Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397270.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_55.0, 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: 4719911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 90628 characters in sequence are not A, C, G, or T
File 6 of 10
Found at i:2168228 original size:29 final size:30
Alignment explanation
Indices: 2168164--2168228 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
2168154 AGTTCTTATT
*
2168164 GATATTGAATATATCTTGCATAGCTACTGTG
1 GATATTGAATATA-CTTGCATAGCTACTATG
* **
2168195 CATATTGAATATA-TTGTTTAGCTACTATG
1 GATATTGAATATACTTGCATAGCTACTATG
2168224 GATAT
1 GATAT
2168229 AGTGAATCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 17 0.59
31 12 0.41
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (30 bp):
GATATTGAATATACTTGCATAGCTACTATG
Found at i:2176117 original size:21 final size:23
Alignment explanation
Indices: 2176093--2176139 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 23
2176083 TATATATATA
2176093 TAATGAAT-ATT-T-TTATGCAAT
1 TAATGAATAATTATATTATG-AAT
*
2176114 TAATTAATAATTATATTATGAAT
1 TAATGAATAATTATATTATGAAT
2176137 TAA
1 TAA
2176140 AAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 7 0.32
22 3 0.14
23 7 0.32
24 5 0.23
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (23 bp):
TAATGAATAATTATATTATGAAT
Found at i:2180256 original size:28 final size:28
Alignment explanation
Indices: 2180220--2180274 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2180210 AATTTGAAAT
2180220 TTTATTTATATTTGATGTAATGTATTTG
1 TTTATTTATATTTGATGTAATGTATTTG
* *
2180248 TTTATTTATTTTTGATGTAATTTATTT
1 TTTATTTATATTTGATGTAATGTATTT
2180275 ATCTGTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (28 bp):
TTTATTTATATTTGATGTAATGTATTTG
Found at i:2221469 original size:14 final size:14
Alignment explanation
Indices: 2221450--2221478 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2221440 AATTATATTG
2221450 TGTTGCTTCATATA
1 TGTTGCTTCATATA
2221464 TGTTGCTTCATATA
1 TGTTGCTTCATATA
2221478 T
1 T
2221479 AAGATCGGAC
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:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (14 bp):
TGTTGCTTCATATA
Found at i:2222772 original size:141 final size:142
Alignment explanation
Indices: 2222582--2222882 Score: 338
Period size: 141 Copynumber: 2.1 Consensus size: 142
2222572 ATTAAATAAT
* ** * *
2222582 AAAAATAGCATGGCAACAACGATGGCAAACTAAATAAGAAAAAAGATAATAAATTGAGCAGAACT
1 AAAAACAGCATGATAACAACGATAGCAAACTAAATAAGAAAAAAGATAATAAATCGAGCAGAACT
* * * * * *
2222647 CAGAAGGTAAGTAACAATGGAAAAATCATATAATATTTTTCAAAT-TTAATTTT-AAAAAATCAA
66 CAAAAGGCAAATAACAATGAAAAAATCACACAATATTTTTCAAATATT-ATTTTAAAAAAATCAA
*
2222710 ATGACTAACAATA
130 ATGACAAACAATA
* * * * *
2222723 AAAAACAGCATGATAACAATGATAGCAAACTAAATCAAG-AAAATGATAATGAATCGTGTAGAAC
1 AAAAACAGCATGATAACAACGATAGCAAACTAAAT-AAGAAAAAAGATAATAAATCGAGCAGAAC
* * *
2222787 TCAAAAGGCAAATAACAATGAAAAAATCACACAATTTTTTTCAAATATTTTTTTAAAAAAATTAA
65 TCAAAAGGCAAATAACAATGAAAAAATCACACAATATTTTTCAAATATTATTTTAAAAAAATCAA
**
2222852 ATTTCAAACAATA
130 ATGACAAACAATA
**
2222865 AAATAACAAAATGATAAC
1 AAA-AACAGCATGATAAC
2222883 TAAAATAGCA
Statistics
Matches: 132, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
141 93 0.70
142 27 0.20
143 12 0.09
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (142 bp):
AAAAACAGCATGATAACAACGATAGCAAACTAAATAAGAAAAAAGATAATAAATCGAGCAGAACT
CAAAAGGCAAATAACAATGAAAAAATCACACAATATTTTTCAAATATTATTTTAAAAAAATCAAA
TGACAAACAATA
Found at i:2223190 original size:39 final size:41
Alignment explanation
Indices: 2223147--2223234 Score: 101
Period size: 41 Copynumber: 2.1 Consensus size: 41
2223137 AACTAAATCG
*
2223147 GCAAAAGTAACATAAA-AAGAAAAA-AAG-AAGAATAAGTAA
1 GCAAAAG-AACATAAATAACAAAAATAAGTAAGAATAAGTAA
*
2223186 GCAAAAAAGGACATAAATAACAAAAATAAGTAAGAATAAGTAA
1 GC--AAAAGAACATAAATAACAAAAATAAGTAAGAATAAGTAA
*
2223229 GAAAAA
1 GCAAAA
2223235 ATAGTAAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
39 2 0.05
40 7 0.17
41 16 0.39
42 3 0.07
43 13 0.32
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.11
Consensus pattern (41 bp):
GCAAAAGAACATAAATAACAAAAATAAGTAAGAATAAGTAA
Found at i:2223228 original size:43 final size:39
Alignment explanation
Indices: 2223156--2223235 Score: 115
Period size: 43 Copynumber: 1.9 Consensus size: 39
2223146 GGCAAAAGTA
*
2223156 ACATAAAAAGAAAAAAAGAAGAATAAGTAAGCAAAAAAGG
1 ACATAAAAACAAAAAAAGAAGAATAAGTAAG-AAAAAAGG
2223196 ACATAAATAACAAAAATAAGTAAGAATAAGTAAGAAAAAA
1 ACATAAA-AACAAAAA-AAG-AAGAATAAGTAAGAAAAAA
2223236 TAGTAAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
40 7 0.19
41 7 0.19
42 9 0.25
43 13 0.36
ACGTcount: A:0.70, C:0.05, G:0.14, T:0.11
Consensus pattern (39 bp):
ACATAAAAACAAAAAAAGAAGAATAAGTAAGAAAAAAGG
Found at i:2223243 original size:23 final size:21
Alignment explanation
Indices: 2223163--2223235 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
2223153 GTAACATAAA
2223163 AAGAAAAAAAGAAGAATAAGT
1 AAGAAAAAAAGAAGAATAAGT
* *
2223184 AAGCAAAAAAG--GACATAAAT
1 AAGAAAAAAAGAAGA-ATAAGT
*
2223204 AACAAAAATAAGTAAGAATAAGT
1 AAGAAAAA-AAG-AAGAATAAGT
2223227 AAGAAAAAA
1 AAGAAAAAA
2223236 TAGTAAGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.05
20 11 0.27
21 13 0.32
22 1 0.02
23 12 0.29
24 2 0.05
ACGTcount: A:0.70, C:0.04, G:0.15, T:0.11
Consensus pattern (21 bp):
AAGAAAAAAAGAAGAATAAGT
Found at i:2225651 original size:30 final size:29
Alignment explanation
Indices: 2225610--2225667 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
2225600 AATGAAAAGT
2225610 AAAAAGAAAGAAGTAAAAATGAGGACATA
1 AAAAAGAAAGAAGTAAAAATGAGGACATA
*
2225639 AAAAAGGAAAGAAGTAAAAATGATGACAT
1 AAAAA-GAAAGAAGTAAAAATGAGGACAT
2225668 TTACTTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.64, C:0.03, G:0.21, T:0.12
Consensus pattern (29 bp):
AAAAAGAAAGAAGTAAAAATGAGGACATA
Found at i:2227128 original size:64 final size:64
Alignment explanation
Indices: 2227054--2227205 Score: 189
Period size: 64 Copynumber: 2.4 Consensus size: 64
2227044 TCACAGGGTA
* * ** *
2227054 TGAGGTAACATTCCACACGTGGTGAATGCATTTAGTATAATGGATGATGGTGTTTCACAC-GATG
1 TGAGGTAACATTCCACACGTGGTGAATGCATCTAGTATAATAGATGATGGCATTCCACACAG-TG
* ** * *
2227118 TGAGGCAACATTTAACACGTGGTGAATGCGTCTAGTATGATAGATGATGGCATTCCACACAGTG
1 TGAGGTAACATTCCACACGTGGTGAATGCATCTAGTATAATAGATGATGGCATTCCACACAGTG
*
2227182 TGAGGTAATATTCCACACGTGGTG
1 TGAGGTAACATTCCACACGTGGTG
2227206 TTAACTCCCG
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 72 0.99
65 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (64 bp):
TGAGGTAACATTCCACACGTGGTGAATGCATCTAGTATAATAGATGATGGCATTCCACACAGTG
Found at i:2227565 original size:29 final size:29
Alignment explanation
Indices: 2227480--2227565 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
2227470 AATGCATTGG
*
2227480 TTGAGTT-TCATGGATT-GGATATTGATTA-
1 TTGAGTTAT-ATGGATTGGGA-AATGATTAC
** *
2227508 TTGAGTTATATGGATTGATAAATGTTTAC
1 TTGAGTTATATGGATTGGGAAATGATTAC
* *
2227537 TTGGGTTATATGGATTGGGAGATGATTAC
1 TTGAGTTATATGGATTGGGAAATGATTAC
2227566 AAAATGTTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 20 0.43
29 26 0.57
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (29 bp):
TTGAGTTATATGGATTGGGAAATGATTAC
Found at i:2229450 original size:20 final size:20
Alignment explanation
Indices: 2229425--2229464 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2229415 TTTTGTTAAG
*
2229425 AATGTATCAATACATTCCTA
1 AATGTATCAATACATCCCTA
*
2229445 AATGTATCGATACATCCCTA
1 AATGTATCAATACATCCCTA
2229465 GACAAAGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (20 bp):
AATGTATCAATACATCCCTA
Found at i:2238108 original size:20 final size:20
Alignment explanation
Indices: 2238083--2238124 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2238073 AATTTAAAGC
2238083 AAAATAACATGAAATT-AACT
1 AAAATAAC-TGAAATTAAACT
*
2238103 AAAATAACTTAAATTAAACT
1 AAAATAACTGAAATTAAACT
2238123 AA
1 AA
2238125 TCAACATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAATAACTGAAATTAAACT
Found at i:2241419 original size:38 final size:38
Alignment explanation
Indices: 2241368--2241445 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2241358 GAAGAGACAG
2241368 AATTGTGCAAGCTAGCCTGAATGTACAAGAAAATATTC
1 AATTGTGCAAGCTAGCCTGAATGTACAAGAAAATATTC
2241406 AATTGTGCAAGCTAGCCTGAATGTACAAGAAAATATTC
1 AATTGTGCAAGCTAGCCTGAATGTACAAGAAAATATTC
2241444 AA
1 AA
2241446 AACTTACTCC
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:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (38 bp):
AATTGTGCAAGCTAGCCTGAATGTACAAGAAAATATTC
Found at i:2247566 original size:78 final size:78
Alignment explanation
Indices: 2247385--2247582 Score: 251
Period size: 78 Copynumber: 2.5 Consensus size: 78
2247375 GGAAGACACA
* * *
2247385 AGGCGTGAGCATGTGGCATTCCTATTAT-CTGTTAAGGTATAATGATGCCAATTTGTAAAAACAT
1 AGGC-TGAGCATGTGGCATTCCTATTATAC-ATTAAGGTATAATAATGCCAATATGTAAAAACAT
*
2247449 CATAGCCCATGTGAT
64 AATAGCCCATGTGAT
* *
2247464 AGGTTG-GCATGTGGCATTCCTATTATACATTAAGGTATAATAATGCCAATATGTAAATACCATG
1 AGGCTGAGCATGTGGCATTCCTATTATACATTAAGGTATAATAATGCCAATATGTAAA-AACAT-
*
2247528 AAT-GTCCATGTGAT
64 AATAGCCCATGTGAT
* *
2247542 A-GCTGAGGATGTGGCATTCCTATTATACATGAAGGTATAAT
1 AGGCTGAGCATGTGGCATTCCTATTATACATTAAGGTATAAT
2247583 GGTGTCATTA
Statistics
Matches: 105, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
77 49 0.47
78 51 0.49
79 5 0.05
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (78 bp):
AGGCTGAGCATGTGGCATTCCTATTATACATTAAGGTATAATAATGCCAATATGTAAAAACATAA
TAGCCCATGTGAT
Found at i:2263186 original size:81 final size:80
Alignment explanation
Indices: 2263046--2263199 Score: 211
Period size: 81 Copynumber: 1.9 Consensus size: 80
2263036 AACGGCCCCT
* * *
2263046 GTCTTCACCAAGAAATTTCGAAAGTGTGTTGACCACATATAAAAGACAAAAGAAGAAAAAATTGC
1 GTCTTCACCAAGAAATTTCAAAAGTGTGTTGACCAAATATAAAAGACAAAAGAACAAAAAATTGC
2263111 TAATGACCGGTCTTA
66 TAATGACCGGTCTTA
* * * * *
2263126 GTCTTCACCAAAGAAGTTTCAAAAGTGTTTTGAGCAAATACT-CAAGACAACAGAACAAAAAATT
1 GTCTTCACC-AAGAAATTTCAAAAGTGTGTTGACCAAATA-TAAAAGACAAAAGAACAAAAAATT
2263190 GCTAATGACC
64 GCTAATGACC
2263200 AAGAGACGTG
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 9 0.14
81 54 0.84
82 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (80 bp):
GTCTTCACCAAGAAATTTCAAAAGTGTGTTGACCAAATATAAAAGACAAAAGAACAAAAAATTGC
TAATGACCGGTCTTA
Found at i:2264927 original size:35 final size:35
Alignment explanation
Indices: 2264806--2264928 Score: 88
Period size: 35 Copynumber: 3.3 Consensus size: 35
2264796 TGACAAATAA
* * *
2264806 TTGACTCAATTGGTAAGTTTAGGCTCATGAAAAGT
1 TTGACTTAATTGGTAAGTTTAAGCTCATGGAAAGT
*
2264841 TTGACTTAATTGATAA-TTTCAAGCCGAGTCGGATGGAGAA-T
1 TTGACTTAATTGGTAAGTTT-AAG-C---TC--ATGGA-AAGT
** * *
2264882 GCGACGTAATTGGTAAGTTTATGCTCATGGAAAGT
1 TTGACTTAATTGGTAAGTTTAAGCTCATGGAAAGT
2264917 TTGACTTAATTG
1 TTGACTTAATTG
2264929 ATCATTTCAG
Statistics
Matches: 66, Mismatches: 12, Indels: 20
0.67 0.12 0.20
Matches are distributed among these distances:
34 5 0.08
35 31 0.47
36 1 0.02
37 2 0.03
39 2 0.03
40 1 0.02
41 19 0.29
42 5 0.08
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
TTGACTTAATTGGTAAGTTTAAGCTCATGGAAAGT
Found at i:2264943 original size:76 final size:76
Alignment explanation
Indices: 2264813--2265004 Score: 296
Period size: 76 Copynumber: 2.5 Consensus size: 76
2264803 TAATTGACTC
*
2264813 AATTGGTAAGTTTAGGCTCATGAAAAGTTTGACTTAATTGATAATTTCAAGCCGAGTC-GGATGG
1 AATTGGTAAGTTTACGCTCATGAAAAGTTTGACTTAATTGATAATTTCAAGCCGAG-CGGGATGG
2264877 AGAATGCGACGT
65 AGAATGCGACGT
* * * *
2264889 AATTGGTAAGTTTATGCTCATGGAAAGTTTGACTTAATTGATCATTTCAGGCCGAGCGGGATGGA
1 AATTGGTAAGTTTACGCTCATGAAAAGTTTGACTTAATTGATAATTTCAAGCCGAGCGGGATGGA
*
2264954 GAATGCGACTT
66 GAATGCGACGT
* *
2264965 AATTGGTAAGTTTACACTCATCAAAAGTTTGACTTAATTG
1 AATTGGTAAGTTTACGCTCATGAAAAGTTTGACTTAATTG
2265005 GTAAAGTTCA
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
75 1 0.01
76 105 0.99
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.32
Consensus pattern (76 bp):
AATTGGTAAGTTTACGCTCATGAAAAGTTTGACTTAATTGATAATTTCAAGCCGAGCGGGATGGA
GAATGCGACGT
Found at i:2268640 original size:38 final size:39
Alignment explanation
Indices: 2268592--2268671 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 39
2268582 TGGAAGCATA
2268592 TTAGGAGTTTAAGGTTATTACACATTTAATGTTTAAGGT
1 TTAGGAGTTTAAGGTTATTACACATTTAATGTTTAAGGT
*
2268631 TTAGG-GTTTAAGGTTATTACACATTTAATGTTTAGGGT
1 TTAGGAGTTTAAGGTTATTACACATTTAATGTTTAAGGT
2268669 TTA
1 TTA
2268672 AAATATTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 35 0.88
39 5 0.12
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (39 bp):
TTAGGAGTTTAAGGTTATTACACATTTAATGTTTAAGGT
Found at i:2271573 original size:2 final size:2
Alignment explanation
Indices: 2271548--2271586 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2271538 GTGGGAGTGG
* * *
2271548 GT GT GG GT GT GG GT GT GG GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
2271587 AGGTCAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.59, T:0.41
Consensus pattern (2 bp):
GT
Found at i:2271586 original size:6 final size:6
Alignment explanation
Indices: 2271531--2271582 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
2271521 CATATATATA
* * *
2271531 TGTGGG TGTGGG AGTGGG TGTGGG TGTGGG TGTGGG TGTGTG TGTGTG
1 TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG
2271579 TGTG
1 TGTG
2271583 TGTGAGGTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.02, C:0.00, G:0.62, T:0.37
Consensus pattern (6 bp):
TGTGGG
Found at i:2275899 original size:105 final size:105
Alignment explanation
Indices: 2275766--2275974 Score: 337
Period size: 105 Copynumber: 2.0 Consensus size: 105
2275756 ACAACCCTTA
* ** *
2275766 TAATGCCTTTTACTAGGAGTGAGCACAACCCATAGTTTTTAACTAGCTTAACCACAAACTCACAC
1 TAATGACTTTTACTAGGAGCAAGCACAACCCATAGTTTTTAACGAGCTTAACCACAAACTCACAC
2275831 TAACTTTTAAAAAATGAGTTAGAACATTTACAAGGAATGT
66 TAACTTTTAAAAAATGAGTTAGAACATTTACAAGGAATGT
* *
2275871 TAATGACTTTTACTATGAGCAAGCACAACCCATAGTTTTTAACGAGCTTAACCACAAACTGACAC
1 TAATGACTTTTACTAGGAGCAAGCACAACCCATAGTTTTTAACGAGCTTAACCACAAACTCACAC
* * *
2275936 TAACTTTTCAAAGATGAGTTAGAGCATTTACAAGGAATG
66 TAACTTTTAAAAAATGAGTTAGAACATTTACAAGGAATG
2275975 GAAATAGTGC
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (105 bp):
TAATGACTTTTACTAGGAGCAAGCACAACCCATAGTTTTTAACGAGCTTAACCACAAACTCACAC
TAACTTTTAAAAAATGAGTTAGAACATTTACAAGGAATGT
Found at i:2276867 original size:24 final size:26
Alignment explanation
Indices: 2276840--2276893 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
2276830 TTGGAGTTCT
2276840 TTTCTCCTTTAGTTTT-C-TTTATAC
1 TTTCTCCTTTAGTTTTACGTTTATAC
**
2276864 TTTCTTGTTTAGTTTTAACGTTTATAC
1 TTTCTCCTTTAGTTTT-ACGTTTATAC
2276891 TTT
1 TTT
2276894 TTTGAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 14 0.56
26 1 0.04
27 10 0.40
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (26 bp):
TTTCTCCTTTAGTTTTACGTTTATAC
Found at i:2278585 original size:22 final size:21
Alignment explanation
Indices: 2278550--2278590 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
2278540 AATTGTTGGT
2278550 ATTCATGGATTGATGCAATCC
1 ATTCATGGATTGATGCAATCC
2278571 ATTCATGAGATTGATGCAAT
1 ATTCATG-GATTGATGCAAT
2278591 TACTCTCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (21 bp):
ATTCATGGATTGATGCAATCC
Found at i:2283927 original size:61 final size:61
Alignment explanation
Indices: 2283854--2283977 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 61
2283844 GATCATCTAT
*
2283854 AGTCAAGAATAGAAGTTCTCTAGTCGATCGACTTTCATAAAGCTTATATTTTTTACATCAA
1 AGTCAAGAATAGAAGTTCTCTAGTCGATCCACTTTCATAAAGCTTATATTTTTTACATCAA
* *
2283915 AGTCAAGAATAGAAGTTCTCTAGTTGATCCACTTTCATAAAGCTTGTATTTTTTACATCAA
1 AGTCAAGAATAGAAGTTCTCTAGTCGATCCACTTTCATAAAGCTTATATTTTTTACATCAA
2283976 AG
1 AG
2283978 CTTAAACGGC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (61 bp):
AGTCAAGAATAGAAGTTCTCTAGTCGATCCACTTTCATAAAGCTTATATTTTTTACATCAA
Found at i:2296682 original size:2 final size:2
Alignment explanation
Indices: 2296675--2296706 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2296665 AAAAGAAAAG
2296675 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2296707 TCGTCTCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2297109 original size:16 final size:16
Alignment explanation
Indices: 2297085--2297122 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2297075 ATCATATTTC
*
2297085 TAAATTATTATTATTA
1 TAAAATATTATTATTA
*
2297101 TAAAATATTTTTATTA
1 TAAAATATTATTATTA
2297117 -AAAATA
1 TAAAATA
2297123 CAAGTATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAATATTATTATTA
Found at i:2299149 original size:30 final size:30
Alignment explanation
Indices: 2299103--2299174 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
2299093 AAATTTTTTG
* *
2299103 AATAAAATTTTAT-TTTTTATTATAT-TTA
1 AATAAATTTTTATATTTTTATTATATATCA
* *
2299131 ATTAAATTTTTATATTTTTATTTTATATCA
1 AATAAATTTTTATATTTTTATTATATATCA
2299161 AATAAATTTTTATA
1 AATAAATTTTTATA
2299175 ATTAATAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 11 0.30
29 11 0.30
30 15 0.41
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (30 bp):
AATAAATTTTTATATTTTTATTATATATCA
Found at i:2299170 original size:29 final size:27
Alignment explanation
Indices: 2299107--2299170 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
2299097 TTTTTGAATA
* *
2299107 AAATTTTATTTTTTATTATATTTAATT
1 AAATTTTATTTTTTATTATATTCAAAT
*
2299134 AAATTTTTATATTTTTATTTTATATCAAAT
1 AAA-TTTTAT-TTTTTATTATAT-TCAAAT
2299164 AAATTTT
1 AAATTTT
2299171 TATAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 3 0.10
28 6 0.19
29 15 0.48
30 7 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
AAATTTTATTTTTTATTATATTCAAAT
Found at i:2302097 original size:13 final size:13
Alignment explanation
Indices: 2302079--2302103 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2302069 TGTCAATATG
2302079 GGCCTAGCCCATC
1 GGCCTAGCCCATC
2302092 GGCCTAGCCCAT
1 GGCCTAGCCCAT
2302104 TTTTAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (13 bp):
GGCCTAGCCCATC
Found at i:2302982 original size:14 final size:14
Alignment explanation
Indices: 2302963--2302994 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2302953 GATCAATCAG
2302963 TTGTGAATTGTTGT
1 TTGTGAATTGTTGT
2302977 TTGTGAATTGTTGT
1 TTGTGAATTGTTGT
2302991 TTGT
1 TTGT
2302995 TGGTCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.59
Consensus pattern (14 bp):
TTGTGAATTGTTGT
Found at i:2302986 original size:37 final size:37
Alignment explanation
Indices: 2302900--2302989 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 37
2302890 TGTGTAAATG
* *
2302900 TGTTTATGAATTCTTGGATCAATTAGTTGTGAATTGT
1 TGTTTATGAATTGTTGGATCAATCAGTTGTGAATTGT
*
2302937 TATTTATGAATTGTTGGATCAATCAGTTGTGAATTGT
1 TGTTTATGAATTGTTGGATCAATCAGTTGTGAATTGT
*
2302974 TGTTTGTGAATTGTTG
1 TGTTTATGAATTGTTG
2302990 TTTGTTGGTC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.49
Consensus pattern (37 bp):
TGTTTATGAATTGTTGGATCAATCAGTTGTGAATTGT
Found at i:2305445 original size:28 final size:28
Alignment explanation
Indices: 2305411--2305479 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
2305401 AATTGAAATT
*
2305411 TTATTTATGTTTGATGTAATGTATTTGC
1 TTATTTATGTTTGATATAATGTATTTGC
* *
2305439 TTATTTATGTTTGATATAATTTATTTGT
1 TTATTTATGTTTGATATAATGTATTTGC
*
2305467 TTGTTATATGTTT
1 TTATT-TATGTTT
2305480 TTATTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 29 0.81
29 7 0.19
ACGTcount: A:0.22, C:0.01, G:0.14, T:0.62
Consensus pattern (28 bp):
TTATTTATGTTTGATATAATGTATTTGC
Found at i:2307157 original size:9 final size:8
Alignment explanation
Indices: 2307123--2307157 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
2307113 AGAGAGGAAG
2307123 AAAAGAAGA
1 AAAAGAA-A
2307132 AAAAGAAA
1 AAAAGAAA
*
2307140 GAAAGAAA
1 AAAAGAAA
2307148 AAAAGAAA
1 AAAAGAAA
2307156 AA
1 AA
2307158 GTAGAGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:2307167 original size:25 final size:24
Alignment explanation
Indices: 2307113--2307167 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
2307103 GGCGAGGGAA
* *
2307113 AGAGAGGAAGAAAAGAAGAAAAAG
1 AGAGAGAAAGAAAAAAAGAAAAAG
2307137 A-A-AGAAAGAAAAAAAGAAAAAG
1 AGAGAGAAAGAAAAAAAGAAAAAG
2307159 TAGAGAGAA
1 -AGAGAGAA
2307168 GAGAGAGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 18 0.69
23 2 0.08
24 2 0.08
25 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (24 bp):
AGAGAGAAAGAAAAAAAGAAAAAG
Found at i:2308358 original size:28 final size:31
Alignment explanation
Indices: 2308326--2308386 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
2308316 CTAATCACTA
*
2308326 ATATGT-TAATTTTA-TATAATATATAT-TT
1 ATATGTATAACTTTATTATAATATATATGTT
* *
2308354 ATATGTATTACTTTATTATTATATATATGTT
1 ATATGTATAACTTTATTATAATATATATGTT
2308385 AT
1 AT
2308387 GAACAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.22
29 6 0.22
30 11 0.41
31 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (31 bp):
ATATGTATAACTTTATTATAATATATATGTT
Found at i:2308411 original size:17 final size:17
Alignment explanation
Indices: 2308378--2308412 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2308368 ATTATTATAT
* *
2308378 ATATGTTATGAACAATA
1 ATATGTTATAAAAAATA
2308395 ATATGTTATAAAAAATA
1 ATATGTTATAAAAAATA
2308412 A
1 A
2308413 GATAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (17 bp):
ATATGTTATAAAAAATA
Found at i:2310750 original size:2 final size:2
Alignment explanation
Indices: 2310743--2310773 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2310733 ACAAAATTAT
2310743 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2310774 TTAAACACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2311183 original size:37 final size:37
Alignment explanation
Indices: 2311142--2311213 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
2311132 CACAAGCTAG
*
2311142 GGTGGAGAAATAGATCACGCTCAATGCTGAAGTAGTT
1 GGTGGAGAAATAGATCACACTCAATGCTGAAGTAGTT
2311179 GGTGGAGAAATAGATCACACTCAATGCTGAAGTAG
1 GGTGGAGAAATAGATCACACTCAATGCTGAAGTAG
2311214 CTGAAAGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.22
Consensus pattern (37 bp):
GGTGGAGAAATAGATCACACTCAATGCTGAAGTAGTT
Found at i:2311224 original size:37 final size:37
Alignment explanation
Indices: 2311146--2311224 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
2311136 AGCTAGGGTG
* * ***
2311146 GAGAAATAGATCACGCTCAATGCTGAAGTAGTTGGTG
1 GAGAAATAGATCACACTCAATGCTGAAGTAGCTGAAA
2311183 GAGAAATAGATCACACTCAATGCTGAAGTAGCTGAAA
1 GAGAAATAGATCACACTCAATGCTGAAGTAGCTGAAA
2311220 GAGAA
1 GAGAA
2311225 TAAATCATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (37 bp):
GAGAAATAGATCACACTCAATGCTGAAGTAGCTGAAA
Found at i:2311849 original size:15 final size:15
Alignment explanation
Indices: 2311829--2311866 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
2311819 ATGTTATGCA
2311829 TTAAGTGCATTTAAC
1 TTAAGTGCATTTAAC
2311844 TTAAGTGCATTTAAC
1 TTAAGTGCATTTAAC
2311859 TTAAGTGC
1 TTAAGTGC
2311867 CACTCATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (15 bp):
TTAAGTGCATTTAAC
Found at i:2312374 original size:22 final size:22
Alignment explanation
Indices: 2312330--2312374 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2312320 ACTTTGAAAT
* **
2312330 AATATATCGATACATTTGGGGC
1 AATATATAGATACATTTAAGGC
2312352 AATATATAGATACATTTAAGGC
1 AATATATAGATACATTTAAGGC
2312374 A
1 A
2312375 GAATGCTCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (22 bp):
AATATATAGATACATTTAAGGC
Found at i:2312480 original size:83 final size:83
Alignment explanation
Indices: 2312334--2312508 Score: 289
Period size: 83 Copynumber: 2.1 Consensus size: 83
2312324 TGAAATAATA
*
2312334 TATCGATACATTTGGGGCAATATATAGATACATTTAAGGCAGAATGCTCCCTACCTAACATGTTT
1 TATCGATACATTTGGGGCAATATATAGATACATTTAAGGCAGAATGCTCCCTACCCAACATGTTT
2312399 CGATACACGTGGGAAATG
66 CGATACACGTGGGAAATG
* * *
2312417 TATCGATATATTTGGGGTAATATATAGATACATTTAAGGCAGAATGC-CCCTTACCCAATATGTT
1 TATCGATACATTTGGGGCAATATATAGATACATTTAAGGCAGAATGCTCCC-TACCCAACATGTT
*
2312481 TTGATACACGTGGGAAATG
65 TCGATACACGTGGGAAATG
2312500 TATCGATAC
1 TATCGATAC
2312509 TTTTCCCCCC
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
82 3 0.04
83 82 0.96
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (83 bp):
TATCGATACATTTGGGGCAATATATAGATACATTTAAGGCAGAATGCTCCCTACCCAACATGTTT
CGATACACGTGGGAAATG
Found at i:2312686 original size:20 final size:20
Alignment explanation
Indices: 2312661--2312711 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
2312651 CTTGCCAAGA
2312661 ATGTATCAATACTTGAGGGG
1 ATGTATCAATACTTGAGGGG
2312681 ATGTATCAATACTTGAGGGG
1 ATGTATCAATACTTGAGGGG
2312701 ATGTATCAATA
1 ATGTATCAATA
2312712 TATCTTCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (20 bp):
ATGTATCAATACTTGAGGGG
Found at i:2317731 original size:21 final size:19
Alignment explanation
Indices: 2317707--2317746 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 19
2317697 TAAAGTATAA
2317707 TATTTAAAAAAATTCTTAAAT
1 TATTT-AAAAAATT-TTAAAT
2317728 TATTTAAAAAATTTTAAAT
1 TATTTAAAAAATTTTAAAT
2317747 AAATTGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 8 0.42
21 5 0.26
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTTAAAAAATTTTAAAT
Found at i:2319354 original size:22 final size:21
Alignment explanation
Indices: 2319329--2319373 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
2319319 TATTTAATTA
2319329 TTTATATTTTATTTTTTATAGT
1 TTTATATTTTATTTTTTA-AGT
*
2319351 TTTATGTTTTATTTTTTAAGT
1 TTTATATTTTATTTTTTAAGT
2319372 TT
1 TT
2319374 AAATATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (21 bp):
TTTATATTTTATTTTTTAAGT
Found at i:2319367 original size:14 final size:14
Alignment explanation
Indices: 2319329--2319373 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2319319 TATTTAATTA
*
2319329 TTTATATTTTATTT
1 TTTATATTTTATGT
2319343 TTTATAGTTTTATGT
1 TTTATA-TTTTATGT
* *
2319358 TTTATTTTTTAAGT
1 TTTATATTTTATGT
2319372 TT
1 TT
2319374 AAATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (14 bp):
TTTATATTTTATGT
Found at i:2326316 original size:20 final size:20
Alignment explanation
Indices: 2326293--2326330 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2326283 TTTTATTACA
2326293 TTTA-ATTAAGTTTTAATATT
1 TTTATATTAAG-TTTAATATT
*
2326313 TTTATTTTAAGTTTAATA
1 TTTATATTAAGTTTAATA
2326331 AGTTTTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTATATTAAGTTTAATATT
Found at i:2330197 original size:2 final size:2
Alignment explanation
Indices: 2330192--2330216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2330182 CAATTTCGTG
2330192 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 T
2330217 TGCAACACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2331245 original size:32 final size:30
Alignment explanation
Indices: 2331197--2331255 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
2331187 TATTTCTTTA
2331197 TTTTTATTATTATATATTATTTTAATTTAGT
1 TTTTTATTATTATATA-TATTTTAATTTAGT
* *
2331228 TTTTATATTATTTTATATATTTTTATTT
1 TTTT-TATTATTATATATATTTTAATTT
2331256 GATAATTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (30 bp):
TTTTTATTATTATATATATTTTAATTTAGT
Found at i:2331250 original size:9 final size:10
Alignment explanation
Indices: 2331194--2331254 Score: 58
Period size: 10 Copynumber: 6.2 Consensus size: 10
2331184 TTCTATTTCT
2331194 TTATTTT-TA
1 TTATTTTATA
*
2331203 TTATTATATA
1 TTATTTTATA
2331213 TTATTTTA-A
1 TTATTTTATA
2331222 TTTAGTTTTTATA
1 -TTA--TTTTATA
2331235 TTATTTTATA
1 TTATTTTATA
2331245 -TATTTT-TA
1 TTATTTTATA
2331253 TT
1 TT
2331255 TGATAATTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
8 2 0.05
9 14 0.32
10 19 0.43
12 8 0.18
13 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTATTTTATA
Found at i:2336871 original size:17 final size:16
Alignment explanation
Indices: 2336835--2336868 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2336825 GAAATCAAAA
*
2336835 TTTAGATTTTGATTCT
1 TTTAGATTTTTATTCT
2336851 TTTAGATTTTTATT-T
1 TTTAGATTTTTATTCT
2336866 TTT
1 TTT
2336869 TTATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.71
Consensus pattern (16 bp):
TTTAGATTTTTATTCT
Found at i:2337232 original size:198 final size:199
Alignment explanation
Indices: 2336886--2337277 Score: 707
Period size: 198 Copynumber: 2.0 Consensus size: 199
2336876 TTTTTATTGA
*
2336886 ATTCAACTGGTTGTTTGCTTATTTACATTAAATATCTTAAGTAAATGTAGAGCAAAAAAAAAGAA
1 ATTCAAATGGTTGTTTGCTTATTTACATTAAATATCTTAAGTAAATGTAGAGCAAAAAAAAAGAA
* *
2336951 GTAAAAATAAAGAAATTTACTCAAACAGTGTTTAATAGTTTTTAATGCCTCAGAAACTATATTTT
66 GTAAAAATAAAAAAATTTACTCAAACAGTGTTTAATAGTATTTAATGCCTCAGAAACTATATTTT
2337016 GTTTCAAAAGTATCGATACATGTTAATAATGTATCGATACAATTTTTTCAAAACCT-AATGTATC
131 GTTTCAAAAGTATCGATACATGTTAATAATGTATCGATACAATTTTTTCAAAA-CTAAATGTATC
2337080 GATAC
195 GATAC
*
2337085 ATTCAAATGGTTGTTTGCTTATTTACATTAAATATCTTAAGTAAATGTAGAG-TAAAAAAAAGAA
1 ATTCAAATGGTTGTTTGCTTATTTACATTAAATATCTTAAGTAAATGTAGAGCAAAAAAAAAGAA
*
2337149 GTAAAAATAAAAAAATTTACTCAAATAGTGTTTAATAGTATTTAATGCCTCAGAAACTATATTTT
66 GTAAAAATAAAAAAATTTACTCAAACAGTGTTTAATAGTATTTAATGCCTCAGAAACTATATTTT
*
2337214 GTTTCAAATGTATCGATACATGTTAATAATGTATCGATACAATTTTTTCAAAACTAAATGTATC
131 GTTTCAAAAGTATCGATACATGTTAATAATGTATCGATACAATTTTTTCAAAACTAAATGTATC
2337278 AATATATGGC
Statistics
Matches: 186, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
197 2 0.01
198 133 0.72
199 51 0.27
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (199 bp):
ATTCAAATGGTTGTTTGCTTATTTACATTAAATATCTTAAGTAAATGTAGAGCAAAAAAAAAGAA
GTAAAAATAAAAAAATTTACTCAAACAGTGTTTAATAGTATTTAATGCCTCAGAAACTATATTTT
GTTTCAAAAGTATCGATACATGTTAATAATGTATCGATACAATTTTTTCAAAACTAAATGTATCG
ATAC
Found at i:2366904 original size:76 final size:76
Alignment explanation
Indices: 2366778--2366935 Score: 232
Period size: 76 Copynumber: 2.1 Consensus size: 76
2366768 AATACCATCT
*
2366778 ATTTTAATTTTGAGTGATCCATAAAAATAGGAAATTATTTCCTACTTT-AAAAACAATTCCTAAA
1 ATTTTAATTTTGAGTGATCCATAAAAATAGGAAATTATTTCCTACTTTAAAAAAAAATT-CTAAA
2366842 ATTATA-GATAGA
65 ATTA-AGGATAGA
* *
2366854 ATTTTAATTTTCG-GTGATTCATAAAAATAGGAAATTGTTTCCTACTTTAAAAAAAAATTCTAAA
1 ATTTTAATTTT-GAGTGATCCATAAAAATAGGAAATTATTTCCTACTTTAAAAAAAAATTCTAAA
*
2366918 ATTAAGGATAGT
65 ATTAAGGATAGA
2366930 ATTTTA
1 ATTTTA
2366936 NNNNNNNNNN
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
75 1 0.01
76 64 0.85
77 10 0.13
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (76 bp):
ATTTTAATTTTGAGTGATCCATAAAAATAGGAAATTATTTCCTACTTTAAAAAAAAATTCTAAAA
TTAAGGATAGA
Found at i:2372883 original size:231 final size:231
Alignment explanation
Indices: 2372450--2372908 Score: 648
Period size: 231 Copynumber: 2.0 Consensus size: 231
2372440 ACAACCACTT
* * *
2372450 TACCTTTTATCTTGGTTAAGGTATAACCACTTAATTTTTACCTTTTCAATTAGTTAAGGTATAAC
1 TACCTTTTATCTTGGTTAAGATATAACCACTTAATTTCTACCTTTTCAATTAGTTAAAGTATAAC
* * * *
2372515 CACTAAAGTGAATACAATAAGAGATGAAAGTATAGCTAAGATGCCTTTTAAAGGCTAAATAGCAA
66 CACTAAAGTGAATACAATAAGAGATAAAAATATAGCTAAGATGCCTCTTAAAGGCCAAATAGCAA
* * * * *
2372580 GTTAAATACAATGTTTGGTGAGAAACAAGATAAGCAATAAAGTCTCTATAAAAAGTACGATAGAA
131 GTTAAATACAATGTTTGGTGAGAAAAAAGACAAGCAATAAAGGCTCTATAAAAAGTACAATAAAA
* *
2372645 TACTTAAATGCAAGAAGAGGAGTACAAAGAGTACTC
196 GACTTAAATGCAAGAAGAGAAGTACAAAGAGTACTC
* * * *
2372681 TACCTTTTATCTTGGTTAATATATAACCACTTAATTTCTACTTTTTCAATTGGTTAAAGTATAAG
1 TACCTTTTATCTTGGTTAAGATATAACCACTTAATTTCTACCTTTTCAATTAGTTAAAGTATAAC
* * * * * * *
2372746 CACTCAAGTGAATATAATAAGAGGTAAAAATGTATCTAGGATGCCTCTTGAAGGCCAAATAGCAA
66 CACTAAAGTGAATACAATAAGAGATAAAAATATAGCTAAGATGCCTCTTAAAGGCCAAATAGCAA
* * * *
2372811 GTTAAGTACAATGTTTGGTGAGAAAAAAGACAAGCAATAAAGGCTCTATGAAAGGTATAATAAAA
131 GTTAAATACAATGTTTGGTGAGAAAAAAGACAAGCAATAAAGGCTCTATAAAAAGTACAATAAAA
*
2372876 GACTTAAATGTAAGAAGAGAAGTACAAAGAGTA
196 GACTTAAATGCAAGAAGAGAAGTACAAAGAGTA
2372909 TTGAATGATT
Statistics
Matches: 198, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
231 198 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (231 bp):
TACCTTTTATCTTGGTTAAGATATAACCACTTAATTTCTACCTTTTCAATTAGTTAAAGTATAAC
CACTAAAGTGAATACAATAAGAGATAAAAATATAGCTAAGATGCCTCTTAAAGGCCAAATAGCAA
GTTAAATACAATGTTTGGTGAGAAAAAAGACAAGCAATAAAGGCTCTATAAAAAGTACAATAAAA
GACTTAAATGCAAGAAGAGAAGTACAAAGAGTACTC
Found at i:2385211 original size:10 final size:11
Alignment explanation
Indices: 2385158--2385213 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
2385148 CTTAAAAATT
2385158 TTTATTTTAAA
1 TTTATTTTAAA
*
2385169 TTCATTTTAAA
1 TTTATTTTAAA
2385180 TTT-TTTT--A
1 TTTATTTTAAA
*
2385188 TTAAGTTTTAAA
1 TTTA-TTTTAAA
2385200 TTTATTTT-AA
1 TTTATTTTAAA
2385210 TTTA
1 TTTA
2385214 GTGAGAGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
8 3 0.08
10 14 0.38
11 16 0.43
12 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:2388080 original size:79 final size:80
Alignment explanation
Indices: 2387983--2388142 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
2387973 AATTTCTTGA
2387983 AACATTAAAGAAAGGCTAATTTTTTGATAAAATATTGAG-ATAAATATAAGATTCTAAAACTTTC
1 AACATTAAAGAAAGGCTAATTTTTTGATAAAATATTGAGAATAAATATAAGATTCTAAAACTTTC
2388047 TCTTTATGATTACAT
66 TCTTTATGATTACAT
2388062 AACATTAAAGAAAGGCTAATTTTTTGATAAAATATTGAGAATAAATATAAGATTCTAAAACTTTC
1 AACATTAAAGAAAGGCTAATTTTTTGATAAAATATTGAGAATAAATATAAGATTCTAAAACTTTC
2388127 TCTTTATGATTACAT
66 TCTTTATGATTACAT
2388142 A
1 A
2388143 CTTTGCACTA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 39 0.49
80 41 0.51
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (80 bp):
AACATTAAAGAAAGGCTAATTTTTTGATAAAATATTGAGAATAAATATAAGATTCTAAAACTTTC
TCTTTATGATTACAT
Found at i:2389956 original size:24 final size:24
Alignment explanation
Indices: 2389923--2389982 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
2389913 GATAAGATCT
* *
2389923 ATGCACAAAGATTGATTTAATGGG
1 ATGCATAAAGATTGATTTAATGCG
*
2389947 ATGCATAAAGAATGATTTAATGCG
1 ATGCATAAAGATTGATTTAATGCG
2389971 ATGCATAAAGAT
1 ATGCATAAAGAT
2389983 GCATAATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (24 bp):
ATGCATAAAGATTGATTTAATGCG
Found at i:2394253 original size:36 final size:35
Alignment explanation
Indices: 2394177--2394289 Score: 118
Period size: 36 Copynumber: 3.1 Consensus size: 35
2394167 CAAGCAATAG
* **
2394177 CTTTTTCACAAGATCAAGCAATAACCGTTACACTTG
1 CTTTTTAACAAGATCAAGCAATAACC-TTACACTAA
*
2394213 CTTTTTAACAAGATCAAGCAATAATCCTTACACCAA
1 CTTTTTAACAAGATCAAGCAATAA-CCTTACACTAA
* * ** *
2394249 CTTTTCAACAAAATCAAGTGATAACCCTCACACTAA
1 CTTTTTAACAAGATCAAGCAATAA-CCTTACACTAA
2394285 CTTTT
1 CTTTT
2394290 CTAGTCTAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 63 0.97
37 2 0.03
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (35 bp):
CTTTTTAACAAGATCAAGCAATAACCTTACACTAA
Found at i:2409250 original size:13 final size:13
Alignment explanation
Indices: 2409197--2409231 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2409187 TGGTCTTATC
2409197 AAAA-TTTA-TAA
1 AAAATTTTATTAA
2409208 AAAATTTTATTAA
1 AAAATTTTATTAA
2409221 AAAATTTTATT
1 AAAATTTTATT
2409232 TAATAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.18
12 4 0.18
13 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATTTTATTAA
Found at i:2409331 original size:12 final size:12
Alignment explanation
Indices: 2409310--2409353 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
2409300 TCTCTATACA
*
2409310 TCTTTCTCTTTC
1 TCTTTTTCTTTC
*
2409322 TCTTTTTCTTTT
1 TCTTTTTCTTTC
2409334 TCTTTTTCTCTTC
1 TCTTTTTCT-TTC
2409347 TCTTTTT
1 TCTTTTT
2409354 TATTTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TCTTTTTCTTTC
Found at i:2409522 original size:17 final size:18
Alignment explanation
Indices: 2409500--2409535 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2409490 AGAGGTAAAG
*
2409500 TTTTCT-TTTATCTTATT
1 TTTTCTATTTATATTATT
2409517 TTTTCTATTTATATTATT
1 TTTTCTATTTATATTATT
2409535 T
1 T
2409536 AACTATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTCTATTTATATTATT
Found at i:2410895 original size:28 final size:28
Alignment explanation
Indices: 2410861--2410914 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
2410851 ATTTGAAATT
2410861 TTATTTATATTTGATGTAATGTATTTGC
1 TTATTTATATTTGATGTAATGTATTTGC
* * *
2410889 TTATTTATGTTTGGTGTAATTTATTT
1 TTATTTATATTTGATGTAATGTATTT
2410915 ATTTGTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.02, G:0.15, T:0.61
Consensus pattern (28 bp):
TTATTTATATTTGATGTAATGTATTTGC
Found at i:2411708 original size:33 final size:35
Alignment explanation
Indices: 2411671--2411743 Score: 114
Period size: 33 Copynumber: 2.1 Consensus size: 35
2411661 TTTTAATGTC
*
2411671 ATATATTTTATTTTTATTT-TTTATTATAA-TCTT
1 ATATATTTTATTTTTATTTCTTTAATATAATTCTT
2411704 ATATATTTTATTTTTATTTCTTTAATATAATTTCTT
1 ATATATTTTATTTTTATTTCTTTAATATAA-TTCTT
2411740 ATAT
1 ATAT
2411744 TATATATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
33 19 0.53
34 9 0.25
36 8 0.22
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (35 bp):
ATATATTTTATTTTTATTTCTTTAATATAATTCTT
Found at i:2411794 original size:31 final size:33
Alignment explanation
Indices: 2411734--2411797 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2411724 TTTAATATAA
* *
2411734 TTTCTTATATTATATATATTATTTGAATTTCTT
1 TTTCCTATATTATATAAATTATTTGAATTTCTT
2411767 TTTCCTATATTATATAAATT-TTT-AATTTCTT
1 TTTCCTATATTATATAAATTATTTGAATTTCTT
2411798 ATATGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 8 0.28
32 3 0.10
33 18 0.62
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (33 bp):
TTTCCTATATTATATAAATTATTTGAATTTCTT
Found at i:2412168 original size:19 final size:18
Alignment explanation
Indices: 2412136--2412175 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
2412126 AAAAATAATT
2412136 AAATAATTCAAAAATTAA
1 AAATAATTCAAAAATTAA
*
2412154 AAATATTTCAAAAAATTAA
1 AAATAATTC-AAAAATTAA
2412173 AAA
1 AAA
2412176 AGAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAATTCAAAAATTAA
Found at i:2412174 original size:18 final size:18
Alignment explanation
Indices: 2412127--2412174 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2412117 TCAATGATAA
2412127 AAAATAATT-AAATAATTC
1 AAAA-AATTAAAATAATTC
*
2412145 -AAAAATTAAAAATATTTC
1 AAAAAATT-AAAATAATTC
2412163 AAAAAATTAAAA
1 AAAAAATTAAAA
2412175 AAGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.15
17 3 0.12
18 12 0.46
19 7 0.27
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATTAAAATAATTC
Found at i:2412181 original size:26 final size:26
Alignment explanation
Indices: 2412126--2412181 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
2412116 TTCAATGATA
* **
2412126 AAAAATAATTAAATAATTCAAAAATT
1 AAAAATAATTAAAAAATTCAAAAAAG
*
2412152 AAAAATATTTCAAAAAATT-AAAAAAG
1 AAAAATAATT-AAAAAATTCAAAAAAG
2412178 AAAA
1 AAAA
2412182 TTAAAGTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (26 bp):
AAAAATAATTAAAAAATTCAAAAAAG
Found at i:2428816 original size:21 final size:21
Alignment explanation
Indices: 2428792--2428833 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2428782 CCTTCTCCAT
* *
2428792 TAGTGACTCCAATAGCAGATG
1 TAGTGACCCCAACAGCAGATG
*
2428813 TAGTGGCCCCAACAGCAGATG
1 TAGTGACCCCAACAGCAGATG
2428834 CAATGGCTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
TAGTGACCCCAACAGCAGATG
Found at i:2428840 original size:21 final size:21
Alignment explanation
Indices: 2428800--2428853 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
2428790 ATTAGTGACT
* * *
2428800 CCAATAGCAGATGTAGTGGCC
1 CCAACAGCAGATGCAATGGCC
*
2428821 CCAACAGCAGATGCAATGGCT
1 CCAACAGCAGATGCAATGGCC
*
2428842 CCAACAGTAGAT
1 CCAACAGCAGAT
2428854 TTACTTGCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (21 bp):
CCAACAGCAGATGCAATGGCC
Found at i:2429633 original size:27 final size:27
Alignment explanation
Indices: 2429576--2429630 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
2429566 TTAAAATTCT
2429576 AATAAAAAAAAATCTCAAACTAAATAA
1 AATAAAAAAAAATCTCAAACTAAATAA
* * *
2429603 AATAAAATAAAATCTTAAA-TTAATAA
1 AATAAAAAAAAATCTCAAACTAAATAA
2429629 AA
1 AA
2429631 ATACTGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (27 bp):
AATAAAAAAAAATCTCAAACTAAATAA
Found at i:2435886 original size:7 final size:7
Alignment explanation
Indices: 2435871--2435903 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2435861 AATAAAAGAA
*
2435871 AAATCCT
1 AAATACT
2435878 AAATACT
1 AAATACT
2435885 AAATACT
1 AAATACT
2435892 AAATACT
1 AAATACT
2435899 AAATA
1 AAATA
2435904 AGAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATACT
Found at i:2436237 original size:22 final size:22
Alignment explanation
Indices: 2436200--2436260 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
2436190 GTAAAGAAAC
*
2436200 TAAATTGAAGAAAATATTAATAA
1 TAAATT-AAGAAAATACTAATAA
* * *
2436223 TAAATTAAGATAATACTAGTAC
1 TAAATTAAGAAAATACTAATAA
2436245 TAAATTAAGAAAATAC
1 TAAATTAAGAAAATAC
2436261 CCTTTGCATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 27 0.82
23 6 0.18
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (22 bp):
TAAATTAAGAAAATACTAATAA
Found at i:2437308 original size:21 final size:21
Alignment explanation
Indices: 2437284--2437326 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2437274 AAAGTTTAAT
2437284 TGCATTAGAAAATGCTTAAAC
1 TGCATTAGAAAATGCTTAAAC
2437305 TGCATTAGAAAATGCTTAAAC
1 TGCATTAGAAAATGCTTAAAC
2437326 T
1 T
2437327 AACTTAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (21 bp):
TGCATTAGAAAATGCTTAAAC
Found at i:2441616 original size:23 final size:24
Alignment explanation
Indices: 2441582--2441630 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
2441572 TTTCTCAATT
2441582 TAGTAATAATTTTTTTAAATTTAG
1 TAGTAATAATTTTTTTAAATTTAG
*
2441606 TAGTAAT-ATTTTTTTCAATTTAG
1 TAGTAATAATTTTTTTAAATTTAG
2441629 TA
1 TA
2441631 TTTTGTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (24 bp):
TAGTAATAATTTTTTTAAATTTAG
Found at i:2445506 original size:22 final size:22
Alignment explanation
Indices: 2445478--2445534 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
2445468 CGGAGACGAC
2445478 TTAGTCGACTAAGTGATAATGG
1 TTAGTCGACTAAGTGATAATGG
2445500 TTAGTCGACTAAGTGATAATGG
1 TTAGTCGACTAAGTGATAATGG
*
2445522 TTAATCGACTAAG
1 TTAGTCGACTAAG
2445535 AGCATTCTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (22 bp):
TTAGTCGACTAAGTGATAATGG
Found at i:2453905 original size:31 final size:31
Alignment explanation
Indices: 2453870--2453944 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
2453860 ATAATAGATC
* **
2453870 TTTGTTCAATTTAGTCTTTATGTTATAAAAT
1 TTTGTTCAATTTAGTCGTTATACTATAAAAT
* * * * *
2453901 TTTGTTTAATATAGTCGTTGTACTCTACAAT
1 TTTGTTCAATTTAGTCGTTATACTATAAAAT
2453932 TTTGTTCAATTTA
1 TTTGTTCAATTTA
2453945 ATTTTTGTAC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (31 bp):
TTTGTTCAATTTAGTCGTTATACTATAAAAT
Found at i:2455146 original size:35 final size:35
Alignment explanation
Indices: 2455077--2455156 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
2455067 CTTAACATGA
*
2455077 AAAATTAAAAGCACATTTAGATATCAAATAAAATT
1 AAAATAAAAAGCACATTTAGATATCAAATAAAATT
* * *
2455112 AGAATAAAAAGTACATTTAGATATTC-AATTAAATT
1 AAAATAAAAAGCACATTTAGATA-TCAAATAAAATT
*
2455147 AAAATTAAAA
1 AAAATAAAAA
2455157 TTTTGTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 36 0.95
36 2 0.05
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (35 bp):
AAAATAAAAAGCACATTTAGATATCAAATAAAATT
Found at i:2469508 original size:4 final size:4
Alignment explanation
Indices: 2469494--2469523 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2469484 TTAGTTTTTC
*
2469494 ATTT GTTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
2469524 AGTAAAGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:2483837 original size:11 final size:11
Alignment explanation
Indices: 2483821--2483848 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2483811 ATTGGTGATC
2483821 ATCAATAAATA
1 ATCAATAAATA
2483832 ATCAATAAATA
1 ATCAATAAATA
2483843 ATCAAT
1 ATCAAT
2483849 TATTTGTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (11 bp):
ATCAATAAATA
Found at i:2490134 original size:18 final size:17
Alignment explanation
Indices: 2490104--2490137 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2490094 TAGAGAGAAT
*
2490104 AAAAAAATGACAAAAAG
1 AAAAAAATAACAAAAAG
2490121 AAAAAATATAACAAAAA
1 AAAAAA-ATAACAAAAA
2490138 ACAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAAAAATAACAAAAAG
Found at i:2493360 original size:31 final size:31
Alignment explanation
Indices: 2493322--2493414 Score: 152
Period size: 31 Copynumber: 3.0 Consensus size: 31
2493312 ATCAAGTTTA
2493322 TTACAATGCCTTTTGTGGATTAAGCACAACT
1 TTACAATGCCTTTTGTGGATTAAGCACAACT
2493353 TTACAATGCCTTTTGTGGATTAAGCACAACT
1 TTACAATGCCTTTTGTGGATTAAGCACAACT
* *
2493384 TTACAATGCTTTTTATGG-TTAAAGCACAACT
1 TTACAATGCCTTTTGTGGATT-AAGCACAACT
2493415 CTACTTTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 2 0.03
31 57 0.97
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (31 bp):
TTACAATGCCTTTTGTGGATTAAGCACAACT
Found at i:2503178 original size:12 final size:11
Alignment explanation
Indices: 2503155--2503196 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
2503145 GTAATTGTTT
2503155 CAAAAAAAACA
1 CAAAAAAAACA
*
2503166 -AAACAAAACA
1 CAAAAAAAACA
*
2503176 CAAGAAAAACAA
1 CAAAAAAAAC-A
2503188 CAAAAAAAA
1 CAAAAAAAA
2503197 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 9 0.36
11 7 0.28
12 9 0.36
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (11 bp):
CAAAAAAAACA
Found at i:2505929 original size:20 final size:20
Alignment explanation
Indices: 2505886--2505930 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2505876 AAGTGAGTTA
* *
2505886 TTTTAATTTTATGTTATTTC
1 TTTTAATTTGATGTGATTTC
2505906 TTTTAATTTGATTGTGATTT-
1 TTTTAATTTGA-TGTGATTTC
2505926 TTTTA
1 TTTTA
2505931 GTTTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (20 bp):
TTTTAATTTGATGTGATTTC
Found at i:2506917 original size:38 final size:39
Alignment explanation
Indices: 2506862--2506950 Score: 162
Period size: 38 Copynumber: 2.3 Consensus size: 39
2506852 AGATCCTTAT
2506862 AAATAAATTAAGACTCTAGGTTAACAATTCAACCCATTG
1 AAATAAATTAAGACTCTAGGTTAACAATTCAACCCATTG
2506901 AAA-AAATTAAGACTCTAGGTTAACAATTCAACCCATTG
1 AAATAAATTAAGACTCTAGGTTAACAATTCAACCCATTG
*
2506939 AAATAAGTTAAG
1 AAATAAATTAAG
2506951 GAAGAAAGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 38 0.79
39 10 0.21
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (39 bp):
AAATAAATTAAGACTCTAGGTTAACAATTCAACCCATTG
Found at i:2520173 original size:21 final size:20
Alignment explanation
Indices: 2520125--2520166 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2520115 TTGAGCTATA
* *
2520125 ATATGAAAAGATAACTTTTT
1 ATATGAAAAGACAACCTTTT
2520145 ATATGAAAAGACAACCTTTT
1 ATATGAAAAGACAACCTTTT
2520165 AT
1 AT
2520167 TTTGAAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
ATATGAAAAGACAACCTTTT
Found at i:2527259 original size:33 final size:33
Alignment explanation
Indices: 2527217--2527300 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
2527207 TTAATATCCA
*
2527217 ATATTTTATTTTTATTTCTTATTATAATCTCAT
1 ATATTTTATTTTTATTTCTTAGTATAATCTCAT
* * *
2527250 ATATTTTATTTTCATTTCTTAGTATAATTTTAT
1 ATATTTTATTTTTATTTCTTAGTATAATCTCAT
*
2527283 ATATTATATATTTTATTT
1 ATATTTTAT-TTTTATTT
2527301 TACTTTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 37 0.84
34 7 0.16
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (33 bp):
ATATTTTATTTTTATTTCTTAGTATAATCTCAT
Found at i:2527751 original size:30 final size:29
Alignment explanation
Indices: 2527710--2527791 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 29
2527700 TATTATGTGC
2527710 TAGCTGTTATGGATATTTAATATATCTTGCT
1 TAGCTGTTATGGATA-TT-ATATATCTTGCT
* *
2527741 TAGCTG-TATGGATATTGTATATCTTGTT
1 TAGCTGTTATGGATATTATATATCTTGCT
* * *
2527769 TAGCTATTGTGAATATTATATAT
1 TAGCTGTTATGGATATTATATAT
2527792 ATTTTATTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 15 0.34
29 15 0.34
30 8 0.18
31 6 0.14
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (29 bp):
TAGCTGTTATGGATATTATATATCTTGCT
Found at i:2541063 original size:40 final size:41
Alignment explanation
Indices: 2540987--2541063 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
2540977 NNGGCTATTC
2540987 TTCACCTTAGTGGGGTATTCTAACCTTGCCAAGATTGATGG
1 TTCACCTTAGTGGGGTATTCTAACCTTGCCAAGATTGATGG
*
2541028 TTCACCTTAGTGGGGT-TTCTAACCTTGCCATGATTG
1 TTCACCTTAGTGGGGTATTCTAACCTTGCCAAGATTG
2541064 GTGTCCTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 19 0.54
41 16 0.46
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
TTCACCTTAGTGGGGTATTCTAACCTTGCCAAGATTGATGG
Found at i:2554234 original size:69 final size:69
Alignment explanation
Indices: 2554112--2554240 Score: 152
Period size: 69 Copynumber: 1.9 Consensus size: 69
2554102 AGATGGTGAA
* * * * * * * *
2554112 AACTCAAGTGTTTCTGTTTATTGCAAAGCATAACATTTCTTTTGTTCTTGATTTTTCTACACTGG
1 AACTCAAGTGTTTCTGTTTATTGCAAAACAAAACACTTATCTTGCTCTCGATTTTACTACACTGG
2554177 TGGG
66 TGGG
* *
2554181 AACTTAAGTGTTTTTGTTTCATT-CAAAACAAAACACTTATCTTGCTCTCGATTTTACTAC
1 AACTCAAGTGTTTCTGTTT-ATTGCAAAACAAAACACTTATCTTGCTCTCGATTTTACTAC
2554241 TCTTGTCTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
69 46 0.94
70 3 0.06
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (69 bp):
AACTCAAGTGTTTCTGTTTATTGCAAAACAAAACACTTATCTTGCTCTCGATTTTACTACACTGG
TGGG
Found at i:2565629 original size:2 final size:2
Alignment explanation
Indices: 2565622--2565649 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2565612 ATTTGGGCGA
2565622 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
2565650 GAAATTCTCC
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:2573166 original size:21 final size:22
Alignment explanation
Indices: 2573137--2573193 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
2573127 TATTATGATT
*
2573137 AAAATAAAGAAAGAAAAG-AAG
1 AAAAAAAAGAAAGAAAAGAAAG
*
2573158 AAAAAAAAGACCA-AAAAGAAAG
1 AAAAAAAAGA-AAGAAAAGAAAG
*
2573180 TAAAAAAAGCAAAG
1 AAAAAAAAG-AAAG
2573194 GGATTTGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 14 0.50
22 13 0.46
23 1 0.04
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAAAAAAGAAAGAAAAGAAAG
Found at i:2575301 original size:17 final size:16
Alignment explanation
Indices: 2575281--2575315 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2575271 GATAAAGAGG
2575281 AAAACAATGTGTTCTCT
1 AAAA-AATGTGTTCTCT
2575298 -AAAAATGTGTTCTCT
1 AAAAAATGTGTTCTCT
2575313 AAA
1 AAA
2575316 GTGACATGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (16 bp):
AAAAAATGTGTTCTCT
Found at i:2575306 original size:15 final size:15
Alignment explanation
Indices: 2575286--2575315 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2575276 AGAGGAAAAC
2575286 AATGTGTTCTCTAAA
1 AATGTGTTCTCTAAA
2575301 AATGTGTTCTCTAAA
1 AATGTGTTCTCTAAA
2575316 GTGACATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
AATGTGTTCTCTAAA
Found at i:2577525 original size:77 final size:70
Alignment explanation
Indices: 2577433--2577745 Score: 250
Period size: 72 Copynumber: 4.3 Consensus size: 70
2577423 TTAGATATCG
* * * *
2577433 TTGACATCTTATCGTGACATACTGAGTTGTTGCAGTATTATAAGGTGACACCCCACACTCCAATT
1 TTGACATCTTGTCGTGACATGCTGAGTCGTTGTAGTATTAT-AGGTGACACCCCACACTCCAA--
*
2577498 TCACCTATGTCA
63 --A--GATGTCA
* * * *
2577510 TTGACATCTTGTCGTGACATGCTAAGTCATTGTAGTATTATTGGGTGACACGCCACACTCCAAAG
1 TTGACATCTTGTCGTGACATGCTGAGTCGTTGTAGTATTA-TAGGTGACACCCCACACTCCAAAG
*
2577575 ATGTCG
65 ATGTCA
* ***
2577581 TTGACATCTTGTCGTGACATGCATGAGTCGTTGTAGTATTATAGGCTGACACGCCATTTTCCAAA
1 TTGACATCTTGTCGTGACATGC-TGAGTCGTTGTAGTATTATAGG-TGACACCCCACACTCCAAA
*
2577646 GATGTCG
64 GATGTCA
* * * * * * ** **
2577653 TTGACATCTTGTCATGACACGGTGCCATGTTGTTATAGTATTATAGGGTAACATGCCACTTTCCA
1 TTGACATCTTGTCGTGACATGCTG--A-GTCGTTGTAGTATTATA-GGTGACACCCCACACTCCA
2577718 AAGATGTCA
62 AAGATGTCA
*
2577727 TT-AGCATCTTGTTGTGACA
1 TTGA-CATCTTGTCGTGACA
2577746 CACCATTAGT
Statistics
Matches: 201, Mismatches: 27, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
71 32 0.16
72 58 0.29
73 3 0.01
74 52 0.26
75 2 0.01
77 53 0.26
78 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (70 bp):
TTGACATCTTGTCGTGACATGCTGAGTCGTTGTAGTATTATAGGTGACACCCCACACTCCAAAGA
TGTCA
Found at i:2577644 original size:72 final size:71
Alignment explanation
Indices: 2577504--2577745 Score: 274
Period size: 72 Copynumber: 3.4 Consensus size: 71
2577494 AATTTCACCT
* * **
2577504 ATGTCATTGACATCTTGTCGTGACATGC-TAAGTCATTGTAGTATTATTGGGTGACACGCCACAC
1 ATGTCATTGACATCTTGTCGTGACATGCAT-AGTCGTTGTAGTATTATAGGGTGACACGCCACTT
2577568 TCCAAAG
65 TCCAAAG
* * *
2577575 ATGTCGTTGACATCTTGTCGTGACATGCATGAGTCGTTGTAGTATTATAGGCTGACACGCCATTT
1 ATGTCATTGACATCTTGTCGTGACATGCAT-AGTCGTTGTAGTATTATAGGGTGACACGCCACTT
2577640 TCCAAAG
65 TCCAAAG
* * * * * *
2577647 ATGTCGTTGACATCTTGTCATGACACGGTGCCAT-GTTGTTATAGTATTATAGGGTAACATGCCA
1 ATGTCATTGACATCTTGTCGTGACA---TG-CATAGTCGTTGTAGTATTATAGGGTGACACGCCA
2577711 CTTTCCAAAG
62 CTTTCCAAAG
*
2577721 ATGTCATT-AGCATCTTGTTGTGACA
1 ATGTCATTGA-CATCTTGTCGTGACA
2577746 CACCATTAGT
Statistics
Matches: 147, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
71 27 0.18
72 60 0.41
73 1 0.01
74 54 0.37
75 2 0.01
76 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (71 bp):
ATGTCATTGACATCTTGTCGTGACATGCATAGTCGTTGTAGTATTATAGGGTGACACGCCACTTT
CCAAAG
Found at i:2578735 original size:23 final size:22
Alignment explanation
Indices: 2578705--2578770 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
2578695 TGTCGCATAT
*
2578705 ATTCTCACCATGCTGTGTCACAG
1 ATTCTCACCATG-TGTGTCACAA
* *
2578728 ATTCTCACCACGTCGTCTCACAA
1 ATTCTCACCATGT-GTGTCACAA
2578751 ATTCTCACCATGGTGTGTCA
1 ATTCTCACCAT-GTGTGTCA
2578771 GAAACTGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 33 0.92
24 2 0.06
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.30
Consensus pattern (22 bp):
ATTCTCACCATGTGTGTCACAA
Found at i:2578880 original size:23 final size:21
Alignment explanation
Indices: 2578827--2578883 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
2578817 CATGCCGTCT
2578827 TACATATTCTCACCATAGTATG
1 TACATATTCTCA-CATAGTATG
*
2578849 T-CATATTCTCACATTGGTATG
1 TACATATTCTCACA-TAGTATG
2578870 TCACATATTCTCAC
1 T-ACATATTCTCAC
2578884 CATGTTGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 2 0.06
21 17 0.55
22 1 0.03
23 11 0.35
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.39
Consensus pattern (21 bp):
TACATATTCTCACATAGTATG
Found at i:2578892 original size:21 final size:22
Alignment explanation
Indices: 2578800--2578953 Score: 97
Period size: 23 Copynumber: 7.0 Consensus size: 22
2578790 TGTCACAGCC
2578800 ATGTCACATATTCTCACCATG-
1 ATGTCACATATTCTCACCATGT
**
2578821 CCGTCTTACATATTCTCACCATAGT
1 ATGTC--ACATATTCTCACCAT-GT
2578846 ATGT--CATATTCTCA-CATTGGT
1 ATGTCACATATTCTCACCA-T-GT
2578867 ATGTCACATATTCTCACCATGT
1 ATGTCACATATTCTCACCATGT
* *
2578889 -TGTCTCATATAATCTCTCCATG-
1 ATGTCACATAT--TCTCACCATGT
* * *
2578911 -GGTCACATATTATCACCCTGT
1 ATGTCACATATTCTCACCATGT
* * *
2578932 CGTGTCACATATTTTCTCCATG
1 -ATGTCACATATTCTCACCATG
2578954 GCGTGTCACA
Statistics
Matches: 104, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
20 9 0.09
21 29 0.28
22 10 0.10
23 51 0.49
24 3 0.03
25 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (22 bp):
ATGTCACATATTCTCACCATGT
Found at i:2578939 original size:23 final size:23
Alignment explanation
Indices: 2578912--2578963 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2578902 CTCTCCATGG
* *
2578912 GTCACATATTATCACCCTGTCGT
1 GTCACATATTATCACCATGGCGT
* *
2578935 GTCACATATTTTCTCCATGGCGT
1 GTCACATATTATCACCATGGCGT
2578958 GTCACA
1 GTCACA
2578964 AATTTTAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (23 bp):
GTCACATATTATCACCATGGCGT
Found at i:2578950 original size:43 final size:43
Alignment explanation
Indices: 2578869--2578954 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
2578859 ACATTGGTAT
* * *
2578869 GTCACATATTCTCACCATGTTGTCTCATATAATCTCTCCATGG
1 GTCACATATTATCACCATGTCGTCTCACATAATCTCTCCATGG
* * * *
2578912 GTCACATATTATCACCCTGTCGTGTCACATATTTTCTCCATGG
1 GTCACATATTATCACCATGTCGTCTCACATAATCTCTCCATGG
2578955 CGTGTCACAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (43 bp):
GTCACATATTATCACCATGTCGTCTCACATAATCTCTCCATGG
Found at i:2579104 original size:23 final size:23
Alignment explanation
Indices: 2579060--2579161 Score: 98
Period size: 23 Copynumber: 4.4 Consensus size: 23
2579050 GTGTTACAGT
* * * *
2579060 CGTGTCATATATTTTCAACATGC
1 CGTGTCACAAATTCTCACCATGC
*
2579083 CGTGTTACAAATTCGT-ACCATGC
1 CGTGTCACAAATTC-TCACCATGC
*
2579106 CGTGTCACGAATTCTCACCATGC
1 CGTGTCACAAATTCTCACCATGC
* * * *
2579129 CGTGTCACACATTCCCACCACGA
1 CGTGTCACAAATTCTCACCATGC
2579152 CGTGTCACAA
1 CGTGTCACAA
2579162 GCTTTAAACC
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
22 1 0.02
23 62 0.97
24 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (23 bp):
CGTGTCACAAATTCTCACCATGC
Found at i:2579218 original size:23 final size:23
Alignment explanation
Indices: 2579188--2579478 Score: 186
Period size: 23 Copynumber: 12.9 Consensus size: 23
2579178 TGTCATAACT
*
2579188 ATGTCACAAATTCTCACCATGCC
1 ATGTCACACATTCTCACCATGCC
*
2579211 ATGTCACACATTCCCACCATGCC
1 ATGTCACACATTCTCACCATGCC
*
2579234 ATGTCACA-A--C-C-CGA--CC
1 ATGTCACACATTCTCACCATGCC
* * * **
2579250 GTGTCACATATTCTCACTATATC
1 ATGTCACACATTCTCACCATGCC
* *
2579273 ATGTCACACATGCTCACCATGTC
1 ATGTCACACATTCTCACCATGCC
* * * **
2579296 GTGTCATAGATTCTCACCACACC
1 ATGTCACACATTCTCACCATGCC
* * *
2579319 ATGTCATACATTCCCACCATTGGC
1 ATGTCACACATTCTCACCA-TGCC
* * * *
2579343 ATGTCACAAACTCTAAACCCTGCC
1 ATGTCACACATTCT-CACCATGCC
* *
2579367 -TGTCACACACTCTCATCATGCC
1 ATGTCACACATTCTCACCATGCC
* * *
2579389 GTGTCACACATTCCCACCATGGC
1 ATGTCACACATTCTCACCATGCC
* * * *
2579412 ATGTCACAAACTCTAAACCTTGCC
1 ATGTCACACATTCT-CACCATGCC
*
2579436 -TGTCACACACTCTCACCATGCC
1 ATGTCACACATTCTCACCATGCC
* *
2579458 GTGTCACACATTCCCACCATG
1 ATGTCACACATTCTCACCATG
2579479 ATGTGTCACA
Statistics
Matches: 205, Mismatches: 51, Indels: 24
0.73 0.18 0.09
Matches are distributed among these distances:
16 9 0.04
17 1 0.00
18 2 0.01
19 2 0.01
20 2 0.01
21 2 0.01
22 14 0.07
23 150 0.73
24 20 0.10
25 3 0.01
ACGTcount: A:0.27, C:0.37, G:0.11, T:0.25
Consensus pattern (23 bp):
ATGTCACACATTCTCACCATGCC
Found at i:2579436 original size:69 final size:69
Alignment explanation
Indices: 2579320--2579510 Score: 310
Period size: 69 Copynumber: 2.7 Consensus size: 69
2579310 CACCACACCA
* *
2579320 TGTCATACATTCCCACCATTGGCATGTCACAAACTCTAAACCCTGCCTGTCACACACTCTCATCA
1 TGTCACACATTCCCACCA-TGGCATGTCACAAACTCTAAACCCTGCCTGTCACACACTCTCACCA
2579385 TGCCG
65 TGCCG
*
2579390 TGTCACACATTCCCACCATGGCATGTCACAAACTCTAAACCTTGCCTGTCACACACTCTCACCAT
1 TGTCACACATTCCCACCATGGCATGTCACAAACTCTAAACCCTGCCTGTCACACACTCTCACCAT
2579455 GCCG
66 GCCG
***
2579459 TGTCACACATTCCCACCATGATGTGTCACAAACTCTAAACCCTGCCGTGTCA
1 TGTCACACATTCCCACCATGGCATGTCACAAACTCTAAACCCTGCC-TGTCA
2579511 TAGCCGTGTC
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
69 91 0.81
70 22 0.19
ACGTcount: A:0.26, C:0.37, G:0.12, T:0.25
Consensus pattern (69 bp):
TGTCACACATTCCCACCATGGCATGTCACAAACTCTAAACCCTGCCTGTCACACACTCTCACCAT
GCCG
Found at i:2579484 original size:23 final size:23
Alignment explanation
Indices: 2579367--2579493 Score: 94
Period size: 23 Copynumber: 5.5 Consensus size: 23
2579357 AAACCCTGCC
* * *
2579367 TGTCACACACTCTCATCATGCCG
1 TGTCACACACTCCCACCATGACG
* * *
2579390 TGTCACACATTCCCACCATGGCA
1 TGTCACACACTCCCACCATGACG
* ** * *
2579413 TGTCACAAACTCTAAACCTTG-CC
1 TGTCACACACTC-CCACCATGACG
* *
2579436 TGTCACACACTCTCACCATGCCG
1 TGTCACACACTCCCACCATGACG
* *
2579459 TGTCACACATTCCCACCATGATG
1 TGTCACACACTCCCACCATGACG
*
2579482 TGTCACAAACTC
1 TGTCACACACTC
2579494 TAAACCCTGC
Statistics
Matches: 80, Mismatches: 22, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
22 5 0.06
23 70 0.88
24 5 0.06
ACGTcount: A:0.26, C:0.38, G:0.12, T:0.24
Consensus pattern (23 bp):
TGTCACACACTCCCACCATGACG
Found at i:2600129 original size:22 final size:22
Alignment explanation
Indices: 2600069--2600140 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
2600059 GTGATGAGCT
*
2600069 TTTAGGCATTACGTTACTAA-C
1 TTTAGGCATTACGTGACTAATC
*
2600090 TTTTGGACATTACGTGACTAATC
1 TTTAGG-CATTACGTGACTAATC
* * *
2600113 TTTAGGCATTGCATGACTGATC
1 TTTAGGCATTACGTGACTAATC
2600135 TTTAGG
1 TTTAGG
2600141 TATTGTGTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
21 5 0.12
22 32 0.74
23 6 0.14
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (22 bp):
TTTAGGCATTACGTGACTAATC
Found at i:2600182 original size:23 final size:23
Alignment explanation
Indices: 2600139--2600183 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2600129 CTGATCTTTA
* * *
2600139 GGTATTGTGTGATTGGTTGATAT
1 GGTATTGTGTGACTAGCTGATAT
2600162 GGTATTGTGTGACTAGCTGATA
1 GGTATTGTGTGACTAGCTGATA
2600184 GGCATTGCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.04, G:0.33, T:0.42
Consensus pattern (23 bp):
GGTATTGTGTGACTAGCTGATAT
Found at i:2600212 original size:23 final size:23
Alignment explanation
Indices: 2600183--2600230 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2600173 ACTAGCTGAT
2600183 AGGCATT-GCATGACTAGTTAATA
1 AGGCATTAGCA-GACTAGTTAATA
* *
2600206 AGGCATTAGTAGACTAGTTAGTA
1 AGGCATTAGCAGACTAGTTAATA
2600229 AG
1 AG
2600231 ATATTGTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (23 bp):
AGGCATTAGCAGACTAGTTAATA
Found at i:2605912 original size:15 final size:15
Alignment explanation
Indices: 2605889--2605930 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
2605879 TATAGCCAAT
* *
2605889 TTCCCTCCAAAAGAG
1 TTCCCTCCAAAAAAA
*
2605904 TTTCCTCCAAAAAAA
1 TTCCCTCCAAAAAAA
2605919 TTCCCTCCAAAA
1 TTCCCTCCAAAA
2605931 CATTTTTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.24
Consensus pattern (15 bp):
TTCCCTCCAAAAAAA
Found at i:2606361 original size:30 final size:30
Alignment explanation
Indices: 2606300--2606361 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
2606290 CGGGCCCCGA
* *
2606300 GCCTGGGTATCGCGCTCCCATGCTATGCGG
1 GCCTGGGTATCGCGCACCCATGCTATACGG
* * * *
2606330 GCCTGGGTGTTGCGCACCCCTGCTGTACGG
1 GCCTGGGTATCGCGCACCCATGCTATACGG
2606360 GC
1 GC
2606362 TGGCACACCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.08, C:0.34, G:0.35, T:0.23
Consensus pattern (30 bp):
GCCTGGGTATCGCGCACCCATGCTATACGG
Found at i:2613623 original size:12 final size:13
Alignment explanation
Indices: 2613605--2613634 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2613595 CATTGGAGAG
2613605 CAAAAAACAAAAA
1 CAAAAAACAAAAA
2613618 -AAAAAACAAAAA
1 CAAAAAACAAAAA
2613630 CAAAA
1 CAAAA
2613635 TGAACTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAACAAAAA
Found at i:2617353 original size:3 final size:3
Alignment explanation
Indices: 2617345--2617373 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2617335 TGTGATGGGT
2617345 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2617374 GCACCAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2617586 original size:15 final size:15
Alignment explanation
Indices: 2617566--2617633 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
2617556 AGGATATAAA
2617566 TTTAAATTTAATTTG
1 TTTAAATTTAATTTG
2617581 TTTAAATTTAA----
1 TTTAAATTTAATTTG
* * *
2617592 -ATAAAGATTAATTATA
1 TTTAAA-TTTAATT-TG
2617608 TTTAAATTTAATTTG
1 TTTAAATTTAATTTG
2617623 TTTAAATTTAA
1 TTTAAATTTAA
2617634 ATATAATATC
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
10 4 0.10
11 4 0.10
15 23 0.56
16 6 0.15
17 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (15 bp):
TTTAAATTTAATTTG
Found at i:2617588 original size:21 final size:21
Alignment explanation
Indices: 2617562--2617640 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
2617552 AGATAGGATA
2617562 TAAATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
* * **
2617583 TAAATTTAAA-TAAAGATTAAT
1 TAAATTTAAATTTAA-TTTGTT
*
2617604 TATATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
*
2617625 TAAATTTAAATATAAT
1 TAAATTTAAATTTAAT
2617641 ATCCTATCAT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTGTT
Found at i:2617804 original size:54 final size:55
Alignment explanation
Indices: 2617740--2617850 Score: 215
Period size: 54 Copynumber: 2.0 Consensus size: 55
2617730 GTTAGAAAAA
2617740 GCAAAAATTCTTTTCTTCTTTTTTCTTTCCC-TCATTCTTGAGGCACCATCAAAG
1 GCAAAAATTCTTTTCTTCTTTTTTCTTTCCCTTCATTCTTGAGGCACCATCAAAG
2617794 GCAAAAATTCTTTTCTTCTTTTTTCTTTCCCTTCATTCTTGAGGCACCATCAAAG
1 GCAAAAATTCTTTTCTTCTTTTTTCTTTCCCTTCATTCTTGAGGCACCATCAAAG
2617849 GC
1 GC
2617851 TAGAAGGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 31 0.55
55 25 0.45
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (55 bp):
GCAAAAATTCTTTTCTTCTTTTTTCTTTCCCTTCATTCTTGAGGCACCATCAAAG
Found at i:2618755 original size:47 final size:47
Alignment explanation
Indices: 2618702--2619039 Score: 239
Period size: 47 Copynumber: 7.4 Consensus size: 47
2618692 TATATTTTGT
*
2618702 TGATTTTACTTATTTGTTTGGTAAAATTTATAAAATGCATGATGTAA
1 TGATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAA
*
2618749 TGATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATAATGTAA
1 TGATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAA
**********
2618796 -GATTTTACTTATTTGTTAGGTAAAATTTNNNNNNNNNNTGATGTAA
1 TGATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAA
* * *
2618842 TTATTTTACTTATTTG-T---T-AAATTTTTAAAATGCATGATGTTA
1 TGATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAA
* **********
2618884 TTATTTTACTTATTTGTTAGGTAAAANNNNNNNNNNGCATGATGTAA
1 TGATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAA
*
2618931 TTATTTTACTTATTT-TT---T-AAATTTATAAAATGCATGATGTAA
1 TGATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAA
********** *
2618973 TNNNNNNNNNNATTTGTTAGGTAAAATTTATAAAAATGCATAATGTAA
1 TGATTTTACTTATTTGTTAGGTAAAATTTAT-AAAATGCATGATGTAA
*
2619021 TTATTTTACTTATTTGTTA
1 TGATTTTACTTATTTGTTA
2619040 AGCAAACTTG
Statistics
Matches: 212, Mismatches: 67, Indels: 23
0.70 0.22 0.08
Matches are distributed among these distances:
42 48 0.23
43 5 0.02
46 40 0.19
47 95 0.45
48 24 0.11
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.45
Consensus pattern (47 bp):
TGATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAA
Found at i:2619665 original size:32 final size:32
Alignment explanation
Indices: 2619628--2619752 Score: 90
Period size: 32 Copynumber: 3.6 Consensus size: 32
2619618 ATATAGGTAG
2619628 AAATTAAATATGTCTAATCTTAATTGATTAGA
1 AAATTAAATATGTCTAATCTTAATTGATTAGA
* * * *
2619660 AAATTAGATATG-CAAAATTTTCAAACTAGTAATATAGGTA
1 AAATTAAATATGTC-TAATCTT--AA-T--TGAT-TA-G-A
2619700 GAAATTAAATATGTCTAATCTTAATTGATTAGA
1 -AAATTAAATATGTCTAATCTTAATTGATTAGA
*
2619733 AAATTAGATATATGCCTAAT
1 AAATTA-A-ATATGTCTAAT
2619753 TGAATCTTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
31 1 0.01
32 22 0.31
33 2 0.03
34 13 0.18
35 3 0.04
36 3 0.04
37 3 0.04
38 3 0.04
39 3 0.04
40 1 0.01
41 16 0.23
42 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (32 bp):
AAATTAAATATGTCTAATCTTAATTGATTAGA
Found at i:2619679 original size:73 final size:73
Alignment explanation
Indices: 2619596--2619743 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
2619586 ACTAGCATGC
2619596 ATGCAAAATTTTCAAACTAGTAATATAGGTAGAAATTAAATATGTCTAATCTTAATTGATTAGAA
1 ATGCAAAATTTTCAAACTAGTAATATAGGTAGAAATTAAATATGTCTAATCTTAATTGATTAGAA
2619661 AATTAGAT
66 AATTAGAT
2619669 ATGCAAAATTTTCAAACTAGTAATATAGGTAGAAATTAAATATGTCTAATCTTAATTGATTAGAA
1 ATGCAAAATTTTCAAACTAGTAATATAGGTAGAAATTAAATATGTCTAATCTTAATTGATTAGAA
2619734 AATTAGAT
66 AATTAGAT
2619742 AT
1 AT
2619744 ATGCCTAATT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (73 bp):
ATGCAAAATTTTCAAACTAGTAATATAGGTAGAAATTAAATATGTCTAATCTTAATTGATTAGAA
AATTAGAT
Found at i:2623525 original size:15 final size:15
Alignment explanation
Indices: 2623504--2623573 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 15
2623494 TAGGATATAA
2623504 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
* *
2623519 GTTTAAATTTAAATT
1 ATTTAAATTTAATTT
* **
2623534 ATCT--A-TCCATTAT
1 ATTTAAATTTAATT-T
2623547 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
*
2623562 GTTTAAATTTAA
1 ATTTAAATTTAA
2623574 ATAAGGATTA
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
12 3 0.08
13 5 0.12
15 28 0.70
16 4 0.10
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:2623601 original size:42 final size:42
Alignment explanation
Indices: 2623504--2623617 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 42
2623494 TAGGATATAA
* * *
2623504 ATTTAAATTTAATTTGTTTAAATTTAAATTATCTATCCATTAT
1 ATTTAAATTTAATTTGTTTAAATTTAAA-TAACGATCAATTAT
* *
2623547 ATTTAAATTTAATTTGTTTAAATTTAAATAAGGATTAATTAT
1 ATTTAAATTTAATTTGTTTAAATTTAAATAACGATCAATTAT
* *
2623589 ATTTAAATTTAATCT-ATTAAATTTAAATA
1 ATTTAAATTTAATTTGTTTAAATTTAAATA
2623618 TAATATCCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
41 13 0.20
42 23 0.36
43 28 0.44
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (42 bp):
ATTTAAATTTAATTTGTTTAAATTTAAATAACGATCAATTAT
Done.