Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 57 of 141
Found at i:17106593 original size:14 final size:14
Alignment explanation
Indices: 17106574--17106608 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
17106564 TATTCAGTAA
*
17106574 TATTATTATTCATC
1 TATTATTATTAATC
*
17106588 TATTATTATTAATT
1 TATTATTATTAATC
17106602 TATTATT
1 TATTATT
17106609 CTTATCATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTATTATTAATC
Found at i:17106674 original size:30 final size:31
Alignment explanation
Indices: 17106588--17106675 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
17106578 ATTATTCATC
* *
17106588 TATTATTATTAATTTATTATTCTTATCATCGT
1 TATTACTATTAATTTATTATT-TAATCATCGT
* * *
17106620 TATTACTACTGATATTATTA-TTAAT-ATTGT
1 TATTACTATTAAT-TTATTATTTAATCATCGT
17106650 TATTA-TATTAATTTATATATTTAATC
1 TATTACTATTAATTTAT-TATTTAATC
17106676 GCCATTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.09
29 7 0.16
30 14 0.31
31 3 0.07
32 11 0.24
33 6 0.13
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTACTATTAATTTATTATTTAATCATCGT
Found at i:17110340 original size:25 final size:25
Alignment explanation
Indices: 17110306--17110356 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
17110296 AAGAAATCCC
17110306 TGTAGTTTTTAGAGCTTATCTAGAG
1 TGTAGTTTTTAGAGCTTATCTAGAG
17110331 TGTAGTTTTTAGAGCTTATCTAGAG
1 TGTAGTTTTTAGAGCTTATCTAGAG
17110356 T
1 T
17110357 AATGTTCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (25 bp):
TGTAGTTTTTAGAGCTTATCTAGAG
Found at i:17114181 original size:3 final size:3
Alignment explanation
Indices: 17114175--17114260 Score: 52
Period size: 3 Copynumber: 28.7 Consensus size: 3
17114165 TATTCAATAA
* * **
17114175 TAT TAT TAT TAAT CTAT TAT TAT TAA T-T TAT TAT TAT TAT CAT CCT
1 TAT TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
17114221 TAT TAC TACT GA- TAT TAT TAT TAA TAT TGT TAT TA- TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17114261 ATTTATATAT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
2 4 0.06
3 53 0.84
4 5 0.08
5 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:17114194 original size:14 final size:14
Alignment explanation
Indices: 17114175--17114213 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
17114165 TATTCAATAA
17114175 TATTATTATTAATC
1 TATTATTATTAATC
*
17114189 TATTATTATTAATT
1 TATTATTATTAATC
17114203 TATTATTATTA
1 TATTATTATTA
17114214 TCATCCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTATTAATC
Found at i:17114197 original size:17 final size:17
Alignment explanation
Indices: 17114175--17114214 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17114165 TATTCAATAA
17114175 TATTATT-ATTAATCTAT
1 TATTATTAATTAAT-TAT
*
17114192 TATTATTAATTTATTAT
1 TATTATTAATTAATTAT
17114209 TATTAT
1 TATTAT
17114215 CATCCTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTAATTAATTAT
Found at i:17114205 original size:11 final size:12
Alignment explanation
Indices: 17114172--17114260 Score: 54
Period size: 14 Copynumber: 6.7 Consensus size: 12
17114162 TACTATTCAA
17114172 TAATATTATTAT
1 TAATATTATTAT
17114184 TAATCTATTATTAT
1 TAA--TATTATTAT
17114198 TAATTTATTATTAT
1 TAA--TATTATTAT
*
17114212 TATCATCCTTATTACT
1 TA--AT-ATTATTA-T
*
17114228 ACTGATATTATTAT
1 --TAATATTATTAT
*
17114242 TAATATTGTTAT
1 TAATATTATTAT
17114254 T-ATATTA
1 TAATATTA
17114261 ATTTATATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
11 5 0.08
12 14 0.23
14 26 0.42
15 12 0.19
16 4 0.06
18 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:17115955 original size:4 final size:4
Alignment explanation
Indices: 17115942--17115976 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
17115932 TGGTTTTTCA
17115942 AATT -ATT AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT
17115977 GAAGTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
AATT
Found at i:17118232 original size:17 final size:18
Alignment explanation
Indices: 17118212--17118245 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17118202 TTTTTTGTGG
17118212 GGATTAT-TTTTGGTTTC
1 GGATTATATTTTGGTTTC
*
17118229 GGATTTTATTTTGGTTT
1 GGATTATATTTTGGTTT
17118246 TCTAGCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.12, C:0.03, G:0.24, T:0.62
Consensus pattern (18 bp):
GGATTATATTTTGGTTTC
Found at i:17120269 original size:20 final size:20
Alignment explanation
Indices: 17120240--17120278 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17120230 CAACATGTAT
*
17120240 TATCTATTAAGGCTTATCTA
1 TATCTATTAAGCCTTATCTA
*
17120260 TATCTTTTAAGCCTTATCT
1 TATCTATTAAGCCTTATCT
17120279 TATGGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Consensus pattern (20 bp):
TATCTATTAAGCCTTATCTA
Found at i:17124083 original size:22 final size:24
Alignment explanation
Indices: 17124050--17124094 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
17124040 GTATAAATTT
*
17124050 AAAATTTTTATT-ATTTATTTATC
1 AAAATTTTTATTGATTTAATTATC
17124073 AAAA-TTTTATTGATTTAATTAT
1 AAAATTTTTATTGATTTAATTAT
17124095 ATAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
AAAATTTTTATTGATTTAATTATC
Found at i:17125146 original size:3 final size:3
Alignment explanation
Indices: 17125138--17125172 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17125128 CTTGTTTCAA
17125138 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17125173 CAACAAAAGT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17125534 original size:3 final size:3
Alignment explanation
Indices: 17125526--17125554 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17125516 AATTTCACAA
17125526 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17125555 GAGCTTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17134048 original size:27 final size:25
Alignment explanation
Indices: 17134017--17134084 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
17134007 CATCTTGACC
17134017 CACAACTTGTGTGAGCAAACCCATATT
1 CACAACTTGTGTGAGC-AA-CCATATT
* **
17134044 CACAACTCGTGTGAGC-ATTATATT
1 CACAACTTGTGTGAGCAACCATATT
*
17134068 CACAACTTATGTGAGCA
1 CACAACTTGTGTGAGCA
17134085 TTTCTATCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 19 0.54
25 1 0.03
27 15 0.43
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (25 bp):
CACAACTTGTGTGAGCAACCATATT
Found at i:17134071 original size:24 final size:24
Alignment explanation
Indices: 17134039--17134086 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
17134029 GAGCAAACCC
*
17134039 ATATTCACAACTCGTGTGAGCATT
1 ATATTCACAACTCATGTGAGCATT
*
17134063 ATATTCACAACTTATGTGAGCATT
1 ATATTCACAACTCATGTGAGCATT
17134087 TCTATCCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (24 bp):
ATATTCACAACTCATGTGAGCATT
Found at i:17138101 original size:21 final size:21
Alignment explanation
Indices: 17138076--17138116 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17138066 TACTGCATTT
*
17138076 ATCCATGACAT-AGATAAATTC
1 ATCCATAACATAAG-TAAATTC
17138097 ATCCATAACATAAGTAAATT
1 ATCCATAACATAAGTAAATT
17138117 TCTCACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (21 bp):
ATCCATAACATAAGTAAATTC
Found at i:17141119 original size:97 final size:97
Alignment explanation
Indices: 17140953--17141146 Score: 334
Period size: 97 Copynumber: 2.0 Consensus size: 97
17140943 CTAGCTTTGA
* *
17140953 CTGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAGGGTTACCACTAATCAGGAAGGTT
1 CTGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGAAGGTT
*
17141018 GAATTTGCTATTGAATTGGCATCGGGAACTTC
66 GAATTTGCTATTGAATTGGCATCGGAAACTTC
* *
17141050 CTGTTCATGAATTTGCTGATGTTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGGAGGTT
1 CTGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGAAGGTT
*
17141115 GAATTTGCTATTGAATTGGCATCTGAAACTTC
66 GAATTTGCTATTGAATTGGCATCGGAAACTTC
17141147 TCCAATATTG
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (97 bp):
CTGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGAAGGTT
GAATTTGCTATTGAATTGGCATCGGAAACTTC
Found at i:17151973 original size:341 final size:341
Alignment explanation
Indices: 17151350--17152031 Score: 1301
Period size: 341 Copynumber: 2.0 Consensus size: 341
17151340 TCATAAATCT
* *
17151350 TCAAGAAAACATCCTAAAAGTTCATAGATTTCATCATCTTCCCCACGTTGTAACGCTGGGGTTTG
1 TCAAGAAAACATCCTAAAAGTTCATAGATTTCACCATCTTCCCCACGTTGTAACGCTAGGGTTTG
17151415 TGCAAGTGTACACAGTCGTTATCAAGTAATAAGTAAGTATTGAGTTATCATCTCCACAGGGATTG
66 TGCAAGTGTACACAGTCGTTATCAAGTAATAAGTAAGTATTGAGTTATCATCTCCACAGGGATTG
17151480 TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
131 TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
*
17151545 TAGTTGAAAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCTT
196 TAGTTGAAAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCCT
17151610 AAGTATGCAAACTATATGAATGAAATAGATTTTAGTAAAATTAAACACAATTTGCAACAATTATA
261 AAGTATGCAAACTATATGAATGAAATAGATTTTAGTAAAATTAAACACAATTTGCAACAATTATA
17151675 ACATAAATAAACTAGG
326 ACATAAATAAACTAGG
*
17151691 TCAAGAAAACATCCTAAAAGTTCATAGATTTCACCATCTTCCCCACGTTGTAACGTTAGGGTTTG
1 TCAAGAAAACATCCTAAAAGTTCATAGATTTCACCATCTTCCCCACGTTGTAACGCTAGGGTTTG
*
17151756 TGCAAGTGTACACAGTCGTTATCAAGTAATAAGTAAGTATTGAGTTATCATCTCTACAGGGATTG
66 TGCAAGTGTACACAGTCGTTATCAAGTAATAAGTAAGTATTGAGTTATCATCTCCACAGGGATTG
17151821 TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
131 TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
*
17151886 TAGTTGAGAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCCT
196 TAGTTGAAAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCCT
*
17151951 AAGTATGCAAACTATATGAATGAAATAGATTTTAGTAAAATTAAATACAATTTGCAACAATTATA
261 AAGTATGCAAACTATATGAATGAAATAGATTTTAGTAAAATTAAACACAATTTGCAACAATTATA
17152016 ACATAAATAAACTAGG
326 ACATAAATAAACTAGG
17152032 ACAATTACTT
Statistics
Matches: 334, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
341 334 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (341 bp):
TCAAGAAAACATCCTAAAAGTTCATAGATTTCACCATCTTCCCCACGTTGTAACGCTAGGGTTTG
TGCAAGTGTACACAGTCGTTATCAAGTAATAAGTAAGTATTGAGTTATCATCTCCACAGGGATTG
TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
TAGTTGAAAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCCT
AAGTATGCAAACTATATGAATGAAATAGATTTTAGTAAAATTAAACACAATTTGCAACAATTATA
ACATAAATAAACTAGG
Found at i:17155830 original size:28 final size:28
Alignment explanation
Indices: 17155785--17155873 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 28
17155775 AACACGATAG
* *
17155785 AAAATAATAGCCTTTGTGGCGAATCGTA
1 AAAAGAATAACCTTTGTGGCGAATCGTA
* * *
17155813 AAAAGAATAACCTCTGTGGAGAATTGTA
1 AAAAGAATAACCTTTGTGGCGAATCGTA
* * *
17155841 AAAAGAA-AAGCCTTTATGGCGGATCATA
1 AAAAGAATAA-CCTTTGTGGCGAATCGTA
17155869 AAAAG
1 AAAAG
17155874 GAAAGCTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 2 0.04
28 47 0.96
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (28 bp):
AAAAGAATAACCTTTGTGGCGAATCGTA
Found at i:17157047 original size:56 final size:56
Alignment explanation
Indices: 17156961--17157192 Score: 446
Period size: 56 Copynumber: 4.1 Consensus size: 56
17156951 ACAAGGGATG
17156961 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
17157017 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
17157073 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
17157129 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
17157185 ATGGGCAA
1 ATGGGCAA
17157193 TAAACTAATA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 174 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:17160445 original size:59 final size:58
Alignment explanation
Indices: 17160341--17160480 Score: 158
Period size: 59 Copynumber: 2.4 Consensus size: 58
17160331 ATTTAATAAA
* * * * *
17160341 TTTAGGTACTAAATTAGGAAAACATGTCAAGTTCAACTATCAAATTGGGCCCAAAAAAGT
1 TTTA-GTACCAAATTAAGAAAAAATGTCAAGTTCAACTATCAAATTGAG-CCAAAAAAAT
* *
17160401 TTTAGTACCAAATTAAGAAAAAATGTCAAGTTCAAGTA-CTAAATTGAGCTAAAAAAAT
1 TTTAGTACCAAATTAAGAAAAAATGTCAAGTTCAACTATC-AAATTGAGCCAAAAAAAT
*
17160459 TTTAAATACCAAATTAA-AAAAA
1 TTT-AGTACCAAATTAAGAAAAA
17160481 TGTTAAGATC
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
58 17 0.24
59 49 0.70
60 4 0.06
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (58 bp):
TTTAGTACCAAATTAAGAAAAAATGTCAAGTTCAACTATCAAATTGAGCCAAAAAAAT
Found at i:17164493 original size:19 final size:19
Alignment explanation
Indices: 17164469--17164508 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
17164459 AGTTTACTTA
17164469 GAGGTGTTCTAAACAATTG
1 GAGGTGTTCTAAACAATTG
17164488 GAGGTGTTCTAAACAATTG
1 GAGGTGTTCTAAACAATTG
17164507 GA
1 GA
17164509 CTGCGGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (19 bp):
GAGGTGTTCTAAACAATTG
Found at i:17164786 original size:11 final size:11
Alignment explanation
Indices: 17164770--17164794 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17164760 CATAATCATA
17164770 TTGTATATTCT
1 TTGTATATTCT
17164781 TTGTATATTCT
1 TTGTATATTCT
17164792 TTG
1 TTG
17164795 GTACCTACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (11 bp):
TTGTATATTCT
Found at i:17166486 original size:46 final size:46
Alignment explanation
Indices: 17166396--17166485 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
17166386 AGGAGAAGGG
* * *
17166396 ACCAAGGTGAAAACCTGCAAAGGGCGCTTTGAGTTTCAAAAAAAAT
1 ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTTCCAAAAAAAAT
* *
17166442 ACCAATGTGAAAACCCGGAAAGGGCACTTTGAG-TCCAAAAAAAA
1 ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTTCCAAAAAAAA
17166486 AAGAAAATAG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 10 0.26
46 29 0.74
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (46 bp):
ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTTCCAAAAAAAAT
Found at i:17167780 original size:45 final size:45
Alignment explanation
Indices: 17167725--17168400 Score: 850
Period size: 45 Copynumber: 15.0 Consensus size: 45
17167715 ATCAGTAAAA
* * * *
17167725 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAA
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * * * * *
17167770 ATAGCAGATCTTGTCTTTCTGTATTGGTAGCAAAGCAGATTGAAA
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * ** *
17167815 ACAGCATATCTTGTCTTCCTATATTGACAGCGAAGTAGATCGAAA
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* *
17167860 ACAACAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * * * * *
17167905 ATAACAGATCTTGTCTTCCTGTATTGGCAGCCAAGTAAATCAAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
*
17167950 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAATAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* *
17167995 ATAACAGATCTTATCTTCCTATATTGGTAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * *
17168040 ATAACAGATTTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
17168085 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * *
17168130 ATAACAGATCTTATCTTCCTATATTGGTAGCGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * * *
17168175 ATAGCAGATCTTGTCTTCTTCTATTGGTAGCAAACTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * * * *
17168220 ATAACGGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * *
17168265 ATAGCAGATCTTGTCTTCTTCTATTGGTAGCAAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * * * * *
17168310 ATAACGGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAA
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
* * * *
17168355 ACAGCAGATCTTATCTTCATGTATTGGCT-GCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGG-TAGCGAAGTAGATCGAAG
17168400 A
1 A
17168401 CAGAAGTAAC
Statistics
Matches: 547, Mismatches: 83, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
45 547 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAG
Found at i:17168553 original size:44 final size:44
Alignment explanation
Indices: 17168503--17168612 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
17168493 ATCCAGTCTC
* * * ** *
17168503 ATCTCCCCGAGGTTGCAGTGGGACAGATTGAATAAGTCAATCTT
1 ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
*
17168547 ATCTCCCTGAGGTTGTAGTGGAACAGATTGAAGAAACCAATCCT
1 ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
*
17168591 ATCTCCCTGAAGTTGCAGTGGA
1 ATCTCCCTGAGGTTGCAGTGGA
17168613 GTGGATCAGA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (44 bp):
ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
Found at i:17175944 original size:50 final size:50
Alignment explanation
Indices: 17175888--17175988 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
17175878 ACCTTAATCA
*
17175888 AATTTTTTATTAACTTTCATCACTTCATAATTTATTTATTATTTTTTTAT
1 AATTTTTTATTAACTTTCATCACTTCATAATTTATTTATTAATTTTTTAT
17175938 AATTTTTTATTAACTTTCATCACTTCATAATTTATTTATTAATTTTTTAT
1 AATTTTTTATTAACTTTCATCACTTCATAATTTATTTATTAATTTTTTAT
17175988 A
1 A
17175989 TATTGGTTAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (50 bp):
AATTTTTTATTAACTTTCATCACTTCATAATTTATTTATTAATTTTTTAT
Found at i:17176468 original size:21 final size:21
Alignment explanation
Indices: 17176434--17176474 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17176424 GGGGGAAAGT
*
17176434 GGGAAGAAGTAAAAGTTTTGA
1 GGGAAGAAGTAAAAGGTTTGA
17176455 GGGAA-AAGTAAAAAGGTTTG
1 GGGAAGAAGT-AAAAGGTTTG
17176475 GGAGTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAGAAGTAAAAGGTTTGA
Found at i:17176526 original size:9 final size:9
Alignment explanation
Indices: 17176512--17176548 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
17176502 TATAATTTGA
17176512 TATTCGAAT
1 TATTCGAAT
17176521 TATTCGAAT
1 TATTCGAAT
*
17176530 TATTCGAGT
1 TATTCGAAT
17176539 TATTCGAAT
1 TATTCGAAT
17176548 T
1 T
17176549 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17176619 original size:9 final size:9
Alignment explanation
Indices: 17176602--17176632 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17176592 TCGAGTTGAT
17176602 TCGAATAAC
1 TCGAATAAC
*
17176611 TCGATTAAC
1 TCGAATAAC
17176620 TCGAATAAC
1 TCGAATAAC
17176629 TCGA
1 TCGA
17176633 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:17176879 original size:58 final size:58
Alignment explanation
Indices: 17176815--17176947 Score: 196
Period size: 58 Copynumber: 2.3 Consensus size: 58
17176805 ATTTATAAGA
* * * *
17176815 TAGTCCTTAATGGACTTCCCAACGCTAGATAGTCCTAACGAACATCCTCTTCATTCGT
1 TAGTCCTTAACGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
**
17176873 TAGTCCTTGGCGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
1 TAGTCCTTAACGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
17176931 TAGT-CTCTAACGGACTT
1 TAGTCCT-TAACGGACTT
17176948 TATATAACAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
57 2 0.03
58 64 0.97
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (58 bp):
TAGTCCTTAACGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
Found at i:17181562 original size:21 final size:21
Alignment explanation
Indices: 17181537--17181592 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
17181527 AACAGCGGTG
*
17181537 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
17181558 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
17181579 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
17181593 AACAATGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:17185233 original size:30 final size:30
Alignment explanation
Indices: 17185197--17185443 Score: 437
Period size: 30 Copynumber: 8.3 Consensus size: 30
17185187 GAATAAATCG
17185197 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17185227 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17185257 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
* *
17185287 AATACGCTACATATA-ATTTTTA-TTTTATA
1 AATACACTACATATATTTTTTTATTTTTA-A
17185316 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17185346 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17185376 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
17185405 AATACACTACATATTTTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17185435 AATACACTA
1 AATACACTA
17185444 ATACAGTGCA
Statistics
Matches: 208, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
28 5 0.02
29 49 0.24
30 149 0.72
31 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (30 bp):
AATACACTACATATATTTTTTTATTTTTAA
Found at i:17185319 original size:59 final size:60
Alignment explanation
Indices: 17185197--17185443 Score: 437
Period size: 59 Copynumber: 4.2 Consensus size: 60
17185187 GAATAAATCG
17185197 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
* *
17185257 AATACACTACATATATTTTTTTATTTTTAAAATACGCTACATATA-ATTTTTA-TTTTATA
1 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTA-A
17185316 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
*
17185376 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATTTTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
17185435 AATACACTA
1 AATACACTA
17185444 ATACAGTGCA
Statistics
Matches: 179, Mismatches: 5, Indels: 7
0.94 0.03 0.04
Matches are distributed among these distances:
58 5 0.03
59 103 0.58
60 66 0.37
61 5 0.03
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (60 bp):
AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
Found at i:17185349 original size:89 final size:89
Alignment explanation
Indices: 17185197--17185443 Score: 442
Period size: 89 Copynumber: 2.8 Consensus size: 89
17185187 GAATAAATCG
17185197 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
17185262 ACTACATATATTTTTTTATTTTTAA
65 ACTACATATATTTTTTTATTTTTAA
* *
17185287 AATACGCTACATATAATTTTTA-TTTTATAAATACACTACATATATTTTTTTATTTTTAAAATAC
1 AATACACTACATATATTTTTTATTTTTA-AAATACACTACATATATTTTTTTATTTTTAAAATAC
17185351 ACTACATATATTTTTTTATTTTTAA
65 ACTACATATATTTTTTTATTTTTAA
*
17185376 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATTTTTTTTTATTTTTAAAATACA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACA
17185441 CTA
66 CTA
17185444 ATACAGTGCA
Statistics
Matches: 150, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
88 5 0.03
89 126 0.84
90 19 0.13
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (89 bp):
AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACA
CTACATATATTTTTTTATTTTTAA
Found at i:17187968 original size:22 final size:21
Alignment explanation
Indices: 17187943--17188006 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
17187933 CCAAGAACAA
17187943 AGCAAAAAAGAGGGGAGAAACC
1 AGCAAAAAA-AGGGGAGAAACC
*
17187965 AGCAAAAACAAGGGG-CAAACC
1 AGCAAAAA-AAGGGGAGAAACC
*
17187986 AGCAAGAACAAGGGGAGAAAC
1 AGCAA-AAAAAGGGGAGAAAC
17188007 TGCTGTTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 16 0.44
22 19 0.53
23 1 0.03
ACGTcount: A:0.53, C:0.17, G:0.30, T:0.00
Consensus pattern (21 bp):
AGCAAAAAAAGGGGAGAAACC
Found at i:17187984 original size:21 final size:22
Alignment explanation
Indices: 17187943--17188006 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
17187933 CCAAGAACAA
*
17187943 AGCAAAAA-AGAGGGGAGAAACC
1 AGCAAAAACA-AGGGGACAAACC
17187965 AGCAAAAACAAGGGG-CAAACC
1 AGCAAAAACAAGGGGACAAACC
* *
17187986 AGCAAGAACAAGGGGAGAAAC
1 AGCAAAAACAAGGGGACAAAC
17188007 TGCTGTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 19 0.51
22 17 0.46
23 1 0.03
ACGTcount: A:0.53, C:0.17, G:0.30, T:0.00
Consensus pattern (22 bp):
AGCAAAAACAAGGGGACAAACC
Found at i:17194370 original size:51 final size:52
Alignment explanation
Indices: 17194268--17194370 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 52
17194258 CGCTATCTTG
*
17194268 GAATTGAGTGAAATTGCATTTTGTGTTTTTTATTGAAAAATGATAAATTAAT
1 GAATTGAGTGAAATTGCATTTTGTGTTTTTTATTGAAAAATAATAAATTAAT
**
17194320 GAATTGAGTGAAATTTTATTTTGTG-TTTTTATTGAAAAATAATAAATTAAT
1 GAATTGAGTGAAATTGCATTTTGTGTTTTTTATTGAAAAATAATAAATTAAT
17194371 CTTATAAGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 25 0.52
52 23 0.48
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.46
Consensus pattern (52 bp):
GAATTGAGTGAAATTGCATTTTGTGTTTTTTATTGAAAAATAATAAATTAAT
Found at i:17194390 original size:24 final size:23
Alignment explanation
Indices: 17194363--17194409 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
17194353 GAAAAATAAT
17194363 AAATTAATCTTATAAGTTAGAAAA
1 AAATTAATCTTATAAGTTA-AAAA
* * *
17194387 AAATTATTTTTTTAAGTTAAAAA
1 AAATTAATCTTATAAGTTAAAAA
17194410 TGTTATCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (23 bp):
AAATTAATCTTATAAGTTAAAAA
Found at i:17195335 original size:18 final size:18
Alignment explanation
Indices: 17195308--17195343 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17195298 AAGTTACATC
17195308 GAGTACTTTGTTAGTAAT
1 GAGTACTTTGTTAGTAAT
*
17195326 GAGTATTTTGTTAGTAAT
1 GAGTACTTTGTTAGTAAT
17195344 ATGTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (18 bp):
GAGTACTTTGTTAGTAAT
Found at i:17198432 original size:21 final size:22
Alignment explanation
Indices: 17198407--17198450 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17198397 CAAATATAAG
*
17198407 TATTGTAT-TAACCAAATCATT
1 TATTGAATATAACCAAATCATT
17198428 TATTGAATATAACCAAATCATT
1 TATTGAATATAACCAAATCATT
17198450 T
1 T
17198451 TCATATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTGAATATAACCAAATCATT
Found at i:17199058 original size:13 final size:13
Alignment explanation
Indices: 17199040--17199077 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
17199030 ACACTCAAAT
17199040 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
17199053 TTCTCAAAAGTAC
1 TTCTCAAAAGCAC
17199066 TTCTCAAAAGCA
1 TTCTCAAAAGCA
17199078 ATAAAGAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.26
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:17199830 original size:22 final size:22
Alignment explanation
Indices: 17199800--17199842 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17199790 ACAGCAGAAC
* *
17199800 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
17199822 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
17199843 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:17200185 original size:42 final size:42
Alignment explanation
Indices: 17199914--17200184 Score: 316
Period size: 42 Copynumber: 6.4 Consensus size: 42
17199904 ACGTCACTAA
* *
17199914 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAATATCATGTT
1 CTTTAGCGGCGCTT--ATAAAAAAACGCCGCTAAAGATCATGTT
* *
17199958 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
* * *
17200000 CTTTAGCGGCGCTTAGAAAGAAACGCCCCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
17200042 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
* * * * * *
17200084 CTTTAGCGACACTT-TGGAAGAAAGCGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAT--AAAAAAACGCCGCTAAAGA-TCATGTT
* *
17200127 CTATAGCGGCGCTTATTAAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGA-TCA-TGTT
17200169 CTTTAGCGGCGCTTAT
1 CTTTAGCGGCGCTTAT
17200185 TTCACAAACG
Statistics
Matches: 198, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.01
42 151 0.76
43 31 0.16
44 14 0.07
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
Found at i:17200621 original size:12 final size:12
Alignment explanation
Indices: 17200604--17200643 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
17200594 TTTTGAACCT
*
17200604 CTGCTTCTATTG
1 CTGCTTCTATCG
*
17200616 CTGCTTCTCTCG
1 CTGCTTCTATCG
*
17200628 CTGCTTCTCTCG
1 CTGCTTCTATCG
17200640 CTGC
1 CTGC
17200644 GGCCTCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTATCG
Found at i:17200654 original size:21 final size:20
Alignment explanation
Indices: 17200628--17200762 Score: 72
Period size: 21 Copynumber: 6.3 Consensus size: 20
17200618 GCTTCTCTCG
17200628 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGC-GCCT
* **
17200649 CTGCTTCTCTTGCTGCTTCT
1 CTGCTTCTCTCGCTGCGCCT
* * * * *
17200669 CTCGCTGCGGTCTCTGTTTCTCTCG
1 CT-GCTTC--TCTC-GCTGCGC-CT
*
17200694 CTGCTTCTCTCGCTGTGGCCT
1 CTGCTTCTCTCGCTG-CGCCT
* * *
17200715 CTGCTTCTCTCGTTGTAGCCG
1 CTGCTTCTCTCGCTG-CGCCT
*
17200736 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTG-CGCCT
17200757 CTGCTT
1 CTGCTT
17200763 TAAGTTGCTG
Statistics
Matches: 85, Mismatches: 23, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
20 4 0.05
21 62 0.73
22 5 0.06
23 3 0.04
24 8 0.09
25 3 0.04
ACGTcount: A:0.01, C:0.39, G:0.21, T:0.39
Consensus pattern (20 bp):
CTGCTTCTCTCGCTGCGCCT
Found at i:17200658 original size:33 final size:33
Alignment explanation
Indices: 17200616--17200726 Score: 186
Period size: 33 Copynumber: 3.4 Consensus size: 33
17200606 GCTTCTATTG
17200616 CTGCTTCTCTCGCTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCTTCTCTCGCTGCGGCCT
* *
17200649 CTGCTTCTCTTGCTGCTTCTCTCGCTGCGGTCT
1 CTGCTTCTCTCGCTGCTTCTCTCGCTGCGGCCT
* *
17200682 CTGTTTCTCTCGCTGCTTCTCTCGCTGTGGCCT
1 CTGCTTCTCTCGCTGCTTCTCTCGCTGCGGCCT
17200715 CTGCTTCTCTCG
1 CTGCTTCTCTCG
17200727 TTGTAGCCGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.00, C:0.39, G:0.21, T:0.41
Consensus pattern (33 bp):
CTGCTTCTCTCGCTGCTTCTCTCGCTGCGGCCT
Found at i:17200666 original size:12 final size:12
Alignment explanation
Indices: 17200649--17200708 Score: 65
Period size: 12 Copynumber: 5.2 Consensus size: 12
17200639 GCTGCGGCCT
*
17200649 CTGCTTCTCTTG
1 CTGCTTCTCTCG
17200661 CTGCTTCTCTCG
1 CTGCTTCTCTCG
*
17200673 CTGCGGTCTCT-G
1 CTGC-TTCTCTCG
17200685 -T--TTCTCTCG
1 CTGCTTCTCTCG
17200694 CTGCTTCTCTCG
1 CTGCTTCTCTCG
17200706 CTG
1 CTG
17200709 TGGCCTCTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 5 0.12
9 1 0.03
10 1 0.03
11 1 0.03
12 27 0.68
13 5 0.12
ACGTcount: A:0.00, C:0.37, G:0.20, T:0.43
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:17212538 original size:115 final size:115
Alignment explanation
Indices: 17212175--17212528 Score: 602
Period size: 115 Copynumber: 3.1 Consensus size: 115
17212165 GCGAATTTGT
17212175 GGCG-TTTTTATAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAATTAAA
1 GGCGTTTTTTA-AATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAATTAAA
17212239 GGCAATTTGTGGCGTTTCTTTGTAAAACACCGGTAATATATCACTTTTAGC
65 GGCAATTTGTGGCGTTTCTTTGTAAAACACCGGTAATATATCACTTTTAGC
17212290 GGCGTTTTTTAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAATTAAAG
1 GGCGTTTTTTAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAATTAAAG
17212355 GCAATTTGTGGCGTTTCTTTGTAAAACACCGGTAATATATCACTTTTAGC
66 GCAATTTGTGGCGTTTCTTTGTAAAACACCGGTAATATATCACTTTTAGC
*
17212405 GGCGTTTTTTAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAGTTAAAG
1 GGCGTTTTTTAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAATTAAAG
* * *** ** * *
17212470 GAAATTTGCGGCGTTTCTTCACAAAACGTCGGTAATATATGACCTTTAGC
66 GCAATTTGTGGCGTTTCTTTGTAAAACACCGGTAATATATCACTTTTAGC
17212520 GGCGTTTTT
1 GGCGTTTTT
17212529 CTGAAGCGCC
Statistics
Matches: 228, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
115 222 0.97
116 6 0.03
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (115 bp):
GGCGTTTTTTAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTCACAATTAAAG
GCAATTTGTGGCGTTTCTTTGTAAAACACCGGTAATATATCACTTTTAGC
Found at i:17213020 original size:21 final size:21
Alignment explanation
Indices: 17212967--17213046 Score: 54
Period size: 21 Copynumber: 3.8 Consensus size: 21
17212957 ATATATACCA
* * * *
17212967 TAAACCTTAAATCTTAAATCC
1 TAAACCATAAACCTAAAACCC
** *
17212988 TAAACCCCAAACCTAAAACTC
1 TAAACCATAAACCTAAAACCC
** *
17213009 TAAACTTTAAA-CTGTAAACCC
1 TAAACCATAAACCT-AAAACCC
17213030 TAAACCATAAACCTAAA
1 TAAACCATAAACCTAAA
17213047 CCATATTTTT
Statistics
Matches: 43, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 2 0.05
21 39 0.91
22 2 0.05
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (21 bp):
TAAACCATAAACCTAAAACCC
Found at i:17217033 original size:41 final size:41
Alignment explanation
Indices: 17216983--17217127 Score: 148
Period size: 41 Copynumber: 3.5 Consensus size: 41
17216973 CTGATTCACA
* * *
17216983 ACACTGGCACGAAGCCTACTACGCCCAAGGTCTGATTTCAT
1 ACACTGGCACGAAGCCTACTAGGCTCAAGGCCTGATTTCAT
* * * *
17217024 ACACCGGCACAAAGCCTGA-TAGGCTTAAGGCCTGATTCCAT
1 ACACTGGCACGAAGCCT-ACTAGGCTCAAGGCCTGATTTCAT
* * * *
17217065 ACACTGACACGAAGCTTGCTAGGCTGAAGGCCTGATTTCAT
1 ACACTGGCACGAAGCCTACTAGGCTCAAGGCCTGATTTCAT
* * *
17217106 ACACTAGCTCGAAGCCTGCTAG
1 ACACTGGCACGAAGCCTACTAG
17217128 ATTCAAAACC
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
41 83 0.99
42 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (41 bp):
ACACTGGCACGAAGCCTACTAGGCTCAAGGCCTGATTTCAT
Found at i:17217121 original size:82 final size:82
Alignment explanation
Indices: 17216973--17217123 Score: 187
Period size: 82 Copynumber: 1.8 Consensus size: 82
17216963 CAACGGTTAT
* * *
17216973 CTGATTCACAACACTGGCACGAAGCCTACTACGCCCAAGGTCTGATTTCATACACCGGCACAAAG
1 CTGATTCACAACACTGACACGAAGCCTACTACGCCCAAGGCCTGATTTCATACACCAGCACAAAG
17217038 CCTGATAGGCTTAAGGC
66 CCTGATAGGCTTAAGGC
* * * ** * * *
17217055 CTGATTC-CATACACTGACACGAAGCTTGCTAGGCTGAAGGCCTGATTTCATACACTAGCTCGAA
1 CTGATTCACA-ACACTGACACGAAGCCTACTACGCCCAAGGCCTGATTTCATACACCAGCACAAA
17217119 GCCTG
65 GCCTG
17217124 CTAGATTCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 2 0.04
82 55 0.96
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (82 bp):
CTGATTCACAACACTGACACGAAGCCTACTACGCCCAAGGCCTGATTTCATACACCAGCACAAAG
CCTGATAGGCTTAAGGC
Found at i:17231924 original size:21 final size:21
Alignment explanation
Indices: 17231892--17231947 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
17231882 ACTGTTGTTG
*
17231892 AGAAGAAAGTTGCTCCTGCAGA
1 AGAAG-AAGTTGCTCCTGAAGA
* * *
17231914 AGAGGAAGTTGTTGCTGAAGA
1 AGAAGAAGTTGCTCCTGAAGA
17231935 AGAAGAAGTTGCT
1 AGAAGAAGTTGCT
17231948 GAAAATAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (21 bp):
AGAAGAAGTTGCTCCTGAAGA
Found at i:17231939 original size:18 final size:18
Alignment explanation
Indices: 17231924--17231959 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17231914 AGAGGAAGTT
17231924 GTTGCTGAAGAAGAAGAA
1 GTTGCTGAAGAAGAAGAA
*
17231942 GTTGCTGAA-AATAAGAA
1 GTTGCTGAAGAAGAAGAA
17231959 G
1 G
17231960 GAAAAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (18 bp):
GTTGCTGAAGAAGAAGAA
Found at i:17232413 original size:17 final size:17
Alignment explanation
Indices: 17232391--17232424 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17232381 GATAAATATA
* *
17232391 TATTGTGATTGCATTTT
1 TATTGTCATTACATTTT
17232408 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
17232425 CATGTTAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:17236945 original size:21 final size:20
Alignment explanation
Indices: 17236904--17236946 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
17236894 ATCACTTTAG
* *
17236904 TATTAAATTAATATAATATT
1 TATTAAATAAATATAAGATT
*
17236924 TATTAAGATAAATATTAGATT
1 TATTAA-ATAAATATAAGATT
17236945 TA
1 TA
17236947 ATTTAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TATTAAATAAATATAAGATT
Found at i:17237016 original size:62 final size:59
Alignment explanation
Indices: 17236904--17237102 Score: 154
Period size: 68 Copynumber: 3.2 Consensus size: 59
17236894 ATCACTTTAG
* * * * *
17236904 TATTAAATTAATATAATATTTATTAAGATAAATATTAGATTTAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
*
17236963 TATTAAAATAATAGAATGTTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAAATAATAGAATATTTAT-T--AAGATAAACATTAAATTAAATTTAATATT---A-AAT-
17237028 ACTT
58 -C-T
* * * * *
17237032 TAATTTTAAATTAATAAAATA-CTATTAAGATAAATATTAAATTTAATTTAATATTAAA-C-
1 T-A--TTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
17237091 -ATTAAAATAATA
1 TATTAAAATAATA
17237103 TTATCTTTGG
Statistics
Matches: 114, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
55 10 0.09
57 1 0.01
59 20 0.18
60 1 0.01
61 1 0.01
62 26 0.23
64 2 0.02
65 2 0.02
66 3 0.03
68 28 0.25
69 2 0.02
70 2 0.02
71 3 0.03
72 13 0.11
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:17237059 original size:25 final size:27
Alignment explanation
Indices: 17237004--17237059 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
17236994 TAAACATTAA
*
17237004 ATTAAATTTAATATTAAGATAATCACT
1 ATTAAATTTAATATTAAGAAAATCACT
* *
17237031 -TTAATTTTAA-ATTAATAAAAT-ACT
1 ATTAAATTTAATATTAAGAAAATCACT
17237055 ATTAA
1 ATTAA
17237060 GATAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTAAATTTAATATTAAGAAAATCACT
Found at i:17238764 original size:20 final size:21
Alignment explanation
Indices: 17238731--17238770 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
17238721 TAAAATCGAT
17238731 TAAACAATAATCTGAAAAATA
1 TAAACAATAATCTGAAAAATA
* *
17238752 TAAA-AATATTCTGGAAAAT
1 TAAACAATAATCTGAAAAAT
17238771 TAATTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.28
Consensus pattern (21 bp):
TAAACAATAATCTGAAAAATA
Found at i:17241097 original size:15 final size:15
Alignment explanation
Indices: 17241077--17241105 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17241067 GTTTTGTTGC
17241077 TTGATAACACGGTGA
1 TTGATAACACGGTGA
17241092 TTGATAACACGGTG
1 TTGATAACACGGTG
17241106 TGTGAAGCAT
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:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:17252219 original size:8 final size:8
Alignment explanation
Indices: 17252206--17252238 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
17252196 GACTATCTTT
17252206 TTCTTTTC
1 TTCTTTTC
*
17252214 TTCTTTAC
1 TTCTTTTC
17252222 TT-TTTTC
1 TTCTTTTC
17252229 TTCTTTTC
1 TTCTTTTC
17252237 TT
1 TT
17252239 TGTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:17252229 original size:15 final size:15
Alignment explanation
Indices: 17252209--17252239 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17252199 TATCTTTTTC
17252209 TTTTCTTCTTTACTT
1 TTTTCTTCTTTACTT
*
17252224 TTTTCTTCTTTTCTT
1 TTTTCTTCTTTACTT
17252239 T
1 T
17252240 GTTAAATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTCTTTACTT
Found at i:17255969 original size:42 final size:42
Alignment explanation
Indices: 17255920--17256111 Score: 205
Period size: 42 Copynumber: 4.6 Consensus size: 42
17255910 CGGCTTTATA
* *
17255920 CTTCAGTTTAGCTGATGATGCACTTATGTACCAATATATTCG
1 CTTCAGTTTAGCTGATGATGCACTTATGTGCCAGTATATTCG
*
17255962 CTTCAGTTTAGCTGATGATGAACTTATGTGCCAGTATATTCG
1 CTTCAGTTTAGCTGATGATGCACTTATGTGCCAGTATATTCG
* *
17256004 CTT-TGTTTTAGCTAATGATGCACTTATGTGCCAGTATAATT-G
1 CTTCAG-TTTAGCTGATGATGCACTTATGTGCCAGTAT-ATTCG
* *
17256046 CCTC-GACTT-GTCTGATGATGCACTTATGTGCCAGTATATTTC-
1 CTTCAG-TTTAG-CTGATGATGCACTTATGTGCCAGTATA-TTCG
* * **
17256088 CTTCGGTTTATCCAATGATGCACT
1 CTTCAGTTTAGCTGATGATGCACT
17256112 GTGGTGCTAG
Statistics
Matches: 127, Mismatches: 15, Indels: 16
0.80 0.09 0.10
Matches are distributed among these distances:
41 3 0.02
42 120 0.94
43 4 0.03
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (42 bp):
CTTCAGTTTAGCTGATGATGCACTTATGTGCCAGTATATTCG
Found at i:17261905 original size:19 final size:19
Alignment explanation
Indices: 17261863--17261905 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17261853 CTACAGAATC
*
17261863 TTTTTTCTTTTTTTCTCAT
1 TTTTTTCTATTTTTCTCAT
* *
17261882 ATTTTTCTATTTTTC-CAC
1 TTTTTTCTATTTTTCTCAT
17261900 TTTTTT
1 TTTTTT
17261906 AATATTCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTCTATTTTTCTCAT
Found at i:17267217 original size:41 final size:41
Alignment explanation
Indices: 17267172--17267369 Score: 220
Period size: 41 Copynumber: 4.8 Consensus size: 41
17267162 AAATTGTTCA
17267172 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
* *
17267213 GACTATACGTCCAGAAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
* * * * *
17267254 GATTATATGTCCAGCAGGCTAAGTGCCGGTGAACTAAATCAG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATC-G
* * ** **
17267296 G-CTATAGGCCTAGCAGGCTAAGTGCCGGTGAACGGAATTA
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
* * *
17267336 GACTATAAGTCTATCAGG-TGAAGTGCCAGTGAAT
1 GACTATACGTCTAGCAGGCT-AAGTGCCGGTGAAT
17267370 CTGTTTAAAT
Statistics
Matches: 134, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.01
41 130 0.97
42 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (41 bp):
GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
Found at i:17276696 original size:17 final size:17
Alignment explanation
Indices: 17276676--17276716 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17276666 ATTTAAATTT
*
17276676 TAAAATTATTATTAATG
1 TAAAATTATTATTAATA
* *
17276693 TAAATTTATTATTTATA
1 TAAAATTATTATTAATA
17276710 TAAAATT
1 TAAAATT
17276717 TTAATATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAAAATTATTATTAATA
Found at i:17276717 original size:18 final size:18
Alignment explanation
Indices: 17276676--17276730 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
17276666 ATTTAAATTT
*
17276676 TAAAA-TTATTATTAATG
1 TAAAATTTATTATTAATA
*
17276693 T-AAATTTATTATTTATA
1 TAAAATTTATTATTAATA
*
17276710 TAAAATTTTAATATTAA-A
1 TAAAA-TTTATTATTAATA
17276728 TAA
1 TAA
17276731 TTTATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 3 0.10
17 12 0.39
18 7 0.23
19 9 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAAAATTTATTATTAATA
Found at i:17276745 original size:16 final size:16
Alignment explanation
Indices: 17276726--17276766 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 16
17276716 TTTAATATTA
17276726 AATAATTTATTAAAAT
1 AATAATTTATTAAAAT
*
17276742 AATAA--T-TTAAATT
1 AATAATTTATTAAAAT
17276755 AATAATTTATTA
1 AATAATTTATTA
17276767 TATTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
13 11 0.52
14 1 0.05
15 1 0.05
16 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAATTTATTAAAAT
Found at i:17276757 original size:26 final size:27
Alignment explanation
Indices: 17276703--17276753 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
17276693 TAAATTTATT
**
17276703 ATTTATATAAAATTTTAATATTAAATA
1 ATTTATATAAAATAATAATATTAAATA
17276730 ATTTAT-TAAAATAATAAT-TTAAAT
1 ATTTATATAAAATAATAATATTAAAT
17276754 TAATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 10 0.45
27 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTATATAAAATAATAATATTAAATA
Found at i:17276771 original size:16 final size:16
Alignment explanation
Indices: 17276720--17276771 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
17276710 TAAAATTTTA
17276720 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
* *
17276737 AAAATAATAATTTA--
1 ATATTAATAATTTATT
17276751 A-ATTAATAATTTATT
1 ATATTAATAATTTATT
17276766 ATATTA
1 ATATTA
17276772 TTAAATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 11 0.38
14 1 0.03
15 1 0.03
16 13 0.45
17 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:17277327 original size:65 final size:65
Alignment explanation
Indices: 17277242--17277364 Score: 210
Period size: 65 Copynumber: 1.9 Consensus size: 65
17277232 TATCGATGTT
*
17277242 TTTAAATATTTTTCACATATATATTTATAATCTAATTTTTAATTTCTTGATAAATTATATATACA
1 TTTAAATATTTTTCACATATATATTTATAATCTAATTTTTAATTTCTTAATAAATTATATATACA
* * *
17277307 TTTAAATATTTTTTACATATATATTTATAGTCTTATTTTTAATTTCTTAATAAATTAT
1 TTTAAATATTTTTCACATATATATTTATAATCTAATTTTTAATTTCTTAATAAATTAT
17277365 TTATTATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.55
Consensus pattern (65 bp):
TTTAAATATTTTTCACATATATATTTATAATCTAATTTTTAATTTCTTAATAAATTATATATACA
Found at i:17283063 original size:42 final size:42
Alignment explanation
Indices: 17282986--17283340 Score: 378
Period size: 42 Copynumber: 8.4 Consensus size: 42
17282976 ACGTCGCAAA
* *
17282986 CTTTTGCGGCGCTTACAGAAAAAAA-GCCCCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCACTAAAGATCATGTT
* *
17283029 CTTTAGCGGCGCTTAGAAAAAAATGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
* * *
17283071 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGACCATGTT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCACTAAAGATCATGTT
* *
17283114 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGACCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
* * *
17283156 CTTTAGCGGCGGTTAGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
* * * *
17283198 CTTTAGCGGTGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GAAAAAAACGCCACTAAAGATCATGTT
* * * * *
17283241 CTTTAGCGGCGCTTTGGAAGAAAATGCCTCTAAA-AGTGATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCACTAAAGA-TCATGTT
* **
17283284 CTATAGCGGCGCTT-GTTCAAAAACGCCACTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCACTAAAGA-TCA-TGTT
17283326 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
17283341 TTTCACAAAC
Statistics
Matches: 273, Mismatches: 31, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
41 11 0.04
42 143 0.52
43 118 0.43
44 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
Found at i:17283154 original size:127 final size:127
Alignment explanation
Indices: 17282986--17283338 Score: 410
Period size: 127 Copynumber: 2.8 Consensus size: 127
17282976 ACGTCGCAAA
* * *
17282986 CTTTTGCGGCGCTTACAGAAAAAAAGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAA
1 CTTTAGCGGCGCTTA-AGAAAAAAAGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAA
*
17283051 ATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGACCATGTT
65 ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGACCATGTT
* * *
17283114 CTTTAGCGGCGCTT-AGAAATAAACGCCACTAAAGACCATGTTCTTTAGCGGCGGTTAGAAATAA
1 CTTTAGCGGCGCTTAAGAAA-AAAAGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAA
* ** * *
17283178 ACGCCGCTAAAGATCATGTTCTTTAGCGGTGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
65 ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGACCATGTT
** * * ** * **
17283241 CTTTAGCGGCGCTTTGGAAGAAAATGCCTCTAAA-AGTGATGTTCTATAGCGGCGCTT-GTTCAA
1 CTTTAGCGGCGCTTAAGAA-AAAAAGCCACTAAAGA-CCATGTTCTTTAGCGGCGCTTAG-AAAA
*
17283304 AAACGCCACTAAA-AGT-AGTGTTCTTTAGCGGCGCT
63 AAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCT
17283339 TATTTCACAA
Statistics
Matches: 194, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
126 5 0.03
127 114 0.59
128 74 0.38
129 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (127 bp):
CTTTAGCGGCGCTTAAGAAAAAAAGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA
CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGACCATGTT
Found at i:17283308 original size:85 final size:85
Alignment explanation
Indices: 17282986--17283339 Score: 373
Period size: 85 Copynumber: 4.2 Consensus size: 85
17282976 ACGTCGCAAA
* * * * *
17282986 CTTTTGCGGCGCTTACAGAAA-AAAAGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAA
1 CTTTAGCGGCGCTT-TAGAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAATA
* *
17283050 AATGCCGCTAAAGATCATGTT
65 AACGCCACTAAAGATCATGTT
** * *
17283071 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAA
1 CTTTAGCGGCGCTTTAGAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAATAA
*
17283136 ACGCCACTAAAGACCATGTT
66 ACGCCACTAAAGATCATGTT
* * * *
17283156 CTTTAGCGGCG-GTTAGAAATAAACGCCGCTAAAGATCATGTTCTTTAGCGGTGCTAAGGAAATA
1 CTTTAGCGGCGCTTTAGAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTA-GAAATA
*
17283220 AACGCCGCTAAAGATCATGTT
65 AACGCCACTAAAGATCATGTT
* * * * * *
17283241 CTTTAGCGGCGCTTTGGAAGA-AAATGCCTCTAAA-AGTGATGTTCTATAGCGGCGCTT-GTTCA
1 CTTTAGCGGCGCTTTAGAA-ATAAACGCCACTAAAGA-TCATGTTCTTTAGCGGCGCTTAG--AA
17283303 A-AAACGCCACTAAA-AGT-AGTGTT
62 ATAAACGCCACTAAAGA-TCA-TGTT
17283326 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
17283340 ATTTCACAAA
Statistics
Matches: 229, Mismatches: 31, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
84 45 0.20
85 148 0.65
86 35 0.15
87 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (85 bp):
CTTTAGCGGCGCTTTAGAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAATAA
ACGCCACTAAAGATCATGTT
Found at i:17283784 original size:78 final size:78
Alignment explanation
Indices: 17283695--17283839 Score: 211
Period size: 78 Copynumber: 1.9 Consensus size: 78
17283685 TTGTTTTGCT
* * *
17283695 CTGCTTCTCTCGATGCCGCATCT-TTTTGAAGTCGTAGCTGTAGTTCTTCATATTTCTTTTGAAC
1 CTGCTTCTCTCGATGCCGCATCTGCTTT-AAGTCGTAGCTGAAGTTCTTCATATTTCCTTTGAAC
17283759 CTCTGTTTCTATCG
65 CTCTGTTTCTATCG
* * * *
17283773 CTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTTGGTGAAGTTCTTCATATTTCCTTTGAACC
1 CTGCTTCTCTCGATGCCGCATCTGCTTTAAGTCGTAGCTGAAGTTCTTCATATTTCCTTTGAACC
17283838 TC
66 TC
17283840 AAATGTGGTC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 56 0.95
79 3 0.05
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (78 bp):
CTGCTTCTCTCGATGCCGCATCTGCTTTAAGTCGTAGCTGAAGTTCTTCATATTTCCTTTGAACC
TCTGTTTCTATCG
Found at i:17285932 original size:45 final size:45
Alignment explanation
Indices: 17285867--17285957 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
17285857 TGAAAGGAGG
** *
17285867 AAGGAGGCAATTTAGGGATTTCGGATTTCAAGAAATTAGGCAAGA
1 AAGGAGGCAATTTACAGATTTCGGAATTCAAGAAATTAGGCAAGA
* * *
17285912 AAGGAGGCGATTTACAGATTTGGGAATTCAAGAAATTGGGCAAGA
1 AAGGAGGCAATTTACAGATTTCGGAATTCAAGAAATTAGGCAAGA
17285957 A
1 A
17285958 GGACACAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.38, C:0.09, G:0.30, T:0.23
Consensus pattern (45 bp):
AAGGAGGCAATTTACAGATTTCGGAATTCAAGAAATTAGGCAAGA
Found at i:17288114 original size:22 final size:22
Alignment explanation
Indices: 17288089--17288132 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17288079 TAGTCATATA
17288089 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* *
17288111 ATAAATTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
17288133 TATTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:17288162 original size:72 final size:75
Alignment explanation
Indices: 17288086--17288247 Score: 172
Period size: 72 Copynumber: 2.2 Consensus size: 75
17288076 ATTTAGTCAT
* * * * *
17288086 ATAATAAATTATT-AATATAATAAATATAAATTATTATT-TTAATAAATTATTTAATAT-TTCAA
1 ATAATAAATT-TTAAAAATAATAAATATAAATAATT-TTATTAACAAATTATTGAAAATATTCAA
17288148 -TTT-TATTTTA
64 TTTTATATTTTA
* * * *
17288158 ATAATAAATTTTAAAAATAATAATTTTAAATAATTTTATTCACATATTATTGAAAATATTCAATT
1 ATAATAAATTTTAAAAATAATAAATATAAATAATTTTATTAACAAATTATTGAAAATATTCAATT
17288223 TTAATATTTTA
66 TT-ATATTTTA
17288234 ATAATAAATATTTA
1 ATAATAAAT-TTTA
17288248 TTACAATTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
71 4 0.05
72 42 0.57
73 5 0.07
74 3 0.04
76 16 0.22
77 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (75 bp):
ATAATAAATTTTAAAAATAATAAATATAAATAATTTTATTAACAAATTATTGAAAATATTCAATT
TTATATTTTA
Found at i:17288184 original size:15 final size:16
Alignment explanation
Indices: 17288157--17288187 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
17288147 ATTTTATTTT
17288157 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
17288173 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
17288188 TAATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:17288245 original size:15 final size:15
Alignment explanation
Indices: 17288225--17288281 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
17288215 ATTCAATTTT
17288225 AATATTTTAATAATA
1 AATATTTTAATAATA
*
17288240 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
17288259 AATATATTAATAATA
1 AATATTTTAATAATA
*
17288274 AATGTTTT
1 AATATTTT
17288282 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:17294410 original size:18 final size:18
Alignment explanation
Indices: 17294373--17294410 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
17294363 ACCAGTACCA
17294373 AAAATGGACGGTGAAGATG
1 AAAATGGAC-GTGAAGATG
17294392 AAAATGGA-GTGACAGATG
1 AAAATGGACGTGA-AGATG
17294410 A
1 A
17294411 GCCAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.45, C:0.05, G:0.34, T:0.16
Consensus pattern (18 bp):
AAAATGGACGTGAAGATG
Found at i:17295329 original size:24 final size:24
Alignment explanation
Indices: 17295302--17295360 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 24
17295292 AGAAGATGCT
*
17295302 CCAAAAGCAGGAGTGCTTGAACCC
1 CCAAAAGCAGGAGTACTTGAACCC
* *
17295326 CCAAAAGCA-GA--ACTTGAAGCT
1 CCAAAAGCAGGAGTACTTGAACCC
17295347 CCAAAAGCAGGAGT
1 CCAAAAGCAGGAGT
17295361 TGCGGAAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 16 0.55
22 2 0.07
23 2 0.07
24 9 0.31
ACGTcount: A:0.39, C:0.25, G:0.24, T:0.12
Consensus pattern (24 bp):
CCAAAAGCAGGAGTACTTGAACCC
Found at i:17295510 original size:24 final size:24
Alignment explanation
Indices: 17295481--17295606 Score: 119
Period size: 24 Copynumber: 5.2 Consensus size: 24
17295471 TTCCAGTTGA
*
17295481 ACCAAATGCAGGGGTGCTCGTGGC
1 ACCAAATGCAGGGGTGCTTGTGGC
* * * *
17295505 ATCAAATGCGGGGGTACTTGAGGC
1 ACCAAATGCAGGGGTGCTTGTGGC
*
17295529 ACCAAACGCAGGGGTGCTTGTGGC
1 ACCAAATGCAGGGGTGCTTGTGGC
* * * *
17295553 ACCGAAA-CCTGGAGTGCTTGAGGC
1 ACC-AAATGCAGGGGTGCTTGTGGC
* * *
17295577 GCCAAACGCAGGGGTGCTTGTCGC
1 ACCAAATGCAGGGGTGCTTGTGGC
17295601 ACCAAA
1 ACCAAA
17295607 AGCCGGGCTA
Statistics
Matches: 79, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
23 3 0.04
24 73 0.92
25 3 0.04
ACGTcount: A:0.24, C:0.25, G:0.35, T:0.17
Consensus pattern (24 bp):
ACCAAATGCAGGGGTGCTTGTGGC
Found at i:17295630 original size:48 final size:47
Alignment explanation
Indices: 17295479--17295636 Score: 147
Period size: 48 Copynumber: 3.3 Consensus size: 47
17295469 ACTTCCAGTT
* * * * *
17295479 GAACCAAATGCAGGGGTGCTCGTGGCATCAAATGCGGGGGTACTTGAG
1 GAACCAAACGCAGGGGTGCTTGTGGCACCAAAAGC-CGGGTACTTGAG
* * *
17295527 GCACCAAACGCAGGGGTGCTTGTGGCACCGAAA-CCTGGAGTGCTTGAG
1 GAACCAAACGCAGGGGTGCTTGTGGCACCAAAAGCC-GG-GTACTTGAG
** * * *
17295575 GCGCCAAACGCAGGGGTGCTTGTCGCACCAAAAGCCGGGCTACTAGTG
1 GAACCAAACGCAGGGGTGCTTGTGGCACCAAAAGCCGGG-TACTTGAG
*
17295623 GAACCAAAGGCAGG
1 GAACCAAACGCAGG
17295637 ACTAGAACCA
Statistics
Matches: 89, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
47 4 0.04
48 83 0.93
49 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.35, T:0.15
Consensus pattern (47 bp):
GAACCAAACGCAGGGGTGCTTGTGGCACCAAAAGCCGGGTACTTGAG
Found at i:17300356 original size:124 final size:126
Alignment explanation
Indices: 17300028--17300379 Score: 539
Period size: 126 Copynumber: 2.8 Consensus size: 126
17300018 TAATTTCGAG
**
17300028 TTGACGTTTCTGATAAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
17300093 AAATCGCGCCCTCGTGGACACGCTTTTGCTATAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
*
17300154 TTGACGTTTCTGAGCAAATAGTATAAAATCACTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * *
17300219 AAATCGCGGCCTCGT-CAGCGTGCTTTTGCTACAGTAGGTCATGTAAGAAATAA-T-TTTTT
66 AAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
* * *
17300278 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTT
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
17300343 AAATCGCGTCCTCGTGGACGCGCTTTTGTTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
17300380 CATGTTTGGG
Statistics
Matches: 206, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
124 97 0.47
125 3 0.01
126 106 0.51
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (126 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
Found at i:17303541 original size:23 final size:23
Alignment explanation
Indices: 17303519--17304241 Score: 500
Period size: 23 Copynumber: 29.4 Consensus size: 23
17303509 TTAAGGTTAG
17303519 GGTTA-GGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
17303541 GGTTAGGGTTTTTAATTAATTTAGGTTAA
1 GGTTAGGGTTTTTAATTAA---A--TT-A
**
17303570 GGTTAGGGTTTTTAAGTT-AA-GG
1 GGTTAGGGTTTTTAA-TTAAATTA
17303592 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
* *
17303615 GGTTAAGGTTAGGGTTT--TTAAGTTAA
1 GGTTAGGGTT----TTTAATTAAATT-A
17303641 GGGTTTAGGGTTTTTAAGTT-AATTA
1 -GG-TTAGGGTTTTTAA-TTAAATTA
17303666 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
17303689 GGTTAGGGTTAGGGTTT--TT-AATTAA
1 GGTTAGGGTT----TTTAATTAAATT-A
17303714 GGGTTTAGGGTTTTTAATTAAATTA
1 -GG-TTAGGGTTTTTAATTAAATTA
* *
17303739 GGTTGGGGTTAAGGTTTTTGATTAAATTA
1 ------GGTTAGGGTTTTTAATTAAATTA
*
17303768 GGTTAGGGTTTCTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
17303791 GGTTAGGGTTTTCAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
17303814 GGTTAGGGTTTTTAATT-AA--G
1 GGTTAGGGTTTTTAATTAAATTA
17303834 GGTTTAGGGTTTTTAATTAAATTAGATTA
1 GG-TTAGGGTTTTTAATT--A--A-ATTA
*
17303863 GGGTTAGGATTTTTAATTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTA
17303887 GGTTAGGGTTAGGGTTT--TT-AATTAA
1 GGTTAGGGTT----TTTAATTAAATT-A
*
17303912 GGGTTTAGGGTTTTCAATTAAATTA
1 -GG-TTAGGGTTTTTAATTAAATTA
*
17303937 GGTTAGGGTTTTCAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
17303960 GGTTAGGGTTTTTAATTAAATTAGGTTAA
1 GGTTAGGGTTTTTAATT-AA--A--TT-A
**
17303989 GGTTAGGGTTTTTAAGTT-AA-GG
1 GGTTAGGGTTTTTAA-TTAAATTA
*
17304011 GGTTAGGGCTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
17304034 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
17304057 GGTTAGGGTTAGGGTTT--TT-AATTAA
1 GGTTAGGGTT----TTTAATTAAATT-A
17304082 GGGGTTAGGGTTTTTAATTAAATTAGATTA
1 --GGTTAGGGTTTTTAATT--A--A-ATTA
*
17304112 GGGCTAGGGTTTTTAATTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTA
17304136 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
* * *
17304159 GGTTAGAGTTAGGGTT--TTCAATTAA
1 GGTTAGGGTT---TTTAATTAAATT-A
17304184 GGGTTTAGGGTTTTTAATTAAATTA
1 -GG-TTAGGGTTTTTAATTAAATTA
17304209 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
17304232 GGTTAAGGTT
1 GGTTAGGGTT
17304242 AGGGTTTAGG
Statistics
Matches: 576, Mismatches: 37, Indels: 175
0.73 0.05 0.22
Matches are distributed among these distances:
20 2 0.00
21 19 0.03
22 42 0.07
23 254 0.44
24 39 0.07
25 28 0.05
26 31 0.05
27 52 0.09
28 12 0.02
29 83 0.14
30 11 0.02
31 3 0.01
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:17303578 original size:29 final size:29
Alignment explanation
Indices: 17303540--17304248 Score: 196
Period size: 29 Copynumber: 28.4 Consensus size: 29
17303530 TAATTAAATT
17303540 AGGTTAGGGTTTTTAA-TTAATTTAGGTTA
1 AGGTTAGGGTTTTTAAGTTAA-TTAGGTTA
17303569 AGGTTAGGGTTTTTAAGTT-A--AGG---
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
17303592 -GGTTAGGGTTTTTAA-TTAAATTAGGTTA
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
17303620 AGGTTAGGGTTTTTAAGTT-A--AGG---
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
*
17303643 -GTTTAGGGTTTTTAAGTT-A--A--TT-
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
17303665 AGGTTAGGGTTTTTAA-TTAAATTAGGTTA
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
*
17303694 GGGTTAGGGTTTTTAA-TT-A--AGG---
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
* *
17303716 -GTTTAGGGTTTTTAA-TTAAATTAGGTTG
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
* * *
17303744 GGGTTAAGGTTTTTGA-TTAA--A--TT-
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
*
17303767 AGGTTAGGGTTTCTAA-TTAA--A--TT-
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
*
17303790 AGGTTAGGGTTTTCAA-TTAA--A--TT-
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
17303813 AGGTTAGGGTTTTTAA-TT-A--AGG---
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
* *
17303835 -GTTTAGGGTTTTTAA-TTAAATTAGATTA
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
* *
17303863 GGGTTAGGATTTTTAA-TTAAATTAGGTTA
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
*
17303892 GGGTTAGGGTTTTTAA-TT-A--AGG---
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
* * *
17303914 -GTTTAGGGTTTTCAA-TTAA-A---TT-
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
*
17303936 AGGTTAGGGTTTTCAA-TTAA--A--TT-
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
17303959 AGGTTAGGGTTTTTAA-TTAAATTAGGTTA
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
17303988 AGGTTAGGGTTTTTAAGTT-A--AGG---
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
*
17304011 -GGTTAGGGCTTTTAA-TTAA--A--TT-
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
17304033 AGGTTAGGGTTTTTAA-TTAAATTAGGTTA
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
*
17304062 GGGTTAGGGTTTTTAA-TT-A--AGG---
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
*
17304084 -GGTTAGGGTTTTTAA-TTAAATTAGATTA
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
* *
17304112 GGGCTAGGGTTTTTAA-TTAA--A--TT-
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
17304135 AGGTTAGGGTTTTTAA-TTAAATTAGGTT-
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
*
17304163 AGAGTTAGGGTTTTCAA-TT-A--AGG---
1 AG-GTTAGGGTTTTTAAGTTAATTAGGTTA
*
17304186 -GTTTAGGGTTTTTAA-TTAA--A--TT-
1 AGGTTAGGGTTTTTAAGTTAATTAGGTTA
17304208 AGGTTAGGGTTTTTAA-TTAAATTAGGTTA
1 AGGTTAGGGTTTTTAAGTT-AATTAGGTTA
17304237 AGGTTAGGGTTT
1 AGGTTAGGGTTT
17304249 AGGGTTTTTA
Statistics
Matches: 560, Mismatches: 35, Indels: 170
0.73 0.05 0.22
Matches are distributed among these distances:
21 82 0.15
22 58 0.10
23 160 0.29
24 13 0.02
25 22 0.04
26 16 0.03
27 4 0.01
28 18 0.03
29 181 0.32
30 6 0.01
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (29 bp):
AGGTTAGGGTTTTTAAGTTAATTAGGTTA
Found at i:17303610 original size:21 final size:22
Alignment explanation
Indices: 17303570--17303610 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17303560 TTTAGGTTAA
17303570 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
17303592 GGTTAGGGTTTTTAA-TTAA
1 GGTTAGGGTTTTTAAGTTAA
17303611 ATTAGGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (22 bp):
GGTTAGGGTTTTTAAGTTAAGG
Found at i:17303649 original size:102 final size:100
Alignment explanation
Indices: 17303512--17304241 Score: 490
Period size: 102 Copynumber: 7.4 Consensus size: 100
17303502 CATTACGTTA
* * *
17303512 AGGTTAGGGTTA-GGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAATTTAGGTTAAGGTTAG
1 AGGTTAAGGTTAGGGTTTTTAATTAAA-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
17303576 GGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATT
65 GGTTTTTAA-TTAAGGGGTTAGGGTTTTTAATT-AATT
*
17303614 AGGTTAAGGTTAGGGTTTTTAAGTT-AA-GGGTTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTT
1 AGGTTAAGGTTAGGGTTTTTAA-TTAAATAGG-TTAGGGTTTTTAA-TTAAATTAGGTTAGGGTT
*
17303676 ----TTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT-A--
63 AGGGTTT--TT-AATTAAG---GGGTTAGGGTTTTTAATTAATT
* * * **
17303713 AGG----GTTTAGGGTTTTTAATTAAATTAGGTTGGGGTTAAGGTTT--TT-GATTAAATTA-GG
1 AGGTTAAGGTTAGGGTTTTTAATTAAA-TAGGTTAGGGTT----TTTAATTAAATTAGGTTAGGG
* ** *
17303770 TTAGGGTTTCTAATTAAATTAGGTTAGGGTTTTCAATTAA--
61 TTAGGGTTTTTAATT-AA-GGGGTTAGGGTTTTTAATTAATT
* *
17303810 A--TT-AGGTTAGGGTTTTTAATT-AA-GGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAG
1 AGGTTAAGGTTAGGGTTTTTAATTAAATAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
* ** **** *
17303870 GATTTTTAATTAAATTAGGTTAGGG-TTAGGGTT-TTT
65 GGTTTTTAATT-AA-GGGGTTAGGGTTTTTAATTAATT
* * *
17303906 A-ATTAAGGGTTTAGGGTTTTCAATTAAATTAGGTTAGGGTTTTCAATTAAATTAGGTTAGGGTT
1 AGGTTAA-GG-TTAGGGTTTTTAATTAAA-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
17303970 ----TTTAATTAAATT-AGGTTAAGGTTAGGGTTTTTAAGTT-A--
63 AGGGTTT--TT-AATTAAGG----GGTTAGGGTTTTTAA-TTAATT
*
17304008 AGG----GGTTAGGGCTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
1 AGGTTAAGGTTAGGGTTTTTAATTAAA-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
17304069 GGTTTTTAATTAAGGGGTTAGGGTTTTTAATTAAATT
65 GGTTTTTAATTAAGGGGTTAGGGTTTTTAATT-AATT
* * * *
17304106 AGATTAGGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAG
1 AGGTTAAGGTTAGGGTTTTTAATTAAA-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
* *
17304171 GGTTTTCAATTAAGGGTTTAGGGTTTTTAATTAA--
65 GGTTTTTAATTAAGGGGTTAGGGTTTTTAATTAATT
*
17304205 A--TT-AGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTT
1 AGGTTAAGGTTAGGGTTTTTAATTAAA-TAGGTTAGGGTT
17304242 AGGGTTTAGG
Statistics
Matches: 512, Mismatches: 52, Indels: 134
0.73 0.07 0.19
Matches are distributed among these distances:
92 3 0.01
94 6 0.01
95 45 0.09
96 96 0.19
97 74 0.14
98 33 0.06
99 12 0.02
100 28 0.05
101 16 0.03
102 160 0.31
103 35 0.07
104 4 0.01
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (100 bp):
AGGTTAAGGTTAGGGTTTTTAATTAAATAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
GTTTTTAATTAAGGGGTTAGGGTTTTTAATTAATT
Found at i:17303658 original size:73 final size:73
Alignment explanation
Indices: 17303519--17304218 Score: 524
Period size: 73 Copynumber: 9.5 Consensus size: 73
17303509 TTAAGGTTAG
**** *
17303519 GGTTA-GGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAATTTAGGTTAA-GGTTAGGGTTTT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTT--TTTAAGTTAAGGGTTAGGGTTTT
**
17303582 TAAGTT-AA-GG
63 TAA-TTAAATTA
*
17303592 GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTA
17303657 AGTT-AATTA
65 A-TTAAATTA
17303666 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTA
17303730 ATTAAATTA
65 ATTAAATTA
* * ** ** *
17303739 GGTTGGGGTTAAGGTTTTTGATTAAATTAGGTTAGGGTT--TCTAATTAAATT-A-GGTTAGGGT
1 ------GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
*
17303800 TTTCAATTAAATTA
60 TTTTAATTAAATTA
* * *
17303814 GGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTT----TTTAATTAAATTAGATTAGGGTTAGGA
1 GGTTAGGGTTTTTAATTAAATTAGG-TTAGGGTTAGGGTTT--TTAAGTT--A--AGGGTTAGGG
17303872 TTTTTAATTAAATTA
59 TTTTTAATTAAATTA
* *
17303887 GGTTAGGGTTAGGGTTT--TT-AATTA----AGGGTTTAGGGTTTTCAA-TTAAATTAGGTTAGG
1 GGTTAGGGTT----TTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAAGTT-AA--GGGTTAGG
*
17303944 GTTTTCAATTAAATTA
58 GTTTTTAATTAAATTA
* *
17303960 GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGCTTTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTA
17304025 ATTAAATTA
65 ATTAAATTA
17304034 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TTAAGGGGTTAGGGTTTTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTA
17304098 ATTAAATTAGATTA
65 ATT--A--A-ATTA
* **** * * *
17304112 GGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT-AGAGTTAGGGTTT
1 -GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTT--TTTAAGTTAAGGGTTAGGGTTT
* *
17304176 TCAATT-AA--G
62 TTAATTAAATTA
17304185 GGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTT
17304219 TTTAATTAAA
Statistics
Matches: 526, Mismatches: 48, Indels: 107
0.77 0.07 0.16
Matches are distributed among these distances:
65 1 0.00
66 2 0.00
67 15 0.03
68 2 0.00
69 18 0.03
71 12 0.02
72 18 0.03
73 168 0.32
74 133 0.25
75 43 0.08
76 8 0.02
77 13 0.02
78 6 0.01
79 61 0.12
80 4 0.01
81 16 0.03
82 4 0.01
83 2 0.00
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (73 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAA
TTAAATTA
Found at i:17303774 original size:125 final size:125
Alignment explanation
Indices: 17303519--17304329 Score: 837
Period size: 125 Copynumber: 6.4 Consensus size: 125
17303509 TTAAGGTTAG
* *
17303519 GGTTA-GGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAATTTAGGTTAAGGTTAGGGTTTTT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT
* *
17303583 AAGTTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTT-AA--G
66 AA-TTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TTAAATTA
17303642 GGTTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
1 GG-TTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
* * * *
17303706 TTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTGGGGTTAAGGTTTTTGATTAAATTA
64 TTAATTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
* *
17303768 GGTTAGGGTTTCTAATTAAATTAGGTTAGGGTTTTCAATT-AA--A--TTA-GGTTAGGGTTTTT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT
* * *
17303827 AATTAAGGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGATTTTTAATTAAATTA
66 AATTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
* *
17303887 GGTTAGGGTTAGGGTTT--TT-AATTAAGGGTTTAGGGTTTTCAATTAAATTAGGTTAGGGTT-T
1 GGTTAGGGTT----TTTAATTAAATT-A-GG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
**** * *
17303948 TCAATTAAATT-A--GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTT-AA
59 GGTTTTTAATTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TTAAA
**
17304009 -GG
123 TTA
*
17304011 GGTTAGGGCTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT
* *
17304076 AATTAAGGGGTTAGGGTTTTTAATTAAATTAGATTAGGGCTAGGGTTTTTAATTAAATTA
66 AATTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
* * *
17304136 GGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTT--TTCAATTA----AGGGTTTAGGGT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT---TTTAATTAAATTAGGTTAGGG-TTAGGGT
**
17304195 TTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTAGGGTTTTTAA
62 TTTTAATT-AA-GGGGTTAGGGTTTTTAATT-AA--A--TT-AGGTTAGGG-TTAGGGTTTTTAA
17304260 TTAAATTA
118 TTAAATTA
* ****
17304268 GGTTAGGGTTAGTGTTTTTAATTAATTTAGGTTAGGGTTTAGGGTTAAATTAGGTTAGGGTT
1 GGTTA--G---G-GTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
17304330 TTTATTGCAT
Statistics
Matches: 578, Mismatches: 55, Indels: 93
0.80 0.08 0.13
Matches are distributed among these distances:
119 78 0.13
120 40 0.07
121 11 0.02
122 11 0.02
123 42 0.07
124 110 0.19
125 179 0.31
126 16 0.03
127 1 0.00
128 12 0.02
129 4 0.01
130 2 0.00
131 8 0.01
132 25 0.04
134 1 0.00
137 8 0.01
138 24 0.04
140 2 0.00
141 4 0.01
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (125 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT
AATTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
Found at i:17304086 original size:21 final size:21
Alignment explanation
Indices: 17304062--17304102 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
17304052 AATTAGGTTA
17304062 GGGTTAGGGTTTTTAATTAAG
1 GGGTTAGGGTTTTTAATTAAG
17304083 GGGTTAGGGTTTTTAATTAA
1 GGGTTAGGGTTTTTAATTAA
17304103 ATTAGATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (21 bp):
GGGTTAGGGTTTTTAATTAAG
Found at i:17304242 original size:102 final size:100
Alignment explanation
Indices: 17303891--17304335 Score: 336
Period size: 102 Copynumber: 4.4 Consensus size: 100
17303881 AAATTAGGTT
* *
17303891 AGGGTTAGGGTTTTTAATT-AA--GGGTTTAGGG--TTT-TCAATTAAATT--AGGTTAGGGTTT
1 AGGGTTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTATTAATTAAATTAGAGGTTAGGGTTT
* **** * *
17303948 TCAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTA
65 TTAATTAAATTAGGTTAGGG-TTAGGGTT--TTTA-ATTA
** *
17303988 A-GGTTAGGGTTTTTAAGTT-AA-GGGGTTAGGG--CTT-TTAATTAAATT--AGGTTAGGGTTT
1 AGGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTATTAATTAAATTAGAGGTTAGGGTTT
17304045 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
65 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
* *
17304081 AGGGGTTAGGGTTTTTAATTAAATTAGATTAGGGCTAGGGTTT-TTAATTAAATT--AGGTTAGG
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-T---TTTTATTAATTAAATTAGAGGTTAGG
* *
17304143 GTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTCAATTA
61 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
17304183 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAG-GGT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTT-ATT-AATTA----AA--TTAGAGG-
*
17304247 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGTGTTTTTAATTA
56 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
* ****
17304292 ATTTAGGTTAGGGTTTAGGGTTAAATTAGGTTAGGGTTTTTATT
1 A---GGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTATT
17304336 GCATCAAATA
Statistics
Matches: 295, Mismatches: 25, Indels: 43
0.81 0.07 0.12
Matches are distributed among these distances:
93 4 0.01
94 5 0.02
95 17 0.06
96 26 0.09
97 54 0.18
98 6 0.02
100 2 0.01
101 9 0.03
102 88 0.30
105 2 0.01
107 2 0.01
108 2 0.01
109 43 0.15
110 3 0.01
111 30 0.10
112 2 0.01
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (100 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTATTAATTAAATTAGAGGTTAGGGTTTT
TAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA
Found at i:17304251 original size:36 final size:36
Alignment explanation
Indices: 17304211--17304284 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
17304201 TTAAATTAGG
17304211 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGT
* *
17304247 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGTGT
1 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGT
17304283 TT
1 TT
17304285 TTAATTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (36 bp):
TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGT
Found at i:17304274 original size:23 final size:23
Alignment explanation
Indices: 17304247--17304333 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 23
17304237 AGGTTAGGGT
17304247 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
17304270 TTAGGGTTAGTGTTTTTAATTAATTTAGG
1 TTA--G---G-GTTTTTAATTAAATTAGG
****
17304299 TTAGGGTTTAGGGTTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
17304322 TTAGGGTTTTTA
1 TTAGGGTTTTTA
17304334 TTGCATCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
23 25 0.51
24 1 0.02
25 1 0.02
27 1 0.02
28 1 0.02
29 20 0.41
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.48
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATTAGG
Found at i:17304284 original size:29 final size:29
Alignment explanation
Indices: 17304083--17304313 Score: 128
Period size: 29 Copynumber: 8.4 Consensus size: 29
17304073 TTTAATTAAG
*
17304083 GGGTTAGGGTTTTTAATTAAATTAGATTA
1 GGGTTAGGGTTTTTAATTAAATTAGGTTA
*
17304112 GGGCTAGGGTTTTTAATT-AA--A--TTA
1 GGGTTAGGGTTTTTAATTAAATTAGGTTA
17304136 -GGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGGTTAGGGTTTTTAATTAAATTAGGTTA
* * *
17304164 GAGTTAGGGTTTTCAATT-AA--GGGTTTA
1 GGGTTAGGGTTTTTAATTAAATTAGG-TTA
*
17304191 GGGTT----TTTAATTAAATT--A-G--GTTA
1 GGGTTAGGGTTT--TT-AATTAAATTAGGTTA
**
17304214 GGGTT----TTTAATTAAATTAGGTTAAGGTTA
1 GGGTTAGGGTTT--TT-AATTAAATT-AGGTTA
17304243 GGGTTTAGGGTTTTTAATTAAATTAGGTTA
1 GGG-TTAGGGTTTTTAATTAAATTAGGTTA
* *
17304273 GGGTTAGTGTTTTTAATTAATTTAGGTTA
1 GGGTTAGGGTTTTTAATTAAATTAGGTTA
17304302 GGGTTTAGGGTT
1 GGG-TTAGGGTT
17304314 AAATTAGGTT
Statistics
Matches: 165, Mismatches: 14, Indels: 45
0.74 0.06 0.20
Matches are distributed among these distances:
23 39 0.24
24 6 0.04
25 2 0.01
26 8 0.05
27 7 0.04
28 7 0.04
29 66 0.40
30 18 0.11
31 7 0.04
32 2 0.01
34 3 0.02
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.45
Consensus pattern (29 bp):
GGGTTAGGGTTTTTAATTAAATTAGGTTA
Found at i:17304300 original size:59 final size:58
Alignment explanation
Indices: 17304183--17304313 Score: 185
Period size: 59 Copynumber: 2.2 Consensus size: 58
17304173 TTTTCAATTA
*
17304183 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTT
1 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTT-ATTAAATTAGATTAAGGTT
* *
17304242 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGTGTT-TTTAATTA-ATTTAGGTT
1 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTT--T-TTATTAAATTAGATTAAGGTT
17304301 AGGGTTTAGGGTT
1 AGGGTTTAGGGTT
17304314 AAATTAGGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
59 56 0.85
60 7 0.11
61 1 0.02
62 2 0.03
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (58 bp):
AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTATTAAATTAGATTAAGGTT
Found at i:17304310 original size:36 final size:33
Alignment explanation
Indices: 17304209--17304314 Score: 121
Period size: 36 Copynumber: 3.2 Consensus size: 33
17304199 AATTAAATTA
17304209 GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAG
1 GGTTAGGGTTTTTAATT-AATTAGGTT-AGGTTAG
17304244 GGTTTAGGGTTTTTAATTAA--A--TTAGGTTAG
1 GG-TTAGGGTTTTTAATTAATTAGGTTAGGTTAG
*
17304274 GGTTAGTGTTTTTAATTAATTTAGGTTAGGGTTTAG
1 GGTTAGGGTTTTTAATTAA-TTAGGTTA-GG-TTAG
17304310 GGTTA
1 GGTTA
17304315 AATTAGGTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 15
0.79 0.01 0.19
Matches are distributed among these distances:
29 16 0.26
30 9 0.15
31 2 0.03
32 1 0.02
33 1 0.02
34 3 0.05
35 6 0.10
36 24 0.39
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.46
Consensus pattern (33 bp):
GGTTAGGGTTTTTAATTAATTAGGTTAGGTTAG
Found at i:17304358 original size:26 final size:26
Alignment explanation
Indices: 17304328--17304397 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
17304318 TAGGTTAGGG
*
17304328 TTTTTATTGCATCAAATAAACTTCTA
1 TTTTTATTACATCAAATAAACTTCTA
*
17304354 TTTTTATTACATCATATAAACTTCTA
1 TTTTTATTACATCAAATAAACTTCTA
17304380 -TTTTATTACATCAAATAA
1 TTTTTATTACATCAAATAA
17304398 TATCAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 17 0.41
26 24 0.59
ACGTcount: A:0.37, C:0.14, G:0.01, T:0.47
Consensus pattern (26 bp):
TTTTTATTACATCAAATAAACTTCTA
Found at i:17305549 original size:7 final size:7
Alignment explanation
Indices: 17305539--17305563 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17305529 TTATATACAT
17305539 AATACTA
1 AATACTA
17305546 AATACTA
1 AATACTA
17305553 AATACTA
1 AATACTA
17305560 AATA
1 AATA
17305564 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:17306770 original size:22 final size:22
Alignment explanation
Indices: 17306745--17306797 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
17306735 TATGGATATA
17306745 AGAGAATTTTGGAAAGAAATTG
1 AGAGAATTTTGGAAAGAAATTG
*
17306767 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAAGAAATTG
17306789 AGAGGAATT
1 AGA-GAATT
17306798 GAGAGGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.26
Consensus pattern (22 bp):
AGAGAATTTTGGAAAGAAATTG
Found at i:17306814 original size:12 final size:11
Alignment explanation
Indices: 17306780--17306814 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
17306770 GAATTTTGGA
17306780 AGGAAATTGAG
1 AGGAAATTGAG
17306791 AGG-AATTGAG
1 AGGAAATTGAG
17306801 AGGAAATATGAG
1 AGGAAAT-TGAG
17306813 AG
1 AG
17306815 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:17312499 original size:60 final size:60
Alignment explanation
Indices: 17312426--17312542 Score: 234
Period size: 60 Copynumber: 1.9 Consensus size: 60
17312416 TAGAATTCAT
17312426 GGATCGAGACATGGGTAAATGATATCCTTTCTTTGGCATTACATGGTTTATGAAAAGAAA
1 GGATCGAGACATGGGTAAATGATATCCTTTCTTTGGCATTACATGGTTTATGAAAAGAAA
17312486 GGATCGAGACATGGGTAAATGATATCCTTTCTTTGGCATTACATGGTTTATGAAAAG
1 GGATCGAGACATGGGTAAATGATATCCTTTCTTTGGCATTACATGGTTTATGAAAAG
17312543 TAAACATGGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (60 bp):
GGATCGAGACATGGGTAAATGATATCCTTTCTTTGGCATTACATGGTTTATGAAAAGAAA
Found at i:17313290 original size:102 final size:102
Alignment explanation
Indices: 17313114--17313309 Score: 304
Period size: 102 Copynumber: 1.9 Consensus size: 102
17313104 TTGAAAGAAC
* * *
17313114 GAGTTTATGTTTTTAAGCTATTTTGAACCCTGAAAATGAAAATAATCCATTCAACCATAGTGAAT
1 GAGTTTATGTTTTTAAGCTATTTTGAACCCTGAAAATAAAAATAATCCATTCAACCACAGTGAAC
17313179 ATGTTGAGTTGTGAAATACTAAATATTTTTTGGAAAT
66 ATGTTGAGTTGTGAAATACTAAATATTTTTTGGAAAT
* ***
17313216 GAGTTTATGTTTTTAAGCTGTTTTGAACCCTGAAAATAAAAATAAAT-CATTCGGTCACAGTGAA
1 GAGTTTATGTTTTTAAGCTATTTTGAACCCTGAAAATAAAAAT-AATCCATTCAACCACAGTGAA
*
17313280 CATGTTGAGTTGTGAAATATTAAATATTTT
65 CATGTTGAGTTGTGAAATACTAAATATTTT
17313310 CTGAAAAAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
102 82 0.96
103 3 0.04
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (102 bp):
GAGTTTATGTTTTTAAGCTATTTTGAACCCTGAAAATAAAAATAATCCATTCAACCACAGTGAAC
ATGTTGAGTTGTGAAATACTAAATATTTTTTGGAAAT
Found at i:17319473 original size:51 final size:50
Alignment explanation
Indices: 17319382--17319508 Score: 141
Period size: 51 Copynumber: 2.5 Consensus size: 50
17319372 TGATAGGTCG
* *
17319382 CATGTGTAGTACTATGTACAGGCTACTATCCGTACCGGATAGCT-TCGATCA
1 CATGTGTAGTACTATGTGCAGGCTAATATCCGTACCGGATAG-TAT-GATCA
* * ** *
17319433 CGTGTGTAGTACTATGTGCAGGCTAATA-CGTGTATTGGATAGTGATGGTCA
1 CATGTGTAGTACTATGTGCAGGCTAATATC-CGTACCGGATAGT-ATGATCA
17319484 CATGTGTAGTACTATGTGCAGGCTA
1 CATGTGTAGTACTATGTGCAGGCTA
17319509 CTATGTGAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
50 2 0.03
51 62 0.95
52 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTATGTGCAGGCTAATATCCGTACCGGATAGTATGATCA
Found at i:17319521 original size:102 final size:101
Alignment explanation
Indices: 17319329--17319521 Score: 271
Period size: 102 Copynumber: 1.9 Consensus size: 101
17319319 AAAGTGATGG
* * *
17319329 TCACGTGTGTAGTACTATGTGTAGGCTACTACGAGTACTAGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTAATACGAGTACTAGAATGATAGGTCACATGTGTAGTAC
*
17319394 TATGTACAGGCTACTATCCGTACCGGATAGCTTCGA
66 TATGTACAGGCTACTATCCGAACCGGATAGCTTCGA
* * *
17319430 TCACGTGTGTAGTACTATGTGCAGGCTAATACGTGTATTGGATAGTGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTAATACGAGTACTAGA-A-TGATAGGTCACATGTGTAGT
* **
17319494 ACTATGTGCAGGCTACTATGTGAACCGG
64 ACTATGTACAGGCTACTATCCGAACCGG
17319522 TATCATTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
101 37 0.46
102 39 0.49
103 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTAATACGAGTACTAGAATGATAGGTCACATGTGTAGTAC
TATGTACAGGCTACTATCCGAACCGGATAGCTTCGA
Found at i:17319590 original size:46 final size:43
Alignment explanation
Indices: 17319517--17319615 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
17319507 TACTATGTGA
*
17319517 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* * *
17319560 ACCGGATATCATTGATTACAAAGGGTGGTTGTTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
17319606 ACCGGGTATC
1 ACC-GGTATC
17319616 TGTTATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.23
45 2 0.04
46 25 0.53
47 4 0.09
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:17319763 original size:16 final size:15
Alignment explanation
Indices: 17319742--17319774 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
17319732 TTGAAAGTGA
17319742 AAAAGTCAAATTATGC
1 AAAAGTCAAATTA-GC
17319758 AAAAGTCAAATTAGC
1 AAAAGTCAAATTAGC
17319773 AA
1 AA
17319775 CAAAATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (15 bp):
AAAAGTCAAATTAGC
Found at i:17322862 original size:37 final size:37
Alignment explanation
Indices: 17322818--17322894 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
17322808 ATTTTATTTC
17322818 CTTAGTTTAAGAAACCTTAAAATTATCTCTTATTTTA
1 CTTAGTTTAAGAAACCTTAAAATTATCTCTTATTTTA
17322855 CTTAGTTTAAGAAACCTTAAAATTATCTCTTATTTTA
1 CTTAGTTTAAGAAACCTTAAAATTATCTCTTATTTTA
17322892 CTT
1 CTT
17322895 TCGTACTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (37 bp):
CTTAGTTTAAGAAACCTTAAAATTATCTCTTATTTTA
Found at i:17332556 original size:13 final size:13
Alignment explanation
Indices: 17332538--17332567 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17332528 TAAATGTATA
17332538 ATATGAAACGGTT
1 ATATGAAACGGTT
*
17332551 ATATGAAATGGTT
1 ATATGAAACGGTT
17332564 ATAT
1 ATAT
17332568 AAAGTAGATG
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:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (13 bp):
ATATGAAACGGTT
Found at i:17332636 original size:54 final size:52
Alignment explanation
Indices: 17332529--17332657 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 52
17332519 ATTGTGTGTT
* * * *
17332529 AAATGTATAATATGAAACGGTTATATGAAATGGTTATATAAAGTAGATGTACA
1 AAATG-ATAATATGAATCAGTTATATGAAATAGTTATATAAAGTAGATATACA
* *
17332582 AAATGATCATATGAATCAGTTATATGGAAAATAGTTATATAAAGT-GTTTATACA
1 AAATGATAATATGAATCAGTTATAT-G-AAATAGTTATATAAAGTAG-ATATACA
* *
17332636 AAATGTTGATATGAAT-AGTTAT
1 AAATGATAATATGAATCAGTTAT
17332658 GTAAAAAGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
52 17 0.26
53 13 0.20
54 35 0.54
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATGATAATATGAATCAGTTATATGAAATAGTTATATAAAGTAGATATACA
Found at i:17332686 original size:13 final size:13
Alignment explanation
Indices: 17332668--17332692 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17332658 GTAAAAAGGG
17332668 ACATTTGAAATGA
1 ACATTTGAAATGA
17332681 ACATTTGAAATG
1 ACATTTGAAATG
17332693 CTAAATGAAA
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:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
ACATTTGAAATGA
Found at i:17351695 original size:16 final size:17
Alignment explanation
Indices: 17351674--17351705 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17351664 ATATACCAAA
17351674 AAAAAT-AAAAACCTGC
1 AAAAATAAAAAACCTGC
17351690 AAAAATAAAAAACCTG
1 AAAAATAAAAAACCTG
17351706 TGGTGGCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.16, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAATAAAAAACCTGC
Found at i:17352356 original size:18 final size:18
Alignment explanation
Indices: 17352335--17352395 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
17352325 AGTAATAACT
17352335 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
** ** *
17352353 CTATTCAAGAAGTAATAACT
1 CTATTTTA-ATTTAATAA-A
17352373 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
17352391 CTATT
1 CTATT
17352396 CTCATCAAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
18 11 0.35
19 14 0.45
20 6 0.19
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:17352366 original size:38 final size:41
Alignment explanation
Indices: 17352324--17352449 Score: 159
Period size: 45 Copynumber: 3.0 Consensus size: 41
17352314 AATTCTAATT
*
17352324 AAGTAATAACTCTATTTTAATTTAATAAACTA-T-TCA-AG
1 AAGTAATAACTCTATTTTAATTTAATAAACTATTCTCACAA
17352362 AAGTAATAACTCTATTTTAATTTAATAAACTATTCTCATCAA
1 AAGTAATAACTCTATTTTAATTTAATAAACTATTCTCA-CAA
* *
17352404 ATTACTTAATAACTCTATTTTAATTTAATAAACTCTTCTCATCAA
1 A--A-GTAATAACTCTATTTTAATTTAATAAACTATTCTCA-CAA
17352449 A
1 A
17352450 TTACCAAAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
38 32 0.41
39 1 0.01
40 3 0.04
42 2 0.03
44 1 0.01
45 39 0.50
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.41
Consensus pattern (41 bp):
AAGTAATAACTCTATTTTAATTTAATAAACTATTCTCACAA
Found at i:17352406 original size:23 final size:23
Alignment explanation
Indices: 17352380--17352451 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 23
17352370 ACTCTATTTT
17352380 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
*
17352403 AATTACTTAATAACTCTATT-T--T--
1 AA-T--TTAATAA-ACTATTCTCATCA
*
17352425 AATTTAATAAACTCTTCTCATCA
1 AATTTAATAAACTATTCTCATCA
17352448 AATT
1 AATT
17352452 ACCAAAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 18
0.64 0.05 0.31
Matches are distributed among these distances:
18 4 0.11
19 8 0.22
21 2 0.05
22 2 0.05
23 6 0.16
24 2 0.05
26 8 0.22
27 5 0.14
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATAAACTATTCTCATCA
Found at i:17352415 original size:45 final size:45
Alignment explanation
Indices: 17352365--17352453 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
17352355 ATTCAAGAAG
17352365 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
*
17352410 TAATAACTCTATTTTAATTTAATAAACTCTTCTCATCAAATTAC
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
17352454 CAAAATAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (45 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
Found at i:17352479 original size:15 final size:15
Alignment explanation
Indices: 17352459--17352508 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
17352449 ATTACCAAAA
17352459 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
17352474 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
17352489 GAGAATAGTTTATTAAAT
1 TAG---AGTTTATTAAAT
17352507 TA
1 TA
17352509 AAATAGAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:17352513 original size:18 final size:18
Alignment explanation
Indices: 17352477--17352514 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17352467 ATTAAATTAG
*
17352477 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
17352495 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
17352513 AG
1 AG
17352515 AGCTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:17353204 original size:26 final size:27
Alignment explanation
Indices: 17353172--17353234 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
17353162 TTTTTTTGGT
*
17353172 ATATTTTGGTAAAT-AAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
17353198 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
17353225 ATATTTTGGT
1 ATATTTTGGT
17353235 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 14 0.40
27 21 0.60
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Done.