Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008162.1 Hibiscus syriacus cultivar Beakdansim tig00110733_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: 3688897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 16
Found at i:2968424 original size:36 final size:36
Alignment explanation
Indices: 2968384--2968522 Score: 233
Period size: 36 Copynumber: 3.9 Consensus size: 36
2968374 TTAAATGGGT
*
2968384 TCATGATAATGATATTGATGTTAATAATGATAGAGA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
2968420 TCATGATAATGATATTGATGTTGATAATGATAGAGA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
* *
2968456 TCATGATAATGATATTGATGTTGAGAATGATAGAAA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
**
2968492 TCATGATAACAATATTGATGTTGATAATGAT
1 TCATGATAATGATATTGATGTTGATAATGAT
2968523 GGTATTTATC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (36 bp):
TCATGATAATGATATTGATGTTGATAATGATAGAGA
Found at i:2969937 original size:69 final size:69
Alignment explanation
Indices: 2969833--2969984 Score: 179
Period size: 69 Copynumber: 2.2 Consensus size: 69
2969823 TACAAATTAA
*
2969833 AATA-TAT-TATTTAATATGAATATTAGTAGGATAATTAT-T-CTTTTAAATATGTCAAATTAAA
1 AATATTATCTATTTAATATGAATATTAGTAAGATAATTATATACTTTTAAATATGTCAAATT-AA
2969894 AACAT
65 AACAT
* * * *
2969899 ATATATTATCTATTTAACTTTGACTATTA-TAAGATAATTATATACTTTTGAATATTTCAAATTA
1 A-ATATTATCTATTTAA-TATGAATATTAGTAAGATAATTATATACTTTTAAATATGTCAAATTA
*
2969963 AAAGAT
64 AAACAT
*
2969969 AATATTATCTGTTTAA
1 AATATTATCTATTTAA
2969985 ATTTAGATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
66 1 0.01
67 3 0.04
68 3 0.04
69 32 0.44
70 17 0.23
71 17 0.23
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.45
Consensus pattern (69 bp):
AATATTATCTATTTAATATGAATATTAGTAAGATAATTATATACTTTTAAATATGTCAAATTAAA
ACAT
Found at i:2970213 original size:13 final size:13
Alignment explanation
Indices: 2970195--2970224 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2970185 ATTTTGTCTC
2970195 GGATTGTTATTTT
1 GGATTGTTATTTT
2970208 GGATTGTTATTTT
1 GGATTGTTATTTT
2970221 GGAT
1 GGAT
2970225 AACAATACAT
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:0.17, C:0.00, G:0.27, T:0.57
Consensus pattern (13 bp):
GGATTGTTATTTT
Found at i:2973275 original size:23 final size:23
Alignment explanation
Indices: 2973249--2973325 Score: 136
Period size: 23 Copynumber: 3.3 Consensus size: 23
2973239 CATGTGTTGG
2973249 TCAAATTTAGTAAACATCAAAGT
1 TCAAATTTAGTAAACATCAAAGT
* *
2973272 TCAAATTTAGCAGACATCAAAGT
1 TCAAATTTAGTAAACATCAAAGT
2973295 TCAAATTTAGTAAACATCAAAGT
1 TCAAATTTAGTAAACATCAAAGT
2973318 TCAAATTT
1 TCAAATTT
2973326 GCTACCACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.31
Consensus pattern (23 bp):
TCAAATTTAGTAAACATCAAAGT
Found at i:2977962 original size:15 final size:19
Alignment explanation
Indices: 2977923--2977961 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2977913 CATACCTAAC
2977923 ATTATATATATTATTTCAT
1 ATTATATATATTATTTCAT
*
2977942 ATTATA-ATATTATTTAAT
1 ATTATATATATTATTTCAT
2977960 AT
1 AT
2977962 ATCAAATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATATATATTATTTCAT
Found at i:2978568 original size:157 final size:159
Alignment explanation
Indices: 2978167--2978591 Score: 432
Period size: 157 Copynumber: 2.7 Consensus size: 159
2978157 TCTTTAGTAA
* * * * * * *
2978167 AAAAAATAGCAATTG-AAGTTACATATGTATTCTATTGTGGTATATGAGCATGTCGTTCAAATTC
1 AAAAAATAGGAATTGAAAG-TACACATGTATTCTACTATGGTATAGGAGCATGT-GATCAAATTT
* * * *
2978231 GGTAAAAAACATGGACTTAAAACAAATCACAAATTGAAGGAA-CAATGAGATTATGAAAAAAATG
64 GGT-AAAAAC-TGGACTTAAAATAAATGACAAATTGAAGAAATAAATGAGATTATGAAAAAAAT-
* *
2978295 AAGGACTAAATTGAAAAAGAAAAAAAATTGTTAC
126 AAGGACCAAATTGAAAAAGAAAAAAAATTATTAC
* * * * * * *
2978329 CAAAAATAGGAATTGAAAGTACGCATGTATTTTACTATGGTTTAGGAGCACGTGGCTTAAATTTG
1 AAAAAATAGGAATTGAAAGTACACATGTATTCTACTATGGTATAGGAGCATGT-GATCAAATTTG
** * *
2978394 GTAAAAA-AAGAGTTAAAATAAATGACAAATTGAAGAAATAAAT-AGATTATG-AAAAATTATAG
65 GTAAAAACTGGACTTAAAATAAATGACAAATTGAAGAAATAAATGAGATTATGAAAAAAATA-AG
* * *
2978456 GACCAAATTGAAAAA-CAAAAAATTTATTAT
129 GACCAAATTGAAAAAGAAAAAAAATTATTAC
* *
2978486 AAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATAGTATA-GAGCATGTGAATCAAATTTG
1 AAAAAATAGGAATTGAAAGTACACATGTATTCTACTATGGTATAGGAGCATGTG-ATCAAATTTG
* * * *
2978550 GTAAAAACTGGACCTAAAATGAACGAGAAATTGAAGAAATAA
65 GTAAAAACTGGACTTAAAATAAATGACAAATTGAAGAAATAA
2978592 TGAAGTCAGG
Statistics
Matches: 215, Mismatches: 43, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
155 1 0.00
156 22 0.10
157 77 0.36
158 22 0.10
159 33 0.15
160 3 0.01
161 5 0.02
162 49 0.23
163 3 0.01
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.26
Consensus pattern (159 bp):
AAAAAATAGGAATTGAAAGTACACATGTATTCTACTATGGTATAGGAGCATGTGATCAAATTTGG
TAAAAACTGGACTTAAAATAAATGACAAATTGAAGAAATAAATGAGATTATGAAAAAAATAAGGA
CCAAATTGAAAAAGAAAAAAAATTATTAC
Found at i:2980438 original size:20 final size:19
Alignment explanation
Indices: 2980384--2980453 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
2980374 CACAATTGTT
*
2980384 TATGAATAGTACTATACTG
1 TATGAATAGTACGATACTG
** *
2980403 TATGAATAAAACCGATATTG
1 TATGAATAGTA-CGATACTG
2980423 TATGAATAGTATCGATACTG
1 TATGAATAGTA-CGATACTG
* *
2980443 TGTGAACAGTA
1 TATGAATAGTA
2980454 ACATCGATAC
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 9 0.22
20 31 0.77
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (19 bp):
TATGAATAGTACGATACTG
Found at i:2984868 original size:17 final size:18
Alignment explanation
Indices: 2984835--2984871 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2984825 TTTAAGATTT
2984835 TATATTCGATTCAAAATTA
1 TATATTCGATT-AAAATTA
2984854 TATATTCGATT-AAATTA
1 TATATTCGATTAAAATTA
2984871 T
1 T
2984872 TTGAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTAAAATTA
Found at i:2988437 original size:13 final size:13
Alignment explanation
Indices: 2988419--2988443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2988409 AGAACCATGG
2988419 TTTGTGAAAATAA
1 TTTGTGAAAATAA
2988432 TTTGTGAAAATA
1 TTTGTGAAAATA
2988444 TTTTTGGGCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TTTGTGAAAATAA
Found at i:2991304 original size:21 final size:21
Alignment explanation
Indices: 2991267--2991314 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2991257 AATAAAATAA
2991267 TGTTTTATTTTTAAATT-TGT
1 TGTTTTATTTTTAAATTATGT
* *
2991287 TGTTTTTTTTATTTAATTATGT
1 TGTTTTATTT-TTAAATTATGT
2991309 TGTTTT
1 TGTTTT
2991315 CATGAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
21 6 0.25
22 9 0.38
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (21 bp):
TGTTTTATTTTTAAATTATGT
Found at i:2991939 original size:15 final size:15
Alignment explanation
Indices: 2991919--2991948 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2991909 TAACACCTTT
2991919 GGTTTAGATAACGAG
1 GGTTTAGATAACGAG
*
2991934 GGTTTATATAACGAG
1 GGTTTAGATAACGAG
2991949 AAATAAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (15 bp):
GGTTTAGATAACGAG
Found at i:2993060 original size:13 final size:13
Alignment explanation
Indices: 2993038--2993071 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2993028 AGGGGGAGTA
*
2993038 ATTTTCAAAATTG
1 ATTTTCAAAAATG
2993051 A-TTTCAAAAATG
1 ATTTTCAAAAATG
2993063 ATTTTCAAA
1 ATTTTCAAA
2993072 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:2993215 original size:17 final size:18
Alignment explanation
Indices: 2993182--2993218 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2993172 TTTAAGATTT
2993182 TATATTCGATTCAAAATTA
1 TATATTCGATT-AAAATTA
2993201 TATATTCGATT-AAATTA
1 TATATTCGATTAAAATTA
2993218 T
1 T
2993219 TCGAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTAAAATTA
Found at i:2993405 original size:20 final size:20
Alignment explanation
Indices: 2993379--2993425 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2993369 AGAGAGGTAC
2993379 CGATACACTCCTTGATGTAT
1 CGATACACTCCTTGATGTAT
*
2993399 TGATACACTCCTTGATGTAT
1 CGATACACTCCTTGATGTAT
2993419 CGATACA
1 CGATACA
2993426 ACCCATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (20 bp):
CGATACACTCCTTGATGTAT
Found at i:3001832 original size:10 final size:10
Alignment explanation
Indices: 3001804--3001833 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3001794 GTTTATTTTT
3001804 CTTTATATTA
1 CTTTATATTA
3001814 CTGTTATATTA
1 CT-TTATATTA
3001825 CTTTATATT
1 CTTTATATT
3001834 CGGTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.60
Consensus pattern (10 bp):
CTTTATATTA
Found at i:3004441 original size:18 final size:18
Alignment explanation
Indices: 3004415--3004453 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3004405 CCATTTCTTG
*
3004415 AGTACAAGGAATAGCTTA
1 AGTACAAGGAATAACTTA
*
3004433 AGTATAAGGAATAACTTA
1 AGTACAAGGAATAACTTA
3004451 AGT
1 AGT
3004454 TTGGGGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.26
Consensus pattern (18 bp):
AGTACAAGGAATAACTTA
Found at i:3009426 original size:5 final size:5
Alignment explanation
Indices: 3009416--3009999 Score: 937
Period size: 5 Copynumber: 120.8 Consensus size: 5
3009406 TAATATTTAT
3009416 ATATC ATATC ATATC ATATC --ATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
*
3009464 ATATC ATATC ATATC --ATC ATATC ATATC ATCTC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
3009512 AT-TC ATATC --ATC ATATC ATATC ATATC AT-TC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
3009558 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
3009608 ATATC ATATC ATATC ATATC ATATC A-ATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
3009657 ATATC ATATC ATATC ATATC -TATC ATATC ATATC ATAT- ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
3009705 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
*
3009755 ATATC ATATC ATATC AAATATC ATATC --ATC ATATC ATATC ATATC ATTTC
1 ATATC ATATC ATATC --ATATC ATATC ATATC ATATC ATATC ATATC ATATC
3009805 ATATC ATATC ATATC ATATC ATATC ATATC ATATC --ATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
3009853 ATATC ATATC ATATC ATATC --ATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
3009901 ATATC ATATC --ATC ATATC ATATC ATAT- -TATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
*
3009947 --ATC ATATC ATATC A-ATC ATATATC ATATC ATATC ATATC ATATC ATATT
1 ATATC ATATC ATATC ATATC --ATATC ATATC ATATC ATATC ATATC ATATC
3009996 ATAT
1 ATAT
3010000 ATACTATATT
Statistics
Matches: 546, Mismatches: 5, Indels: 56
0.90 0.01 0.09
Matches are distributed among these distances:
3 27 0.05
4 23 0.04
5 487 0.89
6 1 0.00
7 8 0.01
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:3010021 original size:14 final size:14
Alignment explanation
Indices: 3010004--3010063 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 14
3009994 TTATATATAC
3010004 TATAT-TTATGTTAT
1 TATATATTATG-TAT
3010018 TATATATTATGTAT
1 TATATATTATGTAT
*
3010032 TAGATATTGTATAGTA-
1 TATATA-T-TAT-GTAT
*
3010048 TATATATTATATAT
1 TATATATTATGTAT
3010062 TA
1 TA
3010064 CTATTGTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
13 2 0.05
14 18 0.47
15 7 0.18
16 8 0.21
17 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (14 bp):
TATATATTATGTAT
Found at i:3010025 original size:16 final size:15
Alignment explanation
Indices: 3010004--3010055 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
3009994 TTATATATAC
3010004 TATATTTATGTTATTA
1 TATATTTATG-TATTA
3010020 TATA-TTATGTATTA
1 TATATTTATGTATTA
*
3010034 GATATTGTATAGTA-TA
1 TATATT-TAT-GTATTA
3010050 TATATT
1 TATATT
3010056 ATATATTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 8 0.26
15 6 0.19
16 14 0.45
17 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.56
Consensus pattern (15 bp):
TATATTTATGTATTA
Found at i:3010097 original size:22 final size:23
Alignment explanation
Indices: 3010072--3010122 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
3010062 TACTATTGTA
3010072 ATTATAGCATATATT-TATATAT
1 ATTATAGCATATATTATATATAT
* * *
3010094 ATTATA-TATATGTTATATTTAT
1 ATTATAGCATATATTATATATAT
3010116 ATTATAG
1 ATTATAG
3010123 TTATTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (23 bp):
ATTATAGCATATATTATATATAT
Found at i:3010126 original size:11 final size:10
Alignment explanation
Indices: 3009965--3010160 Score: 56
Period size: 10 Copynumber: 19.6 Consensus size: 10
3009955 ATATCAATCA
*
3009965 TATATCATAT
1 TATATTATAT
* *
3009975 CATATCATAT
1 TATATTATAT
* *
3009985 CATATCATAT
1 TATATTATAT
*
3009995 TATA-TATAC
1 TATATTATAT
*
3010004 TATATTTATGT
1 TATA-TTATAT
3010015 TAT-TATATAT
1 TATAT-TATAT
*
3010025 TATGTATTAGA-
1 TA--TATTATAT
*
3010036 TAT-TGTATAG
1 TATAT-TATAT
3010046 TATA-TATATT
1 TATATTATA-T
3010056 ATATATTACTAT
1 -TATATTA-TAT
* *
3010068 TGTAATTATAG
1 TAT-ATTATAT
*
3010079 CATA-TAT-T
1 TATATTATAT
3010087 TATA-TATAT
1 TATATTATAT
*
3010096 TATATATATGT
1 TATAT-TATAT
3010107 TATATTTATAT
1 TATA-TTATAT
*
3010118 TATAGT-TAT
1 TATATTATAT
**
3010127 T-TATTACGT
1 TATATTATAT
3010136 TATA-TATAT
1 TATATTATAT
3010145 T-TATTATAAT
1 TATATTAT-AT
3010155 TATATT
1 TATATT
3010161 TACATTATTT
Statistics
Matches: 139, Mismatches: 24, Indels: 45
0.67 0.12 0.22
Matches are distributed among these distances:
8 12 0.09
9 37 0.27
10 38 0.27
11 37 0.27
12 12 0.09
13 3 0.02
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (10 bp):
TATATTATAT
Found at i:3010172 original size:15 final size:16
Alignment explanation
Indices: 3010106--3010172 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 16
3010096 TATATATATG
*
3010106 TTATATTTATATTATA
1 TTATATTTACATTATA
* *
3010122 GTTATTTATTACGTTATA
1 -TTATAT-TTACATTATA
3010140 -TATATTT--ATTATAA
1 TTATATTTACATTAT-A
3010154 TTATATTTACATTAT-
1 TTATATTTACATTATA
3010169 TTAT
1 TTAT
3010173 TTATTTGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
13 4 0.10
14 1 0.03
15 13 0.32
16 4 0.10
17 10 0.25
18 8 0.20
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTATATTTACATTATA
Found at i:3013450 original size:7 final size:7
Alignment explanation
Indices: 3013389--3013455 Score: 59
Period size: 7 Copynumber: 9.9 Consensus size: 7
3013379 TAATTTCTTT
3013389 TATTATCA
1 TATTAT-A
3013397 TATTATA
1 TATTATA
*
3013404 TACTATA
1 TATTATA
*
3013411 TATTATT
1 TATTATA
3013418 TA-TA-A
1 TATTATA
3013423 TATT-TA
1 TATTATA
*
3013429 TATAATA
1 TATTATA
* *
3013436 TCTAATA
1 TATTATA
3013443 TATTATA
1 TATTATA
3013450 TATTAT
1 TATTAT
3013456 TATGTTGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
5 2 0.04
6 7 0.15
7 33 0.69
8 6 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (7 bp):
TATTATA
Found at i:3013466 original size:5 final size:5
Alignment explanation
Indices: 3013458--3013496 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
3013448 TATATTATTA
* *
3013458 TGTTG TGTTG TGTTA TGTTG TGTTG TCTTG TGTGTG TGT
1 TGTTG TGTTG TGTTG TGTTG TGTTG TGTTG TGT-TG TGT
3013497 GTATCATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.03, C:0.03, G:0.36, T:0.59
Consensus pattern (5 bp):
TGTTG
Found at i:3013475 original size:15 final size:15
Alignment explanation
Indices: 3013455--3013483 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3013445 TTATATATTA
3013455 TTATGTTGTGTTGTG
1 TTATGTTGTGTTGTG
3013470 TTATGTTGTGTTGT
1 TTATGTTGTGTTGT
3013484 CTTGTGTGTG
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:0.07, C:0.00, G:0.31, T:0.62
Consensus pattern (15 bp):
TTATGTTGTGTTGTG
Found at i:3013520 original size:9 final size:9
Alignment explanation
Indices: 3013502--3013620 Score: 65
Period size: 9 Copynumber: 13.2 Consensus size: 9
3013492 TGTGTGTATC
*
3013502 ATATAGTAT
1 ATATATTAT
*
3013511 ATATTTTAT
1 ATATATTAT
3013520 ATTACTATTAT
1 A-TA-TATTAT
3013531 A-AT-TATAGT
1 ATATAT-TA-T
3013540 ATATATTAT
1 ATATATTAT
*
3013549 ATAGATTAT
1 ATATATTAT
3013558 ATATATGT-T
1 ATATAT-TAT
3013567 ATAT-TTAT
1 ATATATTAT
*
3013575 ACTATGTTAT
1 A-TATATTAT
*
3013585 AT-TATTAC
1 ATATATTAT
3013593 AT-TA-TAT
1 ATATATTAT
3013600 ATATATT-T
1 ATATATTAT
3013608 ATTATAATTAT
1 A-TAT-ATTAT
3013619 AT
1 AT
3013621 TTACATTATT
Statistics
Matches: 87, Mismatches: 8, Indels: 29
0.70 0.06 0.23
Matches are distributed among these distances:
7 6 0.07
8 18 0.21
9 38 0.44
10 16 0.18
11 9 0.10
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (9 bp):
ATATATTAT
Found at i:3013569 original size:38 final size:38
Alignment explanation
Indices: 3013527--3013629 Score: 94
Period size: 38 Copynumber: 2.8 Consensus size: 38
3013517 TATATTACTA
* *
3013527 TTATAATTATAGTA-TATATTATATAGATTATATATATG
1 TTATAATTATACTATTATATTAT-TACATTATATATATG
* *
3013565 TTATATTTATACTATGTTATATTATTACATTATATATATA
1 TTATAATTATACTA--TTATATTATTACATTATATATATG
3013605 TT-T-ATTATA--ATTATA-T-TTACATTAT
1 TTATAATTATACTATTATATTATTACATTAT
3013630 TTATTTATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
32 9 0.16
33 1 0.02
34 5 0.09
36 1 0.02
38 17 0.30
39 1 0.02
40 15 0.26
41 8 0.14
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (38 bp):
TTATAATTATACTATTATATTATTACATTATATATATG
Found at i:3013580 original size:16 final size:15
Alignment explanation
Indices: 3013557--3013587 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3013547 ATATAGATTA
3013557 TATATATGTTATATT
1 TATATATGTTATATT
3013572 TATACTATGTTATATT
1 TATA-TATGTTATATT
3013588 ATTACATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (15 bp):
TATATATGTTATATT
Found at i:3013621 original size:11 final size:12
Alignment explanation
Indices: 3013510--3013640 Score: 75
Period size: 11 Copynumber: 11.2 Consensus size: 12
3013500 TCATATAGTA
*
3013510 TATATTTTATAT
1 TATATTATATAT
3013522 TACTATTATA-AT
1 TA-TATTATATAT
*
3013534 TATAGTATATAT
1 TATATTATATAT
*
3013546 TATA-TAGATTAT
1 TATATTATA-TAT
3013558 ATATATGT-TATAT
1 -TATAT-TATATAT
*
3013571 T-TA-TACTATGT
1 TATATTA-TATAT
*
3013582 TATATTATTACAT
1 TATATTA-TATAT
3013595 TATA-TATATAT
1 TATATTATATAT
3013606 T-TATTATA-AT
1 TATATTATATAT
*
3013616 TATATT-TACAT
1 TATATTATATAT
*
3013627 TAT-TTATTTAT
1 TATATTATATAT
3013638 TAT
1 TAT
3013641 TATTTCAGAT
Statistics
Matches: 94, Mismatches: 11, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
9 1 0.01
10 9 0.10
11 40 0.43
12 20 0.21
13 22 0.23
14 1 0.01
15 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (12 bp):
TATATTATATAT
Found at i:3023281 original size:23 final size:24
Alignment explanation
Indices: 3023242--3023288 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
3023232 ATTGATCCAA
3023242 ACAGCCTCTTTTGTTCCTTCATTG
1 ACAGCCTCTTTTGTTCCTTCATTG
3023266 ACAGCCTC-TTTGTTCCTTCATTG
1 ACAGCCTCTTTTGTTCCTTCATTG
3023289 GCTACAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.13, C:0.30, G:0.13, T:0.45
Consensus pattern (24 bp):
ACAGCCTCTTTTGTTCCTTCATTG
Found at i:3034213 original size:21 final size:21
Alignment explanation
Indices: 3034187--3034226 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3034177 CAGAACCCCA
*
3034187 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3034208 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3034227 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3034255 original size:20 final size:21
Alignment explanation
Indices: 3034209--3034269 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
3034199 TTCCCCTGTG
3034209 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
3034232 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
3034252 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
3034270 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:3038103 original size:22 final size:21
Alignment explanation
Indices: 3038061--3038100 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3038051 GAGTTTGTTT
*
3038061 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3038082 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3038101 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3044759 original size:3 final size:3
Alignment explanation
Indices: 3044751--3044808 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
3044741 TTTTCTGGTC
3044751 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3044799 TAT TAT TAT T
1 TAT TAT TAT T
3044809 CGAAATGTCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3046842 original size:21 final size:21
Alignment explanation
Indices: 3046818--3046862 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3046808 AGCAATACTA
* *
3046818 TTCAGAATTTTACTTTCTTAT
1 TTCAGAATTTCACTTCCTTAT
3046839 TTCAGAATTTCACTTCCTTAT
1 TTCAGAATTTCACTTCCTTAT
3046860 TTC
1 TTC
3046863 GGGTATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTCAGAATTTCACTTCCTTAT
Found at i:3049852 original size:37 final size:37
Alignment explanation
Indices: 3049776--3049852 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
3049766 TTTTTTATAT
*
3049776 TTTAATTTTGTAAAAAAAAATATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAAATATATAAATATTATCAA
* * *
3049813 TTTAATTTT-TTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAAATATATAAATATTAT-CAA
3049850 TTT
1 TTT
3049853 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 21 0.60
37 14 0.40
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAAATATATAAATATTATCAA
Found at i:3051296 original size:44 final size:44
Alignment explanation
Indices: 3051186--3051612 Score: 640
Period size: 44 Copynumber: 9.7 Consensus size: 44
3051176 CCATTTAATC
* *
3051186 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTAAATCT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA-T-AATTT
** * * * **
3051232 C-TAAGCTAATAAGTTTATTTTACCAATATACTTACCATTATCC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
3051275 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
3051319 CATAAGCTCGTAAGATTATTTTACCAATATACTTACTATAGTTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
3051363 CATAAGCTCGTAGGCTTATTTTACCAATATACTTATTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
3051407 CATAAGCTCATAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* * *
3051451 CATAAGCTCGTAAACTTATTTTACAAATACACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
3051495 CATAAGCTCGTAAGCTTATTTTACTAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
3051539 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACTATAATCTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAAT-TT
3051584 CATAAGCTCGTAAGCTTATTTTACCAATA
1 CATAAGCTCGTAAGCTTATTTTACCAATA
3051613 ATACCAATTG
Statistics
Matches: 347, Mismatches: 32, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
43 4 0.01
44 280 0.81
45 62 0.18
46 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (44 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
Found at i:3055294 original size:21 final size:21
Alignment explanation
Indices: 3055270--3055310 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3055260 AATGTGTATC
*
3055270 GATGCACTTCTACAGTACATA
1 GATGCACTGCTACAGTACATA
3055291 GATGCACTGCTACAGTACAT
1 GATGCACTGCTACAGTACAT
3055311 TTCGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (21 bp):
GATGCACTGCTACAGTACATA
Found at i:3055783 original size:44 final size:44
Alignment explanation
Indices: 3055663--3055963 Score: 392
Period size: 44 Copynumber: 6.8 Consensus size: 44
3055653 ACATACCATT
* *
3055663 TAATC-CATAAGCTCGTAAGCTTATTTTACCAATATTCTTACCAA
1 TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTA-CTA
* *
3055707 TAAATCTC-TAAGCTCGTAAGTTTATTTTACCAATATACTTACCA
1 T-AATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
* *
3055751 -ATATCCCATAAGATCGTAAGCTTATTTTACCAATATACTTACTA
1 TA-ATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
* * * *
3055795 TAATTTCATAAGCTCGTAAGCTTATTTTTCAAATACACTTACTA
1 TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
*
3055839 TAATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
1 TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
* * * * *
3055883 TAATTTCATAAACACGTAAGCTTATTTTACCAATAAATTTACTA
1 TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
*
3055927 TAATCTCCATAAGCTCGTAATCTTATTTTACCAATAT
1 TAATCT-CATAAGCTCGTAAGCTTATTTTACCAATAT
3055964 TACCAATTGT
Statistics
Matches: 226, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
42 1 0.00
43 4 0.02
44 158 0.70
45 62 0.27
46 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (44 bp):
TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
Found at i:3066448 original size:44 final size:44
Alignment explanation
Indices: 3066338--3066868 Score: 839
Period size: 44 Copynumber: 12.0 Consensus size: 44
3066328 CCATTTAATC
* * *
3066338 CATAAGCTCGTAAGCTTATTTTAACAATATACTTAAC-ATTAAATC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTT-ACTA-TAATTT
* ** * * * * *
3066383 CCTAAGCTCGTTTGTTTATTTTATCAATATACTTACCATTATTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
3066427 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
3066471 CATAAGCTCGTAAACTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
3066515 CATAAGCTCGTAAGATTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
3066559 CATAAGCTCGTAAGATTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
3066603 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
3066647 CATAATCTTGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
3066691 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATCTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAAT-TT
* *
3066736 CATAAGCTCGTAAGCTTATTTTACCAGTATACTTACTATAATCTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAAT-TT
*
3066781 CATAAGCTTGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
3066825 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
3066869 GCATCACTGA
Statistics
Matches: 455, Mismatches: 29, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
44 340 0.75
45 115 0.25
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (44 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
Found at i:3067038 original size:59 final size:59
Alignment explanation
Indices: 3066974--3067629 Score: 567
Period size: 59 Copynumber: 11.1 Consensus size: 59
3066964 TTAGCACTCT
* * * *
3066974 TAGTGCTCTATCTGGAATAT-CATATACTTAATATGATTTCCTTCTCATTTTAGCACACGA
1 TAGTGCTCTATATGGAA-ATCCATATACTTAGTATGATTTCCTTATCATTTTAGCACA-TA
* * * *
3067034 -AGTGCCCTAT-TCGAGAATCCATA-CCATTAGTATGA-TTCCTTTACCATTTTTAGCACAT-
1 TAGTGCTCTATATGGA-AATCCATATAC-TTAGTATGATTTCC-TTATCA-TTTTAGCACATA
* * * *
3067092 TAAGTGCGCTAT-TCGAAAATCCATACTA-TTAGTATGA-TCCCTTTACCATTTTTAGCACATGA
1 T-AGTGCTCTATAT-GGAAATCCATA-TACTTAGTATGATTTCC-TTATCA-TTTTAGCACAT-A
* * * * *
3067154 -AGTGC-CTTATATGAAAATCCATACT-GTTAGTATGATTTCCTTATCCTTGTAGCACCCT-
1 TAGTGCTC-TATATGGAAATCCATA-TACTTAGTATGATTTCCTTATCATTTTAGCA-CATA
* * * * * * *
3067212 TAGTGCTTTTTCTGGAAATCCATACAGTCAGTATGA-TTCTCTTACCATTTTAGCACATA
1 TAGTGCTCTATATGGAAATCCATATACTTAGTATGATTTC-CTTATCATTTTAGCACATA
* * * * * *
3067271 TAATTCCCTATCTAGAAATCCATATA-TTCAATATGATTT-CTTATCATTTTAGCACATA
1 TAGTGCTCTATATGGAAATCCATATACTT-AGTATGATTTCCTTATCATTTTAGCACATA
* * * *
3067329 TAATGC-CTTATCTGGAAATCCATATA-TTCAATATGATTTCCTTATCATTTTAGCACACA
1 TAGTGCTC-TATATGGAAATCCATATACTT-AGTATGATTTCCTTATCATTTTAGCACATA
* * * *
3067388 TAATACCCTATATGGAAATCCATATA-TTCAATATGATTTCCTTATCATTTTAGCACATA
1 TAGTGCTCTATATGGAAATCCATATACTT-AGTATGATTTCCTTATCATTTTAGCACATA
* * * * * *
3067447 TAATGCTCCATATGTAAATCCATACACTCAGTATGATTTCATTATCATTTTAGCACATA
1 TAGTGCTCTATATGGAAATCCATATACTTAGTATGATTTCCTTATCATTTTAGCACATA
* *
3067506 TAGTGCTCCATATGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACATA
1 TAGTGCTCTATATGGAAATCCATATACTTAGTATGATTTCCTTATCATTTTAGCACATA
* *
3067565 TAGTGCTCCATATGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACATA
1 TAGTGCTCTATATGGAAATCCATATACTTAGTATGATTTCCTTATCATTTTAGCACATA
3067624 TAGTGC
1 TAGTGC
3067630 CATTTGGTAC
Statistics
Matches: 513, Mismatches: 55, Indels: 57
0.82 0.09 0.09
Matches are distributed among these distances:
57 1 0.00
58 69 0.13
59 339 0.66
60 99 0.19
61 5 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (59 bp):
TAGTGCTCTATATGGAAATCCATATACTTAGTATGATTTCCTTATCATTTTAGCACATA
Found at i:3067559 original size:177 final size:173
Alignment explanation
Indices: 3066986--3067625 Score: 618
Period size: 176 Copynumber: 3.6 Consensus size: 173
3066976 GTGCTCTATC
* * *
3066986 TGGAATAT-CATATACTTAATATGATTTCCTTCTCATTTTAGCACACGA-AGTGCCCTAT-TCGA
1 TGGAA-ATCCATACACTTAATATGATTTCCTTATCATTTTAGCACAC-ATAGTGCCCTATATGGA
* * *
3067048 GAATCCATACCATTAGTATGATTCCTTTACCATTTTTAGCACAT-TAAGTGCGCTAT-TCGAAAA
64 -AATCCATA-CATTAGTATGATTCC-TTACCA-TTTTAGCACATATAA-TGCTCCATAT-GTAAA
* ** *
3067111 TCCATACTATTAGTATGATCCCTTTACCATTTTTAGCACATGA-AGTGCCTTATA
123 TCCATAC-ATCAGTATGATTTC-TTATCA-TTTTAGCACAT-ATAGTGCCTTATA
* ** * * * * * ** * *
3067165 TGAAAATCCATACTGTTAGTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTTTCTGGAAA
1 TGGAAATCCATACACTTAATATGATTTCCTTATCATTTTAGCACACATAGTGCCCTATATGGAAA
* * *
3067230 TCCATACAGTCAGTATGATTCTCTTACCATTTTAGCACATATAAT--TCCCTATCTAGAAATCCA
66 TCCATACA-TTAGTATGATTC-CTTACCATTTTAGCACATATAATGCTCCATATGT--AAATCCA
* * * *
3067293 TATATTCAATATGATTTCTTATCATTTTAGCACATATAATGCCTTATC
127 TACA-TCAGTATGATTTCTTATCATTTTAGCACATATAGTGCCTTATA
* * *
3067341 TGGAAATCCATATA-TTCAATATGATTTCCTTATCATTTTAGCACACATAATACCCTATATGGAA
1 TGGAAATCCATACACTT-AATATGATTTCCTTATCATTTTAGCACACATAGTGCCCTATATGGAA
* * *
3067405 ATCCATATATTCAATATGATTTCCTTATCATTTTAGCACATATAATGCTCCATATGTAAATCCAT
65 ATCCATACATT-AGTATGA-TTCCTTACCATTTTAGCACATATAATGCTCCATATGTAAATCCAT
*
3067470 ACACTCAGTATGATTTCATTATCATTTTAGCACATATAGTG-CTCCATA
128 ACA-TCAGTATGATTTC-TTATCATTTTAGCACATATAGTGCCT-TATA
* *
3067518 TGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCC-ATATGGAA
1 TGGAAATCCATACACTTAATATGATTTCCTTATCATTTTAGCACACATAGTGC-CCTATATGGAA
*
3067582 ATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACATATA
65 ATCCATACA-TTAGTATGA-TTCCTTACCATTTTAGCACATATA
3067626 GTGCCATTTG
Statistics
Matches: 379, Mismatches: 61, Indels: 44
0.78 0.13 0.09
Matches are distributed among these distances:
175 4 0.01
176 129 0.34
177 126 0.33
178 47 0.12
179 69 0.18
180 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.38
Consensus pattern (173 bp):
TGGAAATCCATACACTTAATATGATTTCCTTATCATTTTAGCACACATAGTGCCCTATATGGAAA
TCCATACATTAGTATGATTCCTTACCATTTTAGCACATATAATGCTCCATATGTAAATCCATACA
TCAGTATGATTTCTTATCATTTTAGCACATATAGTGCCTTATA
Found at i:3075220 original size:23 final size:23
Alignment explanation
Indices: 3075177--3075266 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
3075167 CCCGAATAAT
*
3075177 CACATAGATATCTCCCAAAGGAC
1 CACATAGATATGTCCCAAAGGAC
3075200 CACATAGATATGTCCCAAAGGAC
1 CACATAGATATGTCCCAAAGGAC
* * * * *
3075223 CGCGTAGAAATGTCCCGAACGAC
1 CACATAGATATGTCCCAAAGGAC
*
3075246 CACGTAGA-ATTGTCCCGAAAG
1 CACATAGATA-TGTCCC-AAAG
3075267 ACCGCGTAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
22 1 0.02
23 53 0.95
24 2 0.04
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.17
Consensus pattern (23 bp):
CACATAGATATGTCCCAAAGGAC
Found at i:3075269 original size:23 final size:23
Alignment explanation
Indices: 3075189--3075277 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
3075179 CATAGATATC
*
3075189 TCCCAAAGGACCACATAG-ATATG
1 TCCCAAAGGACCACGTAGAAT-TG
* *
3075212 TCCCAAAGGACCGCGTAGAAATG
1 TCCCAAAGGACCACGTAGAATTG
* *
3075235 TCCCGAACGACCACGTAGAATTG
1 TCCCAAAGGACCACGTAGAATTG
*
3075258 TCCCGAAA-GACCGCGTAGAA
1 TCCC-AAAGGACCACGTAGAA
3075278 CTCTTGACTC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 52 0.95
24 3 0.05
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (23 bp):
TCCCAAAGGACCACGTAGAATTG
Found at i:3083807 original size:3 final size:3
Alignment explanation
Indices: 3083793--3083856 Score: 67
Period size: 3 Copynumber: 20.3 Consensus size: 3
3083783 TTTCAATATA
*
3083793 ATT ATAT ATT ATT A-T ATT ATA ATT ACGTT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT A--TT ATT ATT ATT ATT ATT ATT
*
3083840 ATT ATA ATT AATT ATT A
1 ATT ATT ATT -ATT ATT A
3083857 CAATTTTACA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 2 0.04
3 41 0.79
4 6 0.12
5 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:3084210 original size:31 final size:29
Alignment explanation
Indices: 3084141--3084211 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
3084131 AATTTAAATA
*
3084141 GTGACCAAATTGA-AAATTTTGAAAGTTTG
1 GTGACCAAAGT-ATAAATTTTGAAAGTTTG
*
3084170 GTGATCAAAGTATAAATTTTGGAAAAGTTTAG
1 GTGACCAAAGTATAAATTTT-G-AAAGTTT-G
3084202 G-GACCAAAGT
1 GTGACCAAAGT
3084212 GGTAAGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 1 0.03
29 16 0.46
30 1 0.03
31 15 0.43
32 2 0.06
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (29 bp):
GTGACCAAAGTATAAATTTTGAAAGTTTG
Found at i:3085775 original size:18 final size:18
Alignment explanation
Indices: 3085752--3085788 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3085742 AACTGCCGTA
3085752 ATGTTTATACATGGTTAT
1 ATGTTTATACATGGTTAT
3085770 ATGTTTATACATGGTTAT
1 ATGTTTATACATGGTTAT
3085788 A
1 A
3085789 AGTTCAGTGA
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:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (18 bp):
ATGTTTATACATGGTTAT
Found at i:3085923 original size:3 final size:3
Alignment explanation
Indices: 3085909--3085963 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
3085899 TTTCAATATA
* *
3085909 ATT ATAT ATT ATT A-T ATT ATA ATT A-C ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3085953 ATT AATT ATT A
1 ATT -ATT ATT A
3085964 CAATTTTACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 35 0.80
4 6 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:3085938 original size:11 final size:11
Alignment explanation
Indices: 3085905--3085961 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
3085895 TTGATTTCAA
3085905 TATAATTATA-
1 TATAATTATAT
*
3085915 TATTATTATAT
1 TATAATTATAT
*
3085926 TATAATTACAT
1 TATAATTATAT
*
3085937 TATTATTATTAT
1 TATAATTA-TAT
*
3085949 TATTATTA-AT
1 TATAATTATAT
3085959 TAT
1 TAT
3085962 TACAATTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 14 0.35
11 16 0.40
12 10 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TATAATTATAT
Found at i:3086318 original size:31 final size:29
Alignment explanation
Indices: 3086262--3086319 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
3086252 ACCAAATTGG
*
3086262 AAATTTTGAAAGTTTGGTGATCAAAGTAT
1 AAATTTTGAAAGTTTGGTGACCAAAGTAT
3086291 AAATTTTGGAAAAGTTTAGG-GACCAAAGT
1 AAATTTT-G-AAAGTTT-GGTGACCAAAGT
3086320 GGCAAGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
30 1 0.04
31 15 0.60
32 2 0.08
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (29 bp):
AAATTTTGAAAGTTTGGTGACCAAAGTAT
Found at i:3087880 original size:18 final size:18
Alignment explanation
Indices: 3087857--3087893 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3087847 AACTGCCGTA
3087857 ATGTTTATACATGGTTAT
1 ATGTTTATACATGGTTAT
3087875 ATGTTTATACATGGTTAT
1 ATGTTTATACATGGTTAT
3087893 A
1 A
3087894 GGTTCAGTGA
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:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (18 bp):
ATGTTTATACATGGTTAT
Found at i:3088028 original size:3 final size:3
Alignment explanation
Indices: 3088014--3088068 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
3088004 TTTCAATATA
* *
3088014 ATT ATAT ATT ATT A-T ATT ATA ATT A-C ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3088058 ATT AATT ATT A
1 ATT -ATT ATT A
3088069 CAATTTTACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 35 0.80
4 6 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:3088043 original size:11 final size:11
Alignment explanation
Indices: 3088010--3088066 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
3088000 TTGATTTCAA
3088010 TATAATTATA-
1 TATAATTATAT
*
3088020 TATTATTATAT
1 TATAATTATAT
*
3088031 TATAATTACAT
1 TATAATTATAT
*
3088042 TATTATTATTAT
1 TATAATTA-TAT
*
3088054 TATTATTA-AT
1 TATAATTATAT
3088064 TAT
1 TAT
3088067 TACAATTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 14 0.35
11 16 0.40
12 10 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TATAATTATAT
Found at i:3088423 original size:31 final size:29
Alignment explanation
Indices: 3088367--3088424 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
3088357 ACCAAATTGG
*
3088367 AAATTTTGAAAGTTTGGTGATCAAAGTAT
1 AAATTTTGAAAGTTTGGTGACCAAAGTAT
3088396 AAATTTTGGAAAAGTTTAGG-GACCAAAGT
1 AAATTTT-G-AAAGTTT-GGTGACCAAAGT
3088425 GGCAAGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
30 1 0.04
31 15 0.60
32 2 0.08
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (29 bp):
AAATTTTGAAAGTTTGGTGACCAAAGTAT
Found at i:3089294 original size:30 final size:31
Alignment explanation
Indices: 3089254--3089322 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
3089244 ACAAGCCTTA
* * *
3089254 GAAAATTTTGGGGACC-ATTATG-TACTTTTT
1 GAAAAGTTTGGGGACCAATT-TGATAATTTTG
3089284 GAAAAGTTTGGGGACCAATTTGATAATTTTG
1 GAAAAGTTTGGGGACCAATTTGATAATTTTG
3089315 GAAAAGTT
1 GAAAAGTT
3089323 ATGATTGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (31 bp):
GAAAAGTTTGGGGACCAATTTGATAATTTTG
Found at i:3089989 original size:18 final size:18
Alignment explanation
Indices: 3089966--3090002 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3089956 AACTGCCGTA
3089966 ATGTTTATACATGGTTAT
1 ATGTTTATACATGGTTAT
3089984 ATGTTTATACATGGTTAT
1 ATGTTTATACATGGTTAT
3090002 A
1 A
3090003 GGTTCAGTGA
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:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (18 bp):
ATGTTTATACATGGTTAT
Found at i:3090137 original size:3 final size:3
Alignment explanation
Indices: 3090123--3090177 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
3090113 TTTCAATATA
* *
3090123 ATT ATAT ATT ATT A-T ATT ATA ATT A-C ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3090167 ATT AATT ATT A
1 ATT -ATT ATT A
3090178 CAATTTTACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 35 0.80
4 6 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:3090152 original size:11 final size:11
Alignment explanation
Indices: 3090119--3090175 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
3090109 TTGATTTCAA
3090119 TATAATTATA-
1 TATAATTATAT
*
3090129 TATTATTATAT
1 TATAATTATAT
*
3090140 TATAATTACAT
1 TATAATTATAT
*
3090151 TATTATTATTAT
1 TATAATTA-TAT
*
3090163 TATTATTA-AT
1 TATAATTATAT
3090173 TAT
1 TAT
3090176 TACAATTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 14 0.35
11 16 0.40
12 10 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TATAATTATAT
Found at i:3090532 original size:31 final size:29
Alignment explanation
Indices: 3090476--3090533 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
3090466 ACCAAATTGG
*
3090476 AAATTTTGAAAGTTTGGTGATCAAAGTAT
1 AAATTTTGAAAGTTTGGTGACCAAAGTAT
3090505 AAATTTTGGAAAAGTTTAGG-GACCAAAGT
1 AAATTTT-G-AAAGTTT-GGTGACCAAAGT
3090534 GGCAAGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
30 1 0.04
31 15 0.60
32 2 0.08
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (29 bp):
AAATTTTGAAAGTTTGGTGACCAAAGTAT
Found at i:3091402 original size:30 final size:31
Alignment explanation
Indices: 3091363--3091430 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
3091353 ACAAGCCTTA
* *
3091363 GAAAA-TTTGGGGACC-ATTATG-TACTTTTT
1 GAAAAGTTTGGGGACCAATT-TGATAATTTTG
3091392 GAAAAGTTTGGGGACCAATTTGATAATTTTG
1 GAAAAGTTTGGGGACCAATTTGATAATTTTG
3091423 GAAAAGTT
1 GAAAAGTT
3091431 ATGATTGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 5 0.15
30 12 0.35
31 17 0.50
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (31 bp):
GAAAAGTTTGGGGACCAATTTGATAATTTTG
Found at i:3098375 original size:18 final size:18
Alignment explanation
Indices: 3098354--3098389 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3098344 AAAAATGCTA
3098354 TCTTTTGGTACCAATTAT
1 TCTTTTGGTACCAATTAT
3098372 TCTTTTGGTACCAATTAT
1 TCTTTTGGTACCAATTAT
3098390 GCTTACTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (18 bp):
TCTTTTGGTACCAATTAT
Found at i:3098850 original size:30 final size:30
Alignment explanation
Indices: 3098806--3098873 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
3098796 TAAGCCTTAG
*
3098806 GAAAA-TTTGGGGACC-A-TTATGTAATTTTT
1 GAAAAGTTGGGGGACCAATTTA-GTAA-TTTT
3098835 GAAAAGTTGGGGGACCAATTTAGTAATTTT
1 GAAAAGTTGGGGGACCAATTTAGTAATTTT
3098865 GTAAAAGTT
1 G-AAAAGTT
3098874 ATGAATGGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 5 0.15
30 14 0.41
31 12 0.35
32 3 0.09
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (30 bp):
GAAAAGTTGGGGGACCAATTTAGTAATTTT
Found at i:3099438 original size:24 final size:24
Alignment explanation
Indices: 3099411--3099456 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
3099401 GCATGACATG
3099411 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
3099435 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
3099457 ATCAGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:3110963 original size:35 final size:35
Alignment explanation
Indices: 3110920--3111017 Score: 151
Period size: 35 Copynumber: 2.8 Consensus size: 35
3110910 TTTTCTTGCA
*
3110920 AATCAAGCCTTCACAAAAGTGTAGTGAAGAAATGC
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGAAATGC
* * *
3110955 AATCAAGCCTTCATAAAAAAGTAGTGAAGCAATGC
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGAAATGC
*
3110990 AATCAAGCCTTCGCAAAAGAGTAGTGAA
1 AATCAAGCCTTCACAAAAGAGTAGTGAA
3111018 ACAAGATCAG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.19
Consensus pattern (35 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGAAATGC
Found at i:3113294 original size:12 final size:12
Alignment explanation
Indices: 3113279--3113325 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
3113269 AAATCGTTTG
3113279 TAAAACATCAAA
1 TAAAACATCAAA
*
3113291 TAAAACTATC-CA
1 TAAAAC-ATCAAA
*
3113303 TAATAACATGAAA
1 TAA-AACATCAAA
3113316 TAAAACATCA
1 TAAAACATCA
3113326 TAAATCAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.21
Consensus pattern (12 bp):
TAAAACATCAAA
Found at i:3113310 original size:25 final size:23
Alignment explanation
Indices: 3113282--3113328 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
3113272 TCGTTTGTAA
3113282 AACATCAAATAAAACTATCCATAAT
1 AACATCAAATAAAAC-AT-CATAAT
*
3113307 AACATGAAATAAAACATCATAA
1 AACATCAAATAAAACATCATAA
3113329 ATCAGAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 14 0.67
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.21
Consensus pattern (23 bp):
AACATCAAATAAAACATCATAAT
Found at i:3127347 original size:18 final size:19
Alignment explanation
Indices: 3127314--3127349 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3127304 AATATAAAGC
3127314 GACAAAAAGAACTTGTTAT
1 GACAAAAAGAACTTGTTAT
*
3127333 GACAAAAA-AATTTGTTA
1 GACAAAAAGAACTTGTTA
3127350 GTTGCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (19 bp):
GACAAAAAGAACTTGTTAT
Found at i:3132614 original size:136 final size:136
Alignment explanation
Indices: 3132453--3132700 Score: 399
Period size: 136 Copynumber: 1.8 Consensus size: 136
3132443 AATGTATATG
* *
3132453 AATTATATATATAATTAGTATCAATACTTG-ATATGTATATGAATCTTGCAAGAAATATTTATGA
1 AATTATATATATAATTAATATCAATA-TTGAATATGTATATGAATCTTGCAAGAAATACTTATGA
* **
3132517 TTAATAATTAGGGTAAATTACTTGAATGATTATCTAACTATAGAATTGGTGTCGATATGTCCATC
65 TTAATAATTAGGGTAAACTACTTGAATGAACATCTAACTATAGAATTGGTGTCGATATGTCCATC
3132582 ACTTTAA
130 ACTTTAA
* * *
3132589 AATTATATATGTAATTAATATCAATATTGAATATGTATATGAATCTTGTATGAAATACTTATGAT
1 AATTATATATATAATTAATATCAATATTGAATATGTATATGAATCTTGCAAGAAATACTTATGAT
*
3132654 TAATAATTAGGGTAAACTACTTGAATGAACATCTAACTATGGAATTG
66 TAATAATTAGGGTAAACTACTTGAATGAACATCTAACTATAGAATTG
3132701 ACGTTGATAT
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
135 3 0.03
136 99 0.97
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (136 bp):
AATTATATATATAATTAATATCAATATTGAATATGTATATGAATCTTGCAAGAAATACTTATGAT
TAATAATTAGGGTAAACTACTTGAATGAACATCTAACTATAGAATTGGTGTCGATATGTCCATCA
CTTTAA
Found at i:3132710 original size:136 final size:137
Alignment explanation
Indices: 3132453--3132729 Score: 396
Period size: 136 Copynumber: 2.0 Consensus size: 137
3132443 AATGTATATG
* *
3132453 AATTATATATATAATTAGTATCAATACTTGATATGTATATGAATCTTGCAAGAAATATTTATGAT
1 AATTATATATATAATTAATATCAATACTTGATATGTATATGAATCTTGCAAGAAATACTTATGAT
* ** ** * *
3132518 TAATAATTAGGGTAAATTACTTGAATGATTATCTAACTATAGAATTGGTGTCGATATGTCCATCA
66 TAATAATTAGGGTAAACTACTTGAATGAACATCTAACTATAGAATTGACGTCGATATGACCACCA
3132583 CTTT-AA
131 CTTTCAA
* * *
3132589 AATTATATATGTAATTAATATCAATA-TTGAATATGTATATGAATCTTGTATGAAATACTTATGA
1 AATTATATATATAATTAATATCAATACTTG-ATATGTATATGAATCTTGCAAGAAATACTTATGA
* *
3132653 TTAATAATTAGGGTAAACTACTTGAATGAACATCTAACTATGGAATTGACGTTGATATGACCACC
65 TTAATAATTAGGGTAAACTACTTGAATGAACATCTAACTATAGAATTGACGTCGATATGACCACC
*
3132718 ATTTTCAA
130 ACTTTCAA
3132726 AATT
1 AATT
3132730 TTATCAATAT
Statistics
Matches: 124, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
135 3 0.02
136 115 0.93
137 6 0.05
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (137 bp):
AATTATATATATAATTAATATCAATACTTGATATGTATATGAATCTTGCAAGAAATACTTATGAT
TAATAATTAGGGTAAACTACTTGAATGAACATCTAACTATAGAATTGACGTCGATATGACCACCA
CTTTCAA
Found at i:3134886 original size:14 final size:14
Alignment explanation
Indices: 3134867--3134895 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3134857 TATCAATTTT
3134867 ATAAAAATAAATTA
1 ATAAAAATAAATTA
3134881 ATAAAAATAAATTA
1 ATAAAAATAAATTA
3134895 A
1 A
3134896 AATGTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAAATAAATTA
Found at i:3136036 original size:16 final size:16
Alignment explanation
Indices: 3136015--3136046 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3136005 GCATAAGAGC
3136015 ATGACACGTGTTGTTA
1 ATGACACGTGTTGTTA
3136031 ATGACACGTGTTGTTA
1 ATGACACGTGTTGTTA
3136047 GTGATACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (16 bp):
ATGACACGTGTTGTTA
Found at i:3136058 original size:16 final size:16
Alignment explanation
Indices: 3136015--3136058 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
3136005 GCATAAGAGC
*
3136015 ATGACACGTGTTGTTA
1 ATGACACATGTTGTTA
*
3136031 ATGACACGTGTTGTTA
1 ATGACACATGTTGTTA
* *
3136047 GTGATACATGTT
1 ATGACACATGTT
3136059 TTTTAGTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (16 bp):
ATGACACATGTTGTTA
Found at i:3141632 original size:39 final size:39
Alignment explanation
Indices: 3141589--3141707 Score: 168
Period size: 39 Copynumber: 3.1 Consensus size: 39
3141579 TACAACTTGG
*
3141589 AATGTTGGGACATTTTAAAGGCTCATATCAGCAAGAAAT
1 AATGTTGGGACATTTTGAAGGCTCATATCAGCAAGAAAT
* * *
3141628 AATGTTGGGACATTTTGAAGGCTCACATCAACATGAAA-
1 AATGTTGGGACATTTTGAAGGCTCATATCAGCAAGAAAT
* * *
3141666 AATATTGGGGCATTTTGAAGGCTCATATCAGCAATAAAT
1 AATGTTGGGACATTTTGAAGGCTCATATCAGCAAGAAAT
3141705 AAT
1 AAT
3141708 TTTGAATGGA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
38 32 0.46
39 37 0.54
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (39 bp):
AATGTTGGGACATTTTGAAGGCTCATATCAGCAAGAAAT
Found at i:3143149 original size:20 final size:20
Alignment explanation
Indices: 3143126--3143198 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
3143116 CCCAAATTTT
3143126 TAAATCTTTCGGGTCATCAG
1 TAAATCTTTCGGGTCATCAG
* *
3143146 TAAATCTTTCGAG-CATGATG
1 TAAATCTTTCGGGTCATCA-G
*
3143166 TATAAATCTTTCGGGTCATCTG
1 --TAAATCTTTCGGGTCATCAG
3143188 TCAAA-CTTTCG
1 T-AAATCTTTCG
3143199 AGCAAGATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.09
20 20 0.47
21 3 0.07
22 13 0.30
23 3 0.07
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (20 bp):
TAAATCTTTCGGGTCATCAG
Found at i:3143185 original size:42 final size:42
Alignment explanation
Indices: 3143126--3143208 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
3143116 CCCAAATTTT
*
3143126 TAAATCTTTCGGGTCATCAGT-AAATCTTTCGAGCATGATGTA
1 TAAATCTTTCGGGTCATCAGTCAAA-CTTTCGAGCAAGATGTA
*
3143168 TAAATCTTTCGGGTCATCTGTCAAACTTTCGAGCAAGATGT
1 TAAATCTTTCGGGTCATCAGTCAAACTTTCGAGCAAGATGT
3143209 TAAGTCCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (42 bp):
TAAATCTTTCGGGTCATCAGTCAAACTTTCGAGCAAGATGTA
Found at i:3143677 original size:42 final size:41
Alignment explanation
Indices: 3143630--3143709 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
3143620 AAATCATTCG
*
3143630 GTCATCTGTAAGTCCTTCGAGCATGATGCTTAAATCCTTTGA
1 GTCATCTGTAAGTCCTTCGAGCAAGATG-TTAAATCCTTTGA
* * * *
3143672 GTCATCTGTTAGTCTTTTGAGCAAGATGTTAAGTCCTT
1 GTCATCTGTAAGTCCTTCGAGCAAGATGTTAAATCCTT
3143710 CGGGCAAGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 9 0.27
42 24 0.73
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (41 bp):
GTCATCTGTAAGTCCTTCGAGCAAGATGTTAAATCCTTTGA
Found at i:3143701 original size:20 final size:20
Alignment explanation
Indices: 3143678--3143723 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3143668 TTGAGTCATC
* *
3143678 TGTTAGTCTTTTGAGCAAGA
1 TGTTAGTCCTTCGAGCAAGA
*
3143698 TGTTAAGTCCTTCGGGCAAGA
1 TGTT-AGTCCTTCGAGCAAGA
3143719 TGTTA
1 TGTTA
3143724 AGTTCTTCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (20 bp):
TGTTAGTCCTTCGAGCAAGA
Found at i:3143716 original size:21 final size:21
Alignment explanation
Indices: 3143692--3143735 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3143682 AGTCTTTTGA
3143692 GCAAGATGTTAAGTCCTTCGG
1 GCAAGATGTTAAGTCCTTCGG
*
3143713 GCAAGATGTTAAGTTCTTCGG
1 GCAAGATGTTAAGTCCTTCGG
3143734 GC
1 GC
3143736 CATCCATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (21 bp):
GCAAGATGTTAAGTCCTTCGG
Found at i:3147292 original size:14 final size:16
Alignment explanation
Indices: 3147253--3147293 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
3147243 AATTTTGACC
3147253 AAAAATCATTATGATG
1 AAAAATCATTATGATG
3147269 AACAAA-CATT-T-ATG
1 AA-AAATCATTATGATG
3147283 AAAAATCATTA
1 AAAAATCATTA
3147294 AAATAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 1 0.05
16 6 0.27
17 3 0.14
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (16 bp):
AAAAATCATTATGATG
Found at i:3174876 original size:23 final size:23
Alignment explanation
Indices: 3174850--3174895 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3174840 AAACCCACAT
3174850 GCTCTTCCCACCCCATACAAGCA
1 GCTCTTCCCACCCCATACAAGCA
3174873 GCTCTTCCCACCCCATACAAGCA
1 GCTCTTCCCACCCCATACAAGCA
3174896 AACACACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.48, G:0.09, T:0.17
Consensus pattern (23 bp):
GCTCTTCCCACCCCATACAAGCA
Found at i:3182890 original size:20 final size:20
Alignment explanation
Indices: 3182843--3182896 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
3182833 GTTGGAACTC
3182843 AAAGTTTCAAAACTTTAAGG
1 AAAGTTTCAAAACTTTAAGG
* * * *
3182863 AAAATTTCAAAATTTTTATG
1 AAAGTTTCAAAACTTTAAGG
*
3182883 AAAGTTTCGAAACT
1 AAAGTTTCAAAACT
3182897 ATTGAAATGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (20 bp):
AAAGTTTCAAAACTTTAAGG
Found at i:3184151 original size:24 final size:24
Alignment explanation
Indices: 3184124--3184179 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
3184114 CATTTAGTTT
3184124 TTTAA-TATATAATAATATTACATA
1 TTTAATTAT-TAATAATATTACATA
* *
3184148 TTTAATTATTAATAATTTTATATA
1 TTTAATTATTAATAATATTACATA
*
3184172 TTAAATTA
1 TTTAATTA
3184180 AACTAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTAATTATTAATAATATTACATA
Found at i:3185374 original size:19 final size:19
Alignment explanation
Indices: 3185350--3185390 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
3185340 ATTTCGACCG
3185350 TCGGTAAACTTAGAGTGCA
1 TCGGTAAACTTAGAGTGCA
3185369 TCGGTAAACTTAGAGTGCA
1 TCGGTAAACTTAGAGTGCA
3185388 TCG
1 TCG
3185391 ATGCATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (19 bp):
TCGGTAAACTTAGAGTGCA
Found at i:3186649 original size:21 final size:21
Alignment explanation
Indices: 3186625--3186671 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3186615 CCGAAGGAGG
3186625 AGGAGAAGCACGAGAAGAGCT
1 AGGAGAAGCACGAGAAGAGCT
3186646 AGGAGAAGCACGAGAAGAGCT
1 AGGAGAAGCACGAGAAGAGCT
3186667 AGGAG
1 AGGAG
3186672 CAGGAGGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.40, T:0.04
Consensus pattern (21 bp):
AGGAGAAGCACGAGAAGAGCT
Found at i:3188272 original size:23 final size:23
Alignment explanation
Indices: 3188237--3188318 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
3188227 GCATGGCCTT
*
3188237 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAAGA
* *
3188260 GTGCATC-AGTGCACCTTC-ATG-
1 GTGCATCGA-TGCACATTCAAAGA
*
3188281 GTGTATCGATGCACATTCAAAGA
1 GTGCATCGATGCACATTCAAAGA
3188304 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
3188319 TATTAAGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
21 14 0.29
22 6 0.12
23 16 0.33
24 12 0.25
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAAGA
Found at i:3192314 original size:117 final size:117
Alignment explanation
Indices: 3192101--3192315 Score: 247
Period size: 117 Copynumber: 1.8 Consensus size: 117
3192091 ATCAAAATTT
3192101 TCTTTTTCAATACTTTCAAATTTAACTTTTGAAAGCTCTAAATCCTTCTTCAAGAGTTTATTTTG
1 TCTTTTTCAATACTTTCAAATTTAACTTTTGAAAGCTCTAAATCCTTCTTCAAGAGTTTATTTTG
* * * *
3192166 ATTTTCAAAATCCATTTTCGTTTTTAGAAGAAGTTTGTTTAATTTGAAAATG
66 ATTTTCAAAATCCATTTTAGCTTTCAAAAGAAGTTTGTTTAATTTGAAAATG
* * * * * * *
3192218 TCTTTTTCAA-AGTTTTCAGATTTTAGTTTTGAAAGCTCTAACTCCTTTTTCAATA-TTTCATTT
1 TCTTTTTCAATA-CTTTCAAATTTAACTTTTGAAAGCTCTAAATCCTTCTTCAAGAGTTT-ATTT
* * **
3192281 T-ATTTTACCAAGTCTGTTTTAGCTTTCAAAAGAAG
64 TGATTTT-CAAAATCCATTTTAGCTTTCAAAAGAAG
3192316 ATCATTTTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
116 9 0.11
117 71 0.89
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.47
Consensus pattern (117 bp):
TCTTTTTCAATACTTTCAAATTTAACTTTTGAAAGCTCTAAATCCTTCTTCAAGAGTTTATTTTG
ATTTTCAAAATCCATTTTAGCTTTCAAAAGAAGTTTGTTTAATTTGAAAATG
Found at i:3199357 original size:18 final size:19
Alignment explanation
Indices: 3199320--3199357 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3199310 CAGATGCTCT
*
3199320 GAGCTGAAAGTCGATGTTA
1 GAGCTGAAAGTCCATGTTA
*
3199339 GAGCTGAAAG-CCTTGTTA
1 GAGCTGAAAGTCCATGTTA
3199357 G
1 G
3199358 TGCGCACGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (19 bp):
GAGCTGAAAGTCCATGTTA
Found at i:3199709 original size:20 final size:20
Alignment explanation
Indices: 3199684--3199729 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3199674 ATAAAGAGAG
3199684 AAATGTTTGAGTTTGCTGTA
1 AAATGTTTGAGTTTGCTGTA
*
3199704 AAATGTTTGAGTTTGTTGTA
1 AAATGTTTGAGTTTGCTGTA
3199724 AAATGT
1 AAATGT
3199730 CTGGTGTGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.46
Consensus pattern (20 bp):
AAATGTTTGAGTTTGCTGTA
Found at i:3203856 original size:20 final size:21
Alignment explanation
Indices: 3203813--3203880 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 21
3203803 TTTATCCAAC
*
3203813 TTATTAAATATATTTTATT-T
1 TTATAAAATATATTTTATTAT
3203833 TTATTTAAAAATATATTTTATTA-
1 TTA--T-AAAATATATTTTATTAT
* * *
3203856 TTATCAATTATATTTTATTTT
1 TTATAAAATATATTTTATTAT
3203877 TTAT
1 TTAT
3203881 TAACATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 16 0.41
21 5 0.13
22 1 0.03
23 17 0.44
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATAAAATATATTTTATTAT
Found at i:3204026 original size:25 final size:25
Alignment explanation
Indices: 3203986--3204053 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
3203976 AAATTAATTA
*
3203986 AATAATAAAAATATATTTTTTAAGTT
1 AATAA-AAAAATATATTTTTAAAGTT
*
3204012 AATAAAAAAATATATGTTTAAAGTT
1 AATAAAAAAATATATTTTTAAAGTT
* *
3204037 AAGAATAAAATATATTT
1 AATAAAAAAATATATTT
3204054 AATAAGTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 32 0.86
26 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
AATAAAAAAATATATTTTTAAAGTT
Found at i:3204060 original size:25 final size:25
Alignment explanation
Indices: 3203992--3204061 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
3203982 ATTAAATAAT
* *
3203992 AAAAATATATTTTTTAAGTTAATAA
1 AAAAATATATTTTATAAGTTAAGAA
3204017 AAAAATATATGTTTA-AAGTTAAGAA
1 AAAAATATAT-TTTATAAGTTAAGAA
* *
3204042 TAAAATATATTTAATAAGTT
1 AAAAATATATTTTATAAGTT
3204062 GGATATACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.08
25 33 0.85
26 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (25 bp):
AAAAATATATTTTATAAGTTAAGAA
Found at i:3204906 original size:349 final size:348
Alignment explanation
Indices: 3204243--3204941 Score: 1293
Period size: 350 Copynumber: 2.0 Consensus size: 348
3204233 ATGTAATCCC
3204243 AACGCCCTTGGTTTAAATCCCCAAATGCTAATATTTTTTTAATTTGTTTTTTGTAAGAGGGTGTA
1 AACGCCCTTGGTTTAAATCCCCAAATGCTAATATTTTTTTAATTTGTTTTTTGTAAGAGGGTGTA
3204308 TGGGCCACCCTCTGGTTGGAGGAAACTAAATTTAATGAATGAAATAAATTATAAATAAACTTACC
66 TGGGCCACCCTCTGGTTGGAGGAAACTAAATTTAATGAATGAAATAAATTATAAATAAACTTACC
3204373 CATGTAATTAGAGATTGACACTGTCGCAATTTAATTAGAGGACTAAATTTGACATCGTGTAATAA
131 CATGTAATTAGAGATTGACACTGTCGCAATTTAATTAGAGGACTAAATTTGACATCGTGTAATAA
3204438 GTAACAAAGGACCTTATATGCAATTACACCATAAAAATTAACTATGGCGTCATTTCTCTGTTAAA
196 GTAACAAAGGACCTTATATGCAATTACACCATAAAAATTAACTATGGCGTCATTTCTCTGTTAAA
3204503 TTTTAACTTCCACGTCACCGCCACCGTTAAAAGTTAATGGCCAGTGGCTTGGTT-AAGCATTTAA
261 TTTTAACTTCCACGTCACCGCCACCGTTAAAAGTTAATGGCCAGTGGCTTGGTTAAAGCATTTAA
3204567 ATAATTA-GTGGTATGA-TGATT
326 ATAATTATGTGGTATGATTGATT
3204588 AACGCCCTTGGTTTAAATCCCCAAATGCTAATATTTTTTTAATTTGTTTTCTTGTAATTAGAGGG
1 AACGCCCTTGGTTTAAATCCCCAAATGCTAATATTTTTTTAATTTGTTTT-TTGT-A--AGAGGG
3204653 TAGTATGGGCCACCCTCTGGTTGGAGGAAACTAAATTTAATGAATGAAATAAATTATAAATAAAC
62 T-GTATGGGCCACCCTCTGGTTGGAGGAAACTAAATTTAATGAATGAAATAAATTATAAATAAAC
3204718 TTACCCATGTAATTAGAGATTGACACATGTCGCAATTTAATTAGAGGACTAAATTTGACATCGTG
126 TTACCCATGTAATTAGAGATTGACAC-TGTCGCAATTTAATTAGAGGACTAAATTTGACATCGTG
3204783 T-ATAAGTAACAAA-GACCTTATATGCAATTACACCAT-AAAATTAACTATGGCGTCATTTTCTC
190 TAATAAGTAACAAAGGACCTTATATGCAATTACACCATAAAAATTAACTATGGCGTCA-TTTCTC
3204845 TGTTAAATTTTAACTTCCACGTCACCGCCACCGTTAAAAGTTAATGGCCAGTGGCTTGGTTAAAG
254 TGTTAAATTTTAACTTCCACGTCACCGCCACCGTTAAAAGTTAATGGCCAGTGGCTTGGTTAAAG
3204910 CATTTAAATAATTATGTGGTATGATTGATT
319 CATTTAAATAATTATGTGGTATGATTGATT
3204940 AA
1 AA
3204942 ATTGAAACAT
Statistics
Matches: 344, Mismatches: 0, Indels: 13
0.96 0.00 0.04
Matches are distributed among these distances:
345 50 0.15
346 4 0.01
347 1 0.00
348 19 0.06
349 97 0.28
350 118 0.34
351 48 0.14
352 7 0.02
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (348 bp):
AACGCCCTTGGTTTAAATCCCCAAATGCTAATATTTTTTTAATTTGTTTTTTGTAAGAGGGTGTA
TGGGCCACCCTCTGGTTGGAGGAAACTAAATTTAATGAATGAAATAAATTATAAATAAACTTACC
CATGTAATTAGAGATTGACACTGTCGCAATTTAATTAGAGGACTAAATTTGACATCGTGTAATAA
GTAACAAAGGACCTTATATGCAATTACACCATAAAAATTAACTATGGCGTCATTTCTCTGTTAAA
TTTTAACTTCCACGTCACCGCCACCGTTAAAAGTTAATGGCCAGTGGCTTGGTTAAAGCATTTAA
ATAATTATGTGGTATGATTGATT
Found at i:3216726 original size:17 final size:17
Alignment explanation
Indices: 3216704--3216751 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 17
3216694 AGTGTCCCCG
3216704 GTATCGAAACCCTGTGA
1 GTATCGAAACCCTGTGA
3216721 GTATCGATACCACCCTGTGA
1 GTATCGA-A--ACCCTGTGA
*
3216741 GTATCAAAACC
1 GTATCGAAACC
3216752 AGACCAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 10 0.37
18 1 0.04
19 1 0.04
20 15 0.56
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (17 bp):
GTATCGAAACCCTGTGA
Found at i:3216752 original size:20 final size:20
Alignment explanation
Indices: 3216712--3216752 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3216702 CGGTATCGAA
* *
3216712 ACCCTGTGAGTATCGATACC
1 ACCCTGTGAGTATCAAAACC
3216732 ACCCTGTGAGTATCAAAACC
1 ACCCTGTGAGTATCAAAACC
3216752 A
1 A
3216753 GACCAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (20 bp):
ACCCTGTGAGTATCAAAACC
Found at i:3223703 original size:255 final size:247
Alignment explanation
Indices: 3223209--3224148 Score: 1075
Period size: 255 Copynumber: 3.7 Consensus size: 247
3223199 AGTTTCTTAC
* *
3223209 TTAGTAAGTCCTTC-GGCCTATCAGTAAGTCTTTCGAGCATGATGACTAAATCCTTTGGGTTATC
1 TTAGTAAGTCCTTCGGGCC-ATCAGTAAGTCTTTCGAGCATGATGATTAAA--------GTCATC
* * *
3223273 TATAAGCCTTTAGAGCAAGATGATAAGTCTTTCGGGCCA-CCAACAAGACCTTCGGGCAGGATGT
57 TATAAGCCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCC-ATAAGACCTTCGGGCAGGATGT
* * *
3223337 TTTCACATGTTTTTCGAAAAAAATGAGAAAACGATTTCCAAAGTTTATCATTTAAATTTGAAAAT
121 TTTCACATGTTTTT-GAAAAAAAAGAGAAAACGATTT-CAAAGTTTCTCATTTAAATCTGAAAAT
* * * *
3223402 TGAAATCTTTGAAAAGTAAGAAAAAAATTTACAAAGTTTCTTACCTAGTAAACTATTTGCAAAA
184 TGAAATTTTTGAAAAGTAAGAAAAAGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
* * * * **
3223466 TTTGTGAGACCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAA-TCATCTATAAGTAT
1 TTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAAGTCATCTATAAGCCT
* * *
3223530 TTCGAGCAAGATGATAAGTCATTGGGGTCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGT
66 TTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATG-
* *
3223595 TTTTTTGAGAGAAAAAAAACAGAGAAAACGATTTCAAATTTTTCTCACTTAAATCTGAAAATTGA
130 -TTTTT----G-AAAAAAA-AGAGAAAACGATTTCAAA-GTTTCTCATTTAAATCTGAAAATTGA
* *
3223660 AATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTACTTACCTAGTAAACTATTTCCAAAA
187 AATTTTTGAAAAGTAAGAAAAAGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
* *
3223721 TTGGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAAGGTCATCT
1 TTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATT--A-----AA-GTCATCT
* * * * * *
3223786 ATAAGCCTTTCGATCAAGATGATAAGTCTTTCGGGCCATCCATAATATCTTCGAGCAAGATGTTT
58 ATAAGCCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTT
3223851 TCACATGTTTTT-AAAAAAATA-AGAAAACGATTTCTAAAGTTTCTCATTTAAATCTGAAAATTG
123 TCACATGTTTTTGAAAAAAA-AGAGAAAACGATTTC-AAAGTTTCTCATTTAAATCTGAAAATTG
3223914 AAATTTTTGAAAAGTAAGAAAAAGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
186 AAATTTTTGAAAAGTAAGAAAAAGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
* *
3223976 TTAGTAAGTCCTTGGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCTTCGGGTCATCTA
1 TTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA-------GTCATCTA
* * * * * *
3224041 TAAGCCTTTCGAGCAAGATGATAAGTCATTTGGACAATCTATAAGAACTTCGGGTAGGATGTTTT
59 TAAGCCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTT
* * *
3224106 CTCATGTTTTTCG--AAAAATGAGAAAACAATTTCCAAAGTTTCT
124 CACATGTTTTT-GAAAAAAAAGAGAAAACGATTT-CAAAGTTTCT
3224149 TACCTAGTAA
Statistics
Matches: 588, Mismatches: 65, Indels: 63
0.82 0.09 0.09
Matches are distributed among these distances:
248 68 0.12
249 2 0.00
250 5 0.01
253 2 0.00
254 109 0.19
255 272 0.46
256 11 0.02
257 41 0.07
258 4 0.01
262 7 0.01
264 67 0.11
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (247 bp):
TTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAAGTCATCTATAAGCCT
TTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGT
TTTTGAAAAAAAAGAGAAAACGATTTCAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGA
AAAGTAAGAAAAAGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
Found at i:3224170 original size:196 final size:196
Alignment explanation
Indices: 3223917--3224344 Score: 650
Period size: 196 Copynumber: 2.2 Consensus size: 196
3223907 AAAATTGAAA
* *
3223917 TTTTT-GAAAAGTAAGAAAA-AGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAG
1 TTTTTCGAAAAATGAGAAAACA-ATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAG
*
3223980 TAAGTCCTTGGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAAT-CTTCGGGTCATCTATAA
65 TAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAA
* * *
3224044 GCCTTTCGAGCAAGATGATAAGTCATTT-GGACAATCTATAAGAA-CTTCGGGTAGGATGTTTTC
130 GCCTTTCGAGCAAGATGATAAGTC-TTTGGGAC-ATCCATAA-AACCTTCAGGCAGGATGTTTTC
*
3224107 TCATG
192 ACATG
*
3224112 TTTTTCGAAAAATGAGAAAACAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGT
1 TTTTTCGAAAAATGAGAAAACAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAGT
* * * *
3224177 ATGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTATAAT
66 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAG
* *
3224242 CCTTTTGAGCAAGATGATAAGTCTTTGGGTCATCCATAAAACCTTCAGGCAGGATGTTTTCACAT
131 CCTTTCGAGCAAGATGATAAGTCTTTGGGACATCCATAAAACCTTCAGGCAGGATGTTTTCACAT
3224307 G
196 G
*
3224308 TTTTTCGAAAAAAGAGAAAACAATTTCCAAAGTTTCT
1 TTTTTCGAAAAATGAGAAAACAATTTCCAAAGTTTCT
3224345 CATTTAAAAT
Statistics
Matches: 213, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
195 7 0.03
196 163 0.77
197 43 0.20
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (196 bp):
TTTTTCGAAAAATGAGAAAACAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTAGT
AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAG
CCTTTCGAGCAAGATGATAAGTCTTTGGGACATCCATAAAACCTTCAGGCAGGATGTTTTCACAT
G
Found at i:3224227 original size:42 final size:42
Alignment explanation
Indices: 3224180--3224259 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
3224170 AATTGGTATG
*
3224180 TCCTTCGGGCCATC-AGTAAGT-CTTTTGAGCATGATGATTAAA
1 TCCTTCGGGCCATCTA-TAA-TCCTTTTGAGCAAGATGATTAAA
*
3224222 TCCTTCGGGTCATCTATAATCCTTTTGAGCAAGATGAT
1 TCCTTCGGGCCATCTATAATCCTTTTGAGCAAGATGAT
3224260 AAGTCTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 1 0.03
42 32 0.94
43 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (42 bp):
TCCTTCGGGCCATCTATAATCCTTTTGAGCAAGATGATTAAA
Found at i:3224738 original size:3 final size:3
Alignment explanation
Indices: 3224730--3224765 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3224720 TGTCCGAGTT
*
3224730 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3224766 ATTTATGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3226129 original size:53 final size:54
Alignment explanation
Indices: 3226028--3226149 Score: 165
Period size: 53 Copynumber: 2.3 Consensus size: 54
3226018 CCCCATAGGA
* ** * *
3226028 GGAACAGATTCCCCCTAAATGGTTTTGGCCCCGAGATTTCCAGAATGCTCGGAG
1 GGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAAAATTCCAGAATGCTCGGAG
* *
3226082 GGAACCGATTCCCCCTAAACAGTTTT-GCTCCGAAAATTCCAGTATGCTCGGAG
1 GGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAAAATTCCAGAATGCTCGGAG
*
3226135 GGAACCGATCCCCCC
1 GGAACCGATTCCCCC
3226150 AAGGGGGTAC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 37 0.62
54 23 0.38
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (54 bp):
GGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAAAATTCCAGAATGCTCGGAG
Found at i:3232003 original size:21 final size:21
Alignment explanation
Indices: 3231977--3232016 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3231967 CTTCATTTGA
*
3231977 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3231998 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3232017 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3233957 original size:17 final size:17
Alignment explanation
Indices: 3233935--3233982 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
3233925 TTTCAACATT
3233935 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
3233952 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
3233969 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
3233983 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:3234710 original size:76 final size:75
Alignment explanation
Indices: 3234562--3234773 Score: 259
Period size: 76 Copynumber: 2.8 Consensus size: 75
3234552 CAATTCAAAG
* * * *
3234562 CCAAAAATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAA
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCTAA
**
3234627 ATGGTTTTGGCC
65 ACAGTTTT-GCC
* * *
3234639 CCGAGATTTCCAGAATGCTCGGAGGCAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAA
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAA
*
3234704 CAGTTTTGCT
66 CAGTTTTGCC
* * *
3234714 CCAAGAATTCCA-ATATTCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCGATTCCCCCT
1 CCAAGAATTCCAGA-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCT
3234774 TGTACAACGG
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
73 18 0.15
74 9 0.08
75 28 0.24
76 36 0.31
77 27 0.23
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.20
Consensus pattern (75 bp):
CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAA
CAGTTTTGCC
Found at i:3236797 original size:126 final size:123
Alignment explanation
Indices: 3236488--3236967 Score: 508
Period size: 130 Copynumber: 3.9 Consensus size: 123
3236478 TTAATATTGA
* * * * *
3236488 AAATAGTAATATATTTTCATTTCGGTTGGAGTAAT---CGATTGCTCTAAGGCATGAGAGGTCAT
1 AAATAGT-ATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
* * ** * * * * *
3236550 TTATTCCCAATTGGATCTAATTAGATATTATCATTATCTCTTG-AATTAATATT-GA--
65 TTATTCCCGATTGAAAATAATTAGATATTATCGTTTTCTCTCGAAATTGATTTTAGACG
* * * * * * *
3236605 AAATAGTAATATATTTTCAATTCGGTTGGACTAATAAATGACTG-TTCTAAGGCGTGAGAGGTCA
1 AAATAGT-ATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTT-TAAGGCATGAGAGGTCA
* *
3236669 TTTATTCCCGATTGGAAATAATTAGATATCATCGTTTTCTCTCGAAATTGATTTCTGAGACG
64 TTTATTCCCGATTGAAAATAATTAGATATTATCGTTTTCTCTCGAAATTGATTT-T-AGACG
*
3236731 AAATAGTGATATCTCTTCATTTCAATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
1 AAATAGT-ATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
*
3236796 TTATTCTCGATTGAAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGGATTTTAAGAC
65 TTATTCCCGATTGAAAATAATTAGATATTATCGTTTTCTCTCG----AA-ATT-GATTTT-AGAC
3236861 G
123 G
* * * *
3236862 AAATAATATATCTCTTCATTTCGATTGTAGTAATAAATGATTGCTTTAAGACGTGAGAGGTCATT
1 AAATAGTATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATT
* *
3236927 TATTCACGATTGAAAATAATTAGATATTATTGTTTTCTCTC
66 TATTCCCGATTGAAAATAATTAGATATTATCGTTTTCTCTC
3236968 TTAGGATTAT
Statistics
Matches: 311, Mismatches: 35, Indels: 21
0.85 0.10 0.06
Matches are distributed among these distances:
117 33 0.11
119 1 0.00
120 57 0.18
121 7 0.02
122 1 0.00
124 2 0.01
126 93 0.30
127 2 0.01
130 95 0.31
131 15 0.05
132 5 0.02
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (123 bp):
AAATAGTATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATT
TATTCCCGATTGAAAATAATTAGATATTATCGTTTTCTCTCGAAATTGATTTTAGACG
Found at i:3238797 original size:2 final size:2
Alignment explanation
Indices: 3238790--3238815 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3238780 GTAAATTTAC
3238790 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3238816 AGAAATCAAA
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):
TA
Found at i:3247619 original size:21 final size:21
Alignment explanation
Indices: 3247595--3247641 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3247585 TTACCTGTTG
*
3247595 GGGTAAGATGCATTTGTTTGA
1 GGGTAAGATACATTTGTTTGA
3247616 GGGTAAGATACATTTGTTTGA
1 GGGTAAGATACATTTGTTTGA
3247637 GGGTA
1 GGGTA
3247642 TAGAGTATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.04, G:0.34, T:0.36
Consensus pattern (21 bp):
GGGTAAGATACATTTGTTTGA
Found at i:3250976 original size:2 final size:2
Alignment explanation
Indices: 3250969--3251004 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3250959 ATGTCTTTAT
3250969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3251005 AAGTAAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3253810 original size:3 final size:3
Alignment explanation
Indices: 3253802--3253913 Score: 99
Period size: 3 Copynumber: 38.0 Consensus size: 3
3253792 TCTTTATTTG
* * * * *
3253802 TAA TAA TAA T-A TAG TAG TAA TAA TTA TAA TAA TAA T-A TAG TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3253848 TAA TAA T-A TAA TACA TAA TAA TAA T-T TAA TATA TAA TAA TAA T-T
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
3253892 TAA TATA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
3253914 GTAAGATCGT
Statistics
Matches: 91, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
2 8 0.09
3 74 0.81
4 9 0.10
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3253837 original size:26 final size:26
Alignment explanation
Indices: 3253802--3253913 Score: 117
Period size: 26 Copynumber: 4.3 Consensus size: 26
3253792 TCTTTATTTG
3253802 TAATAATAATATAGTAGTAATAAT-TA
1 TAATAATAATATAGTAGT-ATAATATA
3253828 TAATAATAATATAGTAGTAATAATAATA
1 TAATAATAATATAGTAGT-ATAAT-ATA
* *
3253856 TAATACATAATA-A-TAATTTAATATA
1 TAATA-ATAATATAGTAGTATAATATA
* *
3253881 TAATAATAATTTAATA-TATAATA-A
1 TAATAATAATATAGTAGTATAATATA
3253905 TAATAATAA
1 TAATAATAA
3253914 GTAAGATCGT
Statistics
Matches: 77, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
24 15 0.19
25 15 0.19
26 30 0.39
27 3 0.04
28 8 0.10
29 6 0.08
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (26 bp):
TAATAATAATATAGTAGTATAATATA
Found at i:3253868 original size:18 final size:18
Alignment explanation
Indices: 3253821--3253909 Score: 119
Period size: 18 Copynumber: 5.1 Consensus size: 18
3253811 TATAGTAGTA
3253821 ATAAT-TATAATAATAAT
1 ATAATATATAATAATAAT
* *
3253838 ATAGTA-GTAATAATAAT
1 ATAATATATAATAATAAT
*
3253855 ATAATACATAATAATAAT
1 ATAATATATAATAATAAT
*
3253873 TTAATATATAATAATAAT
1 ATAATATATAATAATAAT
*
3253891 TTAATATATAATAATAAT
1 ATAATATATAATAATAAT
3253909 A
1 A
3253910 ATAAGTAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
17 19 0.30
18 44 0.70
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (18 bp):
ATAATATATAATAATAAT
Found at i:3254105 original size:20 final size:20
Alignment explanation
Indices: 3254056--3254109 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
3254046 AAAACATCCT
* *
3254056 ACCCGGAGGTTTTACAGATG
1 ACCCGAAGGTTTTACAAATG
* *
3254076 ACCCGGAGGTTTTACAAATT
1 ACCCGAAGGTTTTACAAATG
*
3254096 ACTCGAAGGTTTTA
1 ACCCGAAGGTTTTA
3254110 ATTTTCTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (20 bp):
ACCCGAAGGTTTTACAAATG
Found at i:3254250 original size:99 final size:98
Alignment explanation
Indices: 3254076--3254420 Score: 451
Period size: 99 Copynumber: 3.5 Consensus size: 98
3254066 TTTACAGATG
* * * *
3254076 ACCCGGAGGTTTTACAAATTACTCGAAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
1 ACCCGGAGGTTTTACAAATGACCCGAAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTAGA
3254141 AAATCGCTTTCTCATTTTCATGCTAAAACATTAT
66 AAATCGCTTTCTCATTTTCATGC-AAAACATTAT
*
3254175 ACCCGAAGGTTTTACAAATGACCC-AGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTAG
1 ACCCGGAGGTTTTACAAATGACCCGA-AGGATTTAATTTTCTAGAACATTAAATGAGAAACTTAG
* * * **
3254239 AAAATCTCTTTCCCATTTCCATGCGAAAACATCCT
65 AAAATCGCTTTCTCATTTTCATGC-AAAACATTAT
* * * *
3254274 ACCCGGAGGTTTTACAGATGACCCGGAGGATTTAATTTTCTAGAACATTAAATTAGAAATTTAGA
1 ACCCGGAGGTTTTACAAATGACCCGAAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTAGA
* * * * *
3254339 AAATCGCTTTCTCACTTTCATACGAATC-TTCTT
66 AAATCGCTTTCTCATTTTCATGCAAAACATT-AT
* *
3254372 ACCCGGAGGTTTTACAGATGATCCGAAGGATTTAATTTTCTAGAACATT
1 ACCCGGAGGTTTTACAAATGACCCGAAGGATTTAATTTTCTAGAACATT
3254421 TGTTGAAAAC
Statistics
Matches: 216, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
97 1 0.00
98 52 0.24
99 163 0.75
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (98 bp):
ACCCGGAGGTTTTACAAATGACCCGAAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTAGA
AAATCGCTTTCTCATTTTCATGCAAAACATTAT
Found at i:3256712 original size:21 final size:21
Alignment explanation
Indices: 3256687--3256726 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3256677 TAAGACTTAT
3256687 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
3256708 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
3256727 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:3260572 original size:22 final size:23
Alignment explanation
Indices: 3260537--3260596 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
3260527 TAGTACAGGA
* *
3260537 GGAATCGATACCCCC-TTGAAGG
1 GGAACCGATTCCCCCTTTGAAGG
* *
3260559 GGAACTGATTCCCCCTTTGAATG
1 GGAACCGATTCCCCCTTTGAAGG
3260582 GGAACCGATTCCCCC
1 GGAACCGATTCCCCC
3260597 CTTTAGGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (23 bp):
GGAACCGATTCCCCCTTTGAAGG
Found at i:3261039 original size:16 final size:18
Alignment explanation
Indices: 3261018--3261050 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3261008 TAAAAAAATG
3261018 AATTATT-AT-TTTTGAA
1 AATTATTGATGTTTTGAA
3261034 AATTATTGATGTTTTGA
1 AATTATTGATGTTTTGA
3261051 TTCAATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
AATTATTGATGTTTTGAA
Found at i:3262866 original size:13 final size:13
Alignment explanation
Indices: 3262848--3262874 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3262838 GAAGTGTTAA
3262848 AGTAAGGGGGAGT
1 AGTAAGGGGGAGT
3262861 AGTAAGGGGGAGT
1 AGTAAGGGGGAGT
3262874 A
1 A
3262875 ATTTCAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (13 bp):
AGTAAGGGGGAGT
Found at i:3272457 original size:3 final size:3
Alignment explanation
Indices: 3272449--3272533 Score: 86
Period size: 3 Copynumber: 29.0 Consensus size: 3
3272439 TCTTTATTTG
* * * *
3272449 TAA TAA TAA TAA TAA T-A TAG TAG TAA TAA TTA TAA TAA TAA T-A TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3272495 TAA TAC TAA TAA -AA TAA TATA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
3272534 GTAAGATCGG
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
2 6 0.09
3 59 0.87
4 3 0.04
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3272485 original size:26 final size:26
Alignment explanation
Indices: 3272449--3272533 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
3272439 TCTTTATTTG
* *
3272449 TAATAATAATAATAATATAGTAGTAA
1 TAATTATAATAATAATATAGTAATAA
*
3272475 TAATTATAATAATAATATAGTAATAC
1 TAATTATAATAATAATATAGTAATAA
* * *
3272501 TAA-TAAAATAAT-ATATAATAATTA
1 TAATTATAATAATAATATAGTAATAA
*
3272525 TAATAATAA
1 TAATTATAA
3272534 GTAAGATCGG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
24 12 0.24
25 11 0.22
26 26 0.53
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (26 bp):
TAATTATAATAATAATATAGTAATAA
Found at i:3272504 original size:29 final size:27
Alignment explanation
Indices: 3272450--3272533 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 27
3272440 CTTTATTTGT
* *
3272450 AATAATAATAATAATATAGTAGTAATAA
1 AATAATAATAAT-ATATAATACTAATAA
*
3272478 TTATAATAATAATATAGTAATACTAATAA
1 -AATAATAATAATATA-TAATACTAATAA
* *
3272507 AATAATATATAATA-ATTATAATAATAA
1 AATAATA-ATAATATATAATACTAATAA
3272534 GTAAGATCGG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 10 0.21
28 10 0.21
29 27 0.57
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.36
Consensus pattern (27 bp):
AATAATAATAATATATAATACTAATAA
Found at i:3278018 original size:2 final size:2
Alignment explanation
Indices: 3278011--3278041 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3278001 AAATGAAATG
3278011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3278042 CATTTTGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3279915 original size:3 final size:3
Alignment explanation
Indices: 3279898--3279981 Score: 105
Period size: 3 Copynumber: 27.7 Consensus size: 3
3279888 AATTTTTTCA
* * * * * *
3279898 TAT TAT TTT TTT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAA AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3279946 TAT TAT TAT TAT ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
3279982 AAAAAATAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Done.