Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:2322928 original size:42 final size:42
Alignment explanation
Indices: 2322862--2322980 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
2322852 GTGAATCGGG
* * * * *
2322862 CTCTTGAACGGCGGGCGGGACCTCTTGAACGATGACAGGGGT
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAAAGGGGC
* * *
2322904 CTCTTGAACGGTGGGAGGGGCCTCTTCAATGATGAAAGTGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAAAGGGGC
* * * * *
2322946 CTCTTAAACGATAGGAGGCGCCTTTTGAACGATGA
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGA
2322981 TAGGTGCATC
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAAAGGGGC
Found at i:2325131 original size:20 final size:20
Alignment explanation
Indices: 2325103--2325241 Score: 146
Period size: 20 Copynumber: 7.2 Consensus size: 20
2325093 AGTAGTTTCT
* *
2325103 GAAACTTAAATTCGCAACGC
1 GAAAATTAAAATCGCAACGC
*
2325123 GAAAATTAAAATCGCAACGT
1 GAAAATTAAAATCGCAACGC
2325143 GAAAATTAAAATCGCAACGC
1 GAAAATTAAAATCGCAACGC
* *
2325163 GAAACTAGAAAATCGCAACGC
1 GAAAAT-TAAAATCGCAACGC
2325184 --AAA-T---ATCGCAACGC
1 GAAAATTAAAATCGCAACGC
* * *
2325198 GAACATGAAAATCGCGACGC
1 GAAAATTAAAATCGCAACGC
*
2325218 GAAAATTAAAATCGCAACTC
1 GAAAATTAAAATCGCAACGC
2325238 GAAA
1 GAAA
2325242 CTAAAATAGC
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
19 2 0.02
20 70 0.72
21 13 0.13
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.15
Consensus pattern (20 bp):
GAAAATTAAAATCGCAACGC
Found at i:2325275 original size:20 final size:20
Alignment explanation
Indices: 2325250--2325338 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
2325240 AACTAAAATA
* *
2325250 GCGTTGCGATTTTTATTTTC
1 GCGTTGCGATTTTCATGTTC
2325270 GCGTTGCGATTTTCATGTTC
1 GCGTTGCGATTTTCATGTTC
2325290 GCGTTGCGATTTTCATGTTC
1 GCGTTGCGATTTTCATGTTC
* *
2325310 GCGTTGCAATTTTCATTTTC
1 GCGTTGCGATTTTCATGTTC
*
2325330 GTGTTGCGA
1 GCGTTGCGA
2325339 ATTTAAGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (20 bp):
GCGTTGCGATTTTCATGTTC
Found at i:2325687 original size:22 final size:22
Alignment explanation
Indices: 2325660--2325716 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
2325650 ATGGAGATAG
*
2325660 ACGGATTTCGCCGGAGATGGGA
1 ACGGATGTCGCCGGAGATGGGA
* *
2325682 ACGGATGTCGCCAGAGATGGGG
1 ACGGATGTCGCCGGAGATGGGA
2325704 ACGGATGTCGCCG
1 ACGGATGTCGCCG
2325717 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.16
Consensus pattern (22 bp):
ACGGATGTCGCCGGAGATGGGA
Found at i:2325889 original size:20 final size:20
Alignment explanation
Indices: 2325864--2325905 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2325854 TAAACGCGCT
2325864 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
2325884 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
2325904 TT
1 TT
2325906 ACGATTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.50
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:2325956 original size:20 final size:20
Alignment explanation
Indices: 2325907--2325969 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
2325897 TTTTGTGTTA
* *
2325907 CGATTTACAAATTCGCATTG
1 CGATTTACATATTCGCGTTG
*
2325927 AGATTTACATATTCGCGTTG
1 CGATTTACATATTCGCGTTG
*
2325947 CGATTTACATAATCGCGTTG
1 CGATTTACATATTCGCGTTG
2325967 CGA
1 CGA
2325970 ATTTGGAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
CGATTTACATATTCGCGTTG
Found at i:2328388 original size:29 final size:29
Alignment explanation
Indices: 2328345--2328427 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
2328335 CTCACCTAAC
*
2328345 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAATT-ATGTAAGCAATGACATCATTAAT
*
2328375 TAAATTATGTAAGCAATGACATCTTTAAT
1 TAAATTATGTAAGCAATGACATCATTAAT
* *
2328404 TAAATGATGTAAGTAATGACATCA
1 TAAATTATGTAAGCAATGACATCA
2328428 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.88
30 6 0.12
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (29 bp):
TAAATTATGTAAGCAATGACATCATTAAT
Found at i:2330531 original size:15 final size:15
Alignment explanation
Indices: 2330511--2330540 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2330501 CTTTCTCATA
2330511 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
2330526 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
2330541 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:2331870 original size:29 final size:29
Alignment explanation
Indices: 2331827--2331909 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
2331817 CTCACCTAAC
* *
2331827 TAAATTGATATAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
2331857 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
2331886 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2331910 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:2335327 original size:90 final size:90
Alignment explanation
Indices: 2335174--2335353 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
2335164 GCATGCTTCC
2335174 ATGTTTGATTAAATTATGTTCAATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGA
1 ATGTTTGATTAAATTATGTTCAATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGA
2335239 ATCCATGTTACAATTCTAAGTTATT
66 ATCCATGTTACAATTCTAAGTTATT
*
2335264 ATGTTTGATTAAATTATGTTCCATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGA
1 ATGTTTGATTAAATTATGTTCAATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGA
2335329 ATCCATGTTACAATTCTAAGTTATT
66 ATCCATGTTACAATTCTAAGTTATT
2335354 GGCCTATCGG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (90 bp):
ATGTTTGATTAAATTATGTTCAATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGA
ATCCATGTTACAATTCTAAGTTATT
Found at i:2335337 original size:47 final size:47
Alignment explanation
Indices: 2335196--2335337 Score: 127
Period size: 47 Copynumber: 3.1 Consensus size: 47
2335186 ATTATGTTCA
2335196 ATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGAATCC
1 ATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGAATCC
* * * * * * ** *
2335243 ATGTT-ACAATT---CT-AAG-TTATTATGTTTGATTAAATT-ATGTTCC
1 ATGTTGATACTTGAGATAAAGCTTGTTGT-TTTCATTGTATTGA--ATCC
2335286 ATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGAATCC
1 ATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGAATCC
2335333 ATGTT
1 ATGTT
2335338 ACAATTCTAA
Statistics
Matches: 67, Mismatches: 18, Indels: 20
0.64 0.17 0.19
Matches are distributed among these distances:
41 6 0.09
42 12 0.18
43 9 0.13
44 4 0.06
46 4 0.06
47 14 0.21
48 12 0.18
49 6 0.09
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (47 bp):
ATGTTGATACTTGAGATAAAGCTTGTTGTTTTCATTGTATTGAATCC
Found at i:2339543 original size:15 final size:16
Alignment explanation
Indices: 2339511--2339543 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2339501 CTCCTCTTTG
*
2339511 CTTTCTCTCAATTTTT
1 CTTTCTCTCAAATTTT
2339527 CTTTCTC-CAAATTTT
1 CTTTCTCTCAAATTTT
2339542 CT
1 CT
2339544 CAAATTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (16 bp):
CTTTCTCTCAAATTTT
Found at i:2343124 original size:21 final size:21
Alignment explanation
Indices: 2343099--2343138 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2343089 AATTTAAAAT
2343099 GTGTATCGATGCACTGCTATA
1 GTGTATCGATGCACTGCTATA
2343120 GTGTATCGATGCACTGCTA
1 GTGTATCGATGCACTGCTA
2343139 CCGTAACTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (21 bp):
GTGTATCGATGCACTGCTATA
Found at i:2343605 original size:45 final size:45
Alignment explanation
Indices: 2343548--2343731 Score: 314
Period size: 45 Copynumber: 4.1 Consensus size: 45
2343538 AATTTCTTAA
* *
2343548 CAATATATTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
2343593 TAATATACTTACCATTTATTCAATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
2343638 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
2343683 CAATATACTTACCATTTATTCCATAATCTCGTAACCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
2343728 CAAT
1 CAAT
2343732 TTATCATTTA
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 131 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:2343641 original size:25 final size:25
Alignment explanation
Indices: 2343613--2343687 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
2343603 ACCATTTATT
2343613 CAATAAGCTCGTAAGCTTATTTTAC
1 CAATAAGCTCGTAAGCTTATTTTAC
* *
2343638 CAATATA-CT--T-A-C-CATTTATTC
1 CAATA-AGCTCGTAAGCTTATTT-TAC
2343659 C-ATAAGCTCGTAAGCTTATTTTAC
1 CAATAAGCTCGTAAGCTTATTTTAC
2343683 CAATA
1 CAATA
2343688 TACTTACCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
19 1 0.03
20 9 0.24
21 4 0.11
22 2 0.05
23 2 0.05
24 4 0.11
25 14 0.38
26 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.37
Consensus pattern (25 bp):
CAATAAGCTCGTAAGCTTATTTTAC
Found at i:2350050 original size:22 final size:21
Alignment explanation
Indices: 2350025--2350069 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2350015 TGACTATAAT
2350025 AACA-ATAATAATTAAATATATA
1 AACATATAA-AATTAAA-ATATA
*
2350047 AACATTTAAAATTAAAATATA
1 AACATATAAAATTAAAATATA
2350068 AA
1 AA
2350070 TAAATAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 11 0.52
23 3 0.14
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
AACATATAAAATTAAAATATA
Found at i:2350120 original size:14 final size:14
Alignment explanation
Indices: 2350062--2350122 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
2350052 TTAAAATTAA
*
2350062 AATA-TAAATAAAT
1 AATATTAAAAAAAT
*
2350075 AATGACTAAAATAAAT
1 AAT-ATTAAAA-AAAT
* **
2350091 AAAATTAAAACTAT
1 AATATTAAAAAAAT
2350105 AATATTAAAAAAAT
1 AATATTAAAAAAAT
2350119 AATA
1 AATA
2350123 AAACTTGTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
13 3 0.08
14 18 0.49
15 10 0.27
16 6 0.16
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (14 bp):
AATATTAAAAAAAT
Found at i:2351972 original size:82 final size:83
Alignment explanation
Indices: 2351876--2352064 Score: 285
Period size: 83 Copynumber: 2.3 Consensus size: 83
2351866 TTCTTCAGAT
* * *
2351876 AAGTTCTTCTCATTATGAACACTT-T-TAGAAATGTTGATGTTGATCTATCTCTTTCTGTGATAG
1 AAGTTCTTCTCATTATGAAC-CTTCTCTAGAAAAGTTGATGCTGATCTATCTATTTCTGTGATAG
2351939 AGTCATGCAAAGGTTGAAC
65 AGTCATGCAAAGGTTGAAC
* *
2351958 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTATTTCTGTGATAGA
1 AAGTTCTTCTCATTATGAACCTTCTCTAGAAAAGTTGATGCTGATCTATCTATTTCTGTGATAGA
2352023 GTCATGCAAAGGTTGAAC
66 GTCATGCAAAGGTTGAAC
* *
2352041 AAGTTTTTATCATTATGAA-CTTCT
1 AAGTTCTTCTCATTATGAACCTTCT
2352065 TCTTCCTCTT
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
81 2 0.02
82 25 0.26
83 70 0.72
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (83 bp):
AAGTTCTTCTCATTATGAACCTTCTCTAGAAAAGTTGATGCTGATCTATCTATTTCTGTGATAGA
GTCATGCAAAGGTTGAAC
Found at i:2352182 original size:128 final size:128
Alignment explanation
Indices: 2351969--2352225 Score: 469
Period size: 128 Copynumber: 2.0 Consensus size: 128
2351959 AGTTCTTCTC
* *
2351969 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTATTTCTGTGATAGAGTCATGCAAAG
1 ATTATGAACTTTATCTGGAAAAGTTGATGCTGATCTATCTATTTATGTGATAGAGTCATGCAAAG
*
2352034 GTTGAACAAGTTTTTATCATTATGAACTTCTTCTTCCTCTTAAGATAAGTTCTTCTCATTATG
66 GTTGAACAAGTTCTTATCATTATGAACTTCTTCTTCCTCTTAAGATAAGTTCTTCTCATTATG
*
2352097 ATTATGAACTTTATCTGGAAAAGTTGATGCTGATCTATCTCTTTATGTGATAGAGTCATGCAAAG
1 ATTATGAACTTTATCTGGAAAAGTTGATGCTGATCTATCTATTTATGTGATAGAGTCATGCAAAG
*
2352162 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTAAGATAAGTTCTTCTCATTATG
66 GTTGAACAAGTTCTTATCATTATGAACTTCTTCTTCCTCTTAAGATAAGTTCTTCTCATTATG
2352225 A
1 A
2352226 ACTTTCTCTG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 124 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (128 bp):
ATTATGAACTTTATCTGGAAAAGTTGATGCTGATCTATCTATTTATGTGATAGAGTCATGCAAAG
GTTGAACAAGTTCTTATCATTATGAACTTCTTCTTCCTCTTAAGATAAGTTCTTCTCATTATG
Found at i:2352648 original size:22 final size:22
Alignment explanation
Indices: 2352614--2352693 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
2352604 AAATCCAATA
* *
2352614 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
* *
2352636 AATGTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
2352658 AATCTATCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
2352680 AATCTATCATCTTT
1 AATCTATCATCTTT
2352694 AAGGAATGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:2353060 original size:20 final size:20
Alignment explanation
Indices: 2353031--2353074 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2353021 CGCAGCATTG
*
2353031 GTTCATCACCAGAATTACTA
1 GTTCAACACCAGAATTACTA
* *
2353051 GTTCAACACCATAATTACTG
1 GTTCAACACCAGAATTACTA
2353071 GTTC
1 GTTC
2353075 GTAAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (20 bp):
GTTCAACACCAGAATTACTA
Found at i:2353350 original size:18 final size:18
Alignment explanation
Indices: 2353327--2353364 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2353317 TATATGAAAG
2353327 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
2353345 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
2353363 AA
1 AA
2353365 GATAAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:2353727 original size:9 final size:9
Alignment explanation
Indices: 2353715--2353768 Score: 60
Period size: 9 Copynumber: 6.0 Consensus size: 9
2353705 TTTTTTCTAT
2353715 ATTTTTTTC
1 ATTTTTTTC
2353724 ATTTCATTTTTC
1 A-TT--TTTTTC
2353736 ATTTTTTTC
1 ATTTTTTTC
2353745 A---TTTTC
1 ATTTTTTTC
2353751 ATTTTTTTC
1 ATTTTTTTC
2353760 ATTTTTTTC
1 ATTTTTTTC
2353769 TTCTTCTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.15
9 22 0.56
10 2 0.05
11 2 0.05
12 7 0.18
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:2353733 original size:24 final size:24
Alignment explanation
Indices: 2353706--2353768 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
2353696 CTTGACCCTT
2353706 TTTTTCTATATTTTTTTCA-TTTCA
1 TTTTTCT-TATTTTTTTCATTTTCA
2353730 TTTTTC--ATTTTTTTCATTTTCA
1 TTTTTCTTATTTTTTTCATTTTCA
2353752 TTTTT-TTCATTTTTTTC
1 TTTTTCTT-ATTTTTTTC
2353769 TTCTTCTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 10 0.29
22 10 0.29
24 15 0.43
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTCTTATTTTTTTCATTTTCA
Found at i:2353746 original size:16 final size:16
Alignment explanation
Indices: 2353725--2353765 Score: 75
Period size: 15 Copynumber: 2.6 Consensus size: 16
2353715 ATTTTTTTCA
2353725 TTTCATTTTTCATTTT
1 TTTCATTTTTCATTTT
2353741 TTTCA-TTTTCATTTT
1 TTTCATTTTTCATTTT
2353756 TTTCATTTTT
1 TTTCATTTTT
2353766 TTCTTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCATTTTTCATTTT
Found at i:2361127 original size:15 final size:16
Alignment explanation
Indices: 2361107--2361138 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2361097 AAAATAATGC
2361107 AATGAATGTATG-AAA
1 AATGAATGTATGCAAA
2361122 AATGAATGTATGCAAA
1 AATGAATGTATGCAAA
2361138 A
1 A
2361139 GGTATTGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
AATGAATGTATGCAAA
Found at i:2364135 original size:29 final size:30
Alignment explanation
Indices: 2364082--2364146 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
2364072 AAAAAGAATT
2364082 AAAAAT-ACAAATAATGATAGAATATA-AAA
1 AAAAATGA-AAATAATGATAGAATATATAAA
* *
2364111 TAAAATGAAAATAATTATA-ATATATATAAA
1 AAAAATGAAAATAATGATAGA-ATATATAAA
2364141 AAAAAT
1 AAAAAT
2364147 TCATGTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 20 0.67
30 9 0.30
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (30 bp):
AAAAATGAAAATAATGATAGAATATATAAA
Found at i:2364518 original size:25 final size:25
Alignment explanation
Indices: 2364490--2364542 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2364480 ATTTGCTGGG
* * *
2364490 ATATGCATCATTTTAATGGGTTAAT
1 ATATACATCATTTTAATAGGATAAT
*
2364515 ATATACATTATTTTAATAGGATAAT
1 ATATACATCATTTTAATAGGATAAT
2364540 ATA
1 ATA
2364543 CATACCTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (25 bp):
ATATACATCATTTTAATAGGATAAT
Found at i:2366149 original size:99 final size:99
Alignment explanation
Indices: 2366010--2366192 Score: 267
Period size: 99 Copynumber: 1.8 Consensus size: 99
2366000 TTGTTAATAG
* * * * * *
2366010 TCAGTCGCCTCTTCGTCGTGAAGTTAAGCTTGTACTGTCTTGGGTCCAATATCCTTCTCTGTGAA
1 TCAGCCGCCCCTTCGTCATGAAGTTAAGCTTGTACTGTCTTGGGACCAATATCATTCGCTGTGAA
*
2366075 GTTGAAATTGGATCTGAAAGTTGTTTGTTGACAA
66 GTTAAAATTGGATCTGAAAGTTGTTTGTTGACAA
* **
2366109 TCAGCCGCCCCTTCGTCATGAAGTTGAGCTTGTGTTGTCTTGGGACCAATATCATTCGCTGTGAA
1 TCAGCCGCCCCTTCGTCATGAAGTTAAGCTTGTACTGTCTTGGGACCAATATCATTCGCTGTGAA
*
2366174 GTTAAAATTGGTTCTGAAA
66 GTTAAAATTGGATCTGAAA
2366193 TTGGAAGCCC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 73 1.00
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (99 bp):
TCAGCCGCCCCTTCGTCATGAAGTTAAGCTTGTACTGTCTTGGGACCAATATCATTCGCTGTGAA
GTTAAAATTGGATCTGAAAGTTGTTTGTTGACAA
Found at i:2367219 original size:11 final size:11
Alignment explanation
Indices: 2367200--2367260 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
2367190 ACCCACCTTA
2367200 TTTTCTTTTCTT
1 TTTTCTTTT-TT
*
2367212 TTTTTTTTTTT
1 TTTTCTTTTTT
*
2367223 TTTTGTTTTTT
1 TTTTCTTTTTT
**
2367234 TTTTCTTTTCC
1 TTTTCTTTTTT
*
2367245 TTTTCTTCTTT
1 TTTTCTTTTTT
2367256 TTTTC
1 TTTTC
2367261 AATTTAGGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
11 33 0.80
12 8 0.20
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:2367259 original size:1 final size:1
Alignment explanation
Indices: 2367200--2367242 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
2367190 ACCCACCTTA
* * * *
2367200 TTTTCTTTTCTTTTTTTTTTTTTTTTTGTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2367243 CCTTTTCTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.91
Consensus pattern (1 bp):
T
Found at i:2372149 original size:17 final size:17
Alignment explanation
Indices: 2372115--2372150 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2372105 TCATATCCTT
*
2372115 CATTCGTACTTACTTGG
1 CATTCGTACTTACATGG
*
2372132 CATTCGTACTTCCATGG
1 CATTCGTACTTACATGG
2372149 CA
1 CA
2372151 CTTATCGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (17 bp):
CATTCGTACTTACATGG
Found at i:2376482 original size:10 final size:10
Alignment explanation
Indices: 2376467--2376498 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2376457 TAAAATGATG
2376467 AAAGGAAGAA
1 AAAGGAAGAA
2376477 AAAGGAAGAA
1 AAAGGAAGAA
*
2376487 AAATGAAGAA
1 AAAGGAAGAA
2376497 AA
1 AA
2376499 CAAAAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (10 bp):
AAAGGAAGAA
Found at i:2378094 original size:27 final size:25
Alignment explanation
Indices: 2378029--2378095 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
2378019 ATTTGCTGGG
* * *
2378029 ATATGCATCATTTTAATTGGTTAAT
1 ATATACATCATTTTAATGGGCTAAT
*
2378054 ATATACATTATTTTAATGGGCTAAT
1 ATATACATCATTTTAATGGGCTAAT
*
2378079 ATACATACCTCATTTTA
1 AT--ATACATCATTTTA
2378096 GATGTAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 23 0.68
27 11 0.32
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (25 bp):
ATATACATCATTTTAATGGGCTAAT
Found at i:2379959 original size:26 final size:26
Alignment explanation
Indices: 2379903--2379959 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
2379893 TTTGAAAAAC
* * *
2379903 AAATAAAAATGAAATTTAATATATGA
1 AAATAAAAATAAAAATTAATATAAGA
*
2379929 AAATAATAATAAAAATTAATA-AAGA
1 AAATAAAAATAAAAATTAATATAAGA
2379954 AGAATA
1 A-AATA
2379960 TATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (26 bp):
AAATAAAAATAAAAATTAATATAAGA
Found at i:2380559 original size:23 final size:21
Alignment explanation
Indices: 2380517--2380560 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2380507 ATATATATAT
* *
2380517 ATATCTTTATTTTTATAAATA
1 ATATATTTATTTTTAGAAATA
2380538 ATATATTTATTTACTTAGAAATA
1 ATATATTTATTT--TTAGAAATA
2380561 CTAGAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (21 bp):
ATATATTTATTTTTAGAAATA
Found at i:2380919 original size:8 final size:8
Alignment explanation
Indices: 2380908--2380945 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
2380898 CAATAATACT
2380908 TAAATATA
1 TAAATATA
2380916 TAAATATA
1 TAAATATA
2380924 TAAATATA
1 TAAATATA
*
2380932 -AATATAAA
1 TAA-ATATA
2380940 TAAATA
1 TAAATA
2380946 ATGACTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 2 0.07
8 23 0.85
9 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TAAATATA
Found at i:2380927 original size:16 final size:16
Alignment explanation
Indices: 2380913--2380945 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2380903 ATACTTAAAT
2380913 ATATAAATAT--ATAA
1 ATATAAATATAAATAA
2380927 ATATAAATATAAATAA
1 ATATAAATATAAATAA
2380943 ATA
1 ATA
2380946 ATGACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAATATAAATAA
Found at i:2385878 original size:15 final size:14
Alignment explanation
Indices: 2385854--2385905 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 14
2385844 TTTGAGCCTG
2385854 TAAAATTATAATTA
1 TAAAATTATAATTA
2385868 TAAATATTATAATTA
1 TAAA-ATTATAATTA
*
2385883 T--AATAATAA-TA
1 TAAAATTATAATTA
*
2385894 TAAAAATATAAT
1 TAAAATTATAAT
2385906 GAAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
11 3 0.10
12 6 0.19
13 7 0.23
14 4 0.13
15 11 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAATTATAATTA
Found at i:2386242 original size:83 final size:84
Alignment explanation
Indices: 2386121--2386286 Score: 246
Period size: 83 Copynumber: 2.0 Consensus size: 84
2386111 GAAGGCTGGA
* *
2386121 TTGACTTGAAAAGAATCTGTTTCACTACTCTTCCGTGAAGATCATATTCGAGGTTGAGTT-ACTT
1 TTGACTTGAAAAGAATATGTTTCACTACTCTTCCGTGAAGATCATATTAGAGGTTGAGTTGA-TT
2386185 -CACTACTCTTTAGTGAAGG
65 CCACTACTCTTTAGTGAAGG
* ** *
2386204 TTGACTTGAAAAGAATATGTTTCACTACTTTTTTGTGAAGATCATATTAGAGGTTGATTTGATTC
1 TTGACTTGAAAAGAATATGTTTCACTACTCTTCCGTGAAGATCATATTAGAGGTTGAGTTGATTC
*
2386269 CACTACTCTTTCGTGAAG
66 CACTACTCTTTAGTGAAG
2386287 ATTAAATTTG
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 56 0.76
84 18 0.24
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (84 bp):
TTGACTTGAAAAGAATATGTTTCACTACTCTTCCGTGAAGATCATATTAGAGGTTGAGTTGATTC
CACTACTCTTTAGTGAAGG
Found at i:2387055 original size:3 final size:3
Alignment explanation
Indices: 2387041--2387124 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
2387031 AGAGATATTC
*
2387041 TCT TCA TCT TCT TCT TC- TCT TCT T-T TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2387087 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2387125 ATGTACGAGA
Statistics
Matches: 77, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 4 0.05
3 73 0.95
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:2387730 original size:64 final size:64
Alignment explanation
Indices: 2387662--2387820 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 64
2387652 TTGAAGGTGT
** ***
2387662 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAATAAT-AAAACATCGAATGCAATTCATG
2387725 C
64 C
* * *
2387726 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
* *
2387790 ACCGATGCATCAGTAGTGCATCGATGCATAC
1 ATCGATGCATAAGTAGTGCATCGATGCATAC
2387821 TTTCATTGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 1 0.01
64 79 0.95
65 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
Found at i:2388513 original size:31 final size:31
Alignment explanation
Indices: 2388475--2388598 Score: 205
Period size: 31 Copynumber: 4.0 Consensus size: 31
2388465 GGGTCGAGGA
2388475 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
* *
2388506 TTTACCTATGTTCTTAGGGATATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
2388537 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTG
*
2388568 TTTACCTAGGTTCTTCGGGATC-TATGGACTG
1 TTTACCTATGTTCTTCGGGA-CATATGGACTG
2388599 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTG
Found at i:2391553 original size:3 final size:3
Alignment explanation
Indices: 2391545--2391595 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
2391535 AGAGATATTC
*
2391545 TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCTT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT
2391591 TCT TC
1 TCT TC
2391596 ATGTACGAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:2392219 original size:19 final size:19
Alignment explanation
Indices: 2392195--2392246 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
2392185 ATGCAATTCA
2392195 TGCATCGATGCATAAGTAG
1 TGCATCGATGCATAAGTAG
2392214 TGCATCGATGCATAAGTAG
1 TGCATCGATGCATAAGTAG
2392233 TGCATCGATGCATA
1 TGCATCGATGCATA
2392247 CCAGTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (19 bp):
TGCATCGATGCATAAGTAG
Found at i:2392221 original size:83 final size:83
Alignment explanation
Indices: 2392134--2392310 Score: 225
Period size: 83 Copynumber: 2.1 Consensus size: 83
2392124 TTGAAGGTGT
** ***
2392134 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAATAAT-AAAACATCGAATGCAATTCATG
*
2392197 CATCGATGCAT-AAGTAGTGC
64 CACCGATGCATCAA-TAGTGC
* * *
2392217 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATACAACATCGAATGCATTTTATGCA
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGCA
2392282 CCGATGCATCAATAGTGC
66 CCGATGCATCAATAGTGC
2392300 ATCGATGCATA
1 ATCGATGCATA
2392311 CTTTCATTGA
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
82 1 0.01
83 76 0.93
84 5 0.06
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (83 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGCA
CCGATGCATCAATAGTGC
Found at i:2393025 original size:31 final size:31
Alignment explanation
Indices: 2392967--2393029 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2392957 AGGGTCGAGG
* **
2392967 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTAGGTTCTTCAAGACATATGGACT
2392998 GTTTACCTAGGTTCTTCAAGATC-TATGGACT
1 GTTTACCTAGGTTCTTCAAGA-CATATGGACT
2393029 G
1 G
2393030 GTCCTTCGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCAAGACATATGGACT
Found at i:2397642 original size:2 final size:2
Alignment explanation
Indices: 2397635--2397678 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2397625 TAAACAAGAG
2397635 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2397677 TA
1 TA
2397679 ATAATAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2397684 original size:3 final size:3
Alignment explanation
Indices: 2397676--2397719 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2397666 ATATATATAT
2397676 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2397720 GCACTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2401309 original size:22 final size:22
Alignment explanation
Indices: 2401271--2401322 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
2401261 ATTTAATAAG
2401271 TATG-AAAAATATAATGT-CAA
1 TATGTAAAAATATAATGTGCAA
*
2401291 -ATGCTAAAAATATTTATGTGCAA
1 TATG-TAAAAATA-TAATGTGCAA
2401314 TATGTAAAA
1 TATGTAAAA
2401323 TGCAAGGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 3 0.12
21 7 0.27
22 5 0.19
23 8 0.31
24 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.33
Consensus pattern (22 bp):
TATGTAAAAATATAATGTGCAA
Found at i:2406809 original size:160 final size:160
Alignment explanation
Indices: 2406506--2406883 Score: 630
Period size: 160 Copynumber: 2.4 Consensus size: 160
2406496 TTAAAATTCA
* ** * * * * *
2406506 AAAAAAATAAAAGTACAATGAGTGAAATAAGAGAGATGATAAAGTTCAGTGAGTAAACGTGGTAT
1 AAAAAATTAAAAGTACGGTGAGTAAAATATGAGAGA-G-TAAAGTTCAGTGAATAAGCATGGTAT
2406571 ATTTTATTATTAAAATAAGCCACATAAGCACCCCGTTACTGAGTAAACAATCAAGTGACAAAAAA
64 ATTTTATTATTAAAATAAGCCACATAAGCACCCCGTTACTGAGTAAACAATCAAGTGACAAAAAA
*
2406636 AGTTCAATGTCTAAAGTTCAGTAAGTAAATTG
129 AGTTAAATGTCTAAAGTTCAGTAAGTAAATTG
2406668 AAAAAATTAAAAGTACGGTGAGTAAAATATGAGAGAGTAAAGTTCAGTGAATAAGCATGGTATAT
1 AAAAAATTAAAAGTACGGTGAGTAAAATATGAGAGAGTAAAGTTCAGTGAATAAGCATGGTATAT
*
2406733 TTTATTATTAAAATAAGCCACATAAGCACCCCGTTACTGAGTAAACAATCAAGTGACCAAAAAAG
66 TTTATTATTAAAATAAGCCACATAAGCACCCCGTTACTGAGTAAACAATCAAGTGACAAAAAAAG
*
2406798 TTAAATGTCTAAAGTTCAGTGAGTAAATTG
131 TTAAATGTCTAAAGTTCAGTAAGTAAATTG
*
2406828 AAAAAATTAAAAGTACGGTGAGTAAAAAATGAGAGAGTAAAGTTCAGTGAATAAGC
1 AAAAAATTAAAAGTACGGTGAGTAAAATATGAGAGAGTAAAGTTCAGTGAATAAGC
2406884 GTACAATTTA
Statistics
Matches: 204, Mismatches: 12, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
160 172 0.84
161 1 0.00
162 31 0.15
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (160 bp):
AAAAAATTAAAAGTACGGTGAGTAAAATATGAGAGAGTAAAGTTCAGTGAATAAGCATGGTATAT
TTTATTATTAAAATAAGCCACATAAGCACCCCGTTACTGAGTAAACAATCAAGTGACAAAAAAAG
TTAAATGTCTAAAGTTCAGTAAGTAAATTG
Found at i:2407413 original size:21 final size:20
Alignment explanation
Indices: 2407389--2407443 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
2407379 TTTTAATTCA
2407389 TAAAATTTAGAATTATTATTT
1 TAAAATTTAGAATTA-TATTT
*
2407410 TAAAAATTATG-ATTATATTT
1 TAAAATTTA-GAATTATATTT
* *
2407430 GAAAATTTATAATT
1 TAAAATTTAGAATT
2407444 TTTGAAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 15 0.54
21 12 0.43
22 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TAAAATTTAGAATTATATTT
Found at i:2415398 original size:15 final size:15
Alignment explanation
Indices: 2415378--2415411 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2415368 TTTTCCTATA
2415378 CTGCCTGTCCCTTTT
1 CTGCCTGTCCCTTTT
2415393 CTGCCTGTCCCTTTT
1 CTGCCTGTCCCTTTT
2415408 CTGC
1 CTGC
2415412 TTCCTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.15, T:0.44
Consensus pattern (15 bp):
CTGCCTGTCCCTTTT
Found at i:2419606 original size:55 final size:55
Alignment explanation
Indices: 2419522--2419865 Score: 441
Period size: 55 Copynumber: 6.3 Consensus size: 55
2419512 ATACTTGAAA
*
2419522 AATCTTCAA-ATAACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
1 AATCTTCAACA-AACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
*
2419577 AATCTTCAACAAACATGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
* * *
2419632 AATCTTTAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAAT
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
* * * * *
2419687 AATCTTCAACAAACGGGTCCGCTCCTTATTCTTTCAGAGAGTATAAGACT----C
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
* * ** * * *
2419738 GATCTTCAATAAACGTGTCCACTCCCTATTCCTTCAGAGAGTATAGGACTCAAAC
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
* *
2419793 AATCTTCAACAAATGTGTCTGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCAAAC
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAG-ACTCAAAC
2419848 AATCTTCATA-AAACGTGT
1 AATCTTCA-ACAAACGTGT
2419866 TCGCGCTCTA
Statistics
Matches: 253, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
51 43 0.17
54 1 0.00
55 207 0.82
56 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (55 bp):
AATCTTCAACAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
Found at i:2419791 original size:161 final size:159
Alignment explanation
Indices: 2419522--2420015 Score: 532
Period size: 161 Copynumber: 3.1 Consensus size: 159
2419512 ATACTTGAAA
* * * *
2419522 AATCTTCAAATAACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAAC
1 AATCTTCAAA-AACGGGTCCGCT-CCTATTCATTCAGAGAGTATAAGACT----CGATCTTCAAT
* * * * * *
2419587 AAACATGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTTAACAAACGTGTCT
60 AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAACGTGTCT
*
2419652 GCTCCCTATTCATTCAGGGAGTATA-AGACTCGAAT
125 GCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAAC
*
2419687 AATCTTCAACAAACGGGTCCGCTCCTTATTCTTTCAGAGAGTATAAGACTCGATCTTCAATAAAC
1 AATCTTCAA-AAACGGGTCCGCTCC-TATTCATTCAGAGAGTATAAGACTCGATCTTCAATAAAC
* *
2419752 GTGTCCACTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAATGTGTCTGCTC
64 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAACGTGTCTGCTC
* *
2419817 CCTATTCGTTCAGGGAGTATAGAACTCAAAC
129 CCTATTCATTCAGGGAGTATAGAACTCGAAC
* *
2419848 AATCTTCATAAAACGTGTTCGCGCT-CTATTCCTTCA-AGAGTAT-AGAACTCGATCTTC-ATAA
1 AATCTTCA-AAAACG-GGTC-CGCTCCTATTCATTCAGAGAGTATAAG-ACTCGATCTTCAAT-A
* * * * * * ** * *
2419909 AACGGGTTCGTTCTCTATTCCTTCCGAGAGTATAGAACTTGAACAATCTTCATA-AAACGGGTCC
61 AACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCA-ACAAACGTGTCT
* * *
2419973 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
125 GCTCCCTATTCATTCAGGGAGTATAGAACTCGAAC
2420008 AATCTTCA
1 AATCTTCA
2420016 GCAAACGTAT
Statistics
Matches: 286, Mismatches: 34, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
159 4 0.01
160 108 0.38
161 119 0.42
162 6 0.02
163 4 0.01
164 2 0.01
165 42 0.15
166 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (159 bp):
AATCTTCAAAAACGGGTCCGCTCCTATTCATTCAGAGAGTATAAGACTCGATCTTCAATAAACGT
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAACGTGTCTGCTCCC
TATTCATTCAGGGAGTATAGAACTCGAAC
Found at i:2419877 original size:55 final size:55
Alignment explanation
Indices: 2419542--2420023 Score: 417
Period size: 55 Copynumber: 8.9 Consensus size: 55
2419532 TAACGGGTCT
* * *
2419542 GCTCCCTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTCAACAAACATG-TC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCAAACAATCTTCAACAAACGTGTTC
* * *
2419596 TGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTTAACAAACGTG-TC
1 -GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCAAACAATCTTCAACAAACGTGTTC
* * * * * *
2419651 TGCTCCCTATTCATTCAGGGAGTATA-AGACTCGAATAATCTTCAACAAACGGGTCC
1 -GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCAAACAATCTTCAACAAACGTGTTC
* * * * *
2419707 GCTCCTTATTCTTTCAGAGAGTATA-AGACT----CGATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCAAACAATCTTCAACAAACGTGTTC
* * *
2419758 ACTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAATGTG-TC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACAAACGTGTTC
* *
2419812 TGCTCCCTATTCGTTCAGGGAGTATAGAACTCAAACAATCTTCATA-AAACGTGTTC
1 -GCTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCA-ACAAACGTGTTC
* * * *
2419868 GCGCTCTATTCCTTCA-AGAGTATAGAACT----CGATCTTCATA-AAACGGGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCA-ACAAACGTGTTC
* * * ** * *
2419918 GTTCTCTATTCCTTCCGAGAGTATAGAACTTGAACAATCTTCATA-AAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCA-ACAAACGTGTTC
* * *
2419973 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAGCAAACGT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACAAACGT
2420024 ATTTGCTTCA
Statistics
Matches: 369, Mismatches: 43, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
50 32 0.09
51 55 0.15
54 13 0.04
55 265 0.72
56 4 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACAAACGTGTTC
Found at i:2420132 original size:37 final size:37
Alignment explanation
Indices: 2420026--2420135 Score: 125
Period size: 37 Copynumber: 3.0 Consensus size: 37
2420016 GCAAACGTAT
* * * *
2420026 TTGCTTCACTATTCTTTCCTGAAGGCTTATA-TATGAT
1 TTGCTTCACAATTCTTTCGTGAAGGCTTA-AGTTTGAA
* * *
2420063 TTGCTTCACCACTCTTAT-GTGAAGTCTTAAGTTTGAA
1 TTGCTTCACAATTCTT-TCGTGAAGGCTTAAGTTTGAA
2420100 TTGCTTCACAATTCTTTCGTGAAGGCTTAAGTTTGA
1 TTGCTTCACAATTCTTTCGTGAAGGCTTAAGTTTGA
2420136 CTTGTTTCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
36 2 0.03
37 58 0.95
38 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (37 bp):
TTGCTTCACAATTCTTTCGTGAAGGCTTAAGTTTGAA
Found at i:2421111 original size:15 final size:15
Alignment explanation
Indices: 2421091--2421146 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 15
2421081 CCCTCCTTTA
2421091 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
2421106 TTTCTTTTTCATTTTTT
1 TTTC-TTTTC-TTTTTT
2421123 TATT-TTTCTCTTTCATTT
1 T-TTCTTT-TCTTT--TTT
2421141 TTTCTT
1 TTTCTT
2421147 CCATTTTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
15 4 0.12
16 11 0.32
17 11 0.32
18 8 0.24
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:2421128 original size:21 final size:20
Alignment explanation
Indices: 2421100--2421283 Score: 94
Period size: 23 Copynumber: 8.7 Consensus size: 20
2421090 ATTTCTTTTC
2421100 TTTTTTTTTCTTTTTCATTT
1 TTTTTTTTTCTTTTTCATTT
*
2421120 TTTTATTTTTCTCTTTCA--T
1 TTTT-TTTTTCTTTTTCATTT
* * *
2421139 TTTTTCTTCCATTTTCCATTT
1 TTTTTTTTTC-TTTTTCATTT
2421160 TTTCTTTTTTC-TTTTCA-TT
1 TTT-TTTTTTCTTTTTCATTT
***
2421179 TTTTTCCATCATTTTTC-TTT
1 TTTTTTTTTC-TTTTTCATTT
2421199 TTTCTTTTTTCTCAATTTTC-TTT
1 TTT-TTTTTTCT---TTTTCATTT
*
2421222 TATTCTTTTTCTTCTTCTCATTT
1 T-TTTTTTTTCTT-TT-TCATTT
2421245 TTATTATTATTAT-TTTTTCATTT
1 TT-TT-TT-TT-TCTTTTTCATTT
2421268 TTTCATTTTTTCTTTT
1 TTT--TTTTTTCTTTT
2421284 CTCTTTTATT
Statistics
Matches: 125, Mismatches: 16, Indels: 44
0.68 0.09 0.24
Matches are distributed among these distances:
18 8 0.06
19 15 0.12
20 21 0.17
21 23 0.18
22 15 0.12
23 31 0.25
24 7 0.06
25 4 0.03
26 1 0.01
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTTTTCTTTTTCATTT
Found at i:2421154 original size:39 final size:38
Alignment explanation
Indices: 2421086--2421210 Score: 132
Period size: 39 Copynumber: 3.2 Consensus size: 38
2421076 TTGAACCCTC
* *
2421086 CTTTATTTCTTTTC-TTTTTTTTTC-TTTTTCATTTTTT
1 CTTT-TTTCTTTTCATTTTTTTTCCATTTTCCATTTTTT
2421123 -TATTTTTCTCTTTCATTTTTTCTTCCATTTTCCATTTTTT
1 CT-TTTTTCT-TTTCATTTTTT-TTCCATTTTCCATTTTTT
* *
2421163 CTTTTTTCTTTTCATTTTTTTCCATCATTTTTC-TTTTTT
1 CTTTTTTCTTTTCATTTTTTTTC--CATTTTCCATTTTTT
2421202 CTTTTTTCT
1 CTTTTTTCT
2421211 CAATTTTCTT
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
36 6 0.08
37 6 0.08
38 8 0.11
39 29 0.38
40 26 0.34
41 1 0.01
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (38 bp):
CTTTTTTCTTTTCATTTTTTTTCCATTTTCCATTTTTT
Found at i:2421174 original size:6 final size:7
Alignment explanation
Indices: 2421086--2421290 Score: 87
Period size: 7 Copynumber: 26.7 Consensus size: 7
2421076 TTGAACCCTC
2421086 CTTTATTT
1 CTTT-TTT
2421094 CTTTTCTT
1 CTTTT-TT
*
2421102 TTTTTTT
1 CTTTTTT
2421109 C-TTTTT
1 CTTTTTT
2421115 CATTTTTT
1 C-TTTTTT
2421123 -TATTTTT
1 CT-TTTTT
*
2421130 C-TCTTT
1 CTTTTTT
2421136 CATTTTTT
1 C-TTTTTT
2421144 CTTCCATTTT
1 CTT---TTTT
2421154 CCATTTTTT
1 -C-TTTTTT
2421163 CTTTTTT
1 CTTTTTT
2421170 CTTTTCATT
1 CTTTT--TT
2421179 -TTTTTCCAT
1 CTTTTT---T
*
2421188 CATTTTT
1 CTTTTTT
2421195 CTTTTTT
1 CTTTTTT
2421202 CTTTTTT
1 CTTTTTT
*
2421209 CTCAATTTT
1 CT--TTTTT
2421218 CTTTTATT
1 CTTTT-TT
2421226 C-TTTTT
1 CTTTTTT
*
2421232 CTTCTTCT
1 CTT-TTTT
*
2421240 CATTTTT
1 CTTTTTT
*
2421247 ATTATTATT
1 CTT-TT-TT
*
2421256 ATTTTTT
1 CTTTTTT
2421263 CATTTTTT
1 C-TTTTTT
2421271 CATTTTTT
1 C-TTTTTT
*
2421279 CTTTTCT
1 CTTTTTT
2421286 CTTTT
1 CTTTT
2421291 ATTTCTTCTT
Statistics
Matches: 156, Mismatches: 15, Indels: 53
0.70 0.07 0.24
Matches are distributed among these distances:
6 16 0.10
7 59 0.38
8 52 0.33
9 18 0.12
10 8 0.05
11 1 0.01
12 2 0.01
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (7 bp):
CTTTTTT
Found at i:2421207 original size:65 final size:65
Alignment explanation
Indices: 2421124--2421246 Score: 155
Period size: 65 Copynumber: 1.9 Consensus size: 65
2421114 TCATTTTTTT
* *
2421124 ATTTTTCTCTTTCATTTTTTCTTCCATTTTCCATTTT-TTC-TTTT-TTCTTTTCATTTTTTTCC
1 ATTTTTCTCTTTCATTTTTTC-TCAATTTT-C-TTTTATTCTTTTTCTTCTTCTCATTTTTTTCC
2421186 ATC
63 ATC
*
2421189 ATTTTTCTTTTTTC-TTTTTTCTCAATTTTCTTTTATTCTTTTTCTTCTTCTCATTTTT
1 ATTTTTC-TCTTTCATTTTTTCTCAATTTTCTTTTATTCTTTTTCTTCTTCTCATTTTT
2421247 ATTATTATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
62 4 0.08
63 4 0.08
64 11 0.22
65 27 0.53
66 5 0.10
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.72
Consensus pattern (65 bp):
ATTTTTCTCTTTCATTTTTTCTCAATTTTCTTTTATTCTTTTTCTTCTTCTCATTTTTTTCCATC
Found at i:2427616 original size:23 final size:23
Alignment explanation
Indices: 2427578--2427622 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2427568 TGATGATCTT
*
2427578 AAAACTTTTGATAAAGTTGGAAC
1 AAAACTTTTGATAAAGGTGGAAC
2427601 AAAACATTTTGA-AAAGGTGGAA
1 AAAAC-TTTTGATAAAGGTGGAA
2427623 ATTCAAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (23 bp):
AAAACTTTTGATAAAGGTGGAAC
Found at i:2433557 original size:31 final size:31
Alignment explanation
Indices: 2433519--2433580 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
2433509 AGTGTGTTTT
2433519 AAGTGTGTTTTTAAAATGATAAATGGGAGAA
1 AAGTGTGTTTTTAAAATGATAAATGGGAGAA
2433550 AAGTGTGTTTTTAAAATGATAAATGGGAGAA
1 AAGTGTGTTTTTAAAATGATAAATGGGAGAA
2433581 GTGTTAAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (31 bp):
AAGTGTGTTTTTAAAATGATAAATGGGAGAA
Found at i:2433618 original size:13 final size:14
Alignment explanation
Indices: 2433600--2433629 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2433590 TAAGGGGGAG
2433600 TAATTTCAAAA-CT
1 TAATTTCAAAATCT
2433613 TAATTTCAAAATCT
1 TAATTTCAAAATCT
2433627 TAA
1 TAA
2433630 AATTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTTCAAAATCT
Found at i:2440546 original size:45 final size:48
Alignment explanation
Indices: 2440479--2440577 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 48
2440469 TGTTATCCAC
* *
2440479 AAAAAGAAATCCTAACCTCATGATATCTAATTTGCATGC-TTATTC-A
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCGA
* *
2440525 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCGA
2440573 AAAAA
1 AAAAA
2440578 ACGAAAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 26 0.57
46 8 0.17
47 6 0.13
48 6 0.13
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.29
Consensus pattern (48 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCGA
Found at i:2442214 original size:2 final size:2
Alignment explanation
Indices: 2442207--2442266 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
2442197 TATAAATTTA
2442207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2442249 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2442267 TAAGATAATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2445780 original size:3 final size:3
Alignment explanation
Indices: 2445772--2445804 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2445762 TAAAAATGGT
2445772 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2445805 ATTTTTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2460813 original size:99 final size:99
Alignment explanation
Indices: 2460697--2460885 Score: 301
Period size: 99 Copynumber: 1.9 Consensus size: 99
2460687 TTTTTTTTTG
** *
2460697 TTTTTTTATTAATTTGTTTGATTTATTATTCGA-TCTTGTGGTGACCCGATCCGGGGTACAATCC
1 TTTTTTTATTAATTTGTTTGATTTATTATTAAACT-TTGTGATGACCCGATCCGGGGTACAATCC
2460761 ACATTATTATGGT-TCGGACTCTACTAACACCTAAT
65 ACATTATTATGGTCT-GGACTCTACTAACACCTAAT
**
2460796 TTTTTTTATTAATTTGTTTGATTTATTATTAAACTTTGTGATGACCCGATCCGGGGTATGATCCA
1 TTTTTTTATTAATTTGTTTGATTTATTATTAAACTTTGTGATGACCCGATCCGGGGTACAATCCA
2460861 CATTATTATGGTCTGGACTCTACTA
66 CATTATTATGGTCTGGACTCTACTA
2460886 CTTTTCTAAC
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
99 81 0.98
100 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.44
Consensus pattern (99 bp):
TTTTTTTATTAATTTGTTTGATTTATTATTAAACTTTGTGATGACCCGATCCGGGGTACAATCCA
CATTATTATGGTCTGGACTCTACTAACACCTAAT
Found at i:2460938 original size:32 final size:32
Alignment explanation
Indices: 2460897--2460989 Score: 134
Period size: 32 Copynumber: 2.9 Consensus size: 32
2460887 TTTTCTAACT
*
2460897 TACTAATATTCTAACTTTTATTTTATTGTTTG
1 TACTAATATTCTAACTTTTATTTTATTGTTCG
*
2460929 TACTAATATTCTAACTTTTATTTCATTGTTCG
1 TACTAATATTCTAACTTTTATTTTATTGTTCG
*
2460961 TACTAACT-TACTAACATTTTATTTTATTG
1 TACTAA-TATTCTAAC-TTTTATTTTATTG
2460990 CACAAACTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 42 0.76
33 13 0.24
ACGTcount: A:0.27, C:0.13, G:0.05, T:0.55
Consensus pattern (32 bp):
TACTAATATTCTAACTTTTATTTTATTGTTCG
Found at i:2461732 original size:18 final size:17
Alignment explanation
Indices: 2461709--2461775 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 17
2461699 TTAGCTTTCT
2461709 TTTTATCTTATTATTTTA
1 TTTTATCTT-TTATTTTA
2461727 TTTTATCTCGTTATATTTTTA
1 TTTTATCT--TT-TA-TTTTA
*
2461748 TTTT-TATTTTATTTTTA
1 TTTTATCTTTTA-TTTTA
2461765 TTTTTATCTTT
1 -TTTTATCTTT
2461776 GATATAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.20
18 14 0.34
19 5 0.12
20 5 0.12
21 9 0.22
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTTATCTTTTATTTTA
Found at i:2461751 original size:6 final size:6
Alignment explanation
Indices: 2461740--2461771 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2461730 TATCTCGTTA
2461740 TATTTT TATTTT TA-TTT TATTTT TATTTT TAT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TAT
2461772 CTTTGATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:2461759 original size:11 final size:11
Alignment explanation
Indices: 2461743--2461768 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2461733 CTCGTTATAT
2461743 TTTTATTTTTA
1 TTTTATTTTTA
2461754 TTTTATTTTTA
1 TTTTATTTTTA
2461765 TTTT
1 TTTT
2461769 TATCTTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:2463388 original size:13 final size:13
Alignment explanation
Indices: 2463372--2463408 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2463362 TTTATTTTCC
2463372 CTTTTACTTTCAT
1 CTTTTACTTTCAT
* *
2463385 CTTTTAATTTTAT
1 CTTTTACTTTCAT
2463398 CTTTTACTTTC
1 CTTTTACTTTC
2463409 TCACTTCAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTTTACTTTCAT
Found at i:2464738 original size:17 final size:15
Alignment explanation
Indices: 2464708--2464741 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
2464698 AGTATAATTG
2464708 AAGTTCAAGAACTAA
1 AAGTTCAAGAACTAA
2464723 AAGTGTCAAGGAACTAA
1 AAGT-TCAA-GAACTAA
2464740 AA
1 AA
2464742 TACCGACCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (15 bp):
AAGTTCAAGAACTAA
Found at i:2466530 original size:44 final size:44
Alignment explanation
Indices: 2466482--2466628 Score: 124
Period size: 44 Copynumber: 3.4 Consensus size: 44
2466472 ATGTCGGTGC
* *
2466482 TGATCTACCTCATTCTGAGATAGAATCGAGCTAAAAGTTGACAT
1 TGATCAACCTCCTTCTGAGATAGAATCGAGCTAAAAGTTGACAT
* * * * * *
2466526 TGATCCAA-CTCCTTCT-ACGATGGATTTGAGC-AAAA-ATAAAAT
1 TGAT-CAACCTCCTTCTGA-GATAGAATCGAGCTAAAAGTTGACAT
* * **
2466568 CGATCAACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGC
1 TGATCAACCTCCTTCTGAGATAGAATCGAGCTAAAAGTTGACAT
2466612 TGATCCAA-CTCCTTCTG
1 TGAT-CAACCTCCTTCTG
2466629 CGATGGATTT
Statistics
Matches: 77, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
41 3 0.04
42 25 0.32
43 9 0.12
44 35 0.45
45 5 0.06
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (44 bp):
TGATCAACCTCCTTCTGAGATAGAATCGAGCTAAAAGTTGACAT
Found at i:2466594 original size:86 final size:86
Alignment explanation
Indices: 2466483--2466652 Score: 268
Period size: 86 Copynumber: 2.0 Consensus size: 86
2466473 TGTCGGTGCT
* *
2466483 GATCTACCTCATTCTGAGATAGAATCGAGCTAAAAGTTGACATTGATCCAACTCCTTCTACGATG
1 GATCAACCTCATTCTGAGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTACGATG
*
2466548 GATTTGAGCAAAAATAAAATC
66 GATTTGAACAAAAATAAAATC
* * * *
2466569 GATCAACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
1 GATCAACCTCATTCTGAGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTACGATG
*
2466634 GATTTGAACGAAAATAAAA
66 GATTTGAACAAAAATAAAA
2466653 ATATTGATCC
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (86 bp):
GATCAACCTCATTCTGAGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTACGATG
GATTTGAACAAAAATAAAATC
Found at i:2466892 original size:218 final size:217
Alignment explanation
Indices: 2466460--2466861 Score: 502
Period size: 218 Copynumber: 1.8 Consensus size: 217
2466450 TTCTGTGACA
*
2466460 GAATCGAACGAGATGTCGGTGCTGATCTACCTCATTCTGAGATAGAATCGAGCTAAAAGTTGACA
1 GAATCGAACAAGATGTCGGTGCTGATCTACCTCATTCTGAGATAGAATCGAGCTAAAAGTTGACA
* *
2466525 TTGATCCAACTCCTTCTACGATGGATTTGAGCAAAAATAAAATCGATCAACCTCCTTCTGTGATA
66 CTGATCCAACTCCTTCTACAATGGATTTGAGCAAAAATAAAATCGATCAACCTCCTTCTGTGATA
* * * * * * * * *
2466590 GAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAACGAAAATAAAAAT
131 GAATCAAACGAAAAGTCGACGATGATCCAACTCCTTCTGCGATAGAATCGAACGAAAATAAAAAG
*
2466655 ATTGATCCACCTCTTCTTTGATG
196 ATTGATCCA-CACTTCTTTGATG
*
2466678 GAATCGAACAAGATGTCGGTGCTGATCTACCTTC-TTCTGTGATAGAATCGAGCTAAAAGTTGAC
1 GAATCGAACAAGATGTCGGTGCTGATCTACC-TCATTCTGAGATAGAATCGAGCTAAAAGTTGAC
* * * * *
2466742 GCTGATCCAACTCCTTGTACAATGGATTTGAGCGAAAATAAAAATACTGATCCACCTTCTTCTGT
65 ACTGATCCAACTCCTTCTACAATGGATTTGAGCAAAAAT-AAAAT-C-GATCAACCTCCTTCTGT
* * * * * * *
2466807 GATGGAATCAAACGAGATA-TCGATGATGATCTACCTCCTTCTGTGATATAATCGA
127 GATAGAATCAAACGA-AAAGTCGACGATGATCCAACTCCTTCTGCGATAGAATCGA
2466862 GCTAAAAGTT
Statistics
Matches: 155, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
218 93 0.60
219 7 0.05
220 1 0.01
221 52 0.34
222 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (217 bp):
GAATCGAACAAGATGTCGGTGCTGATCTACCTCATTCTGAGATAGAATCGAGCTAAAAGTTGACA
CTGATCCAACTCCTTCTACAATGGATTTGAGCAAAAATAAAATCGATCAACCTCCTTCTGTGATA
GAATCAAACGAAAAGTCGACGATGATCCAACTCCTTCTGCGATAGAATCGAACGAAAATAAAAAG
ATTGATCCACACTTCTTTGATG
Found at i:2466918 original size:133 final size:133
Alignment explanation
Indices: 2466569--2467396 Score: 1033
Period size: 133 Copynumber: 6.3 Consensus size: 133
2466559 AAATAAAATC
* * *
2466569 GATCAACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTTCTTCTACGATG
* * * * * * *
2466634 GATTTGAACGAAAATAAAAATATTGATCCACCT-CTTCTTTGATGGAATCGAACAAGATGTCGGT
66 GATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCAGT
*
2466698 GCT
131 GTT
* * * *
2466701 GATCTACCTTCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTGTACAATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTTCTTCTACGATG
* * *
2466766 GATTTGAGCGAAAATAAAAAT-ACTGATCCACCTTCTTCTGTGATGGAATCAAACGAGATATC-G
66 GATTTGAGCGAAAATAAAAATGTC-GATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCAG
*
2466829 ATGAT
130 -TGTT
* * * *
2466834 GATCTACCTCCTTCTGTGATATAATCGAGCTAAAAGTTTACGATGATCCAACTTCTT-TGCGATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTTCTTCTACGATG
* * *
2466898 GATTTTAGCGAAAATAAAAAATGTCAATCCACCTCCTTCTGTGATGGAATCGAACGAGATATTAG
66 GATTTGAGCGAAAAT-AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCAG
2466963 TGTT
130 TGTT
* *
2466967 GATCTACCTCCTTCTGTGATAGAATGGAGCTAAAAGTTGACACTGATCCAAC-TCATTCTACGAT
1 GATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTTC-TTCTACGAT
*
2467031 GGATTTGAGCG---------ATGTCGATCCACCTCCTTCTGTGATGGAATCAAACGAGATATCAG
65 GGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCAG
2467087 TGTT
130 TGTT
* * * *
2467091 GATCTACCTCCTTCTGTAATAGAATTGAGCTAAAAGTTTACGCTAATCCAAC-TCATTCTACGAT
1 GATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTTC-TTCTACGAT
* * ** *
2467155 GGATTTGAGAGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGAAATCGAATAAGATAACAG
65 GGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCAG
2467220 TGTT
130 TGTT
* * * * *
2467224 -ATTCCACCTCATTCTGTGATAGAATCGAGCTAAAATTTGACGTTGATCCAACTTCTTCTGCGAT
1 GA-TCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTTCTTCTACGAT
* * *
2467288 GGATTTGAGCGAAAATAAAAAATGTCGATCCACCTCCTGCTATGATGAAATCGAACG-GATATCA
65 GGATTTGAGCGAAAAT-AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCA
2467352 GTGTT
129 GTGTT
* * *
2467357 GACCCACCTCCTTCTGTGATAGAATCGAGCTAAAATTTGA
1 GATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGA
2467397 ACAAGTTCTT
Statistics
Matches: 610, Mismatches: 65, Indels: 41
0.85 0.09 0.06
Matches are distributed among these distances:
124 115 0.19
132 112 0.18
133 327 0.54
134 56 0.09
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (133 bp):
GATCTACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTTCTTCTACGATG
GATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCAGT
GTT
Found at i:2467123 original size:390 final size:390
Alignment explanation
Indices: 2466569--2467396 Score: 1092
Period size: 390 Copynumber: 2.1 Consensus size: 390
2466559 AAATAAAATC
* * *
2466569 GATCAACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
1 GATCAACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCATTCTACGATG
* * * * *
2466634 GATTTGAACGAAAATAAAAATATTGATCCACCTCTTCTTTGATGGAATCGAACAAGATGTCGGTG
66 GATTTGAACG--------AATATCGATCCACCTCTTCTGTGATGGAATCAAACAAGATATCAGTG
* * * * *
2466699 CTGATCTACCTTCTTCTGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTGTACAA
123 CTGATCTACCTCCTTCTGTAATAGAATCGAGCTAAAAGTTGACGCTAATCCAACTCATTCTACAA
* * * * *
2466764 TGGATTTGAGCGAAAATAAAAATACT-GATCCACCTTCTTCTGTGATGGAATCAAACGAGATATC
188 TGGATTTGAGAGAAAATAAAAAT-CTCGATCCACCTCCTTCTGTGATGAAATCAAACAAGATAAC
* * *
2466828 -GATGATGA-TCTACCTCCTTCTGTGATATAATCGAGCTAAAAGTTT-ACGATGATCCAACTTCT
252 AG-TG-TGATTCCACCTCATTCTGTGATAGAATCGAGCTAAAA-TTTGACGATGATCCAACTTCT
* * * *
2466890 T-TGCGATGGATTTTAGCGAAAATAAAAAATGTCAATCCACCTCCTTCTGTGATGGAATCGAACG
314 TCTGCGATGGATTTGAGCGAAAATAAAAAATGTCAATCCACCTCCTGCTATGATGAAATCGAACG
*
2466954 AGATATTAGTGTT
379 -GATATCAGTGTT
* *
2466967 GATCTACCTCCTTCTGTGATAGAATGGAGCTAAAAGTTGACACTGATCCAACTCATTCTACGATG
1 GATCAACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCATTCTACGATG
* * * *
2467032 GATTTGAGCG-ATGTCGATCCACCTCCTTCTGTGATGGAATCAAACGAGATATCAGTGTTGATCT
66 GATTTGAACGAATATCGATCCACCT-CTTCTGTGATGGAATCAAACAAGATATCAGTGCTGATCT
* * *
2467096 ACCTCCTTCTGTAATAGAATTGAGCTAAAAGTTTACGCTAATCCAACTCATTCTACGATGGATTT
130 ACCTCCTTCTGTAATAGAATCGAGCTAAAAGTTGACGCTAATCCAACTCATTCTACAATGGATTT
* * * *
2467161 GAGAGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGAAATCGAATAAGATAACAGTGTTAT
195 GAGAGAAAATAAAAATCTCGATCCACCTCCTTCTGTGATGAAATCAAACAAGATAACAGTGTGAT
*
2467226 TCCACCTCATTCTGTGATAGAATCGAGCTAAAATTTGACGTTGATCCAACTTCTTCTGCGATGGA
260 TCCACCTCATTCTGTGATAGAATCGAGCTAAAATTTGACGATGATCCAACTTCTTCTGCGATGGA
*
2467291 TTTGAGCGAAAATAAAAAATGTCGATCCACCTCCTGCTATGATGAAATCGAACGGATATCAGTGT
325 TTTGAGCGAAAATAAAAAATGTCAATCCACCTCCTGCTATGATGAAATCGAACGGATATCAGTGT
2467356 T
390 T
* * *
2467357 GACCCACCTCCTTCTGTGATAGAATCGAGCTAAAATTTGA
1 GATCAACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGA
2467397 ACAAGTTCTT
Statistics
Matches: 379, Mismatches: 45, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
389 18 0.05
390 233 0.61
391 59 0.16
398 69 0.18
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (390 bp):
GATCAACCTCCTTCTGTGATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCATTCTACGATG
GATTTGAACGAATATCGATCCACCTCTTCTGTGATGGAATCAAACAAGATATCAGTGCTGATCTA
CCTCCTTCTGTAATAGAATCGAGCTAAAAGTTGACGCTAATCCAACTCATTCTACAATGGATTTG
AGAGAAAATAAAAATCTCGATCCACCTCCTTCTGTGATGAAATCAAACAAGATAACAGTGTGATT
CCACCTCATTCTGTGATAGAATCGAGCTAAAATTTGACGATGATCCAACTTCTTCTGCGATGGAT
TTGAGCGAAAATAAAAAATGTCAATCCACCTCCTGCTATGATGAAATCGAACGGATATCAGTGTT
Found at i:2468265 original size:13 final size:13
Alignment explanation
Indices: 2468249--2468295 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2468239 ATTTTCTTTC
2468249 TCTTTTTTATTTT
1 TCTTTTTTATTTT
*
2468262 TC--TTTTCTTTT
1 TCTTTTTTATTTT
*
2468273 TCTTTTTTCTTTT
1 TCTTTTTTATTTT
2468286 TCTATTTTTA
1 TCT-TTTTTA
2468296 GGCATAGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 10 0.34
13 14 0.48
14 5 0.17
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (13 bp):
TCTTTTTTATTTT
Found at i:2468267 original size:24 final size:24
Alignment explanation
Indices: 2468240--2468288 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2468230 GAACCTCTCA
2468240 TTTTCTTTCTCTTTTTTATTTTTC
1 TTTTCTTTCTCTTTTTTATTTTTC
* *
2468264 TTTTCTTTTTCTTTTTTCTTTTTC
1 TTTTCTTTCTCTTTTTTATTTTTC
2468288 T
1 T
2468289 ATTTTTAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTCTTTCTCTTTTTTATTTTTC
Found at i:2468273 original size:6 final size:6
Alignment explanation
Indices: 2468240--2468293 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
2468230 GAACCTCTCA
* *
2468240 TTTTCT TTCTCTT TTTTAT TTTTC- TTTTCT TTTTCTT TTTTCT TTTTCT
1 TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT
2468289 ATTTT
1 -TTTT
2468294 TAGGCATAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
5 5 0.12
6 21 0.52
7 14 0.35
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:2479347 original size:23 final size:24
Alignment explanation
Indices: 2479308--2479356 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
2479298 AATTGAAATA
*
2479308 ATTAAAACAAAAGATAATA-AAAC
1 ATTAAAACAAAAGATAAAATAAAC
*
2479331 ATTAAAATATAAA-ATAAAATAAAC
1 ATTAAAACA-AAAGATAAAATAAAC
2479355 AT
1 AT
2479357 GAAATAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (24 bp):
ATTAAAACAAAAGATAAAATAAAC
Found at i:2484057 original size:6 final size:7
Alignment explanation
Indices: 2484040--2484074 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
2484030 ATTTTTGAAG
2484040 TTTTTTA
1 TTTTTTA
2484047 TTTTTTA
1 TTTTTTA
*
2484054 TTTTTTGC
1 TTTTTT-A
2484062 TTTTTTA
1 TTTTTTA
2484069 TTTTTT
1 TTTTTT
2484075 GACCATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.09, C:0.03, G:0.03, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:2484058 original size:15 final size:15
Alignment explanation
Indices: 2484040--2484076 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2484030 ATTTTTGAAG
2484040 TTTTTT-ATTTTTTA
1 TTTTTTGATTTTTTA
*
2484054 TTTTTTGCTTTTTTA
1 TTTTTTGATTTTTTA
2484069 TTTTTTGA
1 TTTTTTGA
2484077 CCATTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.11, C:0.03, G:0.05, T:0.81
Consensus pattern (15 bp):
TTTTTTGATTTTTTA
Found at i:2492408 original size:26 final size:28
Alignment explanation
Indices: 2492354--2492409 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
2492344 TAGGGTGGTC
2492354 TTTTGTAGCACATAATAATTGTTTATTTT
1 TTTTGTAGCACATAATAATTG-TTATTTT
2492383 TTTTGTAAG-ACATAATAATTGTT-TTTT
1 TTTTGT-AGCACATAATAATTGTTATTTT
2492410 CTTGAATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 4 0.15
28 2 0.08
29 18 0.69
30 2 0.08
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (28 bp):
TTTTGTAGCACATAATAATTGTTATTTT
Found at i:2500731 original size:2 final size:2
Alignment explanation
Indices: 2500724--2500781 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
2500714 TACGGACACT
2500724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2500766 TA AA TA -A AA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2500782 GATTTTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2501416 original size:16 final size:17
Alignment explanation
Indices: 2501385--2501418 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2501375 AATGAGTTAT
2501385 ATTTATATTCAAATGGA
1 ATTTATATTCAAATGGA
*
2501402 ATTTAT-TTTAAATGGA
1 ATTTATATTCAAATGGA
2501418 A
1 A
2501419 ACTAGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTTATATTCAAATGGA
Found at i:2502311 original size:117 final size:117
Alignment explanation
Indices: 2502105--2502340 Score: 472
Period size: 117 Copynumber: 2.0 Consensus size: 117
2502095 TTCATTTTCC
2502105 AGCAAGGTAATTATCTTTTTCCTTGATTCTTTTTGTGCTTCAATGATTAAATGTGATTAATGATT
1 AGCAAGGTAATTATCTTTTTCCTTGATTCTTTTTGTGCTTCAATGATTAAATGTGATTAATGATT
2502170 TTAATTGAACAATTGTTTTAAAGAGAACTTATGAATTAAAAGTGATTTCCGG
66 TTAATTGAACAATTGTTTTAAAGAGAACTTATGAATTAAAAGTGATTTCCGG
2502222 AGCAAGGTAATTATCTTTTTCCTTGATTCTTTTTGTGCTTCAATGATTAAATGTGATTAATGATT
1 AGCAAGGTAATTATCTTTTTCCTTGATTCTTTTTGTGCTTCAATGATTAAATGTGATTAATGATT
2502287 TTAATTGAACAATTGTTTTAAAGAGAACTTATGAATTAAAAGTGATTTCCGG
66 TTAATTGAACAATTGTTTTAAAGAGAACTTATGAATTAAAAGTGATTTCCGG
2502339 AG
1 AG
2502341 GTATTTATTG
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 119 1.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (117 bp):
AGCAAGGTAATTATCTTTTTCCTTGATTCTTTTTGTGCTTCAATGATTAAATGTGATTAATGATT
TTAATTGAACAATTGTTTTAAAGAGAACTTATGAATTAAAAGTGATTTCCGG
Found at i:2506263 original size:18 final size:17
Alignment explanation
Indices: 2506223--2506267 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2506213 CATTATAGAT
2506223 ATTATAATAAAAATATA
1 ATTATAATAAAAATATA
*
2506240 ACTATAATAAAAATATA
1 ATTATAATAAAAATATA
*
2506257 TTTTATAATAA
1 -ATTATAATAA
2506268 CTCACTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTATAATAAAAATATA
Found at i:2514271 original size:16 final size:17
Alignment explanation
Indices: 2514236--2514287 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
2514226 TTTTAGTAAC
2514236 TTAAAATTAAATATTATT
1 TTAAAATT-AATATTATT
*
2514254 TTAAAATT-ATATTTTT
1 TTAAAATTAATATTATT
* *
2514270 TTACAA-TAATAATATT
1 TTAAAATTAATATTATT
2514286 TT
1 TT
2514288 CACCTCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 20 0.69
18 8 0.28
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAAAATTAATATTATT
Found at i:2514658 original size:60 final size:60
Alignment explanation
Indices: 2514592--2514735 Score: 209
Period size: 60 Copynumber: 2.4 Consensus size: 60
2514582 TATTACCTGG
* * *
2514592 TAATGATTTTTTCCGTGAACCAAACATTAA-AATACAATTCCGGATGATCATTCTCCTTGA
1 TAATGATATTTTCCGTGAACCAAACA-TAAGAATACAATTCCGGAAGATCATTCCCCTTGA
* * *
2514652 TAATGATCTTTTCTGTGAACTAAACATAAGAATACAATTCCGGAAGATCATTCCCCTTGA
1 TAATGATATTTTCCGTGAACCAAACATAAGAATACAATTCCGGAAGATCATTCCCCTTGA
*
2514712 TAATGATATTTTCCGCGAACCAAA
1 TAATGATATTTTCCGTGAACCAAA
2514736 TGCCCTTAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 3 0.04
60 71 0.96
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (60 bp):
TAATGATATTTTCCGTGAACCAAACATAAGAATACAATTCCGGAAGATCATTCCCCTTGA
Found at i:2517211 original size:55 final size:55
Alignment explanation
Indices: 2517121--2517226 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
2517111 CACATGTGAC
* * * * *
2517121 GATGACGTGGCATTTCCATGTCACTATTTTATGCTGATGTGGAATTTACACAAAT
1 GATGACGTGGCATGTCCACGTCACTAATATATGCTGACGTGGAATTTACACAAAT
* *
2517176 GATGATGTGGCATGTCCACGTCACTAATATGTGCTGACGTGGAATTTACAC
1 GATGACGTGGCATGTCCACGTCACTAATATATGCTGACGTGGAATTTACAC
2517227 GTCAGTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (55 bp):
GATGACGTGGCATGTCCACGTCACTAATATATGCTGACGTGGAATTTACACAAAT
Found at i:2518395 original size:195 final size:195
Alignment explanation
Indices: 2518063--2518452 Score: 640
Period size: 195 Copynumber: 2.0 Consensus size: 195
2518053 TGGCTGCCGA
*
2518063 TCTTCGGCAACCTCTTCGATCTTGGCGATAAACCCCACAGGTCATTGGCTAAGCTCGCTCATGTT
1 TCTTCGGCAACCTCTTCGATCTTGGCGATAAACCCCACAGGTCATTGGCTAAGCTCGCTCAGGTT
* *
2518128 CAAGGCCCCGTTATGGGTCTCCAACTCGGCAGCTTATTCACCGCCGTCGTTTCATCGGAAACAAC
66 CAAGGCCCCGTTATGCGTCTCCAACTCGGCAGCTTATTCACCGCCGTCGTTTCATCGAAAACAAC
* * *
2518193 CGCGAAAGAAGTCTTGAAAGAACAGGACCTCGTCTTCTGTAACCGTA-TCATCGTCGATGTCGTC
131 CGCGAAAGAAGTCTTGAAAGAACAAGACCTCGTATTCTGTAACCGAACT-ATCGTCGATGTCGTC
2518257 C
195 C
* *
2518258 TCTTCGGTAACCTCTTCGATCTTGGCGATAAACCCCACAGGTTATTGGCTAAGCTCGCTCAGGTT
1 TCTTCGGCAACCTCTTCGATCTTGGCGATAAACCCCACAGGTCATTGGCTAAGCTCGCTCAGGTT
* * *
2518323 CACA-GCGCCGTTATGCGTCTCCAACTCTGCAGCTTATTCACCGTCGTCGTTTCATCGAAAACAA
66 CA-AGGCCCCGTTATGCGTCTCCAACTCGGCAGCTTATTCACCGCCGTCGTTTCATCGAAAACAA
*
2518387 CCGCGAAAGAAGTCTTGAAAGAACAAGACCTCGTATTCTGTAACTGAACTATCGTCGATGTCGTC
130 CCGCGAAAGAAGTCTTGAAAGAACAAGACCTCGTATTCTGTAACCGAACTATCGTCGATGTCGTC
2518452 C
195 C
2518453 GAGCTTGTCG
Statistics
Matches: 181, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
195 179 0.99
196 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (195 bp):
TCTTCGGCAACCTCTTCGATCTTGGCGATAAACCCCACAGGTCATTGGCTAAGCTCGCTCAGGTT
CAAGGCCCCGTTATGCGTCTCCAACTCGGCAGCTTATTCACCGCCGTCGTTTCATCGAAAACAAC
CGCGAAAGAAGTCTTGAAAGAACAAGACCTCGTATTCTGTAACCGAACTATCGTCGATGTCGTCC
Found at i:2531195 original size:19 final size:19
Alignment explanation
Indices: 2531154--2531196 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2531144 AAACAAGTTT
* *
2531154 TTAATTTTTTTTAAATATT
1 TTAATTTTTTTCAAATATA
2531173 TTAATTTTATTTCAAAT-TA
1 TTAATTTT-TTTCAAATATA
2531192 TTAAT
1 TTAAT
2531197 ATATACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTAATTTTTTTCAAATATA
Found at i:2531947 original size:13 final size:12
Alignment explanation
Indices: 2531915--2531952 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
2531905 AAAATAAATT
*
2531915 AAAAGAAAGAG-
1 AAAAGAAAAAGA
2531926 AAAAGAAAAAGA
1 AAAAGAAAAAGA
2531938 AAAAGAAAAAAGA
1 AAAAG-AAAAAGA
2531951 AA
1 AA
2531953 TATCAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.42
12 5 0.21
13 9 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:2531969 original size:7 final size:6
Alignment explanation
Indices: 2531915--2531952 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
2531905 AAAATAAATT
*
2531915 AAAAGA AAGAG- AAAAGA AAAAGA AAAAGAA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAG-A AAAAGA AA
2531953 TATCAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.14
6 18 0.64
7 6 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:2546585 original size:17 final size:17
Alignment explanation
Indices: 2546541--2546578 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2546531 AAGTATGAAC
2546541 ATGAACATGTGTTTGTT
1 ATGAACATGTGTTTGTT
2546558 ATGAACATGTGTTTGTT
1 ATGAACATGTGTTTGTT
2546575 ATGA
1 ATGA
2546579 GTGTGTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGAACATGTGTTTGTT
Found at i:2547259 original size:2 final size:2
Alignment explanation
Indices: 2547252--2547306 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2547242 ATCTAGGTGA
2547252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2547294 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2547307 GACATAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2547718 original size:23 final size:23
Alignment explanation
Indices: 2547692--2547760 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
2547682 CAACATTATA
2547692 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
2547715 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * *
2547738 CGGCACTACGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
2547761 AACTGTGGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:2547949 original size:28 final size:28
Alignment explanation
Indices: 2547896--2547949 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
2547886 TATGAATGAT
* * *
2547896 ATTATATGATTTATATGATGATATGTGG
1 ATTATATGATTTAAATGATCAAATGTGG
2547924 ATTATATGA-TTAAATGAGTCAAATGT
1 ATTATATGATTTAAATGA-TCAAATGT
2547950 TGGTTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.43
Consensus pattern (28 bp):
ATTATATGATTTAAATGATCAAATGTGG
Found at i:2548677 original size:25 final size:25
Alignment explanation
Indices: 2548643--2548697 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
2548633 AGTTGCGTTG
2548643 GCATCATGGTGCGGCTGAGGGTTCT
1 GCATCATGGTGCGGCTGAGGGTTCT
*
2548668 GCATCATGGTGCGGCTGAGGTTTCT
1 GCATCATGGTGCGGCTGAGGGTTCT
2548693 GCATC
1 GCATC
2548698 TTGAAGCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.13, C:0.22, G:0.36, T:0.29
Consensus pattern (25 bp):
GCATCATGGTGCGGCTGAGGGTTCT
Found at i:2549245 original size:19 final size:20
Alignment explanation
Indices: 2549196--2549247 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2549186 CTCTATTAGG
*
2549196 AGTATCAATACCACTACCTC
1 AGTATCAATACCACTACCTA
* * *
2549216 GGTATCGATACC-CTATCTA
1 AGTATCAATACCACTACCTA
2549235 AGTATCAATACCA
1 AGTATCAATACCA
2549248 AATTTGTACA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.27
Consensus pattern (20 bp):
AGTATCAATACCACTACCTA
Found at i:2572744 original size:31 final size:31
Alignment explanation
Indices: 2572709--2572785 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
2572699 TTCAACGTCC
* * *
2572709 AAGTGACCAAAATTTAATAAAACGATAACAT
1 AAGTGACCAAAACTTAACAAAACAATAACAT
*
2572740 AAGTGACCAAAACTTAACAAAACAATAACGT
1 AAGTGACCAAAACTTAACAAAACAATAACAT
2572771 AAGTGACCAAAACTT
1 AAGTGACCAAAACTT
2572786 TTTTTTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAACAAAACAATAACAT
Found at i:2576190 original size:21 final size:21
Alignment explanation
Indices: 2576135--2576214 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
2576125 GTCGAAGATG
*
2576135 TATGTGGTCCTTCGTG-ACATA
1 TATGTGGTCCTTTG-GAACATA
**
2576156 TATGTAATCCTTTGGAACATA
1 TATGTGGTCCTTTGGAACATA
*
2576177 TATGTGGTCTTTTGAGACACATA
1 TATGTGGTCCTTTG-GA-ACATA
2576200 T-T-TGGTCCTTTGGAA
1 TATGTGGTCCTTTGGAA
2576215 TATGTATATG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.02
20 3 0.06
21 36 0.73
22 3 0.06
23 6 0.12
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (21 bp):
TATGTGGTCCTTTGGAACATA
Found at i:2576317 original size:23 final size:23
Alignment explanation
Indices: 2576268--2576352 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
2576258 ACATTTTATA
*
2576268 TGGCACTCCGGTGCA-TTCTACA
1 TGGCACTCCGGTGCATTTCTACG
2576290 TGGCACTCCGGTGCATTTCTACG
1 TGGCACTCCGGTGCATTTCTACG
* * *
2576313 CGGCACTCAGGTGTATTTCTACG
1 TGGCACTCCGGTGCATTTCTACG
*
2576336 TGGCACTTCGGTGCATT
1 TGGCACTCCGGTGCATT
2576353 ATACGAGCTG
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
22 15 0.28
23 39 0.72
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.31
Consensus pattern (23 bp):
TGGCACTCCGGTGCATTTCTACG
Found at i:2577155 original size:23 final size:23
Alignment explanation
Indices: 2577129--2577172 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2577119 ATTGAACCGA
2577129 AGTGCCACGTAGAATTGCACCAG
1 AGTGCCACGTAGAATTGCACCAG
*
2577152 AGTGCCGCGTAGAATTGCACC
1 AGTGCCACGTAGAATTGCACC
2577173 GTAATGCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCAG
Found at i:2577180 original size:23 final size:23
Alignment explanation
Indices: 2577131--2577181 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
2577121 TGAACCGAAG
*
2577131 TGCCACGTAGAATTGCACCAGAG
1 TGCCACGTAGAATTGCACCAGAA
*
2577154 TGCCGCGTAGAATTGCACC-GTAA
1 TGCCACGTAGAATTGCACCAG-AA
2577177 TGCCA
1 TGCCA
2577182 TATAATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCCACGTAGAATTGCACCAGAA
Found at i:2577429 original size:30 final size:30
Alignment explanation
Indices: 2577388--2577456 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
2577378 TCATATTTTG
* * *
2577388 TATCACGTAGACATATTATTTTCC-TACCTT
1 TATCACATAGACATATCA-TTTCCATACATT
*
2577418 TATCACATAGACATGTCATTTCCATACATT
1 TATCACATAGACATATCATTTCCATACATT
2577448 TATCACATA
1 TATCACATA
2577457 ACTCATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (30 bp):
TATCACATAGACATATCATTTCCATACATT
Found at i:2586053 original size:56 final size:55
Alignment explanation
Indices: 2585950--2586055 Score: 149
Period size: 56 Copynumber: 1.9 Consensus size: 55
2585940 CATAAATCCT
** * *
2585950 ATTCGATGTTTGTATTTAATGGGGTGCATCGATGCACTCCTTATGCATCGATGGC
1 ATTCGATGTTTGTATTTAAAAGAGTGCATCGATGCACTCCATATGCATCGATGGC
* *
2586005 ATTCGATGTTTGTATTTTAAAAGAGTGCATCGATGCACTTCATGTGCATCG
1 ATTCGATGTTTGTA-TTTAAAAGAGTGCATCGATGCACTCCATATGCATCG
2586056 GTACACCTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 14 0.32
56 30 0.68
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (55 bp):
ATTCGATGTTTGTATTTAAAAGAGTGCATCGATGCACTCCATATGCATCGATGGC
Found at i:2592473 original size:7 final size:7
Alignment explanation
Indices: 2592461--2592492 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2592451 ATTTTAAAGT
2592461 TCCCTTC
1 TCCCTTC
2592468 TCCCTTC
1 TCCCTTC
2592475 TCCCTTC
1 TCCCTTC
2592482 TCCCTTC
1 TCCCTTC
2592489 TCCC
1 TCCC
2592493 CAACAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (7 bp):
TCCCTTC
Found at i:2594412 original size:21 final size:21
Alignment explanation
Indices: 2594386--2594430 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2594376 GATTTCTGGG
* *
2594386 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2594407 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2594428 CAA
1 CAA
2594431 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2596277 original size:23 final size:23
Alignment explanation
Indices: 2596244--2596311 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
2596234 ATTATTATAT
2596244 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2596267 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
2596290 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
2596312 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2596536 original size:16 final size:16
Alignment explanation
Indices: 2596485--2596537 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2596475 TGTATGTGAT
*
2596485 ATATGTATATGATTTGTG
1 ATATG-ATAT-ATGTGTG
* **
2596503 ATATGATGTATGCATG
1 ATATGATATATGTGTG
2596519 ATATGATATATGTGTG
1 ATATGATATATGTGTG
2596535 ATA
1 ATA
2596538 GGGGTTATGG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 20 0.71
17 3 0.11
18 5 0.18
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (16 bp):
ATATGATATATGTGTG
Found at i:2599326 original size:21 final size:21
Alignment explanation
Indices: 2599300--2599344 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2599290 GATTTCTGGG
* *
2599300 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2599321 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2599342 CAA
1 CAA
2599345 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2601187 original size:23 final size:23
Alignment explanation
Indices: 2601152--2601219 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2601142 ATTATTATAT
*
2601152 GGCACTACAGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2601175 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
2601198 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
2601220 AGCTGTTGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2605704 original size:45 final size:48
Alignment explanation
Indices: 2605629--2605727 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 48
2605619 ATTTATTTTC
* *
2605629 ATTTTTCGAATAAATGCTTGCGAACTAGATATCATGCGGTTAGG-TTT
1 ATTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTT
* *
2605676 ATTTTTTGAAT-AA-GCATGCGAATTAGATATCATGAGGTTAGGATTT
1 ATTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTT
*
2605722 CTTTTT
1 ATTTTT
2605728 GTGGATAACA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 26 0.57
46 10 0.22
47 10 0.22
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (48 bp):
ATTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTT
Found at i:2615402 original size:8 final size:8
Alignment explanation
Indices: 2615391--2615545 Score: 68
Period size: 8 Copynumber: 19.9 Consensus size: 8
2615381 AAATAAAAGA
2615391 GAAAAAAT
1 GAAAAAAT
2615399 GAAAAAAT
1 GAAAAAAT
2615407 -AAAAAAT
1 GAAAAAAT
*
2615414 AATAAAAAT
1 GA-AAAAAT
*
2615423 GAGAAGAA-
1 GA-AAAAAT
2615431 G-AAAAA-
1 GAAAAAAT
2615437 GAAGAAAA-
1 GAA-AAAAT
2615445 G--AAAAT
1 GAAAAAAT
*
2615451 GAGAAAAAA
1 GA-AAAAAT
2615460 GAAAAATGAT
1 GAAAAA--AT
*
2615470 GGAAAAAAC
1 -GAAAAAAT
*
2615479 GAAAAGA-
1 GAAAAAAT
2615486 -AAAAAAT
1 GAAAAAAT
*
2615493 GGAAAATAGAA
1 -GAAAA-A-AT
2615504 GAAAAAAT
1 GAAAAAAT
2615512 G-AAAAAT
1 GAAAAAAT
2615519 GAAAAAA-
1 GAAAAAAT
2615526 -AAAAAA-
1 GAAAAAAT
2615532 G-AAAAAT
1 GAAAAAAT
2615539 GAAAAAA
1 GAAAAAA
2615546 AAAAGAGAAA
Statistics
Matches: 116, Mismatches: 11, Indels: 40
0.69 0.07 0.24
Matches are distributed among these distances:
5 4 0.03
6 22 0.19
7 16 0.14
8 37 0.32
9 23 0.20
10 7 0.06
11 7 0.06
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:2615464 original size:7 final size:7
Alignment explanation
Indices: 2615375--2615555 Score: 73
Period size: 7 Copynumber: 23.9 Consensus size: 7
2615365 ATTTCGCTTG
*
2615375 AAGAAGA
1 AAGAAAA
*
2615382 AATAAAA
1 AAGAAAA
*
2615389 GAGAAAA
1 AAGAAAA
2615396 AATGAAAA
1 AA-GAAAA
*
2615404 AATAAAA
1 AAGAAAA
*
2615411 AATAATAAA
1 AA-GA-AAA
*
2615420 AATGAGAAG
1 AA-GA-AAA
2615429 AAG-AAA
1 AAGAAAA
2615435 AAGAAGAA
1 AAGAA-AA
2615443 AAGAAAA
1 AAGAAAA
*
2615450 TGAGAAAA
1 -AAGAAAA
2615458 AAGAAAA
1 AAGAAAA
2615465 ATGATGGAAAA
1 A--A--GAAAA
2615476 AACGAAAA
1 AA-GAAAA
2615484 GAA-AAAA
1 -AAGAAAA
*
2615491 ATGGAAAATA
1 A-AG-AAA-A
2615501 GAAGAAAA
1 -AAGAAAA
2615509 AATGAAAA
1 AA-GAAAA
*
2615517 ATGAAAA
1 AAGAAAA
2615524 AA-AAAA
1 AAGAAAA
2615530 AAGAAAA
1 AAGAAAA
*
2615537 ATGAAAA
1 AAGAAAA
2615544 AA-AAAA
1 AAGAAAA
*
2615550 GAGAAA
1 AAGAAA
2615556 TAAAAGGAGG
Statistics
Matches: 134, Mismatches: 21, Indels: 38
0.69 0.11 0.20
Matches are distributed among these distances:
6 17 0.13
7 53 0.40
8 34 0.25
9 21 0.16
10 2 0.01
11 7 0.05
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.08
Consensus pattern (7 bp):
AAGAAAA
Done.