Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 39
Found at i:4212090 original size:14 final size:14
Alignment explanation
Indices: 4212041--4212098 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
4212031 ATAAAAGATA
4212041 AAAAAAAGAAAAGAG
1 AAAAAAAG-AAAGAG
*
4212056 AAAAGATAGAAAAATGAAG
1 AAAA-A-A-AGAAA-G-AG
4212075 AAAAAAAGAAAGAG
1 AAAAAAAGAAAGAG
4212089 AAAAAAAGAA
1 AAAAAAAGAA
4212099 TAAAAGAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
14 12 0.33
15 5 0.14
16 5 0.14
17 5 0.14
18 3 0.08
19 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAGAG
Found at i:4212125 original size:34 final size:34
Alignment explanation
Indices: 4212030--4212125 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 34
4212020 TATTCAAGAC
4212030 AATAAAAG-ATAAAAAAAAGAAAAGAGAAAAGATAG
1 AATAAAAGAAT-AAAAAAAGAAAAGA-AAAAGATAG
* *
4212065 AA-AAATGAAGAAAAAAAGAAAGAGAAAAA-A-AG
1 AATAAAAGAATAAAAAAAGAAA-AGAAAAAGATAG
4212097 AATAAAAGAATAAAAAAGAGAAGAAGAAA
1 AATAAAAGAATAAAAAA-AGAA-AAGAAA
4212126 GAGAACACAT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
32 4 0.08
33 13 0.25
34 28 0.54
35 7 0.13
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (34 bp):
AATAAAAGAATAAAAAAAGAAAAGAAAAAGATAG
Found at i:4213620 original size:45 final size:45
Alignment explanation
Indices: 4213544--4214211 Score: 764
Period size: 45 Copynumber: 14.8 Consensus size: 45
4213534 AATATCAGCA
* ** * *
4213544 TGACTTTCTCATGAAGAAAAGTTAATCTTTTAGTGATGTCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
* ** * *
4213589 TGGCTTTCTCGTGAAGAGGAGTCAATATTTTAGTGTTGTCATTTT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
* * * * *
4213634 TTAATTTCTCGTGAAGAGGAGTCAATCTGTTAGTGTTGTCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
* * * * *
4213679 TAAATTTCTCATGAAGAGGATTCAATCTTTTAGT-ATTGTCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGA-TGTCATTCT
* * *
4213724 TGACTTTCTCATGAAGAGGAGTCAATCTTTTAGCGATGTCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
* *
4213769 TGACTTTCTCGTGAAAAGGAGTCAACCTTTTAGTGATATCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
** *
4213814 TGACTTTCTCGCAAAGAGGAATCAACCTTTTAGTGATGTCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
* * * * * *
4213859 TGACTTTCTCGTGAATATGAGTCAATCTTTTAGAGTTGTCTTTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
*
4213904 TGAATTTCTC-TGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
*
4213948 TGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
** * * *
4213993 TGACTTTCTCGAAAAGAGGAGTCAATCTTTTAGTGTTGTCCTTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
* **
4214038 TAACTTTCTCGCAAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
* ** *
4214083 TGATTTTCTCACGAAGATGAGTCAACCTTTTAGTGATGTCATTCT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
* ** *
4214128 TAACTTTCTCACGAAGAAGAGTCAACCTTTTAGTGATGTCATTTTTAACT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCA---TT--CT
* * * *
4214178 TGACTTTCTCGCGAAGAGGGGTAAACTTTTTAGT
1 TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGT
4214212 AGTATCATTC
Statistics
Matches: 540, Mismatches: 75, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
44 37 0.07
45 470 0.87
46 1 0.00
48 2 0.00
50 30 0.06
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (45 bp):
TGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTCT
Found at i:4214877 original size:55 final size:55
Alignment explanation
Indices: 4214748--4214881 Score: 187
Period size: 55 Copynumber: 2.4 Consensus size: 55
4214738 CTTTGAGGTG
* * * * *
4214748 CACACGTAGTGTCAATACGATAGTTCATAAACATATAATGAATTCCGTGGTTTTG
1 CACACTTAGTGTCAATACGGTCGTTCATAAACATATAATGAATTCCGTAGTTTTA
* * *
4214803 CACACTTAGTGTTAATACGGTCGTTCATAAACATATTATGAATTTCGTAGTTTTA
1 CACACTTAGTGTCAATACGGTCGTTCATAAACATATAATGAATTCCGTAGTTTTA
*
4214858 CACACTTAGTGTCGATACGGTCGT
1 CACACTTAGTGTCAATACGGTCGT
4214882 AATTTTGTGG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 69 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (55 bp):
CACACTTAGTGTCAATACGGTCGTTCATAAACATATAATGAATTCCGTAGTTTTA
Found at i:4214975 original size:55 final size:54
Alignment explanation
Indices: 4214885--4215016 Score: 185
Period size: 55 Copynumber: 2.4 Consensus size: 54
4214875 CGGTCGTAAT
* * **
4214885 TTTGTGG-TTTGCACACTTAGTACCGATACGGTCGTTCATAAACATATTATGAA
1 TTTGTGGTTTTGCACACTTAGTGCCGAGACAATCGTTCATAAACATATTATGAA
* *
4214938 TTATGTGGTTTTGCATACTTAGTGCCGAGACAATCGTTCATAAATATATTATGAA
1 TT-TGTGGTTTTGCACACTTAGTGCCGAGACAATCGTTCATAAACATATTATGAA
4214993 TTTCGTGGTTTTGCACACTTAGTG
1 TTT-GTGGTTTTGCACACTTAGTG
4215017 TCGAAGTACA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.03
54 6 0.09
55 61 0.88
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (54 bp):
TTTGTGGTTTTGCACACTTAGTGCCGAGACAATCGTTCATAAACATATTATGAA
Found at i:4217834 original size:263 final size:263
Alignment explanation
Indices: 4217362--4217841 Score: 574
Period size: 263 Copynumber: 1.8 Consensus size: 263
4217352 TGAAGAACAA
* * * * * *
4217362 TGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCCACATTTTCATAT
1 TGAAGAAAATCAACCTCGATTCAATCCTCCCTGAAGAGAAGTGAAGTGAATCCAAAGTTTCAGAT
* * * * ** *
4217427 ATGATCTACCCTGAAGAGTAGCATATCATATCCCTTTTTTACATATTTGATATTCCATGAAGAGC
66 ATGATCTACCCTGAAAAGCAACAGAGAATATCCCTTTTTTACAAATTTGATATTCCATGAAGAGC
* * * * * * * *
4217492 AGTGAAGTAAATCTACCTCGATTTATTCTTTCTTAAAGAGCATTAAATTGAATCAACGTTTCTAA
131 AGTGAAGCAAATCTACCTCGATTTAATCTTCCCTAAAGAACAGTAAAGTGAATCAACGTTTCCAA
*
4217557 ATCTAATATACCCTGAAAAGCATAGAAGCAAATCCATTTTTTCAGATTTGATCTTCTTTGAGTAG
196 ATATAATATACCCTGAAAAGCATAGAAGCAAATCCATTTTTTCAGATTTGATCTTCTTTGAGTAG
4217622 CAG
261 CAG
* * *
4217625 TGAAGAAAATCTACCTCGATTCAATCCTCCGTGAAGAGAAGTGATGTGAAT-CAAAGTTTCTAGA
1 TGAAGAAAATCAACCTCGATTCAATCCTCCCTGAAGAGAAGTGAAGTGAATCCAAAGTTTC-AGA
* *
4217689 TCTGATCTACCCTGAAAAGCAACAGAGAATATCCCCTTTTTT-CAAATTTGATCTTCTC-TGAAG
65 TATGATCTACCCTGAAAAGCAACAGAGAATAT-CCCTTTTTTACAAATTTGATATTC-CATGAAG
* * *
4217752 AGCAGTGGAA-CAAATCTACCTCGATTTAATCTTCCCTGAGGAACAGTGAAGTGAATCGAA-GTT
128 AGCAGT-GAAGCAAATCTACCTCGATTTAATCTTCCCTAAAGAACAGTAAAGTGAATC-AACGTT
* * * *
4217815 TCCATATATGATCTACCCTGAAGAGCA
191 TCCAAATATAATATACCCTGAAAAGCA
4217842 GCGGAGCATA
Statistics
Matches: 178, Mismatches: 34, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
262 7 0.04
263 156 0.88
264 15 0.08
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (263 bp):
TGAAGAAAATCAACCTCGATTCAATCCTCCCTGAAGAGAAGTGAAGTGAATCCAAAGTTTCAGAT
ATGATCTACCCTGAAAAGCAACAGAGAATATCCCTTTTTTACAAATTTGATATTCCATGAAGAGC
AGTGAAGCAAATCTACCTCGATTTAATCTTCCCTAAAGAACAGTAAAGTGAATCAACGTTTCCAA
ATATAATATACCCTGAAAAGCATAGAAGCAAATCCATTTTTTCAGATTTGATCTTCTTTGAGTAG
CAG
Found at i:4217861 original size:132 final size:132
Alignment explanation
Indices: 4217218--4217875 Score: 608
Period size: 132 Copynumber: 5.0 Consensus size: 132
4217208 TGATATTTTT
* * * * *
4217218 TGAAGAGTAGTGAAGTAAATCAACCCCGATTCAATCTTCCCTGAAGAGTAGTGAAGTGAATCAAA
1 TGAAGAGCAGTGAAGCAAATCTACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAAA
* * * * * *
4217283 CTTTTTAGATCTGATATACCTTGGAACA-CAGCGGAGCATATCCCTTCTTTTTCCATATTTGATC
66 GTTTCTAGATCTGATCTACCCT-GAAAAGCAGCGGAGCATATCCCTT-TTTTT-CAGATTTGATC
*
4217347 TTCCC
128 TTCTC
* * * *
4217352 TGAAGAACAATGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCCAC
1 TGAAGAGCAGTGAAGCAAATCTACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAAT-CAA
* * * * * ** * * * *
4217417 ATTTTC-ATATATGATCTACCCTGAAGAGTAGCATATCATATCCCTTTTTTACATATTTGATATT
65 AGTTTCTAGATCTGATCTACCCTGAAAAGCAGCGGAGCATATCCCTTTTTTTCAGATTTGATCTT
4217481 C-C
130 CTC
* * * * * * * * *
4217483 ATGAAGAGCAGTGAAGTAAATCTACCTCGATTTATTCTTTCTTAAAGAGCATTAAATTGAATCAA
1 -TGAAGAGCAGTGAAGCAAATCTACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAA
* * * * ** * * *
4217548 CGTTTCTAAATCTAATATACCCTGAAAAGCATAGAAGCAAAT-CCATTTTTTCAGATTTGATCTT
65 AGTTTCTAGATCTGATCTACCCTGAAAAGCAGCGGAGCATATCCCTTTTTTTCAGATTTGATCTT
*
4217612 CTT
130 CTC
* * * * *
4217615 TG-AGTAGCAGTGAAGAAAATCTACCTCGATTCAATCCTCCGTGAAGAGAAGTGATGTGAATCAA
1 TGAAG-AGCAGTGAAGCAAATCTACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAA
* * * * *
4217679 AGTTTCTAGATCTGATCTACCCTGAAAAGCAACAGAGAATATCCCCTTTTTTCAAATTTGATCTT
65 AGTTTCTAGATCTGATCTACCCTGAAAAGCAGCGGAGCATATCCCTTTTTTTCAGATTTGATCTT
4217744 CTC
130 CTC
* * * *
4217747 TGAAGAGCAGTGGAA-CAAATCTACCTCGATTTAATCTTCCCTGAGGAACAGTGAAGTGAATCGA
1 TGAAGAGCAGT-GAAGCAAATCTACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAA
* * * * **
4217811 AGTTTCCATATATGATCTACCCTGAAGAGCAGCGGAGCATATACTTTTTTTTTCAGATTTGATCT
65 AGTTTCTAGATCTGATCTACCCTGAAAAGCAGCGGAGCATAT-CCCTTTTTTTCAGATTTGATCT
4217876 CTAAAAATAT
Statistics
Matches: 417, Mismatches: 97, Indels: 21
0.78 0.18 0.04
Matches are distributed among these distances:
130 2 0.00
131 107 0.26
132 190 0.46
133 31 0.07
134 81 0.19
135 6 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (132 bp):
TGAAGAGCAGTGAAGCAAATCTACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAAA
GTTTCTAGATCTGATCTACCCTGAAAAGCAGCGGAGCATATCCCTTTTTTTCAGATTTGATCTTC
TC
Found at i:4219207 original size:24 final size:24
Alignment explanation
Indices: 4219180--4219226 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
4219170 AATACACATC
4219180 AAATTTATTTGAGGATTTTTGTAT
1 AAATTTATTTGAGGATTTTTGTAT
4219204 AAATTTATTTGAGGATTTTTGTA
1 AAATTTATTTGAGGATTTTTGTA
4219227 GAGAACATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (24 bp):
AAATTTATTTGAGGATTTTTGTAT
Found at i:4222287 original size:17 final size:17
Alignment explanation
Indices: 4222265--4222299 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4222255 GGGTGTTACA
4222265 TTTAATGGTATTAGAGC
1 TTTAATGGTATTAGAGC
4222282 TTTAATGGTATTAGAGC
1 TTTAATGGTATTAGAGC
4222299 T
1 T
4222300 AAGGTTTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (17 bp):
TTTAATGGTATTAGAGC
Found at i:4224722 original size:34 final size:32
Alignment explanation
Indices: 4224660--4224729 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
4224650 CCTTACAAAC
* *
4224660 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
4224692 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
4224726 TCCC
1 TCCC
4224730 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:4225035 original size:21 final size:21
Alignment explanation
Indices: 4225011--4225053 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4225001 CCCAGAATAG
*
4225011 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
4225032 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
4225053 A
1 A
4225054 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:4225115 original size:21 final size:21
Alignment explanation
Indices: 4225089--4225132 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
4225079 TTGTTGAACA
*
4225089 GGGGGGGAATCGGTACCCCCT
1 GGGGGGAAATCGGTACCCCCT
4225110 GGGGGGAAATCGGTACCCCCT
1 GGGGGGAAATCGGTACCCCCT
4225131 GG
1 GG
4225133 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (21 bp):
GGGGGGAAATCGGTACCCCCT
Found at i:4225192 original size:21 final size:20
Alignment explanation
Indices: 4225166--4225244 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 20
4225156 AAAACCTGCA
4225166 GGGGGGTATCTGTACCCCCT
1 GGGGGGTATCTGTACCCCCT
4225186 GGGGGGGTATCTGTA--CCC-
1 -GGGGGGTATCTGTACCCCCT
4225204 --GGGGTATCTGTACCCCCT
1 GGGGGGTATCTGTACCCCCT
* * *
4225222 AGGGGGAATCTATACCCCCT
1 GGGGGGTATCTGTACCCCCT
4225242 GGG
1 GGG
4225245 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
20 18 0.36
21 14 0.28
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.23
Consensus pattern (20 bp):
GGGGGGTATCTGTACCCCCT
Found at i:4225209 original size:15 final size:15
Alignment explanation
Indices: 4225189--4225218 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4225179 ACCCCCTGGG
4225189 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
4225204 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
4225219 CCTAGGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:4226677 original size:19 final size:20
Alignment explanation
Indices: 4226636--4226683 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
4226626 TTTAAATCCT
*
4226636 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
*
4226656 TTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
4226675 TTTTCAAAA
1 TTTTCAAAA
4226684 GAAAATCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:4227411 original size:52 final size:53
Alignment explanation
Indices: 4227349--4227453 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 53
4227339 CGGAACGATT
4227349 TGCAAAGAGGGGTCGGAACGGTTTTGTGTTTA-GGGAGTAAGGAGATTGAAAG
1 TGCAAAGAGGGGTCGGAACGGTTTTGTGTTTAGGGGAGTAAGGAGATTGAAAG
4227401 TGCAAAGAGGGGTCGGAACGGTTTTGTGTTTAGGGGAGTAAGGAGATTGAAAG
1 TGCAAAGAGGGGTCGGAACGGTTTTGTGTTTAGGGGAGTAAGGAGATTGAAAG
4227454 ATAGAGAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 32 0.62
53 20 0.38
ACGTcount: A:0.29, C:0.06, G:0.41, T:0.25
Consensus pattern (53 bp):
TGCAAAGAGGGGTCGGAACGGTTTTGTGTTTAGGGGAGTAAGGAGATTGAAAG
Found at i:4227658 original size:34 final size:32
Alignment explanation
Indices: 4227596--4227665 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
4227586 CCTTACAAAC
* *
4227596 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
4227628 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
4227662 TCCC
1 TCCC
4227666 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:4227905 original size:20 final size:22
Alignment explanation
Indices: 4227880--4227919 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4227870 AGTCGTATAT
4227880 AGCCG-TTGGGGATG-TTTTAG
1 AGCCGTTTGGGGATGATTTTAG
4227900 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
4227920 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTAG
Found at i:4227971 original size:21 final size:21
Alignment explanation
Indices: 4227947--4227989 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4227937 CCCAGAATAG
*
4227947 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
4227968 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
4227989 A
1 A
4227990 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:4228107 original size:21 final size:21
Alignment explanation
Indices: 4228081--4228124 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4228071 AAAACCTGTA
* *
4228081 GGGGGGTATCTGTACCCCCTG
1 GGGGGGAATCTATACCCCCTG
4228102 GGGGGGAATCTATACCCCCTG
1 GGGGGGAATCTATACCCCCTG
4228123 GG
1 GG
4228125 CAATCTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.27, G:0.39, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTATACCCCCTG
Found at i:4228245 original size:29 final size:31
Alignment explanation
Indices: 4228213--4228271 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 31
4228203 AAACTTTGAA
4228213 TAAATTCAATT-AAGTCCAAAAA-CATTTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTTT
4228242 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
4228272 GCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTT
Found at i:4232435 original size:44 final size:44
Alignment explanation
Indices: 4232340--4232435 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 44
4232330 AAGAGAACAA
* * *
4232340 GATATAAGCTATGTGATATGATCTACGTGATTACATGAACATGT
1 GATATAAGCTATGTAATATGACCTACGTGATTACATGAACATAT
* * * ***
4232384 GACATAAGCTATGTAATATGACCTAGGTGATTACTTGTTTATAT
1 GATATAAGCTATGTAATATGACCTACGTGATTACATGAACATAT
4232428 GATATAAG
1 GATATAAG
4232436 AAATAATAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.35
Consensus pattern (44 bp):
GATATAAGCTATGTAATATGACCTACGTGATTACATGAACATAT
Found at i:4235758 original size:2 final size:2
Alignment explanation
Indices: 4235753--4235788 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
4235743 TAAAAAAATA
*
4235753 AT AT AT AT AT AT AT AT AT AT AT AT AGT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A
4235789 AACTATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.97
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4235852 original size:11 final size:11
Alignment explanation
Indices: 4235836--4235874 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 11
4235826 ATGTGAACTA
4235836 TATATATAAAC
1 TATATATAAAC
4235847 TATATATAAAC
1 TATATATAAAC
4235858 ATATATGTATAAAC
1 -TATA--TATAAAC
4235872 TAT
1 TAT
4235875 CAAAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.44
12 4 0.16
13 3 0.12
14 7 0.28
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (11 bp):
TATATATAAAC
Found at i:4235907 original size:8 final size:9
Alignment explanation
Indices: 4235894--4236065 Score: 85
Period size: 9 Copynumber: 19.1 Consensus size: 9
4235884 ATTTTATAAA
4235894 ATAT-TATT
1 ATATATATT
*
4235902 ATAT-TAAT
1 ATATATATT
4235910 ATAGTATATT
1 ATA-TATATT
*
4235920 ATATATAAT
1 ATATATATT
4235929 ATATATATAT
1 ATATATAT-T
*
4235939 ATATATATAA
1 ATATATAT-T
4235949 ACTATATATGT
1 A-TATATAT-T
*
4235960 ATA-A-ACT
1 ATATATATT
* *
4235967 ATATAAAAT
1 ATATATATT
4235976 ATATAGT-TT
1 ATATA-TATT
*
4235985 ATATATTATA
1 ATATA-TATT
*
4235995 ATTTATATT
1 ATATATATT
*
4236004 A-ATATAGT
1 ATATATATT
4236012 ATATATATGT
1 ATATATAT-T
4236022 ATATATATGT
1 ATATATAT-T
*
4236032 ATGTATA--
1 ATATATATT
*
4236039 ACTA-ATAAT
1 A-TATATATT
4236048 ATATATA-T
1 ATATATATT
4236056 ATATATATT
1 ATATATATT
4236065 A
1 A
4236066 AAGAAATACT
Statistics
Matches: 129, Mismatches: 20, Indels: 29
0.72 0.11 0.16
Matches are distributed among these distances:
7 8 0.06
8 29 0.22
9 43 0.33
10 41 0.32
11 8 0.06
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (9 bp):
ATATATATT
Found at i:4235918 original size:21 final size:20
Alignment explanation
Indices: 4235894--4235957 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
4235884 ATTTTATAAA
4235894 ATATTATTATATTAATATAGT
1 ATATTATTATATTAATATA-T
4235915 ATATTA-TATA-TAATATAT
1 ATATTATTATATTAATATAT
*
4235933 ATATATATATATATAAACTATAT
1 ATAT-TAT-TATATTAA-TATAT
4235956 AT
1 AT
4235958 GTATAAACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
18 5 0.14
19 9 0.24
20 4 0.11
21 10 0.27
22 2 0.05
23 7 0.19
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATTATTATATTAATATAT
Found at i:4235926 original size:2 final size:2
Alignment explanation
Indices: 4235908--4236063 Score: 107
Period size: 2 Copynumber: 80.0 Consensus size: 2
4235898 TATTATATTA
*
4235908 AT AT AGT AT AT -T AT AT AT A- AT AT AT AT AT AT AT AT AT AT AA
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
4235949 ACT AT AT AT GT AT AA ACT AT AT A- AA AT AT AT AGT TT AT AT AT
1 A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT
* *
4235991 -T AT A- AT TT AT AT -T A- AT AT AGT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* *
4236030 GT AT GT AT A- ACT A- AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
4236064 TAAAGAAATA
Statistics
Matches: 121, Mismatches: 17, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
1 10 0.08
2 103 0.85
3 8 0.07
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4236015 original size:45 final size:49
Alignment explanation
Indices: 4235900--4236038 Score: 121
Period size: 45 Copynumber: 2.9 Consensus size: 49
4235890 TAAAATATTA
4235900 TTATATTAATATAGTATATTATATATAATATATATATATATATATATAAACT
1 TTATATTAATATAG--TA-TATATATAATATATATATATATATATATAAACT
* * * *
4235952 ATATATGT-ATAAACTATATA-A-AATATATAGTTTATATAT-TAT-AA-T
1 TTATAT-TAATATAGTATATATATAATATATA-TATATATATATATAAACT
* * *
4235997 TTATATTAATATAGTATATATAT-GTATATATATGTATGTATA
1 TTATATTAATATAGTATATATATAATATATATATATATATATA
4236039 ACTAATAATA
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
44 1 0.01
45 22 0.31
46 11 0.16
47 11 0.16
48 9 0.13
49 4 0.06
50 2 0.03
52 9 0.13
53 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (49 bp):
TTATATTAATATAGTATATATATAATATATATATATATATATATAAACT
Found at i:4236017 original size:47 final size:49
Alignment explanation
Indices: 4235899--4236038 Score: 137
Period size: 47 Copynumber: 2.9 Consensus size: 49
4235889 ATAAAATATT
4235899 ATTATATTAATATAGTATATTATATATAATATATATATATATATATATAA
1 ATTATATTAATATAGTATA-TATATATAATATATATATATATATATATAA
* * * * *
4235949 ACTATA-T-ATGTA-TAAACTATATAAAATATATAGTTTATATAT-TATAA
1 ATTATATTAATATAGTATA-TATATATAATATATA-TATATATATATATAA
* * * *
4235996 TTTATATTAATATAGTATATATATGT-ATATATATGTATGTATA
1 ATTATATTAATATAGTATATATATATAATATATATATATATATA
4236039 ACTAATAATA
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
47 33 0.46
48 20 0.28
49 10 0.14
50 8 0.11
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (49 bp):
ATTATATTAATATAGTATATATATATAATATATATATATATATATATAA
Found at i:4236141 original size:21 final size:21
Alignment explanation
Indices: 4236115--4236154 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4236105 TATAGTTTAT
*
4236115 AAAAACCCTATACCCTAAAAC
1 AAAAACCCTAAACCCTAAAAC
*
4236136 AAAAACCCTAAATCCTAAA
1 AAAAACCCTAAACCCTAAA
4236155 CTTTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAACCCTAAACCCTAAAAC
Found at i:4236470 original size:7 final size:7
Alignment explanation
Indices: 4236460--4236485 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4236450 TCTTAAACTT
4236460 TAAACCC
1 TAAACCC
4236467 TAAACCC
1 TAAACCC
4236474 TAAACCC
1 TAAACCC
4236481 TAAAC
1 TAAAC
4236486 ACTATACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:4236594 original size:22 final size:20
Alignment explanation
Indices: 4236569--4236622 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
4236559 CTTATAGTAC
4236569 ATGTATCATATATGTATAAACT
1 ATGTAT-ATATAT-TATAAACT
4236591 ATGTATAGTATA-TATAAACT
1 ATGTATA-TATATTATAAACT
4236611 ATGTATATATAT
1 ATGTATATATAT
4236623 AACCTATAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.13
20 15 0.50
21 1 0.03
22 10 0.33
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (20 bp):
ATGTATATATATTATAAACT
Found at i:4236608 original size:20 final size:19
Alignment explanation
Indices: 4236576--4236671 Score: 97
Period size: 20 Copynumber: 4.9 Consensus size: 19
4236566 TACATGTATC
*
4236576 ATATATGTATAAACTATGT
1 ATATATATATAAACTATGT
4236595 ATAGTATATATAAACTATG-
1 ATA-TATATATAAACTATGT
*
4236614 -TATATATATAACCTATAGT
1 ATATATATATAAACTAT-GT
*
4236633 ATATATATATACAATCTATTT
1 ATATATATATA-AA-CTATGT
*
4236654 ATATGTTATATAAACTAT
1 ATAT-ATATATAAACTAT
4236672 ATATGTAACC
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
17 13 0.20
18 3 0.05
19 3 0.05
20 28 0.43
21 8 0.12
22 10 0.15
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (19 bp):
ATATATATATAAACTATGT
Found at i:4236706 original size:21 final size:20
Alignment explanation
Indices: 4236682--4236772 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 20
4236672 ATATGTAACC
4236682 TATAGTTTATAATCAATAGTT
1 TATA-TTTATAATCAATAGTT
* *
4236703 TATATTAGTGTACT-ATATAGTT
1 TATATT--TATAATCA-ATAGTT
* * *
4236725 TATACTTTATAACCTATAGTA
1 TATA-TTTATAATCAATAGTT
* *
4236746 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAATCAATAGTT
4236767 TATATT
1 TATATT
4236773 AATGTACTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
20 5 0.09
21 33 0.60
22 15 0.27
23 2 0.04
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (20 bp):
TATATTTATAATCAATAGTT
Found at i:4236750 original size:57 final size:60
Alignment explanation
Indices: 4236677--4236792 Score: 148
Period size: 64 Copynumber: 1.9 Consensus size: 60
4236667 ACTATATATG
* *
4236677 TAACCTATAGTTTAT-A-AT-CAATAGTTTATATTAGTGTACTATATAGTTTATACTTTA
1 TAACCTATAGTATATAATATACAATAGTTTATATTAATGTACTATATAGTTTATACTTTA
*
4236734 TAACCTATAGTATATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATA
1 TAACCTATAGTATATAA--TAT--ACAATAGTTTATATTAATGTACTATATAGTTTATA
4236793 TTAATGTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
57 14 0.29
58 1 0.02
61 2 0.04
64 32 0.65
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (60 bp):
TAACCTATAGTATATAATATACAATAGTTTATATTAATGTACTATATAGTTTATACTTTA
Found at i:4236796 original size:22 final size:21
Alignment explanation
Indices: 4236697--4236799 Score: 84
Period size: 22 Copynumber: 4.8 Consensus size: 21
4236687 TTTATAATCA
*
4236697 ATAGTTTATATTAGTGTACTAT
1 ATAGTTTATATTAATGTAC-AT
* * *
4236719 ATAGTTTATACTTTAT-AACCT
1 ATAGTTTATA-TTAATGTACAT
* * **
4236740 ATAGTATATAATTTATAAAC-T
1 ATAGTTTAT-ATTAATGTACAT
4236761 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTAC-AT
4236783 ATAGTTTATATTAATGT
1 ATAGTTTATATTAATGT
4236800 TAATTATCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.10
21 23 0.34
22 34 0.51
23 3 0.04
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (21 bp):
ATAGTTTATATTAATGTACAT
Found at i:4236870 original size:65 final size:64
Alignment explanation
Indices: 4236788--4237034 Score: 211
Period size: 65 Copynumber: 3.8 Consensus size: 64
4236778 ACTATATAGT
* * * *
4236788 TTATATTAATGTTAATTATCTTAACTATAATTTATATTAATATAGTACATAGTTTATAAACTATA
1 TTATATTAATATTAATTAT-TTAACTATAATTTATATTAATATAATATATAATTTATAAACTATA
* * *
4236853 TTATAGTAATATTAATTATATTAACTATAGTTTATA--AACTATACTATATAATTTAT-AACATA
1 TTATATTAATATTAATTAT-TTAACTATAATTTATATTAA-TATAATATATAATTTATAAAC-TA
4236915 TA
63 TA
* * *
4236917 GTTTATATTAATATTAATGT-TATAGACTATATTTTATATTAATATTAAT-TATAAATTATAAAC
1 --TTATATTAATATTAAT-TATTTA-ACTATAATTTATATTAATA-TAATATATAATTTATAAAC
4236980 TATA
61 TATA
* *
4236984 TTATATTAATA-TAAGTTAATATTAA-TTTAATTATAAATTAATTATAATATA
1 TTATATTAATATTAA-TT-AT-TTAACTATAATT-TATATTAA-TATAATATA
4237035 ATTATTATAT
Statistics
Matches: 149, Mismatches: 16, Indels: 32
0.76 0.08 0.16
Matches are distributed among these distances:
63 5 0.03
64 22 0.15
65 51 0.34
66 41 0.28
67 22 0.15
68 8 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (64 bp):
TTATATTAATATTAATTATTTAACTATAATTTATATTAATATAATATATAATTTATAAACTATA
Found at i:4236886 original size:43 final size:39
Alignment explanation
Indices: 4236821--4236904 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 39
4236811 ACTATAATTT
*
4236821 ATATTAATATAGTACATAGTTTATAAACTATATTATAGTA
1 ATATTAATATAGTACATAGTTTATAAACTATACTATA-TA
*
4236861 ATATTAATTATATTAACTATAGTTTATAAACTATACTATATA
1 ATATTAA-TATAGT-AC-ATAGTTTATAAACTATACTATATA
4236903 AT
1 AT
4236905 TTATAACATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 7 0.18
41 5 0.13
42 6 0.15
43 21 0.54
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (39 bp):
ATATTAATATAGTACATAGTTTATAAACTATACTATATA
Found at i:4236928 original size:131 final size:133
Alignment explanation
Indices: 4236746--4237020 Score: 316
Period size: 131 Copynumber: 2.1 Consensus size: 133
4236736 ACCTATAGTA
* * * * *
4236746 TATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATATTAATGTTAAT-TATCTT
1 TATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATGT-T-AT
* **
4236810 A-ACTATAATTTATATTAATA-TAGTACATAGTTTATAAACTATATTATAGTAATATTAA-TT-A
64 AGACTATAATTTATATTAATATTAAT-CATAAATTATAAACTATATTATAGTAATA-TAAGTTAA
4236871 TATTAAC
127 TATTAAC
* *
4236878 TATAGTTTATAAACTATACTATATAATTTAT-AAC-ATATAGTTTATATTAATATTAATGTTATA
1 TATAATTTATAAACTATACTATAT-ATTAATGAACTATATAGTTTATATTAATATTAATGTTATA
* * *
4236941 GACTATATTTTATATTAATATTAATTATAAATTATAAACTATATTATATTAATATAAGTTAATAT
65 GACTATAATTTATATTAATATTAATCATAAATTATAAACTATATTATAGTAATATAAGTTAATAT
4237006 TAA-
130 TAAC
*
4237009 TTTAA-TTATAAA
1 TATAATTTATAAA
4237021 TTAATTATAA
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
130 12 0.10
131 71 0.58
132 34 0.28
133 5 0.04
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (133 bp):
TATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATGTTATAG
ACTATAATTTATATTAATATTAATCATAAATTATAAACTATATTATAGTAATATAAGTTAATATT
AAC
Found at i:4236953 original size:31 final size:30
Alignment explanation
Indices: 4236781--4236970 Score: 115
Period size: 31 Copynumber: 6.0 Consensus size: 30
4236771 TTAATGTACT
* *
4236781 ATATAGTTTATATTAATGTTAATTATCTTAAC
1 ATATAGTTTATATTAATATTAATT-T-ATAAC
*
4236813 -TATAATTTATATTAATATAGTACATAGTTTATAA-
1 ATATAGTTTATATTAATAT--T--A-A-TTTATAAC
*
4236847 ACTATA--TTATAGTAATATTAATTATATTAAC
1 A-TATAGTTTATATTAATATTAATT-TA-TAAC
*
4236878 -TATAGTTTATAAACTATACTATATAATTTATAAC
1 ATATAGTTTAT--A-T-TAATAT-TAATTTATAAC
4236912 ATATAGTTTATATTAATATTAATGTTATAGAC
1 ATATAGTTTATATTAATATTAAT-TTATA-AC
*
4236944 -TATATTTTATATTAATATTAA-TTATAA
1 ATATAGTTTATATTAATATTAATTTATAA
4236971 ATTATAAACT
Statistics
Matches: 129, Mismatches: 8, Indels: 46
0.70 0.04 0.25
Matches are distributed among these distances:
28 3 0.02
29 12 0.09
30 8 0.06
31 50 0.39
32 4 0.03
33 3 0.02
34 15 0.12
35 21 0.16
36 11 0.09
37 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (30 bp):
ATATAGTTTATATTAATATTAATTTATAAC
Found at i:4237024 original size:11 final size:11
Alignment explanation
Indices: 4236970--4237057 Score: 60
Period size: 11 Copynumber: 7.9 Consensus size: 11
4236960 ATTAATTATA
*
4236970 AATTATAAACT
1 AATTATAAATT
4236981 ATATTAT--ATT
1 A-ATTATAAATT
*
4236991 AA-TATAAGTT
1 AATTATAAATT
*
4237001 AA-TATTAATTT
1 AATTA-TAAATT
4237012 AATTATAAATT
1 AATTATAAATT
4237023 AATTAT-AATAT
1 AATTATAAAT-T
4237034 AATTATTATATATT
1 AATTA-TA-A-ATT
4237048 AATTATAAAT
1 AATTATAAAT
4237058 AGTTAATTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
8 3 0.05
9 1 0.02
10 12 0.19
11 27 0.43
12 9 0.14
13 2 0.03
14 7 0.11
15 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (11 bp):
AATTATAAATT
Found at i:4237031 original size:22 final size:22
Alignment explanation
Indices: 4236970--4237055 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 22
4236960 ATTAATTATA
*
4236970 AATTATAAACTATATTAT-A-TT
1 AATTATAAATTA-ATTATAATTT
*
4236991 AA-TATAAGTTAA-TATTAATTT
1 AATTATAAATTAATTA-TAATTT
*
4237012 AATTATAAATTAATTATAATAT
1 AATTATAAATTAATTATAATTT
4237034 AATTATTATATATTAATTATAA
1 AATTA-TA-A-ATTAATTATAA
4237056 ATAGTTAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.04
19 2 0.04
20 8 0.15
21 6 0.11
22 19 0.36
23 4 0.08
24 1 0.02
25 11 0.21
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
AATTATAAATTAATTATAATTT
Found at i:4237043 original size:14 final size:14
Alignment explanation
Indices: 4237002--4237066 Score: 57
Period size: 14 Copynumber: 4.7 Consensus size: 14
4236992 ATATAAGTTA
4237002 ATATTAATTTAATTAT
1 ATATTAA-TT-ATTAT
*
4237018 AAATTAATTA-TA-
1 ATATTAATTATTAT
4237030 ATA-TAATTATTAT
1 ATATTAATTATTAT
*
4237043 ATATTAATTA-TAA
1 ATATTAATTATTAT
4237056 ATAGTTAATTA
1 ATA-TTAATTA
4237067 ATAAAAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
11 6 0.14
12 4 0.10
13 10 0.24
14 14 0.33
15 2 0.05
16 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
ATATTAATTATTAT
Found at i:4237053 original size:36 final size:32
Alignment explanation
Indices: 4236988--4237057 Score: 88
Period size: 36 Copynumber: 2.1 Consensus size: 32
4236978 ACTATATTAT
4236988 ATTAATATAAGTTAATATTAATTTAATTATAA
1 ATTAATATAAGTTAATATTAATTTAATTATAA
4237020 ATTAATTATAA-TATAATTATTATATATTAATTATAA
1 ATTAA-TATAAGT-TAA-TATTA-AT-TTAATTATAA
4237056 AT
1 AT
4237058 AGTTAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
32 6 0.18
33 8 0.24
34 5 0.15
35 2 0.06
36 12 0.36
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
ATTAATATAAGTTAATATTAATTTAATTATAA
Found at i:4237066 original size:25 final size:26
Alignment explanation
Indices: 4237000--4237078 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 26
4236990 TAATATAAGT
4237000 TAATATTAATTTAATTATAAATTAATTA
1 TAATA-TAA-TTAATTATAAATTAATTA
*
4237028 TAATATAATT-ATTATATATTAATTA
1 TAATATAATTAATTATAAATTAATTA
*
4237053 TAA-ATAGTTAATTAATAAA--AATTA
1 TAATATAATTAATT-ATAAATTAATTA
4237077 TA
1 TA
4237079 TAGGGATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 12 0.26
25 20 0.43
26 6 0.13
27 3 0.07
28 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
TAATATAATTAATTATAAATTAATTA
Found at i:4237935 original size:17 final size:17
Alignment explanation
Indices: 4237913--4237952 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
4237903 AAACTGTTTA
4237913 ATTTGTAGCTACTGTTG
1 ATTTGTAGCTACTGTTG
**
4237930 ATTTGTTTCTACTGTTG
1 ATTTGTAGCTACTGTTG
4237947 ATTTGT
1 ATTTGT
4237953 TTGTGTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.20, T:0.55
Consensus pattern (17 bp):
ATTTGTAGCTACTGTTG
Found at i:4237963 original size:17 final size:17
Alignment explanation
Indices: 4237921--4237954 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4237911 TAATTTGTAG
4237921 CTACTGTTGATTTGTTT
1 CTACTGTTGATTTGTTT
4237938 CTACTGTTGATTTGTTT
1 CTACTGTTGATTTGTTT
4237955 GTGTTGTTGG
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:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (17 bp):
CTACTGTTGATTTGTTT
Found at i:4238106 original size:102 final size:102
Alignment explanation
Indices: 4237938--4238149 Score: 343
Period size: 102 Copynumber: 2.1 Consensus size: 102
4237928 TGATTTGTTT
* * *
4237938 CTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTTGGATTGCTTCTATAAGGTTGTTAGCTGC
1 CTACTGTTGATTTGTTTGTGTTATTGATTGTTCATTCGGATTGCTTCTATAAGGTTGTTAGCTGC
* *
4238003 CTTTATTTACAGTTTAAATAAATTGTGTAATTTGTAG
66 CTTTATTTAAAATTTAAATAAATTGTGTAATTTGTAG
* *
4238040 CTACTGTTGATTTGTTTGTGTTATTGATTGTTCATTCGGATTGCTTTTATAATGTTGTTAGCTGC
1 CTACTGTTGATTTGTTTGTGTTATTGATTGTTCATTCGGATTGCTTCTATAAGGTTGTTAGCTGC
*
4238105 CTTTATTTAAAATTTAAATAAATTGTTTAATTTGTAG
66 CTTTATTTAAAATTTAAATAAATTGTGTAATTTGTAG
*
4238142 CTATTGTT
1 CTACTGTT
4238150 TGTTGTTCAT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.51
Consensus pattern (102 bp):
CTACTGTTGATTTGTTTGTGTTATTGATTGTTCATTCGGATTGCTTCTATAAGGTTGTTAGCTGC
CTTTATTTAAAATTTAAATAAATTGTGTAATTTGTAG
Found at i:4241296 original size:14 final size:14
Alignment explanation
Indices: 4241277--4241323 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
4241267 ATTTTTTCTT
4241277 TATATAAATTAAAC
1 TATATAAATTAAAC
4241291 TATAT-AATT----
1 TATATAAATTAAAC
4241300 TATATAAATTAAAC
1 TATATAAATTAAAC
*
4241314 TATATTAATT
1 TATATAAATT
4241324 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:4241302 original size:23 final size:24
Alignment explanation
Indices: 4241275--4241324 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
4241265 TTATTTTTTC
4241275 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
4241298 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
4241322 TTT
1 TTT
4241325 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:4241708 original size:35 final size:35
Alignment explanation
Indices: 4241662--4241737 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
4241652 AAAACAATCA
* *
4241662 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
4241697 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
4241732 TCAATT
1 TCAATT
4241738 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:4242265 original size:130 final size:129
Alignment explanation
Indices: 4242129--4242375 Score: 404
Period size: 130 Copynumber: 1.9 Consensus size: 129
4242119 TATTTATATA
* **
4242129 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
4242194 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACAC-TGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
4242259 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
4242324 TTAACACTGATCATGATATATGTTATTGGTGACACGTGTCACCACCTAATTA
66 TTAACACTGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
4242376 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
129 40 0.37
130 68 0.63
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (129 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACTGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:4242859 original size:15 final size:16
Alignment explanation
Indices: 4242835--4242871 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
4242825 TTTAATTTCT
4242835 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
4242849 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
4242865 TGATTCA
1 T-ATTCA
4242872 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:4243488 original size:16 final size:16
Alignment explanation
Indices: 4243467--4243505 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
4243457 CGGATCATTT
4243467 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
4243483 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
4243499 ACAGGTC
1 ACAGGTC
4243506 GGGTAATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:4249152 original size:26 final size:26
Alignment explanation
Indices: 4249093--4249153 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
4249083 TATGTTTTTT
**
4249093 AGATAAAAAAATCTTAAAATTATTGA
1 AGATAAAAAAATCTTAAAATTATAAA
4249119 A-ATGAAAAAAA-CTTATAAATTATAAA
1 AGAT-AAAAAAATCTTA-AAATTATAAA
4249145 AGATAAAAA
1 AGATAAAAA
4249154 TACCTCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 6 0.20
26 22 0.73
27 2 0.07
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (26 bp):
AGATAAAAAAATCTTAAAATTATAAA
Found at i:4249467 original size:31 final size:32
Alignment explanation
Indices: 4249400--4249467 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
4249390 CAGGTCAAAT
*
4249400 TTTTTTTAAAAAAAATCGGGATCAGGTCGGAT
1 TTTTTTTAAAAAAAATCGGGATCAGGTCGGAG
*
4249432 TTTTTTTAAAAAAAATCGGGTTC-GAGTC-GAG
1 TTTTTTTAAAAAAAATCGGGATCAG-GTCGGAG
4249463 TTTTT
1 TTTTT
4249468 AAGTTTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (32 bp):
TTTTTTTAAAAAAAATCGGGATCAGGTCGGAG
Found at i:4249467 original size:32 final size:32
Alignment explanation
Indices: 4249389--4249451 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
4249379 CTTTTGGTAT
**
4249389 TCAGGTCAAATTTTTTTTAAAAAAAATCGGGA
1 TCAGGTCGGATTTTTTTTAAAAAAAATCGGGA
4249421 TCAGGTCGGATTTTTTTTAAAAAAAATCGGG
1 TCAGGTCGGATTTTTTTTAAAAAAAATCGGG
4249452 TTCGAGTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (32 bp):
TCAGGTCGGATTTTTTTTAAAAAAAATCGGGA
Found at i:4249486 original size:26 final size:27
Alignment explanation
Indices: 4249452--4249513 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
4249442 AAAAATCGGG
* *
4249452 TTCGAGTCGAG-TTTTTAAGTTTGATA
1 TTCGGGTCGAGTTTTTTAAGTGTGATA
*
4249478 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGAG-TTTTTTAAGTGTGATA
4249506 TTCGGGTC
1 TTCGGGTC
4249514 AGGGTCGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 9 0.29
28 22 0.71
ACGTcount: A:0.16, C:0.10, G:0.29, T:0.45
Consensus pattern (27 bp):
TTCGGGTCGAGTTTTTTAAGTGTGATA
Found at i:4249504 original size:28 final size:29
Alignment explanation
Indices: 4249463--4249518 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
4249453 TCGAGTCGAG
*
4249463 TTTTTAAGTTTGATATTCGGGTC-GGGTT
1 TTTTTAAGTGTGATATTCGGGTCAGGGTT
4249491 TTTTTAAGTGTGATATTCGGGTCAGGGT
1 TTTTTAAGTGTGATATTCGGGTCAGGGT
4249519 CGGGTTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.16, C:0.07, G:0.30, T:0.46
Consensus pattern (29 bp):
TTTTTAAGTGTGATATTCGGGTCAGGGTT
Found at i:4250396 original size:17 final size:17
Alignment explanation
Indices: 4250370--4250409 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
4250360 CTTTTTTATT
4250370 TTTAAAATAT-TA-AAA
1 TTTAAAATATATAGAAA
4250385 TTTAAAATATATAGAAA
1 TTTAAAATATATAGAAA
4250402 TTTAAAAT
1 TTTAAAAT
4250410 TTTTAAGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 10 0.43
16 2 0.09
17 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
TTTAAAATATATAGAAA
Found at i:4250569 original size:9 final size:9
Alignment explanation
Indices: 4250555--4250585 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
4250545 TATAATCACC
4250555 CAAATTATT
1 CAAATTATT
4250564 CAAATTATT
1 CAAATTATT
4250573 CAAATTATT
1 CAAATTATT
4250582 CAAA
1 CAAA
4250586 AATAGGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (9 bp):
CAAATTATT
Found at i:4251786 original size:56 final size:56
Alignment explanation
Indices: 4251661--4251786 Score: 146
Period size: 56 Copynumber: 2.2 Consensus size: 56
4251651 TGGTCCACCG
* * * * *
4251661 ACTATAAAGTATTGTTTTGTTGAGTATCTCGACCATTAAAAGTTACAAAATAGTCA
1 ACTATAAGGCATTGTTTTGTTAAGTATCTCGACCATCAAAAGTTACAAAATAGCCA
* * * * *
4251717 ATTATAAGGCATTGTTTTGTTAAGTCTTTCGACTATCAAAAGTTACAAAATAGCCG
1 ACTATAAGGCATTGTTTTGTTAAGTATCTCGACCATCAAAAGTTACAAAATAGCCA
4251773 ACTAT-AGGACATTG
1 ACTATAAGG-CATTG
4251787 CTTTATTGAG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 3 0.05
56 55 0.95
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (56 bp):
ACTATAAGGCATTGTTTTGTTAAGTATCTCGACCATCAAAAGTTACAAAATAGCCA
Found at i:4253758 original size:3 final size:3
Alignment explanation
Indices: 4253750--4253807 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
4253740 ACATGTTGTA
4253750 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4253798 TAT TAT TAT T
1 TAT TAT TAT T
4253808 TATGTTATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4263094 original size:24 final size:24
Alignment explanation
Indices: 4263067--4263112 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4263057 TCTTTTGGCA
*
4263067 CTCCAAAAGACATGTTCTTTGATT
1 CTCCAAAAGACACGTTCTTTGATT
* *
4263091 CTCCAAAGGTCACGTTCTTTGA
1 CTCCAAAAGACACGTTCTTTGA
4263113 ATCATGAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (24 bp):
CTCCAAAAGACACGTTCTTTGATT
Found at i:4269100 original size:682 final size:682
Alignment explanation
Indices: 4267795--4269145 Score: 2157
Period size: 682 Copynumber: 2.0 Consensus size: 682
4267785 TATATAGAAC
4267795 TCTAGGAATTTGAAGTATTAGGTTCGAATGAATGACACCACAAGTATAGAAATATACTTGCTTAA
1 TCTAGGAATTTGAAGTATTAGGTTCGAATGAATGACACCACAAGTATAGAAATATACTTGCTTAA
* *
4267860 TAGATAAAGTTTTTAAAGAACTTGGAAGAGAGATTTAACTCACAAATTAATTTGATTAAAAAATG
66 TAGATAAAGTTCTTAAAGAACTTGGAAGAGAGATTTAACTCACAAAGTAATTTGATTAAAAAATG
* *
4267925 AGATAAGATGTTTACAAATGAAGAATGCCTTCTTATTTATAGGATTTGGAAGGCTTGGTCAAAAA
131 AGATAAGATGTTTACAAATGAAGAATGCCTTCCTATTTATAGGATTTGGAAGGCTTGGCCAAAAA
* *
4267990 ACTATGTGCCTTTTCAGCTAAGTACATGATTATAATGAAAGTACATAATTAATTAAGTGAATAAA
196 ACTATGTGCCTTATCAGCTAAGTACATGATTATAATGAAAGTACATAATTAATTAAATGAATAAA
* *
4268055 TGTGTCCATAGGCCTTGTGATAGTTCGAATAATCTTCATAAAGGAGCATGATATTTCGGTCATGC
261 TGTGTCCATAGGCCTTGTGATAGTTCGAATAACCTTCATAAAGGAGCATGATATTTCGGCCATGC
* *
4268120 ATGAATTAACCTCCCTTGGTTGAATGGTGATGTACTTGTTCATCTTGGCGCCAAAGTCTTCATAT
326 ATGAATTAACCTCCCTTGGTCGAATGGTGATGTACTTGTTAATCTTGGCGCCAAAGTCTTCATAT
4268185 GCAAGGCATGTGTTTGGTGGACATATAGACATGATGACTTCCTCATACCTCTTCATGAATTAAGC
391 GCAAGGCATGTGTTTGGTGGACATATAGACATGATGACTTCCTCATACCTCTTCATGAATTAAGC
* *
4268250 ATCTTTTGGATGAAAACTCTTCACCAAAGGGCACCTAAGTTGATAAGGCATTTTCATGGACAACA
456 ATCTTTTGGATGAAAACTCTTCACCAAAGGACACCTAAGTTGATAAGGCATCTTCATGGACAACA
** *
4268315 ACTTTCACAAAAGGTTGCAATGTTTGGAAAGTAACATTTCATGAATGAGCTTGTTCTAATGTGAG
521 ACTTTCACAAAAGGTCACAATGTTTGGAAAGTAACATTTCATGAATGAGCTTGTTCTAAGGTGAG
** * * *
4268380 TGAGCTAAAAGTGAACTGGCCATAGGTGAGTTATATCTTGGTAAGTCTTTTGGCAGCTCCTTGTG
586 TGAGCTAAAAGTGAACAAGCCATAGGTGAGTTATATCTTGGTAAGTCTTTTAGAAGCTCATTGTG
*
4268445 AAAAGTCACTTCCCAGAAATACAACTCCTTGT
651 AAAAGTCACATCCCAGAAATACAACTCCTTGT
* ** *
4268477 TCTAGGAATTTGAAGTATTAGGTTGGAATGAATGAGGCCACAAGTATAGAAATATACTTGTTTAA
1 TCTAGGAATTTGAAGTATTAGGTTCGAATGAATGACACCACAAGTATAGAAATATACTTGCTTAA
* * * * *
4268542 TCGATAAAGTTCTTAAAGAACTTGGAAGAGATATTTAACTCACATAGTAGTTTGATTAAAATATG
66 TAGATAAAGTTCTTAAAGAACTTGGAAGAGAGATTTAACTCACAAAGTAATTTGATTAAAAAATG
* * * *
4268607 AGATGAGATGTTTACAAATGAAGAATGCCTTCCTATTTATAGGATTTGGAGGGCTTGGCCGAATA
131 AGATAAGATGTTTACAAATGAAGAATGCCTTCCTATTTATAGGATTTGGAAGGCTTGGCCAAAAA
* *
4268672 ACTATGTGTCTTATCAGCTAAGTACATGATTATAATGAAAGTACATAATTAATTAAATGAATGAA
196 ACTATGTGCCTTATCAGCTAAGTACATGATTATAATGAAAGTACATAATTAATTAAATGAATAAA
* * * * * *
4268737 TTTGTCCATATGCCTTGTGATGGTTCGGATAACCCTTCATAAAGGAGCGTGATGTTTCGGCCATG
261 TGTGTCCATAGGCCTTGTGATAGTTCGAATAA-CCTTCATAAAGGAGCATGATATTTCGGCCATG
**
4268802 CATGAATTAACCTTTCTTGGTCGAATGGTGATGTACTTGTTAATCTTGGCGCCAAAGTCTTCATA
325 CATGAATTAACCTCCCTTGGTCGAATGGTGATGTACTTGTTAATCTTGGCGCCAAAGTCTTCATA
* * *
4268867 TGCAAGGCATGTGTTTGGTGGTCGA-ATAGACATGATGTCTTCCTCATACCTCTTCGTGAATTAA
390 TGCAAGGCATGTGTTTGGTGGAC-ATATAGACATGATGACTTCCTCATACCTCTTCATGAATTAA
* * *
4268931 GCCTCTTTTGGATGAAAACTCTTCACCAACGTACACCTAAG-TGATAAGGCATCTTCATGGACAA
454 GCATCTTTTGGATGAAAACTCTTCACCAAAGGACACCTAAGTTGATAAGGCATCTTCATGGACAA
* * *
4268995 TAACTTTCACGAAAGGTCACAATGTTTGGAAAGTAACCTTTCATGAATGAGCTTGTTCTAAGGTG
519 CAACTTTCACAAAAGGTCACAATGTTTGGAAAGTAACATTTCATGAATGAGCTTGTTCTAAGGTG
* * *
4269060 AGTGAGCTGAAAGTGAGCAAGCCATAGGTGAGTTATATCTTGGTGAGTCTTTTAGAAGCTCATTG
584 AGTGAGCTAAAAGTGAACAAGCCATAGGTGAGTTATATCTTGGTAAGTCTTTTAGAAGCTCATTG
*
4269125 TGAAAAGTCACATCCCGGAAA
649 TGAAAAGTCACATCCCAGAAA
4269146 GGTAACCCTT
Statistics
Matches: 610, Mismatches: 57, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
682 424 0.70
683 185 0.30
684 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (682 bp):
TCTAGGAATTTGAAGTATTAGGTTCGAATGAATGACACCACAAGTATAGAAATATACTTGCTTAA
TAGATAAAGTTCTTAAAGAACTTGGAAGAGAGATTTAACTCACAAAGTAATTTGATTAAAAAATG
AGATAAGATGTTTACAAATGAAGAATGCCTTCCTATTTATAGGATTTGGAAGGCTTGGCCAAAAA
ACTATGTGCCTTATCAGCTAAGTACATGATTATAATGAAAGTACATAATTAATTAAATGAATAAA
TGTGTCCATAGGCCTTGTGATAGTTCGAATAACCTTCATAAAGGAGCATGATATTTCGGCCATGC
ATGAATTAACCTCCCTTGGTCGAATGGTGATGTACTTGTTAATCTTGGCGCCAAAGTCTTCATAT
GCAAGGCATGTGTTTGGTGGACATATAGACATGATGACTTCCTCATACCTCTTCATGAATTAAGC
ATCTTTTGGATGAAAACTCTTCACCAAAGGACACCTAAGTTGATAAGGCATCTTCATGGACAACA
ACTTTCACAAAAGGTCACAATGTTTGGAAAGTAACATTTCATGAATGAGCTTGTTCTAAGGTGAG
TGAGCTAAAAGTGAACAAGCCATAGGTGAGTTATATCTTGGTAAGTCTTTTAGAAGCTCATTGTG
AAAAGTCACATCCCAGAAATACAACTCCTTGT
Found at i:4271086 original size:19 final size:19
Alignment explanation
Indices: 4271064--4271100 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4271054 CATATTTTTA
4271064 TTTTATACATATATATATT
1 TTTTATACATATATATATT
* *
4271083 TTTTATATATCTATATAT
1 TTTTATACATATATATAT
4271101 ATTATATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATACATATATATATT
Found at i:4271172 original size:40 final size:39
Alignment explanation
Indices: 4271121--4271312 Score: 192
Period size: 37 Copynumber: 5.0 Consensus size: 39
4271111 TTGTAAATGG
4271121 TTTTTGAAAATATGTATATAATATATATATTTTTAAAACA
1 TTTTTGAAAATAT-TATATAATATATATATTTTTAAAACA
* *
4271161 TTTTTGAAAATATGTATAT--TATATAGT-TTTTAAAAAACG
1 TTTTTGAAAATAT-TATATAATATATA-TATTTT-TAAAACA
4271200 TTTTTG-AAA-ATTATATAATATATA-ATTTTTAAAACA
1 TTTTTGAAAATATTATATAATATATATATTTTTAAAACA
* *
4271236 TTTTAGAAAATA-TATATAATATATGTAGTTTTTAAAATCA
1 TTTTTGAAAATATTATATAATATATATA-TTTTTAAAA-CA
4271276 -TTTTG-AAA-A-TATATAATATATAGT-TTTTTGAAAACA
1 TTTTTGAAAATATTATATAATATATA-TATTTTT-AAAACA
4271312 T
1 T
4271313 ATACTATATA
Statistics
Matches: 131, Mismatches: 8, Indels: 29
0.78 0.05 0.17
Matches are distributed among these distances:
36 22 0.17
37 38 0.29
38 25 0.19
39 25 0.19
40 21 0.16
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (39 bp):
TTTTTGAAAATATTATATAATATATATATTTTTAAAACA
Found at i:4271209 original size:39 final size:37
Alignment explanation
Indices: 4271094--4271514 Score: 248
Period size: 39 Copynumber: 11.5 Consensus size: 37
4271084 TTTATATATC
* ***
4271094 TATATATATTATATAGTTTGTAAATGGTTTTTGAAAA
1 TATATATATTATATAGTTTTTAAAACATTTTTGAAAA
4271131 TATGTATATAATATATATA-TTTTTAAAACATTTTTGAAAA
1 TA--TATAT-AT-TATATAGTTTTTAAAACATTTTTGAAAA
* *
4271171 TATGTATATTATATAGTTTTTAAAAAACGTTTTTGAAAA
1 TATATATATTATATAGTTTTT--AAAACATTTTTGAAAA
* * *
4271210 T-TATATAATATATAATTTTTAAAACATTTTAGAAAA
1 TATATATATTATATAGTTTTTAAAACATTTTTGAAAA
*
4271246 TATATATAATATATGTAGTTTTTAAAATCA-TTTTGAAAA
1 TATATAT-AT-TATATAGTTTTTAAAA-CATTTTTGAAAA
* *
4271285 TATATA-A-TATATAGTTTTTTGAAAACA----T-ATAC
1 TATATATATTATATAG-TTTTT-AAAACATTTTTGAAAA
* *
4271317 TATATAGTTTTGAAAATA-TTTTT-AAA-A----T----A
1 TATATA-TATT--ATATAGTTTTTAAAACATTTTTGAAAA
* *
4271346 TATATA-ATTATAGT--TTTTGAAAACATTTTTAAAAA
1 TATATATATTATA-TAGTTTTTAAAACATTTTTGAAAA
* *
4271381 CT-TATATATTATATAGTTTTGAAAACCTTTTTGAAAACA
1 -TATATATATTATATAGTTTTTAAAACATTTTTG-AAA-A
* *
4271420 TTTATATATTATATAGTTTTTAAAACGTTTTTGAAAA
1 TATATATATTATATAGTTTTTAAAACATTTTTGAAAA
* *
4271457 CTTATATATAATATATAG-TTTAAAAATCA-TTTTGAAATA
1 --TATATATATTATATAGTTTTTAAAA-CATTTTTGAAA-A
*
4271496 TATATATATAATATAGTTT
1 TATATATATTATATAGTTT
4271515 ATATTATAAT
Statistics
Matches: 309, Mismatches: 34, Indels: 81
0.73 0.08 0.19
Matches are distributed among these distances:
25 6 0.02
26 4 0.01
27 3 0.01
29 6 0.02
31 1 0.00
32 10 0.03
33 4 0.01
35 18 0.06
36 35 0.11
37 53 0.17
38 45 0.15
39 95 0.31
40 23 0.07
41 6 0.02
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (37 bp):
TATATATATTATATAGTTTTTAAAACATTTTTGAAAA
Found at i:4271304 original size:25 final size:23
Alignment explanation
Indices: 4271276--4271335 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 23
4271266 TTTAAAATCA
4271276 TTTTGAAAATATATAATATATAG
1 TTTTGAAAATATATAATATATAG
* *
4271299 TTTTTTGAAAACATATACTATATAG
1 --TTTTGAAAATATATAATATATAG
4271324 TTTTGAAAATAT
1 TTTTGAAAATAT
4271336 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 11 0.34
25 21 0.66
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (23 bp):
TTTTGAAAATATATAATATATAG
Found at i:4272830 original size:65 final size:65
Alignment explanation
Indices: 4272726--4272875 Score: 300
Period size: 65 Copynumber: 2.3 Consensus size: 65
4272716 AAAGTGACAC
4272726 CTTCGTGTGAATTTATTCACCGTGCGGGCCTAGCAAGTAGCATTCAGGATTCATATACCTTATGT
1 CTTCGTGTGAATTTATTCACCGTGCGGGCCTAGCAAGTAGCATTCAGGATTCATATACCTTATGT
4272791 CTTCGTGTGAATTTATTCACCGTGCGGGCCTAGCAAGTAGCATTCAGGATTCATATACCTTATGT
1 CTTCGTGTGAATTTATTCACCGTGCGGGCCTAGCAAGTAGCATTCAGGATTCATATACCTTATGT
4272856 CTTCGTGTGAATTTATTCAC
1 CTTCGTGTGAATTTATTCAC
4272876 TGCATAGGCA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 85 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (65 bp):
CTTCGTGTGAATTTATTCACCGTGCGGGCCTAGCAAGTAGCATTCAGGATTCATATACCTTATGT
Found at i:4275003 original size:95 final size:94
Alignment explanation
Indices: 4274836--4275018 Score: 296
Period size: 95 Copynumber: 1.9 Consensus size: 94
4274826 TATAATATTA
* *
4274836 TATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGA
* *
4274901 TAATATTCAGTTAGCCTGATAAATGTAAT
66 TAATATTCAGCTAACCTGATAAATGTAAT
*
4274930 TATACTATACAATAAAGCTTGAGATGTCCCTCT-AAGACAATTGGTTAAACGCCTCGACTTTATG
1 TATA-TATACAATAAAGCTTGAGATGTCCCTCTAAAG-CAATTGGTTAAACGCCCCGACTTTATG
4274994 GATAATATTCAGCTAACCTGATAAA
64 GATAATATTCAGCTAACCTGATAAA
4275019 GGTGTTTATA
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
94 7 0.09
95 75 0.91
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGA
TAATATTCAGCTAACCTGATAAATGTAAT
Found at i:4276349 original size:84 final size:83
Alignment explanation
Indices: 4276235--4277385 Score: 1040
Period size: 84 Copynumber: 13.9 Consensus size: 83
4276225 TTTTCTAACA
* * * *
4276235 AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCTA
*
4276300 GAAAGGTTATCTGCCACC
66 GAAGGGTTATCTGCCACC
* * * * * *
4276318 AAAAGACCTTCGAGTTTGACTACGTTTAGCTCCAAGACACATCATTTGCAGTATAACTCAAGGCT
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCT
* *
4276383 AGAAGGGTTATCTACCAAC
65 AGAAGGGTTATCTGCCACC
* * * * * * *
4276402 AAAGACCTTCGAGTTTGACTACACTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCTA
4276467 GAAGGGTTATCTGCCACC
66 GAAGGGTTATCTGCCACC
* * *
4276485 AAAATACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCT
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCT
* *
4276550 AGAAGGGTTATCTACCAAC
65 AGAAGGGTTATCTGCCACC
* * **
4276569 AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAA-ATTG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCT-
*
4276633 AGAAGGGTTACCTG-CA--
65 AGAAGGGTTATCTGCCACC
* * * * * * * * * *
4276649 AAAGACCCTCGAGTTCGATTACACTTAACTTCGAGGGCACATCATTTACAGCATAACTCAAAGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGGCT
*
4276714 AGAAGGGTTATCTGTCACC
65 AGAAGGGTTATCTGCCACC
* * * * * * * * *
4276733 AAAAGACCTTTGATTTTGACTACGCTCAACTCTAAGGCATATCATTTGCATCATAACTTAAGTCG
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCT
*
4276798 AGAAGGGTTATCTGTCAACC
65 AGAAGGGTTATCTG-CCACC
* * * * * *
4276818 AAAGACCTTTGAGTTCGACTATGCTTAGCTCCAAGGCACATCATTTGTAGCATAACTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCTA
* *
4276883 GAAGAGTTATATG---CC
66 GAAGGGTTATCTGCCACC
* * * * * * * * *
4276898 AAAGACCCTT-GAGTTCGATTACACTCAACTTCGAGGGCAAATCATTTACAACACAACTTAAGGC
1 AAAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGGC
* *
4276962 TAGAAGGGTTATTTGTCACC
64 TAGAAGGGTTATCTGCCACC
* * * * *
4276982 AAAAGATCTTCGAGTTCGACTACGCTCAGCTCTAAGACATATCATTTGC-GACATAACTTAAGTC
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG-CATAACTTAAGGC
*
4277046 GAGAAGGGTTATCTGCCAACC
64 TAGAAGGGTTATCTGCC-ACC
* * * * * * *
4277067 AAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTGTAGTATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCTA
* * * *
4277132 AAAAGGCTATTTG---CC
66 GAAGGGTTATCTGCCACC
** * ** * *
4277147 AAAGACCTTTAAGTTCGACTATGCTCAGCTTTGAGGGCACATCATTTGCAGCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGGCT
*
4277212 AGAAGGGTTATCTGCCAAC
65 AGAAGGGTTATCTGCCACC
* * * * * * * *
4277231 AAACACCTTTGAGTTCGATTACACTCAGCT-CAACGGTACATCATTTG-AGGTATAGCTCAAGGC
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCA-GCATAACTTAAGGC
*
4277294 TAGAAGGGCTATCTG---CC
64 TAGAAGGGTTATCTGCCACC
* * * * * * ** *
4277311 AAAGACATTCGAGTTCGACTATGCTCAACTCCAAGGCACATCATTTACAACATAGCACAAGGCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCTA
4277376 GAAGGGTTAT
66 GAAGGGTTAT
4277386 ATGTCAATAA
Statistics
Matches: 863, Mismatches: 177, Indels: 58
0.79 0.16 0.05
Matches are distributed among these distances:
80 127 0.15
81 120 0.14
82 8 0.01
83 178 0.21
84 380 0.44
85 50 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCTA
GAAGGGTTATCTGCCACC
Found at i:4276518 original size:167 final size:165
Alignment explanation
Indices: 4276235--4277385 Score: 1096
Period size: 167 Copynumber: 7.0 Consensus size: 165
4276225 TTTTCTAACA
* *
4276235 AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCAA
* * * *
4276300 GAAAGGTTATCTGCCACCAAAAGACCTTCGAGTTTGACTACGTTTAGCTCCAAGACACATCATTT
66 GAAGGGTTATCTG--ACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTT
* *
4276365 GCAGTATAACTCAAGGCTAGAAGGGTTATCTACCAAC
129 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC
* * *
4276402 AAAGACCTTCGAGTTTGACTACACTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCAA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCAA
*
4276467 GAAGGGTTATCTGCCACCAAAATACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTT
66 GAAGGGTTATCTG--ACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTT
*
4276532 GCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAAC
129 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC
* * * **
4276569 AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAATTGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCAA
* * * * * * *
4276634 GAAGGGTTACCTG--CAAAAGACCCTCGAGTTCGATTACACTT-AACTTCGAGGGCACATCATTT
66 GAAGGGTTATCTGACCAAAAGACCTTCGAGTTCGACTAC-GTTCAGC-TCCAAGGCACATCATTT
* * * *
4276696 ACAGCATAACTCAAAGCTAGAAGGGTTATCTGTCACC
129 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC
* * * * * * *
4276733 AAAAGACCTTTGATTTTGACTACGCTCAACTCTAAGGCATATCATTTGCA-TCATAACTTAAGTC
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGT-ATAGCTTAAGTC
* * *
4276797 GAGAAGGGTTATCTGTCAACC-AAAGACCTTTGAGTTCGACTATGCTT-AGCTCCAAGGCACATC
64 AAGAAGGGTTATCTG---ACCAAAAGACCTTCGAGTTCGACTACG-TTCAGCTCCAAGGCACATC
* * * * * *
4276860 ATTTGTAGCATAACTTAAGTCGAGAAGAGTTATATG-C--C
125 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC
* * * * * * * ** * * *
4276898 AAAGACCCTT-GAGTTCGATTACACTCAACTTCGAGGGCAAATCATTTACAACACAACTTAAGGC
1 AAAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGTATAGCTTAAGTC
* * * * * * *
4276962 TAGAAGGGTTATTTGTCACCAAAAGATCTTCGAGTTCGACTACGCTCAGCTCTAAGACATATCAT
64 AAGAAGGGTTATCTG--ACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCAT
* * *
4277027 TTGC-GACATAACTTAAGTCGAGAAGGGTTATCTGCCAACC
127 TTGCAG-CATAACTCAAGGCTAGAAGGGTTATCTGCCAA-C
* * *
4277067 AAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTGTAGTATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTC-A
* * * ** * * ** *
4277132 A-AAAGGCTATTTG-CC-AAAGACCTTTAAGTTCGACTATGCTCAGCTTTGAGGGCACATCATTT
65 AGAAGGGTTATCTGACCAAAAGACCTTCGAGTTCGACTACGTTCAGC-TCCAAGGCACATCATTT
4277194 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC
129 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC
* * * * * * *
4277231 AAACACCTTTGAGTTCGATTACACTCAGCT-CAACGGTACATCATTTG-AGGTATAGCTCAAGGC
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCA-GTATAGCTTAAGTC
* * * * * *
4277294 TAGAAGGGCTATCTG-CC-AAAGACATTCGAGTTCGACTATGCTCAACTCCAAGGCACATCATTT
64 AAGAAGGGTTATCTGACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTT
* * * * *
4277357 ACAACATAGCACAAGGCAAGAAGGGTTAT
129 GCAGCATAACTCAAGGCTAGAAGGGTTAT
4277386 ATGTCAATAA
Statistics
Matches: 824, Mismatches: 133, Indels: 58
0.81 0.13 0.06
Matches are distributed among these distances:
163 66 0.08
164 186 0.23
165 220 0.27
166 2 0.00
167 229 0.28
168 76 0.09
169 44 0.05
170 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (165 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCAA
GAAGGGTTATCTGACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGC
AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC
Found at i:4276944 original size:249 final size:248
Alignment explanation
Indices: 4276233--4277356 Score: 1192
Period size: 249 Copynumber: 4.5 Consensus size: 248
4276223 TATTTTCTAA
* *
4276233 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTC
* * * * * * *
4276298 AAGAAAGGTTATCTGCCACCAAAAGACCTTCGAGTTTGACTACGTTTAGCTCCAAGACACATCAT
66 GAGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * * * * * *
4276363 TTGCAGTATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGA-CCTTCGAGTTTGACTACACT
130 TTGCAGCATAACTTAAGTCGAGAAGAGTTATCT-GC--CAAAGACCCTT-GAGTTCGACTACACT
* * * * * * * *
4276427 CAGC-TCTAAGGCACATCATTTGCAGTATAGCT-TAAGTCAAGAAGGGTTATCTGCCAC
191 CAACTTCGAGGGCACATCATTTACAGCATAACTCAAAG-CTAGAAGGGTTATCTGCCAC
* * * * *
4276484 CAAAATACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGC
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTC
* * *
4276549 TAGAAGGGTTATCTACCAA-CAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCAT
66 GAGAAGGGTTATCT-GCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * * * * * * * *
4276613 TTGCAGCATAGCTTAAATTGAGAAGGGTTACCTGCAAAAGACCCTCGAGTTCGATTACACTTAAC
130 TTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGCCAAAGACCCTTGAGTTCGACTACACTCAAC
*
4276678 TTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTCAC
195 TTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGCCAC
* * * * * *
4276732 CAAAAGACCTTTGATTTTGACTACGCTCAACTCTAAGGCATATCATTTGCATCATAACTTAAGTC
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTC
* * *
4276797 GAGAAGGGTTATCTGTCAACCAAAGACCTTTGAGTTCGACTATGCTTAGCTCCAAGGCACATCAT
66 GAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * *
4276862 TTGTAGCATAACTTAAGTCGAGAAGAGTTATATGCCAAAGACCCTTGAGTTCGATTACACTCAAC
130 TTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGCCAAAGACCCTTGAGTTCGACTACACTCAAC
* * * * * * *
4276927 TTCGAGGGCAAATCATTTACAACACAACTTAAGGCTAGAAGGGTTATTTGTCAC
195 TTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGCCAC
* * *
4276981 CAAAAGATCTTCGAGTTCGACTACGCTCAGCTCTAAGACATATCATTTGC-GACATAACTTAAGT
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAG-CATAACTTAAGT
* *
4277045 CGAGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTA
65 CGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
* * * * * * * * **
4277110 TTTGTAGTATAGCTTAAGTCGA-AAAAGGCTATTTGCCAAAGACCTTTAAGTTCGACTATGCTCA
129 TTTGCAGCATAACTTAAGTCGAGAAGA-GTTATCTGCCAAAGACCCTTGAGTTCGACTACACTCA
* * * * *
4277174 GCTTTGAGGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
193 ACTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGCCAC
* * * * * * * *
4277230 C-AAACACCTTTGAGTTCGATTACACTCAGCTC-AACGGTACATCATTTG-AGGTATAGCTCAAG
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAA-GGCACATCATTTGCA-GCATAACTTAAG
* * * * * *
4277292 GCTAGAAGGGCTATCTG---CCAAAGACATTCGAGTTCGACTATGCTCAACTCCAAGGCACATCA
64 TCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
4277354 TTT
129 TTT
4277357 ACAACATAGC
Statistics
Matches: 741, Mismatches: 121, Indels: 29
0.83 0.14 0.03
Matches are distributed among these distances:
244 43 0.06
247 22 0.03
248 175 0.24
249 361 0.49
250 66 0.09
251 72 0.10
252 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (248 bp):
CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTC
GAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTTAAGTCGAGAAGAGTTATCTGCCAAAGACCCTTGAGTTCGACTACACTCAACT
TCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGCCAC
Found at i:4277937 original size:37 final size:37
Alignment explanation
Indices: 4277810--4278241 Score: 402
Period size: 37 Copynumber: 11.5 Consensus size: 37
4277800 TTTATATATC
* * ***
4277810 TATATATATTATATAGTTTGTAAATGGTTTTTGAAAA
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAA
*
4277847 TACGTATATAATATATAGTTTTTTATAACATTTTTGAAAA
1 TA--TATATAATATATAG-TTTTTAAAACATTTTTGAAAA
* *
4277887 TATGTATATTATATAGTTTTTAAAAACATTTTTGAAAA
1 TATATATAATATATAGTTTTT-AAAACATTTTTGAAAA
* *
4277925 T-TATATAATATATAATTTTTAAAACATTTTAGAAAA
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAA
*
4277961 TATATATAATATATATAGCTTTTAAAATCA-TTTTG-AAA
1 TATATAT-A-ATATATAGTTTTTAAAA-CATTTTTGAAAA
*
4277999 -ATATATAATATATAGTTTTTTTAAAACATTTTAG-AAA
1 TATATATAATATATAG--TTTTTAAAACATTTTTGAAAA
* * * * *
4278036 -ACATGTACTGTATAGTTTTTAAAATATTTTT-AAAA
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAA
*
4278071 TATATATAAT-TATAGTTGTTGAAAACATTTTTGAAAA
1 TATATATAATATATAGTT-TTTAAAACATTTTTGAAAA
* *
4278108 CT-TATATATTATATAGTTTTGAAAACATTTTTGAAAACA
1 -TATATATAATATATAGTTTTTAAAACATTTTTG-AAA-A
* * *
4278147 TTTATATATTATATAGTTTTTAAAACGTTTTTGAAAA
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAA
*
4278184 CTTATATATAATATATAG-TTTAAAAATCA-TTTTG-AAA
1 --TATATATAATATATAGTTTTTAAAA-CATTTTTGAAAA
4278221 TATATATATATAATATAGTTT
1 TATATATA-AT-ATATAGTTT
4278242 ATATTATAAT
Statistics
Matches: 333, Mismatches: 36, Indels: 51
0.79 0.09 0.12
Matches are distributed among these distances:
35 40 0.12
36 39 0.12
37 96 0.29
38 61 0.18
39 77 0.23
40 20 0.06
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (37 bp):
TATATATAATATATAGTTTTTAAAACATTTTTGAAAA
Found at i:4278141 original size:12 final size:12
Alignment explanation
Indices: 4278124--4278149 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4278114 TATTATATAG
4278124 TTTTGAAAACAT
1 TTTTGAAAACAT
4278136 TTTTGAAAACAT
1 TTTTGAAAACAT
4278148 TT
1 TT
4278150 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:4279427 original size:21 final size:22
Alignment explanation
Indices: 4279401--4279443 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
4279391 ACTGGTTCAC
4279401 TGGTTCAACCG-GGTTCAACCG
1 TGGTTCAACCGTGGTTCAACCG
4279422 TGGTTCAACCGTGGTTCAACCG
1 TGGTTCAACCGTGGTTCAACCG
4279444 AATTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.26
Consensus pattern (22 bp):
TGGTTCAACCGTGGTTCAACCG
Found at i:4279428 original size:11 final size:11
Alignment explanation
Indices: 4279401--4279443 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
4279391 ACTGGTTCAC
4279401 TGGTTCAACCG
1 TGGTTCAACCG
4279412 -GGTTCAACCG
1 TGGTTCAACCG
4279422 TGGTTCAACCG
1 TGGTTCAACCG
4279433 TGGTTCAACCG
1 TGGTTCAACCG
4279444 AATTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.32
11 21 0.68
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.26
Consensus pattern (11 bp):
TGGTTCAACCG
Found at i:4279965 original size:24 final size:24
Alignment explanation
Indices: 4279938--4279999 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
4279928 CTATTCTTTC
4279938 GCTTCAATTGAGCTCGAATTTCAA
1 GCTTCAATTGAGCTCGAATTTCAA
4279962 GCTTCAATTGAGCTCGAATTTCAA
1 GCTTCAATTGAGCTCGAATTTCAA
*
4279986 GCTTCAATCGAGCT
1 GCTTCAATTGAGCT
4280000 TCTAAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (24 bp):
GCTTCAATTGAGCTCGAATTTCAA
Found at i:4280263 original size:30 final size:30
Alignment explanation
Indices: 4280227--4280292 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
4280217 AAAGAACCGG
*
4280227 CGGTTCACACCGATTTTGCTAGTTTTCAGC
1 CGGTTCACACCGATTTTGCTAGTTCTCAGC
* * *
4280257 CGGTTCACCCCGGTTTTGCTGGTTCTCAGC
1 CGGTTCACACCGATTTTGCTAGTTCTCAGC
4280287 CGGTTC
1 CGGTTC
4280293 TTCCGGTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.30, G:0.24, T:0.35
Consensus pattern (30 bp):
CGGTTCACACCGATTTTGCTAGTTCTCAGC
Found at i:4280924 original size:2 final size:2
Alignment explanation
Indices: 4280917--4280951 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4280907 ATACACAAAC
4280917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4280952 ATGAATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4286675 original size:107 final size:107
Alignment explanation
Indices: 4286489--4286703 Score: 385
Period size: 107 Copynumber: 2.0 Consensus size: 107
4286479 TGAATTGTGA
*
4286489 ATGTTTTTAGAGTTAATTGAGAAGCTGAATATAACTCTCTATTTATAGGCTAGAAATAGGGTTAA
1 ATGTTTTTAGAGTGAATTGAGAAGCTGAATATAACTCTCTATTTATAGGCTAGAAATAGGGTTAA
4286554 AATCGTCCATAAAATTTCAGGATTAAACCTCTTATTTGTAAC
66 AATCGTCCATAAAATTTCAGGATTAAACCTCTTATTTGTAAC
* * *
4286596 ATGTTTTTTGAGTGAATTGAGAAGCTGAATATAGCTCTCTATTTATAGGCTAGGAATAGGGTTAA
1 ATGTTTTTAGAGTGAATTGAGAAGCTGAATATAACTCTCTATTTATAGGCTAGAAATAGGGTTAA
*
4286661 AATCGTTCATAAAATTTCAGGATTAAACCTCTTATTTGTAAC
66 AATCGTCCATAAAATTTCAGGATTAAACCTCTTATTTGTAAC
4286703 A
1 A
4286704 GCTGAAACGT
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (107 bp):
ATGTTTTTAGAGTGAATTGAGAAGCTGAATATAACTCTCTATTTATAGGCTAGAAATAGGGTTAA
AATCGTCCATAAAATTTCAGGATTAAACCTCTTATTTGTAAC
Found at i:4287045 original size:6 final size:6
Alignment explanation
Indices: 4287031--4287067 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
4287021 GACACGTATT
* *
4287031 ACCAAG ACCACG ACCACG ACCACA ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
4287068 GCCGAGCCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.41, C:0.46, G:0.14, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4287075 original size:5 final size:5
Alignment explanation
Indices: 4287065--4287091 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4287055 ACCACGACCA
4287065 CGAGC CGAGC CGAGC CGAGC CGAGC CG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CG
4287092 GACAGCGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.41, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:4288656 original size:21 final size:20
Alignment explanation
Indices: 4288619--4288657 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4288609 AATAAAATAA
*
4288619 AATAATAAAACATTTTTAAT
1 AATAATAAAACAATTTTAAT
*
4288639 AATATATAAAATAATTTTA
1 AATA-ATAAAACAATTTTA
4288658 TATTCCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAATAAAACAATTTTAAT
Found at i:4288872 original size:5 final size:5
Alignment explanation
Indices: 4288862--4289035 Score: 334
Period size: 5 Copynumber: 35.2 Consensus size: 5
4288852 CTCTCCGTAT
4288862 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
4288912 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
4288962 TTATA TTATA TTATA TTATA TTATA TTATA -T-TA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
4289010 TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA T
4289036 GTGAGTTCTG
Statistics
Matches: 167, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
3 2 0.01
4 2 0.01
5 163 0.98
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:4290770 original size:419 final size:418
Alignment explanation
Indices: 4289992--4290832 Score: 1592
Period size: 419 Copynumber: 2.0 Consensus size: 418
4289982 TTAGCCATTT
4289992 TTTTTATCCATTTTAGCCAACTGTTGTTTTAAACGAATAACTTCTAATTAGGAAGACTGAGTCTG
1 TTTTTATCCATTTTAGCCAACTGTTGTTTTAAACGAATAACTTCTAATTAGGAAGACTGAGTCTG
4290057 TGACGACATGTACTGAGATGAATTGGATCTAAAATATTTGGTGGGAGTAACGAATGACCCTTGAC
66 TGACGACATGTACTGAGATGAATTGGATCTAAAATATTTGGTGGGAGTAACGAATGACCCTTGAC
*
4290122 AGTGAACCCGACCATATCTTTCAGGACCCAAAACTTCATTAATAACTTTATTTTCGATGTCATCC
131 AGTGAACCCAACCATATCTTTCAGGACCCAAAACTTCATTAATAACTTTATTTTCGATGTCATCC
* *
4290187 GCATTAACAATACCATGACTTGAAGTCGTAGCTTCATACTCCTCCCTTTTATCCATCAATTTTTC
196 GCATTAACAATACCATGACTTAAAGTCATAGCTTCATACTCCTCCCTTTTATCCATCAATTTTTC
4290252 CTAAAAATCAATTCAATAATTATTTTAAATAAGAATGTCATACTATAGATATAAATATAACATAA
261 CTAAAAATCAATTCAATAATTATTTTAAATAAGAATGTCATACTATAGATATAAATATAACATAA
* *
4290317 TTCAAATCATGTGTCCAATAAATGTACCATAATTTCTGCAGCTTCAGCAGTCATAGGAGTGTCAT
326 TTCAAATCATGTGTCCAATAAATATACCATAATTTATGCAGCTTCAGCAGTCATAGGAGTGTCAT
4290382 CCTTTTTCTGTATATGTCATGTCGAAGAG
391 CCTTTTT-TGTATATGTCATGTCGAAGAG
* *
4290411 TTTTTATCCATTTTAGCCAACTGTTGTTTTAAACGACTAACTTCTAATTGGGAAGACTGAGTCTG
1 TTTTTATCCATTTTAGCCAACTGTTGTTTTAAACGAATAACTTCTAATTAGGAAGACTGAGTCTG
4290476 TGACGACATGTACTGAGATGAATTGGATCTAAAATATTTGGTGGGAGTAACGAATGACCCTTGAC
66 TGACGACATGTACTGAGATGAATTGGATCTAAAATATTTGGTGGGAGTAACGAATGACCCTTGAC
4290541 AGTGAACCCAACCATATCTTTCAGGACCCAAAACTTCATTAATAACTTTATTTTCGATGTCATCC
131 AGTGAACCCAACCATATCTTTCAGGACCCAAAACTTCATTAATAACTTTATTTTCGATGTCATCC
4290606 GCATTAACAATACCATGACTTAAAGTCATAGCTTCATACTCCTCCCTTTTATCCATCAATTTTTC
196 GCATTAACAATACCATGACTTAAAGTCATAGCTTCATACTCCTCCCTTTTATCCATCAATTTTTC
*
4290671 CTAATAATCAATTCAATAATTATTTTAAATAAGAATGTCATACTATAGATATAAATATAACATAA
261 CTAAAAATCAATTCAATAATTATTTTAAATAAGAATGTCATACTATAGATATAAATATAACATAA
4290736 TTCAAATCATGTGTCCAATAAATATACCATAATTTATGCAGCTTCAGCAGTCATAGGAGTGTCAT
326 TTCAAATCATGTGTCCAATAAATATACCATAATTTATGCAGCTTCAGCAGTCATAGGAGTGTCAT
*
4290801 CCTTTTTTGTATGTGTCATGTCGAAGAG
391 CCTTTTTTGTATATGTCATGTCGAAGAG
4290829 TTTT
1 TTTT
4290833 ATTCGTCCAA
Statistics
Matches: 413, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
418 24 0.06
419 389 0.94
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (418 bp):
TTTTTATCCATTTTAGCCAACTGTTGTTTTAAACGAATAACTTCTAATTAGGAAGACTGAGTCTG
TGACGACATGTACTGAGATGAATTGGATCTAAAATATTTGGTGGGAGTAACGAATGACCCTTGAC
AGTGAACCCAACCATATCTTTCAGGACCCAAAACTTCATTAATAACTTTATTTTCGATGTCATCC
GCATTAACAATACCATGACTTAAAGTCATAGCTTCATACTCCTCCCTTTTATCCATCAATTTTTC
CTAAAAATCAATTCAATAATTATTTTAAATAAGAATGTCATACTATAGATATAAATATAACATAA
TTCAAATCATGTGTCCAATAAATATACCATAATTTATGCAGCTTCAGCAGTCATAGGAGTGTCAT
CCTTTTTTGTATATGTCATGTCGAAGAG
Found at i:4293909 original size:40 final size:40
Alignment explanation
Indices: 4293854--4293936 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
4293844 TGGATTATTA
4293854 GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACAG
1 GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACAG
4293894 GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACAG
1 GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACAG
4293934 GCG
1 GCG
4293937 AATGCCTGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.14, C:0.20, G:0.36, T:0.29
Consensus pattern (40 bp):
GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACAG
Found at i:4299458 original size:16 final size:16
Alignment explanation
Indices: 4299407--4299463 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
4299397 TCTCCATCAC
*
4299407 AAAAAAAA-TGTTGAAA
1 AAAAAAAACTGTT-AGA
* *
4299423 AAAAAAATAGCAGTTCGA
1 AAAAAAA-A-CTGTTAGA
4299441 AAAAAAAACTGTTAGA
1 AAAAAAAACTGTTAGA
4299457 AAAAAAA
1 AAAAAAA
4299464 GGACATGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 20 0.61
17 2 0.06
18 8 0.24
19 3 0.09
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (16 bp):
AAAAAAAACTGTTAGA
Found at i:4301700 original size:40 final size:40
Alignment explanation
Indices: 4301645--4301723 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
4301635 TGGATTATTA
4301645 GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACAG
1 GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACAG
4301685 GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACA
1 GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACA
4301724 TACGAATGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.15, C:0.20, G:0.34, T:0.30
Consensus pattern (40 bp):
GCGTTGGCTGCTCTGGGGCTTTAGTTACTTGAGACGACAG
Found at i:4302026 original size:42 final size:42
Alignment explanation
Indices: 4301931--4302026 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 42
4301921 AATCACGACG
* *
4301931 TTTATA-ATAAAAACGCCACTAAGGTACATCACTATTGCGTCT
1 TTTATACA-AAAAACGCCACTAAAGTACATCACTATTGCGGCT
* * *
4301973 TTTATTACAAAAAATGCCACTAAAGTCCATGACTATTGCGGCT
1 TTTA-TACAAAAAACGCCACTAAAGTACATCACTATTGCGGCT
4302016 TTTGA-ACAAAA
1 TTT-ATACAAAA
4302027 GCGCCTCTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
42 10 0.22
43 34 0.74
44 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (42 bp):
TTTATACAAAAAACGCCACTAAAGTACATCACTATTGCGGCT
Found at i:4302464 original size:82 final size:82
Alignment explanation
Indices: 4302325--4302538 Score: 279
Period size: 83 Copynumber: 2.6 Consensus size: 82
4302315 TTGTAACGAT
* * *
4302325 GCCACTATATATGAACCTTATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTCTCTGTTGCG
1 GCCACTATATATGAACCCTATTGCGGCATTTGTATAAAAACACCGCTAAAGTACTCTCTGTTGCA
*
4302390 GCGTTTGTTG-AAAAAT
66 GCGTTTGTTGAAAAAAC
* * *
4302406 GTCACTTTATATGAACCCTATTGCGGCATTTGTATAAAAA-ACGTCGCTAAAGTTCTCTCTGTTG
1 GCCACTATATATGAACCCTATTGCGGCATTTGTATAAAAACAC--CGCTAAAGTACTCTCTGTTG
4302470 CAGCGTTTGTTGAAAAAAC
64 CAGCGTTTGTTGAAAAAAC
* * * * * *
4302489 GCCACTATATGTGAAACCTAATGTGGCATTTGTATAAAAACGCTGCTAAA
1 GCCACTATATATGAACCCTATTGCGGCATTTGTATAAAAACACCGCTAAA
4302539 TTTACCATTT
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
80 2 0.02
81 36 0.32
82 36 0.32
83 39 0.34
84 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (82 bp):
GCCACTATATATGAACCCTATTGCGGCATTTGTATAAAAACACCGCTAAAGTACTCTCTGTTGCA
GCGTTTGTTGAAAAAAC
Found at i:4302486 original size:40 final size:41
Alignment explanation
Indices: 4302345--4302486 Score: 123
Period size: 40 Copynumber: 3.5 Consensus size: 41
4302335 ATGAACCTTA
**
4302345 TTGCGGCGTTTGTAT-AAAAACACCGCTAAAGTACTCTCTG
1 TTGCGGCGTTTGTATGAAAAACGTCGCTAAAGTACTCTCTG
* * * * *
4302385 TTGCGGCGTTTGT-TGAAAAATGTCACTTTATATGAAC-C-CTA
1 TTGCGGCGTTTGTATGAAAAACGTCGC--TA-AAGTACTCTCTG
* * *
4302426 TTGCGGCATTTGTATAAAAAACGTCGCTAAAGTTCTCTCTG
1 TTGCGGCGTTTGTATGAAAAACGTCGCTAAAGTACTCTCTG
*
4302467 TTGCAGCGTTTGT-TGAAAAA
1 TTGCGGCGTTTGTATGAAAAA
4302487 ACGCCACTAT
Statistics
Matches: 77, Mismatches: 18, Indels: 14
0.71 0.17 0.13
Matches are distributed among these distances:
39 4 0.05
40 29 0.38
41 27 0.35
42 13 0.17
43 4 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (41 bp):
TTGCGGCGTTTGTATGAAAAACGTCGCTAAAGTACTCTCTG
Found at i:4304396 original size:60 final size:61
Alignment explanation
Indices: 4304313--4304470 Score: 210
Period size: 60 Copynumber: 2.6 Consensus size: 61
4304303 TAAGGTATTA
* * * * * * * *
4304313 TTTTGTTGAGTCTATTGATTATTAAATATTATAAAATGACCCTTCAATTATAGGTTATTGC
1 TTTTGTTAAGTCCATTAACTATTAAAAATTATAAAATGACCCTTCAACTATAGGTCACTGC
* *
4304374 -TTTGTTAAGTCCATTAACTATTAAAAATTACAAAATGACCCTTCGACTATAGGTCACTGC
1 TTTTGTTAAGTCCATTAACTATTAAAAATTATAAAATGACCCTTCAACTATAGGTCACTGC
*
4304434 TTTTGTTAAGTCCACTAACTATTAAAAATTATAAAAT
1 TTTTGTTAAGTCCATTAACTATTAAAAATTATAAAAT
4304471 AATCACTCGA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 50 0.60
61 34 0.40
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (61 bp):
TTTTGTTAAGTCCATTAACTATTAAAAATTATAAAATGACCCTTCAACTATAGGTCACTGC
Found at i:4304481 original size:61 final size:60
Alignment explanation
Indices: 4304332--4304484 Score: 173
Period size: 61 Copynumber: 2.5 Consensus size: 60
4304322 GTCTATTGAT
* * * * * * * * *
4304332 TATTAAATATTATAAAATGACCCTTCAATTATAGGTTATTGCTTTGTTAAGTCCATTAAC
1 TATTAAAAATTACAAAATAACACTTCGACTATAGGTCACTGCTTTGTTAAGTCCACTAAC
* *
4304392 TATTAAAAATTACAAAATGACCCTTCGACTATAGGTCACTGCTTTTGTTAAGTCCACTAAC
1 TATTAAAAATTACAAAATAACACTTCGACTATAGGTCACTGC-TTTGTTAAGTCCACTAAC
*
4304453 TATTAAAAATTATAAAATAATCAC-TCGACTAT
1 TATTAAAAATTACAAAATAA-CACTTCGACTAT
4304485 TTATATATTC
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
60 36 0.44
61 43 0.53
62 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (60 bp):
TATTAAAAATTACAAAATAACACTTCGACTATAGGTCACTGCTTTGTTAAGTCCACTAAC
Found at i:4306268 original size:18 final size:19
Alignment explanation
Indices: 4306225--4306288 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 19
4306215 TTAATGAAAG
4306225 AGATATCAATTGTTAACAAA
1 AGATATCAATTGTTAA-AAA
4306245 AGGATATCAATTGTT-AAAA
1 A-GATATCAATTGTTAAAAA
* *
4306264 AGATACCAATTGTTGAAAA
1 AGATATCAATTGTTAAAAA
*
4306283 ATATAT
1 AGATAT
4306289 GAAAATGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 12 0.31
19 12 0.31
20 2 0.05
21 13 0.33
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (19 bp):
AGATATCAATTGTTAAAAA
Found at i:4307405 original size:20 final size:20
Alignment explanation
Indices: 4307380--4307429 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
4307370 TCTAAATCAT
4307380 TTTTCAAAATTTGATTTTGA
1 TTTTCAAAATTTGATTTTGA
4307400 TTTTCAAAATTTGATTTTGA
1 TTTTCAAAATTTGATTTTGA
4307420 TTTTCAAAAT
1 TTTTCAAAAT
4307430 CAACTATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTTGATTTTGA
Found at i:4309786 original size:18 final size:19
Alignment explanation
Indices: 4309739--4309795 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 19
4309729 ATGTTTAATG
4309739 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
4309758 ACAAAAGGATATCAATTGTT-
1 A-AAAA-GATATCAATTGTTA
*
4309778 AAAAAGATACCAATTGTT
1 AAAAAGATATCAATTGTT
4309796 GGAAAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 12 0.34
19 5 0.14
20 5 0.14
21 13 0.37
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:4312994 original size:20 final size:20
Alignment explanation
Indices: 4312969--4313006 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4312959 TTTGGTTCAC
4312969 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
4312989 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
4313007 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:4313016 original size:16 final size:18
Alignment explanation
Indices: 4312969--4313019 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
4312959 TTTGGTTCAC
4312969 GGAATGTAAGATTACCAGTG
1 GGAA-GTAAGATTACCAG-G
4312989 GGAATGTAAGATTACCA-G
1 GGAA-GTAAGATTACCAGG
4313007 GGAA-TAAGATTAC
1 GGAAGTAAGATTAC
4313020 TGGGAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 5 0.16
20 17 0.55
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGG
Found at i:4314144 original size:12 final size:12
Alignment explanation
Indices: 4314127--4314153 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4314117 ATTTCGGGTT
4314127 GGACATGATTTA
1 GGACATGATTTA
4314139 GGACATGATTTA
1 GGACATGATTTA
4314151 GGA
1 GGA
4314154 ATCGGAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (12 bp):
GGACATGATTTA
Found at i:4314832 original size:23 final size:23
Alignment explanation
Indices: 4314802--4314883 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
4314792 GCATGGCCTT
4314802 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
4314825 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
* *
4314847 -TGTATCAATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
4314869 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
4314884 CTTAATAGTG
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 3 0.07
23 17 0.38
24 12 0.27
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:4314896 original size:45 final size:44
Alignment explanation
Indices: 4314810--4314903 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
4314800 TTGTGCATCG
* * *
4314810 ATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGTATCA
1 ATGCACATTCAAGGAGTGCATCGATGCACCTTAATGATGTATCA
*
4314854 ATGCACATTCAAAGG-GATGCATCGATGCACCTTAAT-AGTGTATCG
1 ATGCACATTC-AAGGAG-TGCATCGATGCACCTTAATGA-TGTATCA
4314899 ATGCA
1 ATGCA
4314904 TTATGCACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
44 12 0.28
45 31 0.72
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
ATGCACATTCAAGGAGTGCATCGATGCACCTTAATGATGTATCA
Found at i:4324228 original size:29 final size:28
Alignment explanation
Indices: 4324173--4324238 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
4324163 TTAAAAGGCT
* *
4324173 TTTTTTTAATAGTCTGTGATGATTATAAGA
1 TTTTTTTAACAGTATGTGA-GATTATAA-A
4324203 TTTTTTTAACAGTATGTGA-ATCTATAAA
1 TTTTTTTAACAGTATGTGAGAT-TATAAA
*
4324231 TATTTTTA
1 TTTTTTTA
4324239 GGGTGGACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 10 0.31
29 5 0.16
30 17 0.53
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.52
Consensus pattern (28 bp):
TTTTTTTAACAGTATGTGAGATTATAAA
Found at i:4324919 original size:20 final size:21
Alignment explanation
Indices: 4324888--4324930 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
4324878 TGTTCACTGG
4324888 TATTTAATTTAAAATGTTATA
1 TATTTAATTTAAAATGTTATA
*
4324909 TATTT-ATTTAAAATTTTATA
1 TATTTAATTTAAAATGTTATA
4324929 TA
1 TA
4324931 ATTGATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTTAATTTAAAATGTTATA
Found at i:4328173 original size:2 final size:2
Alignment explanation
Indices: 4328161--4328191 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4328151 TTGTAGTGAA
4328161 AT AT A- 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
4328192 GATTGTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4329871 original size:14 final size:14
Alignment explanation
Indices: 4329852--4329891 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 14
4329842 TTTACCGGAT
4329852 AAAAAACCGGTTTGA
1 AAAAAACCGGTTT-A
4329867 AAAAAA-CGG-TTA
1 AAAAAACCGGTTTA
4329879 AAAAAACCGGTTT
1 AAAAAACCGGTTT
4329892 TTATCCGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.30
13 5 0.22
14 5 0.22
15 6 0.26
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.20
Consensus pattern (14 bp):
AAAAAACCGGTTTA
Found at i:4332160 original size:19 final size:20
Alignment explanation
Indices: 4332136--4332178 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
4332126 GTTTATTTTA
4332136 TAACTTTATTTCAA-TATCG
1 TAACTTTATTTCAATTATCG
*
4332155 TAACTTTGTTTCAATTATCG
1 TAACTTTATTTCAATTATCG
4332175 -AACT
1 TAACT
4332179 GAAGTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (20 bp):
TAACTTTATTTCAATTATCG
Found at i:4332207 original size:31 final size:32
Alignment explanation
Indices: 4332169--4332264 Score: 133
Period size: 32 Copynumber: 3.0 Consensus size: 32
4332159 TTTGTTTCAA
4332169 TTATCGAAC-TGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
*
4332200 TTATCGAACTTGGAGTTTTTAAGTA-TTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
* * *
4332231 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
4332264 T
1 T
4332265 ATGTTGAGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
31 25 0.44
32 26 0.46
33 6 0.11
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:4332222 original size:32 final size:32
Alignment explanation
Indices: 4332169--4332264 Score: 133
Period size: 31 Copynumber: 3.0 Consensus size: 32
4332159 TTTGTTTCAA
*
4332169 TTATCGAAC-TGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAGTTTTTAAGTATTTGAAT
4332200 TTATCGAACTTGGAGTTTTTAAGTA-TTGAAT
1 TTATCGAACTTGGAGTTTTTAAGTATTTGAAT
* * *
4332231 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGG-AGTTTTTAAGTATTTGAAT
4332264 T
1 T
4332265 ATGTTGAGTT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.47
32 25 0.43
33 6 0.10
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGGAGTTTTTAAGTATTTGAAT
Found at i:4332293 original size:13 final size:13
Alignment explanation
Indices: 4332250--4332304 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
4332240 TTGGAAGTAT
4332250 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
4332263 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
4332277 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
4332290 TTAAGTATTTGAA
1 TTAAGTATTTCAA
4332303 TT
1 TT
4332305 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:4332724 original size:15 final size:16
Alignment explanation
Indices: 4332704--4332745 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
4332694 TTAAATCGGT
* *
4332704 TTTTTTATATAACC-G
1 TTTTTTAAAAAACCGG
4332719 TTTTTTAAAAAACCGG
1 TTTTTTAAAAAACCGG
4332735 TTTTTTTAAAA
1 -TTTTTTAAAA
4332746 CCGAAACCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.52
16 1 0.04
17 10 0.43
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (16 bp):
TTTTTTAAAAAACCGG
Found at i:4332746 original size:15 final size:15
Alignment explanation
Indices: 4332700--4332748 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
4332690 AATATTAAAT
4332700 CGGTTTTTTTATATAAC
1 CGGTTTTTTTA-A-AAC
*
4332717 C-GTTTTTTAAAAAAC
1 CGGTTTTTT-TAAAAC
4332732 CGGTTTTTTTAAAAC
1 CGGTTTTTTTAAAAC
4332747 CG
1 CG
4332749 AAACCGGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 11 0.39
16 15 0.54
17 2 0.07
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (15 bp):
CGGTTTTTTTAAAAC
Found at i:4332865 original size:15 final size:17
Alignment explanation
Indices: 4332839--4332870 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4332829 TTCTATGGGA
4332839 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
4332855 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
4332871 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:4333523 original size:112 final size:112
Alignment explanation
Indices: 4333326--4333544 Score: 438
Period size: 112 Copynumber: 2.0 Consensus size: 112
4333316 ACATCAACAG
4333326 CCACTGTATGTAATAAAGTCTCCCATTACAAATATGTTTCCACTAACCTACATGGTTCTCAAGCA
1 CCACTGTATGTAATAAAGTCTCCCATTACAAATATGTTTCCACTAACCTACATGGTTCTCAAGCA
4333391 CAACTGGAGGCACTTGAGCATCAGGTGACTGTGCATTGGATAGAAAT
66 CAACTGGAGGCACTTGAGCATCAGGTGACTGTGCATTGGATAGAAAT
4333438 CCACTGTATGTAATAAAGTCTCCCATTACAAATATGTTTCCACTAACCTACATGGTTCTCAAGCA
1 CCACTGTATGTAATAAAGTCTCCCATTACAAATATGTTTCCACTAACCTACATGGTTCTCAAGCA
4333503 CAACTGGAGGCACTTGAGCATCAGGTGACTGTGCATTGGATA
66 CAACTGGAGGCACTTGAGCATCAGGTGACTGTGCATTGGATA
4333545 TAGAAATCAG
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 107 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (112 bp):
CCACTGTATGTAATAAAGTCTCCCATTACAAATATGTTTCCACTAACCTACATGGTTCTCAAGCA
CAACTGGAGGCACTTGAGCATCAGGTGACTGTGCATTGGATAGAAAT
Found at i:4334268 original size:98 final size:98
Alignment explanation
Indices: 4334099--4334295 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
4334089 TCATATGAGC
4334099 TGATTCAAGACAACCGCGCTTCCTTCGAACGATCGCACAGTCTATGTGTCCAAAGGCGAGGTATT
1 TGATTCAAGACAACCGCGCTTCCTTCGAACGATCGCACAGTCTATGTGTCCAAAGGCGAGGTATT
4334164 ATGAAGGGTTTCAAATCGCGGTCGCCTTTTAGG
66 ATGAAGGGTTTCAAATCGCGGTCGCCTTTTAGG
4334197 TGATTCAAGACAACCGCGCTTCCTTCGAACGATCGCACAGTCTATGTGTCCAAAGGCGAGGTATT
1 TGATTCAAGACAACCGCGCTTCCTTCGAACGATCGCACAGTCTATGTGTCCAAAGGCGAGGTATT
4334262 ATGAAGGGTTTCAAATCGCGGTCGCCTTTTAGG
66 ATGAAGGGTTTCAAATCGCGGTCGCCTTTTAGG
4334295 T
1 T
4334296 CATTTTGTGT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (98 bp):
TGATTCAAGACAACCGCGCTTCCTTCGAACGATCGCACAGTCTATGTGTCCAAAGGCGAGGTATT
ATGAAGGGTTTCAAATCGCGGTCGCCTTTTAGG
Found at i:4335419 original size:23 final size:23
Alignment explanation
Indices: 4335390--4335442 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
4335380 TTAATATTTT
4335390 TCTTTATAACACGTTTTCTTATG
1 TCTTTATAACACGTTTTCTTATG
** *
4335413 TCTTTATGGCTCGTTTTCTTATG
1 TCTTTATAACACGTTTTCTTATG
*
4335436 TTTTTAT
1 TCTTTAT
4335443 GGCACATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.58
Consensus pattern (23 bp):
TCTTTATAACACGTTTTCTTATG
Found at i:4335443 original size:23 final size:23
Alignment explanation
Indices: 4335401--4335445 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
4335391 CTTTATAACA
4335401 CGTTTTCTTATGTCTTTATGGCT
1 CGTTTTCTTATGTCTTTATGGCT
*
4335424 CGTTTTCTTATGTTTTTATGGC
1 CGTTTTCTTATGTCTTTATGGC
4335446 ACATTTCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.16, G:0.18, T:0.58
Consensus pattern (23 bp):
CGTTTTCTTATGTCTTTATGGCT
Found at i:4335736 original size:11 final size:11
Alignment explanation
Indices: 4335720--4335744 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4335710 AATATAATAT
4335720 ATTTTGAAAAC
1 ATTTTGAAAAC
4335731 ATTTTGAAAAC
1 ATTTTGAAAAC
4335742 ATT
1 ATT
4335745 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
ATTTTGAAAAC
Found at i:4335740 original size:29 final size:29
Alignment explanation
Indices: 4335662--4335751 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 29
4335652 ATAATTTTCA
*
4335662 GAAAACAATTTCGAAAATTTATATATATAGTTTT
1 GAAAAC-ATTTAGAAAA--TATA-ATATA-TTTT
* *
4335696 GAAAATATTTAAAAAATATAATATATTTT
1 GAAAACATTTAGAAAATATAATATATTTT
* * *
4335725 GAAAACATTTTGAAAACATTATATATT
1 GAAAACATTTAGAAAATATAATATATT
4335752 ATATAGTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 26 0.54
30 5 0.10
31 4 0.08
33 8 0.17
34 5 0.10
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (29 bp):
GAAAACATTTAGAAAATATAATATATTTT
Done.