Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1402516 original size:34 final size:34
Alignment explanation
Indices: 1402411--1402517 Score: 142
Period size: 34 Copynumber: 3.1 Consensus size: 34
1402401 ATAAATGTTT
* *
1402411 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCAAAATTTAAAA
* * *
1402445 TAAAAATAAAAATAATATTATTCAAAAATTAAAA
1 TTAAAATAAAAATTATATTATTCAAAATTTAAAA
* * *
1402479 TTAAAATATAAATTATAGTATTCAAAATTTAACA
1 TTAAAATAAAAATTATATTATTCAAAATTTAAAA
1402513 TTAAA
1 TTAAA
1402518 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCAAAATTTAAAA
Found at i:1403169 original size:127 final size:128
Alignment explanation
Indices: 1402882--1403220 Score: 583
Period size: 127 Copynumber: 2.7 Consensus size: 128
1402872 GCAATCCATC
*
1402882 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAAT
* * *
1402947 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGGTACTGATATATC
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTAATATATA
*
1403010 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATGAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAAT
1403075 GGAAGGCGC-CCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTAATATGA-A
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTAATAT-ATA
* * *
1403137 TAGTGTCCCCGAGGGACATGCGTGACGTAATAGGGTAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAAT
1403202 GGAAGGCGCGCCCCCGGGA
66 GGAAGGCGCGCCCCCGGGA
1403221 TAATTGTTGA
Statistics
Matches: 200, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
127 118 0.59
128 82 0.41
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTAATATATA
Found at i:1414495 original size:3 final size:3
Alignment explanation
Indices: 1414487--1414566 Score: 88
Period size: 3 Copynumber: 26.3 Consensus size: 3
1414477 ATGTTATTTA
* * * *
1414487 TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
1414535 AAT AAT TAT TAT TAT TAT TAA TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
1414567 TAATATTCCA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:1419964 original size:15 final size:15
Alignment explanation
Indices: 1419944--1419975 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1419934 ATCAATACCT
1419944 TTTTGCATACATACA
1 TTTTGCATACATACA
*
1419959 TTTTGCATACATTCA
1 TTTTGCATACATACA
1419974 TT
1 TT
1419976 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:1427332 original size:21 final size:21
Alignment explanation
Indices: 1427305--1427368 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
1427295 ATTATGCTTG
1427305 AAGAGAAAAAGAAAAAAAAAA
1 AAGAGAAAAAGAAAAAAAAAA
*
1427326 GAGAGAAAAAGAAAAAAGAAAA
1 AAGAGAAAAAGAAAAAA-AAAA
*
1427348 AAGAGAAAAAAGAAGAAAAAA
1 AAGAG-AAAAAGAAAAAAAAA
1427369 GGGGGGTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 16 0.42
22 11 0.29
23 11 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (21 bp):
AAGAGAAAAAGAAAAAAAAAA
Found at i:1427334 original size:9 final size:9
Alignment explanation
Indices: 1427305--1427369 Score: 64
Period size: 9 Copynumber: 7.3 Consensus size: 9
1427295 ATTATGCTTG
1427305 AAGAGAAAA
1 AAGAGAAAA
* *
1427314 AGAAAAAAAA
1 A-AGAGAAAA
*
1427324 AAGAGAGAA
1 AAGAGAAAA
1427333 AA-AG-AAA
1 AAGAGAAAA
1427340 AA-AGAAAA
1 AAGAGAAAA
1427348 AAGAGAAAA
1 AAGAGAAAA
1427357 AAGAAGAAAA
1 AAG-AGAAAA
1427367 AAG
1 AAG
1427370 GGGGGTCAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
7 6 0.13
8 7 0.15
9 17 0.37
10 16 0.35
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAGAGAAAA
Found at i:1427340 original size:16 final size:15
Alignment explanation
Indices: 1427305--1427357 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
1427295 ATTATGCTTG
1427305 AAGAGAAAAAGAAAA
1 AAGAGAAAAAGAAAA
*
1427320 AA-A-AAAGAGAGAAA
1 AAGAGAAAAAGA-AAA
1427334 AAGA-AAAAAGAAAA
1 AAGAGAAAAAGAAAA
1427348 AAGAGAAAAA
1 AAGAGAAAAA
1427358 AGAAGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 6 0.18
14 13 0.39
15 14 0.42
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAGAGAAAAAGAAAA
Found at i:1427343 original size:7 final size:7
Alignment explanation
Indices: 1427305--1427369 Score: 64
Period size: 7 Copynumber: 9.4 Consensus size: 7
1427295 ATTATGCTTG
1427305 AAGAGAAA
1 AAGA-AAA
1427313 AAGAAAA
1 AAGAAAA
1427320 AA-AAAA
1 AAGAAAA
*
1427326 GAGAGAAA
1 AAGA-AAA
1427334 AAGAAAA
1 AAGAAAA
1427341 AAGAAAA
1 AAGAAAA
*
1427348 AAG-AGA
1 AAGAAAA
*
1427354 AA-AAAG
1 AAGAAAA
1427360 AAGAAAA
1 AAGAAAA
1427367 AAG
1 AAG
1427370 GGGGGTCAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
6 12 0.26
7 25 0.53
8 10 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:1428654 original size:83 final size:83
Alignment explanation
Indices: 1428515--1429118 Score: 940
Period size: 83 Copynumber: 7.2 Consensus size: 83
1428505 GAACAAATGC
*
1428515 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1428580 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
*
1428598 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATGTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
1428663 CATTGAATTTAAAAGATG
66 CATTGAATTTGAAAGATG
1428681 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
1428746 CATTGAATTTGGAAGA-G
66 CATTGAATTTGAAAGATG
*
1428763 TAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACC
1 -AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG----G-----
*
1428828 ACAAAACCAATCATTGAATTTGAAAGATG
56 -TAAAACCAATCATTGAATTTGAAAGATG
* *
1428857 AATGTGGTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
1428922 CATTAAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
* *
1428940 AATGTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
* * *
1429005 TATTGAATTTGGAAGAGG
66 CATTGAATTTGAAAGATG
* *
1429023 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
1429088 CATTAAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
*
1429106 AATTTGCTCATAG
1 AATGTGCTCATAG
1429119 TAGAAATAAG
Statistics
Matches: 478, Mismatches: 31, Indels: 24
0.90 0.06 0.05
Matches are distributed among these distances:
82 1 0.00
83 399 0.83
87 1 0.00
89 1 0.00
93 75 0.16
94 1 0.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
CATTGAATTTGAAAGATG
Found at i:1428973 original size:259 final size:257
Alignment explanation
Indices: 1428515--1429315 Score: 996
Period size: 259 Copynumber: 3.1 Consensus size: 257
1428505 GAACAAATGC
* * *
1428515 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG--G------TA
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAAGAAACCACA
*
1428572 AAACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
66 AAACCAATCATTGAATTTGAAAGATGAATGTGGTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
* * *
1428637 ATGTGATCTGGTTTGGTAAAACCAATCATTGAATTTAAAAGATGAATGTGCTCATAGCATCTTCT
131 ATCTGATCTGGTTTGGTAAAACCAATCATTAAATTTGAAAGATGAATGTGCTCATAGCATCTTCT
*
1428702 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAGAGT
196 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAGAGG
1428764 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCA
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGA-A-GAAACCA
*
1428829 CAAAACCAATCATTGAATTTGAAAGATGAATGTGGTCATAGTATCTTCTGGAAGTGTTCTTTGAG
64 CAAAACCAATCATTGAATTTGAAAGATGAATGTGGTCATAGCATCTTCTGGAAGTGTTCTTTGAG
*
1428894 TTATCTGATCTGGTTTGGTAAAACCAATCATTAAATTTGAAAGATGAATGTGATCATAGCATCTT
129 TTATCTGATCTGGTTTGGTAAAACCAATCATTAAATTTGAAAGATGAATGTGCTCATAGCATCTT
* *
1428959 CTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATTTGGAAGAGG
194 CTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAGAGG
1429023 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAA-AAACCAA
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-GAAGAAACC-A
** ** * *
1429087 TCATTAAATTTGAAAGA-TGAATTTGCTCATAG-TAGAAATAAG-GAGACCCAATAGCATCTTCT
64 -CA--AAA--CCAATCATTGAATTTG---AAAGAT-G-AAT--GTG-G--TC-ATAGCATCTTCT
* * * *
1429149 GGAAGTATTCTTTGAATTATCTGATCTGGTTTGGTATGAACCACATAACCAGTTATTGAATTTGG
113 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AAACCA-AT---CA-TTA---AATTTGA
* * *
1429214 AAGAGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAA
169 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
* *
1429279 ACCAATCATTGAATTTGAAAGATG
234 ACCAATCATTGAATTTGGAAGAGG
* *
1429303 AATTTGCTCATAG
1 AATGTGCTAATAG
1429316 TAGAAATAAG
Statistics
Matches: 482, Mismatches: 33, Indels: 43
0.86 0.06 0.08
Matches are distributed among these distances:
249 52 0.11
253 1 0.00
257 5 0.01
258 1 0.00
259 240 0.50
260 2 0.00
261 3 0.01
262 8 0.02
263 3 0.01
264 1 0.00
265 4 0.01
266 3 0.01
267 1 0.00
268 2 0.00
270 1 0.00
271 45 0.09
272 5 0.01
273 2 0.00
276 2 0.00
277 3 0.01
280 98 0.20
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (257 bp):
AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAAGAAACCACA
AAACCAATCATTGAATTTGAAAGATGAATGTGGTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
ATCTGATCTGGTTTGGTAAAACCAATCATTAAATTTGAAAGATGAATGTGCTCATAGCATCTTCT
GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAGAGG
Found at i:1429282 original size:197 final size:196
Alignment explanation
Indices: 1428949--1429396 Score: 777
Period size: 197 Copynumber: 2.3 Consensus size: 196
1428939 GAATGTGATC
*
1428949 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-AAACCAGTT
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAAACCAGTT
*
1429006 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCT
1429071 GGTTTGGAAAAACCAATCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
131 GGTTTGGAAAAACCAATCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
1429136 A
196 A
*
1429137 ATAGCATCTTCTGGAAGTATTCTTTGAATTATCTGATCTGGTTTGGTATGAACCACATAACCAGT
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA-AACCAGT
1429202 TATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
65 TATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
* *
1429267 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACC
130 TGGTTTGGAAAAACCAATCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACC
1429332 CA
195 CA
1429334 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCA
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA-AACCA
1429397 ATCATTAAAT
Statistics
Matches: 244, Mismatches: 7, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
188 44 0.18
190 1 0.00
195 1 0.00
196 1 0.00
197 197 0.81
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (196 bp):
ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAAACCAGTT
ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCT
GGTTTGGAAAAACCAATCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
A
Found at i:1429522 original size:114 final size:114
Alignment explanation
Indices: 1429228--1429522 Score: 491
Period size: 114 Copynumber: 2.7 Consensus size: 114
1429218 GGAATGTGCT
1429228 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-A-AACCAA
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
*
1429284 TCATTGAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
66 TCATTGAATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
1429333 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
*
1429398 TCATTAAATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
66 TCATTGAATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
*
1429447 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
*
1429512 TTATTGAATTT
66 TCATTGAATTT
1429523 GGAAGAGGAA
Statistics
Matches: 176, Mismatches: 5, Indels: 9
0.93 0.03 0.05
Matches are distributed among these distances:
105 47 0.27
107 1 0.01
112 1 0.01
113 1 0.01
114 126 0.72
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (114 bp):
AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
TCATTGAATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
Found at i:1429585 original size:311 final size:302
Alignment explanation
Indices: 1429031--1429587 Score: 997
Period size: 311 Copynumber: 1.8 Consensus size: 302
1429021 GGAATGTGCT
*
1429031 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAAAAACCAATCATTAAAT
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGAAAAACCAATCATTAAAT
*
1429096 TTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTT
66 TTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTT
*
1429161 TGAATTATCTGATCTGGTTTGGTATGAACCACATAACCAGTTATTGAATTTGGAAGAGGAATGTG
131 TGAATTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATGTG
1429226 CTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
196 CTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
1429291 ATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
261 ATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
1429333 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTT-G---G-A--A-A-AACCAA
1429398 TCATTAAATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGA
57 TCATTAAATTTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGA
*
1429463 AGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTGGAAG
122 AGTATTCTTTGAATTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTGGAAG
1429528 AGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTA
187 AGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTA
1429588 GGAACTACAG
Statistics
Matches: 242, Mismatches: 4, Indels: 9
0.95 0.02 0.04
Matches are distributed among these distances:
302 44 0.18
303 1 0.00
306 1 0.00
307 1 0.00
309 1 0.00
310 1 0.00
311 193 0.80
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (302 bp):
AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGAAAAACCAATCATTAAAT
TTAAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTT
TGAATTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATGTG
CTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
ATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
Found at i:1430021 original size:52 final size:52
Alignment explanation
Indices: 1429959--1430063 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
1429949 TATCGATATC
1429959 TGTGAAATCATCTTG-AAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATC-TGAAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
*
1430011 TGTGAAATCATCTGAAAAGGTCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTGAAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1430063 T
1 T
1430064 TAATATGTTG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 2 0.04
52 49 0.96
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (52 bp):
TGTGAAATCATCTGAAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
Found at i:1430553 original size:113 final size:113
Alignment explanation
Indices: 1430355--1431590 Score: 1913
Period size: 113 Copynumber: 11.0 Consensus size: 113
1430345 GCAAAGATTT
* *
1430355 AAATCCATCACTTGATGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1430420 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
1430468 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1430533 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
1430581 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
1430646 AATGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
1430694 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
1430759 AAGGAAGAATAAGTTCATAATGAG-AGAATTTGTTCAACCTTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCTC
* * **
1430807 AAATCCATCACTTGATGGATTAGCTTTTCCAG-AAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1430871 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
1430920 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1430985 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
1431033 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
1431098 AATGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
1431146 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
1431211 AAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCTC
* * ** * * *
1431260 AAATCCATCACTTGATGGATTAGCTTTTCCAG-AAGAAGTTCATAATGAGAAGAACTCGTTTAAA
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
* *
1431324 GAAGGAAT-AAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
65 GAAGG-ATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * **** *
1431373 AAATCCATCACTTGATGGGTCAGT-TTTTCCAGAGAAAGTTCATAATCAGAAGAACTCATCTGAA
1 AAATCTATCACTTGATGGATTA-TCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
* *
1431437 GAAGGAAT-AAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
65 GAAGG-ATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * * *
1431486 AAACCCATCACTTGGTGGGTCAGT-TTTTCCAG--AGAAGTTCATAATGAGAAAAACTCATC---
1 AAATCTATCACTTGATGGATTA-TCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGA
* * ** *
1431545 AGGA-GAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
64 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
1431591 AATGACTCTA
Statistics
Matches: 1060, Mismatches: 52, Indels: 27
0.93 0.05 0.02
Matches are distributed among these distances:
107 1 0.00
108 34 0.03
109 3 0.00
111 1 0.00
112 38 0.04
113 867 0.82
114 115 0.11
115 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Consensus pattern (113 bp):
AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:1431570 original size:20 final size:20
Alignment explanation
Indices: 1431518--1431573 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
1431508 GTTTTTCCAG
1431518 AGAAGTTCATAATGAG-A-A
1 AGAAGTTCATAATGAGAAGA
* * *
1431536 A-AA-CTCATCAGGAGAAGA
1 AGAAGTTCATAATGAGAAGA
1431554 AGAAGTTCATAATGAGAAGA
1 AGAAGTTCATAATGAGAAGA
1431574 GCTTATTCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 8 0.29
17 3 0.11
18 3 0.11
19 2 0.07
20 12 0.43
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18
Consensus pattern (20 bp):
AGAAGTTCATAATGAGAAGA
Found at i:1431828 original size:3 final size:3
Alignment explanation
Indices: 1431820--1431867 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
1431810 ATGTTATTTA
* *
1431820 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1431868 AATAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1431842 original size:15 final size:15
Alignment explanation
Indices: 1431824--1431870 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
1431814 TATTTATATT
1431824 ATTATTATTATTATA
1 ATTATTATTATTATA
1431839 ATTATTATTATTATA
1 ATTATTATTATTATA
1431854 ATTATTATTATTATA
1 ATTATTATTATTATA
1431869 AT
1 AT
1431871 AATAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATTATTATTATA
Found at i:1431872 original size:3 final size:3
Alignment explanation
Indices: 1431866--1431894 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1431856 TATTATTATT
1431866 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1431895 TATTAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1437163 original size:23 final size:23
Alignment explanation
Indices: 1437137--1437186 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1437127 GCCACTACTA
* *
1437137 ACTGAATCTTCTAGAAGCTATTG
1 ACTGAACCTTCTAAAAGCTATTG
** *
1437160 ACTGGGCCTTCTAAAAGCTGTTG
1 ACTGAACCTTCTAAAAGCTATTG
1437183 ACTG
1 ACTG
1437187 GGCGCCACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (23 bp):
ACTGAACCTTCTAAAAGCTATTG
Found at i:1437187 original size:23 final size:23
Alignment explanation
Indices: 1437144--1437189 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1437134 CTAACTGAAT
*
1437144 CTTCTAGAAGCTATTGACTGGGC
1 CTTCTAAAAGCTATTGACTGGGC
*
1437167 CTTCTAAAAGCTGTTGACTGGGC
1 CTTCTAAAAGCTATTGACTGGGC
1437190 GCCACATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
CTTCTAAAAGCTATTGACTGGGC
Found at i:1442347 original size:16 final size:16
Alignment explanation
Indices: 1442326--1442357 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1442316 TTTATTTGTC
1442326 TAAATGTCATGAAAAG
1 TAAATGTCATGAAAAG
*
1442342 TAAATGTCATGGAAAG
1 TAAATGTCATGAAAAG
1442358 CTTGATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (16 bp):
TAAATGTCATGAAAAG
Found at i:1445433 original size:242 final size:242
Alignment explanation
Indices: 1445008--1445485 Score: 938
Period size: 242 Copynumber: 2.0 Consensus size: 242
1444998 TCTTAACTTG
1445008 TTAAATAGATAGCTCATGGCAGATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
1 TTAAATAGATAGCTCATGGCAGATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
1445073 GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTAAAAGGCAGAGGATACTTAGTCATAACTC
66 GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTAAAAGGCAGAGGATACTTAGTCATAACTC
1445138 CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCAACAAAA
131 CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCAACAAAA
1445203 GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAACTCCTTA
196 GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAACTCCTTA
*
1445250 TTAAATAGATAGCTCATGGCATATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
1 TTAAATAGATAGCTCATGGCAGATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
*
1445315 GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTGAAAGGCAGAGGATACTTAGTCATAACTC
66 GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTAAAAGGCAGAGGATACTTAGTCATAACTC
1445380 CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCAACAAAA
131 CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCAACAAAA
1445445 GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAAC
196 GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAAC
1445486 CCTGTCCAAC
Statistics
Matches: 234, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
242 234 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (242 bp):
TTAAATAGATAGCTCATGGCAGATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTAAAAGGCAGAGGATACTTAGTCATAACTC
CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCAACAAAA
GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAACTCCTTA
Found at i:1447685 original size:3 final size:3
Alignment explanation
Indices: 1447677--1447816 Score: 226
Period size: 3 Copynumber: 46.3 Consensus size: 3
1447667 TATCCATATC
* * **
1447677 ATT ATT ATT AAT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT AGC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1447725 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1447773 ATT ATT ATT ATT ATT ATT ATT ATT AGT ATTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT A
1447817 ATAAATAATT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
3 124 0.98
4 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1449927 original size:18 final size:18
Alignment explanation
Indices: 1449904--1449938 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1449894 CAAATTTTTT
1449904 ATATTTATTAT-TTTTATA
1 ATATTTA-TATGTTTTATA
1449922 ATATTTATATGTTTTAT
1 ATATTTATATGTTTTAT
1449939 TTGCAAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATTTATATGTTTTATA
Found at i:1460530 original size:21 final size:21
Alignment explanation
Indices: 1460499--1460550 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
1460489 ATATATGCTT
*
1460499 GAAAAAAAAAAAAAAAAAG-A
1 GAAAAAGAAAAAAAAAAAGAA
1460519 GAAAAACG-AAAAAAAAAAGAA
1 GAAAAA-GAAAAAAAAAAAGAA
1460540 GAAAAAGAAAA
1 GAAAAAGAAAA
1460551 GGGTCAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAAAAGAA
Found at i:1461457 original size:52 final size:52
Alignment explanation
Indices: 1461390--1461805 Score: 780
Period size: 52 Copynumber: 8.0 Consensus size: 52
1461380 CACTCGAAGA
1461390 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1461442 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1461494 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1461546 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1461598 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1461650 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
1461702 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1461754 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAC
1461806 CAATCATTGA
Statistics
Matches: 355, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
52 352 0.99
53 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:1461911 original size:50 final size:50
Alignment explanation
Indices: 1461836--1461973 Score: 276
Period size: 50 Copynumber: 2.8 Consensus size: 50
1461826 TGAATTTGCC
1461836 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1461886 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1461936 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1461974 ATGGTTTGGT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 88 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:1462814 original size:118 final size:118
Alignment explanation
Indices: 1462624--1463155 Score: 846
Period size: 118 Copynumber: 4.6 Consensus size: 118
1462614 CATCATTTGG
**
1462624 TGGATCATTTTTTCCAGAG-AA-AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
*
1462687 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAGA
66 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACCAGA
1462740 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
**
1462805 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGA
66 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACCAGA
*
1462858 TGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
*
1462923 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAGA
66 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACCAGA
*
1462976 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTAGTCATCTGAAGAAGGAAGAAG
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
* ***
1463041 AAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGA
66 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACCAGA
* ** * *
1463094 TGGAACATCATCCCCAGCAG-AA-AGTT-ATAATGAGAAGAA-AC-TCATCTGAAGAA-AAAGAA
1 TGGATCATCATTTCCAG-AGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAA
1463153 GAA
65 GAA
1463156 TTTATTCAAT
Statistics
Matches: 391, Mismatches: 22, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
113 8 0.02
114 12 0.03
116 30 0.08
117 6 0.02
118 333 0.85
119 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (118 bp):
TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACCAGA
Found at i:1463309 original size:3 final size:3
Alignment explanation
Indices: 1463295--1463399 Score: 147
Period size: 3 Copynumber: 34.3 Consensus size: 3
1463285 TATCCATATC
* * **
1463295 ATT ATT AAT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT AGC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1463343 ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATTT ATT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
1463390 ATT ATT ATT A
1 ATT ATT ATT A
1463400 ATAAATAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
3 85 0.94
4 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1464772 original size:20 final size:20
Alignment explanation
Indices: 1464728--1464772 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1464718 ACTTTTAAAA
1464728 ATATTGTTCTAATTGTATTT
1 ATATTGTTCTAATTGTATTT
* *
1464748 TTATTGTTTTAATTGT-TTAT
1 ATATTGTTCTAATTGTATT-T
1464768 ATATT
1 ATATT
1464773 TAAATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.24, C:0.02, G:0.09, T:0.64
Consensus pattern (20 bp):
ATATTGTTCTAATTGTATTT
Found at i:1469663 original size:15 final size:15
Alignment explanation
Indices: 1469614--1469664 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1469604 ATTTTTTTAA
1469614 TTTAATTACT-TAAC
1 TTTAATTACTCTAAC
1469628 TTTCAAGTTACTCCTAA-
1 TTT-AA-TTACT-CTAAC
*
1469645 TTTAATCACTCTAAC
1 TTTAATTACTCTAAC
1469660 TTTAA
1 TTTAA
1469665 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 7 0.23
15 11 0.35
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.45
Consensus pattern (15 bp):
TTTAATTACTCTAAC
Found at i:1472509 original size:50 final size:50
Alignment explanation
Indices: 1472404--1472510 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 50
1472394 TCACACTTCA
* * * * * *
1472404 ATTTGCCTTTTCATTGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGT
1 ATTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
*
1472454 GTTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACATTATCCATC-T
1 ATTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAGAGACA-TAT-CATCGT
1472504 ATTTTCC
1 ATTTTCC
1472511 GCAAATCCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
49 3 0.06
50 41 0.87
51 3 0.06
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (50 bp):
ATTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
Found at i:1472642 original size:3 final size:3
Alignment explanation
Indices: 1472634--1472765 Score: 239
Period size: 3 Copynumber: 43.7 Consensus size: 3
1472624 TTTCGTCCCG
1472634 TTA TTA TTA GGTTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA --TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1472680 TTA TTA TTA TTA 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
1472728 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1472766 TAAGATTACT
Statistics
Matches: 126, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.02
3 121 0.96
5 3 0.02
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1473337 original size:2 final size:2
Alignment explanation
Indices: 1473330--1473385 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1473320 CTTGCATACA
1473330 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
1473372 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1473386 GCGAGTCTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1474467 original size:2 final size:2
Alignment explanation
Indices: 1474460--1474496 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1474450 ATTTACATAA
1474460 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 A
1474497 ATTTATGCAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1486323 original size:25 final size:23
Alignment explanation
Indices: 1486281--1486344 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 23
1486271 GTATTTTGCC
* *
1486281 TGAAAAGGAAATGAAAAGATTAAAA
1 TGAAAAAGAAAAGAAAAGA--AAAA
*
1486306 TGAAAAAGAAAAGGAAAGAAAAA
1 TGAAAAAGAAAAGAAAAGAAAAA
**
1486329 TGAGGAA-AAAAGAAAA
1 TGAAAAAGAAAAGAAAA
1486345 ATAAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 8 0.24
23 9 0.27
25 16 0.48
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (23 bp):
TGAAAAAGAAAAGAAAAGAAAAA
Found at i:1486355 original size:27 final size:27
Alignment explanation
Indices: 1486308--1486360 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1486298 GATTAAAATG
* *
1486308 AAAAAGAAAAGGAAAGAAAAATGAGGA
1 AAAAAGAAAAAGAAAGAAAAAGGAGGA
*
1486335 AAAAAGAAAAATAAA-ATAAAAGGAGG
1 AAAAAGAAAAAGAAAGA-AAAAGGAGG
1486361 GTTTAAGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.06
Consensus pattern (27 bp):
AAAAAGAAAAAGAAAGAAAAAGGAGGA
Found at i:1487782 original size:111 final size:111
Alignment explanation
Indices: 1487588--1487900 Score: 441
Period size: 111 Copynumber: 2.8 Consensus size: 111
1487578 GTGACAGCGG
* * *
1487588 AATGGATCAACTCCTCTAGATCTGATATTCCCTTAGAAGAAGTGAAACAGATCAC-CATATTCCA
1 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACATATCACTC-TATTCCA
* *
1487652 AGATTTGATATTCCTTGAGTAACAGCAGAACAAGTCTACCCCGATTC
65 AGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCGATTC
**
1487699 AATGGATTGACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACATATCACTCTATTCCAA
1 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACATATCACTCTATTCCAA
*
1487764 GATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCTGATTC
66 GATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCGATTC
* * * * * *
1487810 AATGGATCAACTCCCCCAAATATGATATTCCCTTTAGAAGAAGCGGAACATATCCCTCTCATCCC
1 AATGGATCAACTCCTCCAGATCTGATATTCCC-TTAGAAGAAGTGGAACATATCACTCT-ATTCC
*
1487875 CAGATTTGATA-TCCCTTGAGTGACAG
64 AAGATTTGATATTCCC-TGAGTGACAG
1487901 TGGAACTGAT
Statistics
Matches: 181, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
111 128 0.71
112 29 0.16
113 24 0.13
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (111 bp):
AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACATATCACTCTATTCCAA
GATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCGATTC
Found at i:1488633 original size:2 final size:2
Alignment explanation
Indices: 1488626--1488703 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
1488616 TTTGCATACA
1488626 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
*
1488668 AT AT AG 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
1488704 GCGAGTCTAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1489609 original size:2 final size:2
Alignment explanation
Indices: 1489602--1489895 Score: 216
Period size: 2 Copynumber: 155.5 Consensus size: 2
1489592 TTTTGTAAGG
1489602 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
1489643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1489684 AT TT AGT GT AT -T AT AT AT AT AA AT AT AT AT AT AT AT AA AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1489726 AT AT A- AT AT AT AT -T AT AT AGT AT GT AG A- AT GT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* ** *
1489766 -T TT AT -T CC AT AT -T AT A- AT AT AT AT A- AT AGC AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* ** * * * *
1489803 AC AT GC GT A- AC ACT -T AT AT GT AT AT AT AT A- AT -T AT -T TT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1489841 AT -T A- AT TT AC AT A- 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
1489880 AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1489896 ATTTATGCAT
Statistics
Matches: 233, Mismatches: 34, Indels: 50
0.74 0.11 0.16
Matches are distributed among these distances:
1 21 0.09
2 208 0.89
3 4 0.02
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1499743 original size:24 final size:20
Alignment explanation
Indices: 1499689--1499726 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1499679 TTCCCATTGA
*
1499689 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1499709 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
1499727 TTAACAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1501865 original size:15 final size:15
Alignment explanation
Indices: 1501842--1501917 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
1501832 ATGATTATGC
*
1501842 ATAACGTCACCATAT
1 ATAATGTCACCATAT
1501857 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
* * **
1501871 ATAGTGGCAAAACTA-
1 ATAATGTCACCA-TAT
*
1501886 AAAATTGTCACCATAT
1 ATAA-TGTCACCATAT
1501902 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
1501916 AT
1 AT
1501918 CGTTTTGTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
14 14 0.30
15 23 0.50
16 9 0.20
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (15 bp):
ATAATGTCACCATAT
Found at i:1526981 original size:27 final size:27
Alignment explanation
Indices: 1526943--1526996 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1526933 TTTGATTGTG
** *
1526943 AATGACATTGTCGTGGCAAGTAGAGTT
1 AATGACATTGTCGCAGCAAGTAAAGTT
1526970 AATGACATTGTCGCAGCAAGTAAAGTT
1 AATGACATTGTCGCAGCAAGTAAAGTT
1526997 GCCAAGACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (27 bp):
AATGACATTGTCGCAGCAAGTAAAGTT
Found at i:1529871 original size:19 final size:19
Alignment explanation
Indices: 1529849--1529903 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
1529839 CTAATTAACC
* *
1529849 TGACTTAACCCATTGACTT
1 TGACCTAACCCGTTGACTT
* *
1529868 TGACCCAACTCGTTGACTT
1 TGACCTAACCCGTTGACTT
*
1529887 TGACCTGACCCGTTGAC
1 TGACCTAACCCGTTGAC
1529904 CGTTGACTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (19 bp):
TGACCTAACCCGTTGACTT
Found at i:1531109 original size:15 final size:16
Alignment explanation
Indices: 1531079--1531109 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1531069 GTTCATAAGC
1531079 CAGTAAATCAATAAAT
1 CAGTAAATCAATAAAT
1531095 CAGTAAATC-ATAAAT
1 CAGTAAATCAATAAAT
1531110 TTTTGTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (16 bp):
CAGTAAATCAATAAAT
Found at i:1531282 original size:4 final size:4
Alignment explanation
Indices: 1531273--1531307 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1531263 AGTGTGTACA
* *
1531273 TATG TATG TATG TATG TATG TATG AATG CATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1531308 CAAGTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:1541330 original size:6 final size:6
Alignment explanation
Indices: 1541320--1541401 Score: 67
Period size: 6 Copynumber: 13.2 Consensus size: 6
1541310 CCCTTAACTT
* * * **
1541320 CCTTTC TCTTTC TCTTTC CCTCTC CCTTT- GTTTCTC CCTTTC CCTTTC
1 CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTT-TC CCTTTC CCTTTC
*
1541368 TCTCTTCTC CCTTTC TCTTTC CCTTTC CCTTTC C
1 -C-CTT-TC CCTTTC CCTTTC CCTTTC CCTTTC C
1541402 TTCTCCCTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
5 2 0.03
6 47 0.77
7 6 0.10
8 4 0.07
9 2 0.03
ACGTcount: A:0.00, C:0.45, G:0.01, T:0.54
Consensus pattern (6 bp):
CCTTTC
Found at i:1541347 original size:51 final size:51
Alignment explanation
Indices: 1541290--1541409 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 51
1541280 CACTGTCATG
*
1541290 CTCCCTTCGCTTCTCCCTTTCCCTTAACT-TCCTT-TCTCTTTCTCTTTCCCT
1 CTCCCTTCGCTTCTCCCTTTCCCTT-ACTCT-CTTCTCCCTTTCTCTTTCCCT
* * *
1541341 CTCCCTTTGTTTCTCCCTTTCCCTTTCTCTCTTCTCCCTTTCTCTTTCCCT
1 CTCCCTTCGCTTCTCCCTTTCCCTTACTCTCTTCTCCCTTTCTCTTTCCCT
*
1541392 TTCCCTTTC-CTTCTCCCT
1 CTCCC-TTCGCTTCTCCCT
1541410 AGCTCTTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
50 5 0.08
51 52 0.88
52 2 0.03
ACGTcount: A:0.02, C:0.46, G:0.02, T:0.51
Consensus pattern (51 bp):
CTCCCTTCGCTTCTCCCTTTCCCTTACTCTCTTCTCCCTTTCTCTTTCCCT
Found at i:1541377 original size:21 final size:19
Alignment explanation
Indices: 1541303--1541401 Score: 78
Period size: 18 Copynumber: 5.2 Consensus size: 19
1541293 CCTTCGCTTC
*
1541303 TCCCTTTCCCTTAACTTCCTT
1 TCCCTTTCCCTT--CTCCCTT
* * *
1541324 TCTCTTTCTCTT-TCCCTC
1 TCCCTTTCCCTTCTCCCTT
**
1541342 TCCCTTT-GTTTCTCCCTT
1 TCCCTTTCCCTTCTCCCTT
1541360 TCCCTTTCTCTCTTCTCCCTT
1 TCCCTTTC-C-CTTCTCCCTT
*
1541381 TCTCTTTCCCTT-TCCCTT
1 TCCCTTTCCCTTCTCCCTT
1541399 TCC
1 TCC
1541402 TTCTCCCTAG
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
17 2 0.03
18 30 0.48
19 3 0.05
20 1 0.02
21 26 0.42
ACGTcount: A:0.02, C:0.44, G:0.01, T:0.53
Consensus pattern (19 bp):
TCCCTTTCCCTTCTCCCTT
Found at i:1541380 original size:15 final size:14
Alignment explanation
Indices: 1541350--1541394 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1541340 TCTCCCTTTG
*
1541350 TTTCTCCCTTTCCC
1 TTTCTCTCTTTCCC
1541364 TTTCTCTCTTCTCCC
1 TTTCTCTCTT-TCCC
1541379 -TT-TCTCTTTCCC
1 TTTCTCTCTTTCCC
1541391 TTTC
1 TTTC
1541395 CCTTTCCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 4 0.15
13 8 0.30
14 11 0.41
15 4 0.15
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTCTCTCTTTCCC
Found at i:1541416 original size:30 final size:31
Alignment explanation
Indices: 1541354--1541438 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 31
1541344 CCTTTGTTTC
**
1541354 TCCCTTTCCCTTTCTCTCTTCTCCCTTTCTCTT
1 TCCCTTTCCC-TTCTC-CTTCTCCCTAGCTCTT
1541387 TCCCTTTCCCTT-TCCTTCTCCCTAGCTCTT
1 TCCCTTTCCCTTCTCCTTCTCCCTAGCTCTT
* *
1541417 TCCCTCT-CCTTCTCTTTCTCCC
1 TCCCTTTCCCTTCTCCTTCTCCC
1541439 GTTCCCTGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 4 0.09
30 29 0.62
31 2 0.04
32 2 0.04
33 10 0.21
ACGTcount: A:0.01, C:0.48, G:0.01, T:0.49
Consensus pattern (31 bp):
TCCCTTTCCCTTCTCCTTCTCCCTAGCTCTT
Found at i:1541418 original size:51 final size:51
Alignment explanation
Indices: 1541327--1541423 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
1541317 CTTCCTTTCT
** ** *
1541327 CTTTCTCTTTCCCTCTCCCTTTGTTTCTCCCTTTCCCTTTCTCTCTTCTCC
1 CTTTCTCTTTCCCTCTCCCTTTCCTTCTCCCTAGCCCTTTCCCTCTTCTCC
* *
1541378 CTTTCTCTTTCCCTTTCCCTTTCCTTCTCCCTAGCTCTTTCCCTCT
1 CTTTCTCTTTCCCTCTCCCTTTCCTTCTCCCTAGCCCTTTCCCTCT
1541424 CCTTCTCTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.01, C:0.45, G:0.02, T:0.52
Consensus pattern (51 bp):
CTTTCTCTTTCCCTCTCCCTTTCCTTCTCCCTAGCCCTTTCCCTCTTCTCC
Found at i:1541577 original size:75 final size:75
Alignment explanation
Indices: 1541477--1541769 Score: 390
Period size: 75 Copynumber: 3.9 Consensus size: 75
1541467 TTCACGGTGT
* * * * * *
1541477 TTTTCTTTCTCCTTCTCCTTCTCTCTATCGGAATCACTGCTCTTCTCTCTCTCAGAGCGGCGCCG
1 TTTTCTTTGTCCCTCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCCCTCTCAGAACGACGCCG
1541542 TTCTCGATTC
66 TTCTCGATTC
* * *
1541552 TTTTCTTTTTCCCTCTCTTTTTCTCTATCGGAATCACTGCTCTTCTCCCTCTCAGAAAGACGCCG
1 TTTTCTTTGTCCCTCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCCCTCTCAGAACGACGCCG
1541617 TTCTCG-TTGC
66 TTCTCGATT-C
* * * *
1541627 TTTTCCTTGTCCCTTTCCTTTTCTCTATCGGAATCACTGCTCTTATCCCTCTCGGAACGACGCCG
1 TTTTCTTTGTCCCTCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCCCTCTCAGAACGACGCCG
* *
1541692 TTCACGATGC
66 TTCTCGATTC
* * * * *
1541702 TTTTCTCTGTCCCTTTCCTTTTCTCTATCGGAATCGCCGCTCTTCTCCCTCTCGGAACGACGCCG
1 TTTTCTTTGTCCCTCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCCCTCTCAGAACGACGCCG
1541767 TTC
66 TTC
1541770 CTTATCCCTA
Statistics
Matches: 194, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
74 2 0.01
75 191 0.98
76 1 0.01
ACGTcount: A:0.11, C:0.35, G:0.14, T:0.40
Consensus pattern (75 bp):
TTTTCTTTGTCCCTCTCCTTTTCTCTATCGGAATCACTGCTCTTCTCCCTCTCAGAACGACGCCG
TTCTCGATTC
Found at i:1542112 original size:6 final size:7
Alignment explanation
Indices: 1542094--1542119 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1542084 TTTTTAAAAC
1542094 ATTTTTT
1 ATTTTTT
1542101 ATTTTTT
1 ATTTTTT
1542108 ATTTTTT
1 ATTTTTT
1542115 ATTTT
1 ATTTT
1542120 AGGGTAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:1555022 original size:35 final size:35
Alignment explanation
Indices: 1554924--1555223 Score: 242
Period size: 35 Copynumber: 8.5 Consensus size: 35
1554914 TTTTTAAAAA
* * *
1554924 AAAACATATAATATATAGTTTTTAAAAAAACTGTTTTTG
1 AAAACATATATTATAT-GTTTTT--GAAAAC-ATTTTTG
*
1554963 AAAACATATATAATATATATTTTTGAAAACATTTTTG
1 AAAACATATAT--TATATGTTTTTGAAAACATTTTTG
* *
1555000 AAAACGTATATTATATGTTTTTGAAAACATGTTTG
1 AAAACATATATTATATGTTTTTGAAAACATTTTTG
* *
1555035 AAAACATATAGTATATGGTTTTGAAAACATTTTTG
1 AAAACATATATTATATGTTTTTGAAAACATTTTTG
*
1555070 AAAAC----A-TATA-G-CTTTGAAAACATTTTTG
1 AAAACATATATTATATGTTTTTGAAAACATTTTTG
* * *
1555098 AAAATGTATATAATATATAG-TTTTGAAAACTTTTTTG
1 AAAA--CATATATTATAT-GTTTTTGAAAACATTTTTG
* * ** *
1555135 AAAACGTATATAATATAATTTTGAAAACGTATTTTG
1 AAAACATATATTATATGTTTTTGAAAACAT-TTTTG
*
1555171 AAAACATATA-TATATGTTTTTTTAAAACGAATTTTTG
1 AAAACATATATTATATG-TTTTTGAAAAC--ATTTTTG
1555208 AAAACATA-ATATATAT
1 AAAACATATAT-TATAT
1555224 TATATACTTA
Statistics
Matches: 216, Mismatches: 27, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
28 20 0.09
29 1 0.00
30 4 0.02
31 1 0.00
34 1 0.00
35 85 0.39
36 24 0.11
37 49 0.23
38 11 0.05
39 10 0.05
40 5 0.02
41 5 0.02
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (35 bp):
AAAACATATATTATATGTTTTTGAAAACATTTTTG
Found at i:1555070 original size:12 final size:12
Alignment explanation
Indices: 1555053--1555101 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 12
1555043 TAGTATATGG
1555053 TTTTGAAAACAT
1 TTTTGAAAACAT
1555065 TTTTGAAAACAT
1 TTTTGAAAACAT
1555077 ATAGCTTTGAAAACAT
1 -T---TTTGAAAACAT
1555093 TTTTGAAAA
1 TTTTGAAAA
1555102 TGTATATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 20 0.61
13 1 0.03
15 1 0.03
16 11 0.33
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:1555099 original size:135 final size:136
Alignment explanation
Indices: 1554957--1555215 Score: 380
Period size: 135 Copynumber: 1.9 Consensus size: 136
1554947 AAAAAAACTG
* * **
1554957 TTTTTGAAAACATATATAATATATATTTTTGAAAACATTTTTGAAAACGTATATTATATGTTTTT
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTTGAAAACGTATATAATATAATTTT
1555022 GAAAAC-ATGTTTGAAAACATATAGTATATG-GTTTTGAAAAC-ATTTTTGAAAACATATAGCTT
66 GAAAACGAT-TTTGAAAACATATA-TATATGTGTTTTGAAAACAATTTTTGAAAACATATAGCTT
1555084 TGAAAACA
129 TGAAAACA
** *
1555092 TTTTTGAAAATGTATATAATATATAGTTTTGAAAACTTTTTTGAAAACGTATATAATATAATTTT
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTTGAAAACGTATATAATATAATTTT
* *
1555157 GAAAACGTATTTTGAAAACATATATATATGTTTTTTTAAAACGAATTTTTGAAAACATA
66 GAAAACG-ATTTTGAAAACATATATATATGTGTTTTGAAAAC-AATTTTTGAAAACATA
1555216 ATATATATTA
Statistics
Matches: 110, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
135 70 0.64
136 23 0.21
137 2 0.02
138 15 0.14
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (136 bp):
TTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTTGAAAACGTATATAATATAATTTT
GAAAACGATTTTGAAAACATATATATATGTGTTTTGAAAACAATTTTTGAAAACATATAGCTTTG
AAAACA
Found at i:1555134 original size:65 final size:63
Alignment explanation
Indices: 1555019--1555144 Score: 180
Period size: 65 Copynumber: 2.0 Consensus size: 63
1555009 ATTATATGTT
* *
1555019 TTTGAAAACATGTTTGAAAACATATAGTATATGGTTTTGAAAACATTTTTGAAAACATATAGC
1 TTTGAAAACATGTTTGAAAACATATAATATATAGTTTTGAAAACATTTTTGAAAACATATAGC
* * * *
1555082 TTTGAAAACATTTTTGAAAATGTATATAATATATAGTTTTGAAAACTTTTTTGAAAACGTATA
1 TTTGAAAACATGTTTGAAAA--CATATAATATATAGTTTTGAAAACATTTTTGAAAACATATA
1555145 TAATATAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 19 0.35
65 36 0.65
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (63 bp):
TTTGAAAACATGTTTGAAAACATATAATATATAGTTTTGAAAACATTTTTGAAAACATATAGC
Found at i:1555157 original size:100 final size:99
Alignment explanation
Indices: 1554984--1555180 Score: 274
Period size: 100 Copynumber: 2.0 Consensus size: 99
1554974 AATATATATT
1554984 TTTGAAAACATTTTTGAAAACGTATATTATATGTTTTTGAAAACATGTTTGAAAACATATAGTAT
1 TTTGAAAACATTTTTGAAAACGTATATTATATGTTTTTGAAAACATGTTTGAAAACATATAGTAT
**
1555049 ATGGTTTTGAAAACAT-TTTTGAAAACATATAGC
66 ATAATTTTGAAAACATATTTTGAAAACATATAGC
* * * *
1555082 TTTGAAAACATTTTTGAAAATGTATATAATATATAG-TTTTGAAAACTTTTTTGAAAACGTATA-
1 TTTGAAAACATTTTTGAAAACGTATAT--TATAT-GTTTTTGAAAACATGTTTGAAAACATATAG
*
1555145 TAATATAATTTTGAAAACGTATTTTGAAAACATATA
63 T-ATATAATTTTGAAAACATATTTTGAAAACATATA
1555181 TATATGTTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
98 26 0.30
99 1 0.01
100 44 0.51
101 16 0.18
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.41
Consensus pattern (99 bp):
TTTGAAAACATTTTTGAAAACGTATATTATATGTTTTTGAAAACATGTTTGAAAACATATAGTAT
ATAATTTTGAAAACATATTTTGAAAACATATAGC
Found at i:1555181 original size:36 final size:36
Alignment explanation
Indices: 1555082--1555220 Score: 131
Period size: 37 Copynumber: 3.8 Consensus size: 36
1555072 AACATATAGC
* **
1555082 TTTGAAAACAT-TTTTGAAAATGTATATAATATATAGT
1 TTTGAAAACGTATTTTGAAAACATATATAATATA-A-T
* *
1555119 TTTGAAAAC-TTTTTTGAAAACGTATATAATATAAT
1 TTTGAAAACGTATTTTGAAAACATATATAATATAAT
**
1555154 TTTGAAAACGTATTTTGAAAACATATAT-ATATGTTT
1 TTTGAAAACGTATTTTGAAAACATATATAATAT-AAT
* *
1555190 TTTTAAAACGAATTTTTGAAAACATAATATA
1 TTTGAAAACGTA-TTTTGAAAACAT-ATATA
1555221 TATTATATAC
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
35 14 0.16
36 29 0.33
37 42 0.47
38 4 0.04
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.42
Consensus pattern (36 bp):
TTTGAAAACGTATTTTGAAAACATATATAATATAAT
Found at i:1555236 original size:8 final size:7
Alignment explanation
Indices: 1555217--1555340 Score: 51
Period size: 7 Copynumber: 17.1 Consensus size: 7
1555207 GAAAACATAA
1555217 TATATAT
1 TATATAT
1555224 TATATACT
1 TATATA-T
*
1555232 TATATTT
1 TATATAT
*
1555239 TATATGT
1 TATATAT
1555246 TCATATAT
1 T-ATATAT
*
1555254 TTTCATTACCT
1 TAT-A-TA--T
1555265 TATATAT
1 TATATAT
1555272 TATAT-T
1 TATATAT
* *
1555278 AATACCAT
1 TATA-TAT
1555286 T-TATAT
1 TATATAT
*
1555292 TATTTAT
1 TATATAT
1555299 TA-AT-T
1 TATATAT
* *
1555304 TTTTTAT
1 TATATAT
1555311 TATTATAT
1 TA-TATAT
1555319 TCATATA-
1 T-ATATAT
1555326 TATATAT
1 TATATAT
*
1555333 TATTTAT
1 TATATAT
1555340 T
1 T
1555341 TATTTTCAGG
Statistics
Matches: 87, Mismatches: 16, Indels: 28
0.66 0.12 0.21
Matches are distributed among these distances:
5 2 0.02
6 14 0.16
7 39 0.45
8 23 0.26
9 5 0.06
10 1 0.01
11 3 0.03
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (7 bp):
TATATAT
Found at i:1555332 original size:41 final size:43
Alignment explanation
Indices: 1555264--1555346 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 43
1555254 TTTCATTACC
*
1555264 TTATATATTATATTAATACCATTTATATTATTTATTAATTTTT
1 TTATATATTATATTAATACCATATATATTATTTATTAATTTTT
* * *
1555307 TTAT-TATTATATTCATA-TATATATATTATTTATTTATTTT
1 TTATATATTATATTAATACCATATATATTATTTATTAATTTT
1555347 CAGGTCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 20 0.56
42 12 0.33
43 4 0.11
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.63
Consensus pattern (43 bp):
TTATATATTATATTAATACCATATATATTATTTATTAATTTTT
Found at i:1557939 original size:17 final size:17
Alignment explanation
Indices: 1557912--1557950 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1557902 AATTTACAAT
1557912 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
1557928 TAATTATAAATAATATC
1 TAATTATAAATAATATC
1557945 TAATTA
1 TAATTA
1557951 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:1558433 original size:16 final size:16
Alignment explanation
Indices: 1558412--1558444 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1558402 AAAGTGAATG
1558412 CCAAATTGGGAAGGGC
1 CCAAATTGGGAAGGGC
1558428 CCAAATTGGGAAGGGC
1 CCAAATTGGGAAGGGC
1558444 C
1 C
1558445 TTATATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.21, G:0.36, T:0.12
Consensus pattern (16 bp):
CCAAATTGGGAAGGGC
Found at i:1559767 original size:25 final size:25
Alignment explanation
Indices: 1559714--1559771 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 25
1559704 TTGAAGGTTT
*
1559714 TTTTTTTCTCACTTAAAGATTTATA
1 TTTTTTCCTCACTTAAAGATTTATA
1559739 -TTTTTCCTCACTTAAAGATTTATA
1 TTTTTTCCTCACTTAAAGATTTATA
1559763 TTTTTTCCT
1 TTTTTTCCT
1559772 GGATTCCTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 23 0.74
25 8 0.26
ACGTcount: A:0.24, C:0.16, G:0.03, T:0.57
Consensus pattern (25 bp):
TTTTTTCCTCACTTAAAGATTTATA
Found at i:1569735 original size:36 final size:36
Alignment explanation
Indices: 1569695--1569831 Score: 220
Period size: 36 Copynumber: 3.8 Consensus size: 36
1569685 GGTGCTGGAC
*
1569695 ATTGATACACGAATGTACCAAAGCTGATAGGATAAT
1 ATTGATACACGAATGTACCAAAGCTGATATGATAAT
* *
1569731 ATTGATAAATGAATGTACCAAAGCTGATATGATAAT
1 ATTGATACACGAATGTACCAAAGCTGATATGATAAT
* *
1569767 ATTGATACACGAATGTTCCAAAGCTGATATGATAAC
1 ATTGATACACGAATGTACCAAAGCTGATATGATAAT
*
1569803 ATTGATACACGAATGTGCCAAAGCTGATA
1 ATTGATACACGAATGTACCAAAGCTGATA
1569832 ATACTTAATT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (36 bp):
ATTGATACACGAATGTACCAAAGCTGATATGATAAT
Found at i:1579089 original size:25 final size:25
Alignment explanation
Indices: 1579036--1579134 Score: 64
Period size: 24 Copynumber: 4.0 Consensus size: 25
1579026 CCTTTGATTT
*
1579036 CTTTTTGTTCATTTATTTATTTATA
1 CTTTTTGTTAATTTATTTATTTATA
*
1579061 CTTTTT-TTAATTT-TTTAATTTTTA
1 CTTTTTGTTAATTTATTT-ATTTATA
* **
1579085 GCTTTTTCTTTCTTTTGATTTATTTAGTA
1 -CTTTTT-GTTAATTT-ATTTATTTA-TA
*
1579114 -TTTAT-TT-ATTTATTTATTTAT
1 CTTTTTGTTAATTTATTTATTTAT
1579135 TTTCTCTAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
22 1 0.02
23 12 0.20
24 15 0.25
25 14 0.23
27 9 0.15
28 4 0.07
29 5 0.08
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (25 bp):
CTTTTTGTTAATTTATTTATTTATA
Found at i:1579109 original size:4 final size:4
Alignment explanation
Indices: 1579102--1579136 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1579092 CTTTCTTTTG
*
1579102 ATTT ATTT A-GT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1579137 TCTCTAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 26 0.93
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:1582066 original size:14 final size:12
Alignment explanation
Indices: 1582041--1582102 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 12
1582031 AATCAGAACA
1582041 AAAAGAAAAAGAG
1 AAAA-AAAAAGAG
1582054 AAAAAAATGAAGA-
1 AAAAAAA--AAGAG
1582067 AAAAAGAAAAGAG
1 AAAAA-AAAAGAG
1582080 AAAATAAAAAAGAG
1 -AAA-AAAAAAGAG
1582094 AAACAAAAA
1 AAA-AAAAA
1582103 CAAAGGAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
12 7 0.17
13 17 0.40
14 16 0.38
15 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:1582092 original size:26 final size:27
Alignment explanation
Indices: 1582040--1582128 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
1582030 AAATCAGAAC
*
1582040 AAAAAGAAAAAGAGAAAAAAATGAAGA
1 AAAAAGAAAAAGAGAAAAAAATAAAGA
1582067 AAAAAG-AAAAGAGAAAATAAA-AAAGA
1 AAAAAGAAAAAGAGAAAA-AAATAAAGA
* *
1582093 GAAACAA-AAACAA-AGGAAAAAGTAAAGA
1 -AAA-AAGAAA-AAGAGAAAAAAATAAAGA
1582121 AAAAAGAA
1 AAAAAGAA
1582129 GACAAGACGC
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
26 17 0.33
27 19 0.37
28 14 0.27
29 2 0.04
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAAAAAAATAAAGA
Found at i:1582114 original size:42 final size:40
Alignment explanation
Indices: 1582046--1582125 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 40
1582036 GAACAAAAAG
** *
1582046 AAAAAGAGAAAAAAATGAAGAAAAAAGAAAAGAGAAAATA
1 AAAAAGAGAAAAAAACAAAGAAAAAAGAAAAGAAAAAATA
* *
1582086 AAAAAGAGAAACAAAAACAAAGGAAAAAGTAAAGAAAAAA
1 AAAAAGAG-AA-AAAAACAAAGAAAAAAGAAAAGAAAAAA
1582126 GAAGACAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 8 0.24
41 2 0.06
42 23 0.70
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.04
Consensus pattern (40 bp):
AAAAAGAGAAAAAAACAAAGAAAAAAGAAAAGAAAAAATA
Found at i:1583097 original size:21 final size:21
Alignment explanation
Indices: 1583053--1583097 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1583043 GATTTCTGGG
* * *
1583053 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
1583074 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1583095 CAA
1 CAA
1583098 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1583635 original size:14 final size:14
Alignment explanation
Indices: 1583616--1583651 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1583606 ACATGTGATA
*
1583616 TACATGATATGAAT
1 TACATGAAATGAAT
*
1583630 TACATGAAATGATT
1 TACATGAAATGAAT
1583644 TACATGAA
1 TACATGAA
1583652 TACATGTATA
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:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (14 bp):
TACATGAAATGAAT
Found at i:1583862 original size:31 final size:30
Alignment explanation
Indices: 1583823--1583888 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1583813 GTCGAGGGTT
**
1583823 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAACGA-ACATATGGACAG
*
1583853 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAACGAACATATGGACAG
1583884 TTACC
1 TTACC
1583889 GAGGATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAG
Found at i:1584002 original size:29 final size:30
Alignment explanation
Indices: 1583877--1583999 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
1583867 AAGGAACATA
1583877 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1583907 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1583937 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
1583967 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1583996 TGGA
1 TGGA
1584000 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1588115 original size:21 final size:21
Alignment explanation
Indices: 1588071--1588115 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1588061 GATTTCTGGG
* *
1588071 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCACT
*
1588092 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1588113 CAA
1 CAA
1588116 ACGAACATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1588654 original size:14 final size:14
Alignment explanation
Indices: 1588635--1588670 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1588625 ACATGTGATA
*
1588635 TACATGATATGAAT
1 TACATGAAATGAAT
*
1588649 TACATGAAATGATT
1 TACATGAAATGAAT
1588663 TACATGAA
1 TACATGAA
1588671 TACATGTATA
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:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (14 bp):
TACATGAAATGAAT
Found at i:1588882 original size:31 final size:30
Alignment explanation
Indices: 1588843--1588908 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1588833 GTCGAGGGTT
**
1588843 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAACGA-ACATATGGACAG
*
1588873 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAACGAACATATGGACAG
1588904 TTACC
1 TTACC
1588909 GAGGATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAG
Found at i:1589022 original size:29 final size:30
Alignment explanation
Indices: 1588897--1589019 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
1588887 AAGGAACATA
1588897 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1588927 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1588957 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
1588987 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1589016 TGGA
1 TGGA
1589020 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1593670 original size:14 final size:14
Alignment explanation
Indices: 1593651--1593686 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1593641 ACATGTGATA
*
1593651 TACATGATATGAAT
1 TACATGAAATGAAT
*
1593665 TACATGAAATGATT
1 TACATGAAATGAAT
1593679 TACATGAA
1 TACATGAA
1593687 TACATGTATA
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:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (14 bp):
TACATGAAATGAAT
Found at i:1593898 original size:31 final size:30
Alignment explanation
Indices: 1593859--1593924 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1593849 GTCGAGGGTT
**
1593859 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAACGA-ACATATGGACAG
*
1593889 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAACGAACATATGGACAG
1593920 TTACC
1 TTACC
1593925 GAGGATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAG
Found at i:1594038 original size:29 final size:30
Alignment explanation
Indices: 1593913--1594035 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
1593903 AAGGAACATA
1593913 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1593943 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1593973 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
1594003 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1594032 TGGA
1 TGGA
1594036 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1596476 original size:30 final size:31
Alignment explanation
Indices: 1596440--1596502 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1596430 AGAGGTCACA
1596440 AAGAACCT-CG-ACAACTGTCCATAAGTCTCG
1 AAGAACCTACGTA-AACTGTCCATAAGTCTCG
* *
1596470 AAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAGAACCTACGTAAACTGTCCATAAGTCTCG
1596501 AA
1 AA
1596503 AGACATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 8 0.28
31 20 0.69
32 1 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (31 bp):
AAGAACCTACGTAAACTGTCCATAAGTCTCG
Found at i:1596515 original size:31 final size:31
Alignment explanation
Indices: 1596452--1596516 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1596442 GAACCTCGAC
* *
1596452 AACTGTCCATAAGTCTCGAAGAACCTAGGTA
1 AACTGTCCATAAGTCTCGAAGAACATAAGTA
*
1596483 AACTGTCCATATGTCTCGAA-AGACATAAGTA
1 AACTGTCCATAAGTCTCGAAGA-ACATAAGTA
1596514 AAC
1 AAC
1596517 CCTCGACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (31 bp):
AACTGTCCATAAGTCTCGAAGAACATAAGTA
Found at i:1597441 original size:20 final size:22
Alignment explanation
Indices: 1597409--1597465 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
1597399 TTCCCCTTGA
1597409 AGTGCAT-GATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1597428 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1597451 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1597466 CTACCCATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.21
20 9 0.27
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1597523 original size:64 final size:63
Alignment explanation
Indices: 1597453--1597593 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 63
1597443 TCTTTAACAT
* *
1597453 GTGCATCGATGCACTACC-CATGCATCGATACA-CAAATTACCTTCGATGTTTTCAT-TTTAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACATC-AATTACATTCGATGTTTT-ATCTTTAAAG
*
1597515 G
63 A
* * * *
1597516 GATGCATCGATGCACTCCTTATGCATCGATGCATCAATTGCATTCGATGTTTTTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACATCAATTACATTCGATGTTTTATCTTTAAAGA
1597580 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1597594 ATTAAATATG
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
63 17 0.25
64 49 0.73
65 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACATCAATTACATTCGATGTTTTATCTTTAAAGA
Found at i:1599228 original size:116 final size:116
Alignment explanation
Indices: 1599069--1599298 Score: 370
Period size: 116 Copynumber: 2.0 Consensus size: 116
1599059 CAATATAAGC
*
1599069 TTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCAT
* * *
1599134 CTACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAACATTCA
* * * *
1599185 TTGGATTTCAACTTCACGGCGAAGGATATCCAATTTAAGGCTCAACTTCACAACGAATGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCAT
* *
1599250 CCACGGTTTCAACTTCACGACGAATGGAATTGTACCCACCAGCAACATT
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAACATT
1599299 TATCTTCAGG
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
116 104 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (116 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTACCCACCAGCAACATTCA
Found at i:1599409 original size:37 final size:35
Alignment explanation
Indices: 1599363--1599493 Score: 165
Period size: 37 Copynumber: 3.6 Consensus size: 35
1599353 CAAGGGGTCA
* * *
1599363 TCTCGCTTGAGACTAATTTACTCAAAACAAAGTTTTG
1 TCTCTCTTGAGAC-AGTTT-CTCGAAACAAAGTTTTG
1599400 TCTCTCTTGAGACAGTTTCTCTTGAAACAAA-TTTTG
1 TCTCTCTTGAGACAGTTTCTC--GAAACAAAGTTTTG
*
1599436 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTG
1 TCTCTCTTGAGACAGTTT--CTCGAAACAAAGTTTTG
1599473 TCTCTCTTGAGACAGTTTCTC
1 TCTCTCTTGAGACAGTTTCTC
1599494 TTGAAATACC
Statistics
Matches: 84, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
35 5 0.06
36 35 0.42
37 42 0.50
38 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (35 bp):
TCTCTCTTGAGACAGTTTCTCGAAACAAAGTTTTG
Found at i:1599497 original size:37 final size:37
Alignment explanation
Indices: 1599387--1599499 Score: 210
Period size: 37 Copynumber: 3.1 Consensus size: 37
1599377 AATTTACTCA
1599387 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
1599424 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1599460 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1599497 AAA
1 AAA
1599500 TACCAATATT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
36 35 0.48
37 38 0.52
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (37 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:1599622 original size:38 final size:35
Alignment explanation
Indices: 1599554--1599640 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 35
1599544 CCTTGGGAAA
*
1599554 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
* *
1599589 GTTTCTCTTAAAACACAAAAAAAAAGACTTTTGAAAAT
1 GTTTCTCTTGAAACAC--AAAAAAA-ACCTTTGAAAAT
*
1599627 ATTTCTCTTGAAAC
1 GTTTCTCTTGAAAC
1599641 CCAAGACCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
35 15 0.34
37 7 0.16
38 22 0.50
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
Found at i:1601453 original size:17 final size:16
Alignment explanation
Indices: 1601424--1601482 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
1601414 TATGTTTTCT
*
1601424 TTTCTTTTGTTTTTTA
1 TTTCTTTTATTTTTTA
1601440 TTTCTTTTCATTTTTTA
1 TTTCTTTT-ATTTTTTA
** *
1601457 AATCTAGTTAGTTTTTTA
1 TTTCT-TTTA-TTTTTTA
1601475 TTTCTTTT
1 TTTCTTTT
1601483 TTGTGGTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
16 8 0.24
17 13 0.39
18 12 0.36
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (16 bp):
TTTCTTTTATTTTTTA
Found at i:1601950 original size:25 final size:25
Alignment explanation
Indices: 1601887--1601950 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1601877 TACTTTTCTT
*
1601887 TATTTTTTATTTTAATTTTTTTTAG
1 TATTTTTTATTTTAATTTTATTTAG
* * *
1601912 TTTTTCTTTCTTTTGA-TTTATTTAG
1 TATTT-TTTATTTTAATTTTATTTAG
1601937 TATTTATTTATTTT
1 TATTT-TTTATTTT
1601951 CTCTAACATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 23 0.74
26 8 0.26
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (25 bp):
TATTTTTTATTTTAATTTTATTTAG
Found at i:1603963 original size:26 final size:27
Alignment explanation
Indices: 1603925--1603976 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
1603915 ATGATGTGGC
*
1603925 ATTACTATTATTATTTAATATAAAAAT
1 ATTACTATTATTATTAAATATAAAAAT
*
1603952 ATTA-TATTATTATTAAATTTAAAAA
1 ATTACTATTATTATTAAATATAAAAA
1603977 GACTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTACTATTATTATTAAATATAAAAAT
Found at i:1607627 original size:11 final size:12
Alignment explanation
Indices: 1607611--1607652 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 12
1607601 TTCATGTAAT
1607611 TAAAATAAA-AA
1 TAAAATAAAGAA
1607622 TAAAATAAAGAA
1 TAAAATAAAGAA
1607634 TAATAATTAAAGTAA
1 TAA-AA-TAAAG-AA
1607649 TAAA
1 TAAA
1607653 TTTAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.33
12 5 0.19
13 2 0.07
14 6 0.22
15 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (12 bp):
TAAAATAAAGAA
Found at i:1609070 original size:175 final size:175
Alignment explanation
Indices: 1608775--1609125 Score: 603
Period size: 175 Copynumber: 2.0 Consensus size: 175
1608765 TTTAGGACTG
*
1608775 GTGGATGGCCTTTTTATAGGCCTCATCGACGTTGCTCTCAAACTGGTCACAAAAGTGGCCCTCAG
1 GTGGATGGCCTTTTTATAGGCCTCATCGACGTTGCTCTCAAACCGGTCACAAAAGTGGCCCTCAG
* *
1608840 TATGTCACCGAAGCTATGGTGGTGACTCACCATAGGGTAACGACGTGTGCGGCTGGCCGAGCATC
66 TAAGTCACCGAAGCTATGGTGGTGACTCACCATAGGGCAACGACGTGTGCGGCTGGCCGAGCATC
* *
1608905 TTCTAGAGGCTTCAGTGTTGTGGCAGCAAATCATTGGAGAACATA
131 TTCTAGAGGCTTCAGTGTTGTGGCAACAAATCATTAGAGAACATA
* *
1608950 GTGGATGGCCTTTTTATAGGCCTCATCGATGTTGCTCTCAAACCGGTCACAAAAGTGGCCCTCGG
1 GTGGATGGCCTTTTTATAGGCCTCATCGACGTTGCTCTCAAACCGGTCACAAAAGTGGCCCTCAG
*
1609015 TAAGTCACCGAAGCTATGGTGGTGACTCACCATAGGGCAACGACGTGTTCGGCTGGCCGAGCATC
66 TAAGTCACCGAAGCTATGGTGGTGACTCACCATAGGGCAACGACGTGTGCGGCTGGCCGAGCATC
** *
1609080 TTCTAGAGGCTTTGGTGTTGTGGCAACGAATCATTAGAGAACATA
131 TTCTAGAGGCTTCAGTGTTGTGGCAACAAATCATTAGAGAACATA
1609125 G
1 G
1609126 CAGCAGAGTG
Statistics
Matches: 165, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 165 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (175 bp):
GTGGATGGCCTTTTTATAGGCCTCATCGACGTTGCTCTCAAACCGGTCACAAAAGTGGCCCTCAG
TAAGTCACCGAAGCTATGGTGGTGACTCACCATAGGGCAACGACGTGTGCGGCTGGCCGAGCATC
TTCTAGAGGCTTCAGTGTTGTGGCAACAAATCATTAGAGAACATA
Found at i:1609421 original size:3 final size:3
Alignment explanation
Indices: 1609415--1609460 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1609405 AATTATTATT
1609415 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1609461 GTATGTGACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1611161 original size:42 final size:42
Alignment explanation
Indices: 1611091--1611189 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 42
1611081 AAAAAGCGCT
* * * *
1611091 GCAATAGGTTAGGATATTTAGCAGCGTTTT-TACACAAACAAC
1 GCAATATGTTAGGACATTTAACAGCGTTTTGGA-ACAAACAAC
**
1611133 GCAATATGTTAGGACATTTAAC-GACGTTTTGGGAACAAACGTC
1 GCAATATGTTAGGACATTTAACAG-CGTTTT-GGAACAAACAAC
1611176 GCAATATGTTAGGA
1 GCAATATGTTAGGA
1611190 TATGTAGCGA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
41 1 0.02
42 25 0.52
43 21 0.44
44 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (42 bp):
GCAATATGTTAGGACATTTAACAGCGTTTTGGAACAAACAAC
Found at i:1616481 original size:15 final size:15
Alignment explanation
Indices: 1616463--1616511 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1616453 GTATAACATT
*
1616463 TTCACGTAGAACACA
1 TTCACATAGAACACA
* * *
1616478 TTCATATAAAACACT
1 TTCACATAGAACACA
*
1616493 TTCACATGGAACACA
1 TTCACATAGAACACA
1616508 TTCA
1 TTCA
1616512 TATGTTAATA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (15 bp):
TTCACATAGAACACA
Found at i:1616496 original size:30 final size:30
Alignment explanation
Indices: 1616457--1616514 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1616447 ATCCACGTAT
* *
1616457 AACATTTTCACGTAGAACACATTCATATAA
1 AACACTTTCACATAGAACACATTCATATAA
*
1616487 AACACTTTCACATGGAACACATTCATAT
1 AACACTTTCACATAGAACACATTCATAT
1616515 GTTAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (30 bp):
AACACTTTCACATAGAACACATTCATATAA
Found at i:1622342 original size:17 final size:18
Alignment explanation
Indices: 1622313--1622348 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1622303 TATCCAATAG
*
1622313 TAGTTTGTTATTTTTATT
1 TAGTTTGTTATTTTAATT
1622331 TAGTTT-TTATTTTAATT
1 TAGTTTGTTATTTTAATT
1622348 T
1 T
1622349 TTTAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72
Consensus pattern (18 bp):
TAGTTTGTTATTTTAATT
Found at i:1626134 original size:17 final size:17
Alignment explanation
Indices: 1626087--1626159 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
1626077 ATTCTAAATG
*
1626087 TTTATAGTTATCAGACA
1 TTTATAGTTATCAGATA
*
1626104 TTTCATCGTTATCAGATA
1 TTT-ATAGTTATCAGATA
*
1626122 TTTATAATTATCAGATGA
1 TTTATAGTTATCAGAT-A
* * *
1626140 -TTACAGTTATAAGATG
1 TTTATAGTTATCAGATA
1626156 TTTA
1 TTTA
1626160 CAGAAATAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
17 29 0.64
18 16 0.36
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTATAGTTATCAGATA
Found at i:1626160 original size:17 final size:17
Alignment explanation
Indices: 1626129--1626175 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1626119 ATATTTATAA
* *
1626129 TTATCAGATGATTACAG
1 TTATAAGATGTTTACAG
1626146 TTATAAGATGTTTACAG
1 TTATAAGATGTTTACAG
**
1626163 AAATAAGATGTTT
1 TTATAAGATGTTT
1626176 TTAGTTACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (17 bp):
TTATAAGATGTTTACAG
Found at i:1627599 original size:36 final size:35
Alignment explanation
Indices: 1627551--1627627 Score: 136
Period size: 36 Copynumber: 2.2 Consensus size: 35
1627541 CCCTTACCAG
*
1627551 TTTGAGAAAAATAGTGAGGCATCCTCTGTTGATCC
1 TTTGAAAAAAATAGTGAGGCATCCTCTGTTGATCC
1627586 TTTGAAAACAAATAGTGAGGCATCCTCTGTTGATCC
1 TTTGAAAA-AAATAGTGAGGCATCCTCTGTTGATCC
1627622 TTTGAA
1 TTTGAA
1627628 CCCTTCATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 7 0.17
36 33 0.82
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (35 bp):
TTTGAAAAAAATAGTGAGGCATCCTCTGTTGATCC
Found at i:1630295 original size:20 final size:21
Alignment explanation
Indices: 1630243--1630303 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
1630233 TCCCCTGTGG
1630243 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
1630266 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
1630286 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1630304 TACACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1637048 original size:81 final size:81
Alignment explanation
Indices: 1636907--1637067 Score: 225
Period size: 81 Copynumber: 2.0 Consensus size: 81
1636897 TTATAATTCC
* * * * *
1636907 TTTAGTCTTTTACCCAAAGGCCTTTAACCTTTCATCTAACTTGCATGATTGACACTTTTCTGCCA
1 TTTAGTCTTTTACCCAAAGGCCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTACC-
1636972 AATGCACAGTTAGGCCA
65 AATGCACAGTTAGGCCA
* * * *
1636989 TTTA-TCTTTTACTCAATGGTCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTATCA
1 TTTAGTCTTTTACCCAAAGGCCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTACCA
1637053 ATGCACAGTTAGGCC
66 ATGCACAGTTAGGCC
1637068 TCAAAGGCAC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
80 16 0.23
81 50 0.71
82 4 0.06
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (81 bp):
TTTAGTCTTTTACCCAAAGGCCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTACCA
ATGCACAGTTAGGCCA
Found at i:1637115 original size:67 final size:67
Alignment explanation
Indices: 1637018--1637346 Score: 293
Period size: 67 Copynumber: 4.7 Consensus size: 67
1637008 TCTTTAACCG
*
1637018 TTCATCTAACT-AGCATAATTGACACATTTCTATCAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGA-CATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAG
1637082 CCT
65 CCT
* * *
1637085 TTCATCTAACTGACATAATTGATACCTTTCTGTCAATGCACAGTTAGACCTCAAAGGCACTTAGC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1637150 CT
66 CT
* * * * * * *****
1637152 TTCATCTAAATGGCATACTTGACACATTTCTGTCAATGTACAGTTAGGCTATTTATCTTTTACTC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGC--CTCA-AAGGCACT-
* *
1637217 AATGGTCT
62 --TAGCCT
* * *
1637225 TTAATCATTCATA-TAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGG
1 TTCATC--T-A-ACTGAC--A-T-AATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGG
1637289 CACTTAGCCT
58 CACTTAGCCT
* * * *
1637299 TTCATCTAACTGGCATAATTAACACCTTTCTGTCAATACACAGTTAGG
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGG
1637347 TTATTTATCT
Statistics
Matches: 204, Mismatches: 42, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
67 132 0.65
68 1 0.00
69 3 0.01
70 4 0.02
71 3 0.01
72 1 0.00
73 9 0.04
74 9 0.04
75 1 0.00
76 3 0.01
77 4 0.02
78 3 0.01
80 31 0.15
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (67 bp):
TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:1637291 original size:214 final size:215
Alignment explanation
Indices: 1636921--1637345 Score: 660
Period size: 214 Copynumber: 2.0 Consensus size: 215
1636911 GTCTTTTACC
* * *
1636921 CAAAGGCCTTTAACCTTTCATCTAACTTGCATGATTGACACTTTTCTGCCAAATGCACAGTTAGG
1 CAAAGGCCTTTAACCTTTCATCTAAATGGCATGATTGACACATTTCTGCCAAATGCACAGTTAGG
* *
1636986 CCATTTATCTTTTACTCAATGGTCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTAT
66 CCATTTATCTTTTACTCAATGGTCTTTAACCATTCATATAACTAGCATAATTGACACATTTCTAT
* *
1637051 CAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGATACCTTTCT
131 CAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTAACACCTTTCT
*
1637116 GTCAATGCACAGTTAGACCT
196 GTCAATACACAGTTAGACCT
* * *
1637136 CAAAGGCAC-TTAGCCTTTCATCTAAATGGCAT-ACTTGACACATTTCTGTC-AATGTACAGTTA
1 CAAAGGC-CTTTAACCTTTCATCTAAATGGCATGA-TTGACACATTTCTGCCAAATGCACAGTTA
* *
1637198 GGCTATTTATCTTTTACTCAATGGTCTTTAATCATTCATATAACT-GACATAATTGACACATTTC
64 GGCCATTTATCTTTTACTCAATGGTCTTTAACCATTCATATAACTAG-CATAATTGACACATTTC
* *
1637262 TGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTAACACCTT
128 TATCAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTAACACCTT
1637327 TCTGTCAATACACAGTTAG
193 TCTGTCAATACACAGTTAG
1637346 GTTATTTATC
Statistics
Matches: 192, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
213 1 0.01
214 149 0.78
215 41 0.21
216 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (215 bp):
CAAAGGCCTTTAACCTTTCATCTAAATGGCATGATTGACACATTTCTGCCAAATGCACAGTTAGG
CCATTTATCTTTTACTCAATGGTCTTTAACCATTCATATAACTAGCATAATTGACACATTTCTAT
CAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTAACACCTTTCT
GTCAATACACAGTTAGACCT
Found at i:1637334 original size:147 final size:147
Alignment explanation
Indices: 1637085--1637507 Score: 639
Period size: 147 Copynumber: 2.9 Consensus size: 147
1637075 CACTTAGCCT
* * *
1637085 TTCATCTAACTGACATAATTGATACCTTTCTGTCAATGCACAGTTAGACCTCAAAGGCACTTAGC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* * * *
1637150 CTTTCATCTAAATGGCATACTTGACACATTTCTGTCAATGTACAGTTAGGCTATTTATCTTTTAC
66 CTTTCATCTAAATGGCATAATTAACACCTTTCTGTCAATGCACAGTTAGGCTATTTATCTTTTAC
* *
1637215 TCAATGGTCTTTAATCA
131 TCAATGCTCTTTAACCA
*
1637232 TTCATATAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* * *
1637297 CTTTCATCTAACTGGCATAATTAACACCTTTCTGTCAATACACAGTTAGGTTATTTATCTTTTAC
66 CTTTCATCTAAATGGCATAATTAACACCTTTCTGTCAATGCACAGTTAGGCTATTTATCTTTTAC
*
1637362 TCAATGCTCTTTAACCG
131 TCAATGCTCTTTAACCA
* * *
1637379 TTCATCTAACTAACATAATTGACACATTTTTGTCAATGCACTGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* * * * * *
1637444 CTTTCATCTAATTAGCATAATTTACACCTTTCTGTCAATGCACAATTATGCCATTTATCTTTTA
66 CTTTCATCTAAATGGCATAATTAACACCTTTCTGTCAATGCACAGTTAGGCTATTTATCTTTTA
1637508 TTTTGGAATA
Statistics
Matches: 250, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
147 250 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (147 bp):
TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CTTTCATCTAAATGGCATAATTAACACCTTTCTGTCAATGCACAGTTAGGCTATTTATCTTTTAC
TCAATGCTCTTTAACCA
Found at i:1637734 original size:57 final size:57
Alignment explanation
Indices: 1637668--1637837 Score: 286
Period size: 57 Copynumber: 3.0 Consensus size: 57
1637658 TAAAGTTCTT
*
1637668 ATACGGAAATTCATAAACAAATTATTAATTTCTTAACTTTTTGCACACTCAGTGTCC
1 ATACGGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGTCC
* *
1637725 ATACAGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGCCC
1 ATACGGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGTCC
* * *
1637782 ATACGGAAATTCATAAACATATTATGAATTTCTTAATTTTTTGCACACTCACTGTC
1 ATACGGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGTC
1637838 ATTATGTAAT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 105 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (57 bp):
ATACGGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGTCC
Found at i:1638211 original size:19 final size:19
Alignment explanation
Indices: 1638184--1638224 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1638174 GTATCGATGC
1638184 TACTATACTATGGTACCGA
1 TACTATACTATGGTACCGA
*
1638203 TACTCTACTATGGTACCGA
1 TACTATACTATGGTACCGA
1638222 TAC
1 TAC
1638225 CATTTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (19 bp):
TACTATACTATGGTACCGA
Found at i:1638273 original size:20 final size:19
Alignment explanation
Indices: 1638248--1638316 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1638238 TGTTTCGGAT
1638248 GGTATCGATACCTTCCATTC
1 GGTATCGATACCTTCC-TTC
* *
1638268 GGTATCGATA-CTCCCTCC
1 GGTATCGATACCTTCCTTC
*
1638286 GGTATC-AAACTCTCTCCTTC
1 GGTATCGATAC-CT-TCCTTC
1638306 GGTATCGATAC
1 GGTATCGATAC
1638317 TGATTCATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 2 0.05
18 8 0.21
19 6 0.15
20 20 0.51
21 3 0.08
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (19 bp):
GGTATCGATACCTTCCTTC
Found at i:1638290 original size:18 final size:20
Alignment explanation
Indices: 1638248--1638291 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1638238 TGTTTCGGAT
*
1638248 GGTATCGATACCTTCCATTC
1 GGTATCGATACCTTCCATCC
*
1638268 GGTATCGATA-C-TCCCTCC
1 GGTATCGATACCTTCCATCC
1638286 GGTATC
1 GGTATC
1638292 AAACTCTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (20 bp):
GGTATCGATACCTTCCATCC
Found at i:1641006 original size:24 final size:23
Alignment explanation
Indices: 1640955--1641011 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1640945 TCTCAAATTC
*
1640955 ATTTTATTTTATTCTGATTTACT
1 ATTTTATTTTATTCTAATTTACT
1640978 ATTTTAATTTTATT-TAATTTAC-
1 ATTTT-ATTTTATTCTAATTTACT
*
1641000 ATGTT-TTTTATT
1 ATTTTATTTTATT
1641012 TTACCTCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 7 0.23
22 4 0.13
23 12 0.39
24 8 0.26
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.67
Consensus pattern (23 bp):
ATTTTATTTTATTCTAATTTACT
Found at i:1648986 original size:25 final size:25
Alignment explanation
Indices: 1648952--1649002 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1648942 AAAAGAAAGC
* *
1648952 TTTGATTGTTATTGTGCTTTTGGAT
1 TTTGACTGTTATTGTGCCTTTGGAT
1648977 TTTGACTGTTATTGTGCCTTTGGAT
1 TTTGACTGTTATTGTGCCTTTGGAT
1649002 T
1 T
1649003 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.08, G:0.24, T:0.57
Consensus pattern (25 bp):
TTTGACTGTTATTGTGCCTTTGGAT
Found at i:1649020 original size:6 final size:6
Alignment explanation
Indices: 1649004--1649035 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1648994 CTTTGGATTA
1649004 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
1649036 ATGTTTGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:1649425 original size:208 final size:208
Alignment explanation
Indices: 1649067--1649480 Score: 767
Period size: 208 Copynumber: 2.0 Consensus size: 208
1649057 CATAATCCCT
* *
1649067 AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTTTTTATTTTAATGAAATTTAA
1 AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTCTTTATTTCAATGAAATTTAA
* *
1649132 TATCATTTCAAGATAAAGAATTATAAAAAAAACTCAAGCCAATCAATGATTGACATGTGTCAATT
66 TATCATTTCAAGATAAAAAATTATAAAAAAAACTCAAGCCAATCAATGATTGACATGTGACAATT
1649197 CCCCCTAAAAACACCTTTTACTTAGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTTC
131 CCCCCTAAAAACACCTTTTACTTAGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTTC
1649262 TAATTTTGCCTAA
196 TAATTTTGCCTAA
1649275 AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTCTTTATTTCAATGAAATTTAA
1 AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTCTTTATTTCAATGAAATTTAA
1649340 TATCATTTCAAGATAAAAAAATTAT-AAAAAAACTCAAGCCAATCAATGATTGACATGTGACAAT
66 TATCATTTCAAGAT-AAAAAATTATAAAAAAAACTCAAGCCAATCAATGATTGACATGTGACAAT
*
1649404 TCCCCCTAAAAACACCTTTTACTTGGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTT
130 TCCCCCTAAAAACACCTTTTACTTAGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTT
1649469 CTAATTTTGCCT
195 CTAATTTTGCCT
1649481 TCAATTTTTT
Statistics
Matches: 200, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
208 191 0.95
209 9 0.05
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (208 bp):
AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTCTTTATTTCAATGAAATTTAA
TATCATTTCAAGATAAAAAATTATAAAAAAAACTCAAGCCAATCAATGATTGACATGTGACAATT
CCCCCTAAAAACACCTTTTACTTAGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTTC
TAATTTTGCCTAA
Found at i:1651071 original size:34 final size:36
Alignment explanation
Indices: 1651023--1651124 Score: 154
Period size: 37 Copynumber: 2.9 Consensus size: 36
1651013 TTTCGTCCTA
* *
1651023 CTAGAATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
1651058 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1651093 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1651125 GTTCTACTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.47
35 3 0.05
37 29 0.48
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:1651108 original size:37 final size:35
Alignment explanation
Indices: 1651023--1651122 Score: 148
Period size: 34 Copynumber: 2.8 Consensus size: 35
1651013 TTTCGTCCTA
* * *
1651023 CTAGAATTCAAACTCCTAAAAATATGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1651058 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAA-TTT
1651093 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
1651123 GAGTTCTACT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
34 28 0.47
35 3 0.05
37 28 0.47
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
Found at i:1651148 original size:37 final size:37
Alignment explanation
Indices: 1651020--1651158 Score: 149
Period size: 37 Copynumber: 3.8 Consensus size: 37
1651010 ATTTTTCGTC
* * *
1651020 CTACTAGAATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1651057 -T--TAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
1651091 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
** * * *
1651128 CTACTATTATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1651159 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
34 30 0.34
35 1 0.01
36 1 0.01
37 55 0.63
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Done.