Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 16
Found at i:2666795 original size:12 final size:12
Alignment explanation
Indices: 2666751--2666801 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
2666741 CAAAACATTT
2666751 TTATTTTACTTG
1 TTATTTTACTTG
*
2666763 TTCATTTT-TTTG
1 TT-ATTTTACTTG
2666775 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
2666789 TTATTTTCCTTG
1 TTATTTTACTTG
2666801 T
1 T
2666802 CTTTTTCAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.67
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:2670054 original size:19 final size:19
Alignment explanation
Indices: 2670015--2670058 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2670005 TAAAACTGTG
2670015 AATGATGAAAACCATAAAAA
1 AATGATGAAAA-CATAAAAA
2670035 AATGATGAAAA-ATGAAAAA
1 AATGATGAAAACAT-AAAAA
2670054 AATGA
1 AATGA
2670059 AATTAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 11 0.48
ACGTcount: A:0.66, C:0.05, G:0.14, T:0.16
Consensus pattern (19 bp):
AATGATGAAAACATAAAAA
Found at i:2672873 original size:31 final size:31
Alignment explanation
Indices: 2672832--2672920 Score: 142
Period size: 31 Copynumber: 2.9 Consensus size: 31
2672822 GACCACTATT
* *
2672832 CATATATCCCGAAGGACATAGGTAACCTTTC
1 CATATGTCCCGAAGGACATAGGTAACCTGTC
*
2672863 CATATGTCCCGAAGGACATAGGTAAACTGTC
1 CATATGTCCCGAAGGACATAGGTAACCTGTC
*
2672894 CATATGTCCTGAAGGACATAGGTAACC
1 CATATGTCCCGAAGGACATAGGTAACC
2672921 CTCGACTCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (31 bp):
CATATGTCCCGAAGGACATAGGTAACCTGTC
Found at i:2675190 original size:17 final size:17
Alignment explanation
Indices: 2675152--2675189 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2675142 ACAAAACACG
*
2675152 TAAAATATAATAAAAAA
1 TAAAATAAAATAAAAAA
2675169 TAAAATAAAAT-AAAAA
1 TAAAATAAAATAAAAAA
2675185 TAAAA
1 TAAAA
2675190 AAATGAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAATAAAATAAAAAA
Found at i:2675267 original size:18 final size:18
Alignment explanation
Indices: 2675244--2675291 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2675234 AATTAATGGA
2675244 GTAAAAAAATAAAAAAAG
1 GTAAAAAAATAAAAAAAG
*
2675262 GTAAAAGAAAT-TAAAAAG
1 GTAAAA-AAATAAAAAAAG
2675280 G-AATAAAAATAA
1 GTAA-AAAAATAA
2675292 TGTGTACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.24
18 15 0.60
19 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (18 bp):
GTAAAAAAATAAAAAAAG
Found at i:2675424 original size:16 final size:17
Alignment explanation
Indices: 2675392--2675430 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2675382 ATTAAGGGAA
2675392 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
2675409 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
*
2675425 ATAATA
1 AAAATA
2675431 TATATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:2675478 original size:32 final size:32
Alignment explanation
Indices: 2675409--2675515 Score: 94
Period size: 37 Copynumber: 3.2 Consensus size: 32
2675399 TAGAAAAAAT
* *
2675409 AAAATAAAGTAAAAATATAATATATATA-TAA-
1 AAAATAAA-TAAAAACATAATATAAATATTAAG
2675440 ATAAATAAATAAAAACA-AATATAGAATATTAAG
1 A-AAATAAATAAAAACATAATATA-AATATTAAG
*
2675473 AAAATATATATAAAAACGTATAAAATATAATATTAAG
1 AAAATA-A-ATAAAAAC--ATAATATA-AATATTAAG
2675510 AAAATA
1 AAAATA
2675516 TATATACATA
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
30 6 0.10
31 11 0.17
32 15 0.24
33 2 0.03
34 8 0.13
36 1 0.02
37 20 0.32
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (32 bp):
AAAATAAATAAAAACATAATATAAATATTAAG
Found at i:2675563 original size:2 final size:2
Alignment explanation
Indices: 2675551--2675599 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
2675541 TTAATACATC
* *
2675551 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA TA -A GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
2675592 TA TA TA TA
1 TA TA TA TA
2675600 ATAAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:2675603 original size:14 final size:14
Alignment explanation
Indices: 2675551--2675622 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 14
2675541 TTAATACATC
* *
2675551 TATACATATATATA
1 TATATATATAAATA
*
2675565 TATATATATATATA
1 TATATATATAAATA
2675579 TA-ATGATATAAGATA
1 TATAT-ATATAA-ATA
*
2675594 TATATA-ATAAAAA
1 TATATATATAAATA
2675607 TAATATAATATAAATA
1 T-ATAT-ATATAAATA
2675623 AAAAAGAGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 5 0.10
14 28 0.58
15 7 0.15
16 8 0.17
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (14 bp):
TATATATATAAATA
Found at i:2675612 original size:25 final size:27
Alignment explanation
Indices: 2675564--2675614 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
2675554 ACATATATAT
* *
2675564 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
2675591 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
2675615 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:2675669 original size:12 final size:13
Alignment explanation
Indices: 2675556--2675669 Score: 52
Period size: 14 Copynumber: 8.4 Consensus size: 13
2675546 ACATCTATAC
* *
2675556 ATATATATATATA
1 ATATAAATAAATA
* *
2675569 TATATATATATAATG
1 -ATATAAATA-AATA
2675584 ATATAAGATATATATA
1 ATATAA-ATA-A-ATA
*
2675600 ATAAAAATAATATA
1 ATATAAATAA-ATA
*
2675614 ATATAAATAAAAA
1 ATATAAATAAATA
* ** *
2675627 AGAGGAATATAGTA
1 ATATAAATA-AATA
2675641 A-ATAAATAAATA
1 ATATAAATAAATA
*
2675653 ATATAATTAAA-A
1 ATATAAATAAATA
2675665 ATATA
1 ATATA
2675670 TATAGGGGGC
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
12 10 0.13
13 21 0.27
14 31 0.39
15 10 0.13
16 7 0.09
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (13 bp):
ATATAAATAAATA
Found at i:2676401 original size:39 final size:39
Alignment explanation
Indices: 2676351--2676431 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
2676341 ATTTCAAAAC
2676351 ATTTTCATTCAGTGGAGTTGAAGAATAACTCCTTGTCAA
1 ATTTTCATTCAGTGGAGTTGAAGAATAACTCCTTGTCAA
2676390 ATTTTCATTCAGTGGAGTTGAAGAATAACTCCTTGTCAA
1 ATTTTCATTCAGTGGAGTTGAAGAATAACTCCTTGTCAA
2676429 ATT
1 ATT
2676432 GAATTGCGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (39 bp):
ATTTTCATTCAGTGGAGTTGAAGAATAACTCCTTGTCAA
Found at i:2676874 original size:85 final size:83
Alignment explanation
Indices: 2676753--2676935 Score: 197
Period size: 83 Copynumber: 2.2 Consensus size: 83
2676743 ATTTTGTTGG
* * ** * * * **
2676753 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTAATTTGCCTCT-GTGTTGAATGTAATC
1 CAGATAACCCTTCTTGCCGTGAGCTATGCTACAAA-TT-ATATGCCT-TGGAGCTGAACATAATC
2676817 GAACTCGAAGGTATTTGATGA
63 GAACTCGAAGGTATTTGATGA
* * *
2676838 CAGATAACCCTTCTTGCCGTGAGTTATGCTACAAATTATATGCCTTGGAGCTGAGCATAGTCGAA
1 CAGATAACCCTTCTTGCCGTGAGCTATGCTACAAATTATATGCCTTGGAGCTGAACATAATCGAA
* *
2676903 CTCGAAGGTCTTTGTTGA
66 CTCGAAGGTATTTGATGA
*
2676921 TAGATAACCCTTCTT
1 CAGATAACCCTTCTT
2676936 TGAGTTGGAT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
82 1 0.01
83 49 0.60
84 2 0.02
85 30 0.37
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (83 bp):
CAGATAACCCTTCTTGCCGTGAGCTATGCTACAAATTATATGCCTTGGAGCTGAACATAATCGAA
CTCGAAGGTATTTGATGA
Found at i:2677371 original size:109 final size:108
Alignment explanation
Indices: 2677162--2677363 Score: 332
Period size: 109 Copynumber: 1.9 Consensus size: 108
2677152 TTGGAACTAG
* *
2677162 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTC
1 GAAATTGTTTGTTGACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
* *
2677227 AATATCCTTCGTTATGAAGTTGAAATTGACTCTGAATGAAACT
66 AATATCCCTCGATATGAAGTTGAAATTGACTCTGAATGAAACT
* *
2677270 GAAAGTTGTTTGTTGACAATCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
1 GAAA-TTGTTTGTTGACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTC
*
2677335 CAATATCCCTCGATGTGAAGTTGAAATTG
65 CAATATCCCTCGATATGAAGTTGAAATTG
2677364 GTTCTGAAAC
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
108 4 0.05
109 82 0.95
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (108 bp):
GAAATTGTTTGTTGACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
AATATCCCTCGATATGAAGTTGAAATTGACTCTGAATGAAACT
Found at i:2678100 original size:67 final size:65
Alignment explanation
Indices: 2677969--2678429 Score: 282
Period size: 65 Copynumber: 6.8 Consensus size: 65
2677959 AAGATATCTG
* * * * **
2677969 TTGTTTCATGAGAAAC-GATCTTAAGGGAAACTAAATTTTGTTTTAAGGGAAATAAATTTGAAGA
1 TTGTTTCAAGAGAAACTG-TCTCAAGGGAGAC-AAAATTTGTTTTAAGGGAAATAAATTCAAAGA
2678033 TTT
64 -TT
*
2678036 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
2678101 T
65 T
* * * * * *
2678102 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
* *
2678167 ACAAA-ACT
57 TCAAAGATT
* * * * * * * * * *
2678175 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * *
2678240 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
*
2678305 ACAAA-ATT
57 TCAAAGATT
* * * * * * *** *
2678313 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * *
2678377 TATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTGTTTCAAGTGAAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAA
2678430 CTATCTCAAG
Statistics
Matches: 311, Mismatches: 59, Indels: 49
0.74 0.14 0.12
Matches are distributed among these distances:
64 11 0.04
65 117 0.38
66 18 0.06
67 29 0.09
68 26 0.08
69 1 0.00
70 1 0.00
72 2 0.01
73 96 0.31
74 10 0.03
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:2678153 original size:36 final size:36
Alignment explanation
Indices: 2678101--2678363 Score: 290
Period size: 36 Copynumber: 7.4 Consensus size: 36
2678091 ATTCAAAGAT
*
2678101 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
2678137 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * *
2678173 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
2678210 TTTGTTTCAAAGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
2678239 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
2678275 CTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
2678311 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
2678348 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
2678364 TGTTTTCAAT
Statistics
Matches: 191, Mismatches: 25, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
30 1 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 101 0.53
37 66 0.35
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:2678203 original size:138 final size:138
Alignment explanation
Indices: 2678047--2678449 Score: 520
Period size: 138 Copynumber: 2.9 Consensus size: 138
2678037 ATGTTTCAAG
* * * *
2678047 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAG
*
2678112 GGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
2678177 GTTCCAAA
131 GTTCCAAA
* * * *
2678185 AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAG
* * * *
2678250 GGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTT
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
* *
2678315 GTTTCAAG
131 GTTCCAAA
* * * * * * *
2678323 GGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAA
1 AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAA
* * * * * * *
2678387 GAGAAACTGTCTTAAGGGAGACAAAATTTTGTTTCAAGTGAAACTATCTCAAGTGAGATAAAA
65 GGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2678450 TCTTCTTTTT
Statistics
Matches: 229, Mismatches: 34, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
137 3 0.01
138 195 0.85
139 31 0.14
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:2678267 original size:102 final size:102
Alignment explanation
Indices: 2678137--2678321 Score: 300
Period size: 102 Copynumber: 1.8 Consensus size: 102
2678127 AGAGACGAAA
*
2678137 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-GTTCCAAAAGAAACTGTCTCAAGAG
*
2678202 AGACGAAA-TTTGTTTCAAAGAAAACATATTCAAATAT
65 AGACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
* * **
2678239 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTCCAAAAGAAACTGTCTCAAGAGA
2678304 GACAAAATTTTGTTTCAA
66 GACAAAATTTTGTTTCAA
2678322 GGGAAACTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
101 28 0.37
102 48 0.63
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
Found at i:2678349 original size:37 final size:36
Alignment explanation
Indices: 2678237--2678444 Score: 193
Period size: 37 Copynumber: 5.9 Consensus size: 36
2678227 ATATTCAAAT
2678237 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
**
2678273 AACTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AA
*
2678310 ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAA
1 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AA
* * *
2678347 A-TTTATTTCAAGGGAAA-TGTTTTC-A-A-TG----
1 ATTTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAA
* * *
2678375 -TTTATGTTTCAAGAGAAACTGTCTTAAGGGAGACAAA
1 ATTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AA
* * *
2678412 ATTTTGTTTCAAGTGAAACTATCTCAAGTGAGA
1 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
2678445 TAAAATCTTC
Statistics
Matches: 138, Mismatches: 20, Indels: 27
0.75 0.11 0.15
Matches are distributed among these distances:
28 2 0.01
29 14 0.10
30 3 0.02
32 1 0.01
33 1 0.01
34 1 0.01
35 2 0.01
36 50 0.36
37 61 0.44
38 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (36 bp):
ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:2680012 original size:69 final size:69
Alignment explanation
Indices: 2679901--2680038 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
2679891 TGTCTCTCTC
2679901 TTGATGCTCCATGATCTTCGAGTAGAGTGATGCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTAGAGTGATGCAGTAATTCAGAAATGATTGTGCTTGATCAATC
2679966 TCAT
66 TCAT
* * * *
2679970 TTGATGCTCTATGATCTTCGAGT-GAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAAT
1 TTGATGCTCCATGATCTTCGAGTAG-AGTGATGCAGTAATTCAGAAATGATTGTGCTTGATCAAT
2680034 CTCAT
65 CTCAT
2680039 AGTTTAAATC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 1 0.02
69 63 0.98
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTAGAGTGATGCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:2682536 original size:12 final size:12
Alignment explanation
Indices: 2682519--2682546 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2682509 GGACTAAGTT
2682519 AAACTCGAGAGG
1 AAACTCGAGAGG
2682531 AAACTCGAGAGG
1 AAACTCGAGAGG
2682543 AAAC
1 AAAC
2682547 ATTCCCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.18, G:0.29, T:0.07
Consensus pattern (12 bp):
AAACTCGAGAGG
Found at i:2683324 original size:9 final size:9
Alignment explanation
Indices: 2683312--2683355 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
2683302 AAACACGTAA
2683312 AAAATAAAT
1 AAAATAAAT
2683321 AAAATAAAAT
1 AAAAT-AAAT
*
2683331 AAAAATAAAC
1 -AAAATAAAT
*
2683341 AAAATGAAT
1 AAAATAAAT
2683350 AAAATA
1 AAAATA
2683356 TTAAAAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 17 0.59
10 7 0.24
11 5 0.17
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:2683418 original size:18 final size:18
Alignment explanation
Indices: 2683397--2683444 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2683387 AATTAATGGA
2683397 GTAAAAAAATAAAAAAAG
1 GTAAAAAAATAAAAAAAG
*
2683415 GTAAAAGAAAT-TAAAAAG
1 GTAAAA-AAATAAAAAAAG
2683433 G-AATAAAAATAA
1 GTAA-AAAAATAA
2683445 TGTGTACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.24
18 15 0.60
19 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (18 bp):
GTAAAAAAATAAAAAAAG
Found at i:2683523 original size:23 final size:23
Alignment explanation
Indices: 2683479--2683523 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2683469 CTAAAACAAA
* * *
2683479 TAAAAATAATAAATATATAATAC
1 TAAAAATAACAAATAAAAAATAC
*
2683502 TAAATATAACAAATAAAAAATA
1 TAAAAATAACAAATAAAAAATA
2683524 AGGAAAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAAATAACAAATAAAAAATAC
Found at i:2683563 original size:30 final size:31
Alignment explanation
Indices: 2683507--2683597 Score: 98
Period size: 30 Copynumber: 3.0 Consensus size: 31
2683497 AATACTAAAT
* *
2683507 ATAACAAATAAAAAATAAGGAAAAATATAATAG
1 ATAA-AAATAAAATA-AAGTAAAAATATAATAG
*
2683540 A-AAAAATAAAATAAAGTAAAAATATAATAT
1 ATAAAAATAAAATAAAGTAAAAATATAATAG
* *
2683570 ATATAAAT-AAATAAA-TAAAAATAGAATA
1 ATAAAAATAAAATAAAGTAAAAATATAATA
2683598 TTAAGAAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
29 12 0.23
30 23 0.44
31 14 0.27
32 2 0.04
33 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.22
Consensus pattern (31 bp):
ATAAAAATAAAATAAAGTAAAAATATAATAG
Found at i:2683575 original size:22 final size:22
Alignment explanation
Indices: 2683550--2683635 Score: 56
Period size: 22 Copynumber: 3.9 Consensus size: 22
2683540 AAAAAATAAA
2683550 ATAAAGTAAAAATATAATATAT
1 ATAAAGTAAAAATATAATATAT
*
2683572 ATAAA-TAAATAA-ATAA-AAAT
1 ATAAAGTAAA-AATATAATATAT
* *
2683592 AGAATATTAAGAAAT-T-ATATAT
1 ATAA-AGTAA-AAATATAATATAT
*
2683614 AAAAATGTATAAAATATAATAT
1 ATAAA-GTA-AAAATATAATAT
2683636 TAAGAAACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
20 6 0.12
21 11 0.22
22 25 0.51
23 3 0.06
24 4 0.08
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
ATAAAGTAAAAATATAATATAT
Found at i:2683591 original size:14 final size:14
Alignment explanation
Indices: 2683471--2683597 Score: 69
Period size: 14 Copynumber: 8.7 Consensus size: 14
2683461 AGTATTCACT
*
2683471 AAAACAAATAAA-A
1 AAAATAAATAAATA
* *
2683484 ATAATAAATATATA
1 AAAATAAATAAATA
* * *
2683498 ATACTAAATATAACA
1 AAAATAAATA-AATA
* **
2683513 AATAAAAAATAAGGA
1 AA-AATAAATAAATA
*
2683528 AAAATATAATAGA-A
1 AAAATA-AATAAATA
2683542 AAAATAAAATAAAGTA
1 AAAAT-AAATAAA-TA
*
2683558 AAAATATAATATATA
1 AAAATA-AATAAATA
*
2683573 TAAATAAATAAATA
1 AAAATAAATAAATA
2683587 AAAATAGAATA
1 AAAATA-AATA
2683598 TTAAGAAATT
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
13 9 0.10
14 36 0.42
15 24 0.28
16 17 0.20
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (14 bp):
AAAATAAATAAATA
Found at i:2683606 original size:29 final size:29
Alignment explanation
Indices: 2683543--2683619 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
2683533 ATAATAGAAA
* *
2683543 AAATAAAATAAAGTAAAAATATAATATATAT
1 AAAT-AAATAAA-TAAAAATAGAATATATAG
2683574 AAATAAATAAATAAAAATAGAATAT-TAAG
1 AAATAAATAAATAAAAATAGAATATAT-AG
* *
2683603 AAAT-TATATATAAAAAT
1 AAATAAATAAATAAAAAT
2683620 GTATAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 12 0.29
29 18 0.44
30 7 0.17
31 4 0.10
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (29 bp):
AAATAAATAAATAAAAATAGAATATATAG
Found at i:2683662 original size:42 final size:40
Alignment explanation
Indices: 2683565--2683662 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 40
2683555 GTAAAAATAT
*
2683565 AATATATATA-AATAAATAAATAAAAATAGAATATTAAGA
1 AATATATATATAATAAATGAATAAAAATAGAATATTAAGA
* *
2683604 AAT-TATATATAA-AAATGTAT-AAAATATAATATTAAGAAA
1 AATATATATATAATAAATGAATAAAAATAGAATATTAAG--A
*
2683643 CAATATATACATAATAAATG
1 -AATATATATATAATAAATG
2683663 GAGAAACATT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
37 15 0.31
38 12 0.24
39 6 0.12
40 3 0.06
41 8 0.16
42 5 0.10
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (40 bp):
AATATATATATAATAAATGAATAAAAATAGAATATTAAGA
Found at i:2683693 original size:2 final size:2
Alignment explanation
Indices: 2683681--2683748 Score: 65
Period size: 2 Copynumber: 36.0 Consensus size: 2
2683671 TTAATACATC
* *
2683681 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA TA -A GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
*
2683722 TA TA TA TA -A TA TA AA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2683749 AATAAAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
1 5 0.09
2 48 0.87
3 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (2 bp):
TA
Found at i:2683700 original size:16 final size:16
Alignment explanation
Indices: 2683681--2683749 Score: 72
Period size: 16 Copynumber: 4.3 Consensus size: 16
2683671 TTAATACATC
2683681 TATACATATATATAT-A
1 TATA-ATATATATATAA
*
2683697 TATATATATATATAATGA
1 TATA-ATATATAT-ATAA
*
2683715 TATAAGATATATATAA
1 TATAATATATATATAA
2683731 TATAA-ATA-ATATAA
1 TATAATATATATATAA
2683745 TATAA
1 TATAA
2683750 ATAAAAAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.23
15 3 0.06
16 20 0.42
17 9 0.19
18 5 0.10
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (16 bp):
TATAATATATATATAA
Found at i:2683729 original size:25 final size:25
Alignment explanation
Indices: 2683694--2683744 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2683684 ACATATATAT
*
2683694 ATATATATATATATATAATGATATAAG
1 ATATATATA-ATATA-AATAATATAAG
2683721 ATATATATAATATAAATAATATAA
1 ATATATATAATATAAATAATATAA
2683745 TATAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 5 0.22
27 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
ATATATATAATATAAATAATATAAG
Found at i:2683749 original size:14 final size:14
Alignment explanation
Indices: 2683714--2683753 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 14
2683704 ATATATAATG
2683714 ATATAAGATATATATA
1 ATATAA-ATA-ATATA
2683730 ATATAAATAATATA
1 ATATAAATAATATA
2683744 ATATAAATAA
1 ATATAAATAA
2683754 AAAAAGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.62
15 3 0.12
16 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
ATATAAATAATATA
Found at i:2685424 original size:22 final size:22
Alignment explanation
Indices: 2685394--2685476 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
2685384 GGCATGTTAA
*
2685394 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTCTGT
* * *
2685416 ATTTTTCCCGAAGGACCTCTGC
1 ATTTGTCCCGAATGACCTCTGT
*
2685438 ATATGTCCCGAATGACCTCTGT
1 ATTTGTCCCGAATGACCTCTGT
* * *
2685460 ATATGTCTCGAAGGACC
1 ATTTGTCCCGAATGACC
2685477 GCGTAGACCC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (22 bp):
ATTTGTCCCGAATGACCTCTGT
Found at i:2687828 original size:60 final size:60
Alignment explanation
Indices: 2687756--2687873 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
2687746 TCAAAACGAC
* *
2687756 CTTTCTTATTTTCAGTGATATATCATCTCATATATGATC-TTTTTGACCACATTTAATGTT
1 CTTTCTTATTTTCAGTAATATATCAACTCATATATGA-CGTTTTTGACCACATTTAATGTT
* **
2687816 CTTTCTTCTTTTCAGTAATATATCAACTCATATATGACGTTTTTGACCATTTTTAATG
1 CTTTCTTATTTTCAGTAATATATCAACTCATATATGACGTTTTTGACCACATTTAATG
2687874 AAAAACGTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 1 0.02
60 51 0.98
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49
Consensus pattern (60 bp):
CTTTCTTATTTTCAGTAATATATCAACTCATATATGACGTTTTTGACCACATTTAATGTT
Found at i:2688572 original size:26 final size:26
Alignment explanation
Indices: 2688543--2688602 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
2688533 GTTTCTATTG
*
2688543 TAATGTAATGTAGGAGATAATGTTTC
1 TAATGTAATGTAGGAGATAATGCTTC
** *
2688569 TAATGTAATGTTTGAGTTAATGCTTC
1 TAATGTAATGTAGGAGATAATGCTTC
2688595 TAATGTAA
1 TAATGTAA
2688603 AATTTAGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (26 bp):
TAATGTAATGTAGGAGATAATGCTTC
Found at i:2689418 original size:29 final size:29
Alignment explanation
Indices: 2689375--2689431 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2689365 TTAACGACAG
*
2689375 AAAACACTATGTATGAAA-TCGAGAATTTT
1 AAAACACTATATATGAAACT-GAGAATTTT
*
2689404 AAAACATTATATATGAAACTGAGAATTT
1 AAAACACTATATATGAAACTGAGAATTT
2689432 GATATACTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (29 bp):
AAAACACTATATATGAAACTGAGAATTTT
Found at i:2690529 original size:15 final size:15
Alignment explanation
Indices: 2690509--2690541 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2690499 TTAGCTGGGT
*
2690509 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
2690524 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
2690539 GGG
1 GGG
2690542 TAATGTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:2693320 original size:82 final size:81
Alignment explanation
Indices: 2693169--2693408 Score: 364
Period size: 82 Copynumber: 3.0 Consensus size: 81
2693159 CCCTTATTGA
*
2693169 AGCAAATTAACATATTTAACG--GGCAATTGTTTTGACAC-GTCTTTAAAATCTTGCTAGATAAT
1 AGCAGATTAACATATTTAACGACGG--ATTGTTTTGACACAGTCTTTAAAATCTTGCTAGATAAT
2693231 ATCTTCTAAAAGCTAAAT
64 ATCTTCTAAAAGCTAAAT
* *
2693249 GGCAGATTAACATATTTAACGACGGATTGTTTTGACACGAGCCTTTAAAATCTTGCTAGATAATA
1 AGCAGATTAACATATTTAACGACGGATTGTTTTGACAC-AGTCTTTAAAATCTTGCTAGATAATA
2693314 TCTTCTAAAAGCTAAAT
65 TCTTCTAAAAGCTAAAT
* *
2693331 AGCAGATTAACATATTTAACGACGGATTGTTTTG--ACAGTCTTTAAAATCATGCTAGATAGTAT
1 AGCAGATTAACATATTTAACGACGGATTGTTTTGACACAGTCTTTAAAATCTTGCTAGATAATAT
*
2693394 CTTCTAACAGCTAAA
66 CTTCTAAAAGCTAAA
2693409 ATGTACAAAT
Statistics
Matches: 148, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
79 38 0.26
80 34 0.23
82 76 0.51
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (81 bp):
AGCAGATTAACATATTTAACGACGGATTGTTTTGACACAGTCTTTAAAATCTTGCTAGATAATAT
CTTCTAAAAGCTAAAT
Found at i:2695019 original size:2 final size:2
Alignment explanation
Indices: 2695012--2695039 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2695002 AAGTCTGTGA
2695012 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
2695040 GTACAGTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2695482 original size:32 final size:32
Alignment explanation
Indices: 2695443--2695505 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
2695433 GCATCGAAAT
2695443 ATGTTATAAAATAGGGGAGTTAGATTTTGGGG
1 ATGTTATAAAATAGGGGAGTTAGATTTTGGGG
2695475 ATGTTATAAAATAGGGGAGTTAGATTTTGGG
1 ATGTTATAAAATAGGGGAGTTAGATTTTGGG
2695506 TGAAATCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.33, T:0.35
Consensus pattern (32 bp):
ATGTTATAAAATAGGGGAGTTAGATTTTGGGG
Found at i:2695496 original size:16 final size:16
Alignment explanation
Indices: 2695445--2695496 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2695435 ATCGAAATAT
2695445 GTTATAAAATAGGGGA
1 GTTATAAAATAGGGGA
* ** *
2695461 GTTA-GATTTTGGGGA
1 GTTATAAAATAGGGGA
2695476 TGTTATAAAATAGGGGA
1 -GTTATAAAATAGGGGA
2695493 GTTA
1 GTTA
2695497 GATTTTGGGT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 7 0.27
16 12 0.46
17 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (16 bp):
GTTATAAAATAGGGGA
Found at i:2695834 original size:105 final size:99
Alignment explanation
Indices: 2695656--2695984 Score: 306
Period size: 106 Copynumber: 3.2 Consensus size: 99
2695646 AATTTTATTG
* * *
2695656 TTTTATTTTTTATTTTTATTTGAAATATAAATTAATTAAATTATTTATTTTGATTTTAAATATTA
1 TTTTTTTTTTTATTTTTATTT-AAATATAAATT-ATTAGATTATTTATTTTGATTTTACATATTA
* * *
2695721 AACAGTATTAGAGTGGTTTGGTAAGTTTAATTTAAA
64 AATAGTATTTGAGTGGTTTGGTAAGTTTAGTTTAAA
*
2695757 TTTTCGTGTAATTTTTGTTTTTAATTTAAAT-TATAATTATTAGATTATTTATTTTGATTTTACA
1 TTTT--T-T--TTTTTATTTTT-ATTTAAATATA-AATTATTAGATTATTTATTTTGATTTTACA
* * *** *
2695821 TATTAAGTTGTATTTGAGTAAAACTTGGTAAATTTAGTTTAAA
59 TATTAAATAGTATTTGAGT--GGTTTGGTAAGTTTAGTTTAAA
* *
2695864 TTATTTTTTTTTATTTTTTTATTGAGTAATATAAATTATTAGATTGA-TTATTTTTATTTTAC-T
1 TT-TTTTTTTTTA--TTTTTATTTA--AATATAAATTATTAGATT-ATTTATTTTGATTTTACAT
*
2695927 GATTAAATCGTATTTGAGTGGTTTGGTAAGTTTAGTTT-AA
60 -ATTAAATAGTATTTGAGTGGTTTGGTAAGTTTAGTTTAAA
*
2695967 TTTTTTTTGTTTTTTTTT
1 TTTTTTTT-TTTATTTTT
2695985 GTTTTTATTA
Statistics
Matches: 187, Mismatches: 23, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
101 9 0.05
102 6 0.03
103 12 0.06
104 20 0.11
105 48 0.26
106 64 0.34
107 26 0.14
108 2 0.01
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (99 bp):
TTTTTTTTTTTATTTTTATTTAAATATAAATTATTAGATTATTTATTTTGATTTTACATATTAAA
TAGTATTTGAGTGGTTTGGTAAGTTTAGTTTAAA
Found at i:2695923 original size:106 final size:106
Alignment explanation
Indices: 2695633--2696019 Score: 273
Period size: 106 Copynumber: 3.6 Consensus size: 106
2695623 AGCGATTTGA
* * * * *
2695633 TAAATTTAGTGTAA-ATTTTATTGTTTTATTTTTTATTTTTATT-TGAAATATAAATTAATTAAA
1 TAAATTTAGTTTAATATTAT-TTG-TTT-TTTATTGTTTTTATTATG-AATATAAATT-ATTAGA
* * ***
2695696 TTATTTATTTTGATTTTAAAT-ATTAAA-CAGTATTAGAGTGGTTTGG
61 TTATTTATTTTGATTTT-ACTGATTAAATC-GTATTTGAGTAACTTGG
* * ** *
2695742 TAAGTTTAATTTAA-ATT-TTCGTGTAATTT-TTGTTTTTAATT-TAAAT-TATAATTATTAGAT
1 TAAATTTAGTTTAATATTATT--TGTTTTTTATTGTTTTT-ATTATGAATATA-AATTATTAGAT
* *
2695802 TATTTATTTTGATTTTACAT-ATTAAGTTGTATTTGAGTAAAACTTGG
62 TATTTATTTTGATTTTAC-TGATTAAATCGTATTTGAGT--AACTTGG
2695849 TAAATTTAGTTTAA-ATTATTT-TTTTTTATT-TTTTTATTGA-GTAATATAAATTATTAGATTG
1 TAAATTTAGTTTAATATTATTTGTTTTTTATTGTTTTTATT-ATG-AATATAAATTATTAGATT-
* ***
2695910 A-TTATTTTTATTTTACTGATTAAATCGTATTTGAGTGGTTTGG
63 ATTTATTTTGATTTTACTGATTAAATCGTATTTGAGTAACTTGG
* * * * *
2695953 TAAGTTTAGTTTAATTTTTTTTGTTTTTTTTTGTTTTTATTATGAATATAAATTAATTAGAATAT
1 TAAATTTAGTTTAATATTATTTGTTTTTTATTGTTTTTATTATGAATATAAATT-ATTAGATTAT
2696018 TT
65 TT
2696020 TTTATTTTTA
Statistics
Matches: 225, Mismatches: 31, Indels: 46
0.75 0.10 0.15
Matches are distributed among these distances:
104 21 0.09
105 54 0.24
106 82 0.36
107 48 0.21
108 4 0.02
109 16 0.07
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (106 bp):
TAAATTTAGTTTAATATTATTTGTTTTTTATTGTTTTTATTATGAATATAAATTATTAGATTATT
TATTTTGATTTTACTGATTAAATCGTATTTGAGTAACTTGG
Found at i:2696046 original size:154 final size:154
Alignment explanation
Indices: 2695867--2696180 Score: 472
Period size: 154 Copynumber: 2.0 Consensus size: 154
2695857 GTTTAAATTA
* * *
2695867 TTTTTTTTTATTTTTTTATTGAGTAATATAAATTATTAGATTGATTATTTTTATTTTAC-TGATT
1 TTTTTTTTTATTTTTTTATTCAGTAATATAAATTATTAGACTAATTATTTTTATTTTACAT-ATT
* * * * *
2695931 AAATCGTATTTGAGTGGTTTGGTAAGTTTAGTTTAATTTTTTTTG-TTT-TTTTTTGTTTTTATT
65 AAATCGTATTTGAGTAGTTTGATAAGTTTAGTTCAAATTTTATTGTTTTGTTTTTTGTTTTTATT
*
2695994 ATGAATATAAATTAATTAGAATATT
130 ATAAATATAAATTAATTAGAATATT
2696019 TTTTATTTTTAGTTTTTTTATTCAGTAATATAAATTATTAGACTAATTATTTTTATTTTACATAT
1 TTTT-TTTTTA-TTTTTTTATTCAGTAATATAAATTATTAGACTAATTATTTTTATTTTACATAT
2696084 TAAATCGTATTTGAGTAGTTTGATAAGTTTAGTTCAAATTTTATTGTTTTGTTTTTTGTTTTTAT
64 TAAATCGTATTTGAGTAGTTTGATAAGTTTAGTTCAAATTTTATTGTTTTGTTTTTTGTTTTTAT
* *
2696149 TGTAAATATAAATTAATTAGATTATT
129 TATAAATATAAATTAATTAGAATATT
*
2696175 TATTTT
1 TTTTTT
2696181 GATTTAATAT
Statistics
Matches: 145, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
152 4 0.03
153 6 0.04
154 89 0.61
155 6 0.04
156 40 0.28
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (154 bp):
TTTTTTTTTATTTTTTTATTCAGTAATATAAATTATTAGACTAATTATTTTTATTTTACATATTA
AATCGTATTTGAGTAGTTTGATAAGTTTAGTTCAAATTTTATTGTTTTGTTTTTTGTTTTTATTA
TAAATATAAATTAATTAGAATATT
Found at i:2698430 original size:36 final size:36
Alignment explanation
Indices: 2698349--2698430 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
2698339 ATCGATATTA
* *
2698349 ATCATATTCATTCAAACATAACATCAACAAATATCC
1 ATCAAATTCATTCAAACATAACATCAACAAATAGCC
* ** *
2698385 ATCACATTCATTCAAATTTAACATCAACAAGTAGGCC
1 ATCAAATTCATTCAAACATAACATCAACAAATA-GCC
2698422 AT-AAATTCA
1 ATCAAATTCA
2698431 ATTATTCGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 35 0.90
37 4 0.10
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.28
Consensus pattern (36 bp):
ATCAAATTCATTCAAACATAACATCAACAAATAGCC
Found at i:2702455 original size:59 final size:59
Alignment explanation
Indices: 2702356--2702492 Score: 186
Period size: 59 Copynumber: 2.3 Consensus size: 59
2702346 CAGCAGGCTG
** * *
2702356 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** *
2702415 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
2702474 CATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
2702493 CGGTGCTTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 1 0.02
59 64 0.98
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:2703695 original size:16 final size:17
Alignment explanation
Indices: 2703664--2703695 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2703654 ATAACTACTT
2703664 ATGATTAAATTATAATA
1 ATGATTAAATTATAATA
2703681 ATGATTAAA-TATAAT
1 ATGATTAAATTATAAT
2703696 TAAAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATGATTAAATTATAATA
Found at i:2704126 original size:28 final size:28
Alignment explanation
Indices: 2704094--2704166 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
2704084 ACATAGAGAT
*
2704094 ATTTTATTTGAATAATACTTCAAATAAA
1 ATTTTATTCGAATAATACTTCAAATAAA
*
2704122 ATTTTATTCGAATAATACTTTAAATAAA
1 ATTTTATTCGAATAATACTTCAAATAAA
* *
2704150 GTCTTATTCGAATAATA
1 ATTTTATTCGAATAATA
2704167 TTTACATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (28 bp):
ATTTTATTCGAATAATACTTCAAATAAA
Found at i:2705502 original size:2 final size:2
Alignment explanation
Indices: 2705495--2705533 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2705485 AACTAGTAAT
2705495 TA TA TA 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 TA TA TA T
2705534 TGAATTATGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2706782 original size:3 final size:3
Alignment explanation
Indices: 2706767--2706822 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
2706757 ATTTGGTTTT
* *
2706767 TTA TTA -TA TTTA TTA -TA TTTA TTA TTA TTT TTA TTA TTA ATA TTA
1 TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
2706812 TTA TT- TTA TTA
1 TTA TTA TTA TTA
2706823 CAGATACAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
2 6 0.14
3 34 0.77
4 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2706791 original size:21 final size:20
Alignment explanation
Indices: 2706767--2706822 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
2706757 ATTTGGTTTT
*
2706767 TTATTATATTTATTA-TATTTA
1 TTATTAT-TTTATTATTA-ATA
2706788 TTATTATTTTTATTATTAATA
1 TTATTA-TTTTATTATTAATA
2706809 TTATTATTTTATTA
1 TTATTATTTTATTA
2706823 CAGATACAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.25
21 21 0.66
22 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTATTTTATTATTAATA
Found at i:2707931 original size:2 final size:2
Alignment explanation
Indices: 2707924--2707961 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2707914 TAAAAATAAT
2707924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2707962 TAATAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2708785 original size:18 final size:16
Alignment explanation
Indices: 2708764--2708798 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2708754 TTTTATTGTT
2708764 TATATA-AATAAATATA
1 TATATATAATAAATA-A
2708780 TATATATAATAAATAA
1 TATATATAATAAATAA
2708796 TAT
1 TAT
2708799 TTGTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATAATAAATAA
Found at i:2715596 original size:114 final size:114
Alignment explanation
Indices: 2715388--2715610 Score: 347
Period size: 114 Copynumber: 2.0 Consensus size: 114
2715378 TTCCACGTTA
* * *
2715388 TCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * * * *
2715453 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTTC
66 TTCGGTAGAAACCACAAAACCAATCATTAGAATTGAAAGATGAATTTTC
2715502 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* **
2715567 TTCGGTAGGAACCACTGAACCAATCATTAGAATTGAAAGATGAA
66 TTCGGTAGAAACCACAAAACCAATCATTAGAATTGAAAGATGAA
2715611 CTGCATGATT
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTCGGTAGAAACCACAAAACCAATCATTAGAATTGAAAGATGAATTTTC
Found at i:2716627 original size:124 final size:122
Alignment explanation
Indices: 2716453--2717036 Score: 599
Period size: 124 Copynumber: 4.9 Consensus size: 122
2716443 TGCCATGTAG
*
2716453 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
2716514 TTCAACCTTTTGCATAATTCTATCACATAAGGAGATAGATCAGCATCAGCTTTTCCAAAGAA
63 TTCAACCTTTTGCATAATTCTATCACATAA-GAGATAGATCAGCATCAGCTTTTCC-AAGAA
* * * * * *
2716576 AGTTCATAATGAGAAGAACTAATTTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
2716641 AACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGCATCAGCTTTTCCAGAGAA
66 AACCTTTTGCATAATTCTATCACATAA-GAGATAGATCAGCATCAGCTTTTCCA-AGAA
2716700 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * ** * * * ***
2716765 AACTTTTTTGCTTGAATTC-AT--CAT--TCGATGGATCAGCATTACCAGGT-C--G--
66 AAC-CTTTTGCAT-AATTCTATCACATAAGAGATAGATCAGCATCAGCTTTTCCAAGAA
2716814 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * * * **
2716879 AA-CTTTTCGCTTGAATTC-AT--CAT--TCGATGGATCA--A-CA---TTACCAGGTCG
66 AACCTTTT-GCAT-AATTCTATCACATAAGAGATAGATCAGCATCAGCTTTTCCAAG-AA
2716927 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
2716992 AATCTTTTGCATGATTCTATCACAGAAAGAGATAGATCAACATCA
66 AACCTTTTGCATAATTCTATCACA-TAAGAGATAGATCAGCATCA
2717037 ACATTTCTAG
Statistics
Matches: 404, Mismatches: 33, Indels: 50
0.83 0.07 0.10
Matches are distributed among these distances:
108 1 0.00
110 2 0.00
111 1 0.00
112 8 0.02
113 98 0.24
114 72 0.18
115 2 0.00
116 1 0.00
118 8 0.02
119 1 0.00
120 25 0.06
121 7 0.02
122 1 0.00
123 23 0.06
124 140 0.35
125 9 0.02
126 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (122 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCATAATTCTATCACATAAGAGATAGATCAGCATCAGCTTTTCCAAGAA
Found at i:2716631 original size:20 final size:20
Alignment explanation
Indices: 2716571--2716633 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
2716561 AGCTTTTCCA
2716571 AAGAAAGTTCATAATGAGAAG
1 AAGAAA-TTCATAATGAGAAG
** *
2716592 AACTAATT--TAAAGAAGGAAG
1 AAGAAATTCATAATG-A-GAAG
2716612 AAGAAATTCATAATGAGAAG
1 AAGAAATTCATAATGAGAAG
2716632 AA
1 AA
2716634 TTTGTTTAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 18 0.56
21 5 0.16
22 4 0.12
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.19
Consensus pattern (20 bp):
AAGAAATTCATAATGAGAAG
Found at i:2716825 original size:114 final size:114
Alignment explanation
Indices: 2716700--2716999 Score: 566
Period size: 113 Copynumber: 2.6 Consensus size: 114
2716690 TTCCAGAGAA
2716700 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
2716765 AACTTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCG
66 AACTTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTCG
2716814 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
2716879 AAC-TTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTCG
66 AACTTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTCG
2716927 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
2716992 AATCTTTT
66 AA-CTTTT
2717000 GCATGATTCT
Statistics
Matches: 182, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
113 110 0.60
114 69 0.38
115 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (114 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTCG
Found at i:2717361 original size:9 final size:10
Alignment explanation
Indices: 2717347--2717430 Score: 81
Period size: 9 Copynumber: 8.7 Consensus size: 10
2717337 TATTTGGTTT
2717347 TTTATTA-TA
1 TTTATTATTA
2717356 TTTATTATT-
1 TTTATTATTA
*
2717365 TTTATTACTA
1 TTTATTATTA
2717375 -TTATTATTA
1 TTTATTATTA
2717384 TTT-TTATTA
1 TTTATTATTA
2717393 TTAATATTATT-
1 TT--TATTATTA
2717404 TTTATTATTA
1 TTTATTATTA
*
2717414 -ATATTATTA
1 TTTATTATTA
2717423 TTTTATTA
1 -TTTATTA
2717431 CAGATACAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
9 46 0.74
10 3 0.05
11 8 0.13
12 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATTATTA
Found at i:2717366 original size:18 final size:20
Alignment explanation
Indices: 2717345--2717431 Score: 103
Period size: 18 Copynumber: 4.5 Consensus size: 20
2717335 TATATTTGGT
2717345 TTTTTATTA-TAT-TTATTA
1 TTTTTATTACTATATTATTA
2717363 TTTTTATTACTATTATTATTA
1 TTTTTATTACTA-TATTATTA
*
2717384 TTTTTATTA-T-TAATATTA
1 TTTTTATTACTATATTATTA
*
2717402 TTTTTATTATTAATATTATTA
1 TTTTTATTACT-ATATTATTA
2717423 -TTTTATTAC
1 TTTTTATTAC
2717432 AGATACAACC
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
18 25 0.42
19 3 0.05
20 10 0.17
21 22 0.37
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTATTACTATATTATTA
Found at i:2718806 original size:3 final size:3
Alignment explanation
Indices: 2718798--2718844 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
2718788 TTATTTAAAA
*
2718798 TAT TAT TAT TAT TAT TAT TAT TAT T-T T-T TAT TAT TAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2718844 T
1 T
2718845 TATATAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:2718830 original size:19 final size:19
Alignment explanation
Indices: 2718798--2718847 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
2718788 TTATTTAAAA
2718798 TATTATTA-TTATTATTAT
1 TATTATTATTTATTATTAT
*
2718816 TATTATTTTTTATTATTAT
1 TATTATTATTTATTATTAT
*
2718835 TTTTATTATTTAT
1 TATTATTATTTAT
2718848 ATAAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTATTATTTATTATTAT
Found at i:2718831 original size:22 final size:22
Alignment explanation
Indices: 2718803--2718845 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2718793 TAAAATATTA
2718803 TTATTATTATTATTATTATTTT
1 TTATTATTATTATTATTATTTT
*
2718825 TTATTATTATTTTTATTATTT
1 TTATTATTATTATTATTATTT
2718846 ATATAAATAA
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATTATTATTATTATTATTTT
Found at i:2718870 original size:20 final size:18
Alignment explanation
Indices: 2718845--2718881 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2718835 TTTTATTATT
2718845 TATATA-AATAAATATATA
1 TATATATAATAAATA-ATA
2718863 TATATATAATAAATAATA
1 TATATATAATAAATAATA
2718881 T
1 T
2718882 TTGTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATATATAATAAATAATA
Found at i:2724177 original size:21 final size:20
Alignment explanation
Indices: 2724126--2724177 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
2724116 TTTTCCCAAT
*
2724126 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
2724146 TCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
2724167 TCGCAATGCGA
1 TCGCAATGCGA
2724178 TACTGACTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:2724818 original size:19 final size:19
Alignment explanation
Indices: 2724794--2724841 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
2724784 ACGAGATAAT
*
2724794 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
2724813 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
*
2724832 CGCAATGCGA
1 CGCAACGCGA
2724842 TTTTTGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.50, C:0.25, G:0.19, T:0.06
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:2724883 original size:20 final size:19
Alignment explanation
Indices: 2724837--2724914 Score: 120
Period size: 19 Copynumber: 4.1 Consensus size: 19
2724827 AAAATCGCAA
*
2724837 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
2724856 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
2724875 TGCGATTTTTATTTCGCGGT
1 TGCGATTTTTATTTCGC-GT
*
2724895 TGCGATTTTCATTTCGCGT
1 TGCGATTTTTATTTCGCGT
2724914 T
1 T
2724915 ACAATTGTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 36 0.67
20 18 0.33
ACGTcount: A:0.08, C:0.17, G:0.23, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2724909 original size:39 final size:38
Alignment explanation
Indices: 2724837--2724914 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 38
2724827 AAAATCGCAA
* * *
2724837 TGCGATTTTTGTTTCGCGTTGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGT
2724875 TGCGATTTTTATTTCGCGGTTGCGATTTTCATTTCGCGT
1 TGCGATTTTTATTTCGC-GTTGCGATTTTCATTTCGCGT
2724914 T
1 T
2724915 ACAATTGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 16 0.44
39 20 0.56
ACGTcount: A:0.08, C:0.17, G:0.23, T:0.53
Consensus pattern (38 bp):
TGCGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGT
Found at i:2724985 original size:34 final size:33
Alignment explanation
Indices: 2724903--2724990 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
2724893 GTTGCGATTT
* * * * *
2724903 TCATTTCGCGTTACAATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTAGCGATAG
2724936 TCATTTCGCGTTGCGATTCTCTCGTAGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTAGCGATAG
2724969 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
2724991 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 34 0.69
34 15 0.31
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTAGCGATAG
Found at i:2724992 original size:20 final size:20
Alignment explanation
Indices: 2724969--2725015 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2724959 GTAGCGATAG
2724969 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
2724989 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
2725009 TCATTTC
1 TCATTTC
2725016 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:2727079 original size:42 final size:42
Alignment explanation
Indices: 2727019--2727128 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
2727009 GCCCGACTCG
* *
2727019 CCTATCATCCTTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCTTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
* *
2727061 CCTATCATTCC-TCGAGAGTCCCCTCCTACCGTTCAAGAGGCC
1 CCTATCA-TCCTTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
* * * *
2727103 ACTGTCATCGTTGAAGAGGTCC-CTCC
1 CCTATCATCCTTCAAGA-GTCCACTCC
2727129 CACCATGCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 2 0.04
42 47 0.84
43 7 0.12
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.25
Consensus pattern (42 bp):
CCTATCATCCTTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
Found at i:2729347 original size:20 final size:19
Alignment explanation
Indices: 2729312--2729378 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2729302 GAAACTTAAA
2729312 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
2729331 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
2729351 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
2729370 ATCGCAACG
1 ATCGCAACG
2729379 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2729386 original size:14 final size:14
Alignment explanation
Indices: 2729367--2729424 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2729357 ATGCGAAATG
2729367 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2729381 AAAATCGCAACGTGAA
1 AAAATCGCAAC--GAC
2729397 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2729413 AAAATCGCAACG
1 AAAATCGCAACG
2729425 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.58
16 6 0.16
18 10 0.26
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2729409 original size:32 final size:33
Alignment explanation
Indices: 2729351--2729467 Score: 146
Period size: 32 Copynumber: 3.4 Consensus size: 33
2729341 GGAAATGGCT
*
2729351 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
2729384 ATCGCAACGTGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
**
2729416 ATCGCAACGCGAAACACAAATCGCATCGCAACGACAAA
1 ATCGCAACGCGAAA-TGAAA----ATCGCAACGACAAA
2729454 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2729468 CACAAATCGC
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
32 29 0.40
33 14 0.19
34 2 0.03
38 28 0.38
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2729453 original size:38 final size:38
Alignment explanation
Indices: 2729402--2729479 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2729392 GTGAAATGAA
2729402 ATCGCAACGACAAAATCGCAACGCGAAACACAAATCGC
1 ATCGCAACGACAAAATCGCAACGCGAAACACAAATCGC
2729440 ATCGCAACGACAAAATCGCAACGCGAAACACAAATCGC
1 ATCGCAACGACAAAATCGCAACGCGAAACACAAATCGC
2729478 AT
1 AT
2729480 TGCGATTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.45, C:0.31, G:0.15, T:0.09
Consensus pattern (38 bp):
ATCGCAACGACAAAATCGCAACGCGAAACACAAATCGC
Found at i:2729484 original size:19 final size:19
Alignment explanation
Indices: 2729414--2729478 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
2729404 CGCAACGACA
2729414 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAACAC
*
2729433 AAATCGCATCGC--AACGAC
1 AAATCGCAACGCGAAAC-AC
2729451 AAAATCGCAACGCGAAACAC
1 -AAATCGCAACGCGAAACAC
2729471 AAATCGCA
1 AAATCGCA
2729479 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 3 0.08
18 2 0.05
19 30 0.75
20 2 0.05
21 3 0.08
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (19 bp):
AAATCGCAACGCGAAACAC
Found at i:2729515 original size:14 final size:14
Alignment explanation
Indices: 2729496--2729553 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
2729486 TTTCATTTCG
2729496 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2729510 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
2729526 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
2729542 CGTTGCGATTTT
1 CGTTGCGATTTT
2729554 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2729565 original size:33 final size:33
Alignment explanation
Indices: 2729479--2729569 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
2729469 ACAAATCGCA
*
2729479 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
2729512 TTGCGA-TTTCATTTCACATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2729544 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2729570 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2729588 original size:20 final size:19
Alignment explanation
Indices: 2729554--2729608 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2729544 TTGCGATTTT
*
2729554 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2729573 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2729593 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2729609 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2730110 original size:18 final size:18
Alignment explanation
Indices: 2730084--2730128 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2730074 GTCGATCAGA
*
2730084 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2730102 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2730120 TGATGGCTC
1 TGATGGCTC
2730129 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2731464 original size:20 final size:20
Alignment explanation
Indices: 2731439--2731481 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2731429 AATAGTTTCT
2731439 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
2731459 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
2731479 GAA
1 GAA
2731482 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2732038 original size:20 final size:20
Alignment explanation
Indices: 2731977--2732090 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
2731967 GATTATGTAT
2731977 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2731997 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2732017 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* * *** * *
2732037 TAGCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
2732058 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2732078 TATCGCATTGCGA
1 TATCGCGTTGCGA
2732091 TTTTCCCAAT
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 64 0.84
21 12 0.16
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2732070 original size:21 final size:21
Alignment explanation
Indices: 2732044--2732135 Score: 59
Period size: 20 Copynumber: 4.5 Consensus size: 21
2732034 AAGTAGCTCG
* *
2732044 TTGCGATTTTTTATTATCGCA
1 TTGCGATTTTTCAGTATCGCA
**
2732065 TTGCGA-TAGTCAGTATCGCA
1 TTGCGATTTTTCAGTATCGCA
* * *
2732085 TTGCGATTTTCCCAAT-TCGCG
1 TTGCGATTTT-TCAGTATCGCA
2732106 TTGCGATTTACTT-A-T-TCGCA
1 TTGCGATTT--TTCAGTATCGCA
2732126 TTGCGATTTT
1 TTGCGATTTT
2732136 CCTAATTCGC
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
18 1 0.02
20 30 0.54
21 21 0.38
22 3 0.05
23 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (21 bp):
TTGCGATTTTTCAGTATCGCA
Found at i:2732110 original size:41 final size:41
Alignment explanation
Indices: 2732080--2732172 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
2732070 ATAGTCAGTA
* *
2732080 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
2732121 TCGCATTGCGATTTTCCTAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
*
2732162 TTGCATTGCGA
1 TCGCATTGCGA
2732173 ATTGGTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:2732145 original size:21 final size:20
Alignment explanation
Indices: 2732080--2732172 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2732070 ATAGTCAGTA
* *
2732080 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTAAT
* *
2732101 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
*
2732121 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTACTAAT
* *
2732142 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
*
2732162 TTGCATTGCGA
1 TCGCATTGCGA
2732173 ATTGGTAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 32 0.54
21 27 0.46
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:2732646 original size:28 final size:31
Alignment explanation
Indices: 2732577--2732646 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 31
2732567 TACCAAAAAA
*
2732577 AATTAATATATTATTATTTTTATTTCATTTT
1 AATTAAAATATTATTATTTTTATTTCATTTT
* *
2732608 AATTGAGATA-TATT-TATTTT-TTT-ATTTT
1 AATTAAAATATTATTAT-TTTTATTTCATTTT
2732636 AATTAAAATAT
1 AATTAAAATAT
2732647 GGTAACTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 13 0.39
29 4 0.12
30 8 0.24
31 8 0.24
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (31 bp):
AATTAAAATATTATTATTTTTATTTCATTTT
Found at i:2734958 original size:41 final size:41
Alignment explanation
Indices: 2734876--2734958 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
2734866 ACGTAGGGTA
* *
2734876 ATAGCGCGGGGCAAGGGTCGCGTCTTACTTTTCAATTATAT
1 ATAGCGCGGGGCAAGGGTCGCGCCTTACTTTTCAATGATAT
* *
2734917 ATAGCGCGGGG-AATGGGTCGTGCCTTAGTTTT-AACTGATAT
1 ATAGCGCGGGGCAA-GGGTCGCGCCTTACTTTTCAA-TGATAT
2734958 A
1 A
2734959 ATTATATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 4 0.11
41 32 0.89
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (41 bp):
ATAGCGCGGGGCAAGGGTCGCGCCTTACTTTTCAATGATAT
Found at i:2738961 original size:21 final size:21
Alignment explanation
Indices: 2738932--2738973 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2738922 TCATCATCAC
*
2738932 CATCATCATTGTCGTCGTCGT
1 CATCATCATCGTCGTCGTCGT
*
2738953 CATCGTCATCGTCGTCGTCGT
1 CATCATCATCGTCGTCGTCGT
2738974 GAGCAACTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.31, G:0.21, T:0.36
Consensus pattern (21 bp):
CATCATCATCGTCGTCGTCGT
Found at i:2741005 original size:17 final size:16
Alignment explanation
Indices: 2740966--2741030 Score: 73
Period size: 16 Copynumber: 4.1 Consensus size: 16
2740956 CTGTAAAAAA
*
2740966 ATTAATTAAA-TACAAT
1 ATTAAATAAATTA-AAT
*
2740982 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
2740998 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
2741015 ATTAAAT--ATTAAAT
1 ATTAAATAAATTAAAT
2741029 AT
1 AT
2741031 AATAAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.20
16 18 0.41
17 17 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:2741020 original size:7 final size:7
Alignment explanation
Indices: 2740979--2741030 Score: 59
Period size: 7 Copynumber: 6.7 Consensus size: 7
2740969 AATTAAATAC
2740979 AATATTA
1 AATATTA
2740986 AATAATTTA
1 AAT-A-TTA
2740995 AATACTTA
1 AATA-TTA
2741003 AATAAATTA
1 AAT--ATTA
2741012 AATATTA
1 AATATTA
2741019 AATATTA
1 AATATTA
2741026 AATAT
1 AATAT
2741031 AATAAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 19 0.47
8 8 0.20
9 12 0.30
10 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (7 bp):
AATATTA
Found at i:2741036 original size:16 final size:14
Alignment explanation
Indices: 2740979--2741030 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 14
2740969 AATTAAATAC
2740979 AATATTAAATAATTTA
1 AATATTAAAT-A-TTA
2740995 AATACTTAAATAAATTA
1 AATA-TTAAAT--ATTA
2741012 AATATTAAATATTA
1 AATATTAAATATTA
2741026 AATAT
1 AATAT
2741031 AATAAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.26
16 10 0.29
17 13 0.38
18 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATTAAATATTA
Found at i:2741038 original size:24 final size:24
Alignment explanation
Indices: 2740992--2741040 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
2740982 ATTAAATAAT
*
2740992 TTAAATACTTAAATAAATTAAATA
1 TTAAATACTTAAATAAATAAAATA
2741016 TTAAATA-TTAAATATAATAAAATA
1 TTAAATACTTAAATA-AATAAAATA
2741040 T
1 T
2741041 ACCTTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAAATACTTAAATAAATAAAATA
Found at i:2741717 original size:24 final size:25
Alignment explanation
Indices: 2741668--2741719 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
2741658 ATACACGCAG
**
2741668 ATTTATAAAATTTTAAGAATGATAA
1 ATTTATAAAATTTTAAGAAAAATAA
2741693 ATTTAT-AAATTTT-AGAAAAATTAA
1 ATTTATAAAATTTTAAGAAAAA-TAA
2741717 ATT
1 ATT
2741720 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (25 bp):
ATTTATAAAATTTTAAGAAAAATAA
Found at i:2743760 original size:13 final size:13
Alignment explanation
Indices: 2743732--2743772 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
2743722 GGAAATCATC
*
2743732 AATTAAATACCATA
1 AATTAAA-AACATA
2743746 AATTAAAAACATA
1 AATTAAAAACATA
*
2743759 AAATAAAAACATA
1 AATTAAAAACATA
2743772 A
1 A
2743773 GTGCTTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (13 bp):
AATTAAAAACATA
Found at i:2745135 original size:32 final size:32
Alignment explanation
Indices: 2745098--2745183 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
2745088 ATTGATACTC
2745098 ATGTGCATTATCTGAATGCAAACCTAAACATA
1 ATGTGCATTATCTGAATGCAAACCTAAACATA
* *
2745130 TTGTGCATTATCTGAATGCAAACCTGAACATA
1 ATGTGCATTATCTGAATGCAAACCTAAACATA
* *
2745162 ATGTGCATTATTTGATTGCAAA
1 ATGTGCATTATCTGAATGCAAA
2745184 TGTAACACCC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (32 bp):
ATGTGCATTATCTGAATGCAAACCTAAACATA
Found at i:2746043 original size:24 final size:24
Alignment explanation
Indices: 2745933--2746050 Score: 96
Period size: 24 Copynumber: 4.9 Consensus size: 24
2745923 TGCCAATAGC
* *
2745933 ACACGAATGTACTAACACATGAGT
1 ACACAAATGTACTAATACATGAGT
* * * *
2745957 ACCCAAAGGTACTAATATAGGAGT
1 ACACAAATGTACTAATACATGAGT
* * *
2745981 ACACATATGCAATAATACATGAGT
1 ACACAAATGTACTAATACATGAGT
* * *
2746005 GCAACAAAGGCACTAATAC-TAGAGT
1 AC-ACAAATGTACTAATACAT-GAGT
2746030 ACACAAATGTACTAA-ACATGA
1 ACACAAATGTACTAATACATGA
2746051 TCAATCGATA
Statistics
Matches: 71, Mismatches: 20, Indels: 7
0.72 0.20 0.07
Matches are distributed among these distances:
23 4 0.06
24 49 0.69
25 18 0.25
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.20
Consensus pattern (24 bp):
ACACAAATGTACTAATACATGAGT
Found at i:2750973 original size:21 final size:20
Alignment explanation
Indices: 2750949--2750996 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2750939 ACTATGGTAC
* *
2750949 CGATACTGAGTCTATTAGTAG
1 CGATACTGAATCT-TCAGTAG
* *
2750970 CGATATTGAATCTTCAGTAT
1 CGATACTGAATCTTCAGTAG
2750990 CGATACT
1 CGATACT
2750997 CATCCTTGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (20 bp):
CGATACTGAATCTTCAGTAG
Found at i:2753520 original size:20 final size:18
Alignment explanation
Indices: 2753494--2753541 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2753484 CCCCTATTGG
2753494 GAGTATCGATACTCTACCTT
1 GAGTATCGATA-T-TACCTT
* * *
2753514 TAGTATCAATATTCCCTT
1 GAGTATCGATATTACCTT
2753532 GAGTATCGAT
1 GAGTATCGAT
2753542 TCCAAAAATG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 13 0.57
19 1 0.04
20 9 0.39
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (18 bp):
GAGTATCGATATTACCTT
Found at i:2754378 original size:20 final size:20
Alignment explanation
Indices: 2754355--2754425 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
2754345 CAGTATTTTA
*
2754355 GTATGGAGACCAGTCTTCTG
1 GTATGAAGACCAGTCTTCTG
*
2754375 GTATGAAGACCAGTCTTCCG
1 GTATGAAGACCAGTCTTCTG
* **
2754395 GTATGAAGACCAGTCCTCCA
1 GTATGAAGACCAGTCTTCTG
2754415 GTATGAAGACC
1 GTATGAAGACC
2754426 CATTTTTCGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (20 bp):
GTATGAAGACCAGTCTTCTG
Found at i:2755354 original size:20 final size:20
Alignment explanation
Indices: 2755311--2755362 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2755301 GATTCAATCA
*
2755311 GTATCAATACCAAAGGGGGT
1 GTATCAATACCAAAGGGAGT
*
2755331 GTATCAATACCGAAGGGAAG-
1 GTATCAATACCAAAGGG-AGT
*
2755351 GTATCGATACCA
1 GTATCAATACCA
2755363 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.19
Consensus pattern (20 bp):
GTATCAATACCAAAGGGAGT
Found at i:2755433 original size:20 final size:20
Alignment explanation
Indices: 2755385--2755437 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
2755375 ATGCAAAAAT
*
2755385 GGTATCGATACCATAGTATG
1 GGTATCGATACCATAGTAAG
*
2755405 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGTAAG
2755427 GGTATCGATAC
1 GGTATCGATAC
2755438 TAGACAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.38
22 18 0.62
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:2755959 original size:20 final size:20
Alignment explanation
Indices: 2755934--2756034 Score: 130
Period size: 20 Copynumber: 4.7 Consensus size: 20
2755924 AATTTAAAAA
2755934 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
2755954 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
2755981 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
2756001 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
2756021 GCATGAAAGGATGC
1 GCATGAAAGGATGC
2756035 CATAATTTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
20 49 0.68
21 1 0.01
23 3 0.04
24 3 0.04
26 1 0.01
27 15 0.21
ACGTcount: A:0.41, C:0.11, G:0.29, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:2755984 original size:27 final size:27
Alignment explanation
Indices: 2755954--2756078 Score: 83
Period size: 27 Copynumber: 4.1 Consensus size: 27
2755944 ATGCATTAAG
2755954 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCCATAATTGAAAAT
*
2755981 GCATGAAAGGATG-CATTAAGGCATGAAAGGAT
1 GCATGAAAGGATGCCA-TAA---TTGAAA--AT
*
2756013 GCATTAAGGCATGAAAGGATGCCATAATTTAAAAT
1 GCA-T---G----AAAGGATGCCATAATTGAAAAT
2756048 GCATGAAAGGATGCCATAAATT-AAAAT
1 GCATGAAAGGATGCCAT-AATTGAAAAT
2756075 GCAT
1 GCAT
2756079 AAATGAATGT
Statistics
Matches: 79, Mismatches: 3, Indels: 32
0.69 0.03 0.28
Matches are distributed among these distances:
26 2 0.03
27 37 0.47
28 4 0.05
30 5 0.06
31 1 0.01
32 5 0.06
33 1 0.01
34 1 0.01
35 5 0.06
36 1 0.01
37 4 0.05
40 11 0.14
41 2 0.03
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.22
Consensus pattern (27 bp):
GCATGAAAGGATGCCATAATTGAAAAT
Found at i:2755990 original size:47 final size:47
Alignment explanation
Indices: 2755921--2756014 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
2755911 AAATCGAATT
*
2755921 CATAATTTAAAAAGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAAAGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
2755968 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAAAGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
2756015 ATTAAGGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (47 bp):
CATAATTGAAAAAGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:2756047 original size:67 final size:67
Alignment explanation
Indices: 2755934--2756061 Score: 247
Period size: 67 Copynumber: 1.9 Consensus size: 67
2755924 AATTTAAAAA
2755934 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTA
2755999 AG
66 AG
*
2756001 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTTAAAATGCATGAAAGGATGC
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGC
2756062 CATAAATTAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.21
Consensus pattern (67 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTA
AG
Found at i:2762251 original size:20 final size:20
Alignment explanation
Indices: 2762226--2762277 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2762216 TTGCTAATTA
2762226 GTATCGATACCAAAGGG-AG
1 GTATCGATACCAAAGGGAAG
*
2762245 TGTATCGATACCGAAGGGAAG
1 -GTATCGATACCAAAGGGAAG
2762266 GTATCGATACCA
1 GTATCGATACCA
2762278 TTTCAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (20 bp):
GTATCGATACCAAAGGGAAG
Found at i:2762328 original size:19 final size:19
Alignment explanation
Indices: 2762300--2762373 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 19
2762290 ATGCAAAAAT
* * *
2762300 GGTATTGATACCAAAATAG
1 GGTATCGATACCATAGTAG
2762319 GGTATCGATACCATAGTATG
1 GGTATCGATACCATAGTA-G
*
2762339 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGT-AG
2762361 GGTATCGATACCA
1 GGTATCGATACCA
2762374 GGAAACATCG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 15 0.32
20 14 0.30
22 17 0.36
23 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:2762367 original size:20 final size:20
Alignment explanation
Indices: 2762317--2762373 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 20
2762307 ATACCAAAAT
2762317 AGGGTATCGATACCATAGTA
1 AGGGTATCGATACCATAGTA
* *
2762337 TGGTAGTATCGATACCATGGTA
1 AGG--GTATCGATACCATAGTA
2762359 AGGGTATCGATACCA
1 AGGGTATCGATACCA
2762374 GGAAACATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.44
22 18 0.56
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (20 bp):
AGGGTATCGATACCATAGTA
Found at i:2762897 original size:20 final size:20
Alignment explanation
Indices: 2762872--2762950 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
2762862 ATCTAGAATG
2762872 CATGAAAGGATGTATTAAGA
1 CATGAAAGGATGTATTAAGA
*
2762892 CATGAAAGGATGCCATAATTGAAAA
1 CATGAAAGGATG---T-ATT-AAGA
* *
2762917 TGCATGAAAGGATGCATTAAGG
1 --CATGAAAGGATGTATTAAGA
2762939 CATGAAAGGATG
1 CATGAAAGGATG
2762951 CCATAATTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
20 24 0.50
22 2 0.04
23 4 0.08
24 3 0.06
25 3 0.06
27 12 0.25
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.22
Consensus pattern (20 bp):
CATGAAAGGATGTATTAAGA
Found at i:2762909 original size:47 final size:46
Alignment explanation
Indices: 2762858--2763105 Score: 327
Period size: 47 Copynumber: 5.3 Consensus size: 46
2762848 AAATCGAATT
* * *
2762858 CATAATCTAGAATGCATGAAAGGATGTATTAAGACATGAAAGGATGC
1 CATAAT-TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
2762905 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATT-AAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * *
2762952 CATAATTGCAAATGCATGAAATGATGCATTAAGG-ATTGAAATGATGA
1 CATAATT-AAAATGCATGAAAGGATGCATTAAGGCA-TGAAAGGATGC
* * **
2762999 TATACTTGAAAATGCATGAAATTATGCATTAAGGCATGAAAGGATGC
1 CATAATT-AAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
2763046 CATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAA-TTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
2763093 CATAAATTAAAAT
1 CAT-AATTAAAAT
2763106 CCATAAATAG
Statistics
Matches: 179, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
46 2 0.01
47 172 0.96
48 5 0.03
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (46 bp):
CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:2771478 original size:10 final size:11
Alignment explanation
Indices: 2771455--2771483 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2771445 ATTTTGGATT
2771455 GAATTGATATG
1 GAATTGATATG
2771466 GAATTGA-ATG
1 GAATTGATATG
2771476 GAATTGAT
1 GAATTGAT
2771484 GTTATGAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (11 bp):
GAATTGATATG
Found at i:2779884 original size:21 final size:19
Alignment explanation
Indices: 2779839--2779876 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2779829 TTTTTGGTTT
*
2779839 ATGAAACTAAAATTGAGAA
1 ATGAAACTAAAATTAAGAA
2779858 ATGAAACTAAAATTAAGAA
1 ATGAAACTAAAATTAAGAA
2779877 TAATGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (19 bp):
ATGAAACTAAAATTAAGAA
Found at i:2781745 original size:21 final size:21
Alignment explanation
Indices: 2781716--2781786 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
2781706 TCATATAGGA
*
2781716 GTATCGATACTTGAACCATGG
1 GTATAGATACTTGAACCATGG
* *
2781737 GTATAGATAC-T---CCCTAGA
1 GTATAGATACTTGAACCAT-GG
**
2781755 GTACCGATACTTGAACCATGG
1 GTATAGATACTTGAACCATGG
2781776 GTATAGATACT
1 GTATAGATACT
2781787 CCCTAGAGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
17 3 0.08
18 9 0.25
19 1 0.03
20 1 0.03
21 19 0.53
22 3 0.08
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (21 bp):
GTATAGATACTTGAACCATGG
Found at i:2781763 original size:39 final size:39
Alignment explanation
Indices: 2781714--2781803 Score: 171
Period size: 39 Copynumber: 2.3 Consensus size: 39
2781704 ACTCATATAG
*
2781714 GAGTATCGATACTTGAACCATGGGTATAGATACTCCCTA
1 GAGTACCGATACTTGAACCATGGGTATAGATACTCCCTA
2781753 GAGTACCGATACTTGAACCATGGGTATAGATACTCCCTA
1 GAGTACCGATACTTGAACCATGGGTATAGATACTCCCTA
2781792 GAGTACCGATAC
1 GAGTACCGATAC
2781804 CAAAATGGCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (39 bp):
GAGTACCGATACTTGAACCATGGGTATAGATACTCCCTA
Found at i:2782649 original size:17 final size:17
Alignment explanation
Indices: 2782602--2782651 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2782592 AATTAAGATA
2782602 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * * *
2782619 TATTTTGATGAATGGAC
1 TAGTTTAATAAATGAAC
*
2782636 TAGTTTAATCAATGAA
1 TAGTTTAATAAATGAA
2782652 ATACTTAGTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2785392 original size:37 final size:37
Alignment explanation
Indices: 2785340--2785443 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
2785330 CTTTTCGTCC
*
2785340 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
2785377 TTCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
** * *
2785414 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
2785444 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:2785847 original size:6 final size:6
Alignment explanation
Indices: 2785838--2785893 Score: 50
Period size: 6 Copynumber: 10.2 Consensus size: 6
2785828 TAACCCTTAT
* * *
2785838 TATTTA TATTTA TATGTA TA--TA TATATA TATATA TATTTA -A-TTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
2785882 TATTT- TATTTA T
1 TATTTA TATTTA T
2785894 TTATTTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
4 7 0.16
5 7 0.16
6 29 0.67
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (6 bp):
TATTTA
Found at i:2785883 original size:12 final size:12
Alignment explanation
Indices: 2785842--2785905 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 12
2785832 CCTTATTATT
2785842 TATATTTATATGTA
1 TATATTTA-AT-TA
*
2785856 TATATATATATATA
1 TATATTTA-AT-TA
2785870 TATATTTAATTA
1 TATATTTAATTA
*
2785882 TAT-TTTATTTA
1 TATATTTAATTA
*
2785893 TTTATTT-ATTA
1 TATATTTAATTA
2785904 TA
1 TA
2785906 AGTTTTTACA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
11 13 0.31
12 8 0.19
13 2 0.05
14 19 0.45
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
TATATTTAATTA
Found at i:2785957 original size:2 final size:2
Alignment explanation
Indices: 2785950--2785996 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2785940 ATTCTCCTAT
2785950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2785992 TA TA T
1 TA TA T
2785997 TATTTTTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2786037 original size:14 final size:14
Alignment explanation
Indices: 2785999--2786046 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
2785989 ATATATATTA
2785999 TTTTTTATCTATGTT
1 TTTTTTA-CTATGTT
2786014 TACTTATTTACTATGTT
1 T--TT-TTTACTATGTT
*
2786031 TTTTTTACTATATT
1 TTTTTTACTATGTT
2786045 TT
1 TT
2786047 CCTAACGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.41
15 3 0.10
17 10 0.34
18 4 0.14
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (14 bp):
TTTTTTACTATGTT
Done.