Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014155.1 Corchorus capsularis cultivar CVL-1 contig14176, 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: 58466
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3548 original size:28 final size:28
Alignment explanation
Indices: 3516--3588 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
3506 GGGTCATCCA
3516 GGGGCATTTTGGTCATTTTCACATCTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
** *
3544 GGGGCATTTTGGTCATTTTTGCATTTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
*
3572 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
3589 CTGAATCTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTCACATCTAG
Found at i:7364 original size:55 final size:55
Alignment explanation
Indices: 7303--7626 Score: 504
Period size: 55 Copynumber: 5.9 Consensus size: 55
7293 ATCAGTAAAG
* * * *
7303 AGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
7358 AGTAATAGTAATCAGTAAGTCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* *
7413 AGTAGTAGTAATCAGTAAGTCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* * *
7468 AGTAGTAGTAATCAGTAAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
**
7523 AGTAATAGTAATCAGTAAGTCAGTAATTAAGTAAAAAGAGACCAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* * * *
7578 AGTAGTAGTACTCAGTAAGCCAGTAATTAAGTAAAAAGAGAGTAATCAG
1 AGTAATAGTAATCAGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAG
7627 TAATCAGGTG
Statistics
Matches: 250, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 250 1.00
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.24
Consensus pattern (55 bp):
AGTAATAGTAATCAGTAAGTCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
Found at i:7415 original size:26 final size:26
Alignment explanation
Indices: 7386--7471 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
7376 GTCAGTAATT
7386 AAGTAAAAGGAGATTAATCAGAGTCA
1 AAGTAAAAGGAGATTAATCAGAGTCA
** * * *
7412 AAGTAGTAGTA-ATCAGTAAGTCAGTAAT-T
1 AAGTAAAAGGAGAT---TAA-TCAG-AGTCA
7441 AAGTAAAAGGAGATTAATCAGAGTCA
1 AAGTAAAAGGAGATTAATCAGAGTCA
7467 AAGTA
1 AAGTA
7472 GTAGTAATCA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 4 0.09
26 17 0.40
27 3 0.07
28 3 0.07
29 12 0.28
30 4 0.09
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.23
Consensus pattern (26 bp):
AAGTAAAAGGAGATTAATCAGAGTCA
Found at i:7498 original size:165 final size:165
Alignment explanation
Indices: 7303--7626 Score: 558
Period size: 165 Copynumber: 2.0 Consensus size: 165
7293 ATCAGTAAAG
*
7303 AGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAATAGTA
1 AGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTA
* ** *
7368 ATCAGTAAGTCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGTAAGT
66 ATCAGTAAGTCAGTAATTAAGTAAAAAGAGACCAATCAGAGTCAAAGTAGTAGTAATCAGTAAGC
* *
7433 CAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAA
131 CAGTAATTAAGTAAAAAGAGAGTAATCAGAGTCAA
* *
7468 AGTAGTAGTAATCAGTAAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTA
1 AGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTA
*
7533 ATCAGTAAGTCAGTAATTAAGTAAAAAGAGACCAATCAGAGTCAAAGTAGTAGTACTCAGTAAGC
66 ATCAGTAAGTCAGTAATTAAGTAAAAAGAGACCAATCAGAGTCAAAGTAGTAGTAATCAGTAAGC
7598 CAGTAATTAAGTAAAAAGAGAGTAATCAG
131 CAGTAATTAAGTAAAAAGAGAGTAATCAG
7627 TAATCAGGTG
Statistics
Matches: 149, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
165 149 1.00
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.24
Consensus pattern (165 bp):
AGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTA
ATCAGTAAGTCAGTAATTAAGTAAAAAGAGACCAATCAGAGTCAAAGTAGTAGTAATCAGTAAGC
CAGTAATTAAGTAAAAAGAGAGTAATCAGAGTCAA
Found at i:7627 original size:26 final size:26
Alignment explanation
Indices: 7598--7655 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
7588 CTCAGTAAGC
* *
7598 CAGTAATTAAGTAAAAAGAGAGTAAT
1 CAGTAATCAAGTAAAAACAGAGTAAT
* * *
7624 CAGTAATCAGGTGAAAACATAGTAAT
1 CAGTAATCAAGTAAAAACAGAGTAAT
7650 CAGTAA
1 CAGTAA
7656 ATCGATAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (26 bp):
CAGTAATCAAGTAAAAACAGAGTAAT
Found at i:7910 original size:22 final size:22
Alignment explanation
Indices: 7853--8136 Score: 229
Period size: 21 Copynumber: 13.4 Consensus size: 22
7843 AATAGCATGC
*
7853 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
* * *
7875 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAGAGTAAAAAGGT
*
7895 AATTAGTAAAGAGTAAAATA-GT
1 AATCAGTAAAGAGTAAAA-AGGT
* *
7917 AATCAGTAAAAAGTAACAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
7939 AATC--T-AAGAGTAAAATA-GT
1 AATCAGTAAAGAGTAAAA-AGGT
* * *
7958 AGTCAGTAAAAAGTAAATA-GT
1 AATCAGTAAAGAGTAAAAAGGT
*
7979 AATCAGT-AAGAGTAAAAAAGT
1 AATCAGTAAAGAGTAAAAAGGT
* *
8000 AATAAGT-AAGAAGT-AAAAGGA
1 AATCAGTAAAG-AGTAAAAAGGT
*
8021 AATTAGT-AAGAGTAAAAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
* *
8042 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAGAGTAAAAAGGT
*
8064 AATCAG-CAAGAAGTAAAAAGGT
1 AATCAGTAAAG-AGTAAAAAGGT
* * *
8086 AATCAGTAAAAAG-CAAAAGGC
1 AATCAGTAAAGAGTAAAAAGGT
* *
8107 AATCAGTAAAAAGTAAAGA-GT
1 AATCAGTAAAGAGTAAAAAGGT
8128 AATCAGTAA
1 AATCAGTAA
8137 GAGAAGAATA
Statistics
Matches: 210, Mismatches: 37, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
19 13 0.06
20 26 0.12
21 86 0.41
22 83 0.40
23 2 0.01
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAAAGGT
Found at i:7977 original size:21 final size:21
Alignment explanation
Indices: 7853--8136 Score: 213
Period size: 22 Copynumber: 13.4 Consensus size: 21
7843 AATAGCATGC
7853 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAA-GT
* ** *
7875 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAAAGTAAAA-AGT
* *
7895 AATTAGTAAAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAA-AGT
*
7917 AATCAGTAAAAAGTAACAAGGT
1 AATCAGTAAAAAGTAA-AAAGT
*
7939 AATC--T-AAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAA-AGT
* *
7958 AGTCAGTAAAAAGTAAATAGT
1 AATCAGTAAAAAGTAAAAAGT
*
7979 AATCAGT-AAGAGTAAAAAAGT
1 AATCAGTAAAAAGT-AAAAAGT
* * * *
8000 AATAAGTAAGAAGTAAAAGGA
1 AATCAGTAAAAAGTAAAAAGT
* *
8021 AATTAGT-AAGAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAA-GT
* *
8042 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAAAGTAAAAAG-T
* *
8064 AATCAGCAAGAAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAA-GT
* * *
8086 AATCAGTAAAAAGCAAAAGGC
1 AATCAGTAAAAAGTAAAAAGT
*
8107 AATCAGTAAAAAGTAAAGAGT
1 AATCAGTAAAAAGTAAAAAGT
8128 AATCAGTAA
1 AATCAGTAA
8137 GAGAAGAATA
Statistics
Matches: 204, Mismatches: 44, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
18 2 0.01
19 12 0.06
20 25 0.12
21 74 0.36
22 88 0.43
23 3 0.01
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (21 bp):
AATCAGTAAAAAGTAAAAAGT
Found at i:7979 original size:14 final size:13
Alignment explanation
Indices: 7947--8039 Score: 51
Period size: 14 Copynumber: 6.7 Consensus size: 13
7937 GTAATCTAAG
*
7947 AGTAAAATAGTAGT
1 AGTAAAA-AGTAAT
7961 CAGTAAAAAGTAAAT
1 -AGTAAAAAGT-AAT
** *
7976 AGTAATCAGTAAG
1 AGTAAAAAGTAAT
7989 AGTAAAAAAGTAAT
1 AGT-AAAAAGTAAT
* *
8003 AAGTAAGAAGTAAA
1 -AGTAAAAAGTAAT
* * *
8017 AGGAAATTAGTAAG
1 AGTAAA-AAGTAAT
8031 AGTAAAAAG
1 AGTAAAAAG
8040 GTGATCAGTA
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
13 11 0.19
14 36 0.61
15 12 0.20
ACGTcount: A:0.57, C:0.02, G:0.20, T:0.20
Consensus pattern (13 bp):
AGTAAAAAGTAAT
Found at i:8189 original size:35 final size:35
Alignment explanation
Indices: 8150--8226 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
8140 AAGAATAGTG
* *
8150 AAGAGTAATCAGCAAAGTAAAATGGTAAAAAGTAA
1 AAGAGTAATCAGCAAAGAAAAAGGGTAAAAAGTAA
* *
8185 AAGAGTAATCAGTAAAGAAAAAGGGTAAAGAGTAA
1 AAGAGTAATCAGCAAAGAAAAAGGGTAAAAAGTAA
8220 AA-AGTAA
1 AAGAGTAA
8227 AGAGAAGAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
34 5 0.13
35 33 0.87
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.16
Consensus pattern (35 bp):
AAGAGTAATCAGCAAAGAAAAAGGGTAAAAAGTAA
Found at i:8192 original size:15 final size:15
Alignment explanation
Indices: 8163--8227 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
8153 AGTAATCAGC
8163 AAAGTAAAATG-GTAA
1 AAAGTAAAA-GAGTAA
8178 AAAGTAAAAGAGTAA
1 AAAGTAAAAGAGTAA
**
8193 TCAGT-AAAGA--AA
1 AAAGTAAAAGAGTAA
*
8205 AAGGGT-AAAGAGTAA
1 AA-AGTAAAAGAGTAA
8220 AAAGTAAA
1 AAAGTAAA
8228 GAGAAGAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
12 2 0.05
13 7 0.18
14 8 0.21
15 22 0.56
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.15
Consensus pattern (15 bp):
AAAGTAAAAGAGTAA
Found at i:8206 original size:27 final size:27
Alignment explanation
Indices: 8176--8238 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
8166 GTAAAATGGT
**
8176 AAAAAGTAAAAGAGTAATCAGTAAAGA
1 AAAAAGTAAAAGAGTAAAAAGTAAAGA
*
8203 AAAAGGGT-AAAGAGTAAAAAGTAAAGA
1 AAAA-AGTAAAAGAGTAAAAAGTAAAGA
* *
8230 GAAGAGTAA
1 AAAAAGTAA
8239 TCAGTAAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
26 2 0.07
27 24 0.86
28 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.24, T:0.13
Consensus pattern (27 bp):
AAAAAGTAAAAGAGTAAAAAGTAAAGA
Found at i:8236 original size:19 final size:19
Alignment explanation
Indices: 8212--8248 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8202 AAAAAGGGTA
8212 AAGAGTAAAAAGTAAAGAG
1 AAGAGTAAAAAGTAAAGAG
**
8231 AAGAGTAATCAGTAAAGA
1 AAGAGTAAAAAGTAAAGA
8249 AAAAAATGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.24, T:0.14
Consensus pattern (19 bp):
AAGAGTAAAAAGTAAAGAG
Found at i:8261 original size:41 final size:40
Alignment explanation
Indices: 8149--8309 Score: 116
Period size: 48 Copynumber: 3.8 Consensus size: 40
8139 GAAGAATAGT
* *
8149 GAAGAGTAATCAGCAAAG--TAAAATGGTAAAAAGT-A-A
1 GAAGAGTAATCAGTAAAGAAAAAAATGGTAAAAAGTAAGA
*
8185 -AAGAGTAATCAGTAAAGAAAAAGGGTAAAGAGTAAAAAGTAAAGA
1 GAAGAGTAATCAGTAAAGAAAAA----AATG-GTAAAAAGT-AAGA
*
8230 GAAGAGTAATCAGTAAAGAAAAAAATGGTAAAGGGTAAATAGTAGA
1 GAAGAGTAATCAGTAAAGAAAAAAATGGTAAA----AAGTA--AGA
*
8276 GTAAAGAGTAATCGGTAAAGAAAAAAATGGTAAA
1 G--AAGAGTAATCAGTAAAGAAAAAAATGGTAAA
8310 GAGTGAAGGG
Statistics
Matches: 100, Mismatches: 6, Indels: 26
0.76 0.05 0.20
Matches are distributed among these distances:
35 16 0.16
37 2 0.02
41 8 0.08
42 12 0.12
44 2 0.02
45 4 0.04
46 26 0.26
48 30 0.30
ACGTcount: A:0.57, C:0.03, G:0.24, T:0.16
Consensus pattern (40 bp):
GAAGAGTAATCAGTAAAGAAAAAAATGGTAAAAAGTAAGA
Found at i:8283 original size:48 final size:47
Alignment explanation
Indices: 8184--8313 Score: 183
Period size: 48 Copynumber: 2.8 Consensus size: 47
8174 GTAAAAAGTA
*
8184 AAAGAGTAATCAGTAAAG--AAAAAGGGTAAAGAGTAAAAAGTAAAG
1 AAAGAGTAATCAGTAAAGAAAAAAATGGTAAAGAGTAAAAAGTAAAG
* * *
8229 AGAAGAGTAATCAGTAAAGAAAAAAATGGTAAAGGGTAAATAGTAGAG
1 A-AAGAGTAATCAGTAAAGAAAAAAATGGTAAAGAGTAAAAAGTAAAG
*
8277 TAAAGAGTAATCGGTAAAGAAAAAAATGGTAAAGAGT
1 -AAAGAGTAATCAGTAAAGAAAAAAATGGTAAAGAGT
8314 GAAGGGAAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
45 1 0.01
46 17 0.23
48 56 0.75
49 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.25, T:0.16
Consensus pattern (47 bp):
AAAGAGTAATCAGTAAAGAAAAAAATGGTAAAGAGTAAAAAGTAAAG
Found at i:8330 original size:36 final size:36
Alignment explanation
Indices: 8273--8386 Score: 119
Period size: 36 Copynumber: 3.2 Consensus size: 36
8263 GGTAAATAGT
* *
8273 AGAGTAAAGAGTAAT-CGGTAAAGAAAAAAATGGTAA
1 AGAGTAAAGAGGAATCCAGTAAAG-AAAAAATGGTAA
* * *
8309 AGAGTGAAG-GGAAGT-CAGTAAAG-AAGAATGGTGA
1 AGAGTAAAGAGGAA-TCCAGTAAAGAAAAAATGGTAA
* *
8343 AGAGTAAAGAGTAATCCAGTGAAGAAAAAATGGTAA
1 AGAGTAAAGAGGAATCCAGTAAAGAAAAAATGGTAA
8379 AGAGTAAA
1 AGAGTAAA
8387 ATATTAATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
34 18 0.28
35 13 0.20
36 33 0.52
ACGTcount: A:0.52, C:0.04, G:0.29, T:0.16
Consensus pattern (36 bp):
AGAGTAAAGAGGAATCCAGTAAAGAAAAAATGGTAA
Found at i:9876 original size:2 final size:2
Alignment explanation
Indices: 9871--9919 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
9861 TATACATAAA
*
9871 AT AT AT AT ACT AT GT AT AT AT AT AT AT AT AT AT AT AT AT -T A-
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9912 AT AT AT AT
1 AT AT AT AT
9920 GCTTTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10017 original size:20 final size:18
Alignment explanation
Indices: 9992--10036 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
9982 ACACATGTTT
9992 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
10012 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
10030 TACTAAT
1 TACTAAT
10037 TTTGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:12594 original size:59 final size:58
Alignment explanation
Indices: 12515--12628 Score: 210
Period size: 59 Copynumber: 1.9 Consensus size: 58
12505 TGGTTTTAAA
12515 GAAAAAGCTCTTCTCTTACTGAATTCTAATTTTGGGATTTTCTTTGTTTTATGCATCCG
1 GAAAAAGCTCTTCTCTTACTGAATTCTAATTTT-GGATTTTCTTTGTTTTATGCATCCG
*
12574 GAAAAAGCTCTTCTCTTACTGAATTCTAATTTTTGATTTTCTTTGTTTTATGCAT
1 GAAAAAGCTCTTCTCTTACTGAATTCTAATTTTGGATTTTCTTTGTTTTATGCAT
12629 TGGGTTGATT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
58 21 0.39
59 33 0.61
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (58 bp):
GAAAAAGCTCTTCTCTTACTGAATTCTAATTTTGGATTTTCTTTGTTTTATGCATCCG
Found at i:15950 original size:26 final size:25
Alignment explanation
Indices: 15906--15954 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
15896 ATGATTTAGG
* *
15906 GGTTACTAACGCCCTTTTTCTTTTGA
1 GGTTACTAACACCCATTTT-TTTTGA
*
15932 GGTTACTAACACTCATTTTTTTT
1 GGTTACTAACACCCATTTTTTTT
15955 CAAAGAGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.49
Consensus pattern (25 bp):
GGTTACTAACACCCATTTTTTTTGA
Found at i:33191 original size:25 final size:25
Alignment explanation
Indices: 33163--33214 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
33153 CTTTTCCTTG
*
33163 TACAAAATCATTTATGTAAGTAAAT
1 TACAAAATCATTTATGTAAGAAAAT
33188 TACAAAATCATTTATGTAAGAAAAT
1 TACAAAATCATTTATGTAAGAAAAT
33213 TA
1 TA
33215 TCTCATATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (25 bp):
TACAAAATCATTTATGTAAGAAAAT
Found at i:34128 original size:2 final size:2
Alignment explanation
Indices: 34121--34150 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34111 TGCACAATCA
34121 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34151 GAAAATGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37352 original size:1 final size:1
Alignment explanation
Indices: 37346--37377 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
37336 TGCAAAACAC
37346 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
37378 GCTGAGTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41832 original size:14 final size:14
Alignment explanation
Indices: 41813--41839 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41803 GGAAGTTTTT
41813 GTATGCTCTGCTTC
1 GTATGCTCTGCTTC
41827 GTATGCTCTGCTT
1 GTATGCTCTGCTT
41840 TGCAAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.22, T:0.44
Consensus pattern (14 bp):
GTATGCTCTGCTTC
Found at i:44665 original size:53 final size:52
Alignment explanation
Indices: 44582--44682 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 52
44572 TAATTTGAGA
* *
44582 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAAGACATCTTCATTAAGG
1 TTCCCTTTAATTATTGATATGTTAAATGGGTTTTTAAAACATC-TCATTAAGG
44635 TTCCCTTTAATTATTGATATGTTAAATGGGTTTTTAAAACATCTCATT
1 TTCCCTTTAATTATTGATATGTTAAATGGGTTTTTAAAACATCTCATT
44683 TTGGTAACCC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 5 0.11
53 41 0.89
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.47
Consensus pattern (52 bp):
TTCCCTTTAATTATTGATATGTTAAATGGGTTTTTAAAACATCTCATTAAGG
Found at i:44891 original size:6 final size:6
Alignment explanation
Indices: 44880--44941 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
44870 CCCGAACTCG
**
44880 CCCGAA CCCGAA CCCGAAATA CCCGAA CCC-AA GAC-AA CCCGAA CCCGAA
1 CCCGAA CCCGAA CCCG--A-A CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA
44929 CCC--A CCCGAA CCC
1 CCCGAA CCCGAA CCC
44942 AGCCCGAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
4 4 0.09
5 6 0.13
6 29 0.63
7 1 0.02
8 1 0.02
9 5 0.11
ACGTcount: A:0.35, C:0.50, G:0.13, T:0.02
Consensus pattern (6 bp):
CCCGAA
Found at i:44935 original size:16 final size:15
Alignment explanation
Indices: 44884--44941 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
44874 AACTCGCCCG
44884 AACCCGAACCCGAA-
1 AACCCGAACCCGAAC
*
44898 ATACCCGAACCCAAGAC
1 A-ACCCGAACCCGA-AC
44915 AACCCGAACCCGAACC
1 AACCCGAACCCGAA-C
*
44931 CACCCGAACCC
1 AACCCGAACCC
44942 AGCCCGAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.03
15 12 0.32
16 23 0.62
17 1 0.03
ACGTcount: A:0.38, C:0.48, G:0.12, T:0.02
Consensus pattern (15 bp):
AACCCGAACCCGAAC
Found at i:45717 original size:11 final size:11
Alignment explanation
Indices: 45697--45740 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
45687 TCGAAAATGA
45697 ACCCGAGCCCG
1 ACCCGAGCCCG
*
45708 ACCCGGGCCCG
1 ACCCGAGCCCG
*
45719 AGCCCGAACCCG
1 A-CCCGAGCCCG
*
45731 ATCCGAGCCC
1 ACCCGAGCCC
45741 AAACCCGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.18, C:0.52, G:0.27, T:0.02
Consensus pattern (11 bp):
ACCCGAGCCCG
Found at i:45730 original size:23 final size:23
Alignment explanation
Indices: 45696--45749 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
45686 ATCGAAAATG
* * *
45696 AACCCGAGCCCGACCCGGGCCCG
1 AACCCGAACCCGACCCGAGCCCA
* *
45719 AGCCCGAACCCGATCCGAGCCCA
1 AACCCGAACCCGACCCGAGCCCA
45742 AACCCGAA
1 AACCCGAA
45750 AATACCCGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.48, G:0.24, T:0.02
Consensus pattern (23 bp):
AACCCGAACCCGACCCGAGCCCA
Found at i:45736 original size:17 final size:17
Alignment explanation
Indices: 45716--45748 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45706 CGACCCGGGC
*
45716 CCGAGCCCGAACCCGAT
1 CCGAGCCCAAACCCGAT
45733 CCGAGCCCAAACCCGA
1 CCGAGCCCAAACCCGA
45749 AAATACCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.48, G:0.21, T:0.03
Consensus pattern (17 bp):
CCGAGCCCAAACCCGAT
Found at i:45763 original size:16 final size:16
Alignment explanation
Indices: 45742--45843 Score: 172
Period size: 16 Copynumber: 6.5 Consensus size: 16
45732 TCCGAGCCCA
45742 AACCCGAAAATACCCG
1 AACCCGAAAATACCCG
45758 AACCCGAAAATACCCG
1 AACCCGAAAATACCCG
45774 AACCCG-AAATACCCG
1 AACCCGAAAATACCCG
45789 AACCCGAAAATACCCG
1 AACCCGAAAATACCCG
*
45805 AACCCGAAAATACACG
1 AACCCGAAAATACCCG
*
45821 AACCCG-AAGTACCCG
1 AACCCGAAAATACCCG
45836 AACCCGAA
1 AACCCGAA
45844 TCCGCCCGAA
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
15 28 0.35
16 53 0.65
ACGTcount: A:0.43, C:0.37, G:0.14, T:0.06
Consensus pattern (16 bp):
AACCCGAAAATACCCG
Found at i:45787 original size:31 final size:32
Alignment explanation
Indices: 45742--45843 Score: 172
Period size: 31 Copynumber: 3.2 Consensus size: 32
45732 TCCGAGCCCA
45742 AACCCGAAAATACCCGAACCCGAAAATACCCG
1 AACCCGAAAATACCCGAACCCGAAAATACCCG
45774 AACCCG-AAATACCCGAACCCGAAAATACCCG
1 AACCCGAAAATACCCGAACCCGAAAATACCCG
* *
45805 AACCCGAAAATACACGAACCCG-AAGTACCCG
1 AACCCGAAAATACCCGAACCCGAAAATACCCG
45836 AACCCGAA
1 AACCCGAA
45844 TCCGCCCGAA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
31 47 0.70
32 20 0.30
ACGTcount: A:0.43, C:0.37, G:0.14, T:0.06
Consensus pattern (32 bp):
AACCCGAAAATACCCGAACCCGAAAATACCCG
Found at i:45799 original size:47 final size:47
Alignment explanation
Indices: 45742--45843 Score: 186
Period size: 47 Copynumber: 2.2 Consensus size: 47
45732 TCCGAGCCCA
*
45742 AACCCGAAAATACCCGAACCCGAAAATACCCGAACCCGAAATACCCG
1 AACCCGAAAATACCCGAACCCGAAAATACACGAACCCGAAATACCCG
*
45789 AACCCGAAAATACCCGAACCCGAAAATACACGAACCCGAAGTACCCG
1 AACCCGAAAATACCCGAACCCGAAAATACACGAACCCGAAATACCCG
45836 AACCCGAA
1 AACCCGAA
45844 TCCGCCCGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.43, C:0.37, G:0.14, T:0.06
Consensus pattern (47 bp):
AACCCGAAAATACCCGAACCCGAAAATACACGAACCCGAAATACCCG
Found at i:45852 original size:47 final size:47
Alignment explanation
Indices: 45742--45857 Score: 169
Period size: 47 Copynumber: 2.5 Consensus size: 47
45732 TCCGAGCCCA
* *
45742 AACCCGAAAATACCCGAACCCGAAAATACCCGAACCCGAAATACCCG
1 AACCCGAAAACACCCGAACCCGAAAATACACGAACCCGAAATACCCG
* *
45789 AACCCGAAAATACCCGAACCCGAAAATACACGAACCCGAAGTACCCG
1 AACCCGAAAACACCCGAACCCGAAAATACACGAACCCGAAATACCCG
** *
45836 AACCCGAATCCGCCCGAACCCG
1 AACCCGAAAACACCCGAACCCG
45858 CCCAATTGCC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.40, C:0.40, G:0.15, T:0.06
Consensus pattern (47 bp):
AACCCGAAAACACCCGAACCCGAAAATACACGAACCCGAAATACCCG
Found at i:46186 original size:22 final size:22
Alignment explanation
Indices: 46161--46703 Score: 111
Period size: 22 Copynumber: 24.7 Consensus size: 22
46151 ATGATCCCAT
46161 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCA
* **
46183 TATGAAATTTTAATAACGAT-A
1 TATGAAATTTTGATAACCTTCA
* * ** * * **
46204 CTATGGAGTTTCAAGAATCTTTT
1 -TATGAAATTTTGATAACCTTCA
* ** * *
46227 TAT-AATTTTTTTTAACTTTCT
1 TATGAAATTTTGATAACCTTCA
*
46248 TATGAAATTTTGTTAACC-TCA
1 TATGAAATTTTGATAACCTTCA
* * *
46269 CTAAGGAATTTTGAAAACC-TCAA
1 -TATGAAATTTTGATAACCTTC-A
*
46292 TATGAAATTTTGATAACTTTCCA
1 TATGAAATTTTGATAACCTT-CA
**
46315 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTTCA
* * * *
46336 CTATGAGATGTTGATAAACTCCA
1 -TATGAAATTTTGATAACCTTCA
* * *
46359 TGTGATATATTGATAACCACTT--
1 TATGAAATTTTGATAA-C-CTTCA
* * * * *
46381 TATAAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTTCA
* *
46403 TATG-AATTGTT-AGTAATCATGACA
1 TATGAAATT-TTGA-TAA-CCT-TCA
* * * *
46427 CTTTAAAATTTTGATAATC-ACA
1 -TATGAAATTTTGATAACCTTCA
*
46449 CTATGAAATTTTGATAACC-TCGC
1 -TATGAAATTTTGATAACCTTC-A
* *
46472 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCA
* * *
46495 TATAAAATTTTAATAAACC-TCGC
1 TATGAAATTTTGAT-AACCTTC-A
* *
46518 TATGAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCA
*
46540 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTTCA
* * * *
46557 TA-CAAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCTTCA
** * *
46578 TATGATTTTTTGATTACC-TCGT
1 TATGAAATTTTGATAACCTTC-A
* * * * *
46600 TATGGAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCA
* * *
46622 TATGAAATTTTTGATCTACATAC-
1 TATGAAA-TTTTGAT-AACCTTCA
* * **
46645 TTTGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTTCA
*
46666 CTATGAAAATTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTTCA
46689 TATGAAATTTTGATA
1 TATGAAATTTTGATA
46704 TCCTCACTGA
Statistics
Matches: 373, Mismatches: 110, Indels: 76
0.67 0.20 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 6 0.02
21 25 0.07
22 232 0.62
23 74 0.20
24 10 0.03
25 7 0.02
26 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:46482 original size:44 final size:43
Alignment explanation
Indices: 46248--46703 Score: 178
Period size: 44 Copynumber: 10.3 Consensus size: 43
46238 TTAACTTTCT
* * * * * **
46248 TATGAAATTTTGTTAACCTCACTAAGGAATTTTGAAAACCTCAA
1 TATGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTCGC
* * * *
46292 TATGAAATTTTGATAACTTTCCAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAA-TCTCCTATGAAATTTTGATAACC-TCGC
* * * * * * * **
46337 TATGAGATGTTGATAAACTCCATGTGATATATTGATAACCACTT
1 TATGAAATTTTGATAATCTCC-TATGAAATTTTGATAACCTCGC
* * * * * * *
46381 TATAAAAATTTAAAAACCTCCATATG-AATTGTT-AGTAATCATGACAC
1 TATGAAATTTTGATAATCTCC-TATGAAATT-TTGA-TAA-CCT--CGC
* * *
46428 TTTAAAATTTTGATAATCACACTATGAAATTTTGATAACCTCGC
1 TATGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCTCGC
* *
46472 TATGAAATTTTGATAAATCTTCCTATAAAATTTTAATAAACCTCGC
1 TATGAAATTTTGAT-AATC-TCCTATGAAATTTTGAT-AACCTCGC
* * *
46518 TATGAAATTTTGATAACTTTCTTATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAA-TCTCCTATGAAATTTTGATAACCTCGC
* * ** * *
46557 TA-CAAATTTTGATAAGCTCCCTATGATTTTTTGATTACCTCGT
1 TATGAAATTTTGATAATCT-CCTATGAAATTTTGATAACCTCGC
* * * * *
46600 TATGGAATTTTGTTAATCTCCCTATGAAATTTTTGATCTACAT-AC
1 TATGAAATTTTGATAATCT-CCTATGAAA-TTTTGAT-AACCTCGC
* * * * *
46645 TTTGAAATTTTGA-AAACTAAACTATGAAAATTTGATAACCTTC-A
1 TATGAAATTTTGATAATCT--CCTATGAAATTTTGATAACC-TCGC
46689 TATGAAATTTTGATA
1 TATGAAATTTTGATA
46704 TCCTCACTGA
Statistics
Matches: 304, Mismatches: 80, Indels: 55
0.69 0.18 0.13
Matches are distributed among these distances:
37 1 0.00
38 25 0.08
39 3 0.01
43 7 0.02
44 117 0.38
45 91 0.30
46 30 0.10
47 24 0.08
48 6 0.02
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGATAATCTCCTATGAAATTTTGATAACCTCGC
Found at i:46502 original size:23 final size:24
Alignment explanation
Indices: 46432--46533 Score: 117
Period size: 23 Copynumber: 4.5 Consensus size: 24
46422 TGACACTTTA
* *
46432 AAATTTTGAT-AAT-CACACTATG
1 AAATTTTGATAAATCCTCGCTATG
46454 AAATTTTGAT-AA-CCTCGCTATG
1 AAATTTTGATAAATCCTCGCTATG
* *
46476 AAATTTTGATAAATCTTC-CTATA
1 AAATTTTGATAAATCCTCGCTATG
*
46499 AAATTTTAATAAA-CCTCGCTATG
1 AAATTTTGATAAATCCTCGCTATG
46522 AAATTTTGATAA
1 AAATTTTGATAA
46534 CTTTCTTATG
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
22 32 0.47
23 33 0.49
24 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (24 bp):
AAATTTTGATAAATCCTCGCTATG
Found at i:46521 original size:46 final size:45
Alignment explanation
Indices: 46432--46533 Score: 145
Period size: 46 Copynumber: 2.3 Consensus size: 45
46422 TGACACTTTA
* *
46432 AAATTTTGAT-AATCACACTATGAAATTTTGATAACCTCGCTATG
1 AAATTTTGATAAATCACACTATAAAATTTTAATAACCTCGCTATG
*
46476 AAATTTTGATAAATCTTC-CTATAAAATTTTAATAAACCTCGCTATG
1 AAATTTTGATAAATC-ACACTATAAAATTTTAAT-AACCTCGCTATG
46522 AAATTTTGATAA
1 AAATTTTGATAA
46534 CTTTCTTATG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 10 0.19
45 17 0.33
46 25 0.48
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (45 bp):
AAATTTTGATAAATCACACTATAAAATTTTAATAACCTCGCTATG
Found at i:46747 original size:19 final size:20
Alignment explanation
Indices: 46691--46741 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
46681 AACCTTCATA
*
46691 TGAAATTTTGATATCCTCAC
1 TGAAATTTTGATATCCTCCC
*
46711 TG-AATTTCGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
46730 TGAAATTTTGAT
1 TGAAATTTTGAT
46742 TACTCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:46879 original size:22 final size:22
Alignment explanation
Indices: 46853--47093 Score: 129
Period size: 22 Copynumber: 11.0 Consensus size: 22
46843 ATTTTGATAA
46853 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* *
46875 TTTGATAACATCTTTATAAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * *
46897 TTTGTTGACCCCTCTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * *
46919 TTTGATAATCACATTATGTAAT
1 TTTGATAACCTCTTTATGAAAT
* * *
46941 TTTGATAGCATCGCTT-TGAAAT
1 TTTGATAACCTC-TTTATGAAAT
** ** *
46963 TTTGATAACAACACTAAGAAAT
1 TTTGATAACCTCTTTATGAAAT
46985 TTTGATAA--TCTTCATAT-AAAT
1 TTTGATAACCTCTT--TATGAAAT
47006 TTTGATAATCCTATCTTTATGAAAT
1 TTTGATAA-CC--TCTTTATGAAAT
* * * * *
47031 TTCGATAATCACTGTATGAGA-
1 TTTGATAACCTCTTTATGAAAT
* *
47052 TTTGATAACCT-TCTATCAAAT
1 TTTGATAACCTCTTTATGAAAT
* *
47073 TTTGGT-A-CTCCTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
47093 T
1 T
47094 GAGACTTTTA
Statistics
Matches: 162, Mismatches: 45, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
19 2 0.01
20 16 0.10
21 26 0.16
22 97 0.60
23 2 0.01
24 4 0.02
25 11 0.07
26 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TTTGATAACCTCTTTATGAAAT
Found at i:46936 original size:66 final size:67
Alignment explanation
Indices: 46853--47038 Score: 175
Period size: 66 Copynumber: 2.8 Consensus size: 67
46843 ATTTTGATAA
* * * * * ** * *
46853 TTTGATAACCT-CTTTATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCTCTATGAA
1 TTTGATAATCTACATTATGAAATTTTGATAACATCTTTATGAAATTTTGATAACAACACTAAGAA
46917 AT
66 AT
* * *
46919 TTTGATAATC-ACATTATGTAATTTTGATAGCATCGCTT-TGAAATTTTGATAACAACACTAAGA
1 TTTGATAATCTACATTATGAAATTTTGATAACATC-TTTATGAAATTTTGATAACAACACTAAGA
46982 AAT
65 AAT
* *
46985 TTTGATAATCTTCA-TAT-AAATTTTGATAATCCTATCTTTATGAAATTTCGATAA
1 TTTGATAATCTACATTATGAAATTTTGATAA--C-ATCTTTATGAAATTTTGATAA
47039 TCACTGTATG
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
65 10 0.10
66 63 0.66
67 7 0.07
68 16 0.17
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (67 bp):
TTTGATAATCTACATTATGAAATTTTGATAACATCTTTATGAAATTTTGATAACAACACTAAGAA
AT
Found at i:46942 original size:44 final size:44
Alignment explanation
Indices: 46822--47015 Score: 139
Period size: 44 Copynumber: 4.4 Consensus size: 44
46812 AGAAATACCA
* *
46822 CTATGAAATTTTTG-TAATCACATTTTGATAA-TTTGATAACCTCT
1 CTATGAAA-TTTTGATAATCACATTATG-TAATTTTGATAACCCCT
* * ** * *
46866 TTATGAAATTTTGATAA-CATCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCA-CATTATGTAATTTTGATAACCCCT
* ** *
46910 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAGCATCG
1 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCCCT
* * * * * *
46954 CTTTGAAATTTTGATAA-CAACACTAAGAAATTTTGATAA-TCTT
1 CTATGAAATTTTGATAATC-ACATTATGTAATTTTGATAACCCCT
46997 CATAT-AAATTTTGATAATC
1 C-TATGAAATTTTGATAATC
47016 CTATCTTTAT
Statistics
Matches: 115, Mismatches: 28, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
43 23 0.20
44 90 0.78
45 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCCCT
Found at i:46985 original size:88 final size:88
Alignment explanation
Indices: 46822--46988 Score: 207
Period size: 88 Copynumber: 1.9 Consensus size: 88
46812 AGAAATACCA
* * * *
46822 CTATGAAATTTTTGTAATCACATTTTGATAATTTGATAACCTCTTTATGAAATTTTGATAACATC
1 CTATGAAATTTTTGTAATCACATTATGATAATTTGATAACATCCTTATGAAATTTTGATAACAAC
**
46887 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
*
46910 CTATGAAA-TTTTGATAATCACATTATG-TAATTTTGATAGCATCGCTT-TGAAATTTTGATAAC
1 CTATGAAATTTTTG-TAATCACATTATGATAA-TTTGATAACATC-CTTATGAAATTTTGATAAC
46972 AACACTA-AGAAATTTTG
63 AACACTATA-AAATTTTG
46989 ATAATCTTCA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
87 9 0.13
88 57 0.84
89 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTATGATAATTTGATAACATCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:47031 original size:25 final size:23
Alignment explanation
Indices: 46980--47085 Score: 73
Period size: 21 Copynumber: 4.8 Consensus size: 23
46970 ACAACACTAA
46980 GAAATTTTGATAAT-CTTCATAT
1 GAAATTTTGATAATCCTTCATAT
*
47002 -AAATTTTGATAATCCTATCTTTAT
1 GAAATTTTGATAATCCT-TC-ATAT
* *
47026 GAAATTTCGATAATCAC-T-GTAT
1 GAAATTTTGATAATC-CTTCATAT
*
47048 GAGA-TTTGATAA-CCTTC-TAT
1 GAAATTTTGATAATCCTTCATAT
* * *
47068 CAAATTTTGGTACTCCTT
1 GAAATTTTGATAATCCTT
47086 ATGAAATTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
19 1 0.02
20 7 0.11
21 26 0.39
22 12 0.18
23 2 0.03
24 4 0.06
25 13 0.20
26 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (23 bp):
GAAATTTTGATAATCCTTCATAT
Found at i:47205 original size:22 final size:24
Alignment explanation
Indices: 47180--47229 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
47170 TAACCTTCTA
47180 ATGAAATTTT-GT-TAACCACACT
1 ATGAAATTTTCGTATAACCACACT
* *
47202 ATGAAATTTTCGTATAACCTCGCT
1 ATGAAATTTTCGTATAACCACACT
47226 ATGA
1 ATGA
47230 CATTATGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.42
23 2 0.08
24 12 0.50
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (24 bp):
ATGAAATTTTCGTATAACCACACT
Found at i:47307 original size:22 final size:22
Alignment explanation
Indices: 47275--47322 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
47265 TTGTGATAAT
* *
47275 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTAAGAAATTTCAA
*
47297 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTAAGAAATTTCAA
47319 TAAC
1 TAAC
47323 ATGATCCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTCAA
Found at i:47383 original size:22 final size:22
Alignment explanation
Indices: 47336--47431 Score: 81
Period size: 22 Copynumber: 4.4 Consensus size: 22
47326 ATCCTATTGG
*
47336 TAACTACACTATGAAATTTT-A
1 TAACCACACTATGAAATTTTGA
*
47357 GTAACCACACTATGGAATTTTGA
1 -TAACCACACTATGAAATTTTGA
* * * *
47380 TAACCTC-CTCATGGAATTATAA
1 TAACCACACT-ATGAAATTTTGA
*
47402 TAACCATC-TTATGAAATTTTGA
1 TAACCA-CACTATGAAATTTTGA
47424 TAACCACA
1 TAACCACA
47432 TAGAGACAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.05
22 54 0.90
23 3 0.05
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:47572 original size:6 final size:6
Alignment explanation
Indices: 47561--47586 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
47551 AGTATTGTAC
47561 GTGTTA GTGTTA GTGTTA GTGTTA GT
1 GTGTTA GTGTTA GTGTTA GTGTTA GT
47587 TTAATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
GTGTTA
Found at i:47719 original size:32 final size:31
Alignment explanation
Indices: 47683--47749 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
47673 TTAGTAATGG
*
47683 CAATTAAGAAATATGTTTGAAAAAAAATGGTA
1 CAATT-AGAAATATGTTTGAAAAAAAAGGGTA
* * *
47715 CAATTGGAAATATGTTTTAAAAATAAGGGTA
1 CAATTAGAAATATGTTTGAAAAAAAAGGGTA
47746 CAAT
1 CAAT
47750 CGGAAAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.30
Consensus pattern (31 bp):
CAATTAGAAATATGTTTGAAAAAAAAGGGTA
Found at i:47725 original size:31 final size:31
Alignment explanation
Indices: 47690--47755 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
47680 TGGCAATTAA
* *
47690 GAAATATGTTTGAAAAAAAATGGTACAATTG
1 GAAATATGTTTGAAAAAAAAGGGTACAATCG
* *
47721 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTGAAAAAAAAGGGTACAATCG
47752 GAAA
1 GAAA
47756 ACATAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTGAAAAAAAAGGGTACAATCG
Done.