Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 20
Found at i:3175850 original size:35 final size:34
Alignment explanation
Indices: 3175740--3175853 Score: 111
Period size: 35 Copynumber: 3.2 Consensus size: 34
3175730 CTTGATCAAT
* *
3175740 CTGAACCTATATAAGAAATTACCAATTTGATTGA
1 CTGAACCTATATAAGGAATTACCAGTTTGATTGA
* ** * *
3175774 GTAGAACCTACCGTAAGGAATTACCAGTTCGATTGGT
1 CT-GAACCTA-TATAAGGAATTACCAGTTTGATT-GA
* *
3175811 CTGAACCTATATAAGGAATTACCAGTTTAATCGAA
1 CTGAACCTATATAAGGAATTACCAGTTTGATTG-A
3175846 CTGAACCT
1 CTGAACCT
3175854 GCAGAGACTT
Statistics
Matches: 62, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
34 2 0.03
35 33 0.53
36 25 0.40
37 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (34 bp):
CTGAACCTATATAAGGAATTACCAGTTTGATTGA
Found at i:3180508 original size:20 final size:21
Alignment explanation
Indices: 3180464--3180514 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
3180454 AAGTTAACTT
3180464 AGTATCGATA-CCACCCTACG
1 AGTATCGATACCCACCCTACG
3180484 AGTATCGATACCCTACCCT-CG
1 AGTATCGATACCC-ACCCTACG
*
3180505 -GTATTGATAC
1 AGTATCGATAC
3180515 TTCTGCCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 19 0.68
21 4 0.14
22 5 0.18
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (21 bp):
AGTATCGATACCCACCCTACG
Found at i:3184178 original size:2 final size:2
Alignment explanation
Indices: 3184173--3184211 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3184163 TATTAATAAA
3184173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3184212 AAATTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3184334 original size:54 final size:54
Alignment explanation
Indices: 3184271--3184379 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 54
3184261 TCATCCCTGG
* *
3184271 ATGAGAATGAGATTGACTCAAATGAT-AAAGTCTTAGGTCTTTGGATCTCAATGC
1 ATGAGAATGAGATTGACTCAAACGATGAAA-TCTTAGGTCCTTGGATCTCAATGC
*
3184325 ATGAGAATGAGATTTACTCAAACGATGAAATCTTAGGTCCTTGGATCTCAATGC
1 ATGAGAATGAGATTGACTCAAACGATGAAATCTTAGGTCCTTGGATCTCAATGC
3184379 A
1 A
3184380 AGCAAGTCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 48 0.94
55 3 0.06
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (54 bp):
ATGAGAATGAGATTGACTCAAACGATGAAATCTTAGGTCCTTGGATCTCAATGC
Found at i:3189017 original size:16 final size:16
Alignment explanation
Indices: 3188976--3189018 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
3188966 TAATTAGTAA
*
3188976 TTAGCGGTTAGAAAGG
1 TTAGCGGTTAGAAAAG
**
3188992 TTAGTTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
3189008 TTAGCGGTTAG
1 TTAGCGGTTAG
3189019 CAGAGTCTGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.33
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:3189293 original size:135 final size:130
Alignment explanation
Indices: 3189014--3189410 Score: 391
Period size: 135 Copynumber: 3.0 Consensus size: 130
3189004 AAAGTTAGCG
* * * * * * *
3189014 GTTAGCAGAGTCTGAACTATAATAATGTGGATCATACCCCAGATCTGGTCACCATAAAGTCGAAT
1 GTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCAAAT
** *** * * *
3189079 CGAATA--ATTCA-AATAAATTAACA-AAATAA-AATACAATAATA-TA-AATATAA-AAATGTT
66 CGAATATTATAAACAATAAA-TAA-ATAAATAACAAT-GGTTAA-AGTACAATAAAATAAAAGTC
3189136 AGTA
127 AGTA
* ** ** *
3189140 CTTAGTTGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTTGATT
1 GTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCAAAT
* *
3189205 C-AATTATTAGAAATAATA-AATAAATAAATAAATAAACAATGGTTAGAGTGCAATAAAATAAAA
66 CGAA-TATT----ATAA-ACAATAAATAAATAAAT-AACAATGGTTAAAGTACAATAAAATAAAA
3189268 GTCAGTA
124 GTCAGTA
* *
3189275 GTTAGCAGAGTCTGAACCATAATAATGTGGATCATACCCCGGATCTGGTCACCACAAGGTCAAAT
1 GTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCAAAT
*
3189340 CGAATATTATAAACAATAAATAAATAAATAACAATGGTTAAAGTACAATAAAATAAAAGTTAGTA
66 CGAATATTATAAACAATAAATAAATAAATAACAATGGTTAAAGTACAATAAAATAAAAGTCAGTA
3189405 GTTAGC
1 GTTAGC
3189411 TTTAAATAAA
Statistics
Matches: 223, Mismatches: 32, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
125 2 0.01
126 57 0.26
130 40 0.18
131 20 0.09
132 10 0.04
133 12 0.05
134 9 0.04
135 71 0.32
136 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (130 bp):
GTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCAAAT
CGAATATTATAAACAATAAATAAATAAATAACAATGGTTAAAGTACAATAAAATAAAAGTCAGTA
Found at i:3190820 original size:139 final size:139
Alignment explanation
Indices: 3190636--3191068 Score: 582
Period size: 139 Copynumber: 3.1 Consensus size: 139
3190626 ATTTTTGGAT
* *
3190636 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTACCTGAAGATGACACTGCT
1 ATAAATTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTACCTGAGGATGACACTGCT
* ** * * *
3190701 CATTTGTGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAAGACGTATAGTCA
66 CCTACGTGTTGAGGAGATCTGGTCAGTGGACGACATTGTTCCTACGTGATGAGGACGTATAGCCA
3190766 TCTTTAGGG
131 TCTTTAGGG
* * * * * *
3190775 ATAAATTGGAGATAACACCGTTCCTACATGATGAAGAAGTTTGATTGCCTGAGGATGACGA-TGC
1 ATAAATTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTACCTGAGGATGAC-ACTGC
* * * *
3190839 TCCTACGTGTTGAGGAGATATGGTCAGTGGACGACATTCTTCCGACGTGATGAGGACGTTTAGCC
65 TCCTACGTGTTGAGGAGATCTGGTCAGTGGACGACATTGTTCCTACGTGATGAGGACGTATAGCC
3190904 ATCTTTAGGG
130 ATCTTTAGGG
* * * *
3190914 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCT
1 ATAAATTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTACCTGAGGATGACACTGCT
* * * * * *
3190979 CCTACGTGTTGAGGAGATCTGATTAATGGACAACATTGTTCCTACGTAATGAGGACGTCTAGCCA
66 CCTACGTGTTGAGGAGATCTGGTCAGTGGACGACATTGTTCCTACGTGATGAGGACGTATAGCCA
*
3191044 TTTTTA-GG
131 TCTTTAGGG
3191052 ATAAATTGGAGACAACA
1 ATAAATTGGAGACAACA
3191069 ATCTCAAGTG
Statistics
Matches: 253, Mismatches: 39, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
138 18 0.07
139 234 0.92
140 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (139 bp):
ATAAATTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTACCTGAGGATGACACTGCT
CCTACGTGTTGAGGAGATCTGGTCAGTGGACGACATTGTTCCTACGTGATGAGGACGTATAGCCA
TCTTTAGGG
Found at i:3191162 original size:21 final size:21
Alignment explanation
Indices: 3191108--3191154 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3191098 AGAAATTGCC
*
3191108 TCAAGCGAGACAAAATTTGTT
1 TCAAGCGAGACAAAATTCGTT
3191129 TCAAGCGAGACAAAATTCGTT
1 TCAAGCGAGACAAAATTCGTT
3191150 TCAAG
1 TCAAG
3191155 GGAAACAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (21 bp):
TCAAGCGAGACAAAATTCGTT
Found at i:3192615 original size:18 final size:18
Alignment explanation
Indices: 3192592--3192633 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3192582 AGTATGATGG
3192592 TTGGAACCTTAGAAACAA
1 TTGGAACCTTAGAAACAA
**
3192610 TTGGAATTTTAGAAACAA
1 TTGGAACCTTAGAAACAA
*
3192628 CTGGAA
1 TTGGAA
3192634 TTGAAGGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (18 bp):
TTGGAACCTTAGAAACAA
Found at i:3192634 original size:18 final size:18
Alignment explanation
Indices: 3192600--3192635 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3192590 GGTTGGAACC
*
3192600 TTAGAAACAATTGGAATT
1 TTAGAAACAACTGGAATT
3192618 TTAGAAACAACTGGAATT
1 TTAGAAACAACTGGAATT
3192636 GAAGGTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (18 bp):
TTAGAAACAACTGGAATT
Found at i:3193360 original size:23 final size:23
Alignment explanation
Indices: 3193334--3193399 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
3193324 TTTATTTTCA
3193334 AAAAAATTTGAAAAATATCAATT
1 AAAAAATTTGAAAAATATCAATT
*
3193357 AAAAGAATTTTGAAAAAGGT-TTAATT
1 AAAA-AA-TTTGAAAAA--TATCAATT
*
3193383 -AAAATTTTGAAAAATAT
1 AAAAAATTTGAAAAATAT
3193400 TGCCCCTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
21 1 0.03
22 1 0.03
23 13 0.36
24 3 0.08
25 12 0.33
26 5 0.14
27 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (23 bp):
AAAAAATTTGAAAAATATCAATT
Found at i:3195157 original size:27 final size:27
Alignment explanation
Indices: 3195117--3195169 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
3195107 AAGGAGCATA
*
3195117 AATTCAATCATTAAAAGATAAAAAAATT
1 AATTAAATCATT-AAAGATAAAAAAATT
3195145 AATTAAAT-ATTAAAGATAAAAAAAT
1 AATTAAATCATTAAAGATAAAAAAAT
3195170 GAGTTCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 14 0.58
27 3 0.12
28 7 0.29
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (27 bp):
AATTAAATCATTAAAGATAAAAAAATT
Found at i:3196981 original size:13 final size:13
Alignment explanation
Indices: 3196965--3196993 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3196955 AAAGAAAATG
3196965 AAAAAACC-TGAC
1 AAAAAACCTTGAC
3196977 AAAAAACCTTGAC
1 AAAAAACCTTGAC
3196990 AAAA
1 AAAA
3196994 CTGGAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.62, C:0.21, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAAAACCTTGAC
Found at i:3198305 original size:16 final size:16
Alignment explanation
Indices: 3198281--3198341 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
3198271 CAGTTAATAA
* *
3198281 TTAGCTGTTAGAAAGG
1 TTAGCGGTTAGAAAAG
**
3198297 TTAGTTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
3198313 TTAGCGGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
*
3198329 TTAGTGGTTAGAA
1 TTAGCGGTTAGAA
3198342 GAGTCCGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:3198317 original size:32 final size:32
Alignment explanation
Indices: 3198281--3198341 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3198271 CAGTTAATAA
* * *
3198281 TTAGCTGTTAGAAAGGTTAGTTGTTAGAAAAG
1 TTAGCGGTTAGAAAAGTTAGTGGTTAGAAAAG
3198313 TTAGCGGTTAGAAAAGTTAGTGGTTAGAA
1 TTAGCGGTTAGAAAAGTTAGTGGTTAGAA
3198342 GAGTCCGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (32 bp):
TTAGCGGTTAGAAAAGTTAGTGGTTAGAAAAG
Found at i:3198603 original size:131 final size:131
Alignment explanation
Indices: 3198467--3198865 Score: 602
Period size: 131 Copynumber: 3.0 Consensus size: 131
3198457 ATGGTTAGTT
** *
3198467 GAGTCCGAACCATAATAATGTGGATCATACCCCAAATCGGGTGACCACAAGGTCGATTCAAATAT
1 GAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCGATTCAAATAT
3198532 TAGAAACAATAAATAAATAAATAAACAATGGTTAGAGTGCAATAAAATAAAAGTCAGTAGTTAGC
66 TAGAAACAATAAATAAATAAATAAACAATGGTTAGAGTGCAATAAAATAAAAGTCAGTAGTTAGC
3198597 A
131 A
*
3198598 GAGTCCAAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCGATTCAAATAT
1 GAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCGATTCAAATAT
* *
3198663 TATAAACAATAAATAAATAAATAAATAATGGTTAGAGTGCAATAAAATAAAAGTCAGTAGTTAGC
66 TAGAAACAATAAATAAATAAATAAACAATGGTTAGAGTGCAATAAAATAAAAGTCAGTAGTTAGC
3198728 A
131 A
* ** *
3198729 GAGTCCGAACCATAATAATGTGAATCATACCCCGGATCTAGTCACCACAAGGTCGAAT-AGAATA
1 GAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCGATTCA-AATA
* * *
3198793 TTTGAAACAATAAATAAGTAAATAAATAAATAACAATGGTTAAAGTGCAATAAAATAAAAGTTAG
65 TTAGAAACAAT--A-AA-TAAATAAAT--A-AACAATGGTTAGAGTGCAATAAAATAAAAGTCAG
3198858 TAGTTAGC
123 TAGTTAGC
3198866 TTGAAATAAA
Statistics
Matches: 244, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
130 1 0.00
131 191 0.78
133 1 0.00
134 2 0.01
135 9 0.04
137 1 0.00
138 39 0.16
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (131 bp):
GAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCGATTCAAATAT
TAGAAACAATAAATAAATAAATAAACAATGGTTAGAGTGCAATAAAATAAAAGTCAGTAGTTAGC
A
Found at i:3201216 original size:20 final size:20
Alignment explanation
Indices: 3201191--3201263 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
3201181 GATTTTAGAT
3201191 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
3201211 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
3201231 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
*
3201251 AATCGCAACGCGA
1 AATCGCAATGCGA
3201264 TTCTGACTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:3201275 original size:20 final size:20
Alignment explanation
Indices: 3201252--3201357 Score: 88
Period size: 20 Copynumber: 5.2 Consensus size: 20
3201242 GAATATGTAA
*
3201252 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
* *
3201272 ATCGCAACGATATTCGGACT
1 ATCGCAACGAGATTCTGACT
* * **
3201292 ATTGCAACGCGATAAT-ACGT
1 ATCGCAACGAGATTCTGAC-T
* * *
3201312 GGTCGTAACGTGATTCTGACT
1 -ATCGCAACGAGATTCTGACT
*
3201333 ATCGTAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
3201353 ATCGC
1 ATCGC
3201358 GTTGCGATAA
Statistics
Matches: 65, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
19 2 0.03
20 50 0.77
21 11 0.17
22 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:3201552 original size:22 final size:22
Alignment explanation
Indices: 3201527--3201585 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
3201517 CTACGGTGAC
3201527 ATCCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
* ***
3201549 ATCCGTCCCCATTTCCGGTGAA
1 ATCCGTCCCCATCTCCGACAAA
*
3201571 ATCCGTCCTCATCTC
1 ATCCGTCCCCATCTC
3201586 ATGAAATCCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.20, C:0.42, G:0.12, T:0.25
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:3201997 original size:20 final size:20
Alignment explanation
Indices: 3201957--3202044 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 20
3201947 GTGATTATCT
*
3201957 CGTTGCGATAG-CCATTTCG
1 CGTTGCGATAGTCAATTTCG
*
3201976 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
* * *
3201996 CGTTGCAATAATCATTTTCG
1 CGTTGCGATAGTCAATTTCG
* ** *
3202016 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
*
3202036 TGTTGCGAT
1 CGTTGCGAT
3202045 TTTAAGATTC
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
19 11 0.19
20 47 0.81
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:3202045 original size:20 final size:20
Alignment explanation
Indices: 3202007--3202047 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3201997 GTTGCAATAA
3202007 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
3202027 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
3202047 T
1 T
3202048 AAGATTCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:3203866 original size:31 final size:31
Alignment explanation
Indices: 3203810--3203871 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3203800 TTTGTCTTTG
*
3203810 TTTGTCTTTTGGTTGAAGTTAGTAAATTCATA
1 TTTGTCTTTTGGTTG-ACTTAGTAAATTCATA
3203842 TTTGTCTTTTGGATTG-CTTAGTAAATTCAT
1 TTTGTCTTTTGG-TTGACTTAGTAAATTCAT
3203872 TCGGTAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (31 bp):
TTTGTCTTTTGGTTGACTTAGTAAATTCATA
Found at i:3204063 original size:34 final size:34
Alignment explanation
Indices: 3204024--3204145 Score: 118
Period size: 34 Copynumber: 3.4 Consensus size: 34
3204014 AACGCGAATT
*
3204024 TGACTATCGTAACGGGATAATCGCAATGCGAAAA
1 TGACTATCGCAACGGGATAATCGCAATGCGAAAA
* * * **
3204058 CGACTATCACAACGCGGAAATGACTATCGCAACGCGAATT
1 TGACTATCGCAACG-GG--AT-A--ATCGCAATGCGAAAA
*
3204098 TGACTATCGCAACGGGATAATCGCAATGTGAAAA
1 TGACTATCGCAACGGGATAATCGCAATGCGAAAA
*
3204132 TGACTATTGCAACG
1 TGACTATCGCAACG
3204146 CGAATTTAGT
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
34 35 0.51
35 2 0.03
36 1 0.01
37 4 0.06
38 1 0.01
39 2 0.03
40 24 0.35
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.20
Consensus pattern (34 bp):
TGACTATCGCAACGGGATAATCGCAATGCGAAAA
Found at i:3204084 original size:20 final size:20
Alignment explanation
Indices: 3204043--3204111 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
3204033 TAACGGGATA
* * *
3204043 ATCGCAATGCGAAAACGACT
1 ATCGCAACGCGAATATGACT
*
3204063 ATCACAACGCGGAA-ATGACT
1 ATCGCAACGC-GAATATGACT
*
3204083 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
3204103 ATCGCAACG
1 ATCGCAACG
3204112 GGATAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:3204122 original size:74 final size:74
Alignment explanation
Indices: 3204001--3204147 Score: 231
Period size: 74 Copynumber: 2.0 Consensus size: 74
3203991 CGCAACACGA
* *
3204001 AAATGATTATCACAACGCGAATTTGACTATCGTAACGGGATAATCGCAATGCGAAAACGACTATC
1 AAATGACTATCACAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAACGACTATC
3204066 ACAACGCGG
66 ACAACGCGG
* * * *
3204075 AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGTGAAAATGACTATT
1 AAATGACTATCACAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAACGACTATC
*
3204140 GCAACGCG
66 ACAACGCG
3204148 AATTTAGTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (74 bp):
AAATGACTATCACAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAACGACTATC
ACAACGCGG
Found at i:3204197 original size:33 final size:34
Alignment explanation
Indices: 3204155--3204235 Score: 119
Period size: 33 Copynumber: 2.4 Consensus size: 34
3204145 GCGAATTTAG
* *
3204155 TTTCGCGTTGTGATTTTCTCGTTGCGATAGTC-A
1 TTTCGCGTTGTGATTATCTCGTTGCGACAGTCAA
*
3204188 TTTCGCGTTGCGATTATCTCGTTGCGACAGTCAA
1 TTTCGCGTTGTGATTATCTCGTTGCGACAGTCAA
*
3204222 ATTCGCGTTGTGAT
1 TTTCGCGTTGTGAT
3204236 AGTCAAATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.69
34 13 0.31
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.41
Consensus pattern (34 bp):
TTTCGCGTTGTGATTATCTCGTTGCGACAGTCAA
Found at i:3204239 original size:20 final size:20
Alignment explanation
Indices: 3204207--3204275 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
3204197 GCGATTATCT
*
3204207 CGTTGCGACAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3204227 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
3204247 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
3204267 TGTTGCGAT
1 CGTTGCGAT
3204276 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3204285 original size:20 final size:20
Alignment explanation
Indices: 3204262--3204305 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3204252 CGATAATCAT
*
3204262 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
3204282 TTTCGTGTTGCAATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
3204302 TTTC
1 TTTC
3204306 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTTAAG
Found at i:3204815 original size:21 final size:20
Alignment explanation
Indices: 3204785--3204867 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
3204775 GACTCACCTG
3204785 TCATCGCTCAAGAGGCCCCT
1 TCATCGCTCAAGAGGCCCCT
* *
3204805 ATCATCCCTCAAGAGTCCCCT
1 -TCATCGCTCAAGAGGCCCCT
* *
3204826 CCTATCGTTCAAGAGGCCCCT
1 TC-ATCGCTCAAGAGGCCCCT
* * *
3204847 GTCATCGTTGAAGAGGTCCCT
1 -TCATCGCTCAAGAGGCCCCT
3204868 CCCAACATTC
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 1 0.02
21 49 0.96
22 1 0.02
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.24
Consensus pattern (20 bp):
TCATCGCTCAAGAGGCCCCT
Found at i:3206322 original size:36 final size:30
Alignment explanation
Indices: 3206242--3206307 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
3206232 ATAAGAGTTG
3206242 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
3206272 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
3206302 ATTTGT
1 ATTTGT
3206308 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:3206482 original size:20 final size:20
Alignment explanation
Indices: 3206457--3206713 Score: 167
Period size: 20 Copynumber: 13.8 Consensus size: 20
3206447 GCGATTTTCT
*
3206457 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
3206477 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3206497 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
3206516 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
3206530 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** *
3206550 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCAAATTCG
**
3206570 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* * *
3206590 CATTGC-A-A-T--TA-TCC
1 CGTTGCGATAGTCAAATTCG
3206604 CGTTGCGAT-GTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
3206623 CGCTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* * *
3206643 CATTGTGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
3206657 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
3206677 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
**
3206697 ATTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
3206714 GAATGTGTAA
Statistics
Matches: 184, Mismatches: 34, Indels: 38
0.72 0.13 0.15
Matches are distributed among these distances:
14 27 0.15
15 2 0.01
16 3 0.02
17 2 0.01
18 3 0.02
19 27 0.15
20 120 0.65
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3206483 original size:34 final size:34
Alignment explanation
Indices: 3206423--3206631 Score: 152
Period size: 34 Copynumber: 5.9 Consensus size: 34
3206413 ATCGTATTCG
* * * *
3206423 CGTTGCGATAGTCTAATACACTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* *
3206457 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
* *
3206497 CGTTGCGATAGTC-ATTTCGCGTTGCGATTATCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
3206530 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCAAATTCGCGTTGC----G--ATTTTCT
** * * * *
3206570 CGTTGCGATAGTCATTTTCGCATTGCAATTATCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
3206604 CGTTGCGAT-GTCAAATTCGCGCTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT
3206632 AGTCATTTTC
Statistics
Matches: 139, Mismatches: 23, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
33 29 0.21
34 50 0.36
36 1 0.01
37 1 0.01
38 1 0.01
39 13 0.09
40 44 0.32
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:3206538 original size:73 final size:73
Alignment explanation
Indices: 3206418--3206632 Score: 279
Period size: 73 Copynumber: 2.9 Consensus size: 73
3206408 TCTGCATCGT
* * * * * *
3206418 ATTCGCGTTGCGATAGTCTAATACACTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGC
1 ATTCGCGTTGCGATAGTC-ATTTCGCATTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGC
3206483 GATAATCAA
65 GATAATCAA
*
3206492 ATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCG
1 ATTCGCGTTGCGATAGTCATTTCGCATTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCG
* *
3206557 ATAGTCAT
66 ATAATCAA
* * * * *
3206565 TTTCACGTTGCGATAGTCATTTTCGCATTGCAATTATCCCGTTGCGAT-GTCAAATTCGCGCTGC
1 ATTCGCGTTGCGATAGTCA-TTTCGCATTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGC
3206629 GATA
65 GATA
3206633 GTCATTTTCG
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
73 83 0.66
74 43 0.34
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (73 bp):
ATTCGCGTTGCGATAGTCATTTCGCATTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCG
ATAATCAA
Found at i:3206545 original size:53 final size:54
Alignment explanation
Indices: 3206477--3206578 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 54
3206467 GTCAAATTCC
*
3206477 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCA-TTTCGCGTTGCGATTATCT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCACGTTGCGATTATCT
*
3206530 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCACGTTGCGAT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCACGTTGCGAT
3206579 AGTCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 33 0.72
54 13 0.28
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCACGTTGCGATTATCT
Found at i:3206634 original size:53 final size:54
Alignment explanation
Indices: 3206550--3206696 Score: 215
Period size: 53 Copynumber: 2.7 Consensus size: 54
3206540 GTCAAATTCG
**
3206550 CGTTGCGATAGTCATTTTCACGTTGCGATAGTCATTTTCGCATTGCAATTATCC
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCAATTATCC
* * **
3206604 CGTTGCGAT-GTCAAATTCGCGCTGCGATAGTCATTTTCGCATTGTGATTATCC
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCAATTATCC
* *
3206657 CGTTGCGATATTCAAATTCACGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCG
3206697 ATTTGCGATA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
53 47 0.57
54 35 0.43
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCAATTATCC
Found at i:3206653 original size:127 final size:127
Alignment explanation
Indices: 3206474--3206710 Score: 361
Period size: 127 Copynumber: 1.9 Consensus size: 127
3206464 ATAGTCAAAT
* * *
3206474 TCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGAT
1 TCCCGTTGCGATAATCAAATTCGCGCTGCGATAGTCATTTCGCATTGCGATTATCCCGTTGCGAT
* *
3206539 AGTCAAATTCGCGTTGCGATAGTCATTTTC-ACGTTGCGATAGTCATTTTCGCATTGCAATTA
66 AGTCAAATTCACGTTGCGATAGTCATATTCGA-GTTGCGATAGTCATTTTCGCATTGCAATTA
* *
3206601 TCCCGTTGCGAT-GTCAAATTCGCGCTGCGATAGTCATTTTCGCATTGTGATTATCCCGTTGCGA
1 TCCCGTTGCGATAATCAAATTCGCGCTGCGATAGTCA-TTTCGCATTGCGATTATCCCGTTGCGA
* *
3206665 TATTCAAATTCACGTTGCGATAGTCATATTCGATTTGCGATAGTCA
65 TAGTCAAATTCACGTTGCGATAGTCATATTCGAGTTGCGATAGTCA
3206711 AATGAATGTG
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
126 22 0.22
127 76 0.77
128 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (127 bp):
TCCCGTTGCGATAATCAAATTCGCGCTGCGATAGTCATTTCGCATTGCGATTATCCCGTTGCGAT
AGTCAAATTCACGTTGCGATAGTCATATTCGAGTTGCGATAGTCATTTTCGCATTGCAATTA
Found at i:3206911 original size:18 final size:18
Alignment explanation
Indices: 3206888--3206922 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3206878 AAGCCGGTTG
*
3206888 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3206906 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
3206923 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3212679 original size:14 final size:14
Alignment explanation
Indices: 3212655--3212688 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3212645 TTGCTTGGTC
3212655 AAGGCATATGTCATT
1 AAGG-ATATGTCATT
3212670 AAGGATATGTCATT
1 AAGGATATGTCATT
3212684 AAGGA
1 AAGGA
3212689 GGCTAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (14 bp):
AAGGATATGTCATT
Found at i:3214619 original size:86 final size:85
Alignment explanation
Indices: 3214465--3214632 Score: 198
Period size: 86 Copynumber: 2.0 Consensus size: 85
3214455 ATATAGCAAC
** *
3214465 AAACGCCGCAATAAGTACTGATATTTAGCGGTGTTTTTCTTAAACACGCCGCAATAGCTGTCAAT
1 AAACGCCGCAATAAGTACTGATATTTAGCGGCATTTTTCTTAAAAACGCCGCAATA-CTGTCAAT
*
3214530 ATTTATCGGCATTTTTATCAA
65 ATTTAGCGGCATTTTTATCAA
** *
3214551 AAACGCCGCAATAAGTGTTGATATTTCGCGGCATTTTT-TTATGAAAACGCCGCAATA-TGT-AT
1 AAACGCCGCAATAAGTACTGATATTTAGCGGCATTTTTCTTA--AAAACGCCGCAATACTGTCA-
*
3214613 GGTATTTAGCGGCATTTTTA
63 -ATATTTAGCGGCATTTTTA
3214633 GGATACAAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
84 1 0.01
85 6 0.09
86 50 0.71
87 13 0.19
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (85 bp):
AAACGCCGCAATAAGTACTGATATTTAGCGGCATTTTTCTTAAAAACGCCGCAATACTGTCAATA
TTTAGCGGCATTTTTATCAA
Found at i:3214643 original size:44 final size:44
Alignment explanation
Indices: 3214465--3214647 Score: 157
Period size: 43 Copynumber: 4.2 Consensus size: 44
3214455 ATATAGCAAC
** *
3214465 AAACGCCGCAATAAGTACTGATATTTAGCGG--TGTTTT-TCTTA
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCAT-TTTTATCATA
** *
3214507 AACACGCCGCAAT-AGCTGTCAATATTTATCGGCATTTTTATCA-A
1 AA-ACGCCGCAATAAG-TGTTGATATTTAGCGGCATTTTTATCATA
* *
3214551 AAACGCCGCAATAAGTGTTGATATTTCGCGGCATTTTT-TTATGA
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTTTTATCAT-A
* **
3214595 AAACGCCGCAAT-A-TGTATGGTATTTAGCGGCATTTTTAGGATA
1 AAACGCCGCAATAAGTGT-TGATATTTAGCGGCATTTTTATCATA
3214638 CAAACGCCGC
1 -AAACGCCGC
3214648 TAAAAGTTGG
Statistics
Matches: 115, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
42 9 0.08
43 70 0.61
44 33 0.29
45 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (44 bp):
AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTTTTATCATA
Found at i:3214659 original size:43 final size:43
Alignment explanation
Indices: 3214595--3214692 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 43
3214585 TTTTTTATGA
* ** * *
3214595 AAACGCCGCAATATGTATGGTATTTAGCGGCATTTT-TAGGATAC
1 AAACGCCGCAATAAGTATGGTACATAGAGGCGTTTTGT--GATAC
3214639 AAACGCCGCTAA-AAGT-TGGTACATAGAGGCGTTTTGTGATAC
1 AAACGCCGC-AATAAGTATGGTACATAGAGGCGTTTTGTGATAC
3214681 AAACGCCGCAAT
1 AAACGCCGCAAT
3214693 GGGTTTTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
41 2 0.04
42 14 0.30
43 15 0.33
44 13 0.28
45 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAAGTATGGTACATAGAGGCGTTTTGTGATAC
Found at i:3214892 original size:43 final size:42
Alignment explanation
Indices: 3214843--3215007 Score: 204
Period size: 43 Copynumber: 3.9 Consensus size: 42
3214833 ATTTGAAAGA
*
3214843 ACAAACGCCGCTAATTCTCTTCTTTTTAGTGGTGTTTTCGGCC
1 ACAAACGCCGCTAATTCTCTTATTTTTAGTGGTGTTTT-GGCC
* *
3214886 ACAAACGCCGCTAATTCTCTTATTTTTACTGGCTTTTTTGGCC
1 ACAAACGCCGCTAATTCTCTTATTTTTAGTGG-TGTTTTGGCC
* * * *
3214929 ATAAACGCCGCTAATTCTTTTATCTTTAGTGGTGTTTTTGCC
1 ACAAACGCCGCTAATTCTCTTATTTTTAGTGGTGTTTTGGCC
* * * * *
3214971 ACAAACGACGCTAATTTTGTTGTTTTTAGTGGCGTTT
1 ACAAACGCCGCTAATTCTCTTATTTTTAGTGGTGTTT
3215008 GTAATACAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
42 38 0.36
43 62 0.59
44 5 0.05
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (42 bp):
ACAAACGCCGCTAATTCTCTTATTTTTAGTGGTGTTTTGGCC
Found at i:3221146 original size:8 final size:8
Alignment explanation
Indices: 3221135--3221182 Score: 78
Period size: 8 Copynumber: 5.8 Consensus size: 8
3221125 AAATTTTGGC
3221135 TTTTTTGT
1 TTTTTTGT
3221143 TTTTTTGT
1 TTTTTTGT
3221151 TTTTTTGT
1 TTTTTTGT
3221159 TTTTTTGCCT
1 TTTTTTG--T
3221169 TTTTTTGT
1 TTTTTTGT
3221177 TTTTTT
1 TTTTTT
3221183 TAAATAGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 30 0.79
10 8 0.21
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.85
Consensus pattern (8 bp):
TTTTTTGT
Found at i:3221147 original size:16 final size:16
Alignment explanation
Indices: 3221128--3221181 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
3221118 TTTTTTGAAA
3221128 TTTTGGCTTTTTTGTT
1 TTTTGGCTTTTTTGTT
* *
3221144 TTTTTGTTTTTTTGTTT
1 TTTTGGCTTTTTTG-TT
*
3221161 TTTTGCCTTTTTTTGTT
1 TTTTGGC-TTTTTTGTT
3221178 TTTT
1 TTTT
3221182 TTAAATAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 12 0.39
17 12 0.39
18 7 0.23
ACGTcount: A:0.00, C:0.06, G:0.13, T:0.81
Consensus pattern (16 bp):
TTTTGGCTTTTTTGTT
Found at i:3223468 original size:36 final size:36
Alignment explanation
Indices: 3223421--3223497 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
3223411 TGAGGAATGT
*
3223421 ATTCCACTTGAACATCAACAGTAGAATGTTAATTAA
1 ATTCCACTTGAACAACAACAGTAGAATGTTAATTAA
* *
3223457 ATTCCACTTGAACAACAGCAGTAGAATGTTGATTAA
1 ATTCCACTTGAACAACAACAGTAGAATGTTAATTAA
3223493 ATTCC
1 ATTCC
3223498 CAACCGTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (36 bp):
ATTCCACTTGAACAACAACAGTAGAATGTTAATTAA
Found at i:3226033 original size:41 final size:39
Alignment explanation
Indices: 3226005--3226223 Score: 249
Period size: 41 Copynumber: 5.4 Consensus size: 39
3225995 TTTAAAAAAC
3226005 AAACGCCACTAAAGTACGAGTCTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTAGCGGCGTTTGTATAA
* * * *
3226044 AAATGCCACTAATGTACGAGTCTATAGCGGCATTTGTACAA
1 AAACGCCACTAAAGTACGAGTC--TAGCGGCGTTTGTATAA
*
3226085 AAACGCCACTAAAGTACGAGCCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAG--TCTAGCGGCGTTTGTATAA
** * * *
3226126 AAACGCTGCTAAAGTACTACTCTATCGCGGCGTTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTA--GCGGCG-TTTGTATAA
*
3226168 AAACGCCACTAAAGTACGAGTCTATAGCAGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTC--TAGCGGCGTTTGTATAA
*
3226209 AAACGCCGCTAAAGT
1 AAACGCCACTAAAGT
3226224 TACCATTTTT
Statistics
Matches: 149, Mismatches: 22, Indels: 16
0.80 0.12 0.09
Matches are distributed among these distances:
39 23 0.15
41 92 0.62
42 31 0.21
43 1 0.01
44 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (39 bp):
AAACGCCACTAAAGTACGAGTCTAGCGGCGTTTGTATAA
Found at i:3226201 original size:83 final size:82
Alignment explanation
Indices: 3226005--3226223 Score: 307
Period size: 83 Copynumber: 2.7 Consensus size: 82
3225995 TTTAAAAAAC
* * * *
3226005 AAACGCCACTAAAGTACGAGTC--TAGCGGCGTTTGTATAAAAATGCCACTAATGTACGAGTCTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCGCTAAAGTACGACTCTA
*
3226068 TAGCGGCATTTGTACAA
66 TAGCGGCATTTATACAA
* * *
3226085 AAACGCCACTAAAGTACGAGCCTATAGCGGCGTTTGTATAAAAACGCTGCTAAAGTACTACTCTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCGCTAAAGTACGACTCTA
* * *
3226150 TCGCGGCGTTTTATATAA
66 TAGCGGC-ATTTATACAA
*
3226168 AAACGCCACTAAAGTACGAGTCTATAGCAGCGTTTGTATAAAAACGCCGCTAAAGT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCGCTAAAGT
3226224 TACCATTTTT
Statistics
Matches: 122, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
80 21 0.17
82 41 0.34
83 60 0.49
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (82 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCGCTAAAGTACGACTCTA
TAGCGGCATTTATACAA
Found at i:3230968 original size:29 final size:30
Alignment explanation
Indices: 3230926--3230996 Score: 126
Period size: 31 Copynumber: 2.4 Consensus size: 30
3230916 CTACGCCTAG
3230926 TTTCAGTGTCTATTTTTTT-TGGTGAATAA
1 TTTCAGTGTCTATTTTTTTGTGGTGAATAA
3230955 TTTCAGTGTCTATTTTTTTGGTGGTGAATAA
1 TTTCAGTGTCTATTTTTTT-GTGGTGAATAA
3230986 TTTCAGTGTCT
1 TTTCAGTGTCT
3230997 TTAGTCGCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 19 0.47
31 21 0.52
ACGTcount: A:0.18, C:0.08, G:0.20, T:0.54
Consensus pattern (30 bp):
TTTCAGTGTCTATTTTTTTGTGGTGAATAA
Found at i:3231247 original size:31 final size:31
Alignment explanation
Indices: 3231206--3231273 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
3231196 TTATGCATGT
*
3231206 GTGATCAAAATAGAACA-AAAAGTTAA-TTTG
1 GTGATTAAAAT-GAACATAAAAGTTAACTTTG
*
3231236 AGTGATTAAAATGAACATGAAAGTTAACTTTG
1 -GTGATTAAAATGAACATAAAAGTTAACTTTG
3231268 GTGATT
1 GTGATT
3231274 TATTTGCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 5 0.15
31 24 0.73
32 4 0.12
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (31 bp):
GTGATTAAAATGAACATAAAAGTTAACTTTG
Found at i:3236593 original size:26 final size:26
Alignment explanation
Indices: 3236561--3236610 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3236551 AATACAATTA
3236561 TTTTAGA-CTTCAAGGTATTATGGTTC
1 TTTTAGAGC-TCAAGGTATTATGGTTC
* *
3236587 TTTTAGAGCTCAGGGTATTTTGGT
1 TTTTAGAGCTCAAGGTATTATGGT
3236611 CATTTGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (26 bp):
TTTTAGAGCTCAAGGTATTATGGTTC
Found at i:3238072 original size:23 final size:23
Alignment explanation
Indices: 3238045--3238131 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
3238035 CAGCTTGTAT
* *
3238045 AAATGCACCTAAGTGCCACGTAG
1 AAATGAACCGAAGTGCCACGTAG
*
3238068 AAATGAACCGAAGTGCCATGTAG
1 AAATGAACCGAAGTGCCACGTAG
* *
3238091 AAATGAACCGAAGTGCCGCATAG
1 AAATGAACCGAAGTGCCACGTAG
3238114 AAAT-ACACCGAAGTGCCA
1 AAATGA-ACCGAAGTGCCA
3238132 TATAAAATGT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
22 1 0.02
23 55 0.98
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (23 bp):
AAATGAACCGAAGTGCCACGTAG
Found at i:3238105 original size:46 final size:45
Alignment explanation
Indices: 3238040--3238140 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 45
3238030 CACCACAGCT
* * *
3238040 TGTATAAATGCACCTAAGTGCCACGTAGAAATGA-ACCGAAGTGCCA
1 TGTA-AAATGAACCGAAGTGCCACATAGAAAT-ACACCGAAGTGCCA
*
3238086 TGTAGAAATGAACCGAAGTGCCGCATAGAAATACACCGAAGTGCCA
1 TGTA-AAATGAACCGAAGTGCCACATAGAAATACACCGAAGTGCCA
*
3238132 TATAAAATG
1 TGTAAAATG
3238141 TCCACAAAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 6 0.12
46 42 0.88
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.19
Consensus pattern (45 bp):
TGTAAAATGAACCGAAGTGCCACATAGAAATACACCGAAGTGCCA
Found at i:3244430 original size:23 final size:23
Alignment explanation
Indices: 3244404--3244495 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
3244394 CACCACAGCT
* *
3244404 CGTATATATGCACCT-AAGTGCCA
1 CGTAGATATGCA-CTGAAGTGCCG
* *
3244427 CGTAGAAATACACTGAAGTGCCG
1 CGTAGATATGCACTGAAGTGCCG
*
3244450 CATAGATATGCACTGAAGTGCCG
1 CGTAGATATGCACTGAAGTGCCG
*
3244473 CGTAGATATGCACCGAAGTGCCG
1 CGTAGATATGCACTGAAGTGCCG
3244496 TATAAAATGT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 2 0.03
23 57 0.97
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (23 bp):
CGTAGATATGCACTGAAGTGCCG
Found at i:3245148 original size:17 final size:19
Alignment explanation
Indices: 3245126--3245162 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3245116 CGATACTTCC
3245126 ATTATAAT-G-GTATCGAT
1 ATTATAATCGAGTATCGAT
*
3245143 ATTATACTCGAGTATCGAT
1 ATTATAATCGAGTATCGAT
3245162 A
1 A
3245163 CCCAATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 1 0.06
19 9 0.53
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (19 bp):
ATTATAATCGAGTATCGAT
Found at i:3247134 original size:15 final size:15
Alignment explanation
Indices: 3247110--3247171 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
3247100 TTTTTATCCT
3247110 AAAA-TAAAATATTA
1 AAAATTAAAATATTA
3247124 AAAATTAAAATACTTAA
1 AAAATTAAAATA-TT-A
* * *
3247141 AAAATTAATAGAATA
1 AAAATTAAAATATTA
*
3247156 AAAATCAAAATGATTA
1 AAAATTAAAAT-ATTA
3247172 CTCTAACAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
14 4 0.11
15 16 0.43
16 6 0.16
17 11 0.30
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (15 bp):
AAAATTAAAATATTA
Found at i:3247142 original size:16 final size:16
Alignment explanation
Indices: 3247110--3247148 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
3247100 TTTTTATCCT
3247110 AAAA-TAAAATATT-A
1 AAAATTAAAATATTAA
3247124 AAAATTAAAATACTTAA
1 AAAATTAAAATA-TTAA
3247141 AAAATTAA
1 AAAATTAA
3247149 TAGAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 7 0.32
16 2 0.09
17 9 0.41
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATTAAAATATTAA
Found at i:3248182 original size:4 final size:4
Alignment explanation
Indices: 3248169--3248393 Score: 270
Period size: 4 Copynumber: 56.2 Consensus size: 4
3248159 ATCAGGATAT
* * * * *
3248169 TACA TACA TGCA TGCA TACA TACA TACA TGCA TGCA TACA TACA TACT
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * *
3248217 TATA TACA TGCA TGCA TACA TGCA TGCA TACA TACA TGCA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * *
3248265 TACA TACA TGCA TGCA TACA TGCA TGCA TGCA TACA TACA TACA TAGA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
3248313 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
3248361 TACA TGCA TACA TGCA TACA TGCA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA T
3248394 TTTAGGTATC
Statistics
Matches: 195, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 195 1.00
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:3248521 original size:31 final size:29
Alignment explanation
Indices: 3248460--3248564 Score: 99
Period size: 28 Copynumber: 3.6 Consensus size: 29
3248450 CTTTTTCATT
3248460 TAAGTACCTAAATTATTTTTGGATCAAAA
1 TAAGTACCTAAATTATTTTTGGATCAAAA
*
3248489 TAAGTATCTAAAGTTATCTTTTAGG-TCAAAA
1 TAAGTACCTAAA-TTAT-TTTT-GGATCAAAA
* * *
3248520 T-AGACACCTAAATTTTTTTTAG-TCAAAA
1 TAAG-TACCTAAATTATTTTTGGATCAAAA
* *
3248548 TAGGTACCTAAAGTATT
1 TAAGTACCTAAATTATT
3248565 CATTTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
28 18 0.29
29 16 0.26
30 9 0.15
31 17 0.27
32 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (29 bp):
TAAGTACCTAAATTATTTTTGGATCAAAA
Found at i:3254375 original size:2 final size:2
Alignment explanation
Indices: 3254368--3254410 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
3254358 ATAATTAATC
*
3254368 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
3254411 TAATGTCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 37 0.97
3 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3255807 original size:48 final size:47
Alignment explanation
Indices: 3255727--3255819 Score: 123
Period size: 48 Copynumber: 2.0 Consensus size: 47
3255717 CACCGTTATT
* * *
3255727 CATCTAACTTGCATTAGTGGCATATTTATGCCAAAAAGCACAGTTAGA
1 CATCTAACTTGCATTAATGACACATTTATGCC-AAAAGCACAGTTAGA
* * *
3255775 CATCTAACTTGCATTAATGACACCTTTCTGCCAAATGCACAGTTA
1 CATCTAACTTGCATTAATGACACATTTATGCCAAAAGCACAGTTA
3255820 AGCATTTAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 12 0.31
48 27 0.69
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (47 bp):
CATCTAACTTGCATTAATGACACATTTATGCCAAAAGCACAGTTAGA
Found at i:3256101 original size:55 final size:55
Alignment explanation
Indices: 3255971--3256260 Score: 402
Period size: 55 Copynumber: 5.3 Consensus size: 55
3255961 GCACACCTAA
* * * * * * *
3255971 TGCCAATACAAAAATTCATAAGCTCATTATGAATTTCTTAG-GTTGCACACATAG
1 TGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGTACACACAG
** * *
3256025 TGCTAATACGAAAATTAATAAACTTATTATGAATTTCTTAGTTTTGTACACACAT
1 TGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGTACACACAG
* *
3256080 TGCCCATACGGAAATTCATAAACTTATTATAAATTTCTTAGTTTTGTACACACAG
1 TGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGTACACACAG
* * *
3256135 TGCCTATACGTAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGTACACACAG
* *
3256190 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTTCACACACAG
1 TGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGT-ACACACAG
3256246 TGCCCATACGAAAAT
1 TGCCCATACGAAAAT
3256261 CACCATACAT
Statistics
Matches: 210, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
54 36 0.17
55 152 0.72
56 22 0.10
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (55 bp):
TGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGTACACACAG
Found at i:3259528 original size:22 final size:23
Alignment explanation
Indices: 3259503--3259546 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3259493 AATTAAGTTT
3259503 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
3259525 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
3259547 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:3265470 original size:21 final size:23
Alignment explanation
Indices: 3265449--3265550 Score: 108
Period size: 23 Copynumber: 4.7 Consensus size: 23
3265439 GTACAGAGGA
3265449 AATCGA-TCCCCCCTTG-A-GGG
1 AATCGATTCCCCCCTTGAAGGGG
* *
3265469 AACCGATTCCCCCTTTGAAGGGG
1 AATCGATTCCCCCCTTGAAGGGG
* *
3265492 AACCGATTCCCCCTTTGAAGGGG
1 AATCGATTCCCCCCTTGAAGGGG
3265515 AATCGATTCCCCCC---ACAGGGG
1 AATCGATTCCCCCCTTGA-AGGGG
*
3265536 AATCGATACCCCCCT
1 AATCGATTCCCCCCT
3265551 AGGGTTCTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.08
21 27 0.38
22 1 0.01
23 38 0.53
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.20
Consensus pattern (23 bp):
AATCGATTCCCCCCTTGAAGGGG
Found at i:3265496 original size:23 final size:23
Alignment explanation
Indices: 3265466--3265527 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
3265456 CCCCCCTTGA
3265466 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
3265489 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
3265512 GGGAATCGATTCCCCC
1 GGGAACCGATTCCCCC
3265528 CACAGGGGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:3265554 original size:20 final size:21
Alignment explanation
Indices: 3265510--3265549 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3265500 CCCCCTTTGA
*
3265510 AGGGGAATCGATTCCCCCCAC
1 AGGGGAATCGATACCCCCCAC
3265531 AGGGGAATCGATACCCCCC
1 AGGGGAATCGATACCCCCC
3265550 TAGGGTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAATCGATACCCCCCAC
Found at i:3270058 original size:14 final size:15
Alignment explanation
Indices: 3270033--3270063 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3270023 GCGGTCAATG
3270033 CATTTACCTCTTACT
1 CATTTACCTCTTACT
3270048 CATTT-CCTCTTACT
1 CATTTACCTCTTACT
3270062 CA
1 CA
3270064 AATTAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.45
Consensus pattern (15 bp):
CATTTACCTCTTACT
Found at i:3271172 original size:48 final size:47
Alignment explanation
Indices: 3271118--3271211 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 47
3271108 ACACTGTATT
*
3271118 CATCTAACTTGCATTAGTGGCATCC-TTCTGCCAAAAAGCACAGTTAGG
1 CATCTAACTTGCATTAATGGCA-CCTTTCTGCC-AAAAGCACAGTTAGG
* * *
3271166 CATCTAACTTGCATTAATGTCACCTTTTTGCCAAATGCACAGTTAG
1 CATCTAACTTGCATTAATGGCACCTTTCTGCCAAAAGCACAGTTAG
3271212 ACATTTAGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
47 15 0.37
48 26 0.63
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (47 bp):
CATCTAACTTGCATTAATGGCACCTTTCTGCCAAAAGCACAGTTAGG
Found at i:3271681 original size:172 final size:166
Alignment explanation
Indices: 3271374--3271776 Score: 576
Period size: 172 Copynumber: 2.4 Consensus size: 166
3271364 CCTAATGCCA
** * *
3271374 ATACAGAAATTCATAAACTCGTTATGAATTTATTAG-GTTGCACACACAATGCCAATACGGAAAT
1 ATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACACAATGCCCATACGGAAAT
* *
3271438 TCATAAACTTATTATGAATTTATAAGTTTTGTACATATAGTGCCCATACGAAAATTCATAAACTT
66 TCATAAACTTATTATGAATTTATAAGTTTTGCACACATAGTGCCCATACGAAAATTCATAAACTT
*
3271503 ATTATGAATTTCTTAG-TTTTGCACACATAGTGCAC
131 ATTATGAATTTCTTAGTTTTTGCACACACAGTGCAC
*
3271538 ATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACACACAGTGCCCATATGGAA
1 ATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACACA-A-TGCCCATACGGAA
* * *
3271603 ATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACACATAGTGCCCATACGGAAATTCA
64 ATTCATAAACTTATTATGAATTTATAAG-TTTTG----CACACATAGTGCCCATACGAAAATTCA
* *
3271668 TAAACTTATTATGAATTTCTTAGTTTTTGCACACACGGTGCCC
124 TAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCAC
** *
3271711 ATATGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAATGCCCATACGGAAA
1 ATACAGAAATTCATAAACTTATTATGAATTTATTAG-TTTTGCACACACAATGCCCATACGGAAA
3271776 T
65 T
3271777 CACCATACAT
Statistics
Matches: 212, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
164 34 0.16
165 11 0.05
166 1 0.00
167 37 0.17
168 5 0.02
172 61 0.29
173 50 0.24
174 13 0.06
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (166 bp):
ATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACACAATGCCCATACGGAAAT
TCATAAACTTATTATGAATTTATAAGTTTTGCACACATAGTGCCCATACGAAAATTCATAAACTT
ATTATGAATTTCTTAGTTTTTGCACACACAGTGCAC
Found at i:3271727 original size:56 final size:55
Alignment explanation
Indices: 3271369--3271776 Score: 530
Period size: 55 Copynumber: 7.3 Consensus size: 55
3271359 GCATACCTAA
* * ** * * *
3271369 TGCCAATACAGAAATTCATAAACTCGTTATGAATTTATTAG-GTTGCACACACAA
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * * * * *
3271423 TGCCAATACGGAAATTCATAAACTTATTATGAATTTATAAGTTTTGTACATATAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* *
3271478 TGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * *
3271533 TGCACATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTG--CACACACAG
*
3271590 TGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACACATAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTG--CACACAC--AG
*
3271650 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACGG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAG
* *
3271706 TGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAA
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAG
3271762 TGCCCATACGGAAAT
1 TGCCCATACGGAAAT
3271777 CACCATACAT
Statistics
Matches: 318, Mismatches: 30, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.12
55 99 0.31
56 68 0.21
57 45 0.14
58 21 0.07
60 48 0.15
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (55 bp):
TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
Found at i:3272154 original size:19 final size:19
Alignment explanation
Indices: 3272130--3272177 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
3272120 CTATAGTATG
3272130 GTACCGATACTCCCTTTCA
1 GTACCGATACTCCCTTTCA
*
3272149 GTACCGATACTCCCTTTTA
1 GTACCGATACTCCCTTTCA
*
3272168 GTATCGATAC
1 GTACCGATAC
3272178 CATTTCTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.33
Consensus pattern (19 bp):
GTACCGATACTCCCTTTCA
Found at i:3273268 original size:14 final size:13
Alignment explanation
Indices: 3273249--3273285 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
3273239 TTGTCACTTT
3273249 TTATTTTATTATTA
1 TTATTTTATTA-TA
3273263 TTATTTTATTATA
1 TTATTTTATTATA
3273276 TTA-TTTATTA
1 TTATTTTATTA
3273286 GATATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 7 0.30
13 5 0.22
14 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTTATTATA
Found at i:3273269 original size:19 final size:20
Alignment explanation
Indices: 3273247--3273285 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3273237 GGTTGTCACT
*
3273247 TTTTATTTTATTA-TTATTA
1 TTTTATTATATTATTTATTA
3273266 TTTTATTATATTATTTATTA
1 TTTTATTATATTATTTATTA
3273286 GATATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTATATTATTTATTA
Found at i:3274583 original size:14 final size:14
Alignment explanation
Indices: 3274566--3274595 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3274556 CGTATTTTTA
*
3274566 TATACTATTATTAT
1 TATAATATTATTAT
3274580 TATAATATTATTAT
1 TATAATATTATTAT
3274594 TA
1 TA
3274596 CAAATAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TATAATATTATTAT
Found at i:3276612 original size:18 final size:19
Alignment explanation
Indices: 3276589--3276625 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3276579 CTTTCACTTA
3276589 TTTTTTTAGATA-TTTTAT
1 TTTTTTTAGATACTTTTAT
*
3276607 TTTTTTTATATACTTTTAT
1 TTTTTTTAGATACTTTTAT
3276626 ATATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTTTTTAGATACTTTTAT
Found at i:3276684 original size:18 final size:17
Alignment explanation
Indices: 3276661--3276704 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3276651 GTTTTTCATT
3276661 TTTTATTTAGTCATATTA
1 TTTTATTTAGTCA-ATTA
*
3276679 TTTTATTGTTGTCAATTA
1 TTTTATT-TAGTCAATTA
3276697 TTTTATTT
1 TTTTATTT
3276705 CATTTTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 18 0.75
19 5 0.21
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.66
Consensus pattern (17 bp):
TTTTATTTAGTCAATTA
Found at i:3281604 original size:18 final size:18
Alignment explanation
Indices: 3281554--3281604 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
3281544 CAAGAAGGAA
* *
3281554 CATAGTTGTCTTCAGGTG
1 CATAGTTGTCTTAATGTG
*
3281572 CATAGTTAT-TCTAATGTG
1 CATAGTTGTCT-TAATGTG
*
3281590 TATAGTTGTCTTAAT
1 CATAGTTGTCTTAAT
3281605 CATAAAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.45
Consensus pattern (18 bp):
CATAGTTGTCTTAATGTG
Found at i:3285885 original size:3 final size:3
Alignment explanation
Indices: 3285877--3285917 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3285867 ATGAAACATT
3285877 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3285918 CGTTATTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3294003 original size:34 final size:36
Alignment explanation
Indices: 3293959--3294058 Score: 161
Period size: 34 Copynumber: 2.8 Consensus size: 36
3293949 TTTCGTCCTA
3293959 CTAGGATTCAAACTCCTAAAAATAGGATATA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
3293994 -TAGGATTCAAACTCCTAAAAATAGGATAACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAACATTTT
3294029 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
3294059 GAGTTCTACT
Statistics
Matches: 61, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 29 0.48
35 3 0.05
37 28 0.46
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAACATTTT
Found at i:3294044 original size:37 final size:35
Alignment explanation
Indices: 3293959--3294094 Score: 159
Period size: 37 Copynumber: 3.8 Consensus size: 35
3293949 TTTCGTCCTA
3293959 CTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATATAATTT
3293994 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATATA-A-TTT
* *
3294029 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATATAATT-T
* * * *
3294066 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
3294095 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 53 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATATAATTT
Found at i:3294473 original size:15 final size:15
Alignment explanation
Indices: 3294446--3294488 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3294436 TATTTATTAT
3294446 ATGTATATT-TTATTC
1 ATGT-TATTATTATTC
* *
3294461 ATTTTTTTATTATTC
1 ATGTTATTATTATTC
3294476 ATGTTATTATTAT
1 ATGTTATTATTAT
3294489 ATGTATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (15 bp):
ATGTTATTATTATTC
Found at i:3297578 original size:8 final size:8
Alignment explanation
Indices: 3297565--3297603 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
3297555 GAACATTTCA
*
3297565 TGCATTCT
1 TGCATTTT
3297573 TGCA-TTT
1 TGCATTTT
3297580 TGCATTTT
1 TGCATTTT
*
3297588 TGCCTTTT
1 TGCATTTT
3297596 TGCATTTT
1 TGCATTTT
3297604 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:3298755 original size:22 final size:22
Alignment explanation
Indices: 3298732--3298793 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
3298722 CAAAAAGGGC
3298732 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
3298755 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
3298776 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
3298794 TAAAAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:3298784 original size:20 final size:20
Alignment explanation
Indices: 3298732--3298800 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
3298722 CAAAAAGGGC
*
3298732 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
3298755 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
3298776 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
3298796 AAAAA
1 AAAAA
3298801 AGGGACAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 10 0.24
24 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:3299437 original size:22 final size:22
Alignment explanation
Indices: 3299409--3299459 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3299399 CCCCATCAAT
3299409 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
3299431 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
3299453 CCTTTGA
1 CCTTTGA
3299460 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:3300413 original size:37 final size:37
Alignment explanation
Indices: 3300322--3300428 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
3300312 CTCACCATTG
3300322 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACTTTA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAACTTTA
* *
3300358 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAACTTTA
* *
3300395 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
3300429 ATTGAAAACA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 28 0.44
37 33 0.52
38 3 0.05
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.36
Consensus pattern (37 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAACTTTA
Found at i:3300516 original size:102 final size:102
Alignment explanation
Indices: 3300337--3300692 Score: 586
Period size: 102 Copynumber: 3.5 Consensus size: 102
3300327 CTTGAGACAG
** * * * *
3300337 TTTCCCTTGAAACAAACTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
3300402 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
3300439 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
3300504 TGAGACAATTTCTCTTGAAACATAAACATTGAAAATA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
3300541 TTTGCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
3300606 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
3300643 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
3300693 TAAACATTCA
Statistics
Matches: 234, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 234 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:3300599 original size:37 final size:37
Alignment explanation
Indices: 3300555--3300627 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
3300545 CCTTGAAATG
* *
3300555 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
*
3300592 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
3300628 TAAACATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
Found at i:3300664 original size:167 final size:168
Alignment explanation
Indices: 3300475--3300791 Score: 505
Period size: 167 Copynumber: 1.9 Consensus size: 168
3300465 CTTGAGATAG
*
3300475 TTTCCCTTGAAACAAAATTTCGTCTC-CATTGAGACAATTTCTCTTGAAACATAAACATTGAAAA
1 TTTCCCTTGAAACAAAATTTCGTCTCTC-TTGAGACAATTTCTCTTGAAACATAAACATTCAAAA
* * * *
3300539 TATTTGCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
65 CATTTCCCTTGAAAT-AAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCC
3300604 CTTGAGACAG-TTTCTCTTGAAACATAAACATTGAAAACA
129 CTTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
** * *
3300643 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTCAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCTCTTGAGACAATTTCTCTTGAAACATAAACATTCAAAAC
*
3300707 ATTTCCCTTGAAATAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCCT
66 ATTTCCCTTGAAATAAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
3300772 TGAGACAGTTTTCTCTTGAA
131 TGAGACAGTTTTCTCTTGAA
3300792 GCATCATCTT
Statistics
Matches: 137, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
166 56 0.41
167 68 0.50
168 13 0.09
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (168 bp):
TTTCCCTTGAAACAAAATTTCGTCTCTCTTGAGACAATTTCTCTTGAAACATAAACATTCAAAAC
ATTTCCCTTGAAATAAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:3300682 original size:65 final size:64
Alignment explanation
Indices: 3300577--3300756 Score: 288
Period size: 65 Copynumber: 2.8 Consensus size: 64
3300567 CTTGAGATAG
* * *
3300577 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAA-TAAA-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTCAAAAC
3300642 A
64 A
* *
3300643 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTCAAAACA
1 TTTCCCTTGAAATAAATTT-GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTCAAAACA
3300708 TTTCCCTTGAAATAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
3300757 AAATTTTGTC
Statistics
Matches: 106, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
64 32 0.30
65 62 0.58
66 12 0.11
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (64 bp):
TTTCCCTTGAAATAAATTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTCAAAACA
Found at i:3300767 original size:37 final size:36
Alignment explanation
Indices: 3300708--3300791 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 36
3300698 ATTCAAAACA
* * *
3300708 TTTCCCTTGAAATAAATTTGTCTCTCTTGAGACAG-
1 TTTCTCTTGAAAAAAATTTGTCTCCCTTGAGACAGT
3300743 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
1 TTTCTCTTGAAA-AAAA-TTTGTCTCCCTTGAGACAGT
3300781 TTTCTCTTGAA
1 TTTCTCTTGAA
3300792 GCATCATCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 11 0.26
36 3 0.07
37 18 0.42
38 11 0.26
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAAAAAATTTGTCTCCCTTGAGACAGT
Found at i:3300905 original size:37 final size:37
Alignment explanation
Indices: 3300864--3300935 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
3300854 TGGAACTAAG
* * **
3300864 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
*
3300901 TTTTGTCTCCCTTAAGACCGTTTCCCTTAAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAA
3300936 CAAATATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:3301766 original size:105 final size:105
Alignment explanation
Indices: 3301539--3302304 Score: 1112
Period size: 105 Copynumber: 7.3 Consensus size: 105
3301529 GCCATCTGCG
* * * * * * *
3301539 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTTAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
3301604 GGGA-CGACTGGTTGTAAACAAATAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* *
3301648 ATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3301713 ACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
3301753 ATTTCAACTTCACAACAAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
3301818 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
3301858 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
3301923 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
3301963 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
3302028 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
3302068 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
3302133 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
3302168 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * ** *
3302233 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* *
3302274 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
3302305 TGGAACAATG
Statistics
Matches: 608, Mismatches: 42, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
100 83 0.14
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 408 0.67
106 78 0.13
107 5 0.01
109 21 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:3302976 original size:37 final size:37
Alignment explanation
Indices: 3302848--3302986 Score: 169
Period size: 37 Copynumber: 3.8 Consensus size: 37
3302838 ATTTTTCGTC
*
3302848 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
3302885 -T--TAGGATTCAAACTCCTAAAAATAGGATA-ACATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGA-ATT
* * *
3302919 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
3302956 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3302987 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
33 1 0.01
34 30 0.34
35 1 0.01
36 1 0.01
37 55 0.62
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:3303366 original size:14 final size:15
Alignment explanation
Indices: 3303343--3303380 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3303333 ATTATATGGA
3303343 TATT-TTATTCAT-T
1 TATTATTATTCATGT
*
3303356 TTTTATTATTCATGT
1 TATTATTATTCATGT
3303371 TATTATTATT
1 TATTATTATT
3303381 ATATGTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 3 0.14
14 8 0.38
15 10 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTATTATTCATGT
Found at i:3303408 original size:61 final size:61
Alignment explanation
Indices: 3303343--3303457 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
3303333 ATTATATGGA
*
3303343 TATTTT-A-TTCATTTTTTATTATTCATGTTATTATTATTA-TATGTATATATATATATTAAAT
1 TATTTTCATTTCATTTTTTACTA-T-ATGTTATTATTATTATTAT-TATATATATATATTAAAT
* * *
3303404 TATTTTCATTTGATTTTTTACTATATTTTTTTATTATTATTATTATATATATAT
1 TATTTTCATTTCATTTTTTACTATATGTTATTATTATTATTATTATATATATAT
3303458 TTCTTTAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
61 30 0.64
62 5 0.11
63 12 0.26
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (61 bp):
TATTTTCATTTCATTTTTTACTATATGTTATTATTATTATTATTATATATATATATTAAAT
Found at i:3303464 original size:28 final size:26
Alignment explanation
Indices: 3303425--3303478 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
3303415 GATTTTTTAC
* *
3303425 TATATTTTTTTATTATTATTATTATATA
1 TATATTTCTTTAATATT-TTATT-TATA
3303453 TATATTTCTTTAATATTTTATTTATA
1 TATATTTCTTTAATATTTTATTTATA
3303479 AGTCTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 5 0.21
28 15 0.62
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TATATTTCTTTAATATTTTATTTATA
Found at i:3305328 original size:37 final size:36
Alignment explanation
Indices: 3305200--3305623 Score: 225
Period size: 37 Copynumber: 11.9 Consensus size: 36
3305190 ATGCAGTTTG
* *
3305200 AAAACA-TTTT-AAAATGTATATATAAAATATAGTTTTG
1 AAAACATTTTTGAAAAT-TA-ATATAATATATA-TTTTT
* * * * *
3305237 AAAACATGTTTTAAAACATTTATATATTATAAAGTTTT
1 AAAACAT-TTTTGAAA-ATTAATATAATATATATTTTT
*
3305275 -AAAGATATTTTGAAAATTAATATAATATATATTTTT
1 AAAACAT-TTTTGAAAATTAATATAATATATATTTTT
*
3305311 CAAAACATTTTTGAAAA-TATATATATTATATAATTTTT
1 -AAAACATTTTTGAAAATTA-ATATAATATAT-ATTTTT
*
3305349 AAAA-ATATTTTGAAAATTAATATAATATATAAATTTT
1 AAAACAT-TTTTGAAAATTAATATAATATAT-ATTTTT
* *
3305386 AAAACATTTTT-AAAAATATATATATTATATAGTTTTT
1 AAAACATTTTTGAAAATTA-ATATAATATATA-TTTTT
3305423 AAAACA-TTTT-AAAA--AA-AT-ATATATAGTTTTT
1 AAAACATTTTTGAAAATTAATATAATATATA-TTTTT
* * * *
3305454 AAAAAAACA-TTTTGAAAACATATATATATTATATAGCTTTG
1 ---AAAACATTTTTGAAAA-TTA-ATATAATATATA-TTTTT
* * *
3305495 AAATCA-TTTTGAAAA--CATATAATATATAATTTTA
1 AAAACATTTTTGAAAATTAATATAATATAT-ATTTTT
* *
3305529 AAAACATTTTTTG--AA--AA-CT-ATATA-ATTTTG
1 AAAACA-TTTTTGAAAATTAATATAATATATATTTTT
* * *
3305559 AAAACATTTTTTAAAAAGT-ATATAATATATAATTTT
1 AAAACA-TTTTTGAAAATTAATATAATATATATTTTT
* *
3305595 AAAATATTTTTG-AAATT-ATATATTATATA
1 AAAACATTTTTGAAAATTAATATAATATATA
3305624 GGTTTTGGAA
Statistics
Matches: 313, Mismatches: 41, Indels: 69
0.74 0.10 0.16
Matches are distributed among these distances:
30 17 0.05
31 12 0.04
32 9 0.03
33 3 0.01
34 48 0.15
35 15 0.05
36 50 0.16
37 94 0.30
38 33 0.11
39 14 0.04
40 6 0.02
41 12 0.04
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAACATTTTTGAAAATTAATATAATATATATTTTT
Found at i:3305373 original size:74 final size:73
Alignment explanation
Indices: 3305177--3305641 Score: 359
Period size: 74 Copynumber: 6.4 Consensus size: 73
3305167 ATACATATAT
* * * * * * *
3305177 ATATATATATAATATGCAGTTTGAAAACATTTT-AAAATGTATATATAAAATATAGTTTTGAAAA
1 ATATATATATTATAT-AAGTTTTAAAATATTTTGAAAAT-TA-ATATAATATATAATTTTAAAAA
*
3305241 CATGTTTTAAAA
63 CAT-TTTTGAAA
* * *
3305253 CATTTATATATTATA-AAGTTTTAAAGATATTTTGAAAATTAATATAATATATATTTTTCAAAAC
1 -ATATATATATTATATAAGTTTTAAA-ATATTTTGAAAATTAATATAATATATAATTTTAAAAAC
3305317 ATTTTTGAAA
64 ATTTTTGAAA
*
3305327 ATATATATATTATATAATTTTTAAAAATATTTTGAAAATTAATATAATATATAAATTTT-AAAAC
1 ATATATATATTATATAAGTTTT-AAAATATTTTGAAAATTAATATAATATAT-AATTTTAAAAAC
*
3305391 ATTTTTAAAA
64 ATTTTTGAAA
* *
3305401 ATATATATATTATAT-AGTTTTTAAAACATTTT-AAAA--AA-AT-ATATATAGTTTTTAAAAAA
1 ATATATATATTATATAAG-TTTTAAAATATTTTGAAAATTAATATAATATATA-ATTTT--AAAA
3305460 ACA-TTTTGAAAA
62 ACATTTTTG-AAA
* * *
3305472 CATATATATATTATAT-AGCTTTGAAATCATTTTGAAAA--CATATAATATATAATTTTAAAAAC
1 -ATATATATATTATATAAGTTTTAAAAT-ATTTTGAAAATTAATATAATATATAATTTTAAAAAC
3305534 ATTTTTTGAAA
64 A-TTTTTGAAA
* * * * *
3305545 ACTATATA-ATT-T-TGAA-----AACATTTTTTAAAAAGT-ATATAATATATAATTTT-AAAAT
1 A-TATATATATTATAT-AAGTTTTAAAATATTTTGAAAATTAATATAATATATAATTTTAAAAAC
3305600 ATTTTTG-AA
64 ATTTTTGAAA
*
3305609 AT-TATATATTATATAGGTTTTGGAAAATATTTT
1 ATATATATATTATATAAGTTTT--AAAATATTTT
3305642 TTTATATATA
Statistics
Matches: 325, Mismatches: 30, Indels: 72
0.76 0.07 0.17
Matches are distributed among these distances:
62 4 0.01
63 4 0.01
64 5 0.02
65 7 0.02
66 13 0.04
67 21 0.06
68 10 0.03
69 2 0.01
70 7 0.02
71 24 0.07
72 38 0.12
73 37 0.11
74 83 0.26
75 45 0.14
76 8 0.02
77 17 0.05
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (73 bp):
ATATATATATTATATAAGTTTTAAAATATTTTGAAAATTAATATAATATATAATTTTAAAAACAT
TTTTGAAA
Found at i:3305551 original size:30 final size:30
Alignment explanation
Indices: 3305517--3305584 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
3305507 AAACATATAA
*
3305517 TATATAATTTTAAAAACATTTTTTGAAAAC
1 TATATAATTTTAAAAACATTTTTTAAAAAC
* *
3305547 TATATAATTTTGAAAACATTTTTTAAAAAG
1 TATATAATTTTAAAAACATTTTTTAAAAAC
3305577 TATATAAT
1 TATATAAT
3305585 ATATAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (30 bp):
TATATAATTTTAAAAACATTTTTTAAAAAC
Found at i:3307926 original size:18 final size:18
Alignment explanation
Indices: 3307891--3307933 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3307881 AAAGATATTA
*
3307891 AAAT-AATAAAAATGATT
1 AAATAAATAAAAATAATT
*
3307908 AAATAAATAAAAGTAATT
1 AAATAAATAAAAATAATT
3307926 AAAGTAAA
1 AAA-TAAA
3307934 AATAAGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (18 bp):
AAATAAATAAAAATAATT
Found at i:3308572 original size:23 final size:23
Alignment explanation
Indices: 3308542--3308596 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
3308532 AATAAAAGAA
3308542 AAAAAGAGAAAAACTTGAAAAGT
1 AAAAAGAGAAAAACTTGAAAAGT
3308565 AAAAAGAGAAAAACTTGAAAAGT
1 AAAAAGAGAAAAACTTGAAAAGT
3308588 AAAAAGAGA
1 AAAAAGAGA
3308597 TAACTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.67, C:0.04, G:0.18, T:0.11
Consensus pattern (23 bp):
AAAAAGAGAAAAACTTGAAAAGT
Found at i:3309669 original size:13 final size:14
Alignment explanation
Indices: 3309638--3309676 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3309628 TGTTTTCCAT
*
3309638 TTTTTCTTTCATGTC
1 TTTTTCTTTC-TCTC
3309653 TTTTT-TTTCTCTC
1 TTTTTCTTTCTCTC
3309666 TTTTTCTTTCT
1 TTTTTCTTTCT
3309677 AACAGCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 8 0.36
14 9 0.41
15 5 0.23
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTCTCTC
Found at i:3309691 original size:16 final size:16
Alignment explanation
Indices: 3309652--3309709 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
3309642 TCTTTCATGT
3309652 CTTTTTTTTCT--CT-
1 CTTTTTTTTCTAACTA
3309665 CTTTTTCTTTCTAAC-A
1 CTTTTT-TTTCTAACTA
*
3309681 GCTTTTTTTTCGAACTA
1 -CTTTTTTTTCTAACTA
3309698 CTATTTTTTTCT
1 CT-TTTTTTTCT
3309710 TCTTTCTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 6 0.17
14 5 0.14
16 10 0.28
17 15 0.42
ACGTcount: A:0.12, C:0.21, G:0.03, T:0.64
Consensus pattern (16 bp):
CTTTTTTTTCTAACTA
Found at i:3316186 original size:18 final size:19
Alignment explanation
Indices: 3316165--3316211 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
3316155 GTAAAAAGAT
*
3316165 ATTAAAAT-AATAAAAGTG
1 ATTAAAATAAATAAAAGTA
3316183 ATT-AAATAAATAAAAGTA
1 ATTAAAATAAATAAAAGTA
*
3316201 ATTAAAGTAAA
1 ATTAAAATAAA
3316212 AATAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (19 bp):
ATTAAAATAAATAAAAGTA
Found at i:3321018 original size:120 final size:122
Alignment explanation
Indices: 3320876--3321216 Score: 445
Period size: 120 Copynumber: 2.8 Consensus size: 122
3320866 TGCAACTTAC
* *
3320876 ATTGAATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGTTCAACTTCACAACGAAGGGGCCA
1 ATTGGATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
* *
3320941 TCCACGGTTTCAACTTCACGAAGAATGGAATCGTGCTCACCAGCAACA-AT-AGAAG
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATATCAGAAG
* * * * * **
3320996 CTTGGATTTCAACTTCATGACGAAGGATATTCAAGTCAAGGCTCAACTTCA-AGATGAAGGGGAT
1 ATTGGATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGCTCAACTTCACA-ACGAAGGGGCC
* * ***
3321060 ATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACTAGCAATATTCATCTTTAG
65 ATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACA-T-ATCAGAAG
* * * * *
3321120 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTTACAACGAATGAGCCA
1 ATTGGATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
3321185 TCCACGGTTTCAACTTCACGACGAAGGGAATC
66 TCCACGGTTTCAACTTCACGACGAAGGGAATC
3321217 ATACCCACCA
Statistics
Matches: 188, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
119 1 0.01
120 98 0.52
123 2 0.01
124 86 0.46
125 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (122 bp):
ATTGGATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATATCAGAAG
Found at i:3321236 original size:124 final size:124
Alignment explanation
Indices: 3320876--3321240 Score: 461
Period size: 124 Copynumber: 3.0 Consensus size: 124
3320866 TGCAACTTAC
* *
3320876 ATTGAATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGTTCAACTTCACAACGAAGGGGCCA
1 ATTGGATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
* * **
3320941 TCCACGGTTTCAACTTCACGAAGAATGGAATCGTGCTCACCAGCAACA---AT-AGAAG
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTAAG
* * * * * **
3320996 CTTGGATTTCAACTTCATGACGAAGGATATTCAAGTCAAGGCTCAACTTCA-AGATGAAGGGGAT
1 ATTGGATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGCTCAACTTCACA-ACGAAGGGGCC
* * *
3321060 ATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACTAGCAATATTCATCTTTAG
65 ATCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTAAG
* * * * *
3321120 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTTACAACGAATGAGCCA
1 ATTGGATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
* * * *
3321185 TCCACGGTTTCAACTTCACGACGAAGGGAATCATACCCACCAGTAACATTCATCTT
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTT
3321241 CAGGAACAAG
Statistics
Matches: 206, Mismatches: 33, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
119 1 0.00
120 98 0.48
123 2 0.01
124 104 0.50
125 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (124 bp):
ATTGGATTTCAACTTCAAGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTAAG
Found at i:3321687 original size:84 final size:84
Alignment explanation
Indices: 3321397--3321680 Score: 322
Period size: 84 Copynumber: 3.4 Consensus size: 84
3321387 TCTTGAAACA
* * * * ** **
3321397 CAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCTCAAAATTTGTAGCATAGCTTAAGTCG
1 CAAAGACCTTCAAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCG
*
3321462 AGAAGGGTTATCTGCCAAC
66 AGAAGGGTTATTTGCCAAC
* ** * * *
3321481 CAAAGACCTTCAAGTTCGATTACACTCAGCTCCAAGGCA-ATCATTTACAACATAAATCAAGGCT
1 CAAAGACCTTCAAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCG
3321545 AGAAGGGTTATCTGTGACCAA-
66 AGAAGGGTTAT-T-TG-CCAAC
* *
3321566 -AAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCG
1 CAAAGACCTTCAAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCG
*
3321630 AGAAGGGCTATTTGCCAAC
66 AGAAGGGTTATTTGCCAAC
* * * *
3321649 CGATGACCTTCGAGTTTGATTACACTCAGCTC
1 CAAAGACCTTCAAGTTCGATTACACTCAGCTC
3321681 AGAGGCAAAC
Statistics
Matches: 164, Mismatches: 30, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
82 4 0.02
83 28 0.17
84 97 0.59
85 31 0.19
86 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (84 bp):
CAAAGACCTTCAAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCG
AGAAGGGTTATTTGCCAAC
Found at i:3322303 original size:36 final size:36
Alignment explanation
Indices: 3322260--3322635 Score: 310
Period size: 37 Copynumber: 10.2 Consensus size: 36
3322250 TTTTACACAT
*
3322260 ATATATATATAATATGCAG-TTTGAAAACATTTT-AAA
1 ATATATATATAATAT--AGTTTTTAAAACATTTTGAAA
* * *
3322296 ATGTATATATAATATATAGTTTTGAAAACATGTTTCAAAA
1 ATATATATAT-A-ATATAGTTTTTAAAACAT-TTT-GAAA
* * * * *
3322336 CATTTGTCTATTATATAGTTTTTAAGACATTTTGAAA
1 -ATATATATATAATATAGTTTTTAAAACATTTTGAAA
*
3322373 AT-TA-ATATAATATATAGTTTTCAAAACATTTTTGAAA
1 ATATATATAT-A-ATATAGTTTTTAAAACA-TTTTGAAA
*
3322410 ATATATATATTATATAGTTTTTAAAAACATTTTGAAA
1 ATATATATATAATATAGTTTTT-AAAACATTTTGAAA
3322447 AT-TA-ATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATAT-A-ATATAGTTTTTAAAACA-TTTTGAAA
*
3322484 ATATATATATTATATAGTTTTTAAAACA-TTT-AAA
1 ATATATATATAATATAGTTTTTAAAACATTTTGAAA
3322518 A-A-ATATAT-ATATAGTTTTTAAAAAAACATTTTGAAAA
1 ATATATATATAATATAGTTTTT---AAAACATTTTG-AAA
* * *
3322555 CATATATATATTATATAGTTTTGAAATCATTTTGAAA
1 -ATATATATATAATATAGTTTTTAAAACATTTTGAAA
* *
3322592 ACATATA-AT-ATATAGTTTTAAAAACATTTTTTGAAA
1 ATATATATATAATATAGTTTTTAAAACA--TTTTGAAA
3322628 ACTATATA
1 A-TATATA
3322636 ATTTTGAAAA
Statistics
Matches: 286, Mismatches: 23, Indels: 61
0.77 0.06 0.16
Matches are distributed among these distances:
31 11 0.04
32 6 0.02
33 1 0.00
34 28 0.10
35 13 0.05
36 51 0.18
37 94 0.33
38 31 0.11
39 25 0.09
40 9 0.03
41 17 0.06
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (36 bp):
ATATATATATAATATAGTTTTTAAAACATTTTGAAA
Found at i:3322406 original size:37 final size:35
Alignment explanation
Indices: 3322266--3322724 Score: 309
Period size: 37 Copynumber: 12.8 Consensus size: 35
3322256 ACATATATAT
**
3322266 ATATAATATGCAG-TTTGAAAACATTTT-AAAATGTA
1 ATATAATATATAGTTTTGAAAACATTTTGAAAA--TA
* *
3322301 TATATAATATATAGTTTTGAAAACATGTTTCAAAACATTT
1 -ATATAATATATAGTTTTGAAAACAT-TTT-GAAA-A-TA
* * * * *
3322341 GTCTATTATATAGTTTTTAAGACATTTTGAAAATTA
1 ATATAATATATAGTTTTGAAAACATTTTGAAAA-TA
*
3322377 ATATAATATATAGTTTTCAAAACATTTTTGAAAATA
1 ATATAATATATAGTTTTGAAAACA-TTTTGAAAATA
* *
3322413 TATATATTATATAGTTTTTAAAAACATTTTGAAAATTA
1 -ATATAATATATAG-TTTTGAAAACATTTTGAAAA-TA
*
3322451 ATATAATATATAGTTTTTAAAACATTTTTGAAAATA
1 ATATAATATATAGTTTTGAAAACA-TTTTGAAAATA
* *
3322487 TATATATTATATAGTTTTTAAAACA-TTT-AAAA-A
1 -ATATAATATATAGTTTTGAAAACATTTTGAAAATA
*
3322520 ATAT-ATATATAGTTTTTAAAAAAACATTTTGAAAACATA
1 ATATAATATATAG-TTTT--GAAAACATTTTG-AAA-ATA
* * *
3322559 TATATATTATATAGTTTTGAAATCATTTTGAAAA-C
1 -ATATAATATATAGTTTTGAAAACATTTTGAAAATA
* ***
3322594 ATATAATATATAGTTTTAAAAACATTTTTTGAA-A
1 ATATAATATATAGTTTTGAAAACATTTTGAAAATA
* *
3322628 A-CT-ATATA-A-TTTTGAAAACATTTTTTAAAA-A
1 ATATAATATATAGTTTTGAAAACA-TTTTGAAAATA
* * *
3322659 GTATATAATATATAATTTT-AAAATATTTTTG-AAATT
1 --ATATAATATATAGTTTTGAAAACA-TTTTGAAAATA
* *
3322695 ATATATTATATAGGTTTTGGAAAATATTTT
1 ATATAATATATA-GTTTT-GAAAACATTTT
3322725 TTTTATATAT
Statistics
Matches: 347, Mismatches: 44, Indels: 64
0.76 0.10 0.14
Matches are distributed among these distances:
30 10 0.03
31 16 0.05
32 13 0.04
33 3 0.01
34 50 0.14
35 18 0.05
36 63 0.18
37 104 0.30
38 29 0.08
39 21 0.06
40 12 0.03
41 8 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (35 bp):
ATATAATATATAGTTTTGAAAACATTTTGAAAATA
Found at i:3322459 original size:74 final size:73
Alignment explanation
Indices: 3322260--3322712 Score: 430
Period size: 74 Copynumber: 6.3 Consensus size: 73
3322250 TTTTACACAT
* * *
3322260 ATATATATATAATATGCAG-TTTGAAAACATTTT-AAAATGTATATATAATATATAGTTTTGAAA
1 ATATATATATTATAT--AGTTTTTAAAACATTTTGAAAAT-TA-ATATAATATATAGTTTTAAAA
**
3322323 ACATGTTTCAAAA
62 ACAT-TTTTGAAA
* * * * *
3322336 CATTTGTCTATTATATAGTTTTTAAGACATTTTGAAAATTAATATAATATATAGTTTTCAAAACA
1 -ATATATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATATATAGTTTTAAAAACA
3322401 TTTTTGAAA
65 TTTTTGAAA
*
3322410 ATATATATATTATATAGTTTTTAAAAACATTTTGAAAATTAATATAATATATAGTTTTTAAAACA
1 ATATATATATTATATAGTTTTT-AAAACATTTTGAAAATTAATATAATATATAGTTTTAAAAACA
3322475 TTTTTGAAA
65 TTTTTGAAA
3322484 ATATATATATTATATAGTTTTTAAAACA-TTT-AAAA--AATAT-ATATATAGTTTTTAAAAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATATATAG-TTTT--AAAAA
3322544 CA-TTTTGAAAA
63 CATTTTTG-AAA
* * *
3322555 CATATATATATTATATAGTTTTGAAATCATTTTGAAAA--CATATAATATATAGTTTTAAAAACA
1 -ATATATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATATATAGTTTTAAAAACA
3322618 TTTTTTGAAA
65 -TTTTTGAAA
* * *
3322628 ACTATATA-ATT-T-T-G-----AAAACATTTTTTAAAAAGT-ATATAATATATAATTTT-AAAA
1 A-TATATATATTATATAGTTTTTAAAACA--TTTTGAAAATTAATATAATATATAGTTTTAAAAA
*
3322682 TATTTTTG-AA
63 CATTTTTGAAA
*
3322692 AT-TATATATTATATAGGTTTT
1 ATATATATATTATATAGTTTTT
3322713 GGAAAATATT
Statistics
Matches: 327, Mismatches: 22, Indels: 60
0.80 0.05 0.15
Matches are distributed among these distances:
62 4 0.01
63 4 0.01
64 9 0.03
65 7 0.02
66 14 0.04
67 16 0.05
68 8 0.02
69 10 0.03
70 6 0.02
71 14 0.04
72 40 0.12
73 37 0.11
74 94 0.29
75 34 0.10
76 14 0.04
77 16 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (73 bp):
ATATATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATATATAGTTTTAAAAACAT
TTTTGAAA
Found at i:3322646 original size:30 final size:30
Alignment explanation
Indices: 3322600--3322667 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
3322590 AAACATATAA
* *
3322600 TATATAGTTTTAAAAACATTTTTTGAAAAC
1 TATATAATTTTAAAAACATTTTTTAAAAAC
* *
3322630 TATATAATTTTGAAAACATTTTTTAAAAAG
1 TATATAATTTTAAAAACATTTTTTAAAAAC
3322660 TATATAAT
1 TATATAAT
3322668 ATATAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (30 bp):
TATATAATTTTAAAAACATTTTTTAAAAAC
Found at i:3322698 original size:64 final size:64
Alignment explanation
Indices: 3322564--3322699 Score: 161
Period size: 64 Copynumber: 2.1 Consensus size: 64
3322554 ACATATATAT
* * * *
3322564 ATTATATAGTTTTGAAATCATTTTGAAAACATATAATATATAGTTTTAAAAACATTTTTTGAAA
1 ATTATATAATTTTGAAAACATTTTAAAAACATATAATATATAATTTTAAAAACATTTTTTGAAA
* * *
3322628 ACTATATAATTTTGAAAACATTTTTTAAAAAGTATATAATATATAATTTT-AAAATA-TTTTTG-
1 ATTATATAATTTTGAAAACA--TTTTAAAAA-CATATAATATATAATTTTAAAAACATTTTTTGA
3322690 AA
63 AA
3322692 ATTATATA
1 ATTATATA
3322700 TTATATAGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
64 26 0.43
65 6 0.10
66 13 0.21
67 16 0.26
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (64 bp):
ATTATATAATTTTGAAAACATTTTAAAAACATATAATATATAATTTTAAAAACATTTTTTGAAA
Found at i:3324013 original size:22 final size:22
Alignment explanation
Indices: 3323975--3324024 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3323965 TTTTCCTTTG
*
3323975 TTTTTTTATTTCTTTGATTTAT
1 TTTTTTTATTTCATTGATTTAT
*
3323997 TTTTATTTATTT-ATTGATTTGT
1 TTTT-TTTATTTCATTGATTTAT
3324019 TTTTTT
1 TTTTTT
3324025 CTTTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.64
23 7 0.28
ACGTcount: A:0.14, C:0.02, G:0.06, T:0.78
Consensus pattern (22 bp):
TTTTTTTATTTCATTGATTTAT
Found at i:3324202 original size:6 final size:7
Alignment explanation
Indices: 3324185--3324215 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3324175 TCGAATCGAG
3324185 TTTTTAA
1 TTTTTAA
3324192 TTTTTAA
1 TTTTTAA
3324199 -TTTTAA
1 TTTTTAA
3324205 TTTTTAA
1 TTTTTAA
3324212 TTTT
1 TTTT
3324216 CGCAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:3324204 original size:13 final size:13
Alignment explanation
Indices: 3324186--3324215 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3324176 CGAATCGAGT
3324186 TTTTAATTTTTAA
1 TTTTAATTTTTAA
3324199 TTTTAATTTTTAA
1 TTTTAATTTTTAA
3324212 TTTT
1 TTTT
3324216 CGCAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:3324769 original size:28 final size:27
Alignment explanation
Indices: 3324704--3324762 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
3324694 TTTTGGATCC
* * *
3324704 TAGAGTTTAAGATTTATATTTAGGATT
1 TAGAGTTAAAGTTTTATATTTAAGATT
3324731 TAGAGTTTAAAGTTTTATATTTTAAGATT
1 TAGAG-TTAAAGTTTTATA-TTTAAGATT
3324760 TAG
1 TAG
3324763 CATTAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 11 0.41
29 11 0.41
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (27 bp):
TAGAGTTAAAGTTTTATATTTAAGATT
Found at i:3324945 original size:3 final size:3
Alignment explanation
Indices: 3324937--3325016 Score: 119
Period size: 3 Copynumber: 26.7 Consensus size: 3
3324927 TTTTTGTTAT
*
3324937 TTA TTA TTA TTA -TA TTTA TCT- CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
3324982 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3325017 GCAAAAAACA
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
2 3 0.04
3 65 0.92
4 3 0.04
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3331659 original size:19 final size:20
Alignment explanation
Indices: 3331635--3331673 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3331625 AAGCAAAAAA
3331635 TGATATCAATAC-CAGGGGT
1 TGATATCAATACTCAGGGGT
*
3331654 TGATATCGATACTCAGGGGT
1 TGATATCAATACTCAGGGGT
3331674 CAGTATCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (20 bp):
TGATATCAATACTCAGGGGT
Found at i:3336257 original size:63 final size:63
Alignment explanation
Indices: 3336179--3336303 Score: 250
Period size: 63 Copynumber: 2.0 Consensus size: 63
3336169 CCTATTGGTG
3336179 TCGATACCCTGGTATCGATACTCTTATTTCAGTATCGATACCTTATGAAGATTATCACTCTTA
1 TCGATACCCTGGTATCGATACTCTTATTTCAGTATCGATACCTTATGAAGATTATCACTCTTA
3336242 TCGATACCCTGGTATCGATACTCTTATTTCAGTATCGATACCTTATGAAGATTATCACTCTT
1 TCGATACCCTGGTATCGATACTCTTATTTCAGTATCGATACCTTATGAAGATTATCACTCTT
3336304 CTTCCTTATG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (63 bp):
TCGATACCCTGGTATCGATACTCTTATTTCAGTATCGATACCTTATGAAGATTATCACTCTTA
Found at i:3343457 original size:173 final size:173
Alignment explanation
Indices: 3343160--3343674 Score: 809
Period size: 173 Copynumber: 3.0 Consensus size: 173
3343150 AGAACTCAAG
* * *
3343160 ATTTTAATAGTAGGTTCTATGGGTCACC-TTCATACCAGAATGCTACGAAATAAAACACCAAGTG
1 ATTTTAAGAGTAGGTTCTATGGGTC-CCATTCATACCAGAATGATACGAAATAAAACAACAAGTG
* * * * * *
3343224 AGAATGTTAAATTAAC-TCAGAATATTTAGAAATAACAATTACTAGGATGAAATAAAACTAGCCT
65 GGAATGTTAAATTAACTTC-GAACATTTGGAAACAACAATTGCTAGGATGGAATAAAACTAGCCT
*
3343288 TGTTTGACGCTCGGGACACAGCCAGGACTCCCGAGTCACTCAAAA
129 TGTTTGACGCTCGGGACACAGCCAAGACTCCCGAGTCACTCAAAA
* *
3343333 ATTTTAAGAGTAGGTTCTATGGGTCCCATTTATACCAGAATGATACGAAATAAATCAACAAGTGG
1 ATTTTAAGAGTAGGTTCTATGGGTCCCATTCATACCAGAATGATACGAAATAAAACAACAAGTGG
* *
3343398 GAATGTTAAATTAACTTCGAACATTTGGAAACAACAATTGCTAGAATGGAATTAAACTAGCCTTG
66 GAATGTTAAATTAACTTCGAACATTTGGAAACAACAATTGCTAGGATGGAATAAAACTAGCCTTG
* *
3343463 TTTGACGCTTGGGACACAGCCAAGACTCCCGAGTCACTCAAGA
131 TTTGACGCTCGGGACACAGCCAAGACTCCCGAGTCACTCAAAA
*
3343506 ATTTTAAGAGTTGGTTCTATGGGTCCCATTCATACCAGAATGATACGAAATAAAACAACAAGTGG
1 ATTTTAAGAGTAGGTTCTATGGGTCCCATTCATACCAGAATGATACGAAATAAAACAACAAGTGG
*
3343571 GAATGTTAAATTAACTTAGAACATTTGGAAACAACAATTGCTAGGATGGAATAAAACTAGCCTTG
66 GAATGTTAAATTAACTTCGAACATTTGGAAACAACAATTGCTAGGATGGAATAAAACTAGCCTTG
* * *
3343636 TTTGACACTCAGGACACAGCCATGACTCCCGAGTCACTC
131 TTTGACGCTCGGGACACAGCCAAGACTCCCGAGTCACTC
3343675 TCGCATATGT
Statistics
Matches: 314, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
172 2 0.01
173 310 0.99
174 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (173 bp):
ATTTTAAGAGTAGGTTCTATGGGTCCCATTCATACCAGAATGATACGAAATAAAACAACAAGTGG
GAATGTTAAATTAACTTCGAACATTTGGAAACAACAATTGCTAGGATGGAATAAAACTAGCCTTG
TTTGACGCTCGGGACACAGCCAAGACTCCCGAGTCACTCAAAA
Done.