Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_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: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:2397210 original size:42 final size:42
Alignment explanation
Indices: 2397164--2397296 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
2397154 TCGAAGTTCG
2397164 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * * *
2397206 CGTTGCGA--TAGTCGAAGTACGTGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTC--GTTGCGATTTATTCCAAATT
* * *
2397248 CGTTGCGATTTATTCCAAATTCATTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
2397288 CGTTGCGAT
1 CGTTGCGAT
2397297 AGTCGAAGTT
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
40 26 0.34
42 42 0.55
44 8 0.11
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (42 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
Found at i:2397442 original size:6 final size:6
Alignment explanation
Indices: 2397431--2397455 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2397421 GACACGTATT
2397431 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
2397456 GACGGGACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2397967 original size:6 final size:6
Alignment explanation
Indices: 2397956--2397986 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2397946 TCGTCTGTTC
2397956 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
2397987 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:2398276 original size:48 final size:48
Alignment explanation
Indices: 2398219--2398366 Score: 143
Period size: 48 Copynumber: 3.2 Consensus size: 48
2398209 TTGGACTATC
*
2398219 GCAATGCGAATATGTAAATCGCAATGCGATAGTCGAATTTGGAAAATT
1 GCAACGCGAATATGTAAATCGCAATGCGATAGTCGAATTTGGAAAATT
* * ** *
2398267 GTAACGCGAACT-TCG-ACTATCGCAATGCGA-A--C----TTGGACTATC
1 GCAACGCGAA-TAT-GTA-AATCGCAATGCGATAGTCGAATTTGGAAAATT
*
2398309 GCAATGCGAATATGTAAATCGCAATGCGATAGTCGAATTTGGAAAATT
1 GCAACGCGAATATGTAAATCGCAATGCGATAGTCGAATTTGGAAAATT
2398357 GCAACGCGAA
1 GCAACGCGAA
2398367 CTTCGACTAT
Statistics
Matches: 75, Mismatches: 13, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
41 14 0.19
42 18 0.24
44 1 0.01
46 1 0.01
48 27 0.36
49 14 0.19
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (48 bp):
GCAACGCGAATATGTAAATCGCAATGCGATAGTCGAATTTGGAAAATT
Found at i:2398296 original size:21 final size:21
Alignment explanation
Indices: 2398272--2398540 Score: 231
Period size: 21 Copynumber: 12.2 Consensus size: 21
2398262 AAATTGTAAC
*
2398272 GCGAACTTCGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
2398293 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
* *
2398314 GCGAA-TATGTA-AATCGCAAT
1 GCGAACT-TGGACTATCGCAAT
** * *
2398334 GCGATAGTCGAATTTGGAAAATTGCAAC
1 GCGA-A--C----TTGGACTATCGCAAT
*
2398362 GCGAACTTCGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
*
2398383 GCGAACTTGGACTATCACAAT
1 GCGAACTTGGACTATCGCAAT
2398404 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
* *
2398425 GCGAA-TATGTA-AATCGCAAT
1 GCGAACT-TGGACTATCGCAAT
** *
2398445 GCGATAGTCGAATTTGGAAAATCGCAAC
1 GCGA-A--C----TTGGACTATCGCAAT
*
2398473 GCGAACTTCGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
2398494 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
2398515 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
2398536 GCGAA
1 GCGAA
2398541 TATGTAAATC
Statistics
Matches: 205, Mismatches: 23, Indels: 40
0.76 0.09 0.15
Matches are distributed among these distances:
20 26 0.13
21 144 0.70
25 2 0.01
27 8 0.04
28 25 0.12
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAT
Found at i:2398314 original size:90 final size:90
Alignment explanation
Indices: 2398104--2398408 Score: 418
Period size: 90 Copynumber: 3.4 Consensus size: 90
2398094 TTTGGAATAA
* * * * *
2398104 ATCGCAACGCGAACTTCGACTATCGCAACGCGAATATGTAAATCGCAATGCGATAGTCTAAGTTC
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAATTTG
** * * **
2398169 G--CGTTGCGATA-GTCGAATTTGGAAAA
66 GAAAATTGC-A-ACG-CGAACTTCG-ACT
2398195 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAATTTG
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAATTTG
*
2398260 GAAAATTGTAACGCGAACTTCGACT
66 GAAAATTGCAACGCGAACTTCGACT
*
2398285 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAATTTG
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAATTTG
2398350 GAAAATTGCAACGCGAACTTCGACT
66 GAAAATTGCAACGCGAACTTCGACT
* *
2398375 ATCGCAATGCGAACTTGGACTATCACAATGCGAA
1 ATCGCAACGCGAACTTGGACTATCGCAATGCGAA
2398409 CTTGGACTAT
Statistics
Matches: 196, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
90 122 0.62
91 69 0.35
92 2 0.01
93 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (90 bp):
ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAATTTG
GAAAATTGCAACGCGAACTTCGACT
Found at i:2398396 original size:111 final size:111
Alignment explanation
Indices: 2398272--2398572 Score: 566
Period size: 111 Copynumber: 2.7 Consensus size: 111
2398262 AAATTGTAAC
*
2398272 GCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCG
1 GCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCG
*
2398337 ATAGTCGAATTTGGAAAATTGCAACGCGAACTTCGACTATCGCAAT
66 ATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAT
*
2398383 GCGAACTTGGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCG
1 GCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCG
2398448 ATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAT
66 ATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAT
2398494 GCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCG
1 GCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCG
2398559 ATAGTCGAAGTTTG
66 ATAGTCGAA-TTTG
2398573 CGTTGCGAAT
Statistics
Matches: 185, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
111 181 0.98
112 4 0.02
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (111 bp):
GCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCG
ATAGTCGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAT
Found at i:2399943 original size:2 final size:2
Alignment explanation
Indices: 2399936--2400022 Score: 153
Period size: 2 Copynumber: 45.0 Consensus size: 2
2399926 TAAGATAAGA
2399936 AT AT AT AT AT AT AT A- 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
2399977 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2400017 AT AT AT
1 AT AT AT
2400023 GGGGATAAGG
Statistics
Matches: 82, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 3 0.04
2 79 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2400612 original size:19 final size:19
Alignment explanation
Indices: 2400584--2400620 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2400574 AACATCGAAT
2400584 ACAATAAGTGTATCGATAC
1 ACAATAAGTGTATCGATAC
*
2400603 ACAATCAGTGTATCGATA
1 ACAATAAGTGTATCGATA
2400621 TTCATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (19 bp):
ACAATAAGTGTATCGATAC
Found at i:2401772 original size:19 final size:19
Alignment explanation
Indices: 2401734--2401793 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
2401724 GACTGAAAAT
*
2401734 ACTGTAGCAGTGTACGGTAC
1 ACTGTAGCAGTAT-CGGTAC
*
2401754 ACTTTAGCAGTATCGGTAC
1 ACTGTAGCAGTATCGGTAC
* *
2401773 ACTGTAGCAATATCGATAC
1 ACTGTAGCAGTATCGGTAC
2401792 AC
1 AC
2401794 ATTTTACCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 24 0.69
20 11 0.31
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (19 bp):
ACTGTAGCAGTATCGGTAC
Found at i:2401879 original size:20 final size:20
Alignment explanation
Indices: 2401836--2401879 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2401826 TGTTCATCAG
* * *
2401836 TTCACACAGTATCGGTATTG
1 TTCACACAGTATCGATACTA
2401856 TTCACACAGTATCGATACTA
1 TTCACACAGTATCGATACTA
2401876 TTCA
1 TTCA
2401880 TATAGTACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (20 bp):
TTCACACAGTATCGATACTA
Found at i:2404342 original size:17 final size:17
Alignment explanation
Indices: 2404299--2404338 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2404289 ATTTTGTTAG
2404299 TAATTTATTTAACTATT
1 TAATTTATTTAACTATT
*
2404316 TAAATTATTTAA-TATT
1 TAATTTATTTAACTATT
*
2404332 TTATTTA
1 TAATTTA
2404339 ATTTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATTTATTTAACTATT
Found at i:2407679 original size:22 final size:22
Alignment explanation
Indices: 2407654--2407700 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2407644 AATAATTTTT
*
2407654 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACATAAATAA
2407676 TTTTACACATAAACATAAATAA
1 TTTTACACATAAACATAAATAA
2407698 TTT
1 TTT
2407701 AAATAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTTACACATAAACATAAATAA
Found at i:2411109 original size:14 final size:14
Alignment explanation
Indices: 2411090--2411118 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2411080 CAATCTACTG
2411090 TGTGTGTATATATA
1 TGTGTGTATATATA
2411104 TGTGTGTATATATA
1 TGTGTGTATATATA
2411118 T
1 T
2411119 ATATATATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (14 bp):
TGTGTGTATATATA
Found at i:2411109 original size:16 final size:16
Alignment explanation
Indices: 2411088--2411120 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2411078 TACAATCTAC
*
2411088 TGTGTGTGTATATATA
1 TGTGTGTATATATATA
2411104 TGTGTGTATATATATA
1 TGTGTGTATATATATA
2411120 T
1 T
2411121 ATATATGAGA
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:0.21, T:0.52
Consensus pattern (16 bp):
TGTGTGTATATATATA
Found at i:2411782 original size:42 final size:42
Alignment explanation
Indices: 2411706--2411788 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
2411696 GCTTGCTAAC
* * *
2411706 CTACGAGTAACTATTATAGCCTTACGATTAACACACACGCAA
1 CTACAAGTAACTATTATAGCCTTACAACTAACACACACGCAA
* *
2411748 CTACAAGTAACTATTATAGCCTTACAACTGACACATACGCA
1 CTACAAGTAACTATTATAGCCTTACAACTAACACACACGCA
2411789 CCAACGAGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.24
Consensus pattern (42 bp):
CTACAAGTAACTATTATAGCCTTACAACTAACACACACGCAA
Found at i:2415454 original size:36 final size:36
Alignment explanation
Indices: 2415346--2415619 Score: 287
Period size: 36 Copynumber: 7.6 Consensus size: 36
2415336 GTGCGCTATA
** **
2415346 TCCTTCCGTTTAACTTGAATCGGAAGTGCCGATGTT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* * * * * *
2415382 TCCTTCCTTTCCGACTTGAATTGAAAATGCCAATGCT
1 TCCTTCCGTT-CGACTTGAATCGGAAGTGCCGATGCC
* * * *
2415419 TACTTCCATTCGACTTGAATCGGAAGTGTCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
2415455 TCCTTCCGTTCGACTTGAATCAGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* * * * *
2415491 TCATTCCATTTGACTTGAATCGGAAGTGTCGGTGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* * * **
2415527 TCCTTCTGTTTGACTTGAATCGAAAGTGTTGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* * *
2415563 TCATTCTGTTCGACTTGAATCAGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
2415599 TCCTTCCGTTCGACTTGAATC
1 TCCTTCCGTTCGACTTGAATC
2415620 AGGAGTGTAG
Statistics
Matches: 197, Mismatches: 40, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
36 170 0.86
37 27 0.14
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
Found at i:2420460 original size:25 final size:24
Alignment explanation
Indices: 2420431--2420477 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
2420421 ATTAGGGGTG
2420431 AATTTAT-AATATTTTAGAGGGGATA
1 AATTTATAAAT-TTTTA-AGGGGATA
2420456 AATTTATAAATTTTTAAGGGGA
1 AATTTATAAATTTTTAAGGGGA
2420478 ATTTGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.29
25 12 0.57
26 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (24 bp):
AATTTATAAATTTTTAAGGGGATA
Found at i:2428832 original size:21 final size:20
Alignment explanation
Indices: 2428802--2428844 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2428792 ATATGGTGAC
2428802 AAAAATAAATA-AATAGTAAA
1 AAAAATAAATATAATA-TAAA
2428822 AAAATATAAATATAATATAAA
1 AAAA-ATAAATATAATATAAA
2428843 AA
1 AA
2428845 TAACATCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAATAAATATAATATAAA
Found at i:2430215 original size:3 final size:3
Alignment explanation
Indices: 2430209--2430234 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2430199 ACATAATTAT
2430209 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
2430235 AACCCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2430478 original size:14 final size:14
Alignment explanation
Indices: 2430459--2430485 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2430449 CCCTACAAAT
2430459 AAATCTCTGCATAG
1 AAATCTCTGCATAG
2430473 AAATCTCTGCATA
1 AAATCTCTGCATA
2430486 TAGACAGAAA
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:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (14 bp):
AAATCTCTGCATAG
Found at i:2433454 original size:18 final size:19
Alignment explanation
Indices: 2433431--2433473 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
2433421 ATTTGAGGAT
2433431 AAAAATATAA-TTTCACC-C
1 AAAAATA-AATTTTCACCGC
2433449 AAAAATAAATTTTCACCGC
1 AAAAATAAATTTTCACCGC
2433468 AAAAAT
1 AAAAAT
2433474 TAGAAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.09
18 14 0.61
19 7 0.30
ACGTcount: A:0.53, C:0.19, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATAAATTTTCACCGC
Found at i:2441802 original size:22 final size:22
Alignment explanation
Indices: 2441777--2441842 Score: 118
Period size: 22 Copynumber: 3.1 Consensus size: 22
2441767 TGGTAATCGA
2441777 TAATGAATAACTATTAGATTTC
1 TAATGAATAACTATTAGATTTC
2441799 TAATGAATAACTATTAGATTTC
1 TAATGAATAACTATTAGATTTC
2441821 TAATGAATAAC--TTAGATTTC
1 TAATGAATAACTATTAGATTTC
2441841 TA
1 TA
2441843 TTGTTTGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.25
22 33 0.75
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (22 bp):
TAATGAATAACTATTAGATTTC
Found at i:2449050 original size:20 final size:19
Alignment explanation
Indices: 2449025--2449076 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2449015 GCTGCTGGAA
* *
2449025 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
2449045 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
2449064 AACCGGGTTGACC
1 AACCGGTTTGACC
2449077 CAACTCGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:2449054 original size:10 final size:10
Alignment explanation
Indices: 2449025--2449074 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
2449015 GCTGCTGGAA
2449025 AACCGGTTTG
1 AACCGGTTTG
*
2449035 -ACCAGTTTTG
1 AACC-GGTTTG
2449045 AACCGGTTTG
1 AACCGGTTTG
*
2449055 -ACCGGTCTG
1 AACCGGTTTG
*
2449064 AACCGGGTTG
1 AACCGGTTTG
2449074 A
1 A
2449075 CCCAACTCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.34
10 18 0.56
11 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:2449092 original size:17 final size:17
Alignment explanation
Indices: 2449070--2449110 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2449060 TCTGAACCGG
* *
2449070 GTTGACCCAACTCGACT
1 GTTGACCCAACCCGACA
*
2449087 GTTGACCCGACCCGACA
1 GTTGACCCAACCCGACA
2449104 GTTGACC
1 GTTGACC
2449111 GTTGACCGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.20
Consensus pattern (17 bp):
GTTGACCCAACCCGACA
Found at i:2449116 original size:7 final size:7
Alignment explanation
Indices: 2449104--2449136 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2449094 CGACCCGACA
2449104 GTTGACC
1 GTTGACC
2449111 GTTGACC
1 GTTGACC
2449118 G-TGACC
1 GTTGACC
2449124 GTTGACC
1 GTTGACC
2449131 GTTGAC
1 GTTGAC
2449137 TTTCTTTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GTTGACC
Found at i:2449124 original size:13 final size:13
Alignment explanation
Indices: 2449106--2449132 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2449096 ACCCGACAGT
2449106 TGACCGTTGACCG
1 TGACCGTTGACCG
2449119 TGACCGTTGACCG
1 TGACCGTTGACCG
2449132 T
1 T
2449133 TGACTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.26
Consensus pattern (13 bp):
TGACCGTTGACCG
Found at i:2456342 original size:10 final size:10
Alignment explanation
Indices: 2456313--2456381 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
2456303 GCTGCTGGAA
2456313 AACCGGTTTG
1 AACCGGTTTG
*
2456323 -ACCAGTTTTG
1 AACC-GGTTTG
2456333 AACCGGTTTG
1 AACCGGTTTG
*
2456343 -ACCGGTTCG
1 AACCGGTTTG
2456352 AACCGGTTTG
1 AACCGGTTTG
* *
2456362 -ACCGGTCTA
1 AACCGGTTTG
*
2456371 AACCGGGTTG
1 AACCGGTTTG
2456381 A
1 A
2456382 CCCAACCCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 18 0.39
10 25 0.54
11 3 0.07
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:2456356 original size:19 final size:19
Alignment explanation
Indices: 2456313--2456367 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
2456303 GCTGCTGGAA
* *
2456313 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
2456333 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
2456352 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
2456368 CTAAACCGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:2456374 original size:19 final size:18
Alignment explanation
Indices: 2456312--2456383 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 18
2456302 AGCTGCTGGA
*
2456312 AAACCGGTTTGACCAGTTTT
1 AAACCGGTTTGACC-G-GTT
*
2456332 GAACCGGTTTGACCGGTT
1 AAACCGGTTTGACCGGTT
*
2456350 CGAACCGGTTTGACCGGTCT
1 -AAACCGGTTTGACCGGT-T
*
2456370 AAACCGGGTTGACC
1 AAACCGGTTTGACC
2456384 CAACCCGACT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 2 0.04
19 30 0.65
20 14 0.30
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (18 bp):
AAACCGGTTTGACCGGTT
Found at i:2456399 original size:17 final size:17
Alignment explanation
Indices: 2456377--2456451 Score: 123
Period size: 17 Copynumber: 4.4 Consensus size: 17
2456367 TCTAAACCGG
* *
2456377 GTTGACCCAACCCGACT
1 GTTGACCCGACCCGACC
*
2456394 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
2456411 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2456428 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
2456445 GTTGACC
1 GTTGACC
2456452 GTTGACCGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.19, C:0.43, G:0.23, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:2456451 original size:7 final size:7
Alignment explanation
Indices: 2456441--2456477 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2456431 GACCCGACCC
2456441 GACCGTT
1 GACCGTT
2456448 GACCGTT
1 GACCGTT
2456455 GACCG-T
1 GACCGTT
2456461 GACCGTT
1 GACCGTT
2456468 GACCGTT
1 GACCGTT
2456475 GAC
1 GAC
2456478 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:2456465 original size:13 final size:13
Alignment explanation
Indices: 2456441--2456473 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2456431 GACCCGACCC
2456441 GACCGTTGACCGTT
1 GACCG-TGACCGTT
2456455 GACCGTGACCGTT
1 GACCGTGACCGTT
2456468 GACCGT
1 GACCGT
2456474 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:2458963 original size:32 final size:32
Alignment explanation
Indices: 2458927--2458990 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
2458917 AATATGGTAT
* * *
2458927 GGTCAAAATCAGATCAGTTGGTTTTTTGGTTG
1 GGTCAAAATCAAATCAGTTGATTTTTTAGTTG
* *
2458959 GGTCAATATCAAATCGGTTGATTTTTTAGTTG
1 GGTCAAAATCAAATCAGTTGATTTTTTAGTTG
2458991 AGTTAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.42
Consensus pattern (32 bp):
GGTCAAAATCAAATCAGTTGATTTTTTAGTTG
Found at i:2458999 original size:32 final size:32
Alignment explanation
Indices: 2458928--2458999 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
2458918 ATATGGTATG
* * * * *
2458928 GTCAAAATCAGATCAGTTGGTTTTTTGGTTGG
1 GTCAATATCAAATCAGTTGATTTTTTAGTTGA
*
2458960 GTCAATATCAAATCGGTTGATTTTTTAGTTGA
1 GTCAATATCAAATCAGTTGATTTTTTAGTTGA
*
2458992 GTTAATAT
1 GTCAATAT
2459000 TGGATTGATC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (32 bp):
GTCAATATCAAATCAGTTGATTTTTTAGTTGA
Found at i:2459287 original size:31 final size:31
Alignment explanation
Indices: 2459252--2459326 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
2459242 TTACGTCGGG
2459252 GACCATATTGCAAACGGACTAAATGTTGGGA
1 GACCATATTGCAAACGGACTAAATGTTGGGA
* *
2459283 GACCATATTGCAAATGGACTAAATGTTGGGG
1 GACCATATTGCAAACGGACTAAATGTTGGGA
**
2459314 GACTGTATTGCAA
1 GACCATATTGCAA
2459327 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (31 bp):
GACCATATTGCAAACGGACTAAATGTTGGGA
Found at i:2461588 original size:3 final size:3
Alignment explanation
Indices: 2461577--2461615 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
2461567 AATTATTAAA
2461577 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2461616 ATTATTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2462850 original size:18 final size:17
Alignment explanation
Indices: 2462818--2462851 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2462808 TCAGCCGGTC
2462818 CGGTTTGAACGGTTCAA
1 CGGTTTGAACGGTTCAA
*
2462835 CGGTTCTGACCGGTTCA
1 CGGTT-TGAACGGTTCA
2462852 CTAGTAGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAA
Found at i:2465026 original size:6 final size:6
Alignment explanation
Indices: 2465015--2465057 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
2465005 ACGGCTCGGC
2465015 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
2465058 TCATCTAGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:2470571 original size:5 final size:5
Alignment explanation
Indices: 2470547--2470590 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
2470537 GTCCGTCCGT
* * * *
2470547 CTCGT CTCGT CTCGG CTCGG CTCGG CACGG CACGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
2470591 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.05, C:0.41, G:0.34, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:2470599 original size:6 final size:6
Alignment explanation
Indices: 2470588--2470660 Score: 137
Period size: 6 Copynumber: 12.2 Consensus size: 6
2470578 ACGGCTCGGC
*
2470588 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
2470636 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
2470661 AATACGTGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.01, C:0.16, G:0.49, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:2470963 original size:22 final size:22
Alignment explanation
Indices: 2470938--2470992 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
2470928 TCATGAGTTA
* *
2470938 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
2470960 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
2470982 CGGGAGTTATA
1 CAGGAGTTATA
2470993 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:2471728 original size:36 final size:37
Alignment explanation
Indices: 2471678--2471760 Score: 134
Period size: 36 Copynumber: 2.3 Consensus size: 37
2471668 GGCAACCAAT
2471678 TTTGAAAAAATAGTTTTTC-AAGTTTGGTAAATATTTC
1 TTTG-AAAAATAGTTTTTCAAAGTTTGGTAAATATTTC
*
2471715 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATATTTC
1 TTTGAAAAATAGTTTTTCAAAGTTTGGTAAATATTTC
2471752 -TTGAAAAAT
1 TTTGAAAAAT
2471761 GATAATGGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 23 0.52
37 21 0.48
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (37 bp):
TTTGAAAAATAGTTTTTCAAAGTTTGGTAAATATTTC
Found at i:2486885 original size:16 final size:16
Alignment explanation
Indices: 2486864--2486896 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2486854 TAATAAATAA
2486864 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2486880 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2486896 A
1 A
2486897 AAATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2486990 original size:16 final size:16
Alignment explanation
Indices: 2486969--2487037 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
2486959 TAAATAAACG
2486969 AACATAAACGAACACA
1 AACATAAACGAACACA
*
2486985 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
2487001 AACATAAATGAACACG
1 AACATAAACGAACACA
* *
2487017 AACATAAATGAACATA
1 AACATAAACGAACACA
2487033 AACAT
1 AACAT
2487038 TGGAGACCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.12
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:2487002 original size:32 final size:32
Alignment explanation
Indices: 2486966--2487030 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
2486956 TAATAAATAA
2486966 ACGAACATAAACGAACACAAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
* * *
2486998 ACGAACATAAATGAACACGAACATAAATGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
2487030 A
1 A
2487031 TAAACATTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (32 bp):
ACGAACATAAACGAACACAAACATAAACGAAC
Found at i:2487726 original size:24 final size:24
Alignment explanation
Indices: 2487699--2487761 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
2487689 TAAATAAATG
2487699 AACATAAACGAACATAACCGAACA
1 AACATAAACGAACATAACCGAACA
* *
2487723 AACATAAACGAACATAACTGAACG
1 AACATAAACGAACATAACCGAACA
2487747 AACAT-AACTGAACAT
1 AACATAAAC-GAACAT
2487762 TCACGAACGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 3 0.08
24 33 0.92
ACGTcount: A:0.56, C:0.22, G:0.10, T:0.13
Consensus pattern (24 bp):
AACATAAACGAACATAACCGAACA
Found at i:2487751 original size:14 final size:14
Alignment explanation
Indices: 2487705--2487759 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
2487695 AATGAACATA
*
2487705 AACGAACATAACCG
1 AACGAACATAACTG
*
2487719 AACAAACAT-A---
1 AACGAACATAACTG
2487729 AACGAACATAACTG
1 AACGAACATAACTG
2487743 AACGAACATAACTG
1 AACGAACATAACTG
2487757 AAC
1 AAC
2487760 ATTCACGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.55, C:0.24, G:0.11, T:0.11
Consensus pattern (14 bp):
AACGAACATAACTG
Found at i:2487769 original size:24 final size:23
Alignment explanation
Indices: 2487698--2487783 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 23
2487688 ATAAATAAAT
2487698 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAA-CGAAC
*
2487722 AAACATAAACGAACATAACTGAAC
1 GAACATAAACGAACATAAC-GAAC
*
2487746 GAACAT-AACTGAACATTCACGAAC
1 GAACATAAAC-GAACA-TAACGAAC
*
2487770 GTAA-ATGAACGAAC
1 G-AACATAAACGAAC
2487784 GAGACCTATG
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.07
24 42 0.78
25 8 0.15
ACGTcount: A:0.52, C:0.22, G:0.13, T:0.13
Consensus pattern (23 bp):
GAACATAAACGAACATAACGAAC
Found at i:2490314 original size:14 final size:14
Alignment explanation
Indices: 2490286--2490325 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2490276 TGTTTTTCGT
2490286 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
*
2490299 GTTTATGTTCGTTC
1 GTTTGTGTTCGTTC
2490313 GTTTGTGTTCGTT
1 GTTTGTGTTCGTT
2490326 TATGTTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.03, C:0.10, G:0.28, T:0.60
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:2492685 original size:23 final size:24
Alignment explanation
Indices: 2492657--2492702 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
2492647 CACTGCAAAT
2492657 ATTAT-CTATATATTA-AATGAAAA
1 ATTATCCTAT-TATTATAATGAAAA
2492680 ATTATCCCTATTATTATAATGAA
1 ATTAT-CCTATTATTATAATGAA
2492703 TATAGTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.25
24 5 0.25
25 10 0.50
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (24 bp):
ATTATCCTATTATTATAATGAAAA
Found at i:2495904 original size:17 final size:18
Alignment explanation
Indices: 2495870--2495911 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
2495860 TATTTTAGAT
2495870 ATAATATTATAAAATAAA
1 ATAATATTATAAAATAAA
* *
2495888 ATAA-ATTAT-AATTTAA
1 ATAATATTATAAAATAAA
2495904 ATAATATT
1 ATAATATT
2495912 TATATTCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 9 0.43
17 8 0.38
18 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATATTATAAAATAAA
Found at i:2498654 original size:31 final size:31
Alignment explanation
Indices: 2498612--2498687 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
2498602 TATGTACATG
2498612 CATGTTTTAACATACGCATCATATTCATATA
1 CATGTTTTAACATACGCATCATATTCATATA
* ** * *
2498643 CATGCTTTAACATGTGCATCATTTTCATGTA
1 CATGTTTTAACATACGCATCATATTCATATA
2498674 CATGTTTTAACATA
1 CATGTTTTAACATA
2498688 TGCTTTGGCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (31 bp):
CATGTTTTAACATACGCATCATATTCATATA
Found at i:2498941 original size:22 final size:22
Alignment explanation
Indices: 2498891--2498947 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
2498881 TCTCATTACG
* *
2498891 TTTTAAAACTTTTAAATAATTT
1 TTTTAAAAATTCTAAATAATTT
** *
2498913 TAATAAAAATTCTAATTAATTT
1 TTTTAAAAATTCTAAATAATTT
*
2498935 TTTTAAAAGTTCT
1 TTTTAAAAATTCT
2498948 CACTAAATCT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATTCTAAATAATTT
Found at i:2502031 original size:24 final size:24
Alignment explanation
Indices: 2502003--2502051 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2501993 GTAGTGATAA
2502003 ATTCAATGATAGTATATGAGATTT
1 ATTCAATGATAGTATATGAGATTT
2502027 ATTCAATGATAGTATATGAGATTT
1 ATTCAATGATAGTATATGAGATTT
2502051 A
1 A
2502052 GGGATTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (24 bp):
ATTCAATGATAGTATATGAGATTT
Found at i:2507041 original size:49 final size:50
Alignment explanation
Indices: 2506964--2507069 Score: 187
Period size: 49 Copynumber: 2.1 Consensus size: 50
2506954 AGAATCCGTC
* *
2506964 ATATTATAATAAAGAACGTTATTCTCTTTAAAAGTTTTAGATTCGAATAA
1 ATATTATAATAAAGAACGTTATTATCTTTAAAAGTTTTAAATTCGAATAA
2507014 ATATTAT-ATAAAGAACGTTATTATCTTTAAAAGTTTTAAATTCGAATAA
1 ATATTATAATAAAGAACGTTATTATCTTTAAAAGTTTTAAATTCGAATAA
2507063 ATATTAT
1 ATATTAT
2507070 TTTACAATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
49 47 0.87
50 7 0.13
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (50 bp):
ATATTATAATAAAGAACGTTATTATCTTTAAAAGTTTTAAATTCGAATAA
Found at i:2509822 original size:23 final size:24
Alignment explanation
Indices: 2509794--2509847 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
2509784 TTGACTTTTT
* * *
2509794 GGGTCAAAGTTAGCGGGTTGGGTC
1 GGGTCAAAGTTAACAGGTCGGGTC
2509818 -GGTCAAAGTTAACAGGTCGGGTC
1 GGGTCAAAGTTAACAGGTCGGGTC
2509841 GGGTCAA
1 GGGTCAA
2509848 CAATTCGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (24 bp):
GGGTCAAAGTTAACAGGTCGGGTC
Found at i:2509858 original size:23 final size:23
Alignment explanation
Indices: 2509807--2509909 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 23
2509797 TCAAAGTTAG
*
2509807 CGGGTTGGGTC-GGTCAA-AGTT
1 CGGGTCGGGTCAGGTCAACAGTT
* * *
2509828 AACAGGTCGGGTCGGGTCAACAATT
1 --CGGGTCGGGTCAGGTCAACAGTT
*
2509853 CGGGTCGGCTCAGGTCAAACAGTT
1 CGGGTCGGGTCAGGTC-AACAGTT
* * *
2509877 TGGGTCGAGTCAGGTCAGCAGTT
1 CGGGTCGGGTCAGGTCAACAGTT
*
2509900 CGGGTTGGGT
1 CGGGTCGGGT
2509910 TGGGCCGGTT
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 35 0.56
24 25 0.40
25 3 0.05
ACGTcount: A:0.18, C:0.18, G:0.39, T:0.24
Consensus pattern (23 bp):
CGGGTCGGGTCAGGTCAACAGTT
Found at i:2509881 original size:24 final size:23
Alignment explanation
Indices: 2509832--2509893 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
2509822 AAAGTTAACA
*
2509832 GGTCGGGTCGGGTC-AACAATTCG
1 GGTC-GGTCAGGTCAAACAATTCG
* *
2509855 GGTCGGCTCAGGTCAAACAGTTTG
1 GGTCGG-TCAGGTCAAACAATTCG
2509879 GGTCGAGTCAGGTCA
1 GGTCG-GTCAGGTCA
2509894 GCAGTTCGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 2 0.06
23 10 0.30
24 20 0.61
25 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.23
Consensus pattern (23 bp):
GGTCGGTCAGGTCAAACAATTCG
Found at i:2519870 original size:30 final size:31
Alignment explanation
Indices: 2519836--2519893 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
2519826 AACTTAAAAG
* *
2519836 AGTTTTGCAATACTGAGA-TTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2519866 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2519894 CCATAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2519933 original size:22 final size:22
Alignment explanation
Indices: 2519897--2519951 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2519887 AAATAATCCA
*
2519897 TAAAACTAAAATAATAAAT-TATT
1 TAAAA-TAAATTAATAAATAT-TT
**
2519920 TAAAATAAATTAATCCATATTT
1 TAAAATAAATTAATAAATATTT
2519942 TAAAATAAAT
1 TAAAATAAAT
2519952 CAATCGATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAATAAATTAATAAATATTT
Found at i:2520032 original size:18 final size:17
Alignment explanation
Indices: 2520015--2520065 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 17
2520005 TAAATCAATC
2520015 CATATTTTAAAATAAAT
1 CATATTTTAAAATAAAT
2520032 CA-ATTTATACAAATAAAT
1 CATATTT-TA-AAATAAAT
2520050 --TA-TTTAAAATAAAT
1 CATATTTTAAAATAAAT
2520064 CA
1 CA
2520066 ATCTATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
14 8 0.28
15 2 0.07
16 6 0.21
17 5 0.17
18 8 0.28
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (17 bp):
CATATTTTAAAATAAAT
Found at i:2520059 original size:32 final size:32
Alignment explanation
Indices: 2520020--2520359 Score: 159
Period size: 32 Copynumber: 10.8 Consensus size: 32
2520010 CAATCCATAT
*
2520020 TTTAAAATAAATCAATTTATACAAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
*
2520052 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
*
2520084 TTTAAAATAAATCAATCCATATTTTA-AAATAAATCA
1 TTTAAAATAAATCAAT-C-TA---TACAAATAAATTA
* * * *
2520120 -AT-ACATACTAATAAAT-TATTTA-AAATAAATCAA
1 TTTAAAATA--AATCAATCTA--TACAAATAAAT-TA
* * *
2520153 TCTATACTAATAAAT-TAT-T-TA-AAATAAATCAA
1 T-T-TA-AAATAAATCAATCTATACAAATAAAT-TA
* ** *
2520185 TCTATACAACTACAAT-AATAAAT-C-AATCAATGT-
1 T-T-TA-AAATA-AATCAATCTATACAAATAAAT-TA
*
2520218 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
*
2520250 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
2520282 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACAAATAAATTA
* * * *
2520304 TTTAAAGTTAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
*
2520336 TTTAAAATAAATCAATCCATACAA
1 TTTAAAATAAATCAATCTATACAA
2520360 CTACAATAAT
Statistics
Matches: 247, Mismatches: 30, Indels: 62
0.73 0.09 0.18
Matches are distributed among these distances:
22 15 0.06
23 1 0.00
24 1 0.00
26 3 0.01
28 3 0.01
29 3 0.01
30 10 0.04
31 5 0.02
32 156 0.63
33 10 0.04
34 12 0.05
35 5 0.02
36 18 0.07
37 2 0.01
38 3 0.01
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACAAATAAATTA
Found at i:2520110 original size:22 final size:22
Alignment explanation
Indices: 2520084--2520126 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2520074 TAATAAATTA
*
2520084 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
2520106 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATACATA
2520127 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:2520135 original size:22 final size:22
Alignment explanation
Indices: 2520086--2520134 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2520076 ATAAATTATT
* **
2520086 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATACATATAA
2520108 TAAAATAAATCAATACATACTAA
1 TAAAATAAATCAATACATA-TAA
2520131 TAAA
1 TAAA
2520135 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATACATATAA
Found at i:2520148 original size:14 final size:14
Alignment explanation
Indices: 2520129--2520181 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
2520119 AATACATACT
2520129 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
2520143 AATAAATCAATCTATACT
1 AATAAAT-TAT-T-TA-A
2520161 AATAAATTATTTAA
1 AATAAATTATTTAA
2520175 AATAAAT
1 AATAAAT
2520182 CAATCTATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 4 0.13
16 2 0.06
17 4 0.13
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:2520162 original size:198 final size:198
Alignment explanation
Indices: 2519940--2520647 Score: 857
Period size: 198 Copynumber: 3.6 Consensus size: 198
2519930 TAATCCATAT
* *
2519940 TTTAAAATAAATCAATCGATACTAATAAATTATTTAGAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
* **
2520005 TAAATCAATCCATATTTTAAAATAAATCAATTTATACAAATAAATTATTTAAAATAAATCAATCT
66 TAAATCAATCAATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCT
2520070 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAA
131 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAA
2520135 TTA
196 TTA
*
2520138 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
*
2520203 TAAATCAATCAATGTTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCT
66 TAAATCAATCAATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCT
* * *
2520268 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTTAATCAATCCATACTAATAAA
131 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAA
2520333 TTA
196 TTA
* * *** *
2520336 TTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATA-TTTTAAAATA
1 TTTAAAATAAATCAATCTATACTAA-TAAATTATTTAAAATAAATCAATCCATACAACTACAAT-
* * * *
2520393 AATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAA
64 AATAAATCAAT-C-AAT--A-T-TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAA
** * ** * *
2520458 ATCAATC----C--AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
123 ATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATACA
**
2520513 T-C-AATCCA-TA
186 TACTAATAAATTA
* *
2520523 TTTTAAAGTAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATA
1 -TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
* *
2520588 ATAAATCAATTC-ATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAAT
65 ATAAATCAA-TCAATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAAT
2520648 TATTTTAAAA
Statistics
Matches: 445, Mismatches: 45, Indels: 50
0.82 0.08 0.09
Matches are distributed among these distances:
187 2 0.00
188 90 0.20
189 12 0.03
190 8 0.02
191 5 0.01
192 29 0.07
193 1 0.00
194 29 0.07
195 6 0.01
196 1 0.00
197 3 0.01
198 259 0.58
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (198 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
TAAATCAATCAATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCT
ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAA
TTA
Found at i:2520227 original size:166 final size:167
Alignment explanation
Indices: 2519909--2520647 Score: 693
Period size: 166 Copynumber: 4.4 Consensus size: 167
2519899 AAACTAAAAT
*
2519909 AATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATCAAT-CGATACTAATAAATTAT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATAC-ATACTAATAAATTAT
* * * * *
2519973 TTAGAATAAATCAATCCATAC-AACTACAA-TA-AT-AAATCAATCCATAT-TTTAAAATAAATC
65 TTAAAATAAATCAATCCATACTAA-TA-AATTATTTAAAATAAAT-CA-ATCTATAAACTAAATC
** * *
2520033 AATTTATACAAATAAATTATTTAAAATAAATCAATCTATACT
126 AATAAATACAAATAAATTATTTAAAATAAATCAATCCATACA
2520075 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATT
*
2520140 TAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AAT
66 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATA-AACTA-AATCAAT
*
2520204 AAAT-C-AATCAATGT-TTTAAAATAAATCAATCCATACA
129 AAATACAAATAAAT-TATTTAAAATAAATCAATCCATACA
* ** * ** * * **
2520241 AATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT-C-AATCCA-TA
1 AATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATACATACTAATAAATTA
* * *
2520303 TTTTAAAGTTAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-
64 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATA-AACTA-AATC
**
2520367 AATAAAT-C-AATCCA-TATTTTAAAATAAATCAATCCATACA
126 AATAAATACAAATAAATTA-TTTAAAATAAATCAATCCATACA
* ** * ** * * **
2520407 AATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT-C-AATCCA-TA
1 AATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATACATACTAATAAATTA
*
2520469 TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTAA
64 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-TA---TAAACTAA
** * *
2520534 ATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACA
123 ATCAATAAATACAAATAAATTATTTAAAATAAATCAATCCATACA
* * *
2520579 ACTACA--A--T--AATAAATCAATTCATATTTTAAAATAAATCAATACATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATT
2520638 TAAAATAAAT
66 TAAAATAAAT
2520648 TATTTTAAAA
Statistics
Matches: 498, Mismatches: 49, Indels: 52
0.83 0.08 0.09
Matches are distributed among these distances:
164 7 0.01
165 13 0.03
166 380 0.76
167 23 0.05
168 24 0.05
169 6 0.01
170 10 0.02
171 3 0.01
172 30 0.06
173 2 0.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.35
Consensus pattern (167 bp):
AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATT
TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATAAACTAAATCAATAA
ATACAAATAAATTATTTAAAATAAATCAATCCATACA
Found at i:2520257 original size:14 final size:14
Alignment explanation
Indices: 2520240--2520293 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2520230 CAATCCATAC
2520240 AAATAAATTATTTA
1 AAATAAATTATTTA
*
2520254 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
2520271 CTAATAAATTATTTA
1 -AAATAAATTATTTA
2520286 AAATAAAT
1 AAATAAAT
2520294 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:2520258 original size:112 final size:115
Alignment explanation
Indices: 2520020--2520647 Score: 475
Period size: 112 Copynumber: 5.4 Consensus size: 115
2520010 CAATCCATAT
* *
2520020 TTTAAAATAAATCAATTTATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACTAATAAA-TA-
* *
2520085 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTA
64 TT-AAATAAATCAATCAATATTTTAAAATAAATCAATACATACAAATAAATTA
*
2520138 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATAC-AACTACA-A-
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACTAA-TAAATAT
* *
2520200 T-AATAAATCAATCAATGTTTTAAAATAAATCAATCCATACAAATAAATTA
65 TAAATAAATCAATCAATATTTTAAAATAAATCAATACATACAAATAAATTA
* ** *
2520250 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA-GTT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACTAATAAATATT
* * * *
2520313 -AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAA
66 AAATAAATCAAT-C-AAT--A-T-TTTAAAATAAATCAATACATACAAATA-AAT--T-A
* * * * *
2520372 ATCAATCCATATTTTAAAATAAATCAATCCATACA-AATAAATTATTTAAAATAAATCAATCTAT
1 TTTAA---A-A---T-AAATCAATCTATAC-TA-ATAA---ATTATTTAAAATAAATCAATCTAT
* * *
2520436 ACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
53 ACTAATAAA-TA-TT-AAATAAATCAATCAATATTTTAAAATAAATCAATACATACAAATAAATT
2520501 A
115 A
*
2520502 TTTAAAATAAATCAATC----C--AT--A-T-TTTAAAGTAAATCAATCTATACTAATAAATTAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACTAATAAA-TA-
* * **
2520557 TTAAAATAAATCAATC--TA---TACAACTACAAT-AATAAAT-C-AATTCA-TA
64 TT-AAATAAATCAATCAATATTTTA-AAATA-AATCAATACATACAAATAAATTA
2520603 TTTTAAAATAAATCAATAC-ATACTAATAAATTATTTAAAATAAAT
1 -TTTAAAATAAATCAAT-CTATACTAATAAATTATTTAAAATAAAT
2520648 TATTTTAAAA
Statistics
Matches: 424, Mismatches: 40, Indels: 98
0.75 0.07 0.17
Matches are distributed among these distances:
101 2 0.00
102 20 0.05
103 4 0.01
104 9 0.02
105 3 0.01
106 3 0.01
108 50 0.12
109 1 0.00
110 2 0.00
111 4 0.01
112 118 0.28
113 1 0.00
114 5 0.01
116 1 0.00
117 3 0.01
118 82 0.19
119 3 0.01
121 1 0.00
122 12 0.03
123 1 0.00
125 1 0.00
126 2 0.00
127 1 0.00
129 1 0.00
130 15 0.04
131 5 0.01
132 1 0.00
133 3 0.01
134 49 0.12
135 6 0.01
136 1 0.00
138 4 0.01
139 1 0.00
140 9 0.02
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (115 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACTAATAAATATT
AAATAAATCAATCAATATTTTAAAATAAATCAATACATACAAATAAATTA
Found at i:2520308 original size:22 final size:22
Alignment explanation
Indices: 2520282--2520324 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2520272 TAATAAATTA
2520282 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
* *
2520304 TTTAAAGTTAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2520325 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2520308 original size:54 final size:54
Alignment explanation
Indices: 2520250--2520572 Score: 391
Period size: 54 Copynumber: 5.9 Consensus size: 54
2520240 AAATAAATTA
*
2520250 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * *
2520304 TTTAAAGTTAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** ** * ** * ** **
2520361 TACAATAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACAAATAAAT-T
1 TTTAA-AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCATAT
*
2520415 ATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
2520470 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
2520524 TTTAAAGTAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
2520573 TATACAACTA
Statistics
Matches: 224, Mismatches: 35, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
54 169 0.75
55 13 0.06
56 10 0.04
57 13 0.06
58 19 0.08
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.35
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:2520413 original size:22 final size:22
Alignment explanation
Indices: 2520340--2520413 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
2520330 AAATTATTTA
*
2520340 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAA--A-T
***
2520365 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACAAAT
2520387 AAAATAAATCAATCCATACAAAT
1 -AAATAAATCAATCCATACAAAT
2520410 AAAT
1 AAAT
2520414 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
25 1 0.03
26 16 0.41
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:2520423 original size:14 final size:14
Alignment explanation
Indices: 2520406--2520459 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2520396 CAATCCATAC
2520406 AAATAAATTATTTA
1 AAATAAATTATTTA
*
2520420 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
2520437 CTAATAAATTATTTA
1 -AAATAAATTATTTA
2520452 AAATAAAT
1 AAATAAAT
2520460 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:2520423 original size:32 final size:32
Alignment explanation
Indices: 2520384--2520577 Score: 203
Period size: 32 Copynumber: 6.7 Consensus size: 32
2520374 CAATCCATAT
*
2520384 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
2520416 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2520448 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2520470 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
2520502 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
2520524 TTTAAAGTAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
2520556 TTTAAAATAAATCAATCTATAC
1 TTTAAAATAAATCAATCCATAC
2520578 AACTACAATA
Statistics
Matches: 136, Mismatches: 6, Indels: 40
0.75 0.03 0.22
Matches are distributed among these distances:
22 31 0.23
23 3 0.02
24 2 0.01
26 6 0.04
28 6 0.04
30 2 0.01
31 3 0.02
32 83 0.61
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:2520474 original size:22 final size:22
Alignment explanation
Indices: 2520448--2520490 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2520438 TAATAAATTA
2520448 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2520470 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2520491 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2520499 original size:22 final size:22
Alignment explanation
Indices: 2520450--2520498 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2520440 ATAAATTATT
**
2520450 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2520472 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2520495 TAAA
1 TAAA
2520499 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2520509 original size:220 final size:220
Alignment explanation
Indices: 2520250--2520647 Score: 733
Period size: 220 Copynumber: 1.8 Consensus size: 220
2520240 AAATAAATTA
* *
2520250 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTTAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTAAA
2520315 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCC
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCC
*
2520380 ATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAA
131 ATATTTTAAAATAAATCAATACATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAA
2520445 TTATTTAAAATAAATCAATCCATAT
196 TTATTTAAAATAAATCAATCCATAT
2520470 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTAAA
* * *
2520535 TCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATTC
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCC
*
2520600 ATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAAT
131 ATATTTTAAAATAAATCAATACATACAAATAAATTATTTAAAATAAAT
2520648 TATTTTAAAA
Statistics
Matches: 171, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
220 171 1.00
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (220 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTAAA
TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCC
ATATTTTAAAATAAATCAATACATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAA
TTATTTAAAATAAATCAATCCATAT
Found at i:2520633 original size:22 final size:22
Alignment explanation
Indices: 2520561--2520633 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
2520551 AATTATTTAA
* *
2520561 AATAAATCAATCTATACA-ACT
1 AATAAATAAATCAATACATACT
*
2520582 ACA-ATAATAAATCAATTCATA-T
1 A-ATA-AATAAATCAATACATACT
**
2520604 TTTAAAATAAATCAATACATACT
1 AAT-AAATAAATCAATACATACT
2520627 AATAAAT
1 AATAAAT
2520634 TATTTAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
21 2 0.05
22 32 0.84
23 4 0.11
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
AATAAATAAATCAATACATACT
Found at i:2520656 original size:15 final size:15
Alignment explanation
Indices: 2520627--2520760 Score: 153
Period size: 15 Copynumber: 8.5 Consensus size: 15
2520617 AATACATACT
2520627 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
2520641 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
2520656 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
2520678 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
2520693 AATAAATTATTTTAT
1 AATAAATTATTTTAA
2520708 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
2520723 AATAATTTATTTTTAA
1 AATAAATTA-TTTTAA
2520739 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2520754 AATAAAT
1 AATAAAT
2520761 AACCTTATTA
Statistics
Matches: 103, Mismatches: 8, Indels: 17
0.80 0.06 0.13
Matches are distributed among these distances:
14 9 0.09
15 63 0.61
16 14 0.14
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:2520663 original size:47 final size:47
Alignment explanation
Indices: 2520601--2520760 Score: 169
Period size: 52 Copynumber: 3.3 Consensus size: 47
2520591 AATCAATTCA
*
2520601 TATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAAT
1 TATTTTAAAATAAATCAATACATAATAATAAATTATTTAAAATAAAT
* *
2520648 TATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAATACATA----ATAATAAATTA-TTTAAAATAAAT
* * * ** * **
2520700 TATTTTATAATAAATTATTTTAAAATAATTTATT-TTTAAAATAAAT
1 TATTTTAAAATAAATCAATACATAATAATAAATTATTTAAAATAAAT
2520746 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
2520761 AACCTTATTA
Statistics
Matches: 95, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
46 26 0.27
47 23 0.24
48 7 0.07
51 9 0.09
52 30 0.32
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (47 bp):
TATTTTAAAATAAATCAATACATAATAATAAATTATTTAAAATAAAT
Found at i:2521648 original size:22 final size:22
Alignment explanation
Indices: 2521622--2521668 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2521612 TATATTATTT
*
2521622 AAATTATTTACGTTTATGTGTA
1 AAATTATTTACGTTTATGTATA
2521644 AAATTATTTACGTTTATGTATA
1 AAATTATTTACGTTTATGTATA
2521666 AAA
1 AAA
2521669 AAATTTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (22 bp):
AAATTATTTACGTTTATGTATA
Found at i:2521674 original size:22 final size:22
Alignment explanation
Indices: 2521627--2521675 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2521617 TATTTAAATT
* **
2521627 ATTTACGTTTATGTGTAAAATT
1 ATTTACGTTTATGTATAAAAAA
2521649 ATTTACGTTTATGTATAAAAAA
1 ATTTACGTTTATGTATAAAAAA
2521671 ATTTA
1 ATTTA
2521676 TTGTGTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (22 bp):
ATTTACGTTTATGTATAAAAAA
Found at i:2525013 original size:34 final size:35
Alignment explanation
Indices: 2524973--2525045 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
2524963 AATAAACAAT
* ** *
2524973 TTAAATAAATACA-TTAACTAAAGGTCCAACAAAA
1 TTAAATAAATAAATTTAAAAAAAAGTCCAACAAAA
*
2525007 TTAAATAAATAAATTTAAAAAAAAGTCCAACTAAA
1 TTAAATAAATAAATTTAAAAAAAAGTCCAACAAAA
2525042 TTAA
1 TTAA
2525046 CAAAATTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 12 0.36
35 21 0.64
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.26
Consensus pattern (35 bp):
TTAAATAAATAAATTTAAAAAAAAGTCCAACAAAA
Found at i:2527256 original size:24 final size:24
Alignment explanation
Indices: 2527224--2527279 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
2527214 GACTTTGATC
2527224 GCTCGAACCCCTAACATTCCTAGT
1 GCTCGAACCCCTAACATTCCTAGT
* *
2527248 GCTCGAACCCCTGACGTTCCTAGT
1 GCTCGAACCCCTAACATTCCTAGT
2527272 GCTCGAAC
1 GCTCGAAC
2527280 TCGAAACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (24 bp):
GCTCGAACCCCTAACATTCCTAGT
Found at i:2528338 original size:2 final size:2
Alignment explanation
Indices: 2528331--2528369 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2528321 AAGTTGAAGC
2528331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2528370 AGATGGAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2534968 original size:2 final size:2
Alignment explanation
Indices: 2534961--2535028 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
2534951 GAGTGTGAAC
2534961 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2535003 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
2535029 GTGGTCCAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2535261 original size:3 final size:3
Alignment explanation
Indices: 2535253--2535277 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2535243 CTATCATTCC
2535253 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
2535278 GGGTAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2535505 original size:2 final size:2
Alignment explanation
Indices: 2535493--2535552 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
2535483 CAGAAATTGA
*
2535493 AT AT GT 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
2535535 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2535553 CCTTAAGTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2536178 original size:4 final size:4
Alignment explanation
Indices: 2536169--2536193 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2536159 GTTATGTTCG
2536169 TGTT TGTT TGTT TGTT TGTT TGTT T
1 TGTT TGTT TGTT TGTT TGTT TGTT T
2536194 TCAAAGGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TGTT
Found at i:2536311 original size:33 final size:30
Alignment explanation
Indices: 2536242--2536311 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
2536232 TTTAATATTA
* * *
2536242 TGTTCATGTTTGTCTATTTATTTTTAAAGG
1 TGTTCATGTTCGTCTATTTATTTTCAAACG
*
2536272 TGTTCATGTTCGTTTATTTATTGTTCACGAACG
1 TGTTCATGTTCGTCTATTTATT-TTCA--AACG
2536305 TGTTCAT
1 TGTTCAT
2536312 TTATATATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 20 0.61
31 3 0.09
33 10 0.30
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.53
Consensus pattern (30 bp):
TGTTCATGTTCGTCTATTTATTTTCAAACG
Found at i:2536322 original size:12 final size:12
Alignment explanation
Indices: 2536307--2536362 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
2536297 CACGAACGTG
*
2536307 TTCATTTATATA
1 TTCATTTACATA
**
2536319 TTCATGAACATA
1 TTCATTTACATA
*
2536331 TTCATTTATATA
1 TTCATTTACATA
**
2536343 TTCATGAACATA
1 TTCATTTACATA
2536355 TTCATTTA
1 TTCATTTA
2536363 GCATTTACGA
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (12 bp):
TTCATTTACATA
Found at i:2536327 original size:24 final size:24
Alignment explanation
Indices: 2536307--2536362 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
2536297 CACGAACGTG
2536307 TTCATTTATATATTCATGAACATA
1 TTCATTTATATATTCATGAACATA
2536331 TTCATTTATATATTCATGAACATA
1 TTCATTTATATATTCATGAACATA
2536355 TTCATTTA
1 TTCATTTA
2536363 GCATTTACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (24 bp):
TTCATTTATATATTCATGAACATA
Found at i:2536941 original size:117 final size:117
Alignment explanation
Indices: 2536735--2536966 Score: 464
Period size: 117 Copynumber: 2.0 Consensus size: 117
2536725 ACAAACGAAC
2536735 TTAAACGAATGTTATACGAATAACTCATCAAACGCTTTGTTCATTTACACCCCGAATCTTTGCAT
1 TTAAACGAATGTTATACGAATAACTCATCAAACGCTTTGTTCATTTACACCCCGAATCTTTGCAT
2536800 TATTTGAGTATTGTTAACAATATCTTAAATATTTACTTAATTAGCCACAATT
66 TATTTGAGTATTGTTAACAATATCTTAAATATTTACTTAATTAGCCACAATT
2536852 TTAAACGAATGTTATACGAATAACTCATCAAACGCTTTGTTCATTTACACCCCGAATCTTTGCAT
1 TTAAACGAATGTTATACGAATAACTCATCAAACGCTTTGTTCATTTACACCCCGAATCTTTGCAT
2536917 TATTTGAGTATTGTTAACAATATCTTAAATATTTACTTAATTAGCCACAA
66 TATTTGAGTATTGTTAACAATATCTTAAATATTTACTTAATTAGCCACAA
2536967 ATTTCTTAAT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (117 bp):
TTAAACGAATGTTATACGAATAACTCATCAAACGCTTTGTTCATTTACACCCCGAATCTTTGCAT
TATTTGAGTATTGTTAACAATATCTTAAATATTTACTTAATTAGCCACAATT
Found at i:2539938 original size:24 final size:22
Alignment explanation
Indices: 2539911--2539965 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
2539901 TATGTGACAT
2539911 ATATTTAAATATTAATAAGAAAAA
1 ATATTTAAATATT-ATAA-AAAAA
* *
2539935 ATATTAACAATATTATAAATAAA
1 ATATTTA-AATATTATAAAAAAA
*
2539958 TTATTTAA
1 ATATTTAA
2539966 TTTAAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 9 0.35
24 10 0.38
25 6 0.23
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
ATATTTAAATATTATAAAAAAA
Found at i:2541000 original size:13 final size:13
Alignment explanation
Indices: 2540982--2541009 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2540972 TAGGTAGCGC
2540982 TTAATATAAATAT
1 TTAATATAAATAT
2540995 TTAATATAAATAT
1 TTAATATAAATAT
2541008 TT
1 TT
2541010 CCTGTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATATAAATAT
Found at i:2550820 original size:18 final size:18
Alignment explanation
Indices: 2550797--2550849 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
2550787 AGGGTTATAC
2550797 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
2550815 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
2550833 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
2550850 AATTTCATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2551732 original size:22 final size:21
Alignment explanation
Indices: 2551686--2551732 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2551676 GCAGTACTAT
*
2551686 AGCAGGGTATCAGTACCCTGT
1 AGCAGGGTATCAGTACCCTGA
2551707 AGCAGGGTATC-GATACCCCTGA
1 AGCAGGGTATCAG-TA-CCCTGA
2551729 AGCA
1 AGCA
2551733 ATATGGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 13 0.57
22 9 0.39
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (21 bp):
AGCAGGGTATCAGTACCCTGA
Found at i:2563471 original size:20 final size:20
Alignment explanation
Indices: 2563446--2563483 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2563436 TTAATGACTA
*
2563446 GGGGTATCGATACCCATAAG
1 GGGGTATCAATACCCATAAG
2563466 GGGGTATCAATACCCATA
1 GGGGTATCAATACCCATA
2563484 CGTCATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (20 bp):
GGGGTATCAATACCCATAAG
Found at i:2573032 original size:18 final size:18
Alignment explanation
Indices: 2573009--2573043 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2572999 AGGGTTATAC
* *
2573009 AGTGGTCCTTTGGGACAT
1 AGTGGTCATTCGGGACAT
2573027 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
2573044 AATTTCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:2576271 original size:23 final size:23
Alignment explanation
Indices: 2576245--2576304 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2576235 TAGCTCGTAT
2576245 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* * *
2576268 TTGCACCGGAGTACCGCGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
2576291 TTGCACCGTAGTGC
1 TTGCACCGAAGTGC
2576305 TATATAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:2576444 original size:103 final size:103
Alignment explanation
Indices: 2576314--2576536 Score: 403
Period size: 103 Copynumber: 2.2 Consensus size: 103
2576304 CTATATAATA
* *
2576314 ATGT-CCATAAGGACTACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
2576378 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
2576417 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
2576482 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
2576520 ATGTCCCAAAGGACCAC
1 ATGTCCCAAAGGACCAC
2576537 GTAGACCCTC
Statistics
Matches: 115, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 113 0.98
104 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:2581225 original size:23 final size:23
Alignment explanation
Indices: 2581199--2581267 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
2581189 CACCATAGCT
2581199 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
2581222 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
2581245 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
2581268 TATAATAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2581416 original size:103 final size:103
Alignment explanation
Indices: 2581285--2581497 Score: 365
Period size: 103 Copynumber: 2.1 Consensus size: 103
2581275 ATGTCCATAA
*
2581285 GGACTACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCAGA
1 GGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCAGA
* *
2581350 CTTCACACATGTTCTAAAGAATACATATATGTCCCGAAT
66 CTTCACACATATTCCAAAGAATACATATATGTCCCG-AT
* *
2581389 -GACCACATATCATTCCTTAGGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGA
1 GGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCAGA
2581453 CTTCACACATATTCCAAAGAATACATATATGTCCCGAT
66 CTTCACACATATTCCAAAGAATACATATATGTCCCGAT
2581491 GGACCAC
1 GGACCAC
2581498 GTAGACCCTC
Statistics
Matches: 103, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
102 2 0.02
103 101 0.98
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCAGA
CTTCACACATATTCCAAAGAATACATATATGTCCCGAT
Found at i:2587870 original size:61 final size:61
Alignment explanation
Indices: 2587795--2587917 Score: 176
Period size: 61 Copynumber: 2.0 Consensus size: 61
2587785 GGGTTGTTGG
** * *
2587795 CTTGGCAACCAATTTGGCAATCAATTTCTCCTATT-TCCATTTATTGCACCTGCAAGTTTGA
1 CTTGGCAACCAATTTGAAAACCAATTTCTCCTATTGT-CATTTATTGCACCTACAAGTTTGA
* *
2587856 CTTGGCAACTAATTTGAAAACCAATTTCTCCTATTGTCATTTATTGCACTTACAAGTTTGA
1 CTTGGCAACCAATTTGAAAACCAATTTCTCCTATTGTCATTTATTGCACCTACAAGTTTGA
2587917 C
1 C
2587918 CAACATTATC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 54 0.98
62 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (61 bp):
CTTGGCAACCAATTTGAAAACCAATTTCTCCTATTGTCATTTATTGCACCTACAAGTTTGA
Found at i:2599671 original size:2 final size:2
Alignment explanation
Indices: 2599664--2599689 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2599654 TAAATTAGAT
2599664 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
2599690 CGAAAAGAAT
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):
TA
Found at i:2600406 original size:27 final size:29
Alignment explanation
Indices: 2600356--2600409 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2600346 ATTATATATA
*
2600356 TTTTTTAAAAATTGATAATATTTTAAAGT
1 TTTTTTAAAAAATGATAATATTTTAAAGT
*
2600385 TTTTTTAAAAAAT-A-AATTTTTTAAA
1 TTTTTTAAAAAATGATAATATTTTAAA
2600410 ATTATCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 10 0.43
28 1 0.04
29 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTTTTAAAAAATGATAATATTTTAAAGT
Found at i:2600828 original size:7 final size:7
Alignment explanation
Indices: 2600818--2600844 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2600808 CCAATTCCCA
2600818 AGTCACG
1 AGTCACG
2600825 AGTCACG
1 AGTCACG
2600832 AGTCACG
1 AGTCACG
2600839 AGTCAC
1 AGTCAC
2600845 AAGCCAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (7 bp):
AGTCACG
Found at i:2602156 original size:2 final size:2
Alignment explanation
Indices: 2602149--2602177 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2602139 ACCGACCTAA
2602149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2602178 AGTATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2606311 original size:2 final size:2
Alignment explanation
Indices: 2606304--2606332 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2606294 ACACATTCTA
2606304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2606333 ATAGCTATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2608875 original size:18 final size:17
Alignment explanation
Indices: 2608852--2608904 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 17
2608842 ACTGAATATT
2608852 TGTCCCGAATGACCACTA
1 TGTCCCGAA-GACCACTA
2608870 TGTCCCGAAGAACCACTA
1 TGTCCCGAAG-ACCACTA
2608888 TGTCCCGAAGGACCACT
1 TGTCCCGAA-GACCACT
2608905 GATAATCCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (17 bp):
TGTCCCGAAGACCACTA
Found at i:2609577 original size:64 final size:62
Alignment explanation
Indices: 2609453--2609587 Score: 152
Period size: 64 Copynumber: 2.1 Consensus size: 62
2609443 TCCCTTGACA
** *
2609453 AGTGCATCGATGCACTACCTATGCATCGGTGCATAAATCTCATTCGATGTTTGTATTTTAAACG
1 AGTGCATCGATGCACTACCTATGCATCAATGCATAAATCGCATTCGATGTTTGTATTTT-AA-G
*
2609517 AGTGCATCGATGCACT-CCTTATGCATCAATGCAGT-AATGGCATTCGATGTTCAT-TA-TTTAA
1 AGTGCATCGATGCACTACC-TATGCATCAATGCA-TAAATCGCATTCGATGTT--TGTATTTTAA
2609578 G
62 G
2609579 AGTGCATCG
1 AGTGCATCG
2609588 GTACACATTG
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
62 10 0.16
63 4 0.06
64 45 0.71
65 3 0.05
66 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (62 bp):
AGTGCATCGATGCACTACCTATGCATCAATGCATAAATCGCATTCGATGTTTGTATTTTAAG
Found at i:2614283 original size:21 final size:21
Alignment explanation
Indices: 2614257--2614296 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2614247 CAGAACCCCA
*
2614257 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2614278 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2614297 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2617018 original size:22 final size:21
Alignment explanation
Indices: 2616976--2617015 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2616966 GAGTTTGTTT
*
2616976 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2616997 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2617016 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2623986 original size:20 final size:18
Alignment explanation
Indices: 2623939--2624011 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
2623929 ACTGAATATT
*
2623939 TGTCCCGAAGGACCACTA
1 TGTCCTGAAGGACCACTA
2623957 TGTCCTGAAGGACCACTAA
1 TGTCCTGAAGGACCACT-A
* *
2623976 TTGTTCTGAAGAACCACTA
1 -TGTCCTGAAGGACCACTA
*
2623995 TGTCCCGAAGGACCACT
1 TGTCCTGAAGGACCACT
2624012 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 2 0.04
20 15 0.32
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (18 bp):
TGTCCTGAAGGACCACTA
Found at i:2627225 original size:24 final size:24
Alignment explanation
Indices: 2627198--2627263 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
2627188 AACTTGTATA
*
2627198 AATTTGCACCGTAGTGCCACGTAG
1 AATTTGCACCGTAGTGCCACATAG
* * *
2627222 AATTTGCACCGAAGTACCGCATAG
1 AATTTGCACCGTAGTGCCACATAG
* *
2627246 AA-ATACACCGTAGTGCCA
1 AATTTGCACCGTAGTGCCA
2627264 TATAAGATTG
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 11 0.33
24 22 0.67
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (24 bp):
AATTTGCACCGTAGTGCCACATAG
Found at i:2632810 original size:12 final size:12
Alignment explanation
Indices: 2632792--2632834 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
2632782 AAAATACGGT
2632792 ATGAACATTACC
1 ATGAACATTACC
*
2632804 GTGAACATTACC
1 ATGAACATTACC
*
2632816 ATGAACAATACC
1 ATGAACATTACC
*
2632828 ATTAACA
1 ATGAACA
2632835 GTGAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.23
Consensus pattern (12 bp):
ATGAACATTACC
Found at i:2632913 original size:32 final size:32
Alignment explanation
Indices: 2632870--2632936 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
2632860 TTATTGATGC
2632870 ACTGCTACAGTGCATCGATGCACTGCTACAAT
1 ACTGCTACAGTGCATCGATGCACTGCTACAAT
* * *
2632902 ACTGCTTCAGTGCATCGATGTACTGCTACAGT
1 ACTGCTACAGTGCATCGATGCACTGCTACAAT
2632934 ACT
1 ACT
2632937 TTTGTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (32 bp):
ACTGCTACAGTGCATCGATGCACTGCTACAAT
Found at i:2633678 original size:24 final size:24
Alignment explanation
Indices: 2633651--2633716 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
2633641 AGCTCGTATA
2633651 AATTTACACCGTAGTGCCACGTAG
1 AATTTACACCGTAGTGCCACGTAG
* * *
2633675 AATTTGCACTGAAGTGCCACGTAG
1 AATTTACACCGTAGTGCCACGTAG
*
2633699 AA-ATACACCGTAGTGCCA
1 AATTTACACCGTAGTGCCA
2633717 TATAAGATTG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
23 12 0.34
24 23 0.66
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (24 bp):
AATTTACACCGTAGTGCCACGTAG
Done.