Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 96 of 335
Found at i:30805871 original size:19 final size:20
Alignment explanation
Indices: 30805847--30805887 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
30805837 AATCTTCGAG
30805847 GATATGCAATCTTAG-ATAT
1 GATATGCAATCTTAGAATAT
*
30805866 GATATGTAATCTTAGAATAT
1 GATATGCAATCTTAGAATAT
30805886 GA
1 GA
30805888 GATTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (20 bp):
GATATGCAATCTTAGAATAT
Found at i:30810197 original size:25 final size:24
Alignment explanation
Indices: 30810161--30810208 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
30810151 AAACAAAGAG
30810161 TTTTCACAATAACAAAACAGTTCCT
1 TTTTCACAATAAC-AAACAGTTCCT
*
30810186 TTTTC-CACATAACACACAGTTCC
1 TTTTCACA-ATAACAAACAGTTCC
30810209 ATCCCAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.31
Consensus pattern (24 bp):
TTTTCACAATAACAAACAGTTCCT
Found at i:30812683 original size:16 final size:16
Alignment explanation
Indices: 30812654--30812696 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
30812644 TGAAAGTCGT
*
30812654 AAGAA-AGGGAGAA-G
1 AAGAAGAGGGGGAAGG
30812668 AATGAAGAGGGGGAAGG
1 AA-GAAGAGGGGGAAGG
30812685 AAGAAGAGGGGG
1 AAGAAGAGGGGG
30812697 CTTAAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 17 0.68
17 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.02
Consensus pattern (16 bp):
AAGAAGAGGGGGAAGG
Found at i:30814778 original size:17 final size:18
Alignment explanation
Indices: 30814758--30814791 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30814748 AAACAAGGAA
30814758 AAAT-AAATAAACAATTT
1 AAATCAAATAAACAATTT
*
30814775 AAATCAAATAACCAATT
1 AAATCAAATAAACAATT
30814792 AAGAAGATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATCAAATAAACAATTT
Found at i:30818402 original size:31 final size:32
Alignment explanation
Indices: 30818367--30818434 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 32
30818357 CCAACTTAAG
* *
30818367 AAAAATTGTCAAGTTTAGGTATCAAATTAGA-
1 AAAAATTGTCAAGTTTAGGTACCAAATAAGAC
30818398 AAAAATTGTCAAGTTTAGGTACCAAATAAGAC
1 AAAAATTGTCAAGTTTAGGTACCAAATAAGAC
30818430 AAAAA
1 AAAAA
30818435 AAAGTTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 29 0.85
32 5 0.15
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (32 bp):
AAAAATTGTCAAGTTTAGGTACCAAATAAGAC
Found at i:30818463 original size:29 final size:28
Alignment explanation
Indices: 30818408--30818463 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
30818398 AAAAATTGTC
* *
30818408 AAGTTTAGGTACCAAATAAGACAAAAAA
1 AAGTTTAGGTACAAAATAAGAAAAAAAA
30818436 AAGTTTAGGTACTAAAAT-AGAAAAAAAA
1 AAGTTTAGGTAC-AAAATAAGAAAAAAAA
30818464 TGTTAAGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (28 bp):
AAGTTTAGGTACAAAATAAGAAAAAAAA
Found at i:30819908 original size:2 final size:2
Alignment explanation
Indices: 30819901--30819929 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30819891 TTTATGAAGT
30819901 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 T
30819930 TTTATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30822325 original size:25 final size:25
Alignment explanation
Indices: 30822291--30822340 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
30822281 TTAATAGTTT
30822291 AGGTTTGAGTTTCACCGTGTACAAA
1 AGGTTTGAGTTTCACCGTGTACAAA
*
30822316 AGGTTTGAGTTTCGCCGTGTACAAA
1 AGGTTTGAGTTTCACCGTGTACAAA
30822341 TGCTATGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (25 bp):
AGGTTTGAGTTTCACCGTGTACAAA
Found at i:30825199 original size:4 final size:4
Alignment explanation
Indices: 30825190--30825216 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
30825180 TCTTGATCTG
30825190 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
30825217 TTACATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:30825317 original size:3 final size:3
Alignment explanation
Indices: 30825311--30825339 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30825301 TATTATTATT
30825311 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
30825340 TATTATTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:30832496 original size:23 final size:21
Alignment explanation
Indices: 30832465--30832507 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
30832455 CTATCTCAGT
30832465 AAGAAATTCACTGAATGTGAGAC
1 AAGAAATTCACT-AAT-TGAGAC
*
30832488 AAGATATTCACTAATTGAGA
1 AAGAAATTCACTAATTGAGA
30832508 AGTAGTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.26
Consensus pattern (21 bp):
AAGAAATTCACTAATTGAGAC
Found at i:30834290 original size:44 final size:45
Alignment explanation
Indices: 30834195--30834328 Score: 144
Period size: 44 Copynumber: 3.0 Consensus size: 45
30834185 ACAGGACAGA
* * *
30834195 ACAGAAATGAGCCATGTAAGCCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
30834241 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
30834285 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
30834329 CAGGATAATA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 36 0.49
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:30839194 original size:26 final size:26
Alignment explanation
Indices: 30839165--30839216 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
30839155 TATTTCAGAG
30839165 TTTGTTTCTAGATGCTTGATTTGTCA
1 TTTGTTTCTAGATGCTTGATTTGTCA
30839191 TTTGTTTCTAGATGCTTGATTTGTCA
1 TTTGTTTCTAGATGCTTGATTTGTCA
30839217 ACAGGTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.12, G:0.19, T:0.54
Consensus pattern (26 bp):
TTTGTTTCTAGATGCTTGATTTGTCA
Found at i:30841673 original size:44 final size:45
Alignment explanation
Indices: 30841578--30841711 Score: 144
Period size: 44 Copynumber: 3.0 Consensus size: 45
30841568 ACAGGACAGA
* * *
30841578 ACAGAAATGAGCCATGTAAGCCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
30841624 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
30841668 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
30841712 CAGGATAATA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 36 0.49
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:30845495 original size:50 final size:48
Alignment explanation
Indices: 30845396--30845733 Score: 207
Period size: 50 Copynumber: 7.1 Consensus size: 48
30845386 TAGTGGGACG
* * * * *
30845396 GATTGAAGTTATAATGGCAAATCTTATCTTCCTAAAGTTGTAGTAGAGCA
1 GATTGAAGTTATCA--GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * *
30845446 TATTGAAGTTATCATGGCGAATCTTATCTCCCTGAAGTTGCATTGGAGCA
1 GATTGAAGTTATCA--GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * * * *
30845496 TATTAAAG---CCA-CTAATCTCATCTCCCTAAAGTTGCAGTGGAGTA
1 GATTGAAGTTATCAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
** ** *
30845540 GATTGAAGTTATCATGGTGAATCTTATCTCTTTGAAGTTGCAGTGGAGTA
1 GATTGAAGTTATCA--GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * *
30845590 GGTTAAAG---CCA-CAAATCTTATCTCCCTGAAGTTGCAATGGAGCA
1 GATTGAAGTTATCAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * * * * *
30845634 AATTGAAG---CCA-CAAATCTTATCT-CTTAAAGTTACAATAGAGCT
1 GATTGAAGTTATCAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* *
30845677 TATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCA
1 GATTGAAGTTAT--CAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
30845727 GATTGAA
1 GATTGAA
30845734 ACCACAAAAC
Statistics
Matches: 226, Mismatches: 49, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
43 22 0.10
44 81 0.36
47 6 0.03
48 2 0.01
49 12 0.05
50 103 0.46
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (48 bp):
GATTGAAGTTATCAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
Found at i:30845545 original size:94 final size:94
Alignment explanation
Indices: 30845413--30845641 Score: 305
Period size: 94 Copynumber: 2.4 Consensus size: 94
30845403 GTTATAATGG
* * * *
30845413 CAAATCTTATCTTCCTAAAGTTGTAGTAGAGCATATTGAAGTTATCATGGCGAATCTTATCTCCC
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGTTATCATGGCGAATCTTATCTCCC
* *
30845478 TGAAGTTGCATTGGAGCATATTAAAGCCA
66 TGAAGTTGCAGTGGAGCAGATTAAAGCCA
* * * * * **
30845507 CTAATCTCATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGTTATCATGGTGAATCTTATCTCTT
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGTTATCATGGCGAATCTTATCTCCC
* *
30845572 TGAAGTTGCAGTGGAGTAGGTTAAAGCCA
66 TGAAGTTGCAGTGGAGCAGATTAAAGCCA
* *
30845601 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAG
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAG
30845642 CCACAAATCT
Statistics
Matches: 115, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
94 115 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (94 bp):
CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGTTATCATGGCGAATCTTATCTCCC
TGAAGTTGCAGTGGAGCAGATTAAAGCCA
Found at i:30845622 original size:44 final size:44
Alignment explanation
Indices: 30845465--30845765 Score: 212
Period size: 44 Copynumber: 6.6 Consensus size: 44
30845455 TATCATGGCG
* * *
30845465 AATCTTATCTCCCTGAAGTTGCATTGGAGCATATTAAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * * **
30845509 AATCTCATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGTTATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CA
** * *
30845554 TGGTGAATCTTATCTCTTTGAAGTTGCAGTGGAGTAGGTTAAAGCCACA
1 -----AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * *
30845603 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * * * ** *
30845647 AATCTTATCT-CTTAAAGTTACAATAGAGCTTATTGAAGTTATCACAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA---AGC-CA-CA
*
30845696 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAA-CCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCCACA
* * *
30845740 AAACTTATCTCCC-AAAGTTGTAGTGG
1 AATCTTATCTCCCTGAAGTTGCAGTGG
30845766 GATGGATTGA
Statistics
Matches: 202, Mismatches: 42, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
43 29 0.14
44 95 0.47
45 3 0.01
46 1 0.00
47 3 0.01
48 2 0.01
49 14 0.07
50 55 0.27
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
Found at i:30845723 original size:137 final size:138
Alignment explanation
Indices: 30845465--30845752 Score: 375
Period size: 137 Copynumber: 2.1 Consensus size: 138
30845455 TATCATGGCG
* * * *
30845465 AATCTTATCTCCCTGAAGTTGCATTGGAGCATATTAAAGCCACTAATCTCATCTCCCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAGCCACAAATCTCATCTCCCTAAAGTTA
* * ** ** * * *
30845530 CAGTGGAGTAGATTGAAGTTATCATGGTGAATCTTATCTCTTTGAAGTTGCAGTGGAGTAGGTT-
66 CAATAGAGTAGATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTG
30845594 AAAGCCACA
131 AAA-CCACA
* * *
30845603 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACAAATCTTATCT-CTTAAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAGCCACAAATCTCATCTCCCTAAAGTTA
*
30845667 CAATAGAGCT-TATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATT
66 CAATAGAG-TAGATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATT
30845731 GAAACCACA
130 GAAACCACA
*
30845740 AAACTTATCTCCC
1 AATCTTATCTCCC
30845753 AAAGTTGTAG
Statistics
Matches: 130, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
137 77 0.59
138 53 0.41
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (138 bp):
AATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAGCCACAAATCTCATCTCCCTAAAGTTA
CAATAGAGTAGATTGAAGTTATCACAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTG
AAACCACA
Found at i:30845775 original size:93 final size:93
Alignment explanation
Indices: 30845600--30845798 Score: 222
Period size: 93 Copynumber: 2.1 Consensus size: 93
30845590 GGTTAAAGCC
* * **
30845600 ACAAATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAGCCACAAATCTTATCTCTTAAAGT
1 ACAAATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAACCACAAAACTTATCTCCCAAAGT
* * *
30845665 TACAATAGAGCTTATTGAAGTTATCACAG
66 TACAATAGAGATGATTGAAATTATCA-AG
* * *
30845694 -CAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAACCACAAAACTTATCTCCCAAAGT
1 ACAAATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAACCACAAAACTTATCTCCCAAAGT
** * * *
30845758 TGTAGT-GGGATGGATTGAAATTATTAAG
66 TACAATAGAGAT-GATTGAAATTATCAAG
*
30845786 ACGAATCTTATCT
1 ACAAATCTTATCT
30845799 GAAGCAGATT
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
92 5 0.06
93 82 0.94
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (93 bp):
ACAAATCTTATCTCCCTGAAGTTGCAATGGAGCAAATTGAAACCACAAAACTTATCTCCCAAAGT
TACAATAGAGATGATTGAAATTATCAAG
Found at i:30845870 original size:79 final size:78
Alignment explanation
Indices: 30845723--30845875 Score: 227
Period size: 79 Copynumber: 1.9 Consensus size: 78
30845713 GTTGCAGTGG
* * * *
30845723 AGCAGATTGAAACCACAAAACTTATCTCCCAAAGTTGTAGTGGGATGGATTGAAATTATTAAGAC
1 AGCAGATTGAAACCACAAAACCTATCTCCCAAAGTTGCAGTGGGATGGATTAAAATCATTAAGAC
30845788 GAATCTTATCTGA
66 GAATCTTATCTGA
* *
30845801 AGCAGATTGAAACCACAAATCCTATCTCCCTGAAGTTGCAGTGGGATGGATTAAAATCATTAA-A
1 AGCAGATTGAAACCACAAAACCTATCTCCC-AAAGTTGCAGTGGGATGGATTAAAATCATTAAGA
30845865 GCGAATCTTAT
65 -CGAATCTTAT
30845876 ATCCCTGAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
78 29 0.43
79 38 0.57
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (78 bp):
AGCAGATTGAAACCACAAAACCTATCTCCCAAAGTTGCAGTGGGATGGATTAAAATCATTAAGAC
GAATCTTATCTGA
Found at i:30845971 original size:44 final size:44
Alignment explanation
Indices: 30845902--30846046 Score: 150
Period size: 44 Copynumber: 3.3 Consensus size: 44
30845892 TAGAATAGAT
* *
30845902 TAAAGCTATAAA-CTTTATCTTCTTGAAGATGCAGTGGAGCAGGA
1 TAAAGCTACAAATC-TTATCTACTTGAAGATGCAGTGGAGCAGGA
* * * * *
30845946 TAAAGTTACTAATCTTATCTCCTTGAAGATACAGTGGAGCA-AA
1 TAAAGCTACAAATCTTATCTACTTGAAGATGCAGTGGAGCAGGA
* * * *
30845989 TTGAGGCTACAAATCTTATCTACTTGAAGTTGCAGTGGAGCAGGT
1 -TAAAGCTACAAATCTTATCTACTTGAAGATGCAGTGGAGCAGGA
*
30846034 TAAAGCGACAAAT
1 TAAAGCTACAAAT
30846047 TATATACCTT
Statistics
Matches: 80, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
43 1 0.01
44 78 0.98
45 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (44 bp):
TAAAGCTACAAATCTTATCTACTTGAAGATGCAGTGGAGCAGGA
Found at i:30847685 original size:3 final size:3
Alignment explanation
Indices: 30847677--30847701 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30847667 TGTTTACACA
30847677 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
30847702 GACCATTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:30858076 original size:38 final size:38
Alignment explanation
Indices: 30858020--30858099 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
30858010 GATGTGTATT
* * *
30858020 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
*
30858058 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
30858096 CGGG
1 CGGG
30858100 CCTTCGTGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:30858146 original size:43 final size:43
Alignment explanation
Indices: 30858071--30858259 Score: 256
Period size: 43 Copynumber: 4.4 Consensus size: 43
30858061 GATAAATCCC
* * * * *
30858071 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCTTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCTGGCCTTCGTGCCTA
* * *
30858112 GCAGGCTTGGTGCCGGTGATGTGTATTTTGGCCTTCTTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCTGGCCTTCGTGCCTA
*
30858155 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCTGGCCTTCGTGCCTA
*
30858198 GCAGGCTTCGTGCCGGTGATGTGTATTCTGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCTGGCCTTCGTGCCTA
* *
30858241 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
30858260 AATGATATGT
Statistics
Matches: 129, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
41 14 0.11
42 2 0.02
43 113 0.88
ACGTcount: A:0.12, C:0.23, G:0.33, T:0.32
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCTGGCCTTCGTGCCTA
Found at i:30859854 original size:31 final size:32
Alignment explanation
Indices: 30859813--30859881 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
30859803 TTGGCATAAT
* * *
30859813 TGTAACTTTAATT-ATCAATATTTATACATTA
1 TGTAATTTTAATTCATCAATATTAACACATTA
* *
30859844 TGTAATTTTAATTCCTCAATGTTAACACATTA
1 TGTAATTTTAATTCATCAATATTAACACATTA
30859876 TGTAAT
1 TGTAAT
30859882 AATTTACTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (32 bp):
TGTAATTTTAATTCATCAATATTAACACATTA
Found at i:30861990 original size:39 final size:39
Alignment explanation
Indices: 30861931--30862023 Score: 159
Period size: 39 Copynumber: 2.4 Consensus size: 39
30861921 AAAATTAGTA
* *
30861931 ATTTTTCTCAACTGATACAAAGAAATCCAACATTTTGCTC
1 ATTTTTC-AAACTTATACAAAGAAATCCAACATTTTGCTC
30861971 ATTTTTCAAACTTATACAAAGAAATCCAACATTTTGCTC
1 ATTTTTCAAACTTATACAAAGAAATCCAACATTTTGCTC
30862010 ATTTTTCAAACTTA
1 ATTTTTCAAACTTA
30862024 CATTTCTCAC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 44 0.86
40 7 0.14
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (39 bp):
ATTTTTCAAACTTATACAAAGAAATCCAACATTTTGCTC
Found at i:30863358 original size:31 final size:31
Alignment explanation
Indices: 30863322--30863381 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
30863312 GTAACTTTTC
30863322 ATAATTTAG-TGACTAAAAATAAAATTTATTA
1 ATAA-TTAGATGACTAAAAATAAAATTTATTA
** *
30863353 ATAATTAGATGACTACTAATATAATTTAT
1 ATAATTAGATGACTAAAAATAAAATTTAT
30863382 CCATTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (31 bp):
ATAATTAGATGACTAAAAATAAAATTTATTA
Found at i:30865915 original size:17 final size:17
Alignment explanation
Indices: 30865872--30865916 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
30865862 GTATTTTTCA
*
30865872 TAATATATTATAATATT
1 TAATATTTTATAATATT
*
30865889 TAATAAATTTTATAATTTT
1 TAAT--ATTTTATAATATT
30865908 TAATATTTT
1 TAATATTTT
30865917 TCTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.38
19 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATATTTTATAATATT
Found at i:30869323 original size:19 final size:19
Alignment explanation
Indices: 30869299--30869338 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
30869289 AGAGAATAAG
30869299 GAGAAGAATAGGAGAAGGA
1 GAGAAGAATAGGAGAAGGA
30869318 GAGAAGAATAGGAGAAGGA
1 GAGAAGAATAGGAGAAGGA
30869337 GA
1 GA
30869339 ATGAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.05
Consensus pattern (19 bp):
GAGAAGAATAGGAGAAGGA
Found at i:30872284 original size:25 final size:25
Alignment explanation
Indices: 30872251--30872326 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
30872241 TACCTATTTG
30872251 TTTA-TTAATATTATATAATATATA
1 TTTACTTAATATTATATAATATATA
* *
30872275 TTTACTTAATAATTAAGATAACATAT-
1 TTTACTTAAT-ATT-ATATAATATATA
*
30872301 TTTATCTTTA-ATTATTATAATATATA
1 TTTA-CTTAATATTA-TATAATATATA
30872327 AAATAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 5 0.12
25 16 0.39
26 7 0.17
27 13 0.32
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (25 bp):
TTTACTTAATATTATATAATATATA
Found at i:30874565 original size:7 final size:7
Alignment explanation
Indices: 30874545--30874576 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
30874535 TTGTGTATAG
30874545 ATAAATA
1 ATAAATA
30874552 A-AAATA
1 ATAAATA
30874558 ATAAATA
1 ATAAATA
30874565 ATAAATA
1 ATAAATA
30874572 ATAAA
1 ATAAA
30874577 AAAAGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
ATAAATA
Found at i:30875465 original size:19 final size:17
Alignment explanation
Indices: 30875439--30875492 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
30875429 TTATAAATAT
30875439 TAGTATATATTTATTACA
1 TAGTATATATTTATTA-A
*
30875457 TATGTATATATCT-TTAA
1 TA-GTATATATTTATTAA
30875474 TA-TATATATTTATGTAA
1 TAGTATATATTTAT-TAA
30875491 TA
1 TA
30875493 TTATTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 8 0.26
16 1 0.03
17 8 0.26
18 5 0.16
19 9 0.29
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.52
Consensus pattern (17 bp):
TAGTATATATTTATTAA
Found at i:30875491 original size:17 final size:16
Alignment explanation
Indices: 30875442--30875493 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
30875432 TAAATATTAG
30875442 TATATATTTATTACATA
1 TATATATTTATTA-ATA
*
30875459 TGTATATATCT-TTAATA
1 --TATATATTTATTAATA
30875476 TATATATTTATGTAATA
1 TATATATTTAT-TAATA
30875493 T
1 T
30875494 TATTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 8 0.28
16 1 0.03
17 9 0.31
18 3 0.10
19 8 0.28
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (16 bp):
TATATATTTATTAATA
Found at i:30875800 original size:18 final size:18
Alignment explanation
Indices: 30875765--30875801 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30875755 CTAATATGTA
*
30875765 TATATTATGTAAATATAT
1 TATATTATGTAAACATAT
*
30875783 TATATTATGTATACATAT
1 TATATTATGTAAACATAT
30875801 T
1 T
30875802 TTTATATATT
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:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATTATGTAAACATAT
Found at i:30875817 original size:23 final size:24
Alignment explanation
Indices: 30875783--30875834 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
30875773 GTAAATATAT
*
30875783 TATATTATGTATACATAT-TTTTA
1 TATATTACGTATACATATCTTTTA
*
30875806 TATATTACGTATATATATCTTTTA
1 TATATTACGTATACATATCTTTTA
30875830 -ATATT
1 TATATT
30875835 GTATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TATATTACGTATACATATCTTTTA
Found at i:30875862 original size:36 final size:36
Alignment explanation
Indices: 30875793--30875885 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
30875783 TATATTATGT
*
30875793 ATAC-ATATTTTTATATATTACGTATATATATCTTTTA
1 ATACTATATTTTTATATATTAC-TATATACATC-TTTA
* * * *
30875830 ATATTGTATTTTTATATGTTA-TGTATACATCTTTA
1 ATACTATATTTTTATATATTACTATATACATCTTTA
30875865 ATACTATATTATTTATATATT
1 ATACTATATT-TTTATATATT
30875886 TTTTATTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
35 12 0.26
36 17 0.37
37 3 0.07
38 14 0.30
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (36 bp):
ATACTATATTTTTATATATTACTATATACATCTTTA
Found at i:30876063 original size:28 final size:27
Alignment explanation
Indices: 30876012--30876065 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
30876002 TCCTAGTATG
*
30876012 TATACATTTTTTAAATACTATATTATA
1 TATACATTTTTTAAATACCATATTATA
* *
30876039 TATATATTTTTTAAAATACCGTATTAT
1 TATACATTTTTT-AAATACCATATTAT
30876066 GTACATGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (27 bp):
TATACATTTTTTAAATACCATATTATA
Found at i:30876420 original size:9 final size:9
Alignment explanation
Indices: 30876343--30876450 Score: 53
Period size: 9 Copynumber: 11.7 Consensus size: 9
30876333 GCTTTAATAC
30876343 ATATATGTAT
1 ATATAT-TAT
30876353 ATAT-TTAT
1 ATATATTAT
*
30876361 GTAGTATTAT
1 ATA-TATTAT
30876371 -TA-ATATAT
1 ATATAT-TAT
*
30876379 ATATATTTT
1 ATATATTAT
*
30876388 ATGTTATTAGT
1 AT-ATATTA-T
* * *
30876399 ATTTCTAAT
1 ATATATTAT
*
30876408 ATATTTTAT
1 ATATATTAT
30876417 ATATATTAT
1 ATATATTAT
*
30876426 GTATA-TAT
1 ATATATTAT
30876434 ATATCATGTAT
1 ATAT-AT-TAT
30876445 ATATAT
1 ATATAT
30876451 ATTTAGTATT
Statistics
Matches: 76, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
7 2 0.03
8 14 0.18
9 30 0.39
10 20 0.26
11 10 0.13
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (9 bp):
ATATATTAT
Found at i:30876420 original size:11 final size:13
Alignment explanation
Indices: 30876406--30876468 Score: 62
Period size: 13 Copynumber: 4.9 Consensus size: 13
30876396 AGTATTTCTA
30876406 ATATATT-T-TAT
1 ATATATTATGTAT
30876417 ATATATTATGTAT
1 ATATATTATGTAT
30876430 ATATATATCATGTAT
1 ATATAT-T-ATGTAT
*
30876445 ATATA-TATTTAGT
1 ATATATTATGTA-T
30876458 AT-TATTATGTA
1 ATATATTATGTA
30876469 GACACTTCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
11 7 0.16
12 7 0.16
13 18 0.41
14 1 0.02
15 11 0.25
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (13 bp):
ATATATTATGTAT
Found at i:30876459 original size:15 final size:15
Alignment explanation
Indices: 30876414--30876453 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
30876404 TAATATATTT
30876414 TATATATATTATGTA
1 TATATATATTATGTA
*
30876429 TATATATATCATGTA
1 TATATATATTATGTA
30876444 TATATATATT
1 TATATATATT
30876454 TAGTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (15 bp):
TATATATATTATGTA
Found at i:30880281 original size:22 final size:23
Alignment explanation
Indices: 30880255--30880310 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
30880245 TATTCATGAC
*
30880255 TACATTCATTCGTCATTTATTCA
1 TACATTCATTCGTCATTCATTCA
*
30880278 -ACATTCATTTGTCATTCATTCA
1 TACATTCATTCGTCATTCATTCA
*
30880300 TTCATTCATTC
1 TACATTCATTC
30880311 ATTCATTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.25, C:0.23, G:0.04, T:0.48
Consensus pattern (23 bp):
TACATTCATTCGTCATTCATTCA
Found at i:30880296 original size:4 final size:4
Alignment explanation
Indices: 30880289--30880317 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
30880279 CATTCATTTG
30880289 TCAT TCAT TCAT TCAT TCAT TCAT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT T
30880318 GCATGTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:30888864 original size:74 final size:74
Alignment explanation
Indices: 30888624--30888923 Score: 331
Period size: 74 Copynumber: 4.0 Consensus size: 74
30888614 TTTGTGTTAC
* * * * *
30888624 AAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCAAGACATGCTGAGGTATTTTCAATTTC
*
30888689 TATCTTTCAAAA
66 T-TTTTTC--AA
* *
30888701 AAAAATCAACTCATATTGCGAA-AGGTGAGTTGAGCCTTAAGAC--GCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGC-AAGAGGTGAGTTGAACCTCAAGACATGCTGAGGTATTTTCAATTT
30888763 CTTTTTTGCAA
65 CTTTTTT-CAA
* ** *
30888774 AAAAATCAACTCATATTGTAAGAGGTGAGTTGAACCTCGGGACATGCTGAAGTA-TTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCAAGACATGCTGAGGTATTTTCAATTTC
*
30888838 TGCTTTTC-A
66 T-TTTTTCAA
* ** * *
30888847 AAAAATCAAGCTCATATTGCGAGAGGTGAGTTGAACCTCGGGACATGCTGAGGCATTTTCAGTTT
1 AAAAATCAA-CTCATATTGCAAGAGGTGAGTTGAACCTCAAGACATGCTGAGGTATTTTCAATTT
30888912 CTGTTTTTCAA
65 CT-TTTTTCAA
30888923 A
1 A
30888924 TTTTATTTTT
Statistics
Matches: 196, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
72 2 0.01
73 47 0.24
74 57 0.29
75 49 0.25
76 2 0.01
77 38 0.19
78 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (74 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCAAGACATGCTGAGGTATTTTCAATTTC
TTTTTTCAA
Found at i:30890840 original size:3 final size:3
Alignment explanation
Indices: 30890824--30890895 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
30890814 TTTACCATTT
** *
30890824 TTA TTA TT- TT- TTA TTA TTA -TA TTTA CCA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* * *
30890867 TTA TTA TTA GTA -TA TTT TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30890896 GAATTATTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
2 8 0.15
3 44 0.81
4 2 0.04
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:30890891 original size:20 final size:21
Alignment explanation
Indices: 30890857--30890906 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
30890847 TACCATTATC
* * *
30890857 ATTATTATTATTATTATTAGT
1 ATTATTTTTACTATTATTAGA
30890878 A-TATTTTTACTATTATTAGA
1 ATTATTTTTACTATTATTAGA
30890898 ATTATTTTT
1 ATTATTTTT
30890907 TTTAGTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTATTTTTACTATTATTAGA
Found at i:30891467 original size:25 final size:28
Alignment explanation
Indices: 30891434--30891488 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 28
30891424 CTAATATGTA
30891434 TATACTATGTA-A-ATATCTTTA-ATAT
1 TATACTATGTATACATATCTTTATATAT
* *
30891459 TATATTATGTATACATATTTTTATATAT
1 TATACTATGTATACATATCTTTATATAT
30891487 TA
1 TA
30891489 CGTATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.40
26 1 0.04
27 8 0.32
28 6 0.24
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (28 bp):
TATACTATGTATACATATCTTTATATAT
Found at i:30891487 original size:23 final size:24
Alignment explanation
Indices: 30891459--30891510 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
30891449 TCTTTAATAT
*
30891459 TATATTATGTATACATAT-TTTTA
1 TATATTACGTATACATATCTTTTA
*
30891482 TATATTACGTATATATATCTTTTA
1 TATATTACGTATACATATCTTTTA
30891506 -ATATT
1 TATATT
30891511 GTATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TATATTACGTATACATATCTTTTA
Found at i:30891538 original size:36 final size:36
Alignment explanation
Indices: 30891469--30891561 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
30891459 TATATTATGT
*
30891469 ATAC-ATATTTTTATATATTACGTATATATATCTTTTA
1 ATACTATATTTTTATATATTAC-TATATACATC-TTTA
* * * *
30891506 ATATTGTATTTTTATATGTTA-TGTATACATCTTTA
1 ATACTATATTTTTATATATTACTATATACATCTTTA
30891541 ATACTATATTATTTATATATT
1 ATACTATATT-TTTATATATT
30891562 TTTTATTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
35 12 0.26
36 17 0.37
37 3 0.07
38 14 0.30
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (36 bp):
ATACTATATTTTTATATATTACTATATACATCTTTA
Found at i:30892013 original size:21 final size:20
Alignment explanation
Indices: 30891973--30892035 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 20
30891963 ATAATAATAA
30891973 TTATTAT-TA-GTATAT-GT
1 TTATTATATATGTATATAGT
30891990 TTATTATATATGTATATAGCT
1 TTATTATATATGTATATAG-T
*
30892011 TTAATACATATATGTATATA-T
1 TT-AT-TATATATGTATATAGT
30892032 TTAT
1 TTAT
30892036 GTAGTATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 7 0.18
18 2 0.05
19 6 0.15
20 3 0.08
21 6 0.15
22 2 0.05
23 13 0.33
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
TTATTATATATGTATATAGT
Found at i:30892133 original size:15 final size:15
Alignment explanation
Indices: 30892088--30892127 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
30892078 TAATATAGTT
30892088 TATATATATTACGTA
1 TATATATATTACGTA
*
30892103 TATATATATTATGTA
1 TATATATATTACGTA
30892118 TATATATATT
1 TATATATATT
30892128 TAGTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (15 bp):
TATATATATTACGTA
Found at i:30896878 original size:33 final size:34
Alignment explanation
Indices: 30896836--30896903 Score: 129
Period size: 33 Copynumber: 2.0 Consensus size: 34
30896826 ATTTAAAAAT
30896836 AACATATAATAAATAAT-AAATATAAGGTTTGAA
1 AACATATAATAAATAATAAAATATAAGGTTTGAA
30896869 AACATATAATAAATAATAAAATATAAGGTTTGAA
1 AACATATAATAAATAATAAAATATAAGGTTTGAA
30896903 A
1 A
30896904 TGAATTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (34 bp):
AACATATAATAAATAATAAAATATAAGGTTTGAA
Found at i:30900339 original size:15 final size:15
Alignment explanation
Indices: 30900307--30900349 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
30900297 ATTAAATTTG
*
30900307 TAATATTAATTCTATT
1 TAATATT-ATTATATT
30900323 TAATATTATTATATT
1 TAATATTATTATATT
*
30900338 TACTATTATTAT
1 TAATATTATTAT
30900350 TTATAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATATTATTATATT
Found at i:30900394 original size:17 final size:16
Alignment explanation
Indices: 30900371--30900419 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
30900361 AGTGTACTTT
30900371 GTATGTATATATTATTA
1 GTATGTATATATT-TTA
*
30900388 TTATGTATAT-TTTTA
1 GTATGTATATATTTTA
30900403 GTATGTATATATATTTA
1 GTATGTATATAT-TTTA
30900420 TGAAGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.43
16 3 0.11
17 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
GTATGTATATATTTTA
Found at i:30900398 original size:15 final size:15
Alignment explanation
Indices: 30900378--30900417 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
30900368 TTTGTATGTA
*
30900378 TATATTATTATTATG
1 TATATTATTAGTATG
*
30900393 TATATTTTTAGTATG
1 TATATTATTAGTATG
30900408 TATATATATT
1 TATAT-TATT
30900418 TATGAAGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TATATTATTAGTATG
Found at i:30900500 original size:24 final size:24
Alignment explanation
Indices: 30900463--30900539 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
30900453 TATTCTTTAA
*
30900463 TATATTATGCATATATTTTAATAC
1 TATATTATACATATATTTTAATAC
*
30900487 TATATTATATATATACATTTT-ATAC
1 TATATTATACATAT--ATTTTAATAC
* * *
30900512 TAT-GTATACATA-CTTTTAATAT
1 TATATTATACATATATTTTAATAC
30900534 TATATT
1 TATATT
30900540 TCATATGTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
21 4 0.10
22 6 0.14
23 1 0.02
24 19 0.45
25 7 0.17
26 5 0.12
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.52
Consensus pattern (24 bp):
TATATTATACATATATTTTAATAC
Found at i:30913949 original size:251 final size:250
Alignment explanation
Indices: 30913495--30914141 Score: 860
Period size: 251 Copynumber: 2.5 Consensus size: 250
30913485 ATTCAAAAAT
* * * *
30913495 CAACTCATATTGCGAG-AGCTGAGTTGAGCCTCAGG-ACAC--GCTGAGGTAATTTCAATTTCTG
1 CAACTCATATTGCGAGAAG-TGAGTTGAGCCT-TGGCTCACGTGCTGAGCTATTTTCAATTTCTG
* *
30913556 TTTCTGCTTTTCAAACAAAATCAACTCATATTGCGAGAGGTGAGTTGA-AC-CTTGGCTCACATG
64 --TCTG--TTT---A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTC-AGG---ACACG
* *
30913619 CCGAGGTATTTTCAGTTTTATTTATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGA
117 CTGAGGTATTTTCA----AATTTATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGA
* * * *
30913684 GGTGAGTTGAGCCTCGGGTTGCATGACGAGGTATTTTCAAAAGCTACTTTTTAAATTAAGTTTCA
178 AGTGAGTTGAGCCTCGGGTTACATGACGAGGTATTTTCAAAAGCTACTTCTCAAATTAAGTTTCA
30913749 AAAAAGAC
243 AAAAAGAC
* *
30913757 CAACTCATATTGCTAGAAGTGAGTTGAGCCTTGGCTCACGTGTTGAGCTATTTTCAATTTCTGTC
1 CAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTGTC
30913822 TGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTCAGGACACGCTGAGGTATTTTC
66 TGTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTCAGGACACGCTGAGGTATTTTC
*
30913887 AAATTCTATTT-AATTTATACTTTTCAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTCG
130 AAATT-TATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCG
*
30913951 GGTTACATGACGAGGTATTTTCAAAAGTTACTTCTCAAATTAAGTTTCAAAAAAGAC
194 GGTTACATGACGAGGTATTTTCAAAAGCTACTTCTCAAATTAAGTTTCAAAAAAGAC
*
30914008 CAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTTACGTGCTGAGCTATTTTCAATTTCTGTC
1 CAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTGTC
** * * *
30914073 TGTTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCATGACACGTTGAGGTATTTT-A
66 TGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTCAGGACACGCTGAGGTATTTTCA
30914137 AATTT
131 AATTT
30914142 TTGTTTGTCA
Statistics
Matches: 353, Mismatches: 25, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
248 1 0.00
249 5 0.01
250 53 0.15
251 174 0.49
252 5 0.01
255 17 0.05
257 32 0.09
258 5 0.01
259 1 0.00
260 3 0.01
261 2 0.01
262 34 0.10
263 2 0.01
264 19 0.05
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (250 bp):
CAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTGTC
TGTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGACTCAGGACACGCTGAGGTATTTTCA
AATTTATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGG
TTACATGACGAGGTATTTTCAAAAGCTACTTCTCAAATTAAGTTTCAAAAAAGAC
Found at i:30914220 original size:73 final size:74
Alignment explanation
Indices: 30914008--30914220 Score: 245
Period size: 73 Copynumber: 2.9 Consensus size: 74
30913998 CAAAAAAGAC
* *
30914008 CAACTCATATTGCGAGAAGTGAGTTGAGCCTT-GG-CTTACGTGCTGAGCTATTTTCAATTTCTG
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGAC--AC--GCTGAGCTATTTTCAAATTCTG
* ***
30914071 TCTGTTTTTAAAT
62 TTTGTTCAAAAAT
* * * * *
30914084 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCATGACACGTTGAGGTATTTT-AAATTTTTGTTT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGCTATTTTCAAA-TTCTGTTT
30914148 G-TCAAAAAT
65 GTTCAAAAAT
*
30914157 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACACTGAGCTATTTTCAAATTCTGTTT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGCTATTTTCAAATTCTGTTT
30914221 AATTTATACT
Statistics
Matches: 116, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
73 61 0.53
74 21 0.18
76 32 0.28
77 1 0.01
78 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (74 bp):
CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGCTATTTTCAAATTCTGTTTG
TTCAAAAAT
Found at i:30914341 original size:89 final size:84
Alignment explanation
Indices: 30914149--30914360 Score: 250
Period size: 84 Copynumber: 2.5 Consensus size: 84
30914139 TTTTTGTTTG
* *
30914149 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACACTGAGCTATTTTCAAAT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACAATGAGCTATTTTCAAAT
* * *
30914214 TCTGTTTAATTTATACTTT
66 ACTGTTTAAATTATACGTT
* * * *
30914233 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATGATGAGGTATTTTCAA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA--ATGAGCTATTTTC-A
30914298 AACCTACT-TTTCAAATTA-A-GTT
63 AA--TACTGTTT-AAATTATACGTT
30914320 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
30914361 TAGCTCACGC
Statistics
Matches: 110, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
84 44 0.40
86 11 0.10
87 7 0.06
88 4 0.04
89 44 0.40
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (84 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACAATGAGCTATTTTCAAAT
ACTGTTTAAATTATACGTT
Found at i:30914386 original size:89 final size:86
Alignment explanation
Indices: 30914149--30914386 Score: 270
Period size: 89 Copynumber: 2.7 Consensus size: 86
30914139 TTTTTGTTTG
* *
30914149 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAG-GACACACTGAGCTATTTTC-AA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGTCACACGCTGAGCTATTTTCAAA
* * *
30914212 ATTCTGTTTAATTTATACTTT
66 ATACTGTTTAAATTATACGTT
* ** * * *
30914233 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATGATGAGGTATTTTCAA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TAGTCACACGCTGAGCTATTTTCAA
30914298 AACCTACT-TTTCAAATTA-A-GTT
65 AA--TACTGTTT-AAATTATACGTT
*
30914320 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGCGCTGAGCTATTTTC
1 TC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAG-TCACACGCTGAGCTATTTTC
30914385 AA
63 AA
30914387 TTTCTGTTTT
Statistics
Matches: 127, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
84 38 0.30
85 1 0.01
86 14 0.11
87 7 0.06
88 5 0.04
89 62 0.49
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (86 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGTCACACGCTGAGCTATTTTCAAA
ATACTGTTTAAATTATACGTT
Found at i:30916253 original size:15 final size:15
Alignment explanation
Indices: 30916221--30916263 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
30916211 ATTAAATTTG
*
30916221 TAATATTAATTCTATT
1 TAATATT-ATTATATT
30916237 TAATATTATTATATT
1 TAATATTATTATATT
*
30916252 TACTATTATTAT
1 TAATATTATTAT
30916264 TTATAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATATTATTATATT
Found at i:30916308 original size:17 final size:16
Alignment explanation
Indices: 30916285--30916333 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
30916275 AGTGTACTTT
30916285 GTATGTATATATTATTA
1 GTATGTATATATT-TTA
*
30916302 TTATGTATAT-TTTTA
1 GTATGTATATATTTTA
30916317 GTATGTATATATATTTA
1 GTATGTATATAT-TTTA
30916334 TGAAGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.43
16 3 0.11
17 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
GTATGTATATATTTTA
Found at i:30916312 original size:15 final size:15
Alignment explanation
Indices: 30916292--30916331 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
30916282 TTTGTATGTA
*
30916292 TATATTATTATTATG
1 TATATTATTAGTATG
*
30916307 TATATTTTTAGTATG
1 TATATTATTAGTATG
30916322 TATATATATT
1 TATAT-TATT
30916332 TATGAAGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TATATTATTAGTATG
Found at i:30922105 original size:2 final size:2
Alignment explanation
Indices: 30922098--30922133 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30922088 AGTATAATAC
30922098 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
30922134 TAAAAATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30923961 original size:2 final size:2
Alignment explanation
Indices: 30923954--30923987 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30923944 TTTCTTTTTC
30923954 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
30923988 GAATTAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30926728 original size:54 final size:54
Alignment explanation
Indices: 30926642--30926747 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
30926632 ATGAAGAAAC
* *
30926642 TGGACGTTTCCAAGAATCCCAGTTCAACGAAACTCCGTTTCAGGAGATCAACGG
1 TGGACGTGTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAACGG
* *
30926696 TGGACGTGTCCAAGAATCCCAGTTCCAGGAAACTCCATTTCAGGAGATCAAC
1 TGGACGTGTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAAC
30926748 AACGTCAACA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (54 bp):
TGGACGTGTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAACGG
Found at i:30926793 original size:3 final size:3
Alignment explanation
Indices: 30926780--30926809 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
30926770 AGATCAAGGT
30926780 AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
30926810 TGAACCAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:30926851 original size:36 final size:36
Alignment explanation
Indices: 30926811--30926880 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
30926801 GAAGAAGAAT
*
30926811 GAACCAGAAGTGAGGACTTTTCATTCTATAGGGAAA
1 GAACCAGAAGTGAGGACTTTTCACTCTATAGGGAAA
*
30926847 GAACCAGAAGTGAGGACTTTTCACTCTGTAGGGA
1 GAACCAGAAGTGAGGACTTTTCACTCTATAGGGA
30926881 CTGGAACTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (36 bp):
GAACCAGAAGTGAGGACTTTTCACTCTATAGGGAAA
Found at i:30933138 original size:29 final size:28
Alignment explanation
Indices: 30933074--30933135 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
30933064 TCTATTTTAT
* * *
30933074 TAAATACATAATTTAATTTAACTTTAGTT
1 TAAATATAT-ATTTAATTTAACTTTAATA
30933103 TAAATATATATTTAAATTTAACTATTAATA
1 TAAATATATATTT-AATTTAACT-TTAATA
30933133 TAA
1 TAA
30933136 TATGATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 17 0.61
30 7 0.25
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (28 bp):
TAAATATATATTTAATTTAACTTTAATA
Found at i:30935373 original size:4 final size:4
Alignment explanation
Indices: 30935360--30935395 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
30935350 TGTTCATATA
* *
30935360 TATG TGTG TATG TATG CATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
30935396 CAACTATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:30935419 original size:28 final size:28
Alignment explanation
Indices: 30935388--30935446 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
30935378 TGTATGTATG
30935388 TATGTATGCAACTATTAATCTTTACAAA
1 TATGTATGCAACTATTAATCTTTACAAA
30935416 TATGTATGCAACTATTAATCTTTACAAA
1 TATGTATGCAACTATTAATCTTTACAAA
30935444 TAT
1 TAT
30935447 ATGCATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (28 bp):
TATGTATGCAACTATTAATCTTTACAAA
Found at i:30941848 original size:2 final size:2
Alignment explanation
Indices: 30941841--30941866 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30941831 AATTGATTTC
30941841 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
30941867 TACTTTATTT
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):
AT
Found at i:30943766 original size:24 final size:24
Alignment explanation
Indices: 30943739--30943788 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
30943729 ACCACCAACT
* *
30943739 CCACTTTCGTATCCGGATCCAGAC
1 CCACTTTCATATCCAGATCCAGAC
30943763 CCACTTTCATATCCAGATCCAGAC
1 CCACTTTCATATCCAGATCCAGAC
30943787 CC
1 CC
30943789 TTCTCCACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.24
Consensus pattern (24 bp):
CCACTTTCATATCCAGATCCAGAC
Found at i:30943816 original size:15 final size:15
Alignment explanation
Indices: 30943798--30943826 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30943788 CTTCTCCACT
30943798 GCCACCACCTCCGCC
1 GCCACCACCTCCGCC
30943813 GCCACCACCTCCGC
1 GCCACCACCTCCGC
30943827 TACCACCGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.66, G:0.14, T:0.07
Consensus pattern (15 bp):
GCCACCACCTCCGCC
Found at i:30943832 original size:15 final size:15
Alignment explanation
Indices: 30943799--30943833 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30943789 TTCTCCACTG
*
30943799 CCACCACCTCCGCCG
1 CCACCACCTCCGCCA
*
30943814 CCACCACCTCCGCTA
1 CCACCACCTCCGCCA
30943829 CCACC
1 CCACC
30943834 GCCACCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.66, G:0.09, T:0.09
Consensus pattern (15 bp):
CCACCACCTCCGCCA
Found at i:30943912 original size:36 final size:35
Alignment explanation
Indices: 30943865--30943974 Score: 157
Period size: 36 Copynumber: 3.1 Consensus size: 35
30943855 TATGCCACCA
**
30943865 CCAGACCCATACCCCGATTCCGATCCTGACTTATAC
1 CCAGACCCATACCCCGA-TCCGATCCTGACCCATAC
* *
30943901 CCAGACCCATACCCTGATCTAGATCCTGACCCATAC
1 CCAGACCCATACCCCGATC-CGATCCTGACCCATAC
30943937 CCAGACCCATACCCCGATCCGGATCCTGACCCATAC
1 CCAGACCCATACCCCGATCC-GATCCTGACCCATAC
30943973 CC
1 CC
30943975 TGATCCTTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 2 0.03
36 64 0.97
ACGTcount: A:0.25, C:0.45, G:0.12, T:0.18
Consensus pattern (35 bp):
CCAGACCCATACCCCGATCCGATCCTGACCCATAC
Found at i:30943914 original size:12 final size:12
Alignment explanation
Indices: 30943897--30943950 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
30943887 ATCCTGACTT
30943897 ATACCCAGACCC
1 ATACCCAGACCC
* * *
30943909 ATACCCTGATCT
1 ATACCCAGACCC
* * *
30943921 AGATCCTGACCC
1 ATACCCAGACCC
30943933 ATACCCAGACCC
1 ATACCCAGACCC
30943945 ATACCC
1 ATACCC
30943951 CGATCCGGAT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.30, C:0.44, G:0.09, T:0.17
Consensus pattern (12 bp):
ATACCCAGACCC
Found at i:30944005 original size:24 final size:24
Alignment explanation
Indices: 30943979--30944055 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
30943969 ATACCCTGAT
* *
30943979 CCTTCACCCCCACCACCACCACCT
1 CCTTCACCCCCACCACCACCTCCA
* *
30944003 CCTTCACCCCCTCCCCCACCTCCA
1 CCTTCACCCCCACCACCACCTCCA
* * *
30944027 CCTCCACCTCCACCTCCACCTCCA
1 CCTTCACCCCCACCACCACCTCCA
30944051 CCTTC
1 CCTTC
30944056 TCCAAGACCA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.17
Consensus pattern (24 bp):
CCTTCACCCCCACCACCACCTCCA
Found at i:30944027 original size:6 final size:6
Alignment explanation
Indices: 30944018--30944053 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
30944008 ACCCCCTCCC
30944018 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
30944054 TCTCCAAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CCACCT
Found at i:30944028 original size:18 final size:18
Alignment explanation
Indices: 30943983--30944052 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 18
30943973 CCTGATCCTT
* * *
30943983 CACCCCCACCACCACCAC
1 CACCTCCACCCCCACCCC
* * *
30944001 CTCCTTCACCCCCTCCCC
1 CACCTCCACCCCCACCCC
* *
30944019 CACCTCCACCTCCACCTC
1 CACCTCCACCCCCACCCC
*
30944037 CACCTCCACCTCCACC
1 CACCTCCACCCCCACC
30944053 TTCTCCAAGA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.17, C:0.70, G:0.00, T:0.13
Consensus pattern (18 bp):
CACCTCCACCCCCACCCC
Found at i:30944159 original size:15 final size:15
Alignment explanation
Indices: 30944141--30944181 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
30944131 GGCACCACCC
*
30944141 CCTCCGCCACCTCCA
1 CCTCCACCACCTCCA
* *
30944156 CCTCCACCACTTCCT
1 CCTCCACCACCTCCA
30944171 CCTCCACCACC
1 CCTCCACCACC
30944182 ACTAAGTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.15, C:0.66, G:0.02, T:0.17
Consensus pattern (15 bp):
CCTCCACCACCTCCA
Found at i:30944171 original size:18 final size:18
Alignment explanation
Indices: 30944150--30944184 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30944140 CCCTCCGCCA
*
30944150 CCTCCACCTCCACCACTT
1 CCTCCACCACCACCACTT
*
30944168 CCTCCTCCACCACCACT
1 CCTCCACCACCACCACT
30944185 AAGTGACCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.63, G:0.00, T:0.20
Consensus pattern (18 bp):
CCTCCACCACCACCACTT
Found at i:30950612 original size:13 final size:13
Alignment explanation
Indices: 30950594--30950620 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30950584 AAAAAAGTAG
30950594 AACAGAAGTTTGA
1 AACAGAAGTTTGA
30950607 AACAGAAGTTTGA
1 AACAGAAGTTTGA
30950620 A
1 A
30950621 CAAGGTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
AACAGAAGTTTGA
Found at i:30952054 original size:4 final size:4
Alignment explanation
Indices: 30952045--30952092 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
30952035 TATATAGTTG
*
30952045 ATTT ATTT ATTT A-TT ATTT ATTT CTTT -TTGT ATATT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT-T AT-TT ATTT ATTT ATTT
30952093 TTAAAACTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
3 5 0.13
4 29 0.74
5 4 0.10
6 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:30964011 original size:44 final size:44
Alignment explanation
Indices: 30963956--30964151 Score: 132
Period size: 44 Copynumber: 4.4 Consensus size: 44
30963946 CAAATCTTGC
*
30963956 CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCGC-GAATCTCAT
1 CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCACAG-ATCTCAT
* * * * * * *
30964000 CTCCTTGAAGTTACAGAGGAGTAGATTGAAGTTACAGATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCACAGATCTCAT
** ** * *
30964044 CTCCCTGAAGTTGCAGTGGAATAGATCGAAGAT-AGCA-AACTTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TCA-CAGATC-TCAT
* * * *
30964089 CCCCCTGAAGTTGCAGTGGGGCA-AGTTAAAGTTACA-AGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGTCACAGA-TCTCAT
*
30964133 CTCCCTGAAATTGCAGTGG
1 CTCCCTGAAGTTGCAGTGG
30964152 GGTAGACTGA
Statistics
Matches: 122, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
44 89 0.73
45 33 0.27
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCACAGATCTCAT
Found at i:30964131 original size:89 final size:89
Alignment explanation
Indices: 30964028--30964196 Score: 236
Period size: 89 Copynumber: 1.9 Consensus size: 89
30964018 GAGTAGATTG
*
30964028 AAGTTACAGATCTTATCTCCCTGAAGTTGCAGTGGAATAGA-TCGAAGATAGCAAA-CTTTATCC
1 AAGTTACAGATCTTATCTCCCTGAAATTGCAGTGGAATAGACT-GAAGATAGCAAATC-TTATCC
30964091 CCCTGAAGTTGCAGTGGGGCAAGTTA
64 CCCTGAAGTTGCAGTGGGGCAAGTTA
** ***
30964117 AAGTTACA-AGTCTTATCTCCCTGAAATTGCAGTGGGGTAGACTGAAGATAGCAAATCTTATTTG
1 AAGTTACAGA-TCTTATCTCCCTGAAATTGCAGTGGAATAGACTGAAGATAGCAAATCTTATCCC
30964181 CCTGAAGTTGCAGTGG
65 CCTGAAGTTGCAGTGG
30964197 AACAGGTTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
88 1 0.01
89 68 0.96
90 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (89 bp):
AAGTTACAGATCTTATCTCCCTGAAATTGCAGTGGAATAGACTGAAGATAGCAAATCTTATCCCC
CTGAAGTTGCAGTGGGGCAAGTTA
Found at i:30965207 original size:13 final size:13
Alignment explanation
Indices: 30965189--30965215 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30965179 AAAAAAATAG
30965189 AACAGAAGTTTGA
1 AACAGAAGTTTGA
30965202 AACAGAAGTTTGA
1 AACAGAAGTTTGA
30965215 A
1 A
30965216 CAAGGTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
AACAGAAGTTTGA
Found at i:30965284 original size:9 final size:9
Alignment explanation
Indices: 30965270--30965295 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30965260 TTTAGTTTCC
30965270 TTTTATTTT
1 TTTTATTTT
30965279 TTTTATTTT
1 TTTTATTTT
30965288 TTTTATTT
1 TTTTATTT
30965296 CCTACAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTATTTT
Found at i:30970844 original size:26 final size:26
Alignment explanation
Indices: 30970807--30970941 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
30970797 TGATACAAAT
*
30970807 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
30970833 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
30970859 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
30970885 TGATAATGGGTTAGGTAAATGTT-TA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
30970910 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
30970936 TGATAA
1 TGATAA
30970942 GAATATCATG
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 24 0.24
26 77 0.76
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:30970864 original size:52 final size:51
Alignment explanation
Indices: 30970807--30970941 Score: 243
Period size: 52 Copynumber: 2.6 Consensus size: 51
30970797 TGATACAAAT
30970807 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTT-A
30970859 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTA
* *
30970910 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAA
30970942 GAATATCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
51 31 0.38
52 50 0.62
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.37
Consensus pattern (51 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTA
Found at i:30972967 original size:137 final size:137
Alignment explanation
Indices: 30972721--30972996 Score: 534
Period size: 137 Copynumber: 2.0 Consensus size: 137
30972711 GAGTAGTCTC
30972721 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
30972786 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTTGCCCAGTACC
66 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
30972851 ACTGTTA
131 ACTGTTA
30972858 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
30972923 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
30972988 ACTGTTA
131 ACTGTTA
30972995 CC
1 CC
30972997 TGAATAGGCT
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TATTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:30974672 original size:13 final size:13
Alignment explanation
Indices: 30974654--30974680 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30974644 AAAAAAGTAG
30974654 AACAGAAGTTTGA
1 AACAGAAGTTTGA
30974667 AACAGAAGTTTGA
1 AACAGAAGTTTGA
30974680 A
1 A
30974681 CAAGGTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
AACAGAAGTTTGA
Found at i:30976075 original size:4 final size:4
Alignment explanation
Indices: 30976066--30976113 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
30976056 TATATAGTTG
*
30976066 ATTT ATTT A-TT ATTT ATTT ATTT CTTT -TTGT ATATT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT-T AT-TT ATTT ATTT ATTT
30976114 TTAAAACTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
3 5 0.13
4 29 0.74
5 4 0.10
6 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:30976082 original size:11 final size:11
Alignment explanation
Indices: 30976066--30976116 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
30976056 TATATAGTTG
30976066 ATTTATTTATT
1 ATTTATTTATT
30976077 ATTTATTTATTT
1 ATTTATTTA-TT
* *
30976089 CTTTTTGTATATT
1 ATTTAT-T-TATT
30976102 ATTTATTTATT
1 ATTTATTTATT
30976113 -TTTA
1 ATTTA
30976117 AAACTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 4 0.12
11 13 0.39
12 7 0.21
13 7 0.21
14 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:30977042 original size:15 final size:14
Alignment explanation
Indices: 30977014--30977040 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30977004 ATGCTGCCAA
30977014 AATTTTTATAAAAT
1 AATTTTTATAAAAT
30977028 AATTTTTATAAAA
1 AATTTTTATAAAA
30977041 ATGGAAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTTTATAAAAT
Found at i:30977784 original size:34 final size:34
Alignment explanation
Indices: 30977732--30977798 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
30977722 CAGTCAAATA
30977732 CAGTCTGGGCCTAGGCCCATTTCAGTTTCAGTAG
1 CAGTCTGGGCCTAGGCCCATTTCAGTTTCAGTAG
* *
30977766 CAGTTTGGGCCTTA-GCCCATTTTAGTTTCAGTA
1 CAGTCTGGGCC-TAGGCCCATTTCAGTTTCAGTA
30977799 TCAAATATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (34 bp):
CAGTCTGGGCCTAGGCCCATTTCAGTTTCAGTAG
Found at i:30980294 original size:33 final size:32
Alignment explanation
Indices: 30980247--30980318 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
30980237 AAAAATAATA
* *
30980247 AATTTAAAAATAAAAATGAATTA-AAGAGAAAT
1 AATTTAAAAATAAAAATAAACTAGAA-AGAAAT
*
30980279 AATTTAATAAGTAAAAATAAACTAGAAAGAAAT
1 AATTTAA-AAATAAAAATAAACTAGAAAGAAAT
30980312 -ATTTAAA
1 AATTTAAA
30980319 TTTATTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.03
32 13 0.37
33 19 0.54
34 2 0.06
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.26
Consensus pattern (32 bp):
AATTTAAAAATAAAAATAAACTAGAAAGAAAT
Found at i:30981670 original size:29 final size:29
Alignment explanation
Indices: 30981628--30981684 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
30981618 CATAGCCTTG
*
30981628 ACCTCGGATATTTTGTATGTCAAAACTAA
1 ACCTCAGATATTTTGTATGTCAAAACTAA
30981657 ACCTCAGATATTTTGTATGTCAAAACTA
1 ACCTCAGATATTTTGTATGTCAAAACTA
30981685 CGTTGCAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (29 bp):
ACCTCAGATATTTTGTATGTCAAAACTAA
Found at i:30982634 original size:20 final size:22
Alignment explanation
Indices: 30982606--30982645 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
30982596 AAAGTGATAA
30982606 AAAAGTAAAA-ACAAAAAAAAC
1 AAAAGTAAAATACAAAAAAAAC
30982627 AAAA-TAAAATACAAAAAAA
1 AAAAGTAAAATACAAAAAAA
30982646 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.07
Consensus pattern (22 bp):
AAAAGTAAAATACAAAAAAAAC
Found at i:30982651 original size:21 final size:20
Alignment explanation
Indices: 30982604--30982651 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
30982594 AAAAAGTGAT
30982604 AAAAAAGTAAAAACAAAAAA
1 AAAAAAGTAAAAACAAAAAA
30982624 AACAAAA-TAAAATACAAAAAA
1 AA-AAAAGTAAAA-ACAAAAAA
30982645 ATAAAAA
1 A-AAAAA
30982652 AATATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.28
21 17 0.68
22 1 0.04
ACGTcount: A:0.83, C:0.06, G:0.02, T:0.08
Consensus pattern (20 bp):
AAAAAAGTAAAAACAAAAAA
Found at i:30985759 original size:14 final size:14
Alignment explanation
Indices: 30985740--30985773 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30985730 TGATTTATTA
* *
30985740 TTTTATTTTAGTTT
1 TTTTATTTTAATTG
30985754 TTTTATTTTAATTG
1 TTTTATTTTAATTG
30985768 TTTTAT
1 TTTTAT
30985774 CTGACTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (14 bp):
TTTTATTTTAATTG
Found at i:30987281 original size:9 final size:9
Alignment explanation
Indices: 30987260--30987300 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
30987250 TATAATTTAT
*
30987260 TTAATCAAA
1 TTAATTAAA
30987269 -TAATTAAA
1 TTAATTAAA
30987277 TTAATTAAA
1 TTAATTAAA
*
30987286 TTAACTAAA
1 TTAATTAAA
30987295 TTAATT
1 TTAATT
30987301 TTTCAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (9 bp):
TTAATTAAA
Found at i:30987313 original size:17 final size:17
Alignment explanation
Indices: 30987291--30987323 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30987281 TTAAATTAAC
30987291 TAAATTAATTTTTCAAT
1 TAAATTAATTTTTCAAT
*
30987308 TAAATTATTTTTTCAA
1 TAAATTAATTTTTCAA
30987324 CCTAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATTAATTTTTCAAT
Found at i:30989956 original size:24 final size:24
Alignment explanation
Indices: 30989900--30989949 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
30989890 ACCACCAACT
*
30989900 CCACTTCCGTATCCGGATCCAGAC
1 CCACTTCCATATCCGGATCCAGAC
*
30989924 CCACTTCCATATCTGGATCCAGAC
1 CCACTTCCATATCCGGATCCAGAC
30989948 CC
1 CC
30989950 TTTTCCACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.42, G:0.14, T:0.22
Consensus pattern (24 bp):
CCACTTCCATATCCGGATCCAGAC
Found at i:30990073 original size:36 final size:36
Alignment explanation
Indices: 30990026--30990099 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
30990016 TATGCCACCA
*
30990026 CCAGACCCATACCCCGATCCGGATCCTGACCCATAC
1 CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
*
30990062 CCAGACCCATACCCCGATCTAGATCCTGACCCATAC
1 CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
30990098 CC
1 CC
30990100 TGATCCTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.47, G:0.12, T:0.15
Consensus pattern (36 bp):
CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
Found at i:30990145 original size:23 final size:24
Alignment explanation
Indices: 30990103--30990165 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
30990093 CATACCCTGA
30990103 TCCTTCACCC-CTACCACCACCGCC
1 TCCTTCACCCTCT-CCACCACCGCC
*
30990127 TCCTTCACCCTCTCC-CCACCTCC
1 TCCTTCACCCTCTCCACCACCGCC
* * *
30990150 ACCTCCACCTTCTCCA
1 TCCTTCACCCTCTCCA
30990166 AGACCACTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 19 0.58
24 12 0.36
25 2 0.06
ACGTcount: A:0.14, C:0.62, G:0.02, T:0.22
Consensus pattern (24 bp):
TCCTTCACCCTCTCCACCACCGCC
Found at i:31007189 original size:14 final size:14
Alignment explanation
Indices: 31007170--31007200 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31007160 AGTTTTTTTT
*
31007170 TAATCTAAATTTAC
1 TAATCTAAATTAAC
31007184 TAATCTAAATTAAC
1 TAATCTAAATTAAC
31007198 TAA
1 TAA
31007201 GAACGCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:31019972 original size:28 final size:28
Alignment explanation
Indices: 31019940--31020004 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
31019930 ATTTACTAGA
* *
31019940 ATACCCCTATGTATGCAATATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
31019968 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
31019996 ATACCCCTA
1 ATACCCCTA
31020005 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:31020169 original size:27 final size:28
Alignment explanation
Indices: 31020110--31020199 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 28
31020100 AGGAAGCGTC
*
31020110 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* * **
31020138 ATGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
31020165 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
31020194 CTGGTG
1 CTGGTG
31020200 ACTCTGTCAC
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
27 22 0.44
28 21 0.42
29 7 0.14
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:31020210 original size:29 final size:28
Alignment explanation
Indices: 31020120--31020210 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
31020110 CTGGTGGCTA
* * * *
31020120 TGCCACAAATTATCTGTTATGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
31020148 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
31020175 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
31020204 TGTCACA
1 TGCCACA
31020211 TTTTCTGTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
27 22 0.43
28 14 0.27
29 15 0.29
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:31023607 original size:19 final size:18
Alignment explanation
Indices: 31023567--31023615 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
31023557 AAATTAGGGA
*
31023567 TTTTATTTTATTTTTGTG
1 TTTTATTTTATTTTTCTG
*
31023585 TTTTAATTTTCTTTTTCT-
1 TTTT-ATTTTATTTTTCTG
31023603 TTTT-TTTTATTTT
1 TTTTATTTTATTTT
31023616 CCTTTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.30
18 8 0.30
19 11 0.41
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.82
Consensus pattern (18 bp):
TTTTATTTTATTTTTCTG
Found at i:31029777 original size:18 final size:19
Alignment explanation
Indices: 31029749--31029788 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
31029739 ACGTAAAAAG
31029749 TAAAAAGTAAA-AGATGAAA
1 TAAAAAGTAAATA-ATGAAA
31029768 TAAAAA-TAAATAATGAAA
1 TAAAAAGTAAATAATGAAA
31029786 TAA
1 TAA
31029789 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (19 bp):
TAAAAAGTAAATAATGAAA
Found at i:31030698 original size:16 final size:16
Alignment explanation
Indices: 31030668--31030715 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
31030658 GAAAATTAAT
31030668 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
31030683 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
31030700 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
31030715 A
1 A
31030716 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:31030714 original size:11 final size:11
Alignment explanation
Indices: 31030659--31030729 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
31030649 ATAGCTTAAG
*
31030659 AAAATTAATAT
1 AAAATTAAAAT
31030670 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
31030682 AATAA-T-AATT
1 AA-AATTAAAAT
*
31030692 AAAAAT-AAAT
1 AAAATTAAAAT
31030702 AAAATTAAAAT
1 AAAATTAAAAT
*
31030713 AAACTTAAAAT
1 AAAATTAAAAT
*
31030724 AGAATT
1 AAAATT
31030730 TCCTTGGCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:31031726 original size:28 final size:27
Alignment explanation
Indices: 31031695--31031749 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
31031685 TTTATTATTT
* *
31031695 TTCAATAGCAATTAATCAATCAGTAATA
1 TTCAATAACAATCAATCAATCAG-AATA
* *
31031723 TTCATTAACAATCAGTCAATCAGAATA
1 TTCAATAACAATCAATCAATCAGAATA
31031750 ATTATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (27 bp):
TTCAATAACAATCAATCAATCAGAATA
Found at i:31031806 original size:18 final size:18
Alignment explanation
Indices: 31031784--31031828 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
31031774 TATTTGGTAA
31031784 CAATCAATTATTCAATAAT
1 CAATCAATTATTCAAT-AT
* *
31031803 -AATCAGTTATTCAGTAT
1 CAATCAATTATTCAATAT
31031820 CAATCAATT
1 CAATCAATT
31031829 GATCGGCAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (18 bp):
CAATCAATTATTCAATAT
Found at i:31031809 original size:36 final size:36
Alignment explanation
Indices: 31031721--31031828 Score: 101
Period size: 36 Copynumber: 3.0 Consensus size: 36
31031711 CAATCAGTAA
* * * * * *
31031721 TATTCATTAACAATCAGTCAATCAG-AATAATTATT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* * **
31031756 TATTCAGTAACAGTCAGTTATTTGGTAACAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* *
31031792 TATTCAATAATAATCAGTTATTCAGTATCAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
31031828 T
1 T
31031829 GATCGGCAGG
Statistics
Matches: 57, Mismatches: 15, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
35 19 0.33
36 38 0.67
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (36 bp):
TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
Found at i:31031925 original size:18 final size:19
Alignment explanation
Indices: 31031879--31031925 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
31031869 TCGAGATAAT
*
31031879 GAAAAATAATTACTTTAAA
1 GAAAAATAATTACATTAAA
31031898 -AATAAA-AATTA-ATTAAA
1 GAA-AAATAATTACATTAAA
31031915 GAAAAATAATT
1 GAAAAATAATT
31031926 TAATAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
17 8 0.33
18 13 0.54
19 3 0.12
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
GAAAAATAATTACATTAAA
Found at i:31034497 original size:56 final size:56
Alignment explanation
Indices: 31034425--31034542 Score: 195
Period size: 56 Copynumber: 2.1 Consensus size: 56
31034415 CTTAAAAGAT
* *
31034425 AAAA-AAAATTAATAACTATAAAATAAAATTA-AACTTTAAACTTTAAAACACAATA
1 AAAACAAAATTAATAACTACAAAATAAAATTACAA-TCTAAACTTTAAAACACAATA
31034480 AAAACAAAATTAATAACTACAAAATAAAATTACAATCTAAACTTTAAAACACAATA
1 AAAACAAAATTAATAACTACAAAATAAAATTACAATCTAAACTTTAAAACACAATA
31034536 AAAACAA
1 AAAACAA
31034543 TTGTAAAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
55 4 0.07
56 53 0.90
57 2 0.03
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (56 bp):
AAAACAAAATTAATAACTACAAAATAAAATTACAATCTAAACTTTAAAACACAATA
Found at i:31035083 original size:19 final size:19
Alignment explanation
Indices: 31035018--31035085 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 19
31035008 TGTTGATCGG
* *
31035018 TTATCCAGTAACAGTC-AA
1 TTATTCAGTAACAATCAAA
*
31035036 TTATTCAGTAAAAATCAAA
1 TTATTCAGTAACAATCAAA
* *
31035055 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAATCAAA
31035073 TTATTCAGTAACA
1 TTATTCAGTAACA
31035086 GTCGATCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 28 0.68
19 13 0.32
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:31036614 original size:2 final size:2
Alignment explanation
Indices: 31036607--31036648 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
31036597 TTAGTTTTGT
31036607 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
31036649 CATTATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.