Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 41 of 182
Found at i:15291372 original size:43 final size:42
Alignment explanation
Indices: 15291324--15291420 Score: 113
Period size: 43 Copynumber: 2.3 Consensus size: 42
15291314 GCTTTCCCAA
*
15291324 AAACGCCACTAAAAAACATGATATTTAACGGTGCTTTTACCAC
1 AAACGCCACTAAAAAACATGATATTTAACGGT-ATTTTACCAC
* * * * ** *
15291367 AAACGCCGCTAAAGAACATGGTCTTTAGTGGTATTTTCCCAC
1 AAACGCCACTAAAAAACATGATATTTAACGGTATTTTACCAC
15291409 AAACGCCACTAA
1 AAACGCCACTAA
15291421 TATTAACAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 19 0.42
43 26 0.58
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (42 bp):
AAACGCCACTAAAAAACATGATATTTAACGGTATTTTACCAC
Found at i:15295807 original size:41 final size:41
Alignment explanation
Indices: 15295761--15296030 Score: 337
Period size: 41 Copynumber: 6.6 Consensus size: 41
15295751 TTTTTCAAAT
* * *
15295761 AAGCGCCACTATTACTCTGACCTTTAGCGGTGCTTGCACAA
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCACAA
* *
15295802 AAGCGCCACTATTGCTCTGACCTTTAGCGGCACTTGCACAA
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCACAA
* *
15295843 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCACAA
* * *
15295884 AAGCGCTGTTATTGCTCTGACCTTTAGCAGCGCTTGCACAA
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCACAA
* * * * *
15295925 AAGAG-CGACTATTGCTCTGACCTTTAGTGGCGCTTTCCCAT
1 AAGCGCCG-CTATTGCTCTGACCTTTAGCGGCGCTTGCACAA
* * * * *
15295966 AAGCGTCGCTATTGCTCTGACCTTTAGCGACGCTTTCCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCACAA
15296007 AAGCGCCGCTATTGCTCT-ACCTTT
1 AAGCGCCGCTATTGCTCTGACCTTT
15296031 TACGACATTT
Statistics
Matches: 203, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
40 7 0.03
41 194 0.96
42 2 0.01
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (41 bp):
AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCACAA
Found at i:15295978 original size:123 final size:123
Alignment explanation
Indices: 15295759--15296030 Score: 393
Period size: 123 Copynumber: 2.2 Consensus size: 123
15295749 CGTTTTTCAA
* * * * *
15295759 ATAAGCGCCACTATTACTCTGACCTTTAGCGGTGCTTGCACAAAAGCGCCACTATTGCTCTGACC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTGCACAAAAGAGCCACTATTGCTCTGACC
*
15295824 TTTAGCGGCACTTGCACAAAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
66 TTTAGCGGCACTTGCACAAAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCC
* * *
15295882 ATAAGCGCTGTTATTGCTCTGACCTTTAGCAGCGCTTGCACAAAAGAGCGACTATTGCTCTGACC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTGCACAAAAGAGCCACTATTGCTCTGACC
* * * * * * *
15295947 TTTAGTGGCGCTTTCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCGACGCTTTCCC
66 TTTAGCGGCACTTGCACAAAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCC
15296005 ATAAGCGCCGCTATTGCTCT-ACCTTT
1 ATAAGCGCCGCTATTGCTCTGACCTTT
15296031 TACGACATTT
Statistics
Matches: 131, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
122 6 0.05
123 125 0.95
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (123 bp):
ATAAGCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTGCACAAAAGAGCCACTATTGCTCTGACC
TTTAGCGGCACTTGCACAAAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCC
Found at i:15296054 original size:40 final size:40
Alignment explanation
Indices: 15296010--15296111 Score: 186
Period size: 40 Copynumber: 2.5 Consensus size: 40
15296000 TTCCCATAAG
15296010 CGCCGCTATTGCTCTACCTTTTACGACATTTATGTAGAAA
1 CGCCGCTATTGCTCTACCTTTTACGACATTTATGTAGAAA
*
15296050 CGCCGCTATTGCTCTACCTTTTACGGCATTTATGTAGAAA
1 CGCCGCTATTGCTCTACCTTTTACGACATTTATGTAGAAA
*
15296090 CGCCGCTATTGCTTTACCTTTT
1 CGCCGCTATTGCTCTACCTTTT
15296112 GTGGCGTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (40 bp):
CGCCGCTATTGCTCTACCTTTTACGACATTTATGTAGAAA
Found at i:15296583 original size:17 final size:17
Alignment explanation
Indices: 15296560--15296602 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
15296550 CCACGTTAGC
15296560 AAAAAAT-TAATTATTTT
1 AAAAAATATAATT-TTTT
*
15296577 TAAAAATATAATTTTTT
1 AAAAAATATAATTTTTT
15296594 AAAAAATAT
1 AAAAAATAT
15296603 TTTAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAAATATAATTTTTT
Found at i:15299058 original size:35 final size:35
Alignment explanation
Indices: 15299010--15299090 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
15299000 ATAGTTCTCT
*
15299010 AATACCCTAGGAGTCGAGAACGTATCACCAGCTCA
1 AATACCCTGGGAGTCGAGAACGTATCACCAGCTCA
*
15299045 AATACCCTGGGAGTCGAGAACGTATCACCAGCTTA
1 AATACCCTGGGAGTCGAGAACGTATCACCAGCTCA
15299080 AATACCCTGGG
1 AATACCCTGGG
15299091 GGTACGAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (35 bp):
AATACCCTGGGAGTCGAGAACGTATCACCAGCTCA
Found at i:15299656 original size:4 final size:4
Alignment explanation
Indices: 15299647--15299693 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
15299637 ATTACGATCC
15299647 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
15299694 ATGTTTTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:15301068 original size:2 final size:2
Alignment explanation
Indices: 15301061--15301095 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15301051 ATAAAGAGAT
15301061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15301096 TTAAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15309661 original size:20 final size:21
Alignment explanation
Indices: 15309636--15309677 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
15309626 ACAAAGGGCC
15309636 ACATGGT-TGACGTGGCGATG
1 ACATGGTATGACGTGGCGATG
15309656 ACATGGTACTGACGTGGCGATG
1 ACATGGTA-TGACGTGGCGATG
15309678 CTGACGTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (21 bp):
ACATGGTATGACGTGGCGATG
Found at i:15309683 original size:14 final size:14
Alignment explanation
Indices: 15309664--15309691 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15309654 TGACATGGTA
15309664 CTGACGTGGCGATG
1 CTGACGTGGCGATG
15309678 CTGACGTGGCGATG
1 CTGACGTGGCGATG
15309692 TTGGCTGAAG
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:0.14, C:0.21, G:0.43, T:0.21
Consensus pattern (14 bp):
CTGACGTGGCGATG
Found at i:15310470 original size:49 final size:49
Alignment explanation
Indices: 15310397--15311182 Score: 505
Period size: 49 Copynumber: 16.1 Consensus size: 49
15310387 ATGTCTTTGA
* * * * *
15310397 GGTACAAGGTTCGTCATTGCGACTTAAACCCTTCCCTTTGTATCTTCGT
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * *
15310446 GGTACTAGATTCGCCGTTGTGACTTAAACCTTTCCCTTTGTATCTTCGG
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * * * * * * *
15310495 GGTACTAGATTTGTCGTTACGGCTTAGATCTCTCCCTTCAT-GCTTCTGA
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTC-GT
* * * * * * *
15310544 GGTGCAAGGTTC-ACTATTGCGACTTAAACTTTTCCCTTTATATCTTCGC
1 GGTACTAGATTCGTC-GTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * * * * *
15310593 AGTACTGGATTCGTCATTGC-AGCTTAAACTTTTCCCTTTGTATCTTTGA
1 GGTACTAGATTCGTCGTTGCGA-CTTAAACCTTTCCCTTTATATCTTCGT
* * * * * * * * *
15310642 GGTACTAGATTCATCGTTGTGGCTTAGATCTTTCCCTTCAT-GCCT-GA
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * * *
15310689 GGTACAAGGTTCGCCGTTGCAACTTAAACCTTTCTCTTTATATCTTCGT
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * *
15310738 GATACTAGATT-TTCCGTTGCGGCTTAAATCTTTCCCTTTATATCTTCGT
1 GGTACTAGATTCGT-CGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * * * * *
15310787 GGTACTGGATTCGTTGTTGAGACTTAAATCTTT-CCTTTCGTGT-TTCTGA
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTT-ATATCTTC-GT
* * * * * **
15310836 GGTACAAGGTTCGTCGTTGTGACTTAAACATTTCACTTTGCATCTTCGT
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * * * * *
15310885 GGTAGTAGCTTCGTCGTTGC-AGCTTAAATCTTTTCCTTTAT-GCTTATGA
1 GGTACTAGATTCGTCGTTGCGA-CTTAAACCTTTCCCTTTATATCTT-CGT
* * * *
15310934 GGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTTTATATCTTCGT
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * * *
15310983 GGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCTTTTATATCTTCAT
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * * ** * *
15311032 GGTACTGGATTCGTCGTTGTGGCTTAAATCTTTCCCTTCGT-GCTTCTGA
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTC-GT
* * ** *
15311081 GGTACAAGGTTCACCATTGCGACTTAAACCTTTCCCTTTATATCTTCGT
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
* * * * * * * *
15311130 GGTATTGGATTCGCCGTTACGACTTAAATCTTCCCCTTCATGTCTTCGT
1 GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
15311179 GGTA
1 GGTA
15311183 AACCTGTAGA
Statistics
Matches: 555, Mismatches: 162, Indels: 40
0.73 0.21 0.05
Matches are distributed among these distances:
47 32 0.06
48 26 0.05
49 476 0.86
50 21 0.04
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (49 bp):
GGTACTAGATTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCTTCGT
Found at i:15310635 original size:147 final size:146
Alignment explanation
Indices: 15310384--15311069 Score: 572
Period size: 147 Copynumber: 4.7 Consensus size: 146
15310374 AATTTTTCTT
* * *
15310384 TTCATGTCTT-TGAGGTACAAGGTTCGTCATTGCGACTTAAACCCTTCCCTTTGTATCTTCGTGG
1 TTCATG-CTTCTGAGGTACAAGGTTCCTCATTGCGACTTAAACCTTTCCCTTTATATCTTCGTGG
* * * * *
15310448 TACTAGATTCGCCGTTG-TGACTTAAACCTTTCCCTTTGTATCTTCGGGGTACTAGATTTGTCGT
65 TACTAGATTCGTCGTTGCAG-CTTAAACTTTTCCCTTTGTATCTTCGAGGTACTAGATTCGTCGT
*
15310512 TACGGCTTAGATCTCTCCC
129 TA-GGCTTAGATCTTTCCC
* * **
15310531 TTCATGCTTCTGAGGTGCAAGGTTCACT-ATTGCGACTTAAACTTTTCCCTTTATATCTTCGCAG
1 TTCATGCTTCTGAGGTACAAGGTTC-CTCATTGCGACTTAAACCTTTCCCTTTATATCTTCGTGG
* * * *
15310595 TACTGGATTCGTCATTGCAGCTTAAACTTTTCCCTTTGTATCTTTGAGGTACTAGATTCATCGTT
65 TACTAGATTCGTCGTTGCAGCTTAAACTTTTCCCTTTGTATCTTCGAGGTACTAGATTCGTCGTT
*
15310660 GTGGCTTAGATCTTTCCC
130 -AGGCTTAGATCTTTCCC
* * * *
15310678 TTCATGC--CTGAGGTACAAGGTTCGC-CGTTGCAACTTAAACCTTTCTCTTTATATCTTCGTGA
1 TTCATGCTTCTGAGGTACAAGGTTC-CTCATTGCGACTTAAACCTTTCCCTTTATATCTTCGTGG
* * * * * *
15310740 TACTAGATT-TTCCGTTGCGGCTTAAA-TCTTTCCCTTTATATCTTCGTGGTACTGGATTCGTTG
65 TACTAGATTCGT-CGTTGCAGCTTAAACT-TTTCCCTTTGTATCTTCGAGGTACTAGATTCGTCG
* * *
15310803 TTGAGACTTAAATCTTTCCT
128 TT-AGGCTTAGATCTTTCCC
* * * * * * * **
15310823 TTCGTGTTTCTGAGGTACAAGGTTCGTCGTTGTGACTTAAACATTTCACTTTGCATCTTCGTGGT
1 TTCATGCTTCTGAGGTACAAGGTTCCTCATTGCGACTTAAACCTTTCCCTTTATATCTTCGTGGT
* * * * * *
15310888 AGTAGCTTCGTCGTTGCAGCTTAAATCTTTT-CC-TT-TATGCTTATGAGGTACAAGGTTCGCCG
66 ACTAGATTCGTCGTTGCAGCTTAAA-CTTTTCCCTTTGTAT-CTT-CGAGGTACTAGATTCGTCG
* * *
15310950 TTACGACTTAAACCTTTCCC
128 TTA-GGCTTAGATCTTTCCC
* * * * * * * * * *
15310970 TTTATATCTTC-GTGGTAC-TGGATTCGTCGTTGCGGCTTAAATCTTTCCTTTTATATCTTCATG
1 TTCAT-GCTTCTGAGGTACAAGG-TTCCTCATTGCGACTTAAACCTTTCCCTTTATATCTTCGTG
* **
15311033 GTACTGGATTCGTCGTTGTGGCTTAAA-TCTTTCCCTT
64 GTACTAGATTCGTCGTTGCAGCTTAAACT-TTTCCCTT
15311070 CGTGCTTCTG
Statistics
Matches: 434, Mismatches: 84, Indels: 41
0.78 0.15 0.07
Matches are distributed among these distances:
144 2 0.00
145 119 0.27
146 14 0.03
147 288 0.66
148 10 0.02
149 1 0.00
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (146 bp):
TTCATGCTTCTGAGGTACAAGGTTCCTCATTGCGACTTAAACCTTTCCCTTTATATCTTCGTGGT
ACTAGATTCGTCGTTGCAGCTTAAACTTTTCCCTTTGTATCTTCGAGGTACTAGATTCGTCGTTA
GGCTTAGATCTTTCCC
Found at i:15325790 original size:18 final size:17
Alignment explanation
Indices: 15325759--15325793 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
15325749 GGTTTAGGGT
15325759 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
15325776 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
15325794 AGATTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:15327186 original size:247 final size:247
Alignment explanation
Indices: 15326750--15327245 Score: 992
Period size: 247 Copynumber: 2.0 Consensus size: 247
15326740 TGCAACCCAC
15326750 ACAAAAGCAAGCCAACTGTGGCTTGAAAGCAGCTAATAGGAAGAATGGGAAACTGTTTCTTCAGA
1 ACAAAAGCAAGCCAACTGTGGCTTGAAAGCAGCTAATAGGAAGAATGGGAAACTGTTTCTTCAGA
15326815 TAGTTTGCTACTAGATACAACCCCTAAACAAAATATTTGGATACTTCCACTGCATCATCATAAAC
66 TAGTTTGCTACTAGATACAACCCCTAAACAAAATATTTGGATACTTCCACTGCATCATCATAAAC
15326880 TCTATCCTAGTTTGACAAAAGGGACTAATATAACTTGGTGATGAAACTGCTTCTTCAAAGTGCTT
131 TCTATCCTAGTTTGACAAAAGGGACTAATATAACTTGGTGATGAAACTGCTTCTTCAAAGTGCTT
15326945 TGTTTCGAGGCCTCAATCTTCTGGCAACACAGTCCATATTAGTTCCAGAAGT
196 TGTTTCGAGGCCTCAATCTTCTGGCAACACAGTCCATATTAGTTCCAGAAGT
15326997 ACAAAAGCAAGCCAACTGTGGCTTGAAAGCAGCTAATAGGAAGAATGGGAAACTGTTTCTTCAGA
1 ACAAAAGCAAGCCAACTGTGGCTTGAAAGCAGCTAATAGGAAGAATGGGAAACTGTTTCTTCAGA
15327062 TAGTTTGCTACTAGATACAACCCCTAAACAAAATATTTGGATACTTCCACTGCATCATCATAAAC
66 TAGTTTGCTACTAGATACAACCCCTAAACAAAATATTTGGATACTTCCACTGCATCATCATAAAC
15327127 TCTATCCTAGTTTGACAAAAGGGACTAATATAACTTGGTGATGAAACTGCTTCTTCAAAGTGCTT
131 TCTATCCTAGTTTGACAAAAGGGACTAATATAACTTGGTGATGAAACTGCTTCTTCAAAGTGCTT
15327192 TGTTTCGAGGCCTCAATCTTCTGGCAACACAGTCCATATTAGTTCCAGAAGT
196 TGTTTCGAGGCCTCAATCTTCTGGCAACACAGTCCATATTAGTTCCAGAAGT
15327244 AC
1 AC
15327246 TATGCTTCGG
Statistics
Matches: 249, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
247 249 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (247 bp):
ACAAAAGCAAGCCAACTGTGGCTTGAAAGCAGCTAATAGGAAGAATGGGAAACTGTTTCTTCAGA
TAGTTTGCTACTAGATACAACCCCTAAACAAAATATTTGGATACTTCCACTGCATCATCATAAAC
TCTATCCTAGTTTGACAAAAGGGACTAATATAACTTGGTGATGAAACTGCTTCTTCAAAGTGCTT
TGTTTCGAGGCCTCAATCTTCTGGCAACACAGTCCATATTAGTTCCAGAAGT
Found at i:15328102 original size:234 final size:234
Alignment explanation
Indices: 15327696--15328524 Score: 1610
Period size: 234 Copynumber: 3.6 Consensus size: 234
15327686 TTGTTCCCGA
* *
15327696 AATAGCAACGGTTTGCTTGCAGGATTTTGATGGATAATCGAAGTA-TT--TTCTGGGTATGCTTC
1 AATAGCAACGGTTTGCTTGCAGGATTTTAATGGATAATCGAAGTATTTGGTTCTGAGTATGCTTC
15327758 TTGTTCTTTTTTCTCACTGCTCAAGCCATCCTCTCCAGATTGAGGTTTTGATGTTACAAGCTGAT
66 TTGTTCTTTTTTCTCACTGCTCAAGCCATCCTCTCCAGATTGAGGTTTTGATGTTACAAGCTGAT
15327823 CATCCTTTTCATGTTCACATATGAATTCATCATCTCTCTTGTTCCCGAAATCAAGGTTGATCTTT
131 CATCCTTTTCATGTTCACATATGAATTCATCATCTCTCTTGTTCCCGAAATCAAGGTTGATCTTT
15327888 GTAGACTCCCCTTTCTCAAACTCTGTTTCATTCTTTGAG
196 GTAGACTCCCCTTTCTCAAACTCTGTTTCATTCTTTGAG
15327927 AATAGCAACGGTTTGCTTGCAGGATTTTAATGGATAATCGAAGTATTTGGTTCTGAGTATGCTTC
1 AATAGCAACGGTTTGCTTGCAGGATTTTAATGGATAATCGAAGTATTTGGTTCTGAGTATGCTTC
15327992 TTGTTCTTTTTTCTCACTGCTCAAGCCATCCTCTCCAGATTGAGGTTTTGATGTTACAAGCTGAT
66 TTGTTCTTTTTTCTCACTGCTCAAGCCATCCTCTCCAGATTGAGGTTTTGATGTTACAAGCTGAT
15328057 CATCCTTTTCATGTTCACATATGAATTCATCATCTCTCTTGTTCCCGAAATCAAGGTTGATCTTT
131 CATCCTTTTCATGTTCACATATGAATTCATCATCTCTCTTGTTCCCGAAATCAAGGTTGATCTTT
15328122 GTAGACTCCCCTTTCTCAAACTCTGTTTCATTCTTTGAG
196 GTAGACTCCCCTTTCTCAAACTCTGTTTCATTCTTTGAG
15328161 AATAGCAACGGTTTGCTTGCAGGATTTTAATGGATAATCGAAGTATTTGGTTCTGAGTATGCTTC
1 AATAGCAACGGTTTGCTTGCAGGATTTTAATGGATAATCGAAGTATTTGGTTCTGAGTATGCTTC
15328226 TTGTTCTTTTTTCTCACTGCTCAAGCCATCCTCTCCAGATTGAGGTTTTGATGTTACAAGCTGAT
66 TTGTTCTTTTTTCTCACTGCTCAAGCCATCCTCTCCAGATTGAGGTTTTGATGTTACAAGCTGAT
15328291 CATCCTTTTCATGTTCACATATGAATTCATCATCTCTCTTGTTCCCGAAATCAAGGTTGATCTTT
131 CATCCTTTTCATGTTCACATATGAATTCATCATCTCTCTTGTTCCCGAAATCAAGGTTGATCTTT
15328356 GTAGACTCCCCTTTCTCAAACTCTGTTTCATTCTTTGAG
196 GTAGACTCCCCTTTCTCAAACTCTGTTTCATTCTTTGAG
15328395 AATAGCAACGGTTTGCTTGCAGGATTTTAATGGATAATCGAAGTATTTGGTTCTGAGTATGCTTC
1 AATAGCAACGGTTTGCTTGCAGGATTTTAATGGATAATCGAAGTATTTGGTTCTGAGTATGCTTC
*
15328460 TTGTTCTTTTTTCTCACTGCTCAAGCCATCCTCTCCAGATTGAGGCTTTGATGTTACAAGCTGAT
66 TTGTTCTTTTTTCTCACTGCTCAAGCCATCCTCTCCAGATTGAGGTTTTGATGTTACAAGCTGAT
15328525 TATTATCGAC
Statistics
Matches: 592, Mismatches: 3, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
231 44 0.07
232 2 0.00
234 546 0.92
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (234 bp):
AATAGCAACGGTTTGCTTGCAGGATTTTAATGGATAATCGAAGTATTTGGTTCTGAGTATGCTTC
TTGTTCTTTTTTCTCACTGCTCAAGCCATCCTCTCCAGATTGAGGTTTTGATGTTACAAGCTGAT
CATCCTTTTCATGTTCACATATGAATTCATCATCTCTCTTGTTCCCGAAATCAAGGTTGATCTTT
GTAGACTCCCCTTTCTCAAACTCTGTTTCATTCTTTGAG
Found at i:15331754 original size:10 final size:11
Alignment explanation
Indices: 15331725--15331753 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
15331715 TGCTCAAAAC
15331725 ATACCAAAATG
1 ATACCAAAATG
15331736 AT-CCAAAATG
1 ATACCAAAATG
15331746 ATACCAAA
1 ATACCAAA
15331754 TATATAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (11 bp):
ATACCAAAATG
Found at i:15332154 original size:38 final size:38
Alignment explanation
Indices: 15332087--15332177 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 38
15332077 TATATTGATA
*
15332087 ATAAT-TTTTATTTTTAAAATTATTAAAACATTA-ATAT
1 ATAATATTATATTTTTAAAATTATTAAAACA-TACATAT
*
15332124 ATAATATTATATTTTTCAATATTATT-AAACATACATAT
1 ATAATATTATATTTTT-AAAATTATTAAAACATACATAT
*
15332162 TTAATTATTTATATTT
1 ATAA-TA-TTATATTT
15332178 AGGCATATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
37 7 0.15
38 21 0.46
39 10 0.22
40 8 0.17
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (38 bp):
ATAATATTATATTTTTAAAATTATTAAAACATACATAT
Found at i:15332309 original size:15 final size:15
Alignment explanation
Indices: 15332283--15332346 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
15332273 AAAAATATTC
15332283 AATAAT-AATATTTT
1 AATAATAAATATTTT
15332297 AATAATAAATATTTATT
1 AATAATAAATA-TT-TT
* *
15332314 ACAATTATAAATATATT
1 --AATAATAAATATTTT
15332331 AATAATAAATATTTT
1 AATAATAAATATTTT
15332346 A
1 A
15332347 TAGTATAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 6 0.15
15 18 0.44
16 2 0.05
17 4 0.10
18 1 0.02
19 10 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATAAATATTTT
Found at i:15332773 original size:19 final size:19
Alignment explanation
Indices: 15332741--15332790 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
15332731 ATCCAAACAT
* *
15332741 AAAAAATATTAATTTTTTTC
1 AAAAAA-ATAAATTATTTTC
15332761 AAAAAAATAAATTATTTTC
1 AAAAAAATAAATTATTTTC
* *
15332780 TATAAAATAAA
1 AAAAAAATAAA
15332791 CATAACCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAAAATAAATTATTTTC
Found at i:15332786 original size:21 final size:21
Alignment explanation
Indices: 15332738--15332786 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
15332728 TTCATCCAAA
*
15332738 CATAAAAAATATTAATTTTTTT
1 CATAAAAAATA-TAATTATTTT
15332760 CA-AAAAAATA-AATTATTTT
1 CATAAAAAATATAATTATTTT
15332779 CTATAAAA
1 C-ATAAAA
15332787 TAAACATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 1 0.04
21 12 0.50
22 2 0.08
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (21 bp):
CATAAAAAATATAATTATTTT
Found at i:15333191 original size:15 final size:15
Alignment explanation
Indices: 15333171--15333250 Score: 67
Period size: 14 Copynumber: 5.3 Consensus size: 15
15333161 ATACTATAAA
15333171 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
15333186 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
15333203 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
*
15333220 ATA-TTATTATTGA-
1 ATATTTATTATTAAT
*
15333233 ATATTT-TTAATAAT
1 ATATTTATTATTAAT
15333247 ATAT
1 ATAT
15333251 GAAGAAGATT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
13 8 0.15
14 15 0.28
15 12 0.23
16 1 0.02
17 7 0.13
18 1 0.02
19 9 0.17
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:15333226 original size:14 final size:15
Alignment explanation
Indices: 15333167--15333230 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
15333157 CTTTATACTA
15333167 TAAAATATTTATTAT
1 TAAAATATTTATTAT
* *
15333182 TAATATATTTATAATT
1 TAAAATATTTATTA-T
15333198 GTAATAAATATTTATTAT
1 -T-A-AAATATTTATTAT
15333216 TAAAATA-TTATTAT
1 TAAAATATTTATTAT
15333230 T
1 T
15333231 GAATATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 8 0.20
15 17 0.41
16 2 0.05
17 2 0.05
18 2 0.05
19 10 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TAAAATATTTATTAT
Found at i:15333416 original size:38 final size:38
Alignment explanation
Indices: 15333336--15333426 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 38
15333326 TTATATGGCT
*
15333336 AAATATAAATAATTAAATATGTATGTTTAATAATATTGAA
1 AAATAT-AAT-ATTATATATGTATGTTTAATAATATTGAA
*
15333376 AAATATAATATTATATAT-TAATGTTTTAATAAT-TTTAA
1 AAATATAATATTATATATGT-ATG-TTTAATAATATTGAA
*
15333414 AAATA-AAAATTAT
1 AAATATAATATTAT
15333427 TATCAATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
37 8 0.17
38 20 0.43
39 12 0.26
40 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (38 bp):
AAATATAATATTATATATGTATGTTTAATAATATTGAA
Found at i:15333723 original size:31 final size:31
Alignment explanation
Indices: 15333688--15333764 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
15333678 TTAATATAAC
*
15333688 ATTTGGTACTTAAACTTGACACTTTTT-TCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCT-TA
* *
15333719 ATTTGGTACCTGAGCTTGACACTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCTTA
*
15333750 ATTTGATACCTAAAC
1 ATTTGGTACCTAAAC
15333765 CTTTTTTGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTTA
Found at i:15333804 original size:59 final size:60
Alignment explanation
Indices: 15333718--15333853 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 60
15333708 ACTTTTTTCT
* ** *
15333718 AATTTGGTACCTGAGCTTGACA-CTTTTTCTTAATTTGATACCTAAACCTTTTTT-GACCC
1 AATTTGGTATCTGAATTTGACATCTTTTTCCTAATTTGATACCTAAA-CTTTTTTAGACCC
* * * **
15333777 AATTTGGTATCTGAATTTGATATTTTTTTCCTAATTTGGTACCTAAACTTTTTTAGATTC
1 AATTTGGTATCTGAATTTGACATCTTTTTCCTAATTTGATACCTAAACTTTTTTAGACCC
*
15333837 AATTTGGTATCTAAATT
1 AATTTGGTATCTGAATT
15333854 CATTAAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 25 0.38
60 40 0.62
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (60 bp):
AATTTGGTATCTGAATTTGACATCTTTTTCCTAATTTGATACCTAAACTTTTTTAGACCC
Found at i:15333820 original size:60 final size:60
Alignment explanation
Indices: 15333741--15333853 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
15333731 AGCTTGACAC
* *
15333741 TTTTTCTTAATTTGATACCTAAACCTTTTTT-GACCCAATTTGGTATCTGAATTTGATATT
1 TTTTTCCTAATTTGATACCTAAA-CTTTTTTAGACCCAATTTGGTATCTAAATTTGATATT
* **
15333801 TTTTTCCTAATTTGGTACCTAAACTTTTTTAGATTCAATTTGGTATCTAAATT
1 TTTTTCCTAATTTGATACCTAAACTTTTTTAGACCCAATTTGGTATCTAAATT
15333854 CATTAAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 7 0.15
60 40 0.85
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (60 bp):
TTTTTCCTAATTTGATACCTAAACTTTTTTAGACCCAATTTGGTATCTAAATTTGATATT
Found at i:15336040 original size:15 final size:17
Alignment explanation
Indices: 15336022--15336056 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
15336012 ATAGTTTTCG
15336022 ATCTTT-AATT-TTTTA
1 ATCTTTCAATTATTTTA
15336037 ATCTTTCAATTATTTTA
1 ATCTTTCAATTATTTTA
15336054 ATC
1 ATC
15336057 AATTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 4 0.22
17 8 0.44
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (17 bp):
ATCTTTCAATTATTTTA
Found at i:15337448 original size:10 final size:11
Alignment explanation
Indices: 15337419--15337447 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
15337409 TGCTCAAAAC
15337419 ATACCAAAATG
1 ATACCAAAATG
15337430 AT-CCAAAATG
1 ATACCAAAATG
15337440 ATACCAAA
1 ATACCAAA
15337448 TATATAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (11 bp):
ATACCAAAATG
Found at i:15339907 original size:30 final size:30
Alignment explanation
Indices: 15339872--15340089 Score: 133
Period size: 29 Copynumber: 7.5 Consensus size: 30
15339862 ACCCGGGGGC
* *
15339872 AAAATGGTGATTTTGGTGAAATCGAGGTTA
1 AAAATGGTAATTTTGGTGAAATCGAGGGTA
** *
15339902 AAAATGG-AATTTT--AAAAGATACGGGGGT-
1 AAAATGGTAATTTTGGTGAA-AT-CGAGGGTA
* *
15339930 AAAATGATAATTTTTGGTGAAATCGAGGTTA
1 AAAATGGTAA-TTTTGGTGAAATCGAGGGTA
* *
15339961 AAAATGG-AATTTT--AGAAGATTCGGGGGT-
1 AAAATGGTAATTTTGGTGAA-A-TCGAGGGTA
15339989 AAAATGGTAATTTTCGGTGAAATCG-GGGTA
1 AAAATGGTAATTTT-GGTGAAATCGAGGGTA
** *
15340019 AAAATGG-AATTTT--AAAAGATTCGGGGGT-
1 AAAATGGTAATTTTGGTGAA-A-TCGAGGGTA
*
15340047 AAAATGGTAATTTTTGGTAAAATC-AGGGTA
1 AAAATGGTAA-TTTTGGTGAAATCGAGGGTA
15340077 AAAATGG-AATTTT
1 AAAATGGTAATTTT
15340090 AAAAGATTCG
Statistics
Matches: 147, Mismatches: 19, Indels: 46
0.69 0.09 0.22
Matches are distributed among these distances:
26 2 0.01
27 6 0.04
28 30 0.20
29 50 0.34
30 41 0.28
31 10 0.07
32 8 0.05
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTGAAATCGAGGGTA
Found at i:15339962 original size:59 final size:59
Alignment explanation
Indices: 15339865--15340118 Score: 397
Period size: 58 Copynumber: 4.4 Consensus size: 59
15339855 TGTGGATACC
* * * *
15339865 CGGGGGCAAAATGGTGA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATA
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGGTAAAAATGGAATTTTAAAAGATT
* * *
15339923 CGGGGGTAAAATGATAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGGTAAAAATGGAATTTTAAAAGATT
*
15339982 CGGGGGTAAAATGGTAATTTTCGGTGAAATCG-GGGTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGGTAAAAATGGAATTTTAAAAGATT
*
15340040 CGGGGGTAAAATGGTAATTTTTGGTAAAATC-AGGGTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGGTAAAAATGGAATTTTAAAAGATT
*
15340098 CGGGGTTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
15340119 CAGAAGTTTC
Statistics
Matches: 182, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
58 113 0.62
59 69 0.38
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGGTAAAAATGGAATTTTAAAAGATT
Found at i:15340107 original size:29 final size:28
Alignment explanation
Indices: 15339902--15340118 Score: 136
Period size: 29 Copynumber: 7.5 Consensus size: 28
15339892 ATCGAGGTTA
*
15339902 AAAATGGAATTTTAAAAGATACGGGGGT
1 AAAATGGAATTTTAAAAGATTCGGGGGT
* **** * * *
15339930 AAAATGATAATTTTTGGTGAAATCGAGGTT
1 AAAATG-GAATTTTAAAAG-ATTCGGGGGT
*
15339960 AAAAATGGAATTTTAGAAGATTCGGGGGT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
**** *
15339989 AAAATGGTAATTTTCGGTGAAATC-GGGGT
1 AAAATGG-AATTTTAAAAG-ATTCGGGGGT
15340018 AAAAATGGAATTTTAAAAGATTCGGGGGT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
* *
15340047 AAAATGGTAATTTTTGGTAAA-A-TC-AGGGT
1 AAAATGG-AA-TTTT--AAAAGATTCGGGGGT
*
15340076 AAAAATGGAATTTTAAAAGATTCGGGGTT
1 -AAAATGGAATTTTAAAAGATTCGGGGGT
15340105 AAAATGGTAATTTT
1 AAAATGG-AATTTT
15340119 CAGAAGTTTC
Statistics
Matches: 143, Mismatches: 30, Indels: 31
0.70 0.15 0.15
Matches are distributed among these distances:
26 3 0.02
27 1 0.01
28 36 0.25
29 56 0.39
30 37 0.26
31 7 0.05
32 3 0.02
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (28 bp):
AAAATGGAATTTTAAAAGATTCGGGGGT
Found at i:15340534 original size:162 final size:162
Alignment explanation
Indices: 15340276--15340588 Score: 470
Period size: 162 Copynumber: 1.9 Consensus size: 162
15340266 TTGTAAATCT
** *
15340276 TGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAGTTGATTTGAGGATTAAATTAAAATAAA
1 TGAAAAATTCTTAAGCCAATTTCGTAATTAAATAAAAGTTGATTTGAGGATTAAATTAAAACAAA
*
15340341 TTAAAAAACAAAAGGACTAAATGCATAAATAA-TCGAATAAATGACACGTGGCAGTCC-CTGACA
66 TTAAAAAACAAAAGGACTAAATGCATAAATAATTC-AAAAAATGACACGTGGCAG-CCTCTGACA
15340404 CAGTCAAACAGTCAAAGGACTAATTTATAAACCA
129 CAGTCAAACAGTCAAAGGACTAATTTATAAACCA
15340438 TGAAAAATTCTTAAGCCAATTTCGTAATTAAATAAAAGTTGATTTG-GAGATTAAATTAAAACAA
1 TGAAAAATTCTTAAGCCAATTTCGTAATTAAATAAAAGTTGATTTGAG-GATTAAATTAAAACAA
**** * **
15340502 ATTAAAAATGTCAGGGACTAAATGCATAAATAATTCAAAAAATGACACGTGGCAGCCTCTGGTAC
65 ATTAAAAAACAAAAGGACTAAATGCATAAATAATTCAAAAAATGACACGTGGCAGCCTCTGACAC
*
15340567 AGTCAAACAGTCAGAGGACTAA
130 AGTCAAACAGTCAAAGGACTAA
15340589 ATTGAAAAGC
Statistics
Matches: 136, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
161 3 0.02
162 131 0.96
163 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (162 bp):
TGAAAAATTCTTAAGCCAATTTCGTAATTAAATAAAAGTTGATTTGAGGATTAAATTAAAACAAA
TTAAAAAACAAAAGGACTAAATGCATAAATAATTCAAAAAATGACACGTGGCAGCCTCTGACACA
GTCAAACAGTCAAAGGACTAATTTATAAACCA
Found at i:15340655 original size:34 final size:32
Alignment explanation
Indices: 15340617--15340681 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
15340607 TTACATGGCA
* *
15340617 AAATTGCAAATAATTAAAAAATGCAGAAAGGACT
1 AAATTG-AAACAAATAAAAAATGC-GAAAGGACT
*
15340651 AAATTGAAGCAAATAAAAAATGCGAAAGGAC
1 AAATTGAAACAAATAAAAAATGCGAAAGGAC
15340682 CGATTGTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 8 0.29
33 14 0.50
34 6 0.21
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (32 bp):
AAATTGAAACAAATAAAAAATGCGAAAGGACT
Found at i:15342172 original size:23 final size:20
Alignment explanation
Indices: 15342126--15342169 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
15342116 CTTGGTGGTG
15342126 GCAGATGGAACTGGTGGTCA
1 GCAGATGGAACTGGTGGTCA
*
15342146 GCAGATGGAGCTGGTGGTCA
1 GCAGATGGAACTGGTGGTCA
15342166 GCAG
1 GCAG
15342170 CAGCATAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.43, T:0.18
Consensus pattern (20 bp):
GCAGATGGAACTGGTGGTCA
Found at i:15342408 original size:11 final size:11
Alignment explanation
Indices: 15342392--15342467 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
15342382 TTATAATAAC
15342392 ATTAAATTTAA
1 ATTAAATTTAA
*
15342403 ATTAAATTCAA
1 ATTAAATTTAA
*
15342414 GTTTAAATTTAA
1 -ATTAAATTTAA
*
15342426 ATTGAATTTAA
1 ATTAAATTTAA
*
15342437 AATAAATTTAA
1 ATTAAATTTAA
*
15342448 GATTAAA-ATAA
1 -ATTAAATTTAA
*
15342459 ATTTAATTT
1 ATTAAATTT
15342468 TCAAATGGTT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
10 5 0.10
11 32 0.63
12 14 0.27
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:15342473 original size:17 final size:16
Alignment explanation
Indices: 15342379--15342467 Score: 79
Period size: 17 Copynumber: 5.3 Consensus size: 16
15342369 TTTCTTTTTA
* *
15342379 AATTTATAATAACATTA
1 AATTTAAAATAA-ATTT
* *
15342396 AATTTAAATTAAATTC
1 AATTTAAAATAAATTT
* *
15342412 AAGTTTAAATTTAAATTG
1 AA-TTTAAA-ATAAATTT
15342430 AATTTAAAATAAATTT
1 AATTTAAAATAAATTT
*
15342446 AAGATTAAAATAAATTT
1 AA-TTTAAAATAAATTT
15342463 AATTT
1 AATTT
15342468 TCAAATGGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
16 15 0.25
17 37 0.61
18 9 0.15
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (16 bp):
AATTTAAAATAAATTT
Found at i:15343020 original size:69 final size:69
Alignment explanation
Indices: 15342806--15343488 Score: 888
Period size: 69 Copynumber: 9.7 Consensus size: 69
15342796 ATGTTACTCC
*
15342806 TACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
15342871 CTCT
66 CTCT
* * * * * * *
15342875 TACTTCAATTTCAGAGATAAAGACTTGATATGC-TCTCTACTTCAATTTTAAGGGGATGACATTA
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
15342939 CTCT
66 CTCT
* *
15342943 TACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCAACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
15343008 CTCT
66 CTCT
* *
15343012 TACTTCAATTTCAGAGATAAGGACGTGTTATCC-ACTCTACTTCAATTTCAAG-GGCATGACGTT
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG-ATGACGTT
15343075 GCTCT
65 GCTCT
* * *
15343080 TACTTCAATTTCAGAGATAAAGACTTGATATCCAATTTTACTTCAATTTCAAGAGGATAGGAAAT
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTC-A-A-G--AGG--AT
* *
15343145 GATGTTACTCT
59 GACGTTGCTCT
* * *
15343156 TACTTCAATTTAAGAGATGAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
15343221 CTCT
66 CTCT
* * * *
15343225 TACTTCAATTTCAGAGATAAGGACGTGTTATCC-ACTCTACTTCAATTTCAAAGGGGATGATGTT
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTC-AAGAGGATGACGTT
15343289 GCTCT
65 GCTCT
* * * *
15343294 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCCAGCGGATAGGGAAA
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT---G-AC
15343359 GATCTTGCTCT
62 G---TTGCTCT
* * * *
15343370 TACTTCAATTTCAGAGATAATGGCTTGATATCCAACCCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
15343435 CTCT
66 CTCT
* *
15343439 TGCTTCAATTTCAGAGATAAAGACTTGCTATCCAACTCTACTTCAATTTC
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTC
15343489 CAACGGATAG
Statistics
Matches: 536, Mismatches: 59, Indels: 38
0.85 0.09 0.06
Matches are distributed among these distances:
67 2 0.00
68 136 0.25
69 250 0.47
70 17 0.03
71 4 0.01
72 4 0.01
73 4 0.01
74 1 0.00
75 3 0.01
76 115 0.21
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (69 bp):
TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
CTCT
Found at i:15343234 original size:145 final size:138
Alignment explanation
Indices: 15342742--15343488 Score: 899
Period size: 137 Copynumber: 5.3 Consensus size: 138
15342732 ACTCTTCAGG
* * * * *
15342742 GAGATAAAGACTTTGCTATCCAACTTTACTTCAATTTCTAGAGGATAGGAAATGATGTTACTCCT
1 GAGATAAAGAC-TTGTTATCCAACTCTACTTCAATTTC-A-A-G--AGG--ATGACGTTGCTCTT
*
15342807 ACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGC
58 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGC
15342872 TCTTACTTCAATTTCA
123 TCTTACTTCAATTTCA
* * * * * * *
15342888 GAGATAAAGACTTGATATGC-TCTCTACTTCAATTTTAAGGGGATGACATTACTCTTACTTCAAT
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
* *
15342952 TTCAGAGATGAAGACTTGTTATCCAACTCAACTTCAATTTCAAGAGGATGACGTTGCTCTTACTT
66 TTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTT
15343017 CAATTTCA
131 CAATTTCA
* *
15343025 GAGATAAGGACGTGTTATCC-ACTCTACTTCAATTTCAAG-GGCATGACGTTGCTCTTACTTCAA
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG-ATGACGTTGCTCTTACTTCAA
* * * * *
15343088 TTTCAGAGATAAAGACTTGATATCCAATTTTACTTCAATTTCAAGAGGATAGGAAATGATGTTAC
65 TTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTC-A-A-G--AGG--ATGACGTTGC
*
15343153 TCTTACTTCAATTTAA
123 TCTTACTTCAATTTCA
* *
15343169 GAGATGAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
* * * *
15343234 TTCAGAGATAAGGACGTGTTATCC-ACTCTACTTCAATTTCAAAGGGGATGATGTTGCTCTTACT
66 TTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTC-AAGAGGATGACGTTGCTCTTACT
15343298 TCAATTTCA
130 TCAATTTCA
* * * *
15343307 GAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCCAGCGGATAGGGAAAGATCTTGCTCTTA
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT---G-ACG---TTGCTCTTA
* * * *
15343372 CTTCAATTTCAGAGATAATGGCTTGATATCCAACCCTACTTCAATTTCAAGAGGATGACGTTGCT
59 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCT
*
15343437 CTTGCTTCAATTTCA
124 CTTACTTCAATTTCA
*
15343452 GAGATAAAGACTTGCTATCCAACTCTACTTCAATTTC
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTC
15343489 CAACGGATAG
Statistics
Matches: 529, Mismatches: 54, Indels: 37
0.85 0.09 0.06
Matches are distributed among these distances:
136 2 0.00
137 180 0.34
138 65 0.12
139 3 0.01
140 3 0.01
141 2 0.00
142 7 0.01
143 2 0.00
144 69 0.13
145 168 0.32
146 28 0.05
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (138 bp):
GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAAT
TTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTT
CAATTTCA
Found at i:15343303 original size:32 final size:32
Alignment explanation
Indices: 15342844--15343306 Score: 125
Period size: 31 Copynumber: 13.4 Consensus size: 32
15342834 TATCCAACTC
*
15342844 TACTTCAATTTC-AAGAGGATGACGTTGCTCT
1 TACTTCAATTTCAAAGAGGATGATGTTGCTCT
* ** *
15342875 TACTTCAATTTCAGAGATAAAGACTTGATATGCTCT
1 TACTTCAATTTCAAAGAGGATGA--TG-T-TGCTCT
* * ** *
15342911 CTACTTCAATTT-TAAGGGGATGACATTACTCT
1 -TACTTCAATTTCAAAGAGGATGATGTTGCTCT
* * * * *
15342943 TACTTCAATTTCAGAGATGAAGACTTGTTATCCAACT
1 TACTTCAATTTCAAAGAGGATGA--TG-T-TGC-TCT
* *
15342980 CAACTTCAATTTC-AAGAGGATGACGTTGCTCT
1 -TACTTCAATTTCAAAGAGGATGATGTTGCTCT
* * * *
15343012 TACTTCAATTTCAGAGATAAGGACG-TGTTATCCACT
1 TACTTCAATTTCA-A-A-GAGGATGATG-T-TGCTCT
*
15343048 CTACTTCAATTTC-AAG-GGCATGACGTTGCTCT
1 -TACTTCAATTTCAAAGAGG-ATGATGTTGCTCT
* ** * * *
15343080 TACTTCAATTTCAGAGATAAAGACTTGATATCCAATTT
1 TACTTCAATTTCAAAGAGGATGA--TG-T-TGC--TCT
*
15343118 TACTTCAATTTCAAGAGGATAGGAAATGATGTTACTCT
1 TACTTCAATTTCAA-A-G--AGG--ATGATGTTGCTCT
* * * *
15343156 TACTTCAATTT-AAGAGATGAAGACTTGTTATCCAACTT
1 TACTTCAATTTCAA-AGAGGATGA--TG-T-TGC-TC-T
*
15343194 TACTTCAATTTC-AAGAGGATGACGTTGCTCT
1 TACTTCAATTTCAAAGAGGATGATGTTGCTCT
* * * *
15343225 TACTTCAATTTCAGAGATAAGGACG-TGTTATCCACT
1 TACTTCAATTTCA-A-A-GAGGATGATG-T-TGCTCT
*
15343261 CTACTTCAATTTCAAAGGGGATGATGTTGCTCT
1 -TACTTCAATTTCAAAGAGGATGATGTTGCTCT
15343294 TACTTCAATTTCA
1 TACTTCAATTTCA
15343307 GAGATAAAGA
Statistics
Matches: 308, Mismatches: 73, Indels: 101
0.64 0.15 0.21
Matches are distributed among these distances:
31 59 0.19
32 47 0.15
33 14 0.05
34 19 0.06
35 22 0.07
36 27 0.09
37 57 0.19
38 52 0.17
39 1 0.00
40 3 0.01
41 1 0.00
42 3 0.01
44 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (32 bp):
TACTTCAATTTCAAAGAGGATGATGTTGCTCT
Found at i:15343489 original size:145 final size:142
Alignment explanation
Indices: 15342742--15343510 Score: 858
Period size: 145 Copynumber: 5.4 Consensus size: 142
15342732 ACTCTTCAGG
* * * * * * *
15342742 GAGATAAAGACTTTGCTATCCAACTTTACTTCAATTTCTAGAGGATAGGAAATGATGTTACTCCT
1 GAGATAAAGAC-TTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAA-GA-CTTGCTCTT
15342807 ACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGC
63 ACTTCAATTTCAGAGAT-AAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGC
15342872 TCTTACTTCAATTTCA
127 TCTTACTTCAATTTCA
* * * * * * *
15342888 GAGATAAAGACTTGATATGC-TCTCTACTTCAATTTTAAGGGGAT--G--ACA-TTACTCTTACT
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAGACTTGCTCTTACT
*
15342947 TCAATTTCAGAGATGAAGACTTGTTATCCAACTCAACTTCAATTTCAAGAGGATGACGTTGCTCT
66 TCAATTTCAGAGAT-AAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCT
15343012 TACTTCAATTTCA
130 TACTTCAATTTCA
* * *
15343025 GAGATAAGGACGTGTTATCC-ACTCTACTTCAATTTCAAG-GGCAT--G-ACG--TTGCTCTTAC
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGG-ATAGGAAAGACTTGCTCTTAC
* * * *
15343083 TTCAATTTCAGAGATAAAGACTTGATATCCAATTTTACTTCAATTTCAAGAGGATAGGAAATGAT
65 TTCAATTTCAGAGAT-AAGACTTGTTATCCAACTCTACTTCAATTTC-A-A-G--AGG--ATGAC
* *
15343148 GTTACTCTTACTTCAATTTAA
122 GTTGCTCTTACTTCAATTTCA
* * * *
15343169 GAGATGAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGAT--G-ACG--TTGCTCTTACT
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAGACTTGCTCTTACT
* * *
15343229 TCAATTTCAGAGATAAGGACGTGTTATCC-ACTCTACTTCAATTTCAAAGGGGATGATGTTGCTC
66 TCAATTTCAGAGATAA-GACTTGTTATCCAACTCTACTTCAATTTC-AAGAGGATGACGTTGCTC
15343293 TTACTTCAATTTCA
129 TTACTTCAATTTCA
* *
15343307 GAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCCAGCGGATAGGGAAAGATCTTGCTCTTA
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATA-GGAAAGA-CTTGCTCTTA
* * *
15343372 CTTCAATTTCAGAGATAATGGCTTGATATCCAACCCTACTTCAATTTCAAGAGGATGACGTTGCT
64 CTTCAATTTCAGAGATAA-GACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCT
*
15343437 CTTGCTTCAATTTCA
128 CTTACTTCAATTTCA
*
15343452 GAGATAAAGACTTGCTATCCAACTCTACTTCAATTTCCAA-CGGATAGGGAAAGATCTTG
1 GAGATAAAGACTTGTTATCCAACTCTACTTCAATTT-CAAGCGGATA-GGAAAGA-CTTG
15343511 GTGCGATCTG
Statistics
Matches: 547, Mismatches: 55, Indels: 43
0.85 0.09 0.07
Matches are distributed among these distances:
136 2 0.00
137 174 0.32
138 65 0.12
139 2 0.00
140 4 0.01
141 1 0.00
142 7 0.01
143 1 0.00
144 77 0.14
145 184 0.34
146 30 0.05
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (142 bp):
GAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAGACTTGCTCTTACT
TCAATTTCAGAGATAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTT
ACTTCAATTTCA
Found at i:15355519 original size:29 final size:28
Alignment explanation
Indices: 15355487--15355796 Score: 153
Period size: 29 Copynumber: 10.7 Consensus size: 28
15355477 TGGATACCCG
* * **
15355487 GGGGCAAAATGGTAATTTTTGGTGAAATC
1 GGGGAAAAATGGTAATTTTAGAAG-AATC
*
15355516 GGGGTTAAAAATGG-AATTTTAGAAGATTC
1 GGGG--AAAAATGGTAATTTTAGAAGAATC
* * * *
15355545 GGGGGTAAAATAGTAATTTTCGATGAAATC
1 -GGGGAAAAATGGTAATTTTAGAAG-AATC
* *
15355575 GGGGTAAAAATGG-AATTTTAAAAGATTC
1 GGGG-AAAAATGGTAATTTTAGAAGAATC
* * * **
15355603 AGGGTAAAATGGTAATTTTCGGTGAAATC
1 GGGGAAAAATGGTAATTTTAGAAG-AATC
* * *
15355632 GAGGTAAAAATGG-AATTTTAAAAGATTC
1 G-GGGAAAAATGGTAATTTTAGAAGAATC
* * **
15355660 GGGGGTAAAATGGTAATTTTTGGTGAAATC
1 -GGGGAAAAATGGTAATTTTAGAAG-AATC
* * *
15355690 GGGGTAAAAATAG-AATTTTAAAAGATTC
1 GGGG-AAAAATGGTAATTTTAGAAGAATC
* * **
15355718 AGGGGTAAAATGGTAATTTTCGGTGAAATC
1 -GGGGAAAAATGGTAATTTTAGAAG-AATC
*
15355748 GGGGTTAAAAATGG-AATTTTAGAAGATTC
1 GGGG--AAAAATGGTAATTTTAGAAGAATC
*
15355777 GGGGGTAAAATGGTAATTTT
1 -GGGGAAAAATGGTAATTTT
15355797 TGGAAGTTTC
Statistics
Matches: 203, Mismatches: 58, Indels: 40
0.67 0.19 0.13
Matches are distributed among these distances:
27 7 0.03
28 47 0.23
29 81 0.40
30 54 0.27
31 14 0.07
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.31
Consensus pattern (28 bp):
GGGGAAAAATGGTAATTTTAGAAGAATC
Found at i:15355660 original size:115 final size:117
Alignment explanation
Indices: 15355487--15355796 Score: 534
Period size: 115 Copynumber: 2.7 Consensus size: 117
15355477 TGGATACCCG
* *
15355487 GGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTA
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTA
* *
15355552 AAATAGTAATTTTCGATGAAATCGGGGTAAAAATGGAATTTTAAAAGATTCA
66 AAATGGTAATTTTCGATGAAATCGGGGTAAAAATAGAATTTTAAAAGATTCA
* *
15355604 -GGGTAAAATGGTAATTTTCGGTGAAATCGAGG-TAAAAATGGAATTTTAAAAGATTCGGGGGTA
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTA
* *
15355667 AAATGGTAATTTTTGGTGAAATCGGGGTAAAAATAGAATTTTAAAAGATTCA
66 AAATGGTAATTTTCGATGAAATCGGGGTAAAAATAGAATTTTAAAAGATTCA
15355719 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTA
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTA
15355784 AAATGGTAATTTT
66 AAATGGTAATTTT
15355797 TGGAAGTTTC
Statistics
Matches: 181, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
115 78 0.43
116 60 0.33
117 43 0.24
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.31
Consensus pattern (117 bp):
GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTA
AAATGGTAATTTTCGATGAAATCGGGGTAAAAATAGAATTTTAAAAGATTCA
Found at i:15355689 original size:58 final size:58
Alignment explanation
Indices: 15355485--15355796 Score: 500
Period size: 58 Copynumber: 5.4 Consensus size: 58
15355475 TGTGGATACC
* * *
15355485 CGGGGGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGG-TAAAAATGGAATTTTAAAAGATT
* *
15355544 CGGGGGTAAAATAGTAATTTTCGATGAAATCGGGGTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAATGGAATTTTAAAAGATT
* *
15355602 C-AGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAATGGAATTTTAAAAGATT
* *
15355659 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATAGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAATGGAATTTTAAAAGATT
* *
15355717 CAGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGG-TAAAAATGGAATTTTAAAAGATT
15355776 CGGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
15355797 TGGAAGTTTC
Statistics
Matches: 233, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
57 53 0.23
58 108 0.46
59 72 0.31
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.30
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAATGGAATTTTAAAAGATT
Found at i:15357811 original size:23 final size:20
Alignment explanation
Indices: 15357765--15357808 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
15357755 CTTGGTGGTG
15357765 GCAGATGGAACTGGTGGTCA
1 GCAGATGGAACTGGTGGTCA
*
15357785 GCAGATGGAGCTGGTGGTCA
1 GCAGATGGAACTGGTGGTCA
15357805 GCAG
1 GCAG
15357809 CAGCATAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.43, T:0.18
Consensus pattern (20 bp):
GCAGATGGAACTGGTGGTCA
Found at i:15358024 original size:6 final size:6
Alignment explanation
Indices: 15358015--15358087 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
15358005 GACTTTTCTT
* *
15358015 TTTAAA TTTATAA --TAACA TT-AAA TTTAAA -TTAAA TTCAAG TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
15358061 TTTAAA -TTGAA TTTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
15358088 GATTAAGATA
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
4 1 0.02
5 19 0.37
6 29 0.57
7 2 0.04
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:15358048 original size:11 final size:11
Alignment explanation
Indices: 15358032--15358093 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
15358022 TTATAATAAC
15358032 ATTAAATTTAA
1 ATTAAATTTAA
*
15358043 ATTAAATTCAA
1 ATTAAATTTAA
*
15358054 GTTTAAATTTAA
1 -ATTAAATTTAA
*
15358066 ATTGAATTTAA
1 ATTAAATTTAA
*
15358077 AATAAATTTAA
1 ATTAAATTTAA
15358088 GATTAA
1 -ATTAA
15358094 GATAAATTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
11 28 0.68
12 13 0.32
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:15358099 original size:22 final size:22
Alignment explanation
Indices: 15358057--15358099 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
15358047 AATTCAAGTT
**
15358057 TAAATTTAAATTGAATTTAAAA
1 TAAATTTAAATTGAAGATAAAA
15358079 TAAATTTAAGATT-AAGATAAA
1 TAAATTTAA-ATTGAAGATAAA
15358100 TTTAATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
TAAATTTAAATTGAAGATAAAA
Found at i:15362416 original size:10 final size:11
Alignment explanation
Indices: 15362387--15362415 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
15362377 TTTTCAAAAC
15362387 ATACCAAAATG
1 ATACCAAAATG
15362398 AT-CCAAAATG
1 ATACCAAAATG
15362408 ATACCAAA
1 ATACCAAA
15362416 TATATAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (11 bp):
ATACCAAAATG
Found at i:15364149 original size:20 final size:20
Alignment explanation
Indices: 15364110--15364155 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
15364100 ATAATAGATG
15364110 ATTAAATTTAAAATACATTT
1 ATTAAATTTAAAATACATTT
**
15364130 -TTAATATTTAAAATGTATTT
1 ATTAA-ATTTAAAATACATTT
15364150 ATTAAA
1 ATTAAA
15364156 AAAACATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.18
20 14 0.64
21 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTAAATTTAAAATACATTT
Found at i:15366589 original size:15 final size:16
Alignment explanation
Indices: 15366569--15366598 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15366559 AAGTATAATA
15366569 AAATA-TTAAAAAAAT
1 AAATATTTAAAAAAAT
15366584 AAATATTTAAAAAAA
1 AAATATTTAAAAAAA
15366599 GACACATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATTTAAAAAAAT
Found at i:15366969 original size:17 final size:17
Alignment explanation
Indices: 15366943--15367039 Score: 117
Period size: 17 Copynumber: 5.8 Consensus size: 17
15366933 AATCATTTTA
*
15366943 AAATTCATTTTAAAATT
1 AAATTTATTTTAAAATT
15366960 AAATTTATTTTAAAATT
1 AAATTTATTTTAAAATT
* *
15366977 AAATTTATGTTAAAGTT
1 AAATTTATTTTAAAATT
*
15366994 AAATTTATTTTAAATTT
1 AAATTTATTTTAAAATT
* *
15367011 AGATTTA--TTAAATTT
1 AAATTTATTTTAAAATT
*
15367026 AAATTTAATTTAAA
1 AAATTTATTTTAAA
15367040 TTTAGAATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
15 14 0.20
17 57 0.80
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAAATT
Found at i:15366976 original size:12 final size:12
Alignment explanation
Indices: 15366935--15366959 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15366925 GCCAACCAAA
15366935 TCATTTTAAAAT
1 TCATTTTAAAAT
15366947 TCATTTTAAAAT
1 TCATTTTAAAAT
15366959 T
1 T
15366960 AAATTTATTT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTTTAAAAT
Found at i:15367006 original size:11 final size:11
Alignment explanation
Indices: 15366958--15367043 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
15366948 CATTTTAAAA
*
15366958 TTAAATTTATT
1 TTAAATTTAAT
*
15366969 TTAAAATTAAAT
1 TT-AAATTTAAT
** * *
15366981 TTATGTTAAAG
1 TTAAATTTAAT
*
15366992 TTAAATTTATT
1 TTAAATTTAAT
15367003 TTAAATTTAGAT
1 TTAAATTTA-AT
*
15367015 TT--ATTAAAT
1 TTAAATTTAAT
15367024 TTAAATTTAAT
1 TTAAATTTAAT
15367035 TTAAATTTA
1 TTAAATTTA
15367044 GAATTAATGT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 38 0.66
12 12 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:15367011 original size:6 final size:6
Alignment explanation
Indices: 15366951--15367048 Score: 68
Period size: 6 Copynumber: 17.3 Consensus size: 6
15366941 TAAAATTCAT
* * * *
15366951 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
15366997 TTT-AT TTTAAA TTTAGA TTT--A -TTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
15367040 TTTAGAA TT
1 TTTA-AA TT
15367049 AATGTAAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
3 2 0.03
4 3 0.04
5 16 0.23
6 45 0.63
7 5 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:15367040 original size:17 final size:17
Alignment explanation
Indices: 15366951--15367079 Score: 115
Period size: 17 Copynumber: 7.6 Consensus size: 17
15366941 TAAAATTCAT
* *
15366951 TTTAAAATTAAATTTAT
1 TTTAAATTTAAATTTAA
*
15366968 TTTAAAATTAAATTT-A
1 TTTAAATTTAAATTTAA
* *
15366984 TGTTAAAGTTAAATTTAT
1 T-TTAAATTTAAATTTAA
*
15367002 TTTAAATTTAGATTT-A
1 TTTAAATTTAAATTTAA
15367018 -TTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
15367034 TTTAAATTTAGAA-TTAA
1 TTTAAATTTA-AATTTAA
* *
15367051 TGTAAATTTTAAAATT-A
1 TTTAAA-TTTAAATTTAA
15367068 TTATAAATTTAA
1 TT-TAAATTTAA
15367080 TAGAGTGTCC
Statistics
Matches: 95, Mismatches: 9, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
15 13 0.14
16 2 0.02
17 67 0.71
18 13 0.14
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:15368987 original size:30 final size:30
Alignment explanation
Indices: 15368951--15369208 Score: 308
Period size: 30 Copynumber: 8.6 Consensus size: 30
15368941 TGGACTATTC
15368951 AAAAATTATATTTTGACCCTAAAACTTTCT
1 AAAAATTATATTTTGACCCTAAAACTTTCT
* * *
15368981 AAAAATTATATTTTAACCTTAAAACTTTTT
1 AAAAATTATATTTTGACCCTAAAACTTTCT
* *
15369011 GAAAATTATATTTTGACCCCAAAACTTTCT
1 AAAAATTATATTTTGACCCTAAAACTTTCT
*
15369041 AAAAATTATATTTTAACTCC-AAAACTTTCT
1 AAAAATTATATTTTGAC-CCTAAAACTTTCT
* *
15369071 AAAAATTATATTTTAACTCC-AAAACTTTTT
1 AAAAATTATATTTTGAC-CCTAAAACTTTCT
* *
15369101 GAAAATTACATTTTGA-CCTCAAAACTTTCT
1 AAAAATTATATTTTGACCCT-AAAACTTTCT
* *
15369131 AAAAATTACATTTTGGCACCT-AAACTTTCT
1 AAAAATTATATTTTGAC-CCTAAAACTTTCT
* * *
15369161 AAAAATTACATTTTAACCCTTAAACTTTCT
1 AAAAATTATATTTTGACCCTAAAACTTTCT
*
15369191 AAAAATTACATTTTGACC
1 AAAAATTATATTTTGACC
15369209 TCCAAACTTT
Statistics
Matches: 202, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
28 2 0.01
29 3 0.01
30 192 0.95
31 2 0.01
32 3 0.01
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAAATTATATTTTGACCCTAAAACTTTCT
Found at i:15369104 original size:90 final size:88
Alignment explanation
Indices: 15368951--15369235 Score: 367
Period size: 90 Copynumber: 3.2 Consensus size: 88
15368941 TGGACTATTC
*
15368951 AAAAATTATATTTTGACCCTAAAACTTTCTAAAAATTATATTTTAACCTTAAAACTTTTTGAAAA
1 AAAAATTATATTTTGACCC-AAAACTTTCTAAAAATTATATTTTAACC-CAAAACTTTTTGAAAA
*
15369016 TTATATTTTGACCCCAAAACTTTCT
64 TTACATTTTGACCCCAAAACTTTCT
*
15369041 AAAAATTATATTTTAACTCCAAAACTTTCTAAAAATTATATTTTAACTCCAAAACTTTTTGAAAA
1 AAAAATTATATTTTGAC-CCAAAACTTTCTAAAAATTATATTTTAAC-CCAAAACTTTTTGAAAA
*
15369106 TTACATTTTGACCTCAAAACTTTCT
64 TTACATTTTGACCCCAAAACTTTCT
* * * * * * *
15369131 AAAAATTACATTTTGGCACCTAAACTTTCTAAAAATTACATTTTAACCCTTAAACTTTCTAAAAA
1 AAAAATTATATTTTGAC-CCAAAACTTTCTAAAAATTATATTTTAACCC-AAAACTTTTTGAAAA
15369196 TTACATTTTGACCTCC-AAACTTT-T
64 TTACATTTTGACC-CCAAAACTTTCT
* *
15369220 CCAAAATTAGATTTTG
1 -AAAAATTATATTTTG
15369236 CCTCTGAACT
Statistics
Matches: 174, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
89 3 0.02
90 167 0.96
91 4 0.02
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (88 bp):
AAAAATTATATTTTGACCCAAAACTTTCTAAAAATTATATTTTAACCCAAAACTTTTTGAAAATT
ACATTTTGACCCCAAAACTTTCT
Found at i:15369216 original size:30 final size:30
Alignment explanation
Indices: 15368951--15369253 Score: 273
Period size: 30 Copynumber: 10.1 Consensus size: 30
15368941 TGGACTATTC
*
15368951 AAAAATTATATTTTGACC-CTAAAACTTTCT
1 AAAAATTATATTTTGACCTC-CAAACTTTCT
* ** *
15368981 AAAAATTATATTTTAACCTTAAAACTTTTT
1 AAAAATTATATTTTGACCTCCAAACTTTCT
*
15369011 GAAAATTATATTTTGACC-CCAAAACTTTCT
1 AAAAATTATATTTTGACCTCC-AAACTTTCT
*
15369041 AAAAATTATATTTT-AACTCCAAAACTTTCT
1 AAAAATTATATTTTGACCTCC-AAACTTTCT
* *
15369071 AAAAATTATATTTT-AACTCCAAAACTTTTT
1 AAAAATTATATTTTGACCTCC-AAACTTTCT
* * *
15369101 GAAAATTACATTTTGACCTCAAAACTTTCT
1 AAAAATTATATTTTGACCTCCAAACTTTCT
*
15369131 AAAAATTACATTTTGGCACCT--AAACTTTCT
1 AAAAATTATATTTT-G-ACCTCCAAACTTTCT
* * *
15369161 AAAAATTACATTTTAACC-CTTAAACTTTCT
1 AAAAATTATATTTTGACCTC-CAAACTTTCT
*
15369191 AAAAATTACATTTTGACCTCCAAACTTT-T
1 AAAAATTATATTTTGACCTCCAAACTTTCT
* * ** *
15369220 CCAAAATTAGATTTTG-CCTCTGAACTTTCC
1 -AAAAATTATATTTTGACCTCCAAACTTTCT
15369250 AAAA
1 AAAA
15369254 TCCCATTTTT
Statistics
Matches: 235, Mismatches: 26, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.01
29 16 0.07
30 206 0.88
31 6 0.03
32 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAAATTATATTTTGACCTCCAAACTTTCT
Found at i:15376692 original size:24 final size:23
Alignment explanation
Indices: 15376663--15376708 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
15376653 AAATTCAAGT
*
15376663 AAATTATTCACTT-TTAATATACAC
1 AAATTAATCA-TTCTTAA-ATACAC
15376687 AAATTAATCATTCTTAAATACA
1 AAATTAATCATTCTTAAATACA
15376709 TACACCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATTAATCATTCTTAAATACAC
Found at i:15381279 original size:40 final size:40
Alignment explanation
Indices: 15381224--15381378 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
15381214 ATGTCAATTC
15381224 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACAAATCT
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACAAATCT
***
15381264 TTAT-CTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGCCAATT
1 TTATCCTCT-TGAAGTTATAGTAA-AGTTGGAT-AA----CAAAT--C---T
* *
15381315 CTTATCCTCTTGAAATTATAGTAAAGTTGGATAACGAATCT
1 -TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACAAATCT
15381356 TTAT-CTCTCTGAAGTTATAGTAA
1 TTATCCTCT-TGAAGTTATAGTAA
15381379 GAACAAGATG
Statistics
Matches: 91, Mismatches: 9, Indels: 30
0.70 0.07 0.23
Matches are distributed among these distances:
39 8 0.09
40 35 0.38
41 6 0.07
42 2 0.02
44 1 0.01
46 9 0.10
48 1 0.01
50 2 0.02
51 6 0.07
52 17 0.19
53 4 0.04
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (40 bp):
TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACAAATCT
Found at i:15381336 original size:92 final size:92
Alignment explanation
Indices: 15381179--15381461 Score: 503
Period size: 92 Copynumber: 3.1 Consensus size: 92
15381169 GATGTTATAG
15381179 TCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAG
1 TCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAG
*
15381244 TAAAGTTGGATAACAAATCTTTATCTC
66 TAAAGTTGGATAACGAATCTTTATCTC
* *
15381271 TCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGCCAATTCTTATCCTCTTGAAATTATAG
1 TCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAG
15381336 TAAAGTTGGATAACGAATCTTTATCTC
66 TAAAGTTGGATAACGAATCTTTATCTC
*
15381363 TCTGAAGTTATAGTAAGAACAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAG
1 TCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAG
* *
15381428 TAAAGTTGGATAATGAACCTTTATCTC
66 TAAAGTTGGATAACGAATCTTTATCTC
*
15381455 TTTGAAG
1 TCTGAAG
15381462 ATAAAACCTC
Statistics
Matches: 182, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 182 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (92 bp):
TCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAG
TAAAGTTGGATAACGAATCTTTATCTC
Found at i:15381737 original size:12 final size:12
Alignment explanation
Indices: 15381720--15381744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15381710 GCCAACCAAA
15381720 TCATTTTAAAAT
1 TCATTTTAAAAT
15381732 TCATTTTAAAAT
1 TCATTTTAAAAT
15381744 T
1 T
15381745 AAATTTATGT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTTTAAAAT
Found at i:15381757 original size:17 final size:16
Alignment explanation
Indices: 15381736--15381847 Score: 109
Period size: 17 Copynumber: 6.7 Consensus size: 16
15381726 TAAAATTCAT
*
15381736 TTTAAAATTAAATTTA
1 TTTAAATTTAAATTTA
*
15381752 TGTTAAAGTTAAATTTA
1 T-TTAAATTTAAATTTA
*
15381769 TTTTAAATTTAGATTTA
1 -TTTAAATTTAAATTTA
15381786 -TTAAATTTAAATTTAA
1 TTTAAATTTAAATTT-A
*
15381802 TTTAAATTTAGAATTAA
1 TTTAAATTTA-AATTTA
* *
15381819 TGTAAATTTTAAAATTA
1 TTTAAA-TTTAAATTTA
15381836 TTATAAATTTAA
1 TT-TAAATTTAA
15381848 TAGAGTGTCC
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
15 13 0.16
16 2 0.03
17 52 0.65
18 13 0.16
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:15381774 original size:11 final size:11
Alignment explanation
Indices: 15381760--15381811 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
15381750 TATGTTAAAG
*
15381760 TTAAATTTATT
1 TTAAATTTAAT
15381771 TTAAATTTAGAT
1 TTAAATTTA-AT
*
15381783 TT--ATTAAAT
1 TTAAATTTAAT
15381792 TTAAATTTAAT
1 TTAAATTTAAT
15381803 TTAAATTTA
1 TTAAATTTA
15381812 GAATTAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 4 0.11
10 4 0.11
11 24 0.69
12 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:15381779 original size:6 final size:6
Alignment explanation
Indices: 15381736--15381816 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
15381726 TAAAATTCAT
* * * *
15381736 TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA TTT-AT TTTAAA TTTAGA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
15381782 TTT--A -TTAAA TTTAAA TTT-AA TTTAAA TTTAGAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TT
15381817 AATGTAAATT
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
3 2 0.03
4 3 0.05
5 12 0.20
6 37 0.63
7 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:15383734 original size:30 final size:29
Alignment explanation
Indices: 15383690--15383866 Score: 160
Period size: 30 Copynumber: 5.9 Consensus size: 29
15383680 AAAGTCCCTG
*
15383690 AACTATTCAAAAATTATATTTTAACCCCAA
1 AACT-TTCAAAAATTACATTTTAACCCCAA
* *
15383720 AACTTTCAAAAAATTATATTTTGACCCCAA
1 AACTTTC-AAAAATTACATTTTAACCCCAA
* *
15383750 AACTTTCTAAAAATTACATTTGAACCCCTA
1 AACTTTC-AAAAATTACATTTTAACCCCAA
* *
15383780 AACTTTCTAAAAATTACATTTTGACCCCCA
1 AACTTTC-AAAAATTACATTTTAACCCCAA
* * *
15383810 AACATTTCCAAAATTAGATTTT-ACCTCC-G
1 AAC-TTTCAAAAATTACATTTTAACC-CCAA
* **
15383839 AACTTTCCAAAATCCCATTTTTAACCCC
1 AACTTTCAAAAATTACA-TTTTAACCCC
15383867 GATTTCACCA
Statistics
Matches: 127, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.09
29 15 0.12
30 97 0.76
31 4 0.03
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (29 bp):
AACTTTCAAAAATTACATTTTAACCCCAA
Found at i:15383792 original size:60 final size:59
Alignment explanation
Indices: 15383690--15383830 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 59
15383680 AAAGTCCCTG
* * *
15383690 AACTATTCAAAAATTATATTTTAACCCCAAAACTTTCAAAAAATTATATTTTGACCCCAA
1 AACT-TTCAAAAATTACATTTGAACCCCAAAACTTTCAAAAAATTACATTTTGACCCCAA
* * *
15383750 AACTTTCTAAAAATTACATTTGAACCCCTAAACTTTCTAAAAATTACATTTTGACCCCCA
1 AACTTTC-AAAAATTACATTTGAACCCCAAAACTTTCAAAAAATTACATTTTGACCCCAA
* *
15383810 AACATTTCCAAAATTAGATTT
1 AAC-TTTCAAAAATTACATTT
15383831 TACCTCCGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
59 3 0.04
60 64 0.90
61 4 0.06
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (59 bp):
AACTTTCAAAAATTACATTTGAACCCCAAAACTTTCAAAAAATTACATTTTGACCCCAA
Found at i:15383967 original size:58 final size:59
Alignment explanation
Indices: 15383819--15383952 Score: 157
Period size: 58 Copynumber: 2.3 Consensus size: 59
15383809 AAACATTTCC
* * * * *
15383819 AAAATTA-GATTTTACCTCCGAACTTTCC-AAAATCCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAAC-TTCCAAAAATCCCATTTTTAACCCCAATTCCAACA
* * * *
15383877 AAAATTACCATTTTGCCCCCGAACTTCTAAAAATCCCATTTTTGA-CCCAATTCCAACT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAATTCCAACA
15383935 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
15383953 TCGGGTATCC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 36 0.56
59 28 0.44
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAATTCCAACA
Found at i:15391469 original size:30 final size:31
Alignment explanation
Indices: 15391403--15391498 Score: 117
Period size: 30 Copynumber: 3.1 Consensus size: 31
15391393 TATTCGAGGG
* *
15391403 AAAATGGTAAATTTTGGATAAGTTT-GGGGT-A
1 AAAAT-GT-AATTTTAGAGAAGTTTGGGGGTCA
15391434 AAAATGTAATTTTAG-GAAGTTTGGGGGTCA
1 AAAATGTAATTTTAGAGAAGTTTGGGGGTCA
*
15391464 AAAATGTAATTTTGGAGAAGTTTGAGGGGTCA
1 AAAATGTAATTTTAGAGAAGTTTG-GGGGTCA
15391496 AAA
1 AAA
15391499 TGGGATTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
28 6 0.10
29 12 0.21
30 17 0.29
31 13 0.22
32 10 0.17
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.32
Consensus pattern (31 bp):
AAAATGTAATTTTAGAGAAGTTTGGGGGTCA
Found at i:15391487 original size:31 final size:29
Alignment explanation
Indices: 15391403--15391587 Score: 151
Period size: 29 Copynumber: 6.2 Consensus size: 29
15391393 TATTCGAGGG
* *
15391403 AAAATGGTAAATTTTGGATAAGTTTGGGGTA
1 AAAAT-GT-AATTTTGGAGAAGTTTGGGGTC
*
15391434 AAAATGTAATTTTAG-GAAGTTTGGGGGTC
1 AAAATGTAATTTTGGAGAAGTTT-GGGGTC
15391463 AAAAATGTAATTTTGGAGAAGTTTGAGGGGTC
1 -AAAATGTAATTTTGGAGAAGTTT--GGGGTC
** * * * *
15391495 AAAATGGGATTTTGGAAAATTTTAAGGGTT
1 AAAATGTAATTTTGGAGAAGTTT-GGGGTC
*
15391525 AAAATGTAATTTTGG-GAAAGTTTAGGGTC
1 AAAATGTAATTTTGGAG-AAGTTTGGGGTC
* **
15391554 AAAATATAATTTTGGAAGAA-TTCAGGGTC
1 AAAATGTAATTTTGG-AGAAGTTTGGGGTC
15391583 AAAAT
1 AAAAT
15391588 ATGATTTTTG
Statistics
Matches: 129, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
28 6 0.05
29 44 0.34
30 41 0.32
31 32 0.25
32 6 0.05
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTGGAGAAGTTTGGGGTC
Found at i:15391499 original size:61 final size:58
Alignment explanation
Indices: 15391403--15391571 Score: 164
Period size: 61 Copynumber: 2.8 Consensus size: 58
15391393 TATTCGAGGG
* * **
15391403 AAAATGGTAAATTTTGGATAAGTTT-GGGGTAAAAATGTAATTTTAGGAAGTTTGGGGGTCA
1 AAAAT-GT-AATTTTGGAGAAGTTTAGGGGTCAAAATGTAATTTT-GGAAGTTTAAGGGT-A
** * *
15391464 AAAATGTAATTTTGGAGAAGTTTGAGGGGTCAAAATGGGATTTTGGAAAATTTTAAGGGTT
1 AAAATGTAATTTTGGAGAAGTTT-AGGGGTCAAAATGTAATTTTGG--AAGTTTAAGGGTA
*
15391525 AAAATGTAATTTTGG-GAAAGTTTA-GGGTCAAAATATAATTTTGGAAG
1 AAAATGTAATTTTGGAG-AAGTTTAGGGGTCAAAATGTAATTTTGGAAG
15391572 AATTCAGGGT
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
57 2 0.02
59 32 0.35
60 6 0.07
61 42 0.46
62 9 0.10
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (58 bp):
AAAATGTAATTTTGGAGAAGTTTAGGGGTCAAAATGTAATTTTGGAAGTTTAAGGGTA
Found at i:15391610 original size:30 final size:29
Alignment explanation
Indices: 15391548--15391610 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
15391538 GGGAAAGTTT
* **
15391548 AGGGTCAAAATATAATTTTGGAAGAATTC
1 AGGGTCAAAATATAATTTTGAAAGAAAAC
*
15391577 AGGGTCAAAATATGATTTTTGAAAGAAAAC
1 AGGGTCAAAATAT-AATTTTGAAAGAAAAC
15391607 AGGG
1 AGGG
15391611 GCTTAATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.43, C:0.06, G:0.24, T:0.27
Consensus pattern (29 bp):
AGGGTCAAAATATAATTTTGAAAGAAAAC
Found at i:15393152 original size:17 final size:17
Alignment explanation
Indices: 15393130--15393163 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15393120 CTGAAAACTT
15393130 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
15393147 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
15393164 GCATTGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:15393579 original size:16 final size:17
Alignment explanation
Indices: 15393558--15393592 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15393548 ATGAGAGTAT
15393558 AATAAA-ATATTAAAAA
1 AATAAATATATTAAAAA
*
15393574 AATAAATATTTTAAAAA
1 AATAAATATATTAAAAA
15393591 AA
1 AA
15393593 CATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAATATATTAAAAA
Found at i:15394401 original size:15 final size:16
Alignment explanation
Indices: 15394374--15394403 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15394364 GGAAACATAA
15394374 TAATTTGAATATAAAG
1 TAATTTGAATATAAAG
15394390 TAATTT-AATATAAA
1 TAATTTGAATATAAA
15394404 ATTTAATTAA
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:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
TAATTTGAATATAAAG
Found at i:15402509 original size:2 final size:2
Alignment explanation
Indices: 15402504--15402531 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15402494 TTTTTTTATC
15402504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15402532 GGGGTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15403144 original size:20 final size:20
Alignment explanation
Indices: 15403089--15403132 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
15403079 TTTATTTATT
15403089 TTATTTTTA-T-A-ATTTAA
1 TTATTTTTAGTAATATTTAA
15403106 TTATTTTTAGTAATATTTAA
1 TTATTTTTAGTAATATTTAA
15403126 TTATTTT
1 TTATTTT
15403133 ATATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.38
18 1 0.04
19 1 0.04
20 13 0.54
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTTTTAGTAATATTTAA
Found at i:15403163 original size:30 final size:29
Alignment explanation
Indices: 15403101--15403172 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
15403091 ATTTTTATAA
*
15403101 TTTAATTATTTTTAGTAATATTTAATTAT
1 TTTAATTATTTTTAGTAATAATTAATTAT
15403130 TTTATATTATTTTTA-TAACTTAATTAATT-T
1 TTTA-ATTATTTTTAGTAA--TAATTAATTAT
*
15403160 TTTAAATATTTTT
1 TTTAATTATTTTT
15403173 TTGTAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 15 0.39
30 15 0.39
31 8 0.21
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTAATTATTTTTAGTAATAATTAATTAT
Found at i:15403168 original size:47 final size:46
Alignment explanation
Indices: 15403064--15403170 Score: 132
Period size: 47 Copynumber: 2.3 Consensus size: 46
15403054 AGTTAATTTA
* * *
15403064 AATTTTTTAAA-A-TTATTTATTTATTTTATTTTTATAATTTAATT
1 AATTTTTTAAATATTTAATTATTTATATTATTTTTATAACTTAATT
15403108 -A-TTTTTAGTAATATTTAATTATTTTATATTATTTTTATAACTTAATT
1 AATTTTTTA--AATATTTAATTA-TTTATATTATTTTTATAACTTAATT
15403155 AATTTTTTAAATATTT
1 AATTTTTTAAATATTT
15403171 TTTTGTAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
42 6 0.11
43 1 0.02
44 2 0.04
45 1 0.02
46 6 0.11
47 30 0.57
48 1 0.02
49 6 0.11
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.64
Consensus pattern (46 bp):
AATTTTTTAAATATTTAATTATTTATATTATTTTTATAACTTAATT
Found at i:15404366 original size:68 final size:68
Alignment explanation
Indices: 15404286--15404450 Score: 312
Period size: 68 Copynumber: 2.4 Consensus size: 68
15404276 AAGAAAAAGT
15404286 AAAACTACGTCGTTTTGATAAATATTTACCTTCTAAAGTTTAAAGTGAAAACCATTAAGTTAAAA
1 AAAACTACGTCGTTTTGATAAATATTTACCTTCTAAAGTTTAAAGTGAAAACCATTAAGTTAAAA
15404351 GAC
66 GAC
*
15404354 AAAACTACGTCGTTTTGATAAATATTTACCTTCTAAAGTTTAAAGTGAAAATCATTAAGTTAAAA
1 AAAACTACGTCGTTTTGATAAATATTTACCTTCTAAAGTTTAAAGTGAAAACCATTAAGTTAAAA
15404419 GAC
66 GAC
*
15404422 AAAACTACGTCGTTTTAATAAATATTTAC
1 AAAACTACGTCGTTTTGATAAATATTTAC
15404451 TCATTAAGTT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 95 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (68 bp):
AAAACTACGTCGTTTTGATAAATATTTACCTTCTAAAGTTTAAAGTGAAAACCATTAAGTTAAAA
GAC
Found at i:15406565 original size:142 final size:143
Alignment explanation
Indices: 15406369--15406658 Score: 453
Period size: 142 Copynumber: 2.0 Consensus size: 143
15406359 ATAATGGACT
*
15406369 ATTTAACAATAAATAATAAATATTTATAAAAAAATAATTAAATAATTTGAATAAAAATAAAACAG
1 ATTTAACAATAAATAATAAATACTTAT-AAAAAATAATTAAATAATTTGAATAAAAATAAAAC--
*
15406434 AAAAAATAAAAA-AAA-TTAATTC-TTTCAATTTGTTATGAGTTTTTTACCTAAAATATATAAAA
63 AAAAAATAAAAATAAATTTAA-TCATTTCAATTTGTTATGAGTTTTTTACCTAAAATATACAAAA
* *
15406496 TAAATACTAAAATTGTA
127 TAAATACTAAAACTCTA
15406513 ATTTAACAATAAATAATAAATACTTAT-AAAAATAATTAAATAATTTGAATAAAAATAAAACAAA
1 ATTTAACAATAAATAATAAATACTTATAAAAAATAATTAAATAATTTGAATAAAAATAAAACAAA
* * *
15406577 AAATAAAAATAAATTTAATCATTTTAATTTGTTATGGGTTTTTTACTTAAAATATACAAAATAAA
66 AAATAAAAATAAATTTAATCATTTCAATTTGTTATGAGTTTTTTACCTAAAATATACAAAATAAA
15406642 TACTAAAACTCTA
131 TACTAAAACTCTA
15406655 ATTT
1 ATTT
15406659 TAAAACCCTA
Statistics
Matches: 136, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
140 12 0.09
141 5 0.04
142 93 0.68
144 26 0.19
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (143 bp):
ATTTAACAATAAATAATAAATACTTATAAAAAATAATTAAATAATTTGAATAAAAATAAAACAAA
AAATAAAAATAAATTTAATCATTTCAATTTGTTATGAGTTTTTTACCTAAAATATACAAAATAAA
TACTAAAACTCTA
Found at i:15409747 original size:6 final size:6
Alignment explanation
Indices: 15409733--15409774 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
15409723 GGGATATTAA
* *
15409733 TAAATT TAAACT TAAATT TAAA-A TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T
15409775 TGTTTAGGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:15409757 original size:23 final size:23
Alignment explanation
Indices: 15409731--15409774 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
15409721 AAGGGATATT
15409731 AATAAATTTAAACTTAAATTTAA
1 AATAAATTTAAACTTAAATTTAA
*
15409754 AATAAATTTAAATTTAAATTT
1 AATAAATTTAAACTTAAATTT
15409775 TGTTTAGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAATTTAAACTTAAATTTAA
Found at i:15409764 original size:17 final size:17
Alignment explanation
Indices: 15409739--15409771 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15409729 TTAATAAATT
15409739 TAAACTTAAATTTAAAA
1 TAAACTTAAATTTAAAA
*
15409756 TAAATTTAAATTTAAA
1 TAAACTTAAATTTAAA
15409772 TTTTGTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAACTTAAATTTAAAA
Found at i:15410435 original size:39 final size:38
Alignment explanation
Indices: 15410344--15410512 Score: 115
Period size: 39 Copynumber: 4.3 Consensus size: 38
15410334 TTTCTTTTAG
* ** * *
15410344 AGAGATTGGATGGTTGCAATCTGCCCCAGGCTCGGGGTA
1 AGAGATTGGCTGACTGCAATCTGCCCTAGGCT-AGGGTA
* ** *
15410383 GGAGATTAACTGACTGCAATCTGCCCTAAGCTCAGGGTA
1 AGAGATTGGCTGACTGCAATCTGCCCTAGGCT-AGGGTA
* ** *
15410422 AGAGATTGGCTGACGGTGATCTGCCCTATGCTAGGGGTA
1 AGAGATTGGCTGACTGCAATCTGCCCTAGGCTA-GGGTA
* * * * * *
15410461 AAAGATCGGATGGCTACAATCTG-CCTCAGGCTTGAGGTA
1 AGAGATTGGCTGACTGCAATCTGCCCT-AGGCTAG-GGTA
15410500 AGAGATTGGCTGA
1 AGAGATTGGCTGA
15410513 TGGTGATCTA
Statistics
Matches: 97, Mismatches: 30, Indels: 6
0.73 0.23 0.05
Matches are distributed among these distances:
38 5 0.05
39 92 0.95
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.24
Consensus pattern (38 bp):
AGAGATTGGCTGACTGCAATCTGCCCTAGGCTAGGGTA
Found at i:15410447 original size:78 final size:78
Alignment explanation
Indices: 15410362--15410554 Score: 194
Period size: 78 Copynumber: 2.5 Consensus size: 78
15410352 GATGGTTGCA
** * *
15410362 ATCTGCCCCAGGCTCGGGGTAGGAGAT-TAACTGACTGCAATCTGCC-CTAAGCTCAG-GGTAAG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATCGAA-TGACTACAATCTGCCTC-AAGCT-AGAGGTAAG
15410424 AGATTGGCTGACGGTG
63 AGATTGGCTGACGGTG
* * * * * * *
15410440 ATCTGCCCTATGCTAGGGGTAAAAGATCGGATGGCTACAATCTGCCTCAGGCTTGAGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTACAATCTGCCTCAAGCTAGAGGTAAGAGA
*
15410505 TTGGCTGATGGTG
66 TTGGCTGACGGTG
** * *
15410518 ATCTATCCCAGGCTCGGGGTAAAAGATTGGATGACTA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTA
15410555 TGATGTAACA
Statistics
Matches: 93, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
77 1 0.01
78 90 0.97
79 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (78 bp):
ATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTACAATCTGCCTCAAGCTAGAGGTAAGAGA
TTGGCTGACGGTG
Found at i:15411128 original size:21 final size:21
Alignment explanation
Indices: 15411102--15411177 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 21
15411092 ATACGGAACA
15411102 AACAGAGAGTACCAAAGTACT
1 AACAGAGAGTACCAAAGTACT
* *
15411123 AACAGAGAGCA-CATAAGTGCT
1 AACAGAGAGTACCA-AAGTACT
15411144 GAGAAACAGAGAGTACACAAAGTACT
1 ----AACAGAGAGTAC-CAAAGTACT
15411170 AATCAGAG
1 AA-CAGAG
15411178 GGCACATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
20 2 0.05
21 16 0.37
22 2 0.05
23 5 0.12
25 10 0.23
26 6 0.14
27 2 0.05
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
AACAGAGAGTACCAAAGTACT
Found at i:15411200 original size:46 final size:46
Alignment explanation
Indices: 15411101--15411231 Score: 151
Period size: 46 Copynumber: 2.8 Consensus size: 46
15411091 TATACGGAAC
15411101 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGAG
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACATAAGTGCT--G
*
15411147 AAACAGAGAGTACACAAAGTACTAATCAGAGGGCACATAAAGTGCT-
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACAT-AAGTGCTG
* * * *
15411193 AATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACA
1 AAACAGAGAGTACACAAAGTACTAAT--CAGAGAGCACA
15411232 AGACGTACTA
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
46 35 0.47
47 11 0.15
48 21 0.28
49 7 0.09
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (46 bp):
AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACATAAGTGCTG
Found at i:15411223 original size:71 final size:70
Alignment explanation
Indices: 15411115--15411248 Score: 168
Period size: 71 Copynumber: 1.9 Consensus size: 70
15411105 AGAGAGTACC
* *
15411115 AAAGTACTAACAGAGAGCACATAAGTGCTGAGAAACAGAGAGTACACAA-A-GTACTAATCAGAG
1 AAAGTACTAACAGAGAGCACACAAGTGCTGAGAAACAGAGAG--CACAAGACGTACTAAACAGAG
15411178 GGCACAT
64 GGCACAT
*
15411185 AAAGTGCTAATCAGAGAGCACACACAGTGCT-A-ATAACAGAGAGCACAAGACGTACTAAACAGA
1 AAAGTACTAA-CAGAGAGCACACA-AGTGCTGAGA-AACAGAGAGCACAAGACGTACTAAACAGA
15411248 G
63 G
15411249 AGCGCGCTAG
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
69 5 0.09
70 11 0.20
71 34 0.61
72 6 0.11
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (70 bp):
AAAGTACTAACAGAGAGCACACAAGTGCTGAGAAACAGAGAGCACAAGACGTACTAAACAGAGGG
CACAT
Found at i:15411242 original size:25 final size:23
Alignment explanation
Indices: 15411101--15411251 Score: 94
Period size: 23 Copynumber: 6.5 Consensus size: 23
15411091 TATACGGAAC
* *
15411101 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTACT
* *
15411123 -AACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTACT
* *
15411144 GAGAAACAGAGAGTACACAAAGTACT
1 ---AAACAGAGAGCACACACAGTACT
* * * * *
15411170 AATCAGAGGGCACATAAAGTGCT
1 AAACAGAGAGCACACACAGTACT
* *
15411193 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTACT
*
15411216 AATAACAGAGAGCACA-AGACGTACT
1 -A-AACAGAGAGCACACACA-GTACT
15411241 AAACAGAGAGC
1 AAACAGAGAGC
15411252 GCGCTAGTGT
Statistics
Matches: 103, Mismatches: 17, Indels: 17
0.75 0.12 0.12
Matches are distributed among these distances:
21 16 0.16
22 1 0.01
23 48 0.47
24 4 0.04
25 29 0.28
26 5 0.05
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTACT
Found at i:15411248 original size:48 final size:46
Alignment explanation
Indices: 15411101--15411251 Score: 139
Period size: 48 Copynumber: 3.2 Consensus size: 46
15411091 TATACGGAAC
* *
15411101 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACAT-AAGTGCT
1 AAACAGAGAGCACACAAAGTACTAATCAGAGAGCACATAAAGTACT
* * *
15411144 GAGAAACAGAGAGTACACAAAGTACTAATCAGAGGGCACATAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTACTAATCAGAGAGCACATAAAGTACT
* * * *
15411193 AATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACA-AGACGTACT
1 AAACAGAGAGCACACAAAGTACTAAT--CAGAGAGCACATA-AAGTACT
15411241 AAACAGAGAGC
1 AAACAGAGAGC
15411252 GCGCTAGTGT
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
46 35 0.39
47 12 0.13
48 36 0.40
49 7 0.08
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (46 bp):
AAACAGAGAGCACACAAAGTACTAATCAGAGAGCACATAAAGTACT
Found at i:15415316 original size:39 final size:39
Alignment explanation
Indices: 15415273--15415569 Score: 172
Period size: 39 Copynumber: 7.6 Consensus size: 39
15415263 GATGGTGATT
*
15415273 TGCCCCAGGCTCGGGGTAAGAGATCGGATGACTTCAATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGACTTCAATC
* * * * *
15415312 TGCCCAAAGCTCGGGGTAAGAAAT-TGATTGACAGT-GATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGA-TGAC-TTCAATC
** * ** * *
15415351 TTTCCCAAGCTCGGGGTAAAAGATTAGATAACTGCAATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGACTTCAATC
* * * *
15415390 TGCCCCAAGCACGGGGTAAGAGATTGGCTGA-TGGT-GATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGACT--TCAATC
* * *
15415429 TGCCTCAAGCTCAGGGTAA-ACAATCGGATGACTTCAATC
1 TGCCCCAAGCTCGGGGTAAGA-GATCGGATGACTTCAATC
* * * * * *
15415468 TGTCTCAAGCTCGGGGTAAAAGATCTGATGGCTGCAATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGACTTCAATC
* * * * ** * *
15415507 GGCCCCAAGCTTGGAGTAAAAGATTTGATGGCTACAATC
1 TGCCCCAAGCTCGGGGTAAGAGATCGGATGACTTCAATC
* * * *
15415546 TGTCCGAGGCTCGGGATAAGAGAT
1 TGCCCCAAGCTCGGGGTAAGAGAT
15415570 TGGCTGATGT
Statistics
Matches: 195, Mismatches: 53, Indels: 20
0.73 0.20 0.07
Matches are distributed among these distances:
38 5 0.03
39 185 0.95
40 5 0.03
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (39 bp):
TGCCCCAAGCTCGGGGTAAGAGATCGGATGACTTCAATC
Found at i:15415338 original size:78 final size:76
Alignment explanation
Indices: 15415248--15415578 Score: 256
Period size: 78 Copynumber: 4.2 Consensus size: 76
15415238 TCAGGCTTGA
*
15415248 GGTAAGAGATTGACTGATGGTGATTTGCCCCAGGCTCGGGGTAAGAGATCGGATGACTTCAATCT
1 GGTAAGAGATTGACTGATGGTGATTTGCCCCAAGCTCGGGGTAA-AGATCGGATGACTTCAATCT
15415313 GCCCAAAGCTCGG
65 GCCC-AAGCTCGG
* * ** * ** * *
15415326 GGTAAGAAATTGATTGACAGTGATCTT-TCCCAAGCTCGGGGTAAAAGATTAGATAACTGCAATC
1 GGTAAGAGATTGACTGATGGTGAT-TTGCCCCAAGCTCGGGGT-AAAGATCGGATGACTTCAATC
*
15415390 TGCCCCAAGCACGG
64 TG-CCCAAGCTCGG
* * * * *
15415404 GGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCTCAGGGTAAACAATCGGATGACTTCAATCT
1 GGTAAGAGATTGACTGATGGTGATTTGCCCCAAGCTCGGGGTAAA-GATCGGATGACTTCAATCT
*
15415469 GTCTCAAGCTCGG
65 G-CCCAAGCTCGG
* ** * * ** * *
15415482 GGTAAAAGA-T--CTGATGGCTGCAATCGGCCCCAAGCTTGGAGTAAAAGATTTGATGGCTACAA
1 GGTAAGAGATTGACTGATGG-TG--ATTTGCCCCAAGCTCGGGGT-AAAGATCGGATGACTTCAA
* *
15415544 TCTGTCCGAGGCTCGG
62 TCTG-CCCAAGCTCGG
* *
15415560 GATAAGAGATTGGCTGATG
1 GGTAAGAGATTGACTGATG
15415579 TAGTTTGAAT
Statistics
Matches: 197, Mismatches: 44, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
75 7 0.04
76 2 0.01
77 5 0.03
78 166 0.84
79 11 0.06
81 6 0.03
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (76 bp):
GGTAAGAGATTGACTGATGGTGATTTGCCCCAAGCTCGGGGTAAAGATCGGATGACTTCAATCTG
CCCAAGCTCGG
Found at i:15415545 original size:156 final size:156
Alignment explanation
Indices: 15415248--15415578 Score: 373
Period size: 156 Copynumber: 2.1 Consensus size: 156
15415238 TCAGGCTTGA
* * * * *
15415248 GGTAAGAGATTGACTGATGGTGATTTGCCCCAGGCTCGGGGTAAGAGATCGGATGACTTCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAGAAATCGGATGACTTCAATCT
** *** *
15415313 GCCCAAAGCTCGGGGTAAGAAATTGATTGACAGTGATCTTTCCCAAGCTCGGGGTAAAAGATTAG
66 GCCCAAAGCTCGGGGTAAGAAATTGATTGACAGCAATCGGCCCCAAGCTCGGAGTAAAAGATTAG
*
15415378 ATAACTGCAATCTGCCCCAAGCACGG
131 ATAACTACAATCTGCCCCAAGCACGG
*
15415404 GGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCTCAGGGTAA-ACAATCGGATGACTTCAATC
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAGA-AATCGGATGACTTCAATC
* * * *
15415468 TGTCTC-AAGCTCGGGGTAA-AAGATCTGA-TGGCTGCAATCGGCCCCAAGCTTGGAGTAAAAGA
65 TG-CCCAAAGCTCGGGGTAAGAA-AT-TGATTGACAGCAATCGGCCCCAAGCTCGGAGTAAAAGA
* ** * * * *
15415530 TTTGATGGCTACAATCTGTCCGAGGCTCGG
127 TTAGATAACTACAATCTGCCCCAAGCACGG
*
15415560 GATAAGAGATTGGCTGATG
1 GGTAAGAGATTGGCTGATG
15415579 TAGTTTGAAT
Statistics
Matches: 146, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
155 3 0.02
156 138 0.95
157 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (156 bp):
GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAGAAATCGGATGACTTCAATCT
GCCCAAAGCTCGGGGTAAGAAATTGATTGACAGCAATCGGCCCCAAGCTCGGAGTAAAAGATTAG
ATAACTACAATCTGCCCCAAGCACGG
Found at i:15415979 original size:49 final size:49
Alignment explanation
Indices: 15415926--15416021 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
15415916 TCGCCATTGC
* * *
15415926 GACCTCAACCTTTCACTTC-CAATCTTCATGGTATCGGGTTTACCGTTAT
1 GACCTCAACCTTTCACATCAC-ATCTTCATGGTATCGGATTCACCGTTAT
*
15415975 GACCTCAACCTTTCCCATCACATCTTCATGGTATCGGATTCACCGTT
1 GACCTCAACCTTTCACATCACATCTTCATGGTATCGGATTCACCGTT
15416022 GCAGCCTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 41 0.98
50 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (49 bp):
GACCTCAACCTTTCACATCACATCTTCATGGTATCGGATTCACCGTTAT
Found at i:15416030 original size:49 final size:48
Alignment explanation
Indices: 15415947--15416336 Score: 194
Period size: 50 Copynumber: 8.1 Consensus size: 48
15415937 TTCACTTCCA
* *
15415947 ATCTTCATGGTATCGGGTTTACCGTTA-TGACCTCAACCTTTCCCATCAC
1 ATCTTCATGGTATCGGGTTCACCGTTACAG-CCTCAACC-TTCCCATCAC
* * * *
15415996 ATCTTCATGGTATCGGATTCACCGTTGCAGCCTCAATCCTTCTCATCAT
1 ATCTTCATGGTATCGGGTTCACCGTTACAGCCTCAA-CCTTCCCATCAC
* * * *
15416045 ATCTTTTAAGATATCGGGTTCACCGTTGCAG-CTCAACC-T--C-TC-C
1 ATC-TTCATGGTATCGGGTTCACCGTTACAGCCTCAACCTTCCCATCAC
* ** **
15416088 --CTTCATGGTACCGAATTCGTCGTTAC-GACCTCAATCCTTCCCATCAC
1 ATCTTCATGGTATCGGGTTCACCGTTACAG-CCTCAA-CCTTCCCATCAC
* ** * * *
15416135 ATCTTCTAAGGTA-CTGGGTTTGCCGTTACGGCCTCAACCTTTCCCTTTA-
1 ATCTTC-ATGGTATC-GGGTTCACCGTTACAGCCTCAACC-TTCCCATCAC
* * * * *
15416184 ATATTCATGGTATCGGGTTCACCATTACGGCCTCAACCTTTCCCATAAT
1 ATCTTCATGGTATCGGGTTCACCGTTACAGCCTCAACC-TTCCCATCAC
* * * ** * *
15416233 AT-TTCATGGTACCAGATTTTCCGTTGCAGCCTCAATCCTCCCCATCAC
1 ATCTTCATGGTATCGGGTTCACCGTTACAGCCTCAA-CCTTCCCATCAC
* * * ** ** * *
15416281 ATCTTTTAAGGTACCGGGTTCACTATTATGGCCTCAACCTTTCCCTTCAA
1 ATC-TTCATGGTATCGGGTTCACCGTTACAGCCTCAACC-TTCCCATCAC
15416331 ATCTTC
1 ATCTTC
15416337 GTGTTTTCTT
Statistics
Matches: 258, Mismatches: 60, Indels: 46
0.71 0.16 0.13
Matches are distributed among these distances:
39 1 0.00
40 16 0.06
41 6 0.02
42 2 0.01
43 1 0.00
44 2 0.01
45 2 0.01
46 2 0.01
47 2 0.01
48 70 0.27
49 67 0.26
50 86 0.33
51 1 0.00
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (48 bp):
ATCTTCATGGTATCGGGTTCACCGTTACAGCCTCAACCTTCCCATCAC
Found at i:15417263 original size:6 final size:6
Alignment explanation
Indices: 15417252--15417288 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
15417242 GACCACTCTG
*
15417252 TTTTCT TTTTC- TTCTC- TTTTCT TTTTCT TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTT
15417289 CTTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 8 0.29
6 20 0.71
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:15417271 original size:11 final size:11
Alignment explanation
Indices: 15417252--15417291 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
15417242 GACCACTCTG
15417252 TTTTCTTTTTC
1 TTTTCTTTTTC
*
15417263 TTCTC-TTTTC
1 TTTTCTTTTTC
15417273 TTTTTCTTTTTC
1 -TTTTCTTTTTC
15417285 TTTTCTT
1 TTTTCTT
15417292 CTTTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:15423627 original size:18 final size:18
Alignment explanation
Indices: 15423604--15423640 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15423594 TTTGTGATCA
15423604 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
15423622 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
15423640 A
1 A
15423641 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:15428686 original size:18 final size:18
Alignment explanation
Indices: 15428663--15428699 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15428653 TTTGTGATCA
15428663 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
15428681 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
15428699 A
1 A
15428700 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:15433140 original size:19 final size:22
Alignment explanation
Indices: 15433104--15433163 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
15433094 ACTAAAATTG
*
15433104 TAATTTAACAATAAATAA-TAAA
1 TAATTTAATAA-AAATAATTAAA
15433126 T-ATTT-ATAAAAATAATTAAA
1 TAATTTAATAAAAATAATTAAA
15433146 TAATTTGAATAAAAATAA
1 TAATTT-AATAAAAATAA
15433164 AACATAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
21 8 0.24
22 1 0.03
23 10 0.30
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TAATTTAATAAAAATAATTAAA
Found at i:15433165 original size:141 final size:144
Alignment explanation
Indices: 15432964--15433254 Score: 500
Period size: 143 Copynumber: 2.0 Consensus size: 144
15432954 ATAATGGCCT
15432964 ATTTAACAATAAATAATAAATATTTATAAAAAATAATTAAATAATTTGAATAAAAATAAAACAGA
1 ATTTAACAATAAATAATAAATATTTATAAAAAATAATTAAATAATTTGAATAAAAATAAAACAGA
15433029 AAAAATAAAA-AAA-TTAATTC-TTTCAATTTGTTATGAGTTTTTTACCTAAAATATATAAAATA
66 AAAAATAAAATAAATTTAA-TCATTTCAATTTGTTATGAGTTTTTTACCTAAAATATATAAAATA
* *
15433091 AATACTAAAATTGTA
130 AATACTAAAACTCTA
*
15433106 ATTTAACAATAAATAATAAATATTTAT-AAAAATAATTAAATAATTTGAATAAAAATAAAACATA
1 ATTTAACAATAAATAATAAATATTTATAAAAAATAATTAAATAATTTGAATAAAAATAAAACAGA
* *
15433170 AAAAATAAAATAAATTTAATCATTTTAATTTGTTATGGGTTTTTTACCTAAAATATATAAAATAA
66 AAAAATAAAATAAATTTAATCATTTCAATTTGTTATGAGTTTTTTACCTAAAATATATAAAATAA
15433235 ATACTAAAACTCTA
131 ATACTAAAACTCTA
15433249 ATTTAA
1 ATTTAA
15433255 AAACCCTAAA
Statistics
Matches: 141, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
141 46 0.33
142 32 0.23
143 63 0.45
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (144 bp):
ATTTAACAATAAATAATAAATATTTATAAAAAATAATTAAATAATTTGAATAAAAATAAAACAGA
AAAAATAAAATAAATTTAATCATTTCAATTTGTTATGAGTTTTTTACCTAAAATATATAAAATAA
ATACTAAAACTCTA
Found at i:15439882 original size:11 final size:11
Alignment explanation
Indices: 15439860--15439889 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
15439850 AAGGGATATT
15439860 AATAAA-TTTA
1 AATAAATTTTA
15439870 AATAAATTTTA
1 AATAAATTTTA
15439881 AATAAATTT
1 AATAAATTT
15439890 AAACTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AATAAATTTTA
Found at i:15439892 original size:17 final size:17
Alignment explanation
Indices: 15439872--15439911 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
15439862 TAAATTTAAA
*
15439872 TAAATTTTAAATAAATT
1 TAAATTTAAAATAAATT
*
15439889 TAAACTTAAAATAAATT
1 TAAATTTAAAATAAATT
15439906 TAAATT
1 TAAATT
15439912 CTGTTTGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:15439910 original size:10 final size:10
Alignment explanation
Indices: 15439860--15439892 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
15439850 AAGGGATATT
15439860 AATAAATTTA
1 AATAAATTTA
15439870 AATAAATTTTA
1 AATAAA-TTTA
15439881 AATAAATTTA
1 AATAAATTTA
15439891 AA
1 AA
15439893 CTTAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATAAATTTA
Found at i:15440496 original size:6 final size:6
Alignment explanation
Indices: 15440456--15440480 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15440446 TCTTTTTCAT
15440456 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
15440481 CTATAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:15441303 original size:31 final size:31
Alignment explanation
Indices: 15441240--15441304 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
15441230 TTAAACAGCT
* * *
15441240 AATATACTAAAATTTCAAAATTTGAAAAATA
1 AATAGACTAAAATATCAAAATTGGAAAAATA
*
15441271 AATAGACTAAAATATC-AAATTGGAGAATATA
1 AATAGACTAAAATATCAAAATTGGA-AAAATA
15441302 AAT
1 AAT
15441305 TAAAGTCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (31 bp):
AATAGACTAAAATATCAAAATTGGAAAAATA
Found at i:15441693 original size:22 final size:23
Alignment explanation
Indices: 15441644--15441694 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
15441634 GTTCAAAAAT
*
15441644 GCTCGATCCCGAAAAAATTTGTC
1 GCTCGAACCCGAAAAAATTTGTC
*
15441667 GCTCGAACCTGAAAAAATTTGTC
1 GCTCGAACCCGAAAAAATTTGTC
15441690 -CTCGA
1 GCTCGA
15441695 CCAAACTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (23 bp):
GCTCGAACCCGAAAAAATTTGTC
Found at i:15442335 original size:16 final size:16
Alignment explanation
Indices: 15442285--15442340 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
15442275 CCCGAATCTG
*
15442285 AAAAATTT-GAACTCA
1 AAAAATTTCAAACTCA
* * *
15442300 AAAAAATTCAAACCCG
1 AAAAATTTCAAACTCA
*
15442316 AAAAATTTCAAATTCA
1 AAAAATTTCAAACTCA
15442332 AAAATATTT
1 AAAA-ATTT
15442341 TTAAAAAATC
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
15 7 0.23
16 20 0.65
17 4 0.13
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (16 bp):
AAAAATTTCAAACTCA
Found at i:15443704 original size:25 final size:25
Alignment explanation
Indices: 15443676--15443727 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
15443666 TAAAATGTGT
*
15443676 AAAAAT-TCAAAAAATAATTTATTAG
1 AAAAATATCAAAAAATAA-CTATTAG
*
15443701 AAAAATATTAAAAAATAACTATTAG
1 AAAAATATCAAAAAATAACTATTAG
15443726 AA
1 AA
15443728 TTATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (25 bp):
AAAAATATCAAAAAATAACTATTAG
Found at i:15444666 original size:30 final size:30
Alignment explanation
Indices: 15444622--15444680 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
15444612 CTTTTCATTA
* *
15444622 TTTTAATTAATGATTCAAT-ATATTAATTC
1 TTTTAATTAATGATTAAATAATAATAATTC
*
15444651 TTTTGATTAAATGATTAAATAATAATAATT
1 TTTTAATT-AATGATTAAATAATAATAATT
15444681 TTATCATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 10 0.40
31 8 0.32
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTAATTAATGATTAAATAATAATAATTC
Found at i:15449001 original size:24 final size:24
Alignment explanation
Indices: 15448964--15449009 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
15448954 TCAGTCATTA
*
15448964 AATCTGGATGATATTAAAGAAATG
1 AATCTGGATAATATTAAAGAAATG
* *
15448988 AATCTTGATAATATTCAAGAAA
1 AATCTGGATAATATTAAAGAAA
15449010 ATTAAATGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (24 bp):
AATCTGGATAATATTAAAGAAATG
Found at i:15449174 original size:31 final size:31
Alignment explanation
Indices: 15449130--15449209 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
15449120 GAAAAAGAAG
* *
15449130 CATTAAT-TCCAAGAAGGAAATTAAGCAAAGG
1 CATTAATAT-CAAGAAAGAAATTAAGCAAAGA
* * **
15449161 CATTGATATCAAGAAAGATATTTGGCAAAGA
1 CATTAATATCAAGAAAGAAATTAAGCAAAGA
15449192 CATTAATATCAAGAAAGA
1 CATTAATATCAAGAAAGA
15449210 TATTTGGATG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (31 bp):
CATTAATATCAAGAAAGAAATTAAGCAAAGA
Found at i:15449210 original size:31 final size:31
Alignment explanation
Indices: 15449154--15449216 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
15449144 AGGAAATTAA
* *
15449154 GCAAAGGCATTGATATCAAGAAAGATATTTG
1 GCAAAGACATTAATATCAAGAAAGATATTTG
15449185 GCAAAGACATTAATATCAAGAAAGATATTTG
1 GCAAAGACATTAATATCAAGAAAGATATTTG
15449216 G
1 G
15449217 ATGGGACGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (31 bp):
GCAAAGACATTAATATCAAGAAAGATATTTG
Found at i:15450171 original size:15 final size:16
Alignment explanation
Indices: 15450143--15450174 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
15450133 AGTTCAATTA
15450143 TTTTATTATTTACTTC
1 TTTTATTATTTACTTC
15450159 TTTTATT-TTTACTTC
1 TTTTATTATTTACTTC
15450174 T
1 T
15450175 GTTGTATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTATTTACTTC
Found at i:15453403 original size:31 final size:31
Alignment explanation
Indices: 15453322--15453409 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
15453312 AGAAAAAGAA
* * * * *
15453322 GCATTAATTTCAAGAAGGAAATTAGGTAAAG
1 GCATTAATATCAAGAAAGATATTTGGCAAAG
* *
15453353 GCATTGATATCAAGAAAGATATTTGGCAAAT
1 GCATTAATATCAAGAAAGATATTTGGCAAAG
15453384 GCATTAATATCAAGAAAGATATTTGG
1 GCATTAATATCAAGAAAGATATTTGG
15453410 ATGGGACGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.28
Consensus pattern (31 bp):
GCATTAATATCAAGAAAGATATTTGGCAAAG
Found at i:15463525 original size:21 final size:21
Alignment explanation
Indices: 15463501--15463540 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
15463491 TCATCATTAA
15463501 ATGCATTAAAATAATAATTGT
1 ATGCATTAAAATAATAATTGT
* * *
15463522 ATGCTTTGAAATTATAATT
1 ATGCATTAAAATAATAATT
15463541 TATTTGAAAA
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:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (21 bp):
ATGCATTAAAATAATAATTGT
Found at i:15466815 original size:28 final size:29
Alignment explanation
Indices: 15466784--15466843 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
15466774 CAAGCATGAT
* *
15466784 ATTTGATTTTTA-TTTTTGGGATTTCTCC
1 ATTTAATTTTTATTTTTTGAGATTTCTCC
15466812 ATTTAATTTTTATTTTTTGAGATTTCTCC
1 ATTTAATTTTTATTTTTTGAGATTTCTCC
15466841 ATT
1 ATT
15466844 CTCCATGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (29 bp):
ATTTAATTTTTATTTTTTGAGATTTCTCC
Found at i:15467476 original size:35 final size:36
Alignment explanation
Indices: 15467416--15467484 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
15467406 GATGAAATTA
*
15467416 GCAAAAAGAATAAAAACAAAAGGAGAGGGGGAGAGG
1 GCAAAAAGAATAAAAACAAAAGGAGAGGAGGAGAGG
** *
15467452 GCAAAAAGAAT-AAAACTGAGGGAGAGGAGGAGA
1 GCAAAAAGAATAAAAACAAAAGGAGAGGAGGAGA
15467485 CGACAGGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 18 0.62
36 11 0.38
ACGTcount: A:0.54, C:0.06, G:0.36, T:0.04
Consensus pattern (36 bp):
GCAAAAAGAATAAAAACAAAAGGAGAGGAGGAGAGG
Found at i:15474375 original size:17 final size:16
Alignment explanation
Indices: 15474353--15474385 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
15474343 GCAACTTTTT
15474353 AATAATTATACATTTAA
1 AATAATTATA-ATTTAA
15474370 AATAATTATAATTTAA
1 AATAATTATAATTTAA
15474386 TTAAAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTATAATTTAA
Done.