Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 11 of 34
Found at i:1623470 original size:54 final size:51
Alignment explanation
Indices: 1623403--1623533 Score: 131
Period size: 51 Copynumber: 2.5 Consensus size: 51
1623393 GATTAACGGG
* * **
1623403 GTTGGAGTGTCCCCAATTGTGAAGAAATTGGTGTTTTTTGGAAA-TAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAATG--TTTT-GAAAGTAAAATCGGA
*
1623457 GTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAGTAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAATGTTTTGAAAGTAAAATCGGA
* *
1623508 GTTGGAATATCCTCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
1623534 TTGAGCAACT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
50 4 0.06
51 31 0.48
52 4 0.06
53 9 0.14
54 17 0.26
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAATGTTTTGAAAGTAAAATCGGA
Found at i:1625900 original size:13 final size:13
Alignment explanation
Indices: 1625882--1625907 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1625872 ACAAAGATCC
1625882 ATGTATCGATACA
1 ATGTATCGATACA
1625895 ATGTATCGATACA
1 ATGTATCGATACA
1625908 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1625903 original size:33 final size:33
Alignment explanation
Indices: 1625861--1625927 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1625851 AAAATTTCAA
***
1625861 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1625894 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1625927 A
1 A
1625928 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1625971 original size:19 final size:18
Alignment explanation
Indices: 1625947--1626014 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1625937 CAGTAGCTAA
1625947 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1625966 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1625981 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1625998 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1626015 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1625987 original size:13 final size:13
Alignment explanation
Indices: 1625969--1625993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1625959 ACAATACTTA
1625969 TGTATCGATACAT
1 TGTATCGATACAT
1625982 TGTATCGATACA
1 TGTATCGATACA
1625994 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1625991 original size:32 final size:32
Alignment explanation
Indices: 1625950--1626012 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1625940 TAGCTAATTA
*
1625950 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1625982 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1626013 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1630090 original size:13 final size:13
Alignment explanation
Indices: 1630072--1630097 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1630062 ACATTTTATG
1630072 ATGTATCGATACA
1 ATGTATCGATACA
1630085 ATGTATCGATACA
1 ATGTATCGATACA
1630098 TGCTGTGTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1630110 original size:19 final size:19
Alignment explanation
Indices: 1630086--1630148 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1630076 ATCGATACAA
1630086 TGTATCGATACATGCTGTG
1 TGTATCGATACATGCTGTG
*
1630105 TGTATCGATACA------A
1 TGTATCGATACATGCTGTG
*
1630118 TGTATCAATACATGCTGTG
1 TGTATCGATACATGCTGTG
1630137 TGTATCGATACA
1 TGTATCGATACA
1630149 AGTTTGGCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
13 11 0.32
19 23 0.68
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATGCTGTG
Found at i:1630114 original size:32 final size:32
Alignment explanation
Indices: 1630050--1630149 Score: 155
Period size: 32 Copynumber: 3.1 Consensus size: 32
1630040 CGTTACAAGC
** *
1630050 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATGCTGTG-TGTATCGATA
1630083 CAATGTATCGATACATGCTGTGTGTATCGATA
1 CAATGTATCGATACATGCTGTGTGTATCGATA
*
1630115 CAATGTATCAATACATGCTGTGTGTATCGATA
1 CAATGTATCGATACATGCTGTGTGTATCGATA
1630147 CAA
1 CAA
1630150 GTTTGGCTAC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 44 0.70
33 19 0.30
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATGCTGTGTGTATCGATA
Found at i:1632168 original size:21 final size:21
Alignment explanation
Indices: 1632135--1632184 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1632125 TTGCAAGTTG
*
1632135 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1632157 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1632178 AAATAAA
1 AAATAAA
1632185 AGCTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1636268 original size:21 final size:21
Alignment explanation
Indices: 1636221--1636268 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1636211 TTCCAAACTT
*
1636221 CAAAACTCTTCAAATCTTTTG
1 CAAAATTCTTCAAATCTTTTG
1636242 CAAAATTCTTCAAATCTTTTG
1 CAAAATTCTTCAAATCTTTTG
1636263 CAAAAT
1 CAAAAT
1636269 ACTTGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (21 bp):
CAAAATTCTTCAAATCTTTTG
Found at i:1638013 original size:16 final size:16
Alignment explanation
Indices: 1637992--1638027 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1637982 ACGGGGGAGA
1637992 TAAAGGGGAGAATGCG
1 TAAAGGGGAGAATGCG
1638008 TAAAGGGGAGAATGCG
1 TAAAGGGGAGAATGCG
1638024 TAAA
1 TAAA
1638028 TTGCTACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.39, T:0.14
Consensus pattern (16 bp):
TAAAGGGGAGAATGCG
Found at i:1638729 original size:13 final size:13
Alignment explanation
Indices: 1638711--1638736 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1638701 TACACCAAGT
1638711 ATGTATCGATACA
1 ATGTATCGATACA
1638724 ATGTATCGATACA
1 ATGTATCGATACA
1638737 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1638734 original size:32 final size:33
Alignment explanation
Indices: 1638693--1638756 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1638683 TAGCCAAACT
* **
1638693 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1638725 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1638757 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1643230 original size:20 final size:20
Alignment explanation
Indices: 1643205--1643259 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1643195 CTTCCAGTTT
* *
1643205 CATGTATCAATACAATTGTC
1 CATGTATCGATACAATTGAC
* *
1643225 CATGTATCGATATAA-TGAG
1 CATGTATCGATACAATTGAC
1643244 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1643260 GTATCGATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAC
Found at i:1643263 original size:13 final size:13
Alignment explanation
Indices: 1643245--1643271 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1643235 TATAATGAGC
1643245 ATGTATCGATACA
1 ATGTATCGATACA
1643258 ATGTATCGATACA
1 ATGTATCGATACA
1643271 A
1 A
1643272 AGCAGAATGT
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):
ATGTATCGATACA
Found at i:1643287 original size:33 final size:32
Alignment explanation
Indices: 1643226--1643290 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1643216 ACAATTGTCC
* * *
1643226 ATGTATCGATATAATGAGCATGTATCGATACA
1 ATGTATCGATACAAAGAGAATGTATCGATACA
1643258 ATGTATCGATACAAAGCAGAATGTATCGATACA
1 ATGTATCGATACAAAG-AGAATGTATCGATACA
1643291 TTTGGAAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAGAATGTATCGATACA
Found at i:1645125 original size:41 final size:41
Alignment explanation
Indices: 1645021--1645189 Score: 144
Period size: 41 Copynumber: 4.1 Consensus size: 41
1645011 AAATCATAAT
* * *
1645021 AGTCAATAAGTTAAAAGTGTTGACTAAGATGAAGCCAT-CG
1 AGTCAATAAGTTAAAAGAGTTGACTAGGATGAAACCATACG
** * *
1645061 AGTCAAGGAGTTAGGAA-AGTTGACTAGGATGAAACCATACA
1 AGTCAATAAGTTA-AAAGAGTTGACTAGGATGAAACCATACG
* * * * * **
1645102 AGTCAATGAGTTAAAAGAATTGACCAGGACGAAGCCATTTG
1 AGTCAATAAGTTAAAAGAGTTGACTAGGATGAAACCATACG
* * * * *
1645143 AGTTAACAAGTTAGAAGAGTTGATTGGGATGAAACCATACG
1 AGTCAATAAGTTAAAAGAGTTGACTAGGATGAAACCATACG
1645184 AGTCAA
1 AGTCAA
1645190 CAAATCAAGA
Statistics
Matches: 97, Mismatches: 29, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
40 31 0.32
41 66 0.68
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.22
Consensus pattern (41 bp):
AGTCAATAAGTTAAAAGAGTTGACTAGGATGAAACCATACG
Found at i:1646939 original size:13 final size:14
Alignment explanation
Indices: 1646931--1646962 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1646921 TGATTTTCAG
1646931 AAAATATTTTATGA
1 AAAATATTTTATGA
1646945 AAAATATTTT-TGA
1 AAAATATTTTATGA
1646958 AAAAT
1 AAAAT
1646963 GAGAGACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (14 bp):
AAAATATTTTATGA
Found at i:1648066 original size:18 final size:18
Alignment explanation
Indices: 1648006--1648077 Score: 55
Period size: 18 Copynumber: 4.1 Consensus size: 18
1647996 ATTAACAATT
1648006 ATTAATTTATTATT-AATA
1 ATTAATTTATT-TTAAATA
*
1648024 AAT-ATGTTA-TTT-AATCA
1 ATTAAT-TTATTTTAAAT-A
*
1648041 ATTTATTT-TTTATAAATA
1 ATTAATTTATTT-TAAATA
1648059 ATTAATTTATTTTAAATA
1 ATTAATTTATTTTAAATA
1648077 A
1 A
1648078 AAATAATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
16 5 0.11
17 10 0.23
18 23 0.52
19 6 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
ATTAATTTATTTTAAATA
Found at i:1648067 original size:31 final size:31
Alignment explanation
Indices: 1648009--1648067 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1647999 AACAATTATT
*
1648009 AATTTATTATTAATAAATATGTTATTTAATC
1 AATTTATTATTAATAAATATGTAATTTAATC
* *
1648040 AATTTATTTTTTATAAATAAT-TAATTTA
1 AATTTATTATTAATAAAT-ATGTAATTTA
1648068 TTTTAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.92
32 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (31 bp):
AATTTATTATTAATAAATATGTAATTTAATC
Found at i:1648077 original size:22 final size:22
Alignment explanation
Indices: 1648035--1648078 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1648025 ATATGTTATT
**
1648035 TAATCAATTTATTTTTTATAAA
1 TAATCAATTTATTTTAAATAAA
*
1648057 TAATTAATTTATTTTAAATAAA
1 TAATCAATTTATTTTAAATAAA
1648079 AATAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATCAATTTATTTTAAATAAA
Found at i:1648194 original size:20 final size:21
Alignment explanation
Indices: 1648171--1648210 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1648161 ATATGTAACT
*
1648171 TAATTTGATAA-TAATTAAAA
1 TAATTTGAAAATTAATTAAAA
*
1648191 TAATTTTAAAATTAATTAAA
1 TAATTTGAAAATTAATTAAA
1648211 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TAATTTGAAAATTAATTAAAA
Found at i:1652166 original size:67 final size:67
Alignment explanation
Indices: 1652090--1652227 Score: 258
Period size: 67 Copynumber: 2.1 Consensus size: 67
1652080 CCTTTCTACA
* *
1652090 GAGAAGTATTCATAATCTATAAATAAAGAAAAGATAGAGGCAAAAGAATCTTCCTAAACCGCAGA
1 GAGAAGTATTCATAATCTATAAATAAAGAAAAGATAAAGGCAAAAGAATCTTCCTAAACCACAGA
1652155 AG
66 AG
1652157 GAGAAGTATTCATAATCTATAAATAAAGAAAAGATAAAGGCAAAAGAATCTTCCTAAACCACAGA
1 GAGAAGTATTCATAATCTATAAATAAAGAAAAGATAAAGGCAAAAGAATCTTCCTAAACCACAGA
1652222 AG
66 AG
1652224 GAGA
1 GAGA
1652228 TTAAGTAAAC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.19
Consensus pattern (67 bp):
GAGAAGTATTCATAATCTATAAATAAAGAAAAGATAAAGGCAAAAGAATCTTCCTAAACCACAGA
AG
Found at i:1658894 original size:2 final size:2
Alignment explanation
Indices: 1658889--1658922 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1658879 GGCAAAGACA
*
1658889 AT AT AT AT AT AT CT 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
1658923 GTTGAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1662484 original size:33 final size:33
Alignment explanation
Indices: 1662447--1662513 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1662437 TTCAACGATT
1662447 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1662480 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1662513 T
1 T
1662514 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1662485 original size:13 final size:13
Alignment explanation
Indices: 1662467--1662491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1662457 CATAAAATGT
1662467 TGTATCGATACAA
1 TGTATCGATACAA
1662480 TGTATCGATACA
1 TGTATCGATACA
1662492 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1662717 original size:52 final size:52
Alignment explanation
Indices: 1662589--1662709 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
1662579 CACTGATCTT
* *
1662589 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
*
1662641 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
1662693 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1662710 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
Found at i:1671666 original size:20 final size:20
Alignment explanation
Indices: 1671624--1671677 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1671614 TTCAACAATT
*
1671624 TGTATCGATATAATAAGGCAA
1 TGTATCGATA-CATAAGGCAA
1671645 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAG-GCAA
1671665 TGTATCGATACAT
1 TGTATCGATACAT
1671678 GCCTGAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAGGCAA
Found at i:1671684 original size:20 final size:21
Alignment explanation
Indices: 1671643--1671695 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1671633 ATAATAAGGC
*
1671643 AATGTATCGATACATAAGTG-
1 AATGTATCGATACATAACTGA
**
1671663 AATGTATCGATACATGCCTGA
1 AATGTATCGATACATAACTGA
1671684 AATGTATCGATA
1 AATGTATCGATA
1671696 TAGGATCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (21 bp):
AATGTATCGATACATAACTGA
Found at i:1671743 original size:13 final size:13
Alignment explanation
Indices: 1671725--1671749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1671715 AGAAGGAAAT
1671725 TGTATCGATACAA
1 TGTATCGATACAA
1671738 TGTATCGATACA
1 TGTATCGATACA
1671750 TAGAAATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1682666 original size:6 final size:6
Alignment explanation
Indices: 1682655--1682683 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1682645 GATCGGAGAT
1682655 AGGCAG AGGCAG AGGCAG AGGCAG AGGCA
1 AGGCAG AGGCAG AGGCAG AGGCAG AGGCA
1682684 AAGGGGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.48, T:0.00
Consensus pattern (6 bp):
AGGCAG
Found at i:1683614 original size:25 final size:24
Alignment explanation
Indices: 1683566--1683614 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1683556 TTCGTAGTTA
*
1683566 TTTTTAATATCATATTTTAATTAT
1 TTTTTAATATCATATTATAATTAT
* *
1683590 TTTTTACTATACATATTATATTTAT
1 TTTTTAATAT-CATATTATAATTAT
1683615 CAAGTCTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTTAATATCATATTATAATTAT
Found at i:1683779 original size:16 final size:15
Alignment explanation
Indices: 1683758--1683792 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1683748 TTAAAATAAA
*
1683758 AAAATAAATACTTTTT
1 AAAATAAATA-TTTAT
1683774 AAAATAAATATTTAT
1 AAAATAAATATTTAT
1683789 AAAA
1 AAAA
1683793 GATGCTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATAAATATTTAT
Found at i:1684855 original size:26 final size:26
Alignment explanation
Indices: 1684818--1684882 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
1684808 TATTTTTATT
*
1684818 TTTTATT-TATTTAAAATATT-A-AA
1 TTTTATTAAATTTAAAATATTAATAA
*
1684841 TATTTATATAAATTTTAATATATTAATAA
1 T-TTTAT-TAAA-TTTAAAATATTAATAA
1684870 TTTTATTAAATTT
1 TTTTATTAAATTT
1684883 TAATTCGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
23 1 0.03
24 5 0.15
25 1 0.03
26 4 0.12
27 14 0.41
28 6 0.18
29 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTATTAAATTTAAAATATTAATAA
Found at i:1684886 original size:27 final size:27
Alignment explanation
Indices: 1684827--1684886 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
1684817 TTTTTATTTA
*
1684827 TTTAAAATATTAAATATTTATATAAAT
1 TTTAATATATTAAATATTTATATAAAT
1684854 TTTAATATATT-AATAATTT-TATTAAAT
1 TTTAATATATTAAAT-ATTTATA-TAAAT
1684881 TTTAAT
1 TTTAAT
1684887 TCGTTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTAATATATTAAATATTTATATAAAT
Found at i:1684928 original size:17 final size:18
Alignment explanation
Indices: 1684906--1684943 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1684896 TATTTTTATT
*
1684906 ATTTTATGTTATA-TTTA
1 ATTTTATATTATATTTTA
1684923 ATTTTATATTATATTTTA
1 ATTTTATATTATATTTTA
1684941 ATT
1 ATT
1684944 ATTTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTTTATATTATATTTTA
Found at i:1685589 original size:19 final size:18
Alignment explanation
Indices: 1685545--1685600 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
1685535 AGTTTTATAT
*
1685545 TAATATTTTTATAATTAA
1 TAATAATTTTATAATTAA
* *
1685563 AAAGTAATTTTATTATTCAA
1 TAA-TAATTTTATAATT-AA
*
1685583 TAATAA-TTTAAAATTAA
1 TAATAATTTTATAATTAA
1685600 T
1 T
1685601 TAATTCAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 3 0.10
18 9 0.30
19 14 0.47
20 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TAATAATTTTATAATTAA
Found at i:1692538 original size:18 final size:18
Alignment explanation
Indices: 1692510--1692546 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1692500 CATTGTCTTG
1692510 ATTTTTTAAAAAT-TTAA
1 ATTTTTTAAAAATATTAA
1692527 ATTTTATTAAAAATATTAA
1 ATTTT-TTAAAAATATTAA
1692546 A
1 A
1692547 GAAATGTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTTTAAAAATATTAA
Found at i:1695610 original size:20 final size:20
Alignment explanation
Indices: 1695585--1695642 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1695575 CTACTGCCAA
1695585 GTTCATGTATCGATACAATT
1 GTTCATGTATCGATACAATT
**
1695605 GTTCATGTATAAATACAA-T
1 GTTCATGTATCGATACAATT
**
1695624 GAACATGTATCGATACAAT
1 GTTCATGTATCGATACAAT
1695643 GTATCGATAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (20 bp):
GTTCATGTATCGATACAATT
Found at i:1695646 original size:13 final size:13
Alignment explanation
Indices: 1695628--1695654 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1695618 TACAATGAAC
1695628 ATGTATCGATACA
1 ATGTATCGATACA
1695641 ATGTATCGATACA
1 ATGTATCGATACA
1695654 A
1 A
1695655 AGCATAATGT
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):
ATGTATCGATACA
Found at i:1695695 original size:239 final size:238
Alignment explanation
Indices: 1695254--1695745 Score: 867
Period size: 239 Copynumber: 2.1 Consensus size: 238
1695244 CGTTACAAGC
1695254 AATGTATCGATACAATTCATTAGTATCGATACAATGTATCAATACATTGTACCATGTATCGATAC
1 AATGTATCGATACAATTCATTAGTATCGATACAATGTATCAATACATTGTACCATGTATCGATAC
* **
1695319 AAACAGTAGTAGGGTAGCTACTCCCAAGTTCATGTATCGATACAATTTTTCATGTATCGATACAA
66 AAACAGTAGTAGGGTAGCTACTCCCAAGTTCATGTATCGATACAATTGTTCATGTATAAATACAA
* * *
1695384 CGAACATGTATCGATACAATGTATCAATACAAAGCATAATGTATCGATACATCTGGGTGAGTATG
131 CGAACATGTATCGATACAATGTATCAATACAAAGCATAATGTATCAATACATCTGGGTAAGTATC
1695449 GATATATTCAAGGGTTTTGACCTTTGTAGCCTAAGTCAACCAT
196 GATATATTCAAGGGTTTTGACCTTTGTAGCCTAAGTCAACCAT
* *
1695492 AATGTATCTATACAATTCATTACGTATCGATACAATGTATCGATACATTGTACCATGTATCGATA
1 AATGTATCGATACAATTCATTA-GTATCGATACAATGTATCAATACATTGTACCATGTATCGATA
* *
1695557 CAAACAGTGGTAGGGTAGCTACTGCCAAGTTCATGTATCGATACAATTGTTCATGTATAAATACA
65 CAAACAGTAGTAGGGTAGCTACTCCCAAGTTCATGTATCGATACAATTGTTCATGTATAAATACA
* *
1695622 ATGAACATGTATCGATACAATGTATCGATACAAAGCATAATGTATCAATACATCTGGGTAAGTAT
130 ACGAACATGTATCGATACAATGTATCAATACAAAGCATAATGTATCAATACATCTGGGTAAGTAT
1695687 CGATATATTCAAGGGTTTTGACCTTTGTAGCCTAAGTCAACCAT
195 CGATATATTCAAGGGTTTTGACCTTTGTAGCCTAAGTCAACCAT
1695731 AATGTATCGATACAA
1 AATGTATCGATACAA
1695746 ATACCTATGC
Statistics
Matches: 240, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
238 21 0.09
239 219 0.91
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (238 bp):
AATGTATCGATACAATTCATTAGTATCGATACAATGTATCAATACATTGTACCATGTATCGATAC
AAACAGTAGTAGGGTAGCTACTCCCAAGTTCATGTATCGATACAATTGTTCATGTATAAATACAA
CGAACATGTATCGATACAATGTATCAATACAAAGCATAATGTATCAATACATCTGGGTAAGTATC
GATATATTCAAGGGTTTTGACCTTTGTAGCCTAAGTCAACCAT
Found at i:1696256 original size:24 final size:22
Alignment explanation
Indices: 1696205--1696260 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1696195 AGTTTTCGTT
*
1696205 TTTCTCCCTCTTAATTAAAGAA
1 TTTCTCCCCCTTAATTAAAGAA
* *
1696227 TTTCTCCCCCTTAATTAAGGCA
1 TTTCTCCCCCTTAATTAAAGAA
*
1696249 TTTCTCTCCCTT
1 TTTCTCCCCCTT
1696261 TGTCAAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.30, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTCTCCCCCTTAATTAAAGAA
Found at i:1698222 original size:20 final size:21
Alignment explanation
Indices: 1698191--1698230 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1698181 TATCTAGGTT
1698191 TTTCAGATGTATCGATACATG
1 TTTCAGATGTATCGATACATG
1698212 TTTCA-ATGTATCGATACAT
1 TTTCAGATGTATCGATACAT
1698231 TTTGGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
TTTCAGATGTATCGATACATG
Found at i:1701151 original size:21 final size:21
Alignment explanation
Indices: 1701121--1701161 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1701111 GTCAACCTTG
*
1701121 TGTATTGATACCAGTA-GTATA
1 TGTATCGATA-CAGTACGTATA
1701142 TGTATCGATACAGTACGTAT
1 TGTATCGATACAGTACGTAT
1701162 TTTTACTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (21 bp):
TGTATCGATACAGTACGTATA
Found at i:1702450 original size:13 final size:13
Alignment explanation
Indices: 1702432--1702456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1702422 CATAAAGTGT
1702432 TGTATCGATACAA
1 TGTATCGATACAA
1702445 TGTATCGATACA
1 TGTATCGATACA
1702457 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1702454 original size:33 final size:33
Alignment explanation
Indices: 1702412--1702478 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1702402 TTCAACGATT
1702412 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1702445 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1702478 T
1 T
1702479 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1702581 original size:52 final size:51
Alignment explanation
Indices: 1702518--1702667 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
1702508 CATCACTTAA
** *
1702518 ATGTATCGATACATTGATCTTTGTATCGATACTTGCAGGCAAATTTGCCCAG
1 ATGTATCGATACATT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAG
*
1702570 ATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACATTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAG
*
1702622 ATGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 ATGTATCGATACATTA-TCAATGTATCGATACATGCAGGCAAATTT
1702668 TCATATTTCG
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACATTATCAATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:1711721 original size:30 final size:31
Alignment explanation
Indices: 1711685--1711766 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 31
1711675 ATACCTTTTT
1711685 AAAGTCCACGACTCAGTGGCATTTTGTC-TC
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* *
1711715 AAAGTCCACGACTCAGTGGCATTTTTTCTTT
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* * *
1711746 AAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1711767 CCTTGTTCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 27 0.59
31 19 0.41
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCATTTTGTCTTC
Found at i:1711822 original size:28 final size:28
Alignment explanation
Indices: 1711743--1711990 Score: 167
Period size: 28 Copynumber: 8.1 Consensus size: 28
1711733 GCATTTTTTC
1711743 TTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
1 TTTAAAGCCCACAACTCCGTGGCA-C-----CCT
*
1711777 TTT-AAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACCCT
* **
1711804 TTTAAAGCCCACAATTCCGTGGCACTTT
1 TTTAAAGCCCACAACTCCGTGGCACCCT
*
1711832 TTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
1 TTT-A-----AAGCCCACAACTCCGTGGCACCCT
* * **
1711866 TTTAAAGCCCACAATTCTGTGGCACTTT
1 TTTAAAGCCCACAACTCCGTGGCACCCT
* *
1711894 TTTCATCTTTAAGTCCACAACTCCGTGGCACCCG
1 TTT-A-----AAGCCCACAACTCCGTGGCACCCT
1711928 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCT
1 TTTAAAGCCCACAACTCCGTGGCACC-----CT
*
1711960 TTTAAAGCCCACAACTCCGTGGCACTCT
1 TTTAAAGCCCACAACTCCGTGGCACCCT
1711988 TTT
1 TTT
1711991 TCCCTTTTAA
Statistics
Matches: 172, Mismatches: 23, Indels: 44
0.72 0.10 0.18
Matches are distributed among these distances:
27 27 0.16
28 50 0.29
29 2 0.01
32 5 0.03
33 41 0.24
34 47 0.27
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (28 bp):
TTTAAAGCCCACAACTCCGTGGCACCCT
Found at i:1711850 original size:34 final size:34
Alignment explanation
Indices: 1711682--1712325 Score: 482
Period size: 34 Copynumber: 19.4 Consensus size: 34
1711672 CAAATACCTT
* * * *
1711682 TTTAAAGTCCACGACTCAGTGGCA-TTTTGTCTC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
1711715 ---AAAGTCCACGACTCAGTGGCA--TTTTT-TC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
1711743 TTTAAAGCCCACAACTCCGTGGCACCTTGTTC-C
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* * *
1711776 TTTTAAGTCCACAACTCCGTGGCAC-----CCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
1711804 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TC
* *
1711839 TTT-AAGTCCACAACTCCGTGGCAC-----CCT-
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
1711866 TTTAAAGCCCACAATTCTGTGGCACTTTTTTCATC
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TC
*
1711901 TTT-AAGTCCACAACTCCGTGGCAC------C-C
1 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
1711927 GTTT-AAGCCCACAACTCCGTGGCACCTTTTTCT-
1 -TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
1711960 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
* * *
1711995 TTTTAAGTCCACAACTCCGTGGCA-TCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
* * * *
1712029 TTCCTAAAGCCCACACAAGTCGGTGGCAACCTTCTTCT-
1 TT--TAAAG-CC-CACAACTCCGTGGC-ACTTTTTTCTC
* *
1712067 TTTCAAAGCCCACAACTCCGTGGCACCTTCTTCT-
1 TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
**
1712101 TTTAAAGCCCACAACTTTGTGGCACTCTTTTT-TCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCT-C
*
1712136 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC-C
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
* *
1712171 GTTTAAAGCCCATAACTCCGTGGCACTCTTTTTCCC
1 -TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
1712207 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCT-
1 -TTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTC
*
1712242 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC
* *
1712277 TTTTAAGTCCACAACTCCGTGGCATCTTTTTTC-C
1 TTTAAAGCCCACAACTCCGTGGCA-CTTTTTTCTC
1712311 TTCCTAAAGCCCACA
1 TT--TAAAGCCCACA
1712326 CAAGTCGGTG
Statistics
Matches: 503, Mismatches: 54, Indels: 105
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.00
27 26 0.05
28 45 0.09
29 5 0.01
30 21 0.04
31 18 0.04
32 3 0.01
33 96 0.19
34 107 0.21
35 78 0.16
36 36 0.07
37 47 0.09
38 14 0.03
39 6 0.01
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (34 bp):
TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTC
Found at i:1711862 original size:62 final size:61
Alignment explanation
Indices: 1711743--1712272 Score: 386
Period size: 62 Copynumber: 8.0 Consensus size: 61
1711733 GCATTTTTTC
* *
1711743 TTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCATTTTAAGTCCACAACTCCGTGGCACCCT
* *
1711804 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCAT-TTTAAGTCCACAACTCCGTGGCACCCT
* * * *
1711866 TTTAAAGCCCACAATTCTGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCAT-TTTAAGTCCACAACTCCGTGGCACCCT
*
1711928 TTT-AAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCATTTT-AAGTCCACAACTCCGTGGCA-------
1711991 TCCCT
58 -CCCT
* * * * * * *
1711996 TTT-AAGTCCACAACTCCGTGGCATCTTTTTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAACC
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTT-CATT--TTAAG-TC-CACAACTCCGTGGC-A-C
1712060 TTCTTCT
59 --C--CT
* * **
1712067 TTTCAAAGCCCACAACTCCGTGGCACCTTCTTC-TTTTAAAGCCCACAACTTTGTGGCACTCTTT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCATTTT-AAGTCCACAACTCCGTGGCA--C---
1712131 TTTCCT
59 ---CCT
* * * *
1712137 TTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCATAACTCCGTGGCACTCTTT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTT-CATTTTAAGTCCACAACTCCGTGGCA------
1712202 TTCCCT
58 --CCCT
* * *
1712208 TTTCAAAGCCCACAACTCCGTGGCACTTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACTCT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCATTTT-AAGTCCACAACTCCGTGGCACCCT
1712270 TTT
1 TTT
1712273 TCCCTTTTAA
Statistics
Matches: 396, Mismatches: 35, Indels: 75
0.78 0.07 0.15
Matches are distributed among these distances:
59 3 0.01
60 20 0.05
61 55 0.14
62 96 0.24
67 2 0.01
68 43 0.11
69 8 0.02
70 58 0.15
71 62 0.16
72 10 0.03
73 36 0.09
74 1 0.00
77 2 0.01
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (61 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCATTTTAAGTCCACAACTCCGTGGCACCCT
Found at i:1711939 original size:27 final size:28
Alignment explanation
Indices: 1711747--1711984 Score: 117
Period size: 33 Copynumber: 7.8 Consensus size: 28
1711737 TTTTTCTTTA
*
1711747 AAGCCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGCCCACAACTCCGTGGCACC----T-CGTTT
* *
1711780 AAGTCCACAACTCCGTGGCACC-CTTTT
1 AAGCCCACAACTCCGTGGCACCTCGTTT
*
1711807 AAAGCCCACAATTCCGTGGCACTTTTTTCATC-TTT
1 -AAGCCCACAACTCCGTGGCAC------C-TCGTTT
* *
1711842 AAGTCCACAACTCCGTGGCACC-CTTTT
1 AAGCCCACAACTCCGTGGCACCTCGTTT
* *
1711869 AAAGCCCACAATTCTGTGGCACTTTTTTCATC-TTT
1 -AAGCCCACAACTCCGTGGCAC------C-TCGTTT
*
1711904 AAGTCCACAACTCCGTGGCACC-CGTTT
1 AAGCCCACAACTCCGTGGCACCTCGTTT
*
1711931 AAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1 AAGCCCACAACTCCGTGGCACC----TCGTTT
1711963 AAAGCCCACAACTCCGTGGCAC
1 -AAGCCCACAACTCCGTGGCAC
1711985 TCTTTTTCCC
Statistics
Matches: 166, Mismatches: 13, Indels: 52
0.72 0.06 0.23
Matches are distributed among these distances:
26 2 0.01
27 32 0.19
28 39 0.23
32 4 0.02
33 42 0.25
34 39 0.23
35 6 0.04
36 2 0.01
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.29
Consensus pattern (28 bp):
AAGCCCACAACTCCGTGGCACCTCGTTT
Found at i:1712139 original size:70 final size:70
Alignment explanation
Indices: 1711931--1712325 Score: 507
Period size: 71 Copynumber: 5.6 Consensus size: 70
1711921 GCACCCGTTT
1711931 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1711996 TTT--
66 TTTCA
* * * * * *
1711999 AAGTCCACAACTCCGTGGCATCTTTTTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAAC-CTTC
1 AAGCCCACAACTCCGTGGCACCTTTTT--CTT-TTAAAG-CC-CACAACTCCGTGGC-ACTCTTT
1712063 TT--CTTTTCA
60 TTCCCTTTTCA
* ** *
1712072 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1712137 TTTCA
66 TTTCA
* *
1712142 AAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCATAACTCCGTGGCACTCTTTTTCCC
1 AAGCCCACAACTCCGTGGCACCTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1712207 TTTTCA
65 TTTTCA
*
1712213 AAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1712278 TTT--
66 TTTCA
* * *
1712281 AAGTCCACAACTCCGTGGCATCTTTTTTCCTTCCTAAAGCCCACA
1 AAGCCCACAACTCCGTGGCA-CCTTTTT-CTT-TTAAAGCCCACA
1712326 CAAGTCGGTG
Statistics
Matches: 287, Mismatches: 25, Indels: 27
0.85 0.07 0.08
Matches are distributed among these distances:
67 2 0.01
68 60 0.21
69 9 0.03
70 83 0.29
71 88 0.31
72 2 0.01
73 41 0.14
74 2 0.01
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (70 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
TTTCA
Found at i:1712178 original size:141 final size:139
Alignment explanation
Indices: 1711931--1712347 Score: 608
Period size: 141 Copynumber: 3.0 Consensus size: 139
1711921 GCACCCGTTT
1711931 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
*
1711996 TTTAAGTCCACAACTCCGTGGCATCTTTTTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAACCT
66 TTTAAGTCCACAACTCCGTGGCACCTTTTT-CCTT-CTAAAGCCCACACAAGTCGGTGGCAACCT
1712061 TCTTCTTTTCA
129 TCTTCTTTTCA
* ** *
1712072 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
* * * *
1712137 TTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCGTT-TAAAG-CC-CATAACTCCGTGGC-ACT
66 TTT--AAGTCCACAACTCCGTGGCACCTTTTTCC-TTCTAAAGCCCACACAAGTCGGTGGCAAC-
*
1712198 CTTTTTCCCTTTTCA
127 CTTCTT--CTTTTCA
*
1712213 AAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
*
1712278 TTTAAGTCCACAACTCCGTGGCATCTTTTTTCCTTCCTAAAGCCCACACAAGTCGGTGGCAACCT
66 TTTAAGTCCACAACTCCGTGGCA-CCTTTTTCCTT-CTAAAGCCCACACAAGTCGGTGGCAACCT
1712343 TCTTC
129 TCTTC
1712348 CAAAGCCCAC
Statistics
Matches: 243, Mismatches: 21, Indels: 24
0.84 0.07 0.08
Matches are distributed among these distances:
138 2 0.01
139 37 0.15
140 10 0.04
141 145 0.60
142 4 0.02
143 43 0.18
144 2 0.01
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (139 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
TTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTCTAAAGCCCACACAAGTCGGTGGCAACCTTC
TTCTTTTCA
Found at i:1712346 original size:104 final size:102
Alignment explanation
Indices: 1711866--1712325 Score: 389
Period size: 104 Copynumber: 4.5 Consensus size: 102
1711856 GTGGCACCCT
* * * *
1711866 TTTAAAGCCCACAATTCTGTGGCACT-TTTTTCATCTT-T--AAGTCCACAACTCCGTGGCAC-C
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTCTCAAAGCCCACAACTCCGTGGCACTC
* *
1711926 --CGTTT-AAGCCCACAACTCCGTGGCACCTTTTT-CT
65 TTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCC
* *
1711960 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT-T-TAAGTCCACAACTCCGTGGCATCTT
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTCAAAGCCCACAACTCCGTGGCA-C-T
* * * * * *
1712023 TTTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAACCTTCTT-CT
64 CTT--CTT-TTAAAG-CC-CACAACTCCGTGGC-ACCTTTTTCCC
* * **
1712067 TTTCAAAGCCCACAACTCCGTGGCAC-CTTCTT--CTT-TTAAAGCCCACAACTTTGTGGCACTC
1 TTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTCAAAGCCCACAACTCCGTGGCACTC
*
1712128 TTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCG
65 ----TT-CTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCC
* *
1712172 TTTAAAGCCCATAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTT
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTCAAAGCCCACAACTCCGTGGCAC--T
*
1712237 TTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
64 CTTCTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCC
* * *
1712277 TTTTAAGTCCACAACTCCGTGGCA-TCTTTTTTCCTTC-CTAAAGCCCACA
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTC-AAAGCCCACA
1712326 CAAGTCGGTG
Statistics
Matches: 304, Mismatches: 32, Indels: 50
0.79 0.08 0.13
Matches are distributed among these distances:
94 28 0.09
95 26 0.09
96 1 0.00
102 2 0.01
103 2 0.01
104 75 0.25
105 62 0.20
106 34 0.11
107 28 0.09
108 45 0.15
110 1 0.00
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (102 bp):
TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTCTCAAAGCCCACAACTCCGTGGCACTCT
TCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCC
Found at i:1712353 original size:33 final size:34
Alignment explanation
Indices: 1712310--1712374 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
1712300 ATCTTTTTTC
1712310 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1712344 CTTCC-AAAGCCCACACAAGTCGGTGGCAACC
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC
1712375 CCTCTAAGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.28, C:0.37, G:0.18, T:0.17
Consensus pattern (34 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
Found at i:1712497 original size:49 final size:49
Alignment explanation
Indices: 1712379--1712747 Score: 429
Period size: 49 Copynumber: 7.7 Consensus size: 49
1712369 GCAACCCCTC
* *
1712379 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
1712431 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1712480 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1712529 GAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1712572 TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1712621 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1712664 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTT
* *
1712716 TAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCAC
1712748 GTTGACATCC
Statistics
Matches: 273, Mismatches: 29, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
43 76 0.28
45 2 0.01
47 1 0.00
49 122 0.45
50 3 0.01
52 69 0.25
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:1712591 original size:43 final size:44
Alignment explanation
Indices: 1712525--1712703 Score: 227
Period size: 43 Copynumber: 4.0 Consensus size: 44
1712515 GGCATCTTCA
* * * *
1712525 TCTTGAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* *
1712569 -CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C
* *
1712616 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 -TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1712661 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1712704 ATTTTCCATC
Statistics
Matches: 117, Mismatches: 12, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
43 77 0.66
45 1 0.01
47 1 0.01
49 38 0.32
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (44 bp):
TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:1712598 original size:92 final size:92
Alignment explanation
Indices: 1712477--1712747 Score: 461
Period size: 92 Copynumber: 2.9 Consensus size: 92
1712467 GCACCTTCAT
*
1712477 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
1712542 GCTGGCCTTGACTCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
1712569 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1712634 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
1712661 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAAT
1712726 GTAGCTGGCCTTGAATCAGCAC
63 GTAGCTGGCCTTGAATCAGCAC
1712748 GTTGACATCC
Statistics
Matches: 169, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
92 127 0.75
94 5 0.03
95 37 0.22
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1712953 original size:173 final size:176
Alignment explanation
Indices: 1712661--1713041 Score: 666
Period size: 173 Copynumber: 2.2 Consensus size: 176
1712651 ACATTGGCAC
*
1712661 CTTTAAGTCCAATATAGCTGGCCTTGAAT---CAGCATATTGGCACATTTTCCATCTTTAAGTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAGCATATTGG-ACATCTTCCATCTTTAAGTTC
1712723 AATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTG
65 AATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTG
1712788 GCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
130 GCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
*
1712835 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCAGCATATTGG-CATCTT-CATCTTTAAGTTCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAGCATATTGGACATCTTCCATCTTTAAGTTCA
*
1712897 ATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGG
66 ATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGG
*
1712962 CCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
131 CCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
*
1713008 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCA
1713042 TATTAGCACC
Statistics
Matches: 198, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
173 150 0.76
174 37 0.19
176 11 0.06
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (176 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAGCATATTGGACATCTTCCATCTTTAAGTTCA
ATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGG
CCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
Found at i:1713844 original size:33 final size:33
Alignment explanation
Indices: 1713807--1713873 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1713797 TTCAACGATT
1713807 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1713840 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1713873 T
1 T
1713874 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1713845 original size:13 final size:13
Alignment explanation
Indices: 1713827--1713851 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1713817 CATAAAATGT
1713827 TGTATCGATACAA
1 TGTATCGATACAA
1713840 TGTATCGATACA
1 TGTATCGATACA
1713852 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1713935 original size:13 final size:13
Alignment explanation
Indices: 1713917--1713941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1713907 ATTACTCACA
1713917 TGTATCGATACAT
1 TGTATCGATACAT
1713930 TGTATCGATACA
1 TGTATCGATACA
1713942 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1714078 original size:52 final size:52
Alignment explanation
Indices: 1713950--1714070 Score: 233
Period size: 52 Copynumber: 2.3 Consensus size: 52
1713940 CACTGATCTT
1713950 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACAATATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACAATATTAAA
*
1714002 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACAATATTAAA
1714054 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1714071 ATAAATTTTC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACAATATTAAA
Found at i:1714662 original size:15 final size:15
Alignment explanation
Indices: 1714642--1714670 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1714632 GCTTGTTTAC
1714642 AACCCCAAAGAAGGA
1 AACCCCAAAGAAGGA
1714657 AACCCCAAAGAAGG
1 AACCCCAAAGAAGG
1714671 GTTAAACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.21, T:0.00
Consensus pattern (15 bp):
AACCCCAAAGAAGGA
Found at i:1722315 original size:1 final size:1
Alignment explanation
Indices: 1722309--1722390 Score: 83
Period size: 1 Copynumber: 82.0 Consensus size: 1
1722299 CGTCCTCCAC
* * * * * * *
1722309 AAAAAAAAACAAAAAAAAAAAAAACAAAACAAAACAAAAAAAAACAAAAAAAAAACAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1722374 AAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAA
1722391 GGGGTCCGGG
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.89, C:0.10, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:1722322 original size:10 final size:10
Alignment explanation
Indices: 1722309--1722390 Score: 98
Period size: 10 Copynumber: 8.4 Consensus size: 10
1722299 CGTCCTCCAC
1722309 AAAAAA-AAA
1 AAAAAACAAA
*
1722318 CAAAAA-AAA
1 AAAAAACAAA
1722327 AAAAAACAAA
1 AAAAAACAAA
*
1722337 ACAAAACAAA
1 AAAAAACAAA
1722347 AAAAAACAAAA
1 AAAAAAC-AAA
1722358 AAAAAACAAA
1 AAAAAACAAA
*
1722368 ATAAAA-AAA
1 AAAAAACAAA
*
1722377 CAAAAACAAA
1 AAAAAACAAA
1722387 AAAA
1 AAAA
1722391 GGGGTCCGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
9 20 0.32
10 32 0.52
11 10 0.16
ACGTcount: A:0.89, C:0.10, G:0.00, T:0.01
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:1722329 original size:15 final size:15
Alignment explanation
Indices: 1722307--1722390 Score: 100
Period size: 15 Copynumber: 5.6 Consensus size: 15
1722297 GGCGTCCTCC
1722307 ACAAAAAAAAACAAAA
1 ACAAAAAAAAA-AAAA
*
1722323 A-AAAAAAAAACAAA
1 ACAAAAAAAAAAAAA
*
1722337 ACAAAACAAAAAAAA
1 ACAAAAAAAAAAAAA
1722352 ACAAAAAAAAAACAAA
1 ACAAAAAAAAAA-AAA
* *
1722368 A-TAAAAAAACAAAA
1 ACAAAAAAAAAAAAA
1722382 ACAAAAAAA
1 ACAAAAAAA
1722391 GGGGTCCGGG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
14 8 0.14
15 45 0.78
16 5 0.09
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (15 bp):
ACAAAAAAAAAAAAA
Found at i:1722353 original size:35 final size:34
Alignment explanation
Indices: 1722307--1722387 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 34
1722297 GGCGTCCTCC
1722307 ACAAAAAAAAACAAAAAAAAAA-AAAACAAAACAAA
1 ACAAAAAAAAACAAAAAAAAAACAAAA-AAAA-AAA
*
1722342 ACAAAAAAAAACAAAAAAAAAACAAAATAAAAAA
1 ACAAAAAAAAACAAAAAAAAAACAAAAAAAAAAA
1722376 ACAAAAACAAAA
1 ACAAAAA-AAAA
1722388 AAAGGGGTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
34 10 0.23
35 29 0.67
36 4 0.09
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (34 bp):
ACAAAAAAAAACAAAAAAAAAACAAAAAAAAAAA
Found at i:1722358 original size:30 final size:29
Alignment explanation
Indices: 1722307--1722390 Score: 114
Period size: 31 Copynumber: 2.8 Consensus size: 29
1722297 GGCGTCCTCC
*
1722307 ACAAAAAAAAACAAAAAAAAAAAAAACAAA
1 ACAAAAAAAAA-AAAACAAAAAAAAACAAA
1722337 ACAAAACAAAAAAAAACAAAAAAAAAACAAA
1 ACAAAA-AAAAAAAAAC-AAAAAAAAACAAA
* *
1722368 ATAAAAAAACAAAAACAAAAAAA
1 ACAAAAAAAAAAAAACAAAAAAA
1722391 GGGGTCCGGG
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
29 7 0.14
30 19 0.39
31 23 0.47
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (29 bp):
ACAAAAAAAAAAAAACAAAAAAAAACAAA
Found at i:1723888 original size:30 final size:29
Alignment explanation
Indices: 1723831--1724272 Score: 320
Period size: 30 Copynumber: 14.7 Consensus size: 29
1723821 TCACCCTTCA
1723831 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1723860 AAAGCCCACAAGTCAGTGGCATCTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATC-TTTTTC
* * * *
1723890 AAAAGCCCGCAAGTTAGTGGCACCCTTTTTA
1 -AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
1723921 AAAGCCCACAAATCGGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
1723948 AAAGCCCATAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* *
1723978 GAAGCCCACAAGTCGGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1724007 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* *
1724037 GAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1724066 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * *
1724096 TTTTGTAAGCTCACAACTCTA-TAGCACTTTTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCA-TCTTTTTC
* * * *
1724131 TTTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ----AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
1724164 AAAAGCCCACAAGTTAGTGGCATCTCTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCT-TTTTC
* * *
1724195 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
1724224 AAAGCCCACAAGTTAGTGGCAATC--TTTA
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTTC
1724252 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
1724273 ACCTTCAAAA
Statistics
Matches: 336, Mismatches: 60, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
27 22 0.07
28 43 0.13
29 77 0.23
30 95 0.28
31 51 0.15
32 1 0.00
33 6 0.02
34 18 0.05
35 23 0.07
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1724032 original size:59 final size:59
Alignment explanation
Indices: 1723831--1724292 Score: 386
Period size: 59 Copynumber: 7.7 Consensus size: 59
1723821 TCACCCTTCA
* *
1723831 AAAGCCCACAAGTCAGTGGCATCTTTTTC-AAAGCCCACAAGTCAGTGGCATCTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATC-TTTTTC
* * * * * * *
1723890 AAAAGCCCGCAAGTTAGTGGCACCCTTTTTAAAAGCCCACAAATCGGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
* * ** *
1723948 AAAGCCCATAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
* ** *
1724007 AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * * ** * * * *
1724066 AAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTCACAACTCTA-TAGCACTTTTTTT
1 AAAGCCCACAAGTCAGTGGCAC-CCTTTTC----AAAAGCCCACAAGTC-AGTGGCA-TCTTTTT
1724130 C
59 C
* * *
1724131 TTTTTAAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTTAGTGGCATCTCTTTTC
1 ----AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCT-TTTTC
* * *
1724195 AAAAGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTTAGTGGCAATC--TTTA
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGC-ATCTTTTTC
* *
1724252 AAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCACACAAGT
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGT
1724293 TGATGCAATC
Statistics
Matches: 332, Mismatches: 52, Indels: 40
0.78 0.12 0.09
Matches are distributed among these distances:
55 2 0.01
56 37 0.11
57 47 0.14
58 3 0.01
59 99 0.30
60 36 0.11
61 41 0.12
63 3 0.01
64 34 0.10
65 7 0.02
68 6 0.02
69 17 0.05
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (59 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1724112 original size:35 final size:34
Alignment explanation
Indices: 1724071--1724145 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
1724061 TTTCCAAAGT
* *
1724071 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCATAGCACTCTTTTTCTTTT-TAAGC
* * *
1724106 TCACAACTCTATAGCACTTTTTTTCTTTTTAAGC
1 CCACAACTCCATAGCACTCTTTTTCTTTTTAAGC
1724140 CCACAA
1 CCACAA
1724146 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.39
Consensus pattern (34 bp):
CCACAACTCCATAGCACTCTTTTTCTTTTTAAGC
Found at i:1724276 original size:56 final size:57
Alignment explanation
Indices: 1724136--1724318 Score: 246
Period size: 56 Copynumber: 3.2 Consensus size: 57
1724126 TTTTCTTTTT
* * *
1724136 AAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTTAGTGGCATCTCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTTAGTGGCA-ATCTTTT-AA
1724197 AAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAGTGGCAATC-TTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAGTGGCAATCTTTTAA
* *
1724253 AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCACACAAGTT-GAT-GCAATCCTTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAG-TGGCAAT-CTTTTAA
1724310 AAGCCCACA
1 AAGCCCACA
1724319 CAAGTTGGTG
Statistics
Matches: 114, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
55 6 0.05
56 43 0.38
57 17 0.15
58 2 0.02
59 22 0.19
60 3 0.03
61 21 0.18
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (57 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAGTGGCAATCTTTTAA
Found at i:1724409 original size:52 final size:50
Alignment explanation
Indices: 1724340--1724529 Score: 223
Period size: 52 Copynumber: 3.9 Consensus size: 50
1724330 CGTCTTCTTC
* *
1724340 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT-GTACC-T
* *
1724392 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC----T-CC-
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTACCT
* *
1724436 -AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGT-A-CCT
* *
1724487 TAAGTCCTATATCGCTGGCCTTGAATCAACACATTGGCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
1724530 CATCTTTAAC
Statistics
Matches: 117, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
43 36 0.31
46 2 0.02
47 2 0.02
50 2 0.02
52 75 0.64
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (50 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTACCT
Found at i:1724454 original size:43 final size:44
Alignment explanation
Indices: 1724392--1724528 Score: 141
Period size: 43 Copynumber: 3.0 Consensus size: 44
1724382 TTGGTACCTT
* *
1724392 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCC
* *
1724436 -AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC-AC-----C-TCC
* *
1724486 TTAAGTCCTATATCGCTGGCCTTGAATCAACACATTGGCACCT
1 -TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT
1724529 TCATCTTTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
43 34 0.45
44 1 0.01
45 1 0.01
46 1 0.01
49 1 0.01
50 3 0.04
51 1 0.01
52 34 0.45
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (44 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCC
Found at i:1724504 original size:95 final size:95
Alignment explanation
Indices: 1724341--1724528 Score: 308
Period size: 95 Copynumber: 2.0 Consensus size: 95
1724331 GTCTTCTTCT
*
1724341 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTTTAAGTCCAATGTAG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTTTAAGTCCAATATAG
*
1724406 CTGGCCTTGAATCAGCACATTGGCACCTCC
66 CTGGCCTTGAATCAACACATTGGCACCTCC
*
1724436 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTT-GTCATCC-TTAAGTCCTATAT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGT-A-CCTTTAAGTCCAATAT
*
1724499 CGCTGGCCTTGAATCAACACATTGGCACCT
64 AGCTGGCCTTGAATCAACACATTGGCACCT
1724529 TCATCTTTAA
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
94 2 0.02
95 83 0.95
96 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (95 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTTTAAGTCCAATATAG
CTGGCCTTGAATCAACACATTGGCACCTCC
Found at i:1725422 original size:20 final size:20
Alignment explanation
Indices: 1725378--1725435 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1725368 ATTTCAACGA
***
1725378 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
1725398 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
1725418 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
1725436 AAGCTACTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:1725492 original size:13 final size:13
Alignment explanation
Indices: 1725474--1725498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1725464 ATCACTTAAA
1725474 TGTATCGATACAT
1 TGTATCGATACAT
1725487 TGTATCGATACA
1 TGTATCGATACA
1725499 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1725563 original size:52 final size:52
Alignment explanation
Indices: 1725507--1725616 Score: 184
Period size: 52 Copynumber: 2.1 Consensus size: 52
1725497 CACTGATCTT
* *
1725507 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
1725559 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1725611 TGTATC
1 TGTATC
1725617 TTTTGACTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1727048 original size:21 final size:21
Alignment explanation
Indices: 1727024--1727066 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1727014 AAGTCAACCT
*
1727024 TATGTATTGATACCAGTA-GTA
1 TATGTATCGATA-CAGTACGTA
1727045 TATGTATCGATACAGTACGTA
1 TATGTATCGATACAGTACGTA
1727066 T
1 T
1727067 TTTTACTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (21 bp):
TATGTATCGATACAGTACGTA
Found at i:1728359 original size:20 final size:20
Alignment explanation
Indices: 1728315--1728372 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1728305 ATTTCAACGA
***
1728315 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
1728335 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
1728355 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
1728373 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:1728429 original size:13 final size:13
Alignment explanation
Indices: 1728411--1728435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1728401 ATCACTTAAA
1728411 TGTATCGATACAT
1 TGTATCGATACAT
1728424 TGTATCGATACA
1 TGTATCGATACA
1728436 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1728500 original size:52 final size:52
Alignment explanation
Indices: 1728444--1728572 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1728434 CACTGATCTT
*
1728444 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
1728496 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1728548 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1728573 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1739494 original size:301 final size:301
Alignment explanation
Indices: 1738952--1739514 Score: 1108
Period size: 301 Copynumber: 1.9 Consensus size: 301
1738942 GAACTTTGTG
1738952 CCAATTGATCTCTTACGATTAGTTGAGCAAGAGGAAAAGCAAATCATGCCCCACAAAGATCTGAC
1 CCAATTGATCTCTTACGATTAGTTGAGCAAGAGGAAAAGCAAATCATGCCCCACAAAGATCTGAC
1739017 AGAAGTGATAAACCTGGGTAGTGAAGAAGATCGAAAAGAGGTTAAGATTGGAACCTCAATAAAGT
66 AGAAGTGATAAACCTGGGTAGTGAAGAAGATCGAAAAGAGGTTAAGATTGGAACCTCAATAAAGT
*
1739082 CAACCACTAGGACCGCATTGATAAACCTGCTTCAGAAATATCAGGACGTTTTCGCTTGGTCATAT
131 CAACCACTAGGACCGCATTGATAAACCTGCTTCAGAAATATCAGGACATTTTCGCTTGGTCATAT
1739147 CAAGACATGTCGAGACTGGATGCTGACATAGTGGTTCACAAGCTTCCCATCAAGCTTGGATGCAA
196 CAAGACATGTCGAGACTGGATGCTGACATAGTGGTTCACAAGCTTCCCATCAAGCTTGGATGCAA
1739212 ACTTGATCTCTTACGATTAGTTGAGCAATTGGTCATATCAA
261 ACTTGATCTCTTACGATTAGTTGAGCAATTGGTCATATCAA
1739253 CCAATTGATCTCTTACGATTAGTTGAGCAAGAGGAAAAGCAAATCATGCCCCACAAAGATCTGAC
1 CCAATTGATCTCTTACGATTAGTTGAGCAAGAGGAAAAGCAAATCATGCCCCACAAAGATCTGAC
1739318 AGAAGTGATAAACCTGGGTAGTGAAGAAGATCGAAAAGAGGTTAAGATTGGAACCTCAATAAAGT
66 AGAAGTGATAAACCTGGGTAGTGAAGAAGATCGAAAAGAGGTTAAGATTGGAACCTCAATAAAGT
1739383 CAACCACTAGGACCGCATTGATAAACCTGCTTCAGAAATATCAGGACATTTTCGCTTGGTCATAT
131 CAACCACTAGGACCGCATTGATAAACCTGCTTCAGAAATATCAGGACATTTTCGCTTGGTCATAT
*
1739448 CAAGACATGTCGGGACTGGATGCTGACATAGTGGTTCACAAGCTTCCCATCAAGCTTGGATGCAA
196 CAAGACATGTCGAGACTGGATGCTGACATAGTGGTTCACAAGCTTCCCATCAAGCTTGGATGCAA
1739513 AC
261 AC
1739515 CAATCCAGCA
Statistics
Matches: 260, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
301 260 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (301 bp):
CCAATTGATCTCTTACGATTAGTTGAGCAAGAGGAAAAGCAAATCATGCCCCACAAAGATCTGAC
AGAAGTGATAAACCTGGGTAGTGAAGAAGATCGAAAAGAGGTTAAGATTGGAACCTCAATAAAGT
CAACCACTAGGACCGCATTGATAAACCTGCTTCAGAAATATCAGGACATTTTCGCTTGGTCATAT
CAAGACATGTCGAGACTGGATGCTGACATAGTGGTTCACAAGCTTCCCATCAAGCTTGGATGCAA
ACTTGATCTCTTACGATTAGTTGAGCAATTGGTCATATCAA
Found at i:1742634 original size:1 final size:1
Alignment explanation
Indices: 1742628--1742698 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
1742618 CGTCCTCCAC
* * ** * * * * * *
1742628 AAAAAAAAACAAAACAAAAAAAAACTAAACAAAACAAAAAAAAACAAAACAAAAAAACAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1742693 AAAAAA
1 AAAAAA
1742699 GGGGTCCGGA
Statistics
Matches: 51, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.86, C:0.13, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:1742641 original size:5 final size:5
Alignment explanation
Indices: 1742626--1742695 Score: 81
Period size: 5 Copynumber: 14.2 Consensus size: 5
1742616 GGCGTCCTCC
* * * *
1742626 ACAAA AAAAA ACAAA ACAAA AAAAA ACTAA ACAAA ACAAA AAAAA ACAAA
1 ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA
1742676 AC-AA A-AAA ACAAAA ACAAA A
1 ACAAA ACAAA AC-AAA ACAAA A
1742696 AAAGGGGTCC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
4 6 0.11
5 43 0.80
6 5 0.09
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.01
Consensus pattern (5 bp):
ACAAA
Found at i:1744195 original size:30 final size:29
Alignment explanation
Indices: 1744138--1744579 Score: 293
Period size: 30 Copynumber: 14.7 Consensus size: 29
1744128 TCACCCTTCA
1744138 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1744167 AAAGCCCACAAGTCAGTGGCATCTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATC-TTTTTC
* * * *
1744197 AAAAGCCCGCAAGTTAGTGGCACCCTTTTTA
1 -AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
1744228 AAAGCCCACAAATCGGTGGCAAC--GTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
1744255 AAAGCCCATAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* *
1744285 GAAGCCCACAAGTCGGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1744314 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
1744344 GAAGCCCATAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1744373 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * *
1744403 TTTTGTAAGCTCACAACTCTA-TAGCACTTTTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCA-TCTTTTTC
* * * *
1744438 TTTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ----AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
1744471 AAAAGCCCACAAGTTAGTGGCATCTCTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCT-TTTTC
* * * *
1744502 AAAAGCCCACAAGTCAATGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
1744531 AAAGCCCACAAGTCAGTGGCAATC--TTTA
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTTC
*
1744559 AAAGCCCACAAGTTAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
1744580 ACCTTCAAAA
Statistics
Matches: 332, Mismatches: 64, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
27 22 0.07
28 43 0.13
29 76 0.23
30 93 0.28
31 50 0.15
32 1 0.00
33 6 0.02
34 18 0.05
35 23 0.07
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1744339 original size:59 final size:59
Alignment explanation
Indices: 1744138--1744599 Score: 359
Period size: 59 Copynumber: 7.7 Consensus size: 59
1744128 TCACCCTTCA
* *
1744138 AAAGCCCACAAGTCAGTGGCATCTTTTTC-AAAGCCCACAAGTCAGTGGCATCTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATC-TTTTTC
* * * * * * *
1744197 AAAAGCCCGCAAGTTAGTGGCACCCTTTTTAAAAGCCCACAAATCGGTGGCAAC--GTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
* * ** *
1744255 AAAGCCCATAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
* ** * * *
1744314 AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCATAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * * ** * * * *
1744373 AAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTCACAACTCTA-TAGCACTTTTTTT
1 AAAGCCCACAAGTCAGTGGCAC-CCTTTTC----AAAAGCCCACAAGTC-AGTGGCA-TCTTTTT
1744437 C
59 C
* * *
1744438 TTTTTAAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTTAGTGGCATCTCTTTTC
1 ----AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCT-TTTTC
* * *
1744502 AAAAGCCCACAAGTCAATGGCAACC-TTT-AAAAGCCCACAAGTCAGTGGCAATC--TTTA
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGC-ATCTTTTTC
* * *
1744559 AAAGCCCACAAGTTAGTGGCAACC--TTCAAAAGCACACAAGT
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGT
1744600 TGATGCAATC
Statistics
Matches: 326, Mismatches: 58, Indels: 40
0.77 0.14 0.09
Matches are distributed among these distances:
55 2 0.01
56 35 0.11
57 47 0.14
58 3 0.01
59 98 0.30
60 36 0.11
61 40 0.12
63 3 0.01
64 33 0.10
65 6 0.02
68 6 0.02
69 17 0.05
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (59 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1744419 original size:35 final size:34
Alignment explanation
Indices: 1744378--1744452 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
1744368 TTTCCAAAGT
* *
1744378 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCATAGCACTCTTTTTCTTTT-TAAGC
* * *
1744413 TCACAACTCTATAGCACTTTTTTTCTTTTTAAGC
1 CCACAACTCCATAGCACTCTTTTTCTTTTTAAGC
1744447 CCACAA
1 CCACAA
1744453 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.39
Consensus pattern (34 bp):
CCACAACTCCATAGCACTCTTTTTCTTTTTAAGC
Found at i:1744542 original size:28 final size:29
Alignment explanation
Indices: 1744443--1744625 Score: 214
Period size: 28 Copynumber: 6.3 Consensus size: 29
1744433 TTTTCTTTTT
*
1744443 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGTGGCAACCTTTT-AA
*
1744473 AAGCCCACAAGTTAGTGGCATCTCTTTTCAA
1 AAGCCCACAAGTTAGTGGCAAC-CTTTT-AA
* *
1744504 AAGCCCACAAGTCAATGGCAACC-TTTAA
1 AAGCCCACAAGTTAGTGGCAACCTTTTAA
* *
1744532 AAGCCCACAAGTCAGTGGCAATC-TTTAA
1 AAGCCCACAAGTTAGTGGCAACCTTTTAA
*
1744560 AAGCCCACAAGTTAGTGGCAACC-TTCAA
1 AAGCCCACAAGTTAGTGGCAACCTTTTAA
*
1744588 AAGCACACAAGTT-GAT-GCAATCCTTTTAA
1 AAGCCCACAAGTTAG-TGGCAA-CCTTTTAA
1744617 AAGCCCACA
1 AAGCCCACA
1744626 CAAGTTGGTG
Statistics
Matches: 137, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
27 5 0.04
28 68 0.50
29 15 0.11
30 22 0.16
31 27 0.20
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (29 bp):
AAGCCCACAAGTTAGTGGCAACCTTTTAA
Found at i:1744637 original size:87 final size:88
Alignment explanation
Indices: 1744443--1744625 Score: 241
Period size: 87 Copynumber: 2.1 Consensus size: 88
1744433 TTTTCTTTTT
* *
1744443 AAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTTAGTGGCATCTCTTTTCAAAAGC
1 AAGCCCACAAGTTAGTGGCAACCTTTTCAAAAGCCCACAAGTTAGTGGCAACTC-TTTCAAAAGC
*
1744508 CCACAAGTCAATGGCAACCTTTAA
65 ACACAAGTCAATGGCAACCTTTAA
* *
1744532 AAGCCCACAAGTCAGTGGCAATC-TTT-AAAAGCCCACAAGTTAGTGGCAAC-C-TTCAAAAGCA
1 AAGCCCACAAGTTAGTGGCAACCTTTTCAAAAGCCCACAAGTTAGTGGCAACTCTTTCAAAAGCA
**
1744593 CACAAGTTGAT-GCAATCCTTTTAA
66 CACAAGTCAATGGCAA-CC-TTTAA
1744617 AAGCCCACA
1 AAGCCCACA
1744626 CAAGTTGGTG
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
83 4 0.05
84 20 0.24
85 14 0.16
86 1 0.01
87 23 0.27
88 3 0.04
89 20 0.24
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (88 bp):
AAGCCCACAAGTTAGTGGCAACCTTTTCAAAAGCCCACAAGTTAGTGGCAACTCTTTCAAAAGCA
CACAAGTCAATGGCAACCTTTAA
Found at i:1744709 original size:43 final size:44
Alignment explanation
Indices: 1744646--1744783 Score: 170
Period size: 43 Copynumber: 3.0 Consensus size: 44
1744636 GCGTCTTCTT
1744646 CTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTC
1 CTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTC
* *
1744690 C-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
1 CTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC-AC-----C-TC
*
1744740 CTTAAGTCCTATATCGCTGGCCTTGAATCAGCACATTGGCACCT
1 C-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT
1744784 TCATCTTTAA
Statistics
Matches: 80, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
43 36 0.45
44 2 0.03
45 1 0.01
46 1 0.01
49 1 0.01
50 3 0.04
51 1 0.01
52 35 0.44
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (44 bp):
CTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTC
Found at i:1745688 original size:20 final size:20
Alignment explanation
Indices: 1745632--1745709 Score: 113
Period size: 20 Copynumber: 4.0 Consensus size: 20
1745622 ATTTCAACGA
***
1745632 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
1745652 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
1745672 TTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
1745692 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
1745710 AAGCTACTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 4 0.08
20 49 0.92
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:1745766 original size:13 final size:13
Alignment explanation
Indices: 1745748--1745772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1745738 ATCACTTAAA
1745748 TGTATCGATACAT
1 TGTATCGATACAT
1745761 TGTATCGATACA
1 TGTATCGATACA
1745773 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1745837 original size:52 final size:52
Alignment explanation
Indices: 1745781--1745890 Score: 202
Period size: 52 Copynumber: 2.1 Consensus size: 52
1745771 CACTGATCTT
*
1745781 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1745833 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1745885 TGTATC
1 TGTATC
1745891 TTTTGACTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1747330 original size:21 final size:21
Alignment explanation
Indices: 1747300--1747340 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1747290 GTCAACCTTG
*
1747300 TGTATTGATACTAGTA-GTATA
1 TGTATCGATAC-AGTACGTATA
1747321 TGTATCGATACAGTACGTAT
1 TGTATCGATACAGTACGTAT
1747341 TTTTACTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (21 bp):
TGTATCGATACAGTACGTATA
Found at i:1748634 original size:20 final size:20
Alignment explanation
Indices: 1748590--1748647 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1748580 ATTTCAACGA
***
1748590 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
1748610 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
1748630 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
1748648 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:1748748 original size:52 final size:51
Alignment explanation
Indices: 1748685--1748834 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
1748675 CATCACTTAA
** *
1748685 ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCTAG
1 ATGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAG
* *
1748737 ATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAG
1748789 ATGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 ATGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
1748835 TCATATTTCG
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (51 bp):
ATGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:1753571 original size:21 final size:21
Alignment explanation
Indices: 1753546--1753590 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1753536 CACTTGTAAC
* *
1753546 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATGTTCTCCTCTAAT
**
1753567 TCATTTATGTTCTTTTCTAAT
1 TCATTTATGTTCTCCTCTAAT
1753588 TCA
1 TCA
1753591 CTTAATTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.58
Consensus pattern (21 bp):
TCATTTATGTTCTCCTCTAAT
Found at i:1753600 original size:21 final size:21
Alignment explanation
Indices: 1753561--1753604 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1753551 TCTTTTCTCC
*
1753561 TCTAATTCATTTATGTTCTTT
1 TCTAATTCATTAATGTTCTTT
1753582 TCTAATTCACTTAAT-TTCTTT
1 TCTAATTCA-TTAATGTTCTTT
1753603 TC
1 TC
1753605 AAGAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.59
Consensus pattern (21 bp):
TCTAATTCATTAATGTTCTTT
Found at i:1755191 original size:37 final size:31
Alignment explanation
Indices: 1755133--1755223 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 31
1755123 AATTGTTTAC
* *
1755133 CTTT-AAGGCTAAGGTATAACCTTACACCCCTAT
1 CTTTCAAGGCTAAGATAGAACCTTACA---CTAT
*
1755166 CTTTGACAAAGGCTAAGATAGAACCTTTACACTGT
1 CTTT--C-AAGGCTAAGATAGAACC-TTACACTAT
1755201 CTTTCAAGGCTAAGATAGAACCT
1 CTTTCAAGGCTAAGATAGAACCT
1755224 CTCAATCACT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
31 1 0.02
32 17 0.34
33 5 0.10
35 7 0.14
37 15 0.30
38 5 0.10
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (31 bp):
CTTTCAAGGCTAAGATAGAACCTTACACTAT
Found at i:1755747 original size:10 final size:10
Alignment explanation
Indices: 1755707--1755745 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1755697 GTATCGATAC
1755707 ATGAACAGTG
1 ATGAACAGTG
1755717 ATGAACAGTG
1 ATGAACAGTG
* * *
1755727 GTGAATAGTT
1 ATGAACAGTG
1755737 ATGAACAGT
1 ATGAACAGT
1755746 TAAAAAATGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1755795 original size:13 final size:13
Alignment explanation
Indices: 1755777--1755801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1755767 TGCCAGTTTT
1755777 ATGTATCGATACA
1 ATGTATCGATACA
1755790 ATGTATCGATAC
1 ATGTATCGATAC
1755802 TAAGCAAAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1762427 original size:20 final size:20
Alignment explanation
Indices: 1762384--1762429 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1762374 AAATCTTTTG
1762384 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1762405 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1762425 CAAAA
1 CAAAA
1762430 CCAGTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1764797 original size:13 final size:13
Alignment explanation
Indices: 1764779--1764804 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1764769 TACACCAAGT
1764779 ATGTATCGATACA
1 ATGTATCGATACA
1764792 ATGTATCGATACA
1 ATGTATCGATACA
1764805 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1764802 original size:32 final size:33
Alignment explanation
Indices: 1764761--1764824 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1764751 TAGCCAAACT
* **
1764761 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1764793 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1764825 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1768928 original size:21 final size:22
Alignment explanation
Indices: 1768903--1768948 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1768893 AGTTATTTGG
* *
1768903 ATTTAAATCATTTTATA-TTAA
1 ATTTAAATAATTTTAAATTTAA
*
1768924 ATTTATATAATTTTAAATTTAA
1 ATTTAAATAATTTTAAATTTAA
1768946 ATT
1 ATT
1768949 AATTTAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTAAATAATTTTAAATTTAA
Found at i:1768955 original size:16 final size:16
Alignment explanation
Indices: 1768920--1768953 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1768910 TCATTTTATA
*
1768920 TTAAATTTATATAATT
1 TTAAATTTAAATAATT
1768936 TTAAATTTAAATTAATT
1 TTAAATTTAAA-TAATT
1768953 T
1 T
1768954 AAGTTCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAATTTAAATAATT
Found at i:1769649 original size:22 final size:23
Alignment explanation
Indices: 1769612--1769657 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
1769602 GGTTATGTTA
1769612 ATATAATACTATTAAAAATTATC
1 ATATAATACTATTAAAAATTATC
*
1769635 ATATAATA-TATTAAAGATTATC
1 ATATAATACTATTAAAAATTATC
1769657 A
1 A
1769658 GACAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATAATACTATTAAAAATTATC
Found at i:1769664 original size:22 final size:22
Alignment explanation
Indices: 1769616--1769665 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1769606 ATGTTAATAT
* *
1769616 AATACTATTAAAAATTATCATAT
1 AATA-TATTAAAAATTATCAGAC
*
1769639 AATATATTAAAGATTATCAGAC
1 AATATATTAAAAATTATCAGAC
1769661 AATAT
1 AATAT
1769666 TTTTGCTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (22 bp):
AATATATTAAAAATTATCAGAC
Found at i:1771209 original size:16 final size:16
Alignment explanation
Indices: 1771185--1771223 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1771175 TTTTATGTTA
1771185 TATTCATATTATATTTT
1 TATT-ATATTATATTTT
1771202 TATTATATTATATTTT
1 TATTATATTATATTTT
*
1771218 AATTAT
1 TATTAT
1771224 TTTTCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATATTATATTTT
Found at i:1773444 original size:16 final size:15
Alignment explanation
Indices: 1773425--1773459 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1773415 CTATTTTCCC
*
1773425 TCTTGTTTTCTTTCTT
1 TCTTGTTTTCCTT-TT
1773441 TCTTGTTTTCCTTTT
1 TCTTGTTTTCCTTTT
1773456 TCTT
1 TCTT
1773460 TTTCCTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.74
Consensus pattern (15 bp):
TCTTGTTTTCCTTTT
Found at i:1773458 original size:23 final size:23
Alignment explanation
Indices: 1773430--1773479 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1773420 TTCCCTCTTG
*
1773430 TTTTCTTTCTTTCTT-GTTTTCCT
1 TTTTCTTT-TTCCTTCGTTTTCCT
*
1773453 TTTTCTTTTTCCTTCTTTTTCCT
1 TTTTCTTTTTCCTTCGTTTTCCT
1773476 TTTT
1 TTTT
1773480 AGAATAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTCTTTTTCCTTCGTTTTCCT
Found at i:1773800 original size:25 final size:24
Alignment explanation
Indices: 1773772--1773818 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1773762 AAAATAAAGA
1773772 AAATAGATAATTTTTTTGAAAAACT
1 AAATAGA-AATTTTTTTGAAAAACT
*
1773797 AAATATAAATTTTTTTGAAAAA
1 AAATAGAAATTTTTTTGAAAAA
1773819 AAATCAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (24 bp):
AAATAGAAATTTTTTTGAAAAACT
Found at i:1774070 original size:13 final size:14
Alignment explanation
Indices: 1774042--1774075 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1774032 TGAAAATAAA
*
1774042 TTTAAAAATTATTT
1 TTTAAAAATTAATT
1774056 TTTAAAAA-TAATT
1 TTTAAAAATTAATT
1774069 TTTAAAA
1 TTTAAAA
1774076 TGAACTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAAAATTAATT
Found at i:1775564 original size:22 final size:22
Alignment explanation
Indices: 1775530--1775571 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1775520 AAAACTTATT
*
1775530 ATAAATTACAAAAATTAAAATA
1 ATAAATGACAAAAATTAAAATA
*
1775552 ATAAATGATAAAAATTAAAA
1 ATAAATGACAAAAATTAAAA
1775572 AGCTATAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
ATAAATGACAAAAATTAAAATA
Found at i:1775770 original size:17 final size:17
Alignment explanation
Indices: 1775748--1775781 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1775738 CGATAATTGT
1775748 TTAGATTTAATTAATTA
1 TTAGATTTAATTAATTA
1775765 TTAGATTTAATTAATTA
1 TTAGATTTAATTAATTA
1775782 ATACAAGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTAGATTTAATTAATTA
Found at i:1776677 original size:2 final size:2
Alignment explanation
Indices: 1776670--1776703 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1776660 TGTACATGTA
1776670 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
1776704 CAAGCACAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.