Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 199 of 204
Found at i:58885550 original size:2 final size:2
Alignment explanation
Indices: 58885543--58885571 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58885533 GGTCCCGTTA
58885543 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
58885572 AATATCAATT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:58886825 original size:27 final size:27
Alignment explanation
Indices: 58886761--58886830 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
58886751 GAAGGAGGGC
* *
58886761 CTGCCACAGGCGACACCAATGGTGCCT
1 CTGCCACAGGCGGCACCAATGGTGCCA
* * * *
58886788 GTGGCAGAGGCGGCACCAATGTTGCCA
1 CTGCCACAGGCGGCACCAATGGTGCCA
58886815 CTGCCACAGGCGGCAC
1 CTGCCACAGGCGGCAC
58886831 TCCCCTTTGT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.34, G:0.31, T:0.13
Consensus pattern (27 bp):
CTGCCACAGGCGGCACCAATGGTGCCA
Found at i:58887237 original size:142 final size:145
Alignment explanation
Indices: 58886833--58887333 Score: 649
Period size: 139 Copynumber: 3.4 Consensus size: 145
58886823 GGCGGCACTC
* *
58886833 CCCTTTGTTCGTATTTTTTTTTCGAATTTTATTACTTTTAAAAAATGTACTATTTTTTAATTTTT
1 CCCTATGTTCGTATTTTTTTTTCGAATTTTATTACTTTTAAAAAATATACTA----TT--TTTTT
* * *
58886898 AAATTTTACATTATTTTAGTACATTATATTTGAAATGTTTTGATTTAGTGTGTTTTTTAAATAAA
60 -AATTTTACATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAA
* * *
58886963 TTTTAAAAAAACCTTATTTCAG
124 TTTAAAAAAAATCTTATTTCGG
* * * * *
58886985 CCATTTGTTCTTATTATTTTTTCGGATTTTATTACTTTTAAAAAATATAC---TTTTTT-ATTTT
1 CCCTATGTTCGTATTTTTTTTTCGAATTTTATTACTTTTAAAAAATATACTATTTTTTTAATTTT
* * *
58887046 ACATTATTTTAGTATACTATATTTGAAATGAATTAATTTGGTGTG-TTTTTAAATAAA-TTAAAA
66 ACATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAAAA
*
58887109 AAAATCTTATTTTGG
131 AAAATCTTATTTCGG
58887124 CCCTATGTTCGTATTTTTTTTTCGAATTTTATTACTTTTAAAAAATATACTA-TTTTTTAATTTT
1 CCCTATGTTCGTATTTTTTTTTCGAATTTTATTACTTTTAAAAAATATACTATTTTTTTAATTTT
* *
58887188 ACATTATTTTAGTATATTATATTAGAAATGTATTAATTTAGTATGTTTTTTAAATAAATTTAAAA
66 ACATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTT-AAA
58887253 AAAAATTCTTATTTCGG
130 AAAAA-TCTTATTTCGG
* ** *
58887270 TCCTATGTTCGTA-TTTTTTCCCTGTATTTTATTACTTTTAAAAAATATACTATTTTTTTAATTT
1 CCCTATGTTCGTATTTTTTTTTC-GAATTTTATTACTTTTAAAAAATATACTATTTTTTTAATTT
58887334 AGAGTTCTAC
Statistics
Matches: 310, Mismatches: 30, Indels: 23
0.85 0.08 0.06
Matches are distributed among these distances:
139 62 0.20
140 12 0.04
141 50 0.16
142 45 0.15
143 17 0.05
144 2 0.01
145 16 0.05
146 50 0.16
147 11 0.04
152 45 0.15
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.53
Consensus pattern (145 bp):
CCCTATGTTCGTATTTTTTTTTCGAATTTTATTACTTTTAAAAAATATACTATTTTTTTAATTTT
ACATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAAAA
AAAATCTTATTTCGG
Found at i:58887323 original size:146 final size:142
Alignment explanation
Indices: 58886838--58887333 Score: 599
Period size: 146 Copynumber: 3.4 Consensus size: 142
58886828 CACTCCCCTT
* *
58886838 TGTTCGTATTTTTTTTTCGAATTTTATTACTTTTAAAAAATGTACTATTTTTTAATTTTTAAATT
1 TGTTCGTATTTTTTTCT-GAATTTTATTACTTTTAAAAAATATACTA-----T--TTTTT-AATT
* * * *
58886903 TTACATTATTTTAGTACATTATATTTGAAATGTTTTGATTTAGTGTGTTTTTTAAATAAATTTTA
57 TTACATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAA
* * *
58886968 AAAAAACCTTATTTCAGCCATT
122 AAAAAATCTTATTTCGGCC-TA
* *
58886990 TGTTCTTATTATTTTT-TCGGATTTTATTACTTTTAAAAAATATAC--TTTTTT-ATTTTACATT
1 TGTTCGTATT-TTTTTCT-GAATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTACATT
* * *
58887051 ATTTTAGTATACTATATTTGAAATGAATTAATTTGGTGTG-TTTTTAAATAAA-TTAAAAAAAAT
64 ATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAAT
*
58887114 CTTATTTTGGCCCTA
129 CTTATTTCGG-CCTA
*
58887129 TGTTCGTATTTTTTTTTCGAATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTACATTA
1 TGTTCGTATTTTTTTCT-GAATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTACATTA
* *
58887194 TTTTAGTATATTATATTAGAAATGTATTAATTTAGTATGTTTTTTAAATAAATTTAAAAAAAAAT
65 TTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTT-AAAAAAAA-
58887259 TCTTATTTCGGTCCTA
128 TCTTATTTCGG-CCTA
* *
58887275 TGTTCGTATTTTTTCCCTGTATTTTATTACTTTTAAAAAATATACTATTTTTTTAATTT
1 TGTTCGTATTTTTT-TCTGAATTTTATTACTTTTAAAAAATATACTA-TTTTTTAATTT
58887334 AGAGTTCTAC
Statistics
Matches: 306, Mismatches: 26, Indels: 29
0.85 0.07 0.08
Matches are distributed among these distances:
138 5 0.02
139 55 0.18
140 14 0.05
141 50 0.16
142 45 0.15
143 17 0.06
144 2 0.01
145 9 0.03
146 56 0.18
147 12 0.04
152 36 0.12
153 5 0.02
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (142 bp):
TGTTCGTATTTTTTTCTGAATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTACATTAT
TTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAAAAAAAATCT
TATTTCGGCCTA
Found at i:58888136 original size:28 final size:26
Alignment explanation
Indices: 58888073--58888153 Score: 74
Period size: 28 Copynumber: 3.0 Consensus size: 26
58888063 GCCGTCTTTG
58888073 TTTTTTTTTTG-TATTATTTTGGTAAA
1 TTTTTTTTTTGTTATTATTTTGGT-AA
** *
58888099 TAATTTTTTTGTATATTATTTTGGTAT
1 TTTTTTTTTTGT-TATTATTTTGGTAA
* *
58888126 TTTTTTATTTTTTGTAATATTTTGGTAA
1 TTTTTT-TTTTGT-TATTATTTTGGTAA
58888154 AAAACCTATC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
26 9 0.21
27 5 0.12
28 29 0.67
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (26 bp):
TTTTTTTTTTGTTATTATTTTGGTAA
Found at i:58888491 original size:54 final size:54
Alignment explanation
Indices: 58888409--58888520 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
58888399 TTTTATTCAG
58888409 AGAAATTTAGATCAGTTAGAAGCACTATCAAAGAAGCTTAAGGCAAAAACCTTA
1 AGAAATTTAGATCAGTTAGAAGCACTATCAAAGAAGCTTAAGGCAAAAACCTTA
*
58888463 AGAAATTTAGATCAGTTAGAAGCACTATCAAAGAAGCTTAAGGCAAAAACCTTG
1 AGAAATTTAGATCAGTTAGAAGCACTATCAAAGAAGCTTAAGGCAAAAACCTTA
58888517 AGAA
1 AGAA
58888521 CTGAGGCTCC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.21
Consensus pattern (54 bp):
AGAAATTTAGATCAGTTAGAAGCACTATCAAAGAAGCTTAAGGCAAAAACCTTA
Found at i:58890564 original size:120 final size:120
Alignment explanation
Indices: 58890435--58891274 Score: 1259
Period size: 120 Copynumber: 7.0 Consensus size: 120
58890425 TAGATTATAC
* * * * *
58890435 ATTAT-TTTTATAGCATTACATATTATGATTTTAGTAAATTCATATGATAATATTTAATATTAAA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
58890499 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAACTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
* *
58890554 ATTATATTTTATAGCATTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* * * *
58890619 AATTAATT-TAAAATTATAT-TTTTTATTAAATTATATTTAATAATAATAATGTTCA
66 AATT--TTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
*
58890674 ATTATATTTTATAGTATTCTATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* * *
58890739 AATTTTATTAAATTATATTTTTTTATTAAATTATATTTAAAAATAATTAATTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
58890794 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* * *
58890856 AATTTTATTAAATTATATATTTTT-TCTAAATTATATTTTTAATAATTATTAGTTTAT
66 AATTTTATTAAATTATATATTTTTAT-TAAATTATA--TTTAATAATAATTATTTTAA
* *
58890913 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
58890978 AATTTTATTAAATTATATATATATTTTTATTAAATTATATTTAATAAT-A--ATTTTAA
66 AATTTTATT-AA--AT-TATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
* *
58891034 ATTATATTTTATAGTATTATATATTATGATTTTATTAAATTCATATAACAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* * *
58891099 AATTTTCTTAAATTATATATTTTTATTAAATTATATTTAATAATATTTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
* *
58891154 ATTATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATGTAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* *
58891219 AATTATATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
58891274 A
1 A
58891275 ATATGATTAA
Statistics
Matches: 660, Mismatches: 42, Indels: 37
0.89 0.06 0.05
Matches are distributed among these distances:
116 1 0.00
117 83 0.13
118 4 0.01
119 73 0.11
120 350 0.53
121 84 0.13
122 30 0.05
123 3 0.00
124 9 0.01
125 2 0.00
126 20 0.03
127 1 0.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (120 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
Found at i:58890714 original size:64 final size:61
Alignment explanation
Indices: 58890639--58890834 Score: 176
Period size: 64 Copynumber: 3.2 Consensus size: 61
58890629 AAATTATATT
* *
58890639 TTTTATTAAATTATATTTAATAATAATAATGTTCAATTATATTTTATAGTATTCTATATTATGA
1 TTTTAGTAAATTATATTTAAAAATAATAAT-TT-AATTATATTTTATAGTATT-TATATTATGA
* * * *
58890703 TTTTAGTAAATTCATA--TAAGAATATTTAATATTAA-GA-ATTTTAT--TAAATTATATT-T--
1 TTTTAGTAAATT-ATATTTAAAAATA-ATAAT-TTAATTATATTTTATAGT-ATTTATATTATGA
*
58890759 TTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATATTTTATAGTATTATATATTATGA
1 TTTTAGTAAATTATATTTAAAAATAA-TAATTT-AATTATATTTTATAGTATT-TATATTATGA
58890823 TTTTAGTAAATT
1 TTTTAGTAAATT
58890835 CTAAGAATAT
Statistics
Matches: 105, Mismatches: 12, Indels: 30
0.71 0.08 0.20
Matches are distributed among these distances:
55 3 0.03
56 13 0.12
57 13 0.12
58 2 0.02
59 14 0.13
60 4 0.04
61 14 0.13
62 2 0.02
63 9 0.09
64 28 0.27
65 3 0.03
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (61 bp):
TTTTAGTAAATTATATTTAAAAATAATAATTTAATTATATTTTATAGTATTTATATTATGA
Found at i:58890762 original size:18 final size:18
Alignment explanation
Indices: 58890741--58890776 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
58890731 ATATTAAGAA
58890741 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
58890759 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
58890777 AAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATTAAATTATATTT
Found at i:58890995 original size:22 final size:22
Alignment explanation
Indices: 58890970--58891161 Score: 80
Period size: 22 Copynumber: 9.2 Consensus size: 22
58890960 AGAATATTTA
*
58890970 ATATTAAAAATTTTATTAAATT
1 ATATTAATAATTTTATTAAATT
*
58890992 ATA-TATATATTTTTATTAAATT
1 ATATTA-ATAATTTTATTAAATT
*
58891014 ATATTTAATAATAATT-TTAAATT
1 ATA-TTAATAAT-TTTATTAAATT
* **
58891037 ATATT--TTATAGTATT--A-T
1 ATATTAATAATTTTATTAAATT
*
58891054 ATATT-ATGATTTTATTAAATT
1 ATATTAATAATTTTATTAAATT
* *
58891075 CATA-TAACAA---TATT---TA
1 -ATATTAATAATTTTATTAAATT
* *
58891091 ATATTAAGAATTTTCTTAAATT
1 ATATTAATAATTTTATTAAATT
58891113 ATA-T-AT--TTTTATTAAATT
1 ATATTAATAATTTTATTAAATT
58891131 ATATTTAATAATATTTATGTTAAATT
1 ATA-TTAATAAT-TTTA--TTAAATT
58891157 ATATT
1 ATATT
58891162 TTATAGTATT
Statistics
Matches: 127, Mismatches: 17, Indels: 49
0.66 0.09 0.25
Matches are distributed among these distances:
15 3 0.02
16 6 0.05
17 6 0.05
18 22 0.17
19 9 0.07
20 8 0.06
21 7 0.06
22 31 0.24
23 15 0.12
24 8 0.06
25 2 0.02
26 10 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
ATATTAATAATTTTATTAAATT
Found at i:58891153 original size:26 final size:26
Alignment explanation
Indices: 58891115--58891179 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
58891105 CTTAAATTAT
*
58891115 ATATTTTTATTAAATTATATTTAATA
1 ATATTTATATTAAATTATATTTAATA
* *
58891141 ATATTTATGTTAAATTATATTTTATA
1 ATATTTATATTAAATTATATTTAATA
*
58891167 GTATTATATATTA
1 ATATT-TATATTA
58891180 TGATTTTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
26 27 0.82
27 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (26 bp):
ATATTTATATTAAATTATATTTAATA
Found at i:58895031 original size:52 final size:52
Alignment explanation
Indices: 58894949--58895127 Score: 259
Period size: 52 Copynumber: 3.3 Consensus size: 52
58894939 TTTGAGTACT
*
58894949 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGACTACACTTA
1 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
58895001 TCTCATCAAGTGACAAGTGGAAAGTGATAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAAGT-----G-GA-AAGTGATAAGTGATAGCTTCGGCTACACTTA
*
58895060 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
58895112 TCTGATCAAGAGACAA
1 TCTGATCAAGTGACAA
58895128 AGTGATAAGT
Statistics
Matches: 115, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
52 62 0.54
53 2 0.02
54 1 0.01
57 1 0.01
58 2 0.02
59 47 0.41
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (52 bp):
TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:58895047 original size:59 final size:59
Alignment explanation
Indices: 58894970--58895095 Score: 234
Period size: 59 Copynumber: 2.1 Consensus size: 59
58894960 GACAAGTGGA
58894970 AAGTGATAAGTGATAGCTTCGACTACACTTATCTCATCAAGTGACAAGTGGAAAGTGAT
1 AAGTGATAAGTGATAGCTTCGACTACACTTATCTCATCAAGTGACAAGTGGAAAGTGAT
* *
58895029 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGAT
1 AAGTGATAAGTGATAGCTTCGACTACACTTATCTCATCAAGTGACAAGTGGAAAGTGAT
58895088 AAGTGATA
1 AAGTGATA
58895096 GCTTCGGCTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (59 bp):
AAGTGATAAGTGATAGCTTCGACTACACTTATCTCATCAAGTGACAAGTGGAAAGTGAT
Found at i:58895071 original size:45 final size:46
Alignment explanation
Indices: 58895022--58895143 Score: 147
Period size: 52 Copynumber: 2.5 Consensus size: 46
58895012 GACAAGTGGA
58895022 AAGTGA-TAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC
1 AAGTGACTAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC
*
58895067 AAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATC
1 AAGTGAC---T---AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC
* *
58895119 AAGAGACAAAGTGATAAGTTGATAG
1 AAGTGACTAAGTGATAAG-TGATAG
58895144 TTTCNNNNNN
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
45 6 0.09
46 10 0.15
47 6 0.09
49 1 0.02
52 43 0.65
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (46 bp):
AAGTGACTAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATC
Found at i:58895341 original size:52 final size:52
Alignment explanation
Indices: 58895255--58895373 Score: 177
Period size: 52 Copynumber: 2.2 Consensus size: 52
58895245 NNNATCTGAT
* *
58895255 CAAGTGACAAAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGTTTCAGCTACACTTATCTGATCAAGAGA
58895308 CAAGTGAAAAGTGATAAGTGATAGCTTT-AGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAG-TTTCAGCTACACTTATCTGATCAAGAGA
*
58895360 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
58895374 GCTACACTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
52 40 0.66
53 21 0.34
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGTTTCAGCTACACTTATCTGATCAAGAGA
Found at i:58895381 original size:37 final size:37
Alignment explanation
Indices: 58895337--58895445 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
58895327 GATAGCTTTA
58895337 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
58895374 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
58895411 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
58895446 ATCATACGTA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 12 0.17
36 4 0.06
37 53 0.77
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:58896752 original size:29 final size:28
Alignment explanation
Indices: 58896690--58896752 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
58896680 ATAAAGAATA
* *
58896690 AATAAATATGTATATATACAAAATATGT
1 AATATATATGTATATATACAAAATATGG
*
58896718 ACATATATATGTAGGTATATA-AAATTATGG
1 A-ATATATATGTA--TATATACAAAATATGG
58896748 AATAT
1 AATAT
58896753 GAAAATAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 14 0.48
30 8 0.28
31 6 0.21
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (28 bp):
AATATATATGTATATATACAAAATATGG
Found at i:58896928 original size:16 final size:16
Alignment explanation
Indices: 58896907--58896942 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
58896897 TATGTGAATT
*
58896907 ATAAAAATAAAATAAG
1 ATAAAAATAAAATAAA
58896923 ATAAAAATAAAATAAA
1 ATAAAAATAAAATAAA
58896939 ATAA
1 ATAA
58896943 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
ATAAAAATAAAATAAA
Found at i:58896953 original size:21 final size:21
Alignment explanation
Indices: 58896906--58896954 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
58896896 GTATGTGAAT
58896906 TATA-AAAATAAAATAAGATA
1 TATATAAAATAAAATAAGATA
* * *
58896926 AAAATAAAATAAAATAATATA
1 TATATAAAATAAAATAAGATA
58896947 TATATAAA
1 TATATAAA
58896955 TGAGGAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
TATATAAAATAAAATAAGATA
Found at i:58898694 original size:21 final size:21
Alignment explanation
Indices: 58898655--58898694 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
58898645 AAATTAACTA
* *
58898655 TTGTTATTATTGTGGTTATCT
1 TTGTTATTATTATGATTATCT
*
58898676 TTGTTATTATTATTATTAT
1 TTGTTATTATTATGATTAT
58898695 TTATTTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (21 bp):
TTGTTATTATTATGATTATCT
Found at i:58899511 original size:106 final size:106
Alignment explanation
Indices: 58899298--58899600 Score: 435
Period size: 106 Copynumber: 2.8 Consensus size: 106
58899288 TTTCTAATTG
* *
58899298 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCT
* * * *** **
58899363 CGTTTAACCAAATGGCTTAATATCCTTTTAATTTTTTTAAAATA
63 CGTTTAACCAAATAGCTAAATATCCTTTCAAAAATTACAAAATA
*
58899407 AGGCAATGTTTTGTGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGT
*
58899472 TCAACCAAATAGCTAAATATCCTTTCAAAAATTACAAAATA
66 TTAACCAAATAGCTAAATATCCTTTCAAAAATTACAAAATA
* *
58899513 AGGTAATGTTTTGCGTTTGGAAATTTGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGT
* *
58899578 TTAACCAAATTGCCAAATATCCT
66 TTAACCAAATAGCTAAATATCCT
58899601 ATTGAATTTT
Statistics
Matches: 176, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
106 122 0.69
108 26 0.15
109 28 0.16
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (106 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGT
TTAACCAAATAGCTAAATATCCTTTCAAAAATTACAAAATA
Found at i:58903690 original size:17 final size:17
Alignment explanation
Indices: 58903679--58903712 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
58903669 TATTAATATA
58903679 TAAAAAA-AATTAAAAT
1 TAAAAAATAATTAAAAT
*
58903695 TAAAAAATAATTTAAAT
1 TAAAAAATAATTAAAAT
58903712 T
1 T
58903713 GTGAGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAAATAATTAAAAT
Found at i:58934914 original size:14 final size:12
Alignment explanation
Indices: 58934882--58934908 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58934872 ATCATCAATG
58934882 CAAAGATATATT
1 CAAAGATATATT
58934894 CAAAGATATATT
1 CAAAGATATATT
58934906 CAA
1 CAA
58934909 TGAGATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (12 bp):
CAAAGATATATT
Found at i:58946031 original size:29 final size:29
Alignment explanation
Indices: 58945998--58946053 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
58945988 TTTAATCTTT
*
58945998 ATATTTTTATAATGTTATTAATTAGTTTA
1 ATATTTTTATAATGTAATTAATTAGTTTA
58946027 ATATTTTTATAATGTAATTAATTAGTT
1 ATATTTTTATAATGTAATTAATTAGTT
58946054 CAAATAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (29 bp):
ATATTTTTATAATGTAATTAATTAGTTTA
Found at i:58946924 original size:24 final size:24
Alignment explanation
Indices: 58946892--58946939 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
58946882 TACGATGCTA
58946892 GCCTCCAACCACCACTTGGGGTCC
1 GCCTCCAACCACCACTTGGGGTCC
58946916 GCCTCCAACCACCACTTGGGGTCC
1 GCCTCCAACCACCACTTGGGGTCC
58946940 ATCTTCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.46, G:0.21, T:0.17
Consensus pattern (24 bp):
GCCTCCAACCACCACTTGGGGTCC
Found at i:58957216 original size:21 final size:21
Alignment explanation
Indices: 58957190--58957244 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
58957180 ACAGCGGTGG
*
58957190 CGGTGAGATTAGTTACTGTAA
1 CGGTGAGATTAGATACTGTAA
* *
58957211 CGGTGAGATTGGATACTGTAG
1 CGGTGAGATTAGATACTGTAA
*
58957232 CAGTGAGATTAGA
1 CGGTGAGATTAGA
58957245 AACAATGGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.33, T:0.29
Consensus pattern (21 bp):
CGGTGAGATTAGATACTGTAA
Found at i:58958447 original size:44 final size:44
Alignment explanation
Indices: 58958393--58958500 Score: 146
Period size: 44 Copynumber: 2.5 Consensus size: 44
58958383 CTTGCCTTTA
* *
58958393 GTCTGCCATTTTGGCTTGCACCCACTTGAGCTT-GCATTTAGACC
1 GTCTGCCATTTCGGCTTGCACCCA-TTCAGCTTAGCATTTAGACC
* *
58958437 GTCTGCCATTTCGGCTTGCACCCATTCAGGTTAGCATTTAGACT
1 GTCTGCCATTTCGGCTTGCACCCATTCAGCTTAGCATTTAGACC
* *
58958481 GTCCGCCACTTCGGCTTGCA
1 GTCTGCCATTTCGGCTTGCA
58958501 ATTCGACAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 6 0.11
44 51 0.89
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.32
Consensus pattern (44 bp):
GTCTGCCATTTCGGCTTGCACCCATTCAGCTTAGCATTTAGACC
Found at i:58977652 original size:4 final size:4
Alignment explanation
Indices: 58977643--58977668 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
58977633 TGAATGGAAT
58977643 CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CA
58977669 CTGTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:58979337 original size:31 final size:30
Alignment explanation
Indices: 58979301--58979367 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
58979291 AAGTTAATAA
*
58979301 AAAGACGTGTTTAATAAAATATTTTTACTTT
1 AAAGACGTGATTAA-AAAATATTTTTACTTT
* ** *
58979332 AAAGACTTGATTAAAATGTTTTTTTACTTT
1 AAAGACGTGATTAAAAAATATTTTTACTTT
58979362 AAAGAC
1 AAAGAC
58979368 CAATTTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.43
Consensus pattern (30 bp):
AAAGACGTGATTAAAAAATATTTTTACTTT
Found at i:58979376 original size:30 final size:30
Alignment explanation
Indices: 58979322--58979378 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
58979312 TAATAAAATA
**
58979322 TTTTTACTTTAAAGACTTGATTAAAATGTT
1 TTTTTACTTTAAAGACTCAATTAAAATGTT
58979352 TTTTTACTTTAAAGAC-CAATTTAAAAT
1 TTTTTACTTTAAAGACTCAA-TTAAAAT
58979379 CTAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (30 bp):
TTTTTACTTTAAAGACTCAATTAAAATGTT
Found at i:58986976 original size:6 final size:6
Alignment explanation
Indices: 58986967--58986996 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
58986957 AGGTGTTGGT
*
58986967 GTTGAA GTTGAA ATTGAA GTTGAA GTTGAA
1 GTTGAA GTTGAA GTTGAA GTTGAA GTTGAA
58986997 TTAGCTATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (6 bp):
GTTGAA
Found at i:58987885 original size:26 final size:27
Alignment explanation
Indices: 58987835--58987885 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
58987825 TTTAAATTTT
* *
58987835 TAAAAAAAAAATTAGAATTTCGACAGC
1 TAAAAAAAAAAGTACAATTTCGACAGC
*
58987862 TAAAAAAACAAGTACAATTT-GACA
1 TAAAAAAAAAAGTACAATTTCGACA
58987886 ATTTTTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.22
Consensus pattern (27 bp):
TAAAAAAAAAAGTACAATTTCGACAGC
Found at i:58992174 original size:20 final size:19
Alignment explanation
Indices: 58992147--58992209 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
58992137 AAAGTACCTT
58992147 AAAATATGAGACAATACAA
1 AAAATATGAGACAATACAA
*
58992166 AAAATTATGAGGCAATACTAA
1 AAAA-TATGAGACAATAC-AA
*
58992187 AAAAAATGAAGA-AATACAA
1 AAAATATG-AGACAATACAA
58992206 AAAA
1 AAAA
58992210 AAAATTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 10 0.26
20 20 0.53
21 8 0.21
ACGTcount: A:0.65, C:0.08, G:0.11, T:0.16
Consensus pattern (19 bp):
AAAATATGAGACAATACAA
Found at i:58992211 original size:23 final size:24
Alignment explanation
Indices: 58992185--58992242 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
58992175 AGGCAATACT
58992185 AAAAAAA-ATGAAGA-AATACAAA
1 AAAAAAATATGAAGAGAATACAAA
*
58992207 AAAAAAATTAT-AAGAGAATACGAA
1 AAAAAAA-TATGAAGAGAATACAAA
58992231 AAAAAAATATGA
1 AAAAAAATATGA
58992243 GATAGTACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 7 0.23
23 7 0.23
24 17 0.55
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.14
Consensus pattern (24 bp):
AAAAAAATATGAAGAGAATACAAA
Found at i:58992244 original size:21 final size:21
Alignment explanation
Indices: 58992185--58992258 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 21
58992175 AGGCAATACT
*
58992185 AAAAAAAATGAAGA-AATACAA
1 AAAAAAAAT-ATGAGAATACAA
*
58992206 AAAAAAAATTATAAGAGAATACGA
1 AAAAAAAA-TAT--GAGAATACAA
*
58992230 AAAAAAAATATGAGATAGTACCA
1 AAAAAAAATATGAGA-A-TACAA
58992253 AAAAAA
1 AAAAAA
58992259 TATGATGGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 13 0.30
22 2 0.05
23 15 0.34
24 14 0.32
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (21 bp):
AAAAAAAATATGAGAATACAA
Found at i:58992255 original size:23 final size:24
Alignment explanation
Indices: 58992195--58992258 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
58992185 AAAAAAAATG
*
58992195 AAGA-AATACAAAAAAAAAATTAT
1 AAGAGAATACCAAAAAAAAATTAT
*
58992218 AAGAGAATACGAAAAAAAAA-TAT
1 AAGAGAATACCAAAAAAAAATTAT
* * *
58992241 GAGATAGTACCAAAAAAA
1 AAGAGAATACCAAAAAAA
58992259 TATGATGGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 21 0.60
24 14 0.40
ACGTcount: A:0.69, C:0.06, G:0.11, T:0.14
Consensus pattern (24 bp):
AAGAGAATACCAAAAAAAAATTAT
Found at i:58994964 original size:18 final size:16
Alignment explanation
Indices: 58994943--58994989 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
58994933 CATAAAAAAG
58994943 TATAAAAATCATTAATAT
1 TATAAAAAT-ATTAAT-T
*
58994961 TATAAAAAT-TAAAATT
1 TATAAAAATAT-TAATT
58994977 TATAAAAATATTA
1 TATAAAAATATTA
58994990 GAAATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 12 0.48
17 4 0.16
18 9 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAAAAATATTAATT
Found at i:59000764 original size:41 final size:42
Alignment explanation
Indices: 59000657--59000765 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
59000647 TAAAAGTCTT
* * * * *
59000657 AGCATTAGCGGCGCTATATTAAAAGCGCCGCTAAAAACACTG
1 AGCATTAGCGGCGCTTTATTAAAAACACAGCTAAAAACACAG
* *
59000699 ACCATTAGCGGCGCTTT-TTAAAAAACACAGCTAATAAC-CAG
1 AGCATTAGCGGCGCTTTATT-AAAAACACAGCTAAAAACACAG
*
59000740 AGCATTAGCGGCGCTTTACTAAAAAC
1 AGCATTAGCGGCGCTTTATTAAAAAC
59000766 GCCACTAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 26 0.46
42 30 0.54
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
AGCATTAGCGGCGCTTTATTAAAAACACAGCTAAAAACACAG
Found at i:59000774 original size:41 final size:42
Alignment explanation
Indices: 59000657--59000774 Score: 125
Period size: 41 Copynumber: 2.8 Consensus size: 42
59000647 TAAAAGTCTT
* * * * *
59000657 AGCATTAGCGGCGCTATATTAAAAGCGCCGCTAAAAACACTG
1 AGCATTAGCGGCGCTTTATTAAAAACGCCACTAATAACACAG
* *
59000699 ACCATTAGCGGCGCTTT-TTAAAAAAC-ACAGCTAATAAC-CAG
1 AGCATTAGCGGCGCTTTATT-AAAAACGCCA-CTAATAACACAG
*
59000740 AGCATTAGCGGCGCTTTACTAAAAACGCCACTAAT
1 AGCATTAGCGGCGCTTTATTAAAAACGCCACTAAT
59000775 TCGTCCGAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
41 32 0.52
42 30 0.48
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (42 bp):
AGCATTAGCGGCGCTTTATTAAAAACGCCACTAATAACACAG
Found at i:59003543 original size:19 final size:19
Alignment explanation
Indices: 59003519--59003555 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
59003509 TTCTGATAAT
*
59003519 TTATATGTAAATATTATAG
1 TTATATGCAAATATTATAG
59003538 TTATATGCAAATATTATA
1 TTATATGCAAATATTATA
59003556 TAATAAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (19 bp):
TTATATGCAAATATTATAG
Found at i:59006023 original size:145 final size:145
Alignment explanation
Indices: 59005825--59006108 Score: 370
Period size: 145 Copynumber: 2.0 Consensus size: 145
59005815 AACTGTAAAA
* * *
59005825 ATAGTCACTTTTGTTTGTATTAGATTATATTTTAGTCATTTATATTTGAAATGTTACGTTTTAGT
1 ATAGTCACTTTTGTTTGTATTAGAATACATTTTAGTCACTTATATTTGAAATGTTACGTTTTAGT
** * * * *
59005890 CTTTTACATTATCATTTTGTTATGAAGTAGTCACTCTGCCGTTCAGCTCCATTACCTCCCTAACG
66 CACTTACATTATCATTTTGTTACGAAGTAATCACTCTGCCATTCAGCTCCATTACCTCCCTAACA
*
59005955 ACAATCCTATGTGGG
131 ACAACCCTATGTGGG
* * * *
59005970 ATAGTCACTTTTGTTTGTCTTATAATACATTTTAGTCACTTCTATTTGAAATGTTATGTTTTAGT
1 ATAGTCACTTTTGTTTGTATTAGAATACATTTTAGTCACTTATATTTGAAATGTTACGTTTTAGT
** * * * * * *
59006035 CACTTGTATTATCGTTTTGTTACGAAGTAATCACTTTGTCATTCATCTCCGTTACCTTCCTAACA
66 CACTTACATTATCATTTTGTTACGAAGTAATCACTCTGCCATTCAGCTCCATTACCTCCCTAACA
59006100 ACAACCCTA
131 ACAACCCTA
59006109 GATGGCAGTC
Statistics
Matches: 117, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
145 117 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (145 bp):
ATAGTCACTTTTGTTTGTATTAGAATACATTTTAGTCACTTATATTTGAAATGTTACGTTTTAGT
CACTTACATTATCATTTTGTTACGAAGTAATCACTCTGCCATTCAGCTCCATTACCTCCCTAACA
ACAACCCTATGTGGG
Found at i:59008729 original size:7 final size:7
Alignment explanation
Indices: 59008714--59008743 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
59008704 TGTTTCTTTC
*
59008714 AAAAAAT
1 AAAATAT
59008721 AAAATAT
1 AAAATAT
59008728 AAAATAT
1 AAAATAT
59008735 AAAATAT
1 AAAATAT
59008742 AA
1 AA
59008744 TATTCGTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATAT
Found at i:59023076 original size:12 final size:12
Alignment explanation
Indices: 59023059--59023083 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59023049 TGTTTCTTAC
59023059 AAATAAAATAAA
1 AAATAAAATAAA
59023071 AAATAAAATAAA
1 AAATAAAATAAA
59023083 A
1 A
59023084 TATTCGTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:59023625 original size:5 final size:5
Alignment explanation
Indices: 59023617--59023645 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
59023607 AGGTAAGGGG
59023617 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
59023646 GGTAAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:59024647 original size:57 final size:59
Alignment explanation
Indices: 59024586--59024744 Score: 135
Period size: 57 Copynumber: 2.7 Consensus size: 59
59024576 TATATTTAAA
* *
59024586 TTTTTAGAGTTAGGACTAAATTGATAGATTTTATAAATATTGAGGGTCAAA-T-TTG-TT
1 TTTTTAGAATTAGGA-TAAATTGATAGATTTTATAAATATTGAGGGTCAAACTGTTGATG
** * * * * * *
59024643 TTTTTAGAATTATAATTAAAATGACAAATTTTGTAAACATTGAGGGTTAAATCTGTTGATG
1 TTTTTAGAATTAGGA-TAAATTGATAGATTTTATAAATATTGAGGGTCAAA-CTGTTGATG
* * * *
59024704 TTTTTATATTTAGGATCAAATTGATAGAATGTATAAATATT
1 TTTTTAGAATTAGGAT-AAATTGATAGATTTTATAAATATT
59024745 AGAGAGCTAA
Statistics
Matches: 75, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
57 41 0.55
59 1 0.01
60 4 0.05
61 29 0.39
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.43
Consensus pattern (59 bp):
TTTTTAGAATTAGGATAAATTGATAGATTTTATAAATATTGAGGGTCAAACTGTTGATG
Found at i:59028713 original size:29 final size:29
Alignment explanation
Indices: 59028671--59028730 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
59028661 TCCCGAAACC
59028671 TAGGAGCAATTGTCTCGAGACTAATTAGT
1 TAGGAGCAATTGTCTCGAGACTAATTAGT
59028700 TAGGAGCAATTGTCTCGAGACTAATTAGT
1 TAGGAGCAATTGTCTCGAGACTAATTAGT
59028729 TA
1 TA
59028731 TGTATCGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (29 bp):
TAGGAGCAATTGTCTCGAGACTAATTAGT
Found at i:59036159 original size:16 final size:16
Alignment explanation
Indices: 59036113--59036160 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
59036103 ATTTTGGGAA
59036113 ATTTTTATAAAATTTTT
1 ATTTTTAT-AAATTTTT
* *
59036130 ATTTTTTTAGATTTTT
1 ATTTTTATAAATTTTT
*
59036146 GTTTTTATAAATTTT
1 ATTTTTATAAATTTT
59036161 AATTATTTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (16 bp):
ATTTTTATAAATTTTT
Found at i:59040868 original size:19 final size:20
Alignment explanation
Indices: 59040832--59040869 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
59040822 TTGAGTATTA
* *
59040832 TTTTATTATTATTGATTAAT
1 TTTTATTATAATTAATTAAT
59040852 TTTTATT-TAATTAATTAA
1 TTTTATTATAATTAATTAA
59040870 AAATAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTATTATAATTAATTAAT
Found at i:59041059 original size:81 final size:80
Alignment explanation
Indices: 59040920--59041078 Score: 185
Period size: 81 Copynumber: 2.0 Consensus size: 80
59040910 ATAATTAAGG
* * *
59040920 GTAAAATATTATCATGGAGAATTGATTTGGTGATATAAAATATTTGACATCAAATAATAATCTTT
1 GTAAAATATTAT-ATGGAGAATTGATTTGGTGATATAAAATATATGACATCAAATAATAAACATT
59040985 TAAAAATATATGAAAT
65 TAAAAATATATGAAAT
* ** * * *
59041001 GTAAAATATTAT-TGGGAGGAATTGGTTTGGTGATATAGGATATATGATATTAATTAATAAACAT
1 GTAAAATATTATAT-GGA-GAATTGATTTGGTGATATAAAATATATGACATCAAATAATAAACAT
**
59041065 TTGCAAATATATGA
64 TTAAAAATATATGA
59041079 TTAAAAATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
79 1 0.02
80 3 0.05
81 61 0.94
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (80 bp):
GTAAAATATTATATGGAGAATTGATTTGGTGATATAAAATATATGACATCAAATAATAAACATTT
AAAAATATATGAAAT
Found at i:59045299 original size:3 final size:3
Alignment explanation
Indices: 59045291--59045318 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
59045281 ATTTGAAACT
59045291 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
59045319 AGAGTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:59047172 original size:31 final size:31
Alignment explanation
Indices: 59047127--59047186 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
59047117 TAGCAAGTCT
* * * *
59047127 ACTCTTTTTGAAAGGTTGATGGTCAAATTAG
1 ACTCTTTCTAAAAGGTTAAGGGTCAAATTAG
59047158 ACTCTTTCTAAAAGGTTAAGGGTCAAATT
1 ACTCTTTCTAAAAGGTTAAGGGTCAAATT
59047187 TAACTAAAAA
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:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (31 bp):
ACTCTTTCTAAAAGGTTAAGGGTCAAATTAG
Found at i:59048927 original size:31 final size:31
Alignment explanation
Indices: 59048892--59048992 Score: 111
Period size: 31 Copynumber: 3.3 Consensus size: 31
59048882 CATTTGCATC
* *
59048892 AAAACTGAAATTTTA-AAATTCGAAAAATACA
1 AAAACT-AAATTTGATAAATTCAAAAAATACA
*
59048923 AAAACTAAAATTGATAAATTCAAAAAATACA
1 AAAACTAAATTTGATAAATTCAAAAAATACA
*
59048954 AAAACTAAAATTGATCAAATT---AAAATACA
1 AAAACTAAATTTGAT-AAATTCAAAAAATACA
*
59048983 ATAACTAAAT
1 AAAACTAAAT
59048993 AAACAAATAC
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
29 16 0.25
30 6 0.10
31 36 0.57
32 5 0.08
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.25
Consensus pattern (31 bp):
AAAACTAAATTTGATAAATTCAAAAAATACA
Found at i:59048949 original size:23 final size:23
Alignment explanation
Indices: 59048905--59048948 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
59048895 ACTGAAATTT
59048905 TAAAATTCGAAAAATACAAAAAC
1 TAAAATTCGAAAAATACAAAAAC
* *
59048928 TAAAATT-GATAAATTCAAAAA
1 TAAAATTCGAAAAATACAAAAA
59048949 ATACAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.64, C:0.09, G:0.05, T:0.23
Consensus pattern (23 bp):
TAAAATTCGAAAAATACAAAAAC
Found at i:59048988 original size:29 final size:29
Alignment explanation
Indices: 59048914--59048991 Score: 113
Period size: 31 Copynumber: 2.6 Consensus size: 29
59048904 TTAAAATTCG
59048914 AAAAATACAAAAACTAAAATTGATAAATT
1 AAAAATACAAAAACTAAAATTGATAAATT
59048943 CAAAAAATACAAAAACTAAAATTGATCAAATT
1 --AAAAATACAAAAACTAAAATTGAT-AAATT
*
59048975 -AAAATACAATAACTAAA
1 AAAAATACAAAAACTAAA
59048992 TAAACAAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 16 0.36
31 24 0.53
32 5 0.11
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.22
Consensus pattern (29 bp):
AAAAATACAAAAACTAAAATTGATAAATT
Found at i:59051466 original size:13 final size:13
Alignment explanation
Indices: 59051414--59051466 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
59051404 AGTTCTTCAT
59051414 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
59051427 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
59051440 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
59051453 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
59051466 T
1 T
59051467 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 30 0.88
14 2 0.06
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:59053034 original size:9 final size:9
Alignment explanation
Indices: 59053017--59053132 Score: 60
Period size: 9 Copynumber: 12.7 Consensus size: 9
59053007 TCTATTAAAT
*
59053017 TAATCATTA
1 TAATTATTA
59053026 TAATTATTA
1 TAATTATTA
*
59053035 -AATTA-AA
1 TAATTATTA
59053042 TAATTTATGTA
1 TAA-TTAT-TA
*
59053053 -AATTA-AA
1 TAATTATTA
*
59053060 TTAATTCTTA
1 -TAATTATTA
59053070 TTAATTACTCTA
1 -TAATTA-T-TA
*
59053082 AAATTATTA
1 TAATTATTA
*
59053091 TTATTATTA
1 TAATTATTA
*
59053100 TTATTATTA
1 TAATTATTA
*
59053109 TTATTATTA
1 TAATTATTA
*
59053118 TTATTATTA
1 TAATTATTA
*
59053127 TTATTA
1 TAATTA
59053133 ACTGTTTTTG
Statistics
Matches: 88, Mismatches: 10, Indels: 18
0.76 0.09 0.16
Matches are distributed among these distances:
7 2 0.02
8 7 0.08
9 60 0.68
10 10 0.11
11 7 0.08
12 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (9 bp):
TAATTATTA
Found at i:59053092 original size:3 final size:3
Alignment explanation
Indices: 59053084--59053132 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
59053074 TTACTCTAAA
59053084 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
59053132 A
1 A
59053133 ACTGTTTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:59055748 original size:11 final size:11
Alignment explanation
Indices: 59055732--59055756 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59055722 ATTAATGGCA
59055732 AAATTGTAATT
1 AAATTGTAATT
59055743 AAATTGTAATT
1 AAATTGTAATT
59055754 AAA
1 AAA
59055757 ATAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATTGTAATT
Found at i:59056700 original size:35 final size:34
Alignment explanation
Indices: 59056660--59056806 Score: 104
Period size: 35 Copynumber: 4.3 Consensus size: 34
59056650 ACTATGAACT
*
59056660 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAGTTGGACCATGGCA-TGTTTATATG
* * * *
59056695 TAAGACCATAGTTGGGCTATGGCAT-TCT-GATG
1 TAAGACCATAGTTGGACCATGGCATGTTTATATG
* * ** * * * *
59056727 ATAAGACCATAACTAGG-TTATGGCA-CTATAAACG
1 -TAAGACCAT-AGTTGGACCATGGCATGTTTATATG
*
59056761 TAAGACCATGGTTGGACCATGGCAATGTTTATATG
1 TAAGACCATAGTTGGACCATGGC-ATGTTTATATG
59056796 TAAGACCATAG
1 TAAGACCATAG
59056807 CTGGGATATA
Statistics
Matches: 84, Mismatches: 21, Indels: 14
0.71 0.18 0.12
Matches are distributed among these distances:
32 6 0.07
33 34 0.40
34 8 0.10
35 36 0.43
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (34 bp):
TAAGACCATAGTTGGACCATGGCATGTTTATATG
Found at i:59056800 original size:101 final size:101
Alignment explanation
Indices: 59056625--59056855 Score: 345
Period size: 101 Copynumber: 2.3 Consensus size: 101
59056615 TGAATTCACG
* * * * *
59056625 GATAATACAATAACTGGGTTATGGCACTATGAACTTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATAAACGTAAGACCATGGTTGGACCATGGCAATGTTT
* * * *
59056690 ATATGTAAGACCATAGTTGGGCTATGGCATTCTGAT
66 ATATGTAAGACCATAGCTGGGATATAGAATTCTGAT
*
59056726 GATAAGACCATAACTAGGTTATGGCACTATAAACGTAAGACCATGGTTGGACCATGGCAATGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATAAACGTAAGACCATGGTTGGACCATGGCAATGTTT
*
59056791 ATATGTAAGACCATAGCTGGGATATAGAATTTTGAT
66 ATATGTAAGACCATAGCTGGGATATAGAATTCTGAT
* *
59056827 GAAAAGACCATAACTGGGTTATGACACTA
1 GATAAGACCATAACTGGGTTATGGCACTA
59056856 CGAATGTAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 116 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATAAACGTAAGACCATGGTTGGACCATGGCAATGTTT
ATATGTAAGACCATAGCTGGGATATAGAATTCTGAT
Found at i:59056885 original size:24 final size:24
Alignment explanation
Indices: 59056858--59056908 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
59056848 TGACACTACG
59056858 AATGTAAAGGATGAATTGACGGAA
1 AATGTAAAGGATGAATTGACGGAA
*
59056882 AATGTAAAGGATGAATTGACGGCA
1 AATGTAAAGGATGAATTGACGGAA
59056906 AAT
1 AAT
59056909 TACCCAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.06, G:0.27, T:0.22
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGGAA
Found at i:59058409 original size:9 final size:9
Alignment explanation
Indices: 59058374--59058415 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
59058364 AATTTCTAAA
59058374 ATTTTTAAT
1 ATTTTTAAT
59058383 ATTATTTAAT
1 ATT-TTTAAT
59058393 AATTTTT-AT
1 -ATTTTTAAT
*
59058402 ATTTTTTAT
1 ATTTTTAAT
59058411 ATTTT
1 ATTTT
59058416 ATGTTTCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.20
9 12 0.40
10 9 0.30
11 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:59059338 original size:15 final size:16
Alignment explanation
Indices: 59059310--59059344 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
59059300 TCTAAAAAAT
59059310 ATATTTATATAATTTA
1 ATATTTATATAATTTA
*
59059326 ATATTTA-ATAATTTT
1 ATATTTATATAATTTA
59059341 ATAT
1 ATAT
59059345 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTTATATAATTTA
Found at i:59059353 original size:23 final size:22
Alignment explanation
Indices: 59059313--59059366 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
59059303 AAAAAATATA
59059313 TTTATATAATTTAATATTTAATAAT
1 TTTATAT-ATTTAATA-TTAA-AAT
*
59059338 TTTATATATTT-TTATTAAAAT
1 TTTATATATTTAATATTAAAAT
*
59059359 ATTATATA
1 TTTATATA
59059367 GAATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.37
22 4 0.15
23 2 0.07
24 4 0.15
25 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATATATTTAATATTAAAAT
Found at i:59061067 original size:22 final size:21
Alignment explanation
Indices: 59061024--59061065 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
59061014 TGATTCAAGT
59061024 TTAAATTAAATAATAAACATA
1 TTAAATTAAATAATAAACATA
* *
59061045 TTAAATTTAATCATAAA-ATA
1 TTAAATTAAATAATAAACATA
59061065 T
1 T
59061066 ATGGGCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAATTAAATAATAAACATA
Found at i:59061589 original size:16 final size:18
Alignment explanation
Indices: 59061554--59061589 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
59061544 TAAAAAAGTC
59061554 ATTTTAGCCTTCTATTTA
1 ATTTTAGCCTTCTATTTA
59061572 ATTTTAGCC-TCT-TTTA
1 ATTTTAGCCTTCTATTTA
59061588 AT
1 AT
59061590 CATTGAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 3 0.17
18 9 0.50
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTTTAGCCTTCTATTTA
Found at i:59076843 original size:9 final size:9
Alignment explanation
Indices: 59076829--59076880 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 9
59076819 ACATATTATA
59076829 TTTTATATT
1 TTTTATATT
*
59076838 TTTTATAAT
1 TTTTATATT
*
59076847 TTTAATAATT
1 TTTTAT-ATT
*
59076857 TTGTA-ATT
1 TTTTATATT
59076865 TTTTATGATT
1 TTTTAT-ATT
59076875 TTTTAT
1 TTTTAT
59076881 TTATTTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 7 0.21
9 13 0.38
10 14 0.41
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (9 bp):
TTTTATATT
Found at i:59077021 original size:16 final size:16
Alignment explanation
Indices: 59077000--59077035 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
59076990 TCGAGAACAT
59077000 CTGATAACATTAGGGA
1 CTGATAACATTAGGGA
* *
59077016 CTGATAATATTGGGGA
1 CTGATAACATTAGGGA
59077032 CTGA
1 CTGA
59077036 AGTGGGTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (16 bp):
CTGATAACATTAGGGA
Found at i:59079566 original size:21 final size:21
Alignment explanation
Indices: 59079526--59079566 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
59079516 TTTTTTTTCA
59079526 TATTAATTTTGAGTGTTATTCG
1 TATTAATTTTGAG-GTTATTCG
59079548 TATTAATTTCTGA-GTTATT
1 TATTAATTT-TGAGGTTATT
59079567 GTACAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (21 bp):
TATTAATTTTGAGGTTATTCG
Found at i:59082331 original size:6 final size:6
Alignment explanation
Indices: 59082322--59082360 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
59082312 TACATATACA
*
59082322 TATATG TATATG TTATATG TGTATG TATATG TATATG TA
1 TATATG TATATG -TATATG TATATG TATATG TATATG TA
59082361 AATGCTCACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:59082346 original size:19 final size:18
Alignment explanation
Indices: 59082324--59082359 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
59082314 CATATACATA
59082324 TATGTATATGTTATATGTG
1 TATGTATATG-TATATGTG
59082343 TATGTATATGTATATGT
1 TATGTATATGTATATGT
59082360 AAATGCTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (18 bp):
TATGTATATGTATATGTG
Found at i:59082519 original size:2 final size:2
Alignment explanation
Indices: 59082514--59082554 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
59082504 ATATATATAT
59082514 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
59082555 CGTACCGAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59084998 original size:8 final size:8
Alignment explanation
Indices: 59084987--59085013 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
59084977 AAAAAATTAG
59084987 AAAATTTT
1 AAAATTTT
59084995 AAAATTTT
1 AAAATTTT
59085003 AAAATTTT
1 AAAATTTT
59085011 AAA
1 AAA
59085014 TTGGTAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAAATTTT
Found at i:59085000 original size:16 final size:16
Alignment explanation
Indices: 59084979--59085013 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
59084969 GGCCCTTTAA
59084979 AAAATTAGAAAATTTT
1 AAAATTAGAAAATTTT
**
59084995 AAAATTTTAAAATTTT
1 AAAATTAGAAAATTTT
59085011 AAA
1 AAA
59085014 TTGGTAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
AAAATTAGAAAATTTT
Found at i:59086015 original size:11 final size:11
Alignment explanation
Indices: 59086001--59086027 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
59085991 AAAATAAAAA
59086001 TAAAAGTATTT
1 TAAAAGTATTT
59086012 TAAAAGTATTT
1 TAAAAGTATTT
59086023 TAAAA
1 TAAAA
59086028 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (11 bp):
TAAAAGTATTT
Found at i:59087860 original size:23 final size:23
Alignment explanation
Indices: 59087825--59087876 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
59087815 ACCTACTTTC
* * *
59087825 TTACTGTAATAATTTTCGTGGTA
1 TTACAGTAATAATTTTCGAGATA
*
59087848 TTACAGTAGTAATTTTCGAGATA
1 TTACAGTAATAATTTTCGAGATA
59087871 TTACAG
1 TTACAG
59087877 ATATAGACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (23 bp):
TTACAGTAATAATTTTCGAGATA
Found at i:59088793 original size:30 final size:30
Alignment explanation
Indices: 59088729--59088794 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
59088719 AAAGCTTAAG
**
59088729 TACCAAATTAGAAAAAAAATCAAATTCAGG
1 TACCAAATTAGAAAAAAAATCAAATTCAAA
** *
59088759 TACCAAATTAGAAAAATTATCAAGTTCAAA
1 TACCAAATTAGAAAAAAAATCAAATTCAAA
59088789 TACCAA
1 TACCAA
59088795 TTTAACCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.55, C:0.15, G:0.08, T:0.23
Consensus pattern (30 bp):
TACCAAATTAGAAAAAAAATCAAATTCAAA
Found at i:59090740 original size:6 final size:6
Alignment explanation
Indices: 59090708--59090761 Score: 72
Period size: 6 Copynumber: 8.8 Consensus size: 6
59090698 ACAACACCTA
* * *
59090708 AACAGT AATCAGT AACTGT AGCAGT AACAGT AATAGT AACAGT AACAGT
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT
59090757 AACAG
1 AACAG
59090762 AAATAGTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
6 35 0.85
7 6 0.15
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (6 bp):
AACAGT
Found at i:59090769 original size:12 final size:12
Alignment explanation
Indices: 59090708--59090769 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
59090698 ACAACACCTA
59090708 AACAGTAATCAGT
1 AACAGTAAT-AGT
* **
59090721 AACTGTAGCAGT
1 AACAGTAATAGT
59090733 AACAGTAATAGT
1 AACAGTAATAGT
*
59090745 AACAGTAACAGT
1 AACAGTAATAGT
*
59090757 AACAGAAATAGT
1 AACAGTAATAGT
59090769 A
1 A
59090770 TTCAACACAC
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
12 34 0.85
13 6 0.15
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (12 bp):
AACAGTAATAGT
Found at i:59090769 original size:18 final size:18
Alignment explanation
Indices: 59090707--59090769 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
59090697 CACAACACCT
*
59090707 AAACAGTAATCAGTAACTG
1 AAACAGTAA-CAGTAACAG
* * *
59090726 TAGCAGTAACAGTAATAG
1 AAACAGTAACAGTAACAG
*
59090744 TAACAGTAACAGTAACAG
1 AAACAGTAACAGTAACAG
*
59090762 AAATAGTA
1 AAACAGTA
59090770 TTCAACACAC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
18 29 0.81
19 7 0.19
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (18 bp):
AAACAGTAACAGTAACAG
Found at i:59092142 original size:8 final size:8
Alignment explanation
Indices: 59092129--59092161 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
59092119 TGCTTTATAT
59092129 ATATAATA
1 ATATAATA
59092137 ATATAATA
1 ATATAATA
*
59092145 TTATAATA
1 ATATAATA
59092153 ATATAATA
1 ATATAATA
59092161 A
1 A
59092162 AACAACATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:59092151 original size:16 final size:17
Alignment explanation
Indices: 59092125--59092160 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
59092115 CATTTGCTTT
59092125 ATATATATAATAATATA
1 ATATATATAATAATATA
59092142 ATAT-TATAATAATATA
1 ATATATATAATAATATA
59092158 ATA
1 ATA
59092161 AAACAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATATAATAATATA
Found at i:59093087 original size:3 final size:3
Alignment explanation
Indices: 59093081--59093136 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
59093071 ATGCTCGTAC
59093081 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59093129 ATA ATA AT
1 ATA ATA AT
59093137 TTGTTTTTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:59095456 original size:13 final size:14
Alignment explanation
Indices: 59095440--59095477 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
59095430 AAAACATATG
59095440 TTAAAAATTAAAT-
1 TTAAAAATTAAATA
59095453 TTAAAAA-TAAATA
1 TTAAAAATTAAATA
59095466 TTATAAAATTAA
1 TTA-AAAATTAA
59095478 TAATTTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.23
13 10 0.45
14 4 0.18
15 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAATTAAATA
Found at i:59096180 original size:15 final size:14
Alignment explanation
Indices: 59096155--59096185 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
59096145 TAAATATGAA
59096155 ATTTTTTTATTTTT
1 ATTTTTTTATTTTT
59096169 ATTTTTTATATTTTT
1 ATTTTTT-TATTTTT
59096184 AT
1 AT
59096186 GTAATAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTTTTATTTTT
Found at i:59101238 original size:22 final size:23
Alignment explanation
Indices: 59101189--59101239 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
59101179 AAATTTTCAA
59101189 AGTTGGGTGACCAAAAAAAAATT
1 AGTTGGGTGACCAAAAAAAAATT
*
59101212 TGTTGGGTGA-CAAAAAAAACA-T
1 AGTTGGGTGACCAAAAAAAA-ATT
59101234 AGTTGG
1 AGTTGG
59101240 ATGAACTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.43, C:0.08, G:0.25, T:0.24
Consensus pattern (23 bp):
AGTTGGGTGACCAAAAAAAAATT
Found at i:59102717 original size:63 final size:63
Alignment explanation
Indices: 59102640--59102766 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 63
59102630 TTTGTGTGTC
* *
59102640 TCCTCTTCAAGGAGGTTAATTTCGCTATTTATATAATGT-GATTCTTGCATGTGACGTTTTAGG
1 TCCTCTTCAAGGAGGTTAATTTCGCTATTTATATAATATAG-TTCTTGCATGTGACGTTCTAGG
*
59102703 TCCTCTTCAAGGAGGTTAATTTTGCTATTTATATAATATAGTTCTTGCATGTGACGTTCTAGG
1 TCCTCTTCAAGGAGGTTAATTTCGCTATTTATATAATATAGTTCTTGCATGTGACGTTCTAGG
59102766 T
1 T
59102767 AGACCTCCAT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 59 0.98
64 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (63 bp):
TCCTCTTCAAGGAGGTTAATTTCGCTATTTATATAATATAGTTCTTGCATGTGACGTTCTAGG
Found at i:59106604 original size:14 final size:15
Alignment explanation
Indices: 59106579--59106607 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59106569 ACCCGACCCA
59106579 TATTACTTTTTATAT
1 TATTACTTTTTATAT
59106594 TATTA-TTTTTATAT
1 TATTACTTTTTATAT
59106608 AGTTCTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTACTTTTTATAT
Found at i:59109395 original size:16 final size:16
Alignment explanation
Indices: 59109374--59109406 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59109364 ACAAGTGAGA
59109374 TTAAAAAATTAATTTT
1 TTAAAAAATTAATTTT
*
59109390 TTAAAAAATTACTTTT
1 TTAAAAAATTAATTTT
59109406 T
1 T
59109407 AAATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAAATTAATTTT
Found at i:59111046 original size:6 final size:6
Alignment explanation
Indices: 59111032--59111061 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
59111022 GTGGGAAGGA
*
59111032 AGGGAG AGGGTG AGGGTG AGGGTG AGGGTG
1 AGGGTG AGGGTG AGGGTG AGGGTG AGGGTG
59111062 GCTTGAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.67, T:0.13
Consensus pattern (6 bp):
AGGGTG
Found at i:59117361 original size:2 final size:2
Alignment explanation
Indices: 59117354--59117378 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59117344 CTCTAACTTT
59117354 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
59117379 TTCCAATAAA
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:59118861 original size:2 final size:2
Alignment explanation
Indices: 59118854--59118888 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
59118844 CATATAAAAC
59118854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59118889 CAGTCTGACT
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:59120605 original size:6 final size:6
Alignment explanation
Indices: 59120594--59120634 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
59120584 TAATCTTCAT
59120594 TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCCCC
1 TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCCCCA TCCCC
59120635 CTCCGGCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.15, C:0.68, G:0.00, T:0.17
Consensus pattern (6 bp):
TCCCCA
Found at i:59125022 original size:2 final size:2
Alignment explanation
Indices: 59125015--59125047 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59125005 GTATATCTGG
59125015 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 T
59125048 CTTGTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59141260 original size:26 final size:26
Alignment explanation
Indices: 59141216--59141271 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
59141206 AATTTTAAAA
** * *
59141216 TATTTTTAAAATACTTTTTTATTTTT
1 TATTTTTAAAATAAATTTTTAGTGTT
59141242 TATTTTTAAAATAAATTTTTAGTGTT
1 TATTTTTAAAATAAATTTTTAGTGTT
59141268 TATT
1 TATT
59141272 AAAAAAATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (26 bp):
TATTTTTAAAATAAATTTTTAGTGTT
Found at i:59142296 original size:3 final size:3
Alignment explanation
Indices: 59142288--59142313 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59142278 CATTGCACAT
59142288 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
59142314 AAGTTGTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:59142615 original size:30 final size:30
Alignment explanation
Indices: 59142581--59142651 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
59142571 ATTAATAATA
* *
59142581 ATAAAATTATACGTTCATCTTTCAAAAATT
1 ATAAAATTATAAGTTAATCTTTCAAAAATT
* * *
59142611 ATAAAATT-TAATTTAATTTTTTAAAAATT
1 ATAAAATTATAAGTTAATCTTTCAAAAATT
*
59142640 ATAAAAATATAA
1 ATAAAATTATAA
59142652 ATTATTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (30 bp):
ATAAAATTATAAGTTAATCTTTCAAAAATT
Found at i:59144406 original size:25 final size:25
Alignment explanation
Indices: 59144348--59144398 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
59144338 ACAAATTGAA
59144348 ACAGCAAAAAGAAATGAAGAATGAT
1 ACAGCAAAAAGAAATGAAGAATGAT
59144373 ACAGCAAAAAGAAATGAAGAATGAT
1 ACAGCAAAAAGAAATGAAGAATGAT
59144398 A
1 A
59144399 GTGTAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.61, C:0.08, G:0.20, T:0.12
Consensus pattern (25 bp):
ACAGCAAAAAGAAATGAAGAATGAT
Found at i:59145090 original size:22 final size:22
Alignment explanation
Indices: 59145040--59145090 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
59145030 ATAATAAAAA
59145040 TATATT-TAAAATAATATAATT
1 TATATTATAAAATAATATAATT
* *
59145061 TATTTTATAAAATAAATATATTT
1 TATATTATAAAAT-AATATAATT
59145084 TA-ATTAT
1 TATATTAT
59145091 TACTGAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 10 0.40
23 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTATAAAATAATATAATT
Found at i:59145578 original size:5 final size:5
Alignment explanation
Indices: 59145570--59145596 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
59145560 GAATCAGTTG
59145570 AATTT AATTT AATTT AATTT AATTT AA
1 AATTT AATTT AATTT AATTT AATTT AA
59145597 AAATGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:59146250 original size:3 final size:3
Alignment explanation
Indices: 59146244--59146283 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
59146234 ATTTGACCAA
59146244 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
59146284 GTAGCATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:59151724 original size:5 final size:6
Alignment explanation
Indices: 59151706--59151731 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
59151696 GTTAGGCTAC
59151706 TTCTTT TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TT
59151732 TTCCGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTCTTT
Found at i:59161184 original size:186 final size:187
Alignment explanation
Indices: 59160858--59161218 Score: 462
Period size: 186 Copynumber: 1.9 Consensus size: 187
59160848 AAAATACTCA
** * * * *
59160858 TTTACTAATCTGGTTCTCTTATAGTTGGAATCTATGCTGCCGAAGGAGGAAAAGACCACCGGGAA
1 TTTACTAATCCAGTTCCCTGATAGTTGGAATCTATGCTGCCGAAGCAGGAAAAGACCACCGCGAA
* * *
59160923 CCAAGGGGCTCCGACTCAAAGGGCTTCAGCTTTAGCTGCCTTAACTTCAGCATTCAATAAATCTC
66 CCAAGGGGCTCCGACTCAAAGGGCTTCAGCTTTAGCTGCCTTAACTTAAGCATTCAATAAAGCTA
*
59160988 CTTCCAAATCACCCCCTCCGGTAATAAACTGCTTATGCCAATAAATGATGATACTTG
131 CTTCCAAATCACCCACTCCGGTAATAAACTGCTTATGCCAATAAATGATGATACTTG
* * *
59161045 TTTACTAATCCAGTTCCCTGATCGTTGGAATC-ATGCTGCC-AAGACAGGAAAAGTCCACTGCGA
1 TTTACTAATCCAGTTCCCTGATAGTTGGAATCTATGCTGCCGAAG-CAGGAAAAGACCACCGCGA
* * *
59161108 ACCAAGGGGGTCCTACTCAAAGGGCTTCAGCTTTAGCTGCCTTAAC-TAATGCATTCAA-ATCAG
65 ACCAAGGGGCTCCGACTCAAAGGGCTTCAGCTTTAGCTGCCTTAACTTAA-GCATTCAATA-AAG
* ** * *
59161171 CTAC-TCGCAAATCATCCACTGTGGTAATAAACTTCTTATGCCATTAAA
128 CTACTTC-CAAATCACCCACTCCGGTAATAAACTGCTTATGCCAATAAA
59161219 CTCTTTTTTT
Statistics
Matches: 149, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
185 8 0.05
186 114 0.77
187 27 0.18
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (187 bp):
TTTACTAATCCAGTTCCCTGATAGTTGGAATCTATGCTGCCGAAGCAGGAAAAGACCACCGCGAA
CCAAGGGGCTCCGACTCAAAGGGCTTCAGCTTTAGCTGCCTTAACTTAAGCATTCAATAAAGCTA
CTTCCAAATCACCCACTCCGGTAATAAACTGCTTATGCCAATAAATGATGATACTTG
Found at i:59161455 original size:9 final size:9
Alignment explanation
Indices: 59161441--59161465 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
59161431 ACAAAGAGCT
59161441 GCAGCTTTA
1 GCAGCTTTA
59161450 GCAGCTTTA
1 GCAGCTTTA
59161459 GCAGCTT
1 GCAGCTT
59161466 CATTTAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (9 bp):
GCAGCTTTA
Found at i:59161830 original size:66 final size:65
Alignment explanation
Indices: 59161752--59161883 Score: 192
Period size: 66 Copynumber: 2.0 Consensus size: 65
59161742 TGCAGACTCA
* ** * *
59161752 AGTGAAGTGAACCCTTCTGAAGCTGATGATTCTGTAGGGGTTGCCAAAACCAATAAGGAAGACTT
1 AGTGAAGCGAACCCTTCTGAAGCTGATGATTCTCAAGAGGTTGCCAAAACCAACAAGGAAGA-TT
59161817 G
65 G
* *
59161818 AGTGAAGCGAACCCTTCTGGAGCTGATGATTCTCAAGAGGTTGCTAAAACCAACAAGGAAGATTG
1 AGTGAAGCGAACCCTTCTGAAGCTGATGATTCTCAAGAGGTTGCCAAAACCAACAAGGAAGATTG
59161883 A
1 A
59161884 AAACCGAAGG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
65 4 0.07
66 55 0.93
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (65 bp):
AGTGAAGCGAACCCTTCTGAAGCTGATGATTCTCAAGAGGTTGCCAAAACCAACAAGGAAGATTG
Found at i:59166174 original size:209 final size:210
Alignment explanation
Indices: 59165827--59166221 Score: 551
Period size: 209 Copynumber: 1.9 Consensus size: 210
59165817 GCAAAATTTC
* * *
59165827 ATTTCATTTTTCTTTTTGTCAGTTTTATATCTGTTGTTTGAATATATTTGTTTTCCAATTGGGAA
1 ATTTCATTTCTCTTTTTGTCAGTTTTATATCTGTTGTTTGAATATATTTGTTCTCCAATTGGAAA
* * * * *
59165892 CACTAGTTAGTTCTTTTTGACTGTTTTCAGTTCAAAGATTTCTTCTGGTCTGAGTTCTGTACCAA
66 AACTAGTTAGTGCTTTTTGACTGTTTTCAGTTCAAAGATTTCTTCTGATCTGAATTCTCTACCAA
* * *
59165957 TCAGTGCTATTGAATTACTGATTACTTTGATTTTGTATAGTTTCCCTTTTAATGCAGGTTTCTTT
131 TCAGTGCTACTGAATCACTAATTACTTTGATTTTGTATAGTTT-CCTTTTAATGCAGGTTTCTTT
59166022 AATTACTTGATCCAAA
195 AATTACTTGATCCAAA
* * * * *
59166038 ATTTCATTTCT-TTTTTGTCAGTTTTATGTCTGTTGTTTGGATGTTTTTGTTCT-GAATTGGAAA
1 ATTTCATTTCTCTTTTTGTCAGTTTTATATCTGTTGTTTGAATATATTTGTTCTCCAATTGGAAA
* * ** * *
59166101 AACTAGTTTGTGCTTTTTTACTGTTTTTGGTTCAATGATTTCTTCTGATCTGAATTCTCTACCAG
66 AACTAGTTAGTGCTTTTTGACTGTTTTCAGTTCAAAGATTTCTTCTGATCTGAATTCTCTACCAA
* *
59166166 TGAGTGCTACTGAATCACTAATTTCTTTGATTTTGTATAGTTTCCTTTTAATGCAG
131 TCAGTGCTACTGAATCACTAATTACTTTGATTTTGTATAGTTTCCTTTTAATGCAG
59166222 CTTTATGTTG
Statistics
Matches: 160, Mismatches: 24, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
208 13 0.08
209 100 0.62
210 37 0.23
211 10 0.06
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.50
Consensus pattern (210 bp):
ATTTCATTTCTCTTTTTGTCAGTTTTATATCTGTTGTTTGAATATATTTGTTCTCCAATTGGAAA
AACTAGTTAGTGCTTTTTGACTGTTTTCAGTTCAAAGATTTCTTCTGATCTGAATTCTCTACCAA
TCAGTGCTACTGAATCACTAATTACTTTGATTTTGTATAGTTTCCTTTTAATGCAGGTTTCTTTA
ATTACTTGATCCAAA
Found at i:59166606 original size:21 final size:21
Alignment explanation
Indices: 59166580--59166639 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
59166570 TAGATGCCAA
59166580 CAACAACTATCAGAGGTACGC
1 CAACAACTATCAGAGGTACGC
59166601 CAACAACTATCAGAGGTACGC
1 CAACAACTATCAGAGGTACGC
** *
59166622 GGACAACAATCAGAGGTA
1 CAACAACTATCAGAGGTA
59166640 AGCTAACTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.13
Consensus pattern (21 bp):
CAACAACTATCAGAGGTACGC
Found at i:59172594 original size:15 final size:15
Alignment explanation
Indices: 59172574--59172607 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
59172564 GAAAGTTAAT
59172574 AGAAAAAGAATA-AAA
1 AGAAAAAGAA-ACAAA
59172589 AGAAAAAGAAACAAA
1 AGAAAAAGAAACAAA
59172604 AGAA
1 AGAA
59172608 GAACAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (15 bp):
AGAAAAAGAAACAAA
Found at i:59172638 original size:22 final size:22
Alignment explanation
Indices: 59172592--59172639 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
59172582 AATAAAAAGA
*
59172592 AAAAGAAACAAAAGAAGAACAG
1 AAAAGAAACAAAACAAGAACAG
59172614 AAAAGAAACAGAGAACAA-AAC-G
1 AAAAGAAACA-A-AACAAGAACAG
59172636 AAAA
1 AAAA
59172640 CAGGGGATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 15 0.65
23 4 0.17
24 4 0.17
ACGTcount: A:0.73, C:0.10, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAGAAACAAAACAAGAACAG
Found at i:59173022 original size:22 final size:24
Alignment explanation
Indices: 59172997--59173040 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
59172987 TATGGGAAGA
59172997 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGCTAGAAAAGTAAGTATG
59173019 AATTAAGCTAGAAAAGTAAGTA
1 AATTAAGCTAGAAAAGTAAGTA
59173041 GGTTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.23
Consensus pattern (24 bp):
AATTAAGCTAGAAAAGTAAGTATG
Found at i:59177966 original size:22 final size:24
Alignment explanation
Indices: 59177923--59177966 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
59177913 TAACTAAACC
59177923 TACTTACTTTTCTAGCTTAATTCA
1 TACTTACTTTTCTAGCTTAATTCA
59177947 TACTT-CTTTTCTA-CTTAATT
1 TACTTACTTTTCTAGCTTAATT
59177967 TCTTCCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAGCTTAATTCA
Found at i:59178376 original size:15 final size:15
Alignment explanation
Indices: 59178356--59178389 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
59178346 TTTTCTGTTC
59178356 TTCTTTTGT-TTCTTT
1 TTCTTTT-TATTCTTT
59178371 TTCTTTTTATTCTTT
1 TTCTTTTTATTCTTT
59178386 TTCT
1 TTCT
59178390 ATTAACTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (15 bp):
TTCTTTTTATTCTTT
Found at i:59178378 original size:29 final size:29
Alignment explanation
Indices: 59178321--59178377 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
59178311 TTTTCTTCCC
59178321 CTGTTTTCGTTTTGTTCTCTGTTTCTTTT
1 CTGTTTTCGTTTTGTTCTCTGTTTCTTTT
*
59178350 CTGTTCTTC-TTTTGTT-TCTTTTTCTTTT
1 CTGTT-TTCGTTTTGTTCTCTGTTTCTTTT
59178378 TATTCTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.42
29 12 0.46
30 3 0.12
ACGTcount: A:0.00, C:0.18, G:0.11, T:0.72
Consensus pattern (29 bp):
CTGTTTTCGTTTTGTTCTCTGTTTCTTTT
Found at i:59180071 original size:15 final size:15
Alignment explanation
Indices: 59180048--59180093 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
59180038 GTACATTATG
59180048 ATTATATATTAATAT
1 ATTATATATTAATAT
*
59180063 ATTAAATATT--TAT
1 ATTATATATTAATAT
59180076 ATTATAT-TTATATAT
1 ATTATATATTA-ATAT
59180091 ATT
1 ATT
59180094 TAACCTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 2 0.08
13 9 0.35
15 15 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATATATTAATAT
Found at i:59180076 original size:21 final size:21
Alignment explanation
Indices: 59180052--59180095 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
59180042 ATTATGATTA
59180052 TATATTAATATATTA-A-ATATT
1 TATATT-ATAT-TTATATATATT
59180073 TATATTATATTTATATATATT
1 TATATTATATTTATATATATT
59180094 TA
1 TA
59180096 ACCTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.14
20 5 0.24
21 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATTATATTTATATATATT
Found at i:59182138 original size:17 final size:17
Alignment explanation
Indices: 59182116--59182149 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59182106 TTCGTCCCTG
*
59182116 AGACTAACTACCTGATA
1 AGACTAACTACCAGATA
59182133 AGACTAACTACCAGATA
1 AGACTAACTACCAGATA
59182150 GACAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.21
Consensus pattern (17 bp):
AGACTAACTACCAGATA
Found at i:59186337 original size:22 final size:22
Alignment explanation
Indices: 59186312--59186354 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
59186302 ATGTTTAGTT
59186312 ATTTATT-TTTTAATTTAATTTA
1 ATTTATTGTTTT-ATTTAATTTA
59186334 ATTTATTGTTTTATTTAATTT
1 ATTTATTGTTTTATTTAATTT
59186355 TCATACAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTATTGTTTTATTTAATTTA
Found at i:59189055 original size:14 final size:14
Alignment explanation
Indices: 59189036--59189066 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59189026 GCAGGTATTT
*
59189036 TTTTGATATGTTTA
1 TTTTGACATGTTTA
59189050 TTTTGACATGTTTA
1 TTTTGACATGTTTA
59189064 TTT
1 TTT
59189067 ATTTATTATT
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:0.19, C:0.03, G:0.13, T:0.65
Consensus pattern (14 bp):
TTTTGACATGTTTA
Found at i:59202793 original size:19 final size:19
Alignment explanation
Indices: 59202751--59202795 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
59202741 CTTTCATGCT
*
59202751 TAAAAAAACAAAACAAGAC
1 TAAAAAAAAAAAACAAGAC
* **
59202770 AAAAAAAAAAAAACAATTC
1 TAAAAAAAAAAAACAAGAC
59202789 TAAAAAA
1 TAAAAAA
59202796 TAATCATCCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.78, C:0.11, G:0.02, T:0.09
Consensus pattern (19 bp):
TAAAAAAAAAAAACAAGAC
Found at i:59204541 original size:33 final size:33
Alignment explanation
Indices: 59204481--59204543 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
59204471 TATATTAAAA
* **
59204481 ATTTATTTATAATAATTTATTTGATATTTTTAT
1 ATTTATTTATAATAATATATTAAATATTTTTAT
59204514 ATTTATTTAT-ATAAATATATTAAATATTTT
1 ATTTATTTATAAT-AATATATTAAATATTTT
59204544 AAAAAATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.08
33 24 0.92
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (33 bp):
ATTTATTTATAATAATATATTAAATATTTTTAT
Done.