Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 4 of 167
Found at i:945481 original size:71 final size:71
Alignment explanation
Indices: 945365--946220 Score: 1712
Period size: 71 Copynumber: 12.1 Consensus size: 71
945355 TATCTCAAAA
945365 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
945430 TATTTT
66 TATTTT
945436 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
945501 TATTTT
66 TATTTT
945507 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
945572 TATTTT
66 TATTTT
945578 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
945643 TATTTT
66 TATTTT
945649 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
945714 TATTTT
66 TATTTT
945720 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
945785 TATTTT
66 TATTTT
945791 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
945856 TATTTT
66 TATTTT
945862 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
945927 TATTTT
66 TATTTT
945933 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
945998 TATTTT
66 TATTTT
946004 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
946069 TATTTT
66 TATTTT
946075 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
946140 TATTTT
66 TATTTT
946146 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
1 TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
946211 TATTTT
66 TATTTT
946217 TTTA
1 TTTA
946221 ATCTTATAAT
Statistics
Matches: 785, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 785 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (71 bp):
TTTACAAATCTATTACTTACAACGTTTCTTCTATGAGAAACTAGACTCAATGATATTTAATTTGA
TATTTT
Found at i:951653 original size:5 final size:5
Alignment explanation
Indices: 951619--951652 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
951609 TCAATTCATT
* *
951619 TTTAA TTTAA TTTAA TTTAA TTTAT TTTAT TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
951653 TGCAAGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (5 bp):
TTTAA
Found at i:954497 original size:20 final size:20
Alignment explanation
Indices: 954472--954511 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
954462 TTAATTTTGG
954472 ATTGATTCATTTTTTAGATC
1 ATTGATTCATTTTTTAGATC
954492 ATTGATTCATTTTTTAGATC
1 ATTGATTCATTTTTTAGATC
954512 TTATAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTGATTCATTTTTTAGATC
Found at i:955132 original size:39 final size:39
Alignment explanation
Indices: 955063--955213 Score: 124
Period size: 39 Copynumber: 3.8 Consensus size: 39
955053 AGCGGCGCTT
* *
955063 TTAGCGGCGATTGGACAACAAACGCCGCTAAAAATTAAGCA
1 TTAGCGGCGATT-GAAAAAAAACGCCGCTAAAAA-TAAGCA
* * *
955104 TTAGCGGCGATT-AAAAAAAACGCCGCTAAATATCAGTA
1 TTAGCGGCGATTGAAAAAAAACGCCGCTAAAAATAAGCA
* * ** * * *
955142 TTACCGGCGCTTTTACAAAAACGCCGCTAATAATGAGCA
1 TTAGCGGCGATTGAAAAAAAACGCCGCTAAAAATAAGCA
* *** *
955181 TTAGCGGCGTTTCTTAAAAAGCGCCGCTAAAAA
1 TTAGCGGCGATTGAAAAAAAACGCCGCTAAAAA
955214 CCTAAACCAA
Statistics
Matches: 89, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
38 14 0.16
39 63 0.71
41 12 0.13
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGATTGAAAAAAAACGCCGCTAAAAATAAGCA
Found at i:955502 original size:114 final size:113
Alignment explanation
Indices: 955181--955507 Score: 397
Period size: 113 Copynumber: 2.9 Consensus size: 113
955171 ATAATGAGCA
* * *
955181 TTAGCGGCGTTTCTTAAAAAGCGCCGCTAAAAACCTAAACCAAACGACGTCGTTTTTCTTAGTTT
1 TTAGCGGCGTTTCTTAAAAAGCGCCGC-AAAAACCTAAGCCCAACGACATCGTTTTTCTTAGTTT
* * * *
955246 TCGAGGCTTTGGTGGCGTTTTTGGAGAAGCGCAAG-TAATTCTCAGGGCT
65 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGC-CGCTAATGCTCAAGGCT
* * *
955295 TTAGCAGCGTTTCTTAAAAAGCGCCGCAAAAGACCTAAGCCCAACGTCATC-ATTTTCTTAGTTT
1 TTAGCGGCGTTTCTTAAAAAGCGCCGCAAAA-ACCTAAGCCCAACGACATCGTTTTTCTTAGTTT
* * * *
955359 TCGAGGCTTTGGTGGCGTTTTCGGGAAAGCGCCGCTAATGCTCAATGTT
65 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAGGCT
* * * * *
955408 TTAGCGGCATTTTTTAAAAATCGCCACAAAAAACTGAAGCCCAACGACATCGTTTTTCTTAGTTT
1 TTAGCGGCGTTTCTTAAAAAGCGCCGCAAAAACCT-AAGCCCAACGACATCGTTTTTCTTAGTTT
** * *
955473 GGGAGGCTTTAGTGGCGTTTTTGTAAAAGCGCCGC
65 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCCGC
955508 AAAAAGCCTA
Statistics
Matches: 181, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
112 4 0.02
113 95 0.52
114 82 0.45
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (113 bp):
TTAGCGGCGTTTCTTAAAAAGCGCCGCAAAAACCTAAGCCCAACGACATCGTTTTTCTTAGTTTT
CGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAGGCT
Found at i:956023 original size:21 final size:21
Alignment explanation
Indices: 955999--956051 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
955989 ATGGTTTACA
955999 GTTTAGGGTTTACGAGTTGGG
1 GTTTAGGGTTTACGAGTTGGG
* *
956020 GTTTAAGGTTTACGGGTTGGG
1 GTTTAGGGTTTACGAGTTGGG
*
956041 G-TTGGGGTTTA
1 GTTTAGGGTTTA
956052 AGGTTTACGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.13, C:0.04, G:0.43, T:0.40
Consensus pattern (21 bp):
GTTTAGGGTTTACGAGTTGGG
Found at i:956051 original size:27 final size:27
Alignment explanation
Indices: 956014--956066 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
956004 GGGTTTACGA
956014 GTTGGGGTTTAAGGTTTACGGGTTGGG
1 GTTGGGGTTTAAGGTTTACGGGTTGGG
956041 GTTGGGGTTTAAGGTTTACGGGTTGG
1 GTTGGGGTTTAAGGTTTACGGGTTGG
956067 AGTTTAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.11, C:0.04, G:0.47, T:0.38
Consensus pattern (27 bp):
GTTGGGGTTTAAGGTTTACGGGTTGGG
Found at i:956699 original size:189 final size:189
Alignment explanation
Indices: 956466--956844 Score: 589
Period size: 189 Copynumber: 2.0 Consensus size: 189
956456 GTTTTGTTGG
* * * *
956466 ATTTTGTGTTGACCGAAACGAAATCGTTTTTATGTTTTTAGTGGCGTTTTTGTTAAAACGCCGGA
1 ATTTTGTGTTGACCAAAACGAAACCGTTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCGCA
* * * *
956531 AAAGATCTTGCTTTAGCGGCGCTTATCTTAAAACGCCGCAAGAATGTTATTTTGTGTTTACCAAA
66 AAAGATCTTACTTTAGCGGCGCTTATCTTAAAACGCCACAAAAATGTTATTATGTGTTTACCAAA
956596 ACGTGACCGTTTTTTTATGTATTTAGTGGCGTTTTTATTAAAACGCCGCAAAA-ATGTT
131 ACGTGACCGTTTTTTTATGTATTTAGTGGCGTTTTTATTAAAACGCCGCAAAATATGTT
* **
956654 ATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCGC
1 ATTTTGTGTTGACCAAAACGAAACCG-TTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCGC
* * * *
956719 AAAAGATGTTACTTTAGCGGCGCTTCTTTTAAAATGCCACAAAAATGTTATTATGTGTTTACCAA
65 AAAAGATCTTACTTTAGCGGCGCTTATCTTAAAACGCCACAAAAATGTTATTATGTGTTTACCAA
* *
956784 AACGTGACCGTTTTTTTATGTATTTAGTGGCGTTTTTGTTAAAATGCCGCAAAATATGTT
130 AACGTGACCGTTTTTTTATGTATTTAGTGGCGTTTTTATTAAAACGCCGCAAAATATGTT
956844 A
1 A
956845 CTTTAGCGGC
Statistics
Matches: 172, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
188 21 0.12
189 145 0.84
190 6 0.03
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (189 bp):
ATTTTGTGTTGACCAAAACGAAACCGTTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCGCA
AAAGATCTTACTTTAGCGGCGCTTATCTTAAAACGCCACAAAAATGTTATTATGTGTTTACCAAA
ACGTGACCGTTTTTTTATGTATTTAGTGGCGTTTTTATTAAAACGCCGCAAAATATGTT
Found at i:956721 original size:74 final size:75
Alignment explanation
Indices: 956558--956729 Score: 310
Period size: 75 Copynumber: 2.3 Consensus size: 75
956548 GGCGCTTATC
*
956558 TTAAAACGCCGCAAGAATGTTATTTTGTGTTTACCAAAACGTGACCGTTTTTTTATGTATTTAGT
1 TTAAAACGCCGCAAAAATGTTATTTTGTGTTTACCAAAACGTGACCGTTTTTTTATGTATTTAGT
956623 GGCGTTTTTA
66 GGCGTTTTTA
956633 TTAAAACGCCGCAAAAATGTTATTTTGTGTTTACCAAAACGTGACCG-TTTTTTATGTATTTAGT
1 TTAAAACGCCGCAAAAATGTTATTTTGTGTTTACCAAAACGTGACCGTTTTTTTATGTATTTAGT
*
956697 GGCGTTTTTG
66 GGCGTTTTTA
956707 TTAAAACGCCGCAAAAGATGTTA
1 TTAAAACGCCGCAAAA-ATGTTA
956730 CTTTAGCGGC
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
74 42 0.45
75 52 0.55
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (75 bp):
TTAAAACGCCGCAAAAATGTTATTTTGTGTTTACCAAAACGTGACCGTTTTTTTATGTATTTAGT
GGCGTTTTTA
Found at i:956848 original size:115 final size:114
Alignment explanation
Indices: 956633--956949 Score: 553
Period size: 115 Copynumber: 2.8 Consensus size: 114
956623 GGCGTTTTTA
956633 TTAAAACGCCGCAAAAATGTTATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGTG
1 TTAAAACGCCGCAAAAATGTTATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGTG
* *
956698 GCGTTTTTGTTAAAACGCCGCAAAAGATGTTACTTTAGCGGCGCTTCTT
66 GCGTTTTTGTTAAAACGCCGCAAAAGATGTTACTTTAGCGGCGCTTATC
* * *
956747 TTAAAATGCCACAAAAATGTTATTATGTGTTTACCAAAACGTGACCGTTTTTTTATGTATTTAGT
1 TTAAAACGCCGCAAAAATGTTATTTTGTGTTTACCAAAACGTGACCG-TTTTTTATGTATTTAGT
* *
956812 GGCGTTTTTGTTAAAATGCCGCAAAATATGTTACTTTAGCGGCGCTTATC
65 GGCGTTTTTGTTAAAACGCCGCAAAAGATGTTACTTTAGCGGCGCTTATC
956862 TTAAAACGCCGCAAACAATGTTATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGT
1 TTAAAACGCCGCAAA-AATGTTATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGT
956927 GGCGTTTTTGTTAAAACGCCGCA
65 GGCGTTTTTGTTAAAACGCCGCA
956950 GGTGTTTATT
Statistics
Matches: 190, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
114 44 0.23
115 115 0.61
116 31 0.16
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (114 bp):
TTAAAACGCCGCAAAAATGTTATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGTG
GCGTTTTTGTTAAAACGCCGCAAAAGATGTTACTTTAGCGGCGCTTATC
Found at i:967177 original size:16 final size:16
Alignment explanation
Indices: 967156--967186 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
967146 TTTTTTTCAT
967156 ATATATACATACATAC
1 ATATATACATACATAC
*
967172 ATATATATATACATA
1 ATATATACATACATA
967187 TGGCTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATATACATACATAC
Found at i:971266 original size:21 final size:21
Alignment explanation
Indices: 971242--971281 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
971232 CGTGTCAATA
971242 TTTA-ATTACAAATATTTAATT
1 TTTATATT-CAAATATTTAATT
*
971263 TTTATATTTAAATATTTAA
1 TTTATATTCAAATATTTAA
971282 ATATAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATATTCAAATATTTAATT
Found at i:971934 original size:6 final size:6
Alignment explanation
Indices: 971925--971983 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
971915 AACCCCAATG
971925 CCCATT CCCATT CCCATT CCCATT CCCATT CCCATT CCCATT CCCATT
1 CCCATT CCCATT CCCATT CCCATT CCCATT CCCATT CCCATT CCCATT
971973 CCCATT CCCAT
1 CCCATT CCCAT
971984 ACCAAATCCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.17, C:0.51, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCATT
Found at i:972029 original size:20 final size:20
Alignment explanation
Indices: 972004--972044 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
971994 ATGTTACCTT
972004 TGCCACCACCACGTCCTTTC
1 TGCCACCACCACGTCCTTTC
972024 TGCCACCACCACGTCCTTTC
1 TGCCACCACCACGTCCTTTC
972044 T
1 T
972045 CAACATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.49, G:0.10, T:0.27
Consensus pattern (20 bp):
TGCCACCACCACGTCCTTTC
Found at i:972221 original size:24 final size:24
Alignment explanation
Indices: 972191--972238 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
972181 TCCTCCATTT
972191 CCACCACCTCCACC-CCTGCCTTCA
1 CCACCACCTCCACCTCCT-CCTTCA
*
972215 CCACCACCTCCTCCTCCTCCTTCA
1 CCACCACCTCCACCTCCTCCTTCA
972239 ATGCCAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.15, C:0.62, G:0.02, T:0.21
Consensus pattern (24 bp):
CCACCACCTCCACCTCCTCCTTCA
Found at i:974828 original size:62 final size:62
Alignment explanation
Indices: 974743--974868 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
974733 CAATTTTTTT
*
974743 TTTTTTTTTTTTGCTATCTCCAGTCCAATTTCCCTCAGATCTCTGGAAAATTTCAGGTAACC
1 TTTTTTTTTTTTGCTATCACCAGTCCAATTTCCCTCAGATCTCTGGAAAATTTCAGGTAACC
974805 TTTTTTTTTTTTGCTATCACCAGTCCAATTTCCCTCAGATCTCTGGAAAATTTCAGGTAACC
1 TTTTTTTTTTTTGCTATCACCAGTCCAATTTCCCTCAGATCTCTGGAAAATTTCAGGTAACC
974867 TT
1 TT
974869 ATCCCTTACA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (62 bp):
TTTTTTTTTTTTGCTATCACCAGTCCAATTTCCCTCAGATCTCTGGAAAATTTCAGGTAACC
Found at i:975849 original size:10 final size:10
Alignment explanation
Indices: 975834--975860 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
975824 TCTAAGTTTA
975834 TATATATATG
1 TATATATATG
975844 TATATATATG
1 TATATATATG
975854 TATATAT
1 TATATAT
975861 TCTACTCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:979586 original size:16 final size:16
Alignment explanation
Indices: 979565--979595 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
979555 TTTTTTTCAT
979565 ATATATACATACATAC
1 ATATATACATACATAC
*
979581 ATATATATATACATA
1 ATATATACATACATA
979596 TGGCTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATATACATACATAC
Found at i:983025 original size:20 final size:21
Alignment explanation
Indices: 983000--983056 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 21
982990 AATAATATAA
983000 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTGAAATTTTTGA-AAATT
983020 ATTTTG-AATTTTTGAAAATT
1 ATTTTGAAATTTTTGAAAATT
983040 ATTTTGAATTATTTTTG
1 ATTTTGAA--ATTTTTG
983057 TAATTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 10 0.31
20 14 0.44
21 1 0.03
23 7 0.22
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (21 bp):
ATTTTGAAATTTTTGAAAATT
Found at i:983031 original size:19 final size:20
Alignment explanation
Indices: 983000--983049 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
982990 AATAATATAA
983000 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTG-AATTTTTGA-AAATT
983020 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
983040 ATTTTGAATT
1 ATTTTGAATT
983050 ATTTTTGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:983202 original size:23 final size:23
Alignment explanation
Indices: 983176--983229 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
983166 TCGAACTCAA
* *
983176 AACTCGAATTACT-TATTCGAGTC
1 AACTCGAATAACTCGATTCGA-TC
* *
983199 AACTTGAATAACTCGATTCGATT
1 AACTCGAATAACTCGATTCGATC
983222 AACTCGAA
1 AACTCGAA
983230 ATTCAAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGAATAACTCGATTCGATC
Found at i:997294 original size:31 final size:31
Alignment explanation
Indices: 997259--997319 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
997249 AATTTTGAAA
* *
997259 TTTAAAAAGTACAATGACTGAAATTGATCAT
1 TTTAAAAAGTACAAAGACTAAAATTGATCAT
*
997290 TTTAAAAAGTATAAAGACTAAAATTGATCA
1 TTTAAAAAGTACAAAGACTAAAATTGATCA
997320 AATTAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.31
Consensus pattern (31 bp):
TTTAAAAAGTACAAAGACTAAAATTGATCAT
Found at i:1008847 original size:31 final size:30
Alignment explanation
Indices: 1008781--1008937 Score: 106
Period size: 31 Copynumber: 5.1 Consensus size: 30
1008771 TTATACTCAT
* * **
1008781 TTTTAAAAATTTTAATTAGGTCCAT-CAAATT
1 TTTTAAAAA-TTTAATTAAG-CCTTCCAAAAG
1008812 TTTTAGAAAATTTAATTAAGCCTTCCAAAAG
1 TTTTA-AAAATTTAATTAAGCCTTCCAAAAG
* * *
1008843 TTTTAAAATTTTTAATT-AGACTCTCCAAAAC
1 TTTTAAAA-ATTTAATTAAGCCT-TCCAAAAG
* * * *
1008874 TTTTGAAAATTCTCATTAATCC-TCTCAAAAT
1 TTTTAAAAATT-TAATTAAGCCTTC-CAAAAG
*
1008905 TTTTAAAAATTTTAATTAAACCTTCC-AAAG
1 TTTTAAAAA-TTTAATTAAGCCTTCCAAAAG
1008935 TTT
1 TTT
1008938 ATGGAAATTC
Statistics
Matches: 100, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
30 20 0.20
31 70 0.70
32 10 0.10
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (30 bp):
TTTTAAAAATTTAATTAAGCCTTCCAAAAG
Found at i:1008850 original size:62 final size:62
Alignment explanation
Indices: 1008781--1008986 Score: 162
Period size: 62 Copynumber: 3.3 Consensus size: 62
1008771 TTATACTCAT
* **
1008781 TTTTAAAAATTTTAATTAG-GTC-CATCAAATTTTTTAGAAAATT-TAATTAAGCCT-TCCAAAA
1 TTTTAAAAATTTTAATTAGACTCTC--CAAAACTTTT-GAAAATTCTAATTAAGCCTCT-CAAAA
1008842 G
62 G
* * * *
1008843 TTTTAAAATTTTTAATTAGACTCTCCAAAACTTTTGAAAATTCTCATTAATCCTCTCAAAAT
1 TTTTAAAAATTTTAATTAGACTCTCCAAAACTTTTGAAAATTCTAATTAAGCCTCTCAAAAG
* * * *
1008905 TTTTAAAAATTTTAATTAAAC-CTTCC-AAAGTTTATGGAAATTCTTATTAAG-CTGCT---AAG
1 TTTTAAAAATTTTAATTAGACTC-TCCAAAACTTT-TGAAAATTCTAATTAAGCCT-CTCAAAAG
1008964 TTTTTAGAAAATTTTAATTAGAC
1 -TTTTA-AAAATTTTAATTAGAC
1008987 CTTTGAAATT
Statistics
Matches: 120, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
59 2 0.02
60 5 0.04
61 31 0.26
62 78 0.65
63 3 0.03
64 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (62 bp):
TTTTAAAAATTTTAATTAGACTCTCCAAAACTTTTGAAAATTCTAATTAAGCCTCTCAAAAG
Found at i:1008899 original size:32 final size:32
Alignment explanation
Indices: 1008812--1008933 Score: 110
Period size: 31 Copynumber: 3.9 Consensus size: 32
1008802 CCATCAAATT
* *
1008812 TTTTAGAAAATT-TAATTAAGCCT-TCCAAAAG
1 TTTTA-AAAATTCTAATTAAACCTCTCCAAAAC
* * *
1008843 TTTTAAAATTTTTAATTAGA-CTCTCCAAAAC
1 TTTTAAAAATTCTAATTAAACCTCTCCAAAAC
* * * *
1008874 TTTTGAAAATTCTCATTAATCCTCT-CAAAAT
1 TTTTAAAAATTCTAATTAAACCTCTCCAAAAC
*
1008905 TTTTAAAAATTTTAATTAAACCT-TCCAAA
1 TTTTAAAAATTCTAATTAAACCTCTCCAAA
1008934 GTTTATGGAA
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
30 8 0.11
31 60 0.83
32 4 0.06
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (32 bp):
TTTTAAAAATTCTAATTAAACCTCTCCAAAAC
Found at i:1014630 original size:322 final size:324
Alignment explanation
Indices: 1014112--1014732 Score: 840
Period size: 322 Copynumber: 1.9 Consensus size: 324
1014102 AGTACGTGGT
* * * * * *
1014112 GATAATTGATGGTTGTCTTATCGAAGTGACCTTGTTGTCAGGGGTGGTTGGCTTGCACTTCCTTT
1 GATAAGTGATAGTTGTCTTATCGAAGTGACCTTATTATCAGGGGTGGTTAGCTTGCACTTCCCTT
* * *
1014177 GATCCTGACAAACAATCCTTATGGTGGATGAGATAAGATTGACGAAACCTGATGGGCGGAGTTAG
66 GATCCTGACAAACAATCCTTATGGTGGAAGAGATAAGACTGACGAAACCAGATGGGCGGA--TAG
* * ** *
1014242 GTGGTGAAGTGATCATGGTACTTTGGCGCAGATTGCCAAGTAGCGTATGTATTTGGAACAGTCCT
129 GT-GTGAAGTGATCACGGTACTTTGGCGCAGATTGCCAAGTAGAGTACATATATGGAACAGTCCT
* * *
1014307 TATGGTGGAAGAGATAAGACGGACGAAACCAGATCGGCGGAGTTAGATGATGGTTGTCTTTGATA
193 TATGGTGGAAGAGATAAGACGGACAAAACCAGATCGGCGGAGTTAGAGGATGATTGTC-TTGATA
* * * * *
1014372 GGCTCGTTGCTCCTTCTCATGATCTCTTGTTAGGTGAGTAATGTGACATCACCAAGATTTCAAAA
257 GCCTCGCTGCTCCTTCCCATCATCCCTTGTTAGGTGAGTAATGTGACATCACCAAGATTTCAAAA
1014437 TAC
322 TAC
* **
1014440 GATAAGTGATAGTTGTCTTA-CTGGAGTGACCTTATTATTGGGGGTGGTTAGCTTGCACATTCCC
1 GATAAGTGATAGTTGTCTTATC-GAAGTGACCTTATTATCAGGGGTGGTTAGCTTGCAC-TTCCC
* *
1014504 TTGATCCTGGCAGAACAATCCTTATGGTGGAAGAGATAAGACTGACGAAACCAGATGGG-TGA-A
64 TTGATCCTGACA-AACAATCCTTATGGTGGAAGAGATAAGACTGACGAAACCAGATGGGCGGATA
* *
1014567 -GT-T-AGGTGATCACGGTACTTTGGCGCAGATTGCCAAGTGGAGTACATATATGGAACAGTCCT
128 GGTGTGAAGTGATCACGGTACTTTGGCGCAGATTGCCAAGTAGAGTACATATATGGAACAGTCCT
* * *
1014629 TATGGTGGAAGAGATAAGACTGACAAAACCAGATGGGCGGAGTTAGGGGATGATTGTCTTGATAG
193 TATGGTGGAAGAGATAAGACGGACAAAACCAGATCGGCGGAGTTAGAGGATGATTGTCTTGATAG
*
1014694 CCTCGCTGGTCCTTCCCATCATCCCTTGTTAGGTGAGTA
258 CCTCGCTGCTCCTTCCCATCATCCCTTGTTAGGTGAGTA
1014733 TTGTTAGGTG
Statistics
Matches: 257, Mismatches: 33, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
321 40 0.16
322 104 0.40
323 1 0.00
325 2 0.01
326 1 0.00
327 1 0.00
328 48 0.19
329 17 0.07
330 43 0.17
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (324 bp):
GATAAGTGATAGTTGTCTTATCGAAGTGACCTTATTATCAGGGGTGGTTAGCTTGCACTTCCCTT
GATCCTGACAAACAATCCTTATGGTGGAAGAGATAAGACTGACGAAACCAGATGGGCGGATAGGT
GTGAAGTGATCACGGTACTTTGGCGCAGATTGCCAAGTAGAGTACATATATGGAACAGTCCTTAT
GGTGGAAGAGATAAGACGGACAAAACCAGATCGGCGGAGTTAGAGGATGATTGTCTTGATAGCCT
CGCTGCTCCTTCCCATCATCCCTTGTTAGGTGAGTAATGTGACATCACCAAGATTTCAAAATAC
Found at i:1014738 original size:14 final size:14
Alignment explanation
Indices: 1014719--1014746 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1014709 CCATCATCCC
1014719 TTGTTAGGTGAGTA
1 TTGTTAGGTGAGTA
1014733 TTGTTAGGTGAGTA
1 TTGTTAGGTGAGTA
1014747 ATGTGATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (14 bp):
TTGTTAGGTGAGTA
Found at i:1023515 original size:23 final size:21
Alignment explanation
Indices: 1023489--1023535 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1023479 AACTCAAATA
1023489 ATTCAAATAACTCAAACAATTCG
1 ATTCAAATAACTC-AA-AATTCG
* *
1023512 ATTCGATTAACTCAAAATTCG
1 ATTCAAATAACTCAAAATTCG
1023533 ATT
1 ATT
1023536 TTTTGAATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (21 bp):
ATTCAAATAACTCAAAATTCG
Found at i:1025806 original size:11 final size:11
Alignment explanation
Indices: 1025792--1025817 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1025782 TTTTGGGAAA
1025792 TTTTATAGATT
1 TTTTATAGATT
1025803 TTTTATAGATT
1 TTTTATAGATT
1025814 TTTT
1 TTTT
1025818 GAATTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTATAGATT
Found at i:1028514 original size:73 final size:69
Alignment explanation
Indices: 1028355--1028587 Score: 274
Period size: 69 Copynumber: 3.3 Consensus size: 69
1028345 TTACTTCGGT
* *
1028355 TTTTGCTGATAGCATGAATAATAT-T-ATTACCAAGTATTCAATACTCATACCCGAGTCTGAATA
1 TTTTGCTGATAGCATGAATAAGATCTCA-TACC-TGTATTCAATACTCATACCCGAGTCTGAATA
1028418 AGATGA
64 AGATGA
* * * *
1028424 TTTTGCTGATAGAATGAATAAGATGCTCATACCTGTATTCAGTACTCGTA-CTGAGTCTGAATAA
1 TTTTGCTGATAGCATGAATAAGAT-CTCATACCTGTATTCAATACTCATACCCGAGTCTGAATAA
1028488 GATACTTGA
65 G--A--TGA
* * *
1028497 TTTTGCTGATAGCATGAATAAGACACTCATACATCTGTATTCAATACTCATACCCGAGTCCGAGT
1 TTTTGCTGATAGCATGAATAAGA-TCTCATAC--CTGTATTCAATACTCATACCCGAGTCTGAAT
1028562 AAGATGA
63 AAGATGA
1028569 TTTTGCTGATAGCATGAAT
1 TTTTGCTGATAGCATGAAT
1028588 GTTATTAGGA
Statistics
Matches: 140, Mismatches: 13, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
69 36 0.26
70 14 0.10
71 6 0.04
72 23 0.16
73 32 0.23
74 1 0.01
75 16 0.11
76 12 0.09
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (69 bp):
TTTTGCTGATAGCATGAATAAGATCTCATACCTGTATTCAATACTCATACCCGAGTCTGAATAAG
ATGA
Found at i:1033850 original size:14 final size:14
Alignment explanation
Indices: 1033833--1033870 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1033823 TTTATAAATT
1033833 ACGGGTAGATTTGG
1 ACGGGTAGATTTGG
1033847 ACGGGTAGATTTGG
1 ACGGGTAGATTTGG
*
1033861 ATGGGT-GATT
1 ACGGGTAGATT
1033871 GGATACGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.21, C:0.05, G:0.42, T:0.32
Consensus pattern (14 bp):
ACGGGTAGATTTGG
Found at i:1035571 original size:16 final size:16
Alignment explanation
Indices: 1035545--1035591 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1035535 AAAATTCAAT
*
1035545 AAATAAAAAATATATA
1 AAATAATAAATATATA
* *
1035561 AATTATTAAATAT-TA
1 AAATAATAAATATATA
1035576 AAATAATATAATATAT
1 AAATAATA-AATATAT
1035592 CTTTTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
15 8 0.33
16 15 0.62
17 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATAAATATATA
Found at i:1035572 original size:27 final size:27
Alignment explanation
Indices: 1035528--1035613 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
1035518 TTTAAAAGAC
** *
1035528 TATATAAAAAATTCAATAAATAAAAAA
1 TATATAAATTATTAAATAAATAAAAAA
*
1035555 TATATAAATTATTAAAT-ATTAAAATAA
1 TATATAAATTATTAAATAAATAAAA-AA
* * *
1035582 TATAATATATCTTTTAAAAAAATTAAAAAA
1 TAT-ATAAAT-TATTAAATAAA-TAAAAAA
1035612 TA
1 TA
1035614 ATATGAACGA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
26 6 0.13
27 19 0.41
28 5 0.11
29 6 0.13
30 5 0.11
31 5 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
TATATAAATTATTAAATAAATAAAAAA
Found at i:1040870 original size:3 final size:3
Alignment explanation
Indices: 1040862--1040887 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1040852 TCTTTTAGGA
1040862 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1040888 CAGATTAACA
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:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1044456 original size:20 final size:21
Alignment explanation
Indices: 1044431--1044472 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1044421 AAAAAAAAAG
1044431 AGGATAAACGTA-CAACAAAT
1 AGGATAAACGTACCAACAAAT
*
1044451 AGGATAAATGTATCCAACAAAT
1 AGGATAAACGTA-CCAACAAAT
1044473 TCATTAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (21 bp):
AGGATAAACGTACCAACAAAT
Found at i:1045712 original size:3 final size:3
Alignment explanation
Indices: 1045704--1045729 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1045694 GAATCTAATT
1045704 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1045730 GAAAAAGGTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1054647 original size:29 final size:29
Alignment explanation
Indices: 1054614--1054670 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1054604 GCTCAAAAAA
1054614 TTAAAGACTAAATTGATAAAAGATATAAG
1 TTAAAGACTAAATTGATAAAAGATATAAG
1054643 TTAAAGACTAAATTGATAAAAGATATAA
1 TTAAAGACTAAATTGATAAAAGATATAA
1054671 ATGTTGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.28
Consensus pattern (29 bp):
TTAAAGACTAAATTGATAAAAGATATAAG
Found at i:1055945 original size:29 final size:30
Alignment explanation
Indices: 1055896--1055956 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
1055886 ATATAAAAAC
*
1055896 TATACATGAATTTTAATTTTG-TGCGATTT
1 TATACAAGAATTTTAATTTTGATGCGATTT
* *
1055925 TATACAAGAAATTTTGA-TTTGATTCGATTT
1 TATACAAG-AATTTTAATTTTGATGCGATTT
1055955 TA
1 TA
1055957 AAAAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (30 bp):
TATACAAGAATTTTAATTTTGATGCGATTT
Found at i:1061845 original size:11 final size:11
Alignment explanation
Indices: 1061831--1061872 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
1061821 AAAATTTTAA
1061831 TTTTAAAATAT
1 TTTTAAAATAT
1061842 TTTTAAAATACTTT
1 TTTTAAAATA---T
1061856 TTTTAAAAT-T
1 TTTTAAAATAT
1061866 TTTTAAA
1 TTTTAAA
1061873 TAAATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 8 0.29
11 10 0.36
14 10 0.36
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1061845 original size:17 final size:17
Alignment explanation
Indices: 1061800--1061847 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1061790 CGAATATAAT
*
1061800 AAATATTTTTACTTTTTTA
1 AAATATTTTTA--ATTTTA
* *
1061819 AAAAAATTTTAATTTTA
1 AAATATTTTTAATTTTA
1061836 AAATATTTTTAA
1 AAATATTTTTAA
1061848 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 15 0.62
19 9 0.38
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:1061849 original size:25 final size:23
Alignment explanation
Indices: 1061831--1061882 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 23
1061821 AAAATTTTAA
1061831 TTTTAAAATATTTTTAAAATACTTT
1 TTTTAAAAT-TTTTTAAAATA-TTT
*
1061856 TTTTAAAATTTTTTAAATAAATTT
1 TTTTAAAATTTTTTAAA-ATATTT
1061880 TTT
1 TTT
1061883 ATATTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAAAATTTTTTAAAATATTT
Found at i:1061866 original size:23 final size:24
Alignment explanation
Indices: 1061831--1061883 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1061821 AAAATTTTAA
* **
1061831 TTTTAAAATATTTTTAAAATACTT
1 TTTTTAAATATTTTTAAAATAAAT
*
1061855 TTTTTAAA-ATTTTTTAAATAAAT
1 TTTTTAAATATTTTTAAAATAAAT
1061878 TTTTTA
1 TTTTTA
1061884 TATTTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTTAAATATTTTTAAAATAAAT
Found at i:1068026 original size:16 final size:15
Alignment explanation
Indices: 1067987--1068035 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1067977 CCCGATATAA
1067987 TAATTTTTTTTATTT
1 TAATTTTTTTTATTT
**
1068002 TTTTATTTTTTTATTT
1 TAAT-TTTTTTTATTT
1068018 TAAATTTTTTTTAATTT
1 T-AATTTTTTTT-ATTT
1068035 T
1 T
1068036 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 19 0.70
17 6 0.22
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TAATTTTTTTTATTT
Found at i:1068036 original size:8 final size:8
Alignment explanation
Indices: 1067991--1068018 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1067981 ATATAATAAT
1067991 TTTTTTTA
1 TTTTTTTA
1067999 TTTTTTTA
1 TTTTTTTA
1068007 TTTTTTTA
1 TTTTTTTA
1068015 TTTT
1 TTTT
1068019 AAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1068062 original size:24 final size:23
Alignment explanation
Indices: 1068018--1068064 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1068008 TTTTTTATTT
**
1068018 TAAATTTTTTTTAATTTTTAAAA
1 TAAATTTTTGGTAATTTTTAAAA
*
1068041 TAAATTTTTGGTATTTTATTAAAA
1 TAAATTTTTGGTAATTT-TTAAAA
1068065 AATAGGCTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TAAATTTTTGGTAATTTTTAAAA
Found at i:1073864 original size:18 final size:18
Alignment explanation
Indices: 1073841--1073880 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1073831 GGTTCTCGGT
1073841 TAAATA-AATTATTAAAAA
1 TAAATATAATTATT-AAAA
*
1073859 TAAATATAATTGTTAAAA
1 TAAATATAATTATTAAAA
1073877 TAAA
1 TAAA
1073881 AAAAAAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAATATAATTATTAAAA
Found at i:1077540 original size:6 final size:6
Alignment explanation
Indices: 1077529--1077581 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
1077519 AAATATATAT
*** *
1077529 TTTTTA TTTTTA TTTTTA TTTTTA -AAATA CTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1077576 TTTTTA
1 TTTTTA
1077582 AAATAATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
5 2 0.05
6 37 0.95
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:1077572 original size:29 final size:29
Alignment explanation
Indices: 1077530--1077591 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
1077520 AATATATATT
*
1077530 TTTTATTTTTATTTTTATTTTTAAAATAC
1 TTTTATTTTTATTTTTATTTTTAAAATAA
1077559 TTTTATTTTTATTTTTATTTTTAAAATAA
1 TTTTATTTTTATTTTTATTTTTAAAATAA
1077588 TTTT
1 TTTT
1077592 TTAATGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTTATTTTTATTTTTATTTTTAAAATAA
Found at i:1079049 original size:20 final size:20
Alignment explanation
Indices: 1079014--1079051 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1079004 TGGTCATTTC
1079014 GTAACAAAACGATAACATAA
1 GTAACAAAACGATAACATAA
1079034 GTAATCAAAACG-TAACAT
1 GTAA-CAAAACGATAACAT
1079052 TTCAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (20 bp):
GTAACAAAACGATAACATAA
Found at i:1080097 original size:30 final size:30
Alignment explanation
Indices: 1080057--1080118 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1080047 ATTTATAAAT
*
1080057 AATTAATATTT-AT-TACTTAAAAATATTTAC
1 AATTAATATTTCATATA-TT-AAAATATTAAC
*
1080087 AATTTATATTTCATATATTAAAATATTAAC
1 AATTAATATTTCATATATTAAAATATTAAC
1080117 AA
1 AA
1080119 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 22 0.79
31 4 0.14
32 2 0.07
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTAAC
Found at i:1080306 original size:13 final size:13
Alignment explanation
Indices: 1080285--1080316 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1080275 ATTTTAAACT
*
1080285 AACACTTTTCAAA
1 AACAATTTTCAAA
1080298 AACAATTTTCAAA
1 AACAATTTTCAAA
1080311 AACAAT
1 AACAAT
1080317 AAAGATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (13 bp):
AACAATTTTCAAA
Found at i:1082791 original size:97 final size:96
Alignment explanation
Indices: 1082635--1082923 Score: 332
Period size: 97 Copynumber: 3.0 Consensus size: 96
1082625 AGCACACAAT
* * * * *
1082635 GAGGAAAGATTGAACCATAAAACCAA-AAAAAGCAACCA-AAGCGTTTTGAAGATCAATATAACT
1 GAGG-AAGATGGAACCATAAAGCCAATAAAAAACAACCAGAA-CATTTTGAA-ATCGATATAACT
** *
1082698 CACTAACACGAACCGAGCAATGAAAACTCGAATA
63 TGCTAACACGAACCAAGCAATGAAAACTCGAATA
* * **
1082732 TAGGAAGATGGAACCGTAATTCCAATAAAAAAACAA-CAGAAACATTTTGAAATCGATATAACTT
1 GAGGAAGATGGAACCATAAAGCCAAT-AAAAAACAACCAG-AACATTTTGAAATCGATATAACTT
* * * *
1082796 GCTACCACGAACCAAGCAATGAAAACTTGTATG
64 GCTAACACGAACCAAGCAATGAAAACTCGAATA
* * *
1082829 GAGGAAGATGGAACCATAAAGCCAATAAAAAGCAACCTGAACATTTTGAAAATCGACATAACTTG
1 GAGGAAGATGGAACCATAAAGCCAATAAAAAACAACCAGAACATTTTG-AAATCGATATAACTTG
1082894 CTAACACGAACCAAGCAATGAAAACTCGAA
65 CTAACACGAACCAAGCAATGAAAACTCGAA
1082924 AGTAGGCCAT
Statistics
Matches: 161, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
96 34 0.21
97 109 0.68
98 16 0.10
99 2 0.01
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (96 bp):
GAGGAAGATGGAACCATAAAGCCAATAAAAAACAACCAGAACATTTTGAAATCGATATAACTTGC
TAACACGAACCAAGCAATGAAAACTCGAATA
Found at i:1087067 original size:18 final size:18
Alignment explanation
Indices: 1087046--1087083 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1087036 TCAGGTAGTC
1087046 TTGTCTGTTCAACTTTTA
1 TTGTCTGTTCAACTTTTA
1087064 TTGTCTGTTCAACTTTTA
1 TTGTCTGTTCAACTTTTA
1087082 TT
1 TT
1087084 CATCAGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.58
Consensus pattern (18 bp):
TTGTCTGTTCAACTTTTA
Found at i:1093799 original size:61 final size:63
Alignment explanation
Indices: 1093664--1093807 Score: 204
Period size: 61 Copynumber: 2.3 Consensus size: 63
1093654 AAGCGGGACG
** * *
1093664 AAGTGAGAATTTCATTATAGTGTAAGGAACAAAATGGTAAAAAAAAAATTAGTAAAAGGGCCA
1 AAGTGAGAATTTCATTATAGTCAAAGGAACAAAATGATAAAAAAAAAATTAGTAAAAGGACCA
*
1093727 AGGTGAGAATTTCATTATAGTACAAAGG-ACAAAATGAT-AAAAAAAAA-TAGTAAAAGGACCA
1 AAGTGAGAATTTCATTATAGT-CAAAGGAACAAAATGATAAAAAAAAAATTAGTAAAAGGACCA
*
1093788 AAGTGAGAATTTCACTATAG
1 AAGTGAGAATTTCATTATAG
1093808 GGCCAAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
61 31 0.42
62 9 0.12
63 29 0.40
64 4 0.05
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (63 bp):
AAGTGAGAATTTCATTATAGTCAAAGGAACAAAATGATAAAAAAAAAATTAGTAAAAGGACCA
Found at i:1096262 original size:31 final size:32
Alignment explanation
Indices: 1096201--1096263 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1096191 AATAGACTGG
*
1096201 TGACTTAAATAAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAAACTTTAGAATAGTTCAA
*
1096233 TGACTTAAATAAAACA-TTTCAG-ATAGTTCAA
1 TGACTTAAATAAAAAACTTT-AGAATAGTTCAA
1096264 AGACCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (32 bp):
TGACTTAAATAAAAAACTTTAGAATAGTTCAA
Found at i:1106630 original size:104 final size:104
Alignment explanation
Indices: 1106494--1106918 Score: 647
Period size: 104 Copynumber: 4.1 Consensus size: 104
1106484 ATCAGGCACC
* * * * * * * *
1106494 AACCACTAAGTTAAATACTCGAGTTTATGCGAAAATTA-CAGATCAAAAACAAACTCCTGCTACA
1 AACCTCTAAGTTAAATACTCAAGTTTAAGCGAAAATGATGA-ATCAAAATCAAACTCATTCTACA
*
1106558 ATGTAAGAGCTTTGATTAATTATTTACATAAAAATCTTGA
65 ATGTAAGAGCTTTGATTCATTATTTACATAAAAATCTTGA
1106598 AACCTCTAAGTTAAATACTCAAGTTTAAGCGAAAATGATGAATCAAAATCAAACTCATTCTACAA
1 AACCTCTAAGTTAAATACTCAAGTTTAAGCGAAAATGATGAATCAAAATCAAACTCATTCTACAA
* * *
1106663 TGTAAGAGCTTTGATTCCTTGTTTACATGAAAATCTTGA
66 TGTAAGAGCTTTGATTCATTATTTACATAAAAATCTTGA
*
1106702 AACCTCTAAGTTAAATATTCAAGTTTAAGCGAAAATGATGAATCAAAATCAAACTCATTCTACAA
1 AACCTCTAAGTTAAATACTCAAGTTTAAGCGAAAATGATGAATCAAAATCAAACTCATTCTACAA
* * *
1106767 TGTAAGAGCTTTGATTCATTATTTACATGAAAATTTTTA
66 TGTAAGAGCTTTGATTCATTATTTACATAAAAATCTTGA
*
1106806 AACCTCTAAGTTTAATACTCAAGTTTAAGCGAAAATGATGAATCAAAATCAAACTCATTCTACAA
1 AACCTCTAAGTTAAATACTCAAGTTTAAGCGAAAATGATGAATCAAAATCAAACTCATTCTACAA
*
1106871 TGTAAGAGCTTTGATTCATTACTTACA-AGAAAATCTTGA
66 TGTAAGAGCTTTGATTCATTATTTACATA-AAAATCTTGA
*
1106910 AGCCTCTAA
1 AACCTCTAA
1106919 ATTTACAACA
Statistics
Matches: 295, Mismatches: 24, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
104 294 1.00
105 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (104 bp):
AACCTCTAAGTTAAATACTCAAGTTTAAGCGAAAATGATGAATCAAAATCAAACTCATTCTACAA
TGTAAGAGCTTTGATTCATTATTTACATAAAAATCTTGA
Found at i:1111874 original size:20 final size:21
Alignment explanation
Indices: 1111849--1111887 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1111839 CATAATATCA
1111849 AATTTAATGTTTAT-TTTTTT
1 AATTTAATGTTTATATTTTTT
*
1111869 AATTTAATTTTTATATTTT
1 AATTTAATGTTTATATTTT
1111888 AGTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (21 bp):
AATTTAATGTTTATATTTTTT
Found at i:1118657 original size:5 final size:5
Alignment explanation
Indices: 1118647--1118693 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
1118637 AATTATGTTT
1118647 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA TTAT- TTAT
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
1118694 TCTAGCAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
3 2 0.05
4 6 0.15
5 26 0.67
6 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1118672 original size:19 final size:18
Alignment explanation
Indices: 1118648--1118683 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1118638 ATTATGTTTT
1118648 TATATTATATTATTATTAA
1 TATATTATATTA-TATTAA
1118667 TATATTATATTATATTA
1 TATATTATATTATATTA
1118684 TATTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTATATTATATTAA
Found at i:1119034 original size:29 final size:30
Alignment explanation
Indices: 1118975--1119032 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1118965 TCCGAGCCTT
*
1118975 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
1119005 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
1119033 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:1119262 original size:13 final size:13
Alignment explanation
Indices: 1119244--1119275 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1119234 TTTCCAGCAA
1119244 TTATGAATTTATT
1 TTATGAATTTATT
1119257 TTATGAATTTATT
1 TTATGAATTTATT
*
1119270 TGATGA
1 TTATGA
1119276 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1119483 original size:50 final size:50
Alignment explanation
Indices: 1119370--1119660 Score: 492
Period size: 50 Copynumber: 5.7 Consensus size: 50
1119360 ATTTGGGTAA
* * *
1119370 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
1119426 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1119476 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1119526 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1119576 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1119626 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1119661 TTTGGCATGT
Statistics
Matches: 230, Mismatches: 5, Indels: 6
0.95 0.02 0.02
Matches are distributed among these distances:
50 185 0.80
52 1 0.00
53 3 0.01
55 2 0.01
56 39 0.17
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1121901 original size:19 final size:20
Alignment explanation
Indices: 1121865--1121902 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1121855 AGCAACATGG
*
1121865 TTCATTTTTATGTATTTTTT
1 TTCATTTATATGTATTTTTT
1121885 TTCATTTATAT-TATTTTT
1 TTCATTTATATGTATTTTT
1121903 CCAGTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (20 bp):
TTCATTTATATGTATTTTTT
Found at i:1121937 original size:16 final size:16
Alignment explanation
Indices: 1121910--1121950 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1121900 TTTCCAGTGT
1121910 AAAA-TATTTTTTT-A
1 AAAATTATTTTTTTCA
1121924 AAAATTATTTTTTTCA
1 AAAATTATTTTTTTCA
*
1121940 AATATTATTTT
1 AAAATTATTTT
1121951 CGAGAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 4 0.17
15 9 0.38
16 11 0.46
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
AAAATTATTTTTTTCA
Found at i:1125418 original size:22 final size:22
Alignment explanation
Indices: 1125390--1125441 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1125380 ATGACTACAG
1125390 ACACGTGGACAAAACGTTATCT
1 ACACGTGGACAAAACGTTATCT
* *
1125412 ACACGTGGACTATACGTTATCT
1 ACACGTGGACAAAACGTTATCT
1125434 ACACGTGG
1 ACACGTGG
1125442 CCCAAAATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (22 bp):
ACACGTGGACAAAACGTTATCT
Found at i:1131776 original size:22 final size:23
Alignment explanation
Indices: 1131750--1131797 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1131740 TTTTCACAAA
1131750 TTTA-GAATTTAATCCTTTTATT
1 TTTAGGAATTTAATCCTTTTATT
* *
1131772 TTTAGGAATTTGATCTTTTTATT
1 TTTAGGAATTTAATCCTTTTATT
1131795 TTT
1 TTT
1131798 TAGATTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTAGGAATTTAATCCTTTTATT
Found at i:1132593 original size:30 final size:31
Alignment explanation
Indices: 1132523--1132596 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1132513 AATATTTTAG
*
1132523 TTTAAATCACTGAATAATTTGAAAGCTTCTA
1 TTTAAGTCACTGAATAATTTGAAAGCTTCTA
* *
1132554 TTTAAGTCACTGAATTATTTGGAATG-TT-TA
1 TTTAAGTCACTGAATAATTT-GAAAGCTTCTA
*
1132584 TTTACGTCACTGA
1 TTTAAGTCACTGA
1132597 GTTGTTAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 14 0.37
31 20 0.53
32 4 0.11
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (31 bp):
TTTAAGTCACTGAATAATTTGAAAGCTTCTA
Found at i:1142211 original size:20 final size:20
Alignment explanation
Indices: 1142172--1142210 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1142162 AAACTTATAG
* *
1142172 ATGTATGTAATTTATATTTT
1 ATGTATATAATATATATTTT
1142192 ATGTATATAATATAT-TTTT
1 ATGTATATAATATATATTTT
1142211 TTAGAGAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
ATGTATATAATATATATTTT
Found at i:1147527 original size:17 final size:19
Alignment explanation
Indices: 1147500--1147534 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1147490 TTTGTTTTAG
1147500 TGTTTTATTT-AATTTTTT
1 TGTTTTATTTAAATTTTTT
1147518 TGTTTT-TTTAAATTTTT
1 TGTTTTATTTAAATTTTT
1147535 GATCTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (19 bp):
TGTTTTATTTAAATTTTTT
Found at i:1147534 original size:18 final size:18
Alignment explanation
Indices: 1147500--1147534 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1147490 TTTGTTTTAG
1147500 TGTTTTATTTAATTTTTT
1 TGTTTTATTTAATTTTTT
*
1147518 TGTTTT-TTTAAATTTTT
1 TGTTTTATTTAATTTTTT
1147535 GATCTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (18 bp):
TGTTTTATTTAATTTTTT
Found at i:1147623 original size:21 final size:20
Alignment explanation
Indices: 1147588--1147626 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1147578 ATTAACTTTG
*
1147588 TTTAAAAATATTTTTTTAAT
1 TTTAAAAATAATTTTTTAAT
1147608 TTTAAAAATAAATTTTTTA
1 TTTAAAAAT-AATTTTTTA
1147627 TTCATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAAAAATAATTTTTTAAT
Found at i:1147882 original size:23 final size:23
Alignment explanation
Indices: 1147852--1147899 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1147842 TATGTTAGTC
1147852 TGGTCGATTTCAAGTCTAAGTTT
1 TGGTCGATTTCAAGTCTAAGTTT
1147875 TGGTCGATTTCAAGTCTAAGTTT
1 TGGTCGATTTCAAGTCTAAGTTT
1147898 TG
1 TG
1147900 AATTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (23 bp):
TGGTCGATTTCAAGTCTAAGTTT
Found at i:1158399 original size:16 final size:18
Alignment explanation
Indices: 1158360--1158401 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1158350 TAAGTTTATA
1158360 ATACTT-TATATTATGTT
1 ATACTTATATATTATGTT
*
1158377 ATTCTTATATATTATG-T
1 ATACTTATATATTATGTT
1158394 A-ACTTATA
1 ATACTTATA
1158402 ACACATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (18 bp):
ATACTTATATATTATGTT
Found at i:1158550 original size:20 final size:19
Alignment explanation
Indices: 1158508--1158550 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1158498 ATAGAAAAAT
* *
1158508 ATATAAAATTATTAAATAG
1 ATATAAAATTATTAAAGAA
*
1158527 ATATAAATATTTTTAAAGAA
1 ATATAAA-ATTATTAAAGAA
1158547 ATAT
1 ATAT
1158551 GGGCAGACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
ATATAAAATTATTAAAGAA
Found at i:1162519 original size:2 final size:2
Alignment explanation
Indices: 1162512--1162541 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1162502 TCAAGGTAAT
*
1162512 CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1162542 TCTATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:1170527 original size:20 final size:20
Alignment explanation
Indices: 1170482--1170529 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1170472 CCATTTTTGA
**
1170482 TATTTTATTCAATTTTATGT
1 TATTTTATTCAATCATATGT
1170502 TAATTTTA-TCAATCATATCGT
1 T-ATTTTATTCAATCATAT-GT
1170523 TATTTTA
1 TATTTTA
1170530 AAATTGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.58
Consensus pattern (20 bp):
TATTTTATTCAATCATATGT
Found at i:1182513 original size:31 final size:31
Alignment explanation
Indices: 1182478--1182542 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1182468 TAAAATGGCC
* *
1182478 ACTGAATTATTCAAAAAATTTCATTTAAGTT
1 ACTGAACTATTCAAAAAATTTCATTTAACTT
** *
1182509 ACTGAACTATTCAAAAGTTTTTATTTAACTT
1 ACTGAACTATTCAAAAAATTTCATTTAACTT
1182540 ACT
1 ACT
1182543 AGGCTGTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.43
Consensus pattern (31 bp):
ACTGAACTATTCAAAAAATTTCATTTAACTT
Found at i:1183901 original size:19 final size:19
Alignment explanation
Indices: 1183860--1183901 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 19
1183850 CTAAAAATAT
1183860 TAAAATTGATATTTTTATC
1 TAAAATTGATATTTTTATC
1183879 -AAAATTGATATTTTTATC
1 TAAAATTGATATTTTTATC
1183897 TAAAA
1 TAAAA
1183902 ATTAAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (19 bp):
TAAAATTGATATTTTTATC
Found at i:1185367 original size:24 final size:24
Alignment explanation
Indices: 1185339--1185386 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1185329 GCGTGTCTTC
* *
1185339 CAAGGAAGAGAAGGATAAATCATT
1 CAAGGAAGAGAAAGAGAAATCATT
1185363 CAAGGAAGAGAAAGAGAAATCATT
1 CAAGGAAGAGAAAGAGAAATCATT
1185387 ATCACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.08, G:0.25, T:0.15
Consensus pattern (24 bp):
CAAGGAAGAGAAAGAGAAATCATT
Found at i:1190255 original size:17 final size:15
Alignment explanation
Indices: 1190225--1190258 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
1190215 ACGAAGTCTC
1190225 CCTCCCTTTCCCTCA
1 CCTCCCTTTCCCTCA
1190240 CCTCCCTCTCTCCCTCA
1 CCTCCCT-T-TCCCTCA
1190257 CC
1 CC
1190259 CGTTGCCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.06, C:0.65, G:0.00, T:0.29
Consensus pattern (15 bp):
CCTCCCTTTCCCTCA
Found at i:1195210 original size:11 final size:11
Alignment explanation
Indices: 1195180--1195221 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1195170 ACACCAATTT
*
1195180 TTTTAAAAAAA
1 TTTTAAAAATA
*
1195191 TTTAAAAAAGTA
1 TTTTAAAAA-TA
1195203 TTTTAAAAATA
1 TTTTAAAAATA
1195214 TTTTAAAA
1 TTTTAAAA
1195222 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:1195248 original size:30 final size:30
Alignment explanation
Indices: 1195187--1195245 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
1195177 TTTTTTTAAA
*
1195187 AAAATTTAAAAAAGTATTTTAAAAATATTTT
1 AAAATTTAAAAAAGTA-TTAAAAAATATTTT
1195218 AAAATTTAAAAAA-TA-TAAAAAATATTTT
1 AAAATTTAAAAAAGTATTAAAAAATATTTT
1195246 TTATTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.44
30 2 0.07
31 13 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTTAAAAAAGTATTAAAAAATATTTT
Found at i:1202705 original size:23 final size:22
Alignment explanation
Indices: 1202653--1202705 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1202643 TCCTCGTCTT
*
1202653 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
1202675 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
1202698 TTTCTTTT
1 TTTCTTTT
1202706 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:1256134 original size:33 final size:33
Alignment explanation
Indices: 1256076--1256143 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
1256066 TGGGAGTTAC
* * *
1256076 ATAATGCATGACATAGTTAAGAGATGTAGATTA
1 ATAATGCAGGACATAATTAAGAGATGCAGATTA
*
1256109 ATAATGCAGGACATTAATTAA-AGATGCATATTA
1 ATAATGCAGGACA-TAATTAAGAGATGCAGATTA
1256142 AT
1 AT
1256144 GATGTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 24 0.80
34 6 0.20
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (33 bp):
ATAATGCAGGACATAATTAAGAGATGCAGATTA
Found at i:1257077 original size:23 final size:23
Alignment explanation
Indices: 1257051--1257097 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1257041 ATTTAATCAC
*
1257051 TTCATATTTTATTATAGGTTGTT
1 TTCATATTTTATTATAAGTTGTT
1257074 TTCATATTTTATTATAAGTTGTT
1 TTCATATTTTATTATAAGTTGTT
1257097 T
1 T
1257098 CCACTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.04, G:0.11, T:0.62
Consensus pattern (23 bp):
TTCATATTTTATTATAAGTTGTT
Found at i:1275889 original size:29 final size:29
Alignment explanation
Indices: 1275847--1275915 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
1275837 NNNNNNNNNN
1275847 ACACTTAGTGCTATACAACTTGAACCCGC
1 ACACTTAGTGCTATACAACTTGAACCCGC
*
1275876 ACACTTAGTGCTATACAATTTGAACCCGC
1 ACACTTAGTGCTATACAACTTGAACCCGC
1275905 ACACTTAGTGC
1 ACACTTAGTGC
1275916 CAATTTCATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (29 bp):
ACACTTAGTGCTATACAACTTGAACCCGC
Found at i:1300521 original size:87 final size:88
Alignment explanation
Indices: 1300417--1300594 Score: 261
Period size: 87 Copynumber: 2.0 Consensus size: 88
1300407 ATGATTATAC
* * * * * *
1300417 ATGTGATTGATGATGATATTTGAAATTTGTGTAATGTTAATGATAAGTCAAGAATGGTGAAAGAT
1 ATGTGACTAATGATGATATATGAAATTTGGGTAATGTTAATGATAAGCCAAGAATAGTGAAAGAT
*
1300482 AAAA-GCGC-TATTTATTGAATTA
66 AAAAGGC-CTTATATATTGAATTA
*
1300504 ATGTGACTAATGATGATATATGAAATTTGGGTAATGTTAATGATAAGCCAAGACTAGTGAAAGAT
1 ATGTGACTAATGATGATATATGAAATTTGGGTAATGTTAATGATAAGCCAAGAATAGTGAAAGAT
1300569 AAAAGGCCTTATATATTGAATTA
66 AAAAGGCCTTATATATTGAATTA
1300592 ATG
1 ATG
1300595 ATTAATTTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
87 63 0.78
88 18 0.22
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (88 bp):
ATGTGACTAATGATGATATATGAAATTTGGGTAATGTTAATGATAAGCCAAGAATAGTGAAAGAT
AAAAGGCCTTATATATTGAATTA
Found at i:1309639 original size:30 final size:30
Alignment explanation
Indices: 1309584--1309641 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1309574 TTCGAGCTTT
*
1309584 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGCAAAAGTGTAAATATGAAAAAGTTTA
* * *
1309614 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAGTGTAAATATGAAAAAGTT
1309642 CGAGTCAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (30 bp):
GGGGCAAAAGTGTAAATATGAAAAAGTTTA
Found at i:1310021 original size:33 final size:33
Alignment explanation
Indices: 1309979--1310181 Score: 147
Period size: 33 Copynumber: 5.6 Consensus size: 33
1309969 AATATAAGGG
1309979 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
1310012 GGTTGCTAAGTGTTGATTCCACCGTATCTTAAATGTGAAAG-
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
1310053 GAGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 G-GTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * * *
1310087 GGTTGCTAAGTGCCGATTCCACCATAACTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CC-GAA--T-CAT-TG---GT
* *
1310129 GGTTGCTAAGTGTTGATTCCCTGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
1310162 GGTTGTTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
1310182 ACTGTATCTT
Statistics
Matches: 134, Mismatches: 16, Indels: 40
0.71 0.08 0.21
Matches are distributed among these distances:
33 57 0.43
34 9 0.07
35 2 0.01
36 4 0.03
37 5 0.04
38 5 0.04
39 4 0.03
40 2 0.01
41 8 0.06
42 38 0.28
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:1310072 original size:42 final size:41
Alignment explanation
Indices: 1310013--1310266 Score: 195
Period size: 42 Copynumber: 6.5 Consensus size: 41
1310003 ATCATTGGTG
*
1310013 GTTGCTAAGTGTTGATTCCACCGTATCTTAAATGTGAAAGGA
1 GTTGCTAAGTGCTGATTCCACCGTATCTT-AATGTGAAAGGA
*
1310055 GTTGCTAAGTGCTGATTCC-CCGAATC---AT-TG---GTG-
1 GTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGAAAG-GA
* * * *
1310088 GTTGCTAAGTGCCGATTCCACCATAACTTGAATGTGAAAGGG
1 GTTGCTAAGTGCTGATTCCACCGTATCTT-AATGTGAAAGGA
* * *
1310130 GTTGCTAAGTGTTGATTCC-CTGAATC---AT-TG---GTG-
1 GTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGAAAG-GA
* *
1310163 GTTGTTAAGTGCTGATTCCACTGTATCTTAAATGTGAAA-GA
1 GTTGCTAAGTGCTGATTCCACCGTATCTT-AATGTGAAAGGA
*
1310204 GGTTGCTAAGTGTTGATTCCACCGTATCTTTGAATGTGAAAGGA
1 -GTTGCTAAGTGCTGATTCCACCGTATC-TT-AATGTGAAAGGA
1310248 GTTGCTAAGTGCTGATTCC
1 GTTGCTAAGTGCTGATTCC
1310267 CCGAATCACT
Statistics
Matches: 167, Mismatches: 20, Indels: 49
0.71 0.08 0.21
Matches are distributed among these distances:
33 37 0.22
34 12 0.07
36 4 0.02
37 4 0.02
38 4 0.02
39 4 0.02
40 1 0.01
41 10 0.06
42 60 0.36
43 29 0.17
44 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
GTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGAAAGGA
Found at i:1310105 original size:75 final size:75
Alignment explanation
Indices: 1309980--1310223 Score: 373
Period size: 75 Copynumber: 3.3 Consensus size: 75
1309970 ATATAAGGGG
*
1309980 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATCTTAAA
1 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAA
1310045 TGTGAAAGGA
66 TGTGAAAGGA
* * * *
1310055 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCCGATTCCACCATAACTTGAA
1 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAA
*
1310120 TGTGAAAGGG
66 TGTGAAAGGA
* * * *
1310130 GTTGCTAAGTGTTGATTCCCTGAATCATTGGTGGTTGTTAAGTGCTGATTCCACTGTATCTTAAA
1 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAA
1310195 TGTGAAA-GA
66 TGTGAAAGGA
*
1310204 GGTTGCTAAGTGTTGATTCC
1 -GTTGCTAAGTGCTGATTCC
1310224 ACCGTATCTT
Statistics
Matches: 153, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
74 1 0.01
75 152 0.99
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (75 bp):
GTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAA
TGTGAAAGGA
Found at i:1310254 original size:43 final size:42
Alignment explanation
Indices: 1310162--1310266 Score: 149
Period size: 43 Copynumber: 2.5 Consensus size: 42
1310152 AATCATTGGT
* *
1310162 GGTTGTTAAGTGCTGATTCCACTGTATCTTAAATGTGAAAGA
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGA
* *
1310204 GGTTGCTAAGTGTTGATTCCACCGTATCTTTGAATGTGAAAG-
1 GGTTGCTAAGTGCTGATTCCACCGTATC-TTAAATGTGAAAGA
1310246 GAGTTGCTAAGTGCTGATTCC
1 G-GTTGCTAAGTGCTGATTCC
1310267 CCGAATCACT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
42 26 0.46
43 30 0.54
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGA
Found at i:1310295 original size:118 final size:117
Alignment explanation
Indices: 1310087--1310301 Score: 315
Period size: 118 Copynumber: 1.8 Consensus size: 117
1310077 AATCATTGGT
* * *
1310087 GGTTGCTAAGTGCCGATTCCACCATAACTTGAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCTG
1 GGTTGCTAAGTGCCGATTCCACCATAACTTGAATGTGAAAGGAGTTGCTAAGTGCTGATTCCCCG
* * *
1310152 AATCATTGGTGGTTGTTAAGTGCTGATTCCACTGTATCTTAAATGTGAAAGA
66 AATCACTGGTGGTTGTAAAGTGCTGAATCCACTGTATCTTAAATGTGAAAGA
** * *
1310204 GGTTGCTAAGTGTTGATTCCACCGTATCTTTGAATGTGAAAGGAGTTGCTAAGTGCTGATTCCCC
1 GGTTGCTAAGTGCCGATTCCACCATAAC-TTGAATGTGAAAGGAGTTGCTAAGTGCTGATTCCCC
1310269 GAATCACTGGTGGTTGCTAAAG-GCTGAATCCAC
65 GAATCACTGGTGGTTG-TAAAGTGCTGAATCCAC
1310302 CGAGTAACGG
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
117 24 0.28
118 58 0.67
119 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (117 bp):
GGTTGCTAAGTGCCGATTCCACCATAACTTGAATGTGAAAGGAGTTGCTAAGTGCTGATTCCCCG
AATCACTGGTGGTTGTAAAGTGCTGAATCCACTGTATCTTAAATGTGAAAGA
Found at i:1316184 original size:40 final size:39
Alignment explanation
Indices: 1316062--1316196 Score: 116
Period size: 40 Copynumber: 3.5 Consensus size: 39
1316052 ACCAGTTTGG
* * * *
1316062 CACCCAGTGCCTCATCGGATGATTCGAAGTAATAAATTAA
1 CACCCAGTGCCTCATC-GATAATCCGAAGTAGTAAATTGA
* * * *
1316102 CACCCAGTGCATCATCGGCTAAACCG-A--AGTAAATTGG
1 CACCCAGTGCCTCATC-GATAATCCGAAGTAGTAAATTGA
1316139 CACCCAGTGCCTCAT-GAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCG-A-TAATCCGAAGTAGTAAATTGA
* *
1316179 CACCCAATGTCTCATCGA
1 CACCCAGTGCCTCATCGA
1316197 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
35 1 0.01
37 27 0.36
38 1 0.01
39 1 0.01
40 44 0.59
41 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGATAATCCGAAGTAGTAAATTGA
Found at i:1317150 original size:21 final size:22
Alignment explanation
Indices: 1317125--1317171 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1317115 GTTTCGTTTC
*
1317125 AATTTTGTTTG-TTTGTTTAAT
1 AATTTTATTTGTTTTGTTTAAT
1317146 AA-TTTATTTGTTTTGTTTAAT
1 AATTTTATTTGTTTTGTTTAAT
1317167 AATTT
1 AATTT
1317172 ACTTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 14 0.61
22 2 0.09
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (22 bp):
AATTTTATTTGTTTTGTTTAAT
Found at i:1317172 original size:21 final size:20
Alignment explanation
Indices: 1317132--1317172 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
1317122 TTCAATTTTG
1317132 TTTGTTTGTTTAATAATTTA
1 TTTGTTTGTTTAATAATTTA
1317152 TTTGTTTTGTTTAATAATTTA
1 TTTG-TTTGTTTAATAATTTA
1317173 CTTAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTGTTTGTTTAATAATTTA
Found at i:1318536 original size:23 final size:23
Alignment explanation
Indices: 1318504--1318548 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1318494 GCCTGCACAC
*
1318504 TTAACCCATTCCCATGCTACCCA
1 TTAACACATTCCCATGCTACCCA
1318527 TTAACACATTCCCATGCTACCC
1 TTAACACATTCCCATGCTACCC
1318549 GCAGCCCTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.42, G:0.04, T:0.27
Consensus pattern (23 bp):
TTAACACATTCCCATGCTACCCA
Found at i:1319966 original size:20 final size:23
Alignment explanation
Indices: 1319941--1319985 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 23
1319931 AGTTCGTATG
1319941 GTTAAACTG-T-AATGATA-TAT
1 GTTAAACTGATGAATGATATTAT
*
1319961 GTTAAATTGATGAATGATATTAT
1 GTTAAACTGATGAATGATATTAT
1319984 GT
1 GT
1319986 ATTTATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 1 0.05
22 7 0.33
23 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (23 bp):
GTTAAACTGATGAATGATATTAT
Found at i:1325138 original size:40 final size:40
Alignment explanation
Indices: 1325094--1325177 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
1325084 AATTCCTCAG
1325094 ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
1 ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
1325134 ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
1 ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
1325174 ATTT
1 ATTT
1325178 ATTAATATGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTTCTTATTTAATATGATTTAATATGCTTAGTCCTACA
Found at i:1326562 original size:24 final size:24
Alignment explanation
Indices: 1326526--1326597 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
1326516 TTGAAACCAG
1326526 TTCCACAGCTCCTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
* *
1326550 TTCCACTGTTCCTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
* *
1326574 TTCCACAGCTCTTCTCTCCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
1326598 ATCGATTGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.11, C:0.49, G:0.04, T:0.36
Consensus pattern (24 bp):
TTCCACAGCTCCTCTCTTCACCCT
Found at i:1330237 original size:78 final size:78
Alignment explanation
Indices: 1330137--1330287 Score: 230
Period size: 78 Copynumber: 1.9 Consensus size: 78
1330127 CTCATTTTCT
* *
1330137 ACCATTAAACCATGATCCCTTGATCTCACCAACTGGGAGAGTCGGTGATCATGTTAATAATGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
1330202 ACCATGGAGTTCG
66 ACCATGGAGTTCG
* * * * * *
1330215 ACCATTAAACCATGATCCCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGGTC
1 ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
1330280 ACCATGGA
66 ACCATGGA
1330288 CTTTGTGTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (78 bp):
ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
ACCATGGAGTTCG
Found at i:1332569 original size:13 final size:13
Alignment explanation
Indices: 1332551--1332576 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1332541 ATTTTGACTT
1332551 AGGCTCATTTTTC
1 AGGCTCATTTTTC
1332564 AGGCTCATTTTTC
1 AGGCTCATTTTTC
1332577 TATAGGGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
AGGCTCATTTTTC
Found at i:1335795 original size:9 final size:9
Alignment explanation
Indices: 1335735--1335811 Score: 77
Period size: 9 Copynumber: 8.6 Consensus size: 9
1335725 TTTGGTTAAA
*
1335735 AATTACCCG
1 AATTACTCG
*
1335744 AATTACCCG
1 AATTACTCG
1335753 AATTA-TCCG
1 AATTACT-CG
1335762 AATTA-TCCG
1 AATTACT-CG
*
1335771 AATTAATCG
1 AATTACTCG
1335780 AATTACTCG
1 AATTACTCG
*
1335789 AATTACTTG
1 AATTACTCG
*
1335798 AATTAATCG
1 AATTACTCG
1335807 AATTA
1 AATTA
1335812 ACCTAATTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
9 60 0.98
10 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (9 bp):
AATTACTCG
Found at i:1335819 original size:18 final size:18
Alignment explanation
Indices: 1335735--1335824 Score: 67
Period size: 18 Copynumber: 4.9 Consensus size: 18
1335725 TTTGGTTAAA
* **
1335735 AATTACCCGAATTACCCG
1 AATTAACCGAATTAATCG
*
1335753 AATTATCCGAATT-ATCCG
1 AATTAACCGAATTAAT-CG
* *
1335771 AATTAATCGAATTACTCG
1 AATTAACCGAATTAATCG
*
1335789 AATT-ACTTGAATTAATCG
1 AATTAAC-CGAATTAATCG
*
1335807 AATTAACCTAATTGAATC
1 AATTAACCGAATT-AATC
1335825 ATACATAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
17 1 0.02
18 48 0.86
19 7 0.12
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (18 bp):
AATTAACCGAATTAATCG
Found at i:1335909 original size:18 final size:19
Alignment explanation
Indices: 1335886--1335924 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1335876 TTATAGAATT
* *
1335886 TTATTTTTATTTTTTA-AA
1 TTATTTGTAATTTTTATAA
1335904 TTATTTGTAATTTTTATAA
1 TTATTTGTAATTTTTATAA
1335923 TT
1 TT
1335925 GGGATGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTATTTGTAATTTTTATAA
Found at i:1336291 original size:20 final size:20
Alignment explanation
Indices: 1336266--1336307 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1336256 CATAGCAAAA
1336266 GGACATTAGTGAAATGTTGT
1 GGACATTAGTGAAATGTTGT
*
1336286 GGACATTAGTGCAATGTTGT
1 GGACATTAGTGAAATGTTGT
1336306 GG
1 GG
1336308 TCAGCTACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (20 bp):
GGACATTAGTGAAATGTTGT
Found at i:1347533 original size:31 final size:31
Alignment explanation
Indices: 1347463--1347544 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
1347453 AAATGGGCAG
1347463 AATAAGCACTGAATTTATTTTACAACGTTTT
1 AATAAGCACTGAATTTATTTTACAACGTTTT
* *
1347494 AATGAGCACTAAATTTATTTTACAACGTTTT
1 AATAAGCACTGAATTTATTTTACAACGTTTT
** *
1347525 CGTAAGCACCGAATTTATTT
1 AATAAGCACTGAATTTATTT
1347545 CATTCTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (31 bp):
AATAAGCACTGAATTTATTTTACAACGTTTT
Found at i:1347736 original size:15 final size:15
Alignment explanation
Indices: 1347716--1347765 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1347706 CTGATGTAGT
1347716 TATCCTGGCTTGGGA
1 TATCCTGGCTTGGGA
** *
1347731 TATCCTATTCTAGGGA
1 TATCCT-GGCTTGGGA
*
1347747 TATCCCGGCTTGGGA
1 TATCCTGGCTTGGGA
1347762 TATC
1 TATC
1347766 ACATTCTAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (15 bp):
TATCCTGGCTTGGGA
Found at i:1347782 original size:30 final size:31
Alignment explanation
Indices: 1347716--1347798 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
1347706 CTGATGTAGT
* *
1347716 TATCCTGGCTTGGGATATCCTATTCTAGGGA
1 TATCCCGGCTTGGGATATCCTATTCTAGGAA
1347747 TATCCCGGCTTGGGATATCAC-ATTCTA-GAA
1 TATCCCGGCTTGGGATATC-CTATTCTAGGAA
1347777 TATCCCGGCTTGGGATATCCTA
1 TATCCCGGCTTGGGATATCCTA
1347799 AAAAAGAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 1 0.02
30 22 0.46
31 24 0.50
32 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (31 bp):
TATCCCGGCTTGGGATATCCTATTCTAGGAA
Found at i:1347807 original size:30 final size:30
Alignment explanation
Indices: 1347746--1347807 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
1347736 TATTCTAGGG
****
1347746 ATATCCCGGCTTGGGATATCACATTCTAGA
1 ATATCCCGGCTTGGGATATCACAAAAAAGA
1347776 ATATCCCGGCTTGGGATATC-CTAAAAAAGA
1 ATATCCCGGCTTGGGATATCAC-AAAAAAGA
1347806 AT
1 AT
1347808 TGAGGATGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (30 bp):
ATATCCCGGCTTGGGATATCACAAAAAAGA
Found at i:1348093 original size:22 final size:22
Alignment explanation
Indices: 1348065--1348106 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1348055 GACTCCCGGG
1348065 TAAGAATTTGTGCCTTTGTTGC
1 TAAGAATTTGTGCCTTTGTTGC
1348087 TAAGAATTTGTGCCTTTGTT
1 TAAGAATTTGTGCCTTTGTT
1348107 TCGCAGTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (22 bp):
TAAGAATTTGTGCCTTTGTTGC
Found at i:1348867 original size:44 final size:45
Alignment explanation
Indices: 1348786--1348873 Score: 103
Period size: 44 Copynumber: 2.0 Consensus size: 45
1348776 CTGTTTATGG
*
1348786 TCGTGATTTGTTTTTGTTATAATTGTGTTTTAAAGGTA-TCATGA
1 TCGTGATTTGTTTTTGTTATAATTGCGTTTTAAAGGTATTCATGA
*
1348830 TCGTG-TTGTGTTTTTGTTTCATAATTGCG-TTT-GAGGTATTCATG
1 TCGTGATT-TGTTTTTG-TT-ATAATTGCGTTTTAAAGGTATTCATG
1348874 TTAATAACTG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
43 2 0.05
44 18 0.47
45 10 0.26
46 8 0.21
ACGTcount: A:0.18, C:0.07, G:0.23, T:0.52
Consensus pattern (45 bp):
TCGTGATTTGTTTTTGTTATAATTGCGTTTTAAAGGTATTCATGA
Found at i:1359987 original size:15 final size:15
Alignment explanation
Indices: 1359967--1359995 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1359957 TATGTTCTTG
1359967 ATCATTAAAATTTTA
1 ATCATTAAAATTTTA
1359982 ATCATTAAAATTTT
1 ATCATTAAAATTTT
1359996 CTCACCTTTG
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:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCATTAAAATTTTA
Found at i:1360395 original size:516 final size:518
Alignment explanation
Indices: 1359457--1360407 Score: 1629
Period size: 516 Copynumber: 1.8 Consensus size: 518
1359447 TCGATTTCCT
* *
1359457 TTTTAATTATTAAAATTTTCTCACCTTGTGCAGTTTCTCCCCATAATCCTCAGACTGTATCTTTC
1 TTTTAATCATTAAAATTTTCTCACCTTGTGCAGGTTCTCCCCATAATCCTCAGACTGTATCTTTC
* * *
1359522 TTGGAATTGCTAGATCTTCCTTATGTTCTTGATAATGCATTGGACTCCAGGGATACTCCTGTTTC
66 TTGGAATTGCTAGA--TTCCTTATGTTCTTGACAATGCATCGGACTCCAGGGATACTCCTGCTTC
*
1359587 ATTGCCTCAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATATTACAG
129 ATTGCCTAAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATATTACAG
* *
1359652 CGTCCGGTATGTGATAGGCCAGTTTAGGATTATTCTAGTTCAGGAAAAGACCTTTTCAGGAGTTT
194 CGTCCGGCATGTGATAGGCCAGTTTAGGATTATTCGAGTTCAGGAAAAGACCTTTTCAGGAGTTT
* * * * *
1359717 TGGAGAAATCACCTCGAATAACCAAGCTTTTGAAGCTTTCAAGTCAATAATCCGTTAAACTAATG
259 TGGAGAAATCACCTCGAATAAACAAGCTGTTGAAACTTTCAAGTCAATAATCCGTCAAAATAATG
* *
1359782 AATGGAGGGCTTTAAACAAAGCCAACAGTTTTTTCGGGTTTACCTATTTATTTTAAATATATAAT
324 AATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTTTACCTATTTATTTTAAATATATAAT
*
1359847 ACAGAACACACTCAGATAAATATAATATATTATGAAGCTGATTTTCAGTGAGTTTTTGTCACATC
389 ACAGAACACACTCAGATAAATATAATATATTATAAAGCTGATTTTCAGTGAGTTTTTGTCACATC
1359912 TTTTTATTTCTTGCTCAGCAGAGTATTGTTGGGATTGCTAGATCTTATGTTCTTGATCATTAAAA
454 TTTTTATTTCTTGCTCAGCAGAGTATTGTTGGGATTGCTAGATCTTATGTTCTTGATCATTAAAA
*
1359977 TTTTAATCATTAAAATTTTCTCACCTT-TGTAGGTTCTCCCCATAATCCTCAGACTGTATCTTTC
1 TTTTAATCATTAAAATTTTCTCACCTTGTGCAGGTTCTCCCCATAATCCTCAGACTGTATCTTTC
*
1360041 TTGGGATTGCTAGA-T-CTTATGTTCTTGACAATGCATCGGACTCCAGGGATACTCCTGCTTCAT
66 TTGGAATTGCTAGATTCCTTATGTTCTTGACAATGCATCGGACTCCAGGGATACTCCTGCTTCAT
* *
1360104 TGCTTAAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATGTTACAGCG
131 TGCCTAAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATATTACAGCG
*
1360169 TCCGGCATGTGATAGGCCAGTTTAGGATTATTCGAGTTCAGGAAAAATACCTTTTCAGGAGTTTT
196 TCCGGCATGTGATAGGCCAGTTTAGGATTATTCGAGTTCAGG-AAAAGACCTTTTCAGGAGTTTT
*
1360234 GGAGAAATCACCTCGAATAAACAAGCTGTTGAAACTTTCAAGTTAATAATCCGTCAAAATAATGA
260 GGAGAAATCACCTCGAATAAACAAGCTGTTGAAACTTTCAAGTCAATAATCCGTCAAAATAATGA
*
1360299 ATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTTTACCTATTTATTTTAAATATATAGTA
325 ATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTTTACCTATTTATTTTAAATATATAATA
**
1360364 TGGAACACACTCAGATAAATATAATATATTATAAAGCTGATTTT
390 CAGAACACACTCAGATAAATATAATATATTATAAAGCTGATTTT
1360408 GTCTTTGCCC
Statistics
Matches: 405, Mismatches: 25, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
515 147 0.36
516 184 0.45
519 48 0.12
520 26 0.06
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (518 bp):
TTTTAATCATTAAAATTTTCTCACCTTGTGCAGGTTCTCCCCATAATCCTCAGACTGTATCTTTC
TTGGAATTGCTAGATTCCTTATGTTCTTGACAATGCATCGGACTCCAGGGATACTCCTGCTTCAT
TGCCTAAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATATTACAGCG
TCCGGCATGTGATAGGCCAGTTTAGGATTATTCGAGTTCAGGAAAAGACCTTTTCAGGAGTTTTG
GAGAAATCACCTCGAATAAACAAGCTGTTGAAACTTTCAAGTCAATAATCCGTCAAAATAATGAA
TGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTTTACCTATTTATTTTAAATATATAATAC
AGAACACACTCAGATAAATATAATATATTATAAAGCTGATTTTCAGTGAGTTTTTGTCACATCTT
TTTATTTCTTGCTCAGCAGAGTATTGTTGGGATTGCTAGATCTTATGTTCTTGATCATTAAAA
Found at i:1361271 original size:23 final size:23
Alignment explanation
Indices: 1361232--1361277 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1361222 TAGAAAATGA
*
1361232 AATAAATGAAACTTA-TTTATAT
1 AATAAATGAAACATATTTTATAT
1361254 AATAAATGAAAACATATTTTATAT
1 AATAAATG-AAACATATTTTATAT
1361278 TTATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 7 0.33
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
AATAAATGAAACATATTTTATAT
Found at i:1362082 original size:36 final size:35
Alignment explanation
Indices: 1362006--1362075 Score: 113
Period size: 36 Copynumber: 2.0 Consensus size: 35
1361996 AACCAAGAAC
**
1362006 CCTAAACCCTAAACCCTAAACCTTAAACCATAAAT
1 CCTAAACTTTAAACCCTAAACCTTAAACCATAAAT
1362041 CCTAAACTTTAAACCCTAAAACCTTAAACCATAAA
1 CCTAAACTTTAAACCCT-AAACCTTAAACCATAAA
1362076 CTCTAAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 15 0.47
36 17 0.53
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.21
Consensus pattern (35 bp):
CCTAAACTTTAAACCCTAAACCTTAAACCATAAAT
Found at i:1362092 original size:6 final size:7
Alignment explanation
Indices: 1362003--1362097 Score: 93
Period size: 7 Copynumber: 13.4 Consensus size: 7
1361993 GCAAACCAAG
1362003 AACCCTA
1 AACCCTA
1362010 AACCCTA
1 AACCCTA
1362017 AACCCTA
1 AACCCTA
*
1362024 AACCTTA
1 AACCCTA
*
1362031 AACCATA
1 AACCCTA
*
1362038 AATCCTA
1 AACCCTA
**
1362045 AACTTTA
1 AACCCTA
1362052 AACCCTAA
1 AACCCT-A
*
1362060 AACCTTA
1 AACCCTA
*
1362067 AACCATA
1 AACCCTA
*
1362074 AACTCTAA
1 AACCCT-A
1362082 AACCC-A
1 AACCCTA
1362088 AACCCTA
1 AACCCTA
1362095 AAC
1 AAC
1362098 AATTCAGGGA
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
6 6 0.08
7 54 0.76
8 11 0.15
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (7 bp):
AACCCTA
Found at i:1362398 original size:8 final size:7
Alignment explanation
Indices: 1362380--1362512 Score: 51
Period size: 7 Copynumber: 18.4 Consensus size: 7
1362370 AGTTTTGGAT
*
1362380 TTTAAGG
1 TTTAGGG
1362387 TTTAGGGG
1 TTTA-GGG
*
1362395 TTTAAGG
1 TTTAGGG
1362402 TATTAGGG
1 T-TTAGGG
*
1362410 TTTGGGG
1 TTTAGGG
1362417 TTTTA-GG
1 -TTTAGGG
*
1362424 TTTTGAGG
1 TTTAG-GG
1362432 -TTAGAGG
1 TTTAG-GG
1362439 TTTTAGGG
1 -TTTAGGG
* *
1362447 CTTGGGG
1 TTTAGGG
*
1362454 CTT-GGTG
1 TTTAGG-G
* *
1362461 CTTGGGG
1 TTTAGGG
1362468 TTTAGGG
1 TTTAGGG
1362475 -TTAGGG
1 TTTAGGG
1362481 TTTTAGGG
1 -TTTAGGG
1362489 TTT-GAGG
1 TTTAG-GG
*
1362496 TTTGGGG
1 TTTAGGG
*
1362503 TTTGGGG
1 TTTAGGG
1362510 TTT
1 TTT
1362513 GTGGCGTGGG
Statistics
Matches: 102, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
6 12 0.12
7 58 0.57
8 28 0.27
9 4 0.04
ACGTcount: A:0.12, C:0.02, G:0.43, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:1362398 original size:15 final size:16
Alignment explanation
Indices: 1362380--1362409 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1362370 AGTTTTGGAT
1362380 TTTAAGGT-TTAGGGG
1 TTTAAGGTATTAGGGG
1362395 TTTAAGGTATTAGGG
1 TTTAAGGTATTAGGG
1362410 TTTGGGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (16 bp):
TTTAAGGTATTAGGGG
Found at i:1362433 original size:22 final size:22
Alignment explanation
Indices: 1362408--1362513 Score: 83
Period size: 22 Copynumber: 5.0 Consensus size: 22
1362398 AAGGTATTAG
*
1362408 GGTTTGGGGTTTTAGGTTTTGA
1 GGTTTGGGGTTTTAGGGTTTGA
* * * *
1362430 GGTTAGAGGTTTTAGGGCTTGG
1 GGTTTGGGGTTTTAGGGTTTGA
* * * *
1362452 GGCTTGGTG-CTTGGGGTTT-A
1 GGTTTGGGGTTTTAGGGTTTGA
* *
1362472 GGGTTAGGGTTTTAGGGTTTGA
1 GGTTTGGGGTTTTAGGGTTTGA
*
1362494 GGTTTGGGG-TTTGGGGTTTG
1 GGTTTGGGGTTTTAGGGTTTG
1362514 TGGCGTGGGG
Statistics
Matches: 61, Mismatches: 21, Indels: 5
0.70 0.24 0.06
Matches are distributed among these distances:
20 6 0.10
21 25 0.41
22 30 0.49
ACGTcount: A:0.08, C:0.03, G:0.46, T:0.42
Consensus pattern (22 bp):
GGTTTGGGGTTTTAGGGTTTGA
Done.