Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000065.1 Hibiscus syriacus cultivar Beakdansim tig00000110_pilon, 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: 85859
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2485 original size:55 final size:55
Alignment explanation
Indices: 2330--2488 Score: 210
Period size: 55 Copynumber: 2.9 Consensus size: 55
2320 TTGAAAGAAG
* * * *
2330 TCTTCGATCAACTTCAAACTTCTTCATTCATTGGATGTCTTTCTTAATGGATCGA
1 TCTTCAATCAATTTCAAACTTCTTCATTCATCGGATGTCTTTCTTCATGGATCGA
* * * * * *
2385 TCTTCAATTAGTTTTAAATTTCTTCATTCATCGGATGTCTTTCTTCATGTATCGG
1 TCTTCAATCAATTTCAAACTTCTTCATTCATCGGATGTCTTTCTTCATGGATCGA
* *
2440 TCTTTAATCAATTTCAAACTTCTTCATTCATCGAATGTCTTTCTTCATG
1 TCTTCAATCAATTTCAAACTTCTTCATTCATCGGATGTCTTTCTTCATG
2489 AATCATTTGA
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 88 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.46
Consensus pattern (55 bp):
TCTTCAATCAATTTCAAACTTCTTCATTCATCGGATGTCTTTCTTCATGGATCGA
Found at i:6066 original size:21 final size:22
Alignment explanation
Indices: 6042--6091 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
6032 CTTCTTTTTT
6042 AGGGCATGGGCGT-T-GTGGAGC
1 AGGGCATGGG-GTCTAGTGGAGC
*
6063 AGGGTATGGGGTCTAGTGGAGC
1 AGGGCATGGGGTCTAGTGGAGC
6085 ATGGGCA
1 A-GGGCA
6092 ACAGCTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 10 0.42
22 8 0.33
23 4 0.17
ACGTcount: A:0.18, C:0.12, G:0.50, T:0.20
Consensus pattern (22 bp):
AGGGCATGGGGTCTAGTGGAGC
Found at i:6293 original size:9 final size:9
Alignment explanation
Indices: 6277--6367 Score: 50
Period size: 9 Copynumber: 10.6 Consensus size: 9
6267 AAAATATAAC
6277 TAAT-ATTA
1 TAATAATTA
6285 TAATAATTA
1 TAATAATTA
* **
6294 TTATTTTTA
1 TAATAATTA
*
6303 TTATAA-TA
1 TAATAATTA
*
6311 TAATAGTTA
1 TAATAATTA
**
6320 TAATAACAA
1 TAATAATTA
6329 TAATAA-TA
1 TAATAATTA
6337 T--TAA-TA
1 TAATAATTA
*
6343 TAATATAATA
1 TAATA-ATTA
6353 GTAATAATTA
1 -TAATAATTA
6363 TAATA
1 TAATA
6368 TAATATTTAT
Statistics
Matches: 64, Mismatches: 12, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
6 6 0.09
8 14 0.22
9 34 0.53
10 5 0.08
11 5 0.08
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (9 bp):
TAATAATTA
Found at i:6322 original size:14 final size:13
Alignment explanation
Indices: 6301--6374 Score: 62
Period size: 14 Copynumber: 5.3 Consensus size: 13
6291 TTATTATTTT
6301 TATTATAATATAA
1 TATTATAATATAA
6314 TAGTTATAATA-ACA
1 TA-TTATAATATA-A
*
6328 -ATAATAATATTAA
1 TATTATAATA-TAA
6341 TATAATATAATAGTAA
1 TAT--TATAATA-TAA
6357 TAATTATAATATAA
1 T-ATTATAATATAA
6371 TATT
1 TATT
6375 TATATCCCGG
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
12 7 0.14
13 8 0.16
14 16 0.32
15 7 0.14
16 10 0.20
17 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (13 bp):
TATTATAATATAA
Found at i:6325 original size:3 final size:3
Alignment explanation
Indices: 6305--6372 Score: 54
Period size: 3 Copynumber: 24.0 Consensus size: 3
6295 TATTTTTATT
* * * *
6305 ATA AT- ATA ATA GTT ATA ATA ACA ATA ATA ATA TTA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
6350 ATA GTA ATA ATT ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
6373 TTTATATCCC
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
2 8 0.16
3 41 0.84
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:6349 original size:37 final size:36
Alignment explanation
Indices: 6304--6379 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
6294 TTATTTTTAT
*
6304 TATAATATAATAGTTATAATAACAATAATAATATTAA
1 TATAATATAATAGTAATAATAACAAT-ATAATATTAA
* * *
6341 TATAATATAATAGTAATAATTATAATATAATATTTA
1 TATAATATAATAGTAATAATAACAATATAATATTAA
6377 TAT
1 TAT
6380 CCCGGATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
36 12 0.34
37 23 0.66
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (36 bp):
TATAATATAATAGTAATAATAACAATATAATATTAA
Found at i:6959 original size:2 final size:2
Alignment explanation
Indices: 6952--6977 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6942 CAGATTTCAA
6952 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6978 GAATGTGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9332 original size:14 final size:14
Alignment explanation
Indices: 9309--9342 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
9299 TTTCACCTTT
*
9309 AGGTCGACTACTAA
1 AGGTCAACTACTAA
9323 AGGTCAACTACTAA
1 AGGTCAACTACTAA
9337 AGGTCA
1 AGGTCA
9343 CTTTGGCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
AGGTCAACTACTAA
Found at i:17076 original size:32 final size:33
Alignment explanation
Indices: 16990--17146 Score: 104
Period size: 33 Copynumber: 4.8 Consensus size: 33
16980 CAATCTATGT
* * * * * *
16990 AGCCAAGTGTTAATCCTTATAGCCAACCGCCAC
1 AGCCAAATGCTAATCCATATGGCCAACCTCTAC
* * *
17023 AACCCAATGCTAATCCCTATGGCCAACC-CTAC
1 AGCCAAATGCTAATCCATATGGCCAACCTCTAC
* * * * *
17055 AGCTAAATGCTAATTCATATGGTCAACCTGTGC
1 AGCCAAATGCTAATCCATATGGCCAACCTCTAC
* * *
17088 AGCCAAATGCTAATACA-ACTGGTCAACTTGC-AC
1 AGCCAAATGCTAATCCATA-TGGCCAACCT-CTAC
* *
17121 AACCAAATGCTAATCCATATGACCAA
1 AGCCAAATGCTAATCCATATGGCCAA
17147 ACCATGTAAC
Statistics
Matches: 96, Mismatches: 24, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
32 26 0.27
33 69 0.72
34 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.22
Consensus pattern (33 bp):
AGCCAAATGCTAATCCATATGGCCAACCTCTAC
Found at i:17101 original size:33 final size:33
Alignment explanation
Indices: 17028--17141 Score: 115
Period size: 33 Copynumber: 3.5 Consensus size: 33
17018 GCCACAACCC
* * * *
17028 AATGCTAATCCCTATGGCCAACC-CTACAGCTA
1 AATGCTAATCCATATGGTCAACCTGTACAGCCA
* *
17060 AATGCTAATTCATATGGTCAACCTGTGCAGCCA
1 AATGCTAATCCATATGGTCAACCTGTACAGCCA
* * * *
17093 AATGCTAATACA-ACTGGTCAACTTGCACAACCA
1 AATGCTAATCCATA-TGGTCAACCTGTACAGCCA
17126 AATGCTAATCCATATG
1 AATGCTAATCCATATG
17142 ACCAAACCAT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
32 21 0.31
33 45 0.67
34 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (33 bp):
AATGCTAATCCATATGGTCAACCTGTACAGCCA
Found at i:20234 original size:19 final size:19
Alignment explanation
Indices: 20223--20289 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
20213 TCGGTTGGGC
20223 CAGTCTGAATCGATTGGAA
1 CAGTCTGAATCGATTGGAA
* *
20242 CGGTCTGAATCGATTAGAA
1 CAGTCTGAATCGATTGGAA
*
20261 CGGTCTGAATCGATTGGAA
1 CAGTCTGAATCGATTGGAA
*
20280 CGGTCTGAAT
1 CAGTCTGAAT
20290 TGATCTAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (19 bp):
CAGTCTGAATCGATTGGAA
Found at i:20412 original size:21 final size:21
Alignment explanation
Indices: 20388--20428 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20378 GCTATTAATC
* *
20388 GAGTTAATCGAGCCATTAACT
1 GAGTCAATCGAGCCACTAACT
20409 GAGTCAATCGAGCCACTAAC
1 GAGTCAATCGAGCCACTAAC
20429 AACTAATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
GAGTCAATCGAGCCACTAACT
Found at i:27521 original size:3 final size:3
Alignment explanation
Indices: 27513--27564 Score: 61
Period size: 3 Copynumber: 16.3 Consensus size: 3
27503 CGGGTCTTTT
27513 TTA TTA TTA TT- TATA TATA TTTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA
27561 TTA T
1 TTA T
27565 GTTTATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.02
3 34 0.76
4 9 0.20
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27533 original size:16 final size:16
Alignment explanation
Indices: 27513--27564 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
27503 CGGGTCTTTT
27513 TTATTATTATTTA-TA
1 TTATTATTATTTATTA
27528 -TA-TATT-TATTATTA
1 TTATTATTAT-TTATTA
27542 TTATTATTATTTATTA
1 TTATTATTATTTATTA
27558 TTATTAT
1 TTATTAT
27565 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 1 0.03
13 7 0.22
14 4 0.12
15 2 0.06
16 17 0.53
17 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTATTTATTA
Found at i:27543 original size:10 final size:10
Alignment explanation
Indices: 27512--27562 Score: 79
Period size: 10 Copynumber: 5.2 Consensus size: 10
27502 CCGGGTCTTT
27512 TTTATTATTA
1 TTTATTATTA
27522 TTTA-TATATA
1 TTTATTAT-TA
27532 TTTATTATTA
1 TTTATTATTA
27542 -TTATTATTA
1 TTTATTATTA
27551 TTTATTATTA
1 TTTATTATTA
27561 TT
1 TT
27563 ATGTTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 12 0.32
10 23 0.61
11 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATTATTA
Found at i:27570 original size:19 final size:18
Alignment explanation
Indices: 27512--27576 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
27502 CCGGGTCTTT
*
27512 TTTATTATTATTTATATATA
1 TTTATTATTA-TTAT-TTTA
27532 TTTATTATTATTATTATTA
1 TTTATTATTATTATT-TTA
27551 TTTATTATTATTATGTTTA
1 TTTATTATTATTAT-TTTA
*
27570 TTAATTA
1 TTTATTA
27577 CATATTACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
18 1 0.02
19 29 0.71
20 11 0.27
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTATTATTATTATTTTA
Found at i:27576 original size:13 final size:13
Alignment explanation
Indices: 27514--27572 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
27504 GGGTCTTTTT
*
27514 TATTATTATT-TA
1 TATTATTATTATG
27526 TATATATTTATTAT-
1 TAT-TA-TTATTATG
*
27540 TATTATTATTATT
1 TATTATTATTATG
27553 TATTATTATTATG
1 TATTATTATTATG
27566 T-TTATTA
1 TATTATTA
27573 ATTACATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
12 16 0.38
13 17 0.40
14 8 0.19
15 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:27708 original size:25 final size:25
Alignment explanation
Indices: 27679--27751 Score: 146
Period size: 25 Copynumber: 2.9 Consensus size: 25
27669 ACCAACCCAT
27679 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
27704 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
27729 CAGATTAGGGTTTCAAACCCTAA
1 CAGATTAGGGTTTCAAACCCTAA
27752 TCCCCTAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:28146 original size:10 final size:10
Alignment explanation
Indices: 28131--28161 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
28121 CCACAACCGA
28131 AAAAAAAAAG
1 AAAAAAAAAG
28141 AAAAAAAAAG
1 AAAAAAAAAG
28151 AAAAAAAAAG
1 AAAAAAAAAG
28161 A
1 A
28162 GGAGTAGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:29585 original size:22 final size:22
Alignment explanation
Indices: 29560--29603 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29550 TCAAACGATG
*
29560 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
29582 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
29604 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:31146 original size:30 final size:32
Alignment explanation
Indices: 31111--31171 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 32
31101 ATTTTACATG
31111 TACTAACTTATTT-TTCTC-TTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCATTTGTTTGTGTA
31141 TACTAACTTATTTCTTCTCATTTGTTTGTGT
1 TACTAACTTATTTCTTCTCATTTGTTTGTGT
31172 CAATTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 13 0.45
31 5 0.17
32 11 0.38
ACGTcount: A:0.16, C:0.15, G:0.10, T:0.59
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCATTTGTTTGTGTA
Found at i:34042 original size:17 final size:16
Alignment explanation
Indices: 34022--34056 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
34012 AGATCATATT
*
34022 AAAGCGAAGAGAAAAGA
1 AAAGCAAAGAG-AAAGA
34039 AAAGCAAAGAGAAAGA
1 AAAGCAAAGAGAAAGA
34055 AA
1 AA
34057 CAAAGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.69, C:0.06, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAGCAAAGAGAAAGA
Found at i:35263 original size:4 final size:4
Alignment explanation
Indices: 35254--35303 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
35244 GATCGAGAAA
*
35254 ACAT ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT ACAT ACAT A-AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
35299 ACAT A
1 ACAT A
35304 AAATTTGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 36 0.88
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:35700 original size:36 final size:35
Alignment explanation
Indices: 35645--35782 Score: 161
Period size: 36 Copynumber: 3.9 Consensus size: 35
35635 TTTTGAGAAT
35645 TTTAAAACAAATTTTTGTCTCGCTTGAGACAATTTC
1 TTTAAAACAAA-TTTTGTCTCGCTTGAGACAATTTC
* * *
35681 TTTCAAAGCAAATTTTGTCTCGCTTGAAACAGCTTTC
1 TTT-AAAACAAATTTTGTCTCGCTTGAGACA-ATTTC
* * *
35718 -TAAAAACAAATTTTGTCTCGTTTGAGACAAATTC
1 TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
* *
35752 TCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 T-TTAAAACAAATTTTGTCTCGCTTGAGACA
35783 TTTTTCCTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
34 3 0.04
35 24 0.28
36 47 0.55
37 11 0.13
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (35 bp):
TTTAAAACAAATTTTGTCTCGCTTGAGACAATTTC
Found at i:35876 original size:105 final size:102
Alignment explanation
Indices: 35756--35994 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 102
35746 AAATTCTCTT
* * *
35756 AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* *
35820 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TT-AAACAAAATTAATCTCA-CTTGAGA---TCGTTTC-CTCA
* * *
35861 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* *
35926 TTAAACAAAGTTGATCTCACTTGAGATCGTTTCCTCA
66 TTAAACAAAATTAATCTCACTTGAGATCGTTTCCTCA
*
35963 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
35995 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 32 0.27
103 3 0.03
104 3 0.03
105 76 0.64
106 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACTTGAGATCGTTTCCTCA
Found at i:36002 original size:36 final size:34
Alignment explanation
Indices: 35962--36059 Score: 108
Period size: 36 Copynumber: 2.8 Consensus size: 34
35952 TCGTTTCCTC
*
35962 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCT-T
** *
35998 AAAAACAAATTTTGTCTCATTTGAGACTATATCTT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCTT
*
36033 -AAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTT-GTCTCGCTTGAGACA
36060 TCATTTTCTC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
33 3 0.06
34 19 0.37
35 1 0.02
36 29 0.56
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (34 bp):
AAAAACAAATTTGTCTCGCTTGAGACAATATCTT
Found at i:36334 original size:27 final size:27
Alignment explanation
Indices: 36307--36425 Score: 152
Period size: 27 Copynumber: 4.3 Consensus size: 27
36297 ACAGTTTCTC
*
36307 TTGAAAAAATCTTTGAGTTTGTTCCTC
1 TTGAAAAAATCTTTGAGTTTGTTCCTT
*
36334 TTGAAAAAATC-TTGAAGTTTGCTCCTT
1 TTGAAAAAATCTTTG-AGTTTGTTCCTT
*
36361 TTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTG-A-AAAAATCTTTGAGTTTGTTCCTT
*
36390 TTGAATAAAATCTTTGAG-TTGTTTCTT
1 TTGAA-AAAATCTTTGAGTTTGTTCCTT
36417 TTGAAAAAA
1 TTGAAAAAA
36426 AAAACTTTGA
Statistics
Matches: 81, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.09
27 38 0.47
28 13 0.16
29 21 0.26
30 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (27 bp):
TTGAAAAAATCTTTGAGTTTGTTCCTT
Found at i:36373 original size:56 final size:57
Alignment explanation
Indices: 36310--36437 Score: 163
Period size: 56 Copynumber: 2.3 Consensus size: 57
36300 GTTTCTCTTG
36310 AAAAAATCTTTGAGTTTGTTCCTCTTGAA-AAAATC-TTGAAGTTTGCTCCTTTTG-AA
1 AAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAATCTTTG-AG-TTGCTCCTTTTGAAA
* * * * *
36366 TAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAATCTTTGAGTTGTTTCTTTTGAAA
1 AAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAATCTTTGAGTTGCTCCTTTTGAAA
*
36423 AAAAAAACTTTGAGT
1 AAAAAATCTTTGAGT
36438 CTATTTATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
56 36 0.59
57 22 0.36
58 3 0.05
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (57 bp):
AAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAATCTTTGAGTTGCTCCTTTTGAAA
Found at i:36451 original size:30 final size:29
Alignment explanation
Indices: 36396--36452 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
36386 CCTTTTGAAT
* * *
36396 AAAATCTTTGAGTTGTTTCTTTTGAAAAA
1 AAAAACTTTGAGTTATTTATTTTGAAAAA
36425 AAAAACTTTGAGTCTATTTATTTTGAAA
1 AAAAACTTTGAGT-TATTTATTTTGAAA
36453 CAAATTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (29 bp):
AAAAACTTTGAGTTATTTATTTTGAAAAA
Found at i:36506 original size:52 final size:52
Alignment explanation
Indices: 36446--36602 Score: 278
Period size: 52 Copynumber: 3.0 Consensus size: 52
36436 GTCTATTTAT
*
36446 TTTGAAACAAATTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
1 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
36498 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
1 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
* *
36550 TCTGAAACAAAGTGTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAG
1 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAG
36603 ATTGTTTTTT
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 88 0.87
53 13 0.13
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (52 bp):
TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
Found at i:36626 original size:29 final size:30
Alignment explanation
Indices: 36590--36652 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
36580 AATTTCGTGA
*
36590 AAAAATCTTTGAGATTGTTT-TTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
*
36619 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
36649 AAAA
1 AAAA
36653 TTTTGTCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:37174 original size:31 final size:30
Alignment explanation
Indices: 37098--37182 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 30
37088 ATTTTGACTC
* *
37098 CTTTGAGGCAGTTTCTCTAGAAATACAAAAT
1 CTTTGAGTC-GTTTCTCTTGAAATACAAAAT
*
37129 CTTTGAGTTTGTTTCTCTTGAAATA-AAACCAT
1 CTTTGAG-TCGTTTCTCTTGAAATACAAA--AT
*
37161 CTTTGAGTCGTTTCCCTTGAAA
1 CTTTGAGTCGTTTCTCTTGAAA
37183 CGAATTTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 3 0.07
31 34 0.74
32 9 0.20
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (30 bp):
CTTTGAGTCGTTTCTCTTGAAATACAAAAT
Found at i:37856 original size:28 final size:28
Alignment explanation
Indices: 37824--37877 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
37814 TCAAAATCCA
*
37824 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTTCTATTGAAACAC
*
37852 ATCTTTGAGTTGGTTTCTCTTGAAAC
1 ATCTTTGAGTTGGTTTCTATTGAAAC
37878 CATAGCTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTTCTATTGAAACAC
Found at i:37957 original size:40 final size:40
Alignment explanation
Indices: 37896--38220 Score: 179
Period size: 40 Copynumber: 7.7 Consensus size: 40
37886 CTAAAGATGG
* *
37896 CCAGAACTCCTCATCATGTAGGAACCGTGTCATCCCCAGA
1 CCAGATCTCCTCATCACGTAGGAACCGTGTCATCCCCAGA
* * * * **
37936 CCAGATTTCCTTATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGATCTCCTCATCACGTAGGAACCGTGTCATCCCCAG---A
* * *
37979 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGA
1 CCAGATC-TCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA
* * * * *
38022 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGA
1 ---CCAGATCTCCTCATCACGTAGGAACCGTGTCATCCCCAGA
* * * **
38065 CCAGATCTCCTTATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGATCTCCTCATCACGTAGGAACCGTGTCATCCCCAG---A
* * *
38108 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGATC-TCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA
* * * *
38151 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCC-GA
1 ---CCAGATCTCCTCATCACGTAGGAACCGTGTCA-TCCCCAGA
*
38194 CCAGATGTCCTCATCACGTAGGAACCG
1 CCAGATCTCCTCATCACGTAGGAACCG
38221 CGTTAACCTT
Statistics
Matches: 214, Mismatches: 48, Indels: 46
0.69 0.16 0.15
Matches are distributed among these distances:
40 84 0.39
42 1 0.00
43 63 0.29
44 2 0.01
45 2 0.01
46 58 0.27
47 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTAGGAACCGTGTCATCCCCAGA
Found at i:37996 original size:43 final size:44
Alignment explanation
Indices: 37896--38186 Score: 192
Period size: 40 Copynumber: 6.8 Consensus size: 44
37886 CTAAAGATGG
* * * **
37896 CCAGAACTCCTCATCATGTAGGAACCGTGTCAT-CCCCAG---A
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATAA
** *
37936 CCAGATTTCCTTATCACGTAGGAGCCGTGTCA-ACCATAGATAA
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATAA
* * * **
37979 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGG
1 CCAGACC-TCCTCATCACGTAGGAGCCGTGTCAT-ACCAT-AGATAA
* * * * *
38025 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-CAG---A
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATAA
* *
38065 CCAGATCTCCTTATCACGTAGGAGCCGTGTCA-ACCATAGATAA
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATAA
* * * **
38108 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGACC-TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAA
* * *
38154 CCAGAACTCTTCATCACGTATGAGCCGTGTCAT
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTCAT
38187 TCCCCGACCA
Statistics
Matches: 192, Mismatches: 41, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
39 2 0.01
40 61 0.32
42 1 0.01
43 56 0.29
45 9 0.05
46 61 0.32
47 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.24
Consensus pattern (44 bp):
CCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATAA
Found at i:38044 original size:46 final size:45
Alignment explanation
Indices: 37890--38186 Score: 191
Period size: 46 Copynumber: 6.9 Consensus size: 45
37880 TAGCTCCTAA
* * * *
37890 AGATGGCCAGAACTCCTCATCATGTAGGAACCGTGTCATC-CC-C
1 AGATGGCCAGAACTCTTCATCACGTAGGAGCCGTGTCATCACCTT
** *
37933 AGA---CCAGATTTCCTT-ATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGGCCAGAACT-CTTCATCACGTAGGAGCCGTGTCATCACCTT
** * * * *
37973 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
1 AGATGGCCAGAAC-TCTTCATCACGTAGGAGCCGTGTCATCACCTT
*
38018 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC--
1 -AGATGGCCAGAACTCTTCATCACGTAGGAGCCGTGTCA-TCACCTT
* *
38062 AGA---CCAGATCTCCTT-ATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGGCCAGAACT-CTTCATCACGTAGGAGCCGTGTCATCACCTT
** * * * *
38102 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATGGCCAGAAC-TCTTCATCACGTAGGAGCCGTGTCATCACC-TT
*
38148 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT
1 AGATGGCCAGAACTCTTCATCACGTAGGAGCCGTGTCAT
38187 TCCCCGACCA
Statistics
Matches: 195, Mismatches: 33, Indels: 49
0.70 0.12 0.18
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 56 0.29
41 5 0.03
42 5 0.03
43 52 0.27
45 7 0.04
46 62 0.32
47 4 0.02
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (45 bp):
AGATGGCCAGAACTCTTCATCACGTAGGAGCCGTGTCATCACCTT
Found at i:38119 original size:129 final size:129
Alignment explanation
Indices: 37889--38216 Score: 566
Period size: 129 Copynumber: 2.5 Consensus size: 129
37879 ATAGCTCCTA
* * * * * *
37889 AAGATGGCCAGAACTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATTTCCTTATCACG
1 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
37954 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
66 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
38018 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
1 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
38083 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
66 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
* * * *
38147 TAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATGTCCTCATCACG
1 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
38212 TAGGA
66 TAGGA
38217 ACCGCGTTAA
Statistics
Matches: 189, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 189 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (129 bp):
AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
Found at i:38421 original size:3 final size:3
Alignment explanation
Indices: 38413--38462 Score: 66
Period size: 3 Copynumber: 16.0 Consensus size: 3
38403 CGGGTCTTTT
38413 TTA TTA TTA TT- TATA TATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
38460 TTA
1 TTA
38463 GTTTATTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 36 0.82
4 6 0.14
5 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:38607 original size:25 final size:25
Alignment explanation
Indices: 38578--38649 Score: 144
Period size: 25 Copynumber: 2.9 Consensus size: 25
38568 CCAACCCATT
38578 AGATTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAAAC
38603 AGATTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAAAC
38628 AGATTAGGGTTTCAAACCCTAA
1 AGATTAGGGTTTCAAACCCTAA
38650 TCCCCTAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (25 bp):
AGATTAGGGTTTCAAACCCTAAAAC
Found at i:40473 original size:22 final size:22
Alignment explanation
Indices: 40448--40491 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40438 TCAAACGATG
*
40448 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
40470 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
40492 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:41686 original size:31 final size:31
Alignment explanation
Indices: 41635--41695 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
41625 GATATCCAAA
**
41635 GCCAAATTTAAGAGATAACTAGTTATTTAAG
1 GCCAAATTTAAGAGATAACTAAATATTTAAG
41666 GCCAAATTT-AG-GTATCAACTAAATATTTAA
1 GCCAAATTTAAGAG-AT-AACTAAATATTTAA
41696 AATTAAGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 1 0.04
30 4 0.15
31 21 0.81
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (31 bp):
GCCAAATTTAAGAGATAACTAAATATTTAAG
Found at i:41923 original size:2 final size:2
Alignment explanation
Indices: 41916--41967 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
41906 CTTGGTTCGA
41916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41958 AT AT AT AT AT
1 AT AT AT AT AT
41968 TAATTTTTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42126 original size:25 final size:26
Alignment explanation
Indices: 42074--42127 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
42064 TATATTTTTT
*
42074 TAATTTTAAAAAAATAGAAAACACAA
1 TAATTTTAAAAAAATAAAAAACACAA
*
42100 TAATTTT-TAAAAATAAAAATACA-AA
1 TAATTTTAAAAAAATAAAAA-ACACAA
42125 TAA
1 TAA
42128 AGACATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.28
Consensus pattern (26 bp):
TAATTTTAAAAAAATAAAAAACACAA
Found at i:42446 original size:3 final size:3
Alignment explanation
Indices: 42440--42481 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
42430 AAAAAAATAA
*
42440 TAT TAT TAAT TAA TAT TAAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT T-AT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT T
42482 TCATTTACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:44895 original size:35 final size:35
Alignment explanation
Indices: 44792--44910 Score: 138
Period size: 35 Copynumber: 3.5 Consensus size: 35
44782 TAGTCTATAA
** * *
44792 TCGCTTGAGACCGTCTCTCTCAAAACAAATCTCGTC
1 TCGCTTGAGACAATTTCTCTC-AAACAAATTTCGTC
* *
44828 TCGCTTGAGAC-ATTT-T-TC-CACAAATTTTGTC
1 TCGCTTGAGACAATTTCTCTCAAACAAATTTCGTC
44859 TCGCTTGAGACAATTTCTCTCAAACAAATTTCGTC
1 TCGCTTGAGACAATTTCTCTCAAACAAATTTCGTC
*
44894 TCGCTTGAGACAGTTTC
1 TCGCTTGAGACAATTTC
44911 CTTCGGAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
31 21 0.30
32 4 0.06
33 3 0.04
34 3 0.04
35 29 0.41
36 11 0.15
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.34
Consensus pattern (35 bp):
TCGCTTGAGACAATTTCTCTCAAACAAATTTCGTC
Found at i:45470 original size:131 final size:131
Alignment explanation
Indices: 45233--45572 Score: 423
Period size: 131 Copynumber: 2.6 Consensus size: 131
45223 TTGAAACATT
* * * * * *
45233 ATCCCTAAAGATGGCCAGACGTCTTCATCGCGTAGGAACCATGTCATTCCCCGACCAGACCTCCT
1 ATCCCTAAAGATGGCAAGTCGTCATCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCT
* *
45298 CATAACATAGGAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGAAA-CTGTGTTA
66 CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGAAATC-GTGTTA
45362 TC
130 TC
** * * *
45364 ATCCCTAAAGATGGCTTGTCGTCCTAATCACGTAGAAACCGTGTCATCCCCCGACCAGACCTCCT
1 ATCCCTAAAGATGGCAAGTCGTCATCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCT
* * * *
45429 CATCACGTAGGAGCCGTGTCACTCCTAGATAATCAGTCGTCCTCATCACGTAGGAATCGTGTTAT
66 CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGAAATCGTGTTAT
45494 C
131 C
* * * * * * *
45495 CTCCCTAAAGATGGACAAGAT-GTCATCATCATGTAGGAACAGTATCATCCACTGACCAGATCTC
1 ATCCCTAAAGATGG-CAAG-TCGTCATCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTC
45559 CTCATCACGTAGGA
64 CTCATCACGTAGGA
45573 CCTGTGCTAT
Statistics
Matches: 179, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
131 127 0.71
132 51 0.28
133 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGGCAAGTCGTCATCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCT
CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGAAATCGTGTTAT
C
Found at i:52988 original size:54 final size:52
Alignment explanation
Indices: 52902--53015 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 52
52892 AACTTTTGAT
* * * * *
52902 TTTTACTATTTAGCCCTTTAAGTTTCTGTTTTTGCCATTTTATTCCTTTAAAA
1 TTTTATTATTTAGCCCTTTAAGATTCTATTTTTGCCATTTTAGTCCCTT-AAA
* *
52955 TTTTATTATGTTAGTCCTTTAAGATTCTATTTTTGCTATTTTAGTCCCTTAAA
1 TTTTATTAT-TTAGCCCTTTAAGATTCTATTTTTGCCATTTTAGTCCCTTAAA
53008 TTTATATT
1 TTT-TATT
53016 TTTTTTCTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 14 0.27
54 38 0.73
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (52 bp):
TTTTATTATTTAGCCCTTTAAGATTCTATTTTTGCCATTTTAGTCCCTTAAA
Found at i:52999 original size:30 final size:29
Alignment explanation
Indices: 52826--53070 Score: 114
Period size: 30 Copynumber: 8.4 Consensus size: 29
52816 TTTATGATTC
* * *
52826 AGTCCTTTAAATTTTTTTTTTGTTATTTT
1 AGTCCTTTAAATTCTATTTTTGCTATTTT
* * *
52855 AGTCTTTTAAATGTCTGTATTTGCTA-TTT
1 AGTCCTTTAAAT-TCTATTTTTGCTATTTT
* * *
52884 AGATCC-TTAACTTTTGATTTTTACTA-TTT
1 AG-TCCTTTAAATTCT-ATTTTTGCTATTTT
* * * *
52913 AGCCCTTTAAGTTTCTGTTTTTGCCATTTT
1 AGTCCTTTAA-ATTCTATTTTTGCTATTTT
* *
52943 ATTCCTTTAAA----ATTTTAT--TATGTT
1 AGTCCTTTAAATTCTATTTT-TGCTATTTT
52967 AGTCCTTTAAGATTCTATTTTTGCTATTTT
1 AGTCCTTTAA-ATTCTATTTTTGCTATTTT
* * *
52997 AGTCCCTTAAATTTATATTTTTTTTCTATTTT
1 AGTCCTTTAAA-TTCTA--TTTTTGCTATTTT
* * * *
53029 AGCCCTTTAAGTT-TATGTTTTCACTATTTA
1 AGTCCTTTAAATTCTAT-TTTT-GCTATTTT
*
53059 AGTCATTTAAAT
1 AGTCCTTTAAAT
53071 CGAATATGAT
Statistics
Matches: 161, Mismatches: 36, Indels: 37
0.69 0.15 0.16
Matches are distributed among these distances:
24 13 0.08
25 5 0.03
26 1 0.01
28 6 0.04
29 54 0.34
30 60 0.37
31 2 0.01
32 20 0.12
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.57
Consensus pattern (29 bp):
AGTCCTTTAAATTCTATTTTTGCTATTTT
Found at i:53035 original size:31 final size:33
Alignment explanation
Indices: 52984--53049 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
52974 TAAGATTCTA
52984 TTTTTGCTATTTTAGTCCC-TTAAATTTATATT
1 TTTTTGCTATTTTAGTCCCTTTAAATTTATATT
* * *
53016 TTTTTTCTATTTTAG-CCCTTTAAGTTTATGTT
1 TTTTTGCTATTTTAGTCCCTTTAAATTTATATT
53048 TT
1 TT
53050 CACTATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.18, C:0.12, G:0.08, T:0.62
Consensus pattern (33 bp):
TTTTTGCTATTTTAGTCCCTTTAAATTTATATT
Found at i:61621 original size:24 final size:24
Alignment explanation
Indices: 61594--61681 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 24
61584 GATATCAGAA
*
61594 ATCAAAACATAATTCAGATTAGAT
1 ATCAAAACAGAATTCAGATTAGAT
* * * *
61618 ATCAGAACAGAATCCGGGTTAGGA-
1 ATCAAAACAGAATTCAGATTA-GAT
* * *
61642 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATTAGAT
* *
61666 GTCAAAACATAATTCA
1 ATCAAAACAGAATTCA
61682 AATCAGAAAT
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
23 2 0.04
24 44 0.92
25 2 0.04
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATTAGAT
Found at i:62855 original size:18 final size:18
Alignment explanation
Indices: 62828--62863 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
62818 CGATCTTATT
62828 ATTTAATTCAGTCATTTC
1 ATTTAATTCAGTCATTTC
* *
62846 ATTTACTTCAGTCCTTTC
1 ATTTAATTCAGTCATTTC
62864 GAACAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTAATTCAGTCATTTC
Found at i:64180 original size:17 final size:17
Alignment explanation
Indices: 64158--64197 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
64148 GGTCAACAGT
64158 GGTCAACTCCGGTCAAC
1 GGTCAACTCCGGTCAAC
64175 GGTCAACTCCGGTCAAC
1 GGTCAACTCCGGTCAAC
64192 GGTCAA
1 GGTCAA
64198 TGGGTCAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (17 bp):
GGTCAACTCCGGTCAAC
Found at i:64205 original size:15 final size:15
Alignment explanation
Indices: 64168--64218 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
64158 GGTCAACTCC
*
64168 GGTCAACGGTCAACTCC
1 GGTCAACGGTCAA-T-G
64185 GGTCAACGGTCAATG
1 GGTCAACGGTCAATG
* *
64200 GGTCAATGGTCAACG
1 GGTCAACGGTCAATG
64215 GGTC
1 GGTC
64219 GGGTCAACGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 17 0.55
16 1 0.03
17 13 0.42
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.20
Consensus pattern (15 bp):
GGTCAACGGTCAATG
Found at i:64236 original size:18 final size:18
Alignment explanation
Indices: 64213--64249 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
64203 CAATGGTCAA
64213 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
64231 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
64249 C
1 C
64250 AACGAGTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.24, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:64249 original size:13 final size:13
Alignment explanation
Indices: 64207--64236 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
64197 ATGGGTCAAT
64207 GGTCAACGGGTCG
1 GGTCAACGGGTCG
64220 GGTCAACGGGTCG
1 GGTCAACGGGTCG
64233 GGTC
1 GGTC
64237 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:68005 original size:16 final size:16
Alignment explanation
Indices: 67984--68014 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
67974 ATACAGAGCC
67984 TTTGAATCATTCAGCA
1 TTTGAATCATTCAGCA
68000 TTTGAATCATTCAGC
1 TTTGAATCATTCAGC
68015 GCTTAATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (16 bp):
TTTGAATCATTCAGCA
Found at i:68024 original size:15 final size:16
Alignment explanation
Indices: 67985--68026 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
67975 TACAGAGCCT
*
67985 TTGAATCATTCAGCAT
1 TTGAATCATTCAGCAC
*
68001 TTGAATCATTCAGCGC
1 TTGAATCATTCAGCAC
68017 TT-AATCATTC
1 TTGAATCATTC
68027 TGAAGTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (16 bp):
TTGAATCATTCAGCAC
Found at i:72480 original size:17 final size:17
Alignment explanation
Indices: 72458--72496 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
72448 GTTTTGAAAA
*
72458 TAATTTTGAAAACAATG
1 TAATTTTCAAAACAATG
72475 TAATTTTCAAAACAATG
1 TAATTTTCAAAACAATG
72492 TAATT
1 TAATT
72497 AAATCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (17 bp):
TAATTTTCAAAACAATG
Found at i:75578 original size:28 final size:28
Alignment explanation
Indices: 75546--75604 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
75536 GGGTGCATCG
* *
75546 ATACACTAATTACATTCGATGTTTCAAA
1 ATACACAAAATACATTCGATGTTTCAAA
* *
75574 ATACACAAAATGCATTTGATGTTTCAAA
1 ATACACAAAATACATTCGATGTTTCAAA
75602 ATA
1 ATA
75605 TTCAAGAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (28 bp):
ATACACAAAATACATTCGATGTTTCAAA
Found at i:75964 original size:21 final size:21
Alignment explanation
Indices: 75938--76002 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
75928 ACATCAACAA
75938 ATTTAAAACTTAAAAATTTTT
1 ATTTAAAACTTAAAAATTTTT
* *
75959 ATTTAAAACTTAGAACATTTTC
1 ATTTAAAACTTA-AAAATTTTT
* * *
75981 ACTTTCAAACTTCAATATTTTT
1 A-TTTAAAACTTAAAAATTTTT
76003 TTAAAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 12 0.33
22 15 0.42
23 9 0.25
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTTAAAACTTAAAAATTTTT
Found at i:78797 original size:41 final size:41
Alignment explanation
Indices: 78739--78908 Score: 146
Period size: 41 Copynumber: 4.1 Consensus size: 41
78729 AGGGAGGAGT
* *
78739 CACTGATAATCTAAAGTGAAATTCA-CTCGAAATGATGAATC
1 CACTAATATTCTAAAGTGAAATTCATCTCG-AATGATGAATC
* *
78780 CACTAATATT-TCAAAGTGAAATTCATCTCGAATGGTGAATT
1 CACTAATATTCT-AAAGTGAAATTCATCTCGAATGATGAATC
* * * *
78821 CATTTATATTCTAAAGTGAAATTCATCCCGAATGGTGAATC
1 CACTAATATTCTAAAGTGAAATTCATCTCGAATGATGAATC
** * * * * * * * *
78862 TGCTGATAATCTGAAGTAAAATTCATCCCGAAGGGTGAATA
1 CACTAATATTCTAAAGTGAAATTCATCTCGAATGATGAATC
78903 CACTAA
1 CACTAA
78909 ACTTCCCATA
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
40 1 0.01
41 100 0.94
42 5 0.05
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (41 bp):
CACTAATATTCTAAAGTGAAATTCATCTCGAATGATGAATC
Done.