Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007859.1 Hibiscus syriacus cultivar Beakdansim tig00110221_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: 3538007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:2427774 original size:28 final size:28
Alignment explanation
Indices: 2427734--2427801 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
2427724 TTGTGAAAAA
*
2427734 AAAAAAATC-TTGAGATTGTTTCTTTTG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
*
2427761 AAAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
2427789 AAACAAAAT-TTTG
1 AAA-AAAATCTTTG
2427802 TCTCTCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 9 0.24
28 23 0.62
29 5 0.14
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (28 bp):
AAAAAAATCTTTGAGATTGTTTCTTTGG
Found at i:2427854 original size:64 final size:64
Alignment explanation
Indices: 2427752--2428000 Score: 346
Period size: 64 Copynumber: 3.9 Consensus size: 64
2427742 CTTGAGATTG
2427752 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
2427816 GTTCTTTTAAAACAAAAATCTTTGAG-TTG-TTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTT-GAA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
2427879 AA
64 -A
* * * * *
2427881 TTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTTTTGAAACAAAA-TTT-TATCTCTTAATGACA
1 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAA-GA-T
2427944 A
64 A
2427945 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCCTTT-GAAACAAAATTTTGTCTCTC
1 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTT-CTTTGGAAACAAAATTTTGTCTCTC
2428001 GAGACAACTT
Statistics
Matches: 163, Mismatches: 12, Indels: 18
0.84 0.06 0.09
Matches are distributed among these distances:
63 21 0.13
64 89 0.55
65 35 0.21
66 18 0.11
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45
Consensus pattern (64 bp):
TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:2427894 original size:129 final size:129
Alignment explanation
Indices: 2427752--2428000 Score: 355
Period size: 129 Copynumber: 1.9 Consensus size: 129
2427742 CTTGAGATTG
* * * *
2427752 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAA-GA-T
1 TTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTTTGGAAACAAAA-TTT-TATCTCTTAATGACA
2427815 AGTTCTTTTAAAACAAAAATCTTTGAG-TTG-TT-CTTTGGAAACAAAATTTTGTCTCTCTTAAG
64 AGTTCTTTT-AAA-AAAAATCTTTGAGTTTGTTTCCTTT-GAAACAAAATTTTGTCTCTCTTAAG
2427877 ATAA
126 ATAA
* *
2427881 TTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTTTTGAAACAAAATTTTATCTCTTAATGACAAT
1 TTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTTTGGAAACAAAATTTTATCTCTTAATGACAAG
*
2427946 TTCTTTTGAAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTC
66 TTCTTTTAAAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTC
2428001 GAGACAACTT
Statistics
Matches: 108, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
127 22 0.20
128 10 0.09
129 72 0.67
130 4 0.04
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45
Consensus pattern (129 bp):
TTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTTTGGAAACAAAATTTTATCTCTTAATGACAAG
TTCTTTTAAAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:2428196 original size:15 final size:15
Alignment explanation
Indices: 2428173--2428216 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2428163 TTTTGAGTCG
*
2428173 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
2428188 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
2428203 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
2428217 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:2428845 original size:128 final size:128
Alignment explanation
Indices: 2428612--2428881 Score: 404
Period size: 128 Copynumber: 2.1 Consensus size: 128
2428602 AACCATAACT
* * * *
2428612 CCTAAAGATGGCCAG-CCGTCCTT-ATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTC
1 CCTAAAGATGGCCAGAAC-T-CTTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTC
*
2428675 ATCATGAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
64 ATCATGAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGAAACCGTGTTATCA
**
2428740 CCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC-GACCAGATCTCTTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTCAT
*
2428804 CACAT-AGGAGCTGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGAAACCGTGTTATCA
66 --CATGAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGAAACCGTGTTATCA
2428868 CCTAAAGATGGCCA
1 CCTAAAGATGGCCA
2428882 AGAAACTTCA
Statistics
Matches: 128, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
127 19 0.15
128 105 0.82
129 4 0.03
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (128 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCTTCAT
CATGAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGAAACCGTGTTATCA
Found at i:2429145 original size:3 final size:3
Alignment explanation
Indices: 2429137--2429204 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
2429127 TTTTCGTTAT
** * *
2429137 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TCG TCA -TC TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
2429182 TTA TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
2429205 CAAATTTTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2431370 original size:20 final size:22
Alignment explanation
Indices: 2431334--2431375 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2431324 AATTTCAAGA
*
2431334 TTTCTTATCGAGTTAAA-GGAT
1 TTTCTTATCGAGATAAATGGAT
2431355 TTTCTTATCGA-ATAAATGGAT
1 TTTCTTATCGAGATAAATGGAT
2431376 CATAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.43
Consensus pattern (22 bp):
TTTCTTATCGAGATAAATGGAT
Found at i:2432795 original size:14 final size:14
Alignment explanation
Indices: 2432776--2432806 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2432766 AATCATAATG
2432776 AAGATTAGTCAGCC
1 AAGATTAGTCAGCC
*
2432790 AAGATTAGTTAGCC
1 AAGATTAGTCAGCC
2432804 AAG
1 AAG
2432807 CACAAGCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (14 bp):
AAGATTAGTCAGCC
Found at i:2436482 original size:25 final size:26
Alignment explanation
Indices: 2436448--2436511 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
2436438 TATTGATTTT
*
2436448 AGAAGAAGAAGAAGAAA-TAACGTGG
1 AGAAGAAGAAGAAGAAATTAACCTGG
*
2436473 AGAAGAAGAAGAA-AAATTAACCTGT
1 AGAAGAAGAAGAAGAAATTAACCTGG
*
2436498 AGAAGAAAAAGAAG
1 AGAAGAAGAAGAAG
2436512 GGAGATTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.09
25 31 0.91
ACGTcount: A:0.59, C:0.05, G:0.27, T:0.09
Consensus pattern (26 bp):
AGAAGAAGAAGAAGAAATTAACCTGG
Found at i:2463515 original size:2 final size:2
Alignment explanation
Indices: 2463508--2463549 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2463498 AGTAATCATA
2463508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2463550 CAAATACATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2468550 original size:20 final size:20
Alignment explanation
Indices: 2468527--2468567 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2468517 TATATCCATG
*
2468527 AAATGCAACTATATGCTCCT
1 AAATGCAACTATATGATCCT
* *
2468547 AAATGCATCTTTATGATCCT
1 AAATGCAACTATATGATCCT
2468567 A
1 A
2468568 TATTGGCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (20 bp):
AAATGCAACTATATGATCCT
Found at i:2479124 original size:22 final size:23
Alignment explanation
Indices: 2479094--2479136 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2479084 ATATATATAT
2479094 ATATAATATAGCTTTT-AAAAGC
1 ATATAATATAGCTTTTGAAAAGC
* *
2479116 ATATTATATAGTTTTTGAAAA
1 ATATAATATAGCTTTTGAAAA
2479137 TATATAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (23 bp):
ATATAATATAGCTTTTGAAAAGC
Found at i:2479141 original size:22 final size:21
Alignment explanation
Indices: 2479092--2479142 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2479082 ATATATATAT
2479092 ATATATAATATAGCTTTTAAA
1 ATATATAATATAGCTTTTAAA
* * *
2479113 AGCATATTATATAGTTTTTGAAA
1 A-TATATAATATAGCTTTT-AAA
2479136 ATATATA
1 ATATATA
2479143 GTTTTAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.78
23 4 0.17
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (21 bp):
ATATATAATATAGCTTTTAAA
Found at i:2479153 original size:14 final size:16
Alignment explanation
Indices: 2479120--2479158 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2479110 AAAAGCATAT
2479120 TATATAGTTTTTGAAAA
1 TATATAGTTTTT-AAAA
2479137 TATATAG-TTTTAAATA
1 TATATAGTTTTTAAA-A
2479153 TATATA
1 TATATA
2479159 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 11 0.52
17 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (16 bp):
TATATAGTTTTTAAAA
Found at i:2479986 original size:31 final size:32
Alignment explanation
Indices: 2479927--2480003 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
2479917 TTGGGGTCCG
* * *
2479927 AGAGGCTACCCAAGAAGGTTACTCGGGGCCAC
1 AGAGCCTACCCAAGAAAGATACTCGGGGCCAC
* * *
2479959 GGGGCCTACCCAAGAAAGAT-CTCGGGGCCTC
1 AGAGCCTACCCAAGAAAGATACTCGGGGCCAC
2479990 AGAGCCTACCCAAG
1 AGAGCCTACCCAAG
2480004 GGTCACCTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 22 0.59
32 15 0.41
ACGTcount: A:0.27, C:0.31, G:0.30, T:0.12
Consensus pattern (32 bp):
AGAGCCTACCCAAGAAAGATACTCGGGGCCAC
Found at i:2480881 original size:21 final size:21
Alignment explanation
Indices: 2480829--2480881 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2480819 TCAGGAGTAT
*
2480829 TCAGGATTTTATATTGAATAA
1 TCAGGATTTTGTATTGAATAA
*
2480850 TCAGGATTTTGTATTGAATTA
1 TCAGGATTTTGTATTGAATAA
2480871 TCAGGATTTTG
1 TCAGGATTTTG
2480882 AGTCCAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (21 bp):
TCAGGATTTTGTATTGAATAA
Found at i:2480890 original size:21 final size:21
Alignment explanation
Indices: 2480829--2480891 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
2480819 TCAGGAGTAT
* ** *
2480829 TCAGGATTTTATATTGAATAA
1 TCAGGATTTTGTATCCAATTA
**
2480850 TCAGGATTTTGTATTGAATTA
1 TCAGGATTTTGTATCCAATTA
2480871 TCAGGATTTTG-AGTCCAATTA
1 TCAGGATTTTGTA-TCCAATTA
2480892 CACCAACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (21 bp):
TCAGGATTTTGTATCCAATTA
Found at i:2480979 original size:29 final size:29
Alignment explanation
Indices: 2480914--2480971 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2480904 CAACACTACA
2480914 ATACTTATCAATCATTGGGTCTGTGATAC
1 ATACTTATCAATCATTGGGTCTGTGATAC
2480943 ATACTTATCAATCATTGGGTCTGTGATAC
1 ATACTTATCAATCATTGGGTCTGTGATAC
2480972 TTCATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (29 bp):
ATACTTATCAATCATTGGGTCTGTGATAC
Found at i:2485275 original size:31 final size:29
Alignment explanation
Indices: 2485208--2485280 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
2485198 CGAAGCCACG
2485208 AGCCTACCCAAGAAAGATCTCAGGGCAGT
1 AGCCTACCCAAGAAAGATCTCAGGGCAGT
** *
2485237 AGGGCCTACCCAAGAATTATCTCAGGGCCTCGT
1 A--GCCTACCCAAGAAAGATCTCAGGG-C-AGT
2485270 AGCCTACCCAA
1 AGCCTACCCAA
2485281 TGGTCACCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.03
31 32 0.86
32 1 0.03
33 3 0.08
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.16
Consensus pattern (29 bp):
AGCCTACCCAAGAAAGATCTCAGGGCAGT
Found at i:2488285 original size:31 final size:30
Alignment explanation
Indices: 2488187--2488285 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 30
2488177 GGGCCCGAGA
* * *
2488187 GCCTACCCAAGAAGGTTACTCGGGGCCACAGG
1 GCCTACCCAAGAAGGAT-CTCAGGGCCTC-GG
* * ** * *
2488219 GCCTACCCGAGAAAGATCTCTCGGCTGTAGG
1 GCCTACCCAAGAAGGATCTCAGGGC-CTCGG
2488250 GCCTACCCAAGAAGGATCTCAGGGCCTCGG
1 GCCTACCCAAGAAGGATCTCAGGGCCTCGG
2488280 AGCCTA
1 -GCCTA
2488286 TCGAATGGTC
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
30 3 0.06
31 34 0.67
32 14 0.27
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.15
Consensus pattern (30 bp):
GCCTACCCAAGAAGGATCTCAGGGCCTCGG
Found at i:2501211 original size:199 final size:199
Alignment explanation
Indices: 2500914--2501279 Score: 443
Period size: 196 Copynumber: 1.8 Consensus size: 199
2500904 CATCCCAGTT
* * * * *
2500914 AAATTTTGAACATACCTTAAGGCAATAAGAGCTATTTGTCGACCCAAAGCTTTCACGTTCAATTC
1 AAATTTTGAACATAACTTAAGGAAAAAAGAGCTATTTGTCGACCCAAAACTTTCAAGTTCAATTC
* * *
2500979 CACTCAGCTCGAGAGCATATCAATCGTATGGTAACAAAGAGGAACTATACTCC-AGTCAAAACCC
66 CACTCAGCTCGAGAGCACATCAATCGCATGGTAAC---GAGAAACTATACTCCGA-TCAAAACCC
* * * * *
2501043 AGTTGAGGTCTTTAAGTCTATAAGGAGACCCCAAGACAACTACAATTTGGCAATAAAGAACCAAT
127 AATGGAGGTCTTCAAGTCTAGAAGAAGACCCCAAGACAACTACAATTTGGCAATAAAGAACCAAT
2501108 TCTCAATC
192 TCTCAATC
* * * **
2501116 AAATTTTG-ACATAACTTTAGGAAAAAAGAGCTATTTGT-TA-CCAAAACTTTCAATTTTGATTC
1 AAATTTTGAACATAACTTAAGGAAAAAAGAGCTATTTGTCGACCCAAAACTTTCAAGTTCAATTC
** * * * *
2501178 CACTCAGCTCGAGAGCACATTGATTGCATGGTAACGAGAAATTATCCTCCGATGAAAACCCAATG
66 CACTCAGCTCGAGAGCACATCAATCGCATGGTAACGAGAAACTATACTCCGATCAAAACCCAATG
*
2501243 GAGGTCTTCAAGTCTAGAAGAAGACCCCAAGATAACT
131 GAGGTCTTCAAGTCTAGAAGAAGACCCCAAGACAACT
2501280 GCGATTTAGA
Statistics
Matches: 138, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
196 55 0.40
197 1 0.01
199 47 0.34
200 1 0.01
201 26 0.19
202 8 0.06
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (199 bp):
AAATTTTGAACATAACTTAAGGAAAAAAGAGCTATTTGTCGACCCAAAACTTTCAAGTTCAATTC
CACTCAGCTCGAGAGCACATCAATCGCATGGTAACGAGAAACTATACTCCGATCAAAACCCAATG
GAGGTCTTCAAGTCTAGAAGAAGACCCCAAGACAACTACAATTTGGCAATAAAGAACCAATTCTC
AATC
Found at i:2502024 original size:3 final size:3
Alignment explanation
Indices: 2501997--2502079 Score: 114
Period size: 3 Copynumber: 27.3 Consensus size: 3
2501987 TTTGAAAATA
* * *
2501997 TAT TAT ATAG TAT ATAT TA- TAT TAT TAT TAT TAT TAT TAT TAA TAA
1 TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2502043 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2502080 TCAAGTTCAA
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.03
3 66 0.90
4 5 0.07
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2503507 original size:35 final size:33
Alignment explanation
Indices: 2503433--2503507 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 33
2503423 CAAAATTGTA
**
2503433 ATTA-TTTCTTTTATATTTATTTTATTTATTTT
1 ATTATTTTCTTTTATATTTATTTTATTTATAAT
*
2503465 ATTATTTTCTTTTTCATATTTATTTTGTTT-TAAT
1 ATTATTTTC-TTTT-ATATTTATTTTATTTATAAT
2503499 ATTGATTTT
1 ATT-ATTTT
2503508 ATCTTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 4 0.11
33 4 0.11
34 9 0.25
35 19 0.53
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.72
Consensus pattern (33 bp):
ATTATTTTCTTTTATATTTATTTTATTTATAAT
Found at i:2506230 original size:24 final size:25
Alignment explanation
Indices: 2506170--2506230 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 25
2506160 TTGGACATGA
2506170 GAAAAAGAAT-AAAAATGGAGAAAT
1 GAAAAAGAATGAAAAATGGAGAAAT
2506194 GAAAAAGAA-GAAAAATGGAGAAAT
1 GAAAAAGAATGAAAAATGGAGAAAT
**
2506218 -AAGGAGAATGAAA
1 GAAAAAGAATGAAA
2506231 TGAAAGGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 6 0.18
24 27 0.82
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.10
Consensus pattern (25 bp):
GAAAAAGAATGAAAAATGGAGAAAT
Found at i:2509917 original size:50 final size:49
Alignment explanation
Indices: 2509812--2509917 Score: 110
Period size: 50 Copynumber: 2.1 Consensus size: 49
2509802 TCACTCTCCA
* * *
2509812 ATTTTCCTTTTCATCGTGACTAGGAGGGTTGGTTATAGCCATATTATCGT
1 ATTTTCCTTTTCATCGTGACTAGGAGGGTTCG-TATAGACATATCATCGT
*
2509862 GTTTTCCTTTTCAGT-GTGACTAGGAGGGTTCG-ATAGGACATTATCCATC-T
1 ATTTTCCTTTTCA-TCGTGACTAGGAGGGTTCGTATA-GACA-TAT-CATCGT
2509912 ATTTTC
1 ATTTTC
2509918 ACCAAATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
48 3 0.06
49 3 0.06
50 37 0.79
51 4 0.09
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42
Consensus pattern (49 bp):
ATTTTCCTTTTCATCGTGACTAGGAGGGTTCGTATAGACATATCATCGT
Found at i:2510424 original size:17 final size:17
Alignment explanation
Indices: 2510404--2510440 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2510394 TTGAAATTCA
2510404 AAAAAGTTAAAAAATAC
1 AAAAAGTTAAAAAATAC
* *
2510421 AAAAATTTAAAAATTAC
1 AAAAAGTTAAAAAATAC
2510438 AAA
1 AAA
2510441 TGTAAGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAAAGTTAAAAAATAC
Found at i:2515866 original size:58 final size:60
Alignment explanation
Indices: 2515731--2515878 Score: 178
Period size: 58 Copynumber: 2.5 Consensus size: 60
2515721 GTGTAAGGAC
* * *
2515731 ACTTAGTGCAGGTGGT-GGCACGACTTTATGTGTCATATCCGAATCAACACTAGAGTTTGA
1 ACTTAGTGCAGGTGGTGGGCACGACCTTATGTGTCATATCCGAA-CAACACTAGAGTGTAA
* *
2515791 ACTTAGTACAGGTGGTGGGCACAACCTTATGTGTCATATCC-AA-AATC-CTAGAGTGTAA
1 ACTTAGTGCAGGTGGTGGGCACGACCTTATGTGTCATATCCGAACAA-CACTAGAGTGTAA
* * *
2515849 ACTTATTGCAAGTGGTGGGCATGACCTTAT
1 ACTTAGTGCAGGTGGTGGGCACGACCTTAT
2515879 ATTTCATAGC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
58 36 0.47
59 1 0.01
60 17 0.22
61 22 0.29
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (60 bp):
ACTTAGTGCAGGTGGTGGGCACGACCTTATGTGTCATATCCGAACAACACTAGAGTGTAA
Found at i:2517244 original size:29 final size:29
Alignment explanation
Indices: 2517202--2517260 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2517192 ATTTTCACCT
2517202 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
*
2517231 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
2517260 A
1 A
2517261 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGCAATGACATCAA
Found at i:2530816 original size:13 final size:13
Alignment explanation
Indices: 2530778--2530821 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
2530768 ACAATATTTT
2530778 AAATAAATTAAAA
1 AAATAAATTAAAA
* *
2530791 AAATTTAA-CAAAA
1 AAA-TAAATTAAAA
2530804 AAATAAATTAAAA
1 AAATAAATTAAAA
2530817 AAATA
1 AAATA
2530822 TTTTTATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 19 0.76
14 3 0.12
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATAAATTAAAA
Found at i:2531085 original size:22 final size:24
Alignment explanation
Indices: 2531036--2531085 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2531026 TTTATAAACA
*
2531036 TAAAACTCTTGGTCTTTTAATTTG
1 TAAAACTCTTGGTCTTTAAATTTG
2531060 TAAAACTCTAT-GT-TTTAAATTT-
1 TAAAACTCT-TGGTCTTTAAATTTG
2531082 TAAA
1 TAAA
2531086 GGCTTAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.17
23 8 0.33
24 11 0.46
25 1 0.04
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (24 bp):
TAAAACTCTTGGTCTTTAAATTTG
Found at i:2531984 original size:43 final size:41
Alignment explanation
Indices: 2531936--2532057 Score: 165
Period size: 43 Copynumber: 2.9 Consensus size: 41
2531926 TCGAAATGGA
* *
2531936 GTGCATGGATGCACTGCATGGTGCATCGATGCACT-AGTGGCAG
1 GTGCATGGATGCACTGCAGGGTGCATGGATGCACTCAG-GG--G
2531979 GTGCATGGATGCACTGCAGGGGTGCATGGATGCACTGCAGGGG
1 GTGCATGGATGCACTGCA-GGGTGCATGGATGCACT-CAGGGG
2532022 GTGCATGGATGCACTGCAGGAGTGCATGGATGCACT
1 GTGCATGGATGCACTGCAGG-GTGCATGGATGCACT
2532058 TTGACACCCT
Statistics
Matches: 73, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
42 2 0.03
43 52 0.71
44 15 0.21
45 2 0.03
46 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.39, T:0.21
Consensus pattern (41 bp):
GTGCATGGATGCACTGCAGGGTGCATGGATGCACTCAGGGG
Found at i:2532004 original size:21 final size:21
Alignment explanation
Indices: 2531936--2532057 Score: 158
Period size: 21 Copynumber: 5.7 Consensus size: 21
2531926 TCGAAATGGA
*
2531936 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* *
2531956 GTGCATCGATGCACTAG-TGGCAG
1 GTGCATGGATGCACT-GCAGG--G
2531979 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
2532000 GTGCATGGATGCACTGCAGGGG
1 GTGCATGGATGCACTGCA-GGG
*
2532022 GTGCATGGATGCACTGCAGGA
1 GTGCATGGATGCACTGCAGGG
2532043 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2532058 TTGACACCCT
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
20 14 0.16
21 37 0.41
22 22 0.24
23 17 0.19
ACGTcount: A:0.20, C:0.20, G:0.39, T:0.21
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:2532015 original size:64 final size:63
Alignment explanation
Indices: 2531936--2532057 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 63
2531926 TCGAAATGGA
* *
2531936 GTGCATGGATGCACTGCA-TGGTGCATCGATGCACTAG-TGGCAGGTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGGGGTGCATCGATGCACT-GCAGG-A-GTGCATGGATGCACTGCAGG
2531999 G
63 G
*
2532000 GTGCATGGATGCACTGCAGGGGGTGCATGGATGCACTGCAGGAGTGCATGGATGCACT
1 GTGCATGGATGCACTGCA-GGGGTGCATCGATGCACTGCAGGAGTGCATGGATGCACT
2532058 TTGACACCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
64 33 0.63
65 2 0.04
66 17 0.33
ACGTcount: A:0.20, C:0.20, G:0.39, T:0.21
Consensus pattern (63 bp):
GTGCATGGATGCACTGCAGGGGTGCATCGATGCACTGCAGGAGTGCATGGATGCACTGCAGGG
Found at i:2532361 original size:21 final size:21
Alignment explanation
Indices: 2532332--2532371 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2532322 AAAATATATG
2532332 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
2532353 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
2532372 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:2535492 original size:43 final size:43
Alignment explanation
Indices: 2535431--2535595 Score: 237
Period size: 43 Copynumber: 3.8 Consensus size: 43
2535421 TTGCAGCCTT
*
2535431 GGTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGGCA
1 GGTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTGGCA
*
2535474 GGTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGGCA
1 GGTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTGGCA
* *
2535517 GGTGCATGGATGCACTACAGGGATGCATGGATGCACT-GTAGG--
1 GGTGCATGGATGCACTGCAGGG-TGCATCGATGCACTAGT-GGCA
*
2535559 GGTGCATGGATGCACTGCAGGAGTGCATGGATGCACT
1 GGTGCATGGATGCACTGCAGG-GTGCATCGATGCACT
2535596 TTGACACCCT
Statistics
Matches: 115, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
42 34 0.30
43 66 0.57
44 15 0.13
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (43 bp):
GGTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTGGCA
Found at i:2535545 original size:21 final size:21
Alignment explanation
Indices: 2535431--2535595 Score: 158
Period size: 21 Copynumber: 7.8 Consensus size: 21
2535421 TTGCAGCCTT
*
2535431 GGTGCATGGATGCACTGCA-T
1 GGTGCATGGATGCACTGCAGG
* *
2535451 GGTGCATCGATGCACTAG-TGG
1 GGTGCATGGATGCACT-GCAGG
*
2535472 CAGGTGCATGGATGCACTGCA-T
1 --GGTGCATGGATGCACTGCAGG
* *
2535494 GGTGCATCGATGCACTAG-TGG
1 GGTGCATGGATGCACT-GCAGG
*
2535515 CAGGTGCATGGATGCACTACAGG
1 --GGTGCATGGATGCACTGCAGG
* *
2535538 GATGCATGGATGCACTGTAGG
1 GGTGCATGGATGCACTGCAGG
2535559 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
2535580 AGTGCATGGATGCACT
1 GGTGCATGGATGCACT
2535596 TTGACACCCT
Statistics
Matches: 117, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
20 30 0.26
21 54 0.46
22 1 0.01
23 32 0.27
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:2535898 original size:21 final size:21
Alignment explanation
Indices: 2535869--2535908 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2535859 AAAATATATG
2535869 AAAAAGATATCAATCGTTAAC
1 AAAAAGATATCAATCGTTAAC
* *
2535890 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATCGTTA
2535909 CCAATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATATCAATCGTTAAC
Found at i:2535922 original size:51 final size:51
Alignment explanation
Indices: 2535815--2535923 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
2535805 AAAATGTTTA
* * **
2535815 ATGAAAAAGATACCAATTGTTAACAAAATTATATCAATTGTTTGAAAATAT
1 ATGAAAAAGATACCAATCGTTAACAAAATGATATCAATTGTTACAAAATAT
* * *
2535866 ATGAAAAAGATATCAATCGTTAACAAAATGATATCAATTGTTACCAATTAT
1 ATGAAAAAGATACCAATCGTTAACAAAATGATATCAATTGTTACAAAATAT
*
2535917 TTGAAAA
1 ATGAAAA
2535924 TATATGAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (51 bp):
ATGAAAAAGATACCAATCGTTAACAAAATGATATCAATTGTTACAAAATAT
Found at i:2539039 original size:21 final size:21
Alignment explanation
Indices: 2538970--2539091 Score: 140
Period size: 21 Copynumber: 5.8 Consensus size: 21
2538960 TTGCAGCCTT
*
2538970 GGTGCATGGATGCACTGCA-T
1 GGTGCATGGATGCACTGCAGG
* * * *
2538990 GGTGCGTCGATCCACTAG-TGG
1 GGTGCATGGATGCACT-GCAGG
2539011 AAGGTGCATGGATGCACTGCAGG
1 --GGTGCATGGATGCACTGCAGG
*
2539034 GGTGCATGGATGCACTGTAGG
1 GGTGCATGGATGCACTGCAGG
2539055 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
2539076 AGTGCATGGATGCACT
1 GGTGCATGGATGCACT
2539092 TTGACACCCT
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
20 13 0.15
21 56 0.66
22 1 0.01
23 15 0.18
ACGTcount: A:0.20, C:0.19, G:0.39, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:2539072 original size:42 final size:43
Alignment explanation
Indices: 2538970--2539091 Score: 160
Period size: 42 Copynumber: 2.9 Consensus size: 43
2538960 TTGCAGCCTT
* * * *
2538970 GGTGCATGGATGCACTGCA-TGGTGCGTCGATCCACTAGTGGAA
1 GGTGCATGGATGCACTGCAGGGGTGCATGGATGCACTAGTGG-A
2539013 GGTGCATGGATGCACTGCAGGGGTGCATGGATGCACT-GTAGG-
1 GGTGCATGGATGCACTGCAGGGGTGCATGGATGCACTAGT-GGA
*
2539055 GGTGCATGGATGCACTGCAGGAGTGCATGGATGCACT
1 GGTGCATGGATGCACTGCAGGGGTGCATGGATGCACT
2539092 TTGACACCCT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
42 36 0.50
43 21 0.29
44 15 0.21
ACGTcount: A:0.20, C:0.19, G:0.39, T:0.22
Consensus pattern (43 bp):
GGTGCATGGATGCACTGCAGGGGTGCATGGATGCACTAGTGGA
Found at i:2544728 original size:10 final size:10
Alignment explanation
Indices: 2544715--2544789 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 10
2544705 TAAAAAAACA
2544715 AAAAAAGAAG
1 AAAAAAGAAG
2544725 -AAAAAG-AG
1 AAAAAAGAAG
* *
2544733 ATAAATGAAAG
1 AAAAAAG-AAG
*
2544744 AAAAAAGACAT
1 AAAAAAGA-AG
* *
2544755 AAAAAAGGAT
1 AAAAAAGAAG
2544765 AAAAAAGAAAG
1 AAAAAAG-AAG
2544776 AAAAAA-AA-
1 AAAAAAGAAG
2544784 AAAAAA
1 AAAAAA
2544790 AAAAAATAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
8 8 0.15
9 12 0.23
10 10 0.19
11 22 0.42
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:2546747 original size:55 final size:55
Alignment explanation
Indices: 2546686--2546883 Score: 281
Period size: 55 Copynumber: 3.6 Consensus size: 55
2546676 TGTTTTTAGG
* *
2546686 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTTAAACGAGCTTTTAAATA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTTAAATGAGCTTTTAAAGA
* * *
2546741 AACTAAGTCTGATTTTTAGAAGATTCTTGACGATTTTTAAATGAGCTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTTAAATGAGCTTTTAAAGA
* ** * *
2546796 AACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGATTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTTAAATGAGCTTTTAAAGA
*
2546851 AATTAAGTCTGATTTTCAGATA-TTTCTTGACAA
1 AACTAAGTCTGATTTTCAGA-AGTTTCTTGACAA
2546884 AATGAATTTG
Statistics
Matches: 127, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
55 126 0.99
56 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (55 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTTAAATGAGCTTTTAAAGA
Found at i:2546879 original size:110 final size:103
Alignment explanation
Indices: 2546686--2546967 Score: 300
Period size: 110 Copynumber: 2.7 Consensus size: 103
2546676 TGTTTTTAGG
** * * * * *
2546686 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTTAAACGAGCTTTTAAATAAACTAAGTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGATTTCAAAGAAATTAAGTCT
* * *
2546751 GATTTTTAGAAGATTCTTGACGATTTTTAAATGAGCTTTTAAAGA
66 GATTTTCAGAAGATTCTTGAC-A-----AAATGA-ATTTGAAAGA
*
2546796 AACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGATTTCAAAGAAATTAAGTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGATTTCAAAGAAATTAAGTCT
*
2546861 GATTTTCAGATA-TTTCTTGACAAAATGAATTTGAAAGA
66 GATTTTCAGA-AGATTCTTGACAAAATGAATTTGAAAGA
* * ** * *
2546899 AACTAAGCCTGATTTTTAGGGGTTTCTTGATG-TTTTTAAATGA-ATTTGAAAGAAATTAAGCCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGATTTCAAAGAAATTAAGTCT
*
2546962 AATTTT
66 GATTTT
2546968 TGGGGGTTTC
Statistics
Matches: 151, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
101 23 0.15
102 11 0.07
103 35 0.23
104 6 0.04
109 1 0.01
110 74 0.49
111 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (103 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGATTTCAAAGAAATTAAGTCT
GATTTTCAGAAGATTCTTGACAAAATGAATTTGAAAGA
Found at i:2547019 original size:52 final size:53
Alignment explanation
Indices: 2546882--2547039 Score: 246
Period size: 53 Copynumber: 3.0 Consensus size: 53
2546872 ATTTCTTGAC
*
2546882 AAAATGAATTTGAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTT
1 AAAATGAATTTGAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTT
* * *
2546935 TAAATGAATTTGAAAGAAATTAAGCCTAATTTTTGGGGGTTTCTTGATGTTTT
1 AAAATGAATTTGAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTT
* * *
2546988 AAAATGAATTTGAAA-AAACTAAACCTAATTTTCAGGGGTTTTTTGATGTTTT
1 AAAATGAATTTGAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTT
2547040 CAACATTTCC
Statistics
Matches: 95, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 32 0.34
53 63 0.66
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (53 bp):
AAAATGAATTTGAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTT
Found at i:2547184 original size:22 final size:22
Alignment explanation
Indices: 2547159--2547229 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
2547149 CGGGCTATCA
2547159 GTAAGTCTTTCGAGCATGATGT
1 GTAAGTCTTTCGAGCATGATGT
* * *
2547181 GTAAGTCCTTCGGGCCATCA---
1 GTAAGTCTTTCGAG-CATGATGT
2547201 GTAAGTCTTTCGAGCATGATGT
1 GTAAGTCTTTCGAGCATGATGT
2547223 GTAAGTC
1 GTAAGTC
2547230 CTTTGGGCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 4 0.10
20 12 0.31
22 19 0.49
23 4 0.10
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (22 bp):
GTAAGTCTTTCGAGCATGATGT
Found at i:2547191 original size:42 final size:42
Alignment explanation
Indices: 2547144--2547276 Score: 191
Period size: 42 Copynumber: 3.2 Consensus size: 42
2547134 TCAGCTTAAT
2547144 TCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGTGTAAG
1 TCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGTGTAAG
*
2547186 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTGTAAG
1 TCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGTGTAAG
* * *
2547228 TCCTTTGGGCTATCTA-TAAGTCTTTCAAGCAAGATGATG--AG
1 TCCTTCGGGCTATC-AGTAAGTCTTTCGAGCATGATG-TGTAAG
2547269 TCCTTCGG
1 TCCTTCGG
2547277 ACCATCGATA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
41 9 0.11
42 71 0.86
43 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (42 bp):
TCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGTGTAAG
Found at i:2547206 original size:20 final size:20
Alignment explanation
Indices: 2547144--2547212 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
2547134 TCAGCTTAAT
*
2547144 TCCTTCGGGCTATCAGTAAG
1 TCCTTCGGGCCATCAGTAAG
* * *
2547164 TCTTTCGAG-CATGATGTGTAAG
1 TCCTTCGGGCCATCA---GTAAG
2547186 TCCTTCGGGCCATCAGTAAG
1 TCCTTCGGGCCATCAGTAAG
*
2547206 TCTTTCG
1 TCCTTCG
2547213 AGCATGATGT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.08
20 18 0.49
22 12 0.32
23 4 0.11
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (20 bp):
TCCTTCGGGCCATCAGTAAG
Found at i:2547299 original size:83 final size:83
Alignment explanation
Indices: 2547144--2547305 Score: 204
Period size: 83 Copynumber: 1.9 Consensus size: 83
2547134 TCAGCTTAAT
* * * * *
2547144 TCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGTGTAAGTCCTTCGGGCCATCAGTAAGTCT
1 TCCTTCGGGCTATCAGTAAGTCTTTCAAGCAAGATGTG-AAGTCCTTCGGACCATCAGTAAGACC
*
2547209 TTCGAGCATGATGTGTAAG
65 TTCGAGCAGGATGTGTAAG
*
2547228 TCCTTTGGGCTATCTA-TAAGTCTTTCAAGCAAGATGATG-AGTCCTTCGGACCATC-GATAAGA
1 TCCTTCGGGCTATC-AGTAAGTCTTTCAAGCAAGATG-TGAAGTCCTTCGGACCATCAG-TAAGA
2547290 CCTTCGAGCAGGATGT
63 CCTTCGAGCAGGATGT
2547306 TTTCAACATT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
82 1 0.01
83 33 0.49
84 31 0.46
85 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (83 bp):
TCCTTCGGGCTATCAGTAAGTCTTTCAAGCAAGATGTGAAGTCCTTCGGACCATCAGTAAGACCT
TCGAGCAGGATGTGTAAG
Found at i:2547508 original size:41 final size:42
Alignment explanation
Indices: 2547417--2547515 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
2547407 CTTAATTTTA
* * *
2547417 TCGGGCCATC-AGTAATTCTTTCGAGCAAGATGTGTAAGTCTT
1 TCGGGCCATCTA-TAAGTCTTTCCAGCAAGATGTATAAGTCTT
*
2547459 TCGGGCCATCTATAAGTCTTTCCAGCAATATG-ATAAGTCTT
1 TCGGGCCATCTATAAGTCTTTCCAGCAAGATGTATAAGTCTT
*
2547500 TCGGGCCATATATAAG
1 TCGGGCCATCTATAAG
2547516 ACCTTCGGGC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
41 23 0.45
42 27 0.53
43 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (42 bp):
TCGGGCCATCTATAAGTCTTTCCAGCAAGATGTATAAGTCTT
Found at i:2547510 original size:21 final size:20
Alignment explanation
Indices: 2547451--2547525 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
2547441 GCAAGATGTG
*
2547451 TAAGTCTTTCGGGCCATCTA
1 TAAGTCTTTCGGGCCATATA
** *
2547471 TAAGTCTTTCCAGCAATATGA
1 TAAGTCTTTCGGGCCATAT-A
2547492 TAAGTCTTTCGGGCCATATA
1 TAAGTCTTTCGGGCCATATA
* *
2547512 TAAGACCTTCGGGC
1 TAAGTCTTTCGGGC
2547526 AGGGTGCTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (20 bp):
TAAGTCTTTCGGGCCATATA
Found at i:2547759 original size:81 final size:83
Alignment explanation
Indices: 2547587--2547774 Score: 247
Period size: 81 Copynumber: 2.2 Consensus size: 83
2547577 CAGTAATACC
2547587 TCACTCGAGGGACCAACATTGCCAGTAAAGAATTCATAATGAAGAGCTTGTTCAACCTTTTTCAC
1 TCACTCGAGGGA-CAACATTGCCAGTAAAGAA-T-AT-ATGAAGAGCTTGTTCAACCTTTTTCAC
*
2547652 AACAATTAGAAGCAGCAACGCA
62 AACAATTAGAACCAGCAACGCA
*
2547674 TCACTCGAGGGACGAACATTGCCAGTAAAG-A-AT-TGAAGAGCTTGTTCAACCTTTTTCAGAAC
1 TCACTCGAGGGAC-AACATTGCCAGTAAAGAATATATGAAGAGCTTGTTCAACCTTTTTCACAAC
* * * *
2547736 ACTTCGAACCATCAATGCA
65 AATTAGAACCAGCAACGCA
2547755 TCACTCGAGGGATCAACATT
1 TCACTCGAGGGA-CAACATT
2547775 TCTAATGGAA
Statistics
Matches: 93, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
81 60 0.65
82 1 0.01
83 2 0.02
86 2 0.02
87 28 0.30
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (83 bp):
TCACTCGAGGGACAACATTGCCAGTAAAGAATATATGAAGAGCTTGTTCAACCTTTTTCACAACA
ATTAGAACCAGCAACGCA
Found at i:2551409 original size:15 final size:15
Alignment explanation
Indices: 2551391--2551420 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2551381 AACAACTTGT
*
2551391 CATAAATCAACTACA
1 CATAAATCAAATACA
2551406 CATAAATCAAATACA
1 CATAAATCAAATACA
2551421 TAATATGAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAAATCAAATACA
Found at i:2551683 original size:16 final size:16
Alignment explanation
Indices: 2551650--2551684 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2551640 AGTAGAGAAC
2551650 TTTATTAAAGTAGCTT
1 TTTATTAAAGTAGCTT
*
2551666 TTTA-TAAAGTAGTTT
1 TTTATTAAAGTAGCTT
2551681 TTTA
1 TTTA
2551685 CTTTATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (16 bp):
TTTATTAAAGTAGCTT
Found at i:2556447 original size:3 final size:3
Alignment explanation
Indices: 2556439--2556474 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2556429 TTCTTAATAG
2556439 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2556475 TCACACCACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2564089 original size:31 final size:31
Alignment explanation
Indices: 2564048--2564106 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2564038 ACTGATACTC
2564048 TTGTGCATTATCTGAATGCAAACATGACATA
1 TTGTGCATTATCTGAATGCAAACATGACATA
* * *
2564079 TTGTGTATTATTTGAATGCAAATATGAC
1 TTGTGCATTATCTGAATGCAAACATGAC
2564107 TAGTACATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (31 bp):
TTGTGCATTATCTGAATGCAAACATGACATA
Found at i:2565768 original size:31 final size:31
Alignment explanation
Indices: 2565730--2565854 Score: 214
Period size: 31 Copynumber: 4.0 Consensus size: 31
2565720 AGGGTCGAGG
2565730 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* * *
2565761 GTTTACCTATGTTCTTCAAGATATATTGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
2565792 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
*
2565823 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
2565854 G
1 G
2565855 GTCCTTTGGG
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 87 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCAGGACATATGGACT
Found at i:2566463 original size:16 final size:16
Alignment explanation
Indices: 2566444--2566476 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2566434 AAATGCATAG
2566444 TAATGAATGGTTAAAT
1 TAATGAATGGTTAAAT
2566460 TAATGAATGGTTAAAT
1 TAATGAATGGTTAAAT
2566476 T
1 T
2566477 TTTACAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (16 bp):
TAATGAATGGTTAAAT
Found at i:2569932 original size:7 final size:7
Alignment explanation
Indices: 2569922--2569952 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2569912 ATCTCTTAAC
2569922 TCTTCAT
1 TCTTCAT
2569929 TCTTCAT
1 TCTTCAT
2569936 TCTTCAT
1 TCTTCAT
2569943 TCTTC-T
1 TCTTCAT
2569949 TCTT
1 TCTT
2569953 ATCCAACGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.10, C:0.29, G:0.00, T:0.61
Consensus pattern (7 bp):
TCTTCAT
Found at i:2571299 original size:31 final size:31
Alignment explanation
Indices: 2571261--2571385 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
2571251 AGGGTCGAGA
2571261 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2571292 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2571323 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2571354 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2571385 G
1 G
2571386 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2573427 original size:11 final size:10
Alignment explanation
Indices: 2573393--2573429 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2573383 TGAAGGTACT
2573393 GGTTC-ACT-
1 GGTTCAACTG
2573401 GGTTCAACTG
1 GGTTCAACTG
2573411 GGTTCAACTG
1 GGTTCAACTG
2573421 CGGTTCAAC
1 -GGTTCAAC
2573430 CGGATTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 5 0.19
9 3 0.12
10 10 0.38
11 8 0.31
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (10 bp):
GGTTCAACTG
Found at i:2574181 original size:20 final size:19
Alignment explanation
Indices: 2574127--2574172 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
2574117 AGAGAACCGA
*
2574127 CGGTTCACACCGGTTTTAC
1 CGGTTCTCACCGGTTTTAC
2574146 CGGTTCTCAGCCGGTTTTAC
1 CGGTTCTCA-CCGGTTTTAC
2574166 CGGTTCT
1 CGGTTCT
2574173 TTACCGGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.11, C:0.30, G:0.24, T:0.35
Consensus pattern (19 bp):
CGGTTCTCACCGGTTTTAC
Found at i:2575245 original size:27 final size:27
Alignment explanation
Indices: 2575214--2575273 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
2575204 TCTTTCGGAA
2575214 TCTTTATTTTAGGATGAAATTCAATAT
1 TCTTTATTTTAGGATGAAATTCAATAT
2575241 TCTTTATTTTAGGATGAAATTCAATAT
1 TCTTTATTTTAGGATGAAATTCAATAT
2575268 TCTTTA
1 TCTTTA
2575274 ATCAAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (27 bp):
TCTTTATTTTAGGATGAAATTCAATAT
Found at i:2576756 original size:24 final size:24
Alignment explanation
Indices: 2576729--2576778 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2576719 TGGTGGTTGA
2576729 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
2576753 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
2576777 TT
1 TT
2576779 GGTTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:2583666 original size:19 final size:21
Alignment explanation
Indices: 2583629--2583671 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2583619 TAACTTTTTC
*
2583629 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
2583649 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
2583669 TTT
1 TTT
2583672 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:2586995 original size:24 final size:24
Alignment explanation
Indices: 2586965--2587014 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2586955 TGGTGGTTGA
2586965 TTTAATGGT-TATTTGAACTTTATT
1 TTTAATGGTGTATTT-AACTTTATT
*
2586989 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTTAACTTTATT
2587013 TT
1 TT
2587015 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTTAACTTTATT
Found at i:2588073 original size:31 final size:31
Alignment explanation
Indices: 2588038--2588110 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
2588028 TAATATGTGA
* **
2588038 ATTAAGTTTTGGTCACGT-ACATTATTTTTTT
1 ATTAAGTTTTGGCCAC-TAACATTATCGTTTT
* *
2588069 ATTAAGTTTTTGCCACTAACGTTATCGTTTT
1 ATTAAGTTTTGGCCACTAACATTATCGTTTT
2588100 ATTAAGTTTTG
1 ATTAAGTTTTG
2588111 ATCAATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (31 bp):
ATTAAGTTTTGGCCACTAACATTATCGTTTT
Found at i:2593487 original size:139 final size:137
Alignment explanation
Indices: 2592978--2593504 Score: 689
Period size: 137 Copynumber: 3.8 Consensus size: 137
2592968 CACTATTTAT
* * * * *
2592978 GTGAAAGAGCTTCATGTGGGACGCACT-TTTCCTTTTTGTCAGAAAATA-GATTATAATTTCCCT
1 GTGAAAGCGCTTCTTGTGGGACGC-GTATTTCCTTTTTGTCAGAGAATATG-TTATAATTGCCCT
* ** * * *
2593041 ACTATGTGTGATGTCCCCCGGTGGGGCACTATTCACAACAACACCTATTATGTTTGATGGGACAC
64 ATTATGTGTGATGTCCCCCGACGGGGCACTATTCACATCAACACCTATTATGTTTGAGGGGACGC
2593106 AATAATGTG
129 AATAATGTG
* * *
2593115 GTGAAAGCGCTTCTTGTGGGACGCGTTTTTCCTTTTTGTCAGAAAATAAGTTATAATTGCCCTAT
1 GTGAAAGCGCTTCTTGTGGGACGCGTATTTCCTTTTTGTCAGAGAATATGTTATAATTGCCCTAT
* * *
2593180 TATGTGTGATGTCCCCCGACGGGGCACTATTCACATCAACACCTATTATGTTTGAGAGGAAGAAA
66 TATGTGTGATGTCCCCCGACGGGGCACTATTCACATCAACACCTATTATGTTTGAGGGGACGCAA
2593245 TAATGTG
131 TAATGTG
* * * ** * * *
2593252 ATGAAAGCGCTACTTGTGGGACACGCCTTTCCTTTTTGTCAAAGAATATGTTATAATTTCCTTAT
1 GTGAAAGCGCTTCTTGTGGGACGCGTATTTCCTTTTTGTCAGAGAATATGTTATAATTGCCCTAT
*
2593317 TATGTGTGATGTCCCCCGACGGGGCACTATTCACTTCAACACCTATTATGTTTGAGGGGACGCAA
66 TATGTGTGATGTCCCCCGACGGGGCACTATTCACATCAACACCTATTATGTTTGAGGGGACGCAA
*
2593382 CAATGTG
131 TAATGTG
** * * *
2593389 GTGAAAGTACTTCTTGTGGGATGCGTATTTCCTTTTTTTTTCAGGGAATATGTTATAATTGCCCT
1 GTGAAAGCGCTTCTTGTGGGACGCGTATTTCC--TTTTTGTCAGAGAATATGTTATAATTGCCCT
* * *
2593454 ATTATTTGTGATGTCCCCCGACGGGACACTATTCACGTCAACACCTATTAT
64 ATTATGTGTGATGTCCCCCGACGGGGCACTATTCACATCAACACCTATTAT
2593505 TCGTTATAGG
Statistics
Matches: 342, Mismatches: 44, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
136 1 0.00
137 266 0.78
138 1 0.00
139 74 0.22
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (137 bp):
GTGAAAGCGCTTCTTGTGGGACGCGTATTTCCTTTTTGTCAGAGAATATGTTATAATTGCCCTAT
TATGTGTGATGTCCCCCGACGGGGCACTATTCACATCAACACCTATTATGTTTGAGGGGACGCAA
TAATGTG
Found at i:2593614 original size:21 final size:21
Alignment explanation
Indices: 2593590--2593633 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2593580 TAATAAGTCA
2593590 TTCGAATATATTAAATATTAT
1 TTCGAATATATTAAATATTAT
*
2593611 TTCGAATATATTAATTATTAT
1 TTCGAATATATTAAATATTAT
2593632 TT
1 TT
2593634 AAAGTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
TTCGAATATATTAAATATTAT
Found at i:2594383 original size:21 final size:21
Alignment explanation
Indices: 2594359--2594427 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
2594349 GCTGTCATAA
* *
2594359 AACCCTGCGGGCTAGAAATAT
1 AACCCTGTGGGCTAGGAATAT
* * * *
2594380 AACCTTGTGGGCTGGGTATGT
1 AACCCTGTGGGCTAGGAATAT
*
2594401 ACCCCTGTGGGCTAGGAATAT
1 AACCCTGTGGGCTAGGAATAT
2594422 AACCCT
1 AACCCT
2594428 ATGGAGATGG
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (21 bp):
AACCCTGTGGGCTAGGAATAT
Found at i:2594464 original size:42 final size:41
Alignment explanation
Indices: 2594418--2594554 Score: 118
Period size: 42 Copynumber: 3.3 Consensus size: 41
2594408 TGGGCTAGGA
2594418 ATATAACCCTATGGAGATGGCATATGAACTAAT-GGACTGAGC
1 ATATAACCCT-TGGAGATGGCATATGAACTAATGGGA-TGAGC
* * * * *
2594460 ATATACCCCTGCGGAGATGACATATGAACTGATGGGATGGGC
1 ATATAACCCT-TGGAGATGGCATATGAACTAATGGGATGAGC
* ** * *
2594502 ATAT-ACCCTTGCGGAGATGGCATCTGAACTGGTGGGCTGGGC
1 ATATAACCCTT--GGAGATGGCATATGAACTAATGGGATGAGC
2594544 ATAT-ACCCTTG
1 ATATAACCCTTG
2594555 TGGCCTCATA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
40 1 0.01
41 4 0.05
42 72 0.90
43 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (41 bp):
ATATAACCCTTGGAGATGGCATATGAACTAATGGGATGAGC
Found at i:2595135 original size:17 final size:17
Alignment explanation
Indices: 2595113--2595146 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2595103 ACTGAAACAC
2595113 AAATAT-ATAATTCTAAT
1 AAATATAAT-ATTCTAAT
2595130 AAATATAATATTCTAAT
1 AAATATAATATTCTAAT
2595147 TATATCAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATAATATTCTAAT
Found at i:2596371 original size:22 final size:22
Alignment explanation
Indices: 2596341--2596382 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2596331 ATTTTTAACA
2596341 AACTATTTATAA-AAAATATAAT
1 AACTATTTA-AAGAAAATATAAT
*
2596363 AACTTTTTAAAGAAAATATA
1 AACTATTTAAAGAAAATATA
2596383 CTAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
AACTATTTAAAGAAAATATAAT
Found at i:2597093 original size:14 final size:14
Alignment explanation
Indices: 2597074--2597105 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2597064 TAAGAAATTT
*
2597074 GAGTCAATTTATTC
1 GAGTCAAGTTATTC
2597088 GAGTCAAGTTATTC
1 GAGTCAAGTTATTC
2597102 GAGT
1 GAGT
2597106 TTCTACACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (14 bp):
GAGTCAAGTTATTC
Found at i:2597895 original size:22 final size:22
Alignment explanation
Indices: 2597864--2597935 Score: 108
Period size: 22 Copynumber: 3.3 Consensus size: 22
2597854 AACGAGAGCA
**
2597864 AGAAAAAACAACCAAGTAATAG
1 AGAAAAAACAACCAACCAATAG
*
2597886 AGAAATAACAACCAACCAATAG
1 AGAAAAAACAACCAACCAATAG
*
2597908 AGAAACAACAACCAACCAATAG
1 AGAAAAAACAACCAACCAATAG
2597930 AGAAAA
1 AGAAAA
2597936 TAGAGAGAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.62, C:0.19, G:0.11, T:0.07
Consensus pattern (22 bp):
AGAAAAAACAACCAACCAATAG
Found at i:2603848 original size:286 final size:286
Alignment explanation
Indices: 2603326--2604172 Score: 1541
Period size: 286 Copynumber: 3.0 Consensus size: 286
2603316 AGAAAATGAG
2603326 GTAAATGAAGCAAAGAAATATGAATCCAACAATATCACAGTGTCTCGACCTCAGGATATTGGATC
1 GTAAATGAAGCAAAGAAATATGAATCCAACAATATCACAGTGTCTCGACCTCAGGATATTGGATC
* *
2603391 TTCTACACCAAACTTCACCAAACAAGGGACGAGGGAACCAAGGGTGAAAAGAGAAAAATTTCAGT
66 TTCTACACCAAACTTCGCCAAACAAGGGACGAGGGAACCAAGGGTGGAAAGAGAAAAATTTCAGT
2603456 TTGACCCAATTCTGATGACCTACAAAGAGTTGTACCAGATATTATATGAAAAACATATAATATCA
131 TTGACCCAATTCTGATGACCTACAAAGAGTTGTACCAGATATTATATGAAAAACATATAATATCA
* * *
2603521 TCTTATCATGTATCACCCATACAACCTCAATATCTGAAGTGGTACAATGATAACTTGCAGTGCGA
196 CCTTATCATGTATCACCCATACAACCTCCATATCCGAAGTGGTACAATGATAACTTGCAGTGCGA
2603586 ATATCATGCGGGAGCCTAGGGGCATT
261 ATATCATGCGGGAGCCTAGGGGCATT
*
2603612 GTAAATGAAGCAAAAAAATATGAATCCAACAATATCACAGTGTCTCGACCTCAGGATATTGGATC
1 GTAAATGAAGCAAAGAAATATGAATCCAACAATATCACAGTGTCTCGACCTCAGGATATTGGATC
* * *
2603677 TTCTACAACAAACTTCGCCAAACAAGGTACGAGGGAACCAAGGGTGGAAAGACAAAAATTTCAGT
66 TTCTACACCAAACTTCGCCAAACAAGGGACGAGGGAACCAAGGGTGGAAAGAGAAAAATTTCAGT
*
2603742 TTGACCCAATTCTGATGACCTACAAAGAGTTGTACCATATATTATATGAAAAACATATAATATCA
131 TTGACCCAATTCTGATGACCTACAAAGAGTTGTACCAGATATTATATGAAAAACATATAATATCA
2603807 CCTTATCATGTATCACCCATACAACCTCCATATCCGAAGTGGTACAATGATAACTTGCAGTGCGA
196 CCTTATCATGTATCACCCATACAACCTCCATATCCGAAGTGGTACAATGATAACTTGCAGTGCGA
* *
2603872 ATATCATGCGGAAGCTTAGGGGCATT
261 ATATCATGCGGGAGCCTAGGGGCATT
*
2603898 GTAAATGAAGCAAAGAAATATGAATCCAACAATATCACAGTGTCTCGACCTCAGGATATTAGATC
1 GTAAATGAAGCAAAGAAATATGAATCCAACAATATCACAGTGTCTCGACCTCAGGATATTGGATC
* *
2603963 TTCTATACCAAACTTTGCCAAACAAGGGACGAGGGAACCAAGGGTGGAAAGAGAAAAATTTCAGT
66 TTCTACACCAAACTTCGCCAAACAAGGGACGAGGGAACCAAGGGTGGAAAGAGAAAAATTTCAGT
2604028 TTGACCCAATTCTGATGACCTACAAAGAGTTGTACCAGATATTATATGAAAAACATATAATATCA
131 TTGACCCAATTCTGATGACCTACAAAGAGTTGTACCAGATATTATATGAAAAACATATAATATCA
*
2604093 CCTTATCATGTATCACCCATACAACCTCCATATCCGAAGTGGTACAATGATAACTTGCACTGCGA
196 CCTTATCATGTATCACCCATACAACCTCCATATCCGAAGTGGTACAATGATAACTTGCAGTGCGA
*
2604158 ATATCATGCGAGAGC
261 ATATCATGCGGGAGC
2604173 TCAAGGGCAT
Statistics
Matches: 538, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
286 538 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (286 bp):
GTAAATGAAGCAAAGAAATATGAATCCAACAATATCACAGTGTCTCGACCTCAGGATATTGGATC
TTCTACACCAAACTTCGCCAAACAAGGGACGAGGGAACCAAGGGTGGAAAGAGAAAAATTTCAGT
TTGACCCAATTCTGATGACCTACAAAGAGTTGTACCAGATATTATATGAAAAACATATAATATCA
CCTTATCATGTATCACCCATACAACCTCCATATCCGAAGTGGTACAATGATAACTTGCAGTGCGA
ATATCATGCGGGAGCCTAGGGGCATT
Found at i:2604915 original size:29 final size:29
Alignment explanation
Indices: 2604853--2604910 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
2604843 AAACAAGGTC
* *
2604853 CAGTTGATAAAGGAAAAAAAGTCGAGCTA
1 CAGTTGATAAAGGAAAAAAAGACAAGCTA
2604882 CAGTTGATAAAGGAAAAAAGATGACAAGC
1 CAGTTGATAAAGGAAAAAA-A-GACAAGC
2604911 AAGTTCCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.76
30 1 0.04
31 5 0.20
ACGTcount: A:0.50, C:0.10, G:0.24, T:0.16
Consensus pattern (29 bp):
CAGTTGATAAAGGAAAAAAAGACAAGCTA
Found at i:2610438 original size:21 final size:22
Alignment explanation
Indices: 2610398--2610450 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
2610388 TTTTCCAGAA
* *
2610398 TGCTACAGGGGTATCGATACCC-
1 TGCTACA-GTGTACCGATACCCT
2610420 TGCTACAGTGTACCGATACCCT
1 TGCTACAGTGTACCGATACCCT
2610442 TGCTACAGT
1 TGCTACAGT
2610451 AATTTCGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (22 bp):
TGCTACAGTGTACCGATACCCT
Found at i:2611230 original size:32 final size:32
Alignment explanation
Indices: 2611160--2611411 Score: 339
Period size: 32 Copynumber: 7.9 Consensus size: 32
2611150 TATAATAATT
2611160 TGTCCATATGTCCCG-AAGAACATAGGTAA-AC
1 TGTCCATATGTCCCGAAAG-ACATAGGTAATAC
*
2611191 TGTCCATATGTCCTG-AAGAACATAGGTAATAC
1 TGTCCATATGTCCCGAAAG-ACATAGGTAATAC
* * * *
2611223 TGTCCATATGTCCTGAAATACAAAGGTAATAT
1 TGTCCATATGTCCCGAAAGACATAGGTAATAC
* *
2611255 TGTCCATATGTCTCGAAAGGCATAGGTAATAC
1 TGTCCATATGTCCCGAAAGACATAGGTAATAC
**
2611287 TGTCCATATGTCCCGAAAGACATAGGTAATGT
1 TGTCCATATGTCCCGAAAGACATAGGTAATAC
*
2611319 TGTCCATATGTCCCGAAAGACATAGGTAATAA
1 TGTCCATATGTCCCGAAAGACATAGGTAATAC
* * *
2611351 TGTCCATATATCCCGAAAGAAATAGGTAATAT
1 TGTCCATATGTCCCGAAAGACATAGGTAATAC
*
2611383 TGTCCATATGTCCCAAAAGACATAGGTAA
1 TGTCCATATGTCCCGAAAGACATAGGTAA
2611412 CCCTCGACTC
Statistics
Matches: 197, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
31 28 0.14
32 167 0.85
33 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAGACATAGGTAATAC
Found at i:2613880 original size:38 final size:36
Alignment explanation
Indices: 2613779--2613884 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
2613769 TTCTCAAGTT
*
2613779 AATCAATCCTTCACAAAAGAGTAGTGAAGCAATGCA
1 AATCAAACCTTCACAAAAGAGTAGTGAAGCAATGCA
2613815 AATCAAACCTTCACAAAAGAGTAGTGAAGCAATGCA
1 AATCAAACCTTCACAAAAGAGTAGTGAAGCAATGCA
*
2613851 AATCAAGCCTTCACAAAAAAGAGTAGTGAAGCAA
1 AATCAAACCTTCAC--AAAAGAGTAGTGAAGCAA
2613885 GATCATATCA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 48 0.73
38 18 0.27
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.17
Consensus pattern (36 bp):
AATCAAACCTTCACAAAAGAGTAGTGAAGCAATGCA
Found at i:2614687 original size:22 final size:22
Alignment explanation
Indices: 2614661--2614707 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2614651 CGAGAGTAAC
*
2614661 AAACAGCAACCAAGC-AATAGAG
1 AAACAACAACCAA-CAAATAGAG
*
2614683 AAACAACAACTAACAAATAGAG
1 AAACAACAACCAACAAATAGAG
2614705 AAA
1 AAA
2614708 ATAGAGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.19, G:0.13, T:0.06
Consensus pattern (22 bp):
AAACAACAACCAACAAATAGAG
Found at i:2616472 original size:8 final size:8
Alignment explanation
Indices: 2616456--2616492 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
2616446 TTCGAGTAAC
2616456 TCAAAATTT
1 TCAAAA-TT
*
2616465 TCAAATTT
1 TCAAAATT
2616473 TCAAAATT
1 TCAAAATT
2616481 TCAAAATT
1 TCAAAATT
2616489 TCAA
1 TCAA
2616493 TCTGACTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 21 0.81
9 5 0.19
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (8 bp):
TCAAAATT
Found at i:2620947 original size:15 final size:15
Alignment explanation
Indices: 2620929--2620970 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
2620919 TTACAAACAT
2620929 ATTTTCCTTTGTGAG
1 ATTTTCCTTTGTGAG
2620944 ATTTTCCTTTGTGAG
1 ATTTTCCTTTGTGAG
2620959 ATTTTCCTTTGT
1 ATTTTCCTTTGT
2620971 TTAATACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.57
Consensus pattern (15 bp):
ATTTTCCTTTGTGAG
Found at i:2622315 original size:24 final size:24
Alignment explanation
Indices: 2622286--2622464 Score: 78
Period size: 21 Copynumber: 7.6 Consensus size: 24
2622276 GAATATATTA
2622286 ATATTTTAAAATAATTAAAATAAT
1 ATATTTTAAAATAATTAAAATAAT
* *
2622310 ATATTTTATAATATATATATAATTAGTTATT
1 ATATTTTA-AA-ATA-AT-TAA--A-ATAAT
**
2622341 ATATTTT-AAATGGTTAAAATAAT
1 ATATTTTAAAATAATTAAAATAAT
* *
2622364 ATATTTTATAATAATT--TAT-AT
1 ATATTTTAAAATAATTAAAATAAT
* * *
2622385 ATATTTT-TAACAATT-AAATAAA
1 ATATTTTAAAATAATTAAAATAAT
2622407 ATATTTT--AATAA--AAAATAA-
1 ATATTTTAAAATAATTAAAATAAT
2622426 A-ATTCTTAAAAT-ATTAAATATAAAT
1 ATATT-TTAAAATAATTAAA-AT-AAT
* *
2622451 ATATATAAAAATAA
1 ATATTTTAAAATAA
2622465 AAACTAATCA
Statistics
Matches: 118, Mismatches: 16, Indels: 40
0.68 0.09 0.23
Matches are distributed among these distances:
18 3 0.03
19 3 0.03
20 14 0.12
21 18 0.15
22 13 0.11
23 12 0.10
24 16 0.14
25 9 0.08
26 9 0.08
27 3 0.03
28 5 0.04
29 2 0.02
30 1 0.01
31 10 0.08
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATTTTAAAATAATTAAAATAAT
Found at i:2625810 original size:15 final size:17
Alignment explanation
Indices: 2625790--2625821 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2625780 AAAAGAAGAC
2625790 AAAAATA-TGAA-GAAA
1 AAAAATAGTGAACGAAA
2625805 AAAAATAGTGAACGAAA
1 AAAAATAGTGAACGAAA
2625822 CTAGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.69, C:0.03, G:0.16, T:0.12
Consensus pattern (17 bp):
AAAAATAGTGAACGAAA
Found at i:2637989 original size:24 final size:22
Alignment explanation
Indices: 2637953--2638006 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 22
2637943 ACGTATAATT
*
2637953 ATAAATTAGTTAAAATGTAAAAAG
1 ATAAATTATTTAAAA--TAAAAAG
2637977 ATAAATTATTTAAAATAAAAAG
1 ATAAATTATTTAAAATAAAAAG
2637999 -TAAATTAT
1 ATAAATTAT
2638007 ATGAGTGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 8 0.28
22 7 0.24
24 14 0.48
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (22 bp):
ATAAATTATTTAAAATAAAAAG
Found at i:2640069 original size:31 final size:31
Alignment explanation
Indices: 2640024--2640190 Score: 126
Period size: 31 Copynumber: 5.4 Consensus size: 31
2640014 CGTGATTAGG
* *
2640024 TTCAAGTGTTAAATTGATATTTTATCTAAAT
1 TTCAAGGGTCAAATTGATATTTTATCTAAAT
2640055 TTCAAGGGTCAAATTGATATTTTATCT-AAT
1 TTCAAGGGTCAAATTGATATTTTATCTAAAT
* ** * *
2640085 CTT-TAGAGAACAAATTAATATTTTATATAAAGT
1 -TTCAAG-GGTCAAATTGATATTTTATCTAAA-T
* * * *
2640118 TT-AAAGATCAAATTGATACTTCATCT-AAT
1 TTCAAGGGTCAAATTGATATTTTATCTAAAT
* ** * *
2640147 TTTAAAAGTCAAATTAATATTTTATCTAAAA
1 TTCAAGGGTCAAATTGATATTTTATCTAAAT
*
2640178 TTCAAGAGTCAAA
1 TTCAAGGGTCAAA
2640191 CAAAAATTAA
Statistics
Matches: 108, Mismatches: 22, Indels: 12
0.76 0.15 0.08
Matches are distributed among these distances:
29 3 0.03
30 26 0.24
31 73 0.68
32 5 0.05
33 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (31 bp):
TTCAAGGGTCAAATTGATATTTTATCTAAAT
Found at i:2640131 original size:62 final size:60
Alignment explanation
Indices: 2640034--2640190 Score: 176
Period size: 62 Copynumber: 2.6 Consensus size: 60
2640024 TTCAAGTGTT
* * * * *
2640034 AAATTGATATTTTATCTAAATTTCAAGGGTCAAATTGATATTTTATCTAATCTTTAGAGAA-C
1 AAATTAATATTTTATCTAAATTTCAAAGATCAAATTGATACTTCATCTAAT-TTTA-A-AAGC
*
2640096 AAATTAATATTTTATATAAAGTTT-AAAGATCAAATTGATACTTCATCTAATTTTAAAAGTC
1 AAATTAATATTTTATCTAAA-TTTCAAAGATCAAATTGATACTTCATCTAATTTTAAAAG-C
*
2640157 AAATTAATATTTTATCTAAAATTC-AAGAGTCAAA
1 AAATTAATATTTTATCTAAATTTCAAAGA-TCAAA
2640191 CAAAAATTAA
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
59 2 0.02
60 7 0.09
61 29 0.35
62 41 0.50
63 3 0.04
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (60 bp):
AAATTAATATTTTATCTAAATTTCAAAGATCAAATTGATACTTCATCTAATTTTAAAAGC
Found at i:2648354 original size:3 final size:3
Alignment explanation
Indices: 2648346--2648370 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2648336 TGATTAAAAA
2648346 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2648371 TAAACTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2656239 original size:47 final size:47
Alignment explanation
Indices: 2656170--2656263 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
2656160 AAGTTGCTTA
2656170 AGTGGAGACAAACACCTTGCTTTGCTGGTCACGCACATGGGCTGTTT
1 AGTGGAGACAAACACCTTGCTTTGCTGGTCACGCACATGGGCTGTTT
** * * *
2656217 AGTGGAGACAGGCATCTTGCTTTGCTGGTCACGCATATGGGGTGTTT
1 AGTGGAGACAAACACCTTGCTTTGCTGGTCACGCACATGGGCTGTTT
2656264 TTTGAGTGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (47 bp):
AGTGGAGACAAACACCTTGCTTTGCTGGTCACGCACATGGGCTGTTT
Found at i:2657987 original size:47 final size:47
Alignment explanation
Indices: 2657913--2658004 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 47
2657903 GCACTCAAAG
*
2657913 AACACCCCATATGCGTGACCAGCAAAGCAAGATGCTTGTCTCCACCA
1 AACAACCCATATGCGTGACCAGCAAAGCAAGATGCTTGTCTCCACCA
* * * *
2657960 AACAACCCATGTGTGTGACCAGCAAAGCAAGGTGTTTGTCTCCAC
1 AACAACCCATATGCGTGACCAGCAAAGCAAGATGCTTGTCTCCAC
2658005 TTAAGCACCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (47 bp):
AACAACCCATATGCGTGACCAGCAAAGCAAGATGCTTGTCTCCACCA
Found at i:2678733 original size:15 final size:15
Alignment explanation
Indices: 2678713--2678742 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2678703 GTACACTTGT
2678713 TGAAGAAAAAACAAA
1 TGAAGAAAAAACAAA
*
2678728 TGAAGAAGAAACAAA
1 TGAAGAAAAAACAAA
2678743 AGGAGATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.07
Consensus pattern (15 bp):
TGAAGAAAAAACAAA
Found at i:2683387 original size:13 final size:15
Alignment explanation
Indices: 2683339--2683387 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2683329 TGGCGTTTAT
*
2683339 TATATACTT-TATTA
1 TATATAATTATATTA
*
2683353 AATAATAATTATATTA
1 TAT-ATAATTATATTA
2683369 TATATAATTATATTA
1 TATATAATTATATTA
2683384 TATA
1 TATA
2683388 GCTCGAAGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 2 0.07
15 21 0.70
16 7 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATAATTATATTA
Found at i:2684616 original size:14 final size:16
Alignment explanation
Indices: 2684579--2684616 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
2684569 TATATTTGAT
2684579 TAATATATGTAGTTTA
1 TAATATATGTAGTTTA
2684595 TAATATATGTAGTTTA
1 TAATATATGTAGTTTA
2684611 TAATAT
1 TAATAT
2684617 TTTGAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (16 bp):
TAATATATGTAGTTTA
Found at i:2684662 original size:21 final size:22
Alignment explanation
Indices: 2684629--2684669 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2684619 TGAATTATAG
*
2684629 ACTATAGTTTTATTATTTAACC
1 ACTATAGTTTTATAATTTAACC
2684651 ACTATA-TTTTATAATTTAA
1 ACTATAGTTTTATAATTTAA
2684670 TTTTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (22 bp):
ACTATAGTTTTATAATTTAACC
Found at i:2684784 original size:2 final size:2
Alignment explanation
Indices: 2684777--2684819 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2684767 CAATCATTAT
*
2684777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2684819 T
1 T
2684820 TTAAGTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2691780 original size:83 final size:83
Alignment explanation
Indices: 2691679--2691843 Score: 258
Period size: 83 Copynumber: 2.0 Consensus size: 83
2691669 AAGCAAGAAC
* * * * * *
2691679 AAAAGCAAATCTGAACTCCATGAAAGAGTAGTGGAACGGTTTTTTTAGCAATGTATGAAATCTTC
1 AAAAGCAAATCTGAACTCCACGAAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATAAAATCTTC
*
2691744 ACGGAATAGTAGTGAAGT
66 ACGAAATAGTAGTGAAGT
*
2691762 AAAAGCAAATCTGAACTCCACGAAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATAAAATTTTC
1 AAAAGCAAATCTGAACTCCACGAAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATAAAATCTTC
2691827 ACGAAATAGTAGTGAAG
66 ACGAAATAGTAGTGAAG
2691844 CAAATCATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (83 bp):
AAAAGCAAATCTGAACTCCACGAAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATAAAATCTTC
ACGAAATAGTAGTGAAGT
Found at i:2697029 original size:5 final size:5
Alignment explanation
Indices: 2697019--2697089 Score: 67
Period size: 5 Copynumber: 14.4 Consensus size: 5
2697009 TATTAACTCA
* * * *
2697019 TACAT TACAT TACAT TAACTAA TACGT TACAT TACAT TA-AG TA-A- TACGT
1 TACAT TACAT TACAT T-AC-AT TACAT TACAT TACAT TACAT TACAT TACAT
2697068 TACAT TACAT TACAT TACAT TA
1 TACAT TACAT TACAT TACAT TA
2697090 GAAGCATTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
3 2 0.04
4 4 0.07
5 43 0.78
6 4 0.07
7 2 0.04
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (5 bp):
TACAT
Found at i:2697038 original size:22 final size:22
Alignment explanation
Indices: 2697010--2697079 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
2697000 TCAAACAAGT
* *
2697010 ATTAACTCATACATTACATTAC
1 ATTAACTAATACGTTACATTAC
2697032 ATTAACTAATACGTTACATTAC
1 ATTAACTAATACGTTACATTAC
*
2697054 ATTAAGTAATACGTTACATTAC
1 ATTAACTAATACGTTACATTAC
2697076 ATTA
1 ATTA
2697080 CATTACATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.37
Consensus pattern (22 bp):
ATTAACTAATACGTTACATTAC
Found at i:2697905 original size:115 final size:114
Alignment explanation
Indices: 2697718--2698330 Score: 605
Period size: 115 Copynumber: 5.3 Consensus size: 114
2697708 TGATATTGGG
* * * *
2697718 TGAATAATTAAGATTCTATGTCATTTTAAATTAGTATTATACCAAATATGATTTTTCATTCATAA
1 TGAATAGTTAAGATTCTCTGTCATTTTAAATTATTATTGTACC-AATATGATTTTTCATTCATAA
*
2697783 TTAAACAAGTTCT-ATATGAGGAGATATATCACTAAAAAGAAAAAAAAACA
65 TTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAG-AAAAAAAACA
* *
2697833 TGGATA-TGTAAGATTCTTTGTCATTTTAAATTATTATTGTACCGAATATGATTTTTCATTCATA
1 TGAATAGT-TAAGATTCTCTGTCATTTTAAATTATTATTGTACC-AATATGATTTTTCATTCATA
* * * * **
2697897 ATTTAACAAGTTCTAATATTAGGTG--ATATCAATAAAAAG--AAAAATGA
64 ATTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAAAACA
* ** * * * *
2697944 TGCGATAACTAAGGTTATCTGTTATTTTAAATTATTATTGTACCATACATGATTTTTCATTCATA
1 TG-AATAGTTAAGATTCTCTGTCATTTTAAATTATTATTGTACCA-ATATGATTTTTCATTCATA
* * * * ** *
2698009 ATTAAACAAGTTCAGATATAAGGTGTTATATCACCAAAAAGAAAAAGGACT
64 ATTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAAAACA
* * * * *
2698060 TGAATAGTTAAGATTCTCTATCATTTTAAACTATTATTGTACATGAATAGTTATAATTTACCATT
1 TGAATAGTTAAGATTCTCTGTCATTTTAAATTATTATTGTAC--CAATA-TGAT--TTT-TCATT
* * * * * *
2698125 TATAATTAAACAAGTTTTGAAATGAGGTGATATATCACTAAAAAGGAAAATAATA
60 CATAATTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAAAACA
* * *
2698180 TAAATAGTTAAGATTCTGC-ATCATTTTAAATTATTATTGTACCATATATGA-TTTTCATTTATA
1 TGAATAGTTAAGATTCT-CTGTCATTTTAAATTATTATTGTACCA-ATATGATTTTTCATTCATA
* * * **
2698243 ATTAAACAAGTTTTGATATGAGGTGATATATCACTGAATAGAAAAAGGACA
64 ATTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAAAACA
*
2698294 TGAATAGTTAATATTCTCTGTCATTTTTAAA-TATTAT
1 TGAATAGTTAAGATTCTCTGTCA-TTTTAAATTATTAT
2698331 GATAGAGACT
Statistics
Matches: 412, Mismatches: 67, Indels: 39
0.80 0.13 0.08
Matches are distributed among these distances:
111 9 0.02
112 74 0.18
113 1 0.00
114 102 0.25
115 112 0.27
116 15 0.04
117 4 0.01
118 3 0.01
119 6 0.01
120 85 0.21
121 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (114 bp):
TGAATAGTTAAGATTCTCTGTCATTTTAAATTATTATTGTACCAATATGATTTTTCATTCATAAT
TAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAAAACA
Found at i:2698275 original size:234 final size:224
Alignment explanation
Indices: 2697720--2698330 Score: 681
Period size: 227 Copynumber: 2.7 Consensus size: 224
2697710 ATATTGGGTG
* * *
2697720 AATAATTAAGATTCTATGTCATTTTAAATTAGTATTATACCAAATATGATTTTTCATTCATAATT
1 AATAATTAAGATTC--TGTCATTTTAAATTATTATTGTACCATATATGATTTTTCATTCATAATT
* ** *
2697785 AAACAAGTTCT-ATATGAGGAGATATATCACTAAAAAGAAAAAAAAACATGGATA-TGTAAGATT
64 AAACAAGTTCTGATATGAGGTGATATATCACTAAAAAG-AAAAAGGACATGAATAGT-TAAGATT
* * *
2697848 CTTTGTCATTTTAAATTATTATTGTACCGAATATGATTTTTCATTCATAATTTAACAAGTTCTAA
127 CTCTGTCATTTTAAA-TATTATTGTACCGAATATGATTTTCCATTCATAATTAAACAAGTTCTAA
* * *
2697913 TATTAGGTGATATCAATAAAAAGAAAAATGATGC
191 TATGAGGTGATATCAATAAAAAGAAAAATAATGA
* * * * *
2697947 GATAACTAAGGTTATCTGTTATTTTAAATTATTATTGTACCATACATGATTTTTCATTCATAATT
1 AATAATTAA-GAT-TCTGTCATTTTAAATTATTATTGTACCATATATGATTTTTCATTCATAATT
* * * * *
2698012 AAACAAGTTCAGATATAAGGTGTTATATCACCAAAAAGAAAAAGGACTTGAATAGTTAAGATTCT
64 AAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAGGACATGAATAGTTAAGATTCT
* * * * *
2698077 CTATCATTTTAAACTATTATTGTACATGAATAGTTATAATTTACCATTTATAATTAAACAAGTTT
129 CTGTCATTTTAAA-TATTATTGTAC-CGAATA-TGAT--TTT-CCATTCATAATTAAACAAGTTC
* * *
2698142 TGAA-ATGAGGTGATATATCACTAAAAAGGAAAATAATATA
188 T-AATATGAGGTG--ATATCAATAAAAAGAAAAATAAT-GA
* *
2698182 AATAGTTAAGATTCTGCATCATTTTAAATTATTATTGTACCATATATGA-TTTTCATTTATAATT
1 AATAATTAAGATTCTG--TCATTTTAAATTATTATTGTACCATATATGATTTTTCATTCATAATT
* * * *
2698246 AAACAAGTTTTGATATGAGGTGATATATCACTGAATAGAAAAAGGACATGAATAGTTAATATTCT
64 AAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAGGACATGAATAGTTAAGATTCT
2698311 CTGTCATTTTTAAATATTAT
129 CTGTCA-TTTTAAATATTAT
2698331 GATAGAGACT
Statistics
Matches: 319, Mismatches: 49, Indels: 25
0.81 0.12 0.06
Matches are distributed among these distances:
227 104 0.33
228 30 0.09
229 5 0.02
231 3 0.01
232 26 0.08
233 6 0.02
234 103 0.32
235 42 0.13
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (224 bp):
AATAATTAAGATTCTGTCATTTTAAATTATTATTGTACCATATATGATTTTTCATTCATAATTAA
ACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAGGACATGAATAGTTAAGATTCTCT
GTCATTTTAAATATTATTGTACCGAATATGATTTTCCATTCATAATTAAACAAGTTCTAATATGA
GGTGATATCAATAAAAAGAAAAATAATGA
Found at i:2698318 original size:114 final size:115
Alignment explanation
Indices: 2697718--2698330 Score: 636
Period size: 114 Copynumber: 5.3 Consensus size: 115
2697708 TGATATTGGG
* * * * *
2697718 TGAATAATTAAGATTCTATGTCATTTTAAATTAGTATTATACCAAATATGATTTTTCATTCATAA
1 TGAATAGTTAAGATTCTCTGTCATTTTAAATTATTATTGTACCATATATGATTTTTCATTCATAA
* **
2697783 TTAAACAAGTTCT-ATATGAGGAGATATATCACTAAAAAGAAAAAAAAACA
66 TTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAG-AAAAAGGACA
* *
2697833 TGGATA-TGTAAGATTCTTTGTCATTTTAAATTATTATTGTACCGA-ATATGATTTTTCATTCAT
1 TGAATAGT-TAAGATTCTCTGTCATTTTAAATTATTATTGTACC-ATATATGATTTTTCATTCAT
* * * * *
2697896 AATTTAACAAGTTCTAATATTAGGTG--ATATCAATAAAAAGAAAAATG--A
64 AATTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAGGACA
* ** * * * *
2697944 TGCGATAACTAAGGTTATCTGTTATTTTAAATTATTATTGTACCATACATGATTTTTCATTCATA
1 TG-AATAGTTAAGATTCTCTGTCATTTTAAATTATTATTGTACCATATATGATTTTTCATTCATA
* * * * *
2698009 ATTAAACAAGTTCAGATATAAGGTGTTATATCACCAAAAAGAAAAAGGACT
65 ATTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAGGACA
* * * *
2698060 TGAATAGTTAAGATTCTCTATCATTTTAAACTATTATTGTA-CATGAATAGTTATAATTTACCAT
1 TGAATAGTTAAGATTCTCTGTCATTTTAAATTATTATTGTACCAT--ATA-TGAT--TTT-TCAT
* * * * ** *
2698124 TTATAATTAAACAAGTTTTGAAATGAGGTGATATATCACTAAAAAGGAAAATAATA
60 TCATAATTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAGGACA
* * *
2698180 TAAATAGTTAAGATTCTGC-ATCATTTTAAATTATTATTGTACCATATATGA-TTTTCATTTATA
1 TGAATAGTTAAGATTCT-CTGTCATTTTAAATTATTATTGTACCATATATGATTTTTCATTCATA
* * *
2698243 ATTAAACAAGTTTTGATATGAGGTGATATATCACTGAATAGAAAAAGGACA
65 ATTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAGGACA
*
2698294 TGAATAGTTAATATTCTCTGTCATTTTTAAA-TATTAT
1 TGAATAGTTAAGATTCTCTGTCA-TTTTAAATTATTAT
2698331 GATAGAGACT
Statistics
Matches: 417, Mismatches: 61, Indels: 41
0.80 0.12 0.08
Matches are distributed among these distances:
111 4 0.01
112 74 0.18
113 6 0.01
114 111 0.27
115 110 0.26
116 13 0.03
117 3 0.01
118 2 0.00
119 6 0.01
120 84 0.20
121 4 0.01
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (115 bp):
TGAATAGTTAAGATTCTCTGTCATTTTAAATTATTATTGTACCATATATGATTTTTCATTCATAA
TTAAACAAGTTCTGATATGAGGTGATATATCACTAAAAAGAAAAAGGACA
Found at i:2700044 original size:15 final size:15
Alignment explanation
Indices: 2700024--2700053 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2700014 ACATAATCAC
2700024 ACAAACACAATGATA
1 ACAAACACAATGATA
2700039 ACAAACACAATGATA
1 ACAAACACAATGATA
2700054 GTACATAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.07, T:0.13
Consensus pattern (15 bp):
ACAAACACAATGATA
Found at i:2700213 original size:23 final size:22
Alignment explanation
Indices: 2700187--2700244 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2700177 TATTGAATTG
2700187 CCTTGGCACATAATACTAATA-TT
1 CCTTGGCAC-TAATACTAA-AGTT
*
2700210 CCTTGGCACTGATACTAAAGTT
1 CCTTGGCACTAATACTAAAGTT
* *
2700232 CCTTAGCATTAAT
1 CCTTGGCACTAAT
2700245 TAGAGTAGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 20 0.67
23 9 0.30
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (22 bp):
CCTTGGCACTAATACTAAAGTT
Found at i:2700227 original size:22 final size:23
Alignment explanation
Indices: 2700187--2700235 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2700177 TATTGAATTG
2700187 CCTTGGCACATAATACTAATA-TT
1 CCTTGGCACATAATACTAA-AGTT
*
2700210 CCTTGGCAC-TGATACTAAAGTT
1 CCTTGGCACATAATACTAAAGTT
2700232 CCTT
1 CCTT
2700236 AGCATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 14 0.58
23 9 0.38
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (23 bp):
CCTTGGCACATAATACTAAAGTT
Found at i:2700507 original size:19 final size:19
Alignment explanation
Indices: 2700483--2700528 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2700473 TTGGTGGTCT
*
2700483 TTAACCCATTTTTGGTTCA
1 TTAACCCATTTCTGGTTCA
*
2700502 TTAACCCGTTTCTGGTTCA
1 TTAACCCATTTCTGGTTCA
2700521 TTAACCCA
1 TTAACCCA
2700529 AAGTTAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (19 bp):
TTAACCCATTTCTGGTTCA
Found at i:2700852 original size:49 final size:49
Alignment explanation
Indices: 2700796--2700890 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
2700786 GCTTCACACT
2700796 AAGGATTTCTAACAAATTTACAAATTTGTTCTTTCTTTTTCTAGGACAA
1 AAGGATTTCTAACAAATTTACAAATTTGTTCTTTCTTTTTCTAGGACAA
*
2700845 AAGGATTTCTAACAAATTTACTAATTTGTTCTTTCTTTTTCTAGGA
1 AAGGATTTCTAACAAATTTACAAATTTGTTCTTTCTTTTTCTAGGA
2700891 GAAAGAGTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (49 bp):
AAGGATTTCTAACAAATTTACAAATTTGTTCTTTCTTTTTCTAGGACAA
Found at i:2701499 original size:20 final size:20
Alignment explanation
Indices: 2701476--2701527 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2701466 ACAAGAATAA
*
2701476 TATCAAAATTGTTCATGCGG
1 TATCAATATTGTTCATGCGG
* * *
2701496 TATCGATATTCTTCATGTGG
1 TATCAATATTGTTCATGCGG
2701516 TATCAATATTGT
1 TATCAATATTGT
2701528 AAGAATAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.42
Consensus pattern (20 bp):
TATCAATATTGTTCATGCGG
Found at i:2705066 original size:17 final size:17
Alignment explanation
Indices: 2705044--2705076 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2705034 TGCTCCAAGG
*
2705044 GGAGTATCGATACTATT
1 GGAGTACCGATACTATT
2705061 GGAGTACCGATACTAT
1 GGAGTACCGATACTAT
2705077 AAAGAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (17 bp):
GGAGTACCGATACTATT
Found at i:2711447 original size:13 final size:14
Alignment explanation
Indices: 2711428--2711462 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2711418 CGTTAATTAT
*
2711428 TTATTCTTCGTTTA
1 TTATTCTTCATTTA
2711442 -TATTCTTCATTTA
1 TTATTCTTCATTTA
2711455 TTATTCTT
1 TTATTCTT
2711463 AAATCCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.17, C:0.14, G:0.03, T:0.66
Consensus pattern (14 bp):
TTATTCTTCATTTA
Found at i:2714154 original size:30 final size:31
Alignment explanation
Indices: 2714118--2714187 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
2714108 GCTTCAAAAA
* * *
2714118 TAACAAATTAATCACT-AATTTATCGATTTG
1 TAACAAAATAATCACTGAAGTTATCAATTTG
* *
2714148 TAACAAAATGATCACTGACGTTATCAATTTG
1 TAACAAAATAATCACTGAAGTTATCAATTTG
*
2714179 TAAAAAAAT
1 TAACAAAAT
2714188 GGTCACTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (31 bp):
TAACAAAATAATCACTGAAGTTATCAATTTG
Found at i:2714210 original size:31 final size:30
Alignment explanation
Indices: 2714137--2714210 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
2714127 AATCACTAAT
* *
2714137 TTATCGATTTGTAACAAAATGATCACTGACG
1 TTATC-ATTTGTAAAAAAATGATCACTCACG
*
2714168 TTATCAATTTGTAAAAAAATGGTCACTTCACCG
1 TTATC-ATTTGTAAAAAAATGATCAC-TCA-CG
2714201 TTATC-TTTGT
1 TTATCATTTGT
2714211 TAAATTGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 28 0.76
32 2 0.05
33 7 0.19
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (30 bp):
TTATCATTTGTAAAAAAATGATCACTCACG
Found at i:2714946 original size:26 final size:26
Alignment explanation
Indices: 2714890--2714949 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
2714880 ACTCGTCCTT
*
2714890 TTTTTTAGTATTTTCAAGATATTTTA
1 TTTTTTAATATTTTCAAGATATTTTA
* * *
2714916 ATTTTTAATATTTT-TATATATTCTTA
1 TTTTTTAATATTTTCAAGATATT-TTA
2714942 TTTTTTAA
1 TTTTTTAA
2714950 AAAGTATTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (26 bp):
TTTTTTAATATTTTCAAGATATTTTA
Found at i:2715179 original size:31 final size:31
Alignment explanation
Indices: 2715138--2715209 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
2715128 TGGAGTGACT
*
2715138 ATTTTATTACAAATTGATAACATTAGTAATC
1 ATTTTGTTACAAATTGATAACATTAGTAATC
* * *
2715169 ATTTTGTTACAAATTGATCAGATTAGTTATC
1 ATTTTGTTACAAATTGATAACATTAGTAATC
*
2715200 AATTTGTTAC
1 ATTTTGTTAC
2715210 TTTTAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (31 bp):
ATTTTGTTACAAATTGATAACATTAGTAATC
Found at i:2720759 original size:2 final size:2
Alignment explanation
Indices: 2720754--2720779 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2720744 CACACACACA
2720754 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2720780 TAAATTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2720855 original size:23 final size:22
Alignment explanation
Indices: 2720795--2720851 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
2720785 TATTAAAATA
*
2720795 AATGTAATAAATAAATTATATTT
1 AATGTAAT-AATAAATTATAGTT
* *
2720818 CATATATATAATAAATTATAGTT
1 AATGTA-ATAATAAATTATAGTT
2720841 AATGTAATAAT
1 AATGTAATAAT
2720852 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 5 0.18
23 21 0.75
24 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (22 bp):
AATGTAATAATAAATTATAGTT
Found at i:2721012 original size:2 final size:2
Alignment explanation
Indices: 2720961--2720998 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2720951 TAATATTTTT
2720961 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2720999 TAACATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2729061 original size:19 final size:19
Alignment explanation
Indices: 2729018--2729060 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2729008 ATTCCCCCTG
2729018 TAGGGGAATCGATACCCCA
1 TAGGGGAATCGATACCCCA
2729037 TAGGGGAATCGATACCCCA
1 TAGGGGAATCGATACCCCA
2729056 T-GGGG
1 TAGGGG
2729061 GTTCTGGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.28, C:0.23, G:0.33, T:0.16
Consensus pattern (19 bp):
TAGGGGAATCGATACCCCA
Found at i:2731281 original size:21 final size:23
Alignment explanation
Indices: 2731228--2731281 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
2731218 ATTTAACAGA
*
2731228 AAGGGGGAGAAGTGTTAAGGTGTT
1 AAGGGGGAGAAGTGTTAA-GAGTT
2731252 AAGGGGGAGAAGTGTTAA-AG-T
1 AAGGGGGAGAAGTGTTAAGAGTT
*
2731273 AATGGGGAG
1 AAGGGGGAG
2731282 TAATTTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.32
22 1 0.04
24 18 0.64
ACGTcount: A:0.33, C:0.00, G:0.46, T:0.20
Consensus pattern (23 bp):
AAGGGGGAGAAGTGTTAAGAGTT
Found at i:2737730 original size:45 final size:44
Alignment explanation
Indices: 2737680--2737768 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
2737670 AAACGTTTGA
2737680 ATTTGA-TATGGATGTTTGGAAATGA-TTGAACTTGAATGTTTATAT
1 ATTTGATTATGGATGTTT-G-AATGATTTGAA-TTGAATGTTTATAT
* * *
2737725 ATTTGATTTTGGTTGTTTGAATGATTTGAATTTAATGTTTATAT
1 ATTTGATTATGGATGTTTGAATGATTTGAATTGAATGTTTATAT
2737769 TGTTTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
44 18 0.46
45 12 0.31
46 9 0.23
ACGTcount: A:0.28, C:0.01, G:0.20, T:0.51
Consensus pattern (44 bp):
ATTTGATTATGGATGTTTGAATGATTTGAATTGAATGTTTATAT
Found at i:2738394 original size:54 final size:54
Alignment explanation
Indices: 2738331--2738451 Score: 147
Period size: 54 Copynumber: 2.2 Consensus size: 54
2738321 CTCATAGGGT
*
2738331 GTACCGATACCCCTATTCCAA-TTTTGGCTCCGAGAAAAACAGATTG-CCTAATGG
1 GTACCGATACCCCTA-TCCAAGTTTTGGCTCCGAGAAAAACAGAATGCCCT-ATGG
* * * *
2738385 GTACCGATACCCCTATGCAAGTTTTGGGTCTGAGAAAAACATAATGCCCTATGG
1 GTACCGATACCCCTATCCAAGTTTTGGCTCCGAGAAAAACAGAATGCCCTATGG
**
2738439 GTATTGATACCCC
1 GTACCGATACCCC
2738452 CTTAGAGGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 4 0.07
54 51 0.88
55 3 0.05
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (54 bp):
GTACCGATACCCCTATCCAAGTTTTGGCTCCGAGAAAAACAGAATGCCCTATGG
Done.