Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_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: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1092895 original size:19 final size:19
Alignment explanation
Indices: 1092870--1092941 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 19
1092860 TGCGATTTTG
1092870 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
*
1092889 GCGTTGCGA--TTC---TC
1 TCGTTGCGATTTTCATTTC
*
1092903 TCGTTGCGATTTTTATTCTC
1 TCGTTGCGATTTTCATT-TC
1092923 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
1092942 AACCAAAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 10 0.23
16 2 0.05
17 3 0.07
19 10 0.23
20 18 0.42
ACGTcount: A:0.10, C:0.22, G:0.18, T:0.50
Consensus pattern (19 bp):
TCGTTGCGATTTTCATTTC
Found at i:1092896 original size:33 final size:34
Alignment explanation
Indices: 1092857--1092936 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 34
1092847 TTTGGTTTTT
*
1092857 CGTTGCGATTTTGTCGTTGCGATTTTCATT-TCG
1 CGTTGCGATTTTCTCGTTGCGATTTTCATTCTCG
* * *
1092890 CGTTGCGATTCTCTCGTTGCGATTTTTATTCTCT
1 CGTTGCGATTTTCTCGTTGCGATTTTCATTCTCG
1092924 CGTTGCGATTTTC
1 CGTTGCGATTTTC
1092937 ATTTCAACCA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 27 0.66
34 14 0.34
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.49
Consensus pattern (34 bp):
CGTTGCGATTTTCTCGTTGCGATTTTCATTCTCG
Found at i:1095007 original size:20 final size:20
Alignment explanation
Indices: 1094982--1095043 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
1094972 TTTTGGTTGA
1094982 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
1095002 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
1095021 AATGAAAATCGCAACCAGAG
1 AATGAAAATCGCAACGAGAG
1095041 AAT
1 AAT
1095044 CGCAACGCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1095026 original size:19 final size:19
Alignment explanation
Indices: 1094980--1095072 Score: 115
Period size: 19 Copynumber: 5.1 Consensus size: 19
1094970 TCTTTTGGTT
*
1094980 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
1094999 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
1095019 GAAATGAAAATCGCAAC-C
1 GAAATGAAAATCGCAACGC
*
1095037 ---A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1095052 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1095071 GA
1 GA
1095073 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
14 11 0.17
15 2 0.03
18 2 0.03
19 31 0.48
20 18 0.28
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1095116 original size:33 final size:33
Alignment explanation
Indices: 1095068--1095160 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 33
1095058 AAAATCGCAA
**
1095068 TGCGATTTTGGTTTCGCGTTGCGATTATATCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATATCGT
* * *
1095101 TGCGATTTTCATTTCGCGTTGCGGTTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATATCGT
** *
1095134 TGCGATAGTCATTTTCGTGTTGCGATT
1 TGCGATTTTCA-TTTCGCGTTGCGATT
1095161 TTCATTTTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 37 0.74
34 13 0.26
ACGTcount: A:0.11, C:0.18, G:0.26, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATATCGT
Found at i:1095157 original size:20 final size:20
Alignment explanation
Indices: 1095132--1095180 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1095122 CGGTTCTCTC
*
1095132 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCAT
**
1095152 GTTGCGATTTTCATTTTCAT
1 GTTGCGATAGTCATTTTCAT
1095172 GTTGCGATA
1 GTTGCGATA
1095181 TTAAGTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.47
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAT
Found at i:1095779 original size:20 final size:20
Alignment explanation
Indices: 1095733--1095847 Score: 162
Period size: 20 Copynumber: 5.8 Consensus size: 20
1095723 ATAGTCAGAT
* *
1095733 TCGCATTGCGATTTTCCTAA
1 TCGCATTGCGATTTACGTAA
1095753 TTCGCATTGCGATTTACGTAA
1 -TCGCATTGCGATTTACGTAA
1095774 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
1095794 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
* *
1095814 TCGCGTTGCGAATTATCG--A
1 TCGCATTGCGATTTA-CGTAA
1095833 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
1095848 GTTGGTCATT
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
19 14 0.16
20 53 0.61
21 20 0.23
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:1095806 original size:61 final size:59
Alignment explanation
Indices: 1095733--1095847 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 59
1095723 ATAGTCAGAT
* *
1095733 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTA-CGTAATCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACCTAA-TCGCATTGCGAATTATCG--ATCGCATTGCGATTTACGTAA
* *
1095794 TCGCATTGCGATTTACGTAATCGCGTTGCGAATTATCGATCGCATTGCGATTTA
1 TCGCATTGCGATTTACCTAATCGCATTGCGAATTATCGATCGCATTGCGATTTA
1095848 GTTGGTCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 16 0.33
60 13 0.27
61 20 0.41
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (59 bp):
TCGCATTGCGATTTACCTAATCGCATTGCGAATTATCGATCGCATTGCGATTTACGTAA
Found at i:1096052 original size:25 final size:26
Alignment explanation
Indices: 1095996--1096052 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1095986 TCCATTTCTG
* *
1095996 AATGATTGTGAGGGATTTCTGACCGTA
1 AATGGTTGTGAGGGATTTC-GACCGGA
1096023 AATGGTTGTGAGGGATTTC-ACCGGA
1 AATGGTTGTGAGGGATTTCGACCGGA
*
1096048 GATGG
1 AATGG
1096053 GGACAGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 9 0.33
27 18 0.67
ACGTcount: A:0.25, C:0.11, G:0.35, T:0.30
Consensus pattern (26 bp):
AATGGTTGTGAGGGATTTCGACCGGA
Found at i:1096290 original size:20 final size:20
Alignment explanation
Indices: 1096267--1096423 Score: 190
Period size: 20 Copynumber: 7.8 Consensus size: 20
1096257 ATAGTCAGAT
*
1096267 TCGCATTGCGATTTACATAA
1 TCGCATTGCGATTTACCTAA
**
1096287 TCGCATTGTAATTTACGC-AA
1 TCGCATTGCGATTTAC-CTAA
* *
1096307 TCGCATTACGATTTTCCTAA
1 TCGCATTGCGATTTACCTAA
1096327 TTCGCATTGCGATTTACCTAA
1 -TCGCATTGCGATTTACCTAA
* *
1096348 TCACATTGCGATTTACGTAA
1 TCGCATTGCGATTTACCTAA
* *
1096368 TCGCATTGCAATTTTCCTAA
1 TCGCATTGCGATTTACCTAA
*
1096388 TTCGCATTGCGATTTACGTAA
1 -TCGCATTGCGATTTACCTAA
1096409 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
1096424 TGAAAATTGC
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
19 1 0.01
20 79 0.69
21 35 0.30
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACCTAA
Found at i:1096339 original size:61 final size:61
Alignment explanation
Indices: 1096265--1096423 Score: 237
Period size: 61 Copynumber: 2.6 Consensus size: 61
1096255 CGATAGTCAG
* *
1096265 ATTCGCATTGCGATTTACATAATCGCATTGTAATTTACGCAATCGCATTACGATTTTCCTA
1 ATTCGCATTGCGATTTACATAATCGCATTGCAATTTACGCAATCGCATTACAATTTTCCTA
* * * * *
1096326 ATTCGCATTGCGATTTACCTAATCACATTGCGATTTACGTAATCGCATTGCAATTTTCCTA
1 ATTCGCATTGCGATTTACATAATCGCATTGCAATTTACGCAATCGCATTACAATTTTCCTA
* *
1096387 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTA
1 ATTCGCATTGCGATTTACATAATCGCATTGCAATTTA
1096424 TGAAAATTGC
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 89 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (61 bp):
ATTCGCATTGCGATTTACATAATCGCATTGCAATTTACGCAATCGCATTACAATTTTCCTA
Found at i:1096342 original size:41 final size:40
Alignment explanation
Indices: 1096267--1096423 Score: 199
Period size: 41 Copynumber: 3.9 Consensus size: 40
1096257 ATAGTCAGAT
* *
1096267 TCGCATTGCGATTTACATAATCGCATTGTAATTTACGC-AA
1 TCGCATTGCGATTTACGTAATCGCATTGCAATTTAC-CTAA
* * * *
1096307 TCGCATTACGATTTTCCTAATTCGCATTGCGATTTACCTAA
1 TCGCATTGCGATTTACGTAA-TCGCATTGCAATTTACCTAA
* *
1096348 TCACATTGCGATTTACGTAATCGCATTGCAATTTTCCTAA
1 TCGCATTGCGATTTACGTAATCGCATTGCAATTTACCTAA
*
1096388 TTCGCATTGCGATTTACGTAATCGCATTGCGATTTA
1 -TCGCATTGCGATTTACGTAATCGCATTGCAATTTA
1096424 TGAAAATTGC
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
40 36 0.36
41 64 0.64
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTAATCGCATTGCAATTTACCTAA
Found at i:1096678 original size:27 final size:26
Alignment explanation
Indices: 1096627--1096838 Score: 127
Period size: 27 Copynumber: 8.0 Consensus size: 26
1096617 TTATTTTCTC
*
1096627 TTATATTTATATACTATATACTATAG
1 TTATATTTATATACTATATATTATAG
1096653 TTGATATTTATATACTATATATTATA-
1 TT-ATATTTATATACTATATATTATAG
* *
1096679 TATATAAACTATATAAACTATATA-TATA-
1 T-TAT--A-TTTATATACTATATATTATAG
*
1096707 ATATAGTTTACATATGAACTATATA-TATA-
1 TTATA-TTT--ATAT--ACTATATATTATAG
* * * *
1096736 -TATATATATAAACTATATACTACAG
1 TTATATTTATATACTATATATTATAG
*
1096761 TTGATA-TT-TATACTATATAATATAG
1 TT-ATATTTATATACTATATATTATAG
1096786 TTGATATTTATATACTATAT-TATATAG
1 TT-ATATTTATATACTATATAT-TATAG
* * *
1096813 TTTATACTTATATAATTTATATTATA
1 -TTATATTTATATACTATATATTATA
1096839 TAAATTCAAA
Statistics
Matches: 150, Mismatches: 18, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
23 8 0.05
24 3 0.02
25 26 0.17
26 9 0.06
27 67 0.45
28 12 0.08
29 25 0.17
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (26 bp):
TTATATTTATATACTATATATTATAG
Found at i:1096679 original size:20 final size:19
Alignment explanation
Indices: 1096628--1096743 Score: 92
Period size: 20 Copynumber: 5.9 Consensus size: 19
1096618 TATTTTCTCT
1096628 TATATTTATATACTATATAC
1 TATATTTATATA-TATATAC
* *
1096648 TATAGTTGATATTTATATAC
1 TATA-TTTATATATATATAC
*
1096668 TATATATTATATATATAAAC
1 TATAT-TTATATATATATAC
** *
1096688 TATATAAACTATATATATAA
1 TATATTTA-TATATATATAC
* *
1096708 TATAGTTTACATAT-GA-AC
1 TATA-TTTATATATATATAC
*
1096726 TATATATATATATATATA
1 TATATTTATATATATATA
1096744 TAAACTATAT
Statistics
Matches: 73, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
17 7 0.10
18 6 0.08
19 4 0.05
20 48 0.66
21 8 0.11
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (19 bp):
TATATTTATATATATATAC
Found at i:1096754 original size:2 final size:2
Alignment explanation
Indices: 1096628--1096745 Score: 64
Period size: 2 Copynumber: 56.0 Consensus size: 2
1096618 TATTTTCTCT
* *
1096628 TA TA TT TA TA TA CTA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA
* * *
1096672 TA T- TA TA TA TA TA AA CTA TA TA AA CTA TA TA TA TA -A TA TA GTT
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA -TA
*
1096715 TA CA TA TGA -A CTA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA
1096746 AACTATATAC
Statistics
Matches: 90, Mismatches: 12, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
1 4 0.04
2 73 0.81
3 13 0.14
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1096793 original size:25 final size:25
Alignment explanation
Indices: 1096697--1096824 Score: 95
Period size: 25 Copynumber: 5.2 Consensus size: 25
1096687 CTATATAAAC
* *
1096697 TATA-TATATAATATAGTTTACATAT
1 TATACTATATAATATAGTTGATAT-T
* *
1096722 GA-ACTATAT-ATATA-TAT-ATATA
1 TATACTATATAATATAGT-TGATATT
* * *
1096744 TAAACTATATACTACAGTTGATATT
1 TATACTATATAATATAGTTGATATT
1096769 TATACTATATAATATAGTTGATATTT
1 TATACTATATAATATAGTTGATA-TT
* * *
1096795 ATATACTATATTATATAGTTTATACT
1 -TATACTATATAATATAGTTGATATT
1096821 TATA
1 TATA
1096825 TAATTTATAT
Statistics
Matches: 82, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
22 1 0.01
23 11 0.13
24 11 0.13
25 35 0.43
26 3 0.04
27 21 0.26
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (25 bp):
TATACTATATAATATAGTTGATATT
Found at i:1096844 original size:15 final size:14
Alignment explanation
Indices: 1096801--1096841 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
1096791 ATTTATATAC
*
1096801 TATATTATATAGTT
1 TATATTATATAATT
1096815 TATACTTATATAATT
1 TATA-TTATATAATT
1096830 TATATTATATAA
1 TATATTATATAA
1096842 ATTCAAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
TATATTATATAATT
Found at i:1097516 original size:15 final size:15
Alignment explanation
Indices: 1097496--1097530 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1097486 CTGACGGCCA
1097496 AGGATGAAGCAATTT
1 AGGATGAAGCAATTT
1097511 AGGATGAAGCAATTT
1 AGGATGAAGCAATTT
1097526 AGGAT
1 AGGAT
1097531 TTTTTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.29, T:0.26
Consensus pattern (15 bp):
AGGATGAAGCAATTT
Found at i:1097735 original size:29 final size:29
Alignment explanation
Indices: 1097693--1097757 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
1097683 TCGAACGTAA
1097693 GTCGCCAGGCGCTCCGGGCGACCAAGGAG
1 GTCGCCAGGCGCTCCGGGCGACCAAGGAG
1097722 GTCGCCAGGCGCTCCGGGCGACCAAGGAG
1 GTCGCCAGGCGCTCCGGGCGACCAAGGAG
1097751 GTCGCCA
1 GTCGCCA
1097758 TGCCGTCCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.17, C:0.35, G:0.40, T:0.08
Consensus pattern (29 bp):
GTCGCCAGGCGCTCCGGGCGACCAAGGAG
Found at i:1097771 original size:29 final size:29
Alignment explanation
Indices: 1097693--1097771 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
1097683 TCGAACGTAA
* *
1097693 GTCGCCAGGCGCTCCGGGCGACCAAGGAG
1 GTCGCCAGCCGCTCCCGGCGACCAAGGAG
* *
1097722 GTCGCCAGGCGCTCCGGGCGACCAAGGAG
1 GTCGCCAGCCGCTCCCGGCGACCAAGGAG
*
1097751 GTCGCCATGCCG-TCCCTGCGA
1 GTCGCCA-GCCGCTCCCGGCGA
1097772 ACTGTGGTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 43 0.93
30 3 0.07
ACGTcount: A:0.15, C:0.37, G:0.38, T:0.10
Consensus pattern (29 bp):
GTCGCCAGCCGCTCCCGGCGACCAAGGAG
Found at i:1101107 original size:18 final size:18
Alignment explanation
Indices: 1101086--1101121 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1101076 TAATATGCCA
*
1101086 ACTATATACTATATACAT
1 ACTATATACTATACACAT
*
1101104 ACTATATATTATACACAT
1 ACTATATACTATACACAT
1101122 GCCCACACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (18 bp):
ACTATATACTATACACAT
Found at i:1105425 original size:141 final size:135
Alignment explanation
Indices: 1105080--1105521 Score: 451
Period size: 132 Copynumber: 3.3 Consensus size: 135
1105070 ACGGAGTAAT
* * * * *
1105080 TCCTTCAAAACATGATCATGAACGTAAACAGCACCGTTCGATGGAGGACCCTCCTTCAAAAGAT-
1 TCCTTCAAAACACGATCATCAACCTAAACAGCACCGTTCAATTGAGGACCCTCCTTCAAAAGATG
* ** * * *
1105144 ---ATCCAGAACAAGAAAGAGA-CGCCGCCTCCAGCTCGGAATGCGGAGCAACCAGAAAAAGATA
66 AAGAACCAGAACAA-AACCAGACCGCCGCCTCCAGCTCGGAACGTGGAGCAA-CAGAAAAAGATG
**
1105205 GATTACC
129 GACAACC
* * *
1105212 TCCTTCAAAACACGATCATCAACCTAAGCAGCACCG-TCAGTTGGAGGAGCCTCCTTCAAAAGAT
1 TCCTTCAAAACACGATCATCAACCTAAACAGCACCGTTCAATT-GAGGACCCTCCTTCAAAAGAT
* *
1105276 AGAAAGAACCAGAACCAAAACCAGCCACCCCCGCCTCCAGCTCGGACCGTGGAGCAACAGCAAAA
65 -G-AAGAACCAGAA-CAAAACCAG--ACCGCCGCCTCCAGCTCGGAACGTGGAGCAACAG-AAAA
*
1105341 AGATGGACAAAC
124 AGATGGACAACC
* * *
1105353 TCCTTCAAAACACGATCATCAACGTAACCAGCTCCGTTCAATTGAGGACCCTCCTTCAAAAGATC
1 TCCTTCAAAACACGATCATCAACCTAAACAGCACCGTTCAATTGAGGACCCTCCTTCAAAAGAT-
* *
1105418 GACAGAACCAG-----AACCAG-CTGCCGCCTCCAGCTCGGAACGTGGAACAGACAGAAAAAGAT
65 GA-AGAACCAGAACAAAACCAGACCGCCGCCTCCAGCTCGGAACGTGGAGCA-ACAGAAAAAGAT
1105477 AGG-CAACC
128 -GGACAACC
*
1105485 TCTTTCAAAACACGATCATCAACCTAAACAGCACCGT
1 TCCTTCAAAACACGATCATCAACCTAAACAGCACCGT
1105522 CCGGTGGAGA
Statistics
Matches: 260, Mismatches: 34, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
131 3 0.01
132 122 0.47
133 6 0.02
135 6 0.02
138 11 0.04
139 3 0.01
140 5 0.02
141 99 0.38
142 5 0.02
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (135 bp):
TCCTTCAAAACACGATCATCAACCTAAACAGCACCGTTCAATTGAGGACCCTCCTTCAAAAGATG
AAGAACCAGAACAAAACCAGACCGCCGCCTCCAGCTCGGAACGTGGAGCAACAGAAAAAGATGGA
CAACC
Found at i:1106800 original size:2 final size:2
Alignment explanation
Indices: 1106795--1106820 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1106785 AAAATTAATC
1106795 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
1106821 CCAACAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1107758 original size:102 final size:100
Alignment explanation
Indices: 1107432--1107766 Score: 313
Period size: 108 Copynumber: 3.3 Consensus size: 100
1107422 ATAATCGTGG
*
1107432 TGACAATCAAAGCAGTCATAAAAACTCCAGCCG--CCACCA-CA-ACCAACAACAGAAACAAGCA
1 TGACAATCAAAACAGTCATAAAAACTCCAGCCGCACCACCACCACACCAACAACAGAAACAAGCA
** *
1107493 TCTCCTTTGGTAGTTCTTCCAGAAAACGACAATCC
66 TCTCCTCCGGTGGTTCTTCCAGAAAACGACAATCC
* * * * * * ***
1107528 TGACAATCAAAACAGTCATAAAAATTCCTA-CCATCACCATCACCAGCAGCAGCAGCAGTCGCAA
1 TGACAATCAAAACAGTCATAAAAACTCC-AGCC-GCACCACCACCA-CACCAACAACAGAAAC-A
* * * * * *
1107592 TAGCAACTATCTCCGGTGACGGTTCCTCCA-AGAAACAATAATAC
62 -AGCATCT-CCTCCGGT---GGTTCTTCCAGA-AAACGACAATCC
* * *
1107636 TAACAATCAAAGCAGCCATAAAAACTCCAGCCGCCACCACCACCACCACCAACAACAGAAACAAG
1 TGACAATCAAAACAGTCATAAAAACTCCAGCCG-CACCACCACCA-CACCAACAACAGAAACAAG
1107701 CATCTCCTCCGGTGGTTCTTCCAGAAAACGACAATCC
64 CATCTCCTCCGGTGGTTCTTCCAGAAAACGACAATCC
*
1107738 TGACGATCAAAACAGTCATAAAAACTCCA
1 TGACAATCAAAACAGTCATAAAAACTCCA
1107767 ACCAGCAGCA
Statistics
Matches: 180, Mismatches: 42, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
96 28 0.16
97 1 0.01
99 5 0.03
100 2 0.01
102 52 0.29
103 2 0.01
104 6 0.03
105 12 0.07
106 6 0.03
107 3 0.02
108 63 0.35
ACGTcount: A:0.39, C:0.32, G:0.13, T:0.16
Consensus pattern (100 bp):
TGACAATCAAAACAGTCATAAAAACTCCAGCCGCACCACCACCACACCAACAACAGAAACAAGCA
TCTCCTCCGGTGGTTCTTCCAGAAAACGACAATCC
Found at i:1110858 original size:5 final size:5
Alignment explanation
Indices: 1110848--1110873 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1110838 ATTCATATAT
1110848 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
1110874 GAAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1111565 original size:18 final size:18
Alignment explanation
Indices: 1111528--1111610 Score: 150
Period size: 18 Copynumber: 4.7 Consensus size: 18
1111518 TATGGAATTG
*
1111528 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
1111545 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1111563 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1111581 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1111599 GATTCCAATTCC
1 GATTCCAATTCC
1111611 CTCATAAACA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
17 12 0.19
18 52 0.81
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1111973 original size:20 final size:20
Alignment explanation
Indices: 1111950--1112016 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1111940 ATTTCTTTTC
1111950 CGCAACGCAAATTTGTAATT
1 CGCAACGCAAATTTGTAATT
* *
1111970 CGCAACACAAAATTTGTAAAT
1 CGCAACGC-AAATTTGTAATT
* *
1111991 CGCAACGCACATTTTTAATT
1 CGCAACGCAAATTTGTAATT
1112011 CGCAAC
1 CGCAAC
1112017 ACAGAAGGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 22 0.55
21 18 0.45
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (20 bp):
CGCAACGCAAATTTGTAATT
Found at i:1112030 original size:20 final size:20
Alignment explanation
Indices: 1112007--1112055 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1111997 GCACATTTTT
1112007 AATTCGCAACACAGAAGGCA
1 AATTCGCAACACAGAAGGCA
* **
1112027 AATTCGCAACAGAGAATTCA
1 AATTCGCAACACAGAAGGCA
1112047 AATTCGCAA
1 AATTCGCAA
1112056 AGCGCATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.16
Consensus pattern (20 bp):
AATTCGCAACACAGAAGGCA
Found at i:1112648 original size:14 final size:14
Alignment explanation
Indices: 1112629--1112673 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
1112619 GAAAATGAAA
1112629 TTTGCGTTGCGATT
1 TTTGCGTTGCGATT
*
1112643 TTTGCGTTGCGCTTT
1 TTTGCGTTGCG-ATT
1112658 TTTGCGTTGCGATT
1 TTTGCGTTGCGATT
1112672 TT
1 TT
1112674 CATTTTCGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.04, C:0.16, G:0.27, T:0.53
Consensus pattern (14 bp):
TTTGCGTTGCGATT
Found at i:1112661 original size:15 final size:14
Alignment explanation
Indices: 1112629--1112673 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
1112619 GAAAATGAAA
*
1112629 TTTGCGTTGCGATT
1 TTTGCGTTGCGTTT
1112643 TTTGCGTTGCGCTTT
1 TTTGCGTTGCG-TTT
1112658 TTTGCGTTGCGATTT
1 TTTGCGTTGCG-TTT
1112673 T
1 T
1112674 CATTTTCGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.04, C:0.16, G:0.27, T:0.53
Consensus pattern (14 bp):
TTTGCGTTGCGTTT
Found at i:1113392 original size:21 final size:21
Alignment explanation
Indices: 1113368--1113419 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1113358 ACCTATTTCC
1113368 GAGGACCTAATATTATTGGTA
1 GAGGACCTAATATTATTGGTA
1113389 GAGGACCTAATATTATTGGTA
1 GAGGACCTAATATTATTGGTA
*
1113410 GATGACCTAA
1 GAGGACCTAA
1113420 ATGCATGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (21 bp):
GAGGACCTAATATTATTGGTA
Found at i:1114121 original size:21 final size:21
Alignment explanation
Indices: 1114097--1114146 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1114087 TGGTGCATGG
1114097 CGTGATGAGGTA-AGGTCTTTA
1 CGTGATGAGGTAGAGGT-TTTA
* *
1114118 CGTGGTGAGGTAGATGTTTTA
1 CGTGATGAGGTAGAGGTTTTA
*
1114139 CGCGATGA
1 CGTGATGA
1114147 CAATGGTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.22, C:0.10, G:0.36, T:0.32
Consensus pattern (21 bp):
CGTGATGAGGTAGAGGTTTTA
Found at i:1114518 original size:21 final size:22
Alignment explanation
Indices: 1114488--1114606 Score: 131
Period size: 21 Copynumber: 5.6 Consensus size: 22
1114478 GATTCACCTG
*
1114488 TCATCGTTCAAGAGGCCCCTCC
1 TCATCATTCAAGAGGCCCCTCC
1114510 T-ATCATTCAAGAGGCCCCT-C
1 TCATCATTCAAGAGGCCCCTCC
*
1114530 TCATCATTCAAGAGGCCCCTTC
1 TCATCATTCAAGAGGCCCCTCC
* *
1114552 -CACCGTTCAAGAGGCCCCT-C
1 TCATCATTCAAGAGGCCCCTCC
* *
1114572 TCATCCTTCAAGAGGTCCCTCC
1 TCATCATTCAAGAGGCCCCTCC
* *
1114594 -CACCGTTCAAGAG
1 TCATCATTCAAGAG
1114607 CCCTATTCAC
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
20 3 0.04
21 79 0.93
22 3 0.04
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.23
Consensus pattern (22 bp):
TCATCATTCAAGAGGCCCCTCC
Found at i:1114540 original size:42 final size:41
Alignment explanation
Indices: 1114488--1114606 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 41
1114478 GATTCACCTG
* *
1114488 TCATCGTTCAAGAGGCCCCTCCTATCATTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTCC-ACCATTCAAGAGGCCCCTC
*
1114530 TCATCATTCAAGAGGCCCCTTCCACCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCC-TCCACCATTCAAGAGGCCCCTC
* * *
1114572 TCATCCTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCATTCAAGAGGCCCCT-CCACCATTCAAGAG
1114607 CCCTATTCAC
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
41 1 0.01
42 66 0.94
43 3 0.04
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.23
Consensus pattern (41 bp):
TCATCATTCAAGAGGCCCCTCCACCATTCAAGAGGCCCCTC
Found at i:1116816 original size:18 final size:18
Alignment explanation
Indices: 1116793--1116829 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1116783 AAGCCGGTTG
*
1116793 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1116811 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1116829 T
1 T
1116830 CTTTGGCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.24, T:0.57
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1119287 original size:12 final size:12
Alignment explanation
Indices: 1119266--1119299 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1119256 GGTTGTGGGT
*
1119266 TTTGAGATTGTG
1 TTTGATATTGTG
1119278 TTTGATATTGTG
1 TTTGATATTGTG
*
1119290 TTTGGTATTG
1 TTTGATATTG
1119300 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1120124 original size:20 final size:19
Alignment explanation
Indices: 1120096--1120134 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1120086 AGCTGTTACG
* *
1120096 AAATTAAAATTCGTGTTGC
1 AAATTAAAAATCGAGTTGC
1120115 AAATTCAAAAATCGAGTTGC
1 AAATT-AAAAATCGAGTTGC
1120135 GAAAACAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (19 bp):
AAATTAAAAATCGAGTTGC
Found at i:1120184 original size:20 final size:20
Alignment explanation
Indices: 1120160--1120217 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1120150 ATAGCGATTT
1120160 AGAAAATCT-TGTTGCGAAAA
1 AGAAAAT-TGTGTTGCGAAAA
* *
1120180 GGAAACTTGTGTTGCGAAAA
1 AGAAAATTGTGTTGCGAAAA
* *
1120200 AGAAATTTGGGTTGCGAA
1 AGAAAATTGTGTTGCGAA
1120218 TTTGGAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.26
Consensus pattern (20 bp):
AGAAAATTGTGTTGCGAAAA
Found at i:1120214 original size:40 final size:40
Alignment explanation
Indices: 1120170--1120292 Score: 105
Period size: 40 Copynumber: 3.2 Consensus size: 40
1120160 AGAAAATCTT
* *
1120170 GTTGCGAA-AAGGAAACTTGTGTTGCGAAAAAGAAATTTGG
1 GTTGCGAATAAGGAAA-TCGCGTTGCGAAAAAGAAATTTGG
** *
1120210 GTTGCGAATTTGGAAATCGCGTTGCGAGAAAGAAA--T--
1 GTTGCGAATAAGGAAATCGCGTTGCGAAAAAGAAATTTGG
** * *
1120246 -TTGCGAATTTGGAAATTCGCGTTGCGAGAAAGAAATTTGC
1 GTTGCGAATAAGGAAA-TCGCGTTGCGAAAAAGAAATTTGG
1120286 GTTGCGA
1 GTTGCGA
1120293 TTGCAGAAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
35 15 0.21
36 19 0.27
38 2 0.03
40 24 0.34
41 11 0.15
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.27
Consensus pattern (40 bp):
GTTGCGAATAAGGAAATCGCGTTGCGAAAAAGAAATTTGG
Found at i:1120250 original size:35 final size:36
Alignment explanation
Indices: 1120211--1120286 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
1120201 GAAATTTGGG
1120211 TTGCGAATTTGGAAA-TCGCGTTGCGAGAAAGAAAT
1 TTGCGAATTTGGAAATTCGCGTTGCGAGAAAGAAAT
1120246 TTGCGAATTTGGAAATTCGCGTTGCGAGAAAGAAAT
1 TTGCGAATTTGGAAATTCGCGTTGCGAGAAAGAAAT
1120282 TTGCG
1 TTGCG
1120287 TTGCGATTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 15 0.38
36 25 0.62
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.28
Consensus pattern (36 bp):
TTGCGAATTTGGAAATTCGCGTTGCGAGAAAGAAAT
Found at i:1120330 original size:42 final size:42
Alignment explanation
Indices: 1120277--1120360 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
1120267 TTGCGAGAAA
* *
1120277 GAAATTTGCGTTGCG-A-TTGCAGAAACTGAGTTGCGAATTTGG
1 GAAATTCGCGTTGCGAATTTG--GAAACTGAGTTGCGAAATTGG
*
1120319 GAAATTCGCGTTGCGAATTTGGAAACTGTGTTGCGAAATTGG
1 GAAATTCGCGTTGCGAATTTGGAAACTGAGTTGCGAAATTGG
1120361 AGTTCACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 33 0.89
43 1 0.03
44 3 0.08
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (42 bp):
GAAATTCGCGTTGCGAATTTGGAAACTGAGTTGCGAAATTGG
Found at i:1120353 original size:20 final size:20
Alignment explanation
Indices: 1120298--1120361 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
1120288 TGCGATTGCA
1120298 GAAACTGAGTTGCGAATTTGG
1 GAAACTGAGTTGCGAATTT-G
* *
1120319 GAAATTCGCGTTGCGAATTTG
1 GAAACT-GAGTTGCGAATTTG
* *
1120340 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAATTTG
1120360 GA
1 GA
1120362 GTTCACATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 14 0.38
21 11 0.30
22 12 0.32
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.30
Consensus pattern (20 bp):
GAAACTGAGTTGCGAATTTG
Found at i:1122812 original size:22 final size:22
Alignment explanation
Indices: 1122782--1122836 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1122772 ATTTAGCTGT
*
1122782 TATAACTCCTGAAATTATATCA
1 TATAACTCCTGAAATTAAATCA
*
1122804 TGTAACTCCTGAAATTAAATCA
1 TATAACTCCTGAAATTAAATCA
1122826 TATAACTCCTG
1 TATAACTCCTG
1122837 TAACTCCTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (22 bp):
TATAACTCCTGAAATTAAATCA
Found at i:1127107 original size:19 final size:19
Alignment explanation
Indices: 1127072--1127109 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1127062 TTAATTTATG
*
1127072 ATTGTGATTATAAATATTT
1 ATTGTAATTATAAATATTT
1127091 ATTGTAATT-TAATATATTT
1 ATTGTAATTATAA-ATATTT
1127110 TTTACTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
ATTGTAATTATAAATATTT
Found at i:1127692 original size:2 final size:2
Alignment explanation
Indices: 1127685--1127715 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1127675 CGGAAAGTTA
1127685 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1127716 ATTGTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1128350 original size:183 final size:187
Alignment explanation
Indices: 1128039--1128428 Score: 630
Period size: 183 Copynumber: 2.1 Consensus size: 187
1128029 TTTTCTAATT
* * *
1128039 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
1128103 ATTATAAAATAAAAATGTTATATAAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
66 ATTATAAAATAAAAATGTTATATAAATATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
* *
1128168 ATT-GAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGTCCATATGTTA
131 ATTAG-ATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* *
1128225 TATATAATATATTTAATATTTTTTAATTC-AAAAAATAGTTTACAATTAATTTAAAT-A-ATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
1128287 ATTATAAAATAAAAATTTTATATAAA-ATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
66 ATTATAAAATAAAAATGTTATATAAATATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
*
1128351 ATTAGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGTTGAGCCCATATGTTA
131 ATTAGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
1128408 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
1128429 AAAATTTTAT
Statistics
Matches: 191, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
183 109 0.57
184 31 0.16
185 1 0.01
186 32 0.17
187 18 0.09
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (187 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATGTTATATAAATATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
ATTAGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:1130480 original size:23 final size:23
Alignment explanation
Indices: 1130453--1130569 Score: 175
Period size: 23 Copynumber: 5.2 Consensus size: 23
1130443 AGGGTTCTAG
*
1130453 GTGGTCTTTCGAGACAAAACTAT
1 GTGGTCTTTCGGGACAAAACTAT
* *
1130476 GTGGTCCTTCGAGACAAAACTAT
1 GTGGTCTTTCGGGACAAAACTAT
1130499 GTGGTCTTTCGGGACAAAACTAT
1 GTGGTCTTTCGGGACAAAACTAT
*
1130522 GTGGTCTTTCGGGACAAAACTTT
1 GTGGTCTTTCGGGACAAAACTAT
*
1130545 GTGGTCCTTCGGGAC-AAA-TAT
1 GTGGTCTTTCGGGACAAAACTAT
1130566 GTGG
1 GTGG
1130570 CACTTCGGTG
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
21 6 0.07
22 3 0.03
23 79 0.90
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (23 bp):
GTGGTCTTTCGGGACAAAACTAT
Found at i:1132106 original size:21 final size:21
Alignment explanation
Indices: 1132092--1132148 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1132082 AACTTAAAAT
*
1132092 CCTAAATTATAAACTCTAAAC
1 CCTAAATCATAAACTCTAAAC
*
1132113 CCTAAATCAT-AACTCCATAAC
1 CCTAAATCATAAACTCTA-AAC
*
1132134 ATCTAAATCATAAAC
1 -CCTAAATCATAAAC
1132149 CATAAACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.20
21 12 0.40
22 9 0.30
23 3 0.10
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (21 bp):
CCTAAATCATAAACTCTAAAC
Found at i:1132772 original size:33 final size:34
Alignment explanation
Indices: 1132727--1132793 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
1132717 GTTTATATAT
1132727 ATATATATATACCTCTTGGGAAATAAAAAATTGC
1 ATATATATATACCTCTTGGGAAATAAAAAATTGC
*
1132761 ATATAT-TATACCTCTTGGGAAATAACAAATTGC
1 ATATATATATACCTCTTGGGAAATAAAAAATTGC
1132794 TTGAATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (34 bp):
ATATATATATACCTCTTGGGAAATAAAAAATTGC
Found at i:1133636 original size:14 final size:14
Alignment explanation
Indices: 1133613--1133649 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1133603 AATAGTATAA
1133613 TTAATATTTTA-TT
1 TTAATATTTTACTT
1133626 TTAATTATTTTACTT
1 TTAA-TATTTTACTT
1133641 TTAA-ATTTT
1 TTAATATTTT
1133650 TAACTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 7 0.32
15 6 0.27
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TTAATATTTTACTT
Found at i:1135003 original size:6 final size:6
Alignment explanation
Indices: 1134987--1135018 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1134977 TTTGGATAAT
1134987 AATTT- AATTTA AATTTA AATTTA AA-TTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT
1135019 ATGAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:1136622 original size:32 final size:31
Alignment explanation
Indices: 1136581--1136695 Score: 131
Period size: 32 Copynumber: 3.6 Consensus size: 31
1136571 GTCAAGTAAT
*
1136581 TATCGGATCAATTGTTTTTCGGTTCGGATCAA
1 TATCGGATCAATTGATTTT-GGTTCGGATCAA
* * *
1136613 TATCGGATCAGTTGACTTTTGGGTCGGATTAA
1 TATCGGATCAATTGA-TTTTGGTTCGGATCAA
*
1136645 TATCGGATCAATTAGATTTTGGTTCGGGTCAA
1 TATCGGATCAATT-GATTTTGGTTCGGATCAA
* **
1136677 TATCGAATCTGTTGATTTT
1 TATCGGATCAATTGATTTT
1136696 CGATTTGGGT
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
31 6 0.09
32 58 0.83
33 6 0.09
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (31 bp):
TATCGGATCAATTGATTTTGGTTCGGATCAA
Found at i:1136957 original size:16 final size:16
Alignment explanation
Indices: 1136921--1136969 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1136911 AATTCAATTT
* *
1136921 AGGTTACTTTCGATTC
1 AGGTTGCTTTCGGTTC
*
1136937 GGGTTGCTTTCGGTTC
1 AGGTTGCTTTCGGTTC
*
1136953 AGGTTGTTTTTCGGTTC
1 AGGTTG-CTTTCGGTTC
1136970 GGATCAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.08, C:0.16, G:0.29, T:0.47
Consensus pattern (16 bp):
AGGTTGCTTTCGGTTC
Found at i:1140561 original size:18 final size:18
Alignment explanation
Indices: 1140538--1140577 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1140528 ACAGCAGCCA
* *
1140538 CCGCAGCTATTTATGATG
1 CCGCAGCCATATATGATG
1140556 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
1140574 CCGC
1 CCGC
1140578 CGCCTTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:1144582 original size:14 final size:13
Alignment explanation
Indices: 1144548--1144584 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1144538 AATAAGTATA
1144548 ATAA-AAAAATTT
1 ATAACAAAAATTT
1144560 ATAAC-AAAATTT
1 ATAACAAAAATTT
1144572 ATAACGAAAAATT
1 ATAAC-AAAAATT
1144585 ACACGAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 16 0.73
14 6 0.27
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (13 bp):
ATAACAAAAATTT
Found at i:1150040 original size:34 final size:32
Alignment explanation
Indices: 1149987--1150056 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1149977 ACCTTACAAC
*
1149987 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1150019 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1150053 TCCC
1 TCCC
1150057 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1150305 original size:21 final size:21
Alignment explanation
Indices: 1150271--1150310 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1150261 AGTCGTATAT
1150271 AGCCGTTAGGGATG-TTTTGG
1 AGCCGTTAGGGATGATTTTGG
*
1150291 AGCCGTTTGGGGATGATTTT
1 AGCCG-TTAGGGATGATTTT
1150311 TATGCTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTAGGGATGATTTTGG
Found at i:1150362 original size:21 final size:21
Alignment explanation
Indices: 1150338--1150380 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1150328 CTCAAAATAG
*
1150338 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1150359 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
1150380 A
1 A
1150381 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1150442 original size:21 final size:21
Alignment explanation
Indices: 1150416--1150455 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1150406 CTGTTGAACA
1150416 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
1150437 GGGGGGGAATCGGTACCCC
1 GGGGGGGAATCGGTACCCC
1150456 ATGGACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.28, G:0.45, T:0.12
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:1150695 original size:29 final size:31
Alignment explanation
Indices: 1150663--1150722 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
1150653 AAACTTTGAA
1150663 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1150692 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1150723 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1152648 original size:21 final size:23
Alignment explanation
Indices: 1152597--1152655 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
1152587 ACATATAATT
1152597 TGTCCCGAATGACCACATAGAAA
1 TGTCCCGAATGACCACATAGAAA
* * *
1152620 TGTTCCGAATGACCTCA-A-AGA
1 TGTCCCGAATGACCACATAGAAA
*
1152641 TGTCCCGAAGGACCA
1 TGTCCCGAATGACCA
1152656 TATATAACAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 14 0.47
22 1 0.03
23 15 0.50
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (23 bp):
TGTCCCGAATGACCACATAGAAA
Found at i:1152698 original size:14 final size:14
Alignment explanation
Indices: 1152679--1152712 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1152669 TGTCCCGAAA
1152679 GACCACTCCTTAAG
1 GACCACTCCTTAAG
*
1152693 GACCACTCGTTAAG
1 GACCACTCCTTAAG
1152707 GACCAC
1 GACCAC
1152713 ATACATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (14 bp):
GACCACTCCTTAAG
Found at i:1157329 original size:7 final size:7
Alignment explanation
Indices: 1157316--1157360 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
1157306 ATTGTTAACT
1157316 ATTGACC
1 ATTGACC
*
1157323 GTTGACC
1 ATTGACC
*
1157330 GTTGACC
1 ATTGACC
1157337 ATTGACC
1 ATTGACC
*
1157344 ATTAACC
1 ATTGACC
1157351 -TTGACC
1 ATTGACC
1157357 ATTG
1 ATTG
1157361 GTTGTTGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (7 bp):
ATTGACC
Found at i:1157340 original size:21 final size:20
Alignment explanation
Indices: 1157316--1157360 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
1157306 ATTGTTAACT
* *
1157316 ATTGACCGTTGACCGTTGACC
1 ATTGACCATTAACC-TTGACC
1157337 ATTGACCATTAACCTTGACC
1 ATTGACCATTAACCTTGACC
1157357 ATTG
1 ATTG
1157361 GTTGTTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (20 bp):
ATTGACCATTAACCTTGACC
Found at i:1158366 original size:20 final size:20
Alignment explanation
Indices: 1158343--1158389 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1158333 TCAATATCAG
1158343 TACTGA-CCCTTGATTATCCA
1 TACTGATCCCTTGA-TATCCA
* * *
1158363 TACTCATCCTTTGATATCGA
1 TACTGATCCCTTGATATCCA
1158383 TACTGAT
1 TACTGAT
1158390 ATGACTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (20 bp):
TACTGATCCCTTGATATCCA
Found at i:1162759 original size:19 final size:19
Alignment explanation
Indices: 1162712--1162762 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1162702 GCCCTACCGC
*
1162712 TGAATATAGAGCTAGGCTG
1 TGAATATAGGGCTAGGCTG
1162731 TGAATATAGGGCTAGGCTG
1 TGAATATAGGGCTAGGCTG
1162750 TGAATATAGGGCT
1 TGAATATAGGGCT
1162763 GGTGGAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.27
Consensus pattern (19 bp):
TGAATATAGGGCTAGGCTG
Found at i:1163256 original size:20 final size:20
Alignment explanation
Indices: 1163231--1163270 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1163221 TTACAGGGGC
*
1163231 ATAAAATAGGGGTAGGAGAA
1 ATAAAATAGGGGCAGGAGAA
1163251 ATAAAATAGGGGCAGGAGAA
1 ATAAAATAGGGGCAGGAGAA
1163271 TTCTATTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.35, T:0.12
Consensus pattern (20 bp):
ATAAAATAGGGGCAGGAGAA
Found at i:1180679 original size:21 final size:23
Alignment explanation
Indices: 1180653--1180702 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1180643 TAATTATTAA
1180653 AATATTTAAAAT-ATATT-TATT
1 AATATTTAAAATAATATTATATT
**
1180674 AATATTTTTAATAATATTATATT
1 AATATTTAAAATAATATTATATT
1180697 -ATATTT
1 AATATTT
1180703 TTTAATCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
22 11 0.44
23 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTTAAAATAATATTATATT
Found at i:1180698 original size:26 final size:25
Alignment explanation
Indices: 1180636--1180698 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 25
1180626 CATTTTAATC
1180636 AAAATATTA-ATTATTAAAATATTT
1 AAAATATTATATTATTAAAATATTT
* *
1180660 AAAATA-TAT-TTATTAATATTTTT
1 AAAATATTATATTATTAAAATATTT
1180683 AATAATATTATATTAT
1 AA-AATATTATATTAT
1180699 ATTTTTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 16 0.48
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAAATATTATATTATTAAAATATTT
Found at i:1180708 original size:23 final size:22
Alignment explanation
Indices: 1180646--1180704 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
1180636 AAAATATTAA
* * *
1180646 TTATTAAAATATTTAAAATATAT
1 TTATTAATATTTTTAATA-ATAT
1180669 TTATTAATATTTTTAATAATAT
1 TTATTAATATTTTTAATAATAT
1180691 TATATT-ATATTTTT
1 T-TATTAATATTTTT
1180705 TAATCTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTAATATTTTTAATAATAT
Found at i:1180713 original size:20 final size:22
Alignment explanation
Indices: 1180665--1180714 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1180655 TATTTAAAAT
1180665 ATATT-TATTAATATTTTTAATA
1 ATATTATATTAATATTTTT-ATA
1180687 ATATTATATT-ATATTTTT-TA
1 ATATTATATTAATATTTTTATA
*
1180707 ATCTTATA
1 ATATTATA
1180715 ATAAAATACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTATATTAATATTTTTATA
Found at i:1180948 original size:24 final size:24
Alignment explanation
Indices: 1180909--1180961 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1180899 AATAAAGATA
*
1180909 TTTAAAATATATTAA-TTAATAATT
1 TTTAAAATATACTAACTTAA-AATT
*
1180933 TTTAAAATGTACTAATCTTAAAATT
1 TTTAAAATATACTAA-CTTAAAATT
1180958 TTTA
1 TTTA
1180962 TTAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.52
25 8 0.32
26 4 0.16
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTAAAATATACTAACTTAAAATT
Found at i:1184394 original size:24 final size:20
Alignment explanation
Indices: 1184321--1184398 Score: 111
Period size: 20 Copynumber: 3.7 Consensus size: 20
1184311 TTCCCCTTGA
1184321 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
1184341 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAC
1184361 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1184384 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1184399 CTACCCATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
20 36 0.69
22 1 0.02
23 2 0.04
24 13 0.25
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1187654 original size:29 final size:29
Alignment explanation
Indices: 1187637--1187710 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
1187627 AAGTGAAGGA
1187637 CAAAAG-GTTTTATAAATTATAATGAAGTG
1 CAAAAGTG-TTTATAAATTATAATGAAGTG
* *
1187666 CAAAATTGTTTATAAATTATAATAAAGTG
1 CAAAAGTGTTTATAAATTATAATGAAGTG
* * *
1187695 TAAAACTTTTTATAAA
1 CAAAAGTGTTTATAAA
1187711 ATAAAGTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (29 bp):
CAAAAGTGTTTATAAATTATAATGAAGTG
Found at i:1187767 original size:27 final size:27
Alignment explanation
Indices: 1187718--1187792 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
1187708 AAAATAAAGT
*
1187718 ATTTTTTATAAATTATAATAAAGGACA
1 ATTTTTTATAAATTACAATAAAGGACA
*
1187745 ATTTTTTATGAA-TACAATAAAAGGACA
1 ATTTTTTATAAATTACAAT-AAAGGACA
* * **
1187772 ACTTCTCGTAAATTACAATAA
1 ATTTTTTATAAATTACAATAA
1187793 TACTATCATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 5 0.13
27 28 0.72
28 6 0.15
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (27 bp):
ATTTTTTATAAATTACAATAAAGGACA
Found at i:1187979 original size:22 final size:22
Alignment explanation
Indices: 1187943--1187992 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1187933 GTACGGATGG
1187943 TGGAAGAAGGATGCACGAATGC
1 TGGAAGAAGGATGCACGAATGC
* *
1187965 TGGAAGTAGGTTGCACGAATGC
1 TGGAAGAAGGATGCACGAATGC
1187987 TGGAAG
1 TGGAAG
1187993 CGGGCTGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.32, C:0.12, G:0.38, T:0.18
Consensus pattern (22 bp):
TGGAAGAAGGATGCACGAATGC
Found at i:1188001 original size:22 final size:22
Alignment explanation
Indices: 1187943--1188002 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1187933 GTACGGATGG
* *
1187943 TGGAAGAAGGATGCACGAATGC
1 TGGAAGCAGGCTGCACGAATGC
* *
1187965 TGGAAGTAGGTTGCACGAATGC
1 TGGAAGCAGGCTGCACGAATGC
*
1187987 TGGAAGCGGGCTGCAC
1 TGGAAGCAGGCTGCAC
1188003 AGGTGCTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.38, T:0.17
Consensus pattern (22 bp):
TGGAAGCAGGCTGCACGAATGC
Found at i:1189575 original size:43 final size:41
Alignment explanation
Indices: 1189504--1189663 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 41
1189494 GCTAAAGTTC
* * *
1189504 GCGGCGTTTGTTAACCAAAAACGTCGCAATAGGTAACGATATATA
1 GCGGCGTTTTTTAA-C--AAACGCCGCAATAGGT-ACGATATTTA
*
1189549 GCGCCGTTTGTTTAACAAACGCCGCAATAGGTACTGATATTTA
1 GCGGCGTTT-TTTAACAAACGCCGCAATAGGTAC-GATATTTA
* * *
1189592 GCGGCGTTTATCTTAA-AAATGCCGCAATAGGTGTCAATATTTA
1 GCGGCGTTT-T-TTAACAAACGCCGCAATAGGT-ACGATATTTA
* *
1189635 GCGGCATTTTTATCACAAACGCCGCAATA
1 GCGGCGTTTTT-TAACAAACGCCGCAATA
1189664 AATGTTGATA
Statistics
Matches: 97, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.01
42 5 0.05
43 73 0.75
44 5 0.05
45 9 0.09
46 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTTTTAACAAACGCCGCAATAGGTACGATATTTA
Found at i:1189675 original size:43 final size:43
Alignment explanation
Indices: 1189563--1189676 Score: 120
Period size: 43 Copynumber: 2.7 Consensus size: 43
1189553 CGTTTGTTTA
** * * *
1189563 ACAAACGCCGCAATAGGTACTGATATTTAGCGGCGTTTATCTT
1 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTATATC
* * ** *
1189606 AAAAATGCCGCAATAGGTGTCAATATTTAGCGGCATTTTTATC
1 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTATATC
**
1189649 ACAAACGCCGCAATAAATGTTGATATTT
1 ACAAACGCCGCAATAGGTGTTGATATTT
1189677 CGTGGTATAT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTATATC
Found at i:1189760 original size:44 final size:43
Alignment explanation
Indices: 1189712--1189871 Score: 198
Period size: 44 Copynumber: 3.7 Consensus size: 43
1189702 GTAATAGGTA
* * *
1189712 TGGTATTTAGCGGCGTTTTTAGGATGCAAATGTCGCAATAAGAC
1 TGGTATATAGCGGCGTTTTTAGGATACAAATGCCGCAATAAG-C
* * *
1189756 TGGTATATAGCGGCGTTTTTAGGATACAAACGCCGCGATAGGCC
1 TGGTATATAGCGGCGTTTTTAGGATACAAATGCCGCAATAAG-C
*
1189800 TGGTATATAGCGGCGTTTTTAGGATACAAATGCCGCTAA-AAGT
1 TGGTATATAGCGGCGTTTTTAGGATACAAATGCCGC-AATAAGC
* *
1189843 TGGTACATAGCGGCGTTTTT-TGATACAAA
1 TGGTATATAGCGGCGTTTTTAGGATACAAA
1189872 CGGCACTAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 8 0.08
43 19 0.19
44 74 0.73
45 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (43 bp):
TGGTATATAGCGGCGTTTTTAGGATACAAATGCCGCAATAAGC
Found at i:1189804 original size:88 final size:86
Alignment explanation
Indices: 1189712--1189873 Score: 236
Period size: 88 Copynumber: 1.9 Consensus size: 86
1189702 GTAATAGGTA
* * * *
1189712 TGGTATTTAGCGGCGTTTTTAGGATGCAAATGTCGC-AATAAGACTGGTATATAGCGGCGTTTTT
1 TGGTATATAGCGGCGTTTTTAGGATACAAATGCCGCTAA-AAG-CTGGTACATAGCGGCGTTTTT
1189776 AGGATACAAACGCCGCGATAGGCC
64 -GGATACAAACGCCGCGATAGGCC
* *
1189800 TGGTATATAGCGGCGTTTTTAGGATACAAATGCCGCTAAAAGTTGGTACATAGCGGCGTTTTTTG
1 TGGTATATAGCGGCGTTTTTAGGATACAAATGCCGCTAAAAGCTGGTACATAGCGGCGTTTTTGG
1189865 ATACAAACG
66 ATACAAACG
1189874 GCACTAAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
86 10 0.15
87 19 0.28
88 36 0.54
89 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (86 bp):
TGGTATATAGCGGCGTTTTTAGGATACAAATGCCGCTAAAAGCTGGTACATAGCGGCGTTTTTGG
ATACAAACGCCGCGATAGGCC
Found at i:1194480 original size:71 final size:71
Alignment explanation
Indices: 1194372--1194515 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
1194362 AAATTTTAAA
1194372 TTTTTTTATATTTTAATTTTTAAAATTTTCTATTAATAATCTATTTCACCCCTAAAATTTTATAA
1 TTTTTTTATATTTTAATTTTTAAAATTTTCTATTAATAATCTATTTCACCCCTAAAATTTTATAA
1194437 ATTCTC
66 ATTCTC
1194443 TTTTTTTATATTTTAATTTTTAAAATTTTCTATTAATAATCTATTTCACCCCTAAAATTTTATAA
1 TTTTTTTATATTTTAATTTTTAAAATTTTCTATTAATAATCTATTTCACCCCTAAAATTTTATAA
1194508 ATTCTC
66 ATTCTC
1194514 TT
1 TT
1194516 AACATAAAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (71 bp):
TTTTTTTATATTTTAATTTTTAAAATTTTCTATTAATAATCTATTTCACCCCTAAAATTTTATAA
ATTCTC
Found at i:1195484 original size:42 final size:42
Alignment explanation
Indices: 1195431--1195527 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
1195421 ATTGTGGTGT
*
1195431 TTTTTTGATACAAACGCTGCAAAAGTTAGATCTATGACGGCA
1 TTTTTTGATACAAACGCCGCAAAAGTTAGATCTATGACGGCA
* * * *
1195473 TTTTTTGATACAAACGCCGCAAAAGTTAGGTCTATGGCTGCG
1 TTTTTTGATACAAACGCCGCAAAAGTTAGATCTATGACGGCA
1195515 TTTTTT-ATACAAA
1 TTTTTTGATACAAA
1195528 TGCCACTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (42 bp):
TTTTTTGATACAAACGCCGCAAAAGTTAGATCTATGACGGCA
Found at i:1197159 original size:41 final size:42
Alignment explanation
Indices: 1197034--1197253 Score: 143
Period size: 41 Copynumber: 5.3 Consensus size: 42
1197024 CAAAAATATT
** * *
1197034 AAACGCCGCTAAATTACTTCTCTA-TAGCGTCGTTTATTG-AA
1 AAACGCCGCTAAATTACCACTCTATTA-CGACGTTTGTTGTAA
* * * * *
1197075 CAAACGCCACTATAA--ACAACACTATCACGATGTTTG-TGTAA
1 -AAACGCCGCTA-AATTACCACTCTATTACGACGTTTGTTGTAA
* *
1197116 AAACGCCGCTAAATTACCACTCTATTACGGCGTTTGTTGAAA
1 AAACGCCGCTAAATTACCACTCTATTACGACGTTTGTTGTAA
* * * * * *
1197158 AAACGCCACT--ATAAGCATATCTATTACGACGTTT-TAGCTAT
1 AAACGCCGCTAAATTACCA-CTCTATTACGACGTTTGTTG-TAA
* *
1197199 AAACGCCGCAAAATTACCACTCTATTACGGCGTTTGTT-TAAA
1 AAACGCCGCTAAATTACCACTCTATTACGACGTTTGTTGT-AA
*
1197241 AAATGCCGCTAAA
1 AAACGCCGCTAAA
1197254 GTATCGTTTT
Statistics
Matches: 133, Mismatches: 33, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
39 2 0.02
40 19 0.14
41 54 0.41
42 50 0.38
43 8 0.06
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (42 bp):
AAACGCCGCTAAATTACCACTCTATTACGACGTTTGTTGTAA
Found at i:1197223 original size:83 final size:82
Alignment explanation
Indices: 1197033--1197243 Score: 257
Period size: 82 Copynumber: 2.6 Consensus size: 82
1197023 ACAAAAATAT
** * * *
1197033 TAAACGCCGCTAAATTACTTCTCTA-TAGCGTCGTTTATTGAACAAACGCCACTATAAACAACAC
1 TAAACGCCGCTAAATTACCACTCTATTA-CGGCGTTTGTTGAAAAAACGCCACTATAAACAACAC
*
1197097 TATCACGATGTTTGTGTA
65 TATCACGACGTTTGTGTA
* * *
1197115 AAAACGCCGCTAAATTACCACTCTATTACGGCGTTTGTTGAAAAAACGCCACTATAAGCATA-TC
1 TAAACGCCGCTAAATTACCACTCTATTACGGCGTTTGTTGAAAAAACGCCACTATAAACA-ACAC
*
1197179 TATTACGACGTTT-TAGCTA
65 TATCACGACGTTTGT-G-TA
* *
1197198 TAAACGCCGCAAAATTACCACTCTATTACGGCGTTTGTTTAAAAAA
1 TAAACGCCGCTAAATTACCACTCTATTACGGCGTTTGTTGAAAAAA
1197244 TGCCGCTAAA
Statistics
Matches: 112, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
81 1 0.01
82 63 0.56
83 48 0.43
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (82 bp):
TAAACGCCGCTAAATTACCACTCTATTACGGCGTTTGTTGAAAAAACGCCACTATAAACAACACT
ATCACGACGTTTGTGTA
Found at i:1197233 original size:42 final size:42
Alignment explanation
Indices: 1197106--1197249 Score: 116
Period size: 42 Copynumber: 3.5 Consensus size: 42
1197096 CTATCACGAT
* *
1197106 GTTTGT-GTAAAAACGCCGCTAAATTACCACTCTATTACGGC
1 GTTTGTAGAAAAAACGCCGCAAAATTACCACTCTATTACGGC
* ** * * * *
1197147 GTTTGTTGAAAAAACG-C-CACTATAAGCATATCTATTACGAC
1 GTTTGTAGAAAAAACGCCGCAAAATTACCA-CTCTATTACGGC
* *
1197188 GTTT-TAGCTATAAACGCCGCAAAATTACCACTCTATTACGGC
1 GTTTGTAG-AAAAAACGCCGCAAAATTACCACTCTATTACGGC
** *
1197230 GTTTGTTTAAAAAATGCCGC
1 GTTTGTAGAAAAAACGCCGC
1197250 TAAAGTATCG
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
40 8 0.11
41 27 0.36
42 32 0.43
43 8 0.11
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (42 bp):
GTTTGTAGAAAAAACGCCGCAAAATTACCACTCTATTACGGC
Found at i:1198669 original size:4 final size:4
Alignment explanation
Indices: 1198660--1198687 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1198650 TTGATCTCTC
1198660 TTCT TTCT TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT
1198688 GGAAGCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:1199116 original size:41 final size:41
Alignment explanation
Indices: 1199006--1199167 Score: 146
Period size: 41 Copynumber: 4.0 Consensus size: 41
1198996 CAAATACCGG
* * * * * *
1199006 TAAATACTCATATTTTAGTGGCATTTTTATATAAATGCTGT
1 TAAATACTCGTACTTTAATGGCGTTTTTATACAAACGCTGT
* * * * * *
1199047 TGAATA-TTGTAATTTAGTGTCTTTTTTATACAAACGCTGT
1 TAAATACTCGTACTTTAATGGCGTTTTTATACAAACGCTGT
* * * *
1199087 TAAATACTCGTACTTTAATGGCGTTTTTATATAAACACCGC
1 TAAATACTCGTACTTTAATGGCGTTTTTATACAAACGCTGT
* * *
1199128 TAAAGACTCGTACTTTAATGGTGTTTTTGTACAAACGCTG
1 TAAATACTCGTACTTTAATGGCGTTTTTATACAAACGCTG
1199168 CAATTTATAA
Statistics
Matches: 96, Mismatches: 24, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
40 32 0.33
41 64 0.67
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.42
Consensus pattern (41 bp):
TAAATACTCGTACTTTAATGGCGTTTTTATACAAACGCTGT
Found at i:1205700 original size:40 final size:40
Alignment explanation
Indices: 1205623--1205702 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
1205613 ATATGTGTAT
* * *
1205623 TCTGGCACTTTATATGTGATTTGGCACCATGTGTGCATTA
1 TCTGGCACTTTATATGTGATTTAGCACCATATATGCATTA
* * * *
1205663 TCTGGCACTTTATGTTTGTTTTAGCACTATATATGCATTA
1 TCTGGCACTTTATATGTGATTTAGCACCATATATGCATTA
1205703 CAAGTTTCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (40 bp):
TCTGGCACTTTATATGTGATTTAGCACCATATATGCATTA
Found at i:1206042 original size:17 final size:18
Alignment explanation
Indices: 1206005--1206042 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1205995 ACAATACAAC
*
1206005 AAAAGAATAGTA-ATTGA
1 AAAAGAATAGTACAGTGA
1206022 AAAAGAATAGTACAGTGA
1 AAAAGAATAGTACAGTGA
1206040 AAA
1 AAA
1206043 TATTAGTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.61, C:0.03, G:0.18, T:0.18
Consensus pattern (18 bp):
AAAAGAATAGTACAGTGA
Found at i:1206451 original size:3 final size:3
Alignment explanation
Indices: 1206443--1206475 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1206433 AATCAGGTAA
1206443 AAT AAT AAT AAGT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
1206476 CGGTTGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.04
3 26 0.93
4 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1210200 original size:12 final size:12
Alignment explanation
Indices: 1210183--1210229 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1210173 TTCATCCATT
1210183 TATTTTTATTTA
1 TATTTTTATTTA
1210195 TATTTTTATTTA
1 TATTTTTATTTA
*
1210207 TGTTATTT-TATTA
1 TATT-TTTAT-TTA
*
1210220 TATTATTATT
1 TATTTTTATT
1210230 AATAAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (12 bp):
TATTTTTATTTA
Found at i:1210220 original size:13 final size:14
Alignment explanation
Indices: 1210186--1210226 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
1210176 ATCCATTTAT
1210186 TTTTATTTATA-T-
1 TTTTATTTATATTA
*
1210198 TTTTATTTATGTTA
1 TTTTATTTATATTA
1210212 TTTTA-TTATATTA
1 TTTTATTTATATTA
1210225 TT
1 TT
1210227 ATTAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.40
13 10 0.40
14 5 0.20
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTTATTTATATTA
Found at i:1211692 original size:22 final size:23
Alignment explanation
Indices: 1211666--1211725 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
1211656 AATTATTATT
1211666 ATTATTTTTTAT-A-TATGTTTAA
1 ATTATTTTTTATGATTAT-TTTAA
*
1211688 ATTATTATTTTCATGATTATTTTAT
1 ATTATT-TTTT-ATGATTATTTTAA
1211713 ATTATTTATTTAT
1 ATTATTT-TTTAT
1211726 TTATTCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
22 6 0.19
23 4 0.12
24 5 0.16
25 14 0.44
26 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (23 bp):
ATTATTTTTTATGATTATTTTAA
Found at i:1212579 original size:16 final size:16
Alignment explanation
Indices: 1212560--1212596 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1212550 CTTTCAAAAT
1212560 TTTTTATTAATTATTA
1 TTTTTATTAATTATTA
*
1212576 TTTTTATTACTTATTA
1 TTTTTATTAATTATTA
1212592 TTTTT
1 TTTTT
1212597 TATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTATTAATTATTA
Found at i:1212623 original size:23 final size:22
Alignment explanation
Indices: 1212561--1212623 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
1212551 TTTCAAAATT
*
1212561 TTTTATTAATTATTAT-TTTTA
1 TTTTATTATTTATTATATTTTA
1212582 TTACTTATTATTT-TT-TATTTTA
1 TT--TTATTATTTATTATATTTTA
1212604 TTTTATTTATTTATTATATT
1 TTTTA-TTATTTATTATATT
1212624 CAAGAATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 3 0.09
21 9 0.26
22 11 0.31
23 12 0.34
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTATTTATTATATTTTA
Found at i:1214246 original size:21 final size:21
Alignment explanation
Indices: 1214216--1214258 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1214206 CATATTTACA
*
1214216 TTTACATTTGCATTTGCATTT
1 TTTACATTTGCATTTACATTT
* *
1214237 TTTACGTTTGTATTTACATTT
1 TTTACATTTGCATTTACATTT
1214258 T
1 T
1214259 CATTTTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.12, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTACATTTGCATTTACATTT
Found at i:1216812 original size:17 final size:18
Alignment explanation
Indices: 1216790--1216831 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1216780 AGCAAAGAAA
*
1216790 GAAAAAAGAAAAAAGA-G
1 GAAAAAAGAAAAAAAAGG
1216807 GAAAAAAGAAAAAAAAGG
1 GAAAAAAGAAAAAAAAGG
1216825 GAAAAAA
1 GAAAAAA
1216832 ATAGAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
GAAAAAAGAAAAAAAAGG
Found at i:1216851 original size:10 final size:10
Alignment explanation
Indices: 1216798--1216875 Score: 84
Period size: 10 Copynumber: 7.4 Consensus size: 10
1216788 AAGAAAAAAG
**
1216798 AAAAAAGAGG
1 AAAAAAGAAA
1216808 AAAAAAGAAA
1 AAAAAAGAAA
*
1216818 AAAAAGGGAAA
1 AAAAA-AGAAA
*
1216829 AAAATAGAAAA
1 AAAAAAG-AAA
1216840 AAAAACAGAAA
1 AAAAA-AGAAA
1216851 AGAAAAAGAAA
1 A-AAAAAGAAA
1216862 AAAAAAGAAA
1 AAAAAAGAAA
1216872 AAAA
1 AAAA
1216876 TTGAATCAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
10 27 0.47
11 25 0.43
12 6 0.10
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1216862 original size:33 final size:32
Alignment explanation
Indices: 1216808--1216875 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
1216798 AAAAAAGAGG
* *
1216808 AAAAAAGAAAAAAAAGGGAAAAAAATAGAAAA
1 AAAAAAGAAAAAAAAGAGAAAAAAAAAGAAAA
1216840 AAAAACAGAAAAGAAAA-AGAAAAAAAAAGAAAA
1 AAAAA-AGAAAA-AAAAGAGAAAAAAAAAGAAAA
1216873 AAA
1 AAA
1216876 TTGAATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 5 0.16
33 23 0.72
34 4 0.12
ACGTcount: A:0.84, C:0.01, G:0.13, T:0.01
Consensus pattern (32 bp):
AAAAAAGAAAAAAAAGAGAAAAAAAAAGAAAA
Found at i:1216870 original size:21 final size:22
Alignment explanation
Indices: 1216809--1216872 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
1216799 AAAAAGAGGA
**
1216809 AAAAAGAAAAAAAAGGGAAAA-
1 AAAAAGAAAAAAAACAGAAAAG
*
1216830 AAATAGAAAAAAAAACAGAAAAG
1 AAAAAG-AAAAAAAACAGAAAAG
1216853 AAAAAGAAAAAAAA-AGAAAA
1 AAAAAGAAAAAAAACAGAAAA
1216873 AAATTGAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.30
22 21 0.57
23 5 0.14
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAAAAACAGAAAAG
Found at i:1221381 original size:54 final size:54
Alignment explanation
Indices: 1221299--1221460 Score: 279
Period size: 54 Copynumber: 3.0 Consensus size: 54
1221289 CAATGATTGA
1221299 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
*
1221353 GAACATCTGAGCAGAAACTACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * **
1221407 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1221461 AAACCTGCTA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 102 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:1221847 original size:22 final size:22
Alignment explanation
Indices: 1221821--1221899 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
1221811 ACATCTACAT
1221821 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1221843 TCTTCAAAGATGATAGATTCCC
1 TCTTCAAAGATGATAGATTCTC
* * * *
1221865 TTTTTAAAGATGACATATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1221887 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1221900 AAGCTTTATC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1222525 original size:113 final size:111
Alignment explanation
Indices: 1222317--1222743 Score: 564
Period size: 113 Copynumber: 3.9 Consensus size: 111
1222307 CTCTTTTGAA
*
1222317 GATCAGCATTTCC-GGAAGAGTTCATAATGAGAAGAACTCATCT-----GAAGAAGAAGTTCATA
1 GATCAGCATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAGTTCATA
* *
1222376 ATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTCGATG
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATG
**
1222422 GATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
1 GATCAGCATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG--AGAAGAAGAAGTTCA
* *
1222487 TAATGAGAAGAACTTATTCAA-CTTTTCGCTCAAATTCATCACTCGATG
64 TAATGAGAAGAACTTGTTCAACCTTTT-GCTCGAATTCATCACTCGATG
**
1222535 GATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
1 GATCAGCATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG--AGAAGAAGAAGTTCA
* *
1222600 TAATGAGAAGAACTTGTTCAACTTTTTGCGT-GAATTCATCATTCGATG
64 TAATGAGAAGAACTTGTTCAACCTTTTGC-TCGAATTCATCACTCGATG
* ** * * * * *
1222648 GATCAGCATTTCCAAAAAAATTTCATAATGAGAAGAACTCATCTGAAGAGGATAATAAGTTCATA
1 GATCAGCATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAGTTCATA
*
1222713 ATGAGAAGAATTTGTTCAACCTTTTGCTCGA
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGA
1222744 CTCTATCGCA
Statistics
Matches: 287, Mismatches: 23, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
105 12 0.04
106 28 0.10
110 1 0.00
111 41 0.14
112 5 0.02
113 195 0.68
114 5 0.02
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28
Consensus pattern (111 bp):
GATCAGCATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATG
Found at i:1223194 original size:12 final size:12
Alignment explanation
Indices: 1223177--1223223 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1223167 TTCATCCATT
1223177 TATTTTTATTTA
1 TATTTTTATTTA
1223189 TATTTTTATTTA
1 TATTTTTATTTA
*
1223201 TGTTATTT-TATTA
1 TATT-TTTAT-TTA
*
1223214 TATTATTATT
1 TATTTTTATT
1223224 AATAAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (12 bp):
TATTTTTATTTA
Found at i:1223214 original size:13 final size:14
Alignment explanation
Indices: 1223180--1223220 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
1223170 ATCCATTTAT
1223180 TTTTATTTATA-T-
1 TTTTATTTATATTA
*
1223192 TTTTATTTATGTTA
1 TTTTATTTATATTA
1223206 TTTTA-TTATATTA
1 TTTTATTTATATTA
1223219 TT
1 TT
1223221 ATTAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.40
13 10 0.40
14 5 0.20
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTTATTTATATTA
Found at i:1224687 original size:22 final size:23
Alignment explanation
Indices: 1224661--1224720 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
1224651 AATTATTATT
1224661 ATTATTTTTTAT-A-TATGTTTAA
1 ATTATTTTTTATGATTAT-TTTAA
*
1224683 ATTATTATTTTCATGATTATTTTAT
1 ATTATT-TTTT-ATGATTATTTTAA
1224708 ATTATTTATTTAT
1 ATTATTT-TTTAT
1224721 TTATTCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
22 6 0.19
23 4 0.12
24 5 0.16
25 14 0.44
26 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (23 bp):
ATTATTTTTTATGATTATTTTAA
Found at i:1227608 original size:26 final size:26
Alignment explanation
Indices: 1227577--1227626 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1227567 TTAATTCTTT
* *
1227577 CTTTTTTATCACAGATATTAGCCTCG
1 CTTTTTTATCACAAATATGAGCCTCG
1227603 CTTTTTTATCACAAATATGAGCCT
1 CTTTTTTATCACAAATATGAGCCT
1227627 TGTTCCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (26 bp):
CTTTTTTATCACAAATATGAGCCTCG
Found at i:1229317 original size:18 final size:19
Alignment explanation
Indices: 1229280--1229317 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1229270 TCTTAAATTT
* *
1229280 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
1229299 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
1229317 T
1 T
1229318 AATTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:1229508 original size:16 final size:16
Alignment explanation
Indices: 1229489--1229528 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1229479 TAAATTTTGG
1229489 TTTCGGTTC-GAGTTAA
1 TTTCGGTTCTG-GTTAA
*
1229505 TTTCGGTTCTGGTTGA
1 TTTCGGTTCTGGTTAA
1229521 TTTCGGTT
1 TTTCGGTT
1229529 TCGCTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.10, C:0.12, G:0.28, T:0.50
Consensus pattern (16 bp):
TTTCGGTTCTGGTTAA
Found at i:1234540 original size:16 final size:16
Alignment explanation
Indices: 1234521--1234553 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1234511 TTTTTTTATT
*
1234521 TTTTTTAAATTTTTTA
1 TTTTTTAAATTATTTA
1234537 TTTTTTAAATTATTTA
1 TTTTTTAAATTATTTA
1234553 T
1 T
1234554 CAAATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTAAATTATTTA
Found at i:1235666 original size:37 final size:36
Alignment explanation
Indices: 1235591--1235666 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1235581 TTTTTATATT
*
1235591 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1235627 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1235664 TTT
1 TTT
1235667 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1235848 original size:20 final size:20
Alignment explanation
Indices: 1235812--1235849 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1235802 ATCCTATTCC
**
1235812 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1235832 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1235850 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1237804 original size:19 final size:19
Alignment explanation
Indices: 1237778--1237859 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 19
1237768 AATATAATAT
1237778 TATT-AAAATTATATTATA
1 TATTAAAAATTATATTATA
*
1237796 TATTAAAAATT-T-TAATA
1 TATTAAAAATTATATTATA
* * *
1237813 -ATTAATATTTTTATTAAATGA
1 TATTAAAAATTATATT--AT-A
1237834 TATTAAAATATTATATTA-A
1 TATTAAAA-ATTATATTATA
1237853 TATTAAA
1 TATTAAA
1237860 TAAATAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
16 8 0.16
17 5 0.10
18 6 0.12
19 14 0.29
20 2 0.04
21 2 0.04
22 6 0.12
23 6 0.12
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
TATTAAAAATTATATTATA
Found at i:1240074 original size:21 final size:21
Alignment explanation
Indices: 1240033--1240074 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1240023 CAGTGATTTT
* *
1240033 TATTTTTCTTGTTCTTTTTAA
1 TATTTTTCTTGTTATTCTTAA
1240054 TATTTTGTCTT-TTATTCTTAA
1 TATTTT-TCTTGTTATTCTTAA
1240075 GTTTTTCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TATTTTTCTTGTTATTCTTAA
Found at i:1241146 original size:28 final size:28
Alignment explanation
Indices: 1241114--1241170 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
1241104 TATAATTGAG
*
1241114 TATATTATTATAATATTAA-AAATACTAT
1 TATATTATTAAAATATTAATAAATA-TAT
1241142 TATATTATTAAAATATTAATAAATATAT
1 TATATTATTAAAATATTAATAAATATAT
1241170 T
1 T
1241171 TTAACTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TATATTATTAAAATATTAATAAATATAT
Found at i:1241663 original size:19 final size:18
Alignment explanation
Indices: 1241634--1241676 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1241624 CGGTCGTGAA
1241634 ATTTTTCTAAATGAATTGAT
1 ATTTTTCTAAA--AATTGAT
*
1241654 -TTTTTTTAAAAATTGAT
1 ATTTTTCTAAAAATTGAT
1241671 ATTTTT
1 ATTTTT
1241677 AAAAATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.33
18 5 0.24
19 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (18 bp):
ATTTTTCTAAAAATTGAT
Found at i:1242160 original size:31 final size:31
Alignment explanation
Indices: 1242111--1242182 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
1242101 AAAAATAAAT
* *
1242111 ATATGATTACTTTCGTTTTTGTTTAATTAAG
1 ATATGATCACTTTCGTTTTTATTTAATTAAG
1242142 ATATGATCACTATT-GTTTTTATTTAATTAAG
1 ATATGATCACT-TTCGTTTTTATTTAATTAAG
1242173 ATATGATCAC
1 ATATGATCAC
1242183 CACGAGTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 36 0.95
32 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (31 bp):
ATATGATCACTTTCGTTTTTATTTAATTAAG
Found at i:1242601 original size:246 final size:246
Alignment explanation
Indices: 1242162--1242660 Score: 908
Period size: 246 Copynumber: 2.0 Consensus size: 246
1242152 TATTGTTTTT
*
1242162 ATTTAATTAAGATATGATCACCACGAGTTAATTGTCGTTAAAAATTATCAAATTAGGTGACGTGC
1 ATTTAATTAAGATATGATCACCACGAGTTAATTGTCGTTAAAAATTATCAAATTAGGTGACGTGA
* *
1242227 TGTTTTGGTATAATCACACATTTAGTCCATGTTATTTATACATTCTCTCAGTTTAGTCATACTTT
66 TATTTTGGTATAATCACACATTTAGTCCATGTTATTTACACATTCTCTCAGTTTAGTCATACTTT
*
1242292 TAATAAATTAAAATAAATTTAATCCTCCAATCGAATGATGTCATGTGTCACAGGTGCCACATGTC
131 TAATAAATTAAAATAAATTTAATCCTCCAATCAAATGATGTCATGTGTCACAGGTGCCACATGTC
1242357 ATGCCATGTGTCACTATTTGATTGGAGAACAAACTTTATTTTAATTTATTA
196 ATGCCATGTGTCACTATTTGATTGGAGAACAAACTTTATTTTAATTTATTA
* *
1242408 ATTTAATTAAGATGTGATCACCACGAGTTAATTGTCGTTAAAAATTATCAAATTAGGTGACGTTA
1 ATTTAATTAAGATATGATCACCACGAGTTAATTGTCGTTAAAAATTATCAAATTAGGTGACGTGA
* *
1242473 TATTTTGGTATAATCACACATTTGGTCCATGTTATTTGCACATTCTCTCAGTTTAGTCATACTTT
66 TATTTTGGTATAATCACACATTTAGTCCATGTTATTTACACATTCTCTCAGTTTAGTCATACTTT
*
1242538 TAATAAATTAAAATAAATTTAATCCTCCAATCAAATGATGTCATGTGTCACAGGTGTCACATGTC
131 TAATAAATTAAAATAAATTTAATCCTCCAATCAAATGATGTCATGTGTCACAGGTGCCACATGTC
*
1242603 GTGCCATGTGTCACTATTTGATTGGAGAACAAACTTTATTTTAATTTATTA
196 ATGCCATGTGTCACTATTTGATTGGAGAACAAACTTTATTTTAATTTATTA
1242654 ATTTAAT
1 ATTTAAT
1242661 AGATTTATTT
Statistics
Matches: 243, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
246 243 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (246 bp):
ATTTAATTAAGATATGATCACCACGAGTTAATTGTCGTTAAAAATTATCAAATTAGGTGACGTGA
TATTTTGGTATAATCACACATTTAGTCCATGTTATTTACACATTCTCTCAGTTTAGTCATACTTT
TAATAAATTAAAATAAATTTAATCCTCCAATCAAATGATGTCATGTGTCACAGGTGCCACATGTC
ATGCCATGTGTCACTATTTGATTGGAGAACAAACTTTATTTTAATTTATTA
Found at i:1244857 original size:20 final size:20
Alignment explanation
Indices: 1244832--1244903 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
1244822 AGGGTGTCAA
1244832 AGTGCATCCATGCACTCTGT
1 AGTGCATCCATGCACTCTGT
1244852 AGTGCATCCATGCA---T-T
1 AGTGCATCCATGCACTCTGT
* *
1244868 A-TGCATCGATGCACCCTG-
1 AGTGCATCCATGCACTCTGT
1244886 ATGTGCATCCATGCACTC
1 A-GTGCATCCATGCACTC
1244904 AAACATCGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.26
16 2 0.05
17 1 0.02
18 2 0.05
20 27 0.63
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (20 bp):
AGTGCATCCATGCACTCTGT
Done.