Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007850.1 Hibiscus syriacus cultivar Beakdansim tig00110209_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1775394
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:959146 original size:13 final size:13
Alignment explanation
Indices: 959128--959153 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
959118 ATCTAGTGCC
959128 TCATCCCACTAGA
1 TCATCCCACTAGA
959141 TCATCCCACTAGA
1 TCATCCCACTAGA
959154 ACAACTGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.08, T:0.23
Consensus pattern (13 bp):
TCATCCCACTAGA
Found at i:959256 original size:27 final size:26
Alignment explanation
Indices: 959214--959274 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
959204 ACAAATATAA
959214 TATATTATTTATAATT-AATTTAAGATTT
1 TATATT-TTTATAATTAAATTT-AG-TTT
959242 TAATATTTTTA-AATTAAATTTAGTTT
1 T-ATATTTTTATAATTAAATTTAGTTT
959268 TATATTT
1 TATATTT
959275 ATTTATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 6 0.19
26 4 0.13
27 6 0.19
28 10 0.32
29 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (26 bp):
TATATTTTTATAATTAAATTTAGTTT
Found at i:959279 original size:27 final size:30
Alignment explanation
Indices: 959213--959286 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 30
959203 AACAAATATA
959213 ATATATTATTTATAATTAATTTAAGATTTT
1 ATATATTATTTATAATTAATTTAAGATTTT
959243 A-ATATT-TTTA-AATTAAATTT-AG-TTTT
1 ATATATTATTTATAATT-AATTTAAGATTTT
959269 ATAT-TTATTTATTAATTA
1 ATATATTATTTA-TAATTA
959287 TTATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
26 7 0.18
27 12 0.31
28 10 0.26
29 9 0.23
30 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
ATATATTATTTATAATTAATTTAAGATTTT
Found at i:959641 original size:2 final size:2
Alignment explanation
Indices: 959626--959674 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
959616 TATAATCAAT
959626 TA TA -A TA T- TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
959665 TA -A TA T- TA TA
1 TA TA TA TA TA TA
959675 ATTGATTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
1 5 0.12
2 37 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:959650 original size:15 final size:15
Alignment explanation
Indices: 959626--959674 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
959616 TATAATCAAT
959626 TATA-ATATTATATA
1 TATATATATTATATA
959640 TATATATATTATATA
1 TATATATATTATATA
959655 TATATATA-TATA-A
1 TATATATATTATATA
959668 TAT-TATA
1 TATATATA
959675 ATTGATTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 4 0.12
13 4 0.12
14 8 0.24
15 18 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATATTATATA
Found at i:959656 original size:17 final size:17
Alignment explanation
Indices: 959634--959674 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
959624 ATTATAATAT
*
959634 TATATATATATATATTA
1 TATATATATATATATAA
959651 TATATATATATATATAA
1 TATATATATATATATAA
959668 TAT-TATA
1 TATATATA
959675 ATTGATTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:960889 original size:14 final size:15
Alignment explanation
Indices: 960870--960898 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
960860 TATTATATTC
960870 TATTA-TTTAATTTA
1 TATTATTTTAATTTA
960884 TATTATTTTAATTTA
1 TATTATTTTAATTTA
960899 AAAAACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTATTTTAATTTA
Found at i:961108 original size:2 final size:2
Alignment explanation
Indices: 961101--961125 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
961091 TGACACGTGT
961101 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
961126 TTAAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:961155 original size:17 final size:17
Alignment explanation
Indices: 961112--961171 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
961102 ATATATATAT
961112 ATATATATATATATTTAAA
1 ATATATAT-TAT-TTTAAA
*
961131 CA-AAATATTATTTTAAA
1 -ATATATATTATTTTAAA
961148 ATATATA-TATTTTTAAA
1 ATATATATTA-TTTTAAA
*
961165 AAATATA
1 ATATATA
961172 AATGTGACGC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 3 0.09
17 23 0.66
18 3 0.09
19 5 0.14
20 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATATTATTTTAAA
Found at i:966653 original size:2 final size:2
Alignment explanation
Indices: 966646--966694 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
966636 GAAAAGAATA
966646 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
966687 AT AT AT AT
1 AT AT AT AT
966695 TACTGGTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:969838 original size:52 final size:53
Alignment explanation
Indices: 969760--969865 Score: 205
Period size: 52 Copynumber: 2.0 Consensus size: 53
969750 TGTTGATTCA
969760 TGTAGGTGATTGGGCTTTTCTTTAGATGTGCTTCCTTCAGTCGGGTC-GCGAG
1 TGTAGGTGATTGGGCTTTTCTTTAGATGTGCTTCCTTCAGTCGGGTCTGCGAG
969812 TGTAGGTGATTGGGCTTTTCTTTAGATGTGCTTCCTTCAGTCGGGTCTGCGAG
1 TGTAGGTGATTGGGCTTTTCTTTAGATGTGCTTCCTTCAGTCGGGTCTGCGAG
969865 T
1 T
969866 AATGGACCTG
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 47 0.89
53 6 0.11
ACGTcount: A:0.11, C:0.17, G:0.32, T:0.40
Consensus pattern (53 bp):
TGTAGGTGATTGGGCTTTTCTTTAGATGTGCTTCCTTCAGTCGGGTCTGCGAG
Found at i:971821 original size:3 final size:3
Alignment explanation
Indices: 971805--971897 Score: 82
Period size: 3 Copynumber: 30.7 Consensus size: 3
971795 TTTGGGCTTG
* * * * *
971805 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAA TAA TAT TAG T-A TTA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
971850 TAA TTA TATA TAA TAA TAA TTA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
971896 TA
1 TA
971898 TTTAAATGAA
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
2 3 0.04
3 62 0.85
4 8 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:974178 original size:15 final size:15
Alignment explanation
Indices: 974154--974191 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
974144 ATAATGAAAC
974154 TAAATAAT-AAAGGA
1 TAAATAATAAAAGGA
*
974168 TTAAATCATAAAAGGA
1 -TAAATAATAAAAGGA
974184 TAAATAAT
1 TAAATAAT
974192 GACGCACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (15 bp):
TAAATAATAAAAGGA
Found at i:975325 original size:18 final size:18
Alignment explanation
Indices: 975302--975425 Score: 185
Period size: 18 Copynumber: 6.9 Consensus size: 18
975292 GCGTAGAATT
* *
975302 TGTCCCGTATGACCACTA
1 TGTCCCGAAGGACCACTA
*
975320 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
975338 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
975356 TATCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
975374 TGTCCTGAAGGATCACTA
1 TGTCCCGAAGGACCACTA
975392 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
975410 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
975426 GTAGACCCTC
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 94 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:978325 original size:3 final size:3
Alignment explanation
Indices: 978317--978369 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
978307 TTGTAACCTA
978317 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
978365 AAT AA
1 AAT AA
978370 ATAAGCAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:981021 original size:31 final size:31
Alignment explanation
Indices: 980983--981047 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
980973 ACATTATTAT
*
980983 TTTAAACACATTACATATATTATATCATCAC
1 TTTAAACACATGACATATATTATATCATCAC
* * *
981014 TTTAAACATATGATATGTATTATATCATCAC
1 TTTAAACACATGACATATATTATATCATCAC
981045 TTT
1 TTT
981048 GGATACATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.43
Consensus pattern (31 bp):
TTTAAACACATGACATATATTATATCATCAC
Found at i:991386 original size:7 final size:7
Alignment explanation
Indices: 991369--991436 Score: 59
Period size: 7 Copynumber: 9.7 Consensus size: 7
991359 GTGGTCAGGT
*
991369 TTTATGG
1 TTTAAGG
*
991376 TTTAAGA
1 TTTAAGG
991383 TTT-AGTG
1 TTTAAG-G
991390 TTTAAGG
1 TTTAAGG
*
991397 TTTAAGA
1 TTTAAGG
991404 TTT-AGTG
1 TTTAAG-G
* *
991411 TTTACGA
1 TTTAAGG
991418 TTTAAGG
1 TTTAAGG
991425 TTTAAGG
1 TTTAAGG
991432 TTTAA
1 TTTAA
991437 ATCTTAGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
6 4 0.08
7 41 0.85
8 3 0.06
ACGTcount: A:0.28, C:0.01, G:0.22, T:0.49
Consensus pattern (7 bp):
TTTAAGG
Found at i:991393 original size:21 final size:21
Alignment explanation
Indices: 991369--991436 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
991359 GTGGTCAGGT
*
991369 TTTATGGTTTAAGATTTAGTG
1 TTTAAGGTTTAAGATTTAGTG
991390 TTTAAGGTTTAAGATTTAGTG
1 TTTAAGGTTTAAGATTTAGTG
* * *
991411 TTTACGATTTAAGGTTTAAG-G
1 TTTAAGGTTTAAGATTT-AGTG
991432 TTTAA
1 TTTAA
991437 ATCTTAGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 39 0.95
22 2 0.05
ACGTcount: A:0.28, C:0.01, G:0.22, T:0.49
Consensus pattern (21 bp):
TTTAAGGTTTAAGATTTAGTG
Found at i:991975 original size:11 final size:11
Alignment explanation
Indices: 991959--992015 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
991949 ATTATAGAAA
991959 TTTTAATATAT
1 TTTTAATATAT
991970 TTTTAA-A-AT
1 TTTTAATATAT
991979 TTTATAAT-TAT
1 TTT-TAATATAT
***
991990 CAATAATATAT
1 TTTTAATATAT
992001 TTTTAATATAT
1 TTTTAATATAT
992012 TTTT
1 TTTT
992016 TATAATGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
9 5 0.14
10 8 0.22
11 23 0.64
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:994854 original size:2 final size:2
Alignment explanation
Indices: 994847--994890 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
994837 TGATTCTGAA
994847 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
994889 AG
1 AG
994891 GAGGAGAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:997026 original size:24 final size:25
Alignment explanation
Indices: 996972--997019 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
996962 TAAATATATT
*
996972 TTATTATTAATTTAATTTAAAAAAA
1 TTATTTTTAATTTAATTTAAAAAAA
*
996997 TTATTTTTATTTTAATTTAAAAA
1 TTATTTTTAATTTAATTTAAAAA
997020 TATATTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATTTTTAATTTAATTTAAAAAAA
Found at i:997314 original size:30 final size:31
Alignment explanation
Indices: 997261--997318 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
997251 TCGTGATGAC
997261 CATATCTTAATTAAATAAAAACGAAAGTGAT
1 CATATCTTAATTAAATAAAAACGAAAGTGAT
997292 CATATCTTAATTAAAT-AAAACGAAAGT
1 CATATCTTAATTAAATAAAAACGAAAGT
997319 AATTGTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (31 bp):
CATATCTTAATTAAATAAAAACGAAAGTGAT
Found at i:998523 original size:13 final size:13
Alignment explanation
Indices: 998505--998552 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
998495 TCATAACCCG
998505 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
998518 ACCCGACCTGTTG
1 ACCCGACCCGTTT
998531 ACCCGACCCGTTT
1 ACCCGACCCGTTT
998544 ACCCGACCC
1 ACCCGACCC
998553 ATTGACCGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:998557 original size:26 final size:26
Alignment explanation
Indices: 998504--998559 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
998494 GTCATAACCC
**
998504 GACCCGACCCGTTTACCCGACCTGTT
1 GACCCGACCCGTTTACCCGACCCATT
998530 GACCCGACCCGTTTACCCGACCCATT
1 GACCCGACCCGTTTACCCGACCCATT
998556 GACC
1 GACC
998560 GTTGACCCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.20
Consensus pattern (26 bp):
GACCCGACCCGTTTACCCGACCCATT
Found at i:1002219 original size:37 final size:37
Alignment explanation
Indices: 1002171--1002311 Score: 183
Period size: 37 Copynumber: 3.8 Consensus size: 37
1002161 GTTAGAATTT
* * *
1002171 TACTAGGATTCAAACTCCTAAAAATAGAATATAGTTT
1 TACTAGAATTCAAACTCCTAAAAATAGAATAAAGTTC
* * * * *
1002208 TATTAGAATTCAAACTCTTAATAATAGGATAGAGTTC
1 TACTAGAATTCAAACTCCTAAAAATAGAATAAAGTTC
* *
1002245 TACTATAATTCAAACTCCTAAAAATAGGATAAAGTTC
1 TACTAGAATTCAAACTCCTAAAAATAGAATAAAGTTC
*
1002282 TACTATAATTCAAACTCCTAAAAATAGAAT
1 TACTAGAATTCAAACTCCTAAAAATAGAAT
1002312 CCACAAGCGT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 91 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (37 bp):
TACTAGAATTCAAACTCCTAAAAATAGAATAAAGTTC
Found at i:1002877 original size:2 final size:2
Alignment explanation
Indices: 1002872--1002903 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1002862 TTTAGATTAC
1002872 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1002904 GTTATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1002957 original size:51 final size:50
Alignment explanation
Indices: 1002881--1003032 Score: 121
Period size: 51 Copynumber: 2.9 Consensus size: 50
1002871 CATATATATA
* *
1002881 TATATATATATATATATATATATGTTATTTTTATTATTTGTTTTATTAATT
1 TATATATATAT-TATATTTTTATGTTATTTTTATTATTTGTTTTATTAATT
* * * *
1002932 TATATATATATTACTATTTTTATGTT-TTTATTATATATAT-ATATATTATTT
1 TATATATATATTA-TATTTTTATGTTATTT-TTAT-TATTTGTTTTATTAATT
* * *
1002983 TACTTTAT-TATTATTATTTATTATTATTATTATTATTTATTTGTTTTATT
1 TA-TATATATATTA-TATTT-TTA-TGTTATTTTTA-TTATTTGTTTTATT
1003033 TATATATTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
50 5 0.06
51 45 0.57
52 11 0.14
53 10 0.13
54 8 0.10
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (50 bp):
TATATATATATTATATTTTTATGTTATTTTTATTATTTGTTTTATTAATT
Found at i:1002981 original size:3 final size:3
Alignment explanation
Indices: 1002959--1003019 Score: 63
Period size: 3 Copynumber: 19.7 Consensus size: 3
1002949 TTTTATGTTT
*
1002959 TTA TTA TATA TATA TATA TTA TT- TTA CT- TTA TTA TTA TTA TTTA TTA
1 TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
1003006 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
1003020 TATTTGTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 3 0.06
3 35 0.67
4 14 0.27
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1002993 original size:13 final size:13
Alignment explanation
Indices: 1002905--1003019 Score: 85
Period size: 13 Copynumber: 8.6 Consensus size: 13
1002895 TATATATATG
*
1002905 TTATTTTTATTAT
1 TTATTATTATTAT
*
1002918 TTGTT-TTATTAAT
1 TTATTATTATT-AT
1002931 TTATATATATATTA-
1 TTAT-TAT-TATTAT
* * *
1002945 CTATTTTTATGTTT
1 TTATTATTAT-TAT
1002959 TTATTATATATATAT
1 TTATTAT-TAT-TAT
*
1002974 ATATTATT-TTACT
1 TTATTATTATTA-T
1002987 TTATTATTATTAT
1 TTATTATTATTAT
1003000 TTATTATTATTA-
1 TTATTATTATTAT
1003012 TTATTATT
1 TTATTATT
1003020 TATTTGTTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
12 18 0.22
13 34 0.41
14 13 0.16
15 13 0.16
16 4 0.05
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:1003000 original size:37 final size:33
Alignment explanation
Indices: 1002891--1003039 Score: 117
Period size: 32 Copynumber: 4.3 Consensus size: 33
1002881 TATATATATA
*
1002891 TATATATATATATGTTATTTTTATTATTTGTTTTAT
1 TATATATATATATATTATTTTT-TTA-TT-TTTTAT
* *
1002927 TAATTTATATATATATTACTATTTTTATGTTTTTAT
1 T-ATATATATATATATTA-TTTTTTTAT-TTTTTAT
*
1002963 TATATATATATATATTATTTTACTTTA-TTATTAT
1 TATATATATATATATTATTTT--TTTATTTTTTAT
* *
1002997 TATTTAT-TAT-TATTATTATTATTTATTTGTT-T
1 TATATATATATATATTATT-TT-TTTATTTTTTAT
*
1003029 TATTTATATAT
1 TATATATATAT
1003040 TTTTTCTTCT
Statistics
Matches: 96, Mismatches: 9, Indels: 19
0.77 0.07 0.15
Matches are distributed among these distances:
32 19 0.20
33 12 0.12
34 15 0.16
35 15 0.16
36 13 0.14
37 18 0.19
38 4 0.04
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (33 bp):
TATATATATATATATTATTTTTTTATTTTTTAT
Found at i:1003011 original size:32 final size:31
Alignment explanation
Indices: 1002957--1003077 Score: 96
Period size: 32 Copynumber: 3.9 Consensus size: 31
1002947 ATTTTTATGT
*
1002957 TTTTATTATATATATATATATTATTTTACTTTA
1 TTTTATTATTTAT-TAT-TATTATTTTACTTTA
1002990 TTATTATTATTTATTATTATTATTATTA-TTTA
1 TT-TTATTATTTATTATTATTATT-TTACTTTA
*
1003022 TTTGTTTTATTTA-TA-TATT-TTTT-CTTCT-
1 TTT-TATTATTTATTATTATTATTTTACTT-TA
1003050 TTTT-TTATTT-TTATTTATTTATTTTACT
1 TTTTATTATTTATTA-TTA-TTATTTTACT
1003078 CACTATTTTA
Statistics
Matches: 75, Mismatches: 2, Indels: 24
0.74 0.02 0.24
Matches are distributed among these distances:
26 8 0.11
27 1 0.01
28 9 0.12
29 5 0.07
30 8 0.11
31 5 0.07
32 21 0.28
33 8 0.11
34 10 0.13
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (31 bp):
TTTTATTATTTATTATTATTATTTTACTTTA
Found at i:1003032 original size:19 final size:19
Alignment explanation
Indices: 1002905--1003023 Score: 89
Period size: 19 Copynumber: 5.9 Consensus size: 19
1002895 TATATATATG
* *
1002905 TTATTTTTATTATTTGTT-
1 TTATTATTATTATTTATTA
*
1002923 TTATTAATTTATATATATATTA
1 TTATT-A-TTAT-TATTTATTA
* * *
1002945 CTATTTTTATGTTTTTATTA
1 TTATTATTAT-TATTTATTA
*
1002965 TATATATATATATTATTTTACT-
1 T-TAT-TAT-TATTA-TTTATTA
1002987 TTATTATTATTATTTATTA
1 TTATTATTATTATTTATTA
1003006 TTATTATTATTATTTATT
1 TTATTATTATTATTTATT
1003024 TGTTTTATTT
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
18 10 0.13
19 23 0.29
20 18 0.23
21 12 0.15
22 8 0.10
23 8 0.10
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTATTATTATTTATTA
Found at i:1003074 original size:13 final size:13
Alignment explanation
Indices: 1002977--1003075 Score: 59
Period size: 13 Copynumber: 7.6 Consensus size: 13
1002967 TATATATATA
1002977 TTATTTTACTTTA-
1 TTATTTTA-TTTAT
1002990 TTATTATTATTTA-
1 TTATT-TTATTTAT
1003003 TTATTATTATTATTAT
1 TTATT-TTA-T-TTAT
1003019 TTATTTGT-TTTAT
1 TTATTT-TATTTAT
*
1003032 TTA-TATATTT-T
1 TTATTTTATTTAT
* *
1003043 TTCTTCT-TTT-T
1 TTATTTTATTTAT
1003054 TTATTTTTATTTAT
1 TTA-TTTTATTTAT
1003068 TTATTTTA
1 TTATTTTA
1003076 CTCACTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
11 10 0.14
12 9 0.13
13 33 0.46
14 9 0.13
15 4 0.06
16 6 0.08
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:1006172 original size:31 final size:29
Alignment explanation
Indices: 1006137--1006194 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
1006127 ACAAAAAGAG
1006137 AAAAAGAGAAGA-AAAAAGCAAAGAGAAAATA
1 AAAAAGAGAA-ACAAAAA-CAAAG-GAAAATA
*
1006168 AAAAAGTGAAACAAAAACAAAGGAAAA
1 AAAAAGAGAAACAAAAACAAAGGAAAA
1006195 GGTGAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 5 0.20
30 6 0.24
31 14 0.56
ACGTcount: A:0.74, C:0.05, G:0.17, T:0.03
Consensus pattern (29 bp):
AAAAAGAGAAACAAAAACAAAGGAAAATA
Found at i:1008057 original size:116 final size:116
Alignment explanation
Indices: 1007894--1008123 Score: 318
Period size: 116 Copynumber: 2.0 Consensus size: 116
1007884 CAATATAAGC
* * *
1007894 TTGGATTTCAACTTTACAACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAATGAACCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGGAACCAT
* * *
1007959 CCATGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAACATTCA
** * * ***
1008010 TTGGATTTCAACTTCACGGCGAAGGATATCCAA-TTCAAGGCTGAACTTCACAATGAAGGGGTCA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAAGTT-AAGGCTCAACTTCACAACGAAGGAACCA
*
1008074 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACTAGCAACATT
65 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAACATT
1008124 TATCTTCAGG
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
115 2 0.02
116 97 0.98
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (116 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGGAACCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAACATTCA
Found at i:1008249 original size:21 final size:22
Alignment explanation
Indices: 1008212--1008255 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1008202 AATTTACTCA
*
1008212 AAACAAAGTTTTGTCTCTCTTG
1 AAACAAAGTTTTATCTCTCTTG
1008234 AAACAAA-TTTTATCTCTCTTG
1 AAACAAAGTTTTATCTCTCTTG
1008255 A
1 A
1008256 GACAGTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (22 bp):
AAACAAAGTTTTATCTCTCTTG
Found at i:1008271 original size:36 final size:36
Alignment explanation
Indices: 1008227--1008490 Score: 253
Period size: 37 Copynumber: 7.3 Consensus size: 36
1008217 AAGTTTTGTC
*
1008227 TCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTT
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
* * *
1008263 TCCCTTGAAACAAA------ATCT-TTGA-ATA-TT
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
* *
1008290 TTTACATT-AAACAAATTTTGTCTC-CATTGAGACAATT
1 TCT-C-TTGAAACAAATTTTGTCTCTC-TTGAGACAGTT
* * *
1008327 TCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTT
1 TCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTT
*
1008364 TCTCTTGAAACAAAATTTGCCTTTGTCTCTGTTGAGACAGTT
1 TCTCTTGAAAC-AAA--T---TTTGTCTCTCTTGAGACAGTT
1008406 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
*
1008442 TCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTT
1 TCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTT
1008479 TCTCTTGAAACA
1 TCTCTTGAAACA
1008491 CCAATCTCTG
Statistics
Matches: 187, Mismatches: 20, Indels: 41
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.02
28 10 0.05
29 6 0.03
30 3 0.02
34 2 0.01
35 6 0.03
36 51 0.27
37 69 0.37
38 1 0.01
39 2 0.01
41 3 0.02
42 31 0.17
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
Found at i:1008608 original size:35 final size:36
Alignment explanation
Indices: 1008543--1008625 Score: 123
Period size: 35 Copynumber: 2.3 Consensus size: 36
1008533 CCATGAGACA
*
1008543 ATTTCTCTTGAAACAAAAAAAAAAACCTTTGAAATT
1 ATTTCTCTTGAAACAAAAAAAAAAACCTTTGAAAAT
* *
1008579 ATTTCTCTTGAAAC-ACAAAAAAAAGCTTTGAAAAT
1 ATTTCTCTTGAAACAAAAAAAAAAACCTTTGAAAAT
*
1008614 GTTTCTCTTGAA
1 ATTTCTCTTGAA
1008626 TTCCAAGACC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 29 0.67
36 14 0.33
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (36 bp):
ATTTCTCTTGAAACAAAAAAAAAAACCTTTGAAAAT
Found at i:1009266 original size:37 final size:37
Alignment explanation
Indices: 1009223--1009324 Score: 168
Period size: 37 Copynumber: 2.8 Consensus size: 37
1009213 ACGTTAGAAG
*
1009223 TTTACTAGGATTCAAACTCCTAAACATAGGATAGAGT
1 TTTACTAGGATTCAAACTCCTAAAAATAGGATAGAGT
*
1009260 TTTACTAGAATTCAAACTCCTAAAAATAGGATAGAGT
1 TTTACTAGGATTCAAACTCCTAAAAATAGGATAGAGT
* *
1009297 TCTACTATGATTCAAACTCCTAAAAATA
1 TTTACTAGGATTCAAACTCCTAAAAATA
1009325 AGATCCACAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (37 bp):
TTTACTAGGATTCAAACTCCTAAAAATAGGATAGAGT
Found at i:1010006 original size:42 final size:40
Alignment explanation
Indices: 1009923--1010005 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
1009913 TTTTATAAAT
*
1009923 TTATATATATATATATACTATTTTTTTATGTTTTTATTTA
1 TTATATATATATATATACTATTTTTTAATGTTTTTATTTA
1009963 TTATATATATATATATA-TATTATTTTAACT-TTTTTA-TTA
1 TTATATATATATATATACTATT-TTTTAA-TGTTTTTATTTA
1010002 TTAT
1 TTAT
1010006 TTTATTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
39 11 0.28
40 28 0.70
41 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (40 bp):
TTATATATATATATATACTATTTTTTAATGTTTTTATTTA
Found at i:1014654 original size:116 final size:116
Alignment explanation
Indices: 1014491--1014720 Score: 381
Period size: 116 Copynumber: 2.0 Consensus size: 116
1014481 CAATATAAGC
*
1014491 TTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCAT
* *
1014556 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTAA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCATACTCACCAGCAACATTAA
* * *
1014607 TTGGATTTCAACTTCACGGCGAAGGATATCCAA-TTCAAGGCTTAACTTCACAACGAAGGGGTCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTT-AAGGCTCAACTTCACAACGAAGGGGCCA
*
1014671 TCCACGGTTTCAACTTCACGACGAAGGGAATCATACTCACTAGCAACATT
65 TCCACGGTTTCAACTTCACGACGAAGGGAATCATACTCACCAGCAACATT
1014721 TATCTTCAGG
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 2 0.02
116 104 0.98
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (116 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCATACTCACCAGCAACATTAA
Found at i:1014846 original size:21 final size:21
Alignment explanation
Indices: 1014809--1014888 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
1014799 AATTTACTCA
1014809 AAACAAAGTTTTGTCTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTG
*
1014831 AAACAAATTTTATCTCTCTTG
1 AAACAAATTTTGTCTCTCTTG
* *
1014852 AGAC--A-GTT-TC-C-CTTG
1 AAACAAATTTTGTCTCTCTTG
1014867 AAACAAATTTTGTCTCTCTTG
1 AAACAAATTTTGTCTCTCTTG
1014888 A
1 A
1014889 GACAGTTTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
15 7 0.15
16 1 0.02
17 3 0.06
18 4 0.09
19 3 0.06
20 1 0.02
21 21 0.45
22 7 0.15
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (21 bp):
AAACAAATTTTGTCTCTCTTG
Found at i:1014868 original size:36 final size:36
Alignment explanation
Indices: 1014827--1015123 Score: 299
Period size: 36 Copynumber: 8.2 Consensus size: 36
1014817 TTTTGTCTCT
*
1014827 CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1014863 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
* * * *
1014899 CTTGAAACAAA------ATCT-TTGA-ATATTTTTAC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACA-GTTTCC
* * *
1014928 ATT-AAACAAATTTTGTCTC-CATTGAGACAATTTCT
1 CTTGAAACAAATTTTGTCTCTC-TTGAGACAGTTTCC
* * * *
1014963 TTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCC
*
1015000 CTTGAAACAAATTTTGCCTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAACAAA---T---TTTGTCTCTCTTGAGACAGTTTCC
1015042 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
* *
1015078 CTTGAAACAAAGTTTTGTCTCTTTTGAGACAGTTTCT
1 CTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCC
1015115 CTTGAAACA
1 CTTGAAACA
1015124 CCAATCTCTG
Statistics
Matches: 220, Mismatches: 21, Indels: 39
0.79 0.08 0.14
Matches are distributed among these distances:
28 9 0.04
29 10 0.05
30 3 0.01
34 2 0.01
35 9 0.04
36 87 0.40
37 62 0.28
38 1 0.00
39 2 0.01
42 35 0.16
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
Found at i:1014990 original size:37 final size:37
Alignment explanation
Indices: 1014931--1015123 Score: 248
Period size: 37 Copynumber: 5.1 Consensus size: 37
1014921 TTTTTACATT
* *
1014931 AAACAAA-TTTTGTCTC-CATTGAGACAATTTCTTTTG
1 AAACAAAGTTTTGTCTCTC-TTGAGACAGTTTCTCTTG
* *
1014967 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
1015004 AAACAAATTTTGCCTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA----G-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
1015046 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
1015082 AAACAAAGTTTTGTCTCTTTTGAGACAGTTTCTCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1015119 AAACA
1 AAACA
1015124 CCAATCTCTG
Statistics
Matches: 138, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
36 39 0.28
37 62 0.45
38 1 0.01
41 1 0.01
42 35 0.25
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (37 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:1015220 original size:34 final size:34
Alignment explanation
Indices: 1015177--1015289 Score: 201
Period size: 34 Copynumber: 3.3 Consensus size: 34
1015167 CTTGAGACAA
1015177 TTTCTCTTGAAACA-AAAAAAATCCTTTGAAATTG
1 TTTCTCTTGAAACACAAAAAAA-CCTTTGAAATTG
1015211 TTTCTCTTGAAACACAAAAAAACCTTTGAAATTG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAATTG
*
1015245 TTTCTCTTGAAACACAAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAATTG
1015279 TTTCTCTTGAA
1 TTTCTCTTGAA
1015290 TCCCAAGACC
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
34 70 0.91
35 7 0.09
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.35
Consensus pattern (34 bp):
TTTCTCTTGAAACACAAAAAAACCTTTGAAATTG
Found at i:1015936 original size:37 final size:37
Alignment explanation
Indices: 1015887--1015998 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
1015877 AACATAACGT
* *
1015887 TAGAAGTTTACTAGGATTCAAACTCTTAAAAATAGGA
1 TAGAATTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
1015924 TAGAATTTTACTAGAATTCAAACTCCTAAAAATAGGA
1 TAGAATTTTACTAGGATTCAAACTCCTAAAAATAGGA
* * *
1015961 TAGAGTTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAATTTTACTAGGATTCAAACTCCTAAAAATAGGA
1015998 T
1 T
1015999 CCACAAGCGT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (37 bp):
TAGAATTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:1016521 original size:30 final size:33
Alignment explanation
Indices: 1016471--1016531 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
1016461 GTTAATTTTC
*
1016471 TTTTCTTTTTTTCATGTAATAT-T-TTTTTACA
1 TTTTCTTTTTTACATGTAATATATATTTTTACA
*
1016502 TTTTCTTTTTTAC-TTTAATATATATTTTTA
1 TTTTCTTTTTTACATGTAATATATATTTTTA
1016532 TTTTTTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 13 0.50
32 6 0.23
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (33 bp):
TTTTCTTTTTTACATGTAATATATATTTTTACA
Found at i:1016535 original size:30 final size:29
Alignment explanation
Indices: 1016466--1016535 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 29
1016456 GCTTTGTTAA
* *
1016466 TTTTCTTTTCTTTTTTTCATGTAATATTT
1 TTTTATTTTCTTTTTTACATGTAATATTT
*
1016495 TTTTACATTTTCTTTTTTAC-TTTAATATATAT
1 TTTT--ATTTTCTTTTTTACATGTAATAT-T-T
1016527 TTTTATTTT
1 TTTTATTTT
1016536 TTTAGATTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 4 0.12
30 12 0.35
31 13 0.38
32 5 0.15
ACGTcount: A:0.19, C:0.09, G:0.01, T:0.71
Consensus pattern (29 bp):
TTTTATTTTCTTTTTTACATGTAATATTT
Found at i:1016581 original size:4 final size:4
Alignment explanation
Indices: 1016570--1016703 Score: 57
Period size: 4 Copynumber: 33.8 Consensus size: 4
1016560 ATATATGGTT
* * * * * *
1016570 TTTA -TTA TTTA TTTTA TTAA TTTA TATA TATA TATA TATA TTTA -CTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
1016617 TTT- TTTA TGTT- TTTA TTTA TTATA TATA TATA TATTA TTTT TTTC TTT-
1 TTTA TTTA T-TTA TTTA TTTA TT-TA TTTA TTTA T-TTA TTTA TTTA TTTA
* *
1016665 TTTA -TTA -TTA TTTTA TTTA TTTGT TTTA TTTA TATA TTT
1 TTTA TTTA TTTA -TTTA TTTA TTT-A TTTA TTTA TTTA TTT
1016704 TTTCTTCTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
3 19 0.18
4 67 0.64
5 18 0.17
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:1016624 original size:43 final size:42
Alignment explanation
Indices: 1016547--1016652 Score: 135
Period size: 45 Copynumber: 2.5 Consensus size: 42
1016537 TTAGATTACA
**
1016547 TATATATATATATATATATGGTTTTTATTATTTAT-TTTATTAATT
1 TATATATATATATATATAT--TTACTATTATTTATGTTT-TT-ATT
*
1016592 TATATATATATATATATATTTACTATTTTTTATGTTTTTATT
1 TATATATATATATATATATTTACTATTATTTATGTTTTTATT
1016634 TAT-TATATATATATATATT
1 TATATATATATATATATATT
1016653 ATTTTTTTCT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
41 16 0.28
42 6 0.11
43 13 0.23
44 3 0.05
45 19 0.33
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (42 bp):
TATATATATATATATATATTTACTATTATTTATGTTTTTATT
Found at i:1016666 original size:45 final size:45
Alignment explanation
Indices: 1016526--1016676 Score: 148
Period size: 43 Copynumber: 3.3 Consensus size: 45
1016516 TTAATATATA
* * *
1016526 TTTTTATTTTTTTAGATTACATATATATATATATATATATGGTTTTTAT
1 TTTTTATTTTATTA-ATT-TATATATATATATATAT-TAT-TTTTTTAT
* **
1016575 TATTTATTTTATTAATTTATATATATATATATA-TA-TTTACTAT
1 TTTTTATTTTATTAATTTATATATATATATATATTATTTTTTTAT
*
1016618 TTTTTATGTTT-TT-ATTTATTATATATATATATATTATTTTTTTCT
1 TTTTTAT-TTTATTAATTTA-TATATATATATATATTATTTTTTTAT
1016663 TTTTTATTATTATT
1 TTTTTATT-TTATT
1016677 TTATTTATTT
Statistics
Matches: 86, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
42 5 0.06
43 27 0.31
44 6 0.07
45 16 0.19
46 2 0.02
47 15 0.17
48 3 0.03
49 12 0.14
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (45 bp):
TTTTTATTTTATTAATTTATATATATATATATATTATTTTTTTAT
Found at i:1016675 original size:21 final size:22
Alignment explanation
Indices: 1016649--1016715 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 22
1016639 TATATATATA
1016649 TATTATTTTTTTCTTTTTTA-T
1 TATTATTTTTTTCTTTTTTATT
*
1016670 TATTATTTTATTTATTTGTTTTATT
1 TATTATTTT-TTT-CTT-TTTTATT
1016695 TATATATTTTTTCTTCTTTTT
1 TAT-TA-TTTTT-TTCTTTTT
1016716 CTTTATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 9 0.24
22 3 0.08
23 2 0.05
24 5 0.14
25 7 0.19
26 5 0.14
27 6 0.16
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (22 bp):
TATTATTTTTTTCTTTTTTATT
Found at i:1016715 original size:24 final size:22
Alignment explanation
Indices: 1016645--1016721 Score: 57
Period size: 25 Copynumber: 3.1 Consensus size: 22
1016635 ATTATATATA
1016645 TATATATTATTTTTTTCTTTTTTAT
1 TATATA-T-TTTTTTTCTTTTTT-T
*
1016670 TAT-TATTTTATTTATTTGTTTTATT
1 TATATATTTT-TTT-TCT-TTTT-TT
1016695 TATATATTTTTTCTTCTTTTTCTT
1 TATATATTTTTT-TTCTTTTT-TT
1016719 TAT
1 TAT
1016722 TTTTAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
22 3 0.07
23 4 0.09
24 13 0.30
25 15 0.35
26 8 0.19
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.75
Consensus pattern (22 bp):
TATATATTTTTTTTCTTTTTTT
Found at i:1016720 original size:28 final size:27
Alignment explanation
Indices: 1016615--1016732 Score: 100
Period size: 28 Copynumber: 4.3 Consensus size: 27
1016605 ATATATTTAC
* *
1016615 TATTTTTTATGTTTTTATTTATTATATA
1 TATTTTTTATTTTTTTCTTTATT-TATA
*
1016643 TATATATATTATTTTTTTCTTT-TTTAT-
1 TAT-T-TTTTATTTTTTTCTTTATTTATA
1016670 TATTATTTTATTTATTTGT-TTTATTTATA
1 TATT-TTTTATTT-TTT-TCTTTATTTATA
* *
1016699 TATTTTTTCTTCTTTTTCTTTATTTTTA
1 TATTTTTTATT-TTTTTCTTTATTTATA
1016727 -ATTTTT
1 TATTTTT
1016733 AATTATTTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
26 9 0.12
27 16 0.21
28 30 0.39
29 8 0.11
30 13 0.17
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (27 bp):
TATTTTTTATTTTTTTCTTTATTTATA
Found at i:1017480 original size:20 final size:20
Alignment explanation
Indices: 1017455--1017496 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1017445 TGTATTTCTT
1017455 TTAAATCTTATCTATGTCTA
1 TTAAATCTTATCTATGTCTA
1017475 TTAAATCTTATCTATGTCTA
1 TTAAATCTTATCTATGTCTA
1017495 TT
1 TT
1017497 TGTTAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (20 bp):
TTAAATCTTATCTATGTCTA
Found at i:1019038 original size:34 final size:34
Alignment explanation
Indices: 1018994--1019068 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
1018984 TTTATGTTCA
* *
1018994 TTTATATTCGTTTATTTATGTCGGTGTGTGATCG
1 TTTATGTTCGTTTATTTATGTCGGTGTATGATCG
* *
1019028 TTTATGTTCGTTTATTTATGTCTGTGTATGTTCG
1 TTTATGTTCGTTTATTTATGTCGGTGTATGATCG
*
1019062 TTAATGT
1 TTTATGT
1019069 CCTTTCATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.15, C:0.08, G:0.21, T:0.56
Consensus pattern (34 bp):
TTTATGTTCGTTTATTTATGTCGGTGTATGATCG
Found at i:1019079 original size:34 final size:34
Alignment explanation
Indices: 1019004--1019080 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
1018994 TTTATATTCG
* * *
1019004 TTTATTTATGTCGGTGTGTGATCGTTTATGTTCG
1 TTTATTTATGTCGGTGTATGATCGTTAATGTTCC
* *
1019038 TTTATTTATGTCTGTGTATGTTCGTTAATG-TCC
1 TTTATTTATGTCGGTGTATGATCGTTAATGTTCC
1019071 TTTCATTTAT
1 TTT-ATTTAT
1019081 ATTCAGTCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.14, C:0.10, G:0.19, T:0.56
Consensus pattern (34 bp):
TTTATTTATGTCGGTGTATGATCGTTAATGTTCC
Found at i:1019310 original size:23 final size:23
Alignment explanation
Indices: 1019262--1019310 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1019252 TATTGTTTAC
* *
1019262 GTTCGTTTACGTTCATTTATTGT
1 GTTCGATTACGTTCATTTATTAT
* *
1019285 GTTCGATTATGTTCATTTGTTAT
1 GTTCGATTACGTTCATTTATTAT
1019308 GTT
1 GTT
1019311 TGTACAGGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.14, C:0.10, G:0.18, T:0.57
Consensus pattern (23 bp):
GTTCGATTACGTTCATTTATTAT
Found at i:1019370 original size:37 final size:38
Alignment explanation
Indices: 1019327--1019411 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 38
1019317 GGTTTGTTTA
* *
1019327 TGTTCGTTTAC-GCTAGTTCGTTTCTGTTCATTTA-TTG
1 TGTTCGTTTACATC-AGTTCGTTTATGTTCATTTATTTG
* * *
1019364 TGTTCGTTTACATCCGTTTGTTTATGTTCTTTTATTTG
1 TGTTCGTTTACATCAGTTCGTTTATGTTCATTTATTTG
1019402 TGTTCGTTTA
1 TGTTCGTTTA
1019412 TCATTTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 27 0.66
38 14 0.34
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.58
Consensus pattern (38 bp):
TGTTCGTTTACATCAGTTCGTTTATGTTCATTTATTTG
Found at i:1023368 original size:36 final size:35
Alignment explanation
Indices: 1023327--1023428 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
1023317 CAATATTGGA
*
1023327 AAATATGCTAAATTTAGGTTTTCCCATTAGTATTGC
1 AAATATGCTAAA-TTAGGTTTTCCCACTAGTATTGC
1023363 AAATATGCTAAATTAGG-TTTCCCACTAGTATTGC
1 AAATATGCTAAATTAGGTTTTCCCACTAGTATTGC
*
1023397 AAATATGCTCAAATTAGGTTATCCCACTAGTA
1 AAATATGCT-AAATTAGGTTTTCCCACTAGTA
1023429 GTGGAAATGA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 25 0.40
35 13 0.21
36 24 0.39
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (35 bp):
AAATATGCTAAATTAGGTTTTCCCACTAGTATTGC
Found at i:1024744 original size:394 final size:389
Alignment explanation
Indices: 1024016--1024801 Score: 1336
Period size: 394 Copynumber: 2.0 Consensus size: 389
1024006 AACGTTTGTA
*
1024016 AGTAATGCAATATCTAATAATGCTCCAGATTAAAAAATGCAATTATTACTTGAAACGACAAATGC
1 AGTAATGCAATATCTAATAATGCTCCAGATTAAAAAATGCAATTATTACTTGAAACAACAAATGC
1024081 CATGTCAATGCATTTACAGCATTAATTCTGCAGTTACATGCAAATATGCACATTTCTTTTGGTTA
66 CATGTCAATGCATTTACAGCATTAATTCTGCAGTTACATGCAAATATGCACATTTCTTTTGGTTA
1024146 ATGTGTATTAAATGGCTTTTGGAAATGCACATATTCTAAGCGTTTATGAACATTATGACTATAAT
131 ATGTGTATTAAATGGCTTTTGGAAATGCACATATTCTAAGCGTTTATGAACATTATGACTATAAT
1024211 ATCATTTTAACAAATGGTATTTATTGGTAAGCATGAATGTGTTATAATCATTATGGCATTATTGT
196 ATCATTTTAACAAATGGTATTTATTGGTAAGCATGAATGTGTTATAATCATTATGGCATTATTGT
*
1024276 TATGTTTTAATCATTGAAACTGTTGGTTTATATTAAAGGTGTAAAATCAGTATATACCTGTATAT
261 TATGTTTTAATCATTGAAACTGTTGGTTTATATT-AA-GTGTAAAATCAGTATATACCTATATAT
*
1024341 ATCTATTAGATTGTCAACGTTACG-AGCTACCATAATTGAGTATTAGT-GTATATTCAATGCTTT
324 ATATATTAGATTGTCAACGTTACGAAGCTACCATAATTGAGTATTAGTGGTATATTCAATGCTTT
1024404 G
389 G
1024405 AGTAATGCAATATCTAAATAATGCT-CAGATTAAAAAATGCAATTATTACTTGAAACAACAAAAT
1 AGTAATGCAATATCT-AATAATGCTCCAGATTAAAAAATGCAATTATTACTTGAAACAAC-AAAT
*
1024469 GCCATGTCAATGCATTTACATGCATTAATTCATGCAGTTACATGCAAATATGCATATTTCTTTTG
64 GCCATGTCAATGCATTTACA-GCATTAATTC-TGCAGTTACATGCAAATATGCACATTTCTTTTG
*
1024534 GTTAATGTGTATTAATATGGCTTTTGGAAATGCACATATTCTAAGCGTTTATGAACATTGTGAAC
127 GTTAATGTGTATTAA-ATGGCTTTTGGAAATGCACATATTCTAAGCGTTTATGAACATTATG-AC
1024599 TATAATATCATTTTAACAAATGGTATTTATTGGTAAGCATGAATGTGTTATAATCATTATGGCAT
190 TATAATATCATTTTAACAAATGGTATTTATTGGTAAGCATGAATGTGTTATAATCATTATGGCAT
1024664 TATTGTTATGTTTTAATCATTGAAACTGTTGG-TT-TA-T-A-TGTAAAATCAGGTATATACCTT
255 TATTGTTATGTTTTAATCATTGAAACTGTTGGTTTATATTAAGTGTAAAATCA-GTATATACC--
1024724 TATATATATATATATATTAGATTGTCAACGTTACGAAGCTACCATAATTGAGTATTAGTGGTATA
317 ----TATATATATATATTAGATTGTCAACGTTACGAAGCTACCATAATTGAGTATTAGTGGTATA
1024789 TTCAATGCTTTG
378 TTCAATGCTTTG
1024801 A
1 A
1024802 AGAATGAATG
Statistics
Matches: 377, Mismatches: 5, Indels: 23
0.93 0.01 0.06
Matches are distributed among these distances:
387 10 0.03
388 9 0.02
389 49 0.13
390 33 0.09
391 11 0.03
392 49 0.13
393 47 0.12
394 128 0.34
395 23 0.06
396 18 0.05
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (389 bp):
AGTAATGCAATATCTAATAATGCTCCAGATTAAAAAATGCAATTATTACTTGAAACAACAAATGC
CATGTCAATGCATTTACAGCATTAATTCTGCAGTTACATGCAAATATGCACATTTCTTTTGGTTA
ATGTGTATTAAATGGCTTTTGGAAATGCACATATTCTAAGCGTTTATGAACATTATGACTATAAT
ATCATTTTAACAAATGGTATTTATTGGTAAGCATGAATGTGTTATAATCATTATGGCATTATTGT
TATGTTTTAATCATTGAAACTGTTGGTTTATATTAAGTGTAAAATCAGTATATACCTATATATAT
ATATTAGATTGTCAACGTTACGAAGCTACCATAATTGAGTATTAGTGGTATATTCAATGCTTTG
Found at i:1034734 original size:17 final size:17
Alignment explanation
Indices: 1034714--1034772 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
1034704 TGAAGTCAAC
1034714 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1034731 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
** *
1034748 AATCAGTCCGGTCGGGTCG
1 GGTCA--ACGGTCGGGTCG
1034767 GGTCAA
1 GGTCAA
1034773 ACCGGTCGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 20 0.59
19 14 0.41
ACGTcount: A:0.15, C:0.24, G:0.42, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1034777 original size:19 final size:19
Alignment explanation
Indices: 1034720--1034780 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
1034710 CAACGGTCAA
1034720 CGGTCGGGTCGGGTC-AA-
1 CGGTCGGGTCGGGTCAAAC
** **
1034737 CGGTCGGGTCGAATCAGTC
1 CGGTCGGGTCGGGTCAAAC
1034756 CGGTCGGGTCGGGTCAAAC
1 CGGTCGGGTCGGGTCAAAC
1034775 CGGTCG
1 CGGTCG
1034781 AAACCGGTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 13 0.38
19 21 0.62
ACGTcount: A:0.13, C:0.26, G:0.43, T:0.18
Consensus pattern (19 bp):
CGGTCGGGTCGGGTCAAAC
Found at i:1034793 original size:9 final size:9
Alignment explanation
Indices: 1034767--1034827 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
1034757 GGTCGGGTCG
1034767 GGTCAAACC
1 GGTCAAACC
1034776 GGTCGAAACC
1 GGTC-AAACC
1034786 GGTCAAACC
1 GGTCAAACC
*
1034795 GATCAGAACC
1 GGTCA-AACC
* *
1034805 AGTTGAAAACC
1 -GGT-CAAACC
1034816 GGTCAAACC
1 GGTCAAACC
1034825 GGT
1 GGT
1034828 TTCCATCCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 21 0.49
10 15 0.35
11 6 0.14
12 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.25, T:0.13
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1037383 original size:22 final size:21
Alignment explanation
Indices: 1037355--1037418 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
1037345 GTCGAGGGTT
*
1037355 TCATAGGTCCTTTCGGGACAAC
1 TCATAGGT-CATTCGGGACAAC
*
1037377 TCATAGGTCATTCGGGACATAT
1 TCATAGGTCATTCGGGACA-AC
*
1037399 TCACAGGTCATTCGGGACAA
1 TCATAGGTCATTCGGGACAA
1037419 ATTTCATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.29
22 27 0.71
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
TCATAGGTCATTCGGGACAAC
Found at i:1040579 original size:35 final size:35
Alignment explanation
Indices: 1040533--1040648 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
1040523 TAATGCTCAA
*
1040533 TATTGGAAATATTCTAAATTAGGTTTTCCCACTAG
1 TATTGGAAATATGCTAAATTAGGTTTTCCCACTAG
1040568 TATTGGAAATATGCTAAATTAGGTTTTCCCACTAG
1 TATTGGAAATATGCTAAATTAGGTTTTCCCACTAG
** *
1040603 TATTACAAATATGCTCAAATTAGGTTATCCCACTAG
1 TATTGGAAATATGCT-AAATTAGGTTTTCCCACTAG
1040639 TATTGGAAAT
1 TATTGGAAAT
1040649 GATGATTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 47 0.64
36 27 0.36
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (35 bp):
TATTGGAAATATGCTAAATTAGGTTTTCCCACTAG
Found at i:1041788 original size:28 final size:28
Alignment explanation
Indices: 1041757--1041814 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1041747 GTATATTTCA
1041757 TTGCTAATATATTTGGTTTATT-ATTTAC
1 TTGCTAATATATTTGGTTTATTGA-TTAC
* *
1041785 TTGCTACTATATTTGTTTTATTGATTAC
1 TTGCTAATATATTTGGTTTATTGATTAC
1041813 TT
1 TT
1041815 TTAAATATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.22, C:0.09, G:0.10, T:0.59
Consensus pattern (28 bp):
TTGCTAATATATTTGGTTTATTGATTAC
Found at i:1044565 original size:16 final size:18
Alignment explanation
Indices: 1044535--1044571 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1044525 TATTTTCTTT
1044535 AATTGATTTGAG-TTTAA
1 AATTGATTTGAGTTTTAA
*
1044552 AATT-ATTTGTGTTTTAA
1 AATTGATTTGAGTTTTAA
1044569 AAT
1 AAT
1044572 ATTAATGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (18 bp):
AATTGATTTGAGTTTTAA
Found at i:1044672 original size:25 final size:25
Alignment explanation
Indices: 1044635--1044702 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
1044625 AAACGAACGG
* *
1044635 AAAT-AAACGAACATACACAGACAT
1 AAATGAAACAAACATAAACAGACAT
**
1044659 AAATGAAACAAACATAAAGGGACAT
1 AAATGAAACAAACATAAACAGACAT
1044684 AAATG-AACAAACATAAACA
1 AAATGAAACAAACATAAACA
1044703 AACAGATTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 16 0.43
25 21 0.57
ACGTcount: A:0.62, C:0.16, G:0.10, T:0.12
Consensus pattern (25 bp):
AAATGAAACAAACATAAACAGACAT
Found at i:1044697 original size:24 final size:25
Alignment explanation
Indices: 1044654--1044700 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
1044644 AACATACACA
1044654 GACATAAATGAAACAAACATAAAGG
1 GACATAAATGAAACAAACATAAAGG
1044679 GACATAAATG-AACAAACATAAA
1 GACATAAATGAAACAAACATAAA
1044701 CAAACAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13
Consensus pattern (25 bp):
GACATAAATGAAACAAACATAAAGG
Found at i:1049871 original size:21 final size:21
Alignment explanation
Indices: 1049854--1049929 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
1049844 GGTCTTTGAG
*
1049854 ACATATATGTGGTCCTTTGGA
1 ACATATATGTGGTCATTTGGA
* *
1049875 ACATATATGCGGTCA-TTCGA
1 ACATATATGTGGTCATTTGGA
*
1049895 GACATATATTTGGTCATTTGGA
1 -ACATATATGTGGTCATTTGGA
*
1049917 ATATATATGTGGT
1 ACATATATGTGGT
1049930 TCTACGGGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.09
21 37 0.82
22 4 0.09
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (21 bp):
ACATATATGTGGTCATTTGGA
Found at i:1049948 original size:23 final size:23
Alignment explanation
Indices: 1049922--1050012 Score: 101
Period size: 23 Copynumber: 4.0 Consensus size: 23
1049912 TTGGAATATA
*
1049922 TATGTGGTTCTACGGGACATTTC
1 TATGTGGTCCTACGGGACATTTC
* *
1049945 TATGTGGTCCTACGAGACAATTC
1 TATGTGGTCCTACGGGACATTTC
* *
1049968 TATGTGGTCCTTCAGGACATTTC
1 TATGTGGTCCTACGGGACATTTC
* * **
1049991 TACGCGGTCCTTTGGGACATTT
1 TATGTGGTCCTACGGGACATTT
1050013 TATATGGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (23 bp):
TATGTGGTCCTACGGGACATTTC
Found at i:1053722 original size:12 final size:12
Alignment explanation
Indices: 1053707--1053737 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1053697 TTTCTTATTG
1053707 TACTGTTTCTTT
1 TACTGTTTCTTT
*
1053719 TACTGATTCTTT
1 TACTGTTTCTTT
1053731 TACTGTT
1 TACTGTT
1053738 CTCTATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.16, G:0.10, T:0.61
Consensus pattern (12 bp):
TACTGTTTCTTT
Found at i:1053748 original size:17 final size:17
Alignment explanation
Indices: 1053726--1053773 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1053716 TTTTACTGAT
1053726 TCTTTTACTGT-TCTCTA
1 TCTTTTACTGTAT-TCTA
** *
1053743 TCTTTTGTTGTATTGTA
1 TCTTTTACTGTATTCTA
1053760 TCTTTTACTGTATT
1 TCTTTTACTGTATT
1053774 ATATATATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 24 0.96
18 1 0.04
ACGTcount: A:0.12, C:0.15, G:0.10, T:0.62
Consensus pattern (17 bp):
TCTTTTACTGTATTCTA
Found at i:1053996 original size:52 final size:48
Alignment explanation
Indices: 1053879--1053996 Score: 130
Period size: 48 Copynumber: 2.4 Consensus size: 48
1053869 TAAATTGTTA
* *
1053879 GTAATTGTATGACACATTAGTGCCCTGTGTGCAGAATAATAACTGCTT
1 GTAATTGTATGACACATTAGTGCCCTGTATGCAGAATAATAACTGATT
* * **
1053927 GTAGTTGTATGACACATTAGTGTCCTGTATGCA-ACATATATGCCTGTGATAT
1 GTAATTGTATGACACATTAGTGCCCTGTATGCAGA-ATA-ATAAC--TGAT-T
1053979 GTAATTGTATGACACATT
1 GTAATTGTATGACACATT
1053997 TAATGCAATG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
47 1 0.02
48 33 0.57
49 3 0.05
51 3 0.05
52 18 0.31
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (48 bp):
GTAATTGTATGACACATTAGTGCCCTGTATGCAGAATAATAACTGATT
Found at i:1055834 original size:13 final size:13
Alignment explanation
Indices: 1055818--1055844 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1055808 TAGTTCTATT
1055818 AGCTTATCAAATG
1 AGCTTATCAAATG
1055831 AGCTTATCAAATG
1 AGCTTATCAAATG
1055844 A
1 A
1055845 ACCCATATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AGCTTATCAAATG
Found at i:1060411 original size:31 final size:31
Alignment explanation
Indices: 1060345--1060419 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1060335 ATTCAATGTC
** **
1060345 TAAGTGATCAAAACTTAATAAAATGACAATG
1 TAAGTGATCAAAACTTAATAAAACAACAACA
*
1060376 TAAGTGATCAAAACTTAATAAAACAATAACA
1 TAAGTGATCAAAACTTAATAAAACAACAACA
*
1060407 TAAGTGACCAAAA
1 TAAGTGATCAAAA
1060420 GTATACAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.23
Consensus pattern (31 bp):
TAAGTGATCAAAACTTAATAAAACAACAACA
Found at i:1060682 original size:16 final size:16
Alignment explanation
Indices: 1060661--1060710 Score: 84
Period size: 16 Copynumber: 3.1 Consensus size: 16
1060651 ATAAGGTTAA
1060661 GGTATAAGGTGAAGAC
1 GGTATAAGGTGAAGAC
1060677 GGTATAAGGTGAAGAC
1 GGTATAAGGTGAAGAC
1060693 GGTA-AGAGGTGAAGAC
1 GGTATA-AGGTGAAGAC
1060709 GG
1 GG
1060711 AGTAGAGGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.36, C:0.06, G:0.42, T:0.16
Consensus pattern (16 bp):
GGTATAAGGTGAAGAC
Found at i:1067698 original size:27 final size:28
Alignment explanation
Indices: 1067644--1067705 Score: 117
Period size: 27 Copynumber: 2.2 Consensus size: 28
1067634 CAGGATTTCT
1067644 CCAAGAACAGACCATCCCCCTTCCCAAA
1 CCAAGAACAGACCATCCCCCTTCCCAAA
1067672 CCAAGAACAGACCAT-CCCCTTCCCAAA
1 CCAAGAACAGACCATCCCCCTTCCCAAA
1067699 CCAAGAA
1 CCAAGAA
1067706 AGGAAGTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 19 0.56
28 15 0.44
ACGTcount: A:0.39, C:0.44, G:0.08, T:0.10
Consensus pattern (28 bp):
CCAAGAACAGACCATCCCCCTTCCCAAA
Found at i:1070454 original size:29 final size:29
Alignment explanation
Indices: 1070412--1070471 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1070402 TTGATCTTGG
1070412 TTGCTTCTTTTTCCTTACCCTAAGTTTTA
1 TTGCTTCTTTTTCCTTACCCTAAGTTTTA
1070441 TTGCTTCTTTTTCCTTACCCTAAGTTTTA
1 TTGCTTCTTTTTCCTTACCCTAAGTTTTA
1070470 TT
1 TT
1070472 TGACACTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.13, C:0.23, G:0.07, T:0.57
Consensus pattern (29 bp):
TTGCTTCTTTTTCCTTACCCTAAGTTTTA
Found at i:1075939 original size:31 final size:31
Alignment explanation
Indices: 1075869--1075929 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1075859 CAGGTTCAAG
*
1075869 GGTTAAAATGATATTTTATCTAAAGTTTAGA
1 GGTTAAATTGATATTTTATCTAAAGTTTAGA
* *
1075900 GGTTAAATTGATATTTTATTTAATGTTTAG
1 GGTTAAATTGATATTTTATCTAAAGTTTAG
1075930 GATTTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (31 bp):
GGTTAAATTGATATTTTATCTAAAGTTTAGA
Found at i:1076417 original size:23 final size:23
Alignment explanation
Indices: 1076391--1076438 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1076381 ATAAAGTACA
*
1076391 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1076414 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1076437 AT
1 AT
1076439 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1077185 original size:18 final size:18
Alignment explanation
Indices: 1077162--1077198 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1077152 CGAAATATAT
1077162 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1077180 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1077198 A
1 A
1077199 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1077427 original size:23 final size:23
Alignment explanation
Indices: 1077397--1077461 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1077387 CTACATGCGA
1077397 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
1077420 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
1077443 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
1077462 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:1077876 original size:23 final size:22
Alignment explanation
Indices: 1077814--1077885 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
1077804 ACACTTTACA
*
1077814 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
1077837 ATATAACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
* *
1077859 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
1077882 ATAT
1 ATAT
1077886 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 20 0.47
23 23 0.53
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:1078209 original size:427 final size:427
Alignment explanation
Indices: 1077399--1078412 Score: 1980
Period size: 427 Copynumber: 2.4 Consensus size: 427
1077389 ACATGCGAGA
1077399 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
1077464 TTACCTATTATATTGAAAGTGTCCATAC-TTTTATAAAAAGGATCGATA-TTTTTTAAAACTTAT
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAACTTAT
1077527 GTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAA
131 GTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAA
1077592 TTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTA
196 TTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTA
1077657 ATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAT
261 ATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAT
1077722 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACAC
326 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACAC
1077787 TTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 TTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1077824 TACCTATTACATTATAT-AACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1077888 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTT-AAAACTTA
1077953 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
130 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
1078018 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
195 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
1078083 AATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
260 AATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
1078148 TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACA
325 TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACA
1078213 CTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
390 CTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1078251 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1078316 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAACTTA
1078381 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
130 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
1078413 ACTGCGAATT
Statistics
Matches: 583, Mismatches: 1, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
424 74 0.13
425 37 0.06
426 6 0.01
427 323 0.55
428 137 0.23
429 6 0.01
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (427 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAACTTAT
GTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAA
TTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTA
ATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAT
ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTATGGACAC
TTTTATAAAAAGGATAGACACTTTACAATATAACCAC
Found at i:1078266 original size:21 final size:22
Alignment explanation
Indices: 1078241--1078292 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1078231 ACACTTTACA
*
1078241 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1078264 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1078287 ATATAA
1 ATATAA
1078293 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1078277 original size:23 final size:23
Alignment explanation
Indices: 1078251--1078313 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1078241 ATATAACCAC
1078251 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1078274 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1078297 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1078314 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1079650 original size:197 final size:199
Alignment explanation
Indices: 1079089--1079732 Score: 1231
Period size: 197 Copynumber: 3.2 Consensus size: 199
1079079 ACTATTTAAC
1079089 GCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACAT
1 GCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACAT
1079154 TATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATT
66 TATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATT
1079219 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACGTTTTTATATATGGATCGACACTTTA
131 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTA
1079284 TGGGT
195 TGGGT
1079289 GCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACAT
1 GCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACAT
1079354 TA-TTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATT
66 TATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATT
1079418 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
131 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
* *
1079483 TGAT
196 GGGT
1079487 GCACCTTGTTTTTAATTCATTCTGG-AAAAAAATATCGACACAAACTATATTAGTGTCGACACAT
1 GCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACAT
*
1079551 TATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATT-AAAAATTACATATT
66 TATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATT
1079615 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
131 ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
1079680 GGGT
196 GGGT
1079684 GCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
1 GCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTAT
1079733 TAGTATCGAC
Statistics
Matches: 437, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
197 146 0.33
198 123 0.28
199 101 0.23
200 67 0.15
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (199 bp):
GCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACAT
TATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAGATT
ACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTAT
GGGT
Found at i:1079850 original size:19 final size:19
Alignment explanation
Indices: 1079823--1079867 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1079813 ATATTCACAT
*
1079823 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
1079842 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
1079861 AAAATTA
1 AAAATTA
1079868 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:1081690 original size:33 final size:33
Alignment explanation
Indices: 1081653--1081718 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1081643 CATCTTAATA
*
1081653 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
1081686 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
1081719 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:1083857 original size:24 final size:24
Alignment explanation
Indices: 1083820--1083872 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1083810 CCGTTCTATC
1083820 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1083844 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1083868 TATTT
1 TATTT
1083873 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1084063 original size:20 final size:19
Alignment explanation
Indices: 1084017--1084063 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1084007 TCCGGTATCA
*
1084017 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1084036 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1084057 TTTTACC
1 TTTTACC
1084064 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1084210 original size:20 final size:20
Alignment explanation
Indices: 1084184--1084229 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1084174 CACTTTTAAA
1084184 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1084203 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1084224 TTTACC
1 TTTACC
1084230 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1085688 original size:18 final size:17
Alignment explanation
Indices: 1085649--1085691 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1085639 ATTATATGGA
1085649 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1085665 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1085683 TATTATTAT
1 TATTATTAT
1085692 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1085704 original size:4 final size:4
Alignment explanation
Indices: 1085689--1085787 Score: 68
Period size: 4 Copynumber: 26.2 Consensus size: 4
1085679 TTATTATTAT
* * * * *
1085689 TATA TGTA TATA TATA TATA TATA TATT TA-A T-TA TTTT TATT TAT-
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
1085734 TTTT TACTA TAT- TTTA T-TA T-TA T-TA TATA TATA TATA TATA TATA
1 TATA TA-TA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1085779 TATA TATA T
1 TATA TATA T
1085788 TTCTTTAATA
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
3 16 0.20
4 60 0.76
5 3 0.04
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (4 bp):
TATA
Found at i:1085708 original size:10 final size:10
Alignment explanation
Indices: 1085689--1085787 Score: 68
Period size: 10 Copynumber: 10.5 Consensus size: 10
1085679 TTATTATTAT
*
1085689 TATATGTATA
1 TATATATATA
1085699 TATATATATA
1 TATATATATA
*
1085709 TATATATTTA
1 TATATATATA
* *
1085719 -AT-TATTTT
1 TATATATATA
* *
1085727 TATTTAT-TT
1 TATATATATA
*
1085736 TTTACTATAT-
1 TATA-TATATA
*
1085746 TTTAT-TAT-
1 TATATATATA
1085754 TAT-TATATA
1 TATATATATA
1085763 TATATATATA
1 TATATATATA
1085773 TATATATATA
1 TATATATATA
1085783 TATAT
1 TATAT
1085788 TTCTTTAATA
Statistics
Matches: 76, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
7 1 0.01
8 13 0.17
9 12 0.16
10 49 0.64
11 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (10 bp):
TATATATATA
Found at i:1085766 original size:6 final size:6
Alignment explanation
Indices: 1085757--1085787 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1085747 TTATTATTAT
1085757 TATATA TATATA TATATA TATATA TATATA T
1 TATATA TATATA TATATA TATATA TATATA T
1085788 TTCTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATATA
Found at i:1087443 original size:19 final size:19
Alignment explanation
Indices: 1087419--1087455 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1087409 ACCTTACTAA
1087419 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
1087438 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
1087456 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:1091263 original size:183 final size:183
Alignment explanation
Indices: 1090955--1091483 Score: 878
Period size: 175 Copynumber: 2.9 Consensus size: 183
1090945 ATTAAATCCG
1090955 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
1091020 ATATATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
1091085 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
1091138 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1091203 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
1091268 TTGTCAGGCCAAAGAC-TT-TG-T--GATG-A--CTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
1091313 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGTCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * * *
1091378 ATAGATTACATTCAAA-TCATGACATTGCTCGGACAATTGGTAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* * *
1091442 TTTTTCAGGTCAAAGACTGTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
1091484 TAAACCTGAT
Statistics
Matches: 325, Mismatches: 12, Indels: 18
0.92 0.03 0.05
Matches are distributed among these distances:
174 1 0.00
175 154 0.47
176 1 0.00
177 3 0.01
178 5 0.02
180 5 0.02
181 3 0.01
182 2 0.01
183 151 0.46
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:1092683 original size:36 final size:34
Alignment explanation
Indices: 1092641--1092752 Score: 82
Period size: 36 Copynumber: 3.1 Consensus size: 34
1092631 ACTCAAATTT
1092641 TTTTTCTTAAAACATACTTTGTCTCACTTGAGACTG
1 TTTTTCTTAAAACA-A-TTTGTCTCACTTGAGACTG
* * * ** *
1092677 TTTTTCTCGAAAGA-AGATTTATTTCACTCAAGATTG
1 TTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGACTG
* *
1092713 TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCG
1 TTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGACTG
1092749 TTTT
1 TTTT
1092753 CACTCGAAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 47 0.82
37 5 0.09
38 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (34 bp):
TTTTTCTTAAAACAATTTGTCTCACTTGAGACTG
Found at i:1092717 original size:72 final size:75
Alignment explanation
Indices: 1092624--1092798 Score: 207
Period size: 72 Copynumber: 2.4 Consensus size: 75
1092614 ATGCAGATGA
* * * * *
1092624 TTATCTCACTCAA-ATTTTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCG
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTCG
*
1092686 AAAGAA-G-AT
65 AAAAAAGGCAT
*
1092695 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
1092760 AAAAAGGCAT
66 AAAAAGGCAT
** *
1092770 TTCATTTCACTCAAGGCTGTTTTTTTTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
1092799 GAAGATTTTA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
71 13 0.15
72 38 0.43
73 9 0.10
74 1 0.01
75 4 0.05
76 23 0.26
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAAAAGGCAT
Found at i:1092949 original size:39 final size:39
Alignment explanation
Indices: 1092892--1092966 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
1092882 CCTTGAAATT
* *
1092892 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
1 AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
* *
1092931 AATTTTGTCTC-CCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCC-TGAGACAGTTTCCCTCGAAACA
1092967 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.06
39 29 0.94
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
Found at i:1093052 original size:106 final size:105
Alignment explanation
Indices: 1092869--1093188 Score: 515
Period size: 106 Copynumber: 3.1 Consensus size: 105
1092859 ACAATTTCTC
* *
1092869 TTGAAAACATTTCCCTTGAAATTA-ATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1092933 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
1092973 TTGAAAACATTTCCCTTGAAATGATTTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
1 TTGAAAACATTTCCCTTGAAATGA-TATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
1093038 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
1093079 TTGAAAACATTTCCCTTGAAATGA-ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AA
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
** *
1093140 TTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
1093180 TTGAAAACA
1 TTGAAAACA
1093189 ATTTAATGAA
Statistics
Matches: 204, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
101 48 0.24
103 1 0.00
104 53 0.26
106 102 0.50
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (105 bp):
TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:1093135 original size:36 final size:36
Alignment explanation
Indices: 1093088--1093163 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1093078 ATTGAAAACA
* * *
1093088 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
1093124 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
1093160 TTTC
1 TTTC
1093164 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:1093558 original size:105 final size:105
Alignment explanation
Indices: 1093332--1093993 Score: 920
Period size: 105 Copynumber: 6.3 Consensus size: 105
1093322 AACATCCACG
* * * * * *
1093332 ATTTCAACTCCACGACGGAGGATATCGTGACACACGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATATTG-GACTC-C-AGACAACGCAAGTTCAACTTCACAACGAA
* * * *
1093397 GGGACGGCTGGTTGTGAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
*
1093441 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
*
1093506 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
1093546 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACAATGAAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
*
1093611 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
1093651 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
* *
1093716 ACCGCTGCTTGTCAACAATAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
1093756 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
* * *
1093821 ACCGCTGCTTGTCAA-AA-AAATT-TC-A-TTCAGAGTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
1093856 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
* * * * ** *
1093921 ACGGCTGGTTGTCAACAAATAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
1093962 ATTTCAACTTCACGACGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
1093994 GGAACAATGC
Statistics
Matches: 506, Mismatches: 41, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
100 81 0.16
101 1 0.00
102 3 0.01
103 8 0.02
104 3 0.01
105 302 0.60
106 80 0.16
107 1 0.00
108 4 0.01
109 23 0.05
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:1094565 original size:21 final size:21
Alignment explanation
Indices: 1094540--1094603 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
1094530 TTCGTCCTAC
1094540 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
****
1094561 TAGGA-T-AAACT--T-TTGC
1 TAGGATTCAAACTCCTAAAAA
1094577 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
1094598 TAGGAT
1 TAGGAT
1094604 AGAGTTCTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 5 0.17
17 2 0.07
18 5 0.17
19 5 0.17
20 2 0.07
21 11 0.37
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (21 bp):
TAGGATTCAAACTCCTAAAAA
Found at i:1094632 original size:37 final size:37
Alignment explanation
Indices: 1094536--1094620 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
1094526 CATTTTCGTC
1094536 CTACTAGGATTCAAACTCCTAAAAATAGGATAAACTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAACTT
* * * *
1094573 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAACTT
*
1094610 CTACTAAGATT
1 CTACTAGGATT
1094621 TAAATTTCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAACTT
Found at i:1095037 original size:18 final size:17
Alignment explanation
Indices: 1094998--1095040 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1094988 ATTATATAGA
1094998 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1095014 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1095032 TATTATTAT
1 TATTATTAT
1095041 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1095077 original size:54 final size:53
Alignment explanation
Indices: 1094981--1095113 Score: 128
Period size: 54 Copynumber: 2.5 Consensus size: 53
1094971 TATTTGTCCC
* * * * *
1094981 TTTATTTATTATATAGATATTTTATTCATTTATTTTTATTATTCATGTTA-T-TAT
1 TTTA-TTATTATATATATA-TATATTAAATTATTTTCATTATT-ATGTTACTATAT
* *
1095035 TATTA-TATGTATATATATATATATTAAATTATTTTCATTTATTTTTTTACTATAT
1 T-TTATTAT-TATATATATATATATTAAATTATTTTCA-TTATTATGTTACTATAT
1095090 TTTATTATTATATATATATATATT
1 TTTATTATTATATATATATATATT
1095114 TCTTTAATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
53 21 0.32
54 35 0.53
55 10 0.15
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.62
Consensus pattern (53 bp):
TTTATTATTATATATATATATATTAAATTATTTTCATTATTATGTTACTATAT
Found at i:1100679 original size:12 final size:12
Alignment explanation
Indices: 1100662--1100689 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1100652 TAATCATGGG
1100662 TTTGTTTTTTCA
1 TTTGTTTTTTCA
1100674 TTTGTTTTTTCA
1 TTTGTTTTTTCA
1100686 TTTG
1 TTTG
1100690 ATTATCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.11, T:0.75
Consensus pattern (12 bp):
TTTGTTTTTTCA
Found at i:1101652 original size:2 final size:2
Alignment explanation
Indices: 1101645--1101700 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1101635 ATGGATTGCT
1101645 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1101687 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1101701 AAATTTACGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1101792 original size:13 final size:13
Alignment explanation
Indices: 1101774--1101803 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1101764 AATGACGCGC
1101774 AATGTGCGTCATA
1 AATGTGCGTCATA
*
1101787 AATGTGCGTTATA
1 AATGTGCGTCATA
1101800 AATG
1 AATG
1101804 CATGTCATAA
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:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (13 bp):
AATGTGCGTCATA
Found at i:1102944 original size:185 final size:181
Alignment explanation
Indices: 1102602--1102981 Score: 602
Period size: 185 Copynumber: 2.1 Consensus size: 181
1102592 ACTGAAATTA
* * *
1102602 AATTTAAAATATTAAATATATTATATATAACATATGAGCTCCCAAACCATTTAAAACTAATTAAT
1 AATTAAAAATATTAAAAATATTATATATAACATATGAGCTCCCAAACCATTTAAAACCAATTAAT
1102667 AATTTAAGATTCAATAACTTGTAAACCTAAATCAATATTAATTAATTAAAAAAATTTATAGAAAA
66 AATTTAAGATTCAATAACTTGTAAACCTAAATCAATATTAATTAATTAAAAAAATTTATAGAAAA
*
1102732 TTTTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTG
131 TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTTG
* *
1102784 AATTAAAAATATTAAAAATATTCTATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAAT
1 AATTAAAAATATTAAAAATATTATATATAACATATGAGCT---CCCAAACCATTTAAAA-CCAAT
*
1102849 TAATAATTTAAGA-TCTAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAAATTTATA
62 TAATAATTTAAGATTC-AATAACTTGTAAACCTAAATCAATATTAATTAATTAAAAAAATTTATA
* *
1102912 TAAATTTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTG
126 GAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTG
1102968 AATTAAAAAATATT
1 AATT-AAAAATATT
1102982 TAATTTTTAT
Statistics
Matches: 183, Mismatches: 9, Indels: 9
0.91 0.04 0.04
Matches are distributed among these distances:
182 36 0.20
184 12 0.07
185 84 0.46
186 51 0.28
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (181 bp):
AATTAAAAATATTAAAAATATTATATATAACATATGAGCTCCCAAACCATTTAAAACCAATTAAT
AATTTAAGATTCAATAACTTGTAAACCTAAATCAATATTAATTAATTAAAAAAATTTATAGAAAA
TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTG
Found at i:1122733 original size:17 final size:17
Alignment explanation
Indices: 1122711--1122745 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1122701 CATACTTATG
*
1122711 TTTAAATTATATAAATA
1 TTTAAAATATATAAATA
*
1122728 TTTAAAATATATATATA
1 TTTAAAATATATAAATA
1122745 T
1 T
1122746 AATAAGTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAAATATATAAATA
Found at i:1123684 original size:26 final size:25
Alignment explanation
Indices: 1123636--1123685 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
1123626 TTATTTAAAG
*
1123636 AAATAAAAAGATAAAGATTAAAAAT
1 AAATAAAAAGATAAAGATAAAAAAT
**
1123661 AAATAAAAGAGATAGGGATAAAAAA
1 AAATAAAA-AGATAAAGATAAAAAA
1123686 AACTTATGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (25 bp):
AAATAAAAAGATAAAGATAAAAAAT
Found at i:1124330 original size:85 final size:82
Alignment explanation
Indices: 1124228--1124411 Score: 246
Period size: 85 Copynumber: 2.2 Consensus size: 82
1124218 AGATAATTCC
* * * *
1124228 TAAAATAACATCTTAAATCCTAATT-AAAATATTTAAAAC-TATTTAAATTAAAATACCTAAAAC
1 TAAAATAATATCCTAAATCCTAATTGAAAA-A-CTAAAACATATTTAAACTAAAATACCTAAAAC
1124291 AAAGATAAAATAAAATAATATT
64 AAAGATAAAAT---ATAATATT
*
1124313 TAAAATAATATCCTAAATCCTAATTGAAAAACTAAAACATATTTAAACTAAAATACTTAAAACAA
1 TAAAATAATATCCTAAATCCTAATTGAAAAACTAAAACATATTTAAACTAAAATACCTAAAACAA
*
1124378 AGATAAAATATAATGTT
66 AGATAAAATATAATATT
*
1124395 TAAAATATTATCCTAAA
1 TAAAATAATATCCTAAA
1124412 ACTTGAGTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
82 23 0.26
84 6 0.07
85 57 0.63
86 4 0.04
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (82 bp):
TAAAATAATATCCTAAATCCTAATTGAAAAACTAAAACATATTTAAACTAAAATACCTAAAACAA
AGATAAAATATAATATT
Found at i:1124358 original size:43 final size:42
Alignment explanation
Indices: 1124228--1124366 Score: 108
Period size: 43 Copynumber: 3.3 Consensus size: 42
1124218 AGATAATTCC
* *
1124228 TAAAATAACATCTTAAATCCTAATT-AAAATATTTAAAAC-TATT
1 TAAAATAAAATCCTAAATCCTAATTGAAAA-A--TAAAACATATT
* * * *
1124271 TAAATTAAAATACCTAAA-AC-AA-AGATAAAATAAAATAATATT
1 TAAAATAAAAT-CCTAAATCCTAATTGA-AAAATAAAA-CATATT
*
1124313 TAAAATAATATCCTAAATCCTAATTGAAAAACTAAAACATATT
1 TAAAATAAAATCCTAAATCCTAATTGAAAAA-TAAAACATATT
*
1124356 TAAACTAAAAT
1 TAAAATAAAAT
1124367 ACTTAAAACA
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
40 5 0.07
41 6 0.08
42 18 0.24
43 33 0.45
44 12 0.16
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.31
Consensus pattern (42 bp):
TAAAATAAAATCCTAAATCCTAATTGAAAAATAAAACATATT
Found at i:1125867 original size:21 final size:21
Alignment explanation
Indices: 1125843--1125904 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1125833 GCCACGGTGA
1125843 CGACGAACGAGACGAAGAAGT
1 CGACGAACGAGACGAAGAAGT
1125864 CGACGAACGAGACGAAGAAGT
1 CGACGAACGAGACGAAGAAGT
*
1125885 CGACG-ACGATGGCGAAGAAG
1 CGACGAACGA-GACGAAGAAG
1125905 AAACAGGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.40, C:0.19, G:0.35, T:0.05
Consensus pattern (21 bp):
CGACGAACGAGACGAAGAAGT
Found at i:1127916 original size:21 final size:21
Alignment explanation
Indices: 1127893--1127931 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1127883 ATTATTCTAA
*
1127893 AAAAATATT-TATAATATTAT
1 AAAAATATTATAAAATATTAT
1127913 AAAAATATTATAAAATATT
1 AAAAATATTATAAAATATT
1127932 TATTTAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATATTATAAAATATTAT
Done.