Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002126.1 Hibiscus syriacus cultivar Beakdansim tig00004355_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: 1482737
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1158770 original size:15 final size:13
Alignment explanation
Indices: 1158750--1158813 Score: 80
Period size: 12 Copynumber: 5.0 Consensus size: 13
1158740 TTTGGGCTTG
*
1158750 TAATAAT-ATATT
1 TAATAATAATAAT
1158762 TAATAATAATAA-
1 TAATAATAATAAT
1158774 TAATAATAATAAT
1 TAATAATAATAAT
1158787 T-ATAATAATAATTT
1 TAATAATAATAA--T
1158801 TAATAATAATAAT
1 TAATAATAATAAT
1158814 AAAAACAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
12 29 0.63
13 5 0.11
14 2 0.04
15 10 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:1161743 original size:37 final size:37
Alignment explanation
Indices: 1161693--1161768 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
1161683 AACATAGGCC
1161693 TATATATATTTCAACTTGTAGTGGAGTTGGTGATTTG
1 TATATATATTTCAACTTGTAGTGGAGTTGGTGATTTG
1161730 TATATATATTTCAACTTGTAGTGGAGTTGGTGATTTG
1 TATATATATTTCAACTTGTAGTGGAGTTGGTGATTTG
1161767 TA
1 TA
1161769 GCTAACTTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.05, G:0.24, T:0.46
Consensus pattern (37 bp):
TATATATATTTCAACTTGTAGTGGAGTTGGTGATTTG
Found at i:1162984 original size:3 final size:3
Alignment explanation
Indices: 1162972--1163058 Score: 65
Period size: 3 Copynumber: 29.7 Consensus size: 3
1162962 TTTTTTCCAT
* * * * *
1162972 TTA TTT TTA TTA TTA TTA ATA TTA TT- TCA TT- TATA CTA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* *
1163016 TTA -TA TTA -TA TTA TTTA TTA ATA TTA TTA ATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1163059 TTTACATTTC
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
2 6 0.09
3 55 0.86
4 3 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1163029 original size:16 final size:18
Alignment explanation
Indices: 1162973--1163042 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 18
1162963 TTTTTCCATT
*
1162973 TATT-TTTATTATTATTAA
1 TATTATTTATTAATATT-A
1162991 TATTATTTCATT--TA-TA
1 TATTATTT-ATTAATATTA
1163007 CTATTATTT-TT-ATATTA
1 -TATTATTTATTAATATTA
1163024 TATTATTTATTAATATTA
1 TATTATTTATTAATATTA
1163042 T
1 T
1163043 TAATATTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.04
16 11 0.24
17 13 0.29
18 13 0.29
19 3 0.07
20 3 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTATTTATTAATATTA
Found at i:1164450 original size:3 final size:3
Alignment explanation
Indices: 1164442--1164485 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1164432 AATATATTTA
1164442 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1164486 TAGTCATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1164498 original size:2 final size:2
Alignment explanation
Indices: 1164491--1164528 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1164481 TTATTTAGTC
1164491 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1164529 TTATTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1164714 original size:143 final size:140
Alignment explanation
Indices: 1164555--1164863 Score: 355
Period size: 143 Copynumber: 2.2 Consensus size: 140
1164545 TGTTTTCTAT
* *
1164555 TAAATAAAAATCCTATTTATAAATT-TA-A-T-TTTATATAAATTACTTTTAGGAAAAATAATCA
1 TAAATAAATATTCTATTTATAAATTATATATTATTTATATAAATTACTTTTA-GAAAAAT-AT--
*
1164616 TATT-TTAATATTTATTTATTTTTTAATATTAA-AAAATGGGCTGTCTTAAAGCACCTAGAAGTC
62 T-TTATTAATATTTA--T-TTTTTTAATATTAAGAAAA-AGGCTGTCTTAAAGCACCTAGAAGTC
1164679 ATTTTCTGATA-TTCTTAAA
122 ATTTTCTGATATTTC-TAAA
* * * * *
1164698 TAAATAAATATTCTATTTTTATAAATTATATATTAATTTATTTTAATTATTTTTAGAGAAATGTT
1 TAAATAAATATTCTA--TTTATAAATTATATATT-ATTTATATAAATTACTTTTAGAAAAATATT
1164763 TTATTAATATTTATTTTTTTAATATTAAGAAAAAGGCTGTCTTAAAGCACCTAGAAGTCATTTTC
63 TTATTAATATTTATTTTTTTAATATTAAGAAAAAGGCTGTCTTAAAGCACCTAGAAGTCATTTTC
*
1164828 TGATATTTCTAAG
128 TGATATTTCTAAA
1164841 TAAATAAATA-TCTTATTTATAAA
1 TAAATAAATATTC-TATTTATAAA
1164864 AATATAAATA
Statistics
Matches: 146, Mismatches: 9, Indels: 24
0.82 0.05 0.13
Matches are distributed among these distances:
141 8 0.05
142 2 0.01
143 78 0.53
144 8 0.05
145 12 0.08
146 13 0.09
147 1 0.01
148 2 0.01
149 6 0.04
150 16 0.11
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (140 bp):
TAAATAAATATTCTATTTATAAATTATATATTATTTATATAAATTACTTTTAGAAAAATATTTTA
TTAATATTTATTTTTTTAATATTAAGAAAAAGGCTGTCTTAAAGCACCTAGAAGTCATTTTCTGA
TATTTCTAAA
Found at i:1165195 original size:16 final size:17
Alignment explanation
Indices: 1165174--1165206 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1165164 TGGCGACTCC
*
1165174 CAAAAT-ATTTTTTTAT
1 CAAAATCATTTATTTAT
1165190 CAAAATCATTTATTTAT
1 CAAAATCATTTATTTAT
1165207 TCATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
CAAAATCATTTATTTAT
Found at i:1167337 original size:34 final size:34
Alignment explanation
Indices: 1167294--1167376 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
1167284 CATTTTTTAA
1167294 GACATCAAGTTGGTGTTTAACTTCAAAAGTCAAT
1 GACATCAAGTTGGTGTTTAACTTCAAAAGTCAAT
*
1167328 GACATCAAGTTGGTGTTTAACTTCGAAAGTCAAT
1 GACATCAAGTTGGTGTTTAACTTCAAAAGTCAAT
*
1167362 GGCATCAAGTTGGTG
1 GACATCAAGTTGGTG
1167377 CATTCAAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (34 bp):
GACATCAAGTTGGTGTTTAACTTCAAAAGTCAAT
Found at i:1168152 original size:24 final size:24
Alignment explanation
Indices: 1168118--1168173 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1168108 TAGAAGTTCG
*
1168118 ATTGAAACCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
1168142 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
1168166 ATTGAAGC
1 ATTGAAGC
1168174 GAAAGAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:1168712 original size:8 final size:8
Alignment explanation
Indices: 1168699--1168723 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1168689 TGAACCCGAT
1168699 TGAACCAG
1 TGAACCAG
1168707 TGAACCAG
1 TGAACCAG
1168715 TGAACCAG
1 TGAACCAG
1168723 T
1 T
1168724 ACCTTCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (8 bp):
TGAACCAG
Found at i:1169081 original size:16 final size:16
Alignment explanation
Indices: 1169060--1169101 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1169050 TTGTTTATGA
1169060 GTTCGTTTATCAACTC
1 GTTCGTTTATCAACTC
1169076 GTTCGTTTATCAACTC
1 GTTCGTTTATCAACTC
*
1169092 GTTCATTTAT
1 GTTCGTTTAT
1169102 TTTCATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (16 bp):
GTTCGTTTATCAACTC
Found at i:1169370 original size:12 final size:12
Alignment explanation
Indices: 1169350--1169416 Score: 66
Period size: 12 Copynumber: 5.8 Consensus size: 12
1169340 ACACTAAACA
1169350 AACATGTTCACG
1 AACATGTTCACG
* *
1169362 AACACGTTCGCG
1 AACATGTTCACG
**
1169374 AACAT-TAAACG
1 AACATGTTCACG
1169385 AACATGTTCACG
1 AACATGTTCACG
**
1169397 AACAT-TAAACG
1 AACATGTTCACG
1169408 AACATGTTC
1 AACATGTTC
1169417 GTGAAAAATA
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
11 17 0.41
12 24 0.59
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (12 bp):
AACATGTTCACG
Found at i:1169388 original size:11 final size:11
Alignment explanation
Indices: 1169372--1169412 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1169362 AACACGTTCG
1169372 CGAACATTAAA
1 CGAACATTAAA
**
1169383 CGAACATGTTCA
1 CGAACAT-TAAA
1169395 CGAACATTAAA
1 CGAACATTAAA
1169406 CGAACAT
1 CGAACAT
1169413 GTTCGTGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.46, C:0.22, G:0.12, T:0.20
Consensus pattern (11 bp):
CGAACATTAAA
Found at i:1169428 original size:23 final size:23
Alignment explanation
Indices: 1169359--1169417 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
1169349 AAACATGTTC
*
1169359 ACGAACACGTTCGCGAACATTAA
1 ACGAACATGTTCGCGAACATTAA
*
1169382 ACGAACATGTTCACGAACATTAA
1 ACGAACATGTTCGCGAACATTAA
1169405 ACGAACATGTTCG
1 ACGAACATGTTCG
1169418 TGAAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (23 bp):
ACGAACATGTTCGCGAACATTAA
Found at i:1171873 original size:2 final size:2
Alignment explanation
Indices: 1171866--1171918 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1171856 AAATAGATGC
1171866 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1171908 TA TA TA TA TA T
1 TA TA TA TA TA T
1171919 GCTTTACATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1173536 original size:42 final size:41
Alignment explanation
Indices: 1173490--1173661 Score: 154
Period size: 42 Copynumber: 4.1 Consensus size: 41
1173480 CGTTTGCCAA
* *
1173490 TAAAACGTCATTATAGATCCGTACCTTAATGGCGTTTGTTAC
1 TAAAACG-CATTATAGAGCCGTACCTTAGTGGCGTTTGTTAC
*** * * * *
1173532 TAAAACGCCGCAATAGAGGCGAACCTTAGTAGCGTTTGTCAC
1 TAAAACG-CATTATAGAGCCGTACCTTAGTGGCGTTTGTTAC
*
1173574 TAAAACGCCTCTATAGAGCCGTACCTTAGTGGCGTTTGTTA-
1 TAAAACGCAT-TATAGAGCCGTACCTTAGTGGCGTTTGTTAC
*
1173615 TAAACACACCGCA--ATAGAGGCGTACCTTAGTGGCGTTTGTTA-
1 T-AA-A-A-CGCATTATAGAGCCGTACCTTAGTGGCGTTTGTTAC
1173657 TAAAA
1 TAAAA
1173662 ACGCTACAAT
Statistics
Matches: 106, Mismatches: 19, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 4 0.04
42 95 0.90
43 1 0.01
44 1 0.01
45 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
TAAAACGCATTATAGAGCCGTACCTTAGTGGCGTTTGTTAC
Found at i:1173665 original size:84 final size:84
Alignment explanation
Indices: 1173501--1173654 Score: 247
Period size: 84 Copynumber: 1.8 Consensus size: 84
1173491 AAAACGTCAT
* *
1173501 TATAGATCCGTACCTTAATGGCGTTTGTTACTAAAACGCCGCAATAGAGGCGAACCTTAGTAGCG
1 TATAGAGCCGTACCTTAATGGCGTTTGTTACTAAAACACCGCAATAGAGGCGAACCTTAGTAGCG
1173566 TTTGTCACTAAAACGCCTC
66 TTTGTCACTAAAACGCCTC
* * *
1173585 TATAGAGCCGTACCTTAGTGGCGTTTGTTA-TAAACACACCGCAATAGAGGCGTACCTTAGTGGC
1 TATAGAGCCGTACCTTAATGGCGTTTGTTACTAAA-ACACCGCAATAGAGGCGAACCTTAGTAGC
1173649 GTTTGT
65 GTTTGT
1173655 TATAAAAACG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
83 4 0.06
84 60 0.94
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (84 bp):
TATAGAGCCGTACCTTAATGGCGTTTGTTACTAAAACACCGCAATAGAGGCGAACCTTAGTAGCG
TTTGTCACTAAAACGCCTC
Found at i:1173672 original size:42 final size:42
Alignment explanation
Indices: 1173509--1173694 Score: 216
Period size: 42 Copynumber: 4.5 Consensus size: 42
1173499 ATTATAGATC
*
1173509 CGTACCTTAATGGCGTTTGTTACTAAAACGCCGCAATAGAGG
1 CGTACCTTAGTGGCGTTTGTTACTAAAACGCCGCAATAGAGG
* * * * * *
1173551 CGAACCTTAGTAGCGTTTGTCACTAAAACGCCTCTATAGAGC
1 CGTACCTTAGTGGCGTTTGTTACTAAAACGCCGCAATAGAGG
*
1173593 CGTACCTTAGTGGCGTTTGTTA-TAAACACACCGCAATAGAGG
1 CGTACCTTAGTGGCGTTTGTTACTAAA-ACGCCGCAATAGAGG
**
1173635 CGTACCTTAGTGGCGTTTGTTA-TAAAAACGCTACAATAGAGG
1 CGTACCTTAGTGGCGTTTGTTACT-AAAACGCCGCAATAGAGG
* * *
1173677 TGAACTTTAGTGGC-TTTG
1 CGTACCTTAGTGGCGTTTG
1173695 GTTGTTGAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
41 8 0.07
42 111 0.91
43 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (42 bp):
CGTACCTTAGTGGCGTTTGTTACTAAAACGCCGCAATAGAGG
Found at i:1176572 original size:18 final size:19
Alignment explanation
Indices: 1176524--1176582 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1176514 CACTGAATAT
1176524 TTGTCCCGAATGACCACTGA
1 TTGTCCCGAA-GACCACTGA
*
1176544 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAG-ACCACTGA
1176563 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAA-GACCACTGA
1176582 T
1 T
1176583 AATCCCTCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 14 0.42
19 4 0.12
20 15 0.45
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (19 bp):
TTGTCCCGAAGACCACTGA
Found at i:1177829 original size:2 final size:2
Alignment explanation
Indices: 1177822--1177868 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1177812 CGTGGAGCTA
1177822 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
1177864 AT AT A
1 AT AT A
1177869 AATCCCTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1182528 original size:23 final size:23
Alignment explanation
Indices: 1182496--1182543 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1182486 CATTTACAGG
1182496 CACTCCAGGGGGTGCCTGATCTT
1 CACTCCAGGGGGTGCCTGATCTT
*
1182519 CACTCTAGGGGGTGCCTGATCTT
1 CACTCCAGGGGGTGCCTGATCTT
1182542 CA
1 CA
1182544 ATCTGCCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (23 bp):
CACTCCAGGGGGTGCCTGATCTT
Found at i:1183469 original size:18 final size:20
Alignment explanation
Indices: 1183416--1183474 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1183406 CACTGAATAT
*
1183416 TTGTCCCGAAGGACCACTGA
1 TTGTCTCGAAGGACCACTGA
*
1183436 TTGT-TCCGAAGAACCACT-A
1 TTGTCT-CGAAGGACCACTGA
1183455 -TGTCTCGAAGGACCACTGA
1 TTGTCTCGAAGGACCACTGA
1183474 T
1 T
1183475 AATCCCTCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 14 0.44
19 3 0.09
20 15 0.47
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (20 bp):
TTGTCTCGAAGGACCACTGA
Found at i:1185564 original size:34 final size:34
Alignment explanation
Indices: 1185506--1186078 Score: 402
Period size: 37 Copynumber: 15.9 Consensus size: 34
1185496 CAAATGGATT
* * *
1185506 TGCTCCACTACTATTCGGTGAAGGCTTAATATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* * *
1185540 TGCTTCACCACTCTTCTGTGAAGGCTTAAGGTGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
*
1185574 TGCTTCACTACTCGTTC-GTGAGGGCTTAAGATGG
1 TGCTTCACTACTC-TTCGGTGAAGGCTTAAGATGG
**
1185608 TGCTTCACTACTCTTATGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* *
1185642 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATTGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGA-TG-G
**
1185678 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATTAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGA-TGG
* * *
1185713 TGCTTCACTACTCTCCAGTGAAGGCTTCAA-ATTGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTT-AAGA-TG-G
*
1185749 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGA-TGG
* * *
1185784 TTCTTCACTATTCTCCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* *
1185818 TTTGCTTCACTATTC-TCAGGTGAAGGCTTAAGATTGATT
1 --TGCTTCACTACTCTTC-GGTGAAGGCTTAAGA-TG--G
*
1185857 TGCTTCACTATTC-TCAGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTC-GGTGAAGGCTTAAGATGG
* * * *
1185891 AATTTCTTCACTCCT-TTCCGGTGAAGACTTAAGATTG
1 ---TGCTTCACTACTCTT-CGGTGAAGGCTTAAGATGG
** ** * * * **
1185928 CCCTAAGGACTTAATCATCATGCTCGGAAGGCTTGCTGATGG
1 TGCT--TCAC-TACTCTTC--GGT--GAAGGCTT-AAGATGG
1185970 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGAG
1 ---TGCTTCACTACTCTTCGGTGAAGGCTTAAGA-TG-G
* * * *
1186009 TTACTTCACTATTCTCCGGTGAAGGCTTAAGATGAAAT
1 -TGCTTCACTACTCTTCGGTGAAGGCTTAAGATG---G
*
1186047 TGCTTCACTCCT-TTCCGGTGAAGGCTTAAGAT
1 TGCTTCACTACTCTT-CGGTGAAGGCTTAAGAT
1186079 TGTCCTGAGG
Statistics
Matches: 442, Mismatches: 62, Indels: 67
0.77 0.11 0.12
Matches are distributed among these distances:
33 2 0.00
34 118 0.27
35 66 0.15
36 98 0.22
37 119 0.27
38 13 0.03
39 3 0.01
40 2 0.00
41 7 0.02
42 10 0.02
43 2 0.00
45 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (34 bp):
TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
Found at i:1185748 original size:71 final size:71
Alignment explanation
Indices: 1185505--1186079 Score: 433
Period size: 71 Copynumber: 8.0 Consensus size: 71
1185495 ACAAATGGAT
* * * * * * * *
1185505 TTGCTCCACTACTATTCGGTGAAGGCTTAATA-TG-GTGCTTCACCACTCTTCTGTGAAGGCTTA
1 TTGCTTCACTACTCTCCAGTGAAGGCTTAAGATTGATTGCTTCACTACTCTTCGGTGAAGGCTTA
* *
1185568 AG-GTG
66 AGATTA
* * * * **
1185573 GTGCTTCACTACTCGTTC-GTGAGGGCTTAAGA-TG-GTGCTTCACTACTCTTATGTGAAGGCTT
1 TTGCTTCACTACTC-TCCAGTGAAGGCTTAAGATTGATTGCTTCACTACTCTTCGGTGAAGGCTT
*
1185635 AAGA-TG
65 AAGATTA
* * *
1185641 GTGCTTCACTACTCTTCTGTGAAGGCTTAAGATTGATTGCTTCACTACTCTTCGGTGAAGGCTTA
1 TTGCTTCACTACTCTCCAGTGAAGGCTTAAGATTGATTGCTTCACTACTCTTCGGTGAAGGCTTA
1185706 AGATTA
66 AGATTA
1185712 TTGCTTCACTACTCTCCAGTGAAGGCTTCAA-ATTGATTGCTTCACTACTCTTCGGTGAAGGCTT
1 TTGCTTCACTACTCTCCAGTGAAGGCTT-AAGATTGATTGCTTCACTACTCTTCGGTGAAGGCTT
*
1185776 AAGATTG
65 AAGATTA
* * * * * *
1185783 TTTCTTCACTATTCTCCGGTGAAGGCTTAAGATGGTTTGCTTCACTATTC-TCAGGTGAAGGCTT
1 TTGCTTCACTACTCTCCAGTGAAGGCTTAAGATTGATTGCTTCACTACTCTTC-GGTGAAGGCTT
1185847 AAGATTGA
65 AAGATT-A
* * * * *
1185855 TTTGCTTCACTATTCT-CAGGTGAAGGCTTAAGATGGAATTTCTTCACTCCT-TTCCGGTGAAGA
1 -TTGCTTCACTACTCTCCA-GTGAAGGCTTAAGATTG-ATTGCTTCACTACTCTT-CGGTGAAGG
1185918 CTTAAGATT-
62 CTTAAGATTA
*** ** * ** *
1185927 GCCCTAAGGACTTAATCAT-CATGCTCGGAAGGCTTGCTGATGGATTTGCTTCACTACTCTTCGG
1 TTGCT--TCAC-TACTC-TCCA-G-T--GAAGGCTT-AAGATTGA-TTGCTTCACTACTCTTCGG
1185991 TGAAGGCTTAAGATTGA
56 TGAAGGCTTAAGATT-A
* * * *
1186008 GTTACTTCACTATTCTCCGGTGAAGGCTTAAGA-TGAAATTGCTTCACTCCT-TTCCGGTGAAGG
1 -TTGCTTCACTACTCTCCAGTGAAGGCTTAAGATTG--ATTGCTTCACTACTCTT-CGGTGAAGG
1186071 CTTAAGATT
62 CTTAAGATT
1186080 GTCCTGAGGA
Statistics
Matches: 422, Mismatches: 53, Indels: 58
0.79 0.10 0.11
Matches are distributed among these distances:
67 3 0.01
68 83 0.20
69 5 0.01
70 33 0.08
71 125 0.30
72 3 0.01
73 36 0.09
74 63 0.15
75 14 0.03
76 1 0.00
77 1 0.00
78 11 0.03
79 38 0.09
80 4 0.01
82 2 0.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (71 bp):
TTGCTTCACTACTCTCCAGTGAAGGCTTAAGATTGATTGCTTCACTACTCTTCGGTGAAGGCTTA
AGATTA
Found at i:1185992 original size:79 final size:77
Alignment explanation
Indices: 1185890--1186159 Score: 263
Period size: 79 Copynumber: 3.5 Consensus size: 77
1185880 GCTTAAGATG
* *
1185890 GAATTT-CTTCACTCCTTTCCGGTGAAGACTTAAGATTGCCCTAAGGACTTAATCATCATGCTCG
1 GAATTTGCTTCACTACTTTCCGGTGAAGGCTTAAGATTG-CCT-AGGACTTAATCATCATGCTCG
1185954 GAAGGCTTGCTGAT
64 GAAGGCTTGCTGAT
* * * *
1185968 GGATTTGCTTCACTACTCTT-CGGTGAAGGCTTAAGATTG---AGTTACTTCA-C-T-ATTCTCC
1 GAATTTGCTTCACTACT-TTCCGGTGAAGGCTTAAGATTGCCTAG-GACTTAATCATCATGCT-C
**
1186026 GGTGAAGGCTT-AAGAT
63 -G-GAAGGCTTGCTGAT
* * *
1186042 GAAATTGCTTCACTCCTTTCCGGTGAAGGCTTAAGATTGTCCTGAGGACTTAATCATCGTGCTCG
1 GAATTTGCTTCACTACTTTCCGGTGAAGGCTTAAGATTG-CCT-AGGACTTAATCATCATGCTCG
1186107 GAAGGCTTGCTGAT
64 GAAGGCTTGCTGAT
* *
1186121 GAATTTGCTTTACTACTCTT-CGGTGAAGGCTTAATATTG
1 GAATTTGCTTCACTACT-TTCCGGTGAAGGCTTAAGATTG
1186160 ACTTGCCCCA
Statistics
Matches: 154, Mismatches: 21, Indels: 33
0.74 0.10 0.16
Matches are distributed among these distances:
72 4 0.03
73 4 0.03
74 40 0.26
75 13 0.08
78 18 0.12
79 66 0.43
80 6 0.04
81 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (77 bp):
GAATTTGCTTCACTACTTTCCGGTGAAGGCTTAAGATTGCCTAGGACTTAATCATCATGCTCGGA
AGGCTTGCTGAT
Found at i:1186021 original size:153 final size:150
Alignment explanation
Indices: 1185677--1186165 Score: 590
Period size: 153 Copynumber: 3.3 Consensus size: 150
1185667 TTAAGATTGA
*
1185677 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT-ATTGCTTCACTACTCTCCA-GTGAAGGCTT
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTGCTTCACTATTCT-CAGGTGAAGGCTT
* * * ** *
1185740 CAA-ATTG-ATTGCTTCACTACTCTT-CGGTGAAGGCTTAAGATTGTTTCT-TCAC-TATTC-TC
65 -AAGATGGAATTGCTTCACTCCT-TTCCGGTGAAGGCTTAAGATTG-TCCTAGGACTTAATCATC
* * **
1185799 CGGT--GAAGGCTT-AAGATGG-T
127 TGCTCGGAAGGCTTGCTGATGGAT
*
1185819 TTGCTTCACTATTC-TCAGGTGAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCT
1 TTGCTTCACTACTCTTC-GGTGAAGGCTTAAGATTGA-TTGCTTCACTATTCTCAGGTGAAGGCT
* * *
1185883 TAAGATGGAATTTCTTCACTCCTTTCCGGTGAAGACTTAAGATTGCCCTAAGGACTTAATCATCA
64 TAAGATGGAATTGCTTCACTCCTTTCCGGTGAAGGCTTAAGATTGTCCT-AGGACTTAATCATC-
1185948 TGCTCGGAAGGCTTGCTGATGGAT
127 TGCTCGGAAGGCTTGCTGATGGAT
* *
1185972 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGAGTTACTTCACTATTCTCCGGTGAAGGCTT
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA-TTGCTTCACTATTCTCAGGTGAAGGCTT
*
1186037 AAGATGAAATTGCTTCACTCCTTTCCGGTGAAGGCTTAAGATTGTCCTGAGGACTTAATCATCGT
65 AAGATGGAATTGCTTCACTCCTTTCCGGTGAAGGCTTAAGATTGTCCT-AGGACTTAATCATC-T
*
1186102 GCTCGGAAGGCTTGCTGATGAAT
128 GCTCGGAAGGCTTGCTGATGGAT
* *
1186125 TTGCTTTACTACTCTTCGGTGAAGGCTTAATATTGACTTGC
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA-TTGC
1186166 CCCAATCTCA
Statistics
Matches: 300, Mismatches: 30, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
141 2 0.01
142 30 0.10
143 5 0.02
144 31 0.10
145 30 0.10
146 2 0.01
147 4 0.01
148 2 0.01
149 2 0.01
151 8 0.03
152 5 0.02
153 177 0.59
154 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (150 bp):
TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTGCTTCACTATTCTCAGGTGAAGGCTTA
AGATGGAATTGCTTCACTCCTTTCCGGTGAAGGCTTAAGATTGTCCTAGGACTTAATCATCTGCT
CGGAAGGCTTGCTGATGGAT
Found at i:1190955 original size:55 final size:55
Alignment explanation
Indices: 1190887--1191015 Score: 215
Period size: 55 Copynumber: 2.3 Consensus size: 55
1190877 CTTCAAACTC
1190887 CATTCAT-TGGATGTCCTTCTTCATGAATCCTTCTTCAATCAGGTTCAAATTTCTT
1 CATTCATCT-GATGTCCTTCTTCATGAATCCTTCTTCAATCAGGTTCAAATTTCTT
*
1190942 CATTCATCTGATGTCCTTCTTCATGAATCGTTCTTCAATCAGGTTCAAATTTCTT
1 CATTCATCTGATGTCCTTCTTCATGAATCCTTCTTCAATCAGGTTCAAATTTCTT
* *
1190997 CATTCTTCGGATGTCCTTC
1 CATTCATCTGATGTCCTTC
1191016 ATGAATCATT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
55 69 0.99
56 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (55 bp):
CATTCATCTGATGTCCTTCTTCATGAATCCTTCTTCAATCAGGTTCAAATTTCTT
Found at i:1193016 original size:20 final size:20
Alignment explanation
Indices: 1192993--1193035 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1192983 AATCTACCAC
*
1192993 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
1193013 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
1193033 ATG
1 ATG
1193036 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:1203194 original size:20 final size:20
Alignment explanation
Indices: 1203171--1203213 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1203161 AATCCACCAC
*
1203171 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
1203191 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
1203211 ATG
1 ATG
1203214 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:1203437 original size:46 final size:43
Alignment explanation
Indices: 1203335--1203437 Score: 107
Period size: 46 Copynumber: 2.3 Consensus size: 43
1203325 CCATGCTTTG
* *
1203335 TTATTCACAAAAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAAAACCTAACCGCATGATATCTAATTCGCATAC
* * *
1203379 TTGTTCGAAAAAATAAACCTAACCGCATGATTTCTAGTTCGCATAC
1 TTATTC--AAAAA-AAACCTAACCGCATGATATCTAATTCGCATAC
1203425 ATTTATTCAAAAA
1 --TTATTCAAAAA
1203438 GCGAAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
44 5 0.10
45 4 0.08
46 34 0.71
48 5 0.10
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (43 bp):
TTATTCAAAAAAAACCTAACCGCATGATATCTAATTCGCATAC
Found at i:1206883 original size:3 final size:3
Alignment explanation
Indices: 1206877--1206912 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1206867 ACATTATTAT
1206877 TAA TAA TAA -AA TAA TAA TAA T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1206913 TCCCGGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1206893 original size:11 final size:11
Alignment explanation
Indices: 1206877--1206912 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1206867 ACATTATTAT
1206877 TAATAATAAAA
1 TAATAATAAAA
*
1206888 TAATAATAATA
1 TAATAATAAAA
1206899 TAATAATAATAA
1 TAATAATAA-AA
1206911 TA
1 TA
1206913 TCCCGGACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 19 0.86
12 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:1206913 original size:14 final size:14
Alignment explanation
Indices: 1206877--1206913 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1206867 ACATTATTAT
*
1206877 TAATAATAAAATAA
1 TAATAATATAATAA
1206891 TAATAATATAATAA
1 TAATAATATAATAA
1206905 TAATAATAT
1 TAATAATAT
1206914 CCCGGACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:1212281 original size:41 final size:41
Alignment explanation
Indices: 1212226--1212532 Score: 330
Period size: 41 Copynumber: 7.4 Consensus size: 41
1212216 ATTATAAGTA
* * *
1212226 CGTATTTTAGTGGCGTTTTTATACAAATGCCGCTATAGAAT
1 CGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACT
* ** ** * *
1212267 TGTACTTTAGTGGCGTTTTTATACAAACATCATTATACAAT
1 CGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACT
1212308 CGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACT
1 CGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACT
* * *
1212349 TGTACTTTAGTGGCGTTTCTATACAAACGACGCTATAGACT
1 CGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACT
* * * * *
1212390 CATACTTTAGTGGCGTTTTGAATGCAAATGCCGCTATAAACT
1 CGTACTTTAGTGGCGTTTT-TATACAAACGCCGCTATAGACT
* * * * *
1212432 CGTACTTTAGTGACGTTTTGAATGCAAACGCCACTATATACT
1 CGTACTTTAGTGGCGTTTT-TATACAAACGCCGCTATAGACT
* * *
1212474 CATACTTTAGTGGCATTTTGAATACAAACGCCGCTA-ATGACT
1 CGTACTTTAGTGGCGTTTT-TATACAAACGCCGCTATA-GACT
1212516 CGTAC-TTAGTGGCGTTT
1 CGTACTTTAGTGGCGTTT
1212533 GTATTTACAA
Statistics
Matches: 225, Mismatches: 39, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
41 133 0.59
42 92 0.41
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (41 bp):
CGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACT
Found at i:1213898 original size:16 final size:16
Alignment explanation
Indices: 1213877--1213909 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1213867 TAGTAGAAGG
1213877 GTTCATACAAAACATT
1 GTTCATACAAAACATT
1213893 GTTCATACAAAACATT
1 GTTCATACAAAACATT
1213909 G
1 G
1213910 ATCTTACAAC
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:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (16 bp):
GTTCATACAAAACATT
Found at i:1213917 original size:16 final size:16
Alignment explanation
Indices: 1213879--1213918 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1213869 GTAGAAGGGT
*
1213879 TCATACAAAACATTGT
1 TCATACAAAACATTGA
1213895 TCATACAAAACATTGA
1 TCATACAAAACATTGA
*
1213911 TCTTACAA
1 TCATACAA
1213919 CGATTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (16 bp):
TCATACAAAACATTGA
Found at i:1216162 original size:85 final size:85
Alignment explanation
Indices: 1215984--1216286 Score: 335
Period size: 85 Copynumber: 3.5 Consensus size: 85
1215974 ATGTAATTAG
** * * * *
1215984 CGGCGTTTGTATAAAAAAACGCCGCTATAGATCTAACCTTCTACGGCGTTTGTTCCTAAAACGCA
1 CGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAACGCT
* *
1216049 GCTATAGATCTCAATCTTTTG
65 GCTATAGATCACAATCTTTTA
*
1216070 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCAGCGTTTGTTCCAATAAACGCT
1 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAA-AAACGCT
* *
1216135 GCTATAGATCAGACTC-TTTA
65 GCTATAGATCACAATCTTTTA
* * *
1216155 CGTCGTTTGTTCCAAAAACACCGCTATAGATCTCAACCTTTTGCGGCGTTTGTTCCAAAAACTCT
1 CGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-AACCTTTTGCGGCGTTTGTTCCAAAAACGCT
* * * * *
1216220 ACTATAGATCTCGACCTTTTG
65 GCTATAGATCACAATCTTTTA
**
1216241 CGGCG-TT-TTGGAACAAAC-CCTGCTATAGATCTCAACCTTTTGCGGC
1 CGGCGTTTGTTCCAA-AAACGCC-GCTATAGATCT-AACCTTTTGCGGC
1216287 ATTTTGGAAT
Statistics
Matches: 187, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
84 6 0.03
85 122 0.65
86 59 0.32
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (85 bp):
CGGCGTTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAACGCTG
CTATAGATCACAATCTTTTA
Found at i:1216214 original size:128 final size:129
Alignment explanation
Indices: 1216000--1216248 Score: 360
Period size: 128 Copynumber: 1.9 Consensus size: 129
1215990 TTGTATAAAA
* * *
1216000 AAACGCCGCTATAGATCTAACCTTCTACGGCGTTTGTTCCTAAAACGCAGCTATAGATCTCAATC
1 AAACGCCGCTATAGATCTAACCTTCTACGGCGTTTGTTCCAAAAACACAGCTATAGATCTCAACC
*
1216065 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-AACCTTTTGCAGCGTTTGTTCCAAT
66 TTTTGCGGCGTTTGTTCCAAAAACGCCACTATAGATCTCAACCTTTTGCAGCGTTTGTTCCAAT
* * *
1216128 AAACGCTGCTATAGATC-AGACTCTT-TACGTCGTTTGTTCCAAAAACACCGCTATAGATCTCAA
1 AAACGCCGCTATAGATCTA-AC-CTTCTACGGCGTTTGTTCCAAAAACACAGCTATAGATCTCAA
* * * *
1216191 CCTTTTGCGGCGTTTGTTCCAAAAACTCTACTATAGATCTCGACCTTTTGCGGCGTTT
64 CCTTTTGCGGCGTTTGTTCCAAAAACGCCACTATAGATCTCAACCTTTTGCAGCGTTT
1216249 TGGAACAAAC
Statistics
Matches: 107, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
127 1 0.01
128 88 0.82
129 18 0.17
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (129 bp):
AAACGCCGCTATAGATCTAACCTTCTACGGCGTTTGTTCCAAAAACACAGCTATAGATCTCAACC
TTTTGCGGCGTTTGTTCCAAAAACGCCACTATAGATCTCAACCTTTTGCAGCGTTTGTTCCAAT
Found at i:1216279 original size:42 final size:43
Alignment explanation
Indices: 1215983--1216286 Score: 336
Period size: 43 Copynumber: 7.1 Consensus size: 43
1215973 AATGTAATTA
** *
1215983 GCGGCGTTTGTATAAAAAAACGCCGCTATAGATCT-AACCTTCT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTCAACCTTTT
* * * *
1216026 ACGGCGTTTGTTCCTAAAACGCAGCTATAGATCTCAATCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTT
1216069 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-AACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTT
* *
1216111 GCAGCGTTTGTTCCAATAAACGCTGCTATAGA--TCAGA-CTCTTT
1 GCGGCGTTTGTTCCAA-AAACGCCGCTATAGATCTCA-ACCT-TTT
* * *
1216154 ACGTCGTTTGTTCCAAAAACACCGCTATAGATCTCAACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTT
* ** *
1216197 GCGGCGTTTGTTCCAAAAACTCTACTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTT
**
1216240 GCGGCG-TT-TTGGAACAAAC-CCTGCTATAGATCTCAACCTTTT
1 GCGGCGTTTGTTCCAA-AAACGCC-GCTATAGATCTCAACCTTTT
1216282 GCGGC
1 GCGGC
1216287 ATTTTGGAAT
Statistics
Matches: 222, Mismatches: 29, Indels: 21
0.82 0.11 0.08
Matches are distributed among these distances:
41 6 0.03
42 86 0.39
43 125 0.56
44 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTT
Found at i:1216292 original size:42 final size:41
Alignment explanation
Indices: 1216168--1216314 Score: 154
Period size: 42 Copynumber: 3.5 Consensus size: 41
1216158 CGTTTGTTCC
* **
1216168 AAAAACACC-GCTATAGATCTCAACCTTTTGCGGCGTTTGTTCC
1 AAAAAC-CCTGCTATAGATCTCAACCTTTTGCGGC-ATT-TTGG
* * * *
1216211 AAAAACTCTACTATAGATCTCGACCTTTTGCGGCGTTTTGG
1 AAAAACCCTGCTATAGATCTCAACCTTTTGCGGCATTTTGG
1216252 AACAAACCCTGCTATAGATCTCAACCTTTTGCGGCATTTTGG
1 AA-AAACCCTGCTATAGATCTCAACCTTTTGCGGCATTTTGG
*
1216294 AATAAACGCC-GCAATAGATCT
1 AA-AAAC-CCTGCTATAGATCT
1216315 TGACATATGG
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
41 4 0.04
42 54 0.61
43 31 0.35
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (41 bp):
AAAAACCCTGCTATAGATCTCAACCTTTTGCGGCATTTTGG
Found at i:1216528 original size:44 final size:44
Alignment explanation
Indices: 1216465--1216574 Score: 193
Period size: 44 Copynumber: 2.5 Consensus size: 44
1216455 TGTAGTGGTA
1216465 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATT
* * *
1216509 CCATAAGCCCGTAAGCTTATTTTACCCATATACTTTCCATTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATT
1216553 CCATAAGCTCGTAAGCTTATTT
1 CCATAAGCTCGTAAGCTTATTT
1216575 GCATGCTTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (44 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATT
Found at i:1224856 original size:14 final size:15
Alignment explanation
Indices: 1224837--1224872 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1224827 AAATTCAGTG
1224837 ATAAAATTAAAA-AA
1 ATAAAATTAAAATAA
*
1224851 ATAAAAATAAAATAA
1 ATAAAATTAAAATAA
1224866 ATAAAAT
1 ATAAAAT
1224873 AAGAAAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
ATAAAATTAAAATAA
Found at i:1224860 original size:20 final size:20
Alignment explanation
Indices: 1224837--1224874 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1224827 AAATTCAGTG
1224837 ATAAAATTAAA-AAAATAAAA
1 ATAAAA-TAAATAAAATAAAA
1224857 ATAAAATAAATAAAATAA
1 ATAAAATAAATAAAATAA
1224875 GAAAGAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
ATAAAATAAATAAAATAAAA
Found at i:1226148 original size:70 final size:72
Alignment explanation
Indices: 1226018--1226153 Score: 186
Period size: 70 Copynumber: 1.9 Consensus size: 72
1226008 ATAATACCAG
* * * *
1226018 ATACTCATTATTTCAAAAAGAAATGCTAAGTACTAGTAATAAATAGTGAAAGTCAATACTACCAA
1 ATACTCATTATTTCAAAAAGAAATACTAAATACGAGTAATAAATAATGAAAGTCAATACTACCAA
1226083 ATACTAA
66 ATACTAA
* * * *
1226090 ATACTTATTATTT-AAAAA-AAATACTAAATAGGAGTAATAAATAATGAAAGTTACTACTACCAA
1 ATACTCATTATTTCAAAAAGAAATACTAAATACGAGTAATAAATAATGAAAGTCAATACTACCAA
1226153 A
66 A
1226154 CACCGATTAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 39 0.70
71 5 0.09
72 12 0.21
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.29
Consensus pattern (72 bp):
ATACTCATTATTTCAAAAAGAAATACTAAATACGAGTAATAAATAATGAAAGTCAATACTACCAA
ATACTAA
Found at i:1228552 original size:18 final size:18
Alignment explanation
Indices: 1228529--1228572 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1228519 CAGTAATCCT
*
1228529 ATTCCCTGGTAATCTTAC
1 ATTCCCTAGTAATCTTAC
1228547 ATTCCCACTAGTAATCTTAC
1 ATT-CC-CTAGTAATCTTAC
1228567 ATTCCC
1 ATTCCC
1228573 ACTGGTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.25, C:0.32, G:0.07, T:0.36
Consensus pattern (18 bp):
ATTCCCTAGTAATCTTAC
Found at i:1228562 original size:20 final size:20
Alignment explanation
Indices: 1228537--1228581 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1228527 CTATTCCCTG
1228537 GTAATCTTACATTCCCACTA
1 GTAATCTTACATTCCCACTA
*
1228557 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTA
1228577 GTAAT
1 GTAAT
1228582 GTTGCATACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.36
Consensus pattern (20 bp):
GTAATCTTACATTCCCACTA
Found at i:1229318 original size:18 final size:18
Alignment explanation
Indices: 1229295--1229340 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
1229285 CAACATGTCA
1229295 CATTCAGAGCTTTTGAAT
1 CATTCAGAGCTTTTGAAT
1229313 CATTC--AG-TATTTGAAT
1 CATTCAGAGCT-TTTGAAT
*
1229329 CATTCAGCGCTT
1 CATTCAGAGCTT
1229341 AATCATTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 8
0.72 0.03 0.25
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
18 7 0.30
19 1 0.04
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (18 bp):
CATTCAGAGCTTTTGAAT
Found at i:1230197 original size:178 final size:178
Alignment explanation
Indices: 1229874--1230216 Score: 546
Period size: 178 Copynumber: 1.9 Consensus size: 178
1229864 CCCACGGCAC
*
1229874 AAGTTAACATAACCCATTTGCCCATTTTTATTTGTTTGACACCCATATATCCTATACCTTTATTA
1 AAGTTAACATAACCCATTTGCCCATTTTTATTTGTTTGACACCCATACATCCTATACCTTTATTA
*
1229939 AAAAAATAAAAAAGTTGGTGGTTTTAAAAATTTTCTTAGTATATTTAGACTCACCCTTATGTATA
66 AAAAAATAAAAAAGTTGGTGGGTTTAAAAATTTTCTTAGTATATTTAGACTCACCCTTATGTATA
1230004 TAAAAAAACATATAATTATTCAACTTCCCAAATTACTCCCAACACCAT
131 TAAAAAAACATATAATTATTCAACTTCCCAAATTACTCCCAACACCAT
* * * * * *
1230052 AAGTTAGCATAACTCATTTGTCCTTTTTTATTTGTTTGTCACTCATACA-CCT-TACACTTTTAT
1 AAGTTAACATAACCCATTTGCCCATTTTTATTTGTTTGACACCCATACATCCTATAC-C-TTTAT
* ** *
1230115 TAAAAAAATAAAGAAGTTGGTGGGTTTAGTAATTTTCTTGGTATATTTAGACTCACCCTTATGTA
64 TAAAAAAATAAAAAAGTTGGTGGGTTTAAAAATTTTCTTAGTATATTTAGACTCACCCTTATGTA
1230180 TATAAAAAAACATATAATTATTCAACTTCCCAAATTA
129 TATAAAAAAACATATAATTATTCAACTTCCCAAATTA
1230217 GAGTCATCTT
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
176 3 0.02
177 4 0.03
178 144 0.95
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.38
Consensus pattern (178 bp):
AAGTTAACATAACCCATTTGCCCATTTTTATTTGTTTGACACCCATACATCCTATACCTTTATTA
AAAAAATAAAAAAGTTGGTGGGTTTAAAAATTTTCTTAGTATATTTAGACTCACCCTTATGTATA
TAAAAAAACATATAATTATTCAACTTCCCAAATTACTCCCAACACCAT
Found at i:1230279 original size:15 final size:15
Alignment explanation
Indices: 1230259--1230289 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1230249 CACCAACAGG
1230259 TCGTATTCAAAAGCA
1 TCGTATTCAAAAGCA
1230274 TCGTATTCAAAAGCA
1 TCGTATTCAAAAGCA
1230289 T
1 T
1230290 GAGGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (15 bp):
TCGTATTCAAAAGCA
Found at i:1233056 original size:18 final size:17
Alignment explanation
Indices: 1232998--1233057 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
1232988 CTCTACGGTG
1232998 GATGAATCGACCGAAGGA
1 GATGAA-CGACCGAAGGA
* ** *
1233016 GGTGAACGACTAAAGAA
1 GATGAACGACCGAAGGA
1233033 GTATGAACGACCGAAGGA
1 G-ATGAACGACCGAAGGA
1233051 GAATGAA
1 G-ATGAA
1233058 TCGATTGCAG
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 9 0.28
18 23 0.72
ACGTcount: A:0.43, C:0.13, G:0.32, T:0.12
Consensus pattern (17 bp):
GATGAACGACCGAAGGA
Found at i:1234694 original size:2 final size:2
Alignment explanation
Indices: 1234687--1234715 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1234677 GATGTGCAAG
1234687 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 A
1234716 CAAAAGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1235543 original size:13 final size:14
Alignment explanation
Indices: 1235507--1235552 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
1235497 TATCAATTAC
1235507 ACATGATAACATAT
1 ACATGATAACATAT
*
1235521 ATGATGATAACATAT
1 A-CATGATAACATAT
*
1235536 ACAT-ATAACACAT
1 ACATGATAACATAT
1235549 ACAT
1 ACAT
1235553 TCTCATGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.43
14 3 0.11
15 13 0.46
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (14 bp):
ACATGATAACATAT
Found at i:1235712 original size:18 final size:18
Alignment explanation
Indices: 1235689--1235763 Score: 96
Period size: 18 Copynumber: 4.1 Consensus size: 18
1235679 GCACTGAATA
*
1235689 TTTGTCCCGAATGACCAC
1 TTTGTCCCGAAGGACCAC
1235707 TTTGTCCCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
* *
1235725 TGATTGTTCCGAAGAACCAC
1 T--TTGTCCCGAAGGACCAC
*
1235745 TATGTCCCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
1235763 T
1 T
1235764 GATAATCCCT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 33 0.67
20 16 0.33
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (18 bp):
TTTGTCCCGAAGGACCAC
Found at i:1247617 original size:2 final size:2
Alignment explanation
Indices: 1247579--1247607 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1247569 GCAATCTAAA
1247579 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 A
1247608 AAGGTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1250054 original size:23 final size:21
Alignment explanation
Indices: 1250014--1250055 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
1250004 ATTAATATAT
*
1250014 ATATTTATTTTTATAAATAAG
1 ATATTTATTTTTAGAAATAAG
1250035 ATATTTATTTACTTAGAAATA
1 ATATTTATTT--TTAGAAATA
1250056 TCAGAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
ATATTTATTTTTAGAAATAAG
Found at i:1251761 original size:3 final size:3
Alignment explanation
Indices: 1251755--1251803 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
1251745 TTTTTTTATT
*
1251755 TAA TAA TAT TAA TAA TATA TATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1251802 TA
1 TA
1251804 TGATGAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 36 0.84
4 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1252057 original size:45 final size:45
Alignment explanation
Indices: 1251954--1252272 Score: 480
Period size: 45 Copynumber: 7.1 Consensus size: 45
1251944 CAGGTCCTAT
* * * *
1251954 CATCTTGCACTGTAGGTCTTACAGATGACCCGAATGATTTT--AAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAA-GGTTTTGAAAA
* * * *
1251998 CATCATGCATTGAAGGTCTTACAGATGACCTGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
1252043 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
1252088 CATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
1252133 CATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
1252178 CATCATGCACTGAAGGGCTTACAGATGACACGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
1252223 CATCATGCACTGAAGGGCTTATAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
1252268 TATCA
1 CATCA
1252273 AAAAGCTCTC
Statistics
Matches: 252, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
43 4 0.02
44 30 0.12
45 218 0.87
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (45 bp):
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:1252397 original size:165 final size:165
Alignment explanation
Indices: 1252124--1252437 Score: 495
Period size: 165 Copynumber: 1.9 Consensus size: 165
1252114 GACCCGAAGG
* *
1252124 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTT-AAAACATCATGCACT
* * *
1252189 GAAGGGCTTACAGATGACACGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTATAGATGACCC
65 GAAGAGCTTACAAATGACACGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
*
1252254 GAAGGCTTTGAAAATATCAAAAAGCTCTCGAAGGCT
130 GAAGGCTTTGAAAACATCAAAAAGCTCTCGAAGGCT
* *
1252290 TTTTGAAAACATCTTGCACTGTAGGACTTACAGATGACCCGAAGGATTTT-AAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTAAAACATCATGCACT
* * *
1252354 GAAGATCTTACAAATGACCCGAATGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
65 GAAGAGCTTACAAATGACACGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
*
1252419 GAAGGTTTTGAAAACATCA
130 GAAGGCTTTGAAAACATCA
1252438 TGCACTGAAG
Statistics
Matches: 135, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
165 90 0.67
166 41 0.30
167 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (165 bp):
TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTAAAACATCATGCACTG
AAGAGCTTACAAATGACACGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
AAGGCTTTGAAAACATCAAAAAGCTCTCGAAGGCT
Found at i:1252409 original size:45 final size:45
Alignment explanation
Indices: 1252290--1252459 Score: 254
Period size: 45 Copynumber: 3.8 Consensus size: 45
1252280 CTCGAAGGCT
* * *
1252290 TTTTGAAAACATCTTGCACTGTAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
** * *
1252335 ATTTT--AAACATCATGCACTGAAGATCTTACAAATGACCCGAATG
1 -TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1252379 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1252424 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1252460 TGGGAAATAG
Statistics
Matches: 112, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
43 4 0.04
44 33 0.29
45 71 0.63
46 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:1252447 original size:210 final size:210
Alignment explanation
Indices: 1252079--1252459 Score: 629
Period size: 210 Copynumber: 1.8 Consensus size: 210
1252069 GACCCGAAGG
* *
1252079 TTTTAAAAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTAAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTT-AAAACATCATGCACT
* * *
1252144 GAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACAC
65 GAAGAGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACAC
*
1252209 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGCTTTGAAAATATCAA
130 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAA
1252274 AAAGCTCTCGAAGGCT
195 AAAGCTCTCGAAGGCT
* * *
1252290 TTTTGAAAACATCTTGCACTGTAGGACTTACAGATGACCCGAAGGATTTT-AAACATCATGCACT
1 TTTTAAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTAAAACATCATGCACT
* * *
1252354 GAAGATCTTACAAATGACCCGAATGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
65 GAAGAGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACAC
1252419 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
130 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1252460 TGGGAAATAG
Statistics
Matches: 157, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
210 113 0.72
211 40 0.25
212 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (210 bp):
TTTTAAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTAAAACATCATGCACTG
AAGAGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACACG
AAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAA
AAGCTCTCGAAGGCT
Found at i:1253624 original size:54 final size:54
Alignment explanation
Indices: 1253530--1253686 Score: 208
Period size: 54 Copynumber: 2.9 Consensus size: 54
1253520 AACTGGTTCA
* * * *
1253530 TAAAACATTTGACAACACATTCATCATCTCATGTGGTTTCTGCTCAGATGCTAG
1 TAAAACATTTGACAACACATTCATCATTTCCTGTGCTTTCTGCCCAGATGCTAG
* * * *
1253584 TAAAACATTTGACAATACATTCATTATTTCCTGTGCTTTCTGCCCAGATGTTCG
1 TAAAACATTTGACAACACATTCATCATTTCCTGTGCTTTCTGCCCAGATGCTAG
* *
1253638 TAAAACATTTGACAACACATTCATCATTTCCTATGGC-TTCTGCCAAGAT
1 TAAAACATTTGACAACACATTCATCATTTCCTGT-GCTTTCTGCCCAGAT
1253687 TTATCAATCA
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
54 88 0.98
55 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCATTTCCTGTGCTTTCTGCCCAGATGCTAG
Found at i:1254662 original size:74 final size:74
Alignment explanation
Indices: 1254538--1254723 Score: 234
Period size: 74 Copynumber: 2.5 Consensus size: 74
1254528 TCTTGACACG
* * * *
1254538 TGATGATATGGGCCTTCAGCATGCCCCAATATTTGCTGATACAAACGTTCAAAATGCGTCAAAAT
1 TGATGAAATGGGCTTTCAGTATGCCCCAATATTTGCTGATACAAACGTTCAAAATGAGTCAAAAT
1254603 TCCT-ATTT
66 TCCTGATTT
* *
1254611 CTGATGAAATGGGCTTTCAGTATGCCCCAATATTTGCTGATAC-AACAGTTCAAAATGAGTTAAT
1 -TGATGAAATGGGCTTTCAGTATGCCCCAATATTTGCTGATACAAAC-GTTCAAAATGAGTCAAA
*
1254675 ATTCTTGATTT
64 ATTCCTGATTT
* *
1254686 TGATTGAAATGGGGTTTCA-TCATGCCCCAGTATTTGCT
1 TGA-TGAAATGGGCTTTCAGT-ATGCCCCAATATTTGCT
1254724 TCTTGTTGAT
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
73 3 0.03
74 62 0.63
75 34 0.34
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (74 bp):
TGATGAAATGGGCTTTCAGTATGCCCCAATATTTGCTGATACAAACGTTCAAAATGAGTCAAAAT
TCCTGATTT
Found at i:1260488 original size:43 final size:43
Alignment explanation
Indices: 1260406--1260491 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
1260396 TCGTGCATCA
* * *
1260406 AACAAAACTTTACATATAGGGGACAGCTTTCAGTCCTAACTTC
1 AACAAAACTTTACATACAGGGGACAACTTTCACTCCTAACTTC
* * * *
1260449 AACAAAACTTTATATACAGGGGATAACTTTCCCTTCTAACTTC
1 AACAAAACTTTACATACAGGGGACAACTTTCACTCCTAACTTC
1260492 TCTAAAGTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (43 bp):
AACAAAACTTTACATACAGGGGACAACTTTCACTCCTAACTTC
Found at i:1262742 original size:23 final size:20
Alignment explanation
Indices: 1262690--1262744 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
1262680 AATGAAATTT
*
1262690 AATATCTAAAAATAAAATAAA
1 AATAT-TAATAATAAAATAAA
*
1262711 AACATTAATAATAATAATAAA
1 AATATTAATAATAA-AATAAA
1262732 ATATATATAATAA
1 A-ATAT-TAATAA
1262745 ATATTATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 8 0.29
21 11 0.39
22 3 0.11
23 6 0.21
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
AATATTAATAATAAAATAAA
Found at i:1263800 original size:11 final size:11
Alignment explanation
Indices: 1263784--1263842 Score: 59
Period size: 12 Copynumber: 5.2 Consensus size: 11
1263774 GACTAAGATA
1263784 AAAATAATAAT
1 AAAATAATAAT
1263795 AAAATAATAAT
1 AAAATAATAAT
*
1263806 GAAAGTAATAATT
1 -AAAATAATAA-T
1263819 AAAAT-AT-AT
1 AAAATAATAAT
1263828 CAAAAGTAATAAT
1 -AAAA-TAATAAT
1263841 AA
1 AA
1263843 TATTGCAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 1 0.03
10 5 0.12
11 14 0.35
12 17 0.43
13 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:1265087 original size:3 final size:3
Alignment explanation
Indices: 1265081--1265117 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1265071 TTTTTTTATT
*
1265081 TAA TAA TAT TAA TAA TAA T-A TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1265118 TGATGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1265105 original size:17 final size:17
Alignment explanation
Indices: 1265083--1265118 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1265073 TTTTTATTTA
*
1265083 ATAATATTAATAATAAT
1 ATAATAATAATAATAAT
1265100 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
1265117 AT
1 AT
1265119 GATGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:1271583 original size:20 final size:20
Alignment explanation
Indices: 1271558--1271662 Score: 201
Period size: 20 Copynumber: 5.2 Consensus size: 20
1271548 TTTGGTTCAC
*
1271558 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTACCAGTG
1271578 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1271598 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1271618 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1271638 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1271658 GGAAT
1 GGAAT
1271663 ATGATTACTG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1271887 original size:37 final size:37
Alignment explanation
Indices: 1271814--1271888 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
1271804 GTTAAAAAAT
* *
1271814 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
1271851 ATTTATATATATATT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAT-T-TTCTTTAAAAAATTGAAAATCATAAA
1271888 A
1 A
1271889 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 16 0.48
38 15 0.45
39 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1275839 original size:21 final size:21
Alignment explanation
Indices: 1275815--1275911 Score: 158
Period size: 21 Copynumber: 4.6 Consensus size: 21
1275805 TTACATTATA
1275815 GGTACCGATACCCTATGTAGG
1 GGTACCGATACCCTATGTAGG
**
1275836 GGTATTGATACCCTATGTAGG
1 GGTACCGATACCCTATGTAGG
*
1275857 GGTACCGATACCCTATATAGG
1 GGTACCGATACCCTATGTAGG
1275878 GGTACCGATACCCTATGTAGG
1 GGTACCGATACCCTATGTAGG
*
1275899 GGTACTGATACCC
1 GGTACCGATACCC
1275912 CCCACGCTCC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (21 bp):
GGTACCGATACCCTATGTAGG
Found at i:1276779 original size:18 final size:18
Alignment explanation
Indices: 1276756--1276795 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1276746 AGCATGAAAC
*
1276756 ATCATAGAAGACGGATAT
1 ATCATAGAAGACGAATAT
1276774 ATCATAGAAGACGAATAT
1 ATCATAGAAGACGAATAT
1276792 ATCA
1 ATCA
1276796 AACCTTTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.23
Consensus pattern (18 bp):
ATCATAGAAGACGAATAT
Found at i:1281656 original size:23 final size:23
Alignment explanation
Indices: 1281625--1281677 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1281615 AGGAGGTCTC
* *
1281625 GATAGCCCCTTTGAATGGGTACT
1 GATACCCCCTATGAATGGGTACT
*
1281648 GATACCCCCTATGAATGGGTATT
1 GATACCCCCTATGAATGGGTACT
1281671 GATACCC
1 GATACCC
1281678 TCCCTTAGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (23 bp):
GATACCCCCTATGAATGGGTACT
Found at i:1281694 original size:21 final size:21
Alignment explanation
Indices: 1281670--1281722 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1281660 GAATGGGTAT
1281670 TGATACCCTCCCTTAGGGAAC
1 TGATACCCTCCCTTAGGGAAC
*
1281691 TGATACCCTCCCTTAGGGCAC
1 TGATACCCTCCCTTAGGGAAC
*
1281712 CGATACCCTCC
1 TGATACCCTCC
1281723 ATGGGTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.23
Consensus pattern (21 bp):
TGATACCCTCCCTTAGGGAAC
Found at i:1282077 original size:28 final size:28
Alignment explanation
Indices: 1282037--1282120 Score: 168
Period size: 28 Copynumber: 3.0 Consensus size: 28
1282027 TGTTTATATT
1282037 TTGGTTTAGAACTATAATCTACAACTAA
1 TTGGTTTAGAACTATAATCTACAACTAA
1282065 TTGGTTTAGAACTATAATCTACAACTAA
1 TTGGTTTAGAACTATAATCTACAACTAA
1282093 TTGGTTTAGAACTATAATCTACAACTAA
1 TTGGTTTAGAACTATAATCTACAACTAA
1282121 CTTCATCAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (28 bp):
TTGGTTTAGAACTATAATCTACAACTAA
Found at i:1286470 original size:41 final size:41
Alignment explanation
Indices: 1286425--1286506 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
1286415 ACTAACGGTG
*
1286425 TTGAACATTGATACATAAATATACCAAAGT-TGAACTGATAA
1 TTGAACATTGATACACAAATATACCAAA-TCTGAACTGATAA
* * *
1286466 TTGAACATTGATACACGAATGTATCAAATCTGAACTGATAA
1 TTGAACATTGATACACAAATATACCAAATCTGAACTGATAA
1286507 GCACTCACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (41 bp):
TTGAACATTGATACACAAATATACCAAATCTGAACTGATAA
Found at i:1290365 original size:29 final size:29
Alignment explanation
Indices: 1290323--1290378 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1290313 GTGTTCATTG
1290323 TCAAATAATTGAAAATCTTTATAATATTA
1 TCAAATAATTGAAAATCTTTATAATATTA
1290352 TCAAATAATTGAAAATCTTTATAATAT
1 TCAAATAATTGAAAATCTTTATAATAT
1290379 ATATTATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (29 bp):
TCAAATAATTGAAAATCTTTATAATATTA
Found at i:1292801 original size:32 final size:34
Alignment explanation
Indices: 1292753--1292832 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 34
1292743 TTTAAATAGT
*
1292753 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTATATTAAATAATATTTATATAAA
*
1292785 TATTATATTTTT-TATTAAAATAATATTTATATAAT
1 TATTAT-TTTTTATATT-AAATAATATTTATATAAA
1292820 TATTATTTATTTA
1 TATTATTT-TTTA
1292833 GAATTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
32 10 0.25
33 5 0.12
34 5 0.12
35 20 0.50
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATATTTATATAAA
Found at i:1292812 original size:18 final size:20
Alignment explanation
Indices: 1292775--1292812 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
1292765 TATTAATATA
*
1292775 TTTATGTAAATATTATATTT
1 TTTATGTAAATATAATATTT
1292795 TTTAT-TAAA-ATAATATTT
1 TTTATGTAAATATAATATTT
1292813 ATATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTATGTAAATATAATATTT
Found at i:1292999 original size:17 final size:17
Alignment explanation
Indices: 1292977--1293030 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1292967 AATGTTAATA
1292977 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1292994 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1293011 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1293028 TTT
1 TTT
1293031 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1294604 original size:21 final size:21
Alignment explanation
Indices: 1294561--1294605 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1294551 GCAGGGGTAC
* *
1294561 ATGCCCAGCCCTCTACTTCAT
1 ATGCCAAGCCCACTACTTCAT
* *
1294582 ATGCCAAGCCCACTAGTTTAT
1 ATGCCAAGCCCACTACTTCAT
1294603 ATG
1 ATG
1294606 TCATCTCCGC
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:0.24, C:0.33, G:0.13, T:0.29
Consensus pattern (21 bp):
ATGCCAAGCCCACTACTTCAT
Found at i:1294638 original size:21 final size:21
Alignment explanation
Indices: 1294612--1294705 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
1294602 TATGTCATCT
1294612 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
1294633 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
1294654 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
1294675 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
1294696 CCGCAGGGTT
1 CCGCAGGGTT
1294706 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:1295287 original size:33 final size:34
Alignment explanation
Indices: 1295228--1295324 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
1295218 AAATGTTTTT
*
1295228 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
1295262 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
1295295 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
1295325 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:1295331 original size:34 final size:33
Alignment explanation
Indices: 1295226--1295331 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
1295216 ATAAATGTTT
*
1295226 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
1295260 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
1295292 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
1295327 TTAAA
1 TTAAA
1295332 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:1295953 original size:128 final size:128
Alignment explanation
Indices: 1295725--1296733 Score: 1623
Period size: 128 Copynumber: 7.9 Consensus size: 128
1295715 TTACCTGATT
1295725 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1295790 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
** *
1295853 TACTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *** *
1295918 TGGCAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
*
1295981 TACTAATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1296046 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
** *
1296109 TACTG--ATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * * *** * *
1296172 TGGCAAAATAATGGAAGGCGCGTCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAACAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
1296235 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
1296300 TGATGAAATGATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
** *
1296363 TACTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
1296428 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
1296491 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1296556 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAAG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1296619 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTT
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1296684 TGACGAAATAATGGAAGGCGCGTCCCCGGGAACGCTCCTTCATGTGAATA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
1296734 ATACTCCGAT
Statistics
Matches: 803, Mismatches: 70, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
126 112 0.14
127 4 0.00
128 685 0.85
129 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1296504 original size:256 final size:256
Alignment explanation
Indices: 1295725--1296728 Score: 1850
Period size: 256 Copynumber: 3.9 Consensus size: 256
1295715 TTACCTGATT
1295725 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1295790 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
1295855 CTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG
131 CTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG
*
1295920 GCAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
196 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
*
1295981 TACTAATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1296046 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
1296111 CTG--ATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG
131 CTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG
* * *
1296174 GCAAAATAATGGAAGGCGCGTCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAACAGG
196 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
1296235 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1296300 TGATGAAATGATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
1296365 CTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG
131 CTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG
*
1296430 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
196 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
1296491 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1296556 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAAGTA
66 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
** *
1296621 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTTG
131 CTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG
* * *
1296686 ACGAAATAATGGAAGGCGCGTCCCCGGGAACGCTCCTTCATGT
196 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT
1296729 GAATAATACT
Statistics
Matches: 727, Mismatches: 19, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
254 249 0.34
256 478 0.66
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (256 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
CTGATATATCGGGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATG
ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
Found at i:1299652 original size:23 final size:24
Alignment explanation
Indices: 1299626--1299672 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1299616 TATTTAAATG
*
1299626 AATGTTTTTGT-TTCTA-ATAATTT
1 AATGTTATTGTATT-TATATAATTT
1299649 AATGTTATTGTATTTATATAATTT
1 AATGTTATTGTATTTATATAATTT
1299673 GTCAATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.60
Consensus pattern (24 bp):
AATGTTATTGTATTTATATAATTT
Found at i:1306428 original size:17 final size:18
Alignment explanation
Indices: 1306391--1306431 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1306381 ATATTATGTA
*
1306391 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
1306409 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
1306426 TTTACT
1 TTTACT
1306432 AATATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:1316178 original size:20 final size:21
Alignment explanation
Indices: 1316153--1316245 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1316143 TTTTCCCAAT
*
1316153 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1316173 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1316194 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1316214 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1316235 TCGCAATGCGA
1 TCGCAATGCGA
1316246 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1316198 original size:41 final size:41
Alignment explanation
Indices: 1316153--1316245 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1316143 TTTTCCCAAT
1316153 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1316194 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1316235 TCGCAATGCGA
1 TCGCAATGCGA
1316246 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1316258 original size:41 final size:41
Alignment explanation
Indices: 1316172--1316306 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1316162 GAATAAGTAA
** *
1316172 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1316213 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
1316254 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1316295 TTCGCAACGCGA
1 ATCGCAACGCGA
1316307 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1316259 original size:20 final size:20
Alignment explanation
Indices: 1316234--1316327 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1316224 AATTGGGAAA
*
1316234 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
1316254 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
1316275 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
1316295 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
1316315 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1316328 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:1316881 original size:19 final size:19
Alignment explanation
Indices: 1316843--1316909 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1316833 TTCGAGAATG
1316843 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1316863 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1316882 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1316901 AAAATCGCA
1 AAAATCGCA
1316910 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1316927 original size:19 final size:19
Alignment explanation
Indices: 1316905--1317088 Score: 172
Period size: 19 Copynumber: 10.1 Consensus size: 19
1316895 GAAACCAAAA
*
1316905 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1316924 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1316943 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1316962 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1316982 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1316998 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1317015 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1317029 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1317048 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1317068 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1317088 T
1 T
1317089 TAACCAAAAG
Statistics
Matches: 137, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1316982 original size:39 final size:38
Alignment explanation
Indices: 1316905--1317088 Score: 172
Period size: 33 Copynumber: 5.0 Consensus size: 38
1316895 GAAACCAAAA
*
1316905 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
1316943 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1316982 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
1317015 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
1317048 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1317088 T
1 T
1317089 TAACCAAAAG
Statistics
Matches: 123, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 29 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1319150 original size:42 final size:42
Alignment explanation
Indices: 1319090--1319212 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1319080 GCCCAACTCG
* * *
1319090 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1319132 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1319174 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1319213 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1319170 original size:21 final size:21
Alignment explanation
Indices: 1319146--1319212 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1319136 TCATTCCTCG
1319146 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1319167 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1319188 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1319209 AGAG
1 AGAG
1319213 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1320589 original size:14 final size:14
Alignment explanation
Indices: 1320570--1320605 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1320560 ATTGTTTAAT
1320570 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1320584 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1320598 TGATTTGT
1 TGATTTGT
1320606 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1320788 original size:19 final size:19
Alignment explanation
Indices: 1320766--1320896 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
1320756 CGAAATTAAA
1320766 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
1320785 TTCGCGTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1320801 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1320818 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
1320832 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1320851 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1320867 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1320884 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1320897 AGTAATTTTC
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 23 0.27
16 13 0.15
17 13 0.15
19 35 0.42
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1320814 original size:33 final size:32
Alignment explanation
Indices: 1320772--1320896 Score: 180
Period size: 33 Copynumber: 3.8 Consensus size: 32
1320762 TAAATTCGCA
*
1320772 TTGCGATTTTCATTTCGCGTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATT-CCTCG
**
1320805 TTGCGATTTTCATTTCGCATTGCGAAATT-AGCG
1 TTGCGATTTTCATTTCGCATTGCG--ATTCCTCG
1320838 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTC-CTCG
1320871 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1320897 AGTAATTTTC
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCTCG
Found at i:1320851 original size:66 final size:66
Alignment explanation
Indices: 1320763--1320895 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1320753 ACGCGAAATT
* *
1320763 AAATTCGCATTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1320828 G
66 G
* *
1320829 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1320894 G
66 G
1320895 A
1 A
1320896 TAGTAATTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1323196 original size:12 final size:12
Alignment explanation
Indices: 1323179--1323203 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1323169 TCTTCGGGGA
1323179 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1323191 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1323203 C
1 C
1323204 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1323412 original size:24 final size:24
Alignment explanation
Indices: 1323378--1323431 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1323368 CTGAAACATC
* *
1323378 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1323402 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1323426 ATCAAA
1 ATCAAA
1323432 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1324479 original size:20 final size:20
Alignment explanation
Indices: 1324454--1324511 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1324444 ATTCATTTGA
1324454 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1324474 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1324494 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1324512 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1324571 original size:19 final size:19
Alignment explanation
Indices: 1324530--1324612 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
1324520 GAAATGAAAA
1324530 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1324546 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1324563 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1324582 TCGCATTGCGATTTCCATA
1 TCGCATTGCGATTTTCATT
*
1324601 TCGCGTTGCGAT
1 TCGCATTGCGAT
1324613 AGTCTGTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
14 11 0.19
16 3 0.05
17 3 0.05
19 42 0.71
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1326636 original size:20 final size:19
Alignment explanation
Indices: 1326601--1326667 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1326591 GAAACTTAAA
1326601 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1326620 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1326640 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1326659 ATCGCAACG
1 ATCGCAACG
1326668 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1326675 original size:14 final size:14
Alignment explanation
Indices: 1326656--1326713 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1326646 ATGCGAAATG
1326656 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1326670 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1326686 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1326702 AAAATCGCAACG
1 AAAATCGCAACG
1326714 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1326698 original size:32 final size:33
Alignment explanation
Indices: 1326640--1326718 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1326630 GGAAATGGCT
*
1326640 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1326673 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1326705 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1326719 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1326787 original size:19 final size:19
Alignment explanation
Indices: 1326725--1326788 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1326715 GAAACACAAA
*
1326725 TCGCATTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1326744 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1326760 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1326777 TCGCATTGCGAT
1 TCGCATTGCGAT
1326789 AGCCATTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 6 0.17
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 16 0.44
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1326807 original size:20 final size:19
Alignment explanation
Indices: 1326773--1326826 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
1326763 TTGCGATTTT
*
1326773 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1326792 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1326812 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
1326827 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1326825 original size:19 final size:19
Alignment explanation
Indices: 1326761--1326826 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
1326751 GCGATTTTGT
**
1326761 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
1326780 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1326800 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
1326819 TGTTGCGA
1 CGTTGCGA
1326827 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1327325 original size:18 final size:18
Alignment explanation
Indices: 1327299--1327343 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1327289 GTCGATCAGA
* *
1327299 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
1327317 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1327335 TGATGGCTC
1 TGATGGCTC
1327344 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1328683 original size:20 final size:20
Alignment explanation
Indices: 1328658--1328695 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1328648 AATAGTTTCT
1328658 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1328678 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1328696 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1329258 original size:21 final size:21
Alignment explanation
Indices: 1329234--1329325 Score: 61
Period size: 20 Copynumber: 4.5 Consensus size: 21
1329224 AAGTATCTCG
1329234 TTGCGATTTTGTATTATCGCA
1 TTGCGATTTTGTATTATCGCA
* *
1329255 TTGCGA--TAGTAAGTATCGCA
1 TTGCGATTTTGT-ATTATCGCA
** *
1329275 TTGCGATTTTCCCAAT-TCGCA
1 TTGCGATTTT-GTATTATCGCA
1329296 TTGCGA--TT-TACTTATTCGCA
1 TTGCGATTTTGTA-TTA-TCGCA
1329316 TTGCGATTTT
1 TTGCGATTTT
1329326 CCCAATTCGC
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 5 0.09
20 25 0.46
21 17 0.31
22 5 0.09
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTGTATTATCGCA
Found at i:1329281 original size:20 final size:20
Alignment explanation
Indices: 1329188--1329281 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1329178 GATTATGTAA
* *
1329188 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
1329208 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * *
1329228 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
1329249 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
1329269 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1329282 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:1329295 original size:41 final size:41
Alignment explanation
Indices: 1329209--1329343 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1329199 AAAGTCAGTA
* * * * ** *
1329209 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1329249 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1329291 TCGCATTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
*
1329332 TCGCGTTGCGAT
1 TCGCATTGCGAT
1329344 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1329314 original size:20 final size:21
Alignment explanation
Indices: 1329270--1329362 Score: 109
Period size: 20 Copynumber: 4.5 Consensus size: 21
1329260 ATAGTAAGTA
*
1329270 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
1329291 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
*
1329311 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
1329332 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
1329352 TCGCATTGCGA
1 TCGCATTGCGA
1329363 ATTGGGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 33 0.55
21 27 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:1329344 original size:41 final size:41
Alignment explanation
Indices: 1329270--1329362 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1329260 ATAGTAAGTA
1329270 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
*
1329311 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
1329352 TCGCATTGCGA
1 TCGCATTGCGA
1329363 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
Found at i:1335115 original size:20 final size:20
Alignment explanation
Indices: 1335090--1335136 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1335080 GATTAAGCTA
1335090 TGTTTTGCTTTTAAATATGG
1 TGTTTTGCTTTTAAATATGG
1335110 TGTTTTGCTTTTAAATATGG
1 TGTTTTGCTTTTAAATATGG
1335130 TGTTTTG
1 TGTTTTG
1335137 AATTTTCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.04, G:0.21, T:0.57
Consensus pattern (20 bp):
TGTTTTGCTTTTAAATATGG
Found at i:1347712 original size:23 final size:23
Alignment explanation
Indices: 1347686--1347729 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1347676 AAAATAATTT
*
1347686 CAGAATCGAAAAACCCTATTTAC
1 CAGAACCGAAAAACCCTATTTAC
* *
1347709 CAGAACCGGAAAACTCTATTT
1 CAGAACCGAAAAACCCTATTT
1347730 CTACTAGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (23 bp):
CAGAACCGAAAAACCCTATTTAC
Done.