Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 76 of 125
Found at i:23724713 original size:13 final size:13
Alignment explanation
Indices: 23724697--23724726 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23724687 ATCTAGAAAT
*
23724697 TTTAATATTATAA
1 TTTAATATAATAA
23724710 TTTAATATAATAA
1 TTTAATATAATAA
23724723 TTTA
1 TTTA
23724727 GTAACATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTAATATAATAA
Found at i:23729324 original size:21 final size:21
Alignment explanation
Indices: 23729300--23729341 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
23729290 CCTGCAACTT
23729300 CTACCGATATATGCATACAAA
1 CTACCGATATATGCATACAAA
23729321 CTACCGATATATGCATACAAA
1 CTACCGATATATGCATACAAA
23729342 TTATCATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
CTACCGATATATGCATACAAA
Found at i:23731130 original size:53 final size:53
Alignment explanation
Indices: 23731050--23731153 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
23731040 TATAGTAAAA
*
23731050 TTAATATAAACCATACCAATCCACTAACTAATACTCCTTCGGTTAATTTACAC
1 TTAATATAAACCATACCAATCCACTAACTAAAACTCCTTCGGTTAATTTACAC
23731103 TTAATATAAACCATACCAATCCACTAACTAAAACTCCTTCGGTTAATTTAC
1 TTAATATAAACCATACCAATCCACTAACTAAAACTCCTTCGGTTAATTTAC
23731154 TCATTTGGTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (53 bp):
TTAATATAAACCATACCAATCCACTAACTAAAACTCCTTCGGTTAATTTACAC
Found at i:23737082 original size:27 final size:27
Alignment explanation
Indices: 23737022--23737082 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
23737012 ATCTCGATGA
* *
23737022 ACTACCCCATGTTTAACGTCCCATCGG
1 ACTATCCCATGTTTAACGTCCCATCAG
*
23737049 ACGATCCCATGTTTAACGT-CCAGTCAG
1 ACTATCCCATGTTTAACGTCCCA-TCAG
23737076 ACTATCC
1 ACTATCC
23737083 ATTATACCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (27 bp):
ACTATCCCATGTTTAACGTCCCATCAG
Found at i:23737280 original size:45 final size:45
Alignment explanation
Indices: 23737227--23737394 Score: 183
Period size: 45 Copynumber: 3.7 Consensus size: 45
23737217 ACTTCCGAAG
* * * *
23737227 GATGTCATAGCGTCTTTCAGCCATGGTCTTACTCACTTCCGTCAT
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCACTTACATCAT
* * *
23737272 GATGTCATAGCATCTTTTAGCTATGGTCTTACTCATTTATATCAT
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCACTTACATCAT
** * * ** *
23737317 GAAATCATAACATCTTTCAGCTATGGTCTTACTCATTTTTATCCT
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCACTTACATCAT
* * *
23737362 GATGTCATAGCATTTTTCAACTATGATCTTACT
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACT
23737395 TATTTACAAG
Statistics
Matches: 104, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 104 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (45 bp):
GATGTCATAGCATCTTTCAGCTATGGTCTTACTCACTTACATCAT
Found at i:23741030 original size:31 final size:31
Alignment explanation
Indices: 23740994--23741071 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
23740984 ATTATAAAAA
23740994 TAGTCACTTTTGTTTGCCTCAGATTATATTT
1 TAGTCACTTTTGTTTGCCTCAGATTATATTT
*
23741025 TAGTCACTTTTATTTGCCTCAGATTATATTT
1 TAGTCACTTTTGTTTGCCTCAGATTATATTT
* *
23741056 TAGTTACTTATGTTTG
1 TAGTCACTTTTGTTTG
23741072 AAATGTTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.21, C:0.14, G:0.13, T:0.53
Consensus pattern (31 bp):
TAGTCACTTTTGTTTGCCTCAGATTATATTT
Found at i:23742657 original size:20 final size:20
Alignment explanation
Indices: 23742629--23742674 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
23742619 TGCAGCGAAA
* *
23742629 TTATGTTCTGTCTGATAAGT
1 TTATTTTCTGTCGGATAAGT
23742649 TTATTTTCTGTCGGATAAGT
1 TTATTTTCTGTCGGATAAGT
23742669 TTATTT
1 TTATTT
23742675 ACTTTGGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (20 bp):
TTATTTTCTGTCGGATAAGT
Found at i:23751074 original size:56 final size:56
Alignment explanation
Indices: 23750984--23751096 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
23750974 TCTATGATAA
* * *
23750984 ATGGTTCTCAATTGTCCATAACTTAATGCTAAGCAATCAACTTTCACTAGTAAGAC
1 ATGGTTCTCAATTATCCATAACTTAATACCAAGCAATCAACTTTCACTAGTAAGAC
* * *
23751040 ATGGTTCTCAATTATCCATAACTTAATACCAAGCAATCGATTTTCACTAGTCAGAC
1 ATGGTTCTCAATTATCCATAACTTAATACCAAGCAATCAACTTTCACTAGTAAGAC
23751096 A
1 A
23751097 CAGGAGAACA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (56 bp):
ATGGTTCTCAATTATCCATAACTTAATACCAAGCAATCAACTTTCACTAGTAAGAC
Found at i:23752558 original size:16 final size:15
Alignment explanation
Indices: 23752532--23752564 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
23752522 AAATTATCGT
23752532 TAAAAAAATAAATAA
1 TAAAAAAATAAATAA
23752547 TAAAATAAATAAATAA
1 TAAAA-AAATAAATAA
23752563 TA
1 TA
23752565 CATTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAAAATAAATAA
Found at i:23752583 original size:21 final size:20
Alignment explanation
Indices: 23752552--23752604 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
23752542 AATAATAAAA
23752552 TAAATAAATAATACATTAATTT
1 TAAA-AAATAAT-CATTAATTT
*
23752574 TAAAAAATAATCTTTAATTT
1 TAAAAAATAATCATTAATTT
*
23752594 AAAGAAAATAA
1 TAA-AAAATAA
23752605 ATGTAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.36
21 14 0.50
22 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAAAATAATCATTAATTT
Found at i:23762978 original size:27 final size:25
Alignment explanation
Indices: 23762941--23762991 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
23762931 ATGTTTAAGT
23762941 TATTTTATATTCATAT-AAATTTTAA
1 TATTTTATATT-ATATAAAATTTTAA
*
23762966 TATTTTATTTATTATTTAAAATTTTA
1 TATTTTA--TATTATATAAAATTTTA
23762992 GACATTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.32
26 3 0.14
27 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTTTATATTATATAAAATTTTAA
Found at i:23763947 original size:20 final size:21
Alignment explanation
Indices: 23763922--23764009 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 21
23763912 GGAGTAGAGA
23763922 TATCGATAC-CTG-GTAAAAGG
1 TATCGATACTCTGTG-AAAAGG
*
23763942 TATCGATACTCTTTGAAAAGG
1 TATCGATACTCTGTGAAAAGG
* * *
23763963 TATCGATACTTTTTATAAAAGG
1 TATCGATACTCTGT-GAAAAGG
* * *
23763985 TATCGATACTTTTTGAAAATG
1 TATCGATACTCTGTGAAAAGG
23764006 TATC
1 TATC
23764010 AATATTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.15
21 30 0.50
22 21 0.35
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
TATCGATACTCTGTGAAAAGG
Found at i:23763962 original size:21 final size:21
Alignment explanation
Indices: 23763936--23764020 Score: 116
Period size: 21 Copynumber: 4.0 Consensus size: 21
23763926 GATACCTGGT
*
23763936 AAAAGGTATCGATACTCTTTG
1 AAAAGGTATCGATACTTTTTG
*
23763957 AAAAGGTATCGATACTTTTTAT
1 AAAAGGTATCGATACTTTTT-G
23763979 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
* * *
23764000 AAAATGTATCAATATTTTTTG
1 AAAAGGTATCGATACTTTTTG
23764021 TCATTATTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 37 0.65
22 20 0.35
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.40
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:23763986 original size:43 final size:43
Alignment explanation
Indices: 23763935--23764019 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
23763925 CGATACCTGG
*
23763935 TAAAAGGTATCGATACTCTTTGAAAAGGTATCGATACTTTTTA
1 TAAAAGGTATCGATACTCTTTGAAAAGGTATCAATACTTTTTA
* * *
23763978 TAAAAGGTATCGATACTTTTTGAAAATGTATCAATATTTTTT
1 TAAAAGGTATCGATACTCTTTGAAAAGGTATCAATACTTTTT
23764020 GTCATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.41
Consensus pattern (43 bp):
TAAAAGGTATCGATACTCTTTGAAAAGGTATCAATACTTTTTA
Found at i:23773454 original size:29 final size:29
Alignment explanation
Indices: 23773421--23773483 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
23773411 ATAGGTTCGT
* *
23773421 ACATAGGGGTTCACATACCTAGGATTCAC
1 ACATAAGGGTTCACACACCTAGGATTCAC
*
23773450 ACATAAGGGTTCACACACCTAGGGTTCAC
1 ACATAAGGGTTCACACACCTAGGATTCAC
*
23773479 TCATA
1 ACATA
23773484 CAGTTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (29 bp):
ACATAAGGGTTCACACACCTAGGATTCAC
Found at i:23773475 original size:15 final size:15
Alignment explanation
Indices: 23773427--23773478 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
23773417 TCGTACATAG
*
23773427 GGGTTCACATACCTA
1 GGGTTCACACACCTA
*
23773442 GGATTCACACA--TAA
1 GGGTTCACACACCT-A
23773456 GGGTTCACACACCTA
1 GGGTTCACACACCTA
23773471 GGGTTCAC
1 GGGTTCAC
23773479 TCATACAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 11 0.35
15 18 0.58
16 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (15 bp):
GGGTTCACACACCTA
Found at i:23785509 original size:18 final size:18
Alignment explanation
Indices: 23785483--23785529 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
23785473 ACGAAAACAC
*
23785483 AAGCGCAAGGATAAGAAG
1 AAGCACAAGGATAAGAAG
23785501 AAGCACAAGGATAAGAAG
1 AAGCACAAGGATAAGAAG
23785519 AAGCACAAGGA
1 AAGCACAAGGA
23785530 GGAGTGCCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.53, C:0.13, G:0.30, T:0.04
Consensus pattern (18 bp):
AAGCACAAGGATAAGAAG
Found at i:23786303 original size:17 final size:18
Alignment explanation
Indices: 23786276--23786314 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
23786266 AGTCGAATAA
23786276 AAAAAGAGAAAA-AGAAAG
1 AAAAAGAGAAAAGA-AAAG
23786294 AAAAAG-GAAAAGAAAAG
1 AAAAAGAGAAAAGAAAAG
23786311 AAAA
1 AAAA
23786315 GAAATTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAAGAGAAAAGAAAAG
Found at i:23787104 original size:6 final size:6
Alignment explanation
Indices: 23787095--23787130 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
23787085 AATACTGATG
*
23787095 GAAAAA GAAA-A GAAAGA GAAAGA GAAAGA GAAAGA G
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA G
23787131 GAGGGAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:23787128 original size:18 final size:17
Alignment explanation
Indices: 23787095--23787130 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
23787085 AATACTGATG
23787095 GAAAAAGAAAAGAAAGA
1 GAAAAAGAAAAGAAAGA
*
23787112 GAAAGAGAAAGAGAAAGA
1 GAAAAAGAAA-AGAAAGA
23787130 G
1 G
23787131 GAGGGAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAAAGAAAGA
Found at i:23791639 original size:16 final size:16
Alignment explanation
Indices: 23791618--23791662 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
23791608 GCAAAAATGA
*
23791618 ATGAATGCATGTAAGC
1 ATGAATGCAAGTAAGC
23791634 ATGAATGCAAGTAAGC
1 ATGAATGCAAGTAAGC
23791650 ATGAATGCAAGTA
1 ATGAATGCAAGTA
23791663 TTGCCACGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
ATGAATGCAAGTAAGC
Found at i:23792151 original size:3 final size:3
Alignment explanation
Indices: 23792145--23792179 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
23792135 CTTTTTCTGC
23792145 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23792180 TAAACACTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:23793137 original size:17 final size:18
Alignment explanation
Indices: 23793115--23793156 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
23793105 TATATATTTA
23793115 TTAATTTTATTA-TTATT
1 TTAATTTTATTATTTATT
*
23793132 TTAATTAT-TTATTTATT
1 TTAATTTTATTATTTATT
23793149 TT-ATTTTA
1 TTAATTTTA
23793157 ATTCTTATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTAATTTTATTATTTATT
Found at i:23799142 original size:12 final size:12
Alignment explanation
Indices: 23799104--23799168 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
23799094 CCATTAACTT
23799104 TGTTCGTGAACA
1 TGTTCGTGAACA
* *
23799116 TGTTCAGT-TATA
1 TGTTC-GTGAACA
*
23799128 TGTTCATGAACA
1 TGTTCGTGAACA
**
23799140 TGTTCGTTTA-A
1 TGTTCGTGAACA
23799151 TGTTCGTGAACA
1 TGTTCGTGAACA
23799163 TGTTCG
1 TGTTCG
23799169 ATTAAGTTAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
11 10 0.25
12 28 0.70
13 2 0.05
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.42
Consensus pattern (12 bp):
TGTTCGTGAACA
Found at i:23799160 original size:23 final size:22
Alignment explanation
Indices: 23799104--23799173 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 22
23799094 CCATTAACTT
23799104 TGTTCGTGAACATGTTCAGTTATA
1 TGTTCGTGAACATGTTC-GTTA-A
*
23799128 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCG-TTAA
23799151 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCG-TTAA
23799174 GTTAAATGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 23 0.55
24 19 0.45
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (22 bp):
TGTTCGTGAACATGTTCGTTAA
Found at i:23799183 original size:23 final size:23
Alignment explanation
Indices: 23799110--23799191 Score: 78
Period size: 23 Copynumber: 3.5 Consensus size: 23
23799100 ACTTTGTTCG
*
23799110 TGAACATGTTC-AGTTATATGTTCA
1 TGAACATGTTCGA-TTA-ATGTTAA
* **
23799134 TGAACATGTTCGTTTAATGTTCG
1 TGAACATGTTCGATTAATGTTAA
23799157 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT-AA
*
23799180 TGAACATATTCG
1 TGAACATGTTCG
23799192 TGAATATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
22 3 0.06
23 33 0.66
24 14 0.28
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTAA
Found at i:23800238 original size:32 final size:32
Alignment explanation
Indices: 23800176--23800238 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
23800166 AGTTACTTTA
* * * *
23800176 TTTTTATTTTTAGAGATTTAATTTCTTTATTT
1 TTTTTAATTTTAGAAATTTAAATTCATTATTT
23800208 TTTTTAATTTTA-AAATTTAAATTCAATTATT
1 TTTTTAATTTTAGAAATTTAAATTC-ATTATT
23800239 AATATCTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (32 bp):
TTTTTAATTTTAGAAATTTAAATTCATTATTT
Found at i:23809468 original size:28 final size:28
Alignment explanation
Indices: 23809434--23809519 Score: 145
Period size: 28 Copynumber: 3.1 Consensus size: 28
23809424 CACATAGGTG
23809434 TTCCTTTAACAAAGATAGCCACAAAGGC
1 TTCCTTTAACAAAGATAGCCACAAAGGC
*
23809462 TTCCTTTAATAAAGATAGCCACAAAGGC
1 TTCCTTTAACAAAGATAGCCACAAAGGC
* *
23809490 TTCCTTTAACAAAGATAGCTATAAAGGC
1 TTCCTTTAACAAAGATAGCCACAAAGGC
23809518 TT
1 TT
23809520 TCCTAGTTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (28 bp):
TTCCTTTAACAAAGATAGCCACAAAGGC
Found at i:23827491 original size:28 final size:28
Alignment explanation
Indices: 23827451--23827612 Score: 191
Period size: 28 Copynumber: 5.8 Consensus size: 28
23827441 AAGGTATTCT
*
23827451 TTTAACAA-AGATACCCACAAAGGCTTCC
1 TTTAA-AAGAGATAACCACAAAGGCTTCC
**
23827479 TTTAAAAGAGATAACCACAAAGTTTTCC
1 TTTAAAAGAGATAACCACAAAGGCTTCC
* * * *
23827507 TTTAAAAGAGATCATCTCAAAGGCTTTC
1 TTTAAAAGAGATAACCACAAAGGCTTCC
*
23827535 TTTAACAGAGATAACCACAAAGGCTTCC
1 TTTAAAAGAGATAACCACAAAGGCTTCC
* * *
23827563 TTTAATAGAGATAGCCATAAAGGCTTCC
1 TTTAAAAGAGATAACCACAAAGGCTTCC
* *
23827591 TTTAATAGAGATAGCCACAAAG
1 TTTAAAAGAGATAACCACAAAG
23827613 TTTTTCCTTA
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
27 2 0.02
28 113 0.98
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (28 bp):
TTTAAAAGAGATAACCACAAAGGCTTCC
Found at i:23827612 original size:84 final size:84
Alignment explanation
Indices: 23827451--23827612 Score: 218
Period size: 84 Copynumber: 1.9 Consensus size: 84
23827441 AAGGTATTCT
* **
23827451 TTTAACAAAGATACCCACAAAGGCTTCCTTTAAAAGAGATAACCACAAAGTTTTCCTTTAAAAGA
1 TTTAACAAAGATAACCACAAAGGCTTCCTTTAAAAGAGATAACCACAAAGGCTTCCTTTAAAAGA
* *
23827516 GATCATCTCAAAGGCTTTC
66 GATCACCACAAAGGCTTTC
* * * * *
23827535 TTTAACAGAGATAACCACAAAGGCTTCCTTTAATAGAGATAGCCATAAAGGCTTCCTTTAATAGA
1 TTTAACAAAGATAACCACAAAGGCTTCCTTTAAAAGAGATAACCACAAAGGCTTCCTTTAAAAGA
23827600 GAT-AGCCACAAAG
66 GATCA-CCACAAAG
23827613 TTTTTCCTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
83 1 0.01
84 66 0.99
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (84 bp):
TTTAACAAAGATAACCACAAAGGCTTCCTTTAAAAGAGATAACCACAAAGGCTTCCTTTAAAAGA
GATCACCACAAAGGCTTTC
Found at i:23836034 original size:18 final size:17
Alignment explanation
Indices: 23836003--23836036 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23835993 TGTTTAGCAT
*
23836003 TTTTTTATTTAAAAATA
1 TTTTTTATTCAAAAATA
23836020 TTTTTTATGTCAAAAAT
1 TTTTTTAT-TCAAAAAT
23836037 GCTTCTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTTTATTCAAAAATA
Found at i:23836583 original size:16 final size:16
Alignment explanation
Indices: 23836558--23836609 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
23836548 AAAAATTATG
23836558 TTTTTCAT-CCTTCTAA
1 TTTTTCATCCCTTC-AA
*
23836574 TTTTTTATCCCTTCAA
1 TTTTTCATCCCTTCAA
* * *
23836590 TTTGTCTTCCTTTCAA
1 TTTTTCATCCCTTCAA
23836606 TTTT
1 TTTT
23836610 CTTTCCTCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 24 0.83
17 5 0.17
ACGTcount: A:0.15, C:0.23, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTTCATCCCTTCAA
Found at i:23836615 original size:16 final size:16
Alignment explanation
Indices: 23836572--23836621 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
23836562 TCATCCTTCT
*
23836572 AATTTT-TTATCCCTTC
1 AATTTTCTT-TCCTTTC
23836588 AATTTGTC-TTCCTTTC
1 AATTT-TCTTTCCTTTC
*
23836604 AATTTTCTTTCCTCTC
1 AATTTTCTTTCCTTTC
23836620 AA
1 AA
23836622 CCAAGCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.18, C:0.26, G:0.02, T:0.54
Consensus pattern (16 bp):
AATTTTCTTTCCTTTC
Found at i:23838669 original size:27 final size:27
Alignment explanation
Indices: 23838631--23838755 Score: 132
Period size: 27 Copynumber: 4.8 Consensus size: 27
23838621 TCTTACTCTA
*
23838631 GCTCGAAAGAGCGTTATTTTGATTCTG
1 GCTCGAAAGAGCGTTATTCTGATTCTG
* *
23838658 GCTCGAATGAGCATTATTCTGATTCTG
1 GCTCGAAAGAGCGTTATTCTGATTCTG
* *
23838685 GCTCGAAGGAGCGTTATTCTG--TCTA
1 GCTCGAAAGAGCGTTATTCTGATTCTG
* **
23838710 GCTCGTAAGAGCAATATTCT-A-TCTG
1 GCTCGAAAGAGCGTTATTCTGATTCTG
* *
23838735 GCTCGTAAGAGCGATATTCTG
1 GCTCGAAAGAGCGTTATTCTG
23838756 TTTGGTTCAT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
25 41 0.49
27 43 0.51
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (27 bp):
GCTCGAAAGAGCGTTATTCTGATTCTG
Found at i:23838721 original size:25 final size:25
Alignment explanation
Indices: 23838631--23838862 Score: 155
Period size: 25 Copynumber: 9.0 Consensus size: 25
23838621 TCTTACTCTA
* * *
23838631 GCTCGAAAGAGCGTTATTTTGATTCTG
1 GCTCGTAAGAGCGATATTCTG--TCTG
23838658 GCTCG-AATGAGC-ATTATTCTGATTCTG
1 GCTCGTAA-GAGCGA-TATTCTG--TCTG
* *
23838685 GCTCG-AAGGAGCGTTATTCTGTCTA
1 GCTCGTAA-GAGCGATATTCTGTCTG
* *
23838710 GCTCGTAAGAGCAATATTCTATCTG
1 GCTCGTAAGAGCGATATTCTGTCTG
*
23838735 GCTCGTAAGAGCGATATTCTGTTTG
1 GCTCGTAAGAGCGATATTCTGTCTG
* * * * *
23838760 GTTCATAAGAGTGATATTCTGACTA
1 GCTCGTAAGAGCGATATTCTGTCTG
*
23838785 GCTCGTAAGAGTGATATTCTGTCTGG
1 GCTCGTAAGAGCGATATTCTGTCT-G
* ** * *
23838811 GCTTGTAAGAGTTAAACTCTGTCTAG
1 GCTCGTAAGAGCGATATTCTGTCT-G
* * * *
23838837 GCTTGTAAGAGCTAAACTCTGTCTG
1 GCTCGTAAGAGCGATATTCTGTCTG
23838862 G
1 G
23838863 GCTCATATGA
Statistics
Matches: 172, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
25 85 0.49
26 48 0.28
27 39 0.23
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (25 bp):
GCTCGTAAGAGCGATATTCTGTCTG
Found at i:23838753 original size:50 final size:51
Alignment explanation
Indices: 23838631--23838821 Score: 174
Period size: 50 Copynumber: 3.7 Consensus size: 51
23838621 TCTTACTCTA
* * * *
23838631 GCTCGAAAGAGCGTTATTTTGATTCTGGCTCG-AATGAGCATTATTCTGATTCTG
1 GCTCGTAAGAGCGATATTCTG--TCTGGCTCGTAA-GAGCAATATTCTGA-TCTG
* *
23838685 GCTCG-AAGGAGCGTTATTCTGTCTAGCTCGTAAGAGCAATATTCT-ATCTG
1 GCTCGTAA-GAGCGATATTCTGTCTGGCTCGTAAGAGCAATATTCTGATCTG
* * * ** *
23838735 GCTCGTAAGAGCGATATTCTGTTTGGTTCATAAGAGTGATATTCTGA-CTA
1 GCTCGTAAGAGCGATATTCTGTCTGGCTCGTAAGAGCAATATTCTGATCTG
* *
23838785 GCTCGTAAGAGTGATATTCTGTCTGGGCTTGTAAGAG
1 GCTCGTAAGAGCGATATTCTGTCT-GGCTCGTAAGAG
23838822 TTAAACTCTG
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
50 63 0.54
51 13 0.11
52 19 0.16
53 4 0.03
54 17 0.15
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (51 bp):
GCTCGTAAGAGCGATATTCTGTCTGGCTCGTAAGAGCAATATTCTGATCTG
Found at i:23838878 original size:26 final size:26
Alignment explanation
Indices: 23838802--23838865 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
23838792 AGAGTGATAT
*
23838802 TCTGTCTGGGCTTGTAAGAGTTAAAC
1 TCTGTCTGGGCTTGTAAGAGCTAAAC
*
23838828 TCTGTCTAGGCTTGTAAGAGCTAAAC
1 TCTGTCTGGGCTTGTAAGAGCTAAAC
23838854 TCTGTCTGGGCT
1 TCTGTCTGGGCT
23838866 CATATGAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (26 bp):
TCTGTCTGGGCTTGTAAGAGCTAAAC
Found at i:23840415 original size:21 final size:21
Alignment explanation
Indices: 23840390--23840438 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
23840380 AGTCAAACAT
23840390 TTTCAAATATGTTTTAACCAA
1 TTTCAAATATGTTTTAACCAA
23840411 TTTCAAATATGTTTTAACCAA
1 TTTCAAATATGTTTTAACCAA
23840432 TTTCAAA
1 TTTCAAA
23840439 CAAGTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (21 bp):
TTTCAAATATGTTTTAACCAA
Found at i:23848239 original size:15 final size:15
Alignment explanation
Indices: 23848221--23848292 Score: 76
Period size: 15 Copynumber: 4.8 Consensus size: 15
23848211 AAGTTGCTAG
23848221 CACTCATGTTGCGAA
1 CACTCATGTTGCGAA
*
23848236 CACT-AGAGTTGCGAA
1 CACTCA-TGTTGCGAA
*
23848251 CACT-AGAGTTGCGAA
1 CACTCA-TGTTGCGAA
*
23848266 CACTCATGATGCGAA
1 CACTCATGTTGCGAA
*
23848281 CACTCATTTTGC
1 CACTCATGTTGC
23848293 AGACACACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
14 1 0.02
15 48 0.96
16 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (15 bp):
CACTCATGTTGCGAA
Found at i:23854706 original size:15 final size:15
Alignment explanation
Indices: 23854688--23854754 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 15
23854678 GAACACTGGC
23854688 GTTGCGAACACTCAT
1 GTTGCGAACACTCAT
* * *
23854703 GTTGCGGACACACAC
1 GTTGCGAACACTCAT
** * *
23854718 AATGCGAGCACTGAT
1 GTTGCGAACACTCAT
* *
23854733 GTTGCGAGCACTCGT
1 GTTGCGAACACTCAT
23854748 GTTGCGA
1 GTTGCGA
23854755 GCATGGATGA
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.22
Consensus pattern (15 bp):
GTTGCGAACACTCAT
Found at i:23854755 original size:15 final size:15
Alignment explanation
Indices: 23854720--23854757 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
23854710 ACACACACAA
23854720 TGCGAGCACTGATGT
1 TGCGAGCACTGATGT
23854735 TGCGAGCACTCG-TGT
1 TGCGAGCACT-GATGT
23854750 TGCGAGCA
1 TGCGAGCA
23854758 TGGATGAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.18, C:0.24, G:0.34, T:0.24
Consensus pattern (15 bp):
TGCGAGCACTGATGT
Found at i:23860212 original size:24 final size:24
Alignment explanation
Indices: 23860184--23860234 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
23860174 GTATACTGAT
23860184 TAACTATTCTGGGCTCGTAAGAGC
1 TAACTATTCTGGGCTCGTAAGAGC
* *
23860208 TAACTATTCTGGGCTTGTGAGAGC
1 TAACTATTCTGGGCTCGTAAGAGC
23860232 TAA
1 TAA
23860235 TGTTATCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (24 bp):
TAACTATTCTGGGCTCGTAAGAGC
Found at i:23864779 original size:24 final size:24
Alignment explanation
Indices: 23864751--23864801 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
23864741 GTATACTGGT
23864751 TAACTATTCTGGGCTCGTAAGAGC
1 TAACTATTCTGGGCTCGTAAGAGC
* *
23864775 TAACTATTCTGGGCTTGTGAGAGC
1 TAACTATTCTGGGCTCGTAAGAGC
23864799 TAA
1 TAA
23864802 TGTTATCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (24 bp):
TAACTATTCTGGGCTCGTAAGAGC
Found at i:23865559 original size:21 final size:21
Alignment explanation
Indices: 23865511--23865562 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
23865501 GGAGTTTTTA
*
23865511 GTATCGGTAGAAGCGTGACAT
1 GTATCGGTAGAAGCGTCACAT
* *
23865532 GTTTCGGTAGAAGTC-TCACTT
1 GTATCGGTAGAAG-CGTCACAT
23865553 GTATCGGTAG
1 GTATCGGTAG
23865563 TATTGTCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGCGTCACAT
Found at i:23866047 original size:25 final size:23
Alignment explanation
Indices: 23866019--23866064 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
23866009 GTTGGATCCA
23866019 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
23866044 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
23866065 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:23869760 original size:21 final size:21
Alignment explanation
Indices: 23869734--23869781 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
23869724 CTAGATTTAT
*
23869734 CGATACAAGT-ATGGCTTCTAC
1 CGATACAAGTCAT-GCATCTAC
23869755 CGATACAAGTCATGCATCTAC
1 CGATACAAGTCATGCATCTAC
23869776 CGATAC
1 CGATAC
23869782 CAAAAACTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (21 bp):
CGATACAAGTCATGCATCTAC
Found at i:23877553 original size:6 final size:6
Alignment explanation
Indices: 23877542--23877567 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23877532 ATCTACTCAA
23877542 CTAGAT CTAGAT CTAGAT CTAGAT CT
1 CTAGAT CTAGAT CTAGAT CTAGAT CT
23877568 TGGGTATTAC
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:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (6 bp):
CTAGAT
Found at i:23878677 original size:23 final size:23
Alignment explanation
Indices: 23878643--23878693 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
23878633 TAGGGTCATT
*
23878643 CATTCATTGTTTGCCACAAAGGC
1 CATTCATCGTTTGCCACAAAGGC
* *
23878666 CATTCATCGTTTGTCACGAAGGC
1 CATTCATCGTTTGCCACAAAGGC
23878689 CATTC
1 CATTC
23878694 TTTCATGTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (23 bp):
CATTCATCGTTTGCCACAAAGGC
Found at i:23889137 original size:17 final size:17
Alignment explanation
Indices: 23889111--23889146 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
23889101 CTGAGCGAAA
23889111 GAAAAATAGATGGGATC
1 GAAAAATAGATGGGATC
*
23889128 GAAAATTAGATGGGATC
1 GAAAAATAGATGGGATC
23889145 GA
1 GA
23889147 TCTCATTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (17 bp):
GAAAAATAGATGGGATC
Found at i:23891248 original size:12 final size:12
Alignment explanation
Indices: 23891231--23891255 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23891221 TGTTATCATG
23891231 ATGAATGCTATT
1 ATGAATGCTATT
23891243 ATGAATGCTATT
1 ATGAATGCTATT
23891255 A
1 A
23891256 ATTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:23894368 original size:40 final size:40
Alignment explanation
Indices: 23894301--23894531 Score: 264
Period size: 40 Copynumber: 5.8 Consensus size: 40
23894291 ATTAAAGATG
* * * *
23894301 TAATTCGAGTTACGGCTTAGCAAGCTTTGAGCTGGTGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCCGGTGATA
* ** * *
23894341 TAATTCGAGCTACAACTTATTAGGCTTTGAGTCGATGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCCGGTGATA
* * **
23894381 TAATTCGAGCTACGATTTAGAAGGCTTTGAGCCAATGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCCGGTGATA
* *
23894421 TAATTCGAGCTACGACTTAGCAAGCTTTGAGCCAGTGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCCGGTGATA
* * *
23894461 CAATTCAAGCTACGACTTAACAGGCTTTGAGCCGGTGATA
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAGCCGGTGATA
** * *
23894501 TAATTTAAGCTACGACTTAGCAAGATTTGAG
1 TAATTCGAGCTACGACTTAGCAGGCTTTGAG
23894532 TTGATGATGA
Statistics
Matches: 162, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 162 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (40 bp):
TAATTCGAGCTACGACTTAGCAGGCTTTGAGCCGGTGATA
Found at i:23894514 original size:120 final size:120
Alignment explanation
Indices: 23894301--23894520 Score: 314
Period size: 120 Copynumber: 1.8 Consensus size: 120
23894291 ATTAAAGATG
* * ** * * **
23894301 TAATTCGAGTTACGGCTTAGCAAGCTTTGAGCTGGTGATATAATTCGAGCTACAACTTATTAGGC
1 TAATTCGAGCTACGACTTAGCAAGCTTTGAGCCAGTGATACAATTCAAGCTACAACTTAACAGGC
* * *
23894366 TTTGAGTCGATGATATAATTCGAGCTACGATTTAGAAGGCTTTGAGCCAATGATA
66 TTTGAGCCGATGATATAATTCAAGCTACGACTTAGAAGGCTTTGAGCCAATGATA
*
23894421 TAATTCGAGCTACGACTTAGCAAGCTTTGAGCCAGTGATACAATTCAAGCTACGACTTAACAGGC
1 TAATTCGAGCTACGACTTAGCAAGCTTTGAGCCAGTGATACAATTCAAGCTACAACTTAACAGGC
* *
23894486 TTTGAGCCGGTGATATAATTTAAGCTACGACTTAG
66 TTTGAGCCGATGATATAATTCAAGCTACGACTTAG
23894521 CAAGATTTGA
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
120 86 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (120 bp):
TAATTCGAGCTACGACTTAGCAAGCTTTGAGCCAGTGATACAATTCAAGCTACAACTTAACAGGC
TTTGAGCCGATGATATAATTCAAGCTACGACTTAGAAGGCTTTGAGCCAATGATA
Found at i:23906525 original size:24 final size:24
Alignment explanation
Indices: 23906481--23906527 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
23906471 TTAAACGTTA
* *
23906481 ATTTTATTTAATTTCTTATTAAAT
1 ATTTTATTTAATATCTGATTAAAT
23906505 ATTTTAATTTAATAT-TGATTAAA
1 ATTTT-ATTTAATATCTGATTAAA
23906528 ATAAAATGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTTATTTAATATCTGATTAAAT
Found at i:23912970 original size:50 final size:50
Alignment explanation
Indices: 23912911--23913384 Score: 284
Period size: 50 Copynumber: 9.6 Consensus size: 50
23912901 CCCGCCATGT
** * * *
23912911 TTCTAAGGTATTAGGTTCGCCGTTGCGACCTCAACCTTTCTCTTCACATC
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATC
*
23912961 TTCTAAGGTACCAGGTTTGCCATTGCGGCCTCAACCTTTCCCTTCACATC
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATC
* *
23913011 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAATCTTTCCCTTCATATC
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATC
* ** * * * * * * *
23913061 TTC-ACGGTACCAAATTCACCGTTGTGGCCTTAATC-TTCCTTTCACGTC
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATC
* * ** * ** *
23913109 TTCTAAGGTACCGGGTTCACTGTTACGATCTCAACCTTTCCCTTCATATC
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATC
* * * *** * * * *
23913159 TTC-ATGGTACCAGATTTGTTGTTGTGGCCTTAATCC-TT-CCTATTACTTC
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAA-CCTTTCCCT-TCACATC
** *** * *
23913208 TTCTAAGGTACGGGGTTCGTTGTTGCGGCCTTAACCTTTCCCTT--CGTC
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATC
* * * * * * * * *
23913256 TTC-ATGGTACAAGATTCGCCGTTGTGGCCTTAA-TTCTTCCCATCACGTC
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAACCT-TTCCCTTCACATC
* * ** * * *
23913305 TTCTAAGGTACTAGGTTCGCCGTTATGGCCTTAACCTTTCCCTTTATATC
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATC
* ** *
23913355 TT-TAGGGTATTAGATTCGCCATTGCGGCCT
1 TTCTAAGGTACCAGGTTCGCCATTGCGGCCT
23913385 TAATCTTCCC
Statistics
Matches: 334, Mismatches: 78, Indels: 25
0.76 0.18 0.06
Matches are distributed among these distances:
46 1 0.00
47 29 0.09
48 22 0.07
49 105 0.31
50 173 0.52
51 4 0.01
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37
Consensus pattern (50 bp):
TTCTAAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATC
Found at i:23913142 original size:98 final size:98
Alignment explanation
Indices: 23912924--23913395 Score: 421
Period size: 99 Copynumber: 4.8 Consensus size: 98
23912914 TAAGGTATTA
* * * * * ** * * *
23912924 GGTTCGCCGTTGCGACCTCAACCTTTCTCTTCACATCTTCTAAGGTACCAGGTTTGCCATTGCGG
1 GGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTC-ATGGTACCAAATTCGCCGTTGTGG
* * * *
23912989 CCTCAACCTTTCCCTTCACATCTTCTAAGGTACCA
65 CCTTAATC-TTCCCTTCACGTCTTCTAAGGTACCG
** * * *
23913024 GGTTCGCCATTGCGGCCTCAATCTTTCCCTTCATATCTTCACGGTACCAAATTCACCGTTGTGGC
1 GGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAAATTCGCCGTTGTGGC
*
23913089 CTTAATCTTCCTTTCACGTCTTCTAAGGTACCG
66 CTTAATCTTCCCTTCACGTCTTCTAAGGTACCG
* * ** * * **
23913122 GGTTCACTGTTACGATCTCAACCTTTCCCTTCATATCTTCATGGTACCAGATTTGTTGTTGTGGC
1 GGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAAATTCGCCGTTGTGGC
* * *
23913187 CTTAATCCTT-CCTATTACTTCTTCTAAGGTACGG
66 CTTAAT-CTTCCCT-TCACGTCTTCTAAGGTACCG
* * *
23913221 GGTTCGTTGTTGCGGCCTTAACCTTTCCCTTC--GTCTTCATGGTA-CAAGATTCGCCGTTGTGG
1 GGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAA-ATTCGCCGTTGTGG
* **
23913283 CCTTAATTCTTCCCATCACGTCTTCTAAGGTACTA
65 CCTTAA-TCTTCCCTTCACGTCTTCTAAGGTACCG
* ** * * * * ** * * *
23913318 GGTTCGCCGTTATGGCCTTAACCTTTCCCTTTATATCTTTAGGGTATTAGATTCGCCATTGCGGC
1 GGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAAATTCGCCGTTGTGGC
23913383 CTTAATCTTCCCT
66 CTTAATCTTCCCT
23913396 GTCAAACCTG
Statistics
Matches: 301, Mismatches: 63, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
96 2 0.01
97 74 0.25
98 93 0.31
99 96 0.32
100 36 0.12
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (98 bp):
GGTTCGCTGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAAATTCGCCGTTGTGGC
CTTAATCTTCCCTTCACGTCTTCTAAGGTACCG
Found at i:23914640 original size:60 final size:61
Alignment explanation
Indices: 23914539--23914657 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 61
23914529 GTTTCACTCA
* *
23914539 CATTTATTACTCACGATTGACACAAAATCATCAGACCCTTGTT-CGTATTGGAACTCATTT
1 CATTTAATACTCACGATTGACACAAAATCATCAGACCCTTGTTCCGTATAGGAACTCATTT
* * * * *
23914599 CATTTAATACTCACGA-TGACATATAGTCATCGGACCTCTTGTTCCGTATAGGAATTCAT
1 CATTTAATACTCACGATTGACACAAAATCATCAGACC-CTTGTTCCGTATAGGAACTCAT
23914658 ATACTCACGA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 16 0.32
60 21 0.42
61 13 0.26
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (61 bp):
CATTTAATACTCACGATTGACACAAAATCATCAGACCCTTGTTCCGTATAGGAACTCATTT
Found at i:23914735 original size:51 final size:51
Alignment explanation
Indices: 23914606--23914844 Score: 273
Period size: 51 Copynumber: 4.6 Consensus size: 51
23914596 TTTCATTTAA
* ** ** * *
23914606 TACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTATAGGAATTCATA
1 TACTCACAATGACACCTAGTCATCGGACCT-TTAATCCGTAAAGG-ATTCATT
* * * * * * *
23914659 TACTCACGATAACA-CTAAGTTATCGGGCCTTTAATCCATCATGGATTCATT
1 TACTCACAATGACACCT-AGTCATCGGACCTTTAATCCGTAAAGGATTCATT
23914710 TACTCACAATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACAATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
23914761 TACTCACAATGACACCTAGTCATTGGACCTTTAATCTGTAAAGGATTCATT
1 TACTCACAATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
23914812 TACTCACGATGACACTTAGTCATCGGATCCTTT
1 TACTCACAATGACACCTAGTCATCGGA-CCTTT
23914845 CGTTTATAGT
Statistics
Matches: 160, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
51 120 0.75
52 16 0.10
53 24 0.15
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (51 bp):
TACTCACAATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:23929222 original size:18 final size:19
Alignment explanation
Indices: 23929191--23929226 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
23929181 TTTAACAAAC
23929191 ATTTTATATTTTTTATTTT
1 ATTTTATATTTTTTATTTT
23929210 ATTTTAT-TTTTTTATTT
1 ATTTTATATTTTTTATTT
23929227 GGTTTTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
ATTTTATATTTTTTATTTT
Found at i:23929232 original size:18 final size:19
Alignment explanation
Indices: 23929191--23929232 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
23929181 TTTAACAAAC
*
23929191 ATTTTATATTTTTTATTTT
1 ATTTTATATTTTTTATTTG
23929210 ATTTTAT-TTTTTTATTTG
1 ATTTTATATTTTTTATTTG
*
23929228 GTTTT
1 ATTTT
23929233 GTTGGGCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (19 bp):
ATTTTATATTTTTTATTTG
Found at i:23929845 original size:36 final size:36
Alignment explanation
Indices: 23929788--23929888 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
23929778 GGTAACAGGC
*
23929788 ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* * *
23929824 ATGACCTTTGGATCAATAGGGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
23929860 ATGACCTTTGGGGTCAACAGGGAGTAAAA
1 ATGACCTTT-GGGTCAACAGGGAGTAAAA
23929889 CGAAGAACGA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 41 0.71
37 17 0.29
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.22
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
Found at i:23933596 original size:24 final size:24
Alignment explanation
Indices: 23933563--23933657 Score: 84
Period size: 24 Copynumber: 3.9 Consensus size: 24
23933553 GGTTAAACTC
* *
23933563 TATCTAGGCTCGAATGAGGTAATT
1 TATCTGGGCTCGAATGAGCTAATT
* **
23933587 TATCTGGGCTCGTAA-GAGCTCACC
1 TATCTGGGCTCG-AATGAGCTAATT
**
23933611 TATCTGGGCTCCTATGAGCTAATTT
1 TATCTGGGCTCGAATGAGCTAA-TT
* *
23933636 TGTCTGGGCTCGTATGAGCTAA
1 TATCTGGGCTCGAATGAGCTAA
23933658 ATTTTTGAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.02
24 33 0.59
25 22 0.39
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (24 bp):
TATCTGGGCTCGAATGAGCTAATT
Found at i:23933634 original size:48 final size:49
Alignment explanation
Indices: 23933562--23933655 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
23933552 TGGTTAAACT
* *
23933562 CTATCTAGGCTCGAATGAGGTAA-TTTATCTGGGCTCGTAAGAGCTCAC
1 CTATCTAGGCTCCAATGAGCTAATTTTATCTGGGCTCGTAAGAGCTCAC
* * * *
23933610 CTATCTGGGCTCCTATGAGCTAATTTTGTCTGGGCTCGTATGAGCT
1 CTATCTAGGCTCCAATGAGCTAATTTTATCTGGGCTCGTAAGAGCT
23933656 AAATTTTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 19 0.49
49 20 0.51
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (49 bp):
CTATCTAGGCTCCAATGAGCTAATTTTATCTGGGCTCGTAAGAGCTCAC
Found at i:23933645 original size:25 final size:26
Alignment explanation
Indices: 23933613--23933662 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
23933603 AGCTCACCTA
23933613 TCTGGGCTCCTATGAGCT-AATTTTG
1 TCTGGGCTCCTATGAGCTAAATTTTG
*
23933638 TCTGGGCTCGTATGAGCTAAATTTT
1 TCTGGGCTCCTATGAGCTAAATTTT
23933663 TGAAAGACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (26 bp):
TCTGGGCTCCTATGAGCTAAATTTTG
Found at i:23938099 original size:21 final size:21
Alignment explanation
Indices: 23938075--23938184 Score: 77
Period size: 21 Copynumber: 5.3 Consensus size: 21
23938065 CAAATTTTGA
23938075 GGCATCCTAGTGCAATTCAAG
1 GGCATCCTAGTGCAATTCAAG
* *
23938096 GGCA--CTATATGCAATTCAGG
1 GGCATCCTA-GTGCAATTCAAG
** *
23938116 GGCATTGTAGTGCAATTCAGG
1 GGCATCCTAGTGCAATTCAAG
* *
23938137 GGCA-CCGTAATGCAATGC-AG
1 GGCATCC-TAGTGCAATTCAAG
*
23938157 AGGCACTGC-AGTGCAATTCAAG
1 -GGCA-TCCTAGTGCAATTCAAG
23938179 GGCATC
1 GGCATC
23938185 ACATAATCTT
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
19 3 0.04
20 16 0.24
21 44 0.65
22 4 0.06
23 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (21 bp):
GGCATCCTAGTGCAATTCAAG
Found at i:23938170 original size:42 final size:41
Alignment explanation
Indices: 23938083--23938182 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
23938073 GAGGCATCCT
* * * *
23938083 AGTGCAATTCAAGGGCACTATATGCAATTCAGGGGCATTGT
1 AGTGCAATTCAAGGGCACTATATGCAATGCAGAGGCACTGC
*
23938124 AGTGCAATTCAGGGGCACCGTA-ATGCAATGCAGAGGCACTGC
1 AGTGCAATTCAAGGGCA-C-TATATGCAATGCAGAGGCACTGC
23938166 AGTGCAATTCAAGGGCA
1 AGTGCAATTCAAGGGCA
23938183 TCACATAATC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 16 0.31
42 33 0.65
43 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (41 bp):
AGTGCAATTCAAGGGCACTATATGCAATGCAGAGGCACTGC
Found at i:23951212 original size:21 final size:21
Alignment explanation
Indices: 23951149--23951281 Score: 126
Period size: 21 Copynumber: 6.2 Consensus size: 21
23951139 AACATTACGG
*
23951149 GGGCACCGAAGTGC-ATTCACA
1 GGGCACCGTAGTGCAATTCA-A
23951170 GGGGCACCGTAGTGCAAATTCAA
1 -GGGCACCGTAGTGC-AATTCAA
*
23951193 GGGCATCGTAGTGCAATTC-A
1 GGGCACCGTAGTGCAATTCAA
** * *
23951213 GAGTTACCGTAGTGCTATTCAG
1 G-GGCACCGTAGTGCAATTCAA
* *
23951235 GGGCACTGTAATGCAATTCAA
1 GGGCACCGTAGTGCAATTCAA
*
23951256 GGGCACCGTAGTGTAATTCAA
1 GGGCACCGTAGTGCAATTCAA
*
23951277 AGGCA
1 GGGCA
23951282 TCACATGGTC
Statistics
Matches: 90, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
20 2 0.02
21 55 0.61
22 27 0.30
23 1 0.01
24 5 0.06
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (21 bp):
GGGCACCGTAGTGCAATTCAA
Found at i:23954737 original size:15 final size:15
Alignment explanation
Indices: 23954686--23954738 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
23954676 ATAAAAATAT
23954686 ATTTATATTATTTTTA
1 ATTTATA-TATTTTTA
*
23954702 ATTTA-ATATTTAATA
1 ATTTATATATTT-TTA
*
23954717 ATTTTATATATTTTTT
1 A-TTTATATATTTTTA
23954733 ATTTAT
1 ATTTAT
23954739 TAAAATTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.16
15 9 0.29
16 11 0.35
17 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTATATATTTTTA
Found at i:23955882 original size:21 final size:21
Alignment explanation
Indices: 23955858--23955913 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
23955848 AAGTTATAAG
*
23955858 AAATATATATAAATTATAAAA
1 AAATATATCTAAATTATAAAA
* *
23955879 AAAT-TATCTAAA-TCTAAAC
1 AAATATATCTAAATTATAAAA
23955898 AAATAATATCTAAATT
1 AAAT-ATATCTAAATT
23955914 CAAATAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.31
20 7 0.24
21 12 0.41
22 1 0.03
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATATATCTAAATTATAAAA
Found at i:23964408 original size:32 final size:32
Alignment explanation
Indices: 23964340--23964440 Score: 106
Period size: 31 Copynumber: 3.3 Consensus size: 32
23964330 GGCTTCTTCA
*
23964340 TCAGATTTT-CTTTCTGCATTTTGGATTTTCT
1 TCAGATTTTGGTTTCTGCATTTTGGATTTTCT
* *
23964371 CCAGATTTTGGTTT-TGCATTTTGGGATTTTGT
1 TCAGATTTTGGTTTCTGCATTTT-GGATTTTCT
23964403 TCAGATTTTGG--TCTGC-TCTTTGGATTTTC-
1 TCAGATTTTGGTTTCTGCAT-TTTGGATTTTCT
*
23964432 TCATATTTT
1 TCAGATTTT
23964441 ATTTGGTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
29 8 0.13
30 9 0.15
31 22 0.37
32 21 0.35
ACGTcount: A:0.13, C:0.14, G:0.18, T:0.55
Consensus pattern (32 bp):
TCAGATTTTGGTTTCTGCATTTTGGATTTTCT
Found at i:23964714 original size:17 final size:16
Alignment explanation
Indices: 23964692--23964781 Score: 58
Period size: 17 Copynumber: 5.3 Consensus size: 16
23964682 CTCTTGACTT
23964692 TTAACCTTCCATATTCC
1 TTAACCTTCCAT-TTCC
* *
23964709 TTAACC-TCCCTTGACC
1 TTAACCTTCCATT-TCC
*
23964725 TTTAACCTTTCATCTTCC
1 -TTAACCTTCCAT-TTCC
* *
23964743 TTAACC-TCCCTTGACC
1 TTAACCTTCCATT-TCC
23964759 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCAT-TTCC
23964777 TTAAC
1 TTAAC
23964782 TTTTCATATT
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
15 2 0.04
16 11 0.20
17 29 0.53
18 11 0.20
19 2 0.04
ACGTcount: A:0.20, C:0.38, G:0.02, T:0.40
Consensus pattern (16 bp):
TTAACCTTCCATTTCC
Found at i:23964723 original size:34 final size:34
Alignment explanation
Indices: 23964684--23964781 Score: 169
Period size: 34 Copynumber: 2.9 Consensus size: 34
23964674 TTTCATCTCT
* *
23964684 CTTGACTTTTAACCTTCCATATTCCTTAACCTCC
1 CTTGACCTTTAACCTTCCATCTTCCTTAACCTCC
*
23964718 CTTGACCTTTAACCTTTCATCTTCCTTAACCTCC
1 CTTGACCTTTAACCTTCCATCTTCCTTAACCTCC
23964752 CTTGACCTTTAACCTTCCATCTTCCTTAAC
1 CTTGACCTTTAACCTTCCATCTTCCTTAAC
23964782 TTTTCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.19, C:0.37, G:0.03, T:0.41
Consensus pattern (34 bp):
CTTGACCTTTAACCTTCCATCTTCCTTAACCTCC
Found at i:23965299 original size:33 final size:34
Alignment explanation
Indices: 23965242--23965318 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
23965232 TATTTTTCTG
* * * *
23965242 TTATATTATGCTTGCAAGTTTTGTTAACGGATTAC
1 TTATATT-TACTTGAAAGTTTTGTTAAAGGACTAC
*
23965277 TTATGTTTACTTGAAAG-TTTGTTAAAGGACTAC
1 TTATATTTACTTGAAAGTTTTGTTAAAGGACTAC
23965310 TTATATTTA
1 TTATATTTA
23965319 TATTAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 22 0.61
34 8 0.22
35 6 0.17
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (34 bp):
TTATATTTACTTGAAAGTTTTGTTAAAGGACTAC
Found at i:23970031 original size:2 final size:2
Alignment explanation
Indices: 23970024--23970073 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
23970014 TTCACACTAC
23970024 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
23970066 AT AT AT AT
1 AT AT AT AT
23970074 GGTTGTGATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23970287 original size:17 final size:17
Alignment explanation
Indices: 23970267--23970324 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
23970257 TCCATATTCC
23970267 TTAACCTCCCTTGACCT
1 TTAACCTCCCTTGACCT
*
23970284 TTAACCTTCCATCTT--TC-
1 TTAACC-TCC--CTTGACCT
23970301 TTAACCTCCCTTGACCT
1 TTAACCTCCCTTGACCT
23970318 TTAACCT
1 TTAACCT
23970325 TCTATCTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 3 0.09
16 4 0.12
17 19 0.58
18 4 0.12
20 3 0.09
ACGTcount: A:0.19, C:0.38, G:0.03, T:0.40
Consensus pattern (17 bp):
TTAACCTCCCTTGACCT
Found at i:23970287 original size:34 final size:34
Alignment explanation
Indices: 23970242--23970339 Score: 160
Period size: 34 Copynumber: 2.9 Consensus size: 34
23970232 TTTCATCTCT
* *
23970242 CTTGACTTTTAACCTTCCATATTCCTTAACCTCC
1 CTTGACCTTTAACCTTCCATCTTCCTTAACCTCC
*
23970276 CTTGACCTTTAACCTTCCATCTTTCTTAACCTCC
1 CTTGACCTTTAACCTTCCATCTTCCTTAACCTCC
*
23970310 CTTGACCTTTAACCTTCTATCTTCCTTAAC
1 CTTGACCTTTAACCTTCCATCTTCCTTAAC
23970340 TTTTCATATT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.19, C:0.36, G:0.03, T:0.42
Consensus pattern (34 bp):
CTTGACCTTTAACCTTCCATCTTCCTTAACCTCC
Found at i:23971436 original size:19 final size:19
Alignment explanation
Indices: 23971406--23971471 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
23971396 CACATTCAAA
23971406 TTAAATAATTAAAAACATTT
1 TTAAA-AATTAAAAACATTT
** *
23971426 TTAAAAATTAAATTCAATT
1 TTAAAAATTAAAAACATTT
* *
23971445 ATAAAAATATAAAAATATGTT
1 TTAAAAAT-TAAAAACAT-TT
23971466 TTAAAA
1 TTAAAA
23971472 TTTTTTATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
19 18 0.51
20 10 0.29
21 7 0.20
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (19 bp):
TTAAAAATTAAAAACATTT
Found at i:23972570 original size:2 final size:2
Alignment explanation
Indices: 23972563--23972588 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23972553 ACATACATAC
23972563 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
23972589 GCTGAACCTC
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:23975072 original size:15 final size:15
Alignment explanation
Indices: 23975052--23975082 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
23975042 GCGATATCAG
23975052 ATTTTAAACTAAACA
1 ATTTTAAACTAAACA
23975067 ATTTTAAACTAAACA
1 ATTTTAAACTAAACA
23975082 A
1 A
23975083 GTAATTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTTTAAACTAAACA
Found at i:23981599 original size:6 final size:6
Alignment explanation
Indices: 23981588--23981613 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23981578 CGAAGATGAG
23981588 GACGAT GACGAT GACGAT GACGAT GA
1 GACGAT GACGAT GACGAT GACGAT GA
23981614 GGGTGAAGGT
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:0.35, C:0.15, G:0.35, T:0.15
Consensus pattern (6 bp):
GACGAT
Found at i:23996316 original size:19 final size:18
Alignment explanation
Indices: 23996281--23996319 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
23996271 AAAGCCTAGG
23996281 GAAGAAGAAACACAGGAA
1 GAAGAAGAAACACAGGAA
* *
23996299 GAAGAATGAAAGAGAGGAA
1 GAAGAA-GAAACACAGGAA
23996318 GA
1 GA
23996320 TGAACGTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.59, C:0.05, G:0.33, T:0.03
Consensus pattern (18 bp):
GAAGAAGAAACACAGGAA
Found at i:23996662 original size:21 final size:21
Alignment explanation
Indices: 23996617--23996663 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
23996607 GGTTGATTCG
**
23996617 AAAGATAAGAAGAGAAAGCGT
1 AAAGATAAGAAGAGAAAGCAC
23996638 AAAGATAAGAAGA-AGAAGCAC
1 AAAGATAAGAAGAGA-AAGCAC
23996659 AAAGA
1 AAAGA
23996664 AGAAGGCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.62, C:0.06, G:0.26, T:0.06
Consensus pattern (21 bp):
AAAGATAAGAAGAGAAAGCAC
Found at i:23996686 original size:3 final size:3
Alignment explanation
Indices: 23996680--23996705 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23996670 CAAGCGCCCA
23996680 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
23996706 AACCAAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23996821 original size:17 final size:17
Alignment explanation
Indices: 23996787--23996840 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
23996777 TTTTATTTAG
*
23996787 TTGTCATTGCATTTTCAT
1 TTGTCATTACA-TTTCAT
23996805 TTGTCATTACATTTCAT
1 TTGTCATTACATTTCAT
* *
23996822 TTGTTAGTACATTTGCAT
1 TTGTCATTACATTT-CAT
23996840 T
1 T
23996841 ATAGTTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (17 bp):
TTGTCATTACATTTCAT
Found at i:24001333 original size:49 final size:49
Alignment explanation
Indices: 24001208--24001338 Score: 129
Period size: 49 Copynumber: 2.7 Consensus size: 49
24001198 TGACAGTATA
* * * **
24001208 ACTACAAATTTTTGGTGGCTTGTCCACAACATTTTGTATCTAGTAGTATT
1 ACTAC-AATATTTGGTGGCTTGTCCACAATATTCTGTATCTAGTAGTACG
* * * * * *
24001258 TCTACATTATCTGGTGGCTCGACCACAATATTCTGTTTCTAGTAGCT-CG
1 ACTACAATATTTGGTGGCTTGTCCACAATATTCTGTATCTAGTAG-TACG
*
24001307 ACTACAATATTTGGTGGCTTGTCCACATTATT
1 ACTACAATATTTGGTGGCTTGTCCACAATATT
24001339 AGTGTCTTAT
Statistics
Matches: 63, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
49 58 0.92
50 5 0.08
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (49 bp):
ACTACAATATTTGGTGGCTTGTCCACAATATTCTGTATCTAGTAGTACG
Found at i:24003259 original size:21 final size:20
Alignment explanation
Indices: 24003210--24003259 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
24003200 ATAATCAGGT
24003210 TAAATAAATTATTTAATTGAA
1 TAAAT-AATTATTTAATTGAA
*
24003231 -AAATTAATTAATTTAATTTAA
1 TAAA-TAATT-ATTTAATTGAA
24003252 TAAATAAT
1 TAAATAAT
24003260 GTCTATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 7 0.28
21 15 0.60
22 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TAAATAATTATTTAATTGAA
Found at i:24003424 original size:17 final size:17
Alignment explanation
Indices: 24003402--24003435 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
24003392 GAGGAAGCAC
24003402 ACCCTATTAGCCCCTCT
1 ACCCTATTAGCCCCTCT
24003419 ACCCTATTAGCCCCTCT
1 ACCCTATTAGCCCCTCT
24003436 TTCTCTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.47, G:0.06, T:0.29
Consensus pattern (17 bp):
ACCCTATTAGCCCCTCT
Found at i:24006485 original size:67 final size:67
Alignment explanation
Indices: 24006377--24006511 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
24006367 AACAAAACAG
*
24006377 CCTTAAAAACTTGAAGAAACATTGTCAAAGAAGAGAAGATTGAGAGATGTCGAAGCAATCGCACT
1 CCTTAAAAACTTGAAGAAACATTGTCAAAGAAGAGAAGATTGAGAGATGTCGAAGCAATAGCACT
24006442 TA
66 TA
*
24006444 CCTTAAAAACTTGAAGACACATTGTCAAAGAAGAGAAGATTGAGAGATGTCGAAGCAATAGCACT
1 CCTTAAAAACTTGAAGAAACATTGTCAAAGAAGAGAAGATTGAGAGATGTCGAAGCAATAGCACT
24006509 TA
66 TA
24006511 C
1 C
24006512 TAAAGGGTGC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.21
Consensus pattern (67 bp):
CCTTAAAAACTTGAAGAAACATTGTCAAAGAAGAGAAGATTGAGAGATGTCGAAGCAATAGCACT
TA
Found at i:24007525 original size:34 final size:34
Alignment explanation
Indices: 24007487--24007552 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
24007477 CTGTAGTATA
*
24007487 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* *
24007521 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
24007553 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:24007526 original size:17 final size:17
Alignment explanation
Indices: 24007495--24007552 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
24007485 TAATTGTCCC
* *
24007495 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
24007512 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
24007529 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
24007546 TGCATTT
1 TGCATTT
24007553 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:24008138 original size:17 final size:17
Alignment explanation
Indices: 24008112--24008145 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24008102 ACATAAAAAG
24008112 AAAGAAAAAGAAAATAA
1 AAAGAAAAAGAAAATAA
*
24008129 AAAGAGAAAGAAAATAA
1 AAAGAAAAAGAAAATAA
24008146 TATTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAGAAAAAGAAAATAA
Found at i:24032933 original size:21 final size:21
Alignment explanation
Indices: 24032907--24032958 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
24032897 AAAGTTAGTA
*
24032907 CAAGTGGTTTGGTTCAAAAGT
1 CAAGTGGTTTGGTTCAAAAAT
24032928 CAAGTGGTTTGGTTCAAAAAT
1 CAAGTGGTTTGGTTCAAAAAT
*
24032949 TAAGTGGTTT
1 CAAGTGGTTT
24032959 TAGAAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.37
Consensus pattern (21 bp):
CAAGTGGTTTGGTTCAAAAAT
Found at i:24033764 original size:3 final size:3
Alignment explanation
Indices: 24033750--24033795 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
24033740 AAAATTCATT
24033750 TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
24033796 TAGCTGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:24034238 original size:56 final size:56
Alignment explanation
Indices: 24034175--24034282 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
24034165 CTAAAATTGA
*
24034175 AATAAAATAGTTAATTTTCATGTTTAAGGCATAAGGACTAAATTGAAAAAAAATGG
1 AATAAAATAGTTAATTTGCATGTTTAAGGCATAAGGACTAAATTGAAAAAAAATGG
* * *
24034231 AATAAAATGGTTAATTTGCATGTTTAAGGCTTAAGGACTAAATTGAATAAAA
1 AATAAAATAGTTAATTTGCATGTTTAAGGCATAAGGACTAAATTGAAAAAAA
24034283 TTGAAATGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (56 bp):
AATAAAATAGTTAATTTGCATGTTTAAGGCATAAGGACTAAATTGAAAAAAAATGG
Found at i:24034606 original size:21 final size:18
Alignment explanation
Indices: 24034563--24034607 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
24034553 GCTTAGTAAA
24034563 TATTAAATTGAAGAATTG
1 TATTAAATTGAAGAATTG
*
24034581 AATTAAATTGAAATGAAATTG
1 TATTAAATTG-AA-G-AATTG
24034602 TATTAA
1 TATTAA
24034608 GAAGCATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 1 0.05
21 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (18 bp):
TATTAAATTGAAGAATTG
Found at i:24035095 original size:43 final size:43
Alignment explanation
Indices: 24035043--24035205 Score: 238
Period size: 43 Copynumber: 3.8 Consensus size: 43
24035033 TTGAATTCGT
24035043 AATGGAAGACTTATGTCTCAGG-TAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTC-GGATAGAGCATAAGATTGTTTATA
* *
24035086 AATGGAAGACTTATGTCTCGGTTAGAGAATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGGATAGAGCATAAGATTGTTTATA
* * **
24035129 AATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTATTTGCA
1 AATGGAAGACTTATGTCTCGGATAGAGCATAAGATTGTTTATA
*
24035172 AATGGAAGAACTTATGACTCGGATAGAGCATAAG
1 AATGGAAG-ACTTATGTCTCGGATAGAGCATAAG
24035206 GTTAACTAAG
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
42 2 0.02
43 85 0.77
44 23 0.21
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (43 bp):
AATGGAAGACTTATGTCTCGGATAGAGCATAAGATTGTTTATA
Found at i:24042135 original size:12 final size:11
Alignment explanation
Indices: 24042105--24042185 Score: 51
Period size: 12 Copynumber: 7.0 Consensus size: 11
24042095 ATTGTTAATC
24042105 GTTTGCTTC-TT
1 GTTTG-TTCTTT
24042116 GATTTGTTCTTT
1 G-TTTGTTCTTT
24042128 GTTGTGTTCTTT
1 GTT-TGTTCTTT
** *
24042140 AGTTAATT-TTA
1 -GTTTGTTCTTT
24042151 GTTTGCTTC-TT
1 GTTTG-TTCTTT
24042162 GATTTGTTCTTT
1 G-TTTGTTCTTT
24042174 GTTGTGTTCTTT
1 GTT-TGTTCTTT
24042186 AGTTAATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
10 3 0.05
11 17 0.31
12 32 0.58
13 3 0.05
ACGTcount: A:0.07, C:0.10, G:0.19, T:0.64
Consensus pattern (11 bp):
GTTTGTTCTTT
Found at i:24042137 original size:23 final size:23
Alignment explanation
Indices: 24042111--24042184 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
24042101 AATCGTTTGC
24042111 TTCTTGATTTGTTCTTTGTTGTG
1 TTCTTGATTTGTTCTTTGTTGTG
* ** *
24042134 TTCTTTAGTTAATT-TTAGTT-TG
1 TTCTTGA-TTTGTTCTTTGTTGTG
24042156 CTTCTTGATTTGTTCTTTGTTGTG
1 -TTCTTGATTTGTTCTTTGTTGTG
24042180 TTCTT
1 TTCTT
24042185 TAGTTAATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
22 6 0.15
23 27 0.69
24 6 0.15
ACGTcount: A:0.08, C:0.09, G:0.18, T:0.65
Consensus pattern (23 bp):
TTCTTGATTTGTTCTTTGTTGTG
Found at i:24042160 original size:46 final size:46
Alignment explanation
Indices: 24042105--24042200 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
24042095 ATTGTTAATC
24042105 GTTTGCTTCTTGATTTGTTCTTTGTTGTGTTCTTTAGTTAATTTTA
1 GTTTGCTTCTTGATTTGTTCTTTGTTGTGTTCTTTAGTTAATTTTA
24042151 GTTTGCTTCTTGATTTGTTCTTTGTTGTGTTCTTTAGTTAATTTTA
1 GTTTGCTTCTTGATTTGTTCTTTGTTGTGTTCTTTAGTTAATTTTA
24042197 GTTT
1 GTTT
24042201 TTATCAATCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.10, C:0.08, G:0.18, T:0.64
Consensus pattern (46 bp):
GTTTGCTTCTTGATTTGTTCTTTGTTGTGTTCTTTAGTTAATTTTA
Found at i:24042221 original size:46 final size:45
Alignment explanation
Indices: 24042124--24042214 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 45
24042114 TTGATTTGTT
* ** * * *
24042124 CTTTGTTGTGTTCTTTAGTTAATTTTAGTTTGCTTCTTGATTTGTT
1 CTTTGTTGTGTTCTTTAGTTAATTTTAGTTT-CTTATCAATCTCTC
24042170 CTTTGTTGTGTTCTTTAGTTAATTTTAGTTT-TTATCAATCTCTC
1 CTTTGTTGTGTTCTTTAGTTAATTTTAGTTTCTTATCAATCTCTC
24042214 C
1 C
24042215 AATTTGTCGG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 8 0.21
46 31 0.79
ACGTcount: A:0.13, C:0.12, G:0.14, T:0.60
Consensus pattern (45 bp):
CTTTGTTGTGTTCTTTAGTTAATTTTAGTTTCTTATCAATCTCTC
Found at i:24044155 original size:6 final size:6
Alignment explanation
Indices: 24044138--24044186 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
24044128 ACAAAGCAAA
* *
24044138 GGATAG GTATAG GGATAG GGATAG GGATAG GGATAG GGATAG GGTTAG
1 GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG
24044186 G
1 G
24044187 TTTGCCAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.49, T:0.20
Consensus pattern (6 bp):
GGATAG
Found at i:24044531 original size:26 final size:25
Alignment explanation
Indices: 24044482--24044531 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
24044472 TTTGAGAAGG
* * *
24044482 AATTTTTTTTAATTATTATTTTTAA
1 AATTTTATTTAATTATGATATTTAA
24044507 AATTTTATTTATATTATGATATTTA
1 AATTTTATTTA-ATTATGATATTTA
24044532 TTATTATCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
AATTTTATTTAATTATGATATTTAA
Found at i:24045325 original size:18 final size:19
Alignment explanation
Indices: 24045287--24045327 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
24045277 ATTTTCTGAT
*
24045287 TAAAACTTTTATTTCCCTC
1 TAAAACTTTTACTTCCCTC
*
24045306 TAAAAGTTTTACTT-CCTC
1 TAAAACTTTTACTTCCCTC
24045324 TAAA
1 TAAA
24045328 CTGTCAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.32, C:0.22, G:0.02, T:0.44
Consensus pattern (19 bp):
TAAAACTTTTACTTCCCTC
Found at i:24045634 original size:18 final size:18
Alignment explanation
Indices: 24045611--24045671 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
24045601 TATTTTCACA
24045611 TTTTATCTTTAAAATAAT
1 TTTTATCTTTAAAATAAT
**
24045629 TTTTAT-TAAAAAATCATATT
1 TTTTATCTTTAAAAT-A-A-T
* *
24045649 TTTTATCTTTAATATATT
1 TTTTATCTTTAAAATAAT
24045667 TTTTA
1 TTTTA
24045672 ATTTCAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 6 0.18
18 13 0.39
19 1 0.03
20 8 0.24
21 5 0.15
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATCTTTAAAATAAT
Found at i:24046194 original size:1 final size:1
Alignment explanation
Indices: 24046188--24046212 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
24046178 ATAATGAAAA
24046188 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
24046213 TACAAAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:24053638 original size:9 final size:9
Alignment explanation
Indices: 24053621--24053722 Score: 55
Period size: 10 Copynumber: 10.9 Consensus size: 9
24053611 ATGTGGTTCA
24053621 AAAAATTAT
1 AAAAATTAT
*
24053630 AAAAGTTATT
1 AAAAATTA-T
*
24053640 GAAAA-TAT
1 AAAAATTAT
*
24053648 AAAAATTAA
1 AAAAATTAT
*
24053657 AAATAATTGT
1 AAA-AATTAT
*
24053667 AAATAATTTT
1 AAA-AATTAT
*
24053677 AATAATTATT
1 AAAAATTA-T
*
24053687 TAAAATTAT
1 AAAAATTAT
*
24053696 AATAA-TAT
1 AAAAATTAT
*
24053704 AGAAAAATAT
1 A-AAAATTAT
24053714 AAAATATTA
1 AAAA-ATTA
24053723 AAATTGGATA
Statistics
Matches: 70, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
8 9 0.13
9 28 0.40
10 33 0.47
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (9 bp):
AAAAATTAT
Found at i:24053665 original size:25 final size:27
Alignment explanation
Indices: 24053621--24053671 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
24053611 ATGTGGTTCA
*
24053621 AAAAATTATAAAAGTTATTGAAAATAT
1 AAAAATTATAAAAGTAATTGAAAATAT
*
24053648 AAAAATTA-AAAA-TAATTGTAAATA
1 AAAAATTATAAAAGTAATTGAAAATA
24053672 ATTTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 4 0.18
27 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (27 bp):
AAAAATTATAAAAGTAATTGAAAATAT
Found at i:24053858 original size:26 final size:26
Alignment explanation
Indices: 24053827--24053876 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
24053817 AGATATGGAT
* *
24053827 AAATGGTTCAAGGAGATATTCATGAA
1 AAATGGTTAAAAGAGATATTCATGAA
*
24053853 AAATGGTTAAAAGAGATCTTCATG
1 AAATGGTTAAAAGAGATATTCATG
24053877 TTGAATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (26 bp):
AAATGGTTAAAAGAGATATTCATGAA
Found at i:24054080 original size:19 final size:19
Alignment explanation
Indices: 24054067--24054109 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
24054057 ATTTACATAT
24054067 ATTTATAAT-TTTTAAATAA
1 ATTT-TAATATTTTAAATAA
24054086 ATTTTAATATTTTAAATAA
1 ATTTTAATATTTTAAATAA
24054105 CATTT
1 -ATTT
24054110 AAAATAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.18
19 14 0.64
20 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATATTTTAAATAA
Found at i:24056206 original size:18 final size:18
Alignment explanation
Indices: 24056175--24056219 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
24056165 AATTTAATTT
24056175 TAATATAAATATTCAATA
1 TAATATAAATATTCAATA
24056193 TAAT-TAAATAATTC-A-A
1 TAATATAAAT-ATTCAATA
24056209 TAATATAAATA
1 TAATATAAATA
24056220 GTACAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
17 11 0.44
18 8 0.32
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATATAAATATTCAATA
Found at i:24058612 original size:15 final size:15
Alignment explanation
Indices: 24058588--24058648 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
24058578 TGTTTAGTTT
*
24058588 ATTAATTTTATTTTG
1 ATTAAATTTATTTTG
*
24058603 ATTAAATTTATTATTT
1 ATTAAATTTATT-TTG
* *
24058619 TTTTAATTTCATTTTG
1 ATTAAATTT-ATTTTG
*
24058635 ATTAAAGTTATTTT
1 ATTAAATTTATTTT
24058649 TTATTTTATT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 16 0.44
16 17 0.47
17 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (15 bp):
ATTAAATTTATTTTG
Found at i:24058625 original size:32 final size:33
Alignment explanation
Indices: 24058589--24058656 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
24058579 GTTTAGTTTA
* *
24058589 TTAATTTTATTTTGATTAAATTTATTATTT-TT
1 TTAATTTCATTTTGATTAAAGTTATTATTTATT
*
24058621 TTAATTTCATTTTGATTAAAGTTATTTTTTATT
1 TTAATTTCATTTTGATTAAAGTTATTATTTATT
24058654 TTA
1 TTA
24058657 TTAGGATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 27 0.84
33 5 0.16
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (33 bp):
TTAATTTCATTTTGATTAAAGTTATTATTTATT
Found at i:24058648 original size:27 final size:27
Alignment explanation
Indices: 24058618--24058677 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
24058608 ATTTATTATT
**
24058618 TTTTTAATTTCATTTTGATTAAAGTTA
1 TTTTTAATTTCATTAGGATTAAAGTTA
* * *
24058645 TTTTTTATTTTATTAGGATTTAAGTTA
1 TTTTTAATTTCATTAGGATTAAAGTTA
24058672 TTTTTA
1 TTTTTA
24058678 GTAATCAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (27 bp):
TTTTTAATTTCATTAGGATTAAAGTTA
Found at i:24076428 original size:22 final size:23
Alignment explanation
Indices: 24076394--24076438 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
24076384 TACTTTCATC
24076394 TAGTTGGTAATAT-ATAT-ATAT
1 TAGTTGGTAATATCATATGATAT
*
24076415 TAGTATGGTTATATCATATGATAT
1 TAGT-TGGTAATATCATATGATAT
24076439 GTTAAACTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 4 0.20
24 4 0.20
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (23 bp):
TAGTTGGTAATATCATATGATAT
Found at i:24087197 original size:19 final size:18
Alignment explanation
Indices: 24087173--24087220 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
24087163 TCACTTGAAA
24087173 AAGAAAAAATGAGAAAAAG
1 AAGAAAAAATGA-AAAAAG
*
24087192 AAGAAAGAAAAGAAAAAAG
1 AAGAAA-AAATGAAAAAAG
*
24087211 AAGAATAAAT
1 AAGAAAAAAT
24087221 TGCTGAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 17 0.68
20 5 0.20
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (18 bp):
AAGAAAAAATGAAAAAAG
Found at i:24099408 original size:41 final size:40
Alignment explanation
Indices: 24099363--24099451 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
24099353 GCATTTTTAA
*
24099363 CGGCGTTTAGACAGAAAACGCCGCAAAAGGTAAAGCAATAG
1 CGGCGTTTAGACA-AAAACGCCGCAAAAAGTAAAGCAATAG
*** * *
24099404 CGGCGTTTTTCCATAAACGCCGCAAAAAGTAAAGCATTAG
1 CGGCGTTTAGACAAAAACGCCGCAAAAAGTAAAGCAATAG
24099444 -GGCGTTTA
1 CGGCGTTTA
24099452 TGAGAAAGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 7 0.17
40 24 0.59
41 10 0.24
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (40 bp):
CGGCGTTTAGACAAAAACGCCGCAAAAAGTAAAGCAATAG
Found at i:24099465 original size:39 final size:39
Alignment explanation
Indices: 24099378--24099498 Score: 118
Period size: 40 Copynumber: 3.1 Consensus size: 39
24099368 TTTAGACAGA
* * * *
24099378 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCCAT
1 AAACGCCGCAAAAGGTAAAGCATTAGCGGCGTTTAT-GAG
*
24099418 AAACGCCGCAAAAAGTAAAGCATTAG-GGCGTTTATGAG
1 AAACGCCGCAAAAGGTAAAGCATTAGCGGCGTTTATGAG
* * * * *
24099456 AAAGTGCCGCTAAAGGTCAGAGCATTAGTGACGTTTATGAG
1 AAA-CGCCGCAAAAGGT-AAAGCATTAGCGGCGTTTATGAG
24099497 AA
1 AA
24099499 TGTGTCGCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
38 4 0.06
39 18 0.26
40 33 0.49
41 13 0.19
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (39 bp):
AAACGCCGCAAAAGGTAAAGCATTAGCGGCGTTTATGAG
Found at i:24099494 original size:41 final size:40
Alignment explanation
Indices: 24099436--24099524 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 40
24099426 CAAAAAGTAA
*
24099436 AGCATTAGGGCGTTTATGAGAAAGTGCCGCTAAAGGTCAG
1 AGCATTAGGACGTTTATGAGAAAGTGCCGCTAAAGGTCAG
* *
24099476 AGCATTAGTGACGTTTATGAGAATGTGTCGCTAAAGGTCAG
1 AGCATTAG-GACGTTTATGAGAAAGTGCCGCTAAAGGTCAG
24099517 AGCATTAG
1 AGCATTAG
24099525 CGATCAGAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 8 0.18
41 37 0.82
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.26
Consensus pattern (40 bp):
AGCATTAGGACGTTTATGAGAAAGTGCCGCTAAAGGTCAG
Found at i:24099533 original size:15 final size:15
Alignment explanation
Indices: 24099513--24099541 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24099503 TCGCTAAAGG
24099513 TCAGAGCATTAGCGA
1 TCAGAGCATTAGCGA
24099528 TCAGAGCATTAGCG
1 TCAGAGCATTAGCG
24099542 GCGCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (15 bp):
TCAGAGCATTAGCGA
Found at i:24106507 original size:30 final size:30
Alignment explanation
Indices: 24106440--24106633 Score: 130
Period size: 30 Copynumber: 6.8 Consensus size: 30
24106430 AAGAAAAAAA
*
24106440 AGGGTCAAAAATG-AAATTTTAGAAAGTTTG
1 AGGGTC-AAAATGCAATTTTTAGAAAGTTTG
*
24106470 -GTGGTCAAAATGCAATTCTTAGAAAGTTTG
1 AG-GGTCAAAATGCAATTTTTAGAAAGTTTG
* * *
24106500 A--G-C---GT-CAATTTTTA-AATA-ATTC
1 AGGGTCAAAATGCAATTTTTAGAA-AGTTTG
* *
24106522 AGGGCCAAAATGCAATTTTTAGAAAGTTAG
1 AGGGTCAAAATGCAATTTTTAGAAAGTTTG
*
24106552 -GGGTGCCAAATGCAATTTTTAGAAAGTTT-
1 AGGGT-CAAAATGCAATTTTTAGAAAGTTTG
*
24106581 AGGCGTCAAAATGAAATTTTTAGAAAGTTT-
1 AGG-GTCAAAATGCAATTTTTAGAAAGTTTG
** *
24106611 AGGG-GGAAATGTAATTTTTAGAA
1 AGGGTCAAAATGCAATTTTTAGAA
24106634 TAAAACAAGG
Statistics
Matches: 130, Mismatches: 18, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
22 5 0.04
23 9 0.07
24 2 0.02
25 1 0.01
27 1 0.01
28 18 0.14
29 21 0.16
30 71 0.55
31 2 0.02
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (30 bp):
AGGGTCAAAATGCAATTTTTAGAAAGTTTG
Found at i:24106934 original size:36 final size:36
Alignment explanation
Indices: 24106884--24106969 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
24106874 GGTTATAAGG
* *
24106884 CAAAACGACACCGTTTTGAACCATAGGCATGAGCTT
1 CAAAACGACGCCGTTTTGAACCATAGACATGAGCTT
* * *
24106920 CAAAACGATGCCGTTTTGGACCATAGACATGGGCTT
1 CAAAACGACGCCGTTTTGAACCATAGACATGAGCTT
*
24106956 CAAAATGACGCCGT
1 CAAAACGACGCCGT
24106970 ATAGTGTCCC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (36 bp):
CAAAACGACGCCGTTTTGAACCATAGACATGAGCTT
Done.