Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 78
Found at i:6177246 original size:16 final size:18
Alignment explanation
Indices: 6177225--6177259 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
6177215 TTTACTCATT
6177225 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
6177241 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
6177259 T
1 T
6177260 GTTTTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:6179337 original size:15 final size:15
Alignment explanation
Indices: 6179317--6179355 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
6179307 CTTGATGCCT
6179317 AGTCTGCTAGTCTAC
1 AGTCTGCTAGTCTAC
6179332 AGTCTGCTAGTCTAC
1 AGTCTGCTAGTCTAC
*
6179347 AGTTTGCTA
1 AGTCTGCTA
6179356 TTATCTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (15 bp):
AGTCTGCTAGTCTAC
Found at i:6180098 original size:10 final size:10
Alignment explanation
Indices: 6180083--6180120 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
6180073 GGAGTGGTCG
6180083 ATGGTGGTTC
1 ATGGTGGTTC
*
6180093 ACGGTGG-TC
1 ATGGTGGTTC
6180102 GATGGTGGTTC
1 -ATGGTGGTTC
6180113 ATGGTGGT
1 ATGGTGGT
6180121 GCAACCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.11, C:0.11, G:0.45, T:0.34
Consensus pattern (10 bp):
ATGGTGGTTC
Found at i:6180101 original size:20 final size:20
Alignment explanation
Indices: 6180076--6180120 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
6180066 CAAATTTGGA
6180076 GTGGTCGATGGTGGTTCACG
1 GTGGTCGATGGTGGTTCACG
*
6180096 GTGGTCGATGGTGGTTCATG
1 GTGGTCGATGGTGGTTCACG
6180116 GTGGT
1 GTGGT
6180121 GCAACCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.11, G:0.47, T:0.33
Consensus pattern (20 bp):
GTGGTCGATGGTGGTTCACG
Found at i:6183314 original size:15 final size:15
Alignment explanation
Indices: 6183294--6183344 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
6183284 TTTCGTAAAA
6183294 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
6183309 TGAATTACTGGAAA-A
1 TGAATTACT-GAAATT
*
6183324 TGAATTA-TTAGAATT
1 TGAATTACTGA-AATT
6183339 TGAATT
1 TGAATT
6183345 CTGGAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 3 0.10
15 22 0.73
16 4 0.13
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:6183326 original size:30 final size:30
Alignment explanation
Indices: 6183290--6183360 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
6183280 GGTTTTTCGT
6183290 AAAATGAATTACTGA-AATTTGAATTACTGG
1 AAAATGAATTACTGAGAATTTGAATT-CTGG
*
6183320 AAAATGAATTA-TTAGAATTTGAATTCTGG
1 AAAATGAATTACTGAGAATTTGAATTCTGG
*
6183349 AAAATAAATTAC
1 AAAATGAATTAC
6183361 ATTTCTAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 16 0.43
30 21 0.57
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (30 bp):
AAAATGAATTACTGAGAATTTGAATTCTGG
Found at i:6183595 original size:21 final size:20
Alignment explanation
Indices: 6183552--6183600 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
6183542 ATCATAAAAC
6183552 TTTTTTATTATTAAAAATAA
1 TTTTTTATTATTAAAAATAA
*
6183572 TTTATTTATTATTAAATAGT-A
1 TTT-TTTATTATTAAA-AATAA
6183593 TTTTTTAT
1 TTTTTTAT
6183601 AATTTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTTTATTATTAAAAATAA
Found at i:6183628 original size:30 final size:33
Alignment explanation
Indices: 6183585--6183655 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 33
6183575 ATTTATTATT
* * *
6183585 AAATAGTATTTTTTATA-ATTTTA-T-TAATAA
1 AAATATTAATTTTTATATATTTTAGTGAAATAA
*
6183615 AAATATTAATTTTTGTATATTTTAGTGAAATAA
1 AAATATTAATTTTTATATATTTTAGTGAAATAA
6183648 AAATATTA
1 AAATATTA
6183656 TAAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.41
31 6 0.18
32 1 0.03
33 13 0.38
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (33 bp):
AAATATTAATTTTTATATATTTTAGTGAAATAA
Found at i:6183786 original size:19 final size:20
Alignment explanation
Indices: 6183734--6183786 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
6183724 TTTAAATATT
6183734 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
6183753 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
6183774 TTATTAAATATAT
1 TTATTAAATATAT
6183787 AATAATCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:6189250 original size:148 final size:145
Alignment explanation
Indices: 6188985--6189274 Score: 458
Period size: 148 Copynumber: 2.0 Consensus size: 145
6188975 CAGATTTTAT
* * *
6188985 AGGGGCCTATTTTTAAAAATGATAATAATTTAACTATTAGAAAATAGAAGATATGTAAAACGGTT
1 AGGGGCCCATTTTTAAAAATAATAATAATTTAACTATTAGAAAATAAAAGATATGTAAAACGGTT
6189050 CATAGTGTATATATATAAAAATCAATTTATGGTTTGACTTTTCATCCATCTCTTGTT-TGTCAGC
66 CATAGTGTATATATATAAAAATCAATTTATGGTTTGACTTTTCATCCATCTCTT-TTCTGTCAGC
6189114 TATGTTTTGATGGGAC
130 TATGTTTTGATGGGAC
*
6189130 AGGGGCCCATTTTTAAAAATAATTATAATTTAACTATTAGAAAAGTAAAAGATATGTAAAACGG-
1 AGGGGCCCATTTTTAAAAATAATAATAATTTAACTATTAGAAAA-TAAAAGATATGTAAAACGGT
* * *
6189194 TCTATAGTGTATATATATATATAAATCAATTTGTGGTTTGATTTTTCATCCATCTCTTTTCTGTT
65 TC-ATAGTGTATATATATA-A-AAATCAATTTATGGTTTGACTTTTCATCCATCTCTTTTCTGTC
6189259 AGCTATGTTTTGATGG
127 AGCTATGTTTTGATGG
6189275 AATCCCATAA
Statistics
Matches: 133, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
145 43 0.32
146 34 0.26
147 3 0.02
148 53 0.40
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (145 bp):
AGGGGCCCATTTTTAAAAATAATAATAATTTAACTATTAGAAAATAAAAGATATGTAAAACGGTT
CATAGTGTATATATATAAAAATCAATTTATGGTTTGACTTTTCATCCATCTCTTTTCTGTCAGCT
ATGTTTTGATGGGAC
Found at i:6205281 original size:2 final size:2
Alignment explanation
Indices: 6205276--6205303 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6205266 ACACACACAC
6205276 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
6205304 CATACATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6205633 original size:29 final size:30
Alignment explanation
Indices: 6205598--6205657 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
6205588 CACTTTCATA
*
6205598 TCACATAT-CATATAAG-CTCATAGCTTCTT
1 TCACATATACATAT-AGTCACATAGCTTCTT
*
6205627 TCACATATACATGTAGTCACATAGCTTCTT
1 TCACATATACATATAGTCACATAGCTTCTT
6205657 T
1 T
6205658 TCATATTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
TCACATATACATATAGTCACATAGCTTCTT
Found at i:6206259 original size:20 final size:20
Alignment explanation
Indices: 6206234--6206288 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
6206224 CAAAATTCCC
*
6206234 ATGCATCGATTCACCCCTTA
1 ATGCATCGATGCACCCCTTA
*
6206254 ATGCATCGGTGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
*
6206274 ATGCATCGGTGCACC
1 ATGCATCGATGCACC
6206289 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:6206663 original size:32 final size:32
Alignment explanation
Indices: 6206627--6206691 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
6206617 CCTAACTCCA
6206627 CCATCCTTTGCTTTTAAGATGATTTGAGCTTT
1 CCATCCTTTGCTTTTAAGATGATTTGAGCTTT
*
6206659 CCATCCTTTGCTTTTAAGATGATTTGAGTTTT
1 CCATCCTTTGCTTTTAAGATGATTTGAGCTTT
6206691 C
1 C
6206692 TTTAAGCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (32 bp):
CCATCCTTTGCTTTTAAGATGATTTGAGCTTT
Found at i:6208820 original size:58 final size:58
Alignment explanation
Indices: 6208714--6208843 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 58
6208704 TTGGGTAACA
* * ** *
6208714 ATTTTGTAACTTTTAATAATCAAGGGACTCAACAAAACAATGTCCTATAGTCAGA-GATC
1 ATTTTATAACTTTTAATAAT-AAGGAACTCAACAAAACAACATCCTATAAT-AGATGATC
* *
6208773 ATTTTATAACTTTTAATAAT-TGGAAACTCAACAAAACAACATTCTATAATAGATGATC
1 ATTTTATAACTTTTAATAATAAGG-AACTCAACAAAACAACATCCTATAATAGATGATC
6208831 ATTTGTAT-ACTTT
1 ATTT-TATAACTTT
6208844 ACCCATAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
57 5 0.08
58 34 0.56
59 22 0.36
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (58 bp):
ATTTTATAACTTTTAATAATAAGGAACTCAACAAAACAACATCCTATAATAGATGATC
Found at i:6210826 original size:12 final size:12
Alignment explanation
Indices: 6210811--6210874 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
6210801 TATTGTCTCG
6210811 TTTATAAGCTCC
1 TTTATAAGCTCC
* **
6210823 TTTAT-TGACTTA
1 TTTATAAG-CTCC
6210835 TTTATAAGCTCC
1 TTTATAAGCTCC
* *
6210847 TTTAT-TGACTCA
1 TTTATAAG-CTCC
6210859 TTTATAAGCTCC
1 TTTATAAGCTCC
6210871 TTTA
1 TTTA
6210875 CTCAATCCTC
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (12 bp):
TTTATAAGCTCC
Found at i:6210826 original size:24 final size:24
Alignment explanation
Indices: 6210799--6210874 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 24
6210789 TATTATTTCG
* *
6210799 TTTATTGTCTCGTTTATAAGCTCC
1 TTTATTGACTCATTTATAAGCTCC
*
6210823 TTTATTGACTTATTTATAAGCTCC
1 TTTATTGACTCATTTATAAGCTCC
6210847 TTTATTGACTCATTTATAAGCTCC
1 TTTATTGACTCATTTATAAGCTCC
6210871 TTTA
1 TTTA
6210875 CTCAATCCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.50
Consensus pattern (24 bp):
TTTATTGACTCATTTATAAGCTCC
Found at i:6211128 original size:23 final size:22
Alignment explanation
Indices: 6211069--6211137 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
6211059 AATTAACATA
* *
6211069 TTCACGAACATTAAATGAATATG
1 TTCACGAACATTAAA-AAAAATG
* * **
6211092 TTCGCAAATGTTAAACAAAAATG
1 TTCACGAACATTAAA-AAAAATG
*
6211115 TTCACGAACATTAAAAAACATG
1 TTCACGAACATTAAAAAAAATG
6211137 T
1 T
6211138 CCGCAAACGG
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
22 7 0.21
23 27 0.79
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (22 bp):
TTCACGAACATTAAAAAAAATG
Found at i:6215772 original size:18 final size:18
Alignment explanation
Indices: 6215746--6215780 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6215736 CTAGAATGCA
6215746 AAATAGGTATCGATACTC
1 AAATAGGTATCGATACTC
* *
6215764 AAATGGGTATTGATACT
1 AAATAGGTATCGATACT
6215781 ACTTTACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (18 bp):
AAATAGGTATCGATACTC
Found at i:6217091 original size:19 final size:20
Alignment explanation
Indices: 6217064--6217101 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6217054 TGAAAATGAT
6217064 TTGACTTTG-AAAACAAAAG
1 TTGACTTTGAAAAACAAAAG
*
6217083 TTGATTTTGAAAAACAAAA
1 TTGACTTTGAAAAACAAAA
6217102 TGAAACTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGACTTTGAAAAACAAAAG
Found at i:6218391 original size:20 final size:19
Alignment explanation
Indices: 6218363--6218419 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
6218353 CTGGGTACGT
* *
6218363 AGTACCGATACTGTTCTTAC
1 AGTATCGATACTGTTC-AAC
*
6218383 AGTATCGATACTGCATCAAC
1 AGTATCGATACTG-TTCAAC
*
6218403 AGTATCGATATTGTTCA
1 AGTATCGATACTGTTCA
6218420 TGTGGCAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.10
20 26 0.84
21 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (19 bp):
AGTATCGATACTGTTCAAC
Found at i:6223930 original size:139 final size:139
Alignment explanation
Indices: 6223761--6224038 Score: 493
Period size: 139 Copynumber: 2.0 Consensus size: 139
6223751 GCACTGTTAA
* * *
6223761 GTGTATCGATGCATTAAGCACATAAATGACAAAAATCTGTTTTAAACACTCAAAATACTAAATTA
1 GTGTATCAATGCATTAAGCACAGAAATGACAAAAATCTATTTTAAACACTCAAAATACTAAATTA
*
6223826 ATTAGCTCTAGTGGTATTGGCAACTCATATATTGAAAATTAATCATGTTCAATCAATCAAATTAA
66 ATTAGCTCTAGTGGTACTGGCAACTCATATATTGAAAATTAATCATGTTCAATCAATCAAATTAA
6223891 TCCTTAAGC
131 TCCTTAAGC
*
6223900 GTGTATCAATGCATTAAGCACAGAAATGACAAAAATCTATTTTAAACACTCAAAATGCTAAATTA
1 GTGTATCAATGCATTAAGCACAGAAATGACAAAAATCTATTTTAAACACTCAAAATACTAAATTA
* *
6223965 ATTAGCTTTAGTGGTACTGGCAACTCATATATTGAAAATTAATCGTGTTCAATCAATCAAATTAA
66 ATTAGCTCTAGTGGTACTGGCAACTCATATATTGAAAATTAATCATGTTCAATCAATCAAATTAA
6224030 TCCTTAAGC
131 TCCTTAAGC
6224039 TTCATTTGAA
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 132 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (139 bp):
GTGTATCAATGCATTAAGCACAGAAATGACAAAAATCTATTTTAAACACTCAAAATACTAAATTA
ATTAGCTCTAGTGGTACTGGCAACTCATATATTGAAAATTAATCATGTTCAATCAATCAAATTAA
TCCTTAAGC
Found at i:6229267 original size:19 final size:19
Alignment explanation
Indices: 6229238--6229289 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
6229228 TTGGACCCTT
*
6229238 AGTGCATCGGTGCACTAAG
1 AGTGCAGCGGTGCACTAAG
*
6229257 AGTGTAGCGGTGCACTAAG
1 AGTGCAGCGGTGCACTAAG
*
6229276 AGTGCAGCGATGCA
1 AGTGCAGCGGTGCA
6229290 TCAAGTGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.35, T:0.19
Consensus pattern (19 bp):
AGTGCAGCGGTGCACTAAG
Found at i:6229404 original size:57 final size:56
Alignment explanation
Indices: 6229286--6229394 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 56
6229276 AGTGCAGCGA
* * * *
6229286 TGCATCAAGTGCATTCGATGTTTCAAAATAGCTAGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTACATCGATGCATGGCTGG
6229342 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCT-CAGTACATCGATGCATGG
1 TGCATCAAATGCATTCGATG-TTTCA-AAATA-CCTACAGTACATCGATGCATGG
6229395 TATGTGCATC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
56 19 0.41
57 22 0.48
58 5 0.11
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (56 bp):
TGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTACATCGATGCATGGCTGG
Found at i:6235439 original size:22 final size:23
Alignment explanation
Indices: 6235409--6235461 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
6235399 TATTTTAGTC
*
6235409 ATATAAATATGTATTTA-ATTAA
1 ATATTAATATGTATTTATATTAA
* *
6235431 ATATTAATATTTATTTATTTTTAA
1 ATATTAATATGTATTTA-TATTAA
6235455 ATATTAA
1 ATATTAA
6235462 GAAAGGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 15 0.58
24 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATTAATATGTATTTATATTAA
Found at i:6235682 original size:137 final size:136
Alignment explanation
Indices: 6235432--6235683 Score: 325
Period size: 137 Copynumber: 1.8 Consensus size: 136
6235422 TTTAATTAAA
6235432 TATTAATATTTATTTATTTTTAAATATTAAGAAAGGAACTGTCTTAAAGCACCTAAAAATCATTT
1 TATTAATATTTATTTATTTTTAAATATTAAGAAAGG-ACTGTCTTAAAGCACCTAAAAATCATTT
* *
6235497 TCGAATATTCTTAAATAAATAAAATATTCTATTTTTATAAATTATATATTAATTTATTTTAAAGA
65 TCGAATATTCTTAAATAAATAAAATATTCTATTTATATAAAATATATATTAATTTATTTTAAAGA
6235562 AATATTT
130 AATATTT
* * * * *
6235569 TATTAATATTTATTTATTTTTTAATATTAAGAAATAGG-CTGTCTTCAAGCACCTAGAAGTCCTT
1 TATTAATATTTATTTATTTTTAAATATTAAG-AA-AGGACTGTCTTAAAGCACCTAAAAATCATT
* *
6235633 TTCTAATATT-TCTAAGTAAAT-AAATA-TCTTATTTAAATATAAAAT-TATATT
64 TTCGAATATTCT-TAAATAAATAAAATATTC-TATTT--ATATAAAATATATATT
6235684 TATATATATA
Statistics
Matches: 100, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
135 2 0.02
136 11 0.11
137 75 0.75
138 9 0.09
139 3 0.03
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (136 bp):
TATTAATATTTATTTATTTTTAAATATTAAGAAAGGACTGTCTTAAAGCACCTAAAAATCATTTT
CGAATATTCTTAAATAAATAAAATATTCTATTTATATAAAATATATATTAATTTATTTTAAAGAA
ATATTT
Found at i:6235718 original size:2 final size:2
Alignment explanation
Indices: 6235678--6235707 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6235668 AATATAAAAT
*
6235678 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6235708 AATTAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6237722 original size:16 final size:16
Alignment explanation
Indices: 6237698--6237728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6237688 CAAACTTATA
*
6237698 TCATTCATTAAAATAT
1 TCATCCATTAAAATAT
6237714 TCATCCATTAAAATA
1 TCATCCATTAAAATA
6237729 AGGATTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (16 bp):
TCATCCATTAAAATAT
Found at i:6238431 original size:32 final size:32
Alignment explanation
Indices: 6238355--6238478 Score: 78
Period size: 31 Copynumber: 4.0 Consensus size: 32
6238345 TCCTAAGGGA
*
6238355 ACATCTTAGGGCC-TGAGAGCCTACCCAAGAT
1 ACATCTTAGGGCCGTGAGAGCCTACCCAAGAC
* * * * *
6238386 AGATTTTGGGGCCGTGGGA-CCTACCTAAGAAC
1 ACATCTTAGGGCCGTGAGAGCCTACCCAAG-AC
* ** *
6238418 ACATCTTAGGGCCG-CACTGCCTACCCGAGA-
1 ACATCTTAGGGCCGTGAGAGCCTACCCAAGAC
* * *
6238448 ATGATCTCAGGGCCGT-AGAGCCTACCTAAGA
1 A-CATCTTAGGGCCGTGAGAGCCTACCCAAGA
6238479 GTCACATTAG
Statistics
Matches: 67, Mismatches: 21, Indels: 10
0.68 0.21 0.10
Matches are distributed among these distances:
30 1 0.01
31 42 0.63
32 24 0.36
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (32 bp):
ACATCTTAGGGCCGTGAGAGCCTACCCAAGAC
Found at i:6239385 original size:28 final size:29
Alignment explanation
Indices: 6239294--6239456 Score: 213
Period size: 29 Copynumber: 5.6 Consensus size: 29
6239284 CACATTCGAA
*
6239294 AATTCCCAAAATGTCACCTTTTTGAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
6239323 AATTCCCAAAATGTCACGTTTTTTTCAAAAT
1 AATTCCCAAAATGTCAC--CTTTTTCAAAAT
* * *
6239354 AATT-ACAAAATATCACCTTTTTCAAAAC
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
6239382 AATTCCCAGAATGTCA-CTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
6239410 AATTCCAAAAATATCACCTTTTTTAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
6239439 AATTCCCAAAATGTCACC
1 AATTCCCAAAATGTCACC
6239457 GGGTCGGGTC
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
28 38 0.33
29 52 0.46
30 10 0.09
31 14 0.12
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.34
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:6239395 original size:59 final size:56
Alignment explanation
Indices: 6239300--6239455 Score: 222
Period size: 57 Copynumber: 2.7 Consensus size: 56
6239290 CGAAAATTCC
* *
6239300 CAAAATGTCACCTTTTTGAAAATAATTCCCAAAATGTCACGTTTTTTTCAAAATAATTA
1 CAAAATATCACCTTTTTCAAAATAATTCCCAAAATGTCAC---TTTTTCAAAATAATTA
* * *
6239359 CAAAATATCACCTTTTTCAAAACAATTCCCAGAATGTCACTTTTTCAAAATAATTC
1 CAAAATATCACCTTTTTCAAAATAATTCCCAAAATGTCACTTTTTCAAAATAATTA
*
6239415 CAAAAATATCACCTTTTTTAAAATAATTCCCAAAATGTCAC
1 C-AAAATATCACCTTTTTCAAAATAATTCCCAAAATGTCAC
6239456 CGGGTCGGGT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
56 16 0.18
57 36 0.41
59 36 0.41
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (56 bp):
CAAAATATCACCTTTTTCAAAATAATTCCCAAAATGTCACTTTTTCAAAATAATTA
Found at i:6239489 original size:19 final size:19
Alignment explanation
Indices: 6239465--6239509 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
6239455 CCGGGTCGGG
*
6239465 TCAGACCGATCAACCCGGT
1 TCAGACCGATCAAACCGGT
* *
6239484 TCAGACTGGTCAAACCGGT
1 TCAGACCGATCAAACCGGT
6239503 TCAGACC
1 TCAGACC
6239510 AGTTTGGATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (19 bp):
TCAGACCGATCAAACCGGT
Found at i:6245646 original size:25 final size:25
Alignment explanation
Indices: 6245613--6245665 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
6245603 TACACTAAAC
6245613 AAATCATATTCCAGTAAATCTCATA
1 AAATCATATTCCAGTAAATCTCATA
* **
6245638 AAATTATATTGTAGTAAATCTCATA
1 AAATCATATTCCAGTAAATCTCATA
6245663 AAA
1 AAA
6245666 GAGTTATCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (25 bp):
AAATCATATTCCAGTAAATCTCATA
Found at i:6245760 original size:32 final size:31
Alignment explanation
Indices: 6245724--6245800 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
6245714 CAGGGCCGTG
*
6245724 GGGCCTACCTAAGAACACATCTTAGGGCCACA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
** ** *
6245756 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
6245787 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
6245801 GTCGCATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:6246671 original size:31 final size:29
Alignment explanation
Indices: 6246583--6246717 Score: 171
Period size: 29 Copynumber: 4.6 Consensus size: 29
6246573 CACATTCAAA
*
6246583 AATTCCCAAAATGTCATCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
6246612 AATTCCTAGAATTTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
6246641 AATTCCGAAAATATCACCTTTTTTTTAAAAT
1 AATTCCCAAAATGTCACC--TTTTTCAAAAT
* *
6246672 AATGCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
6246701 AATTCCCAAAATGTCAC
1 AATTCCCAAAATGTCAC
6246718 TGGGTCTGGT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 65 0.73
31 24 0.27
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:6246683 original size:60 final size:60
Alignment explanation
Indices: 6246583--6246717 Score: 184
Period size: 60 Copynumber: 2.3 Consensus size: 60
6246573 CACATTCAAA
* * * * *
6246583 AATTCCCAAAATGTCA--TCTTTTTCAAAATAATTCCTAGAATTTCACCTTTTTCAAAAT
1 AATTCCCAAAATATCACCTTTTTTTCAAAATAATGCCCAGAATGTCACCTTTTTCAAAAT
* *
6246641 AATTCCGAAAATATCACCTTTTTTTTAAAATAATGCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATATCACCTTTTTTTCAAAATAATGCCCAGAATGTCACCTTTTTCAAAAT
*
6246701 AATTCCCAAAATGTCAC
1 AATTCCCAAAATATCAC
6246718 TGGGTCTGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
58 14 0.21
60 52 0.79
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (60 bp):
AATTCCCAAAATATCACCTTTTTTTCAAAATAATGCCCAGAATGTCACCTTTTTCAAAAT
Found at i:6249858 original size:16 final size:15
Alignment explanation
Indices: 6249837--6249867 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
6249827 CTCATTCATC
6249837 AGAAAAAAAGGAAAAA
1 AGAAAAAAA-GAAAAA
6249853 AGAAAAAAAGAAAAA
1 AGAAAAAAAGAAAAA
6249868 GATGAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAGAAAAA
Found at i:6254561 original size:73 final size:71
Alignment explanation
Indices: 6254441--6254665 Score: 290
Period size: 73 Copynumber: 3.1 Consensus size: 71
6254431 TTTTCAAATA
* * *
6254441 GAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGCGTCTCCCTTGAGACAGTTCCAC
1 GAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTT-CAC
6254506 TCGAAAC
65 TCGAAAC
* *
6254513 TGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCT-AAACAGTTTC
1 -GAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCT-TGAGACAG-TTC
*
6254577 ATTCGAAAC
63 ACTCGAAAC
* * * *
6254586 AACAATTTATCTCACTTGAGTTTGTTTTTCTTAAAACAAGATTCGCCTCGCTTGAGACAGTTCAC
1 GA-AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTCAC
*
6254651 TAGAAAC
65 TCGAAAC
6254658 AGAAATTT
1 -GAAATTT
6254666 CCATCACTCG
Statistics
Matches: 132, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
72 17 0.13
73 112 0.85
74 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (71 bp):
GAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTCACT
CGAAAC
Found at i:6254623 original size:37 final size:36
Alignment explanation
Indices: 6254442--6254624 Score: 120
Period size: 36 Copynumber: 5.0 Consensus size: 36
6254432 TTTCAAATAG
6254442 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* *** * ** *** ** *
6254478 AACTGCGTCTCCCTTGAGACAGTTCCACTCGAAACTG
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-A
6254515 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* * * ** *
6254551 AAATTTGTCTCGCTCT-AAACAG--TTTCATTCGAAACA
1 AAATTTATCTCACT-TGAGATTGTTTTTC-TT-AAAACA
*
6254587 ACAATTTATCTCACTTGAGTTTGTTTTTCTTAAAACA
1 A-AATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
6254624 A
1 A
6254625 GATTCGCCTC
Statistics
Matches: 100, Mismatches: 39, Indels: 15
0.65 0.25 0.10
Matches are distributed among these distances:
34 4 0.04
35 2 0.02
36 45 0.45
37 43 0.43
38 2 0.02
39 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
Found at i:6261771 original size:20 final size:21
Alignment explanation
Indices: 6261734--6261781 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6261724 TTCAACAAGT
* *
6261734 TAAACTTTAAAATTAAAA-TTA
1 TAAAATTT-AAATAAAAATTTA
6261755 TAAAATTTAAATAAAAATTTA
1 TAAAATTTAAATAAAAATTTA
6261776 TAAAAT
1 TAAAAT
6261782 ATTTTAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATTTAAATAAAAATTTA
Found at i:6265514 original size:18 final size:18
Alignment explanation
Indices: 6265477--6265516 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
6265467 AGGGTTTTCG
*
6265477 GGCTCTTCAGCGTCAGCA
1 GGCTCTTCAGCGTCAACA
6265495 GGCTCTTCAG-GTTCAACA
1 GGCTCTTCAGCG-TCAACA
6265513 GGCT
1 GGCT
6265517 GGGGACTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (18 bp):
GGCTCTTCAGCGTCAACA
Found at i:6269580 original size:13 final size:13
Alignment explanation
Indices: 6269562--6269587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6269552 GTAGGTATCA
6269562 ACTCGTTATCTTC
1 ACTCGTTATCTTC
6269575 ACTCGTTATCTTC
1 ACTCGTTATCTTC
6269588 CCACGAACTA
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:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (13 bp):
ACTCGTTATCTTC
Found at i:6273681 original size:9 final size:11
Alignment explanation
Indices: 6273654--6273702 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
6273644 AAAAATGAAC
*
6273654 TATAATAAATA
1 TATAATATATA
6273665 -ATAATATAT-
1 TATAATATATA
6273674 TA-AATATATA
1 TATAATATATA
6273684 TATAATATATA
1 TATAATATATA
6273695 TAT-ATATA
1 TATAATATA
6273703 GACATATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 7 0.21
10 16 0.47
11 11 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATAATATATA
Found at i:6273684 original size:11 final size:13
Alignment explanation
Indices: 6273662--6273700 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
6273652 ACTATAATAA
6273662 ATAATA-ATATAT
1 ATAATATATATAT
6273674 -TAA-ATATATAT
1 ATAATATATATAT
6273685 ATAATATATATAT
1 ATAATATATATAT
6273698 ATA
1 ATA
6273701 TAGACATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 9 0.38
12 3 0.12
13 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:6273686 original size:15 final size:15
Alignment explanation
Indices: 6273654--6273702 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
6273644 AAAAATGAAC
6273654 TATAATAAATA-ATAA
1 TATAATAAATATAT-A
*
6273669 TATATTAAATATATA
1 TATAATAAATATATA
*
6273684 TATAATATATATATA
1 TATAATAAATATATA
6273699 TATA
1 TATA
6273703 GACATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 28 0.93
16 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAATAAATATATA
Found at i:6274252 original size:37 final size:37
Alignment explanation
Indices: 6274159--6274260 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
6274149 ATGCTTGTGG
* * ** * *
6274159 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
6274196 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
6274233 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
6274261 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:6275197 original size:106 final size:106
Alignment explanation
Indices: 6275013--6276089 Score: 1516
Period size: 106 Copynumber: 10.3 Consensus size: 106
6275003 GCATTGTTCC
* * * * *
6275013 GAGTCCAATATCCTCCATCGTGAAGTTGAAATTGGCT-CTAGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGA-AATTGGGAAATTGTTTGTTGACA
* * * * *
6275077 ACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
6275119 GAGTCCAATATCTTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
* * *
6275184 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTTTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** ** * *
6275225 AAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTGCGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
* *
6275290 CAAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
6275331 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
*
6275396 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
6275437 GAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
* *
6275502 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
6275543 GAGTCCAATATCTTTAC-CTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTT-CGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
*
6275607 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
6275649 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
6275714 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
6275755 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
*
6275820 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
6275861 GAGTCCAATATCCTTCGTTGTGAAGTT---A---------AAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
* * * *
6275914 CCAGCGATACCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
6275955 GAGTCCAATATCCTTCACTGTGAAGTTGAGATTGGCTCCGAAATTGGGAAATTGTTTATTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
*
6276020 CCAGAGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
6276061 GAGTCCAATATTCTTCGTTGTGAAGTTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGA
6276090 GCCTTGACTT
Statistics
Matches: 874, Mismatches: 82, Indels: 30
0.89 0.08 0.03
Matches are distributed among these distances:
94 84 0.10
97 1 0.00
103 1 0.00
105 1 0.00
106 784 0.90
107 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:6275959 original size:94 final size:96
Alignment explanation
Indices: 6275795--6276089 Score: 369
Period size: 94 Copynumber: 3.0 Consensus size: 96
6275785 ATTGGCTCTG
* * *
6275795 AAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCT
1 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
6275860 GGAGTCCAATATCCTTCGTTGTGAAGTT-A-
66 GGAGTCCAATATCCTTCGTTGTGAAGTTGAC
* * *
6275889 AAATTGGGAAGTTGTTTATTGACAACCAGCGATACCTTCGTCATGAAGTTGAACTTGCGTTGTCT
1 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* **
6275954 TGAGTCCAATATCCTTCACTGTGAAGTTGAGATTGGCTCC
66 GGAGTCCAATATCCTTCGTTGTGAAGTT--GA-------C
* * *
6275994 GAAATTGGGAAATTGTTTATTAACAACCAGAGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 -AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
6276059 TGGAGTCCAATATTCTTCGTTGTGAAGTTGA
65 TGGAGTCCAATATCCTTCGTTGTGAAGTTGA
6276090 GCCTTGACTT
Statistics
Matches: 170, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
94 84 0.49
97 1 0.01
104 2 0.01
106 83 0.49
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (96 bp):
AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
GGAGTCCAATATCCTTCGTTGTGAAGTTGAC
Found at i:6277018 original size:22 final size:22
Alignment explanation
Indices: 6276992--6277046 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
6276982 TTGTGTTTGG
6276992 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
6277014 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
6277036 TCAAAGGTTTG
1 TCAAAGGTTTG
6277047 ATGGGGTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:6277673 original size:8 final size:7
Alignment explanation
Indices: 6277627--6277699 Score: 51
Period size: 7 Copynumber: 9.9 Consensus size: 7
6277617 TTTTTGTCCC
6277627 TTTTTCT
1 TTTTTCT
6277634 TTTTGAT-T
1 TTTT--TCT
6277642 TTTGTTCT
1 TTT-TTCT
*
6277650 TTCTT-T
1 TTTTTCT
*
6277656 TTTTTGT
1 TTTTTCT
6277663 TTTCTTCT
1 TTT-TTCT
6277671 TTTTTGCT
1 TTTTT-CT
6277679 TCTTTTCT
1 T-TTTTCT
*
6277687 TTTTTGT
1 TTTTTCT
6277694 TTTTTC
1 TTTTTC
6277700 CCTTTTTGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
6 5 0.09
7 23 0.43
8 19 0.36
9 6 0.11
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.79
Consensus pattern (7 bp):
TTTTTCT
Found at i:6277673 original size:15 final size:14
Alignment explanation
Indices: 6277640--6277709 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 14
6277630 TTCTTTTTGA
*
6277640 TTTTTGTTCTTTCTTT
1 TTTTTGTT-TTT-TCT
6277656 TTTTTGTTTTCTTCT
1 TTTTTGTTTT-TTCT
6277671 TTTTTGCTTCTTTTCT
1 TTTTTG-TT-TTTTCT
*
6277687 TTTTTGTTTTTTCCC
1 TTTTTGTTTTTT-CT
6277702 TTTTTGTT
1 TTTTTGTT
6277710 CTGATTGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
14 4 0.08
15 21 0.44
16 21 0.44
17 2 0.04
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTGTTTTTTCT
Found at i:6277692 original size:16 final size:15
Alignment explanation
Indices: 6277640--6277711 Score: 76
Period size: 16 Copynumber: 4.7 Consensus size: 15
6277630 TTCTTTTTGA
*
6277640 TTTTTGTTCTTTCTTT
1 TTTTTGTTCTTT-TCT
6277656 TTTTTGTT-TTCTTCT
1 TTTTTGTTCTT-TTCT
6277671 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
*
6277687 TTTTTGTT-TTTTCCC
1 TTTTTGTTCTTTT-CT
6277702 TTTTTGTTCT
1 TTTTTGTTCT
6277712 GATTGAATCT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
14 4 0.08
15 21 0.43
16 22 0.45
17 2 0.04
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:6277705 original size:32 final size:31
Alignment explanation
Indices: 6277640--6277711 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
6277630 TTCTTTTTGA
*
6277640 TTTTTGTTCTTTCTTTTTTTTGTTTTCTTCT
1 TTTTTGTTCTTTCTTTTTTTTGTTTTCTCCT
* * *
6277671 TTTTTGCTTCTTT-TCTTTTTTGTTTTTTCCC
1 TTTTTG-TTCTTTCTTTTTTTTGTTTTCTCCT
6277702 TTTTTGTTCT
1 TTTTTGTTCT
6277712 GATTGAATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 4 0.11
31 26 0.72
32 6 0.17
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (31 bp):
TTTTTGTTCTTTCTTTTTTTTGTTTTCTCCT
Found at i:6282179 original size:26 final size:25
Alignment explanation
Indices: 6282090--6282157 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
6282080 TTAAAAAGAA
* * *
6282090 AAATA-ATAATAAGAACAAAGAAACT
1 AAATATATAATAAAAATAAATAAA-T
*
6282115 AAAAATATAATAAAAATAAATAAAT
1 AAATATATAATAAAAATAAATAAAT
6282140 AAATAGTATAATAAAAAT
1 AAATA-TATAATAAAAAT
6282158 TTATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.25
26 27 0.75
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.22
Consensus pattern (25 bp):
AAATATATAATAAAAATAAATAAAT
Found at i:6282214 original size:21 final size:21
Alignment explanation
Indices: 6282188--6282250 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
6282178 AATGTATGTA
6282188 TAATAATAAAATACTAAATAG
1 TAATAATAAAATACTAAATAG
*
6282209 TAATAATAATAATAATAAAT-G
1 TAATAATAA-AATACTAAATAG
*
6282230 -AAAAATAAATATACTATAATA
1 TAATAATAAA-ATACTA-AATA
6282251 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 1 0.03
20 12 0.34
21 13 0.37
22 9 0.26
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
TAATAATAAAATACTAAATAG
Found at i:6282977 original size:37 final size:37
Alignment explanation
Indices: 6282931--6283020 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
6282921 CTTGTGGATT
* * *
6282931 CTATCTTTAGGAGTTTAAATAATAGTAGAACTCTATC
1 CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTATC
* ** *
6282968 CTATTTTTAGGAGTTTGAATCCTAGCAAAATTCTATC
1 CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTATC
6283005 CTATTTTTAGGAGTTT
1 CTATTTTTAGGAGTTT
6283021 GAATCCTAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTATC
Found at i:6284574 original size:20 final size:20
Alignment explanation
Indices: 6284551--6284593 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
6284541 AATCCACCAT
6284551 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
** * *
6284571 ATGCCTCTACATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
6284591 ATG
1 ATG
6284594 AGCCTTTAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:6284863 original size:3 final size:3
Alignment explanation
Indices: 6284855--6284892 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
6284845 TTTTAATTGT
6284855 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6284893 ATAATATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6287265 original size:18 final size:19
Alignment explanation
Indices: 6287244--6287279 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6287234 TTTTCAAATA
6287244 TAAACA-TAATTGTTTTTT
1 TAAACATTAATTGTTTTTT
6287262 TAAACATTAATTGTTTTT
1 TAAACATTAATTGTTTTT
6287280 AAAAAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (19 bp):
TAAACATTAATTGTTTTTT
Found at i:6290198 original size:21 final size:21
Alignment explanation
Indices: 6290172--6290231 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
6290162 AAAAATCTAG
*
6290172 GAAAAAAAGCAAAGAAAAAAGA
1 GAAAAAAA-CAAAGAAAAAAAA
*
6290194 GAAAAAATCAAAGAAAAAAAA
1 GAAAAAAACAAAGAAAAAAAA
*
6290215 GAAAAAAATAAAGAAAA
1 GAAAAAAACAAAGAAAA
6290232 TGATACAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 27 0.79
22 7 0.21
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (21 bp):
GAAAAAAACAAAGAAAAAAAA
Found at i:6290230 original size:33 final size:33
Alignment explanation
Indices: 6290156--6290231 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 33
6290146 AAATCAAAGC
* *
6290156 AAAGAGAAAAATCTAGGAAAAAAAGCAAAGAAAA
1 AAAGA-AAAAATCAAGAAAAAAAAGCAAAGAAAA
6290190 AAGAGAAAAAATCAAAGAAAAAAAAG-AAA-AAAA
1 AA-AGAAAAAATC-AAGAAAAAAAAGCAAAGAAAA
6290223 TAAAGAAAA
1 -AAAGAAAA
6290232 TGATACAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
33 10 0.27
34 14 0.38
35 13 0.35
ACGTcount: A:0.76, C:0.04, G:0.14, T:0.05
Consensus pattern (33 bp):
AAAGAAAAAATCAAGAAAAAAAAGCAAAGAAAA
Found at i:6294800 original size:20 final size:20
Alignment explanation
Indices: 6294777--6294821 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
6294767 GAACAGTTTT
6294777 GATACTATTCATATGGTATC
1 GATACTATTCATATGGTATC
6294797 GATACTATTCATATGGTATC
1 GATACTATTCATATGGTATC
6294817 GATAC
1 GATAC
6294822 CAAAGATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
GATACTATTCATATGGTATC
Found at i:6296413 original size:18 final size:18
Alignment explanation
Indices: 6296387--6296421 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6296377 ACTGTAAATT
6296387 TGTCCTGAAGGACCACTA
1 TGTCCTGAAGGACCACTA
*
6296405 TGTCTTGAAGGACCACT
1 TGTCCTGAAGGACCACT
6296422 CCTTAAGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (18 bp):
TGTCCTGAAGGACCACTA
Found at i:6297292 original size:21 final size:21
Alignment explanation
Indices: 6297266--6297340 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
6297256 AAGTTTCTCG
6297266 GGTATCGATACTCTCCACATA
1 GGTATCGATACTCTCCACATA
* *
6297287 GGTATCAATAC-CTCTACCATA
1 GGTATCGATACTCTCCA-CATA
* * * *
6297308 TGGTATCGATACTGTTCATACA
1 -GGTATCGATACTCTCCACATA
6297330 GGTATCGATAC
1 GGTATCGATAC
6297341 CCTCTGCAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 4 0.09
21 25 0.58
22 12 0.28
23 2 0.05
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (21 bp):
GGTATCGATACTCTCCACATA
Found at i:6299625 original size:15 final size:15
Alignment explanation
Indices: 6299607--6299638 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6299597 GATTTCATCT
6299607 TCCCGAATTTCTCCA
1 TCCCGAATTTCTCCA
6299622 TCCCGAATTTCTCCA
1 TCCCGAATTTCTCCA
6299637 TC
1 TC
6299639 ATAGTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.41, G:0.06, T:0.34
Consensus pattern (15 bp):
TCCCGAATTTCTCCA
Found at i:6299790 original size:19 final size:21
Alignment explanation
Indices: 6299766--6299805 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
6299756 TATAACCTAA
6299766 TAACAA-AATTTAAA-AATAT
1 TAACAATAATTTAAATAATAT
6299785 TAACAATAATTTAAATAATAT
1 TAACAATAATTTAAATAATAT
6299806 AATTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 8 0.42
21 5 0.26
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAACAATAATTTAAATAATAT
Found at i:6300006 original size:24 final size:24
Alignment explanation
Indices: 6299979--6300034 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
6299969 AATATCAAAT
6299979 GAACT-ATTGAAGAAAATATAGGAG
1 GAACTGATT-AAGAAAATATAGGAG
* *
6300003 GAACTGCTTAAGTAAATATAGGAG
1 GAACTGATTAAGAAAATATAGGAG
*
6300027 GAATTGAT
1 GAACTGAT
6300035 GATGTGATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.45, C:0.05, G:0.25, T:0.25
Consensus pattern (24 bp):
GAACTGATTAAGAAAATATAGGAG
Found at i:6300053 original size:21 final size:22
Alignment explanation
Indices: 6300029--6300069 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6300019 TATAGGAGGA
6300029 ATTG-ATGATGTGATATTTACG
1 ATTGAATGATGTGATATTTACG
* *
6300050 ATTGAATGGTGTGTTATTTA
1 ATTGAATGATGTGATATTTA
6300070 TAGACGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.46
Consensus pattern (22 bp):
ATTGAATGATGTGATATTTACG
Found at i:6302497 original size:17 final size:17
Alignment explanation
Indices: 6302464--6302520 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
6302454 ATTAAAATGA
*
6302464 TTATTTTATTTTATATT
1 TTATTTTATTTAATATT
6302481 TTATTTT-TTTAAGTATT
1 TTATTTTATTTAA-TATT
6302498 TTGA---TA-TTAATATT
1 TT-ATTTTATTTAATATT
6302512 TTATTTTAT
1 TTATTTTAT
6302521 AGTAAATAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
13 1 0.03
14 6 0.19
15 5 0.16
16 6 0.19
17 13 0.41
18 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (17 bp):
TTATTTTATTTAATATT
Found at i:6308425 original size:11 final size:11
Alignment explanation
Indices: 6308403--6308438 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
6308393 CCTATGGAAG
6308403 CTAGAG-GACA
1 CTAGAGTGACA
6308413 CTAGAGTGACA
1 CTAGAGTGACA
6308424 CTAGAGTGACA
1 CTAGAGTGACA
6308435 CTAG
1 CTAG
6308439 GTACCTAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (11 bp):
CTAGAGTGACA
Found at i:6308494 original size:17 final size:16
Alignment explanation
Indices: 6308439--6308495 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
6308429 GTGACACTAG
6308439 GTACCTAGCTAGCTAA
1 GTACCTAGCTAGCTAA
* *
6308455 CTACACTAACTAGCT-A
1 GTAC-CTAGCTAGCTAA
6308471 GCTACCTAGCTAGCTAA
1 G-TACCTAGCTAGCTAA
6308488 GTGACCTA
1 GT-ACCTA
6308496 CCAATCTACC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 14 0.42
17 19 0.58
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (16 bp):
GTACCTAGCTAGCTAA
Found at i:6311149 original size:12 final size:12
Alignment explanation
Indices: 6311114--6311141 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6311104 ATCATTTTCT
6311114 TGGTACTTCTCC
1 TGGTACTTCTCC
6311126 TGGTACTTCTCC
1 TGGTACTTCTCC
6311138 TGGT
1 TGGT
6311142 TTTTCTCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.29, G:0.21, T:0.43
Consensus pattern (12 bp):
TGGTACTTCTCC
Found at i:6312609 original size:27 final size:27
Alignment explanation
Indices: 6312570--6312634 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
6312560 CATGTACAGA
6312570 CAACAAATGCCCCACCAACGCATGCTC
1 CAACAAATGCCCCACCAACGCATGCTC
*
6312597 TAACAAATGCCCCACCAACGCATGCTC
1 CAACAAATGCCCCACCAACGCATGCTC
6312624 CAACAAATGCC
1 CAACAAATGCC
6312635 ACGCCTAATC
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:0.35, C:0.42, G:0.11, T:0.12
Consensus pattern (27 bp):
CAACAAATGCCCCACCAACGCATGCTC
Found at i:6319419 original size:27 final size:27
Alignment explanation
Indices: 6319389--6319457 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
6319379 TTATTTTTTC
* * *
6319389 TACTGTAAATGTTAATATTGAGCACTT
1 TACTGAAAATGTTAATATTAAGAACTT
*
6319416 TACTGGAAATGTTAATATTAAGAACTT
1 TACTGAAAATGTTAATATTAAGAACTT
*
6319443 TGCTGAAAATGTTAA
1 TACTGAAAATGTTAA
6319458 AAAATTAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (27 bp):
TACTGAAAATGTTAATATTAAGAACTT
Found at i:6319481 original size:19 final size:19
Alignment explanation
Indices: 6319457--6319495 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6319447 GAAAATGTTA
6319457 AAAAATTAATGTTTTAGAT
1 AAAAATTAATGTTTTAGAT
6319476 AAAAATTAATGTTTTAGAT
1 AAAAATTAATGTTTTAGAT
6319495 A
1 A
6319496 CTTTTTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (19 bp):
AAAAATTAATGTTTTAGAT
Found at i:6320224 original size:39 final size:39
Alignment explanation
Indices: 6320168--6320295 Score: 202
Period size: 39 Copynumber: 3.3 Consensus size: 39
6320158 TCTATGACTT
6320168 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
* * *
6320207 GTAAGTCCTTACTGCAGGCTCCTAGGCTTTGTGCTTAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
* * *
6320246 ATGAGTCCTTACCGCAAGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
6320285 GTAAGTCCTTA
1 GTAAGTCCTTA
6320296 TAGAAGATAC
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
Found at i:6322237 original size:18 final size:18
Alignment explanation
Indices: 6322214--6322286 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 18
6322204 TGAATATTTG
6322214 TCCCGAAGGACCACTATA
1 TCCCGAAGGACCACTATA
* *
6322232 TCCCGAAAGACCATTATATA
1 TCCCGAAGGACCA--CTATA
* *
6322252 TGTCACGAAGGACCACTATG
1 --TCCCGAAGGACCACTATA
6322272 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
6322287 GTATATCCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
18 26 0.59
20 7 0.16
22 11 0.25
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.19
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:6322276 original size:40 final size:40
Alignment explanation
Indices: 6322207--6322284 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
6322197 GGGGAACTGA
* *
6322207 ATATTTGTCCCGAAGGACCACTATATCCCGAAAGACCATT
1 ATATATGTCACGAAGGACCACTATATCCCGAAAGACCATT
* *
6322247 ATATATGTCACGAAGGACCACTATGTCCCGAAGGACCA
1 ATATATGTCACGAAGGACCACTATATCCCGAAAGACCA
6322285 CTGTATATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (40 bp):
ATATATGTCACGAAGGACCACTATATCCCGAAAGACCATT
Found at i:6329144 original size:22 final size:21
Alignment explanation
Indices: 6329123--6329180 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 21
6329113 CACTGAATAT
6329123 TTGTCCCGAATGACCACTATA
1 TTGTCCCGAATGACCACTATA
6329144 ---TCCCGAATGACCACTATA
1 TTGTCCCGAATGACCACTATA
*
6329162 TATGTCCCGAAGGACCACT
1 T-TGTCCCGAATGACCACT
6329181 GTATATCCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 18 0.56
22 14 0.44
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (21 bp):
TTGTCCCGAATGACCACTATA
Found at i:6329185 original size:22 final size:21
Alignment explanation
Indices: 6329124--6329186 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
6329114 ACTGAATATT
6329124 TGTCCCGAATGACCAC-TATA
1 TGTCCCGAATGACCACTTATA
6329144 --TCCCGAATGACCACTATATA
1 TGTCCCGAATGACCACT-TATA
*
6329164 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAATGACCACT-TATA
6329186 T
1 T
6329187 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 14 0.38
20 4 0.11
22 19 0.51
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (21 bp):
TGTCCCGAATGACCACTTATA
Found at i:6330688 original size:20 final size:20
Alignment explanation
Indices: 6330663--6330706 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
6330653 TTCCAGGAAA
6330663 TCAATTGACTTGGGATCTTT
1 TCAATTGACTTGGGATCTTT
*
6330683 TCAATTGATTTGGGATCTTT
1 TCAATTGACTTGGGATCTTT
6330703 TCAA
1 TCAA
6330707 GGCACGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (20 bp):
TCAATTGACTTGGGATCTTT
Found at i:6335240 original size:10 final size:10
Alignment explanation
Indices: 6335221--6335250 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6335211 TTGCATCATC
6335221 CCGA-GTCCA
1 CCGATGTCCA
6335230 CCGATGTCCA
1 CCGATGTCCA
6335240 CCGATGTCCA
1 CCGATGTCCA
6335250 C
1 C
6335251 TTTGTCTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.17
Consensus pattern (10 bp):
CCGATGTCCA
Found at i:6335882 original size:3 final size:3
Alignment explanation
Indices: 6335874--6335908 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
6335864 TAAATAGGGG
6335874 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6335909 CATATTATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6336388 original size:39 final size:39
Alignment explanation
Indices: 6336330--6336462 Score: 176
Period size: 39 Copynumber: 3.4 Consensus size: 39
6336320 TCTATGACTT
* **
6336330 GTAAGTCTTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCACAGGCTCCTCGGCTTTGTGCTCAGG
* ** *
6336369 ATAAGTAATTACCACAGGCTCCTTGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCACAGGCTCCTCGGCTTTGTGCTCAGG
** *
6336408 GTAAGTCCTTACTGCAGGCTCCTCGACTTTGTGCTCAGG
1 GTAAGTCCTTACCACAGGCTCCTCGGCTTTGTGCTCAGG
6336447 GTAAGTCCTTACCACA
1 GTAAGTCCTTACCACA
6336463 AGTCCTTATG
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (39 bp):
GTAAGTCCTTACCACAGGCTCCTCGGCTTTGTGCTCAGG
Found at i:6338029 original size:3 final size:3
Alignment explanation
Indices: 6338021--6338065 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
6338011 TCTTGTCACA
6338021 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6338066 TGTTTTCTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6350334 original size:31 final size:31
Alignment explanation
Indices: 6350296--6350397 Score: 195
Period size: 31 Copynumber: 3.3 Consensus size: 31
6350286 TAAGGTGGCC
6350296 CTTGGGTAGGCTCCGAGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCCGAGGCCCCGAGATCTTT
6350327 CTTGGGTAGGCTCCGAGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCCGAGGCCCCGAGATCTTT
6350358 CTTGGGTAGGCTCCGAGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCCGAGGCCCCGAGATCTTT
*
6350389 CTTAGGTAG
1 CTTGGGTAG
6350398 TCCCCGTGGC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.14, C:0.27, G:0.32, T:0.26
Consensus pattern (31 bp):
CTTGGGTAGGCTCCGAGGCCCCGAGATCTTT
Found at i:6350409 original size:31 final size:31
Alignment explanation
Indices: 6350300--6350429 Score: 179
Period size: 31 Copynumber: 4.2 Consensus size: 31
6350290 GTGGCCCTTG
*
6350300 GGTAGGCTCCGAGGCCCCGAGATCTTTCTTG
1 GGTAGGCTCCGAGGCCCCGAGATCTTTCTTA
*
6350331 GGTAGGCTCCGAGGCCCCGAGATCTTTCTTG
1 GGTAGGCTCCGAGGCCCCGAGATCTTTCTTA
6350362 GGTAGGCTCCGAGGCCCCGAGATCTTTCTTA
1 GGTAGGCTCCGAGGCCCCGAGATCTTTCTTA
* * * * * *
6350393 GGTAGTCCCCGTGGCCCCAAGTAACCTTCTTA
1 GGTAGGCTCCGAGGCCCCGAG-ATCTTTCTTA
6350425 GGTAG
1 GGTAG
6350430 ACTCTCGGGC
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
31 78 0.86
32 13 0.14
ACGTcount: A:0.15, C:0.29, G:0.30, T:0.25
Consensus pattern (31 bp):
GGTAGGCTCCGAGGCCCCGAGATCTTTCTTA
Found at i:6353674 original size:19 final size:20
Alignment explanation
Indices: 6353642--6353679 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6353632 TACTATATAT
6353642 TACTTGCATCGA-TTGTGTA
1 TACTTGCATCGATTTGTGTA
6353661 TACTTGCA-CAGATTTGTGT
1 TACTTGCATC-GATTTGTGT
6353680 GTCACAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 10 0.59
20 6 0.35
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (20 bp):
TACTTGCATCGATTTGTGTA
Found at i:6355107 original size:27 final size:28
Alignment explanation
Indices: 6355077--6355131 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
6355067 ACAATTTATA
*
6355077 ATGTCTTGGAG-AGGTGCCGATTGGACG
1 ATGTCGTGGAGTAGGTGCCGATTGGACG
* **
6355104 ATGTCGTGGTGTAGGTGTTGATTGGACG
1 ATGTCGTGGAGTAGGTGCCGATTGGACG
6355132 TCTTAAGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.16, C:0.11, G:0.42, T:0.31
Consensus pattern (28 bp):
ATGTCGTGGAGTAGGTGCCGATTGGACG
Found at i:6361547 original size:24 final size:24
Alignment explanation
Indices: 6361516--6361576 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
6361506 AAAGAGAGAG
6361516 GAGCAATTGAGGGGAGTTAAAGCA
1 GAGCAATTGAGGGGAGTTAAAGCA
6361540 GAGCAATTGAGGGGAGTTAAAGCA
1 GAGCAATTGAGGGGAGTTAAAGCA
6361564 GAGCAATTGAGGG
1 GAGCAATTGAGGG
6361577 CGTTGGGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.39, T:0.16
Consensus pattern (24 bp):
GAGCAATTGAGGGGAGTTAAAGCA
Found at i:6363899 original size:19 final size:20
Alignment explanation
Indices: 6363867--6363905 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
6363857 TACACTTTTC
*
6363867 ATTCTATATCAATTTGTTTA
1 ATTCTATATCAATTGGTTTA
*
6363887 ATTC-ATATTAATTGGTTTA
1 ATTCTATATCAATTGGTTTA
6363906 TTTAGCCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTCTATATCAATTGGTTTA
Found at i:6364036 original size:24 final size:24
Alignment explanation
Indices: 6364009--6364131 Score: 117
Period size: 23 Copynumber: 5.2 Consensus size: 24
6363999 GAAGTGTCAT
* *
6364009 GTAGAATTTGGCCCGAAAGACCGC
1 GTAGAATTTGTCCCGAAAGACCAC
* *
6364033 GTAGAATTTGTCACGAACGACCAC
1 GTAGAATTTGTCCCGAAAGACCAC
* *
6364057 TTAG-ATTTTTCCCGAAAGACCAC
1 GTAGAATTTGTCCCGAAAGACCAC
* *
6364080 GTAGAA-TTGACCCGAATGACCAC
1 GTAGAATTTGTCCCGAAAGACCAC
* * * *
6364103 ATAG-ATTTGTCTCGAATGACTAC
1 GTAGAATTTGTCCCGAAAGACCAC
6364126 GTAGAA
1 GTAGAA
6364132 CCCTCGACTC
Statistics
Matches: 79, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
22 1 0.01
23 53 0.67
24 25 0.32
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (24 bp):
GTAGAATTTGTCCCGAAAGACCAC
Found at i:6364128 original size:46 final size:47
Alignment explanation
Indices: 6364014--6364131 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 47
6364004 GTCATGTAGA
* * * *
6364014 ATTTGGCCCGAAAGACCGCGTAGAATTTGTCACGAACGACCACTTAG
1 ATTTGTCCCGAAAGACCACGTAGAATTTGACACGAACGACCACATAG
* * *
6364061 ATTTTTCCCGAAAGACCACGTAGAA-TTGACCCGAATGACCACATAG
1 ATTTGTCCCGAAAGACCACGTAGAATTTGACACGAACGACCACATAG
* * *
6364107 ATTTGTCTCGAATGACTACGTAGAA
1 ATTTGTCCCGAAAGACCACGTAGAA
6364132 CCCTCGACTC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
46 38 0.63
47 22 0.37
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (47 bp):
ATTTGTCCCGAAAGACCACGTAGAATTTGACACGAACGACCACATAG
Found at i:6369319 original size:24 final size:24
Alignment explanation
Indices: 6369284--6369355 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
6369274 TAAAGTGCCA
*
6369284 TTGTTCTGAAGGACCGTGTAGAAT
1 TTGTTCTGAAGGACCATGTAGAAT
* **
6369308 TTGTTCTAAAGGACCACATAG-AT
1 TTGTTCTGAAGGACCATGTAGAAT
*
6369331 TTGTTCTGAAGGACCATGTATAAT
1 TTGTTCTGAAGGACCATGTAGAAT
6369355 T
1 T
6369356 GTCCCGAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 19 0.49
24 20 0.51
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (24 bp):
TTGTTCTGAAGGACCATGTAGAAT
Found at i:6369357 original size:23 final size:23
Alignment explanation
Indices: 6369283--6369357 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
6369273 CTAAAGTGCC
*
6369283 ATTGTTCTGAAGGACCGTGTAGA
1 ATTGTTCTGAAGGACCATGTAGA
* **
6369306 ATTTGTTCTAAAGGACCACATAGA
1 A-TTGTTCTGAAGGACCATGTAGA
* *
6369330 TTTGTTCTGAAGGACCATGTATA
1 ATTGTTCTGAAGGACCATGTAGA
6369353 ATTGT
1 ATTGT
6369358 CCCGAATGAC
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 23 0.56
24 18 0.44
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTGTTCTGAAGGACCATGTAGA
Found at i:6369526 original size:15 final size:15
Alignment explanation
Indices: 6369506--6369542 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
6369496 TCACATAGGT
*
6369506 ATTTTCACGTAGAAC
1 ATTTTCACGTAAAAC
*
6369521 ATTTTCACTTAAAAC
1 ATTTTCACGTAAAAC
6369536 ATTTTCA
1 ATTTTCA
6369543 TATAAACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (15 bp):
ATTTTCACGTAAAAC
Found at i:6373888 original size:23 final size:24
Alignment explanation
Indices: 6373840--6373889 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
6373830 AGTTTTGATT
* *
6373840 TTTAAATAATTTTTATATTTTAAA
1 TTTAAATAACTTCTATATTTTAAA
*
6373864 TTTAAATAACTTCTA-ATTTTTAA
1 TTTAAATAACTTCTATATTTTAAA
6373887 TTT
1 TTT
6373890 TTTATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTAAATAACTTCTATATTTTAAA
Found at i:6376522 original size:21 final size:20
Alignment explanation
Indices: 6376471--6376523 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
6376461 TGTAATTTGG
*
6376471 GATTTA-GGGTTTAAGGTTT
1 GATTTAGGGGTTTAAGGTAT
* *
6376490 GATTTTGAGGTTTAAGGATAT
1 GATTTAGGGGTTTAAGG-TAT
6376511 GATTTAGGGGTTT
1 GATTTAGGGGTTT
6376524 TAATTTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 5 0.19
20 9 0.33
21 13 0.48
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (20 bp):
GATTTAGGGGTTTAAGGTAT
Found at i:6377054 original size:18 final size:18
Alignment explanation
Indices: 6377031--6377067 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6377021 TTCTATGAGA
6377031 AAAAAATATATAAAACTT
1 AAAAAATATATAAAACTT
*
6377049 AAAAAATATATAAATCTT
1 AAAAAATATATAAAACTT
6377067 A
1 A
6377068 TAGTTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAATATATAAAACTT
Found at i:6380083 original size:23 final size:24
Alignment explanation
Indices: 6380057--6380105 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
6380047 TTTTTAACAA
*
6380057 CTCTGCTTTTATAACAC-ATTTTC
1 CTCTGCATTTATAACACTATTTTC
*
6380080 CTCTGCATTTATGACACTATTTTC
1 CTCTGCATTTATAACACTATTTTC
6380104 CT
1 CT
6380106 AGCTTTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.20, C:0.27, G:0.06, T:0.47
Consensus pattern (24 bp):
CTCTGCATTTATAACACTATTTTC
Found at i:6380115 original size:22 final size:23
Alignment explanation
Indices: 6380064--6380115 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
6380054 CAACTCTGCT
* *
6380064 TTTATAACACATTTTCCTCTGCA
1 TTTATGACACATTTTCCTCAGCA
6380087 TTTATGACACTATTTTCCT-AGC-
1 TTTATGACAC-ATTTTCCTCAGCA
6380109 TTTATGA
1 TTTATGA
6380116 AATGTTTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 7 0.27
23 11 0.42
24 8 0.31
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (23 bp):
TTTATGACACATTTTCCTCAGCA
Found at i:6380827 original size:24 final size:25
Alignment explanation
Indices: 6380800--6380848 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
6380790 TTTCTTTTTT
6380800 TAAAATGT-TTATTTTT-TAAAAAAA
1 TAAAAT-TATTATTTTTATAAAAAAA
*
6380824 TAAAATTATTTTTTTTATAAAAAAA
1 TAAAATTATTATTTTTATAAAAAAA
6380849 CCCTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 13 0.59
25 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TAAAATTATTATTTTTATAAAAAAA
Found at i:6383343 original size:24 final size:25
Alignment explanation
Indices: 6383316--6383363 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
6383306 TCTCTTTTCT
* *
6383316 TCTCGGTTTTGTTTT-TTTTATTTG
1 TCTCGCTTTTCTTTTATTTTATTTG
*
6383340 TCTCTCTTTTCTTTTATTTTATTT
1 TCTCGCTTTTCTTTTATTTTATTT
6383364 TCTTACGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.06, C:0.12, G:0.08, T:0.73
Consensus pattern (25 bp):
TCTCGCTTTTCTTTTATTTTATTTG
Found at i:6397351 original size:14 final size:14
Alignment explanation
Indices: 6397330--6397375 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
6397320 AAAATAATAA
*
6397330 AAAAATAC-CAAGT
1 AAAAATACACAAAT
6397343 AAAATATACACAAAT
1 AAAA-ATACACAAAT
*
6397358 AAAAATACAAAAAT
1 AAAAATACACAAAT
6397372 AAAA
1 AAAA
6397376 TGCTCTGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 4 0.14
14 17 0.59
15 8 0.28
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (14 bp):
AAAAATACACAAAT
Found at i:6399882 original size:10 final size:10
Alignment explanation
Indices: 6399867--6399897 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6399857 TTTCTCAATG
6399867 ACAAAATAAA
1 ACAAAATAAA
*
6399877 ATAAAATAAA
1 ACAAAATAAA
6399887 ACAAAATAAA
1 ACAAAATAAA
6399897 A
1 A
6399898 GTGAAAAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (10 bp):
ACAAAATAAA
Found at i:6400277 original size:30 final size:30
Alignment explanation
Indices: 6400243--6400367 Score: 135
Period size: 30 Copynumber: 4.2 Consensus size: 30
6400233 TTAAAATTAC
*
6400243 AAGGGCCAAAATGGGAAAAATAGTAACTTA
1 AAGGGCCAAAATAGGAAAAATAGTAACTTA
*
6400273 AAGGGCCAAAATGGGAAAAATAGTAACTTA
1 AAGGGCCAAAATAGGAAAAATAGTAACTTA
* * * * * *
6400303 AAGGACCAAAATAGTACAAACAGGAATTTA
1 AAGGGCCAAAATAGGAAAAATAGTAACTTA
* * *
6400333 AAGGACTAAAATAGCAAAAATAG-AATCTTA
1 AAGGGCCAAAATAGGAAAAATAGTAA-CTTA
6400363 AAGGG
1 AAGGG
6400368 TTGAGTAGTA
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 2 0.02
30 79 0.98
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (30 bp):
AAGGGCCAAAATAGGAAAAATAGTAACTTA
Found at i:6401747 original size:3 final size:3
Alignment explanation
Indices: 6401739--6401800 Score: 115
Period size: 3 Copynumber: 20.3 Consensus size: 3
6401729 CTACAAAATG
6401739 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6401787 TAA TAA TATA TAA T
1 TAA TAA TA-A TAA T
6401801 CTTTTTGTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:6402583 original size:20 final size:20
Alignment explanation
Indices: 6402558--6402732 Score: 190
Period size: 20 Copynumber: 8.7 Consensus size: 20
6402548 AATTTGGAAA
*
6402558 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
6402578 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
6402598 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
6402619 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
6402639 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
6402659 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
6402679 TTCGCAACACGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
6402699 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
6402719 ATCGCAACGAGATA
1 ATCGCAACGCGATA
6402733 ATACATAATC
Statistics
Matches: 138, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.01
20 119 0.86
21 15 0.11
22 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:6402905 original size:12 final size:12
Alignment explanation
Indices: 6402888--6402919 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
6402878 CTCCGACGAC
6402888 ATCCGTTCCTAT
1 ATCCGTTCCTAT
6402900 ATCCGTTCCTAT
1 ATCCGTTCCTAT
6402912 ATCC-TTCC
1 ATCCGTTCC
6402920 CCATCCGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.16, C:0.38, G:0.06, T:0.41
Consensus pattern (12 bp):
ATCCGTTCCTAT
Found at i:6403501 original size:24 final size:24
Alignment explanation
Indices: 6403474--6403527 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
6403464 GTATTCGAAA
*
6403474 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
6403498 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
6403522 TTTGAT
1 TTTGAT
6403528 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:6406020 original size:20 final size:20
Alignment explanation
Indices: 6405995--6406043 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
6405985 CAACGGGGAA
*
6405995 ATCGCATCGCAAAAATGGCT
1 ATCGCAACGCAAAAATGGCT
*
6406015 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCAAAAATGGCT
6406035 ATCGCAACG
1 ATCGCAACG
6406044 AGAAAATCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGGCT
Found at i:6406048 original size:20 final size:20
Alignment explanation
Indices: 6406006--6406050 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
6405996 TCGCATCGCA
*
6406006 AAAATGGCTATCGCAACGCG
1 AAAATGGCTATCGCAACGAG
6406026 AAAATGGCTATCGCAACGAG
1 AAAATGGCTATCGCAACGAG
6406046 AAAAT
1 AAAAT
6406051 CGTAATGCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
AAAATGGCTATCGCAACGAG
Found at i:6407757 original size:41 final size:42
Alignment explanation
Indices: 6407703--6407794 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
6407693 CCTCTTCAAC
* *
6407703 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
6407744 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
6407786 GATGACAGG
1 GATGACAGG
6407795 TGAGTCAAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:6407759 original size:21 final size:21
Alignment explanation
Indices: 6407730--6407790 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
6407720 GAACGGTGGG
*
6407730 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
6407751 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
6407772 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
6407791 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:6408156 original size:20 final size:20
Alignment explanation
Indices: 6408131--6408183 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
6408121 GAAGAATAGT
*
6408131 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
6408151 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
6408171 TGACTATCGCAAC
1 TTACTTTCGCAAC
6408184 GCGGAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:6408184 original size:20 final size:20
Alignment explanation
Indices: 6408137--6408231 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
6408127 TAGTTTACTT
* * * *
6408137 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
6408157 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
6408177 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
6408197 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
*
6408216 TCGCAATGC-AAAATGA
1 TCGCAACGCGAAAATGA
6408232 AAATTGCAAC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
19 21 0.33
20 43 0.67
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:6408269 original size:19 final size:19
Alignment explanation
Indices: 6408196--6408269 Score: 86
Period size: 19 Copynumber: 4.2 Consensus size: 19
6408186 GGAAATGGCT
6408196 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6408215 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
6408234 ATTGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
6408248 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
6408267 ATC
1 ATC
6408270 ACAACGACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.05
17 1 0.02
18 1 0.02
19 30 0.68
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6408293 original size:33 final size:33
Alignment explanation
Indices: 6408212--6408294 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
6408202 ATGCGAAATG
* **
6408212 AAAATCGCAATGCAAAATGAAAATTGCAACGAC
1 AAAATCGCAATGCGAAATGAAAATCACAACGAC
6408245 AAAATCGCAATGCGAAATGAAAATCACAACGAC
1 AAAATCGCAATGCGAAATGAAAATCACAACGAC
*
6408278 AAAATCGCAACGCGAAA
1 AAAATCGCAATGCGAAA
6408295 CACAAATCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.52, C:0.20, G:0.16, T:0.12
Consensus pattern (33 bp):
AAAATCGCAATGCGAAATGAAAATCACAACGAC
Found at i:6408302 original size:33 final size:33
Alignment explanation
Indices: 6408212--6408305 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
6408202 ATGCGAAATG
* * * **
6408212 AAAATCGCAATGCAAAATGAAAATTGCAACGAC
1 AAAATCGCAACGCGAAATCAAAATCACAACGAC
* *
6408245 AAAATCGCAATGCGAAATGAAAATCACAACGAC
1 AAAATCGCAACGCGAAATCAAAATCACAACGAC
6408278 AAAATCGCAACGCGAAA-CACAAATCACA
1 AAAATCGCAACGCGAAATCA-AAATCACA
6408306 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 1 0.02
33 54 0.98
ACGTcount: A:0.52, C:0.22, G:0.14, T:0.12
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATCAAAATCACAACGAC
Found at i:6408328 original size:19 final size:19
Alignment explanation
Indices: 6408306--6408436 Score: 75
Period size: 19 Copynumber: 7.3 Consensus size: 19
6408296 ACAAATCACA
*
6408306 TTGCGATTTTCATTTCGTG
1 TTGCGATTTTCATTTCGCG
6408325 TTGCGA-TTT--TTT--CG
1 TTGCGATTTTCATTTCGCG
* *
6408339 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
6408358 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
6408372 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
6408391 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
** *
6408411 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
6408431 TTGCGA
1 TTGCGA
6408437 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
14 13 0.15
15 6 0.07
16 5 0.06
17 5 0.06
18 6 0.07
19 25 0.29
20 23 0.27
21 3 0.03
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Done.