Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold139
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: 1720190
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4798 characters in sequence are not A, C, G, or T
File 8 of 11
Found at i:1132809 original size:16 final size:15
Alignment explanation
Indices: 1132788--1132843 Score: 71
Period size: 16 Copynumber: 3.7 Consensus size: 15
1132778 GTGTAAATCT
1132788 AAAAATTTAAATTCAA
1 AAAAATTTAAATT-AA
*
1132804 AAAAATTCAAATTTAA
1 AAAAATTTAAA-TTAA
1132820 AAAAATTTAAA--AA
1 AAAAATTTAAATTAA
1132833 AAAAATTTAAA
1 AAAAATTTAAA
1132844 CACAAGAGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 13 0.35
16 22 0.59
17 2 0.05
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATTTAAATTAA
Found at i:1132835 original size:12 final size:13
Alignment explanation
Indices: 1132818--1132843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1132808 ATTCAAATTT
1132818 AAAAAAATTTAAA
1 AAAAAAATTTAAA
1132831 AAAAAAATTTAAA
1 AAAAAAATTTAAA
1132844 CACAAGAGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAAATTTAAA
Found at i:1136721 original size:18 final size:18
Alignment explanation
Indices: 1136700--1136758 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
1136690 AGGAAGAAGG
*
1136700 GAAAAGAAATGAAGAAAA
1 GAAAAGAAAAGAAGAAAA
* *
1136718 GAAAAAGGAAGGAA-AAAA
1 G-AAAAGAAAAGAAGAAAA
*
1136736 GAAAA-AAAAAAAGAAGAA
1 GAAAAGAAAAGAAGAA-AA
1136754 GAAAA
1 GAAAA
1136759 AAGGAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 13 0.39
19 10 0.30
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (18 bp):
GAAAAGAAAAGAAGAAAA
Found at i:1136743 original size:26 final size:25
Alignment explanation
Indices: 1136711--1136767 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 25
1136701 AAAAGAAATG
* *
1136711 AAGAAAAGAAAAAGGAAG--GAAAA
1 AAGAAAAAAAAAAAGAAGAAGAAAA
1136734 AAGAAAAAAAAAAAGAAGAAGAAAA
1 AAGAAAAAAAAAAAGAAGAAGAAAA
*
1136759 AAGGAAAAA
1 AAGAAAAAA
1136768 TGGTATGGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 16 0.55
25 13 0.45
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (25 bp):
AAGAAAAAAAAAAAGAAGAAGAAAA
Found at i:1137834 original size:81 final size:83
Alignment explanation
Indices: 1137680--1137850 Score: 240
Period size: 81 Copynumber: 2.1 Consensus size: 83
1137670 TAAATAACAT
**
1137680 ATAATTCGGGCACCAAGAGATTGACCTTGAAATAGATCATTACCTAAGATCATAAAGTGGCGTAC
1 ATAATTCGGGCACCAAGAGATTGACCCCGAAATAGATCATTACCTAAGATCATAAAGTGGCGTAC
*
1137745 GAACGCCCTTTATATAGG
66 AAACGCCCTTTATATAGG
* * **
1137763 A-AATTTGGGCACCAA-AGATTGACCCCGAAATAGGTCATTGTCT-AGAGTCATAAAGTGGCGTA
1 ATAATTCGGGCACCAAGAGATTGACCCCGAAATAGATCATTACCTAAGA-TCATAAAGTGGCGTA
*
1137825 CAAATGCCCTTTATATAGG
65 CAAACGCCCTTTATATAGG
1137844 ATAATTC
1 ATAATTC
1137851 ATTTTTTGTA
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 3 0.04
81 56 0.73
82 17 0.22
83 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (83 bp):
ATAATTCGGGCACCAAGAGATTGACCCCGAAATAGATCATTACCTAAGATCATAAAGTGGCGTAC
AAACGCCCTTTATATAGG
Found at i:1140024 original size:156 final size:154
Alignment explanation
Indices: 1139531--1140427 Score: 777
Period size: 156 Copynumber: 5.8 Consensus size: 154
1139521 TTCGACATAT
** * * * * *
1139531 AAGTGCCTAATACCCCTAAAGGACTTAAAAAGGATTATAGATAGAATAAACTTATCCTAAATACT
1 AAGTGCCCGATACCCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACC
* * * * * * *
1139596 CACCATCG-GCATAAAAGCAAACTTGGTGATAATCTAGGACTTGATTTTAAAAAAATTACAAAAA
66 CACCTTCGAGCATAAAAGCAAACCTGGTGACAACCTAAGACTCGATTTTGAAAAAATTACAAAAA
* *
1139660 TACCTTTAATGGATACCTTCCGCA-A-
131 TACCCTTAA-GGAT-CCTTTCG-AGAG
* * * *
1139685 AAGTGCCCAATACTCCTAAAAGACGTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACC
1 AAGTGCCCGATACCCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACC
* * * * * * * *
1139750 CACATT-TAGCATAAAAGCGAACCTGGTGACAACTTAAGATTTGGTTCT-AAAAAATTACAAAAA
66 CACCTTCGAGCATAAAAGCAAACCTGGTGACAACCTAAGACTCGATTTTGAAAAAATTACAAAAA
*
1139813 TACCTCTAAAGGATACC-TTCGAGATG
131 TACC-CTTAAGGAT-CCTTTCGAGA-G
* * * *
1139839 AAAGTGCTCGATACTCCTAAAGGACTTAAAAGGGATTATAGATGGGATGAACTTAT-CTAAATAC
1 -AAGTGCCCGATACCCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATAC
* ** * * *
1139903 TCACCTTCGA-CATAAAAAGCGGACCTAGTGACAACCTAAGACTTGATTTTGAAAAAATTACGAA
65 CCACCTTCGAGCAT-AAAAGCAAACCTGGTGACAACCTAAGACTCGATTTTGAAAAAATTACAAA
1139967 AATACCCTTAAGAGATCCTTTCGATGTAG
129 AATACCCTTAAG-GATCCTTTCGA-G-AG
* * *
1139996 AAGTGCCCGATACCCCTTAAGGACTTAAAAAGGATTATATATGGGATGAACCTATCCTAGATACC
1 AAGTGCCCGATACCCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACC
* * ** * * * * * *
1140061 TACCTTCG-GTATAAAAGCGGACATGGTGACAACTTAAGACTCGGTTATGGAAATATTACAAAAA
66 CACCTTCGAGCATAAAAGCAAACCTGGTGACAACCTAAGACTCGATTTTGAAAAAATTACAAAAA
* * * *
1140125 TGCACC-TATAGGTATACTTTTGACATG
131 TAC-CCTTA-AGG-ATCCTTTCGAGA-G
* * * * * *
1140152 AAAATATCTCGGTAACCCTAAAGAACTT--AAA--A-TATAGATGGGATGAACCTATCCTAAATA
1 -AAGT-GCCCGATACCCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATA
* * * * *
1140212 CACACCTTC-AGCATAAAAGCAAACCCGGTTACAACCTAGGACTCGATTTTGAAAAAATTATAAA
64 CCCACCTTCGAGCATAAAAGCAAACCTGGTGACAACCTAAGACTCGATTTTGAAAAAATTACAAA
* * *
1140276 AATACCCTTAGGGGAT-ATCTTCAACGTAG
129 AATACCCTTA-AGGATCCT-TTCGA-G-AG
* * * * * *
1140305 AAGTGCCTGATACCCTTTAAGGACTTAACAAGGATTACAGATGGGATGAACCTATCTTAAATACC
1 AAGTGCCCGATACCCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACC
* *
1140370 CACCTTC-AGCATAAAAGCAAACCCGGTGACAACCTAAGACTCGATTCTGAAAAAATTA
66 CACCTTCGAGCATAAAAGCAAACCTGGTGACAACCTAAGACTCGATTTTGAAAAAATTA
1140428 TGAAAAATGC
Statistics
Matches: 601, Mismatches: 111, Indels: 60
0.78 0.14 0.08
Matches are distributed among these distances:
151 16 0.03
152 14 0.02
153 111 0.18
154 112 0.19
155 89 0.15
156 209 0.35
157 33 0.05
158 17 0.03
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (154 bp):
AAGTGCCCGATACCCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACC
CACCTTCGAGCATAAAAGCAAACCTGGTGACAACCTAAGACTCGATTTTGAAAAAATTACAAAAA
TACCCTTAAGGATCCTTTCGAGAG
Found at i:1140319 original size:309 final size:310
Alignment explanation
Indices: 1139544--1140482 Score: 1036
Period size: 309 Copynumber: 3.0 Consensus size: 310
1139534 TGCCTAATAC
* * * * * *
1139544 CCCTAAAGGACTTAAAAAGGATTATAGATAGAATAAACTTATCCTAAATACTCACCATCGGCATA
1 CCCTAAAGAACTT-AAAA-GATTATAGATGGGATGAACCTATCCTAAATACTCACCTTC-GCATA
* * * * * *
1139609 AAAGCAAACTTGGTGATAATCTAGGACTTGATTTTAAAAAAATTACAAAAATACCTTTAATGGAT
63 AAAGCAAACCTGGTGACAACCTAGGACTTGATTTTGAAAAAATTACAAAAATACCCTTAAGGGAT
* * * * * * *
1139674 ACCTTC-CGCAAAAGTGCCCAATACTCCTAAAAGACGTAAAAAGGATTATAGATGGGATGAACCT
128 ACCTTCACGTAGAAGTGCCCGATACCCCTTAAGGACTTAAAAAGGATTATAGATGGGATGAACCT
* * * *
1139738 ATCCTAAATACCCACATTTAGCATAAAAGCGAACCTGGTGACAACTTAAGATTTGGTTCT-AAAA
193 ATCCTAAATACCCACCTTCAGCATAAAAGCGAACCTGGTGACAACTTAAGACTCGGTTCTGAAAA
* * * * *
1139802 AATTACAAAAATACCTCTAAAGG-ATACCTTCGAGATGAAAGT-GCTCGAT-A
258 AATTACAAAAATGCCTCTATAGGTATACCTTCGACATGAAAGTATCTCGGTAA
* *
1139852 CTCCTAAAGGACTTAAAAGGGATTATAGATGGGATGAACTTAT-CTAAATACTCACCTTCGACAT
1 C-CCTAAAGAACTTAAAA--GATTATAGATGGGATGAACCTATCCTAAATACTCACCTTCG-CAT
** * * * *
1139916 AAAAAGCGGACCTAGTGACAACCTAAGACTTGATTTTGAAAAAATTACGAAAATACCCTTAAGAG
62 -AAAAGCAAACCTGGTGACAACCTAGGACTTGATTTTGAAAAAATTACAAAAATACCCTTAAGGG
* *
1139981 AT-CCTTTCGATGTAGAAGTGCCCGATACCCCTTAAGGACTTAAAAAGGATTATATATGGGATGA
126 ATACC-TTC-ACGTAGAAGTGCCCGATACCCCTTAAGGACTTAAAAAGGATTATAGATGGGATGA
* * * * * * *
1140045 ACCTATCCTAGATACCTACCTTCGGTATAAAAGCGGACATGGTGACAACTTAAGACTCGGTTATG
189 ACCTATCCTAAATACCCACCTTCAGCATAAAAGCGAACCTGGTGACAACTTAAGACTCGGTTCTG
* * * * *
1140110 GAAATATTACAAAAATGCAC-CTATAGGTATACTTTTGACATGAAAATATCTCGGTAA
254 AAAAAATTACAAAAATGC-CTCTATAGGTATACCTTCGACATGAAAGTATCTCGGTAA
*
1140167 CCCTAAAGAACTT-AAA-A-TATAGATGGGATGAACCTATCCTAAATACACACCTTCAGCATAAA
1 CCCTAAAGAACTTAAAAGATTATAGATGGGATGAACCTATCCTAAATACTCACCTTC-GCATAAA
* * * * * *
1140229 AGCAAACCCGGTTACAACCTAGGACTCGATTTTGAAAAAATTATAAAAATACCCTTAGGGGATAT
65 AGCAAACCTGGTGACAACCTAGGACTTGATTTTGAAAAAATTACAAAAATACCCTTAAGGGATAC
* * * *
1140294 CTTCAACGTAGAAGTGCCTGATACCCTTTAAGGACTTAACAAGGATTACAGATGGGATGAACCTA
130 CTTC-ACGTAGAAGTGCCCGATACCCCTTAAGGACTTAAAAAGGATTATAGATGGGATGAACCTA
* * * * *
1140359 TCTTAAATACCCACCTTCAGCATAAAAGCAAACCCGGTGACAACCTAAGACTCGATTCTGAAAAA
194 TCCTAAATACCCACCTTCAGCATAAAAGCGAACCTGGTGACAACTTAAGACTCGGTTCTGAAAAA
* * * *
1140424 ATTATGAAAAATGCCTCTATGGGTATACCTTCGACATGAAAGTATATCGGGAA
259 ATTA-CAAAAATGCCTCTATAGGTATACCTTCGACATGAAAGTATCTCGGTAA
*
1140477 CTCTAA
1 CCCTAA
1140483 TGGACACTAA
Statistics
Matches: 524, Mismatches: 90, Indels: 32
0.81 0.14 0.05
Matches are distributed among these distances:
307 1 0.00
308 25 0.05
309 277 0.53
310 64 0.12
311 99 0.19
312 21 0.04
313 19 0.04
314 16 0.03
315 2 0.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (310 bp):
CCCTAAAGAACTTAAAAGATTATAGATGGGATGAACCTATCCTAAATACTCACCTTCGCATAAAA
GCAAACCTGGTGACAACCTAGGACTTGATTTTGAAAAAATTACAAAAATACCCTTAAGGGATACC
TTCACGTAGAAGTGCCCGATACCCCTTAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATC
CTAAATACCCACCTTCAGCATAAAAGCGAACCTGGTGACAACTTAAGACTCGGTTCTGAAAAAAT
TACAAAAATGCCTCTATAGGTATACCTTCGACATGAAAGTATCTCGGTAA
Found at i:1142825 original size:163 final size:165
Alignment explanation
Indices: 1142492--1142847 Score: 398
Period size: 164 Copynumber: 2.2 Consensus size: 165
1142482 ATTTATTATA
* * * **
1142492 AATTAAATGATGATATATGATGAATTTTAAAAATTATAAACCATGAAAAAAATCCGTTGAAAACA
1 AATTAAATGATAATATTTGATGAATTTAAAAAATTATAAACCA-GAAAAAAATCCCCTGAAAACA
* * * * * *
1142557 TTTATAGAGTAGAAAACCTTGTATTTCAAAAACAAGAGAATTTTAATGAAAAAATGAAAAATTCA
65 TTTACAGAGTAAAAAACCTGGTATTTCAAAAACAAGAAAATTTAAATGAAAAAATAAAAAATTCA
* * **
1142622 TGAAATAAGCAGAATTTTCAAAATAGATTTAATGTG
130 TGAAATAAGAAAAAAATTCAAAATAGATTTAATGTG
* * * *
1142658 AATTAAATAATAATATTTGATTAATTTAAAAAATTATAAA-CA-AAGAAAATCTCCCTGAAACCA
1 AATTAAATGATAATATTTGATGAATTTAAAAAATTATAAACCAGAAAAAAATC-CCCTGAAAACA
* * * * *
1142721 TTTACGGAGTAAAAAATCTGGTATTTTAAAAATAGGAAAATTTAAA-GTAAAAAATAAAAAATTC
65 TTTACAGAGTAAAAAACCTGGTATTTCAAAAACAAGAAAATTTAAATG-AAAAAATAAAAAATTC
*
1142785 GTGAAATAA-AAAAAAATTCAAAACT-GATTTAATGTG
129 ATGAAATAAGAAAAAAATTCAAAA-TAGATTTAATGTG
* *
1142821 AATTAAATGATAATATTTAAAGAATTT
1 AATTAAATGATAATATTTGATGAATTT
1142848 TGATGTTCAA
Statistics
Matches: 158, Mismatches: 29, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
163 53 0.34
164 68 0.43
165 2 0.01
166 35 0.22
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.31
Consensus pattern (165 bp):
AATTAAATGATAATATTTGATGAATTTAAAAAATTATAAACCAGAAAAAAATCCCCTGAAAACAT
TTACAGAGTAAAAAACCTGGTATTTCAAAAACAAGAAAATTTAAATGAAAAAATAAAAAATTCAT
GAAATAAGAAAAAAATTCAAAATAGATTTAATGTG
Found at i:1143849 original size:2 final size:2
Alignment explanation
Indices: 1143842--1143890 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
1143832 AGAGATAAAG
*
1143842 AT AT AT AT AT AT AT AT AT AT -T A- AT GAT A- AT A- AG 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
1143881 AT AT AT AT AT
1 AT AT AT AT AT
1143891 TAATGATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
1 4 0.10
2 35 0.85
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1143879 original size:29 final size:29
Alignment explanation
Indices: 1143846--1143901 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1143836 ATAAAGATAT
1143846 ATATATATATATATATTAATGATAATAAG
1 ATATATATATATATATTAATGATAATAAG
1143875 ATATATATATATATATTAATGATAATA
1 ATATATATATATATATTAATGATAATA
1143902 TGGCCCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (29 bp):
ATATATATATATATATTAATGATAATAAG
Found at i:1146332 original size:79 final size:79
Alignment explanation
Indices: 1146150--1146332 Score: 242
Period size: 79 Copynumber: 2.3 Consensus size: 79
1146140 ACAACGGGGC
** * * *
1146150 TGGAGTATCCCCGATTATGGGAAATCGGTGTTCTGGAAATAAAATCGGGGTTGGAGTATCCCCTT
1 TGGAGTATCCCCGATTATGAAAAATCGGTATTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
1146215 GAAAATAACAGGAT
66 GAAAATAACAGGAT
* ** *
1146229 TGGAATATCCTTGATTAT-AGAAAATCGGTATTTTGAAAATAAAATCGGGGTTGGAGTATCCCCT
1 TGGAGTATCCCCGATTATGA-AAAATCGGTATTCTGAAAATAAAATCGGGGTTGGAGTATCCCCT
*
1146293 CGAAAATAACAGGGT
65 CGAAAATAACAGGAT
* *
1146308 TGGAGTATCCCCAATTGTGAAAAAT
1 TGGAGTATCCCCGATTATGAAAAAT
1146333 TAATATTTTA
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
79 86 0.99
80 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATGAAAAATCGGTATTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
GAAAATAACAGGAT
Found at i:1146348 original size:79 final size:78
Alignment explanation
Indices: 1146185--1146349 Score: 206
Period size: 79 Copynumber: 2.1 Consensus size: 78
1146175 CGGTGTTCTG
* ***
1146185 GAAATAAAATCGGGGTTGGAGTATCCCCTTGAAAATAACAGGATTGGAATATCCTTGATTATAGA
1 GAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGATTGGAATATCCCCAATTATAGA
**
1146250 AAATCGGTATTTT
66 AAATCAATATTTT
* * *
1146263 GAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATTGT-G
1 G-AAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGATTGGAATATCCCCAATTATAG
*
1146327 AAAAATTAATATTTT
65 -AAAATCAATATTTT
1146342 AGAAATAA
1 -GAAATAA
1146350 GGCCGGGGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
78 2 0.03
79 71 0.96
80 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (78 bp):
GAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGATTGGAATATCCCCAATTATAGA
AAATCAATATTTT
Found at i:1146416 original size:130 final size:128
Alignment explanation
Indices: 1146257--1146577 Score: 344
Period size: 130 Copynumber: 2.5 Consensus size: 128
1146247 AGAAAATCGG
* *
1146257 TATTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAA
1 TATTTTGGAAATAAACT-GGGGTTGGAGTAT-CCCTCGAAAATAACAGGGTTGGAGTATCCCCAA
* **
1146322 TTGTGAAAAATTAATATTTTAGAAATA-AGGCCGGGGTTAAAGTATCTCCGATTATGTGA-AATC
64 TTGTGAAAAATTAATATTTTAGAAATATA-ACCGAAGTTAAAGTATCTCCGATTATG-GAGAATC
1146385 AA
127 AA
* *
1146387 TATTTTGGAAATAAAGCTGGGGTTAGAGTATCCC-CGATGAAATAACAGGGTTGGAGTATCCCCG
1 TATTTTGGAAATAAA-CTGGGGTTGGAGTATCCCTCGA--AAATAACAGGGTTGGAGTATCCCCA
** * * * ** * **
1146451 ATTGTGAAAAATTGGTGTTTTGGAAATATAATCGAAGTTGGAGTATCTTCGATTATGGAGAATTG
63 ATTGTGAAAAATTAATATTTTAGAAATATAACCGAAGTTAAAGTATCTCCGATTATGGAGAATCA
*
1146516 G
128 A
* * * *
1146517 TGTTTTAG-AATAAAACCGGGGTTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCC
1 TATTTTGGAAAT-AAACTGGGGTTGGAGTATCCCTCGAAAATAACAGGGTTGGAGTATCCCC
1146578 GATGAAATAA
Statistics
Matches: 161, Mismatches: 23, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
128 26 0.16
129 24 0.15
130 109 0.68
131 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (128 bp):
TATTTTGGAAATAAACTGGGGTTGGAGTATCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATT
GTGAAAAATTAATATTTTAGAAATATAACCGAAGTTAAAGTATCTCCGATTATGGAGAATCAA
Found at i:1146504 original size:51 final size:51
Alignment explanation
Indices: 1146436--1146703 Score: 186
Period size: 51 Copynumber: 5.2 Consensus size: 51
1146426 AAATAACAGG
* * * * *
1146436 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATATAATCGAA
1 GTTGGAGTATCCTCGATTGTGAAGAATTGGTGTTTTAGAAATAAAATCGGA
* * * * *
1146487 GTTGGAGTATCTTCGATTATGGAGAATTGGTGTTTTAG-AATAAAACCGGG
1 GTTGGAGTATCCTCGATTGTGAAGAATTGGTGTTTTAGAAATAAAATCGGA
*** ** * **
1146537 GTTGGAGTATCCCTCGAAAAT-AACGGGGTTGGAGTATCCCCGATGAAAT--AAT-GGA
1 GTTGGAGTAT-CCTCGATTGTGAA--GAATTGGTGT-T---TTA-GAAATAAAATCGGA
* * * * *
1146592 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTGGAAATAAAATCGAA
1 GTTGGAGTATCCTCGATTGTGAAGAATTGGTGTTTTAGAAATAAAATCGGA
* * * *
1146643 GTTGGAGTATCCTCGATTGTGGAGAATTGGTATTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCTCGATTGTGAAGAATTGGTGTTTTAGAAATAAAATCGGA
1146694 GTTGGAGTAT
1 GTTGGAGTAT
1146704 TCCCTCGGAA
Statistics
Matches: 163, Mismatches: 41, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
48 5 0.03
50 22 0.13
51 95 0.58
52 8 0.05
53 6 0.04
54 6 0.04
55 14 0.09
56 3 0.02
57 1 0.01
58 3 0.02
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCTCGATTGTGAAGAATTGGTGTTTTAGAAATAAAATCGGA
Found at i:1146566 original size:27 final size:27
Alignment explanation
Indices: 1146533--1146607 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 27
1146523 AGAATAAAAC
1146533 CGGGGTTGGAGTATCCCTCGA-AAATAA
1 CGGGGTTGGAGTATCCC-CGAGAAATAA
1146560 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGA-GAAATAA
* *
1146588 TGGAGTTGGAGTATCCCCGA
1 CGGGGTTGGAGTATCCCCGA
1146608 TTGTGAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 3 0.07
27 17 0.39
28 24 0.55
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.23
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGAGAAATAA
Found at i:1146604 original size:156 final size:158
Alignment explanation
Indices: 1146405--1146732 Score: 536
Period size: 156 Copynumber: 2.1 Consensus size: 158
1146395 AAATAAAGCT
* *
1146405 GGGGTTAGAGTATCCCCGATGAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTT
1 GGGGTTGGAGTATCCCCGATGAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATT
* * *
1146470 TTGGAAATATAATCGAAGTTGGAGTATCTTCGATTATGGAGAATTGGTGTTTTAG-AATAAAACC
66 TTGGAAATAAAATCGAAGTTGGAGTATCCTCGATTATGGAGAATTGGTATTTTAGAAATAAAACC
1146534 GGGGTTGGAGTA-TCCCTCGAAAATAAC
131 GGGGTTGGAGTATTCCCTCGAAAATAAC
*
1146561 GGGGTTGGAGTATCCCCGATGAAATAA-TGGAGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT
1 GGGGTTGGAGTATCCCCGATGAAATAACAGG-GTTGGAGTATCCCCGATTGTGAAAAATTGGTAT
*
1146625 TTTGGAAATAAAATCGAAGTTGGAGTATCCTCGATTGTGGAGAATTGGTATTTTAGAAATAAAAC
65 TTTGGAAATAAAATCGAAGTTGGAGTATCCTCGATTATGGAGAATTGGTATTTTAGAAATAAAAC
*
1146690 CGGGGTTGGAGTATTCCCTCGGAAATAAC
130 CGGGGTTGGAGTATTCCCTCGAAAATAAC
* *
1146719 GAGATTGGAGTATC
1 GGGGTTGGAGTATC
1146733 TTCGATTATG
Statistics
Matches: 159, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
155 2 0.01
156 110 0.69
157 21 0.13
158 26 0.16
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (158 bp):
GGGGTTGGAGTATCCCCGATGAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATT
TTGGAAATAAAATCGAAGTTGGAGTATCCTCGATTATGGAGAATTGGTATTTTAGAAATAAAACC
GGGGTTGGAGTATTCCCTCGAAAATAAC
Found at i:1146809 original size:157 final size:154
Alignment explanation
Indices: 1146643--1146940 Score: 400
Period size: 157 Copynumber: 1.9 Consensus size: 154
1146633 TAAAATCGAA
* * ** * *
1146643 GTTGGAGTATCCTCGATTGTG-GAGAATTGGTATTTTAGAAATAAAACCGGGGTTGGAGTATTCC
1 GTTGGAGTATCCGCGATTATGAGA-AATTAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCC
* **
1146707 CTCGGAAATAACGAGATTGGAGTATCTTCGATTATGAAAAATTAATGTTTTAGAAATAAAACCAG
65 CTCAGAAATAACGAGATTGGAGTATCCCCG---ATGAAAAATTAATGTTTTAGAAATAAAACCAG
*
1146772 GGTTGGAGTATCCCCTCAGAAATAACGG
127 GGTTGAAGTATCCCCTCAGAAATAACGG
*
1146800 GTTGGAGTATCCGCGATTATGAGAAATTAATATTTTAGAAATAAAGCCGAGGTTGGAGTATCCCC
1 GTTGGAGTATCCGCGATTATGAGAAATTAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCC
* * * * **
1146865 TCAGAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTGGAAATAAAACTGGGGTT
66 TCAGAAATAACGAGATTGGAGTATCCCCGATGAAAAATTAATGTTTTAGAAATAAAACCAGGGTT
1146930 GAAGTATCCCC
131 GAAGTATCCCC
1146941 GAGATGAAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
154 42 0.34
157 79 0.64
158 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (154 bp):
GTTGGAGTATCCGCGATTATGAGAAATTAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCC
TCAGAAATAACGAGATTGGAGTATCCCCGATGAAAAATTAATGTTTTAGAAATAAAACCAGGGTT
GAAGTATCCCCTCAGAAATAACGG
Found at i:1146854 original size:78 final size:78
Alignment explanation
Indices: 1146643--1146940 Score: 345
Period size: 79 Copynumber: 3.8 Consensus size: 78
1146633 TAAAATCGAA
* ** * *
1146643 GTTGGAGTATCCTCGATTGTG-GAGAATTGGTATTTTAGAAATAAAACCGGGGTTGGAGTATTCC
1 GTTGGAGTATCCTCGATTATGAGA-AATTAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCC
*
1146707 CTCGGAAATAACGAG
65 CTCAGAAATAACG-G
* * * *
1146722 ATTGGAGTATCTTCGATTATGAAAAATTAATGTTTTAGAAATAAAACC-AGGGTTGGAGTATCCC
1 GTTGGAGTATCCTCGATTATGAGAAATTAATATTTTAGAAATAAAACCGA-GGTTGGAGTATCCC
1146786 CTCAGAAATAACGG
65 CTCAGAAATAACGG
* *
1146800 GTTGGAGTATCCGCGATTATGAGAAATTAATATTTTAGAAATAAAGCCGAGGTTGGAGTATCCCC
1 GTTGGAGTATCCTCGATTATGAGAAATTAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCC
1146865 TCAGAAATAACGGG
66 TCAGAAATAAC-GG
* * * * * * * *
1146879 GTTGGAGTATCCCCG---ATGAAAAATTGATGTTTTGGAAATAAAACTGGGGTTGAAGTATCCCC
1 GTTGGAGTATCCTCGATTATGAGAAATTAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCC
1146941 GAGATGAAAA
Statistics
Matches: 190, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
76 39 0.21
78 69 0.36
79 81 0.43
80 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (78 bp):
GTTGGAGTATCCTCGATTATGAGAAATTAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCC
TCAGAAATAACGG
Found at i:1149265 original size:20 final size:20
Alignment explanation
Indices: 1149240--1149299 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1149230 AAAATGCCTG
1149240 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGTAA
* ***
1149260 AATGTATCAATACATCTGGGT
1 AATGTATCGATACAT-TGTAA
*
1149281 AATGTATCGATACAATGTA
1 AATGTATCGATACATTGTA
1149300 TCGATACAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:1149299 original size:13 final size:13
Alignment explanation
Indices: 1149281--1149310 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1149271 ACATCTGGGT
1149281 AATGTATCGATAC
1 AATGTATCGATAC
1149294 AATGTATCGATAC
1 AATGTATCGATAC
1149307 AATG
1 AATG
1149311 AGCAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1149362 original size:13 final size:13
Alignment explanation
Indices: 1149344--1149373 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1149334 GTAAACCCCA
1149344 AATGTATCGATAC
1 AATGTATCGATAC
1149357 AATGTATCGATAC
1 AATGTATCGATAC
1149370 AATG
1 AATG
1149374 AACAGTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1149384 original size:20 final size:20
Alignment explanation
Indices: 1149355--1149411 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1149345 ATGTATCGAT
1149355 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
1149375 ACAGTGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
1149395 ACAATGTATCGATACAA
1 ACAATGTATCGATACAA
1149412 ATTGTGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1152948 original size:236 final size:239
Alignment explanation
Indices: 1152530--1152994 Score: 704
Period size: 236 Copynumber: 2.0 Consensus size: 239
1152520 AGCCATACAA
*
1152530 TCATACAAGCAATAATTAATTTAACAAAAAAATGATTTAAAAAAAAGAAAACATTGATAGTATGT
1 TCATACAAGCAAGAATTAATTTAACAAAAAAATGATTTAAAAAAAAGAAAACATTGATAGTATGT
* * *
1152595 ATTTCAAATTATTTCAGATGTTTGAGAAAATCATCATGTGGAGTTTGAGACAAACTTAAAAGTGA
66 ATCTCAAACTATTTCAGATGTTTGAGAAAATCACCATGTGGAGTTTGAGACAAACTTAAAAGTGA
*
1152660 ATTAGGGTTGAGGCATAAAGTTTTTACATAAAACTAGACGAGCTCAAAAAATAGGAAAGAGAAAA
131 ATTAGGGTTAAGGCATAAAGTTTTTACATAAAACTAGACGAGCTCAAAAAATAGGAAAGAGAAAA
1152725 AAGAAAATA-TTTTTAAAAAAATTTAAAAAGATGGTAAACAAAG
196 AAGAAAATATTTTTTAAAAAAATTTAAAAAGATGGTAAACAAAG
* * * *
1152768 TCATACAATCAAGAATTAATTTAACAAATAAATGATTT-AAATAAA-AAAACATTGATGGTATGT
1 TCATACAAGCAAGAATTAATTTAACAAAAAAATGATTTAAAAAAAAGAAAACATTGATAGTATGT
** *
1152831 ATCTCAAACTATTTTGGATGTTTGAGAAAATCACCATTTGGAGTTTGAGACAAACTTAAAAGTGA
66 ATCTCAAACTATTTCAGATGTTTGAGAAAATCACCATGTGGAGTTTGAGACAAACTTAAAAGTGA
* * * * *
1152896 ATTAGGGTTAAGGCATAAATTTTTTATGA-AAAACTAGATGAGCTCTAAAAATAGGAGAGAGAAA
131 ATTAGGGTTAAGGCATAAAGTTTTTA-CATAAAACTAGACGAGCTCAAAAAATAGGAAAGAGAAA
* * * *
1152960 GAAGAAAATATTTTTTTAGAAATTTTAAAAAGATG
195 AAAGAAAATATTTTTTAAAAAAATTTAAAAAGATG
1152995 ACTTGAAAAA
Statistics
Matches: 204, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
236 141 0.69
237 28 0.14
238 35 0.17
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (239 bp):
TCATACAAGCAAGAATTAATTTAACAAAAAAATGATTTAAAAAAAAGAAAACATTGATAGTATGT
ATCTCAAACTATTTCAGATGTTTGAGAAAATCACCATGTGGAGTTTGAGACAAACTTAAAAGTGA
ATTAGGGTTAAGGCATAAAGTTTTTACATAAAACTAGACGAGCTCAAAAAATAGGAAAGAGAAAA
AAGAAAATATTTTTTAAAAAAATTTAAAAAGATGGTAAACAAAG
Found at i:1154655 original size:18 final size:18
Alignment explanation
Indices: 1154629--1154663 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1154619 CATCTTAGCC
*
1154629 TTTTCTTTTTCCCTTTTT
1 TTTTCTTTTTACCTTTTT
*
1154647 TTTTTTTTTTACCTTTT
1 TTTTCTTTTTACCTTTT
1154664 ATATTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTACCTTTTT
Found at i:1155441 original size:22 final size:22
Alignment explanation
Indices: 1155378--1155458 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
1155368 TAAATATCAA
*
1155378 AACTCAATTCATATT---ATTTG
1 AACTCAATTCA-ATTAACATTTT
* * *
1155398 AACTCATTTTAATTTAATATTTT
1 AACTCAATTCAA-TTAACATTTT
*
1155421 AA-TCCAATTCGATTAACATTTT
1 AACT-CAATTCAATTAACATTTT
1155443 AACTCAATTCAATTAA
1 AACTCAATTCAATTAA
1155459 AACTCTTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
19 1 0.02
20 11 0.23
22 23 0.49
23 12 0.26
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.44
Consensus pattern (22 bp):
AACTCAATTCAATTAACATTTT
Found at i:1156444 original size:16 final size:16
Alignment explanation
Indices: 1156410--1156461 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1156400 CTCAAACCTG
* **
1156410 AAATGACCCAAACCCA
1 AAATGACCTAAACTTA
*
1156426 AAATGACCTGAACTTA
1 AAATGACCTAAACTTA
* *
1156442 AAATGATCTAAACTTG
1 AAATGACCTAAACTTA
1156458 AAAT
1 AAAT
1156462 AACTCGAACA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (16 bp):
AAATGACCTAAACTTA
Found at i:1157283 original size:221 final size:214
Alignment explanation
Indices: 1156972--1157400 Score: 678
Period size: 221 Copynumber: 2.0 Consensus size: 214
1156962 TGGAATTGAA
* *
1156972 AAAAATTGAATCGTGATCAATTCAAAATTCAATCAGATAAATGTTTAAAAAAAACTCTATATGAC
1 AAAAATTGAATCATGATCAATTCAAAATTCAATAAGATAAATGTTTAAAAAAAACTCTATATGAC
* * *
1157037 ATGGCAAGAGGTTGAAATTAATAATTCCATTCGATAATTCTTAAAAATTTAATATTCAAATACAA
66 ATGGCAAGAGGTTGAAATTAATAATTCAATTCGATAATACTTAAAAATTAAATATTCAAATACAA
*
1157102 TGATATACTTTGTTATTTTTCTATTTATAAATGTAAAAAATCTAAAATAACTCAAACCTGATGAA
131 TGATATA-----AT-TTTTTCTATTTATAAATGTAAAAAATCTAAAATAACTCAAACCTGATGAA
1157167 TCCAACTATTAAACCTGATCAATTC
190 TCCAACTATTAAACCTGATCAATTC
* * *
1157192 AAAATTTGAATCATGATCAATTCAAAATTCAATAAGGTAAATGTTTATAAAAAAACTTTATATGA
1 AAAAATTGAATCATGATCAATTCAAAATTCAATAAGATAAATGTTTA-AAAAAAACTCTATATGA
* * * *
1157257 TATGGCAAGAGTTTGGAATTAATAATTCAATTCGATAATACTTGAAAATTAAATATTCAAATACA
65 CATGGCAAGAGGTTGAAATTAATAATTCAATTCGATAATACTTAAAAATTAAATATTCAAATACA
1157322 ATGATATAATTTTTTCTATTTATAAATGTAAAAAATCTAAAATAACTCAAACCTGATGAATCCAA
130 ATGATATAATTTTTTCTATTTATAAATGTAAAAAATCTAAAATAACTCAAACCTGATGAATCCAA
1157387 CTATTAAACCTGAT
195 CTATTAAACCTGAT
1157401 GAATCAGACT
Statistics
Matches: 195, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
215 69 0.35
216 1 0.01
220 43 0.22
221 82 0.42
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (214 bp):
AAAAATTGAATCATGATCAATTCAAAATTCAATAAGATAAATGTTTAAAAAAAACTCTATATGAC
ATGGCAAGAGGTTGAAATTAATAATTCAATTCGATAATACTTAAAAATTAAATATTCAAATACAA
TGATATAATTTTTTCTATTTATAAATGTAAAAAATCTAAAATAACTCAAACCTGATGAATCCAAC
TATTAAACCTGATCAATTC
Found at i:1157395 original size:22 final size:22
Alignment explanation
Indices: 1157370--1157417 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1157360 AAAATAACTC
1157370 AAACCTGATGAATCCA-ACTATT
1 AAACCTGATGAAT-CAGACTATT
1157392 AAACCTGATGAATCAGACTATT
1 AAACCTGATGAATCAGACTATT
1157414 AAAC
1 AAAC
1157418 TTAATTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (22 bp):
AAACCTGATGAATCAGACTATT
Found at i:1166888 original size:32 final size:32
Alignment explanation
Indices: 1166847--1166922 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
1166837 CATTTAATAT
1166847 TGTATCGATACATCTCGGCAAATTTGCCTGCA
1 TGTATCGATACATCTCGGCAAATTTGCCTGCA
* *
1166879 TGTATCGATACATTTGGGCAAATTTGCCTGCA
1 TGTATCGATACATCTCGGCAAATTTGCCTGCA
1166911 TGTATCGATACA
1 TGTATCGATACA
1166923 AAGATCAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATCTCGGCAAATTTGCCTGCA
Found at i:1166949 original size:13 final size:13
Alignment explanation
Indices: 1166931--1166955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1166921 CAAAGATCAG
1166931 TGTATCGATACAA
1 TGTATCGATACAA
1166944 TGTATCGATACA
1 TGTATCGATACA
1166956 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1167035 original size:13 final size:13
Alignment explanation
Indices: 1167017--1167041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1167007 ACAAAACTTA
1167017 TGTATCGATACAT
1 TGTATCGATACAT
1167030 TGTATCGATACA
1 TGTATCGATACA
1167042 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1167037 original size:32 final size:32
Alignment explanation
Indices: 1166996--1167060 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1166986 AGTAGCTTAA
1166996 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
1167028 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
1167060 A
1 A
1167061 ACACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:1167071 original size:20 final size:19
Alignment explanation
Indices: 1166998--1167081 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
1166988 TAGCTTAAAT
*
1166998 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
1167017 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1167030 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1167049 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
1167069 TGTATCGATACAA
1 TGTATCGATACAA
1167082 ATCGTTGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 5 0.09
18 1 0.02
19 25 0.44
20 16 0.28
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1168959 original size:13 final size:13
Alignment explanation
Indices: 1168941--1168966 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1168931 ACAAAGATCC
1168941 ATGTATCGATACA
1 ATGTATCGATACA
1168954 ATGTATCGATACA
1 ATGTATCGATACA
1168967 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1168962 original size:33 final size:33
Alignment explanation
Indices: 1168920--1168986 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1168910 AAAATTTCCA
***
1168920 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1168953 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1168986 A
1 A
1168987 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1169030 original size:19 final size:18
Alignment explanation
Indices: 1169006--1169073 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1168996 CAGTAGCTAA
1169006 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1169025 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1169040 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1169057 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1169074 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1169046 original size:13 final size:13
Alignment explanation
Indices: 1169028--1169052 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1169018 ACAATACTTA
1169028 TGTATCGATACAT
1 TGTATCGATACAT
1169041 TGTATCGATACA
1 TGTATCGATACA
1169053 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1169050 original size:32 final size:32
Alignment explanation
Indices: 1169009--1169071 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1168999 TAGCTAATTA
*
1169009 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1169041 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1169072 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1170204 original size:55 final size:55
Alignment explanation
Indices: 1170074--1171172 Score: 1638
Period size: 55 Copynumber: 19.9 Consensus size: 55
1170064 TGGGAAGGTT
* * * *
1170074 TGCCACTAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTCTGAGGATTGGAAA--
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT-GAAAGG
*
1170128 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCTTGCTCTTTGAGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* ** **
1170183 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
1 TGCCACCAACTTGTGTGGGCTTT---AAG---AGGTGTCCTGCTCTTTGAGGACTGAAAGG
* * * *
1170244 TGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAA-A
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT-GAAAGG
*
1170299 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* * *
1170354 CGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGA
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* * *
1170409 CGCCACCAACTTGTGTGGGCTTTAAGAGGTGTTCTGCTCTTTGGGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
*
1170464 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* * * *
1170519 CGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGGAAGA
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* *
1170574 CGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* *
1170629 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTCCTCTTTGAGGACTGGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* * *
1170684 CGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGTTCTTTGAGGACTGGAAA-A
1 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACT-GAAAGG
*
1170739 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* * *
1170794 CGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
*
1170849 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* * *
1170904 TGCCACCAACTTGTGTAGGCTTTAAGAGGTGTCCTGCTCTTTGAGGATTGGAAA-A
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT-GAAAGG
* *
1170959 TGCCACCAACTTGGGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGGGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
1171014 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
1171069 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
1171124 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
1171173 AAAAAGCGGA
Statistics
Matches: 959, Mismatches: 67, Indels: 37
0.90 0.06 0.03
Matches are distributed among these distances:
53 4 0.00
54 56 0.06
55 835 0.87
56 15 0.02
57 2 0.00
58 2 0.00
61 45 0.05
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
Found at i:1170847 original size:26 final size:26
Alignment explanation
Indices: 1170818--1170905 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
1170808 GTGGGCTTTA
1170818 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** * *
1170844 AAAGGTG-CCACCAACTTGTGTGGG-CTTT
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1170872 AAGAGGTGTCCTGCTCTTTGGGGACTG
1 AA-AGGTGTCCTGCTCTTTGGGGACTG
1170899 AAAGGTG
1 AAAGGTG
1170906 CCACCAACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
25 3 0.06
26 15 0.32
27 9 0.19
28 9 0.19
29 8 0.17
30 3 0.06
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.28
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:1171010 original size:26 final size:26
Alignment explanation
Indices: 1170981--1171125 Score: 82
Period size: 26 Copynumber: 5.3 Consensus size: 26
1170971 GGGTGGGCTT
1170981 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
1171007 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
* *
1171034 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
** *
1171062 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
* *
1171089 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
1171117 TGAAAGGTG
1 TGAAAGGTG
1171126 CCACCAACTT
Statistics
Matches: 86, Mismatches: 19, Indels: 28
0.65 0.14 0.21
Matches are distributed among these distances:
25 6 0.07
26 25 0.29
27 16 0.19
28 17 0.20
29 16 0.19
30 6 0.07
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:1172182 original size:24 final size:24
Alignment explanation
Indices: 1172154--1172212 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1172144 TCTTTTCTCT
* *
1172154 CTTTTTCTTTGTTTTGTTTTTTTTG
1 CTTTTTTTTTGCTTT-TTTTTTTTG
*
1172179 -TTTTTTTTTCCTTTTTTTTTTTG
1 CTTTTTTTTTGCTTTTTTTTTTTG
1172202 CTTTTTTTTTG
1 CTTTTTTTTTG
1172213 AAGAGAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (24 bp):
CTTTTTTTTTGCTTTTTTTTTTTG
Found at i:1172186 original size:11 final size:11
Alignment explanation
Indices: 1172170--1172212 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1172160 CTTTGTTTTG
1172170 TTTTTTTTGTT
1 TTTTTTTTGTT
1172181 TTTTTTTCCT-TT
1 TTTTTTT--TGTT
*
1172193 TTTTTTTTGCT
1 TTTTTTTTGTT
1172204 TTTTTTTTG
1 TTTTTTTTG
1172213 AAGAGAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 1 0.04
11 17 0.61
12 9 0.32
13 1 0.04
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:1172195 original size:13 final size:13
Alignment explanation
Indices: 1172179--1172211 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1172169 GTTTTTTTTG
1172179 TTTTTTTTTCCTT
1 TTTTTTTTTCCTT
*
1172192 TTTTTTTTTGCTT
1 TTTTTTTTTCCTT
1172205 TTTTTTT
1 TTTTTTT
1172212 GAAGAGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTCCTT
Found at i:1184115 original size:33 final size:33
Alignment explanation
Indices: 1184078--1184144 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1184068 TTCAACGATT
1184078 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1184111 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1184144 T
1 T
1184145 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1184116 original size:13 final size:13
Alignment explanation
Indices: 1184098--1184122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184088 CATAAAATGT
1184098 TGTATCGATACAA
1 TGTATCGATACAA
1184111 TGTATCGATACA
1 TGTATCGATACA
1184123 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1184203 original size:13 final size:13
Alignment explanation
Indices: 1184185--1184209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184175 ATTACTCAAA
1184185 TGTATCGATACAT
1 TGTATCGATACAT
1184198 TGTATCGATACA
1 TGTATCGATACA
1184210 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1184259 original size:51 final size:50
Alignment explanation
Indices: 1184198--1184336 Score: 165
Period size: 52 Copynumber: 2.7 Consensus size: 50
1184188 ATCGATACAT
* *
1184198 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGC-AATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAAA
* *
1184249 TGTATCGATACA-TTTTAAAATGTATCGATACATGCAGGCAAATTTTCCCAAA
1 TGTATCGATACACTATT---ATGTATCGATACATGCAGGCAAATTTGCCCAAA
1184301 TGTATCGATACACTATTAAATGTATCGATACATGCA
1 TGTATCGATACACTATT--ATGTATCGATACATGCA
1184337 AGGAACGTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 1 0.01
51 31 0.40
52 41 0.53
53 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAAA
Found at i:1184322 original size:52 final size:51
Alignment explanation
Indices: 1184218--1184336 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 51
1184208 CACTGATCTT
* *
1184218 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTTTAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAAATGTATCGATACATATTAAAA
*
1184269 TGTATCGATACATGCAGGCAAATTTTCCCAAATGTATCGATACACTATT-AAA
1 TGTATCGATACATGCAGGC-AATTTGCCCAAATGTATCGATACA-TATTAAAA
1184321 TGTATCGATACATGCA
1 TGTATCGATACATGCA
1184337 AGGAACGTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
51 19 0.30
52 41 0.65
53 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTGCCCAAATGTATCGATACATATTAAAA
Found at i:1191125 original size:1 final size:1
Alignment explanation
Indices: 1191119--1191196 Score: 57
Period size: 1 Copynumber: 78.0 Consensus size: 1
1191109 AGAAGTGATG
* * * * * * * * * *
1191119 AAAAAAAAAACAAACAAAAAAAAACACACAAAAAAACAAAAAACAAAAAAAAAACAAAAAACAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1191184 AAACAAAAAAAAA
1 AAAAAAAAAAAAA
1191197 GGTGCAAAGG
Statistics
Matches: 55, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1191137 original size:14 final size:14
Alignment explanation
Indices: 1191120--1191196 Score: 97
Period size: 14 Copynumber: 5.6 Consensus size: 14
1191110 GAAGTGATGA
1191120 AAAAAAAAACAAAC
1 AAAAAAAAACAAAC
1191134 AAAAAAAAAC--AC
1 AAAAAAAAACAAAC
*
1191146 ACAAAAAAACAAA-
1 AAAAAAAAACAAAC
*
1191159 AAACAAAAAAAAAAC
1 AAA-AAAAAACAAAC
*
1191174 AAAAAACAACAAAC
1 AAAAAAAAACAAAC
1191188 AAAAAAAAA
1 AAAAAAAAA
1191197 GGTGCAAAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
12 11 0.21
13 2 0.04
14 37 0.70
15 3 0.06
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAC
Found at i:1191140 original size:18 final size:18
Alignment explanation
Indices: 1191119--1191196 Score: 90
Period size: 18 Copynumber: 4.3 Consensus size: 18
1191109 AGAAGTGATG
*
1191119 AAAAAAA-AAACAAACAA
1 AAAAAAACAAACAAAAAA
*
1191136 AAAAAAACACACAAAAAA
1 AAAAAAACAAACAAAAAA
1191154 ACAAAAAACAAA-AAAAAA
1 A-AAAAAACAAACAAAAAA
1191172 ACAAAAAAC-AACAAACAAA
1 A-AAAAAACAAACAAA-AAA
1191191 AAAAAA
1 AAAAAA
1191197 GGTGCAAAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
17 9 0.17
18 32 0.59
19 13 0.24
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAACAAAAAA
Found at i:1191151 original size:25 final size:25
Alignment explanation
Indices: 1191120--1191196 Score: 100
Period size: 25 Copynumber: 2.9 Consensus size: 25
1191110 GAAGTGATGA
1191120 AAAAAAAAACAAACAAAAAAAAACACAC
1 AAAAAAAAACAAAC-AAAAAAAA-A-AC
*
1191148 AAAAAAACAAAAAACAAAAAAAAAAC
1 AAAAAAA-AACAAACAAAAAAAAAAC
*
1191174 AAAAAACAACAAACAAAAAAAAA
1 AAAAAAAAACAAACAAAAAAAAA
1191197 GGTGCAAAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.33
26 8 0.18
27 1 0.02
28 15 0.33
29 6 0.13
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (25 bp):
AAAAAAAAACAAACAAAAAAAAAAC
Found at i:1191466 original size:16 final size:16
Alignment explanation
Indices: 1191435--1191466 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1191425 TGTTCTTTTC
*
1191435 CAAAAAAGAAACAAAA
1 CAAAAAAGAAAAAAAA
1191451 CAAAAAAGAAAAAAAA
1 CAAAAAAGAAAAAAAA
1191467 AGAGAGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (16 bp):
CAAAAAAGAAAAAAAA
Found at i:1192454 original size:30 final size:31
Alignment explanation
Indices: 1192417--1192501 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 31
1192407 CAAATACCTT
1192417 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
1 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
* *
1192448 -TCAAAGTCCACGACTTAGTGGCATTTTTTC
1 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
* * * *
1192478 TTTAAAGCCCACAACTCTGTGGCA
1 TTCAAAGTCCACGACTCAGTGGCA
1192502 CACTTTTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
30 28 0.61
31 18 0.39
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (31 bp):
TTCAAAGTCCACGACTCAGTGGCATTTTGTC
Found at i:1192594 original size:34 final size:33
Alignment explanation
Indices: 1192465--1193254 Score: 674
Period size: 34 Copynumber: 24.3 Consensus size: 33
1192455 CCACGACTTA
* *
1192465 GTGGCA-TTTTTTCT-TTAAAGCCCACAACTCT
1 GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
* * **
1192496 GTGGCACACTTTTTCTTTTTAAAGCCCACAACTTT
1 GTGGCAC-TTTTTTCTCTTT-AAGCCCACAACTCC
1192531 GTGGCACTCTTTTT-TCCTTCTAAGCCCACAACTCC
1 GTGGCACT-TTTTTCT-CTT-TAAGCCCACAACTCC
*
1192566 GTGGCACTTTTTTCATCTTTAAGTCCACAACTCC
1 GTGGCACTTTTTTC-TCTTTAAGCCCACAACTCC
* *
1192600 GTGGCAC--TCTT-T-TTAAAGCCCACAACTCC
1 GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
* *
1192629 GTGGCACCTTTTTCTTTTTAAAGCCCACAACTCC
1 GTGGCACTTTTTTCTCTTT-AAGCCCACAACTCC
*
1192663 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCC
1 GTGGCACT-TTTTTCTC-TTT--AAGCCCACAACTCC
*
1192700 GTGGCACCTTTTTCT-TTTAAAGCCCACAACTCC
1 GTGGCACTTTTTTCTCTTT-AAGCCCACAACTCC
*
1192733 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCC
1 GTGGCACT-TTTTTCTC-TTT--AAGCCCACAACTCC
*
1192770 GTGGCAC-----CCT-TTTAAGCCCACAACTCC
1 GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
* * *
1192797 GTGGTACTTTTTTCAGCTTTAAGTCCACAACTCC
1 GTGGCACTTTTTTC-TCTTTAAGCCCACAACTCC
*
1192831 GTGGCAC-----CCT-TTTAAGCCCACAACTCC
1 GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
*
1192858 GTGGCACTTTTTTCATCTTTAAGTCCACAACTCC
1 GTGGCACTTTTTTC-TCTTTAAGCCCACAACTCC
*
1192892 GTGGCAC-----CCT-TTTAAGCCCACAACTCC
1 GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
* *
1192919 GTGGCACTTTTTTCAGCTTTAAGTCCACAACTCC
1 GTGGCACTTTTTTC-TCTTTAAGCCCACAACTCC
*
1192953 GTGGCAC-----CCT-TTTAAGCCCACAACTCC
1 GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
*
1192980 GTGGCACTTTTTTCATCTTTAAGTCCACAACTCC
1 GTGGCACTTTTTTC-TCTTTAAGCCCACAACTCC
* *
1193014 GTGGCAC--TCTT-T-TTAAAGCCCACAACTCC
1 GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
* *
1193043 GTGGCAC--TCTT-T-TTAAAGCCCACAACTCC
1 GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
* * *
1193072 GTGGCACCTTTTTCTTTTTAAAGCCCACAACTCT
1 GTGGCACTTTTTTCTCTTT-AAGCCCACAACTCC
1193106 GTGGCACTCTTTTTC-CTTCTAAGCCCACAACTCC
1 GTGGCACT-TTTTTCTCTT-TAAGCCCACAACTCC
1193140 GTGGCACTCTTTTTC-CTTCTAAGCCCACAACTCC
1 GTGGCACT-TTTTTCTCTT-TAAGCCCACAACTCC
*
1193174 GTGGCACTTTTTTTTCCCTTTTAAAGCCCACAACTCC
1 GTGGCAC--TTTTTTCTC-TTT-AAGCCCACAACTCC
* * * * *
1193211 GTGGCACCTTGTTCTTTTTAAGTCCACAACTTC
1 GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
1193244 GTGGCATCTTT
1 GTGGCA-CTTT
1193255 CACCCTTTCT
Statistics
Matches: 639, Mismatches: 58, Indels: 121
0.78 0.07 0.15
Matches are distributed among these distances:
27 89 0.14
28 1 0.00
29 79 0.12
30 2 0.00
31 13 0.02
32 12 0.02
33 53 0.08
34 232 0.36
35 74 0.12
36 17 0.03
37 67 0.10
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
GTGGCACTTTTTTCTCTTTAAGCCCACAACTCC
Found at i:1192838 original size:61 final size:62
Alignment explanation
Indices: 1192512--1193218 Score: 698
Period size: 61 Copynumber: 11.0 Consensus size: 62
1192502 CACTTTTTCT
** **
1192512 TTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTC-CTTCTAAGCCCACAACTCCGTGGCACTT
1 TTTTAAAGCCCACAACTCCGTGGCACTC-TTTTTCACTT-TAAGCCCACAACTCCGTGGCACCC
*
1192575 TTTTCATCTTTAAGTCCACAACTCCGTGGCACTCTTTTT-A----AAGCCCACAACTCCGTGGCA
1 TTTT-A-----AAGCCCACAACTCCGTGGCACTCTTTTTCACTTTAAGCCCACAACTCCGTGGCA
1192635 CCTTTTTC
60 CC-----C
*
1192643 TTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACC
1 -TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCAC-TTT--AAGCCCACAACTCCGTGGCACC
1192708 TTTTTC
62 -----C
*
1192714 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCAC-TTT--AAGCCCACAACTCCGTGGCACCC
* *
1192779 TTTT-AAGCCCACAACTCCGTGGTACT-TTTTTCAGCTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCA-CTTTAAGCCCACAACTCCGTGGCACCC
*
1192840 TTTT-AAGCCCACAACTCCGTGGCACT-TTTTTCATCTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCA-CTTTAAGCCCACAACTCCGTGGCACCC
*
1192901 TTTT-AAGCCCACAACTCCGTGGCACT-TTTTTCAGCTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCA-CTTTAAGCCCACAACTCCGTGGCACCC
* *
1192962 TTTT-AAGCCCACAACTCCGTGGCACT-TTTTTCATCTTTAAGTCCACAACTCCGTGGCACTCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCA-CTTTAAGCCCACAACTCCGTGGCAC-CC
1193024 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-A----AAGCCCACAACTCCGTGGCACCTTTT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCACTTTAAGCCCACAACTCCGTGGCACC----
1193084 TC
62 -C
*
1193086 TTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC-CTTCTAAGCCCACAACTCCGTGGCACTCT
1 -TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCACTT-TAAGCCCACAACTCCGTGGCAC-C-
*
1193150 TT
62 -C
* * *
1193152 TTCCTTCTAAGCCCACAACTCCGTGGCACTTTTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCA
1 TT--TT-AAAGCCCACAACTCCGTGGCAC-TCTTTTTCAC-TTT-AAGCCCACAACTCCGTGGCA
1193217 CC
60 CC
1193219 TTGTTCTTTT
Statistics
Matches: 577, Mismatches: 22, Indels: 83
0.85 0.03 0.12
Matches are distributed among these distances:
57 1 0.00
58 20 0.03
61 199 0.34
62 5 0.01
63 116 0.20
64 28 0.05
65 7 0.01
66 2 0.00
67 2 0.00
68 47 0.08
69 32 0.06
70 67 0.12
71 51 0.09
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (62 bp):
TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCACTTTAAGCCCACAACTCCGTGGCACCC
Found at i:1192867 original size:25 final size:26
Alignment explanation
Indices: 1192814--1192869 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
1192804 TTTTTTCAGC
*
1192814 TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAGCCCACAACTCCGTGGCA-CCT
*
1192841 TTTAAGCCCACAACTCCGTGGCACTT
1 TTTAAGCCCACAACTCCGTGGCACCT
1192867 TTT
1 TTT
1192870 TCATCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.30
Consensus pattern (26 bp):
TTTAAGCCCACAACTCCGTGGCACCT
Found at i:1192928 original size:25 final size:26
Alignment explanation
Indices: 1192875--1192930 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
1192865 TTTTTTCATC
*
1192875 TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAGCCCACAACTCCGTGGCA-CCT
*
1192902 TTTAAGCCCACAACTCCGTGGCACTT
1 TTTAAGCCCACAACTCCGTGGCACCT
1192928 TTT
1 TTT
1192931 TCAGCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.30
Consensus pattern (26 bp):
TTTAAGCCCACAACTCCGTGGCACCT
Found at i:1192989 original size:25 final size:26
Alignment explanation
Indices: 1192936--1192991 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
1192926 TTTTTTCAGC
*
1192936 TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAGCCCACAACTCCGTGGCA-CCT
*
1192963 TTTAAGCCCACAACTCCGTGGCACTT
1 TTTAAGCCCACAACTCCGTGGCACCT
1192989 TTT
1 TTT
1192992 TCATCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.30
Consensus pattern (26 bp):
TTTAAGCCCACAACTCCGTGGCACCT
Found at i:1193333 original size:34 final size:34
Alignment explanation
Indices: 1193256--1193362 Score: 184
Period size: 33 Copynumber: 3.2 Consensus size: 34
1193246 GGCATCTTTC
1193256 ACCCTT-TCTAAAGCCCACACAAGTCGGTGGCAA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
1193289 A-CCTTCTCTAAAGCCTACACAAGTCGGTGGCAA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1193322 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGC-A
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1193355 ACCCTTCT
1 ACCCTTCT
1193363 AAGCCCAATA
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
32 4 0.06
33 37 0.53
34 29 0.41
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.21
Consensus pattern (34 bp):
ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:1193420 original size:49 final size:49
Alignment explanation
Indices: 1193362--1193788 Score: 544
Period size: 49 Copynumber: 8.8 Consensus size: 49
1193352 GCAACCCTTC
* *
1193362 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1193411 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1193459 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
1193502 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCGCCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * * * *
1193554 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
1193603 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
1193652 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1193701 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * * *
1193750 TAAGCCCAATATCGTTGGTCGTGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
1193789 TCTTTATCAC
Statistics
Matches: 331, Mismatches: 38, Indels: 18
0.86 0.10 0.05
Matches are distributed among these distances:
43 39 0.12
45 1 0.00
48 44 0.13
49 204 0.62
50 3 0.01
52 40 0.12
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:1193881 original size:49 final size:49
Alignment explanation
Indices: 1193816--1194051 Score: 292
Period size: 49 Copynumber: 4.8 Consensus size: 49
1193806 ACCTTTATCT
* *
1193816 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCA
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCA
* * * *
1193865 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCA
* *
1193914 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCA
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCA
* * * * *
1193963 TTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCA
* ** * * * *
1194012 TTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCA
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
1194052 TCTTTATCAC
Statistics
Matches: 163, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 163 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (49 bp):
TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCA
Found at i:1193893 original size:116 final size:116
Alignment explanation
Indices: 1193700--1193912 Score: 300
Period size: 116 Copynumber: 1.8 Consensus size: 116
1193690 ACCTTCACCA
* * * * * *
1193700 TTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGCCCAATATCGT
1 TTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGCCCAATATAGC
* *
1193765 TGGTCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCACCTTTATCT
66 TGGCCGTGAATCAACATATTGGCACCTTTATCACTTTTCTCACCTTTATCT
* * * *
1193816 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGC
1 TTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGCCCAATATAGC
* *
1193881 TGGCCTTGAATCAGCATATTGGCACCTTTATC
66 TGGCCGTGAATCAACATATTGGCACCTTTATC
1193913 TTTAAGTCCA
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
116 83 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (116 bp):
TTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGCCCAATATAGC
TGGCCGTGAATCAACATATTGGCACCTTTATCACTTTTCTCACCTTTATCT
Found at i:1193953 original size:165 final size:165
Alignment explanation
Indices: 1193640--1193953 Score: 538
Period size: 165 Copynumber: 1.9 Consensus size: 165
1193630 AGCATATTGG
1193640 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
1 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
* * *
1193705 CCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGCCCAATATCGTTGGTC
66 CCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGCCCAATATAGCTGGCC
*
1193770 GTGAATCAACATATTGGCATCTTTATCACTTTTCT
131 GTGAATCAACACATTGGCATCTTTATCACTTTTCT
1193805 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
1 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
* * *
1193870 TCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCC
66 CCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGCCCAATATAGCTGGCC
* * *
1193935 TTGACTCAGCACATTGGCA
131 GTGAATCAACACATTGGCA
1193954 CCTTCACCAT
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
165 139 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (165 bp):
CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
CCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGCCCAATATAGCTGGCC
GTGAATCAACACATTGGCATCTTTATCACTTTTCT
Found at i:1193974 original size:98 final size:98
Alignment explanation
Indices: 1193805--1194022 Score: 418
Period size: 98 Copynumber: 2.2 Consensus size: 98
1193795 TCACTTTTCT
1193805 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
1 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
*
1193870 TCCAATATAGCTGGCCTTGAATCAGCATATTGG
66 CCCAATATAGCTGGCCTTGAATCAGCATATTGG
1193903 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
1 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
1193968 CCCAATATAGCTGGCCTTGAATCAGCATATTGG
66 CCCAATATAGCTGGCCTTGAATCAGCATATTGG
*
1194001 CACCTTTATCTTTAAGCCCAAT
1 CACCTTTATCTTTAAGTCCAAT
1194023 AGCGTTGGCC
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 118 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (98 bp):
CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
CCCAATATAGCTGGCCTTGAATCAGCATATTGG
Found at i:1194016 original size:263 final size:263
Alignment explanation
Indices: 1193548--1194124 Score: 1082
Period size: 263 Copynumber: 2.2 Consensus size: 263
1193538 GCGCCTTTTC
1193548 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAAT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAAT
1193613 ATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACT
66 ATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACT
1193678 CAGCACATTGGCACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
131 CAGCACATTGGCACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
* *
1193743 TTATCTTTAAGCCCAATATCGTTGGTCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCAC
196 TTATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCAC
1193808 CTT
261 CTT
*
1193811 TATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAAT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAAT
1193876 ATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACT
66 ATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACT
1193941 CAGCACATTGGCACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
131 CAGCACATTGGCACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
*
1194006 TTATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCAT
196 TTATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCAC
1194071 CTT
261 CTT
* * * *
1194074 CATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
1194125 TCATCTTTAA
Statistics
Matches: 305, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
263 305 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (263 bp):
CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAAT
ATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACT
CAGCACATTGGCACCTTCACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
TTATCTTTAAGCCCAATAGCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCAC
CTT
Found at i:1194965 original size:33 final size:33
Alignment explanation
Indices: 1194928--1194994 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1194918 TTCAACGATT
1194928 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1194961 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1194994 T
1 T
1194995 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1194966 original size:13 final size:13
Alignment explanation
Indices: 1194948--1194972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1194938 CATAAAATGT
1194948 TGTATCGATACAA
1 TGTATCGATACAA
1194961 TGTATCGATACA
1 TGTATCGATACA
1194973 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1195053 original size:13 final size:13
Alignment explanation
Indices: 1195035--1195059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1195025 ATTACTCAAA
1195035 TGTATCGATACAT
1 TGTATCGATACAT
1195048 TGTATCGATACA
1 TGTATCGATACA
1195060 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1195109 original size:51 final size:50
Alignment explanation
Indices: 1195048--1195186 Score: 165
Period size: 52 Copynumber: 2.7 Consensus size: 50
1195038 ATCGATACAT
* *
1195048 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGC-AATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAAA
* *
1195099 TGTATCGATACA-TTTTAAAATGTATCGATACATGCAGGCAAATTTTCCCAAA
1 TGTATCGATACACTATT---ATGTATCGATACATGCAGGCAAATTTGCCCAAA
1195151 TGTATCGATACACTATTAAATGTATCGATACATGCA
1 TGTATCGATACACTATT--ATGTATCGATACATGCA
1195187 AGTAACGTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 1 0.01
51 31 0.40
52 41 0.53
53 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAAA
Found at i:1195172 original size:52 final size:51
Alignment explanation
Indices: 1195068--1195186 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 51
1195058 CACTGATCTT
* *
1195068 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTTTAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAAATGTATCGATACATATTAAAA
*
1195119 TGTATCGATACATGCAGGCAAATTTTCCCAAATGTATCGATACACTATT-AAA
1 TGTATCGATACATGCAGGC-AATTTGCCCAAATGTATCGATACA-TATTAAAA
1195171 TGTATCGATACATGCA
1 TGTATCGATACATGCA
1195187 AGTAACGTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
51 19 0.30
52 41 0.65
53 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTGCCCAAATGTATCGATACATATTAAAA
Found at i:1198329 original size:19 final size:18
Alignment explanation
Indices: 1198305--1198372 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1198295 CAGTAGCTAA
1198305 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1198324 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1198339 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1198356 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1198373 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1198345 original size:13 final size:13
Alignment explanation
Indices: 1198327--1198351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1198317 ACAATACTTA
1198327 TGTATCGATACAT
1 TGTATCGATACAT
1198340 TGTATCGATACA
1 TGTATCGATACA
1198352 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1198349 original size:32 final size:32
Alignment explanation
Indices: 1198308--1198370 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1198298 TAGCTAATTA
*
1198308 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1198340 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1198371 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1201092 original size:52 final size:52
Alignment explanation
Indices: 1201014--1201162 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 52
1201004 CGAAATATGA
1201014 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
** *
1201066 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
** *
1201118 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACA
1201163 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 88 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
Found at i:1201169 original size:13 final size:13
Alignment explanation
Indices: 1201151--1201175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1201141 CAAAGATTAG
1201151 TGTATCGATACAA
1 TGTATCGATACAA
1201164 TGTATCGATACA
1 TGTATCGATACA
1201176 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1201253 original size:33 final size:33
Alignment explanation
Indices: 1201216--1201282 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1201206 AGTAGCTTAA
1201216 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1201249 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1201282 A
1 A
1201283 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1201256 original size:13 final size:13
Alignment explanation
Indices: 1201238--1201262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1201228 CAAAAAAATA
1201238 TGTATCGATACAT
1 TGTATCGATACAT
1201251 TGTATCGATACA
1 TGTATCGATACA
1201263 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1202194 original size:55 final size:52
Alignment explanation
Indices: 1202100--1202377 Score: 185
Period size: 48 Copynumber: 5.6 Consensus size: 52
1202090 TGATAAAGAT
* * * * * ** *
1202100 GCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAAAAAGGA
1 GCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-AAAAGGA
* *
1202154 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGA
1 -GCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGA
* * *
1202207 GCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T----AAGGT
1 GCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGA
* * * * *
1202249 GCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G--AAGGT
1 GCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGA
* * * * * *
1202298 GCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AA-A-GG-CAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGA
*
1202346 GCCAATATGCTGATTCAAGGCCAGCTATATTG
1 GCCAATATGCTGATTCAAGGCCAGCTACATTG
1202378 GGCTTAAAAG
Statistics
Matches: 189, Mismatches: 25, Indels: 25
0.79 0.10 0.10
Matches are distributed among these distances:
42 36 0.19
43 1 0.01
46 1 0.01
47 2 0.01
48 38 0.20
49 37 0.20
51 1 0.01
52 31 0.16
53 7 0.04
54 1 0.01
55 34 0.18
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (52 bp):
GCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGA
Found at i:1202330 original size:49 final size:49
Alignment explanation
Indices: 1202244--1202388 Score: 204
Period size: 49 Copynumber: 3.0 Consensus size: 49
1202234 TATTGGACTT
* * * *
1202244 AAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATG-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-AGGC
* *
1202293 AAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AAAGGC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGC
*
1202341 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAAGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGG
1202389 AGACGCCACC
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
47 2 0.02
48 41 0.48
49 42 0.49
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (49 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGC
Found at i:1202335 original size:91 final size:94
Alignment explanation
Indices: 1202148--1202385 Score: 302
Period size: 97 Copynumber: 2.5 Consensus size: 94
1202138 AAGCTGAGAA
* *
1202148 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGAGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGAGCCAAT
*
1202213 ATGCTGATTCAAGGCCAGCTATATTGGACTT
64 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1202244 -AAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G-AAGGTGCCAATAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGAGCCAATAT
*
1202306 GCTGATTTAAGGCCAGCGATATTGGACTT
66 GCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1202335 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 --A---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1202386 AGGAGACGCC
Statistics
Matches: 125, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
91 39 0.31
93 1 0.01
94 40 0.32
95 4 0.03
97 41 0.33
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (94 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGAGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:1202360 original size:48 final size:47
Alignment explanation
Indices: 1202157--1202385 Score: 252
Period size: 48 Copynumber: 4.8 Consensus size: 47
1202147 AAAAGGATGT
* * * *
1202157 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGAGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-GG--AAGGTGC
1202209 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGAAGGTGC
* * * *
1202251 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-AGGAAGGTGC
* *
1202300 CAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGGCAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGG-AAGGTGC
*
1202348 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1202386 AGGAGACGCC
Statistics
Matches: 153, Mismatches: 16, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
42 38 0.25
47 2 0.01
48 44 0.29
49 37 0.24
52 32 0.21
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (47 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGAAGGTGC
Found at i:1202476 original size:60 final size:59
Alignment explanation
Indices: 1202429--1202715 Score: 199
Period size: 59 Copynumber: 4.8 Consensus size: 59
1202419 AGGTTTGCAT
* * *
1202429 CACTGACTTGTGGGCTTTT-AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
** *
1202487 CACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGC
1 CACTAACTTGTGGGCTTTT-AAAAGGGTGCCACTAACTTGTGGGCTT---TTG-AAAAGGGTGC
* * * * * ** *
1202551 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGCCACCGACTTGTGGGC-TTCGAAAAAGGGTGC
1 CACTA-ACTTGTGGGCTTT-TAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAAAGGGTGC
* * * * * ***
1202610 CACTGATTTGTGGGC-TTT-GAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGC
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
* * *** * *
1202667 CACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGACTTTTG
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTG
1202716 GAGGGTGATA
Statistics
Matches: 181, Mismatches: 35, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
56 2 0.01
57 39 0.22
58 25 0.14
59 44 0.24
60 25 0.14
62 1 0.01
63 20 0.11
64 25 0.14
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (59 bp):
CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:1202488 original size:30 final size:30
Alignment explanation
Indices: 1202429--1202715 Score: 259
Period size: 30 Copynumber: 9.7 Consensus size: 30
1202419 AGGTTTGCAT
*
1202429 CACTGACTTGTGGGCTTTT--AAAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
1202457 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
1202487 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* ** *
1202517 CACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGC
1 CACTGACTTGTGGGCTT---TTG-AAAAGGGTGC
* * * * *
1202551 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGC
1 CACT-GACTTGTGGGCTTTTGAAAAGGGTGC
* *
1202580 CACCGACTTGTGGGC-TTCGAAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTG-AAAAGGGTGC
* *
1202610 CACTGATTTGTGGGC-TTTG--AAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
***
1202637 CACTGACTTGTGGGCTTTTGAAAAAAATGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
***
1202667 CACTGACTTGTGGGC-TTTGAAAAATATGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
1202696 CACTGACTTGTGGACTTTTG
1 CACTGACTTGTGGGCTTTTG
1202716 GAGGGTGATA
Statistics
Matches: 216, Mismatches: 29, Indels: 26
0.80 0.11 0.10
Matches are distributed among these distances:
27 21 0.10
28 26 0.12
29 44 0.20
30 102 0.47
31 1 0.00
33 2 0.01
34 20 0.09
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (30 bp):
CACTGACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:1204158 original size:1 final size:1
Alignment explanation
Indices: 1204154--1204238 Score: 62
Period size: 1 Copynumber: 85.0 Consensus size: 1
1204144 CCGAACCCCC
* * * * * ** * *
1204154 TTTTTTTGTTTTTGTTTGTTTTTTTTGTTTTTGTTTTTGGTTTTTTTTTGTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
1204219 TTTTGTTTTGTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTT
1204239 GGAGGACGGC
Statistics
Matches: 62, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (1 bp):
T
Found at i:1204175 original size:9 final size:9
Alignment explanation
Indices: 1204154--1204236 Score: 70
Period size: 9 Copynumber: 9.4 Consensus size: 9
1204144 CCGAACCCCC
1204154 TTTT-TTTG
1 TTTTGTTTG
1204162 TTTTTGTTTG
1 -TTTTGTTTG
*
1204172 TTTTTTTTG
1 TTTTGTTTG
1204181 TTTTTGTTT-
1 -TTTTGTTTG
1204190 TTGGTT-TTT-
1 TT--TTGTTTG
*
1204199 TTTTGTTTT
1 TTTTGTTTG
1204208 TTTTGTTT-
1 TTTTGTTTG
1204216 TTTT-TTTG
1 TTTTGTTTG
1204224 TTTTGTTTG
1 TTTTGTTTG
1204233 TTTT
1 TTTT
1204237 TTGGAGGACG
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
7 5 0.08
8 13 0.20
9 33 0.52
10 13 0.20
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (9 bp):
TTTTGTTTG
Found at i:1204177 original size:20 final size:20
Alignment explanation
Indices: 1204154--1204238 Score: 113
Period size: 19 Copynumber: 4.2 Consensus size: 20
1204144 CCGAACCCCC
1204154 TTTTTTTGTTTTTGTTTG-T
1 TTTTTTTGTTTTTGTTTGTT
1204173 TTTTTTTGTTTTTGTTTTTGGTT
1 TTTTTTTGTTTTTG--TTT-GTT
1204196 TTTTTTTGTTTTT-TTTGTT
1 TTTTTTTGTTTTTGTTTGTT
1204215 TTTTTTT-TGTTTTGTTTGTT
1 TTTTTTTGT-TTTTGTTTGTT
1204235 TTTT
1 TTTT
1204239 GGAGGACGGC
Statistics
Matches: 60, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.02
19 28 0.47
20 13 0.22
21 3 0.05
22 1 0.02
23 14 0.23
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (20 bp):
TTTTTTTGTTTTTGTTTGTT
Found at i:1204184 original size:25 final size:25
Alignment explanation
Indices: 1204156--1204237 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 25
1204146 GAACCCCCTT
1204156 TTTTTGTTTTTGTTTGTTTTTTTTG
1 TTTTTGTTTTTGTTTGTTTTTTTTG
*
1204181 TTTTTGTTTTTGGTTT-TTTTTTGTTT
1 TTTTTGTTTTT-GTTTGTTTTTT-TTG
* *
1204207 TTTTTGTTTTTTTTTTGTTTTGTTTG
1 TTTTTG-TTTTTGTTTGTTTTTTTTG
1204233 TTTTT
1 TTTTT
1204238 TGGAGGACGG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
25 17 0.35
26 22 0.45
27 10 0.20
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (25 bp):
TTTTTGTTTTTGTTTGTTTTTTTTG
Found at i:1204191 original size:32 final size:30
Alignment explanation
Indices: 1204154--1204238 Score: 136
Period size: 32 Copynumber: 2.8 Consensus size: 30
1204144 CCGAACCCCC
1204154 TTTTTTTGTTTTTGTTTGTTTTTTTTGTTT
1 TTTTTTTGTTTTTGTTTGTTTTTTTTGTTT
*
1204184 TTGTTTTTGGTTTTTTTTTGTTTTTTTTGTTT
1 TT-TTTTT-GTTTTTGTTTGTTTTTTTTGTTT
1204216 TTTTTTTG-TTTTGTTTGTTTTTT
1 TTTTTTTGTTTTTGTTTGTTTTTT
1204239 GGAGGACGGC
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
29 14 0.27
30 3 0.06
31 10 0.20
32 24 0.47
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (30 bp):
TTTTTTTGTTTTTGTTTGTTTTTTTTGTTT
Found at i:1218109 original size:52 final size:51
Alignment explanation
Indices: 1218031--1218179 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
1218021 CGAAATATGA
*
1218031 AAATTTGCCTGCATGTATTGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
1218083 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
1218135 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1218180 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1218186 original size:13 final size:13
Alignment explanation
Indices: 1218168--1218192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1218158 CAAAGATCAG
1218168 TGTATCGATACAA
1 TGTATCGATACAA
1218181 TGTATCGATACA
1 TGTATCGATACA
1218193 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1218270 original size:33 final size:33
Alignment explanation
Indices: 1218233--1218299 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1218223 AGTAGCTTAA
1218233 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1218266 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1218299 A
1 A
1218300 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1218273 original size:13 final size:13
Alignment explanation
Indices: 1218255--1218279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1218245 CAAAAAAATA
1218255 TGTATCGATACAT
1 TGTATCGATACAT
1218268 TGTATCGATACA
1 TGTATCGATACA
1218280 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1226372 original size:42 final size:42
Alignment explanation
Indices: 1226325--1226406 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
1226315 AAGCAAATTC
*
1226325 TGAAGAAGAAGCAGAGGAAAATAGAAAAATTGAGCGAAATAT
1 TGAAGAAGAAGCAGAGGAAAATAGAAAAATTGAGCAAAATAT
*
1226367 TGAAGAAGAAGCAGAGGGAAATAGAAAAATTGAGCAAAAT
1 TGAAGAAGAAGCAGAGGAAAATAGAAAAATTGAGCAAAAT
1226407 TCTACATTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.55, C:0.05, G:0.27, T:0.13
Consensus pattern (42 bp):
TGAAGAAGAAGCAGAGGAAAATAGAAAAATTGAGCAAAATAT
Found at i:1227611 original size:29 final size:33
Alignment explanation
Indices: 1227562--1227635 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 33
1227552 TTTTAAATAA
1227562 ATTAATAATAATATTAATTTAA-A-AT-AAAATT
1 ATTAA-AATAATATTAATTTAATATATAAAAATT
* *
1227593 -TTAAAATATTATTATTTTAATATATAAAAATT
1 ATTAAAATAATATTAATTTAATATATAAAAATT
*
1227625 ATTAAATTAAT
1 ATTAAAATAAT
1227636 TAACATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 14 0.40
30 5 0.14
31 2 0.06
32 6 0.17
33 8 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATTAAAATAATATTAATTTAATATATAAAAATT
Found at i:1227654 original size:32 final size:34
Alignment explanation
Indices: 1227618--1227686 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
1227608 TTTAATATAT
* *
1227618 AAAAATTATTAAATTAATTAACATAT-TTA-ATA
1 AAAAATTATTAAATCAATTAACAAATCTTACATA
*
1227650 AAAAATTATTAAATCGATTAACAAATCTTACATA
1 AAAAATTATTAAATCAATTAACAAATCTTACATA
1227684 AAA
1 AAA
1227687 TTACTAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 23 0.72
33 3 0.09
34 6 0.19
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (34 bp):
AAAAATTATTAAATCAATTAACAAATCTTACATA
Found at i:1227687 original size:32 final size:31
Alignment explanation
Indices: 1227616--1227695 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
1227606 ATTTTAATAT
* *
1227616 ATAAAAATTATTAAATTAATTAACATATTTA
1 ATAAAAATTATTAAATCAATTAACAAATTTA
*
1227647 ATAAAAAATTATTAAATCGATTAACAAATCTTA
1 AT-AAAAATTATTAAATCAATTAACAAAT-TTA
*
1227680 CAT-AAAATTACTAAAT
1 -ATAAAAATTATTAAAT
1227696 ATTTTAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 2 0.05
32 35 0.83
33 3 0.07
34 2 0.05
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (31 bp):
ATAAAAATTATTAAATCAATTAACAAATTTA
Found at i:1227757 original size:32 final size:32
Alignment explanation
Indices: 1227708--1227777 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1227698 TTTAATAAAG
*
1227708 CGCTAGACACTTTAACAATTCTCACCTAAAAT
1 CGCTAGACACTTCAACAATTCTCACCTAAAAT
* * *
1227740 CGCTAGA-AGCTTCAACAATTTTTACGTAAAAT
1 CGCTAGACA-CTTCAACAATTCTCACCTAAAAT
*
1227772 TGCTAG
1 CGCTAG
1227778 CTGATTCCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 1 0.03
32 31 0.97
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (32 bp):
CGCTAGACACTTCAACAATTCTCACCTAAAAT
Found at i:1227868 original size:19 final size:20
Alignment explanation
Indices: 1227808--1227869 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
1227798 TTGGTAGCCT
* *
1227808 TATTGTTAATTTTATTAAAA
1 TATTATTAATTTTATTAATA
*
1227828 TGTTATT-ATTTT-TTAATAA
1 TATTATTAATTTTATTAAT-A
1227847 TATTATTAATTTTATT-ATA
1 TATTATTAATTTTATTAATA
1227866 TATT
1 TATT
1227870 GATATTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.11
19 17 0.49
20 12 0.34
21 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TATTATTAATTTTATTAATA
Found at i:1228094 original size:28 final size:29
Alignment explanation
Indices: 1228026--1228095 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
1228016 ATTGCAATTG
* *
1228026 TGTAATTATTTTAAAATATTTAATTTAATT
1 TGTAA-TAATTTAAAATATTTAATTTAAGT
* *
1228056 TGT-TTAATTTAAAAT-TTTAATTTAGGT
1 TGTAATAATTTAAAATATTTAATTTAAGT
*
1228083 TGTAATAGTTTAA
1 TGTAATAATTTAA
1228096 TTATTTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 13 0.39
28 17 0.52
30 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (29 bp):
TGTAATAATTTAAAATATTTAATTTAAGT
Found at i:1229282 original size:2 final size:2
Alignment explanation
Indices: 1229275--1229315 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1229265 TTAAAGGCAT
1229275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1229316 TCTAAAACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1232146 original size:22 final size:19
Alignment explanation
Indices: 1232103--1232143 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1232093 TTTATAATAA
1232103 TAATAATATTATCTTTTAT
1 TAATAATATTATCTTTTAT
1232122 TAATAATATTAT-TTTTAT
1 TAATAATATTATCTTTTAT
1232140 TAAT
1 TAAT
1232144 TAAAAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATAATATTATCTTTTAT
Found at i:1232176 original size:26 final size:27
Alignment explanation
Indices: 1232140--1232200 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
1232130 TTATTTTTAT
1232140 TAATTAAAAAAAT-CAACATAACAATA
1 TAATTAAAAAAATACAACATAACAATA
* * *
1232166 TAATTTAAAAAATAACAACATGATAATA
1 TAATTAAAAAAAT-ACAACATAACAATA
1232194 TAATTAA
1 TAATTAA
1232201 CAATATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 12 0.41
28 17 0.59
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (27 bp):
TAATTAAAAAAATACAACATAACAATA
Found at i:1232241 original size:20 final size:19
Alignment explanation
Indices: 1232174--1232242 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
1232164 TATAATTTAA
* *
1232174 AAAATAACAACATGATAAT
1 AAAATAATAACATTATAAT
* * *
1232193 ATAATTAACAATATTATTAA-
1 A-AAATAATAACATTA-TAAT
1232213 AAAATAATAACATTATAAT
1 AAAATAATAACATTATAAT
1232232 AAAATCAATAA
1 AAAAT-AATAA
1232243 TAAGGCGACT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
18 3 0.08
19 17 0.43
20 17 0.43
21 3 0.08
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.29
Consensus pattern (19 bp):
AAAATAATAACATTATAAT
Found at i:1234135 original size:20 final size:20
Alignment explanation
Indices: 1234112--1234149 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1234102 TTCTTAAATA
1234112 AATTAATAA-AATATTATATC
1 AATT-ATAATAATATTATATC
*
1234132 AATTATAATAATCTTATA
1 AATTATAATAATATTATA
1234150 ATAAGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTATAATAATATTATATC
Found at i:1238504 original size:13 final size:13
Alignment explanation
Indices: 1238457--1238505 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1238447 TATGATTACA
1238457 AAATATT-TATAT
1 AAATATTATATAT
*
1238469 AAATATTTTAT-T
1 AAATATTATATAT
1238481 ATAATATTATATAT
1 A-AATATTATATAT
*
1238495 AAATAATATAT
1 AAATATTATAT
1238506 TTATTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 9 0.28
13 21 0.66
14 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AAATATTATATAT
Found at i:1247037 original size:12 final size:11
Alignment explanation
Indices: 1247015--1247066 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
1247005 AGATGTAAAC
1247015 TTTTCACTTTTT
1 TTTTCA-TTTTT
*
1247027 TTTTCCATTTTCA
1 TTTT-CATTTT-T
1247040 TTTTCATTTTT
1 TTTTCATTTTT
1247051 TCTTTC-TTTTT
1 T-TTTCATTTTT
1247062 TTTTC
1 TTTTC
1247067 TTTGGTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 4 0.11
11 7 0.20
12 18 0.51
13 6 0.17
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCATTTTT
Found at i:1248115 original size:20 final size:19
Alignment explanation
Indices: 1248090--1248180 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
1248080 TGCCAGTTTC
1248090 ATGTATCGATACAAATAAGT
1 ATGTATCGATACAAATAA-T
*
1248110 ATGTATCGATAC-AATGAAC
1 ATGTATCGATACAAAT-AAT
* **
1248129 ATGTATTGATACAAAGCAT
1 ATGTATCGATACAAATAAT
**
1248148 AATGTATCGATACATCTAAAT
1 -ATGTATCGATACAAAT-AAT
*
1248169 GTGTATCGATAC
1 ATGTATCGATAC
1248181 TTTTTAGGAT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
19 15 0.27
20 39 0.70
21 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAAATAAT
Found at i:1248411 original size:20 final size:21
Alignment explanation
Indices: 1248374--1248412 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1248364 TTAAAAGAAT
*
1248374 AAAACTTGTTTACGGTTTTTC
1 AAAACTTATTTACGGTTTTTC
1248395 AAAACTTATTT-CGGTTTT
1 AAAACTTATTTACGGTTTT
1248413 ATCCATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (21 bp):
AAAACTTATTTACGGTTTTTC
Found at i:1248767 original size:17 final size:17
Alignment explanation
Indices: 1248745--1248799 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
1248735 TATTTAAAGC
1248745 TTTATAAAACAAATTTA
1 TTTATAAAACAAATTTA
*
1248762 TTTATAAAACACATTTA
1 TTTATAAAACAAATTTA
1248779 TTTTATAAAACAAATTTA
1 -TTTATAAAACAAATTTA
1248797 TTT
1 TTT
1248800 CAAACATTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 19 0.54
18 16 0.46
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATAAAACAAATTTA
Found at i:1248785 original size:18 final size:18
Alignment explanation
Indices: 1248745--1248799 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
1248735 TATTTAAAGC
1248745 TTTATAAAACAAATTTA-
1 TTTATAAAACAAATTTAT
*
1248762 TTTATAAAACACATTTAT
1 TTTATAAAACAAATTTAT
1248780 TTTATAAAACAAATTTAT
1 TTTATAAAACAAATTTAT
1248798 TT
1 TT
1248800 CAAACATTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 16 0.46
18 19 0.54
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTATAAAACAAATTTAT
Found at i:1254809 original size:148 final size:148
Alignment explanation
Indices: 1254541--1254837 Score: 576
Period size: 148 Copynumber: 2.0 Consensus size: 148
1254531 GAATGATTCA
* *
1254541 TGCAAATTTTTGTTTTTCTTTAATAATTCATTATTTTCATTAGTTAAGACTTTATTAATATCTTG
1 TGCAAATTTTTGTTTTTCCTTAATAATTCATTATTTTCATCAGTTAAGACTTTATTAATATCTTG
1254606 TATTTCATTCAATCGATTTTCTAATTTGACCAGTTTTATTTTAAGCTCATTATTCTCTATACTTA
66 TATTTCATTCAATCGATTTTCTAATTTGACCAGTTTTATTTTAAGCTCATTATTCTCTATACTTA
1254671 CCAATTTATTTTCATCAT
131 CCAATTTATTTTCATCAT
1254689 TGCAAATTTTTGTTTTTCCTTAATAATTCATTATTTTCATCAGTTAAGACTTTATTAATATCTTG
1 TGCAAATTTTTGTTTTTCCTTAATAATTCATTATTTTCATCAGTTAAGACTTTATTAATATCTTG
1254754 TATTTCATTCAATCGATTTTCTAATTTGACCAGTTTTATTTTAAGCTCATTATTCTCTATACTTA
66 TATTTCATTCAATCGATTTTCTAATTTGACCAGTTTTATTTTAAGCTCATTATTCTCTATACTTA
1254819 CCAATTTATTTTCATCAT
131 CCAATTTATTTTCATCAT
1254837 T
1 T
1254838 TAGTTTAGAG
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 147 1.00
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (148 bp):
TGCAAATTTTTGTTTTTCCTTAATAATTCATTATTTTCATCAGTTAAGACTTTATTAATATCTTG
TATTTCATTCAATCGATTTTCTAATTTGACCAGTTTTATTTTAAGCTCATTATTCTCTATACTTA
CCAATTTATTTTCATCAT
Found at i:1256931 original size:20 final size:20
Alignment explanation
Indices: 1256906--1256959 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1256896 ATTTGGGACA
* **
1256906 ATGTATCGATACAATTTTTC
1 ATGTATCGATACAATGTGCC
1256926 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
*
1256946 ATGTATCAATACAA
1 ATGTATCGATACAA
1256960 ACAGTGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:1259215 original size:162 final size:163
Alignment explanation
Indices: 1258980--1259379 Score: 463
Period size: 166 Copynumber: 2.4 Consensus size: 163
1258970 ATTTATTTTA
* * * * * *
1258980 GGAAAATTTTTCTTGGTTTATAATTTTTAA-ATTTCTTTAAATATTAAT-ATTTAACTTATATTA
1 GGAAAATTTTTCTTGGTTCA-AAATTTTAATA-TTCATCAAATA-TCATCATTTAACTCATATTA
* * * *
1259043 AATCAGTTTTGAAGAATAT-ATTTTATTCCATGAG-TTT-TTTTCCTTTGGAATTCTTTTTA-TT
63 AATTAGTTTTGAAGAAT-TCATTTTATTCCATGAGTTTTGTTTTCCTTTAGAATTC-TTCTAGTC
* **
1259104 TCTAAAAAACA-GAGTTTTCTACTCCGTAAATGTTTTTGG
126 T-TAAAAAAAAGGAGTTTTCTACTCCGTAAATG-TTTCCG
**
1259143 GGGGAATTTTTCTTGGTTCAAAATTTTAATATTCATCAAATATCATCATTTAACTCATATTAAAT
1 GGAAAATTTTTCTTGGTTCAAAATTTTAATATTCATCAAATATCATCATTTAACTCATATTAAAT
*
1259208 TAGTTTTGAAGAATTCATTTTATTCCATGAGTTTTTTGTTTTCTTTTAGAATTCTTCTAGTCTTA
66 TAGTTTTGAAGAATTCATTTTATTCCATGAG--TTTTGTTTTCCTTTAGAATTCTTCTAGTCTTA
* *
1259273 AAAAAAATGGAGTTTTTTGCTCCGTAAATGTTTCCG
129 AAAAAAA-GGAGTTTTCTACTCCGTAAATGTTTCCG
* * * *
1259309 GGAAAATTTTTTTTGGTTCAAAATTTTAATATTCATCAAATATCATCATTTTATTCATAGTAAAT
1 GGAAAATTTTTCTTGGTTCAAAATTTTAATATTCATCAAATATCATCATTTAACTCATATTAAAT
1259374 TAGTTT
66 TAGTTT
1259380 GGAAATTTTC
Statistics
Matches: 203, Mismatches: 24, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
161 4 0.02
162 62 0.31
163 18 0.09
165 15 0.07
166 85 0.42
167 19 0.09
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.48
Consensus pattern (163 bp):
GGAAAATTTTTCTTGGTTCAAAATTTTAATATTCATCAAATATCATCATTTAACTCATATTAAAT
TAGTTTTGAAGAATTCATTTTATTCCATGAGTTTTGTTTTCCTTTAGAATTCTTCTAGTCTTAAA
AAAAAGGAGTTTTCTACTCCGTAAATGTTTCCG
Found at i:1263189 original size:48 final size:48
Alignment explanation
Indices: 1263118--1263217 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
1263108 CCTAGTGGAA
*
1263118 TAAATTCTCAAAGTCGGGTGAAATGCGCTGCTGGCAGAGCACATGAAG
1 TAAATTCTCAAAGTCGAGTGAAATGCGCTGCTGGCAGAGCACATGAAG
*
1263166 TAAATTCTCAAAGTCGAGTGAAATGTGCTGCTGGCAGAGCACATGAAG
1 TAAATTCTCAAAGTCGAGTGAAATGCGCTGCTGGCAGAGCACATGAAG
1263214 TAAA
1 TAAA
1263218 GGTGTGACAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (48 bp):
TAAATTCTCAAAGTCGAGTGAAATGCGCTGCTGGCAGAGCACATGAAG
Found at i:1263338 original size:9 final size:10
Alignment explanation
Indices: 1263312--1263350 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
1263302 GAAGTTTTTA
1263312 TGAAAAATATT
1 TGAAAAAT-TT
1263323 TGAAAAATTT
1 TGAAAAATTT
1263333 TGAAAAATTT
1 TGAAAAATTT
1263343 TGAAAAAT
1 TGAAAAAT
1263351 CATCTAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (10 bp):
TGAAAAATTT
Found at i:1263994 original size:2 final size:2
Alignment explanation
Indices: 1263989--1264026 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1263979 TTTCAAAATT
1263989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1264027 AATAAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1264419 original size:9 final size:9
Alignment explanation
Indices: 1264406--1264452 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
1264396 TATTTCATAT
*
1264406 TTTTTCTTT
1 TTTTTCTTC
1264415 TTTTTCTTC
1 TTTTTCTTC
*
1264424 TTCTTCTTC
1 TTTTTCTTC
*
1264433 -CTTTCTTC
1 TTTTTCTTC
1264441 TTTTTCCTTC
1 TTTTT-CTTC
1264451 TT
1 TT
1264453 CCCCACCCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
8 6 0.19
9 19 0.61
10 6 0.19
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:1264440 original size:14 final size:13
Alignment explanation
Indices: 1264420--1264453 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1264410 TCTTTTTTTT
1264420 CTTCTTCTTCTTC
1 CTTCTTCTTCTTC
*
1264433 CTTTCTTCTTTTTC
1 C-TTCTTCTTCTTC
1264447 CTTCTTC
1 CTTCTTC
1264454 CCCACCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTCTTCTTCTTC
Done.