Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004507.1 Hibiscus syriacus cultivar Beakdansim tig00009942_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: 1776135
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1088613 original size:7 final size:7
Alignment explanation
Indices: 1088601--1088646 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
1088591 TTAACTAAAA
1088601 TTTTATT
1 TTTTATT
1088608 TTTTATT
1 TTTTATT
1088615 TTTTATT
1 TTTTATT
1088622 TTTTA--
1 TTTTATT
1088627 TTTTATT
1 TTTTATT
1088634 TTTTATT
1 TTTTATT
1088641 TATTTA
1 T-TTTA
1088647 GATGATGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
7 27 0.75
8 4 0.11
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTATT
Found at i:1088622 original size:19 final size:19
Alignment explanation
Indices: 1088600--1088645 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1088590 TTTAACTAAA
1088600 ATTTTATTTTTTATTTTTT
1 ATTTTATTTTTTATTTTTT
1088619 ATTTT-TTATTTTATTTTTT
1 ATTTTATT-TTTTATTTTTT
1088638 A-TTTATTT
1 ATTTTATTT
1088646 AGATGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (19 bp):
ATTTTATTTTTTATTTTTT
Found at i:1089540 original size:20 final size:21
Alignment explanation
Indices: 1089512--1089561 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
1089502 ACAATTATTT
*
1089512 ATATGTATTAAACTA-TTTTTA
1 ATAT-TATTAAAATATTTTTTA
1089533 ATATTATTAAAATATTTTTTTA
1 ATATTATTAAAATA-TTTTTTA
1089555 ATATTAT
1 ATATTAT
1089562 ATTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.35
21 4 0.15
22 13 0.50
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATTATTAAAATATTTTTTA
Found at i:1090294 original size:17 final size:18
Alignment explanation
Indices: 1090272--1090313 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
1090262 TCTTAATCTC
*
1090272 TTATTTTTATGA-CTTAA
1 TTATTTTTAGGACCTTAA
*
1090289 TTATTTTTAGGACCTTAT
1 TTATTTTTAGGACCTTAA
1090307 TTATTTT
1 TTATTTT
1090314 AAATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (18 bp):
TTATTTTTAGGACCTTAA
Found at i:1094522 original size:143 final size:142
Alignment explanation
Indices: 1094249--1094516 Score: 409
Period size: 143 Copynumber: 1.9 Consensus size: 142
1094239 GTCGTATTTC
*
1094249 ACGATTGTGGATATAACAAAATGTTATTACGGTTACCTCGATCTTGTAATAGCAATTTCATACGA
1 ACGATTGTGGATATAACAAAATGTTATTACGGTTACCTCGATCTTGTAATAGCAATTTCAGACGA
** * * *
1094314 CGGTATCATCACTATATACCAGTCATTATTCTGATAACAGACCGCTATTTAAATCTATGGTAAAC
66 CACTATCATCACTATATA-CAATCATTATTATGATAACAGACCGCTATTTAAATCTATGATAAAC
1094379 AAAATGTATTATT
130 AAAATGTATTATT
* * *
1094392 ACGATTGTGGATATAACAAAATGTTATTATGGTTACCTCGATCTT-TAATAGCAATTTCAGATGG
1 ACGATTGTGGATATAACAAAATGTTATTACGGTTACCTCGATCTTGTAATAGCAATTTCAGACGA
*
1094456 CACTATCTTCA-TATA-A-AATCATTATTATGATAACAGACCGCTATTTAAATCTATGATAAAC
66 CACTATCATCACTATATACAATCATTATTATGATAACAGACCGCTATTTAAATCTATGATAAAC
1094517 GAAACAGAGA
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
138 42 0.37
140 1 0.01
141 4 0.03
142 24 0.21
143 44 0.38
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (142 bp):
ACGATTGTGGATATAACAAAATGTTATTACGGTTACCTCGATCTTGTAATAGCAATTTCAGACGA
CACTATCATCACTATATACAATCATTATTATGATAACAGACCGCTATTTAAATCTATGATAAACA
AAATGTATTATT
Found at i:1098574 original size:3 final size:3
Alignment explanation
Indices: 1098566--1098616 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
1098556 TTCGAACATC
*
1098566 TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1098614 TTA
1 TTA
1098617 ACCTAAACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1099261 original size:117 final size:119
Alignment explanation
Indices: 1099118--1099342 Score: 289
Period size: 117 Copynumber: 1.9 Consensus size: 119
1099108 TAAGTTTTGG
* * ** *
1099118 GGAAAAATGAAAGTTTATGTATTAAAACGAAAC-AAATTTGATAGTTTATG-TACTAAACACGTT
1 GGAAAAA-GAAAGTTTATATACTAAAACG-AACTAAAACTGATAGCTTA-GATACTAAACACGTT
*
1099181 AAGTTTTTAA-C-GACGGTACTAAAATGAAACAAAAACTAAACTGTATGTATAATTTT
63 AAGATTTTAACCGGA-GGTACTAAAATGAAACAAAAACTAAACTGTATGTATAATTTT
* *
1099237 GGAAAAA-AAAGTTTATATACTAAAACGGACTAAAACTGATAGCTTAGATACTAAACGCGTTAAG
1 GGAAAAAGAAAGTTTATATACTAAAACGAACTAAAACTGATAGCTTAGATACTAAACACGTTAAG
1099301 ATTTTAACCGTGGAGGTACTAAAATGAAACAAAAACTAAACT
66 ATTTTAACC--GGAGGTACTAAAATGAAACAAAAACTAAACT
1099343 TTAGGCATAA
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
116 3 0.03
117 51 0.55
118 1 0.01
119 7 0.08
120 28 0.30
121 2 0.02
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (119 bp):
GGAAAAAGAAAGTTTATATACTAAAACGAACTAAAACTGATAGCTTAGATACTAAACACGTTAAG
ATTTTAACCGGAGGTACTAAAATGAAACAAAAACTAAACTGTATGTATAATTTT
Found at i:1101363 original size:23 final size:23
Alignment explanation
Indices: 1101333--1101377 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1101323 GAACACAAAC
*
1101333 AAACGAACATAATAAATGAACAT
1 AAACGAACACAATAAATGAACAT
1101356 AAACGAACACAATAAATGAACA
1 AAACGAACACAATAAATGAACA
1101378 ACCAAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.16, G:0.09, T:0.13
Consensus pattern (23 bp):
AAACGAACACAATAAATGAACAT
Found at i:1109682 original size:24 final size:24
Alignment explanation
Indices: 1109651--1109698 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1109641 CAGATGAGAG
1109651 AAAAAAGAGGATTTTTAGGTCTTA
1 AAAAAAGAGGATTTTTAGGTCTTA
1109675 AAAAAAGAGGATTTTTAGGTCTTA
1 AAAAAAGAGGATTTTTAGGTCTTA
1109699 GAACCCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (24 bp):
AAAAAAGAGGATTTTTAGGTCTTA
Found at i:1115302 original size:22 final size:20
Alignment explanation
Indices: 1115257--1115302 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
1115247 TCTTTTAAAA
1115257 ATTT-TAAATTATTATATAT
1 ATTTATAAATTATTATATAT
*
1115276 -CTTATAAATTATTTATATATT
1 ATTTATAAATTA-TTATATA-T
1115297 ATTTAT
1 ATTTAT
1115303 TTATAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 2 0.10
19 7 0.33
20 7 0.33
21 1 0.05
22 4 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTATAAATTATTATATAT
Found at i:1124287 original size:199 final size:199
Alignment explanation
Indices: 1123758--1124435 Score: 852
Period size: 198 Copynumber: 3.4 Consensus size: 199
1123748 TTTTCTAAAA
* * * * **
1123758 GTATCGACCCCAAAAACATCGAAACCTATAATTATAATGTAATATGTAATTTTACAATGAAACCG
1 GTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTATAATGTTACCG
* * * ** *
1123823 GTATAAATATACCGGTTTTATGATAGAATATATCAACATAATGTATCGACAAAAATTTTAAA--A
66 GTATAAATATACCGGTTTTATGAGAGAATATGTCAACATAATGTATC-A-ACACTTTTTAAATTT
* * * * * * * ** *
1123886 ATATCGATACATTTTGTACAGAATGAATG-TCAAACGAGGTGCACGCATAAAGTGTATATATATT
129 GTGTCTATAC-TTTTTTCCAAAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATT
1123950 TATTAAA--
193 TA--AAATT
* * * *
1123957 ATATCGATCCCAAAAATATTGAAA-CTGATAATTACAATGTAATAGGTAAATTTATAATG-TACC
1 GTATCGATCCCAAAAACATCGAAACCT-ATAATTATAATGTAATAGGTAAATTTATAATGTTACC
* * * *
1124020 TGTAGAAATATACCGATTTTATGAGAGAATATGTCAACATAATGTATCGACACTTTTTAAATTTG
65 GGTATAAATATACCGGTTTTATGAGAGAATATGTCAACATAATGTATCAACACTTTTTAAATTTG
1124085 TGTCTATACTTTTTTCCAAAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTA
130 TGTCTATACTTTTTTCCAAAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTA
1124150 AAATT
195 AAATT
* * * *
1124155 GTATCGATCCCAAAAACATCGAAACCAATAATTATAATATAATAGATAAATTTATAATGTTACTG
1 GTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTATAATGTTACCG
*
1124220 GTATAAATATACCAGTTTTATGAGAGAATATGTCAACATAATGTATCAACACTTTTTAAATTTGT
66 GTATAAATATACCGGTTTTATGAGAGAATATGTCAACATAATGTATCAACACTTTTTAAATTTGT
* * **
1124285 GTCGT-TATTTTTTTCCAAAATGAATGCCC-AACGAGATGCAAACATAAAGTGTCGATACATTTA
131 GTC-TATACTTTTTTCCAAAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTA
1124348 AAATT
195 AAATT
* * *
1124353 GTATCGATCCAAAAAATATCAAAACCTATAATTATAATGTAATAGGTAAATTTATAATGTTACCG
1 GTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTATAATGTTACCG
1124418 GTATAAATATACCGGTTT
66 GTATAAATATACCGGTTT
1124436 AGTTAGAAAA
Statistics
Matches: 416, Mismatches: 54, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
196 12 0.03
197 15 0.04
198 249 0.60
199 139 0.33
200 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (199 bp):
GTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTATAATGTTACCG
GTATAAATATACCGGTTTTATGAGAGAATATGTCAACATAATGTATCAACACTTTTTAAATTTGT
GTCTATACTTTTTTCCAAAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTAA
AATT
Found at i:1124566 original size:25 final size:26
Alignment explanation
Indices: 1124535--1124594 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
1124525 AATGCCTATT
* *
1124535 TTATTATATAAACACTACTTATTATA
1 TTATTATATAAACACTACATAATATA
* *
1124561 -TATTATATAAGCGCTACATAATATA
1 TTATTATATAAACACTACATAATATA
1124586 TTATTATAT
1 TTATTATAT
1124595 TTAATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 21 0.72
26 8 0.28
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (26 bp):
TTATTATATAAACACTACATAATATA
Found at i:1128907 original size:193 final size:193
Alignment explanation
Indices: 1128578--1128963 Score: 736
Period size: 193 Copynumber: 2.0 Consensus size: 193
1128568 GTCGGGGTCG
1128578 TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
1 TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
* * *
1128643 CGGGATATTATAATGATAATGGTCCATCAGGACCATTTCCTGGATAGGGTCGTGGTAAATCTATG
66 CGGGATATTATAATGATAATAGTCCATCAGGACCATTTCCTGGACAGGGTCGTGGTAAATATATG
1128708 CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
131 CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
1128771 TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
1 TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
*
1128836 CGGGATATTATACTGATAATAGTCCATCAGGACCATTTCCTGGACAGGGTCGTGGTAAATATATG
66 CGGGATATTATAATGATAATAGTCCATCAGGACCATTTCCTGGACAGGGTCGTGGTAAATATATG
1128901 CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
131 CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
1128964 AAAAACAAAT
Statistics
Matches: 189, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 189 1.00
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (193 bp):
TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
CGGGATATTATAATGATAATAGTCCATCAGGACCATTTCCTGGACAGGGTCGTGGTAAATATATG
CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
Found at i:1129894 original size:80 final size:80
Alignment explanation
Indices: 1129761--1129916 Score: 276
Period size: 80 Copynumber: 1.9 Consensus size: 80
1129751 CGCTTATATA
* * *
1129761 ATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAACGGGAAATATTATCAAGTACAATAA
1 ATGTAATAGATAACGCTTATATAATAAAATAGGTATTTAACAGAAAATATTATCAAGTACAATAA
1129826 CATATTAGGTAACGC
66 CATATTAGGTAACGC
*
1129841 ATGTAATAGATAACGCTTATATAATAAAATATGTATTTAACAGAAAATATTATCAAGTACAATAA
1 ATGTAATAGATAACGCTTATATAATAAAATAGGTATTTAACAGAAAATATTATCAAGTACAATAA
1129906 CATATTAGGTA
66 CATATTAGGTA
1129917 GCGTTTATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.31
Consensus pattern (80 bp):
ATGTAATAGATAACGCTTATATAATAAAATAGGTATTTAACAGAAAATATTATCAAGTACAATAA
CATATTAGGTAACGC
Found at i:1130544 original size:260 final size:250
Alignment explanation
Indices: 1130062--1130579 Score: 778
Period size: 260 Copynumber: 2.0 Consensus size: 250
1130052 CTTTTTATAA
*
1130062 AAGTATCGACACTTTATGCTTGCACCTCGTTAGGCATTAATATTTCATTCTGGACAAAAATATCG
1 AAGTATCGACACTTCATGCTTGCACCTCGTTAGGCATTAATATTTCATTCTGGACAAAAATATCG
1130127 ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTATCATAAAACCGGTATAATTAT
66 ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTATCATAAAACCGGTATAATTAT
* *
1130192 ACCGGTTTCATTGATCATTTACCTATTACATTATACTTATGGGTTTTGATGTTTTAGGGATCAAT
131 ACCGGTTTCATTG----------TA-TACATTATACTTATGGGTTTCGATATTTTAGGGATCAAT
*
1130257 ATTTTTTTAATAAATGTATCGACACTTTTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCG
185 ACTTTTTTAATAAATGTATCGACACTTTTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCG
1130322 T
250 T
**
1130323 AAGTATCGACACTTCATGCTTGCACCTCGTT-GGTTTTAATATTTCATTCTGGACAAAAATATCG
1 AAGTATCGACACTTCATGCTTGCACCTCGTTAGGCATTAATATTTCATTCTGGACAAAAATATCG
* * *
1130387 ACATAAACTAAAAAAGTG-CTGATACATGATTTAGACCTATTCTCTCATAAAACCGGTATAATTA
66 ACACAAACTAAAAAAGTGTC-GATACATGATTTAGACATATTCTATCATAAAACCGGTATAATTA
*
1130451 TACCGGTTTCATTG-A-ACATTATACTTATGGGTTTCGATATTTTAGGGATCGATACTTTTTTAA
130 TACCGGTTTCATTGTATACATTATACTTATGGGTTTCGATATTTTAGGGATCAATACTTTTTTAA
* *
1130514 TAAATGTATCGACAC--TTTAAGGGTACACTTTTTTTTGCATTCATTCTAGACCGT
195 TAAATGTATCGACACTTTTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCGT
1130568 AAGTATCGACAC
1 AAGTATCGACAC
1130580 AACTTTAACA
Statistics
Matches: 244, Mismatches: 12, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
245 49 0.20
247 59 0.24
249 1 0.00
259 1 0.00
260 104 0.43
261 30 0.12
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (250 bp):
AAGTATCGACACTTCATGCTTGCACCTCGTTAGGCATTAATATTTCATTCTGGACAAAAATATCG
ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTATCATAAAACCGGTATAATTAT
ACCGGTTTCATTGTATACATTATACTTATGGGTTTCGATATTTTAGGGATCAATACTTTTTTAAT
AAATGTATCGACACTTTTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCGT
Found at i:1135080 original size:200 final size:200
Alignment explanation
Indices: 1134737--1135368 Score: 1025
Period size: 200 Copynumber: 3.2 Consensus size: 200
1134727 CGATGTTTAT
* ** *
1134737 TGGATCGACACTTTATGGTTACACCCTGTTTGCCATTCATTCTTAACCAAAAATATCGTCACAAA
1 TGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTCGACCAAAAATATCGACACAAA
* * ** * * *
1134802 CTACAAAAATGTCGACACATTATTTAGACACATTCTCTTATAAAACCGATATACTTGTACCGGTT
66 CTACAAAAGTGTCGAAACATTATTTAGACTTATTCTCTCATAAAATCGGTATACTTGTACCGGTT
1134867 AGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTACGGGATCGACACTTTTT
131 AGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTACGGGATCGACACTTTTT
1134932 ATATA
196 ATATA
*
1134937 TGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTCGACCAAAAATATCGACACAAA
1 TGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTCGACCAAAAATATCGACACAAA
1135002 CTACAAAAGTGTCGAAACATTATTTAGACTTATTCTCTCATAAAATCGGTATACTTGTACCGGTT
66 CTACAAAAGTGTCGAAACATTATTTAGACTTATTCTCTCATAAAATCGGTATACTTGTACCGGTT
1135067 AGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATC-GGATCGACACTTTT
131 AGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTA-CGGGATCGACACTTTT
1135131 TATATA
195 TATATA
* * * * *
1135137 TGGATCGACACTTTATTGTTGTACCCTGTTTGCCATTCATTCTGGACCAAAAATATCAATACAAA
1 TGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTCGACCAAAAATATCGACACAAA
* *
1135202 CTACAAAAGTGTCGATACATTATTTAGA-TATATTCTCTCATAAAATCGGTATACTTGTACCGAT
66 CTACAAAAGTGTCGAAACATTATTTAGACT-TATTCTCTCATAAAATCGGTATACTTGTACCGGT
* * * *
1135266 TAGATTGAAAAATTATCTATTACATTATACTTTTGAGTTTCGATGTTTATGGGATCGACACTTTT
130 TAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTACGGGATCGACACTTTT
1135331 TATATA
195 TATATA
1135337 TGGATCGACACTTTATGGTTGCACCCTGTTTG
1 TGGATCGACACTTTATGGTTGCACCCTGTTTG
1135369 TCATATTGTA
Statistics
Matches: 405, Mismatches: 24, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
199 1 0.00
200 403 1.00
201 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (200 bp):
TGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTCGACCAAAAATATCGACACAAA
CTACAAAAGTGTCGAAACATTATTTAGACTTATTCTCTCATAAAATCGGTATACTTGTACCGGTT
AGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTACGGGATCGACACTTTTT
ATATA
Found at i:1135630 original size:19 final size:19
Alignment explanation
Indices: 1135606--1135655 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1135596 TTATATTCAC
*
1135606 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
*
1135625 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
1135644 ATACAAAATTAA
1 ATACAAAATTAA
1135656 CCATACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:1137545 original size:21 final size:21
Alignment explanation
Indices: 1137520--1137582 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1137510 CCCCTTATGC
* *
1137520 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1137541 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1137562 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1137583 ATTGATTGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1140548 original size:21 final size:21
Alignment explanation
Indices: 1140524--1140586 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1140514 GACAATCAAT
*
1140524 AGTCGAAGAGAAACTTGATAG
1 AGTCGAAGAGAAACTTGAGAG
1140545 AGTCGAAGAGAAACTTGAGAG
1 AGTCGAAGAGAAACTTGAGAG
* * *
1140566 AGTTGAAGATACACTTGAGAG
1 AGTCGAAGAGAAACTTGAGAG
1140587 GCATAAGGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.41, C:0.10, G:0.30, T:0.19
Consensus pattern (21 bp):
AGTCGAAGAGAAACTTGAGAG
Found at i:1142491 original size:19 final size:19
Alignment explanation
Indices: 1142467--1142515 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1142457 AATGTAGGGT
1142467 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1142486 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1142505 TAATTTTGTAT
1 TAATTTTGTAT
1142516 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1144536 original size:183 final size:182
Alignment explanation
Indices: 1144196--1144597 Score: 617
Period size: 183 Copynumber: 2.2 Consensus size: 182
1144186 CAAAGTTTTC
* * * *
1144196 ACACTTTTTAATATTGTGTCGATACTTTATGTCCATAATAGAAGAAAAATGTGTTAATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCAATACCTTGT
* *
1144261 CAAATAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATA
66 CAAAAAGTGTCGATT--AAAAACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
*
1144326 TAATCGGTATAAATATACCGATTTTATGAGCGAATAAATCTACAACCTATATCG
129 TAACCGGTATAAATATACCGATTTTATGAGCGAATAAATCTACAACCTATATCG
* *
1144380 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCAATACCTTGT
* * *
1144445 CAAAAAGTGTCGACATT-TACACATTGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
66 CAAAAAGTGTCG--ATTAAAAACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
* **
1144509 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
129 TAACCGGTATAAATATACCGATTTTATGAGCGAATAAATCTACAACCTATATCG
*
1144563 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCA
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
1144598 TAATTATAAT
Statistics
Matches: 200, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
183 127 0.63
184 70 0.35
186 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (182 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCAATACCTTGT
CAAAAAGTGTCGATTAAAAACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
ACCGGTATAAATATACCGATTTTATGAGCGAATAAATCTACAACCTATATCG
Found at i:1144692 original size:120 final size:120
Alignment explanation
Indices: 1144479--1144717 Score: 424
Period size: 120 Copynumber: 2.0 Consensus size: 120
1144469 TGGAACCCAG
*
1144479 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
*
1144544 AGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAT
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAT
* * *
1144599 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
*
1144664 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
1144718 GAATGGAAGA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 113 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAT
Found at i:1144875 original size:302 final size:303
Alignment explanation
Indices: 1144292--1145188 Score: 1616
Period size: 302 Copynumber: 3.0 Consensus size: 303
1144282 ACATCGGAAC
* * * *
1144292 CCATAATTATAATGTAATAGATAATTTTGTAATATAATCGGTATAAATATACCGATTTTATGAGC
1 CCATAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGC
** *
1144357 GAATAAATCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
*
1144422 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAA
131 AGAAAAATGTGTAGATACCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAA
1144487 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
1144552 AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
261 AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
1144595 CCATAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGC
1 CCATAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGC
1144660 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
* * *
1144725 AGAAAAATG-GTTGATATCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCATAATTATAA
131 AGAAAAATGTGTAGATACCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAA
*
1144789 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
*
1144854 AACCTATATCGACACTTTTTAATTTTATGTCGGTACTTTATGT
261 AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
* *
1144897 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGT
1 CCATAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGC
1144962 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
* *
1145027 AGAAAAATGTGTAGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTTTAA
131 AGAAAAATGTGTAGATACCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAA
*
1145092 TGTAATAGATAATTTTGTAATATAACTGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
*
1145157 AACCTATATCGACACTTTTTAATATTGTGTCG
261 AACCTATATCGACACTTTTTAATTTTGTGTCG
1145189 CTAATTTTAA
Statistics
Matches: 570, Mismatches: 23, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
302 295 0.52
303 275 0.48
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (303 bp):
CCATAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGC
GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
AGAAAAATGTGTAGATACCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAA
TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
Found at i:1144994 original size:120 final size:120
Alignment explanation
Indices: 1144781--1145023 Score: 423
Period size: 120 Copynumber: 2.0 Consensus size: 120
1144771 TGGAACCCAT
1144781 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
*
1144846 AGGTCTACAACCTATATCGACACTTTTTAATTTTATGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACACTTTTTAATATTATGTCGGTACTTTATGTCCAG
* * * *
1144901 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGTGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
* *
1144966 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACACTTTTTAATATTATGTCGGTACTTTATGTCCAG
1145021 AAT
1 AAT
1145024 GGAAGAAAAA
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTATGTCGGTACTTTATGTCCAG
Found at i:1147870 original size:87 final size:87
Alignment explanation
Indices: 1147766--1148015 Score: 446
Period size: 87 Copynumber: 2.9 Consensus size: 87
1147756 AAATAGGTCA
* *
1147766 ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTATTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
*
1147831 CTCATTAAATACCTATTTTATT
66 CCCATTAAATACCTATTTTATT
1147853 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
*
1147918 CCCGTTAAATACCTATTTTATT
66 CCCATTAAATACCTATTTTATT
1147940 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
**
1148005 CCGGTTAAATA
66 CCCATTAAATA
1148016 ATATAACATA
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 158 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
CCCATTAAATACCTATTTTATT
Found at i:1147900 original size:23 final size:23
Alignment explanation
Indices: 1147850--1147894 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1147840 TACCTATTTT
* *
1147850 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
1147873 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1147895 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1147987 original size:23 final size:23
Alignment explanation
Indices: 1147937--1147981 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1147927 TACCTATTTT
* *
1147937 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
1147960 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1147982 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1154984 original size:30 final size:29
Alignment explanation
Indices: 1154934--1154999 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
1154924 TAATGAATTC
1154934 TTTTTTATAATGATCCTTTTTTGTTTTTA
1 TTTTTTATAATGATCCTTTTTTGTTTTTA
1154963 TTTTTTATAATGATCCTTTTTTGTTTTTA
1 TTTTTTATAATGATCCTTTTTTGTTTTTA
1154992 TTTTTTAT
1 TTTTTTAT
1155000 TTTATATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (29 bp):
TTTTTTATAATGATCCTTTTTTGTTTTTA
Found at i:1155685 original size:2 final size:2
Alignment explanation
Indices: 1155680--1155706 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1155670 TATAATTTTA
1155680 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1155707 ATGTCATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1155814 original size:19 final size:20
Alignment explanation
Indices: 1155767--1155815 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1155757 AATGTAATTG
*
1155767 TAGTATTTTTTTAATATAAA
1 TAGTATATTTTTAATATAAA
* *
1155787 TAGTCTATTTTTAGTATAAA
1 TAGTATATTTTTAATATAAA
1155807 TA-TATATTT
1 TAGTATATTT
1155816 AATTTTTCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (20 bp):
TAGTATATTTTTAATATAAA
Found at i:1156100 original size:28 final size:28
Alignment explanation
Indices: 1156012--1156104 Score: 93
Period size: 27 Copynumber: 3.4 Consensus size: 28
1156002 ATTACATCAT
**
1156012 TTAAAAAAATAGATA-CTAATTGGACCA
1 TTAAAAAAATAGATACCTAATTATACCA
* * *
1156039 TTAAAAAGATATG-TGCCTAATTATACTA
1 TTAAAAAAATA-GATACCTAATTATACCA
* *
1156067 TTAAAAAATTA-ATACCTAATTTTACCA
1 TTAAAAAAATAGATACCTAATTATACCA
1156094 TTAAAAAAATA
1 TTAAAAAAATA
1156105 AATTATACTA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
27 33 0.63
28 19 0.37
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (28 bp):
TTAAAAAAATAGATACCTAATTATACCA
Found at i:1157060 original size:31 final size:31
Alignment explanation
Indices: 1157025--1157135 Score: 177
Period size: 31 Copynumber: 3.6 Consensus size: 31
1157015 TTTAACGTCC
* *
1157025 AAGTGACCAAAACTTAATAAAACGATAACTT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
* *
1157056 AAGTGACCACAACTTAATAAAACAATGACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
*
1157087 AAGTGACCAAAATTTAATAAAACAATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
1157118 AAGTGACCAAAACTTAAT
1 AAGTGACCAAAACTTAAT
1157136 CAAAGTATAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:1157679 original size:21 final size:21
Alignment explanation
Indices: 1157637--1157680 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1157627 AATTCTTAAA
* *
1157637 TATTTTAATTAAAATAATATT
1 TATTTAAATAAAAATAATATT
1157658 TATTTAAATAAAACATAA-ATT
1 TATTTAAATAAAA-ATAATATT
1157679 TA
1 TA
1157681 ATAGATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTAAATAAAAATAATATT
Found at i:1160927 original size:23 final size:22
Alignment explanation
Indices: 1160895--1160952 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
1160885 ATTACAAGCC
* *
1160895 CAAAAAAAAATTGGGCCCCTTTA
1 CAAAATAAAATCGGG-CCCTTTA
1160918 CAAAATAAAACTCGGGCCCTTTA
1 CAAAATAAAA-TCGGGCCCTTTA
1160941 CAAAATAAAATC
1 CAAAATAAAATC
1160953 CATATCCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 2 0.06
23 26 0.81
24 4 0.12
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.21
Consensus pattern (22 bp):
CAAAATAAAATCGGGCCCTTTA
Found at i:1173341 original size:13 final size:14
Alignment explanation
Indices: 1173320--1173367 Score: 89
Period size: 14 Copynumber: 3.5 Consensus size: 14
1173310 TGGGGAGTAA
1173320 TTTCAAAAATTGAT
1 TTTCAAAAATTGAT
1173334 TTTCAAAAATTGAT
1 TTTCAAAAATTGAT
1173348 TTTCAAAAATTGA-
1 TTTCAAAAATTGAT
1173361 TTTCAAA
1 TTTCAAA
1173368 TGATTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 7 0.21
14 27 0.79
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (14 bp):
TTTCAAAAATTGAT
Found at i:1176486 original size:29 final size:29
Alignment explanation
Indices: 1176444--1176503 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1176434 CAATTAAACA
*
1176444 ACCGAATAATTGTCAAGATGGGTGAATTG
1 ACCGAATAATTGTCAAGAGGGGTGAATTG
1176473 ACCGAATAATTGTCAAGAGGGGTGAATTG
1 ACCGAATAATTGTCAAGAGGGGTGAATTG
1176502 AC
1 AC
1176504 TTTTTGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (29 bp):
ACCGAATAATTGTCAAGAGGGGTGAATTG
Found at i:1176526 original size:7 final size:7
Alignment explanation
Indices: 1176514--1176543 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1176504 TTTTTGAGAT
1176514 TAAGGAG
1 TAAGGAG
1176521 TAAGGAG
1 TAAGGAG
*
1176528 TAAGAAG
1 TAAGGAG
1176535 TAAGGAG
1 TAAGGAG
1176542 TA
1 TA
1176544 TAAATATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.37, T:0.17
Consensus pattern (7 bp):
TAAGGAG
Found at i:1180703 original size:21 final size:23
Alignment explanation
Indices: 1180668--1180709 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
1180658 AAAAGGACGA
1180668 GTAATAAATATATGTCTTGAAGC
1 GTAATAAATATATGTCTTGAAGC
1180691 GTAA-AAA-ATATGTCTTGAA
1 GTAATAAATATATGTCTTGAA
1180710 TCAAACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (23 bp):
GTAATAAATATATGTCTTGAAGC
Found at i:1184928 original size:2 final size:2
Alignment explanation
Indices: 1184921--1184992 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
1184911 GGTTACTGCC
1184921 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
1184963 TA T- 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 T
1184993 TTTTGTCAGT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1185619 original size:15 final size:15
Alignment explanation
Indices: 1185601--1185634 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1185591 CCCCTCTCTC
1185601 CCTTCCCCCCTTCCT
1 CCTTCCCCCCTTCCT
1185616 CCTT-CCCCCTTCCT
1 CCTTCCCCCCTTCCT
1185630 -CTTCC
1 CCTTCC
1185635 ATGGTCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 11 0.61
15 4 0.22
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (15 bp):
CCTTCCCCCCTTCCT
Found at i:1187580 original size:20 final size:21
Alignment explanation
Indices: 1187547--1187585 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1187537 TCGACTCATA
*
1187547 TTAACATATCTAAATATATCT
1 TTAACATATATAAATATATCT
1187568 TTAA-ATATATAAATATAT
1 TTAACATATATAAATATAT
1187586 TTAAAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAACATATATAAATATATCT
Found at i:1187593 original size:20 final size:20
Alignment explanation
Indices: 1187547--1187591 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1187537 TCGACTCATA
* *
1187547 TTAACATATCTAAATATATC
1 TTAAAATATATAAATATATC
*
1187567 TTTAAATATATAAATATAT-
1 TTAAAATATATAAATATATC
1187586 TTAAAA
1 TTAAAA
1187592 ATGGATTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAATATATAAATATATC
Found at i:1190385 original size:20 final size:20
Alignment explanation
Indices: 1190360--1190452 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1190350 TTTTCCCTAT
1190360 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1190380 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1190400 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1190421 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1190442 TCGCAATGCGA
1 TCGCAATGCGA
1190453 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1190406 original size:21 final size:20
Alignment explanation
Indices: 1190360--1190452 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1190350 TTTTCCCTAT
*
1190360 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1190380 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1190400 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1190421 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1190442 TCGCAATGCGA
1 TCGCAATGCGA
1190453 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1190406 original size:41 final size:41
Alignment explanation
Indices: 1190358--1190452 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
1190348 GATTTTCCCT
1190358 ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1 ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1190399 ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1 ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
*
1190440 AATCGCAATGCGA
1 ATTCGCAATGCGA
1190453 TACTGACTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
ATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
Found at i:1190465 original size:41 final size:41
Alignment explanation
Indices: 1190379--1190513 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1190369 GAATAAGTAA
* * *
1190379 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1190420 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1190461 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1190502 TTCGCAACGCGA
1 ATCGCAACGCGA
1190514 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1190466 original size:20 final size:20
Alignment explanation
Indices: 1190441--1190535 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1190431 AATTGGGAAA
*
1190441 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1190461 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1190482 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1190502 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1190522 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1190536 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1190748 original size:22 final size:22
Alignment explanation
Indices: 1190720--1190763 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1190710 CACTCTCTCA
1190720 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1190742 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1190764 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1192396 original size:18 final size:18
Alignment explanation
Indices: 1192375--1192419 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1192365 TCCACTTCGG
*
1192375 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1192393 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1192411 GAGCCATCA
1 GAGCCATCA
1192420 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1192946 original size:19 final size:20
Alignment explanation
Indices: 1192892--1192958 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1192882 TAGTTTACTT
* *
1192892 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1192912 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1192932 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1192951 TCGCAACG
1 TCGCAACG
1192959 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1192966 original size:14 final size:14
Alignment explanation
Indices: 1192947--1193005 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
1192937 ATGCGAAATG
1192947 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1192961 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1192977 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1192993 AAAAATCGCAACG
1 -AAAATCGCAACG
1193006 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 10 0.26
15 11 0.29
16 7 0.18
17 1 0.03
18 9 0.24
ACGTcount: A:0.49, C:0.25, G:0.17, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1192976 original size:33 final size:34
Alignment explanation
Indices: 1192931--1193022 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 34
1192921 GGAAATGGCT
*
1192931 ATCGCAATGCGAAATGAAAATCGCAACGAC-AAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAAA
1192964 ATCGCAACGCGAAATG-AAATCGCAACGACAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAAA
1192997 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1193023 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 13 0.23
33 34 0.61
34 9 0.16
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (34 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAAA
Found at i:1193058 original size:14 final size:14
Alignment explanation
Indices: 1193039--1193096 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1193029 TTGTGTTTCG
1193039 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1193053 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1193069 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1193085 CGTTGCGATTTT
1 CGTTGCGATTTT
1193097 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1193073 original size:32 final size:33
Alignment explanation
Indices: 1193034--1193112 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1193024 GCGATTTGTG
1193034 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1193066 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1193099 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1193113 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1193111 original size:19 final size:19
Alignment explanation
Indices: 1193053--1193170 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
1193043 GCGATTTTGT
1193053 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1193071 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1193085 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1193104 CATTGCGATAGCCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
**
1193124 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1193143 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1193163 TGTTGCGA
1 CGTTGCGA
1193171 AAGTAAACTG
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1193162 original size:39 final size:37
Alignment explanation
Indices: 1193034--1193170 Score: 105
Period size: 39 Copynumber: 3.9 Consensus size: 37
1193024 GCGATTTGTG
1193034 TTTCGCGTTGCGATTTT-G--T--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTAGTTTCGCGTTGCGATTTCA
1193066 TTTCGCGTTGCGATTTT-G--T--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTAGTTTCGCGTTGCGA-TTTCA
* *** * *
1193099 TTTCGCATTGCGATAGCCATTTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGAT-TTTAGTTTCGCGTTGCGAT-TTCA
*
1193138 TTTCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TTTCGCGTTGCGATTTT-AGTTTCGCGTTGCGA
1193171 AAGTAAACTG
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
32 27 0.32
33 18 0.21
37 1 0.01
38 1 0.01
39 37 0.44
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (37 bp):
TTTCGCGTTGCGATTTTAGTTTCGCGTTGCGATTTCA
Found at i:1195163 original size:14 final size:15
Alignment explanation
Indices: 1195144--1195219 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
1195134 CGAAATGGCT
1195144 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
1195158 ATCGCAATGCGA-ATGAA
1 ATCGCAA-GCGAGA--AA
1195175 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
1195194 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
1195208 ATCGCAATGCGA
1 ATCGCAA-GCGA
1195220 TTATCATTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
14 18 0.35
15 2 0.04
16 6 0.12
17 15 0.29
19 10 0.19
21 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:1195178 original size:17 final size:18
Alignment explanation
Indices: 1195154--1195219 Score: 88
Period size: 17 Copynumber: 3.9 Consensus size: 18
1195144 ATCGCAACGA
1195154 GAAAATCGCAATGCGAAT
1 GAAAATCGCAATGCGAAT
1195172 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCG-AAT
1195190 GAAAATCGCAA--CG-A-
1 GAAAATCGCAATGCGAAT
1195204 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1195220 TTATCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 15 0.35
18 5 0.12
19 9 0.21
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (18 bp):
GAAAATCGCAATGCGAAT
Found at i:1195200 original size:50 final size:50
Alignment explanation
Indices: 1195125--1195219 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 50
1195115 AAAACAGACT
***
1195125 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGAATGAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAATGAA
*
1195175 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
1195220 TTATCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (50 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAATGAA
Found at i:1195295 original size:20 final size:20
Alignment explanation
Indices: 1195245--1195295 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1195235 GCGATATTCT
*
1195245 CGTTGCGATAACCATTTTCA
1 CGTTGCGATAGCCATTTTCA
1195265 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
1195285 CGTTGCGATAG
1 CGTTGCGATAG
1195296 TCAAATGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:1195653 original size:14 final size:14
Alignment explanation
Indices: 1195634--1195669 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1195624 ATTGTTTAAT
1195634 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1195648 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1195662 TGATTTGT
1 TGATTTGT
1195670 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1196959 original size:24 final size:24
Alignment explanation
Indices: 1196908--1196961 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1196898 GTATTCAAAA
* * *
1196908 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGAAC
* *
1196932 TTTGATATTGGTCAATACACTAAT
1 TTTGATATTGGTCAATACACGAAC
1196956 TTTGAT
1 TTTGAT
1196962 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGAAC
Found at i:1199479 original size:32 final size:33
Alignment explanation
Indices: 1199407--1199499 Score: 179
Period size: 32 Copynumber: 2.8 Consensus size: 33
1199397 GGAAATTACT
1199407 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1199440 ATCGCAATGCGAAATGAAAATCGCAACGAG-GA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1199472 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1199500 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 30 0.50
33 30 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1199529 original size:18 final size:19
Alignment explanation
Indices: 1199503--1199542 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1199493 CGCAACGCGA
1199503 ATTTAA-TTTCGCGTTGCG
1 ATTTAATTTTCGCGTTGCG
*
1199521 ATTTCATTTTCGCGTTGCG
1 ATTTAATTTTCGCGTTGCG
1199540 ATT
1 ATT
1199543 CTCTAGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.47
Consensus pattern (19 bp):
ATTTAATTTTCGCGTTGCG
Found at i:1201110 original size:21 final size:21
Alignment explanation
Indices: 1201044--1201110 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1201034 GTGAATCGGG
*
1201044 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1201064 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1201086 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1201107 CTCT
1 CTCT
1201111 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1201129 original size:42 final size:41
Alignment explanation
Indices: 1201044--1201166 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1201034 GTGAATCGGG
* * * * *
1201044 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1201086 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1201128 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1201167 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1201502 original size:18 final size:18
Alignment explanation
Indices: 1201479--1201524 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1201469 CCAAGCAATC
1201479 TAAGTGAAATGGTTAATT
1 TAAGTGAAATGGTTAATT
1201497 TAAGTGAAATGGTTAATT
1 TAAGTGAAATGGTTAATT
1201515 TAAGTGAAAT
1 TAAGTGAAAT
1201525 TACGAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (18 bp):
TAAGTGAAATGGTTAATT
Found at i:1203208 original size:39 final size:38
Alignment explanation
Indices: 1203165--1203243 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 38
1203155 TCTTTTGGTT
*
1203165 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGA-AATGAAAATCGCAACGC
* *
1203204 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGC
1203242 GA
1 GA
1203244 TTTTGGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 17 0.46
39 20 0.54
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGC
Found at i:1203215 original size:19 final size:19
Alignment explanation
Indices: 1203165--1203243 Score: 122
Period size: 19 Copynumber: 4.1 Consensus size: 19
1203155 TCTTTTGGTT
*
1203165 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1203184 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
1203204 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1203223 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1203242 GA
1 GA
1203244 TTTTGGTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 38 0.69
20 17 0.31
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1203273 original size:18 final size:18
Alignment explanation
Indices: 1203239--1203302 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
1203229 AAAATCGCAA
*
1203239 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
1203258 TGCGATTTTATTTCGCGT
1 TGCGATTTTATTTCGCGT
* *
1203276 TGCGATAGTCATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
1203296 TGCGATT
1 TGCGATT
1203303 CTCATTCTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 14 0.36
19 14 0.36
20 11 0.28
ACGTcount: A:0.11, C:0.19, G:0.27, T:0.44
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:1203307 original size:20 final size:18
Alignment explanation
Indices: 1203250--1203308 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 18
1203240 GCGATTTTGG
*
1203250 TTTCGCGTTGCGATTTTA
1 TTTCGCGTTGCGATTTCA
*
1203268 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGAT-TTCA
1203287 TTTCCGCGTTGCGATTCTCA
1 TTT-CGCGTTGCGATT-TCA
1203307 TT
1 TT
1203309 CTCGAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.40
19 5 0.14
20 16 0.46
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:1203910 original size:20 final size:20
Alignment explanation
Indices: 1203817--1203910 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1203807 CGCTAAGTAA
*
1203817 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
1203837 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1203857 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1203878 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1203898 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1203911 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1203929 original size:41 final size:41
Alignment explanation
Indices: 1203838--1203971 Score: 119
Period size: 41 Copynumber: 3.3 Consensus size: 41
1203828 AAAGTCAGTA
* * * * ** *
1203838 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
1203878 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* * ** *
1203920 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1203961 TCGCATTGCGA
1 TCGCATTGCGA
1203972 ATAGGGAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 71 0.93
42 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (41 bp):
TCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1203972 original size:21 final size:21
Alignment explanation
Indices: 1203899--1203973 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
1203889 ATAGTCAGTA
*
1203899 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGAATTTCCCAAT
* * **
1203920 TCGCGTTGCG-ATTTACTTAT
1 TCGCATTGCGAATTTCCCAAT
1203940 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGAATTTCCCAAT
1203961 TCGCATTGCGAAT
1 TCGCATTGCGAAT
1203974 AGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGAATTTCCCAAT
Found at i:1207032 original size:20 final size:20
Alignment explanation
Indices: 1207009--1207055 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1206999 GTTTGAGTCT
1207009 TGATATTTTGATAT-TATTTA
1 TGAT-TTTTGATATATATTTA
*
1207029 TGATTTTTTATATATATTTA
1 TGATTTTTGATATATATTTA
*
1207049 TAATTTT
1 TGATTTT
1207056 AAAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (20 bp):
TGATTTTTGATATATATTTA
Found at i:1216879 original size:25 final size:26
Alignment explanation
Indices: 1216839--1216891 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
1216829 TAACAATAGG
1216839 GATTGAAAATTGTATATTTTTTTATA
1 GATTGAAAATTGTATATTTTTTTATA
1216865 GATTG-AAATTGTATATTTTTTTATA
1 GATTGAAAATTGTATATTTTTTTATA
1216890 GA
1 GA
1216892 CAAAAAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (26 bp):
GATTGAAAATTGTATATTTTTTTATA
Found at i:1217362 original size:2 final size:2
Alignment explanation
Indices: 1217355--1217387 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1217345 TTTGACCTTT
1217355 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 T
1217388 TGGATCAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1218715 original size:11 final size:11
Alignment explanation
Indices: 1218685--1218715 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1218675 GTTTGTATAG
1218685 TTTTTTTTTCT
1 TTTTTTTTTCT
*
1218696 TTTCTTTTTCT
1 TTTTTTTTTCT
1218707 TTTTTTTTT
1 TTTTTTTTT
1218716 TCACTTTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:1220865 original size:24 final size:23
Alignment explanation
Indices: 1220838--1220882 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1220828 GCTCGATCTG
1220838 ATTTGATTTGACATAAATAAAAAT
1 ATTTGATTTGACA-AAATAAAAAT
* *
1220862 ATTTTATTTGATAAAATAAAA
1 ATTTGATTTGACAAAATAAAA
1220883 TGATAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (23 bp):
ATTTGATTTGACAAAATAAAAAT
Found at i:1228620 original size:17 final size:18
Alignment explanation
Indices: 1228581--1228627 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1228571 CGTTTCGGAG
*
1228581 GGAATTGAAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
1228599 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
*
1228616 GGAATTTGAATC
1 GGAATTGGAATC
1228628 CAATTTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.30
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:1230053 original size:25 final size:26
Alignment explanation
Indices: 1230019--1230074 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1230009 ATACTTTTAA
* * *
1230019 TAAATTAAAAT-AAATTATATAATTT
1 TAAATAAAAATGAAAATAAATAATTT
*
1230044 TAAATAAAAATGAAAATAAATATTTT
1 TAAATAAAAATGAAAATAAATAATTT
1230070 TAAAT
1 TAAAT
1230075 TCAGTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAATAAAAATGAAAATAAATAATTT
Found at i:1230103 original size:28 final size:27
Alignment explanation
Indices: 1230061--1230155 Score: 115
Period size: 28 Copynumber: 3.6 Consensus size: 27
1230051 AAATGAAAAT
1230061 AAATATTTTTAAATTCAGTTAATAATA
1 AAATATTTTTAAATTCAGTTAATAATA
*
1230088 AAATATTTTTTAAATTCAATTAATAATA
1 AAATA-TTTTTAAATTCAGTTAATAATA
** *
1230116 ATCTATTTTT-AA-TAAGTTAAT-ATAA
1 AAATATTTTTAAATTCAGTTAATAAT-A
1230141 AAATATTTTTAAATT
1 AAATATTTTTAAATT
1230156 AATATATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
24 2 0.04
25 16 0.28
26 4 0.07
27 11 0.19
28 24 0.42
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (27 bp):
AAATATTTTTAAATTCAGTTAATAATA
Found at i:1230453 original size:39 final size:39
Alignment explanation
Indices: 1230398--1230521 Score: 119
Period size: 39 Copynumber: 3.2 Consensus size: 39
1230388 AAATAAATAT
*
1230398 TTAAAAAATTAAAACGTTAATGTGAAATAATTTAAGAAA
1 TTAAAAATTTAAAACGTTAATGTGAAATAATTTAAGAAA
* *
1230437 TTAAAAATTTAGAACG-TAATGGTGTCAA-AATTTAAGAAA
1 TTAAAAATTTAAAACGTTAAT-GTG-AAATAATTTAAGAAA
** * * * *
1230476 TTAGGATTTTAAAATGTTATTGTGAAATAATTTGAG-AA
1 TTAAAAATTTAAAACGTTAATGTGAAATAATTTAAGAAA
*
1230514 TTATAAAT
1 TTAAAAAT
1230522 AAAAATTTTA
Statistics
Matches: 67, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
38 13 0.19
39 49 0.73
40 5 0.07
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.35
Consensus pattern (39 bp):
TTAAAAATTTAAAACGTTAATGTGAAATAATTTAAGAAA
Found at i:1235439 original size:23 final size:23
Alignment explanation
Indices: 1235401--1235485 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
1235391 TGTAAACTAT
* *
1235401 CAAAAGACATAGAAAAACGTGCCA
1 CAAAAG-CAGAGAAAAACGTGCTA
*
1235425 CAAAAGCAGAGAAAAATGTGCTA
1 CAAAAGCAGAGAAAAACGTGCTA
* *
1235448 TAAAAACAGAGAAAAACGTGCTA
1 CAAAAGCAGAGAAAAACGTGCTA
* *
1235471 TAAAGGCAGAGAAAA
1 CAAAAGCAGAGAAAA
1235486 TGTCACAAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 47 0.89
24 6 0.11
ACGTcount: A:0.55, C:0.14, G:0.20, T:0.11
Consensus pattern (23 bp):
CAAAAGCAGAGAAAAACGTGCTA
Found at i:1235737 original size:2 final size:2
Alignment explanation
Indices: 1235732--1235770 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1235722 TGATTGTTAC
1235732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1235771 CACGTACAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1258596 original size:17 final size:17
Alignment explanation
Indices: 1258550--1258597 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
1258540 TATAGCACAT
*
1258550 ATATTAGTAAAATAAAA
1 ATATTAATAAAATAAAA
* *
1258567 A-ATTCATATAATAAAA
1 ATATTAATAAAATAAAA
1258583 ATATTAATAAAATAA
1 ATATTAATAAAATAA
1258598 GATAAAGTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
ATATTAATAAAATAAAA
Found at i:1268778 original size:2 final size:2
Alignment explanation
Indices: 1268771--1268805 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1268761 CACGTGAGTG
1268771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1268806 CATCAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1274567 original size:57 final size:57
Alignment explanation
Indices: 1274479--1274604 Score: 173
Period size: 57 Copynumber: 2.2 Consensus size: 57
1274469 ACCATTTAAT
* * * *
1274479 TATTTCACATAGTATTAATCAAATTGTCATTTGTTCATATAAAAC-ATATACTCATAG
1 TATTTCACATAGCATTAATCAAATTATCATTTATTCACATAAAACAAT-TACTCATAG
* *
1274536 TATTTCACATAGCATTACTCAAATTATCATTTATTCACATAAAACAATTACTCATTG
1 TATTTCACATAGCATTAATCAAATTATCATTTATTCACATAAAACAATTACTCATAG
*
1274593 CATTTCACATAG
1 TATTTCACATAG
1274605 TATATATACT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 59 0.97
58 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (57 bp):
TATTTCACATAGCATTAATCAAATTATCATTTATTCACATAAAACAATTACTCATAG
Found at i:1276008 original size:62 final size:62
Alignment explanation
Indices: 1275937--1276060 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
1275927 ATTTATTAAT
*
1275937 TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAATTATATAAAG
1 TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAACTATATAAAG
1275999 TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAACTATATAAAG
1 TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAACTATATAAAG
1276061 GGTATAATAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (62 bp):
TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAACTATATAAAG
Found at i:1276282 original size:74 final size:68
Alignment explanation
Indices: 1276124--1276287 Score: 157
Period size: 74 Copynumber: 2.2 Consensus size: 68
1276114 CTGGAACTCA
* * * * *
1276124 AATTTCTTTATATTAGTTGTTCATTTTATTGAAGGTGTTCATCCTAAAATTATATTGTGCCCATC
1 AATTTTTTTATATTAGTTGTTCATTTTACTGAAGGTGTCCACCCTAAAATTATATTGTGCCCATA
1276189 TGG
66 TGG
*
1276192 AATTTGGATTTCTTTATATTAGTTGTTCATTTTACTGAAGGTGTCCACCCTAAAATTTTATTTGT
1 AA--T---TTT-TTTATATTAGTTGTTCATTTTACTGAAGGTGTCCACCCTAAAA--TTA--TAT
1276257 GTGTGACCCATATGG
56 -TGTG-CCCATATGG
1276272 AATTTTTTTATTATTA
1 AATTTTTTTA-TATTA
1276288 ATACATATGT
Statistics
Matches: 77, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
68 2 0.03
70 1 0.01
73 2 0.03
74 44 0.57
75 8 0.10
76 3 0.04
78 3 0.04
79 4 0.05
80 10 0.13
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (68 bp):
AATTTTTTTATATTAGTTGTTCATTTTACTGAAGGTGTCCACCCTAAAATTATATTGTGCCCATA
TGG
Found at i:1285892 original size:96 final size:96
Alignment explanation
Indices: 1285726--1285913 Score: 295
Period size: 96 Copynumber: 2.0 Consensus size: 96
1285716 ACAAGATTAT
* * *
1285726 TCAAGCCAGGAGATGAAACTCTTCCTAATTCAGACCCAAACTGTCTTTCTTCAGCACCAAGTGAA
1 TCAAGCCAGGAGATGAAACCCTTCCTAATTCAGACCCAAACAGTCTTTCTTCAGCACCAAGCGAA
*
1285791 GGAAAATCACGTTCAAAAGCAGATTTACTAA
66 GGAAAATCACGCTCAAAAGCAGATTTACTAA
* * *
1285822 TCAAGCCAGGAGATGAAACCCTTCCTATTTCAGACCCTACCAGTCTTTCTTCAGCACCAAGCGAA
1 TCAAGCCAGGAGATGAAACCCTTCCTAATTCAGACCCAAACAGTCTTTCTTCAGCACCAAGCGAA
* *
1285887 TGAAAATCACGCTCAAATGCAGATTTA
66 GGAAAATCACGCTCAAAAGCAGATTTA
1285914 TCACGGACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 83 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (96 bp):
TCAAGCCAGGAGATGAAACCCTTCCTAATTCAGACCCAAACAGTCTTTCTTCAGCACCAAGCGAA
GGAAAATCACGCTCAAAAGCAGATTTACTAA
Found at i:1298469 original size:19 final size:19
Alignment explanation
Indices: 1298419--1298472 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1298409 CACTAAAAAA
1298419 AATATTATTTT-ATACATTT
1 AATATTATTTTAATA-ATTT
**
1298438 AATATTAAATTAATAATTT
1 AATATTATTTTAATAATTT
*
1298457 AATATCATTTTAATAA
1 AATATTATTTTAATAA
1298473 AAATATTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 26 0.90
20 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTATTTTAATAATTT
Found at i:1298650 original size:19 final size:19
Alignment explanation
Indices: 1298612--1298657 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1298602 TAATAATGAC
*
1298612 TAATATTAATTTATATATT
1 TAATATTAATTAATATATT
1298631 TAATATTAATATAATA-ATT
1 TAATATTAAT-TAATATATT
*
1298650 TATTATTA
1 TAATATTA
1298658 TGTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATATTAATTAATATATT
Found at i:1298982 original size:29 final size:30
Alignment explanation
Indices: 1298940--1299016 Score: 111
Period size: 29 Copynumber: 2.6 Consensus size: 30
1298930 CCGGAAAATG
1298940 TAATTCATTTTACGTAAAACAATTTT-AGA
1 TAATTCATTTTACGTAAAACAATTTTCAGA
* *
1298969 TAATTCATTTTACGTAAAACAGTTTTCAGG
1 TAATTCATTTTACGTAAAACAATTTTCAGA
* *
1298999 TAATTCATCTTACATAAA
1 TAATTCATTTTACGTAAA
1299017 TTATTTTCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 25 0.58
30 18 0.42
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (30 bp):
TAATTCATTTTACGTAAAACAATTTTCAGA
Found at i:1299765 original size:35 final size:35
Alignment explanation
Indices: 1299719--1299789 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1299709 TTATTCATAA
* *
1299719 AGCACGATAATGTTTTAAGGTGTATGTATGTATGT
1 AGCACGATAATGTTTTAAGGTATATGTATGCATGT
1299754 AGCACGATAATGTTTTAAGGTATATGTATGCATGT
1 AGCACGATAATGTTTTAAGGTATATGTATGCATGT
1299789 A
1 A
1299790 TGTATGTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (35 bp):
AGCACGATAATGTTTTAAGGTATATGTATGCATGT
Found at i:1299792 original size:4 final size:4
Alignment explanation
Indices: 1299776--1299810 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1299766 TTTTAAGGTA
* *
1299776 TATG TATG CATG TATG TATG TATG CATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1299811 AACACTCTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:1299797 original size:16 final size:16
Alignment explanation
Indices: 1299776--1299810 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1299766 TTTTAAGGTA
1299776 TATGTATGCATGTATG
1 TATGTATGCATGTATG
1299792 TATGTATGCATGTATG
1 TATGTATGCATGTATG
1299808 TAT
1 TAT
1299811 AACACTCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (16 bp):
TATGTATGCATGTATG
Found at i:1301575 original size:17 final size:17
Alignment explanation
Indices: 1301534--1301576 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1301524 ATATTTTACG
*
1301534 GGATTATTTCCCTTTTTT
1 GGATT-TTTTCCTTTTTT
*
1301552 GTATTTTTTCCTTTTTT
1 GGATTTTTTCCTTTTTT
*
1301569 GGCTTTTT
1 GGATTTTT
1301577 GTGTATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.07, C:0.14, G:0.12, T:0.67
Consensus pattern (17 bp):
GGATTTTTTCCTTTTTT
Found at i:1301610 original size:3 final size:3
Alignment explanation
Indices: 1301587--1301645 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
1301577 GTGTATTTTT
* *
1301587 TAA T-A TAA CAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1301634 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1301646 ATAAAATAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1303304 original size:28 final size:27
Alignment explanation
Indices: 1303222--1303294 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
1303212 GAGATACTAA
1303222 ATTATTAAAAAGTTTAATATATAAAAC
1 ATTATTAAAAAGTTTAATATATAAAAC
1303249 ATTATTAAAAAGTTTAATATATAAAAC
1 ATTATTAAAAAGTTTAATATATAAAAC
1303276 ATTATTAAAAAAGTTTAAT
1 ATTATT-AAAAAGTTTAAT
1303295 TTCTTTAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 33 0.73
28 12 0.27
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (27 bp):
ATTATTAAAAAGTTTAATATATAAAAC
Found at i:1303366 original size:19 final size:20
Alignment explanation
Indices: 1303327--1303366 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1303317 GGTTTGCGTA
1303327 TATGAAAAATACTGATTAAT
1 TATGAAAAATACTGATTAAT
* *
1303347 TATGTAAAATA-TGTTTAAT
1 TATGAAAAATACTGATTAAT
1303366 T
1 T
1303367 TGAGGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (20 bp):
TATGAAAAATACTGATTAAT
Found at i:1311164 original size:2 final size:2
Alignment explanation
Indices: 1311157--1311181 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1311147 TTGAATGCTA
1311157 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1311182 CTAATCATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1312622 original size:30 final size:31
Alignment explanation
Indices: 1312542--1312625 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
1312532 TTTATAAAAT
* *
1312542 GTGTATAACTGAAT-TAAATCAAAATTTTAA
1 GTGTACAACTGAATCAAAATCAAAATTTTAA
* * *
1312572 GTGTTCAATTGAATCAAAATCAAAATTTTAT
1 GTGTACAACTGAATCAAAATCAAAATTTTAA
*
1312603 GTGTACAACTGCA-CAAAATCAAA
1 GTGTACAACTGAATCAAAATCAAA
1312626 CTTATGTATC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
30 21 0.47
31 24 0.53
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (31 bp):
GTGTACAACTGAATCAAAATCAAAATTTTAA
Found at i:1317310 original size:135 final size:135
Alignment explanation
Indices: 1317060--1317335 Score: 462
Period size: 135 Copynumber: 2.0 Consensus size: 135
1317050 TCGAGGGTTG
* * * * * *
1317060 GTCGCCAGGTCTTTCGGGCAACCTCTATAGGTCGTCATATCCTCTAAACGTTCAAGCATTGGTTT
1 GTCGTCAGGTCCTTCGGGCAACCTCCATAGGTCGTCATATCCTCCAAACATTCAAACATTGGTTT
1317125 CCTAGATTTCTCATAAGTTACAGTTATTACCTATATCGGTAATTACGTTTTTATTCGAAGACCTC
66 CCTAGATTTCTCATAAGTTACAGTTATTACCTATATCGGTAATTACGTTTTTATTCGAAGACCTC
1317190 CATAA
131 CATAA
* *
1317195 GTCGTCAGGTCCTTCGGGCGACCTCCATAGGTCGTCATGTCCTCCAAACATTCAAACATTGGTTT
1 GTCGTCAGGTCCTTCGGGCAACCTCCATAGGTCGTCATATCCTCCAAACATTCAAACATTGGTTT
*
1317260 CCTAGATTTCTCATAAGTTACAGTTATTACCTATATCGGTAATTAGGTTTTTATTCGAAGACCTC
66 CCTAGATTTCTCATAAGTTACAGTTATTACCTATATCGGTAATTACGTTTTTATTCGAAGACCTC
*
1317325 CATAG
131 CATAA
1317330 GTCGTC
1 GTCGTC
1317336 TGGTACCTCC
Statistics
Matches: 131, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 131 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (135 bp):
GTCGTCAGGTCCTTCGGGCAACCTCCATAGGTCGTCATATCCTCCAAACATTCAAACATTGGTTT
CCTAGATTTCTCATAAGTTACAGTTATTACCTATATCGGTAATTACGTTTTTATTCGAAGACCTC
CATAA
Found at i:1318928 original size:57 final size:57
Alignment explanation
Indices: 1318859--1318969 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
1318849 ACTGCTTTCT
** * *
1318859 CCATGCAAAACCTTTTGAGAACCAATCAGATCACCGCCTTCTTCATGCAAAAACTCG
1 CCATGCAAAACCTCGTGAGAACCAATCAGACCACCACCTTCTTCATGCAAAAACTCG
* *
1318916 CCATGCAAAACCTCGTGAGAACCAATCAGACCATCACCTTCTTCATGTAAAAAC
1 CCATGCAAAACCTCGTGAGAACCAATCAGACCACCACCTTCTTCATGCAAAAAC
1318970 ACGTACGAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.35, C:0.32, G:0.12, T:0.22
Consensus pattern (57 bp):
CCATGCAAAACCTCGTGAGAACCAATCAGACCACCACCTTCTTCATGCAAAAACTCG
Found at i:1330540 original size:6 final size:6
Alignment explanation
Indices: 1330474--1330538 Score: 85
Period size: 6 Copynumber: 10.8 Consensus size: 6
1330464 ATATATGTGT
* * *
1330474 GCGTGC GCGTGT GCGTAC GCGTGC GCGTGC GCGTGC GCGTGT GCGTGC
1 GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC GCGTGC
* *
1330522 GCGTGT GCGTGT GCGTG
1 GCGTGC GCGTGC GCGTG
1330539 TGTATTATGT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.02, C:0.26, G:0.49, T:0.23
Consensus pattern (6 bp):
GCGTGC
Found at i:1332609 original size:31 final size:31
Alignment explanation
Indices: 1332574--1332667 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
1332564 AATTCGGTGA
*
1332574 ATTCAATATGTCATTCTCACTAGGAATTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
*
1332605 ATTCAATATTTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
*
1332636 ATTCAATATGTCATTCTCACTAGAAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
1332667 A
1 A
1332668 AAATCTTGGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGGAACTCCC
Found at i:1334731 original size:19 final size:19
Alignment explanation
Indices: 1334707--1334751 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1334697 TTGTTATGAG
1334707 TTTTAACCATAAAACTATA
1 TTTTAACCATAAAACTATA
1334726 TTTTAACCATAAAACTATA
1 TTTTAACCATAAAACTATA
1334745 TTTTAAC
1 TTTTAAC
1334752 AAACTCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTAACCATAAAACTATA
Found at i:1335884 original size:19 final size:19
Alignment explanation
Indices: 1335860--1335917 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
1335850 AGAGTTGACA
1335860 TTTATTTTCAACTTACTAT
1 TTTATTTTCAACTTACTAT
1335879 TTTATTTTCAACTTACTAT
1 TTTATTTTCAACTTACTAT
*
1335898 TTTATTTTCAACTTAATAT
1 TTTATTTTCAACTTACTAT
1335917 T
1 T
1335918 CAGAAACTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATTTTCAACTTACTAT
Found at i:1337216 original size:21 final size:21
Alignment explanation
Indices: 1337190--1337248 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1337180 ATTTACCATG
1337190 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
** *
1337211 ATTGCGGTTGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGGCGCT
* *
1337232 ATTGAGGCCATCGCGGG
1 ATTGCGGCCGTCGCGGG
1337249 TAACTCGGAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Found at i:1347758 original size:191 final size:191
Alignment explanation
Indices: 1347412--1347794 Score: 734
Period size: 191 Copynumber: 2.0 Consensus size: 191
1347402 ACATAACTTC
1347412 TCTAGGATCAAGTCCCAAAACTTCCGCCTGTCAGGAAACTCGAGAAAAATCGCATATAAGGAGTA
1 TCTAGGATCAAGTCCCAAAACTTCCGCCTGTCAGGAAACTCGAGAAAAATCGCATATAAGGAGTA
1347477 AAAACAGAAATGCTGCAAATTTCTTGGTGTTCTATTAGAAAATTTGAGGACTGTATAAAAAGGTC
66 AAAACAGAAATGCTGCAAATTTCTTGGTGTTCTATTAGAAAATTTGAGGACTGTATAAAAAGGTC
1347542 GCATATAAAAGTGTTAGCTCTGACAACAGCAATAG-TGTAACTCCCAAAAGTCGTTTCGGG
131 GCATATAAAAGTGTTAGCTCTGACAACAGCAATAGTTGTAACTCCCAAAAGTCGTTTCGGG
1347602 TCTAGGATCAAGTCCCAAAACTTCCGCCTGTCAGGAAACTCGAGAAAAATCGCATATAAGGAGTA
1 TCTAGGATCAAGTCCCAAAACTTCCGCCTGTCAGGAAACTCGAGAAAAATCGCATATAAGGAGTA
1347667 AAAACCAGAAATGCTGCAAATTTCTTGGTGTTCTATTAGAAAATTTGAGGACTGTAATAAAAAGG
66 AAAA-CAGAAATGCTGCAAATTTCTTGGTGTTCTATTAGAAAATTTGAGGACTGT-ATAAAAAGG
1347732 TCGCATAT-AAAGTGTTAGCTCTGACAACAGCAATAGTTGTAACTCCCAAAAGTCGTTTCGGG
129 TCGCATATAAAAGTGTTAGCTCTGACAACAGCAATAGTTGTAACTCCCAAAAGTCGTTTCGGG
1347794 T
1 T
1347795 ATAAGTACTG
Statistics
Matches: 190, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
190 69 0.36
191 78 0.41
192 43 0.23
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (191 bp):
TCTAGGATCAAGTCCCAAAACTTCCGCCTGTCAGGAAACTCGAGAAAAATCGCATATAAGGAGTA
AAAACAGAAATGCTGCAAATTTCTTGGTGTTCTATTAGAAAATTTGAGGACTGTATAAAAAGGTC
GCATATAAAAGTGTTAGCTCTGACAACAGCAATAGTTGTAACTCCCAAAAGTCGTTTCGGG
Found at i:1349045 original size:28 final size:29
Alignment explanation
Indices: 1349005--1349060 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
1348995 ACGAGAAATT
*
1349005 AGTCATGATTATT-ACGATAGATACTCCG
1 AGTCATGATTATTGACAATAGATACTCCG
*
1349033 AGTCATGATTATTGACAATAGATGCTCC
1 AGTCATGATTATTGACAATAGATACTCC
1349061 AAGAAGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (29 bp):
AGTCATGATTATTGACAATAGATACTCCG
Found at i:1349120 original size:37 final size:37
Alignment explanation
Indices: 1349057--1349150 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 37
1349047 ACAATAGATG
* *
1349057 CTCCAAGAAGATT-GTTAT-AGTTATCGACA-ACGGATA
1 CTCCAAGAAGATTAGTTATGA-TAATCGA-AGACGAATA
* *
1349093 CTCCGAGAAGATTAGTTATGATAATCGAAGATGAATA
1 CTCCAAGAAGATTAGTTATGATAATCGAAGACGAATA
*
1349130 CTCCTAGAAGATTAG-TATGAT
1 CTCCAAGAAGATTAGTTATGAT
1349151 GAATACTGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
36 19 0.38
37 30 0.60
38 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (37 bp):
CTCCAAGAAGATTAGTTATGATAATCGAAGACGAATA
Found at i:1351671 original size:3 final size:3
Alignment explanation
Indices: 1351660--1351710 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
1351650 TCTTCTTGTT
1351660 TTA TT- TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
1351704 TT- TTA TT
1 TTA TTA TT
1351711 GGCATCTACA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.14
3 35 0.80
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1351689 original size:20 final size:20
Alignment explanation
Indices: 1351660--1351701 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1351650 TCTTCTTGTT
*
1351660 TTATTTTATTATTATTATTA
1 TTATTATATTATTATTATTA
1351680 TTATTATATTATTATTATTA
1 TTATTATATTATTATTATTA
1351700 TT
1 TT
1351702 GATTTTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTATATTATTATTATTA
Found at i:1351691 original size:23 final size:23
Alignment explanation
Indices: 1351658--1351709 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1351648 TTTCTTCTTG
*
1351658 TTTTATTTTATTATTATTATT-A
1 TTTTATATTATTATTATTATTGA
1351680 TTATTATATTATTATTATTATTGA
1 TT-TTATATTATTATTATTATTGA
1351704 TTTTAT
1 TTTTAT
1351710 TGGCATCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 22 0.81
24 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTATATTATTATTATTATTGA
Found at i:1357071 original size:30 final size:30
Alignment explanation
Indices: 1357037--1357103 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
1357027 CATGATACAT
*
1357037 GTCACATTATCACTTTAAGTGATATGTCAC
1 GTCACACTATCACTTTAAGTGATATGTCAC
*
1357067 GTCACACTATCACTTTGAGTGATATGTCAC
1 GTCACACTATCACTTTAAGTGATATGTCAC
1357097 GTCACAC
1 GTCACAC
1357104 ATCTTGACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (30 bp):
GTCACACTATCACTTTAAGTGATATGTCAC
Found at i:1361311 original size:18 final size:19
Alignment explanation
Indices: 1361270--1361311 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1361260 TTGGTTCACA
1361270 GAATGTAAAATTATCAGCGG
1 GAATGTAAAATTATCA-CGG
*
1361290 GAATGTAAGATTATCA-GG
1 GAATGTAAAATTATCACGG
1361308 GAAT
1 GAAT
1361312 AGGATTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.26
Consensus pattern (19 bp):
GAATGTAAAATTATCACGG
Found at i:1368566 original size:16 final size:17
Alignment explanation
Indices: 1368534--1368566 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1368524 TTTCTATTTC
*
1368534 TATTTTATATTTTAAAT
1 TATTTTATATATTAAAT
1368551 TATTTT-TATATTAAAT
1 TATTTTATATATTAAAT
1368567 AATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTTATATATTAAAT
Found at i:1370275 original size:21 final size:23
Alignment explanation
Indices: 1370251--1370298 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
1370241 ATTTTTTAAT
1370251 TTTTTAA-T-AATAAAAAAATTA
1 TTTTTAATTAAATAAAAAAATTA
1370272 TTTTTAATTAAAATAAAAAAATTA
1 TTTTTAATT-AAATAAAAAAATTA
1370296 TTT
1 TTT
1370299 ATAAAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.29
22 1 0.04
24 16 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTTTAATTAAATAAAAAAATTA
Done.