Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009000.1 Hibiscus syriacus cultivar Beakdansim tig00112382_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1742898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1092107 original size:31 final size:32
Alignment explanation
Indices: 1092067--1092137 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 32
1092057 TATGTGCTTC
*
1092067 TTATCTTTTTTCTTT-CT-TTTGTTCTTTTTCTT
1 TTATCTTTTTTCTTTGCTCTTT-TT-TCTTTCTT
1092099 TTAT-TTTTTTCTTTGCTCTTTTTTCTTTCTT
1 TTATCTTTTTTCTTTGCTCTTTTTTCTTTCTT
1092130 TTATCTTT
1 TTATCTTT
1092138 GTTTTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
31 21 0.60
32 11 0.31
33 3 0.09
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.77
Consensus pattern (32 bp):
TTATCTTTTTTCTTTGCTCTTTTTTCTTTCTT
Found at i:1092136 original size:18 final size:18
Alignment explanation
Indices: 1092073--1092137 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 18
1092063 CTTCTTATCT
*
1092073 TTTTTCTTTCTTT-TGTTC
1 TTTTTCTTTATTTCT-TTC
*
1092091 TTTTTCTTTTATTTTTTTC
1 TTTTTC-TTTATTTCTTTC
*
1092110 TTTGCTCTTT-TTTCTTTC
1 TTT-TTCTTTATTTCTTTC
1092128 TTTTATCTTT
1 TTTT-TCTTT
1092138 GTTTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 21 0.54
19 15 0.38
20 3 0.08
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTATTTCTTTC
Found at i:1092145 original size:14 final size:14
Alignment explanation
Indices: 1092128--1092171 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1092118 TTTTTCTTTC
1092128 TTTTATCTTTGTTT
1 TTTTATCTTTGTTT
* *
1092142 TTTTTTCTTTGCTTA
1 TTTTATCTTTG-TTT
*
1092157 TTTTCTCTTTGTTT
1 TTTTATCTTTGTTT
1092171 T
1 T
1092172 GATTGAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.05, C:0.11, G:0.07, T:0.77
Consensus pattern (14 bp):
TTTTATCTTTGTTT
Found at i:1094097 original size:10 final size:10
Alignment explanation
Indices: 1094082--1094111 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1094072 TCGCAATGAT
1094082 AAAATAAAAG
1 AAAATAAAAG
*
1094092 AAAATAAAAC
1 AAAATAAAAG
1094102 AAAATAAAAG
1 AAAATAAAAG
1094112 TGAAAAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (10 bp):
AAAATAAAAG
Found at i:1095693 original size:3 final size:3
Alignment explanation
Indices: 1095681--1095749 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
1095671 GCAAAAAATG
1095681 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1095728 TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
1095750 GATGATGATG
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1095754 original size:3 final size:3
Alignment explanation
Indices: 1095748--1095773 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1095738 AATAATAATA
1095748 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
1095774 AATAATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:1097144 original size:4 final size:4
Alignment explanation
Indices: 1097135--1097159 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1097125 CTTATTTCAG
1097135 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
1097160 GGATTGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:1101517 original size:3 final size:3
Alignment explanation
Indices: 1101509--1101547 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1101499 GCTCATTCAC
* *
1101509 ATT ATT ATT ATT ATT ATT ATT GTTT AGT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT AT
1101548 ATGCCAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1102895 original size:47 final size:48
Alignment explanation
Indices: 1102825--1102963 Score: 154
Period size: 51 Copynumber: 2.8 Consensus size: 48
1102815 TTCATACTAC
* * * *
1102825 AAAAAATATAGCATTTAATACATACTTACA-TTGTAAGTGAATAAAAT
1 AAAAAATGTAGCACTTAACACATACTTACACATGTAAGTGAATAAAAT
*
1102872 AAAAAATGTAGCACTTAACACATACTTACACCGATGTAAGTTAATAAAAT
1 AAAAAATGTAGCACTTAACACATACTTACA-C-ATGTAAGTGAATAAAAT
** *
1102922 AAAAAAGTGTTTCACTTAACAAATACTTACACCAATGTAAGT
1 AAAAAA-TGTAGCACTTAACACATACTTACA-C-ATGTAAGT
1102964 ATATACATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
47 27 0.34
50 21 0.27
51 31 0.39
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (48 bp):
AAAAAATGTAGCACTTAACACATACTTACACATGTAAGTGAATAAAAT
Found at i:1102948 original size:51 final size:50
Alignment explanation
Indices: 1102856--1102963 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 50
1102846 ATACTTACAT
* *
1102856 TGTAAGTGAATAAAATAAAAAATGTAGCACTTAACACATACTTACACCGA
1 TGTAAGTGAATAAAATAAAAAATGTAGCACTTAACAAATACTTACACCAA
* **
1102906 TGTAAGTTAATAAAATAAAAAAGTGTTTCACTTAACAAATACTTACACCAA
1 TGTAAGTGAATAAAATAAAAAA-TGTAGCACTTAACAAATACTTACACCAA
1102957 TGTAAGT
1 TGTAAGT
1102964 ATATACATCT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
50 21 0.40
51 31 0.60
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (50 bp):
TGTAAGTGAATAAAATAAAAAATGTAGCACTTAACAAATACTTACACCAA
Found at i:1103302 original size:29 final size:29
Alignment explanation
Indices: 1103246--1103316 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1103236 TCATCATTTG
*
1103246 TAGTGACTAAAATATAAGTTTTGAAAGTT
1 TAGTGACTAAAATAAAAGTTTTGAAAGTT
* *
1103275 TAGTGAC-AAAGTAAAATTTTTGAGAAGTT
1 TAGTGACTAAAATAAAAGTTTTGA-AAGTT
* *
1103304 TAGGGACCAAAAT
1 TAGTGACTAAAAT
1103317 GTAAATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 13 0.37
29 18 0.51
30 4 0.11
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (29 bp):
TAGTGACTAAAATAAAAGTTTTGAAAGTT
Found at i:1104559 original size:20 final size:21
Alignment explanation
Indices: 1104520--1104559 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1104510 AGGGAAAAAT
* *
1104520 AAAATAAATAAGTAAGATAAG
1 AAAAAAAATAAGTAAAATAAG
1104541 AAAAAAAAT-AGTAAAATAA
1 AAAAAAAATAAGTAAAATAA
1104560 TAATTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAAAAAATAAGTAAAATAAG
Found at i:1104863 original size:28 final size:28
Alignment explanation
Indices: 1104799--1104887 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
1104789 AGGTTTTTAA
* * *
1104799 AAAAAATAATAATAATAATGAATAAAAAAT
1 AAAAAATAATAAAAATAAT--ATAATATAT
**
1104829 CGAAAATAATAAAAATAATATAATATAT
1 AAAAAATAATAAAAATAATATAATATAT
*
1104857 AAAAAATAATATAAAT-ATATAAATATAT
1 AAAAAATAATAAAAATAATAT-AATATAT
1104885 AAA
1 AAA
1104888 GATAATATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 4 0.08
28 30 0.60
30 16 0.32
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAATAATAAAAATAATATAATATAT
Found at i:1104873 original size:20 final size:19
Alignment explanation
Indices: 1104839--1104898 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 19
1104829 CGAAAATAAT
1104839 AAAAATAATATAATATATA
1 AAAAATAATATAATATATA
1104858 AAAAATAATATAAATATATA
1 AAAAATAATAT-AATATATA
* *
1104878 AATATATAAAGATAATATATA
1 AA-AAAT-AATATAATATATA
1104899 CATAATAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.31
20 10 0.28
21 11 0.31
22 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAATAATATAATATATA
Found at i:1104941 original size:19 final size:19
Alignment explanation
Indices: 1104840--1104941 Score: 55
Period size: 21 Copynumber: 5.1 Consensus size: 19
1104830 GAAAATAATA
1104840 AAAATA-ATATA-ATATAT
1 AAAATATATATATATATAT
* *
1104857 AAAAAATAATATAAATATAT
1 AAAATAT-ATATATATATAT
* *
1104877 AAATATATAAAGATAATATAT
1 AAA-ATATATATAT-ATATAT
* * * *
1104898 ACATAATAAAGAAATAATCAAAT
1 A-A-AATATATATAT-AT-ATAT
1104921 AAAATATATATATATATAT
1 AAAATATATATATATATAT
1104940 AA
1 AA
1104942 TAACAGGTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
17 5 0.08
19 10 0.16
20 14 0.22
21 18 0.28
22 12 0.19
23 5 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATATATATATATATAT
Found at i:1105545 original size:37 final size:37
Alignment explanation
Indices: 1105463--1105564 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
1105453 GTGCTTGTGG
* * * * * *
1105463 ATCCTATATTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
1105500 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
1105537 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1105565 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:1106411 original size:105 final size:105
Alignment explanation
Indices: 1106107--1106737 Score: 880
Period size: 105 Copynumber: 6.0 Consensus size: 105
1106097 GCATTGTTCC
* * *** *
1106107 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCAGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTGTTT-TTGACA
* * * * *
1106171 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1106213 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTTTTGACAAG
* *
1106273 CAGCGGTCCCTTCATCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1106313 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTTTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTTTTGACAAG
1106378 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1106418 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTTTTGACAAG
1106483 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1106523 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTTTTGACAAG
1106588 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1106628 GAGTCCAATATCATTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTT-TTGACAA
* * * * *
1106693 CCAGAC-GTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1106734 GAGT
1 GAGT
1106738 GTCACGATAT
Statistics
Matches: 481, Mismatches: 36, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
100 80 0.17
101 3 0.01
102 7 0.01
104 5 0.01
105 305 0.63
106 80 0.17
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTTTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1106977 original size:36 final size:36
Alignment explanation
Indices: 1106937--1107008 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
1106927 TGTTTGGAGA
* **
1106937 GAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGG
1 GAAACTATCTCAAGGGAGACAAAATTCATTTCAAGG
* *
1106973 GAAACTATCTCAAGTGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGGGAGACAAAATTCATTTCAAGG
1107009 AAAATGTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
GAAACTATCTCAAGGGAGACAAAATTCATTTCAAGG
Found at i:1107133 original size:106 final size:103
Alignment explanation
Indices: 1106912--1107231 Score: 477
Period size: 106 Copynumber: 3.1 Consensus size: 103
1106902 TTCGTTAAAT
* ** *
1106912 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA-TT-TGTTTCAAGGGA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCTGTTTCGAGGGA
* *
1106975 AACTATCTCAAGTGAG-ATAAAATTCATTTCAAGGAAAA
66 AACTATCTCAAG-GAGAAAAAAATTCATTTCAAGGGAAA
*
1107013 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTCTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TCTGTTTCGAGGG
*
1107078 AAACTATCTCAAGAGAGAAAAAAAAATCATTTCAAGGGAAA
65 AAACTATCTCAAG-GAG-AAAAAAATTCATTTCAAGGGAAA
1107119 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTCTGTTTCGAGGG
*
1107184 AAACTATCTC-AGGAGAGAAAAAATTAATTTCAAGGGAAA
65 AAACTATCTCAAGGAGA-AAAAAATTCATTTCAAGGGAAA
1107223 TGTTTTCAA
1 TGTTTTCAA
1107232 GAGAAACTGT
Statistics
Matches: 200, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
101 45 0.22
102 1 0.00
103 2 0.01
104 58 0.29
105 2 0.01
106 90 0.45
107 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (103 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCTGTTTCGAGGGA
AACTATCTCAAGGAGAAAAAAATTCATTTCAAGGGAAA
Found at i:1107188 original size:39 final size:39
Alignment explanation
Indices: 1107134--1107208 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
1107124 TCAATGTTTA
* *
1107134 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
1107173 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
1107209 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:1107388 original size:36 final size:36
Alignment explanation
Indices: 1107348--1107461 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
1107338 ATTTCGAGTG
* *
1107348 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * * * **
1107384 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
*
1107420 AAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TCTTGTTTTAAGA
1107456 AAAACA
1 AAAACA
1107462 AATTTGAGTG
Statistics
Matches: 58, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:1107440 original size:72 final size:74
Alignment explanation
Indices: 1107302--1107477 Score: 207
Period size: 72 Copynumber: 2.4 Consensus size: 74
1107292 TAAAATCTTC
* ** * *
1107302 TTAAAAAAAACAGCCTTGAGTGAAATGAAATGCCTTATTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTATTTCGAGTAAAAACAGTCTCAAGCGAGA
*
1107367 CAAA-TCTTGTT
64 CAAAGT-ATGTT
* *
1107378 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTATTTCGAGTAAAAACAGTCTCAAGCGAGACA
1107441 AAGTATGTT
66 AAGTATGTT
*
1107450 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
1107478 TCATCTGCAT
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
72 48 0.54
73 14 0.16
75 4 0.04
76 23 0.26
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTATTTCGAGTAAAAACAGTCTCAAGCGAGACA
AAGTATGTT
Found at i:1108929 original size:183 final size:183
Alignment explanation
Indices: 1108621--1109153 Score: 906
Period size: 183 Copynumber: 2.9 Consensus size: 183
1108611 GGTTTAACTG
*
1108621 AAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* **
1108686 AGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCC
66 AGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCC
1108750 TCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTA
130 TCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTA
* *
1108804 AAGGGTTCGTCTCATCACAAAGTCTTTGGCTTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1108869 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
* * *
1108934 CTATAACCAATTGCCTTAGTGGAATAGTTTAGCTTTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTA
** * *
1108987 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAAAAGTAGAGCAAACACCAAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* * *
1109052 AGTGTCCAAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGTTTTCAAGTTTCCT
66 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
1109117 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
1109154 CGGATTTAAT
Statistics
Matches: 329, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
183 328 1.00
184 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTA
Found at i:1114808 original size:3 final size:3
Alignment explanation
Indices: 1114802--1114838 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1114792 TTTTTTAAAA
1114802 AAT AAT AAT AAT AAT AAT AAT GAAT AA- AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
1114839 AAAATACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1114840 original size:9 final size:9
Alignment explanation
Indices: 1114799--1114841 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1114789 GTTTTTTTTA
1114799 AAAAATAAT
1 AAAAATAAT
*
1114808 AATAATAAT
1 AAAAATAAT
*
1114817 AATAATGAAT
1 AAAAAT-AAT
1114827 AAAAAATAAT
1 -AAAAATAAT
1114837 AAAAA
1 AAAAA
1114842 ATACTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 19 0.63
10 6 0.20
11 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (9 bp):
AAAAATAAT
Found at i:1114851 original size:12 final size:10
Alignment explanation
Indices: 1114797--1114844 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
1114787 ATGTTTTTTT
1114797 TAAAAAATAA
1 TAAAAAATAA
*
1114807 T-AATAATAA
1 TAAAAAATAA
*
1114816 T-AATAATGAA
1 TAAAAAAT-AA
1114826 TAAAAAATAA
1 TAAAAAATAA
1114836 TAAAAAATA
1 TAAAAAATA
1114845 CTATAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 14 0.41
10 15 0.44
11 5 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:1115124 original size:18 final size:17
Alignment explanation
Indices: 1115101--1115143 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1115091 ATATATACAT
1115101 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1115119 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1115136 ATAA-AATA
1 ATAATAATA
1115144 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1115151 original size:56 final size:55
Alignment explanation
Indices: 1115033--1115151 Score: 125
Period size: 58 Copynumber: 2.1 Consensus size: 55
1115023 TATTAAAGAA
* * * *
1115033 ATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTAATATAT
1 ATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATAA--TAATATAC
*
1115091 ATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-AATATCC
1 ATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAATAATATAC
1115147 ATATA
1 ATATA
1115152 ATAAATAAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
56 10 0.19
58 19 0.36
59 9 0.17
60 4 0.08
61 11 0.21
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (55 bp):
ATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATAATAATATAC
Found at i:1117769 original size:19 final size:19
Alignment explanation
Indices: 1117742--1117780 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1117732 ACATTGAATG
*
1117742 CATATCATGCATCGATGCA
1 CATACCATGCATCGATGCA
1117761 CATACCATGCATCGATGCA
1 CATACCATGCATCGATGCA
1117780 C
1 C
1117781 TCAAGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (19 bp):
CATACCATGCATCGATGCA
Found at i:1117861 original size:65 final size:65
Alignment explanation
Indices: 1117731--1117890 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 65
1117721 AAATAAATTG
* *
1117731 AACATTGAATGCATATCATGCATCGATGCA-CATACCATGCATCGATGCACTCAAGGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAAGGTTTTATG-
1117795 A
65 A
* * **
1117796 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACT-TTGGCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAAGG-T-TTTAT
1117858 GA
64 GA
* *
1117860 AACATCGAATGCATTTTATGAATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
1117891 TAAGGTTCCA
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 32 0.38
65 47 0.56
66 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAAGGTTTTATGA
Found at i:1123335 original size:21 final size:21
Alignment explanation
Indices: 1123270--1123364 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 21
1123260 TTGTGCTTAA
*
1123270 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
*
1123290 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
1123312 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
1123333 TGCACCGATGCACGCCTTGAATG
1 TGCATCGAT--ACACCTTGAATG
1123356 TGCATCGAT
1 TGCATCGAT
1123365 GCACAAGGCC
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 17 0.28
22 13 0.22
23 19 0.32
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:1123358 original size:23 final size:23
Alignment explanation
Indices: 1123289--1123369 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
1123279 ACACCTAACA
*
1123289 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
1123311 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
1123332 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
1123355 GTGCATCGATGCACA
1 GTGCATCGATGCACA
1123370 AGGCCATGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
22 10 0.21
23 21 0.45
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:1123360 original size:44 final size:42
Alignment explanation
Indices: 1123270--1123364 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
1123260 TTGTGCTTAA
* *
1123270 TGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
*
1123312 TGCATCGATACACCATGAA-GGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCA-GCCTTGAATG
1123356 TGCATCGAT
1 TGCATCGAT
1123365 GCACAAGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 20 0.43
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
Found at i:1123385 original size:43 final size:42
Alignment explanation
Indices: 1123288--1123387 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 42
1123278 TACACCTAAC
* * *
1123288 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
* * *
1123330 AGGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-GCCTTGAATGTGCATCGATACACAAGG-A
1123375 A-TGCATCGATGCA
1 AGTGCATCGATGCA
1123388 TCCGTTGGGT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.48
44 23 0.48
45 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
Found at i:1126048 original size:65 final size:63
Alignment explanation
Indices: 1125975--1126133 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 63
1125965 AAATAAATTG
* *
1125975 AACATCGAATGCATTTGATGTATCGATGCACATACCATGCATCGATGCACTCAAGG-T-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCGATACACTC-AGGATATTT-T-
1126038 AA
62 AA
* * * *
1126040 AACATCGAATGCATTTGATACATCGATGCGCCAGCCATGCATCGATACACTCTGGATATTTTAA
1 AACATCGAATGCATTTGATGCATCGATGC-ACAACCATGCATCGATACACTCAGGATATTTTAA
*
1126104 AACATCGAATGCATTTTATGCATCG-TGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1126134 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 3 0.04
64 27 0.33
65 46 0.56
66 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCGATACACTCAGGATATTTTAA
Found at i:1129775 original size:10 final size:10
Alignment explanation
Indices: 1129760--1129789 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1129750 ATGTTTGGTC
1129760 ATTTATTTTA
1 ATTTATTTTA
1129770 ATTTATTTTA
1 ATTTATTTTA
1129780 ATTTATTTTA
1 ATTTATTTTA
1129790 TTGGGGCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTATTTTA
Found at i:1130152 original size:26 final size:27
Alignment explanation
Indices: 1130115--1130168 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
1130105 TTAATCAAAA
1130115 AAAAATAATTTAATTCATATTT-AATTT
1 AAAAATAATTTAATTCAT-TTTAAATTT
1130142 AAAAA-AATTTAATTCATTTTAAATTT
1 AAAAATAATTTAATTCATTTTAAATTT
1130168 A
1 A
1130169 TTTTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 3 0.12
26 18 0.69
27 5 0.19
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (27 bp):
AAAAATAATTTAATTCATTTTAAATTT
Found at i:1130434 original size:24 final size:23
Alignment explanation
Indices: 1130402--1130449 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1130392 TATTTATTTA
* *
1130402 TTTATCATATTATCTTGTTTATT
1 TTTATCATAATATCTTGTATATT
*
1130425 TTTATGCATAATATTTTGTATATT
1 TTTAT-CATAATATCTTGTATATT
1130449 T
1 T
1130450 ATTAATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (23 bp):
TTTATCATAATATCTTGTATATT
Found at i:1132650 original size:177 final size:179
Alignment explanation
Indices: 1132389--1132747 Score: 550
Period size: 177 Copynumber: 2.0 Consensus size: 179
1132379 ATTAAATTTT
* * *
1132389 AATATTATATATATTATATATAACATATGGGCTTAGCCCAAACATTTAAAATCCAATTAATAATT
1 AATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACATTTAAAACCCAATTAATAATT
*
1132454 TAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATT-AAAAA-TT-T-T-A-TATAAT
66 TAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTAATTATAAT
*
1132513 TTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTAATTAAAA
131 TTTATAATTATATATTATTTAAATTAATTATAAAC---TTTTTTAATTAAAA
1132565 AATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACTATTTAAAACCCAATTAATAAT
1 AATATTAAATATATTATATATAACATATGGGCTCAGCCCAAAC-ATTTAAAACCCAATTAATAAT
*
1132630 TTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATTTT
65 TTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCT--AATTAT
* *
1132695 TATTTTATAATTCTATATTATTTAAATTAATTATAAACTTTTTTAATTAAAA
128 AATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAATTAAAA
1132747 A
1 A
1132748 CATTTAATTT
Statistics
Matches: 166, Mismatches: 8, Indels: 12
0.89 0.04 0.06
Matches are distributed among these distances:
176 41 0.25
177 63 0.38
178 5 0.03
179 2 0.01
180 1 0.01
181 1 0.01
182 15 0.09
184 1 0.01
185 37 0.22
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (179 bp):
AATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACATTTAAAACCCAATTAATAATT
TAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTAATTATAAT
TTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAATTAAAA
Found at i:1134344 original size:31 final size:31
Alignment explanation
Indices: 1134309--1134382 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
1134299 TTCAACGTTC
* * *
1134309 AAGTGACCAAAACTTAATAAAACGATAACTT
1 AAGTGACCAAAACTTAAGAAAAAGATAACAT
*
1134340 AAGTGACCATAACTTAAGAAAAAGATAACAT
1 AAGTGACCAAAACTTAAGAAAAAGATAACAT
*
1134371 GAGTGACCAAAA
1 AAGTGACCAAAA
1134383 GTGTACAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.53, C:0.15, G:0.14, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAAGAAAAAGATAACAT
Found at i:1134531 original size:20 final size:20
Alignment explanation
Indices: 1134506--1134557 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1134496 GTATGATAAT
1134506 GAACCGGCTGAAAACCAGTA
1 GAACCGGCTGAAAACCAGTA
** *
1134526 GAACCGGCCAAAAACCGGTA
1 GAACCGGCTGAAAACCAGTA
* *
1134546 AAACCGGGTGAA
1 GAACCGGCTGAA
1134558 CCGGCTGAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.25, G:0.27, T:0.08
Consensus pattern (20 bp):
GAACCGGCTGAAAACCAGTA
Found at i:1137616 original size:13 final size:13
Alignment explanation
Indices: 1137597--1137633 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1137587 GTCACAACCC
1137597 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1137610 TACCCGACCCGTT
1 GACCCGACCCGTT
1137623 GACCCGACCCG
1 GACCCGACCCG
1137634 ACCCATTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1137631 original size:31 final size:31
Alignment explanation
Indices: 1137593--1137657 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1137583 ACCGGTCACA
* *
1137593 ACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCATTGACCCGACCCGTTG
*
1137624 ACCCGACCCGACCCATTGACTCGACCCGTTG
1 ACCCGACCCGACCCATTGACCCGACCCGTTG
1137655 ACC
1 ACC
1137658 GTTGACCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.18, C:0.48, G:0.18, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGACCCATTGACCCGACCCGTTG
Found at i:1137632 original size:18 final size:18
Alignment explanation
Indices: 1137611--1137651 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1137601 CGACCCGTTT
*
1137611 ACCCGACCCGTTGACCCG
1 ACCCGACCCATTGACCCG
*
1137629 ACCCGACCCATTGACTCG
1 ACCCGACCCATTGACCCG
1137647 ACCCG
1 ACCCG
1137652 TTGACCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCATTGACCCG
Found at i:1137670 original size:15 final size:15
Alignment explanation
Indices: 1137632--1137673 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1137622 TGACCCGACC
1137632 CGACCCATTGA-C-T
1 CGACCCATTGACCGT
*
1137645 CGACCCGTTGACCGT
1 CGACCCATTGACCGT
*
1137660 TGACCCATTGACCG
1 CGACCCATTGACCG
1137674 GCGTTGACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 13 0.54
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.21
Consensus pattern (15 bp):
CGACCCATTGACCGT
Found at i:1140191 original size:12 final size:12
Alignment explanation
Indices: 1140176--1140245 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
1140166 GATACATTAC
1140176 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1140188 CTGATTTCTGAT
1 CTGAATTCTGTT
1140200 CT-AGATTCTGTT
1 CTGA-ATTCTGTT
*
1140212 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
1140224 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1140236 TTGATTTCTG
1 CTGAATTCTG
1140246 ATATCTCCGT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 3 0.07
12 41 0.89
13 2 0.04
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1140207 original size:24 final size:24
Alignment explanation
Indices: 1140139--1140247 Score: 116
Period size: 24 Copynumber: 4.5 Consensus size: 24
1140129 AAATATTTTA
*
1140139 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* * *
1140163 TCTGA-TACATTACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
1140187 TCTGATTTCTGATCT-AGATTCTGT
1 TCTGATTTCTGATCTGA-ATTCTGT
*
1140211 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
1140235 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1140248 ATCTCCGTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
23 3 0.04
24 64 0.90
25 4 0.06
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:1140244 original size:48 final size:48
Alignment explanation
Indices: 1140139--1140247 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
1140129 AAATATTTTA
* * *
1140139 TCTGATTTCCGA-CTTGAATTCTGTTCTGATACATTACCTGAATTCTGT
1 TCTGATTTCTGATCTAG-ATTCTGTTCTGATACATGACCTGAATTCTGT
*
1140187 TCTGATTTCTGATCTAGATTCTGTTCTGATATC-TGATCTGAATTCTGT
1 TCTGATTTCTGATCTAGATTCTGTTCTGATA-CATGACCTGAATTCTGT
*
1140235 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1140248 ATCTCCGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 50 0.93
49 4 0.07
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTAGATTCTGTTCTGATACATGACCTGAATTCTGT
Found at i:1142369 original size:8 final size:8
Alignment explanation
Indices: 1142356--1142402 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
1142346 AACCCGGCCC
1142356 GACCCGTT
1 GACCCGTT
1142364 GACCCGTT
1 GACCCGTT
1142372 GA-CCGTT
1 GACCCGTT
1142379 GACCGACGTT
1 GACC--CGTT
1142389 GACCACTGTT
1 GACC-C-GTT
1142399 GACC
1 GACC
1142403 AAAACTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.20
8 11 0.31
9 2 0.06
10 15 0.43
ACGTcount: A:0.17, C:0.34, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:1142379 original size:15 final size:16
Alignment explanation
Indices: 1142359--1142392 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1142349 CCGGCCCGAC
1142359 CCGTTGACC-CGTTGA
1 CCGTTGACCACGTTGA
1142374 CCGTTGACCGACGTTGA
1 CCGTTGACC-ACGTTGA
1142391 CC
1 CC
1142393 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (16 bp):
CCGTTGACCACGTTGA
Found at i:1143710 original size:18 final size:18
Alignment explanation
Indices: 1143684--1143724 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1143674 AATTGTTCGA
* *
1143684 AAGACTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
*
1143702 AAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
1143720 AAGAT
1 AAGAT
1143725 CGGATGGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:1144903 original size:12 final size:12
Alignment explanation
Indices: 1144888--1144956 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1144878 GATACATTAC
1144888 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1144900 CTGATTTCTGAT
1 CTGAATTCTGTT
1144912 CT-AGATTCTGTT
1 CTGA-ATTCTGTT
*
1144924 -TG-ATATCTGAT
1 CTGAAT-TCTGTT
1144935 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1144947 TTGATTTCTG
1 CTGAATTCTG
1144957 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
10 2 0.05
11 7 0.16
12 33 0.75
13 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1144932 original size:23 final size:23
Alignment explanation
Indices: 1144888--1144958 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 23
1144878 GATACATTAC
1144888 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTT-TGATTTCTGAT
*
1144912 CT-AGATTCTGTTTGATATCTGAT
1 CTGA-ATTCTGTTTGATTTCTGAT
1144935 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTG-TTTGATTTCTGAT
1144959 ATCTCCGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 19 0.45
24 23 0.55
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (23 bp):
CTGAATTCTGTTTGATTTCTGAT
Found at i:1151229 original size:29 final size:31
Alignment explanation
Indices: 1151155--1151231 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 31
1151145 AATTTTTAGG
*
1151155 AAAATTACCACTTTGGTCCCTAAACTTTTCCA
1 AAAATTA-TACTTTGGTCCCTAAACTTTTCCA
*
1151187 AAATTTATACTTTGG-CCACTAAAC-TTT-CA
1 AAAATTATACTTTGGTCC-CTAAACTTTTCCA
*
1151216 AAAATTATATTTTGGT
1 AAAATTATACTTTGGT
1151232 AATTTTGGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 15 0.38
30 5 0.13
31 13 0.33
32 6 0.15
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (31 bp):
AAAATTATACTTTGGTCCCTAAACTTTTCCA
Found at i:1153569 original size:15 final size:15
Alignment explanation
Indices: 1153521--1153561 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1153511 ATCTATCTTT
*
1153521 ATCAGCATCACCATC
1 ATCACCATCACCATC
* *
1153536 ATAACCACCACCATC
1 ATCACCATCACCATC
1153551 ATCACCATCAC
1 ATCACCATCAC
1153562 TATTATCATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.37, C:0.44, G:0.02, T:0.17
Consensus pattern (15 bp):
ATCACCATCACCATC
Found at i:1160039 original size:95 final size:94
Alignment explanation
Indices: 1159871--1160053 Score: 226
Period size: 95 Copynumber: 1.9 Consensus size: 94
1159861 GATGTGGGTA
* * * * **
1159871 TCGATACTATGAGGAAGATATCGATACCATTGATTTAGAATGCAGAAATGGTATTGATACTGTGA
1 TCGATACTAAGAGGAAGATATCAATACCATGGATTCAGAATGCAGAAATGGTATTGATACTGAAA
* *
1159936 TGGAGTATC-GATACTATAGTATATGAGTG
66 GGGAGTATCAG-TACCATAGTATATGAGTG
* *
1159965 TCGATACTAAGAGGAAGGTATTAATACCATGGATTCCAGAATGTCA-AAATGGTATTGATACTGA
1 TCGATACTAAGAGGAAGATATCAATACCATGGATT-CAGAATG-CAGAAATGGTATTGATACTGA
*
1160029 AAGGGGGTATCAGTACCATAGTATA
64 AAGGGAGTATCAGTACCATAGTATA
1160054 GAAGAATCGA
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
94 30 0.40
95 42 0.56
96 3 0.04
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.30
Consensus pattern (94 bp):
TCGATACTAAGAGGAAGATATCAATACCATGGATTCAGAATGCAGAAATGGTATTGATACTGAAA
GGGAGTATCAGTACCATAGTATATGAGTG
Found at i:1160438 original size:54 final size:53
Alignment explanation
Indices: 1160407--1160747 Score: 390
Period size: 54 Copynumber: 6.4 Consensus size: 53
1160397 TATGAATTTT
1160407 CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATA-TTGATGAACAAC
1 CGTATAGGCACTAAGTGTGCAACCCAC-AAATTCATCATA-AGTTGATGAACAAC
* * *
1160461 TGTATGGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAAC
1 CGTATAGGCACTAAGTGTGCAACCCAC-AAATTCATCATAAGTTGATGAACAAC
* *
1160515 CATATAGGCACTAAGTGTGCAACCCACGAAATTTATCATATA-TTGATGAACAAC
1 CGTATAGGCACTAAGTGTGCAACCCAC-AAATTCATCATA-AGTTGATGAACAAC
*
1160569 CGTATAGGCACTAAGTGT--AACCCACAGAATTCATCATATGTTGATGAACAAC
1 CGTATAGGCACTAAGTGTGCAACCCACA-AATTCATCATAAGTTGATGAACAAC
* * *
1160621 CGTATAGGCACTAAGTGTGCAATCCACATTATTCATCATAGGTTGATGAACGAA-
1 CGTATAGGCACTAAGTGTGCAACCCACA-AATTCATCATAAGTTGATGAAC-AAC
* * * **
1160675 CGTATAGGCACTATATGTGTG-AA-CCACAGAATTCATAATATGTTTATGAATGAC
1 CGTATAGGCACTA-A-GTGTGCAACCCACA-AATTCATCATAAGTTGATGAACAAC
* *
1160729 CGTATAGGTACTACGTGTG
1 CGTATAGGCACTAAGTGTG
1160748 AATCTCAACG
Statistics
Matches: 251, Mismatches: 26, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
51 1 0.00
52 52 0.21
53 1 0.00
54 187 0.75
55 5 0.02
56 5 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (53 bp):
CGTATAGGCACTAAGTGTGCAACCCACAAATTCATCATAAGTTGATGAACAAC
Found at i:1160558 original size:108 final size:106
Alignment explanation
Indices: 1160407--1160747 Score: 472
Period size: 108 Copynumber: 3.2 Consensus size: 106
1160397 TATGAATTTT
*
1160407 CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAACTGTATGGGCAC
1 CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAAC-GTATAGGCAC
*
1160472 TAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAAC
65 TAAGTGTG-AACCCACAGAATTCATCATATGTTGATGAACAAC
* *
1160515 CATATAGGCACTAAGTGTGCAACCCACGAAATTTATCATATATTGATGAACAACCGTATAGGCAC
1 CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAA-CGTATAGGCAC
1160580 TAAGTGT-AACCCACAGAATTCATCATATGTTGATGAACAAC
65 TAAGTGTGAACCCACAGAATTCATCATATGTTGATGAACAAC
* * **
1160621 CGTATAGGCACTAAGTGTGCAATCCAC-ATTATTCATCATAGGTTGATGAACGAACGTATAGGCA
1 CGTATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATATTGATGAAC-AACGTATAGGCA
* * **
1160685 CTATATGTGTGAA-CCACAGAATTCATAATATGTTTATGAATGAC
64 CTA-A-GTGTGAACCCACAGAATTCATCATATGTTGATGAACAAC
* *
1160729 CGTATAGGTACTACGTGTG
1 CGTATAGGCACTAAGTGTG
1160748 AATCTCAACG
Statistics
Matches: 211, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
105 1 0.00
106 89 0.42
107 3 0.01
108 115 0.55
109 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (106 bp):
CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATATTGATGAACAACGTATAGGCACT
AAGTGTGAACCCACAGAATTCATCATATGTTGATGAACAAC
Found at i:1160733 original size:160 final size:161
Alignment explanation
Indices: 1160380--1160746 Score: 458
Period size: 160 Copynumber: 2.3 Consensus size: 161
1160370 TGCAAACTAA
* ***
1160380 GAAATTCATAATAAGTTTATGAATTTTCGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCA
1 GAAATTCATAATATGTTTATGAATAACCGTATAGGCACTAAGTGT-CAACCCACGAAATTCATCA
* * *
1160445 TATATTGATGAACAACTGTATGGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGA
65 TATATTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACAAAATTCATCATAGGTTGATGA
1160510 ACAACCATATAGGCACTAAGTGTGCAACCCAC
130 ACAACCATATAGGCACTAAGTGTGCAACCCAC
* * * * *
1160542 GAAATTTATCATATATTGATGAACAACCGTATAGGCACTAAGTGT-AACCCAC-AGAATTCATCA
1 GAAATTCATAATATGTTTATGAATAACCGTATAGGCACTAAGTGTCAACCCACGA-AATTCATCA
* * **
1160605 TATGTTGATGAACAACCGTATAGGCACTAAGTGTGCAATCCACATTATTCATCATAGGTTGATGA
65 TATATTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACAAAATTCATCATAGGTTGATGA
*
1160670 ACGAA-CGTATAGGCACTATATGTGTG-AA-CCAC
130 AC-AACCATATAGGCACTA-A-GTGTGCAACCCAC
* * *
1160702 -AGAATTCATAATATGTTTATGAATGACCGTATAGGTACTACGTGT
1 GA-AATTCATAATATGTTTATGAATAACCGTATAGGCACTAAGTGT
1160747 GAATCTCAAC
Statistics
Matches: 175, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
159 2 0.01
160 127 0.73
161 5 0.03
162 41 0.23
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (161 bp):
GAAATTCATAATATGTTTATGAATAACCGTATAGGCACTAAGTGTCAACCCACGAAATTCATCAT
ATATTGATGAACAACCGTATAGGCACTAAGTGTGCAACCCACAAAATTCATCATAGGTTGATGAA
CAACCATATAGGCACTAAGTGTGCAACCCAC
Found at i:1167000 original size:94 final size:94
Alignment explanation
Indices: 1166810--1167006 Score: 236
Period size: 94 Copynumber: 2.1 Consensus size: 94
1166800 TGTGGAATAA
* * * * * *
1166810 TATCGATAATATGAGAAATGTATCGATACCATTGATTCCAGAATTCATAAATGGTATCGATATTG
1 TATCGATACTAAGAGGAAGGTATCGATACCATGGATTCCAGAATTCATAAATGGTATCGATACTG
* * * **
1166875 TGATGGAGTATCGGTACTATAGATATGAG
66 TAAAGGAGTATCGGTACCATAGATAAAAG
* *
1166904 TATTGATACTAAGAGGAAGGTATCGATACCATGGATTCCAGAGTGTCA-AAATGGTATCGATACT
1 TATCGATACTAAGAGGAAGGTATCGATACCATGGATTCCAGAAT-TCATAAATGGTATCGATACT
*
1166968 G-AAAGGGGTATCGGTACCATAGTATAAAAG
65 GTAAAGGAGTATCGGTACCATAG-ATAAAAG
1166998 TATCGATAC
1 TATCGATAC
1167007 CAGGGTAGGG
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
93 17 0.20
94 66 0.77
95 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (94 bp):
TATCGATACTAAGAGGAAGGTATCGATACCATGGATTCCAGAATTCATAAATGGTATCGATACTG
TAAAGGAGTATCGGTACCATAGATAAAAG
Found at i:1167449 original size:54 final size:54
Alignment explanation
Indices: 1167402--1167844 Score: 449
Period size: 54 Copynumber: 8.2 Consensus size: 54
1167392 TGAATTTCCT
* * * *
1167402 TATAGGCACTAAATGTGCATCCCAAAAAATTGATCATATGTTAATGAACAACTG
1 TATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTAATGAACAACCG
***
1167456 TATAGGCACTAAGTGTGCAACCCACGTAATTCATCATATGTTAATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTAATGAACAACCG
* * *
1167510 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTAATGAACAACCG
* * * * * *
1167564 TATAGGCACCAAGTGTGCAACCCAAGAAATTCATCATATATTGATGATCAACCA
1 TATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTAATGAACAACCG
* *** * *
1167618 TATAAGCACTAAGTGTGCAACCCATGGAATTCATCATATATTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTAATGAACAACCG
*** * * * *
1167672 TATAGGCACTAAGTGTGCAACCCATGGAATTAATCATATATTGATGAACAACCA
1 TATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTAATGAACAACCG
* ** * * * *
1167726 TATAGGCACTAAGTGTGTAACCCACGAAATTCATCATAGGTTGATGAACGATCG
1 TATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTAATGAACAACCG
* * * * * * * **
1167780 TATAGACACTATATATGTG-AA-CCACATAATTCATAATATTTTTATGAATGACCG
1 TATAGGCACTA-A-GTGTGCAACCCAAAAAATTCATCATATGTTAATGAACAACCG
1167834 TATAGGCACTA
1 TATAGGCACTA
1167845 TGTGCGCATG
Statistics
Matches: 341, Mismatches: 46, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
54 334 0.98
55 3 0.01
56 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTAATGAACAACCG
Found at i:1167546 original size:108 final size:108
Alignment explanation
Indices: 1167402--1167844 Score: 532
Period size: 108 Copynumber: 4.1 Consensus size: 108
1167392 TGAATTTCCT
* * * * * * *
1167402 TATAGGCACTAAATGTGCATCCCAAAAAATTGATCATATGTTAATGAACAACTGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGCACTA
* * *
1167467 AGTGTGCAACCCACGTAATTCATCATATGTTAATGAACAACCG
66 AGTGTGCAACCCACGTAATTCATCATATATTGATGAACAACCA
*
1167510 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGCACCA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGCACTA
* * *
1167575 AGTGTGCAACCCAAGAAATTCATCATATATTGATGATCAACCA
66 AGTGTGCAACCCACGTAATTCATCATATATTGATGAACAACCA
* ** *
1167618 TATAAGCACTAAGTGTGCAACCCATGGAATTCATCATATATTGATGAACAACCGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGCACTA
* * *
1167683 AGTGTGCAACCCATGGAATTAATCATATATTGATGAACAACCA
66 AGTGTGCAACCCACGTAATTCATCATATATTGATGAACAACCA
* * * * *
1167726 TATAGGCACTAAGTGTGTAACCCAC-GAAATTCATCATAGGTTGATGAACGATCGTATAGACACT
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACAACCGTATAGGCACT
* * * * * ** *
1167790 ATATATGTG-AA-CCACATAATTCATAATATTTTTATGAATGACCG
65 A-A-GTGTGCAACCCACGTAATTCATCATATATTGATGAACAACCA
1167834 TATAGGCACTA
1 TATAGGCACTA
1167845 TGTGCGCATG
Statistics
Matches: 290, Mismatches: 42, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
107 1 0.00
108 282 0.97
109 3 0.01
110 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (108 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGCACTA
AGTGTGCAACCCACGTAATTCATCATATATTGATGAACAACCA
Found at i:1167651 original size:162 final size:162
Alignment explanation
Indices: 1167402--1167774 Score: 539
Period size: 162 Copynumber: 2.3 Consensus size: 162
1167392 TGAATTTCCT
* * * * * ** *
1167402 TATAGGCACTAAATGTGCATCCCAAAAAATTGATCATATGTTAATGAACAACTGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACAACCATATAAGCACTA
* *
1167467 AGTGTGCAACCCACGTAATTCATCATATGTTAATGAACAACCGTATAGGCACTAAGTGTGCAACC
66 AGTGTGCAACCCACGGAATTCATCATATATTAATGAACAACCGTATAGGCACTAAGTGTGCAACC
* * *
1167532 CACAGAATTCATCATATGTTGATGAACAACCG
131 CACAGAATTAATCATATATTGATGAACAACCA
* * *
1167564 TATAGGCACCAAGTGTGCAACCCAAGAAATTCATCATATATTGATGATCAACCATATAAGCACTA
1 TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACAACCATATAAGCACTA
* *
1167629 AGTGTGCAACCCATGGAATTCATCATATATTGATGAACAACCGTATAGGCACTAAGTGTGCAACC
66 AGTGTGCAACCCACGGAATTCATCATATATTAATGAACAACCGTATAGGCACTAAGTGTGCAACC
**
1167694 CATGGAATTAATCATATATTGATGAACAACCA
131 CACAGAATTAATCATATATTGATGAACAACCA
* * *
1167726 TATAGGCACTAAGTGTGTAACCCACGAAATTCATCATAGGTTGATGAAC
1 TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAAC
1167775 GATCGTATAG
Statistics
Matches: 185, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
162 185 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (162 bp):
TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACAACCATATAAGCACTA
AGTGTGCAACCCACGGAATTCATCATATATTAATGAACAACCGTATAGGCACTAAGTGTGCAACC
CACAGAATTAATCATATATTGATGAACAACCA
Found at i:1167813 original size:162 final size:160
Alignment explanation
Indices: 1167402--1167844 Score: 532
Period size: 162 Copynumber: 2.7 Consensus size: 160
1167392 TGAATTTCCT
* * * * * *
1167402 TATAGGCACTAAATGTGCATCCCAAAAAATTGATCATATGTTAATGAACAACTGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACAAC-GTATAGACACTA
* *
1167467 AGTGTGCAACCCACGTAATTCATCATATGTTAATGAACAACCGTATAGGCACTAAGTGTGCAACC
65 AGTGTGCAA-CCACATAATTCATCATATATTAATGAACAACCGTATAGGCACTAAGTGTGCAACC
* * *
1167532 CACAGAATTCATCATATGTTGATGAACAACCG
129 CACAGAATTAATCATATATTGATGAACAACCA
* * * *
1167564 TATAGGCACCAAGTGTGCAACCCAAGAAATTCATCATATATTGATGATCAACCATATA-AGCACT
1 TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACAA-CGTATAGA-CACT
*
1167628 AAGTGTGCAACC-CATGGAATTCATCATATATTGATGAACAACCGTATAGGCACTAAGTGTGCAA
64 AAGTGTGCAACCACAT--AATTCATCATATATTAATGAACAACCGTATAGGCACTAAGTGTGCAA
**
1167692 CCCATGGAATTAATCATATATTGATGAACAACCA
127 CCCACAGAATTAATCATATATTGATGAACAACCA
* * * *
1167726 TATAGGCACTAAGTGTGTAACCCACGAAATTCATCATAGGTTGATGAACGATCGTATAGACACTA
1 TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAAC-AACGTATAGACACTA
* * * * **
1167791 TATATGTG-AACCACATAATTCATAATATTTTTATGAATGACCGTATAGGCACTA
65 -A-GTGTGCAACCACATAATTCATCATATATTAATGAACAACCGTATAGGCACTA
1167845 TGTGCGCATG
Statistics
Matches: 240, Mismatches: 32, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
160 2 0.01
161 2 0.01
162 221 0.92
163 8 0.03
164 7 0.03
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (160 bp):
TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACAACGTATAGACACTAA
GTGTGCAACCACATAATTCATCATATATTAATGAACAACCGTATAGGCACTAAGTGTGCAACCCA
CAGAATTAATCATATATTGATGAACAACCA
Found at i:1170036 original size:4 final size:4
Alignment explanation
Indices: 1170029--1170075 Score: 53
Period size: 4 Copynumber: 11.5 Consensus size: 4
1170019 TTGTAAATAA
1170029 AAAT AAAT AAAT AAAT -AAT AATAT AAAT AAA- ATAAT AATAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT A-AAT AA-AT AAAT AA
1170076 TTTATAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 4 0.11
4 25 0.66
5 9 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:1170063 original size:17 final size:16
Alignment explanation
Indices: 1170022--1170089 Score: 86
Period size: 17 Copynumber: 4.2 Consensus size: 16
1170012 CCTATTTTTG
1170022 TAAATAAA-AATAA-A
1 TAAATAAATAATAATA
1170036 TAAATAAATAATAATA
1 TAAATAAATAATAATA
1170052 TAAATAAAATAATAATA
1 TAAAT-AAATAATAATA
* *
1170069 TAAATAATTTATAATAA
1 TAAATAAATAATAAT-A
1170086 TAAA
1 TAAA
1170090 CTATATAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.17
15 5 0.10
16 14 0.29
17 21 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAATAAATAATAATA
Found at i:1170140 original size:15 final size:15
Alignment explanation
Indices: 1170103--1170141 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
1170093 TATAACATAT
*
1170103 ATTATATTTTCAAAA
1 ATTATGTTTTCAAAA
1170118 ATAATATGTTTTCAAAA
1 AT--TATGTTTTCAAAA
1170135 ATTATGT
1 ATTATGT
1170142 ATTATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.33
17 14 0.67
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (15 bp):
ATTATGTTTTCAAAA
Found at i:1170285 original size:77 final size:76
Alignment explanation
Indices: 1170176--1170408 Score: 235
Period size: 77 Copynumber: 3.0 Consensus size: 76
1170166 TTTAAAAAAC
*
1170176 TATATATATGTTTTCAAAATAC-GTTTTCAAAACTATAT-TATATACGTTTTCAAAAACCATTTT
1 TATATATATATTTTCAAAA-ACTGTTTTCAAAACTATATAT-TATACGTTTTCAAAAACCATTTT
*
1170239 TTAAAACTATATA
64 TAAAAACTATATA
*
1170252 TAT-TATACGT-TTTTCAAAAACGTGTTTTCAAAACTATATATTATACTTTTTCAAAAA-CATAT
1 TATATATA--TATTTTCAAAAAC-TGTTTTCAAAACTATATATTATACGTTTTCAAAAACCAT-T
* * *
1170314 TTTCAAAGCCATACTA
62 TTTAAAAACTATA-TA
* * * * *
1170330 TATATATATATATTCAAAAACTGATTTTTAAAAACTATATATTATATGCTTTC-AAAACCGTTTT
1 TATATATATATTTTCAAAAACTG--TTTTCAAAACTATATATTATACGTTTTCAAAAACCATTTT
1170394 CTAAAAACTATATA
64 -TAAAAACTATATA
1170408 T
1 T
1170409 TACATGTTTT
Statistics
Matches: 131, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
75 6 0.05
76 15 0.11
77 46 0.35
78 26 0.20
79 38 0.29
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.42
Consensus pattern (76 bp):
TATATATATATTTTCAAAAACTGTTTTCAAAACTATATATTATACGTTTTCAAAAACCATTTTTA
AAAACTATATA
Found at i:1170317 original size:37 final size:36
Alignment explanation
Indices: 1170171--1170410 Score: 170
Period size: 37 Copynumber: 6.4 Consensus size: 36
1170161 ATCTTTTTAA
* *
1170171 AAAACTATATA-TAT--GTTTTCAAAATAC-GTTTTC
1 AAAACTATATATTATACTTTTTCAAAA-ACATTTTTC
* *
1170204 AAAACTATAT-TATATACGTTTTCAAAAACCATTTTTT
1 AAAACTATATAT-TATACTTTTTCAAAAA-CATTTTTC
*
1170241 AAAACTATATATATTATACGTTTTTCAAAAACGTGTTTTC
1 AAAAC--TATATATTATAC-TTTTTCAAAAACAT-TTTTC
1170281 AAAACTATATATTATACTTTTTCAAAAACATATTTTC
1 AAAACTATATATTATACTTTTTCAAAAACAT-TTTTC
* * *
1170318 AAAGCCATACTATATATATA-TATATTCAAAAACTGATTTTTA
1 AAA-AC-TA-TATAT-TATACT-TTTTCAAAAAC--ATTTTTC
* * * *
1170360 AAAACTATATATTATA-TGCTTTCAAAACCGTTTTCTA
1 AAAACTATATATTATACT-TTTTCAAAAACATTTT-TC
1170397 AAAACTATATATTA
1 AAAACTATATATTA
1170411 CATGTTTTCG
Statistics
Matches: 172, Mismatches: 16, Indels: 34
0.77 0.07 0.15
Matches are distributed among these distances:
33 10 0.06
34 3 0.02
35 1 0.01
36 15 0.09
37 46 0.27
38 26 0.15
39 19 0.11
40 28 0.16
41 15 0.09
42 7 0.04
43 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.41
Consensus pattern (36 bp):
AAAACTATATATTATACTTTTTCAAAAACATTTTTC
Found at i:1170437 original size:37 final size:37
Alignment explanation
Indices: 1170359--1170441 Score: 89
Period size: 37 Copynumber: 2.3 Consensus size: 37
1170349 ACTGATTTTT
* * * *
1170359 AAAAACTATATATTATATGCTTTCAAAACCGTTTTCT
1 AAAAACTATATATTACATGCTTTCAAAACCATTTCCA
* *
1170396 AAAAACTATATATTACATGTTTTCGAAAA-TATTTCCA
1 AAAAACTATATATTACATGCTTTC-AAAACCATTTCCA
1170433 AAAAA-TATA
1 AAAAACTATA
1170442 CTATATTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
36 4 0.10
37 31 0.79
38 4 0.10
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (37 bp):
AAAAACTATATATTACATGCTTTCAAAACCATTTCCA
Found at i:1171133 original size:72 final size:72
Alignment explanation
Indices: 1171020--1171160 Score: 185
Period size: 72 Copynumber: 2.0 Consensus size: 72
1171010 GAAGTTAAGC
* * * * * *
1171020 CAATCTATTGGGCATGATATCTTTTGTTGTGAAATTTAAATCGTAGGTGACTCATTCATTGTGAA
1 CAATCTATTGGGCATGATATCCTTCGTCGCGAAATTGAAATCGTAGGTGACTCATTCATCGTGAA
1171085 GTTGGAT
66 GTTGGAT
* * *
1171092 CAATCT-TCTGGGCATGATATCCTTCGTCGCGAAGTTGAAATCGTGGGTGACTCATTCGTCGTGA
1 CAATCTAT-TGGGCATGATATCCTTCGTCGCGAAATTGAAATCGTAGGTGACTCATTCATCGTGA
1171156 AGTTG
65 AGTTG
1171161 AGTCCCAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 1 0.02
72 58 0.98
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (72 bp):
CAATCTATTGGGCATGATATCCTTCGTCGCGAAATTGAAATCGTAGGTGACTCATTCATCGTGAA
GTTGGAT
Found at i:1185401 original size:22 final size:22
Alignment explanation
Indices: 1185376--1185424 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1185366 CACCACAGCT
1185376 CACATAATTTG-CACCGAA-GTAC
1 CACATAATTTGTC-CCGAATG-AC
1185398 CACAT-ATTTGTCCCGAATGAC
1 CACATAATTTGTCCCGAATGAC
1185419 CACATA
1 CACATA
1185425 GTTTTGCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (22 bp):
CACATAATTTGTCCCGAATGAC
Found at i:1185477 original size:23 final size:23
Alignment explanation
Indices: 1185404--1185477 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
1185394 GTACCACATA
* *
1185404 TTTGTCCCGAATGACCACATAGT
1 TTTGTTCCGAATGACCACTTAGT
* **
1185427 TTTGCTCTAAATGACCACTTAGT
1 TTTGTTCCGAATGACCACTTAGT
1185450 TTTGTTCCGAATGACCACTTAGT
1 TTTGTTCCGAATGACCACTTAGT
1185473 TTTGT
1 TTTGT
1185478 CCCAAACATA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (23 bp):
TTTGTTCCGAATGACCACTTAGT
Found at i:1186138 original size:22 final size:22
Alignment explanation
Indices: 1186113--1186154 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1186103 CCAATATTTT
1186113 TCTTCTATGGTA-CTGATACCTC
1 TCTTCTATGGTATC-GATACCTC
1186135 TCTTCTATGGTATCGATACC
1 TCTTCTATGGTATCGATACC
1186155 CACTTCAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.40
Consensus pattern (22 bp):
TCTTCTATGGTATCGATACCTC
Found at i:1192831 original size:19 final size:20
Alignment explanation
Indices: 1192794--1192838 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1192784 ACATTTTTTA
1192794 AATAAAAATAAATAAATAAT
1 AATAAAAATAAATAAATAAT
* *
1192814 AATATAAAT-AATATATAAT
1 AATAAAAATAAATAAATAAT
1192833 AATAAA
1 AATAAA
1192839 CTATGTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAAAATAAATAAATAAT
Found at i:1192948 original size:20 final size:22
Alignment explanation
Indices: 1192923--1192969 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
1192913 ATCATTTTAA
1192923 AAAACTATA-TATAT-GTTTTC
1 AAAACTATATTATATAGTTTTC
1192943 AAAACTATATTATATACGTTTTC
1 AAAACTATATTATATA-GTTTTC
1192966 AAAA
1 AAAA
1192970 ACCATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.38
21 5 0.21
23 10 0.42
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (22 bp):
AAAACTATATTATATAGTTTTC
Found at i:1192969 original size:58 final size:59
Alignment explanation
Indices: 1192872--1192983 Score: 140
Period size: 57 Copynumber: 1.9 Consensus size: 59
1192862 TTCAAAAAAA
*
1192872 ATATGTTTTCAAAAATTATATATTATATATAGTTCCAAAAAATCATTTTAAAAAACTATAT
1 ATATGTTTTCAAAAA-TATATATTATATATAGTTCC-AAAAACCATTTTAAAAAACTATAT
* * *
1192933 ATATGTTTTC-AAAA-CTATATTATATA-CGTTTTCAAAAACCATTTTAAAAAA
1 ATATGTTTTCAAAAATATATATTATATATAG-TTCCAAAAACCATTTTAAAAAA
1192984 AAAAACTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
57 18 0.39
58 14 0.30
60 4 0.09
61 10 0.22
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (59 bp):
ATATGTTTTCAAAAATATATATTATATATAGTTCCAAAAACCATTTTAAAAAACTATAT
Found at i:1193088 original size:38 final size:38
Alignment explanation
Indices: 1193027--1193129 Score: 136
Period size: 38 Copynumber: 2.7 Consensus size: 38
1193017 TTAAAACCAT
*
1193027 ACTATATATATATAT-ATATTCAAAAATCGTTTTTTAAAA
1 ACTATATAT-TATATGAT-TTCAAAAATCGTTTTCTAAAA
* *
1193066 ACTATATATTATATGCTTTCAAAAACCGTTTTCTAAAA
1 ACTATATATTATATGATTTCAAAAATCGTTTTCTAAAA
* *
1193104 ACTATATATTACATGTTTTCAAAAAT
1 ACTATATATTATATGATTTCAAAAAT
1193130 ATTTCCAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 47 0.82
39 10 0.18
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.42
Consensus pattern (38 bp):
ACTATATATTATATGATTTCAAAAATCGTTTTCTAAAA
Found at i:1193140 original size:36 final size:36
Alignment explanation
Indices: 1193062--1193145 Score: 98
Period size: 38 Copynumber: 2.3 Consensus size: 36
1193052 ATCGTTTTTT
* *
1193062 AAAAACTATATATTATATGCTTTCAAAAACCGTTTTCT
1 AAAAACTATATATTACATGCTTTCAAAAA-C-TTTTCC
*
1193100 AAAAACTATATATTACATGTTTTCAAAAA-TATTTCC
1 AAAAACTATATATTACATGCTTTCAAAAACT-TTTCC
*
1193136 AAAAATTATA
1 AAAAACTATA
1193146 CTATATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 1 0.02
36 13 0.32
38 27 0.66
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (36 bp):
AAAAACTATATATTACATGCTTTCAAAAACTTTTCC
Found at i:1194648 original size:25 final size:26
Alignment explanation
Indices: 1194588--1194648 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
1194578 TATATTTATT
*
1194588 TTTTAATTTTTATATATAATCATTAA
1 TTTTAATTTTTATATATAATCAATAA
* *
1194614 -ATTAATTTTT-TAATATAATTAATAA
1 TTTTAATTTTTAT-ATATAATCAATAA
1194639 TTTTAATTTT
1 TTTTAATTTT
1194649 ATTTAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 20 0.69
26 8 0.28
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTAATTTTTATATATAATCAATAA
Found at i:1194836 original size:25 final size:24
Alignment explanation
Indices: 1194808--1194860 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1194798 ACTTTTATAC
* * *
1194808 ATATTAAATTTATTATTATTTTTAA
1 ATATTAAATTAACTA-TATTTTAAA
*
1194833 ATATTATATTAACTATATTTTAAA
1 ATATTAAATTAACTATATTTTAAA
1194857 ATAT
1 ATAT
1194861 ATATGAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATTAAATTAACTATATTTTAAA
Found at i:1200796 original size:35 final size:35
Alignment explanation
Indices: 1200747--1200844 Score: 135
Period size: 35 Copynumber: 2.8 Consensus size: 35
1200737 AATTTTCATT
* *
1200747 GTTCGAACAGTGCAGAAAAATATAGTGCATATTTG
1 GTTCGAACAGTGCAGAAAAATACAGTGCAGATTTG
* * *
1200782 GTTCAAACATTGCAGAAAAATACAGTGTAGATTTG
1 GTTCGAACAGTGCAGAAAAATACAGTGCAGATTTG
*
1200817 CTTCGAACAGTGCAG-AAAATACAGTGCA
1 GTTCGAACAGTGCAGAAAAATACAGTGCA
1200845 ATGCGGATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 12 0.22
35 42 0.78
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (35 bp):
GTTCGAACAGTGCAGAAAAATACAGTGCAGATTTG
Found at i:1205866 original size:21 final size:21
Alignment explanation
Indices: 1205842--1205933 Score: 70
Period size: 21 Copynumber: 4.6 Consensus size: 21
1205832 TCCTAATGCT
*
1205842 TAAACCTTAAAACTTAAACCA
1 TAAACCTTAAAACTTAAACCC
1205863 TAAA-CTCT--AACTTAAACCC
1 TAAACCT-TAAAACTTAAACCC
* **
1205882 CAAACC-CCAAACTCTAAACCC
1 TAAACCTTAAAACT-TAAACCC
* *
1205903 TAAACTTTAACACTTAAACCC
1 TAAACCTTAAAACTTAAACCC
1205924 T-AA-CTTAAAA
1 TAAACCTTAAAA
1205934 TTCTAAAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
19 18 0.33
20 9 0.16
21 24 0.44
22 4 0.07
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCTTAAAACTTAAACCC
Found at i:1205940 original size:20 final size:22
Alignment explanation
Indices: 1205890--1205940 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
1205880 CCCAAACCCC
1205890 AAACTCTAAACCCTAAACTTTA
1 AAACTCTAAACCCTAAACTTTA
*
1205912 ACACT-TAAACCCT-AAC-TTA
1 AAACTCTAAACCCTAAACTTTA
*
1205931 AAATTCTAAA
1 AAACTCTAAA
1205941 ATTAATAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 6 0.24
20 7 0.28
21 8 0.32
22 4 0.16
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (22 bp):
AAACTCTAAACCCTAAACTTTA
Found at i:1206847 original size:22 final size:22
Alignment explanation
Indices: 1206812--1206874 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
1206802 TTACGTAACA
**
1206812 CCACAACACGCTATAAATTGAG
1 CCACAACAAACTATAAATTGAG
*
1206834 CCGCAACAAACTATAAATTGAG
1 CCACAACAAACTATAAATTGAG
1206856 CCACAACAAACTATAAATT
1 CCACAACAAACTATAAATT
1206875 ATCTGAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.19
Consensus pattern (22 bp):
CCACAACAAACTATAAATTGAG
Found at i:1207043 original size:16 final size:17
Alignment explanation
Indices: 1207022--1207057 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1207012 TAAACGTTAT
1207022 TTTAAAATTAAATT-AA
1 TTTAAAATTAAATTGAA
*
1207038 TTTAAATTTAAATTGAA
1 TTTAAAATTAAATTGAA
1207055 TTT
1 TTT
1207058 TTTTCATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAATTAAATTGAA
Found at i:1218739 original size:25 final size:25
Alignment explanation
Indices: 1218692--1218744 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1218682 TATGTTTATT
* *
1218692 TTATTTTATATTTGTAATGTTTTTA
1 TTATTTTATATTTGTAATATTTTAA
* *
1218717 TTATTTTATATTTTTATTATTTTAA
1 TTATTTTATATTTGTAATATTTTAA
1218742 TTA
1 TTA
1218745 AGCTTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (25 bp):
TTATTTTATATTTGTAATATTTTAA
Found at i:1223614 original size:39 final size:39
Alignment explanation
Indices: 1223536--1223614 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
1223526 TTGTTTTTAA
* * *
1223536 AGAATATTTTATCTCACTTAAGATGGTTTCTCTCGAAAC
1 AGAATATTTTATCTCACTTAAGATAGTTTCACTCAAAAC
* * *
1223575 AGAATATTTTA-CTCCGCTTGAGATAGTTTCACTTAAAAC
1 AGAATATTTTATCT-CACTTAAGATAGTTTCACTCAAAAC
1223614 A
1 A
1223615 AGAGTTGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (39 bp):
AGAATATTTTATCTCACTTAAGATAGTTTCACTCAAAAC
Found at i:1223724 original size:78 final size:77
Alignment explanation
Indices: 1223621--1224150 Score: 401
Period size: 78 Copynumber: 7.1 Consensus size: 77
1223611 AACAAGAGTT
* *
1223621 GTTTCGCTTGAAACAGAAGATTTTATCTCGCTTTAGTAGTTTCCCTTGAAACAGAAGATTTTGTC
1 GTTTCCCTCGAAACAGAAGATTTTATCTCGCTTTAGTAGTTTCCCTTGAAACAGAAGATTTTGTC
*
1223686 TCGCTTGAGACA
66 TCGCTTGAGATA
** * * * * ** *
1223698 GTTTTTACTCGAAACAAGAAGA-TTTATTTCACTCAATA-TTGTTTTTCTT-AAA-ACAAGA-TT
1 G-TTTCCCTCGAAAC-AGAAGATTTTATCTCGCT--TTAGTAGTTTCCCTTGAAACAGAAGATTT
*
1223758 TGTCTCGCTTGAGACA
62 TGTCTCGCTTGAGATA
** * * ** *
1223774 GTTTTTACTC-AAA-AGAAGACATTTCT-TTTCACTCAAG-A-TTT--TTTG-AA-AGAAGATTT
1 G-TTTCCCTCGAAACAGAAG--ATTT-TATCTCGCTTTAGTAGTTTCCCTTGAAACAGAAGATTT
*
1223830 TATCTCGCTTGAGATA
62 TGTCTCGCTTGAGATA
* * * * * *
1223846 GTTTCCCTTGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACATAAGATTTTAT
1 GTTTCCCTCGAAACAGAAGATTTTATCTCGCTTTAG-TAGTTTCCCTTGAAACAGAAGATTTTGT
1223911 CTCGCTTGAGATA
65 CTCGCTTGAGATA
* * *
1223924 GTTTCCCTCGAAACAGAAGATTTTATCTCGC-TTATGATAGTTTTCCTCGAAATAGAAGATTTTG
1 GTTTCCCTCGAAACAGAAGATTTTATCTCGCTTTA-G-TAGTTTCCCTTGAAACAGAAGATTTTG
1223988 TCTCGCTTGAGATA
64 TCTCGCTTGAGATA
* * * *
1224002 GTTTCCCTTGAAACAAAAGATTTTGTCT--C---A-T--TTTCCCTCGAAACAGAAGATTTTGTC
1 GTTTCCCTCGAAACAGAAGATTTTATCTCGCTTTAGTAGTTTCCCTTGAAACAGAAGATTTTGTC
1224059 TCGCTTGAGATA
66 TCGCTTGAGATA
* * * * *
1224071 GTTTCCCTCGAAACAGAAGATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC--AA-ATTTTGT
1 GTTTCCCTCGAAACAGAAGATTTTATCTCGCTTTAG-TAGTTTCCCTTGAAACAGAAGATTTTGT
* *
1224133 CTCTCTTGAGACA
65 CTCGCTTGAGATA
1224146 GTTTC
1 GTTTC
1224151 TCTTGAAATG
Statistics
Matches: 376, Mismatches: 46, Indels: 64
0.77 0.09 0.13
Matches are distributed among these distances:
69 62 0.16
70 1 0.00
71 27 0.07
72 20 0.05
73 14 0.04
74 6 0.02
75 27 0.07
76 42 0.11
77 11 0.03
78 150 0.40
79 14 0.04
80 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (77 bp):
GTTTCCCTCGAAACAGAAGATTTTATCTCGCTTTAGTAGTTTCCCTTGAAACAGAAGATTTTGTC
TCGCTTGAGATA
Found at i:1223769 original size:76 final size:76
Alignment explanation
Indices: 1223675--1223849 Score: 209
Period size: 76 Copynumber: 2.4 Consensus size: 76
1223665 CTTGAAACAG
* * *
1223675 AAGATTTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTT-ATTTCACTCAATATTG
1 AAGATTTTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAG-ACATTTCATTTCACTCAAGATT-
1223739 TTTTTCTTAAAAC
64 TTTTTCTTAAAAC
* *
1223752 AAGA-TTTGTCTCGCTTGAGACAGTTTTTACTCAAAAGAAGACATTTCTTTTCACTCAAGA---T
1 AAGATTTTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAGACATTTCATTTCACTCAAGATTTT
* *
1223813 TTT-TTGAAAG
66 TTTCTTAAAAC
* *
1223823 AAGATTTTATCTCGCTTGAGATAGTTT
1 AAGATTTTGTCTCGCTTGAGACAGTTT
1223850 CCCTTGAAAC
Statistics
Matches: 87, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
71 9 0.10
72 24 0.28
75 5 0.06
76 45 0.52
77 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (76 bp):
AAGATTTTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAGACATTTCATTTCACTCAAGATTTT
TTTCTTAAAAC
Found at i:1223868 original size:39 final size:39
Alignment explanation
Indices: 1223821--1224213 Score: 437
Period size: 39 Copynumber: 10.5 Consensus size: 39
1223811 ATTTTTTGAA
* *
1223821 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1223860 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
1223899 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
1223938 AGAAGATTTTATCTCGCTT-ATGATAGTTTTCCTCGAAAT
1 AGAAGATTTTGTCTCGCTTGA-GATAGTTTCCCTCGAAAC
*
1223977 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
1224016 AAAAGATTTTGTCT--C-----AT--TTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1224046 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
1224085 AGAAGATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
1224124 --AA-ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
1224159 TG-A-ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
*
1224196 --AA-ATTTTGTCTCTCTTGA
1 AGAAGATTTTGTCTCGCTTGA
1224214 AACAAATTTT
Statistics
Matches: 321, Mismatches: 18, Indels: 33
0.86 0.05 0.09
Matches are distributed among these distances:
30 25 0.08
32 3 0.01
36 84 0.26
37 5 0.02
38 1 0.00
39 202 0.63
40 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:1224039 original size:30 final size:30
Alignment explanation
Indices: 1224003--1224060 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1223993 CTTGAGATAG
*
1224003 TTTCCCTTGAAACAAAAGATTTTGTCTCAT
1 TTTCCCTCGAAACAAAAGATTTTGTCTCAT
*
1224033 TTTCCCTCGAAACAGAAGATTTTGTCTC
1 TTTCCCTCGAAACAAAAGATTTTGTCTC
1224061 GCTTGAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (30 bp):
TTTCCCTCGAAACAAAAGATTTTGTCTCAT
Found at i:1224084 original size:69 final size:68
Alignment explanation
Indices: 1223964--1224099 Score: 236
Period size: 69 Copynumber: 2.0 Consensus size: 68
1223954 CTTATGATAG
* *
1223964 TTTTCCTCGAAATAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAAAAGATTTTGTC
1 TTTTCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGTC
1224029 TCA
66 TCA
*
1224032 TTTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTGT
1 TTTT-CCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGT
1224097 CTC
65 CTC
1224100 TCTTGAGACA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 4 0.06
69 60 0.94
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (68 bp):
TTTTCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGTC
TCA
Found at i:1224114 original size:108 final size:108
Alignment explanation
Indices: 1223925--1224126 Score: 334
Period size: 108 Copynumber: 1.9 Consensus size: 108
1223915 CTTGAGATAG
* *
1223925 TTTCCCTCGAAACAGAAGATTTTATCTCGCTTATGATAGTTTTCCTCGAAATAGAAGATTTTGTC
1 TTTCCCTCGAAACAGAAGATTTTATCTCGCTTATGATAGTTTCCCTCGAAACAGAAGATTTTGTC
*
1223990 TCGCTTGAGATAGTTTCCCTTGAAACAAAAGATTTTGTCTCAT
66 TCGCTTGAGACAGTTTCCCTTGAAACAAAAGATTTTGTCTCAT
*
1224033 TTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGA-GATAGTTTCCCTCGAAACAGAAGATTTTGT
1 TTTCCCTCGAAACAGAAGATTTTATCTCGCTT-ATGATAGTTTCCCTCGAAACAGAAGATTTTGT
* *
1224097 CTCTCTTGAGACAGTTTCTCTTGAAACAAA
65 CTCGCTTGAGACAGTTTCCCTTGAAACAAA
1224127 TTTTGTCTCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 86 0.99
109 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (108 bp):
TTTCCCTCGAAACAGAAGATTTTATCTCGCTTATGATAGTTTCCCTCGAAACAGAAGATTTTGTC
TCGCTTGAGACAGTTTCCCTTGAAACAAAAGATTTTGTCTCAT
Found at i:1224137 original size:36 final size:36
Alignment explanation
Indices: 1224051--1224213 Score: 245
Period size: 36 Copynumber: 4.4 Consensus size: 36
1224041 GAAACAGAAG
* * * *
1224051 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAGAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC--AA
1224089 GATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 -ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
**
1224126 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATGA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1224162 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1224198 ATTTTGTCTCTCTTGA
1 ATTTTGTCTCTCTTGA
1224214 AACAAATTTT
Statistics
Matches: 116, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
36 84 0.72
37 2 0.02
39 30 0.26
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
Found at i:1224138 original size:21 final size:21
Alignment explanation
Indices: 1224113--1224234 Score: 106
Period size: 21 Copynumber: 6.4 Consensus size: 21
1224103 TGAGACAGTT
1224113 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
1224134 TCTCTTGAGAC--A----GTT
1 TCTCTTGAAACAAATTTTGTC
**
1224149 TCTCTTGAAATGAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
1224170 TCTCTTGAGAC--A----GTT
1 TCTCTTGAAACAAATTTTGTC
1224185 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
1224206 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
1224227 TCTCTTGA
1 TCTCTTGA
1224235 GACAGTTTCC
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
15 23 0.29
17 2 0.03
19 2 0.03
21 52 0.66
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:1224210 original size:57 final size:57
Alignment explanation
Indices: 1224149--1224270 Score: 181
Period size: 57 Copynumber: 2.1 Consensus size: 57
1224139 TGAGACAGTT
** * *
1224149 TCTCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
**
1224206 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATGAATTTTATC
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
*
1224263 TATCTTGA
1 TCTCTTGA
1224271 GACATTTCCA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.43
Consensus pattern (57 bp):
TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
Found at i:1224218 original size:93 final size:92
Alignment explanation
Indices: 1224113--1224305 Score: 325
Period size: 93 Copynumber: 2.1 Consensus size: 92
1224103 TGAGACAGTT
* * *
1224113 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATGAATTTTGTCTCTCTTGA
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATGAATTTTATCTATCTTGA
*
1224178 GACAGTTTCTC-TTGAAACAAATTTTGTC
66 GACA-TTTC-CATTGAAACAAATTCTGTC
1224206 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATGAATTTTATCTATCTTGA
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATGAATTTTATCTATCTTGA
1224271 GACATTTCCATTGAAACAAATTCTGTC
66 GACATTTCCATTGAAACAAATTCTGTC
1224298 TCTCTTGA
1 TCTCTTGA
1224306 GATATTCCCT
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
91 1 0.01
92 28 0.29
93 66 0.69
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (92 bp):
TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATGAATTTTATCTATCTTGA
GACATTTCCATTGAAACAAATTCTGTC
Found at i:1224286 original size:35 final size:36
Alignment explanation
Indices: 1224218--1224286 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1224208 TCTTGAAACA
* * *
1224218 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATG
1 AATTTTATCTATCTTGAGACAGTTTCCATTGAAATG
1224254 AATTTTATCTATCTTGAGACA-TTTCCATTGAAA
1 AATTTTATCTATCTTGAGACAGTTTCCATTGAAA
1224287 CAAATTCTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (36 bp):
AATTTTATCTATCTTGAGACAGTTTCCATTGAAATG
Found at i:1224304 original size:35 final size:35
Alignment explanation
Indices: 1224209--1224323 Score: 151
Period size: 35 Copynumber: 3.3 Consensus size: 35
1224199 TTTTGTCTCT
1224209 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACA-TTTCC
** * *
1224245 CTTGAAATGAATTTTATCTATCTTGAGACATTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACATTTCC
* * *
1224280 ATTGAAACAAATTCTGTCTCTCTTGAGATA-TTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACATTTCC
1224314 CTTGAAACAA
1 CTTGAAACAA
1224324 GAAATGTATC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
34 13 0.19
35 28 0.42
36 26 0.39
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (35 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACATTTCC
Found at i:1224334 original size:71 final size:73
Alignment explanation
Indices: 1224210--1224419 Score: 207
Period size: 71 Copynumber: 2.9 Consensus size: 73
1224200 TTTGTCTCTC
* * * *
1224210 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG-AA-ATGAATTTTATCT-ATCTTGAG
1 TTGAAACAAATTTTGTCTCTCTTGAGATA-TTTCCCTTGAAACAAGAAATGTATCTCA-CTTGAG
1224272 A-CATTTCCA
64 AGCATTTCCA
*
1224281 TTGAAACAAATTCTGTCTCTCTTGAGATA-TTCCCTTGAAACAAGAAATGTATCTCACTTGAGAT
1 TTGAAACAAATTTTGTCTCTCTTGAGATATTTCCCTTGAAACAAGAAATGTATCTCACTTGAGA-
** *
1224345 GGTTTTTCA
65 GCATTTCCA
* * * * *
1224354 -TAAAACCAATTTTGTCTCGCTTGAGATAATTTTCCCTTGAAACAAGAAATTTTATCTCACTCGA
1 TTGAAACAAATTTTGTCTCTCTTGAGAT-A-TTTCCCTTGAAACAAGAAA-TGTATCTCACTTGA
1224418 GA
63 GA
1224420 TAGCTTCTCT
Statistics
Matches: 116, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
69 8 0.07
70 2 0.02
71 44 0.38
72 24 0.21
73 6 0.05
75 18 0.16
76 14 0.12
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (73 bp):
TTGAAACAAATTTTGTCTCTCTTGAGATATTTCCCTTGAAACAAGAAATGTATCTCACTTGAGAG
CATTTCCA
Found at i:1224869 original size:64 final size:64
Alignment explanation
Indices: 1224762--1224887 Score: 216
Period size: 64 Copynumber: 2.0 Consensus size: 64
1224752 AGTTCATAAC
* *
1224762 GAGAAGAACTTGTTCAACCTTGCATCAACATTTCTAGCAGGGAGTTCATAATGAGAAAAACTAT
1 GAGAAAAACTTGTTCAACCTTGCATCAACATTTCCAGCAGGGAGTTCATAATGAGAAAAACTAT
* *
1224826 GAGAAAAACTTGTTCAACCTTGCATCAACATTTCCAGCGGGGAGTTCATAATGAGAAGAACT
1 GAGAAAAACTTGTTCAACCTTGCATCAACATTTCCAGCAGGGAGTTCATAATGAGAAAAACT
1224888 CATCCAACGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (64 bp):
GAGAAAAACTTGTTCAACCTTGCATCAACATTTCCAGCAGGGAGTTCATAATGAGAAAAACTAT
Found at i:1224979 original size:91 final size:92
Alignment explanation
Indices: 1224824--1225030 Score: 319
Period size: 91 Copynumber: 2.3 Consensus size: 92
1224814 GAGAAAAACT
*
1224824 ATGAGAAAAACTTGTTCAACCTT-GCATCAACATTTCCAGCGGGGAGTTCATAATGAGAAGAACT
1 ATGAGAAAAACTTGTTCAACCTTGGCATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACT
*
1224888 CATCCAACGAGGGAAAAGAAGTTCGTA
66 CATCCAACGAGGGAAAAGAAGTTCATA
* * *
1224915 ATGAGAAAAACGTGTTCAACCTTGGC-TCAGCATTTCCAGTGGAGAGTTCATAATGAGAAGAACT
1 ATGAGAAAAACTTGTTCAACCTTGGCATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACT
* * *
1224979 CATCCAACGGGGGAGAATAAGTTCATA
66 CATCCAACGAGGGAAAAGAAGTTCATA
*
1225006 ATGAGAAAAACTTATTCAACCTTGG
1 ATGAGAAAAACTTGTTCAACCTTGG
1225031 TTCGATTTCA
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
91 103 0.98
92 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (92 bp):
ATGAGAAAAACTTGTTCAACCTTGGCATCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACT
CATCCAACGAGGGAAAAGAAGTTCATA
Found at i:1226477 original size:11 final size:10
Alignment explanation
Indices: 1226460--1226551 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 10
1226450 ACAATTAGGT
1226460 TTTTATTTTA
1 TTTTATTTTA
1226470 TGTTTATTTTA
1 T-TTTATTTTA
*
1226481 TTTTA-TGT-
1 TTTTATTTTA
*
1226489 TTTTATTGT-
1 TTTTATTTTA
1226498 TTTTATTATT-
1 TTTTATT-TTA
*
1226508 TTATATTTTA
1 TTTTATTTTA
*
1226518 -ATTATTTTA
1 TTTTATTTTA
* * *
1226527 ATTAAGTTTA
1 TTTTATTTTA
*
1226537 TTATTATTTAA
1 TT-TTATTTTA
1226548 TTTT
1 TTTT
1226552 TTTGTAATTT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
8 5 0.08
9 21 0.33
10 21 0.33
11 17 0.27
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:1226500 original size:16 final size:16
Alignment explanation
Indices: 1226460--1226490 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1226450 ACAATTAGGT
1226460 TTTTATTTTATGTTTA
1 TTTTATTTTATGTTTA
1226476 TTTTATTTTATGTTT
1 TTTTATTTTATGTTT
1226491 TTATTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTATTTTATGTTTA
Found at i:1226516 original size:7 final size:8
Alignment explanation
Indices: 1226478--1226541 Score: 51
Period size: 9 Copynumber: 7.6 Consensus size: 8
1226468 TATGTTTATT
1226478 TTATTTTA
1 TTATTTTA
1226486 TGT-TTTTA
1 T-TATTTTA
*
1226494 TTGTTTTTA
1 TT-ATTTTA
1226503 TTATTTTA
1 TTATTTTA
1226511 -TATTTTAA
1 TTATTTT-A
1226519 TTATTTTAA
1 TTATTTT-A
*
1226528 TTAAGTTTA
1 TT-ATTTTA
1226537 TTATT
1 TTATT
1226542 ATTTAATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
7 7 0.15
8 15 0.32
9 21 0.45
10 4 0.09
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (8 bp):
TTATTTTA
Found at i:1226530 original size:25 final size:25
Alignment explanation
Indices: 1226478--1226530 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1226468 TATGTTTATT
* * * *
1226478 TTATTTTATGTTTTTATTGTTTTTA
1 TTATTTTATATTTTAATTATTTTAA
1226503 TTATTTTATATTTTAATTATTTTAA
1 TTATTTTATATTTTAATTATTTTAA
1226528 TTA
1 TTA
1226531 AGTTTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (25 bp):
TTATTTTATATTTTAATTATTTTAA
Found at i:1229570 original size:12 final size:13
Alignment explanation
Indices: 1229539--1229595 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
1229529 AGAAATAAAT
1229539 AAAATAAGGAAAG
1 AAAATAAGGAAAG
1229552 AAAATAAGGAAA-
1 AAAATAAGGAAAG
* *
1229564 CAAATAAGCAAAGAG
1 AAAATAAG-GAA-AG
*
1229579 AAAATAAGCAAAG
1 AAAATAAGGAAAG
1229592 AAAA
1 AAAA
1229596 AAACAAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 7 0.19
13 20 0.54
14 3 0.08
15 7 0.19
ACGTcount: A:0.70, C:0.05, G:0.18, T:0.07
Consensus pattern (13 bp):
AAAATAAGGAAAG
Found at i:1229580 original size:27 final size:27
Alignment explanation
Indices: 1229550--1229613 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
1229540 AAATAAGGAA
* *
1229550 AGAAAATAAGGAAACAAATAAGCAAAG
1 AGAAAATAAGGAAACAAAAAAACAAAG
* *
1229577 AGAAAATAAGCAAAGAAAAAAACAAAG
1 AGAAAATAAGGAAACAAAAAAACAAAG
*
1229604 A-AAAAAAAGG
1 AGAAAATAAGG
1229614 GACAAGAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.72, C:0.06, G:0.17, T:0.05
Consensus pattern (27 bp):
AGAAAATAAGGAAACAAAAAAACAAAG
Found at i:1229585 original size:15 final size:14
Alignment explanation
Indices: 1229539--1229608 Score: 69
Period size: 12 Copynumber: 5.3 Consensus size: 14
1229529 AGAAATAAAT
*
1229539 AAAATAAGGAAAG-
1 AAAATAAGCAAAGA
*
1229552 AAAATAAG-GAA-A
1 AAAATAAGCAAAGA
*
1229564 CAAATAAGCAAAGA
1 AAAATAAGCAAAGA
1229578 GAAAATAAGCAAAGA
1 -AAAATAAGCAAAGA
1229593 AAAA-AA-CAAAGA
1 AAAATAAGCAAAGA
1229605 AAAA
1 AAAA
1229609 AAAGGGACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
12 19 0.39
13 12 0.24
14 5 0.10
15 13 0.27
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.06
Consensus pattern (14 bp):
AAAATAAGCAAAGA
Found at i:1230859 original size:20 final size:20
Alignment explanation
Indices: 1230834--1230895 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 20
1230824 CTAAAAAATA
1230834 AATTTTGTCTCGCTTGAGAC
1 AATTTTGTCTCGCTTGAGAC
* *
1230854 AA-TTT-TCT---TTAAAAGC
1 AATTTTGTCTCGCTTGAGA-C
1230870 AAGTTTTGTCTCGCTTGAGAC
1 AA-TTTTGTCTCGCTTGAGAC
1230891 AATTT
1 AATTT
1230896 CTCTCAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 14
0.63 0.08 0.29
Matches are distributed among these distances:
15 4 0.13
16 3 0.10
18 6 0.19
19 6 0.19
20 5 0.16
21 3 0.10
22 4 0.13
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
AATTTTGTCTCGCTTGAGAC
Found at i:1230918 original size:36 final size:37
Alignment explanation
Indices: 1230841--1230925 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
1230831 ATAAATTTTG
* **
1230841 TCTCGCTTGAGACAATTTTCTTTAAAAGCAAGTTTTG
1 TCTCGCTTGAGACAATTTTCTCTAAAAGCAAGTTTCA
*
1230878 TCTCGCTTGAGACAA-TTTCTCTCAAAGACAA-TTTCA
1 TCTCGCTTGAGACAATTTTCTCTAAAAG-CAAGTTTCA
*
1230914 TCTCGTTTGAGA
1 TCTCGCTTGAGA
1230926 TGATTCCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 24 0.57
37 18 0.43
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (37 bp):
TCTCGCTTGAGACAATTTTCTCTAAAAGCAAGTTTCA
Found at i:1231121 original size:67 final size:67
Alignment explanation
Indices: 1231041--1231229 Score: 280
Period size: 65 Copynumber: 2.9 Consensus size: 67
1231031 TTTTTACTCA
* * *
1231041 AAACAAA--TTTGTCTCTCTTTAGACATTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCTCT
1 AAACAAAGTTTTGTCTCTCTTTAGACAGTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCCCC
1231104 TG
66 TG
*
1231106 AAACAAAGTTTTGTCTCTCTTTAGACAGTTTCTCTT-AAA-AATAATCTTTGAGT-TGTTTCCCC
1 AAACAAAGTTTTGTCTCTCTTTAGACAGTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCCCC
1231168 TG
66 TG
* *
1231170 AAACAAAGTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGT
1 AAACAAAG-TTTTGTCTCTCTTTAGACAGTTTCTCTTGAAATAAAAATCTTTGAGTATGT
1231230 AGTTTTGTCT
Statistics
Matches: 111, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
64 17 0.15
65 47 0.42
66 6 0.05
67 38 0.34
68 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (67 bp):
AAACAAAGTTTTGTCTCTCTTTAGACAGTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCCCC
TG
Found at i:1231307 original size:120 final size:118
Alignment explanation
Indices: 1231112--1231330 Score: 359
Period size: 120 Copynumber: 1.8 Consensus size: 118
1231102 CTTGAAACAA
* * *
1231112 AGTTTTGTCTCTCTTTAGACAGTTTCTCTTAAAAATAATCTTTGAGTTGTTTCCCCTGAAACAAA
1 AGTTTTGTCTCTCTTGAGACAGTTACTCTTAAAAAAAATCTTTGAGTTGTTTCCCCTGAAACAAA
1231177 GTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGT
66 GTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGT
* *
1231230 AGTTTTGTCTCTCTTGAGACGGTTACTCTTAAAACAAAAGTCTTTGAGTTTGTTTCCCTTGAAAC
1 AGTTTTGTCTCTCTTGAGACAGTTACTCTTAAAA-AAAA-TCTTTGAG-TTGTTTCCCCTGAAAC
1231295 AAAG-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
63 AAAGTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1231331 CATCATCTTT
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
118 31 0.33
119 3 0.03
120 40 0.43
121 19 0.20
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (118 bp):
AGTTTTGTCTCTCTTGAGACAGTTACTCTTAAAAAAAATCTTTGAGTTGTTTCCCCTGAAACAAA
GTTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGT
Found at i:1231370 original size:185 final size:184
Alignment explanation
Indices: 1231048--1231395 Score: 509
Period size: 185 Copynumber: 1.9 Consensus size: 184
1231038 TCAAAACAAA
* * * * * *
1231048 TTTGTCTCTCTTTAGACATTTTCTCTTGAAATAAAAATCTTTGAGTATGTTTCTCTTGAAACAAA
1 TTTGTCTCTCTTGAGACAGTTACTCTTAAAACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAA
* *
1231113 GTTTTGTCTCTCTTTAGACAGTTTCTCTTAAAAATAATCTTTGAGTTGTTTCCCCTGAAACAAAG
66 GTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAATAATCTTTGAGTCGTTTCCCCTGAAACAAAG
*
1231178 TTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAAATCTTTGTGTATGTAGT
131 -TTTTGTCTCTCTTGAGACAGTTTCTCATGAAATAAAAATCTTTGTGTATGTAGT
* * *
1231233 TTTGTCTCTCTTGAGACGGTTACTCTTAAAACAAAAGTCTTTGAGTTTGTTTCCCTTGAAACAAA
1 TTTGTCTCTCTTGAGACAGTTACTCTTAAAACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAA
* * * *
1231298 GTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGA
66 GTTTTGTCTCTCTTGAGACAGTTTCTCTT-AAAAATAATCTTTGAG-TCGTTTCCCCTGAAACAA
*
1231363 A-TTTTGTCTCTCTTGAGATAGTTTCTCATGAAA
129 AGTTTTGTCTCTCTTGAGACAGTTTCTCATGAAA
1231396 CATCATCTTT
Statistics
Matches: 144, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
185 114 0.79
186 14 0.10
187 16 0.11
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (184 bp):
TTTGTCTCTCTTGAGACAGTTACTCTTAAAACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAA
GTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAATAATCTTTGAGTCGTTTCCCCTGAAACAAAG
TTTTGTCTCTCTTGAGACAGTTTCTCATGAAATAAAAATCTTTGTGTATGTAGT
Found at i:1231386 original size:65 final size:65
Alignment explanation
Indices: 1231232--1231463 Score: 329
Period size: 65 Copynumber: 3.5 Consensus size: 65
1231222 GTGTATGTAG
* * * **
1231232 TTTTGTCTCTCTTGAGACGGTTACTCTTAAAACAAAAGTCTTTGAGTTTGTTTCCCTTGAAACAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCA-TCTTTGAGTTTGTTTCCCTTGAAACAA
1231297 A
65 A
* * *
1231298 GTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGA
1 -TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTTTGTTTCCCTTGAAACAA
1231363 A
65 A
* * *
1231364 TTTTGTCTCTCTTGAGATAGTTTCTCATGAAACATCATCTTTGAGTTTGTTTCCCTTGAAGCAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTTTGTTTCCCTTGAAACAAA
* *
1231429 TTTTGTCTCTCTTGAGATAGCTTCTCTTGAAACAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAT
1231464 TATCCCTATA
Statistics
Matches: 149, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
65 92 0.62
66 25 0.17
67 32 0.21
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTTTGTTTCCCTTGAAACAAA
Found at i:1231387 original size:36 final size:35
Alignment explanation
Indices: 1231281--1231462 Score: 122
Period size: 29 Copynumber: 5.4 Consensus size: 35
1231271 CTTTGAGTTT
*
1231281 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AA-TTTTGTCTCTCTTGAGATA
* *
1231318 GTTTCTCTTGAAAC-A-----TCATCT-TTGAGATC
1 GTTTCCCTTGAAACAATTTTGTC-TCTCTTGAGATA
1231347 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGATA
* * * *
1231383 GTTTCTCATGAAAC-A-----TCATCT-TTGAGTTT
1 GTTTCCCTTGAAACAATTTTGTC-TCTCTTGAGATA
*
1231412 GTTTCCCTTGAAGCAAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGATA
* *
1231448 GCTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
1231463 TTATCCCTAT
Statistics
Matches: 110, Mismatches: 17, Indels: 38
0.67 0.10 0.23
Matches are distributed among these distances:
29 40 0.36
30 6 0.05
31 2 0.02
34 1 0.01
35 8 0.07
36 40 0.36
37 13 0.12
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (35 bp):
GTTTCCCTTGAAACAATTTTGTCTCTCTTGAGATA
Found at i:1231648 original size:131 final size:133
Alignment explanation
Indices: 1231475--1231857 Score: 486
Period size: 134 Copynumber: 2.9 Consensus size: 133
1231465 ATCCCTATAA
* * * * *
1231475 ATGGCTAGCAGTCCTCATCGCATAGGAATAGTGTCATCCACCGACCAGATATCCTCATCACATAG
1 ATGGCCAGCCGTCCTCATCGCATAGGAACAGTGTCATCCACCGACCAAATCTCCTCATCACATAG
* * *
1231540 GAGCCGTGTCACCCTTAGATAACCAGTCGTCCTTATCAAATAGGAATCGTG-TTATCATC-CCTA
66 GAGCCGCGTCACCCTTAGATAACCAGTCGTCCTCATCAAATAGGAACCGTGTTTATCATCACCTA
1231603 AAG
131 AAG
* * * *
1231606 ATGG-CATGTCGTCCTCATCACATTGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACATA
1 ATGGCCA-GCCGTCCTCATCGCATAGGAACAGTGTCATCCACCGACCAAATCTCCTCATCACATA
* *
1231670 GGAGCCGCATCACCCTTAGATAACCAGTCGTCCTCATCAAGTAGGAACCGTGTTTATCATCATCC
65 GGAGCCGCGTCACCCTTAGATAACCAGTCGTCCTCATCAAATAGGAACCGTGTTTATCATCA-CC
1231735 TAAAG
129 TAAAG
* * * *
1231740 ATGGCCAGCCGTCCTCATCGCATAGGAACTGTGTCATCCACCAACCATATCTCCTCATCACGTAG
1 ATGGCCAGCCGTCCTCATCGCATAGGAACAGTGTCATCCACCGACCAAATCTCCTCATCACATAG
* * * * * **
1231805 GAGCTGCGTCAACCTTAGATAATCA-TCTGTCATAATCACGTAGGAACCGTGTT
66 GAGCCGCGTCACCCTTAGATAACCAGTC-GTCCTCATCAAATAGGAACCGTGTT
1231858 ATCTCCAACT
Statistics
Matches: 218, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
130 1 0.00
131 100 0.46
132 8 0.04
133 2 0.01
134 105 0.48
135 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (133 bp):
ATGGCCAGCCGTCCTCATCGCATAGGAACAGTGTCATCCACCGACCAAATCTCCTCATCACATAG
GAGCCGCGTCACCCTTAGATAACCAGTCGTCCTCATCAAATAGGAACCGTGTTTATCATCACCTA
AAG
Found at i:1231807 original size:134 final size:132
Alignment explanation
Indices: 1231465--1231857 Score: 499
Period size: 131 Copynumber: 3.0 Consensus size: 132
1231455 TTGAAACATT
* * * *
1231465 ATCCCTATAA-ATGGCTAGCAGTCCTCATCGCATAGGAA-TAGTGTCATCCACCGACCAGATATC
1 ATCCCTA-AAGATGGCCAGCCGTCCTCATCGCATAGGAACT-GTGTCATCCACCGACCAAATCTC
* * * *
1231528 CTCATCACATAGGAGCCGTGTCACCCTTAGATAACCAGTCGTCCTTATCAAATAGGAATCGTG-T
64 CTCATCACATAGGAGCCGCGTCACCCTTAGATAACCAGTCGTCCTAATCAAGTAGGAACCGTGTT
1231592 TATC
129 TATC
* * * *
1231596 ATCCCTAAAGATGG-CATGTCGTCCTCATCACATTGGAACCGTGTCATCCACCGACCAAATCTCC
1 ATCCCTAAAGATGGCCA-GCCGTCCTCATCGCATAGGAACTGTGTCATCCACCGACCAAATCTCC
* *
1231660 TCATCACATAGGAGCCGCATCACCCTTAGATAACCAGTCGTCCTCATCAAGTAGGAACCGTGTTT
65 TCATCACATAGGAGCCGCGTCACCCTTAGATAACCAGTCGTCCTAATCAAGTAGGAACCGTGTTT
1231725 ATC
130 ATC
* *
1231728 ATCATCCTAAAGATGGCCAGCCGTCCTCATCGCATAGGAACTGTGTCATCCACCAACCATATCTC
1 ATC--CCTAAAGATGGCCAGCCGTCCTCATCGCATAGGAACTGTGTCATCCACCGACCAAATCTC
* * * * * *
1231793 CTCATCACGTAGGAGCTGCGTCAACCTTAGATAATCA-TCTGTCATAATCACGTAGGAACCGTGT
64 CTCATCACATAGGAGCCGCGTCACCCTTAGATAACCAGTC-GTCCTAATCAAGTAGGAACCGTGT
1231857 T
128 T
1231858 ATCTCCAACT
Statistics
Matches: 227, Mismatches: 27, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
130 3 0.01
131 107 0.47
132 8 0.04
133 2 0.01
134 105 0.46
135 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (132 bp):
ATCCCTAAAGATGGCCAGCCGTCCTCATCGCATAGGAACTGTGTCATCCACCGACCAAATCTCCT
CATCACATAGGAGCCGCGTCACCCTTAGATAACCAGTCGTCCTAATCAAGTAGGAACCGTGTTTA
TC
Found at i:1232384 original size:20 final size:21
Alignment explanation
Indices: 1232351--1232391 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1232341 GCACTAAATC
*
1232351 AGTCAGAGAAAACAACACCAA
1 AGTCAGAGAAAACAAAACCAA
1232372 AGTCAGA-AAAACAAAACCAA
1 AGTCAGAGAAAACAAAACCAA
1232392 TAAAAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.61, C:0.22, G:0.12, T:0.05
Consensus pattern (21 bp):
AGTCAGAGAAAACAAAACCAA
Done.