Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 35
Found at i:1462861 original size:3 final size:3
Alignment explanation
Indices: 1462855--1462942 Score: 81
Period size: 3 Copynumber: 29.7 Consensus size: 3
1462845 TAATATTTAT
* * *
1462855 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TTA TTA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1462902 TAA TAA TTA TTA TTA TTA TTA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
1462943 TTCAAATGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
2 4 0.05
3 72 0.92
4 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1462878 original size:30 final size:30
Alignment explanation
Indices: 1462842--1462933 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
1462832 ATTGGGCCTG
* * *
1462842 TAATAATATTTATTAATAATAAAATAATAA
1 TAATAATATTTATTATTATTATAATAATAA
* *
1462872 TAATAATAATAATTATTATTATAATAATAA
1 TAATAATATTTATTATTATTATAATAATAA
1462902 TAATAAT-TATTATTATTATTATAATAATAA
1 TAATAATAT-TTATTATTATTATAATAATAA
1462932 TA
1 TA
1462934 TAAATAATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAATAATATTTATTATTATTATAATAATAA
Found at i:1462895 original size:24 final size:24
Alignment explanation
Indices: 1462868--1462932 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
1462858 TAATAAAATA
1462868 ATAATAATAATAATAATTATTATT
1 ATAATAATAATAATAATTATTATT
1462892 ATAATAATAATAATAATTATTATT
1 ATAATAATAATAATAATTATTATT
* *
1462916 ATTATTATAATAATAAT
1 ATAATAATAATAATAAT
1462933 ATAAATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAATAATAATAATAATTATTATT
Found at i:1462895 original size:27 final size:27
Alignment explanation
Indices: 1462865--1462933 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
1462855 TAATAATAAA
1462865 ATAATAATAATAATAATAATTATTATT
1 ATAATAATAATAATAATAATTATTATT
*
1462892 ATAATAATAATAATAATTATTATTATT
1 ATAATAATAATAATAATAATTATTATT
*
1462919 ATTATAATAATAATA
1 ATAATAATAATAATA
1462934 TAAATAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
ATAATAATAATAATAATAATTATTATT
Found at i:1463420 original size:113 final size:113
Alignment explanation
Indices: 1463297--1463826 Score: 747
Period size: 113 Copynumber: 4.7 Consensus size: 113
1463287 TCGAACAAGC
* *
1463297 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
*
1463362 AAAAGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAAT
66 AAATGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAAT
* * **
1463410 TCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
* * * * * * *
1463475 CACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGT
66 AAATGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAAT
* *
1463523 TATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
* * *
1463588 AAAAGTTGATCCATCAAGTGGTGAATTTAAGAAAAAGGTTGAACAAAT
66 AAATGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAAT
* * ** *
1463636 TCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
* * * * * * *
1463701 CACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGT
66 AAATGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAAT
* * *
1463749 TTTTCTCATTATGAACTTGTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-ACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
1463813 AAATGTTGATCCAT
66 AAATGTTGATCCAT
1463827 TGAATGATGG
Statistics
Matches: 361, Mismatches: 56, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
112 14 0.04
113 347 0.96
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGG
AAATGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAAT
Found at i:1463544 original size:226 final size:226
Alignment explanation
Indices: 1463279--1463826 Score: 974
Period size: 226 Copynumber: 2.4 Consensus size: 226
1463269 ATAGAGTCAT
* * * *
1463279 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1463344 ATTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAA
66 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAA
1463409 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
131 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
1463474 GCACTGCTGATCCACCGAGTGATGAATTTAA
196 GCACTGCTGATCCACCGAGTGATGAATTTAA
1463505 GCAAAAAGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1463570 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGGTGAATTTAAGAAAAAGGTTGAACAAA
66 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAA
1463635 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
131 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
*
1463700 TCACTGCTGATCCACCGAGTGATGAATTTAA
196 GCACTGCTGATCCACCGAGTGATGAATTTAA
* *
1463731 GCAAAAAGTTGAACAAGTTTTTCTCATTATGAACTTGTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1463796 ATTATGAAC--TCTACTGGAAATGTTGATCCAT
66 ATTATGAACTTTCT-CTGGAAAAGTTGATCCAT
1463827 TGAATGATGG
Statistics
Matches: 310, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
224 3 0.01
225 17 0.05
226 290 0.94
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (226 bp):
GCAAAAAGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGAAAAAAGTTGAACAAA
TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
GCACTGCTGATCCACCGAGTGATGAATTTAA
Found at i:1465009 original size:18 final size:17
Alignment explanation
Indices: 1464986--1465035 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1464976 AAAATAAAAG
*
1464986 AATAAATTGAATTTCGAA
1 AATAAATTGAATTT-AAA
* *
1465004 AATAAATTAAATCTAAA
1 AATAAATTGAATTTAAA
*
1465021 AAAAAATTGAATTTA
1 AATAAATTGAATTTA
1465036 GGGAAACTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (17 bp):
AATAAATTGAATTTAAA
Found at i:1465408 original size:8 final size:8
Alignment explanation
Indices: 1465391--1465421 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1465381 ACCCTCCTTT
1465391 TTTTTTTC
1 TTTTTTTC
*
1465399 TTTTTCTC
1 TTTTTTTC
1465407 TTTTTTTC
1 TTTTTTTC
1465415 TTTTTTT
1 TTTTTTT
1465422 ATTTCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1475893 original size:18 final size:18
Alignment explanation
Indices: 1475867--1475924 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1475857 AATATATTAC
1475867 AAATAAACATATAAAATT
1 AAATAAACATATAAAATT
*
1475885 AAATCAACA-ACTAAAA-T
1 AAATAAACATA-TAAAATT
*
1475902 AAATGAA-AT-TAAAATT
1 AAATAAACATATAAAATT
*
1475918 ATATAAA
1 AAATAAA
1475925 AATGATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 8 0.24
18 13 0.39
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAACATATAAAATT
Found at i:1477272 original size:27 final size:27
Alignment explanation
Indices: 1477233--1477299 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
1477223 ATTGGGCTTG
*
1477233 TAATAATATTTATTAATAATAAAATAA
1 TAATAATAATTATTAATAATAAAATAA
* * *
1477260 TAATAATAATTATTATTATTATAATAA
1 TAATAATAATTATTAATAATAAAATAA
1477287 TAAT-ATAAATTAT
1 TAATAAT-AATTAT
1477300 ATTCAAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAATAATAATTATTAATAATAAAATAA
Found at i:1477298 original size:21 final size:21
Alignment explanation
Indices: 1477259--1477299 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1477249 TAATAAAATA
*
1477259 ATAATAATAATTATTATTATT
1 ATAATAATAATTATAATTATT
1477280 ATAATAATAA-TATAAATTAT
1 ATAATAATAATTAT-AATTAT
1477300 ATTCAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAATAATAATTATAATTATT
Found at i:1477490 original size:16 final size:16
Alignment explanation
Indices: 1477469--1477502 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1477459 TGAGATAGAT
1477469 ATAATTAA-TAAAATAA
1 ATAATTAACTAAAA-AA
1477485 ATAATTAACTAAAAAA
1 ATAATTAACTAAAAAA
1477501 AT
1 AT
1477503 TAAACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAATTAACTAAAAAA
Found at i:1481760 original size:17 final size:17
Alignment explanation
Indices: 1481738--1481771 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1481728 TGTAAAATTC
*
1481738 GTAAAATTATTAAAAAT
1 GTAAAATAATTAAAAAT
*
1481755 GTAAAATAATTATAAAT
1 GTAAAATAATTAAAAAT
1481772 AATAAGAAAA
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:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
GTAAAATAATTAAAAAT
Found at i:1481765 original size:29 final size:29
Alignment explanation
Indices: 1481710--1481765 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
1481700 TTAGGAACAT
* **
1481710 TAAAATTTATTTAAAATGTGTAAAATTCG
1 TAAAATTTATTAAAAATGTAAAAAATTCG
1481739 TAAAA-TTATTAAAAATGTAAAATAATT
1 TAAAATTTATTAAAAATGTAAAA-AATT
1481766 ATAAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (29 bp):
TAAAATTTATTAAAAATGTAAAAAATTCG
Found at i:1483274 original size:18 final size:18
Alignment explanation
Indices: 1483251--1483299 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
1483241 ATATTTTTTT
1483251 TCATAAAACTCCCTCAAA
1 TCATAAAACTCCCTCAAA
1483269 TCATAAAACTCCCTCAAA
1 TCATAAAACTCCCTCAAA
1483287 TCATAAAACTCCC
1 TCATAAAACTCCC
1483300 AAATACTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (18 bp):
TCATAAAACTCCCTCAAA
Found at i:1483959 original size:20 final size:19
Alignment explanation
Indices: 1483927--1483969 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1483917 TATTTTTAAT
*
1483927 ATCATATTCATATTAAATA
1 ATCATATTCATATCAAATA
* *
1483946 ATCATATCTTATATCAAATT
1 ATCATAT-TCATATCAAATA
1483966 ATCA
1 ATCA
1483970 GAGTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (19 bp):
ATCATATTCATATCAAATA
Found at i:1489018 original size:22 final size:22
Alignment explanation
Indices: 1488942--1489029 Score: 104
Period size: 22 Copynumber: 3.9 Consensus size: 22
1488932 AAAAATTCAA
* *
1488942 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTCAAGCTC--GATTC
* *
1488966 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGA-TTC
1488989 GAGCTCGATTCAAGCTCGATTC
1 GAGCTCGATTCAAGCTCGATTC
*
1489011 AAGCTCGATTCAAGCTCGA
1 GAGCTCGATTCAAGCTCGA
1489030 ACTCGATTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
22 22 0.38
23 19 0.33
24 17 0.29
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (22 bp):
GAGCTCGATTCAAGCTCGATTC
Found at i:1489036 original size:17 final size:17
Alignment explanation
Indices: 1489014--1489050 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1489004 TCGATTCAAG
*
1489014 CTCGATTCAAGCTCGAA
1 CTCGATTAAAGCTCGAA
1489031 CTCGATTAAAGCTCGAA
1 CTCGATTAAAGCTCGAA
1489048 CTC
1 CTC
1489051 AAACTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTAAAGCTCGAA
Found at i:1489046 original size:11 final size:11
Alignment explanation
Indices: 1488943--1489029 Score: 93
Period size: 11 Copynumber: 7.6 Consensus size: 11
1488933 AAAATTCAAG
*
1488943 AGCTCGATTGA
1 AGCTCGATTCA
* *
1488954 AGCTCGAGACTCG
1 AGCTC--GATTCA
*
1488967 AGCTCGATTGA
1 AGCTCGATTCA
**
1488978 AGCTCGATTTTG
1 AGCTCGA-TTCA
1488990 AGCTCGATTCA
1 AGCTCGATTCA
1489001 AGCTCGATTCA
1 AGCTCGATTCA
1489012 AGCTCGATTCA
1 AGCTCGATTCA
1489023 AGCTCGA
1 AGCTCGA
1489030 ACTCGATTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
11 46 0.73
12 9 0.14
13 8 0.13
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:1489353 original size:21 final size:21
Alignment explanation
Indices: 1489328--1489374 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1489318 TGGCATAACT
*
1489328 TAAACCTTAACACATAAACCC
1 TAAACCTTAACACATAAACCA
1489349 TAAACCTTAACACATAAACCA
1 TAAACCTTAACACATAAACCA
1489370 TAAAC
1 TAAAC
1489375 TCTAAACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCTTAACACATAAACCA
Found at i:1489381 original size:35 final size:35
Alignment explanation
Indices: 1489342--1489429 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 35
1489332 CCTTAACACA
1489342 TAAACCCTAAACCTTAACA-CATAA-ACCATAAACTC
1 TAAACCCTAAACCTTAA-ATCATAACA-CATAAACTC
** * *
1489377 TAAACTTTAAACCTTAAATCCTATCACATAAACTC
1 TAAACCCTAAACCTTAAATCATAACACATAAACTC
* *
1489412 TAAATCCTAAACCCTAAA
1 TAAACCCTAAACCTTAAA
1489430 CCTGATCACA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
34 1 0.02
35 41 0.95
36 1 0.02
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (35 bp):
TAAACCCTAAACCTTAAATCATAACACATAAACTC
Found at i:1489438 original size:35 final size:35
Alignment explanation
Indices: 1489368--1489442 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 35
1489358 ACACATAAAC
* *
1489368 CATAAACTCTAAACTTTAAACCTTAAATCCTATCA
1 CATAAACTCTAAACTCTAAACCCTAAATCCTATCA
1489403 CATAAACTCTAAA-TCCTAAACCCTAAA-CCTGATCA
1 CATAAACTCTAAACT-CTAAACCCTAAATCCT-ATCA
1489438 CATAA
1 CATAA
1489443 TTAGTTATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
34 4 0.11
35 32 0.89
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.27
Consensus pattern (35 bp):
CATAAACTCTAAACTCTAAACCCTAAATCCTATCA
Found at i:1489712 original size:14 final size:14
Alignment explanation
Indices: 1489695--1489735 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1489685 TTTATTCATC
1489695 AATAATGTATTTTT
1 AATAATGTATTTTT
1489709 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
1489720 AATAATGTAATTTT
1 AATAATGTATTTTT
1489734 AA
1 AA
1489736 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:1506904 original size:19 final size:19
Alignment explanation
Indices: 1506866--1506905 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1506856 TTTAATAATA
* *
1506866 ATATTTATAATATAATAAT
1 ATATTTATAACATAAGAAT
*
1506885 ATATTTATAACATACGAAT
1 ATATTTATAACATAAGAAT
1506904 AT
1 AT
1506906 TTTTTTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (19 bp):
ATATTTATAACATAAGAAT
Found at i:1507617 original size:31 final size:32
Alignment explanation
Indices: 1507548--1507624 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
1507538 CGGGGCTGTG
* *
1507548 GAGCCTACCTAAGAACACATCTTAGGGTCGCA
1 GAGCCTACCTAAGAACACATCTCAGGGCCGCA
* * **
1507580 GGGCCTACCTGAGAA-TGATCTCAGGGCCGCA
1 GAGCCTACCTAAGAACACATCTCAGGGCCGCA
1507611 GAGCCTACCTAAGA
1 GAGCCTACCTAAGA
1507625 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (32 bp):
GAGCCTACCTAAGAACACATCTCAGGGCCGCA
Found at i:1508553 original size:29 final size:29
Alignment explanation
Indices: 1508512--1508585 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
1508502 CATATTCAAA
*
1508512 AATT-CCAATAATGTCACCTTTTTCAAAAT
1 AATTCCCAA-AATGTCACCATTTTCAAAAT
* *
1508541 AATTTCCAGAATGTCACCATTTTCAAAAT
1 AATTCCCAAAATGTCACCATTTTCAAAAT
1508570 AATTCCCAAAATGTCA
1 AATTCCCAAAATGTCA
1508586 ACGGGTCGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 37 0.93
30 3 0.08
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCATTTTCAAAAT
Found at i:1508677 original size:11 final size:13
Alignment explanation
Indices: 1508650--1508678 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1508640 ACTCCCCCAT
1508650 GCGCAGGGGCGGC
1 GCGCAGGGGCGGC
1508663 GCGCAGGGGCGGC
1 GCGCAGGGGCGGC
1508676 GCG
1 GCG
1508679 TGAGACCGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.31, G:0.62, T:0.00
Consensus pattern (13 bp):
GCGCAGGGGCGGC
Found at i:1514859 original size:63 final size:63
Alignment explanation
Indices: 1514758--1514879 Score: 174
Period size: 63 Copynumber: 1.9 Consensus size: 63
1514748 CTAAGGAAAT
* * *
1514758 ATCTTAGGGCCTCAGAGCCTACCCAAGATAGATTTCAGGGCCGTGGAGCCTACCTAAGAACAC
1 ATCTTAGGGCCGCAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAACAC
* **
1514821 ATCTTAGGGCCGCAGGGCCTACCTGAGA-ATGATCTCAGGGCCGTAGAGCCTACCTAAGA
1 ATCTTAGGGCCGCAGAGCCTACCCAAGATA-GATCTCAGGGCCGTAGAGCCTACCTAAGA
1514880 GTCACATTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 1 0.02
63 51 0.98
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (63 bp):
ATCTTAGGGCCGCAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAACAC
Found at i:1514872 original size:31 final size:31
Alignment explanation
Indices: 1514758--1514879 Score: 113
Period size: 31 Copynumber: 3.9 Consensus size: 31
1514748 CTAAGGAAAT
* *
1514758 ATCTTAGGGCC-TCAGAGCCTACCCAAG-ATAG
1 ATCTCAGGGCCGT-AGAGCCTACCTAAGAAT-G
* * **
1514789 ATTTCAGGGCCGTGGAGCCTACCTAAGAACAC
1 ATCTCAGGGCCGTAGAGCCTACCTAAGAA-TG
* * * *
1514821 ATCTTAGGGCCGCAGGGCCTACCTGAGAATG
1 ATCTCAGGGCCGTAGAGCCTACCTAAGAATG
1514852 ATCTCAGGGCCGTAGAGCCTACCTAAGA
1 ATCTCAGGGCCGTAGAGCCTACCTAAGA
1514880 GTCACATTAG
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
31 45 0.64
32 25 0.36
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (31 bp):
ATCTCAGGGCCGTAGAGCCTACCTAAGAATG
Found at i:1515807 original size:29 final size:29
Alignment explanation
Indices: 1515760--1515839 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
1515750 ATAGTCCACA
*
1515760 TTCAAAA-AA-TCCCATAATGTCA-CATTT
1 TTCAAAATAATTCCCAAAATGTCACCA-TT
*
1515787 TTCAAAATAATTCCCAGAATGTCACCATT
1 TTCAAAATAATTCCCAAAATGTCACCATT
1515816 TTCAAAATAATTCCCAAAATGTCA
1 TTCAAAATAATTCCCAAAATGTCA
1515840 ACGGGTCGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.15
28 2 0.04
29 37 0.77
30 2 0.04
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (29 bp):
TTCAAAATAATTCCCAAAATGTCACCATT
Found at i:1515858 original size:17 final size:17
Alignment explanation
Indices: 1515836--1515868 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1515826 TTCCCAAAAT
1515836 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
1515853 GTCAACGGGTCGGGTC
1 GTCAACGGGTCGGGTC
1515869 AGACCTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GTCAACGGGTCGGGTCG
Found at i:1515903 original size:30 final size:30
Alignment explanation
Indices: 1515867--1515925 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1515857 ACGGGTCGGG
*
1515867 TCAGACCTGTTCGGA-TCGGTCAAACCGGTT
1 TCAGACCGGTTCGGACT-GGTCAAACCGGTT
*
1515897 TCAGACCGGTTTGGACTGGTCAAACCGGT
1 TCAGACCGGTTCGGACTGGTCAAACCGGT
1515926 CATAACATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.25
Consensus pattern (30 bp):
TCAGACCGGTTCGGACTGGTCAAACCGGTT
Found at i:1518915 original size:81 final size:82
Alignment explanation
Indices: 1518816--1518979 Score: 294
Period size: 81 Copynumber: 2.0 Consensus size: 82
1518806 TTAAGTTGTC
1518816 TTTTTTTTTTAAATTTTGTTGTTAATGTGAATAATGTGGTTAGTGCTTCAAATAAGAG-ACAAAA
1 TTTTTTTTTTAAATTTTGTTGTTAATGTGAATAATGTGGTTAGTGCTTCAAATAAGAGAACAAAA
*
1518880 TTCTTCAATCTAATCAA
66 TTCTACAATCTAATCAA
*
1518897 TTTTTTTTTTTAATTTTGTTGTTAATGTGAATAATGTGGTTAGTGCTTCAAATAAGAGAAACAAA
1 TTTTTTTTTTAAATTTTGTTGTTAATGTGAATAATGTGGTTAGTGCTTCAAATAAGAG-AACAAA
1518962 ATTCTACAATCTAATCAA
65 ATTCTACAATCTAATCAA
1518980 ATGATTAAGG
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
81 57 0.72
83 22 0.28
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (82 bp):
TTTTTTTTTTAAATTTTGTTGTTAATGTGAATAATGTGGTTAGTGCTTCAAATAAGAGAACAAAA
TTCTACAATCTAATCAA
Found at i:1521232 original size:18 final size:17
Alignment explanation
Indices: 1521199--1521237 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1521189 ACTTTGACCC
*
1521199 GAAAAGTCAAAATTTTT
1 GAAAAATCAAAATTTTT
1521216 GAAAAATCAAAATTTTT
1 GAAAAATCAAAATTTTT
1521233 GAAAA
1 GAAAA
1521238 GTTATATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (17 bp):
GAAAAATCAAAATTTTT
Found at i:1523374 original size:23 final size:23
Alignment explanation
Indices: 1523340--1523395 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1523330 TTGGTCAAAA
*
1523340 TCAAAGTCAACGATCAACTCTGG
1 TCAAAGTCAACGATCAACTCTAG
*
1523363 TCAAAGTTAACGATCAACTCTAG
1 TCAAAGTCAACGATCAACTCTAG
1523386 TCAAAGTCAA
1 TCAAAGTCAA
1523396 AGGGTCGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.23
Consensus pattern (23 bp):
TCAAAGTCAACGATCAACTCTAG
Found at i:1525373 original size:32 final size:32
Alignment explanation
Indices: 1525303--1525376 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
1525293 CCTAAGGTGA
1525303 CCCTTGGGTAGGCTCCGAGGCCCCAAGAAACT
1 CCCTTGGGTAGGCTCCGAGGCCCCAAGAAACT
**
1525335 TTCTTGGGTAGGCTCTC-AGGCCCCAA-AACACT
1 CCCTTGGGTAGGCTC-CGAGGCCCCAAGAA-ACT
1525367 CCCTTGGGTA
1 CCCTTGGGTA
1525377 AATCATAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 2 0.06
32 33 0.92
33 1 0.03
ACGTcount: A:0.20, C:0.32, G:0.26, T:0.22
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCCGAGGCCCCAAGAAACT
Found at i:1527696 original size:37 final size:37
Alignment explanation
Indices: 1527585--1527765 Score: 146
Period size: 37 Copynumber: 4.9 Consensus size: 37
1527575 CGTTTGTATG
* * * * * *
1527585 TTACTGACAACTTATCGCACTAAGCTTGAGCTCCCAT
1 TTACTGGCGACTTATCGCACTGAGCTTCAACTCTCAT
* * * * * *
1527622 TTACTGGCAACTTATTGCACTGAACATCAGCTTTCAT
1 TTACTGGCGACTTATCGCACTGAGCTTCAACTCTCAT
* *
1527659 TTACTGGTGACTTATCGCACTGAGCTTCAATTCTCAT
1 TTACTGGCGACTTATCGCACTGAGCTTCAACTCTCAT
* * * ** *
1527696 TTACTAGAGATTTATCAAACTGAGCTTCGACTCTCAT
1 TTACTGGCGACTTATCGCACTGAGCTTCAACTCTCAT
* * * *
1527733 TTACTGGCGACTTACCGCATTGAGTTTCGACTC
1 TTACTGGCGACTTATCGCACTGAGCTTCAACTC
1527766 CTATTTGAAG
Statistics
Matches: 113, Mismatches: 31, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
37 113 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (37 bp):
TTACTGGCGACTTATCGCACTGAGCTTCAACTCTCAT
Found at i:1546951 original size:27 final size:27
Alignment explanation
Indices: 1546920--1546984 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
1546910 TCTATTTACA
1546920 AAATCATCTCTCTATAGGAATGGTAAC
1 AAATCATCTCTCTATAGGAATGGTAAC
*
1546947 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATCTCTCTATAGGAATGGTAAC
1546974 AAATCATCTCT
1 AAATCATCTCT
1546985 ATAATTCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATCTCTCTATAGGAATGGTAAC
Found at i:1554587 original size:16 final size:16
Alignment explanation
Indices: 1554566--1554602 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1554556 AGGTATTAAC
1554566 AGAGTTGAAAAATTAT
1 AGAGTTGAAAAATTAT
1554582 AGAGTTGAAAAATTAT
1 AGAGTTGAAAAATTAT
1554598 AGAGT
1 AGAGT
1554603 AGAATTGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.30
Consensus pattern (16 bp):
AGAGTTGAAAAATTAT
Found at i:1559335 original size:51 final size:54
Alignment explanation
Indices: 1559272--1559375 Score: 160
Period size: 51 Copynumber: 2.0 Consensus size: 54
1559262 TTGAGTTACC
*
1559272 TACTTGTAATAGGACTTTTCTAAT-AA-AT-ACTTCTATCTAGATTATGAATCA
1 TACTTCTAATAGGACTTTTCTAATAAATATAACTTCTATCTAGATTATGAATCA
*
1559323 TACTTCTAATAGGACTTTTCTAATAAATATAAACTTCTATCTAGATTGTGAAT
1 TACTTCTAATAGGACTTTTCTAATAAATAT-AACTTCTATCTAGATTATGAAT
1559376 ACTCCTAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
51 23 0.49
52 2 0.04
53 2 0.04
55 20 0.43
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (54 bp):
TACTTCTAATAGGACTTTTCTAATAAATATAACTTCTATCTAGATTATGAATCA
Found at i:1563432 original size:132 final size:132
Alignment explanation
Indices: 1563219--1563456 Score: 467
Period size: 132 Copynumber: 1.8 Consensus size: 132
1563209 TGCTCACCCA
1563219 ATGCCTATGGCAATTAGTGCGGGGTTTGGGTCATAGGTGCAAGTATAGATGGCTGCGGCGGGCGG
1 ATGCCTATGGCAATTAGTGCGGGGTTTGGGTCATAGGTGCAAGTATAGATGGCTGCGGCGGGCGG
*
1563284 TTTTTCCTTGCCCTACCACACCCGGTTTCTCGGAGGTTCTCGGATGTCTACTGCTCACCCAATGC
66 TTTTTCCTCGCCCTACCACACCCGGTTTCTCGGAGGTTCTCGGATGTCTACTGCTCACCCAATGC
1563349 CT
131 CT
1563351 ATGCCTATGGCAATTAGTGCGGGGTTTGGGTCATAGGTGCAAGTATAGATGGCTGCGGCGGGCGG
1 ATGCCTATGGCAATTAGTGCGGGGTTTGGGTCATAGGTGCAAGTATAGATGGCTGCGGCGGGCGG
1563416 TTTTTCCTCGCCCTACCACACCCGGTTTCTCGGAGGTTCTC
66 TTTTTCCTCGCCCTACCACACCCGGTTTCTCGGAGGTTCTC
1563457 ATGTGCGGCA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 105 1.00
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.29
Consensus pattern (132 bp):
ATGCCTATGGCAATTAGTGCGGGGTTTGGGTCATAGGTGCAAGTATAGATGGCTGCGGCGGGCGG
TTTTTCCTCGCCCTACCACACCCGGTTTCTCGGAGGTTCTCGGATGTCTACTGCTCACCCAATGC
CT
Found at i:1567468 original size:20 final size:20
Alignment explanation
Indices: 1567443--1567485 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1567433 TCTAAGAGCC
*
1567443 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
1567463 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1567483 CAT
1 CAT
1567486 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1574991 original size:19 final size:19
Alignment explanation
Indices: 1574969--1575012 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1574959 TTCTAAAAAA
1574969 TTCAATCTGAGCTGCAAAT
1 TTCAATCTGAGCTGCAAAT
1574988 TTCAATCTGAGCTGCAAAT
1 TTCAATCTGAGCTGCAAAT
1575007 TTCAAT
1 TTCAAT
1575013 ACTAACAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (19 bp):
TTCAATCTGAGCTGCAAAT
Found at i:1575836 original size:75 final size:75
Alignment explanation
Indices: 1575713--1575912 Score: 294
Period size: 75 Copynumber: 2.7 Consensus size: 75
1575703 ACTGAAAAAC
* * * * *
1575713 CAGATTGCCCAGAGGGTACCAATACCCCACAAGAGGGTATTGATACCCCATGTAAAATTTGGCTC
1 CAGATTGCTCAGAGGGTACCGATACCCCCCAAGAGGGTATCGATACCCCATGTAAAATCTGGCTC
1575778 CAAAAAATAA
66 CAAAAAATAA
* * * *
1575788 CAGATTGCTCGGAGGGTACCGATACCCCCCAAGAGGGTACCGATACCCCATGTAAGATCTGGCTT
1 CAGATTGCTCAGAGGGTACCGATACCCCCCAAGAGGGTATCGATACCCCATGTAAAATCTGGCTC
*
1575853 CAAGAAATAA
66 CAAAAAATAA
*
1575863 CAGATTGCTCAGAGGGTACCGATACCCCCCAGGA-GGTATCGATACCCCAT
1 CAGATTGCTCAGAGGGTACCGATACCCCCCAAGAGGGTATCGATACCCCAT
1575913 CTCATAACGA
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 15 0.13
75 97 0.87
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (75 bp):
CAGATTGCTCAGAGGGTACCGATACCCCCCAAGAGGGTATCGATACCCCATGTAAAATCTGGCTC
CAAAAAATAA
Found at i:1577018 original size:149 final size:149
Alignment explanation
Indices: 1576748--1577051 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
1576738 CGAAGTACCC
1576748 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* *
1576813 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
1576878 CATATGTCCTAAAGAACCG
131 CATATGTCCCAAAGAACCG
1576897 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1576962 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
1577027 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
1577046 CGTAGA
1 CGTAGA
1577052 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:1577565 original size:19 final size:20
Alignment explanation
Indices: 1577528--1577565 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1577518 TTTTTTCTCA
1577528 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGGTTCCCCCC
*
1577548 TGGGGGTATCGGTTCCCC
1 TGGGGGAATCGGTTCCCC
1577566 TCTAGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.32, G:0.37, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGGTTCCCCCC
Found at i:1586885 original size:23 final size:23
Alignment explanation
Indices: 1586859--1586919 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1586849 CTCGTATAAA
*
1586859 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1586882 TGCATCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1586905 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1586920 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1592856 original size:19 final size:19
Alignment explanation
Indices: 1592829--1592897 Score: 111
Period size: 19 Copynumber: 3.6 Consensus size: 19
1592819 CCTTAACATG
1592829 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
* *
1592848 TGCACCGATGTACTCCTTA
1 TGCATCGATGCACTCCTTA
1592867 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
1592886 TGTATCGATGCA
1 TGCATCGATGCA
1592898 TTAATTGCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:1593497 original size:13 final size:13
Alignment explanation
Indices: 1593479--1593503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1593469 ACGGGAGGAG
1593479 AGGAAGAAGAAGA
1 AGGAAGAAGAAGA
1593492 AGGAAGAAGAAG
1 AGGAAGAAGAAG
1593504 TTCTGGAGAA
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:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
AGGAAGAAGAAGA
Found at i:1596691 original size:23 final size:21
Alignment explanation
Indices: 1596645--1596723 Score: 88
Period size: 23 Copynumber: 3.6 Consensus size: 21
1596635 TTCAGCGCTA
*
1596645 GGTATCGATACCCCCTTGCATG
1 GGTACCGATACCCCCTTG-ATG
*
1596667 GGTACCAATACCCCCTTTGAGTG
1 GGTACCGATACCCCC-TTGA-TG
*
1596690 GGTATCGATACCCCCCTTGA-G
1 GGTACCGATA-CCCCCTTGATG
1596711 GGTACCGATACCC
1 GGTACCGATACCC
1596724 TCCACGGGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 3 0.06
21 10 0.20
22 14 0.29
23 17 0.35
24 5 0.10
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.24
Consensus pattern (21 bp):
GGTACCGATACCCCCTTGATG
Found at i:1599460 original size:21 final size:20
Alignment explanation
Indices: 1599434--1599472 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1599424 GATTGCTCGG
*
1599434 AGGGTACTGATACCACCCAAT
1 AGGGTACCGATACC-CCCAAT
1599455 AGGGTACCGATACCCCCA
1 AGGGTACCGATACCCCCA
1599473 TTTAAGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.33, G:0.21, T:0.15
Consensus pattern (20 bp):
AGGGTACCGATACCCCCAAT
Found at i:1599505 original size:76 final size:76
Alignment explanation
Indices: 1599377--1599545 Score: 234
Period size: 76 Copynumber: 2.2 Consensus size: 76
1599367 CAGATTGCCC
* * **
1599377 AGAGGGTACTGATACCCCCATGTAAAATTTGGCTCTGAGAAATAACAGATTGCTCGGAGGGT-AC
1 AGAGGGTACCGATACCCCCATGTAAAATCTGGCTCCAAGAAATAACAGATTGCTCGGAGGGTAAC
1599441 TGATACCACCCA
66 -GATACCACCCA
* * *
1599453 ATAGGGTACCGATACCCCCATTTAAGATCTGGCTCCAAGAAATAACAGATTGCTCGGAGGGTAAC
1 AGAGGGTACCGATACCCCCATGTAAAATCTGGCTCCAAGAAATAACAGATTGCTCGGAGGGTAAC
*
1599518 GATACCCCCCA
66 GATACCACCCA
*
1599529 GGA-GGTACCGATACCCC
1 AGAGGGTACCGATACCCC
1599546 AATCTCATAA
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
75 14 0.17
76 66 0.80
77 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (76 bp):
AGAGGGTACCGATACCCCCATGTAAAATCTGGCTCCAAGAAATAACAGATTGCTCGGAGGGTAAC
GATACCACCCA
Found at i:1601145 original size:143 final size:143
Alignment explanation
Indices: 1600981--1601242 Score: 461
Period size: 143 Copynumber: 1.8 Consensus size: 143
1600971 AAAAAATAAT
*
1600981 CCAATTAATCCTTATAATTTATTACTACTTATGCATAACTACTTAATCACCTATTATATTTTATT
1 CCAATTAATCCTTATAATTTATTACTACTTATACATAACTACTTAATCACCTATTATATTTTATT
* *
1601046 CTTTCTTTATTACGATTTCTCATATTATATTACTCTATGATTTTAGCACAACTTTTATCATATAC
66 CTTTCTTTACTACGATTTCTCATATTATATTACTCTACGATTTTAGCACAACTTTTATCATATAC
1601111 TTTTATATCACCA
131 TTTTATATCACCA
* *
1601124 CCAATTAATCCTTATAATTTATTACTACTTATACATAACTACTTAATCACTTATTATATTTTCTT
1 CCAATTAATCCTTATAATTTATTACTACTTATACATAACTACTTAATCACCTATTATATTTTATT
* *
1601189 CTTTCTTTACTACGATTTGTCATATTATATTACTCTACGGTTTTAGCACAACTT
66 CTTTCTTTACTACGATTTCTCATATTATATTACTCTACGATTTTAGCACAACTT
1601243 ATATACCTTT
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
143 112 1.00
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.47
Consensus pattern (143 bp):
CCAATTAATCCTTATAATTTATTACTACTTATACATAACTACTTAATCACCTATTATATTTTATT
CTTTCTTTACTACGATTTCTCATATTATATTACTCTACGATTTTAGCACAACTTTTATCATATAC
TTTTATATCACCA
Found at i:1601858 original size:17 final size:17
Alignment explanation
Indices: 1601817--1601865 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1601807 TACTCTCTTT
* *
1601817 TTCATGTACTGT-TCCT
1 TTCATGTACTATATCCC
1601833 TTCATTGTACTATATCCC
1 TTCA-TGTACTATATCCC
1601851 TTCATGTACTATATC
1 TTCATGTACTATATC
1601866 TTTTACAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 4 0.14
17 18 0.62
18 7 0.24
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.47
Consensus pattern (17 bp):
TTCATGTACTATATCCC
Found at i:1602172 original size:39 final size:38
Alignment explanation
Indices: 1602108--1602219 Score: 127
Period size: 39 Copynumber: 2.9 Consensus size: 38
1602098 ACCCATAATA
* *
1602108 CACATAAAGTGTCAGATAATTCACACATAGTGCATATTG
1 CACATAAAGTG-CCGATAATGCACACATAGTGCATATTG
* * *
1602147 CACATAAAGTGCCGGCTAATGCACACATAGCGCCAAATTG
1 CACATAAAGTGCC-GATAATGCACACATAGTG-CATATTG
* *
1602187 CACATAAAATGCC-ATAATGCACATATAGTGCAT
1 CACATAAAGTGCCGATAATGCACACATAGTGCAT
1602220 GGCAGATGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
37 2 0.03
38 15 0.25
39 26 0.43
40 18 0.30
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (38 bp):
CACATAAAGTGCCGATAATGCACACATAGTGCATATTG
Found at i:1603923 original size:18 final size:17
Alignment explanation
Indices: 1603891--1603924 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1603881 TATTATACTT
*
1603891 ATCTCTTATTTCATATG
1 ATCTCTTAATTCATATG
1603908 ATCTCTTACATTCATAT
1 ATCTCTTA-ATTCATAT
1603925 TCTATAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (17 bp):
ATCTCTTAATTCATATG
Found at i:1605113 original size:65 final size:62
Alignment explanation
Indices: 1605042--1605183 Score: 162
Period size: 65 Copynumber: 2.2 Consensus size: 62
1605032 TCTTTAACAT
* * *
1605042 GTGCATCGATGCACTATCC-ATGCATTGATACACAAATTACCTTCGATGTTTTCATT-TTTAAAG
1 GTGCATCGATGCAC--TCCTATGCATCGATACACAAATTACATTCGAT-ATTTC-TTCTTTAAAG
*
1605105 G
62 A
* *
1605106 GATGCATCGATGCACTCCTTATGCATCGATACACCAATTGCATTCGATATTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCC-TATGCATCGATACACAAATTACATTCGATATTTCTTCTTTAAAGA
1605170 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1605184 ATTGAATGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
63 18 0.26
64 13 0.19
65 37 0.54
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATTACATTCGATATTTCTTCTTTAAAGA
Found at i:1607916 original size:30 final size:30
Alignment explanation
Indices: 1607877--1607934 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
1607867 TTAAATAAGC
1607877 CCTTAAACTTTAT-AAAAAACCTAATTAAT
1 CCTTAAACTTTATAAAAAAACCTAATTAAT
*
1607906 CCTTCAAACTTTATAAAAAAACTTAATTA
1 CCTT-AAACTTTATAAAAAAACCTAATTA
1607935 TGTCATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 9 0.35
31 13 0.50
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (30 bp):
CCTTAAACTTTATAAAAAAACCTAATTAAT
Found at i:1608209 original size:30 final size:30
Alignment explanation
Indices: 1608158--1608236 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
1608148 CTTTTTTCTT
* *
1608158 AATTTAACG-GTCACATCGAATACATAAATA
1 AATTTAA-GAGTCACATTGAATACACAAATA
* *
1608188 AGTTTAAGAGTCATATTGAATACACAAATA
1 AATTTAAGAGTCACATTGAATACACAAATA
*
1608218 AATTTAGGAGTCACATTGA
1 AATTTAAGAGTCACATTGA
1608237 TTTTTTAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 1 0.02
30 40 0.98
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (30 bp):
AATTTAAGAGTCACATTGAATACACAAATA
Found at i:1609037 original size:2 final size:2
Alignment explanation
Indices: 1609030--1609064 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1609020 TTGGAGATTA
1609030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1609065 ATAGAAGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1613017 original size:42 final size:42
Alignment explanation
Indices: 1612970--1613116 Score: 294
Period size: 42 Copynumber: 3.5 Consensus size: 42
1612960 AAAGAAACAC
1612970 ATGCATTTGCAAGTGGGCACAAACAACATAAATGAACTATAG
1 ATGCATTTGCAAGTGGGCACAAACAACATAAATGAACTATAG
1613012 ATGCATTTGCAAGTGGGCACAAACAACATAAATGAACTATAG
1 ATGCATTTGCAAGTGGGCACAAACAACATAAATGAACTATAG
1613054 ATGCATTTGCAAGTGGGCACAAACAACATAAATGAACTATAG
1 ATGCATTTGCAAGTGGGCACAAACAACATAAATGAACTATAG
1613096 ATGCATTTGCAAGTGGGCACA
1 ATGCATTTGCAAGTGGGCACA
1613117 TACATTTATA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 105 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (42 bp):
ATGCATTTGCAAGTGGGCACAAACAACATAAATGAACTATAG
Found at i:1623873 original size:12 final size:12
Alignment explanation
Indices: 1623856--1623891 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1623846 TATCATGTTT
1623856 TCATATCACATG
1 TCATATCACATG
*
1623868 TCATATCACATA
1 TCATATCACATG
*
1623880 TTATATCACATG
1 TCATATCACATG
1623892 AACATATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1624305 original size:64 final size:63
Alignment explanation
Indices: 1624197--1624417 Score: 239
Period size: 64 Copynumber: 3.5 Consensus size: 63
1624187 TAATGAAGGT
* * ** * **
1624197 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* ** *
1624261 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGAAGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
* **
1624325 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT-TTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTA--TTAATGGG
**
1624388 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1624418 ACACCTTCAA
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
62 3 0.02
63 4 0.03
64 127 0.95
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:1630878 original size:20 final size:20
Alignment explanation
Indices: 1630853--1630920 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
1630843 AACCAACAAA
1630853 TTCGCAACGCGATCTCCAAT
1 TTCGCAACGCGATCTCCAAT
* * * *
1630873 TTCGCAACAC-AGTTTTCAAA
1 TTCGCAACGCGA-TCTCCAAT
1630893 TTCGCAACGCGATCTCCAAT
1 TTCGCAACGCGATCTCCAAT
1630913 TTCGCAAC
1 TTCGCAAC
1630921 ACAGTTTTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGATCTCCAAT
Found at i:1630904 original size:40 final size:40
Alignment explanation
Indices: 1630849--1630962 Score: 192
Period size: 40 Copynumber: 2.9 Consensus size: 40
1630839 AAATAACCAA
1630849 CAAATTCGCAACGCGATCTCCAATTTCGCAACACAGTTTT
1 CAAATTCGCAACGCGATCTCCAATTTCGCAACACAGTTTT
1630889 CAAATTCGCAACGCGATCTCCAATTTCGCAACACAGTTTT
1 CAAATTCGCAACGCGATCTCCAATTTCGCAACACAGTTTT
* * * *
1630929 CAAATTCGCAACGTGATTTCTAAATTCGCAACAC
1 CAAATTCGCAACGCGATCTCCAATTTCGCAACAC
1630963 GGAATTTAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (40 bp):
CAAATTCGCAACGCGATCTCCAATTTCGCAACACAGTTTT
Found at i:1630936 original size:20 final size:20
Alignment explanation
Indices: 1630873--1630962 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
1630863 GATCTCCAAT
1630873 TTCGCAACACAGTTTTCAAA
1 TTCGCAACACAGTTTTCAAA
* * * *
1630893 TTCGCAACGC-GATCTCCAAT
1 TTCGCAACACAG-TTTTCAAA
1630913 TTCGCAACACAGTTTTCAAA
1 TTCGCAACACAGTTTTCAAA
** *
1630933 TTCGCAAC-GTGATTTCTAAA
1 TTCGCAACACAGTTTTC-AAA
1630953 TTCGCAACAC
1 TTCGCAACAC
1630963 GGAATTTAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 6 0.11
20 47 0.87
21 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (20 bp):
TTCGCAACACAGTTTTCAAA
Found at i:1631054 original size:20 final size:20
Alignment explanation
Indices: 1631032--1631101 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
1631022 CAAGTTTCCT
*
1631032 TTTCGCAACACGAATTTTGT
1 TTTCGCAACACGAATTTTGA
* *
1631052 TTTCGCAACTCGATTTTTGA
1 TTTCGCAACACGAATTTTGA
* *
1631072 ATTCGCAACACGAATTTTAA
1 TTTCGCAACACGAATTTTGA
1631092 TTTCGCAACA
1 TTTCGCAACA
1631102 GCTTTTATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (20 bp):
TTTCGCAACACGAATTTTGA
Found at i:1631077 original size:40 final size:40
Alignment explanation
Indices: 1630913--1631100 Score: 138
Period size: 40 Copynumber: 4.7 Consensus size: 40
1630903 GATCTCCAAT
* * * *
1630913 TTCGCAACAC-AGTTTTCAAATTCGCAACGT-GATTTCTAAA
1 TTCGCAACACGAATTTT-AATTTCGCAAC-TCGATTTTTGAA
*
1630953 TTCGCAACACGGAATTTAAAATTT-GCAACTCGA-TTTTGAA
1 TTCGCAACAC-GAATTT-TAATTTCGCAACTCGATTTTTGAA
* * * ****
1630993 TTCGCAACGCGAATCTCTT--TTTCGCAA-TACAAGTTTCCTT
1 TTCGCAACACGAAT-T-TTAATTTCGCAACT-CGATTTTTGAA
**
1631033 TTCGCAACACGAATTTTGTTTTCGCAACTCGATTTTTGAA
1 TTCGCAACACGAATTTTAATTTCGCAACTCGATTTTTGAA
1631073 TTCGCAACACGAATTTTAATTTCGCAAC
1 TTCGCAACACGAATTTTAATTTCGCAAC
1631101 AGCTTTTATT
Statistics
Matches: 115, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
38 6 0.05
39 11 0.10
40 81 0.70
41 9 0.08
42 8 0.07
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (40 bp):
TTCGCAACACGAATTTTAATTTCGCAACTCGATTTTTGAA
Found at i:1634366 original size:6 final size:6
Alignment explanation
Indices: 1634355--1634390 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1634345 CAAGCAAACA
**
1634355 AAAATC AAAATC AAAATC GCAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1634391 CCAATCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.61, C:0.19, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:1634380 original size:18 final size:18
Alignment explanation
Indices: 1634357--1634397 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1634347 AGCAAACAAA
*
1634357 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
1634375 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
1634393 AATCA
1 AATCA
1634398 CAACCGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:1634628 original size:20 final size:20
Alignment explanation
Indices: 1634603--1634725 Score: 113
Period size: 20 Copynumber: 6.2 Consensus size: 20
1634593 GAATTGAATG
**
1634603 GAAAGTCAAATTCGCATTGC
1 GAAAGTCAAATTCGCAACGC
* *
1634623 GAAAGTTAAATTCGAAACGC
1 GAAAGTCAAATTCGCAACGC
1634643 GAAAGTCAAATTCGCAACGC
1 GAAAGTCAAATTCGCAACGC
* * *
1634663 AAAAATCAAATTCGCAACAC
1 GAAAGTCAAATTCGCAACGC
* *
1634683 GAAAATCGAATTCG-ACACGC
1 GAAAGTCAAATTCGCA-ACGC
* * **
1634703 GAAAATTAAAAGCGCAACGC
1 GAAAGTCAAATTCGCAACGC
1634723 GAA
1 GAA
1634726 TTTGATTTTC
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 83 0.98
21 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAGTCAAATTCGCAACGC
Found at i:1636360 original size:21 final size:21
Alignment explanation
Indices: 1636336--1636433 Score: 119
Period size: 21 Copynumber: 4.7 Consensus size: 21
1636326 AGGTGGATCA
* *
1636336 TGAATGATGGAAGGGGCATCT
1 TGAACGATGGAAGGGGCCTCT
*
1636357 TGAATGAT-GAGAGGGGCCTCT
1 TGAACGATGGA-AGGGGCCTCT
1636378 TGAACGAT-GAGAGGGGCCTCT
1 TGAACGATGGA-AGGGGCCTCT
*
1636399 TGAACGATGGGAGGGGCCTCT
1 TGAACGATGGAAGGGGCCTCT
*
1636420 TGAACGATGAAAGG
1 TGAACGATGGAAGG
1636434 TGAATTGGGC
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
20 2 0.03
21 67 0.96
22 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.39, T:0.20
Consensus pattern (21 bp):
TGAACGATGGAAGGGGCCTCT
Found at i:1636413 original size:42 final size:42
Alignment explanation
Indices: 1636347--1636429 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
1636337 GAATGATGGA
*
1636347 AGGGGCATCTTGAATGATGAGAGGGGCCTCTTGAACGATGAG
1 AGGGGCATCTTGAACGATGAGAGGGGCCTCTTGAACGATGAG
* *
1636389 AGGGGCCTCTTGAACGATGGGAGGGGCCTCTTGAACGATGA
1 AGGGGCATCTTGAACGATGAGAGGGGCCTCTTGAACGATGA
1636430 AAGGTGAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (42 bp):
AGGGGCATCTTGAACGATGAGAGGGGCCTCTTGAACGATGAG
Found at i:1636809 original size:21 final size:21
Alignment explanation
Indices: 1636732--1636811 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 21
1636722 CGTAGAGCGG
* **
1636732 CTACCTCATCACGTAAAGTAGA
1 CTACCTCACCACGTAAAACA-A
1636754 -TACCTCACCACGTAAAAC-A
1 CTACCTCACCACGTAAAACAA
* ** * *
1636773 CCATTGTCATCGCGTAAAACAA
1 CTA-CCTCACCACGTAAAACAA
1636795 CTACCTCACCACGTAAA
1 CTACCTCACCACGTAAA
1636812 GACCGTACCT
Statistics
Matches: 42, Mismatches: 13, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 37 0.88
22 3 0.07
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.20
Consensus pattern (21 bp):
CTACCTCACCACGTAAAACAA
Found at i:1636886 original size:21 final size:21
Alignment explanation
Indices: 1636847--1636887 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1636837 CATTATCGTC
* *
1636847 ACGTAAAGTACCGACCTCATT
1 ACGTAAAGCACCGAACTCATT
*
1636868 ACGTAAAGCACTGAACTCAT
1 ACGTAAAGCACCGAACTCAT
1636888 CATGTAACTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.22
Consensus pattern (21 bp):
ACGTAAAGCACCGAACTCATT
Found at i:1637070 original size:42 final size:42
Alignment explanation
Indices: 1637011--1637107 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
1637001 GATGGAATAG
* *
1637011 GTGATGGATCTCGGTGTCGA-AGTGTATAATCAGCTCGATCAA
1 GTGATGGCTCTCGGTGTCGAGA-TGTAGAATCAGCTCGATCAA
* *
1637053 GTGATGGCTCTCGGTGTCGAGATGTAGAATCGGCTCGATCAG
1 GTGATGGCTCTCGGTGTCGAGATGTAGAATCAGCTCGATCAA
1637095 GTGATGGCTCTCG
1 GTGATGGCTCTCG
1637108 AAGTGGGGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 49 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.28
Consensus pattern (42 bp):
GTGATGGCTCTCGGTGTCGAGATGTAGAATCAGCTCGATCAA
Found at i:1639625 original size:23 final size:23
Alignment explanation
Indices: 1639567--1639625 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 23
1639557 ATCTTACATA
* * *
1639567 GCACTCCGGTACATTTCTACGCG
1 GCACTACGGTGCAATTCTACGCG
** *
1639590 GCACTACAATGCAATTCTACGTG
1 GCACTACGGTGCAATTCTACGCG
*
1639613 GCACTTCGGTGCA
1 GCACTACGGTGCA
1639626 TTTATATGAG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCG
Found at i:1640569 original size:67 final size:68
Alignment explanation
Indices: 1640488--1640639 Score: 225
Period size: 67 Copynumber: 2.2 Consensus size: 68
1640478 ACCCATTCAA
* * * *
1640488 GGGGAACCGATACCCTCTCAATGAATATGAATTTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
1640552 AGG
66 AGG
* *
1640555 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGTTAGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
*
1640620 GGG
66 AGG
*
1640623 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1640640 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
67 53 0.70
68 23 0.30
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.16
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
AGG
Found at i:1641388 original size:149 final size:149
Alignment explanation
Indices: 1641118--1641421 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
1641108 GGATAGAGGG
1641118 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1641183 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
1641248 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
1641267 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1641332 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1641397 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1641416 TCTACG
1 TCTACG
1641422 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1641444 original size:23 final size:23
Alignment explanation
Indices: 1641400--1641444 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1641390 ATCATTATAT
*
1641400 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1641423 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1641445 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1647362 original size:67 final size:67
Alignment explanation
Indices: 1647281--1647431 Score: 221
Period size: 67 Copynumber: 2.3 Consensus size: 67
1647271 ACCCATTCAA
* * * * *
1647281 GGGGAACCGATACCCTCTCAATGAATATGAATTTCCAGAATGCTAGAGGGGAATCGATACCCCAA
1 GGGGAACCGATACCCCCTCAACGAACATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAA
1647346 GG
66 GG
* * *
1647348 GGGGAACCGATACCCCCTCAACGGACATGAAATTCCAGAATGTTAGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAACATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAA
1647413 GG
66 GG
*
1647415 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1647432 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 75 1.00
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.16
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAACATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAA
GG
Found at i:1647420 original size:20 final size:20
Alignment explanation
Indices: 1647395--1647432 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1647385 GAATGTTAGA
1647395 GGGGAACCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
1647415 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1647433 TGAGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.37, G:0.32, T:0.08
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:1648179 original size:149 final size:149
Alignment explanation
Indices: 1647909--1648212 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
1647899 GGGTAGAGGG
*
1647909 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTAGAACCTGTGTGAAGTCTTGAAAGACACAT
1647974 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1648039 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1648058 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTAGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTAGAACCTGTGTGAAGTCTTGAAAGACACAT
1648123 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1648188 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1648207 TCTACG
1 TCTACG
1648213 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTAGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1648235 original size:23 final size:23
Alignment explanation
Indices: 1648191--1648235 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1648181 ATCATTATAT
*
1648191 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1648214 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1648236 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1654159 original size:23 final size:23
Alignment explanation
Indices: 1654124--1654183 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1654114 AATCTTACAT
* **
1654124 GGCACTTCAGTGCGTTTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
1654147 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
1654170 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1654184 TTTATATGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1657242 original size:22 final size:22
Alignment explanation
Indices: 1657217--1657266 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
1657207 ATAGAGGGGG
* * *
1657217 GTCGTCAGATATGGGGACGGAT
1 GTCGTCAGAGATAGAGACGGAT
* *
1657239 GTCGCCGGAGATAGAGACGGAT
1 GTCGTCAGAGATAGAGACGGAT
1657261 GTCGTC
1 GTCGTC
1657267 GTAGAAAGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.40, T:0.20
Consensus pattern (22 bp):
GTCGTCAGAGATAGAGACGGAT
Found at i:1657401 original size:19 final size:20
Alignment explanation
Indices: 1657379--1657416 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1657369 AATATTGTGT
1657379 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
1657398 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
1657417 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:1657501 original size:22 final size:22
Alignment explanation
Indices: 1657474--1657517 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1657464 TTGCGGAAAA
1657474 GAAATTC-AAGTTGCGAATCTGG
1 GAAATTCGAA-TTGCGAATCTGG
*
1657496 GAAATTCGCATTGCGAATCTGG
1 GAAATTCGAATTGCGAATCTGG
1657518 AAACTATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (22 bp):
GAAATTCGAATTGCGAATCTGG
Found at i:1657988 original size:33 final size:32
Alignment explanation
Indices: 1657944--1658024 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
1657934 AAAAATTAGG
* *
1657944 TTCGAGTCGGGTTTGGTTGTTTTAAGTTTGATA
1 TTCGGGTCGGGTTTGGTT-TTTTAAGTGTGATA
*
1657977 TTCGGGTCGGGTTGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTGGTTTTTTAAGTGTGATA
* *
1658009 TTCGGGTAGGGGTTGG
1 TTCGGGTCGGGTTTGG
1658025 GTTTAGGGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 26 0.62
33 16 0.38
ACGTcount: A:0.12, C:0.06, G:0.38, T:0.43
Consensus pattern (32 bp):
TTCGGGTCGGGTTTGGTTTTTTAAGTGTGATA
Found at i:1658027 original size:33 final size:32
Alignment explanation
Indices: 1657944--1658028 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 32
1657934 AAAAATTAGG
* * *
1657944 TTCGAGTCGGGTTTGGTTGTTTTAAGTTTGATA
1 TTCGGGTCGGGTTGGGTT-TTTTAAGTGTGATA
1657977 TTCGGGTCGGGTTGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTGGGTTTTTTAAGTGTGATA
*
1658009 TTCGGGTAGGGGTTGGGTTT
1 TTCGGGT-CGGGTTGGGTTT
1658029 AGGGTGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
32 20 0.43
33 27 0.57
ACGTcount: A:0.12, C:0.06, G:0.38, T:0.45
Consensus pattern (32 bp):
TTCGGGTCGGGTTGGGTTTTTTAAGTGTGATA
Found at i:1658234 original size:21 final size:21
Alignment explanation
Indices: 1658208--1658257 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1658198 GTCGGTCGAG
1658208 TCTCGGGTGGAGGTTCCTTGT
1 TCTCGGGTGGAGGTTCCTTGT
1658229 TCTCGGGTGGAGGTTCCTTGT
1 TCTCGGGTGGAGGTTCCTTGT
1658250 TCTCGGGT
1 TCTCGGGT
1658258 CGGGTCGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.04, C:0.20, G:0.38, T:0.38
Consensus pattern (21 bp):
TCTCGGGTGGAGGTTCCTTGT
Found at i:1658611 original size:16 final size:18
Alignment explanation
Indices: 1658590--1658635 Score: 69
Period size: 16 Copynumber: 2.7 Consensus size: 18
1658580 GTTTTAGATT
1658590 CAGATTCCAATTCC-T-A
1 CAGATTCCAATTCCTTCA
*
1658606 CAGATTGCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
1658624 CAGATTCCAATT
1 CAGATTCCAATT
1658636 TCCTCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 13 0.50
17 1 0.04
18 12 0.46
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:1659933 original size:22 final size:22
Alignment explanation
Indices: 1659902--1659973 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
1659892 CTGAGTGGCA
1659902 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
1659925 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
1659947 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
1659968 TATGAA
1 TATGAA
1659974 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:1659958 original size:21 final size:21
Alignment explanation
Indices: 1659910--1659972 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1659900 CATATGAAAT
* *
1659910 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
1659932 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
1659953 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
1659973 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:1660542 original size:18 final size:16
Alignment explanation
Indices: 1660495--1660542 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 16
1660485 TATTACTGGG
1660495 ATGCATCGATGCATGACTT
1 ATGCATCGATGC---ACTT
1660514 ATGCATCGATGCACTT
1 ATGCATCGATGCACTT
1660530 ATTGCATTCGATG
1 A-TGCA-TCGATG
1660543 TTTCTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 4 0.15
18 6 0.22
19 12 0.44
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (16 bp):
ATGCATCGATGCACTT
Found at i:1666747 original size:22 final size:22
Alignment explanation
Indices: 1666716--1666787 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
1666706 CTGAGTGGCA
*
1666716 TATGAAATTTATCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
1666739 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
1666761 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
1666782 TATGAA
1 TATGAA
1666788 ACCCTCGACT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 20 0.45
22 21 0.48
23 3 0.07
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:1666772 original size:21 final size:21
Alignment explanation
Indices: 1666727--1666786 Score: 93
Period size: 21 Copynumber: 2.8 Consensus size: 21
1666717 ATGAAATTTA
* *
1666727 TCCCGAAGGACCTGTGAATTTG
1 TCCCGAAGGACCTATG-AGTTG
1666749 TCCCGAAGGACCTATGAGTTG
1 TCCCGAAGGACCTATGAGTTG
1666770 TCCCGAAGGACCTATGA
1 TCCCGAAGGACCTATGA
1666787 AACCCTCGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (21 bp):
TCCCGAAGGACCTATGAGTTG
Found at i:1667357 original size:18 final size:16
Alignment explanation
Indices: 1667310--1667357 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 16
1667300 TATTACTGGG
1667310 ATGCATCGATGCATGACTT
1 ATGCATCGATGC---ACTT
1667329 ATGCATCGATGCACTT
1 ATGCATCGATGCACTT
1667345 ATTGCATTCGATG
1 A-TGCA-TCGATG
1667358 TTTCTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 4 0.15
18 6 0.22
19 12 0.44
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (16 bp):
ATGCATCGATGCACTT
Found at i:1675463 original size:18 final size:18
Alignment explanation
Indices: 1675440--1675478 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1675430 TTTTACATAG
1675440 TTTATCATATTGATTATA
1 TTTATCATATTGATTATA
1675458 TTTATCATATTGATTATA
1 TTTATCATATTGATTATA
1675476 TTT
1 TTT
1675479 CTATTTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTATCATATTGATTATA
Found at i:1686882 original size:18 final size:15
Alignment explanation
Indices: 1686839--1686873 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1686829 CGAGGGTATT
1686839 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1686854 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1686869 GTAGT
1 GTAGT
1686874 GGTCCTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:1689247 original size:2 final size:2
Alignment explanation
Indices: 1689240--1689285 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1689230 GTTATGATTC
1689240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1689282 AT AT
1 AT AT
1689286 GAATGATGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1712089 original size:24 final size:24
Alignment explanation
Indices: 1712062--1712107 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1712052 ATGTGTTTTC
1712062 TTTTTAAAAAATATATAATTTTAT
1 TTTTTAAAAAATATATAATTTTAT
***
1712086 TTTTTAAATTTTATATAATTTT
1 TTTTTAAAAAATATATAATTTT
1712108 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTTAAAAAATATATAATTTTAT
Found at i:1715276 original size:23 final size:22
Alignment explanation
Indices: 1715232--1715276 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1715222 TCAGGAGTTA
1715232 CAGGAGTTATCTGATTTAATTT
1 CAGGAGTTATCTGATTTAATTT
1715254 CAGGAGTTATAACTG-TTTAATTT
1 CAGGAGTTAT--CTGATTTAATTT
1715277 TTATGCAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 8 0.38
24 3 0.14
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (22 bp):
CAGGAGTTATCTGATTTAATTT
Found at i:1716270 original size:22 final size:22
Alignment explanation
Indices: 1716244--1716293 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1716234 TTACATTTCC
1716244 ATAATGCATACGTTTTATTATA
1 ATAATGCATACGTTTTATTATA
1716266 ATAATGCATACGTTTTATTATA
1 ATAATGCATACGTTTTATTATA
1716288 ATAATG
1 ATAATG
1716294 TATAATAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (22 bp):
ATAATGCATACGTTTTATTATA
Found at i:1718470 original size:14 final size:14
Alignment explanation
Indices: 1718451--1718480 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1718441 CATTTTTGAA
1718451 AGGAGATCTAGATG
1 AGGAGATCTAGATG
*
1718465 AGGAGATCTATATG
1 AGGAGATCTAGATG
1718479 AG
1 AG
1718481 AACAATGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (14 bp):
AGGAGATCTAGATG
Found at i:1735388 original size:59 final size:59
Alignment explanation
Indices: 1735308--1735421 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 59
1735298 AAATGATCCA
* *
1735308 GACTATAGGATATTACTTTGTTGAGTCTC-CTGACTGTAAAAAGTTACGAAATGGTCTCCT
1 GACTATAGGATATTACTTTGTTGAGTCACTC-GACTATAAAAAGTTAC-AAATGGTCTCCT
* *
1735368 GACTATAGGA-GTTACTTTGTTGAGTCACTCGACTATTAAAAGTTACAAATGGTC
1 GACTATAGGATATTACTTTGTTGAGTCACTCGACTATAAAAAGTTACAAATGGTC
1735422 ATCCGATTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 8 0.16
59 30 0.61
60 11 0.22
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (59 bp):
GACTATAGGATATTACTTTGTTGAGTCACTCGACTATAAAAAGTTACAAATGGTCTCCT
Found at i:1747686 original size:6 final size:6
Alignment explanation
Indices: 1747675--1747699 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1747665 TCATTTTTAA
1747675 TAAAAT TAAAAT TAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT T
1747700 TAATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAAAT
Found at i:1747815 original size:21 final size:21
Alignment explanation
Indices: 1747790--1747834 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1747780 ATTACATTAT
1747790 ATTTTT-ATTGAATTTTATTC
1 ATTTTTAATTGAATTTTATTC
* * *
1747810 ATTTTTAATTTATTTTTATTT
1 ATTTTTAATTGAATTTTATTC
1747831 ATTT
1 ATTT
1747835 CTAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTTAATTGAATTTTATTC
Found at i:1747824 original size:11 final size:10
Alignment explanation
Indices: 1747789--1747834 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
1747779 CATTACATTA
1747789 TATTTTTATT
1 TATTTTTATT
* *
1747799 GAATTTTATT
1 TATTTTTATT
*
1747809 CATTTTTAATT
1 TATTTTT-ATT
1747820 TATTTTTATT
1 TATTTTTATT
1747830 TATTT
1 TATTT
1747835 CTAAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1748313 original size:6 final size:6
Alignment explanation
Indices: 1748302--1748346 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1748292 TAACTTATCT
1748302 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTT
1748347 TTCACTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:1751681 original size:2 final size:2
Alignment explanation
Indices: 1751669--1751723 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1751659 AACAGATGGA
1751669 AG AG AG A- 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
1751710 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
1751724 TGATGGAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1753604 original size:40 final size:43
Alignment explanation
Indices: 1753545--1753629 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 43
1753535 CTTTGAGATA
1753545 TTGTTTTCTACTTTCATACAACAAAATCTAA-CC-TC-CCTTT
1 TTGTTTTCTACTTTCATACAACAAAATCTAATCCATCACCTTT
* *
1753585 TTGTTTTCTATTTTGATACAACAAAATCTAATCCATCACCTTT
1 TTGTTTTCTACTTTCATACAACAAAATCTAATCCATCACCTTT
1753628 TT
1 TT
1753630 ATTTATTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 29 0.73
41 2 0.05
42 2 0.05
43 7 0.17
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.45
Consensus pattern (43 bp):
TTGTTTTCTACTTTCATACAACAAAATCTAATCCATCACCTTT
Found at i:1754019 original size:7 final size:7
Alignment explanation
Indices: 1754003--1754049 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
1753993 TGCCAGACTT
*
1754003 TAAACTC
1 TAAACCC
1754010 TAAACCC
1 TAAACCC
1754017 TAAACCC
1 TAAACCC
1754024 TAAACCC
1 TAAACCC
**
1754031 TAAAATC
1 TAAACCC
1754038 TAAACTCC
1 TAAAC-CC
1754046 TAAA
1 TAAA
1754050 TATTAAGTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 29 0.85
8 5 0.15
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:1754050 original size:14 final size:14
Alignment explanation
Indices: 1754003--1754049 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
1753993 TGCCAGACTT
1754003 TAAACTCTAAACCC
1 TAAACTCTAAACCC
*
1754017 TAAACCCTAAACCC
1 TAAACTCTAAACCC
*
1754031 TAAAATCTAAACTCC
1 TAAACTCTAAAC-CC
1754046 TAAA
1 TAAA
1754050 TATTAAGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 23 0.79
15 6 0.21
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACTCTAAACCC
Found at i:1757811 original size:15 final size:17
Alignment explanation
Indices: 1757780--1757812 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1757770 GAATATTTAT
1757780 TATTAAATAATTAAAAA
1 TATTAAATAATTAAAAA
1757797 TATTAAA-AA-TAAAAA
1 TATTAAATAATTAAAAA
1757812 T
1 T
1757813 TATTTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATTAAATAATTAAAAA
Found at i:1757816 original size:16 final size:18
Alignment explanation
Indices: 1757778--1757816 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1757768 TTGAATATTT
1757778 ATTATTAAATAATTAAAA
1 ATTATTAAATAATTAAAA
1757796 A-TATTAAA-AA-TAAAA
1 ATTATTAAATAATTAAAA
1757811 ATTATT
1 ATTATT
1757817 TTATTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.30
16 6 0.30
17 7 0.35
18 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTATTAAATAATTAAAA
Found at i:1762733 original size:13 final size:13
Alignment explanation
Indices: 1762715--1762740 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1762705 GTATATAGCT
1762715 GATCTTTATTTAG
1 GATCTTTATTTAG
1762728 GATCTTTATTTAG
1 GATCTTTATTTAG
1762741 TATGTACTTC
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:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
GATCTTTATTTAG
Found at i:1771293 original size:34 final size:36
Alignment explanation
Indices: 1771249--1771350 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1771239 TTTCGTCCTA
1771249 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
1771284 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1771319 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1771351 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:1771800 original size:2 final size:2
Alignment explanation
Indices: 1771795--1771825 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1771785 TTAGTGTTAT
1771795 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1771826 TTCCTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1773239 original size:5 final size:5
Alignment explanation
Indices: 1773229--1773266 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
1773219 TCTTTTCATC
1773229 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1773267 CATCACTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Done.