGAAGTAGACCAAATCAATAAAACAAAGCTCAATACGAATGAAA
*
71686 CTTCAAACCC
66 CTCCAAACCC
71696 CATCTTCCTGATGAGATAC
1 CATCTTCCTGATGAGATAC
71715 GAAAAGTGTG
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 26 0.32
76 55 0.68
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (75 bp):
CATCTTCCTGATGAGATACACAGAAGTAGACCAAATCAATAAAACAAAGCTCAATACGAATGAAA
CTCCAAACCC
Found at i:71917 original size:283 final size:283
Alignment explanation
Indices: 71405--71928 Score: 777
Period size: 283 Copynumber: 1.9 Consensus size: 283
71395 TGTGAGTGGA
* **
71405 TCAAACCCCACTTCCTAATGAGATACAGAGAAGTGGGTCGAAGCAATAAATTGATCATCTTCCTG
1 TCAAACCCCACTTCCTAATGAGATACAGAAAAGTGGGTCGAAGCAATAAAGCGATCATCTTCCTG
*
71470 ACGAGATGCAGAGAAGTGAACCAAATCCGTCTTCTTAATGACATACAGAGAAGTGGATTAAAATA
66 ACGAGATACAGAGAAGTGAACCAAATCCGTCTTCTTAATGACATACAGAGAAGTGGATTAAAATA
*
71535 ATGAAGCGGTCATCTTCCTGATGAAATACACAGAAGTAGACCAATTCAATAAAACAAAGCTCAAT
131 ATGAAGCGGTCATCTTCCTGATGAAATACACAGAAGTAGACCAAATCAATAAAACAAAGCTCAAT
* * *
71600 GTGAGTGAAACATCCAAACCCCATCTTTCTGATGAGATACAGAGAAGTAGACTAAATCAATGAAG
196 ATGAATGAAACATCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTAGACTAAATCAATGAAG
71665 CAAAGCTCAATACGAATGAGACT
261 CAAAGCTCAATACGAATGAGACT
* *
71688 TCAAACCCCATCTTCCTGATGAGATAC-GAAAAGTGTGTCGAAGCAATAAAGCGATCATCTTCCT
1 TCAAACCCCA-CTTCCTAATGAGATACAGAAAAGTGGGTCGAAGCAATAAAGCGATCATCTTCCT
* * * *
71752 GATGAGATACAGAGAAGT-AGACCAAATCCGTCTTCTTGATGAGATACAGAGTAGTGGATT-AAA
65 GACGAGATACAGAGAAGTGA-ACCAAATCCGTCTTCTTAATGACATACAGAGAAGTGGATTAAAA
* * * * * * *
71815 TCGATGAAGCGGTTATCTTCCTGATGAGATACAGAGAAGTAGATCAAATCAATGAAGCAAAGCTC
129 T-AATGAAGCGGTCATCTTCCTGATGAAATACACAGAAGTAGACCAAATCAATAAAACAAAGCTC
* *
71880 AATATGAATGAGAC-TTCAAACCCCCATCTTCCTGATGAGATACAGAGAA
193 AATATGAATGAAACATCCAAA-CCCCATCTTCCTGATGAGATACAGAGAA
71929 ATGGGTCGAA
Statistics
Matches: 214, Mismatches: 23, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
282 10 0.05
283 189 0.88
284 15 0.07
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (283 bp):
TCAAACCCCACTTCCTAATGAGATACAGAAAAGTGGGTCGAAGCAATAAAGCGATCATCTTCCTG
ACGAGATACAGAGAAGTGAACCAAATCCGTCTTCTTAATGACATACAGAGAAGTGGATTAAAATA
ATGAAGCGGTCATCTTCCTGATGAAATACACAGAAGTAGACCAAATCAATAAAACAAAGCTCAAT
ATGAATGAAACATCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTAGACTAAATCAATGAAG
CAAAGCTCAATACGAATGAGACT
Found at i:72050 original size:209 final size:207
Alignment explanation
Indices: 71621--72066 Score: 650
Period size: 209 Copynumber: 2.1 Consensus size: 207
71611 ATCCAAACCC
*
71621 CATCTTTCTGATGAGATACAGAGAAGTAGACTAAATCAATGAAGCAAAGCTCAATACGAATGAGA
1 CATCTTCCTGATGAGATACAGAGAAGTAGACTAAATCAATGAAGCAAAGCTCAATACGAATGAGA
*
71686 CTTCAAACCCCATCTTCCTGATGAGATACGAAAAGTGTGTCGAAGCAATAAAGCGATCATCTTCC
66 CTTCAAACCCCATCTTCCTGATGAGATACGAAAAGTGGGTCGAAGCAATAAAGCGATCATCTTCC
* * * * * * *
71751 TGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCTTGATGAGATACAGAGTAGTGGATTAAAT
131 TGATGAGATACAGAAAAGTACACCAAATCCATCTTCCTGATGAGATACAAAGAAGTGGATTAAAA
*
71816 CGATGAAGCGGT
196 CAATGAAGCGGT
* *
71828 TATCTTCCTGATGAGATACAGAGAAGTAGA-TCAAATCAATGAAGCAAAGCTCAATATGAATGAG
1 CATCTTCCTGATGAGATACAGAGAAGTAGACT-AAATCAATGAAGCAAAGCTCAATACGAATGAG
* *
71892 ACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAA-TGGGTCGAAGTAATAAAGCGGTCATC
65 ACTTCAAA-CCCCATCTTCCTGATGAGATAC-GA-AAAGTGGGTCGAAGCAATAAAGCGATCATC
*
71956 TTCCTGATGCA-ATAC-GAAAAAGTACACCAAATCCATCTTCCTGATTAGATACAAAGAAGTGGA
127 TTCCTGATG-AGATACAG-AAAAGTACACCAAATCCATCTTCCTGATGAGATACAAAGAAGTGGA
*
72019 -TAAACACAATGAAGTGGT
190 TTAAA-ACAATGAAGCGGT
72037 CATCTTCCTGATGAGATACAGAGAAGTAGA
1 CATCTTCCTGATGAGATACAGAGAAGTAGA
72067 ACAAGAGATG
Statistics
Matches: 215, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
206 1 0.00
207 67 0.31
208 27 0.13
209 116 0.54
210 4 0.02
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (207 bp):
CATCTTCCTGATGAGATACAGAGAAGTAGACTAAATCAATGAAGCAAAGCTCAATACGAATGAGA
CTTCAAACCCCATCTTCCTGATGAGATACGAAAAGTGGGTCGAAGCAATAAAGCGATCATCTTCC
TGATGAGATACAGAAAAGTACACCAAATCCATCTTCCTGATGAGATACAAAGAAGTGGATTAAAA
CAATGAAGCGGT
Found at i:73633 original size:30 final size:28
Alignment explanation
Indices: 73580--73812 Score: 110
Period size: 30 Copynumber: 7.9 Consensus size: 28
73570 TTAAAAACTA
*
73580 TATTTTACCCCAAACTTTTCCAAAATTG
1 TATTTTACCCCAAACTTCTCCAAAATTG
* *
73608 TATTTTGACTCCCACACTTCTCCAAAATTA
1 TATTTT-AC-CCCAAACTTCTCCAAAATTG
* * * * *
73638 CATTTAACCCTTAAACTTTTCTAAAATTG
1 TATTTTACCC-CAAACTTCTCCAAAATTG
* * * *
73667 CATTTTGGCCCTTAAACTTCTCTAAAATTG
1 TATTTT-ACCC-CAAACTTCTCCAAAATTG
* * * *
73697 TATTTTAACCCTAAACTTTTTCAAAATTA
1 TATTTT-ACCCCAAACTTCTCCAAAATTG
* * * *
73726 CATTTTA-ACAATTAAGCTTCTCTAAAATTG
1 TATTTTACCCCA--AA-CTTCTCCAAAATTG
* * * *
73756 CATTTTGACACCTAAACTTTTCCAAAATTA
1 TATTTT-AC-CCCAAACTTCTCCAAAATTG
*
73786 CATTTTGACCCCCAAACTT-TCCAAAAT
1 TATTTT-A-CCCCAAACTTCTCCAAAAT
73813 CACATTTTAA
Statistics
Matches: 161, Mismatches: 33, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
27 2 0.01
28 9 0.06
29 51 0.32
30 93 0.58
31 4 0.02
33 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (28 bp):
TATTTTACCCCAAACTTCTCCAAAATTG
Found at i:73686 original size:59 final size:59
Alignment explanation
Indices: 73591--73940 Score: 245
Period size: 59 Copynumber: 5.9 Consensus size: 59
73581 ATTTTACCCC
* ** * * *
73591 AAACTTTTCCAAAATTGTATTTTGACTCCCACACTTCTCCAAAATTACA-TTTAACCCTT
1 AAACTTTTCTAAAATTACATTTTGAC-CCTAAACTTCTCTAAAATTACATTTTAACCCTT
* * **
73650 AAACTTTTCTAAAATTGCATTTTGGCCCTTAAACTTCTCTAAAATTGTATTTTAACCC-T
1 AAACTTTTCTAAAATTACATTTTGACCC-TAAACTTCTCTAAAATTACATTTTAACCCTT
* ** * * *
73709 AAACTTTT-TCAAAATTACATTTTAACAATTAAGCTTCTCTAAAATTGCATTTTGACACC-T
1 AAACTTTTCT-AAAATTACATTTTGAC-CCTAAACTTCTCTAAAATTACATTTTAAC-CCTT
* * * *
73769 AAACTTTTCCAAAATTACATTTTGACCCCCAAACTT-TCCAAAATCACATTTTAACCCTT
1 AAACTTTTCTAAAATTACATTTTGA-CCCTAAACTTCTCTAAAATTACATTTTAACCCTT
* * * *
73828 TAATTTTTCTTAAATT-CATGTTTTAGA-CCTAAAGCTTC-CTAAAATCACATTTTAA-CCTT
1 AAACTTTTCTAAAATTACA--TTTT-GACCCTAAA-CTTCTCTAAAATTACATTTTAACCCTT
* * ** *
73887 AAAC-TTTCATAAAATTACCTTTAGACCCCCGAA-TTCTTCCAAAATTACATTTTA
1 AAACTTTTC-TAAAATTACATTTTGA-CCCTAAACTTC-TCTAAAATTACATTTTA
73941 GCATCAAATT
Statistics
Matches: 231, Mismatches: 41, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
57 5 0.02
58 14 0.06
59 147 0.64
60 62 0.27
61 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (59 bp):
AAACTTTTCTAAAATTACATTTTGACCCTAAACTTCTCTAAAATTACATTTTAACCCTT
Found at i:73733 original size:89 final size:89
Alignment explanation
Indices: 73591--73860 Score: 287
Period size: 89 Copynumber: 3.0 Consensus size: 89
73581 ATTTTACCCC
* * *
73591 AAACTTTTCCAAAATTGTATTTTGACTCCCACACTTCTCCAAAATTACA-TTTAACCCTTAAACT
1 AAACTTTTCCAAAATTGTATTTTAAC-CCCAAACTTTTCCAAAATTACATTTTAACCCTTAAACT
*
73655 TTTCTAAAATTGCATTTTGGC-CCTT
65 TTTCTAAAATTGCATTTTGACACC-T
* * * * ** *
73680 AAACTTCTCTAAAATTGTATTTTAACCCTAAACTTTTTCAAAATTACATTTTAACAATTAAGCTT
1 AAACTTTTCCAAAATTGTATTTTAACCCCAAACTTTTCCAAAATTACATTTTAACCCTTAAACTT
*
73745 CTCTAAAATTGCATTTTGACACCT
66 TTCTAAAATTGCATTTTGACACCT
** * * * *
73769 AAACTTTTCCAAAATTACATTTTGACCCCCAAAC-TTTCCAAAATCACATTTTAACCCTTTAATT
1 AAACTTTTCCAAAATTGTATTTT-AACCCCAAACTTTTCCAAAATTACATTTTAACCCTTAAACT
* * *
73833 TTTCTTAAATT-CATGTTTTAGACCT
65 TTTCTAAAATTGCAT-TTTGACACCT
73858 AAA
1 AAA
73861 GCTTCCTAAA
Statistics
Matches: 148, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
88 21 0.14
89 117 0.79
90 10 0.07
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (89 bp):
AAACTTTTCCAAAATTGTATTTTAACCCCAAACTTTTCCAAAATTACATTTTAACCCTTAAACTT
TTCTAAAATTGCATTTTGACACCT
Found at i:77342 original size:28 final size:28
Alignment explanation
Indices: 77311--77392 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
77301 GTTCTTTTCT
*
77311 AGAGATAGCCACAAA-GACGTTCTTTCAC
1 AGAGATAGCCACAAATG-CGTTCTTTAAC
*
77339 AGAGATCA-CCACAAATGCTTTCTTTAAC
1 AGAGAT-AGCCACAAATGCGTTCTTTAAC
*
77367 AGAGATCGCCACAAATGC-TTCTTTAA
1 AGAGATAGCCACAAATGCGTTCTTTAA
77393 AAAAGATCAC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 8 0.17
28 38 0.79
29 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (28 bp):
AGAGATAGCCACAAATGCGTTCTTTAAC
Found at i:77418 original size:55 final size:55
Alignment explanation
Indices: 77313--77465 Score: 191
Period size: 55 Copynumber: 2.8 Consensus size: 55
77303 TCTTTTCTAG
* * * * * * * * *
77313 AGATAGCCACAAAGACGTTCTTTCACAGAGATCACCACAAATGCTTTCTTTAACAG
1 AGATCGCCACAAAGGCTTTCTTTAAAAAAGATCACCACAAAGGCTATCTTTAA-AA
*
77369 AGATCGCCACAAATGC-TTCTTTAAAAAAGATCACCACAAAGGCTATCTTTAAAA
1 AGATCGCCACAAAGGCTTTCTTTAAAAAAGATCACCACAAAGGCTATCTTTAAAA
*
77423 AGATCGTCACAAAGGCTTTCTTTAAAAAAGATCACCACAAAGG
1 AGATCGCCACAAAGGCTTTCTTTAAAAAAGATCACCACAAAGG
77466 ATTCTTCACA
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
54 15 0.18
55 57 0.67
56 13 0.15
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.24
Consensus pattern (55 bp):
AGATCGCCACAAAGGCTTTCTTTAAAAAAGATCACCACAAAGGCTATCTTTAAAA
Found at i:77450 original size:28 final size:28
Alignment explanation
Indices: 77341--77465 Score: 164
Period size: 27 Copynumber: 4.5 Consensus size: 28
77331 TCTTTCACAG
* * *
77341 AGATCACCACAAATGCTTTCTTTAACAG
1 AGATCACCACAAAGGCTTTCTTTAAAAA
* *
77369 AGATCGCCACAAATGC-TTCTTTAAAAA
1 AGATCACCACAAAGGCTTTCTTTAAAAA
*
77396 AGATCACCACAAAGGCTATCTTT-AAAA
1 AGATCACCACAAAGGCTTTCTTTAAAAA
**
77423 AGATCGTCACAAAGGCTTTCTTTAAAAA
1 AGATCACCACAAAGGCTTTCTTTAAAAA
77451 AGATCACCACAAAGG
1 AGATCACCACAAAGG
77466 ATTCTTCACA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 47 0.56
28 37 0.44
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (28 bp):
AGATCACCACAAAGGCTTTCTTTAAAAA
Done.