Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008796.1 Hibiscus syriacus cultivar Beakdansim tig00111941_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: 1607457
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 7 of 7
Found at i:1377554 original size:20 final size:21
Alignment explanation
Indices: 1377531--1377594 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1377521 GAACGGTGGG
1377531 GGGGACTC-TGAGGGATGATA
1 GGGGACTCTTGAGGGATGATA
* * *
1377551 GGGGCCTCTTGAAGGATTG-GA
1 GGGGACTCTTGAGGGA-TGATA
1377572 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGATA
1377593 GG
1 GG
1377595 TGAGTCGGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 9 0.26
21 24 0.69
22 2 0.06
ACGTcount: A:0.22, C:0.11, G:0.45, T:0.22
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGATA
Found at i:1377563 original size:40 final size:41
Alignment explanation
Indices: 1377513--1377594 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 41
1377503 ACGATGACGT
*
1377513 GGCCTCTTGAACGG-TGGGGGGGACTC-TGAGGGATGATAGG
1 GGCCTCTTGAA-GGATGGAGGGGACTCTTGAGGGATGATAGG
1377553 GGCCTCTTGAAGGATTGGAGGGGACTCTTGAGGGATGATAGG
1 GGCCTCTTGAAGGA-TGGAGGGGACTCTTGAGGGATGATAGG
1377595 TGAGTCGGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
39 2 0.05
40 11 0.29
41 11 0.29
42 14 0.37
ACGTcount: A:0.20, C:0.13, G:0.45, T:0.22
Consensus pattern (41 bp):
GGCCTCTTGAAGGATGGAGGGGACTCTTGAGGGATGATAGG
Found at i:1377956 original size:20 final size:20
Alignment explanation
Indices: 1377931--1377983 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1377921 GAAGAATAGT
*
1377931 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
* *
1377951 TTACTTTCACAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
1377971 TGACTATCGCAAC
1 TTACTTTCGCAAC
1377984 GCGGAAATGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:1377984 original size:20 final size:20
Alignment explanation
Indices: 1377937--1378023 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 20
1377927 TAGTTTACTT
* * * *
1377937 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
*
1377957 TCACAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
1377977 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
1377997 TCGCAAAGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
1378016 TCGCAACG
1 TCGCAACG
1378024 ACAAAATCGC
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
19 13 0.24
20 41 0.76
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1378018 original size:19 final size:19
Alignment explanation
Indices: 1377996--1378054 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1377986 GGAAATGGCT
1377996 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
1378015 ATCGC-AA-CG--A-CAAA
1 ATCGCAAAGCGAAATGAAA
*
1378029 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
1378048 ATCGCAA
1 ATCGCAA
1378055 CGACAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 8 0.25
15 2 0.06
16 2 0.06
17 2 0.06
18 3 0.09
19 15 0.47
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:1378031 original size:14 final size:14
Alignment explanation
Indices: 1378012--1378070 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1378002 AAGCGAAATG
1378012 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1378026 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1378045 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1378059 AAAATCGCAACG
1 AAAATCGCAACG
1378071 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1378086 original size:33 final size:33
Alignment explanation
Indices: 1377996--1378075 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1377986 GGAAATGGCT
1377996 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
*
1378029 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
*
1378062 ATCGCAACGCGAAA
1 ATCGCAAAGCGAAA
1378076 CACAAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.49, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
Found at i:1378123 original size:14 final size:14
Alignment explanation
Indices: 1378104--1378162 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1378094 TTTCATTTCG
1378104 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1378118 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
*
1378135 CGCATTGTGATTTTGT
1 CG--TTGCGATTTTGT
1378151 CGTTGCGATTTT
1 CGTTGCGATTTT
1378163 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 17 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 5 0.14
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1378134 original size:33 final size:33
Alignment explanation
Indices: 1378087--1378178 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
1378077 ACAAATCGCA
* *
1378087 TTGCAATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1378120 TTGCGATTTTCATTTCGCATTGTGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1378153 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1378179 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1378177 original size:19 final size:19
Alignment explanation
Indices: 1378082--1378178 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
1378072 GAAACACAAA
*
1378082 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1378101 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1378117 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1378134 TCGCATTGTGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1378150 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1378167 TCGCATTGCGAT
1 TCGCATTGCGAT
1378179 AGCCATTTCC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 11 0.18
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 21 0.35
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1378197 original size:20 final size:19
Alignment explanation
Indices: 1378163--1378216 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
1378153 TTGCGATTTT
*
1378163 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1378182 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1378202 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
1378217 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1378215 original size:19 final size:19
Alignment explanation
Indices: 1378151--1378216 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
1378141 GTGATTTTGT
**
1378151 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
1378170 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1378190 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
1378209 TGTTGCGA
1 CGTTGCGA
1378217 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1378781 original size:18 final size:18
Alignment explanation
Indices: 1378755--1378799 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1378745 GTCGATCAGA
1378755 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
*
1378773 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
1378791 TGATGGCTC
1 TGATGGCTC
1378800 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGG
Found at i:1380414 original size:22 final size:22
Alignment explanation
Indices: 1380387--1380430 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1380377 GATGGAGATA
1380387 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1380409 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1380431 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1380716 original size:41 final size:41
Alignment explanation
Indices: 1380597--1380734 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
1380587 CGCTTTGAAA
* * *
1380597 ATCGCATTGTGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * * * *
1380638 ATTG-AGTTGCGAAATT-AAGTATCGAGTTACGAAAGTCAGT
1 ATCGCA-TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
1380678 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
1380719 ATCGCGTTGCGATTTT
1 ATCGCATTGCGATTTT
1380735 CCAAATTCGC
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
40 31 0.41
41 44 0.59
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1380731 original size:20 final size:20
Alignment explanation
Indices: 1380617--1380730 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
1380607 GATTATGTAT
*
1380617 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
1380637 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
* *
1380657 TATCGAGTTACGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
1380677 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1380698 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1380718 TATCGCGTTGCGA
1 TATCGCGTTGCGA
1380731 TTTTCCAAAT
Statistics
Matches: 73, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
19 3 0.04
20 55 0.75
21 13 0.18
22 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1380750 original size:41 final size:41
Alignment explanation
Indices: 1380671--1380751 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
1380661 GAGTTACGAA
** * *
1380671 AGTCAGTATCGCATTGCGATTTTGTATTATCGCGTTGCGAT
1 AGTCAGTATCGCATTGCGATTTTCAAATATCGCATTGCGAT
*
1380712 AGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCATTGCGA
1 AGTCAGTATCGCATTGCGATTTT-CAAATATCGCATTGCGA
1380752 ATTGGGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
AGTCAGTATCGCATTGCGATTTTCAAATATCGCATTGCGAT
Found at i:1380765 original size:21 final size:20
Alignment explanation
Indices: 1380741--1380793 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
1380731 TTTTCCAAAT
1380741 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
1380762 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
1380783 TCGCATTGCGA
1 TCGCATTGCGA
1380794 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:1381647 original size:2 final size:2
Alignment explanation
Indices: 1381640--1381672 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1381630 ATATTTAAAG
1381640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1381673 GAAGTTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1383322 original size:21 final size:21
Alignment explanation
Indices: 1383296--1383337 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1383286 TTAGAATGGG
*
1383296 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1383317 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1383338 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1383468 original size:19 final size:19
Alignment explanation
Indices: 1383444--1383509 Score: 105
Period size: 19 Copynumber: 3.5 Consensus size: 19
1383434 AGCCTCGGGA
*
1383444 TACTGTTCAAATAGTGATT
1 TACTGTTCAAATAGTAATT
1383463 TACTGTTCAAATAGTAATT
1 TACTGTTCAAATAGTAATT
*
1383482 TACTGTTCAAATAGTAAAT
1 TACTGTTCAAATAGTAATT
*
1383501 TACTATTCA
1 TACTGTTCA
1383510 TAAAACCATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (19 bp):
TACTGTTCAAATAGTAATT
Found at i:1383601 original size:31 final size:32
Alignment explanation
Indices: 1383566--1383633 Score: 97
Period size: 29 Copynumber: 2.2 Consensus size: 32
1383556 ATTTTTGTAA
*
1383566 ATTTTGGATAAATTCAATT-AAGTCCAAATA-C
1 ATTTTGG-TAAATTCAATTCAAGTCCAAAAATC
1383597 ATTTT-GTAAATTCAATTCAAGTCCAAAAATC
1 ATTTTGGTAAATTCAATTCAAGTCCAAAAATC
1383628 ATTTTG
1 ATTTTG
1383634 CCTTAAATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 11 0.33
30 11 0.33
31 11 0.33
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (32 bp):
ATTTTGGTAAATTCAATTCAAGTCCAAAAATC
Found at i:1402441 original size:11 final size:10
Alignment explanation
Indices: 1402424--1402448 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1402414 TGGGTATGCA
1402424 ATTTTTTTTT
1 ATTTTTTTTT
1402434 ATTTTTTTTT
1 ATTTTTTTTT
1402444 ATTTT
1 ATTTT
1402449 CATTAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:1405498 original size:202 final size:202
Alignment explanation
Indices: 1405152--1405555 Score: 772
Period size: 202 Copynumber: 2.0 Consensus size: 202
1405142 GCACCGAACC
1405152 ACTGCCATCCCTAATCAATCCACCTATTCCACCCTTATCCCAACCTTTGACCATTGCACCATCTA
1 ACTGCCATCCCTAATCAATCCACCTATTCCACCCTTATCCCAACCTTTGACCATTGCACCATCTA
**
1405217 CGTTTACTTTTAAGAACCCTTCTGGAGGAGGACTCCACCTAGAAGAAGGTGGAGACCTCTTTTTC
66 CGTTTACTTTTAAGAACCCTTCCAGAGGAGGACTCCACCTAGAAGAAGGTGGAGACCTCTTTTTC
*
1405282 AGATTGTCATTCAAGTCTGCTAGTTTTAAATCCCCCATCAAAGAATCGAAAGGAATATGAACATC
131 AGATTGCCATTCAAGTCTGCTAGTTTTAAATCCCCCATCAAAGAATCGAAAGGAATATGAACATC
1405347 CTTAAAT
196 CTTAAAT
*
1405354 ACTGCCATCTCTAATCAATCCACCTATTCCACCCTTATCCCAACCTTTGACCATTGCACCATCTA
1 ACTGCCATCCCTAATCAATCCACCTATTCCACCCTTATCCCAACCTTTGACCATTGCACCATCTA
1405419 CGTTTACTTTTAAGAACCCTTCCAGAGGAGGACTCCACCTAGAAGAAGGTGGAGACCTCTTTTTC
66 CGTTTACTTTTAAGAACCCTTCCAGAGGAGGACTCCACCTAGAAGAAGGTGGAGACCTCTTTTTC
1405484 AGATTGCCATTCAAGTCTGCTAGTTTTAAATCCCCCATCAAAGAATCGAAAGGAATATGAACATC
131 AGATTGCCATTCAAGTCTGCTAGTTTTAAATCCCCCATCAAAGAATCGAAAGGAATATGAACATC
1405549 CTTAAAT
196 CTTAAAT
1405556 GAAGTTCCAA
Statistics
Matches: 198, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
202 198 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (202 bp):
ACTGCCATCCCTAATCAATCCACCTATTCCACCCTTATCCCAACCTTTGACCATTGCACCATCTA
CGTTTACTTTTAAGAACCCTTCCAGAGGAGGACTCCACCTAGAAGAAGGTGGAGACCTCTTTTTC
AGATTGCCATTCAAGTCTGCTAGTTTTAAATCCCCCATCAAAGAATCGAAAGGAATATGAACATC
CTTAAAT
Found at i:1411373 original size:22 final size:20
Alignment explanation
Indices: 1411346--1411393 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
1411336 TTTATTTGAA
1411346 TTTTATAAATTTAATAATTATT
1 TTTTATAAATTT-ATAA-TATT
**
1411368 TTTTATTTATTTATAATATT
1 TTTTATAAATTTATAATATT
1411388 TTTTAT
1 TTTTAT
1411394 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 4 0.17
22 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATAAATTTATAATATT
Found at i:1411383 original size:21 final size:21
Alignment explanation
Indices: 1411354--1411395 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1411344 AATTTTATAA
1411354 ATTTAATAATTATTTTTTATTT
1 ATTTAATAA-TATTTTTTATTT
1411376 ATTT-ATAATATTTTTTATTT
1 ATTTAATAATATTTTTTATTT
1411396 TTAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
21 4 0.20
22 4 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTAATAATATTTTTTATTT
Found at i:1411394 original size:16 final size:17
Alignment explanation
Indices: 1411354--1411407 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
1411344 AATTTTATAA
*
1411354 ATTTAATAATTATTTTTT
1 ATTT-ATAAATATTTTTT
1411372 ATTTATTTATAATATTTTTT
1 ATTTA--TA-AATATTTTTT
*
1411392 ATTTTTAAATATTTTT
1 ATTTATAAATATTTTT
1411408 GATGACATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 10 0.32
18 6 0.19
19 2 0.06
20 13 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTATAAATATTTTTT
Found at i:1411404 original size:17 final size:20
Alignment explanation
Indices: 1411354--1411407 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 20
1411344 AATTTTATAA
1411354 ATTTAATAATTATTTTTTATTT
1 ATTT-ATAA-TATTTTTTATTT
1411376 ATTTATAATATTTTTTA-TT
1 ATTTATAATATTTTTTATTT
1411395 -TTTA-AATATTTTT
1 ATTTATAATATTTTT
1411408 GATGACATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.28
18 4 0.12
19 2 0.06
20 9 0.28
21 4 0.12
22 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTATAATATTTTTTATTT
Found at i:1411517 original size:5 final size:5
Alignment explanation
Indices: 1411502--1411539 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
1411492 ATGCGGTGTG
1411502 TATTGT TATTT TATTT TATTT TATTT TGATTT T-TTT TA
1 TATT-T TATTT TATTT TATTT TATTT T-ATTT TATTT TA
1411540 ACTTTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.13
5 17 0.57
6 9 0.30
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:1423396 original size:2 final size:2
Alignment explanation
Indices: 1423389--1423430 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1423379 TCTGGTTGGA
1423389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1423431 TCTACTGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1425839 original size:30 final size:29
Alignment explanation
Indices: 1425803--1425914 Score: 179
Period size: 30 Copynumber: 3.8 Consensus size: 29
1425793 TGCTGTTGCT
* *
1425803 ACTTATTTTCCCTTTAATATCTCCTCTGGC
1 ACTTATTTTCCCTTTAATACCT-CTCGGGC
1425833 ACTTATTTTCCCTTTAATACCTTCTCGGGC
1 ACTTATTTTCCCTTTAATACC-TCTCGGGC
1425863 ACTTATTTTCCCTTTAATACCATCTCGGGC
1 ACTTATTTTCCCTTTAATACC-TCTCGGGC
1425893 ACTTATTTTCCCTTTAATACCT
1 ACTTATTTTCCCTTTAATACCT
1425915 TCTGATTTTA
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
29 1 0.01
30 76 0.97
31 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.07, T:0.45
Consensus pattern (29 bp):
ACTTATTTTCCCTTTAATACCTCTCGGGC
Found at i:1427575 original size:63 final size:63
Alignment explanation
Indices: 1427476--1427613 Score: 258
Period size: 63 Copynumber: 2.2 Consensus size: 63
1427466 TAACCTAATT
1427476 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATAACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATAACAATTTACAATGCTAGTTGAA
*
1427539 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATAACAATTTACAATGCTAGTTGAA
*
1427602 TTAACATTATCA
1 TTAGCATTATCA
1427614 AGAAATGACA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATAACAATTTACAATGCTAGTTGAA
Found at i:1427622 original size:41 final size:41
Alignment explanation
Indices: 1427561--1427693 Score: 230
Period size: 41 Copynumber: 3.2 Consensus size: 41
1427551 TTATCAAAAT
1427561 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
* *
1427602 TTAACATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
* *
1427643 TGAGCAGTACCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1427684 TGAGCATTAT
1 TGAGCATTAT
1427694 ACAATACTCA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (41 bp):
TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:1433103 original size:63 final size:63
Alignment explanation
Indices: 1433022--1433159 Score: 249
Period size: 63 Copynumber: 2.2 Consensus size: 63
1433012 TAACCTAATT
*
1433022 TTAGCATTATCATTATCAAAATTGAGCATTGTCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
*
1433085 TTAGTATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
*
1433148 TTAACATTATCA
1 TTAGCATTATCA
1433160 AGAAATGACA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:1433168 original size:41 final size:41
Alignment explanation
Indices: 1433107--1433283 Score: 318
Period size: 41 Copynumber: 4.3 Consensus size: 41
1433097 TTATCAAAAT
1433107 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
* *
1433148 TTAACATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
* *
1433189 TTAGCATTATCAAGAAATGACAATTTACAAAGCTAGTTGAA
1 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1433230 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1433271 TGAGCATTATCAA
1 TGAGCATTATCAA
1433284 CAGTATCTTT
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 130 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (41 bp):
TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:1439403 original size:37 final size:37
Alignment explanation
Indices: 1439319--1439388 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 37
1439309 TAATAAGTTA
*
1439319 AAAAATATTTATATATTTTCTTTAAAAAATTTAAATTC
1 AAAAA-ATTTATATATTTTCTTTAAAAAATTAAAATTC
* *
1439357 ATAAAATTTATA-ATTTT-TTTATAAAATTAAAA
1 AAAAAATTTATATATTTTCTTTAAAAAATTAAAA
1439389 ATATAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 13 0.45
36 5 0.17
37 7 0.24
38 4 0.14
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (37 bp):
AAAAAATTTATATATTTTCTTTAAAAAATTAAAATTC
Found at i:1444379 original size:19 final size:21
Alignment explanation
Indices: 1444357--1444400 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1444347 TAAATTTTTT
1444357 AAAT-AAAAAAATATTT-ATA
1 AAATAAAAAAAATATTTAATA
1444376 AAATAAAAAAAAATATTTAATA
1 AAAT-AAAAAAAATATTTAATA
1444398 AAA
1 AAA
1444401 CTAGTCACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
21 12 0.55
22 6 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAAAAAAATATTTAATA
Found at i:1460360 original size:24 final size:24
Alignment explanation
Indices: 1460328--1460382 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1460318 ATTGACTTCC
1460328 GCAGCTGTTGCAATA-GCAGCAGCT
1 GCAGCTGTTGCAA-AGGCAGCAGCT
* *
1460352 GCTGCTGTTGCAAAGGCTGCAGCT
1 GCAGCTGTTGCAAAGGCAGCAGCT
1460376 GCAGCTG
1 GCAGCTG
1460383 CCAATGTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (24 bp):
GCAGCTGTTGCAAAGGCAGCAGCT
Found at i:1473814 original size:19 final size:20
Alignment explanation
Indices: 1473790--1473829 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1473780 ATAATATAAA
1473790 ATTTT-AAAAAATAATTTTT
1 ATTTTAAAAAAATAATTTTT
1473809 ATTTTAAAAAAATAATTTTT
1 ATTTTAAAAAAATAATTTTT
1473829 A
1 A
1473830 AACCATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTAAAAAAATAATTTTT
Found at i:1474329 original size:2 final size:2
Alignment explanation
Indices: 1474324--1474357 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1474314 AAAATAAAAT
1474324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1474358 AAAGAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1474736 original size:18 final size:20
Alignment explanation
Indices: 1474705--1474741 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1474695 AAATGAATGT
1474705 TTTCAAAGTTTTTG-GTTTA
1 TTTCAAAGTTTTTGTGTTTA
1474724 TTTCAAA-TTTTTGTGTTT
1 TTTCAAAGTTTTTGTGTTT
1474742 TCTTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.62
Consensus pattern (20 bp):
TTTCAAAGTTTTTGTGTTTA
Found at i:1482372 original size:14 final size:15
Alignment explanation
Indices: 1482353--1482385 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1482343 CTTTAACTCA
1482353 TTATTATT-TAAAAT
1 TTATTATTATAAAAT
1482367 TTATTATTGATAAAAT
1 TTATTATT-ATAAAAT
1482383 TTA
1 TTA
1482386 AAAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
16 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATTATTATAAAAT
Found at i:1494153 original size:2 final size:2
Alignment explanation
Indices: 1494148--1494189 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1494138 TATTCAAAGC
1494148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1494190 TCTTTATTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1498195 original size:25 final size:25
Alignment explanation
Indices: 1498157--1498211 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1498147 TACGCCCAAT
*
1498157 TGCCAGCCTCCCAAGAGGGGACCAC
1 TGCCAGCCACCCAAGAGGGGACCAC
*
1498182 TGCCAGCCAGCCAAGAGGGGACCAC
1 TGCCAGCCACCCAAGAGGGGACCAC
1498207 TGCCA
1 TGCCA
1498212 CCTTTATACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.38, G:0.29, T:0.07
Consensus pattern (25 bp):
TGCCAGCCACCCAAGAGGGGACCAC
Found at i:1498708 original size:22 final size:22
Alignment explanation
Indices: 1498666--1498708 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1498656 TAATGGATGA
*
1498666 TTGTTTTTCTTTATGTTCTTAT
1 TTGTTTTTCTTTATGTGCTTAT
1498688 TTGTTTTTC-TTATGGTGCTTA
1 TTGTTTTTCTTTAT-GTGCTTA
1498709 ATGTCTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.09, C:0.09, G:0.14, T:0.67
Consensus pattern (22 bp):
TTGTTTTTCTTTATGTGCTTAT
Found at i:1506252 original size:396 final size:397
Alignment explanation
Indices: 1505520--1506313 Score: 1446
Period size: 396 Copynumber: 2.0 Consensus size: 397
1505510 TGCTCAGAAG
*
1505520 CAAAATTCAGACGTTGTTACACAAATATATGCCACATTTGTTGAAGTGTATGCGGTTCATGGTAT
1 CAAAATTCAGACGATGTTACACAAATATATGCCACATTTGTTGAAGTGTATGCGGTTCATGGTAT
*
1505585 GTCATTATACTTCCATTATGGGTTGGCTCAACAAGTTGATCAAGTTGACAGCCCAACTCAAGTAA
66 GTCATTATACTTCCATTATGGGTTGGCTCAACAAGCTGATCAAGTTGACAGCCCAACTCAAGTAA
* * *
1505650 TGTGTAATGATTTTAAGTCGTTAATGGGAAATCTACATCCTGATACCATTTCATCAAGTTCAATG
131 TGTGTAATGATTTTAAGTCATTAATGGGAAATCCACATCCTGATACCATTCCATCAAGTTCAATG
1505715 GGGAGACATTCATTAGTAACTTGTTACGATCTCTACCGAGGTGGCTCTATGAACAATCTGTATGT
196 GGGAGACATTCATTAGTAACTTGTTACGATCTCTACCGAGGTGGCTCTATGAACAATCTGTATGT
*
1505780 CAACATTGCTTCCAATTTAAGGAGAATGCATTCTTTTACCAATTTCTTTGACCTTAATATGAAGT
261 CAACATTGCTTCCAATTTAAGGAGAATGCATTCTTTTACCAATTTCTTTGACCTTAATATGAAGA
*
1505845 TTCCCTCGACACAACAATATGTTCAGTACCCATTTGACACGATG-CTTCAAGTTCTAGAGGAAGA
326 TGCCCTCGACACAACAATATGTTCAGTACCCATTTGACACGATGCCTTCAAGTTCTAGAGGAAGA
1505909 CATTCAA
391 CATTCAA
* * *
1505916 CAAAATTCAGACGATGTTACACAAATGTATGCCACATTTGTTGAAGTGTCTGTGGTTCATGGTAT
1 CAAAATTCAGACGATGTTACACAAATATATGCCACATTTGTTGAAGTGTATGCGGTTCATGGTAT
*
1505981 GTCATTATACTTCCATTATGGGTTGGCTCAACAAGCTGATCAAGTTGACAGCTCAACTCAAGTAA
66 GTCATTATACTTCCATTATGGGTTGGCTCAACAAGCTGATCAAGTTGACAGCCCAACTCAAGTAA
*
1506046 TGTGTAATGATTTTAAGTCATTAATGGGAAATCCACATCCTGGTACCATTCCATCAAGTTCAATG
131 TGTGTAATGATTTTAAGTCATTAATGGGAAATCCACATCCTGATACCATTCCATCAAGTTCAATG
1506111 GGGAGACATTCATTAGTAACTTGTTACGATCTCTACCGAGGTGGCTCTATGAACAATCTGTATGT
196 GGGAGACATTCATTAGTAACTTGTTACGATCTCTACCGAGGTGGCTCTATGAACAATCTGTATGT
* *
1506176 TAACATTGCTTCCAATTTAAGGAGAATGCATTCTTTTACCAATTTCTTTGACTTTAATATGAAGA
261 CAACATTGCTTCCAATTTAAGGAGAATGCATTCTTTTACCAATTTCTTTGACCTTAATATGAAGA
*
1506241 TGCTCTCGACACAACAATATGTTCAGTACCCATTTGACACGATGCCTTCAAGTTCTAGAGGAAGA
326 TGCCCTCGACACAACAATATGTTCAGTACCCATTTGACACGATGCCTTCAAGTTCTAGAGGAAGA
1506306 CATTCAA
391 CATTCAA
1506313 C
1 C
1506314 TACGAGTTGT
Statistics
Matches: 382, Mismatches: 15, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
396 354 0.93
397 28 0.07
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (397 bp):
CAAAATTCAGACGATGTTACACAAATATATGCCACATTTGTTGAAGTGTATGCGGTTCATGGTAT
GTCATTATACTTCCATTATGGGTTGGCTCAACAAGCTGATCAAGTTGACAGCCCAACTCAAGTAA
TGTGTAATGATTTTAAGTCATTAATGGGAAATCCACATCCTGATACCATTCCATCAAGTTCAATG
GGGAGACATTCATTAGTAACTTGTTACGATCTCTACCGAGGTGGCTCTATGAACAATCTGTATGT
CAACATTGCTTCCAATTTAAGGAGAATGCATTCTTTTACCAATTTCTTTGACCTTAATATGAAGA
TGCCCTCGACACAACAATATGTTCAGTACCCATTTGACACGATGCCTTCAAGTTCTAGAGGAAGA
CATTCAA
Found at i:1509343 original size:18 final size:18
Alignment explanation
Indices: 1509315--1509353 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1509305 TCAAAAATAT
1509315 TATTTTATATA-TTTTAA
1 TATTTTATATATTTTTAA
1509332 TATTTATATATATTTTTAA
1 TATTT-TATATATTTTTAA
1509351 TAT
1 TAT
1509354 CATTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTATATATTTTTAA
Found at i:1509358 original size:12 final size:10
Alignment explanation
Indices: 1509310--1509363 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 10
1509300 AACACTCAAA
1509310 AATATTATTTT
1 AATA-TATTTT
1509321 -ATATATTTT
1 AATATATTTT
*
1509330 AATAT-TTAT
1 AATATATTTT
1509339 -ATATATTTTT
1 AATATA-TTTT
1509349 AATATCATTTT
1 AATAT-ATTTT
1509360 AATA
1 AATA
1509364 AAATATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
8 4 0.11
9 9 0.25
10 10 0.28
11 12 0.33
12 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
AATATATTTT
Found at i:1509588 original size:14 final size:14
Alignment explanation
Indices: 1509554--1509580 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1509544 TTTAATATAT
1509554 AAAATAATATTTTA
1 AAAATAATATTTTA
1509568 AAAATAATATTTT
1 AAAATAATATTTT
1509581 TCTAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATAATATTTTA
Found at i:1512873 original size:28 final size:28
Alignment explanation
Indices: 1512833--1512890 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1512823 CTTTATATTG
1512833 TTTTTTCTTGCTGAAGAGTTCTACTTGT
1 TTTTTTCTTGCTGAAGAGTTCTACTTGT
1512861 TTTTTTCTTGCTGAAGAGTTCTACTTGT
1 TTTTTTCTTGCTGAAGAGTTCTACTTGT
1512889 TT
1 TT
1512891 ATAATCATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (28 bp):
TTTTTTCTTGCTGAAGAGTTCTACTTGT
Found at i:1513288 original size:225 final size:226
Alignment explanation
Indices: 1512895--1513351 Score: 898
Period size: 225 Copynumber: 2.0 Consensus size: 226
1512885 TTGTTTATAA
1512895 TCATGTCTGGAAGTTGCATCATAGTATGATACGCATTGATCGAGATCGATGCTTTTTTACTCGTG
1 TCATGTCTGGAAGTTGCATCATAGTATGATAC-CATTGATCGAGATCGATGCTTTTTTACTCGTG
1512960 ATATGGCCTATTTTCTATTACAGTATTTACATCAGTATGTTGGAGCATGATAATTGATCTAATTT
65 ATATGGCCTATTTTCTATTACAGTATTTACATCAGTATGTTGGAGCATGATAATTGATCTAATTT
1513025 ACTACGAAAATACTTCCTAATAGTGAGTTTTAAATTTATCTGAGTGTTATTTCTGTCAAGGGAAT
130 ACTACGAAAATACTTCCTAATAGTGAGTTTTAAATTTATCTGAGTGTTATTTCTGTCAAGGGAAT
1513090 GTCTAATTTCTCAAAGCCTGCAAGATATCTCT
195 GTCTAATTTCTCAAAGCCTGCAAGATATCTCT
1513122 TCATGTCTGGAAGTTGCATCATAGTATGATA-CATTGATCGAGATCGATGCTTTTTTACTCGTGA
1 TCATGTCTGGAAGTTGCATCATAGTATGATACCATTGATCGAGATCGATGCTTTTTTACTCGTGA
1513186 TATGGCCTATTTTCTATTACAGTATTTACATCAGTATGTTGGAGCATGATAATTGATCTAATTTA
66 TATGGCCTATTTTCTATTACAGTATTTACATCAGTATGTTGGAGCATGATAATTGATCTAATTTA
1513251 CTACGAAAATACTTCCTAATAGTGAGTTTTAAATTTATCTGAGTGTTATTTCTGTCAAGGGAATG
131 CTACGAAAATACTTCCTAATAGTGAGTTTTAAATTTATCTGAGTGTTATTTCTGTCAAGGGAATG
1513316 TCTAATTTCTCAAAGCCTGCAAGATATCTCT
196 TCTAATTTCTCAAAGCCTGCAAGATATCTCT
1513347 TCATG
1 TCATG
1513352 GAAATTCAGA
Statistics
Matches: 230, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
225 199 0.87
227 31 0.13
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (226 bp):
TCATGTCTGGAAGTTGCATCATAGTATGATACCATTGATCGAGATCGATGCTTTTTTACTCGTGA
TATGGCCTATTTTCTATTACAGTATTTACATCAGTATGTTGGAGCATGATAATTGATCTAATTTA
CTACGAAAATACTTCCTAATAGTGAGTTTTAAATTTATCTGAGTGTTATTTCTGTCAAGGGAATG
TCTAATTTCTCAAAGCCTGCAAGATATCTCT
Found at i:1517009 original size:68 final size:68
Alignment explanation
Indices: 1516900--1517038 Score: 260
Period size: 68 Copynumber: 2.0 Consensus size: 68
1516890 CATTTTTTTA
1516900 TTACTAAATGACGTACATTTAATGCGATGTTGATACAGCACAAATGTAATAACCCTCGATGATAC
1 TTACTAAATGACGTACATTTAATGCGATGTTGATACAGCACAAATGTAATAACCCTCGATGATAC
1516965 TTT
66 TTT
* *
1516968 TTACTAAATGACTTACATTTAATGCGATGTTGATACAGCACAAATGTAATAACCCTTGATGATAC
1 TTACTAAATGACGTACATTTAATGCGATGTTGATACAGCACAAATGTAATAACCCTCGATGATAC
1517033 TTT
66 TTT
1517036 TTA
1 TTA
1517039 TAATTGCAGG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (68 bp):
TTACTAAATGACGTACATTTAATGCGATGTTGATACAGCACAAATGTAATAACCCTCGATGATAC
TTT
Found at i:1519885 original size:76 final size:76
Alignment explanation
Indices: 1519759--1519912 Score: 281
Period size: 76 Copynumber: 2.0 Consensus size: 76
1519749 AATGGCACGG
* *
1519759 AAAGACAGGGGCAAAGATTAAACTATGATTGAAGTTACAATTCTAACAAATGATACCATCAAAGT
1 AAAGACAGAGGCAAAGATTAAACTATGATTGAAGTTACAATTCTAACAAATGATACCATCAAAGC
1519824 ATACAACTTGC
66 ATACAACTTGC
1519835 AAAGACAGAGGCAAAGATTAAACTATGATTGAAGTTACAATTCTAACAAATGATACCATCAAAGC
1 AAAGACAGAGGCAAAGATTAAACTATGATTGAAGTTACAATTCTAACAAATGATACCATCAAAGC
*
1519900 ATACAATTTGC
66 ATACAACTTGC
1519911 AA
1 AA
1519913 TAATTTGGTA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (76 bp):
AAAGACAGAGGCAAAGATTAAACTATGATTGAAGTTACAATTCTAACAAATGATACCATCAAAGC
ATACAACTTGC
Found at i:1521497 original size:31 final size:32
Alignment explanation
Indices: 1521454--1521524 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
1521444 AATATGTAAA
*
1521454 ATTTTAAT-AATAT-TTAAAAATAATTT-ACT-T
1 ATTTTATTAAATATATT-AAAAT-ATTTAACTGT
*
1521484 ATTTTATTAAATATATTTAAATATTTAACTGT
1 ATTTTATTAAATATATTAAAATATTTAACTGT
1521516 ATTTTATTA
1 ATTTTATTA
1521525 TTATTATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 11 0.31
31 12 0.34
32 12 0.34
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (32 bp):
ATTTTATTAAATATATTAAAATATTTAACTGT
Found at i:1521527 original size:3 final size:3
Alignment explanation
Indices: 1521515--1521573 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
1521505 TATTTAACTG
1521515 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1521562 TAT TAT TAT TAT
1 TAT TAT TAT TAT
1521574 AACAAATCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1523435 original size:27 final size:27
Alignment explanation
Indices: 1523397--1523451 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1523387 GGCTCATACT
1523397 TGTAGTCCTCAGTTTGTTATTGGTAGA
1 TGTAGTCCTCAGTTTGTTATTGGTAGA
1523424 TGTAGTCCTCAGTTTGTTATTGGTAGA
1 TGTAGTCCTCAGTTTGTTATTGGTAGA
1523451 T
1 T
1523452 CAGTTACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.45
Consensus pattern (27 bp):
TGTAGTCCTCAGTTTGTTATTGGTAGA
Found at i:1525611 original size:2 final size:2
Alignment explanation
Indices: 1525604--1525639 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1525594 CCGATTAGTT
1525604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1525640 ATGGATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1526659 original size:18 final size:18
Alignment explanation
Indices: 1526617--1526660 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1526607 GACTGCCTTC
*
1526617 AGATGAGCCGCAGGGTGT
1 AGATGATCCGCAGGGTGT
1526635 AGATGATCCGCAGGGTGT
1 AGATGATCCGCAGGGTGT
1526653 AGATGATC
1 AGATGATC
1526661 AGGAACTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.39, T:0.20
Consensus pattern (18 bp):
AGATGATCCGCAGGGTGT
Found at i:1532176 original size:18 final size:18
Alignment explanation
Indices: 1532139--1532176 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1532129 AATACATTTC
**
1532139 TTTAAAATGATACCTTTG
1 TTTAAAATGATACCGATG
1532157 TTTAAAATGATACCGATG
1 TTTAAAATGATACCGATG
1532175 TT
1 TT
1532177 GGTCGTCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (18 bp):
TTTAAAATGATACCGATG
Found at i:1532614 original size:39 final size:39
Alignment explanation
Indices: 1532560--1532639 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
1532550 ATCGTTTGGC
1532560 TGCTTTGTTTTCTTTTATGCTTGTGGAAACCTTAGGTGT
1 TGCTTTGTTTTCTTTTATGCTTGTGGAAACCTTAGGTGT
1532599 TGCTTTGTTTTCTTTTATGCTTGTGGAAACCTTAGGTGT
1 TGCTTTGTTTTCTTTTATGCTTGTGGAAACCTTAGGTGT
1532638 TG
1 TG
1532640 AATCGGTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.51
Consensus pattern (39 bp):
TGCTTTGTTTTCTTTTATGCTTGTGGAAACCTTAGGTGT
Found at i:1533642 original size:34 final size:35
Alignment explanation
Indices: 1533604--1533670 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 35
1533594 TGTATGAACC
* *
1533604 ATATATATGCA-TATCTTGTGCTCTACGTATGTGA
1 ATATATATACACTACCTTGTGCTCTACGTATGTGA
1533638 ATATATATACACGTACCTTGTGCTCTACGTATG
1 ATATATATACAC-TACCTTGTGCTCTACGTATG
1533671 GATGCTGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 10 0.34
36 19 0.66
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (35 bp):
ATATATATACACTACCTTGTGCTCTACGTATGTGA
Found at i:1538637 original size:20 final size:20
Alignment explanation
Indices: 1538591--1538638 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1538581 ATTCGCTACA
*
1538591 ATCGATACTAACCCTTCAGT
1 ATCGATACTAACCCTTCAAT
* *
1538611 ATTGATACTGAA-CCTTGAAT
1 ATCGATACT-AACCCTTCAAT
1538631 ATCGATAC
1 ATCGATAC
1538639 CCATATGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (20 bp):
ATCGATACTAACCCTTCAAT
Found at i:1541663 original size:79 final size:79
Alignment explanation
Indices: 1541527--1541707 Score: 335
Period size: 79 Copynumber: 2.3 Consensus size: 79
1541517 TAAAGAAATT
* *
1541527 AATAATTCAAATATTAATAATTATATATAAAGGAATTATTATAATGAATTTTGCATTACTTAATC
1 AATAATTCAAATATTAATAATTATATATAAAGAAATTATTATAATGAATTTTACATTACTTAATC
1541592 TAAATTAGTCAATC
66 TAAATTAGTCAATC
*
1541606 AATAATTCAAATATTAATAATTATCTATAAAGAAATTATTATAATGAATTTTACATTACTTAATC
1 AATAATTCAAATATTAATAATTATATATAAAGAAATTATTATAATGAATTTTACATTACTTAATC
1541671 TAAATTAGTCAATC
66 TAAATTAGTCAATC
1541685 AATAATTCAAATATTAATAATTA
1 AATAATTCAAATATTAATAATTA
1541708 GGGTAAAATA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 99 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (79 bp):
AATAATTCAAATATTAATAATTATATATAAAGAAATTATTATAATGAATTTTACATTACTTAATC
TAAATTAGTCAATC
Found at i:1543071 original size:14 final size:14
Alignment explanation
Indices: 1543052--1543079 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1543042 TTAGAGATTA
1543052 TTTATATATTTTAC
1 TTTATATATTTTAC
1543066 TTTATATATTTTAC
1 TTTATATATTTTAC
1543080 CCTAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTATATATTTTAC
Found at i:1544384 original size:17 final size:18
Alignment explanation
Indices: 1544364--1544397 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1544354 TTTATAAGGT
1544364 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
1544381 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
1544398 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:1544428 original size:20 final size:20
Alignment explanation
Indices: 1544405--1544446 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1544395 TTTTATTTAA
* *
1544405 TTATTGTATTATTTAATTAT
1 TTATTATATTATTTAAATAT
*
1544425 TTATTATTTTATTTAAATAT
1 TTATTATATTATTTAAATAT
1544445 TT
1 TT
1544447 TATTTTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTATATTATTTAAATAT
Found at i:1544435 original size:8 final size:8
Alignment explanation
Indices: 1544365--1544437 Score: 60
Period size: 8 Copynumber: 9.1 Consensus size: 8
1544355 TTATAAGGTA
1544365 TATTTTAT
1 TATTTTAT
*
1544373 TATATTTAA
1 TAT-TTTAT
*
1544382 TATTTTGT
1 TATTTTAT
*
1544390 TAGTATT-T
1 TA-TTTTAT
*
1544398 TATTTAAT
1 TATTTTAT
*
1544406 TATTGTAT
1 TATTTTAT
*
1544414 TATTTAAT
1 TATTTTAT
1544422 TA-TTTAT
1 TATTTTAT
1544429 TATTTTAT
1 TATTTTAT
1544437 T
1 T
1544438 TAAATATTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
7 8 0.16
8 32 0.64
9 10 0.20
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (8 bp):
TATTTTAT
Found at i:1544435 original size:16 final size:16
Alignment explanation
Indices: 1544397--1544433 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1544387 TGTTAGTATT
1544397 TTATTTAATTATTGTA
1 TTATTTAATTATTGTA
1544413 TTATTTAATTATT-TA
1 TTATTTAATTATTGTA
1544428 TTATTT
1 TTATTT
1544434 TATTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTATTTAATTATTGTA
Found at i:1544529 original size:13 final size:13
Alignment explanation
Indices: 1544508--1544568 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
1544498 ATTTTGTTAG
1544508 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
1544521 TATTGTA-TTATT
1 TATTTTATTTAAT
*
1544533 TAATTTT-TTTTAT
1 T-ATTTTATTTAAT
*
1544546 TATTTTATTTAAA
1 TATTTTATTTAAT
1544559 TATTTTATTT
1 TATTTTATTT
1544569 CTTTACAGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
12 10 0.26
13 28 0.74
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:1544548 original size:17 final size:17
Alignment explanation
Indices: 1544512--1544556 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1544502 TGTTAGTATT
1544512 TTATTTAA-TTATTGTA
1 TTATTTAATTTATTGTA
* *
1544528 TTATTTAATTTTTTTTA
1 TTATTTAATTTATTGTA
*
1544545 TTATTTTATTTA
1 TTATTTAATTTA
1544557 AATATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTAATTTATTGTA
Found at i:1544553 original size:38 final size:39
Alignment explanation
Indices: 1544490--1544567 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
1544480 TACTTCGTTA
*
1544490 TATTTAATATTTTGTTAGTATTTTATTTAATTATTGTAT
1 TATTTAATATTTTGTTAGTATTTTATTTAAATATTGTAT
* * *
1544529 TATTTAAT-TTTTTTTATTATTTTATTTAAATATTTTAT
1 TATTTAATATTTTGTTAGTATTTTATTTAAATATTGTAT
1544567 T
1 T
1544568 TCTTTACAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 27 0.77
39 8 0.23
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (39 bp):
TATTTAATATTTTGTTAGTATTTTATTTAAATATTGTAT
Found at i:1544604 original size:117 final size:115
Alignment explanation
Indices: 1544372--1544666 Score: 475
Period size: 117 Copynumber: 2.5 Consensus size: 115
1544362 GTATATTTTA
1544372 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTATTTATTATTTTAT
1 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTATTTATTATTTTAT
* ** *
1544437 TTAAATATTTTATTTTTTTGTAGTTATAAAATGGAAAGCGGTCTACTTCG
66 TTAAATATTTTATTTCTTTACAGTTATAAAATGGAAAGCGGTATACTTCG
*
1544487 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTTTTTTTATTATTTT
1 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAA--TTATTTATTATTTT
**
1544552 ATTTAAATATTTTATTTCTTTACAGTTATAAAATGGAAAGCGGTATGTTTCG
64 ATTTAAATATTTTATTTCTTTACAGTTATAAAATGGAAAGCGGTATACTTCG
* *
1544604 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATT-TTTTATTATTTTATTTTTTT
1 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTA-TTTATTATTTT
1544667 GCAGTTATAA
Statistics
Matches: 167, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
114 2 0.01
115 59 0.35
116 4 0.02
117 102 0.61
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (115 bp):
TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTATTTATTATTTTAT
TTAAATATTTTATTTCTTTACAGTTATAAAATGGAAAGCGGTATACTTCG
Found at i:1544656 original size:15 final size:15
Alignment explanation
Indices: 1544636--1544665 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1544626 ATTTTATTTA
1544636 ATTATTGTATTTTTT
1 ATTATTGTATTTTTT
*
1544651 ATTATTTTATTTTTT
1 ATTATTGTATTTTTT
1544666 TGCAGTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTATTGTATTTTTT
Found at i:1545406 original size:14 final size:15
Alignment explanation
Indices: 1545387--1545428 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1545377 TTAAAAATTA
1545387 TTAATAAATAT-GTT
1 TTAATAAATATAGTT
*
1545401 TTAATAATTAATAGTT
1 TTAATAAAT-ATAGTT
*
1545417 TTTATAAATATA
1 TTAATAAATATA
1545429 TATATTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 8 0.35
15 5 0.22
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (15 bp):
TTAATAAATATAGTT
Found at i:1555471 original size:18 final size:19
Alignment explanation
Indices: 1555448--1555490 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1555438 CAGCAGCACA
*
1555448 TAACTGCTC-TTAACAAGC
1 TAACTGCTCGTTAACAAAC
1555466 TAACTGCTCGTTTAACAAAC
1 TAACTGCTCG-TTAACAAAC
1555486 TAACT
1 TAACT
1555491 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (19 bp):
TAACTGCTCGTTAACAAAC
Found at i:1557500 original size:63 final size:63
Alignment explanation
Indices: 1557396--1557519 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 63
1557386 TATTAATCAT
*
1557396 CTCGTCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
1 CTCGGCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
* * *
1557459 CTCGGCTTCATTATGTACTT-CTGCATTAC-CATCTTCTTCATGCACGGTGGTGGTATTTGGT
1 CTCGGCTTCATTATG-AATTGCTGCATTACTCA-CTTCTTCATGCACGGTGATGATATTTGGT
1557520 AACTGACTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.91
64 3 0.05
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (63 bp):
CTCGGCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
Found at i:1560100 original size:18 final size:19
Alignment explanation
Indices: 1560077--1560119 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1560067 CAGCAGCACA
*
1560077 TAACTGCTC-TTAACAAGC
1 TAACTGCTCGTTAACAAAC
1560095 TAACTGCTCGTTTAACAAAC
1 TAACTGCTCG-TTAACAAAC
1560115 TAACT
1 TAACT
1560120 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (19 bp):
TAACTGCTCGTTAACAAAC
Found at i:1567102 original size:20 final size:21
Alignment explanation
Indices: 1567077--1567117 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1567067 GTCATGATGG
*
1567077 AAGA-GGAATTAGGGTTGAAA
1 AAGAGGGAATTAGGGATGAAA
*
1567097 AAGAGGGAATTGGGGATGAAA
1 AAGAGGGAATTAGGGATGAAA
1567118 TCGATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.17
Consensus pattern (21 bp):
AAGAGGGAATTAGGGATGAAA
Found at i:1578382 original size:20 final size:20
Alignment explanation
Indices: 1578354--1578465 Score: 161
Period size: 20 Copynumber: 5.5 Consensus size: 20
1578344 TTCCTAATTT
1578354 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* ** *
1578374 GCAACGCGAATTTGGAAAATC
1 GCAATGCGAA-TACGTAAATC
1578395 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
1578415 ACAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
1578435 GCAATGCGAATACGTAAATT
1 GCAATGCGAATACGTAAATC
1578455 GCAATGCGAAT
1 GCAATGCGAAT
1578466 CTGACTATCG
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 64 0.80
21 16 0.20
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:1578476 original size:40 final size:39
Alignment explanation
Indices: 1578354--1578480 Score: 157
Period size: 40 Copynumber: 3.2 Consensus size: 39
1578344 TTCCTAATTT
* *
1578354 GCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATC
1 GCAATGCGAATACGTAAATCGCAATGCGAATCT-G-AAATC
*
1578395 GCAATGCGAATACGTAAATCACAATGCGAATAC-GTAAATC
1 GCAATGCGAATACGTAAATCGCAATGCGAAT-CTG-AAATC
* *
1578435 GCAATGCGAATACGTAAATTGCAATGCGAATCTGACTATC
1 GCAATGCGAATACGTAAATCGCAATGCGAATCTGA-AATC
1578475 GCAATG
1 GCAATG
1578481 TGATTTACAT
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.03
40 45 0.59
41 29 0.38
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (39 bp):
GCAATGCGAATACGTAAATCGCAATGCGAATCTGAAATC
Found at i:1578686 original size:22 final size:22
Alignment explanation
Indices: 1578661--1578726 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1578651 GGCGACATCC
1578661 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1578683 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
1578705 GTCTCCATCTCCGACAAAATCA
1 GTCCCCATCTCCGACGAAATCA
1578727 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.27, C:0.39, G:0.12, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1579108 original size:20 final size:20
Alignment explanation
Indices: 1579083--1579129 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1579073 GATTCTTGCA
1579083 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
1579103 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
1579123 TTGCGAT
1 TTGCGAT
1579130 TTAAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:1581043 original size:20 final size:20
Alignment explanation
Indices: 1581018--1581194 Score: 157
Period size: 20 Copynumber: 9.5 Consensus size: 20
1581008 AATAGTTTAT
1581018 TATCGCAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
* *
1581038 TATCGCAACGTGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
1581058 TATCGCAA--CG-AGA-GA-
1 TATCGCAATGCGAAAATGAC
*
1581073 -ATCGCAATGCG-AAATGAA
1 TATCGCAATGCGAAAATGAC
*
1581091 AATCGCAA--C-AACAA--A-
1 TATCGCAATGCGAA-AATGAC
*
1581106 -ATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
1581125 TATCGCAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
1581145 TATCGTAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
** *
1581165 TATCGCAATGCGAATTTGAT
1 TATCGCAATGCGAAAATGAC
1581185 TATCGCAATG
1 TATCGCAATG
1581195 AAAGAATCGC
Statistics
Matches: 132, Mismatches: 11, Indels: 28
0.77 0.06 0.16
Matches are distributed among these distances:
14 14 0.11
16 10 0.08
17 8 0.06
18 4 0.03
19 7 0.05
20 89 0.67
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
TATCGCAATGCGAAAATGAC
Found at i:1581375 original size:20 final size:20
Alignment explanation
Indices: 1581239--1581365 Score: 173
Period size: 20 Copynumber: 6.3 Consensus size: 20
1581229 GATTCTCTCG
* **
1581239 TTGCGATAGTTAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* **
1581259 CTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1581279 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
1581299 TTGCGATATTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1581319 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1581339 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1581359 TTGCGAT
1 TTGCGAT
1581366 TTTAAGTTTC
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1581922 original size:21 final size:20
Alignment explanation
Indices: 1581850--1581947 Score: 72
Period size: 21 Copynumber: 4.7 Consensus size: 20
1581840 ACTCACCTGT
*
1581850 CATCATTCAAGAGGCCTCC-C
1 CATCGTTCAAGAGGCC-CCTC
*
1581870 CTATCGTTCAAGAGGCCCCTAT
1 C-ATCGTTCAAGAGGCCCCT-C
** *
1581892 CATCCCTCAAGAGTCCCCTC
1 CATCGTTCAAGAGGCCCCTC
* *
1581912 CAATCGTTCAAGAGGCCACTGT
1 C-ATCGTTCAAGAGGCCCCT-C
*
1581934 CATCGTTGAAGAGG
1 CATCGTTCAAGAGG
1581948 TCCGTCCCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
20 4 0.07
21 55 0.90
22 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.22
Consensus pattern (20 bp):
CATCGTTCAAGAGGCCCCTC
Found at i:1581946 original size:42 final size:42
Alignment explanation
Indices: 1581846--1581947 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
1581836 CCAGACTCAC
* *
1581846 CTGTCATCATTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCATTCAAGAGGCCTCCCCAATCGTTCAAGAGGCCA
* ** *
1581888 CTATCATCCCTCAAGAGTCC-CCTCCAATCGTTCAAGAGGCCA
1 CTGTCATCATTCAAGAGGCCTCC-CCAATCGTTCAAGAGGCCA
* *
1581930 CTGTCATCGTTGAAGAGG
1 CTGTCATCATTCAAGAGG
1581948 TCCGTCCCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 2 0.04
42 46 0.96
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (42 bp):
CTGTCATCATTCAAGAGGCCTCCCCAATCGTTCAAGAGGCCA
Found at i:1583526 original size:33 final size:34
Alignment explanation
Indices: 1583481--1583556 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
1583471 GGAAATGACT
*
1583481 ATCGCAATGAGAGAATCACAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCACAATGCGAAAATGAAA
* *
1583514 ATTGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCACAATGCGAAAATGAAA
1583548 ATCGCAACG
1 ATCGCAACG
1583557 CGAAACTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCACAATGCGAAAATGAAA
Found at i:1583628 original size:33 final size:34
Alignment explanation
Indices: 1583571--1583642 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
1583561 ACTAAATTCG
*
1583571 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCAATTCACT
*
1583605 CGTTGCGATTTTCA-TTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCAATTCACT
1583638 CGTTG
1 CGTTG
1583643 TGATAGTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 22 0.61
34 14 0.39
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCAATTCACT
Found at i:1583653 original size:33 final size:33
Alignment explanation
Indices: 1583571--1583655 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
1583561 ACTAAATTCG
** *
1583571 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATAGTCA-TTTCGCATTGCAATTCACT
** *
1583605 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATAGTCATTTCGCATTGCAATTCACT
*
1583638 CGTTGTGATAGTCATTTC
1 CGTTGCGATAGTCATTTC
1583656 CGCGTAGCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 32 0.70
34 14 0.30
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCATTGCAATTCACT
Found at i:1583706 original size:20 final size:20
Alignment explanation
Indices: 1583645--1583712 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
1583635 TCTCGTTGTG
*
1583645 ATAGTCATTTCCGCG-TAGCG
1 ATAGTCATTTCCGCGTTA-CA
* *
1583665 ATAGTCAATTCCGCGTTGCA
1 ATAGTCATTTCCGCGTTACA
*
1583685 ATAGTCATTTCCGTGTTACA
1 ATAGTCATTTCCGCGTTACA
1583705 ATAGTCAT
1 ATAGTCAT
1583713 ATTTGCGTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 40 0.98
21 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (20 bp):
ATAGTCATTTCCGCGTTACA
Found at i:1586190 original size:24 final size:24
Alignment explanation
Indices: 1586156--1586209 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1586146 CTAAAAAATC
1586156 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1586180 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1586204 ATCAAA
1 ATCAAA
1586210 TTTTGAATAC
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:1587112 original size:20 final size:20
Alignment explanation
Indices: 1587037--1587144 Score: 119
Period size: 20 Copynumber: 5.4 Consensus size: 20
1587027 GAAATTCAGT
* *
1587037 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGATTCGC
* * * *
1587057 GTTGCGATAGTCAAAATCTC
1 ATTGCGATAGTCAGATTCGC
*
1587077 GTTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGATTCGC
1587097 ATTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGATTCGC
* *
1587117 ATTGCGAT-TTACATATTCGC
1 ATTGCGATAGT-CAGATTCGC
1587137 ATTGCGAT
1 ATTGCGAT
1587145 TTACGTATTC
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
19 1 0.01
20 78 0.99
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (20 bp):
ATTGCGATAGTCAGATTCGC
Found at i:1587145 original size:20 final size:20
Alignment explanation
Indices: 1587111--1587244 Score: 178
Period size: 20 Copynumber: 6.7 Consensus size: 20
1587101 CGATAGTCAG
*
1587111 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
1587131 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1587151 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1587171 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1587191 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
1587212 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1587232 ATTCACATTGCGA
1 ATTCGCATTGCGA
1587245 ATTAGGAAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 82 0.85
21 15 0.15
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1587269 original size:21 final size:21
Alignment explanation
Indices: 1587241--1587328 Score: 149
Period size: 21 Copynumber: 4.2 Consensus size: 21
1587231 TATTCACATT
1587241 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
1587262 GTGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
1587283 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1587304 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1587325 GCGA
1 GCGA
1587329 TAGTCAGAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1587767 original size:14 final size:14
Alignment explanation
Indices: 1587718--1587767 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1587708 AGAGATGAAC
1587718 AAATAATTATTAAA
1 AAATAATTATTAAA
*
1587732 TAATTAA--ATTAAA
1 -AAATAATTATTAAA
*
1587745 ATATAATTATTAAA
1 AAATAATTATTAAA
*
1587759 AAATCATTA
1 AAATAATTA
1587768 CATAATTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 13 0.46
15 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATAATTATTAAA
Found at i:1590453 original size:45 final size:45
Alignment explanation
Indices: 1590387--1590490 Score: 190
Period size: 45 Copynumber: 2.3 Consensus size: 45
1590377 AGAGAACCCT
1590387 TAGAAACTTGGTAATTCTATTTCTATTTTTGTGCAAATAGACATG
1 TAGAAACTTGGTAATTCTATTTCTATTTTTGTGCAAATAGACATG
* *
1590432 TTGAAACTCGGTAATTCTATTTCTATTTTTGTGCAAATAGACATG
1 TAGAAACTTGGTAATTCTATTTCTATTTTTGTGCAAATAGACATG
1590477 TAGAAACTTGGTAA
1 TAGAAACTTGGTAA
1590491 CATATTCCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (45 bp):
TAGAAACTTGGTAATTCTATTTCTATTTTTGTGCAAATAGACATG
Found at i:1595547 original size:20 final size:20
Alignment explanation
Indices: 1595522--1595575 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1595512 AATTGGGAAA
1595522 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1595542 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
1595562 ATCGCAATGCGATA
1 ATCGCAATGCGATA
1595576 ATACAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1596196 original size:18 final size:18
Alignment explanation
Indices: 1596137--1596216 Score: 78
Period size: 18 Copynumber: 4.5 Consensus size: 18
1596127 TTCGAGAATG
1596137 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGC-GAAAT
* *
1596156 AACTATCGCAA--CGAGAT
1 AA-AATCGCAACGCGAAAT
1596173 --AATCGCAACGCGAAAT
1 AAAATCGCAACGCGAAAT
*
1596189 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-T
1596208 AAAATCGCA
1 AAAATCGCA
1596217 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 16 0.32
19 11 0.22
20 7 0.14
ACGTcount: A:0.46, C:0.25, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAT
Found at i:1596234 original size:19 final size:19
Alignment explanation
Indices: 1596212--1596396 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
1596202 GAAACCAAAA
*
1596212 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1596231 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1596250 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1596269 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1596289 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
**
1596305 T-G-GTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1596322 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1596336 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1596355 TCCGCGTTTCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1596375 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1596395 TC
1 TC
1596397 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 21 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 61 0.44
20 47 0.34
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1596289 original size:39 final size:38
Alignment explanation
Indices: 1596212--1596396 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
1596202 GAAACCAAAA
*
1596212 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
1596250 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* **
1596289 TCGCGTTGCGATTGTC---T-G-GTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
1596322 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
1596355 TCCGCGTTTCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1596395 TC
1 TC
1596397 AACCAAAAGA
Statistics
Matches: 125, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 40 0.32
34 9 0.07
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.14
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1596373 original size:20 final size:20
Alignment explanation
Indices: 1596339--1596396 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1596329 GCGATTCTCT
**
1596339 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
* *
1596359 CGTTTCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1596379 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1596397 AACCAAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1598473 original size:42 final size:42
Alignment explanation
Indices: 1598393--1598485 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1598383 GCCCGACTCG
* *
1598393 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
* * *
1598435 CCTATCATTCCTCGAGAGTCCCCTTCC-ACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCAC-TCCTACCGTTCAAGAGGCC
* *
1598477 ACTGTCATC
1 CCTATCATC
1598486 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.25
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
Found at i:1599886 original size:14 final size:14
Alignment explanation
Indices: 1599867--1599902 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1599857 ATTGTTTAAT
1599867 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1599881 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1599895 TGATTTGT
1 TGATTTGT
1599903 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1600066 original size:20 final size:19
Alignment explanation
Indices: 1600009--1600076 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
1599999 AAAAAGTACT
1600009 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1600028 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1600042 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCG-AAATGAAA
*
1600062 ATCGCAACGCGAAAT
1 ATCGCAATGCGAAAT
1600077 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1600112 original size:19 final size:19
Alignment explanation
Indices: 1600081--1600198 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
1600071 CGAAATTAAA
1600081 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
1600100 TTCGCGTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1600115 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1600133 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1600148 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1600166 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1600185 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1600199 GGACATTAAG
Statistics
Matches: 75, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
14 18 0.24
16 6 0.08
17 6 0.08
19 35 0.47
20 10 0.13
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1600127 original size:33 final size:33
Alignment explanation
Indices: 1600085--1600178 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1600075 ATTAAATTCG
*
1600085 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1600118 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1600151 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1600179 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1600158 original size:14 final size:14
Alignment explanation
Indices: 1600104--1600160 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1600094 TTTCATTTCG
*
1600104 CGTTGCGATTCCCT
1 CGTTGCGATTCTCT
*
1600118 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
1600135 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
1600151 CGTTGCGATT
1 CGTTGCGATT
1600161 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 7 0.20
17 6 0.17
19 6 0.17
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1602687 original size:23 final size:24
Alignment explanation
Indices: 1602654--1602706 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1602644 CTGAAACATC
* *
1602654 ATCAAAATCCGTG-ATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1602677 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1602701 ATCAAA
1 ATCAAA
1602707 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1603792 original size:20 final size:20
Alignment explanation
Indices: 1603767--1603824 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1603757 ATTCATTTGA
*
1603767 CTATCGTAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1603787 CTATCGCAAC-CTGAAAATGG
1 CTATCGCAACGC-GAAAATGG
* *
1603807 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1603825 CGCAATGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1603887 original size:19 final size:19
Alignment explanation
Indices: 1603865--1603910 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1603855 TTTCTCGTTA
1603865 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
1603884 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
1603903 CGATTTTC
1 CGATTTTC
1603911 TCGTTGCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:1604044 original size:14 final size:14
Alignment explanation
Indices: 1604025--1604061 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1604015 CATCAATTAA
1604025 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1604039 ACAAATCATCTTTT
1 ACAAATCAACATTT
1604053 ACAAATCAA
1 ACAAATCAA
1604062 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1605936 original size:20 final size:19
Alignment explanation
Indices: 1605901--1605966 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
1605891 GAAACTTAAA
1605901 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1605920 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1605940 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1605959 ATCGCAAC
1 ATCGCAAC
1605967 AACAAAATCG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1605998 original size:32 final size:33
Alignment explanation
Indices: 1605940--1606018 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1605930 GGAAATGGCT
*
1605940 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
*
1605973 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
1606005 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1606019 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:1606013 original size:14 final size:14
Alignment explanation
Indices: 1605956--1606013 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1605946 ATGCGAAATG
*
1605956 AAAATCGCAACAAC
1 AAAATCGCAACGAC
*
1605970 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1605986 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1606002 AAAATCGCAACG
1 AAAATCGCAACG
1606014 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1606066 original size:14 final size:14
Alignment explanation
Indices: 1606047--1606104 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1606037 TTTCATTTCG
1606047 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1606061 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1606077 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1606093 TGTTGCGATTTT
1 CGTTGCGATTTT
1606105 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1606111 original size:33 final size:33
Alignment explanation
Indices: 1606030--1606120 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1606020 ACAAATCGCA
*
1606030 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1606063 TTGCGA-TTTCATTTCGCATTGCGATTTTGTTG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1606095 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1606121 AGCCATTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1606132 original size:20 final size:20
Alignment explanation
Indices: 1606107--1606151 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1606097 GCGATTTTCA
*
1606107 TTTCGCATTGCGATAGCCAT
1 TTTCGCATTACGATAGCCAT
* *
1606127 TTTCGCGTTACGATAGTCAT
1 TTTCGCATTACGATAGCCAT
1606147 TTTCG
1 TTTCG
1606152 TGTTGCGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (20 bp):
TTTCGCATTACGATAGCCAT
Found at i:1606662 original size:18 final size:18
Alignment explanation
Indices: 1606636--1606675 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1606626 GTCGATCAGA
* *
1606636 TGATGGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
1606654 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
1606672 TGAT
1 TGAT
1606676 GGACTCCCGA
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:0.15, C:0.12, G:0.45, T:0.28
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Done.