Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009247.1 Hibiscus syriacus cultivar Beakdansim tig00112888_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: 1479039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1177798 original size:22 final size:22
Alignment explanation
Indices: 1177772--1177814 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177762 TAATAAATTA
1177772 TTTAAAATAAACCAATCCATAT
1 TTTAAAATAAACCAATCCATAT
* *
1177794 TTTAAAATAAAGCATTCCATA
1 TTTAAAATAAACCAATCCATA
1177815 CTAATAAATT
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:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
TTTAAAATAAACCAATCCATAT
Found at i:1177849 original size:134 final size:134
Alignment explanation
Indices: 1177518--1177980 Score: 854
Period size: 134 Copynumber: 3.4 Consensus size: 134
1177508 GAATGATTTC
1177518 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
1 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
1177583 ACAATAATAAATCAATCCATATTTTAAAATACAATCAATCCATACTAATAAATTATTTAAAATAA
66 ACAATAATAAATCAATCCATATTTTAAAATA-AATCAATCCATACTAATAAATTATTTAAAATAA
1177648 ATCAA
130 ATCAA
1177653 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
1 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
*
1177718 ACAATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
66 ACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
*
1177783 CCAA
131 TCAA
* * *
1177787 TCCATATTTTAAAATAAAGCATTCCATACTAATAAATTATTTAAAATAAATCAATCTATACAACT
1 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
*
1177852 ACAATAATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAA
66 ACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
1177917 TCAA
131 TCAA
*
1177921 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATA
1 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1177981 TTTTAAAATA
Statistics
Matches: 316, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
134 221 0.70
135 95 0.30
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (134 bp):
TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
ACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
TCAA
Found at i:1177903 original size:22 final size:22
Alignment explanation
Indices: 1177831--1177903 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
1177821 AATTATTTAA
* *
1177831 AATAAATCAATCTATACAACTAC-
1 AATAAATAAATCAAT-CAA-TACT
*
1177854 AAT-AATAAATCAATCCATA-T
1 AATAAATAAATCAATCAATACT
**
1177874 TTTAAAATAAATCAATCAATACT
1 AAT-AAATAAATCAATCAATACT
1177897 AATAAAT
1 AATAAAT
1177904 TATTTAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
20 3 0.08
21 2 0.05
22 28 0.74
23 5 0.13
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAATAAATCAATCAATACT
Found at i:1177917 original size:188 final size:186
Alignment explanation
Indices: 1177588--1178025 Score: 600
Period size: 188 Copynumber: 2.3 Consensus size: 186
1177578 CAACTACAAT
1177588 AATAAATCAATCCATATTTTAAAATACAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATA-AATCAATCCATACTAATAAATTATTTAAAATAAATCAA
* ** *
1177653 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACT
65 TCCATACTACAAAATAAATCAATCCATACTAATAAA-TA-TTAAAATAAATCAATCAATACAACT
*
1177718 ACAATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
128 ACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
1177777 AATAAACCAATCCATATTTTAAAATAAAGCATTCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* ** *
1177842 CTATACAACTACAATAATAAATCAATCCATA-TTTTAAA-A-T-AAATCAATCAATACTAATA-A
66 CCAT---ACTACAA-AATAAATCAATCCATACTAATAAATATTAAAATAAATCAAT-C-AATACA
* *
1177902 ATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
125 ACTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1177965 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1178026 TATTTTAAAA
Statistics
Matches: 223, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
186 11 0.05
187 6 0.03
188 153 0.69
189 28 0.13
191 9 0.04
192 16 0.07
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (186 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACTACAAAATAAATCAATCCATACTAATAAATATTAAAATAAATCAATCAATACAACTACA
ATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:1177932 original size:22 final size:22
Alignment explanation
Indices: 1177906--1177948 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177896 TAATAAATTA
1177906 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1177928 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1177949 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1177957 original size:22 final size:22
Alignment explanation
Indices: 1177908--1177956 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1177898 ATAAATTATT
**
1177908 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1177930 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1177953 TAAA
1 TAAA
1177957 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1177986 original size:22 final size:22
Alignment explanation
Indices: 1177960--1178002 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177950 TAATAAATTA
*
1177960 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
1177982 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1178003 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1178011 original size:22 final size:22
Alignment explanation
Indices: 1177962--1178010 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1177952 ATAAATTATT
* **
1177962 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
1177984 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1178007 TAAA
1 TAAA
1178011 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1178024 original size:14 final size:15
Alignment explanation
Indices: 1178005--1178040 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1177995 AATCCATACT
1178005 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1178019 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1178034 AATAAAT
1 AATAAAT
1178041 AACCTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1179962 original size:12 final size:12
Alignment explanation
Indices: 1179928--1179967 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
1179918 TCCACTGATC
1179928 TTTGAATCAAAATT
1 TTTGAATC--AATT
1179942 TTTGTAATCAATT
1 TTTG-AATCAATT
1179955 TTTGAATCAATT
1 TTTGAATCAATT
1179967 T
1 T
1179968 ATTTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.36
13 8 0.32
14 4 0.16
15 4 0.16
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (12 bp):
TTTGAATCAATT
Found at i:1202335 original size:75 final size:75
Alignment explanation
Indices: 1202245--1202418 Score: 217
Period size: 75 Copynumber: 2.3 Consensus size: 75
1202235 AAATATCAAA
* * * *
1202245 ACTCAAACAACAATATTAAGTTTAGAACAGTAAAATCCATAA-ACAAATCACAATATTAAAATGT
1 ACTCAAACCATAATATTAAGTCTAGAACAATAAAATCCATAATA-AAATCACAATATTAAAATGT
*
1202309 CAAAT-TTCAAG
65 CAAATCCT-AAG
* * * * * *
1202320 ATTCAAATCATAATATTAACTCTAGAATAATAAAATCCATAATAAAATCATAATATTAAAGTGTC
1 ACTCAAACCATAATATTAAGTCTAGAACAATAAAATCCATAATAAAATCACAATATTAAAATGTC
1202385 AAATCCTAAG
66 AAATCCTAAG
1202395 ACTCAAACCATAATATTAAGTCTA
1 ACTCAAACCATAATATTAAGTCTA
1202419 TAAAATATTA
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
75 81 0.98
76 2 0.02
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.28
Consensus pattern (75 bp):
ACTCAAACCATAATATTAAGTCTAGAACAATAAAATCCATAATAAAATCACAATATTAAAATGTC
AAATCCTAAG
Found at i:1202373 original size:11 final size:12
Alignment explanation
Indices: 1202346--1202374 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1202336 TAACTCTAGA
1202346 ATAATAAAATCC
1 ATAATAAAATCC
1202358 ATAATAAAAT-C
1 ATAATAAAATCC
1202369 ATAATA
1 ATAATA
1202375 TTAAAGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAATAAAATCC
Found at i:1207237 original size:50 final size:50
Alignment explanation
Indices: 1207139--1207262 Score: 160
Period size: 51 Copynumber: 2.5 Consensus size: 50
1207129 AACAGTAAAA
**
1207139 CACGCCCCTGCACCGCGCTATACGATGATTTGGCGTCACGTGGGGTATAG
1 CACGCCCCTGCACCGCGCTATACGATGAGCTGGCGTCACGTGGGGTATAG
* * *
1207189 CACGCCCCCTGCACTGTGCTATACGGTGAGCTGGCGTCACGT-GGGTATAG
1 CACG-CCCCTGCACCGCGCTATACGATGAGCTGGCGTCACGTGGGGTATAG
* *
1207239 CGCGGCCCCTGCAGCGCGCTATAC
1 CAC-GCCCCTGCACCGCGCTATAC
1207263 TTGTATATCT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 30 0.48
51 33 0.52
ACGTcount: A:0.16, C:0.33, G:0.31, T:0.20
Consensus pattern (50 bp):
CACGCCCCTGCACCGCGCTATACGATGAGCTGGCGTCACGTGGGGTATAG
Found at i:1207373 original size:51 final size:49
Alignment explanation
Indices: 1207283--1207404 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 49
1207273 GACACGTGGG
* **
1207283 GTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGG-CGCGCTATACCCACGTGGCGCCAAATCACC
*
1207333 GTATAGCGCGGTGCAAGGGGCGCGCTATACCACACGTGGCGCCAAATCATC
1 GTATAGCGCGGTGC-AGGGGCGCGCTATACC-CACGTGGCGCCAAATCACC
**
1207384 GTATAGCATGGTGCAGGGGCG
1 GTATAGCGCGGTGCAGGGGCG
1207405 TGCTTTACTG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
50 31 0.48
51 33 0.52
ACGTcount: A:0.20, C:0.30, G:0.34, T:0.16
Consensus pattern (49 bp):
GTATAGCGCGGTGCAGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:1211599 original size:12 final size:12
Alignment explanation
Indices: 1211582--1211612 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1211572 ATTAAAATCA
1211582 TTAAAATTTATT
1 TTAAAATTTATT
1211594 TTAAAATTTATT
1 TTAAAATTTATT
1211606 TTAAAAT
1 TTAAAAT
1211613 ATAGATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:1211627 original size:22 final size:22
Alignment explanation
Indices: 1211599--1212031 Score: 647
Period size: 22 Copynumber: 19.6 Consensus size: 22
1211589 TTATTTTAAA
*
1211599 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
1211621 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1211643 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
*
1211665 ATGTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1211687 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1211709 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1211731 ATTTAATTTTAAAATATGGATTG
1 ATTT-ATTTTAAAATATGGATTG
1211754 ATTTAATTTTAAAATATGGATTG
1 ATTT-ATTTTAAAATATGGATTG
**
1211777 ATTTATTTTAAAATATGGA-CA
1 ATTTATTTTAAAATATGGATTG
1211798 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
1211821 ATTTATTTTAAAATATGGGTTG
1 ATTTATTTTAAAATATGGATTG
**
1211843 ATTTATTTTAAAATATGGA-CA
1 ATTTATTTTAAAATATGGATTG
1211864 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
* **
1211887 ATTTATTTTAAAATATGTA-AA
1 ATTTATTTTAAAATATGGATTG
1211908 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
* ***
1211931 ATTTATTTTAAAATATGTAAAA
1 ATTTATTTTAAAATATGGATTG
1211953 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1211975 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
1211997 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
1212019 ATTTATTTTAAAA
1 ATTTATTTTAAAA
1212032 AAATTATTAT
Statistics
Matches: 372, Mismatches: 32, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
21 3 0.01
22 321 0.86
23 48 0.13
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1212112 original size:31 final size:31
Alignment explanation
Indices: 1212055--1212113 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1212045 AGTTGTATGG
* *
1212055 ATTATTTAAATTTTAATATTATAAAACTAAA
1 ATTATTTAAATTTCAATATTACAAAACTAAA
*
1212086 ATTATTTAAATTTCAATATTGCAAAACT
1 ATTATTTAAATTTCAATATTACAAAACT
1212114 CTTTCAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTACAAAACTAAA
Found at i:1218624 original size:91 final size:91
Alignment explanation
Indices: 1218515--1218699 Score: 370
Period size: 91 Copynumber: 2.0 Consensus size: 91
1218505 AAGATGTCTA
1218515 GGGGGTTACGCCAAGGGTGTTCGTTATCACCGCTATTGTTTAATTTAGTGGGTGAGATGTTAAGT
1 GGGGGTTACGCCAAGGGTGTTCGTTATCACCGCTATTGTTTAATTTAGTGGGTGAGATGTTAAGT
1218580 TTGATGTTGTCTAAGGCAGTTAAGAT
66 TTGATGTTGTCTAAGGCAGTTAAGAT
1218606 GGGGGTTACGCCAAGGGTGTTCGTTATCACCGCTATTGTTTAATTTAGTGGGTGAGATGTTAAGT
1 GGGGGTTACGCCAAGGGTGTTCGTTATCACCGCTATTGTTTAATTTAGTGGGTGAGATGTTAAGT
1218671 TTGATGTTGTCTAAGGCAGTTAAGAT
66 TTGATGTTGTCTAAGGCAGTTAAGAT
1218697 GGG
1 GGG
1218700 CCTTTCTAGC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.22, C:0.11, G:0.32, T:0.36
Consensus pattern (91 bp):
GGGGGTTACGCCAAGGGTGTTCGTTATCACCGCTATTGTTTAATTTAGTGGGTGAGATGTTAAGT
TTGATGTTGTCTAAGGCAGTTAAGAT
Found at i:1221802 original size:23 final size:23
Alignment explanation
Indices: 1221766--1221812 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1221756 CCTCTGAATG
* *
1221766 AAAACTGTGCTGAATGATTCAGC
1 AAAACAGTGCTGAATCATTCAGC
*
1221789 AAAACAGTGTTGAATCATTCAGC
1 AAAACAGTGCTGAATCATTCAGC
1221812 A
1 A
1221813 CATAAGTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (23 bp):
AAAACAGTGCTGAATCATTCAGC
Found at i:1221927 original size:15 final size:16
Alignment explanation
Indices: 1221889--1221929 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1221879 ACAGAGGCTC
1221889 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
*
1221905 TGAATCATTCAGCGTT
1 TGAATCATTCAGCATT
1221921 T-AATCATTC
1 TGAATCATTC
1221930 TGAAGTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:1221989 original size:18 final size:18
Alignment explanation
Indices: 1221963--1222006 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1221953 GTTTGATTAT
*
1221963 TGAAATAACATTATTCAA
1 TGAACTAACATTATTCAA
* *
1221981 TGAACTAACTTTATTTAA
1 TGAACTAACATTATTCAA
1221999 TGAACTAA
1 TGAACTAA
1222007 ATGCATGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (18 bp):
TGAACTAACATTATTCAA
Found at i:1223178 original size:21 final size:21
Alignment explanation
Indices: 1223154--1223193 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1223144 CTCATTTTCA
1223154 CTCTCAAT-TCTCTTTTCAATG
1 CTCTCAATGTCT-TTTTCAATG
1223175 CTCTCAATGTCTTTTTCAA
1 CTCTCAATGTCTTTTTCAA
1223194 CTCTCGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.20, C:0.28, G:0.05, T:0.47
Consensus pattern (21 bp):
CTCTCAATGTCTTTTTCAATG
Found at i:1223994 original size:27 final size:27
Alignment explanation
Indices: 1223963--1224026 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1223953 TAATGGAATA
1223963 TAAAGATGAAGTAAAATTTTTTTTCTT
1 TAAAGATGAAGTAAAATTTTTTTTCTT
*
1223990 TAAAGATGAAGTAAATTTTTTTTTCTT
1 TAAAGATGAAGTAAAATTTTTTTTCTT
1224017 TAAAGATGAA
1 TAAAGATGAA
1224027 AAGAATTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.45
Consensus pattern (27 bp):
TAAAGATGAAGTAAAATTTTTTTTCTT
Found at i:1224286 original size:14 final size:14
Alignment explanation
Indices: 1224267--1224316 Score: 100
Period size: 14 Copynumber: 3.6 Consensus size: 14
1224257 ATAAGAAGGG
1224267 AAATATGTATATAT
1 AAATATGTATATAT
1224281 AAATATGTATATAT
1 AAATATGTATATAT
1224295 AAATATGTATATAT
1 AAATATGTATATAT
1224309 AAATATGT
1 AAATATGT
1224317 GTATGAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (14 bp):
AAATATGTATATAT
Found at i:1225631 original size:18 final size:18
Alignment explanation
Indices: 1225603--1225648 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1225593 TAGTTTGATT
*
1225603 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
* *
1225621 ATTGAACTAACTTTATTC
1 AATGAACTAACATTATTC
1225639 AATGAACTAA
1 AATGAACTAA
1225649 ATGCATGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:1228000 original size:33 final size:33
Alignment explanation
Indices: 1227963--1228081 Score: 107
Period size: 33 Copynumber: 3.6 Consensus size: 33
1227953 TTGTTCCGGA
* *
1227963 CAAGTAGCAGGGATGATGCCCCCACATGCAGCC
1 CAAGTAGCAGGAATGATGCCCCCACATGAAGCC
* * * * * *
1227996 CAAGTAGTACGAATGATGCCCCTATAAGAAGGC
1 CAAGTAGCAGGAATGATGCCCCCACATGAAGCC
* * *
1228029 CAAGTAGCAGGGATGATGCCCCCGCAAT-TAGCC
1 CAAGTAGCAGGAATGATGCCCCCAC-ATGAAGCC
1228062 CAAGTAGTC-GGAATGATGCC
1 CAAGTAG-CAGGAATGATGCC
1228082 TCTATAAGCA
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
33 64 0.97
34 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (33 bp):
CAAGTAGCAGGAATGATGCCCCCACATGAAGCC
Found at i:1228039 original size:66 final size:66
Alignment explanation
Indices: 1227963--1228114 Score: 209
Period size: 66 Copynumber: 2.3 Consensus size: 66
1227953 TTGTTCCGGA
1227963 CAAGTAGCAGGGATGATGCCCCCAC-ATGCAGCCCAAGTAGTAC-GAATGATGCCCCTATAAGAA
1 CAAGTAGCAGGGATGATGCCCCCACAAT-CAGCCCAAGTAGT-CGGAATGATGCCCCTATAAGAA
1228026 GGC
64 GGC
* * * *
1228029 CAAGTAGCAGGGATGATGCCCCCGCAATTAGCCCAAGTAGTCGGAATGATGCCTCTATAAGCAGG
1 CAAGTAGCAGGGATGATGCCCCCACAATCAGCCCAAGTAGTCGGAATGATGCCCCTATAAGAAGG
*
1228094 T
66 C
* *
1228095 CAAGTAGCAGTGACGATGCC
1 CAAGTAGCAGGGATGATGCC
1228115 TCCATAAGCA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 74 0.96
67 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.17
Consensus pattern (66 bp):
CAAGTAGCAGGGATGATGCCCCCACAATCAGCCCAAGTAGTCGGAATGATGCCCCTATAAGAAGG
C
Found at i:1234517 original size:12 final size:14
Alignment explanation
Indices: 1234488--1234518 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1234478 CATGAAAGCA
1234488 TGTGACAGTGTTTG
1 TGTGACAGTGTTTG
1234502 TGTGACAGTGTTTG
1 TGTGACAGTGTTTG
1234516 TGT
1 TGT
1234519 ATGCAAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.06, G:0.35, T:0.45
Consensus pattern (14 bp):
TGTGACAGTGTTTG
Found at i:1234992 original size:21 final size:21
Alignment explanation
Indices: 1234959--1235011 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1234949 ATTCTGACTA
1234959 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
1234980 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1235001 TCGCAATGCGA
1 TCGCATTGCGA
1235012 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1235026 original size:20 final size:20
Alignment explanation
Indices: 1235001--1235091 Score: 164
Period size: 20 Copynumber: 4.5 Consensus size: 20
1234991 TTTTCCTAAT
1235001 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1235021 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1235041 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1235061 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1235081 TCGCAATGCGA
1 TCGCAATGCGA
1235092 TTTACATAGC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1235705 original size:33 final size:34
Alignment explanation
Indices: 1235657--1235727 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
1235647 ACTATCGCAA
**
1235657 TGCGATTCTGTCGTTGCGATTTTCA-TTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCATTTTCGCGT
*
1235690 TGCGATTCT-TGCGTTGCGATAGTCATTTTCGTGT
1 TGCGATTCTGT-CGTTGCGATAGTCATTTTCGCGT
1235724 TGCG
1 TGCG
1235728 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 1 0.03
33 21 0.64
34 11 0.33
ACGTcount: A:0.10, C:0.20, G:0.27, T:0.44
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCATTTTCGCGT
Found at i:1235727 original size:20 final size:20
Alignment explanation
Indices: 1235702--1235771 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
1235692 CGATTCTTGC
**
1235702 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
1235722 GTTGCGCTTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
* *
1235742 GTTGCGCTTTTTATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1235762 GTTGCGATTT
1 GTTGCGATTT
1235772 AAAGTTTCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.09, C:0.16, G:0.23, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:1237680 original size:20 final size:20
Alignment explanation
Indices: 1237655--1237798 Score: 174
Period size: 20 Copynumber: 7.5 Consensus size: 20
1237645 AGAATAGTTT
1237655 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
1237675 ACTATCGCAACGCGAAAATA
1 ACTATCGCAATGCGAAAATG
*
1237695 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1237711 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1237729 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
1237749 ACTATCCCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
1237769 ACTATCACAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1237789 ACTATCGCAA
1 ACTATCGCAA
1237799 CGAAAGAATC
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.07
16 3 0.03
17 4 0.04
18 4 0.04
20 88 0.83
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1237780 original size:40 final size:40
Alignment explanation
Indices: 1237655--1237836 Score: 174
Period size: 40 Copynumber: 4.9 Consensus size: 40
1237645 AGAATAGTTT
* *
1237655 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATA
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
*
1237695 ACTATCGCAA--CG-AGA-GA--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* *
1237729 ACTATCGCAATGCGAAAATGACTATCCCAATACGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* **
1237769 ACTATCACAATGCGAATTTGACTATCGCAA--CG-AAA-G
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
1237805 A--ATCGCAATGCG-AAATGAAAATCGCATTGCGA
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGA
1237837 TTCTCTCGTT
Statistics
Matches: 117, Mismatches: 16, Indels: 22
0.75 0.10 0.14
Matches are distributed among these distances:
33 10 0.09
34 35 0.30
35 2 0.02
36 6 0.05
37 7 0.06
38 6 0.05
40 51 0.44
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
Found at i:1237816 original size:94 final size:93
Alignment explanation
Indices: 1237655--1237836 Score: 256
Period size: 94 Copynumber: 1.9 Consensus size: 93
1237645 AGAATAGTTT
* * * *
1237655 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATAACTATCGCAACGAGAGAATCGCAAT
1 ACTATCCCAATACGAAAATGACTATCACAACGCGAAAATAACTATCGCAACGAAAGAATCGCAAT
**
1237720 GCGAAAATGACTATCGCAATGCGAAAATG
66 GCG-AAATGAAAATCGCAATGCGAAAATG
* ** *
1237749 ACTATCCCAATACGAAAATGACTATCACAATGCGAATTTGACTATCGCAACGAAAGAATCGCAAT
1 ACTATCCCAATACGAAAATGACTATCACAACGCGAAAATAACTATCGCAACGAAAGAATCGCAAT
*
1237814 GCGAAATGAAAATCGCATTGCGA
66 GCGAAATGAAAATCGCAATGCGA
1237837 TTCTCTCGTT
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
93 17 0.22
94 60 0.78
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (93 bp):
ACTATCCCAATACGAAAATGACTATCACAACGCGAAAATAACTATCGCAACGAAAGAATCGCAAT
GCGAAATGAAAATCGCAATGCGAAAATG
Found at i:1237897 original size:20 final size:20
Alignment explanation
Indices: 1237845--1238018 Score: 142
Period size: 20 Copynumber: 9.3 Consensus size: 20
1237835 GATTCTCTCG
**
1237845 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1237865 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* **
1237885 TTGCGATAATCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
1237905 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
1237919 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
1237938 TTACGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
1237952 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1237972 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1237992 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1238012 TTGCGAT
1 TTGCGAT
1238019 TTTAAGTTTC
Statistics
Matches: 128, Mismatches: 12, Indels: 28
0.76 0.07 0.17
Matches are distributed among these distances:
14 13 0.10
16 11 0.09
17 6 0.05
18 5 0.04
19 6 0.05
20 87 0.68
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1237970 original size:107 final size:107
Alignment explanation
Indices: 1237826--1238021 Score: 338
Period size: 107 Copynumber: 1.8 Consensus size: 107
1237816 GAAATGAAAA
*
1237826 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGA
1 TCGCATTACGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGA
*
1237891 TAATCATTTTCGTGTTGCGATTTTGTTGTTGCGATTTTCATT
66 TAATCATTTTCGCGTTGCGATTTTGTTGTTGCGATTTTCATT
* **
1237933 TCGCATTACGATTCTCTCGTTGCGATAGTTATTTTCGCATTGCGATAGTCATTTTCGCATTGCGA
1 TCGCATTACGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGA
*
1237998 TAGTCATTTTCGCGTTGCGATTTT
66 TAATCATTTTCGCGTTGCGATTTT
1238022 AAGTTTCAGA
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 83 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.43
Consensus pattern (107 bp):
TCGCATTACGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGA
TAATCATTTTCGCGTTGCGATTTTGTTGTTGCGATTTTCATT
Found at i:1237997 original size:40 final size:35
Alignment explanation
Indices: 1237826--1238019 Score: 146
Period size: 40 Copynumber: 5.4 Consensus size: 35
1237816 GAAATGAAAA
* **
1237826 TCGCATTGCGATTC-TCTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATTCTTTTCGTTGCGATAGTCATTT
*
1237860 TCGCATTGCGATAGTCATTTTCGCATTGCGATAATCATTT
1 TCGCATTGCGAT--TC-TTTTCG--TTGCGATAGTCATTT
** **
1237900 TCGTGTTGCGATT-TTGTT-GTTGCGATTTTCA-TT
1 TCGCATTGCGATTCTT-TTCGTTGCGATAGTCATTT
* * *
1237933 TCGCATTACGATTC-TCTCGTTGCGATAGTTATTT
1 TCGCATTGCGATTCTTTTCGTTGCGATAGTCATTT
1237967 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGAT--TC-TTTTCG--TTGCGATAGTCATTT
*
1238007 TCGCGTTGCGATT
1 TCGCATTGCGATT
1238020 TTAAGTTTCA
Statistics
Matches: 125, Mismatches: 19, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
32 1 0.01
33 23 0.18
34 35 0.28
36 7 0.06
37 2 0.02
38 10 0.08
40 47 0.38
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.42
Consensus pattern (35 bp):
TCGCATTGCGATTCTTTTCGTTGCGATAGTCATTT
Found at i:1238593 original size:21 final size:21
Alignment explanation
Indices: 1238502--1238606 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
1238492 GACTCACCTG
*
1238502 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1238524 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1238544 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1238565 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1238586 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1238607 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1238599 original size:42 final size:42
Alignment explanation
Indices: 1238499--1238609 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1238489 CCCGACTCAC
* * * *
1238499 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1238541 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1238583 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1238610 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1239985 original size:14 final size:14
Alignment explanation
Indices: 1239966--1240001 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1239956 ATTGTTTAAT
1239966 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1239980 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1239994 TGATTTGT
1 TGATTTGT
1240002 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1240153 original size:33 final size:33
Alignment explanation
Indices: 1240114--1240177 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1240104 TCGCAACGCG
** *
1240114 GAAATGACTATCGCAACTAGAGAATCGCAATAC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATAC
*
1240147 GAAATGAAAATCGCAACGAGTGAATCGCAAT
1 GAAATGAAAATCGCAACGAGAGAATCGCAAT
1240178 GCGATTTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATAC
Found at i:1240232 original size:20 final size:20
Alignment explanation
Indices: 1240207--1240300 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
1240197 GTGATTCTCT
1240207 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
1240227 CGTTGCGATAGTCAATTCTG
1 CGTTGCGATAGTCATTTCCG
*
1240247 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1240267 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
1240287 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1240301 AATGAATGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 63 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1240256 original size:40 final size:40
Alignment explanation
Indices: 1240209--1240300 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
1240199 GATTCTCTCG
1240209 TTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCTGCA
1 TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTC-GCA
* *
1240249 TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCGCG
1 TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCGCA
1240289 TTGCGATAGTCA
1 TTGCGATAGTCA
1240301 AATGAATGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 45 0.92
41 4 0.08
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (40 bp):
TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCGCA
Found at i:1242739 original size:24 final size:24
Alignment explanation
Indices: 1242705--1242758 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1242695 CTGAAAAATC
1242705 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1242729 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1242753 ATCAAA
1 ATCAAA
1242759 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1242772 original size:24 final size:24
Alignment explanation
Indices: 1242705--1242772 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1242695 CTGAAAAATC
* * *
1242705 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1242729 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1242753 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1242773 TAATACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1243638 original size:20 final size:20
Alignment explanation
Indices: 1243612--1243754 Score: 180
Period size: 20 Copynumber: 7.1 Consensus size: 20
1243602 CAGAATCTCG
*
1243612 TTGCGATTCACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
* *
1243632 TTACGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
1243652 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1243672 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
1243692 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
1243712 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
*
1243733 TTGCGATTTACGTATTTGCA
1 TTGCGATTTACGTATTCGCA
1243753 TT
1 TT
1243755 ACGAATTAGG
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 1 0.01
20 89 0.85
21 15 0.14
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1243782 original size:21 final size:21
Alignment explanation
Indices: 1243756--1243800 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1243746 ATTTGCATTA
1243756 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* * *
1243777 CGAATTTGGGAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
1243798 CGA
1 CGA
1243801 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:1244257 original size:3 final size:3
Alignment explanation
Indices: 1244249--1244348 Score: 173
Period size: 3 Copynumber: 33.3 Consensus size: 3
1244239 TTCCATTTGG
1244249 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
1244297 ATT ATT ATT ATT ACT ATT ATT ATT ATG ATT ATT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1244345 ATT A
1 ATT A
1244349 AAAAAAAATT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1245673 original size:3 final size:3
Alignment explanation
Indices: 1245665--1245697 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1245655 AATATATTTA
*
1245665 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1245698 TAGTCATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1248013 original size:42 final size:43
Alignment explanation
Indices: 1247950--1248031 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
1247940 CGGCTTTAGA
* *
1247950 GAAGTTAGGAGGGAAATTTATCCCC-ATATGTAAAGTTTTATT
1 GAAGTTAGGACGGAAAGTTATCCCCTATATGTAAAGTTTTATT
*
1247992 GAAGTTAGGACTGAAAGTTATCCCCTATATGTAAAGTTTT
1 GAAGTTAGGACGGAAAGTTATCCCCTATATGTAAAGTTTT
1248032 GTTTGATGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 22 0.61
43 14 0.39
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (43 bp):
GAAGTTAGGACGGAAAGTTATCCCCTATATGTAAAGTTTTATT
Found at i:1249708 original size:2 final size:2
Alignment explanation
Indices: 1249697--1249749 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1249687 TTATCCTTTC
1249697 AT AT -T 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
1249738 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1249750 CCCTTGTTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1250075 original size:14 final size:16
Alignment explanation
Indices: 1250052--1250086 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1250042 AGAGAAAAAA
*
1250052 AAGAAAAAAATGAA-C
1 AAGAAAAAATTGAATC
1250067 AAGAAAAAATTGAATC
1 AAGAAAAAATTGAATC
1250083 AAGA
1 AAGA
1250087 TGGGTGACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.69, C:0.06, G:0.14, T:0.11
Consensus pattern (16 bp):
AAGAAAAAATTGAATC
Found at i:1254124 original size:54 final size:54
Alignment explanation
Indices: 1254036--1254215 Score: 297
Period size: 54 Copynumber: 3.3 Consensus size: 54
1254026 CTGACCAGAA
* *
1254036 ATCTGTGCAGAAGCCACATGAAAGGATGAATGTATTGTCAAATGTTTTACAAAC
1 ATCTGAGCAGAAGCCACATGAAAAGATGAATGTATTGTCAAATGTTTTACAAAC
*
1254090 ATTTGAGCAGAAGCCACATGAAAAGATGAATGTATTGTCAAATGTTTTACAAAC
1 ATCTGAGCAGAAGCCACATGAAAAGATGAATGTATTGTCAAATGTTTTACAAAC
* * * *
1254144 ATCTGAACAGAAACCACAGGAAAAGATGAATGTATTGTCAAATATTTTACAAAC
1 ATCTGAGCAGAAGCCACATGAAAAGATGAATGTATTGTCAAATGTTTTACAAAC
1254198 ATCTGAGCAGAAGCCACA
1 ATCTGAGCAGAAGCCACA
1254216 ACTGAATGAA
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 116 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACATGAAAAGATGAATGTATTGTCAAATGTTTTACAAAC
Found at i:1254625 original size:21 final size:22
Alignment explanation
Indices: 1254575--1254628 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1254565 ACATCTACAT
1254575 TCTTCAAAGATGATAGATTCTA
1 TCTTCAAAGATGATAGATTCTA
* *
1254597 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATAGATTCTA
1254619 T-TTCAAAGAT
1 TCTTCAAAGAT
1254629 AAACGTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTA
Found at i:1255034 original size:113 final size:110
Alignment explanation
Indices: 1254892--1255299 Score: 393
Period size: 114 Copynumber: 3.6 Consensus size: 110
1254882 CATTCATGCA
1254892 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
*
1254957 CTTTTGCTCGTATTCATCACTTGATGGATCAACATTGCCAGGCAGAGT
65 CTTTTGCT-GTATTCATCACTTGATGGATCAACATTTCCAGG-AGAGT
* * *
1255005 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCCAA
1 TCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTT-CAA
* * *
1255070 CCTTTTGCTTTAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGT
64 CCTTTTGCTGT-ATTCATCACTTGATGGATCAACATTTCCAG-GAGAGT
* * * *
1255119 TCGTAATGAGAATAACTTATCTGAAG-AG--GAAGAA-TACATAAT--G-AGAACTTGTTCAACC
1 TCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
* * ** ** *
1255177 -TTTG-TTTGATTCTATCACAGAAGAAGATAGATCAACATCAACATTTCCAAAAGTGT
66 TTTTGCTGT-ATTC-ATCAC---------TTGAT--GGATCAACATTTCCAGGAGAGT
* *
1255233 TCATAATGAGAATAACTCATCTAAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
1 TCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
1255298 TT
66 TT
1255300 GCCTTAATTC
Statistics
Matches: 246, Mismatches: 26, Indels: 37
0.80 0.08 0.12
Matches are distributed among these distances:
103 7 0.03
104 9 0.04
105 5 0.02
106 9 0.04
107 1 0.00
109 7 0.03
110 5 0.02
112 1 0.00
113 64 0.26
114 93 0.38
115 15 0.06
117 6 0.02
118 7 0.03
120 1 0.00
121 15 0.06
122 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (110 bp):
TCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
TTTTGCTGTATTCATCACTTGATGGATCAACATTTCCAGGAGAGT
Found at i:1255145 original size:114 final size:113
Alignment explanation
Indices: 1254892--1255179 Score: 389
Period size: 113 Copynumber: 2.6 Consensus size: 113
1254882 CATTCATGCA
* *
1254892 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAACTTGTTCAAC
*
1254957 CTTTTGCTCGTATTCATCACTTGATGGATCAACATTGCCAGGCAGAGT
66 CTTTTGCTCGTATTCATCACTTGATGGATCAACATTGCCAGGCAAAGT
*
1255005 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCCAA
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAACTTGTT-CAA
* * *
1255070 CCTTTTGCT-TTAATTCATCACTTGATGGATCAACTTTTCCAGAG-AAAGT
65 CCTTTTGCTCGT-ATTCATCACTTGATGGATCAACATTGCCAG-GCAAAGT
* * *
1255119 TCGTAATGAGAATAACTTATCTGAAG-AGGAAGAAT--A--CATAAT--G-AGAACTTGTTCAAC
1 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAACTTGTTCAAC
1255176 CTTT
66 CTTT
1255180 GTTTGATTCT
Statistics
Matches: 161, Mismatches: 11, Indels: 14
0.87 0.06 0.08
Matches are distributed among these distances:
105 8 0.05
106 9 0.06
107 1 0.01
109 6 0.04
111 1 0.01
113 68 0.42
114 67 0.42
115 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAACTTGTTCAAC
CTTTTGCTCGTATTCATCACTTGATGGATCAACATTGCCAGGCAAAGT
Found at i:1255654 original size:3 final size:3
Alignment explanation
Indices: 1255646--1255670 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1255636 TTCCATTTGG
1255646 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1255671 AATAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1257042 original size:15 final size:15
Alignment explanation
Indices: 1257010--1257047 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1257000 ATTGTTTATT
1257010 TATATTTATATTTTA
1 TATATTTATATTTTA
*
1257025 TATGTTTAT-TTTTAA
1 TATATTTATATTTT-A
1257040 TATATTTA
1 TATATTTA
1257048 ATTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TATATTTATATTTTA
Found at i:1257056 original size:3 final size:3
Alignment explanation
Indices: 1257048--1257077 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1257038 AATATATTTA
*
1257048 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1257078 TAGTCATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1260738 original size:20 final size:21
Alignment explanation
Indices: 1260715--1260790 Score: 86
Period size: 20 Copynumber: 3.8 Consensus size: 21
1260705 ACCGGTAAAG
* *
1260715 AACC-GGAAGAATCGGTTGAA
1 AACCGGGAAGAACCGGCTGAA
**
1260735 AACCGGGGTGAACCGGCTGAA
1 AACCGGGAAGAACCGGCTGAA
1260756 AACCGGGAA-AACCGGCTGAA
1 AACCGGGAAGAACCGGCTGAA
*
1260776 AACCGGCAA-AACCGG
1 AACCGGGAAGAACCGG
1260791 TTTGAACCGC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 29 0.60
21 19 0.40
ACGTcount: A:0.37, C:0.24, G:0.32, T:0.08
Consensus pattern (21 bp):
AACCGGGAAGAACCGGCTGAA
Found at i:1260761 original size:11 final size:10
Alignment explanation
Indices: 1260745--1260790 Score: 60
Period size: 9 Copynumber: 4.6 Consensus size: 10
1260735 AACCGGGGTG
1260745 AACCGGCTGAA
1 AACCGGC-GAA
1260756 AACCGG-GAA
1 AACCGGCGAA
1260765 AACCGGCTGAA
1 AACCGGC-GAA
1260776 AACCGGC-AA
1 AACCGGCGAA
1260785 AACCGG
1 AACCGG
1260791 TTTGAACCGC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 17 0.52
11 16 0.48
ACGTcount: A:0.39, C:0.28, G:0.28, T:0.04
Consensus pattern (10 bp):
AACCGGCGAA
Found at i:1261053 original size:24 final size:24
Alignment explanation
Indices: 1261023--1261078 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1261013 TAGAAGTTCG
*
1261023 ATTGAAGCCTAAAATTTGAGGTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
1261047 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
1261071 ATTGAAGC
1 ATTGAAGC
1261079 GAAAGAATAG
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:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:1262194 original size:21 final size:21
Alignment explanation
Indices: 1262145--1262195 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1262135 TATTACTATT
1262145 GCAATGCGATTTTCCAATTTC
1 GCAATGCGATTTTCCAATTTC
**
1262166 GCGTTGCGATTTTCCCAA-TTC
1 GCAATGCGATTTT-CCAATTTC
1262187 GCAATGCGA
1 GCAATGCGA
1262196 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (21 bp):
GCAATGCGATTTTCCAATTTC
Found at i:1262249 original size:41 final size:39
Alignment explanation
Indices: 1262204--1262338 Score: 135
Period size: 41 Copynumber: 3.3 Consensus size: 39
1262194 GAATAAGTAA
* * *
1262204 ATCGCAATGCGAATTTGGAAAATCTCAATGCGATACTGACT
1 ATCGCAACGCGAATAT--AAAATCGCAATGCGATACTGACT
* * *
1262245 ATCGCAACACTATAATATAAAATCGCAATGCGATACTGGCT
1 ATCGCAACGC--GAATATAAAATCGCAATGCGATACTGACT
* *
1262286 ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCG--AATATAAAATCGCAATGCGATACTGACT
*
1262327 TTCGCAACGCGA
1 ATCGCAACGCGA
1262339 TACTGACTTG
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
39 1 0.01
41 73 0.94
43 4 0.05
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (39 bp):
ATCGCAACGCGAATATAAAATCGCAATGCGATACTGACT
Found at i:1262339 original size:41 final size:41
Alignment explanation
Indices: 1262222--1262340 Score: 175
Period size: 41 Copynumber: 2.9 Consensus size: 41
1262212 GCGAATTTGG
* * * *
1262222 AAAATCTCAATGCGATACTGACTATCGCAACACTATAATAT
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
*
1262263 AAAATCGCAATGCGATACTGGCTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* *
1262304 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATA
1262341 CTGACTTGCG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1262347 original size:20 final size:20
Alignment explanation
Indices: 1262233--1262346 Score: 95
Period size: 20 Copynumber: 5.6 Consensus size: 20
1262223 AAATCTCAAT
1262233 GCGATACTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
* * * * ** *
1262253 ACTATAATATAAAATCGCAAT
1 GCGATACT-GACTATCGCAAC
*
1262274 GCGATACTGGCTATCGCAAC
1 GCGATACTGACTATCGCAAC
* *
1262294 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
*
1262315 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
1262335 GCGATACTGACT
1 GCGATACTGACT
1262347 TGCGAATCTG
Statistics
Matches: 69, Mismatches: 21, Indels: 8
0.70 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 38 0.55
21 28 0.41
22 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:1263647 original size:13 final size:14
Alignment explanation
Indices: 1263611--1263648 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1263601 GCACAATATG
1263611 ATATTTTAAAATTT
1 ATATTTTAAAATTT
*
1263625 ATTTTTTAAAATTT
1 ATATTTTAAAATTT
*
1263639 -TATTATAAAA
1 ATATTTTAAAA
1263649 AGCTTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTTAAAATTT
Found at i:1264168 original size:9 final size:9
Alignment explanation
Indices: 1264154--1264181 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1264144 ATCTAAATAG
1264154 GTAACGTTT
1 GTAACGTTT
1264163 GTAACGTTT
1 GTAACGTTT
1264172 GTAACGTTT
1 GTAACGTTT
1264181 G
1 G
1264182 ACACCTAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.43
Consensus pattern (9 bp):
GTAACGTTT
Found at i:1264858 original size:20 final size:20
Alignment explanation
Indices: 1264808--1264862 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1264798 AACCAATAAT
*
1264808 AATAAACATAAAAT-AATTTG
1 AATAAA-ATAAAATAAAATTG
1264828 -ATGAAAA-AAAATAAAATTG
1 AAT-AAAATAAAATAAAATTG
1264847 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
1264863 TGAAGATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 12 0.40
20 13 0.43
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (20 bp):
AATAAAATAAAATAAAATTG
Found at i:1264863 original size:19 final size:19
Alignment explanation
Indices: 1264808--1264863 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1264798 AACCAATAAT
*
1264808 AATAAACATAAAATAATTTG
1 AATAAA-ATAAAATAAATTG
1264828 -ATGAAAA-AAAATAAAATTG
1 AAT-AAAATAAAAT-AAATTG
1264847 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
1264864 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 5 0.16
19 16 0.52
20 10 0.32
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:1265077 original size:15 final size:17
Alignment explanation
Indices: 1264946--1265083 Score: 75
Period size: 19 Copynumber: 7.4 Consensus size: 17
1264936 AAAAAACTAA
1264946 AAATATAATGAAAATAAAT
1 AAATATAAT-AAAAT-AAT
*
1264965 AAATAGTATAAATAAAATATT
1 -AA-A-TAT-AATAAAATAAT
*
1264986 AAAATATATATATATATATAT
1 -AAATATA-ATA-AAATA-AT
* *
1265007 AAATATAA-AAATGTATGT
1 AAATATAATAAA-ATA-AT
*
1265025 ATAATATAATAAAATACT
1 A-AATATAATAAAATAAT
1265043 AAATAATAATAATAATAAT
1 AAAT-ATAATAA-AATAAT
1265062 AAATA-AATAAAA-AAT
1 AAATATAATAAAATAAT
1265077 AAATATA
1 AAATATA
1265084 CATATAATAT
Statistics
Matches: 97, Mismatches: 9, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
15 8 0.08
16 3 0.03
17 9 0.09
18 17 0.18
19 25 0.26
20 17 0.18
21 7 0.07
22 8 0.08
23 3 0.03
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (17 bp):
AAATATAATAAAATAAT
Found at i:1265297 original size:2 final size:2
Alignment explanation
Indices: 1265290--1265316 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1265280 ATATAATTAA
1265290 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1265317 AATAGTAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1265772 original size:37 final size:37
Alignment explanation
Indices: 1265717--1265809 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 37
1265707 ATGCTTGTGG
* * ** *
1265717 ATCCTATCTTTAAAAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAAGAGTTTAAATAATAACAAAACTCT
* * * *
1265754 ATCCTATTTTTAGGAGTTTGAATCATAACAAAATTCT
1 ATCCTATTTTTAAGAGTTTAAATAATAACAAAACTCT
*
1265791 ATCCCATTTTTAAGAGTTT
1 ATCCTATTTTTAAGAGTTT
1265810 GAATCCTAGT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTAAATAATAACAAAACTCT
Found at i:1271478 original size:16 final size:17
Alignment explanation
Indices: 1271457--1271488 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1271447 TAAAAACAAC
1271457 TCTCTCATA-TATTATT
1 TCTCTCATATTATTATT
1271473 TCTCTCATATTATTAT
1 TCTCTCATATTATTAT
1271489 GGCTAGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (17 bp):
TCTCTCATATTATTATT
Found at i:1271565 original size:4 final size:4
Alignment explanation
Indices: 1271556--1271742 Score: 78
Period size: 4 Copynumber: 45.8 Consensus size: 4
1271546 GGCAATAATT
*
1271556 TTTA TTTA TTTA TTTA TTTA TTTCAAA TTTA TTTA TTTA TTTCAAA TTTG
1 TTTA TTTA TTTA TTTA TTTA TTT---A TTTA TTTA TTTA TTT---A TTTA
* * * * **
1271606 TGTA TTCA TTTA TTT- CTAA TTTA TTTA TTTA TTT- TGAA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *** **
1271652 TTTA TTCCA CTTGAA TTTA -TTA TTTA TTTA GGAA TTT- TGAA TTTA TTTA
1 TTTA TT-TA -TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * ** *
1271701 TTTA TTTG TTTG TTTG TTT- TGAA ATTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1271743 GAAGGGAATT
Statistics
Matches: 135, Mismatches: 35, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
3 7 0.05
4 114 0.84
5 3 0.02
6 3 0.02
7 8 0.06
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:1271585 original size:23 final size:22
Alignment explanation
Indices: 1271559--1271681 Score: 107
Period size: 23 Copynumber: 5.8 Consensus size: 22
1271549 AATAATTTTT
1271559 ATTTATTTATTTATTTATTTCA
1 ATTTATTTATTTATTTATTTCA
1271581 A---ATTTATTTATTTATTTCAA
1 ATTTATTTATTTATTTATTTC-A
* * *
1271601 ATTTGTGTATTCATTTATTTCTA
1 ATTTATTTATTTATTTATTTC-A
*
1271624 ATTTATTTATTTA--T-TTTGA
1 ATTTATTTATTTATTTATTTCA
* * *
1271643 ATTTATTTATTTATTCCACTTGA
1 ATTTATTTATTTATT-TATTTCA
1271666 ATTTA-TTATTTATTTA
1 ATTTATTTATTTATTTA
1271682 GGAATTTTGA
Statistics
Matches: 82, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
19 31 0.38
20 5 0.06
21 2 0.02
22 10 0.12
23 34 0.41
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (22 bp):
ATTTATTTATTTATTTATTTCA
Found at i:1271587 original size:19 final size:19
Alignment explanation
Indices: 1271563--1271657 Score: 118
Period size: 19 Copynumber: 4.8 Consensus size: 19
1271553 ATTTTTATTT
1271563 ATTTATTTATTTATTTCAA
1 ATTTATTTATTTATTTCAA
1271582 ATTTATTTATTTATTTCAA
1 ATTTATTTATTTATTTCAA
* *
1271601 ATTTGTGTATTCATTTATTTCTA
1 A--T-T-TATTTATTTATTTCAA
**
1271624 ATTTATTTATTTATTTTGA
1 ATTTATTTATTTATTTCAA
1271643 ATTTATTTATTTATT
1 ATTTATTTATTTATT
1271658 CCACTTGAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
19 48 0.72
20 1 0.01
21 2 0.03
22 1 0.01
23 15 0.22
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTATTTATTTATTTCAA
Found at i:1271686 original size:19 final size:20
Alignment explanation
Indices: 1271563--1271740 Score: 104
Period size: 19 Copynumber: 8.9 Consensus size: 20
1271553 ATTTTTATTT
1271563 ATTTATTTATTTATTTCA--A
1 ATTTATTTATTTATTT-ATGA
1271582 ATTTATTTATTTATTTCA--A
1 ATTTATTTATTTATTT-ATGA
* *
1271601 ATTTGTGTATTCATTTATTTCT-A
1 A--T-T-TATTTATTTATTTATGA
1271624 ATTTATTTATTTATTT-TGA
1 ATTTATTTATTTATTTATGA
*
1271643 ATTTATTTATTTATTCCACTTGA
1 ATTTATTTATTTATT-TA--TGA
*
1271666 ATTTA-TTATTTATTTAGGA
1 ATTTATTTATTTATTTATGA
** **
1271685 ATTT-TGAATTTATTTATTT
1 ATTTATTTATTTATTTATGA
* * *
1271704 ATTTGTTTGTTTGTTT-TGA
1 ATTTATTTATTTATTTATGA
*
1271723 AATTATTTATTTATTTAT
1 ATTTATTTATTTATTTAT
1271741 TTGAAGGGAA
Statistics
Matches: 125, Mismatches: 21, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
18 1 0.01
19 80 0.64
20 9 0.07
21 3 0.02
22 10 0.08
23 22 0.18
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.63
Consensus pattern (20 bp):
ATTTATTTATTTATTTATGA
Found at i:1273826 original size:52 final size:52
Alignment explanation
Indices: 1273764--1273866 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
1273754 AAATTGGACA
1273764 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
1273816 CATAGAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1273867 AATATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:1278422 original size:52 final size:52
Alignment explanation
Indices: 1278360--1278462 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
1278350 AAATTGGACA
1278360 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
1278412 CATAGAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1278463 AATATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:1278742 original size:28 final size:28
Alignment explanation
Indices: 1278708--1278767 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1278698 TTTATAATTC
* * * *
1278708 TTTTAGTTATTTGAACTGTATTTTCTTT
1 TTTTAGTTAATCGAACTCTATTTTATTT
*
1278736 TTTTAGTTAATCGAACTCTGTTTTATTT
1 TTTTAGTTAATCGAACTCTATTTTATTT
1278764 TTTT
1 TTTT
1278768 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.63
Consensus pattern (28 bp):
TTTTAGTTAATCGAACTCTATTTTATTT
Found at i:1278855 original size:17 final size:17
Alignment explanation
Indices: 1278810--1278860 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1278800 AGTTTTTAAA
*
1278810 AATTTGTTTAAATTATT
1 AATTTCTTTAAATTATT
**
1278827 AATCAACTTTAAATTATT
1 AAT-TTCTTTAAATTATT
*
1278845 AATTTCTTTAAGTTAT
1 AATTTCTTTAAATTAT
1278861 CCTTGAACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTCTTTAAATTATT
Found at i:1291168 original size:2 final size:2
Alignment explanation
Indices: 1291158--1291481 Score: 145
Period size: 2 Copynumber: 167.0 Consensus size: 2
1291148 ATTGAAAAAA
*
1291158 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AC 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
* * *
1291199 A- AT AT A- AGT TT AT AT AT AA ACT AT AT A- AT -T AT -T AT A- AG
1 AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * * *
1291237 CT AT AT AT AA AT -T AT GT TT AT GT GA- ACT AT AT AT AT AT AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT A-T
* * * * *
1291280 AT AT AT GT AT AA ACT AT A- AA AGT AT AT AGT TT AT A- AA AT AT
1 AT AT AT AT AT AT A-T AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* *
1291321 -T AT TT AT AT -T A- AT AT AGT AT AT AT AT AT AT AT AA AGT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT
* * * *
1291362 AT AT GT AT AA ACT AT AT A- AA AT AT AT AGT TT AT AT AT -T AT A-
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
1291403 AT TT AT AT -T A- AT AT A- AT AT AT AT AT GT AT GT AT -T ACT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
1291441 AT AT AT GT A- 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
1291482 TAAAGAAATA
Statistics
Matches: 241, Mismatches: 45, Indels: 72
0.67 0.13 0.20
Matches are distributed among these distances:
1 23 0.10
2 205 0.85
3 13 0.05
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1291241 original size:29 final size:31
Alignment explanation
Indices: 1291163--1291247 Score: 83
Period size: 29 Copynumber: 2.9 Consensus size: 31
1291153 AAAAAATATA
* *
1291163 ATATATAT-ATAT-A-TATATATATATACAT
1 ATATATATAATATAAGTCTATATATAAACAT
*
1291191 ATATATATAATATAAGTTTATATATAAAC-T
1 ATATATATAATATAAGTCTATATATAAACAT
*
1291221 ATATA-ATTATTATAAG-CTATATATAAA
1 ATATATA-TAATATAAGTCTATATATAAA
1291248 TTATGTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
28 8 0.16
29 15 0.31
30 15 0.31
31 11 0.22
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (31 bp):
ATATATATAATATAAGTCTATATATAAACAT
Found at i:1291304 original size:15 final size:15
Alignment explanation
Indices: 1291272--1291305 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1291262 ACTATATATA
* *
1291272 TATAAACTATATATG
1 TATAAACTATAAAAG
1291287 TATAAACTATAAAAG
1 TATAAACTATAAAAG
1291302 TATA
1 TATA
1291306 TAGTTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
TATAAACTATAAAAG
Found at i:1291445 original size:81 final size:81
Alignment explanation
Indices: 1291264--1291479 Score: 255
Period size: 81 Copynumber: 2.7 Consensus size: 81
1291254 TTATGTGAAC
* * * *
1291264 TATATATATATAAAC--TATATATGTATAAACTATA-AAAGTATATAGTTTATAAAATATTATTT
1 TATATATATATAAACTATATATATGTATAAACTATATAAAATATATAGTTTATATATTATAATTT
*
1291326 ATATTAATATAGTATA
66 ATATTAATATAATATA
*
1291342 TATATATATATAAAGTATATATATGTATAAACTATATAAAATATATAGTTTATATATTATAATTT
1 TATATATATATAAACTATATATATGTATAAACTATATAAAATATATAGTTTATATATTATAATTT
1291407 ATATTAATATAATATA
66 ATATTAATATAATATA
* * * * * *
1291423 TATATGTATGTATTACTA-ATATATGTAATATA-TATATATATATATATA-TATATATAT
1 TATATATATATA-AACTATATATATGT-ATAAACTATATA-AAATATATAGTTTATATAT
1291480 ATTAAAGAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
78 14 0.12
80 19 0.16
81 71 0.60
82 15 0.13
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (81 bp):
TATATATATATAAACTATATATATGTATAAACTATATAAAATATATAGTTTATATATTATAATTT
ATATTAATATAATATA
Found at i:1291876 original size:7 final size:7
Alignment explanation
Indices: 1291866--1291908 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
1291856 ATAGTTTATA
1291866 AAACCCT
1 AAACCCT
*
1291873 AAACCTT
1 AAACCCT
1291880 AAACCCT
1 AAACCCT
*
1291887 AAACTCT
1 AAACCCT
*
1291894 AAGCCCT
1 AAACCCT
1291901 AAACCCT
1 AAACCCT
1291908 A
1 A
1291909 TACATAAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.42, C:0.37, G:0.02, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:1292020 original size:22 final size:20
Alignment explanation
Indices: 1291995--1292101 Score: 76
Period size: 20 Copynumber: 5.1 Consensus size: 20
1291985 CTTATAGTAC
1291995 ATGTATCATATATGTATAAACT
1 ATGTAT-ATATAT-TATAAACT
1292017 ATGTATAGTATA-TATAAACT
1 ATGTATA-TATATTATAAACT
* *
1292037 ATATATATATA-TATAACCT
1 ATGTATATATATTATAAACT
*
1292056 ATAGTATATGTATATATACAATCT
1 AT-GTATATATAT-TATA-AA-CT
* *
1292080 ATTTATATGT-TATATAAACT
1 ATGTATATATAT-TATAAACT
1292100 AT
1 AT
1292102 ATATGTAACC
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
19 13 0.18
20 25 0.34
21 3 0.04
22 20 0.27
23 8 0.11
24 4 0.05
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (20 bp):
ATGTATATATATTATAAACT
Found at i:1292034 original size:20 final size:21
Alignment explanation
Indices: 1291995--1292108 Score: 105
Period size: 22 Copynumber: 5.5 Consensus size: 21
1291985 CTTATAGTAC
* *
1291995 ATGTATCATATATGTATAAACT
1 ATGTAT-ATGTATATATAAACT
1292017 ATGTATA-GTATATATAAACT
1 ATGTATATGTATATATAAACT
* *
1292037 A--TATATATATATATAACCT
1 ATGTATATGTATATATAAACT
1292056 ATAGTATATGTATATATACAATCT
1 AT-GTATATGTATATATA-AA-CT
*
1292080 ATTTATATGT-TATATAAACT
1 ATGTATATGTATATATAAACT
1292100 A--TATATGTA
1 ATGTATATGTA
1292109 ACCTATAGTT
Statistics
Matches: 78, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
18 11 0.14
19 12 0.15
20 15 0.19
21 3 0.04
22 25 0.32
23 8 0.10
24 4 0.05
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (21 bp):
ATGTATATGTATATATAAACT
Found at i:1292047 original size:24 final size:22
Alignment explanation
Indices: 1292009--1292105 Score: 86
Period size: 20 Copynumber: 4.7 Consensus size: 22
1291999 ATCATATATG
*
1292009 TATAAACTA-TGTATA-GTATA
1 TATAAACTATTATATATGTATA
1292029 TATAAACTA-TATATA--TATA
1 TATAAACTATTATATATGTATA
*
1292048 TATAACCTA-TAGTATATGTATA
1 TATAAACTATTA-TATATGTATA
1292070 TATACAATCTATT-TATATGT-TA
1 TATA-AA-CTATTATATATGTATA
1292092 TATAAACTA-TATAT
1 TATAAACTATTATAT
1292106 GTAACCTATA
Statistics
Matches: 67, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
19 15 0.22
20 24 0.36
21 2 0.03
22 14 0.21
23 8 0.12
24 3 0.04
25 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (22 bp):
TATAAACTATTATATATGTATA
Found at i:1292179 original size:21 final size:20
Alignment explanation
Indices: 1292155--1292224 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 20
1292145 CTATATATTT
1292155 TATACTTTATAACCTATAGTA
1 TATA-TTTATAACCTATAGTA
* *
1292176 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAACCTATAGTA
* *
1292197 TATATTAATGTACTCTATAGTA
1 TATATTTAT-AAC-CTATAGTA
1292219 TATATT
1 TATATT
1292225 AATGTTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.12
21 21 0.52
22 14 0.35
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.47
Consensus pattern (20 bp):
TATATTTATAACCTATAGTA
Found at i:1292237 original size:22 final size:22
Alignment explanation
Indices: 1292190--1292268 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
1292180 ATTTATAAAC
* *
1292190 TATAGTTTATATTAATG-TACT
1 TATAGTATATATTAATGTTAAT
1292211 CTATAGTATATATTAATGTTAAT
1 -TATAGTATATATTAATGTTAAT
* * *
1292234 TATATTAACTATAATTTATATTAA-
1 TATAGT-A-TAT-ATTAATGTTAAT
1292258 TATAGTATATA
1 TATAGTATATA
1292269 GTTTATAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
21 1 0.02
22 24 0.51
23 5 0.11
24 8 0.17
25 9 0.19
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (22 bp):
TATAGTATATATTAATGTTAAT
Found at i:1292273 original size:22 final size:22
Alignment explanation
Indices: 1292169--1292445 Score: 70
Period size: 21 Copynumber: 12.7 Consensus size: 22
1292159 CTTTATAACC
*
1292169 TATAGTATATAATTTATA--AAC
1 TATAGTATAT-ATTTATATTAAT
* *
1292190 TATAGTTTATA-TTA-ATGTACT
1 TATAGTATATATTTATAT-TAAT
* *
1292211 CTATAGTATATATTAATGTTAAT
1 -TATAGTATATATTTATATTAAT
*
1292234 TATATTAACTATAATTTATATTAA-
1 TATAGT-A-TAT-ATTTATATTAAT
*
1292258 TATAGTATATAGTTTATA--AAC
1 TATAGTATATA-TTTATATTAAT
*
1292279 TATA-T-TATATTAATATTAAT
1 TATAGTATATATTTATATTAAT
* *
1292299 TATATTTACTATAGTTTATA--AAC
1 TATA-GTA-TATA-TTTATATTAAT
** **
1292322 TATACCATATAATTTATA-GCA-
1 TATAGTATAT-ATTTATATTAAT
* *
1292343 TATAGTTTATATTAATATTAAT
1 TATAGTATATATTTATATTAAT
* *
1292365 TATA-AATTATAAATTATATTATAT
1 TATAGTA-TAT-ATTTATATTA-AT
*
1292389 TA-A-TATA-AGTTAATATTAA-
1 TATAGTATATA-TTTATATTAAT
* *
1292408 TATTAAT-TATATTAATATTAAT
1 TA-TAGTATATATTTATATTAAT
* *
1292430 TATAATATATAATTAT
1 TATAGTATATATTTAT
1292446 TATAATATTA
Statistics
Matches: 191, Mismatches: 33, Indels: 63
0.67 0.11 0.22
Matches are distributed among these distances:
18 6 0.03
19 9 0.05
20 18 0.09
21 56 0.29
22 48 0.25
23 23 0.12
24 17 0.09
25 14 0.07
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
TATAGTATATATTTATATTAAT
Found at i:1292362 original size:6 final size:6
Alignment explanation
Indices: 1292351--1292471 Score: 64
Period size: 6 Copynumber: 20.3 Consensus size: 6
1292341 CATATAGTTT
*
1292351 ATATTA ATATTA AT-TATA A-ATTA TAAATT- ATATT- ATATTA ATA-TA
1 ATATTA ATATTA ATAT-TA ATATTA -ATATTA ATATTA ATATTA ATATTA
*
1292396 A-GTTA ATATTA ATATT- A-ATT- ATATTA ATATTA AT-TATA ATATATA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATAT-TA ATAT-TA
*
1292441 ATTATTATA ATATTA ATTATAA ATAGTTA AT
1 A-TA-T-TA ATATTA A-TATTA ATA-TTA AT
1292472 TAATAAAAAT
Statistics
Matches: 95, Mismatches: 5, Indels: 29
0.74 0.04 0.22
Matches are distributed among these distances:
4 4 0.04
5 23 0.24
6 41 0.43
7 18 0.19
8 4 0.04
9 5 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:1292370 original size:50 final size:50
Alignment explanation
Indices: 1292232--1292463 Score: 138
Period size: 50 Copynumber: 4.8 Consensus size: 50
1292222 ATTAATGTTA
* * *** *
1292232 ATTATATTAACTATAA-TTTATATTAATA-TAGTATATAGTTTATAAACTAT
1 ATTATATTAA-TATAAGTTAATATTAATATTAAT-TATAAACTATAAATTAT
* * *
1292282 ATTATATTAATATTAA-TT-ATATTTACTA-TAGTTTATAAACTATACCA-TAT
1 ATTATATTAATA-TAAGTTAATA-TTAATATTA-ATTATAAACTATA-AATTAT
* *
1292332 AATT-TA-TAGCATAT-AGTTTATATTAATATTAATTATAAATTATAAATTAT
1 -ATTATATTA--ATATAAGTTAATATTAATATTAATTATAAACTATAAATTAT
1292382 ATTATATTAATATAAGTTAATATTAATATTAATTAT--A-T-TAATATTA-
1 ATTATATTAATATAAGTTAATATTAATATTAATTATAAACTATAA-ATTAT
* *
1292428 ATTATAAT-ATATAA-TTATTA-TAATATTAATTATAAA
1 ATTATATTAATATAAGTTAATATTAATATTAATTATAAA
1292464 TAGTTAATTA
Statistics
Matches: 152, Mismatches: 13, Indels: 39
0.75 0.06 0.19
Matches are distributed among these distances:
43 13 0.09
44 5 0.03
45 7 0.05
46 10 0.07
47 5 0.03
48 1 0.01
49 16 0.11
50 80 0.53
51 15 0.10
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (50 bp):
ATTATATTAATATAAGTTAATATTAATATTAATTATAAACTATAAATTAT
Found at i:1292406 original size:16 final size:14
Alignment explanation
Indices: 1292349--1292461 Score: 86
Period size: 15 Copynumber: 7.4 Consensus size: 14
1292339 AGCATATAGT
1292349 TTATATTAATATTAA
1 TTATATTAATA-TAA
*
1292364 TTATAAATTATAAATTATA
1 TTAT--ATTA-ATA-TA-A
1292383 TTATATTAATATAA
1 TTATATTAATATAA
1292397 GTTAATATTAATATTAA
1 -TT-ATATTAATA-TAA
1292414 TTATATTAATATTAA
1 TTATATTAATA-TAA
*
1292429 TTATAAT-ATATAA
1 TTATATTAATATAA
1292442 TTAT-TATAATATTAA
1 TTATAT-TAATA-TAA
1292457 TTATA
1 TTATA
1292462 AATAGTTAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.10
14 7 0.08
15 34 0.41
16 13 0.16
17 11 0.13
18 5 0.06
19 5 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (14 bp):
TTATATTAATATAA
Found at i:1292406 original size:21 final size:21
Alignment explanation
Indices: 1292353--1292462 Score: 93
Period size: 21 Copynumber: 5.0 Consensus size: 21
1292343 TATAGTTTAT
*
1292353 ATTAATATTAATTATAAATTATAA
1 ATTAATATTAA-TATTAA-TAT-A
1292377 ATT-ATATT-ATATTAATATA
1 ATTAATATTAATATTAATATA
1292396 AGTTAATATTAATATTAAT-TA
1 A-TTAATATTAATATTAATATA
*
1292417 TATTAATATTAATTATAATATATA
1 -ATTAATATTAA-TATTA-ATATA
*
1292441 ATTATTA-TAATATTAATTATA
1 ATTAATATTAATATTAA-TATA
1292462 A
1 A
1292463 ATAGTTAATT
Statistics
Matches: 74, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
19 2 0.03
20 6 0.08
21 31 0.42
22 17 0.23
23 13 0.18
24 5 0.07
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
ATTAATATTAATATTAATATA
Found at i:1292451 original size:28 final size:27
Alignment explanation
Indices: 1292357--1292473 Score: 105
Period size: 28 Copynumber: 4.0 Consensus size: 27
1292347 GTTTATATTA
*
1292357 ATATTAATTATAAATTATAA-ATTATATT
1 ATATTAA-TATTAATTATAATATTA-ATT
1292385 ATATTAATA-TAAGTTAATATTAATATTAATT
1 ATATTAATATTAA--T--TA-TAATATTAATT
1292416 ATATTAATATTAATTATAATATATAATT
1 ATATTAATATTAATTATAATAT-TAATT
1292444 AT-TATAATATTAATTATAAATAGTTAATT
1 ATAT-TAATATTAATTAT-AATA-TTAATT
1292473 A
1 A
1292474 ATAAAAATTA
Statistics
Matches: 77, Mismatches: 1, Indels: 21
0.78 0.01 0.21
Matches are distributed among these distances:
26 2 0.03
27 9 0.12
28 30 0.39
29 10 0.13
30 4 0.05
31 15 0.19
32 7 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTAATATTAATTATAATATTAATT
Found at i:1292477 original size:15 final size:14
Alignment explanation
Indices: 1292406--1292483 Score: 72
Period size: 15 Copynumber: 5.5 Consensus size: 14
1292396 AGTTAATATT
*
1292406 AATATTAATTATATT
1 AATATTAATTA-ATA
1292421 AATATTAATT-AT-
1 AATATTAATTAATA
*
1292433 AATATATAATTATTA
1 AATAT-TAATTAATA
1292448 TAATATTAATT-ATA
1 -AATATTAATTAATA
1292462 AATAGTTAATTAATA
1 AATA-TTAATTAATA
*
1292477 AAAATTA
1 AATATTA
1292484 TATAGGGATG
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
12 5 0.09
13 11 0.20
14 12 0.22
15 21 0.39
16 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (14 bp):
AATATTAATTAATA
Found at i:1292732 original size:18 final size:19
Alignment explanation
Indices: 1292709--1292754 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1292699 TTTTGCTCTA
*
1292709 TCTCTCTAGCTCTATG-TT
1 TCTCTCTAGATCTATGTTT
*
1292727 TCTCTC-AAATCTATGTTT
1 TCTCTCTAGATCTATGTTT
1292745 TCTCTCTAGA
1 TCTCTCTAGA
1292755 AGTTCATCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.30
18 14 0.61
19 2 0.09
ACGTcount: A:0.17, C:0.26, G:0.09, T:0.48
Consensus pattern (19 bp):
TCTCTCTAGATCTATGTTT
Found at i:1293178 original size:6 final size:6
Alignment explanation
Indices: 1293169--1293278 Score: 71
Period size: 6 Copynumber: 18.5 Consensus size: 6
1293159 CCCTAACTTG
* * * * *
1293169 AACCCA AACCTCA AACCAA AACCCA AACCCG AACCCA AATCCT AA-CCG
1 AACCCA AACC-CA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * * * * * *
1293217 AACCCA AACCTA AACCTA AACCCA AGCCCT AACCCT AACCTA AA-TCG
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
*
1293264 AACCCG AACCCA AAC
1 AACCCA AACCCA AAC
1293279 TCGAATCTGA
Statistics
Matches: 81, Mismatches: 20, Indels: 6
0.76 0.19 0.06
Matches are distributed among these distances:
5 6 0.07
6 69 0.85
7 6 0.07
ACGTcount: A:0.45, C:0.43, G:0.05, T:0.08
Consensus pattern (6 bp):
AACCCA
Found at i:1293206 original size:19 final size:19
Alignment explanation
Indices: 1293169--1293224 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
1293159 CCCTAACTTG
*
1293169 AACCCAAACCTC-AAACCAA
1 AACCCAAACC-CGAACCCAA
1293188 AACCCAAACCCGAACCC-A
1 AACCCAAACCCGAACCCAA
* *
1293206 AATCCTAA-CCGAACCCAA
1 AACCCAAACCCGAACCCAA
1293224 A
1 A
1293225 CCTAAACCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 8 0.25
18 10 0.31
19 14 0.44
ACGTcount: A:0.48, C:0.43, G:0.04, T:0.05
Consensus pattern (19 bp):
AACCCAAACCCGAACCCAA
Found at i:1293215 original size:12 final size:12
Alignment explanation
Indices: 1293169--1293317 Score: 50
Period size: 12 Copynumber: 12.4 Consensus size: 12
1293159 CCCTAACTTG
*
1293169 AACCCAAACCTCA
1 AACCCGAACC-CA
**
1293182 AACCAAAACCCA
1 AACCCGAACCCA
1293194 AACCCGAACCCA
1 AACCCGAACCCA
* * *
1293206 AATCCTAA-CCG
1 AACCCGAACCCA
* *
1293217 AACCCAAACCTA
1 AACCCGAACCCA
**
1293229 AACCTAAACCCA
1 AACCCGAACCCA
* * *
1293241 AGCCCTAACCCT
1 AACCCGAACCCA
* ** *
1293253 AA-CCTAAATCG
1 AACCCGAACCCA
1293264 AACCCGAACCCA
1 AACCCGAACCCA
* * **
1293276 AACTCGAATCTG
1 AACCCGAACCCA
* *
1293288 AACCTGAATCCAA
1 AACCCGAA-CCCA
*
1293301 AACCCGAACCCG
1 AACCCGAACCCA
1293313 AACCC
1 AACCC
1293318 AAACTAAAAT
Statistics
Matches: 97, Mismatches: 36, Indels: 7
0.69 0.26 0.05
Matches are distributed among these distances:
11 16 0.16
12 64 0.66
13 17 0.18
ACGTcount: A:0.42, C:0.42, G:0.07, T:0.09
Consensus pattern (12 bp):
AACCCGAACCCA
Found at i:1293219 original size:17 final size:16
Alignment explanation
Indices: 1293197--1293229 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1293187 AAACCCAAAC
1293197 CCGAACCCAAATCCTAA
1 CCGAACCCAAA-CCTAA
1293214 CCGAACCCAAACCTAA
1 CCGAACCCAAACCTAA
1293230 ACCTAAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.42, C:0.42, G:0.06, T:0.09
Consensus pattern (16 bp):
CCGAACCCAAACCTAA
Found at i:1293232 original size:35 final size:35
Alignment explanation
Indices: 1293182--1293278 Score: 88
Period size: 35 Copynumber: 2.7 Consensus size: 35
1293172 CCAAACCTCA
*
1293182 AACCAAAACCCAAACCCGAACCCAAATCCTAA-CCG
1 AACCAAAA-CCAAACCCGAACCCAAACCCTAACCCG
* ** * *
1293217 AACCCAAACCTAAACCTAAACCCAAGCCCTAACCCT
1 AACCAAAACC-AAACCCGAACCCAAACCCTAACCCG
* * *
1293253 AACCTAAATCGAACCCGAACCCAAAC
1 AACCAAAACCAAACCCGAACCCAAAC
1293279 TCGAATCTGA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
34 2 0.04
35 36 0.75
36 10 0.21
ACGTcount: A:0.44, C:0.42, G:0.05, T:0.08
Consensus pattern (35 bp):
AACCAAAACCAAACCCGAACCCAAACCCTAACCCG
Found at i:1293240 original size:47 final size:47
Alignment explanation
Indices: 1293168--1293278 Score: 134
Period size: 47 Copynumber: 2.3 Consensus size: 47
1293158 ACCCTAACTT
1293168 GAACCCAAACCTCAAACCAAAACCCAAACCCGAACCCAAATCCT-AACC
1 GAACCCAAACCT-AAACCAAAACCCAAACCCGAACCCAAA-CCTAAACC
* * * * *
1293216 GAACCCAAACCTAAACCTAAACCCAAGCCCTAACCCTAACCTAAATC
1 GAACCCAAACCTAAACCAAAACCCAAACCCGAACCCAAACCTAAACC
* *
1293263 GAACCCGAACCCAAAC
1 GAACCCAAACCTAAAC
1293279 TCGAATCTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
46 3 0.05
47 40 0.73
48 12 0.22
ACGTcount: A:0.44, C:0.42, G:0.05, T:0.08
Consensus pattern (47 bp):
GAACCCAAACCTAAACCAAAACCCAAACCCGAACCCAAACCTAAACC
Found at i:1293344 original size:43 final size:43
Alignment explanation
Indices: 1293262--1293353 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
1293252 TAACCTAAAT
** ** * *
1293262 CGAACCCGAACCCAAACTCGAATCTGAACCTGAATCCAAAACC
1 CGAACCCGAACCCAAACTAAAATCCAAACCTAAACCCAAAACC
1293305 CGAACCCGAACCCAAACTAAAATCCAAA-CTCAAACCCAAAACC
1 CGAACCCGAACCCAAACTAAAATCCAAACCT-AAACCCAAAACC
*
1293348 CTAACC
1 CGAACC
1293354 TAACCCCTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 2 0.05
43 39 0.95
ACGTcount: A:0.43, C:0.39, G:0.08, T:0.10
Consensus pattern (43 bp):
CGAACCCGAACCCAAACTAAAATCCAAACCTAAACCCAAAACC
Found at i:1293674 original size:17 final size:17
Alignment explanation
Indices: 1293632--1293665 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1293622 TAATTTATAG
1293632 CTACTGTTGATTTGTTT
1 CTACTGTTGATTTGTTT
1293649 CTACTGTTGATTTGTTT
1 CTACTGTTGATTTGTTT
1293666 GTGTTGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (17 bp):
CTACTGTTGATTTGTTT
Found at i:1293833 original size:101 final size:102
Alignment explanation
Indices: 1293649--1293860 Score: 363
Period size: 101 Copynumber: 2.1 Consensus size: 102
1293639 TGATTTGTTT
* * *
1293649 CTACTGTTGATTTGTTTGTGTTGTTGGTTGTTAATTCGGATTGTTTTTATAAGGTTGTTAGCTGT
1 CTACTGTTGATTTGTTTGTGTTATTGGTTGTTAATTCGGATTGCTTTTATAAGGTTGTTAGCTGA
1293714 CTTTATTTACAGTTTAAATAAACTGTTTAATTTGTAG
66 CTTTATTTACAGTTTAAATAAACTGTTTAATTTGTAG
* *
1293751 CTATTGTTGATTTGTTTGTGTTATTGGTTGTTCATTCGGATTGCTTTT-TAAGGTTGTTAGCTGA
1 CTACTGTTGATTTGTTTGTGTTATTGGTTGTTAATTCGGATTGCTTTTATAAGGTTGTTAGCTGA
*
1293815 CTTTATTTAGAGTTTAAATAAACTGTTTAATTTGTAG
66 CTTTATTTACAGTTTAAATAAACTGTTTAATTTGTAG
1293852 CTACTGTTG
1 CTACTGTTG
1293861 GTTGTTCATT
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 59 0.57
102 44 0.43
ACGTcount: A:0.20, C:0.08, G:0.21, T:0.51
Consensus pattern (102 bp):
CTACTGTTGATTTGTTTGTGTTATTGGTTGTTAATTCGGATTGCTTTTATAAGGTTGTTAGCTGA
CTTTATTTACAGTTTAAATAAACTGTTTAATTTGTAG
Found at i:1299681 original size:95 final size:94
Alignment explanation
Indices: 1299503--1299698 Score: 268
Period size: 95 Copynumber: 2.1 Consensus size: 94
1299493 TAATATTATA
* * * * *
1299503 TATATATACAATAAAGCTTGAGTTGTCCCTCCAGAGCAATTGGTTAAATGCCCCGGCTTTATGGA
1 TATATATACAATAAAGCTTAAGCTGTCCCTCAAGAGCAATTGGTTAAACGCCCCGACTTTATGGA
* * *
1299568 TAATATTCGACTAGCCTGATAAAGGTGAT
66 TAAGATTCAACTAACCTGATAAAGGTGAT
*
1299597 TATACTATACAATAAAGCTTAAGCTGTCCCTCTAAG-GTAATTGGTTAAACGCCCCGACTTTATG
1 TATA-TATACAATAAAGCTTAAGCTGTCCCTC-AAGAGCAATTGGTTAAACGCCCCGACTTTATG
*
1299661 GATAAGATTCAACTAACCTGATAAAGGTGTT
64 GATAAGATTCAACTAACCTGATAAAGGTGAT
*
1299692 TACATAT
1 TATATAT
1299699 TGAGCTGTTC
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
94 7 0.08
95 80 0.90
96 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (94 bp):
TATATATACAATAAAGCTTAAGCTGTCCCTCAAGAGCAATTGGTTAAACGCCCCGACTTTATGGA
TAAGATTCAACTAACCTGATAAAGGTGAT
Found at i:1301138 original size:86 final size:85
Alignment explanation
Indices: 1300954--1301140 Score: 216
Period size: 85 Copynumber: 2.2 Consensus size: 85
1300944 CTCGAAGCCA
* * * * * * * *
1300954 AACTTCACAACAAAGGGGCCATCCACGGTTTCAACTTCACGGCGAAGAGAATCGTGTCCATCGTA
1 AACTTCACGACGAAGGGGCCACCCACGATTTCAACTTCACGACAAAGAGAATCGTGACCATCGCA
1301019 ACATACAATACTTGGATTTC
66 ACATACAATACTTGGATTTC
* * *
1301039 AATTTCACGACGAAGGGGCCACCCACGATTTCAACTTCACGACAAAGGGAATTGTGCACACAT-G
1 AACTTCACGACGAAGGGGCCACCCACGATTTCAACTTCACGACAAAGAGAATCGTG-AC-CATCG
* *
1301103 CAACATCCATCTA-TTGGATTTC
64 CAACATACA-ATACTTGGATTTC
1301125 AACTTCACGACGAAGG
1 AACTTCACGACGAAGG
1301141 ATATCCAACT
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
85 47 0.55
86 33 0.39
87 5 0.06
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (85 bp):
AACTTCACGACGAAGGGGCCACCCACGATTTCAACTTCACGACAAAGAGAATCGTGACCATCGCA
ACATACAATACTTGGATTTC
Found at i:1301459 original size:125 final size:125
Alignment explanation
Indices: 1301237--1301463 Score: 373
Period size: 125 Copynumber: 1.8 Consensus size: 125
1301227 GAAACAACAC
* * * * * * *
1301237 AAATATTTGGATTTCAACTTCACGACGAAGGATATCTAATTCGAGGCTCAGCTTCACAACGAATA
1 AAATATTTGGATTTCAACTTCACAAAGAAGGACATCCAATTCAAGGCTCAACTTCACAACGAAGA
1301302 GGCCATCCACGGTTTTAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCA
66 GGCCATCCACGGTTTTAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCA
*
1301362 AAATATTTGGATTTCAACTTCACAAAGAAGGACATCCAATTCAAGGCTCAACTTCACAACGAAGG
1 AAATATTTGGATTTCAACTTCACAAAGAAGGACATCCAATTCAAGGCTCAACTTCACAACGAAGA
*
1301427 GGCCATCCATGGTTTTAACTTCACGACGAAGGGAATC
66 GGCCATCCACGGTTTTAACTTCACGACGAAGGGAATC
1301464 TTGCCATAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 93 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (125 bp):
AAATATTTGGATTTCAACTTCACAAAGAAGGACATCCAATTCAAGGCTCAACTTCACAACGAAGA
GGCCATCCACGGTTTTAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCA
Found at i:1301683 original size:36 final size:36
Alignment explanation
Indices: 1301635--1301806 Score: 137
Period size: 36 Copynumber: 4.9 Consensus size: 36
1301625 CAAAATAAAG
*
1301635 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1301671 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
1301707 ----A--TCT-TTGA-ATATGCTTT-CCTCGAAACAAA
1 TTTTATCTCTCTTGAGACA-G-TTTCCCTTGAAACAAA
** * * ** * *
1301736 TTTCGTCTCCCTTGAGACTGTTTCTTTTGGAACTAAG
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
1301773 TTTTTTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACA
1301807 CCAATCTTTG
Statistics
Matches: 106, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 2 0.02
29 16 0.15
30 6 0.06
32 1 0.01
35 5 0.05
36 46 0.43
37 30 0.28
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1301982 original size:84 final size:83
Alignment explanation
Indices: 1301839--1302038 Score: 271
Period size: 84 Copynumber: 2.4 Consensus size: 83
1301829 TTAAAACACC
* * * * *
1301839 AAACCTTCGAGTTCGGTTAGACTCAGCTCAAAGACACATCATTTGCAGTATAACTCAAGGCT-AG
1 AAACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAGTATAACTCAAGG-TGAG
1301903 AAGGGTTATC-TGCCAATAA
65 AAGGGTTATCTTG-CAATAA
* *
1301922 AAGACCTTCGAGTTTGATTACACTCAGCTCCAAGGCACATCATTTACAGTATAGCTCAAGGTGAG
1 AA-ACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAGTATAACTCAAGGTGAG
1301987 AAGGGTTATCTTGCAATAA
65 AAGGGTTATCTTGCAATAA
* *
1302006 AAACCTTCGAGTTCGATTCCATTCAGCT-CAAGG
1 AAACCTTCGAGTTCGATTACACTCAGCTCCAAGG
1302039 GCATGACAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
82 5 0.05
83 26 0.25
84 71 0.68
85 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (83 bp):
AAACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAGTATAACTCAAGGTGAGA
AGGGTTATCTTGCAATAA
Found at i:1302082 original size:85 final size:82
Alignment explanation
Indices: 1301839--1302121 Score: 234
Period size: 84 Copynumber: 3.4 Consensus size: 82
1301829 TTAAAACACC
* ** * * * *
1301839 AAACCTTCGAGTTCGGTTAGACTCAGCTCAAAGACACATCATTTGCAGTATAACTCAAGGCT-AG
1 AAACCTTCGAGTTCGATTCCACTCAGCTC-AAGGCACATAATTTACAGTATAGCTCAAGG-TGAG
** * *
1301903 AAGGGTTATCTGCCAATAA
64 AAAAGCTATCTGTCAATAA
* * *
1301922 AAGACCTTCGAGTTTGATTACACTCAGCTCCAAGGCACATCATTTACAGTATAGCTCAAGGTGAG
1 AA-ACCTTCGAGTTCGATTCCACTCAGCT-CAAGGCACATAATTTACAGTATAGCTCAAGGTGAG
** *
1301987 AAGGGTTATCT-TGCAATAA
64 AAAAGCTATCTGT-CAATAA
* *
1302006 AAACCTTCGAGTTCGATTCCATTCAGCTCAAGGGCATGACA-AATTTACAGTATAGCTTAA-GTC
1 AAACCTTCGAGTTCGATTCCACTCAGCTCAA-GGC---ACATAATTTACAGTATAGCTCAAGGT-
*
1302069 GAGAAAAGCTATCTGTCGATAA
61 GAGAAAAGCTATCTGTCAATAA
* *
1302091 AAA-TTATCGAGTTCGGTTCCACTCAGCTCAA
1 AAACCT-TCGAGTTCGATTCCACTCAGCTCAA
1302122 TGACACATCA
Statistics
Matches: 170, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
82 3 0.02
83 29 0.17
84 74 0.44
85 60 0.35
86 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (82 bp):
AAACCTTCGAGTTCGATTCCACTCAGCTCAAGGCACATAATTTACAGTATAGCTCAAGGTGAGAA
AAGCTATCTGTCAATAA
Found at i:1303754 original size:16 final size:17
Alignment explanation
Indices: 1303722--1303754 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1303712 AATTGTCCCC
*
1303722 CAATTTGGTTTTCATTA
1 CAATTTGGTTCTCATTA
1303739 CAATTTGG-TCTCATTA
1 CAATTTGGTTCTCATTA
1303755 TGATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (17 bp):
CAATTTGGTTCTCATTA
Found at i:1303846 original size:2 final size:2
Alignment explanation
Indices: 1303837--1303911 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
1303827 TATTTTTTTA
1303837 AT AT -T 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
1303878 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
1303912 CTTTTTTGTT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1304052 original size:11 final size:11
Alignment explanation
Indices: 1304024--1304065 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1304014 TATACCTTAC
*
1304024 TATATATATATA
1 TATATAT-TATT
1304036 TATATATTATT
1 TATATATTATT
1304047 TATATATTATT
1 TATATATTATT
*
1304058 TATTTATT
1 TATATATT
1304066 TTCCTCTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 21 0.75
12 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATATTATT
Found at i:1304052 original size:15 final size:15
Alignment explanation
Indices: 1304030--1304064 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
1304020 TTACTATATA
1304030 TATATATATATATTATT
1 TATATAT-TAT-TTATT
1304047 TATATATTATTTATT
1 TATATATTATTTATT
1304062 TAT
1 TAT
1304065 TTTCCTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 3 0.17
17 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATATTATTTATT
Done.