Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009405.1 Hibiscus syriacus cultivar Beakdansim tig00113337_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: 1310060
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:1005750 original size:31 final size:31
Alignment explanation
Indices: 1005715--1005819 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 31
1005705 GTAACTTACA
1005715 TATTATCTAATTTATGTTTTGGTCACTCGAT
1 TATTATCTAATTTATGTTTTGGTCACTCGAT
* ** ** *
1005746 TATTATTTAGGGTAAACTACCTATTTGGTCACT-TAT
1 TATTA--T---CTAATTTATGT-TTTGGTCACTCGAT
1005782 ATATTATCTAATTTATGTTTTGGTCACTCGAT
1 -TATTATCTAATTTATGTTTTGGTCACTCGAT
1005814 TATTAT
1 TATTAT
1005820 TTAGGGTAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
31 21 0.39
32 8 0.15
33 1 0.02
35 1 0.02
36 8 0.15
37 15 0.28
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (31 bp):
TATTATCTAATTTATGTTTTGGTCACTCGAT
Found at i:1010024 original size:15 final size:15
Alignment explanation
Indices: 1010004--1010041 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1009994 TTGAGACCTT
*
1010004 ACCCGCCCCGCATCC
1 ACCCGCCCCACATCC
1010019 ACCCGCCCCACATCC
1 ACCCGCCCCACATCC
*
1010034 GCCCGCCC
1 ACCCGCCC
1010042 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.68, G:0.13, T:0.05
Consensus pattern (15 bp):
ACCCGCCCCACATCC
Found at i:1018236 original size:27 final size:27
Alignment explanation
Indices: 1018205--1018278 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
1018195 ATTTCTCTTT
1018205 CAAAATCACGATTGAGAAACAAAATCC
1 CAAAATCACGATTGAGAAACAAAATCC
* *
1018232 CAAAATCAGGATTGAGAAACAATATCC
1 CAAAATCACGATTGAGAAACAAAATCC
* *
1018259 CAAAAACACGATTGATAAAC
1 CAAAATCACGATTGAGAAAC
1018279 TCTCCCAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.16
Consensus pattern (27 bp):
CAAAATCACGATTGAGAAACAAAATCC
Found at i:1018974 original size:3 final size:3
Alignment explanation
Indices: 1018963--1019032 Score: 61
Period size: 3 Copynumber: 22.7 Consensus size: 3
1018953 CGGGTTTTTT
** * *
1018963 TTA TATA TTA TTA TTA TCG TTA TTT TTA TTT TTA TTA TTTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
1019010 TTA -TA TTCA TTA TCA TTA TTA TT
1 TTA TTA TT-A TTA TTA TTA TTA TT
1019033 TACATATTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.04
3 42 0.79
4 9 0.17
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1019032 original size:34 final size:34
Alignment explanation
Indices: 1018963--1019032 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 34
1018953 CGGGTTTTTT
* * * *
1018963 TTATATATTATTATTATCGTTATTTTTATTTTTA
1 TTATATATTATTATTATCATTATTATCATTATTA
*
1018997 TTATTTATTATTATTAT-ATTCATTATCATTATTA
1 TTATATATTATTATTATCATT-ATTATCATTATTA
1019031 TT
1 TT
1019033 TACATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 2 0.07
34 28 0.93
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (34 bp):
TTATATATTATTATTATCATTATTATCATTATTA
Found at i:1020242 original size:20 final size:23
Alignment explanation
Indices: 1020195--1020248 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
1020185 TCAGTCATTA
*
1020195 ATTTATATATTATGTTTGCTGAT
1 ATTTATATATTATGGTTGCTGAT
1020218 A-TTATA-ATT-TGGTTG-TGAT
1 ATTTATATATTATGGTTGCTGAT
1020237 ATTTATAT-TTAT
1 ATTTATATATTAT
1020249 TTCGTATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 4 0.15
22 5 0.19
23 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (23 bp):
ATTTATATATTATGGTTGCTGAT
Found at i:1024051 original size:26 final size:25
Alignment explanation
Indices: 1024022--1024099 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
1024012 AATTTTTGAC
1024022 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
1024048 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
1024068 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
1024094 ATTCTT
1 ATTCTT
1024100 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:1024060 original size:20 final size:20
Alignment explanation
Indices: 1024037--1024111 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
1024027 ATCTCTTTGA
1024037 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
1024057 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
1024083 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
1024102 CACCTTGAAA
1 GACCTTGAAA
1024112 AACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:1024770 original size:11 final size:11
Alignment explanation
Indices: 1024742--1024779 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1024732 AAGAGCAAAG
1024742 AGAAAAATCAA
1 AGAAAAATCAA
1024753 AGCAAAAATCAA
1 AG-AAAAATCAA
*
1024765 AGAAAAAGCAA
1 AGAAAAATCAA
1024776 AGAA
1 AGAA
1024780 CAAAAAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:1025700 original size:24 final size:23
Alignment explanation
Indices: 1025647--1025703 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
1025637 TGAAAGGGGT
1025647 AATATTTTCAAAATCTTTGATTA
1 AATATTTTCAAAATCTTTGATTA
* *
1025670 AACATTTTTAAAACTCTTTTGA-TA
1 AATATTTTCAAAA-TC-TTTGATTA
*
1025694 GATATTTTCA
1 AATATTTTCA
1025704 TACTTTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 11 0.41
24 11 0.41
25 5 0.19
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (23 bp):
AATATTTTCAAAATCTTTGATTA
Found at i:1026704 original size:105 final size:102
Alignment explanation
Indices: 1026563--1026801 Score: 268
Period size: 105 Copynumber: 2.3 Consensus size: 102
1026553 TGAGAATTTT
** * * *
1026563 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAAATACAAATTTCGAATTTGATTCACA
* *
1026627 TTAAAACAAAATTAACCTCACCTT-AGATTGTTGTTTCTTTC-
66 TT-AAACAAAATTAACATC-CCTTGAGATCG-T-TTTC--TCA
* * *
1026668 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAAATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAAATACAAATTTCGAATTTGATTCACA
* * *
1026733 TTAAACAAAGTTGACATCTCTTGAGATCGTTTTCTCA
66 TTAAACAAAATTAACATCCCTTGAGATCGTTTTCTCA
* *
1026770 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
1026802 TCTAAAAACA
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
101 2 0.02
102 29 0.25
103 4 0.03
104 4 0.03
105 74 0.64
106 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAAATACAAATTTCGAATTTGATTCACA
TTAAACAAAATTAACATCCCTTGAGATCGTTTTCTCA
Found at i:1026792 original size:36 final size:36
Alignment explanation
Indices: 1026763--1026866 Score: 117
Period size: 36 Copynumber: 3.0 Consensus size: 36
1026753 TTGAGATCGT
1026763 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
* ** *
1026798 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
* *
1026834 TATCT-T-AAAGCAAA-TTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAACTTT-GTCTCGCTTGAGACA
1026867 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
33 3 0.05
34 19 0.33
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAACTTTGTCTCGCTTGAGACAA
Found at i:1027150 original size:28 final size:28
Alignment explanation
Indices: 1027112--1027171 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
1027102 GACAATTTTG
*
1027112 TGAAAAAAATCTTTGAGAT-TGTTTCTTT
1 TGAAAAAAATCTTTGAG-TCTATTTCTTT
1027140 TGAAAAAAATCTTTGAGTCTATTTCTTT
1 TGAAAAAAATCTTTGAGTCTATTTCTTT
1027168 TGAA
1 TGAA
1027172 GCAAAGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGTCTATTTCTTT
Found at i:1027236 original size:143 final size:142
Alignment explanation
Indices: 1027079--1027344 Score: 412
Period size: 143 Copynumber: 1.9 Consensus size: 142
1027069 GAATCTTTTA
1027079 AAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTG-AAAAAAATCTTTGAGATTGTTTCTTTTG-
1 AAACAAAGTTTTG--TCTCTTGAGACAATTTTGTGAAAAAAAATCTTTGAGATTGTTTCTTTTGA
* * *
1027142 AA-AAAAATCTTTGAGTCTATTTCTTTTGAAGCAAAGTTTTGTCTCTCTTAAGACAATTTCGTGA
64 AACAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCT-T-TTAAGACAATTTCGTGA
1027206 AAAATCTTTGAGTCTG
127 AAAATCTTTGAGTCTG
1027222 AAACAAAGTTTTGTCTCTTGAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTTGAA
1 AAACAAAGTTTTGTCTCTTGAGACAATTTTGTG-AAAAAAAATCTTTGAGATTGTTTCTTTTGAA
* * *
1027287 ACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTTTTAAGATAATTTC
65 ACAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTTTTAAGACAATTTC
1027345 TTTTGAAACA
Statistics
Matches: 113, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
141 20 0.18
143 53 0.47
144 3 0.03
145 37 0.33
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (142 bp):
AAACAAAGTTTTGTCTCTTGAGACAATTTTGTGAAAAAAAATCTTTGAGATTGTTTCTTTTGAAA
CAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTTTTAAGACAATTTCGTGAAAAA
TCTTTGAGTCTG
Found at i:1027293 original size:30 final size:30
Alignment explanation
Indices: 1027253--1027387 Score: 137
Period size: 30 Copynumber: 4.3 Consensus size: 30
1027243 GACAATTTTG
*
1027253 TGAAAAAAAAATCTTTGAGATTGTTTCTTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTTT
*
1027283 TGAAACAAAAATCTTTGAGTTTGTTTCTTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTTT
* * * **
1027313 GGAAACAAAATTTTGTCTTTTAAGATAATTTCTTT
1 TGAAACAAAA----ATC-TTTGAGATTGTTTCTTT
1027348 TGAAACAAAAATCTTTGAG-TCTGTTTCTTT
1 TGAAACAAAAATCTTTGAGAT-TGTTTCTTT
*
1027378 GGAAACAAAA
1 TGAAACAAAA
1027388 TTTTGTCTCT
Statistics
Matches: 85, Mismatches: 14, Indels: 12
0.77 0.13 0.11
Matches are distributed among these distances:
29 1 0.01
30 58 0.68
31 2 0.02
34 2 0.02
35 22 0.26
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (30 bp):
TGAAACAAAAATCTTTGAGATTGTTTCTTT
Found at i:1027349 original size:65 final size:67
Alignment explanation
Indices: 1027276--1027441 Score: 284
Period size: 65 Copynumber: 2.5 Consensus size: 67
1027266 TTTGAGATTG
*
1027276 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCT-T-TTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1027339 AA
66 AA
1027341 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
*
1027406 AT
66 AA
*
1027408 TTTCTTTTGAAA-AAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT
1027442 CTTAAAATGA
Statistics
Matches: 96, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
65 54 0.56
66 22 0.23
67 20 0.21
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:1027477 original size:65 final size:65
Alignment explanation
Indices: 1027270--1027483 Score: 247
Period size: 65 Copynumber: 3.3 Consensus size: 65
1027260 AAAATCTTTG
* * * *
1027270 AGATTGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTG-TCTTTT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTTT-GAAACAAAATTTTGTTCTCTT
1027334 A
65 A
* *
1027335 AGATAATTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTTT-GAAACAAAATTTTGT-TCTCT
1027400 TA
64 TA
* *
1027402 AGATATTTTCTTTTGAAA-AAAAATCTTTGAATCTGTTTCTCTT-AAA-ATGAATTTTGTATCTC
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCT-TTGAAACA-AAATTTTGT-TCTC
*
1027464 TTG
63 TTA
* *
1027467 AGACAGTTTCTCTTGAA
1 AGATAGTTTCTTTTGAA
1027484 GTAAATCTTT
Statistics
Matches: 133, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
64 1 0.01
65 86 0.65
66 21 0.16
67 25 0.19
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (65 bp):
AGATAGTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTTTGAAACAAAATTTTGTTCTCTTA
Found at i:1028453 original size:28 final size:28
Alignment explanation
Indices: 1028407--1028483 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 28
1028397 GAGACAGTTG
1028407 CTTTTGAAACACATTATCTTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
1028438 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
1028466 CTTTTGAAACAAATCTTT
1 CTTTTGAAACAAATCTTT
1028484 AATTTGGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
28 29 0.67
29 3 0.07
30 3 0.07
31 8 0.19
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:1028493 original size:28 final size:28
Alignment explanation
Indices: 1028433--1028503 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
1028423 TCTTTGAGCT
* *
1028433 TGTTTTTCTTGAAACAAATCTTTGAGTC
1 TGTTTCTCTTGAAACAAATCTTTGAATC
* *
1028461 TGTTTCTTTTGAAACAAATCTTT-AATT
1 TGTTTCTCTTGAAACAAATCTTTGAATC
1028488 TGGTTTCTCTTGAAAC
1 T-GTTTCTCTTGAAAC
1028504 CATAACTCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.08
28 34 0.92
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (28 bp):
TGTTTCTCTTGAAACAAATCTTTGAATC
Found at i:1028921 original size:3 final size:3
Alignment explanation
Indices: 1028910--1028979 Score: 70
Period size: 3 Copynumber: 22.7 Consensus size: 3
1028900 CGGGTTTTTT
** *
1028910 TTA TATA TTA TTA TTA TCG TTA TTT TTA TTA TTA TTA TTTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
1028957 TTA -TA TTCA TTA TCA TTA TTA TT
1 TTA TTA TT-A TTA TTA TTA TTA TT
1028980 TACATATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 44 0.80
4 9 0.16
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1028951 original size:28 final size:28
Alignment explanation
Indices: 1028904--1028981 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
1028894 TTTGTCCGGG
* *
1028904 TTTTTTTTATATATTA-TTATTATCGTTA
1 TTTTTATTAT-TATTATTTATTATCATTA
*
1028932 TTTTTATTATTATTATTTATTATTATTA
1 TTTTTATTATTATTATTTATTATCATTA
*
1028960 TATTCATTATCATTATTATTTA
1 T-TT--TTATTATTATTATTTA
1028982 CATATTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 5 0.12
28 20 0.48
29 2 0.05
31 15 0.36
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (28 bp):
TTTTTATTATTATTATTTATTATCATTA
Found at i:1028975 original size:34 final size:34
Alignment explanation
Indices: 1028910--1028979 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
1028900 CGGGTTTTTT
* * *
1028910 TTATATATTATTATTATCGTTATTTTTATTATTA
1 TTATATATTATTATTATCATTATTATCATTATTA
*
1028944 TTATTTATTATTATTAT-ATTCATTATCATTATTA
1 TTATATATTATTATTATCATT-ATTATCATTATTA
1028978 TT
1 TT
1028980 TACATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 2 0.06
34 29 0.94
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (34 bp):
TTATATATTATTATTATCATTATTATCATTATTA
Found at i:1030162 original size:19 final size:21
Alignment explanation
Indices: 1030124--1030172 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
1030114 AGTCATTAAT
*
1030124 TTATATATTTGTTTGCTGATA
1 TTATATATTTGGTTGCTGATA
1030145 TTATA-ATTTGGTTG-TGATA
1 TTATATATTTGGTTGCTGATA
1030164 TT-TATATTT
1 TTATATATTT
1030173 ATTTCGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 11 0.42
20 8 0.31
21 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.59
Consensus pattern (21 bp):
TTATATATTTGGTTGCTGATA
Found at i:1030168 original size:20 final size:22
Alignment explanation
Indices: 1030122--1030170 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
1030112 TCAGTCATTA
*
1030122 ATTTATATATTTGTTTGCTGAT
1 ATTTATATATTTGGTTGCTGAT
1030144 A-TTATA-ATTTGGTTG-TGAT
1 ATTTATATATTTGGTTGCTGAT
1030163 ATTTATAT
1 ATTTATAT
1030171 TTATTTCGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 13 0.54
21 5 0.21
22 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (22 bp):
ATTTATATATTTGGTTGCTGAT
Found at i:1036462 original size:20 final size:21
Alignment explanation
Indices: 1036414--1036462 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1036404 GGTATAAGTG
* *
1036414 TCAATTGTAGAATAATAATTA
1 TCAATTATAGAATAATAATAA
* *
1036435 TCATTTATAGATTAATAA-AA
1 TCAATTATAGAATAATAATAA
1036455 TCAATTAT
1 TCAATTAT
1036463 TTAGACTATC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (21 bp):
TCAATTATAGAATAATAATAA
Found at i:1041357 original size:1 final size:1
Alignment explanation
Indices: 1041351--1041383 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
1041341 TCTTCTTCTC
1041351 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1041384 GAGAAATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1046870 original size:2 final size:2
Alignment explanation
Indices: 1046863--1046899 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1046853 TAAATTGATT
1046863 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1046900 CTTTTCTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1047849 original size:21 final size:21
Alignment explanation
Indices: 1047757--1047912 Score: 112
Period size: 21 Copynumber: 7.7 Consensus size: 21
1047747 AATGACCAAC
*
1047757 AAATTCGCAACGCGAT-CTC-
1 AAATTCGCAACGCGATAGTCT
* * *
1047776 AAATTCGCAACTC-A-GGTTCC
1 AAATTCGCAACGCGATAG-TCT
* * *
1047796 AAATTCGCAACACGAAAGTCG
1 AAATTCGCAACGCGATAGTCT
*
1047817 AAATTCGTAACGCGATAGTCT
1 AAATTCGCAACGCGATAGTCT
* *
1047838 AAAATCGCAACGCGAT--TTT
1 AAATTCGCAACGCGATAGTCT
*
1047857 AAGATTCGCAACGCGAT--TTT
1 AA-ATTCGCAACGCGATAGTCT
* *
1047877 AAGATTCGTAACGCGATAGTCG
1 AA-ATTCGCAACGCGATAGTCT
1047899 AAATTCGCAACGCG
1 AAATTCGCAACGCG
1047913 TTTGTTTTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
18 1 0.01
19 18 0.16
20 44 0.39
21 45 0.40
22 4 0.04
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (21 bp):
AAATTCGCAACGCGATAGTCT
Found at i:1047867 original size:20 final size:20
Alignment explanation
Indices: 1047842--1047893 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1047832 TAGTCTAAAA
1047842 TCGCAACGCGATTTTAAGAT
1 TCGCAACGCGATTTTAAGAT
1047862 TCGCAACGCGATTTTAAGAT
1 TCGCAACGCGATTTTAAGAT
*
1047882 TCGTAACGCGAT
1 TCGCAACGCGAT
1047894 AGTCGAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTTTAAGAT
Found at i:1048302 original size:31 final size:31
Alignment explanation
Indices: 1048267--1048326 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1048257 GTCACTTATG
* *
1048267 TTATTGTTTTATTAAGTTTTAGACACTTACA
1 TTATTATTTTATTAAATTTTAGACACTTACA
* *
1048298 TTATTATTTTATTAAATTTTGGTCACTTA
1 TTATTATTTTATTAAATTTTAGACACTTA
1048327 GACGTTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.55
Consensus pattern (31 bp):
TTATTATTTTATTAAATTTTAGACACTTACA
Found at i:1048947 original size:54 final size:53
Alignment explanation
Indices: 1048877--1049012 Score: 193
Period size: 54 Copynumber: 2.5 Consensus size: 53
1048867 CAACTCACAG
* *
1048877 ACACTATTTGTTCAACTCAC-AGAATTCATCATGTGTTGATGAACAACCGTACAA
1 ACACTATGTGTGCAACTCACGA-AATTCATCATGTGTTGATGAACAACC-TACAA
* *
1048931 ACACTATGTGTGCAACTCACGAAATTCATCATGTGTTGATGAACAAGCTACAT
1 ACACTATGTGTGCAACTCACGAAATTCATCATGTGTTGATGAACAACCTACAA
* *
1048984 GCACTATGTGTGCAACCCACGAAATTCAT
1 ACACTATGTGTGCAACTCACGAAATTCAT
1049013 AATAAGTTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
53 31 0.41
54 43 0.57
55 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (53 bp):
ACACTATGTGTGCAACTCACGAAATTCATCATGTGTTGATGAACAACCTACAA
Found at i:1049119 original size:55 final size:54
Alignment explanation
Indices: 1048991--1049147 Score: 163
Period size: 55 Copynumber: 2.9 Consensus size: 54
1048981 CATGCACTAT
* * * **
1048991 GTGTGCAACCCACGAAATTCATAATAAGTTTATGAAGTTCCGTATGGGTACTTT
1 GTGTGAAACCCACGAAATTCATAATAAGTTTATGAATTTCCGTATTGGTACTGG
* * * * *
1049045 GTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGTAGTGG
1 GTGTG-AAACCCACGAAATTCATAATAAGTTTATGAATTTCCGTATTGGTACTGG
* ** *
1049100 GTGTGTAACCCACGTAAATT-ATAATAAGTTCGTGAATTACCGTATTGG
1 GTGTGAAACCCACG-AAATTCATAATAAGTTTATGAATTTCCGTATTGG
1049148 CACTACTTAT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
54 34 0.41
55 49 0.59
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (54 bp):
GTGTGAAACCCACGAAATTCATAATAAGTTTATGAATTTCCGTATTGGTACTGG
Found at i:1049449 original size:46 final size:46
Alignment explanation
Indices: 1049382--1049562 Score: 263
Period size: 46 Copynumber: 3.9 Consensus size: 46
1049372 TTGGATGAAG
* *
1049382 AACAATGCATAATTGGCATGAAATGATGTCATAAATGAAAATATAT
1 AACAATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATATAT
* * * *
1049428 AACAATGCATAATTGACATGAAAGTATGTCATAAATGAAAATGTAT
1 AACAATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATATAT
* * *
1049474 AACAGTGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGTAA
1 AACAATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATATAT
* *
1049520 AACAGTGCATAATTGGCATGAAAGGGTGCCATAAATGAAAATA
1 AACAATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATA
1049563 CATAGCGGTA
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 124 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (46 bp):
AACAATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATATAT
Found at i:1049507 original size:22 final size:22
Alignment explanation
Indices: 1049481--1049553 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1049471 TATAACAGTG
1049481 CATAATTGGCATGAAAGGATGC
1 CATAATTGGCATGAAAGGATGC
* ** **
1049503 CATAAATGAAAATGTAAAACAGTG-
1 CATAATTG-GCATG-AAAGGA-TGC
*
1049527 CATAATTGGCATGAAAGGGTGC
1 CATAATTGGCATGAAAGGATGC
1049549 CATAA
1 CATAA
1049554 ATGAAAATAC
Statistics
Matches: 36, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 2 0.06
22 15 0.42
23 6 0.17
24 11 0.31
25 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (22 bp):
CATAATTGGCATGAAAGGATGC
Found at i:1050328 original size:23 final size:23
Alignment explanation
Indices: 1050300--1050370 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
1050290 TAAGCTAACA
*
1050300 AAAGACAGAGAAAAATATGTCAC
1 AAAGACAGAGAAAAACATGTCAC
* * *
1050323 AAAGACAGAGATAAACGTGTCAT
1 AAAGACAGAGAAAAACATGTCAC
*
1050346 AAATACAGAG---AACATGTCAC
1 AAAGACAGAGAAAAACATGTCAC
1050366 AAAGA
1 AAAGA
1050371 TATAATTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 12 0.30
23 28 0.70
ACGTcount: A:0.54, C:0.14, G:0.18, T:0.14
Consensus pattern (23 bp):
AAAGACAGAGAAAAACATGTCAC
Found at i:1054241 original size:48 final size:48
Alignment explanation
Indices: 1054177--1054282 Score: 196
Period size: 48 Copynumber: 2.2 Consensus size: 48
1054167 CCACGAGAAT
*
1054177 AAGA-TGATGAATATGAACGAACGATCCCTCCTTGATCTTCCACCACG
1 AAGACTGAGGAATATGAACGAACGATCCCTCCTTGATCTTCCACCACG
1054224 AAGACTGAGGAATATGAACGAACGATCCCTCCTTGATCTTCCACCACG
1 AAGACTGAGGAATATGAACGAACGATCCCTCCTTGATCTTCCACCACG
1054272 AAGACTGAGGA
1 AAGACTGAGGA
1054283 GAATATCTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
47 4 0.07
48 53 0.93
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (48 bp):
AAGACTGAGGAATATGAACGAACGATCCCTCCTTGATCTTCCACCACG
Found at i:1061654 original size:23 final size:23
Alignment explanation
Indices: 1061619--1061666 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1061609 ATCAAGTACA
*
1061619 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* **
1061642 ATAATGTAATAGGTAGTGCTTAT
1 ATAATATAATAGGTAACGCTTAT
1061665 AT
1 AT
1061667 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:1061918 original size:20 final size:20
Alignment explanation
Indices: 1061895--1061933 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1061885 CCAGTATATT
*
1061895 TTTACCGGTTACATTATAAA
1 TTTACCGGTTACATAATAAA
*
1061915 TTTACCTGTTACATAATAA
1 TTTACCGGTTACATAATAA
1061934 TTATCGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTACCGGTTACATAATAAA
Found at i:1062598 original size:182 final size:182
Alignment explanation
Indices: 1062285--1062740 Score: 680
Period size: 182 Copynumber: 2.5 Consensus size: 182
1062275 ACTTTTTTAC
* * *
1062285 TACCGGTTTTATCATTTCGAGATCGATTTTGTCATATATTTACATGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
* * *
1062350 TATATTTTTATAAAGTATCGACACTTTATTGACGCTATAATTTCTTTTCTTTTAAATTTCAAAAG
66 TATATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTTCAAAAG
* * **
1062415 TGTCGATACTTATAATAAAGTATCGACATTTTCAACATATCCGGTAGTTCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
* * *
1062467 TACCGGTTTTGTCATTTCGATACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
*
1062532 TACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTCTCTTTTAAA-TTCTAAAA
66 TATATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTTC-AAAA
*
1062596 GTGTCGATACTTATAATAAAGTATCGGCACTATCAACATATCCGGTAGCGCTT
130 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
** ** * * * **
1062649 TACTTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTATAGATTAA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
1062714 TATATTTTTATAAAGTATCGACACTTT
66 TATATTTTTATAAAGTATCGACACTTT
1062741 CAATATATCC
Statistics
Matches: 245, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
181 3 0.01
182 242 0.99
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.45
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
TATATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTCTTCTCTTTTAAATTTCAAAAG
TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
Found at i:1062847 original size:111 final size:111
Alignment explanation
Indices: 1062611--1062961 Score: 578
Period size: 111 Copynumber: 3.1 Consensus size: 111
1062601 GATACTTATA
* * *
1062611 ATAAAGTATCGGCACTATCAACATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCG-T
1062676 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATTAATATATTTTT
65 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATTAATATATTTTT
*
1062723 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACATGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGAC-CGT
1062788 TTTGTCA-TTTTTTACCTGTTATATTGTTATAGATTAATATATTTTT
65 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATTAATATATTTTT
* * *
1062834 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTCTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACC-GT
* *
1062899 TTTGTCATTTTTTTTATCTGTTATATTGTTATTGATTAATATATTTTT
65 TTTGTCA-TTTTTTTACCTGTTATATTGTTATAGATTAATATATTTTT
1062947 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
1062962 AAACCGACAA
Statistics
Matches: 225, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
111 106 0.47
112 66 0.29
113 53 0.24
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (111 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGTT
TTGTCATTTTTTTACCTGTTATATTGTTATAGATTAATATATTTTT
Found at i:1072547 original size:138 final size:138
Alignment explanation
Indices: 1072378--1072653 Score: 543
Period size: 138 Copynumber: 2.0 Consensus size: 138
1072368 AAAGGCAAGC
*
1072378 ATGCTATTTTCTTTGCCATTTTATAATTCAAAAGGGATACTAAACAATCAGTATGAAGTACATTT
1 ATGCTATTTTCTCTGCCATTTTATAATTCAAAAGGGATACTAAACAATCAGTATGAAGTACATTT
1072443 CATGTTAATAGAAAATAAGTAAATAGAGCATCAGTCTCCGAACAGACCTCAAGATCAGCAGGGGA
66 CATGTTAATAGAAAATAAGTAAATAGAGCATCAGTCTCCGAACAGACCTCAAGATCAGCAGGGGA
1072508 AATAGGCT
131 AATAGGCT
1072516 ATGCTATTTTCTCTGCCATTTTATAATTCAAAAGGGATACTAAACAATCAGTATGAAGTACATTT
1 ATGCTATTTTCTCTGCCATTTTATAATTCAAAAGGGATACTAAACAATCAGTATGAAGTACATTT
1072581 CATGTTAATAGAAAATAAGTAAATAGAGCATCAGTCTCCGAACAGACCTCAAGATCAGCAGGGGA
66 CATGTTAATAGAAAATAAGTAAATAGAGCATCAGTCTCCGAACAGACCTCAAGATCAGCAGGGGA
1072646 AATAGGCT
131 AATAGGCT
1072654 CATCATTTAG
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 137 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (138 bp):
ATGCTATTTTCTCTGCCATTTTATAATTCAAAAGGGATACTAAACAATCAGTATGAAGTACATTT
CATGTTAATAGAAAATAAGTAAATAGAGCATCAGTCTCCGAACAGACCTCAAGATCAGCAGGGGA
AATAGGCT
Found at i:1079345 original size:2 final size:2
Alignment explanation
Indices: 1079340--1079395 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1079330 ATTTAAAATG
1079340 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
1079382 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1079396 TTGAGTTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1080876 original size:2 final size:2
Alignment explanation
Indices: 1080869--1080894 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1080859 ATTTGTGGTT
1080869 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
1080895 CACACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1083197 original size:18 final size:16
Alignment explanation
Indices: 1083166--1083202 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
1083156 AAAATAATTT
1083166 TATTTTATATATTTAA
1 TATTTTATATATTTAA
1083182 TATTTATATAATATTTAA
1 TATTT-TAT-ATATTTAA
1083200 TAT
1 TAT
1083203 CATTTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 3 0.16
18 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTATATATTTAA
Found at i:1083350 original size:55 final size:54
Alignment explanation
Indices: 1083259--1083363 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 54
1083249 TTAATATTTC
* *
1083259 TAATAATGTAATATTATATTTTCTTATATTTATAATAATATACTCAATTATGTTA
1 TAATAATGTAATATTATATTTTCTTATATTTATAAT-ATATAATAAATTATGTTA
1083314 TAATAATGTAAGATATTATA-TTT-TTAT-TTTAATAATATATAATAAATTAT
1 TAATAATGT-A-ATATTATATTTTCTTATATTT-ATAATATATAATAAATTAT
1083364 TAATAAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
54 15 0.33
55 18 0.40
56 4 0.09
57 8 0.18
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (54 bp):
TAATAATGTAATATTATATTTTCTTATATTTATAATATATAATAAATTATGTTA
Found at i:1083493 original size:23 final size:22
Alignment explanation
Indices: 1083443--1083513 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 22
1083433 TGTTTATGTG
* *
1083443 TTTAATAAAATAATATAATAATAG
1 TTTAATAAAAT-ATTTAA-AATAT
1083467 TTTAATAAAGATATTTAAAATAT
1 TTTAATAAA-ATATTTAAAATAT
1083490 TTTAATTAATAA-ATTTCAAAATAT
1 TTTAA-TAA-AATATTT-AAAATAT
1083514 AATATAATAC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
23 13 0.32
24 25 0.61
25 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (22 bp):
TTTAATAAAATATTTAAAATAT
Found at i:1085645 original size:7 final size:7
Alignment explanation
Indices: 1085628--1085657 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1085618 TATTCAAATT
1085628 AAATT-A
1 AAATTAA
1085634 AAATTAA
1 AAATTAA
1085641 AAATTAA
1 AAATTAA
1085648 AAATTAA
1 AAATTAA
1085655 AAA
1 AAA
1085658 AATGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATTAA
Found at i:1085665 original size:23 final size:24
Alignment explanation
Indices: 1085623--1085672 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1085613 TTAATTATTC
* *
1085623 AAATTAAATTAAAATTAAAAATTAA
1 AAATTAAA-TAAAATGAAAAATGAA
1085648 AAATTAAA-AAAATGAAAAATGAA
1 AAATTAAATAAAATGAAAAATGAA
1085671 AA
1 AA
1085673 TGACAAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
25 8 0.35
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (24 bp):
AAATTAAATAAAATGAAAAATGAA
Found at i:1085965 original size:2 final size:2
Alignment explanation
Indices: 1085953--1085987 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1085943 TTTTATAGGG
1085953 TA TA T- 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
1085988 GTAGAGTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1087185 original size:19 final size:19
Alignment explanation
Indices: 1087161--1087213 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
1087151 AAAATGTTTA
1087161 AAAGTATCAATACTTATAT
1 AAAGTATCAATACTTATAT
1087180 AAAGTATCAATACTTATAT
1 AAAGTATCAATACTTATAT
1087199 AAAGTATCAATACTT
1 AAAGTATCAATACTT
1087214 TTTCAGGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (19 bp):
AAAGTATCAATACTTATAT
Found at i:1088842 original size:23 final size:23
Alignment explanation
Indices: 1088816--1088879 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1088806 CAGCTCATAT
1088816 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1088839 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1088862 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1088880 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1089069 original size:103 final size:103
Alignment explanation
Indices: 1088890--1089112 Score: 419
Period size: 103 Copynumber: 2.2 Consensus size: 103
1088880 TATAATAATG
* *
1088890 TCCCGAAGGACTATATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1088955 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
1088993 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1089058 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
*
1089096 TCTCGAAGGACCACATA
1 TCCCGAAGGACCACATA
1089113 GACCCTCGAC
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
103 117 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:1089977 original size:64 final size:64
Alignment explanation
Indices: 1089864--1090088 Score: 244
Period size: 64 Copynumber: 3.5 Consensus size: 64
1089854 TAATGAAGGT
* * * * *
1089864 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
1089927 G
64 G
* * *
1089928 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCAATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* * **
1089992 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
1090055 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
1090089 CTTCAAACAA
Statistics
Matches: 138, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
63 4 0.03
64 128 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:1091809 original size:18 final size:18
Alignment explanation
Indices: 1091788--1091838 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
1091778 CTGCTAAAAC
1091788 TTATAATTATTTTA-AAT
1 TTATAATTATTTTATAAT
*
1091805 ATTATATTTATATTTATAAT
1 -TTATAATTAT-TTTATAAT
*
1091825 TTAAAATGTATTTT
1 TTATAAT-TATTTT
1091839 TATATTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 12 0.44
20 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTATAATTATTTTATAAT
Found at i:1092297 original size:2 final size:2
Alignment explanation
Indices: 1092290--1092324 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1092280 CTAAAACTTG
1092290 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
1092325 AGGTTTGTTA
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:1101103 original size:25 final size:23
Alignment explanation
Indices: 1101028--1101108 Score: 74
Period size: 25 Copynumber: 3.4 Consensus size: 23
1101018 GTATAAATAG
* *
1101028 TTAAATTCATAATATTTTTTATATA
1 TTAAATTAAAAATA-TTTTTAT-TA
*
1101053 TTAAATTAAAAATATTTTTA-TG
1 TTAAATTAAAAATATTTTTATTA
* *
1101075 TTAACTTATCAAATATATTTTATTA
1 TTAAATTA-AAAATAT-TTTTATTA
1101100 TTAAATTAA
1 TTAAATTAA
1101109 TTTAAAAACA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
22 8 0.18
23 6 0.13
24 11 0.24
25 20 0.44
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (23 bp):
TTAAATTAAAAATATTTTTATTA
Found at i:1101586 original size:21 final size:21
Alignment explanation
Indices: 1101521--1101586 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1101511 GAAGTTCGCA
1101521 TTGCGATTCATTCC-AATTCG
1 TTGCGATTCATTCCAAATTCG
** *
1101541 TTGCGA--CAGGCGAAATTCG
1 TTGCGATTCATTCCAAATTCG
1101560 CATTGCGATTCATTCCAAATTCG
1 --TTGCGATTCATTCCAAATTCG
1101583 TTGC
1 TTGC
1101587 AATTGGCGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
18 3 0.09
19 6 0.17
20 6 0.17
21 10 0.29
23 10 0.29
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (21 bp):
TTGCGATTCATTCCAAATTCG
Found at i:1101595 original size:42 final size:41
Alignment explanation
Indices: 1101479--1101610 Score: 201
Period size: 41 Copynumber: 3.2 Consensus size: 41
1101469 TACGATTTTG
*
1101479 ATTGCGATTCATTCCAATTTGTTGCGATAGGCGAAGTTCGC
1 ATTGCGATTCATTCCAATTCGTTGCGATAGGCGAAGTTCGC
* *
1101520 ATTGCGATTCATTCCAATTCGTTGCGACAGGCGAAATTCGC
1 ATTGCGATTCATTCCAATTCGTTGCGATAGGCGAAGTTCGC
* *
1101561 ATTGCGATTCATTCCAAATTCGTTGCAATTGGCGAAGTTCGC
1 ATTGCGATTCATTCC-AATTCGTTGCGATAGGCGAAGTTCGC
*
1101603 GTTGCGAT
1 ATTGCGAT
1101611 AGTCCAAATA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 53 0.65
42 29 0.35
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (41 bp):
ATTGCGATTCATTCCAATTCGTTGCGATAGGCGAAGTTCGC
Found at i:1102401 original size:6 final size:6
Alignment explanation
Indices: 1102385--1102422 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1102375 TCCCGTCTCG
1102385 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1102423 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1102526 original size:21 final size:20
Alignment explanation
Indices: 1102502--1102570 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
1102492 TATTTAGACT
1102502 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAA-TTGGAATGA
* **
1102523 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAA-TTGGAATGA
1102544 ATCGCAACGAATTGGAATGA
1 ATCGCAACGAATTGGAATGA
1102564 ATCGCAA
1 ATCGCAA
1102571 TGCGAAAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 7 0.19
21 14 0.38
23 8 0.22
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAATTGGAATGA
Found at i:1102569 original size:41 final size:41
Alignment explanation
Indices: 1102500--1102715 Score: 279
Period size: 41 Copynumber: 5.2 Consensus size: 41
1102490 AATATTTAGA
1102500 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
* *
1102542 CTATCGCAACGAATTGGAATGAATCGCAATGCGAAAACTTCAC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCG--AACTTCGC
* * * * *
1102585 CTGTCGCAACGATTTGTAATGAATCGCAACGTGAACTTCGA
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
* * *
1102626 CTATCGCAACGATTTAGAATGAATCGCAACGCGAACTTCAC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
* * *
1102667 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGA
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
1102709 CTATCGC
1 CTATCGC
1102716 GTTGCGAATA
Statistics
Matches: 150, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
41 72 0.48
42 43 0.29
43 35 0.23
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (41 bp):
CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
Found at i:1102606 original size:84 final size:83
Alignment explanation
Indices: 1102500--1102715 Score: 326
Period size: 84 Copynumber: 2.6 Consensus size: 83
1102490 AATATTTAGA
* *
1102500 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTAGAATGAA
*
1102565 TCGCAATGCGAAAACTTCAC
66 TCGCAACGCG--AACTTCAC
* * * *
1102585 CTGTCGCAACG-ATTTGTAATGAATCGCAACGTGAACTTCGACTATCGCAACGATTTAGAATGAA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTAGAATGAA
1102649 TCGCAACGCGAACTTCAC
66 TCGCAACGCGAACTTCAC
* *
1102667 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGC
1102716 GTTGCGAATA
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
82 18 0.15
83 33 0.28
84 57 0.48
85 10 0.08
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (83 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTAGAATGAA
TCGCAACGCGAACTTCAC
Found at i:1102714 original size:21 final size:20
Alignment explanation
Indices: 1102607--1102715 Score: 55
Period size: 21 Copynumber: 5.2 Consensus size: 20
1102597 TTTGTAATGA
*
1102607 ATCGCAACGTGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
* * *
1102628 ATCGCAA-CG-ATTTAGAAT
1 ATCGCAAGCGAACTTCGACT
1102646 GAATCGCAACGCGAACTTC-ACCT
1 --ATCGCAA-GCGAACTTCGA-CT
* * *
1102669 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTCGACT
1102688 AAATCGCAATGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTCGACT
1102711 ATCGC
1 ATCGC
1102716 GTTGCGAATA
Statistics
Matches: 64, Mismatches: 13, Indels: 22
0.65 0.13 0.22
Matches are distributed among these distances:
18 6 0.09
19 8 0.12
20 8 0.12
21 26 0.41
22 3 0.05
23 13 0.20
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAAGCGAACTTCGACT
Found at i:1103720 original size:2 final size:2
Alignment explanation
Indices: 1103713--1103737 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1103703 ATATTAAGCT
1103713 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1103738 CAATTTGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1104422 original size:112 final size:112
Alignment explanation
Indices: 1104085--1104660 Score: 902
Period size: 113 Copynumber: 5.1 Consensus size: 112
1104075 TTGTCGTTTT
* * * *
1104085 GTGTCAATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1104150 GGTCTATAAATGACAAAACGGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1104197 GTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1104261 GATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1104308 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * **
1104373 GGTCTATAAATGACAAAACAGGTAAAACGCTATCAAATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1104420 GTGTCGATACTTTATAAAAATGTATGGGTCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
* * * *
1104485 CGATTTATAAATGACATAACAGGTAAAGCGCTACCAGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1104533 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGATAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
** * * *
1104598 CGGTCTATAAATGACAAAACAAATAAAGCGCTACCGAATATGTTGATA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
1104646 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
1104661 TATAAGTATC
Statistics
Matches: 425, Mismatches: 37, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
111 106 0.25
112 146 0.34
113 173 0.41
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1104855 original size:182 final size:182
Alignment explanation
Indices: 1104530--1104986 Score: 659
Period size: 182 Copynumber: 2.5 Consensus size: 182
1104520 AGATATATTG
* *
1104530 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGATAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAATATGACAA
** ** * *
1104595 AACCGGTCTATAAATGACAAAA-CAAATAAAGCGCTACCGAATATGTTGATAGTGTCGATACTTT
65 AACCGGTCTCGAAATGACAAAATC-GGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTT
* * *
1104659 ATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCG-CTAAT
129 ATAATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTC-AAT
* * * *
1104713 AAAGTGTCGATGCTTTATAAAAATGTATCGGTCCATAACAATATAAAAGATAAAAATATGACAGA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACA-A
* *
1104778 AA-CGGTTTCGAAATGACAAAATCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTA
65 AACCGGTCTCGAAATGACAAAATCGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTA
*
1104842 TAATAAATATCGACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGTCAAT
130 TAATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAAT
* *
1104895 AAAGTGTTGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
1104960 ATCGATCTCGAAATGACAAAATCGGTA
66 ACCGGTCTCGAAATGACAAAATCGGTA
1104987 GTAAAAAAAA
Statistics
Matches: 244, Mismatches: 26, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
181 3 0.01
182 189 0.77
183 52 0.21
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAATCGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
AATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAAT
Found at i:1105467 original size:23 final size:23
Alignment explanation
Indices: 1105411--1105467 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1105401 TTAGTTAGAA
1105411 AATATGTTAATATAAGCGCTACCT
1 AATATGTT-ATATAAGCGCTACCT
* ** *
1105435 ATTACATTATATAAGCGGTACCT
1 AATATGTTATATAAGCGCTACCT
1105458 AATATGTTAT
1 AATATGTTAT
1105468 TGTACTTGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (23 bp):
AATATGTTATATAAGCGCTACCT
Found at i:1105641 original size:23 final size:23
Alignment explanation
Indices: 1105615--1105674 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1105605 ATTAAACACA
* *
1105615 ATAATATATTAGGTACCGCTTAT
1 ATAATATAATAGGTACCACTTAT
* *
1105638 ATAATGTAATAGGTATCACTTAT
1 ATAATATAATAGGTACCACTTAT
*
1105661 ATAATAAAATAGGT
1 ATAATATAATAGGT
1105675 TAATTACTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGGTACCACTTAT
Found at i:1105671 original size:87 final size:87
Alignment explanation
Indices: 1105525--1105758 Score: 380
Period size: 87 Copynumber: 2.7 Consensus size: 87
1105515 ATTACCAAGT
*
1105525 ACAATAACATATTAGGTGCCGCTTATATAATGTAATAGGTAGCTA-TTATATAATAAAATAGGTT
1 ACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGC-ACTTATATAATAAAATAGGTT
*
1105589 AATTACTGAAAACATTATTAAAC
65 AATTACTGAAAACATTATCAAAC
* *
1105612 ACAATAATATATTAGGTACCGCTTATATAATGTAATAGGTATCACTTATATAATAAAATAGGTTA
1 ACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTA
* *
1105677 ATTACTGGAAACATTATCATAC
66 ATTACTGAAAACATTATCAAAC
* *
1105699 ACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATA
1 ACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATA
1105759 AGTAGCGCTT
Statistics
Matches: 136, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
86 1 0.01
87 135 0.99
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (87 bp):
ACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTA
ATTACTGAAAACATTATCAAAC
Found at i:1105728 original size:23 final size:23
Alignment explanation
Indices: 1105702--1105784 Score: 112
Period size: 23 Copynumber: 3.6 Consensus size: 23
1105692 ATCATACACA
* *
1105702 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1105725 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
* *
1105748 ATAATAAAATAAGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1105771 ATAATAAAATAGGT
1 ATAATATAATAGGT
1105785 TAATTACTGG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:1105738 original size:110 final size:110
Alignment explanation
Indices: 1105615--1105871 Score: 390
Period size: 110 Copynumber: 2.3 Consensus size: 110
1105605 ATTAAACACA
* * * ** *
1105615 ATAATATATTAGGTACCGCTTATATAATGTAATAGGTATCACTTATATAATAAAATAGGTTAATT
1 ATAATGTAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATT
* *
1105680 ACTGGAAACATTATC-ATACACAATAACATATTAGGTAGCGCTTAT
66 ACTGGAAACATTATCAAT-CACAATAACATATTAGGTACCACTTAT
* * *
1105725 ATAATGTAATAGGTAGCGCTTATATAATAAAATAAGTAGCGCTTATATAATAAAATAGGTTAATT
1 ATAATGTAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATT
1105790 ACTGGAAACATTATCAATCACAATAACATATTAGGTACCACTTAT
66 ACTGGAAACATTATCAATCACAATAACATATTAGGTACCACTTAT
*
1105835 ATAATGTAATAGGTAACACTTATATAATAAAATAGGT
1 ATAATGTAATAGGTAACGCTTATATAATAAAATAGGT
1105872 TAATTACTGG
Statistics
Matches: 133, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
110 131 0.98
111 2 0.02
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (110 bp):
ATAATGTAATAGGTAACGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGGTTAATT
ACTGGAAACATTATCAATCACAATAACATATTAGGTACCACTTAT
Found at i:1105825 original size:87 final size:86
Alignment explanation
Indices: 1105734--1105964 Score: 356
Period size: 87 Copynumber: 2.7 Consensus size: 86
1105724 TATAATGTAA
** *
1105734 TAGGTAGCGCTTATATAATAAAATAAGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAAC
1 TAGGTAGCGCTTATATAATGTAATAGGTA-CGCTTATATAATAAAATAGGTTAATTACTGGAAAC
*
1105799 ATTATCAATCACAATAACATAT
65 ATTATCAAACACAATAACATAT
* * *
1105821 TAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAATTACTGGAAAC
1 TAGGTAGCGCTTATATAATGTAATAGGT-ACGCTTATATAATAAAATAGGTTAATTACTGGAAAC
1105886 ATTATCAAACACAATAACATAT
65 ATTATCAAACACAATAACATAT
* *
1105908 TAGGTAGCGCTTATATAACGTAATAGGTA-GCTTATATAATAAAATAAGTTAATTACT
1 TAGGTAGCGCTTATATAATGTAATAGGTACGCTTATATAATAAAATAGGTTAATTACT
1105965 TAATTTGTTA
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
85 26 0.20
86 1 0.01
87 103 0.79
88 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (86 bp):
TAGGTAGCGCTTATATAATGTAATAGGTACGCTTATATAATAAAATAGGTTAATTACTGGAAACA
TTATCAAACACAATAACATAT
Found at i:1105838 original size:23 final size:23
Alignment explanation
Indices: 1105812--1105871 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1105802 ATCAATCACA
* *
1105812 ATAACATATTAGGTACCACTTAT
1 ATAACATAATAGGTAACACTTAT
**
1105835 ATAATGTAATAGGTAACACTTAT
1 ATAACATAATAGGTAACACTTAT
* *
1105858 ATAATAAAATAGGT
1 ATAACATAATAGGT
1105872 TAATTACTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACACTTAT
Found at i:1105879 original size:197 final size:196
Alignment explanation
Indices: 1105544--1105956 Score: 693
Period size: 197 Copynumber: 2.1 Consensus size: 196
1105534 TATTAGGTGC
** * * *
1105544 CGCTTATATAATGTAATAGGTAGCTATTATATAATAAAATAGGTTAATTACTGAAAACATTATTA
1 CGCTTATATAATAAAATAAGTAGCGATTATATAATAAAATAGGTTAATTACTGAAAACATTATCA
* * *
1105609 AACACAATAATATATTAGGTACCGCTTATATAATGTAATAGGTATCACTTATATAATAAAATAGG
66 AACACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAGG
* *
1105674 TTAATTACTGGAAACATTATCATACACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
131 TTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGT
1105739 A
196 A
* *
1105740 GCGCTTATATAATAAAATAAGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATTATC
1 -CGCTTATATAATAAAATAAGTAGCGATTATATAATAAAATAGGTTAATTACTGAAAACATTATC
*
1105805 AATCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAG
65 AAACACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAG
1105870 GTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTATATAACGTAATAGG
130 GTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTATATAACGTAATAGG
1105935 TA
195 TA
1105937 -GCTTATATAATAAAATAAGT
1 CGCTTATATAATAAAATAAGT
1105957 TAATTACTTA
Statistics
Matches: 203, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
195 20 0.10
197 183 0.90
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (196 bp):
CGCTTATATAATAAAATAAGTAGCGATTATATAATAAAATAGGTTAATTACTGAAAACATTATCA
AACACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAACACTTATATAATAAAATAGG
TTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGT
A
Found at i:1105925 original size:23 final size:21
Alignment explanation
Indices: 1105899--1105946 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
1105889 ATCAAACACA
*
1105899 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTA--GCTTAT
*
1105922 ATAACGTAATAGGTAGCTTAT
1 ATAACATAATAGGTAGCTTAT
1105943 ATAA
1 ATAA
1105947 TAAAATAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
23 13 0.57
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
ATAACATAATAGGTAGCTTAT
Found at i:1106820 original size:198 final size:197
Alignment explanation
Indices: 1106503--1106941 Score: 616
Period size: 198 Copynumber: 2.2 Consensus size: 197
1106493 TAAAATAAAT
* *
1106503 ATTGCAAATTTATCTATTACATTATAATTATCGATTTCGATGTTTTTGGGATCGATACAATTTTA
1 ATTGTAAATTTATCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTTTA
* *
1106568 AATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAATGTATCGACACAA
66 AATGTATCGACACTTTAT-CGTGCACCTCGTTGGACATTCATTATGGAAAAATGTATCGACAC-A
* *
1106633 ACTTAAA-ATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAATCGGTATATTTATACTGA
129 ACTTAAATATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCG-
1106697 G-TAC
193 GTTAC
* * *
1106701 ATTGTAAATTTGTCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAA
1 ATTGTAAATTTATCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT--
*
1106765 TAAATGTATCGACACTTTAT-GTGCACCTCGTTTGACATTCATTATGGACAAAATGTATCGACAC
64 TAAATGTATCGACACTTTATCGTGCACCTCGTTGGACATTCATTATGGA-AAAATGTATCGACAC
*** * * * *
1106829 TTTTTAAATTTGTGTCGATATATTATGTTGATCTATTCTCTCATAAAATCGGTATATTTATACCG
128 AACTTAAATATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCG
*
1106894 GTTAT
193 GTTAC
* *
1106899 ATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
1 ATTGTAAATTTATCTATTACATTATAATTATCGGTTTCGATGT
1106942 AACATATGTG
Statistics
Matches: 214, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
197 34 0.16
198 160 0.75
199 20 0.09
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (197 bp):
ATTGTAAATTTATCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTTTA
AATGTATCGACACTTTATCGTGCACCTCGTTGGACATTCATTATGGAAAAATGTATCGACACAAC
TTAAATATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCGGTT
AC
Found at i:1107169 original size:20 final size:22
Alignment explanation
Indices: 1107146--1107186 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1107136 ATTGACATAA
*
1107146 TAATA-TTAAATAAAT-TATTC
1 TAATATTTAAAAAAATATATTC
1107166 TAATATTTAAAAAAATATATT
1 TAATATTTAAAAAAATATATT
1107187 ATTTTGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATATTTAAAAAAATATATTC
Found at i:1110592 original size:24 final size:23
Alignment explanation
Indices: 1110559--1110614 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
1110549 CCACTAGGGG
* *
1110559 CACTGAATATTTATCTCGAAGGAC
1 CACTGTATA-TTATCCCGAAGGAC
*
1110583 CACTGTATA-TGTCCCGAAGGAC
1 CACTGTATATTATCCCGAAGGAC
1110605 CACTGTATAT
1 CACTGTATAT
1110615 CCCTCGACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 20 0.71
24 8 0.29
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (23 bp):
CACTGTATATTATCCCGAAGGAC
Found at i:1117076 original size:23 final size:22
Alignment explanation
Indices: 1117033--1117080 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
1117023 ATTTTTTATA
1117033 TATTATAATATTAATATTTAAT
1 TATTATAATATTAATATTTAAT
* *
1117055 TATTAATAATTTTATATATTAAAT
1 TATT-ATAATATTA-ATATTTAAT
1117079 TA
1 TA
1117081 AACTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 8 0.36
24 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATAATATTAATATTTAAT
Found at i:1126934 original size:2 final size:2
Alignment explanation
Indices: 1126927--1126954 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1126917 TAGACTAAAT
1126927 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
1126955 CAAAAGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1127689 original size:6 final size:6
Alignment explanation
Indices: 1127678--1127709 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1127668 CTACCTAGAG
1127678 TGGTAC TGGTAC TGGTAC TGGTAC TGGTAC TG
1 TGGTAC TGGTAC TGGTAC TGGTAC TGGTAC TG
1127710 TGTAGAGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (6 bp):
TGGTAC
Found at i:1129488 original size:31 final size:31
Alignment explanation
Indices: 1129453--1129549 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
1129443 AAAAATTAAG
1129453 TTACTTAATAGTAAGCTTAATCTTTAATAAT
1 TTACTTAATAGTAAGCTTAATCTTTAATAAT
** * * **
1129484 TTAC-TAATTTTCAA-TTTCACA-CTTTGAT-CG
1 TTACTTAATAGT-AAGCTT-A-ATCTTTAATAAT
1129514 TTACTTAATAGTAAGCTTAATCTTTAATAAT
1 TTACTTAATAGTAAGCTTAATCTTTAATAAT
1129545 TTACT
1 TTACT
1129550 AATTTTCAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 14
0.64 0.16 0.19
Matches are distributed among these distances:
29 1 0.02
30 20 0.43
31 25 0.53
32 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.46
Consensus pattern (31 bp):
TTACTTAATAGTAAGCTTAATCTTTAATAAT
Found at i:1129547 original size:61 final size:61
Alignment explanation
Indices: 1129452--1129573 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
1129442 AAAAAATTAA
1129452 GTTACTTAATAGTAAGCTTAATCTTTAATAATTTACTAATTTTCAATTTCACACTTTGATC
1 GTTACTTAATAGTAAGCTTAATCTTTAATAATTTACTAATTTTCAATTTCACACTTTGATC
1129513 GTTACTTAATAGTAAGCTTAATCTTTAATAATTTACTAATTTTCAATTTCACACTTTGATC
1 GTTACTTAATAGTAAGCTTAATCTTTAATAATTTACTAATTTTCAATTTCACACTTTGATC
1129574 TTTAAAAATC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (61 bp):
GTTACTTAATAGTAAGCTTAATCTTTAATAATTTACTAATTTTCAATTTCACACTTTGATC
Found at i:1130730 original size:20 final size:20
Alignment explanation
Indices: 1130692--1130731 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1130682 CATACAAATA
1130692 TTTTAATAGTTATACTATCTT
1 TTTTAATAGTTATA-TATCTT
1130713 TTTTATATAGTTAT-TATCT
1 TTTTA-ATAGTTATATATCT
1130732 AACTTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTAATAGTTATATATCTT
Found at i:1131184 original size:14 final size:14
Alignment explanation
Indices: 1131165--1131194 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1131155 ACCATTTTAA
1131165 TTAAAAAATACTAT
1 TTAAAAAATACTAT
*
1131179 TTAAAAAATATTAT
1 TTAAAAAATACTAT
1131193 TT
1 TT
1131195 CCTAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAAATACTAT
Found at i:1134032 original size:31 final size:31
Alignment explanation
Indices: 1133994--1134061 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1133984 ATGACGTCGT
1133994 CCGGTTATTCCGACTGATCGGACCGGTTCGA
1 CCGGTTATTCCGACTGATCGGACCGGTTCGA
*
1134025 CCGGTTATTCCGACTGGTCGGACCGGTTCGA
1 CCGGTTATTCCGACTGATCGGACCGGTTCGA
1134056 CCGGTT
1 CCGGTT
1134062 GAACCAGTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.13, C:0.29, G:0.31, T:0.26
Consensus pattern (31 bp):
CCGGTTATTCCGACTGATCGGACCGGTTCGA
Found at i:1134403 original size:6 final size:6
Alignment explanation
Indices: 1134392--1134428 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1134382 GACACGTATT
1134392 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1134429 GACGAGACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1135082 original size:22 final size:22
Alignment explanation
Indices: 1135057--1135105 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1135047 TGGAAAATCA
1135057 CAACGACAACTGTAAACTATCG
1 CAACGACAACTGTAAACTATCG
*
1135079 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAAACTATCG
1135101 CAACG
1 CAACG
1135106 CGAAATGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.16
Consensus pattern (22 bp):
CAACGACAACTGTAAACTATCG
Found at i:1135424 original size:2 final size:2
Alignment explanation
Indices: 1135417--1135477 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1135407 ATAAAACAAC
1135417 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
1135459 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1135478 CATGTCACTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1136290 original size:18 final size:18
Alignment explanation
Indices: 1136264--1136300 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1136254 CATTATGGAA
*
1136264 ATAATCCATATTTAAAAT
1 ATAAACCATATTTAAAAT
*
1136282 ATAAACCATATTTTAAAT
1 ATAAACCATATTTAAAAT
1136300 A
1 A
1136301 ATATAAGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAACCATATTTAAAAT
Found at i:1136834 original size:6 final size:6
Alignment explanation
Indices: 1136827--1136873 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
1136817 CCAAATGAAA
*
1136827 CAGAAA CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAA
1 CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAA
1136874 AATAAAGGCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.53, C:0.17, G:0.30, T:0.00
Consensus pattern (6 bp):
CAGAAG
Found at i:1139428 original size:55 final size:56
Alignment explanation
Indices: 1139314--1139430 Score: 182
Period size: 56 Copynumber: 2.1 Consensus size: 56
1139304 TTCAATCAAA
* * *
1139314 TTTTTTGAGTTATTTAAATTGACAAATCTTATTTTATTTCTAAAATTTATTTGATT
1 TTTTTTGAGTTATTTAAATTGAAAAATCTTACTTTATTACTAAAATTTATTTGATT
*
1139370 TTTTTTGAGTTATTTTAAA-TGAAAAATCTTACTTTATTACTAAATTTTATTTGATT
1 TTTTTTGAGTTA-TTTAAATTGAAAAATCTTACTTTATTACTAAAATTTATTTGATT
1139426 TTTTT
1 TTTTT
1139431 AAAAATCAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
56 50 0.89
57 6 0.11
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (56 bp):
TTTTTTGAGTTATTTAAATTGAAAAATCTTACTTTATTACTAAAATTTATTTGATT
Found at i:1148110 original size:19 final size:19
Alignment explanation
Indices: 1148086--1148128 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1148076 AAAGCATAAA
1148086 TAAGGATTTGATCATGACC
1 TAAGGATTTGATCATGACC
1148105 TAAGGATTTGATCATGACC
1 TAAGGATTTGATCATGACC
1148124 TAAGG
1 TAAGG
1148129 TTTATGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (19 bp):
TAAGGATTTGATCATGACC
Found at i:1148362 original size:15 final size:14
Alignment explanation
Indices: 1148338--1148396 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
1148328 GTAATTGGTT
* *
1148338 TTCTGGAAATTGAA
1 TTCTAGAAAATGAA
1148352 TTCTAGAAAATGAA
1 TTCTAGAAAATGAA
* **
1148366 TTACTGGAATTTGAA
1 TT-CTAGAAAATGAA
1148381 TTCTAGAAAATGAA
1 TTCTAGAAAATGAA
1148395 TT
1 TT
1148397 ACATTTCTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (14 bp):
TTCTAGAAAATGAA
Found at i:1148382 original size:29 final size:29
Alignment explanation
Indices: 1148340--1148398 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1148330 AATTGGTTTT
1148340 CTGGAAATTGAATTCTAGAAAATGAATTA
1 CTGGAAATTGAATTCTAGAAAATGAATTA
*
1148369 CTGGAATTTGAATTCTAGAAAATGAATTA
1 CTGGAAATTGAATTCTAGAAAATGAATTA
1148398 C
1 C
1148399 ATTTCTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (29 bp):
CTGGAAATTGAATTCTAGAAAATGAATTA
Found at i:1148689 original size:31 final size:29
Alignment explanation
Indices: 1148621--1148690 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
1148611 AATATTATTT
*
1148621 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
1148651 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
1148684 TTATATT
1 TTATATT
1148691 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:1148770 original size:23 final size:23
Alignment explanation
Indices: 1148721--1148771 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1148711 GTGTTAAATT
**
1148721 ATATTTTAAAAATATTGATTAGT
1 ATATTTTAAAAATATTGATTAAA
* * *
1148744 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTGATTAAA
1148767 ATATT
1 ATATT
1148772 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTGATTAAA
Found at i:1148827 original size:19 final size:19
Alignment explanation
Indices: 1148759--1148827 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
1148749 TTAAATATCT
1148759 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATT-GA
*
1148778 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTGA
*
1148797 TATATAAATAATATTATTGA
1 T-TATTAATAATATTATTGA
1148817 TTATTAATAAT
1 TTATTAATAAT
1148828 TTAATAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
18 8 0.20
19 18 0.45
20 7 0.17
22 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTGA
Found at i:1148985 original size:22 final size:21
Alignment explanation
Indices: 1148953--1149014 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
1148943 TTTTATTATA
*
1148953 ATATTAAAAATA-TAATATAAT
1 ATATTATAAATATTAATA-AAT
1148974 ATTATTATAAATATTAATAAAT
1 A-TATTATAAATATTAATAAAT
*
1148996 ATATTTTAAATAATTAATA
1 ATATTATAAAT-ATTAATA
1149015 TTTTGATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 10 0.28
22 21 0.58
23 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTATAAATATTAATAAAT
Found at i:1148993 original size:10 final size:10
Alignment explanation
Indices: 1148952--1148997 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
1148942 ATTTTATTAT
1148952 AATATTAA-A
1 AATATTAATA
1148961 AATA-TAATA
1 AATATTAATA
1148970 TAATATTATTATA
1 -AATATTA--ATA
1148983 AATATTAATA
1 AATATTAATA
1148993 AATAT
1 AATAT
1148998 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 5 0.16
10 12 0.38
11 2 0.06
12 7 0.22
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:1149275 original size:42 final size:42
Alignment explanation
Indices: 1149216--1149309 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
1149206 TGCTCAAACC
* * *
1149216 AAACACTGGAAAACATTTTCTGTAAAACGAATTACATGAAAA
1 AAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAAA
* *
1149258 AAACACGGGAAAACATTTTCCGGAAAACGAATTACGTGAAAC
1 AAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAAA
1149300 AAACACGGGA
1 AAACACGGGA
1149310 TTTCGGGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (42 bp):
AAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAAA
Found at i:1152409 original size:25 final size:25
Alignment explanation
Indices: 1152373--1152424 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1152363 GCACTATTTG
*
1152373 TGCGTTTTGTTTTAGCAGTTACGAC
1 TGCGTTTAGTTTTAGCAGTTACGAC
*
1152398 TGCGTTTAGTTTTGGCAGTTACGAC
1 TGCGTTTAGTTTTAGCAGTTACGAC
1152423 TG
1 TG
1152425 TATATTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (25 bp):
TGCGTTTAGTTTTAGCAGTTACGAC
Found at i:1153966 original size:14 final size:14
Alignment explanation
Indices: 1153947--1153989 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1153937 TGTATTTTTT
* *
1153947 AATTTCTGCCTTTA
1 AATTTCAGCATTTA
1153961 AATTTCAGCATTTA
1 AATTTCAGCATTTA
* *
1153975 CATTTCAGTATTTA
1 AATTTCAGCATTTA
1153989 A
1 A
1153990 TTTTTGCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (14 bp):
AATTTCAGCATTTA
Found at i:1154812 original size:18 final size:18
Alignment explanation
Indices: 1154791--1154826 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1154781 ATGATCTCAC
1154791 TTAAAATTTGGGAACAAG
1 TTAAAATTTGGGAACAAG
*
1154809 TTAAATTTTGGGAACAAG
1 TTAAAATTTGGGAACAAG
1154827 GGAAAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTAAAATTTGGGAACAAG
Found at i:1154983 original size:98 final size:94
Alignment explanation
Indices: 1154809--1155077 Score: 359
Period size: 89 Copynumber: 2.9 Consensus size: 94
1154799 TGGGAACAAG
* * * * *
1154809 TTAAATTTTGGGAACAAGGGAAAAAGAGAATGTTCGTCTATTTAAATTCACTGGTAAAAGATCGT
1 TTAAAATTTGGGAACGAGGGAAAAAGAGAATGTTCGTCTATTTAAATTCACCGATAAAATATCGT
*
1154874 TAGAATGCATAAAAGGTACGATCATGATATCAC
66 TAGAACGCATAAAAGGTA--A--ATGATATCAC
*
1154907 TTAAAATTTGGGAACGAGGGAAAAAGATAATGTTCGTCTATTTAAATTCACCGATAAAATATCGT
1 TTAAAATTTGGGAACGAGGGAAAAAGAGAATGTTCGTCTATTTAAATTCACCGATAAAATATCGT
* *
1154972 TAGAACACAT--AA---AAATGATCTCAC
66 TAGAACGCATAAAAGGTAAATGATATCAC
* * *
1154996 GTAAAATTTGGGAACGAGGGAAAAAGAGAATGTTCTTCTATTTAAATTTACCGATAAAATATCGT
1 TTAAAATTTGGGAACGAGGGAAAAAGAGAATGTTCGTCTATTTAAATTCACCGATAAAATATCGT
1155061 TAGAACGCATAAAAGGT
66 TAGAACGCATAAAAGGT
1155078 CTGATTTTGA
Statistics
Matches: 152, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
89 79 0.52
91 3 0.02
93 1 0.01
96 2 0.01
98 67 0.44
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (94 bp):
TTAAAATTTGGGAACGAGGGAAAAAGAGAATGTTCGTCTATTTAAATTCACCGATAAAATATCGT
TAGAACGCATAAAAGGTAAATGATATCAC
Found at i:1157151 original size:13 final size:13
Alignment explanation
Indices: 1157133--1157158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1157123 GAAACTATCC
1157133 GTGAAATATTTAA
1 GTGAAATATTTAA
1157146 GTGAAATATTTAA
1 GTGAAATATTTAA
1157159 ATAACAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
GTGAAATATTTAA
Found at i:1158805 original size:21 final size:21
Alignment explanation
Indices: 1158780--1158853 Score: 94
Period size: 21 Copynumber: 3.3 Consensus size: 21
1158770 ACAAATATTT
1158780 TTTTATAATTTAATCTTTTAA
1 TTTTATAATTTAATCTTTTAA
1158801 TTTTATAATTTAATCTTTTAATA
1 TTTTATAATTTAATCTTTT-A-A
*
1158824 GTTTTTTATAATTTAATCTTTTAG
1 ---TTTTATAATTTAATCTTTTAA
1158848 TTTTAT
1 TTTTAT
1158854 TTTATTTAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
21 25 0.53
22 1 0.02
23 1 0.02
25 1 0.02
26 19 0.40
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (21 bp):
TTTTATAATTTAATCTTTTAA
Found at i:1158830 original size:26 final size:25
Alignment explanation
Indices: 1158773--1158846 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 25
1158763 TCTAATTACA
1158773 AATATTTTTTTATAATTTAATCTTTT
1 AATA-TTTTTTATAATTTAATCTTTT
1158799 -A-A--TTTTATAATTTAATCTTTT
1 AATATTTTTTATAATTTAATCTTTT
1158820 AATAGTTTTTTATAATTTAATCTTTT
1 AATA-TTTTTTATAATTTAATCTTTT
1158846 A
1 A
1158847 GTTTTATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
21 19 0.44
22 1 0.02
23 1 0.02
24 1 0.02
25 1 0.02
26 20 0.47
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (25 bp):
AATATTTTTTATAATTTAATCTTTT
Found at i:1158856 original size:26 final size:24
Alignment explanation
Indices: 1158775--1158858 Score: 88
Period size: 26 Copynumber: 3.5 Consensus size: 24
1158765 TAATTACAAA
1158775 TATTT-TTTTATAATTTAATCTTT
1 TATTTATTTTATAATTTAATCTTT
1158798 TA---ATTTTATAATTTAATCTTT
1 TATTTATTTTATAATTTAATCTTT
1158819 TAATAGTT-TTTTATAATTTAATCTTT
1 T-AT--TTATTTTATAATTTAATCTTT
1158845 TAGTTTTATTTTAT
1 TA--TTTATTTTAT
1158859 TTAGTCTTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
21 19 0.37
22 1 0.02
23 2 0.04
25 3 0.06
26 25 0.49
27 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (24 bp):
TATTTATTTTATAATTTAATCTTT
Found at i:1158974 original size:19 final size:20
Alignment explanation
Indices: 1158937--1158980 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1158927 AAAAAAGTTT
**
1158937 ATAAA-TTTAAAATTTAATA
1 ATAAATTTTAAAATAAAATA
1158956 A-AAATTTTAAAATAAAATA
1 ATAAATTTTAAAATAAAATA
1158975 ATAAAT
1 ATAAAT
1158981 CATTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 14 0.67
20 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAATTTTAAAATAAAATA
Found at i:1163066 original size:2 final size:2
Alignment explanation
Indices: 1163059--1163093 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1163049 ACATTTTAAC
1163059 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
1163094 AATTTGCCAA
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:1167385 original size:3 final size:3
Alignment explanation
Indices: 1167379--1167442 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
1167369 CATCATCATC
1167379 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1167427 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
1167443 GCATTAATCC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1170141 original size:11 final size:12
Alignment explanation
Indices: 1170125--1170160 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
1170115 ATGATTAACA
1170125 AATATATAA-AT
1 AATATATAATAT
1170136 AATATATATATAT
1 AATATATA-ATAT
1170149 AATATATAATAT
1 AATATATAATAT
1170161 TAAATATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.35
12 5 0.22
13 10 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATATAATAT
Found at i:1171333 original size:36 final size:36
Alignment explanation
Indices: 1171286--1171388 Score: 118
Period size: 36 Copynumber: 2.9 Consensus size: 36
1171276 GATCGGAACA
* * * *
1171286 GATAAGCACACACAGTGCTATTATATCGGAAATCAC
1 GATATGCACACAAAGTGCTATTACATCGGAAATAAC
* *
1171322 GATATGCACACAAAGTGCAATCACATCGGAAATAAC
1 GATATGCACACAAAGTGCTATTACATCGGAAATAAC
* *
1171358 AATATGCACACAAAGTG-TATTCAGATCGGAA
1 GATATGCACACAAAGTGCTATT-ACATCGGAA
1171389 TATATATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 2 0.04
36 54 0.96
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (36 bp):
GATATGCACACAAAGTGCTATTACATCGGAAATAAC
Found at i:1171395 original size:2 final size:2
Alignment explanation
Indices: 1171388--1171412 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1171378 TCAGATCGGA
1171388 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 A
1171413 CTAGTGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1174163 original size:7 final size:7
Alignment explanation
Indices: 1174151--1174187 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
1174141 GTCAAAGAAA
1174151 GTCAACG
1 GTCAACG
1174158 GTCAACG
1 GTCAACG
1174165 GTC-ACG
1 GTCAACG
1174171 GTCAACG
1 GTCAACG
1174178 GTCAACG
1 GTCAACG
1174185 GTC
1 GTC
1174188 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1174173 original size:13 final size:14
Alignment explanation
Indices: 1174151--1174187 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
1174141 GTCAAAGAAA
1174151 GTCAACGGTCAACG
1 GTCAACGGTCAACG
1174165 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
1174178 GTCAACGGTC
1 GTCAACGGTC
1174188 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:1174199 original size:17 final size:17
Alignment explanation
Indices: 1174177--1174234 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
1174167 CACGGTCAAC
*
1174177 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
1174194 GGTCAACAGTCGGGTTG
1 GGTCAACAGTCGGGTCG
1174211 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1174228 GGTCAAC
1 GGTCAAC
1174235 CCGGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.22, G:0.41, T:0.19
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1181461 original size:17 final size:17
Alignment explanation
Indices: 1181441--1181498 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
1181431 GAAAGTCAAC
*
1181441 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
* *
1181458 GGTCAACATTCGGGTTG
1 GGTCAACAGTCGGGTCG
1181475 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1181492 GGTCAAC
1 GGTCAAC
1181499 CCGGTTCAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.40, T:0.21
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1181522 original size:19 final size:19
Alignment explanation
Indices: 1181494--1181563 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1181484 TCGGGTCGGG
* *
1181494 TCAACCCGGTTCAGACTGA
1 TCAAACCGGTTCAGACCGA
* *
1181513 TCAAATCGGTTCAGACCGG
1 TCAAACCGGTTCAGACCGA
*
1181532 TCAAACCGGTTC-GAACCGG
1 TCAAACCGGTTCAG-ACCGA
*
1181551 TTAAACCGGTTCA
1 TCAAACCGGTTCA
1181564 AAACTGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 1 0.02
19 42 0.98
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (19 bp):
TCAAACCGGTTCAGACCGA
Done.