Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008056.1 Hibiscus syriacus cultivar Beakdansim tig00110551_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: 2370532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1159066 original size:35 final size:36
Alignment explanation
Indices: 1159012--1159097 Score: 140
Period size: 35 Copynumber: 2.4 Consensus size: 36
1159002 CGCAATGCGA
*
1159012 TTTTCAAAGTACC-ATTATTATCGCAACACGTA-TTT
1 TTTTCAAA-TACCAAATATTATCGCAACACGTATTTT
1159047 TTTTCAAATACCAAATATTATCGCAACACGTATTTT
1 TTTTCAAATACCAAATATTATCGCAACACGTATTTT
1159083 TTTTCAAATACCAAA
1 TTTTCAAATACCAAA
1159098 CACGAATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
34 4 0.08
35 26 0.54
36 18 0.38
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (36 bp):
TTTTCAAATACCAAATATTATCGCAACACGTATTTT
Found at i:1159248 original size:22 final size:22
Alignment explanation
Indices: 1159223--1159265 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1159213 GGCGACATCC
*
1159223 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATATCCGACGAAATCA
*
1159245 GTCCCCATATCCGGCGAAATC
1 GTCCCCATATCCGACGAAATC
1159266 CGTCTTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.40, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATATCCGACGAAATCA
Found at i:1159552 original size:80 final size:80
Alignment explanation
Indices: 1159455--1159602 Score: 269
Period size: 80 Copynumber: 1.9 Consensus size: 80
1159445 GCGAAAGTAA
* * *
1159455 ACTATTCTTCTTCTGCAAATTGAAACTTGAATGGATTGCTTAGTAAATTCATTCGGTTGTTGCCA
1 ACTATTCTTCATATGCAAATTGAAACTTGAATGGATTGCTTAGTAAATTCATTCGGTTGCTGCCA
1159520 ATAGTTGCGAAAATG
66 ATAGTTGCGAAAATG
1159535 ACTATTCTTCATATGCAAATTGAAACTTGAATGGATTGCTTAGTAAATTCATTCGGTTGCTGCCA
1 ACTATTCTTCATATGCAAATTGAAACTTGAATGGATTGCTTAGTAAATTCATTCGGTTGCTGCCA
1159600 ATA
66 ATA
1159603 CTGCTAAACT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (80 bp):
ACTATTCTTCATATGCAAATTGAAACTTGAATGGATTGCTTAGTAAATTCATTCGGTTGCTGCCA
ATAGTTGCGAAAATG
Found at i:1159744 original size:20 final size:20
Alignment explanation
Indices: 1159719--1159786 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
1159709 TAGTTTACTT
1159719 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
1159739 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
1159759 TCGCAACGC-AAATTTTACTA
1 TCGCAACGCGAAA-ATGACTA
1159779 TCGCAACG
1 TCGCAACG
1159787 AAAGAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 3 0.07
20 42 0.93
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1161883 original size:14 final size:14
Alignment explanation
Indices: 1161846--1161884 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1161836 TTGCTTGTTT
*
1161846 AATTGATTTATAAA
1 AATTGATTTGTAAA
1161860 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1161874 AGTTGATTTGT
1 AATTGATTTGT
1161885 TTATATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1162026 original size:20 final size:20
Alignment explanation
Indices: 1162001--1162053 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1161991 AGGTACACTT
* *
1162001 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACACAAAA
* *
1162021 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAACACAAAA
*
1162041 TCACAACGCGAAA
1 TCGCAACGCGAAA
1162054 GTCAATTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACACAAAA
Found at i:1162126 original size:20 final size:20
Alignment explanation
Indices: 1162097--1162225 Score: 195
Period size: 20 Copynumber: 6.5 Consensus size: 20
1162087 GCGATTTTCT
* *
1162097 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCA
* * *
1162117 CGTTGTGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCA
1162137 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
1162157 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
1162177 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
* *
1162197 CGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
1162217 CGTTGCGAT
1 CGTTGCGAT
1162226 TTTGAGTTGC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 99 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:1162487 original size:133 final size:132
Alignment explanation
Indices: 1162263--1162514 Score: 461
Period size: 133 Copynumber: 1.9 Consensus size: 132
1162253 AATCAAATTC
* *
1162263 GCGTTGCGATATTCAAATGAATGTAAAAGTGATAACAATGAACATATCATAGCAGTGTTCAAACT
1 GCGTTGCGATATTCAAATGAATGTAAAAGTGATAACAATGAACAGATCATAGCAATGTTCAAACT
1162328 CAAGTTACTAATACATGCCTAACTG-AAAATGTTAAAAGTTTACACATAATACACATAATAGTCA
66 CAAGTTACTAATACATGCCTAACTGAAAAATGTTAAAAGTTTACACATAATACACATAATAGTCA
1162392 AT
131 AT
1162394 GCGTTGCGATATTCAAATGAATGTATAAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAA
1 GCGTTGCGATATTCAAATGAATGTA-AAAGTGATAACAA-TGAACAGATCATAGCAATGTTCAAA
1162459 CTCAAGTTACTAATACATGCCTAACTGAAAAATGTTAAAAGTTTACACATAATACA
64 CTCAAGTTACTAATACATGCCTAACTGAAAAATGTTAAAAGTTTACACATAATACA
1162515 ACGATCATTA
Statistics
Matches: 116, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
131 25 0.22
132 13 0.11
133 50 0.43
134 28 0.24
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (132 bp):
GCGTTGCGATATTCAAATGAATGTAAAAGTGATAACAATGAACAGATCATAGCAATGTTCAAACT
CAAGTTACTAATACATGCCTAACTGAAAAATGTTAAAAGTTTACACATAATACACATAATAGTCA
AT
Found at i:1162590 original size:18 final size:18
Alignment explanation
Indices: 1162567--1162601 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1162557 AAGCCGGTTG
*
1162567 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1162585 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1162602 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1164849 original size:24 final size:24
Alignment explanation
Indices: 1164822--1164868 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1164812 CAAAATCCGA
1164822 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1164846 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1164869 AATACCGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1165714 original size:20 final size:20
Alignment explanation
Indices: 1165683--1165810 Score: 175
Period size: 20 Copynumber: 6.4 Consensus size: 20
1165673 GAAATTCAGT
*
1165683 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
1165703 GTTGTGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
1165723 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1165743 GTTGCTATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
1165763 ATTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
1165783 ATTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1165803 ATTGCGAT
1 GTTGCGAT
1165811 TTACATATTT
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 99 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1165824 original size:20 final size:20
Alignment explanation
Indices: 1165759--1165849 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1165749 ATAGTCAGAA
* *
1165759 TCGCATTGCGATAGT-CATAA
1 TCGCATTGCGAT-TTACATAT
* *
1165779 TCGCATTGCGATAGT-CATAA
1 TCGCATTGCGAT-TTACATAT
1165799 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
1165819 TTGCATTGTGATTTACATAT
1 TCGCATTGCGATTTACATAT
1165839 TCGCATTGCGA
1 TCGCATTGCGA
1165850 ATTCGGAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 1 0.02
20 63 0.98
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1165912 original size:21 final size:21
Alignment explanation
Indices: 1165846--1165912 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
1165836 TATTCGCATT
1165846 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
*
1165867 ACGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
1165888 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
1165909 GCGA
1 GCGA
1165913 TAGTCAGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:1173565 original size:13 final size:13
Alignment explanation
Indices: 1173549--1173575 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1173539 AGTTAAATAT
1173549 TTTAAGAATTATC
1 TTTAAGAATTATC
1173562 TTTAAGAATTATC
1 TTTAAGAATTATC
1173575 T
1 T
1173576 CTTATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTAAGAATTATC
Found at i:1178341 original size:23 final size:23
Alignment explanation
Indices: 1178311--1178355 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1178301 AATTATTCCA
1178311 CTTTAAGATATTTGATCATGCAG
1 CTTTAAGATATTTGATCATGCAG
*
1178334 CTTTAAGATATTTGATGATGCA
1 CTTTAAGATATTTGATCATGCA
1178356 AAAAGGAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (23 bp):
CTTTAAGATATTTGATCATGCAG
Found at i:1182081 original size:15 final size:14
Alignment explanation
Indices: 1182066--1182108 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
1182056 TAAAAATAAG
*
1182066 AGATAATTCCT-AA
1 AGATAATTCTTAAA
1182079 AGATAATTCTTATAA
1 AGATAATTCTTA-AA
1182094 AGATAATTCTTAAA
1 AGATAATTCTTAAA
1182108 A
1 A
1182109 TATTTAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.37
14 3 0.11
15 14 0.52
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (14 bp):
AGATAATTCTTAAA
Found at i:1191362 original size:20 final size:20
Alignment explanation
Indices: 1191337--1191387 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1191327 CACTTAGGGA
1191337 ACCGATTCCCCATAGGGGGT
1 ACCGATTCCCCATAGGGGGT
1191357 ACCGATTCCCCATAGGGGGT
1 ACCGATTCCCCATAGGGGGT
1191377 ACCGATTCCCC
1 ACCGATTCCCC
1191388 CCACGCTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (20 bp):
ACCGATTCCCCATAGGGGGT
Found at i:1193493 original size:286 final size:286
Alignment explanation
Indices: 1192981--1193552 Score: 1074
Period size: 286 Copynumber: 2.0 Consensus size: 286
1192971 TAATAGAGGT
1192981 ATTTGAACTTGTTTGATCGATTAGAGCGGAGAACATGCCACGACGTTTCAATAGAGGCATCCCCA
1 ATTTGAACTTGTTTGATCGATTAGAGCGGAGAACATGCCACGACGTTTCAATAGAGGCATCCCCA
*
1193046 CTTCTTGGAAAACGGGTTCAGCAGGCCTCAAGGTCGATGGTGTTATGTCAGTCATAAAGCACTAG
66 CTTCTTGGAAAACGGGCTCAGCAGGCCTCAAGGTCGATGGTGTTATGTCAGTCATAAAGCACTAG
* *
1193111 TTAGGGGAATAATCCGAGTGATGAGAGCATGTTATGTTGTCCTCATTGTTTTTCGAGGGATATTC
131 TTAGGGGAATAATCCGAGTGATGAGAGCATGTTATGTTATCCTCATTATTTTTCGAGGGATATTC
* *
1193176 GTCCCCACATACAAGTACTGCAGGTCGAATATGCTTGAGAGATTATATATGGACTCGTTAGTGTA
196 GTCCCCACATACAAGTACTGCAGGTCGAATATGCTCGAGAGATTATATATGGACTCATTAGTGTA
1193241 TGTGTCAGCCATAAGGATATGATGGC
261 TGTGTCAGCCATAAGGATATGATGGC
1193267 ATTTGAACTTGTTTGATCGATTA-ATGCGGAGAACATGCCACGACGTTTCAATAGAGGCATCCCC
1 ATTTGAACTTGTTTGATCGATTAGA-GCGGAGAACATGCCACGACGTTTCAATAGAGGCATCCCC
1193331 ACTTCTTGGAAAACGGGCTCAGCAGGCCTCAAGGTCGATGGTGTTATGTCAGTCATAAAGCACTA
65 ACTTCTTGGAAAACGGGCTCAGCAGGCCTCAAGGTCGATGGTGTTATGTCAGTCATAAAGCACTA
1193396 GTTAGGGGAATAATCCGAGTGATGAGAGCATGTTATGTTATCCTCATTATTTTTCGAGGGATATT
130 GTTAGGGGAATAATCCGAGTGATGAGAGCATGTTATGTTATCCTCATTATTTTTCGAGGGATATT
*
1193461 TGTCCCCACATACAAGTACTGCAGGTCGAATATGCTCGAGAGATTATATATGGACTCATTAGTGT
195 CGTCCCCACATACAAGTACTGCAGGTCGAATATGCTCGAGAGATTATATATGGACTCATTAGTGT
1193526 ATGTGTCAGCCATAAGGATATGATGGC
260 ATGTGTCAGCCATAAGGATATGATGGC
1193553 TACTCATAAG
Statistics
Matches: 279, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
285 1 0.00
286 278 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (286 bp):
ATTTGAACTTGTTTGATCGATTAGAGCGGAGAACATGCCACGACGTTTCAATAGAGGCATCCCCA
CTTCTTGGAAAACGGGCTCAGCAGGCCTCAAGGTCGATGGTGTTATGTCAGTCATAAAGCACTAG
TTAGGGGAATAATCCGAGTGATGAGAGCATGTTATGTTATCCTCATTATTTTTCGAGGGATATTC
GTCCCCACATACAAGTACTGCAGGTCGAATATGCTCGAGAGATTATATATGGACTCATTAGTGTA
TGTGTCAGCCATAAGGATATGATGGC
Found at i:1195023 original size:60 final size:60
Alignment explanation
Indices: 1194950--1195081 Score: 246
Period size: 60 Copynumber: 2.2 Consensus size: 60
1194940 ATTATTTTTC
*
1194950 TACTCTTATTTTGGTCATTAAAGTTTAAACATTTTCAATTGAATTACCCAACTTTTGAAT
1 TACTCTTATTTTGGTCATTAAAGTTTAAACATTTTCAATTGAATCACCCAACTTTTGAAT
*
1195010 TACTCTTATTTTGGTCATTAAAGTTTAAATATTTTCAATTGAATCACCCAACTTTTGAAT
1 TACTCTTATTTTGGTCATTAAAGTTTAAACATTTTCAATTGAATCACCCAACTTTTGAAT
1195070 TACTCTTATTTT
1 TACTCTTATTTT
1195082 AATCACTTTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (60 bp):
TACTCTTATTTTGGTCATTAAAGTTTAAACATTTTCAATTGAATCACCCAACTTTTGAAT
Found at i:1195140 original size:3 final size:3
Alignment explanation
Indices: 1195134--1195174 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1195124 TGACATTTTT
*
1195134 TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1195175 ATATATGTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1195150 original size:18 final size:18
Alignment explanation
Indices: 1195128--1195174 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1195118 ATAGTGTGAC
1195128 ATTTTT-TTATTATTATT
1 ATTTTTATTATTATTATT
1195145 ATTTTTATTATTATTATT
1 ATTTTTATTATTATTATT
*
1195163 ATTATTA-TATTA
1 ATTTTTATTATTA
1195175 ATATATGTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTATTATTATTATT
Found at i:1201036 original size:90 final size:90
Alignment explanation
Indices: 1200794--1201036 Score: 335
Period size: 90 Copynumber: 2.7 Consensus size: 90
1200784 TTAAGATTTT
* *
1200794 TCGGTTGTAA-TCGAAATTATTATCAATTATTTAACTTTTTAAAGTAGACATGTAACATTTTAAG
1 TCGGTTGTAACT-GAAATTATTATCAATTATTTAACTTTTTAGAGTAGACATGTAACATTTTAGG
* * *
1200858 TTAAAACATGTTGCAATGTAATATTT
65 CTAAAACACGTTGCAATGTAATATTC
** * ** * * *
1200884 TCGGTTGTAACAAAAATTATTATCAATTATATAACGCTTTCGAATAGACATGTAATATTTTAGGC
1 TCGGTTGTAACTGAAATTATTATCAATTATTTAACTTTTTAGAGTAGACATGTAACATTTTAGGC
*
1200949 TAAAACACGTTGTAATGTAATATTC
66 TAAAACACGTTGCAATGTAATATTC
*
1200974 TCGGTTGTAACTGAAATTATTATTAATTATTTAACTTTTTAGAGTAGACATGTAACATTTTAG
1 TCGGTTGTAACTGAAATTATTATCAATTATTTAACTTTTTAGAGTAGACATGTAACATTTTAG
1201037 ATAAAAATCT
Statistics
Matches: 129, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
90 129 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (90 bp):
TCGGTTGTAACTGAAATTATTATCAATTATTTAACTTTTTAGAGTAGACATGTAACATTTTAGGC
TAAAACACGTTGCAATGTAATATTC
Found at i:1201060 original size:90 final size:89
Alignment explanation
Indices: 1200794--1201064 Score: 314
Period size: 90 Copynumber: 3.0 Consensus size: 89
1200784 TTAAGATTTT
*
1200794 TCGGTTGTAA-TCGAAATTATTATCAATTATTTAACTTTTTAAAGTAGACATGTAACATTTTAAG
1 TCGGTTGTAACT-GAAATTATTATCAATTATTTAACTTTTTAGAGTAGACATGTAACATTTT-AG
* * * *
1200858 TTAAAACATGTTGCAATGTAATATTT
64 ATAAAACATCTTGTAATGTAATATTC
** * ** * * * *
1200884 TCGGTTGTAACAAAAATTATTATCAATTATATAACGCTTTCGAATAGACATGTAATATTTTAGGC
1 TCGGTTGTAACTGAAATTATTATCAATTATTTAACTTTTTAGAGTAGACATGTAACATTTTA-GA
1200949 TAAAACA-CGTTGTAATGTAATATTC
65 TAAAACATC-TTGTAATGTAATATTC
*
1200974 TCGGTTGTAACTGAAATTATTATTAATTATTTAACTTTTTAGAGTAGACATGTAACATTTTAGAT
1 TCGGTTGTAACTGAAATTATTATCAATTATTTAACTTTTTAGAGTAGACATGTAACATTTTAGAT
* *
1201039 AAAA-ATCTAATGTAGTATAATATTC
66 AAAACATCT--TGTAATGTAATATTC
1201064 T
1 T
1201065 TGATTTTTAA
Statistics
Matches: 150, Mismatches: 25, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
88 2 0.01
89 8 0.05
90 140 0.93
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (89 bp):
TCGGTTGTAACTGAAATTATTATCAATTATTTAACTTTTTAGAGTAGACATGTAACATTTTAGAT
AAAACATCTTGTAATGTAATATTC
Found at i:1203409 original size:11 final size:11
Alignment explanation
Indices: 1203386--1203455 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
1203376 AAAATTGATC
*
1203386 ATTT-ATTAAA
1 ATTTAATTATA
1203396 ATTTAATTATA
1 ATTTAATTATA
1203407 ATTTAAATT-TA
1 ATTT-AATTATA
*
1203418 ATTATAATTTTA
1 ATT-TAATTATA
**
1203430 ATAGAATTATA
1 ATTTAATTATA
* *
1203441 ATTAAATTGTA
1 ATTTAATTATA
1203452 ATTT
1 ATTT
1203456 TTAATAGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
10 4 0.08
11 35 0.73
12 9 0.19
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
ATTTAATTATA
Found at i:1203414 original size:17 final size:17
Alignment explanation
Indices: 1203394--1203454 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
1203384 TCATTTATTA
1203394 AAATTTAATTATAATTT
1 AAATTTAATTATAATTT
1203411 AAATTTAATTATAATTT
1 AAATTTAATTATAATTT
* **
1203428 TAATAGAATTATAA-TT
1 AAATTTAATTATAATTT
1203444 AAATTGTAATT
1 AAATT-TAATT
1203455 TTTAATAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
16 5 0.14
17 32 0.86
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
AAATTTAATTATAATTT
Found at i:1203425 original size:6 final size:6
Alignment explanation
Indices: 1203390--1203454 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
1203380 TTGATCATTT
* * *
1203390 ATTAAA ATT-TA ATTATA ATT-TAA ATT-TA ATTATA ATTTTA A-TAGA
1 ATTATA ATTATA ATTATA ATTAT-A ATTATA ATTATA ATTATA ATTATA
*
1203435 ATTATA ATTA-A ATTGTA ATT
1 ATTATA ATTATA ATTATA ATT
1203455 TTTAATAGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
5 16 0.33
6 32 0.67
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (6 bp):
ATTATA
Found at i:1203469 original size:28 final size:28
Alignment explanation
Indices: 1203412--1203476 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
1203402 TTATAATTTA
* *
1203412 AATTTAATTATAATTTTAATAGAATTAT
1 AATTAAATTATAATTTTAATAGAATAAT
*
1203440 AATTAAATTGTAATTTTTAATAGAAAATAAT
1 AATTAAATTATAA-TTTTAATAG--AATAAT
1203471 AATTAA
1 AATTAA
1203477 TTTAAGCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 11 0.35
29 9 0.29
31 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (28 bp):
AATTAAATTATAATTTTAATAGAATAAT
Found at i:1203942 original size:3 final size:3
Alignment explanation
Indices: 1203934--1204005 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
1203924 TATCGGACTA
1203934 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1203982 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
1204006 GGCATGATAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1205636 original size:46 final size:46
Alignment explanation
Indices: 1205099--1205633 Score: 784
Period size: 46 Copynumber: 11.6 Consensus size: 46
1205089 CATTTTTCAA
* * **
1205099 TTTA-TTATGGCAGTCCTTTCCATGCCTTAATACATTCGTTCATATAT
1 TTTAGTTATGGCA-TCCTTT-CATGCCTTAATGCATCCGTTCATGCAT
* *
1205146 TTTTGTTATGGCATCCTTTCATGCCTTAATGCATTCGTTCATGCAT
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
* *
1205192 TTTAGTTATGACATCCTTTCATGCCTTAATGCATCCATTCATGCAT
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
* * * *
1205238 TTTAGTTATGTCATCCTTTCATGCCTTAGTACATCCGTTTATGCAT
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
* * * *
1205284 TTTAGTTATGGAATCCTTTCATGGCTTAGTGCATCCGTTCATGCAC
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
1205330 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
* *
1205376 TTTAGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCAC
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
1205422 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
* * *
1205468 TTTAGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATACAC
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
* * *
1205514 TTTATTTATGGCATCCTTTCATGCCTTAATACATCCGTTCATACAT
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
* * * * *
1205560 TTTAGTTATGGCATTCTTTCGTTCCTTAGTGCATCCGTTCATGCAC
1 TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
1205606 TTTAGTTATGGCATCCTTTCATGCCTTA
1 TTTAGTTATGGCATCCTTTCATGCCTTA
1205634 GTGATAACAT
Statistics
Matches: 442, Mismatches: 45, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
46 425 0.96
47 9 0.02
48 8 0.02
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.42
Consensus pattern (46 bp):
TTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCAT
Found at i:1206991 original size:18 final size:18
Alignment explanation
Indices: 1206913--1206998 Score: 100
Period size: 18 Copynumber: 4.8 Consensus size: 18
1206903 TAGAATTTGC
*
1206913 CCCGTAGGACCACTATGT
1 CCCGAAGGACCACTATGT
* * *
1206931 ACCGAAAGACCACTGTGT
1 CCCGAAGGACCACTATGT
*
1206949 CCCGAATGACCACTATGT
1 CCCGAAGGACCACTATGT
* *
1206967 TCTGAAGGACCACTATGT
1 CCCGAAGGACCACTATGT
*
1206985 CCCGAAGAACCACT
1 CCCGAAGGACCACT
1206999 CCTTAAGAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (18 bp):
CCCGAAGGACCACTATGT
Found at i:1211685 original size:17 final size:17
Alignment explanation
Indices: 1211647--1211679 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1211637 GTTTACCCAA
1211647 AAAATTATAATTTAATT
1 AAAATTATAATTTAATT
1211664 AAAATTAT-ATTTAATT
1 AAAATTATAATTTAATT
1211680 TTAAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATTATAATTTAATT
Found at i:1211880 original size:15 final size:16
Alignment explanation
Indices: 1211855--1211884 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1211845 AAATATTCAT
1211855 ATATAAATAATATAAC
1 ATATAAATAATATAAC
1211871 ATAT-AATAATATAA
1 ATATAAATAATATAA
1211885 TAACAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAATAATATAAC
Found at i:1211882 original size:32 final size:31
Alignment explanation
Indices: 1211812--1211883 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
1211802 TATAAATAAT
* *
1211812 ATAATATATGATATATAATAATATAATAAAA
1 ATAATATATCATATATAATAATATAACAAAA
* *
1211843 ACAA-ATATTCATATATAAATAATATAACATATA
1 ATAATATA-TCATATAT-AATAATATAACA-AAA
1211876 ATAATATA
1 ATAATATA
1211884 ATAACAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 3 0.09
31 10 0.31
32 11 0.34
33 5 0.16
34 3 0.09
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (31 bp):
ATAATATATCATATATAATAATATAACAAAA
Found at i:1211908 original size:47 final size:45
Alignment explanation
Indices: 1211801--1211909 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 45
1211791 AAAATTTTTC
* * *
1211801 ATATAAATAATATAATATATGATATATAATAATATAATAAAAACAA
1 ATATTAATAATA-AATATATAACATATAATAATATAATAAAAACAA
* * *
1211847 ATATTCATATATAAATAATATAACATATAATAATATAATAACAACAT
1 ATATTAATA-ATAAAT-ATATAACATATAATAATATAATAAAAACAA
1211894 ATATTTAATAATAAAT
1 ATA-TTAATAATAAAT
1211910 CCAAATGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
46 10 0.19
47 38 0.72
48 5 0.09
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.35
Consensus pattern (45 bp):
ATATTAATAATAAATATATAACATATAATAATATAATAAAAACAA
Found at i:1212182 original size:31 final size:31
Alignment explanation
Indices: 1212138--1212198 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1212128 ACTGAGGAAC
*
1212138 TAAAATAGAACGGATCGATAACATTTGGGAT
1 TAAAATAGAACGGATCGATAACATTAGGGAT
1212169 TAAAATCAG-ACGGATCGATAACATTAGGGA
1 TAAAAT-AGAACGGATCGATAACATTAGGGA
1212199 CCATGTACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (31 bp):
TAAAATAGAACGGATCGATAACATTAGGGAT
Found at i:1212501 original size:22 final size:20
Alignment explanation
Indices: 1212475--1212524 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1212465 TATTTTCTAA
*
1212475 TTTATATATTACTATTTATTT
1 TTTATATATTACT-TATATTT
*
1212496 TATTATATTTTTACTTATATTT
1 T-TTATA-TATTACTTATATTT
1212518 TTTATAT
1 TTTATAT
1212525 TTATTTTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 12 0.48
23 6 0.24
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATATATTACTTATATTT
Found at i:1212600 original size:22 final size:22
Alignment explanation
Indices: 1212562--1212607 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1212552 AAGAAAATAA
*
1212562 TATTTTATTACACATTTTTAAT
1 TATTTTATTACACATTTGTAAT
*
1212584 TATTTTATTA-ATTATTTGTAAT
1 TATTTTATTACA-CATTTGTAAT
1212606 TA
1 TA
1212608 AATTCAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTTTATTACACATTTGTAAT
Found at i:1213087 original size:23 final size:24
Alignment explanation
Indices: 1213061--1213107 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1213051 TATACGACCA
*
1213061 AAATAGAA-TTAAAACATAATATT
1 AAATAGAATTTAAAAAATAATATT
* *
1213084 AAATATAATTTAAAAAATGATATT
1 AAATAGAATTTAAAAAATAATATT
1213108 TAAGTAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (24 bp):
AAATAGAATTTAAAAAATAATATT
Found at i:1214358 original size:42 final size:41
Alignment explanation
Indices: 1214297--1214376 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
1214287 CGTTTTTCGA
1214297 AAAATATTTCCTGTATTTGTTTCACGTAATTCATTTTCTGG
1 AAAATATTTCCTGTATTTGTTTCACGTAATTCATTTTCTGG
* *
1214338 AAAATATTTTCCTGTGTTTGTTTCACGTAATTTATTTTC
1 AAAATA-TTTCCTGTATTTGTTTCACGTAATTCATTTTC
1214377 CTAGTAACAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 6 0.17
42 30 0.83
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (41 bp):
AAAATATTTCCTGTATTTGTTTCACGTAATTCATTTTCTGG
Found at i:1214577 original size:21 final size:24
Alignment explanation
Indices: 1214534--1214584 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 24
1214524 CATTTTCATC
1214534 AAAATATTATTTATTTAAATATTT
1 AAAATATTATTTATTTAAATATTT
1214558 AAAATA-TATTTA-TT-AATATTT
1 AAAATATTATTTATTTAAATATTT
*
1214579 ATAATA
1 AAAATA
1214585 ATATAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 2 0.08
23 6 0.23
24 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAAATATTATTTATTTAAATATTT
Found at i:1214700 original size:30 final size:28
Alignment explanation
Indices: 1214639--1214733 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 28
1214629 TTATAATAAT
*
1214639 ATAATATA-AGATATTATATTTTTAT-TTTA
1 ATAATATATA-ATATT-T-TTTATATATTTA
1214668 ATAATATATAATAATTTTTTTATATATTTA
1 ATAATATATAAT-A-TTTTTTATATATTTA
* *
1214698 ATAATAAATAATATTATTTATATATTTAA
1 ATAATATATAATATTTTTTATATATTT-A
1214727 ATAATAT
1 ATAATAT
1214734 TTTAGTAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
28 13 0.23
29 24 0.42
30 18 0.32
31 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
ATAATATATAATATTTTTTATATATTTA
Found at i:1214726 original size:28 final size:30
Alignment explanation
Indices: 1214655--1214732 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
1214645 TAAGATATTA
* *
1214655 TATTTTTAT-TTTAATAATATATAATAATT
1 TATTTATATATTTAATAATAAATAATAATT
*
1214684 TTTTTATATATTTAATAATAAATAAT-A-T
1 TATTTATATATTTAATAATAAATAATAATT
1214712 TATTTATATATTTAAATAATA
1 TATTTATATATTT-AATAATA
1214733 TTTTAGTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 13 0.30
29 15 0.35
30 15 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TATTTATATATTTAATAATAAATAATAATT
Found at i:1214861 original size:90 final size:86
Alignment explanation
Indices: 1214749--1214918 Score: 200
Period size: 90 Copynumber: 1.9 Consensus size: 86
1214739 TAAAGATATT
* * * * * *
1214749 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACACTATTACTTTAATAAATAATTAA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATA-TTTAAT-AATAAATAA
1214812 TATAATTTATAATATTTTATTTCAC
64 -ATAATTT-TAATATTTTATTTCAC
*
1214837 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATATA-CAA-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
*
1214902 ATTATTTTAATATTTTA
64 ATAATTTTAATATTTTA
1214919 AAATAATAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 19 0.27
89 8 0.11
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
AATTTTAATATTTTATTTCAC
Found at i:1215106 original size:29 final size:30
Alignment explanation
Indices: 1215073--1215139 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
1215063 TTCCAGAAAT
*
1215073 GTAATTCATTTTCCAG-AATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
1215102 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
1215132 GTAATTCA
1 GTAATTCA
1215140 AATTGCAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 15 0.43
30 20 0.57
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1215107 original size:15 final size:15
Alignment explanation
Indices: 1215089--1215148 Score: 84
Period size: 15 Copynumber: 4.0 Consensus size: 15
1215079 CATTTTCCAG
1215089 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
**
1215104 AATTCATTTTTCAGT
1 AATTCAAATTTCAGT
*
1215119 AATTCAAATTCCAGT
1 AATTCAAATTTCAGT
*
1215134 AATTCAAATTGCAGT
1 AATTCAAATTTCAGT
1215149 TTCCGGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (15 bp):
AATTCAAATTTCAGT
Found at i:1216605 original size:37 final size:37
Alignment explanation
Indices: 1216555--1216637 Score: 148
Period size: 37 Copynumber: 2.2 Consensus size: 37
1216545 TAGAAAGCCC
*
1216555 AGGATTAGGATTTGGGTTAGAGAATAAATACTTTTTT
1 AGGATTAGGATTTGAGTTAGAGAATAAATACTTTTTT
*
1216592 AGGATTAGGATTTGAGTTAGAGAATAAATATTTTTTT
1 AGGATTAGGATTTGAGTTAGAGAATAAATACTTTTTT
1216629 AGGATTAGG
1 AGGATTAGG
1216638 GGTCAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.34, C:0.01, G:0.25, T:0.40
Consensus pattern (37 bp):
AGGATTAGGATTTGAGTTAGAGAATAAATACTTTTTT
Found at i:1217243 original size:2 final size:2
Alignment explanation
Indices: 1217236--1217268 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1217226 AATAATCTTA
1217236 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 A
1217269 AGTTCATGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1220333 original size:6 final size:6
Alignment explanation
Indices: 1220322--1220372 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
1220312 CAAGAGTAAT
* *
1220322 GGGTGA GGGTGA GGGTGA GGGTGA GGGTGG GGGTGG GGGTGA GGGTGA
1 GGGTGA GGGTGA GGGTGA GGGTGA GGGTGA GGGTGA GGGTGA GGGTGA
1220370 GGG
1 GGG
1220373 AGAGATTAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.12, C:0.00, G:0.73, T:0.16
Consensus pattern (6 bp):
GGGTGA
Found at i:1220384 original size:24 final size:24
Alignment explanation
Indices: 1220334--1220385 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1220324 GTGAGGGTGA
* * * *
1220334 GGGTGAGGGTGAGGGTGGGGGTGG
1 GGGTGAGGGTGAGGGAGAGAGTAG
*
1220358 GGGTGAGGGTGAGGGAGAGATTAG
1 GGGTGAGGGTGAGGGAGAGAGTAG
1220382 GGGT
1 GGGT
1220386 TAACGTTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.67, T:0.17
Consensus pattern (24 bp):
GGGTGAGGGTGAGGGAGAGAGTAG
Found at i:1224484 original size:21 final size:20
Alignment explanation
Indices: 1224436--1224484 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1224426 CAATTGTTAT
1224436 GAAGAAAAACTAAGGAGAAG
1 GAAGAAAAACTAAGGAGAAG
1224456 GAAGAAAAACTAAGGAGAAG
1 GAAGAAAAACTAAGGAGAAG
*
1224476 GGAGAAAAA
1 GAAGAAAAA
1224485 TTTAGTGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.61, C:0.04, G:0.31, T:0.04
Consensus pattern (20 bp):
GAAGAAAAACTAAGGAGAAG
Found at i:1229788 original size:20 final size:20
Alignment explanation
Indices: 1229763--1229811 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1229753 ATAAGCATAG
1229763 GTATTGGACTACCTTTAAAA
1 GTATTGGACTACCTTTAAAA
*
1229783 GTATTGGATTACCTTTAAAA
1 GTATTGGACTACCTTTAAAA
*
1229803 GTAATGGAC
1 GTATTGGAC
1229812 ACAATTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (20 bp):
GTATTGGACTACCTTTAAAA
Found at i:1236235 original size:23 final size:23
Alignment explanation
Indices: 1236207--1236257 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
1236197 TACTGATAAA
1236207 TTTATTTTGTATTCATAAATCAT
1 TTTATTTTGTATTCATAAATCAT
1236230 TTTATTTTGTATTCATAAATCAT
1 TTTATTTTGTATTCATAAATCAT
1236253 TTTAT
1 TTTAT
1236258 GAGTTTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.59
Consensus pattern (23 bp):
TTTATTTTGTATTCATAAATCAT
Found at i:1238642 original size:7 final size:7
Alignment explanation
Indices: 1238632--1238680 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
1238622 ACTGTTGACC
*
1238632 ACCGTTT
1 ACCGTTG
1238639 ACCGTTG
1 ACCGTTG
1238646 ACCGTTG
1 ACCGTTG
*
1238653 A-CTTTG
1 ACCGTTG
*
1238659 ACCGTTT
1 ACCGTTG
1238666 ACCGTTG
1 ACCGTTG
1238673 ACCGTTG
1 ACCGTTG
1238680 A
1 A
1238681 GTCTATTGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (7 bp):
ACCGTTG
Found at i:1242021 original size:7 final size:7
Alignment explanation
Indices: 1242011--1242059 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
1242001 ACTGTTGACC
*
1242011 ACCGTTT
1 ACCGTTG
1242018 ACCGTTG
1 ACCGTTG
1242025 ACCGTTG
1 ACCGTTG
*
1242032 A-CTTTG
1 ACCGTTG
*
1242038 ACCGTTT
1 ACCGTTG
1242045 ACCGTTG
1 ACCGTTG
1242052 ACCGTTG
1 ACCGTTG
1242059 A
1 A
1242060 GTCTATTGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (7 bp):
ACCGTTG
Found at i:1244790 original size:12 final size:11
Alignment explanation
Indices: 1244763--1244789 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1244753 TTTCATTTAA
1244763 TTTTTCTTTGT
1 TTTTTCTTTGT
1244774 TTTTTCTTTGT
1 TTTTTCTTTGT
1244785 TTTTT
1 TTTTT
1244790 TAAAGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTGT
Found at i:1244839 original size:24 final size:24
Alignment explanation
Indices: 1244801--1244856 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1244791 AAAGGTTTTA
1244801 ACATGTTTTTATCTATCTTTATGAC
1 ACAT-TTTTTATCTATCTTTATGAC
* * *
1244826 ATATTTTTTTTCTATTTTTATGAC
1 ACATTTTTTATCTATCTTTATGAC
1244850 ACATTTT
1 ACATTTT
1244857 CGATTGTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.59
Consensus pattern (24 bp):
ACATTTTTTATCTATCTTTATGAC
Found at i:1245406 original size:60 final size:58
Alignment explanation
Indices: 1245336--1245504 Score: 162
Period size: 60 Copynumber: 2.9 Consensus size: 58
1245326 ACTACGACAA
*
1245336 TCATTTTAAATTAATCCTTAAACTTTTAAATATTTCAATTTCATTCTCAAACTATGAC
1 TCATTCTAAATTAATCCTTAAACTTTTAAATATTTCAATTTCATTCTCAAACTATGAC
* * * * * * *
1245394 TTTCATTCTAAATTAGTTCTTATACTTTTGAACATTAT-AATTTCATCCCCAAACTATGAC
1 --TCATTCTAAATTAATCCTTAAACTTTTAAATATT-TCAATTTCATTCTCAAACTATGAC
** * * * *
1245454 TCATTCTAAATTGCTCAC-CAAACTTTTTAATTTTTCAATTCCATTCTCAAA
1 TCATTCTAAATTAATC-CTTAAACTTTTAAATATTTCAATTTCATTCTCAAA
1245505 GTCAAATATG
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
57 1 0.01
58 36 0.41
59 1 0.01
60 48 0.55
61 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.44
Consensus pattern (58 bp):
TCATTCTAAATTAATCCTTAAACTTTTAAATATTTCAATTTCATTCTCAAACTATGAC
Found at i:1245735 original size:58 final size:59
Alignment explanation
Indices: 1245624--1245735 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 59
1245614 TATATACATA
* ** *
1245624 TAGTTTAGGATAAAATTGAAATATTCAAAAAGTTTAGGGACTAATTTAGAATAAAGGTC
1 TAGTTTAGGATAAAAATGAAATATTCAAAAAGTTTAAAGACTAATTTAAAATAAAGGTC
*
1245683 TAGTTTGAGGATAAAAATGAAA-ATTTAAAAA-TTTAAAGACTAATTTAAAATAA
1 TAGTTT-AGGATAAAAATGAAATATTCAAAAAGTTTAAAGACTAATTTAAAATAA
1245736 TAGTCATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 19 0.40
59 14 0.30
60 14 0.30
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (59 bp):
TAGTTTAGGATAAAAATGAAATATTCAAAAAGTTTAAAGACTAATTTAAAATAAAGGTC
Found at i:1246480 original size:108 final size:106
Alignment explanation
Indices: 1246350--1246851 Score: 425
Period size: 108 Copynumber: 4.6 Consensus size: 106
1246340 TGCATTTTTA
* * *
1246350 AAGCTGATAGGGCCATAGAAATCTGACGATAACAAAATATGTTAATTACTTGATTTGTTATCAAT
1 AAGCTGAT-GGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTT-ATTTGTTATCAAT
1246415 ATTATCAACATATTAGGTAGTGCCTAAAATGTTACCAAAGTTT
64 ATTATCAACATATTAGGTAGTGCCTAAAATGTTACCAAAGTTT
* * **** *
1246458 AAGCTGATGGAGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTGGAAACATTATCAGT
1 AAGCTGATGG-GCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACT-TATTTGTTATCAAT
* ** * *** * * **
1246523 CATAAT-AACATAACAAGTAACGCTTATTTAATGTAATAGGTAGCACATTTTT
64 -ATTATCAACATATTAGGT-A-G--TGCCTAA---AAT-GTTACCA-AAGTTT
1246575 AAAGCTGATAGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAA
1 -AAGCTGAT-GGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTT-ATTTGTTATCAA
* ** * * *
1246640 TATTGTCAATTTATTAGGTA-TCGTCT-AAATATTATCAAAGTTT
63 TATTATCAACATATTAGGTAGT-GCCTAAAATGTTACCAAAGTTT
* * *
1246683 AAGTTGATGGGGCCTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTATTTTGTTATTAAT
1 AAGCTGAT-GGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTA-TTTGTTATCAAT
* *
1246748 ATTATCAACATATTATGTAGTGCCTAAAATGTTACTAAAGTTT
64 ATTATCAACATATTAGGTAGTGCCTAAAATGTTACCAAAGTTT
* * * * * * * *
1246791 AAGTTGATGGGACATTCGAAATCCCATGACAACAAAATATGTTAATTTCTTATTTTGTTAT
1 AAGCTGATGGG-CCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTA-TTTGTTAT
1246852 GTTGAAAATA
Statistics
Matches: 315, Mismatches: 58, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
106 1 0.00
107 82 0.26
108 132 0.42
109 9 0.03
110 4 0.01
112 4 0.01
113 2 0.01
114 2 0.01
115 3 0.01
116 5 0.02
117 8 0.03
118 61 0.19
119 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (106 bp):
AAGCTGATGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTATTTGTTATCAATAT
TATCAACATATTAGGTAGTGCCTAAAATGTTACCAAAGTTT
Found at i:1249103 original size:21 final size:21
Alignment explanation
Indices: 1249078--1249117 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1249068 AAGACTCTAT
1249078 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
1249099 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
1249118 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:1252968 original size:23 final size:22
Alignment explanation
Indices: 1252926--1252986 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
1252916 TTGGTGCAGA
* *
1252926 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
1252948 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
1252971 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
1252987 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:1253012 original size:20 final size:22
Alignment explanation
Indices: 1252926--1253007 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 22
1252916 TTGGTGCAGA
*
1252926 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
1252948 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
*
1252971 GGGAACCGATTCCCCC---ACAG
1 GGGAACCGATACCCCCTTGA-AG
*
1252991 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
1253008 GAGGGTTCTG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.02
20 16 0.30
22 14 0.26
23 22 0.42
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:1256553 original size:22 final size:22
Alignment explanation
Indices: 1256526--1256570 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1256516 AATTTCAAAA
1256526 ATATATAATATATAGCTTTTGAAG
1 ATATAT-A-ATATAGCTTTTGAAG
*
1256550 ATATATAATATAGTTTTTGAA
1 ATATATAATATAGCTTTTGAA
1256571 AACATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 1 0.05
24 6 0.30
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (22 bp):
ATATATAATATAGCTTTTGAAG
Found at i:1256577 original size:22 final size:22
Alignment explanation
Indices: 1256535--1256577 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1256525 AATATATAAT
* *
1256535 ATATAGCTTTTGAAGATATATA
1 ATATAGCTTTTGAAAACATATA
*
1256557 ATATAGTTTTTGAAAACATAT
1 ATATAGCTTTTGAAAACATAT
1256578 TTTTGAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (22 bp):
ATATAGCTTTTGAAAACATATA
Found at i:1256590 original size:36 final size:36
Alignment explanation
Indices: 1256542--1256722 Score: 160
Period size: 36 Copynumber: 5.0 Consensus size: 36
1256532 AATATATAGC
*
1256542 TTTTGAAGATATATAATATAGTTTTTGAAAACATAT
1 TTTTGAAAATATATAATATAGTTTTTGAAAACATAT
*
1256578 TTTTGAAAATATATAATATATAGTTTTT--AAA-ATGGT
1 TTTTGAAAATATAT-A-ATATAGTTTTTGAAAACAT-AT
*
1256614 TTTTAAAAAATATATAATATAGTTTTTGAAAACAT-T
1 TTTT-GAAAATATATAATATAGTTTTTGAAAACATAT
* ** *
1256650 ATTTTGAAAAAATATAATATATAGTTTTAAAAAACA-GT
1 -TTTTGAAAATATAT-A-ATATAGTTTTTGAAAACATAT
* *
1256688 TTTTGAAAACATAT-ATAATA-TTTTTGAAAAAATAT
1 TTTTGAAAATATATAAT-ATAGTTTTTGAAAACATAT
1256723 AACATAGTTT
Statistics
Matches: 120, Mismatches: 12, Indels: 27
0.75 0.08 0.17
Matches are distributed among these distances:
34 11 0.09
35 17 0.14
36 31 0.26
37 31 0.26
38 30 0.25
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTTGAAAATATATAATATAGTTTTTGAAAACATAT
Found at i:1256632 original size:73 final size:75
Alignment explanation
Indices: 1256550--1256708 Score: 243
Period size: 73 Copynumber: 2.1 Consensus size: 75
1256540 GCTTTTGAAG
* * **
1256550 ATATATAATATAGTTTTTGAAAACA-TATTTTTGAAAATATATAATATATAGTTTT-TAAAATGG
1 ATATATAATATAGTTTTTGAAAACATTA-TTTTGAAAAAATATAATATATAGTTTTAAAAAACAG
1256613 TTTTT-AAAAA
65 TTTTTGAAAAA
1256623 ATATATAATATAGTTTTTGAAAACATTATTTTGAAAAAATATAATATATAGTTTTAAAAAACAGT
1 ATATATAATATAGTTTTTGAAAACATTATTTTGAAAAAATATAATATATAGTTTTAAAAAACAGT
*
1256688 TTTTGAAAAC
66 TTTTGAAAAA
1256698 ATATATAATAT
1 ATATATAATAT
1256709 TTTTGAAAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
73 51 0.65
74 12 0.15
75 15 0.19
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (75 bp):
ATATATAATATAGTTTTTGAAAACATTATTTTGAAAAAATATAATATATAGTTTTAAAAAACAGT
TTTTGAAAAA
Found at i:1256633 original size:37 final size:37
Alignment explanation
Indices: 1256550--1256708 Score: 150
Period size: 38 Copynumber: 4.3 Consensus size: 37
1256540 GCTTTTGAAG
**
1256550 ATATAT-A-ATATAGTTTTTGAAAACA-TATTTTTGAAA
1 ATATATAATATATAGTTTTT-AAAACAGT-TTTTAAAAA
**
1256586 ATATATAATATATAGTTTTTAAAATGGTTTTTAAAAA
1 ATATATAATATATAGTTTTTAAAACAGTTTTTAAAAA
* *
1256623 ATATAT-A-ATATAGTTTTTGAAAACATTATTTTGAAAA
1 ATATATAATATATAGTTTTT-AAAACAGT-TTTTAAAAA
* *
1256660 A-ATATAATATATAGTTTTAAAAAACAGTTTTTGAAAAC
1 ATATATAATATATAGTTTT-TAAAACAGTTTTT-AAAAA
1256698 ATATATAATAT
1 ATATATAATAT
1256709 TTTTGAAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
35 11 0.11
36 16 0.16
37 32 0.32
38 33 0.33
39 9 0.09
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTAAAACAGTTTTTAAAAA
Found at i:1256713 original size:21 final size:21
Alignment explanation
Indices: 1256685--1256773 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 21
1256675 TTTAAAAAAC
1256685 AGTTTTTGAAAACATATATAAT
1 AGTTTTTGAAAACATATAT-AT
* *
1256707 A-TTTTTGAAAAAATATAACAT
1 AGTTTTTGAAAACATAT-ATAT
*
1256728 AGTTTTT-AAAA-AGAT-T-T
1 AGTTTTTGAAAACATATATAT
1256745 --TTTTTGAAAACATA-ATAT
1 AGTTTTTGAAAACATATATAT
1256763 AGTTTTTGAAA
1 AGTTTTTGAAA
1256774 TATAATGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
15 5 0.09
16 4 0.07
17 4 0.07
18 1 0.02
20 12 0.22
21 21 0.39
22 7 0.13
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (21 bp):
AGTTTTTGAAAACATATATAT
Found at i:1256719 original size:58 final size:57
Alignment explanation
Indices: 1256651--1256800 Score: 153
Period size: 58 Copynumber: 2.5 Consensus size: 57
1256641 GAAAACATTA
1256651 TTTTGAAAAAATATAATATATAGTTTTAAAAA-ACAGTTTTTGAAAACATATATAATA-T
1 TTTTGAAAAAATAT-ATATATAGTTTTAAAAAGACAGTTTTTGAAAACATA-AT-ATAGT
* ***
1256709 TTTTGAAAAAATATA-ACATAGTTTTTAAAAAGATTTTTTTTGAAAACATAATATAGT
1 TTTTGAAAAAATATATATATAG-TTTTAAAAAGACAGTTTTTGAAAACATAATATAGT
*
1256766 TTTTGAAATATAATGTATGTTATATAGTTTTAAAA
1 TTTTGAAA-A-AA--TAT-ATATATAGTTTTAAAA
1256801 TAAATATAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
56 8 0.10
57 21 0.27
58 30 0.39
59 2 0.03
61 3 0.04
62 8 0.10
63 5 0.06
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (57 bp):
TTTTGAAAAAATATATATATAGTTTTAAAAAGACAGTTTTTGAAAACATAATATAGT
Found at i:1256853 original size:8 final size:9
Alignment explanation
Indices: 1256823--1256875 Score: 51
Period size: 8 Copynumber: 6.1 Consensus size: 9
1256813 ACGTGTTATT
1256823 TATTATATA
1 TATTATATA
1256832 TATATATATA
1 TAT-TATATA
1256842 TATTATAT-
1 TATTATATA
1256850 TATTAT-TA
1 TATTATATA
*
1256858 -AGTTATATT
1 TA-TTATATA
1256867 TATTA-ATA
1 TATTATATA
1256875 T
1 T
1256876 GTTTTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
7 2 0.05
8 13 0.35
9 12 0.32
10 10 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
TATTATATA
Found at i:1258615 original size:18 final size:18
Alignment explanation
Indices: 1258592--1258635 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1258582 ATGATGGTTG
* *
1258592 ATACTTTAGCAAGTATCC
1 ATACTTTAGCAAATATCA
*
1258610 ATACTTACAGCAAATATCA
1 ATACTT-TAGCAAATATCA
1258629 ATACTTT
1 ATACTTT
1258636 TAGAGTAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (18 bp):
ATACTTTAGCAAATATCA
Found at i:1258670 original size:17 final size:17
Alignment explanation
Indices: 1258645--1258680 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1258635 TTAGAGTAAG
* *
1258645 TATGGATACATTATTAT
1 TATGAATACATTATAAT
1258662 TATGAATACATTATAAT
1 TATGAATACATTATAAT
1258679 TA
1 TA
1258681 ACCTTTAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (17 bp):
TATGAATACATTATAAT
Found at i:1258994 original size:23 final size:23
Alignment explanation
Indices: 1258967--1259038 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
1258957 CGGTAGCTAG
* *
1258967 TTTAACGTAATATGTAGCGCTTA
1 TTTAACGTAATAGGTAGCGCCTA
*
1258990 TTTAACGTAATAGGTAGTGCCTA
1 TTTAACGTAATAGGTAGCGCCTA
* **
1259013 TTTAACATAATAGGTAGAACCTA
1 TTTAACGTAATAGGTAGCGCCTA
1259036 TTT
1 TTT
1259039 TATTTTACCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (23 bp):
TTTAACGTAATAGGTAGCGCCTA
Found at i:1259146 original size:75 final size:75
Alignment explanation
Indices: 1259013--1259178 Score: 233
Period size: 75 Copynumber: 2.2 Consensus size: 75
1259003 GTAGTGCCTA
* * * *
1259013 TTTAACATAATAGGTAGAACCTATTTTATTTTACCTTTTACATTTTTAGTAATCTTTAAACAAAT
1 TTTAACGTAATAGGTAGAACATATTTTATTTTACCGTTTACATTATTAGTAATCTTTAAACAAAT
*
1259078 CGATAGATAT
66 CGATAGATAG
* ** * *
1259088 TTTAATGTAATAGGTATCACATATTTTATTTTACCGTTTACATTATTATTAATTTTTAAACAAAT
1 TTTAACGTAATAGGTAGAACATATTTTATTTTACCGTTTACATTATTAGTAATCTTTAAACAAAT
*
1259153 CGATAGCTAG
66 CGATAGATAG
1259163 TTTAACGTAATAGGTA
1 TTTAACGTAATAGGTA
1259179 ACGCTTATTT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.44
Consensus pattern (75 bp):
TTTAACGTAATAGGTAGAACATATTTTATTTTACCGTTTACATTATTAGTAATCTTTAAACAAAT
CGATAGATAG
Found at i:1259193 original size:23 final size:23
Alignment explanation
Indices: 1259163--1259234 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
1259153 CGATAGCTAG
* *
1259163 TTTAACGTAATAGGTAACGCTTA
1 TTTAACGTAATAGGTAACACCTA
*
1259186 TTTAACGTAATAGGTAGCACCTA
1 TTTAACGTAATAGGTAACACCTA
* *
1259209 TTTAACATAATAGGTAAGACCTA
1 TTTAACGTAATAGGTAACACCTA
1259232 TTT
1 TTT
1259235 TATTTTACTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (23 bp):
TTTAACGTAATAGGTAACACCTA
Found at i:1259252 original size:196 final size:196
Alignment explanation
Indices: 1258918--1259316 Score: 570
Period size: 196 Copynumber: 2.0 Consensus size: 196
1258908 AAGTTGTATA
* * *
1258918 TATTTTATCGTTTACATTATTATTAACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATATGTA
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGATAGCTAGTTTAACGTAATAGGTA
* **
1258983 GCGCTTATTTAACGTAATAGGTAGTGCCTATTTAACATAATAGGTAGAACCTATTTTATTTTACC
66 ACGCTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGTAGAACCTATTTTATTTTACC
* * * * * * ** *
1259048 TTTTACATTTTTAGTAATCTTTAAACAAATCGATAGATATTTTAATGTAATAGGTATC-ACATAT
131 TGTTACATTATTAGTAACCTTCAAACAAACCGATAGATAGTTTAACATAATAGGTAGCGAC-TAT
1259112 TT
195 TT
** *
1259114 TATTTTACCGTTTACATTATTATTAATTTTTAAACAAATCGATAGCTAGTTTAACGTAATAGGTA
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGATAGCTAGTTTAACGTAATAGGTA
1259179 ACGCTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGTA-AGACCTATTTTATTTTA-
66 ACGCTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGTAGA-ACCTATTTTATTTTAC
* *
1259242 CTGGTTACATTATTAGTAACCTTCAAACAAACCGGTAGGTAGTTTAACATAATAGGTAGCGACTA
130 CT-GTTACATTATTAGTAACCTTCAAACAAACCGATAGATAGTTTAACATAATAGGTAGCGACTA
1259307 TTT
194 TTT
1259310 TATTTTA
1 TATTTTA
1259317 ACCGATTAAA
Statistics
Matches: 180, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
195 3 0.02
196 175 0.97
197 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (196 bp):
TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCGATAGCTAGTTTAACGTAATAGGTA
ACGCTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGTAGAACCTATTTTATTTTACC
TGTTACATTATTAGTAACCTTCAAACAAACCGATAGATAGTTTAACATAATAGGTAGCGACTATT
T
Found at i:1263158 original size:16 final size:16
Alignment explanation
Indices: 1263139--1263186 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1263129 TTTAGTTATA
1263139 TTTTCATTGATGAAAG
1 TTTTCATTGATGAAAG
1263155 TTTT-ACTTGAT---A-
1 TTTTCA-TTGATGAAAG
1263167 TTTTCATTGATGAAAG
1 TTTTCATTGATGAAAG
1263183 TTTT
1 TTTT
1263187 ACTTGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
12 9 0.35
13 2 0.08
15 2 0.08
16 13 0.50
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTTCATTGATGAAAG
Found at i:1263192 original size:16 final size:16
Alignment explanation
Indices: 1263145--1263193 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1263135 TATATTTTCA
1263145 TTGATGAAAGTTTTAC
1 TTGATGAAAGTTTTAC
1263161 TTGAT---A-TTTT-C
1 TTGATGAAAGTTTTAC
1263172 ATTGATGAAAGTTTTAC
1 -TTGATGAAAGTTTTAC
1263189 TTGAT
1 TTGAT
1263194 ATTTATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
11 1 0.04
12 9 0.33
13 1 0.04
15 1 0.04
16 14 0.52
17 1 0.04
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (16 bp):
TTGATGAAAGTTTTAC
Found at i:1263213 original size:28 final size:28
Alignment explanation
Indices: 1263128--1263197 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
1263118 AGCTATTAAA
*
1263128 TTTTAGTT-ATATTTTCATTGATGAAAG
1 TTTTACTTGATATTTTCATTGATGAAAG
1263155 TTTTACTTGATATTTTCATTGATGAAAG
1 TTTTACTTGATATTTTCATTGATGAAAG
1263183 TTTTACTTGATATTT
1 TTTTACTTGATATTT
1263198 ATTATGATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 34 0.83
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.54
Consensus pattern (28 bp):
TTTTACTTGATATTTTCATTGATGAAAG
Found at i:1267930 original size:22 final size:23
Alignment explanation
Indices: 1267881--1267936 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1267871 AATTTGACTT
1267881 TTTGGTCAAA-TTCAAAATCAAC
1 TTTGGTCAAAGTTCAAAATCAAC
** *
1267903 GCTGGTCAAAGTT-AAAGTCAAC
1 TTTGGTCAAAGTTCAAAATCAAC
*
1267925 TTTGGTTAAAGT
1 TTTGGTCAAAGT
1267937 CAACAAGTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (23 bp):
TTTGGTCAAAGTTCAAAATCAAC
Found at i:1268746 original size:23 final size:23
Alignment explanation
Indices: 1268720--1268767 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1268710 TTGGATTTAA
1268720 GATAGTTTTCTATAATCAATTTG
1 GATAGTTTTCTATAATCAATTTG
1268743 GATAGTTTTCTATAATCAATTTG
1 GATAGTTTTCTATAATCAATTTG
1268766 GA
1 GA
1268768 CCGTTGGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (23 bp):
GATAGTTTTCTATAATCAATTTG
Found at i:1273999 original size:30 final size:30
Alignment explanation
Indices: 1273963--1274019 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1273953 GAGTTGAGGG
*
1273963 TTACCTATG-TCCTTCGGGACATATGGACAA
1 TTACCTATGCT-CTTCGGAACATATGGACAA
*
1273993 TTACCTATGCTCTTTGGAACATATGGA
1 TTACCTATGCTCTTCGGAACATATGGA
1274020 TAGCGGTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (30 bp):
TTACCTATGCTCTTCGGAACATATGGACAA
Found at i:1275210 original size:18 final size:18
Alignment explanation
Indices: 1275187--1275231 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1275177 TTCATGTATC
1275187 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGT
**
1275205 TAGTTCATTGAATAATTT
1 TAGTTCATTGAATAAAGT
1275223 TAGTTCATT
1 TAGTTCATT
1275232 AATCAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (18 bp):
TAGTTCATTGAATAAAGT
Found at i:1279450 original size:23 final size:23
Alignment explanation
Indices: 1279399--1279452 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1279389 TGAAGGACTA
1279399 CATAGAATTGTCCCGAAAGACCG
1 CATAGAATTGTCCCGAAAGACCG
**
1279422 TGTAGAATTGTCCC-AAAGGACCG
1 CATAGAATTGTCCCGAAA-GACCG
1279445 CATAGAAT
1 CATAGAAT
1279453 CCCTCATCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (23 bp):
CATAGAATTGTCCCGAAAGACCG
Found at i:1281247 original size:19 final size:19
Alignment explanation
Indices: 1281223--1281273 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1281213 GAAAATATTC
1281223 AGAGTGCATTGATGCATGG
1 AGAGTGCATTGATGCATGG
* *
1281242 AGAGTGCATCGGTGCATGG
1 AGAGTGCATTGATGCATGG
1281261 A-A-TGCATTCGATG
1 AGAGTGCATT-GATG
1281274 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 18 0.67
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATTGATGCATGG
Found at i:1281249 original size:65 final size:65
Alignment explanation
Indices: 1281131--1281275 Score: 177
Period size: 65 Copynumber: 2.2 Consensus size: 65
1281121 ATGCATCATG
* ***
1281131 AAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTTGTGCATCGATGCATC
1 AAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGAGTGCATCGATGCATC
** * *
1281195 AAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATTGATGCATGGAGAGTGCATCGGTGCAT
1 AAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAGAGTGCATCGATGCAT
*
1281259 G
65 C
*
1281260 GAATGCATTCGATGTT
1 AAATGCATTCGATGTT
1281276 CAATTAATTC
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 23 0.33
65 46 0.67
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (65 bp):
AAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGAGTGCATCGATGCATC
Found at i:1287781 original size:22 final size:21
Alignment explanation
Indices: 1287739--1287778 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1287729 GAGTTTGTTT
*
1287739 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1287760 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1287779 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1289774 original size:64 final size:64
Alignment explanation
Indices: 1289703--1289932 Score: 219
Period size: 64 Copynumber: 3.6 Consensus size: 64
1289693 TTGGAACACT
* ***
1289703 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCC
** * * ** **
1289767 TGATGCATCGATGCATGGCTTGTGAATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCC
* * * * * ** * *
1289831 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTCAATTAAT-TCA
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCC
* *
1289895 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
1289933 CCTTTGAATA
Statistics
Matches: 133, Mismatches: 30, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
64 72 0.54
65 61 0.46
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (64 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCC
Found at i:1289855 original size:19 final size:19
Alignment explanation
Indices: 1289831--1289881 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1289821 GAAAATATTC
1289831 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1289850 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1289869 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1289882 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1289873 original size:65 final size:63
Alignment explanation
Indices: 1289724--1289932 Score: 199
Period size: 65 Copynumber: 3.2 Consensus size: 63
1289714 TGCACCAAGT
* ** * ***
1289724 GTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTT-TAAAATATTCAGATGCATCGATGCATGGAGA
* *
1289788 GTGAATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTT-AAAATATTCAGA-TGCATCGATGCATGGAGA
* * * *
1289853 GTGCATCGGTGCATGGAATGCATTCGATG--TTCAATTAATTCATCGATGCATCGATGCATGGAC
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTAAAAT-ATTCA--GATGCATCGATGCATGGA-
1289916 TGA
62 -GA
*
1289919 -TGCATCGGTGCATG
1 GTGCATCGATGCATG
1289933 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
62 3 0.02
63 7 0.06
64 55 0.45
65 56 0.46
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTAAAATATTCAGATGCATCGATGCATGGAGA
Found at i:1295922 original size:24 final size:25
Alignment explanation
Indices: 1295872--1295924 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
1295862 TTGCAGTTGA
* *
1295872 AAGTACCGCATAGAATTTTGCACCG
1 AAGTACCACATAGAATTATGCACCG
*
1295897 AAGTACCACGTAGAA-TATGCACCG
1 AAGTACCACATAGAATTATGCACCG
1295921 AAGT
1 AAGT
1295925 GCCGCTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (25 bp):
AAGTACCACATAGAATTATGCACCG
Found at i:1295934 original size:24 final size:25
Alignment explanation
Indices: 1295872--1295934 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
1295862 TTGCAGTTGA
*
1295872 AAGTACCGCATAGAATTTTGCACCG
1 AAGTACCGCATAGAATTATGCACCG
* *
1295897 AAGTACCACGTAGAA-TATGCACCG
1 AAGTACCGCATAGAATTATGCACCG
* *
1295921 AAGTGCCGCTTAGA
1 AAGTACCGCATAGA
1295935 TTTGTCTCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 19 0.59
25 13 0.41
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (25 bp):
AAGTACCGCATAGAATTATGCACCG
Found at i:1295957 original size:23 final size:23
Alignment explanation
Indices: 1295931--1295996 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
1295921 AAGTGCCGCT
*
1295931 TAGATTTGTCTCGAAGGACCACA
1 TAGATTTGTCCCGAAGGACCACA
*
1295954 TAGATTTGTCCCGAAGGACCATA
1 TAGATTTGTCCCGAAGGACCACA
* * *
1295977 TATAATTATCCCGAAGGACC
1 TAGATTTGTCCCGAAGGACC
1295997 GCGTAGAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (23 bp):
TAGATTTGTCCCGAAGGACCACA
Found at i:1300876 original size:72 final size:73
Alignment explanation
Indices: 1300763--1300933 Score: 265
Period size: 72 Copynumber: 2.4 Consensus size: 73
1300753 TTTTCTACCG
* * * **
1300763 TGTTTACCGATGTCGGTATTTAA-GTTGGGAAATTGGCGAATTCAATTTGTGAAAATAACGTTGC
1 TGTTTACCTATATCGGTAATTAACGTTACGAAATTGGCGAATTCAATTTGTGAAAATAACGTTGC
1300827 GATAGTA-
66 GATAGTAC
*
1300834 TGTTTACCTATATCGGTAATTAGCGTTACGAAATTGGCGAATTCAATTTGTGAAAATAACGTTGC
1 TGTTTACCTATATCGGTAATTAACGTTACGAAATTGGCGAATTCAATTTGTGAAAATAACGTTGC
1300899 GATAGTAC
66 GATAGTAC
*
1300907 TTTTTACCTATATCGGTAATTAACGTT
1 TGTTTACCTATATCGGTAATTAACGTT
1300934 GCGATTTTCC
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
71 19 0.21
72 46 0.51
73 25 0.28
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (73 bp):
TGTTTACCTATATCGGTAATTAACGTTACGAAATTGGCGAATTCAATTTGTGAAAATAACGTTGC
GATAGTAC
Found at i:1300981 original size:57 final size:57
Alignment explanation
Indices: 1300893--1301015 Score: 210
Period size: 57 Copynumber: 2.2 Consensus size: 57
1300883 GTGAAAATAA
*
1300893 CGTTGCGATAGTACTTTTTACCTATATCGGTAATTAACGTTGCGATTTTCCTATTCG
1 CGTTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTGCGATTTTCCTATTCG
* *
1300950 CGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGATTTTGCTATTCG
1 CGTTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTGCGATTTTCCTATTCG
*
1301007 TGTTGCGAT
1 CGTTGCGAT
1301016 TTTCCAATTC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (57 bp):
CGTTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTGCGATTTTCCTATTCG
Found at i:1301013 original size:20 final size:20
Alignment explanation
Indices: 1300981--1301039 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
1300971 CTATATCGGT
*
1300981 AATTAGCGTTGCGATTTTGC
1 AATTCGCGTTGCGATTTTGC
* * *
1301001 TATTCGTGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTGC
1301021 AATTCGCGTTGCGATTTTG
1 AATTCGCGTTGCGATTTTG
1301040 GAACCTGTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.44
Consensus pattern (20 bp):
AATTCGCGTTGCGATTTTGC
Found at i:1306053 original size:12 final size:12
Alignment explanation
Indices: 1306036--1306081 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1306026 TGTATATCAC
1306036 ATATGAGAAAAA
1 ATATGAGAAAAA
*
1306048 ATATGA-AGAAAC
1 ATATGAGA-AAAA
1306060 AT-TGAGAAAAA
1 ATATGAGAAAAA
1306071 ATATGAAGAAA
1 ATATG-AGAAA
1306082 CATATATCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.17
Consensus pattern (12 bp):
ATATGAGAAAAA
Found at i:1306065 original size:23 final size:24
Alignment explanation
Indices: 1306034--1306086 Score: 99
Period size: 23 Copynumber: 2.2 Consensus size: 24
1306024 TATGTATATC
1306034 ACATATGAGAAAAAATATGAAGAA
1 ACATATGAGAAAAAATATGAAGAA
1306058 ACAT-TGAGAAAAAATATGAAGAA
1 ACATATGAGAAAAAATATGAAGAA
1306081 ACATAT
1 ACATAT
1306087 ATCTATTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (24 bp):
ACATATGAGAAAAAATATGAAGAA
Found at i:1314114 original size:55 final size:55
Alignment explanation
Indices: 1314058--1314686 Score: 903
Period size: 55 Copynumber: 11.7 Consensus size: 55
1314048 CGGGTTCGCT
* * * * * *
1314058 CCCTCTTTCTTTAGAGAGTAT-AGAACTCGGACAATCTTCAATAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGCGTCTGCC
* ** *
1314113 CCCTATTTCTTCAGAGAGTATAAGAC-CCAA-TTTCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
1314166 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTTTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
1314221 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT-GCGTCTGTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
1314275 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTG-C
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
1314329 CCCTATTTCTTCAGAGAGTATAAGAC-C---CAATCTTCATA-AATCGCGTATGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAATCGCGTCTGCC
* *
1314380 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
1314435 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
1314490 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
1314545 CCCTATTTCTTC--AGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTG-C
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
1314597 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATA-AAGCGCGTATGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAATCGCGTCTGCC
1314650 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCT
1314687 CCATCAAACG
Statistics
Matches: 521, Mismatches: 36, Indels: 34
0.88 0.06 0.06
Matches are distributed among these distances:
50 18 0.03
51 28 0.05
52 32 0.06
53 112 0.21
54 95 0.18
55 234 0.45
56 2 0.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
Found at i:1314212 original size:108 final size:110
Alignment explanation
Indices: 1314058--1314686 Score: 896
Period size: 108 Copynumber: 5.8 Consensus size: 110
1314048 CGGGTTCGCT
* * * * *
1314058 CCCTCTTTCTTTAGAGAGTAT-AGAACTCG-GACAATCTTCAATAATCGTGTCTGCTCCCTATTT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAG-CAATCTTCAACAATCGCGTCTGCCCCCTATTT
* ** *
1314121 CTTCAGAGAGTATAAGAC-CCAA-TTTCTTCATCAATCGCGTCTGCC
64 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
1314166 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTTTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGCGTCTGCCCCCTATTTCT
*
1314231 TCAGAGAGTATAAGACTCGAACAATCTTCAACAAT-GCGTCTGTC
66 TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
1314275 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTG-CCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGCGTCTGCCCCCTATTTCT
*
1314339 TCAGAGAGTATAAGAC-C---CAATCTTCATA-AATCGCGTATGCC
66 TCAGAGAGTATAAGACTCGAACAATCTTCA-ACAATCGCGTCTGCC
*
1314380 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGCGTCTGCCCCCTATTTCT
*
1314445 TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGTC
66 TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
1314490 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGCGTCTGCCCCCTATTTCT
*
1314555 TC--AGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTG-C
66 TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
1314597 CCCTATTTCTTCAGAGAGTATAAGAC-CCA-CAATCTTCATA-AAGCGCGTATGCCCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCA-ACAATCGCGTCTGCCCCCTATTTC
1314659 TTCAGAGAGTATAAGACTCGAACAATCT
65 TTCAGAGAGTATAAGACTCGAACAATCT
1314687 CCATCAAACG
Statistics
Matches: 477, Mismatches: 29, Indels: 31
0.89 0.05 0.06
Matches are distributed among these distances:
104 12 0.03
105 89 0.19
106 30 0.06
107 52 0.11
108 136 0.29
109 64 0.13
110 94 0.20
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (110 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGCGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
Found at i:1314563 original size:214 final size:214
Alignment explanation
Indices: 1314058--1314686 Score: 959
Period size: 214 Copynumber: 2.9 Consensus size: 214
1314048 CGGGTTCGCT
* * * ** * *
1314058 CCCTCTTTCTTTAGAGAGTAT-AGAACTCGGACAATCTTCAATAATCGTGTCTGCTCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTC
*
1314122 TTCAGAGAGTATAAGACCCAATTTCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTAT
65 TTCA-AGAGTATAAGACCCAA--TCTTCATAAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTAT
*
1314187 AAGACTCGAGCAATCTTCAACAATCGTGTTTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA
127 AAGACTCGAGCAATCTTCAACAATCGTGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA
1314252 CAATCTTCAACAATGCGTCTGTC
192 CAATCTTCAACAATGCGTCTGTC
1314275 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTG-CCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
*
1314339 TCAGAGAGTATAAGACCCAATCTTCATAAATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAG
66 TCA-AGAGTATAAGACCCAATCTTCATAAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
1314404 ACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
130 ACTCGAGCAATCTTCAACAATCGTGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1314469 TCTTCAACAATCGCGTCTGTC
195 TCTTCAACAAT-GCGTCTGTC
1314490 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
*
1314555 TC-AGAGTATAAGACTCGAACAATCTTCA-ACGATCGCGTCTG-CCCCTATTTCTTCAGAGAGTA
66 TCAAGAGTATAAGAC-C---CAATCTTCATA-AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTA
* * *
1314617 TAAGAC-CCA-CAATCTTCATA-AAGCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
126 TAAGACTCGAGCAATCTTCA-ACAATCGTGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
1314679 AACAATCT
190 AACAATCT
1314687 CCATCAAACG
Statistics
Matches: 387, Mismatches: 16, Indels: 20
0.91 0.04 0.05
Matches are distributed among these distances:
214 130 0.34
215 119 0.31
216 46 0.12
217 72 0.19
218 20 0.05
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (214 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
TCAAGAGTATAAGACCCAATCTTCATAAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA
CTCGAGCAATCTTCAACAATCGTGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
CTTCAACAATGCGTCTGTC
Found at i:1315690 original size:18 final size:19
Alignment explanation
Indices: 1315663--1315703 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1315653 TGAACCTCAT
1315663 TTTTTCATTTTTTCATTCA
1 TTTTTCATTTTTTCATTCA
**
1315682 TTTTT-ATTTTTTTTTTCA
1 TTTTTCATTTTTTCATTCA
1315700 TTTT
1 TTTT
1315704 CACTCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTCATTTTTTCATTCA
Found at i:1331310 original size:57 final size:57
Alignment explanation
Indices: 1331219--1331334 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
1331209 GGAGGTAATC
*
1331219 CACTGGAAAAACAGAATCAATGCACAATTAACTTTGAGTGGCAATGTGGAAACACAT
1 CACTGGAAAAACAGAATCAATGCACAATTAACTTTGAGAGGCAATGTGGAAACACAT
*
1331276 CACTGGAAAAACAGAATCAATGCACAATTGACTTTGAGAGGCAATGTGGAAACACAT
1 CACTGGAAAAACAGAATCAATGCACAATTAACTTTGAGAGGCAATGTGGAAACACAT
1331333 CA
1 CA
1331335 AAGGAAATAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (57 bp):
CACTGGAAAAACAGAATCAATGCACAATTAACTTTGAGAGGCAATGTGGAAACACAT
Found at i:1332087 original size:21 final size:21
Alignment explanation
Indices: 1332061--1332108 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1332051 GTAGCTAGCA
*
1332061 TTAAACCTAGGAGAACCAATG
1 TTAAACCGAGGAGAACCAATG
* *
1332082 TTAAACCGGGGAGAATCAATG
1 TTAAACCGAGGAGAACCAATG
*
1332103 GTAAAC
1 TTAAAC
1332109 TCTGAAGCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.19
Consensus pattern (21 bp):
TTAAACCGAGGAGAACCAATG
Found at i:1334936 original size:39 final size:38
Alignment explanation
Indices: 1334889--1334970 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 38
1334879 ATGTAATCAC
1334889 CACAACACACGATTACTAGGCACGAGAATCACACAAAA
1 CACAACACACGATTACTAGGCACGAGAATCACACAAAA
1334927 CACAGACACACGATTACTAGGCACGAGAATCACACAAAA
1 CACA-ACACACGATTACTAGGCACGAGAATCACACAAAA
1334966 CACAA
1 CACAA
1334971 GAGAAATCGC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 5 0.12
39 38 0.88
ACGTcount: A:0.48, C:0.29, G:0.13, T:0.10
Consensus pattern (38 bp):
CACAACACACGATTACTAGGCACGAGAATCACACAAAA
Found at i:1335704 original size:15 final size:15
Alignment explanation
Indices: 1335659--1335709 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1335649 CTTATTTAAA
* *
1335659 TATTTGATTATATATA
1 TATTTGATTAT-TTTT
*
1335675 TATTTTAATTA-TTTT
1 TA-TTTGATTATTTTT
1335690 TATTTGATTATTTTT
1 TATTTGATTATTTTT
1335705 TATTT
1 TATTT
1335710 AAAAACTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 7 0.24
15 13 0.45
16 2 0.07
17 7 0.24
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (15 bp):
TATTTGATTATTTTT
Found at i:1335808 original size:14 final size:14
Alignment explanation
Indices: 1335791--1335817 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1335781 GCACATATAT
1335791 TTTGATTATTTTTA
1 TTTGATTATTTTTA
1335805 TTTGATTATTTTT
1 TTTGATTATTTTT
1335818 TTGTTTAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (14 bp):
TTTGATTATTTTTA
Found at i:1335875 original size:110 final size:111
Alignment explanation
Indices: 1335672--1335911 Score: 322
Period size: 110 Copynumber: 2.2 Consensus size: 111
1335662 TTGATTATAT
1335672 ATATATTTTAATTATTTTTATTTGATTATTTTTTATTTAAAAACTATATTTTATCATTTTATATA
1 ATATATTTTAATTATTTTTATTTGATTATTTTTTATTTAAAAACTATATTTTATCA-TTTATATA
* * * *
1335737 TGTATATATATTTTTAATATTTTATTTATAAGCCTATTATTATTGCAC
65 -GTATATATACTCTTAATAGTTTATTTATAAGCCTATTATTATTACAC
* * ***
1335785 ATATATTTTGATTATTTTTATTTGATTATTTTTTTGTTTAAGCGCTATATTTTATCA-TTATATA
1 ATATATTTTAATTATTTTTATTTGATTA-TTTTTTATTTAAAAACTATATTTTATCATTTATATA
* * * *
1335849 -TATATATACTCTTAATAGTTTATTTATACGTCTATTATTATTATAT
65 GTATATATACTCTTAATAGTTTATTTATAAGCCTATTATTATTACAC
1335895 ATATATTTTAATTATTT
1 ATATATTTTAATTATTT
1335912 GATTATTTTT
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
110 54 0.48
112 7 0.06
113 27 0.24
114 24 0.21
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (111 bp):
ATATATTTTAATTATTTTTATTTGATTATTTTTTATTTAAAAACTATATTTTATCATTTATATAG
TATATATACTCTTAATAGTTTATTTATAAGCCTATTATTATTACAC
Found at i:1336065 original size:1 final size:1
Alignment explanation
Indices: 1336059--1336103 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
1336049 TAGATTATTA
* * * *
1336059 TTTTTTTTATTTTTTTTTTTTTTTTCTTTTTTTTTCTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1336104 CCTTTTCTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.02, C:0.07, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:1336081 original size:17 final size:17
Alignment explanation
Indices: 1336059--1336098 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
1336049 TAGATTATTA
1336059 TTTTTTTTATTTTTTTT
1 TTTTTTTTATTTTTTTT
*
1336076 TTTTTTTTCTTTTTTTT
1 TTTTTTTTATTTTTTTT
1336093 TCTTTT
1 T-TTTT
1336099 CTTTTCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.03, C:0.05, G:0.00, T:0.93
Consensus pattern (17 bp):
TTTTTTTTATTTTTTTT
Found at i:1336108 original size:6 final size:5
Alignment explanation
Indices: 1336059--1336114 Score: 57
Period size: 5 Copynumber: 11.8 Consensus size: 5
1336049 TAGATTATTA
* *
1336059 TTTT- TTTTA TTTT- TTTT- TTTT- TTTTC TTTTT TTTTC TTTTC TTTTCC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT-C
1336106 TTTTC TTTT
1 TTTTC TTTT
1336115 TATTCCTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
4 16 0.34
5 26 0.55
6 5 0.11
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.88
Consensus pattern (5 bp):
TTTTC
Found at i:1336108 original size:11 final size:11
Alignment explanation
Indices: 1336059--1336115 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
1336049 TAGATTATTA
*
1336059 TTTT-TTTTAT
1 TTTTCTTTTCT
* *
1336069 TTTTTTTTTTT
1 TTTTCTTTTCT
1336080 TTTTCTTTT-T
1 TTTTCTTTTCT
1336090 TTTTCTTTTCT
1 TTTTCTTTTCT
*
1336101 TTTCCTTTTCT
1 TTTTCTTTTCT
1336112 TTTT
1 TTTT
1336116 ATTCCTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
10 14 0.34
11 27 0.66
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:1336125 original size:27 final size:25
Alignment explanation
Indices: 1336080--1336144 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
1336070 TTTTTTTTTT
* * **
1336080 TTTTCTTTTTTTTTCTTTTCTTTTCC
1 TTTTCTTTTTATTCCTTTTAATTT-C
1336106 TTTTCTTTTTATTCCTTTTTAATTTC
1 TTTTCTTTTTATTCC-TTTTAATTTC
1336132 TTTATCTTTTTAT
1 TTT-TCTTTTTAT
1336145 CTTCATGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 17 0.52
27 16 0.48
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTCTTTTTATTCCTTTTAATTTC
Found at i:1336134 original size:11 final size:10
Alignment explanation
Indices: 1336056--1336134 Score: 51
Period size: 11 Copynumber: 8.0 Consensus size: 10
1336046 ATATAGATTA
1336056 TTATTT-TTT
1 TTATTTCTTT
1336065 TTATTT-TTT
1 TTATTTCTTT
1336074 TT-TTT-TTT
1 TTATTTCTTT
* *
1336082 TTCTTTTTTT
1 TTATTTCTTT
*
1336092 TTCTTTTCTTT
1 TT-ATTTCTTT
1336103 TCCT-TTTCTTT
1 T--TATTTCTTT
*
1336114 TTATTCCTTT
1 TTATTTCTTT
1336124 TTAATTTCTTT
1 TT-ATTTCTTT
1336135 ATCTTTTTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.14
9 15 0.25
10 13 0.22
11 22 0.37
13 1 0.02
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.82
Consensus pattern (10 bp):
TTATTTCTTT
Found at i:1340081 original size:34 final size:34
Alignment explanation
Indices: 1340043--1340127 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
1340033 AACAAACCCG
*
1340043 AAAATATTTTATATATAATTAATATAAAAAATAA
1 AAAATATTATATATATAATTAATATAAAAAATAA
*
1340077 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAA
1340111 AAAATATTATATATATA
1 AAAATATTATATATATA
1340128 TATATATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAA
Found at i:1340123 original size:2 final size:2
Alignment explanation
Indices: 1340114--1340143 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1340104 AAAATATAAA
1340114 AT AT -T 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 A
1340144 ATCGAGGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1346802 original size:35 final size:35
Alignment explanation
Indices: 1346756--1346827 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1346746 TTGATATGAT
1346756 CAGCTGAACCTGATAGATAAAAAGAGATTGAAAGC
1 CAGCTGAACCTGATAGATAAAAAGAGATTGAAAGC
1346791 CAGCTGAACCTGATAGATAAAAAGAGATTGAAAGC
1 CAGCTGAACCTGATAGATAAAAAGAGATTGAAAGC
1346826 CA
1 CA
1346828 TTCATCATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (35 bp):
CAGCTGAACCTGATAGATAAAAAGAGATTGAAAGC
Found at i:1347143 original size:13 final size:13
Alignment explanation
Indices: 1347125--1347150 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1347115 TAAGTCGAAG
1347125 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
1347138 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
1347151 GCACAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:1347231 original size:22 final size:21
Alignment explanation
Indices: 1347206--1347253 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1347196 CCTAAATGGA
1347206 AAAAAAGAGAAAAAAACAAAAG
1 AAAAAAGAGAAAAAAA-AAAAG
* * *
1347228 AAAACAGAGAAAAGAAAAAGG
1 AAAAAAGAGAAAAAAAAAAAG
1347249 AAAAA
1 AAAAA
1347254 TAAGGTGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAAAAGAGAAAAAAAAAAAG
Found at i:1348520 original size:124 final size:124
Alignment explanation
Indices: 1348124--1348713 Score: 923
Period size: 124 Copynumber: 4.8 Consensus size: 124
1348114 AACCAATTTA
* * * *
1348124 GATTTCAACTTCTCGATGAAAGATATCCAATTCGAGGCTCAACTTCACGACGAATGGGCCATCTA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCATCCA
* * * *
1348189 CGATTTCAACTTCACGACGAAGGATATCATGTCCACCAGAAACATTCATTCTTAGATTG
66 CGATTTCAACTTCACGACGAAGGATATCGTGTCTACCAGCAACATTCATCCTTAGATTG
* *
1348248 GATTTCAACTTCACGATGAAGGATATCTAATTCGAGGCTCAACTTCACGACGAAGGGGCTATCCA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCATCCA
* * *
1348313 CGATTTCAACTTCACGACAAATGATAT--TGTCTACCAGCAACATTCATTCTTAGATTG
66 CGATTTCAACTTCACGACGAAGGATATCGTGTCTACCAGCAACATTCATCCTTAGATTG
*
1348370 GATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTTAACTTCACGACGAAGGGGCCATCCA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCATCCA
* * *
1348435 CTATTTCAACTCCACGAAGAAGGATATCGTGTCTACCAGCAACATTCATCCTTAGATTG
66 CGATTTCAACTTCACGACGAAGGATATCGTGTCTACCAGCAACATTCATCCTTAGATTG
* * *
1348494 GATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGTCATCCA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCATCCA
**
1348559 CGATTTCAACTTCACGACGAAGGATATCGTGTCTACCAGCATTATTCATCCTTAGATTG
66 CGATTTCAACTTCACGACGAAGGATATCGTGTCTACCAGCAACATTCATCCTTAGATTG
* * * * *
1348618 GATTTCAACTTCACGACGAAGGATATCTAATTCGAGGCTCAACTTCACAACGAAAGGGTCATCCA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCATCCA
1348683 CGATTTCAACTTCACGACGAAGGATATCGTG
66 CGATTTCAACTTCACGACGAAGGATATCGTG
1348714 CCCATAAGTA
Statistics
Matches: 434, Mismatches: 30, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
122 112 0.26
124 322 0.74
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (124 bp):
GATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCATCCA
CGATTTCAACTTCACGACGAAGGATATCGTGTCTACCAGCAACATTCATCCTTAGATTG
Done.