Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009017.1 Hibiscus syriacus cultivar Beakdansim tig00112407_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1192163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:985788 original size:26 final size:26
Alignment explanation
Indices: 985759--985812 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
985749 CATAATTTCT
*
985759 TATATTCACATAGAT-CATATAACAAA
1 TATAATCACATA-ATACATATAACAAA
* *
985785 TATAATCATATAATACATTTAACAAA
1 TATAATCACATAATACATATAACAAA
985811 TA
1 TA
985813 CGTGTACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (26 bp):
TATAATCACATAATACATATAACAAA
Found at i:987341 original size:30 final size:30
Alignment explanation
Indices: 987252--987362 Score: 118
Period size: 30 Copynumber: 3.7 Consensus size: 30
987242 AAATATATAT
* * *
987252 GAAATTTTAAGGGACCAAAATA-AAAATAACA
1 GAAATTTGAA-GGACTAAAATAGAAAA-AATA
* *
987283 GAAACTTAAAGGACTAAAATAG-AAAAATA
1 GAAATTTGAAGGACTAAAATAGAAAAAATA
*
987312 GAAATTTGAAGTACTAAAATAGAAAAAATA
1 GAAATTTGAAGGACTAAAATAGAAAAAATA
* *
987342 GAACTTTGAAGGACTATAATA
1 GAAATTTGAAGGACTAAAATA
987363 TCAAAAACAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.32
30 38 0.56
31 8 0.12
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.22
Consensus pattern (30 bp):
GAAATTTGAAGGACTAAAATAGAAAAAATA
Found at i:987369 original size:30 final size:29
Alignment explanation
Indices: 987238--987362 Score: 115
Period size: 30 Copynumber: 4.2 Consensus size: 29
987228 ATAAATAGTC
* * * *
987238 AAATAAATATATATGAAATTTTAAGGGACCA
1 AAATAAAAAAATA-GAAATTTGAA-GGACTA
* * *
987269 AAATAAAAATAACAGAAACTTAAAGGACTA
1 AAATAAAAA-AATAGAAATTTGAAGGACTA
* *
987299 AAATAGAAAAATAGAAATTTGAAGTACTA
1 AAATAAAAAAATAGAAATTTGAAGGACTA
*
987328 AAATAGAAAAAATAGAACTTTGAAGGACTA
1 AAATA-AAAAAATAGAAATTTGAAGGACTA
*
987358 TAATA
1 AAATA
987363 TCAAAAACAT
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
29 21 0.27
30 38 0.49
31 16 0.21
32 2 0.03
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (29 bp):
AAATAAAAAAATAGAAATTTGAAGGACTA
Found at i:988853 original size:3 final size:3
Alignment explanation
Indices: 988847--988906 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
988837 GGTAAGTAAT
* * *
988847 TAA TAA TAA TAA TAA TAA TAA TAA TAA -CA TAA TAA TAA CAA -CA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
988893 TAA T-A TAA TTAA TA
1 TAA TAA TAA -TAA TA
988907 CTATTTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:988880 original size:14 final size:14
Alignment explanation
Indices: 988847--988897 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
988837 GGTAAGTAAT
*
988847 TAATAATAATAATAA
1 TAATAATAATAA-CA
988862 TAATAATAATAACA
1 TAATAATAATAACA
*
988876 TAATAATAACAACA
1 TAATAATAATAACA
988890 TAATAATA
1 TAATAATA
988898 TAATTAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAATAATAACA
Found at i:990155 original size:28 final size:26
Alignment explanation
Indices: 990079--990155 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 26
990069 AAAGATATAT
*
990079 ATAAAAAAATGCATAGAATAAA-GAAG
1 ATAAAAAAATG-ATAAAATAAATGAAG
* *
990105 ATAATAAAAATAACAATAA-AAATGGAAG
1 ATAA-AAAAATGATAA-AATAAAT-GAAG
990133 ATAAAAAAATGATAAAATGAAAT
1 ATAAAAAAATGATAAAAT-AAAT
990156 TTACAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 11 0.28
27 17 0.43
28 12 0.30
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (26 bp):
ATAAAAAAATGATAAAATAAATGAAG
Found at i:990246 original size:30 final size:30
Alignment explanation
Indices: 990185--990246 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
990175 CATAACATGT
* *
990185 AATAATAGTAATAAAGAAAATATATATATA
1 AATAATAATAATAAAGAAAAGATATATATA
990215 AATAATAATAATAAAGGCAAAAGA-ATA-ATA
1 AATAATAATAATAAA-G-AAAAGATATATATA
990245 AA
1 AA
990247 ATAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 4 0.14
32 5 0.18
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (30 bp):
AATAATAATAATAAAGAAAAGATATATATA
Found at i:992371 original size:43 final size:43
Alignment explanation
Indices: 992310--992431 Score: 192
Period size: 43 Copynumber: 2.8 Consensus size: 43
992300 CTCAAATGGC
* *
992310 ACGATATCCTCCGTCGTGGAGTTAAAATCGTGGATGTATGGGT
1 ACGATATCCTCCTTCGTGGAGTTGAAATCGTGGATGTATGGGT
* *
992353 ACGATATCCTCCTTCGTGGAGTTGAAATCGTGGATTTGTGGGT
1 ACGATATCCTCCTTCGTGGAGTTGAAATCGTGGATGTATGGGT
992396 ACGATATCCT-CTATCGTGGAGTTGAAATCGTGGATG
1 ACGATATCCTCCT-TCGTGGAGTTGAAATCGTGGATG
992432 GCCCCTTCAT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 2 0.03
43 71 0.97
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (43 bp):
ACGATATCCTCCTTCGTGGAGTTGAAATCGTGGATGTATGGGT
Found at i:993476 original size:11 final size:11
Alignment explanation
Indices: 993437--993475 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
993427 ACCCACCTTA
993437 TTTTTCTTTTC
1 TTTTTCTTTTC
*
993448 TTTTTCTTTTG
1 TTTTTCTTTTC
*
993459 TTCTTTTTTTTC
1 TT-TTTCTTTTC
993471 TTTTT
1 TTTTT
993476 TCAATTTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:993476 original size:19 final size:19
Alignment explanation
Indices: 993440--993474 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
993430 CACCTTATTT
993440 TTCTTTTCTTTTTCTTTTG
1 TTCTTTTCTTTTTCTTTTG
993459 TTC-TTT-TTTTTCTTTT
1 TTCTTTTCTTTTTCTTTT
993475 TTCAATTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 3 0.19
19 3 0.19
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (19 bp):
TTCTTTTCTTTTTCTTTTG
Found at i:997788 original size:23 final size:22
Alignment explanation
Indices: 997762--997824 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
997752 CATCTTATAT
*
997762 GGCACTTTGGTGCATTTCTACGC
1 GGCACTTAGGTGCATTT-TACGC
*
997785 GGCACTTAGGTGCAATTTTACGT
1 GGCACTTAGGTGC-ATTTTACGC
*
997808 GGCACTTCGGTGCATTT
1 GGCACTTAGGTGCATTT
997825 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.11
23 28 0.78
24 4 0.11
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (22 bp):
GGCACTTAGGTGCATTTTACGC
Found at i:1003300 original size:6 final size:6
Alignment explanation
Indices: 1003289--1003323 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1003279 TTGTGAAACA
* *
1003289 ATATGT ATATGT ATATGT ATATAT ATATAT ATATG
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATG
1003324 CGTTTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (6 bp):
ATATGT
Found at i:1020482 original size:77 final size:77
Alignment explanation
Indices: 1020377--1020578 Score: 266
Period size: 77 Copynumber: 2.6 Consensus size: 77
1020367 GACCGTTGAA
* * * *
1020377 CAGGGGGGAATCGGTACCCCCT-TGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCATACTGGAAATCTCGA
**
1020441 AACAAAAACTGTT
66 AAC-AAAACCATT
* * *
1020454 TAGGGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCTGAGCATTCTGGAAATCTCGG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCATACTGGAAATCTCGA
* *
1020517 AGCCAAACCATT
66 AACAAAACCATT
*
1020529 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGATTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1020579 ATCTGTAATT
Statistics
Matches: 109, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
75 29 0.27
76 37 0.34
77 42 0.39
78 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (77 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCATACTGGAAATCTCGA
AACAAAACCATT
Found at i:1023195 original size:21 final size:21
Alignment explanation
Indices: 1023169--1023208 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1023159 CAGAACCCCA
*
1023169 GGGGGGTATCGATTCCCCTGT
1 GGGGGGGATCGATTCCCCTGT
*
1023190 GGGGGGGATCGGTTCCCCT
1 GGGGGGGATCGATTCCCCT
1023209 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.25, G:0.42, T:0.25
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCCTGT
Found at i:1029103 original size:76 final size:76
Alignment explanation
Indices: 1028999--1029198 Score: 262
Period size: 76 Copynumber: 2.6 Consensus size: 76
1028989 GACCGTTGAA
* * *
1028999 CAGGGGGGAATCGGTACCCCCT-TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGAA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGAA
**
1029063 ACAAAAACTGTT
66 AC-AAAACCATT
* * *
1029075 TAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGAA
* *
1029139 GCCAAACCATT
66 ACAAAACCATT
*
1029150 CA-GGGGGAATCGGTTCCTCCTATGGGGGGAAATCGGTTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGG-AATCGGTTCCCTCCGAGCA
1029199 ATCTGTAATT
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
74 21 0.19
75 12 0.11
76 75 0.69
77 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGAA
ACAAAACCATT
Found at i:1031224 original size:34 final size:34
Alignment explanation
Indices: 1031152--1031224 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
1031142 CATAACATAT
* * * *
1031152 AATAATAGTAATAAAGAAAATATATATATATAAT
1 AATAATAATAATAAAGAAAAGATATATATAAAAA
1031186 AATAATAATAATAAAGGCAAAAGA-ATA-ATAAAAA
1 AATAATAATAATAAA-G-AAAAGATATATATAAAAA
1031220 AATAA
1 AATAA
1031225 AACTAGTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
34 24 0.73
35 4 0.12
36 5 0.15
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (34 bp):
AATAATAATAATAAAGAAAAGATATATATAAAAA
Found at i:1031370 original size:15 final size:15
Alignment explanation
Indices: 1031347--1031408 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
1031337 AACTATACAA
* * *
1031347 ATATTAATAATAAGT
1 ATATAAATAAAAAAT
1031362 ATATAAATAAAAAAT
1 ATATAAATAAAAAAT
* *
1031377 ATATAAA-AACATAT
1 ATATAAATAAAAAAT
1031391 ATATAATATAAAATAAT
1 ATATAA-ATAAAA-AAT
1031408 A
1 A
1031409 AAAATACTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 11 0.30
15 20 0.54
16 3 0.08
17 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
ATATAAATAAAAAAT
Found at i:1031421 original size:29 final size:30
Alignment explanation
Indices: 1031356--1031422 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
1031346 AATATTAATA
*
1031356 ATAAGTATATAAATAAAAAATATATAAAAAC
1 ATAA-TATATAAATAAAAAATATATAAAAAT
*
1031387 AT-ATATAT-AATATAAAATA-ATAAAAAT
1 ATAATATATAAATAAAAAATATATAAAAAT
1031414 ACTAATATA
1 A-TAATATA
1031423 AGGATCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 8 0.25
28 11 0.34
29 10 0.31
30 1 0.03
31 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (30 bp):
ATAATATATAAATAAAAAATATATAAAAAT
Found at i:1031423 original size:27 final size:28
Alignment explanation
Indices: 1031361--1031412 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1031351 TAATAATAAG
1031361 TATATA-AATAAAAAATATATAAAAACA
1 TATATATAATAAAAAATATATAAAAACA
*
1031388 TATATATAATATAAAATA-ATAAAAA
1 TATATATAATAAAAAATATATAAAAA
1031413 TACTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (28 bp):
TATATATAATAAAAAATATATAAAAACA
Found at i:1033857 original size:2 final size:2
Alignment explanation
Indices: 1033850--1033891 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1033840 ATATTATCTC
1033850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1033892 CACCCATGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1043758 original size:20 final size:20
Alignment explanation
Indices: 1043722--1043759 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1043712 CACACCACCT
* *
1043722 ACAAAATTATTATTATTAAA
1 ACAAAATTAATAATATTAAA
1043742 ACAAAATTAATAATATTA
1 ACAAAATTAATAATATTA
1043760 GTGTGTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
ACAAAATTAATAATATTAAA
Found at i:1044524 original size:184 final size:184
Alignment explanation
Indices: 1044215--1044573 Score: 673
Period size: 184 Copynumber: 2.0 Consensus size: 184
1044205 GTTAACCCCT
*
1044215 CCTTCTTCTTCTTCTTCTACTACTACTACTACTATGCGTTTACTACTAAACTCTTTAGCTGTTGC
1 CCTTCTTCTTCTTCTTCTACTACTACTACTACTATGCGTTTACTACTAAACTCTTTAGCTGATGC
1044280 AGGTTTTGCAATTCGGCTCCGTTCCGCCACAAATATATTAGTTTACTACAACCTTCAATCTGCAG
66 AGGTTTTGCAATTCGGCTCCGTTCCGCCACAAATATATTAGTTTACTACAACCTTCAATCTGCAG
* *
1044345 AATTTTGAGTTTCGTTAAGGCCTTGGATAGCTCCTCAATTATGTACTAATATAA
131 AATTTTGAGTTTCGTTAAGACCTTGGATACCTCCTCAATTATGTACTAATATAA
*
1044399 CCTTCTTCTTCTTCTTCTTCTACTACTACTACTATGCGTTTACTACTAAACTCTTTAGCTGATGC
1 CCTTCTTCTTCTTCTTCTACTACTACTACTACTATGCGTTTACTACTAAACTCTTTAGCTGATGC
1044464 AGGTTTTGCAATTCGGCTCCGTTCCGCCACAAATATATTAGTTTACTACAACCTTCAATCTGCAG
66 AGGTTTTGCAATTCGGCTCCGTTCCGCCACAAATATATTAGTTTACTACAACCTTCAATCTGCAG
*
1044529 AATTTTGAGTTTCGTTAAGACCTTTGATACCTCCTCAATTATGTA
131 AATTTTGAGTTTCGTTAAGACCTTGGATACCTCCTCAATTATGTA
1044574 GGTAAGGTTT
Statistics
Matches: 170, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 170 1.00
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.39
Consensus pattern (184 bp):
CCTTCTTCTTCTTCTTCTACTACTACTACTACTATGCGTTTACTACTAAACTCTTTAGCTGATGC
AGGTTTTGCAATTCGGCTCCGTTCCGCCACAAATATATTAGTTTACTACAACCTTCAATCTGCAG
AATTTTGAGTTTCGTTAAGACCTTGGATACCTCCTCAATTATGTACTAATATAA
Found at i:1047018 original size:23 final size:23
Alignment explanation
Indices: 1046988--1047034 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1046978 TGTTATAGCA
*
1046988 TAACTAATATTCCTATCTTTGAT
1 TAACTAATATTCCTATCCTTGAT
1047011 TAACTAATATTCCTATCCTTGAT
1 TAACTAATATTCCTATCCTTGAT
1047034 T
1 T
1047035 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (23 bp):
TAACTAATATTCCTATCCTTGAT
Found at i:1057422 original size:39 final size:39
Alignment explanation
Indices: 1057378--1057461 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
1057368 GATGGTGAAG
* *
1057378 TAGGGAGTGAGATGCGA-AGGAGAAATGAAAAAGGGGAAT
1 TAGGGAGTGAGAGGCAAGAGGA-AAATGAAAAAGGGGAAT
* * *
1057417 TAGGGATTGAGGGGCAAGAGGAAAATGAAAATGGGGAAT
1 TAGGGAGTGAGAGGCAAGAGGAAAATGAAAAAGGGGAAT
1057456 TAGGGA
1 TAGGGA
1057462 TTATGGCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 35 0.90
40 4 0.10
ACGTcount: A:0.42, C:0.02, G:0.42, T:0.14
Consensus pattern (39 bp):
TAGGGAGTGAGAGGCAAGAGGAAAATGAAAAAGGGGAAT
Found at i:1066564 original size:21 final size:21
Alignment explanation
Indices: 1066538--1066590 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1066528 ATTCTGACTA
1066538 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
1066559 TCGCATTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
1066580 TCGCAATGCGA
1 TCGCATTGCGA
1066591 ATATGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1066691 original size:20 final size:20
Alignment explanation
Indices: 1066599--1066685 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
1066589 GAATATGTAA
* *
1066599 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
1066619 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1066639 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1066659 ATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
1066679 ATCGCAA
1 ATCGCAA
1066686 TACGATTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1066891 original size:22 final size:22
Alignment explanation
Indices: 1066866--1066910 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1066856 CACTCTCTAA
* *
1066866 GACGACATCCGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
1066888 GACGAAATCAGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
1066910 G
1 G
1066911 GCAAAATCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.44, G:0.16, T:0.18
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCC
Found at i:1066917 original size:22 final size:22
Alignment explanation
Indices: 1066876--1066918 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1066866 GACGACATCC
*
1066876 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACAAAATCA
*
1066898 GTCCCCATCTCCGGCAAAATC
1 GTCCCCATCTCCGACAAAATC
1066919 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.42, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCA
Found at i:1067438 original size:20 final size:20
Alignment explanation
Indices: 1067316--1067431 Score: 144
Period size: 20 Copynumber: 5.8 Consensus size: 20
1067306 GTGATTTTAG
1067316 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
** *
1067335 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTTTCAT
* **
1067355 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCAT
*
1067375 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
1067395 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
1067415 TTTCGTGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
1067432 AAGTTTCAGA
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
19 17 0.19
20 71 0.81
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.47
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:1069178 original size:18 final size:18
Alignment explanation
Indices: 1069155--1069204 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1069145 TTTACTCGTA
* *
1069155 ATTTCAATTAGATTAATC
1 ATTTCACTTAGATTAACC
1069173 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1069191 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1069205 GCTTAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1069383 original size:20 final size:20
Alignment explanation
Indices: 1069354--1069397 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1069344 GTTTACTTTT
*
1069354 GCAACGCGAAAATGACTATC
1 GCAACACGAAAATGACTATC
**
1069374 GCAACACGAATTTGACTATC
1 GCAACACGAAAATGACTATC
1069394 GCAA
1 GCAA
1069398 TGAAAGAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
GCAACACGAAAATGACTATC
Found at i:1069467 original size:20 final size:19
Alignment explanation
Indices: 1069442--1069508 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
1069432 GCGATTCTCT
1069442 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
* *
1069462 CGTTGCGGTAGTCATTTTCG
1 CGTTGCGATAGTCA-ATTCG
1069482 CGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
1069500 TGTTGCGAT
1 CGTTGCGAT
1069509 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 12 0.29
19 1 0.02
20 28 0.68
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:1070054 original size:21 final size:21
Alignment explanation
Indices: 1069963--1070067 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
1069953 TACTCAGCTG
*
1069963 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1069985 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1070005 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1070026 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1070047 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1070068 CCAACATTTT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1070060 original size:42 final size:42
Alignment explanation
Indices: 1069960--1070070 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1069950 CCTTACTCAG
* * * *
1069960 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1070002 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1070044 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1070071 ACATTTTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1071248 original size:20 final size:20
Alignment explanation
Indices: 1071223--1071317 Score: 103
Period size: 20 Copynumber: 5.0 Consensus size: 20
1071213 TGTTGTTAAG
1071223 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
1071243 TTCGCGTTGCGAT--T----
1 TTCGCGTTGCGATAGTCAAA
* * *
1071257 TTTGAGTTGCGATAATCAAA
1 TTCGCGTTGCGATAGTCAAA
*
1071277 TTCGTGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
*
1071297 TTCGCGTTGCGATATTCAAA
1 TTCGCGTTGCGATAGTCAAA
1071317 T
1 T
1071318 GAATGTGTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
14 11 0.18
16 1 0.02
18 1 0.02
20 49 0.79
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:1071511 original size:18 final size:18
Alignment explanation
Indices: 1071488--1071522 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1071478 AAGCCGGTTG
*
1071488 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1071506 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1071523 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1073809 original size:24 final size:24
Alignment explanation
Indices: 1073777--1073852 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
1073767 GAAACATCAT
*
1073777 CAAAATCCGAGTATTGACCAAGAC
1 CAAAGTCCGAGTATTGACCAAGAC
1073801 CAAAGTCCGAGTATTGACCAAGAC
1 CAAAGTCCGAGTATTGACCAAGAC
*
1073825 CAAAGTCCGAGTATTGACCAAGAT
1 CAAAGTCCGAGTATTGACCAAGAC
1073849 CAAA
1 CAAA
1073853 TTTTGAATAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (24 bp):
CAAAGTCCGAGTATTGACCAAGAC
Found at i:1074780 original size:20 final size:20
Alignment explanation
Indices: 1074673--1074771 Score: 135
Period size: 20 Copynumber: 5.0 Consensus size: 20
1074663 GAAATTCAGT
*
1074673 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
1074693 GTTACGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
1074713 GTTGCGATAATCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1074733 GTTGCGATAGTCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
* *
1074753 ATTGCGATAGTCATAATCG
1 GTTGCGATAGTCAGAATCG
1074772 TATTGCGATT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1074787 original size:20 final size:20
Alignment explanation
Indices: 1074773--1074839 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
1074763 TCATAATCGT
1074773 ATTGCGATTTACATATTCGC
1 ATTGCGATTTACATATTCGC
1074793 ATTGCGATTTACATATTCGC
1 ATTGCGATTTACATATTCGC
1074813 ATTGCGATTTACATATTCGC
1 ATTGCGATTTACATATTCGC
1074833 ATTGCGA
1 ATTGCGA
1074840 ATTCGGAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (20 bp):
ATTGCGATTTACATATTCGC
Found at i:1074796 original size:40 final size:40
Alignment explanation
Indices: 1074752--1074839 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
1074742 GTCAGAATCA
*
1074752 CATTGCGATAGT-CATAATCGTATTGCGATTTACATATTCG
1 CATTGCGAT-GTACATAATCGCATTGCGATTTACATATTCG
* *
1074792 CATTGCGATTTACATATTCGCATTGCGATTTACATATTCG
1 CATTGCGATGTACATAATCGCATTGCGATTTACATATTCG
1074832 CATTGCGA
1 CATTGCGA
1074840 ATTCGGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (40 bp):
CATTGCGATGTACATAATCGCATTGCGATTTACATATTCG
Found at i:1074860 original size:21 final size:21
Alignment explanation
Indices: 1074836--1074881 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1074826 TATTCGCATT
1074836 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
1074857 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
1074878 GCGA
1 GCGA
1074882 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:1075409 original size:27 final size:28
Alignment explanation
Indices: 1075349--1075410 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
1075339 AATTCTAGGT
1075349 AATTTAAAGATTTTATGTTTGTTTAGAA
1 AATTTAAAGATTTTATGTTTGTTTAGAA
*
1075377 AA-TTAACA-ATTTTA-GTTT-TTTAATAA
1 AATTTAA-AGATTTTATGTTTGTTT-AGAA
1075403 AATTTAAA
1 AATTTAAA
1075411 AAAAACATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
25 3 0.10
26 10 0.33
27 14 0.47
28 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (28 bp):
AATTTAAAGATTTTATGTTTGTTTAGAA
Found at i:1075962 original size:35 final size:35
Alignment explanation
Indices: 1075916--1076006 Score: 173
Period size: 35 Copynumber: 2.6 Consensus size: 35
1075906 AATTAAGTTG
*
1075916 TATCTTTTCTTCAATTAATTAGAGGCTAACTATGC
1 TATCTTTTCTTCAATTAATTAGAGGCTAAATATGC
1075951 TATCTTTTCTTCAATTAATTAGAGGCTAAATATGC
1 TATCTTTTCTTCAATTAATTAGAGGCTAAATATGC
1075986 TATCTTTTCTTCAATTAATTA
1 TATCTTTTCTTCAATTAATTA
1076007 CCTCATTATT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (35 bp):
TATCTTTTCTTCAATTAATTAGAGGCTAAATATGC
Found at i:1083689 original size:36 final size:35
Alignment explanation
Indices: 1083614--1083693 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
1083604 ACACAATCAT
*
1083614 CAATTACATTATAAACCCTAAATTCCAAAATACTT
1 CAATTACATTATAAACCCTAAATTCCAAAATACTC
*
1083649 CAATTACATTCTAAA-CCTCAAATTCCAAAAATA-TGC
1 CAATTACATTATAAACCCT-AAATTCC-AAAATACT-C
1083685 CAATTACAT
1 CAATTACAT
1083694 AACCAACCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 3 0.08
35 22 0.55
36 15 0.38
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.30
Consensus pattern (35 bp):
CAATTACATTATAAACCCTAAATTCCAAAATACTC
Found at i:1083981 original size:34 final size:35
Alignment explanation
Indices: 1083938--1084016 Score: 124
Period size: 34 Copynumber: 2.3 Consensus size: 35
1083928 AGGGTTGGAC
1083938 ATATAATTGAAGTATTTTGGAATTTGAGG-TTAGA
1 ATATAATTGAAGTATTTTGGAATTTGAGGTTTAGA
* *
1083972 ATATAATTGAAGTATTTTGGATTTTGTGGTTTAGA
1 ATATAATTGAAGTATTTTGGAATTTGAGGTTTAGA
*
1084007 ATGTAATTGA
1 ATATAATTGA
1084017 TTAACGTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 27 0.66
35 14 0.34
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
ATATAATTGAAGTATTTTGGAATTTGAGGTTTAGA
Found at i:1086745 original size:43 final size:43
Alignment explanation
Indices: 1086698--1086812 Score: 207
Period size: 42 Copynumber: 2.7 Consensus size: 43
1086688 ATAATTAAAT
*
1086698 AATAAAATATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
1 AATAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
1086741 AATAAAACATTAAGAAACAAAATAAAT-AAAAGTCCATAATTA
1 AATAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
1086783 AATAAAACATTAAGAAAC-AAATAAATAAAA
1 AATAAAACATTAAGAAACAAAATAAATAAAA
1086813 CATATCTATC
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
41 8 0.11
42 36 0.51
43 26 0.37
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (43 bp):
AATAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
Found at i:1089709 original size:20 final size:20
Alignment explanation
Indices: 1089684--1089735 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1089674 AACAAGAAAA
*
1089684 AAATGACAAAACCGGTTTAT
1 AAATGACAAAACCGGTCTAT
1089704 AAATGACAAAACCGGTCTAT
1 AAATGACAAAACCGGTCTAT
1089724 AAATGACAAAAC
1 AAATGACAAAAC
1089736 TGGTAAAGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.19
Consensus pattern (20 bp):
AAATGACAAAACCGGTCTAT
Found at i:1089906 original size:112 final size:110
Alignment explanation
Indices: 1089708--1090001 Score: 473
Period size: 112 Copynumber: 2.6 Consensus size: 110
1089698 GTTTATAAAT
1089708 GACAAAACCGGTCTATAAATGACAAAACTGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATA
1 GACAAAACCGGTCTATAAATGACAAAACTGGTAAAGCGCTACC-GATATATTGAAAGTGTCGATA
1089773 CTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAA
65 CTTTATAAAAATGTATCGATCCATAACAATATAACAGGT--AAAAAAA
*
1089821 GACAAAACCGGTCTATAAATGAC-AAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATA
1 GACAAAACCGGTCTATAAATGACAAAACTGGTAAAGCGCTACC-GATATATTGAAAGTGTCGATA
* *
1089885 CTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAT
65 CTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAA
* * *
1089931 GACGAAACCGGTCTATAAATGACAAAACTGGTAAAGCGCTACCGAATATGTTGATAGTGTCGATA
1 GACAAAACCGGTCTATAAATGACAAAACTGGTAAAGCGCTACCG-ATATATTGAAAGTGTCGATA
*
1089996 TTTTAT
65 CTTTAT
1090002 TATAAGTATC
Statistics
Matches: 170, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
110 29 0.17
111 41 0.24
112 77 0.45
113 23 0.14
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (110 bp):
GACAAAACCGGTCTATAAATGACAAAACTGGTAAAGCGCTACCGATATATTGAAAGTGTCGATAC
TTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAA
Found at i:1090308 original size:178 final size:180
Alignment explanation
Indices: 1089873--1090316 Score: 675
Period size: 181 Copynumber: 2.5 Consensus size: 180
1089863 AGATATATTG
* *
1089873 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAA-ATGACGAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** * ** * * *
1089937 ACCGGTCTATAAATGACAAAACTGGTAAAGCGCTACCGAATATGTTGATAGTGTCGATATTTTAT
66 ACC-GTCTCGAAATGAC-AAACCGGTAAAAAGCAACCGAATATGTTGAAAGTGTCGATACTTTAT
* *
1090002 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
129 TATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGCTAAT
1090054 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATATGACAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAATATGACAA
1090119 AACCGTCTCGAAATGACAAACCGGTAAAAAGCAACC-AGATATGTTGAAAGTGTCGATACTTTAT
65 AACCGTCTCGAAATGACAAACCGGTAAAAAGCAACCGA-ATATGTTGAAAGTGTCGATACTTTAT
1090183 TATAAGTATCGACACTTTT-AAATTT-AAAGAAAAGAAGTTATAGCG-TCAAT
129 TATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGCT-AAT
1090233 AAAGTGTCGATAC-TTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
1090297 ATCGATCTCGAAATGACAAA
66 ACCG-TCTCGAAATGACAAA
1090317 TCGATAGTAA
Statistics
Matches: 245, Mismatches: 13, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
177 17 0.07
178 53 0.22
179 35 0.14
180 6 0.02
181 108 0.44
182 16 0.07
183 10 0.04
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (180 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGTCTCGAAATGACAAACCGGTAAAAAGCAACCGAATATGTTGAAAGTGTCGATACTTTATTA
TAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGCTAAT
Found at i:1094041 original size:68 final size:68
Alignment explanation
Indices: 1093922--1094054 Score: 250
Period size: 68 Copynumber: 2.0 Consensus size: 68
1093912 AGCCTTTTGT
1093922 TGTAGGACCGGGCATCGGCATTCTCGTCCCAAACATCATCGATCAAAGGTTTAAGTCTTTCCGTA
1 TGTAGGACCGGGCATCGGCATTCTCGTCCCAAACATCATCGATCAAAGGTTTAAGTCTTTCCGTA
1093987 TTG
66 TTG
1093990 TGTAGGACCGGGCATCGGCATTCTCGTCCCAAA-ATCATCGATCAAAGGGTTTAAGTCTTTCCGT
1 TGTAGGACCGGGCATCGGCATTCTCGTCCCAAACATCATCGATCAAA-GGTTTAAGTCTTTCCGT
1094054 A
65 A
1094055 ATTAGGACCG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
67 13 0.20
68 51 0.80
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (68 bp):
TGTAGGACCGGGCATCGGCATTCTCGTCCCAAACATCATCGATCAAAGGTTTAAGTCTTTCCGTA
TTG
Found at i:1095028 original size:202 final size:200
Alignment explanation
Indices: 1094668--1095074 Score: 735
Period size: 202 Copynumber: 2.0 Consensus size: 200
1094658 GTGTATTTCC
*
1094668 GGTATCAACAGTGGAATCGCCAAAGATGAGAATAGAGGTGGAATTCGGCACGGTTGCAGCGTGGT
1 GGTATCAACAGTGGAATCGCCAAAGATGAGAATAGAGGTGAAATTCGGCACGGTTGCAGCGTGGT
1094733 CGGAATCTGATGAGGACTATAGTGACTTGGAGCGTATTAGAAAGTGGCGTGTGGTGAGAGCCATT
66 CGGAATCTGATGAGGACTATAGTGACTTGGAGCGTATTAGAAAGTGGCGTGTGGTGAGAGCCATT
1094798 TTGAACCGTGTGTGAGATCATATTACAGACGGATAG-TTTTATAGTAAAATTAAAGGGTGAAACA
131 TTGAACCGTGTGTGAGATCATATTACAGACGGATAGTTTTTATAGTAAAATTAAAGGGTGAAACA
1094862 AGTGT
196 AGTGT
1094867 GGTATCAACAGTGGAATCGCCAAAGATGAGAATAGAGGTGAAATTCGGCACGGTTGCAGCGCTGG
1 GGTATCAACAGTGGAATCGCCAAAGATGAGAATAGAGGTGAAATTCGGCACGGTTGCAGCG-TGG
1094932 TCGGAATACTGATGAGGACTATAGTGACTTGGAGCAGTATTAGAAAGTGGCGTGTGGTGAGAGCC
65 TCGGAAT-CTGATGAGGACTATAGTGACTTGGAGC-GTATTAGAAAGTGGCGTGTGGTGAGAGCC
*
1094997 ATTTTGAACCGTGTGTGAGATGATATTACAGACGGATAGTTATTTTTATAGTAAAATTAAAGGGT
128 ATTTTGAACCGTGTGTGAGATCATATTACAGACGGATAG---TTTTTATAGTAAAATTAAAGGGT
1095062 GAAACAAGTGT
190 GAAACAAGTGT
1095073 GG
1 GG
1095075 AACTAAGCTG
Statistics
Matches: 199, Mismatches: 2, Indels: 7
0.96 0.01 0.03
Matches are distributed among these distances:
199 60 0.30
200 10 0.05
201 27 0.14
202 67 0.34
206 35 0.18
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (200 bp):
GGTATCAACAGTGGAATCGCCAAAGATGAGAATAGAGGTGAAATTCGGCACGGTTGCAGCGTGGT
CGGAATCTGATGAGGACTATAGTGACTTGGAGCGTATTAGAAAGTGGCGTGTGGTGAGAGCCATT
TTGAACCGTGTGTGAGATCATATTACAGACGGATAGTTTTTATAGTAAAATTAAAGGGTGAAACA
AGTGT
Found at i:1098793 original size:3 final size:3
Alignment explanation
Indices: 1098764--1098829 Score: 66
Period size: 3 Copynumber: 22.0 Consensus size: 3
1098754 TAAAAATGAT
*
1098764 TAA TAA -AA TAA TTAA TAA -ACC TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
1098809 T-T TATA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
1098830 AAAAACCCGG
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 4 0.08
3 43 0.81
4 6 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1099079 original size:40 final size:40
Alignment explanation
Indices: 1099019--1099123 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 40
1099009 CGTCTAAAGG
* * * *
1099019 TGACACGGCTCCTACGTGATGAGGAAATCTAGTCAAGGGA
1 TGACACTGCTCATACATGATGAAGAAATCTAGTCAAGGGA
** * *
1099059 TGACACTGCTCATACATGATGAAGAGTTTTGGTCAAGGGA
1 TGACACTGCTCATACATGATGAAGAAATCTAGTCAAGGGA
1099099 TGACACTGCTCATACATGATGAAGA
1 TGACACTGCTCATACATGATGAAGA
1099124 TTCTGGTCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (40 bp):
TGACACTGCTCATACATGATGAAGAAATCTAGTCAAGGGA
Found at i:1099247 original size:40 final size:40
Alignment explanation
Indices: 1099188--1099265 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1099178 TGGTTATCTA
* *
1099188 GGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGG
1 GGATGACACGGCTCATACGTGATGAAGAGGTCTGGTCAGG
* * *
1099228 GGATGGCACTGCTCATACGTGATGAAGAGTTCTGGTCA
1 GGATGACACGGCTCATACGTGATGAAGAGGTCTGGTCA
1099266 TCTTTAGGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (40 bp):
GGATGACACGGCTCATACGTGATGAAGAGGTCTGGTCAGG
Found at i:1099314 original size:133 final size:133
Alignment explanation
Indices: 1099056--1099369 Score: 470
Period size: 132 Copynumber: 2.4 Consensus size: 133
1099046 TCTAGTCAAG
* * * * * * *
1099056 GGATGACACTGCTCATACATGATGAAGAGTTTTGGTCAAGGGATGACACTGCTCATACATGATGA
1 GGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACATGATGA
* *
1099121 AGATTCTGGTCATATTTAGGAGGAGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATC
66 AGATTCTGGTCATATTTAGGAGGAGCGATAACACGATTCCTACGTGATGAGGACGACTGGTTATC
1099186 TA-
131 TAT
* * *
1099188 GGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGGCACTGCTCATACGTGATGA
1 GGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACATGATGA
*
1099253 AGAGTTCTGGTCATCTTTAGGTAGG-GCGATAACACGATTCCTACGTGATGAGGACGACTGGTTA
66 AGA-TTCTGGTCATATTTAGG-AGGAGCGATAACACGATTCCTACGTGATGAGGACGACTGGTTA
1099317 TCTAT
129 TCTAT
*
1099322 GGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACA
1 GGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACA
1099370 TGATTCCTAC
Statistics
Matches: 164, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
132 59 0.36
133 57 0.35
134 48 0.29
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (133 bp):
GGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACATGATGA
AGATTCTGGTCATATTTAGGAGGAGCGATAACACGATTCCTACGTGATGAGGACGACTGGTTATC
TAT
Found at i:1099345 original size:43 final size:43
Alignment explanation
Indices: 1099291--1099440 Score: 186
Period size: 43 Copynumber: 3.6 Consensus size: 43
1099281 ATAACACGAT
1099291 TCCTACGTGATGAGGACGA-CTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTATGGTTGACACGGC
* * * **
1099334 TCCTACGTGATGAGGAGATCTGG---TC-AGGGGATGACATGAT
1 TCCTACGTGATGAGGAGATCTGGTTATCTA-TGGTTGACACGGC
1099374 TCCTACGTGATGAGGACGA-CTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTATGGTTGACACGGC
1099417 TCCTACGTGATGAGGAGATCTGGT
1 TCCTACGTGATGAGGAGATCTGGT
1099441 CAGGGGATGA
Statistics
Matches: 89, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
39 1 0.01
40 30 0.34
41 2 0.02
42 4 0.04
43 51 0.57
44 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (43 bp):
TCCTACGTGATGAGGAGATCTGGTTATCTATGGTTGACACGGC
Found at i:1099380 original size:40 final size:40
Alignment explanation
Indices: 1099334--1099472 Score: 174
Period size: 40 Copynumber: 3.4 Consensus size: 40
1099324 TTGACACGGC
1099334 TCCTACGTGATGAGGAGATCTGGTCAGGGGATGACATGAT
1 TCCTACGTGATGAGGAGATCTGGTCAGGGGATGACATGAT
* * * **
1099374 TCCTACGTGATGAGGACGA-CTGGTTATCTA-TGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGG---TC-AGGGGATGACATGAT
1099417 TCCTACGTGATGAGGAGATCTGGTCAGGGGATGACATGAT
1 TCCTACGTGATGAGGAGATCTGGTCAGGGGATGACATGAT
1099457 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
1099473 CGACTGGCCA
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
39 1 0.01
40 46 0.56
41 2 0.02
42 2 0.02
43 30 0.37
44 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGATCTGGTCAGGGGATGACATGAT
Found at i:1099397 original size:134 final size:133
Alignment explanation
Indices: 1099056--1099386 Score: 452
Period size: 134 Copynumber: 2.5 Consensus size: 133
1099046 TCTAGTCAAG
* * * * * * * *
1099056 GGATGACACTGCTCATACATGATGAAGAGTTTTGGTCAAGGGATGACACTGCTCATACATGATGA
1 GGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGA
* * * *
1099121 AGA-TTCTGGTCATATTTAGGAGGAGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTAT
66 AGAGTACTGGTCATCTTTAGGAGGAGCGATAACACGATTCCTACGTGATGAGGACGACTGGTTAT
1099185 CTA
131 CTA
* *
1099188 GGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGGCACTGCTCATACGTGATGA
1 GGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGA
*
1099253 AGAGTTCTGGTCATCTTTAGGTAGG-GCGATAACACGATTCCTACGTGATGAGGACGACTGGTTA
66 AGAGTACTGGTCATCTTTAGG-AGGAGCGATAACACGATTCCTACGTGATGAGGACGACTGGTTA
1099317 TCTA
130 TCTA
* * *
1099321 TGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACA-TGATTCCTACGTGAT
1 -GGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTG-CTCATACGTGAT
1099385 GA
64 GA
1099387 GGACGACTGG
Statistics
Matches: 178, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
132 59 0.33
133 59 0.33
134 60 0.34
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.27
Consensus pattern (133 bp):
GGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGA
AGAGTACTGGTCATCTTTAGGAGGAGCGATAACACGATTCCTACGTGATGAGGACGACTGGTTAT
CTA
Found at i:1099427 original size:83 final size:83
Alignment explanation
Indices: 1099288--1099479 Score: 384
Period size: 83 Copynumber: 2.3 Consensus size: 83
1099278 GCGATAACAC
1099288 GATTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGAT
1 GATTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGAT
1099353 CTGGTCAGGGGATGACAT
66 CTGGTCAGGGGATGACAT
1099371 GATTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGAT
1 GATTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGAT
1099436 CTGGTCAGGGGATGACAT
66 CTGGTCAGGGGATGACAT
1099454 GATTCCTACGTGATGAGGACGACTGG
1 GATTCCTACGTGATGAGGACGACTGG
1099480 CCATCTCTAG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 109 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (83 bp):
GATTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGAT
CTGGTCAGGGGATGACAT
Found at i:1099631 original size:35 final size:35
Alignment explanation
Indices: 1099591--1099664 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1099581 GACAAAATTC
*
1099591 GTTTCAAGGGAAAC-GATCTCAAAGATATTTGCTTT
1 GTTTCAAGGGAAACAAAT-TCAAAGATATTTGCTTT
1099626 GTTTCAAGGGAAACAAATTCAAAGATATTTGCTTT
1 GTTTCAAGGGAAACAAATTCAAAGATATTTGCTTT
1099661 GTTT
1 GTTT
1099665 TTCAGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
35 35 0.95
36 2 0.05
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (35 bp):
GTTTCAAGGGAAACAAATTCAAAGATATTTGCTTT
Found at i:1099991 original size:62 final size:63
Alignment explanation
Indices: 1099919--1100038 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 63
1099909 AAGGTGGGTA
* * * *
1099919 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAATGATT
1 TTTTCAAAAGAAATTGCCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAATGATT
* * *
1099981 TTTTCAAAAGAAATTGCCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAATCTCAA
1 TTTTCAAAAGAAATTGCCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAA
1100039 AAGTTAGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
62 16 0.32
63 34 0.68
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGCCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAATGATT
Found at i:1100512 original size:52 final size:52
Alignment explanation
Indices: 1100466--1100698 Score: 167
Period size: 52 Copynumber: 4.7 Consensus size: 52
1100456 TCAAATTTTT
1100466 TTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAAGATTC
1 TTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAAGATTC
* * * ***
1100518 TTCACGAAATTGTCTTAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGA--C
1 TTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAA-AGATTC
* * *** *
1100569 -TCA-AATATTTTGT-TCAA-A-AGA-AACAA-----TCTCA-A---AGATTTTTT
1 TTCACAA-A-ATTGTCTCAAGAGAGACAA-AACTTTGTTTCAGACTCA-AAGATTC
*
1100610 TTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTTAAAGATTC
1 TTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAAGATTC
* *
1100662 TTCACGAAATTGTCTTAAGAGAGACAAAACTTTGTTT
1 TTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTT
1100699 TAAAAGATTC
Statistics
Matches: 137, Mismatches: 22, Indels: 44
0.67 0.11 0.22
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 4 0.03
42 9 0.07
43 7 0.05
44 5 0.04
45 2 0.01
47 2 0.01
48 5 0.04
49 6 0.04
50 8 0.06
51 5 0.04
52 78 0.57
53 4 0.03
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.32
Consensus pattern (52 bp):
TTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAAGATTC
Found at i:1100549 original size:144 final size:145
Alignment explanation
Indices: 1100243--1100705 Score: 785
Period size: 144 Copynumber: 3.2 Consensus size: 145
1100233 AAAGAAAATA
* * *
1100243 TCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGA-TTTTTGTTTCAAAAGAAA
1 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAGATTTTTTGTTTCAAAAGAAA
** *
1100307 TTATCTTAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTC-AAGA
66 CAATCTCAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAAGA
1100371 TTCTTCACGAAATTG
131 TTCTTCACGAAATTG
1100386 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAGATTTTTTGTTTCAAAAGAAA
1 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAGATTTTTTGTTTCAAAAGAAA
1100451 CAATCTCAA-ATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAAGA
66 CAATCTCAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAAGA
1100515 TTCTTCACGAAATTG
131 TTCTTCACGAAATTG
*
1100530 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTC-AA-ATATTTTG-TTCAAAAGAAA
1 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAGATTTTTTGTTTCAAAAGAAA
*
1100592 CAATCTCAAAGATTTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTTAAA
66 CAATCTC-AAGA-TTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAA
1100657 GATTCTTCACGAAATTG
129 GATTCTTCACGAAATTG
*
1100674 TCTTAAGAGAGACAAAACTTTGTTTTAAAAGA
1 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGA
1100706 TTCAAAGATT
Statistics
Matches: 306, Mismatches: 9, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
141 18 0.06
142 9 0.03
143 96 0.31
144 183 0.60
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (145 bp):
TCTTAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAGATTTTTTGTTTCAAAAGAAA
CAATCTCAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAAGA
TTCTTCACGAAATTG
Found at i:1100599 original size:28 final size:29
Alignment explanation
Indices: 1100548--1100613 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
1100538 GAGACAAAAC
* *
1100548 TTTGTTTCAAAAGAAATAGACTCAAATAT
1 TTTGTTTCAAAAGAAACAGACTCAAAGAT
1100577 TTTG-TTCAAAAGAAACA-ATCTCAAAGAT
1 TTTGTTTCAAAAGAAACAGA-CTCAAAGAT
*
1100605 TTTTTTTCA
1 TTTGTTTCA
1100614 CAAAATTGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 23 0.72
29 8 0.25
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:1100756 original size:144 final size:140
Alignment explanation
Indices: 1100243--1100757 Score: 584
Period size: 144 Copynumber: 3.6 Consensus size: 140
1100233 AAAGAAAATA
* *
1100243 TCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGA--T-TTTTGTTTCAAAAGA
1 TCTTAAGAGAGACAAAACTTTGTTT-C----AAA-AGATTCAAAGATTTATTTTGTTT-AAAAGA
** * *
1100305 AATTATCT-TAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGAC-TCA
59 AACAATCTCAAAG-TTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTTAA
1100368 AGATTCTTCACGAAATTG
123 AGATTCTTCACGAAATTG
1100386 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAGA-TT-TTTTGTTTCAAAAGA
1 TCTTAAGAGAGACAAAACTTTGTTTCAAAAG--AT----TCAAAGATTTATTTTGTTT-AAAAGA
*
1100449 AACAATCTCAAA-TTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTCAAA
59 AACAATCTCAAAGTTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTTAAA
1100513 GATTCTTCACGAAATTG
124 GATTCTTCACGAAATTG
* *
1100530 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGA---AATAGACTCAAATATTTTGTTCAAAAGAAA
1 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGATTCAA-AGA-T---TTATTTTGTTTAAAAGAAA
1100592 CAATCTCAAAGATTTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTTAAA
61 CAATCTCAAAG--TTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTTAAA
1100657 GATTCTTCACGAAATTG
124 GATTCTTCACGAAATTG
* ** *
1100674 TCTTAAGAGAGACAAAACTTTGTTTTAAAAGATTCAAAGATTGTCGATTTTGTTTATATGGAAAT
1 TCTTAAGAGAGACAAAACTTTGTTTCAAAAGATTCAAAGATT-T--ATTTTGTTTA-AAAGAAAC
* *
1100739 AATCTCAAAGGTGTTTTCA
62 AATCTCAAAGTTTTTTTCA
1100758 AAAGTGTTTA
Statistics
Matches: 328, Mismatches: 18, Indels: 51
0.83 0.05 0.13
Matches are distributed among these distances:
135 2 0.01
136 3 0.01
137 2 0.01
138 3 0.01
139 1 0.00
141 19 0.06
142 9 0.03
143 79 0.24
144 178 0.54
145 12 0.04
146 18 0.05
147 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (140 bp):
TCTTAAGAGAGACAAAACTTTGTTTCAAAAGATTCAAAGATTTATTTTGTTTAAAAGAAACAATC
TCAAAGTTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGACTTAAAGATTCTT
CACGAAATTG
Found at i:1101023 original size:35 final size:35
Alignment explanation
Indices: 1100969--1101041 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
1100959 AAAATTTGTT
* *
1100969 TTTTTAGAGAAATTGTCTCAAGCGAGA-CAAGTTTG
1 TTTTTAGAGAAAATGTCTC-AGCGAGATCAACTTTG
*
1101004 TTTTT-GAGAAAATGATCTCAGTGAGATCAACTTTG
1 TTTTTAGAGAAAATG-TCTCAGCGAGATCAACTTTG
1101039 TTT
1 TTT
1101042 AATGTGAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 14 0.42
35 19 0.58
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (35 bp):
TTTTTAGAGAAAATGTCTCAGCGAGATCAACTTTG
Found at i:1101160 original size:105 final size:105
Alignment explanation
Indices: 1101024--1101213 Score: 276
Period size: 105 Copynumber: 1.8 Consensus size: 105
1101014 AATGATCTCA
* *
1101024 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAA-TTTGGATCTCCAAGGGAAAAGGTCTC
1 GTGAGATCAACTTTGTTTAATGTGAAACAAATTC-AAATTTTGGATCTCAAAGGAAAAAGGTCTC
1101088 AAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAG
65 AAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAG
* * * * *
1101129 GTGAGATTAATTTTGTTTTAA-GTGAATCAAATTCAAATTTTGTATCTCAAAGGAAAAATGTCTC
1 GTGAGATCAACTTTG-TTTAATGTGAAACAAATTCAAATTTTGGATCTCAAAGGAAAAAGGTCTC
*
1101193 AAGCGAGACGCAATTTGTTTT
65 AAGCGAGACGAAATTTGTTTT
1101214 AAAATTCTCA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
104 3 0.04
105 67 0.89
106 5 0.07
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (105 bp):
GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAATTTTGGATCTCAAAGGAAAAAGGTCTCA
AGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAG
Found at i:1104957 original size:31 final size:32
Alignment explanation
Indices: 1104901--1104962 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1104891 TGATAAAATG
1104901 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1104933 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
1104963 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:1106719 original size:2 final size:2
Alignment explanation
Indices: 1106714--1106798 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
1106704 GCATAAATGA
*
1106714 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1106756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1106798 A
1 A
1106799 CATGCATATG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1108859 original size:13 final size:13
Alignment explanation
Indices: 1108841--1108926 Score: 63
Period size: 12 Copynumber: 6.7 Consensus size: 13
1108831 AATTGGCCTG
*
1108841 TAAAAATGATTAA
1 TAAAAATAATTAA
1108854 TAAAAATAATTAA
1 TAAAAATAATTAA
1108867 TAAACCTAATAA-TAA
1 TAAA---AATAATTAA
*
1108882 TAATAATAA-TAA
1 TAAAAATAATTAA
* *
1108894 TAATAA-AATTTA
1 TAAAAATAATTAA
*
1108906 TATAAATAA-TAA
1 TAAAAATAATTAA
*
1108918 TAATAATAA
1 TAAAAATAA
1108927 AAAAGACCCG
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
11 2 0.03
12 29 0.48
13 18 0.30
15 6 0.10
16 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (13 bp):
TAAAAATAATTAA
Found at i:1108881 original size:3 final size:3
Alignment explanation
Indices: 1108851--1108926 Score: 68
Period size: 3 Copynumber: 25.0 Consensus size: 3
1108841 TAAAAATGAT
* *
1108851 TAA TAA AAA TAA TTAA TAA -ACC TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
1108897 TAA -AA T-T TATA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A T-AA TAA TAA TAA TAA TAA
1108927 AAAAGACCCG
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
2 4 0.07
3 48 0.80
4 7 0.12
5 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1111562 original size:24 final size:24
Alignment explanation
Indices: 1111535--1111592 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1111525 TCAATATTGG
* *
1111535 TATCCATACTTGCATCAATACTAC
1 TATCAATACTTGCATCAATACTAA
* *
1111559 TATCAATACCTGCATCTATACTAA
1 TATCAATACTTGCATCAATACTAA
1111583 TATCAATACT
1 TATCAATACT
1111593 GTCCAATACC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (24 bp):
TATCAATACTTGCATCAATACTAA
Found at i:1114869 original size:35 final size:35
Alignment explanation
Indices: 1114823--1114895 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
1114813 AATAAAATCG
1114823 AATAAATTTTAGTTTATATACATATATCTTACTGT
1 AATAAATTTTAGTTTATATACATATATCTTACTGT
*
1114858 AATAAATTTTAGTTTATATACATATATCTTATTGT
1 AATAAATTTTAGTTTATATACATATATCTTACTGT
1114893 AAT
1 AAT
1114896 GAATAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.49
Consensus pattern (35 bp):
AATAAATTTTAGTTTATATACATATATCTTACTGT
Found at i:1119836 original size:36 final size:36
Alignment explanation
Indices: 1119747--1119847 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
1119737 CCTTTTCATC
*
1119747 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCT-AAAATAGAATAGAATT
* ** *
1119784 TTGTTAGGATTCAAACTCCTAAAATAGAATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAATAGAATAGAATT
* * *
1119820 CTACTATGATTTAAACTCTTAAAGATAG
1 CTACTAGGATTCAAACTCCTAAA-ATAG
1119848 GATCCACAAG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
36 31 0.60
37 21 0.40
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGAATAGAATT
Found at i:1120228 original size:14 final size:13
Alignment explanation
Indices: 1120209--1120247 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1120199 TATATGGATA
1120209 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
1120223 TTTTATTATTTAT
1 TTTTATTATTTAT
1120236 GTTATTATTATT
1 -TT-TTATTATT
1120248 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:1120246 original size:18 final size:17
Alignment explanation
Indices: 1120207--1120249 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1120197 ATTATATGGA
1120207 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
1120223 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
1120241 TATTATTAT
1 TATTATTAT
1120250 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1120498 original size:25 final size:25
Alignment explanation
Indices: 1120448--1120498 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1120438 ATCTTATAAC
* *
1120448 TTTATATATATTATTATTTTCGTTT
1 TTTATATATATTATTATATTAGTTT
1120473 TTTAT-TATTATTATTATATTA-TTT
1 TTTATATA-TATTATTATATTAGTTT
1120497 TT
1 TT
1120499 AAAAAATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTATATATATTATTATATTAGTTT
Found at i:1120650 original size:2 final size:2
Alignment explanation
Indices: 1120645--1120681 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1120635 TACTTTGATG
1120645 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 T
1120682 TTTCCTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1120776 original size:31 final size:29
Alignment explanation
Indices: 1120723--1120787 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
1120713 ATTACTTTAC
*
1120723 TATTTTTTTTTCCTTTATCTTATTT-ATT
1 TATTTTTTTTTCCTTTACCTTATTTGATT
*
1120751 TATTTTATTTTTCCCTTTTACCTTATTTGTTT
1 TATTTT-TTTTT-CC-TTTACCTTATTTGATT
1120783 TATTT
1 TATTT
1120788 ACCTTGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 6 0.19
29 5 0.16
30 2 0.06
31 11 0.35
32 7 0.23
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (29 bp):
TATTTTTTTTTCCTTTACCTTATTTGATT
Found at i:1123223 original size:8 final size:8
Alignment explanation
Indices: 1123210--1123248 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1123200 GAACATTTCA
*
1123210 TGCATTCT
1 TGCATTTT
1123218 TGCA-TTT
1 TGCATTTT
1123225 TGCATTTT
1 TGCATTTT
*
1123233 TGCCTTTT
1 TGCATTTT
1123241 TGCATTTT
1 TGCATTTT
1123249 CATCTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:1124405 original size:9 final size:8
Alignment explanation
Indices: 1124362--1124433 Score: 67
Period size: 8 Copynumber: 9.0 Consensus size: 8
1124352 AATCAAGAAC
1124362 AAAAAAGA
1 AAAAAAGA
*
1124370 AAAGAAGCA
1 AAAAAAG-A
1124379 AAAAAAGCA
1 AAAAAAG-A
1124388 AAAAAA-A
1 AAAAAAGA
*
1124395 AACAAAGA
1 AAAAAAGA
*
1124403 AAAAGAG-
1 AAAAAAGA
*
1124410 AAACAAGA
1 AAAAAAGA
*
1124418 ACAAAAGA
1 AAAAAAGA
1124426 AAAAAAGA
1 AAAAAAGA
1124434 GCAAAAATCA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
7 11 0.22
8 25 0.49
9 15 0.29
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1124405 original size:22 final size:23
Alignment explanation
Indices: 1124380--1124463 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 23
1124370 AAAGAAGCAA
1124380 AAAAAGCA-AAAAAAAAAC-AAAG
1 AAAAAG-AGAAAAAAAAACAAAAG
* *
1124402 AAAAAGAGAAACAAGAACAAAAG
1 AAAAAGAGAAAAAAAAACAAAAG
* ** *
1124425 AAAAAAAGAGCAAAAATCAAAAAG
1 AAAAAGAGAAAAAAAAAC-AAAAG
* *
1124449 AAAAAGGGACAAAAA
1 AAAAAGAGAAAAAAA
1124464 GCACATGCAA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.02
22 14 0.30
23 16 0.34
24 16 0.34
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.01
Consensus pattern (23 bp):
AAAAAGAGAAAAAAAAACAAAAG
Found at i:1125109 original size:22 final size:22
Alignment explanation
Indices: 1125084--1125154 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
1125074 CCATCAATCT
*
1125084 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
1125106 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
*
1125128 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGTCAAACC
1125150 TTTGA
1 TTTGA
1125155 CCAAACACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:1125598 original size:18 final size:19
Alignment explanation
Indices: 1125569--1125605 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1125559 TCAACATCAA
*
1125569 ATATTGGGGCATTTTTTGG
1 ATATTGGGGCATTATTTGG
1125588 ATATT-GGGCATTATTTGG
1 ATATTGGGGCATTATTTGG
1125606 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.19, C:0.05, G:0.30, T:0.46
Consensus pattern (19 bp):
ATATTGGGGCATTATTTGG
Found at i:1126073 original size:36 final size:36
Alignment explanation
Indices: 1126033--1126154 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 36
1126023 ACTCATGATT
* * *
1126033 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
* * * * *
1126069 GTTT-TCACTAGAA-GAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAGATTTGTCTCCCTTGAGACA
* *
1126104 GTTTCCCTTGAAACAA-ATTTTGTCTCCCTTGAGACA
1 GTTTCTCTTAAAACAAGA-TTTGTCTCCCTTGAGACA
*
1126140 GTTTCTCTTGAAACA
1 GTTTCTCTTAAAACA
1126155 TAAACATTGA
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
35 27 0.40
36 41 0.60
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
Found at i:1126237 original size:37 final size:36
Alignment explanation
Indices: 1126170--1126294 Score: 162
Period size: 36 Copynumber: 3.4 Consensus size: 36
1126160 ATTGAAAACA
* * *
1126170 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
1126206 TTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
* *
1126243 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAG
1126279 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
1126295 ATCTTTGAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
35 4 0.05
36 42 0.54
37 32 0.41
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1126332 original size:138 final size:138
Alignment explanation
Indices: 1126083--1126357 Score: 374
Period size: 138 Copynumber: 2.0 Consensus size: 138
1126073 TCACTAGAAG
* * *
1126083 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 AGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTACCTTGAGACAGTTTCCCT
* * * * * *
1126148 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCTCT
66 TGAAACATAAACATTGAAAACATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAGTTACTCT
1126213 TGAAACAA
131 TGAAACAA
* *
1126221 AGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCC
1 AGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTACCTTGAGACAGTTTCCC
* *** *
1126285 TTGAAACA-AAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACT
65 TTGAAACATAAA-CATTGAAAACATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAGTTACT
1126349 CTTGAAACA
129 CTTGAAACA
1126358 CAAAATCTTC
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
137 9 0.08
138 110 0.92
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (138 bp):
AGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTACCTTGAGACAGTTTCCCT
TGAAACATAAACATTGAAAACATTTCCCCTAAAACAAATTTCGTCTCCCTTGAGACAGTTACTCT
TGAAACAA
Found at i:1126356 original size:65 final size:65
Alignment explanation
Indices: 1126252--1126426 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 65
1126242 GTTTCTCTTG
** * **
1126252 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCT
1126316 A
65 A
* *
1126317 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
1126382 TA
64 TA
* * *
1126384 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1126427 CAGATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 25 0.26
66 12 0.13
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:1126386 original size:67 final size:67
Alignment explanation
Indices: 1126105--1126425 Score: 242
Period size: 65 Copynumber: 4.7 Consensus size: 67
1126095 CTTGAGACAG
* * *
1126105 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-TAAA-CATTGAAA-
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATC-TTCAAAT
**
1126167 ACA
65 TTA
* * * * * ** * ***
1126170 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAGTTTTGTCTCCC
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCT-TC-AAA
*
1126234 TTGAGACA
64 TT----TA
* * ** * **
1126242 GTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAA
1 -TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAA
1126304 TTTA
64 TTTA
* *
1126308 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1126373 TA
66 TA
* * *
1126375 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1126426 ACAGATATCT
Statistics
Matches: 200, Mismatches: 41, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
65 79 0.40
66 10 0.05
67 29 0.14
68 32 0.16
70 2 0.01
71 2 0.01
72 13 0.06
73 33 0.17
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:1127507 original size:100 final size:104
Alignment explanation
Indices: 1127030--1127721 Score: 988
Period size: 105 Copynumber: 6.6 Consensus size: 104
1127020 GCCATCCGCG
* * * * * * *
1127030 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGGCAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
1127095 GGGACGGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTTC-CAA-TTCAGAGCCA
*
1127139 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
1127204 ACCGCTGGTTGTCAATAAATAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAACTTT-CCAA-TTCAGAGCCA
*
1127246 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1127311 ACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGTCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAAT-TCAGAGCCA
1127351 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1127416 ACCTCTGCTTGTCAACAA-AA-TTT-C-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATTCAGAGCCA
* *
1127451 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1127516 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAAT-TCAGAGCCA
1127556 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1127621 ACCGCTGCTTGTCAACAA-AA-TTT-C-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATTCAGAGCCA
* ** * * *
1127656 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATTCAGGCTCAACTTCACGAAGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1127721 A
66 A
1127722 ATCATGCACA
Statistics
Matches: 541, Mismatches: 33, Indels: 27
0.90 0.05 0.04
Matches are distributed among these distances:
100 157 0.29
101 6 0.01
102 5 0.01
103 7 0.01
104 7 0.01
105 182 0.34
106 57 0.11
107 97 0.18
108 1 0.00
109 22 0.04
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTTCCAATTCAGAGCCA
Found at i:1127530 original size:205 final size:205
Alignment explanation
Indices: 1127074--1127721 Score: 1082
Period size: 205 Copynumber: 3.1 Consensus size: 205
1127064 CGAGGCAACA
* * *
1127074 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTTC-CAATCTCAGAGCC
*
1127138 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGG
64 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
1127203 GACCGCTGGTTGTCAATAAATAATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
129 GACCGCTGCTTGTCAA-CAA-AA-TTT--C-A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGA
*
1127268 TATTGGACTCCAGACAACG
187 TATTGGACTCCAGACAATG
*
1127287 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGTCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAA
1127352 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
*
1127417 CCTCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
131 CCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
1127482 CCAGACAATG
196 CCAGACAATG
*
1127492 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAA
1127557 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
1127622 CCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
131 CCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
1127687 CCAGACAATT
196 CCAGACAATG
* * *
1127697 CAGGCTCAACTTCACGAAGAAGGGA
1 CAAGTTCAACTTCACGACGAAGGGA
1127722 ATCATGCACA
Statistics
Matches: 418, Mismatches: 16, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
205 273 0.65
206 1 0.00
207 1 0.00
209 3 0.01
210 2 0.00
211 2 0.00
212 95 0.23
213 41 0.10
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (205 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCAA
TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
CCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
CCAGACAATG
Found at i:1128431 original size:36 final size:36
Alignment explanation
Indices: 1128342--1128442 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
1128332 CCTTTTCGTC
*
1128342 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCT-AAAATAGAATAGAATT
* ** *
1128379 TTGTTAGGATTCAAACTCCTAAAATAGAATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAATAGAATAGAATT
* * *
1128415 CTACTATGATTTAAACTCTTAAAGATAG
1 CTACTAGGATTCAAACTCCTAAA-ATAG
1128443 GATCCACAAG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
36 31 0.60
37 21 0.40
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGAATAGAATT
Found at i:1128823 original size:14 final size:13
Alignment explanation
Indices: 1128804--1128842 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1128794 TATATGGATA
1128804 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
1128818 TTTTATTATTTAT
1 TTTTATTATTTAT
1128831 GTTATTATTATT
1 -TT-TTATTATT
1128843 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:1128841 original size:18 final size:17
Alignment explanation
Indices: 1128802--1128844 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1128792 ATTATATGGA
1128802 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
1128818 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
1128836 TATTATTAT
1 TATTATTAT
1128845 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1128855 original size:2 final size:2
Alignment explanation
Indices: 1128842--1128903 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
1128832 TTATTATTAT
*
1128842 TA TA TG 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 TA TA
1128884 TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1128904 TTCTTTAATA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1129046 original size:3 final size:3
Alignment explanation
Indices: 1129038--1129095 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
1129028 TCTAATTTTA
*
1129038 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATGT -TT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT
1129084 ATT ATT ATT ATT
1 ATT ATT ATT ATT
1129096 TTTGCAGGCC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 1 0.02
3 45 0.90
4 4 0.08
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1130849 original size:19 final size:19
Alignment explanation
Indices: 1130808--1130850 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1130798 ATTCCTTTTG
* **
1130808 TATGTACTTATTTTTATGT
1 TATGTACTTATTTATATCA
*
1130827 TATGTATTTATTTATATCA
1 TATGTACTTATTTATATCA
1130846 TATGT
1 TATGT
1130851 GAATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (19 bp):
TATGTACTTATTTATATCA
Found at i:1136864 original size:4 final size:4
Alignment explanation
Indices: 1136855--1136898 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1136845 AGAAAAGTAT
*
1136855 ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATCC ATA- ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1136899 ACATTTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 3 0.09
4 30 0.86
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:1136874 original size:14 final size:14
Alignment explanation
Indices: 1136855--1136881 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1136845 AGAAAAGTAT
1136855 ATACATACATACAC
1 ATACATACATACAC
1136869 ATACATACATACA
1 ATACATACATACA
1136882 TACATCCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (14 bp):
ATACATACATACAC
Found at i:1136878 original size:18 final size:18
Alignment explanation
Indices: 1136855--1136898 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1136845 AGAAAAGTAT
1136855 ATACATACATACA-CATA
1 ATACATACATACACCATA
1136872 CATACATACATACATCCATA
1 -ATACATACATACA-CCATA
1136892 ATACATA
1 ATACATA
1136899 ACATTTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.54
19 7 0.29
20 4 0.17
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (18 bp):
ATACATACATACACCATA
Found at i:1137319 original size:36 final size:35
Alignment explanation
Indices: 1137236--1137365 Score: 115
Period size: 36 Copynumber: 3.7 Consensus size: 35
1137226 AAATAATAAT
* *
1137236 AACAAAGTTGATCTCACTTGAGATC-GTTTCTC-AAA
1 AACAAATTTG-TCTCACTTGAGA-CAATTTCTCTAAA
*
1137271 AACAAACTTTGTCTCGCTTGAGACAATTTCTCTAAA
1 AACAAA-TTTGTCTCACTTGAGACAATTTCTCTAAA
* * *
1137307 AACAAATGTTGTCTCATTTGAGACTATATCT-T-AA
1 AACAAAT-TTGTCTCACTTGAGACAATTTCTCTAAA
* *
1137341 AGCAAATTTCGTCTCGCTTGAGACA
1 AACAAATTT-GTCTCACTTGAGACA
1137366 TCATTTTCTC
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
33 2 0.03
34 21 0.27
35 25 0.32
36 31 0.39
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (35 bp):
AACAAATTTGTCTCACTTGAGACAATTTCTCTAAA
Found at i:1137657 original size:28 final size:27
Alignment explanation
Indices: 1137617--1137711 Score: 113
Period size: 28 Copynumber: 3.5 Consensus size: 27
1137607 TTCTCTTGAA
1137617 AAAATCTTTGAGTTAGTTCCTTTTAAAT
1 AAAATCTTTGAGTT-GTTCCTTTTAAAT
* *
1137645 AAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAATCTTTGAG-TTGTTCCTTTTAAAT
* *
1137673 AAATATCTTTGAGTTGTTTCTTTT-GA-
1 AAA-ATCTTTGAGTTGTTCCTTTTAAAT
1137699 AAAATCTTTGAGT
1 AAAATCTTTGAGT
1137712 CTATTTATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.17
26 3 0.05
27 1 0.02
28 36 0.60
29 10 0.17
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.47
Consensus pattern (27 bp):
AAAATCTTTGAGTTGTTCCTTTTAAAT
Found at i:1137723 original size:54 final size:55
Alignment explanation
Indices: 1137612--1137726 Score: 128
Period size: 54 Copynumber: 2.1 Consensus size: 55
1137602 ACAGTTTCTC
* * *
1137612 TTGAAAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTCTATTCATT
* * * *
1137667 TTGAATAAATATCTTTGAGTT-GTTTCTTTT-GA-AAAATCTTTGAGTCTATTTATT
1 TTGAA-AAA-ATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTCTATTCATT
1137721 TTGAAA
1 TTGAAA
1137727 CAAAGTTTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
53 1 0.02
54 22 0.43
55 6 0.12
56 11 0.22
57 11 0.22
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.48
Consensus pattern (55 bp):
TTGAAAAAATCTTTGAGTTAGTTCCTTTTAAATAAAATCTTGGAGTCTATTCATT
Found at i:1137868 original size:28 final size:29
Alignment explanation
Indices: 1137814--1137882 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
1137804 CAATTTTGTG
1137814 AAAAAATCTTTGAGATTGTTTCTTTTGGA
1 AAAAAATCTTTGAGATTGTTTCTTTTGGA
*
1137843 AAAAAATCTTTGAGTTTGTTTC-TTTGGA
1 AAAAAATCTTTGAGATTGTTTCTTTTGGA
1137871 AACAAAAT-TTTG
1 AA-AAAATCTTTG
1137883 TCTCTCTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 12 0.32
29 26 0.68
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.43
Consensus pattern (29 bp):
AAAAAATCTTTGAGATTGTTTCTTTTGGA
Found at i:1137911 original size:37 final size:37
Alignment explanation
Indices: 1137861--1137981 Score: 121
Period size: 37 Copynumber: 3.5 Consensus size: 37
1137851 TTTGAGTTTG
1137861 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* * * * **
1137898 TTTCTTTTGAAACAAAA------ATCT-TTGAGTTTG
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1137928 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* *
1137965 TTTCTTTTGAAAAAAAA
1 TTTCTTTGGAAACAAAA
1137982 AAATCTTTGA
Statistics
Matches: 63, Mismatches: 14, Indels: 14
0.69 0.15 0.15
Matches are distributed among these distances:
30 21 0.33
31 3 0.05
36 3 0.05
37 36 0.57
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:1137915 original size:67 final size:66
Alignment explanation
Indices: 1137832--1137981 Score: 282
Period size: 67 Copynumber: 2.3 Consensus size: 66
1137822 TTTGAGATTG
*
1137832 TTTCTTTTGGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 TTTCTTTTGAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1137897 A
66 A
1137898 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1137963 AA
65 AA
1137965 TTTCTTTTGAAAAAAAA
1 TTTCTTTTGAAAAAAAA
1137982 AAATCTTTGA
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
66 16 0.20
67 66 0.80
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.45
Consensus pattern (66 bp):
TTTCTTTTGAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
A
Found at i:1137915 original size:69 final size:69
Alignment explanation
Indices: 1137842--1138001 Score: 279
Period size: 67 Copynumber: 2.3 Consensus size: 69
1137832 TTTCTTTTGG
1137842 AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG
1137907 --AA
66 AAAA
*
1137909 ACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG
1137974 AAAA
66 AAAA
* *
1137978 AAAAAAATCTTTGAATCTGTTTCT
1 AAAAAAATCTTTGAGTTTGTTTCT
1138002 CTTAAAATGA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
67 64 0.74
69 23 0.26
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (69 bp):
AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG
AAAA
Found at i:1138182 original size:63 final size:62
Alignment explanation
Indices: 1138104--1138226 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 62
1138094 AACAAAATCC
* * *
1138104 ATCTTTGAGTCTGTTTCTTTTAAAACAAAATTTTATCTCTTAACGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTTATCTCTCAA-GACAACTTCTTTTGAAAAA
* * *
1138167 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAA
1 ATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAA
1138227 CCACCCACAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 16 0.30
63 38 0.70
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (62 bp):
ATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAAAA
Found at i:1138304 original size:252 final size:251
Alignment explanation
Indices: 1137816--1138307 Score: 579
Period size: 252 Copynumber: 1.9 Consensus size: 251
1137806 ATTTTGTGAA
* * *
1137816 AAAATCTTTGAGATTGTTTCTTTTGGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTT
1 AAAATCTTTGAGATTGTTTCTCTT-GAAAAAAATCTTTGAGTCTGTTTCTTTGAAAACAAAATTT
* * *
1137881 TGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAAT
65 TGTATCTCTTAAGACAATTTCTTTTG-AACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAAT
* * * **
1137946 TTTGTCTCTCTTAAGATAATTTCTTTTGAAAAAAAAAAATCTTTGAATCTGTTTCTCTTAAAATG
129 TTTGTCTCTC-TAAGACAACTTCTTTTGAAAAAAAAAAATCTTTGAATCTGTTTCTATTAAAACA
* * * *
1138011 AATTTTGTGTCTCTTGAGACAGTTTCTCTTGAAGTAAATCTTTGAATATGTTCATTTTG
193 AATTTTGTGTCCCTTAAGACAGTTTCTCTTAAAATAAATCTTTGAATATGTTCATTTTG
* *
1138070 AAAATCTTTGAGTTTGTTTCTCTT-AACAAAATCCATCTTTGAGTCTGTTTCTTTTAAAACAAAA
1 AAAATCTTTGAGATTGTTTCTCTTGAA-AAAA---ATCTTTGAGTCTGTTTCTTTGAAAACAAAA
1138134 -TTT-TATCTCTTAACGACAATTTCTTTTG-A-AAAAATCTTTGAGTCTGTTTCTTTGGAAACAA
62 TTTTGTATCTCTTAA-GACAATTTCTTTTGAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAA
* * *** *
1138195 AATTTTGTCTCTC-GAGACAACTTCTTTTGAAACCACCCACAT-TTT-AGATC-GTTTCTATTAA
126 AATTTTGTCTCTCTAAGACAACTTCTTTTGAAA-AAAAAAAATCTTTGA-ATCTGTTTCTATTAA
* *
1138256 AACAAATTTTGTTTCCCTTAAGGCAGTTTCTCTATAAATATAAAATCTTTGA
189 AACAAATTTTGTGTCCCTTAAGACAGTTTCTCT-TAAA-AT-AAATCTTTGA
1138308 GTTTGTTTCT
Statistics
Matches: 203, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
249 38 0.19
250 25 0.12
251 5 0.02
252 56 0.28
253 5 0.02
254 31 0.15
255 16 0.08
256 27 0.13
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (251 bp):
AAAATCTTTGAGATTGTTTCTCTTGAAAAAAATCTTTGAGTCTGTTTCTTTGAAAACAAAATTTT
GTATCTCTTAAGACAATTTCTTTTGAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTT
TGTCTCTCTAAGACAACTTCTTTTGAAAAAAAAAAATCTTTGAATCTGTTTCTATTAAAACAAAT
TTTGTGTCCCTTAAGACAGTTTCTCTTAAAATAAATCTTTGAATATGTTCATTTTG
Found at i:1138447 original size:36 final size:36
Alignment explanation
Indices: 1138374--1138448 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
1138364 AACAAACATC
*
1138374 TTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCA
1 TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
* *
1138410 TTTGAGA-CAGTTTTCCTTTAAAC-AATCTTTGAGTCA
1 TTTGAGATCA-TTTCCCTTTAAACGAAT-TTTGACTCA
1138446 TTT
1 TTT
1138449 CCTTTGAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (36 bp):
TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
Found at i:1138465 original size:63 final size:63
Alignment explanation
Indices: 1138367--1138486 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
1138357 GAAACAAAAC
*
1138367 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTT-GAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTAGAGACAGTTTTCCTTT
*
1138429 AAACAATCTTTGAG-TCATTT-CCTTTGAAACAAAATTTTGTCTCTTTTAAGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCCTTT-AAAC-AAATTTTGTCTCATTT-AGAGACAGTT
1138487 GCTTTTGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
61 5 0.10
62 14 0.27
63 23 0.45
65 9 0.18
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (63 bp):
AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTAGAGACAGTTTTCCTTT
Found at i:1138634 original size:46 final size:45
Alignment explanation
Indices: 1138566--1138982 Score: 269
Period size: 46 Copynumber: 9.7 Consensus size: 45
1138556 ACCATAACTT
* * * *
1138566 TTAGATGGCCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC
*
1138611 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT-ACC
1 -TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
** *
1138656 -CCGA---CCAGATCTCTTCATCACGTATGAGCCGTG---TCACC
1 TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
* ** * * * *
1138694 CTAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC
*
1138739 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT-ACC
1 -TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
** *
1138784 -CCGA---CCAGATCTCTTCATCACGTATGAGCCGTG---TCACC
1 TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
* ** * * * *
1138822 CTAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 TTAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC
*
1138867 TTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC
1 -TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTA-TCACC
* * * *
1138913 --CGA---CCAGATCTCTTCATCACGTAGGAGCCGTGTCA--ACC
1 TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
* **
1138951 ATAGATAACCA-AACTCTTCATCACGTATGAGC
1 TTAGATGGCCAGAACTCTTCATCACGTATGAGC
1138983 AGTGGCGTCC
Statistics
Matches: 296, Mismatches: 45, Indels: 64
0.73 0.11 0.16
Matches are distributed among these distances:
37 2 0.01
38 8 0.03
39 4 0.01
40 88 0.30
41 2 0.01
42 65 0.22
43 9 0.03
45 16 0.05
46 97 0.33
47 5 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (45 bp):
TTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
Found at i:1138675 original size:40 final size:40
Alignment explanation
Indices: 1138620--1138982 Score: 247
Period size: 40 Copynumber: 8.6 Consensus size: 40
1138610 CTTTAGATGG
*
1138620 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCCGA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCAGA
*
1138660 CCAGATCTCTTCATCACGTATGAGCCGTGTC--ACCCTAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCC-AG---A
* * * * * *
1138702 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCAT-ACC--CAGA
*
1138745 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCCGA
1 ---CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCAGA
*
1138788 CCAGATCTCTTCATCACGTATGAGCCGTGTC--ACCCTAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCC-AG---A
* * * * * *
1138830 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTCAT-ACC--CAGA
* *
1138873 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 ---CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCAGA
* * *
1138916 CCAGATCTCTTCATCACGTAGGAGCCGTGTCA-ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATACC-CAG---A
1138959 CCA-AACTCTTCATCACGTATGAGC
1 CCAGAACTCTTCATCACGTATGAGC
1138983 AGTGGCGTCC
Statistics
Matches: 253, Mismatches: 38, Indels: 62
0.72 0.11 0.18
Matches are distributed among these distances:
38 8 0.03
39 4 0.02
40 91 0.36
41 2 0.01
42 69 0.27
43 10 0.04
45 11 0.04
46 56 0.22
47 2 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTCATACCCAGA
Found at i:1138977 original size:128 final size:128
Alignment explanation
Indices: 1138574--1138961 Score: 740
Period size: 128 Copynumber: 3.0 Consensus size: 128
1138564 TTTTAGATGG
1138574 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1138639 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
66 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
1138702 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1138767 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
66 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
1138830 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
* * *
1138895 ATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
66 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACCCTAGATAA
1138959 CCA
1 CCA
1138962 AACTCTTCAT
Statistics
Matches: 256, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
128 243 0.95
129 13 0.05
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (128 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
Found at i:1139162 original size:3 final size:3
Alignment explanation
Indices: 1139154--1139211 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
1139144 TCTAATTTTA
*
1139154 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATGT -TT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT
1139200 ATT ATT ATT ATT
1 ATT ATT ATT ATT
1139212 TTTGCAGGCC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 1 0.02
3 45 0.90
4 4 0.08
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1140939 original size:19 final size:19
Alignment explanation
Indices: 1140898--1140940 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1140888 ATTCCTTTTG
* **
1140898 TATGTACTTATTTTTATGT
1 TATGTACTTATTTATATCA
*
1140917 TATGTATTTATTTATATCA
1 TATGTACTTATTTATATCA
1140936 TATGT
1 TATGT
1140941 GAATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (19 bp):
TATGTACTTATTTATATCA
Found at i:1141984 original size:26 final size:26
Alignment explanation
Indices: 1141856--1141985 Score: 66
Period size: 26 Copynumber: 4.8 Consensus size: 26
1141846 TTTATATACC
* * * *
1141856 TATTATTAATATATATATATTCTTAAT
1 TATTATTATTATAT-TATTTTTTTATT
*
1141883 TATTTTTATT-TGATTATTTTTTTATT
1 TATTATTATTAT-ATTATTTTTTTATT
* * * * * *
1141909 TACGTAATA-TATCTTATAACTTTATATA
1 TA-TTATTATTATATTAT--TTTTTTATT
* **
1141937 TATATATTATTATTTTCGTTTTTTATT
1 TAT-TATTATTATATTATTTTTTTATT
1141964 TATTATTATTATATTATTTTTT
1 TATTATTATTATATTATTTTTT
1141986 AAAAAATCTT
Statistics
Matches: 73, Mismatches: 23, Indels: 15
0.66 0.21 0.14
Matches are distributed among these distances:
26 33 0.45
27 23 0.32
28 12 0.16
29 5 0.07
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (26 bp):
TATTATTATTATATTATTTTTTTATT
Found at i:1142142 original size:2 final size:2
Alignment explanation
Indices: 1142137--1142183 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1142127 TACTTTGATG
1142137 TA TA 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 TA TA
1142179 TA TA T
1 TA TA T
1142184 TTCCTTTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1142257 original size:9 final size:9
Alignment explanation
Indices: 1142236--1142269 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1142226 TTTTTTTTCC
1142236 TTTATCTTA-
1 TTTAT-TTAT
1142245 TTTATTTAT
1 TTTATTTAT
1142254 TTTATTTAT
1 TTTATTTAT
1142263 TTTATTT
1 TTTATTT
1142270 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:1142258 original size:13 final size:14
Alignment explanation
Indices: 1142236--1142270 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1142226 TTTTTTTTCC
*
1142236 TTTATCTTATTTA-
1 TTTATTTTATTTAT
1142249 TTTATTTTATTTAT
1 TTTATTTTATTTAT
1142263 TTTATTTT
1 TTTATTTT
1142271 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Done.